From c7ff439015a2066315fb631138a35ee34093951b Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Tue, 12 Jul 2022 21:31:55 -0700
Subject: [PATCH 001/192] CHG: Some bug fixes / optimizations related to COSI
 calibrations

---
 .../base/src/MCalibrateEnergyFindLines.cxx    |  3 +-
 src/fretalon/base/src/MCalibrationModel.cxx   | 47 ++++++++++++++-----
 .../melinator/src/MGUIMainMelinator.cxx       |  5 +-
 src/fretalon/melinator/src/MMelinator.cxx     |  4 +-
 4 files changed, 42 insertions(+), 17 deletions(-)

diff --git a/src/fretalon/base/src/MCalibrateEnergyFindLines.cxx b/src/fretalon/base/src/MCalibrateEnergyFindLines.cxx
index 82b4a4c90..2e94f07bf 100644
--- a/src/fretalon/base/src/MCalibrateEnergyFindLines.cxx
+++ b/src/fretalon/base/src/MCalibrateEnergyFindLines.cxx
@@ -676,6 +676,7 @@ bool MCalibrateEnergyFindLines::CheckPeaks()
     }
   }
   
+  /*
   if (FWHMes.size() >= 3) {
     // Calculate outliers via the modified thomson tau method
     MMath M;
@@ -699,7 +700,7 @@ bool MCalibrateEnergyFindLines::CheckPeaks()
   } else {
     if (g_Verbosity >= c_Info) cout<<"Not enough FWHMes found for FWHM sanity check!"<<endl; 
   }
-  
+  */
   
   return true;
 }
diff --git a/src/fretalon/base/src/MCalibrationModel.cxx b/src/fretalon/base/src/MCalibrationModel.cxx
index de4a14c23..2e9ad7041 100644
--- a/src/fretalon/base/src/MCalibrationModel.cxx
+++ b/src/fretalon/base/src/MCalibrationModel.cxx
@@ -148,25 +148,39 @@ double MCalibrationModel::Fit(const vector<MCalibrationSpectralPoint> Points)
   // Prepare the array for ROOT
   m_ROOTParameters.resize(NPar(), 0);
    
-  // SEt up the fitter
+  // Set up the fitter
   ROOT::Math::MinimizerOptions::SetDefaultMaxFunctionCalls(20000);
 
-  ROOT::Fit::BinData TheData;
-  TheData.Initialize(Points.size(), 1, ROOT::Fit::BinData::kValueError);
+  // Locally store the data - we need it later
+  vector<double> X;
+  vector<double> Y;
+  vector<double> dY;
   for (unsigned int p = 0; p < Points.size(); ++p) {
     double FWHM = Points[p].GetEnergyFWHM();
     // If we do not yet have a FWHM use a dummy linear calibration through zero
-    if (FWHM == 0.0) {
+    if (FWHM < 1E-10) {
       FWHM = Points[p].GetFWHM() * Points[p].GetEnergy() / Points[p].GetPeak();
     }
     if (m_Type == MCalibrationModelType::c_LineWidth) {
       if (fabs(Points[p].GetEnergy() - 511) < 0.1) continue; // Always exclude any 511 line, since it is larger than usual (positron range)
-      TheData.Add(Points[p].GetEnergy(), FWHM, 0.1*FWHM); // Arbitrary width...
+      X.push_back(Points[p].GetEnergy());
+      Y.push_back(FWHM);
+      dY.push_back(0.1*FWHM); // Arbitrary width...
     } else {
-      TheData.Add(Points[p].GetPeak(), Points[p].GetEnergy(), FWHM/2.35);
+      X.push_back(Points[p].GetPeak());
+      Y.push_back(Points[p].GetEnergy());
+      dY.push_back(FWHM/2.35);
     }
   }
 
+  // Fill the fitting data set
+  ROOT::Fit::BinData TheData;
+  TheData.Initialize(Points.size(), 1, ROOT::Fit::BinData::kValueError);
+  for (unsigned int d = 0; d < X.size(); ++d) {
+    TheData.Add(X[d], Y[d], dY[d]);
+  }
+
+
   ROOT::Fit::Fitter TheFitter; 
   TheFitter.Config().SetMinimizer("Minuit2", "Migrad");
   if (g_Verbosity >= c_Info) TheFitter.Config().MinimizerOptions().SetPrintLevel(2);
@@ -175,7 +189,7 @@ double MCalibrationModel::Fit(const vector<MCalibrationSpectralPoint> Points)
   InitializeFitParameters(TheFitter);
   
   // Fit
-  if (g_Verbosity >= c_Info) cout<<"Round 1 of line fitting started"<<endl;
+  if (g_Verbosity >= c_Info) cout<<endl<<"Round 1 of line fitting started"<<endl;
   bool ReturnCode = TheFitter.Fit(TheData);
   ROOT::Fit::FitResult& TheFitResult = const_cast<ROOT::Fit::FitResult&>(TheFitter.Result());
 
@@ -202,7 +216,7 @@ double MCalibrationModel::Fit(const vector<MCalibrationSpectralPoint> Points)
   if (ReturnCode == false) {
     // Try a different fitting approach 
     
-    if (g_Verbosity >= c_Info) cout<<"Round 2 of line fitting started"<<endl;
+    if (g_Verbosity >= c_Info) cout<<endl<<"Round 2 of line fitting started"<<endl;
     ROOT::Fit::Fitter TheFitter2; 
     TheFitter2.Config().SetMinimizer("Minuit2", "Minimize");
     if (g_Verbosity >= c_Info) TheFitter2.Config().MinimizerOptions().SetPrintLevel(2);
@@ -226,7 +240,7 @@ double MCalibrationModel::Fit(const vector<MCalibrationSpectralPoint> Points)
       }
       if (ReturnCode == true) {
         TheFitResult = const_cast<ROOT::Fit::FitResult&>(TheFitter2.Result()); 
-        if (g_Verbosity >= c_Info) cout<<"Successfully fit line model in round 2."<<endl;
+        if (g_Verbosity >= c_Info) cout<<"Successfully fit line model in round 2 (chisquare: "<<TheFitResult.Chi2()<<")"<<endl;
       }
     } else {
       if (g_Verbosity >= c_Info) cout<<"Unable to fit calibration model in round 2."<<endl;
@@ -239,7 +253,7 @@ double MCalibrationModel::Fit(const vector<MCalibrationSpectralPoint> Points)
   if (ReturnCode == false) {
     // Try a different fitting approach 
     
-    if (g_Verbosity >= c_Info) cout<<"Round 3 of line fitting started"<<endl;
+    if (g_Verbosity >= c_Info) cout<<endl<<"Round 3 of line fitting started"<<endl;
     ROOT::Fit::Fitter TheFitter3; 
     TheFitter3.Config().SetMinimizer("Fumili");
     if (g_Verbosity >= c_Info) TheFitter3.Config().MinimizerOptions().SetPrintLevel(2);
@@ -284,17 +298,24 @@ double MCalibrationModel::Fit(const vector<MCalibrationSpectralPoint> Points)
     m_Fit = new TF1("", this, 0, 1.1*Points.back().GetPeak(), NPar());
     TThread::UnLock();
     
-    m_Fit->SetChisquare(TheFitResult.Chi2());
-    m_Fit->SetNDF(TheFitResult.Ndf());
     m_Fit->SetNumberFitPoints(TheData.Size());
-
     m_Fit->SetParameters( &(TheFitResult.Parameters().front()) ); 
     if (int(TheFitResult.Errors().size()) >= m_Fit->GetNpar()) { 
       m_Fit->SetParErrors( &(TheFitResult.Errors().front()) );
     }
 
+    // Let's do our own chi-square calculation, since it needs to be uniform over all fit approaches and independent of fit errors
+    double Chisquare = 0;
+    for (unsigned int d = 0; d < X.size(); ++d) {
+      Chisquare += (m_Fit->Eval(X[d]) - Y[d])*(m_Fit->Eval(X[d]) - Y[d]) / (dY[d]*dY[d]);
+    }
+    m_Fit->SetChisquare(Chisquare);
+    m_Fit->SetNDF(TheFitResult.Ndf());
+
+
     if (m_Fit->GetNDF() > 0) {
       m_FitQuality = m_Fit->GetChisquare()/m_Fit->GetNDF(); // Used to determine the quality of fit, thus critically important    
+      //if (g_Verbosity >= c_Info) cout<<"Fit quality: "<<m_FitQuality<<" (chi-square: "<<m_Fit->GetChisquare()<<", NDF: "<<m_Fit->GetNDF()<<")"<<endl;
     } else {
       m_FitQuality = 0; 
     }
diff --git a/src/fretalon/melinator/src/MGUIMainMelinator.cxx b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
index 01cc411b9..b0809a785 100644
--- a/src/fretalon/melinator/src/MGUIMainMelinator.cxx
+++ b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
@@ -1693,7 +1693,10 @@ void MGUIMainMelinator::UpdateCalibration(unsigned int Collection, bool DrawEner
   
   // RMS with outlier detection:
   MMath M;
-  vector<bool> IsOutlier = M.ModifiedThomsonTauTest(FitQualities, 0.01, KnownOutliers);
+  vector<bool> IsOutlier = KnownOutliers;
+  if (FitQualities.size() >= 3) {
+    IsOutlier = M.ModifiedThomsonTauTest(FitQualities, 0.01, KnownOutliers);
+  }
   
   unsigned int GoodEntries = 0;
   double RMS = 0;
diff --git a/src/fretalon/melinator/src/MMelinator.cxx b/src/fretalon/melinator/src/MMelinator.cxx
index 3d8f2330b..6bcd37cd6 100644
--- a/src/fretalon/melinator/src/MMelinator.cxx
+++ b/src/fretalon/melinator/src/MMelinator.cxx
@@ -673,7 +673,7 @@ void MMelinator::DrawSpectrum(TCanvas& Canvas, unsigned int Collection, unsigned
         Names += ", ";
       }
     }
-    Legend->AddEntry(m_Histograms[h], Names);
+    Legend->AddEntry(m_Histograms[h], Names, "l");
   }
   Legend->Draw("SAME");
   
@@ -850,7 +850,7 @@ void MMelinator::DrawLineFit(TCanvas& Canvas, unsigned int Collection, unsigned
             Spectrum->GetXaxis()->SetTitleOffset(0.9);
             Spectrum->GetXaxis()->CenterTitle(true);
             Spectrum->GetXaxis()->SetMoreLogLabels(true);
-            Spectrum->GetXaxis()->SetNdivisions(509, true);
+            Spectrum->GetXaxis()->SetNdivisions(506, true);
     
             //Spectrum->GetYaxis()->SetLabelOffset(0.001);
             Spectrum->GetYaxis()->SetLabelSize(0.05);

From d3b29b627760eb098ee7719dd24f2366f2785015 Mon Sep 17 00:00:00 2001
From: GallegoSav <savitri.gallego@laposte.net>
Date: Thu, 16 Feb 2023 10:22:53 +0100
Subject: [PATCH 002/192] update for geant4.11

---
 config/AllowedGeant4Versions.txt      |   1 +
 config/AllowedROOTVersions.txt        |   3 +-
 config/Makefile.linuxgcc              |   6 +--
 config/env.sh                         | Bin 7289 -> 7422 bytes
 src/cosima/inc/MCSteppingAction.hh    |   3 +-
 src/cosima/src/MCActivator.cc         |  75 ++++++++++++++++----------
 src/cosima/src/MCGeometryConverter.cc |   2 +-
 src/cosima/src/MCPhysicsList.cc       |  14 ++---
 src/cosima/src/MCSteppingAction.cc    |  33 ++++++++----
 9 files changed, 84 insertions(+), 53 deletions(-)

diff --git a/config/AllowedGeant4Versions.txt b/config/AllowedGeant4Versions.txt
index 257e56326..8339415de 100644
--- a/config/AllowedGeant4Versions.txt
+++ b/config/AllowedGeant4Versions.txt
@@ -1 +1,2 @@
 102
+111
diff --git a/config/AllowedROOTVersions.txt b/config/AllowedROOTVersions.txt
index 212eb6fb8..8339415de 100644
--- a/config/AllowedROOTVersions.txt
+++ b/config/AllowedROOTVersions.txt
@@ -1 +1,2 @@
-618 624 
+102
+111
diff --git a/config/Makefile.linuxgcc b/config/Makefile.linuxgcc
index a0a10661c..691725b40 100644
--- a/config/Makefile.linuxgcc
+++ b/config/Makefile.linuxgcc
@@ -9,7 +9,7 @@
 #----------------------------------------------------------------
 
 
-CMODE         = "Linux with gcc and support for C++11"
+CMODE         = "Linux with gcc and support for C++17"
 DLL           = so
 
 # Basic flags generated by ROOT
@@ -19,7 +19,7 @@ ROOTGLIBS     = $(shell root-config --glibs)
 
 # Compiler & linker options:
 CXX           = g++
-CXXFLAGS      = $(OPT) -std=c++11 -Wall -Wno-deprecated -fPIC -D_REENTRANT -I$(IN) -I$(CT) -I. $(ROOTCFLAGS) -D___LINUX___ -D___CLING___
+CXXFLAGS      = $(OPT) -std=c++17 -Wall -Wno-deprecated -fPIC -D_REENTRANT -I$(IN) -I$(CT) -I. $(ROOTCFLAGS) -D___LINUX___ -D___CLING___
 DEFINES       = -UHARDWARE
 LD            = g++
 LDFLAGS       = $(OPT) -D___LINUX___
@@ -33,7 +33,7 @@ LINK          = ln -s -f
 # HEASoft
 HEACFLAGS     = 
 HEALIBS       =
-ifneq ("$(wildcard $(LHEASOFT)/include/fitsio.h)", "")
+ifneq ("$(wildcard $(LHEASOFT)/include/cfitsio.h)", "")
 	HEACFLAGS += -I$(LHEASOFT)/include
 	HEALIBS += -L$(LHEASOFT)/lib 
 else ifeq ("$(shell pkg-config --exists cfitsio 1>&2 2> /dev/null; echo $$?)", "0")
diff --git a/config/env.sh b/config/env.sh
index e364447aae7a72135db20049aba608daba73a5f2..be9c4f4b149cfa67f9f0d85a05a88537f8508f3d 100755
GIT binary patch
delta 103
ucmexq@y~KYIya;8<aF*rAU5F9PftzED>2DU%ueOne3^ThfHMQdfC~U+u?-Xe

delta 20
ccmexo`O{)UI``z8+y;|pa64|6;#nvF0Aw2oGXMYp

diff --git a/src/cosima/inc/MCSteppingAction.hh b/src/cosima/inc/MCSteppingAction.hh
index 7c0677cba..098d4b0b3 100644
--- a/src/cosima/inc/MCSteppingAction.hh
+++ b/src/cosima/inc/MCSteppingAction.hh
@@ -87,7 +87,8 @@ public:
   static const int c_ProcessIDIonization;
   static const int c_ProcessIDTransportation;
   static const int c_ProcessIDUncovered;
-  
+  static const int c_ProcessIDNoProcess; //added in g4.11 : New class G4NoProcess, representing an empty process not assigned to any particle, and used only in G4SteppingManager::InvokeAtRestDoItProcs() for stable ions at rest, in order to avoid that radioactive decay appears as process defining their last step. Note that the method IsApplicable(), retunrs false, as this process should not be set to any particle. (see release note)
+
   
   // protected methods:
 protected:
diff --git a/src/cosima/src/MCActivator.cc b/src/cosima/src/MCActivator.cc
index ad54f053e..1c54f81f3 100644
--- a/src/cosima/src/MCActivator.cc
+++ b/src/cosima/src/MCActivator.cc
@@ -36,11 +36,18 @@
 #include "G4DecayTable.hh"
 #include "G4VDecayChannel.hh"
 #include "G4ParticleTable.hh"
-#include "G4RIsotopeTable.hh"
-#include "G4IsotopeProperty.hh"
-#include "G4NuclearLevelManager.hh"
-#include "G4NuclearLevel.hh"
-#include "G4NuclearLevelStore.hh"
+//#include "G4RIsotopeTable.hh"
+// from g4 v10.2 release note : G4RIsotopeTable: added object name in constructor; removed
+//G4RIsotopeTable (now redundant) and all associated pointers from G4RadioactiveDecay
+
+#include "G4IsotopeProperty.hh"    
+//#include "G4NuclearLevelManager.hh" //not found anymore in v11.1
+//#include "G4NuclearLevel.hh" //same
+//#include "G4NuclearLevelSI woultore.hh" //same
+#include "G4NuclearLevelData.hh" //replace libs upper ? see release note 10.2
+#include "G4LevelManager.hh"
+#include "G4NucLevel.hh"
+
 #include "G4IonTable.hh"
 
 // Standard lib:
@@ -163,7 +170,7 @@ bool MCActivator::LoadCountsFiles()
     Counts.Load(m_CountsFiles[i]);
 
     if (Counts.GetTime() == 0) {
-      merr<<"Isotope file does not contain a time for rates calculation!"<<endl;
+      merr<<"Isotope file does not contain a time for rates calculation: "<<m_CountsFiles[i]<<endl;
       return false;
     }
 
@@ -423,33 +430,38 @@ bool MCActivator::CalculateEquilibriumRates()
               G4Ions* Nucleus = dynamic_cast<G4Ions*>(Tree[b].back().GetDefinition()); 
               
               bool LevelsOK = true;
-              G4NuclearLevelManager* M = G4NuclearLevelStore::GetInstance()->GetManager(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass());
-              if (M->IsValid() == true) {
+              //G4NucLearLevelManager* M = G4NucLevelStore::GetInstance()->GetManager(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass());
+              const G4LevelManager* M = G4NuclearLevelData::GetInstance()->GetLevelManager(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass());
+	      
+	      //if (M->IsValid() == true) {
+	      bool IsValid = true; // IsValid() Method no longer exist for G4LevelManager, is all level are registered now ? 
+	      if (IsValid == true) {
+
                 //M->PrintAll();
-                const G4NuclearLevel* NuclearLevel = M->NearestLevel(Nucleus->GetExcitationEnergy());
-                cout<<"Nearest level: "<<NuclearLevel->Energy()/keV<<" vs. "<<Nucleus->GetExcitationEnergy()/keV<<endl;
+                const G4NucLevel* NuclearLevel = M->NearestLevel(Nucleus->GetExcitationEnergy());
+                cout<<"Nearest level: "<<M->NearestLevelEnergy(Nucleus->GetExcitationEnergy())/keV<<" vs. "<<Nucleus->GetExcitationEnergy()/keV<<endl;
                 if (NuclearLevel != 0) {
                   // Create new levels...
-                  cout<<"Number of gammas: "<<NuclearLevel->NumberOfGammas()<<endl;
-                  for (int h = 0; h < NuclearLevel->NumberOfGammas(); ++h) {
+                  cout<<"Number of gammas: "<<NuclearLevel->NumberOfTransitions()<<endl;
+                  for (int h = 0; h < int(NuclearLevel->NumberOfTransitions()); ++h) {
                     vector<MCActivatorParticle> ABranch = Tree[b];
-                    cout<<"Gamma energy: "<<NuclearLevel->GammaEnergies()[h]/keV<<endl;
+                    cout<<"Gamma energy: "<<M->LevelEnergy(NuclearLevel->FinalExcitationIndex(h))/keV<<endl;
                     
                     double NewLevelEnergy = 0.0;
                     double NewHalfLife = 0.0;
-                    if (fabs(NuclearLevel->Energy() - NuclearLevel->GammaEnergies()[h]) > 1*keV && /* NuclearLevel->GammaEnergies()[h] > 1*keV && */
-                        NuclearLevel->Energy() != M->HighestLevel()->Energy()) { // table has some significant uncertainties...
+                    if (fabs(M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()) - M->LevelEnergy(NuclearLevel->FinalExcitationIndex(h))) > 1*keV && /* NuclearLevel->GammaEnergies()[h] > 1*keV && */
+                        M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()) != M->MaxLevelEnergy()) { // table has some significant uncertainties...
                       // Make sure we know the exact energy of the new level:
-                      const G4NuclearLevel* NewNuclearLevel = M->NearestLevel(NuclearLevel->Energy() - NuclearLevel->GammaEnergies()[h]);
+                      const G4NucLevel* NewNuclearLevel = M->NearestLevel(M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()) - M->LevelEnergy(NuclearLevel->FinalExcitationIndex(h)));
                       if (NewNuclearLevel != 0) {
-                        NewLevelEnergy = NewNuclearLevel->Energy();
-                        if (NewNuclearLevel->HalfLife() > m_HalfLifeCutOff) {
-                          NewHalfLife = NewNuclearLevel->HalfLife();
+                        NewLevelEnergy = M->NearestLevelEnergy(M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()) - M->LevelEnergy(NuclearLevel->FinalExcitationIndex(h)));
+                        if (NewNuclearLevel->GetTimeGamma () > m_HalfLifeCutOff) {
+                          NewHalfLife = NewNuclearLevel->GetTimeGamma ();
                         } else {
                           NewHalfLife = 0.0;
                         }
                       } else {
-                        mout<<"Error: No nearest level found for: "<<Nucleus->GetParticleName()<<" Excitation: "<<NuclearLevel->Energy() - NuclearLevel->GammaEnergies()[h]<<endl;
+                        mout<<"Error: No nearest level found for: "<<Nucleus->GetParticleName()<<" Excitation: "<<M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()) - M->LevelEnergy(NuclearLevel->FinalExcitationIndex(h))<<endl;
                         mout<<"       This isotope is excluded from further analysis!"<<endl;
                         LevelsOK = false;                        
                       }
@@ -472,8 +484,8 @@ bool MCActivator::CalculateEquilibriumRates()
                     MCActivatorParticle NewParticle;
                     NewParticle.SetIDAndExcitation(MCSteppingAction::GetParticleType(Nucleus->GetParticleName()), 
                                                 NewLevelEnergy);
-                    NewParticle.SetBranchingRatio(Tree[b].back().GetBranchingRatio()*NuclearLevel->GammaProbabilities()[h]);
-                    NewParticle.SetProductionRate(Tree[b].back().GetProductionRate()*NuclearLevel->GammaProbabilities()[h]);
+                    NewParticle.SetBranchingRatio(Tree[b].back().GetBranchingRatio()*NuclearLevel->GammaProbability(h));
+                    NewParticle.SetProductionRate(Tree[b].back().GetProductionRate()*NuclearLevel->GammaProbability(h));
                     // The PDGLifeTime is not always ok for excited states, thus we have to get it this way:
                     if (NewLevelEnergy > 0.0) {
                       NewParticle.SetHalfLife(NewHalfLife);
@@ -503,7 +515,7 @@ bool MCActivator::CalculateEquilibriumRates()
                       cout<<"Adding entry with energy: "<<NewParticle.GetExcitation()/keV<<endl;
                     }
                   } // all possible gammas
-                  if (NuclearLevel->NumberOfGammas() > 0 && LevelsOK == true) {
+                  if (NuclearLevel->NumberOfTransitions() > 0 && LevelsOK == true) {
                     Tree[b].clear(); // mark for removal
                     TreeChanged = true;
                     cout<<"Original tree cleared"<<endl;
@@ -1268,21 +1280,26 @@ bool MCActivator::DetermineHalfLife(G4ParticleDefinition* ParticleDef, double& H
         }
       }
     } else {
-      G4NuclearLevelManager* M = G4NuclearLevelStore::GetInstance()->GetManager(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass());
+      //G4NucLevelManager* M = G4NucLevelStore::GetInstance()->GetManager(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass());
+      const G4LevelManager* M = G4NuclearLevelData::GetInstance()->GetLevelManager(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass());
+
       //M->PrintAll();
-      if (M->IsValid() == true) {
-        const G4NuclearLevel* Level = M->NearestLevel(Nucleus->GetExcitationEnergy());
+      bool IsValid = true; // IsValid() Method no longer exist for G4LevelManager, is all level are registered now ? 
+      if (IsValid == true) {
+        //const G4NucLevel* Level = M->NearestLevel(Nucleus->GetExcitationEnergy());
+	const G4NucLevel* Level = M->NearestLevel(Nucleus->GetExcitationEnergy());
+
         //Level->PrintAll();
         if (Level != 0) {
-          if (Level->HalfLife() > m_HalfLifeCutOff || IgnoreCutOff == true) {
+          if (Level->GetTimeGamma() > m_HalfLifeCutOff || IgnoreCutOff == true) {
             //cout<<"Half life: "<<Level->HalfLife()<<endl;
-            HalfLife = Level->HalfLife();
+            HalfLife = Level->GetTimeGamma ();
           } else {
             //cout<<"Half life: "<<Level->HalfLife()<<" ---> Declared as immdiate decay!"<<endl;
             HalfLife = 0.0;
           }
           // This excitation energy is more exact:
-          ExcitationEnergy = Level->Energy();
+          ExcitationEnergy = M->NearestLevelEnergy(Nucleus->GetExcitationEnergy());
         } else {
           mout<<"Error: No nearest level found for: "<<Nucleus->GetParticleName()<<endl;
           mout<<"       This isotope is excluded from further analysis!"<<endl;
diff --git a/src/cosima/src/MCGeometryConverter.cc b/src/cosima/src/MCGeometryConverter.cc
index ecd45ca5a..943c59cf9 100644
--- a/src/cosima/src/MCGeometryConverter.cc
+++ b/src/cosima/src/MCGeometryConverter.cc
@@ -221,7 +221,7 @@ bool MCGeometryConverter::ConvertShape(ofstream& fout, G4String& Name, G4VSolid*
   } else if (S->GetEntityType() == "G4Sphere") {
     G4Sphere* Sphere = (G4Sphere*) S;
     fout<<Init
-    <<Sphere->GetInsideRadius()/cm<<" "
+    <<Sphere->GetInnerRadius()/cm<<" "
     <<Sphere->GetOuterRadius()/cm<<" "
     <<Sphere->GetStartThetaAngle()/deg<<" "
     <<Sphere->GetStartThetaAngle()/deg + Sphere->GetDeltaThetaAngle()/deg<<" "
diff --git a/src/cosima/src/MCPhysicsList.cc b/src/cosima/src/MCPhysicsList.cc
index 986688ee8..ba19afc23 100644
--- a/src/cosima/src/MCPhysicsList.cc
+++ b/src/cosima/src/MCPhysicsList.cc
@@ -46,7 +46,7 @@
 #include "G4VEnergyLossProcess.hh"
 #include "G4ProcessVector.hh"
 #include "G4ProcessManager.hh"
-#include "G4LivermorePolarizedPhotoElectricModel.hh"
+//#include "G4LivermorePolarizedPhotoElectricModel.hh" removed in g4 v11
 #include "G4LivermorePhotoElectricModel.hh"
 #include "G4PenelopePhotoElectricModel.hh"
 #include "G4LivermoreIonisationModel.hh"
@@ -196,21 +196,21 @@ void MCPhysicsList::ConstructProcess()
   G4VModularPhysicsList::ConstructProcess();
   
   // Do some additional modifications to the default lists:
-  theParticleIterator->reset();
-  while ((*theParticleIterator)() == true) {
-    G4ParticleDefinition* particle = theParticleIterator->value();
+  GetParticleIterator()->reset();
+  while ((*GetParticleIterator())() == true) {
+    G4ParticleDefinition* particle = GetParticleIterator()->value();
     G4ProcessManager* pmanager = particle->GetProcessManager();
     G4ProcessVector* pvector = pmanager->GetProcessList();
     //cout<<particle->GetParticleName()<<endl;
     //cout<<"Gamma processes: "<<pvector->size()<<endl;
-    for (G4int p = 0; p < pvector->size(); ++p) {
+    for (G4int p = 0; p < int(pvector->size()); ++p) {
       G4VProcess* P = (*pvector)[p];
       //cout<<P->GetProcessName()<<endl;
       if (dynamic_cast<G4RadioactiveDecay*>(P) != 0) {
         G4RadioactiveDecay* RadioactiveDecay = dynamic_cast<G4RadioactiveDecay*>(P);
-        RadioactiveDecay->SetICM(true);  // Internal Conversion
+        //RadioactiveDecay->SetICM(true);  // Internal Conversion -> removed from PhysicList in v10.2 see release note
         RadioactiveDecay->SetARM(true);  // Atomic Rearrangement, i.e. filling of shell vacancies
-        RadioactiveDecay->SetHLThreshold(1.0E-9*second);  // Half life cut-off of isomeruic states
+        //RadioactiveDecay->SetHLThreshold(1.0E-9*second);  // Half life cut-off of isomeric states | no longer exist in g4 v11 , no track of that on the release notes 
       }
     }
   }
diff --git a/src/cosima/src/MCSteppingAction.cc b/src/cosima/src/MCSteppingAction.cc
index d9f582acf..9370b6b9b 100644
--- a/src/cosima/src/MCSteppingAction.cc
+++ b/src/cosima/src/MCSteppingAction.cc
@@ -36,9 +36,13 @@
 #include "G4ParticleDefinition.hh"
 #include "G4ParticleTypes.hh"
 #include "G4EventManager.hh"
-#include "G4NuclearLevel.hh"
-#include "G4NuclearLevelManager.hh"
-#include "G4NuclearLevelStore.hh"
+//#include "G4NuclearLevel.hh" //no longer exist in g4 v11
+//#include "G4NuclearLevelManager.hh" // same
+//#include "G4NuclearLevelStore.hh" // same
+#include "G4NuclearLevelData.hh" //replace libs upper ? see release note 10.2
+#include "G4LevelManager.hh"
+#include "G4NucLevel.hh"
+
 #include "G4Ions.hh"
 #include "G4IonTable.hh"
 
@@ -73,6 +77,7 @@ const int MCSteppingAction::c_ProcessIDDecay                  = 11;
 const int MCSteppingAction::c_ProcessIDRadioactiveDecay       = 12;
 const int MCSteppingAction::c_ProcessIDIonization             = 13;
 const int MCSteppingAction::c_ProcessIDTransportation         = 14;
+const int MCSteppingAction::c_ProcessIDNoProcess              = 15;
 
 
 /******************************************************************************
@@ -118,6 +123,8 @@ MCSteppingAction::MCSteppingAction(MCParameterFile& RunParameters) :
   m_KnownProcess.push_back("LowEnConversion"); m_KnownProcessID.push_back(c_ProcessIDPair);
   m_KnownProcess.push_back("LowEnPolarizConversion"); m_KnownProcessID.push_back(c_ProcessIDPair);
   m_KnownProcess.push_back("muPairProd"); m_KnownProcessID.push_back(c_ProcessIDPair);
+  m_KnownProcess.push_back("ePairProd"); m_KnownProcessID.push_back(c_ProcessIDPair);
+
   
   m_KnownProcess.push_back("annihil"); m_KnownProcessID.push_back(c_ProcessIDAnnihilation);
   m_KnownProcess.push_back("PenAnnih"); m_KnownProcessID.push_back(c_ProcessIDAnnihilation);
@@ -154,6 +161,7 @@ MCSteppingAction::MCSteppingAction(MCParameterFile& RunParameters) :
   m_KnownProcess.push_back("KaonPlusInelastic"); m_KnownProcessID.push_back(c_ProcessIDInelasticScattering);
   m_KnownProcess.push_back("KaonMinusInelastic"); m_KnownProcessID.push_back(c_ProcessIDInelasticScattering);
   m_KnownProcess.push_back("LambdaInelastic"); m_KnownProcessID.push_back(c_ProcessIDInelasticScattering);
+  m_KnownProcess.push_back("anti_lambdaInelastic"); m_KnownProcessID.push_back(c_ProcessIDInelasticScattering);
   m_KnownProcess.push_back("AntiLambdaInelastic"); m_KnownProcessID.push_back(c_ProcessIDInelasticScattering);
   m_KnownProcess.push_back("SigmaMinusInelastic"); m_KnownProcessID.push_back(c_ProcessIDInelasticScattering);
   m_KnownProcess.push_back("SigmaPlusInelastic"); m_KnownProcessID.push_back(c_ProcessIDInelasticScattering);
@@ -207,6 +215,8 @@ MCSteppingAction::MCSteppingAction(MCParameterFile& RunParameters) :
   m_KnownProcess.push_back("CoulombScat"); m_KnownProcessID.push_back(c_ProcessIDIonization);
 
   m_KnownProcess.push_back("Transportation"); m_KnownProcessID.push_back(c_ProcessIDTransportation);
+  m_KnownProcess.push_back("NoProcess"); m_KnownProcessID.push_back(c_ProcessIDNoProcess);
+
 
   // To lower all processes:
   for (unsigned int i = 0; i < m_KnownProcess.size(); ++i) m_KnownProcessFrequency.push_back(0);  
@@ -910,12 +920,13 @@ void MCSteppingAction::UserSteppingAction(const G4Step* Step)
           //cout<<"Storing: "<<Nucleus->GetParticleName()<<endl;
           if (Nucleus->GetExcitationEnergy() > 1*keV) {
             //cout<<"Alignment > 1 keV"<<endl;
-            G4NuclearLevelManager* M = G4NuclearLevelStore::GetInstance()->GetManager(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass());
-            if (M->IsValid() == true) {
-              const G4NuclearLevel* Level = M->NearestLevel(Nucleus->GetExcitationEnergy());
+            const G4LevelManager* M = G4NuclearLevelData::GetInstance()->GetLevelManager(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass());
+	    bool IsValid =true ;// IsValid() method no longer available for G4LevelManager, always true for now , need to check 
+            if (IsValid == true) {
+              const G4NucLevel* Level = M->NearestLevel(Nucleus->GetExcitationEnergy());
               if (Level != 0) {
                 G4IonTable* Table = G4IonTable::GetIonTable();
-                Nucleus = dynamic_cast<G4Ions*>(Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), Level->Energy()));
+                Nucleus = dynamic_cast<G4Ions*>(Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy())));
               }
             }
           } else {
@@ -991,8 +1002,8 @@ void MCSteppingAction::UserSteppingAction(const G4Step* Step)
           //cout<<Track->GetDefinition()->GetParticleName()<<" --> "<<Step->GetPostStepPoint()->GetGlobalTime()/second<<" sec "<<Step->GetPreStepPoint()->GetGlobalTime()/second<<" sec"<<endl;
           G4TouchableHistory* Hist = (G4TouchableHistory*) (Step->GetPreStepPoint()->GetTouchable());
           G4LogicalVolume* V = Hist->GetVolume(0)->GetLogicalVolume();
-          G4String Name = V->GetName();
-          Name.remove(Name.size()-3, 3);
+          G4String Name = V->GetName(); 
+          Name.erase(Name.size()-3, 3);
           MCRunManager::GetMCRunManager()->GetCurrentRun().SkipOneEvent(Track->GetDefinition(), Name);
         }
         
@@ -1003,7 +1014,7 @@ void MCSteppingAction::UserSteppingAction(const G4Step* Step)
           G4TouchableHistory* Hist = (G4TouchableHistory*) (Step->GetPreStepPoint()->GetTouchable());
           G4LogicalVolume* V = Hist->GetVolume(0)->GetLogicalVolume();
           G4String Name = V->GetName();
-          Name.remove(Name.size()-3, 3);
+          Name.erase(Name.size()-3, 3);
 
           double GlobalTime = Step->GetPostStepPoint()->GetGlobalTime();
 //           if (Track->GetDefinition()->GetParticleName() == "Ge73[66.7]") {
@@ -1409,7 +1420,7 @@ int MCSteppingAction::GetProcessId(const G4String& Name)
       return m_KnownProcessID[i];
     }
   }
-  
+  //cout<<Name<<endl;
   return c_ProcessIDUncovered;
 }
   

From e97c49a0d69848f355834aed091b03c208c17a54 Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Thu, 16 Feb 2023 10:58:55 +0100
Subject: [PATCH 003/192] Update AllowedROOTVersions.txt

---
 config/AllowedROOTVersions.txt | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/config/AllowedROOTVersions.txt b/config/AllowedROOTVersions.txt
index 8339415de..212eb6fb8 100644
--- a/config/AllowedROOTVersions.txt
+++ b/config/AllowedROOTVersions.txt
@@ -1,2 +1 @@
-102
-111
+618 624 

From e51a2663d2c9af649473900ffc63bbe889e22eef Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Thu, 16 Feb 2023 14:49:47 -0800
Subject: [PATCH 004/192] CHG: Fixed automatic compilation

---
 config/AllowedROOTVersions.txt |  2 +-
 config/build-geant4.sh         | 50 ++++++++++++++++++++--------------
 config/build-root.sh           |  2 +-
 config/check-geant4version.sh  |  4 +--
 4 files changed, 33 insertions(+), 25 deletions(-)

diff --git a/config/AllowedROOTVersions.txt b/config/AllowedROOTVersions.txt
index 212eb6fb8..a0595b546 100644
--- a/config/AllowedROOTVersions.txt
+++ b/config/AllowedROOTVersions.txt
@@ -1 +1 @@
-618 624 
+618 626 
diff --git a/config/build-geant4.sh b/config/build-geant4.sh
index 58f342f1d..302e024b1 100755
--- a/config/build-geant4.sh
+++ b/config/build-geant4.sh
@@ -7,9 +7,8 @@ if [ $? -eq 0 ]; then
     # echo "g++ compiler found - using it as default!";
     CONFIGUREOPTIONS="-DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++"
 fi
-CONFIGUREOPTIONS="${CONFIGUREOPTIONS} -DCMAKE_INSTALL_PREFIX=.. -DGEANT4_INSTALL_DATA=ON -DGEANT4_USE_OPENGL_X11=OFF -DGEANT4_INSTALL_DATA_TIMEOUT=14400 -DGEANT4_USE_SYSTEM_EXPAT=OFF -DGEANT4_BUILD_CXXSTD=c++11"
-# For compilation with ROOT 6.06 
-#CONFIGUREOPTIONS="${CONFIGUREOPTIONS} -DCMAKE_CXX_FLAGS=-D_GLIBCXX_USE_CXX11_ABI=0"
+CONFIGUREOPTIONS="${CONFIGUREOPTIONS} -DCMAKE_INSTALL_PREFIX=.. -DGEANT4_INSTALL_DATA=ON -DGEANT4_USE_OPENGL_X11=OFF -DGEANT4_INSTALL_DATA_TIMEOUT=14400 -DGEANT4_USE_SYSTEM_EXPAT=OFF -DCMAKE_CXX_STANDARD=17"
+
 # Reduce the warning messages:
 WARNINGS="-Wno-shadow -Wno-implicit-fallthrough -Wno-overloaded-virtual -Wno-deprecated-copy -Wno-unused-result -Wno-format-overflow="
 
@@ -291,23 +290,32 @@ else
   echo "Looking for Geant4 version ${WANTEDVERSION} with latest patch on the Geant4 website --- sometimes this takes a few minutes..."
   
   # Now check Geant4 repository for the given version:
-  TESTTARBALL="geant4.${WANTEDVERSION}.tar.gz"
-  echo "Trying to find ${TESTTARBALL}..."
-  EXISTS=`curl -s --head ${WEBSITE}/${TESTTARBALL} | grep gzip`
-  if [ "${EXISTS}" == "" ]; then
-    echo "ERROR: Unable to find suitable Geant4 tar ball at the Geant4 website"
-    exit 1
-  fi
-  TARBALL=${TESTTARBALL}
-  for s in `seq -w 01 10`; do
-    TESTTARBALL="geant4.${WANTEDVERSION}.p${s}.tar.gz"
+  #TESTTARBALL="geant4_v${WANTEDVERSION}.tar.gz"
+  #echo "Trying to find ${TESTTARBALL}..."
+  #EXISTS=`curl -s --head ${WEBSITE}/${TESTTARBALL} | grep gzip`
+  #if [ "${EXISTS}" == "" ]; then
+  #  echo "ERROR: Unable to find suitable Geant4 tar ball at the Geant4 website"
+  #  exit 1
+  #fi
+  TARBALL=""
+  MAX_TRIALS=3
+  for s in `seq 0 100`; do
+    TESTTARBALL="geant4-v${WANTEDVERSION}.${s}.tar.gz"
     echo "Trying to find ${TESTTARBALL}..."
     EXISTS=`curl -s --head ${WEBSITE}/${TESTTARBALL} | grep gzip`
-    if [ "${EXISTS}" == "" ]; then
-      break
+    if [[ ${EXISTS} == "" ]]; then # sometimes version 00 does not exist...
+      MAX_TRIALS=$(( MAX_TRIALS - 1 ))
+      if [[ ${MAX_TRIALS} -eq 0 ]]; then
+        break
+      fi
+    else
+      TARBALL=${TESTTARBALL}
     fi
-    TARBALL=${TESTTARBALL}
   done
+  if [ "${TARBALL}" == "" ]; then
+    echo "ERROR: Unable to find suitable Geant4 tar ball at the Geant4 website"
+    exit 1
+  fi
   echo "Using Geant4 tar ball ${TARBALL}"
   
   # Check if it already exists locally
@@ -350,10 +358,10 @@ fi
 
 
 
-GEANT4CORE=geant4_v${VER}
-GEANT4DIR=geant4_v${VER}${DEBUGSTRING}
-GEANT4SOURCEDIR=geant4_v${VER}-source   # Attention: the cleanup checks this name pattern before removing it
-GEANT4BUILDDIR=geant4_v${VER}-build     # Attention: the cleanup checks this name pattern before removing it
+GEANT4CORE=geant4_${VER}
+GEANT4DIR=geant4_${VER}${DEBUGSTRING}
+GEANT4SOURCEDIR=geant4_${VER}-source   # Attention: the cleanup checks this name pattern before removing it
+GEANT4BUILDDIR=geant4_${VER}-build     # Attention: the cleanup checks this name pattern before removing it
 
 echo "Checking for old installation..."
 if [ -d ${GEANT4DIR} ]; then
@@ -437,7 +445,7 @@ if [ "$?" != "0" ]; then
 fi
 mkdir ${GEANT4DIR}
 cd ${GEANT4DIR}
-mv ../geant4.${VER} ${GEANT4SOURCEDIR}
+mv ../geant4-${VER} ${GEANT4SOURCEDIR}
 mkdir ${GEANT4BUILDDIR}
 
 
diff --git a/config/build-root.sh b/config/build-root.sh
index 102090152..4caef8570 100755
--- a/config/build-root.sh
+++ b/config/build-root.sh
@@ -16,7 +16,7 @@ if [[ $? -eq 0 ]]; then
   CONFIGUREOPTIONS+=" -DCMAKE_IGNORE_PATH=${PORTPATH};${PORTPATH}/bin;${PORTPATH}/include;${PORTPATH}/include/libxml2;${PORTPATH}/include/unicode"
 fi
 # Until ROOT 6.24: C++ 11
-CONFIGUREOPTIONS+=" -DCMAKE_CXX_STANDARD=11"
+CONFIGUREOPTIONS+=" -DCMAKE_CXX_STANDARD=17"
 # To compile ROOT 6.06 with gcc 5.x --- no longer  needed for ROOT 6.08 and higher
 #CONFIGUREOPTIONS+=" -DCMAKE_CXX_FLAGS=-D_GLIBCXX_USE_CXX11_ABI=0"
 # We want a minimal system and enable what we really need:
diff --git a/config/check-geant4version.sh b/config/check-geant4version.sh
index 779a29ea1..b9aefe6a9 100755
--- a/config/check-geant4version.sh
+++ b/config/check-geant4version.sh
@@ -99,13 +99,13 @@ Geant4VersionMin=`echo ${VERSIONS} | awk -F" " '{ print $1 }'`
 Geant4VersionMax=`echo ${VERSIONS} | awk -F" " '{ print $NF }'`
 
 Sep=$((${#Geant4VersionMin}-1))
-if [ ${Geant4VersionMin:0:${Sep}} -ge 10 ]; then 
+if [ ${Geant4VersionMin:0:${Sep}} -eq 10 ]; then 
   Geant4VersionMinString="${Geant4VersionMin:0:${Sep}}.0${Geant4VersionMin:${Sep}:1}"
 else 
   Geant4VersionMinString="${Geant4VersionMin:0:${Sep}}.${Geant4VersionMin:${Sep}:1}"
 fi
 Sep=$((${#Geant4VersionMax}-1))
-if [ ${Geant4VersionMax:0:${Sep}} -ge 10 ]; then 
+if [ ${Geant4VersionMax:0:${Sep}} -eq 10 ]; then 
   Geant4VersionMaxString="${Geant4VersionMax:0:${Sep}}.0${Geant4VersionMax:${Sep}:1}"
 else
   Geant4VersionMaxString="${Geant4VersionMax:0:${Sep}}.${Geant4VersionMax:${Sep}:1}"

From 56833c13f2e78b0ee1628178d681c42b8a90e25f Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Tue, 21 Feb 2023 14:55:27 -0800
Subject: [PATCH 005/192] CHG: More compile compatibilty - but still not
 running

---
 config/AllowedGeant4Versions.txt |   2 +-
 config/build-geant4.sh           |   5 +++--
 config/env.sh                    | Bin 7422 -> 7461 bytes
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/config/AllowedGeant4Versions.txt b/config/AllowedGeant4Versions.txt
index 8339415de..fc1db2732 100644
--- a/config/AllowedGeant4Versions.txt
+++ b/config/AllowedGeant4Versions.txt
@@ -1,2 +1,2 @@
-102
+110
 111
diff --git a/config/build-geant4.sh b/config/build-geant4.sh
index 302e024b1..530267132 100755
--- a/config/build-geant4.sh
+++ b/config/build-geant4.sh
@@ -261,7 +261,8 @@ if [ "${TARBALL}" != "" ]; then
   
   # Check if it has the correct version:
   VER=`echo ${TARBALL} | awk -Fgeant4. '{ print $2 }' | awk -F.t '{ print $1 }'`;
-  SHORTVER=`echo ${TARBALL} | awk -Fgeant4. '{ print $2 }' | awk -F.t '{ print $1 }' | awk -F.p '{ print $1 }'`;
+  CHECKVER=`echo ${TARBALL} | awk -Fgeant4-v '{ print $2 }' | awk -F.t '{ print $1 }'`;
+  SHORTVER=`echo ${TARBALL} | awk -Fgeant4-v '{ print $2 }' | awk -F.t '{ print $1 }' | awk -F.p '{ print $1 }'`;
   echo "Version of Geant4 is: ${VER}"
   
   if [[ ${WANTEDVERSION} != "" ]]; then
@@ -270,7 +271,7 @@ if [ "${TARBALL}" != "" ]; then
       exit 1
     fi
   else 
-    bash ${MEGALIB}/config/check-geant4version.sh --good-version=${VER}
+    bash ${MEGALIB}/config/check-geant4version.sh --good-version=${CHECKVER}
     if [ "$?" != "0" ]; then
       echo "ERROR: The Geant4 tarball you supplied does not contain an acceptable Geant4 version!"
       exit 1
diff --git a/config/env.sh b/config/env.sh
index be9c4f4b149cfa67f9f0d85a05a88537f8508f3d..42f92f19f2146b5b78b6e150f9fa4d0d9042cf75 100755
GIT binary patch
delta 23
fcmexoxzuWd2oH;bvWmv!jojjlnwvR!z6t;US@s6k

delta 12
TcmZ2#_0MvH2+w9~o>u|@BKic|


From 182bd39c212a6afe9690acd27115a1f34b1bfb8c Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Tue, 21 Feb 2023 15:23:20 -0800
Subject: [PATCH 006/192] CHG: Hack to fix random number seed issue

---
 src/cosima/src/MCMain.cc | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/cosima/src/MCMain.cc b/src/cosima/src/MCMain.cc
index 4ab1d4e0a..9dfbfd607 100644
--- a/src/cosima/src/MCMain.cc
+++ b/src/cosima/src/MCMain.cc
@@ -394,8 +394,12 @@ unsigned int MCMain::ParseCommandLine(int argc, char** argv)
   }
 
   // Set the initial seed - Geant4 & ROOT !
-  CLHEP::HepRandom::setTheSeed(m_Seed);
+  //CLHEP::HepRandom::setTheSeed(m_Seed);
+  //G4Random::setTheSeed(m_Seed);
   gRandom->SetSeed(m_Seed);
+  /// FIXME
+  cout<<endl<<endl<<"FIXME: Switch to G4Random for random numbers throughout the code"<<endl<<endl;
+  gSystem->Sleep(1000);
 
   return 0;
 }

From c672257898ad2d672eced3b512ddc6b92806a8ca Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Wed, 22 Feb 2023 10:29:30 +0100
Subject: [PATCH 007/192] Update MCSteppingAction.cc

---
 src/cosima/src/MCSteppingAction.cc | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/cosima/src/MCSteppingAction.cc b/src/cosima/src/MCSteppingAction.cc
index 9370b6b9b..0d7672907 100644
--- a/src/cosima/src/MCSteppingAction.cc
+++ b/src/cosima/src/MCSteppingAction.cc
@@ -144,7 +144,8 @@ MCSteppingAction::MCSteppingAction(MCParameterFile& RunParameters) :
   m_KnownProcess.push_back("phot"); m_KnownProcessID.push_back(c_ProcessIDPhoto);
   
   m_KnownProcess.push_back("hadElastic"); m_KnownProcessID.push_back(c_ProcessIDElasticScattering);
-  
+  m_KnownProcess.push_back("ionElastic"); m_KnownProcessID.push_back(c_ProcessIDElasticScattering);
+
   m_KnownProcess.push_back("nFission"); m_KnownProcessID.push_back(c_ProcessIDFission);
   
   m_KnownProcess.push_back("PhotonInelastic"); m_KnownProcessID.push_back(c_ProcessIDInelasticScattering);
@@ -192,6 +193,8 @@ MCSteppingAction::MCSteppingAction(MCParameterFile& RunParameters) :
   m_KnownProcess.push_back("xi-Inelastic"); m_KnownProcessID.push_back(c_ProcessIDInelasticScattering);
   m_KnownProcess.push_back("xi+Inelastic"); m_KnownProcessID.push_back(c_ProcessIDInelasticScattering);
   m_KnownProcess.push_back("xi0Inelastic"); m_KnownProcessID.push_back(c_ProcessIDInelasticScattering);
+  m_KnownProcess.push_back("anti_xi-Inelastic"); m_KnownProcessID.push_back(c_ProcessIDInelasticScattering);
+
   
   m_KnownProcess.push_back("HadronCapture"); m_KnownProcessID.push_back(c_ProcessIDCapture);
   m_KnownProcess.push_back("nCapture"); m_KnownProcessID.push_back(c_ProcessIDCapture);

From b807efce629d5a2b03654b2d4978f04152e4449e Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Fri, 3 Mar 2023 14:31:03 +0100
Subject: [PATCH 008/192] ADD : EM parameters updated

`SetDeexcitationIgnoreCut` was set to true for version 11 instead of false for version 10.02. Put it explicitly false on the physic list solved the issue of the factor 10 for the computation time.

Some comments about this option :

In Geant4 version 11, the `SetDeexcitationIgnoreCut` method is used to control the behavior of the `G4RadioactiveDecay`process during the simulation. This method sets a flag to ignore the cut imposed by the user on the production of secondary particles by radioactive decays.

By default, when a radioactive decay occurs and produces one or more secondary particles (e.g. electrons, positrons, photons), these particles are subject to the same range cut and production thresholds as any other particle in the simulation. This means that if the range of a secondary particle is smaller than the range cut or the production threshold, it may be discarded by the simulation.

However, in some cases it may be desirable to ignore these cuts for secondary particles produced by radioactive decays. This can be achieved by calling the `SetDeexcitationIgnoreCut` method with a value of true. This will cause the range cut and production thresholds to be ignored for all secondary particles produced by the `G4RadioactiveDecay` process.

It should be noted that ignoring the range cut and production thresholds can lead to longer simulation times and may affect the accuracy of the simulation. Therefore, this feature should be used with caution and only when it is necessary to model the specific physics of the problem being studied.
---
 src/cosima/src/MCPhysicsList.cc | 29 +++++++++++++++++++++++++----
 1 file changed, 25 insertions(+), 4 deletions(-)

diff --git a/src/cosima/src/MCPhysicsList.cc b/src/cosima/src/MCPhysicsList.cc
index ba19afc23..2ca9708fe 100644
--- a/src/cosima/src/MCPhysicsList.cc
+++ b/src/cosima/src/MCPhysicsList.cc
@@ -58,6 +58,8 @@
 #include "G4LossTableManager.hh"  
 #include "G4NuclideTable.hh"
 
+#include "G4EmParameters.hh"
+
 // MEGAlib:
 #include "MStreams.h"
 
@@ -208,12 +210,20 @@ void MCPhysicsList::ConstructProcess()
       //cout<<P->GetProcessName()<<endl;
       if (dynamic_cast<G4RadioactiveDecay*>(P) != 0) {
         G4RadioactiveDecay* RadioactiveDecay = dynamic_cast<G4RadioactiveDecay*>(P);
-        //RadioactiveDecay->SetICM(true);  // Internal Conversion -> removed from PhysicList in v10.2 see release note
+        //RadioactiveDecay->SetICMode(true);  // Internal Conversion geant4 11  removed SetICM() method, as deprecated for some time and no longer used. ICM now set exclusively in G4PhotonEvaporation. Added printout of the flag of atomic relaxation.
         RadioactiveDecay->SetARM(true);  // Atomic Rearrangement, i.e. filling of shell vacancies
         //RadioactiveDecay->SetHLThreshold(1.0E-9*second);  // Half life cut-off of isomeric states | no longer exist in g4 v11 , no track of that on the release notes 
       }
-    }
-  }
+      
+     // if (dynamic_cast<G4ComptonScattering*>(P) != 0) {
+     //   cout<< "compton here !"<<endl;
+      
+     //   G4ComptonScattering* ComptonScat = dynamic_cast<G4ComptonScattering*>(P);
+     //    ComptonScat->SetMinKinEnergy(1*GeV);
+     // }
+      
+    } //end for loop
+  }//end while loop
   
   G4VAtomDeexcitation* D = G4LossTableManager::Instance()->AtomDeexcitation();
   D->SetFluo(true);
@@ -223,8 +233,19 @@ void MCPhysicsList::ConstructProcess()
   G4NuclideTable::GetInstance()->SetLevelTolerance(100*eV);
   G4NuclideTable::GetInstance()->SetThresholdOfHalfLife(0.0001*ns);
   
-
+  // for geant4 v11 in order to have same EM parameters as v10.02
+  G4EmParameters* emParameters = G4EmParameters::Instance();
+  emParameters->SetFluo(true);
+  emParameters->SetPixe(true);
+  emParameters->SetAuger(true);
+  emParameters->SetDeexcitationIgnoreCut(false);
   
+  //remove the comments below if you want exactly the same paramameters as v10.02
+  //Not sure of the result if you do that
+  //emParameters->SetMuHadLateralDisplacement(false);
+  //emParameters->SetMscRangeFactor(0.04);
+  //emParameters->SetMscSkin(1);
+  //emParameters->SetAugerCascade(false);
   
   /* unnecessary as of Geant4 9.6
   // Do some additional modifications to the default lists:

From 469b90818bf0d4721bc58a0fb4f5f7ac0243afc1 Mon Sep 17 00:00:00 2001
From: GallegoSav <savitri.gallego@laposte.net>
Date: Tue, 23 May 2023 15:30:59 +0200
Subject: [PATCH 009/192] update for geant11 activation part

---
 src/cosima/src/MCActivator.cc         | 124 +++++++++++++-----
 src/cosima/src/MCActivatorParticle.cc |  41 +++++-
 src/cosima/src/MCIsotopeStore.cc      |  39 +++++-
 src/cosima/src/MCMain.cc              |   6 +-
 src/cosima/src/MCPhysicsList.cc       |   4 +
 src/cosima/src/MCRunManager.cc        |   4 +-
 src/cosima/src/MCSteppingAction.cc    | 174 ++++++++++++++++++++++++--
 src/cosima/src/MCVHit.cc              |   9 +-
 8 files changed, 353 insertions(+), 48 deletions(-)

diff --git a/src/cosima/src/MCActivator.cc b/src/cosima/src/MCActivator.cc
index 1c54f81f3..d8e8570e3 100644
--- a/src/cosima/src/MCActivator.cc
+++ b/src/cosima/src/MCActivator.cc
@@ -32,6 +32,8 @@
 // Geant4:
 #include "G4SystemOfUnits.hh"
 #include "G4RadioactiveDecay.hh"
+#include "G4Radioactivation.hh"
+
 #include "G4ParticleDefinition.hh"
 #include "G4DecayTable.hh"
 #include "G4VDecayChannel.hh"
@@ -164,6 +166,9 @@ bool MCActivator::LoadCountsFiles()
 
   m_Rates.Reset();
 
+
+
+
   for (unsigned int i = 0; i < m_CountsFiles.size(); ++i) {
     mout<<"Loading and merging isotopes file "<<m_CountsFiles[i]<<endl;
     MCIsotopeStore Counts;
@@ -206,23 +211,65 @@ bool MCActivator::CalculateEquilibriumRates()
 {
   // Determine the activation after ActivationTime & Cool-down time
 
-  /*
+  
   // Some test
-  G4IonTable* IonTable = G4IonTable::GetIonTable();
-  int Z = 30;
-  for (int A = 60; A <= 72; ++A) {
-    G4Ions* Ion = dynamic_cast<G4Ions*>(IonTable->GetIon(Z, A, 0));
-    if (Ion == 0) continue;
-    //Ion->DumpTable();
+  /*G4IonTable* IonTable = G4IonTable::GetIonTable();
+
+  int Z = 70;
+  for (int A = 157; A <= 157; ++A) {
+    G4Ions* Ion = dynamic_cast<G4Ions*>(IonTable->GetIon(Z, A, 0.5293,G4Ions::G4FloatLevelBase::no_Float));
+    if (Ion == 0) {cout<<"ion not found !"<<endl; continue;}
+    Ion->DumpTable();
+    
+   
+    
+    cout<<"Life time :"<<IonTable->GetLifeTime(Z, A, 0,G4Ions::G4FloatLevelBase::plus_Y)<<endl;
+    G4ParticleDefinition* part = IonTable->GetIon(Z, A, 0,G4Ions::G4FloatLevelBase::plus_Y);
+    cout<<"Life time from PDG def:"<<part->GetPDGLifeTime()/s<<endl;
+
+
 
     G4RadioactiveDecay* Decay = new G4RadioactiveDecay();
     G4DecayTable* DecayTable = Decay->LoadDecayTable(*Ion);
     if (DecayTable == 0) continue;
     if (DecayTable->entries() == 0) continue;
     DecayTable->DumpInfo();
+    
+    //G4Radioactivation* Decay_bis = new G4Radioactivation();
+    //G4DecayTable* DecayTable_bis = Decay_bis->LoadDecayTable(*Ion);
+    //if (DecayTable_bis == 0) continue;
+    //if (DecayTable_bis->entries() == 0) continue;
+    //DecayTable_bis->DumpInfo();
+  
+  
+    const G4LevelManager* M = G4NuclearLevelData::GetInstance()->GetLevelManager(Z, A);
+    const G4NucLevel* NuclearLevel = M->NearestLevel(Ion->GetExcitationEnergy());
+    cout<<"Number of gammas: "<<NuclearLevel->NumberOfTransitions()<<endl;
+    cout<<"Number of transition from G4LevelManager: "<<M->NumberOfTransitions()<<endl;
+
+    for (int h = 0; h < int(NuclearLevel->NumberOfTransitions()); ++h) {
+                    cout<<"final excitation index : "<< NuclearLevel->FinalExcitationIndex(h)<<endl; 
+
+                    cout<<"Gamma energy: "<<M->NearestLevelEnergy(Ion->GetExcitationEnergy(),NuclearLevel->FinalExcitationIndex(h))/keV<<endl;
+		    cout<<"level density: "<<M->LevelDensity(Ion->GetExcitationEnergy())<<endl;
+
+		     
+		    double NewLevelEnergy =0.;
+        NewLevelEnergy = M->NearestLevelEnergy(M->NearestLevelEnergy(Ion->GetExcitationEnergy()) - M->LevelEnergy(NuclearLevel->FinalExcitationIndex(h)));
+	cout<< "new level energy : " <<NewLevelEnergy<<endl;
+	const G4NucLevel* NewNuclearLevel = M->NearestLevel(M->NearestLevelEnergy(Ion->GetExcitationEnergy()) - M->LevelEnergy(NuclearLevel->FinalExcitationIndex(h)));
+
+
+        if (NewNuclearLevel!=0){ cout<< "new Half life : "<< NewNuclearLevel->GetTimeGamma()<<endl;}
+        else {
+                  cout<<"Error: No nearest level found for: "<<Ion->GetParticleName()<<" Excitation: "<<M->NearestLevelEnergy(Ion->GetExcitationEnergy()) - M->LevelEnergy(NuclearLevel->FinalExcitationIndex(h))<<endl;
+                  cout<<"       This isotope is excluded from further analysis!"<<endl;
+
+               }
+		    }
   }
-  return true;
-  */
+  return true;*/
+  
   
 
   // We utilize G4RadioactiveDecay to retrieve the decay tables
@@ -241,7 +288,13 @@ bool MCActivator::CalculateEquilibriumRates()
     for (unsigned int i = 0; i < m_Rates.GetNIDs(v); ++i) {
       cout<<"Start: ID: "<<m_Rates.GetID(v, i)<<"  #Ex: "<<m_Rates.GetNExcitations(v, i)<<endl;      
 
-      if (m_Rates.GetID(v, i) == 72154 || m_Rates.GetID(v, i) == 71154 || m_Rates.GetID(v, i) == 70154 || m_Rates.GetID(v, i) == 73158 || m_Rates.GetID(v, i) == 74158) {
+      //73192 because it create W192 unknow isotope ?
+      //44090 because  Ru90 -> Tc90[0.000X]  with HL = 0 which lead to a bug when trying to get this isotope
+      // and then goes to Tc90[0.000Y] with HL 8.7s which lead to geant4 loop
+      // hope it will be corrected in the next patch (here v11.01)
+       
+      if (m_Rates.GetID(v, i) == 44090 || m_Rates.GetID(v, i) == 73192 )  
+      {
         cout<<"Warning: This element sends Geant4 in an infinite loop -- skipping!"<<endl;
         continue;
       }
@@ -356,6 +409,14 @@ bool MCActivator::CalculateEquilibriumRates()
                       MCActivatorParticle NewParticle;
                       NewParticle.SetIDAndExcitation(MCSteppingAction::GetParticleType(ParticleDef->GetParticleName()), 
                                                   ExcitationEnergy);
+		      //NewParticle.GetDefinition()->DumpTable();
+		      // have to compute get the Halflife with the good def (ex Tb145[0.000Y] and not Tb145 ) #g4v11.01 bug
+		      DetermineHalfLife(NewParticle.GetDefinition(), HalfLife, ExcitationEnergy, false);
+		      //cout<< "Name :" <<NewParticle.GetDefinition()->GetParticleName()<<endl;
+		      //cout<< NewParticle.GetDefinition()->GetPDGLifeTime()*log(2.0)/s<<" sec"<<endl;
+		      //cout<< "Name : " << ParticleName<<endl;
+		      //cout<< ParticleDef->GetPDGLifeTime()*log(2.0)/s<<" sec"<<endl; 		  
+ 		  
                       if (Tree[b].back().GetBranchingRatio()* Channel->GetBR() > 1.01) {
                         mout<<"Error (DecayLoop): Branching ratio of "<<Tree[b].back().GetName()<<" larger than one: "<<Tree[b].back().GetBranchingRatio()* Channel->GetBR()<<endl;
                         continue;
@@ -364,6 +425,7 @@ bool MCActivator::CalculateEquilibriumRates()
                       //cout<<"Adding to branch "<<b<<", after "<<ABranch.back().GetName()<<": "<<ParticleDef->GetParticleName()<<" -> BR="<<Channel->GetBR()<<endl;
                       NewParticle.SetBranchingRatio(Tree[b].back().GetBranchingRatio()* Channel->GetBR());
                       NewParticle.SetHalfLife(HalfLife);
+		      //cout<<"HALFLIFE after SetHalfLife = "<<NewParticle.GetHalfLife()<<endl;
                       
                       //cout<<"ID: "<<MCSteppingAction::GetParticleType(Nucleus->GetParticleName())<<":"<<Nucleus->GetExcitationEnergy()<<endl;
                       ABranch.push_back(NewParticle);
@@ -418,50 +480,55 @@ bool MCActivator::CalculateEquilibriumRates()
 
             NChanges = 0;
             unsigned int b_max = Tree.size(); // The tree will grow, thus do not go beyond the original max size --- we will visit the new branches later!
+	    
+
+	    
             for (unsigned int b = 0; b < b_max; ++b) {
-              if (Tree[b].size() == 0 || Tree[b].back().GetExcitation() < 1.0*keV) continue;
-              
+              if (Tree[b].size() == 0 || Tree[b].back().GetExcitation() < 1.0*keV) {
+	      continue;
+                       }
               // We have to make sure that in the first round only all immidiate decays are handled, which replace individial elements
               // in the chain, only in the second round we ONCE add to the chain and then test immidiate decays again
               if (Tree[b].back().GetHalfLife() > m_HalfLifeCutOff && ImmidiateDecayRound == true) {
                 continue;
               }
-              
               G4Ions* Nucleus = dynamic_cast<G4Ions*>(Tree[b].back().GetDefinition()); 
-              
+
+	      
               bool LevelsOK = true;
               //G4NucLearLevelManager* M = G4NucLevelStore::GetInstance()->GetManager(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass());
               const G4LevelManager* M = G4NuclearLevelData::GetInstance()->GetLevelManager(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass());
-	      
+
+
 	      //if (M->IsValid() == true) {
-	      bool IsValid = true; // IsValid() Method no longer exist for G4LevelManager, is all level are registered now ? 
-	      if (IsValid == true) {
+	      if (M != nullptr) {
+               const G4NucLevel* NuclearLevel = M->NearestLevel(Nucleus->GetExcitationEnergy());
 
                 //M->PrintAll();
-                const G4NucLevel* NuclearLevel = M->NearestLevel(Nucleus->GetExcitationEnergy());
                 cout<<"Nearest level: "<<M->NearestLevelEnergy(Nucleus->GetExcitationEnergy())/keV<<" vs. "<<Nucleus->GetExcitationEnergy()/keV<<endl;
                 if (NuclearLevel != 0) {
                   // Create new levels...
                   cout<<"Number of gammas: "<<NuclearLevel->NumberOfTransitions()<<endl;
+
                   for (int h = 0; h < int(NuclearLevel->NumberOfTransitions()); ++h) {
                     vector<MCActivatorParticle> ABranch = Tree[b];
-                    cout<<"Gamma energy: "<<M->LevelEnergy(NuclearLevel->FinalExcitationIndex(h))/keV<<endl;
+                    //cout<<"Gamma energy: "<<M->LevelEnergy(NuclearLevel->FinalExcitationIndex(h))/keV<<endl;
                     
                     double NewLevelEnergy = 0.0;
                     double NewHalfLife = 0.0;
-                    if (fabs(M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()) - M->LevelEnergy(NuclearLevel->FinalExcitationIndex(h))) > 1*keV && /* NuclearLevel->GammaEnergies()[h] > 1*keV && */
+                    if (/*fabs(M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()) - M->LevelEnergy(NuclearLevel->FinalExcitationIndex(h))) > 1*keV &&*/ /* NuclearLevel->GammaEnergies()[h] > 1*keV && */
                         M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()) != M->MaxLevelEnergy()) { // table has some significant uncertainties...
                       // Make sure we know the exact energy of the new level:
-                      const G4NucLevel* NewNuclearLevel = M->NearestLevel(M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()) - M->LevelEnergy(NuclearLevel->FinalExcitationIndex(h)));
+                      const G4NucLevel* NewNuclearLevel = M->GetLevel(NuclearLevel->FinalExcitationIndex(h));
                       if (NewNuclearLevel != 0) {
-                        NewLevelEnergy = M->NearestLevelEnergy(M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()) - M->LevelEnergy(NuclearLevel->FinalExcitationIndex(h)));
-                        if (NewNuclearLevel->GetTimeGamma () > m_HalfLifeCutOff) {
-                          NewHalfLife = NewNuclearLevel->GetTimeGamma ();
+                        NewLevelEnergy = M->LevelEnergy(NuclearLevel->FinalExcitationIndex(h));
+                        if (NewNuclearLevel->GetTimeGamma() > m_HalfLifeCutOff) {
+                          NewHalfLife = NewNuclearLevel->GetTimeGamma();
                         } else {
                           NewHalfLife = 0.0;
                         }
                       } else {
-                        mout<<"Error: No nearest level found for: "<<Nucleus->GetParticleName()<<" Excitation: "<<M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()) - M->LevelEnergy(NuclearLevel->FinalExcitationIndex(h))<<endl;
+                        mout<<"Error: No nearest level found for: "<<Nucleus->GetParticleName()<<" Excitation: "<< M->LevelEnergy(NuclearLevel->FinalExcitationIndex(h))<<endl;
                         mout<<"       This isotope is excluded from further analysis!"<<endl;
                         LevelsOK = false;                        
                       }
@@ -515,6 +582,7 @@ bool MCActivator::CalculateEquilibriumRates()
                       cout<<"Adding entry with energy: "<<NewParticle.GetExcitation()/keV<<endl;
                     }
                   } // all possible gammas
+		  
                   if (NuclearLevel->NumberOfTransitions() > 0 && LevelsOK == true) {
                     Tree[b].clear(); // mark for removal
                     TreeChanged = true;
@@ -1284,10 +1352,10 @@ bool MCActivator::DetermineHalfLife(G4ParticleDefinition* ParticleDef, double& H
       const G4LevelManager* M = G4NuclearLevelData::GetInstance()->GetLevelManager(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass());
 
       //M->PrintAll();
-      bool IsValid = true; // IsValid() Method no longer exist for G4LevelManager, is all level are registered now ? 
-      if (IsValid == true) {
+      if (M!=nullptr) {
+       const G4NucLevel* Level = M->NearestLevel(Nucleus->GetExcitationEnergy());
+
         //const G4NucLevel* Level = M->NearestLevel(Nucleus->GetExcitationEnergy());
-	const G4NucLevel* Level = M->NearestLevel(Nucleus->GetExcitationEnergy());
 
         //Level->PrintAll();
         if (Level != 0) {
diff --git a/src/cosima/src/MCActivatorParticle.cc b/src/cosima/src/MCActivatorParticle.cc
index ec9473ea9..eab14baff 100644
--- a/src/cosima/src/MCActivatorParticle.cc
+++ b/src/cosima/src/MCActivatorParticle.cc
@@ -129,7 +129,46 @@ void MCActivatorParticle::SetIDAndExcitation(unsigned int ID, double Excitation)
   G4IonTable* Table = G4IonTable::GetIonTable();
   int AtomicNumber = int(m_ID/1000);
   int AtomicMass = m_ID - int(m_ID/1000)*1000;
-  m_Definition = Table->GetIon(AtomicNumber, AtomicMass, Excitation);
+  //m_Definition = Table->GetIon(AtomicNumber, AtomicMass, Excitation);
+
+
+   if(   Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::no_Float)!= -1001)
+  {m_Definition =     Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::no_Float);}
+  
+  //if the level state of the isotope is a floating level , loop over the levels until we Get
+ //the isotope in order to not get 0s lifetime . Will be probably fixed in the next patch
+  else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_X)!= -1001) {m_Definition =  Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_X);}
+  
+  else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_Y)!= -1001) {m_Definition =  Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_Y);}
+  
+  else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_Z)!= -1001) {m_Definition =  Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_Z);}
+  
+  else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_U)!= -1001) {m_Definition =  Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_U);}
+  
+  else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_V)!= -1001) {m_Definition =  Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_V);}
+  
+   else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_W)!= -1001) {m_Definition =  Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_W);}
+  
+   else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_R)!= -1001) {m_Definition =  Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_R);}
+   
+    else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_S)!= -1001) {m_Definition =  Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_S);}
+    
+   else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_T)!= -1001) {m_Definition =  Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_T);}
+   
+   else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_A)!= -1001) {m_Definition =  Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_A);}
+  
+   else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_B)!= -1001) {m_Definition =  Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_B);}
+   
+    else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_C)!= -1001) {m_Definition =  Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_C);}
+    
+   else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_D)!= -1001) {m_Definition =  Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_D);}
+  
+   else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_E)!= -1001) {m_Definition =  Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_E);}
+  
+  
+  else if(m_Definition==0){cout<<"Half Life time below the SetThresholdOfHalfLife or no isotope found with this excitation energy -> create a isotope with 0s of half-time  ! Z = "<<AtomicNumber
+  << " A = "<< AtomicMass<< " E = "<<Excitation<<endl;
+  m_Definition =     Table->GetIon(AtomicNumber, AtomicMass, Excitation);}
 
   massert(m_Definition != 0);
 }
diff --git a/src/cosima/src/MCIsotopeStore.cc b/src/cosima/src/MCIsotopeStore.cc
index ff4c4ec4d..2424469d8 100644
--- a/src/cosima/src/MCIsotopeStore.cc
+++ b/src/cosima/src/MCIsotopeStore.cc
@@ -66,7 +66,44 @@ G4ParticleDefinition* MCIsotopeStore::GetParticleDefinition(int IonID, double Ex
   int AtomicNumber = int(IonID/1000);
   int AtomicMass = IonID - int(IonID/1000)*1000;
   
-  return Table->GetIon(AtomicNumber, AtomicMass, Excitation);
+  
+  if(   Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::no_Float)!= -1001)
+  {return    Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::no_Float);}
+  
+  //if the level state of the isotope is a floating level , loop over the levels until we Get
+ //the isotope in order to not get 0s lifetime . Will be probably fixed in the next patch
+  else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_X)!= -1001) {return Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_X);}
+  
+  else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_Y)!= -1001) {return Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_Y);}
+  
+  else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_Z)!= -1001) {return Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_Z);}
+  
+  else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_U)!= -1001) {return Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_U);}
+  
+  else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_V)!= -1001) {return Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_V);}
+  
+   else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_W)!= -1001) {return Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_W);}
+  
+   else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_R)!= -1001) {return Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_R);}
+   
+    else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_S)!= -1001) {return Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_S);}
+    
+   else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_T)!= -1001) {return Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_T);}
+   
+   else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_A)!= -1001) {return Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_A);}
+  
+   else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_B)!= -1001) {return Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_B);}
+   
+    else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_C)!= -1001) {return Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_C);}
+    
+   else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_D)!= -1001) {return Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_D);}
+  
+   else if (Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_E)!= -1001) {return Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_E);}
+  
+  
+  else {cout<<"ERROR no correct lifetime found for this isotope ->"
+  <<"Z = "<<AtomicNumber<< " A = "<< AtomicMass<< " E = "<<Excitation<<endl; 
+  return nullptr;}
 }
 
 
diff --git a/src/cosima/src/MCMain.cc b/src/cosima/src/MCMain.cc
index 9dfbfd607..4ab1d4e0a 100644
--- a/src/cosima/src/MCMain.cc
+++ b/src/cosima/src/MCMain.cc
@@ -394,12 +394,8 @@ unsigned int MCMain::ParseCommandLine(int argc, char** argv)
   }
 
   // Set the initial seed - Geant4 & ROOT !
-  //CLHEP::HepRandom::setTheSeed(m_Seed);
-  //G4Random::setTheSeed(m_Seed);
+  CLHEP::HepRandom::setTheSeed(m_Seed);
   gRandom->SetSeed(m_Seed);
-  /// FIXME
-  cout<<endl<<endl<<"FIXME: Switch to G4Random for random numbers throughout the code"<<endl<<endl;
-  gSystem->Sleep(1000);
 
   return 0;
 }
diff --git a/src/cosima/src/MCPhysicsList.cc b/src/cosima/src/MCPhysicsList.cc
index 2ca9708fe..ff44a6504 100644
--- a/src/cosima/src/MCPhysicsList.cc
+++ b/src/cosima/src/MCPhysicsList.cc
@@ -41,6 +41,7 @@
 #include "G4EmPenelopePhysics.hh"
 #include "G4EmStandardPhysics.hh"
 #include "G4RadioactiveDecayPhysics.hh"
+
 #include "G4VProcess.hh"
 #include "G4VEmProcess.hh"
 #include "G4VEnergyLossProcess.hh"
@@ -178,6 +179,9 @@ void MCPhysicsList::Register()
   // We always register all sorts of decays:
   RegisterPhysics(new G4RadioactiveDecayPhysics());
   
+  
+  
+  
   // Check what we got:
   cout<<"Chosen physics: "<<endl;
   for (unsigned int p = 0; ; ++p) {
diff --git a/src/cosima/src/MCRunManager.cc b/src/cosima/src/MCRunManager.cc
index 380db1038..f574456dd 100644
--- a/src/cosima/src/MCRunManager.cc
+++ b/src/cosima/src/MCRunManager.cc
@@ -98,7 +98,9 @@ void MCRunManager::StartBeam()
     mout<<"Starting activator \""<<m_RunParameters.GetActivator(a).GetName()<<"\":"<<endl;
     mout<<endl;
 
-    m_RunParameters.GetActivator(a).LoadCountsFiles();
+    if (m_RunParameters.GetActivator(a).LoadCountsFiles() == false) {
+      return;
+    }
     m_RunParameters.GetActivator(a).CalculateEquilibriumRates();
     m_RunParameters.GetActivator(a).SaveOutputFile();
   }
diff --git a/src/cosima/src/MCSteppingAction.cc b/src/cosima/src/MCSteppingAction.cc
index 0d7672907..dfae26def 100644
--- a/src/cosima/src/MCSteppingAction.cc
+++ b/src/cosima/src/MCSteppingAction.cc
@@ -929,13 +929,123 @@ void MCSteppingAction::UserSteppingAction(const G4Step* Step)
               const G4NucLevel* Level = M->NearestLevel(Nucleus->GetExcitationEnergy());
               if (Level != 0) {
                 G4IonTable* Table = G4IonTable::GetIonTable();
-                Nucleus = dynamic_cast<G4Ions*>(Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy())));
+		
+		 if(Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::no_Float)!=-1001){ 
+    Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::no_Float));}
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_X)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_X)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_Y)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_Y)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_Z)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_Z)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_U)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_U)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_V)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_V)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_W)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_W)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_R)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_R)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_S)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_S)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_T)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_T)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_T)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_T)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_A)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_A)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_B)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_B)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_C)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_C)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_D)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_D)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_E)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy()),G4Ions::G4FloatLevelBase::plus_E)); }
+		
+    else { cout<<"Isotope not found from MCSteppingAction"<<endl;
+           cout<< Nucleus->GetAtomicNumber() << Nucleus->GetAtomicMass()<< M->NearestLevelEnergy(Nucleus->GetExcitationEnergy())<<endl;
+           Nucleus = nullptr;
+    }	 	
+		
+               // Nucleus = dynamic_cast<G4Ions*>(Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), M->NearestLevelEnergy(Nucleus->GetExcitationEnergy())));
               }
             }
           } else {
             //cout<<"Alignment < 1 keV"<<endl;
             G4IonTable* Table = G4IonTable::GetIonTable();
-            Nucleus = dynamic_cast<G4Ions*>(Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0));
+            //Nucleus = dynamic_cast<G4Ions*>(Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0));
+	    
+	    
+	    if(Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::no_Float)!=-1001){ 
+    Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::no_Float));}
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_X)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_X)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_Y)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_Y)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_Z)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_Z)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_U)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_U)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_V)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_V)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_W)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_W)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_R)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_R)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_S)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_S)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_T)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_T)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_T)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_T)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_A)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_A)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_B)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_B)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_C)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_C)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_D)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_D)); }
+    
+    else if( Table->GetLifeTime(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_E)!=-1001)
+    { Nucleus = dynamic_cast<G4Ions*>( Table->GetIon(Nucleus->GetAtomicNumber(), Nucleus->GetAtomicMass(), 0.0,G4Ions::G4FloatLevelBase::plus_E)); }
+		
+    else { cout<<"Isotope not found from MCSteppingAction"<<endl;
+           cout<< "Z : "<<Nucleus->GetAtomicNumber()<< "A :"<< Nucleus->GetAtomicMass()<<"E : " <<0.0<<endl;
+           Nucleus = nullptr;
+    }	 	
+	    
+	    
           }
           //cout<<"NE: "<<Nucleus->GetExcitationEnergy()/keV<<"keV"<<endl;
 
@@ -1796,17 +1906,65 @@ G4ParticleDefinition* MCSteppingAction::GetParticleDefinition(int ID, double Exc
   
   // Check for ions first
   if (ID > 1000) {
-    G4ParticleDefinition* Ion = 0;
+    
     G4IonTable* Table = G4IonTable::GetIonTable();
     int AtomicNumber = int(ID/1000);
     int AtomicMass = ID - int(ID/1000)*1000;
-    Ion = Table->GetIon(AtomicNumber, AtomicMass, Excitation);
-    if (Ion == 0) {
+    
+    
+    if(Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::no_Float)!=-1001){ 
+    ParticleDefinition = Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::no_Float);}
+    
+    else if( Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_X)!=-1001)
+    { ParticleDefinition = Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_X); }
+    
+    else if( Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_Y)!=-1001)
+    { ParticleDefinition = Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_Y); }
+    
+    else if( Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_Z)!=-1001)
+    { ParticleDefinition = Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_Z); }
+    
+    else if( Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_U)!=-1001)
+    { ParticleDefinition = Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_U); }
+    
+    else if( Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_V)!=-1001)
+    { ParticleDefinition = Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_V); }
+    
+    else if( Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_W)!=-1001)
+    { ParticleDefinition = Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_W); }
+    
+    else if( Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_R)!=-1001)
+    { ParticleDefinition = Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_R); }
+    
+    else if( Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_S)!=-1001)
+    { ParticleDefinition = Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_S); }
+    
+    else if( Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_T)!=-1001)
+    { ParticleDefinition = Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_T); }
+    
+    else if( Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_T)!=-1001)
+    { ParticleDefinition = Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_T); }
+    
+    else if( Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_A)!=-1001)
+    { ParticleDefinition = Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_A); }
+    
+    else if( Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_B)!=-1001)
+    { ParticleDefinition = Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_B); }
+    
+    else if( Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_C)!=-1001)
+    { ParticleDefinition = Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_C); }
+    
+    else if( Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_D)!=-1001)
+    { ParticleDefinition = Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_D); }
+    
+    else if( Table->GetLifeTime(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_E)!=-1001)
+    { ParticleDefinition = Table->GetIon(AtomicNumber, AtomicMass, Excitation,G4Ions::G4FloatLevelBase::plus_E); }
+    
+    
+    else {
       merr<<"Particle type not yet implemented!"<<endl;
       ParticleDefinition = nullptr;
-    } else {
-      ParticleDefinition = Ion;
-    }
+    } 
   } else if (ID == MCSource::c_Gamma) {
     ParticleDefinition = G4Gamma::Gamma();
   } else if (ID == MCSource::c_Positron) {
diff --git a/src/cosima/src/MCVHit.cc b/src/cosima/src/MCVHit.cc
index 70dec9f63..e9b626599 100644
--- a/src/cosima/src/MCVHit.cc
+++ b/src/cosima/src/MCVHit.cc
@@ -45,7 +45,7 @@ MCVHit::MCVHit()
   m_Name = "Unknown";
   m_DetectorType = MDDetector::c_NoDetectorType;
 
-  m_LastAddedOrigin = -1; 
+  m_LastAddedOrigin = g_UnsignedIntNotDefined; 
 }
 
 
@@ -61,7 +61,7 @@ MCVHit::~MCVHit()
 /******************************************************************************
  * Add a track ID as origin to this hit
  */
-void MCVHit::AddOrigin(int TrackId)
+void MCVHit::AddOrigin(unsigned int TrackId)
 {
   // Since m_origin is a set, the origin is not added if it already exists!
 
@@ -72,9 +72,9 @@ void MCVHit::AddOrigin(int TrackId)
 /******************************************************************************
  * Add several origins to the list
  */
-void MCVHit::AddOrigins(const set<int>& Origins)
+void MCVHit::AddOrigins(const set<unsigned int>& Origins)
 {
-  set<int>::const_iterator Iter;
+  set<unsigned int>::const_iterator Iter;
   for (Iter = Origins.begin(); Iter != Origins.end(); ++Iter) {
     AddOrigin(*Iter);
   }
@@ -97,6 +97,7 @@ MSimHT* MCVHit::GetCalibrated()
 {
   MSimHT* HT = new MSimHT();
   HT->Set(m_DetectorType, MVector(m_Position.getX()/cm, m_Position.getY()/cm, m_Position.getZ()/cm), m_Energy/keV, m_Time/s, m_Origins, false);
+
   return HT;
 }
 

From d46c65972ed6cc77325dbef3fe43d850f5d3eab7 Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Tue, 23 May 2023 15:38:29 +0200
Subject: [PATCH 010/192] Update MCMain.cc

---
 src/cosima/src/MCMain.cc | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/cosima/src/MCMain.cc b/src/cosima/src/MCMain.cc
index 4ab1d4e0a..9dfbfd607 100644
--- a/src/cosima/src/MCMain.cc
+++ b/src/cosima/src/MCMain.cc
@@ -394,8 +394,12 @@ unsigned int MCMain::ParseCommandLine(int argc, char** argv)
   }
 
   // Set the initial seed - Geant4 & ROOT !
-  CLHEP::HepRandom::setTheSeed(m_Seed);
+  //CLHEP::HepRandom::setTheSeed(m_Seed);
+  //G4Random::setTheSeed(m_Seed);
   gRandom->SetSeed(m_Seed);
+  /// FIXME
+  cout<<endl<<endl<<"FIXME: Switch to G4Random for random numbers throughout the code"<<endl<<endl;
+  gSystem->Sleep(1000);
 
   return 0;
 }

From 49f2c094faba6979a9cf72957ccda24ef4d0ff2b Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Tue, 23 May 2023 15:39:51 +0200
Subject: [PATCH 011/192] Update MCVHit.cc

---
 src/cosima/src/MCVHit.cc | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/cosima/src/MCVHit.cc b/src/cosima/src/MCVHit.cc
index e9b626599..70dec9f63 100644
--- a/src/cosima/src/MCVHit.cc
+++ b/src/cosima/src/MCVHit.cc
@@ -45,7 +45,7 @@ MCVHit::MCVHit()
   m_Name = "Unknown";
   m_DetectorType = MDDetector::c_NoDetectorType;
 
-  m_LastAddedOrigin = g_UnsignedIntNotDefined; 
+  m_LastAddedOrigin = -1; 
 }
 
 
@@ -61,7 +61,7 @@ MCVHit::~MCVHit()
 /******************************************************************************
  * Add a track ID as origin to this hit
  */
-void MCVHit::AddOrigin(unsigned int TrackId)
+void MCVHit::AddOrigin(int TrackId)
 {
   // Since m_origin is a set, the origin is not added if it already exists!
 
@@ -72,9 +72,9 @@ void MCVHit::AddOrigin(unsigned int TrackId)
 /******************************************************************************
  * Add several origins to the list
  */
-void MCVHit::AddOrigins(const set<unsigned int>& Origins)
+void MCVHit::AddOrigins(const set<int>& Origins)
 {
-  set<unsigned int>::const_iterator Iter;
+  set<int>::const_iterator Iter;
   for (Iter = Origins.begin(); Iter != Origins.end(); ++Iter) {
     AddOrigin(*Iter);
   }
@@ -97,7 +97,6 @@ MSimHT* MCVHit::GetCalibrated()
 {
   MSimHT* HT = new MSimHT();
   HT->Set(m_DetectorType, MVector(m_Position.getX()/cm, m_Position.getY()/cm, m_Position.getZ()/cm), m_Energy/keV, m_Time/s, m_Origins, false);
-
   return HT;
 }
 

From 00f94b4d314272d9118493a8484b10a703915826 Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Thu, 15 Jun 2023 11:48:55 +0200
Subject: [PATCH 012/192] Update MCCrossSections.cc

I had to modified this file because the folder `rayl,pair,phot` are no more present. The cross sections are loaded differently but the results are the same with the version 10.2
---
 src/cosima/src/MCCrossSections.cc | 56 ++++++++++++++++++++++---------
 1 file changed, 40 insertions(+), 16 deletions(-)

diff --git a/src/cosima/src/MCCrossSections.cc b/src/cosima/src/MCCrossSections.cc
index 508ca0105..4e1e69d3b 100644
--- a/src/cosima/src/MCCrossSections.cc
+++ b/src/cosima/src/MCCrossSections.cc
@@ -31,6 +31,12 @@
 #include "G4Material.hh"
 #include "G4MaterialTable.hh"
 #include "G4Version.hh"
+#include "G4LivermorePhotoElectricModel.hh"
+#include "G4LivermoreRayleighModel.hh"
+#include "G4LivermoreGammaConversionModel.hh"
+#include "G4ParticleTable.hh"
+#include "G4ParticleDefinition.hh"
+#include "G4DataVector.hh"
 
 // ROOT:
 #include "TSystem.h"
@@ -70,21 +76,37 @@ bool MCCrossSections::CreateCrossSectionFiles(MString Path)
   // Make sure the path exists
   gSystem->mkdir(Path, true);
 
-  G4CrossSectionHandler* CrossSectionHandlerPhoto = new G4CrossSectionHandler;
-  CrossSectionHandlerPhoto->Clear();
-  CrossSectionHandlerPhoto->LoadData("phot/pe-cs-");
-
-  G4CrossSectionHandler* CrossSectionHandlerRayleigh = new G4CrossSectionHandler;
-  CrossSectionHandlerRayleigh->Clear();
-  CrossSectionHandlerRayleigh->LoadData("rayl/re-cs-");
+  
+  // Get the G4ParticleTable
+  G4ParticleTable* particleTable = G4ParticleTable::GetParticleTable();
 
+  // Get the G4ParticleDefinition for a photon
+  G4ParticleDefinition* gamma = particleTable->FindParticle("gamma");
+    
   G4CrossSectionHandler* CrossSectionHandlerCompton = new G4CrossSectionHandler;
   CrossSectionHandlerCompton->Clear();
   CrossSectionHandlerCompton->LoadData("comp/ce-cs-");
 
-  G4CrossSectionHandler* CrossSectionHandlerPair = new G4CrossSectionHandler;
-  CrossSectionHandlerPair->Clear();
-  CrossSectionHandlerPair->LoadData("pair/pp-cs-");
+  G4LivermorePhotoElectricModel* CrossSectionHandlerPhoto = new G4LivermorePhotoElectricModel;
+  G4DataVector Data;
+  CrossSectionHandlerPhoto->Initialise(gamma,Data);
+ 
+  
+  //G4CrossSectionHandler* CrossSectionHandlerPhoto = new G4CrossSectionHandler;
+  //CrossSectionHandlerPhoto->Clear();
+  //CrossSectionHandlerPhoto->LoadData("phot/pe-cs-");
+
+  G4LivermoreRayleighModel* CrossSectionHandlerRayleigh = new G4LivermoreRayleighModel;
+  //G4CrossSectionHandler* CrossSectionHandlerRayleigh = new G4CrossSectionHandler;
+  //CrossSectionHandlerRayleigh->Clear();
+  //CrossSectionHandlerRayleigh->LoadData("rayl/re-cs-");
+
+  G4LivermoreGammaConversionModel*  CrossSectionHandlerPair = new G4LivermoreGammaConversionModel;
+  //G4CrossSectionHandler* CrossSectionHandlerPair = new G4CrossSectionHandler;
+  //CrossSectionHandlerPair->Clear();
+  //CrossSectionHandlerPair->LoadData("pair/pp-cs-");
+
+  cout<<"Cross-section Data loaded !"<<endl;
 
   // Loop over all materials and write the cross-section files
   double eMin = 1*keV;
@@ -99,6 +121,8 @@ bool MCCrossSections::CreateCrossSectionFiles(MString Path)
   const G4MaterialTable* Table = G4Material::GetMaterialTable();
   //const G4ProductionCutsTable* Table = G4ProductionCutsTable::GetProductionCutsTable();
 
+  
+
   for (unsigned int mat = 0; mat < Table->size(); ++mat) {
     //const G4Material* M = Table->GetMaterialCutsCouple(mat)->GetMaterial();
     const G4Material* M = Table->at(mat);
@@ -127,7 +151,7 @@ bool MCCrossSections::CreateCrossSectionFiles(MString Path)
       for (int e = 0; e <= eBins; ++e) {
         out<<"R1 "
            <<fixed<<setw(16)<<exp(eMin+e*eDist)/keV<<" "
-           <<scientific<<CrossSectionHandlerPhoto->ValueForMaterial(M, exp(eMin+e*eDist))/(1/cm)<<endl;
+           <<scientific<<CrossSectionHandlerPhoto->CrossSectionPerVolume(M, gamma,exp(eMin+e*eDist))/(1/cm)<<endl;
       }
       out<<endl;
     } else {
@@ -154,7 +178,7 @@ bool MCCrossSections::CreateCrossSectionFiles(MString Path)
       for (int e = 0; e <= eBins; ++e) {
         out<<"R1 "
            <<fixed<<setw(16)<<exp(eMin+e*eDist)/keV<<" "
-           <<scientific<<CrossSectionHandlerRayleigh->ValueForMaterial(M, exp(eMin+e*eDist))/(1/cm)<<endl;
+           <<scientific<<CrossSectionHandlerRayleigh->CrossSectionPerVolume(M,gamma, exp(eMin+e*eDist))/(1/cm)<<endl;
       }
       out<<endl;
     } else {
@@ -208,7 +232,7 @@ bool MCCrossSections::CreateCrossSectionFiles(MString Path)
       for (int e = 0; e <= eBins; ++e) {
         out<<"R1 "
            <<fixed<<setw(16)<<exp(eMin+e*eDist)/keV<<" "
-           <<scientific<<CrossSectionHandlerPair->ValueForMaterial(M, exp(eMin+e*eDist))/(1/cm)<<endl;
+           <<scientific<<CrossSectionHandlerPair->CrossSectionPerVolume(M, gamma,exp(eMin+e*eDist))/(1/cm)<<endl;
       }
       out<<endl;
     } else {
@@ -235,10 +259,10 @@ bool MCCrossSections::CreateCrossSectionFiles(MString Path)
       for (int e = 0; e <= eBins; ++e) {
         out<<"R1 "
            <<fixed<<setw(16)<<exp(eMin+e*eDist)/keV<<" "
-           <<scientific<<(CrossSectionHandlerPhoto->ValueForMaterial(M, exp(eMin+e*eDist)) + 
-                          CrossSectionHandlerRayleigh->ValueForMaterial(M, exp(eMin+e*eDist)) + 
+           <<scientific<<(CrossSectionHandlerPhoto->CrossSectionPerVolume(M, gamma,exp(eMin+e*eDist)) + 
+                          CrossSectionHandlerRayleigh->CrossSectionPerVolume(M,gamma ,exp(eMin+e*eDist)) + 
                           CrossSectionHandlerCompton->ValueForMaterial(M, exp(eMin+e*eDist)) + 
-                          CrossSectionHandlerPair->ValueForMaterial(M, exp(eMin+e*eDist)))/(1/cm)<<endl;
+                          CrossSectionHandlerPair->CrossSectionPerVolume(M, gamma,exp(eMin+e*eDist)))/(1/cm)<<endl;
       }
       out<<endl;
     } else {

From a4c021d51c3380f9e34dbeee05b7c79d6b79128e Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Thu, 6 Jul 2023 12:10:04 -0700
Subject: [PATCH 013/192] ADD: Flag to really exclude excluded lines

---
 src/global/misc/inc/MIsotope.h        |  2 +-
 src/global/misc/inc/MIsotopeStore.h   |  2 +-
 src/global/misc/src/MIsotope.cxx      | 16 +++++++++-------
 src/global/misc/src/MIsotopeStore.cxx |  6 +++---
 4 files changed, 14 insertions(+), 12 deletions(-)

diff --git a/src/global/misc/inc/MIsotope.h b/src/global/misc/inc/MIsotope.h
index 9bbe5f869..8fc56f57f 100644
--- a/src/global/misc/inc/MIsotope.h
+++ b/src/global/misc/inc/MIsotope.h
@@ -58,7 +58,7 @@ class MIsotope
   unsigned int GetNucleons() const { return m_Nucleons; }
   
   //! Add line parameters:
-  virtual void AddLine(double Energy, double BranchingRatio, const MString& Flags);
+  virtual void AddLine(double Energy, double BranchingRatio, const MString& Flags, bool ExcludeExcludedLines = false);
   //! Return the number of lines
   unsigned GetNLines() const { return m_LineEnergies.size(); }
   //! Return the line energy
diff --git a/src/global/misc/inc/MIsotopeStore.h b/src/global/misc/inc/MIsotopeStore.h
index b7bc6bfbf..9018c99b8 100644
--- a/src/global/misc/inc/MIsotopeStore.h
+++ b/src/global/misc/inc/MIsotopeStore.h
@@ -41,7 +41,7 @@ class MIsotopeStore
   virtual ~MIsotopeStore();
 
   //! Load all isotopes form a standard MEGAlib isotope file
-  bool Load(MString FileName);
+  bool Load(MString FileName, bool ExcludeExcludedLines = false);
 
   //! Return the number of isotopes
   unsigned int GetNumberOfIsotopes() const { return m_Isotopes.size(); }
diff --git a/src/global/misc/src/MIsotope.cxx b/src/global/misc/src/MIsotope.cxx
index 100aed932..67aef9c4f 100644
--- a/src/global/misc/src/MIsotope.cxx
+++ b/src/global/misc/src/MIsotope.cxx
@@ -111,14 +111,16 @@ MString MIsotope::GetName() const
 
 
 //! Add line parameters:
-void MIsotope::AddLine(double Energy, double BranchingRatio, const MString& Flags) 
+void MIsotope::AddLine(double Energy, double BranchingRatio, const MString& Flags, bool ExcludeExcludedLines)
 { 
-  m_LineEnergies.push_back(Energy); 
-  m_LineBranchingRatios.push_back(BranchingRatio);
-  m_LineExcludeFlags.push_back(false);
-  m_LineDefaultFlags.push_back(false);
-  if (Flags.Contains("E") == true) m_LineExcludeFlags.back() = true;
-  if (Flags.Contains("D") == true) m_LineDefaultFlags.back() = true;
+  if (ExcludeExcludedLines == false || (ExcludeExcludedLines == true && Flags.Contains("E") == false)) {
+    m_LineEnergies.push_back(Energy);
+    m_LineBranchingRatios.push_back(BranchingRatio);
+    m_LineExcludeFlags.push_back(false);
+    m_LineDefaultFlags.push_back(false);
+    if (Flags.Contains("E") == true) m_LineExcludeFlags.back() = true;
+    if (Flags.Contains("D") == true) m_LineDefaultFlags.back() = true;
+  }
 }
 
 ////////////////////////////////////////////////////////////////////////////////
diff --git a/src/global/misc/src/MIsotopeStore.cxx b/src/global/misc/src/MIsotopeStore.cxx
index c5c094ed1..2e695f9d8 100644
--- a/src/global/misc/src/MIsotopeStore.cxx
+++ b/src/global/misc/src/MIsotopeStore.cxx
@@ -59,7 +59,7 @@ MIsotopeStore::~MIsotopeStore()
 
 
 //! Load all isotopes form a standard MEGAlib isotope file
-bool MIsotopeStore::Load(MString FileName)
+bool MIsotopeStore::Load(MString FileName, bool ExcludeExcludedLines)
 {
   MFile::ExpandFileName(FileName);
   if (MFile::Exists(FileName) == false) return false;
@@ -85,7 +85,7 @@ bool MIsotopeStore::Load(MString FileName)
       if (m_Isotopes[s].GetElement() == Name && m_Isotopes[s].GetNucleons() == Nucleons) {
         m_Isotopes[s].AddLine(iParser.GetTokenizerAt(i)->GetTokenAtAsDouble(2), 
                               iParser.GetTokenizerAt(i)->GetTokenAtAsDouble(3),
-                              Flags);
+                              Flags, ExcludeExcludedLines);
         Found = true;
         break;
       }
@@ -96,7 +96,7 @@ bool MIsotopeStore::Load(MString FileName)
       Isotope.SetNucleons(Nucleons);
       Isotope.AddLine(iParser.GetTokenizerAt(i)->GetTokenAtAsDouble(2), 
                       iParser.GetTokenizerAt(i)->GetTokenAtAsDouble(3),
-                      Flags);
+                      Flags, ExcludeExcludedLines);
       m_Isotopes.push_back(Isotope);
     }
   }

From 250f752fbb2e860f452a299e18cb52a8f5202237 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Thu, 6 Jul 2023 12:10:30 -0700
Subject: [PATCH 014/192] CHG: Minimum bin ID is now 25

---
 src/fretalon/base/src/MCalibrateEnergyFindLines.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/fretalon/base/src/MCalibrateEnergyFindLines.cxx b/src/fretalon/base/src/MCalibrateEnergyFindLines.cxx
index 2e94f07bf..b057e7f56 100644
--- a/src/fretalon/base/src/MCalibrateEnergyFindLines.cxx
+++ b/src/fretalon/base/src/MCalibrateEnergyFindLines.cxx
@@ -111,7 +111,7 @@ bool MCalibrateEnergyFindLines::FindPeaks(unsigned int ROGID)
   
   int Prior = 8;
   
-  int FirstPeakMinimumBinID = 3;
+  int FirstPeakMinimumBinID = 25;
   double FirstPeakMinimumPeakCounts = 300; 
   
   double MinimumPeakCounts = 100; 

From 4ef81d8be98f2a3edc519c634ae559f03d527f53 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Thu, 6 Jul 2023 12:10:45 -0700
Subject: [PATCH 015/192] CHG: Exclude excluded lines

---
 src/fretalon/melinator/src/MGUIMainMelinator.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/fretalon/melinator/src/MGUIMainMelinator.cxx b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
index b0809a785..c2927eb5b 100644
--- a/src/fretalon/melinator/src/MGUIMainMelinator.cxx
+++ b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
@@ -1279,7 +1279,7 @@ bool MGUIMainMelinator::OnLoadLast()
   vector<unsigned int> AllGroupIDs;
   
   MIsotopeStore Store;
-  if (Store.Load("$(MEGALIB)/resource/libraries/Calibration.isotopes") == false) {
+  if (Store.Load("$(MEGALIB)/resource/libraries/Calibration.isotopes", true) == false) {
     merr<<"Unable to load calibration isotopes..."<<show;
     return false;
   }

From fdab3364dec38dbbb0bb7fcbc7321acde6413220 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Wed, 19 Jul 2023 12:51:28 -0700
Subject: [PATCH 016/192] ADD: Command line option to select on a specific side

---
 src/fretalon/base/inc/MFileReadOuts.h         |  9 +++++++--
 src/fretalon/base/src/MFileReadOuts.cxx       | 14 +++++++------
 src/fretalon/melinator/inc/MMelinator.h       | 10 ++++++++--
 .../melinator/inc/MSettingsMelinator.h        | 13 +++++++++---
 .../melinator/src/MGUIMainMelinator.cxx       |  1 +
 .../melinator/src/MInterfaceMelinator.cxx     | 20 ++++++++++++-------
 src/fretalon/melinator/src/MMelinator.cxx     |  7 ++++---
 .../melinator/src/MSettingsMelinator.cxx      | 11 ++++++++--
 8 files changed, 60 insertions(+), 25 deletions(-)

diff --git a/src/fretalon/base/inc/MFileReadOuts.h b/src/fretalon/base/inc/MFileReadOuts.h
index bfc5b7d0c..04a563ff5 100644
--- a/src/fretalon/base/inc/MFileReadOuts.h
+++ b/src/fretalon/base/inc/MFileReadOuts.h
@@ -48,8 +48,13 @@ class MFileReadOuts : public MFileEvents
   virtual bool Open(MString FileName, unsigned int Way = MFile::c_Read);
 
   //! Return the next event
-  //! If SelectedDetectorID >= 0 then restrict yourself to SelectedDetectorID
-  bool ReadNext(MReadOutSequence& Sequence, int SelectedDetectorID = -1);
+  //! If SelectedDetectorID is non-negative then restrict yourself to SelectedDetectorID
+  //! SelectedDetectorSide:
+  //!   < 0: all
+  //!     0: negative side
+  //!     1: positive side
+  //!   >=2: all
+  bool ReadNext(MReadOutSequence& Sequence, int SelectedDetectorID = -1, int SelectedDetectorSide = -1);
 
   
   // protected methods:
diff --git a/src/fretalon/base/src/MFileReadOuts.cxx b/src/fretalon/base/src/MFileReadOuts.cxx
index 755e4d7bb..43eb067c0 100644
--- a/src/fretalon/base/src/MFileReadOuts.cxx
+++ b/src/fretalon/base/src/MFileReadOuts.cxx
@@ -248,7 +248,7 @@ bool MFileReadOuts::ParseFooter(const MString& Line)
 ////////////////////////////////////////////////////////////////////////////////
 
 
-bool MFileReadOuts::ReadNext(MReadOutSequence& ROS, int SelectedDetectorID)
+bool MFileReadOuts::ReadNext(MReadOutSequence& ROS, int SelectedDetectorID, int SelectedDetectorSide)
 {
   // Return next single event from file... or 0 if there are no more.
   
@@ -267,7 +267,7 @@ bool MFileReadOuts::ReadNext(MReadOutSequence& ROS, int SelectedDetectorID)
 
   // If we have an include file, we get the event from it!
   if (m_IncludeFileUsed == true) {
-    bool Return = dynamic_cast<MFileReadOuts*>(m_IncludeFile)->ReadNext(ROS, SelectedDetectorID);
+    bool Return = dynamic_cast<MFileReadOuts*>(m_IncludeFile)->ReadNext(ROS, SelectedDetectorID, SelectedDetectorSide);
     if (ROS.GetNumberOfReadOuts() == 0 || Return == false) {
       m_IncludeFile->Close();
       m_IncludeFileUsed = false;
@@ -313,7 +313,7 @@ bool MFileReadOuts::ReadNext(MReadOutSequence& ROS, int SelectedDetectorID)
       if (OpenIncludeFile(Line) == true) {
         //mout<<"Switched to new include file: "<<m_IncludeFile->GetFileName()<<endl;
         // Now we have to read the first event:
-        bool Return = dynamic_cast<MFileReadOuts*>(m_IncludeFile)->ReadNext(ROS, SelectedDetectorID);
+        bool Return = dynamic_cast<MFileReadOuts*>(m_IncludeFile)->ReadNext(ROS, SelectedDetectorID, SelectedDetectorSide);
         if (ROS.GetNumberOfReadOuts() == 0 || Return == false) {
           //mout<<"Closing: "<<m_IncludeFile->GetFileName()<<endl;
           m_IncludeFile->Close();
@@ -340,9 +340,11 @@ bool MFileReadOuts::ReadNext(MReadOutSequence& ROS, int SelectedDetectorID)
       // cout<<"Combined: "<<m_ROD->ToString()<<" vs. "<<m_ROD->GetCombinedType()<<endl;
       
       if (SelectedDetectorID < 0 || (SelectedDetectorID >= 0 && (int) m_ROE->GetDetectorID() == SelectedDetectorID)) {
-        MReadOut RO(*m_ROE, *m_ROD);
-        ROS.AddReadOut(RO);
-        //cout<<"Added: "<<RO.ToString()<<endl;
+        if (SelectedDetectorSide < 0 || SelectedDetectorSide >= 2 || (dynamic_cast<MReadOutElementDoubleStrip*>(m_ROE) != nullptr && (int) dynamic_cast<MReadOutElementDoubleStrip*>(m_ROE)->IsPositiveStrip() == SelectedDetectorSide)) {
+          MReadOut RO(*m_ROE, *m_ROD);
+          ROS.AddReadOut(RO);
+          //cout<<"Added: "<<RO.ToString()<<endl;
+        }
       }
       continue;
     }
diff --git a/src/fretalon/melinator/inc/MMelinator.h b/src/fretalon/melinator/inc/MMelinator.h
index 0f36788b5..d89f22f38 100644
--- a/src/fretalon/melinator/inc/MMelinator.h
+++ b/src/fretalon/melinator/inc/MMelinator.h
@@ -57,7 +57,10 @@ class MMelinator
   
   //! Set the ID of the selected detector (use all detectors when negative)
   void SetSelectedTemperatureWindow(double Min, double Max) { m_SelectedTemperatureMin = Min; m_SelectedTemperatureMax = Max; }
-  
+
+  //! Set the ID of the selected detector side (< 0: all, 0: negative side, 1: positive side, >=2: all)
+  void SetSelectedDetectorSide(int SelectedDetectorSide) { m_SelectedDetectorSide = SelectedDetectorSide; }
+
   //! Load the calibration data containing the given isotopes and eventually merge files with identical data groups
   //! Return false if an error occurred
   //! This function performs parallel loading of all given files
@@ -199,7 +202,10 @@ class MMelinator
   double m_SelectedTemperatureMin;
   //! The selected temperature window maximum
   double m_SelectedTemperatureMax;
-  
+
+  //! The selected detector side (< 0: all, 0: negative side, 1: positive side, >=2: all)
+  int m_SelectedDetectorSide;
+
   //! The group IDs
   vector<unsigned int> m_GroupIDs;
   //! The calibration file names
diff --git a/src/fretalon/melinator/inc/MSettingsMelinator.h b/src/fretalon/melinator/inc/MSettingsMelinator.h
index cc030a42c..ddebda59e 100644
--- a/src/fretalon/melinator/inc/MSettingsMelinator.h
+++ b/src/fretalon/melinator/inc/MSettingsMelinator.h
@@ -133,12 +133,17 @@ class MSettingsMelinator : public MSettings
   void SetSaveAsFileName(const MString& SaveAsFileName) { m_SaveAsFileName = SaveAsFileName; }
   //! Get the save-as file name
   MString GetSaveAsFileName() const { return m_SaveAsFileName; }
-  
+
   //! Set the single detector to use (negative means use all)
   void SetSelectedDetectorID(int ID) { m_SelectedDetectorID = ID; }
   //! Get the single detector to use (negative means use all)
   int GetSelectedDetectorID() const { return m_SelectedDetectorID; }
-  
+
+  //! Set the detector side to use (< 0: all, 0: negative side, 1: positive side, >=2: all)
+  void SetSelectedDetectorSide(int Side) { m_SelectedDetectorSide = Side; }
+  //! Get the detector side to use (< 0: all, 0: negative side, 1: positive side, >=2: all)
+  int GetSelectedDetectorSide() const { return m_SelectedDetectorSide; }
+
   //! Set the minimum allowed detector temperature
   void SetMinimumTemperature(double MinimumTemperature) { m_MinimumTemperature = MinimumTemperature; }
   //! Get the minimum allowed detector temperate
@@ -206,7 +211,9 @@ class MSettingsMelinator : public MSettings
   
   //! Set the single detector to use (negative means use all)
   int m_SelectedDetectorID;
-  
+  //! Set the detector side to use (< 0: all, 0: negative side, 1: positive side, >=2: all)
+  int m_SelectedDetectorSide;
+
   //! Set the minimum allowed detector temperature
   double m_MinimumTemperature;
   //! Set the maximum allowed detector temperature
diff --git a/src/fretalon/melinator/src/MGUIMainMelinator.cxx b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
index c2927eb5b..db3babc7c 100644
--- a/src/fretalon/melinator/src/MGUIMainMelinator.cxx
+++ b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
@@ -1267,6 +1267,7 @@ bool MGUIMainMelinator::OnLoadLast()
    
   m_Melinator.Clear();
   m_Melinator.SetSelectedDetectorID(m_Settings->GetSelectedDetectorID());
+  m_Melinator.SetSelectedDetectorSide(m_Settings->GetSelectedDetectorSide());
   m_Melinator.SetSelectedTemperatureWindow(m_Settings->GetMinimumTemperature(), m_Settings->GetMaximumTemperature());
   
   MString FileName;
diff --git a/src/fretalon/melinator/src/MInterfaceMelinator.cxx b/src/fretalon/melinator/src/MInterfaceMelinator.cxx
index 0c39c6db2..dcbea0910 100644
--- a/src/fretalon/melinator/src/MInterfaceMelinator.cxx
+++ b/src/fretalon/melinator/src/MInterfaceMelinator.cxx
@@ -95,16 +95,18 @@ bool MInterfaceMelinator::ParseCommandLine(int argc, char** argv)
   Usage<<endl;
   Usage<<"  Usage: Melinator <options>"<<endl;
   Usage<<endl;
-  Usage<<"      -l:"<<endl;
+  Usage<<"      -l"<<endl;
   Usage<<"             Load the last used calibration files"<<endl;
-  Usage<<"      -p:"<<endl;
+  Usage<<"      -p"<<endl;
   Usage<<"             Load the last used calibration files and parametrize all peaks"<<endl;
-  Usage<<"      -a:"<<endl;
+  Usage<<"      -a"<<endl;
   Usage<<"             Load the last used calibration files, parametrize all peaks, save the result, and exit"<<endl;
-  Usage<<"      -s <filename>.ecal:"<<endl;
-  Usage<<"             Save file name"<<endl;
+  Usage<<"      -e <filename>.ecal:"<<endl;
+  Usage<<"             ecal file name"<<endl;
   Usage<<"      -d --detector <int>:"<<endl;
   Usage<<"             Only look at this detector"<<endl;
+  Usage<<"      -s --side <int>:"<<endl;
+  Usage<<"             Only look at this detector side (0: negative, 1: positive, else: all)"<<endl;
   Usage<<"      -t --temperature <double> <double>:"<<endl;
   Usage<<"             Only look at this temperature window: [min...max]"<<endl;
   Usage<<"      -v --verbosity <0..5>:"<<endl;
@@ -134,7 +136,8 @@ bool MInterfaceMelinator::ParseCommandLine(int argc, char** argv)
     
     // Single argument
     if (Option == "-c" || Option == "--configuration" ||
-        Option == "-s" || Option == "--save" ||
+        Option == "-s" || Option == "--side" ||
+        Option == "-e" || Option == "--ecal" ||
         Option == "-d" || Option == "--detector" ||
         Option == "-v" || Option == "--verbosity") {
       if (!((argc > i+1) && argv[i+1][0] != '-')){
@@ -164,12 +167,15 @@ bool MInterfaceMelinator::ParseCommandLine(int argc, char** argv)
   // Now parse all low level options
   for (int i = 1; i < argc; i++) {
     Option = argv[i];
-    if (Option == "--save" || Option == "-s") {
+    if (Option == "--ecal" || Option == "-e") {
       m_Data->SetSaveAsFileName(argv[++i]);
       cout<<"Command-line parser: Use save as file name "<<m_Data->GetSaveAsFileName()<<endl;
     } else if (Option == "--detector" || Option == "-d") {
       m_Data->SetSelectedDetectorID(atoi(argv[++i]));
       cout<<"Command-line parser: Use only this detector: "<<m_Data->GetSelectedDetectorID()<<endl;
+    } else if (Option == "--side" || Option == "-s") {
+      m_Data->SetSelectedDetectorSide(atoi(argv[++i]));
+      cout<<"Command-line parser: Use only this detector side (0: neg, 1: pos, else: all): "<<m_Data->GetSelectedDetectorSide()<<endl;
     } else if (Option == "--temperature" || Option == "-t") {
       m_Data->SetMinimumTemperature(atof(argv[++i]));
       m_Data->SetMaximumTemperature(atof(argv[++i]));
diff --git a/src/fretalon/melinator/src/MMelinator.cxx b/src/fretalon/melinator/src/MMelinator.cxx
index 6bcd37cd6..544026941 100644
--- a/src/fretalon/melinator/src/MMelinator.cxx
+++ b/src/fretalon/melinator/src/MMelinator.cxx
@@ -126,10 +126,11 @@ void MMelinator::Clear()
   m_Isotopes.clear();
   
   m_SelectedDetectorID = -1;
-  
+  m_SelectedDetectorSide = -1;
+
   m_SelectedTemperatureMin = -numeric_limits<double>::max();
   m_SelectedTemperatureMax = +numeric_limits<double>::max();
-  
+
   m_HistogramChanged = true;
   m_HistogramCollection = -1;
   for (auto H: m_Histograms) delete H;
@@ -420,7 +421,7 @@ bool MMelinator::LoadParallel(unsigned int ThreadID)
       MReadOutSequence Sequence;
       long Counter = 0;
       long NewCounter = 0;
-      while (Reader.ReadNext(Sequence, m_SelectedDetectorID) == true) {
+      while (Reader.ReadNext(Sequence, m_SelectedDetectorID, m_SelectedDetectorSide) == true) {
         // Since we do energy calibration, exclude everything with more than the number of good hits
         //if (Sequence.HasIdenticalReadOutElementTypes() == true) {
         //  if (Sequence.GetNumberOfReadOuts() > 0 && 
diff --git a/src/fretalon/melinator/src/MSettingsMelinator.cxx b/src/fretalon/melinator/src/MSettingsMelinator.cxx
index 710f1bf65..8b438fe1b 100644
--- a/src/fretalon/melinator/src/MSettingsMelinator.cxx
+++ b/src/fretalon/melinator/src/MSettingsMelinator.cxx
@@ -77,6 +77,7 @@ MSettingsMelinator::MSettingsMelinator(bool AutoLoad) : MSettings("MelinatorConf
   m_SaveAsFileName = "Out.ecal";
   
   m_SelectedDetectorID = -1;
+  m_SelectedDetectorSide = -1;
   
   m_MinimumTemperature = -numeric_limits<double>::max();
   m_MaximumTemperature = +numeric_limits<double>::max();
@@ -169,8 +170,10 @@ bool MSettingsMelinator::WriteXml(MXmlNode* Node)
   
   new MXmlNode(Node, "SaveAsFileName", m_SaveAsFileName);
   
-  //new MXmlNode(Node, "SelectedDetectorID", m_SelectedDetectorID);
-  
+  // Not stored, since command line options:
+  // new MXmlNode(Node, "SelectedDetectorID", m_SelectedDetectorID);
+  // new MXmlNode(Node, "SelectedDetectorSide", m_SelectedDetectorSide);
+
   return true;
 }
 
@@ -279,9 +282,13 @@ bool MSettingsMelinator::ReadXml(MXmlNode* Node)
   }
  
   /*
+  // Not stored since command line options
   if ((aNode = Node->GetNode("SelectedDetectorID")) != 0) {
     m_SelectedDetectorID = aNode->GetValueAsInt();
   }
+  if ((aNode = Node->GetNode("SelectedDetectorSide")) != 0) {
+    m_SelectedDetectorSide = aNode->GetValueAsInt();
+  }
   */
  
   return true;

From a93fe4fa29aa52dff87a135998d0cf895dc1560d Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Wed, 19 Jul 2023 18:38:22 -0700
Subject: [PATCH 017/192] CHG: Disallow cfg loading in the UI

---
 src/fretalon/melinator/src/MGUIMainMelinator.cxx   | 9 +++++++--
 src/fretalon/melinator/src/MInterfaceMelinator.cxx | 2 +-
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/src/fretalon/melinator/src/MGUIMainMelinator.cxx b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
index db3babc7c..492f46959 100644
--- a/src/fretalon/melinator/src/MGUIMainMelinator.cxx
+++ b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
@@ -168,7 +168,8 @@ void MGUIMainMelinator::Create()
   MenuFiles->AddEntry("Save", c_Save);
   MenuFiles->AddSeparator();
   MenuFiles->AddLabel("Configuration file");
-  MenuFiles->AddEntry("Open", c_LoadConfig);
+  //MenuFiles->AddEntry("Open", c_LoadConfig);
+  MenuFiles->AddEntry("Open -> use command line at launch", c_LoadConfig);
   MenuFiles->AddEntry("Save As", c_SaveConfig);
   MenuFiles->AddSeparator();
   MenuFiles->AddLabel("Geometry file");
@@ -1864,6 +1865,9 @@ bool MGUIMainMelinator::OnFitAll()
 //! Load a configuration file from disk
 bool MGUIMainMelinator::OnLoadConfiguration()
 {
+  //! Loading can leave the app in an inconsistent state, thus not do it now
+
+  /*
   const char** Types = new const char*[4];
   Types[0] = "Configuration file";
   Types[1] = "*.cfg";
@@ -1880,7 +1884,8 @@ bool MGUIMainMelinator::OnLoadConfiguration()
   // Get the filename ...
   if ((char *) Info.fFilename != 0) {
     m_Interface->LoadConfiguration(MString(Info.fFilename));
-  } 
+  }
+  */
 
   return true;
 }
diff --git a/src/fretalon/melinator/src/MInterfaceMelinator.cxx b/src/fretalon/melinator/src/MInterfaceMelinator.cxx
index dcbea0910..b21d2cd5f 100644
--- a/src/fretalon/melinator/src/MInterfaceMelinator.cxx
+++ b/src/fretalon/melinator/src/MInterfaceMelinator.cxx
@@ -260,7 +260,7 @@ bool MInterfaceMelinator::LoadConfiguration(MString FileName)
 {  
   // Load the configuration file
 
-  if (m_Data == 0) {
+  if (m_Data == nullptr) {
     m_Data = new MSettingsMelinator();
     m_BasicGuiData = dynamic_cast<MSettings*>(m_Data);
     //m_Gui->SetConfiguration(m_Data);

From c012e63a9eb875d24272c2ece967b282c5507dc8 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Fri, 8 Sep 2023 15:25:06 -0700
Subject: [PATCH 018/192] CHG: Switch from n/p side to high and low voltage
 side

---
 .../base/inc/MReadOutElementDoubleStrip.h      | 16 +++++++++++-----
 .../base/src/MReadOutElementDoubleStrip.cxx    | 18 +++++++++---------
 2 files changed, 20 insertions(+), 14 deletions(-)

diff --git a/src/fretalon/base/inc/MReadOutElementDoubleStrip.h b/src/fretalon/base/inc/MReadOutElementDoubleStrip.h
index c39fed83d..569b44395 100644
--- a/src/fretalon/base/inc/MReadOutElementDoubleStrip.h
+++ b/src/fretalon/base/inc/MReadOutElementDoubleStrip.h
@@ -64,10 +64,16 @@ class MReadOutElementDoubleStrip : public MReadOutElementStrip
   //! I.e. for a double strip it is two (n and p side), otherwise it is usually 1
   virtual unsigned int GetMinimumNumberOfReadOutsForGoodInteraction() const { return 2; }
 
-  //! Set the strip type (x/y)
-  void IsPositiveStrip(bool IsPositiveStrip) { m_IsPositiveStrip = IsPositiveStrip; }
-  //! Return the strip type (x/y)
-  bool IsPositiveStrip() const { return m_IsPositiveStrip; }
+  //! Set the strip type (positive equals the lowest voltage value side of the detector)
+  void IsPositiveStrip(bool IsPositiveStrip) { m_IsLowVoltageStrip = IsPositiveStrip; }
+  //! Return the strip type (positive equals the lowest voltage value side of the detector)
+  bool IsPositiveStrip() const { return m_IsLowVoltageStrip; }
+
+  //! Is this the low voltage strip (= negative in ols nomenclature)
+  void IsLowVoltageStrip(bool IsLowVoltageStrip) { m_IsLowVoltageStrip = IsLowVoltageStrip; }
+  //! Return true if this is a high-volatge strip
+  bool IsLowVoltageStrip() const { return m_IsLowVoltageStrip; }
+
 
   //! Return the number of parsable elements
   virtual unsigned int GetNumberOfParsableElements() const;  
@@ -91,7 +97,7 @@ class MReadOutElementDoubleStrip : public MReadOutElementStrip
   // protected members:
  protected:
   //! The side of double sided strip detector
-  bool m_IsPositiveStrip;
+  bool m_IsLowVoltageStrip;
 
   // private members:
  private:
diff --git a/src/fretalon/base/src/MReadOutElementDoubleStrip.cxx b/src/fretalon/base/src/MReadOutElementDoubleStrip.cxx
index 3570a8f40..f97bacd38 100644
--- a/src/fretalon/base/src/MReadOutElementDoubleStrip.cxx
+++ b/src/fretalon/base/src/MReadOutElementDoubleStrip.cxx
@@ -46,7 +46,7 @@ ClassImp(MReadOutElementDoubleStrip)
 
 
 //! Default constructor
-MReadOutElementDoubleStrip::MReadOutElementDoubleStrip(): MReadOutElementStrip(), m_IsPositiveStrip(true)
+MReadOutElementDoubleStrip::MReadOutElementDoubleStrip(): MReadOutElementStrip(), m_IsLowVoltageStrip(true)
 {
 }
 
@@ -55,7 +55,7 @@ MReadOutElementDoubleStrip::MReadOutElementDoubleStrip(): MReadOutElementStrip()
 
 
 //! Read out element of a DOUBLE-SIDED strip detector  
-MReadOutElementDoubleStrip::MReadOutElementDoubleStrip(unsigned int DetectorID, unsigned int StripID, bool IsPositiveStrip) : MReadOutElementStrip(DetectorID, StripID), m_IsPositiveStrip(IsPositiveStrip)
+MReadOutElementDoubleStrip::MReadOutElementDoubleStrip(unsigned int DetectorID, unsigned int StripID, bool IsLowVoltageStrip) : MReadOutElementStrip(DetectorID, StripID), m_IsLowVoltageStrip(IsLowVoltageStrip)
 {
 }
 
@@ -75,7 +75,7 @@ MReadOutElementDoubleStrip::~MReadOutElementDoubleStrip()
 //! Clone this read-out element - the returned element must be deleted!
 MReadOutElementDoubleStrip* MReadOutElementDoubleStrip::Clone() const
 {
-  MReadOutElementDoubleStrip* R = new MReadOutElementDoubleStrip(m_DetectorID, m_StripID, m_IsPositiveStrip);
+  MReadOutElementDoubleStrip* R = new MReadOutElementDoubleStrip(m_DetectorID, m_StripID, m_IsLowVoltageStrip);
   return R;
 }
 
@@ -87,7 +87,7 @@ MReadOutElementDoubleStrip* MReadOutElementDoubleStrip::Clone() const
 void MReadOutElementDoubleStrip::Clear()
 {
   MReadOutElementStrip::Clear();
-  m_IsPositiveStrip = true;
+  m_IsLowVoltageStrip = true;
 }
 
 
@@ -124,7 +124,7 @@ bool MReadOutElementDoubleStrip::operator==(const MReadOutElement& R) const
   
   if (m_StripID != S->m_StripID) return false;
   if (m_DetectorID != S->m_DetectorID) return false;
-  if (m_IsPositiveStrip != S->m_IsPositiveStrip) return false;
+  if (m_IsLowVoltageStrip != S->m_IsLowVoltageStrip) return false;
   
   return true;
 }
@@ -143,7 +143,7 @@ bool MReadOutElementDoubleStrip::operator<(const MReadOutElement& R) const
   if (m_DetectorID == S->m_DetectorID) {
     if (m_StripID < S->m_StripID) return true;
     if (m_StripID == S->m_StripID) {
-      if (m_IsPositiveStrip == false && S->m_IsPositiveStrip == true) return true;
+      if (m_IsLowVoltageStrip == false && S->m_IsLowVoltageStrip == true) return true;
     }  
   }
   
@@ -174,7 +174,7 @@ bool MReadOutElementDoubleStrip::Parse(const MTokenizer& T, unsigned int StartEl
   
   m_DetectorID = T.GetTokenAtAsUnsignedIntFast(StartElement);
   m_StripID = T.GetTokenAtAsUnsignedIntFast(StartElement+1);
-  m_IsPositiveStrip = (T.GetTokenAt(StartElement+2) == "p") ? true : false;
+  m_IsLowVoltageStrip = (T.GetTokenAt(StartElement+2) == "l" || T.GetTokenAt(StartElement+2) == "p") ? true : false;
   
   return true;
 }
@@ -194,7 +194,7 @@ MString MReadOutElementDoubleStrip::ToParsableString(bool WithDescriptor) const
   Return += " ";
   Return += m_StripID;
   Return += " ";
-  Return += (m_IsPositiveStrip ? "p" : "n");
+  Return += (m_IsLowVoltageStrip ? "l" : "h");
 
   return Return;
 }
@@ -207,7 +207,7 @@ MString MReadOutElementDoubleStrip::ToParsableString(bool WithDescriptor) const
 MString MReadOutElementDoubleStrip::ToString() const
 {
   ostringstream os;
-  os<<"Detector: "<<m_DetectorID<<", side: "<<((m_IsPositiveStrip == true) ? "pos" : "neg")<<", strip: "<<m_StripID;
+  os<<"Detector: "<<m_DetectorID<<", side: "<<((m_IsLowVoltageStrip == true) ? "LV" : "HV")<<", strip: "<<m_StripID;
   return os.str();
 }
 

From 6b24b154ffeff3a69da0195405e33cb0eac6cbe4 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Tue, 12 Sep 2023 00:53:14 -0700
Subject: [PATCH 019/192] CHG: More switching from neg/pos to LV/HV

---
 src/fretalon/base/inc/MReadOutElementDoubleStrip.h | 4 ++--
 src/fretalon/melinator/src/MInterfaceMelinator.cxx | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/fretalon/base/inc/MReadOutElementDoubleStrip.h b/src/fretalon/base/inc/MReadOutElementDoubleStrip.h
index 569b44395..f37d327f5 100644
--- a/src/fretalon/base/inc/MReadOutElementDoubleStrip.h
+++ b/src/fretalon/base/inc/MReadOutElementDoubleStrip.h
@@ -69,9 +69,9 @@ class MReadOutElementDoubleStrip : public MReadOutElementStrip
   //! Return the strip type (positive equals the lowest voltage value side of the detector)
   bool IsPositiveStrip() const { return m_IsLowVoltageStrip; }
 
-  //! Is this the low voltage strip (= negative in ols nomenclature)
+  //! Is this the-low voltage strip (= negative in old nomenclature)
   void IsLowVoltageStrip(bool IsLowVoltageStrip) { m_IsLowVoltageStrip = IsLowVoltageStrip; }
-  //! Return true if this is a high-volatge strip
+  //! Return true if this is a low-voltage strip
   bool IsLowVoltageStrip() const { return m_IsLowVoltageStrip; }
 
 
diff --git a/src/fretalon/melinator/src/MInterfaceMelinator.cxx b/src/fretalon/melinator/src/MInterfaceMelinator.cxx
index b21d2cd5f..7e91587e2 100644
--- a/src/fretalon/melinator/src/MInterfaceMelinator.cxx
+++ b/src/fretalon/melinator/src/MInterfaceMelinator.cxx
@@ -106,7 +106,7 @@ bool MInterfaceMelinator::ParseCommandLine(int argc, char** argv)
   Usage<<"      -d --detector <int>:"<<endl;
   Usage<<"             Only look at this detector"<<endl;
   Usage<<"      -s --side <int>:"<<endl;
-  Usage<<"             Only look at this detector side (0: negative, 1: positive, else: all)"<<endl;
+  Usage<<"             Only look at this detector side (0: HV/negative, 1: LV/positive, else: all)"<<endl;
   Usage<<"      -t --temperature <double> <double>:"<<endl;
   Usage<<"             Only look at this temperature window: [min...max]"<<endl;
   Usage<<"      -v --verbosity <0..5>:"<<endl;
@@ -175,7 +175,7 @@ bool MInterfaceMelinator::ParseCommandLine(int argc, char** argv)
       cout<<"Command-line parser: Use only this detector: "<<m_Data->GetSelectedDetectorID()<<endl;
     } else if (Option == "--side" || Option == "-s") {
       m_Data->SetSelectedDetectorSide(atoi(argv[++i]));
-      cout<<"Command-line parser: Use only this detector side (0: neg, 1: pos, else: all): "<<m_Data->GetSelectedDetectorSide()<<endl;
+      cout<<"Command-line parser: Use only this detector side (0: HV/neg, 1: LV/pos, else: all): "<<m_Data->GetSelectedDetectorSide()<<endl;
     } else if (Option == "--temperature" || Option == "-t") {
       m_Data->SetMinimumTemperature(atof(argv[++i]));
       m_Data->SetMaximumTemperature(atof(argv[++i]));

From 772f8c37100acc0b43fd93252654e6bb20a187d8 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Wed, 13 Sep 2023 00:06:36 -0700
Subject: [PATCH 020/192] CHG: Added peak finding options to UI, scrollbar for
 options, include errors for peak fitting, minor canvas chnages

---
 .../base/inc/MCalibrateEnergyFindLines.h      |  21 +-
 .../src/MCalibrateEnergyAssignEnergies.cxx    |   4 +-
 .../base/src/MCalibrateEnergyFindLines.cxx    |  35 ++--
 .../base/src/MCalibrationFitGaussian.cxx      |   2 +-
 .../melinator/inc/MGUIMainMelinator.h         |  12 +-
 src/fretalon/melinator/inc/MMelinator.h       |  17 +-
 .../melinator/inc/MSettingsMelinator.h        |  27 ++-
 .../melinator/src/MGUIEReadOutElementView.cxx |   2 +-
 .../melinator/src/MGUIMainMelinator.cxx       | 197 ++++++++++++------
 src/fretalon/melinator/src/MMelinator.cxx     |  21 +-
 .../melinator/src/MSettingsMelinator.cxx      |  20 +-
 src/global/misc/src/MBinner.cxx               |  12 +-
 12 files changed, 267 insertions(+), 103 deletions(-)

diff --git a/src/fretalon/base/inc/MCalibrateEnergyFindLines.h b/src/fretalon/base/inc/MCalibrateEnergyFindLines.h
index f780235a0..28fbc6c6a 100644
--- a/src/fretalon/base/inc/MCalibrateEnergyFindLines.h
+++ b/src/fretalon/base/inc/MCalibrateEnergyFindLines.h
@@ -60,6 +60,16 @@ class MCalibrateEnergyFindLines : public MCalibrateEnergy
   //! Set the selected temperature window
   void SetTemperatureWindow(double Min, double Max) { m_TemperatureMin = Min; m_TemperatureMax = Max; }
   
+  //! Set the prior
+  void SetBayesianBlockPrior(unsigned int Prior) { m_Prior = Prior; }
+
+  //! Set the number of bins which are excluded from peak finding at low energies
+  //! to avoid noise peaks
+  void SetNumberOfExcludedBinsAtLowEnergies(unsigned int Bins) { m_ExcludeFirstNumberOfBins = Bins; }
+
+  //! Set the minimum number of counts in accepted peaks
+  void SetMinimumNumberOfPeakCounts(unsigned int Counts) { m_MinimumPeakCounts = Counts; }
+
   //! Perform the calibration
   virtual bool Calibrate();
   
@@ -108,7 +118,16 @@ class MCalibrateEnergyFindLines : public MCalibrateEnergy
   //! The selected temperature window maximum
   double m_TemperatureMax;
   
-  
+  // User adjustable flags
+
+  //! The prior for the Bayesian block binning
+  unsigned int m_Prior;
+  //! Ignore peaks found in the first X number of bins
+  unsigned int m_ExcludeFirstNumberOfBins;
+  //! Minimum number of counts in accepted peak
+  unsigned int m_MinimumPeakCounts;
+
+
 #ifdef ___CLING___
  public:
   ClassDef(MCalibrateEnergyFindLines, 0) // no description
diff --git a/src/fretalon/base/src/MCalibrateEnergyAssignEnergies.cxx b/src/fretalon/base/src/MCalibrateEnergyAssignEnergies.cxx
index 360ce37da..bb077d8d4 100644
--- a/src/fretalon/base/src/MCalibrateEnergyAssignEnergies.cxx
+++ b/src/fretalon/base/src/MCalibrateEnergyAssignEnergies.cxx
@@ -316,9 +316,9 @@ bool MCalibrateEnergyAssignEnergies::CalibrateLinear()
           }
           if (AllIncreasing == true) {
             NewSetsOfMatches.push_back(NewSet);
-            //cout<<"Increasing: "<<OldSet.ToString()<<" with "<<SubSet.ToString()<<endl; 
+            //cout<<"Increasing: "<<OldSet.ToString()<<" with "<<SubSet.ToString()<<endl;
           } else {
-            //cout<<"Not increasing: "<<OldSet.ToString()<<" with "<<SubSet.ToString()<<endl; 
+            //cout<<"Not increasing: "<<OldSet.ToString()<<" with "<<SubSet.ToString()<<endl;
           }
         }
       }
diff --git a/src/fretalon/base/src/MCalibrateEnergyFindLines.cxx b/src/fretalon/base/src/MCalibrateEnergyFindLines.cxx
index b057e7f56..3248fca7f 100644
--- a/src/fretalon/base/src/MCalibrateEnergyFindLines.cxx
+++ b/src/fretalon/base/src/MCalibrateEnergyFindLines.cxx
@@ -66,6 +66,10 @@ MCalibrateEnergyFindLines::MCalibrateEnergyFindLines() : MCalibrateEnergy()
   
   m_TemperatureMin = -numeric_limits<double>::max();
   m_TemperatureMax = +numeric_limits<double>::max();
+
+  m_Prior = 8;
+  m_ExcludeFirstNumberOfBins = 25;
+  m_MinimumPeakCounts = 100;
 }
 
 
@@ -109,12 +113,9 @@ bool MCalibrateEnergyFindLines::FindPeaks(unsigned int ROGID)
 {
   if (g_Verbosity >= c_Info) cout<<endl<<"Finding peaks for ROG ID: "<<ROGID<<" ("<<m_ROGs[ROGID]->GetName()<<")"<<endl;
   
-  int Prior = 8;
-  
-  int FirstPeakMinimumBinID = 25;
+  // Other options are in the constructor
   double FirstPeakMinimumPeakCounts = 300; 
-  
-  double MinimumPeakCounts = 100; 
+
   double MinimumHeight = 1.5; 
   double MinimumBinWidthForBayesianBinner = 8;
   double ComptonEdgeThreshold = 0.5;
@@ -126,7 +127,7 @@ bool MCalibrateEnergyFindLines::FindPeaks(unsigned int ROGID)
   MBinnerBayesianBlocks Binner;
   Binner.SetMinimumBinWidth(MinimumBinWidthForBayesianBinner);
   Binner.SetMinMax(m_RangeMinimum, m_RangeMaximum);
-  Binner.SetPrior(Prior);
+  Binner.SetPrior(m_Prior);
   for (unsigned int d = 0; d < m_ROGs[ROGID]->GetNumberOfReadOutDatas(); ++d) {
     MReadOutDataTemperature* T = dynamic_cast<MReadOutDataTemperature*>(m_ROGs[ROGID]->GetReadOutData(d).Get(MReadOutDataTemperature::m_TypeID));
     if (T != nullptr) {
@@ -259,11 +260,11 @@ bool MCalibrateEnergyFindLines::FindPeaks(unsigned int ROGID)
       if (g_Verbosity >= c_Chatty) cout<<FirstDerivation->GetBinLowEdge(b+1)<<": Height etc. : "<<CountsPerBinBefore<<":"<<Height<<":"<<CountsPerBinAfter<<endl;
       Height -= 0.5*(CountsPerBinBefore + CountsPerBinAfter);
       
-      if (CountsPerBin*Width < MinimumPeakCounts) {
-        if (g_Verbosity >= c_Info) cout<<FirstDerivation->GetBinLowEdge(b+1)<<" - Rejected: Not enough counts per bin: "<<CountsPerBin*Width<<" (min: "<<MinimumPeakCounts<<")"<<endl;
+      if (CountsPerBin*Width < m_MinimumPeakCounts) {
+        if (g_Verbosity >= c_Info) cout<<FirstDerivation->GetBinLowEdge(b+1)<<" - Rejected: Not enough counts per bin: "<<CountsPerBin*Width<<" (min: "<<m_MinimumPeakCounts<<")"<<endl;
         continue;
       } else {
-        if (g_Verbosity >= c_Info) cout<<FirstDerivation->GetBinLowEdge(b+1)<<" - Passed: Enough counts per bin: "<<CountsPerBin*Width<<" (min: "<<MinimumPeakCounts<<")"<<endl;        
+        if (g_Verbosity >= c_Info) cout<<FirstDerivation->GetBinLowEdge(b+1)<<" - Passed: Enough counts per bin: "<<CountsPerBin*Width<<" (min: "<<m_MinimumPeakCounts<<")"<<endl;
       }
       P.SetCounts(CountsPerBin*Width);
         
@@ -323,14 +324,14 @@ bool MCalibrateEnergyFindLines::FindPeaks(unsigned int ROGID)
       if (g_Verbosity >= c_Chatty) cout<<"Peak bin: "<<PeakBin<<endl;
       
       // If this is the first peak it must be at least 3 bins away from the first bin and from any bin with less than 1 counts:
-      if (FirstPeak == true) {
-        if (PeakBin < FirstPeakMinimumBinID) {
-          if (g_Verbosity >= c_Info) cout<<FirstDerivation->GetBinLowEdge(b+1)<<" - Rejected: First peak must be at least "<<FirstPeakMinimumBinID<<" bins away from start, and not only "<<PeakBin<<endl;
+      //if (FirstPeak == true) {
+        if (PeakBin < m_ExcludeFirstNumberOfBins) {
+          if (g_Verbosity >= c_Info) cout<<FirstDerivation->GetBinLowEdge(b+1)<<" - Rejected: First peak must be at least "<<m_ExcludeFirstNumberOfBins<<" bins away from start, and not only "<<PeakBin<<endl;
           continue;          
         } else {
-          if (g_Verbosity >= c_Info) cout<<FirstDerivation->GetBinLowEdge(b+1)<<" - Passed: First peak is at least "<<FirstPeakMinimumBinID<<" bins away from start: "<<PeakBin<<endl;          
+          if (g_Verbosity >= c_Info) cout<<FirstDerivation->GetBinLowEdge(b+1)<<" - Passed: First peak is at least "<<m_ExcludeFirstNumberOfBins<<" bins away from start: "<<PeakBin<<endl;
         }
-      }
+      //}
       
       
       
@@ -390,7 +391,7 @@ bool MCalibrateEnergyFindLines::FindPeaks(unsigned int ROGID)
           if (g_Verbosity >= c_Info) cout<<FirstDerivation->GetBinLowEdge(b+1)<<" - Passed: Enough peak counts for a first peak: "<<Excess<<endl;          
         }
       } else {
-        if (Excess < MinimumPeakCounts) {
+        if (Excess < m_MinimumPeakCounts) {
           if (g_Verbosity >= c_Info) cout<<FirstDerivation->GetBinLowEdge(b+1)<<" - Rejected: Not enough peak counts: "<<Excess<<endl;
           continue;
         } else {          
@@ -591,8 +592,8 @@ bool MCalibrateEnergyFindLines::FitPeaks(unsigned int ROGID)
       if (Fit.Evaluate(P.GetLowEdge()) < 0.8*Fit.Evaluate(P.GetHighEdge()) &&
         Fit.Evaluate(P.GetHighEdge()) > 3.0 && Fit.Evaluate(P.GetPeak())/Fit.Evaluate(P.GetHighEdge()) < 10) {
         if (g_Verbosity >= c_Info) cout<<P.GetPeak()<<" - Rejected: The peak sits on a strong increasing incline (left "<<Fit.Evaluate(P.GetLowEdge())<<" is less than 80% of right "<<Fit.Evaluate(P.GetHighEdge())<<" and right has at least an 3 count average and the peak-to-right-edge ratio is smaller than 10)"<<endl;  
-        P.IsGood(false);
-        continue;
+        //P.IsGood(false);
+        //continue;
       } else {
         if (g_Verbosity >= c_Info) cout<<P.GetPeak()<<" - Passed: The peak sits NOT on a strong increasing incline (left "<<Fit.Evaluate(P.GetLowEdge())<<" is more than 80% of right "<<Fit.Evaluate(P.GetHighEdge())<<" or right has less than a 3 count average and the peak-to-right-edge ratio is not smaller than 10)"<<endl;          
       }
diff --git a/src/fretalon/base/src/MCalibrationFitGaussian.cxx b/src/fretalon/base/src/MCalibrationFitGaussian.cxx
index 73d9c4ed3..5a4ef3f00 100644
--- a/src/fretalon/base/src/MCalibrationFitGaussian.cxx
+++ b/src/fretalon/base/src/MCalibrationFitGaussian.cxx
@@ -196,7 +196,7 @@ bool MCalibrationFitGaussian::Fit(TH1D& Histogram, double Min, double Max)
   ROOT::Fit::DataOptions Options; 
   ROOT::Fit::DataRange Range; 
   Range.SetRange(Min, Max);
-  ROOT::Fit::BinData TheData(Options, Range); 
+  ROOT::Fit::BinData TheData(Options, Range);
   ROOT::Fit::FillData(TheData, &Histogram);
 
   ROOT::Fit::Fitter TheFitter; 
diff --git a/src/fretalon/melinator/inc/MGUIMainMelinator.h b/src/fretalon/melinator/inc/MGUIMainMelinator.h
index f723d9f00..1f7e916b0 100644
--- a/src/fretalon/melinator/inc/MGUIMainMelinator.h
+++ b/src/fretalon/melinator/inc/MGUIMainMelinator.h
@@ -78,6 +78,8 @@ class MGUIMainMelinator : public TGMainFrame
 
   // protected members:
 protected:
+  //! Update melinator with the latest options
+  void UpdateMelinator();
   //! Set the active collection
   void UpdateCollection(unsigned int Collection, unsigned int Line);
   //! Set the active collection
@@ -89,7 +91,7 @@ class MGUIMainMelinator : public TGMainFrame
   bool UpdateDisplay(unsigned int Collection, unsigned int Line, bool ActiveResultIsEnergy);
 
   //! Update the saved GUI data
-  bool Update();
+  bool UpdateSettings();
   
   //! Create the selection GUI element    
   void CreateSelection();
@@ -207,6 +209,14 @@ class MGUIMainMelinator : public TGMainFrame
   //! Check button indicating that the Y-axis should be logarithmic
   TGCheckButton* m_HistogramLogY;
   
+
+  //! Entry representing the prior for bayesian block peak fining
+  TGNumberEntry* m_PeakFindingPrior;
+  //! Entry representing the number of ignored bins
+  TGNumberEntry* m_PeakFindingExcludeFirstNumberOfBins;
+  //! Entry representing the minimum number of counts in an accepted peak
+  TGNumberEntry* m_PeakFindingMinimumPeakCounts;
+
   
   //! Choose the binning mode (fixed bins, fixed number of counts, Bayesian block)
   TGComboBox* m_PeakHistogramBinningMode;
diff --git a/src/fretalon/melinator/inc/MMelinator.h b/src/fretalon/melinator/inc/MMelinator.h
index d89f22f38..b0234da87 100644
--- a/src/fretalon/melinator/inc/MMelinator.h
+++ b/src/fretalon/melinator/inc/MMelinator.h
@@ -74,6 +74,14 @@ class MMelinator
     if (m_HistogramBinningModeValue != HistogramBinningModeValue) { m_HistogramBinningModeValue = HistogramBinningModeValue; m_HistogramChanged = true; }
   }
   
+  //! Set the peak finding Bayesian block prior
+  void SetPeakFindingPrior(unsigned int PeakFindingPrior) { m_PeakFindingPrior = PeakFindingPrior; }
+  //! Set the peak finding number of bins excluded at lower energies
+  void SetPeakFindingExcludeFirstNumberOfBins(unsigned int PeakFindingExcludeFirstNumberOfBins) { m_PeakFindingExcludeFirstNumberOfBins = PeakFindingExcludeFirstNumberOfBins; }
+  //! Set the peak finding minimum number of counts in a peak
+  void SetPeakFindingMinimumPeakCounts(unsigned int PeakFindingMinimumPeakCounts) { m_PeakFindingMinimumPeakCounts = PeakFindingMinimumPeakCounts; }
+
+
   //! Set the peak parametrization method
   void SetPeakParametrizationMethod(unsigned int Method) { m_PeakParametrizationMethod = Method; }
   
@@ -232,7 +240,14 @@ class MMelinator
   unsigned int m_HistogramCollection;
   //! The current histograms
   vector<TH1D*> m_Histograms;
- 
+
+  //! Peak finding: Bayesian block prior
+  unsigned int m_PeakFindingPrior;
+  //! Peak finding: the number of bins excluded at lower energies
+  unsigned int m_PeakFindingExcludeFirstNumberOfBins;
+  //! Peak finding: the minimum number of counts in a peak
+  unsigned int m_PeakFindingMinimumPeakCounts;
+
   //! The peak parametrization method in during calibration of the lines
   unsigned int m_PeakParametrizationMethod;
   
diff --git a/src/fretalon/melinator/inc/MSettingsMelinator.h b/src/fretalon/melinator/inc/MSettingsMelinator.h
index ddebda59e..aec6cc4d7 100644
--- a/src/fretalon/melinator/inc/MSettingsMelinator.h
+++ b/src/fretalon/melinator/inc/MSettingsMelinator.h
@@ -79,7 +79,25 @@ class MSettingsMelinator : public MSettings
   bool GetHistogramLogY() const { return m_HistogramLogY; }
   //! Set a flag indicating the y-axis is displayed logarithmic
   void SetHistogramLogY(bool HistogramLogY) { m_HistogramLogY = HistogramLogY; }
-  
+
+
+
+  //! Get the peak finding Bayesian block prior
+  unsigned int GetPeakFindingPrior() const { return m_PeakFindingPrior; }
+  //! Set the peak finding Bayesian block prior
+  void SetPeakFindingPrior(unsigned int PeakFindingPrior) { m_PeakFindingPrior = PeakFindingPrior; }
+
+  //! Get the peak finding number of bins excluded at lower energies
+  unsigned int GetPeakFindingExcludeFirstNumberOfBins() const { return m_PeakFindingExcludeFirstNumberOfBins; }
+  //! Set the peak finding number of bins excluded at lower energies
+  void SetPeakFindingExcludeFirstNumberOfBins(unsigned int PeakFindingExcludeFirstNumberOfBins) { m_PeakFindingExcludeFirstNumberOfBins = PeakFindingExcludeFirstNumberOfBins; }
+
+  //! Get the peak finding minimum number of counts in a peak
+  unsigned int GetPeakFindingMinimumPeakCounts() const { return m_PeakFindingMinimumPeakCounts; }
+  //! Set the peak finding minimum number of counts in a peak
+  void SetPeakFindingMinimumPeakCounts(unsigned int PeakFindingMinimumPeakCounts) { m_PeakFindingMinimumPeakCounts = PeakFindingMinimumPeakCounts; }
+
+
   
   //! Get the peak binning mode: 0: fixed number of bins, 1: fixed cts per bin, 2: Bayesian block
   unsigned int GetPeakHistogramBinningMode() const { return m_PeakHistogramBinningMode; }
@@ -183,6 +201,13 @@ class MSettingsMelinator : public MSettings
   //! Flag indicating that the y-axis is displayed logarithmic
   bool m_HistogramLogY;
   
+  //! Peak finding: Bayesian block prior
+  unsigned int m_PeakFindingPrior;
+  //! Peak finding: the number of bins excluded at lower energies
+  unsigned int m_PeakFindingExcludeFirstNumberOfBins;
+  //! Peak finding: the minimum number of counts in a peak
+  unsigned int m_PeakFindingMinimumPeakCounts;
+
   //! The binning mode for the peak histogram: fixed number of bins, fixed cts per bin, Bayesian block
   unsigned int m_PeakHistogramBinningMode;
   //! Depending on the binning mode, either bins, cts/bin, or prior
diff --git a/src/fretalon/melinator/src/MGUIEReadOutElementView.cxx b/src/fretalon/melinator/src/MGUIEReadOutElementView.cxx
index 6b4b26125..70a099ad1 100644
--- a/src/fretalon/melinator/src/MGUIEReadOutElementView.cxx
+++ b/src/fretalon/melinator/src/MGUIEReadOutElementView.cxx
@@ -47,7 +47,7 @@ MGUIEReadOutElementView::MGUIEReadOutElementView(const TGWindow* Parent) :
   m_Parent = (TGWindow *) Parent;
   
   // Since we do not create the element in the constructor, 
-  // we have initialze some pointers:
+  // we have to initialize some pointers:
   m_Container = new TGCompositeFrame(GetViewPort(), 50, 50);
   SetContainer(m_Container);
   
diff --git a/src/fretalon/melinator/src/MGUIMainMelinator.cxx b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
index 492f46959..4d2d95bf5 100644
--- a/src/fretalon/melinator/src/MGUIMainMelinator.cxx
+++ b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
@@ -107,6 +107,9 @@ void MGUIMainMelinator::Create()
 
   double FontScaler = MGUIDefaults::GetInstance()->GetFontScaler();
   
+  int ScrollBarWidth = 50;
+  int ControlColumnWidth = 225 + ScrollBarWidth;
+
   // Give it a default size
   Resize(FontScaler*1200, 250 + FontScaler*600);
   
@@ -125,10 +128,14 @@ void MGUIMainMelinator::Create()
   TGLayoutHints* TopLeftTextLayout = new TGLayoutHints(kLHintsTop | kLHintsLeft, 0, 0, FontScaler*3, 0);
   TGLayoutHints* TopRightLayout = new TGLayoutHints(kLHintsTop | kLHintsExpandX | kLHintsRight, FontScaler*10, 0, 0, 0);
   TGLayoutHints* ButtonLayout = new TGLayoutHints(kLHintsTop | kLHintsRight, 2, 2, FontScaler*3, 3);
+
+  TGLayoutHints* CenterYLeftLayout = new TGLayoutHints(kLHintsCenterY | kLHintsLeft, 0, 0, 0, 0);
+  TGLayoutHints* CenterYRightEntryLayout = new TGLayoutHints(kLHintsCenterY | kLHintsRight, 0, 0, 0, 0);
+
   
   //TGLayoutHints* TopRightLayout = new TGLayoutHints(kLHintsTop | kLHintsRight, 2, 2, 2, 3);
 
-  TGLayoutHints* GroupLayout = new TGLayoutHints(kLHintsTop | kLHintsLeft | kLHintsExpandX, 2, 2, 5, 5);
+  TGLayoutHints* GroupLayout = new TGLayoutHints(kLHintsTop | kLHintsLeft | kLHintsExpandX, 2, 2 + ScrollBarWidth, 5, 5);
   
   // We have three main columns - the control column on the left, data column in the center, and selection on the right 
 
@@ -140,9 +147,7 @@ void MGUIMainMelinator::Create()
 
 
   // Left column: control column
-  
-  int ControlColumnWidth = 225;
-  
+
   TGLayoutHints* ControlColumnLayout = new TGLayoutHints(kLHintsTop | kLHintsLeft | kLHintsExpandY, 5, 0, 0, 0);
   TGVerticalFrame* ControlColumn = new TGVerticalFrame(Columns, ControlColumnWidth, ControlColumnWidth); //, kRaisedFrame);
   Columns->AddFrame(ControlColumn, ControlColumnLayout);
@@ -218,9 +223,22 @@ void MGUIMainMelinator::Create()
   ControlColumn->AddFrame(SubTitle, SubTitleLayout);
 
   
+
+  // Options section
+
+  TGLayoutHints* OptionsLayout = new TGLayoutHints(kLHintsTop | kLHintsLeft | kLHintsExpandY, 5, 0, 0, 0);
+  TGCanvas* OptionsCanvas = new TGCanvas(Columns, ControlColumnWidth, ControlColumnWidth, 0);
+
+  TGVerticalFrame* OptionsFrame = new TGVerticalFrame(OptionsCanvas->GetViewPort(), ControlColumnWidth, ControlColumnWidth, 0);
+  OptionsCanvas->SetContainer(OptionsFrame);
+  OptionsCanvas->SetScrolling(TGCanvas::kCanvasScrollVertical);
+
+  ControlColumn->AddFrame(OptionsCanvas, OptionsLayout);
+
+
   //  Section: Main spectrum
-  TGGroupFrame* HistogramGroup = new TGGroupFrame(ControlColumn, "Options for Main Spectrum", kVerticalFrame);
-  ControlColumn->AddFrame(HistogramGroup, GroupLayout);
+  TGGroupFrame* HistogramGroup = new TGGroupFrame(OptionsFrame, "Display of spectrum", kVerticalFrame);
+  OptionsFrame->AddFrame(HistogramGroup, GroupLayout);
   
   
   TGHorizontalFrame* ADCFrame = new TGHorizontalFrame(HistogramGroup);
@@ -306,11 +324,57 @@ void MGUIMainMelinator::Create()
   HistogramGroup->AddFrame(m_UpdateHistogramButton, TopExpandXLayout);
   
 
+
+
+  // Section: Peak finding
+  TGGroupFrame* PeakFindingGroup = new TGGroupFrame(OptionsFrame, "Peak finding options", kVerticalFrame);
+  OptionsFrame->AddFrame(PeakFindingGroup, GroupLayout);
+
+  TGHorizontalFrame* PeakFindingPriorFrame = new TGHorizontalFrame(PeakFindingGroup);
+  PeakFindingGroup->AddFrame(PeakFindingPriorFrame, TopLeftLayout);
+
+  TGLabel* PeakFindingPriorLabel = new TGLabel(PeakFindingPriorFrame, "Bayesian block prior:  ");
+  PeakFindingPriorLabel->SetWrapLength(FontScaler*150);
+  PeakFindingPriorFrame->AddFrame(PeakFindingPriorLabel, CenterYLeftLayout);
+
+  m_PeakFindingPrior = new TGNumberEntry(PeakFindingPriorFrame, m_Settings->GetPeakFindingPrior());
+  m_PeakFindingPrior->SetLimits(TGNumberFormat::kNELLimitMinMax, 1, 1000000);
+  m_PeakFindingPrior->SetWidth(FontScaler*70);
+  PeakFindingPriorFrame->AddFrame(m_PeakFindingPrior, CenterYRightEntryLayout);
+
+
+  TGHorizontalFrame* PeakFindingExcludeFirstNumberOfBinsFrame = new TGHorizontalFrame(PeakFindingGroup);
+  PeakFindingGroup->AddFrame(PeakFindingExcludeFirstNumberOfBinsFrame, TopLeftLayout);
+
+  TGLabel* PeakFindingExcludeFirstNumberOfBinsLabel = new TGLabel(PeakFindingExcludeFirstNumberOfBinsFrame, "Number of low-energy bins to exclude:  ");
+  PeakFindingExcludeFirstNumberOfBinsLabel->SetWrapLength(FontScaler*150);
+  PeakFindingExcludeFirstNumberOfBinsFrame->AddFrame(PeakFindingExcludeFirstNumberOfBinsLabel, CenterYLeftLayout);
+
+  m_PeakFindingExcludeFirstNumberOfBins = new TGNumberEntry(PeakFindingExcludeFirstNumberOfBinsFrame, m_Settings->GetPeakFindingExcludeFirstNumberOfBins());
+  m_PeakFindingExcludeFirstNumberOfBins->SetLimits(TGNumberFormat::kNELLimitMinMax, 1, 1000000);
+  m_PeakFindingExcludeFirstNumberOfBins->SetWidth(FontScaler*70);
+  PeakFindingExcludeFirstNumberOfBinsFrame->AddFrame(m_PeakFindingExcludeFirstNumberOfBins, CenterYRightEntryLayout);
+
+
+  TGHorizontalFrame* PeakFindingMinimumPeakCountsFrame = new TGHorizontalFrame(PeakFindingGroup);
+  PeakFindingGroup->AddFrame(PeakFindingMinimumPeakCountsFrame, TopLeftLayout);
+
+  TGLabel* PeakFindingMinimumPeakCountsLabel = new TGLabel(PeakFindingMinimumPeakCountsFrame, "Minimum counts in peak:  ");
+  PeakFindingMinimumPeakCountsLabel->SetWrapLength(FontScaler*150);
+  PeakFindingMinimumPeakCountsFrame->AddFrame(PeakFindingMinimumPeakCountsLabel, CenterYLeftLayout);
+
+  m_PeakFindingMinimumPeakCounts = new TGNumberEntry(PeakFindingMinimumPeakCountsFrame, m_Settings->GetPeakFindingMinimumPeakCounts());
+  m_PeakFindingMinimumPeakCounts->SetLimits(TGNumberFormat::kNELLimitMinMax, 1, 1000000);
+  m_PeakFindingMinimumPeakCounts->SetWidth(FontScaler*70);
+  PeakFindingMinimumPeakCountsFrame->AddFrame(m_PeakFindingMinimumPeakCounts, CenterYRightEntryLayout);
+
+
+
+
   
   //  Section: Secondary spectrum
-  TGGroupFrame* PeakGroup = new TGGroupFrame(ControlColumn, "Options for Peak Spectrum", kVerticalFrame);
-  ControlColumn->AddFrame(PeakGroup, GroupLayout);
-
+  TGGroupFrame* PeakGroup = new TGGroupFrame(OptionsFrame, "Display of peak spectrum", kVerticalFrame);
+  OptionsFrame->AddFrame(PeakGroup, GroupLayout);
   
   TGHorizontalFrame* PeakBinningModeFrame = new TGHorizontalFrame(PeakGroup);
   PeakGroup->AddFrame(PeakBinningModeFrame, TopLeftLayout);
@@ -374,8 +438,8 @@ void MGUIMainMelinator::Create()
   
   
   // Peak parametrization section
-  TGGroupFrame* FitGroup = new TGGroupFrame(ControlColumn, "Peak parametrization options", kVerticalFrame);
-  ControlColumn->AddFrame(FitGroup, GroupLayout);
+  TGGroupFrame* FitGroup = new TGGroupFrame(OptionsFrame, "Peak parametrization options", kVerticalFrame);
+  OptionsFrame->AddFrame(FitGroup, GroupLayout);
 
   TGHorizontalFrame* PeakParametrizationMethodFrame = new TGHorizontalFrame(FitGroup);
   FitGroup->AddFrame(PeakParametrizationMethodFrame, TopLeftLayout);
@@ -404,8 +468,8 @@ void MGUIMainMelinator::Create()
   
   
   // Calibration model determination section
-  TGGroupFrame* CalibrationModel = new TGGroupFrame(ControlColumn, "Calibration model options", kVerticalFrame);
-  ControlColumn->AddFrame(CalibrationModel, GroupLayout);
+  TGGroupFrame* CalibrationModel = new TGGroupFrame(OptionsFrame, "Calibration model options", kVerticalFrame);
+  OptionsFrame->AddFrame(CalibrationModel, GroupLayout);
 
   m_CalibrationModelZeroCrossing = new TGCheckButton(CalibrationModel, "Energy assignment only: Assume the energy calibration crosses (0/0)", c_CalibrationModelZeroCrossing);
   m_CalibrationModelZeroCrossing->Associate(this);
@@ -500,9 +564,7 @@ void MGUIMainMelinator::Create()
 
   m_SpectrumCanvas = new MGUIEReadOutUnitsCanvas(this, "SpectrumCanvas", MainDataView);
   MainDataView->AddFrame(m_SpectrumCanvas, CanvasLayout);
-  
- 
- 
+
     
   // The calibration view:
   TGHorizontalFrame* CalibrationView = new TGHorizontalFrame(DataColumn, 100, 100); //, kRaisedFrame);
@@ -902,7 +964,7 @@ void MGUIMainMelinator::CloseWindow()
 
 
 //! Update the setting with the GUI data
-bool MGUIMainMelinator::Update()
+bool MGUIMainMelinator::UpdateSettings()
 {
   m_Settings->SetHistogramMin(m_HistogramRangeMin->GetNumber());
   m_Settings->SetHistogramMax(m_HistogramRangeMax->GetNumber());
@@ -921,6 +983,10 @@ bool MGUIMainMelinator::Update()
   m_Settings->SetPeakHistogramBinningMode(m_PeakHistogramBinningMode->GetSelected());
   m_Settings->SetPeakHistogramBinningModeValue(m_PeakHistogramBinningModeValue->GetNumber());
   
+  m_Settings->SetPeakFindingPrior(m_PeakFindingPrior->GetNumber());
+  m_Settings->SetPeakFindingExcludeFirstNumberOfBins(m_PeakFindingExcludeFirstNumberOfBins->GetNumber());
+  m_Settings->SetPeakFindingMinimumPeakCounts(m_PeakFindingMinimumPeakCounts->GetNumber());
+
   m_Settings->SetPeakParametrizationMethod(m_PeakParametrizationMethod->GetSelected());
   if (m_PeakParametrizationMethod->GetSelected() == MCalibrateEnergyFindLines::c_PeakParametrizationMethodFittedPeak) {
     m_Settings->SetPeakParametrizationMethodFittingBackgroundModel(m_PeakParametrizationMethodFittingBackgroundModel->GetSelected());
@@ -948,7 +1014,7 @@ bool MGUIMainMelinator::Update()
 //! Close the applictaion
 bool MGUIMainMelinator::OnExit()
 {
-  Update();
+  UpdateSettings();
   m_Settings->Write(); // Update alreday writes, but it is logical that we write here too so keep it
   
   //m_Interface->Exit();
@@ -1270,6 +1336,10 @@ bool MGUIMainMelinator::OnLoadLast()
   m_Melinator.SetSelectedDetectorID(m_Settings->GetSelectedDetectorID());
   m_Melinator.SetSelectedDetectorSide(m_Settings->GetSelectedDetectorSide());
   m_Melinator.SetSelectedTemperatureWindow(m_Settings->GetMinimumTemperature(), m_Settings->GetMaximumTemperature());
+  m_Melinator.SetPeakFindingPrior(m_Settings->GetPeakFindingPrior());
+  m_Melinator.SetPeakFindingExcludeFirstNumberOfBins(m_Settings->GetPeakFindingExcludeFirstNumberOfBins());
+  m_Melinator.SetPeakFindingMinimumPeakCounts(m_Settings->GetPeakFindingMinimumPeakCounts());
+
   
   MString FileName;
   MString IsotopeName;
@@ -1527,6 +1597,37 @@ bool MGUIMainMelinator::OnToggleResults()
 ////////////////////////////////////////////////////////////////////////////////
 
 
+//! Update all graphs
+void MGUIMainMelinator::UpdateMelinator()
+{
+  UpdateSettings();
+
+  m_Melinator.SetPeakFindingPrior(m_Settings->GetPeakFindingPrior());
+  m_Melinator.SetPeakFindingExcludeFirstNumberOfBins(m_Settings->GetPeakFindingExcludeFirstNumberOfBins());
+  m_Melinator.SetPeakFindingMinimumPeakCounts(m_Settings->GetPeakFindingMinimumPeakCounts());
+
+  if (m_Melinator.GetNumberOfCollections() > 0) {
+    m_Melinator.SetPeakParametrizationMethod(m_PeakParametrizationMethod->GetSelected());
+    if (m_PeakParametrizationMethod->GetSelected() == MCalibrateEnergyFindLines::c_PeakParametrizationMethodFittedPeak) {
+      m_Melinator.SetPeakParametrizationMethodFittedPeakOptions(m_PeakParametrizationMethodFittingBackgroundModel->GetSelected(), m_PeakParametrizationMethodFittingEnergyLossModel->GetSelected(), m_PeakParametrizationMethodFittingPeakShapeModel->GetSelected());
+    }
+
+    if (m_CalibrationModelZeroCrossing->GetState() == kButtonDown) {
+      m_Melinator.SetCalibrationModelEnergyAssignmentMethod(MCalibrateEnergyAssignEnergyModes::e_LinearZeroCrossing);
+    } else {
+      m_Melinator.SetCalibrationModelEnergyAssignmentMethod(MCalibrateEnergyAssignEnergyModes::e_Linear);
+    }
+    m_Melinator.SetCalibrationModelDeterminationMethod(m_CalibrationModelDeterminationMethod->GetSelected());
+    if (m_CalibrationModelDeterminationMethod->GetSelected() == MCalibrateEnergyDetermineModel::c_CalibrationModelFit) {
+      m_Melinator.SetCalibrationModelDeterminationMethodFittingEnergyOptions(m_CalibrationModelDeterminationMethodFittingEnergyModel->GetSelected());
+      m_Melinator.SetCalibrationModelDeterminationMethodFittingFWHMOptions(m_CalibrationModelDeterminationMethodFittingFWHMModel->GetSelected());
+    }
+  }
+}
+
+////////////////////////////////////////////////////////////////////////////////
+
+
 //! Update all graphs
 bool MGUIMainMelinator::UpdateDisplay(unsigned int Collection, unsigned int Line, bool ActiveResultIsEnergy)
 {
@@ -1544,7 +1645,7 @@ bool MGUIMainMelinator::UpdateDisplay(unsigned int Collection, unsigned int Line
 //! Set the active collection and put it to the screen
 void MGUIMainMelinator::UpdateCollection(unsigned int Collection, unsigned int Line)
 {
-  Update();
+  UpdateSettings();
   
   if (Collection < m_Melinator.GetNumberOfCollections()) {
     m_ActiveCollection = Collection;
@@ -1566,7 +1667,7 @@ void MGUIMainMelinator::UpdateCollection(unsigned int Collection, unsigned int L
     m_Melinator.SetHistogramProperties(m_Settings->GetHistogramMin(), m_Settings->GetHistogramMax(), 
       m_Settings->GetHistogramBinningMode(), m_Settings->GetHistogramBinningModeValue());
     m_Melinator.DrawSpectrum(*(m_SpectrumCanvas->GetCanvas()), m_ActiveCollection, Line);
-    
+
     OnXAxis(m_Settings->GetHistogramLogX());
     OnYAxis(m_Settings->GetHistogramLogY());
 
@@ -1772,23 +1873,9 @@ void MGUIMainMelinator::SwitchToLine(double X)
 //! Fit the current histogram
 bool MGUIMainMelinator::OnFit()
 {
-  if (m_ActiveCollection < m_Melinator.GetNumberOfCollections()) {
-    m_Melinator.SetPeakParametrizationMethod(m_PeakParametrizationMethod->GetSelected());
-    if (m_PeakParametrizationMethod->GetSelected() == MCalibrateEnergyFindLines::c_PeakParametrizationMethodFittedPeak) {
-      m_Melinator.SetPeakParametrizationMethodFittedPeakOptions(m_PeakParametrizationMethodFittingBackgroundModel->GetSelected(), m_PeakParametrizationMethodFittingEnergyLossModel->GetSelected(), m_PeakParametrizationMethodFittingPeakShapeModel->GetSelected());
-    }
-    
-    if (m_CalibrationModelZeroCrossing->GetState() == kButtonDown) {
-      m_Melinator.SetCalibrationModelEnergyAssignmentMethod(MCalibrateEnergyAssignEnergyModes::e_LinearZeroCrossing);
-    } else {
-      m_Melinator.SetCalibrationModelEnergyAssignmentMethod(MCalibrateEnergyAssignEnergyModes::e_Linear);      
-    }
-    m_Melinator.SetCalibrationModelDeterminationMethod(m_CalibrationModelDeterminationMethod->GetSelected());
-    if (m_CalibrationModelDeterminationMethod->GetSelected() == MCalibrateEnergyDetermineModel::c_CalibrationModelFit) {
-      m_Melinator.SetCalibrationModelDeterminationMethodFittingEnergyOptions(m_CalibrationModelDeterminationMethodFittingEnergyModel->GetSelected());
-      m_Melinator.SetCalibrationModelDeterminationMethodFittingFWHMOptions(m_CalibrationModelDeterminationMethodFittingFWHMModel->GetSelected());
-    }
+  UpdateMelinator();
 
+  if (m_ActiveCollection < m_Melinator.GetNumberOfCollections()) {
     m_Melinator.Calibrate(m_ActiveCollection, false);
     OnUpdateHistogram();
   }
@@ -1803,23 +1890,9 @@ bool MGUIMainMelinator::OnFit()
 //! Fit the current histogram
 bool MGUIMainMelinator::OnFitWithDiagnostics()
 {
-  if (m_ActiveCollection < m_Melinator.GetNumberOfCollections()) {
-    m_Melinator.SetPeakParametrizationMethod(m_PeakParametrizationMethod->GetSelected());
-    if (m_PeakParametrizationMethod->GetSelected() == MCalibrateEnergyFindLines::c_PeakParametrizationMethodFittedPeak) {
-      m_Melinator.SetPeakParametrizationMethodFittedPeakOptions(m_PeakParametrizationMethodFittingBackgroundModel->GetSelected(), m_PeakParametrizationMethodFittingEnergyLossModel->GetSelected(), m_PeakParametrizationMethodFittingPeakShapeModel->GetSelected());
-    }
+  UpdateMelinator();
 
-    if (m_CalibrationModelZeroCrossing->GetState() == kButtonDown) {
-      m_Melinator.SetCalibrationModelEnergyAssignmentMethod(MCalibrateEnergyAssignEnergyModes::e_LinearZeroCrossing);
-    } else {
-      m_Melinator.SetCalibrationModelEnergyAssignmentMethod(MCalibrateEnergyAssignEnergyModes::e_Linear);      
-    }
-    m_Melinator.SetCalibrationModelDeterminationMethod(m_CalibrationModelDeterminationMethod->GetSelected());
-    if (m_CalibrationModelDeterminationMethod->GetSelected() == MCalibrateEnergyDetermineModel::c_CalibrationModelFit) {
-      m_Melinator.SetCalibrationModelDeterminationMethodFittingEnergyOptions(m_CalibrationModelDeterminationMethodFittingEnergyModel->GetSelected());
-      m_Melinator.SetCalibrationModelDeterminationMethodFittingFWHMOptions(m_CalibrationModelDeterminationMethodFittingFWHMModel->GetSelected());
-    }
-    
+  if (m_ActiveCollection < m_Melinator.GetNumberOfCollections()) {
     m_Melinator.Calibrate(m_ActiveCollection, true);
     OnUpdateHistogram();
   }
@@ -1834,23 +1907,9 @@ bool MGUIMainMelinator::OnFitWithDiagnostics()
 //! Fit the current histogram
 bool MGUIMainMelinator::OnFitAll()
 {
-  if (m_Melinator.GetNumberOfCollections() > 0) {
-    m_Melinator.SetPeakParametrizationMethod(m_PeakParametrizationMethod->GetSelected());
-    if (m_PeakParametrizationMethod->GetSelected() == MCalibrateEnergyFindLines::c_PeakParametrizationMethodFittedPeak) {
-      m_Melinator.SetPeakParametrizationMethodFittedPeakOptions(m_PeakParametrizationMethodFittingBackgroundModel->GetSelected(), m_PeakParametrizationMethodFittingEnergyLossModel->GetSelected(), m_PeakParametrizationMethodFittingPeakShapeModel->GetSelected());
-    }
+  UpdateMelinator();
 
-    if (m_CalibrationModelZeroCrossing->GetState() == kButtonDown) {
-      m_Melinator.SetCalibrationModelEnergyAssignmentMethod(MCalibrateEnergyAssignEnergyModes::e_LinearZeroCrossing);
-    } else {
-      m_Melinator.SetCalibrationModelEnergyAssignmentMethod(MCalibrateEnergyAssignEnergyModes::e_Linear);      
-    }
-    m_Melinator.SetCalibrationModelDeterminationMethod(m_CalibrationModelDeterminationMethod->GetSelected());
-    if (m_CalibrationModelDeterminationMethod->GetSelected() == MCalibrateEnergyDetermineModel::c_CalibrationModelFit) {
-      m_Melinator.SetCalibrationModelDeterminationMethodFittingEnergyOptions(m_CalibrationModelDeterminationMethodFittingEnergyModel->GetSelected());
-      m_Melinator.SetCalibrationModelDeterminationMethodFittingFWHMOptions(m_CalibrationModelDeterminationMethodFittingFWHMModel->GetSelected());
-    }
-    
+  if (m_Melinator.GetNumberOfCollections() > 0) {
     m_Melinator.Calibrate(false);
     OnUpdateHistogram();
   }
@@ -1912,7 +1971,7 @@ bool MGUIMainMelinator::OnSaveConfiguration()
   
   // Get the filename and store all the data in the settings...
   if ((char *) Info.fFilename != 0) {
-    Update();
+    UpdateSettings();
     m_Interface->SaveConfiguration(MString(Info.fFilename));
   } 
 
diff --git a/src/fretalon/melinator/src/MMelinator.cxx b/src/fretalon/melinator/src/MMelinator.cxx
index 544026941..fa6074177 100644
--- a/src/fretalon/melinator/src/MMelinator.cxx
+++ b/src/fretalon/melinator/src/MMelinator.cxx
@@ -90,6 +90,10 @@ MMelinator::MMelinator()
   m_HistogramChanged = true;
   m_HistogramCollection = -1;
 
+  m_PeakFindingPrior = 8;
+  m_PeakFindingExcludeFirstNumberOfBins = 25;
+  m_PeakFindingMinimumPeakCounts = 100;
+
   m_PeakParametrizationMethod = MCalibrateEnergyFindLines::c_PeakParametrizationMethodBayesianBlockPeak;
   m_PeakParametrizationMethodFittedPeakBackgroundModel = MCalibrationFit::c_BackgroundModelLinear;
   m_PeakParametrizationMethodFittedPeakEnergyLossModel = MCalibrationFit::c_EnergyLossModelNone;
@@ -543,10 +547,10 @@ void MMelinator::DrawSpectrum(TCanvas& Canvas, unsigned int Collection, unsigned
   Canvas.SetGridy();
   //Canvas.SetLogy();
   
-  Canvas.SetLeftMargin(0.08);
+  Canvas.SetLeftMargin(0.1);
   Canvas.SetRightMargin(0.05);
   Canvas.SetTopMargin(0.05);
-  Canvas.SetBottomMargin(0.12);
+  Canvas.SetBottomMargin(0.14);
   
   
   
@@ -595,14 +599,14 @@ void MMelinator::DrawSpectrum(TCanvas& Canvas, unsigned int Collection, unsigned
       //m_Histograms[h]->GetXaxis()->SetLabelOffset(0.0);
       m_Histograms[h]->GetXaxis()->SetLabelSize(0.05);
       m_Histograms[h]->GetXaxis()->SetTitleSize(0.06);
-      m_Histograms[h]->GetXaxis()->SetTitleOffset(0.9);
+      m_Histograms[h]->GetXaxis()->SetTitleOffset(1.1);
       m_Histograms[h]->GetXaxis()->CenterTitle(true);
       m_Histograms[h]->GetXaxis()->SetMoreLogLabels(true);
       
       //m_Histograms[h]->GetYaxis()->SetLabelOffset(0.001);
       m_Histograms[h]->GetYaxis()->SetLabelSize(0.05);
       m_Histograms[h]->GetYaxis()->SetTitleSize(0.06);
-      m_Histograms[h]->GetYaxis()->SetTitleOffset(0.6);
+      m_Histograms[h]->GetYaxis()->SetTitleOffset(0.8);
       m_Histograms[h]->GetYaxis()->CenterTitle(true);
     }
   }
@@ -611,9 +615,9 @@ void MMelinator::DrawSpectrum(TCanvas& Canvas, unsigned int Collection, unsigned
     if (m_Histograms[h] == 0) continue;
     
     if (h == 0) {
-      m_Histograms[h]->DrawCopy();
+      m_Histograms[h]->DrawCopy("HIST");
     } else {
-      m_Histograms[h]->DrawCopy("SAME");
+      m_Histograms[h]->DrawCopy("HIST SAME");
     }
   }
   
@@ -964,7 +968,7 @@ void MMelinator::DrawCalibration(TCanvas& Canvas, unsigned int Collection, bool
   Graph->GetXaxis()->CenterTitle(true);
   Graph->GetXaxis()->SetMoreLogLabels(true);
   Graph->GetXaxis()->SetLimits(0.0, 1.1*MaximumX);
-  Graph->GetXaxis()->SetNdivisions(509, true);
+  Graph->GetXaxis()->SetNdivisions(505, true);
   
   if (UseEnergy == true) {
     Graph->GetYaxis()->SetTitle("energy [keV]");
@@ -1263,6 +1267,9 @@ bool MMelinator::Calibrate(unsigned int Collection, bool ShowDiagnostics)
     FindLines.SetDiagnosticsMode(ShowDiagnostics);
     FindLines.SetRange(m_HistogramMin, m_HistogramMax);
     FindLines.SetTemperatureWindow(m_SelectedTemperatureMin, m_SelectedTemperatureMax);
+    FindLines.SetBayesianBlockPrior(m_PeakFindingPrior);
+    FindLines.SetNumberOfExcludedBinsAtLowEnergies(m_PeakFindingExcludeFirstNumberOfBins);
+    FindLines.SetMinimumNumberOfPeakCounts(m_PeakFindingMinimumPeakCounts);
     //cout<<"T1: "<<Timer.GetElapsed()<<endl;
     for (unsigned int g = 0; g < C.GetNumberOfReadOutDataGroups(); ++g) {
       FindLines.AddReadOutDataGroup(C.GetReadOutDataGroup(g), m_Isotopes[distance(m_GroupIDs.begin(), find(m_GroupIDs.begin(), m_GroupIDs.end(), g))]);
diff --git a/src/fretalon/melinator/src/MSettingsMelinator.cxx b/src/fretalon/melinator/src/MSettingsMelinator.cxx
index 8b438fe1b..b64697542 100644
--- a/src/fretalon/melinator/src/MSettingsMelinator.cxx
+++ b/src/fretalon/melinator/src/MSettingsMelinator.cxx
@@ -60,6 +60,10 @@ MSettingsMelinator::MSettingsMelinator(bool AutoLoad) : MSettings("MelinatorConf
   m_HistogramLogX = false;
   m_HistogramLogY = false;
 
+  m_PeakFindingPrior = 8;
+  m_PeakFindingExcludeFirstNumberOfBins = 25;
+  m_PeakFindingMinimumPeakCounts = 100;
+
   m_PeakHistogramBinningMode = 0;
   m_PeakHistogramBinningModeValue = 100;
 
@@ -155,6 +159,10 @@ bool MSettingsMelinator::WriteXml(MXmlNode* Node)
   new MXmlNode(Node, "HistogramLogX", m_HistogramLogX);
   new MXmlNode(Node, "HistogramLogY", m_HistogramLogY);
 
+  new MXmlNode(Node, "PeakFindingPrior", m_PeakFindingPrior);
+  new MXmlNode(Node, "PeakFindingExcludeFirstNumberOfBins", m_PeakFindingExcludeFirstNumberOfBins);
+  new MXmlNode(Node, "PeakFindingMinimumPeakCounts", m_PeakFindingMinimumPeakCounts);
+
   new MXmlNode(Node, "PeakHistogramBinningMode", m_PeakHistogramBinningMode);
   new MXmlNode(Node, "PeakHistogramBinningModeValue", m_PeakHistogramBinningModeValue);
 
@@ -236,7 +244,17 @@ bool MSettingsMelinator::ReadXml(MXmlNode* Node)
   if ((aNode = Node->GetNode("HistogramLogY")) != 0) {
     m_HistogramLogY = aNode->GetValueAsBoolean();
   }
- 
+
+  if ((aNode = Node->GetNode("PeakFindingPrior")) != 0) {
+    m_PeakFindingPrior = aNode->GetValueAsUnsignedInt();
+  }
+  if ((aNode = Node->GetNode("PeakFindingExcludeFirstNumberOfBins")) != 0) {
+    m_PeakFindingExcludeFirstNumberOfBins = aNode->GetValueAsUnsignedInt();
+  }
+  if ((aNode = Node->GetNode("PeakFindingMinimumPeakCounts")) != 0) {
+    m_PeakFindingMinimumPeakCounts = aNode->GetValueAsUnsignedInt();
+  }
+
   if ((aNode = Node->GetNode("PeakHistogramBinningMode")) != 0) {
     m_PeakHistogramBinningMode = aNode->GetValueAsUnsignedInt();
   }
diff --git a/src/global/misc/src/MBinner.cxx b/src/global/misc/src/MBinner.cxx
index 3b6e6b396..96d5c375d 100644
--- a/src/global/misc/src/MBinner.cxx
+++ b/src/global/misc/src/MBinner.cxx
@@ -129,6 +129,11 @@ TH1D* MBinner::GetHistogram(const MString& Title, const MString& xTitle, const M
   
   for (unsigned int i = 0; i < m_BinnedData.size(); ++i) {
     Hist->SetBinContent(i+1, m_BinnedData[i]);
+    if (m_BinnedData[i] > 0) {
+      Hist->SetBinError(i+1, sqrt(m_BinnedData[i]));
+    } else {
+      Hist->SetBinError(i+1, 1);
+    }
   }
   
   return Hist;
@@ -143,9 +148,14 @@ TH1D* MBinner::GetNormalizedHistogram(const MString& Title, const MString& xTitl
 {
   TH1D* Hist = GetHistogram(Title, xTitle, yTitle);
  
-  for (int b = 0; b <= Hist->GetNbinsX(); ++b) {
+  for (int b = 1; b <= Hist->GetNbinsX(); ++b) {
     if (Hist->GetBinWidth(b) > 0) {
       Hist->SetBinContent(b, Hist->GetBinContent(b)/Hist->GetBinWidth(b));
+      if (Hist->GetBinContent(b) > 0) {
+        Hist->SetBinError(b, sqrt(Hist->GetBinContent(b))/Hist->GetBinWidth(b));
+      } else {
+        Hist->SetBinError(b, 1/Hist->GetBinWidth(b));
+      }
     }
   }
  

From 86b5459ca2eb7492d3a431b22f0cae742a9ab976 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Wed, 13 Sep 2023 11:49:29 -0700
Subject: [PATCH 021/192] CHG: Parallelize spectrum creation

---
 src/fretalon/melinator/inc/MMelinator.h       |  18 +-
 .../melinator/src/MGUIMainMelinator.cxx       |  15 +-
 src/fretalon/melinator/src/MMelinator.cxx     | 157 +++++++++++++++---
 3 files changed, 160 insertions(+), 30 deletions(-)

diff --git a/src/fretalon/melinator/inc/MMelinator.h b/src/fretalon/melinator/inc/MMelinator.h
index b0234da87..86685900d 100644
--- a/src/fretalon/melinator/inc/MMelinator.h
+++ b/src/fretalon/melinator/inc/MMelinator.h
@@ -178,6 +178,8 @@ class MMelinator
   bool CalibrateParallel(unsigned int ThreadID);
   //! This function is executed by the parallel loading threads
   bool LoadParallel(unsigned int ThreadID);
+  //! The function is executed by the parallel spectrum creation threads
+  bool CreateSpectrumParallel(unsigned int ThreadID, unsigned int CollectionID, unsigned int DataGroupID);
   
   
   // protected methods:
@@ -308,21 +310,32 @@ class MMelinatorThreadCaller
 {
  public:
   //! Standard constructor
-  MMelinatorThreadCaller(MMelinator* M, unsigned int ThreadID) {
+  //! ID1 and ID2 can be any ID/index we need to pass on
+  MMelinatorThreadCaller(MMelinator* M, unsigned int ThreadID, unsigned int ID1 = 0, unsigned int ID2 = 0) {
     m_Melinator = M;
     m_ThreadID = ThreadID;
+    m_ID1 = ID1;
+    m_ID2 = ID2;
   }
 
   //! Return the calling class
   MMelinator* GetThreadCaller() { return m_Melinator; }
   //! Return the thread ID
   unsigned int GetThreadID() { return m_ThreadID; }
+  //! Return ID1
+  unsigned int GetID1() { return m_ID1; }
+  //! Return ID2
+  unsigned int GetID2() { return m_ID2; }
 
  private:
   //! Store the calling class for retrieval
   MMelinator* m_Melinator;
   //! ID of the worker thread
   unsigned int m_ThreadID;
+  //! Special ID/index
+  unsigned int m_ID1;
+  //! Special ID/index
+  unsigned int m_ID2;
 };
 
 
@@ -335,6 +348,9 @@ void MMelinatorCallParallelCalibrationThread(void* address);
 //! Thread entry point for the parallel calibration
 void MMelinatorCallParallelLoadingThread(void* address);
 
+//! Thread entry point for the parallel spectrum creation
+void MMelinatorCallParallelSpectrumCreationThread(void* address);
+
 //! Streamify the read-out data
 std::ostream& operator<<(std::ostream& os, const MMelinator& R);
 
diff --git a/src/fretalon/melinator/src/MGUIMainMelinator.cxx b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
index 4d2d95bf5..af4d56ad9 100644
--- a/src/fretalon/melinator/src/MGUIMainMelinator.cxx
+++ b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
@@ -42,6 +42,7 @@ using namespace std;
 
 // MEGAlib libs:
 #include "MStreams.h"
+#include "MTimer.h"
 #include "MGUIDefaults.h"
 #include "MFile.h"
 #include "MMath.h"
@@ -292,7 +293,7 @@ void MGUIMainMelinator::Create()
   m_HistogramBinningModeValue->SetLimits(TGNumberFormat::kNELLimitMinMax, 1, 1000000); 
   BinningValueFrame->AddFrame(m_HistogramBinningModeValue, TopLeftLayout);
   
-  m_HistogramBinningModeValueLabel = new TGLabel(BinningValueFrame, "To be determined later");
+  m_HistogramBinningModeValueLabel = new TGLabel(BinningValueFrame, "   TBD later   ");
   BinningValueFrame->AddFrame(m_HistogramBinningModeValueLabel, TopLeftTextLayout);
   
   OnSwitchHistogramBinningMode(m_Settings->GetHistogramBinningMode());
@@ -407,7 +408,7 @@ void MGUIMainMelinator::Create()
   m_PeakHistogramBinningModeValue->SetLimits(TGNumberFormat::kNELLimitMinMax, 1, 1000000); 
   PeakBinningValueFrame->AddFrame(m_PeakHistogramBinningModeValue, TopLeftLayout);
   
-  m_PeakHistogramBinningModeValueLabel = new TGLabel(PeakBinningValueFrame, "To be determined later");
+  m_PeakHistogramBinningModeValueLabel = new TGLabel(PeakBinningValueFrame, "  TBD later");
   PeakBinningValueFrame->AddFrame(m_PeakHistogramBinningModeValueLabel, TopLeftTextLayout);
   
   OnSwitchPeakHistogramBinningMode(m_Settings->GetPeakHistogramBinningMode());
@@ -1040,9 +1041,9 @@ bool MGUIMainMelinator::OnSwitchHistogramBinningMode(unsigned int ID)
     m_HistogramBinningModeValueLabel->SetText("ERROR");
   }
 
-  MapSubwindows();
-  MapWindow();  
-  Layout();  
+  //MapSubwindows();
+  MapWindow();
+  //Layout();
   
   return true;
 }
@@ -1634,7 +1635,7 @@ bool MGUIMainMelinator::UpdateDisplay(unsigned int Collection, unsigned int Line
   UpdateCollection(Collection, Line);
   UpdateLineFit(Collection, Line);
   UpdateCalibration(Collection, ActiveResultIsEnergy);
-  
+
   return true;
 }
 
@@ -1645,6 +1646,7 @@ bool MGUIMainMelinator::UpdateDisplay(unsigned int Collection, unsigned int Line
 //! Set the active collection and put it to the screen
 void MGUIMainMelinator::UpdateCollection(unsigned int Collection, unsigned int Line)
 {
+
   UpdateSettings();
   
   if (Collection < m_Melinator.GetNumberOfCollections()) {
@@ -1666,6 +1668,7 @@ void MGUIMainMelinator::UpdateCollection(unsigned int Collection, unsigned int L
     
     m_Melinator.SetHistogramProperties(m_Settings->GetHistogramMin(), m_Settings->GetHistogramMax(), 
       m_Settings->GetHistogramBinningMode(), m_Settings->GetHistogramBinningModeValue());
+
     m_Melinator.DrawSpectrum(*(m_SpectrumCanvas->GetCanvas()), m_ActiveCollection, Line);
 
     OnXAxis(m_Settings->GetHistogramLogX());
diff --git a/src/fretalon/melinator/src/MMelinator.cxx b/src/fretalon/melinator/src/MMelinator.cxx
index fa6074177..645ef1424 100644
--- a/src/fretalon/melinator/src/MMelinator.cxx
+++ b/src/fretalon/melinator/src/MMelinator.cxx
@@ -80,6 +80,19 @@ ClassImp(MMelinator)
 ////////////////////////////////////////////////////////////////////////////////
 
 
+//! Thread entry point for the parallel calibration
+void MMelinatorCallParallelSpectrumCreationThread(void* Address)
+{
+  MMelinatorThreadCaller* Caller = (MMelinatorThreadCaller*) Address;
+
+  MMelinator* M = Caller->GetThreadCaller();
+  M->CreateSpectrumParallel(Caller->GetThreadID(), Caller->GetID1(), Caller->GetID2());
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
 //! Default constructor
 MMelinator::MMelinator()
 {
@@ -287,14 +300,14 @@ bool MMelinator::Load(const vector<MString>& FileNames, const vector<vector<MIso
     m_CalibrationFileLoadingProgress[c] = 0.0;
   }
   
-  unsigned int NThreads = m_CalibrationFileNames.size();  
+  unsigned int NThreads = m_CalibrationFileNames.size();
 
   m_ThreadNextItem = 0;
   m_Threads.resize(NThreads);
   m_ThreadIsInitialized.resize(NThreads);
   m_ThreadShouldTerminate.resize(NThreads);
   m_ThreadIsFinished.resize(NThreads);
-  
+
   if (NThreads > 0) {
     
     // Start threads
@@ -552,25 +565,90 @@ void MMelinator::DrawSpectrum(TCanvas& Canvas, unsigned int Collection, unsigned
   Canvas.SetTopMargin(0.05);
   Canvas.SetBottomMargin(0.14);
   
-  
-  
+
   if (m_HistogramChanged == true) {
-    
+
     for (auto H: m_Histograms) delete H;
     m_Histograms.clear();
     
-    //! Create the histograms
-    for (unsigned int g = 0; g < C.GetNumberOfReadOutDataGroups(); ++g) {
-      MReadOutDataGroup& G = C.GetReadOutDataGroup(g);
-      TH1D* H = CreateSpectrum(G.GetName(), G, m_HistogramMin, m_HistogramMax, m_HistogramBinningMode, m_HistogramBinningModeValue);
-      if (H->GetMaximum() > 0) {
-        m_Histograms.push_back(H); //C.GetReadOutElement().ToString(), G));
-      } else {
-        m_Histograms.push_back(0);
-        delete H;
+
+    // <-- Begin time critical
+
+    unsigned int NThreads = C.GetNumberOfReadOutDataGroups();
+
+    if (NThreads > 1) {
+      m_Histograms.resize(NThreads);
+
+      m_ThreadNextItem = 0;
+      m_Threads.resize(NThreads);
+      m_ThreadIsInitialized.resize(NThreads);
+      m_ThreadShouldTerminate.resize(NThreads);
+      m_ThreadIsFinished.resize(NThreads);
+
+      // Start threads
+      for (unsigned int t = 0; t < NThreads; ++t) {
+        TString Name = "Loading thread #";
+        Name += t;
+        //cout<<"Creating thread: "<<Name<<endl;
+        TThread* Thread = new TThread(Name, (void(*) (void *)) &MMelinatorCallParallelSpectrumCreationThread, (void*) new MMelinatorThreadCaller(this, t, Collection, t));
+        m_Threads[t] = Thread;
+        m_ThreadIsInitialized[t] = false;
+        m_ThreadShouldTerminate[t] = false;
+        m_ThreadIsFinished[t] = false;
+
+        Thread->Run();
+
+        // Wait until thread is initialized:
+        while (m_ThreadIsInitialized[t] == false && m_ThreadIsFinished[t] == false) {
+          // Sleep for a while...
+          TThread::Sleep(0, 10000000);
+        }
+
+      }
+
+      long Counter = 0;
+      bool ThreadsAreRunning = true;
+      while (ThreadsAreRunning == true) {
+
+        // Sleep for a 10 ms
+        TThread::Sleep(0, 10000000);
+        // Whenever we slept ~0.1 sec update the UI
+        if (++Counter % 10 == 0) {
+          gSystem->ProcessEvents();
+        }
+
+        int Running = 0;
+        ThreadsAreRunning = false;
+        for (unsigned int t = 0; t < NThreads; ++t) {
+          if (m_ThreadIsFinished[t] == false) {
+            ThreadsAreRunning = true;
+            Running++;
+          }
+        }
+      }
+
+      // None of the threads are running any more --- kill them
+      for (unsigned int t = 0; t < NThreads; ++t) {
+        m_Threads[t]->Kill();
+        m_Threads[t] = 0;
+      }
+
+    } else {
+      //! Create the histograms
+      for (unsigned int g = 0; g < C.GetNumberOfReadOutDataGroups(); ++g)  {
+        MReadOutDataGroup& G = C.GetReadOutDataGroup(g);
+        TH1D* H = CreateSpectrum(G.GetName(), G, m_HistogramMin, m_HistogramMax, m_HistogramBinningMode, m_HistogramBinningModeValue);
+        if (H->GetMaximum() > 0) {
+          m_Histograms.push_back(H);
+        } else {
+          m_Histograms.push_back(nullptr);
+          delete H;
+        }
       }
     }
-    
+    // --> end time critical
+
+
     double Max = 0;
     double Min = numeric_limits<double>::max();
     for (unsigned int h = 0; h < m_Histograms.size(); ++h) {
@@ -584,7 +662,8 @@ void MMelinator::DrawSpectrum(TCanvas& Canvas, unsigned int Collection, unsigned
         }
       }
     }
-    
+
+
     for (unsigned int h = 0; h < m_Histograms.size(); ++h) {
       if (m_Histograms[h] == 0) continue;
       m_Histograms[h]->SetMaximum(1.1*Max);
@@ -610,7 +689,7 @@ void MMelinator::DrawSpectrum(TCanvas& Canvas, unsigned int Collection, unsigned
       m_Histograms[h]->GetYaxis()->CenterTitle(true);
     }
   }
-  
+
   for (unsigned int h = 0; h < m_Histograms.size(); ++h) {
     if (m_Histograms[h] == 0) continue;
     
@@ -620,7 +699,7 @@ void MMelinator::DrawSpectrum(TCanvas& Canvas, unsigned int Collection, unsigned
       m_Histograms[h]->DrawCopy("HIST SAME");
     }
   }
-  
+
   
   vector<int> ColorOffsets;
   ColorOffsets.push_back(-4);
@@ -689,7 +768,7 @@ void MMelinator::DrawSpectrum(TCanvas& Canvas, unsigned int Collection, unsigned
     m_Histograms[h]->DrawCopy("AXIS SAME");
     break;
   }
-  
+
   Canvas.Update();
   m_HistogramChanged = false;
 }
@@ -1064,9 +1143,41 @@ void MMelinator::DrawCalibration(TCanvas& Canvas, unsigned int Collection, bool
 ////////////////////////////////////////////////////////////////////////////////
 
 
+//! Perform parallel spectrum creation
+bool MMelinator::CreateSpectrumParallel(unsigned int ThreadID, unsigned int CollectionID, unsigned int DataGroupID)
+{
+  if (g_Verbosity >= c_Info) cout<<"Parallel spectrum creation thread #"<<ThreadID<<" has started"<<endl;
+
+  m_ThreadIsInitialized[ThreadID] = true;
+
+  MReadOutCollection& C = GetCollection(CollectionID);
+  MReadOutDataGroup& G = C.GetReadOutDataGroup(DataGroupID);
+  TH1D* H = CreateSpectrum(G.GetName(), G, m_HistogramMin, m_HistogramMax, m_HistogramBinningMode, m_HistogramBinningModeValue);
+  if (H->GetMaximum() > 0) {
+    m_Histograms[DataGroupID] = H;
+  } else {
+    m_Histograms[DataGroupID] = nullptr;
+    {
+      TLockGuard G(g_Mutex);
+      delete H;
+    }
+  }
+
+  m_ThreadIsFinished[ThreadID] = true;
+
+  if (g_Verbosity >= c_Info) cout<<"Parallel spectrum creation thread #"<<ThreadID<<" has finished"<<endl;
+
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
 //! Create the histogram for the given read-out data group
 TH1D* MMelinator::CreateSpectrum(const MString& Title, MReadOutDataGroup& G, double Min, double Max, unsigned int HistogramBinningMode, double HistogramBinningModeValue)
 {
+
   MBinner* Binner = 0;
   if (HistogramBinningMode == c_HistogramBinningModeFixedNumberOfBins) {
     MBinnerFixedNumberOfBins* B = new MBinnerFixedNumberOfBins();
@@ -1083,7 +1194,7 @@ TH1D* MMelinator::CreateSpectrum(const MString& Title, MReadOutDataGroup& G, dou
     B->SetPrior(HistogramBinningModeValue);
     Binner = B;
   }
-  
+
   Binner->SetMinMax(Min, Max);
   for (unsigned int d = 0; d < G.GetNumberOfReadOutDatas(); ++d) {
     MReadOutDataADCValue* ADC = dynamic_cast<MReadOutDataADCValue*>(G.GetReadOutData(d).Get(MReadOutDataADCValue::m_TypeID));
@@ -1091,7 +1202,7 @@ TH1D* MMelinator::CreateSpectrum(const MString& Title, MReadOutDataGroup& G, dou
       Binner->Add(ADC->GetADCValue());
     }
   }
-  
+
   TH1D* Histogram = 0;
   Histogram = Binner->GetNormalizedHistogram(Title, "read-out units", "counts / read-out unit");
   Histogram->SetBit(kCanDelete);
@@ -1099,7 +1210,7 @@ TH1D* MMelinator::CreateSpectrum(const MString& Title, MReadOutDataGroup& G, dou
   Histogram->SetFillStyle(0);
 
   delete Binner;
-  
+
   return Histogram;
 }
 
@@ -1144,7 +1255,7 @@ bool MMelinator::Calibrate(bool ShowDiagnostics)
     for (unsigned int t = 0; t < m_NThreads; ++t) {
       MString Name = "Calibration thread #";
       Name += t;
-      //cout<<"Creatung thread: "<<Name<<endl;
+      //cout<<"Creating thread: "<<Name<<endl;
       TThread* Thread = new TThread(Name, (void(*) (void *)) &MMelinatorCallParallelCalibrationThread, (void*) new MMelinatorThreadCaller(this, t));
       m_Threads[t] = Thread;
       m_ThreadIsInitialized[t] = false;

From 85796022a69b52bbb3e3df7fc497a6ce9096a9f9 Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Thu, 9 Nov 2023 11:06:30 +0100
Subject: [PATCH 022/192] Update MFunction3D.h

---
 src/global/misc/inc/MFunction3D.h | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/src/global/misc/inc/MFunction3D.h b/src/global/misc/inc/MFunction3D.h
index 3d1b363a7..09e11c738 100644
--- a/src/global/misc/inc/MFunction3D.h
+++ b/src/global/misc/inc/MFunction3D.h
@@ -151,16 +151,25 @@ class MFunction3D
 
   //! The x-axis data
   vector<double> m_X;
+  //! If the edges are equidistant this is the distance
+  double m_XDistance;
   //! The y-axis data
   vector<double> m_Y;
+  //! If the edges are equidistant this is the distance
+  double m_YDistance;
   //! The z-axis data
   vector<double> m_Z;
+  //! If the edges are equidistant this is the distance
+  double m_ZDistance;
   //! The value-axis data
   vector<double> m_V;
 
   //! For random number generation store the maximum
   double m_Maximum;
 
+  //! The cumulative function for faster random number generation
+  vector<double> m_Cumulative;
+
   // private members:
  private:
   

From 68f0c8d8960356bed5ff1b719bd3d1b26cf38e36 Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Thu, 9 Nov 2023 11:07:12 +0100
Subject: [PATCH 023/192] Update MFunction3D.cxx

---
 src/global/misc/src/MFunction3D.cxx | 108 +++++++++++++++++++++++++++-
 1 file changed, 105 insertions(+), 3 deletions(-)

diff --git a/src/global/misc/src/MFunction3D.cxx b/src/global/misc/src/MFunction3D.cxx
index 26de4025f..0d386c020 100644
--- a/src/global/misc/src/MFunction3D.cxx
+++ b/src/global/misc/src/MFunction3D.cxx
@@ -62,7 +62,7 @@ const unsigned int MFunction3D::c_InterpolationLinear   = 2;
 
 
 MFunction3D::MFunction3D() 
-  : m_InterpolationType(c_InterpolationUnknown)
+  : m_InterpolationType(c_InterpolationUnknown), m_XDistance(0), m_YDistance(0), m_ZDistance(0)
 {
   // Construct an instance of MFunction3D
 }
@@ -78,8 +78,11 @@ MFunction3D::MFunction3D(const MFunction3D& F)
   m_InterpolationType = F.m_InterpolationType;
 
   m_X = F.m_X;
+  m_XDistance = F.m_XDistance;
   m_Y = F.m_Y;
+  m_YDistance = F.m_YDistance;
   m_Z = F.m_Z;
+  m_ZDistance = F.m_ZDistance;
   m_V = F.m_V;
   m_Maximum = F.m_Maximum;
 }
@@ -104,8 +107,11 @@ const MFunction3D& MFunction3D::operator=(const MFunction3D& F)
   m_InterpolationType = F.m_InterpolationType;
 
   m_X = F.m_X;
+  m_XDistance = F.m_XDistance;
   m_Y = F.m_Y;
+  m_YDistance = F.m_YDistance;
   m_Z = F.m_Z;
+  m_ZDistance = F.m_ZDistance;
   m_V = F.m_V;
   m_Maximum = F.m_Maximum;
 
@@ -224,6 +230,54 @@ bool MFunction3D::Set(const MString FileName, const MString KeyWord,
     }
   }
 
+  // Are m_X equidistant?
+  bool Equidistant = true;
+  double Equidistance = (m_X.back() - m_X.front()) / (m_X.size()-1);
+  for (unsigned int i = 2; i < m_X.size(); ++i) {
+    if (fabs((m_X[i] - m_X[i-1]) - Equidistance) > 1E-10) {
+      Equidistant = false;
+      break;
+    }
+  }
+  if (Equidistant == true) {
+    m_XDistance = Equidistance;
+    cout<<"X is equidistant"<<endl;
+  } else {
+    m_XDistance = 0;
+    cout<<"X not equidistant"<<endl;
+  }
+  // Are m_Y equidistant?
+  Equidistant = true;
+  Equidistance = (m_Y.back() - m_Y.front()) / (m_Y.size()-1);
+  for (unsigned int i = 2; i < m_Y.size(); ++i) {
+    if (fabs((m_Y[i] - m_Y[i-1]) - Equidistance) > 1E-10) {
+      Equidistant = false;
+      break;
+    }
+  }
+  if (Equidistant == true) {
+    m_YDistance = Equidistance;
+  } else {
+    m_YDistance = 0;
+    cout<<"Y not equidistant"<<endl;
+  }
+  // Are m_Z equidistant?
+  Equidistant = true;
+  Equidistance = (m_Z.back() - m_Z.front()) / (m_Z.size()-1);
+  for (unsigned int i = 2; i < m_Z.size(); ++i) {
+    if (fabs((m_Z[i] - m_Z[i-1]) - Equidistance) > 1E-10) {
+      Equidistant = false;
+      break;
+    }
+  }
+  if (Equidistant == true) {
+    m_ZDistance = Equidistance;
+  } else {
+    m_ZDistance = 0;
+    cout<<"Z not equidistant"<<endl;
+  }
+
+
   // Round two: Parse the actual data
   for (unsigned int i = 0; i < Parser.GetNLines(); ++i) {
     if (Parser.GetTokenizerAt(i)->GetNTokens() == 0) continue;
@@ -574,7 +628,7 @@ double MFunction3D::Evaluate(double x, double y, double z) const
   }
 
   if (m_InterpolationType == c_InterpolationConstant) {
-    return m_Z[0];
+    return m_V[0];
   } else if (m_InterpolationType == c_InterpolationLinear) {
 
     // Get Position:
@@ -770,8 +824,23 @@ double MFunction3D::GetVMax()
 
 int MFunction3D::FindXBin(double x) const 
 {
-  //! Find the z bin fast (switches between linear search and binary search)
+  //! Find the x bin fast (switches between linear search and binary search)
+
+  if (m_XDistance == 0) {
+    auto I = lower_bound(m_X.begin(), m_X.end(), x);
+    if (I == m_X.begin()) {
+      return -1;  // Smaller than the lowest bin edge
+    } else if (I == m_X.end()) {
+      return m_X.size();  // Greater than or equal to the largest bin edge
+    } else {
+      return distance(m_X.begin(), I);
+    }
+  } else {
+    // Equidistant case
+    return (int) ((x - m_X[0]) / m_XDistance);
+  }
 
+  /*
   massert(m_X.size() >= 2);
 
   if (x < m_X.front()) return -1;
@@ -806,6 +875,7 @@ int MFunction3D::FindXBin(double x) const
     }
     return int(lower);
   }
+  */
 }
 
 
@@ -816,6 +886,21 @@ int MFunction3D::FindYBin(double y) const
 {
   //! Find the z bin fast (switches between linear search and binary search)
 
+  if (m_YDistance == 0) {
+    auto I = lower_bound(m_Y.begin(), m_Y.end(), y);
+    if (I == m_Y.begin()) {
+      return -1;  // Smaller than the lowest bin edge
+    } else if (I == m_Y.end()) {
+      return m_Y.size();  // Greater than or equal to the largest bin edge
+    } else {
+      return distance(m_Y.begin(), I);
+    }
+  } else {
+    // Equidistant case
+    return (int) ((y - m_Y[0]) / m_YDistance);
+  }
+
+  /*
   massert(m_Y.size() >= 2);
 
   if (y < m_Y.front()) return -1;
@@ -850,6 +935,7 @@ int MFunction3D::FindYBin(double y) const
     }
     return int(lower);
   }
+  */
 }
 
 
@@ -860,6 +946,21 @@ int MFunction3D::FindZBin(double z) const
 {
   //! Find the z bin fast (switches between linear search and binary search)
 
+  if (m_ZDistance == 0) {
+    auto I = lower_bound(m_Z.begin(), m_Z.end(), z);
+    if (I == m_Z.begin()) {
+      return -1;  // Smaller than the lowest bin edge
+    } else if (I == m_Z.end()) {
+      return m_Z.size();  // Greater than or equal to the largest bin edge
+    } else {
+      return distance(m_Z.begin(), I);
+    }
+  } else {
+    // Equidistant case
+    return (int) ((z - m_Z[0]) / m_ZDistance);
+  }
+
+  /*
   massert(m_Z.size() >= 2);
 
   if (z < m_Z.front()) return -1;
@@ -894,6 +995,7 @@ int MFunction3D::FindZBin(double z) const
     }
     return int(lower);
   }
+  */
 }
 
 

From 418b9032f7150693a00d88880423beb583f3e1cf Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Thu, 9 Nov 2023 11:07:38 +0100
Subject: [PATCH 024/192] Update MFunction3DSpherical.cxx

---
 src/global/misc/src/MFunction3DSpherical.cxx | 192 +++++++++++++++++--
 1 file changed, 178 insertions(+), 14 deletions(-)

diff --git a/src/global/misc/src/MFunction3DSpherical.cxx b/src/global/misc/src/MFunction3DSpherical.cxx
index 97be65905..4f5e55d98 100644
--- a/src/global/misc/src/MFunction3DSpherical.cxx
+++ b/src/global/misc/src/MFunction3DSpherical.cxx
@@ -224,6 +224,53 @@ bool MFunction3DSpherical::Set(const MString FileName, const MString KeyWord,
     }
   }
 
+  // Are m_X equidistant?
+  bool Equidistant = true;
+  double Equidistance = (m_X.back() - m_X.front()) / (m_X.size()-1);
+  for (unsigned int i = 2; i < m_X.size(); ++i) {
+    if (fabs((m_X[i] - m_X[i-1]) - Equidistance) > 1E-10) {
+      Equidistant = false;
+      break;
+    }
+  }
+  if (Equidistant == true) {
+    m_XDistance = Equidistance;
+    cout<<"X is equidistant"<<endl;
+  } else {
+    m_XDistance = 0;
+    cout<<"X not equidistant"<<endl;
+  }
+  // Are m_Y equidistant?
+  Equidistant = true;
+  Equidistance = (m_Y.back() - m_Y.front()) / (m_Y.size()-1);
+  for (unsigned int i = 2; i < m_Y.size(); ++i) {
+    if (fabs((m_Y[i] - m_Y[i-1]) - Equidistance) > 1E-10) {
+      Equidistant = false;
+      break;
+    }
+  }
+  if (Equidistant == true) {
+    m_YDistance = Equidistance;
+  } else {
+    m_YDistance = 0;
+    cout<<"Y not equidistant"<<endl;
+  }
+  // Are m_Z equidistant?
+  Equidistant = true;
+  Equidistance = (m_Z.back() - m_Z.front()) / (m_Z.size()-1);
+  for (unsigned int i = 2; i < m_Z.size(); ++i) {
+    if (fabs((m_Z[i] - m_Z[i-1]) - Equidistance) > 1E-10) {
+      Equidistant = false;
+      break;
+    }
+  }
+  if (Equidistant == true) {
+    m_ZDistance = Equidistance;
+  } else {
+    m_ZDistance = 0;
+    cout<<"Z not equidistant"<<endl;
+  }
+
   // Round two: Parse the actual data
   for (unsigned int i = 0; i < Parser.GetNLines(); ++i) {
     if (Parser.GetTokenizerAt(i)->GetNTokens() == 0) continue;
@@ -389,16 +436,92 @@ double MFunction3DSpherical::Integrate() const
 
   return Integral;
 }
-  
+
 
 ////////////////////////////////////////////////////////////////////////////////
 
 
-void MFunction3DSpherical::GetRandom(double& x, double& y, double& z)
+void MFunction3DSpherical::GetRandom(double& X, double& Y, double& Z)
 {
   // Return a random number distributed as the underlying function
   // The following is an accurate and safe version but rather slow...
 
+  if (m_Cumulative.size() == 0) {
+    m_Cumulative.resize(m_X.size()*m_Y.size()*m_Z.size());
+    for (unsigned int x = 0; x < m_X.size()-1; ++x) {
+      double xCenter = 0.5*(m_X[x+1] + m_X[x]);
+      double xSize = fabs((m_X[x+1] - m_X[x]))*c_Rad;
+      for (unsigned int y = 0; y < m_Y.size()-1; ++y) {
+        double yCenter = 0.5*(m_Y[y+1] + m_Y[y]);
+        double ySize = fabs(cos(m_Y[y]*c_Rad) - cos(m_Y[y+1]*c_Rad));
+        for (unsigned int z = 0; z < m_Z.size()-1; ++z) {
+          double zCenter = 0.5*(m_Z[z+1] + m_Z[z]);
+          double zSize = fabs(m_Z[z+1] - m_Z[z]);
+
+          unsigned long Bin = x + y*m_X.size() + z*m_X.size()*m_Y.size();
+          m_Cumulative[Bin] = xSize*ySize*zSize*Evaluate(xCenter, yCenter, zCenter);
+        }
+      }
+    }
+    for (unsigned int i = 1; i < m_Cumulative.size(); ++i) {
+      m_Cumulative[i] += m_Cumulative[i-1];
+    }
+  }
+
+
+  // Find a random bin
+  double RandomCumulative = gRandom->Rndm()*m_Cumulative.back();
+  auto upperBoundIt = upper_bound(m_Cumulative.begin(), m_Cumulative.end(), RandomCumulative);
+
+  if (upperBoundIt == m_Cumulative.end()) {
+    cout<<"Error: We should never, ever reach that part of the code..."<<endl;
+    return;
+  }
+  unsigned long Bin = distance(m_Cumulative.begin(), upperBoundIt);
+
+  //cout<<"Bin: "<<Bin<<" for "<<RandomCumulative<<endl;
+  unsigned int xBin = Bin % m_X.size();
+  Bin -= xBin;
+  Bin /= m_X.size();
+  unsigned int yBin = Bin % m_Y.size();
+  Bin -= yBin;
+  Bin /= m_Y.size();
+  unsigned int zBin = Bin;
+  //cout<<"Bins: "<<xBin<<":"<<yBin<<":"<<zBin<<endl;
+
+  // Find the maximum value in that bin
+  double Max = -numeric_limits<double>::max();
+  for (unsigned int x = xBin; x <= xBin+1; ++x) {
+    for (unsigned int y = yBin; y <= yBin+1; ++y) {
+      for (unsigned int z = zBin; z <= zBin+1; ++z) {
+        double V = m_V[x + y*m_X.size() + z*m_X.size()*m_Y.size()];
+        if (V > Max) Max = V;
+      }
+    }
+  }
+  //cout<<"Max: "<<Max<<endl;
+
+  // Find a random position inside the bin
+  double x_min = m_X[xBin];
+  double x_diff = m_X[xBin+1] - m_X[xBin];
+
+  double y_min = cos(m_Y[yBin]*c_Rad);
+  double y_diff = cos(m_Y[yBin]*c_Rad) - cos(m_Y[yBin+1]*c_Rad);
+
+  double z_min = m_Z[zBin];
+  double z_diff = m_Z[zBin+1] - m_Z[zBin];
+
+  double V = 0;
+  do {
+    X = gRandom->Rndm()*x_diff + x_min;
+    Y = acos(y_min - gRandom->Rndm()*y_diff)*c_Deg;
+    Z = gRandom->Rndm()*z_diff + z_min;
+
+    V = Evaluate(X, Y, Z);
+  } while (Max*gRandom->Rndm() > V);
+  //cout<<"Final: "<<X<<":"<<Y<<":"<<Z<<endl;
+
+  /*
   if (m_Maximum == g_DoubleNotDefined) {
     m_Maximum = GetVMax();
   }
@@ -414,12 +537,13 @@ void MFunction3DSpherical::GetRandom(double& x, double& y, double& z)
   
   double v = 0;
   do {
-    x = gRandom->Rndm()*x_diff + x_min;
-    y = acos(y_min - gRandom->Rndm()*y_diff)*c_Deg;
-    z = gRandom->Rndm()*z_diff + z_min;
+    X = gRandom->Rndm()*x_diff + x_min;
+    Y = acos(y_min - gRandom->Rndm()*y_diff)*c_Deg;
+    Z = gRandom->Rndm()*z_diff + z_min;
     
-    v = Evaluate(x, y, z);
+    v = Evaluate(X, Y, Z);
   } while (m_Maximum*gRandom->Rndm() > v);
+  */
 }
 
 
@@ -432,19 +556,24 @@ void MFunction3DSpherical::Plot(bool Random)
   
   if (m_X.size() >= 2 && m_Y.size() >= 2 && m_Z.size() >= 2) {
 
-    TH3D* Hist = new TH3D("MFunction3DSpherical", "MFunction3DSpherical", m_X.size(), m_X.front(), m_X.back(), m_Y.size(), m_Y.front(), m_Y.back(), m_Z.size(), m_Z.front(), m_Z.back());
+    TH3D* Hist = new TH3D("MFunction3DSpherical", "MFunction3DSpherical",  m_X.size()-1, &m_X[0], m_Y.size()-1, &m_Y[0], m_Z.size()-1, &m_Z[0]);
     Hist->SetXTitle("phi in degree");
     Hist->SetYTitle("theta in degree");
     Hist->SetZTitle("energy in keV");
 
-    TH2D* Projection = new TH2D("MFunction3DSpherical-P", "MFunction3DSpherical-P", 
-                          m_X.size(), m_X.front(), m_X.back(), 
-                          m_Y.size(), m_Y.front(), m_Y.back());
+    TH2D* Projection = new TH2D("MFunction3DSpherical-P", "MFunction3DSpherical-P", m_X.size()-1, &m_X[0], m_Y.size()-1, &m_Y[0]);
     Projection->SetXTitle("phi in degree");
     Projection->SetYTitle("theta in degree");
 
+
+    TH1D* ProjectionZ = new TH1D("MFunction3DSpherical-Z", "MFunction3DSpherical-Z", m_Z.size()-1, &m_Z[0]);
+    ProjectionZ->SetXTitle("energy in [keV]");
+
     TCanvas* Canvas = new TCanvas("DiagnosticsCanvas", "DiagnosticsCanvas");
     Canvas->cd();
+    if (m_Z.back() / (m_Z.front() > 0 ? m_Z.front() : 1) > 1000) {
+      Canvas->SetLogz();
+    }
 
     if (Random == true) {
       double x, y, z;
@@ -458,13 +587,39 @@ void MFunction3DSpherical::Plot(bool Random)
         }
         GetRandom(x, y, z);
         Hist->Fill(x, y, z, 1);
+        Projection->Fill(x, y, 1);
+        ProjectionZ->Fill(z, 1);
+      }
+      for (int bx = 1; bx <= Hist->GetXaxis()->GetNbins(); ++bx) {
+        for (int by = 1; by <= Hist->GetYaxis()->GetNbins(); ++by) {
+          double Area = c_Pi*(Hist->GetXaxis()->GetBinUpEdge(bx)*c_Rad - Hist->GetXaxis()->GetBinLowEdge(bx)*c_Rad);
+          Area *= cos(Hist->GetYaxis()->GetBinLowEdge(by)*c_Rad) - cos(Hist->GetYaxis()->GetBinUpEdge(by)*c_Rad);
+          for (int bz = 1; bz <= Hist->GetZaxis()->GetNbins(); ++bz) {
+            Hist->SetBinContent(bx, by, bz, Hist->GetBinContent(bx, by, bz) / Area / Hist->GetZaxis()->GetBinWidth(bz));
+          }
+        }
+      }
+      for (int bx = 1; bx <= Hist->GetXaxis()->GetNbins(); ++bx) {
+        for (int by = 1; by <= Hist->GetYaxis()->GetNbins(); ++by) {
+          double Area = c_Pi*(Projection->GetXaxis()->GetBinUpEdge(bx)*c_Rad - Projection->GetXaxis()->GetBinLowEdge(bx)*c_Rad);
+          Area *= cos(Projection->GetYaxis()->GetBinLowEdge(by)*c_Rad) - cos(Projection->GetYaxis()->GetBinUpEdge(by)*c_Rad);
+          Projection->SetBinContent(bx, by, Projection->GetBinContent(bx, by) / Area);
+        }
+      }
+      for (int bz = 1; bz <= Hist->GetZaxis()->GetNbins(); ++bz) {
+        ProjectionZ->SetBinContent(bz, ProjectionZ->GetBinContent(bz) / ProjectionZ->GetXaxis()->GetBinWidth(bz));
       }
     } else {
       for (int bx = 1; bx <= Hist->GetXaxis()->GetNbins(); ++bx) {
         for (int by = 1; by <= Hist->GetYaxis()->GetNbins(); ++by) {
           for (int bz = 1; bz <= Hist->GetZaxis()->GetNbins(); ++bz) {
-            Hist->SetBinContent(bx, by, bz, Evaluate(Hist->GetXaxis()->GetBinCenter(bx), Hist->GetYaxis()->GetBinCenter(by), Hist->GetZaxis()->GetBinCenter(bz)));
-            Projection->SetBinContent(bx, by, Projection->GetBinContent(bx, by) + Evaluate(Hist->GetXaxis()->GetBinCenter(bx), Hist->GetYaxis()->GetBinCenter(by), Hist->GetZaxis()->GetBinCenter(bz)));
+            double x = Hist->GetXaxis()->GetBinCenter(bx);
+            double y = Hist->GetYaxis()->GetBinCenter(by);
+            double z = Hist->GetZaxis()->GetBinCenter(bz);
+            double v = Evaluate(x, y, z);
+            Hist->Fill(x, y, z, v);
+            Projection->Fill(x, y, v);
+            ProjectionZ->Fill(z, v);
           }
         }
       }
@@ -478,8 +633,17 @@ void MFunction3DSpherical::Plot(bool Random)
     ProjectionCanvas->cd();
     Projection->Draw("colz");
     ProjectionCanvas->Update();
-    
-    
+
+
+    TCanvas* ProjectionZCanvas = new TCanvas();
+    if (m_Z.back() / (m_Z.front() > 0 ? m_Z.front() : 1) > 1000) {
+      ProjectionZCanvas->SetLogx();
+    }
+    ProjectionZCanvas->cd();
+    ProjectionZ->Draw();
+    ProjectionZCanvas->Update();
+
+
     gSystem->ProcessEvents();
 
     for (unsigned int i = 0; i < 10; ++i) {

From 8edb8780b337f0618d86a7b3e1d690bb4fc76647 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Thu, 7 Dec 2023 15:30:30 -0800
Subject: [PATCH 025/192] CHG: Make sure we have an example finalize

---
 src/fretalon/framework/inc/MModuleTemplate.h   |  3 +++
 src/fretalon/framework/src/MModuleTemplate.cxx | 13 +++++++++++++
 2 files changed, 16 insertions(+)

diff --git a/src/fretalon/framework/inc/MModuleTemplate.h b/src/fretalon/framework/inc/MModuleTemplate.h
index 607c8022e..2e3efe7cc 100644
--- a/src/fretalon/framework/inc/MModuleTemplate.h
+++ b/src/fretalon/framework/inc/MModuleTemplate.h
@@ -47,6 +47,9 @@ class MModuleTemplate : public MModule
 
   //! Main data analysis routine, which updates the event to a new level 
   virtual bool AnalyzeEvent(MReadOutAssembly* Event);
+  
+  //! Finalize the module
+  virtual void Finalize();
 
   //! Show the options GUI
   virtual void ShowOptionsGUI();
diff --git a/src/fretalon/framework/src/MModuleTemplate.cxx b/src/fretalon/framework/src/MModuleTemplate.cxx
index e35f5d746..2c42047ae 100644
--- a/src/fretalon/framework/src/MModuleTemplate.cxx
+++ b/src/fretalon/framework/src/MModuleTemplate.cxx
@@ -122,6 +122,19 @@ bool MModuleTemplate::AnalyzeEvent(MReadOutAssembly* Event)
 ////////////////////////////////////////////////////////////////////////////////
 
 
+void MModuleTemplate::Finalize()
+{
+  // Initialize the module 
+
+  MModule::Finalize();
+  
+  // Your code here
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
 void MModuleTemplate::ShowOptionsGUI()
 {
   //! Show the options GUI --- has to be overwritten!

From 1d630c9a03b8e45de60c487a4f72e8bb08a82093 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Mon, 11 Dec 2023 13:47:46 -0800
Subject: [PATCH 026/192] CHG: Allow phi from -180 to 360

---
 src/mimrec/src/MGUIEventSelection.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mimrec/src/MGUIEventSelection.cxx b/src/mimrec/src/MGUIEventSelection.cxx
index 37fc5e6ab..4c642b83e 100644
--- a/src/mimrec/src/MGUIEventSelection.cxx
+++ b/src/mimrec/src/MGUIEventSelection.cxx
@@ -617,7 +617,7 @@ void MGUIEventSelection::Create()
 
   m_SourceSpheric = new MGUIEEntryList(SourceFrame, "Location (Theta, Phi) [deg]", MGUIEEntryList::c_SingleLine);
   m_SourceSpheric->Add("", m_Settings->GetSourceTheta(), kTRUE, 0.0, 180.0);
-  m_SourceSpheric->Add("", m_Settings->GetSourcePhi(), kTRUE, 0.0, 360.0);
+  m_SourceSpheric->Add("", m_Settings->GetSourcePhi(), kTRUE, -180.0, 360.0);
   m_SourceSpheric->SetEntryFieldSize(FieldSize);
   m_SourceSpheric->Create();
   SourceFrame->AddFrame(m_SourceSpheric, SourceLayout);

From cc4a4503f61c6c683ce976ae172ff2c9c2463a77 Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Mon, 8 Jan 2024 14:38:37 +0100
Subject: [PATCH 027/192] Apply MFunction.cxx correction for high value of x

see the commit https://github.com/zoglauer/megalib/commit/dc0d7b576cc9f80f8e1f13d53774e6fb1898f4fd
---
 src/global/misc/src/MFunction.cxx | 79 ++++++++++++++++++-------------
 1 file changed, 47 insertions(+), 32 deletions(-)

diff --git a/src/global/misc/src/MFunction.cxx b/src/global/misc/src/MFunction.cxx
index 7f1040a0f..ece0f8bdc 100644
--- a/src/global/misc/src/MFunction.cxx
+++ b/src/global/misc/src/MFunction.cxx
@@ -29,6 +29,7 @@
 // Standard libs:
 #include <algorithm>
 #include <cmath>
+#include <iomanip>
 using namespace std;
 
 // ROOT libs:
@@ -90,6 +91,7 @@ MFunction::MFunction(const MFunction& F)
   m_InterpolationType = F.m_InterpolationType;
 
   m_X = F.m_X;
+  m_XZero = F.m_XZero;
   m_Y = F.m_Y;
   m_Cumulative = F.m_Cumulative;
   m_YNonNegative = F.m_YNonNegative;
@@ -124,6 +126,7 @@ const MFunction& MFunction::operator=(const MFunction& F)
   m_InterpolationType = F.m_InterpolationType;
 
   m_X = F.m_X;
+  m_XZero = F.m_XZero;
   m_Y = F.m_Y;
   m_Cumulative = F.m_Cumulative;
   m_YNonNegative = F.m_YNonNegative;
@@ -271,6 +274,10 @@ bool MFunction::Set(const MString FileName, const MString KeyWord)
     CreateSplines();
   }
 
+  for (auto x: m_X) {
+    m_XZero.push_back(x - m_X[0]);
+  }
+
   return true;
 }
 
@@ -339,6 +346,10 @@ bool MFunction::Set(const MResponseMatrixO1& Response)
   // Clean up:
   m_Cumulative.clear();
 
+  for (auto x: m_X) {
+    m_XZero.push_back(x - m_X[0]);
+  }
+
   return true;
 }
 
@@ -364,6 +375,10 @@ bool MFunction::Set(const vector<double>& X, const vector<double>& Y, unsigned i
   // Clean up:
   m_Cumulative.clear();
 
+  for (auto x: m_X) {
+    m_XZero.push_back(x - m_X[0]);
+  }
+
   return true;
 }
 
@@ -379,13 +394,16 @@ bool MFunction::Add(const double x, const double y)
   if (m_X.size() == 0) {
     m_X.push_back(x);
     m_Y.push_back(y);
+    m_XZero.push_back(x - m_X[0]);
   } else {
     if (x < m_X[0]) {
       m_X.insert(m_X.begin(), x);
       m_Y.insert(m_Y.begin(), y);
+      m_XZero.insert(m_X.begin(), x - m_X[0]);
     } else if (x > m_X.back()) {
       m_X.push_back(x);
       m_Y.push_back(y);
+      m_XZero.push_back(x - m_X[0]);
     } else {
       for (unsigned int i = 0; i < m_X.size(); ++i) {
         if (x == m_X[i]) {
@@ -395,6 +413,7 @@ bool MFunction::Add(const double x, const double y)
         } else if (x < m_X[i]) {
           m_X.insert(m_X.begin()+i, x);
           m_Y.insert(m_Y.begin()+i, y);
+          m_XZero.insert(m_XZero.begin()+i, x - m_X[0]);
           break;
         }
       }
@@ -438,9 +457,10 @@ void MFunction::ScaleX(double Scaler)
 {
   // Multiple the x-axis by some value
 
-   for (unsigned int i = 0; i < m_X.size(); ++i) {
+  for (unsigned int i = 0; i < m_X.size(); ++i) {
     m_X[i] *= Scaler;
-  }  
+    m_XZero[i] = m_X[i] - m_X[0];
+  }
 
   // We clear the cumulative function:
   m_Cumulative.clear();
@@ -1117,8 +1137,8 @@ double MFunction::FindX(double XStart, double Integral, bool Cyclic)
   //! Find the x value starting from Start which would be achieved after integrating for "Integral"
   //! If we go beyond x_max, x_max is returned if we are not cyclic, otherwise we continue at x_0
 
-  //cout<<"XStart: "<<XStart<<"  Integral: "<<Integral<<endl;
-  
+  // To reign in larger number rounding issues, use the offset x-values offset everything
+
   double Modulo = 0;
   if (Cyclic == true) {
     // Project XStart into the frame of this function
@@ -1132,24 +1152,24 @@ double MFunction::FindX(double XStart, double Integral, bool Cyclic)
     }
   }
 
-  double X = XStart + Modulo;
+  double X = XStart + Modulo - m_X[0]; // To reign in larger number rounding issues, offset everything
 
   // Find the bin X is in: 
-  if (X < m_X.front()) {
+  if (X < m_XZero.front()) {
     //merr<<"XStart ("<<XStart<<") smaller than minimum x-value ("<<m_X.front()<<") --- starting at minimum x-value"<<endl;
-    X = m_X.front();
+    X = m_XZero.front();
   }
-  if (X > m_X.back()) {
+  if (X > m_XZero.back()) {
     //merr<<"XStart ("<<XStart<<") larger than maximum x-value ("<<m_X.back()<<") --- starting at minimum x-value"<<endl;
-    X = m_X.front();
+    X = m_XZero.front();
   }
 
   // Step 1: Go from bin to bin until we find an upper limit bin, where iIntegral > I
 
   unsigned int BinStart = 0;
-  if (X > m_X.front()) {
-    //BinStart = find_if(m_X.begin(), m_X.end(), bind2nd(greater<double>(), X)) - m_X.begin() - 1;
-    BinStart = find_if(m_X.begin(), m_X.end(), bind(greater<double>(), placeholders::_1, X)) - m_X.begin() - 1;
+  if (X > m_XZero.front()) {
+    //BinStart = find_if(m_XZero.begin(), m_XZero.end(), bind2nd(greater<double>(), X)) - m_XZero.begin() - 1;
+    BinStart = find_if(m_XZero.begin(), m_XZero.end(), bind(greater<double>(), placeholders::_1, X)) - m_XZero.begin() - 1;
   }
 
   //cout<<"x: "<<X<<" Bin start: "<<BinStart<<endl;
@@ -1159,38 +1179,33 @@ double MFunction::FindX(double XStart, double Integral, bool Cyclic)
   double iIntegral = 0.0;
   do {
     NewUpperBin++;
-    tIntegral = Integrate(X, m_X[NewUpperBin]);
+    tIntegral = Integrate(X+m_X[0], m_X[NewUpperBin]);
     //cout<<"Int from "<<X<<" to "<<m_X[NewUpperBin]<<": "<<tIntegral<<" (total: "<<iIntegral<<")"<<endl;
     if (iIntegral + tIntegral < Integral) {
-      X = m_X[NewUpperBin];
+      X = m_XZero[NewUpperBin];
       iIntegral += tIntegral;
     } else {
       //cout<<"Found it"<<endl;
       break;
     }
-    if (X == m_X.back()) {
+    if (X == m_XZero.back()) {
       if (Cyclic == false) {
         break;
       } else {
         X = 0;
         NewUpperBin = 0;
-        Modulo -= m_X.back() - m_X.front();
-        cout<<"New Modulo (while): "<<Modulo<<endl;
+        Modulo -= m_XZero.back() - m_XZero.front();
       }
     }
   } while (true);
   
   // Non-cyclic exit case
-  if (X == m_X.back() && iIntegral < Integral) return numeric_limits<double>::max();
-  
-  //cout<<"UpperBin: "<<NewUpperBin<<endl;
-  
+  if (X == m_XZero.back() && iIntegral < Integral) return numeric_limits<double>::max();
+
   // Step 2: Interpolate --- only linear at the moment --- within the given bin to find the right x-value
-  
-  double m = (m_Y[NewUpperBin-1] - m_Y[NewUpperBin]) / (m_X[NewUpperBin-1] - m_X[NewUpperBin]);
-  double t = m_Y[NewUpperBin] - m*m_X[NewUpperBin];
-  
-  //cout<<"m: "<<m<<" t: "<<t<<endl;
+
+  double m = (m_Y[NewUpperBin-1] - m_Y[NewUpperBin]) / (m_XZero[NewUpperBin-1] - m_XZero[NewUpperBin]);
+  double t = m_Y[NewUpperBin] - m*m_XZero[NewUpperBin];
   
   double x1 = 0; 
   double x2 = 0;
@@ -1208,21 +1223,21 @@ double MFunction::FindX(double XStart, double Integral, bool Cyclic)
   }
   //cout<<"x1: "<<x1<<" x2: "<<x2<<endl;
   
-  if (x1 >= m_X[NewUpperBin-1] && x1 <= m_X[NewUpperBin] && (x2 < m_X[NewUpperBin-1] || x2 > m_X[NewUpperBin])) {
+  if (x1 >= m_XZero[NewUpperBin-1] && x1 <= m_XZero[NewUpperBin] && (x2 < m_XZero[NewUpperBin-1] || x2 > m_XZero[NewUpperBin])) {
     //mout<<"x="<<x1<<endl;
     X = x1;
-  } else if (x2 >= m_X[NewUpperBin-1] && x2 <= m_X[NewUpperBin] && (x1 < m_X[NewUpperBin-1] || x1 > m_X[NewUpperBin])) {
+  } else if (x2 >= m_XZero[NewUpperBin-1] && x2 <= m_XZero[NewUpperBin] && (x1 < m_XZero[NewUpperBin-1] || x1 > m_XZero[NewUpperBin])) {
     //mout<<"x="<<x2<<endl;
     X = x2; 
-  } else if ((x2 < m_X[NewUpperBin-1] || x2 > m_X[NewUpperBin]) && (x1 < m_X[NewUpperBin-1] || x1 > m_X[NewUpperBin])) {
-    merr<<"FindX: Both possible results are outside choosen bin ["<<m_X[NewUpperBin-1]<<"-"<<m_X[NewUpperBin]<<"]: x1="<<x1<<" x2="<<x2<<endl;
+  } else if ((x2 < m_XZero[NewUpperBin-1] || x2 > m_XZero[NewUpperBin]) && (x1 < m_XZero[NewUpperBin-1] || x1 > m_XZero[NewUpperBin])) {
+    merr<<std::setprecision(20)<<"FindX: Both possible results are outside choosen bin ["<<m_XZero[NewUpperBin-1]<<"-"<<m_XZero[NewUpperBin]<<"]: x1="<<x1<<" x2="<<x2<<endl;
   } else {
-    merr<<"FindX: Both possible results are within choosen bin ["<<m_X[NewUpperBin-1]<<"-"<<m_X[NewUpperBin]<<"]: x1="<<x1<<" x2="<<x2<<endl;    
+    merr<<std::setprecision(20)<<"FindX: Both possible results are within choosen bin ["<<m_X[NewUpperBin-1]<<"-"<<m_X[NewUpperBin]<<"]: x1="<<x1<<" x2="<<x2<<endl;
   }
   
   //cout<<"XStart: "<<XStart<<" X: "<<X<<" modulo: "<<Modulo<<endl;
   
-  return X - Modulo;
+  return X - Modulo + m_X[0];
 }
 
 

From 44c32d07586b56e25d35ad35be33a5f58aa14a66 Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Mon, 8 Jan 2024 14:40:00 +0100
Subject: [PATCH 028/192] apply the  MFunction.h correction for high value of x

see the commit : https://github.com/zoglauer/megalib/commit/dc0d7b576cc9f80f8e1f13d53774e6fb1898f4fd
---
 src/global/misc/inc/MFunction.h | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/global/misc/inc/MFunction.h b/src/global/misc/inc/MFunction.h
index 798d29b21..9e1289f68 100644
--- a/src/global/misc/inc/MFunction.h
+++ b/src/global/misc/inc/MFunction.h
@@ -160,6 +160,8 @@ class MFunction
 
   //! The x-axis data
   vector<double> m_X;
+  //! The x-axis data starting at 0
+  vector<double> m_XZero;
   //! The y-axis data
   vector<double> m_Y;
 

From 20c47ba01a99ff26ecee3e33e916548ec16df88e Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Fri, 26 Jan 2024 01:14:22 -0800
Subject: [PATCH 029/192] CHG: Add energy windows to Bayesian and TMVA
 reconstrcution

---
 src/response/Makefile                         |    1 +
 src/response/inc/MResponseCreator.h           |    2 +-
 src/response/inc/MResponseMultipleCompton.h   |   47 +-
 .../inc/MResponseMultipleComptonBayes.h       |  198 ++
 src/response/src/MResponseCreator.cxx         |   13 +-
 src/response/src/MResponseMultipleCompton.cxx |  475 +---
 .../src/MResponseMultipleComptonBayes.cxx     | 1980 +++++++++++++++++
 .../src/MResponseMultipleComptonEventFile.cxx |   20 +-
 .../src/MResponseMultipleComptonTMVA.cxx      |   18 +-
 9 files changed, 2229 insertions(+), 525 deletions(-)
 create mode 100644 src/response/inc/MResponseMultipleComptonBayes.h
 create mode 100644 src/response/src/MResponseMultipleComptonBayes.cxx

diff --git a/src/response/Makefile b/src/response/Makefile
index 9f4bfb97d..07d03fa35 100644
--- a/src/response/Makefile
+++ b/src/response/Makefile
@@ -30,6 +30,7 @@ FILES := MResponseCreator \
 	MResponseClusteringDSS \
 	MResponseTracking \
 	MResponseMultipleCompton \
+	MResponseMultipleComptonBayes \
 	MResponseMultipleComptonEventFile \
 	MResponseMultipleComptonLens \
 	MResponseMultipleComptonTMVA \
diff --git a/src/response/inc/MResponseCreator.h b/src/response/inc/MResponseCreator.h
index b78ec935a..e8c839104 100644
--- a/src/response/inc/MResponseCreator.h
+++ b/src/response/inc/MResponseCreator.h
@@ -110,7 +110,7 @@ class MResponseCreator
   enum MResponseModes {
     c_ModeUnknown,
     c_ModeTracks,
-    c_ModeComptons,
+    c_ModeComptonsBayes,
     c_ModeComptonsEventFile,
     c_ModeComptonsLens,
     c_ModeComptonsNeuralNetwork,
diff --git a/src/response/inc/MResponseMultipleCompton.h b/src/response/inc/MResponseMultipleCompton.h
index e97692fa2..74511b7ea 100644
--- a/src/response/inc/MResponseMultipleCompton.h
+++ b/src/response/inc/MResponseMultipleCompton.h
@@ -52,25 +52,10 @@ class MResponseMultipleCompton : public MResponseBuilder
   void SetDoAbsorptions(const bool Flag = true) { m_DoAbsorptions = Flag; }
   //! Set whether or not absorptions should be considered
   void SetMaxNInteractions(const unsigned int MaxNInteractions) { m_MaxNInteractions = MaxNInteractions; }
-  
-  //! Initialize the response matrices and their generation
-  virtual bool Initialize();
-
-  //! Analyze th events (all if in file mode, one if in event-by-event mode)
-  virtual bool Analyze();
-    
-  //! Finalize the response generation (i.e. save the data a final time )
-  virtual bool Finalize();
-
 
   // protected methods:
  protected:
 
-  //! Save the response matrices
-  virtual bool Save();
-
-      
-
   bool IsTrackStart(MRESE& Start, MRESE& Central, double Energy);
   bool IsTrackStop(MRESE& Central, MRESE& Stop, double Energy);
 
@@ -126,6 +111,11 @@ class MResponseMultipleCompton : public MResponseBuilder
 
   // protected members:
  protected:
+  //! Minimum energy range
+  double m_EnergyMinimum;
+  //! Maximum energy range
+  double m_EnergyMaximum;
+
   //! Do or not to do absorptions
   bool m_DoAbsorptions;
   //! MaximumSequenceLength up to which absorptions are considered
@@ -139,33 +129,6 @@ class MResponseMultipleCompton : public MResponseBuilder
   double m_MaxTrackEnergyDifference;
   double m_MaxTrackEnergyDifferencePercent;
 
-  // The event/pdf matrices:
-  //!
-  MResponseMatrixO2 m_GoodBadTable;
-  //!
-  MResponseMatrixO4 m_PdfStartGood;
-
-  MResponseMatrixO4 m_PdfStartBad;
-
-  MResponseMatrixO6 m_PdfTrackGood;
-
-  MResponseMatrixO6 m_PdfTrackBad;
-
-  MResponseMatrixO4 m_PdfComptonScatterProbabilityGood;
-
-  MResponseMatrixO4 m_PdfComptonScatterProbabilityBad;
-
-  MResponseMatrixO4 m_PdfPhotoAbsorptionProbabilityGood;
-
-  MResponseMatrixO4 m_PdfPhotoAbsorptionProbabilityBad;
-
-  MResponseMatrixO6 m_PdfComptonGood;
-
-  MResponseMatrixO6 m_PdfComptonBad;
-
-  MResponseMatrixO4 m_PdfDualGood;
-
-  MResponseMatrixO4 m_PdfDualBad;
 
 
   // private members:
diff --git a/src/response/inc/MResponseMultipleComptonBayes.h b/src/response/inc/MResponseMultipleComptonBayes.h
new file mode 100644
index 000000000..a5bf91791
--- /dev/null
+++ b/src/response/inc/MResponseMultipleComptonBayes.h
@@ -0,0 +1,198 @@
+/*
+ * MResponseMultipleComptonBayes.h
+ *
+ * Copyright (C) by Andreas Zoglauer.
+ * All rights reserved.
+ *
+ * Please see the source-file for the copyright-notice.
+ *
+ */
+
+
+#ifndef __MResponseMultipleComptonBayes__
+#define __MResponseMultipleComptonBayes__
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+// Standard libs:
+
+// ROOT libs:
+
+// MEGAlib libs:
+#include "MGlobal.h"
+#include "MResponseBuilder.h"
+#include "MResponseMultipleCompton.h"
+#include "MRESE.h"
+#include "MRETrack.h"
+#include "MResponseMatrixO1.h"
+#include "MResponseMatrixO2.h"
+#include "MResponseMatrixO3.h"
+#include "MResponseMatrixO4.h"
+#include "MResponseMatrixO5.h"
+#include "MResponseMatrixO6.h"
+#include "MResponseMatrixO7.h"
+
+// Forward declarations:
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+//! Create a Bayesian Compton sequenceing response 
+class MResponseMultipleComptonBayes : public MResponseMultipleCompton
+{
+  // public interface:
+ public:
+  //! Default constructor
+  MResponseMultipleComptonBayes();
+  //! Default destructor
+  virtual ~MResponseMultipleComptonBayes();
+
+  //! Return a brief description of this response class
+  static MString Description();
+  //! Return information on the parsable options for this response class
+  static MString Options();
+  //! Parse the options
+  virtual bool ParseOptions(const MString& Options);
+
+  //! Set whether or not absorptions should be considered
+  void SetDoAbsorptions(const bool Flag = true) { m_DoAbsorptions = Flag; }
+  //! Set whether or not absorptions should be considered
+  void SetMaxNInteractions(const unsigned int MaxNInteractions) { m_MaxNInteractions = MaxNInteractions; }
+  
+  //! Initialize the response matrices and their generation
+  virtual bool Initialize();
+
+  //! Analyze th events (all if in file mode, one if in event-by-event mode)
+  virtual bool Analyze();
+    
+  //! Finalize the response generation (i.e. save the data a final time )
+  virtual bool Finalize();
+
+
+  // protected methods:
+ protected:
+
+  //! Save the response matrices
+  virtual bool Save();
+
+      
+
+  bool IsTrackStart(MRESE& Start, MRESE& Central, double Energy);
+  bool IsTrackStop(MRESE& Central, MRESE& Stop, double Energy);
+
+  bool IsComptonStart(MRESE& Start, double Etot, double Eres);
+  bool IsComptonTrack(MRESE& Start, MRESE& Central, int StartPosition, 
+                      double Etot, double Eres);
+  bool IsComptonEnd(MRESE& Stop);
+  bool IsComptonSequence(MRESE& Start, MRESE& Stop,
+                         int StartPosition, double StopEnergy, double Eres);
+  bool IsComptonSequence(MRESE& Start, MRESE& Central, MRESE& Stop,
+                         int StartPosition, double StopEnergy, double Eres);
+  bool IsSingleCompton(MRESE& Start);
+
+  bool AreInComptonSequence(const vector<int>& StartOriginIds, 
+                            const vector<int>& CentralOriginIds,
+                            int StartPosition);
+  bool AreReseInSequence(MRESE& Start, MRESE& Central, MRESE& Stop, double Energy);
+
+  bool ContainsOnlyComptonDependants(vector<int> AllSimIds);
+  bool IsAbsorbed(const vector<int>& AllSimIds, double Energy, double EnergyResolution);
+  bool IsTotalAbsorbed(const vector<int>& AllSimIds, double Energy, double EnergyResolution);
+  bool IsTrackCompletelyAbsorbed(const vector<int>& Ids, double Energy);
+  double GetIdealDepositedEnergy(int MinId);
+
+  //! Return the number of Compton interaction from the Sim ID with the given origin
+  unsigned int NumberOfComptonInteractions(vector<int> AllSimIds, int Origin);
+  
+  
+  int GetMaterial(MRESE& RESE);
+
+  double CalculateDCosPhi(MRESE& Start, MRESE& Central, MRESE& Stop, double Etot);
+  double CalculateDPhiInDegree(MRESE& Start, MRESE& Central, MRESE& Stop, double Etot);
+  double CalculateCosPhiE(MRESE& Central, double Etot);
+  double CalculatePhiEInDegree(MRESE& Central, double Etot);
+  double CalculateCosPhiG(MRESE& Start, MRESE& Central, MRESE& Stop);
+  double CalculatePhiGInDegree(MRESE& Start, MRESE& Central, MRESE& Stop);
+  double CalculateCosAlphaE(MRETrack& Start, MRESE& Central, double Etot);
+  double CalculateAlphaEInDegree(MRETrack& Start, MRESE& Central, double Etot);
+  double CalculateCosAlphaG(MRETrack& Start, MRESE& Central, double Etot);
+  double CalculateAlphaGInDegree(MRETrack& Start, MRESE& Central, double Etot);
+  double CalculateDCosAlpha(MRETrack& Start, MRESE& Central, double Etot);
+  double CalculateDAlphaInDegree(MRETrack& Start, MRESE& Central, double Etot);
+  double CalculateMinLeverArm(MRESE& Start, MRESE& Central, MRESE& Stop);
+
+  double CalculateAbsorptionProbabilityPhoto(MRESE& Start, MRESE& Stop, double Etot);
+  double CalculateAbsorptionProbabilityCompton(MRESE& Start, MRESE& Stop, double Etot);
+  double CalculateAbsorptionProbabilityTotal(MRESE& Start, MRESE& Stop, double Etot);
+
+  // private methods:
+ private:
+
+
+
+  // protected members:
+ protected:
+  //! Minimum energy range
+  double m_EnergyMinimum;
+  //! Maximum energy range
+  double m_EnergyMaximum;
+
+  //! Do or not to do absorptions
+  bool m_DoAbsorptions;
+  //! MaximumSequenceLength up to which absorptions are considered
+  unsigned int m_MaxAbsorptions;
+  //! Maximum number of individual Compton interactions to be considered
+  unsigned int m_MaxNInteractions;
+
+  double m_MaxEnergyDifference;
+  double m_MaxEnergyDifferencePercent;
+
+  double m_MaxTrackEnergyDifference;
+  double m_MaxTrackEnergyDifferencePercent;
+
+  // The event/pdf matrices:
+  //!
+  MResponseMatrixO2 m_GoodBadTable;
+  //!
+  MResponseMatrixO4 m_PdfStartGood;
+
+  MResponseMatrixO4 m_PdfStartBad;
+
+  MResponseMatrixO6 m_PdfTrackGood;
+
+  MResponseMatrixO6 m_PdfTrackBad;
+
+  MResponseMatrixO4 m_PdfComptonScatterProbabilityGood;
+
+  MResponseMatrixO4 m_PdfComptonScatterProbabilityBad;
+
+  MResponseMatrixO4 m_PdfPhotoAbsorptionProbabilityGood;
+
+  MResponseMatrixO4 m_PdfPhotoAbsorptionProbabilityBad;
+
+  MResponseMatrixO6 m_PdfComptonGood;
+
+  MResponseMatrixO6 m_PdfComptonBad;
+
+  MResponseMatrixO4 m_PdfDualGood;
+
+  MResponseMatrixO4 m_PdfDualBad;
+
+
+  // private members:
+ private:
+
+
+#ifdef ___CLING___
+ public:
+  ClassDef(MResponseMultipleComptonBayes, 0) // no description
+#endif
+
+};
+
+#endif
+
+
+////////////////////////////////////////////////////////////////////////////////
diff --git a/src/response/src/MResponseCreator.cxx b/src/response/src/MResponseCreator.cxx
index 1cf4325ef..ce87dc1bb 100644
--- a/src/response/src/MResponseCreator.cxx
+++ b/src/response/src/MResponseCreator.cxx
@@ -39,7 +39,7 @@ using namespace std;
 #include "MAssert.h"
 #include "MStreams.h"
 #include "MResponseClusteringDSS.h"
-#include "MResponseMultipleCompton.h"
+#include "MResponseMultipleComptonBayes.h"
 #include "MResponseMultipleComptonEventFile.h"
 #include "MResponseMultipleComptonLens.h"
 #include "MResponseMultipleComptonTMVA.h"
@@ -160,7 +160,8 @@ bool MResponseCreator::ParseCommandLine(int argc, char** argv)
   Usage<<"      t  : track"<<endl;
   Usage<<"      cf : "<<MResponseMultipleComptonEventFile::Description()<<endl;
   Usage<<MResponseMultipleComptonEventFile::Options()<<endl;
-  Usage<<"      cb : compton (Bayesian)"<<endl;
+  Usage<<"      cb : "<<MResponseMultipleComptonBayes::Description()<<endl;
+  Usage<<MResponseMultipleComptonBayes::Options()<<endl;
   Usage<<"      ct : "<<MResponseMultipleComptonTMVA::Description()<<endl;
   Usage<<MResponseMultipleComptonTMVA::Options()<<endl;
   Usage<<"      cl : compton (Laue lens or collimated)"<<endl;
@@ -265,7 +266,7 @@ bool MResponseCreator::ParseCommandLine(int argc, char** argv)
       } else if (SubOption == "cd") {
         m_Mode = c_ModeClusteringDSS;
       } else if (SubOption == "cb") {
-        m_Mode = c_ModeComptons;
+        m_Mode = c_ModeComptonsBayes;
         cout<<"Choosing Compton mode (Bayesian)"<<endl;
       } else if (SubOption == "ct") {
         m_Mode = c_ModeComptonsTMVA;
@@ -398,7 +399,7 @@ bool MResponseCreator::ParseCommandLine(int argc, char** argv)
     while (m_TestRun == false && m_Interrupt == false && Response.Analyze() == true);
     if (Response.Finalize() == false) return false;
 
-  } else if (m_Mode == c_ModeComptons) {
+  } else if (m_Mode == c_ModeComptonsBayes) {
 
     if (m_RevanCfgFileName == g_StringNotDefined) {
       cout<<"Error: No revan configuration file name given!"<<endl;
@@ -406,14 +407,14 @@ bool MResponseCreator::ParseCommandLine(int argc, char** argv)
       return false;
     }
 
-    MResponseMultipleCompton Response;
+    MResponseMultipleComptonBayes Response;
 
     Response.SetDataFileName(m_FileName);
     Response.SetGeometryFileName(m_GeometryFileName);
     Response.SetResponseName(m_ResponseName);
     Response.SetCompression(m_Compress);
 
-    Response.SetMaxNInteractions(m_MaxNInteractions);
+    //Response.SetMaxNInteractions(m_MaxNInteractions);
     Response.SetMaxNumberOfEvents(m_MaxNEvents);
     Response.SetSaveAfterNumberOfEvents(m_SaveAfter);
 
diff --git a/src/response/src/MResponseMultipleCompton.cxx b/src/response/src/MResponseMultipleCompton.cxx
index faed8069e..d76143dca 100644
--- a/src/response/src/MResponseMultipleCompton.cxx
+++ b/src/response/src/MResponseMultipleCompton.cxx
@@ -67,6 +67,9 @@ MResponseMultipleCompton::MResponseMultipleCompton()
 
   m_MaxTrackEnergyDifference = 30; // keV
   m_MaxTrackEnergyDifferencePercent = 0.1;
+
+  m_EnergyMinimum = 100; // keV
+  m_EnergyMaximum = 10000; // keV
 }
 
 
@@ -79,478 +82,6 @@ MResponseMultipleCompton::~MResponseMultipleCompton()
   // Nothing to delete
 }
 
-  
-////////////////////////////////////////////////////////////////////////////////
-
-
-//! Initialize the response matrices and their generation
-bool MResponseMultipleCompton::Initialize() 
-{ 
-  // Initialize next matching event, save if necessary
-  if (MResponseBuilder::Initialize() == false) return false;
-  
-  m_MaxNInteractions = m_RevanSettings.GetCSRMaxNHits();
-  //m_MaxNInteractions = 3;
-  m_ReReader->SetCSROnlyCreateSequences(true);
-
-  if (m_ReReader->PreAnalysis() == false) return false;
-
-  double MaxCosineLimit = 10;
-
-  // Axis representing the sequence length:
-  vector<float> AxisSequenceLength;
-  for (unsigned int i = 2; i <= m_MaxNInteractions+1; ++i) {
-    AxisSequenceLength.push_back(i);
-  }
-  MString NameAxisSequenceLength = "Sequence length";
-
-  double MaxEnergy = 5000;
-  
-  // Material: 0: unknown, 1: Si, 2: Ge, 3: Xe, 4: CsI
-  // Make sure this is identical with: MERCSRBayesian::GetMaterial()
-  vector<float> AxisMaterial;
-  AxisMaterial = CreateEquiDist(-0.5, 4.5, 5);
-  MString NameAxisMaterial = "Material (0: ?, 1: Si, 2: Ge, 3: Xe, 4: CsI)";
-
-  // Compton scatter angle axis:
-  // Make sure it starts, well below 0 and exceeds (slightly) 1!
-  vector<float> AxisComptonScatterAngleStart;
-  AxisComptonScatterAngleStart = CreateEquiDist(-1.5, 1.1, 26, -MaxCosineLimit, +MaxCosineLimit);
-  MString NameAxisComptonScatterAngleStart = "cos#varphi";
-
-  // Scatter probability axis
-  vector<float> AxisScatterProbability = CreateEquiDist(-0.025, 1.025, 42);
-  MString NameAxisScatterProbability = "Scatter probability";
-
-  // Total energy axis for scatter probabilities
-  vector<float> AxisTotalEnergyDistances = CreateLogDist(15, MaxEnergy, 38, 1, 20000);
-  MString NameAxisTotalEnergyDistances = "Energy [keV]";
-
-  // Total energy axis for scatter probabilities
-  vector<float> AxisTotalEnergyStart = CreateLogDist(100, MaxEnergy, 38, 1, 20000);
-  MString NameAxisTotalEnergyStart = "Energy [keV]";
-
-
-  // Make sure it starts, well below 0 and exceeds (slightly) 1!
-  vector<float> AxisComptonScatterAngleDual;
-  AxisComptonScatterAngleDual = CreateEquiDist(-1.5, 1.1, 26, -MaxCosineLimit, +MaxCosineLimit);
-  MString NameAxisComptonScatterAngleDual = "cos#varphi";
-
-  // Total energy axis for scatter probabilities
-  vector<float> AxisTotalEnergyDual = CreateLogDist(100, MaxEnergy, 18, 1, 20000);
-  MString NameAxisTotalEnergyDual = "Energy [keV]";
-
-  // Scatter probability axis
-  vector<float> AxisScatterProbabilityDual = CreateEquiDist(0, 1, 15, -0.025, 1.025);
-  MString NameAxisScatterProbabilityDual = "Scatter probability";
-  
-
-
-  // Global good/bad:
-  m_GoodBadTable = MResponseMatrixO2("MC: Good/Bad ratio (=prior)", 
-                                     CreateEquiDist(0, 2, 2), 
-                                     AxisSequenceLength); 
-  m_GoodBadTable.SetAxisNames("GoodBad", 
-                              NameAxisSequenceLength);
-
-  // Dual:
-  m_PdfDualGood = MResponseMatrixO4("MC: Dual (good)", 
-                                    AxisTotalEnergyDual,
-                                    AxisComptonScatterAngleDual,  
-                                    AxisScatterProbabilityDual,
-                                    AxisMaterial);
-  m_PdfDualGood.SetAxisNames(NameAxisTotalEnergyStart, 
-                             NameAxisComptonScatterAngleStart, 
-                             NameAxisScatterProbabilityDual, 
-                             NameAxisMaterial);
-  m_PdfDualBad = MResponseMatrixO4("MC: Dual (bad)", 
-                                   AxisTotalEnergyDual,
-                                   AxisComptonScatterAngleDual,  
-                                   AxisScatterProbabilityDual,
-                                   AxisMaterial);
-  m_PdfDualBad.SetAxisNames(NameAxisTotalEnergyStart, 
-                            NameAxisComptonScatterAngleStart, 
-                            NameAxisScatterProbabilityDual, 
-                            NameAxisMaterial);
-  
-
-  // Start point:
-  m_PdfStartGood = MResponseMatrixO4("MC: Start (good)", 
-                                     AxisTotalEnergyStart,
-                                     AxisComptonScatterAngleStart, 
-                                     AxisSequenceLength, 
-                                     AxisMaterial);
-  m_PdfStartGood.SetAxisNames(NameAxisTotalEnergyStart, 
-                              NameAxisComptonScatterAngleStart, 
-                              NameAxisSequenceLength, 
-                              NameAxisMaterial);
-  m_PdfStartBad = MResponseMatrixO4("MC: Start (bad)", 
-                                    AxisTotalEnergyStart, 
-                                    AxisComptonScatterAngleStart, 
-                                    AxisSequenceLength, 
-                                    AxisMaterial);
-  m_PdfStartBad.SetAxisNames(NameAxisTotalEnergyStart, 
-                             NameAxisComptonScatterAngleStart, 
-                             NameAxisSequenceLength, 
-                             NameAxisMaterial);
-
-
-  // Track:
-  m_PdfTrackGood = MResponseMatrixO6("MC: Track (good)", 
-                                     CreateEquiDist(-0.5, 1.5, 36, c_NoBound, MaxCosineLimit),
-                                     CreateEquiDist(-0.5, 1.5, 1, c_NoBound, MaxCosineLimit),
-                                     CreateEquiDist(0, 1000000, 1),
-                                     CreateLogDist(500, 10000, 10, 0, 100000, 0, false),
-                                     AxisSequenceLength, 
-                                     AxisMaterial);
-  m_PdfTrackGood.SetAxisNames("#Delta #alpha [deg]", 
-                              "#alpha_{G} [deg]", 
-                              "d [cm]", 
-                              "E_{e}", 
-                              NameAxisSequenceLength, 
-                              NameAxisMaterial);
-  m_PdfTrackBad = MResponseMatrixO6("MC: Track (bad)", 
-                                    CreateEquiDist(-0.5, 1.5, 36, c_NoBound, MaxCosineLimit),
-                                    CreateEquiDist(-0.5, 1.5, 1, c_NoBound, MaxCosineLimit),
-                                    CreateEquiDist(0, 1000000, 1),
-                                    CreateLogDist(500, 10000, 10, 0, 100000, 0, false),
-                                    AxisSequenceLength, 
-                                    AxisMaterial);
-  m_PdfTrackBad.SetAxisNames("#Delta cos#alpha [deg]", 
-                             "cos#alpha_{G} [deg]", 
-                             "d [cm]", 
-                             "E_{e}", 
-                             NameAxisSequenceLength, 
-                             NameAxisMaterial);
-
-  
-  // Compton scatter distance:
-  m_PdfComptonScatterProbabilityGood = MResponseMatrixO4("MC: Compton distance (good)", 
-                                        AxisScatterProbability,
-                                        AxisTotalEnergyDistances, 
-                                        AxisSequenceLength, 
-                                        AxisMaterial);
-  m_PdfComptonScatterProbabilityGood.SetAxisNames(NameAxisScatterProbability, 
-                                 NameAxisTotalEnergyDistances, 
-                                 NameAxisSequenceLength, 
-                                 NameAxisMaterial);
-  m_PdfComptonScatterProbabilityBad = MResponseMatrixO4("MC: Compton distance (bad)", 
-                                       AxisScatterProbability, 
-                                       AxisTotalEnergyDistances, 
-                                       AxisSequenceLength, 
-                                       AxisMaterial);
-  m_PdfComptonScatterProbabilityBad.SetAxisNames(NameAxisScatterProbability, 
-                                NameAxisTotalEnergyDistances, 
-                                NameAxisSequenceLength, 
-                                NameAxisMaterial);
-
-
-  // Lastdistance:
-  m_PdfPhotoAbsorptionProbabilityGood = MResponseMatrixO4("MC: Photo distance (good)", 
-                                            AxisScatterProbability, 
-                                            AxisTotalEnergyDistances, 
-                                            AxisSequenceLength, 
-                                            AxisMaterial);
-  m_PdfPhotoAbsorptionProbabilityGood.SetAxisNames(NameAxisScatterProbability, 
-                                     NameAxisTotalEnergyDistances, 
-                                     NameAxisSequenceLength, 
-                                     NameAxisMaterial);
-  m_PdfPhotoAbsorptionProbabilityBad = MResponseMatrixO4("MC: Photo distance (bad)", 
-                                           AxisScatterProbability, 
-                                           AxisTotalEnergyDistances, 
-                                           AxisSequenceLength, 
-                                           AxisMaterial);
-  m_PdfPhotoAbsorptionProbabilityBad.SetAxisNames(NameAxisScatterProbability, 
-                                    NameAxisTotalEnergyDistances, 
-                                    NameAxisSequenceLength, 
-                                    NameAxisMaterial);
-
-
-  // CentralCompton:
-  
-  // Assymetries would be best handled if -1 .. 1
-  //vector<float> AxisDifferenceComptonScatterAngle = 
-  //  CreateLogDist(1E-3, 2, 18, 0.0000001, MaxCosineLimit);
-  vector<float> AxisDifferenceComptonScatterAngle; 
-  vector<float> A = CreateLogDist(0.003, 2, 14, c_NoBound, MaxCosineLimit);
-  for (unsigned int i = A.size()-1; i < A.size(); --i) {
-    AxisDifferenceComptonScatterAngle.push_back(-A[i]);
-  }
-  for (unsigned int i = 0; i < A.size(); ++i) {
-    AxisDifferenceComptonScatterAngle.push_back(A[i]);
-  }
-  MString NameAxisDifferenceComptonScatterAngle = "cos#varphi_{E} - cos#varphi_{G}";
-
-  vector<float> AxisComptonScatterAngle;
-  AxisComptonScatterAngle = CreateEquiDist(-1.4, 1.2, 13, -MaxCosineLimit, c_NoBound);
-  MString NameAxisComptonScatterAngle = NameAxisComptonScatterAngleStart;
-
-
-  vector<float> AxisDistance = 
-    CreateLogDist(0.2, 10, 7, 0.01, 100, 0, false); 
-  MString NameAxisDistance = "Distance [cm]";
-
-  vector<float> AxisTotalEnergy = CreateLogDist(100, MaxEnergy, 4, 1, 10000, 0, false);
-  //CreateLogDist(1, 10000, 1); //, 1, 10000, 0, false);
-  //mimp<<"No total energy bins!"<<show;
-  MString NameAxisTotalEnergy = "E_{tot} [keV]";
-
-  m_PdfComptonGood = MResponseMatrixO6("MC: Central (good)", 
-                                       AxisDifferenceComptonScatterAngle,
-                                       AxisComptonScatterAngle, 
-                                       AxisDistance,
-                                       AxisTotalEnergy,
-                                       AxisSequenceLength, 
-                                       AxisMaterial);
-  m_PdfComptonGood.SetAxisNames(NameAxisDifferenceComptonScatterAngle, 
-                                NameAxisComptonScatterAngle, 
-                                NameAxisDistance, 
-                                NameAxisTotalEnergy, 
-                                NameAxisSequenceLength, 
-                                NameAxisMaterial);
-  m_PdfComptonBad = MResponseMatrixO6("MC: Central (bad)", 
-                                      AxisDifferenceComptonScatterAngle, 
-                                      AxisComptonScatterAngle,
-                                      AxisDistance,
-                                      AxisTotalEnergy,
-                                      AxisSequenceLength, 
-                                      AxisMaterial);
-  m_PdfComptonBad.SetAxisNames(NameAxisDifferenceComptonScatterAngle, 
-                               NameAxisComptonScatterAngle, 
-                               NameAxisDistance, 
-                               NameAxisTotalEnergy, 
-                               NameAxisSequenceLength, 
-                               NameAxisMaterial);
-
-  return true;
-}
-
-
-////////////////////////////////////////////////////////////////////////////////
-
-
-//! Save the responses
-bool MResponseMultipleCompton::Save()
-{
-  MResponseBuilder::Save(); 
-
-  m_GoodBadTable.Write(GetFilePrefix() + ".goodbad" + m_Suffix, true);
-  
-  m_PdfDualGood.Write(GetFilePrefix() + ".dual.good" + m_Suffix, true);
-  m_PdfDualBad.Write(GetFilePrefix() + ".dual.bad" + m_Suffix, true);
-  
-  m_PdfStartGood.Write(GetFilePrefix() + ".start.good" + m_Suffix, true);
-  m_PdfStartBad.Write(GetFilePrefix() + ".start.bad" + m_Suffix, true);
-  
-  m_PdfTrackGood.Write(GetFilePrefix() + ".track.good" + m_Suffix, true);
-  m_PdfTrackBad.Write(GetFilePrefix() + ".track.bad" + m_Suffix, true);
-  
-  m_PdfComptonGood.Write(GetFilePrefix() + ".compton.good" + m_Suffix, true);
-  m_PdfComptonBad.Write(GetFilePrefix() + ".compton.bad" + m_Suffix, true);
-  
-  m_PdfComptonScatterProbabilityGood.Write(GetFilePrefix() + ".comptondistance.good" + m_Suffix, true);
-  m_PdfComptonScatterProbabilityBad.Write(GetFilePrefix() + ".comptondistance.bad" + m_Suffix, true);
-      
-  m_PdfPhotoAbsorptionProbabilityGood.Write(GetFilePrefix() + ".photodistance.good" + m_Suffix, true);
-  m_PdfPhotoAbsorptionProbabilityBad.Write(GetFilePrefix() + ".photodistance.bad" + m_Suffix, true);
-      
-  return true;
-}
-
-  
-////////////////////////////////////////////////////////////////////////////////
-
-
-//! Analyze the current event
-bool MResponseMultipleCompton::Analyze() 
-{ 
-  // Initlize next matching event, save if necessary
-  if (MResponseBuilder::Analyze() == false) return false;
-  
-  
-  //g_Verbosity = 1;
-  double Etot = 0;
-  double Eres = 0;
- 
-  
-  for (auto RE: m_ReEvents) {
-    if (RE == nullptr) continue;
-    
-    if (RE->GetNRESEs() <= 1) {
-      mdebug<<"GeneratePdf: Not enough hits!"<<endl;
-      continue;
-    }
-    
-    mdebug<<endl<<endl;
-    mdebug<<RE->ToString()<<endl;
-    
-    if (RE->GetStartPoint() == 0) continue;
-    
-    // Check if complete sequence is ok:
-    bool SequenceOk = true;
-    unsigned int SequenceLength = RE->GetNRESEs();
-    int PreviousPosition = 0;
-    
-    if (SequenceLength > m_MaxNInteractions) continue;
-    
-    if (SequenceLength == 2) {
-      // Look at start:
-      MRESEIterator Iter;
-      Iter.Start(RE->GetStartPoint());
-      Iter.GetNextRESE();
-      Etot = RE->GetEnergy();
-      Eres = RE->GetEnergyResolution();
-      
-      double CosPhiE = CalculateCosPhiE(*Iter.GetCurrent(), Etot);
-      double PhotoDistance = CalculateAbsorptionProbabilityTotal(*Iter.GetCurrent(), *Iter.GetNext(), Iter.GetNext()->GetEnergy());
-      
-      if (IsComptonStart(*Iter.GetCurrent(), Etot, Eres) == true) {
-        mdebug<<"--------> Found GOOD dual Compton event!"<<endl;
-        m_PdfDualGood.Add(Etot, CosPhiE, PhotoDistance, GetMaterial(*Iter.GetCurrent()));
-      } else {
-        mdebug<<"--------> Found bad dual Compton event!"<<endl;
-        m_PdfDualBad.Add(Etot, CosPhiE, PhotoDistance, GetMaterial(*Iter.GetCurrent()));
-        SequenceOk = false;
-      }
-    } else {
-      // Look at start:
-      MRESEIterator Iter;
-      Iter.Start(RE->GetStartPoint());
-      Iter.GetNextRESE();
-      Etot = RE->GetEnergy();
-      Eres = RE->GetEnergyResolution();
-      if (IsComptonStart(*Iter.GetCurrent(), Etot, Eres) == true) {
-        mdebug<<"--------> Found GOOD Compton start!"<<endl;
-        m_PdfStartGood.Add(Etot, CalculateCosPhiE(*Iter.GetCurrent(), Etot), SequenceLength, GetMaterial(*Iter.GetCurrent()));
-      } else {
-        mdebug<<"--------> Found bad Compton start!"<<endl;
-        m_PdfStartBad.Add(Etot, CalculateCosPhiE(*Iter.GetCurrent(), Etot), SequenceLength, GetMaterial(*Iter.GetCurrent()));
-        SequenceOk = false;
-      }
-      
-      // Track at start?
-      if (Iter.GetCurrent()->GetType() == MRESE::c_Track) {
-        double dAlpha = CalculateDCosAlpha(*((MRETrack*) Iter.GetCurrent()), *Iter.GetNext(), Etot);
-        double Alpha = CalculateCosAlphaG(*((MRETrack*) Iter.GetCurrent()), *Iter.GetNext(), Etot);
-        if (IsComptonTrack(*Iter.GetCurrent(), *Iter.GetNext(), PreviousPosition, Etot, Eres) == true) {
-          mdebug<<"--------> Found GOOD Track start!"<<endl;
-          m_PdfTrackGood.Add(dAlpha, Alpha, 1, Iter.GetCurrent()->GetEnergy(), SequenceLength, GetMaterial(*Iter.GetCurrent()));
-        } else {
-          mdebug<<"--------> Found bad Track start!"<<endl;
-          m_PdfTrackBad.Add(dAlpha, Alpha, 1, Iter.GetCurrent()->GetEnergy(), SequenceLength, GetMaterial(*Iter.GetCurrent()));
-          SequenceOk = false;
-        }
-      }
-      
-      
-      // Central part of the Compton track
-      Iter.GetNextRESE();
-      while (Iter.GetNext() != 0) {
-        // Add here
-        Etot -= Iter.GetPrevious()->GetEnergy();
-        Eres = sqrt(Eres*Eres - Iter.GetPrevious()->GetEnergyResolution()*Iter.GetPrevious()->GetEnergyResolution());
-        PreviousPosition++;
-        
-        // In the current implementation/simulation the hits have to be in increasing order...
-        if (m_DoAbsorptions == true && SequenceLength <= m_MaxAbsorptions) {
-          double ComptonDistance = 
-          CalculateAbsorptionProbabilityCompton(*Iter.GetPrevious(), *Iter.GetCurrent(), Etot);
-          mdebug<<"Dist C: "<<ComptonDistance<<": real:"<<(Iter.GetCurrent()->GetPosition() - Iter.GetPrevious()->GetPosition()).Mag()<<endl;
-          if (IsComptonSequence(*Iter.GetPrevious(), *Iter.GetCurrent(), PreviousPosition, Etot, Eres) == true) {
-            mdebug<<"--------> Found GOOD Distance sequence!"<<endl;
-            // Retrieve the data:
-            m_PdfComptonScatterProbabilityGood.Add(ComptonDistance, Etot, SequenceLength, GetMaterial(*Iter.GetCurrent()));
-          } else {
-            mdebug<<"--------> Found bad Distance sequence!"<<endl;
-            // Retrieve the data:
-            m_PdfComptonScatterProbabilityBad.Add(ComptonDistance, Etot, SequenceLength, GetMaterial(*Iter.GetCurrent()));
-            SequenceOk = false;
-          } // Add good / bad
-        }
-        
-        // Decide if it is good or bad...
-        // In the current implementation/simulation the hits have to be in increasing order...
-        double dPhi = CalculateDCosPhi(*Iter.GetPrevious(), *Iter.GetCurrent(), *Iter.GetNext(), Etot);
-        double PhiE = CalculateCosPhiE(*Iter.GetCurrent(), Etot);
-        double Lever = CalculateMinLeverArm(*Iter.GetPrevious(), *Iter.GetCurrent(), *Iter.GetNext());
-        int Material = GetMaterial(*Iter.GetCurrent());
-        
-        if (IsComptonSequence(*Iter.GetPrevious(), *Iter.GetCurrent(), *Iter.GetNext(), PreviousPosition, Etot, Eres) == true) {
-          mdebug<<"--------> Found GOOD internal Compton sequence!"<<endl;
-          // Retrieve the data:
-          m_PdfComptonGood.Add(dPhi, PhiE, Lever, Etot, SequenceLength, Material);
-          
-        } else {
-          mdebug<<"--------> Found bad internal Compton sequence!"<<endl;
-          // Retrieve the data:
-          m_PdfComptonBad.Add(dPhi, PhiE, Lever, Etot, SequenceLength, Material);
-          SequenceOk = false;
-        } // Add good / bad
-        
-        // Track at central?
-        if (Iter.GetCurrent()->GetType() == MRESE::c_Track) {
-          //MRETrack* T = (MRETrack*) Iter.GetCurrent();
-          double dAlpha = CalculateDCosAlpha(*((MRETrack*) Iter.GetCurrent()), *Iter.GetNext(), Etot);
-          double Alpha = CalculateCosAlphaG(*((MRETrack*) Iter.GetCurrent()), *Iter.GetNext(), Etot);
-          if (IsComptonTrack(*Iter.GetCurrent(), *Iter.GetNext(), PreviousPosition, Etot, Eres) == true) {
-            mdebug<<"--------> Found GOOD Track start (central)!"<<endl;
-            m_PdfTrackGood.Add(dAlpha, Alpha, 1, Iter.GetCurrent()->GetEnergy(), SequenceLength, GetMaterial(*Iter.GetCurrent()));
-          } else {
-            mdebug<<"--------> Found bad Track start (central)!"<<endl;
-            m_PdfTrackBad.Add(dAlpha, Alpha, 1, Iter.GetCurrent()->GetEnergy(), SequenceLength, GetMaterial(*Iter.GetCurrent()));
-            SequenceOk = false;
-          }
-        }
-        Iter.GetNextRESE();
-      }
-      
-      Etot -= Iter.GetPrevious()->GetEnergy();
-      Eres = sqrt(Eres*Eres - Iter.GetPrevious()->GetEnergyResolution()*Iter.GetPrevious()->GetEnergyResolution());
-      PreviousPosition++;
-      
-      // Decide if it is good or bad...
-      // In the current implementation/simulation the hits have to be in increasing order...
-      if (m_DoAbsorptions == true && SequenceLength <= m_MaxAbsorptions) {
-        double LastDistance = CalculateAbsorptionProbabilityPhoto(*Iter.GetPrevious(), *Iter.GetCurrent(), Etot);
-        mdebug<<"Dist P: "<<LastDistance<<": real:"<<(Iter.GetCurrent()->GetPosition() - Iter.GetPrevious()->GetPosition()).Mag()<<endl;
-        if (IsComptonSequence(*Iter.GetPrevious(), *Iter.GetCurrent(), PreviousPosition, Etot, Eres) == true) {
-          mdebug<<"--------> Found GOOD Lastdistance sequence!"<<endl;
-          // Retrieve the data:
-          m_PdfPhotoAbsorptionProbabilityGood.Add(CalculateAbsorptionProbabilityPhoto(*Iter.GetPrevious(), *Iter.GetCurrent(), Etot), 
-                                                  Etot, SequenceLength, GetMaterial(*Iter.GetCurrent()));
-        } else {
-          mdebug<<"--------> Found bad Lastdistance sequence!"<<endl;
-          // Retrieve the data:
-          m_PdfPhotoAbsorptionProbabilityBad.Add(CalculateAbsorptionProbabilityPhoto(*Iter.GetPrevious(), *Iter.GetCurrent(), Etot), 
-                                                 Etot, SequenceLength, GetMaterial(*Iter.GetCurrent()));
-          SequenceOk = false;
-        } // Add good / bad
-      }
-    }
-    
-    if (SequenceOk == false) {
-      m_GoodBadTable.Add(0.5, SequenceLength, 1);
-      //mdebug<<"No good sequence exists"<<endl<<endl<<endl<<endl;
-    } else {
-      m_GoodBadTable.Add(1.5, SequenceLength, 1);
-      mdebug<<"One good sequence exists"<<endl<<endl<<endl<<endl;
-    }
-  } // For each raw event...
-  
-  
-  return true;
-}
-
-  
-////////////////////////////////////////////////////////////////////////////////
-
-
-//! Finalize the response generation (i.e. save the data a final time )
-bool MResponseMultipleCompton::Finalize() 
-{ 
-  return MResponseBuilder::Finalize(); 
-}
-
 
 ////////////////////////////////////////////////////////////////////////////////
 
diff --git a/src/response/src/MResponseMultipleComptonBayes.cxx b/src/response/src/MResponseMultipleComptonBayes.cxx
new file mode 100644
index 000000000..90a28a0ee
--- /dev/null
+++ b/src/response/src/MResponseMultipleComptonBayes.cxx
@@ -0,0 +1,1980 @@
+/*
+ * MResponseMultipleComptonBayes.cxx
+ *
+ *
+ * Copyright (C) by Andreas Zoglauer.
+ * All rights reserved.
+ *
+ *
+ * This code implementation is the intellectual property of
+ * Andreas Zoglauer.
+ *
+ * By copying, distributing or modifying the Program (or any work
+ * based on the Program) you indicate your acceptance of this statement,
+ * and all its terms.
+ *
+ */
+
+
+////////////////////////////////////////////////////////////////////////////////
+//
+// MResponseMultipleComptonBayes
+//
+////////////////////////////////////////////////////////////////////////////////
+
+
+// Include the header:
+#include "MResponseMultipleComptonBayes.h"
+
+// Standard libs:
+#include <limits>
+#include <algorithm>
+#include <vector>
+using namespace std;
+
+// ROOT libs:
+
+// MEGAlib libs:
+#include "MAssert.h"
+#include "MStreams.h"
+#include "MSettingsRevan.h"
+#include "MRESEIterator.h"
+#include "MERCSRBayesian.h"
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+#ifdef ___CLING___
+ClassImp(MResponseMultipleComptonBayes)
+#endif
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Default constructor
+MResponseMultipleComptonBayes::MResponseMultipleComptonBayes()
+{  
+  m_ResponseNameSuffix = "mc";
+  
+  m_DoAbsorptions = true;
+  m_MaxAbsorptions = 5;
+  m_MaxNInteractions = 7;
+
+  m_MaxEnergyDifference = 5; // keV
+  m_MaxEnergyDifferencePercent = 0.02;
+
+  m_MaxTrackEnergyDifference = 30; // keV
+  m_MaxTrackEnergyDifferencePercent = 0.1;
+
+  m_EnergyMinimum = 100; // keV
+  m_EnergyMaximum = 10000; // keV
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Default destructor
+MResponseMultipleComptonBayes::~MResponseMultipleComptonBayes()
+{
+  // Nothing to delete
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Return a brief description of this response class
+MString MResponseMultipleComptonBayes::Description()
+{
+  return MString("Compton event reconstruction (Bayes)");
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Return information on the parsable options for this response class
+MString MResponseMultipleComptonBayes::Options()
+{
+  ostringstream out;
+  out<<"             maxia:                 the maximum number of interactions (default: 7)"<<endl;
+  out<<"             emin:                  minimum energy (default: 100 keV)"<<endl;
+  out<<"             emax:                  maximum energy (default: 10000 keV)"<<endl;
+
+  return MString(out);
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Parse the options
+bool MResponseMultipleComptonBayes::ParseOptions(const MString& Options)
+{
+  // Split the different options
+  vector<MString> Split1 = Options.Tokenize(":");
+  // Split Option <-> Value
+  vector<vector<MString>> Split2;
+  for (MString S: Split1) {
+    Split2.push_back(S.Tokenize("="));
+  }
+
+  // Basic sanity check and to lower for all options
+  for (unsigned int i = 0; i < Split2.size(); ++i) {
+    if (Split2[i].size() == 0) {
+      mout<<"Error: Empty option in string "<<Options<<endl;
+      return false;
+    }
+    if (Split2[i].size() == 1) {
+      mout<<"Error: Option has no value: "<<Split2[i][0]<<endl;
+      return false;
+    }
+    if (Split2[i].size() > 2) {
+      mout<<"Error: Option has more than one value or you used the wrong separator (not \":\"): "<<Split1[i]<<endl;
+      return false;
+    }
+    Split2[i][0].ToLowerInPlace();
+  }
+
+  // Parse
+  for (unsigned int i = 0; i < Split2.size(); ++i) {
+    string Value = Split2[i][1].Data();
+
+    if (Split2[i][0] == "emin") {
+      m_EnergyMinimum = stod(Value);
+    } else if (Split2[i][0] == "emax") {
+      m_EnergyMaximum = stod(Value);
+    } else if (Split2[i][0] == "maxia") {
+      m_MaxNInteractions = stoi(Value);
+    } else {
+      mout<<"Error: Unrecognized option "<<Split2[i][0]<<endl;
+      return false;
+    }
+  }
+
+  // Sanity checks:
+  if (m_EnergyMinimum <= 0 || m_EnergyMaximum <= 0) {
+    mout<<"Error: All energy values must be positive (larger than zero)"<<endl;
+    return false;
+  }
+  if (m_EnergyMinimum >= m_EnergyMaximum) {
+    mout<<"Error: The minimum energy must be smaller than the maximum energy"<<endl;
+    return false;
+  }
+  if (m_MaxNInteractions < 2) {
+    mout<<"Error: You need at least 2 interactions"<<endl;
+    return false;
+  }
+
+  // Dump it for user info
+  mout<<endl;
+  mout<<"Choosen options for binned imaging response:"<<endl;
+  mout<<"  Minimum energy:                                     "<<m_EnergyMinimum<<endl;
+  mout<<"  Maximum energy:                                     "<<m_EnergyMaximum<<endl;
+  mout<<"  Maximum number of interactions:                     "<<m_MaxNInteractions<<endl;
+  mout<<endl;
+
+  return true;
+}
+
+
+  
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Initialize the response matrices and their generation
+bool MResponseMultipleComptonBayes::Initialize()
+{ 
+  // Initialize next matching event, save if necessary
+  if (MResponseBuilder::Initialize() == false) return false;
+  
+  m_MaxNInteractions = m_RevanSettings.GetCSRMaxNHits();
+  //m_MaxNInteractions = 3;
+  m_ReReader->SetCSROnlyCreateSequences(true);
+
+  if (m_ReReader->PreAnalysis() == false) return false;
+
+  double MaxCosineLimit = 10;
+
+  // Axis representing the sequence length:
+  vector<float> AxisSequenceLength;
+  for (unsigned int i = 2; i <= m_MaxNInteractions+1; ++i) {
+    AxisSequenceLength.push_back(i);
+  }
+  MString NameAxisSequenceLength = "Sequence length";
+
+  // Material: 0: unknown, 1: Si, 2: Ge, 3: Xe, 4: CsI
+  // Make sure this is identical with: MERCSRBayesian::GetMaterial()
+  vector<float> AxisMaterial;
+  AxisMaterial = CreateEquiDist(-0.5, 4.5, 5);
+  MString NameAxisMaterial = "Material (0: ?, 1: Si, 2: Ge, 3: Xe, 4: CsI)";
+
+  // Compton scatter angle axis:
+  // Make sure it starts, well below 0 and exceeds (slightly) 1!
+  vector<float> AxisComptonScatterAngleStart;
+  AxisComptonScatterAngleStart = CreateEquiDist(-1.5, 1.1, 26, -MaxCosineLimit, +MaxCosineLimit);
+  MString NameAxisComptonScatterAngleStart = "cos#varphi";
+
+  // Scatter probability axis
+  vector<float> AxisScatterProbability = CreateEquiDist(-0.025, 1.025, 42);
+  MString NameAxisScatterProbability = "Scatter probability";
+
+  // Total energy axis for scatter probabilities
+  vector<float> AxisTotalEnergyDistances = CreateLogDist(15, m_EnergyMaximum, 38, 1, 20000);
+  MString NameAxisTotalEnergyDistances = "Energy [keV]";
+
+  // Total energy axis for scatter probabilities
+  vector<float> AxisTotalEnergyStart = CreateLogDist(m_EnergyMinimum, m_EnergyMaximum, 38, 1, 20000);
+  MString NameAxisTotalEnergyStart = "Energy [keV]";
+
+
+  // Make sure it starts, well below 0 and exceeds (slightly) 1!
+  vector<float> AxisComptonScatterAngleDual;
+  AxisComptonScatterAngleDual = CreateEquiDist(-1.5, 1.1, 26, -MaxCosineLimit, +MaxCosineLimit);
+  MString NameAxisComptonScatterAngleDual = "cos#varphi";
+
+  // Total energy axis for scatter probabilities
+  vector<float> AxisTotalEnergyDual = CreateLogDist(m_EnergyMinimum, m_EnergyMaximum, 18, 1, 20000);
+  MString NameAxisTotalEnergyDual = "Energy [keV]";
+
+  // Scatter probability axis
+  vector<float> AxisScatterProbabilityDual = CreateEquiDist(0, 1, 15, -0.025, 1.025);
+  MString NameAxisScatterProbabilityDual = "Scatter probability";
+  
+
+
+  // Global good/bad:
+  m_GoodBadTable = MResponseMatrixO2("MC: Good/Bad ratio (=prior)", 
+                                     CreateEquiDist(0, 2, 2), 
+                                     AxisSequenceLength); 
+  m_GoodBadTable.SetAxisNames("GoodBad", 
+                              NameAxisSequenceLength);
+
+  // Dual:
+  m_PdfDualGood = MResponseMatrixO4("MC: Dual (good)", 
+                                    AxisTotalEnergyDual,
+                                    AxisComptonScatterAngleDual,  
+                                    AxisScatterProbabilityDual,
+                                    AxisMaterial);
+  m_PdfDualGood.SetAxisNames(NameAxisTotalEnergyStart, 
+                             NameAxisComptonScatterAngleStart, 
+                             NameAxisScatterProbabilityDual, 
+                             NameAxisMaterial);
+  m_PdfDualBad = MResponseMatrixO4("MC: Dual (bad)", 
+                                   AxisTotalEnergyDual,
+                                   AxisComptonScatterAngleDual,  
+                                   AxisScatterProbabilityDual,
+                                   AxisMaterial);
+  m_PdfDualBad.SetAxisNames(NameAxisTotalEnergyStart, 
+                            NameAxisComptonScatterAngleStart, 
+                            NameAxisScatterProbabilityDual, 
+                            NameAxisMaterial);
+  
+
+  // Start point:
+  m_PdfStartGood = MResponseMatrixO4("MC: Start (good)", 
+                                     AxisTotalEnergyStart,
+                                     AxisComptonScatterAngleStart, 
+                                     AxisSequenceLength, 
+                                     AxisMaterial);
+  m_PdfStartGood.SetAxisNames(NameAxisTotalEnergyStart, 
+                              NameAxisComptonScatterAngleStart, 
+                              NameAxisSequenceLength, 
+                              NameAxisMaterial);
+  m_PdfStartBad = MResponseMatrixO4("MC: Start (bad)", 
+                                    AxisTotalEnergyStart, 
+                                    AxisComptonScatterAngleStart, 
+                                    AxisSequenceLength, 
+                                    AxisMaterial);
+  m_PdfStartBad.SetAxisNames(NameAxisTotalEnergyStart, 
+                             NameAxisComptonScatterAngleStart, 
+                             NameAxisSequenceLength, 
+                             NameAxisMaterial);
+
+
+  // Track:
+  m_PdfTrackGood = MResponseMatrixO6("MC: Track (good)", 
+                                     CreateEquiDist(-0.5, 1.5, 36, c_NoBound, MaxCosineLimit),
+                                     CreateEquiDist(-0.5, 1.5, 1, c_NoBound, MaxCosineLimit),
+                                     CreateEquiDist(0, 1000000, 1),
+                                     CreateLogDist(500, 10000, 10, 0, 100000, 0, false),
+                                     AxisSequenceLength, 
+                                     AxisMaterial);
+  m_PdfTrackGood.SetAxisNames("#Delta #alpha [deg]", 
+                              "#alpha_{G} [deg]", 
+                              "d [cm]", 
+                              "E_{e}", 
+                              NameAxisSequenceLength, 
+                              NameAxisMaterial);
+  m_PdfTrackBad = MResponseMatrixO6("MC: Track (bad)", 
+                                    CreateEquiDist(-0.5, 1.5, 36, c_NoBound, MaxCosineLimit),
+                                    CreateEquiDist(-0.5, 1.5, 1, c_NoBound, MaxCosineLimit),
+                                    CreateEquiDist(0, 1000000, 1),
+                                    CreateLogDist(500, 10000, 10, 0, 100000, 0, false),
+                                    AxisSequenceLength, 
+                                    AxisMaterial);
+  m_PdfTrackBad.SetAxisNames("#Delta cos#alpha [deg]", 
+                             "cos#alpha_{G} [deg]", 
+                             "d [cm]", 
+                             "E_{e}", 
+                             NameAxisSequenceLength, 
+                             NameAxisMaterial);
+
+  
+  // Compton scatter distance:
+  m_PdfComptonScatterProbabilityGood = MResponseMatrixO4("MC: Compton distance (good)", 
+                                        AxisScatterProbability,
+                                        AxisTotalEnergyDistances, 
+                                        AxisSequenceLength, 
+                                        AxisMaterial);
+  m_PdfComptonScatterProbabilityGood.SetAxisNames(NameAxisScatterProbability, 
+                                 NameAxisTotalEnergyDistances, 
+                                 NameAxisSequenceLength, 
+                                 NameAxisMaterial);
+  m_PdfComptonScatterProbabilityBad = MResponseMatrixO4("MC: Compton distance (bad)", 
+                                       AxisScatterProbability, 
+                                       AxisTotalEnergyDistances, 
+                                       AxisSequenceLength, 
+                                       AxisMaterial);
+  m_PdfComptonScatterProbabilityBad.SetAxisNames(NameAxisScatterProbability, 
+                                NameAxisTotalEnergyDistances, 
+                                NameAxisSequenceLength, 
+                                NameAxisMaterial);
+
+
+  // Lastdistance:
+  m_PdfPhotoAbsorptionProbabilityGood = MResponseMatrixO4("MC: Photo distance (good)", 
+                                            AxisScatterProbability, 
+                                            AxisTotalEnergyDistances, 
+                                            AxisSequenceLength, 
+                                            AxisMaterial);
+  m_PdfPhotoAbsorptionProbabilityGood.SetAxisNames(NameAxisScatterProbability, 
+                                     NameAxisTotalEnergyDistances, 
+                                     NameAxisSequenceLength, 
+                                     NameAxisMaterial);
+  m_PdfPhotoAbsorptionProbabilityBad = MResponseMatrixO4("MC: Photo distance (bad)", 
+                                           AxisScatterProbability, 
+                                           AxisTotalEnergyDistances, 
+                                           AxisSequenceLength, 
+                                           AxisMaterial);
+  m_PdfPhotoAbsorptionProbabilityBad.SetAxisNames(NameAxisScatterProbability, 
+                                    NameAxisTotalEnergyDistances, 
+                                    NameAxisSequenceLength, 
+                                    NameAxisMaterial);
+
+
+  // CentralCompton:
+  
+  // Assymetries would be best handled if -1 .. 1
+  //vector<float> AxisDifferenceComptonScatterAngle = 
+  //  CreateLogDist(1E-3, 2, 18, 0.0000001, MaxCosineLimit);
+  vector<float> AxisDifferenceComptonScatterAngle; 
+  vector<float> A = CreateLogDist(0.003, 2, 14, c_NoBound, MaxCosineLimit);
+  for (unsigned int i = A.size()-1; i < A.size(); --i) {
+    AxisDifferenceComptonScatterAngle.push_back(-A[i]);
+  }
+  for (unsigned int i = 0; i < A.size(); ++i) {
+    AxisDifferenceComptonScatterAngle.push_back(A[i]);
+  }
+  MString NameAxisDifferenceComptonScatterAngle = "cos#varphi_{E} - cos#varphi_{G}";
+
+  vector<float> AxisComptonScatterAngle;
+  AxisComptonScatterAngle = CreateEquiDist(-1.4, 1.2, 13, -MaxCosineLimit, c_NoBound);
+  MString NameAxisComptonScatterAngle = NameAxisComptonScatterAngleStart;
+
+
+  vector<float> AxisDistance = CreateLogDist(0.2, 10, 7, 0.01, 100, 0, false);
+  MString NameAxisDistance = "Distance [cm]";
+
+  vector<float> AxisTotalEnergy = CreateLogDist(100, m_EnergyMaximum, 4, 1, 10000, 0, false);
+  //CreateLogDist(1, 10000, 1); //, 1, 10000, 0, false);
+  //mimp<<"No total energy bins!"<<show;
+  MString NameAxisTotalEnergy = "E_{tot} [keV]";
+
+  m_PdfComptonGood = MResponseMatrixO6("MC: Central (good)", 
+                                       AxisDifferenceComptonScatterAngle,
+                                       AxisComptonScatterAngle, 
+                                       AxisDistance,
+                                       AxisTotalEnergy,
+                                       AxisSequenceLength, 
+                                       AxisMaterial);
+  m_PdfComptonGood.SetAxisNames(NameAxisDifferenceComptonScatterAngle, 
+                                NameAxisComptonScatterAngle, 
+                                NameAxisDistance, 
+                                NameAxisTotalEnergy, 
+                                NameAxisSequenceLength, 
+                                NameAxisMaterial);
+  m_PdfComptonBad = MResponseMatrixO6("MC: Central (bad)", 
+                                      AxisDifferenceComptonScatterAngle, 
+                                      AxisComptonScatterAngle,
+                                      AxisDistance,
+                                      AxisTotalEnergy,
+                                      AxisSequenceLength, 
+                                      AxisMaterial);
+  m_PdfComptonBad.SetAxisNames(NameAxisDifferenceComptonScatterAngle, 
+                               NameAxisComptonScatterAngle, 
+                               NameAxisDistance, 
+                               NameAxisTotalEnergy, 
+                               NameAxisSequenceLength, 
+                               NameAxisMaterial);
+
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Save the responses
+bool MResponseMultipleComptonBayes::Save()
+{
+  MResponseBuilder::Save(); 
+
+  m_GoodBadTable.Write(GetFilePrefix() + ".goodbad" + m_Suffix, true);
+  
+  m_PdfDualGood.Write(GetFilePrefix() + ".dual.good" + m_Suffix, true);
+  m_PdfDualBad.Write(GetFilePrefix() + ".dual.bad" + m_Suffix, true);
+  
+  m_PdfStartGood.Write(GetFilePrefix() + ".start.good" + m_Suffix, true);
+  m_PdfStartBad.Write(GetFilePrefix() + ".start.bad" + m_Suffix, true);
+  
+  m_PdfTrackGood.Write(GetFilePrefix() + ".track.good" + m_Suffix, true);
+  m_PdfTrackBad.Write(GetFilePrefix() + ".track.bad" + m_Suffix, true);
+  
+  m_PdfComptonGood.Write(GetFilePrefix() + ".compton.good" + m_Suffix, true);
+  m_PdfComptonBad.Write(GetFilePrefix() + ".compton.bad" + m_Suffix, true);
+  
+  m_PdfComptonScatterProbabilityGood.Write(GetFilePrefix() + ".comptondistance.good" + m_Suffix, true);
+  m_PdfComptonScatterProbabilityBad.Write(GetFilePrefix() + ".comptondistance.bad" + m_Suffix, true);
+      
+  m_PdfPhotoAbsorptionProbabilityGood.Write(GetFilePrefix() + ".photodistance.good" + m_Suffix, true);
+  m_PdfPhotoAbsorptionProbabilityBad.Write(GetFilePrefix() + ".photodistance.bad" + m_Suffix, true);
+      
+  return true;
+}
+
+  
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Analyze the current event
+bool MResponseMultipleComptonBayes::Analyze()
+{ 
+  // Initlize next matching event, save if necessary
+  if (MResponseBuilder::Analyze() == false) return false;
+  
+  
+  //g_Verbosity = 1;
+  double Etot = 0;
+  double Eres = 0;
+ 
+  
+  for (auto RE: m_ReEvents) {
+    if (RE == nullptr) continue;
+    
+    if (RE->GetNRESEs() <= 1) {
+      mdebug<<"GeneratePdf: Not enough hits!"<<endl;
+      continue;
+    }
+    
+    if (RE->GetEnergy() < m_EnergyMinimum || RE->GetEnergy() > m_EnergyMaximum) {
+      mdebug<<"GeneratePdf: Energy out of bounds!"<<endl;
+      continue;
+    }
+
+    mdebug<<endl<<endl;
+    mdebug<<RE->ToString()<<endl;
+    
+    if (RE->GetStartPoint() == 0) continue;
+    
+    // Check if complete sequence is ok:
+    bool SequenceOk = true;
+    unsigned int SequenceLength = RE->GetNRESEs();
+    int PreviousPosition = 0;
+    
+    if (SequenceLength > m_MaxNInteractions) continue;
+    
+    if (SequenceLength == 2) {
+      // Look at start:
+      MRESEIterator Iter;
+      Iter.Start(RE->GetStartPoint());
+      Iter.GetNextRESE();
+      Etot = RE->GetEnergy();
+      Eres = RE->GetEnergyResolution();
+      
+      double CosPhiE = CalculateCosPhiE(*Iter.GetCurrent(), Etot);
+      double PhotoDistance = CalculateAbsorptionProbabilityTotal(*Iter.GetCurrent(), *Iter.GetNext(), Iter.GetNext()->GetEnergy());
+      
+      if (IsComptonStart(*Iter.GetCurrent(), Etot, Eres) == true) {
+        mdebug<<"--------> Found GOOD dual Compton event!"<<endl;
+        m_PdfDualGood.Add(Etot, CosPhiE, PhotoDistance, GetMaterial(*Iter.GetCurrent()));
+      } else {
+        mdebug<<"--------> Found bad dual Compton event!"<<endl;
+        m_PdfDualBad.Add(Etot, CosPhiE, PhotoDistance, GetMaterial(*Iter.GetCurrent()));
+        SequenceOk = false;
+      }
+    } else {
+      // Look at start:
+      MRESEIterator Iter;
+      Iter.Start(RE->GetStartPoint());
+      Iter.GetNextRESE();
+      Etot = RE->GetEnergy();
+      Eres = RE->GetEnergyResolution();
+      if (IsComptonStart(*Iter.GetCurrent(), Etot, Eres) == true) {
+        mdebug<<"--------> Found GOOD Compton start!"<<endl;
+        m_PdfStartGood.Add(Etot, CalculateCosPhiE(*Iter.GetCurrent(), Etot), SequenceLength, GetMaterial(*Iter.GetCurrent()));
+      } else {
+        mdebug<<"--------> Found bad Compton start!"<<endl;
+        m_PdfStartBad.Add(Etot, CalculateCosPhiE(*Iter.GetCurrent(), Etot), SequenceLength, GetMaterial(*Iter.GetCurrent()));
+        SequenceOk = false;
+      }
+      
+      // Track at start?
+      if (Iter.GetCurrent()->GetType() == MRESE::c_Track) {
+        double dAlpha = CalculateDCosAlpha(*((MRETrack*) Iter.GetCurrent()), *Iter.GetNext(), Etot);
+        double Alpha = CalculateCosAlphaG(*((MRETrack*) Iter.GetCurrent()), *Iter.GetNext(), Etot);
+        if (IsComptonTrack(*Iter.GetCurrent(), *Iter.GetNext(), PreviousPosition, Etot, Eres) == true) {
+          mdebug<<"--------> Found GOOD Track start!"<<endl;
+          m_PdfTrackGood.Add(dAlpha, Alpha, 1, Iter.GetCurrent()->GetEnergy(), SequenceLength, GetMaterial(*Iter.GetCurrent()));
+        } else {
+          mdebug<<"--------> Found bad Track start!"<<endl;
+          m_PdfTrackBad.Add(dAlpha, Alpha, 1, Iter.GetCurrent()->GetEnergy(), SequenceLength, GetMaterial(*Iter.GetCurrent()));
+          SequenceOk = false;
+        }
+      }
+      
+      
+      // Central part of the Compton track
+      Iter.GetNextRESE();
+      while (Iter.GetNext() != 0) {
+        // Add here
+        Etot -= Iter.GetPrevious()->GetEnergy();
+        Eres = sqrt(Eres*Eres - Iter.GetPrevious()->GetEnergyResolution()*Iter.GetPrevious()->GetEnergyResolution());
+        PreviousPosition++;
+        
+        // In the current implementation/simulation the hits have to be in increasing order...
+        if (m_DoAbsorptions == true && SequenceLength <= m_MaxAbsorptions) {
+          double ComptonDistance = 
+          CalculateAbsorptionProbabilityCompton(*Iter.GetPrevious(), *Iter.GetCurrent(), Etot);
+          mdebug<<"Dist C: "<<ComptonDistance<<": real:"<<(Iter.GetCurrent()->GetPosition() - Iter.GetPrevious()->GetPosition()).Mag()<<endl;
+          if (IsComptonSequence(*Iter.GetPrevious(), *Iter.GetCurrent(), PreviousPosition, Etot, Eres) == true) {
+            mdebug<<"--------> Found GOOD Distance sequence!"<<endl;
+            // Retrieve the data:
+            m_PdfComptonScatterProbabilityGood.Add(ComptonDistance, Etot, SequenceLength, GetMaterial(*Iter.GetCurrent()));
+          } else {
+            mdebug<<"--------> Found bad Distance sequence!"<<endl;
+            // Retrieve the data:
+            m_PdfComptonScatterProbabilityBad.Add(ComptonDistance, Etot, SequenceLength, GetMaterial(*Iter.GetCurrent()));
+            SequenceOk = false;
+          } // Add good / bad
+        }
+        
+        // Decide if it is good or bad...
+        // In the current implementation/simulation the hits have to be in increasing order...
+        double dPhi = CalculateDCosPhi(*Iter.GetPrevious(), *Iter.GetCurrent(), *Iter.GetNext(), Etot);
+        double PhiE = CalculateCosPhiE(*Iter.GetCurrent(), Etot);
+        double Lever = CalculateMinLeverArm(*Iter.GetPrevious(), *Iter.GetCurrent(), *Iter.GetNext());
+        int Material = GetMaterial(*Iter.GetCurrent());
+        
+        if (IsComptonSequence(*Iter.GetPrevious(), *Iter.GetCurrent(), *Iter.GetNext(), PreviousPosition, Etot, Eres) == true) {
+          mdebug<<"--------> Found GOOD internal Compton sequence!"<<endl;
+          // Retrieve the data:
+          m_PdfComptonGood.Add(dPhi, PhiE, Lever, Etot, SequenceLength, Material);
+          
+        } else {
+          mdebug<<"--------> Found bad internal Compton sequence!"<<endl;
+          // Retrieve the data:
+          m_PdfComptonBad.Add(dPhi, PhiE, Lever, Etot, SequenceLength, Material);
+          SequenceOk = false;
+        } // Add good / bad
+        
+        // Track at central?
+        if (Iter.GetCurrent()->GetType() == MRESE::c_Track) {
+          //MRETrack* T = (MRETrack*) Iter.GetCurrent();
+          double dAlpha = CalculateDCosAlpha(*((MRETrack*) Iter.GetCurrent()), *Iter.GetNext(), Etot);
+          double Alpha = CalculateCosAlphaG(*((MRETrack*) Iter.GetCurrent()), *Iter.GetNext(), Etot);
+          if (IsComptonTrack(*Iter.GetCurrent(), *Iter.GetNext(), PreviousPosition, Etot, Eres) == true) {
+            mdebug<<"--------> Found GOOD Track start (central)!"<<endl;
+            m_PdfTrackGood.Add(dAlpha, Alpha, 1, Iter.GetCurrent()->GetEnergy(), SequenceLength, GetMaterial(*Iter.GetCurrent()));
+          } else {
+            mdebug<<"--------> Found bad Track start (central)!"<<endl;
+            m_PdfTrackBad.Add(dAlpha, Alpha, 1, Iter.GetCurrent()->GetEnergy(), SequenceLength, GetMaterial(*Iter.GetCurrent()));
+            SequenceOk = false;
+          }
+        }
+        Iter.GetNextRESE();
+      }
+      
+      Etot -= Iter.GetPrevious()->GetEnergy();
+      Eres = sqrt(Eres*Eres - Iter.GetPrevious()->GetEnergyResolution()*Iter.GetPrevious()->GetEnergyResolution());
+      PreviousPosition++;
+      
+      // Decide if it is good or bad...
+      // In the current implementation/simulation the hits have to be in increasing order...
+      if (m_DoAbsorptions == true && SequenceLength <= m_MaxAbsorptions) {
+        double LastDistance = CalculateAbsorptionProbabilityPhoto(*Iter.GetPrevious(), *Iter.GetCurrent(), Etot);
+        mdebug<<"Dist P: "<<LastDistance<<": real:"<<(Iter.GetCurrent()->GetPosition() - Iter.GetPrevious()->GetPosition()).Mag()<<endl;
+        if (IsComptonSequence(*Iter.GetPrevious(), *Iter.GetCurrent(), PreviousPosition, Etot, Eres) == true) {
+          mdebug<<"--------> Found GOOD Lastdistance sequence!"<<endl;
+          // Retrieve the data:
+          m_PdfPhotoAbsorptionProbabilityGood.Add(CalculateAbsorptionProbabilityPhoto(*Iter.GetPrevious(), *Iter.GetCurrent(), Etot), 
+                                                  Etot, SequenceLength, GetMaterial(*Iter.GetCurrent()));
+        } else {
+          mdebug<<"--------> Found bad Lastdistance sequence!"<<endl;
+          // Retrieve the data:
+          m_PdfPhotoAbsorptionProbabilityBad.Add(CalculateAbsorptionProbabilityPhoto(*Iter.GetPrevious(), *Iter.GetCurrent(), Etot), 
+                                                 Etot, SequenceLength, GetMaterial(*Iter.GetCurrent()));
+          SequenceOk = false;
+        } // Add good / bad
+      }
+    }
+    
+    if (SequenceOk == false) {
+      m_GoodBadTable.Add(0.5, SequenceLength, 1);
+      //mdebug<<"No good sequence exists"<<endl<<endl<<endl<<endl;
+    } else {
+      m_GoodBadTable.Add(1.5, SequenceLength, 1);
+      mdebug<<"One good sequence exists"<<endl<<endl<<endl<<endl;
+    }
+  } // For each raw event...
+  
+  
+  return true;
+}
+
+  
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Finalize the response generation (i.e. save the data a final time )
+bool MResponseMultipleComptonBayes::Finalize()
+{ 
+  return MResponseBuilder::Finalize(); 
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MResponseMultipleComptonBayes::IsComptonTrack(MRESE& Start, MRESE& Center,
+                                       int PreviousPosition, double Etot, double Eres)
+{
+  // A good start point of the track consists of the following:
+  // (1) Start is a track
+  // (2) Start is only one Compton interaction
+  // (3) One of Centers Compton interactions directly follows the IA of start
+  // (4) The first hit of start is the first hit of the track
+  //     The second hit of start is the second hit of the track
+
+  mdebug<<"IsComptonTrack: Looking at: "<<Start.GetID()<<"("<<Etot<<")"<<endl;
+
+  // (1) 
+  if (Start.GetType() != MRESE::c_Track) {
+    mdebug<<"IsComptonTrack: No track!"<<endl;
+    return false;    
+  }
+
+  // (2)
+  if (IsSingleCompton(Start) == false) {
+    mdebug<<"IsComptonTrack: Start has multiple Comptons!"<<endl;
+    return false;        
+  }
+
+  // (3)
+  if (IsComptonSequence(Start, Center, PreviousPosition, Etot-Start.GetEnergy(), Eres) == false) {
+    // Attention: Eres is a little to large...
+    mdebug<<"IsComptonTrack: No Compton sequence!"<<endl;
+    return false;        
+  }
+
+  // (4)
+  MRESEIterator Iter;
+  MRETrack* Track = (MRETrack*) &Start;
+  Iter.Start(Track->GetStartPoint());
+  Iter.GetNextRESE();
+  if (IsTrackStart(*Iter.GetCurrent(), *Iter.GetNext(), Track->GetEnergy()) == false) {
+    mdebug<<"IsComptonTrack: Track is wrong!"<<endl;
+    return false;    
+  }
+    
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MResponseMultipleComptonBayes::IsTrackStart(MRESE& Start, MRESE& Central, double Energy)
+{
+  // According to the current simulation (GMega), the RESEs are in sequence if
+  // (1) the IDs of their hits are in increasing order without holes
+  // (2) all originate from the same IA
+  // (3) The start condition is fullfilled, when the start hit has the lowest 
+  //     time-tag of all hits with this origin
+
+  const int IdOffset = 2;
+
+  vector<int> StartIds = GetReseIds(&Start);
+  vector<int> CentralIds = GetReseIds(&Central);
+  if (StartIds.size() == 0) return false;
+  if (CentralIds.size() == 0) return false;
+
+
+  // Test (1)
+  if (AreIdsInSequence(StartIds) == false) {
+    mdebug<<"   Is track start: Start IDs not in sequence"<<endl;
+    return false;
+  }
+  if (AreIdsInSequence(CentralIds) == false) {
+    mdebug<<"Is track Start: Central IDs not in sequence"<<endl;
+    return false;
+  }
+
+  // Test for holes:
+  // The hit after the last one from start is the first from central:
+  double TimeLastFirst = m_SiEvent->GetHTAt(StartIds.back()-IdOffset)->GetTime();
+  double TimeFirstLast = m_SiEvent->GetHTAt(CentralIds.front()-IdOffset)->GetTime();
+  for (unsigned int h = 0; h < m_SiEvent->GetNHTs(); ++h) {
+    if (m_SiEvent->GetHTAt(h)->GetTime() > TimeLastFirst && 
+        m_SiEvent->GetHTAt(h)->GetTime() < TimeFirstLast) {
+      mdebug<<"   Is track start: Hit between first and central according to time: "
+            <<h<<endl;
+      mdebug<<"LF: "<<TimeLastFirst<<" FL: "<<TimeFirstLast<<endl;
+      return false;      
+    }
+  } 
+
+
+//   if (abs(CentralIds[0] - StartIds[StartIds.size()-1]) != 1 && 
+//       abs(CentralIds[CentralIds.size()-1] - StartIds[0]) != 1) {
+//     mdebug<<"   Is track start: Distance not equal 1: "
+//           <<abs(CentralIds[0] - StartIds[StartIds.size()-1])<<", "
+//           <<abs(CentralIds[CentralIds.size()-1] - StartIds[0])<<endl;
+//     return false;
+//   }
+  
+  // Test (2)
+  int CommonOrigin = -1;
+  for (unsigned int i = 0; i < StartIds.size(); ++i) {
+    for (unsigned int j = 0; j < CentralIds.size(); ++j) {
+      for (unsigned int oi = 0; oi < m_SiEvent->GetHTAt(StartIds[i]-IdOffset)->GetNOrigins(); ++oi) {
+        for (unsigned int oj = 0; oj < m_SiEvent->GetHTAt(CentralIds[j]-IdOffset)->GetNOrigins(); ++oj) {
+          if (m_SiEvent->GetHTAt(StartIds[i]-IdOffset)->GetOriginAt(oi) == 
+              m_SiEvent->GetHTAt(CentralIds[j]-IdOffset)->GetOriginAt(oj)) {
+            CommonOrigin = m_SiEvent->GetHTAt(CentralIds[j]-IdOffset)->GetOriginAt(oj);
+            break;
+          }
+        }
+      }
+    }
+  }
+
+  if (CommonOrigin == -1) {
+    mdebug<<"   Is track start: No common origin!"<<endl;
+    return false;
+  }
+
+  // Test (3)
+  double Timing = numeric_limits<double>::max();
+  for (unsigned int i = 0; i < StartIds.size(); ++i) {
+    if (m_SiEvent->GetHTAt(StartIds[i]-IdOffset)->GetTime() < Timing) {
+      Timing = m_SiEvent->GetHTAt(StartIds[i]-IdOffset)->GetTime();
+    }
+  }
+  unsigned int i_max = m_SiEvent->GetNHTs();
+  for (unsigned int i = 0; i < i_max; ++i) {
+    if (m_SiEvent->GetHTAt(i)->IsOrigin(CommonOrigin)) {
+      if (m_SiEvent->GetHTAt(i)->GetTime() < Timing) {
+        mdebug<<"   Is track start: Not first hit (timing)"<<endl;
+        return false;
+      }
+    }
+  }
+
+  if (Energy > 0) {
+    if (IsTrackCompletelyAbsorbed(StartIds, Energy) == false) {
+      mdebug<<"   Is track start: Not completely absorbed"<<endl;
+      return false;
+    }
+  }
+
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MResponseMultipleComptonBayes::IsTrackStop(MRESE& Central,
+                                           MRESE& Stop, double Energy)
+{
+  // According to the current simulation (GMega), the RESEs are in sequence if
+  // (1) the IDs of their hits are in increasing order without holes
+  // (2) all originate from the same IA (espec. the first and last hit in the 
+  //     sequence)
+  // (3) The start condition is fullfilled, when the start hit has the highest 
+  //     time-tag of all hits with this origin
+
+  const int IdOffset = 2;
+
+  vector<int> CentralIds = GetReseIds(&Central);
+  vector<int> StopIds = GetReseIds(&Stop);
+  
+  // Test (1)
+  if (AreIdsInSequence(CentralIds) == false) {
+    mdebug<<"   IsStop: Central IDs not in sequence"<<endl;
+    return false;
+  }
+  if (AreIdsInSequence(StopIds) == false) {
+    mdebug<<"   IsStop: Stop IDs not in sequence"<<endl;
+    return false;
+  }
+  // Test for holes:
+  // The hit after the last one from start is the first from central:
+  double TimeLastFirst = m_SiEvent->GetHTAt(CentralIds.back()-IdOffset)->GetTime();
+  double TimeFirstLast = m_SiEvent->GetHTAt(StopIds.front()-IdOffset)->GetTime();
+  for (unsigned int h = 0; h < m_SiEvent->GetNHTs(); ++h) {
+    if (m_SiEvent->GetHTAt(h)->GetTime() > TimeLastFirst && 
+        m_SiEvent->GetHTAt(h)->GetTime() < TimeFirstLast) {
+      mdebug<<"   IsStop: Hit between first and central according to time!"<<endl;
+      return false;      
+    }
+  } 
+//   if (abs(StopIds[0] - CentralIds[CentralIds.size()-1]) != 1 && 
+//       abs(StopIds[StopIds.size()-1] - CentralIds[0]) != 1) {
+//     mdebug<<"   IsStop: Distance not equal 1"<<endl;
+//     return false;
+//   }
+
+
+  // Test (2)
+  int CommonOrigin = -1;
+  for (unsigned int i = 0; i < CentralIds.size(); ++i) {
+    for (unsigned int j = 0; j < StopIds.size(); ++j) {
+      for (unsigned int oi = 0; oi < m_SiEvent->GetHTAt(CentralIds[i]-IdOffset)->GetNOrigins(); ++oi) {
+        for (unsigned int oj = 0; oj < m_SiEvent->GetHTAt(StopIds[j]-IdOffset)->GetNOrigins(); ++oj) {
+          if (m_SiEvent->GetHTAt(CentralIds[i]-IdOffset)->GetOriginAt(oi) == 
+              m_SiEvent->GetHTAt(StopIds[j]-IdOffset)->GetOriginAt(oj)) {
+            CommonOrigin = m_SiEvent->GetHTAt(StopIds[j]-IdOffset)->GetOriginAt(oj);
+            break;
+          }
+        }
+      }
+    }
+  }
+
+  if (CommonOrigin == -1) {
+    mdebug<<"   IsStop: No common origin!"<<endl;
+    return false;
+  }
+
+  // Test (3)
+  double Timing = -numeric_limits<double>::max();
+  for (unsigned int i = 0; i < StopIds.size(); ++i) {
+    if (m_SiEvent->GetHTAt(StopIds[i]-IdOffset)->GetTime() > Timing) {
+      Timing = m_SiEvent->GetHTAt(StopIds[i]-IdOffset)->GetTime();
+    }
+  }
+  unsigned int i_max = m_SiEvent->GetNHTs();
+  for (unsigned int i = 0; i < i_max; ++i) {
+    if (m_SiEvent->GetHTAt(i)->IsOrigin(CommonOrigin)) {
+      if (m_SiEvent->GetHTAt(i)->GetTime() > Timing) {
+        mdebug<<"   IsStop: Not last hit (timing)"<<endl;
+        return false;
+      }
+    }
+  }
+
+  if (IsTrackCompletelyAbsorbed(StopIds, Energy) == false) {
+    mdebug<<"   Is track stop: Not completely absorbed"<<endl;
+    return false;
+  }
+
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MResponseMultipleComptonBayes::AreReseInSequence(MRESE& Start,
+                                                 MRESE& Central, 
+                                                 MRESE& Stop, 
+                                                 double Energy)
+{
+  // Return true if the given RESEs are in sequence
+  //
+  // According to the current simulation (GMega), the RESEs are in sequence if
+  // (1) the IDs of their hits are in increasing order without holes
+  // (2) all originate from the same IA (espec. the first and last hit in the 
+  //     sequence)
+
+  const int IdOffset = 2;
+
+  vector<int> StartIds = GetReseIds(&Start);
+  vector<int> CentralIds = GetReseIds(&Central);
+  vector<int> StopIds = GetReseIds(&Stop);
+  
+  // Test (1)
+  if (AreIdsInSequence(StartIds) == false) {
+    mdebug<<"   IsCentral: Start IDs not in sequence"<<endl;
+    return false;
+  }
+  if (AreIdsInSequence(CentralIds) == false) {
+    mdebug<<"   IsCentral: Central IDs not in sequence"<<endl;
+    return false;
+  }
+  if (AreIdsInSequence(StopIds) == false) {
+    mdebug<<"   IsCentral: Stop IDs not in sequence"<<endl;
+    return false;
+  }
+  // Test for holes:
+  // The hit after the last one from start is the first from central:
+  double TimeLastFirst = m_SiEvent->GetHTAt(StartIds.back()-IdOffset)->GetTime();
+  double TimeFirstLast = m_SiEvent->GetHTAt(CentralIds.front()-IdOffset)->GetTime();
+  for (unsigned int h = 0; h < m_SiEvent->GetNHTs(); ++h) {
+    if (m_SiEvent->GetHTAt(h)->GetTime() > TimeLastFirst && 
+        m_SiEvent->GetHTAt(h)->GetTime() < TimeFirstLast) {
+      mdebug<<"   IsCentral: Hit between first and central according to time!"<<endl;
+      return false;      
+    }
+  } 
+  TimeLastFirst = m_SiEvent->GetHTAt(CentralIds.back()-IdOffset)->GetTime();
+  TimeFirstLast = m_SiEvent->GetHTAt(StopIds.front()-IdOffset)->GetTime();
+  for (unsigned int h = 0; h < m_SiEvent->GetNHTs(); ++h) {
+    if (m_SiEvent->GetHTAt(h)->GetTime() > TimeLastFirst && 
+        m_SiEvent->GetHTAt(h)->GetTime() < TimeFirstLast) {
+      mdebug<<"   IsCentral: Hit between first and central according to time!"<<endl;
+      return false;      
+    }
+  } 
+
+
+  // Test (2)
+  int CommonOrigin = -1;
+  for (unsigned int i = 0; i < StartIds.size(); ++i) {
+    for (unsigned int j = 0; j < CentralIds.size(); ++j) {
+      for (unsigned int k = 0; k < StopIds.size(); ++k) {
+        for (unsigned int oi = 0; oi < m_SiEvent->GetHTAt(StartIds[i]-IdOffset)->GetNOrigins(); ++oi) {
+          for (unsigned int oj = 0; oj < m_SiEvent->GetHTAt(CentralIds[j]-IdOffset)->GetNOrigins(); ++oj) {
+            for (unsigned int ok = 0; ok < m_SiEvent->GetHTAt(StopIds[k]-IdOffset)->GetNOrigins(); ++ok) {
+              if (m_SiEvent->GetHTAt(StartIds[i]-IdOffset)->GetOriginAt(oi) == 
+                  m_SiEvent->GetHTAt(CentralIds[j]-IdOffset)->GetOriginAt(oj) && 
+                  m_SiEvent->GetHTAt(StartIds[i]-IdOffset)->GetOriginAt(oi) == 
+                  m_SiEvent->GetHTAt(StopIds[k]-IdOffset)->GetOriginAt(ok)) {
+                CommonOrigin = m_SiEvent->GetHTAt(CentralIds[j]-IdOffset)->GetOriginAt(oj);
+                break;
+              }
+            }
+          }
+        }
+      }
+    }
+  }
+  if (CommonOrigin == -1) {
+    mdebug<<"   IsCentral: No common origin!"<<endl;
+    return false;
+  }
+
+  // (3) Timing:
+  if (m_SiEvent->GetHTAt(StartIds[0]-IdOffset)->GetTime() > 
+      m_SiEvent->GetHTAt(CentralIds[0]-IdOffset)->GetTime() ||
+      m_SiEvent->GetHTAt(CentralIds[0]-IdOffset)->GetTime() >
+      m_SiEvent->GetHTAt(StopIds[0]-IdOffset)->GetTime()) {
+    mdebug<<"   IsCentral: Timing wrong"<<endl;
+    return false;
+  }
+
+
+  if (IsTrackCompletelyAbsorbed(CentralIds, Energy) == false) {
+    mdebug<<"   IsCentral: Not completely absorbed"<<endl;
+    return false;
+  }
+
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MResponseMultipleComptonBayes::IsComptonStart(MRESE& Start, double Etot, double Eres)
+{
+  // Return true if the given RESEs are in sequence
+  //
+  // A good start point for tripple Comptons requires:
+  // (1) An absorption better than 3 sigma energy resolution + 2 keV for the fuirst hitr and the while sequence...
+  // (2) The origin is or produced a photon
+  // (3) We have exactly one Compton interaction and maybe some other, secondary interaction
+
+  if (g_Verbosity >= c_Chatty) mout<<"IsComptonStart: Looking at: "<<Start.GetID()<<endl;
+
+
+  // Get the origin IDs of the RESEs
+  vector<int> StartOriginIds = GetOriginIds(&Start);
+  if (StartOriginIds.size() == 0) {
+    if (g_Verbosity >= c_Chatty) mout<<"IsComptonStart: Start has no Sim IDs!"<<endl;
+    return false;
+  }
+  
+  // Find the smallest origin ID in the sequence
+  int SmallestOriginID = numeric_limits<int>::max();
+  for (unsigned int i = 0; i < StartOriginIds.size(); ++i) {
+    if (StartOriginIds[i] < SmallestOriginID) SmallestOriginID = StartOriginIds[i];
+  }
+  
+  // Find the real Origin
+  int TrueOrigin = m_SiEvent->GetIAAt(SmallestOriginID-1)->GetOriginID();
+  
+  // Test (1) - Absorption:
+  if (Etot > 0) {
+    // First hit
+    if (IsAbsorbed(StartOriginIds, Start.GetEnergy(), Start.GetEnergyResolution()) == false) {
+      if (g_Verbosity >= c_Chatty) mout<<"IsComptonStart: IA not completely absorbed!"<<endl;
+      return false;
+    }
+    // Full sequence
+    if (IsTotalAbsorbed(StartOriginIds, Etot, Eres) == false) {
+      if (g_Verbosity >= c_Chatty) mout<<"IsComptonStart: Not completely absorbed!"<<endl;
+      return false;
+    }
+  }
+  
+  // Test (2) - the start IA must be a photon (and create nothing) or be anything and create a photon
+  MSimIA* OriginIA = m_SiEvent->GetIAAt(m_SiEvent->GetIAAt(SmallestOriginID-1)->GetOriginID()-1);
+  if (OriginIA->GetSecondaryParticleID() == 1 || // create photon
+     (OriginIA->GetSecondaryParticleID() == 0 && OriginIA->GetMotherParticleID() == 1)) { // create nothing and be a photon
+    // good...
+  } else {
+    // Only photons can be good...
+    if (g_Verbosity >= c_Chatty) mout<<"IsComptonStart: IA which triggered first RESE did not create a photon or is not photon and create nothing"<<endl;
+    return false;
+  }
+  
+  // Check if the IA only contains Compton dependants
+  if (ContainsOnlyComptonDependants(StartOriginIds) == false) {
+    if (g_Verbosity >= c_Chatty) mout<<"IsComptonStart: Start contains not only Compton dependants"<<endl;
+    return false;
+  }
+  
+  // Check if we really have only one Compton interaction
+  if (NumberOfComptonInteractions(StartOriginIds, TrueOrigin) != 1) {
+    if (g_Verbosity >= c_Chatty) mout<<"IsComptonStart: Not exactly one Compton in interaction"<<endl;
+      return false;       
+  }
+  
+  if (g_Verbosity >= c_Chatty) mout<<"IsComptonStart: Passed!"<<endl;
+  
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+unsigned int MResponseMultipleComptonBayes::NumberOfComptonInteractions(vector<int> AllSimIds, int Origin)
+{
+  unsigned int N = 0;
+  
+  for (unsigned int i = 0; i < AllSimIds.size(); ++i) {
+    if (m_SiEvent->GetIAAt(AllSimIds[i]-1)->GetProcess() == "COMP" && m_SiEvent->GetIAAt(AllSimIds[i]-1)->GetOriginID() == Origin)  {
+      ++N;
+    }
+  }
+  
+  return N;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MResponseMultipleComptonBayes::IsComptonSequence(MRESE& Start, MRESE& Central,
+                                          int StartPosition, double Etot, 
+                                          double Eres)
+{
+  // Return true if the given RESEs are in sequence
+  //
+  // A good start point for double Comptons requires:
+  // (1) An absorption better than 99%
+  // (2) the IDs of their hits are in increasing order without holes
+  // (3) Start is the StartPosition's Compton IA
+
+  mdebug<<"IsComptonSequence2: Looking at: "<<Start.GetID()<<" - "<<Central.GetID()<<endl;
+
+
+  // Test (2)
+  //vector<int> StartIds = GetReseIds(Start);
+  vector<int> StartOriginIds = GetOriginIds(&Start);
+  if (StartOriginIds.size() == 0) {
+    mdebug<<"IsComptonSequence2: Start has no Sim IDs!"<<endl;
+    return false;
+  }
+  
+  //vector<int> CentralIds = GetReseIds(Central);
+  vector<int> CentralOriginIds = GetOriginIds(&Central);
+  if (CentralOriginIds.size() == 0) {
+    mdebug<<"IsComptonSequence2: Central has no Sim IDs!"<<endl;
+    return false;
+  }
+  
+
+  if (ContainsOnlyComptonDependants(CentralOriginIds) == false) {
+    mdebug<<"IsComptonSequence2: Central contains not only Compton dependants"<<endl;
+    return false;
+  }
+  if (AreInComptonSequence(StartOriginIds, CentralOriginIds, StartPosition) == false) {
+    mdebug<<"IsComptonSequence2: Not in Compton sequence!"<<endl;
+    return false;
+  }
+
+  if (Etot > 0) {
+    if (IsTotalAbsorbed(CentralOriginIds, Etot, Eres) == false) {
+      mdebug<<"IsComptonSequence2: Not completely absorbed!"<<endl;
+      return false;
+    }
+  }
+
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MResponseMultipleComptonBayes::IsComptonSequence(MRESE& Start, MRESE& Central,
+                                          MRESE& Stop, int StartPosition, 
+                                          double Etot, double Eres)
+{
+  // Return true if the given RESEs are in sequence
+
+  // A good start point for tripple Comptons requires:
+  // (1) An absorption better than 98%
+  // (2) the IDs of their hits are in increasing order without holes
+
+  mdebug<<"IsComptonSequence3: Looking at: "
+        <<Start.GetID()<<" - "<<Central.GetID()<<" - "<<Stop.GetID()<<endl;
+
+
+  // Test (2)
+  //vector<int> StartIds = GetReseIds(Start);
+  vector<int> StartOriginIds = GetOriginIds(&Start);
+  if (StartOriginIds.size() == 0) {
+    mdebug<<"IsComptonSequence3: Start has no Sim IDs!"<<endl;
+    return false;
+  }
+  
+//   // Absorption:
+//   if (IsAbsorbed(StartOriginIds, Start.GetEnergy()) == false) {
+//     mdebug<<"IsComptonSequence3: Start not completely absorbed!"<<endl;
+//     return false;
+//   }
+  
+  //vector<int> CentralIds = GetReseIds(Central);
+  vector<int> CentralOriginIds = GetOriginIds(&Central);
+  if (CentralOriginIds.size() == 0) {
+    mdebug<<"IsComptonSequence3: Central has no Sim IDs!"<<endl;
+    return false;
+  }
+  
+  // Absorption:
+  if (IsAbsorbed(CentralOriginIds, Central.GetEnergy(), Central.GetEnergyResolution()) == false) {
+    mdebug<<"IsComptonSequence3: Central not completely absorbed!"<<endl;
+    return false;
+  }
+  
+  //vector<int> StopIds = GetReseIds(Stop);
+  vector<int> StopOriginIds = GetOriginIds(&Stop);
+  if (StopOriginIds.size() == 0) {
+    mdebug<<"IsComptonSequence3: Stop has no Sim IDs!"<<endl;
+    return false;
+  }
+  
+//   // Absorption:
+//   if (IsAbsorbed(StopOriginIds, Stop.GetEnergy()) == false) {
+//     mdebug<<"IsComptonSequence3: Stop not completely absorbed!"<<endl;
+//     return false;
+//   }
+  
+  //cout<<"Cont only Start!"<<endl;
+//   if (ContainsOnlyComptonDependants(StartOriginIds) == false) {
+//     mdebug<<"IsComptonSequence3: Start contains not only Compton dependants"<<endl;
+//     return false;
+//   }
+  //cout<<"Cont only Central!"<<endl;
+  if (ContainsOnlyComptonDependants(CentralOriginIds) == false) {
+    mdebug<<"IsComptonSequence3: Central contains not only Compton dependants"<<endl;
+    return false;
+  }
+  if (ContainsOnlyComptonDependants(StopOriginIds) == false) {
+    mdebug<<"IsComptonSequence3: Stop contains not only Compton dependants"<<endl;
+    return false;
+  }
+  if (AreInComptonSequence(StartOriginIds, CentralOriginIds, StartPosition) == false) {
+    mdebug<<"IsComptonSequence3: Not in Compton sequence!"<<endl;
+    return false;
+  }
+  if (AreInComptonSequence(CentralOriginIds, StopOriginIds, 0) == false) {
+    mdebug<<"IsComptonSequence3: Not in Compton sequence!"<<endl;
+    return false;
+  }
+
+  if (IsTotalAbsorbed(CentralOriginIds, Etot, Eres) == false) {
+    mdebug<<"IsComptonSequence3: Not completely absorbed!"<<endl;
+    return false;
+  }
+
+  bool FoundBehind = false;
+  for (unsigned int i = 0; i < StartOriginIds.size(); ++i) {
+    if (StopOriginIds[0] - StartOriginIds[i] == 2) {
+      FoundBehind = true;
+    }
+  }
+  if (FoundBehind == false) {
+    mdebug<<"IsComptonSequence3: More than one Compton between start and stop!"<<endl;
+    return false;
+  }
+
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MResponseMultipleComptonBayes::IsComptonEnd(MRESE& End)
+{
+  // A good start point for tripple Comptons requires:
+  // (1) An absorption better than 98%
+  // (2) the IDs of their hits are in increasing order without holes
+  // (3) We have one Compton interaction and some other interaction
+  // (4) The origin is only the first Compton interaction
+
+  mdebug<<"IsComptonEnd: Looking at: "<<End.GetID()<<endl;
+
+
+
+  // Test (2)
+//   vector<int> CentralIds = GetReseIds(Central);
+//   vector<int> CentralOriginIds = GetOriginIds(CentralIds);
+//   if (CentralOriginIds.size() == 0) {
+//     mdebug<<"IsComptonEnd: Central has no Sim IDs!"<<endl;
+//     return false;
+//   }
+  
+  //vector<int> EndIds = GetReseIds(End);
+  vector<int> EndOriginIds = GetOriginIds(&End);
+  if (EndOriginIds.size() == 0) {
+    mdebug<<"IsComptonEnd: End has no Sim IDs!"<<endl;
+    return false;
+  }
+  
+  // Absorption:
+  if (IsTotalAbsorbed(EndOriginIds, End.GetEnergy(), End.GetEnergyResolution()) == false) {
+    mdebug<<"IsComptonEnd: Not completely absorbed!"<<endl;
+    return false;
+  }
+
+//   if (ContainsOnlyComptonDependants(CentralOriginIds) == false) {
+//     mdebug<<"IsComptonEnd: Central contains not only Compton dependants"<<endl;
+//     return false;
+//   }
+  if (ContainsOnlyComptonDependants(EndOriginIds) == false) {
+    mdebug<<"IsComptonEnd: End contains not only Compton dependants"<<endl;
+    return false;
+  }
+//   if (AreInComptonSequence(CentralOriginIds, EndOriginIds) == false) {
+//     mdebug<<"IsComptonEnd: Not in Compton sequence!"<<endl;
+//     return false;
+//   }
+  
+  // Test (3)
+  if (m_SiEvent->GetNIAs() < 3) { 
+    mdebug<<"IsComptonEnd: Not enough interactions!"<<endl;
+    return false;    
+  }
+  
+//   // Test (4)
+//   // End needs to contain the last interaction of track 1 
+//   int LastIA = 0;
+//   for (unsigned int i = 1; i < m_SiEvent->GetNIAs(); ++i) {
+//     if (m_SiEvent->GetIAAt(i)->GetOriginID() == 1) {
+//       LastIA = i+1;
+//     } else {     
+//       break;
+//     }
+//   }
+//   bool FoundLastIA = false;
+//   for (unsigned int i = 0; i < EndOriginIds.size(); ++i) {
+//     if (EndOriginIds[i] == LastIA) {
+//       FoundLastIA = true;
+//       break;
+//     }
+//   }
+//   if (FoundLastIA == false) {
+//     mdebug<<"IsComptonEnd: Last interaction of track 1 not part of last hit"<<endl;
+//     return false;    
+//   }
+
+  // Motherparticle of smallest ID needs to be a photon:
+  int Smallest = EndOriginIds[0];
+  for (unsigned int i = 1; i < EndOriginIds.size(); ++i) {
+    if (EndOriginIds[i] < Smallest) Smallest = EndOriginIds[i];
+  }
+
+  if (m_SiEvent->GetIAAt(Smallest-1)->GetOriginID() == 0) {
+    if (m_SiEvent->GetIAAt(Smallest-1)->GetProcess() != "ANNI" &&
+        m_SiEvent->GetIAAt(Smallest-1)->GetProcess() != "INIT") {
+      return false;
+    }
+  } else {
+    if (m_SiEvent->GetIAAt(m_SiEvent->GetIAAt(Smallest-1)->GetOriginID()-1)->GetProcess() != "ANNI" &&
+        m_SiEvent->GetIAAt(m_SiEvent->GetIAAt(Smallest-1)->GetOriginID()-1)->GetProcess() != "INIT") {
+      return false;
+    }
+  }
+
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MResponseMultipleComptonBayes::IsSingleCompton(MRESE& Start)
+{
+  // Check if all interaction in start are from one single Compton interaction:
+
+  //cout<<Start.ToString()<<endl;
+
+  //vector<int> StartIds = GetReseIds(Start);
+  vector<int> StartOriginIds = GetOriginIds(&Start);
+  if (StartOriginIds.size() == 0) {
+    mdebug<<"IsSingleCompton: Start has no Sim IDs!"<<endl;
+    return false;
+  }
+
+  int NPhotos = 0;
+  int NComptons = 0;
+  for (unsigned int i = 0; i < StartOriginIds.size(); ++i) {
+    //cout<<"Id:"<<StartOriginIds[i]<<endl;
+    if (m_SiEvent->GetIAAt(StartOriginIds[i]-1)->GetProcess() == "COMP") {
+      NComptons++;
+    } else if (m_SiEvent->GetIAAt(StartOriginIds[i]-1)->GetProcess() == "PHOT") {
+      NPhotos++;
+    }
+  }
+
+  if (NComptons == 1 && NPhotos >= 0) {
+    mdebug<<"IsSingleCompton: Single Compton: C="<<NComptons<<" P="<<NPhotos<<endl;
+    return true;
+  } else if (NComptons == 0 && NPhotos >= 1) {
+    mdebug<<"IsSingleCompton: No Compton but photo: C="<<NComptons<<" P="<<NPhotos<<endl;
+    return true;
+  } else {
+    mdebug<<"IsSingleCompton: No single Compton or photo: C="<<NComptons<<" P="<<NPhotos<<endl;
+  }
+
+  return false;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MResponseMultipleComptonBayes::AreInComptonSequence(const vector<int>& StartOriginIds,
+                                                    const vector<int>& CentralOriginIds,
+                                                    int StartPosition)
+{
+  // They are in good sequence if 
+  //  (1) Both smallest IDs originate from 1
+  //  (2) The IDs are in sequence
+
+  massert(StartOriginIds.size() > 0);
+  massert(CentralOriginIds.size() > 0);
+  
+  if (m_SiEvent->GetIAAt(StartOriginIds[0]-1)->GetProcess() != "COMP") {
+    mdebug<<"CS: No COMP"<<endl;
+    return false;
+  }
+
+  if (m_SiEvent->GetIAAt(StartOriginIds[0]-1)->GetOriginID() != 
+      m_SiEvent->GetIAAt(CentralOriginIds[0]-1)->GetOriginID()) {
+    mdebug<<"CS: No common origin"<<endl;
+    return false;
+  }
+
+//   if (m_SiEvent->GetIAAt(StartOriginIds[0]-1)->GetMotherParticleNumber() != 1) {
+//     mdebug<<"CS: Mother is no photon: "<<m_SiEvent->GetIAAt(StartOriginIds[0]-1)->GetMotherParticleNumber()<<endl;
+//     return false;
+//   }
+
+  bool FoundBehind = false;
+  for (unsigned int i = 0; i < StartOriginIds.size(); ++i) {
+    //cout<<"testing: "<<CentralOriginIds[0]<<"-"<<StartOriginIds[i]<<endl;
+    if (CentralOriginIds[0] - StartOriginIds[i] == 1) {
+      FoundBehind = true;
+      break;
+    }
+  }
+  if (FoundBehind == false) {
+    mdebug<<"CS: Not behind each other!"<<endl;
+    return false;
+  }
+
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MResponseMultipleComptonBayes::ContainsOnlyComptonDependants(vector<int> AllSimIds)
+{
+  // We do two checks here, one down the tree and one up the tree
+  
+  // First check upwards: Is everything in there originating from somewhere else in there or is it an initial process (COMP, INIT, produced a photon)
+  for (unsigned int i = 0; i < AllSimIds.size(); ++i) {
+    int ID = AllSimIds[i];
+    int HighestOriginID = ID;
+    while (true) {
+      // Get new origin ID
+      ID = m_SiEvent->GetIAAt(ID-1)->GetOriginID();
+      // Check if included
+      for (unsigned int j = 0; j < AllSimIds.size(); ++j) {
+        if (i != j && ID == AllSimIds[j]) {
+          HighestOriginID = ID;
+          break;
+        }
+      }
+      
+      // Check if we are done
+      if (m_SiEvent->GetIAAt(ID-1)->GetProcess() == "INIT") break; // Compton dependents, remember?
+    }
+    
+    // We are good if the end point is a Compton scatter or a photo effect which is preceeded by a Compton in the list:
+    bool IsGood = false;
+    if (m_SiEvent->GetIAAt(HighestOriginID-1)->GetProcess() == "COMP") {
+      IsGood = true;
+    } else if (m_SiEvent->GetIAAt(HighestOriginID-1)->GetProcess() == "PHOT") {
+      int Predeccessor = HighestOriginID-1;
+      while (true) {
+        if (Predeccessor == 1) break; // we reached init
+        if (m_SiEvent->GetIAAt(Predeccessor-1)->GetOriginID() == m_SiEvent->GetIAAt(HighestOriginID-1)->GetOriginID()) {
+          if (m_SiEvent->GetIAAt(Predeccessor-1)->GetProcess() == "COMP") {
+            if (find(AllSimIds.begin(), AllSimIds.end(), Predeccessor) != AllSimIds.end()) {
+              IsGood = true;
+              break;
+            } else {
+              mdebug<<"ContainsOnlyComptonDependants: Preceeding Compton IA is missing"<<endl;
+              return false;
+            }
+          }
+        }
+        --Predeccessor;
+      }
+    }
+    if (IsGood == false) {
+      mdebug<<"ContainsOnlyComptonDependants: Hits other than dependants for ID="<<ID<<endl;
+      return false;
+    }
+  }
+
+  
+  // The second check is downward: Are all particles generated from this process contained?
+  for (unsigned int i = 0; i < AllSimIds.size(); ++i) {
+    vector<int> Descendents;
+    Descendents.push_back(AllSimIds[i]);
+    unsigned int Size = 1;
+    do {
+      Size = Descendents.size();
+      for (unsigned int j = 0; j < m_SiEvent->GetNIAs(); ++j) {
+        for (unsigned int d = 0; d < Descendents.size(); ++d) {
+          if (m_SiEvent->GetIAAt(j)->GetOriginID() == Descendents[d]) {
+            if (find(Descendents.begin(), Descendents.end(), j+1) != Descendents.end()) {
+              Descendents.push_back(j+1);
+            }
+          }
+        }
+      }
+    } while (Size < Descendents.size());
+    
+    // Now check if all are contianed:
+    for (unsigned int d = 0; d < Descendents.size(); ++d) {
+      if (m_SiEvent->GetIAAt(Descendents[d]-1)->GetSecondaryParticleID() != 0 && m_SiEvent->GetIAAt(Descendents[d]-1)->GetSecondaryParticleID() != 1) {
+        bool Found = false;
+        for (unsigned int i = 0; i < AllSimIds.size(); ++i) {
+          if (d == i) {
+            Found = true; 
+          }
+        }
+        if (Found == false) {
+          mdebug<<"ContainsOnlyComptonDependants: Originates but not contained: ID="<<d<<endl; 
+        }
+      }
+    }
+  }
+  
+  
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MResponseMultipleComptonBayes::IsAbsorbed(const vector<int>& AllSimIds,
+                                          double Energy, double EnergyResolution)
+{
+  // Rules:
+  // If a Compton scattering is included, the energy of the of the recoild electron plus any instant deposits, bremsstrahlug, etc. must be contained
+  // If a photo is included, the energy of the INCOMING gamma-ray must be contained
+  
+  EnergyResolution = 3.0*EnergyResolution + 2.0;
+  
+  double IdealEnergy = 0.0;
+  
+  vector<int> SimIDs = AllSimIds;
+  
+  // (1) First clean the IDs
+  vector<int> CleanedSimIDs;
+  // (a) If we have secondaries, remove them if the parent is contained
+  //     Or inverse, keep all IAs whose parents are not included
+  for (unsigned int i = 0; i < SimIDs.size(); ++i) {
+    bool Found = false;
+    for (unsigned int j = 0; j < SimIDs.size(); ++j) {
+      if (i != j) {
+        if (m_SiEvent->GetIAAt(SimIDs[i]-1)->GetOriginID() == SimIDs[j]) {
+          Found = true;
+          break;
+        }
+      }
+    }
+    if (Found == false) {
+      CleanedSimIDs.push_back(SimIDs[i]);
+    }
+  }
+  SimIDs = CleanedSimIDs;
+  CleanedSimIDs.clear();
+  
+  // (b) Keep only the smallest PHOT IA since we require it to be contained
+  for (unsigned int i = 0; i < SimIDs.size(); ++i) {
+    if (m_SiEvent->GetIAAt(SimIDs[i]-1)->GetProcess() == "PHOT") {
+      if (m_SiEvent->GetIAAt(SimIDs[i]-1)->GetOriginID() == m_SiEvent->GetIAAt(SimIDs[i]-2)->GetOriginID() && m_SiEvent->GetIAAt(SimIDs[i]-2)->GetProcess() != "PHOT") {
+        CleanedSimIDs.push_back(SimIDs[i]);
+      }
+    } else {
+      CleanedSimIDs.push_back(SimIDs[i]);
+    }
+  }
+  SimIDs = CleanedSimIDs;
+  CleanedSimIDs.clear();
+    
+  // (c) Exclude fluoresence COMP
+  for (unsigned int i = 0; i < SimIDs.size(); ++i) {
+    if (m_SiEvent->GetIAAt(SimIDs[i]-1)->GetProcess() == "COMP") {
+      if (m_SiEvent->GetIAAt(SimIDs[i]-1)->GetSecondaryParticleID() == 3) {
+        CleanedSimIDs.push_back(SimIDs[i]);
+      }
+    } else {
+      CleanedSimIDs.push_back(SimIDs[i]);
+    }
+  }
+  SimIDs = CleanedSimIDs;
+  CleanedSimIDs.clear();
+  
+  mdebug<<"SimIDs: "; for (int i: SimIDs) mdebug<<i<<" "; mdebug<<endl;
+  
+  // (d) Sanity check - we just should have COMP & PHOT in our list
+  for (unsigned int i = 0; i < SimIDs.size(); ++i) {
+    if (m_SiEvent->GetIAAt(SimIDs[i]-1)->GetProcess() != "COMP" && m_SiEvent->GetIAAt(SimIDs[i]-1)->GetProcess() != "PHOT") {
+      cout<<"Error: We only should have COMP and PHOT IA's at this point and not \""<<m_SiEvent->GetIAAt(SimIDs[i]-1)->GetProcess()<<"\". Did you use hadronic processes for the simulations?"<<endl;
+    }
+  }
+  
+  // (2) Now add the energies
+  for (unsigned int i = 0; i < SimIDs.size(); ++i) {
+    if (m_SiEvent->GetIAAt(SimIDs[i]-1)->GetProcess() == "COMP") {
+      if (m_SiEvent->GetIAAt(SimIDs[i]-2)->GetProcess() == "COMP" || m_SiEvent->GetIAAt(SimIDs[i]-2)->GetProcess() == "RAYL") {
+        mdebug<<"COMP with COMP/RAYL predeccessor: Adding mother difference energy: "<<m_SiEvent->GetIAAt(SimIDs[i]-2)->GetMotherEnergy() - m_SiEvent->GetIAAt(SimIDs[i]-1)->GetMotherEnergy()<<endl;
+        IdealEnergy += m_SiEvent->GetIAAt(SimIDs[i]-2)->GetMotherEnergy() - m_SiEvent->GetIAAt(SimIDs[i]-1)->GetMotherEnergy();
+      } else {
+        mdebug<<"COMP WITHOUT COMP/RAYL predeccessor: Adding secondary-mother difference energy: "<<m_SiEvent->GetIAAt(SimIDs[i]-2)->GetSecondaryEnergy() - m_SiEvent->GetIAAt(SimIDs[i]-1)->GetMotherEnergy()<<endl;
+        IdealEnergy += m_SiEvent->GetIAAt(SimIDs[i]-2)->GetSecondaryEnergy() - m_SiEvent->GetIAAt(SimIDs[i]-1)->GetMotherEnergy();
+      }
+    } else if (m_SiEvent->GetIAAt(SimIDs[i]-1)->GetProcess() == "PHOT") {
+      if (m_SiEvent->GetIAAt(SimIDs[i]-2)->GetProcess() == "COMP" || m_SiEvent->GetIAAt(SimIDs[i]-2)->GetProcess() == "RAYL") {
+        mdebug<<"PHOT with COMP/RAYL predeccessor: Adding mother energy: "<<m_SiEvent->GetIAAt(SimIDs[i]-2)->GetMotherEnergy()<<endl;
+        IdealEnergy += m_SiEvent->GetIAAt(SimIDs[i]-2)->GetMotherEnergy();
+      } else {
+        mdebug<<"PHOT withOUT COMP/RAYL predeccessor: Adding secondary energy: "<<m_SiEvent->GetIAAt(SimIDs[i]-2)->GetSecondaryEnergy()<<endl;
+        IdealEnergy += m_SiEvent->GetIAAt(SimIDs[i]-2)->GetSecondaryEnergy();
+      }      
+    } else {
+      cout<<"Error: We only should have COMP and PHOT IA's at this point. Did you use hadronic processes for the simulations?"<<endl;      
+    }
+  }
+  
+  // (3) Check for absorption
+  if (fabs(Energy - IdealEnergy) > EnergyResolution) {
+    mdebug<<"IsAbsorbed(): Not completely absorbed: ideal="<<IdealEnergy<<"  observed="<<Energy<<"  3*Eres+2="<<EnergyResolution<<endl;
+    return false;
+  } else {
+    mdebug<<"IsAbsorbed(): Completely absorbed: ideal="<<IdealEnergy<<" observed="<<Energy<<endl;
+  }
+  return true;  
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MResponseMultipleComptonBayes::IsTotalAbsorbed(const vector<int>& AllSimIds,
+                                               double Energy, double EnergyResolution)
+{
+  massert(AllSimIds.size() > 0);
+
+  EnergyResolution = 3*EnergyResolution+2;
+
+  int MinId = numeric_limits<int>::max();
+  for (unsigned int i = 0; i < AllSimIds.size(); ++i) {
+    if (MinId > AllSimIds[i] && AllSimIds[i] > 1) MinId = AllSimIds[i];
+  }
+
+  if (MinId == numeric_limits<int>::max()) return false;
+
+  double Ideal;
+  MSimIA* Top = 0;
+  if (m_SiEvent->GetIAAt(MinId-2)->GetOriginID() == m_SiEvent->GetIAAt(MinId-1)->GetOriginID()) {
+    Top = m_SiEvent->GetIAAt(MinId-2);
+  } else {
+    Top = m_SiEvent->GetIAAt(m_SiEvent->GetIAAt(MinId-1)->GetOriginID()-1);
+  }
+
+  if (m_SiEvent->GetIAAt(MinId-2)->GetProcess() == "COMP") {
+    Ideal = Top->GetMotherEnergy();
+  } else {
+    Ideal = Top->GetSecondaryEnergy();
+  }
+
+  if (MinId-2 != 0) {
+    Ideal = m_SiEvent->GetIAAt(MinId-2)->GetMotherEnergy();
+  } else {
+    Ideal = m_SiEvent->GetIAAt(MinId-2)->GetSecondaryEnergy();
+  }
+
+  if (fabs(Ideal - Energy) > EnergyResolution) {
+      mdebug<<"Is totally absorbed: Not completely absorbed: Tot abs: i="<<Ideal<<"  r="<<Energy<<"  3*Eres+2="<<EnergyResolution<<endl;
+    return false;
+  } else {
+    mdebug<<"Is totally absorbed: Completely absorbed: Tot abs: i="<<Ideal<<"  r="<<Energy<<"  3*Eres+2="<<EnergyResolution<<endl;
+  }
+//   if (fabs((Ideal - Energy)/Ideal) > m_MaxEnergyDifferencePercent &&
+//       fabs(Ideal - Energy) > m_MaxEnergyDifference ) {
+//       mdebug<<"Is totally absorbed: Not completely absorbed: Tot abs: i="<<Ideal<<" r="<<Energy<<endl;
+//     return false;
+//   }
+
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+double MResponseMultipleComptonBayes::GetIdealDepositedEnergy(int MinId)
+{
+  //  
+
+  double Ideal = 0;
+
+  MSimIA* Top = 0;
+  MSimIA* Bottom = 0;
+  if (m_SiEvent->GetIAAt(MinId-2)->GetOriginID() == m_SiEvent->GetIAAt(MinId-1)->GetOriginID()) {
+    Top = m_SiEvent->GetIAAt(MinId-2);
+    Bottom = m_SiEvent->GetIAAt(MinId-1);
+  } else {
+    Top = m_SiEvent->GetIAAt(m_SiEvent->GetIAAt(MinId-1)->GetOriginID()-1);
+    Bottom = m_SiEvent->GetIAAt(MinId-1);
+  }
+
+  if (m_SiEvent->GetIAAt(MinId-2)->GetProcess() == "COMP") {
+    Ideal = Top->GetMotherEnergy()-Bottom->GetMotherEnergy();
+  } else {
+    Ideal = Top->GetSecondaryEnergy()-Bottom->GetMotherEnergy();
+  }
+
+  return Ideal;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MResponseMultipleComptonBayes::IsTrackCompletelyAbsorbed(const vector<int>& Ids, double Energy)
+{
+  // Return true if the track is completely absorbed
+  //
+  // Prerequisites: Ids have only one common origin!
+  // Realization: Nothing originates from this ID AFTER this hit:
+
+  const int IdOffset = 2;
+
+  // Get origin Id
+  int Origin = -1;
+  for (unsigned int i = 0; i < Ids.size(); ++i) {
+    for (unsigned int oi = 0; oi < m_SiEvent->GetHTAt(Ids[i]-IdOffset)->GetNOrigins(); ++oi) {
+      if (m_SiEvent->GetHTAt(Ids[i]-IdOffset)->GetOriginAt(oi) != 1) { 
+        Origin = m_SiEvent->GetHTAt(Ids[i]-IdOffset)->GetOriginAt(oi);
+        break;
+      }
+    }
+  } 
+  if (Origin <= 1) {
+    mdebug<<"   IsTrackCompletelyAbsorbed: No origin"<<endl;
+    return false;
+  }
+
+//   // Check if we do haven an IA originating from this - which is not part of this track:
+//   for (unsigned int i = 0; i < m_SiEvent->GetNIAs(); ++i) {
+//     if (m_SiEvent->GetIAAt(i)->GetOriginID() == Origin) {
+//       if (m_SiEvent->GetIAAt(i)->GetProcess() == "BREM") {
+//         // Search the closest hit:
+//         int MinHT = -1;
+//         double MinDist = numeric_limits<double>::max();
+//         for (unsigned int h = 0; h < m_SiEvent->GetNHTs(); ++h) {
+//           if (m_SiEvent->GetHTAt(h)->IsOrigin(Origin) == true) {
+//             if ((m_SiEvent->GetIAAt(i)->GetPosition() - m_SiEvent->GetHTAt(h)->GetPosition()).Mag() < MinDist) {
+//               MinDist = (m_SiEvent->GetIAAt(i)->GetPosition() - m_SiEvent->GetHTAt(h)->GetPosition()).Mag();
+//               MinHT = h;
+//             }
+//           }
+//         }
+//         if (MinHT > 0) {
+//           if (m_SiEvent->GetHTAt(MinHT)->GetTime() >= m_SiEvent->GetHTAt(Ids[0]-IdOffset)->GetTime()) {
+//             mdebug<<"   IsTrackCompletelyAbsorbed: Bremsstrahlung emitted after this hit!"<<endl;
+//             return false;
+//           }
+//         }
+//       } else {
+//         mdebug<<"   IsTrackCompletelyAbsorbed: Originating interaction: "<<m_SiEvent->GetIAAt(i)->GetProcess()<<endl;
+//         return false;
+//       }
+//     }
+//   }
+
+  // Check for complete absorption:
+  const double EnergyLimitPercent = 0.15; // %
+  const double EnergyLimit = 20; //keV
+
+  double RealEnergy = 0;
+  for (unsigned int h = 0; h < m_SiEvent->GetNHTs(); ++h) {
+    if (m_SiEvent->GetHTAt(h)->IsOrigin(Origin) == true) {
+      if (m_SiEvent->GetHTAt(h)->GetTime() >= m_SiEvent->GetHTAt(Ids[0]-IdOffset)->GetTime()) {
+        RealEnergy += m_SiEvent->GetHTAt(h)->GetEnergy();
+      }
+    }
+  }
+  
+  if (fabs(Energy - RealEnergy) > EnergyLimit &&
+      fabs(Energy - RealEnergy)/RealEnergy > EnergyLimitPercent) {
+    mdebug<<"   IsTrackCompletelyAbsorbed: Missing/Not much energy: i="
+          <<RealEnergy<<" r="<<Energy<<endl;
+    return false;   
+  }
+
+
+  return  true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+double MResponseMultipleComptonBayes::CalculateMinLeverArm(MRESE& Start, MRESE& Central,
+                                               MRESE& Stop)
+{
+  return MERCSRBayesian::CalculateMinLeverArm(Start.GetPosition(),
+                                              Central.GetPosition(),
+                                              Stop.GetPosition());
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+double MResponseMultipleComptonBayes::CalculateDPhiInDegree(MRESE& Start, MRESE& Central,
+                                        MRESE& Stop, double Energy)
+{
+  return MERCSRBayesian::CalculateDPhiInDegree(&Start, &Central, &Stop, Energy);
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+double MResponseMultipleComptonBayes::CalculateDCosPhi(MRESE& Start, MRESE& Central,
+                                                  MRESE& Stop, double Energy)
+{
+  return MERCSRBayesian::CalculateDCosPhi(&Start, &Central, &Stop, Energy);
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+double MResponseMultipleComptonBayes::CalculateDCosAlpha(MRETrack& Track, MRESE& Central, double Energy)
+{
+  return MERCSRBayesian::CalculateDCosAlpha(&Track, &Central, Energy);
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+double MResponseMultipleComptonBayes::CalculateDAlphaInDegree(MRETrack& Track, MRESE& Central, double Energy)
+{
+  return MERCSRBayesian::CalculateDAlphaInDegree(&Track, &Central, Energy);
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+double MResponseMultipleComptonBayes::CalculateCosAlphaE(MRETrack& Track, MRESE& Central, double Energy)
+{
+  return MERCSRBayesian::CalculateCosAlphaE(&Track, &Central, Energy);
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+double MResponseMultipleComptonBayes::CalculateAlphaEInDegree(MRETrack& Track, MRESE& Central, double Energy)
+{
+  return MERCSRBayesian::CalculateAlphaEInDegree(&Track, &Central, Energy);
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+double MResponseMultipleComptonBayes::CalculateCosAlphaG(MRETrack& Track, MRESE& Central, double Energy)
+{
+  return MERCSRBayesian::CalculateCosAlphaG(&Track, &Central, Energy);
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+double MResponseMultipleComptonBayes::CalculateAlphaGInDegree(MRETrack& Track, MRESE& Central, double Energy)
+{
+  return MERCSRBayesian::CalculateAlphaGInDegree(&Track, &Central, Energy);
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+double MResponseMultipleComptonBayes::CalculateAbsorptionProbabilityPhoto(MRESE& Start,
+                                                                     MRESE& Stop, 
+                                                                     double Etot)
+{
+  double Probability = 
+    m_ReGeometry->GetPhotoAbsorptionProbability(Start.GetPosition(), 
+                                                Stop.GetPosition(), Etot); 
+
+  //cout<<"Probability: "<<Probability<<" E: "<<Etot<<endl;
+  //cout<<Start.GetPosition()<<":"<<Stop.GetPosition()<<":"<<(Stop.GetPosition()-Start.GetPosition()).Mag()<<endl;
+  return Probability;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+double MResponseMultipleComptonBayes::CalculateAbsorptionProbabilityTotal(MRESE& Start,
+                                                                     MRESE& Stop, 
+                                                                     double Etot)
+{
+  double Probability = 
+    m_ReGeometry->GetAbsorptionProbability(Start.GetPosition(), 
+                                           Stop.GetPosition(), Etot); 
+
+  //cout<<"Probability: "<<Probability<<" E: "<<Etot<<endl;
+  //cout<<Start.GetPosition()<<":"<<Stop.GetPosition()<<":"<<(Stop.GetPosition()-Start.GetPosition()).Mag()<<endl;
+  return Probability;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+double MResponseMultipleComptonBayes::CalculateAbsorptionProbabilityCompton(MRESE& Start,
+                                                                       MRESE& Stop, 
+                                                                       double Etot)
+{
+  double Distance = 
+    m_ReGeometry->GetComptonAbsorptionProbability(Start.GetPosition(), 
+                                                  Stop.GetPosition(), Etot); 
+
+  //cout<<"Distance: "<<Distance<<" E: "<<Etot<<endl;
+  //cout<<Start.ToString()<<endl;
+  //cout<<Stop.ToString()<<endl;
+  return Distance;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+double MResponseMultipleComptonBayes::CalculatePhiEInDegree(MRESE& Central, double Etot)
+{
+  return MERCSRBayesian::CalculatePhiEInDegree(&Central, Etot);
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+double MResponseMultipleComptonBayes::CalculatePhiGInDegree(MRESE& Start, MRESE& Central,
+                                                       MRESE& Stop)
+{
+  return MERCSRBayesian::CalculatePhiGInDegree(&Start, &Central, &Stop);
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+double MResponseMultipleComptonBayes::CalculateCosPhiG(MRESE& Start, MRESE& Central,
+                                                  MRESE& Stop)
+{
+  return MERCSRBayesian::CalculateCosPhiG(&Start, &Central, &Stop);
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+double MResponseMultipleComptonBayes::CalculateCosPhiE(MRESE& Central, double Etot)
+{
+  return MERCSRBayesian::CalculateCosPhiE(&Central, Etot);
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+int MResponseMultipleComptonBayes::GetMaterial(MRESE& Hit)
+{
+  return MERCSRBayesian::GetMaterial(&Hit);
+}
+
+
+// MResponseMultipleComptonBayes.cxx: the end...
+////////////////////////////////////////////////////////////////////////////////
diff --git a/src/response/src/MResponseMultipleComptonEventFile.cxx b/src/response/src/MResponseMultipleComptonEventFile.cxx
index 9b2e62479..e3755268f 100644
--- a/src/response/src/MResponseMultipleComptonEventFile.cxx
+++ b/src/response/src/MResponseMultipleComptonEventFile.cxx
@@ -68,6 +68,9 @@ MResponseMultipleComptonEventFile::MResponseMultipleComptonEventFile()
   m_MaxTrackEnergyDifference = 30; // keV
   m_MaxTrackEnergyDifferencePercent = 0.1;
   
+  m_EnergyMinimum = 100; // keV
+  m_EnergyMaximum = 10000; // keV
+
   // We can save much more frequently here, since the files are a lot smaller
   m_SaveAfter = numeric_limits<long>::max();
   
@@ -102,7 +105,9 @@ MString MResponseMultipleComptonEventFile::Options()
 {
   ostringstream out;
   out<<"             initial:   use the path to the initial IA (default: true)"<<endl;
-  
+  out<<"             emin:                  minimum energy (default: 100 keV)"<<endl;
+  out<<"             emax:                  maximum energy (default: 10000 keV)"<<endl;
+
   return MString(out);
 }
 
@@ -150,6 +155,10 @@ bool MResponseMultipleComptonEventFile::ParseOptions(const MString& Options)
       } else {
         mout<<"Error: Unrecognized value ("<<Value<<") for option "<<Value<<endl;
       }
+    } else if (Split2[i][0] == "emin") {
+      m_EnergyMinimum = stod(Value);
+    } else if (Split2[i][0] == "emax") {
+      m_EnergyMaximum = stod(Value);
     } else {
       mout<<"Error: Unrecognized option "<<Split2[i][0]<<endl;
       return false;
@@ -160,6 +169,8 @@ bool MResponseMultipleComptonEventFile::ParseOptions(const MString& Options)
   mout<<endl;
   mout<<"Choosen options for creating TMVA data files:"<<endl;
   mout<<"  Path to first IA:          "<<(m_UsePathToFirstIA == true ? "true" : "false")<<endl;
+  mout<<"  Minimum energy:            "<<m_EnergyMinimum<<endl;
+  mout<<"  Maximum energy:            "<<m_EnergyMaximum<<endl;
   mout<<endl;
   
   return true;
@@ -274,7 +285,12 @@ bool MResponseMultipleComptonEventFile::Analyze()
       mdebug<<"CreateResponse: Too many hits: "<<SequenceLength<<endl;
       continue;
     }
-    
+
+    if (RE->GetEnergy() < m_EnergyMinimum || RE->GetEnergy() > m_EnergyMaximum) {
+      mdebug<<"CreateResponse: Energy out of bounds!"<<endl;
+      continue;
+    }
+
     if (RE->GetRejectionReason() == MRERawEvent::c_RejectionTotalEnergyOutOfLimits ||
         RE->GetRejectionReason() == MRERawEvent::c_RejectionLeverArmOutOfLimits ||
         RE->GetRejectionReason() == MRERawEvent::c_RejectionEventIdOutOfLimits) {
diff --git a/src/response/src/MResponseMultipleComptonTMVA.cxx b/src/response/src/MResponseMultipleComptonTMVA.cxx
index f6da9a951..f2e156379 100644
--- a/src/response/src/MResponseMultipleComptonTMVA.cxx
+++ b/src/response/src/MResponseMultipleComptonTMVA.cxx
@@ -73,9 +73,12 @@ MResponseMultipleComptonTMVA::MResponseMultipleComptonTMVA()
   
   m_ResponseNameSuffix = "tmva";
   m_MaxNEvents = 10000000; // 10 Mio
-  m_MaxNInteractions = 5;
+  m_MaxNInteractions = 7;
   m_MethodsString = "BDTD";
-  
+
+  m_EnergyMinimum = 100; // keV
+  m_EnergyMaximum = 10000; // keV
+
   SetDefaultOptions();
 }
 
@@ -148,6 +151,8 @@ MString MResponseMultipleComptonTMVA::Options()
   ostringstream out;
   out<<"             methods:               the selected TMVA methods (default: BDTD)"<<endl;
   out<<"             maxia:                 the maximum number of interactions (default: 5)"<<endl;
+  out<<"             emin:                  minimum energy (default: 100 keV)"<<endl;
+  out<<"             emax:                  maximum energy (default: 10000 keV)"<<endl;
   out<<"             mlp_options:           MLP options (default: ["<<m_MLPOptionsDefault<<"])"<<endl;
   out<<"             bdtd_options:          BDTD options (default: ["<<m_BDTDOptionsDefault<<"])"<<endl;
   out<<"             pdefoamboost_options:  PDE foam boost options (default: ["<<m_PDEFoamBoostOptionsDefault<<"])"<<endl;
@@ -268,6 +273,10 @@ bool MResponseMultipleComptonTMVA::ParseOptions(const MString& Options)
       m_MethodsString = Value;
     } else if (Split2[i][0] == "maxia") {
       m_MaxNInteractions = stoi(Value);
+    } else if (Split2[i][0] == "emin") {
+      m_EnergyMinimum = stod(Value);
+    } else if (Split2[i][0] == "emax") {
+      m_EnergyMaximum = stod(Value);
     } else if (Split2[i][0] == "mlp_options") {
       m_MLPOptions = Value;
     } else if (Split2[i][0] == "bdtd_options") {
@@ -295,6 +304,8 @@ bool MResponseMultipleComptonTMVA::ParseOptions(const MString& Options)
   mout<<"Choosen options for Compton event reconstruction using TMVA:"<<endl;
   mout<<"  TMVA methods:                            "<<m_MethodsString<<endl;
   mout<<"  Maximum number of interactions:          "<<m_MaxNInteractions<<endl;
+  mout<<"  Minimum energy:                          "<<m_EnergyMinimum<<endl;
+  mout<<"  Maximum energy:                          "<<m_EnergyMaximum<<endl;
   if (m_MLPOptions != m_MLPOptionsDefault) {
     mout<<"  MLP options:                             "<<m_MLPOptions<<endl; 
   }
@@ -421,6 +432,9 @@ bool MResponseMultipleComptonTMVA::Initialize()
     out<<s<<" ";
   }
   out<<endl;
+  out<<"# Energy window"<<endl;
+  out<<"EW "<<m_EnergyMinimum<<" "<<m_EnergyMaximum<<endl;
+  out<<endl;
   out<<endl;
   out<<"# Trained Algorithms (e.g. MLP, BDTD, PDEFoamBoost, DNN_GPU, DNN_CPU)"<<endl;
   out<<"TA "<<m_Methods.GetUsedMethodsString()<<endl;

From 678fa08c325a6353291521c1e0412af4cb82e084 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Fri, 26 Jan 2024 01:16:32 -0800
Subject: [PATCH 030/192] CHG: Changes to internal cfitsio

---
 config/Makefile.linuxgcc | 10 +++++-----
 config/Makefile.macosx   |  6 +++---
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/config/Makefile.linuxgcc b/config/Makefile.linuxgcc
index d9f7ca68b..a1dcf0d73 100644
--- a/config/Makefile.linuxgcc
+++ b/config/Makefile.linuxgcc
@@ -33,11 +33,11 @@ LINK          := ln -s -f
 # HEASoft
 HEACFLAGS     := 
 HEALIBS       :=
-ifneq ("$(wildcard $(LHEASOFT)/include/fitsio.h)", "")
-	HEACFLAGS += -I$(LHEASOFT)/include
-	HEALIBS += -L$(LHEASOFT)/lib 
+ifeq ("$(shell PKG_CONFIG_PATH=$(LHEASOFT)/lib/pkgconfig pkg-config --exists cfitsio 1>&2 2> /dev/null; echo $$?)", "0")
+	HEACFLAGS += $(shell PKG_CONFIG_PATH=$(LHEASOFT)/lib/pkgconfig pkg-config --cflags cfitsio)
+	HEALIBS += $(shell PKG_CONFIG_PATH=$(LHEASOFT)/lib/pkgconfig pkg-config --libs cfitsio --static)
 else ifeq ("$(shell pkg-config --exists cfitsio 1>&2 2> /dev/null; echo $$?)", "0")
-        HEACFLAGS += $(shell pkg-config --cflags cfitsio)
-        HEALIBS += $(shell pkg-config --libs cfitsio)
+	HEACFLAGS += $(shell pkg-config --cflags cfitsio)
+	HEALIBS += $(shell pkg-config --libs cfitsio)
 endif
 
diff --git a/config/Makefile.macosx b/config/Makefile.macosx
index 7ed957113..1cd2fa743 100644
--- a/config/Makefile.macosx
+++ b/config/Makefile.macosx
@@ -34,9 +34,9 @@ LINK          := ln -s -f
 # HEASoft
 HEACFLAGS     :=
 HEALIBS       :=
-ifneq ("$(wildcard $(LHEASOFT)/include/fitsio.h)", "")
-        HEACFLAGS += -I$(LHEASOFT)/include
-        HEALIBS += -L$(LHEASOFT)/lib
+ifeq ("$(shell PKG_CONFIG_PATH=$(LHEASOFT)/lib/pkgconfig pkg-config --exists cfitsio 1>&2 2> /dev/null; echo $$?)", "0")
+        HEACFLAGS += $(shell PKG_CONFIG_PATH=$(LHEASOFT)/lib/pkgconfig pkg-config --cflags cfitsio)
+        HEALIBS += $(shell PKG_CONFIG_PATH=$(LHEASOFT)/lib/pkgconfig pkg-config --libs cfitsio --static)
 else ifeq ("$(shell pkg-config --exists cfitsio 1>&2 2> /dev/null; echo $$?)", "0")
         HEACFLAGS += $(shell pkg-config --cflags cfitsio)
         HEALIBS += $(shell pkg-config --libs cfitsio)

From fda5eb17ebebd1de2cb1ec3bb3dfc68c1630e12f Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Fri, 26 Jan 2024 11:11:20 -0800
Subject: [PATCH 031/192] ADD: Save the cfg file via command line in revan and
 mimrec

---
 src/mimrec/src/MInterfaceMimrec.cxx | 8 +++++++-
 src/revan/src/MInterfaceRevan.cxx   | 6 ++++++
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/src/mimrec/src/MInterfaceMimrec.cxx b/src/mimrec/src/MInterfaceMimrec.cxx
index a8251e42e..d9a2c920e 100644
--- a/src/mimrec/src/MInterfaceMimrec.cxx
+++ b/src/mimrec/src/MInterfaceMimrec.cxx
@@ -159,6 +159,8 @@ bool MInterfaceMimrec::ParseCommandLine(int argc, char** argv)
   Usage<<"             Perform polarization analysis. If the -o option is given then the image is saved to this file."<<endl;
   Usage<<"         --interaction-distance:"<<endl;
   Usage<<"             Create interaction distance plots. If the -o option is given then the image is saved to this file."<<endl;
+  Usage<<"         --save-cfg:"<<endl;
+  Usage<<"             Safe the configuration. If the -o option is given then the configuration is saved to this file."<<endl;
   Usage<<"         --scatter-angles:"<<endl;
   Usage<<"             Create the scatter-angle distributions. If the -o option is given then the image is saved to this file."<<endl;
   Usage<<"         --sequence-length:"<<endl;
@@ -349,9 +351,13 @@ bool MInterfaceMimrec::ParseCommandLine(int argc, char** argv)
       Polarization();
       return KeepAlive;
     } else if (Option == "--scatter-angles") {
-      cout<<"Command-line parser: Generating scatter-angles plot..."<<endl;  
+      cout<<"Command-line parser: Generating scatter-angles plot..."<<endl;
       ScatterAnglesDistribution();
       return KeepAlive;
+    } else if (Option == "--save-cfg") {
+      cout<<"Command-line parser: Save the configuration..."<<endl;
+      SaveConfiguration(m_OutputFileName != "" ? m_OutputFileName : "NewConfiguration.cfg");
+      return KeepAlive;
     } else if (Option == "--interaction-distance") {
       cout<<"Command-line parser: Generating interaction-distance plot..."<<endl;  
       DistanceDistribution();
diff --git a/src/revan/src/MInterfaceRevan.cxx b/src/revan/src/MInterfaceRevan.cxx
index 632f8df67..122aa8c27 100644
--- a/src/revan/src/MInterfaceRevan.cxx
+++ b/src/revan/src/MInterfaceRevan.cxx
@@ -143,6 +143,8 @@ bool MInterfaceRevan::ParseCommandLine(int argc, char** argv)
   Usage<<"             Analyze the evta-file given with the -f option, otherwise the file in the configuration file"<<endl;
   Usage<<"      -s --generate spectra:"<<endl;
   Usage<<"             Generate spectra using the options previously set in the GUI and stored in the configuration file"<<endl;
+  Usage<<"         --save-cfg:"<<endl;
+  Usage<<"             Safe the configuration. If the -o option is given then the configuration is saved to this file."<<endl;
   Usage<<endl;
   Usage<<"      -t  --test:"<<endl;
   Usage<<"             Perform a test run."<<endl;
@@ -291,6 +293,10 @@ bool MInterfaceRevan::ParseCommandLine(int argc, char** argv)
       cout<<"Command-line parser: Analyzing..."<<endl;
       AnalyzeEvents();
       return true;
+    } else if (Option == "--save-cfg") {
+      cout<<"Command-line parser: Save the configuration..."<<endl;
+      SaveConfiguration(m_OutputFilenName != "" ? m_OutputFilenName : "NewConfiguration.cfg");
+      return false;
     } else if (Option == "--generate-spectra" || Option == "-s") {
       cout<<"Command-line parser: Generate spectra (use the options from the configuration file)"<<endl;
       GenerateSpectra();

From 7fe0e4ba840d4bac46fd7a8df1cd3b7e99c3eb2f Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Thu, 8 Feb 2024 11:31:56 -0800
Subject: [PATCH 032/192] CHG: Minimum energy must be 0

---
 src/mimrec/src/MInterfaceMimrec.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mimrec/src/MInterfaceMimrec.cxx b/src/mimrec/src/MInterfaceMimrec.cxx
index d9a2c920e..f13a7c4dc 100644
--- a/src/mimrec/src/MInterfaceMimrec.cxx
+++ b/src/mimrec/src/MInterfaceMimrec.cxx
@@ -4056,7 +4056,7 @@ void MInterfaceMimrec::EnergyDistributionElectronPhoton()
   if (InitializeEventLoader() == false) return;
 
   bool xLog = m_Settings->GetLogBinningSpectrum();
-  double xMin = GetTotalEnergyMin();
+  double xMin = 0;
   double xMax = GetTotalEnergyMax();
   
   if (xLog == true) {

From 896ef505732b8b46e0752cf085a1b3dcce918304 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Thu, 8 Feb 2024 16:06:56 -0800
Subject: [PATCH 033/192] CHG: Sort masses by name

---
 src/geomega/src/MDGeometry.cxx | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/src/geomega/src/MDGeometry.cxx b/src/geomega/src/MDGeometry.cxx
index 3aa595eb8..d8810d48d 100644
--- a/src/geomega/src/MDGeometry.cxx
+++ b/src/geomega/src/MDGeometry.cxx
@@ -4646,16 +4646,25 @@ void MDGeometry::CalculateMasses()
     }
   }
 
+  map<MString, double> MassByName;
+  for (MassesIter = Masses.begin(); MassesIter != Masses.end(); ++MassesIter) {
+    MassByName[(*MassesIter).first->GetName()] = (*MassesIter).second;
+  }
+
   ostringstream out;
   out.setf(ios_base::fixed, ios_base::floatfield);
   out.precision(3);
   out<<endl;
   out<<"Mass summary by material: "<<endl;
   out<<endl;
-  for (MassesIter = (Masses.begin());
-       MassesIter != Masses.end(); MassesIter++) {
-    out<<setw(NameWidth+2)<<(*MassesIter).first->GetName()<<" :  "<<setw(12)<<(*MassesIter).second<<" g"<<endl;
-    Total += (*MassesIter).second;
+  //for (MassesIter = (Masses.begin());
+  //     MassesIter != Masses.end(); MassesIter++) {
+  //  out<<setw(NameWidth+2)<<(*MassesIter).first->GetName()<<" :  "<<setw(12)<<(*MassesIter).second<<" g"<<endl;
+  //  Total += (*MassesIter).second;
+  //}
+  for (auto I = MassByName.begin(); I != MassByName.end(); ++I) {
+    out<<setw(NameWidth+2)<<(*I).first<<" :  "<<setw(12)<<(*I).second<<" g"<<endl;
+    Total += (*I).second;
   }
   out<<endl;
   out<<setw(NameWidth+2)<<"Total"<<" :  "<<setw(12)<<Total<<" g"<<endl;

From 798a4c110b4f3ecd8c1d890725e6237468e22387 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Thu, 23 May 2024 17:15:51 -0700
Subject: [PATCH 034/192] CHG: More ROOTPATH sanity checks

---
 config/check-rootversion.sh | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/config/check-rootversion.sh b/config/check-rootversion.sh
index 19769d1e9..60df5477b 100755
--- a/config/check-rootversion.sh
+++ b/config/check-rootversion.sh
@@ -126,9 +126,15 @@ if [ "${GOOD}" == "true" ]; then
 fi  
 
 if [ "${CHECK}" == "true" ]; then
+  if [ ! -d ${ROOTPATH} ]; then
+    echo " "
+    echo "ERROR: The given directory ${ROOTPATH} does no exist."
+    exit 1;
+  fi
+
   if [ ! -f ${ROOTPATH}/bin/root-config ]; then
     echo " "
-    echo "ERROR: The given directory ${ROOTPATH} does no contain a correct ROOT installation"
+    echo "ERROR: The file ${ROOTPATH}/bin/root-config does exist and thus you do not have a standard ROOT installation"
     exit 1;
   fi
 

From e9a32b745b9654e00d0ae74c18f593bdccdb052a Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Thu, 23 May 2024 17:16:17 -0700
Subject: [PATCH 035/192] CHG: Update Doxyfile to latest version

---
 resource/Doxyfile | 2829 +++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 2735 insertions(+), 94 deletions(-)
 mode change 100755 => 100644 resource/Doxyfile

diff --git a/resource/Doxyfile b/resource/Doxyfile
old mode 100755
new mode 100644
index df3d13543..260e2c928
--- a/resource/Doxyfile
+++ b/resource/Doxyfile
@@ -1,181 +1,2822 @@
-# Doxyfile 0.1
+# Doxyfile 1.9.8
+
+# This file describes the settings to be used by the documentation system
+# doxygen (www.doxygen.org) for a project.
+#
+# All text after a double hash (##) is considered a comment and is placed in
+# front of the TAG it is preceding.
+#
+# All text after a single hash (#) is considered a comment and will be ignored.
+# The format is:
+# TAG = value [value, ...]
+# For lists, items can also be appended using:
+# TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (\" \").
+#
+# Note:
+#
+# Use doxygen to compare the used configuration file with the template
+# configuration file:
+# doxygen -x [configFile]
+# Use doxygen to compare the used configuration file with the template
+# configuration file without replacing the environment variables or CMake type
+# replacement variables:
+# doxygen -x_noenv [configFile]
 
 #---------------------------------------------------------------------------
-# General configuration options
+# Project related configuration options
 #---------------------------------------------------------------------------
+
+# This tag specifies the encoding used for all characters in the configuration
+# file that follow. The default is UTF-8 which is also the encoding used for all
+# text before the first occurrence of this tag. Doxygen uses libiconv (or the
+# iconv built into libc) for the transcoding. See
+# https://www.gnu.org/software/libiconv/ for the list of possible encodings.
+# The default value is: UTF-8.
+
+DOXYFILE_ENCODING      = UTF-8
+
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
+# double-quotes, unless you are using Doxywizard) that should identify the
+# project for which the documentation is generated. This name is used in the
+# title of most generated pages and in a few other places.
+# The default value is: My Project.
+
 PROJECT_NAME           = "MEGAlib"
-PROJECT_NUMBER         = 2.XX
+
+# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
+# could be handy for archiving the generated documentation or if some version
+# control system is used.
+
+PROJECT_NUMBER         =
+
+# Using the PROJECT_BRIEF tag one can provide an optional one line description
+# for a project that appears at the top of each page and should give viewer a
+# quick idea about the purpose of the project. Keep the description short.
+
+PROJECT_BRIEF          = "the medium-energy gamma-ray astronomy library"
+
+# With the PROJECT_LOGO tag one can specify a logo or an icon that is included
+# in the documentation. The maximum height of the logo should not exceed 55
+# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy
+# the logo to the output directory.
+
+PROJECT_LOGO           =
+
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
+# into which the generated documentation will be written. If a relative path is
+# entered, it will be relative to the location where doxygen was started. If
+# left blank the current directory will be used.
+
 OUTPUT_DIRECTORY       = doc
+
+# If the CREATE_SUBDIRS tag is set to YES then doxygen will create up to 4096
+# sub-directories (in 2 levels) under the output directory of each output format
+# and will distribute the generated files over these directories. Enabling this
+# option can be useful when feeding doxygen a huge amount of source files, where
+# putting all generated files in the same directory would otherwise causes
+# performance problems for the file system. Adapt CREATE_SUBDIRS_LEVEL to
+# control the number of sub-directories.
+# The default value is: NO.
+
+CREATE_SUBDIRS         = NO
+
+# Controls the number of sub-directories that will be created when
+# CREATE_SUBDIRS tag is set to YES. Level 0 represents 16 directories, and every
+# level increment doubles the number of directories, resulting in 4096
+# directories at level 8 which is the default and also the maximum value. The
+# sub-directories are organized in 2 levels, the first level always has a fixed
+# number of 16 directories.
+# Minimum value: 0, maximum value: 8, default value: 8.
+# This tag requires that the tag CREATE_SUBDIRS is set to YES.
+
+CREATE_SUBDIRS_LEVEL   = 8
+
+# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII
+# characters to appear in the names of generated files. If set to NO, non-ASCII
+# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode
+# U+3044.
+# The default value is: NO.
+
+ALLOW_UNICODE_NAMES    = NO
+
+# The OUTPUT_LANGUAGE tag is used to specify the language in which all
+# documentation generated by doxygen is written. Doxygen will use this
+# information to generate all constant output in the proper language.
+# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Bulgarian,
+# Catalan, Chinese, Chinese-Traditional, Croatian, Czech, Danish, Dutch, English
+# (United States), Esperanto, Farsi (Persian), Finnish, French, German, Greek,
+# Hindi, Hungarian, Indonesian, Italian, Japanese, Japanese-en (Japanese with
+# English messages), Korean, Korean-en (Korean with English messages), Latvian,
+# Lithuanian, Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese,
+# Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish,
+# Swedish, Turkish, Ukrainian and Vietnamese.
+# The default value is: English.
+
 OUTPUT_LANGUAGE        = English
-EXTRACT_ALL            = YES
-EXTRACT_PRIVATE        = YES
-EXTRACT_STATIC         = YES
-EXTRACT_LOCAL_CLASSES  = YES
-HIDE_UNDOC_MEMBERS     = NO
-HIDE_UNDOC_CLASSES     = NO
-BRIEF_MEMBER_DESC      = NO
+
+# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member
+# descriptions after the members that are listed in the file and class
+# documentation (similar to Javadoc). Set to NO to disable this.
+# The default value is: YES.
+
+BRIEF_MEMBER_DESC      = YES
+
+# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief
+# description of a member or function before the detailed description
+#
+# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
+# brief descriptions will be completely suppressed.
+# The default value is: YES.
+
 REPEAT_BRIEF           = YES
-ALWAYS_DETAILED_SEC    = YES
+
+# This tag implements a quasi-intelligent brief description abbreviator that is
+# used to form the text in various listings. Each string in this list, if found
+# as the leading text of the brief description, will be stripped from the text
+# and the result, after processing the whole list, is used as the annotated
+# text. Otherwise, the brief description is used as-is. If left blank, the
+# following values are used ($name is automatically replaced with the name of
+# the entity):The $name class, The $name widget, The $name file, is, provides,
+# specifies, contains, represents, a, an and the.
+
+ABBREVIATE_BRIEF       = "The $name class" \
+                         "The $name widget" \
+                         "The $name file" \
+                         is \
+                         provides \
+                         specifies \
+                         contains \
+                         represents \
+                         a \
+                         an \
+                         the
+
+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
+# doxygen will generate a detailed section even if there is only a brief
+# description.
+# The default value is: NO.
+
+ALWAYS_DETAILED_SEC    = NO
+
+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
+# inherited members of a class in the documentation of that class as if those
+# members were ordinary class members. Constructors, destructors and assignment
+# operators of the base classes will not be shown.
+# The default value is: NO.
+
 INLINE_INHERITED_MEMB  = NO
-FULL_PATH_NAMES        = NO
-STRIP_FROM_PATH        = 
-INTERNAL_DOCS          = NO
-STRIP_CODE_COMMENTS    = NO
-CASE_SENSE_NAMES       = YES
+
+# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path
+# before files name in the file list and in the header files. If set to NO the
+# shortest path that makes the file name unique will be used
+# The default value is: YES.
+
+FULL_PATH_NAMES        = YES
+
+# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
+# Stripping is only done if one of the specified strings matches the left-hand
+# part of the path. The tag can be used to show relative paths in the file list.
+# If left blank the directory from which doxygen is run is used as the path to
+# strip.
+#
+# Note that you can specify absolute paths here, but also relative paths, which
+# will be relative from the directory where doxygen is started.
+# This tag requires that the tag FULL_PATH_NAMES is set to YES.
+
+STRIP_FROM_PATH        =
+
+# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
+# path mentioned in the documentation of a class, which tells the reader which
+# header file to include in order to use a class. If left blank only the name of
+# the header file containing the class definition is used. Otherwise one should
+# specify the list of include paths that are normally passed to the compiler
+# using the -I flag.
+
+STRIP_FROM_INC_PATH    =
+
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
+# less readable) file names. This can be useful is your file systems doesn't
+# support long names like on DOS, Mac, or CD-ROM.
+# The default value is: NO.
+
 SHORT_NAMES            = NO
-HIDE_SCOPE_NAMES       = NO
-VERBATIM_HEADERS       = NO
-SHOW_INCLUDE_FILES     = NO
+
+# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the
+# first line (until the first dot) of a Javadoc-style comment as the brief
+# description. If set to NO, the Javadoc-style will behave just like regular Qt-
+# style comments (thus requiring an explicit @brief command for a brief
+# description.)
+# The default value is: NO.
+
 JAVADOC_AUTOBRIEF      = NO
+
+# If the JAVADOC_BANNER tag is set to YES then doxygen will interpret a line
+# such as
+# /***************
+# as being the beginning of a Javadoc-style comment "banner". If set to NO, the
+# Javadoc-style will behave just like regular comments and it will not be
+# interpreted by doxygen.
+# The default value is: NO.
+
+JAVADOC_BANNER         = NO
+
+# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first
+# line (until the first dot) of a Qt-style comment as the brief description. If
+# set to NO, the Qt-style will behave just like regular Qt-style comments (thus
+# requiring an explicit \brief command for a brief description.)
+# The default value is: NO.
+
+QT_AUTOBRIEF           = NO
+
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a
+# multi-line C++ special comment block (i.e. a block of //! or /// comments) as
+# a brief description. This used to be the default behavior. The new default is
+# to treat a multi-line C++ comment block as a detailed description. Set this
+# tag to YES if you prefer the old behavior instead.
+#
+# Note that setting this tag to YES also means that rational rose comments are
+# not recognized any more.
+# The default value is: NO.
+
+MULTILINE_CPP_IS_BRIEF = NO
+
+# By default Python docstrings are displayed as preformatted text and doxygen's
+# special commands cannot be used. By setting PYTHON_DOCSTRING to NO the
+# doxygen's special commands can be used and the contents of the docstring
+# documentation blocks is shown as doxygen documentation.
+# The default value is: YES.
+
+PYTHON_DOCSTRING       = YES
+
+# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
+# documentation from any documented member that it re-implements.
+# The default value is: YES.
+
 INHERIT_DOCS           = YES
+
+# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new
+# page for each member. If set to NO, the documentation of a member will be part
+# of the file/class/namespace that contains it.
+# The default value is: NO.
+
+SEPARATE_MEMBER_PAGES  = NO
+
+# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen
+# uses this value to replace tabs by spaces in code fragments.
+# Minimum value: 1, maximum value: 16, default value: 4.
+
+TAB_SIZE               = 4
+
+# This tag can be used to specify a number of aliases that act as commands in
+# the documentation. An alias has the form:
+# name=value
+# For example adding
+# "sideeffect=@par Side Effects:^^"
+# will allow you to put the command \sideeffect (or @sideeffect) in the
+# documentation, which will result in a user-defined paragraph with heading
+# "Side Effects:". Note that you cannot put \n's in the value part of an alias
+# to insert newlines (in the resulting output). You can put ^^ in the value part
+# of an alias to insert a newline as if a physical newline was in the original
+# file. When you need a literal { or } or , in the value part of an alias you
+# have to escape them by means of a backslash (\), this can lead to conflicts
+# with the commands \{ and \} for these it is advised to use the version @{ and
+# @} or use a double escape (\\{ and \\})
+
+ALIASES                =
+
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
+# only. Doxygen will then generate output that is more tailored for C. For
+# instance, some of the names that are used will be different. The list of all
+# members will be omitted, etc.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_FOR_C  = NO
+
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
+# Python sources only. Doxygen will then generate output that is more tailored
+# for that language. For instance, namespaces will be presented as packages,
+# qualified scopes will look different, etc.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_JAVA   = NO
+
+# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
+# sources. Doxygen will then generate output that is tailored for Fortran.
+# The default value is: NO.
+
+OPTIMIZE_FOR_FORTRAN   = NO
+
+# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
+# sources. Doxygen will then generate output that is tailored for VHDL.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_VHDL   = NO
+
+# Set the OPTIMIZE_OUTPUT_SLICE tag to YES if your project consists of Slice
+# sources only. Doxygen will then generate output that is more tailored for that
+# language. For instance, namespaces will be presented as modules, types will be
+# separated into more groups, etc.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_SLICE  = NO
+
+# Doxygen selects the parser to use depending on the extension of the files it
+# parses. With this tag you can assign which parser to use for a given
+# extension. Doxygen has a built-in mapping, but you can override or extend it
+# using this tag. The format is ext=language, where ext is a file extension, and
+# language is one of the parsers supported by doxygen: IDL, Java, JavaScript,
+# Csharp (C#), C, C++, Lex, D, PHP, md (Markdown), Objective-C, Python, Slice,
+# VHDL, Fortran (fixed format Fortran: FortranFixed, free formatted Fortran:
+# FortranFree, unknown formatted Fortran: Fortran. In the later case the parser
+# tries to guess whether the code is fixed or free formatted code, this is the
+# default for Fortran type files). For instance to make doxygen treat .inc files
+# as Fortran files (default is PHP), and .f files as C (default is Fortran),
+# use: inc=Fortran f=C.
+#
+# Note: For files without extension you can use no_extension as a placeholder.
+#
+# Note that for custom extensions you also need to set FILE_PATTERNS otherwise
+# the files are not read by doxygen. When specifying no_extension you should add
+# * to the FILE_PATTERNS.
+#
+# Note see also the list of default file extension mappings.
+
+EXTENSION_MAPPING      =
+
+# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
+# according to the Markdown format, which allows for more readable
+# documentation. See https://daringfireball.net/projects/markdown/ for details.
+# The output of markdown processing is further processed by doxygen, so you can
+# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in
+# case of backward compatibilities issues.
+# The default value is: YES.
+
+MARKDOWN_SUPPORT       = YES
+
+# When the TOC_INCLUDE_HEADINGS tag is set to a non-zero value, all headings up
+# to that level are automatically included in the table of contents, even if
+# they do not have an id attribute.
+# Note: This feature currently applies only to Markdown headings.
+# Minimum value: 0, maximum value: 99, default value: 5.
+# This tag requires that the tag MARKDOWN_SUPPORT is set to YES.
+
+TOC_INCLUDE_HEADINGS   = 5
+
+# The MARKDOWN_ID_STYLE tag can be used to specify the algorithm used to
+# generate identifiers for the Markdown headings. Note: Every identifier is
+# unique.
+# Possible values are: DOXYGEN use a fixed 'autotoc_md' string followed by a
+# sequence number starting at 0 and GITHUB use the lower case version of title
+# with any whitespace replaced by '-' and punctuation characters removed.
+# The default value is: DOXYGEN.
+# This tag requires that the tag MARKDOWN_SUPPORT is set to YES.
+
+MARKDOWN_ID_STYLE      = DOXYGEN
+
+# When enabled doxygen tries to link words that correspond to documented
+# classes, or namespaces to their corresponding documentation. Such a link can
+# be prevented in individual cases by putting a % sign in front of the word or
+# globally by setting AUTOLINK_SUPPORT to NO.
+# The default value is: YES.
+
+AUTOLINK_SUPPORT       = YES
+
+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
+# to include (a tag file for) the STL sources as input, then you should set this
+# tag to YES in order to let doxygen match functions declarations and
+# definitions whose arguments contain STL classes (e.g. func(std::string);
+# versus func(std::string) {}). This also make the inheritance and collaboration
+# diagrams that involve STL classes more complete and accurate.
+# The default value is: NO.
+
+BUILTIN_STL_SUPPORT    = NO
+
+# If you use Microsoft's C++/CLI language, you should set this option to YES to
+# enable parsing support.
+# The default value is: NO.
+
+CPP_CLI_SUPPORT        = NO
+
+# Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
+# https://www.riverbankcomputing.com/software/sip/intro) sources only. Doxygen
+# will parse them like normal C++ but will assume all classes use public instead
+# of private inheritance when no explicit protection keyword is present.
+# The default value is: NO.
+
+SIP_SUPPORT            = NO
+
+# For Microsoft's IDL there are propget and propput attributes to indicate
+# getter and setter methods for a property. Setting this option to YES will make
+# doxygen to replace the get and set methods by a property in the documentation.
+# This will only work if the methods are indeed getting or setting a simple
+# type. If this is not the case, or you want to show the methods anyway, you
+# should set this option to NO.
+# The default value is: YES.
+
+IDL_PROPERTY_SUPPORT   = YES
+
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
+# tag is set to YES then doxygen will reuse the documentation of the first
+# member in the group (if any) for the other members of the group. By default
+# all members of a group must be documented explicitly.
+# The default value is: NO.
+
+DISTRIBUTE_GROUP_DOC   = NO
+
+# If one adds a struct or class to a group and this option is enabled, then also
+# any nested class or struct is added to the same group. By default this option
+# is disabled and one has to add nested compounds explicitly via \ingroup.
+# The default value is: NO.
+
+GROUP_NESTED_COMPOUNDS = NO
+
+# Set the SUBGROUPING tag to YES to allow class member groups of the same type
+# (for instance a group of public functions) to be put as a subgroup of that
+# type (e.g. under the Public Functions section). Set it to NO to prevent
+# subgrouping. Alternatively, this can be done per class using the
+# \nosubgrouping command.
+# The default value is: YES.
+
+SUBGROUPING            = YES
+
+# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions
+# are shown inside the group in which they are included (e.g. using \ingroup)
+# instead of on a separate page (for HTML and Man pages) or section (for LaTeX
+# and RTF).
+#
+# Note that this feature does not work in combination with
+# SEPARATE_MEMBER_PAGES.
+# The default value is: NO.
+
+INLINE_GROUPED_CLASSES = NO
+
+# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
+# with only public data fields or simple typedef fields will be shown inline in
+# the documentation of the scope in which they are defined (i.e. file,
+# namespace, or group documentation), provided this scope is documented. If set
+# to NO, structs, classes, and unions are shown on a separate page (for HTML and
+# Man pages) or section (for LaTeX and RTF).
+# The default value is: NO.
+
+INLINE_SIMPLE_STRUCTS  = NO
+
+# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
+# enum is documented as struct, union, or enum with the name of the typedef. So
+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
+# with name TypeT. When disabled the typedef will appear as a member of a file,
+# namespace, or class. And the struct will be named TypeS. This can typically be
+# useful for C code in case the coding convention dictates that all compound
+# types are typedef'ed and only the typedef is referenced, never the tag name.
+# The default value is: NO.
+
+TYPEDEF_HIDES_STRUCT   = NO
+
+# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
+# cache is used to resolve symbols given their name and scope. Since this can be
+# an expensive process and often the same symbol appears multiple times in the
+# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
+# doxygen will become slower. If the cache is too large, memory is wasted. The
+# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
+# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
+# symbols. At the end of a run doxygen will report the cache usage and suggest
+# the optimal cache size from a speed point of view.
+# Minimum value: 0, maximum value: 9, default value: 0.
+
+LOOKUP_CACHE_SIZE      = 0
+
+# The NUM_PROC_THREADS specifies the number of threads doxygen is allowed to use
+# during processing. When set to 0 doxygen will based this on the number of
+# cores available in the system. You can set it explicitly to a value larger
+# than 0 to get more control over the balance between CPU load and processing
+# speed. At this moment only the input processing can be done using multiple
+# threads. Since this is still an experimental feature the default is set to 1,
+# which effectively disables parallel processing. Please report any issues you
+# encounter. Generating dot graphs in parallel is controlled by the
+# DOT_NUM_THREADS setting.
+# Minimum value: 0, maximum value: 32, default value: 1.
+
+NUM_PROC_THREADS       = 1
+
+# If the TIMESTAMP tag is set different from NO then each generated page will
+# contain the date or date and time when the page was generated. Setting this to
+# NO can help when comparing the output of multiple runs.
+# Possible values are: YES, NO, DATETIME and DATE.
+# The default value is: NO.
+
+TIMESTAMP              = NO
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in
+# documentation are documented, even if no documentation was available. Private
+# class members and static file members will be hidden unless the
+# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
+# Note: This will also disable the warnings about undocumented members that are
+# normally produced when WARNINGS is set to YES.
+# The default value is: NO.
+
+EXTRACT_ALL            = NO
+
+# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
+# be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PRIVATE        = NO
+
+# If the EXTRACT_PRIV_VIRTUAL tag is set to YES, documented private virtual
+# methods of a class will be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PRIV_VIRTUAL   = NO
+
+# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
+# scope will be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PACKAGE        = NO
+
+# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be
+# included in the documentation.
+# The default value is: NO.
+
+EXTRACT_STATIC         = NO
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
+# locally in source files will be included in the documentation. If set to NO,
+# only classes defined in header files are included. Does not have any effect
+# for Java sources.
+# The default value is: YES.
+
+EXTRACT_LOCAL_CLASSES  = YES
+
+# This flag is only useful for Objective-C code. If set to YES, local methods,
+# which are defined in the implementation section but not in the interface are
+# included in the documentation. If set to NO, only methods in the interface are
+# included.
+# The default value is: NO.
+
+EXTRACT_LOCAL_METHODS  = NO
+
+# If this flag is set to YES, the members of anonymous namespaces will be
+# extracted and appear in the documentation as a namespace called
+# 'anonymous_namespace{file}', where file will be replaced with the base name of
+# the file that contains the anonymous namespace. By default anonymous namespace
+# are hidden.
+# The default value is: NO.
+
+EXTRACT_ANON_NSPACES   = NO
+
+# If this flag is set to YES, the name of an unnamed parameter in a declaration
+# will be determined by the corresponding definition. By default unnamed
+# parameters remain unnamed in the output.
+# The default value is: YES.
+
+RESOLVE_UNNAMED_PARAMS = YES
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
+# undocumented members inside documented classes or files. If set to NO these
+# members will be included in the various overviews, but no documentation
+# section is generated. This option has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
+
+HIDE_UNDOC_MEMBERS     = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy. If set
+# to NO, these classes will be included in the various overviews. This option
+# will also hide undocumented C++ concepts if enabled. This option has no effect
+# if EXTRACT_ALL is enabled.
+# The default value is: NO.
+
+HIDE_UNDOC_CLASSES     = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
+# declarations. If set to NO, these declarations will be included in the
+# documentation.
+# The default value is: NO.
+
+HIDE_FRIEND_COMPOUNDS  = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
+# documentation blocks found inside the body of a function. If set to NO, these
+# blocks will be appended to the function's detailed documentation block.
+# The default value is: NO.
+
+HIDE_IN_BODY_DOCS      = NO
+
+# The INTERNAL_DOCS tag determines if documentation that is typed after a
+# \internal command is included. If the tag is set to NO then the documentation
+# will be excluded. Set it to YES to include the internal documentation.
+# The default value is: NO.
+
+INTERNAL_DOCS          = NO
+
+# With the correct setting of option CASE_SENSE_NAMES doxygen will better be
+# able to match the capabilities of the underlying filesystem. In case the
+# filesystem is case sensitive (i.e. it supports files in the same directory
+# whose names only differ in casing), the option must be set to YES to properly
+# deal with such files in case they appear in the input. For filesystems that
+# are not case sensitive the option should be set to NO to properly deal with
+# output files written for symbols that only differ in casing, such as for two
+# classes, one named CLASS and the other named Class, and to also support
+# references to files without having to specify the exact matching casing. On
+# Windows (including Cygwin) and MacOS, users should typically set this option
+# to NO, whereas on Linux or other Unix flavors it should typically be set to
+# YES.
+# Possible values are: SYSTEM, NO and YES.
+# The default value is: SYSTEM.
+
+CASE_SENSE_NAMES       = SYSTEM
+
+# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
+# their full class and namespace scopes in the documentation. If set to YES, the
+# scope will be hidden.
+# The default value is: NO.
+
+HIDE_SCOPE_NAMES       = NO
+
+# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will
+# append additional text to a page's title, such as Class Reference. If set to
+# YES the compound reference will be hidden.
+# The default value is: NO.
+
+HIDE_COMPOUND_REFERENCE= NO
+
+# If the SHOW_HEADERFILE tag is set to YES then the documentation for a class
+# will show which file needs to be included to use the class.
+# The default value is: YES.
+
+SHOW_HEADERFILE        = YES
+
+# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
+# the files that are included by a file in the documentation of that file.
+# The default value is: YES.
+
+SHOW_INCLUDE_FILES     = YES
+
+# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
+# grouped member an include statement to the documentation, telling the reader
+# which file to include in order to use the member.
+# The default value is: NO.
+
+SHOW_GROUPED_MEMB_INC  = NO
+
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
+# files with double quotes in the documentation rather than with sharp brackets.
+# The default value is: NO.
+
+FORCE_LOCAL_INCLUDES   = NO
+
+# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
+# documentation for inline members.
+# The default value is: YES.
+
 INLINE_INFO            = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
+# (detailed) documentation of file and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order.
+# The default value is: YES.
+
 SORT_MEMBER_DOCS       = YES
-DISTRIBUTE_GROUP_DOC   = NO
-TAB_SIZE               = 16
-GENERATE_TODOLIST      = NO
-GENERATE_TESTLIST      = NO
-GENERATE_BUGLIST       = NO
-ALIASES                = 
-ENABLED_SECTIONS       = 
+
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
+# descriptions of file, namespace and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order. Note that
+# this will also influence the order of the classes in the class list.
+# The default value is: NO.
+
+SORT_BRIEF_DOCS        = NO
+
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
+# (brief and detailed) documentation of class members so that constructors and
+# destructors are listed first. If set to NO the constructors will appear in the
+# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
+# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
+# member documentation.
+# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
+# detailed member documentation.
+# The default value is: NO.
+
+SORT_MEMBERS_CTORS_1ST = NO
+
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
+# of group names into alphabetical order. If set to NO the group names will
+# appear in their defined order.
+# The default value is: NO.
+
+SORT_GROUP_NAMES       = NO
+
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
+# fully-qualified names, including namespaces. If set to NO, the class list will
+# be sorted only by class name, not including the namespace part.
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
+# Note: This option applies only to the class list, not to the alphabetical
+# list.
+# The default value is: NO.
+
+SORT_BY_SCOPE_NAME     = NO
+
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
+# type resolution of all parameters of a function it will reject a match between
+# the prototype and the implementation of a member function even if there is
+# only one candidate or it is obvious which candidate to choose by doing a
+# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
+# accept a match between prototype and implementation in such cases.
+# The default value is: NO.
+
+STRICT_PROTO_MATCHING  = NO
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo
+# list. This list is created by putting \todo commands in the documentation.
+# The default value is: YES.
+
+GENERATE_TODOLIST      = YES
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test
+# list. This list is created by putting \test commands in the documentation.
+# The default value is: YES.
+
+GENERATE_TESTLIST      = YES
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug
+# list. This list is created by putting \bug commands in the documentation.
+# The default value is: YES.
+
+GENERATE_BUGLIST       = YES
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO)
+# the deprecated list. This list is created by putting \deprecated commands in
+# the documentation.
+# The default value is: YES.
+
+GENERATE_DEPRECATEDLIST= YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional documentation
+# sections, marked by \if <section_label> ... \endif and \cond <section_label>
+# ... \endcond blocks.
+
+ENABLED_SECTIONS       =
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
+# initial value of a variable or macro / define can have for it to appear in the
+# documentation. If the initializer consists of more lines than specified here
+# it will be hidden. Use a value of 0 to hide initializers completely. The
+# appearance of the value of individual variables and macros / defines can be
+# controlled using \showinitializer or \hideinitializer command in the
+# documentation regardless of this setting.
+# Minimum value: 0, maximum value: 10000, default value: 30.
+
 MAX_INITIALIZER_LINES  = 30
-OPTIMIZE_OUTPUT_FOR_C  = NO
-SHOW_USED_FILES        = NO
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
+# the bottom of the documentation of classes and structs. If set to YES, the
+# list will mention the files that were used to generate the documentation.
+# The default value is: YES.
+
+SHOW_USED_FILES        = YES
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
+# will remove the Files entry from the Quick Index and from the Folder Tree View
+# (if specified).
+# The default value is: YES.
+
+SHOW_FILES             = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
+# page. This will remove the Namespaces entry from the Quick Index and from the
+# Folder Tree View (if specified).
+# The default value is: YES.
+
+SHOW_NAMESPACES        = YES
+
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
+# popen()) the command command input-file, where command is the value of the
+# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
+# by doxygen. Whatever the program writes to standard output is used as the file
+# version. For an example see the documentation.
+
+FILE_VERSION_FILTER    =
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
+# by doxygen. The layout file controls the global structure of the generated
+# output files in an output format independent way. To create the layout file
+# that represents doxygen's defaults, run doxygen with the -l option. You can
+# optionally specify a file name after the option, if omitted DoxygenLayout.xml
+# will be used as the name of the layout file. See also section "Changing the
+# layout of pages" for information.
+#
+# Note that if you run doxygen from a directory containing a file called
+# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
+# tag is left empty.
+
+LAYOUT_FILE            =
+
+# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
+# the reference definitions. This must be a list of .bib files. The .bib
+# extension is automatically appended if omitted. This requires the bibtex tool
+# to be installed. See also https://en.wikipedia.org/wiki/BibTeX for more info.
+# For LaTeX the style of the bibliography can be controlled using
+# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
+# search path. See also \cite for info how to create references.
+
+CITE_BIB_FILES         =
+
 #---------------------------------------------------------------------------
-# configuration options related to warning and progress messages
+# Configuration options related to warning and progress messages
 #---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated to
+# standard output by doxygen. If QUIET is set to YES this implies that the
+# messages are off.
+# The default value is: NO.
+
 QUIET                  = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
+# this implies that the warnings are on.
+#
+# Tip: Turn warnings on while writing the documentation.
+# The default value is: YES.
+
 WARNINGS               = YES
+
+# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate
+# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
+# will automatically be disabled.
+# The default value is: YES.
+
 WARN_IF_UNDOCUMENTED   = YES
+
+# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as documenting some parameters in
+# a documented function twice, or documenting parameters that don't exist or
+# using markup commands wrongly.
+# The default value is: YES.
+
+WARN_IF_DOC_ERROR      = YES
+
+# If WARN_IF_INCOMPLETE_DOC is set to YES, doxygen will warn about incomplete
+# function parameter documentation. If set to NO, doxygen will accept that some
+# parameters have no documentation without warning.
+# The default value is: YES.
+
+WARN_IF_INCOMPLETE_DOC = YES
+
+# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
+# are documented, but have no documentation for their parameters or return
+# value. If set to NO, doxygen will only warn about wrong parameter
+# documentation, but not about the absence of documentation. If EXTRACT_ALL is
+# set to YES then this flag will automatically be disabled. See also
+# WARN_IF_INCOMPLETE_DOC
+# The default value is: NO.
+
+WARN_NO_PARAMDOC       = NO
+
+# If WARN_IF_UNDOC_ENUM_VAL option is set to YES, doxygen will warn about
+# undocumented enumeration values. If set to NO, doxygen will accept
+# undocumented enumeration values. If EXTRACT_ALL is set to YES then this flag
+# will automatically be disabled.
+# The default value is: NO.
+
+WARN_IF_UNDOC_ENUM_VAL = NO
+
+# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when
+# a warning is encountered. If the WARN_AS_ERROR tag is set to FAIL_ON_WARNINGS
+# then doxygen will continue running as if WARN_AS_ERROR tag is set to NO, but
+# at the end of the doxygen process doxygen will return with a non-zero status.
+# If the WARN_AS_ERROR tag is set to FAIL_ON_WARNINGS_PRINT then doxygen behaves
+# like FAIL_ON_WARNINGS but in case no WARN_LOGFILE is defined doxygen will not
+# write the warning messages in between other messages but write them at the end
+# of a run, in case a WARN_LOGFILE is defined the warning messages will be
+# besides being in the defined file also be shown at the end of a run, unless
+# the WARN_LOGFILE is defined as - i.e. standard output (stdout) in that case
+# the behavior will remain as with the setting FAIL_ON_WARNINGS.
+# Possible values are: NO, YES, FAIL_ON_WARNINGS and FAIL_ON_WARNINGS_PRINT.
+# The default value is: NO.
+
+WARN_AS_ERROR          = NO
+
+# The WARN_FORMAT tag determines the format of the warning messages that doxygen
+# can produce. The string should contain the $file, $line, and $text tags, which
+# will be replaced by the file and line number from which the warning originated
+# and the warning text. Optionally the format may contain $version, which will
+# be replaced by the version of the file (if it could be obtained via
+# FILE_VERSION_FILTER)
+# See also: WARN_LINE_FORMAT
+# The default value is: $file:$line: $text.
+
 WARN_FORMAT            = "$file:$line: $text"
-WARN_LOGFILE           = 
+
+# In the $text part of the WARN_FORMAT command it is possible that a reference
+# to a more specific place is given. To make it easier to jump to this place
+# (outside of doxygen) the user can define a custom "cut" / "paste" string.
+# Example:
+# WARN_LINE_FORMAT = "'vi $file +$line'"
+# See also: WARN_FORMAT
+# The default value is: at line $line of file $file.
+
+WARN_LINE_FORMAT       = "at line $line of file $file"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning and error
+# messages should be written. If left blank the output is written to standard
+# error (stderr). In case the file specified cannot be opened for writing the
+# warning and error messages are written to standard error. When as file - is
+# specified the warning and error messages are written to standard output
+# (stdout).
+
+WARN_LOGFILE           =
+
 #---------------------------------------------------------------------------
-# configuration options related to the input files
+# Configuration options related to the input files
 #---------------------------------------------------------------------------
-INPUT                  = /tmp/doxygen
-FILE_PATTERNS          = *.cpp \
-                         *.h \
-                         *.cxx \
+
+# The INPUT tag is used to specify the files and/or directories that contain
+# documented source files. You may enter file names like myfile.cpp or
+# directories like /usr/src/myproject. Separate the files or directories with
+# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
+# Note: If this tag is empty the current directory is searched.
+
+INPUT                  = src
+
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
+# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
+# documentation (see:
+# https://www.gnu.org/software/libiconv/) for the list of possible encodings.
+# See also: INPUT_FILE_ENCODING
+# The default value is: UTF-8.
+
+INPUT_ENCODING         = UTF-8
+
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses The INPUT_FILE_ENCODING tag can be used to specify
+# character encoding on a per file pattern basis. Doxygen will compare the file
+# name with each pattern and apply the encoding instead of the default
+# INPUT_ENCODING) if there is a match. The character encodings are a list of the
+# form: pattern=encoding (like *.php=ISO-8859-1). See cfg_input_encoding
+# "INPUT_ENCODING" for further information on supported encodings.
+
+INPUT_FILE_ENCODING    =
+
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
+# *.h) to filter out the source-files in the directories.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# read by doxygen.
+#
+# Note the list of default checked file patterns might differ from the list of
+# default file extension mappings.
+#
+# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cxxm,
+# *.cpp, *.cppm, *.c++, *.c++m, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl,
+# *.ddl, *.odl, *.h, *.hh, *.hxx, *.hpp, *.h++, *.ixx, *.l, *.cs, *.d, *.php,
+# *.php4, *.php5, *.phtml, *.inc, *.m, *.markdown, *.md, *.mm, *.dox (to be
+# provided as doxygen C comment), *.py, *.pyw, *.f90, *.f95, *.f03, *.f08,
+# *.f18, *.f, *.for, *.vhd, *.vhdl, *.ucf, *.qsf and *.ice.
+
+FILE_PATTERNS          = *.c \
                          *.cc \
+                         *.cxx \
+                         *.cxxm \
+                         *.cpp \
+                         *.cppm \
+                         *.c++ \
+                         *.c++m \
+                         *.java \
+                         *.ii \
+                         *.ixx \
+                         *.ipp \
+                         *.i++ \
+                         *.inl \
+                         *.idl \
+                         *.ddl \
+                         *.odl \
+                         *.h \
                          *.hh \
+                         *.hxx \
+                         *.hpp \
+                         *.h++ \
+                         *.ixx \
+                         *.l \
+                         *.cs \
+                         *.d \
+                         *.php \
+                         *.php4 \
+                         *.php5 \
+                         *.phtml \
+                         *.inc \
+                         *.m \
+                         *.markdown \
+                         *.md \
+                         *.mm \
+                         *.dox \
+                         *.py \
+                         *.pyw \
+                         *.f90 \
+                         *.f95 \
+                         *.f03 \
+                         *.f08 \
+                         *.f18 \
+                         *.f \
+                         *.for \
+                         *.vhd \
+                         *.vhdl \
+                         *.ucf \
+                         *.qsf \
+                         *.ice
+
+# The RECURSIVE tag can be used to specify whether or not subdirectories should
+# be searched for input files as well.
+# The default value is: NO.
+
 RECURSIVE              = YES
-EXCLUDE                = 
-EXCLUDE_PATTERNS       = 
-EXAMPLE_PATH           = 
-EXAMPLE_PATTERNS       = 
+
+# The EXCLUDE tag can be used to specify files and/or directories that should be
+# excluded from the INPUT source files. This way you can easily exclude a
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+#
+# Note that relative paths are relative to the directory from which doxygen is
+# run.
+
+EXCLUDE                =
+
+# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
+# directories that are symbolic links (a Unix file system feature) are excluded
+# from the input.
+# The default value is: NO.
+
+EXCLUDE_SYMLINKS       = NO
+
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories.
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories for example use the pattern */test/*
+
+EXCLUDE_PATTERNS       =
+
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
+# (namespaces, classes, functions, etc.) that should be excluded from the
+# output. The symbol name can be a fully qualified name, a word, or if the
+# wildcard * is used, a substring. Examples: ANamespace, AClass,
+# ANamespace::AClass, ANamespace::*Test
+
+EXCLUDE_SYMBOLS        =
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or directories
+# that contain example code fragments that are included (see the \include
+# command).
+
+EXAMPLE_PATH           =
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
+# *.h) to filter out the source-files in the directories. If left blank all
+# files are included.
+
+EXAMPLE_PATTERNS       = *
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
+# searched for input files to be used with the \include or \dontinclude commands
+# irrespective of the value of the RECURSIVE tag.
+# The default value is: NO.
+
 EXAMPLE_RECURSIVE      = NO
-IMAGE_PATH             = 
-INPUT_FILTER           = 
+
+# The IMAGE_PATH tag can be used to specify one or more files or directories
+# that contain images that are to be included in the documentation (see the
+# \image command).
+
+IMAGE_PATH             =
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should
+# invoke to filter for each input file. Doxygen will invoke the filter program
+# by executing (via popen()) the command:
+#
+# <filter> <input-file>
+#
+# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the
+# name of an input file. Doxygen will then use the output that the filter
+# program writes to standard output. If FILTER_PATTERNS is specified, this tag
+# will be ignored.
+#
+# Note that the filter must not add or remove lines; it is applied before the
+# code is scanned, but not when the output code is generated. If lines are added
+# or removed, the anchors will not be placed correctly.
+#
+# Note that doxygen will use the data processed and written to standard output
+# for further processing, therefore nothing else, like debug statements or used
+# commands (so in case of a Windows batch file always use @echo OFF), should be
+# written to standard output.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
+
+INPUT_FILTER           =
+
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
+# basis. Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match. The filters are a list of the form: pattern=filter
+# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
+# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
+# patterns match the file name, INPUT_FILTER is applied.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
+
+FILTER_PATTERNS        =
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+# INPUT_FILTER) will also be used to filter the input files that are used for
+# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
+# The default value is: NO.
+
 FILTER_SOURCE_FILES    = NO
+
+# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
+# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
+# it is also possible to disable source filtering for a specific pattern using
+# *.ext= (so without naming a filter).
+# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
+
+FILTER_SOURCE_PATTERNS =
+
+# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
+# is part of the input, its contents will be placed on the main page
+# (index.html). This can be useful if you have a project on for instance GitHub
+# and want to reuse the introduction page also for the doxygen output.
+
+USE_MDFILE_AS_MAINPAGE =
+
+# The Fortran standard specifies that for fixed formatted Fortran code all
+# characters from position 72 are to be considered as comment. A common
+# extension is to allow longer lines before the automatic comment starts. The
+# setting FORTRAN_COMMENT_AFTER will also make it possible that longer lines can
+# be processed before the automatic comment starts.
+# Minimum value: 7, maximum value: 10000, default value: 72.
+
+FORTRAN_COMMENT_AFTER  = 72
+
 #---------------------------------------------------------------------------
-# configuration options related to source browsing
+# Configuration options related to source browsing
 #---------------------------------------------------------------------------
-SOURCE_BROWSER         = YES
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
+# generated. Documented entities will be cross-referenced with these sources.
+#
+# Note: To get rid of all source code in the generated output, make sure that
+# also VERBATIM_HEADERS is set to NO.
+# The default value is: NO.
+
+SOURCE_BROWSER         = NO
+
+# Setting the INLINE_SOURCES tag to YES will include the body of functions,
+# classes and enums directly into the documentation.
+# The default value is: NO.
+
 INLINE_SOURCES         = NO
-REFERENCED_BY_RELATION = YES
-REFERENCES_RELATION    = YES
+
+# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
+# special comment blocks from generated source code fragments. Normal C, C++ and
+# Fortran comments will always remain visible.
+# The default value is: YES.
+
+STRIP_CODE_COMMENTS    = YES
+
+# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
+# entity all documented functions referencing it will be listed.
+# The default value is: NO.
+
+REFERENCED_BY_RELATION = NO
+
+# If the REFERENCES_RELATION tag is set to YES then for each documented function
+# all documented entities called/used by that function will be listed.
+# The default value is: NO.
+
+REFERENCES_RELATION    = NO
+
+# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
+# to YES then the hyperlinks from functions in REFERENCES_RELATION and
+# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
+# link to the documentation.
+# The default value is: YES.
+
+REFERENCES_LINK_SOURCE = YES
+
+# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
+# source code will show a tooltip with additional information such as prototype,
+# brief description and links to the definition and documentation. Since this
+# will make the HTML file larger and loading of large files a bit slower, you
+# can opt to disable this feature.
+# The default value is: YES.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+SOURCE_TOOLTIPS        = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code will
+# point to the HTML generated by the htags(1) tool instead of doxygen built-in
+# source browser. The htags tool is part of GNU's global source tagging system
+# (see https://www.gnu.org/software/global/global.html). You will need version
+# 4.8.6 or higher.
+#
+# To use it do the following:
+# - Install the latest version of global
+# - Enable SOURCE_BROWSER and USE_HTAGS in the configuration file
+# - Make sure the INPUT points to the root of the source tree
+# - Run doxygen as normal
+#
+# Doxygen will invoke htags (and that will in turn invoke gtags), so these
+# tools must be available from the command line (i.e. in the search path).
+#
+# The result: instead of the source browser generated by doxygen, the links to
+# source code will now point to the output of htags.
+# The default value is: NO.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+USE_HTAGS              = NO
+
+# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
+# verbatim copy of the header file for each class for which an include is
+# specified. Set to NO to disable this.
+# See also: Section \class.
+# The default value is: YES.
+
+VERBATIM_HEADERS       = YES
+
 #---------------------------------------------------------------------------
-# configuration options related to the alphabetical class index
+# Configuration options related to the alphabetical class index
 #---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
+# compounds will be generated. Enable this if the project contains a lot of
+# classes, structs, unions or interfaces.
+# The default value is: YES.
+
 ALPHABETICAL_INDEX     = YES
-COLS_IN_ALPHA_INDEX    = 4
-IGNORE_PREFIX          = ZD
+
+# The IGNORE_PREFIX tag can be used to specify a prefix (or a list of prefixes)
+# that should be ignored while generating the index headers. The IGNORE_PREFIX
+# tag works for classes, function and member names. The entity will be placed in
+# the alphabetical list under the first letter of the entity name that remains
+# after removing the prefix.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
+
+IGNORE_PREFIX          =
+
 #---------------------------------------------------------------------------
-# configuration options related to the HTML output
+# Configuration options related to the HTML output
 #---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
+# The default value is: YES.
+
 GENERATE_HTML          = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
 HTML_OUTPUT            = html
-HTML_HEADER            = 
-HTML_FOOTER            = 
-HTML_STYLESHEET        = 
-HTML_ALIGN_MEMBERS     = YES
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
+# generated HTML page (for example: .htm, .php, .asp).
+# The default value is: .html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FILE_EXTENSION    = .html
+
+# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
+# each generated HTML page. If the tag is left blank doxygen will generate a
+# standard header.
+#
+# To get valid HTML the header file that includes any scripts and style sheets
+# that doxygen needs, which is dependent on the configuration options used (e.g.
+# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
+# default header using
+# doxygen -w html new_header.html new_footer.html new_stylesheet.css
+# YourConfigFile
+# and then modify the file new_header.html. See also section "Doxygen usage"
+# for information on how to generate the default header that doxygen normally
+# uses.
+# Note: The header is subject to change so you typically have to regenerate the
+# default header when upgrading to a newer version of doxygen. For a description
+# of the possible markers and block names see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_HEADER            =
+
+# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
+# generated HTML page. If the tag is left blank doxygen will generate a standard
+# footer. See HTML_HEADER for more information on how to generate a default
+# footer and what special commands can be used inside the footer. See also
+# section "Doxygen usage" for information on how to generate the default footer
+# that doxygen normally uses.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FOOTER            =
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
+# sheet that is used by each HTML page. It can be used to fine-tune the look of
+# the HTML output. If left blank doxygen will generate a default style sheet.
+# See also section "Doxygen usage" for information on how to generate the style
+# sheet that doxygen normally uses.
+# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
+# it is more robust and this tag (HTML_STYLESHEET) will in the future become
+# obsolete.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_STYLESHEET        =
+
+# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# cascading style sheets that are included after the standard style sheets
+# created by doxygen. Using this option one can overrule certain style aspects.
+# This is preferred over using HTML_STYLESHEET since it does not replace the
+# standard style sheet and is therefore more robust against future updates.
+# Doxygen will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list).
+# Note: Since the styling of scrollbars can currently not be overruled in
+# Webkit/Chromium, the styling will be left out of the default doxygen.css if
+# one or more extra stylesheets have been specified. So if scrollbar
+# customization is desired it has to be added explicitly. For an example see the
+# documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_STYLESHEET  =
+
+# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the HTML output directory. Note
+# that these files will be copied to the base HTML output directory. Use the
+# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
+# files will be copied as-is; there are no commands or markers available.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_FILES       =
+
+# The HTML_COLORSTYLE tag can be used to specify if the generated HTML output
+# should be rendered with a dark or light theme.
+# Possible values are: LIGHT always generate light mode output, DARK always
+# generate dark mode output, AUTO_LIGHT automatically set the mode according to
+# the user preference, use light mode if no preference is set (the default),
+# AUTO_DARK automatically set the mode according to the user preference, use
+# dark mode if no preference is set and TOGGLE allow to user to switch between
+# light and dark mode via a button.
+# The default value is: AUTO_LIGHT.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE        = AUTO_LIGHT
+
+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
+# will adjust the colors in the style sheet and background images according to
+# this color. Hue is specified as an angle on a color-wheel, see
+# https://en.wikipedia.org/wiki/Hue for more information. For instance the value
+# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
+# purple, and 360 is red again.
+# Minimum value: 0, maximum value: 359, default value: 220.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_HUE    = 220
+
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
+# in the HTML output. For a value of 0 the output will use gray-scales only. A
+# value of 255 will produce the most vivid colors.
+# Minimum value: 0, maximum value: 255, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_SAT    = 100
+
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
+# luminance component of the colors in the HTML output. Values below 100
+# gradually make the output lighter, whereas values above 100 make the output
+# darker. The value divided by 100 is the actual gamma applied, so 80 represents
+# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
+# change the gamma.
+# Minimum value: 40, maximum value: 240, default value: 80.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_GAMMA  = 80
+
+# If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML
+# documentation will contain a main index with vertical navigation menus that
+# are dynamically created via JavaScript. If disabled, the navigation index will
+# consists of multiple levels of tabs that are statically embedded in every HTML
+# page. Disable this option to support browsers that do not have JavaScript,
+# like the Qt help browser.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_DYNAMIC_MENUS     = YES
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
+# page has loaded.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_DYNAMIC_SECTIONS  = NO
+
+# If the HTML_CODE_FOLDING tag is set to YES then classes and functions can be
+# dynamically folded and expanded in the generated HTML source code.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_CODE_FOLDING      = YES
+
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
+# shown in the various tree structured indices initially; the user can expand
+# and collapse entries dynamically later on. Doxygen will expand the tree to
+# such a level that at most the specified number of entries are visible (unless
+# a fully collapsed tree already exceeds this amount). So setting the number of
+# entries 1 will produce a full collapsed tree by default. 0 is a special value
+# representing an infinite number of entries and will result in a full expanded
+# tree by default.
+# Minimum value: 0, maximum value: 9999, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
+# If the GENERATE_DOCSET tag is set to YES, additional index files will be
+# generated that can be used as input for Apple's Xcode 3 integrated development
+# environment (see:
+# https://developer.apple.com/xcode/), introduced with OSX 10.5 (Leopard). To
+# create a documentation set, doxygen will generate a Makefile in the HTML
+# output directory. Running make will produce the docset in that directory and
+# running make install will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
+# startup. See https://developer.apple.com/library/archive/featuredarticles/Doxy
+# genXcode/_index.html for more information.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_DOCSET        = NO
+
+# This tag determines the name of the docset feed. A documentation feed provides
+# an umbrella under which multiple documentation sets from a single provider
+# (such as a company or product suite) can be grouped.
+# The default value is: Doxygen generated docs.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_FEEDNAME        = "Doxygen generated docs"
+
+# This tag determines the URL of the docset feed. A documentation feed provides
+# an umbrella under which multiple documentation sets from a single provider
+# (such as a company or product suite) can be grouped.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_FEEDURL         =
+
+# This tag specifies a string that should uniquely identify the documentation
+# set bundle. This should be a reverse domain-name style string, e.g.
+# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_BUNDLE_ID       = org.doxygen.Project
+
+# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
+# the documentation publisher. This should be a reverse domain-name style
+# string, e.g. com.mycompany.MyDocSet.documentation.
+# The default value is: org.doxygen.Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
+
+# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
+# The default value is: Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_PUBLISHER_NAME  = Publisher
+
+# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
+# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
+# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
+# on Windows. In the beginning of 2021 Microsoft took the original page, with
+# a.o. the download links, offline the HTML help workshop was already many years
+# in maintenance mode). You can download the HTML help workshop from the web
+# archives at Installation executable (see:
+# http://web.archive.org/web/20160201063255/http://download.microsoft.com/downlo
+# ad/0/A/9/0A939EF6-E31C-430F-A3DF-DFAE7960D564/htmlhelp.exe).
+#
+# The HTML Help Workshop contains a compiler that can convert all HTML output
+# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
+# files are now used as the Windows 98 help format, and will replace the old
+# Windows help format (.hlp) on all Windows platforms in the future. Compressed
+# HTML files also contain an index, a table of contents, and you can search for
+# words in the documentation. The HTML workshop also contains a viewer for
+# compressed HTML files.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
 GENERATE_HTMLHELP      = NO
+
+# The CHM_FILE tag can be used to specify the file name of the resulting .chm
+# file. You can add a path in front of the file if the result should not be
+# written to the html output directory.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_FILE               =
+
+# The HHC_LOCATION tag can be used to specify the location (absolute path
+# including file name) of the HTML help compiler (hhc.exe). If non-empty,
+# doxygen will try to run the HTML help compiler on the generated index.hhp.
+# The file has to be specified with full path.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+HHC_LOCATION           =
+
+# The GENERATE_CHI flag controls if a separate .chi index file is generated
+# (YES) or that it should be included in the main .chm file (NO).
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
 GENERATE_CHI           = NO
+
+# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc)
+# and project file content.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_INDEX_ENCODING     =
+
+# The BINARY_TOC flag controls whether a binary table of contents is generated
+# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it
+# enables the Previous and Next buttons.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
 BINARY_TOC             = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members to
+# the table of contents of the HTML help documentation and to the tree view.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
 TOC_EXPAND             = NO
+
+# The SITEMAP_URL tag is used to specify the full URL of the place where the
+# generated documentation will be placed on the server by the user during the
+# deployment of the documentation. The generated sitemap is called sitemap.xml
+# and placed on the directory specified by HTML_OUTPUT. In case no SITEMAP_URL
+# is specified no sitemap is generated. For information about the sitemap
+# protocol see https://www.sitemaps.org
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+SITEMAP_URL            =
+
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
+# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
+# (.qch) of the generated HTML documentation.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_QHP           = NO
+
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
+# the file name of the resulting .qch file. The path specified is relative to
+# the HTML output folder.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QCH_FILE               =
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
+# Project output. For more information please see Qt Help Project / Namespace
+# (see:
+# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#namespace).
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_NAMESPACE          = org.doxygen.Project
+
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
+# Help Project output. For more information please see Qt Help Project / Virtual
+# Folders (see:
+# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#virtual-folders).
+# The default value is: doc.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_VIRTUAL_FOLDER     = doc
+
+# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
+# filter to add. For more information please see Qt Help Project / Custom
+# Filters (see:
+# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_NAME   =
+
+# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
+# custom filter to add. For more information please see Qt Help Project / Custom
+# Filters (see:
+# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_ATTRS  =
+
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
+# project's filter section matches. Qt Help Project / Filter Attributes (see:
+# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#filter-attributes).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_SECT_FILTER_ATTRS  =
+
+# The QHG_LOCATION tag can be used to specify the location (absolute path
+# including file name) of Qt's qhelpgenerator. If non-empty doxygen will try to
+# run qhelpgenerator on the generated .qhp file.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHG_LOCATION           =
+
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
+# generated, together with the HTML files, they form an Eclipse help plugin. To
+# install this plugin and make it available under the help contents menu in
+# Eclipse, the contents of the directory containing the HTML and XML files needs
+# to be copied into the plugins directory of eclipse. The name of the directory
+# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
+# After copying Eclipse needs to be restarted before the help appears.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_ECLIPSEHELP   = NO
+
+# A unique identifier for the Eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have this
+# name. Each documentation set should have its own identifier.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
+
+ECLIPSE_DOC_ID         = org.doxygen.Project
+
+# If you want full control over the layout of the generated HTML pages it might
+# be necessary to disable the index and replace it with your own. The
+# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
+# of each HTML page. A value of NO enables the index and the value YES disables
+# it. Since the tabs in the index contain the same information as the navigation
+# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
 DISABLE_INDEX          = NO
+
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
+# structure should be generated to display hierarchical information. If the tag
+# value is set to YES, a side panel will be generated containing a tree-like
+# index structure (just like the one that is generated for HTML Help). For this
+# to work a browser that supports JavaScript, DHTML, CSS and frames is required
+# (i.e. any modern browser). Windows users are probably better off using the
+# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can
+# further fine tune the look of the index (see "Fine-tuning the output"). As an
+# example, the default style sheet generated by doxygen has an example that
+# shows how to put an image at the root of the tree instead of the PROJECT_NAME.
+# Since the tree basically has the same information as the tab index, you could
+# consider setting DISABLE_INDEX to YES when enabling this option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_TREEVIEW      = NO
+
+# When both GENERATE_TREEVIEW and DISABLE_INDEX are set to YES, then the
+# FULL_SIDEBAR option determines if the side bar is limited to only the treeview
+# area (value NO) or if it should extend to the full height of the window (value
+# YES). Setting this to YES gives a layout similar to
+# https://docs.readthedocs.io with more room for contents, but less room for the
+# project logo, title, and description. If either GENERATE_TREEVIEW or
+# DISABLE_INDEX is set to NO, this option has no effect.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FULL_SIDEBAR           = NO
+
+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
+# doxygen will group on one line in the generated HTML documentation.
+#
+# Note that a value of 0 will completely suppress the enum values from appearing
+# in the overview section.
+# Minimum value: 0, maximum value: 20, default value: 4.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
 ENUM_VALUES_PER_LINE   = 4
-GENERATE_TREEVIEW      = YES
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
+# to set the initial width (in pixels) of the frame in which the tree is shown.
+# Minimum value: 0, maximum value: 1500, default value: 250.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
 TREEVIEW_WIDTH         = 250
+
+# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to
+# external symbols imported via tag files in a separate window.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+EXT_LINKS_IN_WINDOW    = NO
+
+# If the OBFUSCATE_EMAILS tag is set to YES, doxygen will obfuscate email
+# addresses.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+OBFUSCATE_EMAILS       = YES
+
+# If the HTML_FORMULA_FORMAT option is set to svg, doxygen will use the pdf2svg
+# tool (see https://github.com/dawbarton/pdf2svg) or inkscape (see
+# https://inkscape.org) to generate formulas as SVG images instead of PNGs for
+# the HTML output. These images will generally look nicer at scaled resolutions.
+# Possible values are: png (the default) and svg (looks nicer but requires the
+# pdf2svg or inkscape tool).
+# The default value is: png.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FORMULA_FORMAT    = png
+
+# Use this tag to change the font size of LaTeX formulas included as images in
+# the HTML documentation. When you change the font size after a successful
+# doxygen run you need to manually remove any form_*.png images from the HTML
+# output directory to force them to be regenerated.
+# Minimum value: 8, maximum value: 50, default value: 10.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FORMULA_FONTSIZE       = 10
+
+# The FORMULA_MACROFILE can contain LaTeX \newcommand and \renewcommand commands
+# to create new LaTeX commands to be used in formulas as building blocks. See
+# the section "Including formulas" for details.
+
+FORMULA_MACROFILE      =
+
+# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
+# https://www.mathjax.org) which uses client side JavaScript for the rendering
+# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX
+# installed or if you want to formulas look prettier in the HTML output. When
+# enabled you may also need to install MathJax separately and configure the path
+# to it using the MATHJAX_RELPATH option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+USE_MATHJAX            = NO
+
+# With MATHJAX_VERSION it is possible to specify the MathJax version to be used.
+# Note that the different versions of MathJax have different requirements with
+# regards to the different settings, so it is possible that also other MathJax
+# settings have to be changed when switching between the different MathJax
+# versions.
+# Possible values are: MathJax_2 and MathJax_3.
+# The default value is: MathJax_2.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_VERSION        = MathJax_2
+
+# When MathJax is enabled you can set the default output format to be used for
+# the MathJax output. For more details about the output format see MathJax
+# version 2 (see:
+# http://docs.mathjax.org/en/v2.7-latest/output.html) and MathJax version 3
+# (see:
+# http://docs.mathjax.org/en/latest/web/components/output.html).
+# Possible values are: HTML-CSS (which is slower, but has the best
+# compatibility. This is the name for Mathjax version 2, for MathJax version 3
+# this will be translated into chtml), NativeMML (i.e. MathML. Only supported
+# for NathJax 2. For MathJax version 3 chtml will be used instead.), chtml (This
+# is the name for Mathjax version 3, for MathJax version 2 this will be
+# translated into HTML-CSS) and SVG.
+# The default value is: HTML-CSS.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_FORMAT         = HTML-CSS
+
+# When MathJax is enabled you need to specify the location relative to the HTML
+# output directory using the MATHJAX_RELPATH option. The destination directory
+# should contain the MathJax.js script. For instance, if the mathjax directory
+# is located at the same level as the HTML output directory, then
+# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
+# Content Delivery Network so you can quickly see the result without installing
+# MathJax. However, it is strongly recommended to install a local copy of
+# MathJax from https://www.mathjax.org before deployment. The default value is:
+# - in case of MathJax version 2: https://cdn.jsdelivr.net/npm/mathjax@2
+# - in case of MathJax version 3: https://cdn.jsdelivr.net/npm/mathjax@3
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_RELPATH        =
+
+# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
+# extension names that should be enabled during MathJax rendering. For example
+# for MathJax version 2 (see
+# https://docs.mathjax.org/en/v2.7-latest/tex.html#tex-and-latex-extensions):
+# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
+# For example for MathJax version 3 (see
+# http://docs.mathjax.org/en/latest/input/tex/extensions/index.html):
+# MATHJAX_EXTENSIONS = ams
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_EXTENSIONS     =
+
+# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
+# of code that will be used on startup of the MathJax code. See the MathJax site
+# (see:
+# http://docs.mathjax.org/en/v2.7-latest/output.html) for more details. For an
+# example see the documentation.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_CODEFILE       =
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
+# the HTML output. The underlying search engine uses javascript and DHTML and
+# should work on any modern browser. Note that when using HTML help
+# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
+# there is already a search function so this one should typically be disabled.
+# For large projects the javascript based search engine can be slow, then
+# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
+# search using the keyboard; to jump to the search box use <access key> + S
+# (what the <access key> is depends on the OS and browser, but it is typically
+# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
+# key> to jump into the search results window, the results can be navigated
+# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
+# the search. The filter options can be selected when the cursor is inside the
+# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
+# to select a filter and <Enter> or <escape> to activate or cancel the filter
+# option.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+SEARCHENGINE           = YES
+
+# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
+# implemented using a web server instead of a web client using JavaScript. There
+# are two flavors of web server based searching depending on the EXTERNAL_SEARCH
+# setting. When disabled, doxygen will generate a PHP script for searching and
+# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing
+# and searching needs to be provided by external tools. See the section
+# "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SERVER_BASED_SEARCH    = NO
+
+# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP
+# script for searching. Instead the search results are written to an XML file
+# which needs to be processed by an external indexer. Doxygen will invoke an
+# external search engine pointed to by the SEARCHENGINE_URL option to obtain the
+# search results.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see:
+# https://xapian.org/).
+#
+# See the section "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH        = NO
+
+# The SEARCHENGINE_URL should point to a search engine hosted by a web server
+# which will return the search results when EXTERNAL_SEARCH is enabled.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see:
+# https://xapian.org/). See the section "External Indexing and Searching" for
+# details.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHENGINE_URL       =
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
+# search data is written to a file for indexing by an external tool. With the
+# SEARCHDATA_FILE tag the name of this file can be specified.
+# The default file is: searchdata.xml.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHDATA_FILE        = searchdata.xml
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the
+# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
+# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
+# projects and redirect the results back to the right project.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH_ID     =
+
+# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
+# projects other than the one defined by this configuration file, but that are
+# all added to the same external search index. Each project needs to have a
+# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of
+# to a relative location where the documentation can be found. The format is:
+# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ...
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTRA_SEARCH_MAPPINGS  =
+
 #---------------------------------------------------------------------------
-# configuration options related to the LaTeX output
+# Configuration options related to the LaTeX output
 #---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
+# The default value is: YES.
+
 GENERATE_LATEX         = NO
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
 LATEX_OUTPUT           = latex
+
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
+# invoked.
+#
+# Note that when not enabling USE_PDFLATEX the default is latex when enabling
+# USE_PDFLATEX the default is pdflatex and when in the later case latex is
+# chosen this is overwritten by pdflatex. For specific output languages the
+# default can have been set differently, this depends on the implementation of
+# the output language.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_CMD_NAME         =
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
+# index for LaTeX.
+# Note: This tag is used in the Makefile / make.bat.
+# See also: LATEX_MAKEINDEX_CMD for the part in the generated output file
+# (.tex).
+# The default file is: makeindex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+MAKEINDEX_CMD_NAME     = makeindex
+
+# The LATEX_MAKEINDEX_CMD tag can be used to specify the command name to
+# generate index for LaTeX. In case there is no backslash (\) as first character
+# it will be automatically added in the LaTeX code.
+# Note: This tag is used in the generated output file (.tex).
+# See also: MAKEINDEX_CMD_NAME for the part in the Makefile / make.bat.
+# The default value is: makeindex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_MAKEINDEX_CMD    = makeindex
+
+# If the COMPACT_LATEX tag is set to YES, doxygen generates more compact LaTeX
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
 COMPACT_LATEX          = NO
-PAPER_TYPE             = a4wide
-EXTRA_PACKAGES         = 
-LATEX_HEADER           = 
-PDF_HYPERLINKS         = NO
-USE_PDFLATEX           = NO
+
+# The PAPER_TYPE tag can be used to set the paper type that is used by the
+# printer.
+# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x
+# 14 inches) and executive (7.25 x 10.5 inches).
+# The default value is: a4.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+PAPER_TYPE             = a4
+
+# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
+# that should be included in the LaTeX output. The package can be specified just
+# by its name or with the correct syntax as to be used with the LaTeX
+# \usepackage command. To get the times font for instance you can specify :
+# EXTRA_PACKAGES=times or EXTRA_PACKAGES={times}
+# To use the option intlimits with the amsmath package you can specify:
+# EXTRA_PACKAGES=[intlimits]{amsmath}
+# If left blank no extra packages will be included.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+EXTRA_PACKAGES         =
+
+# The LATEX_HEADER tag can be used to specify a user-defined LaTeX header for
+# the generated LaTeX document. The header should contain everything until the
+# first chapter. If it is left blank doxygen will generate a standard header. It
+# is highly recommended to start with a default header using
+# doxygen -w latex new_header.tex new_footer.tex new_stylesheet.sty
+# and then modify the file new_header.tex. See also section "Doxygen usage" for
+# information on how to generate the default header that doxygen normally uses.
+#
+# Note: Only use a user-defined header if you know what you are doing!
+# Note: The header is subject to change so you typically have to regenerate the
+# default header when upgrading to a newer version of doxygen. The following
+# commands have a special meaning inside the header (and footer): For a
+# description of the possible markers and block names see the documentation.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_HEADER           =
+
+# The LATEX_FOOTER tag can be used to specify a user-defined LaTeX footer for
+# the generated LaTeX document. The footer should contain everything after the
+# last chapter. If it is left blank doxygen will generate a standard footer. See
+# LATEX_HEADER for more information on how to generate a default footer and what
+# special commands can be used inside the footer. See also section "Doxygen
+# usage" for information on how to generate the default footer that doxygen
+# normally uses. Note: Only use a user-defined footer if you know what you are
+# doing!
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_FOOTER           =
+
+# The LATEX_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# LaTeX style sheets that are included after the standard style sheets created
+# by doxygen. Using this option one can overrule certain style aspects. Doxygen
+# will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list).
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_STYLESHEET =
+
+# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the LATEX_OUTPUT output
+# directory. Note that the files will be copied as-is; there are no commands or
+# markers available.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_FILES      =
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
+# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will
+# contain links (just like the HTML output) instead of page references. This
+# makes the output suitable for online browsing using a PDF viewer.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+PDF_HYPERLINKS         = YES
+
+# If the USE_PDFLATEX tag is set to YES, doxygen will use the engine as
+# specified with LATEX_CMD_NAME to generate the PDF file directly from the LaTeX
+# files. Set this option to YES, to get a higher quality PDF documentation.
+#
+# See also section LATEX_CMD_NAME for selecting the engine.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+USE_PDFLATEX           = YES
+
+# The LATEX_BATCHMODE tag signals the behavior of LaTeX in case of an error.
+# Possible values are: NO same as ERROR_STOP, YES same as BATCH, BATCH In batch
+# mode nothing is printed on the terminal, errors are scrolled as if <return> is
+# hit at every error; missing files that TeX tries to input or request from
+# keyboard input (\read on a not open input stream) cause the job to abort,
+# NON_STOP In nonstop mode the diagnostic message will appear on the terminal,
+# but there is no possibility of user interaction just like in batch mode,
+# SCROLL In scroll mode, TeX will stop only for missing files to input or if
+# keyboard input is necessary and ERROR_STOP In errorstop mode, TeX will stop at
+# each error, asking for user intervention.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
 LATEX_BATCHMODE        = NO
+
+# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the
+# index chapters (such as File Index, Compound Index, etc.) in the output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_HIDE_INDICES     = NO
+
+# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
+# bibliography, e.g. plainnat, or ieeetr. See
+# https://en.wikipedia.org/wiki/BibTeX and \cite for more info.
+# The default value is: plain.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_BIB_STYLE        = plain
+
+# The LATEX_EMOJI_DIRECTORY tag is used to specify the (relative or absolute)
+# path from which the emoji images will be read. If a relative path is entered,
+# it will be relative to the LATEX_OUTPUT directory. If left blank the
+# LATEX_OUTPUT directory will be used.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EMOJI_DIRECTORY  =
+
 #---------------------------------------------------------------------------
-# configuration options related to the RTF output
+# Configuration options related to the RTF output
 #---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES, doxygen will generate RTF output. The
+# RTF output is optimized for Word 97 and may not look too pretty with other RTF
+# readers/editors.
+# The default value is: NO.
+
 GENERATE_RTF           = NO
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: rtf.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
 RTF_OUTPUT             = rtf
+
+# If the COMPACT_RTF tag is set to YES, doxygen generates more compact RTF
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
 COMPACT_RTF            = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will
+# contain hyperlink fields. The RTF file will contain links (just like the HTML
+# output) instead of page references. This makes the output suitable for online
+# browsing using Word or some other Word compatible readers that support those
+# fields.
+#
+# Note: WordPad (write) and others do not support links.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
 RTF_HYPERLINKS         = NO
-RTF_STYLESHEET_FILE    = 
-RTF_EXTENSIONS_FILE    = 
+
+# Load stylesheet definitions from file. Syntax is similar to doxygen's
+# configuration file, i.e. a series of assignments. You only have to provide
+# replacements, missing definitions are set to their default value.
+#
+# See also section "Doxygen usage" for information on how to generate the
+# default style sheet that doxygen normally uses.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_STYLESHEET_FILE    =
+
+# Set optional variables used in the generation of an RTF document. Syntax is
+# similar to doxygen's configuration file. A template extensions file can be
+# generated using doxygen -e rtf extensionFile.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_EXTENSIONS_FILE    =
+
 #---------------------------------------------------------------------------
-# configuration options related to the man page output
+# Configuration options related to the man page output
 #---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for
+# classes and files.
+# The default value is: NO.
+
 GENERATE_MAN           = NO
+
+# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it. A directory man3 will be created inside the directory specified by
+# MAN_OUTPUT.
+# The default directory is: man.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
 MAN_OUTPUT             = man
+
+# The MAN_EXTENSION tag determines the extension that is added to the generated
+# man pages. In case the manual section does not start with a number, the number
+# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is
+# optional.
+# The default value is: .3.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
 MAN_EXTENSION          = .3
+
+# The MAN_SUBDIR tag determines the name of the directory created within
+# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by
+# MAN_EXTENSION with the initial . removed.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_SUBDIR             =
+
+# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it
+# will generate one additional man file for each entity documented in the real
+# man page(s). These additional files only source the real man page, but without
+# them the man command would be unable to find the correct page.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
 MAN_LINKS              = NO
+
 #---------------------------------------------------------------------------
-# configuration options related to the XML output
+# Configuration options related to the XML output
 #---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES, doxygen will generate an XML file that
+# captures the structure of the code including all documentation.
+# The default value is: NO.
+
 GENERATE_XML           = NO
+
+# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: xml.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_OUTPUT             = xml
+
+# If the XML_PROGRAMLISTING tag is set to YES, doxygen will dump the program
+# listings (including syntax highlighting and cross-referencing information) to
+# the XML output. Note that enabling this will significantly increase the size
+# of the XML output.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_PROGRAMLISTING     = YES
+
+# If the XML_NS_MEMB_FILE_SCOPE tag is set to YES, doxygen will include
+# namespace members in file scope as well, matching the HTML output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_NS_MEMB_FILE_SCOPE = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the DOCBOOK output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_DOCBOOK tag is set to YES, doxygen will generate Docbook files
+# that can be used to generate PDF.
+# The default value is: NO.
+
+GENERATE_DOCBOOK       = NO
+
+# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
+# front of it.
+# The default directory is: docbook.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_OUTPUT         = docbook
+
 #---------------------------------------------------------------------------
-# configuration options for the AutoGen Definitions output
+# Configuration options for the AutoGen Definitions output
 #---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an
+# AutoGen Definitions (see https://autogen.sourceforge.net/) file that captures
+# the structure of the code including all documentation. Note that this feature
+# is still experimental and incomplete at the moment.
+# The default value is: NO.
+
 GENERATE_AUTOGEN_DEF   = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to Sqlite3 output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_SQLITE3 tag is set to YES doxygen will generate a Sqlite3
+# database with symbols found by doxygen stored in tables.
+# The default value is: NO.
+
+GENERATE_SQLITE3       = NO
+
+# The SQLITE3_OUTPUT tag is used to specify where the Sqlite3 database will be
+# put. If a relative path is entered the value of OUTPUT_DIRECTORY will be put
+# in front of it.
+# The default directory is: sqlite3.
+# This tag requires that the tag GENERATE_SQLITE3 is set to YES.
+
+SQLITE3_OUTPUT         = sqlite3
+
+# The SQLITE3_OVERWRITE_DB tag is set to YES, the existing doxygen_sqlite3.db
+# database file will be recreated with each doxygen run. If set to NO, doxygen
+# will warn if an a database file is already found and not modify it.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_SQLITE3 is set to YES.
+
+SQLITE3_RECREATE_DB    = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES, doxygen will generate a Perl module
+# file that captures the structure of the code including all documentation.
+#
+# Note that this feature is still experimental and incomplete at the moment.
+# The default value is: NO.
+
+GENERATE_PERLMOD       = NO
+
+# If the PERLMOD_LATEX tag is set to YES, doxygen will generate the necessary
+# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI
+# output from the Perl module output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_LATEX          = NO
+
+# If the PERLMOD_PRETTY tag is set to YES, the Perl module output will be nicely
+# formatted so it can be parsed by a human reader. This is useful if you want to
+# understand what is going on. On the other hand, if this tag is set to NO, the
+# size of the Perl module output will be much smaller and Perl will parse it
+# just the same.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_PRETTY         = YES
+
+# The names of the make variables in the generated doxyrules.make file are
+# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful
+# so different doxyrules.make files included by the same Makefile don't
+# overwrite each other's variables.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_MAKEVAR_PREFIX =
+
 #---------------------------------------------------------------------------
-# Configuration options related to the preprocessor   
+# Configuration options related to the preprocessor
 #---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all
+# C-preprocessor directives found in the sources and include files.
+# The default value is: YES.
+
 ENABLE_PREPROCESSING   = YES
+
+# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names
+# in the source code. If set to NO, only conditional compilation will be
+# performed. Macro expansion can be done in a controlled way by setting
+# EXPAND_ONLY_PREDEF to YES.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
 MACRO_EXPANSION        = NO
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
+# the macro expansion is limited to the macros specified with the PREDEFINED and
+# EXPAND_AS_DEFINED tags.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
 EXPAND_ONLY_PREDEF     = NO
+
+# If the SEARCH_INCLUDES tag is set to YES, the include files in the
+# INCLUDE_PATH will be searched if a #include is found.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
 SEARCH_INCLUDES        = YES
-INCLUDE_PATH           = 
-INCLUDE_FILE_PATTERNS  = 
-PREDEFINED             = 
-EXPAND_AS_DEFINED      = 
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that
+# contain include files that are not input files but should be processed by the
+# preprocessor. Note that the INCLUDE_PATH is not recursive, so the setting of
+# RECURSIVE has no effect here.
+# This tag requires that the tag SEARCH_INCLUDES is set to YES.
+
+INCLUDE_PATH           =
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
+# patterns (like *.h and *.hpp) to filter out the header-files in the
+# directories. If left blank, the patterns specified with FILE_PATTERNS will be
+# used.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+INCLUDE_FILE_PATTERNS  =
+
+# The PREDEFINED tag can be used to specify one or more macro names that are
+# defined before the preprocessor is started (similar to the -D option of e.g.
+# gcc). The argument of the tag is a list of macros of the form: name or
+# name=definition (no spaces). If the definition and the "=" are omitted, "=1"
+# is assumed. To prevent a macro definition from being undefined via #undef or
+# recursively expanded use the := operator instead of the = operator.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+PREDEFINED             =
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
+# tag can be used to specify a list of macro names that should be expanded. The
+# macro definition that is found in the sources will be used. Use the PREDEFINED
+# tag if you want to use a different macro definition that overrules the
+# definition found in the source code.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+EXPAND_AS_DEFINED      =
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
+# remove all references to function-like macros that are alone on a line, have
+# an all uppercase name, and do not end with a semicolon. Such function macros
+# are typically used for boiler-plate code, and will confuse the parser if not
+# removed.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
 SKIP_FUNCTION_MACROS   = YES
+
 #---------------------------------------------------------------------------
-# Configuration::addtions related to external references   
+# Configuration options related to external references
 #---------------------------------------------------------------------------
-TAGFILES               = 
-GENERATE_TAGFILE       = 
+
+# The TAGFILES tag can be used to specify one or more tag files. For each tag
+# file the location of the external documentation should be added. The format of
+# a tag file without this location is as follows:
+# TAGFILES = file1 file2 ...
+# Adding location for the tag files is done as follows:
+# TAGFILES = file1=loc1 "file2 = loc2" ...
+# where loc1 and loc2 can be relative or absolute paths or URLs. See the
+# section "Linking to external documentation" for more information about the use
+# of tag files.
+# Note: Each tag file must have a unique name (where the name does NOT include
+# the path). If a tag file is not located in the directory in which doxygen is
+# run, you must also specify the path to the tagfile here.
+
+TAGFILES               =
+
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create a
+# tag file that is based on the input files it reads. See section "Linking to
+# external documentation" for more information about the usage of tag files.
+
+GENERATE_TAGFILE       =
+
+# If the ALLEXTERNALS tag is set to YES, all external classes and namespaces
+# will be listed in the class and namespace index. If set to NO, only the
+# inherited external classes will be listed.
+# The default value is: NO.
+
 ALLEXTERNALS           = NO
-PERL_PATH              = /usr/bin/perl
+
+# If the EXTERNAL_GROUPS tag is set to YES, all external groups will be listed
+# in the topic index. If set to NO, only the current project's groups will be
+# listed.
+# The default value is: YES.
+
+EXTERNAL_GROUPS        = YES
+
+# If the EXTERNAL_PAGES tag is set to YES, all external pages will be listed in
+# the related pages index. If set to NO, only the current project's pages will
+# be listed.
+# The default value is: YES.
+
+EXTERNAL_PAGES         = YES
+
 #---------------------------------------------------------------------------
-# Configuration options related to the dot tool   
+# Configuration options related to diagram generator tools
 #---------------------------------------------------------------------------
-CLASS_DIAGRAMS         = YES
-HAVE_DOT               = YES
+
+# If set to YES the inheritance and collaboration graphs will hide inheritance
+# and usage relations if the target is undocumented or is not a class.
+# The default value is: YES.
+
+HIDE_UNDOC_RELATIONS   = YES
+
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
+# available from the path. This tool is part of Graphviz (see:
+# https://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
+# Bell Labs. The other options in this section have no effect if this option is
+# set to NO
+# The default value is: NO.
+
+HAVE_DOT               = NO
+
+# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed
+# to run in parallel. When set to 0 doxygen will base this on the number of
+# processors available in the system. You can set it explicitly to a value
+# larger than 0 to get control over the balance between CPU load and processing
+# speed.
+# Minimum value: 0, maximum value: 32, default value: 0.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_NUM_THREADS        = 0
+
+# DOT_COMMON_ATTR is common attributes for nodes, edges and labels of
+# subgraphs. When you want a differently looking font in the dot files that
+# doxygen generates you can specify fontname, fontcolor and fontsize attributes.
+# For details please see <a href=https://graphviz.org/doc/info/attrs.html>Node,
+# Edge and Graph Attributes specification</a> You need to make sure dot is able
+# to find the font, which can be done by putting it in a standard location or by
+# setting the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the
+# directory containing the font. Default graphviz fontsize is 14.
+# The default value is: fontname=Helvetica,fontsize=10.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_COMMON_ATTR        = "fontname=Helvetica,fontsize=10"
+
+# DOT_EDGE_ATTR is concatenated with DOT_COMMON_ATTR. For elegant style you can
+# add 'arrowhead=open, arrowtail=open, arrowsize=0.5'. <a
+# href=https://graphviz.org/doc/info/arrows.html>Complete documentation about
+# arrows shapes.</a>
+# The default value is: labelfontname=Helvetica,labelfontsize=10.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_EDGE_ATTR          = "labelfontname=Helvetica,labelfontsize=10"
+
+# DOT_NODE_ATTR is concatenated with DOT_COMMON_ATTR. For view without boxes
+# around nodes set 'shape=plain' or 'shape=plaintext' <a
+# href=https://www.graphviz.org/doc/info/shapes.html>Shapes specification</a>
+# The default value is: shape=box,height=0.2,width=0.4.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_NODE_ATTR          = "shape=box,height=0.2,width=0.4"
+
+# You can set the path where dot can find font specified with fontname in
+# DOT_COMMON_ATTR and others dot attributes.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_FONTPATH           =
+
+# If the CLASS_GRAPH tag is set to YES or GRAPH or BUILTIN then doxygen will
+# generate a graph for each documented class showing the direct and indirect
+# inheritance relations. In case the CLASS_GRAPH tag is set to YES or GRAPH and
+# HAVE_DOT is enabled as well, then dot will be used to draw the graph. In case
+# the CLASS_GRAPH tag is set to YES and HAVE_DOT is disabled or if the
+# CLASS_GRAPH tag is set to BUILTIN, then the built-in generator will be used.
+# If the CLASS_GRAPH tag is set to TEXT the direct and indirect inheritance
+# relations will be shown as texts / links.
+# Possible values are: NO, YES, TEXT, GRAPH and BUILTIN.
+# The default value is: YES.
+
 CLASS_GRAPH            = YES
+
+# If the COLLABORATION_GRAPH tag is set to YES then doxygen will generate a
+# graph for each documented class showing the direct and indirect implementation
+# dependencies (inheritance, containment, and class references variables) of the
+# class with other documented classes. Explicit enabling a collaboration graph,
+# when COLLABORATION_GRAPH is set to NO, can be accomplished by means of the
+# command \collaborationgraph. Disabling a collaboration graph can be
+# accomplished by means of the command \hidecollaborationgraph.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
 COLLABORATION_GRAPH    = YES
-TEMPLATE_RELATIONS     = YES
-HIDE_UNDOC_RELATIONS   = YES
+
+# If the GROUP_GRAPHS tag is set to YES then doxygen will generate a graph for
+# groups, showing the direct groups dependencies. Explicit enabling a group
+# dependency graph, when GROUP_GRAPHS is set to NO, can be accomplished by means
+# of the command \groupgraph. Disabling a directory graph can be accomplished by
+# means of the command \hidegroupgraph. See also the chapter Grouping in the
+# manual.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+GROUP_GRAPHS           = YES
+
+# If the UML_LOOK tag is set to YES, doxygen will generate inheritance and
+# collaboration diagrams in a style similar to the OMG's Unified Modeling
+# Language.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+UML_LOOK               = NO
+
+# If the UML_LOOK tag is enabled, the fields and methods are shown inside the
+# class node. If there are many fields or methods and many nodes the graph may
+# become too big to be useful. The UML_LIMIT_NUM_FIELDS threshold limits the
+# number of items for each type to make the size more manageable. Set this to 0
+# for no limit. Note that the threshold may be exceeded by 50% before the limit
+# is enforced. So when you set the threshold to 10, up to 15 fields may appear,
+# but if the number exceeds 15, the total amount of fields shown is limited to
+# 10.
+# Minimum value: 0, maximum value: 100, default value: 10.
+# This tag requires that the tag UML_LOOK is set to YES.
+
+UML_LIMIT_NUM_FIELDS   = 10
+
+# If the DOT_UML_DETAILS tag is set to NO, doxygen will show attributes and
+# methods without types and arguments in the UML graphs. If the DOT_UML_DETAILS
+# tag is set to YES, doxygen will add type and arguments for attributes and
+# methods in the UML graphs. If the DOT_UML_DETAILS tag is set to NONE, doxygen
+# will not generate fields with class member information in the UML graphs. The
+# class diagrams will look similar to the default class diagrams but using UML
+# notation for the relationships.
+# Possible values are: NO, YES and NONE.
+# The default value is: NO.
+# This tag requires that the tag UML_LOOK is set to YES.
+
+DOT_UML_DETAILS        = NO
+
+# The DOT_WRAP_THRESHOLD tag can be used to set the maximum number of characters
+# to display on a single line. If the actual line length exceeds this threshold
+# significantly it will wrapped across multiple lines. Some heuristics are apply
+# to avoid ugly line breaks.
+# Minimum value: 0, maximum value: 1000, default value: 17.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_WRAP_THRESHOLD     = 17
+
+# If the TEMPLATE_RELATIONS tag is set to YES then the inheritance and
+# collaboration graphs will show the relations between templates and their
+# instances.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+TEMPLATE_RELATIONS     = NO
+
+# If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to
+# YES then doxygen will generate a graph for each documented file showing the
+# direct and indirect include dependencies of the file with other documented
+# files. Explicit enabling an include graph, when INCLUDE_GRAPH is is set to NO,
+# can be accomplished by means of the command \includegraph. Disabling an
+# include graph can be accomplished by means of the command \hideincludegraph.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
 INCLUDE_GRAPH          = YES
+
+# If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are
+# set to YES then doxygen will generate a graph for each documented file showing
+# the direct and indirect include dependencies of the file with other documented
+# files. Explicit enabling an included by graph, when INCLUDED_BY_GRAPH is set
+# to NO, can be accomplished by means of the command \includedbygraph. Disabling
+# an included by graph can be accomplished by means of the command
+# \hideincludedbygraph.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
 INCLUDED_BY_GRAPH      = YES
+
+# If the CALL_GRAPH tag is set to YES then doxygen will generate a call
+# dependency graph for every global function or class method.
+#
+# Note that enabling this option will significantly increase the time of a run.
+# So in most cases it will be better to enable call graphs for selected
+# functions only using the \callgraph command. Disabling a call graph can be
+# accomplished by means of the command \hidecallgraph.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+CALL_GRAPH             = NO
+
+# If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller
+# dependency graph for every global function or class method.
+#
+# Note that enabling this option will significantly increase the time of a run.
+# So in most cases it will be better to enable caller graphs for selected
+# functions only using the \callergraph command. Disabling a caller graph can be
+# accomplished by means of the command \hidecallergraph.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+CALLER_GRAPH           = NO
+
+# If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical
+# hierarchy of all classes instead of a textual one.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
 GRAPHICAL_HIERARCHY    = YES
-DOT_PATH               = 
-DOTFILE_DIRS           = 
-MAX_DOT_GRAPH_WIDTH    = 1024
-MAX_DOT_GRAPH_HEIGHT   = 1024
+
+# If the DIRECTORY_GRAPH tag is set to YES then doxygen will show the
+# dependencies a directory has on other directories in a graphical way. The
+# dependency relations are determined by the #include relations between the
+# files in the directories. Explicit enabling a directory graph, when
+# DIRECTORY_GRAPH is set to NO, can be accomplished by means of the command
+# \directorygraph. Disabling a directory graph can be accomplished by means of
+# the command \hidedirectorygraph.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DIRECTORY_GRAPH        = YES
+
+# The DIR_GRAPH_MAX_DEPTH tag can be used to limit the maximum number of levels
+# of child directories generated in directory dependency graphs by dot.
+# Minimum value: 1, maximum value: 25, default value: 1.
+# This tag requires that the tag DIRECTORY_GRAPH is set to YES.
+
+DIR_GRAPH_MAX_DEPTH    = 1
+
+# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
+# generated by dot. For an explanation of the image formats see the section
+# output formats in the documentation of the dot tool (Graphviz (see:
+# https://www.graphviz.org/)).
+# Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order
+# to make the SVG files visible in IE 9+ (other browsers do not have this
+# requirement).
+# Possible values are: png, jpg, gif, svg, png:gd, png:gd:gd, png:cairo,
+# png:cairo:gd, png:cairo:cairo, png:cairo:gdiplus, png:gdiplus and
+# png:gdiplus:gdiplus.
+# The default value is: png.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_IMAGE_FORMAT       = png
+
+# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
+# enable generation of interactive SVG images that allow zooming and panning.
+#
+# Note that this requires a modern browser other than Internet Explorer. Tested
+# and working are Firefox, Chrome, Safari, and Opera.
+# Note: For IE 9+ you need to set HTML_FILE_EXTENSION to xhtml in order to make
+# the SVG files visible. Older versions of IE do not have SVG support.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+INTERACTIVE_SVG        = NO
+
+# The DOT_PATH tag can be used to specify the path where the dot tool can be
+# found. If left blank, it is assumed the dot tool can be found in the path.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_PATH               =
+
+# The DOTFILE_DIRS tag can be used to specify one or more directories that
+# contain dot files that are included in the documentation (see the \dotfile
+# command).
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOTFILE_DIRS           =
+
+# You can include diagrams made with dia in doxygen documentation. Doxygen will
+# then run dia to produce the diagram and insert it in the documentation. The
+# DIA_PATH tag allows you to specify the directory where the dia binary resides.
+# If left empty dia is assumed to be found in the default search path.
+
+DIA_PATH               =
+
+# The DIAFILE_DIRS tag can be used to specify one or more directories that
+# contain dia files that are included in the documentation (see the \diafile
+# command).
+
+DIAFILE_DIRS           =
+
+# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the
+# path where java can find the plantuml.jar file or to the filename of jar file
+# to be used. If left blank, it is assumed PlantUML is not used or called during
+# a preprocessing step. Doxygen will generate a warning when it encounters a
+# \startuml command in this case and will not generate output for the diagram.
+
+PLANTUML_JAR_PATH      =
+
+# When using plantuml, the PLANTUML_CFG_FILE tag can be used to specify a
+# configuration file for plantuml.
+
+PLANTUML_CFG_FILE      =
+
+# When using plantuml, the specified paths are searched for files specified by
+# the !include statement in a plantuml block.
+
+PLANTUML_INCLUDE_PATH  =
+
+# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of nodes
+# that will be shown in the graph. If the number of nodes in a graph becomes
+# larger than this value, doxygen will truncate the graph, which is visualized
+# by representing a node as a red box. Note that doxygen if the number of direct
+# children of the root node in a graph is already larger than
+# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note that
+# the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+# Minimum value: 0, maximum value: 10000, default value: 50.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_GRAPH_MAX_NODES    = 50
+
+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the graphs
+# generated by dot. A depth value of 3 means that only nodes reachable from the
+# root by following a path via at most 3 edges will be shown. Nodes that lay
+# further from the root node will be omitted. Note that setting this option to 1
+# or 2 may greatly reduce the computation time needed for large code bases. Also
+# note that the size of a graph can be further restricted by
+# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
+# Minimum value: 0, maximum value: 1000, default value: 0.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+MAX_DOT_GRAPH_DEPTH    = 0
+
+# Set the DOT_MULTI_TARGETS tag to YES to allow dot to generate multiple output
+# files in one run (i.e. multiple -o and -T options on the command line). This
+# makes dot run faster, but since only newer versions of dot (>1.8.10) support
+# this, this feature is disabled by default.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_MULTI_TARGETS      = NO
+
+# If the GENERATE_LEGEND tag is set to YES doxygen will generate a legend page
+# explaining the meaning of the various boxes and arrows in the dot generated
+# graphs.
+# Note: This tag requires that UML_LOOK isn't set, i.e. the doxygen internal
+# graphical representation for inheritance and collaboration diagrams is used.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
 GENERATE_LEGEND        = YES
+
+# If the DOT_CLEANUP tag is set to YES, doxygen will remove the intermediate
+# files that are used to generate the various graphs.
+#
+# Note: This setting is not only used for dot files but also for msc temporary
+# files.
+# The default value is: YES.
+
 DOT_CLEANUP            = YES
-#---------------------------------------------------------------------------
-# Configuration::addtions related to the search engine   
-#---------------------------------------------------------------------------
-SEARCHENGINE           = NO
-CGI_NAME               = search.cgi
-CGI_URL                = 
-DOC_URL                = 
-DOC_ABSPATH            = 
-BIN_ABSPATH            = /usr/local/bin/
-EXT_DOC_PATHS          = 
+
+# You can define message sequence charts within doxygen comments using the \msc
+# command. If the MSCGEN_TOOL tag is left empty (the default), then doxygen will
+# use a built-in version of mscgen tool to produce the charts. Alternatively,
+# the MSCGEN_TOOL tag can also specify the name an external tool. For instance,
+# specifying prog as the value, doxygen will call the tool as prog -T
+# <outfile_format> -o <outputfile> <inputfile>. The external tool should support
+# output file formats "png", "eps", "svg", and "ismap".
+
+MSCGEN_TOOL            =
+
+# The MSCFILE_DIRS tag can be used to specify one or more directories that
+# contain msc files that are included in the documentation (see the \mscfile
+# command).
+
+MSCFILE_DIRS           =

From 756ef92a7f9c6b04e8153e4ad54a74963e2274a2 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Sun, 2 Jun 2024 23:33:25 -0700
Subject: [PATCH 036/192] CHG: Add code of conduct

---
 CodeOfConduct.md | 133 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 133 insertions(+)
 create mode 100644 CodeOfConduct.md

diff --git a/CodeOfConduct.md b/CodeOfConduct.md
new file mode 100644
index 000000000..5f1f64d88
--- /dev/null
+++ b/CodeOfConduct.md
@@ -0,0 +1,133 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official email address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[INSERT CONTACT METHOD].
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations
+

From 67a77ddfabb72d93078b7fe35706140a1ab17b5d Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Sun, 2 Jun 2024 23:34:55 -0700
Subject: [PATCH 037/192] CHG: Update CodeOfConduct.md

---
 CodeOfConduct.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CodeOfConduct.md b/CodeOfConduct.md
index 5f1f64d88..e565fec70 100644
--- a/CodeOfConduct.md
+++ b/CodeOfConduct.md
@@ -60,7 +60,7 @@ representative at an online or offline event.
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported to the community leaders responsible for enforcement at
-[INSERT CONTACT METHOD].
+andreas@megalibtoolkit.com.
 All complaints will be reviewed and investigated promptly and fairly.
 
 All community leaders are obligated to respect the privacy and security of the

From 0cd96e90ed0f90c046bd891b28028d4e9522c1a6 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Sun, 2 Jun 2024 23:53:59 -0700
Subject: [PATCH 038/192] ADD: Contributor guide

---
 Contribute.md | 59 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 59 insertions(+)
 create mode 100644 Contribute.md

diff --git a/Contribute.md b/Contribute.md
new file mode 100644
index 000000000..2f88064c6
--- /dev/null
+++ b/Contribute.md
@@ -0,0 +1,59 @@
+# Contributor Guide
+
+Welcome to the MEGAlib contributor guide! We're excited to have you interested in contributing to our project. This guide will help you get started, understand our workflow, and know what to expect when contributing.
+How to Contribute
+
+We use a fork and pull request workflow for contributions. Here’s a step-by-step guide to help you get started:
+
+## Fork the Repository
+Go to our GitHub repository and click the "Fork" button at the top right corner of the page. This will create a copy of the repository under your GitHub account.
+
+## Clone Your Fork
+
+Clone your fork to your local machine using the following command:
+
+```
+git clone https://github.com/zoglauer/MEGAlib.git
+cd MEGAlib
+```
+
+## Create a Branch
+Create a new branch for your feature or bug fix. Use a descriptive name for your branch:
+
+```
+git checkout -b feature/your-feature-name
+```
+
+## Make Your Changes
+Make your changes in your local repository. Be sure to follow the same coding standards as in the rest of MEGAlib.
+
+## Commit Your Changes
+Commit your changes with a clear and concise commit message:
+
+```
+git add .
+git commit -m "Add feature: your feature name"
+```
+
+## Push to Your Fork
+Push your changes to your forked repository on GitHub:
+
+```
+git push origin feature/your-feature-name
+```
+
+## Open a Pull Request
+Go to your forked repository on GitHub and click the "New pull request" button. Select the branch you created and make sure the base repository is set to the original repository. Provide a clear and descriptive title and description for your pull request.
+
+## Respond to Feedback
+Your pull request will be reviewed by the project maintainers. Be prepared to make additional changes based on their feedback. Engage in constructive discussions to refine your contribution.
+
+## Merge Your Pull Request
+
+Once your pull request is approved, it will be merged into the main repository. Congratulations on your contribution!
+
+## Final words
+
+If you need help or have questions, feel free to open an issue or discussion on GitHub.
+
+

From 6cc89cd7aa5e4ff78f115034b5ecdb9a0b94cfe2 Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Fri, 7 Jun 2024 12:07:06 +0200
Subject: [PATCH 039/192] Update AllowedGeant4Versions.txt increase version to
 11.2

---
 config/AllowedGeant4Versions.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/config/AllowedGeant4Versions.txt b/config/AllowedGeant4Versions.txt
index fc1db2732..efd8ca582 100644
--- a/config/AllowedGeant4Versions.txt
+++ b/config/AllowedGeant4Versions.txt
@@ -1,2 +1,3 @@
 110
 111
+112

From 6ee15515c8c51e153254c640f86b22ce8509146a Mon Sep 17 00:00:00 2001
From: GallegoSav <savitri.gallego@laposte.net>
Date: Fri, 7 Jun 2024 13:44:00 +0200
Subject: [PATCH 040/192] modify MCActivator for compiling with geant4 v11.2

---
 src/cosima/src/MCActivator.cc | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/cosima/src/MCActivator.cc b/src/cosima/src/MCActivator.cc
index d8e8570e3..797002a89 100644
--- a/src/cosima/src/MCActivator.cc
+++ b/src/cosima/src/MCActivator.cc
@@ -375,7 +375,8 @@ bool MCActivator::CalculateEquilibriumRates()
               if (Tree[b].back().GetHalfLife() == numeric_limits<double>::max()) continue;
               
               //cout<<<<endl;
-              DecayTable = Decay->LoadDecayTable(*(Tree[b].back().GetDefinition()));
+	      const G4Ions* ion = dynamic_cast<const G4Ions*>(*(Tree[b].back().GetDefinition()));
+              DecayTable = Decay->LoadDecayTable(ion);
               if (DecayTable == 0) {
                 mout<<"Error: Decay table not found for: "<<m_Rates.GetID(v, i)<<endl;
                 continue;

From 8ef0f2d92da04279eab815c8412970086621b92a Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Fri, 7 Jun 2024 14:58:40 +0200
Subject: [PATCH 041/192] increase Allowed root version to 6.28

---
 config/AllowedROOTVersions.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/AllowedROOTVersions.txt b/config/AllowedROOTVersions.txt
index a0595b546..225336c96 100644
--- a/config/AllowedROOTVersions.txt
+++ b/config/AllowedROOTVersions.txt
@@ -1 +1 @@
-618 626 
+618 626 628

From 2546f20a1808140783483a8c93b90b2aef6eb5e8 Mon Sep 17 00:00:00 2001
From: GallegoSav <savitri.gallego@laposte.net>
Date: Fri, 7 Jun 2024 15:46:09 +0200
Subject: [PATCH 042/192] MCActivator add the process Radioactivation and link
 it to RadioactiveDecay process | add long time limit for lifetime of isotope
 in the Physic list | other modif for compiling cosima with geant4v11.2

---
 src/cosima/src/MCActivator.cc      | 2 +-
 src/cosima/src/MCPhysicsList.cc    | 7 ++++++-
 src/cosima/src/MCSteppingAction.cc | 3 ++-
 3 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/src/cosima/src/MCActivator.cc b/src/cosima/src/MCActivator.cc
index 797002a89..d8f184a05 100644
--- a/src/cosima/src/MCActivator.cc
+++ b/src/cosima/src/MCActivator.cc
@@ -375,7 +375,7 @@ bool MCActivator::CalculateEquilibriumRates()
               if (Tree[b].back().GetHalfLife() == numeric_limits<double>::max()) continue;
               
               //cout<<<<endl;
-	      const G4Ions* ion = dynamic_cast<const G4Ions*>(*(Tree[b].back().GetDefinition()));
+	      const G4Ions* ion = dynamic_cast<const G4Ions*>((Tree[b].back().GetDefinition()));
               DecayTable = Decay->LoadDecayTable(ion);
               if (DecayTable == 0) {
                 mout<<"Error: Decay table not found for: "<<m_Rates.GetID(v, i)<<endl;
diff --git a/src/cosima/src/MCPhysicsList.cc b/src/cosima/src/MCPhysicsList.cc
index ff44a6504..f47f21d71 100644
--- a/src/cosima/src/MCPhysicsList.cc
+++ b/src/cosima/src/MCPhysicsList.cc
@@ -60,7 +60,6 @@
 #include "G4NuclideTable.hh"
 
 #include "G4EmParameters.hh"
-
 // MEGAlib:
 #include "MStreams.h"
 
@@ -216,6 +215,8 @@ void MCPhysicsList::ConstructProcess()
         G4RadioactiveDecay* RadioactiveDecay = dynamic_cast<G4RadioactiveDecay*>(P);
         //RadioactiveDecay->SetICMode(true);  // Internal Conversion geant4 11  removed SetICM() method, as deprecated for some time and no longer used. ICM now set exclusively in G4PhotonEvaporation. Added printout of the flag of atomic relaxation.
         RadioactiveDecay->SetARM(true);  // Atomic Rearrangement, i.e. filling of shell vacancies
+	RadioactiveDecay->SetThresholdForVeryLongDecayTime(1.0e+60*CLHEP::year); // Ignore radioactive decays at rest of nuclides happening after this (very long) time threshold
+
         //RadioactiveDecay->SetHLThreshold(1.0E-9*second);  // Half life cut-off of isomeric states | no longer exist in g4 v11 , no track of that on the release notes 
       }
       
@@ -244,6 +245,10 @@ void MCPhysicsList::ConstructProcess()
   emParameters->SetAuger(true);
   emParameters->SetDeexcitationIgnoreCut(false);
   
+ 
+  
+  
+  
   //remove the comments below if you want exactly the same paramameters as v10.02
   //Not sure of the result if you do that
   //emParameters->SetMuHadLateralDisplacement(false);
diff --git a/src/cosima/src/MCSteppingAction.cc b/src/cosima/src/MCSteppingAction.cc
index dfae26def..3484565aa 100644
--- a/src/cosima/src/MCSteppingAction.cc
+++ b/src/cosima/src/MCSteppingAction.cc
@@ -205,7 +205,8 @@ MCSteppingAction::MCSteppingAction(MCParameterFile& RunParameters) :
   m_KnownProcess.push_back("Decay"); m_KnownProcessID.push_back(c_ProcessIDDecay);
   
   m_KnownProcess.push_back("RadioactiveDecay"); m_KnownProcessID.push_back(c_ProcessIDRadioactiveDecay);
-  
+  m_KnownProcess.push_back("Radioactivation"); m_KnownProcessID.push_back(c_ProcessIDRadioactiveDecay);
+
   m_KnownProcess.push_back("LowEnergyIoni"); m_KnownProcessID.push_back(c_ProcessIDIonization);
   m_KnownProcess.push_back("hLowEIoni"); m_KnownProcessID.push_back(c_ProcessIDIonization);
   m_KnownProcess.push_back("ionIoni"); m_KnownProcessID.push_back(c_ProcessIDIonization);

From 094c1339c56fbce6c9a0d75586b085e4fec2fa1f Mon Sep 17 00:00:00 2001
From: GallegoSav <savitri.gallego@laposte.net>
Date: Fri, 7 Jun 2024 15:50:02 +0200
Subject: [PATCH 043/192] merge

---
 config/AllowedROOTVersions.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/AllowedROOTVersions.txt b/config/AllowedROOTVersions.txt
index a0595b546..225336c96 100644
--- a/config/AllowedROOTVersions.txt
+++ b/config/AllowedROOTVersions.txt
@@ -1 +1 @@
-618 626 
+618 626 628

From 8db810c984a1665ce40936e13552912279649275 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Mon, 17 Jun 2024 16:14:15 -0700
Subject: [PATCH 044/192] CHG: Large number fix

---
 src/cosima/src/MCSource.cc        |  30 +++++--
 src/global/misc/src/MFunction.cxx | 139 ++++++++++++++++++------------
 2 files changed, 105 insertions(+), 64 deletions(-)

diff --git a/src/cosima/src/MCSource.cc b/src/cosima/src/MCSource.cc
index 73a5f62ae..7153503bc 100644
--- a/src/cosima/src/MCSource.cc
+++ b/src/cosima/src/MCSource.cc
@@ -510,13 +510,13 @@ bool MCSource::SetStartAreaParameters(double StartAreaParam1,
   }
 
   // We have to update the start area parameters
-  UpgradeStartArea();
+  if (UpgradeStartArea() == false) return false;
   // We have to update the position vectors
-  UpgradePosition();
+  if (UpgradePosition() == false) return false;
   // and the flux normalization
-  UpgradeFlux();
+  if (UpgradeFlux() == false) return false;
   // and the light curve information
-  UpgradeLightCurve();
+  if (UpgradeLightCurve() == false) return false;
   
   return true;
 }
@@ -2116,13 +2116,25 @@ bool MCSource::UpgradeLightCurve()
   if (m_LightCurveType == c_LightCurveFile) {
     // Make sure the y-value is the flux in particles/second
     
-    cout<<"Lightcurve integration: "<<m_LightCurveFunction.Integrate()<<endl;
+    // Sanity check:
+    auto LightCurveIntegral = m_LightCurveFunction.Integrate();
+    if (std::isfinite(LightCurveIntegral) == false) {
+      mout<<"  ***  ERROR  ***   "<<m_Name<<": The light curve integral is not finite: " <<LightCurveIntegral<<endl;
+      return false;
+    }
+
+    cout<<"Lightcurve integration: "<<LightCurveIntegral<<endl;
     cout<<"Flux: "<<m_Flux*second<<" ph/s"<<endl;
-    if (m_Flux > 0 && m_LightCurveFunction.Integrate() > 0) {
-      m_LightCurveFunction.ScaleY((m_LightCurveFunction.GetXMax() - m_LightCurveFunction.GetXMin())/m_LightCurveFunction.Integrate());
+    if (m_Flux > 0 && LightCurveIntegral > 0) {
+      m_LightCurveFunction.ScaleY((m_LightCurveFunction.GetXMax() - m_LightCurveFunction.GetXMin())/LightCurveIntegral);
     }
-    cout<<"Final light-curve integration: "<<m_LightCurveFunction.Integrate()<<endl;
-    
+    LightCurveIntegral = m_LightCurveFunction.Integrate();
+    cout<<"Final light-curve integration: "<<LightCurveIntegral<<endl;
+    if (std::isfinite(LightCurveIntegral) == false) {
+      mout<<"  ***  ERROR  ***   "<<m_Name<<": The light curve integral is not finite:" <<LightCurveIntegral<<endl;
+      return false;
+    }
+
     if (m_NextEmission < m_LightCurveFunction.GetXMin()) {
       m_NextEmission = m_LightCurveFunction.GetXMin();
     }
diff --git a/src/global/misc/src/MFunction.cxx b/src/global/misc/src/MFunction.cxx
index ece0f8bdc..c3d61fd3c 100644
--- a/src/global/misc/src/MFunction.cxx
+++ b/src/global/misc/src/MFunction.cxx
@@ -520,7 +520,9 @@ double MFunction::Evaluate(double x) const
 {
   // Evalute the function considering the different interpolation types
 
-  if (m_InterpolationType == c_InterpolationUnknown) {
+  auto InterpolationType = m_InterpolationType;
+
+  if (InterpolationType == c_InterpolationUnknown) {
     merr<<"Unknown interpolation type: "<<c_InterpolationUnknown<<show;
     return 0;
   }
@@ -531,13 +533,20 @@ double MFunction::Evaluate(double x) const
     return 0;
   }
 
-  if (m_InterpolationType == c_InterpolationConstant || m_X.size() == 1) {
+  if (InterpolationType == c_InterpolationLinLog) {
+    if (m_X.back() > 1E+09) {
+      merr<<"Info: Large x-axis values make LinLog interpolation fail. Switching to LinLin!"<<endl;
+      InterpolationType = c_InterpolationLinLin;
+    }
+  }
+
+  if (InterpolationType == c_InterpolationConstant || m_X.size() == 1) {
     return m_Y[0];
-  } else if (m_InterpolationType == c_InterpolationSpline3) {
+  } else if (InterpolationType == c_InterpolationSpline3) {
     return m_Spline3->Eval(x);
-  } else if (m_InterpolationType == c_InterpolationSpline5) {
+  } else if (InterpolationType == c_InterpolationSpline5) {
     return m_Spline5->Eval(x);
-  } else if (m_InterpolationType == c_InterpolationNone) {
+  } else if (InterpolationType == c_InterpolationNone) {
 
     // Get Position:
     int xPosition = -1; 
@@ -556,10 +565,10 @@ double MFunction::Evaluate(double x) const
 
     return m_Y[xPosition];
 
-  } else if (m_InterpolationType == c_InterpolationLinLin ||
-             m_InterpolationType == c_InterpolationLinLog ||
-             m_InterpolationType == c_InterpolationLogLin ||
-             m_InterpolationType == c_InterpolationLogLog) {
+  } else if (InterpolationType == c_InterpolationLinLin ||
+             InterpolationType == c_InterpolationLinLog ||
+             InterpolationType == c_InterpolationLogLin ||
+             InterpolationType == c_InterpolationLogLog) {
 
     double y = 0.0;
 
@@ -595,11 +604,11 @@ double MFunction::Evaluate(double x) const
     }
 
     // Attention for log interpolation make sure all values are positive!
-    if (m_InterpolationType == c_InterpolationLinLog || m_InterpolationType == c_InterpolationLogLog) {
+    if (InterpolationType == c_InterpolationLinLog || InterpolationType == c_InterpolationLogLog) {
       y1 = log(y1);
       y2 = log(y2);
     }
-    if (m_InterpolationType == c_InterpolationLogLin || m_InterpolationType == c_InterpolationLogLog) {
+    if (InterpolationType == c_InterpolationLogLin || InterpolationType == c_InterpolationLogLog) {
       x = log(x);
       x1 = log(x1);
       x2 = log(x2);
@@ -608,14 +617,14 @@ double MFunction::Evaluate(double x) const
     double m = (y2-y1)/(x2-x1);
     double t = y2 - m*x2;
 
-    if (m_InterpolationType == c_InterpolationLinLog || m_InterpolationType == c_InterpolationLogLog) {
+    if (InterpolationType == c_InterpolationLinLog || InterpolationType == c_InterpolationLogLog) {
       y = exp(m*x+t);
     } else {
       y = m*x+t;
     }
     
     if (std::isnan(y)) { // std:: is required here due to multiple definitions
-      merr<<"Interpolation error for interpolation type "<<m_InterpolationType<<": y is NaN!"<<endl;;
+      merr<<"Interpolation error for interpolation type "<<InterpolationType<<": y is NaN!"<<endl;;
       merr<<"   m="<<m<<"  t="<<t<<"  x1="<<x1<<"  y1="<<y1<<"  x2="<<x2<<"  y2="<<y2<<show;
     }
 
@@ -643,6 +652,8 @@ double MFunction::Integrate(double XMin, double XMax) const
 {
   // Integrate the data from min to max
   
+  auto InterpolationType = m_InterpolationType;
+
   if (XMin < m_X.front()) {
     merr<<"XMin ("<<XMin<<") smaller than minimum x-value ("<<m_X.front()<<") --- starting at minimum x-value"<<endl;
     XMin = m_X.front();
@@ -656,20 +667,34 @@ double MFunction::Integrate(double XMin, double XMax) const
     return 0.0;    
   }
 
+  // Switch to XZero to handle very large numbers
+  XMin -= m_X.front();
+  XMax -= m_X.front();
+
+  // ... use m_XZero from now on for x-axis
+
+  // More sanity checks
+  if (InterpolationType == c_InterpolationLinLog) {
+    if (m_X.back() > 1E+09) {
+      merr<<"Info: Large x-axis values make LinLog interpolation fail. Switching to LinLin!"<<endl;
+      InterpolationType = c_InterpolationLinLin;
+    }
+  }
+
   int BinMin = 0;
-  if (XMin > m_X.front()) {
-    // BinMin = find_if(m_X.begin(), m_X.end(), bind2nd(greater<double>(), XMin)) - m_X.begin() - 1;
-    BinMin = find_if(m_X.begin(), m_X.end(), bind(greater<double>(), placeholders::_1, XMin)) - m_X.begin() - 1;
+  if (XMin > m_XZero.front()) {
+    // BinMin = find_if(m_XZero.begin(), m_XZero.end(), bind2nd(greater<double>(), XMin)) - m_XZero.begin() - 1;
+    BinMin = find_if(m_XZero.begin(), m_XZero.end(), bind(greater<double>(), placeholders::_1, XMin)) - m_XZero.begin() - 1;
 //     unsigned int upper = m_Cumulative.size();
 //     unsigned int center = 1;
 //     unsigned int lower = 0;
     
 //     while (upper-lower > 1) {
 //       center = (upper+lower) >> 1;
-//       if (XMin == m_X[center]) {
+//       if (XMin == m_XZero[center]) {
 //         BinMin = int(center)+1;
 //       }
-//       if (XMin < m_X[center]) {
+//       if (XMin < m_XZero[center]) {
 //         upper = center;
 //       } else {
 //         lower = center;
@@ -677,20 +702,20 @@ double MFunction::Integrate(double XMin, double XMax) const
 //     }
 //     BinMin = int(lower)+1;
   }
-  int BinMax = m_X.size()-1;
-  if (XMax < m_X.back()) {
-    //BinMax = find_if(m_X.begin(), m_X.end(), bind2nd(greater_equal<double>(), XMax)) - m_X.begin();
-    BinMax = find_if(m_X.begin(), m_X.end(), bind(greater_equal<double>(), placeholders::_1, XMax)) - m_X.begin();
+  int BinMax = m_XZero.size()-1;
+  if (XMax < m_XZero.back()) {
+    //BinMax = find_if(m_XZero.begin(), m_XZero.end(), bind2nd(greater_equal<double>(), XMax)) - m_XZero.begin();
+    BinMax = find_if(m_XZero.begin(), m_XZero.end(), bind(greater_equal<double>(), placeholders::_1, XMax)) - m_XZero.begin();
 //     unsigned int upper = m_Cumulative.size();
 //     unsigned int center = 1;
 //     unsigned int lower = 0;
     
 //     while (upper-lower > 1) {
 //       center = (upper+lower) >> 1;
-//       if (XMax == m_X[center]) {
+//       if (XMax == m_XZero[center]) {
 //         BinMax = int(center)+1;
 //       }
-//       if (XMax < m_X[center]) {
+//       if (XMax < m_XZero[center]) {
 //         upper = center;
 //       } else {
 //         lower = center;
@@ -700,30 +725,30 @@ double MFunction::Integrate(double XMin, double XMax) const
   }
   
   double Integral = 0.0;
-  if (m_InterpolationType == c_InterpolationConstant) {
+  if (InterpolationType == c_InterpolationConstant) {
     Integral = (XMax - XMin) * m_Y[0];
-  } else if (m_InterpolationType == c_InterpolationNone) {
+  } else if (InterpolationType == c_InterpolationNone) {
     // Just sum rectangular bins:
 
-    double BinCenterMin = m_X[BinMin-1] + 0.5*(m_X[BinMin] - m_X[BinMin-1]);
-    double BinCenterMax = m_X[BinMax-1] + 0.5*(m_X[BinMax] - m_X[BinMax-1]);
+    double BinCenterMin = m_XZero[BinMin-1] + 0.5*(m_XZero[BinMin] - m_XZero[BinMin-1]);
+    double BinCenterMax = m_XZero[BinMax-1] + 0.5*(m_XZero[BinMax] - m_XZero[BinMax-1]);
 
     if (BinMin != BinMax) {
       if (XMin < BinCenterMin) {
         Integral += (BinCenterMin - XMin)*m_Y[BinMin-1];
-        Integral += (m_X[BinMin] - BinCenterMin)*m_Y[BinMin];
+        Integral += (m_XZero[BinMin] - BinCenterMin)*m_Y[BinMin];
       } else {
-        Integral += (m_X[BinMin] - XMin)*m_Y[BinMin];
+        Integral += (m_XZero[BinMin] - XMin)*m_Y[BinMin];
       }
       for (int b = BinMin; b < BinMax; ++b) {
-        Integral += 0.5*(m_X[BinMin+1] - m_X[BinMin])*m_Y[BinMin];
-        Integral += 0.5*(m_X[BinMin+1] - m_X[BinMin])*m_Y[BinMin+1];
+        Integral += 0.5*(m_XZero[BinMin+1] - m_XZero[BinMin])*m_Y[BinMin];
+        Integral += 0.5*(m_XZero[BinMin+1] - m_XZero[BinMin])*m_Y[BinMin+1];
       }
       if (XMax > BinCenterMax) {
-        Integral += (BinCenterMax - m_X[BinMax-1])*m_Y[BinMax-1];
+        Integral += (BinCenterMax - m_XZero[BinMax-1])*m_Y[BinMax-1];
         Integral += (XMax - BinCenterMax)*m_Y[BinMax];
       } else {
-        Integral += (XMax - m_X[BinMax-1])*m_Y[BinMax-1];
+        Integral += (XMax - m_XZero[BinMax-1])*m_Y[BinMax-1];
       }
     } else {
       if (XMin < BinCenterMin && XMax < BinCenterMin) {
@@ -735,10 +760,10 @@ double MFunction::Integrate(double XMin, double XMax) const
         Integral += (XMax - BinCenterMax)*m_Y[BinMin];
       }
     }      
-  } else if (m_InterpolationType == c_InterpolationLinLin ||
-             m_InterpolationType == c_InterpolationLinLog ||
-             m_InterpolationType == c_InterpolationLogLin ||
-             m_InterpolationType == c_InterpolationLogLog) {
+  } else if (InterpolationType == c_InterpolationLinLin ||
+             InterpolationType == c_InterpolationLinLog ||
+             InterpolationType == c_InterpolationLogLin ||
+             InterpolationType == c_InterpolationLogLog) {
     
     double x1, x2, y1, y2;
     for (int i = BinMin; i < BinMax; ++i) {
@@ -747,25 +772,25 @@ double MFunction::Integrate(double XMin, double XMax) const
         x1 = XMin;
         y1 = Evaluate(x1);
       } else {
-        x1 = m_X[i];
+        x1 = m_XZero[i];
         y1 = m_Y[i];
       }
       if (i == BinMax) {
         x2 = XMax;
         y2 = Evaluate(x2);
       } else {
-        x2 = m_X[i+1];
+        x2 = m_XZero[i+1];
         y2 = m_Y[i+1];
       }
       
       // Attention for log interpolation make sure all values are positive!
-      if (m_InterpolationType == c_InterpolationLinLog || 
-          m_InterpolationType == c_InterpolationLogLog) {
+      if (InterpolationType == c_InterpolationLinLog ||
+          InterpolationType == c_InterpolationLogLog) {
         y1 = log(y1);
         y2 = log(y2);
       }
-      if (m_InterpolationType == c_InterpolationLogLin || 
-          m_InterpolationType == c_InterpolationLogLog) {
+      if (InterpolationType == c_InterpolationLogLin ||
+          InterpolationType == c_InterpolationLogLog) {
         x1 = log(x1);
         x2 = log(x2);
       }
@@ -777,32 +802,34 @@ double MFunction::Integrate(double XMin, double XMax) const
       double t = y2 - m*x2;
 
       // Switch back
-      if (m_InterpolationType == c_InterpolationLinLog || 
-          m_InterpolationType == c_InterpolationLogLog) {
+      if (InterpolationType == c_InterpolationLinLog ||
+          InterpolationType == c_InterpolationLogLog) {
         y1 = exp(y1);
         y2 = exp(y2);
       }
-      if (m_InterpolationType == c_InterpolationLogLin || 
-          m_InterpolationType == c_InterpolationLogLog) {
+      if (InterpolationType == c_InterpolationLogLin ||
+          InterpolationType == c_InterpolationLogLog) {
         x1 = exp(x1);
         x2 = exp(x2);
       }
       
       // Do the integration using the correct formula for the various modi:
-      if (m_InterpolationType == c_InterpolationLinLin) {
+      if (InterpolationType == c_InterpolationLinLin) {
         // y=m*x+t --> int(m*x+t)
         Integral += 0.5*m*(x2*x2-x1*x1) + t*(x2-x1);      
-      } else if (m_InterpolationType == c_InterpolationLinLog) {
+      } else if (InterpolationType == c_InterpolationLinLog) {
         // ln(y) = m*x+t --> int(exp(m*x+t))
         if (fabs(m) < 10E-8) {
           Integral += exp(t)*(x2-x1); 
+          cout<<"x1:"<<x1<<" x2:"<<x2<<" y1:"<<y1<<" y2:"<<y2<<" m:"<<m<<" t:"<<t<<":"<<exp(t)<<":"<<x2-x1<<endl;
         } else {
           Integral += 1/m * (exp(m*x2+t) - exp(m*x1+t));
+          cout<<1/m<<":"<<exp(m*x2+t)<<":"<<exp(m*x1+t)<<endl;
         }
-      } else if (m_InterpolationType == c_InterpolationLogLin) {
+      } else if (InterpolationType == c_InterpolationLogLin) {
         // y = m*ln(x) + t --> int(m*ln(x) + t)
         Integral += x2*(m*(log(x2) - 1) + t) - x1*(m*(log(x1) - 1) + t);
-      } else if (m_InterpolationType == c_InterpolationLogLog) {
+      } else if (InterpolationType == c_InterpolationLogLog) {
         // ln(y) = m*ln(x) + t --> y = exp(t)*x^m --> int(exp(t)*x^m)
         if (fabs(m+1) < 10E-8) {
           Integral += exp(t)*(log(x2)-log(x1)); 
@@ -810,8 +837,10 @@ double MFunction::Integrate(double XMin, double XMax) const
           Integral += exp(t)/(m+1) * (pow(x2, m+1) - pow(x1, m+1));
         }
       }
+      if (std::isfinite(Integral) == false) {
+        merr<<"Error: Integral is no longer finite at bin: "<<i<<endl;
+      }
     }
-
   } else {
     merr<<"This interpolation type is no longer supported..."<<endl;
   }
@@ -1230,9 +1259,9 @@ double MFunction::FindX(double XStart, double Integral, bool Cyclic)
     //mout<<"x="<<x2<<endl;
     X = x2; 
   } else if ((x2 < m_XZero[NewUpperBin-1] || x2 > m_XZero[NewUpperBin]) && (x1 < m_XZero[NewUpperBin-1] || x1 > m_XZero[NewUpperBin])) {
-    merr<<std::setprecision(20)<<"FindX: Both possible results are outside choosen bin ["<<m_XZero[NewUpperBin-1]<<"-"<<m_XZero[NewUpperBin]<<"]: x1="<<x1<<" x2="<<x2<<endl;
+    merr<<std::setprecision(20)<<"FindX: Both possible results are outside choosen bin ["<<m_XZero[NewUpperBin-1]<<"-"<<m_XZero[NewUpperBin]<<"] with bin ID="<<NewUpperBin-1<<" and y range ["<<m_Y[NewUpperBin-1]<<"-"<<m_Y[NewUpperBin]<<"]: x1="<<x1<<" x2="<<x2<<endl;
   } else {
-    merr<<std::setprecision(20)<<"FindX: Both possible results are within choosen bin ["<<m_X[NewUpperBin-1]<<"-"<<m_X[NewUpperBin]<<"]: x1="<<x1<<" x2="<<x2<<endl;
+    merr<<std::setprecision(20)<<"FindX: Both possible results are within choosen bin ["<<m_X[NewUpperBin-1]<<"-"<<m_X[NewUpperBin]<<"] with bin ID="<<NewUpperBin-1<<" and y range ["<<m_Y[NewUpperBin-1]<<"-"<<m_Y[NewUpperBin]<<"]: x1="<<x1<<" x2="<<x2<<endl;
   }
   
   //cout<<"XStart: "<<XStart<<" X: "<<X<<" modulo: "<<Modulo<<endl;

From 2637e4d9b71795803260e2d08b0955ad746d67e9 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Thu, 11 Jul 2024 14:56:07 -0700
Subject: [PATCH 045/192] CHG: Foxes for C++ 17 on macOS

---
 src/cosima/inc/MCRun.hh                 | 2 +-
 src/global/misc/inc/MResponseMatrixO1.h | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/cosima/inc/MCRun.hh b/src/cosima/inc/MCRun.hh
index a58b3e3e7..3c7eb6467 100644
--- a/src/cosima/inc/MCRun.hh
+++ b/src/cosima/inc/MCRun.hh
@@ -42,7 +42,7 @@ using namespace std;
 
 /******************************************************************************/
 
-struct NextEmissionSort : public binary_function<const MCSource*, const MCSource*, bool> {
+struct NextEmissionSort {
 public:
   bool operator() (const MCSource* S1, const MCSource* S2) const {
 
diff --git a/src/global/misc/inc/MResponseMatrixO1.h b/src/global/misc/inc/MResponseMatrixO1.h
index 2689532d0..580ce8bd7 100644
--- a/src/global/misc/inc/MResponseMatrixO1.h
+++ b/src/global/misc/inc/MResponseMatrixO1.h
@@ -35,7 +35,7 @@ using namespace std;
 ////////////////////////////////////////////////////////////////////////////////
 
 
-template< class T > class greater_than : public unary_function< T, bool > 
+template< class T > class greater_than
 {
  public:
   explicit greater_than( const T& x ) : arg2( x ) { }

From 4c6179ae4e1a6cd86f14cab414e77e0e4ffbdcb7 Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Fri, 12 Jul 2024 11:00:57 +0200
Subject: [PATCH 046/192] resolve conflict  MFunction.cxx

---
 src/global/misc/src/MFunction.cxx | 139 ++++++++++++++++++------------
 1 file changed, 84 insertions(+), 55 deletions(-)

diff --git a/src/global/misc/src/MFunction.cxx b/src/global/misc/src/MFunction.cxx
index ece0f8bdc..c3d61fd3c 100644
--- a/src/global/misc/src/MFunction.cxx
+++ b/src/global/misc/src/MFunction.cxx
@@ -520,7 +520,9 @@ double MFunction::Evaluate(double x) const
 {
   // Evalute the function considering the different interpolation types
 
-  if (m_InterpolationType == c_InterpolationUnknown) {
+  auto InterpolationType = m_InterpolationType;
+
+  if (InterpolationType == c_InterpolationUnknown) {
     merr<<"Unknown interpolation type: "<<c_InterpolationUnknown<<show;
     return 0;
   }
@@ -531,13 +533,20 @@ double MFunction::Evaluate(double x) const
     return 0;
   }
 
-  if (m_InterpolationType == c_InterpolationConstant || m_X.size() == 1) {
+  if (InterpolationType == c_InterpolationLinLog) {
+    if (m_X.back() > 1E+09) {
+      merr<<"Info: Large x-axis values make LinLog interpolation fail. Switching to LinLin!"<<endl;
+      InterpolationType = c_InterpolationLinLin;
+    }
+  }
+
+  if (InterpolationType == c_InterpolationConstant || m_X.size() == 1) {
     return m_Y[0];
-  } else if (m_InterpolationType == c_InterpolationSpline3) {
+  } else if (InterpolationType == c_InterpolationSpline3) {
     return m_Spline3->Eval(x);
-  } else if (m_InterpolationType == c_InterpolationSpline5) {
+  } else if (InterpolationType == c_InterpolationSpline5) {
     return m_Spline5->Eval(x);
-  } else if (m_InterpolationType == c_InterpolationNone) {
+  } else if (InterpolationType == c_InterpolationNone) {
 
     // Get Position:
     int xPosition = -1; 
@@ -556,10 +565,10 @@ double MFunction::Evaluate(double x) const
 
     return m_Y[xPosition];
 
-  } else if (m_InterpolationType == c_InterpolationLinLin ||
-             m_InterpolationType == c_InterpolationLinLog ||
-             m_InterpolationType == c_InterpolationLogLin ||
-             m_InterpolationType == c_InterpolationLogLog) {
+  } else if (InterpolationType == c_InterpolationLinLin ||
+             InterpolationType == c_InterpolationLinLog ||
+             InterpolationType == c_InterpolationLogLin ||
+             InterpolationType == c_InterpolationLogLog) {
 
     double y = 0.0;
 
@@ -595,11 +604,11 @@ double MFunction::Evaluate(double x) const
     }
 
     // Attention for log interpolation make sure all values are positive!
-    if (m_InterpolationType == c_InterpolationLinLog || m_InterpolationType == c_InterpolationLogLog) {
+    if (InterpolationType == c_InterpolationLinLog || InterpolationType == c_InterpolationLogLog) {
       y1 = log(y1);
       y2 = log(y2);
     }
-    if (m_InterpolationType == c_InterpolationLogLin || m_InterpolationType == c_InterpolationLogLog) {
+    if (InterpolationType == c_InterpolationLogLin || InterpolationType == c_InterpolationLogLog) {
       x = log(x);
       x1 = log(x1);
       x2 = log(x2);
@@ -608,14 +617,14 @@ double MFunction::Evaluate(double x) const
     double m = (y2-y1)/(x2-x1);
     double t = y2 - m*x2;
 
-    if (m_InterpolationType == c_InterpolationLinLog || m_InterpolationType == c_InterpolationLogLog) {
+    if (InterpolationType == c_InterpolationLinLog || InterpolationType == c_InterpolationLogLog) {
       y = exp(m*x+t);
     } else {
       y = m*x+t;
     }
     
     if (std::isnan(y)) { // std:: is required here due to multiple definitions
-      merr<<"Interpolation error for interpolation type "<<m_InterpolationType<<": y is NaN!"<<endl;;
+      merr<<"Interpolation error for interpolation type "<<InterpolationType<<": y is NaN!"<<endl;;
       merr<<"   m="<<m<<"  t="<<t<<"  x1="<<x1<<"  y1="<<y1<<"  x2="<<x2<<"  y2="<<y2<<show;
     }
 
@@ -643,6 +652,8 @@ double MFunction::Integrate(double XMin, double XMax) const
 {
   // Integrate the data from min to max
   
+  auto InterpolationType = m_InterpolationType;
+
   if (XMin < m_X.front()) {
     merr<<"XMin ("<<XMin<<") smaller than minimum x-value ("<<m_X.front()<<") --- starting at minimum x-value"<<endl;
     XMin = m_X.front();
@@ -656,20 +667,34 @@ double MFunction::Integrate(double XMin, double XMax) const
     return 0.0;    
   }
 
+  // Switch to XZero to handle very large numbers
+  XMin -= m_X.front();
+  XMax -= m_X.front();
+
+  // ... use m_XZero from now on for x-axis
+
+  // More sanity checks
+  if (InterpolationType == c_InterpolationLinLog) {
+    if (m_X.back() > 1E+09) {
+      merr<<"Info: Large x-axis values make LinLog interpolation fail. Switching to LinLin!"<<endl;
+      InterpolationType = c_InterpolationLinLin;
+    }
+  }
+
   int BinMin = 0;
-  if (XMin > m_X.front()) {
-    // BinMin = find_if(m_X.begin(), m_X.end(), bind2nd(greater<double>(), XMin)) - m_X.begin() - 1;
-    BinMin = find_if(m_X.begin(), m_X.end(), bind(greater<double>(), placeholders::_1, XMin)) - m_X.begin() - 1;
+  if (XMin > m_XZero.front()) {
+    // BinMin = find_if(m_XZero.begin(), m_XZero.end(), bind2nd(greater<double>(), XMin)) - m_XZero.begin() - 1;
+    BinMin = find_if(m_XZero.begin(), m_XZero.end(), bind(greater<double>(), placeholders::_1, XMin)) - m_XZero.begin() - 1;
 //     unsigned int upper = m_Cumulative.size();
 //     unsigned int center = 1;
 //     unsigned int lower = 0;
     
 //     while (upper-lower > 1) {
 //       center = (upper+lower) >> 1;
-//       if (XMin == m_X[center]) {
+//       if (XMin == m_XZero[center]) {
 //         BinMin = int(center)+1;
 //       }
-//       if (XMin < m_X[center]) {
+//       if (XMin < m_XZero[center]) {
 //         upper = center;
 //       } else {
 //         lower = center;
@@ -677,20 +702,20 @@ double MFunction::Integrate(double XMin, double XMax) const
 //     }
 //     BinMin = int(lower)+1;
   }
-  int BinMax = m_X.size()-1;
-  if (XMax < m_X.back()) {
-    //BinMax = find_if(m_X.begin(), m_X.end(), bind2nd(greater_equal<double>(), XMax)) - m_X.begin();
-    BinMax = find_if(m_X.begin(), m_X.end(), bind(greater_equal<double>(), placeholders::_1, XMax)) - m_X.begin();
+  int BinMax = m_XZero.size()-1;
+  if (XMax < m_XZero.back()) {
+    //BinMax = find_if(m_XZero.begin(), m_XZero.end(), bind2nd(greater_equal<double>(), XMax)) - m_XZero.begin();
+    BinMax = find_if(m_XZero.begin(), m_XZero.end(), bind(greater_equal<double>(), placeholders::_1, XMax)) - m_XZero.begin();
 //     unsigned int upper = m_Cumulative.size();
 //     unsigned int center = 1;
 //     unsigned int lower = 0;
     
 //     while (upper-lower > 1) {
 //       center = (upper+lower) >> 1;
-//       if (XMax == m_X[center]) {
+//       if (XMax == m_XZero[center]) {
 //         BinMax = int(center)+1;
 //       }
-//       if (XMax < m_X[center]) {
+//       if (XMax < m_XZero[center]) {
 //         upper = center;
 //       } else {
 //         lower = center;
@@ -700,30 +725,30 @@ double MFunction::Integrate(double XMin, double XMax) const
   }
   
   double Integral = 0.0;
-  if (m_InterpolationType == c_InterpolationConstant) {
+  if (InterpolationType == c_InterpolationConstant) {
     Integral = (XMax - XMin) * m_Y[0];
-  } else if (m_InterpolationType == c_InterpolationNone) {
+  } else if (InterpolationType == c_InterpolationNone) {
     // Just sum rectangular bins:
 
-    double BinCenterMin = m_X[BinMin-1] + 0.5*(m_X[BinMin] - m_X[BinMin-1]);
-    double BinCenterMax = m_X[BinMax-1] + 0.5*(m_X[BinMax] - m_X[BinMax-1]);
+    double BinCenterMin = m_XZero[BinMin-1] + 0.5*(m_XZero[BinMin] - m_XZero[BinMin-1]);
+    double BinCenterMax = m_XZero[BinMax-1] + 0.5*(m_XZero[BinMax] - m_XZero[BinMax-1]);
 
     if (BinMin != BinMax) {
       if (XMin < BinCenterMin) {
         Integral += (BinCenterMin - XMin)*m_Y[BinMin-1];
-        Integral += (m_X[BinMin] - BinCenterMin)*m_Y[BinMin];
+        Integral += (m_XZero[BinMin] - BinCenterMin)*m_Y[BinMin];
       } else {
-        Integral += (m_X[BinMin] - XMin)*m_Y[BinMin];
+        Integral += (m_XZero[BinMin] - XMin)*m_Y[BinMin];
       }
       for (int b = BinMin; b < BinMax; ++b) {
-        Integral += 0.5*(m_X[BinMin+1] - m_X[BinMin])*m_Y[BinMin];
-        Integral += 0.5*(m_X[BinMin+1] - m_X[BinMin])*m_Y[BinMin+1];
+        Integral += 0.5*(m_XZero[BinMin+1] - m_XZero[BinMin])*m_Y[BinMin];
+        Integral += 0.5*(m_XZero[BinMin+1] - m_XZero[BinMin])*m_Y[BinMin+1];
       }
       if (XMax > BinCenterMax) {
-        Integral += (BinCenterMax - m_X[BinMax-1])*m_Y[BinMax-1];
+        Integral += (BinCenterMax - m_XZero[BinMax-1])*m_Y[BinMax-1];
         Integral += (XMax - BinCenterMax)*m_Y[BinMax];
       } else {
-        Integral += (XMax - m_X[BinMax-1])*m_Y[BinMax-1];
+        Integral += (XMax - m_XZero[BinMax-1])*m_Y[BinMax-1];
       }
     } else {
       if (XMin < BinCenterMin && XMax < BinCenterMin) {
@@ -735,10 +760,10 @@ double MFunction::Integrate(double XMin, double XMax) const
         Integral += (XMax - BinCenterMax)*m_Y[BinMin];
       }
     }      
-  } else if (m_InterpolationType == c_InterpolationLinLin ||
-             m_InterpolationType == c_InterpolationLinLog ||
-             m_InterpolationType == c_InterpolationLogLin ||
-             m_InterpolationType == c_InterpolationLogLog) {
+  } else if (InterpolationType == c_InterpolationLinLin ||
+             InterpolationType == c_InterpolationLinLog ||
+             InterpolationType == c_InterpolationLogLin ||
+             InterpolationType == c_InterpolationLogLog) {
     
     double x1, x2, y1, y2;
     for (int i = BinMin; i < BinMax; ++i) {
@@ -747,25 +772,25 @@ double MFunction::Integrate(double XMin, double XMax) const
         x1 = XMin;
         y1 = Evaluate(x1);
       } else {
-        x1 = m_X[i];
+        x1 = m_XZero[i];
         y1 = m_Y[i];
       }
       if (i == BinMax) {
         x2 = XMax;
         y2 = Evaluate(x2);
       } else {
-        x2 = m_X[i+1];
+        x2 = m_XZero[i+1];
         y2 = m_Y[i+1];
       }
       
       // Attention for log interpolation make sure all values are positive!
-      if (m_InterpolationType == c_InterpolationLinLog || 
-          m_InterpolationType == c_InterpolationLogLog) {
+      if (InterpolationType == c_InterpolationLinLog ||
+          InterpolationType == c_InterpolationLogLog) {
         y1 = log(y1);
         y2 = log(y2);
       }
-      if (m_InterpolationType == c_InterpolationLogLin || 
-          m_InterpolationType == c_InterpolationLogLog) {
+      if (InterpolationType == c_InterpolationLogLin ||
+          InterpolationType == c_InterpolationLogLog) {
         x1 = log(x1);
         x2 = log(x2);
       }
@@ -777,32 +802,34 @@ double MFunction::Integrate(double XMin, double XMax) const
       double t = y2 - m*x2;
 
       // Switch back
-      if (m_InterpolationType == c_InterpolationLinLog || 
-          m_InterpolationType == c_InterpolationLogLog) {
+      if (InterpolationType == c_InterpolationLinLog ||
+          InterpolationType == c_InterpolationLogLog) {
         y1 = exp(y1);
         y2 = exp(y2);
       }
-      if (m_InterpolationType == c_InterpolationLogLin || 
-          m_InterpolationType == c_InterpolationLogLog) {
+      if (InterpolationType == c_InterpolationLogLin ||
+          InterpolationType == c_InterpolationLogLog) {
         x1 = exp(x1);
         x2 = exp(x2);
       }
       
       // Do the integration using the correct formula for the various modi:
-      if (m_InterpolationType == c_InterpolationLinLin) {
+      if (InterpolationType == c_InterpolationLinLin) {
         // y=m*x+t --> int(m*x+t)
         Integral += 0.5*m*(x2*x2-x1*x1) + t*(x2-x1);      
-      } else if (m_InterpolationType == c_InterpolationLinLog) {
+      } else if (InterpolationType == c_InterpolationLinLog) {
         // ln(y) = m*x+t --> int(exp(m*x+t))
         if (fabs(m) < 10E-8) {
           Integral += exp(t)*(x2-x1); 
+          cout<<"x1:"<<x1<<" x2:"<<x2<<" y1:"<<y1<<" y2:"<<y2<<" m:"<<m<<" t:"<<t<<":"<<exp(t)<<":"<<x2-x1<<endl;
         } else {
           Integral += 1/m * (exp(m*x2+t) - exp(m*x1+t));
+          cout<<1/m<<":"<<exp(m*x2+t)<<":"<<exp(m*x1+t)<<endl;
         }
-      } else if (m_InterpolationType == c_InterpolationLogLin) {
+      } else if (InterpolationType == c_InterpolationLogLin) {
         // y = m*ln(x) + t --> int(m*ln(x) + t)
         Integral += x2*(m*(log(x2) - 1) + t) - x1*(m*(log(x1) - 1) + t);
-      } else if (m_InterpolationType == c_InterpolationLogLog) {
+      } else if (InterpolationType == c_InterpolationLogLog) {
         // ln(y) = m*ln(x) + t --> y = exp(t)*x^m --> int(exp(t)*x^m)
         if (fabs(m+1) < 10E-8) {
           Integral += exp(t)*(log(x2)-log(x1)); 
@@ -810,8 +837,10 @@ double MFunction::Integrate(double XMin, double XMax) const
           Integral += exp(t)/(m+1) * (pow(x2, m+1) - pow(x1, m+1));
         }
       }
+      if (std::isfinite(Integral) == false) {
+        merr<<"Error: Integral is no longer finite at bin: "<<i<<endl;
+      }
     }
-
   } else {
     merr<<"This interpolation type is no longer supported..."<<endl;
   }
@@ -1230,9 +1259,9 @@ double MFunction::FindX(double XStart, double Integral, bool Cyclic)
     //mout<<"x="<<x2<<endl;
     X = x2; 
   } else if ((x2 < m_XZero[NewUpperBin-1] || x2 > m_XZero[NewUpperBin]) && (x1 < m_XZero[NewUpperBin-1] || x1 > m_XZero[NewUpperBin])) {
-    merr<<std::setprecision(20)<<"FindX: Both possible results are outside choosen bin ["<<m_XZero[NewUpperBin-1]<<"-"<<m_XZero[NewUpperBin]<<"]: x1="<<x1<<" x2="<<x2<<endl;
+    merr<<std::setprecision(20)<<"FindX: Both possible results are outside choosen bin ["<<m_XZero[NewUpperBin-1]<<"-"<<m_XZero[NewUpperBin]<<"] with bin ID="<<NewUpperBin-1<<" and y range ["<<m_Y[NewUpperBin-1]<<"-"<<m_Y[NewUpperBin]<<"]: x1="<<x1<<" x2="<<x2<<endl;
   } else {
-    merr<<std::setprecision(20)<<"FindX: Both possible results are within choosen bin ["<<m_X[NewUpperBin-1]<<"-"<<m_X[NewUpperBin]<<"]: x1="<<x1<<" x2="<<x2<<endl;
+    merr<<std::setprecision(20)<<"FindX: Both possible results are within choosen bin ["<<m_X[NewUpperBin-1]<<"-"<<m_X[NewUpperBin]<<"] with bin ID="<<NewUpperBin-1<<" and y range ["<<m_Y[NewUpperBin-1]<<"-"<<m_Y[NewUpperBin]<<"]: x1="<<x1<<" x2="<<x2<<endl;
   }
   
   //cout<<"XStart: "<<XStart<<" X: "<<X<<" modulo: "<<Modulo<<endl;

From 894f3d0d033330167afa715d430115b1c5adce27 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Tue, 23 Jul 2024 10:16:55 -0700
Subject: [PATCH 047/192] CHG: Revert "CHG: Large number fix"

This reverts commit 8db810c984a1665ce40936e13552912279649275.
---
 src/cosima/src/MCSource.cc        |  30 ++-----
 src/global/misc/src/MFunction.cxx | 139 ++++++++++++------------------
 2 files changed, 64 insertions(+), 105 deletions(-)

diff --git a/src/cosima/src/MCSource.cc b/src/cosima/src/MCSource.cc
index 7153503bc..73a5f62ae 100644
--- a/src/cosima/src/MCSource.cc
+++ b/src/cosima/src/MCSource.cc
@@ -510,13 +510,13 @@ bool MCSource::SetStartAreaParameters(double StartAreaParam1,
   }
 
   // We have to update the start area parameters
-  if (UpgradeStartArea() == false) return false;
+  UpgradeStartArea();
   // We have to update the position vectors
-  if (UpgradePosition() == false) return false;
+  UpgradePosition();
   // and the flux normalization
-  if (UpgradeFlux() == false) return false;
+  UpgradeFlux();
   // and the light curve information
-  if (UpgradeLightCurve() == false) return false;
+  UpgradeLightCurve();
   
   return true;
 }
@@ -2116,25 +2116,13 @@ bool MCSource::UpgradeLightCurve()
   if (m_LightCurveType == c_LightCurveFile) {
     // Make sure the y-value is the flux in particles/second
     
-    // Sanity check:
-    auto LightCurveIntegral = m_LightCurveFunction.Integrate();
-    if (std::isfinite(LightCurveIntegral) == false) {
-      mout<<"  ***  ERROR  ***   "<<m_Name<<": The light curve integral is not finite: " <<LightCurveIntegral<<endl;
-      return false;
-    }
-
-    cout<<"Lightcurve integration: "<<LightCurveIntegral<<endl;
+    cout<<"Lightcurve integration: "<<m_LightCurveFunction.Integrate()<<endl;
     cout<<"Flux: "<<m_Flux*second<<" ph/s"<<endl;
-    if (m_Flux > 0 && LightCurveIntegral > 0) {
-      m_LightCurveFunction.ScaleY((m_LightCurveFunction.GetXMax() - m_LightCurveFunction.GetXMin())/LightCurveIntegral);
+    if (m_Flux > 0 && m_LightCurveFunction.Integrate() > 0) {
+      m_LightCurveFunction.ScaleY((m_LightCurveFunction.GetXMax() - m_LightCurveFunction.GetXMin())/m_LightCurveFunction.Integrate());
     }
-    LightCurveIntegral = m_LightCurveFunction.Integrate();
-    cout<<"Final light-curve integration: "<<LightCurveIntegral<<endl;
-    if (std::isfinite(LightCurveIntegral) == false) {
-      mout<<"  ***  ERROR  ***   "<<m_Name<<": The light curve integral is not finite:" <<LightCurveIntegral<<endl;
-      return false;
-    }
-
+    cout<<"Final light-curve integration: "<<m_LightCurveFunction.Integrate()<<endl;
+    
     if (m_NextEmission < m_LightCurveFunction.GetXMin()) {
       m_NextEmission = m_LightCurveFunction.GetXMin();
     }
diff --git a/src/global/misc/src/MFunction.cxx b/src/global/misc/src/MFunction.cxx
index c3d61fd3c..ece0f8bdc 100644
--- a/src/global/misc/src/MFunction.cxx
+++ b/src/global/misc/src/MFunction.cxx
@@ -520,9 +520,7 @@ double MFunction::Evaluate(double x) const
 {
   // Evalute the function considering the different interpolation types
 
-  auto InterpolationType = m_InterpolationType;
-
-  if (InterpolationType == c_InterpolationUnknown) {
+  if (m_InterpolationType == c_InterpolationUnknown) {
     merr<<"Unknown interpolation type: "<<c_InterpolationUnknown<<show;
     return 0;
   }
@@ -533,20 +531,13 @@ double MFunction::Evaluate(double x) const
     return 0;
   }
 
-  if (InterpolationType == c_InterpolationLinLog) {
-    if (m_X.back() > 1E+09) {
-      merr<<"Info: Large x-axis values make LinLog interpolation fail. Switching to LinLin!"<<endl;
-      InterpolationType = c_InterpolationLinLin;
-    }
-  }
-
-  if (InterpolationType == c_InterpolationConstant || m_X.size() == 1) {
+  if (m_InterpolationType == c_InterpolationConstant || m_X.size() == 1) {
     return m_Y[0];
-  } else if (InterpolationType == c_InterpolationSpline3) {
+  } else if (m_InterpolationType == c_InterpolationSpline3) {
     return m_Spline3->Eval(x);
-  } else if (InterpolationType == c_InterpolationSpline5) {
+  } else if (m_InterpolationType == c_InterpolationSpline5) {
     return m_Spline5->Eval(x);
-  } else if (InterpolationType == c_InterpolationNone) {
+  } else if (m_InterpolationType == c_InterpolationNone) {
 
     // Get Position:
     int xPosition = -1; 
@@ -565,10 +556,10 @@ double MFunction::Evaluate(double x) const
 
     return m_Y[xPosition];
 
-  } else if (InterpolationType == c_InterpolationLinLin ||
-             InterpolationType == c_InterpolationLinLog ||
-             InterpolationType == c_InterpolationLogLin ||
-             InterpolationType == c_InterpolationLogLog) {
+  } else if (m_InterpolationType == c_InterpolationLinLin ||
+             m_InterpolationType == c_InterpolationLinLog ||
+             m_InterpolationType == c_InterpolationLogLin ||
+             m_InterpolationType == c_InterpolationLogLog) {
 
     double y = 0.0;
 
@@ -604,11 +595,11 @@ double MFunction::Evaluate(double x) const
     }
 
     // Attention for log interpolation make sure all values are positive!
-    if (InterpolationType == c_InterpolationLinLog || InterpolationType == c_InterpolationLogLog) {
+    if (m_InterpolationType == c_InterpolationLinLog || m_InterpolationType == c_InterpolationLogLog) {
       y1 = log(y1);
       y2 = log(y2);
     }
-    if (InterpolationType == c_InterpolationLogLin || InterpolationType == c_InterpolationLogLog) {
+    if (m_InterpolationType == c_InterpolationLogLin || m_InterpolationType == c_InterpolationLogLog) {
       x = log(x);
       x1 = log(x1);
       x2 = log(x2);
@@ -617,14 +608,14 @@ double MFunction::Evaluate(double x) const
     double m = (y2-y1)/(x2-x1);
     double t = y2 - m*x2;
 
-    if (InterpolationType == c_InterpolationLinLog || InterpolationType == c_InterpolationLogLog) {
+    if (m_InterpolationType == c_InterpolationLinLog || m_InterpolationType == c_InterpolationLogLog) {
       y = exp(m*x+t);
     } else {
       y = m*x+t;
     }
     
     if (std::isnan(y)) { // std:: is required here due to multiple definitions
-      merr<<"Interpolation error for interpolation type "<<InterpolationType<<": y is NaN!"<<endl;;
+      merr<<"Interpolation error for interpolation type "<<m_InterpolationType<<": y is NaN!"<<endl;;
       merr<<"   m="<<m<<"  t="<<t<<"  x1="<<x1<<"  y1="<<y1<<"  x2="<<x2<<"  y2="<<y2<<show;
     }
 
@@ -652,8 +643,6 @@ double MFunction::Integrate(double XMin, double XMax) const
 {
   // Integrate the data from min to max
   
-  auto InterpolationType = m_InterpolationType;
-
   if (XMin < m_X.front()) {
     merr<<"XMin ("<<XMin<<") smaller than minimum x-value ("<<m_X.front()<<") --- starting at minimum x-value"<<endl;
     XMin = m_X.front();
@@ -667,34 +656,20 @@ double MFunction::Integrate(double XMin, double XMax) const
     return 0.0;    
   }
 
-  // Switch to XZero to handle very large numbers
-  XMin -= m_X.front();
-  XMax -= m_X.front();
-
-  // ... use m_XZero from now on for x-axis
-
-  // More sanity checks
-  if (InterpolationType == c_InterpolationLinLog) {
-    if (m_X.back() > 1E+09) {
-      merr<<"Info: Large x-axis values make LinLog interpolation fail. Switching to LinLin!"<<endl;
-      InterpolationType = c_InterpolationLinLin;
-    }
-  }
-
   int BinMin = 0;
-  if (XMin > m_XZero.front()) {
-    // BinMin = find_if(m_XZero.begin(), m_XZero.end(), bind2nd(greater<double>(), XMin)) - m_XZero.begin() - 1;
-    BinMin = find_if(m_XZero.begin(), m_XZero.end(), bind(greater<double>(), placeholders::_1, XMin)) - m_XZero.begin() - 1;
+  if (XMin > m_X.front()) {
+    // BinMin = find_if(m_X.begin(), m_X.end(), bind2nd(greater<double>(), XMin)) - m_X.begin() - 1;
+    BinMin = find_if(m_X.begin(), m_X.end(), bind(greater<double>(), placeholders::_1, XMin)) - m_X.begin() - 1;
 //     unsigned int upper = m_Cumulative.size();
 //     unsigned int center = 1;
 //     unsigned int lower = 0;
     
 //     while (upper-lower > 1) {
 //       center = (upper+lower) >> 1;
-//       if (XMin == m_XZero[center]) {
+//       if (XMin == m_X[center]) {
 //         BinMin = int(center)+1;
 //       }
-//       if (XMin < m_XZero[center]) {
+//       if (XMin < m_X[center]) {
 //         upper = center;
 //       } else {
 //         lower = center;
@@ -702,20 +677,20 @@ double MFunction::Integrate(double XMin, double XMax) const
 //     }
 //     BinMin = int(lower)+1;
   }
-  int BinMax = m_XZero.size()-1;
-  if (XMax < m_XZero.back()) {
-    //BinMax = find_if(m_XZero.begin(), m_XZero.end(), bind2nd(greater_equal<double>(), XMax)) - m_XZero.begin();
-    BinMax = find_if(m_XZero.begin(), m_XZero.end(), bind(greater_equal<double>(), placeholders::_1, XMax)) - m_XZero.begin();
+  int BinMax = m_X.size()-1;
+  if (XMax < m_X.back()) {
+    //BinMax = find_if(m_X.begin(), m_X.end(), bind2nd(greater_equal<double>(), XMax)) - m_X.begin();
+    BinMax = find_if(m_X.begin(), m_X.end(), bind(greater_equal<double>(), placeholders::_1, XMax)) - m_X.begin();
 //     unsigned int upper = m_Cumulative.size();
 //     unsigned int center = 1;
 //     unsigned int lower = 0;
     
 //     while (upper-lower > 1) {
 //       center = (upper+lower) >> 1;
-//       if (XMax == m_XZero[center]) {
+//       if (XMax == m_X[center]) {
 //         BinMax = int(center)+1;
 //       }
-//       if (XMax < m_XZero[center]) {
+//       if (XMax < m_X[center]) {
 //         upper = center;
 //       } else {
 //         lower = center;
@@ -725,30 +700,30 @@ double MFunction::Integrate(double XMin, double XMax) const
   }
   
   double Integral = 0.0;
-  if (InterpolationType == c_InterpolationConstant) {
+  if (m_InterpolationType == c_InterpolationConstant) {
     Integral = (XMax - XMin) * m_Y[0];
-  } else if (InterpolationType == c_InterpolationNone) {
+  } else if (m_InterpolationType == c_InterpolationNone) {
     // Just sum rectangular bins:
 
-    double BinCenterMin = m_XZero[BinMin-1] + 0.5*(m_XZero[BinMin] - m_XZero[BinMin-1]);
-    double BinCenterMax = m_XZero[BinMax-1] + 0.5*(m_XZero[BinMax] - m_XZero[BinMax-1]);
+    double BinCenterMin = m_X[BinMin-1] + 0.5*(m_X[BinMin] - m_X[BinMin-1]);
+    double BinCenterMax = m_X[BinMax-1] + 0.5*(m_X[BinMax] - m_X[BinMax-1]);
 
     if (BinMin != BinMax) {
       if (XMin < BinCenterMin) {
         Integral += (BinCenterMin - XMin)*m_Y[BinMin-1];
-        Integral += (m_XZero[BinMin] - BinCenterMin)*m_Y[BinMin];
+        Integral += (m_X[BinMin] - BinCenterMin)*m_Y[BinMin];
       } else {
-        Integral += (m_XZero[BinMin] - XMin)*m_Y[BinMin];
+        Integral += (m_X[BinMin] - XMin)*m_Y[BinMin];
       }
       for (int b = BinMin; b < BinMax; ++b) {
-        Integral += 0.5*(m_XZero[BinMin+1] - m_XZero[BinMin])*m_Y[BinMin];
-        Integral += 0.5*(m_XZero[BinMin+1] - m_XZero[BinMin])*m_Y[BinMin+1];
+        Integral += 0.5*(m_X[BinMin+1] - m_X[BinMin])*m_Y[BinMin];
+        Integral += 0.5*(m_X[BinMin+1] - m_X[BinMin])*m_Y[BinMin+1];
       }
       if (XMax > BinCenterMax) {
-        Integral += (BinCenterMax - m_XZero[BinMax-1])*m_Y[BinMax-1];
+        Integral += (BinCenterMax - m_X[BinMax-1])*m_Y[BinMax-1];
         Integral += (XMax - BinCenterMax)*m_Y[BinMax];
       } else {
-        Integral += (XMax - m_XZero[BinMax-1])*m_Y[BinMax-1];
+        Integral += (XMax - m_X[BinMax-1])*m_Y[BinMax-1];
       }
     } else {
       if (XMin < BinCenterMin && XMax < BinCenterMin) {
@@ -760,10 +735,10 @@ double MFunction::Integrate(double XMin, double XMax) const
         Integral += (XMax - BinCenterMax)*m_Y[BinMin];
       }
     }      
-  } else if (InterpolationType == c_InterpolationLinLin ||
-             InterpolationType == c_InterpolationLinLog ||
-             InterpolationType == c_InterpolationLogLin ||
-             InterpolationType == c_InterpolationLogLog) {
+  } else if (m_InterpolationType == c_InterpolationLinLin ||
+             m_InterpolationType == c_InterpolationLinLog ||
+             m_InterpolationType == c_InterpolationLogLin ||
+             m_InterpolationType == c_InterpolationLogLog) {
     
     double x1, x2, y1, y2;
     for (int i = BinMin; i < BinMax; ++i) {
@@ -772,25 +747,25 @@ double MFunction::Integrate(double XMin, double XMax) const
         x1 = XMin;
         y1 = Evaluate(x1);
       } else {
-        x1 = m_XZero[i];
+        x1 = m_X[i];
         y1 = m_Y[i];
       }
       if (i == BinMax) {
         x2 = XMax;
         y2 = Evaluate(x2);
       } else {
-        x2 = m_XZero[i+1];
+        x2 = m_X[i+1];
         y2 = m_Y[i+1];
       }
       
       // Attention for log interpolation make sure all values are positive!
-      if (InterpolationType == c_InterpolationLinLog ||
-          InterpolationType == c_InterpolationLogLog) {
+      if (m_InterpolationType == c_InterpolationLinLog || 
+          m_InterpolationType == c_InterpolationLogLog) {
         y1 = log(y1);
         y2 = log(y2);
       }
-      if (InterpolationType == c_InterpolationLogLin ||
-          InterpolationType == c_InterpolationLogLog) {
+      if (m_InterpolationType == c_InterpolationLogLin || 
+          m_InterpolationType == c_InterpolationLogLog) {
         x1 = log(x1);
         x2 = log(x2);
       }
@@ -802,34 +777,32 @@ double MFunction::Integrate(double XMin, double XMax) const
       double t = y2 - m*x2;
 
       // Switch back
-      if (InterpolationType == c_InterpolationLinLog ||
-          InterpolationType == c_InterpolationLogLog) {
+      if (m_InterpolationType == c_InterpolationLinLog || 
+          m_InterpolationType == c_InterpolationLogLog) {
         y1 = exp(y1);
         y2 = exp(y2);
       }
-      if (InterpolationType == c_InterpolationLogLin ||
-          InterpolationType == c_InterpolationLogLog) {
+      if (m_InterpolationType == c_InterpolationLogLin || 
+          m_InterpolationType == c_InterpolationLogLog) {
         x1 = exp(x1);
         x2 = exp(x2);
       }
       
       // Do the integration using the correct formula for the various modi:
-      if (InterpolationType == c_InterpolationLinLin) {
+      if (m_InterpolationType == c_InterpolationLinLin) {
         // y=m*x+t --> int(m*x+t)
         Integral += 0.5*m*(x2*x2-x1*x1) + t*(x2-x1);      
-      } else if (InterpolationType == c_InterpolationLinLog) {
+      } else if (m_InterpolationType == c_InterpolationLinLog) {
         // ln(y) = m*x+t --> int(exp(m*x+t))
         if (fabs(m) < 10E-8) {
           Integral += exp(t)*(x2-x1); 
-          cout<<"x1:"<<x1<<" x2:"<<x2<<" y1:"<<y1<<" y2:"<<y2<<" m:"<<m<<" t:"<<t<<":"<<exp(t)<<":"<<x2-x1<<endl;
         } else {
           Integral += 1/m * (exp(m*x2+t) - exp(m*x1+t));
-          cout<<1/m<<":"<<exp(m*x2+t)<<":"<<exp(m*x1+t)<<endl;
         }
-      } else if (InterpolationType == c_InterpolationLogLin) {
+      } else if (m_InterpolationType == c_InterpolationLogLin) {
         // y = m*ln(x) + t --> int(m*ln(x) + t)
         Integral += x2*(m*(log(x2) - 1) + t) - x1*(m*(log(x1) - 1) + t);
-      } else if (InterpolationType == c_InterpolationLogLog) {
+      } else if (m_InterpolationType == c_InterpolationLogLog) {
         // ln(y) = m*ln(x) + t --> y = exp(t)*x^m --> int(exp(t)*x^m)
         if (fabs(m+1) < 10E-8) {
           Integral += exp(t)*(log(x2)-log(x1)); 
@@ -837,10 +810,8 @@ double MFunction::Integrate(double XMin, double XMax) const
           Integral += exp(t)/(m+1) * (pow(x2, m+1) - pow(x1, m+1));
         }
       }
-      if (std::isfinite(Integral) == false) {
-        merr<<"Error: Integral is no longer finite at bin: "<<i<<endl;
-      }
     }
+
   } else {
     merr<<"This interpolation type is no longer supported..."<<endl;
   }
@@ -1259,9 +1230,9 @@ double MFunction::FindX(double XStart, double Integral, bool Cyclic)
     //mout<<"x="<<x2<<endl;
     X = x2; 
   } else if ((x2 < m_XZero[NewUpperBin-1] || x2 > m_XZero[NewUpperBin]) && (x1 < m_XZero[NewUpperBin-1] || x1 > m_XZero[NewUpperBin])) {
-    merr<<std::setprecision(20)<<"FindX: Both possible results are outside choosen bin ["<<m_XZero[NewUpperBin-1]<<"-"<<m_XZero[NewUpperBin]<<"] with bin ID="<<NewUpperBin-1<<" and y range ["<<m_Y[NewUpperBin-1]<<"-"<<m_Y[NewUpperBin]<<"]: x1="<<x1<<" x2="<<x2<<endl;
+    merr<<std::setprecision(20)<<"FindX: Both possible results are outside choosen bin ["<<m_XZero[NewUpperBin-1]<<"-"<<m_XZero[NewUpperBin]<<"]: x1="<<x1<<" x2="<<x2<<endl;
   } else {
-    merr<<std::setprecision(20)<<"FindX: Both possible results are within choosen bin ["<<m_X[NewUpperBin-1]<<"-"<<m_X[NewUpperBin]<<"] with bin ID="<<NewUpperBin-1<<" and y range ["<<m_Y[NewUpperBin-1]<<"-"<<m_Y[NewUpperBin]<<"]: x1="<<x1<<" x2="<<x2<<endl;
+    merr<<std::setprecision(20)<<"FindX: Both possible results are within choosen bin ["<<m_X[NewUpperBin-1]<<"-"<<m_X[NewUpperBin]<<"]: x1="<<x1<<" x2="<<x2<<endl;
   }
   
   //cout<<"XStart: "<<XStart<<" X: "<<X<<" modulo: "<<Modulo<<endl;

From d9afacb2657c07307742f51f9abdd54261709acc Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Tue, 23 Jul 2024 10:32:26 -0700
Subject: [PATCH 048/192] VER: 4.0

---
 config/Version.txt |  2 +-
 doc/ChangeLog.txt  | 20 ++++++++++++++++----
 2 files changed, 17 insertions(+), 5 deletions(-)

diff --git a/config/Version.txt b/config/Version.txt
index 847b845c4..4e7283627 100644
--- a/config/Version.txt
+++ b/config/Version.txt
@@ -1 +1 @@
-3.99.02
+4.00.00
diff --git a/doc/ChangeLog.txt b/doc/ChangeLog.txt
index 1c73d56c1..b58b802e8 100644
--- a/doc/ChangeLog.txt
+++ b/doc/ChangeLog.txt
@@ -7,12 +7,13 @@
 
 
 
-Version 3.99/4.00
-=================
+Version 4.00
+============
 
 General:
 + License is now LPGL v3
-+ Default ROOT version is 6.24
++ Default ROOT version is 6.28
++ C++-2014 is now default
 + Updates for Apple M1 and Ubuntu 22.04
 + Updates to the dmegalib parallel simulation environment
 
@@ -23,19 +24,30 @@ Geomega:
 + The geometry view is now restored after a reload of the mass-model
 + Do not allow to define multiple surrounding spheres
 + Fix path in which cross-section are stored
++ Voxel3D is allowed to be non-box detector if it an intersection or subtraction
 
 Cosima:
 + mcosima has the new option "-a" to not generated concatenation files
++ gzip'ing sim files is now default
 
 Response:
 + Parallel reading of spares rsp files
 + Cleanup interface in responsemanipulator
 
 Mimrec:
-+ Chenges for near-filed imaging
++ Changes for near-field imaging
 + Fixes in binned-mode imaging
 + Spherical images now can have hammer projection too
++ Save the cfg file via command line
+
+Revan:
++ Save the cfg file via command line
++ Add energy windows to Bayesian and TMVA reconstrcution
+
+Fretalon / Melinator:
++ Significant speed ups and optimizations to handle new COSI calibrations
 
+And many smaller bug fixes and optimizations
 
 
 

From 9bddb3bf759e9ed3187e0289ae12554053d1e6df Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Tue, 23 Jul 2024 11:43:31 -0700
Subject: [PATCH 049/192] CHG: REvert to Geant4 11.1

---
 config/AllowedGeant4Versions.txt | 1 -
 1 file changed, 1 deletion(-)

diff --git a/config/AllowedGeant4Versions.txt b/config/AllowedGeant4Versions.txt
index efd8ca582..fc1db2732 100644
--- a/config/AllowedGeant4Versions.txt
+++ b/config/AllowedGeant4Versions.txt
@@ -1,3 +1,2 @@
 110
 111
-112

From b61d0569d42707ad863ebdd3bcbe036d177916bb Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Tue, 23 Jul 2024 15:38:07 -0700
Subject: [PATCH 050/192] ADD: More 4.0 changes

---
 doc/ChangeLog.txt | 23 ++++++++++++++++++++---
 1 file changed, 20 insertions(+), 3 deletions(-)

diff --git a/doc/ChangeLog.txt b/doc/ChangeLog.txt
index b58b802e8..c4a71a120 100644
--- a/doc/ChangeLog.txt
+++ b/doc/ChangeLog.txt
@@ -14,31 +14,42 @@ General:
 + License is now LPGL v3
 + Default ROOT version is 6.28
 + C++-2014 is now default
-+ Updates for Apple M1 and Ubuntu 22.04
-+ Updates to the dmegalib parallel simulation environment
++ Updates for all the latest OS'es
++ Improvements to the dmegalib parallel simulation environment
++ Improved event and file writting
 
 Geomega:
 + Speed ups reading large files
 + Fixed if-statement evaluations
 + Voxel3D is now allowed not to be a box detector
 + The geometry view is now restored after a reload of the mass-model
++ Option to automatically view the geometry upon launch
 + Do not allow to define multiple surrounding spheres
 + Fix path in which cross-section are stored
-+ Voxel3D is allowed to be non-box detector if it an intersection or subtraction
 
 Cosima:
 + mcosima has the new option "-a" to not generated concatenation files
 + gzip'ing sim files is now default
++ Improvements to the orientation handling to enable COSI data challenge simulations
++ Enable a timeout (stop simulating) if no new events are stored after 30 minutes
++ Added Comptonization model as spectrum
++ Added cutoff power law
++ Added more unit tests
 
 Response:
 + Parallel reading of spares rsp files
 + Cleanup interface in responsemanipulator
++ Option to collapse response matrices
++ Store simulation parameters in rsp files
 
 Mimrec:
 + Changes for near-field imaging
 + Fixes in binned-mode imaging
++ Default color palette now is Viridis
 + Spherical images now can have hammer projection too
 + Save the cfg file via command line
++ Enable polarization analysis in Galactic coordinates
++ Feature to perform box selections on first and second interactio
 
 Revan:
 + Save the cfg file via command line
@@ -46,6 +57,12 @@ Revan:
 
 Fretalon / Melinator:
 + Significant speed ups and optimizations to handle new COSI calibrations
++ Parallelization of spectrum generation
++ UI: Added peak finding options to UI, scrollbar for options, include errors for peak fitting, minor canvas changes
+
+Examples:
++ Sensitivity optimizer
++ Add test data for MEGAlib's getting started guide
 
 And many smaller bug fixes and optimizations
 

From 9843bcd30d34ad467b8e9a56ea1b6841a9f87723 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Wed, 24 Jul 2024 11:23:25 -0700
Subject: [PATCH 051/192] CHG: Geant4 11.1 compatibility on macOS

---
 config/env.sh | Bin 7461 -> 6994 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/config/env.sh b/config/env.sh
index 42f92f19f2146b5b78b6e150f9fa4d0d9042cf75..4976e25abb701a9848b37aebdbe3b3e354fc90fe 100755
GIT binary patch
delta 495
zcmZ2#b;)dkA*1p{LoKGH#ECI7(h7;i3W-HUiIrTwA-)0e&b}_T8VX7(4oV7|8&5bg
z3Mi>m!z7{|Vr!K)i!e!ZT5%}=L1vmlbhLtQo`OnLut$8DYf!MKzn?;EthGW(Mrs~d
ziGqTYBTz2bKQzeMHQFH7R%!AqZdn(-;tVB))ZEgX#FA8n?BWas-DCxIJ)pJKsLE@V
z)S<=%IEHwH_`AD0`h}SII(oYT4SL0`Rj-7@7L{sr4Ym5|sfl?dCb@~(saUNq&Mz%W
zPQ~qp)STi}sBLhilV@|w$bwA6>q;w_G+ZA+*MZGT%jBBu$Y(K`jZ<jyW1h{E|MTfh
uHs|+J4aiANEKXGb`9z_(v?x`<9qcoO%wmPiyyB9?oSf7Yz0EuV*LVQ-t&Si7

delta 696
zcmbu6L2DC17=}$jCDTm{6-20#*UcW9;%2R_f~F~~F|<%pL&>dao3K00F5S$^&TfL#
zw11&x@CSJC2T1>bSFawtd+}$KP9`e}wm0WA%=f(S_kHjDeD(Fs`O3wM<;?NL!Q%$0
zH|veVYW-bB*U7;11B$&p7zLQ!7|*f4k22hl029tQ`FkJ2SkYyTd;U>O+>lZ7?X#Vk
zogyy(WEQjcd6+~Fg(%OWfDKqK?OQAf0;vTG4ZFG3e7{+<cbaQ;d%IQ<r&@l-Y)kyf
zs_BI6$nU~5`!wQy$l6wyc38aD>l{<1zfHb;hJvv)25&eNryZ1qT4<}bTdTA`4BWPQ
zb6glF|9THqDP3nWM~QnAjWWACavO@@+Lic0@^2~YOQu*x>`^xDkw!IMe$;JfjoIm#
z07ArkE-!kyN8<a!L!o7#%>bg2TNhsTf%uXO?u8MgP-N$J&TP(;p3k}%P;?>+Cy64;
z;@~5E#^X*9jB1-IM1*pnXy9{-QJ&z5<l_)g!qC!7R#k;BA6q(>Qpq}AmtGbj8@6;u
asZ!gN(d6e~qoSy%m!IZ-Y1KRbeaJQIcfbGu


From bea0a76db4add04af90e8dfd0434ccd2af30b111 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Wed, 24 Jul 2024 13:51:50 -0700
Subject: [PATCH 052/192] CHG: Addd bzip2lib

---
 config/configure_packages | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/config/configure_packages b/config/configure_packages
index 104927c96..b862c4f5f 100755
--- a/config/configure_packages
+++ b/config/configure_packages
@@ -59,9 +59,9 @@ if [[ ${IsDebianClone} -eq 1 ]]; then
     elif [[ ${VERSIONID} == 20.04 ]]; then
       REQUIRED="git gawk dpkg-dev make g++ gcc gfortran gdb valgrind binutils libx11-dev libxpm-dev libxft-dev libxext-dev libssl-dev libpcre3-dev libglu1-mesa-dev libglew-dev libftgl-dev libmysqlclient-dev libfftw3-dev libgraphviz-dev libavahi-compat-libdnssd-dev libldap2-dev python3 python3-dev python3-tk python3-venv libxml2-dev libkrb5-dev libgsl-dev cmake libxmu-dev curl doxygen libblas-dev liblapack-dev expect dos2unix libncurses5-dev libboost-all-dev libcfitsio-dev mlocate"
     elif [[ ${VERSIONID} == 22.04 ]]; then
-      REQUIRED="git gawk dpkg-dev make g++ gcc gfortran gdb valgrind binutils libx11-dev libxpm-dev libxft-dev libxext-dev libssl-dev libpcre3-dev libglu1-mesa-dev libglew-dev libftgl-dev libmysqlclient-dev libfftw3-dev libgraphviz-dev libavahi-compat-libdnssd-dev libldap2-dev python3 python3-dev python3-tk python3-venv libxml2-dev libkrb5-dev libgsl-dev cmake libxmu-dev curl doxygen libblas-dev liblapack-dev expect dos2unix libncurses5-dev libboost-all-dev libcfitsio-dev mlocate"
+      REQUIRED="git gawk dpkg-dev make g++ gcc gfortran gdb valgrind binutils libx11-dev libxpm-dev libxft-dev libxext-dev libssl-dev libpcre3-dev libglu1-mesa-dev libglew-dev libftgl-dev libmysqlclient-dev libfftw3-dev libgraphviz-dev libavahi-compat-libdnssd-dev libldap2-dev python3 python3-dev python3-tk python3-venv libxml2-dev libkrb5-dev libgsl-dev cmake libxmu-dev curl doxygen libblas-dev liblapack-dev expect dos2unix libncurses5-dev libboost-all-dev libcfitsio-dev mlocate libbz2-dev"
     else
-      REQUIRED="git gawk dpkg-dev make g++ gcc gfortran gdb valgrind binutils libx11-dev libxpm-dev libxft-dev libxext-dev libssl-dev libpcre3-dev libglu1-mesa-dev libglew-dev libftgl-dev libmysqlclient-dev libfftw3-dev libgraphviz-dev libavahi-compat-libdnssd-dev libldap2-dev python3 python3-dev python3-tk python3-venv libxml2-dev libkrb5-dev libgsl-dev cmake libxmu-dev curl doxygen libblas-dev liblapack-dev expect dos2unix libncurses5-dev libboost-all-dev libcfitsio-dev mlocate"
+      REQUIRED="git gawk dpkg-dev make g++ gcc gfortran gdb valgrind binutils libx11-dev libxpm-dev libxft-dev libxext-dev libssl-dev libpcre3-dev libglu1-mesa-dev libglew-dev libftgl-dev libmysqlclient-dev libfftw3-dev libgraphviz-dev libavahi-compat-libdnssd-dev libldap2-dev python3 python3-dev python3-tk python3-venv libxml2-dev libkrb5-dev libgsl-dev cmake libxmu-dev curl doxygen libblas-dev liblapack-dev expect dos2unix libncurses5-dev libboost-all-dev libcfitsio-dev mlocate libbz2-dev"
       
       echo "This script has not yet been adapted for your version of Ubuntu: ${VERSIONID}"
       echo "Feel free to write the MEGAlib maintainers an email to update this script and send them the content of the file: /etc/os-release"
@@ -86,7 +86,7 @@ if [[ ${IsDebianClone} -eq 1 ]]; then
       exit 0  
     fi
   else
-    REQUIRED="bc git gawk dpkg-dev make g++ gcc gdb valgrind binutils libx11-dev libxpm-dev libxft-dev libxext-dev libssl-dev libpcre3-dev libglu1-mesa-dev libglew-dev libftgl-dev libfftw3-dev libgraphviz-dev libavahi-compat-libdnssd-dev libldap2-dev python python3-dev python3-tk python3-venv libxml2-dev libkrb5-dev libgsl-dev cmake libxmu-dev curl doxygen libblas-dev liblapack-dev expect dos2unix libncurses5-dev libboost-all-dev libcfitsio-dev"
+    REQUIRED="bc git gawk dpkg-dev make g++ gcc gdb valgrind binutils libx11-dev libxpm-dev libxft-dev libxext-dev libssl-dev libpcre3-dev libglu1-mesa-dev libglew-dev libftgl-dev libfftw3-dev libgraphviz-dev libavahi-compat-libdnssd-dev libldap2-dev python python3-dev python3-tk python3-venv libxml2-dev libkrb5-dev libgsl-dev cmake libxmu-dev curl doxygen libblas-dev liblapack-dev expect dos2unix libncurses5-dev libboost-all-dev libcfitsio-dev libbz2-dev"
  
     echo "This script has not yet been adapted for your version of Linux: Debian-derivative ${OS}"
     echo "Feel free to write the MEGAlib maintainers an email to update this script and send them the content of the file: /etc/os-release"

From 1eaad14c51ec52ad1cb2399a7357fe2ca1074f79 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Wed, 24 Jul 2024 14:14:33 -0700
Subject: [PATCH 053/192] CHG: Added known issues

---
 doc/ChangeLog.txt | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/doc/ChangeLog.txt b/doc/ChangeLog.txt
index c4a71a120..f8cab2c45 100644
--- a/doc/ChangeLog.txt
+++ b/doc/ChangeLog.txt
@@ -64,8 +64,11 @@ Examples:
 + Sensitivity optimizer
 + Add test data for MEGAlib's getting started guide
 
-And many smaller bug fixes and optimizations
+Known issues:
++ Cosima: Activation simulations still miss some important lines
++ Cosima: Using light curves with large time numbers (i.e. corresponding to current date in seconds) can create artificial spikes
 
+And many smaller bug fixes and optimizations
 
 
 Version 3.03/3.04

From 8f1a2dcfaf15bcf453c8981a3b863545c5331281 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Sat, 27 Jul 2024 21:34:37 -0700
Subject: [PATCH 054/192] CHG: More env.sh fixes for macOS

---
 config/env.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/config/env.sh b/config/env.sh
index 4976e25ab..ecbd32310 100755
--- a/config/env.sh
+++ b/config/env.sh
@@ -1,6 +1,6 @@
 # Set all MEGAlib-related environment variables
 
-#if [ -n "$ZSH_VERSION" ]; then emulate -L bash; fi
+if [ -n "$ZSH_VERSION" ]; then emulate -L ksh; fi
 
 # Store command line as array
 MTMP_CMD=( "$@" )
@@ -97,6 +97,7 @@ if [ "${MTMP_GEANT4PATH}" != "${MTMP_NODEFAULT}" ]; then
   if (test -f ${MTMP_GEANT4PATH}/bin/geant4.sh); then
     
     if [[ -n $ZSH_VERSION ]]; then
+      BASH_SOURCE=()
       BASH_SOURCE[0]="${MTMP_GEANT4PATH}/bin/geant4.sh" emulate ksh -c '. "${BASH_SOURCE[0]}"'
       PATHTOGEANT4MAKE="${MTMP_GEANT4PATH}/share/Geant4/geant4make"
       BASH_SOURCE[0]="${PATHTOGEANT4MAKE}/geant4make.sh" emulate ksh -c 'source "${BASH_SOURCE[0]}"'

From dcddb2bff46d9d7554423018898130d2463b8504 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Sat, 27 Jul 2024 22:27:35 -0700
Subject: [PATCH 055/192] CHG: Only Geant4 11.2 allowed

---
 config/AllowedGeant4Versions.txt | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/config/AllowedGeant4Versions.txt b/config/AllowedGeant4Versions.txt
index fc1db2732..194b81caa 100644
--- a/config/AllowedGeant4Versions.txt
+++ b/config/AllowedGeant4Versions.txt
@@ -1,2 +1 @@
-110
-111
+112

From c807e0d547617e485820bad47607a62aadff92c1 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Tue, 13 Aug 2024 09:47:52 -0700
Subject: [PATCH 056/192] CHG: Changes for ROOT 6.32

---
 config/AllowedROOTVersions.txt | 2 +-
 config/build-root.sh           | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/config/AllowedROOTVersions.txt b/config/AllowedROOTVersions.txt
index 6193b76c1..cfee3c9ec 100644
--- a/config/AllowedROOTVersions.txt
+++ b/config/AllowedROOTVersions.txt
@@ -1 +1 @@
-628 
+632 
diff --git a/config/build-root.sh b/config/build-root.sh
index f270bff6d..71db2a6dc 100755
--- a/config/build-root.sh
+++ b/config/build-root.sh
@@ -24,7 +24,7 @@ CONFIGUREOPTIONS+=" -Dopengl=ON"
 # Mathmore -- needed for fitting, e.g. ARMs"
 CONFIGUREOPTIONS+=" -Dmathmore=ON"
 # Minuit2 -- needed for parallel fitting with melinator
-CONFIGUREOPTIONS+=" -Dminuit2=ON"
+# Minuit 2 is default startin g ROOT 6.30: CONFIGUREOPTIONS+=" -Dminuit2=ON"
 # XFT -- needed for smoothed fonts
 CONFIGUREOPTIONS+=" -Dxft=ON"
 # Afterimage -- support to draw images in pads and save as png, etc.

From 2ce372d2f9d3377102b14888eb568fb0c02d7545 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Thu, 29 Aug 2024 08:32:40 -0700
Subject: [PATCH 057/192] CHG: Option to create a string in correct
 value/uncertainty format

---
 src/global/misc/inc/MString.h   | 16 +++++++++----
 src/global/misc/src/MString.cxx | 40 +++++++++++++++++++++++++++++++++
 2 files changed, 52 insertions(+), 4 deletions(-)

diff --git a/src/global/misc/inc/MString.h b/src/global/misc/inc/MString.h
index e29be6c82..26af68617 100644
--- a/src/global/misc/inc/MString.h
+++ b/src/global/misc/inc/MString.h
@@ -43,13 +43,15 @@ class MString
 {
   // public interface:
  public:
-  //! Deafult constructor
+  //! Default constructor
   MString() {};
-  // Copy constructor
+  //! Copy constructor
   MString(const MString& String) : m_String(String.m_String) {}
-  // Move constructor
+  //! Move constructor
   MString(MString&& String) : m_String(std::move(String.m_String)) {}
+  //! Initialize with string
   MString(const string& S) { m_String = S; }
+  //! Initilaize with ostringstream
   MString(const ostringstream& S) { m_String = S.str(); }
   MString(const char* S) { if (S!= nullptr) m_String = S; }
   //! Copy first n characters of S
@@ -63,6 +65,11 @@ class MString
   MString(const unsigned long i) { operator+=(i); }
   MString(const float i) { operator+=(i); }
   MString(const double i) { operator+=(i); }
+  //! Construct from value, uncertainty, unit using scientific rounding
+  //! If Latex is true, the +- will be repalce by #pm for display with ROOT
+  //! Will be something like (12.345, 1.872, "mm") -> "(12.3 +- 1.9) mm"
+  MString(double Value, double Uncertainty, MString Units = "", bool Latex = false);
+  //! Default destructor
   virtual ~MString() {}
 
   // Move
@@ -255,9 +262,10 @@ class MString
   //! Test if the string is a positive integer -- ignores whitespace at beginning and end
   bool IsPositiveInteger() const;
 
-  // General type test (use for int, long, etc.)
+  //! General type test (use for int, long, etc.)
   template <typename T> bool Is() const;
 
+  //! For compatibility with ???
   static const size_t npos;
 
   // protected methods:
diff --git a/src/global/misc/src/MString.cxx b/src/global/misc/src/MString.cxx
index fe1b89d1f..6cb0b5a85 100644
--- a/src/global/misc/src/MString.cxx
+++ b/src/global/misc/src/MString.cxx
@@ -71,6 +71,46 @@ ostream& operator<<(ostream& out, const MString& S)
 ////////////////////////////////////////////////////////////////////////////////
 
 
+MString::MString(double Value, double Uncertainty, MString Units, bool Latex)
+{
+  //! Construct from value, uncertainty, unit using scientific rounding
+  //! Will be something like (12.345, 1.872, "mm") -> "(12.3 +- 1.9) mm"
+
+  // Find at which position the first digit is, e.g.:
+  // 187.2 = 2, 3.23 = 0, 0.348 = -1, etc.
+  int RoundOffDigit = int(log10(Uncertainty));
+  if (Uncertainty < 1) RoundOffDigit -= 1; // Due to how rounding using int() works
+
+  // If the uncertainty starts with 1 & 2, we have one more significant digit.
+  if (round(Uncertainty * pow(10, -RoundOffDigit)) < 3) RoundOffDigit -= 1;
+
+  // Now round
+  double Scale = pow(10, -RoundOffDigit);
+  Value = round(Value * Scale) / Scale;
+  Uncertainty = round(Uncertainty * Scale) / Scale;
+
+  // Print the result
+  ostringstream out;
+  if (Units != "") {
+    if (Latex == true) {
+      out<<"("<<Value<<" #pm "<<Uncertainty<<") "<<Units;
+    } else {
+      out<<"("<<Value<<" ± "<<Uncertainty<<") "<<Units;
+    }
+  } else {
+    if (Latex == true) {
+      out<<Value<<" #pm "<<Uncertainty;
+    } else {
+      out<<Value<<" ± "<<Uncertainty;
+    }
+  }
+
+  m_String = out.str();
+}
+
+////////////////////////////////////////////////////////////////////////////////
+
+
 bool MString::operator<(const MString& N) const
 {
   // Is lower operator for sorting by name

From c88913498cb4df356461f1309f4e5ff92e5433ae Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Thu, 29 Aug 2024 08:33:24 -0700
Subject: [PATCH 058/192] ADD: New ARM fitter

---
 src/mimrec/Makefile                  |   12 +-
 src/mimrec/inc/MARMFitter.h          |  289 ++++++
 src/mimrec/inc/MGUIMimrecMain.h      |    5 +-
 src/mimrec/inc/MInterfaceMimrec.h    |    4 +-
 src/mimrec/src/MARMFitter.cxx        | 1261 ++++++++++++++++++++++++++
 src/mimrec/src/MGUIMimrecMain.cxx    |   10 +-
 src/mimrec/src/MInterfaceMimrec.cxx  |  142 ++-
 src/mimrec/unittests/UTARMFitter.cxx |  349 +++++++
 8 files changed, 2033 insertions(+), 39 deletions(-)
 create mode 100644 src/mimrec/inc/MARMFitter.h
 create mode 100644 src/mimrec/src/MARMFitter.cxx
 create mode 100644 src/mimrec/unittests/UTARMFitter.cxx

diff --git a/src/mimrec/Makefile b/src/mimrec/Makefile
index c48e80ced..bac15eb0f 100644
--- a/src/mimrec/Makefile
+++ b/src/mimrec/Makefile
@@ -54,6 +54,7 @@ FILES := MSettingsMimrec \
 	MExposure \
 	MEarthHorizon \
 	MStandardAnalysis \
+	MARMFitter \
 	MVariableSourceDetector \
 
 LIBRARY_UI := MimrecGui
@@ -117,12 +118,16 @@ ROOTPCM_UI:=lib$(LIBRARY_UI)_rdict.pcm
 OBJECT_MAIN:=$(patsubst %, $(LB)/%.o, $(MAIN))
 EXECUTABLE:=$(BN)/$(PROGRAM)
 
+CXX_UT := $(wildcard unittests/*.cxx)
+EXE_UT := $(patsubst %.cxx,%,$(CXX_UT))
+EXE_UT := $(patsubst unittests/%,$(BN)/%,$(EXE_UT))
+
 
 #----------------------------------------------------------------
 # Commands:
 #
 
-all: $(EXECUTABLE)
+all: $(EXECUTABLE) $(EXE_UT)
 
 lib: $(SHAREDLIB) 
 
@@ -196,6 +201,11 @@ $(EXECUTABLE): $(SHAREDLIB_UI) $(SHAREDLIB) $(OBJECT_MAIN)
 	@echo "Linking $(subst $(BN)/,,$@) ..."
 	@$(LD) $(LDFLAGS) $(OBJECT_MAIN) $(SHAREDLIB_UI) $(SHAREDLIB) $(LIBRARIES) $(GLIBS) $(LIBS) -o $(EXECUTABLE)
 
+
+$(EXE_UT): $(BN)/%: unittests/%.cxx $(SHAREDLIB)
+	@echo "Compiling and linking $(subst $(BN)/,,$@) ..."
+	@$(LD) $(CXXFLAGS) $(LDFLAGS) $< $(SHAREDLIB) $(LIBRARIES) $(GLIBS) $(LIBS) -o $@
+
 	
 #
 #----------------------------------------------------------------
diff --git a/src/mimrec/inc/MARMFitter.h b/src/mimrec/inc/MARMFitter.h
new file mode 100644
index 000000000..5d1915bbe
--- /dev/null
+++ b/src/mimrec/inc/MARMFitter.h
@@ -0,0 +1,289 @@
+/*
+ * MARMFitter.h
+ *
+ * Copyright (C) by Andreas Zoglauer.
+ * All rights reserved.
+ *
+ * Please see the source-file for the copyright-notice.
+ *
+ */
+
+
+#ifndef __MARMFitter__
+#define __MARMFitter__
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+// Standard libs:
+#include <vector>
+#include <random>
+#include <mutex>
+#include <condition_variable>
+using namespace std;
+
+// ROOT libs:
+#include "TH1.h"
+#include "Fit/Fitter.h"
+
+// MEGAlib libs:
+#include "MGlobal.h"
+#include "MCoordinateSystem.h"
+#include "MComptonEvent.h"
+
+// Forward declarations:
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! List of the available fit functions
+enum class MARMFitFunctionID {
+  c_Gauss,
+  c_Lorentz,
+  c_GeneralizedNormal,
+  c_GaussLorentz,
+  c_GaussLorentzLorentz,
+  c_AsymmetricGaussLorentzLorentz,
+  c_AsymmetricGaussGaussLorentzLorentz,
+  c_AsymmetricGeneralizedNormalGeneralizedNormal,
+  c_AsymmetricGeneralizedNormalGeneralizedNormalGeneralizedNormal
+};
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! A class to fit ARM's
+class MARMFitter
+{
+  // public interface:
+ public:
+  //! Default constructor
+  MARMFitter();
+  //! Default destuctor 
+  virtual ~MARMFitter();
+
+  // Interface to set up the fitter
+
+  //! Set the number of bins for the ARM fit hisogram
+  //! The deafult is 101
+  void SetNumberOfBins(unsigned int NumberOfBins = 101);
+
+  //! Set the maximum range of the ARM values
+  //! The maximum value is 180
+  //! The histogram will go from [-MaxARM, MaxARM]
+  //! The defaulkt is 180
+  void SetMaxARM(double MaxARM = 180);
+
+  //! Set the test position, and its coordinate system
+  //! Do not call this function while adding events
+  void SetTestPosition(MVector TestPosition, MCoordinateSystem);
+
+  //! If this is set we try to optimize the binning
+  //! Especially if we have too many bins we iterate until we have at least 50 counts in one bin - if possible
+  void UseOptimizedBinning(bool DoIt = true) { m_OptimizeBinning = DoIt; }
+
+  //! If this is set we use an unbinned-likelihood fit
+  void UseUnbinnedFitting(bool DoIt = true) { m_UnbinnedFitting = DoIt; }
+
+  //! Fit this function to the data
+  //! One of: c_Gauss, c_Lorentz, c_GaussLorentz, c_GaussDoubleLorentz, c_AsymmetricGaussDoubleLorentz
+  //! If not set,  default is c_AsymmetricGaussDoubleLorentz
+  void SetFitFunction(MARMFitFunctionID ID) { m_ARMFitFunction = ID; }
+
+  // Interface to set the data
+
+  //! Reset the internally stored ARM values
+  void Reset();
+
+  //! Add Event - only stores the actual ARM value
+  void AddEvent(MComptonEvent* Event);
+  //! Add an ARM value
+  void AddARMValue(double ARMValue) { m_OriginalARMValues.push_back(ARMValue); }
+
+  // Interface to do the fits
+
+  //! Perform a single fit with the chosen fit function
+  bool FitOnce();
+
+  //! Perform fits with all fit functions and report Baker-Cousin results
+  bool FitAll();
+
+  //! Performs N fits.
+  //! Each fit samples randomly form the stored ARM values to determine the average width and error correctly
+  bool FitMultiple(unsigned int NumberOfFits = 100);
+
+
+  // Interface to retrieve the results
+
+  //! Returns true if we have a successful fit and have the results
+  bool WasFittingSuccessful() const { return m_FitSuccessful; }
+
+  //! Return the bootstrapped FWHM'es
+  vector<double> GetBootstrappedFWHMSamples() { return m_BootStrappedFWHMSamples; }
+
+  //! Return the FWHM result
+  double GetFWHM() const;
+
+  //! Return the FWHM uncertainty result
+  double GetFWHMUncertainty() const;
+
+  //! Return a summary string
+  MString ToString();
+
+  //! Draw an ARM histogram
+  void Draw();
+
+
+
+  // protected methods:
+ protected:
+  //! Optimize binning - check sif the binning is OK, otherwise check for a better one
+  bool OptimizeBinning();
+  //! Perform a single fit
+  bool PerformFit(unsigned int FitID, vector<double>& ARMValues);
+  //! Thread entry for parallel fitting
+  void ParallelFitting(int id, condition_variable& CV);
+  //! Bootstrap the ARM values and return them as vector
+  vector<double> BootstrapARMValues();
+  //! Calculate the average metrics from boot strapping (FWHM & uncertainty)
+  void CalculateBootStrappedMetrics();
+  //! Calculate the metrics of the ARM (containment etc.)
+  void CalculateARMMetrics();
+
+  //! Setup the fit function - ARMFitID is one of the members of the MARMFitFunctions enum
+  void SetupARMFit(MARMFitFunctionID ARMFitID, ROOT::Fit::Fitter& Fitter, TF1** FitFunction);
+  //! Setup a Gauss-function
+  void SetupARMFitGauss(ROOT::Fit::Fitter& Fitter, TF1** FitFunction);
+  //! Setup a Gauss-Lorentz-function
+  void SetupARMFitLorentz(ROOT::Fit::Fitter& Fitter, TF1** FitFunction);
+  //! Setup a GeneralizedNormal-function
+  void SetupARMFitGeneralizedNormal(ROOT::Fit::Fitter& Fitter, TF1** FitFunction);
+  //! Setup a Gauss-Lorentz-function
+  void SetupARMFitGaussLorentz(ROOT::Fit::Fitter& Fitter, TF1** FitFunction);
+  //! Setup a Gauss-Double-Lorentz-function
+  void SetupARMFitGaussLorentzLorentz(ROOT::Fit::Fitter& Fitter, TF1** FitFunction);
+  //! Setup an Assymetric-Gauss-Double-Lorentz-function
+  void SetupARMFitAsymmetricGaussLorentzLorentz(ROOT::Fit::Fitter& Fitter, TF1** FitFunction);
+  //! Setup an Assymetric-Gauss-Double-Lorentz-function
+  void SetupARMFitAsymmetricGaussGaussLorentzLorentz(ROOT::Fit::Fitter& Fitter, TF1** FitFunction);
+  //! Setup an Assymetric-Gauss-Double-Lorentz-function
+  void SetupARMFitAsymmetricGeneralizedNormalGeneralizedNormal(ROOT::Fit::Fitter& Fitter, TF1** FitFunction);
+  //! Setup an Assymetric-Gauss-Double-Lorentz-function
+  void SetupARMFitAsymmetricGeneralizedNormalGeneralizedNormalGeneralizedNormal(ROOT::Fit::Fitter& Fitter, TF1** FitFunction);
+
+  //! Return the function of the fit given the fit function ID
+  MString GetARMFitFunction(MARMFitFunctionID ARMFitID);
+  //! Return the name of the fit given the fit function ID
+  MString GetARMFitFunctionName(MARMFitFunctionID ARMFitID);
+  //! Return the number of parameters of the fit given the fit function ID
+  unsigned int GetARMFitFunctionNumberOfParameters(MARMFitFunctionID ARMFitID);
+
+  // private methods:
+ private:
+
+
+
+  // protected members:
+ protected:
+
+
+  // private members:
+ private:
+  //! The number of bins
+  unsigned int m_NumberOfBins;
+  //! The maximum ARM value
+  double m_MaxARMValue;
+  //! The test position
+  MVector m_TestPosition;
+  //! The coordinate system of the test position
+  MCoordinateSystem m_CoordinateSystem;
+  //! The function to use for fitting
+  MARMFitFunctionID m_ARMFitFunction;
+
+  //! Perform binning optimization
+  bool m_OptimizeBinning;
+  //! Use unbinned fitting
+  bool m_UnbinnedFitting;
+
+  //! Random device
+  std::mt19937 m_MersenneTwister;
+
+  //! Store for the ARM values
+  vector<double> m_OriginalARMValues;
+
+  //! The boot-strapped FWHM samples
+  vector<double> m_BootStrappedFWHMSamples;
+  //! The boot-strapped fit parameters:
+  vector<vector<double>> m_BootStrappedFitParameters;
+  //! The boot-strapped Baker-Cousins-Likelihood ratio values:
+  vector<double> m_BootStrappedBakerCousins;
+
+  //! The maximum number of allowed threads
+  unsigned int m_MaximumNumberOfThreads;
+  //! The number of currently running threads
+  unsigned int m_NumberOfRunningThreads;
+  //! The global mutex
+  std::mutex m_Mutex;
+
+  //! Check is we have a final results
+  bool m_FitSuccessful;
+
+  //! The final (average) FWHM of the ARM
+  double m_FinalFWHM;
+
+  //! The final FWHM uncertainty
+  double m_FinalFWHMUncertainty;
+
+  //! The final (average) baker-Cousins likelihood ratio
+  double m_FinalBakerCousins;
+
+  //! The final baker-Cousins likelihood ratio uncertainty
+  double m_FinalBakerCousinsUncertainty;
+
+  //! The final fit parameters
+  vector<double> m_FinalFitParameters;
+
+  //! The 50% containment radius (accurate to the next largest bin in the histogram)
+  double m_Containment50Percent;
+  //! The 1-sigmna containment radius (accurate to the next largest bin in the histogra)
+  double m_Containment1Sigma;
+  //! The 2-sigma containment radius (accurate to the next largest bin in the histogra)
+  double m_Containment2Sigma;
+  //! The 3-sigma containment radius (accurate to the next largest bin in the histogra)
+  double m_Containment3Sigma;
+
+  //! Minimum height for fitting
+  double m_MinHeight;
+  //! Maximum height for fitting
+  double m_MaxHeight;
+  //! Minimum width for fitting
+  double m_MinWidth;
+  //! Maximum width for fitting
+  double m_MaxWidth;
+  //! Minimum scale of generalized normal function for fitting
+  double m_MinScale;
+  //! Maximum scale of generalized normal functiofor fitting
+  double m_MaxScale;
+
+  //! Guess for the widths for fitting
+  double m_WidthGuess;
+  //! Guess for the height for fitting
+  double m_HeightGuess;
+  //! Guess for the scale for fitting
+  double m_ScaleGuess;
+
+
+#ifdef ___CLING___
+ public:
+  ClassDef(MARMFitter, 1)
+#endif
+
+};
+
+#endif
+
+
+////////////////////////////////////////////////////////////////////////////////
diff --git a/src/mimrec/inc/MGUIMimrecMain.h b/src/mimrec/inc/MGUIMimrecMain.h
index c0949fa49..4e3c2f8c5 100644
--- a/src/mimrec/inc/MGUIMimrecMain.h
+++ b/src/mimrec/inc/MGUIMimrecMain.h
@@ -90,8 +90,9 @@ class MGUIMimrecMain : public MGUIMain
                    c_StopReconstruction,
                    c_ThetaOriginDistribution,
                    c_SpectralAnalyzer,
-                   c_ResponseArmGamma, 
-                   c_ResponseArmGammaVsCompton, 
+                   c_ResponseArmGamma,
+                   c_ResponseArmGammaClassic,
+                   c_ResponseArmGammaVsCompton,
                    c_ResponseArmGammaVsDistance, 
                    c_ResponsePhiKinVsPhiGeo, 
                    c_ResponseSignificanceMap, 
diff --git a/src/mimrec/inc/MInterfaceMimrec.h b/src/mimrec/inc/MInterfaceMimrec.h
index ce7ace6c2..1c2565423 100644
--- a/src/mimrec/inc/MInterfaceMimrec.h
+++ b/src/mimrec/inc/MInterfaceMimrec.h
@@ -86,8 +86,10 @@ class MInterfaceMimrec : public MInterface
 
   void ThetaOriginDistribution();
 
-  //! The classic ARM gamma distribution
+  //! The ARM gamma distribution calculated in unbinned mode
   void ARMGamma();
+  //! The classic ARM gamma calculation
+  void ARMGammaClassic();
   //! Distribution of ARM values of the gamma-ray vs. the Compton scatter angle
   void ARMGammaVsComptonScatterAngle();
   //! 2D Histogram of Phi Calculated via kinemetics vs. Phi calculated via geometry
diff --git a/src/mimrec/src/MARMFitter.cxx b/src/mimrec/src/MARMFitter.cxx
new file mode 100644
index 000000000..035f2962f
--- /dev/null
+++ b/src/mimrec/src/MARMFitter.cxx
@@ -0,0 +1,1261 @@
+/*
+ * MARMFitter.cxx
+ *
+ *
+ * Copyright (C) by Andreas Zoglauer.
+ * All rights reserved.
+ *
+ *
+ * This code implementation is the intellectual property of
+ * Andreas Zoglauer.
+ *
+ * By copying, distributing or modifying the Program (or any work
+ * based on the Program) you indicate your acceptance of this statement,
+ * and all its terms.
+ *
+ */
+
+
+// Include the header:
+#include "MARMFitter.h"
+
+// Standard libs:
+#include <cmath>
+#include <cstring>
+#include <ctime>
+#include <vector>
+#include <algorithm>
+#include <iomanip>
+#include <thread>
+#include <mutex>
+#include <condition_variable>
+#include <atomic>
+#include <functional>
+
+// ROOT libs:
+#include "TH1.h"
+#include "TF1.h"
+#include "TCanvas.h"
+#include "TVirtualFitter.h"
+#include "TFitResult.h"
+#include "Math/MinimizerOptions.h"
+#include "Math/WrappedTF1.h"
+#include "Math/WrappedMultiTF1.h"
+#include "Fit/BinData.h"
+#include "Fit/UnBinData.h"
+#include "HFitInterface.h"
+#include "Fit/Fitter.h"
+#include "TLatex.h"
+#include "TStyle.h"
+
+// MEGAlib libs:
+#include "MExceptions.h"
+#include "MComptonEvent.h"
+#include "MFitFunctions.h"
+#include "MInterface.h"
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+#ifdef ___CLING___
+ClassImp(MARMFitter)
+#endif
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Default constructor
+MARMFitter::MARMFitter()
+{
+  ROOT::Math::MinimizerOptions::SetDefaultMaxFunctionCalls(250000);
+
+  std::random_device RD; // <-- should use MEGAlib global
+  std::mt19937 m_MersenneTwister(RD());
+
+  m_NumberOfBins = 101;
+  m_MaxARMValue = 180;
+  m_ARMFitFunction = MARMFitFunctionID::c_AsymmetricGaussLorentzLorentz;
+
+  m_OptimizeBinning = false;
+  m_UnbinnedFitting = true;
+
+  m_MinHeight = 0;
+  m_MaxHeight = 1E20;
+  m_MinWidth = 0.05;
+  m_MaxWidth = 180;
+  m_MinScale = 0.1;
+  m_MaxScale = 1000;
+
+  m_WidthGuess = 2;
+  m_HeightGuess = 2;
+  m_ScaleGuess = 2;
+
+  m_MaximumNumberOfThreads = 2*std::thread::hardware_concurrency();
+  if (m_MaximumNumberOfThreads < 1) m_MaximumNumberOfThreads = 1;
+
+  Reset();
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Default destructor
+MARMFitter::~MARMFitter()
+{
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//!
+void MARMFitter::SetNumberOfBins(unsigned int NumberOfBins)
+{
+  m_NumberOfBins = NumberOfBins;
+  if (m_NumberOfBins < 10) {
+    merr<<"You need at least 10 bins to be able to fit an ARM, and not "<<NumberOfBins<<". Setting it to 10."<<endl;
+    m_NumberOfBins = 10;
+  }
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+
+//!
+void MARMFitter::SetMaxARM(double MaxARMValue)
+{
+  m_MaxARMValue = MaxARMValue;
+  if (m_MaxARMValue <= 0 || m_MaxARMValue > 180) {
+    merr<<"The maximum ARM value must be within (0,180] and not "<<MaxARMValue<<endl<<"Setting it to 180"<<endl;
+  }
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Set the test position, and its coordinate system
+void MARMFitter::SetTestPosition(MVector TestPosition, MCoordinateSystem CoordinateSystem)
+{
+  m_TestPosition = TestPosition;
+  m_CoordinateSystem = CoordinateSystem;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Reset the internally stored ARM values
+void MARMFitter::Reset()
+{
+  m_OriginalARMValues.clear();
+
+  m_BootStrappedFWHMSamples.clear();
+  m_BootStrappedFitParameters.clear();
+  m_BootStrappedBakerCousins.clear();
+
+  m_FitSuccessful = false;
+  m_FinalFWHM = g_DoubleNotDefined;
+  m_FinalFWHMUncertainty = g_DoubleNotDefined;
+  m_FinalFitParameters.clear();
+  m_FinalBakerCousins = g_DoubleNotDefined;
+  m_FinalBakerCousinsUncertainty = g_DoubleNotDefined;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Add event - only stores the actual ARM value
+void MARMFitter::AddEvent(MComptonEvent* ComptonEvent)
+{
+  m_OriginalARMValues.push_back(ComptonEvent->GetARMGamma(m_TestPosition, m_CoordinateSystem));
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Optimize binning - check sif the binning is OK, otherwise check for a better one
+bool MARMFitter::OptimizeBinning()
+{
+  const unsigned int MinimumBinContent = 50;
+  const unsigned int MinimumBins = 5;
+
+  bool BinningOptimized = false;
+
+  unsigned int NumberOfBins = m_NumberOfBins;
+
+  while (BinningOptimized == false) {
+
+    double BinWidth = 2*m_MaxARMValue / NumberOfBins;
+    vector<unsigned int> BinnedData(NumberOfBins, 0);
+
+    for (auto A: m_OriginalARMValues) {
+      if (A >= -m_MaxARMValue && A <= m_MaxARMValue) {
+        unsigned int BinIndex = static_cast<unsigned int>((A + m_MaxARMValue) / BinWidth);
+
+        // Sanity check: Do we have a correct bin
+        if (BinIndex >= 0 && BinIndex < NumberOfBins) {
+          BinnedData[BinIndex]++;
+        } else {
+          new MExceptionIndexOutOfBounds(0, NumberOfBins, BinIndex);
+          return false;
+        }
+      }
+    }
+
+    // We need at least 1 bin with more than >>MinimumBinContent<< counts in it:
+    auto MaximumIterator = std::max_element(BinnedData.begin(), BinnedData.end());
+
+    if (MaximumIterator == BinnedData.end()) {
+      new MExceptionObjectDoesNotExist("Unable to find maximum of array.");
+      return false;
+    }
+    unsigned int Maximum = *MaximumIterator;
+
+    if (Maximum < MinimumBinContent) {
+      if (NumberOfBins == MinimumBins) {
+        mout<<"Unable to find a good number of bins. Using "<<MinimumBins<<endl;
+        m_NumberOfBins = MinimumBins;
+        return false;
+      }
+
+      mout<<"We do not have at least "<<MinimumBinContent<<" counts in any bin of the ARM histogram, but only "<<Maximum<<endl;
+
+      // Make sure we alsways have a reduction
+      unsigned int Reduction = NumberOfBins - static_cast<unsigned int>(static_cast<double>(NumberOfBins) * Maximum / MinimumBinContent);
+      if (Reduction == 0) Reduction = 1;
+      NumberOfBins -= Reduction;
+      // Make sure we have always an odd number
+      if (NumberOfBins % 2 == 0) NumberOfBins -= 1;
+      // Make sure we do not go below our limit
+      if (NumberOfBins < MinimumBins) NumberOfBins = MinimumBins;
+
+      mout<<"Reducing the bin number to "<<NumberOfBins<<" and checking again"<<endl;
+
+    } else {
+      BinningOptimized = true;
+    }
+  }
+
+  m_NumberOfBins = NumberOfBins;
+
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Return the name of the fit given the fit function ID
+MString MARMFitter::GetARMFitFunctionName(MARMFitFunctionID ID)
+{
+  if (ID == MARMFitFunctionID::c_Gauss) {
+    return MString("Gauss");
+  } else if (ID == MARMFitFunctionID::c_Lorentz) {
+    return MString("Lorentz");
+  } else if (ID == MARMFitFunctionID::c_GeneralizedNormal) {
+    return MString("GeneralizedNormal");
+  } else if (ID == MARMFitFunctionID::c_GaussLorentz) {
+    return MString("Gauss+Lorentz");
+  } else if (ID == MARMFitFunctionID::c_GaussLorentzLorentz) {
+    return MString("Gauss+Lorentz+Lorentz");
+  } else if (ID == MARMFitFunctionID::c_AsymmetricGaussLorentzLorentz) {
+    return MString("AsymmetricGauss+Lorentz+Lorentz");
+  } else if (ID == MARMFitFunctionID::c_AsymmetricGaussGaussLorentzLorentz) {
+    return MString("AsymmetricGauss+Gauss+Lorentz+Lorentz");
+  } else if (ID == MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormal) {
+    return MString("AsymmetricGeneralizedNormal+GeneralizedNormal");
+  } else if (ID == MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormalGeneralizedNormal) {
+    return MString("AsymmetricGeneralizedNormal+GeneralizedNormal+GeneralizedNormal");
+  } else {
+    new MExceptionObjectDoesNotExist("Unknown ARM fit function ID");
+    return MString("Unknown ARM fit function ID");
+  }
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Return the function of the fit given the fit function ID
+MString MARMFitter::GetARMFitFunction(MARMFitFunctionID ID)
+{
+  if (ID == MARMFitFunctionID::c_Gauss) {
+    return MString("[&](double *x, double *p){ return p[0] + p[2]*exp(-0.5*pow((x[0]-p[1])/p[3], 2)); }");
+  } else if (ID == MARMFitFunctionID::c_Lorentz) {
+    return MString("[&](double *x, double *p){ return p[0] + p[2]/(p[3]*p[3] + (x[0]-p[1])*(x[0]-p[1])); }");
+  } else if (ID == MARMFitFunctionID::c_GeneralizedNormal) {
+    return MString("[&](double *x, double *p){ return p[0] + p[2]*exp(-0.5*pow(fabs(x[0]-p[1])/p[3], p[4])); }");
+  } else if (ID == MARMFitFunctionID::c_GaussLorentz) {
+    return MString("[&](double *x, double *p){ return p[0] + p[2]*exp(-0.5*pow((x[0]-p[1])/p[3], 2)) + p[4]/(p[5]*p[5] + (x[0]-p[1])*(x[0]-p[1])); }");
+  } else if (ID == MARMFitFunctionID::c_GaussLorentzLorentz) {
+    return MString("[&](double *x, double *p){ return p[0] + p[2]*exp(-0.5*pow((x[0]-p[1])/p[3], 2)) + p[4]/(p[5]*p[5] + (x[0]-p[1])*(x[0]-p[1])) + p[6]/(p[7]*p[7] + (x[0]-p[1])*(x[0]-p[1])); }");
+  } else if (ID == MARMFitFunctionID::c_AsymmetricGaussLorentzLorentz) {
+    return MString("[&](double *x, double *p){ return p[0] + (x[0] - p[1] >= 0 ? p[2]*exp(-0.5*pow((x[0]-p[1])/p[3], 2)) : p[2]*exp(-0.5*pow((x[0]-p[1])/p[4], 2)) ) + p[5]/(p[6]*p[6] + (x[0]-p[1])*(x[0]-p[1])) + p[7]/(p[8]*p[8] + (x[0]-p[1])*(x[0]-p[1])); }");
+  } else if (ID == MARMFitFunctionID::c_AsymmetricGaussGaussLorentzLorentz) {
+    return MString("[&](double *x, double *p){ return p[0] + (x[0] - p[1] >= 0 ? p[2]*exp(-0.5*pow((x[0]-p[1])/p[3], 2)) : p[2]*exp(-0.5*pow((x[0]-p[1])/p[4], 2)) )  +  p[5]*exp(-0.5*pow((x[0]-p[1])/p[6], 2))  +  p[7]/(p[8]*p[8] + (x[0]-p[1])*(x[0]-p[1]))  +  p[9]/(p[10]*p[10] + (x[0]-p[1])*(x[0]-p[1])); }");
+  } else if (ID == MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormal) {
+    return MString("[&](double *x, double *p){ return p[0] + (x[0] - p[1] >= 0 ? p[2]*exp(-0.5*pow(fabs(x[0]-p[1])/p[3], p[4])) : p[2]*exp(-0.5*pow(fabs(x[0]-p[1])/p[5], p[6])) )  +  p[7]*exp(-0.5*pow(fabs(x[0]-p[1])/p[8], p[9])) ; }");
+  } else if (ID == MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormalGeneralizedNormal) {
+    return MString("[&](double *x, double *p){ return p[0] + (x[0] - p[1] >= 0 ? p[2]*exp(-0.5*pow(fabs(x[0]-p[1])/p[3], p[4])) : p[2]*exp(-0.5*pow(fabs(x[0]-p[1])/p[5], p[6])) )  +  p[7]*exp(-0.5*pow(fabs(x[0]-p[1])/p[8], p[9]))  +  p[10]*exp(-0.5*pow(fabs(x[0]-p[1])/p[11], p[12])) ; }");
+  } else {
+    new MExceptionObjectDoesNotExist("Unknown ARM fit function ID");
+    return MString("Unknown ARM fit function ID");
+  }
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Return the number of parameters of the fit given the fit function ID
+unsigned int MARMFitter::GetARMFitFunctionNumberOfParameters(MARMFitFunctionID ID)
+{
+   if (ID == MARMFitFunctionID::c_Gauss) {
+    return 4;
+  } else if (ID == MARMFitFunctionID::c_Lorentz) {
+    return 4;
+  } else if (ID == MARMFitFunctionID::c_GeneralizedNormal) {
+    return 5;
+  } else if (ID == MARMFitFunctionID::c_GaussLorentz) {
+    return 6;
+  } else if (ID == MARMFitFunctionID::c_GaussLorentzLorentz) {
+    return 8;
+  } else if (ID == MARMFitFunctionID::c_AsymmetricGaussLorentzLorentz) {
+    return 9;
+  } else if (ID == MARMFitFunctionID::c_AsymmetricGaussGaussLorentzLorentz) {
+    return 11;
+  } else if (ID == MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormal) {
+    return 10;
+  } else if (ID == MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormalGeneralizedNormal) {
+    return 13;
+  } else {
+    new MExceptionObjectDoesNotExist("Unknown ARM fit function ID");
+    return 0;
+  }
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Switch between the fit functions
+void MARMFitter::SetupARMFit(MARMFitFunctionID ARMFitID, ROOT::Fit::Fitter& Fitter, TF1** FitFunction)
+{
+  if (ARMFitID == MARMFitFunctionID::c_Gauss) {
+    SetupARMFitGauss(Fitter, FitFunction);
+  } else if (ARMFitID == MARMFitFunctionID::c_Lorentz) {
+    SetupARMFitLorentz(Fitter, FitFunction);
+  } else if (ARMFitID == MARMFitFunctionID::c_GeneralizedNormal) {
+    SetupARMFitGeneralizedNormal(Fitter, FitFunction);
+  } else if (ARMFitID == MARMFitFunctionID::c_GaussLorentz) {
+    SetupARMFitGaussLorentz(Fitter, FitFunction);
+  } else if (ARMFitID == MARMFitFunctionID::c_GaussLorentzLorentz) {
+    SetupARMFitGaussLorentzLorentz(Fitter, FitFunction);
+  } else if (ARMFitID == MARMFitFunctionID::c_AsymmetricGaussLorentzLorentz) {
+    SetupARMFitAsymmetricGaussLorentzLorentz(Fitter, FitFunction);
+  } else if (ARMFitID == MARMFitFunctionID::c_AsymmetricGaussGaussLorentzLorentz) {
+    SetupARMFitAsymmetricGaussGaussLorentzLorentz(Fitter, FitFunction);
+  } else if (ARMFitID == MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormal) {
+    SetupARMFitAsymmetricGeneralizedNormalGeneralizedNormal(Fitter, FitFunction);
+  } else if (ARMFitID == MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormalGeneralizedNormal) {
+    SetupARMFitAsymmetricGeneralizedNormalGeneralizedNormalGeneralizedNormal(Fitter, FitFunction);
+  } else {
+    new MExceptionObjectDoesNotExist("Unknown ARM fit function ID");
+  }
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Setup a Gauss fit function
+void MARMFitter::SetupARMFitGauss(ROOT::Fit::Fitter& Fitter, TF1** FitFunction)
+{
+  *FitFunction = new TF1(GetARMFitFunctionName(MARMFitFunctionID::c_Gauss).Data(), GetARMFitFunction(MARMFitFunctionID::c_Gauss).Data(), -m_MaxARMValue, m_MaxARMValue, 4);
+  ROOT::Math::WrappedMultiTF1 WrappedFitFunction(**FitFunction, 1);
+
+  Fitter.Config().SetMinimizer("Minuit2", "Migrad");
+  if (g_Verbosity >= c_Info) Fitter.Config().MinimizerOptions().SetPrintLevel(1);
+  Fitter.SetFunction(WrappedFitFunction, false);
+
+  vector<double> Parameters = { 1, 1, 1, 1};
+  Fitter.Config().SetParamsSettings(Parameters.size(), Parameters.data());
+
+  Fitter.Config().ParSettings(0).SetName("Offset");
+  Fitter.Config().ParSettings(0).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(1).SetName("Shift");
+  Fitter.Config().ParSettings(1).SetLimits(-m_MaxARMValue, m_MaxARMValue);
+
+  Fitter.Config().ParSettings(2).SetName("Gauss - height");
+  Fitter.Config().ParSettings(2).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(3).SetName("Gauss - sigma");
+  Fitter.Config().ParSettings(3).SetLimits(m_MinWidth, m_MaxWidth);
+
+  Fitter.Config().SetUpdateAfterFit();
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Setup a Lorentz fit function
+//! Return: The fitter
+void MARMFitter::SetupARMFitLorentz(ROOT::Fit::Fitter& Fitter, TF1** FitFunction)
+{
+  *FitFunction = new TF1(GetARMFitFunctionName(MARMFitFunctionID::c_Lorentz).Data(), GetARMFitFunction(MARMFitFunctionID::c_Lorentz).Data(), -m_MaxARMValue, m_MaxARMValue, 4);
+  ROOT::Math::WrappedMultiTF1 WrappedFitFunction(**FitFunction, 1);
+
+  Fitter.Config().SetMinimizer("Minuit2", "Migrad");
+  if (g_Verbosity >= c_Info) Fitter.Config().MinimizerOptions().SetPrintLevel(1);
+  Fitter.SetFunction(WrappedFitFunction, false);
+
+  vector<double> Parameters = { 1, 1, 1, 1 };
+  Fitter.Config().SetParamsSettings(Parameters.size(), Parameters.data());
+
+  Fitter.Config().ParSettings(0).SetName("Offset");
+  Fitter.Config().ParSettings(0).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(1).SetName("Shift");
+  Fitter.Config().ParSettings(1).SetLimits(-m_MaxARMValue, m_MaxARMValue);
+
+  Fitter.Config().ParSettings(2).SetName("Lorentz - height");
+  Fitter.Config().ParSettings(2).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(3).SetName("Lorentz - width");
+  Fitter.Config().ParSettings(3).SetLimits(m_MinWidth, m_MaxWidth);
+
+  Fitter.Config().SetUpdateAfterFit();
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Setup a generalzied normal distribution fit function
+void MARMFitter::SetupARMFitGeneralizedNormal(ROOT::Fit::Fitter& Fitter, TF1** FitFunction)
+{
+  *FitFunction = new TF1(GetARMFitFunctionName(MARMFitFunctionID::c_GeneralizedNormal).Data(), GetARMFitFunction(MARMFitFunctionID::c_GeneralizedNormal).Data(), -m_MaxARMValue, m_MaxARMValue, 5);
+  ROOT::Math::WrappedMultiTF1 WrappedFitFunction(**FitFunction, 1);
+
+  Fitter.Config().SetMinimizer("Minuit2", "Migrad");
+  if (g_Verbosity >= c_Info) Fitter.Config().MinimizerOptions().SetPrintLevel(10);
+  Fitter.SetFunction(WrappedFitFunction, false);
+
+  vector<double> Parameters = { 1, 1, 1, 1, 1.5};
+  Fitter.Config().SetParamsSettings(Parameters.size(), Parameters.data());
+
+  Fitter.Config().ParSettings(0).SetName("Offset");
+  Fitter.Config().ParSettings(0).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(1).SetName("Shift");
+  Fitter.Config().ParSettings(1).SetLimits(-m_MaxARMValue, m_MaxARMValue);
+
+  Fitter.Config().ParSettings(2).SetName("Generalized normal - height");
+  Fitter.Config().ParSettings(2).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(3).SetName("Generalized normal - sigma");
+  Fitter.Config().ParSettings(3).SetLimits(m_MinWidth, m_MaxWidth);
+  Fitter.Config().ParSettings(4).SetName("Generalized normal - scale");
+  Fitter.Config().ParSettings(4).SetLimits(m_MinScale, m_MaxScale);
+
+  Fitter.Config().SetUpdateAfterFit();
+}
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Setup an Gauss-Lorentz fit function
+void MARMFitter::SetupARMFitGaussLorentz(ROOT::Fit::Fitter& Fitter, TF1** FitFunction)
+{
+  *FitFunction = new TF1(GetARMFitFunctionName(MARMFitFunctionID::c_GaussLorentz).Data(), GetARMFitFunction(MARMFitFunctionID::c_GaussLorentz).Data(), -m_MaxARMValue, m_MaxARMValue, 6);
+  ROOT::Math::WrappedMultiTF1 WrappedFitFunction(**FitFunction, 1);
+
+  Fitter.Config().SetMinimizer("Minuit2", "Migrad");
+  if (g_Verbosity >= c_Info) Fitter.Config().MinimizerOptions().SetPrintLevel(1);
+  Fitter.SetFunction(WrappedFitFunction, false);
+
+  vector<double> Parameters = { 1, 1, 1, 1, 1, 1};
+  Fitter.Config().SetParamsSettings(Parameters.size(), Parameters.data());
+
+  Fitter.Config().ParSettings(0).SetName("Offset");
+  Fitter.Config().ParSettings(0).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(1).SetName("Shift");
+  Fitter.Config().ParSettings(1).SetLimits(-m_MaxARMValue, m_MaxARMValue);
+
+  Fitter.Config().ParSettings(2).SetName("Gauss - height");
+  Fitter.Config().ParSettings(2).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(3).SetName("Gauss - sigma");
+  Fitter.Config().ParSettings(3).SetLimits(m_MinWidth, m_MaxWidth);
+
+  Fitter.Config().ParSettings(4).SetName("Lorentz - height");
+  Fitter.Config().ParSettings(4).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(5).SetName("Lorentz - width");
+  Fitter.Config().ParSettings(5).SetLimits(m_MinWidth, m_MaxWidth);
+
+  Fitter.Config().SetUpdateAfterFit();
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Setup an Gauss-Double-Lorentz fit function
+void MARMFitter::SetupARMFitGaussLorentzLorentz(ROOT::Fit::Fitter& Fitter, TF1** FitFunction)
+{
+  *FitFunction = new TF1(GetARMFitFunctionName(MARMFitFunctionID::c_GaussLorentzLorentz).Data(), GetARMFitFunction(MARMFitFunctionID::c_GaussLorentzLorentz).Data(), -m_MaxARMValue, m_MaxARMValue, 8);
+  ROOT::Math::WrappedMultiTF1 WrappedFitFunction(**FitFunction, 1);
+
+  Fitter.Config().SetMinimizer("Minuit2", "Migrad");
+  if (g_Verbosity >= c_Info) Fitter.Config().MinimizerOptions().SetPrintLevel(1);
+  Fitter.SetFunction(WrappedFitFunction, false);
+
+  vector<double> Parameters = { 1, 1, 1, 1, 1, 1, 1, 1};
+  Fitter.Config().SetParamsSettings(Parameters.size(), Parameters.data());
+
+  Fitter.Config().ParSettings(0).SetName("Offset");
+  Fitter.Config().ParSettings(0).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(1).SetName("Shift");
+  Fitter.Config().ParSettings(1).SetLimits(-m_MaxARMValue, m_MaxARMValue);
+
+  Fitter.Config().ParSettings(2).SetName("Gauss - height");
+  Fitter.Config().ParSettings(2).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(3).SetName("Gauss - sigma");
+  Fitter.Config().ParSettings(3).SetLimits(m_MinWidth, m_MaxWidth);
+
+  Fitter.Config().ParSettings(4).SetName("Lorentz #1 - height");
+  Fitter.Config().ParSettings(4).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(5).SetName("Lorentz #1 - width");
+  Fitter.Config().ParSettings(5).SetLimits(m_MinWidth, m_MaxWidth);
+
+  Fitter.Config().ParSettings(6).SetName("Lorentz #2 - height");
+  Fitter.Config().ParSettings(6).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(7).SetName("Lorentz #2 - width");
+  Fitter.Config().ParSettings(7).SetLimits(m_MinWidth, m_MaxWidth);
+
+  Fitter.Config().SetUpdateAfterFit();
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Setup an Asymmetric-Gauss-Double-Lorentz fit function
+void MARMFitter::SetupARMFitAsymmetricGaussLorentzLorentz(ROOT::Fit::Fitter& Fitter, TF1** FitFunction)
+{
+  *FitFunction  = new TF1(GetARMFitFunctionName(MARMFitFunctionID::c_AsymmetricGaussLorentzLorentz).Data(), GetARMFitFunction(MARMFitFunctionID::c_AsymmetricGaussLorentzLorentz).Data(), -m_MaxARMValue, m_MaxARMValue, 9);
+  ROOT::Math::WrappedMultiTF1 WrappedFitFunction(**FitFunction, 1);
+
+  Fitter.Config().SetMinimizer("Minuit2", "Migrad");
+  if (g_Verbosity >= c_Info) Fitter.Config().MinimizerOptions().SetPrintLevel(1);
+  //Fitter.Config().MinimizerOptions().SetPrintLevel(0);
+  Fitter.SetFunction(WrappedFitFunction, false);
+
+  //vector<double> Parameters = { 0, 1, 1, 1, 1, 1, 1, 1, 1};
+  vector<double> Parameters = { 0, 0, m_HeightGuess, 0.9*m_WidthGuess, 1.1*m_WidthGuess, 0.9*m_HeightGuess, 0.95*m_WidthGuess, 1.1*m_HeightGuess, 1.05*m_WidthGuess };
+  Fitter.Config().SetParamsSettings(Parameters.size(), Parameters.data());
+
+
+  Fitter.Config().ParSettings(0).SetName("Offset");
+  Fitter.Config().ParSettings(0).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(1).SetName("Shift");
+  Fitter.Config().ParSettings(1).SetLimits(-m_MaxARMValue, m_MaxARMValue);
+
+  Fitter.Config().ParSettings(2).SetName("Gauss - height");
+  Fitter.Config().ParSettings(2).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(3).SetName("Gauss - sigma left");
+  Fitter.Config().ParSettings(3).SetLimits(m_MinWidth, m_MaxWidth);
+  Fitter.Config().ParSettings(4).SetName("Gauss - sigma right");
+  Fitter.Config().ParSettings(4).SetLimits(m_MinWidth, m_MaxWidth);
+
+  Fitter.Config().ParSettings(5).SetName("Lorentz #1 - height");
+  Fitter.Config().ParSettings(5).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(6).SetName("Lorentz #1 - width");
+  Fitter.Config().ParSettings(6).SetLimits(m_MinWidth, m_MaxWidth);
+
+  Fitter.Config().ParSettings(7).SetName("Lorentz #2 - height");
+  Fitter.Config().ParSettings(7).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(8).SetName("Lorentz #2 - width");
+  Fitter.Config().ParSettings(8).SetLimits(m_MinWidth, m_MaxWidth);
+
+  Fitter.Config().SetUpdateAfterFit();
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Setup an Asymmetric-Gauss-Double-Lorentz fit function
+void MARMFitter::SetupARMFitAsymmetricGaussGaussLorentzLorentz(ROOT::Fit::Fitter& Fitter, TF1** FitFunction)
+{
+  *FitFunction  = new TF1(GetARMFitFunctionName(MARMFitFunctionID::c_AsymmetricGaussGaussLorentzLorentz).Data(), GetARMFitFunction(MARMFitFunctionID::c_AsymmetricGaussGaussLorentzLorentz).Data(), -m_MaxARMValue, m_MaxARMValue, 11);
+  ROOT::Math::WrappedMultiTF1 WrappedFitFunction(**FitFunction, 1);
+
+  Fitter.Config().SetMinimizer("Minuit2", "Migrad");
+  if (g_Verbosity >= c_Info) Fitter.Config().MinimizerOptions().SetPrintLevel(1);
+  //Fitter.Config().MinimizerOptions().SetPrintLevel(0);
+  Fitter.SetFunction(WrappedFitFunction, false);
+
+  vector<double> Parameters = { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1};
+  Fitter.Config().SetParamsSettings(Parameters.size(), Parameters.data());
+
+
+  Fitter.Config().ParSettings(0).SetName("Offset");
+  Fitter.Config().ParSettings(0).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(1).SetName("Shift");
+  Fitter.Config().ParSettings(1).SetLimits(-m_MaxARMValue, m_MaxARMValue);
+
+  Fitter.Config().ParSettings(2).SetName("Gauss #1 - height");
+  Fitter.Config().ParSettings(2).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(3).SetName("Gauss #1 - sigma left");
+  Fitter.Config().ParSettings(3).SetLimits(m_MinWidth, m_MaxWidth);
+  Fitter.Config().ParSettings(4).SetName("Gauss #1 - sigma right");
+  Fitter.Config().ParSettings(4).SetLimits(m_MinWidth, m_MaxWidth);
+
+  Fitter.Config().ParSettings(5).SetName("Gauss #2 - height");
+  Fitter.Config().ParSettings(5).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(6).SetName("Gauss #2 - sigma");
+  Fitter.Config().ParSettings(6).SetLimits(m_MinWidth, m_MaxWidth);
+
+  Fitter.Config().ParSettings(7).SetName("Lorentz #1 - height");
+  Fitter.Config().ParSettings(7).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(8).SetName("Lorentz #1 - width");
+  Fitter.Config().ParSettings(8).SetLimits(m_MinWidth, m_MaxWidth);
+
+  Fitter.Config().ParSettings(9).SetName("Lorentz #2 - height");
+  Fitter.Config().ParSettings(9).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(10).SetName("Lorentz #2 - width");
+  Fitter.Config().ParSettings(10).SetLimits(m_MinWidth, m_MaxWidth);
+
+  Fitter.Config().SetUpdateAfterFit();
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Setup an Asymmetric-GeneralizedNormal+GeneralizedNormal fit function
+void MARMFitter::SetupARMFitAsymmetricGeneralizedNormalGeneralizedNormal(ROOT::Fit::Fitter& Fitter, TF1** FitFunction)
+{
+  *FitFunction  = new TF1(GetARMFitFunctionName(MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormal).Data(), GetARMFitFunction(MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormal).Data(), -m_MaxARMValue, m_MaxARMValue, 10);
+  ROOT::Math::WrappedMultiTF1 WrappedFitFunction(**FitFunction, 1);
+
+  Fitter.Config().SetMinimizer("Minuit2", "Migrad");
+  if (g_Verbosity >= c_Info) Fitter.Config().MinimizerOptions().SetPrintLevel(1);
+  //Fitter.Config().MinimizerOptions().SetPrintLevel(0);
+  Fitter.SetFunction(WrappedFitFunction, false);
+
+  vector<double> Parameters = { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 };
+  Fitter.Config().SetParamsSettings(Parameters.size(), Parameters.data());
+
+  Fitter.Config().ParSettings(0).SetName("Offset");
+  Fitter.Config().ParSettings(0).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(1).SetName("Shift");
+  Fitter.Config().ParSettings(1).SetLimits(-m_MaxARMValue, m_MaxARMValue);
+
+  Fitter.Config().ParSettings(2).SetName("GeneralizedNormal #1 - height");
+  Fitter.Config().ParSettings(2).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(3).SetName("GeneralizedNormal #1 - sigma left");
+  Fitter.Config().ParSettings(3).SetLimits(m_MinWidth, m_MaxWidth);
+  Fitter.Config().ParSettings(4).SetName("GeneralizedNormal #1 - scale left");
+  Fitter.Config().ParSettings(4).SetLimits(m_MinScale, m_MaxScale);
+  Fitter.Config().ParSettings(5).SetName("GeneralizedNormal #1 - sigma right");
+  Fitter.Config().ParSettings(5).SetLimits(m_MinWidth, m_MaxWidth);
+  Fitter.Config().ParSettings(6).SetName("GeneralizedNormal #1 - scale right");
+  Fitter.Config().ParSettings(6).SetLimits(m_MinScale, m_MaxScale);
+
+  Fitter.Config().ParSettings(7).SetName("GeneralizedNormal #2 - height");
+  Fitter.Config().ParSettings(7).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(8).SetName("GeneralizedNormal #2 - sigma");
+  Fitter.Config().ParSettings(8).SetLimits(m_MinWidth, m_MaxWidth);
+  Fitter.Config().ParSettings(9).SetName("GeneralizedNormal #2 - scale");
+  Fitter.Config().ParSettings(9).SetLimits(m_MinScale, m_MaxScale);
+
+  Fitter.Config().SetUpdateAfterFit();
+}
+
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Setup an Asymmetric-GeneralizedNormal+GeneralizedNormal+GeneralizedNormal fit function
+void MARMFitter::SetupARMFitAsymmetricGeneralizedNormalGeneralizedNormalGeneralizedNormal(ROOT::Fit::Fitter& Fitter, TF1** FitFunction)
+{
+  *FitFunction  = new TF1(GetARMFitFunctionName(MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormalGeneralizedNormal).Data(), GetARMFitFunction(MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormalGeneralizedNormal).Data(), -m_MaxARMValue, m_MaxARMValue, 13);
+  ROOT::Math::WrappedMultiTF1 WrappedFitFunction(**FitFunction, 1);
+
+  Fitter.Config().SetMinimizer("Minuit2", "Migrad");
+  if (g_Verbosity >= c_Info) Fitter.Config().MinimizerOptions().SetPrintLevel(0);
+  //Fitter.Config().MinimizerOptions().SetPrintLevel(0);
+  Fitter.SetFunction(WrappedFitFunction, false);
+
+  vector<double> Parameters = { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 };
+  Fitter.Config().SetParamsSettings(Parameters.size(), Parameters.data());
+
+  Fitter.Config().ParSettings(0).SetName("Offset");
+  Fitter.Config().ParSettings(0).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(1).SetName("Shift");
+  Fitter.Config().ParSettings(1).SetLimits(-m_MaxARMValue, m_MaxARMValue);
+
+  Fitter.Config().ParSettings(2).SetName("GeneralizedNormal #1 - height");
+  Fitter.Config().ParSettings(2).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(3).SetName("GeneralizedNormal #1 - sigma left");
+  Fitter.Config().ParSettings(3).SetLimits(m_MinWidth, m_MaxWidth);
+  Fitter.Config().ParSettings(4).SetName("GeneralizedNormal #1 - scale left");
+  Fitter.Config().ParSettings(4).SetLimits(m_MinScale, m_MaxScale);
+  Fitter.Config().ParSettings(5).SetName("GeneralizedNormal #1 - sigma right");
+  Fitter.Config().ParSettings(5).SetLimits(m_MinWidth, m_MaxWidth);
+  Fitter.Config().ParSettings(6).SetName("GeneralizedNormal #1 - scale right");
+  Fitter.Config().ParSettings(6).SetLimits(m_MinScale, m_MaxScale);
+
+  Fitter.Config().ParSettings(7).SetName("GeneralizedNormal #2 - height");
+  Fitter.Config().ParSettings(7).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(8).SetName("GeneralizedNormal #2 - sigma");
+  Fitter.Config().ParSettings(8).SetLimits(m_MinWidth, m_MaxWidth);
+  Fitter.Config().ParSettings(9).SetName("GeneralizedNormal #2 - scale");
+  Fitter.Config().ParSettings(9).SetLimits(m_MinScale, m_MaxScale);
+
+  Fitter.Config().ParSettings(10).SetName("GeneralizedNormal #3 - height");
+  Fitter.Config().ParSettings(10).SetLimits(m_MinHeight, m_MaxHeight);
+  Fitter.Config().ParSettings(11).SetName("GeneralizedNormal #3 - sigma");
+  Fitter.Config().ParSettings(11).SetLimits(m_MinWidth, m_MaxWidth);
+  Fitter.Config().ParSettings(12).SetName("GeneralizedNormal #3 - scale");
+  Fitter.Config().ParSettings(12).SetLimits(m_MinScale, m_MaxScale);
+
+  Fitter.Config().SetUpdateAfterFit();
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Perform a series of fits to find the best match
+bool MARMFitter::PerformFit(unsigned int FitID, vector<double>& ARMValues)
+{
+  // Clean the data
+  vector<double> CleanedData;
+  CleanedData.reserve(ARMValues.size());
+  for (auto A: ARMValues) {
+    if (A >= -m_MaxARMValue && A <= m_MaxARMValue) {
+      CleanedData.push_back(A);
+    }
+  }
+
+  // Set up for fitting
+  ROOT::Fit::DataOptions DataOptions;
+  DataOptions.fIntegral = true;
+
+  ROOT::Fit::DataRange Range(-m_MaxARMValue, m_MaxARMValue);
+
+  TF1* FitFunction = nullptr;
+  ROOT::Fit::Fitter Fitter; // need a new one every time
+  SetupARMFit(m_ARMFitFunction, Fitter, &FitFunction);
+
+  // Do the fitting
+  if (m_UnbinnedFitting == true) {
+    cout<<"Unbinned fit"<<endl;
+    ROOT::Fit::UnBinData UnbinnedData(CleanedData.size(), CleanedData.data(), Range);
+    Fitter.LikelihoodFit(UnbinnedData, true);
+  } else {
+    cout<<"Binned fit"<<endl;
+    DataOptions.fIntegral = true;
+    DataOptions.fUseRange =true;
+    ROOT::Fit::BinData BinnedData(DataOptions, Range);
+    // Easiest option to fill the binned data set is via a histogram:
+    TH1D* D = new TH1D("", "", m_NumberOfBins, -m_MaxARMValue, m_MaxARMValue);
+    for (auto& V: CleanedData) D->Fill(V);
+    for (int b = 1; b <= D->GetNbinsX(); ++b) D->SetBinError(b, sqrt(D->GetBinContent(b)));
+    ROOT::Fit::FillData(BinnedData, D);
+    delete D;
+    //Fitter.LikelihoodFit(BinnedData, true);
+    Fitter.LeastSquareFit(BinnedData);
+  }
+
+  // Retrieve results
+  TFitResult Result = Fitter.Result();
+
+  //cout<<"Best fit: "<<GetARMFitFunctionName(m_ARMFitFunction)<<" (Baker-Cousins likelihood ratio: "<<std::fixed<<Result.MinFcnValue()<<")"<<endl;
+
+  FitFunction->SetParameters(Result.GetParams());
+
+  // Calculate FWHM ...
+  double FWHM = MInterface::GetFWHM(FitFunction, -m_MaxARMValue, m_MaxARMValue);
+
+  {
+    std::unique_lock<std::mutex> Lock(m_Mutex);
+
+    m_BootStrappedFWHMSamples[FitID] = FWHM;
+
+    m_BootStrappedFitParameters[FitID] = vector<double>();
+    for (unsigned int i = 0; i < GetARMFitFunctionNumberOfParameters(m_ARMFitFunction); ++i) {
+      m_BootStrappedFitParameters[FitID].push_back(Result.Parameter(i));
+    }
+
+    m_BootStrappedBakerCousins[FitID] = Result.MinFcnValue();
+
+    Result.Print();
+  }
+
+  delete FitFunction;
+
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Perform a single fit with the chosen fit function
+bool MARMFitter::FitOnce()
+{
+  m_FitSuccessful = false;
+
+  // Pre-calculate limits on fits
+  m_MinHeight = 0;
+  m_MaxHeight = m_OriginalARMValues.size();
+
+  vector<double> MinHeightData;
+  MinHeightData.reserve(m_OriginalARMValues.size());
+  for (double V: m_OriginalARMValues) {
+    if (V > -15 && V < 15) {
+      MinHeightData.push_back(V); // The ARM width should be within that...
+    }
+  }
+  // If the above is not working look at the value and zoom in or out
+  double SumOfSquares = 0.0;
+  for (double V: MinHeightData) {
+    SumOfSquares += V*V;
+  }
+  m_MinWidth = 0.5*sqrt(SumOfSquares / MinHeightData.size());
+  m_MaxWidth = 180;
+
+  m_WidthGuess = sqrt(SumOfSquares / MinHeightData.size());
+  m_HeightGuess = 0.3*MinHeightData.size();
+  m_ScaleGuess = 2;
+
+
+  // Right size the result storage
+  m_BootStrappedFWHMSamples.clear();
+  m_BootStrappedFWHMSamples.resize(1);
+
+  m_BootStrappedFitParameters.clear();
+  m_BootStrappedFitParameters.resize(1);
+
+  m_BootStrappedBakerCousins.clear();
+  m_BootStrappedBakerCousins.resize(1);
+
+  // Fit
+  if (PerformFit(0, m_OriginalARMValues) == true) {
+    CalculateBootStrappedMetrics();
+    m_FitSuccessful = true;
+  }
+
+  return m_FitSuccessful;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Perform fits with all fit functions and report Baker-Cousin likelihood ratios
+bool MARMFitter::FitAll()
+{
+  unsigned int NFits = 500;
+
+  MARMFitFunctionID Best;
+  double BestBC = 0;
+
+  cout<<"Fitting through all functions (except Lorentz) with "<<NFits<<" samples."<<endl;
+
+  m_ARMFitFunction = MARMFitFunctionID::c_Gauss;
+  FitMultiple(NFits);
+  if (m_FinalBakerCousins < BestBC) { BestBC = m_FinalBakerCousins; Best = m_ARMFitFunction; }
+  cout<<GetARMFitFunctionName(m_ARMFitFunction)<<" - BC: "<<MString(m_FinalBakerCousins, m_FinalBakerCousinsUncertainty)<<endl;
+
+  //m_ARMFitFunction = MARMFitFunctionID::c_Lorentz;
+  //FitMultiple(NFits);
+  //if (m_FinalBakerCousins < BestBC) { BestBC = m_FinalBakerCousins; Best = m_ARMFitFunction; }
+  //cout<<GetARMFitFunctionName(m_ARMFitFunction)<<" - BC: "<<MString(m_FinalBakerCousins, m_FinalBakerCousinsUncertainty)<<endl;
+
+  m_ARMFitFunction = MARMFitFunctionID::c_GeneralizedNormal;
+  FitMultiple(NFits);
+  if (m_FinalBakerCousins < BestBC) { BestBC = m_FinalBakerCousins; Best = m_ARMFitFunction; }
+  cout<<GetARMFitFunctionName(m_ARMFitFunction)<<" - BC: "<<MString(m_FinalBakerCousins, m_FinalBakerCousinsUncertainty)<<endl;
+
+  m_ARMFitFunction = MARMFitFunctionID::c_GaussLorentz;
+  FitMultiple(NFits);
+  if (m_FinalBakerCousins < BestBC) { BestBC = m_FinalBakerCousins; Best = m_ARMFitFunction; }
+  cout<<GetARMFitFunctionName(m_ARMFitFunction)<<" - BC: "<<MString(m_FinalBakerCousins, m_FinalBakerCousinsUncertainty)<<endl;
+
+  m_ARMFitFunction = MARMFitFunctionID::c_GaussLorentzLorentz;
+  FitMultiple(NFits);
+  if (m_FinalBakerCousins < BestBC) { BestBC = m_FinalBakerCousins; Best = m_ARMFitFunction; }
+  cout<<GetARMFitFunctionName(m_ARMFitFunction)<<" - BC: "<<MString(m_FinalBakerCousins, m_FinalBakerCousinsUncertainty)<<endl;
+
+  m_ARMFitFunction = MARMFitFunctionID::c_AsymmetricGaussLorentzLorentz;
+  FitMultiple(NFits);
+  if (m_FinalBakerCousins < BestBC) { BestBC = m_FinalBakerCousins; Best = m_ARMFitFunction; }
+  cout<<GetARMFitFunctionName(m_ARMFitFunction)<<" - BC: "<<MString(m_FinalBakerCousins, m_FinalBakerCousinsUncertainty)<<endl;
+
+  m_ARMFitFunction = MARMFitFunctionID::c_AsymmetricGaussGaussLorentzLorentz;
+  FitMultiple(NFits);
+  if (m_FinalBakerCousins < BestBC) { BestBC = m_FinalBakerCousins; Best = m_ARMFitFunction; }
+  cout<<GetARMFitFunctionName(m_ARMFitFunction)<<" - BC: "<<MString(m_FinalBakerCousins, m_FinalBakerCousinsUncertainty)<<endl;
+
+  m_ARMFitFunction = MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormal;
+  FitMultiple(NFits);
+  if (m_FinalBakerCousins < BestBC) { BestBC = m_FinalBakerCousins; Best = m_ARMFitFunction; }
+  cout<<GetARMFitFunctionName(m_ARMFitFunction)<<" - BC: "<<MString(m_FinalBakerCousins, m_FinalBakerCousinsUncertainty)<<endl;
+
+  m_ARMFitFunction = MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormalGeneralizedNormal;
+  FitMultiple(NFits);
+  if (m_FinalBakerCousins < BestBC) { BestBC = m_FinalBakerCousins; Best = m_ARMFitFunction; }
+  cout<<GetARMFitFunctionName(m_ARMFitFunction)<<" - BC: "<<MString(m_FinalBakerCousins, m_FinalBakerCousinsUncertainty)<<endl;
+
+  // Do the best again:
+  m_ARMFitFunction = Best;
+  FitMultiple(2*NFits);
+  cout<<"Best: "<<GetARMFitFunctionName(m_ARMFitFunction)<<" - BC: "<<MString(m_FinalBakerCousins, m_FinalBakerCousinsUncertainty)<<endl;
+
+  return m_FitSuccessful;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Bootstrap the ARM values and return them as vector
+vector<double> MARMFitter::BootstrapARMValues()
+{
+  std::uniform_int_distribution<> Distributor(0, m_OriginalARMValues.size() - 1);
+
+  // Bootstrapping: sample with replacement
+  vector<double> ARMValues;
+  ARMValues.reserve(m_OriginalARMValues.size());
+  for (size_t i = 0; i < m_OriginalARMValues.size(); ++i) {
+    int D = Distributor(m_MersenneTwister);
+    ARMValues.push_back(m_OriginalARMValues[D]);
+  }
+
+  return ARMValues;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Calculate all ARM metrics from the bootstrapped results
+void MARMFitter::CalculateBootStrappedMetrics()
+{
+  m_FinalFWHM = g_DoubleNotDefined;
+  m_FinalFWHMUncertainty = g_DoubleNotDefined;
+  m_FinalFitParameters.clear();
+  m_FinalBakerCousins = g_DoubleNotDefined;
+  m_FinalBakerCousinsUncertainty = g_DoubleNotDefined;
+
+  if (m_BootStrappedFWHMSamples.size() > 0) {
+    // Calculate the average
+    double SumFWHM = std::accumulate(m_BootStrappedFWHMSamples.begin(), m_BootStrappedFWHMSamples.end(), 0.0);
+    m_FinalFWHM = SumFWHM / m_BootStrappedFWHMSamples.size();
+
+    // Calculate the standard deviation
+    double SquaredSumFWHM = std::accumulate(m_BootStrappedFWHMSamples.begin(), m_BootStrappedFWHMSamples.end(), 0.0,
+        [FWHM = m_FinalFWHM](double acc, double x) {
+            return acc + (x - FWHM) * (x - FWHM);
+        });
+    m_FinalFWHMUncertainty = std::sqrt(SquaredSumFWHM / m_BootStrappedFWHMSamples.size());
+
+    // Find the bin with the FWHM closest to the average to choose the best fit parameters
+    unsigned int ClosestBin = 0;
+    double ClosestValue = m_BootStrappedFWHMSamples[0];
+    double MinDifference = std::abs(m_BootStrappedFWHMSamples[0] - m_FinalFWHM);
+
+    for (unsigned int b = 1; b < m_BootStrappedFWHMSamples.size(); ++b) {
+      double Difference = std::abs(m_BootStrappedFWHMSamples[b] - m_FinalFWHM);
+      if (Difference < MinDifference) {
+        MinDifference = Difference;
+        ClosestValue = m_BootStrappedFWHMSamples[b];
+        ClosestBin = b;
+      }
+    }
+    m_FinalFitParameters = m_BootStrappedFitParameters[ClosestBin];
+
+    // The average Baker-Cousins value
+    double SumBakerCousins = std::accumulate(m_BootStrappedBakerCousins.begin(), m_BootStrappedBakerCousins.end(), 0.0);
+    m_FinalBakerCousins = SumBakerCousins / m_BootStrappedBakerCousins.size();
+
+    // Calculate its standard deviation
+    double SquaredSumBakerCousins = std::accumulate(m_BootStrappedBakerCousins.begin(), m_BootStrappedBakerCousins.end(), 0.0,
+        [BC = m_FinalBakerCousins](double acc, double x) {
+            return acc + (x - BC) * (x - BC);
+        });
+    m_FinalBakerCousinsUncertainty = std::sqrt(SquaredSumBakerCousins / m_BootStrappedBakerCousins.size());
+
+  } else {
+    merr<<"Cannot calculate ARM metrics, since we don't have any bootstrapped values."<<endl;
+  }
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Calculate all ARM metrics from the distribution itself
+void MARMFitter::CalculateARMMetrics()
+{
+  // Determine containment radii
+
+  /*
+  double Sigma0 = 0.5;
+  m_Containment50Percent = g_DoubleNotDefined;
+  double Sigma1 = 0.6826;
+  m_Containment1Sigma = g_DoubleNotDefined;
+  double Sigma2 = 0.9546;
+  m_Containment2Sigma = g_DoubleNotDefined;
+  double Sigma3 = 0.9973;
+  m_Containment3Sigma = g_DoubleNotDefined;
+
+  int CentralBin = Histogram->FindBin(0);
+  double All = Histogram->Integral(1, m_NumberOfBins);
+  double Content = 0.0;
+  for (int b = 0; b + CentralBin <= Histogram->GetNbinsX(); ++b) {
+    if (b == 0) {
+      Content += Histogram->GetBinContent(CentralBin);
+    } else {
+      Content += Histogram->GetBinContent(CentralBin + b) + Histogram->GetBinContent(CentralBin - b);
+    }
+    if (m_Containment50Percent == g_DoubleNotDefined && Content >= Sigma0*All) {
+      m_Containment50Percent = Histogram->GetBinCenter(CentralBin + b);
+    }
+    if (m_Containment1Sigma == g_DoubleNotDefined && Content >= Sigma1*All) {
+      m_Containment1Sigma = Histogram->GetBinCenter(CentralBin + b);
+    }
+    if (m_Containment2Sigma == g_DoubleNotDefined && Content >= Sigma2*All) {
+      m_Containment2Sigma = Histogram->GetBinCenter(CentralBin + b);
+    }
+    if (m_Containment3Sigma == g_DoubleNotDefined && Content >= Sigma3*All) {
+      m_Containment3Sigma = Histogram->GetBinCenter(CentralBin + b);
+    }
+  }
+  */
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+void MARMFitter::ParallelFitting(int FitID, std::condition_variable& CV)
+{
+  { // lock the mutex while we wait
+    std::unique_lock<std::mutex> Lock(m_Mutex);
+    CV.wait(Lock, [this]() { return m_NumberOfRunningThreads < m_MaximumNumberOfThreads; }); // the condition_variable releases the lock while waiting.
+    ++m_NumberOfRunningThreads;
+    //cout<<"Fit "<<FitID<<endl;
+  }
+
+  vector<double> ARMValues = BootstrapARMValues();
+  PerformFit(FitID, ARMValues);
+
+  { // lock the mutex while we wait
+    std::unique_lock<std::mutex> lock(m_Mutex);
+    --m_NumberOfRunningThreads;
+    CV.notify_all();
+  }
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Performs N fits.
+//! Each fit samples randomly from the stored ARM values to determine the average width and error correctly
+bool MARMFitter::FitMultiple(unsigned int NumberOfFits)
+{
+  if (NumberOfFits <= 0) return false;
+
+  m_FitSuccessful = true;
+
+  // Pre-calculate limits on fits
+  m_MinHeight = 0;
+  m_MaxHeight = m_OriginalARMValues.size();
+
+  vector<double> MinHeightData;
+  MinHeightData.reserve(m_OriginalARMValues.size());
+  for (double V: m_OriginalARMValues) {
+    if (V > -15 && V < 15) {
+      MinHeightData.push_back(V); // The ARM width should be within that...
+    }
+  }
+  // If the above is not working look at the value and zoom in or out
+  double SumOfSquares = 0.0;
+  for (double V: MinHeightData) {
+    SumOfSquares += V*V;
+  }
+  m_MinWidth = 0.5*sqrt(SumOfSquares / MinHeightData.size());
+  m_MaxWidth = m_MaxARMValue;
+
+
+  // Right size the result storage
+  m_BootStrappedFWHMSamples.clear();
+  m_BootStrappedFWHMSamples.resize(NumberOfFits);
+
+  m_BootStrappedFitParameters.clear();
+  m_BootStrappedFitParameters.resize(NumberOfFits);
+
+  m_BootStrappedBakerCousins.clear();
+  m_BootStrappedBakerCousins.resize(NumberOfFits);
+
+
+  // Start the threads
+  m_NumberOfRunningThreads = 0;
+  vector<thread> Threads;
+  condition_variable CV;
+
+  for (unsigned int i = 0; i < NumberOfFits; ++i) {
+    Threads.emplace_back([this, &CV, i]() { this->ParallelFitting(i, CV); } );
+  }
+
+  // Join all threads with the main thread
+  for (thread& T: Threads) {
+    T.join();
+  }
+
+  // Caluclate the results
+  CalculateBootStrappedMetrics();
+
+  return m_FitSuccessful;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Return the the FWHM result
+double MARMFitter::GetFWHM() const
+{
+  return m_FitSuccessful ? m_FinalFWHM : g_DoubleNotDefined;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Return the FWHM uncertainty result
+double MARMFitter::GetFWHMUncertainty() const
+{
+  return m_FitSuccessful ? m_FinalFWHMUncertainty : g_DoubleNotDefined;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Convert the results into a string
+MString MARMFitter::ToString()
+{
+  unsigned int SelectedEvents = 0;
+  for (auto A: m_OriginalARMValues) {
+    if (A >= -m_MaxARMValue && A <= m_MaxARMValue) {
+      SelectedEvents++;
+    }
+  }
+
+  ostringstream out;
+  out<<endl;
+  out<<"ARM fit results:"<<endl;
+  out<<"================"<<endl;
+  out<<endl;
+  if (m_FitSuccessful == false) {
+    out<<"Fit not yet performed or fit failed."<<endl;
+    return out;
+  }
+  out<<"Events:"<<endl;
+  out<<"  Total: "<<m_OriginalARMValues.size()<<endl;
+  out<<"  In selection (+- "<<m_MaxARMValue<<" deg): "<<SelectedEvents<<endl;
+  out<<endl;
+  out<<"Fit:"<<endl;
+  out<<"  Fit mode: "<<(m_UnbinnedFitting == true ? "Unbinned" : "Binned")<<" likelihood fit"<<endl;
+  out<<"  Fit function: "<<GetARMFitFunctionName(m_ARMFitFunction)<<endl;
+  out<<"  Average FWHM after "<<m_BootStrappedFWHMSamples.size()<<" boot straps: "<<MString(m_FinalFWHM, m_FinalFWHMUncertainty, "degree")<<endl;
+  out<<endl;
+
+  return out;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Draw the ARM histogram
+void MARMFitter::Draw()
+{
+  if (m_OptimizeBinning == true) {
+    OptimizeBinning();
+  }
+
+
+  TH1D* Histogram = new TH1D("ARMComptonCone", "Angular Resolution Measure", m_NumberOfBins, -m_MaxARMValue, m_MaxARMValue);
+  Histogram->SetBit(kCanDelete);
+  Histogram->SetDirectory(0);
+  Histogram->SetXTitle("ARM [#circ]");
+  Histogram->SetYTitle("counts");
+  Histogram->SetTitleOffset(1.3f, "Y");
+  Histogram->SetStats(false);
+  Histogram->SetLineColor(kBlack);
+  Histogram->SetMinimum(0);
+
+  for (double& ARMValue: m_OriginalARMValues) {
+    Histogram->Fill(ARMValue);
+  }
+  Histogram->Draw("HIST"); // This defines all scales
+
+  // Create a new fit since we need to scale the existing one,
+  // since there the scaler height is a function of the bins (and we did an unbinned fit)
+  unsigned int NumberOfParameters = GetARMFitFunctionNumberOfParameters(m_ARMFitFunction);
+  MString FitString = GetARMFitFunction(m_ARMFitFunction);
+  FitString.ReplaceAll("return", "return (");
+  MString Addendum = ") * p[";
+  Addendum += NumberOfParameters;
+  Addendum += "]; }";
+  FitString.ReplaceAll("; }", Addendum);
+
+  TF1* ScaledFit = new TF1("ScaledFit", FitString.Data(), -m_MaxARMValue, m_MaxARMValue, NumberOfParameters+1);
+  for (unsigned int f = 0; f < m_BootStrappedFitParameters.size(); ++f) {
+    //cout<<"Fit "<<f<<endl;
+    ScaledFit->SetName(MString("ScaledFit")+f);
+    for (unsigned int i = 0; i < NumberOfParameters; ++i) {
+      ScaledFit->FixParameter(i, m_BootStrappedFitParameters[f][i]);
+    }
+
+    Histogram->Fit(ScaledFit, "QR");
+    double Alpha = 1.0 / (0.1 * m_BootStrappedFitParameters.size());
+    if (Alpha > 1.0) Alpha = 1.0;
+    if (Alpha < 0.005) Alpha = 0.005;
+    ScaledFit->SetLineColorAlpha(kAzure-2, Alpha);
+    ScaledFit->SetLineWidth(4);
+    ScaledFit->DrawCopy("SAME");
+  }
+  delete ScaledFit;
+
+  Histogram->Draw("HIST SAME"); // Overdraws the fits
+
+  MString Text("FWHM of fit function: ");
+  Text += MString(m_FinalFWHM, m_FinalFWHMUncertainty, "#circ", true);
+
+  TLatex* Latex = new TLatex();
+  Latex->SetTextFont(gStyle->GetLabelFont());
+  Latex->SetTextSize(gStyle->GetLabelSize());
+  Latex->SetTextAlign(21);
+  Latex->DrawLatexNDC(0.5, 0.02, Text.Data());
+
+  // No delete Histogram - Histogramn deletion managed by ROOT
+
+  return;
+}
+
+
+// MARMFitter.cxx: the end...
+////////////////////////////////////////////////////////////////////////////////
diff --git a/src/mimrec/src/MGUIMimrecMain.cxx b/src/mimrec/src/MGUIMimrecMain.cxx
index 36621bc15..a6e1e4349 100644
--- a/src/mimrec/src/MGUIMimrecMain.cxx
+++ b/src/mimrec/src/MGUIMimrecMain.cxx
@@ -235,6 +235,7 @@ void MGUIMimrecMain::Create()
   MenuResponse->AddLabel("Compton specific");
   MenuResponse->AddSeparator();
   MenuResponse->AddEntry("ARM of scattered gamma ray", c_ResponseArmGamma);
+  MenuResponse->AddEntry("ARM of scattered gamma ray (classic binned mode)", c_ResponseArmGammaClassic);
   MenuResponse->AddEntry("SPD of recoil electron", c_ResponseSpdElectron);
   MenuResponse->AddPopup("All ARM/SPD options", MenuARM);
   MenuResponse->AddSeparator();
@@ -429,7 +430,14 @@ bool MGUIMimrecMain::ProcessMessage(long Message, long Parameter1,
           m_Interface->ARMGamma();
         }
         break;
-        
+
+      case c_ResponseArmGammaClassic:
+        new MGUIARM(gClient->GetRoot(), this, m_Data, MGUIARMModes::m_ARMGamma, OKPressed);
+        if (OKPressed == true) {
+          m_Interface->ARMGammaClassic();
+        }
+        break;
+
       case c_ResponsePhiKinVsPhiGeo:
         new MGUIARM(gClient->GetRoot(), this, m_Data, MGUIARMModes::m_ARMGamma, OKPressed);
         if (OKPressed == true) {
diff --git a/src/mimrec/src/MInterfaceMimrec.cxx b/src/mimrec/src/MInterfaceMimrec.cxx
index f13a7c4dc..4a871e3f1 100644
--- a/src/mimrec/src/MInterfaceMimrec.cxx
+++ b/src/mimrec/src/MInterfaceMimrec.cxx
@@ -74,6 +74,7 @@ using namespace std;
 #include "MResponsePRM.h"
 #include "MResponseEnergyLeakage.h"
 #include "MBinnerBayesianBlocks.h"
+#include "MARMFitter.h"
 
 
 ////////////////////////////////////////////////////////////////////////////////
@@ -1115,10 +1116,84 @@ void MInterfaceMimrec::ARMGamma()
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
+  MVector TestPosition = GetTestPosition();
+
+  MARMFitter Fitter;
+  Fitter.SetNumberOfBins(m_Settings->GetHistBinsARMGamma());
+  Fitter.SetMaxARM(m_Settings->GetTPDistanceTrans());
+  //Fitter.SetFitFunction(MARMFitFunctionID::c_GeneralizedNormal);
+  //Fitter.SetFitFunction(MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormal);
+  //Fitter.SetFitFunction(MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormalGeneralizedNormal);
+  Fitter.SetFitFunction(MARMFitFunctionID::c_AsymmetricGaussLorentzLorentz);
+  Fitter.UseUnbinnedFitting(false);
+  Fitter.UseOptimizedBinning();
+
+  bool FoundEvents = false;
+  MPhysicalEvent* Event = nullptr;
+  MComptonEvent* ComptonEvent = nullptr;
+  // ... loop over all events and save a count in the belonging bin ...
+  while ((Event = GetNextEvent()) != nullptr) {
+
+    // Only accept Comptons within the selected ranges...
+    if (m_Selector->IsQualifiedEventFast(Event) == true) {
+      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+        ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
+        Fitter.AddARMValue(ComptonEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem())*c_Deg);
+        FoundEvents = true;
+      }
+    }
+
+    delete Event;
+  } 
+  
+  // Close the event loader
+  FinalizeEventLoader();
+
+  if (FoundEvents == false) {
+    mgui<<"No events passed the event selections."<<error;
+  }
+
+  Fitter.FitOnce();
+  //Fitter.FitMultiple(100);
+  //Fitter.FitAll();
+
+  if (Fitter.WasFittingSuccessful() == true) {
+    // Draw the histogram
+    TCanvas* FitterCanvas = new TCanvas();
+    FitterCanvas->SetTitle("ARM of Compton cone");
+    FitterCanvas->cd();
+    Fitter.Draw();
+    FitterCanvas->Modified();
+    FitterCanvas->Update();
+    if (m_OutputFileName.IsEmpty() == false) {
+      FitterCanvas->SaveAs(m_OutputFileName);
+    }
+
+    // Dump the results
+    mout<<Fitter.ToString()<<endl;
+  }
+
+  return;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+void MInterfaceMimrec::ARMGammaClassic()
+{
+  // Display the angular resolution measurement for the gamma-ray
+  // The ARM value for the scattered gamma-ray is the minimum angle between
+  // the gamma-cone-surface and the line connecting the cone-apex with the
+  // (Test-)position
+
+  // Start with the event file loader first (just in case something goes wrong here)
+  if (InitializeEventLoader() == false) return;
+
 
   //double ConfidenceLevel = 0.9; // 90%
   MString ConfidenceLevelString = "90%";
-  
+
   int NEvents = 0;
   double Value = 0;
   int NAverages = 0;
@@ -1129,7 +1204,7 @@ void MInterfaceMimrec::ARMGamma()
   double Disk = m_Settings->GetTPDistanceTrans();
   MVector TestPosition = GetTestPosition();
   double BinWidth = 2.0*Disk/NBins;
-  
+
   // Initalize the image size (x-axis)
   TH1D* Hist = new TH1D("ARMComptonCone", "ARM (Compton cone)", NBins, -Disk, Disk);
   Hist->SetBit(kCanDelete);
@@ -1144,8 +1219,8 @@ void MInterfaceMimrec::ARMGamma()
   Hist->SetMinimum(0);
 
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* ComptonEvent = nullptr; 
-//   MPairEvent* PairEvent = 0; 
+  MComptonEvent* ComptonEvent = nullptr;
+//   MPairEvent* PairEvent = 0;
   // ... loop over all events and save a count in the belonging bin ...
   while ((Event = GetNextEvent()) != 0) {
 
@@ -1174,8 +1249,8 @@ void MInterfaceMimrec::ARMGamma()
     }
 
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -1228,7 +1303,6 @@ void MInterfaceMimrec::ARMGamma()
       mout<<"  "<<100*Sigma3<<"% containment (radius): "<<Hist->GetBinCenter(CentralBin + b)<<endl;
       Sigma3Found = true;
     }
-    
   }
 
 
@@ -1241,10 +1315,10 @@ void MInterfaceMimrec::ARMGamma()
 
   TF1* Fit = 0;
   ROOT::Math::MinimizerOptions::SetDefaultMaxFunctionCalls(20000);
-  Fit = new TF1("DoubleLorentzAsymGausArm", DoubleLorentzAsymGausArm, 
+  Fit = new TF1("DoubleLorentzAsymGausArm", DoubleLorentzAsymGausArm,
                 -Disk*0.99, Disk*0.99, 9);
   Fit->SetBit(kCanDelete);
-  Fit->SetParNames("Offset", "Mean", 
+  Fit->SetParNames("Offset", "Mean",
                    "Lorentz Width 1", "Lorentz Height 1",
                    "Lorentz Width 2", "Lorentz Height 2",
                    "Gaus Height", "Gaus Sigma 1", "Gaus Sigma 2");
@@ -1258,7 +1332,7 @@ void MInterfaceMimrec::ARMGamma()
   Fit->SetParLimits(6, 0, 2*Hist->GetMaximum());
   Fit->SetParLimits(7, 0.5*SigmaGuess, 180);
   Fit->SetParLimits(8, 0.5*SigmaGuess, 180);
-  
+
   Canvas->cd();
   TFitResultPtr FitResult;
   TH1D* Confidence = 0;
@@ -1275,7 +1349,7 @@ void MInterfaceMimrec::ARMGamma()
       if (TVirtualFitter::GetFitter() != nullptr) {
         (TVirtualFitter::GetFitter())->GetConfidenceIntervals(Confidence, ConfidenceLevel);
       } else {
-        merr<<"Virtual fitter is nullptr -- confidence intervals are wrong!"<<endl; 
+        merr<<"Virtual fitter is nullptr -- confidence intervals are wrong!"<<endl;
       }
       Hist->SetTitle(MString("ARM (Compton cone) with ") + ConfidenceLevelString + MString(" confidence intervals"));
     }
@@ -1289,7 +1363,7 @@ void MInterfaceMimrec::ARMGamma()
       Confidence->Draw("E5 SAME");
     }
     */
-    Fit->Draw("SAME");      
+    Fit->Draw("SAME");
   }
   Hist->Draw("HIST SAME");
   Canvas->Modified();
@@ -1297,16 +1371,16 @@ void MInterfaceMimrec::ARMGamma()
   if (m_OutputFileName.IsEmpty() == false) {
     Canvas->SaveAs(m_OutputFileName);
   }
-  
+
   // Calculate FWHM and its uncertainty using the confidence intervals
   double FWHM = GetFWHM(Fit, -180, 180);
   double MinFWHM = -1;
   double MaxFWHM = -1;
-  
+
   bool FWHMConfidenceGood = false;
   if (Confidence != 0) {
     FWHMConfidenceGood = true;
-    
+
     // Sub-step a1: Find maximum of upper error curve
     int MaxBin = 0;
     double MaxContent = 0;
@@ -1317,10 +1391,10 @@ void MInterfaceMimrec::ARMGamma()
       }
     }
     MaxContent = Fit->GetMaximum(); // Use the fit itstself since it is more accurate (and the Confidence is anyway derived from it)
-    
+
     // Sub-step a2: Find left half value
     int LeftBelow = 0;
-    for (int b = MaxBin; b >= 1; --b) { 
+    for (int b = MaxBin; b >= 1; --b) {
       if (Confidence->GetBinContent(b) + Confidence->GetBinError(b) < 0.5*MaxContent) {
         LeftBelow = b;
         break;
@@ -1342,10 +1416,10 @@ void MInterfaceMimrec::ARMGamma()
     double m = (y2-y1) / (x2-x1);
     double t = y2 - m*x2;
     double LeftFWHMBoarder = (0.5*MaxContent - t) / m;
-    
+
     // Sub-step a3: Find right half value
     int RightBelow = Confidence->GetNbinsX()+1;
-    for (int b = MaxBin; b <= Confidence->GetNbinsX(); ++b) { 
+    for (int b = MaxBin; b <= Confidence->GetNbinsX(); ++b) {
       if (Confidence->GetBinContent(b) + Confidence->GetBinError(b) < 0.5*MaxContent) {
         RightBelow = b;
         break;
@@ -1367,17 +1441,17 @@ void MInterfaceMimrec::ARMGamma()
     m = (y2-y1) / (x2-x1);
     t = y2 - m*x2;
     double RightFWHMBoarder = (0.5*MaxContent - t) / m;
-    
+
     MaxFWHM = RightFWHMBoarder - LeftFWHMBoarder;
     //cout<<"Boarders: "<<LeftFWHMBoarder<<":"<<RightFWHMBoarder<<endl;
-    
-    
+
+
     // Sub-step b1: Find maximum of lower error curve
     // --> no need to redo
-    
+
     // Sub-step b2: Find left half value
     LeftBelow = 0;
-    for (int b = MaxBin; b >= 1; --b) { 
+    for (int b = MaxBin; b >= 1; --b) {
       if (Confidence->GetBinContent(b) - Confidence->GetBinError(b) < 0.5*MaxContent) {
         LeftBelow = b;
         break;
@@ -1399,10 +1473,10 @@ void MInterfaceMimrec::ARMGamma()
     m = (y2-y1) / (x2-x1);
     t = y2 - m*x2;
     LeftFWHMBoarder = (0.5*MaxContent - t) / m;
-    
+
     // Sub-step b3: Find right half value
     RightBelow = Confidence->GetNbinsX()+1;
-    for (int b = MaxBin; b <= Confidence->GetNbinsX(); ++b) { 
+    for (int b = MaxBin; b <= Confidence->GetNbinsX(); ++b) {
       if (Confidence->GetBinContent(b) - Confidence->GetBinError(b) < 0.5*MaxContent) {
         RightBelow = b;
         break;
@@ -1424,14 +1498,14 @@ void MInterfaceMimrec::ARMGamma()
     m = (y2-y1) / (x2-x1);
     t = y2 - m*x2;
     RightFWHMBoarder = (0.5*MaxContent - t) / m;
-    
+
     MinFWHM = RightFWHMBoarder - LeftFWHMBoarder;
     //cout<<"Boarders: "<<LeftFWHMBoarder<<":"<<RightFWHMBoarder<<endl;
   }
-  
-  
+
+
   // Dump all the information
-  
+
   cout<<endl;
   cout<<endl;
   cout<<"Statistics of ARM histogram and fit"<<endl;
@@ -1445,11 +1519,11 @@ void MInterfaceMimrec::ARMGamma()
   if (Fit != 0) {
     cout<<"Total FWHM of fit (not of data!):        "<<FWHM<<" deg";
     if (FWHMConfidenceGood == true) {
-      cout<<" ("<<ConfidenceLevelString<<" confidence interval: "<<MinFWHM<<" deg ... "<<MaxFWHM<<" deg)"; 
+      cout<<" ("<<ConfidenceLevelString<<" confidence interval: "<<MinFWHM<<" deg ... "<<MaxFWHM<<" deg)";
     }
-    if (FitResult->Parameter(2) < 0.5*BinWidth || 
-        FitResult->Parameter(4) < 0.5*BinWidth || 
-        FitResult->Parameter(7) < 0.5*BinWidth || 
+    if (FitResult->Parameter(2) < 0.5*BinWidth ||
+        FitResult->Parameter(4) < 0.5*BinWidth ||
+        FitResult->Parameter(7) < 0.5*BinWidth ||
         FitResult->Parameter(8) < 0.5*BinWidth) {
       cout<<" --- WARNING: One of the widths is smaller than one bin --- fit result my be inaccurate!"<<endl;
     } else {
diff --git a/src/mimrec/unittests/UTARMFitter.cxx b/src/mimrec/unittests/UTARMFitter.cxx
new file mode 100644
index 000000000..356b55f6d
--- /dev/null
+++ b/src/mimrec/unittests/UTARMFitter.cxx
@@ -0,0 +1,349 @@
+/*
+ * UTARMFitter.cxx
+ *
+ *
+ * Copyright (C) by Andreas Zoglauer.
+ * All rights reserved.
+ *
+ *
+ * This code implementation is the intellectual property of
+ * Andreas Zoglauer.
+ *
+ * By copying, distributing or modifying the Program (or any work
+ * based on the Program) you indicate your acceptance of this statement,
+ * and all its terms.
+ *
+ */
+
+
+// Cosima:
+
+// MEGAlib:
+#include "MGlobal.h"
+#include "MFitFunctions.h"
+#include "MARMFitter.h"
+#include "MInterface.h"
+
+// Geant4:
+
+// ROOT:
+#include "TH1.h"
+#include "TF1.h"
+#include "TApplication.h"
+#include "TCanvas.h"
+#include "TRandom.h"
+
+// Standard lib:
+#include <sstream>
+#include <fstream>
+#include <future>
+#include <cmath>
+#include <chrono>
+#include <thread>
+using namespace std;
+
+
+//! Unit test class for the ARM fitter
+class UTARMFitter
+{
+  // public interface:
+public:
+  //! Default constructor
+  UTARMFitter();
+  //! Default destructor
+  virtual ~UTARMFitter() {};
+
+  //! Run all tests
+  bool Run();
+
+  //! Run a single tests
+  bool RunSingle();
+
+  // protected methods:
+protected:
+  //! Test single fitting
+  double TestSingleFit();
+  //! Test bootstrapping
+  double TestBootstrapping();
+
+
+
+  // protected members:
+protected:
+
+
+  // private members:
+private:
+  //! Single mode
+  bool m_SingleMode;
+};
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Default constructor
+UTARMFitter::UTARMFitter()
+{
+  //m_MassModelFileName = "$(MEGALIB)/src/cosima/unittests/GiganticSphere.geo.setup";
+  //m_NumberOfTriggers = 100000;
+  m_SingleMode = false;
+
+  //gROOT->SetBatch(true);
+  gRandom->SetSeed(0);
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Run a single tests
+bool UTARMFitter::RunSingle()
+{
+  m_SingleMode = true;
+  
+  cout<<"Test single fit: "<<TestSingleFit()<<endl;
+  //cout<<"Test single fit: "<<TestSingleFit()<<endl;
+
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Run all tests
+bool UTARMFitter::Run()
+{
+  //cout<<"Test single fit: "<<TestSingleFit()<<endl;
+  cout<<"Test bootstrapping: "<<TestBootstrapping()<<endl;
+
+
+
+  /*
+  future<double> TestPowerLawResult = async(launch::async, &UTARMFitter::TestPowerLaw, this);
+  std::this_thread::sleep_for(std::chrono::milliseconds(5));
+  future<double> TestCutOffPowerLawResult = async(launch::async, &UTARMFitter::TestCutOffPowerLaw, this);
+  std::this_thread::sleep_for(std::chrono::milliseconds(5));
+  future<double> TestComptonization = async(launch::async, &UTARMFitter::TestComptonization, this);
+  std::this_thread::sleep_for(std::chrono::milliseconds(5));
+
+  bool AllPassed = true;
+
+  double TestPowerLawSigma = TestPowerLawResult.get();
+  double TestCutOffPowerLawSigma = TestCutOffPowerLawResult.get();
+  double TestComptonizationSigma = TestComptonization.get();
+
+  if (TestPowerLawSigma < 0) {
+    cout<<"Failed: Power law test did not finish"<<endl;
+    AllPassed = false;
+  } else if (TestPowerLawSigma >= 3 || std::isnan(TestPowerLawSigma) == true) {
+    cout<<"Failed: Power law significance: "<<TestPowerLawSigma<<" sigma"<<endl;
+    AllPassed = false;
+  } else {
+    cout<<"Passed: Power law significance: "<<TestPowerLawSigma<<" sigma"<<endl;
+  }
+
+  if (TestCutOffPowerLawSigma < 0) {
+    cout<<"Failed: Cutoff power law test did not finish"<<endl;
+    AllPassed = false;
+  } else if (TestCutOffPowerLawSigma >= 3 || std::isnan(TestCutOffPowerLawSigma) == true) {
+    cout<<"Failed: Cutoff power law significance: "<<TestCutOffPowerLawSigma<<" sigma"<<endl;
+    AllPassed = false;
+  } else {
+    cout<<"Passed: Cutoff power law significance: "<<TestCutOffPowerLawSigma<<" sigma"<<endl;
+  }
+
+  if (TestComptonizationSigma < 0) {
+    cout<<"Failed: Comptonization test did not finish"<<endl;
+    AllPassed = false;
+  } else if (TestComptonizationSigma >= 3 || std::isnan(TestComptonizationSigma) == true) {
+    cout<<"Failed: Comptonization significance: "<<TestComptonizationSigma<<" sigma"<<endl;
+    AllPassed = false;
+  } else {
+    cout<<"Passed: Comptonization significance: "<<TestComptonizationSigma<<" sigma"<<endl;
+  }
+
+  if (AllPassed == true) {
+    cout<<"Passed: All passed"<<endl;
+  }
+  */
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Test a single fit
+double UTARMFitter::TestSingleFit()
+{
+  cout<<"Started test single fit"<<endl;
+
+  // Basics
+  constexpr unsigned int Counts = 200;
+  constexpr unsigned int NumberOfBins = 201;
+  constexpr double MaxARM = 20;
+
+  vector<double> ARMValues;
+  ARMValues.reserve(Counts);
+
+  // Create the ARM data
+  TF1* Sampler = new TF1("DoubleLorentzAsymGausArm", DoubleLorentzAsymGausArm, -MaxARM, MaxARM, 9);
+  Sampler->SetBit(kCanDelete);
+  Sampler->SetParNames("Offset",
+                       "Mean",
+                       "Lorentz Width 1",
+                       "Lorentz Height 1",
+                       "Lorentz Width 2",
+                       "Lorentz Height 2",
+                       "Gaus Height",
+                       "Gaus Sigma 1",
+                       "Gaus Sigma 2");
+  //Sampler->SetParameters(100, -1.0, 1.0, 200, 3.0, 300, 500, 1.5, 4.5);
+  Sampler->SetParameters(0, 0.0, 1.0, 0, 3.0, 0, 500, 2.5, 2.5);
+
+  for (unsigned int i = 0; i < Counts; ++i) {
+    ARMValues.push_back(Sampler->GetRandom(-MaxARM, MaxARM));
+  }
+
+  delete Sampler;
+
+  // Set up the fitter and fit
+  MARMFitter Fitter;
+  Fitter.SetNumberOfBins(NumberOfBins);
+  Fitter.SetMaxARM(MaxARM);
+
+  for (unsigned int i = 0; i < Counts; ++i) {
+    Fitter.AddARMValue(ARMValues[i]);
+  }
+
+  Fitter.FitOnce();
+
+  if (Fitter.WasFittingSuccessful() == true) {
+    cout<<"FWHM: "<<Fitter.GetFWHM()<<endl;
+  }
+
+  TCanvas* FitterCanvas = new TCanvas();
+  FitterCanvas->SetTitle("ARM of Compton cone");
+  FitterCanvas->cd();
+  Fitter.Draw();
+  FitterCanvas->Modified();
+  FitterCanvas->Update();
+
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Test a single fit
+double UTARMFitter::TestBootstrapping()
+{
+  cout<<"Started test bootstrapping"<<endl;
+
+  // Basics
+  constexpr unsigned int Counts = 1000;
+  constexpr unsigned int NumberOfBins = 201;
+  constexpr double MaxARM = 20;
+
+  vector<double> ARMValues;
+  ARMValues.reserve(Counts);
+
+  // Create the ARM data
+  TF1* Sampler = new TF1("DoubleLorentzAsymGausArm", DoubleLorentzAsymGausArm, -MaxARM, MaxARM, 9);
+  Sampler->SetBit(kCanDelete);
+  Sampler->SetParNames("Offset",
+                       "Mean",
+                       "Lorentz Width 1",
+                       "Lorentz Height 1",
+                       "Lorentz Width 2",
+                       "Lorentz Height 2",
+                       "Gaus Height",
+                       "Gaus Sigma 1",
+                       "Gaus Sigma 2");
+  Sampler->SetParameters(0, 1.0, 2.0, 150, 3.0, 800, 500, 2.5, 5.5);
+
+  for (unsigned int i = 0; i < Counts; ++i) {
+    ARMValues.push_back(Sampler->GetRandom(-MaxARM, MaxARM));
+  }
+
+  double OriginalFWHM = MInterface::GetFWHM(Sampler, -MaxARM, MaxARM);
+  cout<<"Original FWHM: "<<OriginalFWHM<<endl;
+
+  delete Sampler;
+
+  // Set up the fitter and fit
+  MARMFitter Fitter;
+  Fitter.SetNumberOfBins(NumberOfBins);
+  Fitter.SetMaxARM(MaxARM);
+  Fitter.SetFitFunction(MARMFitFunctionID::c_AsymmetricGaussLorentzLorentz);
+  Fitter.UseOptimizedBinning();
+
+  for (unsigned int i = 0; i < Counts; ++i) {
+    Fitter.AddARMValue(ARMValues[i]);
+  }
+
+  Fitter.FitMultiple(200);
+
+  if (Fitter.WasFittingSuccessful() == true) {
+    cout<<"Average FWHM: "<<Fitter.GetFWHM()<<endl;
+    cout<<"FWHM Uncertainty: "<<Fitter.GetFWHMUncertainty()<<endl;
+    cout<<"Sigma difference: "<<fabs(OriginalFWHM - Fitter.GetFWHM())/Fitter.GetFWHMUncertainty()<<endl;
+
+    vector<double> FWHMes = Fitter.GetBootstrappedFWHMSamples();
+    if (FWHMes.size() > 0) {
+
+      // Use std::min_element to find the minimum value
+      auto MinValueIter = std::min_element(FWHMes.begin(), FWHMes.end());
+      double MinValue = *MinValueIter;
+      auto MaxValueIter = std::max_element(FWHMes.begin(), FWHMes.end());
+      double MaxValue = *MaxValueIter;
+
+      TH1D* H = new TH1D("H", "H", 100, MinValue, MaxValue + 0.5);
+      for (auto F: FWHMes) {
+        H->Fill(F);
+      }
+
+      TCanvas* C = new TCanvas();
+      C->cd();
+      H->Draw();
+      C->Update();
+    }
+
+    TCanvas* FitterCanvas = new TCanvas();
+    FitterCanvas->SetTitle("ARM of Compton cone");
+    FitterCanvas->cd();
+    Fitter.Draw();
+    FitterCanvas->Modified();
+    FitterCanvas->Update();
+  }
+
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Main program
+int main(int argc, char** argv)
+{
+  // Initialize ROOT:
+  TApplication ROOT("ROOT", 0, 0);
+
+  // Initialize global MEGAlib variables, especially mgui, etc.
+  MGlobal::Initialize("ARMFitter", "unit test the ARM fitting class");
+
+  UTARMFitter Test;
+  //Test.Run();
+  
+  Test.Run();
+  ROOT.Run();
+
+  return 0;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////

From 2fb1d4f00faa3b2d3e2ace94076fce705b233557 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Fri, 30 Aug 2024 13:07:24 -0700
Subject: [PATCH 059/192] CHG: More improvments for the new ARM fitter

---
 src/mimrec/inc/MARMFitter.h          |  65 +++--
 src/mimrec/src/MARMFitter.cxx        | 347 ++++++++++++++++-----------
 src/mimrec/src/MInterfaceMimrec.cxx  |   9 +-
 src/mimrec/unittests/UTARMFitter.cxx |  16 +-
 4 files changed, 269 insertions(+), 168 deletions(-)

diff --git a/src/mimrec/inc/MARMFitter.h b/src/mimrec/inc/MARMFitter.h
index 5d1915bbe..044380f57 100644
--- a/src/mimrec/inc/MARMFitter.h
+++ b/src/mimrec/inc/MARMFitter.h
@@ -68,14 +68,14 @@ class MARMFitter
   // Interface to set up the fitter
 
   //! Set the number of bins for the ARM fit hisogram
-  //! The deafult is 101
+  //! The default is 101
   void SetNumberOfBins(unsigned int NumberOfBins = 101);
 
   //! Set the maximum range of the ARM values
   //! The maximum value is 180
   //! The histogram will go from [-MaxARM, MaxARM]
-  //! The defaulkt is 180
-  void SetMaxARM(double MaxARM = 180);
+  //! The default is 180
+  void SetMaximumARMValue(double MaxARM = 180);
 
   //! Set the test position, and its coordinate system
   //! Do not call this function while adding events
@@ -86,7 +86,7 @@ class MARMFitter
   void UseOptimizedBinning(bool DoIt = true) { m_OptimizeBinning = DoIt; }
 
   //! If this is set we use an unbinned-likelihood fit
-  void UseUnbinnedFitting(bool DoIt = true) { m_UnbinnedFitting = DoIt; }
+  void UseBinnedFitting(bool DoIt = true) { m_UnbinnedFitting = !DoIt; }
 
   //! Fit this function to the data
   //! One of: c_Gauss, c_Lorentz, c_GaussLorentz, c_GaussDoubleLorentz, c_AsymmetricGaussDoubleLorentz
@@ -103,18 +103,19 @@ class MARMFitter
   //! Add an ARM value
   void AddARMValue(double ARMValue) { m_OriginalARMValues.push_back(ARMValue); }
 
-  // Interface to do the fits
-
-  //! Perform a single fit with the chosen fit function
-  bool FitOnce();
+  //! Load the ARM value from file
+  bool LoadARMValues(MString FileName);
+  //! Save the the ARM values to file
+  bool SaveARMValues(MString FileName);
 
-  //! Perform fits with all fit functions and report Baker-Cousin results
-  bool FitAll();
+  // Interface to do the fits
 
   //! Performs N fits.
   //! Each fit samples randomly form the stored ARM values to determine the average width and error correctly
-  bool FitMultiple(unsigned int NumberOfFits = 100);
+  bool Fit(unsigned int NumberOfFits = 1);
 
+  //! Perform fits with all fit functions and report Baker-Cousin results
+  bool FitAll();
 
   // Interface to retrieve the results
 
@@ -124,16 +125,29 @@ class MARMFitter
   //! Return the bootstrapped FWHM'es
   vector<double> GetBootstrappedFWHMSamples() { return m_BootStrappedFWHMSamples; }
 
-  //! Return the FWHM result
-  double GetFWHM() const;
+  //! Return the FWHM result or g_DoubleNotDefined if fit was not successful or not done yet
+  double GetAverageFWHM() const;
 
-  //! Return the FWHM uncertainty result
-  double GetFWHMUncertainty() const;
+  //! Return the FWHM uncertainty result or g_DoubleNotDefined if fit was not successful or not done yet
+  double GetAverageFWHMUncertainty() const;
+
+  //! Return the 50.0% containment for events with +- maximum ARM value or g_DoubleNotDefined if fit was not successful or not done yet
+  double Get50p0PercentContainment() const;
+  //! Return the 68.3% containment for events with +- maximum ARM value or g_DoubleNotDefined if fit was not successful or not done yet
+  double Get68p3PercentContainment() const;
+  //! Return the 95.5% containment for events with +- maximum ARM value or g_DoubleNotDefined if fit was not successful or not done yet
+  double Get95p5PercentContainment() const;
+  //! Return the 99.7% containment for events with +- maximum ARM value or g_DoubleNotDefined if fit was not successful or not done yet
+  double Get99p7PercentContainment() const;
 
   //! Return a summary string
   MString ToString();
 
   //! Draw an ARM histogram
+  //! This works like a root histogram, you would do:
+  //! Canvas->cd();
+  //! ARMFitter->Draw();
+  //! Canvas->Update();
   void Draw();
 
 
@@ -228,6 +242,9 @@ class MARMFitter
   //! The global mutex
   std::mutex m_Mutex;
 
+  //! True if the binning has already been optimized
+  bool m_IsBinningOptimized;
+
   //! Check is we have a final results
   bool m_FitSuccessful;
 
@@ -246,13 +263,13 @@ class MARMFitter
   //! The final fit parameters
   vector<double> m_FinalFitParameters;
 
-  //! The 50% containment radius (accurate to the next largest bin in the histogram)
+  //! The 50% containment radius within the ARM window (accurate to the next largest value in the data set)
   double m_Containment50Percent;
-  //! The 1-sigmna containment radius (accurate to the next largest bin in the histogra)
+  //! The 1-sigmna containment radius within the ARM window (accurate to the next largest value in the data set)
   double m_Containment1Sigma;
-  //! The 2-sigma containment radius (accurate to the next largest bin in the histogra)
+  //! The 2-sigma containment radius within the ARM window (accurate to the next largest value in the data set)
   double m_Containment2Sigma;
-  //! The 3-sigma containment radius (accurate to the next largest bin in the histogra)
+  //! The 3-sigma containment radius within the ARM window (accurate to the next largest value in the data set)
   double m_Containment3Sigma;
 
   //! Minimum height for fitting
@@ -269,11 +286,15 @@ class MARMFitter
   double m_MaxScale;
 
   //! Guess for the widths for fitting
-  double m_WidthGuess;
+  double m_GuessWidth;
   //! Guess for the height for fitting
-  double m_HeightGuess;
+  double m_GuessHeight;
   //! Guess for the scale for fitting
-  double m_ScaleGuess;
+  double m_GuessScale;
+  //! Guess for the low-x maximum for fitting
+  double m_GuessMaximumLow;
+  //! Guess for the high-x maximum for fitting
+  double m_GuessMaximumHigh;
 
 
 #ifdef ___CLING___
diff --git a/src/mimrec/src/MARMFitter.cxx b/src/mimrec/src/MARMFitter.cxx
index 035f2962f..e7ab50235 100644
--- a/src/mimrec/src/MARMFitter.cxx
+++ b/src/mimrec/src/MARMFitter.cxx
@@ -31,6 +31,7 @@
 #include <condition_variable>
 #include <atomic>
 #include <functional>
+#include <fstream>
 
 // ROOT libs:
 #include "TH1.h"
@@ -78,6 +79,8 @@ MARMFitter::MARMFitter()
   m_ARMFitFunction = MARMFitFunctionID::c_AsymmetricGaussLorentzLorentz;
 
   m_OptimizeBinning = false;
+  m_IsBinningOptimized = false;
+
   m_UnbinnedFitting = true;
 
   m_MinHeight = 0;
@@ -87,9 +90,9 @@ MARMFitter::MARMFitter()
   m_MinScale = 0.1;
   m_MaxScale = 1000;
 
-  m_WidthGuess = 2;
-  m_HeightGuess = 2;
-  m_ScaleGuess = 2;
+  m_GuessWidth = 2;
+  m_GuessHeight = 2;
+  m_GuessScale = 2;
 
   m_MaximumNumberOfThreads = 2*std::thread::hardware_concurrency();
   if (m_MaximumNumberOfThreads < 1) m_MaximumNumberOfThreads = 1;
@@ -118,6 +121,7 @@ void MARMFitter::SetNumberOfBins(unsigned int NumberOfBins)
     merr<<"You need at least 10 bins to be able to fit an ARM, and not "<<NumberOfBins<<". Setting it to 10."<<endl;
     m_NumberOfBins = 10;
   }
+  m_IsBinningOptimized = false;
 }
 
 
@@ -126,7 +130,7 @@ void MARMFitter::SetNumberOfBins(unsigned int NumberOfBins)
 
 
 //!
-void MARMFitter::SetMaxARM(double MaxARMValue)
+void MARMFitter::SetMaximumARMValue(double MaxARMValue)
 {
   m_MaxARMValue = MaxARMValue;
   if (m_MaxARMValue <= 0 || m_MaxARMValue > 180) {
@@ -164,6 +168,11 @@ void MARMFitter::Reset()
   m_FinalFitParameters.clear();
   m_FinalBakerCousins = g_DoubleNotDefined;
   m_FinalBakerCousinsUncertainty = g_DoubleNotDefined;
+
+  m_Containment50Percent = g_DoubleNotDefined;
+  m_Containment1Sigma = g_DoubleNotDefined;
+  m_Containment2Sigma = g_DoubleNotDefined;
+  m_Containment3Sigma = g_DoubleNotDefined;
 }
 
 
@@ -183,6 +192,8 @@ void MARMFitter::AddEvent(MComptonEvent* ComptonEvent)
 //! Optimize binning - check sif the binning is OK, otherwise check for a better one
 bool MARMFitter::OptimizeBinning()
 {
+  if (m_IsBinningOptimized == true) return true;
+
   const unsigned int MinimumBinContent = 50;
   const unsigned int MinimumBins = 5;
 
@@ -244,6 +255,7 @@ bool MARMFitter::OptimizeBinning()
   }
 
   m_NumberOfBins = NumberOfBins;
+  m_IsBinningOptimized = true;
 
   return true;
 }
@@ -289,17 +301,18 @@ MString MARMFitter::GetARMFitFunction(MARMFitFunctionID ID)
   if (ID == MARMFitFunctionID::c_Gauss) {
     return MString("[&](double *x, double *p){ return p[0] + p[2]*exp(-0.5*pow((x[0]-p[1])/p[3], 2)); }");
   } else if (ID == MARMFitFunctionID::c_Lorentz) {
-    return MString("[&](double *x, double *p){ return p[0] + p[2]/(p[3]*p[3] + (x[0]-p[1])*(x[0]-p[1])); }");
+    return MString("[&](double *x, double *p){ return p[0] + p[2]*(p[3]*p[3])/(p[3]*p[3] + (x[0]-p[1])*(x[0]-p[1])); }");
   } else if (ID == MARMFitFunctionID::c_GeneralizedNormal) {
     return MString("[&](double *x, double *p){ return p[0] + p[2]*exp(-0.5*pow(fabs(x[0]-p[1])/p[3], p[4])); }");
   } else if (ID == MARMFitFunctionID::c_GaussLorentz) {
     return MString("[&](double *x, double *p){ return p[0] + p[2]*exp(-0.5*pow((x[0]-p[1])/p[3], 2)) + p[4]/(p[5]*p[5] + (x[0]-p[1])*(x[0]-p[1])); }");
   } else if (ID == MARMFitFunctionID::c_GaussLorentzLorentz) {
-    return MString("[&](double *x, double *p){ return p[0] + p[2]*exp(-0.5*pow((x[0]-p[1])/p[3], 2)) + p[4]/(p[5]*p[5] + (x[0]-p[1])*(x[0]-p[1])) + p[6]/(p[7]*p[7] + (x[0]-p[1])*(x[0]-p[1])); }");
+    return MString("[&](double *x, double *p){ return p[0] + p[2]*exp(-0.5*pow((x[0]-p[1])/p[3], 2)) + p[4]*(p[5]*p[5])/(p[5]*p[5] + (x[0]-p[1])*(x[0]-p[1])) + p[6]*(p[7]*p[7])/(p[7]*p[7] + (x[0]-p[1])*(x[0]-p[1])); }");
   } else if (ID == MARMFitFunctionID::c_AsymmetricGaussLorentzLorentz) {
-    return MString("[&](double *x, double *p){ return p[0] + (x[0] - p[1] >= 0 ? p[2]*exp(-0.5*pow((x[0]-p[1])/p[3], 2)) : p[2]*exp(-0.5*pow((x[0]-p[1])/p[4], 2)) ) + p[5]/(p[6]*p[6] + (x[0]-p[1])*(x[0]-p[1])) + p[7]/(p[8]*p[8] + (x[0]-p[1])*(x[0]-p[1])); }");
+    return MString("[&](double *x, double *p){ return p[0] + (x[0] - p[1] >= 0 ? p[2]*exp(-0.5*pow((x[0]-p[1])/p[3], 2)) : p[2]*exp(-0.5*pow((x[0]-p[1])/p[4], 2)) ) + p[5]*(p[6]*p[6])/(p[6]*p[6] + (x[0]-p[1])*(x[0]-p[1])) + p[7]*(p[8]*p[8])/(p[8]*p[8] + (x[0]-p[1])*(x[0]-p[1])); }");
   } else if (ID == MARMFitFunctionID::c_AsymmetricGaussGaussLorentzLorentz) {
-    return MString("[&](double *x, double *p){ return p[0] + (x[0] - p[1] >= 0 ? p[2]*exp(-0.5*pow((x[0]-p[1])/p[3], 2)) : p[2]*exp(-0.5*pow((x[0]-p[1])/p[4], 2)) )  +  p[5]*exp(-0.5*pow((x[0]-p[1])/p[6], 2))  +  p[7]/(p[8]*p[8] + (x[0]-p[1])*(x[0]-p[1]))  +  p[9]/(p[10]*p[10] + (x[0]-p[1])*(x[0]-p[1])); }");
+    //return MString("[&](double *x, double *p){ return p[0] + (x[0] - p[1] >= 0 ? p[2]*exp(-0.5*pow((x[0]-p[1])/p[3], 2)) : p[2]*exp(-0.5*pow((x[0]-p[1])/p[4], 2)) )  +  p[5]*exp(-0.5*pow((x[0]-p[1])/p[6], 2))  +  p[7]*(p[8]*p[8])/(p[8]*p[8] + (x[0]-p[1])*(x[0]-p[1]))  +  p[9]*(p[10]*p[10])/(p[10]*p[10] + (x[0]-p[1])*(x[0]-p[1])); }");
+    return MString("[&](double *x, double *p){ return p[0] + (x[0] - p[1] >= 0 ? p[2]*exp(-0.5*pow((x[0]-p[1])/p[3], 2)) : p[2]*exp(-0.5*pow((x[0]-p[1])/p[4], 2)) )  +  p[5]*exp(-0.5*pow((x[0]-p[1])/p[6], 2))  +  p[7]*p[8]/(p[8]*p[8] + (x[0]-p[1])*(x[0]-p[1]))  +  p[9]*p[10]/(p[10]*p[10] + (x[0]-p[1])*(x[0]-p[1])); }");
   } else if (ID == MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormal) {
     return MString("[&](double *x, double *p){ return p[0] + (x[0] - p[1] >= 0 ? p[2]*exp(-0.5*pow(fabs(x[0]-p[1])/p[3], p[4])) : p[2]*exp(-0.5*pow(fabs(x[0]-p[1])/p[5], p[6])) )  +  p[7]*exp(-0.5*pow(fabs(x[0]-p[1])/p[8], p[9])) ; }");
   } else if (ID == MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormalGeneralizedNormal) {
@@ -385,13 +398,13 @@ void MARMFitter::SetupARMFitGauss(ROOT::Fit::Fitter& Fitter, TF1** FitFunction)
   if (g_Verbosity >= c_Info) Fitter.Config().MinimizerOptions().SetPrintLevel(1);
   Fitter.SetFunction(WrappedFitFunction, false);
 
-  vector<double> Parameters = { 1, 1, 1, 1};
+  vector<double> Parameters = { 1, 0.5*(m_GuessMaximumLow+m_GuessMaximumHigh), m_GuessHeight, m_GuessWidth };
   Fitter.Config().SetParamsSettings(Parameters.size(), Parameters.data());
 
   Fitter.Config().ParSettings(0).SetName("Offset");
   Fitter.Config().ParSettings(0).SetLimits(m_MinHeight, m_MaxHeight);
   Fitter.Config().ParSettings(1).SetName("Shift");
-  Fitter.Config().ParSettings(1).SetLimits(-m_MaxARMValue, m_MaxARMValue);
+  Fitter.Config().ParSettings(1).SetLimits(m_GuessMaximumLow, m_GuessMaximumHigh);
 
   Fitter.Config().ParSettings(2).SetName("Gauss - height");
   Fitter.Config().ParSettings(2).SetLimits(m_MinHeight, m_MaxHeight);
@@ -416,13 +429,13 @@ void MARMFitter::SetupARMFitLorentz(ROOT::Fit::Fitter& Fitter, TF1** FitFunction
   if (g_Verbosity >= c_Info) Fitter.Config().MinimizerOptions().SetPrintLevel(1);
   Fitter.SetFunction(WrappedFitFunction, false);
 
-  vector<double> Parameters = { 1, 1, 1, 1 };
+  vector<double> Parameters = { 1, 0.5*(m_GuessMaximumLow+m_GuessMaximumHigh), m_GuessHeight, m_GuessWidth };
   Fitter.Config().SetParamsSettings(Parameters.size(), Parameters.data());
 
   Fitter.Config().ParSettings(0).SetName("Offset");
   Fitter.Config().ParSettings(0).SetLimits(m_MinHeight, m_MaxHeight);
   Fitter.Config().ParSettings(1).SetName("Shift");
-  Fitter.Config().ParSettings(1).SetLimits(-m_MaxARMValue, m_MaxARMValue);
+  Fitter.Config().ParSettings(1).SetLimits(m_GuessMaximumLow, m_GuessMaximumHigh);
 
   Fitter.Config().ParSettings(2).SetName("Lorentz - height");
   Fitter.Config().ParSettings(2).SetLimits(m_MinHeight, m_MaxHeight);
@@ -446,13 +459,13 @@ void MARMFitter::SetupARMFitGeneralizedNormal(ROOT::Fit::Fitter& Fitter, TF1** F
   if (g_Verbosity >= c_Info) Fitter.Config().MinimizerOptions().SetPrintLevel(10);
   Fitter.SetFunction(WrappedFitFunction, false);
 
-  vector<double> Parameters = { 1, 1, 1, 1, 1.5};
+  vector<double> Parameters = { 1, 0.5*(m_GuessMaximumLow+m_GuessMaximumHigh), m_GuessHeight, m_GuessWidth, m_GuessScale };
   Fitter.Config().SetParamsSettings(Parameters.size(), Parameters.data());
 
   Fitter.Config().ParSettings(0).SetName("Offset");
   Fitter.Config().ParSettings(0).SetLimits(m_MinHeight, m_MaxHeight);
   Fitter.Config().ParSettings(1).SetName("Shift");
-  Fitter.Config().ParSettings(1).SetLimits(-m_MaxARMValue, m_MaxARMValue);
+  Fitter.Config().ParSettings(1).SetLimits(m_GuessMaximumLow, m_GuessMaximumHigh);
 
   Fitter.Config().ParSettings(2).SetName("Generalized normal - height");
   Fitter.Config().ParSettings(2).SetLimits(m_MinHeight, m_MaxHeight);
@@ -477,13 +490,13 @@ void MARMFitter::SetupARMFitGaussLorentz(ROOT::Fit::Fitter& Fitter, TF1** FitFun
   if (g_Verbosity >= c_Info) Fitter.Config().MinimizerOptions().SetPrintLevel(1);
   Fitter.SetFunction(WrappedFitFunction, false);
 
-  vector<double> Parameters = { 1, 1, 1, 1, 1, 1};
+  vector<double> Parameters = { 1, 0.5*(m_GuessMaximumLow+m_GuessMaximumHigh), m_GuessHeight, m_GuessWidth, m_GuessHeight, m_GuessWidth };
   Fitter.Config().SetParamsSettings(Parameters.size(), Parameters.data());
 
   Fitter.Config().ParSettings(0).SetName("Offset");
   Fitter.Config().ParSettings(0).SetLimits(m_MinHeight, m_MaxHeight);
   Fitter.Config().ParSettings(1).SetName("Shift");
-  Fitter.Config().ParSettings(1).SetLimits(-m_MaxARMValue, m_MaxARMValue);
+  Fitter.Config().ParSettings(1).SetLimits(m_GuessMaximumLow, m_GuessMaximumHigh);
 
   Fitter.Config().ParSettings(2).SetName("Gauss - height");
   Fitter.Config().ParSettings(2).SetLimits(m_MinHeight, m_MaxHeight);
@@ -512,13 +525,13 @@ void MARMFitter::SetupARMFitGaussLorentzLorentz(ROOT::Fit::Fitter& Fitter, TF1**
   if (g_Verbosity >= c_Info) Fitter.Config().MinimizerOptions().SetPrintLevel(1);
   Fitter.SetFunction(WrappedFitFunction, false);
 
-  vector<double> Parameters = { 1, 1, 1, 1, 1, 1, 1, 1};
+  vector<double> Parameters = { 1 , 0.5*(m_GuessMaximumLow+m_GuessMaximumHigh), m_GuessHeight, m_GuessWidth, m_GuessHeight, m_GuessWidth, m_GuessHeight, m_GuessWidth };
   Fitter.Config().SetParamsSettings(Parameters.size(), Parameters.data());
 
   Fitter.Config().ParSettings(0).SetName("Offset");
   Fitter.Config().ParSettings(0).SetLimits(m_MinHeight, m_MaxHeight);
   Fitter.Config().ParSettings(1).SetName("Shift");
-  Fitter.Config().ParSettings(1).SetLimits(-m_MaxARMValue, m_MaxARMValue);
+  Fitter.Config().ParSettings(1).SetLimits(m_GuessMaximumLow, m_GuessMaximumHigh);
 
   Fitter.Config().ParSettings(2).SetName("Gauss - height");
   Fitter.Config().ParSettings(2).SetLimits(m_MinHeight, m_MaxHeight);
@@ -553,15 +566,14 @@ void MARMFitter::SetupARMFitAsymmetricGaussLorentzLorentz(ROOT::Fit::Fitter& Fit
   //Fitter.Config().MinimizerOptions().SetPrintLevel(0);
   Fitter.SetFunction(WrappedFitFunction, false);
 
-  //vector<double> Parameters = { 0, 1, 1, 1, 1, 1, 1, 1, 1};
-  vector<double> Parameters = { 0, 0, m_HeightGuess, 0.9*m_WidthGuess, 1.1*m_WidthGuess, 0.9*m_HeightGuess, 0.95*m_WidthGuess, 1.1*m_HeightGuess, 1.05*m_WidthGuess };
+  vector<double> Parameters = { 1, 0.5*(m_GuessMaximumLow+m_GuessMaximumHigh), m_GuessHeight, 0.9*m_GuessWidth, 1.1*m_GuessWidth, 0.9*m_GuessHeight, 0.5*m_GuessWidth, 1.1*m_GuessHeight, 2*m_GuessWidth };
   Fitter.Config().SetParamsSettings(Parameters.size(), Parameters.data());
 
 
   Fitter.Config().ParSettings(0).SetName("Offset");
   Fitter.Config().ParSettings(0).SetLimits(m_MinHeight, m_MaxHeight);
   Fitter.Config().ParSettings(1).SetName("Shift");
-  Fitter.Config().ParSettings(1).SetLimits(-m_MaxARMValue, m_MaxARMValue);
+  Fitter.Config().ParSettings(1).SetLimits(m_GuessMaximumLow, m_GuessMaximumHigh);
 
   Fitter.Config().ParSettings(2).SetName("Gauss - height");
   Fitter.Config().ParSettings(2).SetLimits(m_MinHeight, m_MaxHeight);
@@ -598,14 +610,14 @@ void MARMFitter::SetupARMFitAsymmetricGaussGaussLorentzLorentz(ROOT::Fit::Fitter
   //Fitter.Config().MinimizerOptions().SetPrintLevel(0);
   Fitter.SetFunction(WrappedFitFunction, false);
 
-  vector<double> Parameters = { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1};
+  vector<double> Parameters = { 1, 0.5*(m_GuessMaximumLow+m_GuessMaximumHigh), m_GuessHeight, m_GuessWidth, m_GuessWidth, m_GuessHeight, m_GuessWidth, m_GuessHeight, m_GuessWidth, m_GuessHeight, m_GuessWidth };
   Fitter.Config().SetParamsSettings(Parameters.size(), Parameters.data());
 
 
   Fitter.Config().ParSettings(0).SetName("Offset");
   Fitter.Config().ParSettings(0).SetLimits(m_MinHeight, m_MaxHeight);
   Fitter.Config().ParSettings(1).SetName("Shift");
-  Fitter.Config().ParSettings(1).SetLimits(-m_MaxARMValue, m_MaxARMValue);
+  Fitter.Config().ParSettings(1).SetLimits(m_GuessMaximumLow, m_GuessMaximumHigh);
 
   Fitter.Config().ParSettings(2).SetName("Gauss #1 - height");
   Fitter.Config().ParSettings(2).SetLimits(m_MinHeight, m_MaxHeight);
@@ -647,13 +659,13 @@ void MARMFitter::SetupARMFitAsymmetricGeneralizedNormalGeneralizedNormal(ROOT::F
   //Fitter.Config().MinimizerOptions().SetPrintLevel(0);
   Fitter.SetFunction(WrappedFitFunction, false);
 
-  vector<double> Parameters = { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 };
+  vector<double> Parameters = { 1, 0.5*(m_GuessMaximumLow+m_GuessMaximumHigh), m_GuessHeight, m_GuessWidth, m_GuessScale, m_GuessWidth, m_GuessHeight, m_GuessScale, m_GuessHeight, m_GuessWidth, m_GuessScale };
   Fitter.Config().SetParamsSettings(Parameters.size(), Parameters.data());
 
   Fitter.Config().ParSettings(0).SetName("Offset");
   Fitter.Config().ParSettings(0).SetLimits(m_MinHeight, m_MaxHeight);
   Fitter.Config().ParSettings(1).SetName("Shift");
-  Fitter.Config().ParSettings(1).SetLimits(-m_MaxARMValue, m_MaxARMValue);
+  Fitter.Config().ParSettings(1).SetLimits(m_GuessMaximumLow, m_GuessMaximumHigh);
 
   Fitter.Config().ParSettings(2).SetName("GeneralizedNormal #1 - height");
   Fitter.Config().ParSettings(2).SetLimits(m_MinHeight, m_MaxHeight);
@@ -692,13 +704,13 @@ void MARMFitter::SetupARMFitAsymmetricGeneralizedNormalGeneralizedNormalGenerali
   //Fitter.Config().MinimizerOptions().SetPrintLevel(0);
   Fitter.SetFunction(WrappedFitFunction, false);
 
-  vector<double> Parameters = { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 };
+  vector<double> Parameters = { 1, 0.5*(m_GuessMaximumLow+m_GuessMaximumHigh), m_GuessHeight, m_GuessWidth, m_GuessScale, m_GuessWidth, m_GuessHeight, m_GuessScale, m_GuessHeight, m_GuessWidth, m_GuessScale, m_GuessHeight, m_GuessWidth, m_GuessScale };
   Fitter.Config().SetParamsSettings(Parameters.size(), Parameters.data());
 
   Fitter.Config().ParSettings(0).SetName("Offset");
   Fitter.Config().ParSettings(0).SetLimits(m_MinHeight, m_MaxHeight);
   Fitter.Config().ParSettings(1).SetName("Shift");
-  Fitter.Config().ParSettings(1).SetLimits(-m_MaxARMValue, m_MaxARMValue);
+  Fitter.Config().ParSettings(1).SetLimits(m_GuessMaximumLow, m_GuessMaximumHigh);
 
   Fitter.Config().ParSettings(2).SetName("GeneralizedNormal #1 - height");
   Fitter.Config().ParSettings(2).SetLimits(m_MinHeight, m_MaxHeight);
@@ -744,6 +756,9 @@ bool MARMFitter::PerformFit(unsigned int FitID, vector<double>& ARMValues)
     }
   }
 
+  // Calculate the ARM metrics not depending on a fit
+  CalculateARMMetrics();
+
   // Set up for fitting
   ROOT::Fit::DataOptions DataOptions;
   DataOptions.fIntegral = true;
@@ -770,8 +785,8 @@ bool MARMFitter::PerformFit(unsigned int FitID, vector<double>& ARMValues)
     for (int b = 1; b <= D->GetNbinsX(); ++b) D->SetBinError(b, sqrt(D->GetBinContent(b)));
     ROOT::Fit::FillData(BinnedData, D);
     delete D;
-    //Fitter.LikelihoodFit(BinnedData, true);
-    Fitter.LeastSquareFit(BinnedData);
+    Fitter.LikelihoodFit(BinnedData, true);
+    //Fitter.LeastSquareFit(BinnedData);
   }
 
   // Retrieve results
@@ -808,58 +823,6 @@ bool MARMFitter::PerformFit(unsigned int FitID, vector<double>& ARMValues)
 ////////////////////////////////////////////////////////////////////////////////
 
 
-//! Perform a single fit with the chosen fit function
-bool MARMFitter::FitOnce()
-{
-  m_FitSuccessful = false;
-
-  // Pre-calculate limits on fits
-  m_MinHeight = 0;
-  m_MaxHeight = m_OriginalARMValues.size();
-
-  vector<double> MinHeightData;
-  MinHeightData.reserve(m_OriginalARMValues.size());
-  for (double V: m_OriginalARMValues) {
-    if (V > -15 && V < 15) {
-      MinHeightData.push_back(V); // The ARM width should be within that...
-    }
-  }
-  // If the above is not working look at the value and zoom in or out
-  double SumOfSquares = 0.0;
-  for (double V: MinHeightData) {
-    SumOfSquares += V*V;
-  }
-  m_MinWidth = 0.5*sqrt(SumOfSquares / MinHeightData.size());
-  m_MaxWidth = 180;
-
-  m_WidthGuess = sqrt(SumOfSquares / MinHeightData.size());
-  m_HeightGuess = 0.3*MinHeightData.size();
-  m_ScaleGuess = 2;
-
-
-  // Right size the result storage
-  m_BootStrappedFWHMSamples.clear();
-  m_BootStrappedFWHMSamples.resize(1);
-
-  m_BootStrappedFitParameters.clear();
-  m_BootStrappedFitParameters.resize(1);
-
-  m_BootStrappedBakerCousins.clear();
-  m_BootStrappedBakerCousins.resize(1);
-
-  // Fit
-  if (PerformFit(0, m_OriginalARMValues) == true) {
-    CalculateBootStrappedMetrics();
-    m_FitSuccessful = true;
-  }
-
-  return m_FitSuccessful;
-}
-
-
-////////////////////////////////////////////////////////////////////////////////
-
-
 //! Perform fits with all fit functions and report Baker-Cousin likelihood ratios
 bool MARMFitter::FitAll()
 {
@@ -871,7 +834,7 @@ bool MARMFitter::FitAll()
   cout<<"Fitting through all functions (except Lorentz) with "<<NFits<<" samples."<<endl;
 
   m_ARMFitFunction = MARMFitFunctionID::c_Gauss;
-  FitMultiple(NFits);
+  Fit(NFits);
   if (m_FinalBakerCousins < BestBC) { BestBC = m_FinalBakerCousins; Best = m_ARMFitFunction; }
   cout<<GetARMFitFunctionName(m_ARMFitFunction)<<" - BC: "<<MString(m_FinalBakerCousins, m_FinalBakerCousinsUncertainty)<<endl;
 
@@ -881,43 +844,43 @@ bool MARMFitter::FitAll()
   //cout<<GetARMFitFunctionName(m_ARMFitFunction)<<" - BC: "<<MString(m_FinalBakerCousins, m_FinalBakerCousinsUncertainty)<<endl;
 
   m_ARMFitFunction = MARMFitFunctionID::c_GeneralizedNormal;
-  FitMultiple(NFits);
+  Fit(NFits);
   if (m_FinalBakerCousins < BestBC) { BestBC = m_FinalBakerCousins; Best = m_ARMFitFunction; }
   cout<<GetARMFitFunctionName(m_ARMFitFunction)<<" - BC: "<<MString(m_FinalBakerCousins, m_FinalBakerCousinsUncertainty)<<endl;
 
   m_ARMFitFunction = MARMFitFunctionID::c_GaussLorentz;
-  FitMultiple(NFits);
+  Fit(NFits);
   if (m_FinalBakerCousins < BestBC) { BestBC = m_FinalBakerCousins; Best = m_ARMFitFunction; }
   cout<<GetARMFitFunctionName(m_ARMFitFunction)<<" - BC: "<<MString(m_FinalBakerCousins, m_FinalBakerCousinsUncertainty)<<endl;
 
   m_ARMFitFunction = MARMFitFunctionID::c_GaussLorentzLorentz;
-  FitMultiple(NFits);
+  Fit(NFits);
   if (m_FinalBakerCousins < BestBC) { BestBC = m_FinalBakerCousins; Best = m_ARMFitFunction; }
   cout<<GetARMFitFunctionName(m_ARMFitFunction)<<" - BC: "<<MString(m_FinalBakerCousins, m_FinalBakerCousinsUncertainty)<<endl;
 
   m_ARMFitFunction = MARMFitFunctionID::c_AsymmetricGaussLorentzLorentz;
-  FitMultiple(NFits);
+  Fit(NFits);
   if (m_FinalBakerCousins < BestBC) { BestBC = m_FinalBakerCousins; Best = m_ARMFitFunction; }
   cout<<GetARMFitFunctionName(m_ARMFitFunction)<<" - BC: "<<MString(m_FinalBakerCousins, m_FinalBakerCousinsUncertainty)<<endl;
 
   m_ARMFitFunction = MARMFitFunctionID::c_AsymmetricGaussGaussLorentzLorentz;
-  FitMultiple(NFits);
+  Fit(NFits);
   if (m_FinalBakerCousins < BestBC) { BestBC = m_FinalBakerCousins; Best = m_ARMFitFunction; }
   cout<<GetARMFitFunctionName(m_ARMFitFunction)<<" - BC: "<<MString(m_FinalBakerCousins, m_FinalBakerCousinsUncertainty)<<endl;
 
   m_ARMFitFunction = MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormal;
-  FitMultiple(NFits);
+  Fit(NFits);
   if (m_FinalBakerCousins < BestBC) { BestBC = m_FinalBakerCousins; Best = m_ARMFitFunction; }
   cout<<GetARMFitFunctionName(m_ARMFitFunction)<<" - BC: "<<MString(m_FinalBakerCousins, m_FinalBakerCousinsUncertainty)<<endl;
 
   m_ARMFitFunction = MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormalGeneralizedNormal;
-  FitMultiple(NFits);
+  Fit(NFits);
   if (m_FinalBakerCousins < BestBC) { BestBC = m_FinalBakerCousins; Best = m_ARMFitFunction; }
   cout<<GetARMFitFunctionName(m_ARMFitFunction)<<" - BC: "<<MString(m_FinalBakerCousins, m_FinalBakerCousinsUncertainty)<<endl;
 
   // Do the best again:
   m_ARMFitFunction = Best;
-  FitMultiple(2*NFits);
+  Fit(2*NFits);
   cout<<"Best: "<<GetARMFitFunctionName(m_ARMFitFunction)<<" - BC: "<<MString(m_FinalBakerCousins, m_FinalBakerCousinsUncertainty)<<endl;
 
   return m_FitSuccessful;
@@ -1008,7 +971,6 @@ void MARMFitter::CalculateARMMetrics()
 {
   // Determine containment radii
 
-  /*
   double Sigma0 = 0.5;
   m_Containment50Percent = g_DoubleNotDefined;
   double Sigma1 = 0.6826;
@@ -1018,29 +980,29 @@ void MARMFitter::CalculateARMMetrics()
   double Sigma3 = 0.9973;
   m_Containment3Sigma = g_DoubleNotDefined;
 
-  int CentralBin = Histogram->FindBin(0);
-  double All = Histogram->Integral(1, m_NumberOfBins);
-  double Content = 0.0;
-  for (int b = 0; b + CentralBin <= Histogram->GetNbinsX(); ++b) {
-    if (b == 0) {
-      Content += Histogram->GetBinContent(CentralBin);
-    } else {
-      Content += Histogram->GetBinContent(CentralBin + b) + Histogram->GetBinContent(CentralBin - b);
+  vector<double> SortedAbs;
+  for (double& A: m_OriginalARMValues) {
+    if (A >= -m_MaxARMValue && A <= m_MaxARMValue) {
+      SortedAbs.push_back(fabs(A));
     }
-    if (m_Containment50Percent == g_DoubleNotDefined && Content >= Sigma0*All) {
-      m_Containment50Percent = Histogram->GetBinCenter(CentralBin + b);
+  }
+  std::sort(SortedAbs.begin(), SortedAbs.end());
+
+  double Total = SortedAbs.size();
+  for (int b = 0; b < SortedAbs.size(); ++b) {
+    if (m_Containment50Percent == g_DoubleNotDefined && b >= Sigma0*Total) {
+      m_Containment50Percent = SortedAbs[b];
     }
-    if (m_Containment1Sigma == g_DoubleNotDefined && Content >= Sigma1*All) {
-      m_Containment1Sigma = Histogram->GetBinCenter(CentralBin + b);
+    if (m_Containment1Sigma == g_DoubleNotDefined && b >= Sigma1*Total) {
+      m_Containment1Sigma = SortedAbs[b];
     }
-    if (m_Containment2Sigma == g_DoubleNotDefined && Content >= Sigma2*All) {
-      m_Containment2Sigma = Histogram->GetBinCenter(CentralBin + b);
+    if (m_Containment2Sigma == g_DoubleNotDefined && b >= Sigma2*Total) {
+      m_Containment2Sigma = SortedAbs[b];
     }
-    if (m_Containment3Sigma == g_DoubleNotDefined && Content >= Sigma3*All) {
-      m_Containment3Sigma = Histogram->GetBinCenter(CentralBin + b);
+    if (m_Containment3Sigma == g_DoubleNotDefined && b >= Sigma3*Total) {
+      m_Containment3Sigma = SortedAbs[b];
     }
   }
-  */
 }
 
 
@@ -1070,32 +1032,44 @@ void MARMFitter::ParallelFitting(int FitID, std::condition_variable& CV)
 ////////////////////////////////////////////////////////////////////////////////
 
 
-//! Performs N fits.
+//! Performs N fits. N must be 1 or larger.
 //! Each fit samples randomly from the stored ARM values to determine the average width and error correctly
-bool MARMFitter::FitMultiple(unsigned int NumberOfFits)
+bool MARMFitter::Fit(unsigned int NumberOfFits)
 {
   if (NumberOfFits <= 0) return false;
 
   m_FitSuccessful = true;
 
+  if (m_OptimizeBinning == true) {
+    OptimizeBinning();
+  }
+
   // Pre-calculate limits on fits
-  m_MinHeight = 0;
-  m_MaxHeight = m_OriginalARMValues.size();
 
-  vector<double> MinHeightData;
-  MinHeightData.reserve(m_OriginalARMValues.size());
+  // We need a histogram, to do it easily
+  unsigned int NEvents = 0;
+  TH1D* Hist = new TH1D("", "", m_NumberOfBins, -m_MaxARMValue, m_MaxARMValue);
   for (double V: m_OriginalARMValues) {
-    if (V > -15 && V < 15) {
-      MinHeightData.push_back(V); // The ARM width should be within that...
+    if (V >= -15 && V <= 15) {
+      Hist->Fill(V);
+      NEvents++;
     }
   }
-  // If the above is not working look at the value and zoom in or out
-  double SumOfSquares = 0.0;
-  for (double V: MinHeightData) {
-    SumOfSquares += V*V;
+  m_MinHeight = 0;
+  if (m_UnbinnedFitting == false) {
+    m_MaxHeight = 1.25 * Hist->GetMaximum();
+  } else {
+    m_MaxHeight = 0.5*NEvents;
   }
-  m_MinWidth = 0.5*sqrt(SumOfSquares / MinHeightData.size());
+  m_GuessHeight = 0.5*m_MaxHeight;
+
+  m_MinWidth = 0.25*Hist->GetRMS();
   m_MaxWidth = m_MaxARMValue;
+  m_GuessWidth = Hist->GetRMS();
+
+  double MaxX = Hist->GetBinCenter(Hist->GetMaximumBin());
+  m_GuessMaximumLow = MaxX - 0.5*Hist->GetRMS();
+  m_GuessMaximumHigh = MaxX + 0.5*Hist->GetRMS();
 
 
   // Right size the result storage
@@ -1108,19 +1082,22 @@ bool MARMFitter::FitMultiple(unsigned int NumberOfFits)
   m_BootStrappedBakerCousins.clear();
   m_BootStrappedBakerCousins.resize(NumberOfFits);
 
+  if (NumberOfFits > 1) {
+    // Start the threads
+    m_NumberOfRunningThreads = 0;
+    vector<thread> Threads;
+    condition_variable CV;
 
-  // Start the threads
-  m_NumberOfRunningThreads = 0;
-  vector<thread> Threads;
-  condition_variable CV;
-
-  for (unsigned int i = 0; i < NumberOfFits; ++i) {
-    Threads.emplace_back([this, &CV, i]() { this->ParallelFitting(i, CV); } );
-  }
+    for (unsigned int i = 0; i < NumberOfFits; ++i) {
+      Threads.emplace_back([this, &CV, i]() { this->ParallelFitting(i, CV); } );
+    }
 
-  // Join all threads with the main thread
-  for (thread& T: Threads) {
-    T.join();
+    // Join all threads with the main thread
+    for (thread& T: Threads) {
+      T.join();
+    }
+  } else {
+    PerformFit(0, m_OriginalARMValues);
   }
 
   // Caluclate the results
@@ -1134,7 +1111,7 @@ bool MARMFitter::FitMultiple(unsigned int NumberOfFits)
 
 
 //! Return the the FWHM result
-double MARMFitter::GetFWHM() const
+double MARMFitter::GetAverageFWHM() const
 {
   return m_FitSuccessful ? m_FinalFWHM : g_DoubleNotDefined;
 }
@@ -1144,7 +1121,7 @@ double MARMFitter::GetFWHM() const
 
 
 //! Return the FWHM uncertainty result
-double MARMFitter::GetFWHMUncertainty() const
+double MARMFitter::GetAverageFWHMUncertainty() const
 {
   return m_FitSuccessful ? m_FinalFWHMUncertainty : g_DoubleNotDefined;
 }
@@ -1153,6 +1130,46 @@ double MARMFitter::GetFWHMUncertainty() const
 ////////////////////////////////////////////////////////////////////////////////
 
 
+//! Return the 50.0% containment for events with +- maximum ARM value
+double MARMFitter::Get50p0PercentContainment() const
+{
+  return m_FitSuccessful ? m_Containment50Percent : g_DoubleNotDefined;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Return the 68.3% containment for events with +- maximum ARM value
+double MARMFitter::Get68p3PercentContainment() const
+{
+  return m_FitSuccessful ? m_Containment1Sigma : g_DoubleNotDefined;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Return the 95.5% containment for events with +- maximum ARM value
+double MARMFitter::Get95p5PercentContainment() const
+{
+  return m_FitSuccessful ? m_Containment2Sigma : g_DoubleNotDefined;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Return the 99.7% containment for events with +- maximum ARM value
+double MARMFitter::Get99p7PercentContainment() const
+{
+  return m_FitSuccessful ? m_Containment3Sigma : g_DoubleNotDefined;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
 //! Convert the results into a string
 MString MARMFitter::ToString()
 {
@@ -1181,6 +1198,12 @@ MString MARMFitter::ToString()
   out<<"  Fit function: "<<GetARMFitFunctionName(m_ARMFitFunction)<<endl;
   out<<"  Average FWHM after "<<m_BootStrappedFWHMSamples.size()<<" boot straps: "<<MString(m_FinalFWHM, m_FinalFWHMUncertainty, "degree")<<endl;
   out<<endl;
+  out<<"Containment (with +- "<<m_MaxARMValue<<" deg):"<<endl;
+  out<<"  50.0 %: "<<m_Containment50Percent<<" deg"<<endl;
+  out<<"  68.3 %: "<<m_Containment1Sigma<<" deg"<<endl;
+  out<<"  95.5 %: "<<m_Containment2Sigma<<" deg"<<endl;
+  out<<"  99.7 %: "<<m_Containment3Sigma<<" deg"<<endl;
+  out<<endl;
 
   return out;
 }
@@ -1257,5 +1280,61 @@ void MARMFitter::Draw()
 }
 
 
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Load the ARM value from file
+bool MARMFitter::LoadARMValues(MString FileName)
+{
+  m_OriginalARMValues.clear();
+
+  ifstream fin;
+  fin.open(FileName);
+  if (fin.is_open() == false) {
+    merr<<"Unable to open "<<FileName<<endl;
+    return false;
+  }
+
+  string Line;
+  string Prefix;
+  double Value;
+  while (getline(fin, Line)) {
+    if (Line.size() < 4 || Line.substr(0, 2) != "DP") continue;
+    istringstream iss(Line);
+    // Read the prefix ("DP") and the value
+    if (iss>>Prefix>>Value) {
+      m_OriginalARMValues.push_back(Value);
+    }
+  }
+
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Save the the ARM values to a file
+bool MARMFitter::SaveARMValues(MString FileName)
+{
+  if (m_OriginalARMValues.size() > 0) {
+    ofstream fout;
+    fout.open(FileName);
+    if (fout.is_open() == false) {
+      merr<<"Unable to open "<<FileName<<endl;
+      return false;
+    }
+    fout<<"# ARM data file"<<endl;
+    fout<<endl;
+    for (auto& A: m_OriginalARMValues) {
+      fout<<"DP "<<A<<endl;
+    }
+    fout<<endl;
+    fout.close();
+  }
+
+  return true;
+}
+
 // MARMFitter.cxx: the end...
 ////////////////////////////////////////////////////////////////////////////////
diff --git a/src/mimrec/src/MInterfaceMimrec.cxx b/src/mimrec/src/MInterfaceMimrec.cxx
index 4a871e3f1..e776eaeb4 100644
--- a/src/mimrec/src/MInterfaceMimrec.cxx
+++ b/src/mimrec/src/MInterfaceMimrec.cxx
@@ -1120,12 +1120,12 @@ void MInterfaceMimrec::ARMGamma()
 
   MARMFitter Fitter;
   Fitter.SetNumberOfBins(m_Settings->GetHistBinsARMGamma());
-  Fitter.SetMaxARM(m_Settings->GetTPDistanceTrans());
+  Fitter.SetMaximumARMValue(m_Settings->GetTPDistanceTrans());
   //Fitter.SetFitFunction(MARMFitFunctionID::c_GeneralizedNormal);
   //Fitter.SetFitFunction(MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormal);
   //Fitter.SetFitFunction(MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormalGeneralizedNormal);
   Fitter.SetFitFunction(MARMFitFunctionID::c_AsymmetricGaussLorentzLorentz);
-  Fitter.UseUnbinnedFitting(false);
+  Fitter.UseBinnedFitting(true);
   Fitter.UseOptimizedBinning();
 
   bool FoundEvents = false;
@@ -1146,6 +1146,8 @@ void MInterfaceMimrec::ARMGamma()
     delete Event;
   } 
   
+  Fitter.SaveARMValues("Data.dat");
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -1153,8 +1155,7 @@ void MInterfaceMimrec::ARMGamma()
     mgui<<"No events passed the event selections."<<error;
   }
 
-  Fitter.FitOnce();
-  //Fitter.FitMultiple(100);
+  Fitter.Fit(100);
   //Fitter.FitAll();
 
   if (Fitter.WasFittingSuccessful() == true) {
diff --git a/src/mimrec/unittests/UTARMFitter.cxx b/src/mimrec/unittests/UTARMFitter.cxx
index 356b55f6d..ed9b19efb 100644
--- a/src/mimrec/unittests/UTARMFitter.cxx
+++ b/src/mimrec/unittests/UTARMFitter.cxx
@@ -212,16 +212,16 @@ double UTARMFitter::TestSingleFit()
   // Set up the fitter and fit
   MARMFitter Fitter;
   Fitter.SetNumberOfBins(NumberOfBins);
-  Fitter.SetMaxARM(MaxARM);
+  Fitter.SetMaximumARMValue(MaxARM);
 
   for (unsigned int i = 0; i < Counts; ++i) {
     Fitter.AddARMValue(ARMValues[i]);
   }
 
-  Fitter.FitOnce();
+  Fitter.Fit(1);
 
   if (Fitter.WasFittingSuccessful() == true) {
-    cout<<"FWHM: "<<Fitter.GetFWHM()<<endl;
+    cout<<"FWHM: "<<Fitter.GetAverageFWHM()<<endl;
   }
 
   TCanvas* FitterCanvas = new TCanvas();
@@ -277,7 +277,7 @@ double UTARMFitter::TestBootstrapping()
   // Set up the fitter and fit
   MARMFitter Fitter;
   Fitter.SetNumberOfBins(NumberOfBins);
-  Fitter.SetMaxARM(MaxARM);
+  Fitter.SetMaximumARMValue(MaxARM);
   Fitter.SetFitFunction(MARMFitFunctionID::c_AsymmetricGaussLorentzLorentz);
   Fitter.UseOptimizedBinning();
 
@@ -285,12 +285,12 @@ double UTARMFitter::TestBootstrapping()
     Fitter.AddARMValue(ARMValues[i]);
   }
 
-  Fitter.FitMultiple(200);
+  Fitter.Fit(200);
 
   if (Fitter.WasFittingSuccessful() == true) {
-    cout<<"Average FWHM: "<<Fitter.GetFWHM()<<endl;
-    cout<<"FWHM Uncertainty: "<<Fitter.GetFWHMUncertainty()<<endl;
-    cout<<"Sigma difference: "<<fabs(OriginalFWHM - Fitter.GetFWHM())/Fitter.GetFWHMUncertainty()<<endl;
+    cout<<"Average FWHM: "<<Fitter.GetAverageFWHM()<<endl;
+    cout<<"FWHM Uncertainty: "<<Fitter.GetAverageFWHMUncertainty()<<endl;
+    cout<<"Sigma difference: "<<fabs(OriginalFWHM - Fitter.GetAverageFWHM())/Fitter.GetAverageFWHMUncertainty()<<endl;
 
     vector<double> FWHMes = Fitter.GetBootstrappedFWHMSamples();
     if (FWHMes.size() > 0) {

From 80806e0c4855b191e7f0b9d0eb19a6cc1aad7d6c Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Mon, 2 Sep 2024 23:33:58 -0700
Subject: [PATCH 060/192] CHG: References to class enum seem not to work nicely
 in python, thus replaced

---
 src/global/misc/inc/MComptonEvent.h   | 8 ++++----
 src/global/misc/src/MComptonEvent.cxx | 8 ++++----
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/global/misc/inc/MComptonEvent.h b/src/global/misc/inc/MComptonEvent.h
index cd9149d7e..01271780b 100644
--- a/src/global/misc/inc/MComptonEvent.h
+++ b/src/global/misc/inc/MComptonEvent.h
@@ -203,14 +203,14 @@ class MComptonEvent : public MPhysicalEvent
 
 
   //! Return the Angular Resolution Measure value for the gamma cone for the given test position in the given coordinate system
-  double GetARMGamma(const MVector& TestPosition, const MCoordinateSystem& CS = MCoordinateSystem::c_Cartesian2D);
+  double GetARMGamma(const MVector& TestPosition, const MCoordinateSystem CS = MCoordinateSystem::c_Cartesian2D);
   //! Return the Angular Resolution Measure value for the electron cone for the given test position in the given coordinate system
-  double GetARMElectron(const MVector& TestPosition, const MCoordinateSystem& CS = MCoordinateSystem::c_Cartesian2D);
+  double GetARMElectron(const MVector& TestPosition, const MCoordinateSystem CS = MCoordinateSystem::c_Cartesian2D);
   //! Return the Scatter Plane Deviation value for the given test position in the given coordinate system
-  double GetSPDElectron(const MVector& TestPosition, const MCoordinateSystem& CS = MCoordinateSystem::c_Cartesian2D);
+  double GetSPDElectron(const MVector& TestPosition, const MCoordinateSystem CS = MCoordinateSystem::c_Cartesian2D);
 
   //! Return the azimuthal scatter angle value for the given test position in the given coordinate system
-  double GetAzimuthalScatterAngle(const MVector& Position, const MCoordinateSystem& CS = MCoordinateSystem::c_Cartesian2D);
+  double GetAzimuthalScatterAngle(const MVector& Position, const MCoordinateSystem CS = MCoordinateSystem::c_Cartesian2D);
 
 
   //! Representation of the Kleine Nishina cross-section value of this events data
diff --git a/src/global/misc/src/MComptonEvent.cxx b/src/global/misc/src/MComptonEvent.cxx
index 5ce071888..91d609c84 100644
--- a/src/global/misc/src/MComptonEvent.cxx
+++ b/src/global/misc/src/MComptonEvent.cxx
@@ -486,7 +486,7 @@ double MComptonEvent::GetRandomPhi(const double Ei)
 ////////////////////////////////////////////////////////////////////////////////
 
 
-double MComptonEvent::GetARMGamma(const MVector& Position, const MCoordinateSystem& CS) 
+double MComptonEvent::GetARMGamma(const MVector& Position, const MCoordinateSystem CS)
 {
   // The ARM value for the scattered gamma-ray is the minimum angle between 
   // the gamma-cone-surface and the line connecting the cone-apex with the 
@@ -507,7 +507,7 @@ double MComptonEvent::GetARMGamma(const MVector& Position, const MCoordinateSyst
 ////////////////////////////////////////////////////////////////////////////////
 
 
-double MComptonEvent::GetARMElectron(const MVector& Position, const MCoordinateSystem& CS) 
+double MComptonEvent::GetARMElectron(const MVector& Position, const MCoordinateSystem CS)
 {
   // The ARM value for the recoil electron is the minimum angle between 
   // the elctron-cone-surface and the line connecting the cone-apex with the 
@@ -525,7 +525,7 @@ double MComptonEvent::GetARMElectron(const MVector& Position, const MCoordinateS
 ////////////////////////////////////////////////////////////////////////////////
 
 
-double MComptonEvent::GetSPDElectron(const MVector& Position, const MCoordinateSystem& CS)
+double MComptonEvent::GetSPDElectron(const MVector& Position, const MCoordinateSystem CS)
 {
   // The SPD value for the recoil electron is the minimum angle between 
   // the electron-cone-surface and the line connecting the cone-apex with the 
@@ -543,7 +543,7 @@ double MComptonEvent::GetSPDElectron(const MVector& Position, const MCoordinateS
 ////////////////////////////////////////////////////////////////////////////////
 
 
-double MComptonEvent::GetAzimuthalScatterAngle(const MVector& Position, const MCoordinateSystem& CS)
+double MComptonEvent::GetAzimuthalScatterAngle(const MVector& Position, const MCoordinateSystem CS)
 {
   //! Return the azimuthal scatter angle value for the given test position in the given coordinate system
 

From b58dd4d9a7bdc546fbd74c1c70679066a603e9cd Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Mon, 2 Sep 2024 23:34:54 -0700
Subject: [PATCH 061/192] CHG: ARM fitting improvements for python and work on
 GUI

---
 resource/examples/python/ARMFitter.py     |  81 ++++++++
 resource/examples/python/AnalyzeEvents.py |  10 +-
 resource/examples/python/Test.geo.setup   | 211 ++++++++++++++++++++
 resource/examples/python/Test.source      |   4 +-
 resource/examples/python/TraRewriter.py   |  10 +-
 src/mimrec/Makefile                       |   1 +
 src/mimrec/inc/MARMFitter.h               |  40 ++--
 src/mimrec/inc/MGUIARMExtended.h          | 100 ++++++++++
 src/mimrec/src/MARMFitter.cxx             | 150 +++++++++++----
 src/mimrec/src/MGUIARMExtended.cxx        | 224 ++++++++++++++++++++++
 src/mimrec/src/MGUIMimrecMain.cxx         |   3 +-
 11 files changed, 775 insertions(+), 59 deletions(-)
 create mode 100644 resource/examples/python/ARMFitter.py
 create mode 100644 resource/examples/python/Test.geo.setup
 create mode 100644 src/mimrec/inc/MGUIARMExtended.h
 create mode 100644 src/mimrec/src/MGUIARMExtended.cxx

diff --git a/resource/examples/python/ARMFitter.py b/resource/examples/python/ARMFitter.py
new file mode 100644
index 000000000..6a235c804
--- /dev/null
+++ b/resource/examples/python/ARMFitter.py
@@ -0,0 +1,81 @@
+import math
+import ctypes
+import ROOT as M
+
+# Load MEGAlib into ROOT
+M.gSystem.Load("$(MEGALIB)/lib/libMEGAlib.so")
+
+# Initialize MEGAlib
+G = M.MGlobal()
+G.Initialize()
+
+# We are good to go ...
+
+FileName = "Test.inc1.id1.tra.gz"
+GeometryFileName = "Test.geo.setup"
+SettingsFileName = "Test.mimrec.cfg"
+TestPosition = M.MVector(0, 0, 1E20)
+CoordinateSystem = M.MCoordinateSystem.c_Spheric
+
+# Load geometry:
+Geometry = M.MDGeometryQuest()
+if Geometry.ScanSetupFile(M.MString(GeometryFileName)) == True:
+  print("Geometry " + GeometryFileName + " loaded!")
+else:
+  print("Unable to load geometry " + GeometryFileName + " - Aborting!")
+  quit()
+    
+# Load the data
+Reader = M.MFileEventsTra()
+if Reader.Open(M.MString(FileName)) == False:
+  print("Unable to open file " + FileName + ". Aborting!")
+  quit()
+
+# Set up the event selector
+Settings = M.MSettingsMimrec()
+Settings.Read(SettingsFileName)
+
+Selector = M.MEventSelector()
+Selector.SetGeometry(Geometry)
+Selector.SetSettings(Settings);
+
+# Set up the fitter
+Fitter = M.MARMFitter()
+Fitter.SetNumberOfBins(101);
+Fitter.SetMaximumARMValue(15);
+Fitter.SetFitFunction(M.MARMFitFunctionID.c_AsymmetricGaussLorentzLorentz);
+Fitter.UseOptimizedBinning();
+
+
+C = M.MComptonEvent()
+
+while True: 
+  Event = Reader.GetNextEvent()
+  if not Event:
+    break
+  M.SetOwnership(Event, True)
+  
+  if Selector.IsQualifiedEvent(Event):
+    if Event.GetType() == M.MPhysicalEvent.c_Compton:
+      C = Event
+      Fitter.AddARMValue(math.degrees(Event.GetARMGamma(TestPosition, CoordinateSystem)))
+
+
+Fitter.Fit(20);
+
+if Fitter.WasFittingSuccessful():
+  FitterCanvas = M.TCanvas();
+  FitterCanvas.SetTitle("ARM of Compton cone");
+  FitterCanvas.cd();
+  Fitter.Draw();
+  FitterCanvas.Modified();
+  FitterCanvas.Update();
+
+  print(Fitter.ToString())
+
+
+# Prevent the canvases from being closed
+import os
+print("ATTENTION: Please exit by clicking: File -> Close ROOT! Do not just close the window by clicking \"x\"")
+print("           ... and if you didn't honor this warning, and are stuck, execute the following in a new terminal: kill " + str(os.getpid()))
+M.gApplication.Run()
diff --git a/resource/examples/python/AnalyzeEvents.py b/resource/examples/python/AnalyzeEvents.py
index f09f1c5f7..01f6ed1aa 100644
--- a/resource/examples/python/AnalyzeEvents.py
+++ b/resource/examples/python/AnalyzeEvents.py
@@ -9,15 +9,15 @@
 
 # We are good to go ...
 
-GeometryName = "$(MEGALIB)/resource/examples/geomega/special/Max.geo.setup"
-FileName = "Test.inc1.id1.tra"
+GeometryFileName = "Test.geo.setup"
+FileName = "Test.inc1.id1.tra.gz"
 
 # Load geometry:
 Geometry = M.MDGeometryQuest()
-if Geometry.ScanSetupFile(M.MString(GeometryName)) == True:
-  print("Geometry " + GeometryName + " loaded!")
+if Geometry.ScanSetupFile(M.MString(GeometryFileName)) == True:
+  print("Geometry " + GeometryFileName + " loaded!")
 else:
-  print("Unable to load geometry " + GeometryName + " - Aborting!")
+  print("Unable to load geometry " + GeometryFileName + " - Aborting!")
   quit()
     
 
diff --git a/resource/examples/python/Test.geo.setup b/resource/examples/python/Test.geo.setup
new file mode 100644
index 000000000..952cbba25
--- /dev/null
+++ b/resource/examples/python/Test.geo.setup
@@ -0,0 +1,211 @@
+#---------------------------------------------------------
+# Very simple Germanium ACT - similar to NCT 
+
+
+Name Max
+Version 2.0
+
+SurroundingSphere 10  0.0  0.0  0.0  10.0
+
+# Use this volume, to test the surrounding sphere:
+#Volume Sphere
+#Sphere.Material Vacuum
+#Sphere.Shape SPHE 0.0 10.0 0.0 180.0 0.0 360.
+#Sphere.Position 0.0 0.0 0.0
+#Sphere.Mother WorldVolume
+
+
+Include $(MEGALIB)/resource/examples/geomega/materials/Materials.geo
+
+
+
+#------------------------------------------------------------
+# Volume section:
+
+
+Volume WorldVolume             
+WorldVolume.Material Vacuum
+WorldVolume.Visibility 0   
+WorldVolume.Shape BRIK 5000. 5000. 5000.
+WorldVolume.Mother 0
+
+
+
+//------------------------------------------------------------
+// Define Germanium strip detector:
+
+// One layer of the tracker
+// GeStripDetector is the aluminum cryostat surrounding the 
+// Ge detectors - they are called 'GeWafer' ....
+
+Constant DetectorHalfWidth  4.0
+Constant DetectorHalfHeight 0.75
+Constant GuardRingSize      0.3
+Constant IngotRadius        { 2* 2.54}
+
+Constant CryoThickness  0.1
+Constant CryoOffset     0.5
+
+Constant CryoTotalHeight { 2*(DetectorHalfHeight + CryoOffset + CryoThickness ) } 
+
+Volume GeStripDetector           
+GeStripDetector.Material Aluminium
+GeStripDetector.Visibility 1
+GeStripDetector.Color 2
+GeStripDetector.Shape BRIK  { DetectorHalfWidth + CryoOffset + CryoThickness }  { DetectorHalfWidth + CryoOffset  + CryoThickness }  { DetectorHalfHeight + CryoOffset  + CryoThickness } 
+
+Volume CryoInnerHull 
+CryoInnerHull.Material Vacuum 
+CryoInnerHull.Visibility 1
+CryoInnerHull.Shape BRIK  { DetectorHalfWidth + CryoOffset }  { DetectorHalfWidth + CryoOffset }  { DetectorHalfHeight + CryoOffset } 
+
+
+# Create the whole wafer
+Shape BRIK WaferOuterBox
+WaferOuterBox.Parameters DetectorHalfWidth  DetectorHalfWidth  DetectorHalfHeight
+
+Shape TUBE WaferCutDisk
+WaferCutDisk.Parameters 0.0 IngotRadius DetectorHalfHeight
+
+Shape Intersection WholeWafer
+WholeWafer.Parameters WaferOuterBox WaferCutDisk
+
+# Create the active wafer
+Shape BRIK ActiveWaferOuterBox
+ActiveWaferOuterBox.Parameters { DetectorHalfWidth - GuardRingSize }  { DetectorHalfWidth - GuardRingSize }  DetectorHalfHeight
+
+Shape TUBE ActiveWaferCutDisk
+ActiveWaferCutDisk.Parameters 0.0 { IngotRadius - GuardRingSize } DetectorHalfHeight
+
+Shape Intersection ActiveWafer
+ActiveWafer.Parameters ActiveWaferOuterBox ActiveWaferCutDisk
+
+# Create the guard ring
+Shape Subtraction GuardRing_AlmostThere
+GuardRing_AlmostThere.Parameters WholeWafer ActiveWafer
+
+# A little trick, to get the Strip detector to work: we have to do another intersection, so that the first volume is a box:
+Shape Intersection GuardRing
+GuardRing.Parameters WaferOuterBox GuardRing_AlmostThere
+
+
+Volume GeWafer
+GeWafer.Material Germanium
+GeWafer.Visibility 1
+GeWafer.Color 6
+GeWafer.Shape ActiveWafer
+GeWafer.Position  0.0 0.0 0.0
+GeWafer.Mother CryoInnerHull
+
+Volume GeWaferGuardRing
+GeWaferGuardRing.Material Germanium
+GeWaferGuardRing.Visibility 1
+GeWaferGuardRing.Color 3
+GeWaferGuardRing.Shape GuardRing
+GeWaferGuardRing.Position  0.0 0.0 0.0
+GeWaferGuardRing.Mother CryoInnerHull
+
+CryoInnerHull.Copy Cryo
+Cryo.Position 0.0 0.0 0.0
+Cryo.Mother GeStripDetector
+
+
+
+// Line-Up some Ge-Detector 
+GeStripDetector.Copy GeE1N001
+GeE1N001.Position  0.0  0.0  {  1.5*CryoTotalHeight } 
+GeE1N001.Mother WorldVolume
+
+GeStripDetector.Copy GeE1N002
+GeE1N002.Position  0.0  0.0  {  0.5*CryoTotalHeight } 
+GeE1N002.Mother WorldVolume
+
+GeStripDetector.Copy GeE1N003
+GeE1N003.Position  0.0  0.0  { -0.5*CryoTotalHeight } 
+GeE1N003.Mother WorldVolume
+
+GeStripDetector.Copy GeE1N004
+GeE1N004.Position  0.0  0.0  { -1.5*CryoTotalHeight } 
+GeE1N004.Mother WorldVolume
+
+
+
+
+
+
+#------------------------------------------------------------
+# Detector and trigger section:
+
+
+MDStrip3D                  ActiveDetector
+
+ActiveDetector.DetectorVolume      GeWafer
+ActiveDetector.SensitiveVolume     GeWafer
+
+ActiveDetector.StructuralPitch     0.0   0.0    CryoTotalHeight
+ActiveDetector.StructuralOffset    0.0   0.0    0.0
+
+ActiveDetector.Offset              0.0   0.0
+ActiveDetector.StripNumber         40    40
+
+ActiveDetector.NoiseThreshold      15
+ActiveDetector.TriggerThreshold    30
+
+ActiveDetector.DepthResolution     10  0.02
+ActiveDetector.DepthResolution     100  0.02
+ActiveDetector.DepthResolution     1000  0.02
+
+ActiveDetector.EnergyResolution Gaus 10      10        0.417   
+ActiveDetector.EnergyResolution Gaus 20      20        0.425           
+ActiveDetector.EnergyResolution Gaus 50      50        0.4375    
+ActiveDetector.EnergyResolution Gaus 100     100       0.454     
+ActiveDetector.EnergyResolution Gaus 200     200       0.492     
+ActiveDetector.EnergyResolution Gaus 500     500       0.5875      
+ActiveDetector.EnergyResolution Gaus 1000    1000      0.7217       
+ActiveDetector.EnergyResolution Gaus 2000    2000      0.9317      
+ActiveDetector.EnergyResolution Gaus 5000    5000      1.3819       
+ActiveDetector.EnergyResolution Gaus 10000   10000     1.9094                     
+ActiveDetector.EnergyResolution Gaus 100000  100000    5.907         
+
+ActiveDetector.FailureRate 0.0
+
+ActiveDetector.Named D1
+D1.Assign 0.0  0.0  {  1.5*CryoTotalHeight }
+ActiveDetector.Named D2
+D2.Assign 0.0  0.0  {  0.5*CryoTotalHeight }
+ActiveDetector.Named D3
+D3.Assign  0.0  0.0  { -0.5*CryoTotalHeight }
+ActiveDetector.Named D4  
+D4.Assign 0.0  0.0  { -1.5*CryoTotalHeight }
+
+
+Simple GuardRingDetector
+
+GuardRingDetector.DetectorVolume      GeWaferGuardRing
+GuardRingDetector.SensitiveVolume     GeWaferGuardRing
+
+GuardRingDetector.TriggerThreshold      40
+GuardRingDetector.NoiseThresholdEqualsTriggerThreshold true
+
+GuardRingDetector.EnergyResolution Gaus 10      10        3   
+GuardRingDetector.EnergyResolution Gaus 20      20        3           
+GuardRingDetector.EnergyResolution Gaus 50      50        3    
+GuardRingDetector.EnergyResolution Gaus 100     100       3     
+GuardRingDetector.EnergyResolution Gaus 200     200       3     
+GuardRingDetector.EnergyResolution Gaus 500     500       3      
+GuardRingDetector.EnergyResolution Gaus 1000    1000      3       
+GuardRingDetector.EnergyResolution Gaus 2000    2000      3      
+GuardRingDetector.EnergyResolution Gaus 5000    5000      3       
+
+
+
+// Trigger: at least one hit in one Germanium detector  
+Trigger ActiveDetectorTrigger
+ActiveDetectorTrigger.Veto false
+ActiveDetectorTrigger.TriggerByChannel true
+ActiveDetectorTrigger.Detector ActiveDetector 1
+
+Trigger GuardRingVeto
+GuardRingVeto.Veto true
+GuardRingVeto.TriggerByChannel true
+GuardRingVeto.Detector GuardRingDetector 1
diff --git a/resource/examples/python/Test.source b/resource/examples/python/Test.source
index 07a311306..1061bf796 100644
--- a/resource/examples/python/Test.source
+++ b/resource/examples/python/Test.source
@@ -1,10 +1,8 @@
 # Example run for Cosima
-# A Crab-like source in the zenith on cosmic and albedo photon background
-
 
 # Global parameters
 Version         1
-Geometry        $(MEGALIB)/resource/examples/geomega/special/Max.geo.setup
+Geometry        Test.geo.setup
 
 # Physics list
 PhysicsListEM               LivermorePol
diff --git a/resource/examples/python/TraRewriter.py b/resource/examples/python/TraRewriter.py
index 32d2e1109..92433bdcb 100644
--- a/resource/examples/python/TraRewriter.py
+++ b/resource/examples/python/TraRewriter.py
@@ -9,15 +9,15 @@
 
 # We are good to go ...
 
-GeometryName = "$(MEGALIB)/resource/examples/geomega/special/Max.geo.setup"
-FileName = "Test.inc1.id1.tra"
+GeometryFileName = "Test.geo.setup"
+FileName = "Test.inc1.id1.tra.gz"
 
 # Load geometry:
 Geometry = M.MDGeometryQuest()
-if Geometry.ScanSetupFile(M.MString(GeometryName)) == True:
-  print("Geometry " + GeometryName + " loaded!")
+if Geometry.ScanSetupFile(M.MString(GeometryFileName)) == True:
+  print("Geometry " + GeometryFileName + " loaded!")
 else:
-  print("Unable to load geometry " + GeometryName + " - Aborting!")
+  print("Unable to load geometry " + GeometryFileName + " - Aborting!")
   quit()
     
 # Open the tra reader
diff --git a/src/mimrec/Makefile b/src/mimrec/Makefile
index bac15eb0f..d72240760 100644
--- a/src/mimrec/Makefile
+++ b/src/mimrec/Makefile
@@ -64,6 +64,7 @@ FILES_UI := \
 	MGUIMimrecMain \
 	MGUIHistogramData \
 	MGUIARM \
+	MGUIARMExtended \
 	MGUIAnimation \
 	MGUICoordinateSystem \
 	MGUIEventSelection \
diff --git a/src/mimrec/inc/MARMFitter.h b/src/mimrec/inc/MARMFitter.h
index 044380f57..a8a28fa3f 100644
--- a/src/mimrec/inc/MARMFitter.h
+++ b/src/mimrec/inc/MARMFitter.h
@@ -79,7 +79,7 @@ class MARMFitter
 
   //! Set the test position, and its coordinate system
   //! Do not call this function while adding events
-  void SetTestPosition(MVector TestPosition, MCoordinateSystem);
+  void SetTestPosition(MVector TestPosition, MCoordinateSystem CoordinateSystem);
 
   //! If this is set we try to optimize the binning
   //! Especially if we have too many bins we iterate until we have at least 50 counts in one bin - if possible
@@ -98,9 +98,9 @@ class MARMFitter
   //! Reset the internally stored ARM values
   void Reset();
 
-  //! Add Event - only stores the actual ARM value
+  //! Add Event - only stores the actual ARM value - do not do any prior ARM selections
   void AddEvent(MComptonEvent* Event);
-  //! Add an ARM value
+  //! Add an ARM value - do not do any prior ARM selections
   void AddARMValue(double ARMValue) { m_OriginalARMValues.push_back(ARMValue); }
 
   //! Load the ARM value from file
@@ -132,13 +132,22 @@ class MARMFitter
   double GetAverageFWHMUncertainty() const;
 
   //! Return the 50.0% containment for events with +- maximum ARM value or g_DoubleNotDefined if fit was not successful or not done yet
-  double Get50p0PercentContainment() const;
+  double Get50p0PercentContainmentUsingARMSelection() const;
   //! Return the 68.3% containment for events with +- maximum ARM value or g_DoubleNotDefined if fit was not successful or not done yet
-  double Get68p3PercentContainment() const;
+  double Get68p3PercentContainmentUsingARMSelection() const;
   //! Return the 95.5% containment for events with +- maximum ARM value or g_DoubleNotDefined if fit was not successful or not done yet
-  double Get95p5PercentContainment() const;
+  double Get95p5PercentContainmentUsingARMSelection() const;
   //! Return the 99.7% containment for events with +- maximum ARM value or g_DoubleNotDefined if fit was not successful or not done yet
-  double Get99p7PercentContainment() const;
+  double Get99p7PercentContainmentUsingARMSelection() const;
+
+  //! Return the 50.0% containment using all data or g_DoubleNotDefined if fit was not successful or not done yet
+  double Get50p0PercentContainmentUsingAllData() const;
+  //! Return the 68.3% containment using all data or g_DoubleNotDefined if fit was not successful or not done yet
+  double Get68p3PercentContainmentUsingAllData() const;
+  //! Return the 95.5% containment using all data or g_DoubleNotDefined if fit was not successful or not done yet
+  double Get95p5PercentContainmentUsingAllData() const;
+  //! Return the 99.7% containment using all data or g_DoubleNotDefined if fit was not successful or not done yet
+  double Get99p7PercentContainmentUsingAllData() const;
 
   //! Return a summary string
   MString ToString();
@@ -264,13 +273,22 @@ class MARMFitter
   vector<double> m_FinalFitParameters;
 
   //! The 50% containment radius within the ARM window (accurate to the next largest value in the data set)
-  double m_Containment50Percent;
+  double m_Containment50PercentUsingARMSelection;
   //! The 1-sigmna containment radius within the ARM window (accurate to the next largest value in the data set)
-  double m_Containment1Sigma;
+  double m_Containment1SigmaUsingARMSelection;
   //! The 2-sigma containment radius within the ARM window (accurate to the next largest value in the data set)
-  double m_Containment2Sigma;
+  double m_Containment2SigmaUsingARMSelection;
   //! The 3-sigma containment radius within the ARM window (accurate to the next largest value in the data set)
-  double m_Containment3Sigma;
+  double m_Containment3SigmaUsingARMSelection;
+
+  //! The 50% containment radius using all data (accurate to the next largest value in the data set)
+  double m_Containment50PercentUsingAllData;
+  //! The 1-sigmna containment radius using all data (accurate to the next largest value in the data set)
+  double m_Containment1SigmaUsingAllData;
+  //! The 2-sigma containment radius using all data (accurate to the next largest value in the data set)
+  double m_Containment2SigmaUsingAllData;
+  //! The 3-sigma containment radius using all data (accurate to the next largest value in the data set)
+  double m_Containment3SigmaUsingAllData;
 
   //! Minimum height for fitting
   double m_MinHeight;
diff --git a/src/mimrec/inc/MGUIARMExtended.h b/src/mimrec/inc/MGUIARMExtended.h
new file mode 100644
index 000000000..4f5014049
--- /dev/null
+++ b/src/mimrec/inc/MGUIARMExtended.h
@@ -0,0 +1,100 @@
+/*
+ * MGUIARMExtended.h
+ *
+ * Copyright (C) by Andreas Zoglauer.
+ * All rights reserved.
+ *
+ * Please see the source-file for the copyright-notice.
+ *
+ */
+
+
+#ifndef __MGUIARMExtended__
+#define __MGUIARMExtended__
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+// ROOT libs:
+#include <TApplication.h>
+#include <TGButton.h>
+#include <TGFrame.h>
+#include <TGLabel.h>
+#include <TGTextBuffer.h>
+#include <TGTextEntry.h>
+
+// MEGAlib libs:
+#include "MGlobal.h"
+#include "MGUIDialog.h"
+#include "MSettingsMimrec.h"
+#include "MGUIEEntry.h"
+
+// Forward declarations:
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+//! The position selection dialog box called by all interfaces which allow
+//! this selection
+//! It has 3 modes: ARM Gamma, ARM Electron, Spectrum
+//! This window will wait for being unmapped and not be deleted on close
+class MGUIARMExtended : public MGUIDialog
+{
+  // Public Interface:
+ public:
+  //! Standard constructor
+  MGUIARMExtended(const TGWindow* Parent, const TGWindow* Main, MSettingsMimrec* Data, bool& OkPressed);
+  //! Default destructor
+  virtual ~MGUIARMExtended();
+
+  // protected methods:
+ protected:
+  virtual void Create();
+  virtual bool ProcessMessage(long Message, long Parameter1, long Parameter2);
+  virtual bool OnApply();
+
+
+  // private methods:
+ private:
+
+
+  // protected members:
+ protected:
+
+
+  // private members:
+ private:
+  //! The user settings data
+  MSettingsMimrec* m_Settings;
+
+
+  //! The return message that OK was pressed
+  bool& m_OkPressed;
+
+  //! Check button indicating if we do want to use a test position in spectral mode
+  TGCheckButton* m_UseTestPosition;
+  const int m_UseTestPositionID = 140;
+
+  //! Check button indicating if we do want to use a logarithmic binning in spectral mode
+  TGCheckButton* m_UseLog;
+  const int m_UseLogID = 141;
+  
+  MGUIEEntry* m_ThetaIsX;
+  MGUIEEntry* m_PhiIsY;
+  MGUIEEntry* m_RadiusIsZ;
+  MGUIEEntry* m_Distance;
+  MGUIEEntry* m_Bins;
+
+  
+#ifdef ___CLING___
+ public:
+  ClassDef(MGUIARMExtended, 0) // Dialogbox: Select the ARM-parameters
+#endif
+
+};
+
+#endif
+
+
+////////////////////////////////////////////////////////////////////////////////
diff --git a/src/mimrec/src/MARMFitter.cxx b/src/mimrec/src/MARMFitter.cxx
index e7ab50235..a7a75e694 100644
--- a/src/mimrec/src/MARMFitter.cxx
+++ b/src/mimrec/src/MARMFitter.cxx
@@ -169,10 +169,15 @@ void MARMFitter::Reset()
   m_FinalBakerCousins = g_DoubleNotDefined;
   m_FinalBakerCousinsUncertainty = g_DoubleNotDefined;
 
-  m_Containment50Percent = g_DoubleNotDefined;
-  m_Containment1Sigma = g_DoubleNotDefined;
-  m_Containment2Sigma = g_DoubleNotDefined;
-  m_Containment3Sigma = g_DoubleNotDefined;
+  m_Containment50PercentUsingARMSelection = g_DoubleNotDefined;
+  m_Containment1SigmaUsingARMSelection = g_DoubleNotDefined;
+  m_Containment2SigmaUsingARMSelection = g_DoubleNotDefined;
+  m_Containment3SigmaUsingARMSelection = g_DoubleNotDefined;
+
+  m_Containment50PercentUsingAllData = g_DoubleNotDefined;
+  m_Containment1SigmaUsingAllData = g_DoubleNotDefined;
+  m_Containment2SigmaUsingAllData = g_DoubleNotDefined;
+  m_Containment3SigmaUsingAllData = g_DoubleNotDefined;
 }
 
 
@@ -972,37 +977,67 @@ void MARMFitter::CalculateARMMetrics()
   // Determine containment radii
 
   double Sigma0 = 0.5;
-  m_Containment50Percent = g_DoubleNotDefined;
   double Sigma1 = 0.6826;
-  m_Containment1Sigma = g_DoubleNotDefined;
   double Sigma2 = 0.9546;
-  m_Containment2Sigma = g_DoubleNotDefined;
   double Sigma3 = 0.9973;
-  m_Containment3Sigma = g_DoubleNotDefined;
 
-  vector<double> SortedAbs;
+  m_Containment50PercentUsingARMSelection = g_DoubleNotDefined;
+  m_Containment1SigmaUsingARMSelection = g_DoubleNotDefined;
+  m_Containment2SigmaUsingARMSelection = g_DoubleNotDefined;
+  m_Containment3SigmaUsingARMSelection = g_DoubleNotDefined;
+
+  vector<double> SortedAbsSelected;
   for (double& A: m_OriginalARMValues) {
     if (A >= -m_MaxARMValue && A <= m_MaxARMValue) {
-      SortedAbs.push_back(fabs(A));
+      SortedAbsSelected.push_back(fabs(A));
     }
   }
-  std::sort(SortedAbs.begin(), SortedAbs.end());
+  std::sort(SortedAbsSelected.begin(), SortedAbsSelected.end());
 
-  double Total = SortedAbs.size();
-  for (int b = 0; b < SortedAbs.size(); ++b) {
-    if (m_Containment50Percent == g_DoubleNotDefined && b >= Sigma0*Total) {
-      m_Containment50Percent = SortedAbs[b];
+  double Total = SortedAbsSelected.size();
+  for (int b = 0; b < SortedAbsSelected.size(); ++b) {
+    if (m_Containment50PercentUsingARMSelection == g_DoubleNotDefined && b >= Sigma0*Total) {
+      m_Containment50PercentUsingARMSelection = SortedAbsSelected[b];
     }
-    if (m_Containment1Sigma == g_DoubleNotDefined && b >= Sigma1*Total) {
-      m_Containment1Sigma = SortedAbs[b];
+    if (m_Containment1SigmaUsingARMSelection == g_DoubleNotDefined && b >= Sigma1*Total) {
+      m_Containment1SigmaUsingARMSelection = SortedAbsSelected[b];
     }
-    if (m_Containment2Sigma == g_DoubleNotDefined && b >= Sigma2*Total) {
-      m_Containment2Sigma = SortedAbs[b];
+    if (m_Containment2SigmaUsingARMSelection == g_DoubleNotDefined && b >= Sigma2*Total) {
+      m_Containment2SigmaUsingARMSelection = SortedAbsSelected[b];
     }
-    if (m_Containment3Sigma == g_DoubleNotDefined && b >= Sigma3*Total) {
-      m_Containment3Sigma = SortedAbs[b];
+    if (m_Containment3SigmaUsingARMSelection == g_DoubleNotDefined && b >= Sigma3*Total) {
+      m_Containment3SigmaUsingARMSelection = SortedAbsSelected[b];
     }
   }
+
+
+  m_Containment50PercentUsingAllData = g_DoubleNotDefined;
+  m_Containment1SigmaUsingAllData = g_DoubleNotDefined;
+  m_Containment2SigmaUsingAllData = g_DoubleNotDefined;
+  m_Containment3SigmaUsingAllData = g_DoubleNotDefined;
+
+  vector<double> SortedAbsAll;
+  for (double& A: m_OriginalARMValues) {
+    SortedAbsAll.push_back(fabs(A));
+  }
+  std::sort(SortedAbsAll.begin(), SortedAbsAll.end());
+
+  Total = SortedAbsAll.size();
+  for (int b = 0; b < SortedAbsAll.size(); ++b) {
+    if (m_Containment50PercentUsingAllData == g_DoubleNotDefined && b >= Sigma0*Total) {
+      m_Containment50PercentUsingAllData = SortedAbsAll[b];
+    }
+    if (m_Containment1SigmaUsingAllData == g_DoubleNotDefined && b >= Sigma1*Total) {
+      m_Containment1SigmaUsingAllData = SortedAbsAll[b];
+    }
+    if (m_Containment2SigmaUsingAllData == g_DoubleNotDefined && b >= Sigma2*Total) {
+      m_Containment2SigmaUsingAllData = SortedAbsAll[b];
+    }
+    if (m_Containment3SigmaUsingAllData == g_DoubleNotDefined && b >= Sigma3*Total) {
+      m_Containment3SigmaUsingAllData = SortedAbsAll[b];
+    }
+  }
+
 }
 
 
@@ -1127,13 +1162,14 @@ double MARMFitter::GetAverageFWHMUncertainty() const
 }
 
 
+
 ////////////////////////////////////////////////////////////////////////////////
 
 
 //! Return the 50.0% containment for events with +- maximum ARM value
-double MARMFitter::Get50p0PercentContainment() const
+double MARMFitter::Get50p0PercentContainmentUsingARMSelection() const
 {
-  return m_FitSuccessful ? m_Containment50Percent : g_DoubleNotDefined;
+  return m_FitSuccessful ? m_Containment50PercentUsingARMSelection : g_DoubleNotDefined;
 }
 
 
@@ -1141,9 +1177,9 @@ double MARMFitter::Get50p0PercentContainment() const
 
 
 //! Return the 68.3% containment for events with +- maximum ARM value
-double MARMFitter::Get68p3PercentContainment() const
+double MARMFitter::Get68p3PercentContainmentUsingARMSelection() const
 {
-  return m_FitSuccessful ? m_Containment1Sigma : g_DoubleNotDefined;
+  return m_FitSuccessful ? m_Containment1SigmaUsingARMSelection : g_DoubleNotDefined;
 }
 
 
@@ -1151,9 +1187,9 @@ double MARMFitter::Get68p3PercentContainment() const
 
 
 //! Return the 95.5% containment for events with +- maximum ARM value
-double MARMFitter::Get95p5PercentContainment() const
+double MARMFitter::Get95p5PercentContainmentUsingARMSelection() const
 {
-  return m_FitSuccessful ? m_Containment2Sigma : g_DoubleNotDefined;
+  return m_FitSuccessful ? m_Containment2SigmaUsingARMSelection : g_DoubleNotDefined;
 }
 
 
@@ -1161,9 +1197,49 @@ double MARMFitter::Get95p5PercentContainment() const
 
 
 //! Return the 99.7% containment for events with +- maximum ARM value
-double MARMFitter::Get99p7PercentContainment() const
+double MARMFitter::Get99p7PercentContainmentUsingARMSelection() const
+{
+  return m_FitSuccessful ? m_Containment3SigmaUsingARMSelection : g_DoubleNotDefined;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Return the 50.0% containment for all events
+double MARMFitter::Get50p0PercentContainmentUsingAllData() const
+{
+  return m_FitSuccessful ? m_Containment50PercentUsingAllData : g_DoubleNotDefined;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Return the 68.3% containment for all events
+double MARMFitter::Get68p3PercentContainmentUsingAllData() const
+{
+  return m_FitSuccessful ? m_Containment1SigmaUsingAllData : g_DoubleNotDefined;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Return the 95.5% containment for all events
+double MARMFitter::Get95p5PercentContainmentUsingAllData() const
+{
+  return m_FitSuccessful ? m_Containment2SigmaUsingAllData : g_DoubleNotDefined;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Return the 99.7% containment for all events
+double MARMFitter::Get99p7PercentContainmentUsingAllData() const
 {
-  return m_FitSuccessful ? m_Containment3Sigma : g_DoubleNotDefined;
+  return m_FitSuccessful ? m_Containment3SigmaUsingAllData : g_DoubleNotDefined;
 }
 
 
@@ -1198,11 +1274,17 @@ MString MARMFitter::ToString()
   out<<"  Fit function: "<<GetARMFitFunctionName(m_ARMFitFunction)<<endl;
   out<<"  Average FWHM after "<<m_BootStrappedFWHMSamples.size()<<" boot straps: "<<MString(m_FinalFWHM, m_FinalFWHMUncertainty, "degree")<<endl;
   out<<endl;
-  out<<"Containment (with +- "<<m_MaxARMValue<<" deg):"<<endl;
-  out<<"  50.0 %: "<<m_Containment50Percent<<" deg"<<endl;
-  out<<"  68.3 %: "<<m_Containment1Sigma<<" deg"<<endl;
-  out<<"  95.5 %: "<<m_Containment2Sigma<<" deg"<<endl;
-  out<<"  99.7 %: "<<m_Containment3Sigma<<" deg"<<endl;
+  out<<"Containment:"<<endl;
+  out<<"  using +- "<<m_MaxARMValue<<" deg ARM selection:"<<endl;
+  out<<"    50.0 %:\t"<<m_Containment50PercentUsingARMSelection<<" deg"<<endl;
+  out<<"    68.3 %:\t"<<m_Containment1SigmaUsingARMSelection<<" deg"<<endl;
+  out<<"    95.5 %:\t"<<m_Containment2SigmaUsingARMSelection<<" deg"<<endl;
+  out<<"    99.7 %:\t"<<m_Containment3SigmaUsingARMSelection<<" deg"<<endl;
+  out<<"  using all data:"<<endl;
+  out<<"    50.0 %:\t"<<m_Containment50PercentUsingAllData<<" deg"<<endl;
+  out<<"    68.3 %:\t"<<m_Containment1SigmaUsingAllData<<" deg"<<endl;
+  out<<"    95.5 %:\t"<<m_Containment2SigmaUsingAllData<<" deg"<<endl;
+  out<<"    99.7 %:\t"<<m_Containment3SigmaUsingAllData<<" deg"<<endl;
   out<<endl;
 
   return out;
diff --git a/src/mimrec/src/MGUIARMExtended.cxx b/src/mimrec/src/MGUIARMExtended.cxx
new file mode 100644
index 000000000..e1bb09859
--- /dev/null
+++ b/src/mimrec/src/MGUIARMExtended.cxx
@@ -0,0 +1,224 @@
+/*
+ * MGUIARMExtended.cxx
+ *
+ *
+ * Copyright (C) by Andreas Zoglauer.
+ * All rights reserved.
+ *
+ *
+ * This code implementation is the intellectual property of
+ * Andreas Zoglauer.
+ *
+ * By copying, distributing or modifying the Program (or any work
+ * based on the Program) you indicate your acceptance of this statement,
+ * and all its terms.
+ *
+ */
+
+
+////////////////////////////////////////////////////////////////////////////////
+//
+// MGUIARMExtended
+//
+//
+// Dialog box, which provides entry-boxes for ARM-parameter (theta, phi, radius)
+//
+////////////////////////////////////////////////////////////////////////////////
+
+
+// Include the header:
+#include "MGUIARMExtended.h"
+
+// Standard libs:
+
+// ROOT libs:
+
+// MEGAlib libs:
+#include "MCoordinateSystem.h"
+#include "MGUIEEntry.h"
+#include "MGUIDefaults.h"
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+#ifdef ___CLING___
+ClassImp(MGUIARMExtended)
+#endif
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+MGUIARMExtended::MGUIARMExtended(const TGWindow* p, const TGWindow* main, MSettingsMimrec* Data, bool& OkPressed)
+  : MGUIDialog(p, main), m_OkPressed(OkPressed)
+{
+  // standard constructor
+
+  m_Settings = Data;
+  m_OkPressed = false;
+  
+  m_UseTestPosition = nullptr;  
+  
+  m_ThetaIsX = nullptr;
+  m_PhiIsY = nullptr;
+  m_RadiusIsZ = nullptr;
+  m_Distance = nullptr;
+  
+  // use hierarchical cleaning
+  SetCleanup(kDeepCleanup);
+
+  Create();
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+MGUIARMExtended::~MGUIARMExtended()
+{
+  // standard destructor --- deep clean up activated!
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+void MGUIARMExtended::Create()
+{
+  // Create the main window
+
+  double Scaler = MGUIDefaults::GetInstance()->GetFontScaler();
+  
+  SetWindowName("Angular Resolution Measure");
+  AddSubTitle("Choose the fitting and histogram binning options for creating the\nAngular Resolution Measure (ARM) for Compton events");
+
+
+  TGLabel* TestPositionLabel = new TGLabel(this, "Choose the source location and the ARM acceptance window:");
+  TGLayoutHints* TestPositionLayout = new TGLayoutHints(kLHintsLeft | kLHintsTop, 50*Scaler, 50*Scaler, 10*Scaler, 2*Scaler);
+  AddFrame(TestPositionLabel, TestPositionLayout);
+    
+  TGLayoutHints* SelectorLayout = new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, 50*Scaler, 50*Scaler, 2*Scaler, 2*Scaler);
+  TGLayoutHints* SelectorSubLayout = new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, (50+20)*Scaler, 50*Scaler, 2*Scaler, 2*Scaler);
+ 
+  if (m_Settings->GetCoordinateSystem() == MCoordinateSystem::c_Spheric) {
+    
+    m_ThetaIsX = new MGUIEEntry(this, "Theta (0 - 180 deg):", false, m_Settings->GetTPTheta());
+    AddFrame(m_ThetaIsX, SelectorSubLayout);
+    m_PhiIsY = new MGUIEEntry(this, "Phi (-180 - 360 deg):", false, m_Settings->GetTPPhi());
+    AddFrame(m_PhiIsY, SelectorSubLayout);
+
+    
+  } else if (m_Settings->GetCoordinateSystem() == MCoordinateSystem::c_Galactic) {
+    
+    m_ThetaIsX = new MGUIEEntry(this, "Latitude (-90 - 90 deg):", false, m_Settings->GetTPGalLatitude());
+    AddFrame(m_ThetaIsX, SelectorSubLayout);
+    m_PhiIsY = new MGUIEEntry(this, "Longitude (0 - 360 deg):", false, m_Settings->GetTPGalLongitude());
+    AddFrame(m_PhiIsY, SelectorSubLayout);
+
+    
+  } else if (m_Settings->GetCoordinateSystem() == MCoordinateSystem::c_Cartesian2D ||
+             m_Settings->GetCoordinateSystem() == MCoordinateSystem::c_Cartesian3D) {
+
+    m_ThetaIsX = new MGUIEEntry(this, "x [cm]:", false, m_Settings->GetTPX());
+    AddFrame(m_ThetaIsX, SelectorSubLayout);
+    m_PhiIsY = new MGUIEEntry(this, "y [cm]:", false, m_Settings->GetTPY());
+    AddFrame(m_PhiIsY, SelectorSubLayout);
+    m_RadiusIsZ = new MGUIEEntry(this, "z [cm]:", false, m_Settings->GetTPZ());
+    AddFrame(m_RadiusIsZ, SelectorSubLayout);
+
+  }
+
+  m_Distance = new MGUIEEntry(this, "Acceptance radius (0 - 180 deg):", false, m_Settings->GetTPDistanceTrans());
+  AddFrame(m_Distance, SelectorSubLayout);
+  
+  // All histogram types have the number of bins
+  m_Bins = new MGUIEEntry(this, "Number of bins in histogram (odd numbers preferred):", false, m_Settings->GetHistBinsARMGamma());
+  TGLayoutHints* BinsLayout = new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, 50*Scaler, 50*Scaler, 10*Scaler, 2*Scaler);
+  AddFrame(m_Bins, BinsLayout);
+
+
+
+
+  AddButtons();
+  
+  // Let's resize and position the window, 
+  PositionWindow(GetDefaultWidth(), GetDefaultHeight(), false);
+  
+  // and bring it to the screen.
+  MapSubwindows();
+  MapWindow();  
+  Layout();
+
+  fClient->WaitFor(this);
+ 
+  return;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MGUIARMExtended::ProcessMessage(long Message, long Parameter1,
+                                        long Parameter2)
+{
+  // Process the messages for this application
+  
+  return MGUIDialog::ProcessMessage(Message, Parameter1, Parameter2);
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MGUIARMExtended::OnApply()
+{
+  // First test the data (m_RadiusIsZ has not to be checked!)
+  if (m_Settings->GetCoordinateSystem() == MCoordinateSystem::c_Spheric) {
+    if (m_ThetaIsX->IsDouble(0, 180) == false || 
+        m_PhiIsY->IsDouble(-360, 360) == false || 
+        m_Distance->IsDouble(-180, 180) == false) {
+      return false;
+    }
+  } else if (m_Settings->GetCoordinateSystem() == MCoordinateSystem::c_Galactic) {
+    if (m_ThetaIsX->IsDouble(-90, 90) == false || 
+        m_PhiIsY->IsDouble(-360, 360) == false || 
+        m_Distance->IsDouble(-180, 180) == false) {
+      return false;
+    }
+  } else if (m_Settings->GetCoordinateSystem() == MCoordinateSystem::c_Cartesian2D ||
+             m_Settings->GetCoordinateSystem() == MCoordinateSystem::c_Cartesian3D) {
+    if (m_Distance->IsDouble(-180, 180) == false) {
+      return false;
+    }
+  }
+  
+  if (m_UseTestPosition != nullptr) {
+    m_Settings->SetTPUse(m_UseTestPosition->GetState() == kButtonDown ? true : false);
+  }
+  
+  // Otherwise update the data:
+  if (m_Settings->GetCoordinateSystem() == MCoordinateSystem::c_Spheric) {
+    m_Settings->SetTPTheta(m_ThetaIsX->GetAsDouble());
+    m_Settings->SetTPPhi(m_PhiIsY->GetAsDouble());
+  } else if (m_Settings->GetCoordinateSystem() == MCoordinateSystem::c_Galactic) {
+    m_Settings->SetTPGalLatitude(m_ThetaIsX->GetAsDouble());
+    m_Settings->SetTPGalLongitude(m_PhiIsY->GetAsDouble());
+  } else if (m_Settings->GetCoordinateSystem() == MCoordinateSystem::c_Cartesian2D ||
+             m_Settings->GetCoordinateSystem() == MCoordinateSystem::c_Cartesian3D) {
+    m_Settings->SetTPX(m_ThetaIsX->GetAsDouble());
+    m_Settings->SetTPY(m_PhiIsY->GetAsDouble());
+    m_Settings->SetTPZ(m_RadiusIsZ->GetAsDouble());
+  }
+
+  m_Settings->SetTPDistanceTrans(m_Distance->GetAsDouble());
+  m_Settings->SetHistBinsARMGamma(m_Bins->GetAsInt());
+  
+  m_OkPressed = true;
+  
+  return true;
+}
+
+
+// MGUIARMExtended: the end...
+////////////////////////////////////////////////////////////////////////////////
diff --git a/src/mimrec/src/MGUIMimrecMain.cxx b/src/mimrec/src/MGUIMimrecMain.cxx
index a6e1e4349..e4ac6ba75 100644
--- a/src/mimrec/src/MGUIMimrecMain.cxx
+++ b/src/mimrec/src/MGUIMimrecMain.cxx
@@ -40,6 +40,7 @@
 #include "MGUIResponseParameterConeShapes.h"
 #include "MGUIResponseParameterPRM.h"
 #include "MGUIARM.h"
+#include "MGUIARMExtended.h"
 #include "MGUISignificance.h"
 #include "MGUIExposure.h"
 #include "MGUIAnimation.h"
@@ -425,7 +426,7 @@ bool MGUIMimrecMain::ProcessMessage(long Message, long Parameter1,
         break;
         
       case c_ResponseArmGamma:
-        new MGUIARM(gClient->GetRoot(), this, m_Data, MGUIARMModes::m_ARMGamma, OKPressed);
+        new MGUIARMExtended(gClient->GetRoot(), this, m_Data, OKPressed);
         if (OKPressed == true) {
           m_Interface->ARMGamma();
         }

From 1e318921dd16b9f1859177601152aa64e9cdb4f3 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Tue, 3 Sep 2024 14:44:00 -0700
Subject: [PATCH 062/192] CHG: Improved ARM GUI

---
 src/mimrec/inc/MARMFitter.h         |  26 +++--
 src/mimrec/inc/MGUIARMExtended.h    |  18 +++-
 src/mimrec/inc/MSettingsMimrec.h    |  18 ++++
 src/mimrec/src/MARMFitter.cxx       |  81 ++++++++++++----
 src/mimrec/src/MGUIARMExtended.cxx  | 142 ++++++++++++++++++++++------
 src/mimrec/src/MInterfaceMimrec.cxx |  10 +-
 src/mimrec/src/MSettingsMimrec.cxx  |  28 +++++-
 7 files changed, 257 insertions(+), 66 deletions(-)

diff --git a/src/mimrec/inc/MARMFitter.h b/src/mimrec/inc/MARMFitter.h
index a8a28fa3f..0b25299b1 100644
--- a/src/mimrec/inc/MARMFitter.h
+++ b/src/mimrec/inc/MARMFitter.h
@@ -88,11 +88,19 @@ class MARMFitter
   //! If this is set we use an unbinned-likelihood fit
   void UseBinnedFitting(bool DoIt = true) { m_UnbinnedFitting = !DoIt; }
 
+  //! Get a list of all fit functions:
+  vector<MARMFitFunctionID> GetListOfFitFunctions() const;
+
   //! Fit this function to the data
-  //! One of: c_Gauss, c_Lorentz, c_GaussLorentz, c_GaussDoubleLorentz, c_AsymmetricGaussDoubleLorentz
-  //! If not set,  default is c_AsymmetricGaussDoubleLorentz
+  //! One of: c_Gauss, c_Lorentz, c_GaussLorentz, c_GaussDoubleLorentz, c_AsymmetricGaussLorentzLorentz, etc.
+  //! If not set,  default is c_AsymmetricGaussLorentzLorentz
   void SetFitFunction(MARMFitFunctionID ID) { m_ARMFitFunction = ID; }
 
+  //! Fit this function to the data
+  //! The ID corresponds to the position of the corresponding MARMFitFunctionID in the vector retuned by GetListOfFitFunctions()
+  //! If it's not in there use c_AsymmetricGaussLorentzLorentz
+  void SetFitFunction(unsigned int ID);
+
   // Interface to set the data
 
   //! Reset the internally stored ARM values
@@ -159,6 +167,14 @@ class MARMFitter
   //! Canvas->Update();
   void Draw();
 
+  //! Return the function of the fit given the fit function ID
+  MString GetARMFitFunction(MARMFitFunctionID ARMFitID);
+  //! Return the name of the fit given the fit function ID
+  MString GetARMFitFunctionName(MARMFitFunctionID ARMFitID);
+  //! Return the number of parameters of the fit given the fit function ID
+  unsigned int GetARMFitFunctionNumberOfParameters(MARMFitFunctionID ARMFitID);
+
+
 
 
   // protected methods:
@@ -197,12 +213,6 @@ class MARMFitter
   //! Setup an Assymetric-Gauss-Double-Lorentz-function
   void SetupARMFitAsymmetricGeneralizedNormalGeneralizedNormalGeneralizedNormal(ROOT::Fit::Fitter& Fitter, TF1** FitFunction);
 
-  //! Return the function of the fit given the fit function ID
-  MString GetARMFitFunction(MARMFitFunctionID ARMFitID);
-  //! Return the name of the fit given the fit function ID
-  MString GetARMFitFunctionName(MARMFitFunctionID ARMFitID);
-  //! Return the number of parameters of the fit given the fit function ID
-  unsigned int GetARMFitFunctionNumberOfParameters(MARMFitFunctionID ARMFitID);
 
   // private methods:
  private:
diff --git a/src/mimrec/inc/MGUIARMExtended.h b/src/mimrec/inc/MGUIARMExtended.h
index 4f5014049..1dc7cb598 100644
--- a/src/mimrec/inc/MGUIARMExtended.h
+++ b/src/mimrec/inc/MGUIARMExtended.h
@@ -23,6 +23,7 @@
 #include <TGLabel.h>
 #include <TGTextBuffer.h>
 #include <TGTextEntry.h>
+#include <TGComboBox.h>
 
 // MEGAlib libs:
 #include "MGlobal.h"
@@ -73,12 +74,12 @@ class MGUIARMExtended : public MGUIDialog
   bool& m_OkPressed;
 
   //! Check button indicating if we do want to use a test position in spectral mode
-  TGCheckButton* m_UseTestPosition;
-  const int m_UseTestPositionID = 140;
+  MGUIEEntry* m_NumberOfFits;
+  //const int m_NumberOfFitsID = 140;
 
   //! Check button indicating if we do want to use a logarithmic binning in spectral mode
-  TGCheckButton* m_UseLog;
-  const int m_UseLogID = 141;
+  TGCheckButton* m_OptimizedBinning;
+  const int m_OptimizedBinningID = 141;
   
   MGUIEEntry* m_ThetaIsX;
   MGUIEEntry* m_PhiIsY;
@@ -86,7 +87,14 @@ class MGUIARMExtended : public MGUIDialog
   MGUIEEntry* m_Distance;
   MGUIEEntry* m_Bins;
 
-  
+  //! The fit function combo box
+  TGComboBox* m_FitFunctions;
+
+
+  //! Check button indicating if we do want to use a logarithmic binning in spectral mode
+  TGCheckButton* m_UseUnbinnedFitting;
+  const int m_UseUnbinnedFittingID = 142;
+
 #ifdef ___CLING___
  public:
   ClassDef(MGUIARMExtended, 0) // Dialogbox: Select the ARM-parameters
diff --git a/src/mimrec/inc/MSettingsMimrec.h b/src/mimrec/inc/MSettingsMimrec.h
index 5f17bbbc3..346ea067c 100644
--- a/src/mimrec/inc/MSettingsMimrec.h
+++ b/src/mimrec/inc/MSettingsMimrec.h
@@ -101,6 +101,18 @@ class MSettingsMimrec : public MSettings, public MSettingsEventSelections, publi
   int GetHistBinsPolarization() const { return m_HistBinsPolarization; }
   void SetHistBinsPolarization(int HistBinsPolarization) { m_HistBinsPolarization = HistBinsPolarization; } 
 
+  // Log binning
+  bool GetOptimizeBinningARMGamma() const { return m_OptimizeBinningARMGamma; }
+  void SetOptimizeBinningARMGamma(bool OptimizeBinningARMGamma) { m_OptimizeBinningARMGamma = OptimizeBinningARMGamma; }
+
+  unsigned int GetNumberOfFitsARMGamma() const { return m_NumberOfFitsARMGamma; }
+  void SetNumberOfFitsARMGamma(unsigned int NumberOfFitsARMGamma) { m_NumberOfFitsARMGamma = NumberOfFitsARMGamma; }
+
+  unsigned int GetFitFunctionIDARMGamma() const { return m_FitFunctionIDARMGamma; }
+  void SetFitFunctionIDARMGamma(unsigned int FitFunctionIDARMGamma) { m_FitFunctionIDARMGamma = FitFunctionIDARMGamma; }
+
+  bool GetUseUnbinnedFittingARMGamma() const { return m_UseUnbinnedFittingARMGamma; }
+  void SetUseUnbinnedFittingARMGamma(bool UseUnbinnedFittingARMGamma) { m_UseUnbinnedFittingARMGamma = UseUnbinnedFittingARMGamma; }
 
 
   // protected members:
@@ -136,6 +148,12 @@ class MSettingsMimrec : public MSettings, public MSettingsEventSelections, publi
   int m_HistBinsSpectrum;
   int m_HistBinsPolarization;
 
+  //
+  bool m_OptimizeBinningARMGamma;
+  unsigned int m_NumberOfFitsARMGamma;
+  unsigned int m_FitFunctionIDARMGamma;
+  bool m_UseUnbinnedFittingARMGamma;
+
   // Polarization:
   MString m_PolarizationBackgroundFileName;
   double m_PolarizationArmCut;
diff --git a/src/mimrec/src/MARMFitter.cxx b/src/mimrec/src/MARMFitter.cxx
index a7a75e694..4b3f1e0c2 100644
--- a/src/mimrec/src/MARMFitter.cxx
+++ b/src/mimrec/src/MARMFitter.cxx
@@ -153,6 +153,25 @@ void MARMFitter::SetTestPosition(MVector TestPosition, MCoordinateSystem Coordin
 ////////////////////////////////////////////////////////////////////////////////
 
 
+//! Fit this function to the data
+//! The ID corresponds to the position of the corresponding MARMFitFunctionID in the vector retuned by GetListOfFitFunctions()
+//! If it's not in there use c_AsymmetricGaussLorentzLorentz
+void MARMFitter::SetFitFunction(unsigned int ID)
+{
+  vector<MARMFitFunctionID> IDs = GetListOfFitFunctions();
+
+  if (ID < IDs.size()) {
+    m_ARMFitFunction = IDs[ID];
+  } else {
+    merr<<"There is no function with ID n"<<ID<<". Choosing assymmetric gauss + Lorentz + Lorentz"<<endl;
+    m_ARMFitFunction = MARMFitFunctionID::c_AsymmetricGaussLorentzLorentz;
+  }
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
 //! Reset the internally stored ARM values
 void MARMFitter::Reset()
 {
@@ -277,19 +296,19 @@ MString MARMFitter::GetARMFitFunctionName(MARMFitFunctionID ID)
   } else if (ID == MARMFitFunctionID::c_Lorentz) {
     return MString("Lorentz");
   } else if (ID == MARMFitFunctionID::c_GeneralizedNormal) {
-    return MString("GeneralizedNormal");
+    return MString("Generalized-Normal");
   } else if (ID == MARMFitFunctionID::c_GaussLorentz) {
-    return MString("Gauss+Lorentz");
+    return MString("Gauss + Lorentz");
   } else if (ID == MARMFitFunctionID::c_GaussLorentzLorentz) {
-    return MString("Gauss+Lorentz+Lorentz");
+    return MString("Gauss + Lorentz + Lorentz");
   } else if (ID == MARMFitFunctionID::c_AsymmetricGaussLorentzLorentz) {
-    return MString("AsymmetricGauss+Lorentz+Lorentz");
+    return MString("Asymmetric-Gauss + Lorentz + Lorentz");
   } else if (ID == MARMFitFunctionID::c_AsymmetricGaussGaussLorentzLorentz) {
-    return MString("AsymmetricGauss+Gauss+Lorentz+Lorentz");
+    return MString("Asymmetric-Gauss + Gauss + Lorentz + Lorentz");
   } else if (ID == MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormal) {
-    return MString("AsymmetricGeneralizedNormal+GeneralizedNormal");
+    return MString("Asymmetric-Generalized-Normal + Generalized-Normal");
   } else if (ID == MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormalGeneralizedNormal) {
-    return MString("AsymmetricGeneralizedNormal+GeneralizedNormal+GeneralizedNormal");
+    return MString("Asymmetric-Generalized-Normal + Generalized-Normal + Generalized-Normal");
   } else {
     new MExceptionObjectDoesNotExist("Unknown ARM fit function ID");
     return MString("Unknown ARM fit function ID");
@@ -363,6 +382,27 @@ unsigned int MARMFitter::GetARMFitFunctionNumberOfParameters(MARMFitFunctionID I
 ////////////////////////////////////////////////////////////////////////////////
 
 
+//! Get a list of all fit functions:
+vector<MARMFitFunctionID> MARMFitter::GetListOfFitFunctions() const
+{
+  vector<MARMFitFunctionID> List;
+  List.push_back(MARMFitFunctionID::c_Gauss);
+  List.push_back(MARMFitFunctionID::c_Lorentz);
+  List.push_back(MARMFitFunctionID::c_GeneralizedNormal);
+  List.push_back(MARMFitFunctionID::c_GaussLorentz);
+  List.push_back(MARMFitFunctionID::c_GaussLorentzLorentz);
+  List.push_back(MARMFitFunctionID::c_AsymmetricGaussLorentzLorentz);
+  List.push_back(MARMFitFunctionID::c_AsymmetricGaussGaussLorentzLorentz);
+  List.push_back(MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormal);
+  List.push_back(MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormalGeneralizedNormal);
+
+  return List;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
 //! Switch between the fit functions
 void MARMFitter::SetupARMFit(MARMFitFunctionID ARMFitID, ROOT::Fit::Fitter& Fitter, TF1** FitFunction)
 {
@@ -482,6 +522,7 @@ void MARMFitter::SetupARMFitGeneralizedNormal(ROOT::Fit::Fitter& Fitter, TF1** F
   Fitter.Config().SetUpdateAfterFit();
 }
 
+
 ////////////////////////////////////////////////////////////////////////////////
 
 
@@ -709,7 +750,7 @@ void MARMFitter::SetupARMFitAsymmetricGeneralizedNormalGeneralizedNormalGenerali
   //Fitter.Config().MinimizerOptions().SetPrintLevel(0);
   Fitter.SetFunction(WrappedFitFunction, false);
 
-  vector<double> Parameters = { 1, 0.5*(m_GuessMaximumLow+m_GuessMaximumHigh), m_GuessHeight, m_GuessWidth, m_GuessScale, m_GuessWidth, m_GuessHeight, m_GuessScale, m_GuessHeight, m_GuessWidth, m_GuessScale, m_GuessHeight, m_GuessWidth, m_GuessScale };
+  vector<double> Parameters = { 1, 0.5*(m_GuessMaximumLow+m_GuessMaximumHigh), m_GuessHeight, m_GuessWidth, m_GuessScale, m_GuessWidth, m_GuessScale, m_GuessHeight, m_GuessWidth, m_GuessScale, m_GuessHeight, m_GuessWidth, m_GuessScale };
   Fitter.Config().SetParamsSettings(Parameters.size(), Parameters.data());
 
   Fitter.Config().ParSettings(0).SetName("Offset");
@@ -1071,8 +1112,6 @@ void MARMFitter::ParallelFitting(int FitID, std::condition_variable& CV)
 //! Each fit samples randomly from the stored ARM values to determine the average width and error correctly
 bool MARMFitter::Fit(unsigned int NumberOfFits)
 {
-  if (NumberOfFits <= 0) return false;
-
   m_FitSuccessful = true;
 
   if (m_OptimizeBinning == true) {
@@ -1131,12 +1170,14 @@ bool MARMFitter::Fit(unsigned int NumberOfFits)
     for (thread& T: Threads) {
       T.join();
     }
-  } else {
+  } else if (NumberOfFits == 1) {
     PerformFit(0, m_OriginalARMValues);
   }
 
-  // Caluclate the results
-  CalculateBootStrappedMetrics();
+  if (NumberOfFits >= 1) {
+    // Caluclate the results
+    CalculateBootStrappedMetrics();
+  }
 
   return m_FitSuccessful;
 }
@@ -1270,9 +1311,17 @@ MString MARMFitter::ToString()
   out<<"  In selection (+- "<<m_MaxARMValue<<" deg): "<<SelectedEvents<<endl;
   out<<endl;
   out<<"Fit:"<<endl;
-  out<<"  Fit mode: "<<(m_UnbinnedFitting == true ? "Unbinned" : "Binned")<<" likelihood fit"<<endl;
-  out<<"  Fit function: "<<GetARMFitFunctionName(m_ARMFitFunction)<<endl;
-  out<<"  Average FWHM after "<<m_BootStrappedFWHMSamples.size()<<" boot straps: "<<MString(m_FinalFWHM, m_FinalFWHMUncertainty, "degree")<<endl;
+  if (m_BootStrappedFWHMSamples.size() > 0) {
+    out<<"  Fit mode: "<<(m_UnbinnedFitting == true ? "Unbinned" : "Binned")<<" likelihood fit"<<endl;
+    out<<"  Fit function: "<<GetARMFitFunctionName(m_ARMFitFunction)<<endl;
+    if (m_BootStrappedFWHMSamples.size() > 1) {
+      out<<"  Average FWHM after "<<m_BootStrappedFWHMSamples.size()<<" boot straps: "<<MString(m_FinalFWHM, m_FinalFWHMUncertainty, "degree")<<endl;
+    } else {
+      out<<"  FWHM after 1 fit: "<<m_FinalFWHM<<" degree"<<endl;
+    }
+  } else {
+    out<<"  No fits performed"<<endl;
+  }
   out<<endl;
   out<<"Containment:"<<endl;
   out<<"  using +- "<<m_MaxARMValue<<" deg ARM selection:"<<endl;
diff --git a/src/mimrec/src/MGUIARMExtended.cxx b/src/mimrec/src/MGUIARMExtended.cxx
index e1bb09859..527ef650e 100644
--- a/src/mimrec/src/MGUIARMExtended.cxx
+++ b/src/mimrec/src/MGUIARMExtended.cxx
@@ -34,6 +34,8 @@
 // ROOT libs:
 
 // MEGAlib libs:
+#include "MARMFitter.h"
+#include "MGUIEText.h"
 #include "MCoordinateSystem.h"
 #include "MGUIEEntry.h"
 #include "MGUIDefaults.h"
@@ -57,9 +59,7 @@ MGUIARMExtended::MGUIARMExtended(const TGWindow* p, const TGWindow* main, MSetti
 
   m_Settings = Data;
   m_OkPressed = false;
-  
-  m_UseTestPosition = nullptr;  
-  
+
   m_ThetaIsX = nullptr;
   m_PhiIsY = nullptr;
   m_RadiusIsZ = nullptr;
@@ -90,56 +90,132 @@ void MGUIARMExtended::Create()
 
   double Scaler = MGUIDefaults::GetInstance()->GetFontScaler();
   
+  double WrapLength = 600*Scaler;
+
   SetWindowName("Angular Resolution Measure");
-  AddSubTitle("Choose the fitting and histogram binning options for creating the\nAngular Resolution Measure (ARM) for Compton events");
+  AddSubTitle("Choose the source location, histogramming, and fitting options for creating the\nAngular Resolution Measure (ARM) for Compton events");
 
+  TGLayoutHints* SectionFirstLayout = new TGLayoutHints(kLHintsLeft | kLHintsTop, 50*Scaler, 50*Scaler, 2*Scaler, 2*Scaler);
+  TGLayoutHints* SectionTopLayout = new TGLayoutHints(kLHintsLeft | kLHintsTop, 50*Scaler, 50*Scaler, 30*Scaler, 2*Scaler);
+  TGLayoutHints* SectionLayout = new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, 50*Scaler, 50*Scaler, 2*Scaler, 2*Scaler);
 
-  TGLabel* TestPositionLabel = new TGLabel(this, "Choose the source location and the ARM acceptance window:");
-  TGLayoutHints* TestPositionLayout = new TGLayoutHints(kLHintsLeft | kLHintsTop, 50*Scaler, 50*Scaler, 10*Scaler, 2*Scaler);
-  AddFrame(TestPositionLabel, TestPositionLayout);
-    
-  TGLayoutHints* SelectorLayout = new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, 50*Scaler, 50*Scaler, 2*Scaler, 2*Scaler);
-  TGLayoutHints* SelectorSubLayout = new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, (50+20)*Scaler, 50*Scaler, 2*Scaler, 2*Scaler);
- 
+  TGLayoutHints* LeftLayout = new TGLayoutHints(kLHintsLeft | kLHintsTop, 0, 10*Scaler, 0, 0);
+  TGLayoutHints* RightLayout = new TGLayoutHints(kLHintsRight | kLHintsTop, 10*Scaler, 0, 0, 0);
+
+  MString TestPositionIntro;
   if (m_Settings->GetCoordinateSystem() == MCoordinateSystem::c_Spheric) {
-    
+    TestPositionIntro += "Source location in spheric coordinates:\n";
+  } else if (m_Settings->GetCoordinateSystem() == MCoordinateSystem::c_Galactic) {
+    TestPositionIntro += "Source location in Galactic coordinates:\n";
+  } else if (m_Settings->GetCoordinateSystem() == MCoordinateSystem::c_Cartesian2D ||
+             m_Settings->GetCoordinateSystem() == MCoordinateSystem::c_Cartesian3D) {
+    TestPositionIntro += "Source location in Cartesian coordinates:\n";
+  }
+  TestPositionIntro += "Change the coordiante system in the menu Selections -> Coordinate System:";
+  TGLabel* TestPositionLabel = new TGLabel(this, TestPositionIntro);
+  TestPositionLabel->SetWrapLength(WrapLength);
+  AddFrame(TestPositionLabel, SectionFirstLayout);
+
+  if (m_Settings->GetCoordinateSystem() == MCoordinateSystem::c_Spheric) {
+
     m_ThetaIsX = new MGUIEEntry(this, "Theta (0 - 180 deg):", false, m_Settings->GetTPTheta());
-    AddFrame(m_ThetaIsX, SelectorSubLayout);
+    AddFrame(m_ThetaIsX, SectionLayout);
     m_PhiIsY = new MGUIEEntry(this, "Phi (-180 - 360 deg):", false, m_Settings->GetTPPhi());
-    AddFrame(m_PhiIsY, SelectorSubLayout);
-
+    AddFrame(m_PhiIsY, SectionLayout);
     
   } else if (m_Settings->GetCoordinateSystem() == MCoordinateSystem::c_Galactic) {
     
     m_ThetaIsX = new MGUIEEntry(this, "Latitude (-90 - 90 deg):", false, m_Settings->GetTPGalLatitude());
-    AddFrame(m_ThetaIsX, SelectorSubLayout);
+    AddFrame(m_ThetaIsX, SectionLayout);
     m_PhiIsY = new MGUIEEntry(this, "Longitude (0 - 360 deg):", false, m_Settings->GetTPGalLongitude());
-    AddFrame(m_PhiIsY, SelectorSubLayout);
+    AddFrame(m_PhiIsY, SectionLayout);
 
-    
   } else if (m_Settings->GetCoordinateSystem() == MCoordinateSystem::c_Cartesian2D ||
              m_Settings->GetCoordinateSystem() == MCoordinateSystem::c_Cartesian3D) {
 
     m_ThetaIsX = new MGUIEEntry(this, "x [cm]:", false, m_Settings->GetTPX());
-    AddFrame(m_ThetaIsX, SelectorSubLayout);
+    AddFrame(m_ThetaIsX, SectionLayout);
     m_PhiIsY = new MGUIEEntry(this, "y [cm]:", false, m_Settings->GetTPY());
-    AddFrame(m_PhiIsY, SelectorSubLayout);
+    AddFrame(m_PhiIsY, SectionLayout);
     m_RadiusIsZ = new MGUIEEntry(this, "z [cm]:", false, m_Settings->GetTPZ());
-    AddFrame(m_RadiusIsZ, SelectorSubLayout);
+    AddFrame(m_RadiusIsZ, SectionLayout);
 
   }
 
-  m_Distance = new MGUIEEntry(this, "Acceptance radius (0 - 180 deg):", false, m_Settings->GetTPDistanceTrans());
-  AddFrame(m_Distance, SelectorSubLayout);
-  
+
+  // Fitting section:
+  MString HistogramIntro;
+  HistogramIntro += "Histogram options:";
+  TGLabel* HistogramIntroLabel = new TGLabel(this, HistogramIntro);
+  HistogramIntroLabel->SetWrapLength(WrapLength);
+  AddFrame(HistogramIntroLabel, SectionTopLayout);
+
+  m_Distance = new MGUIEEntry(this, "Maximum ARM value in histogram (0 - 180 deg):", false, m_Settings->GetTPDistanceTrans(), true, 0.0, 180.0);
+  AddFrame(m_Distance, SectionLayout);
+
   // All histogram types have the number of bins
-  m_Bins = new MGUIEEntry(this, "Number of bins in histogram (odd numbers preferred):", false, m_Settings->GetHistBinsARMGamma());
-  TGLayoutHints* BinsLayout = new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, 50*Scaler, 50*Scaler, 10*Scaler, 2*Scaler);
-  AddFrame(m_Bins, BinsLayout);
+  m_Bins = new MGUIEEntry(this, "Number of bins in histogram (odd numbers preferred):", false, m_Settings->GetHistBinsARMGamma(), true, 1);
+  AddFrame(m_Bins, SectionLayout);
 
+  m_OptimizedBinning = new TGCheckButton(this, "Optimize the binning, i.e., make bins larger until there are at least 50 counts in one bin if possible", m_OptimizedBinningID);
+  m_OptimizedBinning->Associate(this);
+  m_OptimizedBinning->SetState(m_Settings->GetOptimizeBinningARMGamma() ? kButtonDown : kButtonUp);
+  AddFrame(m_OptimizedBinning, SectionLayout);
 
 
 
+
+  // Fitting section:
+  MString FittingIntro;
+  FittingIntro += "Fitting options:\n";
+  FittingIntro += "Zero fits means only the ARM is created, one fit does exactly that, multiple fits calculates also the uncertainty of the FWHM from bootstrapping the data and re-fitting. Concerning the fit function, start with asymmetric Gauss + Lorentz + Lorentz.";
+  TGLabel* FittingIntroLabel = new TGLabel(this, FittingIntro);
+  FittingIntroLabel->SetWrapLength(WrapLength);
+  //FittingIntroLabel->ChangeOptions(FittingIntroLabel->GetOptions() | kRaisedFrame);
+  AddFrame(FittingIntroLabel, SectionTopLayout);
+
+  m_NumberOfFits = new MGUIEEntry(this, "Number of fits:", false, (int) m_Settings->GetNumberOfFitsARMGamma(), true, 0);
+  AddFrame(m_NumberOfFits, SectionLayout);
+
+  TGHorizontalFrame* FitFunctionFrame = new TGHorizontalFrame(this);
+  AddFrame(FitFunctionFrame, SectionLayout);
+
+  TGLabel* FitFunctionLabel = new TGLabel(FitFunctionFrame, "Fit function:");
+  FitFunctionFrame->AddFrame(FitFunctionLabel, LeftLayout);
+
+  MARMFitter Fitter;
+  vector<MARMFitFunctionID> FitFunctions = Fitter.GetListOfFitFunctions();
+
+  m_FitFunctions = new TGComboBox(FitFunctionFrame);
+  for (unsigned int f = 0; f < FitFunctions.size(); ++f) {
+    m_FitFunctions->AddEntry(Fitter.GetARMFitFunctionName(FitFunctions[f]), f);
+  }
+  m_FitFunctions->Select(m_Settings->GetFitFunctionIDARMGamma());
+  m_FitFunctions->Associate(this);
+  m_FitFunctions->SetHeight(Scaler*18);
+  m_FitFunctions->SetWidth(Scaler*475);
+  FitFunctionFrame->AddFrame(m_FitFunctions, RightLayout);
+
+  m_UseUnbinnedFitting = new TGCheckButton(this, "Use unbinned fitting. This works better for a lower number of counts, but is slower for a large number of counts.", m_UseUnbinnedFittingID);
+  m_UseUnbinnedFitting->SetWrapLength(WrapLength);
+  m_UseUnbinnedFitting->Associate(this);
+  m_UseUnbinnedFitting->SetState(m_Settings->GetUseUnbinnedFittingARMGamma() ? kButtonDown : kButtonUp);
+  AddFrame(m_UseUnbinnedFitting, SectionLayout);
+
+
+
+  MString ARMComment;
+  ARMComment += "Some comments on the ARM:\n";
+  ARMComment += "1. The ARM is the angular resolution of the detector, not of point sources in the final image. The angular resolution achieved in images depends on the ARM, the number of counts, and the imaging algorithm. It is also not a measure for the localization accuracy of a point source. This is a function of the number of counts in the core of the ARM. The ARM is also just a proxy for how good two close by point sources can be resolved. That depends on the shape of the ARM, the imaging algorithm, and the number of counts.\n";
+  ARMComment += "2. The ARM depends on the used event selections. Therefore, always quote the event selections when quoting an ARM. A typical event selection is to use a +-3 sigma cut on the (calibration) line you are using and then quoting the effective area calculated by using all events falling withing [-FWHM, +FWHM] of the ARM.\n";
+  ARMComment += "3. If you are fitting the ARM, the FWHM uncertainty is only reliable if the fit is OK. If the fit is not good, you will have an additional systematic uncertainty which is not included in the FWHM uncertainty. For a good fit, try to use an ARM window of 2-4 FWHM'es, and try to start with the asymmetric-gaussian + Lorentz + Lorentz fit function. If the fit still fails, make the ARM window smaller.";
+
+  TGLabel* ARMCommentsLabel = new TGLabel(this, ARMComment);
+  ARMCommentsLabel->SetWrapLength(WrapLength);
+  //ARMCommentsLabel->ChangeOptions(ARMCommentsLabel->GetOptions() | kRaisedFrame);
+  AddFrame(ARMCommentsLabel, SectionTopLayout);
+
+
   AddButtons();
   
   // Let's resize and position the window, 
@@ -193,10 +269,6 @@ bool MGUIARMExtended::OnApply()
     }
   }
   
-  if (m_UseTestPosition != nullptr) {
-    m_Settings->SetTPUse(m_UseTestPosition->GetState() == kButtonDown ? true : false);
-  }
-  
   // Otherwise update the data:
   if (m_Settings->GetCoordinateSystem() == MCoordinateSystem::c_Spheric) {
     m_Settings->SetTPTheta(m_ThetaIsX->GetAsDouble());
@@ -214,6 +286,14 @@ bool MGUIARMExtended::OnApply()
   m_Settings->SetTPDistanceTrans(m_Distance->GetAsDouble());
   m_Settings->SetHistBinsARMGamma(m_Bins->GetAsInt());
   
+  m_Settings->SetOptimizeBinningARMGamma(m_OptimizedBinning->GetState() == kButtonDown ? true : false);
+  m_Settings->SetNumberOfFitsARMGamma(m_NumberOfFits->GetAsInt());
+  m_Settings->SetFitFunctionIDARMGamma(m_FitFunctions->GetSelected());
+  m_Settings->SetUseUnbinnedFittingARMGamma(m_UseUnbinnedFitting->GetState() == kButtonDown ? true : false);
+
+
+
+
   m_OkPressed = true;
   
   return true;
diff --git a/src/mimrec/src/MInterfaceMimrec.cxx b/src/mimrec/src/MInterfaceMimrec.cxx
index e776eaeb4..eab35716e 100644
--- a/src/mimrec/src/MInterfaceMimrec.cxx
+++ b/src/mimrec/src/MInterfaceMimrec.cxx
@@ -1124,9 +1124,9 @@ void MInterfaceMimrec::ARMGamma()
   //Fitter.SetFitFunction(MARMFitFunctionID::c_GeneralizedNormal);
   //Fitter.SetFitFunction(MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormal);
   //Fitter.SetFitFunction(MARMFitFunctionID::c_AsymmetricGeneralizedNormalGeneralizedNormalGeneralizedNormal);
-  Fitter.SetFitFunction(MARMFitFunctionID::c_AsymmetricGaussLorentzLorentz);
-  Fitter.UseBinnedFitting(true);
-  Fitter.UseOptimizedBinning();
+  Fitter.SetFitFunction(m_Settings->GetFitFunctionIDARMGamma());
+  Fitter.UseBinnedFitting(!m_Settings->GetUseUnbinnedFittingARMGamma());
+  Fitter.UseOptimizedBinning(m_Settings->GetOptimizeBinningARMGamma());
 
   bool FoundEvents = false;
   MPhysicalEvent* Event = nullptr;
@@ -1146,7 +1146,7 @@ void MInterfaceMimrec::ARMGamma()
     delete Event;
   } 
   
-  Fitter.SaveARMValues("Data.dat");
+  //Fitter.SaveARMValues("Data.dat");
 
   // Close the event loader
   FinalizeEventLoader();
@@ -1155,7 +1155,7 @@ void MInterfaceMimrec::ARMGamma()
     mgui<<"No events passed the event selections."<<error;
   }
 
-  Fitter.Fit(100);
+  Fitter.Fit(m_Settings->GetNumberOfFitsARMGamma());
   //Fitter.FitAll();
 
   if (Fitter.WasFittingSuccessful() == true) {
diff --git a/src/mimrec/src/MSettingsMimrec.cxx b/src/mimrec/src/MSettingsMimrec.cxx
index 1d83f0f4b..7b8483888 100644
--- a/src/mimrec/src/MSettingsMimrec.cxx
+++ b/src/mimrec/src/MSettingsMimrec.cxx
@@ -80,6 +80,12 @@ MSettingsMimrec::MSettingsMimrec(bool AutoLoad) : MSettings("MimrecConfiguration
   m_HistBinsSpectrum = 200;
   m_HistBinsPolarization = 90;
 
+  // More options for the ARM
+  m_OptimizeBinningARMGamma = false;
+  m_NumberOfFitsARMGamma = 0;
+  m_FitFunctionIDARMGamma = 5;
+  m_UseUnbinnedFittingARMGamma = false;
+
   // Polarization
   m_PolarizationBackgroundFileName = "";
   m_PolarizationArmCut = 10;
@@ -147,6 +153,13 @@ bool MSettingsMimrec::WriteXml(MXmlNode* Node)
   new MXmlNode(aNode, "Spectrum", m_HistBinsSpectrum);
   new MXmlNode(aNode, "Polarization", m_HistBinsPolarization);
 
+  // ARM Gamma additional options
+  aNode = new MXmlNode(Node, "ARMGammaExtra");
+  new MXmlNode(aNode, "OptimizeBinning", m_OptimizeBinningARMGamma);
+  new MXmlNode(aNode, "NumberOfFits", m_NumberOfFitsARMGamma);
+  new MXmlNode(aNode, "FitFunctionID", m_FitFunctionIDARMGamma);
+  new MXmlNode(aNode, "UseUnbinnedFitting", m_UseUnbinnedFittingARMGamma);
+
   // Menu Polarization
   aNode = new MXmlNode(Node, "Polarization");
   new MXmlNode(aNode, "BackgroundFile", MSettings::CleanPath(m_PolarizationBackgroundFileName));
@@ -235,6 +248,20 @@ bool MSettingsMimrec::ReadXml(MXmlNode* Node)
     }
   }
 
+  if ((aNode = Node->GetNode("ARMGammaExtra")) != 0) {
+    if ((bNode = aNode->GetNode("OptimizeBinning")) != 0) {
+      m_OptimizeBinningARMGamma = bNode->GetValueAsBoolean();
+    }
+    if ((bNode = aNode->GetNode("NumberOfFits")) != 0) {
+      m_NumberOfFitsARMGamma = bNode->GetValueAsUnsignedInt();
+    }
+    if ((bNode = aNode->GetNode("FitFunctionID")) != 0) {
+      m_FitFunctionIDARMGamma = bNode->GetValueAsUnsignedInt();
+    }
+    if ((bNode = aNode->GetNode("UseUnbinnedFitting")) != 0) {
+      m_UseUnbinnedFittingARMGamma = bNode->GetValueAsBoolean();
+    }
+  }
 
   if ((aNode = Node->GetNode("Polarization")) != 0) {
     if ((bNode = aNode->GetNode("BackgroundFile")) != 0) {
@@ -244,7 +271,6 @@ bool MSettingsMimrec::ReadXml(MXmlNode* Node)
       m_PolarizationArmCut = bNode->GetValueAsDouble();
     }
   }
-    
 
   return true;
 }

From a9447170e8bae1c8ee53b739d8d80f731357bdb5 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Wed, 4 Sep 2024 21:12:13 -0700
Subject: [PATCH 063/192] ADD: Counts in FWHM window into ARMFitter

---
 src/mimrec/inc/MARMFitter.h        | 15 +++++++
 src/mimrec/inc/MGUIARMExtended.h   | 24 +++++++-----
 src/mimrec/src/MARMFitter.cxx      | 63 ++++++++++++++++++++++++++++--
 src/mimrec/src/MGUIARMExtended.cxx |  3 --
 4 files changed, 89 insertions(+), 16 deletions(-)

diff --git a/src/mimrec/inc/MARMFitter.h b/src/mimrec/inc/MARMFitter.h
index 0b25299b1..dde49d93f 100644
--- a/src/mimrec/inc/MARMFitter.h
+++ b/src/mimrec/inc/MARMFitter.h
@@ -157,6 +157,14 @@ class MARMFitter
   //! Return the 99.7% containment using all data or g_DoubleNotDefined if fit was not successful or not done yet
   double Get99p7PercentContainmentUsingAllData() const;
 
+  //! Get the counts in the FWHM window or g_DoubleNotDefined if we don't have a FWHM
+  unsigned int GetFWHMWindowCounts() const;
+  //! Get the counts in the FWHM minus uncertainty window or g_DoubleNotDefined if we don't have a FWHM uncertainty
+  unsigned int GetFWHMWindowCountsMinimum() const;
+  //! Get the counts in the FWHM plus uncertainty window or g_DoubleNotDefined if we don't have a FWHM uncertainty
+  unsigned int GetFWHMWindowCountsMaximum() const;
+
+
   //! Return a summary string
   MString ToString();
 
@@ -300,6 +308,13 @@ class MARMFitter
   //! The 3-sigma containment radius using all data (accurate to the next largest value in the data set)
   double m_Containment3SigmaUsingAllData;
 
+  //! The counts in the FWHM window or g_UnsignedIntNotDefined if we don't have a FWHM
+  unsigned int m_CountsFWHMWindow;
+  //! The counts in the FWHM minus uncertainty window or g_UnsignedIntNotDefined if we don't have a FWHM uncertainty
+  unsigned int m_CountsFWHMWindowMinimum;
+  //! The counts in the FWHM plus uncertainty window or g_UnsignedIntNotDefined if we don't have a FWHM uncertainty
+  unsigned int m_CountsFWHMWindowMaximum;
+
   //! Minimum height for fitting
   double m_MinHeight;
   //! Maximum height for fitting
diff --git a/src/mimrec/inc/MGUIARMExtended.h b/src/mimrec/inc/MGUIARMExtended.h
index 1dc7cb598..0d1f0660d 100644
--- a/src/mimrec/inc/MGUIARMExtended.h
+++ b/src/mimrec/inc/MGUIARMExtended.h
@@ -36,10 +36,7 @@
 
 ////////////////////////////////////////////////////////////////////////////////
 
-//! The position selection dialog box called by all interfaces which allow
-//! this selection
-//! It has 3 modes: ARM Gamma, ARM Electron, Spectrum
-//! This window will wait for being unmapped and not be deleted on close
+//! This is the UI window for the extended ARM fitting dialog
 class MGUIARMExtended : public MGUIDialog
 {
   // Public Interface:
@@ -51,8 +48,11 @@ class MGUIARMExtended : public MGUIDialog
 
   // protected methods:
  protected:
+  //! Create the window
   virtual void Create();
+  //! Process all messages
   virtual bool ProcessMessage(long Message, long Parameter1, long Parameter2);
+  //! Save the data when OK was pressed
   virtual bool OnApply();
 
 
@@ -69,29 +69,33 @@ class MGUIARMExtended : public MGUIDialog
   //! The user settings data
   MSettingsMimrec* m_Settings;
 
-
   //! The return message that OK was pressed
   bool& m_OkPressed;
 
-  //! Check button indicating if we do want to use a test position in spectral mode
+  //! The number of fits to use
   MGUIEEntry* m_NumberOfFits;
-  //const int m_NumberOfFitsID = 140;
 
-  //! Check button indicating if we do want to use a logarithmic binning in spectral mode
+  //! Check button indicating if we do want to use optimized binninf
   TGCheckButton* m_OptimizedBinning;
   const int m_OptimizedBinningID = 141;
   
+  //! Entry for the theta / latitude / X value
   MGUIEEntry* m_ThetaIsX;
+  //! Entry fir the phi / longitude / Y value
   MGUIEEntry* m_PhiIsY;
+  //! Entry for the radius / Z value
   MGUIEEntry* m_RadiusIsZ;
+
+  //! Entry for the ARM window
   MGUIEEntry* m_Distance;
+
+  //! Enetry for the number of bins
   MGUIEEntry* m_Bins;
 
   //! The fit function combo box
   TGComboBox* m_FitFunctions;
 
-
-  //! Check button indicating if we do want to use a logarithmic binning in spectral mode
+  //! Check button indicating if we do want to use unbinned fitting
   TGCheckButton* m_UseUnbinnedFitting;
   const int m_UseUnbinnedFittingID = 142;
 
diff --git a/src/mimrec/src/MARMFitter.cxx b/src/mimrec/src/MARMFitter.cxx
index 4b3f1e0c2..26e03980d 100644
--- a/src/mimrec/src/MARMFitter.cxx
+++ b/src/mimrec/src/MARMFitter.cxx
@@ -197,6 +197,10 @@ void MARMFitter::Reset()
   m_Containment1SigmaUsingAllData = g_DoubleNotDefined;
   m_Containment2SigmaUsingAllData = g_DoubleNotDefined;
   m_Containment3SigmaUsingAllData = g_DoubleNotDefined;
+
+  m_CountsFWHMWindow = g_UnsignedIntNotDefined;
+  m_CountsFWHMWindowMinimum = g_UnsignedIntNotDefined;
+  m_CountsFWHMWindowMaximum = g_UnsignedIntNotDefined;
 }
 
 
@@ -1003,8 +1007,28 @@ void MARMFitter::CalculateBootStrappedMetrics()
         });
     m_FinalBakerCousinsUncertainty = std::sqrt(SquaredSumBakerCousins / m_BootStrappedBakerCousins.size());
 
-  } else {
-    merr<<"Cannot calculate ARM metrics, since we don't have any bootstrapped values."<<endl;
+
+    m_CountsFWHMWindow = g_UnsignedIntNotDefined;
+    m_CountsFWHMWindowMinimum = g_UnsignedIntNotDefined;
+    m_CountsFWHMWindowMaximum = g_UnsignedIntNotDefined;
+
+    vector<double> SortedAbs;
+    for (double& A: m_OriginalARMValues) {
+      SortedAbs.push_back(fabs(A));
+    }
+    std::sort(SortedAbs.begin(), SortedAbs.end());
+
+    for (int b = 0; b < SortedAbs.size(); ++b) {
+      if (m_CountsFWHMWindowMinimum == g_UnsignedIntNotDefined && SortedAbs[b] >= m_FinalFWHM - m_FinalFWHMUncertainty) {
+        m_CountsFWHMWindowMinimum = b;
+      }
+      if (m_CountsFWHMWindow == g_UnsignedIntNotDefined && SortedAbs[b] >= m_FinalFWHM) {
+        m_CountsFWHMWindow = b;
+      }
+      if (m_CountsFWHMWindowMaximum == g_UnsignedIntNotDefined && SortedAbs[b] >= m_FinalFWHM + m_FinalFWHMUncertainty) {
+        m_CountsFWHMWindowMaximum = b;
+      }
+    }
   }
 }
 
@@ -1280,7 +1304,38 @@ double MARMFitter::Get95p5PercentContainmentUsingAllData() const
 //! Return the 99.7% containment for all events
 double MARMFitter::Get99p7PercentContainmentUsingAllData() const
 {
-  return m_FitSuccessful ? m_Containment3SigmaUsingAllData : g_DoubleNotDefined;
+  return m_FitSuccessful ? m_Containment3SigmaUsingAllData : g_UnsignedIntNotDefined;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Get the counts in the FWHM window or g_DoubleNotDefined if we don't have a FWHM
+unsigned int MARMFitter::GetFWHMWindowCounts() const
+{
+  return m_FitSuccessful ? m_CountsFWHMWindow : g_UnsignedIntNotDefined;
+}
+
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Get the counts in the FWHM minus uncertainty window or g_DoubleNotDefined if we don't have a FWHM uncertainty
+unsigned int MARMFitter::GetFWHMWindowCountsMinimum() const
+{
+  return m_FitSuccessful ? m_CountsFWHMWindowMinimum : g_UnsignedIntNotDefined;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Get the counts in the FWHM plus uncertainty window or g_DoubleNotDefined if we don't have a FWHM uncertainty
+unsigned int MARMFitter::GetFWHMWindowCountsMaximum() const
+{
+  return m_FitSuccessful ? m_CountsFWHMWindowMaximum : g_UnsignedIntNotDefined;
 }
 
 
@@ -1316,8 +1371,10 @@ MString MARMFitter::ToString()
     out<<"  Fit function: "<<GetARMFitFunctionName(m_ARMFitFunction)<<endl;
     if (m_BootStrappedFWHMSamples.size() > 1) {
       out<<"  Average FWHM after "<<m_BootStrappedFWHMSamples.size()<<" boot straps: "<<MString(m_FinalFWHM, m_FinalFWHMUncertainty, "degree")<<endl;
+      out<<"  Counts in +-FWHM window: "<<m_CountsFWHMWindow<<" (-"<<m_CountsFWHMWindow-m_CountsFWHMWindowMinimum<<", +"<<m_CountsFWHMWindowMaximum-m_CountsFWHMWindow<<")"<<endl;
     } else {
       out<<"  FWHM after 1 fit: "<<m_FinalFWHM<<" degree"<<endl;
+      out<<"  Counts in +-FWHM window: "<<m_CountsFWHMWindow<<endl;
     }
   } else {
     out<<"  No fits performed"<<endl;
diff --git a/src/mimrec/src/MGUIARMExtended.cxx b/src/mimrec/src/MGUIARMExtended.cxx
index 527ef650e..06a0117da 100644
--- a/src/mimrec/src/MGUIARMExtended.cxx
+++ b/src/mimrec/src/MGUIARMExtended.cxx
@@ -291,9 +291,6 @@ bool MGUIARMExtended::OnApply()
   m_Settings->SetFitFunctionIDARMGamma(m_FitFunctions->GetSelected());
   m_Settings->SetUseUnbinnedFittingARMGamma(m_UseUnbinnedFitting->GetState() == kButtonDown ? true : false);
 
-
-
-
   m_OkPressed = true;
   
   return true;

From e51e9325c501fd2b400a066680db1e94698e106b Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Wed, 4 Sep 2024 21:27:25 -0700
Subject: [PATCH 064/192] CHG: Verbosity

---
 src/mimrec/src/MARMFitter.cxx | 14 ++++----------
 1 file changed, 4 insertions(+), 10 deletions(-)

diff --git a/src/mimrec/src/MARMFitter.cxx b/src/mimrec/src/MARMFitter.cxx
index 26e03980d..fbfb12807 100644
--- a/src/mimrec/src/MARMFitter.cxx
+++ b/src/mimrec/src/MARMFitter.cxx
@@ -505,7 +505,7 @@ void MARMFitter::SetupARMFitGeneralizedNormal(ROOT::Fit::Fitter& Fitter, TF1** F
   ROOT::Math::WrappedMultiTF1 WrappedFitFunction(**FitFunction, 1);
 
   Fitter.Config().SetMinimizer("Minuit2", "Migrad");
-  if (g_Verbosity >= c_Info) Fitter.Config().MinimizerOptions().SetPrintLevel(10);
+  if (g_Verbosity >= c_Info) Fitter.Config().MinimizerOptions().SetPrintLevel(1);
   Fitter.SetFunction(WrappedFitFunction, false);
 
   vector<double> Parameters = { 1, 0.5*(m_GuessMaximumLow+m_GuessMaximumHigh), m_GuessHeight, m_GuessWidth, m_GuessScale };
@@ -613,7 +613,6 @@ void MARMFitter::SetupARMFitAsymmetricGaussLorentzLorentz(ROOT::Fit::Fitter& Fit
 
   Fitter.Config().SetMinimizer("Minuit2", "Migrad");
   if (g_Verbosity >= c_Info) Fitter.Config().MinimizerOptions().SetPrintLevel(1);
-  //Fitter.Config().MinimizerOptions().SetPrintLevel(0);
   Fitter.SetFunction(WrappedFitFunction, false);
 
   vector<double> Parameters = { 1, 0.5*(m_GuessMaximumLow+m_GuessMaximumHigh), m_GuessHeight, 0.9*m_GuessWidth, 1.1*m_GuessWidth, 0.9*m_GuessHeight, 0.5*m_GuessWidth, 1.1*m_GuessHeight, 2*m_GuessWidth };
@@ -657,7 +656,6 @@ void MARMFitter::SetupARMFitAsymmetricGaussGaussLorentzLorentz(ROOT::Fit::Fitter
 
   Fitter.Config().SetMinimizer("Minuit2", "Migrad");
   if (g_Verbosity >= c_Info) Fitter.Config().MinimizerOptions().SetPrintLevel(1);
-  //Fitter.Config().MinimizerOptions().SetPrintLevel(0);
   Fitter.SetFunction(WrappedFitFunction, false);
 
   vector<double> Parameters = { 1, 0.5*(m_GuessMaximumLow+m_GuessMaximumHigh), m_GuessHeight, m_GuessWidth, m_GuessWidth, m_GuessHeight, m_GuessWidth, m_GuessHeight, m_GuessWidth, m_GuessHeight, m_GuessWidth };
@@ -706,7 +704,6 @@ void MARMFitter::SetupARMFitAsymmetricGeneralizedNormalGeneralizedNormal(ROOT::F
 
   Fitter.Config().SetMinimizer("Minuit2", "Migrad");
   if (g_Verbosity >= c_Info) Fitter.Config().MinimizerOptions().SetPrintLevel(1);
-  //Fitter.Config().MinimizerOptions().SetPrintLevel(0);
   Fitter.SetFunction(WrappedFitFunction, false);
 
   vector<double> Parameters = { 1, 0.5*(m_GuessMaximumLow+m_GuessMaximumHigh), m_GuessHeight, m_GuessWidth, m_GuessScale, m_GuessWidth, m_GuessHeight, m_GuessScale, m_GuessHeight, m_GuessWidth, m_GuessScale };
@@ -750,8 +747,7 @@ void MARMFitter::SetupARMFitAsymmetricGeneralizedNormalGeneralizedNormalGenerali
   ROOT::Math::WrappedMultiTF1 WrappedFitFunction(**FitFunction, 1);
 
   Fitter.Config().SetMinimizer("Minuit2", "Migrad");
-  if (g_Verbosity >= c_Info) Fitter.Config().MinimizerOptions().SetPrintLevel(0);
-  //Fitter.Config().MinimizerOptions().SetPrintLevel(0);
+  if (g_Verbosity >= c_Info) Fitter.Config().MinimizerOptions().SetPrintLevel(1);
   Fitter.SetFunction(WrappedFitFunction, false);
 
   vector<double> Parameters = { 1, 0.5*(m_GuessMaximumLow+m_GuessMaximumHigh), m_GuessHeight, m_GuessWidth, m_GuessScale, m_GuessWidth, m_GuessScale, m_GuessHeight, m_GuessWidth, m_GuessScale, m_GuessHeight, m_GuessWidth, m_GuessScale };
@@ -821,11 +817,11 @@ bool MARMFitter::PerformFit(unsigned int FitID, vector<double>& ARMValues)
 
   // Do the fitting
   if (m_UnbinnedFitting == true) {
-    cout<<"Unbinned fit"<<endl;
+    //cout<<"Unbinned fit"<<endl;
     ROOT::Fit::UnBinData UnbinnedData(CleanedData.size(), CleanedData.data(), Range);
     Fitter.LikelihoodFit(UnbinnedData, true);
   } else {
-    cout<<"Binned fit"<<endl;
+    //cout<<"Binned fit"<<endl;
     DataOptions.fIntegral = true;
     DataOptions.fUseRange =true;
     ROOT::Fit::BinData BinnedData(DataOptions, Range);
@@ -842,8 +838,6 @@ bool MARMFitter::PerformFit(unsigned int FitID, vector<double>& ARMValues)
   // Retrieve results
   TFitResult Result = Fitter.Result();
 
-  //cout<<"Best fit: "<<GetARMFitFunctionName(m_ARMFitFunction)<<" (Baker-Cousins likelihood ratio: "<<std::fixed<<Result.MinFcnValue()<<")"<<endl;
-
   FitFunction->SetParameters(Result.GetParams());
 
   // Calculate FWHM ...

From da6128eb21c29293ab66f9f2cfb7fadb6b655e15 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Thu, 5 Sep 2024 01:25:35 -0700
Subject: [PATCH 065/192] CHG: Minor formatting and output fixes

---
 src/global/misc/inc/MString.h   |  2 ++
 src/global/misc/src/MString.cxx | 16 ++++++++++++++++
 src/mimrec/src/MARMFitter.cxx   | 33 +++++++++++++++++++++------------
 3 files changed, 39 insertions(+), 12 deletions(-)

diff --git a/src/global/misc/inc/MString.h b/src/global/misc/inc/MString.h
index 26af68617..20eae0270 100644
--- a/src/global/misc/inc/MString.h
+++ b/src/global/misc/inc/MString.h
@@ -65,6 +65,8 @@ class MString
   MString(const unsigned long i) { operator+=(i); }
   MString(const float i) { operator+=(i); }
   MString(const double i) { operator+=(i); }
+  //! Constrcut with double of given precision
+  MString(const double i, unsigned int Precision);
   //! Construct from value, uncertainty, unit using scientific rounding
   //! If Latex is true, the +- will be repalce by #pm for display with ROOT
   //! Will be something like (12.345, 1.872, "mm") -> "(12.3 +- 1.9) mm"
diff --git a/src/global/misc/src/MString.cxx b/src/global/misc/src/MString.cxx
index 6cb0b5a85..b8f1e4ec7 100644
--- a/src/global/misc/src/MString.cxx
+++ b/src/global/misc/src/MString.cxx
@@ -28,6 +28,7 @@
 
 // Standard libs:
 #include <locale>
+#include <iomanip>
 using namespace std;
 
 // ROOT libs:
@@ -68,6 +69,21 @@ ostream& operator<<(ostream& out, const MString& S)
   return out; 
 }
 
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+MString::MString(const double D, unsigned int Precision)
+{
+  //! Construct with double of given precision
+
+  ostringstream in;
+  in<<setprecision(Precision)<<D;
+
+  m_String = in.str();
+}
+
+
 ////////////////////////////////////////////////////////////////////////////////
 
 
diff --git a/src/mimrec/src/MARMFitter.cxx b/src/mimrec/src/MARMFitter.cxx
index fbfb12807..ec7719e2b 100644
--- a/src/mimrec/src/MARMFitter.cxx
+++ b/src/mimrec/src/MARMFitter.cxx
@@ -802,9 +802,6 @@ bool MARMFitter::PerformFit(unsigned int FitID, vector<double>& ARMValues)
     }
   }
 
-  // Calculate the ARM metrics not depending on a fit
-  CalculateARMMetrics();
-
   // Set up for fitting
   ROOT::Fit::DataOptions DataOptions;
   DataOptions.fIntegral = true;
@@ -1136,6 +1133,9 @@ bool MARMFitter::Fit(unsigned int NumberOfFits)
     OptimizeBinning();
   }
 
+  // Calculate the ARM metrics not depending on a fit
+  CalculateARMMetrics();
+
   // Pre-calculate limits on fits
 
   // We need a histogram, to do it easily
@@ -1364,10 +1364,10 @@ MString MARMFitter::ToString()
     out<<"  Fit mode: "<<(m_UnbinnedFitting == true ? "Unbinned" : "Binned")<<" likelihood fit"<<endl;
     out<<"  Fit function: "<<GetARMFitFunctionName(m_ARMFitFunction)<<endl;
     if (m_BootStrappedFWHMSamples.size() > 1) {
-      out<<"  Average FWHM after "<<m_BootStrappedFWHMSamples.size()<<" boot straps: "<<MString(m_FinalFWHM, m_FinalFWHMUncertainty, "degree")<<endl;
+      out<<"  Average FWHM after "<<m_BootStrappedFWHMSamples.size()<<" bootstraps: "<<MString(m_FinalFWHM, m_FinalFWHMUncertainty, "degree")<<endl;
       out<<"  Counts in +-FWHM window: "<<m_CountsFWHMWindow<<" (-"<<m_CountsFWHMWindow-m_CountsFWHMWindowMinimum<<", +"<<m_CountsFWHMWindowMaximum-m_CountsFWHMWindow<<")"<<endl;
     } else {
-      out<<"  FWHM after 1 fit: "<<m_FinalFWHM<<" degree"<<endl;
+      out<<"  FWHM after 1 fit: "<<setprecision(3)<<m_FinalFWHM<<" degree"<<endl;
       out<<"  Counts in +-FWHM window: "<<m_CountsFWHMWindow<<endl;
     }
   } else {
@@ -1376,6 +1376,7 @@ MString MARMFitter::ToString()
   out<<endl;
   out<<"Containment:"<<endl;
   out<<"  using +- "<<m_MaxARMValue<<" deg ARM selection:"<<endl;
+  out<<fixed<<setprecision(2);
   out<<"    50.0 %:\t"<<m_Containment50PercentUsingARMSelection<<" deg"<<endl;
   out<<"    68.3 %:\t"<<m_Containment1SigmaUsingARMSelection<<" deg"<<endl;
   out<<"    95.5 %:\t"<<m_Containment2SigmaUsingARMSelection<<" deg"<<endl;
@@ -1447,14 +1448,21 @@ void MARMFitter::Draw()
 
   Histogram->Draw("HIST SAME"); // Overdraws the fits
 
-  MString Text("FWHM of fit function: ");
-  Text += MString(m_FinalFWHM, m_FinalFWHMUncertainty, "#circ", true);
+  if (m_BootStrappedFWHMSamples.size() > 0) {
+    MString Text("FWHM of fit function: ");
+    if (m_BootStrappedFWHMSamples.size() == 1) {
+      Text += MString(m_FinalFWHM, 3u);
+      Text += "#circ";
+    } else {
+      Text += MString(m_FinalFWHM, m_FinalFWHMUncertainty, "#circ", true);
+    }
 
-  TLatex* Latex = new TLatex();
-  Latex->SetTextFont(gStyle->GetLabelFont());
-  Latex->SetTextSize(gStyle->GetLabelSize());
-  Latex->SetTextAlign(21);
-  Latex->DrawLatexNDC(0.5, 0.02, Text.Data());
+    TLatex* Latex = new TLatex();
+    Latex->SetTextFont(gStyle->GetLabelFont());
+    Latex->SetTextSize(gStyle->GetLabelSize());
+    Latex->SetTextAlign(21);
+    Latex->DrawLatexNDC(0.5, 0.02, Text.Data());
+  }
 
   // No delete Histogram - Histogramn deletion managed by ROOT
 
@@ -1518,5 +1526,6 @@ bool MARMFitter::SaveARMValues(MString FileName)
   return true;
 }
 
+
 // MARMFitter.cxx: the end...
 ////////////////////////////////////////////////////////////////////////////////

From 194f7110f9223dd1e25f3f784793986f014dab52 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Thu, 5 Sep 2024 13:57:43 -0700
Subject: [PATCH 066/192] ADD: Feature to get volume positions in the mother
 volume

---
 resource/examples/python/GeometryTricks.py | 34 ++++++++++++++++++++++
 src/geomega/inc/MDVolume.h                 |  2 ++
 src/geomega/src/MDVolume.cxx               | 28 ++++++++++++++++++
 3 files changed, 64 insertions(+)
 create mode 100644 resource/examples/python/GeometryTricks.py

diff --git a/resource/examples/python/GeometryTricks.py b/resource/examples/python/GeometryTricks.py
new file mode 100644
index 000000000..c43951a49
--- /dev/null
+++ b/resource/examples/python/GeometryTricks.py
@@ -0,0 +1,34 @@
+import ROOT as M
+
+# Load MEGAlib into ROOT
+M.gSystem.Load("$(MEGALIB)/lib/libMEGAlib.so")
+
+# Initialize MEGAlib
+G = M.MGlobal()
+G.Initialize()
+
+# We are good to go ...
+
+GeometryFileName = "Test.geo.setup"
+
+# Load geometry:
+Geometry = M.MDGeometryQuest()
+if Geometry.ScanSetupFile(M.MString(GeometryFileName)) == True:
+  print("Geometry " + GeometryFileName + " loaded!")
+else:
+  print("Unable to load geometry " + GeometryFileName + " - Aborting!")
+  quit()
+    
+# Find a volume location by volume name
+VolumeName = M.MString("GeWafer")
+
+World = Geometry.GetWorldVolume()
+Locations = World.GetCenterLocations(VolumeName)
+
+if Locations.size() > 0:
+  print(f"Center locations for volume {VolumeName}")
+  for L in Locations:
+    print(f"({L[0]}, {L[1]}, {L[2]}) cm")
+else:
+  print(f"Volume {VolumeName} not found in volume tree")
+
diff --git a/src/geomega/inc/MDVolume.h b/src/geomega/inc/MDVolume.h
index 9df6308ff..25ec5562e 100644
--- a/src/geomega/inc/MDVolume.h
+++ b/src/geomega/inc/MDVolume.h
@@ -225,6 +225,8 @@ class MDVolume
   //! Find the number of placements of a volume
   bool GetNPlacements(MDVolume* Volume, vector<int>& Placements, int& TreeDepth);
 
+  //! Return the center locations of the volumes
+  vector<MVector> GetCenterLocations(const MString& VolumeName);
 
   //! Recursively return a geomega setup file type string
   MString GetGeomega();
diff --git a/src/geomega/src/MDVolume.cxx b/src/geomega/src/MDVolume.cxx
index c44c45481..b430368a6 100644
--- a/src/geomega/src/MDVolume.cxx
+++ b/src/geomega/src/MDVolume.cxx
@@ -2324,6 +2324,34 @@ MVector MDVolume::GetRandomPositionInVolume(MDVolume* Volume, vector<int>& Place
 ////////////////////////////////////////////////////////////////////////////////
 
 
+vector<MVector> MDVolume::GetCenterLocations(const MString& VolumeName)
+{
+  //! Return the center locations of all volumes named VolumeName
+
+  vector<MVector> Positions;
+
+  for (unsigned int d = 0; d < GetNDaughters(); ++d) {
+    if (GetDaughterAt(d)->GetName() == VolumeName) {
+      Positions.push_back(GetDaughterAt(d)->GetPosition());
+    } else {
+      // Get the locations
+      vector<MVector> Interim = GetDaughterAt(d)->GetCenterLocations(VolumeName);
+      // Rotate them into this volume and add them to the main vector
+      for (MVector& P: Interim) {
+        P = m_InvertedRotMatrix*P;
+        P += m_Position;
+        Positions.push_back(P);
+      }
+    }
+  }
+
+  return Positions;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
 void MDVolume::VirtualizeNonDetectorVolumes()
 {
   // Check the list of daughters, those not containing sensitive detectors

From 39e41cdaed8c87546f671dd3a537c2d98c256976 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Thu, 19 Sep 2024 22:36:26 -0700
Subject: [PATCH 067/192] ADD: Check for OS version and store it in a global
 string

---
 src/global/misc/inc/MGlobal.h   |  4 ++++
 src/global/misc/src/MGlobal.cxx | 23 +++++++++++++++++++++--
 2 files changed, 25 insertions(+), 2 deletions(-)

diff --git a/src/global/misc/inc/MGlobal.h b/src/global/misc/inc/MGlobal.h
index 4a5813c96..b26d88d9b 100644
--- a/src/global/misc/inc/MGlobal.h
+++ b/src/global/misc/inc/MGlobal.h
@@ -132,6 +132,10 @@ extern TMutex* g_Mutex;
 //! The ID of the main thread
 extern Long_t g_MainThreadID;
 
+//! The OS name
+extern MString g_OSType;
+
+
 // And here a lot of other useful constants:
 extern const double c_Pi;
 extern const double c_TwoPi;
diff --git a/src/global/misc/src/MGlobal.cxx b/src/global/misc/src/MGlobal.cxx
index 551e78ccf..a9eb7e937 100644
--- a/src/global/misc/src/MGlobal.cxx
+++ b/src/global/misc/src/MGlobal.cxx
@@ -59,13 +59,15 @@ ClassImp(MGlobal)
 
 
 // Make this part of a future singleton class MGlobal
+MString g_OSType = "Unknown";
+
 unsigned int g_MajorVersion = 100;
 unsigned int g_MinorVersion = 0;
 unsigned int g_Version = 10000;
 MString g_VersionString = "1.00.00";
 
 // Remove year of copyright and replace with (C) by ....
-const MString g_CopyrightYear = "2016";
+const MString g_CopyrightYear = "2024";
 const MString g_Homepage = "http://megalibtoolkit.com";
 const MString g_MEGAlibPath = "$(MEGALIB)";
 
@@ -137,6 +139,20 @@ bool MGlobal::Initialize(MString ProgramName, MString ProgramDescription)
   g_Verbosity = 1;
 #endif
 
+  // Find the operating systenm type
+#if defined(_WIN32) || defined(_WIN64)
+  g_OSType = "Windows";
+#elif defined(__linux__)
+  g_OSType = "Linux";
+#elif defined(__APPLE__) && defined(__MACH__)
+  g_OSType = "macOS";
+#elif defined(__FreeBSD__)
+  g_OSType = "FreeBSD";
+#else
+  g_OSType = "Unknown";
+#endif
+
+
   // Load the GUI defaults by initializing the singleton
   MGUIDefaults::GetInstance();
 
@@ -182,8 +198,11 @@ bool MGlobal::Initialize(MString ProgramName, MString ProgramDescription)
 
   // Speeds up drawing of canvas if an openGL capable GPU is available and we are not remote
   MString SSHClient(getenv("SSH_CLIENT"));
+  gStyle->SetCanvasPreferGL(false);
   if (SSHClient.IsEmpty()) {
-    gStyle->SetCanvasPreferGL(true);
+    if (g_OSType != "macOS") {
+      gStyle->SetCanvasPreferGL(true);
+    }
   }
   
   // Change the region where the drawing starts in canvases:

From d0b2937d8d6d020f99a3abbce029cd34a9708379 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Thu, 19 Sep 2024 23:50:20 -0700
Subject: [PATCH 068/192] CHG: Sonoma compatibility

---
 config/build-root.sh                 |    2 +
 resource/patches/root_v6.28.12.patch | 6241 ++++++++++++++++++++++++++
 setup.sh                             |    2 +-
 3 files changed, 6244 insertions(+), 1 deletion(-)
 create mode 100644 resource/patches/root_v6.28.12.patch

diff --git a/config/build-root.sh b/config/build-root.sh
index f270bff6d..ddb1a8789 100755
--- a/config/build-root.sh
+++ b/config/build-root.sh
@@ -31,6 +31,8 @@ CONFIGUREOPTIONS+=" -Dxft=ON"
 CONFIGUREOPTIONS+=" -Dasimage=ON"
 # Stuff for linking, paths in so files, versioning etc
 CONFIGUREOPTIONS+=" -Dexplicitlink=ON -Drpath=ON -Dsoversion=ON"
+# enable builtin glew
+CONFIGUREOPTIONS+=" -Dbuiltin_glew=ON"
 
 # In case you have trouble with anything related to freetype, try to comment in this option
 # CONFIGUREOPTIONS+=" -Dbuiltin-freetype=ON"
diff --git a/resource/patches/root_v6.28.12.patch b/resource/patches/root_v6.28.12.patch
new file mode 100644
index 000000000..6a9cc312a
--- /dev/null
+++ b/resource/patches/root_v6.28.12.patch
@@ -0,0 +1,6241 @@
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/CMakeLists.txt root_v6.28.12_patched/root_v6.28.12-source/CMakeLists.txt
+--- root_v6.28.12_unpatched/root_v6.28.12-source/CMakeLists.txt	2024-09-18 13:23:14
++++ root_v6.28.12_patched/root_v6.28.12-source/CMakeLists.txt	2024-09-18 13:49:27
+@@ -400,16 +400,21 @@ file(TO_NATIVE_PATH "${CMAKE_BINARY_DIR}/include/modul
+   set(_os_cat "cat")
+ endif()
+ file(TO_NATIVE_PATH "${CMAKE_BINARY_DIR}/include/module.modulemap.extra" _from_native)
+-file(TO_NATIVE_PATH "${CMAKE_BINARY_DIR}/include/module.modulemap" _to_native)
++#file(TO_NATIVE_PATH "${CMAKE_BINARY_DIR}/include/module.modulemap" _to_native)
++file(TO_NATIVE_PATH "${CMAKE_BINARY_DIR}/include/ROOT.modulemap" _to_native)
+ 
+-add_custom_target(copymodulemap DEPENDS "${CMAKE_BINARY_DIR}/include/module.modulemap")
++#add_custom_target(copymodulemap DEPENDS "${CMAKE_BINARY_DIR}/include/module.modulemap")
++add_custom_target(copymodulemap DEPENDS "${CMAKE_BINARY_DIR}/include/ROOT.modulemap")
+ add_custom_command(
+-                  OUTPUT "${CMAKE_BINARY_DIR}/include/module.modulemap"
++                  #OUTPUT "${CMAKE_BINARY_DIR}/include/module.modulemap"
++		  OUTPUT "${CMAKE_BINARY_DIR}/include/ROOT.modulemap"
+                   DEPENDS build/unix/module.modulemap "${CMAKE_BINARY_DIR}/include/module.modulemap.extra"
+-                  COMMAND ${CMAKE_COMMAND} -E copy "${CMAKE_SOURCE_DIR}/build/unix/module.modulemap" "${CMAKE_BINARY_DIR}/include/module.modulemap"
++		  #COMMAND ${CMAKE_COMMAND} -E copy "${CMAKE_SOURCE_DIR}/build/unix/module.modulemap" "${CMAKE_BINARY_DIR}/include/module.modulemap"
++		  COMMAND ${CMAKE_COMMAND} -E copy "${CMAKE_SOURCE_DIR}/build/unix/module.modulemap" "${CMAKE_BINARY_DIR}/include/ROOT.modulemap"
+                   COMMAND ${_os_cat} "${_from_native}" >> "${_to_native}"
+ )
+-install(FILES "${CMAKE_BINARY_DIR}/include/module.modulemap" DESTINATION ${CMAKE_INSTALL_INCLUDEDIR} COMPONENT headers)
++#install(FILES "${CMAKE_BINARY_DIR}/include/module.modulemap" DESTINATION ${CMAKE_INSTALL_INCLUDEDIR} COMPONENT headers)
++install(FILES "${CMAKE_BINARY_DIR}/include/ROOT.modulemap" DESTINATION ${CMAKE_INSTALL_INCLUDEDIR} COMPONENT headers)
+ 
+ add_dependencies(move_headers copymodulemap)
+ 
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/README/ReleaseNotes/v628/index.md root_v6.28.12_patched/root_v6.28.12-source/README/ReleaseNotes/v628/index.md
+--- root_v6.28.12_unpatched/root_v6.28.12-source/README/ReleaseNotes/v628/index.md	2024-09-18 13:23:15
++++ root_v6.28.12_patched/root_v6.28.12-source/README/ReleaseNotes/v628/index.md	2024-09-18 13:49:27
+@@ -989,12 +989,20 @@ List of issues solved:
+ Besides the items below, this patch release features some improvements relative to run time performance. Firstly, the memory footprint of the plugin manager has been reduced. Moreover, the mechanism by which symbols are looked up by the interpreter was improved, avoiding to open and close a large number of libraries at startup, which improves considerably the user experience as well as cpu efficiency on batch jobs. More verbose output is now provided if wrong settings are used for the web-based widgets, the loopback device is always used and only one connection is allowed to `RBrowser`.
+ 
+ List of issues solved:
++
+ * [[ROOT-10234](https://its.cern.ch/jira/browse/ROOT-10234)] - Mistake in rs301_splot.C
+-* [[#8126] (https://github.com/root-project/root/issues/8126)] - cling interpreter crash while autocomplete
+-* [[#10178] (https://github.com/root-project/root/issues/10178)] - [cling] crash / compilation exception after undo
+-* [[#11746] (https://github.com/root-project/root/issues/11746)] - TH2::Fill(const char *namex, const char *namey, Double_t w) doesn't update fTsumwxy
++* [[#8126](https://github.com/root-project/root/issues/8126)] - cling interpreter crash while autocomplete
++* [[#10178](https://github.com/root-project/root/issues/10178)] - [cling] crash / compilation exception after undo
++* [[#11746](https://github.com/root-project/root/issues/11746)] - TH2::Fill(const char *namex, const char *namey, Double_t w) doesn't update fTsumwxy
+ 
+ ## HEAD of the v6-28-00-patches branch
++
++The next patch release removes the `RooPower` and `RooExpPoly` classes from this release branch.
++It is an unfortunate but unavoidable change: different classes with the same name were used in the CMS collaboration since at least the Higgs discovery.
++This name collision caused massive problems in backwards compatibility and was blocking CMS from picking up ROOT 6.28+ for statistical analysis.
++These classes were only introduced with ROOT 6.28.00 and were not widely advertised, so you should not be affected by this removal.
++If you were using one of these classes, please copy the sources from a previous ROOT tag in your analysis as a temporary solution, and report this unsupported usecase by opening a GitHub issue.
++Based on the feedback to this patch release, the `RooPower` and `RooExpPoly` classes will either be removed or renamed in the upcoming ROOT 6.32.
+ 
+ These changes will be part of a future 6.28/14.
+ 
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/bindings/pyroot/pythonizations/python/ROOT/_pythonization/_rvec.py root_v6.28.12_patched/root_v6.28.12-source/bindings/pyroot/pythonizations/python/ROOT/_pythonization/_rvec.py
+--- root_v6.28.12_unpatched/root_v6.28.12-source/bindings/pyroot/pythonizations/python/ROOT/_pythonization/_rvec.py	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/bindings/pyroot/pythonizations/python/ROOT/_pythonization/_rvec.py	2024-09-18 13:49:27
+@@ -66,9 +66,10 @@ from . import pythonization
+ '''
+ 
+ from . import pythonization
+-from libROOTPythonizations import GetEndianess, GetDataPointer, GetSizeOfType
++from libROOTPythonizations import GetEndianess
++import cppyy
++from cppyy import ll
+ 
+-
+ _array_interface_dtype_map = {
+     "float": "f",
+     "double": "f",
+@@ -86,7 +87,7 @@ def get_array_interface(self):
+     for dtype in _array_interface_dtype_map:
+         if cppname.endswith("<{}>".format(dtype)):
+             dtype_numpy = _array_interface_dtype_map[dtype]
+-            dtype_size = GetSizeOfType(dtype)
++            dtype_size = cppyy.sizeof(dtype)
+             endianess = GetEndianess()
+             size = self.size()
+             # Numpy breaks for data pointer of 0 even though the array is empty.
+@@ -94,7 +95,7 @@ def get_array_interface(self):
+             if self.empty():
+                 pointer = 1
+             else:
+-                pointer = GetDataPointer(self, cppname, "data")
++                pointer = ll.addressof(self.data())
+             return {
+                 "shape": (size, ),
+                 "typestr": "{}{}{}".format(endianess, dtype_numpy, dtype_size),
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/bindings/pyroot/pythonizations/python/ROOT/_pythonization/_tmva/_rbdt.py root_v6.28.12_patched/root_v6.28.12-source/bindings/pyroot/pythonizations/python/ROOT/_pythonization/_tmva/_rbdt.py
+--- root_v6.28.12_unpatched/root_v6.28.12-source/bindings/pyroot/pythonizations/python/ROOT/_pythonization/_tmva/_rbdt.py	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/bindings/pyroot/pythonizations/python/ROOT/_pythonization/_tmva/_rbdt.py	2024-09-18 13:49:27
+@@ -35,11 +35,24 @@ def Compute(self, x):
+     # As fall-through we go to the original compute function and use the error-handling from cppyy
+     return self._OriginalCompute(x)
+ 
++def RBDTInit(self, *args, **kwargs):
++    import warnings
++    warnings.warn(
++        ("Usage of xgboost models through RBDT is known to be limited and may "
++         "lead to unexpected behaviour. Proceed with caution if the input model "
++         "was obtained via `SaveXGBoost`. See https://github.com/root-project/root/issues/15197 "
++         "for more details."), UserWarning, stacklevel=2)
++    
++    return self._original_init(*args, **kwargs)
++    
+ 
+ @pythonization("RBDT", ns="TMVA::Experimental", is_prefix=True)
+ def pythonize_rbdt(klass):
+     # Parameters:
+     # klass: class to be pythonized
++
++    klass._original_init = klass.__init__
++    klass.__init__ = RBDTInit
+ 
+     klass._OriginalCompute = klass.Compute
+     klass.Compute = Compute
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/bindings/pyroot/pythonizations/python/ROOT/_pythonization/_tmva/_rtensor.py root_v6.28.12_patched/root_v6.28.12-source/bindings/pyroot/pythonizations/python/ROOT/_pythonization/_tmva/_rtensor.py
+--- root_v6.28.12_unpatched/root_v6.28.12-source/bindings/pyroot/pythonizations/python/ROOT/_pythonization/_tmva/_rtensor.py	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/bindings/pyroot/pythonizations/python/ROOT/_pythonization/_tmva/_rtensor.py	2024-09-18 13:49:27
+@@ -10,8 +10,9 @@ from .._rvec import _array_interface_dtype_map
+ 
+ from .. import pythonization
+ from .._rvec import _array_interface_dtype_map
+-from libROOTPythonizations import GetEndianess, GetDataPointer, GetSizeOfType
++from libROOTPythonizations import GetEndianess
+ import cppyy
++from cppyy import ll
+ 
+ 
+ def get_array_interface(self):
+@@ -28,13 +29,13 @@ def get_array_interface(self):
+     idx2 = cppname.find(",", idx1)
+     dtype = cppname[idx1 + 8 : idx2]
+     dtype_numpy = _array_interface_dtype_map[dtype]
+-    dtype_size = GetSizeOfType(dtype)
++    dtype_size = cppyy.sizeof(dtype)
+     endianess = GetEndianess()
+     shape = self.GetShape()
+     strides = self.GetStrides()
+     # Numpy breaks for data pointer of 0 even though the array is empty.
+     # We set the pointer to 1 but the value itself is arbitrary and never accessed.
+-    pointer = GetDataPointer(self, cppname, "GetData")
++    pointer = ll.addressof(self.GetData())
+     if pointer == 0:
+         pointer == 1
+     return {
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/bindings/pyroot/pythonizations/python/ROOT/_pythonization/_tmva/_tree_inference.py root_v6.28.12_patched/root_v6.28.12-source/bindings/pyroot/pythonizations/python/ROOT/_pythonization/_tmva/_tree_inference.py
+--- root_v6.28.12_unpatched/root_v6.28.12-source/bindings/pyroot/pythonizations/python/ROOT/_pythonization/_tmva/_tree_inference.py	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/bindings/pyroot/pythonizations/python/ROOT/_pythonization/_tmva/_tree_inference.py	2024-09-18 13:49:27
+@@ -12,12 +12,18 @@ import cppyy
+ import cppyy
+ 
+ 
+-def SaveXGBoost(self, xgb_model, key_name, output_path, num_inputs=None, tmp_path="/tmp", threshold_dtype="float"):
++def SaveXGBoost(self, xgb_model, key_name, output_path, num_inputs, tmp_path="/tmp", threshold_dtype="float"):
++    import warnings
++    warnings.warn(
++        ("Usage of xgboost models through RBDT is known to be limited and may "
++         "lead to unexpected behaviour. See https://github.com/root-project/root/issues/15197 "
++         "for more details."), UserWarning, stacklevel=2)
+     # Extract objective
+     objective_map = {
+         "multi:softprob": "softmax",  # Naming the objective softmax is more common today
+         "binary:logistic": "logistic",
+         "reg:linear": "identity",
++        "reg:squarederror": "identity",
+     }
+     model_objective = xgb_model.objective
+     if not model_objective in objective_map:
+@@ -48,7 +54,8 @@ def SaveXGBoost(self, xgb_model, key_name, output_path
+ 
+     import json
+ 
+-    forest = json.load(open(tmp_path, "r"))
++    with open(tmp_path, "r") as json_file:
++        forest = json.load(json_file)
+ 
+     # Determine whether the model has a bias paramter and write bias trees
+     if hasattr(xgb_model, "base_score") and "reg:" in model_objective:
+@@ -95,16 +102,6 @@ def SaveXGBoost(self, xgb_model, key_name, output_path
+     if num_outputs != 1:
+         for i in range(num_trees):
+             outputs[i] = int(i % num_outputs)
+-
+-    # Determine number of input variables
+-    if not num_inputs is None:
+-        pass
+-    elif hasattr(xgb_model, "_features_count"):
+-        num_inputs = xgb_model._features_count
+-    else:
+-        raise Exception(
+-            "Failed to get number of input variables from XGBoost model. Please provide the additional keyword argument 'num_inputs' to this function."
+-        )
+ 
+     # Store arrays in a ROOT file in a folder with the given key name
+     # TODO: Write single values as simple integers and not vectors.
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/bindings/pyroot/pythonizations/src/PyROOTModule.cxx root_v6.28.12_patched/root_v6.28.12-source/bindings/pyroot/pythonizations/src/PyROOTModule.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/bindings/pyroot/pythonizations/src/PyROOTModule.cxx	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/bindings/pyroot/pythonizations/src/PyROOTModule.cxx	2024-09-18 13:49:27
+@@ -68,9 +68,6 @@ static PyMethodDef gPyROOTMethods[] = {
+    {(char *)"AddPrettyPrintingPyz", (PyCFunction)PyROOT::AddPrettyPrintingPyz, METH_VARARGS,
+     (char *)"Add pretty printing pythonization"},
+    {(char *)"GetEndianess", (PyCFunction)PyROOT::GetEndianess, METH_NOARGS, (char *)"Get endianess of the system"},
+-   {(char *)"GetDataPointer", (PyCFunction)PyROOT::GetDataPointer, METH_VARARGS,
+-    (char *)"Get pointer to data of a C++ object"},
+-   {(char *)"GetSizeOfType", (PyCFunction)PyROOT::GetSizeOfType, METH_VARARGS, (char *)"Get size of data-type"},
+    {(char *)"AsRVec", (PyCFunction)PyROOT::AsRVec, METH_O, (char *)"Get object with array interface as RVec"},
+ #ifdef R__HAS_DATAFRAME
+    {(char *)"AsRTensor", (PyCFunction)PyROOT::AsRTensor, METH_O, (char *)"Get object with array interface as RTensor"},
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/bindings/pyroot/pythonizations/src/PyROOTPythonize.h root_v6.28.12_patched/root_v6.28.12-source/bindings/pyroot/pythonizations/src/PyROOTPythonize.h
+--- root_v6.28.12_unpatched/root_v6.28.12-source/bindings/pyroot/pythonizations/src/PyROOTPythonize.h	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/bindings/pyroot/pythonizations/src/PyROOTPythonize.h	2024-09-18 13:49:27
+@@ -43,8 +43,6 @@ PyObject *GetEndianess(PyObject *self, PyObject *args)
+ PyObject *CPPInstanceExpand(PyObject *self, PyObject *args);
+ 
+ PyObject *GetEndianess(PyObject *self, PyObject *args);
+-PyObject *GetDataPointer(PyObject *self, PyObject *args);
+-PyObject *GetSizeOfType(PyObject *self, PyObject *args);
+ 
+ PyObject *MakeNumpyDataFrameImpl(PyObject *self, PyObject *obj);
+ 
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/bindings/pyroot/pythonizations/src/PyzPythonHelpers.cxx root_v6.28.12_patched/root_v6.28.12-source/bindings/pyroot/pythonizations/src/PyzPythonHelpers.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/bindings/pyroot/pythonizations/src/PyzPythonHelpers.cxx	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/bindings/pyroot/pythonizations/src/PyzPythonHelpers.cxx	2024-09-18 13:49:27
+@@ -36,66 +36,6 @@ namespace CPyCppyy {
+ }
+ 
+ ////////////////////////////////////////////////////////////////////////////
+-/// \brief Get size of C++ data-type
+-/// \param[in] self Always null, since this is a module function.
+-/// \param[in] args C++ data-type as Python string
+-///
+-/// This function returns the length of a C++ data-type in bytes
+-/// as a Python integer.
+-PyObject *PyROOT::GetSizeOfType(PyObject * /*self*/, PyObject *args)
+-{
+-   // Get name of data-type
+-   PyObject *pydtype = PyTuple_GetItem(args, 0);
+-   std::string dtype = CPyCppyy_PyText_AsString(pydtype);
+-
+-   // Call interpreter to get size of data-type using `sizeof`
+-   size_t size = 0;
+-   std::stringstream code;
+-   code << "*((size_t*)" << std::showbase << (uintptr_t)&size << ") = (size_t)sizeof(" << dtype << ")";
+-   gInterpreter->Calc(code.str().c_str());
+-
+-   // Return size of data-type as integer
+-   PyObject *pysize = PyInt_FromLong(size);
+-   return pysize;
+-}
+-
+-////////////////////////////////////////////////////////////////////////////
+-/// \brief Get pointer to the data of an object
+-/// \param[in] self Always null, since this is a module function.
+-/// \param[in] args [0] Python representation of the C++ object.
+-///                 [1] Data-type of the C++ object as Python string.
+-///                 [2] Method to be called on the C++ object to get the data pointer as Python string
+-///
+-/// This function returns the pointer to the data of an object as an Python
+-/// integer retrieved by the given method.
+-PyObject *PyROOT::GetDataPointer(PyObject * /*self*/, PyObject *args)
+-{
+-   // Get pointer of C++ object
+-   PyObject *pyobj = PyTuple_GetItem(args, 0);
+-   auto instance = (CPyCppyy::CPPInstance *)(pyobj);
+-   auto cppobj = instance->GetObject();
+-
+-   // Get name of C++ object as string
+-   PyObject *pycppname = PyTuple_GetItem(args, 1);
+-   std::string cppname = CPyCppyy_PyText_AsString(pycppname);
+-
+-   // Get name of method to be called to get the data pointer
+-   PyObject *pymethodname = PyTuple_GetItem(args, 2);
+-   std::string methodname = CPyCppyy_PyText_AsString(pymethodname);
+-
+-   // Call interpreter to get pointer to data
+-   uintptr_t pointer = 0;
+-   std::stringstream code;
+-   code << "*((intptr_t*)" << std::showbase << (uintptr_t)&pointer << ") = reinterpret_cast<uintptr_t>(reinterpret_cast<"
+-        << cppname << "*>(" << std::showbase << (uintptr_t)cppobj << ")->" << methodname << "())";
+-   gInterpreter->Calc(code.str().c_str());
+-
+-   // Return pointer as integer
+-   PyObject *pypointer = PyLong_FromUnsignedLongLong(pointer);
+-   return pypointer;
+-}
+-
+-////////////////////////////////////////////////////////////////////////////
+ /// \brief Get endianess of the system
+ /// \param[in] self Always null, since this is a module function.
+ /// \param[in] args Pointer to an empty Python tuple.
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/bindings/pyroot/pythonizations/test/CMakeLists.txt root_v6.28.12_patched/root_v6.28.12-source/bindings/pyroot/pythonizations/test/CMakeLists.txt
+--- root_v6.28.12_unpatched/root_v6.28.12-source/bindings/pyroot/pythonizations/test/CMakeLists.txt	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/bindings/pyroot/pythonizations/test/CMakeLists.txt	2024-09-18 13:49:27
+@@ -14,11 +14,6 @@ ROOT_ADD_PYUNITTEST(pyroot_root_module root_module.py)
+ # Test ROOT module
+ ROOT_ADD_PYUNITTEST(pyroot_root_module root_module.py)
+ 
+-# Test versions of Python dependencies
+-if(NOT MSVC)
+-    ROOT_ADD_PYUNITTEST(pyroot_dependency_versions dependency_versions.py)
+-endif()
+-
+ # @pythonization decorator
+ ROOT_ADD_PYUNITTEST(pyroot_pyz_decorator pythonization_decorator.py)
+ 
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/bindings/pyroot/pythonizations/test/dependency_versions.py root_v6.28.12_patched/root_v6.28.12-source/bindings/pyroot/pythonizations/test/dependency_versions.py
+--- root_v6.28.12_unpatched/root_v6.28.12-source/bindings/pyroot/pythonizations/test/dependency_versions.py	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/bindings/pyroot/pythonizations/test/dependency_versions.py	1969-12-31 16:00:00
+@@ -1,68 +0,0 @@
+-import unittest
+-import pkg_resources
+-import subprocess
+-import os
+-import sys
+-
+-
+-# Compile list of packages to be ignored in the test
+-ignore = []
+-
+-# Dependencies of distributed RDataFrame are ignored in this test because they
+-# are checked through specific build options (`test_distrdf_*`).
+-# The dependencies are checked at configuration time so that we know whether the
+-# CTest environment would be ready for the tests of the distributed RDF backends
+-ignore.append('pyspark')
+-ignore.append('dask')
+-ignore.append('distributed')
+-ignore.append('dask-jobqueue')
+-
+-if sys.version_info[0] == 2 and 'ROOTTEST_IGNORE_NUMBA_PY2' in os.environ or \
+-   sys.version_info[0] == 3 and 'ROOTTEST_IGNORE_NUMBA_PY3' in os.environ:
+-    ignore += ['numba', 'cffi']
+-
+-if sys.version_info[0] == 2 and 'ROOTTEST_IGNORE_JUPYTER_PY2' in os.environ or \
+-   sys.version_info[0] == 3 and 'ROOTTEST_IGNORE_JUPYTER_PY3' in os.environ:
+-    ignore += ['notebook', 'metakernel']
+-
+-
+-class DependencyVersions(unittest.TestCase):
+-    def test_versions(self):
+-        '''
+-        Test the versions of the installed packages versus the
+-        requirements file in ROOT
+-        '''
+-        # For implementation details see
+-        # https://stackoverflow.com/questions/16294819/check-if-my-python-has-all-required-packages/45474387#45474387
+-
+-        # Get source directory with requirements.txt
+-        p = subprocess.Popen(['root-config', '--srcdir'], stdout=subprocess.PIPE)
+-        r, _ = p.communicate()
+-        rootsrc = r.decode('UTF-8').strip()
+-
+-        # Check each requirement separately
+-        path = os.path.join(rootsrc, 'requirements.txt')
+-        f = open(path)
+-        requirements = pkg_resources.parse_requirements(f)
+-        errors = []
+-        for requirement in requirements:
+-            requirement_str = str(requirement)
+-            name = requirement.project_name
+-            if name in ignore:
+-                print('Ignore dependency {}'.format(requirement_str))
+-                continue
+-            try:
+-                pkg_resources.require(requirement_str)
+-            except Exception as e:
+-                errors.append(e)
+-        f.close()
+-        if errors:
+-            print()
+-            print('Full path to requirements.txt: {}'.format(path))
+-            print('Details about not matched dependencies:')
+-            print('\n'.join([' - ' + e.report() for e in errors]))
+-            raise Exception('Found not matched dependencies declared in the requirements.txt, see test output for details')
+-
+-
+-if __name__ == '__main__':
+-    unittest.main()
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/cmake/modules/RootMacros.cmake root_v6.28.12_patched/root_v6.28.12-source/cmake/modules/RootMacros.cmake
+--- root_v6.28.12_unpatched/root_v6.28.12-source/cmake/modules/RootMacros.cmake	2024-09-18 13:23:14
++++ root_v6.28.12_patched/root_v6.28.12-source/cmake/modules/RootMacros.cmake	2024-09-18 13:49:27
+@@ -551,8 +551,9 @@ function(ROOT_GENERATE_DICTIONARY dictionary)
+       if(cpp_module)
+         set(cpp_module_file ${library_output_dir}/${cpp_module}.pcm)
+         # The module depends on its modulemap file.
+-        if (cpp_module_file)
+-          set (runtime_cxxmodule_dependencies copymodulemap "${CMAKE_BINARY_DIR}/include/module.modulemap")
++        if (cpp_module_file AND CMAKE_PROJECT_NAME STREQUAL ROOT)
++		#set (runtime_cxxmodule_dependencies copymodulemap "${CMAKE_BINARY_DIR}/include/module.modulemap")
++		set (runtime_cxxmodule_dependencies copymodulemap "${CMAKE_BINARY_DIR}/include/ROOT.modulemap")
+         endif()
+       endif(cpp_module)
+     endif()
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/core/clingutils/CMakeLists.txt root_v6.28.12_patched/root_v6.28.12-source/core/clingutils/CMakeLists.txt
+--- root_v6.28.12_unpatched/root_v6.28.12-source/core/clingutils/CMakeLists.txt	2024-09-18 13:23:14
++++ root_v6.28.12_patched/root_v6.28.12-source/core/clingutils/CMakeLists.txt	2024-09-18 13:49:27
+@@ -113,6 +113,13 @@ if (runtime_cxxmodules)
+   # some systems install it under /usr/include/Vc/Vc which allows rootcling to
+   # discover it and assert that the modulemap is not found.
+   set(custom_modulemaps ${custom_modulemaps} vc.modulemap)
++
++  # We need to override the default modulemap because instead of producing a
++  # single std.pcm, produces millions of pcms. This changed with sdk 15.3.
++  if (CMAKE_SYSTEM_NAME MATCHES Darwin AND CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 15.0.0.15000309)
++    set(custom_modulemaps ${custom_modulemaps} std_darwin.modulemap)
++  endif()
++
+   if (NOT libcxx)
+     if (MSVC)
+       set(custom_modulemaps ${custom_modulemaps} vcruntime.modulemap)
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/core/dictgen/src/rootcling_impl.cxx root_v6.28.12_patched/root_v6.28.12-source/core/dictgen/src/rootcling_impl.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/core/dictgen/src/rootcling_impl.cxx	2024-09-18 13:23:14
++++ root_v6.28.12_patched/root_v6.28.12-source/core/dictgen/src/rootcling_impl.cxx	2024-09-18 13:49:27
+@@ -4265,7 +4265,8 @@ int RootClingMain(int argc,
+ 
+       clingArgsInterpreter.push_back("-fmodule-map-file=" +
+                                      std::string(gDriverConfig->fTROOT__GetIncludeDir()) +
+-                                     "/module.modulemap");
++                                     // "/module.modulemap");
++                                     "/ROOT.modulemap");
+       std::string ModuleMapCWD = ROOT::FoundationUtils::GetCurrentDir() + "/module.modulemap";
+       if (llvm::sys::fs::exists(ModuleMapCWD))
+          clingArgsInterpreter.push_back("-fmodule-map-file=" + ModuleMapCWD);
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/core/lzma/src/ZipLZMA.c root_v6.28.12_patched/root_v6.28.12-source/core/lzma/src/ZipLZMA.c
+--- root_v6.28.12_unpatched/root_v6.28.12-source/core/lzma/src/ZipLZMA.c	2024-09-18 13:23:14
++++ root_v6.28.12_patched/root_v6.28.12-source/core/lzma/src/ZipLZMA.c	2024-09-18 13:26:22
+@@ -68,7 +68,7 @@ void R__zipLZMA(int cxlevel, int *srcsize, char *src, 
+    stream.avail_in  = (size_t)(*srcsize);
+ 
+    stream.next_out  = (uint8_t *)(&tgt[kHeaderSize]);
+-   stream.avail_out = (size_t)(*tgtsize);
++   stream.avail_out = (size_t)(*tgtsize) - kHeaderSize;
+ 
+    returnStatus = lzma_code(&stream, LZMA_FINISH);
+    if (returnStatus != LZMA_STREAM_END) {
+@@ -117,7 +117,7 @@ void R__unzipLZMA(int *srcsize, unsigned char *src, in
+    }
+ 
+    stream.next_in   = (const uint8_t *)(&src[kHeaderSize]);
+-   stream.avail_in  = (size_t)(*srcsize);
++   stream.avail_in  = (size_t)(*srcsize) - kHeaderSize;
+    stream.next_out  = (uint8_t *)tgt;
+    stream.avail_out = (size_t)(*tgtsize);
+ 
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/core/metacling/src/TCling.cxx root_v6.28.12_patched/root_v6.28.12-source/core/metacling/src/TCling.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/core/metacling/src/TCling.cxx	2024-09-18 13:23:14
++++ root_v6.28.12_patched/root_v6.28.12-source/core/metacling/src/TCling.cxx	2024-09-18 13:49:27
+@@ -1491,7 +1491,8 @@ TCling::TCling(const char *name, const char *title, co
+    if (fCxxModulesEnabled && !fromRootCling) {
+       // For now we prefer rootcling to enumerate explicitly its modulemaps.
+       std::vector<std::string> ModuleMaps;
+-      std::string ModuleMapSuffix = ROOT::FoundationUtils::GetPathSeparator() + "module.modulemap";
++      //std::string ModuleMapSuffix = ROOT::FoundationUtils::GetPathSeparator() + "module.modulemap";
++      std::string ModuleMapSuffix = ROOT::FoundationUtils::GetPathSeparator() + "ROOT.modulemap";
+       ModuleMaps.push_back(TROOT::GetIncludeDir().Data() + ModuleMapSuffix);
+       GetEnvVarPath("CLING_MODULEMAP_FILES", ModuleMaps);
+ 
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/core/zip/CMakeLists.txt root_v6.28.12_patched/root_v6.28.12-source/core/zip/CMakeLists.txt
+--- root_v6.28.12_unpatched/root_v6.28.12-source/core/zip/CMakeLists.txt	2024-09-18 13:23:14
++++ root_v6.28.12_patched/root_v6.28.12-source/core/zip/CMakeLists.txt	2024-09-18 13:49:27
+@@ -28,3 +28,5 @@ ROOT_INSTALL_HEADERS()
+ )
+ 
+ ROOT_INSTALL_HEADERS()
++
++ROOT_ADD_TEST_SUBDIRECTORY(test)
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/core/zip/src/RZip.cxx root_v6.28.12_patched/root_v6.28.12-source/core/zip/src/RZip.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/core/zip/src/RZip.cxx	2024-09-18 13:23:14
++++ root_v6.28.12_patched/root_v6.28.12-source/core/zip/src/RZip.cxx	2024-09-18 13:26:22
+@@ -78,14 +78,18 @@ void R__zipMultipleAlgorithm(int cxlevel, int *srcsize
+ /*                      3 = old */
+ void R__zipMultipleAlgorithm(int cxlevel, int *srcsize, char *src, int *tgtsize, char *tgt, int *irep, ROOT::RCompressionSetting::EAlgorithm::EValues compressionAlgorithm)
+ {
++  *irep = 0;
+ 
++  // Performance optimization: avoid compressing tiny source buffers.
+   if (*srcsize < 1 + HDRSIZE + 1) {
+-     *irep = 0;
+      return;
+   }
++  // Correctness check: we need at least enough bytes to prepend the header!
++  if (*tgtsize <= HDRSIZE) {
++     return;
++  }
+ 
+   if (cxlevel <= 0) {
+-    *irep = 0;
+     return;
+   }
+ 
+@@ -197,7 +201,7 @@ static void R__zipZLIB(int cxlevel, int *srcsize, char
+     stream.avail_in  = (uInt)(*srcsize);
+ 
+     stream.next_out  = (Bytef*)(&tgt[HDRSIZE]);
+-    stream.avail_out = (uInt)(*tgtsize);
++    stream.avail_out = (uInt)(*tgtsize) - HDRSIZE;
+ 
+     stream.zalloc    = (alloc_func)0;
+     stream.zfree     = (free_func)0;
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/core/zip/test/CMakeLists.txt root_v6.28.12_patched/root_v6.28.12-source/core/zip/test/CMakeLists.txt
+--- root_v6.28.12_unpatched/root_v6.28.12-source/core/zip/test/CMakeLists.txt	1969-12-31 16:00:00
++++ root_v6.28.12_patched/root_v6.28.12-source/core/zip/test/CMakeLists.txt	2024-09-18 13:26:22
+@@ -0,0 +1,7 @@
++# Copyright (C) 1995-2024, Rene Brun and Fons Rademakers.
++# All rights reserved.
++#
++# For the licensing terms see $ROOTSYS/LICENSE.
++# For the list of contributors see $ROOTSYS/README/CREDITS.
++
++ROOT_ADD_GTEST(ZipTest ZipTest.cxx LIBRARIES Core)
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/core/zip/test/ZipTest.cxx root_v6.28.12_patched/root_v6.28.12-source/core/zip/test/ZipTest.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/core/zip/test/ZipTest.cxx	1969-12-31 16:00:00
++++ root_v6.28.12_patched/root_v6.28.12-source/core/zip/test/ZipTest.cxx	2024-09-18 13:26:22
+@@ -0,0 +1,70 @@
++#include <Compression.h>
++#include <RZip.h>
++
++#include <gtest/gtest.h>
++
++#include <memory>
++
++static void testZipBufferSizes(ROOT::RCompressionSetting::EAlgorithm::EValues compressionAlgorithm)
++{
++   static constexpr size_t BufferSize = 256;
++   static constexpr size_t MaxBytes = 128;
++   static_assert(MaxBytes <= BufferSize, "MaxBytes must be smaller than BufferSize");
++   static constexpr size_t StartOffset = (BufferSize - MaxBytes) / 2;
++   // For extra "safety", allocate the buffers on the heap to avoid corrupting the stack should anything go wrong.
++   std::unique_ptr<char[]> source(new char[BufferSize]);
++   std::unique_ptr<char[]> target(new char[BufferSize]);
++
++   // Fill the buffers with monotonically increasing numbers. This is easy to compress, but that's fine because we scan
++   // through all possible sizes.
++   for (size_t i = 0; i < BufferSize; i++) {
++      source[i] = static_cast<char>(i);
++      target[i] = static_cast<char>(i);
++   }
++
++   // Now test all possible combinations of target and source sizes. The outer loop is for the target sizes because that
++   // allows us to check that nothing got overwritten.
++   for (size_t targetSize = 1; targetSize <= MaxBytes; targetSize++) {
++      for (size_t sourceSize = 1; sourceSize <= MaxBytes; sourceSize++) {
++         for (int cxlevel = 1; cxlevel <= 9; cxlevel++) {
++            int srcsize = static_cast<int>(sourceSize);
++            int tgtsize = static_cast<int>(targetSize);
++            int irep = -1;
++            R__zipMultipleAlgorithm(cxlevel, &srcsize, source.get(), &tgtsize, target.get() + StartOffset, &irep,
++                                    compressionAlgorithm);
++
++            for (size_t i = 0; i < StartOffset; i++) {
++               EXPECT_EQ(target[i], static_cast<char>(i));
++            }
++            for (size_t i = StartOffset + targetSize + 1; i < BufferSize; i++) {
++               EXPECT_EQ(target[i], static_cast<char>(i));
++            }
++         }
++      }
++   }
++}
++
++TEST(RZip, ZipBufferSizesOld)
++{
++   testZipBufferSizes(ROOT::RCompressionSetting::EAlgorithm::kOldCompressionAlgo);
++}
++
++TEST(RZip, ZipBufferSizesZLIB)
++{
++   testZipBufferSizes(ROOT::RCompressionSetting::EAlgorithm::kZLIB);
++}
++
++TEST(RZip, ZipBufferSizesLZMA)
++{
++   testZipBufferSizes(ROOT::RCompressionSetting::EAlgorithm::kLZMA);
++}
++
++TEST(RZip, ZipBufferSizesLZ4)
++{
++   testZipBufferSizes(ROOT::RCompressionSetting::EAlgorithm::kLZ4);
++}
++
++TEST(RZip, ZipBufferSizesZSTD)
++{
++   testZipBufferSizes(ROOT::RCompressionSetting::EAlgorithm::kZSTD);
++}
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/etc/RooFitHS3_wsexportkeys.json root_v6.28.12_patched/root_v6.28.12-source/etc/RooFitHS3_wsexportkeys.json
+--- root_v6.28.12_unpatched/root_v6.28.12-source/etc/RooFitHS3_wsexportkeys.json	2024-09-18 13:23:15
++++ root_v6.28.12_patched/root_v6.28.12-source/etc/RooFitHS3_wsexportkeys.json	2024-09-18 13:49:27
+@@ -102,14 +102,6 @@
+             "mean": "mean"
+         }
+     },
+-    "RooPower": {
+-        "type": "power_dist",
+-        "proxies": {
+-            "coefList": "coefficients",
+-            "expList": "exponents",
+-            "x": "x"
+-        }
+-    },
+     "RooProdPdf": {
+         "type": "product_dist",
+         "proxies": {
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/etc/RooFitHS3_wsfactoryexpressions.json root_v6.28.12_patched/root_v6.28.12-source/etc/RooFitHS3_wsfactoryexpressions.json
+--- root_v6.28.12_unpatched/root_v6.28.12-source/etc/RooFitHS3_wsfactoryexpressions.json	2024-09-18 13:23:15
++++ root_v6.28.12_patched/root_v6.28.12-source/etc/RooFitHS3_wsfactoryexpressions.json	2024-09-18 13:49:27
+@@ -90,14 +90,6 @@
+             "mean"
+         ]
+     },
+-    "power_dist": {
+-        "class": "RooPower",
+-        "arguments": [
+-            "x",
+-            "coefficients",
+-            "exponents"
+-        ]
+-    },
+     "product": {
+         "class": "RooProduct",
+         "arguments": [
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/graf2d/asimage/CMakeLists.txt root_v6.28.12_patched/root_v6.28.12-source/graf2d/asimage/CMakeLists.txt
+--- root_v6.28.12_unpatched/root_v6.28.12-source/graf2d/asimage/CMakeLists.txt	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/graf2d/asimage/CMakeLists.txt	2024-09-18 13:49:27
+@@ -33,6 +33,7 @@ ROOT_STANDARD_LIBRARY_PACKAGE(ASImage
+   DEPENDENCIES
+     Core
+     Graf
++    Postscript
+   BUILTINS
+     AFTERIMAGE
+ )
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/graf2d/asimage/src/TASImage.cxx root_v6.28.12_patched/root_v6.28.12-source/graf2d/asimage/src/TASImage.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/graf2d/asimage/src/TASImage.cxx	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/graf2d/asimage/src/TASImage.cxx	2024-09-18 13:49:27
+@@ -61,37 +61,39 @@ ROOT tutorials: `$ROOTSYS/tutorials/image/`
+ #include FT_FREETYPE_H
+ #include FT_GLYPH_H
+ 
++#include "RConfigure.h"
++#include "TArrayD.h"
++#include "TArrayL.h"
+ #include "TASImage.h"
+ #include "TASImagePlugin.h"
+-#include "TROOT.h"
+ #include "TBuffer.h"
+-#include "TMath.h"
+-#include "TSystem.h"
+-#include "TVirtualX.h"
+-#include "TVirtualPad.h"
+-#include "TArrayD.h"
+-#include "TVectorD.h"
+-#include "TVirtualPS.h"
+-#include "TGaxis.h"
+ #include "TColor.h"
+-#include "TObjArray.h"
+-#include "TArrayL.h"
+-#include "TPoint.h"
++#include "TEnv.h"
+ #include "TFrame.h"
+-#include "TTF.h"
+-#include "TRandom.h"
+-#include <iostream>
++#include "TGaxis.h"
+ #include "THashTable.h"
++#include "TImageDump.h"
++#include "TMath.h"
++#include "TObjArray.h"
+ #include "TPluginManager.h"
+-#include "TEnv.h"
++#include "TPoint.h"
++#include "TRandom.h"
++#include "TROOT.h"
+ #include "TStyle.h"
++#include "TSystem.h"
+ #include "TText.h"
+-#include "RConfigure.h"
++#include "TTF.h"
++#include "TVectorD.h"
++#include "TVirtualPad.h"
+ #include "TVirtualPadPainter.h"
+-#include "snprintf.h"
++#include "TVirtualPS.h"
++#include "TVirtualX.h"
+ 
++#include <iostream>
+ #include <memory>
+ 
++#include "snprintf.h"
++
+ #ifndef WIN32
+ #ifndef R__HAS_COCOA
+ #   include <X11/Xlib.h>
+@@ -1095,7 +1097,7 @@ void TASImage::FromPad(TVirtualPad *pad, Int_t x, Int_
+ 
+    if (gROOT->IsBatch()) { // in batch mode
+       TVirtualPS *psave = gVirtualPS;
+-      gVirtualPS = (TVirtualPS*)gROOT->ProcessLineFast("new TImageDump()");
++      gVirtualPS = new TImageDump();
+       gVirtualPS->Open(pad->GetName(), 114); // in memory
+       gVirtualPS->SetBit(BIT(11)); //kPrintingPS
+ 
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/interpreter/cling/include/cling/std_darwin.modulemap root_v6.28.12_patched/root_v6.28.12-source/interpreter/cling/include/cling/std_darwin.modulemap
+--- root_v6.28.12_unpatched/root_v6.28.12-source/interpreter/cling/include/cling/std_darwin.modulemap	1969-12-31 16:00:00
++++ root_v6.28.12_patched/root_v6.28.12-source/interpreter/cling/include/cling/std_darwin.modulemap	2024-09-18 13:49:27
+@@ -0,0 +1,2064 @@
++module std [system] {
++export *
++// Main C++ standard library interfaces
++module std_algorithm [system] {
++  header "algorithm"
++  export *
++}
++module std_any [system] {
++  header "any"
++  export *
++}
++module std_array [system] {
++  header "array"
++  export *
++}
++module std_atomic [system] {
++  header "atomic"
++  export *
++}
++module std_barrier [system] {
++  header "barrier"
++  export *
++}
++module std_bit [system] {
++  header "bit"
++  export *
++}
++module std_bitset [system] {
++  header "bitset"
++  export *
++}
++module std_charconv [system] {
++  header "charconv"
++  export *
++}
++module std_chrono [system] {
++  header "chrono"
++  export *
++}
++module std_codecvt [system] {
++  header "codecvt"
++  export *
++}
++module std_compare [system] {
++  header "compare"
++  export *
++}
++module std_complex [system] {
++  header "complex"
++  export *
++}
++module std_concepts [system] {
++  header "concepts"
++  export *
++}
++module std_condition_variable [system] {
++  header "condition_variable"
++  export *
++}
++module std_coroutine [system] {
++  header "coroutine"
++  export *
++}
++module std_deque [system] {
++  header "deque"
++  export *
++}
++module std_exception [system] {
++  header "exception"
++  export *
++}
++module std_execution [system] {
++  header "execution"
++  export *
++}
++module std_expected [system] {
++  header "expected"
++  export *
++}
++module std_filesystem [system] {
++  header "filesystem"
++  export *
++}
++module std_format [system] {
++  header "format"
++  export *
++}
++module std_forward_list [system] {
++  header "forward_list"
++  export *
++}
++module std_fstream [system] {
++  header "fstream"
++  export *
++}
++module std_functional [system] {
++  header "functional"
++  export *
++}
++module std_future [system] {
++  header "future"
++  export *
++}
++module std_initializer_list [system] {
++  header "initializer_list"
++  export *
++}
++module std_iomanip [system] {
++  header "iomanip"
++  export *
++}
++module std_ios [system] {
++  header "ios"
++  export *
++}
++module std_iosfwd [system] {
++  header "iosfwd"
++  export *
++}
++module std_iostream [system] {
++  header "iostream"
++  export *
++}
++module std_istream [system] {
++  header "istream"
++  export *
++}
++module std_iterator [system] {
++  header "iterator"
++  export *
++}
++module std_latch [system] {
++  header "latch"
++  export *
++}
++module std_limits [system] {
++  header "limits"
++  export *
++}
++module std_list [system] {
++  header "list"
++  export *
++}
++module std_locale [system] {
++  header "locale"
++  export *
++}
++module std_map [system] {
++  header "map"
++  export *
++}
++module std_mdspan [system] {
++  header "mdspan"
++  export *
++}
++module std_memory [system] {
++  header "memory"
++  export *
++}
++module std_memory_resource [system] {
++  header "memory_resource"
++  export *
++}
++module std_mutex [system] {
++  header "mutex"
++  export *
++}
++module std_new [system] {
++  header "new"
++  export *
++}
++module std_numbers [system] {
++  header "numbers"
++  export *
++}
++module std_numeric [system] {
++  header "numeric"
++  export *
++}
++module std_optional [system] {
++  header "optional"
++  export *
++}
++module std_ostream [system] {
++  header "ostream"
++  export *
++}
++module std_print [system] {
++  header "print"
++  export *
++}
++module std_queue [system] {
++  header "queue"
++  export *
++}
++module std_random [system] {
++  header "random"
++  export *
++}
++module std_ranges [system] {
++  header "ranges"
++  export *
++}
++module std_ratio [system] {
++  header "ratio"
++  export *
++}
++module std_regex [system] {
++  header "regex"
++  export *
++}
++module std_scoped_allocator [system] {
++  header "scoped_allocator"
++  export *
++}
++module std_semaphore [system] {
++  header "semaphore"
++  export *
++}
++module std_set [system] {
++  header "set"
++  export *
++}
++module std_shared_mutex [system] {
++  header "shared_mutex"
++  export std_version
++}
++module std_source_location [system] {
++  header "source_location"
++  export *
++}
++module std_span [system] {
++  header "span"
++  export std_private_ranges_enable_borrowed_range
++  export std_version
++  export std_private_span_span_fwd
++}
++module std_sstream [system] {
++  header "sstream"
++  export *
++}
++module std_stack [system] {
++  header "stack"
++  export *
++}
++module std_stdexcept [system] {
++  header "stdexcept"
++  export *
++}
++module std_stop_token {
++  header "stop_token"
++  export *
++}
++module std_streambuf [system] {
++  header "streambuf"
++  export *
++}
++module std_string [system] {
++  header "string"
++  export *
++}
++module std_string_view [system] {
++  header "string_view"
++  export *
++}
++module std_strstream [system] {
++  header "strstream"
++  export *
++}
++module std_system_error [system] {
++  header "system_error"
++  export *
++}
++module std_thread [system] {
++  header "thread"
++  export *
++}
++module std_tuple [system] {
++  header "tuple"
++  export *
++}
++module std_type_traits [system] {
++  header "type_traits"
++  export *
++}
++module std_typeindex [system] {
++  header "typeindex"
++  export *
++}
++module std_typeinfo [system] {
++  header "typeinfo"
++  export *
++}
++module std_unordered_map [system] {
++  header "unordered_map"
++  export *
++}
++module std_unordered_set [system] {
++  header "unordered_set"
++  export *
++}
++module std_utility [system] {
++  header "utility"
++  export *
++}
++module std_valarray [system] {
++  header "valarray"
++  export *
++}
++module std_variant [system] {
++  header "variant"
++  export *
++}
++module std_vector [system] {
++  header "vector"
++  export *
++}
++module std_version [system] {
++  header "version"
++  export *
++}
++
++// C standard library interface wrappers
++module std_cassert [system] {
++  // <cassert>'s use of NDEBUG requires textual inclusion.
++  textual header "cassert"
++}
++module std_ccomplex [system] {
++  header "ccomplex"
++  export *
++}
++module std_cctype [system] {
++  header "cctype"
++  export *
++}
++module std_cerrno [system] {
++  header "cerrno"
++  export *
++}
++module std_cfenv [system] {
++  header "cfenv"
++  export *
++}
++module std_cfloat [system] {
++  header "cfloat"
++  export *
++}
++module std_cinttypes [system] {
++  header "cinttypes"
++  export *
++}
++module std_ciso646 [system] {
++  header "ciso646"
++  export *
++}
++module std_climits [system] {
++  header "climits"
++  export *
++}
++module std_clocale [system] {
++  header "clocale"
++  export *
++}
++module std_cmath [system] {
++  header "cmath"
++  export *
++}
++module std_csetjmp [system] {
++  header "csetjmp"
++  export *
++}
++module std_csignal [system] {
++  header "csignal"
++  export *
++}
++// FIXME: <cstdalign> is missing.
++module std_cstdarg [system] {
++  header "cstdarg"
++  export *
++}
++module std_cstdbool [system] {
++  header "cstdbool"
++  export *
++}
++module std_cstddef [system] {
++  header "cstddef"
++  export *
++}
++module std_cstdint [system] {
++  header "cstdint"
++  export *
++}
++module std_cstdio [system] {
++  header "cstdio"
++  export *
++}
++module std_cstdlib [system] {
++  header "cstdlib"
++  export *
++}
++module std_cstring [system] {
++  header "cstring"
++  export *
++}
++module std_ctgmath [system] {
++  header "ctgmath"
++  export *
++}
++module std_ctime [system] {
++  header "ctime"
++  export *
++}
++module std_cuchar [system] {
++  header "cuchar"
++  export *
++}
++module std_cwchar [system] {
++  header "cwchar"
++  export *
++}
++module std_cwctype [system] {
++  header "cwctype"
++  export *
++}
++
++// C standard library interfaces augmented/replaced in C++
++// <assert.h> provided by C library.
++module std_complex_h [system] {
++  header "complex.h"
++  export *
++}
++module std_ctype_h [system] {
++  header "ctype.h"
++  export *
++}
++module std_errno_h [system] {
++  header "errno.h"
++  export *
++}
++module std_fenv_h [system] {
++  header "fenv.h"
++  export *
++}
++module std_float_h [system] {
++  header "float.h"
++  export *
++}
++module std_inttypes_h [system] {
++  header "inttypes.h"
++  export *
++}
++// <iso646.h> provided by compiler.
++module std_limits_h [system] {
++  header "limits.h"
++  export *
++}
++module std_locale_h [system] {
++  header "locale.h"
++  export *
++}
++module std_math_h [system] {
++  header "math.h"
++  export *
++}
++module std_setjmp_h [system] {
++  header "setjmp.h"
++  export *
++}
++// <signal.h> provided by C library.
++// FIXME: <stdalign.h> is missing.
++// <stdarg.h> provided by compiler.
++module std_stdatomic_h [system] {
++  header "stdatomic.h"
++  export *
++}
++module std_stdbool_h [system] {
++  // <stdbool.h>'s __bool_true_false_are_defined macro requires textual inclusion.
++  textual header "stdbool.h"
++  export *
++}
++module std_stddef_h [system] {
++  // <stddef.h>'s __need_* macros require textual inclusion.
++  textual header "stddef.h"
++  export *
++}
++module std_stdint_h [system] {
++  header "stdint.h"
++  export *
++}
++module std_stdio_h [system] {
++  // <stdio.h>'s __need_* macros require textual inclusion.
++  textual header "stdio.h"
++  export *
++}
++module std_stdlib_h [system] {
++  // <stdlib.h>'s __need_* macros require textual inclusion.
++  textual header "stdlib.h"
++  export *
++}
++module std_string_h [system] {
++  header "string.h"
++  export *
++}
++module std_tgmath_h [system] {
++  header "tgmath.h"
++  export *
++}
++module std_uchar_h [system] {
++  header "uchar.h"
++  export *
++}
++// <time.h> provided by C library.
++module std_wchar_h [system] {
++  // <wchar.h>'s __need_* macros require textual inclusion.
++  textual header "wchar.h"
++  export *
++}
++module std_wctype_h [system] {
++  header "wctype.h"
++  export *
++}
++
++// Experimental C++ standard library interfaces
++module std_experimental [system] {
++  module deque {
++    header "experimental/deque"
++    export *
++  }
++  module forward_list {
++    header "experimental/forward_list"
++    export *
++  }
++  module iterator {
++    header "experimental/iterator"
++    export *
++  }
++  module list {
++    header "experimental/list"
++    export *
++  }
++  module map {
++    header "experimental/map"
++    export *
++  }
++  module memory_resource {
++    header "experimental/memory_resource"
++    export *
++  }
++  module propagate_const {
++    header "experimental/propagate_const"
++    export *
++  }
++  module regex {
++    
++    header "experimental/regex"
++    export *
++  }
++  module simd {
++    header "experimental/simd"
++    export *
++  }
++  module set {
++    header "experimental/set"
++    export *
++  }
++  module string {
++    header "experimental/string"
++    export *
++  }
++  module type_traits {
++    header "experimental/type_traits"
++    export *
++  }
++  module unordered_map {
++    header "experimental/unordered_map"
++    export *
++  }
++  module unordered_set {
++    header "experimental/unordered_set"
++    export *
++  }
++  module utility {
++    header "experimental/utility"
++    export *
++  }
++  module vector {
++    header "experimental/vector"
++    export *
++  }
++  module __config {
++    private textual header "experimental/__config"
++    export *
++  }
++  // FIXME these should be private
++  module __memory {
++    header "experimental/__memory"
++    export *
++  }
++}
++
++// Convenience method to get all of the above modules in a single import statement.
++// Importing only the needed modules is likely to be more performant.
++//module std [system] {
++//  header "__std_clang_module"
++//  export *
++//}
++
++// Implementation detail headers that are private to libc++. These modules
++// must not be directly imported.
++module std_private_assert            [system] {
++  header "__assert"
++  export *
++}
++module std_private_availability      [system] {
++  header "__availability"
++  export *
++}
++module std_private_bit_reference     [system] {
++  header "__bit_reference"
++  export *
++}
++module std_private_config            [system] {
++  textual header "__config"
++  export *
++}
++module std_private_hash_table        [system] {
++  header "__hash_table"
++  export *
++}
++module std_private_locale            [system] {
++  header "__locale"
++  export *
++}
++module std_private_mbstate_t         [system] {
++  header "__mbstate_t.h"
++  export *
++}
++module std_private_node_handle       [system] {
++  header "__node_handle"
++  export *
++}
++module std_private_split_buffer      [system] {
++  header "__split_buffer"
++  export *
++}
++module std_private_std_mbstate_t     [system] {
++  header "__std_mbstate_t.h"
++  export *
++}
++module std_private_threading_support [system] {
++  header "__threading_support"
++  export *
++}
++module std_private_tree              [system] {
++  header "__tree"
++  export *
++}
++module std_private_undef_macros      [system] {
++  textual header "__undef_macros"
++  export *
++}
++module std_private_verbose_abort     [system] {
++  header "__verbose_abort"
++  export *
++}
++
++module std_private_algorithm_adjacent_find                               [system] { header "__algorithm/adjacent_find.h" }
++module std_private_algorithm_all_of                                      [system] { header "__algorithm/all_of.h" }
++module std_private_algorithm_any_of                                      [system] { header "__algorithm/any_of.h" }
++module std_private_algorithm_binary_search                               [system] { header "__algorithm/binary_search.h" }
++module std_private_algorithm_clamp                                       [system] { header "__algorithm/clamp.h" }
++module std_private_algorithm_comp                                        [system] { header "__algorithm/comp.h" }
++module std_private_algorithm_comp_ref_type                               [system] { header "__algorithm/comp_ref_type.h" }
++module std_private_algorithm_copy                                        [system] {
++  header "__algorithm/copy.h"
++  export std_private_algorithm_copy_move_common
++}
++module std_private_algorithm_copy_backward                               [system] { header "__algorithm/copy_backward.h" }
++module std_private_algorithm_copy_if                                     [system] { header "__algorithm/copy_if.h" }
++module std_private_algorithm_copy_move_common                            [system] {
++  header "__algorithm/copy_move_common.h"
++  export std_private_type_traits_is_trivially_copyable
++}
++module std_private_algorithm_copy_n                                      [system] { header "__algorithm/copy_n.h" }
++module std_private_algorithm_count                                       [system] { header "__algorithm/count.h" }
++module std_private_algorithm_count_if                                    [system] { header "__algorithm/count_if.h" }
++module std_private_algorithm_equal                                       [system] { header "__algorithm/equal.h" }
++module std_private_algorithm_equal_range                                 [system] { header "__algorithm/equal_range.h" }
++module std_private_algorithm_fill                                        [system] { header "__algorithm/fill.h" }
++module std_private_algorithm_fill_n                                      [system] { header "__algorithm/fill_n.h" }
++module std_private_algorithm_find                                        [system] {
++  header "__algorithm/find.h"
++  export std_private_algorithm_unwrap_iter
++}
++module std_private_algorithm_find_end                                    [system] { header "__algorithm/find_end.h" }
++module std_private_algorithm_find_first_of                               [system] { header "__algorithm/find_first_of.h" }
++module std_private_algorithm_find_if                                     [system] { header "__algorithm/find_if.h" }
++module std_private_algorithm_find_if_not                                 [system] { header "__algorithm/find_if_not.h" }
++module std_private_algorithm_for_each                                    [system] { header "__algorithm/for_each.h" }
++module std_private_algorithm_for_each_n                                  [system] { header "__algorithm/for_each_n.h" }
++module std_private_algorithm_for_each_segment                            [system] { header "__algorithm/for_each_segment.h" }
++module std_private_algorithm_generate                                    [system] { header "__algorithm/generate.h" }
++module std_private_algorithm_generate_n                                  [system] { header "__algorithm/generate_n.h" }
++module std_private_algorithm_half_positive                               [system] { header "__algorithm/half_positive.h" }
++module std_private_algorithm_in_found_result                             [system] { header "__algorithm/in_found_result.h" }
++module std_private_algorithm_in_fun_result                               [system] { header "__algorithm/in_fun_result.h" }
++module std_private_algorithm_in_in_out_result                            [system] { header "__algorithm/in_in_out_result.h" }
++module std_private_algorithm_in_in_result                                [system] { header "__algorithm/in_in_result.h" }
++module std_private_algorithm_in_out_out_result                           [system] { header "__algorithm/in_out_out_result.h" }
++module std_private_algorithm_in_out_result                               [system] { header "__algorithm/in_out_result.h" }
++module std_private_algorithm_includes                                    [system] { header "__algorithm/includes.h" }
++module std_private_algorithm_inplace_merge                               [system] { header "__algorithm/inplace_merge.h" }
++module std_private_algorithm_is_heap                                     [system] { header "__algorithm/is_heap.h" }
++module std_private_algorithm_is_heap_until                               [system] { header "__algorithm/is_heap_until.h" }
++module std_private_algorithm_is_partitioned                              [system] { header "__algorithm/is_partitioned.h" }
++module std_private_algorithm_is_permutation                              [system] { header "__algorithm/is_permutation.h" }
++module std_private_algorithm_is_sorted                                   [system] { header "__algorithm/is_sorted.h" }
++module std_private_algorithm_is_sorted_until                             [system] { header "__algorithm/is_sorted_until.h" }
++module std_private_algorithm_iter_swap                                   [system] { header "__algorithm/iter_swap.h" }
++module std_private_algorithm_iterator_operations                         [system] {
++  header "__algorithm/iterator_operations.h"
++  export *
++}
++module std_private_algorithm_lexicographical_compare                     [system] { header "__algorithm/lexicographical_compare.h" }
++module std_private_algorithm_lexicographical_compare_three_way           [system] { header "__algorithm/lexicographical_compare_three_way.h" }
++module std_private_algorithm_lower_bound                                 [system] { header "__algorithm/lower_bound.h" }
++module std_private_algorithm_make_heap                                   [system] { header "__algorithm/make_heap.h" }
++module std_private_algorithm_make_projected                              [system] { header "__algorithm/make_projected.h" }
++module std_private_algorithm_max                                         [system] { header "__algorithm/max.h" }
++module std_private_algorithm_max_element                                 [system] { header "__algorithm/max_element.h" }
++module std_private_algorithm_merge                                       [system] { header "__algorithm/merge.h" }
++module std_private_algorithm_min                                         [system] { header "__algorithm/min.h" }
++module std_private_algorithm_min_element                                 [system] { header "__algorithm/min_element.h" }
++module std_private_algorithm_min_max_result                              [system] { header "__algorithm/min_max_result.h" }
++module std_private_algorithm_minmax                                      [system] {
++  header "__algorithm/minmax.h"
++  export *
++}
++module std_private_algorithm_minmax_element                              [system] { header "__algorithm/minmax_element.h" }
++module std_private_algorithm_mismatch                                    [system] { header "__algorithm/mismatch.h" }
++module std_private_algorithm_move                                        [system] { header "__algorithm/move.h" }
++module std_private_algorithm_move_backward                               [system] { header "__algorithm/move_backward.h" }
++module std_private_algorithm_next_permutation                            [system] { header "__algorithm/next_permutation.h" }
++module std_private_algorithm_none_of                                     [system] { header "__algorithm/none_of.h" }
++module std_private_algorithm_nth_element                                 [system] { header "__algorithm/nth_element.h" }
++module std_private_algorithm_partial_sort                                [system] { header "__algorithm/partial_sort.h" }
++module std_private_algorithm_partial_sort_copy                           [system] { header "__algorithm/partial_sort_copy.h" }
++module std_private_algorithm_partition                                   [system] { header "__algorithm/partition.h" }
++module std_private_algorithm_partition_copy                              [system] { header "__algorithm/partition_copy.h" }
++module std_private_algorithm_partition_point                             [system] { header "__algorithm/partition_point.h" }
++module std_private_algorithm_pop_heap                                    [system] { header "__algorithm/pop_heap.h" }
++module std_private_algorithm_prev_permutation                            [system] { header "__algorithm/prev_permutation.h" }
++module std_private_algorithm_pstl_any_all_none_of                        [system] { header "__algorithm/pstl_any_all_none_of.h" }
++module std_private_algorithm_pstl_backend                                [system] {
++  header "__algorithm/pstl_backend.h"
++  export *
++}
++module std_private_algorithm_pstl_backends_cpu_backend                   [system] {
++  header "__algorithm/pstl_backends/cpu_backend.h"
++  export *
++}
++module std_private_algorithm_pstl_backends_cpu_backends_any_of           [system] { header "__algorithm/pstl_backends/cpu_backends/any_of.h" }
++module std_private_algorithm_pstl_backends_cpu_backends_backend          [system] {
++  header "__algorithm/pstl_backends/cpu_backends/backend.h"
++  export *
++}
++module std_private_algorithm_pstl_backends_cpu_backends_fill             [system] { header "__algorithm/pstl_backends/cpu_backends/fill.h" }
++module std_private_algorithm_pstl_backends_cpu_backends_find_if          [system] { header "__algorithm/pstl_backends/cpu_backends/find_if.h" }
++module std_private_algorithm_pstl_backends_cpu_backends_for_each         [system] { header "__algorithm/pstl_backends/cpu_backends/for_each.h" }
++module std_private_algorithm_pstl_backends_cpu_backends_libdispatch      [system] { header "__algorithm/pstl_backends/cpu_backends/libdispatch.h" }
++module std_private_algorithm_pstl_backends_cpu_backends_merge            [system] { header "__algorithm/pstl_backends/cpu_backends/merge.h" }
++module std_private_algorithm_pstl_backends_cpu_backends_serial           [system] { textual header "__algorithm/pstl_backends/cpu_backends/serial.h" }
++module std_private_algorithm_pstl_backends_cpu_backends_stable_sort      [system] { header "__algorithm/pstl_backends/cpu_backends/stable_sort.h" }
++module std_private_algorithm_pstl_backends_cpu_backends_thread           [system] { textual header "__algorithm/pstl_backends/cpu_backends/thread.h" }
++module std_private_algorithm_pstl_backends_cpu_backends_transform        [system] {
++  header "__algorithm/pstl_backends/cpu_backends/transform.h"
++  export std_private_algorithm_transform
++}
++module std_private_algorithm_pstl_backends_cpu_backends_transform_reduce [system] { header "__algorithm/pstl_backends/cpu_backends/transform_reduce.h" }
++module std_private_algorithm_pstl_copy                                   [system] { header "__algorithm/pstl_copy.h" }
++module std_private_algorithm_pstl_count                                  [system] { header "__algorithm/pstl_count.h" }
++module std_private_algorithm_pstl_fill                                   [system] { header "__algorithm/pstl_fill.h" }
++module std_private_algorithm_pstl_find                                   [system] {
++  header "__algorithm/pstl_find.h"
++  export *
++}
++module std_private_algorithm_pstl_for_each                               [system] {
++  header "__algorithm/pstl_for_each.h"
++  export *
++}
++module std_private_algorithm_pstl_frontend_dispatch                      [system] {
++  header "__algorithm/pstl_frontend_dispatch.h"
++  export std_private_utility_forward
++}
++module std_private_algorithm_pstl_generate                               [system] { header "__algorithm/pstl_generate.h" }
++module std_private_algorithm_pstl_is_partitioned                         [system] { header "__algorithm/pstl_is_partitioned.h" }
++module std_private_algorithm_pstl_merge                                  [system] { header "__algorithm/pstl_merge.h" }
++module std_private_algorithm_pstl_replace                                [system] { header "__algorithm/pstl_replace.h" }
++module std_private_algorithm_pstl_sort                                   [system] { header "__algorithm/pstl_sort.h" }
++module std_private_algorithm_pstl_stable_sort                            [system] {
++  header "__algorithm/pstl_stable_sort.h"
++  export std_private_functional_operations
++}
++module std_private_algorithm_pstl_transform                              [system] { header "__algorithm/pstl_transform.h" }
++module std_private_algorithm_push_heap                                   [system] { header "__algorithm/push_heap.h" }
++module std_private_algorithm_ranges_adjacent_find                        [system] { header "__algorithm/ranges_adjacent_find.h" }
++module std_private_algorithm_ranges_all_of                               [system] { header "__algorithm/ranges_all_of.h" }
++module std_private_algorithm_ranges_any_of                               [system] { header "__algorithm/ranges_any_of.h" }
++module std_private_algorithm_ranges_binary_search                        [system] {
++  header "__algorithm/ranges_binary_search.h"
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_clamp                                [system] {
++  header "__algorithm/ranges_clamp.h"
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_copy                                 [system] {
++  header "__algorithm/ranges_copy.h"
++  export std_private_algorithm_in_out_result
++}
++module std_private_algorithm_ranges_copy_backward                        [system] {
++  header "__algorithm/ranges_copy_backward.h"
++  export std_private_algorithm_in_out_result
++}
++module std_private_algorithm_ranges_copy_if                              [system] {
++  header "__algorithm/ranges_copy_if.h"
++  export std_private_algorithm_in_out_result
++}
++module std_private_algorithm_ranges_copy_n                               [system] {
++  header "__algorithm/ranges_copy_n.h"
++  export std_private_algorithm_in_out_result
++}
++module std_private_algorithm_ranges_count                                [system] { header "__algorithm/ranges_count.h" }
++module std_private_algorithm_ranges_count_if                             [system] { header "__algorithm/ranges_count_if.h" }
++module std_private_algorithm_ranges_equal                                [system] { header "__algorithm/ranges_equal.h" }
++module std_private_algorithm_ranges_equal_range                          [system] {
++  header "__algorithm/ranges_equal_range.h"
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_fill                                 [system] { header "__algorithm/ranges_fill.h" }
++module std_private_algorithm_ranges_fill_n                               [system] { header "__algorithm/ranges_fill_n.h" }
++module std_private_algorithm_ranges_find                                 [system] { header "__algorithm/ranges_find.h" }
++module std_private_algorithm_ranges_find_end                             [system] { header "__algorithm/ranges_find_end.h" }
++module std_private_algorithm_ranges_find_first_of                        [system] { header "__algorithm/ranges_find_first_of.h" }
++module std_private_algorithm_ranges_find_if                              [system] { header "__algorithm/ranges_find_if.h" }
++module std_private_algorithm_ranges_find_if_not                          [system] { header "__algorithm/ranges_find_if_not.h" }
++module std_private_algorithm_ranges_for_each                             [system] {
++  header "__algorithm/ranges_for_each.h"
++  export std_private_algorithm_in_fun_result
++}
++module std_private_algorithm_ranges_for_each_n                           [system] {
++  header "__algorithm/ranges_for_each_n.h"
++  export std_private_algorithm_in_fun_result
++}
++module std_private_algorithm_ranges_generate                             [system] { header "__algorithm/ranges_generate.h" }
++module std_private_algorithm_ranges_generate_n                           [system] { header "__algorithm/ranges_generate_n.h" }
++module std_private_algorithm_ranges_includes                             [system] {
++  header "__algorithm/ranges_includes.h"
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_inplace_merge                        [system] {
++  header "__algorithm/ranges_inplace_merge.h"
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_is_heap                              [system] {
++  header "__algorithm/ranges_is_heap.h"
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_is_heap_until                        [system] {
++  header "__algorithm/ranges_is_heap_until.h"
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_is_partitioned                       [system] { header "__algorithm/ranges_is_partitioned.h" }
++module std_private_algorithm_ranges_is_permutation                       [system] { header "__algorithm/ranges_is_permutation.h" }
++module std_private_algorithm_ranges_is_sorted                            [system] {
++  header "__algorithm/ranges_is_sorted.h"
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_is_sorted_until                      [system] {
++  header "__algorithm/ranges_is_sorted_until.h"
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_iterator_concept                     [system] { header "__algorithm/ranges_iterator_concept.h" }
++module std_private_algorithm_ranges_lexicographical_compare              [system] {
++  header "__algorithm/ranges_lexicographical_compare.h"
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_lower_bound                          [system] {
++  header "__algorithm/ranges_lower_bound.h"
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_make_heap                            [system] {
++  header "__algorithm/ranges_make_heap.h"
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_max                                  [system] {
++  header "__algorithm/ranges_max.h"
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_max_element                          [system] {
++  header "__algorithm/ranges_max_element.h"
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_merge                                [system] {
++  header "__algorithm/ranges_merge.h"
++  export std_private_algorithm_in_in_out_result
++}
++module std_private_algorithm_ranges_min                                  [system] {
++  header "__algorithm/ranges_min.h"
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_min_element                          [system] {
++  header "__algorithm/ranges_min_element.h"
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_minmax                               [system] {
++  header "__algorithm/ranges_minmax.h"
++  export std_private_functional_ranges_operations
++  export std_private_algorithm_min_max_result
++}
++module std_private_algorithm_ranges_minmax_element                       [system] {
++  header "__algorithm/ranges_minmax_element.h"
++  export std_private_functional_ranges_operations
++  export std_private_algorithm_min_max_result
++}
++module std_private_algorithm_ranges_mismatch                             [system] {
++  header "__algorithm/ranges_mismatch.h"
++  export std_private_algorithm_in_in_result
++}
++module std_private_algorithm_ranges_move                                 [system] {
++  header "__algorithm/ranges_move.h"
++  export std_private_algorithm_in_out_result
++}
++module std_private_algorithm_ranges_move_backward                        [system] {
++  header "__algorithm/ranges_move_backward.h"
++  export std_private_algorithm_in_out_result
++}
++module std_private_algorithm_ranges_next_permutation                     [system] {
++  header "__algorithm/ranges_next_permutation.h"
++  export std_private_algorithm_in_found_result
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_none_of                              [system] { header "__algorithm/ranges_none_of.h" }
++module std_private_algorithm_ranges_nth_element                          [system] {
++  header "__algorithm/ranges_nth_element.h"
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_partial_sort                         [system] {
++  header "__algorithm/ranges_partial_sort.h"
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_partial_sort_copy                    [system] {
++  header "__algorithm/ranges_partial_sort_copy.h"
++  export std_private_algorithm_in_out_result
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_partition                            [system] { header "__algorithm/ranges_partition.h" }
++module std_private_algorithm_ranges_partition_copy                       [system] { header "__algorithm/ranges_partition_copy.h" }
++module std_private_algorithm_ranges_partition_point                      [system] { header "__algorithm/ranges_partition_point.h" }
++module std_private_algorithm_ranges_pop_heap                             [system] {
++  header "__algorithm/ranges_pop_heap.h"
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_prev_permutation                     [system] {
++  header "__algorithm/ranges_prev_permutation.h"
++  export std_private_algorithm_in_found_result
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_push_heap                            [system] {
++  header "__algorithm/ranges_push_heap.h"
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_remove                               [system] { header "__algorithm/ranges_remove.h" }
++module std_private_algorithm_ranges_remove_copy                          [system] {
++  header "__algorithm/ranges_remove_copy.h"
++  export std_private_algorithm_in_out_result
++}
++module std_private_algorithm_ranges_remove_copy_if                       [system] {
++  header "__algorithm/ranges_remove_copy_if.h"
++  export std_private_algorithm_in_out_result
++}
++module std_private_algorithm_ranges_remove_if                            [system] { header "__algorithm/ranges_remove_if.h" }
++module std_private_algorithm_ranges_replace                              [system] { header "__algorithm/ranges_replace.h" }
++module std_private_algorithm_ranges_replace_copy                         [system] {
++  header "__algorithm/ranges_replace_copy.h"
++  export std_private_algorithm_in_out_result
++}
++module std_private_algorithm_ranges_replace_copy_if                      [system] {
++  header "__algorithm/ranges_replace_copy_if.h"
++  export std_private_algorithm_in_out_result
++}
++module std_private_algorithm_ranges_replace_if                           [system] { header "__algorithm/ranges_replace_if.h" }
++module std_private_algorithm_ranges_reverse                              [system] { header "__algorithm/ranges_reverse.h" }
++module std_private_algorithm_ranges_reverse_copy                         [system] {
++  header "__algorithm/ranges_reverse_copy.h"
++  export std_private_algorithm_in_out_result
++}
++module std_private_algorithm_ranges_rotate                               [system] { header "__algorithm/ranges_rotate.h" }
++module std_private_algorithm_ranges_rotate_copy                          [system] {
++  header "__algorithm/ranges_rotate_copy.h"
++  export std_private_algorithm_in_out_result
++}
++module std_private_algorithm_ranges_sample                               [system] { header "__algorithm/ranges_sample.h" }
++module std_private_algorithm_ranges_search                               [system] { header "__algorithm/ranges_search.h" }
++module std_private_algorithm_ranges_search_n                             [system] { header "__algorithm/ranges_search_n.h" }
++module std_private_algorithm_ranges_set_difference                       [system] {
++  header "__algorithm/ranges_set_difference.h"
++  export std_private_algorithm_in_out_result
++}
++module std_private_algorithm_ranges_set_intersection                     [system] {
++  header "__algorithm/ranges_set_intersection.h"
++  export std_private_algorithm_in_in_out_result
++}
++module std_private_algorithm_ranges_set_symmetric_difference             [system] {
++  header "__algorithm/ranges_set_symmetric_difference.h"
++  export std_private_algorithm_in_in_out_result
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_set_union                            [system] {
++  header "__algorithm/ranges_set_union.h"
++  export std_private_algorithm_in_in_out_result
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_shuffle                              [system] { header "__algorithm/ranges_shuffle.h" }
++module std_private_algorithm_ranges_sort                                 [system] {
++  header "__algorithm/ranges_sort.h"
++  export std_private_algorithm_make_projected
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_sort_heap                            [system] {
++  header "__algorithm/ranges_sort_heap.h"
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_stable_partition                     [system] { header "__algorithm/ranges_stable_partition.h" }
++module std_private_algorithm_ranges_stable_sort                          [system] {
++  header "__algorithm/ranges_stable_sort.h"
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_ranges_starts_with                          [system] { header "__algorithm/ranges_starts_with.h" }
++module std_private_algorithm_ranges_swap_ranges                          [system] {
++  header "__algorithm/ranges_swap_ranges.h"
++  export std_private_algorithm_in_in_result
++}
++module std_private_algorithm_ranges_transform                            [system] {
++  header "__algorithm/ranges_transform.h"
++  export std_private_algorithm_in_in_out_result
++  export std_private_algorithm_in_out_result
++}
++module std_private_algorithm_ranges_unique                               [system] { header "__algorithm/ranges_unique.h" }
++module std_private_algorithm_ranges_unique_copy                          [system] {
++  header "__algorithm/ranges_unique_copy.h"
++  export std_private_algorithm_in_out_result
++}
++module std_private_algorithm_ranges_upper_bound                          [system] {
++  header "__algorithm/ranges_upper_bound.h"
++  export std_private_functional_ranges_operations
++}
++module std_private_algorithm_remove                                      [system] { header "__algorithm/remove.h" }
++module std_private_algorithm_remove_copy                                 [system] { header "__algorithm/remove_copy.h" }
++module std_private_algorithm_remove_copy_if                              [system] { header "__algorithm/remove_copy_if.h" }
++module std_private_algorithm_remove_if                                   [system] { header "__algorithm/remove_if.h" }
++module std_private_algorithm_replace                                     [system] { header "__algorithm/replace.h" }
++module std_private_algorithm_replace_copy                                [system] { header "__algorithm/replace_copy.h" }
++module std_private_algorithm_replace_copy_if                             [system] { header "__algorithm/replace_copy_if.h" }
++module std_private_algorithm_replace_if                                  [system] { header "__algorithm/replace_if.h" }
++module std_private_algorithm_reverse                                     [system] { header "__algorithm/reverse.h" }
++module std_private_algorithm_reverse_copy                                [system] { header "__algorithm/reverse_copy.h" }
++module std_private_algorithm_rotate                                      [system] { header "__algorithm/rotate.h" }
++module std_private_algorithm_rotate_copy                                 [system] { header "__algorithm/rotate_copy.h" }
++module std_private_algorithm_sample                                      [system] { header "__algorithm/sample.h" }
++module std_private_algorithm_search                                      [system] { header "__algorithm/search.h" }
++module std_private_algorithm_search_n                                    [system] { header "__algorithm/search_n.h" }
++module std_private_algorithm_set_difference                              [system] { header "__algorithm/set_difference.h" }
++module std_private_algorithm_set_intersection                            [system] { header "__algorithm/set_intersection.h" }
++module std_private_algorithm_set_symmetric_difference                    [system] { header "__algorithm/set_symmetric_difference.h" }
++module std_private_algorithm_set_union                                   [system] { header "__algorithm/set_union.h" }
++module std_private_algorithm_shift_left                                  [system] { header "__algorithm/shift_left.h" }
++module std_private_algorithm_shift_right                                 [system] { header "__algorithm/shift_right.h" }
++module std_private_algorithm_shuffle                                     [system] { header "__algorithm/shuffle.h" }
++module std_private_algorithm_sift_down                                   [system] { header "__algorithm/sift_down.h" }
++module std_private_algorithm_sort                                        [system] {
++  header "__algorithm/sort.h"
++  export std_private_debug_utils_strict_weak_ordering_check
++}
++module std_private_algorithm_sort_heap                                   [system] { header "__algorithm/sort_heap.h" }
++module std_private_algorithm_stable_partition                            [system] { header "__algorithm/stable_partition.h" }
++module std_private_algorithm_stable_sort                                 [system] { header "__algorithm/stable_sort.h" }
++module std_private_algorithm_swap_ranges                                 [system] {
++  header "__algorithm/swap_ranges.h"
++  export std_private_algorithm_iterator_operations
++}
++module std_private_algorithm_three_way_comp_ref_type                     [system] { header "__algorithm/three_way_comp_ref_type.h" }
++module std_private_algorithm_transform                                   [system] { header "__algorithm/transform.h" }
++module std_private_algorithm_uniform_random_bit_generator_adaptor        [system] { header "__algorithm/uniform_random_bit_generator_adaptor.h" }
++module std_private_algorithm_unique                                      [system] { header "__algorithm/unique.h" }
++module std_private_algorithm_unique_copy                                 [system] { header "__algorithm/unique_copy.h" }
++module std_private_algorithm_unwrap_iter                                 [system] {
++  header "__algorithm/unwrap_iter.h"
++  export std_private_iterator_iterator_traits
++}
++module std_private_algorithm_unwrap_range                                [system] {
++  header "__algorithm/unwrap_range.h"
++  export std_private_utility_pair
++}
++module std_private_algorithm_upper_bound                                 [system] { header "__algorithm/upper_bound.h" }
++
++module std_private_array_array_fwd [system] { header "__fwd/array.h" }
++
++module std_private_atomic_aliases             [system] {
++  header "__atomic/aliases.h"
++  export std_private_atomic_atomic
++}
++module std_private_atomic_atomic              [system] {
++  header "__atomic/atomic.h"
++  export std_private_atomic_atomic_base
++}
++module std_private_atomic_atomic_base         [system] { header "__atomic/atomic_base.h" }
++module std_private_atomic_atomic_flag         [system] {
++  header "__atomic/atomic_flag.h"
++  export *
++}
++module std_private_atomic_atomic_init         [system] { header "__atomic/atomic_init.h" }
++module std_private_atomic_atomic_lock_free    [system] { header "__atomic/atomic_lock_free.h" }
++module std_private_atomic_atomic_sync         [system] { header "__atomic/atomic_sync.h" }
++module std_private_atomic_check_memory_order  [system] { header "__atomic/check_memory_order.h" }
++module std_private_atomic_contention_t        [system] { header "__atomic/contention_t.h" }
++module std_private_atomic_cxx_atomic_impl     [system] { header "__atomic/cxx_atomic_impl.h" }
++module std_private_atomic_fence               [system] { header "__atomic/fence.h" }
++module std_private_atomic_is_always_lock_free [system] { header "__atomic/is_always_lock_free.h" }
++module std_private_atomic_kill_dependency     [system] { header "__atomic/kill_dependency.h" }
++module std_private_atomic_memory_order        [system] { header "__atomic/memory_order.h" }
++
++module std_private_bit_bit_cast       [system] { header "__bit/bit_cast.h" }
++module std_private_bit_bit_ceil       [system] { header "__bit/bit_ceil.h" }
++module std_private_bit_bit_floor      [system] { header "__bit/bit_floor.h" }
++module std_private_bit_bit_log2       [system] { header "__bit/bit_log2.h" }
++module std_private_bit_bit_width      [system] { header "__bit/bit_width.h" }
++module std_private_bit_blsr           [system] { header "__bit/blsr.h" }
++module std_private_bit_byteswap       [system] { header "__bit/byteswap.h" }
++module std_private_bit_countl         [system] { header "__bit/countl.h" }
++module std_private_bit_countr         [system] { header "__bit/countr.h" }
++module std_private_bit_endian         [system] { header "__bit/endian.h" }
++module std_private_bit_has_single_bit [system] { header "__bit/has_single_bit.h" }
++module std_private_bit_popcount       [system] { header "__bit/popcount.h" }
++module std_private_bit_rotate         [system] { header "__bit/rotate.h" }
++
++module std_private_charconv_chars_format            [system] { header "__charconv/chars_format.h" }
++module std_private_charconv_from_chars_integral     [system] { header "__charconv/from_chars_integral.h" }
++module std_private_charconv_from_chars_result       [system] { header "__charconv/from_chars_result.h" }
++module std_private_charconv_tables                  [system] { header "__charconv/tables.h" }
++module std_private_charconv_to_chars                [system] { header "__charconv/to_chars.h" }
++module std_private_charconv_to_chars_base_10        [system] { header "__charconv/to_chars_base_10.h" }
++module std_private_charconv_to_chars_floating_point [system] { header "__charconv/to_chars_floating_point.h" }
++module std_private_charconv_to_chars_integral       [system] { header "__charconv/to_chars_integral.h" }
++module std_private_charconv_to_chars_result         [system] { header "__charconv/to_chars_result.h" }
++module std_private_charconv_traits                  [system] { header "__charconv/traits.h" }
++
++module std_private_chrono_calendar               [system] { header "__chrono/calendar.h" }
++module std_private_chrono_concepts               [system] { header "__chrono/concepts.h" }
++module std_private_chrono_convert_to_timespec    [system] { header "__chrono/convert_to_timespec.h" }
++module std_private_chrono_convert_to_tm          [system] { header "__chrono/convert_to_tm.h" }
++module std_private_chrono_day                    [system] { header "__chrono/day.h" }
++module std_private_chrono_duration               [system] {
++  header "__chrono/duration.h"
++  export std_private_type_traits_is_convertible
++}
++module std_private_chrono_file_clock             [system] { header "__chrono/file_clock.h" }
++module std_private_chrono_formatter              [system] {
++  header "__chrono/formatter.h"
++}
++module std_private_chrono_hh_mm_ss               [system] { header "__chrono/hh_mm_ss.h" }
++module std_private_chrono_high_resolution_clock  [system] {
++  header "__chrono/high_resolution_clock.h"
++  export std_private_chrono_steady_clock
++  export std_private_chrono_system_clock
++}
++module std_private_chrono_literals               [system] { header "__chrono/literals.h" }
++module std_private_chrono_month                  [system] { header "__chrono/month.h" }
++module std_private_chrono_month_weekday          [system] { header "__chrono/month_weekday.h" }
++module std_private_chrono_monthday               [system] { header "__chrono/monthday.h" }
++module std_private_chrono_ostream                [system] {
++  header "__chrono/ostream.h"
++}
++module std_private_chrono_parser_std_format_spec [system] {
++  header "__chrono/parser_std_format_spec.h"
++}
++module std_private_chrono_statically_widen       [system] { header "__chrono/statically_widen.h" }
++module std_private_chrono_steady_clock           [system] {
++  header "__chrono/steady_clock.h"
++  export std_private_chrono_time_point
++}
++module std_private_chrono_system_clock           [system] {
++  header "__chrono/system_clock.h"
++  export std_private_chrono_time_point
++}
++module std_private_chrono_time_point             [system] { header "__chrono/time_point.h" }
++module std_private_chrono_weekday                [system] { header "__chrono/weekday.h" }
++module std_private_chrono_year                   [system] { header "__chrono/year.h" }
++module std_private_chrono_year_month             [system] { header "__chrono/year_month.h" }
++module std_private_chrono_year_month_day         [system] { header "__chrono/year_month_day.h" }
++module std_private_chrono_year_month_weekday     [system] { header "__chrono/year_month_weekday.h" }
++
++module std_private_compare_common_comparison_category     [system] { header "__compare/common_comparison_category.h" }
++module std_private_compare_compare_partial_order_fallback [system] { header "__compare/compare_partial_order_fallback.h" }
++module std_private_compare_compare_strong_order_fallback  [system] { header "__compare/compare_strong_order_fallback.h" }
++module std_private_compare_compare_three_way              [system] { header "__compare/compare_three_way.h" }
++module std_private_compare_compare_three_way_result       [system] { header "__compare/compare_three_way_result.h" }
++module std_private_compare_compare_weak_order_fallback    [system] { header "__compare/compare_weak_order_fallback.h" }
++module std_private_compare_is_eq                          [system] { header "__compare/is_eq.h" }
++module std_private_compare_ordering                       [system] { header "__compare/ordering.h" }
++module std_private_compare_partial_order                  [system] { header "__compare/partial_order.h" }
++module std_private_compare_strong_order                   [system] { header "__compare/strong_order.h" }
++module std_private_compare_synth_three_way                [system] { header "__compare/synth_three_way.h" }
++module std_private_compare_three_way_comparable           [system] { header "__compare/three_way_comparable.h" }
++module std_private_compare_weak_order                     [system] { header "__compare/weak_order.h" }
++
++module std_private_concepts_arithmetic            [system] { header "__concepts/arithmetic.h" }
++module std_private_concepts_assignable            [system] { header "__concepts/assignable.h" }
++module std_private_concepts_boolean_testable      [system] { header "__concepts/boolean_testable.h" }
++module std_private_concepts_class_or_enum         [system] { header "__concepts/class_or_enum.h" }
++module std_private_concepts_common_reference_with [system] { header "__concepts/common_reference_with.h" }
++module std_private_concepts_common_with           [system] { header "__concepts/common_with.h" }
++module std_private_concepts_constructible         [system] {
++  header "__concepts/constructible.h"
++  export std_private_concepts_destructible
++}
++module std_private_concepts_convertible_to        [system] { header "__concepts/convertible_to.h" }
++module std_private_concepts_copyable              [system] { header "__concepts/copyable.h" }
++module std_private_concepts_derived_from          [system] { header "__concepts/derived_from.h" }
++module std_private_concepts_destructible          [system] {
++  header "__concepts/destructible.h"
++  export std_private_type_traits_is_nothrow_destructible
++}
++module std_private_concepts_different_from        [system] { header "__concepts/different_from.h" }
++module std_private_concepts_equality_comparable   [system] {
++  header "__concepts/equality_comparable.h"
++  export std_private_type_traits_common_reference
++}
++module std_private_concepts_invocable             [system] { header "__concepts/invocable.h" }
++module std_private_concepts_movable               [system] {
++  header "__concepts/movable.h"
++  export std_private_type_traits_is_object
++}
++module std_private_concepts_predicate             [system] { header "__concepts/predicate.h" }
++module std_private_concepts_regular               [system] { header "__concepts/regular.h" }
++module std_private_concepts_relation              [system] { header "__concepts/relation.h" }
++module std_private_concepts_same_as               [system] {
++  header "__concepts/same_as.h"
++  export std_private_type_traits_is_same
++}
++module std_private_concepts_semiregular           [system] { header "__concepts/semiregular.h" }
++module std_private_concepts_swappable             [system] { header "__concepts/swappable.h" }
++module std_private_concepts_totally_ordered       [system] { header "__concepts/totally_ordered.h" }
++
++module std_private_condition_variable_condition_variable [system] {
++  header "__condition_variable/condition_variable.h"
++  export *
++}
++
++module std_private_coroutine_coroutine_handle      [system] { header "__coroutine/coroutine_handle.h" }
++module std_private_coroutine_coroutine_traits      [system] { header "__coroutine/coroutine_traits.h" }
++module std_private_coroutine_noop_coroutine_handle [system] { header "__coroutine/noop_coroutine_handle.h" }
++module std_private_coroutine_trivial_awaitables    [system] { header "__coroutine/trivial_awaitables.h" }
++
++module std_private_debug_utils_randomize_range            [system] { header "__debug_utils/randomize_range.h" }
++module std_private_debug_utils_strict_weak_ordering_check [system] {
++  header "__debug_utils/strict_weak_ordering_check.h"
++  export std_private_type_traits_is_constant_evaluated
++}
++
++module std_private_exception_exception        [system] { header "__exception/exception.h" }
++module std_private_exception_exception_ptr    [system] {
++  header "__exception/exception_ptr.h"
++  export std_private_exception_operations
++}
++module std_private_exception_nested_exception [system] { header "__exception/nested_exception.h" }
++module std_private_exception_operations       [system] { header "__exception/operations.h" }
++module std_private_exception_terminate        [system] { header "__exception/terminate.h" }
++
++module std_private_expected_bad_expected_access [system] { header "__expected/bad_expected_access.h" }
++module std_private_expected_expected            [system] { header "__expected/expected.h" }
++module std_private_expected_unexpect            [system] { header "__expected/unexpect.h" }
++module std_private_expected_unexpected          [system] { header "__expected/unexpected.h" }
++
++module std_private_filesystem_copy_options                 [system] { header "__filesystem/copy_options.h" }
++module std_private_filesystem_directory_entry              [system] {
++  header "__filesystem/directory_entry.h"
++  export *
++}
++module std_private_filesystem_directory_iterator           [system] {
++  header "__filesystem/directory_iterator.h"
++  export *
++}
++module std_private_filesystem_directory_options            [system] { header "__filesystem/directory_options.h" }
++module std_private_filesystem_file_status                  [system] { header "__filesystem/file_status.h" }
++module std_private_filesystem_file_time_type               [system] { header "__filesystem/file_time_type.h" }
++module std_private_filesystem_file_type                    [system] { header "__filesystem/file_type.h" }
++module std_private_filesystem_filesystem_error             [system] {
++  header "__filesystem/filesystem_error.h"
++  export *
++}
++module std_private_filesystem_operations                   [system] { header "__filesystem/operations.h" }
++module std_private_filesystem_path                         [system] {
++  header "__filesystem/path.h"
++  export *
++}
++module std_private_filesystem_path_iterator                [system] { header "__filesystem/path_iterator.h" }
++module std_private_filesystem_perm_options                 [system] { header "__filesystem/perm_options.h" }
++module std_private_filesystem_perms                        [system] { header "__filesystem/perms.h" }
++module std_private_filesystem_recursive_directory_iterator [system] {
++  header "__filesystem/recursive_directory_iterator.h"
++  export *
++}
++module std_private_filesystem_space_info                   [system] { header "__filesystem/space_info.h" }
++module std_private_filesystem_u8path                       [system] { header "__filesystem/u8path.h" }
++
++module std_private_format_buffer                          [system] { header "__format/buffer.h" }
++module std_private_format_concepts                        [system] { header "__format/concepts.h" }
++module std_private_format_container_adaptor               [system] { header "__format/container_adaptor.h" }
++module std_private_format_enable_insertable               [system] { header "__format/enable_insertable.h" }
++module std_private_format_escaped_output_table            [system] { header "__format/escaped_output_table.h" }
++module std_private_format_extended_grapheme_cluster_table [system] { header "__format/extended_grapheme_cluster_table.h" }
++module std_private_format_format_arg                      [system] { header "__format/format_arg.h" }
++module std_private_format_format_arg_store                [system] { header "__format/format_arg_store.h" }
++module std_private_format_format_args                     [system] { header "__format/format_args.h" }
++module std_private_format_format_context                  [system] {
++  header "__format/format_context.h"
++  export *
++}
++module std_private_format_format_error                    [system] { header "__format/format_error.h" }
++module std_private_format_format_functions                [system] {
++  header "__format/format_functions.h"
++  export std_string
++}
++module std_private_format_format_fwd                      [system] { header "__format/format_fwd.h" }
++module std_private_format_format_parse_context            [system] { header "__format/format_parse_context.h" }
++module std_private_format_format_string                   [system] { header "__format/format_string.h" }
++module std_private_format_format_to_n_result              [system] {
++  header "__format/format_to_n_result.h"
++  export std_private_iterator_incrementable_traits
++}
++module std_private_format_formatter                       [system] { header "__format/formatter.h" }
++module std_private_format_formatter_bool                  [system] { header "__format/formatter_bool.h" }
++module std_private_format_formatter_char                  [system] { header "__format/formatter_char.h" }
++module std_private_format_formatter_floating_point        [system] { header "__format/formatter_floating_point.h" }
++module std_private_format_formatter_integer               [system] { header "__format/formatter_integer.h" }
++module std_private_format_formatter_integral              [system] { header "__format/formatter_integral.h" }
++module std_private_format_formatter_output                [system] { header "__format/formatter_output.h" }
++module std_private_format_formatter_pointer               [system] { header "__format/formatter_pointer.h" }
++module std_private_format_formatter_string                [system] { header "__format/formatter_string.h" }
++module std_private_format_formatter_tuple                 [system] { header "__format/formatter_tuple.h" }
++module std_private_format_parser_std_format_spec          [system] { header "__format/parser_std_format_spec.h" }
++module std_private_format_range_default_formatter         [system] { header "__format/range_default_formatter.h" }
++module std_private_format_range_formatter                 [system] { header "__format/range_formatter.h" }
++module std_private_format_unicode                         [system] {
++  header "__format/unicode.h"
++  export std_private_format_extended_grapheme_cluster_table
++}
++module std_private_format_width_estimation_table          [system] { header "__format/width_estimation_table.h" }
++module std_private_format_write_escaped                   [system] { header "__format/write_escaped.h" }
++
++module std_private_functional_binary_function            [system] { header "__functional/binary_function.h" }
++module std_private_functional_binary_negate              [system] { header "__functional/binary_negate.h" }
++module std_private_functional_bind                       [system] { header "__functional/bind.h" }
++module std_private_functional_bind_back                  [system] { header "__functional/bind_back.h" }
++module std_private_functional_bind_front                 [system] { header "__functional/bind_front.h" }
++module std_private_functional_binder1st                  [system] { header "__functional/binder1st.h" }
++module std_private_functional_binder2nd                  [system] { header "__functional/binder2nd.h" }
++module std_private_functional_boyer_moore_searcher       [system] {
++  header "__functional/boyer_moore_searcher.h"
++  export std_private_memory_shared_ptr
++}
++module std_private_functional_compose                    [system] {
++  header "__functional/compose.h"
++  export std_private_functional_perfect_forward
++}
++module std_private_functional_default_searcher           [system] { header "__functional/default_searcher.h" }
++module std_private_functional_function                   [system] { header "__functional/function.h" }
++module std_private_functional_hash                       [system] {
++  header "__functional/hash.h"
++  export std_cstdint
++  export std_private_type_traits_underlying_type
++  export std_private_utility_pair
++}
++module std_private_functional_hash_fwd                   [system] { header "__fwd/hash.h" }
++module std_private_functional_identity                   [system] { header "__functional/identity.h" }
++module std_private_functional_invoke                     [system] {
++  header "__functional/invoke.h"
++  export *
++}
++module std_private_functional_is_transparent             [system] { header "__functional/is_transparent.h" }
++module std_private_functional_mem_fn                     [system] { header "__functional/mem_fn.h" }
++module std_private_functional_mem_fun_ref                [system] { header "__functional/mem_fun_ref.h" }
++module std_private_functional_not_fn                     [system] { header "__functional/not_fn.h" }
++module std_private_functional_operations                 [system] { header "__functional/operations.h" }
++module std_private_functional_perfect_forward            [system] {
++  header "__functional/perfect_forward.h"
++  export *
++}
++module std_private_functional_pointer_to_binary_function [system] { header "__functional/pointer_to_binary_function.h" }
++module std_private_functional_pointer_to_unary_function  [system] { header "__functional/pointer_to_unary_function.h" }
++module std_private_functional_ranges_operations          [system] { header "__functional/ranges_operations.h" }
++module std_private_functional_reference_wrapper          [system] { header "__functional/reference_wrapper.h" }
++module std_private_functional_unary_function             [system] { header "__functional/unary_function.h" }
++module std_private_functional_unary_negate               [system] { header "__functional/unary_negate.h" }
++module std_private_functional_weak_result_type           [system] { header "__functional/weak_result_type.h" }
++
++module std_private_ios_fpos [system] { header "__ios/fpos.h" }
++
++module std_private_iosfwd_fstream_fwd   [system] { header "__fwd/fstream.h" }
++module std_private_iosfwd_ios_fwd       [system] { header "__fwd/ios.h" }
++module std_private_iosfwd_istream_fwd   [system] { header "__fwd/istream.h" }
++module std_private_iosfwd_ostream_fwd   [system] { header "__fwd/ostream.h" }
++module std_private_iosfwd_sstream_fwd   [system] { header "__fwd/sstream.h" }
++module std_private_iosfwd_streambuf_fwd [system] { header "__fwd/streambuf.h" }
++
++module std_private_iterator_access                  [system] { header "__iterator/access.h" }
++module std_private_iterator_advance                 [system] { header "__iterator/advance.h" }
++module std_private_iterator_back_insert_iterator    [system] { header "__iterator/back_insert_iterator.h" }
++module std_private_iterator_bounded_iter            [system] { header "__iterator/bounded_iter.h" }
++module std_private_iterator_common_iterator         [system] { header "__iterator/common_iterator.h" }
++module std_private_iterator_concepts                [system] {
++  header "__iterator/concepts.h"
++  export std_private_concepts_constructible
++  export std_private_concepts_equality_comparable
++  export std_private_concepts_movable
++  export std_private_type_traits_common_reference
++  export std_private_type_traits_is_reference
++  export std_private_type_traits_remove_cvref
++}
++module std_private_iterator_counted_iterator        [system] { header "__iterator/counted_iterator.h" }
++module std_private_iterator_cpp17_iterator_concepts [system] { header "__iterator/cpp17_iterator_concepts.h" }
++module std_private_iterator_data                    [system] { header "__iterator/data.h" }
++module std_private_iterator_default_sentinel        [system] { header "__iterator/default_sentinel.h" }
++module std_private_iterator_distance                [system] {
++  header "__iterator/distance.h"
++  export std_private_ranges_size
++}
++module std_private_iterator_empty                   [system] { header "__iterator/empty.h" }
++module std_private_iterator_erase_if_container      [system] { header "__iterator/erase_if_container.h" }
++module std_private_iterator_front_insert_iterator   [system] { header "__iterator/front_insert_iterator.h" }
++module std_private_iterator_incrementable_traits    [system] { header "__iterator/incrementable_traits.h" }
++module std_private_iterator_indirectly_comparable   [system] { header "__iterator/indirectly_comparable.h" }
++module std_private_iterator_insert_iterator         [system] { header "__iterator/insert_iterator.h" }
++module std_private_iterator_istream_iterator        [system] { header "__iterator/istream_iterator.h" }
++module std_private_iterator_istreambuf_iterator     [system] { header "__iterator/istreambuf_iterator.h" }
++module std_private_iterator_iter_move               [system] { header "__iterator/iter_move.h" }
++module std_private_iterator_iter_swap               [system] { header "__iterator/iter_swap.h" }
++module std_private_iterator_iterator                [system] { header "__iterator/iterator.h" }
++module std_private_iterator_iterator_traits         [system] {
++  header "__iterator/iterator_traits.h"
++  export std_private_type_traits_is_primary_template
++}
++module std_private_iterator_iterator_with_data      [system] { header "__iterator/iterator_with_data.h" }
++module std_private_iterator_mergeable               [system] {
++  header "__iterator/mergeable.h"
++  export std_private_functional_ranges_operations
++}
++module std_private_iterator_move_iterator           [system] { header "__iterator/move_iterator.h" }
++module std_private_iterator_move_sentinel           [system] { header "__iterator/move_sentinel.h" }
++module std_private_iterator_next                    [system] { header "__iterator/next.h" }
++module std_private_iterator_ostream_iterator        [system] { header "__iterator/ostream_iterator.h" }
++module std_private_iterator_ostreambuf_iterator     [system] {
++  header "__iterator/ostreambuf_iterator.h"
++  export *
++}
++module std_private_iterator_permutable              [system] { header "__iterator/permutable.h" }
++module std_private_iterator_prev                    [system] { header "__iterator/prev.h" }
++module std_private_iterator_projected               [system] { header "__iterator/projected.h" }
++module std_private_iterator_ranges_iterator_traits  [system] { header "__iterator/ranges_iterator_traits.h" }
++module std_private_iterator_readable_traits         [system] { header "__iterator/readable_traits.h" }
++module std_private_iterator_reverse_access          [system] { header "__iterator/reverse_access.h" }
++module std_private_iterator_reverse_iterator        [system] { header "__iterator/reverse_iterator.h" }
++module std_private_iterator_segmented_iterator      [system] { header "__iterator/segmented_iterator.h" }
++module std_private_iterator_size                    [system] { header "__iterator/size.h" }
++module std_private_iterator_sortable                [system] {
++  header "__iterator/sortable.h"
++  export std_private_functional_ranges_operations
++}
++module std_private_iterator_unreachable_sentinel    [system] { header "__iterator/unreachable_sentinel.h" }
++module std_private_iterator_wrap_iter               [system] { header "__iterator/wrap_iter.h" }
++
++module std_private_locale_locale_base_api_bsd_locale_defaults  [system] { textual header "__locale_dir/locale_base_api/bsd_locale_defaults.h" }
++module std_private_locale_locale_base_api_bsd_locale_fallbacks [system] { textual header "__locale_dir/locale_base_api/bsd_locale_fallbacks.h" }
++module std_private_locale_locale_base_api_locale_guard         [system] { header "__locale_dir/locale_base_api/locale_guard.h" }
++
++module std_private_mdspan_default_accessor [system] { header "__mdspan/default_accessor.h" }
++module std_private_mdspan_extents          [system] {
++  header "__mdspan/extents.h"
++  export *
++}
++module std_private_mdspan_layout_left      [system] { header "__mdspan/layout_left.h" }
++module std_private_mdspan_layout_right     [system] { header "__mdspan/layout_right.h" }
++module std_private_mdspan_mdspan           [system] { header "__mdspan/mdspan.h" }
++module std_private_mdspan_mdspan_fwd       [system] { header "__fwd/mdspan.h" }
++
++module std_private_memory_addressof                       [system] { header "__memory/addressof.h" }
++module std_private_memory_align                           [system] { header "__memory/align.h" }
++module std_private_memory_aligned_alloc                   [system] { header "__memory/aligned_alloc.h" }
++module std_private_memory_allocate_at_least               [system] { header "__memory/allocate_at_least.h" }
++module std_private_memory_allocation_guard                [system] { header "__memory/allocation_guard.h" }
++module std_private_memory_allocator                       [system] { header "__memory/allocator.h" }
++module std_private_memory_allocator_arg_t                 [system] { header "__memory/allocator_arg_t.h" }
++module std_private_memory_allocator_destructor            [system] { header "__memory/allocator_destructor.h" }
++module std_private_memory_allocator_traits                [system] { header "__memory/allocator_traits.h" }
++module std_private_memory_assume_aligned                  [system] { header "__memory/assume_aligned.h" }
++module std_private_memory_auto_ptr                        [system] { header "__memory/auto_ptr.h" }
++module std_private_memory_builtin_new_allocator           [system] {
++  header "__memory/builtin_new_allocator.h"
++  export *
++}
++module std_private_memory_compressed_pair                 [system] { header "__memory/compressed_pair.h" }
++module std_private_memory_concepts                        [system] {
++  header "__memory/concepts.h"
++  export std_private_type_traits_remove_reference
++}
++module std_private_memory_construct_at                    [system] { header "__memory/construct_at.h" }
++module std_private_memory_destruct_n                      [system] { header "__memory/destruct_n.h" }
++module std_private_memory_pointer_traits                  [system] { header "__memory/pointer_traits.h" }
++module std_private_memory_ranges_construct_at             [system] { header "__memory/ranges_construct_at.h" }
++module std_private_memory_ranges_uninitialized_algorithms [system] {
++  header "__memory/ranges_uninitialized_algorithms.h"
++  export std_private_algorithm_in_out_result
++}
++module std_private_memory_raw_storage_iterator            [system] { header "__memory/raw_storage_iterator.h" }
++module std_private_memory_shared_ptr                      [system] {
++  header "__memory/shared_ptr.h"
++  export std_private_memory_uninitialized_algorithms
++}
++module std_private_memory_swap_allocator                  [system] { header "__memory/swap_allocator.h" }
++module std_private_memory_temp_value                      [system] { header "__memory/temp_value.h" }
++module std_private_memory_temporary_buffer                [system] { header "__memory/temporary_buffer.h" }
++module std_private_memory_uninitialized_algorithms        [system] {
++  header "__memory/uninitialized_algorithms.h"
++  export std_private_algorithm_copy
++}
++module std_private_memory_unique_ptr                      [system] {
++  header "__memory/unique_ptr.h"
++  export std_private_type_traits_add_lvalue_reference
++  export std_private_type_traits_is_pointer
++  export std_private_type_traits_type_identity
++}
++module std_private_memory_uses_allocator                  [system] { header "__memory/uses_allocator.h" }
++module std_private_memory_uses_allocator_construction     [system] { header "__memory/uses_allocator_construction.h" }
++module std_private_memory_voidify                         [system] { header "__memory/voidify.h" }
++
++module std_private_memory_resource_memory_resource              [system] { header "__memory_resource/memory_resource.h" }
++module std_private_memory_resource_memory_resource_fwd          [system] { header "__fwd/memory_resource.h" }
++module std_private_memory_resource_monotonic_buffer_resource    [system] { header "__memory_resource/monotonic_buffer_resource.h" }
++module std_private_memory_resource_polymorphic_allocator        [system] { header "__memory_resource/polymorphic_allocator.h" }
++module std_private_memory_resource_pool_options                 [system] { header "__memory_resource/pool_options.h" }
++module std_private_memory_resource_synchronized_pool_resource   [system] {
++  header "__memory_resource/synchronized_pool_resource.h"
++  export *
++}
++module std_private_memory_resource_unsynchronized_pool_resource [system] { header "__memory_resource/unsynchronized_pool_resource.h" }
++
++module std_private_mutex_lock_guard  [system] { header "__mutex/lock_guard.h" }
++module std_private_mutex_mutex       [system] { header "__mutex/mutex.h" }
++module std_private_mutex_tag_types   [system] { header "__mutex/tag_types.h" }
++module std_private_mutex_unique_lock [system] { header "__mutex/unique_lock.h" }
++
++module std_private_numeric_accumulate               [system] { header "__numeric/accumulate.h" }
++module std_private_numeric_adjacent_difference      [system] { header "__numeric/adjacent_difference.h" }
++module std_private_numeric_exclusive_scan           [system] { header "__numeric/exclusive_scan.h" }
++module std_private_numeric_gcd_lcm                  [system] { header "__numeric/gcd_lcm.h" }
++module std_private_numeric_inclusive_scan           [system] { header "__numeric/inclusive_scan.h" }
++module std_private_numeric_inner_product            [system] { header "__numeric/inner_product.h" }
++module std_private_numeric_iota                     [system] { header "__numeric/iota.h" }
++module std_private_numeric_midpoint                 [system] { header "__numeric/midpoint.h" }
++module std_private_numeric_partial_sum              [system] { header "__numeric/partial_sum.h" }
++module std_private_numeric_pstl_reduce              [system] { header "__numeric/pstl_reduce.h" }
++module std_private_numeric_pstl_transform_reduce    [system] {
++  header "__numeric/pstl_transform_reduce.h"
++  export *
++}
++module std_private_numeric_reduce                   [system] { header "__numeric/reduce.h" }
++module std_private_numeric_transform_exclusive_scan [system] { header "__numeric/transform_exclusive_scan.h" }
++module std_private_numeric_transform_inclusive_scan [system] { header "__numeric/transform_inclusive_scan.h" }
++module std_private_numeric_transform_reduce         [system] { header "__numeric/transform_reduce.h" }
++
++module std_private_random_bernoulli_distribution          [system] { header "__random/bernoulli_distribution.h" }
++module std_private_random_binomial_distribution           [system] { header "__random/binomial_distribution.h" }
++module std_private_random_cauchy_distribution             [system] { header "__random/cauchy_distribution.h" }
++module std_private_random_chi_squared_distribution        [system] { header "__random/chi_squared_distribution.h" }
++module std_private_random_clamp_to_integral               [system] { header "__random/clamp_to_integral.h" }
++module std_private_random_default_random_engine           [system] { header "__random/default_random_engine.h" }
++module std_private_random_discard_block_engine            [system] { header "__random/discard_block_engine.h" }
++module std_private_random_discrete_distribution           [system] {
++  header "__random/discrete_distribution.h"
++  export *
++}
++module std_private_random_exponential_distribution        [system] { header "__random/exponential_distribution.h" }
++module std_private_random_extreme_value_distribution      [system] { header "__random/extreme_value_distribution.h" }
++module std_private_random_fisher_f_distribution           [system] { header "__random/fisher_f_distribution.h" }
++module std_private_random_gamma_distribution              [system] { header "__random/gamma_distribution.h" }
++module std_private_random_generate_canonical              [system] { header "__random/generate_canonical.h" }
++module std_private_random_geometric_distribution          [system] { header "__random/geometric_distribution.h" }
++module std_private_random_independent_bits_engine         [system] { header "__random/independent_bits_engine.h" }
++module std_private_random_is_seed_sequence                [system] { header "__random/is_seed_sequence.h" }
++module std_private_random_is_valid                        [system] { header "__random/is_valid.h" }
++module std_private_random_knuth_b                         [system] { header "__random/knuth_b.h" }
++module std_private_random_linear_congruential_engine      [system] { header "__random/linear_congruential_engine.h" }
++module std_private_random_log2                            [system] { header "__random/log2.h" }
++module std_private_random_lognormal_distribution          [system] { header "__random/lognormal_distribution.h" }
++module std_private_random_mersenne_twister_engine         [system] { header "__random/mersenne_twister_engine.h" }
++module std_private_random_negative_binomial_distribution  [system] { header "__random/negative_binomial_distribution.h" }
++module std_private_random_normal_distribution             [system] { header "__random/normal_distribution.h" }
++module std_private_random_piecewise_constant_distribution [system] {
++  header "__random/piecewise_constant_distribution.h"
++  export *
++}
++module std_private_random_piecewise_linear_distribution   [system] {
++  header "__random/piecewise_linear_distribution.h"
++  export *
++}
++module std_private_random_poisson_distribution            [system] { header "__random/poisson_distribution.h" }
++module std_private_random_random_device                   [system] {
++  header "__random/random_device.h"
++  export *
++}
++module std_private_random_ranlux                          [system] { header "__random/ranlux.h" }
++module std_private_random_seed_seq                        [system] {
++  header "__random/seed_seq.h"
++  export *
++}
++module std_private_random_shuffle_order_engine            [system] { header "__random/shuffle_order_engine.h" }
++module std_private_random_student_t_distribution          [system] { header "__random/student_t_distribution.h" }
++module std_private_random_subtract_with_carry_engine      [system] { header "__random/subtract_with_carry_engine.h" }
++module std_private_random_uniform_int_distribution        [system] { header "__random/uniform_int_distribution.h" }
++module std_private_random_uniform_random_bit_generator    [system] { header "__random/uniform_random_bit_generator.h" }
++module std_private_random_uniform_real_distribution       [system] { header "__random/uniform_real_distribution.h" }
++module std_private_random_weibull_distribution            [system] { header "__random/weibull_distribution.h" }
++
++module std_private_ranges_access                     [system] { header "__ranges/access.h" }
++module std_private_ranges_all                        [system] {
++  header "__ranges/all.h"
++  export std_private_functional_compose
++  export std_private_functional_perfect_forward
++  export std_private_ranges_owning_view
++}
++module std_private_ranges_as_rvalue_view             [system] { header "__ranges/as_rvalue_view.h" }
++module std_private_ranges_common_view                [system] { header "__ranges/common_view.h" }
++module std_private_ranges_concepts                   [system] {
++  header "__ranges/concepts.h"
++  export std_private_iterator_concepts
++}
++module std_private_ranges_container_compatible_range [system] { header "__ranges/container_compatible_range.h" }
++module std_private_ranges_counted                    [system] {
++  header "__ranges/counted.h"
++  export std_span
++}
++module std_private_ranges_dangling                   [system] { header "__ranges/dangling.h" }
++module std_private_ranges_data                       [system] { header "__ranges/data.h" }
++module std_private_ranges_drop_view                  [system] { header "__ranges/drop_view.h" }
++module std_private_ranges_drop_while_view            [system] { header "__ranges/drop_while_view.h" }
++module std_private_ranges_elements_view              [system] { header "__ranges/elements_view.h" }
++module std_private_ranges_empty                      [system] { header "__ranges/empty.h" }
++module std_private_ranges_empty_view                 [system] { header "__ranges/empty_view.h" }
++module std_private_ranges_enable_borrowed_range      [system] { header "__ranges/enable_borrowed_range.h" }
++module std_private_ranges_enable_view                [system] { header "__ranges/enable_view.h" }
++module std_private_ranges_filter_view                [system] {
++  header "__ranges/filter_view.h"
++  export std_private_ranges_range_adaptor
++}
++module std_private_ranges_from_range                 [system] { header "__ranges/from_range.h" }
++module std_private_ranges_iota_view                  [system] { header "__ranges/iota_view.h" }
++module std_private_ranges_istream_view               [system] {
++  header "__ranges/istream_view.h"
++}
++module std_private_ranges_join_view                  [system] {
++  header "__ranges/join_view.h"
++  export std_private_iterator_iterator_with_data
++  export std_private_iterator_segmented_iterator
++}
++module std_private_ranges_lazy_split_view            [system] {
++  header "__ranges/lazy_split_view.h"
++  export std_private_ranges_non_propagating_cache
++}
++module std_private_ranges_movable_box                [system] { header "__ranges/movable_box.h" }
++module std_private_ranges_non_propagating_cache      [system] { header "__ranges/non_propagating_cache.h" }
++module std_private_ranges_owning_view                [system] { header "__ranges/owning_view.h" }
++module std_private_ranges_range_adaptor              [system] { header "__ranges/range_adaptor.h" }
++module std_private_ranges_rbegin                     [system] { header "__ranges/rbegin.h" }
++module std_private_ranges_ref_view                   [system] { header "__ranges/ref_view.h" }
++module std_private_ranges_rend                       [system] { header "__ranges/rend.h" }
++module std_private_ranges_repeat_view                [system] { header "__ranges/repeat_view.h" }
++module std_private_ranges_reverse_view               [system] { header "__ranges/reverse_view.h" }
++module std_private_ranges_single_view                [system] { header "__ranges/single_view.h" }
++module std_private_ranges_size                       [system] {
++  header "__ranges/size.h"
++  export std_private_type_traits_make_unsigned
++}
++module std_private_ranges_split_view                 [system] { header "__ranges/split_view.h" }
++module std_private_ranges_subrange                   [system] {
++  header "__ranges/subrange.h"
++  export std_private_ranges_subrange_fwd
++}
++module std_private_ranges_subrange_fwd               [system] {
++  header "__fwd/subrange.h"
++  export std_private_iterator_concepts
++}
++module std_private_ranges_take_view                  [system] { header "__ranges/take_view.h" }
++module std_private_ranges_take_while_view            [system] { header "__ranges/take_while_view.h" }
++module std_private_ranges_to                         [system] { header "__ranges/to.h" }
++module std_private_ranges_transform_view             [system] {
++  header "__ranges/transform_view.h"
++  export std_private_functional_bind_back
++  export std_private_functional_perfect_forward
++  export std_private_ranges_movable_box
++}
++module std_private_ranges_view_interface             [system] { header "__ranges/view_interface.h" }
++module std_private_ranges_views                      [system] { header "__ranges/views.h" }
++module std_private_ranges_zip_view                   [system] { header "__ranges/zip_view.h" }
++
++module std_private_span_span_fwd [system] { header "__fwd/span.h" }
++
++module std_private_stop_token_atomic_unique_lock   [system] { header "__stop_token/atomic_unique_lock.h" }
++module std_private_stop_token_intrusive_list_view  [system] { header "__stop_token/intrusive_list_view.h" }
++module std_private_stop_token_intrusive_shared_ptr [system] { header "__stop_token/intrusive_shared_ptr.h" }
++module std_private_stop_token_stop_callback        [system] { header "__stop_token/stop_callback.h" }
++module std_private_stop_token_stop_source          [system] {
++  header "__stop_token/stop_source.h"
++  export *
++}
++module std_private_stop_token_stop_state           [system] {
++  header "__stop_token/stop_state.h"
++  export *
++}
++module std_private_stop_token_stop_token           [system] {
++  header "__stop_token/stop_token.h"
++  export *
++}
++
++module std_private_string_char_traits           [system] {
++  header "__string/char_traits.h"
++  export *
++}
++module std_private_string_constexpr_c_functions [system] {
++  header "__string/constexpr_c_functions.h"
++  export std_private_type_traits_is_equality_comparable
++}
++module std_private_string_extern_template_lists [system] { header "__string/extern_template_lists.h" }
++module std_private_string_string_fwd            [system] { header "__fwd/string.h" }
++
++module std_private_string_view_string_view_fwd [system] { header "__fwd/string_view.h" }
++
++module std_private_system_error_errc            [system] { header "__system_error/errc.h" }
++module std_private_system_error_error_category  [system] { header "__system_error/error_category.h" }
++module std_private_system_error_error_code      [system] {
++  header "__system_error/error_code.h"
++  export std_private_functional_hash
++  export std_private_functional_unary_function
++}
++module std_private_system_error_error_condition [system] {
++  header "__system_error/error_condition.h"
++  export std_private_functional_hash
++  export std_private_functional_unary_function
++}
++module std_private_system_error_system_error    [system] { header "__system_error/system_error.h" }
++
++module std_private_thread_formatter            [system] { header "__thread/formatter.h" }
++module std_private_thread_id                   [system] { header "__thread/id.h" }
++module std_private_thread_poll_with_backoff    [system] { header "__thread/poll_with_backoff.h" }
++module std_private_thread_this_thread          [system] { header "__thread/this_thread.h" }
++module std_private_thread_thread               [system] {
++  header "__thread/thread.h"
++  export *
++}
++module std_private_thread_timed_backoff_policy [system] { header "__thread/timed_backoff_policy.h" }
++
++module std_private_tuple_get_fwd          [system] { header "__fwd/get.h" }
++module std_private_tuple_make_tuple_types [system] { header "__tuple/make_tuple_types.h" }
++module std_private_tuple_pair_like        [system] {
++  header "__tuple/pair_like.h"
++  export std_private_tuple_tuple_like
++}
++module std_private_tuple_sfinae_helpers   [system] { header "__tuple/sfinae_helpers.h" }
++module std_private_tuple_tuple_element    [system] { header "__tuple/tuple_element.h" }
++module std_private_tuple_tuple_fwd        [system] { header "__fwd/tuple.h" }
++module std_private_tuple_tuple_indices    [system] { header "__tuple/tuple_indices.h" }
++module std_private_tuple_tuple_like       [system] { header "__tuple/tuple_like.h" }
++module std_private_tuple_tuple_like_ext   [system] { header "__tuple/tuple_like_ext.h" }
++module std_private_tuple_tuple_size       [system] { header "__tuple/tuple_size.h" }
++module std_private_tuple_tuple_types      [system] { header "__tuple/tuple_types.h" }
++
++module std_private_type_traits_add_const                                 [system] { header "__type_traits/add_const.h" }
++module std_private_type_traits_add_cv                                    [system] { header "__type_traits/add_cv.h" }
++module std_private_type_traits_add_lvalue_reference                      [system] {
++  header "__type_traits/add_lvalue_reference.h"
++  export std_private_type_traits_is_referenceable
++}
++module std_private_type_traits_add_pointer                               [system] { header "__type_traits/add_pointer.h" }
++module std_private_type_traits_add_rvalue_reference                      [system] { header "__type_traits/add_rvalue_reference.h" }
++module std_private_type_traits_add_volatile                              [system] { header "__type_traits/add_volatile.h" }
++module std_private_type_traits_aligned_storage                           [system] { header "__type_traits/aligned_storage.h" }
++module std_private_type_traits_aligned_union                             [system] { header "__type_traits/aligned_union.h" }
++module std_private_type_traits_alignment_of                              [system] { header "__type_traits/alignment_of.h" }
++module std_private_type_traits_apply_cv                                  [system] {
++  header "__type_traits/apply_cv.h"
++  export std_private_type_traits_is_const
++  export std_private_type_traits_is_volatile
++}
++module std_private_type_traits_can_extract_key                           [system] { header "__type_traits/can_extract_key.h" }
++module std_private_type_traits_common_reference                          [system] {
++  header "__type_traits/common_reference.h"
++  export std_private_type_traits_remove_cvref
++}
++module std_private_type_traits_common_type                               [system] {
++  header "__type_traits/common_type.h"
++  export std_private_utility_declval
++}
++module std_private_type_traits_conditional                               [system] { header "__type_traits/conditional.h" }
++module std_private_type_traits_conjunction                               [system] { header "__type_traits/conjunction.h" }
++module std_private_type_traits_copy_cv                                   [system] { header "__type_traits/copy_cv.h" }
++module std_private_type_traits_copy_cvref                                [system] { header "__type_traits/copy_cvref.h" }
++module std_private_type_traits_datasizeof                                [system] { header "__type_traits/datasizeof.h" }
++module std_private_type_traits_decay                                     [system] {
++  header "__type_traits/decay.h"
++  export std_private_type_traits_add_pointer
++}
++module std_private_type_traits_dependent_type                            [system] { header "__type_traits/dependent_type.h" }
++module std_private_type_traits_disjunction                               [system] { header "__type_traits/disjunction.h" }
++module std_private_type_traits_enable_if                                 [system] { header "__type_traits/enable_if.h" }
++module std_private_type_traits_extent                                    [system] { header "__type_traits/extent.h" }
++module std_private_type_traits_has_unique_object_representation          [system] { header "__type_traits/has_unique_object_representation.h" }
++module std_private_type_traits_has_virtual_destructor                    [system] { header "__type_traits/has_virtual_destructor.h" }
++module std_private_type_traits_integral_constant                         [system] { header "__type_traits/integral_constant.h" }
++module std_private_type_traits_invoke                                    [system] {
++  header "__type_traits/invoke.h"
++  export std_private_type_traits_conditional
++  export std_private_type_traits_decay
++  export std_private_type_traits_decay
++  export std_private_type_traits_enable_if
++  export std_private_type_traits_is_base_of
++  export std_private_type_traits_is_core_convertible
++  export std_private_type_traits_is_reference_wrapper
++  export std_private_type_traits_is_same
++  export std_private_type_traits_is_void
++  export std_private_type_traits_nat
++  export std_private_type_traits_remove_cv
++}
++module std_private_type_traits_is_abstract                               [system] { header "__type_traits/is_abstract.h" }
++module std_private_type_traits_is_aggregate                              [system] { header "__type_traits/is_aggregate.h" }
++module std_private_type_traits_is_allocator                              [system] { header "__type_traits/is_allocator.h" }
++module std_private_type_traits_is_always_bitcastable                     [system] { header "__type_traits/is_always_bitcastable.h" }
++module std_private_type_traits_is_arithmetic                             [system] {
++  header "__type_traits/is_arithmetic.h"
++  export std_private_type_traits_integral_constant
++}
++module std_private_type_traits_is_array                                  [system] {
++  header "__type_traits/is_array.h"
++  export std_private_type_traits_integral_constant
++}
++module std_private_type_traits_is_assignable                             [system] { header "__type_traits/is_assignable.h" }
++module std_private_type_traits_is_base_of                                [system] { header "__type_traits/is_base_of.h" }
++module std_private_type_traits_is_bounded_array                          [system] { header "__type_traits/is_bounded_array.h" }
++module std_private_type_traits_is_callable                               [system] { header "__type_traits/is_callable.h" }
++module std_private_type_traits_is_char_like_type                         [system] { header "__type_traits/is_char_like_type.h" }
++module std_private_type_traits_is_class                                  [system] { header "__type_traits/is_class.h" }
++module std_private_type_traits_is_compound                               [system] { header "__type_traits/is_compound.h" }
++module std_private_type_traits_is_const                                  [system] { header "__type_traits/is_const.h" }
++module std_private_type_traits_is_constant_evaluated                     [system] { header "__type_traits/is_constant_evaluated.h" }
++module std_private_type_traits_is_constructible                          [system] { header "__type_traits/is_constructible.h" }
++module std_private_type_traits_is_convertible                            [system] {
++  header "__type_traits/is_convertible.h"
++  export std_private_type_traits_is_array
++}
++module std_private_type_traits_is_copy_assignable                        [system] { header "__type_traits/is_copy_assignable.h" }
++module std_private_type_traits_is_copy_constructible                     [system] { header "__type_traits/is_copy_constructible.h" }
++module std_private_type_traits_is_core_convertible                       [system] {
++  header "__type_traits/is_core_convertible.h"
++  export std_private_type_traits_integral_constant
++}
++module std_private_type_traits_is_default_constructible                  [system] { header "__type_traits/is_default_constructible.h" }
++module std_private_type_traits_is_destructible                           [system] { header "__type_traits/is_destructible.h" }
++module std_private_type_traits_is_empty                                  [system] { header "__type_traits/is_empty.h" }
++module std_private_type_traits_is_enum                                   [system] {
++  header "__type_traits/is_enum.h"
++  export std_private_type_traits_integral_constant
++}
++module std_private_type_traits_is_equality_comparable                    [system] {
++  header "__type_traits/is_equality_comparable.h"
++  export std_private_type_traits_integral_constant
++}
++module std_private_type_traits_is_execution_policy                       [system] {
++  header "__type_traits/is_execution_policy.h"
++  export std_private_type_traits_remove_cvref
++}
++module std_private_type_traits_is_final                                  [system] { header "__type_traits/is_final.h" }
++module std_private_type_traits_is_floating_point                         [system] { header "__type_traits/is_floating_point.h" }
++module std_private_type_traits_is_function                               [system] { header "__type_traits/is_function.h" }
++module std_private_type_traits_is_fundamental                            [system] { header "__type_traits/is_fundamental.h" }
++module std_private_type_traits_is_implicitly_default_constructible       [system] { header "__type_traits/is_implicitly_default_constructible.h" }
++module std_private_type_traits_is_integral                               [system] { header "__type_traits/is_integral.h" }
++module std_private_type_traits_is_literal_type                           [system] { header "__type_traits/is_literal_type.h" }
++module std_private_type_traits_is_member_function_pointer                [system] { header "__type_traits/is_member_function_pointer.h" }
++module std_private_type_traits_is_member_object_pointer                  [system] { header "__type_traits/is_member_object_pointer.h" }
++module std_private_type_traits_is_member_pointer                         [system] { header "__type_traits/is_member_pointer.h" }
++module std_private_type_traits_is_move_assignable                        [system] { header "__type_traits/is_move_assignable.h" }
++module std_private_type_traits_is_move_constructible                     [system] { header "__type_traits/is_move_constructible.h" }
++module std_private_type_traits_is_nothrow_assignable                     [system] { header "__type_traits/is_nothrow_assignable.h" }
++module std_private_type_traits_is_nothrow_constructible                  [system] { header "__type_traits/is_nothrow_constructible.h" }
++module std_private_type_traits_is_nothrow_convertible                    [system] { header "__type_traits/is_nothrow_convertible.h" }
++module std_private_type_traits_is_nothrow_copy_assignable                [system] { header "__type_traits/is_nothrow_copy_assignable.h" }
++module std_private_type_traits_is_nothrow_copy_constructible             [system] { header "__type_traits/is_nothrow_copy_constructible.h" }
++module std_private_type_traits_is_nothrow_default_constructible          [system] { header "__type_traits/is_nothrow_default_constructible.h" }
++module std_private_type_traits_is_nothrow_destructible                   [system] {
++  header "__type_traits/is_nothrow_destructible.h"
++  export std_private_type_traits_is_destructible
++}
++module std_private_type_traits_is_nothrow_move_assignable                [system] { header "__type_traits/is_nothrow_move_assignable.h" }
++module std_private_type_traits_is_nothrow_move_constructible             [system] {
++  header "__type_traits/is_nothrow_move_constructible.h"
++  export std_private_type_traits_is_nothrow_constructible
++}
++module std_private_type_traits_is_null_pointer                           [system] {
++  header "__type_traits/is_null_pointer.h"
++  export std_cstddef
++}
++module std_private_type_traits_is_object                                 [system] {
++  header "__type_traits/is_object.h"
++  export std_private_type_traits_is_scalar
++}
++module std_private_type_traits_is_pod                                    [system] { header "__type_traits/is_pod.h" }
++module std_private_type_traits_is_pointer                                [system] { header "__type_traits/is_pointer.h" }
++module std_private_type_traits_is_polymorphic                            [system] { header "__type_traits/is_polymorphic.h" }
++module std_private_type_traits_is_primary_template                       [system] {
++  header "__type_traits/is_primary_template.h"
++  export std_private_type_traits_enable_if
++}
++module std_private_type_traits_is_reference                              [system] { header "__type_traits/is_reference.h" }
++module std_private_type_traits_is_reference_wrapper                      [system] { header "__type_traits/is_reference_wrapper.h" }
++module std_private_type_traits_is_referenceable                          [system] { header "__type_traits/is_referenceable.h" }
++module std_private_type_traits_is_same                                   [system] {
++  header "__type_traits/is_same.h"
++  export std_private_type_traits_integral_constant
++}
++module std_private_type_traits_is_scalar                                 [system] {
++  header "__type_traits/is_scalar.h"
++  export std_private_type_traits_is_null_pointer
++}
++module std_private_type_traits_is_scoped_enum                            [system] { header "__type_traits/is_scoped_enum.h" }
++module std_private_type_traits_is_signed                                 [system] { header "__type_traits/is_signed.h" }
++module std_private_type_traits_is_signed_integer                         [system] { header "__type_traits/is_signed_integer.h" }
++module std_private_type_traits_is_specialization                         [system] { header "__type_traits/is_specialization.h" }
++module std_private_type_traits_is_standard_layout                        [system] { header "__type_traits/is_standard_layout.h" }
++module std_private_type_traits_is_swappable                              [system] {
++  header "__type_traits/is_swappable.h"
++  export std_private_type_traits_is_move_constructible
++}
++module std_private_type_traits_is_trivial                                [system] { header "__type_traits/is_trivial.h" }
++module std_private_type_traits_is_trivially_assignable                   [system] { header "__type_traits/is_trivially_assignable.h" }
++module std_private_type_traits_is_trivially_constructible                [system] { header "__type_traits/is_trivially_constructible.h" }
++module std_private_type_traits_is_trivially_copy_assignable              [system] { header "__type_traits/is_trivially_copy_assignable.h" }
++module std_private_type_traits_is_trivially_copy_constructible           [system] { header "__type_traits/is_trivially_copy_constructible.h" }
++module std_private_type_traits_is_trivially_copyable                     [system] { header "__type_traits/is_trivially_copyable.h" }
++module std_private_type_traits_is_trivially_default_constructible        [system] { header "__type_traits/is_trivially_default_constructible.h" }
++module std_private_type_traits_is_trivially_destructible                 [system] { header "__type_traits/is_trivially_destructible.h" }
++module std_private_type_traits_is_trivially_lexicographically_comparable [system] { header "__type_traits/is_trivially_lexicographically_comparable.h" }
++module std_private_type_traits_is_trivially_move_assignable              [system] { header "__type_traits/is_trivially_move_assignable.h" }
++module std_private_type_traits_is_trivially_move_constructible           [system] { header "__type_traits/is_trivially_move_constructible.h" }
++module std_private_type_traits_is_unbounded_array                        [system] { header "__type_traits/is_unbounded_array.h" }
++module std_private_type_traits_is_union                                  [system] { header "__type_traits/is_union.h" }
++module std_private_type_traits_is_unsigned                               [system] { header "__type_traits/is_unsigned.h" }
++module std_private_type_traits_is_unsigned_integer                       [system] { header "__type_traits/is_unsigned_integer.h" }
++module std_private_type_traits_is_valid_expansion                        [system] { header "__type_traits/is_valid_expansion.h" }
++module std_private_type_traits_is_void                                   [system] {
++  header "__type_traits/is_void.h"
++  export std_private_type_traits_integral_constant
++}
++module std_private_type_traits_is_volatile                               [system] { header "__type_traits/is_volatile.h" }
++module std_private_type_traits_lazy                                      [system] { header "__type_traits/lazy.h" }
++module std_private_type_traits_make_32_64_or_128_bit                     [system] { header "__type_traits/make_32_64_or_128_bit.h" }
++module std_private_type_traits_make_const_lvalue_ref                     [system] { header "__type_traits/make_const_lvalue_ref.h" }
++module std_private_type_traits_make_signed                               [system] { header "__type_traits/make_signed.h" }
++module std_private_type_traits_make_unsigned                             [system] {
++  header "__type_traits/make_unsigned.h"
++  export std_private_type_traits_is_unsigned
++}
++module std_private_type_traits_maybe_const                               [system] { header "__type_traits/maybe_const.h" }
++module std_private_type_traits_nat                                       [system] { header "__type_traits/nat.h" }
++module std_private_type_traits_negation                                  [system] { header "__type_traits/negation.h" }
++module std_private_type_traits_noexcept_move_assign_container            [system] { header "__type_traits/noexcept_move_assign_container.h" }
++module std_private_type_traits_operation_traits                          [system] { header "__type_traits/operation_traits.h" }
++module std_private_type_traits_predicate_traits                          [system] { header "__type_traits/predicate_traits.h" }
++module std_private_type_traits_promote                                   [system] { header "__type_traits/promote.h" }
++module std_private_type_traits_rank                                      [system] { header "__type_traits/rank.h" }
++module std_private_type_traits_remove_all_extents                        [system] { header "__type_traits/remove_all_extents.h" }
++module std_private_type_traits_remove_const                              [system] { header "__type_traits/remove_const.h" }
++module std_private_type_traits_remove_const_ref                          [system] { header "__type_traits/remove_const_ref.h" }
++module std_private_type_traits_remove_cv                                 [system] {
++  header "__type_traits/remove_cv.h"
++  export std_private_type_traits_remove_const
++  export std_private_type_traits_remove_volatile
++}
++module std_private_type_traits_remove_cvref                              [system] { header "__type_traits/remove_cvref.h" }
++module std_private_type_traits_remove_extent                             [system] { header "__type_traits/remove_extent.h" }
++module std_private_type_traits_remove_pointer                            [system] { header "__type_traits/remove_pointer.h" }
++module std_private_type_traits_remove_reference                          [system] { header "__type_traits/remove_reference.h" }
++module std_private_type_traits_remove_volatile                           [system] { header "__type_traits/remove_volatile.h" }
++module std_private_type_traits_result_of                                 [system] { header "__type_traits/result_of.h" }
++module std_private_type_traits_strip_signature                           [system] { header "__type_traits/strip_signature.h" }
++module std_private_type_traits_type_identity                             [system] { header "__type_traits/type_identity.h" }
++module std_private_type_traits_type_list                                 [system] { header "__type_traits/type_list.h" }
++module std_private_type_traits_underlying_type                           [system] {
++  header "__type_traits/underlying_type.h"
++  export std_private_type_traits_is_enum
++}
++module std_private_type_traits_unwrap_ref                                [system] { header "__type_traits/unwrap_ref.h" }
++module std_private_type_traits_void_t                                    [system] { header "__type_traits/void_t.h" }
++
++module std_private_utility_as_const               [system] { header "__utility/as_const.h" }
++module std_private_utility_auto_cast              [system] {
++  header "__utility/auto_cast.h"
++  export std_private_type_traits_decay
++}
++module std_private_utility_cmp                    [system] {
++  header "__utility/cmp.h"
++  export std_private_type_traits_make_unsigned
++}
++module std_private_utility_convert_to_integral    [system] { header "__utility/convert_to_integral.h" }
++module std_private_utility_declval                [system] { header "__utility/declval.h" }
++module std_private_utility_exception_guard        [system] { header "__utility/exception_guard.h" }
++module std_private_utility_exchange               [system] { header "__utility/exchange.h" }
++module std_private_utility_forward                [system] { header "__utility/forward.h" }
++module std_private_utility_forward_like           [system] { header "__utility/forward_like.h" }
++module std_private_utility_in_place               [system] { header "__utility/in_place.h" }
++module std_private_utility_integer_sequence       [system] { header "__utility/integer_sequence.h" }
++module std_private_utility_is_pointer_in_range    [system] { header "__utility/is_pointer_in_range.h" }
++module std_private_utility_move                   [system] {
++  header "__utility/move.h"
++  export std_private_type_traits_is_copy_constructible
++  export std_private_type_traits_is_nothrow_move_constructible
++  export std_private_type_traits_remove_reference
++}
++module std_private_utility_pair                   [system] {
++  header "__utility/pair.h"
++  export std_private_ranges_subrange_fwd
++  export std_private_tuple_pair_like
++  export std_private_type_traits_is_assignable
++  export std_private_type_traits_is_constructible
++  export std_private_type_traits_is_convertible
++  export std_private_type_traits_is_copy_assignable
++  export std_private_type_traits_is_move_assignable
++  export std_private_type_traits_is_nothrow_copy_constructible
++  export std_private_type_traits_is_nothrow_default_constructible
++  export std_private_type_traits_is_nothrow_move_assignable
++  export std_private_utility_pair_fwd
++}
++module std_private_utility_pair_fwd               [system] { header "__fwd/pair.h" }
++module std_private_utility_piecewise_construct    [system] { header "__utility/piecewise_construct.h" }
++module std_private_utility_priority_tag           [system] { header "__utility/priority_tag.h" }
++module std_private_utility_rel_ops                [system] { header "__utility/rel_ops.h" }
++module std_private_utility_swap                   [system] {
++  header "__utility/swap.h"
++  export std_private_type_traits_is_swappable
++}
++module std_private_utility_terminate_on_exception [system] { header "__utility/terminate_on_exception.h" }
++module std_private_utility_to_underlying          [system] { header "__utility/to_underlying.h" }
++module std_private_utility_unreachable            [system] { header "__utility/unreachable.h" }
++
++module std_private_variant_monostate [system] { header "__variant/monostate.h" }
++}
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/interpreter/cling/lib/Interpreter/CIFactory.cpp root_v6.28.12_patched/root_v6.28.12-source/interpreter/cling/lib/Interpreter/CIFactory.cpp
+--- root_v6.28.12_unpatched/root_v6.28.12-source/interpreter/cling/lib/Interpreter/CIFactory.cpp	2024-09-18 13:23:13
++++ root_v6.28.12_patched/root_v6.28.12-source/interpreter/cling/lib/Interpreter/CIFactory.cpp	2024-09-18 13:49:27
+@@ -609,7 +609,7 @@ namespace {
+       llvm::sys::path::append(systemLoc, modulemapFilename);
+       // Check if we need to mount a custom modulemap. We may have it, for
+       // instance when we are on osx or using libc++.
+-      if (AllowModulemapOverride &&llvm::sys::fs::exists(systemLoc.str())) {
++      if (AllowModulemapOverride && llvm::sys::fs::exists(systemLoc.str())) {
+         if (HSOpts.Verbose)
+           cling::log() << "Loading '" << systemLoc.str() << "'\n";
+ 
+@@ -651,6 +651,8 @@ namespace {
+         ModuleMapFiles.push_back(systemLoc.str().str());
+     };
+ 
++    const llvm::Triple &Triple = CI.getTarget().getTriple();
++
+     if (!HSOpts.ImplicitModuleMaps) {
+       // Register the modulemap files.
+       llvm::SmallString<512> resourceDirLoc(HSOpts.ResourceDir);
+@@ -659,17 +661,20 @@ namespace {
+       llvm::SmallString<512> clingModuleMap(clingIncLoc);
+       llvm::sys::path::append(clingModuleMap, "module.modulemap");
+       ModuleMapFiles.push_back(clingModuleMap.str().str());
+-#ifdef __APPLE__
+-      llvm::SmallString<512> libcModuleMap(cIncLoc);
+-      llvm::sys::path::append(libcModuleMap, "module.modulemap");
+-      ModuleMapFiles.push_back(libcModuleMap.str().str());
+-      llvm::SmallString<512> stdModuleMap(stdIncLoc);
+-      llvm::sys::path::append(stdModuleMap, "module.modulemap");
+-      ModuleMapFiles.push_back(stdModuleMap.str().str());
+-#endif // __APPLE__
++      if (Triple.isMacOSX()) {
++        llvm::SmallString<512> libcModuleMap(cIncLoc);
++        llvm::sys::path::append(libcModuleMap, "module.modulemap");
++        ModuleMapFiles.push_back(libcModuleMap.str().str());
++        if (CI.getTarget().getSDKVersion() < VersionTuple(14, 4)) {
++          llvm::SmallString<512> stdModuleMap(stdIncLoc);
++          llvm::sys::path::append(stdModuleMap, "module.modulemap");
++          ModuleMapFiles.push_back(stdModuleMap.str().str());
++        }
++      }
+     }
+ 
+     std::string MOverlay;
++
+ #ifdef _WIN32
+     maybeAppendOverlayEntry(vcIncLoc.str(), "vcruntime.modulemap",
+                             clingIncLoc.str().str(), MOverlay,
+@@ -687,6 +692,12 @@ namespace {
+                             clingIncLoc.str().str(), MOverlay,
+                             /*RegisterModuleMap=*/ true,
+                             /*AllowModulemapOverride=*/ false);
++#elif __APPLE__
++    if (Triple.isMacOSX() && CI.getTarget().getSDKVersion() >= VersionTuple(14, 4))
++      maybeAppendOverlayEntry(stdIncLoc.str(), "std_darwin.modulemap",
++                              clingIncLoc.str().str(), MOverlay,
++                              /*RegisterModuleMap=*/ true,
++                              /*AllowModulemapOverride=*/ false);
+ #else
+     maybeAppendOverlayEntry(cIncLoc.str(), "libc.modulemap",
+                             clingIncLoc.str().str(), MOverlay,
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/interpreter/cling/lib/Interpreter/IncrementalJIT.cpp root_v6.28.12_patched/root_v6.28.12-source/interpreter/cling/lib/Interpreter/IncrementalJIT.cpp
+--- root_v6.28.12_unpatched/root_v6.28.12-source/interpreter/cling/lib/Interpreter/IncrementalJIT.cpp	2024-09-18 13:23:13
++++ root_v6.28.12_patched/root_v6.28.12-source/interpreter/cling/lib/Interpreter/IncrementalJIT.cpp	2024-09-18 13:49:27
+@@ -36,7 +36,7 @@ using namespace llvm::orc;
+ using namespace llvm;
+ using namespace llvm::orc;
+ 
+-namespace {
++namespace cling {
+ 
+   class ClingMMapper final : public SectionMemoryManager::MemoryMapper {
+   public:
+@@ -65,8 +65,10 @@ namespace {
+     }
+   };
+ 
+-  ClingMMapper MMapperInstance;
++}
+ 
++namespace {
++
+   // A memory manager for Cling that reserves memory for code and data sections
+   // to keep them contiguous for the emission of one module. This is required
+   // for working exception handling support since one .eh_frame section will
+@@ -128,7 +130,7 @@ namespace {
+     AllocInfo m_RWData;
+ 
+   public:
+-    ClingMemoryManager() : Super(&MMapperInstance) {}
++    ClingMemoryManager(cling::ClingMMapper& MMapper) : Super(&MMapper) {}
+ 
+     uint8_t* allocateCodeSection(uintptr_t Size, unsigned Alignment,
+                                  unsigned SectionID,
+@@ -397,7 +399,10 @@ IncrementalJIT::IncrementalJIT(
+   // Create ObjectLinkingLayer with our own MemoryManager.
+   Builder.setObjectLinkingLayerCreator([&](ExecutionSession& ES,
+                                            const Triple& TT) {
+-    auto GetMemMgr = []() { return std::make_unique<ClingMemoryManager>(); };
++    m_MMapper = std::make_unique<ClingMMapper>();
++    auto GetMemMgr = [this]() {
++      return std::make_unique<ClingMemoryManager>(*m_MMapper);
++    };
+     auto Layer =
+         std::make_unique<RTDyldObjectLinkingLayer>(ES, std::move(GetMemMgr));
+ 
+@@ -506,6 +511,8 @@ IncrementalJIT::IncrementalJIT(
+   };
+   Jit->getExecutionSession().setErrorReporter(ErrorReporter);
+ }
++
++IncrementalJIT::~IncrementalJIT() = default;
+ 
+ std::unique_ptr<llvm::orc::DefinitionGenerator> IncrementalJIT::getGenerator() {
+   return std::make_unique<DelegateGenerator>(
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/interpreter/cling/lib/Interpreter/IncrementalJIT.h root_v6.28.12_patched/root_v6.28.12-source/interpreter/cling/lib/Interpreter/IncrementalJIT.h
+--- root_v6.28.12_unpatched/root_v6.28.12-source/interpreter/cling/lib/Interpreter/IncrementalJIT.h	2024-09-18 13:23:13
++++ root_v6.28.12_patched/root_v6.28.12-source/interpreter/cling/lib/Interpreter/IncrementalJIT.h	2024-09-18 13:49:27
+@@ -33,6 +33,7 @@ namespace cling {
+ 
+ namespace cling {
+ 
++class ClingMMapper;
+ class IncrementalExecutor;
+ class Transaction;
+ 
+@@ -59,6 +60,7 @@ class IncrementalJIT { (public)
+                  const clang::CompilerInstance &CI,
+                  std::unique_ptr<llvm::orc::ExecutorProcessControl> EPC,
+                  llvm::Error &Err, void *ExtraLibHandle, bool Verbose);
++  ~IncrementalJIT();
+ 
+   /// Register a DefinitionGenerator to dynamically provide symbols for
+   /// generated code that are not already available within the process.
+@@ -102,6 +104,7 @@ class IncrementalJIT { (public)
+   llvm::TargetMachine &getTargetMachine() { return *TM; }
+ 
+ private:
++  std::unique_ptr<ClingMMapper> m_MMapper;
+   std::unique_ptr<llvm::orc::LLJIT> Jit;
+   llvm::orc::SymbolMap m_InjectedSymbols;
+   SharedAtomicFlag SkipHostProcessLookup;
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/interpreter/llvm/src/lib/ExecutionEngine/Orc/LLJIT.cpp root_v6.28.12_patched/root_v6.28.12-source/interpreter/llvm/src/lib/ExecutionEngine/Orc/LLJIT.cpp
+--- root_v6.28.12_unpatched/root_v6.28.12-source/interpreter/llvm/src/lib/ExecutionEngine/Orc/LLJIT.cpp	2024-09-18 13:23:13
++++ root_v6.28.12_patched/root_v6.28.12-source/interpreter/llvm/src/lib/ExecutionEngine/Orc/LLJIT.cpp	2024-09-18 13:49:28
+@@ -481,8 +481,8 @@ GlobalCtorDtorScraper::operator()(ThreadSafeModule TSM
+     std::vector<std::pair<Function *, unsigned>> Inits;
+     for (auto E : getConstructors(M))
+       Inits.push_back(std::make_pair(E.Func, E.Priority));
+-    llvm::sort(Inits, [](const std::pair<Function *, unsigned> &LHS,
+-                         const std::pair<Function *, unsigned> &RHS) {
++    llvm::stable_sort(Inits, [](const std::pair<Function *, unsigned> &LHS,
++                                const std::pair<Function *, unsigned> &RHS) {
+       return LHS.second < RHS.second;
+     });
+     auto *EntryBlock = BasicBlock::Create(Ctx, "entry", InitFunc);
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/interpreter/llvm/src/tools/clang/include/clang/AST/ComputeDependence.h root_v6.28.12_patched/root_v6.28.12-source/interpreter/llvm/src/tools/clang/include/clang/AST/ComputeDependence.h
+--- root_v6.28.12_unpatched/root_v6.28.12-source/interpreter/llvm/src/tools/clang/include/clang/AST/ComputeDependence.h	2024-09-18 13:23:11
++++ root_v6.28.12_patched/root_v6.28.12-source/interpreter/llvm/src/tools/clang/include/clang/AST/ComputeDependence.h	2024-09-18 13:49:28
+@@ -30,7 +30,8 @@ class CompoundLiteralExpr;
+ class ArraySubscriptExpr;
+ class MatrixSubscriptExpr;
+ class CompoundLiteralExpr;
+-class CastExpr;
++class ImplicitCastExpr;
++class ExplicitCastExpr;
+ class BinaryOperator;
+ class ConditionalOperator;
+ class BinaryConditionalOperator;
+@@ -70,6 +71,7 @@ class CXXConstructExpr;
+ class OverloadExpr;
+ class DependentScopeDeclRefExpr;
+ class CXXConstructExpr;
++class CXXTemporaryObjectExpr;
+ class CXXDefaultInitExpr;
+ class CXXDefaultArgExpr;
+ class LambdaExpr;
+@@ -114,7 +116,8 @@ ExprDependence computeDependence(CompoundLiteralExpr *
+ ExprDependence computeDependence(ArraySubscriptExpr *E);
+ ExprDependence computeDependence(MatrixSubscriptExpr *E);
+ ExprDependence computeDependence(CompoundLiteralExpr *E);
+-ExprDependence computeDependence(CastExpr *E);
++ExprDependence computeDependence(ImplicitCastExpr *E);
++ExprDependence computeDependence(ExplicitCastExpr *E);
+ ExprDependence computeDependence(BinaryOperator *E);
+ ExprDependence computeDependence(ConditionalOperator *E);
+ ExprDependence computeDependence(BinaryConditionalOperator *E);
+@@ -156,6 +159,7 @@ ExprDependence computeDependence(CXXConstructExpr *E);
+                                  bool KnownContainsUnexpandedParameterPack);
+ ExprDependence computeDependence(DependentScopeDeclRefExpr *E);
+ ExprDependence computeDependence(CXXConstructExpr *E);
++ExprDependence computeDependence(CXXTemporaryObjectExpr *E);
+ ExprDependence computeDependence(CXXDefaultInitExpr *E);
+ ExprDependence computeDependence(CXXDefaultArgExpr *E);
+ ExprDependence computeDependence(LambdaExpr *E,
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/interpreter/llvm/src/tools/clang/include/clang/AST/DependenceFlags.h root_v6.28.12_patched/root_v6.28.12-source/interpreter/llvm/src/tools/clang/include/clang/AST/DependenceFlags.h
+--- root_v6.28.12_unpatched/root_v6.28.12-source/interpreter/llvm/src/tools/clang/include/clang/AST/DependenceFlags.h	2024-09-18 13:23:11
++++ root_v6.28.12_patched/root_v6.28.12-source/interpreter/llvm/src/tools/clang/include/clang/AST/DependenceFlags.h	2024-09-18 13:49:28
+@@ -130,6 +130,14 @@ class Dependence { (public)
+ 
+     // Dependence that is propagated syntactically, regardless of semantics.
+     Syntactic = UnexpandedPack | Instantiation | Error,
++    // Dependence that is propagated semantically, even in cases where the
++    // type doesn't syntactically appear. This currently excludes only
++    // UnexpandedPack. Even though Instantiation dependence is also notionally
++    // syntactic, we also want to propagate it semantically because anything
++    // that semantically depends on an instantiation-dependent entity should
++    // always be instantiated when that instantiation-dependent entity is.
++    Semantic =
++        Instantiation | Type | Value | Dependent | Error | VariablyModified,
+ 
+     LLVM_MARK_AS_BITMASK_ENUM(/*LargestValue=*/VariablyModified)
+   };
+@@ -175,6 +183,14 @@ class Dependence { (public)
+     return Result;
+   }
+ 
++  /// Extract the semantic portions of this type's dependence that apply even
++  /// to uses where the type does not appear syntactically.
++  Dependence semantic() {
++    Dependence Result = *this;
++    Result.V &= Semantic;
++    return Result;
++  }
++
+   TypeDependence type() const {
+     return translate(V, UnexpandedPack, TypeDependence::UnexpandedPack) |
+            translate(V, Instantiation, TypeDependence::Instantiation) |
+@@ -231,7 +247,10 @@ inline ExprDependence toExprDependence(TemplateArgumen
+ inline ExprDependence toExprDependence(TemplateArgumentDependence TA) {
+   return Dependence(TA).expr();
+ }
+-inline ExprDependence toExprDependence(TypeDependence D) {
++inline ExprDependence toExprDependenceForImpliedType(TypeDependence D) {
++  return Dependence(D).semantic().expr();
++}
++inline ExprDependence toExprDependenceAsWritten(TypeDependence D) {
+   return Dependence(D).expr();
+ }
+ // Note: it's often necessary to strip `Dependent` from qualifiers.
+@@ -268,6 +287,9 @@ inline TypeDependence toSyntacticDependence(TypeDepend
+ 
+ inline TypeDependence toSyntacticDependence(TypeDependence D) {
+   return Dependence(D).syntactic().type();
++}
++inline TypeDependence toSemanticDependence(TypeDependence D) {
++  return Dependence(D).semantic().type();
+ }
+ 
+ inline NestedNameSpecifierDependence
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/interpreter/llvm/src/tools/clang/include/clang/AST/Expr.h root_v6.28.12_patched/root_v6.28.12-source/interpreter/llvm/src/tools/clang/include/clang/AST/Expr.h
+--- root_v6.28.12_unpatched/root_v6.28.12-source/interpreter/llvm/src/tools/clang/include/clang/AST/Expr.h	2024-09-18 13:23:11
++++ root_v6.28.12_patched/root_v6.28.12-source/interpreter/llvm/src/tools/clang/include/clang/AST/Expr.h	2024-09-18 13:49:28
+@@ -3485,7 +3485,6 @@ class CastExpr : public Expr { (protected)
+     CastExprBits.BasePathSize = BasePathSize;
+     assert((CastExprBits.BasePathSize == BasePathSize) &&
+            "BasePathSize overflow!");
+-    setDependence(computeDependence(this));
+     assert(CastConsistency());
+     CastExprBits.HasFPFeatures = HasFPFeatures;
+   }
+@@ -3619,6 +3618,7 @@ class ImplicitCastExpr final
+                    ExprValueKind VK)
+       : CastExpr(ImplicitCastExprClass, ty, VK, kind, op, BasePathLength,
+                  FPO.requiresTrailingStorage()) {
++    setDependence(computeDependence(this));
+     if (hasStoredFPFeatures())
+       *getTrailingFPFeatures() = FPO;
+   }
+@@ -3696,7 +3696,9 @@ class ExplicitCastExpr : public CastExpr { (protected)
+                    CastKind kind, Expr *op, unsigned PathSize,
+                    bool HasFPFeatures, TypeSourceInfo *writtenTy)
+       : CastExpr(SC, exprTy, VK, kind, op, PathSize, HasFPFeatures),
+-        TInfo(writtenTy) {}
++        TInfo(writtenTy) {
++    setDependence(computeDependence(this));
++  }
+ 
+   /// Construct an empty explicit cast.
+   ExplicitCastExpr(StmtClass SC, EmptyShell Shell, unsigned PathSize,
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/interpreter/llvm/src/tools/clang/lib/AST/ComputeDependence.cpp root_v6.28.12_patched/root_v6.28.12-source/interpreter/llvm/src/tools/clang/lib/AST/ComputeDependence.cpp
+--- root_v6.28.12_unpatched/root_v6.28.12-source/interpreter/llvm/src/tools/clang/lib/AST/ComputeDependence.cpp	2024-09-18 13:23:11
++++ root_v6.28.12_patched/root_v6.28.12-source/interpreter/llvm/src/tools/clang/lib/AST/ComputeDependence.cpp	2024-09-18 13:49:28
+@@ -26,7 +26,7 @@ ExprDependence clang::computeDependence(OpaqueValueExp
+ }
+ 
+ ExprDependence clang::computeDependence(OpaqueValueExpr *E) {
+-  auto D = toExprDependence(E->getType()->getDependence());
++  auto D = toExprDependenceForImpliedType(E->getType()->getDependence());
+   if (auto *S = E->getSourceExpr())
+     D |= S->getDependence();
+   assert(!(D & ExprDependence::UnexpandedPack));
+@@ -39,8 +39,10 @@ ExprDependence clang::computeDependence(UnaryOperator 
+ 
+ ExprDependence clang::computeDependence(UnaryOperator *E,
+                                         const ASTContext &Ctx) {
+-  ExprDependence Dep = toExprDependence(E->getType()->getDependence()) |
+-                       E->getSubExpr()->getDependence();
++  ExprDependence Dep =
++      // FIXME: Do we need to look at the type?
++      toExprDependenceForImpliedType(E->getType()->getDependence()) |
++      E->getSubExpr()->getDependence();
+ 
+   // C++ [temp.dep.constexpr]p5:
+   //   An expression of the form & qualified-id where the qualified-id names a
+@@ -77,7 +79,7 @@ ExprDependence clang::computeDependence(UnaryExprOrTyp
+   // Value-dependent if the argument is type-dependent.
+   if (E->isArgumentType())
+     return turnTypeToValueDependence(
+-        toExprDependence(E->getArgumentType()->getDependence()));
++        toExprDependenceAsWritten(E->getArgumentType()->getDependence()));
+ 
+   auto ArgDeps = E->getArgumentExpr()->getDependence();
+   auto Deps = ArgDeps & ~ExprDependence::TypeValue;
+@@ -120,21 +122,36 @@ ExprDependence clang::computeDependence(CompoundLitera
+ }
+ 
+ ExprDependence clang::computeDependence(CompoundLiteralExpr *E) {
+-  return toExprDependence(E->getTypeSourceInfo()->getType()->getDependence()) |
++  return toExprDependenceAsWritten(
++             E->getTypeSourceInfo()->getType()->getDependence()) |
++         toExprDependenceForImpliedType(E->getType()->getDependence()) |
+          turnTypeToValueDependence(E->getInitializer()->getDependence());
+ }
+ 
+-ExprDependence clang::computeDependence(CastExpr *E) {
++ExprDependence clang::computeDependence(ImplicitCastExpr *E) {
++  // We model implicit conversions as combining the dependence of their
++  // subexpression, apart from its type, with the semantic portion of the
++  // target type.
++  ExprDependence D =
++      toExprDependenceForImpliedType(E->getType()->getDependence());
++  if (auto *S = E->getSubExpr())
++    D |= S->getDependence() & ~ExprDependence::Type;
++  return D;
++}
++
++ExprDependence clang::computeDependence(ExplicitCastExpr *E) {
+   // Cast expressions are type-dependent if the type is
+   // dependent (C++ [temp.dep.expr]p3).
+   // Cast expressions are value-dependent if the type is
+   // dependent or if the subexpression is value-dependent.
+-  auto D = toExprDependence(E->getType()->getDependence());
+-  if (E->getStmtClass() == Stmt::ImplicitCastExprClass) {
+-    // An implicit cast expression doesn't (lexically) contain an
+-    // unexpanded pack, even if its target type does.
+-    D &= ~ExprDependence::UnexpandedPack;
+-  }
++  //
++  // Note that we also need to consider the dependence of the actual type here,
++  // because when the type as written is a deduced type, that type is not
++  // dependent, but it may be deduced as a dependent type.
++  ExprDependence D =
++      toExprDependenceAsWritten(
++          cast<ExplicitCastExpr>(E)->getTypeAsWritten()->getDependence()) |
++      toExprDependenceForImpliedType(E->getType()->getDependence());
+   if (auto *S = E->getSubExpr())
+     D |= S->getDependence() & ~ExprDependence::Type;
+   return D;
+@@ -158,7 +175,7 @@ ExprDependence clang::computeDependence(StmtExpr *E, u
+ }
+ 
+ ExprDependence clang::computeDependence(StmtExpr *E, unsigned TemplateDepth) {
+-  auto D = toExprDependence(E->getType()->getDependence());
++  auto D = toExprDependenceForImpliedType(E->getType()->getDependence());
+   // Propagate dependence of the result.
+   if (const auto *CompoundExprResult =
+           dyn_cast_or_null<ValueStmt>(E->getSubStmt()->getStmtExprResult()))
+@@ -174,7 +191,8 @@ ExprDependence clang::computeDependence(ConvertVectorE
+ }
+ 
+ ExprDependence clang::computeDependence(ConvertVectorExpr *E) {
+-  auto D = toExprDependence(E->getType()->getDependence()) |
++  auto D = toExprDependenceAsWritten(
++               E->getTypeSourceInfo()->getType()->getDependence()) |
+            E->getSrcExpr()->getDependence();
+   if (!E->getType()->isDependentType())
+     D &= ~ExprDependence::Type;
+@@ -206,14 +224,14 @@ ExprDependence clang::computeDependence(VAArgExpr *E) 
+ }
+ 
+ ExprDependence clang::computeDependence(VAArgExpr *E) {
+-  auto D =
+-      toExprDependence(E->getWrittenTypeInfo()->getType()->getDependence()) |
+-      (E->getSubExpr()->getDependence() & ~ExprDependence::Type);
++  auto D = toExprDependenceAsWritten(
++               E->getWrittenTypeInfo()->getType()->getDependence()) |
++           (E->getSubExpr()->getDependence() & ~ExprDependence::Type);
+   return D & ~ExprDependence::Value;
+ }
+ 
+ ExprDependence clang::computeDependence(NoInitExpr *E) {
+-  return toExprDependence(E->getType()->getDependence()) &
++  return toExprDependenceForImpliedType(E->getType()->getDependence()) &
+          (ExprDependence::Instantiation | ExprDependence::Error);
+ }
+ 
+@@ -226,7 +244,7 @@ ExprDependence clang::computeDependence(ImplicitValueI
+ }
+ 
+ ExprDependence clang::computeDependence(ImplicitValueInitExpr *E) {
+-  return toExprDependence(E->getType()->getDependence()) &
++  return toExprDependenceForImpliedType(E->getType()->getDependence()) &
+          ExprDependence::Instantiation;
+ }
+ 
+@@ -235,14 +253,16 @@ ExprDependence clang::computeDependence(BlockExpr *E) 
+ }
+ 
+ ExprDependence clang::computeDependence(BlockExpr *E) {
+-  auto D = toExprDependence(E->getType()->getDependence());
++  auto D = toExprDependenceForImpliedType(E->getType()->getDependence());
+   if (E->getBlockDecl()->isDependentContext())
+     D |= ExprDependence::Instantiation;
+-  return D & ~ExprDependence::UnexpandedPack;
++  return D;
+ }
+ 
+ ExprDependence clang::computeDependence(AsTypeExpr *E) {
+-  auto D = toExprDependence(E->getType()->getDependence()) |
++  // FIXME: AsTypeExpr doesn't store the type as written. Assume the expression
++  // type has identical sugar for now, so is a type-as-written.
++  auto D = toExprDependenceAsWritten(E->getType()->getDependence()) |
+            E->getSrcExpr()->getDependence();
+   if (!E->getType()->isDependentType())
+     D &= ~ExprDependence::Type;
+@@ -255,15 +275,14 @@ ExprDependence clang::computeDependence(CXXStdInitiali
+ 
+ ExprDependence clang::computeDependence(CXXStdInitializerListExpr *E) {
+   auto D = turnTypeToValueDependence(E->getSubExpr()->getDependence());
+-  D |= toExprDependence(E->getType()->getDependence()) &
+-       (ExprDependence::Type | ExprDependence::Error);
++  D |= toExprDependenceForImpliedType(E->getType()->getDependence());
+   return D;
+ }
+ 
+ ExprDependence clang::computeDependence(CXXTypeidExpr *E) {
+   auto D = ExprDependence::None;
+   if (E->isTypeOperand())
+-    D = toExprDependence(
++    D = toExprDependenceAsWritten(
+         E->getTypeOperandSourceInfo()->getType()->getDependence());
+   else
+     D = turnTypeToValueDependence(E->getExprOperand()->getDependence());
+@@ -281,7 +300,7 @@ ExprDependence clang::computeDependence(CXXUuidofExpr 
+ 
+ ExprDependence clang::computeDependence(CXXUuidofExpr *E) {
+   if (E->isTypeOperand())
+-    return turnTypeToValueDependence(toExprDependence(
++    return turnTypeToValueDependence(toExprDependenceAsWritten(
+         E->getTypeOperandSourceInfo()->getType()->getDependence()));
+ 
+   return turnTypeToValueDependence(E->getExprOperand()->getDependence());
+@@ -290,7 +309,7 @@ ExprDependence clang::computeDependence(CXXThisExpr *E
+ ExprDependence clang::computeDependence(CXXThisExpr *E) {
+   // 'this' is type-dependent if the class type of the enclosing
+   // member function is dependent (C++ [temp.dep.expr]p2)
+-  auto D = toExprDependence(E->getType()->getDependence());
++  auto D = toExprDependenceForImpliedType(E->getType()->getDependence());
+   assert(!(D & ExprDependence::UnexpandedPack));
+   return D;
+ }
+@@ -307,8 +326,10 @@ ExprDependence clang::computeDependence(CXXScalarValue
+ }
+ 
+ ExprDependence clang::computeDependence(CXXScalarValueInitExpr *E) {
+-  return toExprDependence(E->getType()->getDependence()) &
+-         ~ExprDependence::TypeValue;
++  auto D = toExprDependenceForImpliedType(E->getType()->getDependence());
++  if (auto *TSI = E->getTypeSourceInfo())
++    D |= toExprDependenceAsWritten(TSI->getType()->getDependence());
++  return D;
+ }
+ 
+ ExprDependence clang::computeDependence(CXXDeleteExpr *E) {
+@@ -316,7 +337,7 @@ ExprDependence clang::computeDependence(ArrayTypeTrait
+ }
+ 
+ ExprDependence clang::computeDependence(ArrayTypeTraitExpr *E) {
+-  auto D = toExprDependence(E->getQueriedType()->getDependence());
++  auto D = toExprDependenceAsWritten(E->getQueriedType()->getDependence());
+   if (auto *Dim = E->getDimensionExpression())
+     D |= Dim->getDependence();
+   return turnTypeToValueDependence(D);
+@@ -366,7 +387,7 @@ ExprDependence clang::computeDependence(ObjCEncodeExpr
+ }
+ 
+ ExprDependence clang::computeDependence(ObjCEncodeExpr *E) {
+-  return toExprDependence(E->getEncodedType()->getDependence());
++  return toExprDependenceAsWritten(E->getEncodedType()->getDependence());
+ }
+ 
+ ExprDependence clang::computeDependence(ObjCIvarRefExpr *E) {
+@@ -377,7 +398,8 @@ ExprDependence clang::computeDependence(ObjCPropertyRe
+   if (E->isObjectReceiver())
+     return E->getBase()->getDependence() & ~ExprDependence::Type;
+   if (E->isSuperReceiver())
+-    return toExprDependence(E->getSuperReceiverType()->getDependence()) &
++    return toExprDependenceForImpliedType(
++               E->getSuperReceiverType()->getDependence()) &
+            ~ExprDependence::TypeValue;
+   assert(E->isClassReceiver());
+   return ExprDependence::None;
+@@ -406,19 +428,22 @@ ExprDependence clang::computeDependence(OMPArrayShapin
+ }
+ 
+ ExprDependence clang::computeDependence(OMPArrayShapingExpr *E) {
+-  auto D = E->getBase()->getDependence() |
+-           toExprDependence(E->getType()->getDependence());
++  auto D = E->getBase()->getDependence();
+   for (Expr *Dim: E->getDimensions())
+     if (Dim)
+-      D |= Dim->getDependence();
++      D |= turnValueToTypeDependence(Dim->getDependence());
+   return D;
+ }
+ 
+ ExprDependence clang::computeDependence(OMPIteratorExpr *E) {
+-  auto D = toExprDependence(E->getType()->getDependence());
++  auto D = toExprDependenceForImpliedType(E->getType()->getDependence());
+   for (unsigned I = 0, End = E->numOfIterators(); I < End; ++I) {
+-    if (auto *VD = cast_or_null<ValueDecl>(E->getIteratorDecl(I)))
+-      D |= toExprDependence(VD->getType()->getDependence());
++    if (auto *DD = cast_or_null<DeclaratorDecl>(E->getIteratorDecl(I))) {
++      // If the type is omitted, it's 'int', and is not dependent in any way.
++      if (auto *TSI = DD->getTypeSourceInfo()) {
++        D |= toExprDependenceAsWritten(TSI->getType()->getDependence());
++      }
++    }
+     OMPIteratorExpr::IteratorRange IR = E->getIteratorRange(I);
+     if (Expr *BE = IR.Begin)
+       D |= BE->getDependence();
+@@ -451,7 +476,8 @@ ExprDependence clang::computeDependence(DeclRefExpr *E
+ 
+   if (Decl->isParameterPack())
+     Deps |= ExprDependence::UnexpandedPack;
+-  Deps |= toExprDependence(Type->getDependence()) & ExprDependence::Error;
++  Deps |= toExprDependenceForImpliedType(Type->getDependence()) &
++          ExprDependence::Error;
+ 
+   // C++ [temp.dep.expr]p3:
+   //   An id-expression is type-dependent if it contains:
+@@ -547,7 +573,7 @@ ExprDependence clang::computeDependence(RecoveryExpr *
+   //   - type-dependent if we don't know the type (fallback to an opaque
+   //     dependent type), or the type is known and dependent, or it has
+   //     type-dependent subexpressions.
+-  auto D = toExprDependence(E->getType()->getDependence()) |
++  auto D = toExprDependenceForImpliedType(E->getType()->getDependence()) |
+            ExprDependence::ErrorDependent;
+   // FIXME: remove the type-dependent bit from subexpressions, if the
+   // RecoveryExpr has a non-dependent type.
+@@ -557,12 +583,12 @@ ExprDependence clang::computeDependence(SYCLUniqueStab
+ }
+ 
+ ExprDependence clang::computeDependence(SYCLUniqueStableNameExpr *E) {
+-  return toExprDependence(E->getTypeSourceInfo()->getType()->getDependence());
++  return toExprDependenceAsWritten(
++      E->getTypeSourceInfo()->getType()->getDependence());
+ }
+ 
+ ExprDependence clang::computeDependence(PredefinedExpr *E) {
+-  return toExprDependence(E->getType()->getDependence()) &
+-         ~ExprDependence::UnexpandedPack;
++  return toExprDependenceForImpliedType(E->getType()->getDependence());
+ }
+ 
+ ExprDependence clang::computeDependence(CallExpr *E,
+@@ -578,8 +604,8 @@ ExprDependence clang::computeDependence(OffsetOfExpr *
+ }
+ 
+ ExprDependence clang::computeDependence(OffsetOfExpr *E) {
+-  auto D = turnTypeToValueDependence(
+-      toExprDependence(E->getTypeSourceInfo()->getType()->getDependence()));
++  auto D = turnTypeToValueDependence(toExprDependenceAsWritten(
++      E->getTypeSourceInfo()->getType()->getDependence()));
+   for (unsigned I = 0, N = E->getNumExpressions(); I < N; ++I)
+     D |= turnTypeToValueDependence(E->getIndexExpr(I)->getDependence());
+   return D;
+@@ -615,7 +641,7 @@ ExprDependence clang::computeDependence(ShuffleVectorE
+ }
+ 
+ ExprDependence clang::computeDependence(ShuffleVectorExpr *E) {
+-  auto D = toExprDependence(E->getType()->getDependence());
++  auto D = toExprDependenceForImpliedType(E->getType()->getDependence());
+   for (auto *C : llvm::makeArrayRef(E->getSubExprs(), E->getNumSubExprs()))
+     D |= C->getDependence();
+   return D;
+@@ -666,7 +692,9 @@ ExprDependence clang::computeDependence(CXXNewExpr *E)
+ }
+ 
+ ExprDependence clang::computeDependence(CXXNewExpr *E) {
+-  auto D = toExprDependence(E->getType()->getDependence());
++  auto D = toExprDependenceAsWritten(
++      E->getAllocatedTypeSourceInfo()->getType()->getDependence());
++  D |= toExprDependenceForImpliedType(E->getAllocatedType()->getDependence());
+   auto Size = E->getArraySize();
+   if (Size.hasValue() && *Size)
+     D |= turnTypeToValueDependence((*Size)->getDependence());
+@@ -679,11 +707,11 @@ ExprDependence clang::computeDependence(CXXPseudoDestr
+ 
+ ExprDependence clang::computeDependence(CXXPseudoDestructorExpr *E) {
+   auto D = E->getBase()->getDependence();
+-  if (!E->getDestroyedType().isNull())
+-    D |= toExprDependence(E->getDestroyedType()->getDependence());
++  if (auto *TSI = E->getDestroyedTypeInfo())
++    D |= toExprDependenceAsWritten(TSI->getType()->getDependence());
+   if (auto *ST = E->getScopeTypeInfo())
+     D |= turnTypeToValueDependence(
+-        toExprDependence(ST->getType()->getDependence()));
++        toExprDependenceAsWritten(ST->getType()->getDependence()));
+   if (auto *Q = E->getQualifier())
+     D |= toExprDependence(Q->getDependence() &
+                           ~NestedNameSpecifierDependence::Dependent);
+@@ -738,12 +766,20 @@ ExprDependence clang::computeDependence(CXXConstructEx
+ }
+ 
+ ExprDependence clang::computeDependence(CXXConstructExpr *E) {
+-  auto D = toExprDependence(E->getType()->getDependence());
++  ExprDependence D =
++      toExprDependenceForImpliedType(E->getType()->getDependence());
+   for (auto *A : E->arguments())
+     D |= A->getDependence() & ~ExprDependence::Type;
+   return D;
+ }
+ 
++ExprDependence clang::computeDependence(CXXTemporaryObjectExpr *E) {
++  CXXConstructExpr *BaseE = E;
++  return toExprDependenceAsWritten(
++             E->getTypeSourceInfo()->getType()->getDependence()) |
++         computeDependence(BaseE);
++}
++
+ ExprDependence clang::computeDependence(CXXDefaultInitExpr *E) {
+   return E->getExpr()->getDependence();
+ }
+@@ -754,7 +790,7 @@ ExprDependence clang::computeDependence(LambdaExpr *E,
+ 
+ ExprDependence clang::computeDependence(LambdaExpr *E,
+                                         bool ContainsUnexpandedParameterPack) {
+-  auto D = toExprDependence(E->getType()->getDependence());
++  auto D = toExprDependenceForImpliedType(E->getType()->getDependence());
+   if (ContainsUnexpandedParameterPack)
+     D |= ExprDependence::UnexpandedPack;
+   return D;
+@@ -762,7 +798,8 @@ ExprDependence clang::computeDependence(CXXUnresolvedC
+ 
+ ExprDependence clang::computeDependence(CXXUnresolvedConstructExpr *E) {
+   auto D = ExprDependence::ValueInstantiation;
+-  D |= toExprDependence(E->getType()->getDependence());
++  D |= toExprDependenceAsWritten(E->getTypeAsWritten()->getDependence());
++  D |= toExprDependenceForImpliedType(E->getType()->getDependence());
+   for (auto *A : E->arguments())
+     D |= A->getDependence() &
+          (ExprDependence::UnexpandedPack | ExprDependence::Error);
+@@ -797,8 +834,8 @@ ExprDependence clang::computeDependence(TypeTraitExpr 
+ ExprDependence clang::computeDependence(TypeTraitExpr *E) {
+   auto D = ExprDependence::None;
+   for (const auto *A : E->getArgs())
+-    D |=
+-        toExprDependence(A->getType()->getDependence()) & ~ExprDependence::Type;
++    D |= toExprDependenceAsWritten(A->getType()->getDependence()) &
++         ~ExprDependence::Type;
+   return D;
+ }
+ 
+@@ -845,7 +882,7 @@ ExprDependence clang::computeDependence(ObjCMessageExp
+   if (auto *R = E->getInstanceReceiver())
+     D |= R->getDependence();
+   else
+-    D |= toExprDependence(E->getType()->getDependence());
++    D |= toExprDependenceForImpliedType(E->getType()->getDependence());
+   for (auto *A : E->arguments())
+     D |= A->getDependence();
+   return D;
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/interpreter/llvm/src/tools/clang/lib/AST/ExprCXX.cpp root_v6.28.12_patched/root_v6.28.12-source/interpreter/llvm/src/tools/clang/lib/AST/ExprCXX.cpp
+--- root_v6.28.12_unpatched/root_v6.28.12-source/interpreter/llvm/src/tools/clang/lib/AST/ExprCXX.cpp	2024-09-18 13:23:11
++++ root_v6.28.12_patched/root_v6.28.12-source/interpreter/llvm/src/tools/clang/lib/AST/ExprCXX.cpp	2024-09-18 13:49:28
+@@ -989,7 +989,9 @@ CXXTemporaryObjectExpr::CXXTemporaryObjectExpr(
+           Cons, /* Elidable=*/false, Args, HadMultipleCandidates,
+           ListInitialization, StdInitListInitialization, ZeroInitialization,
+           CXXConstructExpr::CK_Complete, ParenOrBraceRange),
+-      TSI(TSI) {}
++      TSI(TSI) {
++  setDependence(computeDependence(this));
++}
+ 
+ CXXTemporaryObjectExpr::CXXTemporaryObjectExpr(EmptyShell Empty,
+                                                unsigned NumArgs)
+@@ -1075,7 +1077,9 @@ CXXConstructExpr::CXXConstructExpr(
+     TrailingArgs[I] = Args[I];
+   }
+ 
+-  setDependence(computeDependence(this));
++  // CXXTemporaryObjectExpr does this itself after setting its TypeSourceInfo.
++  if (SC == CXXConstructExprClass)
++    setDependence(computeDependence(this));
+ }
+ 
+ CXXConstructExpr::CXXConstructExpr(StmtClass SC, EmptyShell Empty,
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/interpreter/llvm/src/tools/clang/lib/AST/Type.cpp root_v6.28.12_patched/root_v6.28.12-source/interpreter/llvm/src/tools/clang/lib/AST/Type.cpp
+--- root_v6.28.12_unpatched/root_v6.28.12-source/interpreter/llvm/src/tools/clang/lib/AST/Type.cpp	2024-09-18 13:23:11
++++ root_v6.28.12_patched/root_v6.28.12-source/interpreter/llvm/src/tools/clang/lib/AST/Type.cpp	2024-09-18 13:49:28
+@@ -722,8 +722,7 @@ ObjCTypeParamType::ObjCTypeParamType(const ObjCTypePar
+ 
+ ObjCTypeParamType::ObjCTypeParamType(const ObjCTypeParamDecl *D, QualType can,
+                                      ArrayRef<ObjCProtocolDecl *> protocols)
+-    : Type(ObjCTypeParam, can,
+-           can->getDependence() & ~TypeDependence::UnexpandedPack),
++    : Type(ObjCTypeParam, can, toSemanticDependence(can->getDependence())),
+       OTPDecl(const_cast<ObjCTypeParamDecl *>(D)) {
+   initialize(protocols);
+ }
+@@ -3383,7 +3382,7 @@ TypedefType::TypedefType(TypeClass tc, const TypedefNa
+ 
+ TypedefType::TypedefType(TypeClass tc, const TypedefNameDecl *D,
+                          QualType underlying, QualType can)
+-    : Type(tc, can, underlying->getDependence()),
++    : Type(tc, can, toSemanticDependence(underlying->getDependence())),
+       Decl(const_cast<TypedefNameDecl *>(D)) {
+   assert(!isa<TypedefType>(can) && "Invalid canonical type");
+ }
+@@ -3639,8 +3638,7 @@ TemplateSpecializationType::TemplateSpecializationType
+     : Type(TemplateSpecialization, Canon.isNull() ? QualType(this, 0) : Canon,
+            (Canon.isNull()
+                 ? TypeDependence::DependentInstantiation
+-                : Canon->getDependence() & ~(TypeDependence::VariablyModified |
+-                                             TypeDependence::UnexpandedPack)) |
++                : toSemanticDependence(Canon->getDependence())) |
+                (toTypeDependence(T.getDependence()) &
+                 TypeDependence::UnexpandedPack)),
+       Template(T) {
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/io/io/src/TFile.cxx root_v6.28.12_patched/root_v6.28.12-source/io/io/src/TFile.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/io/io/src/TFile.cxx	2024-09-18 13:23:15
++++ root_v6.28.12_patched/root_v6.28.12-source/io/io/src/TFile.cxx	2024-09-18 13:49:29
+@@ -4249,8 +4249,9 @@ TFile *TFile::Open(const char *url, Option_t *options,
+                   f = (TFile*) h->ExecPlugin(4, name.Data(), option, ftitle, compress);
+             } else {
+                // Just try to open it locally but via TFile::Open, so that we pick-up the correct
+-               // plug-in in the case file name contains information about a special backend (e.g.
+-               f = TFile::Open(urlname.GetFileAndOptions(), option, ftitle, compress);
++               // plug-in in the case file name contains information about a special backend (e.g.)
++               if (strcmp(name, urlname.GetFileAndOptions()) != 0)
++                  f = TFile::Open(urlname.GetFileAndOptions(), option, ftitle, compress);
+             }
+          }
+       }
+@@ -4258,7 +4259,7 @@ TFile *TFile::Open(const char *url, Option_t *options,
+       if (f && f->IsZombie()) {
+          TString newUrl = f->GetNewUrl();
+          delete f;
+-         if( newUrl.Length() && gEnv->GetValue("TFile.CrossProtocolRedirects", 1) )
++         if( newUrl.Length() && (newUrl != name) && gEnv->GetValue("TFile.CrossProtocolRedirects", 1) )
+             f = TFile::Open( newUrl, option, ftitle, compress );
+          else
+             f = nullptr;
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/math/mathcore/src/FitUtil.cxx root_v6.28.12_patched/root_v6.28.12-source/math/mathcore/src/FitUtil.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/math/mathcore/src/FitUtil.cxx	2024-09-18 13:23:15
++++ root_v6.28.12_patched/root_v6.28.12-source/math/mathcore/src/FitUtil.cxx	2024-09-18 13:49:29
+@@ -1118,7 +1118,7 @@ double FitUtil::EvaluateLogL(const IModelFunction &fun
+          } else {
+             // use (-inf +inf)
+             data.Range().GetRange(&xmin[0],&xmax[0]);
+-            // check if funcition is zero at +- inf
++            // check if function is zero at +- inf
+             if (func(xmin.data(), p) != 0 || func(xmax.data(), p) != 0) {
+                MATH_ERROR_MSG("FitUtil::EvaluateLogLikelihood","A range has not been set and the function is not zero at +/- inf");
+                return 0;
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/math/mathcore/src/Fitter.cxx root_v6.28.12_patched/root_v6.28.12-source/math/mathcore/src/Fitter.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/math/mathcore/src/Fitter.cxx	2024-09-18 13:23:15
++++ root_v6.28.12_patched/root_v6.28.12-source/math/mathcore/src/Fitter.cxx	2024-09-18 13:49:29
+@@ -870,14 +870,16 @@ bool Fitter::DoWeightMinimization(std::unique_ptr<ObjF
+ template<class ObjFunc_t>
+ bool Fitter::DoWeightMinimization(std::unique_ptr<ObjFunc_t> objFunc, const ROOT::Math::IMultiGenFunction * chi2func) {
+    // perform the minimization initializing the minimizer starting from a given obj function
+-   // and apply afterwards the correction for weights. This applyies only for logL fitting
++   // and apply afterwards the correction for weights. This applies only for logL fitting
+    this->fFitType = objFunc->Type();
+    fExtObjFunction = nullptr;
+-   fObjFunction = std::move(objFunc);
++   // need to use a temporary shared pointer to the objective function since we cannot use the unique pointer when it has been moved
++   std::shared_ptr<ObjFunc_t> sObjFunc{ std::move(objFunc)};
++   fObjFunction = sObjFunc;
+    if (!DoInitMinimizer()) return false;
+    if (!DoMinimization(chi2func)) return false;
+-   objFunc->UseSumOfWeightSquare();
+-   return ApplyWeightCorrection(*objFunc);
++   sObjFunc->UseSumOfWeightSquare();
++   return ApplyWeightCorrection(*sObjFunc);
+ }
+ 
+ 
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/requirements.txt root_v6.28.12_patched/root_v6.28.12-source/requirements.txt
+--- root_v6.28.12_unpatched/root_v6.28.12-source/requirements.txt	2024-09-18 13:23:14
++++ root_v6.28.12_patched/root_v6.28.12-source/requirements.txt	2024-09-18 13:49:29
+@@ -1,8 +1,18 @@
+ # ROOT requirements for third-party Python packages
+ 
+ # PyROOT: Interoperability with numpy arrays
+-# TMVA: PyMVA interfaces
+ numpy>=1.4.1
++
++# TMVA: SOFIE
++# graph_nets
++onnx
++# sonnet # used for GNNs
++
++# TMVA: PyMVA interfaces
++scikit-learn
++tensorflow<2.16
++torch
++xgboost
+ 
+ # PyROOT: ROOT.Numba.Declare decorator
+ numba>=0.47.0
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/roofit/hs3/src/JSONFactories_RooFitCore.cxx root_v6.28.12_patched/root_v6.28.12-source/roofit/hs3/src/JSONFactories_RooFitCore.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/roofit/hs3/src/JSONFactories_RooFitCore.cxx	2024-09-18 13:23:15
++++ root_v6.28.12_patched/root_v6.28.12-source/roofit/hs3/src/JSONFactories_RooFitCore.cxx	2024-09-18 13:49:29
+@@ -17,7 +17,6 @@
+ #include <RooBinWidthFunction.h>
+ #include <RooCategory.h>
+ #include <RooDataHist.h>
+-#include <RooExpPoly.h>
+ #include <RooFit/Detail/JSONInterface.h>
+ #include <RooFitHS3/JSONIO.h>
+ #include <RooFormulaVar.h>
+@@ -213,37 +212,6 @@ class RooPolynomialFactory : public RooFit::JSONIO::Im
+    }
+ };
+ 
+-class RooExpPolyFactory : public RooFit::JSONIO::Importer {
+-public:
+-   bool importArg(RooJSONFactoryWSTool *tool, const JSONNode &p) const override
+-   {
+-      std::string name(RooJSONFactoryWSTool::name(p));
+-      if (!p.has_child("coefficients")) {
+-         RooJSONFactoryWSTool::error("no coefficients given in '" + name + "'");
+-      }
+-      RooAbsReal *x = tool->requestArg<RooAbsReal>(p, "x");
+-      RooArgList coefs;
+-      int order = 0;
+-      int lowestOrder = 0;
+-      for (const auto &coef : p["coefficients"].children()) {
+-         // As long as the coefficients match the default coefficients in
+-         // RooFit, we don't have to instantiate RooFit objects but can
+-         // increase the lowestOrder flag.
+-         if (order == 0 && coef.val() == "1.0") {
+-            ++lowestOrder;
+-         } else if (coefs.empty() && coef.val() == "0.0") {
+-            ++lowestOrder;
+-         } else {
+-            coefs.add(*tool->request<RooAbsReal>(coef.val(), name));
+-         }
+-         ++order;
+-      }
+-
+-      tool->wsEmplace<RooExpPoly>(name, *x, coefs, lowestOrder);
+-      return true;
+-   }
+-};
+-
+ class RooMultiVarGaussianFactory : public RooFit::JSONIO::Importer {
+ public:
+    bool importArg(RooJSONFactoryWSTool *tool, const JSONNode &p) const override
+@@ -445,28 +413,6 @@ class RooPolynomialStreamer : public RooFit::JSONIO::E
+    }
+ };
+ 
+-class RooExpPolyStreamer : public RooFit::JSONIO::Exporter {
+-public:
+-   std::string const &key() const override;
+-   bool exportObject(RooJSONFactoryWSTool *, const RooAbsArg *func, JSONNode &elem) const override
+-   {
+-      auto *pdf = static_cast<const RooExpPoly *>(func);
+-      elem["type"] << key();
+-      elem["x"] << pdf->x().GetName();
+-      auto &coefs = elem["coefficients"].set_seq();
+-      // Write out the default coefficient that RooFit uses for the lower
+-      // orders before the order of the first coefficient. Like this, the
+-      // output is more self-documenting.
+-      for (int i = 0; i < pdf->lowestOrder(); ++i) {
+-         coefs.append_child() << (i == 0 ? "1.0" : "0.0");
+-      }
+-      for (const auto &coef : pdf->coefList()) {
+-         coefs.append_child() << coef->GetName();
+-      }
+-      return true;
+-   }
+-};
+-
+ class RooMultiVarGaussianStreamer : public RooFit::JSONIO::Exporter {
+ public:
+    std::string const &key() const override;
+@@ -519,7 +465,6 @@ DEFINE_EXPORTER_KEY(RooBinWidthFunctionStreamer, "binw
+ DEFINE_EXPORTER_KEY(RooHistPdfStreamer, "histogram_dist");
+ DEFINE_EXPORTER_KEY(RooBinSamplingPdfStreamer, "binsampling");
+ DEFINE_EXPORTER_KEY(RooBinWidthFunctionStreamer, "binwidth");
+-DEFINE_EXPORTER_KEY(RooExpPolyStreamer, "exp_poly_dist");
+ DEFINE_EXPORTER_KEY(RooPolynomialStreamer, "polynomial_dist");
+ DEFINE_EXPORTER_KEY(RooMultiVarGaussianStreamer, "multinormal_dist");
+ DEFINE_EXPORTER_KEY(RooTFnBindingStreamer, "generic_function");
+@@ -540,7 +485,6 @@ STATIC_EXECUTE([]() {
+    registerImporter<RooBinWidthFunctionFactory>("binwidth", false);
+    registerImporter<RooRealSumPdfFactory>("weighted_sum_dist", false);
+    registerImporter<RooRealSumFuncFactory>("weighted_sum", false);
+-   registerImporter<RooExpPolyFactory>("exp_poly_dist", false);
+    registerImporter<RooPolynomialFactory>("polynomial_dist", false);
+    registerImporter<RooMultiVarGaussianFactory>("multinormal_dist", false);
+ 
+@@ -552,7 +496,6 @@ STATIC_EXECUTE([]() {
+    registerExporter<RooFormulaArgStreamer<RooFormulaVar>>(RooFormulaVar::Class(), false);
+    registerExporter<RooRealSumPdfStreamer>(RooRealSumPdf::Class(), false);
+    registerExporter<RooRealSumFuncStreamer>(RooRealSumFunc::Class(), false);
+-   registerExporter<RooExpPolyStreamer>(RooExpPoly::Class(), false);
+    registerExporter<RooPolynomialStreamer>(RooPolynomial::Class(), false);
+    registerExporter<RooMultiVarGaussianStreamer>(RooMultiVarGaussian::Class(), false);
+    registerExporter<RooTFnBindingStreamer>(RooTFnBinding::Class(), false);
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/roofit/hs3/test/testRooFitHS3.cxx root_v6.28.12_patched/root_v6.28.12-source/roofit/hs3/test/testRooFitHS3.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/roofit/hs3/test/testRooFitHS3.cxx	2024-09-18 13:23:15
++++ root_v6.28.12_patched/root_v6.28.12-source/roofit/hs3/test/testRooFitHS3.cxx	2024-09-18 13:49:29
+@@ -155,21 +155,6 @@ TEST(RooFitHS3, RooExponential)
+    EXPECT_EQ(status, 0);
+ }
+ 
+-TEST(RooFitHS3, RooExpPoly)
+-{
+-   // To silence the numeric integration
+-   RooHelpers::LocalChangeMsgLevel changeMsgLvl(RooFit::WARNING);
+-
+-   // Test different values for "lowestOrder"
+-   int status = 0;
+-   status = validate({"ExpPoly::exppoly0(x[0, 10], {a_0[3.0], a_1[-0.3, -10, 10], a_2[0.01, -10, 10]}, 0)"});
+-   EXPECT_EQ(status, 0);
+-   status = validate({"ExpPoly::exppoly1(x[0, 10], {a_1[-0.1, -10, 10], a_2[0.003, -10, 10]}, 1)"});
+-   EXPECT_EQ(status, 0);
+-   status = validate({"ExpPoly::exppoly1(x[0, 10], {a_2[0.003, -10, 10]}, 2)"});
+-   EXPECT_EQ(status, 0);
+-}
+-
+ TEST(RooFitHS3, RooGamma)
+ {
+    int status = validate({"Gamma::gamma_dist(x[5.0, 10.0], gamma[1.0, 0.1, 10.0], beta[1.0, 0.1, 10.0], mu[5.0])"});
+@@ -255,13 +240,6 @@ TEST(RooFitHS3, RooPolynomial)
+    status = validate({"Polynomial::poly1(x[0, 10], {a_1[-0.1, -10, 10], a_2[0.003, -10, 10]}, 1)"});
+    EXPECT_EQ(status, 0);
+    status = validate({"Polynomial::poly1(x[0, 10], {a_2[0.003, -10, 10]}, 2)"});
+-   EXPECT_EQ(status, 0);
+-}
+-
+-TEST(RooFitHS3, RooPower)
+-{
+-   int status = 0;
+-   status = validate({"Power::power(x[0, 10], {a_0[3.0], a_1[-0.3, -10, 10]}, {1.0, 2.0})"});
+    EXPECT_EQ(status, 0);
+ }
+ 
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/roofit/jsoninterface/CMakeLists.txt root_v6.28.12_patched/root_v6.28.12-source/roofit/jsoninterface/CMakeLists.txt
+--- root_v6.28.12_unpatched/root_v6.28.12-source/roofit/jsoninterface/CMakeLists.txt	2024-09-18 13:23:15
++++ root_v6.28.12_patched/root_v6.28.12-source/roofit/jsoninterface/CMakeLists.txt	2024-09-18 13:49:29
+@@ -12,8 +12,14 @@
+ # If RapidYAML can be found on the system, we will also compile the RapidYAML backend besides the
+ # nlohmann-json backend. Like this we can also convert to yaml.
+ 
+-message(STATUS "Looking for RapidYAML (used by RooFit)")
+-find_package(ryml)
++# The RapidYAML backend is always disabled because it doesn't work anymore for
++# RooFitHS3. The nlohmann_json interface is always used and works well, hence
++# rapidyaml was not tested anymore. The relevant code is still left in the
++# CMakeLists.txt in case someone wants to revive the RapilYAML backend.
++
++# message(STATUS "Looking for RapidYAML (used by RooFit)")
++# find_package(ryml)
++
+ if(${RYML_FOUND})
+   message(STATUS "RapidYAML found, compiling also RooFit JSON Interface with RapidYAML parser")
+   set(ParserSources src/JSONParser.cxx src/RYMLParser.cxx)
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/roofit/roofit/CMakeLists.txt root_v6.28.12_patched/root_v6.28.12-source/roofit/roofit/CMakeLists.txt
+--- root_v6.28.12_unpatched/root_v6.28.12-source/roofit/roofit/CMakeLists.txt	2024-09-18 13:23:15
++++ root_v6.28.12_patched/root_v6.28.12-source/roofit/roofit/CMakeLists.txt	2024-09-18 13:49:29
+@@ -35,8 +35,6 @@ ROOT_STANDARD_LIBRARY_PACKAGE(RooFit
+     RooDecay.h
+     RooDstD0BG.h
+     RooExponential.h
+-    RooExpPoly.h
+-    RooPower.h    
+     RooFunctor1DBinding.h
+     RooFunctorBinding.h
+     RooGamma.h
+@@ -98,8 +96,6 @@ ROOT_STANDARD_LIBRARY_PACKAGE(RooFit
+     src/RooDecay.cxx
+     src/RooDstD0BG.cxx
+     src/RooExponential.cxx
+-    src/RooExpPoly.cxx
+-    src/RooPower.cxx
+     src/RooFunctor1DBinding.cxx
+     src/RooFunctorBinding.cxx
+     src/RooGamma.cxx
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/roofit/roofit/inc/LinkDef1.h root_v6.28.12_patched/root_v6.28.12-source/roofit/roofit/inc/LinkDef1.h
+--- root_v6.28.12_unpatched/root_v6.28.12-source/roofit/roofit/inc/LinkDef1.h	2024-09-18 13:23:15
++++ root_v6.28.12_patched/root_v6.28.12-source/roofit/roofit/inc/LinkDef1.h	2024-09-18 13:49:29
+@@ -18,8 +18,6 @@
+ #pragma link C++ class RooDecay+ ;
+ #pragma link C++ class RooDstD0BG+ ;
+ #pragma link C++ class RooExponential+ ;
+-#pragma link C++ class RooExpPoly+ ;
+-#pragma link C++ class RooPower+ ;
+ #pragma link C++ class RooGaussian+ ;
+ #pragma link C++ class RooLognormal+ ;
+ #pragma link C++ class RooGamma+ ;
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/roofit/roofit/inc/RooExpPoly.h root_v6.28.12_patched/root_v6.28.12-source/roofit/roofit/inc/RooExpPoly.h
+--- root_v6.28.12_unpatched/root_v6.28.12-source/roofit/roofit/inc/RooExpPoly.h	2024-09-18 13:23:15
++++ root_v6.28.12_patched/root_v6.28.12-source/roofit/roofit/inc/RooExpPoly.h	1969-12-31 16:00:00
+@@ -1,56 +0,0 @@
+-/*
+- * Project: RooFit
+- *
+- * Copyright (c) 2022, CERN
+- *
+- * Redistribution and use in source and binary forms,
+- * with or without modification, are permitted according to the terms
+- * listed in LICENSE (http://roofit.sourceforge.net/license.txt)
+- */
+-
+-#ifndef RooFit_RooExpPoly_h
+-#define RooFit_RooExpPoly_h
+-
+-#include <RooAbsPdf.h>
+-#include <RooRealProxy.h>
+-#include <RooListProxy.h>
+-
+-class RooExpPoly : public RooAbsPdf {
+-public:
+-   RooExpPoly() {}
+-   RooExpPoly(const char *name, const char *title, RooAbsReal &x, const RooArgList &coefList, int lowestOrder = 1);
+-
+-   RooExpPoly(const RooExpPoly &other, const char *name = nullptr);
+-   TObject *clone(const char *newname) const override { return new RooExpPoly(*this, newname); }
+-
+-   /// Get the x variable.
+-   RooAbsReal const &x() const { return _x.arg(); }
+-
+-   /// Get the coefficient list.
+-   RooArgList const &coefList() const { return _coefList; }
+-
+-   /// Return the order for the first coefficient in the list.
+-   int lowestOrder() const { return _lowestOrder; }
+-
+-   double getLogVal(const RooArgSet *nset) const override;
+-
+-   std::string getFormulaExpression(bool expand) const;
+-
+-   int getAnalyticalIntegral(RooArgSet &allVars, RooArgSet &analVars, const char *rangeName = nullptr) const override;
+-   double analyticalIntegral(int code, const char *rangeName = nullptr) const override;
+-
+-   void adjustLimits();
+-
+-protected:
+-   RooRealProxy _x;
+-   RooListProxy _coefList;
+-   int _lowestOrder;
+-
+-   /// Evaluation
+-   double evaluate() const override;
+-   double evaluateLog() const;
+-
+-   ClassDefOverride(RooExpPoly, 1) // ExpPoly PDF
+-};
+-
+-#endif
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/roofit/roofit/inc/RooPower.h root_v6.28.12_patched/root_v6.28.12-source/roofit/roofit/inc/RooPower.h
+--- root_v6.28.12_unpatched/root_v6.28.12-source/roofit/roofit/inc/RooPower.h	2024-09-18 13:23:15
++++ root_v6.28.12_patched/root_v6.28.12-source/roofit/roofit/inc/RooPower.h	1969-12-31 16:00:00
+@@ -1,55 +0,0 @@
+-/*
+- * Project: RooFit
+- *
+- * Copyright (c) 2022, CERN
+- *
+- * Redistribution and use in source and binary forms,
+- * with or without modification, are permitted according to the terms
+- * listed in LICENSE (http://roofit.sourceforge.net/license.txt)
+- */
+-
+-#ifndef RooFit_RooPower_h
+-#define RooFit_RooPower_h
+-
+-#include <RooAbsPdf.h>
+-#include <RooRealProxy.h>
+-#include <RooListProxy.h>
+-
+-#include <vector>
+-
+-class RooPower : public RooAbsPdf {
+-public:
+-   RooPower() {}
+-   RooPower(const char *name, const char *title, RooAbsReal &x, const RooArgList &coefList, const RooArgList &expList);
+-
+-   RooPower(const RooPower &other, const char *name = nullptr);
+-   TObject *clone(const char *newname) const override { return new RooPower(*this, newname); }
+-
+-   /// Get the base of the exponentiated terms (aka. x variable).
+-   RooAbsReal const &base() const { return *_x; }
+-
+-   /// Get the list of coefficients.
+-   RooArgList const &coefList() const { return _coefList; }
+-
+-   /// Get the list of exponents.
+-   RooArgList const &expList() const { return _expList; }
+-
+-   std::string getFormulaExpression(bool expand) const;
+-
+-   int getAnalyticalIntegral(RooArgSet &allVars, RooArgSet &analVars, const char *rangeName = nullptr) const override;
+-   double analyticalIntegral(int code, const char *rangeName = nullptr) const override;
+-
+-protected:
+-   RooRealProxy _x;
+-   RooListProxy _coefList;
+-   RooListProxy _expList;
+-
+-   mutable std::vector<double> _wksp; //! do not persist
+-
+-   /// Evaluation
+-   double evaluate() const override;
+-
+-   ClassDefOverride(RooPower, 1) // Power PDF
+-};
+-
+-#endif
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/roofit/roofit/src/RooExpPoly.cxx root_v6.28.12_patched/root_v6.28.12-source/roofit/roofit/src/RooExpPoly.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/roofit/roofit/src/RooExpPoly.cxx	2024-09-18 13:23:15
++++ root_v6.28.12_patched/root_v6.28.12-source/roofit/roofit/src/RooExpPoly.cxx	1969-12-31 16:00:00
+@@ -1,301 +0,0 @@
+-/*
+- * Project: RooFit
+- *
+- * Copyright (c) 2022, CERN
+- *
+- * Redistribution and use in source and binary forms,
+- * with or without modification, are permitted according to the terms
+- * listed in LICENSE (http://roofit.sourceforge.net/license.txt)
+- */
+-
+-/** \class RooExpPoly
+-    \ingroup Roofit
+-
+-RooExpPoly implements a polynomial PDF of the form \f[ f(x) =
+-\mathcal{N} \cdot \exp( \sum_{i} a_{i} * x^{i} ) \f] \f$ \mathcal{N}
+-\f$ is a normalisation constant that is automatically calculated when
+-the function is used in computations.
+-
+-The sum can be truncated at the low end. See the main constructor
+-RooExpPoly::RooExpPoly(const char*, const char*, RooAbsReal&, const RooArgList&, int)
+-
+-\image html RooExpPoly.png
+-
+-**/
+-
+-#include <RooExpPoly.h>
+-
+-#include <RooAbsReal.h>
+-#include <RooArgList.h>
+-#include <RooMath.h>
+-#include <RooMsgService.h>
+-#include <RooRealVar.h>
+-
+-#include <TMath.h>
+-#include <TError.h>
+-
+-#include <cmath>
+-#include <sstream>
+-#include <cassert>
+-#include <complex>
+-
+-ClassImp(RooExpPoly);
+-
+-////////////////////////////////////////////////////////////////////////////////
+-/// Create a polynomial in the variable `x`.
+-/// \param[in] name Name of the PDF
+-/// \param[in] title Title for plotting the PDF
+-/// \param[in] x The variable of the polynomial
+-/// \param[in] coefList The coefficients \f$ a_i \f$
+-/// \param[in] lowestOrder [optional] Truncate the sum such that it skips the lower orders:
+-/// \f[
+-///     1. + \sum_{i=0}^{\mathrm{coefList.size()}} a_{i} * x^{(i + \mathrm{lowestOrder})}
+-/// \f]
+-///
+-/// This means that
+-/// \code{.cpp}
+-/// RooExpPoly pol("pol", "pol", x, RooArgList(a, b), lowestOrder = 2)
+-/// \endcode
+-/// computes
+-/// \f[
+-///   \mathrm{pol}(x) = 1 * x^0 + (0 * x^{\ldots}) + a * x^2 + b * x^3.
+-/// \f]
+-
+-RooExpPoly::RooExpPoly(const char *name, const char *title, RooAbsReal &x, const RooArgList &coefList, int lowestOrder)
+-   : RooAbsPdf(name, title),
+-     _x("x", "Dependent", this, x),
+-     _coefList("coefList", "List of coefficients", this),
+-     _lowestOrder(lowestOrder)
+-{
+-   // Check lowest order
+-   if (_lowestOrder < 0) {
+-      coutE(InputArguments) << "RooExpPoly::ctor(" << GetName()
+-                            << ") WARNING: lowestOrder must be >=0, setting value to 0" << std::endl;
+-      _lowestOrder = 0;
+-   }
+-
+-   for (auto coef : coefList) {
+-      if (!dynamic_cast<RooAbsReal *>(coef)) {
+-         coutE(InputArguments) << "RooExpPoly::ctor(" << GetName() << ") ERROR: coefficient " << coef->GetName()
+-                               << " is not of type RooAbsReal" << std::endl;
+-         R__ASSERT(0);
+-      }
+-      _coefList.add(*coef);
+-   }
+-}
+-
+-////////////////////////////////////////////////////////////////////////////////
+-/// Copy constructor
+-
+-RooExpPoly::RooExpPoly(const RooExpPoly &other, const char *name)
+-   : RooAbsPdf(other, name),
+-     _x("x", this, other._x),
+-     _coefList("coefList", this, other._coefList),
+-     _lowestOrder(other._lowestOrder)
+-{
+-}
+-
+-////////////////////////////////////////////////////////////////////////////////
+-
+-double RooExpPoly::evaluateLog() const
+-{
+-   // Calculate and return value of polynomial
+-
+-   const unsigned sz = _coefList.size();
+-   const int lowestOrder = _lowestOrder;
+-   if (!sz)
+-      return lowestOrder ? 1. : 0.;
+-   std::vector<double> coefs;
+-   coefs.reserve(sz);
+-
+-   const RooArgSet *nset = _coefList.nset();
+-   for (auto coef : _coefList) {
+-      coefs.push_back(static_cast<RooAbsReal *>(coef)->getVal(nset));
+-   };
+-   const double x = _x;
+-   double xpow = std::pow(x, lowestOrder);
+-   double retval = 0;
+-   for (size_t i = 0; i < sz; ++i) {
+-      retval += coefs[i] * xpow;
+-      xpow *= x;
+-   }
+-
+-   if (std::numeric_limits<double>::max_exponent < retval) {
+-      coutE(InputArguments) << "RooExpPoly::evaluateLog(" << GetName() << ") ERROR: exponent at " << x
+-                            << " larger than allowed maximum, result will be infinite! " << retval << " > "
+-                            << std::numeric_limits<double>::max_exponent << " in " << this->getFormulaExpression(true)
+-                            << std::endl;
+-   }
+-   return retval;
+-}
+-
+-////////////////////////////////////////////////////////////////////////////////
+-
+-void RooExpPoly::adjustLimits()
+-{
+-   // Adjust the limits of all the coefficients to reflect the numeric boundaries
+-
+-   const unsigned sz = _coefList.size();
+-   double max = std::numeric_limits<double>::max_exponent / sz;
+-   const int lowestOrder = _lowestOrder;
+-   std::vector<double> coefs;
+-   coefs.reserve(sz);
+-
+-   RooRealVar *x = dynamic_cast<RooRealVar *>(&(*_x));
+-   if (x) {
+-      const double xmax = x->getMax();
+-      double xmaxpow = std::pow(xmax, lowestOrder);
+-      for (size_t i = 0; i < sz; ++i) {
+-         double thismax = max / xmaxpow;
+-         RooRealVar *coef = dynamic_cast<RooRealVar *>(this->_coefList.at(i));
+-         if (coef) {
+-            coef->setVal(thismax);
+-            coef->setMax(thismax);
+-         }
+-         xmaxpow *= xmax;
+-      }
+-   }
+-}
+-
+-////////////////////////////////////////////////////////////////////////////////
+-
+-double RooExpPoly::evaluate() const
+-{
+-   // Calculate and return value of function
+-
+-   const double logval = this->evaluateLog();
+-   const double val = exp(logval);
+-   if (std::isinf(val)) {
+-      coutE(InputArguments) << "RooExpPoly::evaluate(" << GetName()
+-                            << ") ERROR: result of exponentiation is infinite! exponent was " << logval << std::endl;
+-   }
+-   return val;
+-}
+-
+-////////////////////////////////////////////////////////////////////////////////
+-
+-double RooExpPoly::getLogVal(const RooArgSet *nset) const
+-{
+-   return RooAbsPdf::getLogVal(nset);
+-   //  return this->evaluateLog();
+-}
+-
+-////////////////////////////////////////////////////////////////////////////////
+-
+-int RooExpPoly::getAnalyticalIntegral(RooArgSet &allVars, RooArgSet &analVars, const char * /*rangeName*/) const
+-{
+-
+-   if ((_coefList.size() + _lowestOrder < 4) &&
+-       ((_coefList.size() + _lowestOrder < 3) ||
+-        (static_cast<RooAbsReal *>(_coefList.at(2 - _lowestOrder))->getVal() <= 0)) &&
+-       matchArgs(allVars, analVars, _x)) {
+-      return 0;
+-   }
+-   return 0;
+-}
+-
+-////////////////////////////////////////////////////////////////////////////////
+-
+-#define PI TMath::Pi()
+-
+-namespace {
+-double deltaerf(long double x1, long double x2)
+-{
+-   // several things happening here
+-   // 1. use "erf(x) = -erf(-x)" to evaluate the function only ever for the positive side (higher precision)
+-   // 2. use "erf(x) = 1.-erfc(x)" and, instead of "erf(x1) - erf(x2)", do "(1.-erfc(x1)) - (1.-erfc(x2)) = erfc(x2) -
+-   // erfc(x1)"
+-   double y2 = x1 > 0 ? erfc(x1) : -erfc(-x1);
+-   double y1 = x2 > 0 ? erfc(x2) : -erfc(-x2);
+-   if (y1 == y2) {
+-      std::cout << "WARNING in calculation of analytical integral limited by numerical precision" << std::endl;
+-      std::cout << "x: " << x1 << " , " << x2 << std::endl;
+-      std::cout << "y: " << y1 << " , " << y2 << std::endl;
+-   }
+-   return y1 - y2;
+-}
+-
+-double deltaerfi(double x1, double x2)
+-{
+-   std::complex<double> u1 = {x1, 0.};
+-   std::complex<double> u2 = {x2, 0.};
+-
+-   std::complex<double> y2 = x2 > 0 ? RooMath::faddeeva(u2) : RooMath::faddeeva(-u2);
+-   std::complex<double> y1 = x1 > 0 ? RooMath::faddeeva(u1) : RooMath::faddeeva(-u1);
+-   if (y1 == y2) {
+-      std::cout << "WARNING in calculation of analytical integral limited by numerical precision" << std::endl;
+-      std::cout << "x: " << x1 << " , " << x2 << std::endl;
+-      std::cout << "y: " << y1 << " , " << y2 << std::endl;
+-   }
+-   return y1.imag() - y2.imag();
+-}
+-} // namespace
+-
+-double RooExpPoly::analyticalIntegral(int /*code*/, const char *rangeName) const
+-{
+-   const double xmin = _x.min(rangeName), xmax = _x.max(rangeName);
+-   const unsigned sz = _coefList.size();
+-   if (!sz)
+-      return xmax - xmin;
+-
+-   std::vector<double> coefs;
+-   coefs.reserve(sz);
+-   const RooArgSet *nset = _coefList.nset();
+-   for (auto c : _coefList) {
+-      coefs.push_back(static_cast<RooAbsReal *>(c)->getVal(nset));
+-   }
+-
+-   switch (_coefList.size() + _lowestOrder) {
+-   case 1: return xmax - xmin;
+-   case 2: {
+-      const double a = coefs[1 - _lowestOrder];
+-      if (a != 0) {
+-         return 1. / a * (exp(a * xmax) - exp(a * xmin)) * (_lowestOrder == 0 ? exp(coefs[0]) : 1);
+-      } else {
+-         return xmax - xmin;
+-      }
+-   }
+-   case 3: {
+-      const double a = coefs[2 - _lowestOrder];
+-      const double b = _lowestOrder == 2 ? 0. : coefs[1 - _lowestOrder];
+-      const double c = _lowestOrder == 0 ? coefs[0] : 0.;
+-      const double absa = std::abs(a);
+-      const double sqrta = std::sqrt(absa);
+-      if (a < 0) {
+-         double d = ::deltaerf((-b + 2 * absa * xmax) / (2 * sqrta), (-b + 2 * absa * xmin) / (2 * sqrta));
+-         double retval = exp(b * b / (4 * absa) + c) * std::sqrt(PI) * d / (2 * sqrta);
+-         return retval;
+-      } else if (a > 0) {
+-         double d = ::deltaerfi((b + 2 * absa * xmax) / (2 * sqrta), (b + 2 * absa * xmin) / (2 * sqrta));
+-         double retval = exp(-b * b / (4 * absa) + c) * std::sqrt(PI) * d / (2 * sqrta);
+-         return retval;
+-      } else if (b != 0) {
+-         return 1. / b * (std::exp(b * xmax) - exp(b * xmin)) * exp(c);
+-      } else {
+-         return xmax - xmin;
+-      }
+-   }
+-   }
+-   return 0.;
+-}
+-
+-////////////////////////////////////////////////////////////////////////////////
+-
+-std::string RooExpPoly::getFormulaExpression(bool expand) const
+-{
+-   std::stringstream ss;
+-   ss << "exp(";
+-   int order = _lowestOrder;
+-   for (auto coef : _coefList) {
+-      if (order != _lowestOrder)
+-         ss << "+";
+-      if (expand)
+-         ss << ((RooAbsReal *)coef)->getVal();
+-      else
+-         ss << coef->GetName();
+-      ss << "*pow(" << _x.GetName() << "," << order << ")";
+-      ++order;
+-   }
+-   ss << ")";
+-   return ss.str();
+-}
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/roofit/roofit/src/RooPower.cxx root_v6.28.12_patched/root_v6.28.12-source/roofit/roofit/src/RooPower.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/roofit/roofit/src/RooPower.cxx	2024-09-18 13:23:15
++++ root_v6.28.12_patched/root_v6.28.12-source/roofit/roofit/src/RooPower.cxx	1969-12-31 16:00:00
+@@ -1,186 +0,0 @@
+-/*
+- * Project: RooFit
+- *
+- * Copyright (c) 2022, CERN
+- *
+- * Redistribution and use in source and binary forms,
+- * with or without modification, are permitted according to the terms
+- * listed in LICENSE (http://roofit.sourceforge.net/license.txt)
+- */
+-
+-/** \class RooPower
+-    \ingroup Roofit
+-
+-RooPower implements a power law PDF of the form
+-\f[ f(x) = \mathcal{N} \cdot \sum_{i} a_{i} * x^{b_i} \f]
+-
+-\image html RooPower.png
+-**/
+-
+-#include <RooPower.h>
+-
+-#include <RooAbsReal.h>
+-#include <RooArgList.h>
+-#include <RooMsgService.h>
+-
+-#include <TError.h>
+-
+-#include <cmath>
+-#include <cassert>
+-#include <sstream>
+-
+-ClassImp(RooPower);
+-
+-////////////////////////////////////////////////////////////////////////////////
+-/// Create a power law in the variable `x`.
+-/// \param[in] name Name of the PDF
+-/// \param[in] title Title for plotting the PDF
+-/// \param[in] x The variable of the polynomial
+-/// \param[in] coefList The coefficients \f$ a_i \f$
+-/// \param[in] expList The exponentials \f$ b_i \f$
+-/// \f[
+-///     \sum_{i=0}^{n} a_{i} * x^{b_{i}}
+-/// \f]
+-///
+-/// This means that
+-/// \code{.cpp}
+-/// RooPower powl("pow", "pow", x, RooArgList(a1, a2), RooArgList(b1,b2))
+-/// \endcode
+-/// computes
+-/// \f[
+-///   \mathrm{pol}(x) = a1 * x^b1 + a2 * x^b2
+-/// \f]
+-
+-RooPower::RooPower(const char *name, const char *title, RooAbsReal &x, const RooArgList &coefList,
+-                   const RooArgList &expList)
+-   : RooAbsPdf(name, title),
+-     _x("x", "Dependent", this, x),
+-     _coefList("coefList", "List of coefficients", this),
+-     _expList("expList", "List of exponents", this)
+-{
+-   if (coefList.size() != expList.size()) {
+-      coutE(InputArguments) << "RooPower::ctor(" << GetName()
+-                            << ") ERROR: coefficient list and exponent list must be of same length" << std::endl;
+-      return;
+-   }
+-   for (auto coef : coefList) {
+-      if (!dynamic_cast<RooAbsReal *>(coef)) {
+-         coutE(InputArguments) << "RooPower::ctor(" << GetName() << ") ERROR: coefficient " << coef->GetName()
+-                               << " is not of type RooAbsReal" << std::endl;
+-         R__ASSERT(0);
+-      }
+-      _coefList.add(*coef);
+-   }
+-   for (auto exp : expList) {
+-      if (!dynamic_cast<RooAbsReal *>(exp)) {
+-         coutE(InputArguments) << "RooPower::ctor(" << GetName() << ") ERROR: coefficient " << exp->GetName()
+-                               << " is not of type RooAbsReal" << std::endl;
+-         R__ASSERT(0);
+-      }
+-      _expList.add(*exp);
+-   }
+-}
+-
+-////////////////////////////////////////////////////////////////////////////////
+-/// Copy constructor
+-
+-RooPower::RooPower(const RooPower &other, const char *name)
+-   : RooAbsPdf(other, name),
+-     _x("x", this, other._x),
+-     _coefList("coefList", this, other._coefList),
+-     _expList("expList", this, other._expList)
+-{
+-}
+-
+-////////////////////////////////////////////////////////////////////////////////
+-
+-double RooPower::evaluate() const
+-{
+-   // Calculate and return value of polynomial
+-
+-   const unsigned sz = _coefList.size();
+-   if (!sz) {
+-      return 0.;
+-   }
+-
+-   std::vector<double> coefs;
+-   std::vector<double> exps;
+-   coefs.reserve(sz);
+-   exps.reserve(sz);
+-   const RooArgSet *nset = _coefList.nset();
+-   for (auto c : _coefList) {
+-      coefs.push_back(static_cast<RooAbsReal *>(c)->getVal(nset));
+-   }
+-   for (auto c : _expList) {
+-      exps.push_back(static_cast<RooAbsReal *>(c)->getVal(nset));
+-   }
+-   double x = this->_x;
+-   double retval = 0;
+-   for (unsigned int i = 0; i < sz; ++i) {
+-      retval += coefs[i] * pow(x, exps[i]);
+-   }
+-   return retval;
+-}
+-
+-////////////////////////////////////////////////////////////////////////////////
+-/// Advertise to RooFit that this function can be analytically integrated.
+-int RooPower::getAnalyticalIntegral(RooArgSet &allVars, RooArgSet &analVars, const char * /*rangeName*/) const
+-{
+-   if (matchArgs(allVars, analVars, _x))
+-      return 1;
+-   return 0;
+-}
+-
+-////////////////////////////////////////////////////////////////////////////////
+-/// Do the analytical integral according to the code that was returned by getAnalyticalIntegral().
+-double RooPower::analyticalIntegral(int /*code*/, const char *rangeName) const
+-{
+-   const double xmin = _x.min(rangeName);
+-   const double xmax = _x.max(rangeName);
+-   const unsigned sz = _coefList.size();
+-   if (!sz) {
+-      return xmax - xmin;
+-   }
+-
+-   std::vector<double> coefs;
+-   std::vector<double> exps;
+-   coefs.reserve(sz);
+-   exps.reserve(sz);
+-   const RooArgSet *nset = _coefList.nset();
+-   for (auto c : _coefList) {
+-      coefs.push_back(static_cast<RooAbsReal *>(c)->getVal(nset));
+-   }
+-   for (auto c : _expList) {
+-      exps.push_back(static_cast<RooAbsReal *>(c)->getVal(nset));
+-   }
+-
+-   double retval = 0;
+-   for (unsigned int i = 0; i < sz; ++i) {
+-      if (exps[i] == -1) {
+-         retval += coefs[i] * (log(xmax) - log(xmin));
+-      } else {
+-         retval += coefs[i] / (exps[i] + 1) * (pow(xmax, (exps[i] + 1)) - pow(xmin, (exps[i] + 1)));
+-      }
+-   }
+-   return retval;
+-}
+-
+-std::string RooPower::getFormulaExpression(bool expand) const
+-{
+-   std::stringstream ss;
+-   for (std::size_t i = 0; i < _coefList.size(); ++i) {
+-      if (i != 0)
+-         ss << "+";
+-      if (expand)
+-         ss << static_cast<RooAbsReal *>(_coefList.at(i))->getVal();
+-      else
+-         ss << _coefList.at(i)->GetName();
+-      ss << "*pow(" << _x.GetName() << ",";
+-      if (expand)
+-         ss << static_cast<RooAbsReal *>(_expList.at(i))->getVal();
+-      else
+-         ss << _expList.at(i)->GetName();
+-      ss << ")";
+-   }
+-   return ss.str().c_str();
+-}
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/roofit/roofitcore/test/testTestStatistics.cxx root_v6.28.12_patched/root_v6.28.12-source/roofit/roofitcore/test/testTestStatistics.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/roofit/roofitcore/test/testTestStatistics.cxx	2024-09-18 13:23:15
++++ root_v6.28.12_patched/root_v6.28.12-source/roofit/roofitcore/test/testTestStatistics.cxx	2024-09-18 13:49:29
+@@ -73,7 +73,7 @@ TEST_P(TestStatisticTest, IntegrateBins)
+ TEST_P(TestStatisticTest, IntegrateBins)
+ {
+    RooWorkspace ws;
+-   ws.factory("Power::pow(x[0.1, 5.1], {1.0}, {a[-0.3, -5., 5.]})");
++   ws.factory("EXPR::pow('std::pow(x, a)', {x[0.1, 5.1], a[-0.3, -5., 5.]})");
+ 
+    RooRealVar &x = *ws.var("x");
+    RooRealVar &a = *ws.var("a");
+@@ -120,7 +120,7 @@ TEST_P(TestStatisticTest, IntegrateBins_SubRange)
+ TEST_P(TestStatisticTest, IntegrateBins_SubRange)
+ {
+    RooWorkspace ws;
+-   ws.factory("Power::pow(x[0.1, 5.1], {1.0}, {a[-0.3, -5., 5.]})");
++   ws.factory("EXPR::pow('std::pow(x, a)', {x[0.1, 5.1], a[-0.3, -5., 5.]})");
+ 
+    RooRealVar &x = *ws.var("x");
+    RooRealVar &a = *ws.var("a");
+@@ -169,7 +169,7 @@ TEST_P(TestStatisticTest, IntegrateBins_CustomBinning)
+ TEST_P(TestStatisticTest, IntegrateBins_CustomBinning)
+ {
+    RooWorkspace ws;
+-   ws.factory("Power::pow(x[1.0, 5.], {1.0}, {a[-0.3, -5., 5.]})");
++   ws.factory("EXPR::pow('std::pow(x, a)', {x[1.0, 5.], a[-0.3, -5., 5.]})");
+ 
+    RooRealVar &x = *ws.var("x");
+    RooRealVar &a = *ws.var("a");
+@@ -222,7 +222,7 @@ TEST_P(TestStatisticTest, IntegrateBins_RooDataHist)
+ TEST_P(TestStatisticTest, IntegrateBins_RooDataHist)
+ {
+    RooWorkspace ws;
+-   ws.factory("Power::pow(x[0.1, 5.0], {1.0}, {a[-0.3, -5., 5.]})");
++   ws.factory("EXPR::pow('std::pow(x, a)', {x[0.1, 5.], a[-0.3, -5., 5.]})");
+ 
+    RooRealVar &x = *ws.var("x");
+    RooRealVar &a = *ws.var("a");
+@@ -270,7 +270,7 @@ TEST(RooChi2Var, IntegrateBins)
+    RooRandom::randomGenerator()->SetSeed(1337ul);
+ 
+    RooWorkspace ws;
+-   ws.factory("Power::pow(x[0.1, 5.1], {1.0}, {a[-0.3, -5., 5.]})");
++   ws.factory("EXPR::pow('std::pow(x, a)', {x[0.1, 5.1], a[-0.3, -5., 5.]})");
+ 
+    RooRealVar &x = *ws.var("x");
+    RooRealVar &a = *ws.var("a");
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/test/stressHistoFit.cxx root_v6.28.12_patched/root_v6.28.12-source/test/stressHistoFit.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/test/stressHistoFit.cxx	2024-09-18 13:23:14
++++ root_v6.28.12_patched/root_v6.28.12-source/test/stressHistoFit.cxx	2024-09-18 13:49:29
+@@ -771,6 +771,7 @@ int test1DObjects(vector< vector<algoType> >& listH,
+       for (int i = 1; i <= h1->GetNbinsX() + 1; ++i)
+          h1->SetBinContent(i, rndm.Poisson(func->Eval(h1->GetBinCenter(i))));
+ 
++      h1->Sumw2(); // make as a weighted histo to test weighted fits
+       gTestIndex++;
+       if (gSelectedTest == 0 || gSelectedTest == gTestIndex) {
+          // fill equal bin 1D  histogram
+@@ -803,7 +804,7 @@ int test1DObjects(vector< vector<algoType> >& listH,
+                                              h2->GetXaxis()->GetBinUpEdge(i));
+             h2->SetBinContent(i,rndm.Poisson(expValue));
+          }
+-
++         h2->Sumw2(); // make as a weighted histo to test weighted fits
+          if (c0 && !__DRAW__) delete c0;
+          c0 = new TCanvas(TString::Format("c%d_H1D", gTestIndex), "Histogram1D Variable");
+          ObjectWrapper<TH1D *> owh2(h2);
+@@ -1219,6 +1220,7 @@ void init_structures()
+    noGraphAlgos.push_back( algoType( "Minuit2",     "Migrad",      "EX", CompareResult()) );
+    noGraphAlgos.push_back( algoType( "Minuit",      "Migrad",      "L", CompareResult(defCmpOpt,3,0.1)) );  // normal binned likelihood fit
+    noGraphAlgos.push_back( algoType( "Minuit2",     "Migrad",      "L", CompareResult(defCmpOpt,3,0.1)) );
++   noGraphAlgos.push_back( algoType( "Minuit2",     "Migrad",      "WL", CompareResult(defCmpOpt,3,0.1)) );
+    noGraphAlgos.push_back( algoType( "Minuit2",     "Migrad",      "G", CompareResult()) ); // gradient chi2 fit
+    //noGraphAlgos.push_back( algoType( "Minuit",      "Migrad",      "G", CompareResult()) );   // skip TMinuit with G
+    noGraphAlgos.push_back( algoType( "Minuit2",     "Minimize",    "G", CompareResult()) );
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tmva/pymva/src/MethodPyAdaBoost.cxx root_v6.28.12_patched/root_v6.28.12-source/tmva/pymva/src/MethodPyAdaBoost.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tmva/pymva/src/MethodPyAdaBoost.cxx	2024-09-18 13:23:14
++++ root_v6.28.12_patched/root_v6.28.12-source/tmva/pymva/src/MethodPyAdaBoost.cxx	2024-09-18 13:49:29
+@@ -231,7 +231,7 @@ void MethodPyAdaBoost::Train()
+    }
+ 
+    // Create classifier object
+-   PyRunString("classifier = sklearn.ensemble.AdaBoostClassifier(base_estimator=baseEstimator, n_estimators=nEstimators, learning_rate=learningRate, algorithm=algorithm, random_state=randomState)",
++   PyRunString("classifier = sklearn.ensemble.AdaBoostClassifier(estimator=baseEstimator, n_estimators=nEstimators, learning_rate=learningRate, algorithm=algorithm, random_state=randomState)",
+       "Failed to setup classifier");
+ 
+    // Fit classifier
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tmva/pymva/src/MethodPyGTB.cxx root_v6.28.12_patched/root_v6.28.12-source/tmva/pymva/src/MethodPyGTB.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tmva/pymva/src/MethodPyGTB.cxx	2024-09-18 13:23:14
++++ root_v6.28.12_patched/root_v6.28.12-source/tmva/pymva/src/MethodPyGTB.cxx	2024-09-18 13:49:29
+@@ -301,7 +301,7 @@ void MethodPyGTB::ProcessOptions()
+    pVerbose = Eval(Form("%i", fVerbose));
+    PyDict_SetItemString(fLocalNS, "verbose", pVerbose);
+ 
+-   pWarmStart = Eval(Form("%i", UInt_t(fWarmStart)));
++   pWarmStart = (fWarmStart) ? Eval("True") : Eval("False");
+    PyDict_SetItemString(fLocalNS, "warmStart", pWarmStart);
+ 
+    // If no filename is given, set default
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tmva/pymva/src/MethodPyRandomForest.cxx root_v6.28.12_patched/root_v6.28.12-source/tmva/pymva/src/MethodPyRandomForest.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tmva/pymva/src/MethodPyRandomForest.cxx	2024-09-18 13:23:14
++++ root_v6.28.12_patched/root_v6.28.12-source/tmva/pymva/src/MethodPyRandomForest.cxx	2024-09-18 13:49:29
+@@ -284,13 +284,13 @@ void MethodPyRandomForest::ProcessOptions()
+    pNjobs = Eval(Form("%i", fNjobs));
+    PyDict_SetItemString(fLocalNS, "nJobs", pNjobs);
+ 
+-   pBootstrap = Eval(Form("%i", UInt_t(fBootstrap)));
++   pBootstrap = (fBootstrap) ? Eval("True") : Eval("False");
+    PyDict_SetItemString(fLocalNS, "bootstrap", pBootstrap);
+-   pOobScore = Eval(Form("%i", UInt_t(fOobScore)));
++   pOobScore = (fOobScore) ? Eval("True") : Eval("False");
+    PyDict_SetItemString(fLocalNS, "oobScore", pOobScore);
+    pVerbose = Eval(Form("%i", fVerbose));
+    PyDict_SetItemString(fLocalNS, "verbose", pVerbose);
+-   pWarmStart = Eval(Form("%i", UInt_t(fWarmStart)));
++   pWarmStart = (fWarmStart) ? Eval("True") : Eval("False");
+    PyDict_SetItemString(fLocalNS, "warmStart", pWarmStart);
+ 
+    // If no filename is given, set default
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tmva/pymva/src/RModelParser_PyTorch.cxx root_v6.28.12_patched/root_v6.28.12-source/tmva/pymva/src/RModelParser_PyTorch.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tmva/pymva/src/RModelParser_PyTorch.cxx	2024-09-18 13:23:14
++++ root_v6.28.12_patched/root_v6.28.12-source/tmva/pymva/src/RModelParser_PyTorch.cxx	2024-09-18 13:26:26
+@@ -398,7 +398,7 @@ RModel Parse(std::string filename, std::vector<std::ve
+     PyRunString("import torch",fGlobalNS,fLocalNS);
+     PyRunString("print('Torch Version: '+torch.__version__)",fGlobalNS,fLocalNS);
+     PyRunString("from torch.onnx.utils import _model_to_graph",fGlobalNS,fLocalNS);
+-    PyRunString("from torch.onnx.symbolic_helper import _set_onnx_shape_inference",fGlobalNS,fLocalNS);
++    //PyRunString("from torch.onnx.symbolic_helper import _set_onnx_shape_inference",fGlobalNS,fLocalNS);
+     PyRunString(TString::Format("model= torch.jit.load('%s')",filename.c_str()),fGlobalNS,fLocalNS);
+     PyRunString("globals().update(locals())",fGlobalNS,fLocalNS);
+     PyRunString("model.cpu()",fGlobalNS,fLocalNS);
+@@ -416,7 +416,7 @@ RModel Parse(std::string filename, std::vector<std::ve
+ 
+ 
+     //Getting the ONNX graph from model using the dummy inputs and example outputs
+-    PyRunString("_set_onnx_shape_inference(True)",fGlobalNS,fLocalNS);
++    //PyRunString("_set_onnx_shape_inference(True)",fGlobalNS,fLocalNS);
+     PyRunString("graph=_model_to_graph(model,dummyInputs)",fGlobalNS,fLocalNS);
+ 
+ 
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tmva/pymva/test/CMakeLists.txt root_v6.28.12_patched/root_v6.28.12-source/tmva/pymva/test/CMakeLists.txt
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tmva/pymva/test/CMakeLists.txt	2024-09-18 13:23:14
++++ root_v6.28.12_patched/root_v6.28.12-source/tmva/pymva/test/CMakeLists.txt	2024-09-18 13:49:29
+@@ -88,7 +88,6 @@ if(PY_TORCH_FOUND)
+          LIBRARIES
+          ROOTTMVASofie
+          TMVA
+-         blas
+          ${PYTHON_LIBRARIES}
+          INCLUDE_DIRS
+          SYSTEM
+@@ -96,6 +95,7 @@ if(PY_TORCH_FOUND)
+          ${NUMPY_INCLUDE_DIRS}
+          ${CMAKE_CURRENT_BINARY_DIR}
+       )
++   target_link_libraries(TestRModelParserPyTorch ${BLAS_LINKER_FLAGS} ${BLAS_LIBRARIES})
+    if(APPLE)
+       target_link_options(TestRModelParserPyTorch PRIVATE ${PYTHON_LINK_OPTIONS_Development_Main})
+    endif()
+@@ -183,7 +183,6 @@ endif()
+    ROOT_ADD_GTEST(TestRModelParserKeras TestRModelParserKeras.C
+     LIBRARIES
+     ROOTTMVASofie
+-    blas
+     ${PYTHON_LIBRARIES}
+     INCLUDE_DIRS
+     SYSTEM
+@@ -191,6 +190,7 @@ endif()
+     ${NUMPY_INCLUDE_DIRS}
+     ${CMAKE_CURRENT_BINARY_DIR}
+    )
++   target_link_libraries(TestRModelParserKeras ${BLAS_LINKER_FLAGS} ${BLAS_LIBRARIES})
+    if(APPLE)
+    target_link_options(TestRModelParserKeras PRIVATE ${PYTHON_LINK_OPTIONS_Development_Main})
+    endif()
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tmva/pymva/test/Classification.C root_v6.28.12_patched/root_v6.28.12-source/tmva/pymva/test/Classification.C
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tmva/pymva/test/Classification.C	2024-09-18 13:23:14
++++ root_v6.28.12_patched/root_v6.28.12-source/tmva/pymva/test/Classification.C	2024-09-18 13:49:29
+@@ -21,7 +21,7 @@ void Classification()
+    TMVA::Tools::Instance();
+    TMVA::PyMethodBase::PyInitialize();
+ 
+-   TString outfileName("TMVA.root");
++   TString outfileName("RMVAC.root");
+    TFile *outputFile = TFile::Open(outfileName, "RECREATE");
+ 
+    TMVA::Factory *factory = new TMVA::Factory("TMVAClassification", outputFile,
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tmva/pymva/test/EmitCustomModel.cxx root_v6.28.12_patched/root_v6.28.12-source/tmva/pymva/test/EmitCustomModel.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tmva/pymva/test/EmitCustomModel.cxx	2024-09-18 13:23:14
++++ root_v6.28.12_patched/root_v6.28.12-source/tmva/pymva/test/EmitCustomModel.cxx	2024-09-18 13:49:29
+@@ -34,7 +34,7 @@ model.fit(x_train, y_train, epochs=10, batch_size=1)\n
+ \n\
+ model.compile(loss='mean_squared_error', optimizer=SGD(learning_rate=0.01))\n\
+ model.fit(x_train, y_train, epochs=10, batch_size=1)\n\
+-model.save('KerasModelForCustomOp.keras')\n";
++model.save('KerasModelForCustomOp.h5')\n";
+ 
+ int main(){
+    Py_Initialize();
+@@ -43,7 +43,7 @@ int main(){
+    PyRun_SimpleString(pythonSrc);
+ 
+     //Parsing the saved Keras .keras file into RModel object
+-    RModel model = PyKeras::Parse("KerasModelForCustomOp.keras");
++    RModel model = PyKeras::Parse("KerasModelForCustomOp.h5");
+     model.Generate();
+ 
+     std::unique_ptr<ROperator> op;
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tmva/pymva/test/EmitFromKeras.cxx root_v6.28.12_patched/root_v6.28.12-source/tmva/pymva/test/EmitFromKeras.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tmva/pymva/test/EmitFromKeras.cxx	2024-09-18 13:23:14
++++ root_v6.28.12_patched/root_v6.28.12-source/tmva/pymva/test/EmitFromKeras.cxx	2024-09-18 13:49:29
+@@ -22,49 +22,49 @@ int main(){
+    PyRun_SimpleFile(fKerasModels, "generateKerasModels.py");
+ 
+    //Emitting header file for Keras Sequential Model
+-   RModel modelSequential = TMVA::Experimental::SOFIE::PyKeras::Parse("KerasModelSequential.keras");
++   RModel modelSequential = TMVA::Experimental::SOFIE::PyKeras::Parse("KerasModelSequential.h5");
+    modelSequential.Generate();
+    modelSequential.OutputGenerated("KerasSequentialModel.hxx");
+ 
+    //Emitting header file for Keras Functional API Model
+-   RModel modelFunctional = TMVA::Experimental::SOFIE::PyKeras::Parse("KerasModelFunctional.keras");
++   RModel modelFunctional = TMVA::Experimental::SOFIE::PyKeras::Parse("KerasModelFunctional.h5");
+    modelFunctional.Generate();
+    modelFunctional.OutputGenerated("KerasFunctionalModel.hxx");
+ 
+    //Emitting header file for Keras BatchNorm Model
+-   RModel modelBatchNorm = TMVA::Experimental::SOFIE::PyKeras::Parse("KerasModelBatchNorm.keras");
++   RModel modelBatchNorm = TMVA::Experimental::SOFIE::PyKeras::Parse("KerasModelBatchNorm.h5");
+    modelBatchNorm.Generate();
+    modelBatchNorm.OutputGenerated("KerasBatchNormModel.hxx");
+ 
+ #if PY_MAJOR_VERSION >= 3  // parsing of convolutional models supported only for Python3
+    // Emitting header file for Keras Conv2D Model with valid padding
+-   RModel modelConv2D_Valid = TMVA::Experimental::SOFIE::PyKeras::Parse("KerasModelConv2D_Valid.keras");
++   RModel modelConv2D_Valid = TMVA::Experimental::SOFIE::PyKeras::Parse("KerasModelConv2D_Valid.h5");
+    modelConv2D_Valid.Generate();
+    modelConv2D_Valid.OutputGenerated("KerasConv2D_Valid.hxx");
+ 
+    // Emitting header file for Keras Conv2D Model with valid padding
+-   RModel modelConv2D_Same = TMVA::Experimental::SOFIE::PyKeras::Parse("KerasModelConv2D_Same.keras");
++   RModel modelConv2D_Same = TMVA::Experimental::SOFIE::PyKeras::Parse("KerasModelConv2D_Same.h5");
+    modelConv2D_Same.Generate();
+    modelConv2D_Same.OutputGenerated("KerasConv2D_Same.hxx");
+ #endif
+ 
+    //Emitting header file for Keras model with Reshape layer
+-   RModel modelReshape = TMVA::Experimental::SOFIE::PyKeras::Parse("KerasModelReshape.keras");
++   RModel modelReshape = TMVA::Experimental::SOFIE::PyKeras::Parse("KerasModelReshape.h5");
+    modelReshape.Generate();
+    modelReshape.OutputGenerated("KerasReshapeModel.hxx");
+ 
+    //Emitting header file for Keras model with Concatenate layer
+-   RModel modelConcatenate = TMVA::Experimental::SOFIE::PyKeras::Parse("KerasModelConcatenate.keras");
++   RModel modelConcatenate = TMVA::Experimental::SOFIE::PyKeras::Parse("KerasModelConcatenate.h5");
+    modelConcatenate.Generate();
+    modelConcatenate.OutputGenerated("KerasConcatenateModel.hxx");
+ 
+    // Emitting header file for Keras Binary Op Model
+-   RModel modelBinaryOp = TMVA::Experimental::SOFIE::PyKeras::Parse("KerasModelBinaryOp.keras");
++   RModel modelBinaryOp = TMVA::Experimental::SOFIE::PyKeras::Parse("KerasModelBinaryOp.h5");
+    modelBinaryOp.Generate();
+    modelBinaryOp.OutputGenerated("KerasBinaryOpModel.hxx");
+ 
+    //Emitting header file for Keras activation functions model
+-   RModel modelActivations = TMVA::Experimental::SOFIE::PyKeras::Parse("KerasModelActivations.keras");
++   RModel modelActivations = TMVA::Experimental::SOFIE::PyKeras::Parse("KerasModelActivations.h5");
+    modelActivations.Generate();
+    modelActivations.OutputGenerated("KerasActivationsModel.hxx");
+ 
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tmva/pymva/test/TestRModelParserKeras.C root_v6.28.12_patched/root_v6.28.12-source/tmva/pymva/test/TestRModelParserKeras.C
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tmva/pymva/test/TestRModelParserKeras.C	2024-09-18 13:23:14
++++ root_v6.28.12_patched/root_v6.28.12-source/tmva/pymva/test/TestRModelParserKeras.C	2024-09-18 13:49:29
+@@ -47,7 +47,7 @@ TEST(RModelParser_Keras, SEQUENTIAL)
+     PyRun_String("os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("from tensorflow.keras.models import load_model",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("import numpy",Py_single_input,fGlobalNS,fLocalNS);
+-    PyRun_String("model=load_model('KerasModelSequential.keras')",Py_single_input,fGlobalNS,fLocalNS);
++    PyRun_String("model=load_model('KerasModelSequential.h5')",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("input=numpy.array([0.12107884, 0.89718615, 0.89123899, 0.32197549,"
+                                     "0.17891638, 0.83555135, 0.98680066, 0.14496809,"
+                                     "0.07255503, 0.55386989, 0.6628149 , 0.29843291,"
+@@ -94,7 +94,7 @@ TEST(RModelParser_Keras, FUNCTIONAL)
+     PyRun_String("os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("from tensorflow.keras.models import load_model",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("import numpy",Py_single_input,fGlobalNS,fLocalNS);
+-    PyRun_String("model=load_model('KerasModelFunctional.keras')",Py_single_input,fGlobalNS,fLocalNS);
++    PyRun_String("model=load_model('KerasModelFunctional.h5')",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("input=numpy.array([0.60828574, 0.50069386, 0.75186709, 0.14968806, 0.7692464 ,0.77027585, 0.75095316, 0.96651197,"
+                                     "0.38536308, 0.95565917, 0.62796356, 0.13818375, 0.65484891,0.89220363, 0.23879365, 0.00635323]).reshape(2,8)",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("output=model(input).numpy()",Py_single_input,fGlobalNS,fLocalNS);
+@@ -135,7 +135,7 @@ TEST(RModelParser_Keras, BATCH_NORM)
+     PyRun_String("os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("from tensorflow.keras.models import load_model",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("import numpy",Py_single_input,fGlobalNS,fLocalNS);
+-    PyRun_String("model=load_model('KerasModelBatchNorm.keras')",Py_single_input,fGlobalNS,fLocalNS);
++    PyRun_String("model=load_model('KerasModelBatchNorm.h5')",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("input=numpy.array([0.22308163, 0.95274901, 0.44712538, 0.84640867,"
+                                     "0.69947928, 0.29743695, 0.81379782, 0.39650574]).reshape(2,4)",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("output=model(input).numpy()",Py_single_input,fGlobalNS,fLocalNS);
+@@ -182,7 +182,7 @@ TEST(DISABLED_RModelParser_Keras, CONV_VALID)
+     PyRun_String("os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("from tensorflow.keras.models import load_model",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("import numpy",Py_single_input,fGlobalNS,fLocalNS);
+-    PyRun_String("model=load_model('KerasModelConv2D_Valid.keras')",Py_single_input,fGlobalNS,fLocalNS);
++    PyRun_String("model=load_model('KerasModelConv2D_Valid.h5')",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("input=numpy.ones((1,4,4,1))",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("output=model(input).numpy()",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("outputSize=output.size",Py_single_input,fGlobalNS,fLocalNS);
+@@ -228,7 +228,7 @@ TEST(DISABLED_RModelParser_Keras, CONV_SAME)
+     PyRun_String("os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("from tensorflow.keras.models import load_model",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("import numpy",Py_single_input,fGlobalNS,fLocalNS);
+-    PyRun_String("model=load_model('KerasModelConv2D_Same.keras')",Py_single_input,fGlobalNS,fLocalNS);
++    PyRun_String("model=load_model('KerasModelConv2D_Same.h5')",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("input=numpy.ones((1,4,4,1))",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("output=model(input).numpy()",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("outputSize=output.size",Py_single_input,fGlobalNS,fLocalNS);
+@@ -270,7 +270,7 @@ TEST(RModelParser_Keras, RESHAPE)
+     PyRun_String("os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("from tensorflow.keras.models import load_model",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("import numpy",Py_single_input,fGlobalNS,fLocalNS);
+-    PyRun_String("model=load_model('KerasModelReshape.keras')",Py_single_input,fGlobalNS,fLocalNS);
++    PyRun_String("model=load_model('KerasModelReshape.h5')",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("input=numpy.ones((1,4,4,1))",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("output=model(input).numpy()",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("outputSize=output.size",Py_single_input,fGlobalNS,fLocalNS);
+@@ -311,7 +311,7 @@ TEST(RModelParser_Keras, CONCATENATE)
+     PyRun_String("os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("from tensorflow.keras.models import load_model",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("import numpy",Py_single_input,fGlobalNS,fLocalNS);
+-    PyRun_String("model=load_model('KerasModelConcatenate.keras')",Py_single_input,fGlobalNS,fLocalNS);
++    PyRun_String("model=load_model('KerasModelConcatenate.h5')",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("input_1=numpy.ones((1,2))",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("input_2=numpy.ones((1,2))",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("output=model([input_1,input_2]).numpy()",Py_single_input,fGlobalNS,fLocalNS);
+@@ -353,7 +353,7 @@ TEST(RModelParser_Keras, BINARY_OP)
+     PyRun_String("os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("from tensorflow.keras.models import load_model",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("import numpy",Py_single_input,fGlobalNS,fLocalNS);
+-    PyRun_String("model=load_model('KerasModelBinaryOp.keras')",Py_single_input,fGlobalNS,fLocalNS);
++    PyRun_String("model=load_model('KerasModelBinaryOp.h5')",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("input1=numpy.array([1,1])",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("input2=numpy.array([1,1])",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("output=model([input1,input2]).numpy()",Py_single_input,fGlobalNS,fLocalNS);
+@@ -393,7 +393,7 @@ TEST(RModelParser_Keras, ACTIVATIONS)
+     PyRun_String("os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("from tensorflow.keras.models import load_model",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("import numpy",Py_single_input,fGlobalNS,fLocalNS);
+-    PyRun_String("model=load_model('KerasModelActivations.keras')",Py_single_input,fGlobalNS,fLocalNS);
++    PyRun_String("model=load_model('KerasModelActivations.h5')",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("input=numpy.ones((1,8))",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("output=model(input).numpy()",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("outputSize=output.size",Py_single_input,fGlobalNS,fLocalNS);
+@@ -436,7 +436,7 @@ TEST(RModel, CUSTOM_OP)
+ 
+     PyRun_String("from tensorflow.keras.layers import Lambda",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("import numpy",Py_single_input,fGlobalNS,fLocalNS);
+-    PyRun_String("model=load_model('KerasModelForCustomOp.keras')",Py_single_input,fGlobalNS,fLocalNS);
++    PyRun_String("model=load_model('KerasModelForCustomOp.h5')",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("model.add(Lambda(lambda x: x * 2))",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("input=numpy.array([1,1,1,1,1,1,1,1]).reshape(1,8)",Py_single_input,fGlobalNS,fLocalNS);
+     PyRun_String("output=model(input).numpy()",Py_single_input,fGlobalNS,fLocalNS);
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tmva/pymva/test/generateKerasModels.py root_v6.28.12_patched/root_v6.28.12-source/tmva/pymva/test/generateKerasModels.py
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tmva/pymva/test/generateKerasModels.py	2024-09-18 13:23:14
++++ root_v6.28.12_patched/root_v6.28.12-source/tmva/pymva/test/generateKerasModels.py	2024-09-18 13:49:29
+@@ -24,7 +24,7 @@ def generateFunctionalModel():
+ 
+     model.compile(loss='mean_squared_error', optimizer=SGD(learning_rate=0.01))
+     model.fit(x_train, y_train, epochs=10, batch_size=2)
+-    model.save('KerasModelFunctional.keras')
++    model.save('KerasModelFunctional.h5')
+ 
+ def generateSequentialModel():
+     model=Sequential()
+@@ -39,7 +39,7 @@ def generateSequentialModel():
+ 
+     model.compile(loss='mean_squared_error', optimizer=SGD(learning_rate=0.01))
+     model.fit(x_train, y_train, epochs=10, batch_size=4)
+-    model.save('KerasModelSequential.keras')
++    model.save('KerasModelSequential.h5')
+ 
+ def generateBatchNormModel():
+     model=Sequential()
+@@ -53,7 +53,7 @@ def generateBatchNormModel():
+ 
+     model.compile(loss='mean_squared_error', optimizer=SGD(learning_rate=0.01))
+     model.fit(x_train, y_train, epochs=10, batch_size=2)
+-    model.save('KerasModelBatchNorm.keras')
++    model.save('KerasModelBatchNorm.h5')
+ 
+ def generateConv2DModel_ValidPadding():
+     model=Sequential()
+@@ -65,7 +65,7 @@ def generateConv2DModel_ValidPadding():
+ 
+     model.compile(loss='mean_squared_error', optimizer=SGD(learning_rate=0.01))
+     model.fit(x_train, y_train, epochs=10, batch_size=2)
+-    model.save('KerasModelConv2D_Valid.keras')
++    model.save('KerasModelConv2D_Valid.h5')
+ 
+ def generateConv2DModel_SamePadding():
+     model=Sequential()
+@@ -77,7 +77,7 @@ def generateConv2DModel_SamePadding():
+ 
+     model.compile(loss='mean_squared_error', optimizer=SGD(learning_rate=0.01))
+     model.fit(x_train, y_train, epochs=10, batch_size=2)
+-    model.save('KerasModelConv2D_Same.keras')
++    model.save('KerasModelConv2D_Same.h5')
+ 
+ def generateReshapeModel():
+     model = Sequential()
+@@ -90,7 +90,7 @@ def generateReshapeModel():
+ 
+     model.compile(loss='mean_squared_error', optimizer=SGD(learning_rate=0.01))
+     model.fit(x_train, y_train, epochs=10, batch_size=2)
+-    model.save('KerasModelReshape.keras')
++    model.save('KerasModelReshape.h5')
+ 
+ def generateConcatModel():
+     input_1 = Input(shape=(2,))
+@@ -107,7 +107,7 @@ def generateConcatModel():
+ 
+     model.compile(loss='mean_squared_error', optimizer=SGD(learning_rate=0.01))
+     model.fit([x1_train,x2_train], y_train, epochs=10, batch_size=1)
+-    model.save('KerasModelConcatenate.keras')
++    model.save('KerasModelConcatenate.h5')
+ 
+ def generateBinaryOpModel():
+     input1 = Input(shape=(2, ))
+@@ -124,7 +124,7 @@ def generateBinaryOpModel():
+ 
+     model.compile(loss='mean_squared_error', optimizer=SGD(learning_rate=0.01))
+     model.fit([x1_train,x2_train], y_train, epochs=10, batch_size=2)
+-    model.save('KerasModelBinaryOp.keras')
++    model.save('KerasModelBinaryOp.h5')
+ 
+ def generateActivationModel():
+     input=Input(shape=(8,))
+@@ -140,8 +140,8 @@ def generateActivationModel():
+ 
+     model.compile(loss='mean_squared_error', optimizer=SGD(learning_rate=0.01))
+     model.fit(x_train, y_train, epochs=10, batch_size=1)
+-    model.save('KerasModelActivations.keras')
+-    
++    model.save('KerasModelActivations.h5')
++
+ 
+ generateFunctionalModel()
+ generateSequentialModel()
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tmva/pymva/test/testPyKerasClassification.C root_v6.28.12_patched/root_v6.28.12-source/tmva/pymva/test/testPyKerasClassification.C
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tmva/pymva/test/testPyKerasClassification.C	2024-09-18 13:23:14
++++ root_v6.28.12_patched/root_v6.28.12-source/tmva/pymva/test/testPyKerasClassification.C	2024-09-18 13:49:29
+@@ -30,19 +30,20 @@ int testPyKerasClassification(){
+    TFile *input = TFile::Open(fname);
+ 
+    // Build model from python file
+-   std::cout << "Generate keras model..." << std::endl;
+-   UInt_t ret;
+-   ret = gSystem->Exec("echo '"+pythonSrc+"' > generateKerasModelClassification.py");
+-   if(ret!=0){
+-       std::cout << "[ERROR] Failed to write python code to file" << std::endl;
+-       return 1;
++   if (gSystem->AccessPathName("kerasModelClassification.h5")) {
++      std::cout << "Generate keras model..." << std::endl;
++      UInt_t ret;
++      ret = gSystem->Exec("echo '"+pythonSrc+"' > generateKerasModelClassification.py");
++      if(ret!=0){
++         std::cout << "[ERROR] Failed to write python code to file" << std::endl;
++         return 1;
++      }
++      ret = gSystem->Exec(TMVA::Python_Executable() + " generateKerasModelClassification.py");
++      if(ret!=0){
++         std::cout << "[ERROR] Failed to generate model using python" << std::endl;
++         return 1;
++      }
+    }
+-   ret = gSystem->Exec(TMVA::Python_Executable() + " generateKerasModelClassification.py");
+-   if(ret!=0){
+-       std::cout << "[ERROR] Failed to generate model using python" << std::endl;
+-       return 1;
+-   }
+-
+    // Setup PyMVA and factory
+    std::cout << "Setup TMVA..." << std::endl;
+    TMVA::PyMethodBase::PyInitialize();
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tmva/rmva/test/Classification.C root_v6.28.12_patched/root_v6.28.12-source/tmva/rmva/test/Classification.C
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tmva/rmva/test/Classification.C	2024-09-18 13:23:14
++++ root_v6.28.12_patched/root_v6.28.12-source/tmva/rmva/test/Classification.C	2024-09-18 13:49:29
+@@ -23,7 +23,7 @@ void Classification()
+    TMVA::Tools::Instance();
+    ROOT::R::TRInterface &r = ROOT::R::TRInterface::Instance();
+ 
+-   TString outfileName("TMVA.root");
++   TString outfileName("RMVA.root");
+    TFile *outputFile = TFile::Open(outfileName, "RECREATE");
+ 
+    TMVA::Factory *factory = new TMVA::Factory("RMVAClassification", outputFile,
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tmva/sofie/test/TestSofieModels.cxx root_v6.28.12_patched/root_v6.28.12-source/tmva/sofie/test/TestSofieModels.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tmva/sofie/test/TestSofieModels.cxx	2024-09-18 13:23:14
++++ root_v6.28.12_patched/root_v6.28.12-source/tmva/sofie/test/TestSofieModels.cxx	2024-09-18 13:26:26
+@@ -94,11 +94,7 @@ void TestLinear(int nbatches, bool useBN = false, int 
+       f >> refValue[i];
+       if (verbose)
+          std::cout << " result " << result.at(i) << " reference " << refValue[i] << std::endl;
+-      if (std::abs(refValue[i]) > 0.5)
+-         EXPECT_FLOAT_EQ(result.at(i), refValue[i]);
+-      else
+-         // expect float fails for small values
+-         EXPECT_NEAR(result.at(i), refValue[i], 10 * std::numeric_limits<float>::epsilon());
++      EXPECT_NEAR(result.at(i), refValue[i], 10 * std::numeric_limits<float>::epsilon());
+    }
+ }
+ 
+@@ -177,11 +173,7 @@ void TestConv( std::string type, int nbatches, bool us
+    for (size_t i = 0; i < refValue.size(); ++i) {
+       f >> refValue[i];
+       if (verbose) std::cout << " result " << result.at(i) << " reference " << refValue[i] << std::endl;
+-      if (std::abs(refValue[i]) > 0.5)
+-         EXPECT_FLOAT_EQ(result.at(i), refValue[i]);
+-      else
+-         // expect float fails for small values
+-         EXPECT_NEAR(result.at(i), refValue[i], 10 * std::numeric_limits<float>::epsilon());
++      EXPECT_NEAR(result.at(i), refValue[i], 10 * std::numeric_limits<float>::epsilon());
+    }
+ }
+ 
+@@ -253,11 +245,7 @@ void TestRecurrent(std::string type, int nbatches, int
+       f >> refValue[i];
+       if (verbose)
+          std::cout << " result " << result.at(i) << " reference " << refValue[i] << std::endl;
+-      if (std::abs(refValue[i]) > 0.5)
+-         EXPECT_FLOAT_EQ(result.at(i), refValue[i]);
+-      else
+-         // expect float fails for small values
+-         EXPECT_NEAR(result.at(i), refValue[i], 10 * std::numeric_limits<float>::epsilon());
++      EXPECT_NEAR(result.at(i), refValue[i], 10 * std::numeric_limits<float>::epsilon());
+    }
+ }
+ 
+@@ -336,11 +324,7 @@ void TestConvTranspose( std::string type, int nbatches
+    for (size_t i = 0; i < refValue.size(); ++i) {
+       f >> refValue[i];
+       if (verbose) std::cout << " result " << result.at(i) << " reference " << refValue[i] << std::endl;
+-      if (std::abs(refValue[i]) > 0.5)
+-         EXPECT_FLOAT_EQ(result.at(i), refValue[i]);
+-      else
+-         // expect float fails for small values
+-         EXPECT_NEAR(result.at(i), refValue[i], 10 * std::numeric_limits<float>::epsilon());
++      EXPECT_NEAR(result.at(i), refValue[i], 10 * std::numeric_limits<float>::epsilon());
+    }
+ }
+ 
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tmva/tmva/test/CMakeLists.txt root_v6.28.12_patched/root_v6.28.12-source/tmva/tmva/test/CMakeLists.txt
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tmva/tmva/test/CMakeLists.txt	2024-09-18 13:23:14
++++ root_v6.28.12_patched/root_v6.28.12-source/tmva/tmva/test/CMakeLists.txt	2024-09-18 13:49:29
+@@ -33,9 +33,12 @@ endif()
+     endif()
+ endif()
+ 
+-if(dataframe AND NOT pyroot_legacy)
+-  find_python_module(xgboost QUIET)
+-  if (PY_XGBOOST_FOUND)
+-    ROOT_ADD_PYUNITTEST(rbdt_xgboost rbdt_xgboost.py)
+-  endif()
+-endif()
++# Disabled because RBDT doesn't support the imbalanced tree structure of
++# XGBoost models. See https://github.com/root-project/root/issues/15197
++# TODO: Re-enable once fixed
++# if(dataframe)
++#   find_python_module(xgboost QUIET)
++#   if (PY_XGBOOST_FOUND)
++#     ROOT_ADD_PYUNITTEST(rbdt_xgboost rbdt_xgboost.py)
++#   endif()
++# endif()
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tmva/tmva/test/rbdt_xgboost.py root_v6.28.12_patched/root_v6.28.12-source/tmva/tmva/test/rbdt_xgboost.py
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tmva/tmva/test/rbdt_xgboost.py	2024-09-18 13:23:14
++++ root_v6.28.12_patched/root_v6.28.12-source/tmva/tmva/test/rbdt_xgboost.py	2024-09-18 13:49:29
+@@ -21,7 +21,7 @@ def _test_XGBBinary(backend, label):
+     x, y = create_dataset(1000, 10, 2)
+     xgb = xgboost.XGBClassifier(n_estimators=100, max_depth=3)
+     xgb.fit(x, y)
+-    ROOT.TMVA.Experimental.SaveXGBoost(xgb, "myModel", "testXGBBinary{}.root".format(label))
++    ROOT.TMVA.Experimental.SaveXGBoost(xgb, "myModel", "testXGBBinary{}.root".format(label), num_inputs=10)
+     bdt = ROOT.TMVA.Experimental.RBDT[backend]("myModel", "testXGBBinary{}.root".format(label))
+ 
+     y_xgb = xgb.predict_proba(x)[:, 1].squeeze()
+@@ -51,7 +51,7 @@ def _test_XGBMulticlass(backend, label):
+     x, y = create_dataset(1000, 10, 3)
+     xgb = xgboost.XGBClassifier(n_estimators=100, max_depth=3)
+     xgb.fit(x, y)
+-    ROOT.TMVA.Experimental.SaveXGBoost(xgb, "myModel", "testXGBMulticlass{}.root".format(label))
++    ROOT.TMVA.Experimental.SaveXGBoost(xgb, "myModel", "testXGBMulticlass{}.root".format(label), num_inputs=10)
+     bdt = ROOT.TMVA.Experimental.RBDT[backend]("myModel", "testXGBMulticlass{}.root".format(label))
+ 
+     y_xgb = xgb.predict_proba(x)
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tree/dataframe/inc/ROOT/RDF/RAction.hxx root_v6.28.12_patched/root_v6.28.12-source/tree/dataframe/inc/ROOT/RDF/RAction.hxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tree/dataframe/inc/ROOT/RDF/RAction.hxx	2024-09-18 13:23:13
++++ root_v6.28.12_patched/root_v6.28.12-source/tree/dataframe/inc/ROOT/RDF/RAction.hxx	2024-09-18 13:49:29
+@@ -102,7 +102,8 @@ class R__CLING_PTRCHECK(off) RAction : public RActionB
+    template <typename... ColTypes, std::size_t... S>
+    void CallExec(unsigned int slot, Long64_t entry, TypeList<ColTypes...>, std::index_sequence<S...>)
+    {
+-      fHelper.Exec(slot, fValues[slot][S]->template Get<ColTypes>(entry)...);
++      ROOT::Internal::RDF::CallGuaranteedOrder{[&](auto &&...args) { return fHelper.Exec(slot, args...); },
++                                               fValues[slot][S]->template Get<ColTypes>(entry)...};
+       (void)entry; // avoid unused parameter warning (gcc 12.1)
+    }
+ 
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tree/dataframe/inc/ROOT/RDF/Utils.hxx root_v6.28.12_patched/root_v6.28.12-source/tree/dataframe/inc/ROOT/RDF/Utils.hxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tree/dataframe/inc/ROOT/RDF/Utils.hxx	2024-09-18 13:23:13
++++ root_v6.28.12_patched/root_v6.28.12-source/tree/dataframe/inc/ROOT/RDF/Utils.hxx	2024-09-18 13:49:29
+@@ -283,6 +283,23 @@ std::vector<T> Union(const std::vector<T> &v1, const s
+    return res;
+ }
+ 
++/**
++ * \brief Struct to wrap the call to a function with a guaranteed order of
++ *        execution of its arguments.
++ * \tparam F Type of the callable.
++ * \tparam Args Variadic types of the arguments to the callable.
++ *
++ * The execution order is guaranteed by calling the function in the constructor
++ * thus enabling the exploitation of the list-initialization sequenced-before
++ * feature (See rule 9 at https://en.cppreference.com/w/cpp/language/eval_order).
++ */
++struct CallGuaranteedOrder {
++   template <typename F, typename... Args>
++   CallGuaranteedOrder(F &&f, Args &&...args)
++   {
++      f(std::forward<Args>(args)...);
++   }
++};
+ } // end NS RDF
+ } // end NS Internal
+ } // end NS ROOT
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tree/dataframe/src/RDataFrame.cxx root_v6.28.12_patched/root_v6.28.12-source/tree/dataframe/src/RDataFrame.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tree/dataframe/src/RDataFrame.cxx	2024-09-18 13:23:13
++++ root_v6.28.12_patched/root_v6.28.12-source/tree/dataframe/src/RDataFrame.cxx	2024-09-18 13:49:29
+@@ -611,6 +611,22 @@ for el in df.Take[int]("x"):
+     print(f"Element: {el}")
+ ~~~
+ 
++### Actions and readers
++
++An action that needs values for its computations will request it from a reader, e.g. a column created via `Define` or
++available from the input dataset. The action will request values from each column of the list of input columns (either
++inferred or specified by the user), in order. For example:
++
++~~~{.cpp}
++ROOT::RDataFrame df{1};
++auto df1 = df.Define("x", []{ return 11; });
++auto df2 = df1.Define("y", []{ return 22; });
++auto graph = df2.Graph<int, int>("x","y");
++~~~
++
++The `Graph` action is going to request first the value from column "x", then that of column "y". Specifically, the order
++of execution of the operations of nodes in this branch of the computation graph is guaranteed to be top to bottom.
++
+ \anchor distrdf
+ ## Distributed execution
+ 
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tree/dataframe/test/CMakeLists.txt root_v6.28.12_patched/root_v6.28.12-source/tree/dataframe/test/CMakeLists.txt
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tree/dataframe/test/CMakeLists.txt	2024-09-18 13:23:13
++++ root_v6.28.12_patched/root_v6.28.12-source/tree/dataframe/test/CMakeLists.txt	2024-09-18 13:49:29
+@@ -53,6 +53,7 @@ ROOT_ADD_GTEST(dataframe_vary dataframe_vary.cxx LIBRA
+ ROOT_ADD_GTEST(dataframe_merge_results dataframe_merge_results.cxx LIBRARIES ROOTDataFrame)
+ ROOT_ADD_GTEST(dataframe_samplecallback dataframe_samplecallback.cxx CounterHelper.h LIBRARIES ROOTDataFrame)
+ ROOT_ADD_GTEST(dataframe_vary dataframe_vary.cxx LIBRARIES ROOTDataFrame)
++ROOT_ADD_GTEST(dataframe_compgraph dataframe_compgraph.cxx LIBRARIES ROOTDataFrame)
+ 
+ #### TESTS FOR DIFFERENT DATASOURCES ####
+ if(MSVC AND MSVC_VERSION GREATER_EQUAL 1925 AND MSVC_VERSION LESS 1929 OR CMAKE_CXX_STANDARD LESS 17)
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tree/dataframe/test/dataframe_compgraph.cxx root_v6.28.12_patched/root_v6.28.12-source/tree/dataframe/test/dataframe_compgraph.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tree/dataframe/test/dataframe_compgraph.cxx	1969-12-31 16:00:00
++++ root_v6.28.12_patched/root_v6.28.12-source/tree/dataframe/test/dataframe_compgraph.cxx	2024-09-18 13:26:26
+@@ -0,0 +1,86 @@
++#include "TInterpreter.h"
++#include "ROOT/RDataFrame.hxx"
++#include "gtest/gtest.h"
++
++TEST(CompGraphTests, ExecOrderTwoDefines)
++{
++   ROOT::RDataFrame d{1};
++   int i{42};
++   auto graph = d.Define("x",
++                         [&i]() {
++                            auto ret = i;
++                            i = 10;
++                            return ret;
++                         })
++                   .Define("y", [&i]() { return i; })
++                   .Graph<int, int>("x", "y");
++
++   // Expected x=42,y=10
++   EXPECT_EQ(graph->GetN(), 1);
++   EXPECT_EQ(graph->GetPointX(0), 42);
++   EXPECT_EQ(graph->GetPointY(0), 10);
++}
++
++TEST(CompGraphTests, ExecOrderTwoDefinesInterpreted)
++{
++   ROOT::RDataFrame d{1};
++   gInterpreter->Declare(R"(
++    namespace ROOT::Internal::RDF::Testing{
++        int myInt{42};
++    }
++   )");
++   auto graph =
++      d.Define("x", "return [&i = ROOT::Internal::RDF::Testing::myInt]() { auto ret = i; i = 10; return ret; }();")
++         .Define("y", "return [&i = ROOT::Internal::RDF::Testing::myInt]() { return i; }();")
++         .Graph<int, int>("x", "y");
++
++   // Expected x=42,y=10
++   EXPECT_EQ(graph->GetN(), 1);
++   EXPECT_EQ(graph->GetPointX(0), 42);
++   EXPECT_EQ(graph->GetPointY(0), 10);
++}
++
++TEST(CompGraphTests, ExecOrderThreeDefines)
++{
++   struct Filler {
++      int fA;
++      float fB;
++      std::string fC;
++      void Fill(int a, float b, const std::string &c)
++      {
++         fA = a;
++         fB = b;
++         fC = c;
++      }
++      void Merge(const std::vector<Filler *> &)
++      {
++         // no-op to comply with interface for RInterface::Fill
++      }
++   };
++
++   int i{};
++   ROOT::RDataFrame d{1};
++   auto obj = d.Define("x",
++                       [&i]() {
++                          auto ret{i == 0 ? 33 : 999};
++                          i = 10;
++                          return ret;
++                       })
++                 .Define("y",
++                         [&i]() {
++                            auto ret{i == 10 ? 42.f : 33.f};
++                            i = 20;
++                            return ret;
++                         })
++                 .Define("z",
++                         [&i]() {
++                            std::string ret{i == 20 ? "correct" : "wrong"};
++                            i = 30;
++                            return ret;
++                         })
++                 .Fill<int, float, std::string>(Filler{}, {"x", "y", "z"});
++
++   EXPECT_EQ(obj->fA, 33);
++   EXPECT_EQ(obj->fB, 42.f);
++   EXPECT_EQ(obj->fC, "correct");
++}
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tree/ntuple/v7/test/ntuple_storage.cxx root_v6.28.12_patched/root_v6.28.12-source/tree/ntuple/v7/test/ntuple_storage.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tree/ntuple/v7/test/ntuple_storage.cxx	2024-09-18 13:23:13
++++ root_v6.28.12_patched/root_v6.28.12-source/tree/ntuple/v7/test/ntuple_storage.cxx	2024-09-18 13:49:29
+@@ -397,7 +397,11 @@ TEST(RPageSinkBuf, ParallelZip) {
+             auto *parallel_zip = ntuple->GetMetrics().GetCounter(
+                "RNTupleWriter.RPageSinkBuf.ParallelZip");
+             ASSERT_FALSE(parallel_zip == nullptr);
++#ifdef R__USE_IMT
+             EXPECT_EQ(1, parallel_zip->GetValueAsInt());
++#else
++            EXPECT_EQ(0, parallel_zip->GetValueAsInt());
++#endif
+          }
+       }
+    }
+@@ -455,10 +459,15 @@ TEST(RPageSinkBuf, CommitSealedPageV)
+       ntuple->Fill();
+       ntuple->Fill();
+       ntuple->CommitCluster();
++#ifdef R__USE_IMT
+       // All pages in all columns committed via a single call to `CommitSealedPageV()`
+       EXPECT_EQ(0, counters.fNCommitPage);
+-      EXPECT_EQ(0, counters.fNCommitSealedPage);
+       EXPECT_EQ(1, counters.fNCommitSealedPageV);
++#else
++      EXPECT_EQ(2, counters.fNCommitPage);
++      EXPECT_EQ(0, counters.fNCommitSealedPageV);
++#endif
++      EXPECT_EQ(0, counters.fNCommitSealedPage);
+    }
+ }
+ 
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tree/tree/src/TBranch.cxx root_v6.28.12_patched/root_v6.28.12-source/tree/tree/src/TBranch.cxx
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tree/tree/src/TBranch.cxx	2024-09-18 13:23:13
++++ root_v6.28.12_patched/root_v6.28.12-source/tree/tree/src/TBranch.cxx	2024-09-18 13:49:29
+@@ -350,7 +350,7 @@ void TBranch::Init(const char* name, const char* leafl
+          }
+          if (lenName == 0 || ctype == leafname) {
+             Warning("TBranch","No name was given to the leaf number '%d' in the leaflist of the branch '%s'.",fNleaves,name);
+-            snprintf(leafname,640,"__noname%d",fNleaves);
++            snprintf(leafname, len + 1, "__noname%d", fNleaves);
+          }
+          TLeaf* leaf = 0;
+          if (leaftype[1] == '[' && !strchr(leaftype, ',')) {
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/CMakeLists.txt root_v6.28.12_patched/root_v6.28.12-source/tutorials/CMakeLists.txt
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/CMakeLists.txt	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/tutorials/CMakeLists.txt	2024-09-18 13:49:29
+@@ -145,6 +145,10 @@ else()
+     if(CMAKE_SIZEOF_VOID_P EQUAL 8)
+       list(APPEND roofit_veto roofit/rf409_NumPyPandasToRooFit.py)
+     endif()
++    # The following tutorials are failing with this error:
++    # IncrementalExecutor::executeFunction: symbol '__std_find_trivial_4@12' unresolved while linking [cling interface function]!
++    # with Visual Studio v17.8
++    list(APPEND roofit_veto roofit/rf509_wsinteractive.C roofit/rf614_binned_fit_problems.C)
+   endif()
+ endif()
+ 
+@@ -256,6 +260,12 @@ if(MSVC)
+ if(MSVC)
+   #---Multiproc is not supported on Windows
+   set(imt_veto ${imt_veto} multicore/mp*.C multicore/mtbb201_parallelHistoFill.C)
++  if(NOT win_broken_tests)
++    # std::this_thread::sleep_for(std::chrono::duration<double, std::nano>(500));
++    # fails on Windows 32 bit and Visual Studio v17.9 with the following error:
++    # IncrementalExecutor::executeFunction: symbol '_Thrd_sleep_for@4' unresolved while linking [cling interface function]!
++    set(imt_veto ${imt_veto} multicore/mt201_parallelHistoFill.C)
++  endif()
+ endif()
+ 
+ if(ROOT_CLASSIC_BUILD)
+@@ -287,15 +297,21 @@ else()
+ if (NOT ROOT_tmva_FOUND)
+   list(APPEND tmva_veto tmva/*.C tmva/*.py tmva/envelope/*.C tmva/keras/*.C tmva/keras/*.py tmva/pytorch/*.py )
+ else()
++  # RBDT with xgboost is currently broken, disable all tutorials that use it
++  # See https://github.com/root-project/root/issues/15197
++  # TODO: Re-enable once fixed
++  list(APPEND tmva_veto tmva/tmva10[0-2]_*.py)
+   #---These do not need to run for TMVA
+   list(APPEND tmva_veto tmva/createData.C)
+   if(MSVC AND NOT win_broken_tests)
+     list(APPEND tmva_veto tmva/envelope/classification.C)
+   endif()
+   #these depends on external packages
+-  find_python_module(torch QUIET)
+-  find_python_module(keras QUIET)
+-  find_python_module(sklearn QUIET)
++  if (tmva-pymva)
++    find_python_module(torch QUIET)
++    find_python_module(keras QUIET)
++    find_python_module(sklearn QUIET)
++  endif()
+   if (NOT PY_KERAS_FOUND)
+     list(APPEND tmva_veto tmva/TMVA_SOFIE_Keras.C)
+     list(APPEND tmva_veto tmva/TMVA_SOFIE_Keras_HiggsModel.C)
+@@ -305,6 +321,11 @@ else()
+     list(APPEND tmva_veto tmva/TMVA_SOFIE_Inference.py)
+     list(APPEND tmva_veto tmva/TMVA_SOFIE_RSofieReader.C)
+   endif()
++  # The TMVA_SOFIE_RSofieReader test is disabled because it uses two differnt
++  # openblas versions via SOFIE and NumPy (indirectly from Keras) at the same
++  # time. This can cause crashes, for example on alma9.
++  # TODO: remove the next line once this problem is fixed.
++  list(APPEND tmva_veto tmva/TMVA_SOFIE_RSofieReader.C)
+   if (NOT PY_SKLEARN_FOUND)
+     list(APPEND tmva_veto tmva/TMVA_SOFIE_Models.py)
+   endif()
+@@ -560,19 +581,11 @@ set (tmva-tmva004_RStandardScaler-depends tutorial-tmv
+ set (tmva-tmva102_Testing-depends tutorial-tmva-tmva101_Training-py)
+ set (tmva-tmva003_RReader-depends tutorial-tmva-TMVAClassification)
+ set (tmva-tmva004_RStandardScaler-depends tutorial-tmva-tmva003_RReader)
+-if (PY_TORCH_FOUND)
+-  set (tmva-pytorch-ApplicationClassificationPyTorch-depends tutorial-tmva-pytorch-ClassificationPyTorch-py)
+-  set (tmva-pytorch-RegressionPyTorch-depends tutorial-tmva-pytorch-ApplicationClassificationPyTorch-py)
+-  set (tmva-pytorch-ApplicationRegressionPyTorch-depends tutorial-tmva-pytorch-RegressionPyTorch-py)
+-endif()
+ if (PY_KERAS_FOUND)
+   set (tmva-TMVA_SOFIE_Keras_HiggsModel-depends tutorial-tmva-TMVA_Higgs_Classification)
+   set (tmva-TMVA_SOFIE_RDataFrame-depends tutorial-tmva-TMVA_SOFIE_Keras_HiggsModel)
+   set (tmva-TMVA_SOFIE_RDataFrame_JIT-depends tutorial-tmva-TMVA_SOFIE_Keras_HiggsModel)
+-  set (tmva-TMVA_SOFIE_Inference-depends tutorial-tmva-TMVA_Higgs_Classification)
+-  set (tmva-TMVA_SOFIE_RSofieReader-depends tutorial-tmva-TMVA_Higgs_Classification)
+-  set (tmva-keras-ApplicationRegressionKeras-depends tutorial-tmva-keras-RegressionKeras-py)
+-  set (tmva-keras-ApplicationClassificationKeras-depends tutorial-tmva-keras-ClassificationKeras-py)
++  set (tmva-TMVA_SOFIE_RSofieReader-depends tutorial-tmva-TMVA_SOFIE_RDataFrame_JIT)
+ endif()
+ 
+ #--List long-running tutorials to label them as "longtest"
+@@ -755,7 +768,7 @@ if(ROOT_pyroot_FOUND)
+   endif()
+ 
+   find_python_module(keras QUIET)
+-  if(NOT PY_KERAS_FOUND)
++  if(NOT tmva-pymva OR NOT PY_KERAS_FOUND)
+     file(GLOB tmva_veto_py RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} tmva/keras/*.py)
+     list(APPEND pyveto ${tmva_veto_py})
+   elseif(ROOT_ARCHITECTURE MATCHES macosx)
+@@ -766,7 +779,7 @@ if(ROOT_pyroot_FOUND)
+   endif()
+ 
+   find_python_module(torch QUIET)
+-  if(NOT PY_TORCH_FOUND)
++  if(NOT tmva-pymva OR NOT PY_TORCH_FOUND)
+     file(GLOB tmva_veto_py RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} tmva/pytorch/*.py)
+     list(APPEND pyveto ${tmva_veto_py})
+   endif()
+@@ -796,13 +809,22 @@ if(ROOT_pyroot_FOUND)
+   set(pyroot-na49view-depends tutorial-pyroot-geometry-py)
+   set(roofit-rf503_wspaceread-depends tutorial-roofit-rf502_wspacewrite-py)
+ 
+-  # Avoid a race condition: make sure Python tutorial is ran after C++ tutorial
++  # Avoid a race condition: make sure Python tutorial is run after C++ tutorial
+   set(roofit-rf104_classfactory-depends tutorial-roofit-rf104_classfactory)
+   set(roofit-rf512_wsfactory_oper-depends tutorial-roofit-rf512_wsfactory_oper)
+-  set (tmva-Higgs_CNN_Classification-depends tutorial-tmva-TMVA_Higgs_Classification)
++  set (tmva-TMVA_Higgs_Classification-depends tutorial-tmva-TMVA_Higgs_Classification)
+   set (tmva-TMVA_CNN_Classification-depends tutorial-tmva-TMVA_CNN_Classification)
+   set (tmva-TMVA_RNN_Classification-depends tutorial-tmva-TMVA_RNN_Classification)
+-
++  if(PY_KERAS_FOUND)
++    set (tmva-TMVA_SOFIE_Inference-depends tutorial-tmva-TMVA_Higgs_Classification)
++    set (tmva-keras-ApplicationRegressionKeras-depends tutorial-tmva-keras-RegressionKeras-py)
++    set (tmva-keras-ApplicationClassificationKeras-depends tutorial-tmva-keras-ClassificationKeras-py)
++  endif()
++  if(PY_TORCH_FOUND)
++    set (tmva-pytorch-ApplicationClassificationPyTorch-depends tutorial-tmva-pytorch-ClassificationPyTorch-py)
++    set (tmva-pytorch-RegressionPyTorch-depends tutorial-tmva-pytorch-ApplicationClassificationPyTorch-py)
++    set (tmva-pytorch-ApplicationRegressionPyTorch-depends tutorial-tmva-pytorch-RegressionPyTorch-py)
++  endif()
+   #----------------------------------------------------------------------
+   # List requirements for python tutorials.
+   # To add a new requirement, add a glob expression that's named requires_<packageName>,
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/roofit/rf614_binned_fit_problems.C root_v6.28.12_patched/root_v6.28.12-source/tutorials/roofit/rf614_binned_fit_problems.C
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/roofit/rf614_binned_fit_problems.C	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/tutorials/roofit/rf614_binned_fit_problems.C	2024-09-18 13:49:29
+@@ -105,7 +105,7 @@ void rf614_binned_fit_problems()
+ 
+    // Let's not look at another example: a power law \f[x^a\f].
+    RooRealVar a{"a", "a", -0.3, -5.0, 5.0};
+-   RooPower powerlaw{"powerlaw", "powerlaw", x, RooConst(1.0), a};
++   RooGenericPdf powerlaw{"powerlaw", "std::pow(x, a)", {x, a}};
+    std::unique_ptr<RooAbsData> powerlawData{generateBinnedAsimov(powerlaw, x, 10000)};
+ 
+    // Again, if you do a vanilla fit, you'll get a bias
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/roofit/rf614_binned_fit_problems.py root_v6.28.12_patched/root_v6.28.12-source/tutorials/roofit/rf614_binned_fit_problems.py
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/roofit/rf614_binned_fit_problems.py	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/tutorials/roofit/rf614_binned_fit_problems.py	2024-09-18 13:49:29
+@@ -110,7 +110,7 @@ a = ROOT.RooRealVar("a", "a", -0.3, -5.0, 5.0)
+ 
+ # Let's not look at another example: a power law \f[x^a\f].
+ a = ROOT.RooRealVar("a", "a", -0.3, -5.0, 5.0)
+-powerlaw = ROOT.RooPower("powerlaw", "powerlaw", x, ROOT.RooFit.RooConst(1.0), a)
++powerlaw = ROOT.RooGenericPdf("powerlaw", "std::pow(x, a)", [x, a]);
+ powerlaw_data = generateBinnedAsimov(powerlaw, x, 10000)
+ 
+ # Again, if you do a vanilla fit, you'll get a bias
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/TMVAClassification.C root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/TMVAClassification.C
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/TMVAClassification.C	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/TMVAClassification.C	2024-09-18 13:49:29
+@@ -13,7 +13,7 @@
+ ///
+ /// (note that the backslashes are mandatory)
+ /// If no method given, a default set of classifiers is used.
+-/// The output file "TMVA.root" can be analysed with the use of dedicated
++/// The output file "TMVAC.root" can be analysed with the use of dedicated
+ /// macros (simply say: root -l <macro.C>), which can be conveniently
+ /// invoked through a GUI that will appear at the end of the run of this macro.
+ /// Launch the GUI via the command:
+@@ -193,7 +193,7 @@ int TMVAClassification( TString myMethodList = "" )
+    TTree *background     = (TTree*)input->Get("TreeB");
+ 
+    // Create a ROOT output file where TMVA will store ntuples, histograms, etc.
+-   TString outfileName( "TMVA.root" );
++   TString outfileName( "TMVAC.root" );
+    TFile* outputFile = TFile::Open( outfileName, "RECREATE" );
+ 
+    // Create the factory object. Later you can choose the methods
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/TMVAClassificationCategory.C root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/TMVAClassificationCategory.C
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/TMVAClassificationCategory.C	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/TMVAClassificationCategory.C	2024-09-18 13:26:26
+@@ -15,7 +15,7 @@
+ ///
+ ///     root -l TMVAClassificationCategory.C
+ ///
+-/// The output file "TMVA.root" can be analysed with the use of dedicated
++/// The output file "TMVACC.root" can be analysed with the use of dedicated
+ /// macros (simply say: root -l <macro.C>), which can be conveniently
+ /// invoked through a GUI that will appear at the end of the run of this macro.
+ ///
+@@ -60,7 +60,7 @@ void TMVAClassificationCategory()
+    bool batchMode = false;
+ 
+    // Create a new root output file.
+-   TString outfileName( "TMVA.root" );
++   TString outfileName( "TMVACC.root" );
+    TFile* outputFile = TFile::Open( outfileName, "RECREATE" );
+ 
+    // Create the factory object (see TMVAClassification.C for more information)
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/TMVACrossValidation.C root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/TMVACrossValidation.C
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/TMVACrossValidation.C	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/TMVACrossValidation.C	2024-09-18 13:49:29
+@@ -7,13 +7,13 @@
+ /// As input data is used a toy-MC sample consisting of two gaussian
+ /// distributions.
+ ///
+-/// The output file "TMVA.root" can be analysed with the use of dedicated
++/// The output file "TMVACV.root" can be analysed with the use of dedicated
+ /// macros (simply say: root -l <macro.C>), which can be conveniently
+ /// invoked through a GUI that will appear at the end of the run of this macro.
+ /// Launch the GUI via the command:
+ ///
+ /// ```
+-/// root -l -e 'TMVA::TMVAGui("TMVA.root")'
++/// root -l -e 'TMVA::TMVAGui("TMVACV.root")'
+ /// ```
+ ///
+ /// ## Cross Evaluation
+@@ -121,7 +121,7 @@ int TMVACrossValidation(bool useRandomSplitting = fals
+    TTree *bkgTree = genTree(1000, -1.0, 1.0, 101);
+ 
+    // Create a ROOT output file where TMVA will store ntuples, histograms, etc.
+-   TString outfileName("TMVA.root");
++   TString outfileName("TMVACV.root");
+    TFile *outputFile = TFile::Open(outfileName, "RECREATE");
+ 
+    // DataLoader definitions; We declare variables in the tree so that TMVA can
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/TMVACrossValidationRegression.C root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/TMVACrossValidationRegression.C
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/TMVACrossValidationRegression.C	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/TMVACrossValidationRegression.C	2024-09-18 13:49:29
+@@ -7,13 +7,13 @@
+ /// As input data is used a toy-MC sample consisting of two gaussian
+ /// distributions.
+ ///
+-/// The output file "TMVA.root" can be analysed with the use of dedicated
++/// The output file "TMVARegCv.root" can be analysed with the use of dedicated
+ /// macros (simply say: root -l <macro.C>), which can be conveniently
+ /// invoked through a GUI that will appear at the end of the run of this macro.
+ /// Launch the GUI via the command:
+ ///
+ /// ```
+-/// root -l -e 'TMVA::TMVAGui("TMVA.root")'
++/// root -l -e 'TMVA::TMVAGui("TMVARegCv.root")'
+ /// ```
+ ///
+ /// ## Cross Evaluation
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/TMVA_CNN_Classification.C root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/TMVA_CNN_Classification.C
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/TMVA_CNN_Classification.C	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/TMVA_CNN_Classification.C	2024-09-18 13:26:26
+@@ -32,6 +32,7 @@ void MakeImagesTree(int n, int nh, int nw)
+    // image size (nh x nw)
+    const int ntot = nh * nw;
+    const TString fileOutName = TString::Format("images_data_%dx%d.root", nh, nw);
++   TFile f(fileOutName, "RECREATE");
+ 
+    const int nRndmEvts = 10000; // number of events we use to fill each image
+    double delta_sigma = 0.1;    // 5% difference in the sigma
+@@ -42,15 +43,15 @@ void MakeImagesTree(int n, int nh, int nw)
+    double sX2 = sX1 + delta_sigma;
+    double sY2 = sY1 - delta_sigma;
+ 
+-   auto h1 = new TH2D("h1", "h1", nh, 0, 10, nw, 0, 10);
+-   auto h2 = new TH2D("h2", "h2", nh, 0, 10, nw, 0, 10);
++   TH2D h1("h1", "h1", nh, 0, 10, nw, 0, 10);
++   TH2D h2("h2", "h2", nh, 0, 10, nw, 0, 10);
+ 
+-   auto f1 = new TF2("f1", "xygaus");
+-   auto f2 = new TF2("f2", "xygaus");
++   TF2 f1("f1", "xygaus");
++   TF2 f2("f2", "xygaus");
++
+    TTree sgn("sig_tree", "signal_tree");
+    TTree bkg("bkg_tree", "background_tree");
+ 
+-   TFile f(fileOutName, "RECREATE");
+ 
+    std::vector<float> x1(ntot);
+    std::vector<float> x2(ntot);
+@@ -69,30 +70,30 @@ void MakeImagesTree(int n, int nh, int nw)
+    sgn.SetDirectory(&f);
+    bkg.SetDirectory(&f);
+ 
+-   f1->SetParameters(1, 5, sX1, 5, sY1);
+-   f2->SetParameters(1, 5, sX2, 5, sY2);
++   f1.SetParameters(1, 5, sX1, 5, sY1);
++   f2.SetParameters(1, 5, sX2, 5, sY2);
+    gRandom->SetSeed(0);
+    std::cout << "Filling ROOT tree " << std::endl;
+    for (int i = 0; i < n; ++i) {
+       if (i % 1000 == 0)
+          std::cout << "Generating image event ... " << i << std::endl;
+-      h1->Reset();
+-      h2->Reset();
++      h1.Reset();
++      h2.Reset();
+       // generate random means in range [3,7] to be not too much on the border
+-      f1->SetParameter(1, gRandom->Uniform(3, 7));
+-      f1->SetParameter(3, gRandom->Uniform(3, 7));
+-      f2->SetParameter(1, gRandom->Uniform(3, 7));
+-      f2->SetParameter(3, gRandom->Uniform(3, 7));
++      f1.SetParameter(1, gRandom->Uniform(3, 7));
++      f1.SetParameter(3, gRandom->Uniform(3, 7));
++      f2.SetParameter(1, gRandom->Uniform(3, 7));
++      f2.SetParameter(3, gRandom->Uniform(3, 7));
+ 
+-      h1->FillRandom("f1", nRndmEvts);
+-      h2->FillRandom("f2", nRndmEvts);
++      h1.FillRandom("f1", nRndmEvts);
++      h2.FillRandom("f2", nRndmEvts);
+ 
+       for (int k = 0; k < nh; ++k) {
+          for (int l = 0; l < nw; ++l) {
+             int m = k * nw + l;
+             // add some noise in each bin
+-            x1[m] = h1->GetBinContent(k + 1, l + 1) + gRandom->Gaus(0, pixelNoise);
+-            x2[m] = h2->GetBinContent(k + 1, l + 1) + gRandom->Gaus(0, pixelNoise);
++            x1[m] = h1.GetBinContent(k + 1, l + 1) + gRandom->Gaus(0, pixelNoise);
++            x2[m] = h2.GetBinContent(k + 1, l + 1) + gRandom->Gaus(0, pixelNoise);
+          }
+       }
+       sgn.Fill();
+@@ -119,6 +120,16 @@ void TMVA_CNN_Classification(int nevts = 1000, std::ve
+ void TMVA_CNN_Classification(int nevts = 1000, std::vector<bool> opt = {1, 1, 1, 1, 1})
+ {
+ 
++   int imgSize = 16 * 16;
++   TString inputFileName = "images_data_16x16.root";
++
++   bool fileExist = !gSystem->AccessPathName(inputFileName);
++
++   // if file does not exists create it
++   if (!fileExist) {
++      MakeImagesTree(nevts, 16, 16);
++   }
++
+    bool useTMVACNN = (opt.size() > 0) ? opt[0] : false;
+    bool useKerasCNN = (opt.size() > 1) ? opt[1] : false;
+    bool useTMVADNN = (opt.size() > 2) ? opt[2] : false;
+@@ -202,7 +213,7 @@ void TMVA_CNN_Classification(int nevts = 1000, std::ve
+ 
+    **/
+ 
+-   TMVA::DataLoader *loader = new TMVA::DataLoader("dataset");
++   TMVA::DataLoader loader("dataset");
+ 
+    /***
+ 
+@@ -212,19 +223,7 @@ void TMVA_CNN_Classification(int nevts = 1000, std::ve
+ 
+    **/
+ 
+-   int imgSize = 16 * 16;
+-   TString inputFileName = "images_data_16x16.root";
+-
+-   bool fileExist = !gSystem->AccessPathName(inputFileName);
+-
+-   // if file does not exists create it
+-   if (!fileExist) {
+-      MakeImagesTree(nevts, 16, 16);
+-   }
+-
+-   // TString inputFileName = "tmva_class_example.root";
+-
+-   auto inputFile = TFile::Open(inputFileName);
++   std::unique_ptr<TFile> inputFile{TFile::Open(inputFileName)};
+    if (!inputFile) {
+       Error("TMVA_CNN_Classification", "Error opening input file %s - exit", inputFileName.Data());
+       return;
+@@ -232,9 +231,18 @@ void TMVA_CNN_Classification(int nevts = 1000, std::ve
+ 
+    // --- Register the training and test trees
+ 
+-   TTree *signalTree = (TTree *)inputFile->Get("sig_tree");
+-   TTree *backgroundTree = (TTree *)inputFile->Get("bkg_tree");
++   auto signalTree = inputFile->Get<TTree>("sig_tree");
++   auto backgroundTree = inputFile->Get<TTree>("bkg_tree");
+ 
++   if (!signalTree) {
++      Error("TMVA_CNN_Classification", "Could not find signal tree in file '%s'", inputFileName.Data());
++      return;
++   }
++   if (!backgroundTree) {
++      Error("TMVA_CNN_Classification", "Could not find background tree in file '%s'", inputFileName.Data());
++      return;
++   }
++
+    int nEventsSig = signalTree->GetEntries();
+    int nEventsBkg = backgroundTree->GetEntries();
+ 
+@@ -243,17 +251,17 @@ void TMVA_CNN_Classification(int nevts = 1000, std::ve
+    Double_t backgroundWeight = 1.0;
+ 
+    // You can add an arbitrary number of signal or background trees
+-   loader->AddSignalTree(signalTree, signalWeight);
+-   loader->AddBackgroundTree(backgroundTree, backgroundWeight);
++   loader.AddSignalTree(signalTree, signalWeight);
++   loader.AddBackgroundTree(backgroundTree, backgroundWeight);
+ 
+    /// add event variables (image)
+    /// use new method (from ROOT 6.20 to add a variable array for all image data)
+-   loader->AddVariablesArray("vars", imgSize);
++   loader.AddVariablesArray("vars", imgSize);
+ 
+    // Set individual event weights (the variables must exist in the original TTree)
+    //    for signal    : factory->SetSignalWeightExpression    ("weight1*weight2");
+    //    for background: factory->SetBackgroundWeightExpression("weight1*weight2");
+-   // loader->SetBackgroundWeightExpression( "weight" );
++   // loader.SetBackgroundWeightExpression( "weight" );
+ 
+    // Apply additional cuts on the signal and background samples (can be different)
+    TCut mycuts = ""; // for example: TCut mycuts = "abs(var1)<0.5 && abs(var2-0.5)<1";
+@@ -263,7 +271,7 @@ void TMVA_CNN_Classification(int nevts = 1000, std::ve
+    //
+    // If no numbers of events are given, half of the events in the tree are used
+    // for training, and the other half for testing:
+-   //    loader->PrepareTrainingAndTestTree( mycut, "SplitMode=random:!V" );
++   //    loader.PrepareTrainingAndTestTree( mycut, "SplitMode=random:!V" );
+    // It is possible also to specify the number of training and testing events,
+    // note we disable the computation of the correlation matrix of the input variables
+ 
+@@ -275,7 +283,7 @@ void TMVA_CNN_Classification(int nevts = 1000, std::ve
+       "nTrain_Signal=%d:nTrain_Background=%d:SplitMode=Random:SplitSeed=100:NormMode=NumEvents:!V:!CalcCorrelations",
+       nTrainSig, nTrainBkg);
+ 
+-   loader->PrepareTrainingAndTestTree(mycuts, mycutb, prepareOptions);
++   loader.PrepareTrainingAndTestTree(mycuts, mycutb, prepareOptions);
+ 
+    /***
+ 
+@@ -288,8 +296,6 @@ void TMVA_CNN_Classification(int nevts = 1000, std::ve
+ 
+    **/
+ 
+-   // signalTree->Print();
+-
+    /****
+         # Booking Methods
+ 
+@@ -299,7 +305,7 @@ void TMVA_CNN_Classification(int nevts = 1000, std::ve
+ 
+    // Boosted Decision Trees
+    if (useTMVABDT) {
+-      factory.BookMethod(loader, TMVA::Types::kBDT, "BDT",
++      factory.BookMethod(&loader, TMVA::Types::kBDT, "BDT",
+                          "!V:NTrees=200:MinNodeSize=2.5%:MaxDepth=2:BoostType=AdaBoost:AdaBoostBeta=0.5:"
+                          "UseBaggedBoost:BaggedSampleFraction=0.5:SeparationType=GiniIndex:nCuts=20");
+    }
+@@ -346,7 +352,7 @@ void TMVA_CNN_Classification(int nevts = 1000, std::ve
+       dnnOptions += ":Architecture=CPU";
+ #endif
+ 
+-      factory.BookMethod(loader, TMVA::Types::kDL, dnnMethodName, dnnOptions);
++      factory.BookMethod(&loader, TMVA::Types::kDL, dnnMethodName, dnnOptions);
+    }
+ 
+    /***
+@@ -419,7 +425,7 @@ void TMVA_CNN_Classification(int nevts = 1000, std::ve
+       cnnMethodName = "TMVA_CNN_CPU";
+ #endif
+ 
+-      factory.BookMethod(loader, TMVA::Types::kDL, cnnMethodName, cnnOptions);
++      factory.BookMethod(&loader, TMVA::Types::kDL, cnnMethodName, cnnOptions);
+    }
+ 
+    /**
+@@ -427,6 +433,11 @@ void TMVA_CNN_Classification(int nevts = 1000, std::ve
+ 
+    **/
+ 
++#ifdef R__HAS_PYMVA
++   // The next section uses Python packages, execute it only if PyMVA is available
++   TString tmva_python_exe{TMVA::Python_Executable()};
++   TString python_exe = tmva_python_exe.IsNull() ? "python" : tmva_python_exe;
++
+    if (useKerasCNN) {
+ 
+       Info("TMVA_CNN_Classification", "Building convolutional keras model");
+@@ -457,8 +468,6 @@ void TMVA_CNN_Classification(int nevts = 1000, std::ve
+ 
+       m.SaveSource("make_cnn_model.py");
+       // execute
+-      auto ret = (TString *)gROOT->ProcessLine("TMVA::Python_Executable()");
+-      TString python_exe = (ret) ? *(ret) : "python";
+       gSystem->Exec(python_exe + " make_cnn_model.py");
+ 
+       if (gSystem->AccessPathName("model_cnn.h5")) {
+@@ -467,7 +476,7 @@ void TMVA_CNN_Classification(int nevts = 1000, std::ve
+          // book PyKeras method only if Keras model could be created
+          Info("TMVA_CNN_Classification", "Booking tf.Keras CNN model");
+          factory.BookMethod(
+-            loader, TMVA::Types::kPyKeras, "PyKeras",
++            &loader, TMVA::Types::kPyKeras, "PyKeras",
+             "H:!V:VarTransform=None:FilenameModel=model_cnn.h5:tf.keras:"
+             "FilenameTrainedModel=trained_model_cnn.h5:NumEpochs=10:BatchSize=100:"
+             "GpuOptions=allow_growth=True"); // needed for RTX NVidia card and to avoid TF allocates all GPU memory
+@@ -478,9 +487,8 @@ void TMVA_CNN_Classification(int nevts = 1000, std::ve
+ 
+       Info("TMVA_CNN_Classification", "Using Convolutional PyTorch Model");
+       TString pyTorchFileName = gROOT->GetTutorialDir() + TString("/tmva/PyTorch_Generate_CNN_Model.py");
+-      // check that pytorch can be imported and file defining the model and used later when booking the method is existing
+-      auto ret = (TString *)gROOT->ProcessLine("TMVA::Python_Executable()");
+-      TString python_exe = (ret) ? *(ret) : "python";
++      // check that pytorch can be imported and file defining the model and used later when booking the method is
++      // existing
+       if (gSystem->Exec(python_exe + " -c 'import torch'") || gSystem->AccessPathName(pyTorchFileName)) {
+          Warning("TMVA_CNN_Classification", "PyTorch is not installed or model building file is not existing - skip using PyTorch");
+       } else {
+@@ -489,11 +497,11 @@ void TMVA_CNN_Classification(int nevts = 1000, std::ve
+          TString methodOpt = "H:!V:VarTransform=None:FilenameModel=PyTorchModelCNN.pt:"
+                              "FilenameTrainedModel=PyTorchTrainedModelCNN.pt:NumEpochs=10:BatchSize=100";
+          methodOpt += TString(":UserCode=") + pyTorchFileName;
+-         factory.BookMethod(loader, TMVA::Types::kPyTorch, "PyTorch", methodOpt);
++         factory.BookMethod(&loader, TMVA::Types::kPyTorch, "PyTorch", methodOpt);
+       }
+    }
++#endif
+ 
+-
+    ////  ## Train Methods
+ 
+    factory.TrainAllMethods();
+@@ -506,7 +514,7 @@ void TMVA_CNN_Classification(int nevts = 1000, std::ve
+ 
+    /// ## Plot ROC Curve
+ 
+-   auto c1 = factory.GetROCCurve(loader);
++   auto c1 = factory.GetROCCurve(&loader);
+    c1->Draw();
+ 
+    // close outputfile to save output file
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/TMVA_CNN_Classification.py root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/TMVA_CNN_Classification.py
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/TMVA_CNN_Classification.py	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/TMVA_CNN_Classification.py	2024-09-18 13:49:29
+@@ -22,7 +22,34 @@
+ ## The difference between signal and background is in the gaussian width.
+ ## The width for the background gaussian is slightly larger than the signal width by few % values
+ 
++import os
++import importlib.util
+ 
++opt = [1, 1, 1, 1, 1]
++useTMVACNN = opt[0] if len(opt) > 0  else False
++useKerasCNN = opt[1] if len(opt) > 1 else False
++useTMVADNN = opt[2] if len(opt) > 2 else False
++useTMVABDT = opt[3] if len(opt) > 3 else False
++usePyTorchCNN = opt[4] if len(opt) > 4 else False
++
++tf_spec = importlib.util.find_spec("tensorflow")
++if tf_spec is None:
++    useKerasCNN = False
++    print("TMVA_CNN_Classificaton","Skip using Keras since tensorflow is not installed")
++else:
++    import tensorflow
++
++# PyTorch has to be imported before ROOT to avoid crashes because of clashing
++# std::regexp symbols that are exported by cppyy.
++# See also: https://github.com/wlav/cppyy/issues/227
++torch_spec = importlib.util.find_spec("torch")
++if torch_spec is None:
++    usePyTorchCNN = False
++    print("TMVA_CNN_Classificaton","Skip using PyTorch since torch is not installed")
++else:
++    import torch
++
++
+ import ROOT
+ 
+ #switch off MT in OpenMP (BLAS)
+@@ -30,10 +57,6 @@ TFile = ROOT.TFile
+ TMVA = ROOT.TMVA
+ TFile = ROOT.TFile
+ 
+-
+-import os
+-import importlib
+-
+ TMVA.Tools.Instance()
+ 
+ def MakeImagesTree(n, nh, nw):
+@@ -108,12 +131,6 @@ nevt = 1000    # use a larger value to get better resu
+ hasCPU = "tmva-cpu" in ROOT.gROOT.GetConfigFeatures()
+ 
+ nevt = 1000    # use a larger value to get better results
+-opt = [1, 1, 1, 1, 1]
+-useTMVACNN = opt[0] if len(opt) > 0  else False
+-useKerasCNN = opt[1] if len(opt) > 1 else False
+-useTMVADNN = opt[2] if len(opt) > 2 else False
+-useTMVABDT = opt[3] if len(opt) > 3 else False
+-usePyTorchCNN = opt[4] if len(opt) > 4 else False
+ 
+ if (not hasCPU and not hasGPU) :
+     ROOT.Warning("TMVA_CNN_Classificaton","ROOT is not supporting tmva-cpu and tmva-gpu skip using TMVA-DNN and TMVA-CNN")
+@@ -125,16 +142,6 @@ else:
+     usePyTorchCNN = False
+ else:
+     TMVA.PyMethodBase.PyInitialize()
+-
+-tf_spec = importlib.util.find_spec("tensorflow")
+-if tf_spec is None:
+-    useKerasCNN = False
+-    ROOT.Warning("TMVA_CNN_Classificaton","Skip using Keras since tensorflow is not installed")
+-
+-torch_spec = importlib.util.find_spec("torch")
+-if torch_spec is None:
+-    usePyTorchCNN = False
+-    ROOT.Warning("TMVA_CNN_Classificaton","Skip using PyTorch since torch is not installed")
+ 
+ if not useTMVACNN:
+     ROOT.Warning(
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/TMVA_RNN_Classification.C root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/TMVA_RNN_Classification.C
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/TMVA_RNN_Classification.C	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/TMVA_RNN_Classification.C	2024-09-18 13:26:26
+@@ -55,9 +55,9 @@ void MakeTimeData(int n, int ntime, int ndim )
+    auto f1 = new TF1("f1", "gaus");
+    auto f2 = new TF1("f2", "gaus");
+ 
++   TFile f(fname, "RECREATE");
+    TTree sgn("sgn", "sgn");
+    TTree bkg("bkg", "bkg");
+-   TFile f(fname, "RECREATE");
+ 
+    std::vector<std::vector<float>> x1(ntime);
+    std::vector<std::vector<float>> x2(ntime);
+@@ -192,8 +192,10 @@ void TMVA_RNN_Classification(int nevts = 2000, int use
+ #endif
+ 
+ #ifdef R__USE_IMT
+-   int num_threads = 4;   // use by default all threads
+-   gSystem->Setenv("OMP_NUM_THREADS", "1"); // switch off MT in OpenBLAS
++   int num_threads = 4; // use max 4 threads
++   // switch off MT in OpenBLAS to avoid conflict with tbb
++   gSystem->Setenv("OMP_NUM_THREADS", "1");
++
+    // do enable MT running
+    if (num_threads >= 0) {
+       ROOT::EnableImplicitMT(num_threads);
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/TMVA_SOFIE_Inference.py root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/TMVA_SOFIE_Inference.py
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/TMVA_SOFIE_Inference.py	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/TMVA_SOFIE_Inference.py	2024-09-18 13:49:29
+@@ -31,7 +31,7 @@ model = ROOT.TMVA.Experimental.SOFIE.PyKeras.Parse(mod
+ # parse the input Keras model into RModel object
+ model = ROOT.TMVA.Experimental.SOFIE.PyKeras.Parse(modelFile)
+ 
+-generatedHeaderFile = modelFile.replace(".h5",".hxx")
++generatedHeaderFile = "generatedSofieHiggsModel.hxx" #modelFile.replace(".h5",".hxx")
+ print("Generating inference code for the Keras model from ",modelFile,"in the header ", generatedHeaderFile)
+ #Generating inference code
+ model.Generate()
+@@ -44,7 +44,6 @@ ROOT.gInterpreter.Declare('#include "' + generatedHead
+ ROOT.gInterpreter.Declare('#include "' + generatedHeaderFile + '"')
+ 
+ 
+-generatedHeaderFile = modelFile.replace(".h5",".hxx")
+ print("Generating inference code for the Keras model from ",modelFile,"in the header ", generatedHeaderFile)
+ #Generating inference
+ 
+@@ -67,7 +66,7 @@ print("size of data", dataset_size)
+ print("size of data", dataset_size)
+ 
+ #instantiate SOFIE session class 
+-session = ROOT.TMVA_SOFIE_Higgs_trained_model.Session()
++session = ROOT.TMVA_SOFIE_Higgs_trained_model.Session("generatedSofieHiggsModel.dat")
+ 
+ hs = ROOT.TH1D("hs","Signal result",100,0,1)
+ for i in range(0,dataset_size):
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/TMVA_SOFIE_RDataFrame.py root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/TMVA_SOFIE_RDataFrame.py
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/TMVA_SOFIE_RDataFrame.py	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/TMVA_SOFIE_RDataFrame.py	2024-09-18 13:49:29
+@@ -27,14 +27,14 @@ model.Generate()
+ 
+ # generating inference code
+ model.Generate()
+-model.OutputGenerated("Higgs_trained_model.hxx")
++model.OutputGenerated("Higgs_generated_Sofie_model.hxx")
+ model.PrintGenerated()
+ 
+ # compile using ROOT JIT trained model
+ print("compiling SOFIE model and functor....")
+-ROOT.gInterpreter.Declare('#include "Higgs_trained_model.hxx"')
++ROOT.gInterpreter.Declare('#include "Higgs_generated_Sofie_model.hxx"')
+ modelName = "Higgs_trained_model"
+-ROOT.gInterpreter.Declare('auto sofie_functor = TMVA::Experimental::SofieFunctor<7,TMVA_SOFIE_'+modelName+'::Session>(0);')
++ROOT.gInterpreter.Declare('auto sofie_functor = TMVA::Experimental::SofieFunctor<7,TMVA_SOFIE_'+modelName+'::Session>(0,"Higgs_generated_Sofie_model.dat");')
+ 
+ # run inference over input data
+ inputFile = "http://root.cern/files/Higgs_data.root"
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/keras/ApplicationClassificationKeras.py root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/keras/ApplicationClassificationKeras.py
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/keras/ApplicationClassificationKeras.py	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/keras/ApplicationClassificationKeras.py	2024-09-18 13:49:29
+@@ -20,10 +20,11 @@ reader = TMVA.Reader("Color:!Silent")
+ reader = TMVA.Reader("Color:!Silent")
+ 
+ # Load data
+-if not isfile('tmva_class_example.root'):
+-    call(['curl', '-L', '-O', 'http://root.cern.ch/files/tmva_class_example.root'])
++TFile.SetCacheFileDir(".")
++data = TFile.Open("http://root.cern.ch/files/tmva_class_example.root", "CACHEREAD");
++if data is None:
++    raise FileNotFoundError("Input file cannot be downloaded - exit")
+ 
+-data = TFile.Open('tmva_class_example.root')
+ signal = data.Get('TreeS')
+ background = data.Get('TreeB')
+ 
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/keras/ApplicationRegressionKeras.py root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/keras/ApplicationRegressionKeras.py
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/keras/ApplicationRegressionKeras.py	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/keras/ApplicationRegressionKeras.py	2024-09-18 13:49:29
+@@ -20,10 +20,11 @@ reader = TMVA.Reader("Color:!Silent")
+ reader = TMVA.Reader("Color:!Silent")
+ 
+ # Load data
+-if not isfile('tmva_reg_example.root'):
+-    call(['curl', '-L', '-O', 'http://root.cern.ch/files/tmva_reg_example.root'])
++TFile.SetCacheFileDir(".")
++data = TFile.Open("http://root.cern.ch/files/tmva_reg_example.root", "CACHEREAD")
++if data is None:
++    raise FileNotFoundError("Input file cannot be downloaded - exit")
+ 
+-data = TFile.Open('tmva_reg_example.root')
+ tree = data.Get('TreeR')
+ 
+ branches = {}
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/keras/ClassificationKeras.py root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/keras/ClassificationKeras.py
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/keras/ClassificationKeras.py	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/keras/ClassificationKeras.py	2024-09-18 13:49:29
+@@ -22,15 +22,15 @@ TMVA.PyMethodBase.PyInitialize()
+ TMVA.Tools.Instance()
+ TMVA.PyMethodBase.PyInitialize()
+ 
+-output = TFile.Open('TMVA.root', 'RECREATE')
++output = TFile.Open('TMVA_Classification_Keras..root', 'RECREATE')
+ factory = TMVA.Factory('TMVAClassification', output,
+                        '!V:!Silent:Color:DrawProgressBar:Transformations=D,G:AnalysisType=Classification')
+ 
+ # Load data
+-if not isfile('tmva_class_example.root'):
+-    call(['curl', '-L', '-O', 'http://root.cern.ch/files/tmva_class_example.root'])
+-
+-data = TFile.Open('tmva_class_example.root')
++TFile.SetCacheFileDir(".")
++data = TFile.Open("http://root.cern.ch/files/tmva_class_example.root", "CACHEREAD")
++if data is None:
++    raise FileNotFoundError("Input file cannot be downloaded - exit")
+ signal = data.Get('TreeS')
+ background = data.Get('TreeB')
+ 
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/keras/MulticlassKeras.py root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/keras/MulticlassKeras.py
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/keras/MulticlassKeras.py	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/keras/MulticlassKeras.py	2024-09-18 13:49:29
+@@ -21,7 +21,7 @@ TMVA.PyMethodBase.PyInitialize()
+ TMVA.Tools.Instance()
+ TMVA.PyMethodBase.PyInitialize()
+ 
+-output = TFile.Open('TMVA.root', 'RECREATE')
++output = TFile.Open('TMVA_multiclass.root', 'RECREATE')
+ factory = TMVA.Factory('TMVAClassification', output,
+     '!V:!Silent:Color:DrawProgressBar:Transformations=D,G:AnalysisType=multiclass')
+ 
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/keras/RegressionKeras.py root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/keras/RegressionKeras.py
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/keras/RegressionKeras.py	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/keras/RegressionKeras.py	2024-09-18 13:49:29
+@@ -22,15 +22,16 @@ TMVA.PyMethodBase.PyInitialize()
+ TMVA.Tools.Instance()
+ TMVA.PyMethodBase.PyInitialize()
+ 
+-output = TFile.Open('TMVA.root', 'RECREATE')
++output = TFile.Open('TMVA_Regression_Keras.root', 'RECREATE')
+ factory = TMVA.Factory('TMVARegression', output,
+         '!V:!Silent:Color:DrawProgressBar:Transformations=D,G:AnalysisType=Regression')
+ 
+ # Load data
+-if not isfile('tmva_reg_example.root'):
+-    call(['curl', '-L', '-O', 'http://root.cern.ch/files/tmva_reg_example.root'])
++TFile.SetCacheFileDir(".")
++data = TFile.Open("http://root.cern.ch/files/tmva_reg_example.root", "CACHEREAD")
++if data is None:
++    raise FileNotFoundError("Input file cannot be downloaded - exit")
+ 
+-data = TFile.Open('tmva_reg_example.root')
+ tree = data.Get('TreeR')
+ 
+ dataloader = TMVA.DataLoader('dataset')
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/pytorch/ApplicationClassificationPyTorch.py root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/pytorch/ApplicationClassificationPyTorch.py
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/pytorch/ApplicationClassificationPyTorch.py	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/pytorch/ApplicationClassificationPyTorch.py	2024-09-18 13:49:29
+@@ -10,6 +10,11 @@
+ ## \author Anirudh Dagar <anirudhdagar6@gmail.com> - IIT, Roorkee
+ 
+ 
++# PyTorch has to be imported before ROOT to avoid crashes because of clashing
++# std::regexp symbols that are exported by cppyy.
++# See also: https://github.com/wlav/cppyy/issues/227
++import torch
++
+ from ROOT import TMVA, TFile, TString
+ from array import array
+ from subprocess import call
+@@ -23,10 +28,11 @@ reader = TMVA.Reader("Color:!Silent")
+ 
+ 
+ # Load data
+-if not isfile('tmva_class_example.root'):
+-    call(['curl', '-L', '-O', 'http://root.cern.ch/files/tmva_class_example.root'])
++TFile.SetCacheFileDir(".")
++data = TFile.Open("http://root.cern.ch/files/tmva_class_example.root", "CACHEREAD")
++if data is None:
++    raise FileNotFoundError("Input file cannot be downloaded - exit")
+ 
+-data = TFile.Open('tmva_class_example.root')
+ signal = data.Get('TreeS')
+ background = data.Get('TreeB')
+ 
+@@ -43,7 +49,7 @@ def predict(model, test_X, batch_size=32):
+ def predict(model, test_X, batch_size=32):
+     # Set to eval mode
+     model.eval()
+-   
++
+     test_dataset = torch.utils.data.TensorDataset(torch.Tensor(test_X))
+     test_loader = torch.utils.data.DataLoader(test_dataset, batch_size=batch_size, shuffle=False)
+ 
+@@ -54,7 +60,7 @@ def predict(model, test_X, batch_size=32):
+             outputs = model(X)
+             predictions.append(outputs)
+         preds = torch.cat(predictions)
+-   
++
+     return preds.numpy()
+ 
+ 
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/pytorch/ApplicationRegressionPyTorch.py root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/pytorch/ApplicationRegressionPyTorch.py
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/pytorch/ApplicationRegressionPyTorch.py	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/pytorch/ApplicationRegressionPyTorch.py	2024-09-18 13:49:29
+@@ -10,6 +10,11 @@
+ ## \author Anirudh Dagar <anirudhdagar6@gmail.com> - IIT, Roorkee
+ 
+ 
++# PyTorch has to be imported before ROOT to avoid crashes because of clashing
++# std::regexp symbols that are exported by cppyy.
++# See also: https://github.com/wlav/cppyy/issues/227
++import torch
++
+ from ROOT import TMVA, TFile, TString
+ from array import array
+ from subprocess import call
+@@ -23,10 +28,11 @@ reader = TMVA.Reader("Color:!Silent")
+ 
+ 
+ # Load data
+-if not isfile('tmva_reg_example.root'):
+-    call(['curl', '-L', '-O', 'http://root.cern.ch/files/tmva_reg_example.root'])
++TFile.SetCacheFileDir(".")
++data = TFile.Open("http://root.cern.ch/files/tmva_reg_example.root", "CACHEREAD")
++if data is None:
++    raise FileNotFoundError("Input file cannot be downloaded - exit")
+ 
+-data = TFile.Open('tmva_reg_example.root')
+ tree = data.Get('TreeR')
+ 
+ branches = {}
+@@ -46,7 +52,7 @@ def predict(model, test_X, batch_size=32):
+ def predict(model, test_X, batch_size=32):
+     # Set to eval mode
+     model.eval()
+-   
++
+     test_dataset = torch.utils.data.TensorDataset(torch.Tensor(test_X))
+     test_loader = torch.utils.data.DataLoader(test_dataset, batch_size=batch_size, shuffle=False)
+ 
+@@ -57,7 +63,7 @@ def predict(model, test_X, batch_size=32):
+             outputs = model(X)
+             predictions.append(outputs)
+         preds = torch.cat(predictions)
+-   
++
+     return preds.numpy()
+ 
+ load_model_custom_objects = {"optimizer": None, "criterion": None, "train_func": None, "predict_func": predict}
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/pytorch/ClassificationPyTorch.py root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/pytorch/ClassificationPyTorch.py
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/pytorch/ClassificationPyTorch.py	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/pytorch/ClassificationPyTorch.py	2024-09-18 13:49:29
+@@ -11,28 +11,32 @@
+ ## \author Anirudh Dagar <anirudhdagar6@gmail.com> - IIT, Roorkee
+ 
+ 
++# PyTorch has to be imported before ROOT to avoid crashes because of clashing
++# std::regexp symbols that are exported by cppyy.
++# See also: https://github.com/wlav/cppyy/issues/227
++import torch
++from torch import nn
++
+ from ROOT import TMVA, TFile, TTree, TCut
+ from subprocess import call
+ from os.path import isfile
+ 
+-import torch
+-from torch import nn
+ 
+-
+ # Setup TMVA
+ TMVA.Tools.Instance()
+ TMVA.PyMethodBase.PyInitialize()
+ 
+-output = TFile.Open('TMVA.root', 'RECREATE')
+-factory = TMVA.Factory('TMVAClassification', output,
++# create factory without output file since it is not needed
++factory = TMVA.Factory('TMVAClassification',
+                        '!V:!Silent:Color:DrawProgressBar:Transformations=D,G:AnalysisType=Classification')
+ 
+ 
+ # Load data
+-if not isfile('tmva_class_example.root'):
+-    call(['curl', '-L', '-O', 'http://root.cern.ch/files/tmva_class_example.root'])
++TFile.SetCacheFileDir(".")
++data = TFile.Open("http://root.cern.ch/files/tmva_class_example.root", "CACHEREAD")
++if data is None:
++    raise FileNotFoundError("Input file cannot be downloaded - exit")
+ 
+-data = TFile.Open('tmva_class_example.root')
+ signal = data.Get('TreeS')
+ background = data.Get('TreeB')
+ 
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/pytorch/MulticlassPyTorch.py root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/pytorch/MulticlassPyTorch.py
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/pytorch/MulticlassPyTorch.py	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/pytorch/MulticlassPyTorch.py	2024-09-18 13:26:26
+@@ -11,19 +11,22 @@
+ ## \author Anirudh Dagar <anirudhdagar6@gmail.com> - IIT, Roorkee
+ 
+ 
+-from ROOT import TMVA, TFile, TTree, TCut, gROOT
+-from os.path import isfile
+-
++# PyTorch has to be imported before ROOT to avoid crashes because of clashing
++# std::regexp symbols that are exported by cppyy.
++# See also: https://github.com/wlav/cppyy/issues/227
+ import torch
+ from torch import nn
+ 
++from ROOT import TMVA, TFile, TTree, TCut, gROOT
++from os.path import isfile
+ 
++
+ # Setup TMVA
+ TMVA.Tools.Instance()
+ TMVA.PyMethodBase.PyInitialize()
+ 
+-output = TFile.Open('TMVA.root', 'RECREATE')
+-factory = TMVA.Factory('TMVAClassification', output,
++# create factory without output file since it is not needed
++factory = TMVA.Factory('TMVAClassification',
+     '!V:!Silent:Color:DrawProgressBar:Transformations=D,G:AnalysisType=multiclass')
+ 
+ 
+@@ -163,4 +166,4 @@ roc = factory.GetROCCurve(dataloader)
+ 
+ # Plot ROC Curves
+ roc = factory.GetROCCurve(dataloader)
+-roc.SaveAs('ROC_MulticlassPyTorch.png')
+\ No newline at end of file
++roc.SaveAs('ROC_MulticlassPyTorch.png')
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/pytorch/RegressionPyTorch.py root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/pytorch/RegressionPyTorch.py
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/pytorch/RegressionPyTorch.py	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/pytorch/RegressionPyTorch.py	2024-09-18 13:49:29
+@@ -11,28 +11,32 @@
+ ## \author Anirudh Dagar <anirudhdagar6@gmail.com> - IIT, Roorkee
+ 
+ 
++# PyTorch has to be imported before ROOT to avoid crashes because of clashing
++# std::regexp symbols that are exported by cppyy.
++# See also: https://github.com/wlav/cppyy/issues/227
++import torch
++from torch import nn
++
+ from ROOT import TMVA, TFile, TTree, TCut
+ from subprocess import call
+ from os.path import isfile
+ 
+-import torch
+-from torch import nn
+ 
+-
+ # Setup TMVA
+ TMVA.Tools.Instance()
+ TMVA.PyMethodBase.PyInitialize()
+ 
+-output = TFile.Open('TMVA.root', 'RECREATE')
+-factory = TMVA.Factory('TMVARegression', output,
++# create factory without output file since it is not needed
++factory = TMVA.Factory('TMVARegression',
+         '!V:!Silent:Color:DrawProgressBar:Transformations=D,G:AnalysisType=Regression')
+ 
+ 
+ # Load data
+-if not isfile('tmva_reg_example.root'):
+-    call(['curl', '-L', '-O', 'http://root.cern.ch/files/tmva_reg_example.root'])
++TFile.SetCacheFileDir(".")
++data = TFile.Open("http://root.cern.ch/files/tmva_reg_example.root", "CACHEREAD")
++if data is None:
++    raise FileNotFoundError("Input file cannot be downloaded - exit")
+ 
+-data = TFile.Open('tmva_reg_example.root')
+ tree = data.Get('TreeR')
+ 
+ dataloader = TMVA.DataLoader('dataset')
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/tmva003_RReader.C root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/tmva003_RReader.C
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/tmva003_RReader.C	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/tmva003_RReader.C	2024-09-18 13:49:29
+@@ -15,7 +15,7 @@ void train(const std::string &filename)
+ void train(const std::string &filename)
+ {
+    // Create factory
+-   auto output = TFile::Open("TMVA.root", "RECREATE");
++   auto output = TFile::Open("TMVARR.root", "RECREATE");
+    auto factory = new TMVA::Factory("tmva003",
+            output, "!V:!DrawProgressBar:AnalysisType=Classification");
+ 
+diff -rupN --exclude=.git* root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/tmva101_Training.py root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/tmva101_Training.py
+--- root_v6.28.12_unpatched/root_v6.28.12-source/tutorials/tmva/tmva101_Training.py	2024-09-18 13:23:16
++++ root_v6.28.12_patched/root_v6.28.12-source/tutorials/tmva/tmva101_Training.py	2024-09-18 13:26:26
+@@ -12,9 +12,13 @@
+ ## \date August 2019
+ ## \author Stefan Wunsch
+ 
++# XGBoost has to be imported before ROOT to avoid crashes because of clashing
++# std::regexp symbols that are exported by cppyy.
++# See also: https://github.com/wlav/cppyy/issues/227
++from xgboost import XGBClassifier
++
+ import ROOT
+ import numpy as np
+-import pickle
+ 
+ from tmva100_DataPreparation import variables
+ 
+@@ -45,7 +49,6 @@ if __name__ == "__main__":
+     x, y, w = load_data("train_signal.root", "train_background.root")
+ 
+     # Fit xgboost model
+-    from xgboost import XGBClassifier
+     bdt = XGBClassifier(max_depth=3, n_estimators=500)
+     bdt.fit(x, y, sample_weight=w)
+ 
diff --git a/setup.sh b/setup.sh
index e91e4d8bb..fbb9099a1 100755
--- a/setup.sh
+++ b/setup.sh
@@ -168,7 +168,7 @@ OSTYPE=$(uname -s)
 OPT="normal"
 DEBUG="off"
 UPDATES="off"
-PATCH="off"
+PATCH="on"
 CLEANUP="off"
 BRANCH=""
 

From 3e8121d3963146e434b2e1a3d1465939c7fef00d Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Mon, 23 Sep 2024 13:49:57 -0700
Subject: [PATCH 069/192] CHG: EventTransmitter now can handle gzip'ed files

---
 src/realta/src/MEventTransmitter.cxx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/realta/src/MEventTransmitter.cxx b/src/realta/src/MEventTransmitter.cxx
index b0df953a4..49e059719 100644
--- a/src/realta/src/MEventTransmitter.cxx
+++ b/src/realta/src/MEventTransmitter.cxx
@@ -206,12 +206,12 @@ bool MEventTransmitter::Analyze()
   vector<MFileEvents*> Readers;
   for (unsigned int s = 0; s < m_SimFileNames.size(); ++s) {
     MFileEvents* Reader;
-    if (m_SimFileNames[s].EndsWith("sim")) {
+    if (m_SimFileNames[s].EndsWith("sim") || m_SimFileNames[s].EndsWith("sim.gz")) {
       Reader = new MFileEventsSim(Geometry);
-    } else if (m_SimFileNames[s].EndsWith("evta")) {
+    } else if (m_SimFileNames[s].EndsWith("evta") || m_SimFileNames[s].EndsWith("evta.gz")) {
       Reader = new MFileEventsEvta(Geometry);
     } else {
-      cout<<"Error: File must either have sim or evta suffix: "<<m_SimFileNames[s]<<endl;
+      cout<<"Error: File must either have sim(.gz) or evta(.gz) suffix: "<<m_SimFileNames[s]<<endl;
       return false;
     }
     if (Reader->Open(m_SimFileNames[s]) == false) {

From e4082aa052338ff9900c336788bbce93fe4b422f Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Thu, 11 Jul 2024 14:56:07 -0700
Subject: [PATCH 070/192] CHG: Foxes for C++ 17 on macOS

---
 src/cosima/inc/MCRun.hh                 | 2 +-
 src/global/misc/inc/MResponseMatrixO1.h | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/cosima/inc/MCRun.hh b/src/cosima/inc/MCRun.hh
index a58b3e3e7..3c7eb6467 100644
--- a/src/cosima/inc/MCRun.hh
+++ b/src/cosima/inc/MCRun.hh
@@ -42,7 +42,7 @@ using namespace std;
 
 /******************************************************************************/
 
-struct NextEmissionSort : public binary_function<const MCSource*, const MCSource*, bool> {
+struct NextEmissionSort {
 public:
   bool operator() (const MCSource* S1, const MCSource* S2) const {
 
diff --git a/src/global/misc/inc/MResponseMatrixO1.h b/src/global/misc/inc/MResponseMatrixO1.h
index 2689532d0..580ce8bd7 100644
--- a/src/global/misc/inc/MResponseMatrixO1.h
+++ b/src/global/misc/inc/MResponseMatrixO1.h
@@ -35,7 +35,7 @@ using namespace std;
 ////////////////////////////////////////////////////////////////////////////////
 
 
-template< class T > class greater_than : public unary_function< T, bool > 
+template< class T > class greater_than
 {
  public:
   explicit greater_than( const T& x ) : arg2( x ) { }

From 35d118a36c693785606cf8065b2f45bcee94150c Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Mon, 23 Sep 2024 15:28:35 -0700
Subject: [PATCH 071/192] CHG: Compatibility with ROOT 6.32

---
 config/build-root.sh | 31 +++++++++++++++++++++++--------
 1 file changed, 23 insertions(+), 8 deletions(-)

diff --git a/config/build-root.sh b/config/build-root.sh
index 50d85e31e..e1d4eb28c 100755
--- a/config/build-root.sh
+++ b/config/build-root.sh
@@ -16,7 +16,7 @@ if [[ $? -eq 0 ]]; then
   CONFIGUREOPTIONS+=" -DCMAKE_IGNORE_PATH=${PORTPATH};${PORTPATH}/bin;${PORTPATH}/include;${PORTPATH}/include/libxml2;${PORTPATH}/include/unicode"
 fi
 # Until ROOT 6.24: C++ 11
-CONFIGUREOPTIONS+=" -DCMAKE_CXX_STANDARD=14"
+CONFIGUREOPTIONS+=" -DCMAKE_CXX_STANDARD=17"
 # We want a minimal system and enable what we really need:
 #CONFIGUREOPTIONS+=" -Dgminimal=ON"
 # Open GL -- needed by geomega
@@ -333,10 +333,17 @@ if [ "${TARBALL}" != "" ]; then
   fi
 
   # Check if it has the correct version:
-  VER=`tar xfzO ${TARBALL} ${ROOTTOPDIR}/build/version_number | sed 's|/|.|g'`
-  RESULT=$?
-  if [ "${RESULT}" != "0" ]; then
-    echo "ERROR: Something went wrong unpacking the ROOT tarball!"
+  VER=""
+  if tar -tf ${TARBALL} | grep -q "${ROOTTOPDIR}/build/version_number"; then  
+    VER=`tar xfzO ${TARBALL} ${ROOTTOPDIR}/build/version_number | sed 's|/|.|g'`
+  elif tar -tf ${TARBALL} | grep -q "${ROOTTOPDIR}/core/foundation/inc/ROOT/RVersion.hxx"; then
+    VER+=$(tar xfzO ${TARBALL} ${ROOTTOPDIR}/core/foundation/inc/ROOT/RVersion.hxx | grep "ROOT_VERSION_MAJOR" | head -n 1 | awk '{ print $3 }')
+    VER+="."
+    VER+=$(tar xfzO ${TARBALL} ${ROOTTOPDIR}/core/foundation/inc/ROOT/RVersion.hxx | grep "ROOT_VERSION_MINOR" | head -n 1 | awk '{ print $3 }')
+    VER+="."
+    VER+=$(tar xfzO ${TARBALL} ${ROOTTOPDIR}/core/foundation/inc/ROOT/RVersion.hxx | grep "ROOT_VERSION_PATCH" | head -n 1 | awk '{ print $3 }')
+  else
+    echo "ERROR: Cannot find the ROOT version in the tarball!"
     exit 1
   fi
   if echo ${VER} | grep -E '[ "]' >/dev/null; then
@@ -430,9 +437,17 @@ else
     exit 1
   fi
 
-  VER=`tar xfzO ${TARBALL} ${ROOTTOPDIR}/build/version_number | sed 's|/|.|g'`
-  if [ "$?" != "0" ]; then
-    echo "ERROR: Something went wrong unpacking the ROOT tarball!"
+  VER=""
+  if tar -tf ${TARBALL} | grep -q "${ROOTTOPDIR}/build/version_number"; then
+    VER=`tar xfzO ${TARBALL} ${ROOTTOPDIR}/build/version_number | sed 's|/|.|g'`
+  elif tar -tf ${TARBALL} | grep -q "${ROOTTOPDIR}/core/foundation/inc/ROOT/RVersion.hxx"; then
+    VER+=$(tar xfzO ${TARBALL} ${ROOTTOPDIR}/core/foundation/inc/ROOT/RVersion.hxx | grep "ROOT_VERSION_MAJOR" | head -n 1 | awk '{ print $3 }')
+    VER+="."
+    VER+=$(tar xfzO ${TARBALL} ${ROOTTOPDIR}/core/foundation/inc/ROOT/RVersion.hxx | grep "ROOT_VERSION_MINOR" | head -n 1 | awk '{ print $3 }')
+    VER+="."
+    VER+=$(tar xfzO ${TARBALL} ${ROOTTOPDIR}/core/foundation/inc/ROOT/RVersion.hxx | grep "ROOT_VERSION_PATCH" | head -n 1 | awk '{ print $3 }')
+  else
+    echo "ERROR: Cannot find the ROOT version in the tarball!"
     exit 1
   fi
   if echo ${VER} | grep -E '[ "]' >/dev/null; then

From 425699881c228131465bac7b51a6fa064bce2fdf Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Mon, 23 Sep 2024 15:29:04 -0700
Subject: [PATCH 072/192] CHG: Moved dependencies out of MGlobal

---
 src/fretalon/melinator/src/MGUIMainMelinator.cxx | 1 +
 src/geomega/src/MDGDMLImport.cxx                 | 1 +
 src/geomega/src/MGUIGeomegaMain.cxx              | 3 ++-
 src/geomega/src/MInterfaceGeomega.cxx            | 1 +
 src/global/misc/inc/MGlobal.h                    | 3 ---
 src/global/misc/src/MBinnerFISBEL.cxx            | 1 +
 src/mimrec/src/MGUIMimrecMain.cxx                | 3 ++-
 src/revan/src/MGUIRevanMain.cxx                  | 3 ++-
 src/sivan/src/MGUISivanMain.cxx                  | 5 +++--
 9 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/src/fretalon/melinator/src/MGUIMainMelinator.cxx b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
index af4d56ad9..f1e94ad9b 100644
--- a/src/fretalon/melinator/src/MGUIMainMelinator.cxx
+++ b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
@@ -26,6 +26,7 @@
 using namespace std;
 
 // ROOT libs:
+#include <TSystem.h>
 #include <KeySymbols.h>
 #include <TApplication.h>
 #include <TGPicture.h>
diff --git a/src/geomega/src/MDGDMLImport.cxx b/src/geomega/src/MDGDMLImport.cxx
index f9e9e07b3..3ecb10a87 100644
--- a/src/geomega/src/MDGDMLImport.cxx
+++ b/src/geomega/src/MDGDMLImport.cxx
@@ -22,6 +22,7 @@
 // Standard libs:
 
 // ROOT libs:
+#include "TSystem.h"
 #include "TList.h"
 #include "TGeoBBox.h"
 #include "TGeoNode.h"
diff --git a/src/geomega/src/MGUIGeomegaMain.cxx b/src/geomega/src/MGUIGeomegaMain.cxx
index 86de7efb7..4ee9d11fe 100644
--- a/src/geomega/src/MGUIGeomegaMain.cxx
+++ b/src/geomega/src/MGUIGeomegaMain.cxx
@@ -22,7 +22,8 @@
 // Standard libs:
 
 // ROOT libs:
-#include <TGPicture.h>
+#include "TGPicture.h"
+#include "TSystem.h"
 
 // MEBAlib libs:
 #include "MGUIAbout.h"
diff --git a/src/geomega/src/MInterfaceGeomega.cxx b/src/geomega/src/MInterfaceGeomega.cxx
index 92521c6bb..c5d32097b 100644
--- a/src/geomega/src/MInterfaceGeomega.cxx
+++ b/src/geomega/src/MInterfaceGeomega.cxx
@@ -34,6 +34,7 @@ using namespace std;
 
 // ROOT libs:
 #include "TROOT.h"
+#include "TSystem.h"
 #include "MString.h"
 #include "TCanvas.h"
 #include "TView.h"
diff --git a/src/global/misc/inc/MGlobal.h b/src/global/misc/inc/MGlobal.h
index b26d88d9b..02f0ce5d5 100644
--- a/src/global/misc/inc/MGlobal.h
+++ b/src/global/misc/inc/MGlobal.h
@@ -80,10 +80,7 @@
 #ifndef __MGlobal__
 #define __MGlobal__
 
-#include "TROOT.h"
-#include "TSystem.h"
 #include "TMutex.h"
-#include "TVirtualMutex.h"
 
 #include "MVector.h"
 #include "MString.h"
diff --git a/src/global/misc/src/MBinnerFISBEL.cxx b/src/global/misc/src/MBinnerFISBEL.cxx
index 78c7d2da0..e33e6a349 100644
--- a/src/global/misc/src/MBinnerFISBEL.cxx
+++ b/src/global/misc/src/MBinnerFISBEL.cxx
@@ -29,6 +29,7 @@ using namespace std;
 #include "TMath.h"
 #include "TH2.h"
 #include "TCanvas.h"
+#include "TSystem.h"
 
 // MEGAlib libs:
 #include "MExceptions.h"
diff --git a/src/mimrec/src/MGUIMimrecMain.cxx b/src/mimrec/src/MGUIMimrecMain.cxx
index e4ac6ba75..be10273a1 100644
--- a/src/mimrec/src/MGUIMimrecMain.cxx
+++ b/src/mimrec/src/MGUIMimrecMain.cxx
@@ -22,7 +22,8 @@
 // Standard libs:
 
 // ROOT libs:
-#include <TGPicture.h>
+#include "TSystem.h"
+#include "TGPicture.h"
 
 // MEGAlib libs:
 #include "MStreams.h"
diff --git a/src/revan/src/MGUIRevanMain.cxx b/src/revan/src/MGUIRevanMain.cxx
index a5ae48088..079dd4ebf 100644
--- a/src/revan/src/MGUIRevanMain.cxx
+++ b/src/revan/src/MGUIRevanMain.cxx
@@ -24,7 +24,8 @@
 using namespace std;
 
 // ROOT libs:
-#include <TGPicture.h>
+#include "TSystem.h"
+#include "TGPicture.h"
 
 // MEGAlib libs:
 #include "MGUIAbout.h"
diff --git a/src/sivan/src/MGUISivanMain.cxx b/src/sivan/src/MGUISivanMain.cxx
index e8d42d906..de71c3b5d 100644
--- a/src/sivan/src/MGUISivanMain.cxx
+++ b/src/sivan/src/MGUISivanMain.cxx
@@ -22,8 +22,9 @@
 // Standard libs:
 
 // ROOT libs:
-#include <TGPicture.h>
-#include <TStyle.h>
+#include "TSystem.h"
+#include "TGPicture.h"
+#include "TStyle.h"
 
 // MEGAlib libs:
 #include "MGUIAbout.h"

From b3cc0b1d37f91ff21c1099ae458cd9139ca485da Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Tue, 24 Sep 2024 11:19:40 -0700
Subject: [PATCH 073/192] CHG: Port C++-17 fixes back to Geant4 10.2

---
 config/build-geant4.sh                   |   4 +-
 resource/patches/geant4_v10.02.p03.patch | 224 +++++++++++++++++++++++
 2 files changed, 226 insertions(+), 2 deletions(-)

diff --git a/config/build-geant4.sh b/config/build-geant4.sh
index 51372e7a8..c603a9c54 100755
--- a/config/build-geant4.sh
+++ b/config/build-geant4.sh
@@ -10,7 +10,7 @@ if [[ $(uname -a) != *arwin* ]]; then
     CONFIGUREOPTIONS="-DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++"
   fi
 fi
-CONFIGUREOPTIONS="${CONFIGUREOPTIONS} -DCMAKE_INSTALL_PREFIX=.. -DGEANT4_INSTALL_DATA=ON -DGEANT4_USE_OPENGL_X11=OFF -DGEANT4_INSTALL_DATA_TIMEOUT=14400 -DGEANT4_USE_SYSTEM_EXPAT=OFF -DGEANT4_BUILD_CXXSTD=c++14"
+CONFIGUREOPTIONS="${CONFIGUREOPTIONS} -DCMAKE_INSTALL_PREFIX=.. -DGEANT4_INSTALL_DATA=ON -DGEANT4_USE_OPENGL_X11=OFF -DGEANT4_INSTALL_DATA_TIMEOUT=14400 -DGEANT4_USE_SYSTEM_EXPAT=OFF -DGEANT4_BUILD_CXXSTD=c++17"
 #CONFIGUREOPTIONS="${CONFIGUREOPTIONS} -DCMAKE_CXX_FLAGS=-D_GLIBCXX_USE_CXX11_ABI=0"
 # Reduce the warning messages:
 WARNINGS="-Wno-shadow -Wno-implicit-fallthrough -Wno-overloaded-virtual -Wno-deprecated-copy -Wno-unused-result -Wno-format-overflow="
@@ -456,7 +456,7 @@ PATCHAPPLIED="Patch not applied"
 if [[ ${PATCH} == on ]]; then
   echo "Patching..."
   if [ -f "${MEGALIB}/resource/patches/${GEANT4CORE}.patch" ]; then
-    patch -p1 < ${MEGALIB}/resource/patches/${GEANT4CORE}.patch
+    patch -p1 -l < ${MEGALIB}/resource/patches/${GEANT4CORE}.patch
     PATCHMD5=`openssl md5 "${MEGALIB}/resource/patches/${GEANT4CORE}.patch" | awk -F" " '{ print $2 }'`
     PATCHAPPLIED="Patch applied ${PATCHMD5}"
     echo "Applied patch: ${MEGALIB}/resource/patches/${GEANT4CORE}.patch"
diff --git a/resource/patches/geant4_v10.02.p03.patch b/resource/patches/geant4_v10.02.p03.patch
index 125c99dc5..e0dca1c56 100644
--- a/resource/patches/geant4_v10.02.p03.patch
+++ b/resource/patches/geant4_v10.02.p03.patch
@@ -1,3 +1,227 @@
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLNNToMultiPionsChannel.cc geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLNNToMultiPionsChannel.cc
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLNNToMultiPionsChannel.cc	2017-01-27 04:24:56
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLNNToMultiPionsChannel.cc	2024-09-24 11:08:46
+@@ -209,7 +209,15 @@ namespace G4INCL {
+             }
+         }
+
+-        std::random_shuffle(isosp,isosp+npion,Random::getAdapter());
++        //std::random_shuffle(isosp,isosp+npion,Random::getAdapter());
++        auto&& r = Random::getAdapter();
++        auto first = isosp;
++        auto last = isosp+npion;
++        for (auto i = last - first - 1; i > 0; --i) {
++            using std::swap;
++            swap(first[i], first[r(i + 1)]);
++        }
++
+         inter2Part(0.5);
+     }
+
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLPhaseSpaceKopylov.cc geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLPhaseSpaceKopylov.cc
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLPhaseSpaceKopylov.cc	2017-01-27 04:24:56
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLPhaseSpaceKopylov.cc	2024-09-24 10:55:25
+@@ -69,7 +69,7 @@ namespace G4INCL {
+     const size_t N = particles.size();
+     masses.resize(N);
+     sumMasses.resize(N);
+-    std::transform(particles.begin(), particles.end(), masses.begin(), std::mem_fun(&Particle::getMass));
++    std::transform(particles.begin(), particles.end(), masses.begin(), std::mem_fn(&Particle::getMass));
+     std::partial_sum(masses.begin(), masses.end(), sumMasses.begin());
+
+     G4double PFragMagCM = 0.0;
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLPhaseSpaceRauboldLynch.cc geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLPhaseSpaceRauboldLynch.cc
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLPhaseSpaceRauboldLynch.cc	2017-01-27 04:24:56
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLPhaseSpaceRauboldLynch.cc	2024-09-24 10:54:24
+@@ -240,7 +240,7 @@ namespace G4INCL {
+     // masses and sum of masses
+     masses.resize(nParticles);
+     sumMasses.resize(nParticles);
+-    std::transform(particles.begin(), particles.end(), masses.begin(), std::mem_fun(&Particle::getMass));
++    std::transform(particles.begin(), particles.end(), masses.begin(), std::mem_fn(&Particle::getMass));
+     std::partial_sum(masses.begin(), masses.end(), sumMasses.begin());
+
+     // sanity check
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLPiNToMultiPionsChannel.cc geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLPiNToMultiPionsChannel.cc
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLPiNToMultiPionsChannel.cc	2017-01-27 04:24:56
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLPiNToMultiPionsChannel.cc	2024-09-24 10:52:09
+@@ -269,7 +269,15 @@ namespace G4INCL {
+             }
+         }
+
+-        std::random_shuffle(isosp,isosp+npion,Random::getAdapter()); // isospin randomly distributed
++        //std::random_shuffle(isosp,isosp+npion,Random::getAdapter()); // isospin randomly distributed
++        auto&& r = Random::getAdapter();
++        auto first = isosp;
++        auto last = isosp+npion;
++        for (auto i = last - first - 1; i > 0; --i) {
++            using std::swap;
++            swap(first[i], first[r(i + 1)]);
++        }
++
+     }
+
+ }
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLCascade.cc geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLCascade.cc
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLCascade.cc	2017-01-27 04:24:56
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLCascade.cc	2024-09-24 10:43:55
+@@ -490,7 +490,15 @@ namespace G4INCL {
+     ParticleList const &initialProjectileComponents = theProjectileRemnant->getParticles();
+     std::vector<Particle *> shuffledComponents(initialProjectileComponents.begin(), initialProjectileComponents.end());
+     // Shuffle the list of potential participants
+-    std::random_shuffle(shuffledComponents.begin(), shuffledComponents.end(), Random::getAdapter());
++    //std::random_shuffle(shuffledComponents.begin(), shuffledComponents.end(), Random::getAdapter());
++    auto&& r = Random::getAdapter();
++    auto first = shuffledComponents.begin();
++    auto last = shuffledComponents.end();
++    for (auto i = last - first - 1; i > 0; --i) {
++      using std::swap;
++      swap(first[i], first[r(i + 1)]);
++    }
++
+
+     G4bool success = true;
+     G4bool atLeastOneNucleonEntering = false;
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLCDPP.cc geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLCDPP.cc
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLCDPP.cc	2017-01-27 04:24:56
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLCDPP.cc	2024-09-24 10:41:28
+@@ -59,8 +59,12 @@ namespace G4INCL {
+     Sk = 0.0;
+     TbelowTf = 0.0;
+
+-    std::for_each(remnantParticles.begin(), remnantParticles.end(), std::bind1st(std::mem_fun(&G4INCL::CDPP::processOneParticle), this));
+-    std::for_each(created.begin(), created.end(), std::bind1st(std::mem_fun(&G4INCL::CDPP::processOneParticle), this));
++    std::for_each(remnantParticles.begin(), remnantParticles.end(),
++                  [this](Particle const * const p){ this->G4INCL::CDPP::processOneParticle(p); }
++                  );
++    std::for_each(created.begin(), created.end(),
++                  [this](Particle const * const p){ this->G4INCL::CDPP::processOneParticle(p); }
++                  );
+
+     const G4double Tinitial = nucleus->getInitialInternalEnergy();
+     const G4double Eblock = TbelowTf - Tinitial - Sk - S;
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/include/G4INCLProjectileRemnant.hh geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/include/G4INCLProjectileRemnant.hh
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/include/G4INCLProjectileRemnant.hh	2017-01-27 04:24:56
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/include/G4INCLProjectileRemnant.hh	2024-09-23 19:31:52
+@@ -227,7 +227,14 @@ namespace G4INCL {
+     /// \brief Shuffle the list of stored projectile components
+     ParticleList shuffleStoredComponents() {
+       ParticleList pL = getStoredComponents();
+-      std::random_shuffle(pL.begin(), pL.end(), Random::getAdapter());
++      auto&& r = Random::getAdapter();
++      auto first = pL.begin();
++      auto last = pL.end();
++      //std::iterator_traits<ParticleList>::difference_type diff_t;
++      for (auto i = last - first - 1; i > 0; --i) {
++        using std::swap;
++        swap(first[i], first[r(i + 1)]);
++      }
+       return pL;
+     }
+
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/utils/src/G4INCLInterpolationTable.cc geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/utils/src/G4INCLInterpolationTable.cc
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/utils/src/G4INCLInterpolationTable.cc	2017-01-27 04:24:56
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/utils/src/G4INCLInterpolationTable.cc	2024-09-23 16:58:22
+@@ -67,14 +67,14 @@ namespace G4INCL {
+   std::vector<G4double> InterpolationTable::getNodeAbscissae() const {
+     std::vector<G4double> x(nodes.size());
+     std::transform(nodes.begin(), nodes.end(), x.begin(),
+-                   std::mem_fun_ref(&InterpolationNode::getX));
++                   std::mem_fn(&InterpolationNode::getX));
+     return x;
+   }
+
+   std::vector<G4double> InterpolationTable::getNodeValues() const {
+     std::vector<G4double> y(nodes.size());
+     std::transform(nodes.begin(), nodes.end(), y.begin(),
+-                   std::mem_fun_ref(&InterpolationNode::getY));
++                   std::mem_fn(&InterpolationNode::getY));
+     return y;
+   }
+
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/de_excitation/multifragmentation/src/G4StatMFChannel.cc geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/de_excitation/multifragmentation/src/G4StatMFChannel.cc
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/de_excitation/multifragmentation/src/G4StatMFChannel.cc	2017-01-27 04:24:56
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/de_excitation/multifragmentation/src/G4StatMFChannel.cc	2024-09-23 16:40:59
+@@ -43,7 +43,7 @@
+ #include "G4Pow.hh"
+ #include "G4Exp.hh"
+
+-class SumCoulombEnergy : public std::binary_function<G4double,G4double,G4double>
++class SumCoulombEnergy
+ {
+ public:
+   SumCoulombEnergy() : total(0.0) {}
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/cascade/cascade/src/G4NucleiModel.cc geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/cascade/cascade/src/G4NucleiModel.cc
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/cascade/cascade/src/G4NucleiModel.cc	2024-09-23 16:21:30
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/cascade/cascade/src/G4NucleiModel.cc	2024-09-23 16:23:47
+@@ -1264,7 +1264,7 @@ void G4NucleiModel::choosePointAlongTraj(G4CascadParti
+
+   // Normalize CDF to unit integral
+   std::transform(wtlen.begin(), wtlen.end(), wtlen.begin(),
+-		 std::bind2nd(std::divides<G4double>(), wtlen.back()));
++		 std::bind(std::divides<G4double>(), std::placeholders::_1, wtlen.back()));
+
+   if (verboseLevel > 3) {
+     G4cout << " weights";
+
+
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/de_excitation/multifragmentation/include/G4StatMFMicroCanonical.hh geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/de_excitation/multifragmentation/include/G4StatMFMicroCanonical.hh
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/de_excitation/multifragmentation/include/G4StatMFMicroCanonical.hh	2017-01-27 04:24:56
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/de_excitation/multifragmentation/include/G4StatMFMicroCanonical.hh	2024-09-23 16:02:54
+@@ -110,7 +110,7 @@ class G4StatMFMicroCanonical : public G4VStatMFEnsembl
+     }
+   };
+
+-  class SumProbabilities : public std::binary_function<G4double,G4double,G4double>
++  class SumProbabilities
+   {
+   public:
+     SumProbabilities() : total(0.0) {}
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/geometry/management/include/G4SmartVoxelStat.hh geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/geometry/management/include/G4SmartVoxelStat.hh
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/geometry/management/include/G4SmartVoxelStat.hh	2017-01-27 04:24:59
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/geometry/management/include/G4SmartVoxelStat.hh	2024-09-23 15:56:26
+@@ -106,8 +106,6 @@ class G4SmartVoxelStat
+     // Functor objects for sorting
+     //
+     struct ByCpu
+-      : public std::binary_function< const G4SmartVoxelStat,
+-                                     const G4SmartVoxelStat, G4bool >
+     {
+       G4bool operator()( const G4SmartVoxelStat &a, const G4SmartVoxelStat &b )
+       {
+@@ -116,8 +114,6 @@ class G4SmartVoxelStat
+     };
+
+     struct ByMemory
+-      : public std::binary_function< const G4SmartVoxelStat,
+-                                     const G4SmartVoxelStat, G4bool >
+     {
+       G4bool operator()( const G4SmartVoxelStat &a, const G4SmartVoxelStat &b )
+       {
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/externals/clhep/src/mixmax.cc geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/externals/clhep/src/mixmax.cc
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/externals/clhep/src/mixmax.cc	2017-01-27 04:24:58
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/externals/clhep/src/mixmax.cc	2024-09-23 15:48:28
+@@ -254,7 +254,7 @@ inline myuint fmodmulM61(myuint cum, myuint s, myuint
+
+ inline myuint fmodmulM61(myuint cum, myuint s, myuint a)
+ {
+-    register myuint o,ph,pl,ah,al;
++    myuint o,ph,pl,ah,al;
+     o=(s)*a;
+     ph = ((s)>>32);
+     pl = (s) & MASK32;
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/cmake/Modules/Geant4LibraryBuildOptions.cmake geant4_v10.02.p03_patched/geant4_v10.02.p03-source/cmake/Modules/Geant4LibraryBuildOptions.cmake
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/cmake/Modules/Geant4LibraryBuildOptions.cmake	2017-01-27 04:25:00
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/cmake/Modules/Geant4LibraryBuildOptions.cmake	2024-09-23 15:35:43
+@@ -76,7 +76,7 @@ enum_option(GEANT4_BUILD_CXXSTD
+ # Mark as advanced because most users will not need it
+ enum_option(GEANT4_BUILD_CXXSTD
+   DOC "C++ Standard to compile against"
+-  VALUES 11 14 c++11 c++14
++  VALUES 11 14 17 c++11 c++14 c++17
+   CASE_INSENSITIVE
+   )
+
 diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/cmake/Modules/Geant4InstallData.cmake geant4_v10.02.p03_patched/geant4_v10.02.p03-source/cmake/Modules/Geant4InstallData.cmake
 --- geant4_v10.02.p03/geant4_v10.02.p03-source/cmake/Modules/Geant4InstallData.cmake	2017-01-27 04:25:00.000000000 -0800
 +++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/cmake/Modules/Geant4InstallData.cmake	2023-02-17 10:38:59.000000000 -0800

From 1f909ab7bb6b29ffdc5978d53c4e6410a035785a Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Thu, 3 Oct 2024 19:47:23 +0200
Subject: [PATCH 074/192] Update MCParameterFile.cc

---
 src/cosima/src/MCParameterFile.cc | 63 +++++++++++++++++++++++++++++--
 1 file changed, 59 insertions(+), 4 deletions(-)

diff --git a/src/cosima/src/MCParameterFile.cc b/src/cosima/src/MCParameterFile.cc
index bc685c6f1..e16cd16da 100644
--- a/src/cosima/src/MCParameterFile.cc
+++ b/src/cosima/src/MCParameterFile.cc
@@ -324,8 +324,12 @@ bool MCParameterFile::Parse()
           m_DecayMode = c_DecayModeIgnore;  
         } else if  (Mode == "activationbuildup") {
           m_DecayMode = c_DecayModeActivationBuildUp;
+	  Typo(i, "Cannot use this activation option for this current MEGAlib branch. Please use the option Buildup");
+          return false;	
         } else if  (Mode == "activationdelayeddecay") {
           m_DecayMode = c_DecayModeActivationDelayedDecay;
+	  Typo(i, "Cannot use this activation option for this current MEGAlib branch. Please use the option Buildup");
+          return false;		
         } else {
           Typo(i, "Cannot parse token DecayMode correctly:"
                " Unknown Decay mode!");
@@ -797,7 +801,16 @@ bool MCParameterFile::Parse()
                " Number of tokens is not correct!");
           return false;
         }
-      } else if (T->IsTokenAt(1, "Triggers", true) == true || 
+      } else if (T->IsTokenAt(1, "Reconstruction", true) == true) {
+        if (T->GetNTokens() == 4) {
+          Run->SetRevanConfigurationFileName(T->GetTokenAtAsString(2));
+          Run->SetTraFileName(T->GetTokenAtAsString(3));
+        } else {
+          Typo(i, "Cannot parse token Reconstruction correctly:"
+               " Number of tokens is not correct!");
+          return false;
+        }
+      } else if (T->IsTokenAt(1, "Triggers", true) == true ||
                  T->IsTokenAt(1, "Trigger", true) == true ||
                  T->IsTokenAt(1, "NTrigger", true) == true ||
                  T->IsTokenAt(1, "NTriggers", true) == true) {
@@ -852,14 +865,15 @@ bool MCParameterFile::Parse()
           if (O.Parse(*T) == false) {
             Typo(i, "Cannot parse token \"OrientationSky\" correctly");
             return false;
-          }          
+          }
+	  
           // The sky can only be rotated if in Galactic coordinates
-          if (O.GetCoordinateSystem() != MCOrientationCoordinateSystem::c_Galactic && O.IsOriented() == true) {
+          if ( O.GetCoordinateSystem() != MCOrientationCoordinateSystem::c_Galactic  && O.IsOriented() == true) {
             Typo(i, "\"OrientationSky\" can only have an orientation in Galactic coordinates!");
             return false;            
           }
           Run->SetSkyOrientation(O);
-          
+
         } else {
           Typo(i, "Cannot parse token \"OrientationSky\" correctly: Number of tokens is not correct!");
           return false;
@@ -1435,6 +1449,18 @@ bool MCParameterFile::Parse()
               return false;
             }
           }
+	  else if (Type == "farfieldearthoccultation" ) {
+            if (T->GetNTokens() >= 3) {
+              Source->SetBeamType(MCSource::c_FarField,
+                                  MCSource::c_FarFieldEarthOccultation);
+              
+              mdebug<<"Using beam: "<<Type<<endl;
+            } else {
+              Typo(i, "Cannot parse token \"Beam - far field file zenith dependent\" correctly:"
+                   " Number of tokens must be larger than 2!");
+              return false;
+            }
+          }
           else if (Type == "farfieldnormalizedenergybeamfluxfunction") {
             if (T->GetNTokens() >= 4) {
               Source->SetBeamType(MCSource::c_FarField,
@@ -2319,6 +2345,7 @@ bool MCParameterFile::Parse()
       } else if (T->IsTokenAt(1, "Flux", true) == true) {
       } else if (T->IsTokenAt(1, "FarFieldTransmissionProbability", true) == true) {
       } else if (T->IsTokenAt(1, "EventList", true) == true) {
+      } else if (T->IsTokenAt(1, "EarthOccultation", true) == true) {
       } else {      
         Typo(i, MString("Unknown keyword: ") + T->GetTokenAt(1));
         return false;
@@ -2870,6 +2897,34 @@ bool MCParameterFile::Parse()
           return false;
         }
       }
+      
+      else if (T->IsTokenAt(1, "EarthOccultation", true)) {
+       
+        if (T->GetNTokens() == 4) {
+	  double Theta = T->GetTokenAtAsDouble(3);
+	  bool InverseCut = T->GetTokenAtAsBoolean(2);
+	  if(Source->SetEarthOccultation(Theta,InverseCut)==true){
+	     mdebug<<"Setting Earth Occultation"<<endl;
+	  } else{
+	     Typo(i, "Cannot set Earth Occultation");
+             return false;
+	  }
+       }
+	if (T->GetNTokens() == 3) {
+	  //if theta is not specify we set it to 0 and will calculate it from the ori file
+	  // depending on the altitude
+	  double Theta = 0.0;
+	  bool InverseCut = T->GetTokenAtAsBoolean(2);
+	  if(Source->SetEarthOccultation(Theta,InverseCut)==true){
+	     mdebug<<"Setting Earth Occultation"<<endl;
+	  } else{
+	     Typo(i, "Cannot set Earth Occultation");
+             return false;
+	  }
+	
+       }
+      }    
+      
     } // is source
   } // Step 6
 

From 501b6ff4e6b92f16491f02bb4ee47edf8d56d4d5 Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Thu, 3 Oct 2024 19:48:22 +0200
Subject: [PATCH 075/192] Update MCParameterFile.hh


From b86134bc572352bba47fac95dea55a2bca0256ab Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Thu, 3 Oct 2024 19:50:55 +0200
Subject: [PATCH 076/192] Update MCParameterFile.cc

---
 src/cosima/src/MCParameterFile.cc | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/cosima/src/MCParameterFile.cc b/src/cosima/src/MCParameterFile.cc
index e16cd16da..c4780c053 100644
--- a/src/cosima/src/MCParameterFile.cc
+++ b/src/cosima/src/MCParameterFile.cc
@@ -866,9 +866,8 @@ bool MCParameterFile::Parse()
             Typo(i, "Cannot parse token \"OrientationSky\" correctly");
             return false;
           }
-	  
           // The sky can only be rotated if in Galactic coordinates
-          if ( O.GetCoordinateSystem() != MCOrientationCoordinateSystem::c_Galactic  && O.IsOriented() == true) {
+          if (O.GetCoordinateSystem() != MCOrientationCoordinateSystem::c_Galactic && O.IsOriented() == true) {
             Typo(i, "\"OrientationSky\" can only have an orientation in Galactic coordinates!");
             return false;            
           }

From 4bf4826b95db29b7ac596ddfbd67f9f33526dbe5 Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Thu, 3 Oct 2024 19:52:52 +0200
Subject: [PATCH 077/192] Update MCOrientation.cc

---
 src/cosima/src/MCOrientation.cc | 46 +++++++++++++++++++++++++++++----
 1 file changed, 41 insertions(+), 5 deletions(-)

diff --git a/src/cosima/src/MCOrientation.cc b/src/cosima/src/MCOrientation.cc
index 7ac4f5550..d3a03f8de 100644
--- a/src/cosima/src/MCOrientation.cc
+++ b/src/cosima/src/MCOrientation.cc
@@ -71,6 +71,9 @@ void MCOrientation::Clear()
   m_XPhiLong.clear();
   m_ZThetaLat.clear();
   m_ZPhiLong.clear();
+  m_EarthAlt.clear();
+  m_EarthLat.clear();
+  m_EarthLong.clear();
   
   m_Translations.clear();
   
@@ -233,10 +236,12 @@ bool MCOrientation::Parse(const MTokenizer& Tokenizer)
 
     
   } else if (Tokenizer.IsTokenAt(3, "File") == true) {
-    if (Tokenizer.GetNTokens() != 6) {
+    if (Tokenizer.GetNTokens() != 6 ) {
       mlog<<"   ***  Error  ***  You need exactly 6 tokens to for an orientation read from file"<<endl;
       return false;
     }
+    
+    
     if (Tokenizer.IsTokenAt(4, "Loop") == true) {
       m_IsLooping = true;
     } else if (Tokenizer.IsTokenAt(4, "NoLoop") == true) {
@@ -246,10 +251,13 @@ bool MCOrientation::Parse(const MTokenizer& Tokenizer)
       return false;        
     }
     
+    
     if (Read(Tokenizer.GetTokenAtAsString(5)) == false) {
       mlog<<"   ***  Error  ***  Unable to read orientation file correctly: \""<<Tokenizer.GetTokenAtAsString(5)<<"\""<<endl;
       return false; 
-    }
+     }
+    
+    
     
     if (m_Times.size() > 0) {
       m_IsOriented = true;
@@ -281,8 +289,8 @@ bool MCOrientation::Read(MString FileName)
   for (unsigned int l = 0; l < P.GetNLines(); ++l) {
     MTokenizer* T = P.GetTokenizerAt(l);
     if (T->IsTokenAt(0, "OG") == true) {
-      if (T->GetNTokens() != 6) {
-        mlog<<"   ***  Error  ***  Number of tokens for OG keyword must be 6"<<endl;
+      if (T->GetNTokens() != 6 && T->GetNTokens() != 9 &&(m_CoordianteSystem == MCOrientationCoordinateSystem::c_Galactic || m_CoordianteSystem == MCOrientationCoordinateSystem::c_Local) ) {
+        mlog<<"   ***  Error  ***  Number of tokens for OG keyword must be 6 or 9"<<endl;
         return false;          
       }
       
@@ -290,7 +298,14 @@ bool MCOrientation::Read(MString FileName)
       m_XThetaLat.push_back(T->GetTokenAtAsDouble(2)*deg);
       m_XPhiLong.push_back(T->GetTokenAtAsDouble(3)*deg);
       m_ZThetaLat.push_back(T->GetTokenAtAsDouble(4)*deg);
-      m_ZPhiLong.push_back(T->GetTokenAtAsDouble(5)*deg); 
+      m_ZPhiLong.push_back(T->GetTokenAtAsDouble(5)*deg);
+      
+      if (T->GetNTokens() == 9){
+        m_EarthAlt.push_back(T->GetTokenAtAsDouble(6)*km);
+        m_EarthLat.push_back(T->GetTokenAtAsDouble(7)*deg);
+        m_EarthLong.push_back(T->GetTokenAtAsDouble(8)*deg);
+      }
+       
       
       if (m_XThetaLat.back() > 90 || m_XThetaLat.back() < -90) {
         mlog<<"   ***  Error  ***  Latitude value for X axis not within [-90, 90]: "<<m_XThetaLat.back()<<endl;
@@ -382,6 +397,7 @@ bool MCOrientation::Read(MString FileName)
   }
  
  
+ 
   return true;
 }
 
@@ -462,6 +478,26 @@ bool MCOrientation::GetOrientation(double Time, double& XThetaLat, double& XPhiL
 }
 
 
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Get the Earth coordinates of the current spacecraft orbit position 
+bool MCOrientation::GetEarthCoordinate(double Time, double& Alt, double& Lat, double& Long) const
+{
+  if (InRange(Time) == true) {
+    unsigned int Index = FindClosestIndex(Time);
+    Alt = m_EarthAlt[Index];
+    Lat = m_EarthLat[Index];
+    Long = m_EarthLong[Index];
+    
+    return true;
+  }
+  
+  return false;
+}
+
+
 ////////////////////////////////////////////////////////////////////////////////
 
 

From e7982fb30b95f4fdb4f6f4270d98940b795d2c03 Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Thu, 3 Oct 2024 19:53:20 +0200
Subject: [PATCH 078/192] Update MCOrientation.hh

---
 src/cosima/inc/MCOrientation.hh | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/src/cosima/inc/MCOrientation.hh b/src/cosima/inc/MCOrientation.hh
index 9ebf90d7c..380ebda70 100644
--- a/src/cosima/inc/MCOrientation.hh
+++ b/src/cosima/inc/MCOrientation.hh
@@ -42,7 +42,7 @@ using namespace std;
 
 //! This class represents all orientations in Cosima
 enum class MCOrientationCoordinateSystem : int { 
-  c_Local = 0, c_Galactic = 1
+  c_Local = 0, c_Galactic = 1 
 };
 
 //! I/O for MCOrientationCoordinateSystem
@@ -84,6 +84,9 @@ class MCOrientation
   //! Get the orientation
   bool GetOrientation(double Time, double& XThetaLat, double& XPhiLong, double& ZThetaLat, double& ZPhiLong) const;
   
+  //! Get the Earth coordinates
+  bool GetEarthCoordinate(double Time, double& Alt, double& Lat, double& Long) const;
+  
   //! Perform the orientation for the given time for a position and a direction from local to oriented coordiante system
   bool OrientPositionAndDirection(double Time, G4ThreeVector& Position, G4ThreeVector& Direction) const;  
   //! Perform the invers orientation for the given time for a position and a direction from oriented to local coordiante system
@@ -144,6 +147,13 @@ class MCOrientation
   //! The z-Axis phi / longitude
   vector<double> m_ZPhiLong;
   
+  //! The Earth altitude
+  vector<double> m_EarthAlt;
+  //! The Earth  lat in galactic coordinate
+  vector<double> m_EarthLat;
+  //! The Earth  lat in galactic coordinate
+  vector<double> m_EarthLong;
+  
   //! The translation
   vector<MVector> m_Translations;
   

From 0ee391beaaf5cc2438b1538a25635d677ff105d7 Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Thu, 3 Oct 2024 19:54:09 +0200
Subject: [PATCH 079/192] Update MCSource.hh

---
 src/cosima/inc/MCSource.hh | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/src/cosima/inc/MCSource.hh b/src/cosima/inc/MCSource.hh
index 35b18cb54..646552668 100644
--- a/src/cosima/inc/MCSource.hh
+++ b/src/cosima/inc/MCSource.hh
@@ -202,6 +202,9 @@ public:
   /// Return true, if the far field transmission probability file could be set and read correctly
   bool SetFarFieldTransmissionProbability(const MString& FileName);
 
+
+  /// Set the Earth occultation option to true
+  bool SetEarthOccultation(double Theta,bool InverseCut);
   
   /// Return true, if the successor flag couls be set correctly
   bool SetIsSuccessor(const bool& IsSuccessorFlag) { m_IsSuccessor = IsSuccessorFlag; return true; }
@@ -371,6 +374,9 @@ public:
   static const int c_FarFieldIsotropic;
   /// Id of an far-field disk 
   static const int c_FarFieldDisk;
+  /// Id of an far-field where we apply the Earth occultation 
+  static const int c_FarFieldEarthOccultation;
+  
   
   /// Id of a point like source in Cartesian coordinates
   static const int c_NearFieldPoint;
@@ -747,6 +753,13 @@ private:
   
   /// Flag indicating we should apply the far field transmission probabilities
   bool m_UseFarFieldTransmissionProbability;
+  /// Flag indicating we should apply the Earth occultation
+  bool m_UseEarthOccultation;
+  /// Theta max use for the Earth Occultation
+  double m_ThetaMaxEarthOccultation;
+  /// Flag indicating if we want a Inverse Earth occultation for albedo
+  bool m_EarthOccultation_InverseCut;
+  
   /// Far field transmission probabilities
   MFunction2D m_FarFieldTransmissionProbability;
   

From c0edb043f3961a51b397905148784f6127fa6057 Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Thu, 3 Oct 2024 19:59:44 +0200
Subject: [PATCH 080/192] Update MCSource.cc

---
 src/cosima/src/MCSource.cc | 162 ++++++++++++++++++++++++++++++++++---
 1 file changed, 153 insertions(+), 9 deletions(-)

diff --git a/src/cosima/src/MCSource.cc b/src/cosima/src/MCSource.cc
index 73a5f62ae..da549e8c9 100644
--- a/src/cosima/src/MCSource.cc
+++ b/src/cosima/src/MCSource.cc
@@ -85,6 +85,7 @@ const int MCSource::c_FarFieldFileZenithDependent                  = 5;
 const int MCSource::c_FarFieldNormalizedEnergyBeamFluxFunction     = 6;
 const int MCSource::c_FarFieldIsotropic                            = 7;
 const int MCSource::c_FarFieldDisk                                 = 8;
+const int MCSource::c_FarFieldEarthOccultation                     = 9;
 
 const int MCSource::c_NearFieldPoint                               = 10;
 const int MCSource::c_NearFieldRestrictedPoint                     = 11;
@@ -272,6 +273,9 @@ void MCSource::Initialize()
   m_PolarizationDegree = 0.0;
   
   m_UseFarFieldTransmissionProbability = false;
+  m_UseEarthOccultation = false;
+  m_ThetaMaxEarthOccultation = 0.0;
+  m_EarthOccultation_InverseCut = false;
   
   m_NGeneratedParticles = 0;
   
@@ -402,7 +406,74 @@ bool MCSource::GenerateParticles(G4GeneralParticleSource* ParticleGun)
     }
   }
   
+  // if we use the Earth Occultation , we skip the event if the direction is coming from the Earth
+  if (m_UseEarthOccultation == true) {
   
+    G4ThreeVector Dir = -ParticleGun->GetCurrentSource()->GetAngDist()->GenerateOne();
+    
+    
+    
+   //get the Earth aspect information from the orientation file
+    const MCOrientation& Sky = MCRunManager::GetMCRunManager()->GetCurrentRun().GetSkyOrientationReference();
+    double Alt,Lat,Lon=0;
+    if (Sky.GetEarthCoordinate(m_NextEmission,  Alt,  Lat, Lon)==true){
+     
+      double ThetaMax;
+      
+      //if Theta max is set by the user
+      if (m_ThetaMaxEarthOccultation != 0.0){
+      
+          ThetaMax = m_ThetaMaxEarthOccultation;
+      }
+     
+      else{
+      
+      //Compute the theta max (angle between the particle direction and Earth-based zenith) 
+      //using the altitude from ori file
+      double R_Earth = 6378; //km
+      ThetaMax =  ( c_Pi - asin( R_Earth/(R_Earth+Alt/km) ) )/deg;
+      
+      }
+     
+     
+      //cout<< "Alt,Lat,Lon : "<<Alt/km<<" "<<Lat/deg<<" "<<Lon/deg<<endl;
+      //cout<<"Theta max: "<<ThetaMax <<endl;
+       
+      // convert the Earth galactic l,b coordinate into cartesian representation  
+      G4ThreeVector EarthZenith(cos(Lat)*cos(Lon) , cos(Lat)*sin(Lon) , sin(Lat)); 
+     
+      //rotate the oriented coordinate system of the event into the local coordinate system
+      //Sky.OrientDirectionInvers(m_NextEmission, Dir);
+      Sky.OrientDirection(m_NextEmission, Dir);
+      
+      //For some reason Z of particle dir needs to be *-1 #reverseingeniering
+      Dir[2] = Dir[2]*-1;
+      
+      //cout<< "particle Dir: "<<Dir[0]<<" " <<Dir[1] <<" "<<Dir[2]<<endl;
+      //cout<<"Earth zenith: "<< EarthZenith[0]<<" "<<EarthZenith[1]<<" "<<EarthZenith[2]<<endl;
+      //cout<<"Angle between 2 vector : "<<EarthZenith.angle(Dir)/deg<<endl;
+      
+      
+            
+      //Do the Theta cut
+      if (m_EarthOccultation_InverseCut){
+      if (EarthZenith.angle(Dir)/deg <ThetaMax ){
+       ParticleGun->GetCurrentSource()->GetEneDist()->SetMonoEnergy(0);
+       }
+       
+      } else {
+       if (EarthZenith.angle(Dir)/deg >=ThetaMax ){
+       ParticleGun->GetCurrentSource()->GetEneDist()->SetMonoEnergy(0);
+       }
+      }
+    }
+    else{
+    merr<<"the time is not in the ori time range : "<<m_NextEmission<< " ["<< Sky.GetStartTime()<<","<< Sky.GetStopTime() <<"]"<<endl;
+    }
+    
+    
+    
+  }
   return true;
 }
 
@@ -510,13 +581,13 @@ bool MCSource::SetStartAreaParameters(double StartAreaParam1,
   }
 
   // We have to update the start area parameters
-  UpgradeStartArea();
+  if (UpgradeStartArea() == false) return false;
   // We have to update the position vectors
-  UpgradePosition();
+  if (UpgradePosition() == false) return false;
   // and the flux normalization
-  UpgradeFlux();
+  if (UpgradeFlux() == false) return false;
   // and the light curve information
-  UpgradeLightCurve();
+  if (UpgradeLightCurve() == false) return false;
   
   return true;
 }
@@ -964,6 +1035,7 @@ bool MCSource::SetBeamType(const int& CoordinateSystem, const int& BeamType)
   case c_FarFieldGaussian:
   case c_FarFieldAssymetricGaussian:
   case c_FarFieldFileZenithDependent:
+  case c_FarFieldEarthOccultation:
   case c_FarFieldNormalizedEnergyBeamFluxFunction:
   case c_FarFieldIsotropic:
   case c_FarFieldDisk:
@@ -1064,6 +1136,9 @@ string MCSource::GetBeamTypeAsString() const
   case c_FarFieldFileZenithDependent:
     Name = "FarFieldFileZenithDependent";
     break;
+  case c_FarFieldEarthOccultation:
+    Name = "FarFieldEarthOccultation";
+    break;
   case c_FarFieldNormalizedEnergyBeamFluxFunction:
     Name = "FarFieldNormalizedEnergyBeamFluxFunction";
     break;
@@ -1167,6 +1242,9 @@ string MCSource::GetBeamAsString() const
   case c_FarFieldFileZenithDependent:
     Name<<"FarFieldFileZenithDependent";
     break;
+  case c_FarFieldEarthOccultation:
+    Name<<"FarFieldEarthOccultation";
+    break;  
   case c_FarFieldNormalizedEnergyBeamFluxFunction:
     Name<<"FarFieldNormalizedEnergyBeamFluxFunction";
     break;
@@ -1293,6 +1371,8 @@ bool MCSource::SetPosition(double PositionParam1,
     }
   } else if (m_BeamType == c_FarFieldFileZenithDependent) {
     // nothing
+  } else if (m_BeamType == c_FarFieldEarthOccultation) {
+    // nothing
   } else if (m_BeamType == c_FarFieldNormalizedEnergyBeamFluxFunction) {
     // nothing
   } else if (m_BeamType == c_NearFieldPoint) {
@@ -2075,7 +2155,25 @@ bool MCSource::SetFarFieldTransmissionProbability(const MString& FileName)
   return true;
 }
 
+/******************************************************************************
+ * Return true, if the Earth occultation option is choose
+ */
+bool MCSource::SetEarthOccultation(double Theta,bool InverseCut)
+{
+
+  if (m_CoordinateSystem != c_FarField) {
+    mout<<"  ***  ERROR  ***   "<<m_Name<<": Earth Occultation : You can only use Earth Occultation for far field sources!"<<endl;
+    return false;
+  }
 
+  mout<<"Source : Earth occultation is activated !"<<endl;
+  mout<<"Earth occultation inverted ?"<<InverseCut<<endl;
+  m_UseEarthOccultation = true;
+  m_ThetaMaxEarthOccultation = Theta;
+  m_EarthOccultation_InverseCut = InverseCut;
+  
+  return true;
+}
 /******************************************************************************
  * Return true, if the light curve could be set correctly
  */
@@ -2116,13 +2214,25 @@ bool MCSource::UpgradeLightCurve()
   if (m_LightCurveType == c_LightCurveFile) {
     // Make sure the y-value is the flux in particles/second
     
-    cout<<"Lightcurve integration: "<<m_LightCurveFunction.Integrate()<<endl;
+    // Sanity check:
+    auto LightCurveIntegral = m_LightCurveFunction.Integrate();
+    if (std::isfinite(LightCurveIntegral) == false) {
+      mout<<"  ***  ERROR  ***   "<<m_Name<<": The light curve integral is not finite: " <<LightCurveIntegral<<endl;
+      return false;
+    }
+
+    cout<<"Lightcurve integration: "<<LightCurveIntegral<<endl;
     cout<<"Flux: "<<m_Flux*second<<" ph/s"<<endl;
-    if (m_Flux > 0 && m_LightCurveFunction.Integrate() > 0) {
-      m_LightCurveFunction.ScaleY((m_LightCurveFunction.GetXMax() - m_LightCurveFunction.GetXMin())/m_LightCurveFunction.Integrate());
+    if (m_Flux > 0 && LightCurveIntegral > 0) {
+      m_LightCurveFunction.ScaleY((m_LightCurveFunction.GetXMax() - m_LightCurveFunction.GetXMin())/LightCurveIntegral);
     }
-    cout<<"Final light-curve integration: "<<m_LightCurveFunction.Integrate()<<endl;
-    
+    LightCurveIntegral = m_LightCurveFunction.Integrate();
+    cout<<"Final light-curve integration: "<<LightCurveIntegral<<endl;
+    if (std::isfinite(LightCurveIntegral) == false) {
+      mout<<"  ***  ERROR  ***   "<<m_Name<<": The light curve integral is not finite:" <<LightCurveIntegral<<endl;
+      return false;
+    }
+
     if (m_NextEmission < m_LightCurveFunction.GetXMin()) {
       m_NextEmission = m_LightCurveFunction.GetXMin();
     }
@@ -2418,6 +2528,7 @@ bool MCSource::CalculateNextEmission(double Time, double /*Scale*/)
     if (m_LightCurveType == c_LightCurveFile) {
       double dIntegral = CLHEP::RandExponential::shoot(1.0/GetFlux());
       //cout<<"dIntegral: "<<dIntegral<<endl;
+      //cout<<m_NextEmission<<endl;
       NextEmission = m_LightCurveFunction.FindX(m_NextEmission, dIntegral, m_IsRepeatingLightCurve);
       if (m_IsRepeatingLightCurve == false && NextEmission >= m_LightCurveFunction.GetXMax()) {
         m_IsActive = false;
@@ -2809,6 +2920,7 @@ bool MCSource::GeneratePosition(G4GeneralParticleSource* Gun)
         m_BeamType == c_FarFieldDisk ||
         m_BeamType == c_FarFieldAssymetricGaussian ||
         m_BeamType == c_FarFieldFileZenithDependent ||
+	m_BeamType == c_FarFieldEarthOccultation ||
         m_BeamType == c_FarFieldNormalizedEnergyBeamFluxFunction ||
         m_BeamType == c_FarFieldIsotropic) {
       if (m_BeamType == c_FarFieldPoint || m_BeamType == c_FarFieldNormalizedEnergyBeamFluxFunction) {
@@ -2985,6 +3097,38 @@ bool MCSource::GeneratePosition(G4GeneralParticleSource* Gun)
         } else {
           mout<<m_Name<<": Unknown start area type for position generation"<<endl;
         }
+      
+      
+      } else if (m_BeamType == c_FarFieldEarthOccultation) {
+        // Determine a random position on the sphere between 
+        // theta min and theta max that are computed each time
+	      // according to the pointing of the spacecraft in order
+	      //to take into account the Earth Occultation
+        
+        if (m_StartAreaType == c_StartAreaSphere) {
+	
+	       //determine the theta range 
+	
+	      //get the Earth aspect information from the orientation file
+            const MCOrientation& Sky = MCRunManager::GetMCRunManager()->GetCurrentRun().GetSkyOrientationReference();
+            double Alt,Lat,Lon=0;
+            if (Sky.GetEarthCoordinate(m_NextEmission,  Alt,  Lat, Lon)==true){
+     
+             
+           }
+          else{
+                merr<<"the time is not in the ori time range : "<<m_NextEmission<< " ["<<Sky.GetStartTime()<<","<< Sky.GetStopTime() <<"]"<<endl;
+           }
+	   
+	    //sort theta and phi 
+        
+            Theta = acos(cos(0*deg) - CLHEP::RandFlat::shoot(1)*(cos(0*deg) - cos(5*deg)));
+            Phi = CLHEP::RandFlat::shoot(1)*360*deg;
+              
+        
+        } else {
+          mout<<m_Name<<": Earth Occultation only handle StartAreaSphere for position generation"<<endl;
+        }
       }
       
       // Generate start direction:

From dee391d2a32168686bd045e5c7980e0adae7fda8 Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Thu, 3 Oct 2024 20:00:29 +0200
Subject: [PATCH 081/192] Update MCOrientation.hh

---
 src/cosima/inc/MCOrientation.hh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/cosima/inc/MCOrientation.hh b/src/cosima/inc/MCOrientation.hh
index 380ebda70..41084f688 100644
--- a/src/cosima/inc/MCOrientation.hh
+++ b/src/cosima/inc/MCOrientation.hh
@@ -42,7 +42,7 @@ using namespace std;
 
 //! This class represents all orientations in Cosima
 enum class MCOrientationCoordinateSystem : int { 
-  c_Local = 0, c_Galactic = 1 
+  c_Local = 0, c_Galactic = 1
 };
 
 //! I/O for MCOrientationCoordinateSystem

From 772dfd329bbd06378a3f2898a3be341eef9cb9b0 Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Thu, 3 Oct 2024 20:02:46 +0200
Subject: [PATCH 082/192] Update MCOrientation.cc

---
 src/cosima/src/MCOrientation.cc | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/src/cosima/src/MCOrientation.cc b/src/cosima/src/MCOrientation.cc
index d3a03f8de..ff4982b73 100644
--- a/src/cosima/src/MCOrientation.cc
+++ b/src/cosima/src/MCOrientation.cc
@@ -236,12 +236,10 @@ bool MCOrientation::Parse(const MTokenizer& Tokenizer)
 
     
   } else if (Tokenizer.IsTokenAt(3, "File") == true) {
-    if (Tokenizer.GetNTokens() != 6 ) {
+    if (Tokenizer.GetNTokens() != 6) {
       mlog<<"   ***  Error  ***  You need exactly 6 tokens to for an orientation read from file"<<endl;
       return false;
-    }
-    
-    
+    }  
     if (Tokenizer.IsTokenAt(4, "Loop") == true) {
       m_IsLooping = true;
     } else if (Tokenizer.IsTokenAt(4, "NoLoop") == true) {
@@ -251,7 +249,6 @@ bool MCOrientation::Parse(const MTokenizer& Tokenizer)
       return false;        
     }
     
-    
     if (Read(Tokenizer.GetTokenAtAsString(5)) == false) {
       mlog<<"   ***  Error  ***  Unable to read orientation file correctly: \""<<Tokenizer.GetTokenAtAsString(5)<<"\""<<endl;
       return false; 
@@ -401,7 +398,6 @@ bool MCOrientation::Read(MString FileName)
   return true;
 }
 
-
 ////////////////////////////////////////////////////////////////////////////////
 
 

From 9b05f41ef7f741af1c2760ff395a798ab220941f Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Thu, 3 Oct 2024 20:20:51 +0200
Subject: [PATCH 083/192] Create EarthOccultation.source

---
 .../EarthOccultation/EarthOccultation.source  | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 resource/examples/advanced/EarthOccultation/EarthOccultation.source

diff --git a/resource/examples/advanced/EarthOccultation/EarthOccultation.source b/resource/examples/advanced/EarthOccultation/EarthOccultation.source
new file mode 100644
index 000000000..3851557e6
--- /dev/null
+++ b/resource/examples/advanced/EarthOccultation/EarthOccultation.source
@@ -0,0 +1,34 @@
+Geometry $(MEGALIB)/resource/examples/geomega/mpesatellitebaseline/SatelliteWithACS.geo.setup
+StoreSimulationInfo  init-only 
+PhysicsListEM LivermorePol
+
+
+Run SpaceSim
+SpaceSim.FileName  crab
+SpaceSim.Time  1843467255.0
+SpaceSim.OrientationSky Galactic File NoLoop Equatorial_orbit_530km_Galactic_zenith.ori
+
+SpaceSim.Source crab
+crab.ParticleType	       1
+crab.Beam                       FarFieldPointSource 0 0
+crab.Orientation                Galactic Fixed -5.78 184.56
+crab.Spectrum                   File crab_spec.dat
+crab.Flux                       0.048977e-3
+
+# False means you want to reject all event > thetamax i.e rejecting all events coming from the Earth
+# This is what you want to use for a source like the crab
+
+crab.EarthOccultation False 
+
+# You can specify the maximum angle between the direction of the particle and the Earth zenith vector 
+# This is what you want to use for a source like the crab and a specic angle between the particle direction
+# if Thetamax is not specify, cosima will compute it from the Orientation file and the corresponding altitude
+# and the Earth zenith vector 
+
+#crab.EarthOccultation False 20
+
+# True means you want to reject all event <= thetamax i.e rejecting all events that are not coming from the Earth
+# This is what you want to use for a source coming from the Earth like albedo
+
+#crab.EarthOccultation True 
+

From de2e2d9c9b313642a53aadf5177af13cad0fd744 Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Thu, 3 Oct 2024 20:28:05 +0200
Subject: [PATCH 084/192] Create Equatorial_orbit_530km_Galactic_zenith.ori

---
 ...Equatorial_orbit_530km_Galactic_zenith.ori | 10002 ++++++++++++++++
 1 file changed, 10002 insertions(+)
 create mode 100644 resource/examples/advanced/EarthOccultation/Equatorial_orbit_530km_Galactic_zenith.ori

diff --git a/resource/examples/advanced/EarthOccultation/Equatorial_orbit_530km_Galactic_zenith.ori b/resource/examples/advanced/EarthOccultation/Equatorial_orbit_530km_Galactic_zenith.ori
new file mode 100644
index 000000000..cd1b64bb9
--- /dev/null
+++ b/resource/examples/advanced/EarthOccultation/Equatorial_orbit_530km_Galactic_zenith.ori
@@ -0,0 +1,10002 @@
+# time lat_y (galactic) lon_y (galactic) lat_z (galactic) lon_z (galactic) Eart_alt (km) Earth_lat (galactic) Eart_lon (galactic)
+# see cosima documentation for the orientation file. This is similar to OrientationsGalactic but with Earth coord in addition and in the galactic coord system
+Type OrientationsGalactic
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+OG 1835637015.0 86.13768003799427 185.9156736281111 -3.86231996200573 185.9156736281111 527.7860971557658 -14.813834505326772 205.14226623840926
+OG 1835637030.0 86.8358113907319 186.338071193617 -3.164188609268108 186.338071193617 527.7315705171308 -14.038508648479176 205.5695607357679
+OG 1835637045.0 87.53650509306361 186.75589319402206 -2.4634949069363907 186.75589319402206 527.6767833117731 -13.26244450794904 205.99396818391304
+OG 1835637060.0 88.23969579751206 187.1692575317211 -1.7603042024879376 187.1692575317211 527.6217504407849 -12.485689198137365 206.41566950184924
+OG 1835637075.0 88.9453192758217 187.5782809570337 -1.054680724178297 187.5782809570337 527.5664868720751 -11.70828878166179 206.8348419351509
+OG 1835637090.0 89.65331577662424 187.98307561203728 -0.346684223375759 187.98307561203728 527.5110076362977 -10.930288405936333 207.25165928052687
+OG 1835637105.0 89.63637333222681 8.38375248673765 0.3636266677731993 188.38375248673765 527.4553278227642 -10.15173231957611 207.66629216582183
+OG 1835637120.0 88.92380668287791 8.780422571147932 1.076193317122101 188.78042257114794 527.3994625753394 -9.372663925144893 208.07890830129998
+OG 1835637135.0 88.20904189065764 9.173195841402078 1.7909581093423592 189.17319584140205 527.3434270883231 -8.593125833204157 208.48967272227645
+OG 1835637150.0 87.49213250362305 9.562178218133358 2.507867496376947 189.56217821813334 527.2872366023164 -7.813159882573092 208.8987480422398
+OG 1835637165.0 86.77313105301327 9.947474608103205 3.226868946986728 189.94747460810322 527.2309064000776 -7.032807253254633 209.30629465031248
+OG 1835637180.0 86.05209007006744 10.329189918065829 3.9479099299325657 190.32918991806582 527.1744518023653 -6.252108546123218 209.7124709209586
+OG 1835637195.0 85.32906120602125 10.70742817422977 4.670938793978747 190.7074281742298 527.1178881637711 -5.471103847308884 210.11743342663
+OG 1835637210.0 84.60409259209675 11.08228988057818 5.395907407903259 191.08228988057817 527.0612308685437 -4.689832795284595 210.52133714440137
+OG 1835637225.0 83.87723147951249 11.453874660550369 6.122768520487516 191.45387466055035 527.0044953264047 -3.9083346342996834 210.92433566517647
+OG 1835637240.0 83.14852511948708 11.822282137578473 6.851474880512927 191.82228213757844 526.9476969683574 -3.1266482708317844 211.3265813977475
+OG 1835637255.0 82.4180199973901 12.187611215773357 7.581980002609897 192.18761121577336 526.8908512424898 -2.344812338874474 211.72822576530615
+OG 1835637270.0 81.68575953519522 12.549957921954043 8.314240464804792 192.54995792195405 526.8339736097732 -1.5628652798211875 212.12941939202304

From 105dc7c2ade7346e1279a76deeda299fb6d1495c Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Thu, 3 Oct 2024 20:28:48 +0200
Subject: [PATCH 085/192] Create crab_spec.dat

---
 .../advanced/EarthOccultation/crab_spec.dat   | 56 +++++++++++++++++++
 1 file changed, 56 insertions(+)
 create mode 100644 resource/examples/advanced/EarthOccultation/crab_spec.dat

diff --git a/resource/examples/advanced/EarthOccultation/crab_spec.dat b/resource/examples/advanced/EarthOccultation/crab_spec.dat
new file mode 100644
index 000000000..26d93adf1
--- /dev/null
+++ b/resource/examples/advanced/EarthOccultation/crab_spec.dat
@@ -0,0 +1,56 @@
+#Format: <DP> <Energy in keV> <Spectrum in ph cm^-2 s^-1 keV^-1>
+#flux (100.0 - 10000.0 keV): 0.048977 ph/cm^2/s
+
+
+IP LINLIN
+
+DP	1.00000e+02	6.22916e-04
+DP	1.09854e+02	5.07161e-04
+DP	1.20679e+02	4.12162e-04
+DP	1.32571e+02	3.34285e-04
+DP	1.45635e+02	2.70525e-04
+DP	1.59986e+02	2.18397e-04
+DP	1.75751e+02	1.75844e-04
+DP	1.93070e+02	1.41395e-04
+DP	2.12095e+02	1.13695e-04
+DP	2.32995e+02	9.14211e-05
+DP	2.55955e+02	7.35111e-05
+DP	2.81177e+02	5.91097e-05
+DP	3.08884e+02	4.75297e-05
+DP	3.39322e+02	3.82183e-05
+DP	3.72759e+02	3.07310e-05
+DP	4.09492e+02	2.47106e-05
+DP	4.49843e+02	1.98696e-05
+DP	4.94171e+02	1.59770e-05
+DP	5.42868e+02	1.28470e-05
+DP	5.96362e+02	1.03302e-05
+DP	6.55129e+02	8.30642e-06
+DP	7.19686e+02	6.67913e-06
+DP	7.90604e+02	5.37064e-06
+DP	8.68511e+02	4.31849e-06
+DP	9.54095e+02	3.47247e-06
+DP	1.04811e+03	2.79219e-06
+DP	1.15140e+03	2.24518e-06
+DP	1.26486e+03	1.80533e-06
+DP	1.38950e+03	1.45165e-06
+DP	1.52642e+03	1.16726e-06
+DP	1.67683e+03	9.38588e-07
+DP	1.84207e+03	7.54712e-07
+DP	2.02359e+03	6.06858e-07
+DP	2.22300e+03	4.87970e-07
+DP	2.44205e+03	3.92373e-07
+DP	2.68270e+03	3.15505e-07
+DP	2.94705e+03	2.53695e-07
+DP	3.23746e+03	2.03994e-07
+DP	3.55648e+03	1.64030e-07
+DP	3.90694e+03	1.31896e-07
+DP	4.29193e+03	1.06056e-07
+DP	4.71487e+03	8.52791e-08
+DP	5.17947e+03	6.85723e-08
+DP	5.68987e+03	5.51385e-08
+DP	6.25055e+03	4.43364e-08
+DP	6.86649e+03	3.56506e-08
+DP	7.54312e+03	2.86664e-08
+DP	8.28643e+03	2.30504e-08
+DP	9.10298e+03	1.85347e-08
+DP	1.00000e+04	1.49036e-08

From 3b5eaa2730bd9aca9a6ca482e54bdb7ddb06f8a1 Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Thu, 3 Oct 2024 20:29:42 +0200
Subject: [PATCH 086/192] Create README.md

---
 resource/examples/advanced/EarthOccultation/README.md | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 resource/examples/advanced/EarthOccultation/README.md

diff --git a/resource/examples/advanced/EarthOccultation/README.md b/resource/examples/advanced/EarthOccultation/README.md
new file mode 100644
index 000000000..065189db0
--- /dev/null
+++ b/resource/examples/advanced/EarthOccultation/README.md
@@ -0,0 +1 @@
+Will put future DC3 github page here 

From 710c75920acb8e699b4952302e8d3fee37f57c96 Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Thu, 3 Oct 2024 20:36:43 +0200
Subject: [PATCH 087/192] correct typo

---
 .../advanced/EarthOccultation/EarthOccultation.source         | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/resource/examples/advanced/EarthOccultation/EarthOccultation.source b/resource/examples/advanced/EarthOccultation/EarthOccultation.source
index 3851557e6..ac4f1eb8f 100644
--- a/resource/examples/advanced/EarthOccultation/EarthOccultation.source
+++ b/resource/examples/advanced/EarthOccultation/EarthOccultation.source
@@ -21,9 +21,9 @@ crab.Flux                       0.048977e-3
 crab.EarthOccultation False 
 
 # You can specify the maximum angle between the direction of the particle and the Earth zenith vector 
-# This is what you want to use for a source like the crab and a specic angle between the particle direction
+# This is what you want to use for a source like the crab and a specic angle between the particle direction and the Earth zenith vector 
 # if Thetamax is not specify, cosima will compute it from the Orientation file and the corresponding altitude
-# and the Earth zenith vector 
+
 
 #crab.EarthOccultation False 20
 

From 7023b21ec83939414fe793d70ba82a4b35979641 Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Thu, 3 Oct 2024 20:38:44 +0200
Subject: [PATCH 088/192] correct typo

---
 src/cosima/src/MCOrientation.cc | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/cosima/src/MCOrientation.cc b/src/cosima/src/MCOrientation.cc
index ff4982b73..5a30f32ba 100644
--- a/src/cosima/src/MCOrientation.cc
+++ b/src/cosima/src/MCOrientation.cc
@@ -239,7 +239,7 @@ bool MCOrientation::Parse(const MTokenizer& Tokenizer)
     if (Tokenizer.GetNTokens() != 6) {
       mlog<<"   ***  Error  ***  You need exactly 6 tokens to for an orientation read from file"<<endl;
       return false;
-    }  
+    }
     if (Tokenizer.IsTokenAt(4, "Loop") == true) {
       m_IsLooping = true;
     } else if (Tokenizer.IsTokenAt(4, "NoLoop") == true) {
@@ -254,8 +254,6 @@ bool MCOrientation::Parse(const MTokenizer& Tokenizer)
       return false; 
      }
     
-    
-    
     if (m_Times.size() > 0) {
       m_IsOriented = true;
     } else {
@@ -394,10 +392,10 @@ bool MCOrientation::Read(MString FileName)
   }
  
  
- 
   return true;
 }
 
+
 ////////////////////////////////////////////////////////////////////////////////
 
 

From b8e09a850f394e1e99709dafef826b683bec49d8 Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Thu, 3 Oct 2024 20:39:45 +0200
Subject: [PATCH 089/192] correct typo

---
 src/cosima/src/MCOrientation.cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/cosima/src/MCOrientation.cc b/src/cosima/src/MCOrientation.cc
index 5a30f32ba..61a917b99 100644
--- a/src/cosima/src/MCOrientation.cc
+++ b/src/cosima/src/MCOrientation.cc
@@ -252,7 +252,7 @@ bool MCOrientation::Parse(const MTokenizer& Tokenizer)
     if (Read(Tokenizer.GetTokenAtAsString(5)) == false) {
       mlog<<"   ***  Error  ***  Unable to read orientation file correctly: \""<<Tokenizer.GetTokenAtAsString(5)<<"\""<<endl;
       return false; 
-     }
+    }
     
     if (m_Times.size() > 0) {
       m_IsOriented = true;

From b965389bc85363e3b7fa5d404dc2bd185ca858c0 Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Thu, 3 Oct 2024 20:40:58 +0200
Subject: [PATCH 090/192] correct typo

---
 src/cosima/src/MCParameterFile.cc | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/cosima/src/MCParameterFile.cc b/src/cosima/src/MCParameterFile.cc
index c4780c053..02e9f5306 100644
--- a/src/cosima/src/MCParameterFile.cc
+++ b/src/cosima/src/MCParameterFile.cc
@@ -865,14 +865,14 @@ bool MCParameterFile::Parse()
           if (O.Parse(*T) == false) {
             Typo(i, "Cannot parse token \"OrientationSky\" correctly");
             return false;
-          }
+          }	
           // The sky can only be rotated if in Galactic coordinates
           if (O.GetCoordinateSystem() != MCOrientationCoordinateSystem::c_Galactic && O.IsOriented() == true) {
             Typo(i, "\"OrientationSky\" can only have an orientation in Galactic coordinates!");
             return false;            
           }
           Run->SetSkyOrientation(O);
-
+	
         } else {
           Typo(i, "Cannot parse token \"OrientationSky\" correctly: Number of tokens is not correct!");
           return false;

From af1fcf79c7561c0a2239bf0b93d4eeccf062c7c2 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Tue, 8 Oct 2024 09:13:38 -0700
Subject: [PATCH 091/192] CHG: Frtalon regression

---
 src/fretalon/framework/src/MGUIMainFretalon.cxx | 1 +
 src/fretalon/framework/src/MModule.cxx          | 1 +
 2 files changed, 2 insertions(+)

diff --git a/src/fretalon/framework/src/MGUIMainFretalon.cxx b/src/fretalon/framework/src/MGUIMainFretalon.cxx
index e1cc62710..db7401d98 100644
--- a/src/fretalon/framework/src/MGUIMainFretalon.cxx
+++ b/src/fretalon/framework/src/MGUIMainFretalon.cxx
@@ -32,6 +32,7 @@
 #include <TGFrame.h>
 #include <TGClient.h>
 #include <TGResourcePool.h>
+#include <TSystem.h>
 
 // MEGAlib libs:
 #include "MStreams.h"
diff --git a/src/fretalon/framework/src/MModule.cxx b/src/fretalon/framework/src/MModule.cxx
index b6d9f3c48..d20bc31dd 100644
--- a/src/fretalon/framework/src/MModule.cxx
+++ b/src/fretalon/framework/src/MModule.cxx
@@ -29,6 +29,7 @@
 // Standard libs:
 
 // ROOT libs:
+#include "TSystem.h"
 
 // MEGAlib libs:
 #include "MModuleReadOutAssemblyQueues.h"

From 7586df2fc614509eebbe210a733606ebdb5e094d Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Tue, 8 Oct 2024 23:08:24 -0700
Subject: [PATCH 092/192] CHG: Display improvements - skip similar results

---
 resource/examples/benchmarks/Benchmark.py     | 34 ++++++++++++--
 .../examples/benchmarks/References/galatea.bm | 47 +++++++++++++++++++
 2 files changed, 78 insertions(+), 3 deletions(-)
 create mode 100644 resource/examples/benchmarks/References/galatea.bm

diff --git a/resource/examples/benchmarks/Benchmark.py b/resource/examples/benchmarks/Benchmark.py
index f25f0d198..015a71789 100644
--- a/resource/examples/benchmarks/Benchmark.py
+++ b/resource/examples/benchmarks/Benchmark.py
@@ -185,7 +185,7 @@
 
 
 # Sorting:
-IsGood.sort(key=dict(zip(IsGood, RunMulti)).get)
+#IsGood.sort(key=dict(zip(IsGood, RunMulti)).get)
 
 IsGood = [x for _,x in sorted(zip(RunMulti, IsGood))]
 Reference = [x for _,x in sorted(zip(RunMulti, Reference))]
@@ -197,13 +197,41 @@
 RunSingle = [x for _,x in sorted(zip(RunMulti, RunSingle))]
 RunMulti = [x for _,x in sorted(zip(RunMulti, RunMulti))]
 
-# If we have more than (RefernceCount+1) delete the weakest referneces
+# If we have more than (RefernceCount+1) first cull results which are within 5% of an higher value
+HighestRef=-1
+for i in range(len(Reference) - 1, -1, -1):
+  if HighestRef < 0:
+    if IsGood[i] == True:
+      HighestRef = i
+  else:
+    if Reference[0] == "*** this ***":
+      HighestRef = i
+      continue
+
+    if RunMulti[i] > 0.95*RunMulti[HighestRef]:
+      IsGood[i] = False
+      print("Deleting {}".format(CPUNames[i]))
+    else: 
+      HighestRef = i
+
+Reference = [a for a, keep in zip(Reference, IsGood) if keep]
+HostNames = [a for a, keep in zip(HostNames, IsGood) if keep]
+CPUSockets = [a for a, keep in zip(CPUSockets, IsGood) if keep]
+CPUNames = [a for a, keep in zip(CPUNames, IsGood) if keep]
+OSNames = [a for a, keep in zip(OSNames, IsGood) if keep]
+OSVersions = [a for a, keep in zip(OSVersions, IsGood) if keep]
+RunSingle = [a for a, keep in zip(RunSingle, IsGood) if keep]
+RunMulti = [a for a, keep in zip(RunMulti, IsGood) if keep]
+IsGood = [a for a, keep in zip(IsGood, IsGood) if keep]
+
+
+# If we have more than (RefernceCount+1) delete the weakest references
 while len(Reference) > ReferenceCount+1:
   # Find which one to delete
   ToDelete = 0
   if Reference[0] == "*** this ***":
     ToDelete = 1
-  print("Deleting %: %".format(ToDelete, CPUNames[ToDelete]))
+  print("Deleting {}".format(CPUNames[ToDelete]))
   del IsGood[ToDelete]
   del Reference[ToDelete]
   del HostNames[ToDelete]
diff --git a/resource/examples/benchmarks/References/galatea.bm b/resource/examples/benchmarks/References/galatea.bm
new file mode 100644
index 000000000..86d571b97
--- /dev/null
+++ b/resource/examples/benchmarks/References/galatea.bm
@@ -0,0 +1,47 @@
+# Benchmark summary file
+ 
+HostName:                                  galatea
+ 
+OSFlavour:                                 ubuntu
+OSVersion:                                 24.04
+Kernel:                                    6.8.0-45-generic
+ 
+CPUModel:                                  AMD Ryzen 9 9950X 16-Core Processor
+CPUName:                                   Ryzen 9 9950X
+CPUSockets:                                1
+CPUCoresPerSocket:                         16
+CPUThreadsPerCore:                         2
+Cores:                                     16
+Threads:                                   32
+ 
+ROOTVersion:                               6.28/12
+Geant4Version:                             10.2.3
+ 
+MEGAlibVersion:                            4.00.00
+MEGAlibGitHash:                            d9afacb2657c07307742f51f9abdd54261709acc 2024-07-23
+MEGAlibOptimization:                       
+ 
+# Cosima
+DurationCosimaSingle:                      12.482
+EventsPerSecondCosimaSingle:               8011.536
+DurationCosimaMultiple:                    20.526
+EventsPerSecondCosimaMultiple:             155899.834
+ 
+# Revan
+DurationRevanSingle:                       5.411
+EventsPerSecondRevanSingle:                18480.872
+DurationRevanMultiple:                     5.094
+EventsPerSecondRevanMultiple:              628190.027
+ 
+# ResponseCreator
+DurationResponseCreatorSingle:             6.013
+EventsPerSecondResponseCreatorSingle:      16630.633
+DurationResponseCreatorMultiple:           12.838
+EventsPerSecondResponseCreatorMultiple:    249260.009
+ 
+# MimrecImaging
+DurationMimrecImagingSingle:               24.462
+EventsPerSecondMimrecImagingSingle:        4087.973
+DurationMimrecImagingMultiple:             4.330
+EventsPerSecondMimrecImagingMultiple:      23094.688
+ 

From c17a9a8fdebccccb0853f3b3e066f324c11e56d3 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Tue, 8 Oct 2024 23:35:31 -0700
Subject: [PATCH 093/192] ADD: Despina benchmark

---
 .../examples/benchmarks/References/despina.bm | 47 +++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 resource/examples/benchmarks/References/despina.bm

diff --git a/resource/examples/benchmarks/References/despina.bm b/resource/examples/benchmarks/References/despina.bm
new file mode 100644
index 000000000..8b6b12b99
--- /dev/null
+++ b/resource/examples/benchmarks/References/despina.bm
@@ -0,0 +1,47 @@
+# Benchmark summary file
+ 
+HostName:                                  despina
+ 
+OSFlavour:                                 ubuntu
+OSVersion:                                 20.04
+Kernel:                                    5.13.0-51-generic
+ 
+CPUModel:                                  AMD Ryzen Threadripper 3960X 24-Core Processor
+CPUName:                                   Ryzen Threadripper 3960X
+CPUSockets:                                1
+CPUCoresPerSocket:                         24
+CPUThreadsPerCore:                         2
+Cores:                                     24
+Threads:                                   48
+ 
+ROOTVersion:                               6.24/06
+Geant4Version:                             10.2.3
+ 
+MEGAlibVersion:                            3.99.01
+MEGAlibGitHash:                            b8755b560e62eeadc96bcb25b267d2e4b4bcdc90 2022-06-15
+MEGAlibOptimization:                       -O3 -mtune=native -fno-strict-aliasing -DNDEBUG
+ 
+# Cosima
+DurationCosimaSingle:                      24.217
+EventsPerSecondCosimaSingle:               4129.330
+DurationCosimaMultiple:                    39.557
+EventsPerSecondCosimaMultiple:             121343.883
+ 
+# Revan
+DurationRevanSingle:                       5.361
+EventsPerSecondRevanSingle:                18653.236
+DurationRevanMultiple:                     8.832
+EventsPerSecondRevanMultiple:              543478.260
+ 
+# ResponseCreator
+DurationResponseCreatorSingle:             14.362
+EventsPerSecondResponseCreatorSingle:      6962.818
+DurationResponseCreatorMultiple:           25.726
+EventsPerSecondResponseCreatorMultiple:    186581.668
+ 
+# MimrecImaging
+DurationMimrecImagingSingle:               .417
+EventsPerSecondMimrecImagingSingle:        239808.153
+DurationMimrecImagingMultiple:             .410
+EventsPerSecondMimrecImagingMultiple:      243902.439
+ 

From 2f22b7933f8d49bb1d416ce0c648c6050b56e0e2 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Fri, 18 Oct 2024 09:08:04 -0700
Subject: [PATCH 094/192] CHG: When the complain about too many sim rounds
 happens

---
 src/geomega/src/MDShape.cxx | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/geomega/src/MDShape.cxx b/src/geomega/src/MDShape.cxx
index cd9568513..94676d0fd 100644
--- a/src/geomega/src/MDShape.cxx
+++ b/src/geomega/src/MDShape.cxx
@@ -227,13 +227,14 @@ MVector MDShape::GetRandomPositionInside()
     R.SetZ((2.0*gRandom->Rndm()-1.0)*BBox->GetDZ() + BBox->GetOrigin()[2]);
 
     Counter++;
-    if (Counter > 1 && Counter%100 == 0) {
-      mout<<"   ***  Warning  ***  in shape "<<m_Type<<endl;
-      mout<<"GetRandomPositionInside() required more than "<<Counter<<" trials."<<endl;
-      mout<<"You might want to ask the developers to write an optimized version of GetRandomPositionInside() for type "<<m_Type<<endl;
-    }
   } while (IsInside(R) == false);
 
+  if (Counter > 100) {
+    mout<<"   ***  Warning  ***  in shape "<<m_Name<<endl;
+    mout<<"GetRandomPositionInside() required "<<Counter<<" trials."<<endl;
+    mout<<"You might want to ask the developers to write an optimized version of GetRandomPositionInside() for type "<<m_Type<<endl;
+  }
+
   return R;
 }
 

From f2f8fda0155622115587d7470b6ba325ec71c138 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Fri, 18 Oct 2024 09:09:31 -0700
Subject: [PATCH 095/192] ADD: Feature which shows in which volume the
 activation happened

---
 src/sivan/inc/MGUISivanMain.h     |  1 +
 src/sivan/inc/MInterfaceSivan.h   |  3 ++
 src/sivan/src/MGUISivanMain.cxx   | 20 ++++--------
 src/sivan/src/MInterfaceSivan.cxx | 52 ++++++++++++++++++++++++++++++-
 4 files changed, 61 insertions(+), 15 deletions(-)

diff --git a/src/sivan/inc/MGUISivanMain.h b/src/sivan/inc/MGUISivanMain.h
index ec58bac04..4265c9562 100644
--- a/src/sivan/inc/MGUISivanMain.h
+++ b/src/sivan/inc/MGUISivanMain.h
@@ -99,6 +99,7 @@ class MGUISivanMain : public MGUIMain
                    c_NInteractions,
                    c_SecondaryGenerationPattern,
                    c_EnergyLossByMaterial,
+                   c_OriginVolumesOfActivation,
                    c_Test };
 
 
diff --git a/src/sivan/inc/MInterfaceSivan.h b/src/sivan/inc/MInterfaceSivan.h
index f9881177f..b6d0dfa73 100644
--- a/src/sivan/inc/MInterfaceSivan.h
+++ b/src/sivan/inc/MInterfaceSivan.h
@@ -103,6 +103,9 @@ class MInterfaceSivan : public MInterface
   
   void SecondaryGenerationPattern();
 
+  //! List the top volumes, where activation is originating
+  void OriginVolumesOfActivation();
+
   void TriggerPatternEfficiency();
   void BeamMonitorEfficiency();
 
diff --git a/src/sivan/src/MGUISivanMain.cxx b/src/sivan/src/MGUISivanMain.cxx
index e8d42d906..8f6458412 100644
--- a/src/sivan/src/MGUISivanMain.cxx
+++ b/src/sivan/src/MGUISivanMain.cxx
@@ -112,23 +112,11 @@ void MGUISivanMain::Create()
   m_MenuAnalysis->AddEntry("Newly generated isotopes distribution", c_IsotopeGeneration);
   m_MenuAnalysis->AddEntry("Energy distribution by decayed isotope", c_EnergyPerNucleus);
   m_MenuAnalysis->AddEntry("Activation per incidence energy", c_ActivationPerIncidenceEnergy);
+  m_MenuAnalysis->AddEntry("Origin volume of activation", c_OriginVolumesOfActivation);
   // m_MenuAnalysis->AddEntry("Charge sharing between voxels...", c_ChargeSharing);
   m_MenuAnalysis->AddSeparator();
   m_MenuAnalysis->AddEntry("Doppler broadening", c_DopplerARM);
 
-
-//   m_MenuAnalysis->AddEntry("Event selections", M_SV_EVENTSELECTION);
-//   m_MenuAnalysis->AddSeparator();
-//   m_MenuAnalysis->AddEntry("Options", M_SV_OPTIONS);
-//   m_MenuAnalysis->AddSeparator();
-//   m_MenuAnalysis->AddEntry("Start creating tra-file", M_SV_START);
-//   m_MenuAnalysis->AddEntry("View hits", M_SV_VIEWHITS);
-//   m_MenuAnalysis->AddEntry("Energy loss", M_SV_ENERGYLOSS);
-//   m_MenuAnalysis->AddEntry("Crystals with certain deposited energies", M_SV_ENERGYCRYSTAL);
-//   m_MenuAnalysis->AddEntry("Distance and angular error of multiple comptons", M_SV_MULTIPLECOMPTONS);
-//   m_MenuAnalysis->AddEntry("Create Response", M_SV_CREATERESPONSE);
-//   m_MenuAnalysis->AddEntry("Doppler Broadening", M_SV_DOPPLER);
-
   // m_MenuAnalysis->AddSeparator();
   // m_MenuAnalysis->AddEntry("Some testing...", c_Test);
   m_MenuAnalysis->Associate(this);
@@ -327,7 +315,11 @@ bool MGUISivanMain::ProcessMessage(long Message, long Parameter1,
       case c_ActivationPerIncidenceEnergy:
         m_Interface->ActivationPerIncidenceEnergy();
         break;
-      
+
+      case c_OriginVolumesOfActivation:
+        m_Interface->OriginVolumesOfActivation();
+        break;
+
       default:
         break;
       }
diff --git a/src/sivan/src/MInterfaceSivan.cxx b/src/sivan/src/MInterfaceSivan.cxx
index afadff70f..0c7c479e2 100644
--- a/src/sivan/src/MInterfaceSivan.cxx
+++ b/src/sivan/src/MInterfaceSivan.cxx
@@ -6282,7 +6282,7 @@ void MInterfaceSivan::IsotopeGeneration()
   
   return;
 }
-  
+
 
 ////////////////////////////////////////////////////////////////////////////////
 
@@ -6411,5 +6411,55 @@ void MInterfaceSivan::ActivationPerIncidenceEnergy()
 }
 
 
+////////////////////////////////////////////////////////////////////////////////
+
+
+void MInterfaceSivan::OriginVolumesOfActivation()
+{
+  // List the top volumes, where activation is originating
+
+  map<MString, unsigned int> m_CountsPerVolume;
+  double MinEnergy = 0;
+  double MaxEnergy = 2000;
+
+
+  // Open the simulation file:
+  MFileEventsSim EventFile(m_Geometry);
+  if (EventFile.Open(m_Data->GetCurrentFileName()) == false) {
+    mgui<<"Unable to open file"<<error;
+    return;
+  }
+  EventFile.ShowProgress();
+
+  MSimEvent* Event = nullptr;
+  while ((Event = EventFile.GetNextEvent()) != 0) {
+    if (Event->GetNIAs() > 0) {
+      if (Event->GetIAAt(0)->GetSecondaryParticleID() > 1000) {
+        cout<<Event->GetIAAt(0)->GetSecondaryParticleID()<<":"<<Event->GetVeto()<<":"<<Event->GetNClusters()<<endl;
+        if (Event->GetVeto() == false) {
+          if (Event->GetREnergy() >= MinEnergy && Event->GetREnergy() <= MaxEnergy) {
+            MDVolumeSequence S = m_Geometry->GetVolumeSequence(Event->GetIAAt(0)->GetPosition());
+            m_CountsPerVolume[S.GetDeepestVolume()->GetName()] += 1;
+          }
+        }
+      }
+    }
+    delete Event;
+  }
+
+  // Create a vector to hold the map elements to allow sorting
+  vector<pair<string, int>> V(m_CountsPerVolume.begin(), m_CountsPerVolume.end());
+
+  sort(V.begin(), V.end(), [](const auto& a, const auto& b) {
+    return a.second > b.second; // Sort in descending order
+  });
+
+  for (const auto& Pair: V) {
+    cout<<Pair.first<< ": "<<Pair.second<<endl;
+  }
+
+  return;
+}
+
 // MInterfaceSivan: the end...
 ////////////////////////////////////////////////////////////////////////////////

From 3325d650e8250e9b24b89f796f31fe8d378dbc00 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Fri, 18 Oct 2024 10:59:33 -0700
Subject: [PATCH 096/192] BUG: Fixed random number seeding regression

---
 src/cosima/src/MCMain.cc | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/src/cosima/src/MCMain.cc b/src/cosima/src/MCMain.cc
index 57292c1ba..4b82a54d2 100644
--- a/src/cosima/src/MCMain.cc
+++ b/src/cosima/src/MCMain.cc
@@ -389,7 +389,7 @@ unsigned int MCMain::ParseCommandLine(int argc, char** argv)
     mout<<"--> Assuming we are in test condition..."<<endl;
     mout<<"--> Using default parameter file from "<<m_ParameterFileName
         <<"    and enabling debugging"<<endl;
-    m_Seed = 0;
+    m_Seed = 1;
   } 
 
   if (m_RunParameters.Open(m_ParameterFileName) == false) {
@@ -403,12 +403,9 @@ unsigned int MCMain::ParseCommandLine(int argc, char** argv)
   }
 
   // Set the initial seed - Geant4 & ROOT !
-  //CLHEP::HepRandom::setTheSeed(m_Seed);
-  //G4Random::setTheSeed(m_Seed);
+  CLHEP::HepRandom::setTheSeed(m_Seed);
   gRandom->SetSeed(m_Seed);
-  /// FIXME
-  cout<<endl<<endl<<"FIXME: Switch to G4Random for random numbers throughout the code"<<endl<<endl;
-  gSystem->Sleep(1000);
+  // FIXME: Switch to G4Random for random numbers throughout the code
 
   return 0;
 }

From 5ea17b6772512e6c8f47bd2d70ec4b54a4c4f6ef Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Fri, 25 Oct 2024 00:37:31 -0700
Subject: [PATCH 097/192] BUG: Make sure filtered events are not deleted or a
 timeout would be triggered

---
 src/fretalon/framework/src/MModule.cxx     | 13 ++++++-------
 src/fretalon/framework/src/MSupervisor.cxx | 20 ++++++++------------
 2 files changed, 14 insertions(+), 19 deletions(-)

diff --git a/src/fretalon/framework/src/MModule.cxx b/src/fretalon/framework/src/MModule.cxx
index b6d9f3c48..68f497cf5 100644
--- a/src/fretalon/framework/src/MModule.cxx
+++ b/src/fretalon/framework/src/MModule.cxx
@@ -306,14 +306,13 @@ bool MModule::DoSingleAnalysis()
   }
   
   if (E != 0) {
-    if (FullfillsRequirements(E) == true) {
+    if (FullfillsRequirements(E) == true && E->IsFilteredOut() == false) {
       AnalyzeEvent(E);
-      if (m_IsFinished == true) {
-        delete E;
-        E = 0;
-      } else {
-        ++m_NAnalyzedEvents;
-      }
+    }
+    ++m_NAnalyzedEvents; // Analyzed actually just means passed through...
+    if (m_IsFinished == true) {
+      delete E;
+      E = 0;
     }
     if (E != 0) {
       m_Queues->AddOutgoing(E);
diff --git a/src/fretalon/framework/src/MSupervisor.cxx b/src/fretalon/framework/src/MSupervisor.cxx
index 21cfeaad3..bf9d15ddf 100644
--- a/src/fretalon/framework/src/MSupervisor.cxx
+++ b/src/fretalon/framework/src/MSupervisor.cxx
@@ -892,19 +892,15 @@ bool MSupervisor::Analyze(bool TestRun)
             TimeAssemblyExitedStartModule.Now();
           }
           MReadOutAssembly* ROA = M->GetAnalyzedReadOutAssembly();
-          if (ROA->IsFilteredOut() == true) {
-            //cout<<"ROA "<<ROA->GetID()<<" has been filterered out"<<endl;
-            delete ROA;
+          // Do not deleting filtered events, because it would triggers the timeout below
+          if (m < Modules.size()-1) {
+            //cout<<"Adding ROA "<<ROA->GetID()<<" to module "<<Modules[m+1][0]->GetName()<<endl;
+            Modules[m+1][0]->AddReadOutAssembly(ROA);
+            // Remark: the modules share their queue, so it does not matter to which we add the event
           } else {
-            if (m < Modules.size()-1) {
-              //cout<<"Adding ROA "<<ROA->GetID()<<" to module "<<Modules[m+1][0]->GetName()<<endl;
-              Modules[m+1][0]->AddReadOutAssembly(ROA); 
-              // Remark: the modules share their queue, so it does not matter to which we add the event
-            } else {
-              if (m == Modules.size()-1) {
-                //cout<<"ROA "<<ROA->GetID()<<" passed through all modules"<<endl;
-                delete ROA;
-              }
+            if (m == Modules.size()-1) {
+              //cout<<"ROA "<<ROA->GetID()<<" passed through all modules"<<endl;
+              delete ROA;
             }
           }
         }

From 8ee692e8257976755e8aedb9749bd069be7ca279 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Fri, 25 Oct 2024 00:38:07 -0700
Subject: [PATCH 098/192] ADD: Comment

---
 src/global/misc/src/MComptonEvent.cxx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/global/misc/src/MComptonEvent.cxx b/src/global/misc/src/MComptonEvent.cxx
index 91d609c84..eb144e76d 100644
--- a/src/global/misc/src/MComptonEvent.cxx
+++ b/src/global/misc/src/MComptonEvent.cxx
@@ -552,6 +552,8 @@ double MComptonEvent::GetAzimuthalScatterAngle(const MVector& Position, const MC
   if (m_HasDetectorRotation == true) RotPosition = GetDetectorRotationMatrix().Invert()*RotPosition;
   if (CS == MCoordinateSystem::c_Galactic && m_HasGalacticPointing == true) RotPosition = GetGalacticPointingInverseRotationMatrix()*RotPosition;
 
+  // Rotate the direction of the scattered gamma-ray as if it would come from zenith:
+  // First around Z then around Y
   MVector Plain = Dg();
   Plain.RotateZ(-RotPosition.Phi());
   Plain.RotateY(-RotPosition.Theta());

From 9d2790a0ba58a42a3fbb898cc25b9f2042bc4807 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Mon, 28 Oct 2024 10:57:06 -0700
Subject: [PATCH 099/192] CHG: Throw out positive / x strip and replace it with
 high/low volatge strip

---
 src/fretalon/base/inc/MReadOutElementDoubleStrip.h | 6 +++---
 src/fretalon/base/src/MFileReadOuts.cxx            | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/fretalon/base/inc/MReadOutElementDoubleStrip.h b/src/fretalon/base/inc/MReadOutElementDoubleStrip.h
index f37d327f5..4368bd1a9 100644
--- a/src/fretalon/base/inc/MReadOutElementDoubleStrip.h
+++ b/src/fretalon/base/inc/MReadOutElementDoubleStrip.h
@@ -65,11 +65,11 @@ class MReadOutElementDoubleStrip : public MReadOutElementStrip
   virtual unsigned int GetMinimumNumberOfReadOutsForGoodInteraction() const { return 2; }
 
   //! Set the strip type (positive equals the lowest voltage value side of the detector)
-  void IsPositiveStrip(bool IsPositiveStrip) { m_IsLowVoltageStrip = IsPositiveStrip; }
+  //void IsPositiveStrip(bool IsPositiveStrip) { m_IsLowVoltageStrip = IsPositiveStrip; }
   //! Return the strip type (positive equals the lowest voltage value side of the detector)
-  bool IsPositiveStrip() const { return m_IsLowVoltageStrip; }
+  //bool IsPositiveStrip() const { return m_IsLowVoltageStrip; }
 
-  //! Is this the-low voltage strip (= negative in old nomenclature)
+  //! Is this the-low voltage strip (= positive in old nomenclature)
   void IsLowVoltageStrip(bool IsLowVoltageStrip) { m_IsLowVoltageStrip = IsLowVoltageStrip; }
   //! Return true if this is a low-voltage strip
   bool IsLowVoltageStrip() const { return m_IsLowVoltageStrip; }
diff --git a/src/fretalon/base/src/MFileReadOuts.cxx b/src/fretalon/base/src/MFileReadOuts.cxx
index 43eb067c0..2655c62bc 100644
--- a/src/fretalon/base/src/MFileReadOuts.cxx
+++ b/src/fretalon/base/src/MFileReadOuts.cxx
@@ -340,7 +340,7 @@ bool MFileReadOuts::ReadNext(MReadOutSequence& ROS, int SelectedDetectorID, int
       // cout<<"Combined: "<<m_ROD->ToString()<<" vs. "<<m_ROD->GetCombinedType()<<endl;
       
       if (SelectedDetectorID < 0 || (SelectedDetectorID >= 0 && (int) m_ROE->GetDetectorID() == SelectedDetectorID)) {
-        if (SelectedDetectorSide < 0 || SelectedDetectorSide >= 2 || (dynamic_cast<MReadOutElementDoubleStrip*>(m_ROE) != nullptr && (int) dynamic_cast<MReadOutElementDoubleStrip*>(m_ROE)->IsPositiveStrip() == SelectedDetectorSide)) {
+        if (SelectedDetectorSide < 0 || SelectedDetectorSide >= 2 || (dynamic_cast<MReadOutElementDoubleStrip*>(m_ROE) != nullptr && (int) dynamic_cast<MReadOutElementDoubleStrip*>(m_ROE)->IsLowVoltageStrip() == SelectedDetectorSide)) {
           MReadOut RO(*m_ROE, *m_ROD);
           ROS.AddReadOut(RO);
           //cout<<"Added: "<<RO.ToString()<<endl;

From 2d70b21e3f27fb0d5afa0f36c734b390274ff283 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Mon, 28 Oct 2024 12:18:39 -0700
Subject: [PATCH 100/192] BUG: Need to finalize modules if initialization
 failed

---
 src/fretalon/framework/src/MSupervisor.cxx | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/fretalon/framework/src/MSupervisor.cxx b/src/fretalon/framework/src/MSupervisor.cxx
index bf9d15ddf..12885cc55 100644
--- a/src/fretalon/framework/src/MSupervisor.cxx
+++ b/src/fretalon/framework/src/MSupervisor.cxx
@@ -777,6 +777,11 @@ bool MSupervisor::Analyze(bool TestRun)
         break;
       }
       mout<<"Initialization of module "<<GetModule(m)->GetName()<<" failed"<<endl;
+
+      // Finalize already initialized modules since threads are already running:
+      for (unsigned int r = 0; r <= m; ++r) {
+        GetModule(r)->Finalize();
+      }
       m_IsAnalysisRunning = false;
       return false;
     }
@@ -1100,7 +1105,7 @@ void MSupervisor::View()
 void MSupervisor::Exit()
 {
   // Prepare to exit the application
-  
+
   if (m_IsAnalysisRunning == true) {
     m_SoftInterrupt = true;
     m_HardInterrupt = true;

From 9ec92cca7c1178c66d4376255339823be0045f77 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Tue, 29 Oct 2024 00:23:16 -0700
Subject: [PATCH 101/192] CHG: Work around ROOT bug on macOS

---
 .../framework/src/MGUIMainFretalon.cxx        | 28 +++++++++++++++++--
 1 file changed, 26 insertions(+), 2 deletions(-)

diff --git a/src/fretalon/framework/src/MGUIMainFretalon.cxx b/src/fretalon/framework/src/MGUIMainFretalon.cxx
index e1cc62710..ea19e5fc6 100644
--- a/src/fretalon/framework/src/MGUIMainFretalon.cxx
+++ b/src/fretalon/framework/src/MGUIMainFretalon.cxx
@@ -233,9 +233,33 @@ void MGUIMainFretalon::UpdateModules()
 {
   // Remove all existing modules:
 
-  m_ModuleFrame->RemoveAll();  // Deletes everyting too, especially the m_Modules.
+  // The next few lines are to work around a ROOT bug on macOS
+  double FontScaler = MGUIDefaults::GetInstance()->GetFontScaler();
+
+  TGFrameElement *el;
+  TIter next(m_ModuleFrame->GetList());
+  while ((el = (TGFrameElement *) next())) {
+    m_ModuleFrame->HideFrame(el->fFrame);
+    m_ModuleFrame->RemoveFrame(el->fFrame);
+    delete el->fFrame;
+  }
+
   m_ModuleFrame->Resize();
-  m_Modules.clear(); // Modules itself already deleted via m_ModuleFrame->RemoveAll()
+  m_Modules.clear();
+
+  HideFrame(m_ModuleFrame);
+  RemoveFrame(m_ModuleFrame);
+  delete m_ModuleFrame;
+
+  m_ModuleFrame = new TGVerticalFrame(this);
+  TGLayoutHints* SectionLayout = new TGLayoutHints(kLHintsTop | kLHintsCenterX | kLHintsExpandX, 40*FontScaler, 20*FontScaler, 0, 10*FontScaler);
+  AddFrame(m_ModuleFrame, SectionLayout);
+  // end ROOT bug work around
+
+  // The non-ROOT-bug-on-macOS version was:
+  // m_ModuleFrame->RemoveAll();  // Deletes everyting too, especially the m_Modules.
+  // m_ModuleFrame->Resize();
+  // m_Modules.clear(); // Modules itself already deleted via m_ModuleFrame->RemoveAll()
 
   for (unsigned int m = 0; m < m_Supervisor->GetNModules(); ++m) {
     MGUIEModule* GuiModule = new MGUIEModule(m_ModuleFrame, m, m_Supervisor->GetModule(m));

From 09026d7d8f0babf4bf07e4ecfe75f3b3d001b1d6 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Wed, 13 Nov 2024 11:16:12 -0800
Subject: [PATCH 102/192] ADD: Feature to scale just one axis

---
 src/geomega/inc/MDOrientation.h         | 18 +++++++-
 src/geomega/inc/MDShape.h               | 15 ++++--
 src/geomega/inc/MDShapeBRIK.h           |  4 +-
 src/geomega/inc/MDShapeCONE.h           |  4 +-
 src/geomega/inc/MDShapeCONS.h           |  4 +-
 src/geomega/inc/MDShapeGTRA.h           |  4 +-
 src/geomega/inc/MDShapeIntersection.h   |  5 +-
 src/geomega/inc/MDShapePCON.h           |  4 +-
 src/geomega/inc/MDShapePGON.h           |  4 +-
 src/geomega/inc/MDShapeSPHE.h           |  4 +-
 src/geomega/inc/MDShapeSubtraction.h    |  5 +-
 src/geomega/inc/MDShapeTRAP.h           | 17 +++++--
 src/geomega/inc/MDShapeTRD1.h           |  4 +-
 src/geomega/inc/MDShapeTRD2.h           |  4 +-
 src/geomega/inc/MDShapeTUBS.h           |  4 +-
 src/geomega/inc/MDShapeUnion.h          |  7 +--
 src/geomega/inc/MDVolume.h              |  5 +-
 src/geomega/src/MDGeometry.cxx          | 47 +++++++++++++------
 src/geomega/src/MDOrientation.cxx       | 51 +++++++++++++++++++++
 src/geomega/src/MDShape.cxx             | 61 +++++++++++++++++++++----
 src/geomega/src/MDShapeBRIK.cxx         | 30 +++++++++---
 src/geomega/src/MDShapeCONE.cxx         | 41 +++++++++++++----
 src/geomega/src/MDShapeCONS.cxx         | 39 ++++++++++++----
 src/geomega/src/MDShapeGTRA.cxx         | 48 +++++++++++--------
 src/geomega/src/MDShapeIntersection.cxx | 52 ++++++++++++++++++---
 src/geomega/src/MDShapePCON.cxx         | 35 ++++++++++----
 src/geomega/src/MDShapePGON.cxx         | 35 ++++++++++----
 src/geomega/src/MDShapeSPHE.cxx         | 29 +++++++++---
 src/geomega/src/MDShapeSubtraction.cxx  | 60 ++++++++++++++++++------
 src/geomega/src/MDShapeTRAP.cxx         | 43 +++++++++++------
 src/geomega/src/MDShapeTRD1.cxx         | 31 +++++++++----
 src/geomega/src/MDShapeTRD2.cxx         | 37 +++++++++++----
 src/geomega/src/MDShapeTUBS.cxx         | 33 ++++++++++---
 src/geomega/src/MDShapeUnion.cxx        | 56 +++++++++++++++++++----
 src/geomega/src/MDVolume.cxx            | 20 ++++++--
 src/sivan/src/MInterfaceSivan.cxx       | 29 ++++++++++--
 36 files changed, 690 insertions(+), 199 deletions(-)

diff --git a/src/geomega/inc/MDOrientation.h b/src/geomega/inc/MDOrientation.h
index 4e13c43a2..57c43dedb 100644
--- a/src/geomega/inc/MDOrientation.h
+++ b/src/geomega/inc/MDOrientation.h
@@ -54,6 +54,17 @@ class MDOrientation
   //! Set the name of the orientation
   void SetName(const MString& Name) { m_Name = Name; }
 
+  //! Scale this shape by Factor, optionally give the axis.
+  //! The options for the latter are "X", "Y", "Z", and any combination thereof
+  //! For anything but "XYZ", the daughter volumes are not allowed to have orientations
+  virtual bool Scale(const double Scaler, const MString Axes = "XYZ");
+  //! Get the current scale factor
+  double GetScaler() const { return m_Scaler; }
+  //! Get scaler axid
+  MString GetScalingAxis() const { return m_ScalingAxis; }
+  //! True if we are scaled
+  bool IsScaled() const;
+
   //! Validate the data and create the shape 
   bool Validate();  
   
@@ -86,7 +97,7 @@ class MDOrientation
   //! Return the inverted rotation matrix
   MRotation GetInvRotationMatrix() const { return m_InvertedRotMatrix; }
   //! The if we have a rotation
-  bool IsRotated() const;
+  bool IsRotated() const { return m_IsRotated; }
 
   //! Dump content into a string
   MString ToString() const;
@@ -127,6 +138,11 @@ class MDOrientation
   //! The whole thing as ROOT matrix
   TGeoMatrix* m_RootMatrix;
 
+  //! The scale factor
+  double m_Scaler;
+  //! The scaling axis "X", "Y", "Z", and any combination thereof
+  MString m_ScalingAxis;
+
 #ifdef ___CLING___
  public:
   ClassDef(MDOrientation, 0) // no description
diff --git a/src/geomega/inc/MDShape.h b/src/geomega/inc/MDShape.h
index e4498ac61..4de77a7d5 100644
--- a/src/geomega/inc/MDShape.h
+++ b/src/geomega/inc/MDShape.h
@@ -69,10 +69,17 @@ class MDShape
   virtual double GetVolume() = 0;
   virtual MVector GetRandomPositionInside(); 
 
-  //! Scale this shape by Factor
-  virtual void Scale(const double Scale);
+  //! Scale this shape by Factor, optionally give the axis.
+  //! The options for the latter are "X", "Y", "Z", and any combination thereof
+  //! For anything but "XYZ", the daughter volumes are not allowed to have orientations
+  virtual bool Scale(const double Scaler, const MString Axes = "XYZ");
   //! Get the current scale factor
   double GetScaler() const { return m_Scaler; }
+  //! Get scaler axid
+  MString GetScalingAxis() const { return m_ScalingAxis; }
+  //! True if we are scaled
+  bool IsScaled() const;
+
 
   //! Return a unique position within the volume of the detector (center if possible)
   virtual MVector GetUniquePosition() const = 0;
@@ -113,7 +120,9 @@ class MDShape
 
   //! The scale factor
   double m_Scaler;
-  
+  //! The scaling axis "X", "Y", "Z", and any combination thereof
+  MString m_ScalingAxis;
+
   //! If this shape consists of other shapes, they are stored here
   vector<MDShape*> m_SubShapes;
   
diff --git a/src/geomega/inc/MDShapeBRIK.h b/src/geomega/inc/MDShapeBRIK.h
index 2afd40277..497bebbd3 100644
--- a/src/geomega/inc/MDShapeBRIK.h
+++ b/src/geomega/inc/MDShapeBRIK.h
@@ -69,8 +69,8 @@ class MDShapeBRIK : public MDShape
 
   double GetVolume();
 
-  //! Scale this shape by Factor
-  virtual void Scale(const double Factor);
+  //! Scale the axes given in Axes by a factor Scaler
+  virtual bool Scale(const double Scaler, const MString Axes = "XYZ");
 
   //! Return a unique position within the volume of the detector (center if possible)
   virtual MVector GetUniquePosition() const;
diff --git a/src/geomega/inc/MDShapeCONE.h b/src/geomega/inc/MDShapeCONE.h
index bf7f8ec93..17e3e84c5 100644
--- a/src/geomega/inc/MDShapeCONE.h
+++ b/src/geomega/inc/MDShapeCONE.h
@@ -62,8 +62,8 @@ class MDShapeCONE : public MDShape
 
   double GetVolume();
 
-  //! Scale this shape by Factor
-  virtual void Scale(const double Factor);
+  //! Scale the axes given in Axes by a factor Scaler
+  virtual bool Scale(const double Scaler, const MString Axes = "XYZ");
 
   //! Return a unique position within the volume of the detector (center if possible)
   virtual MVector GetUniquePosition() const;
diff --git a/src/geomega/inc/MDShapeCONS.h b/src/geomega/inc/MDShapeCONS.h
index 7b0454e3e..4972fb1b5 100644
--- a/src/geomega/inc/MDShapeCONS.h
+++ b/src/geomega/inc/MDShapeCONS.h
@@ -66,8 +66,8 @@ class MDShapeCONS : public MDShape
 
   double GetVolume();
 
-  //! Scale this shape by Factor
-  virtual void Scale(const double Factor);
+  //! Scale the axes given in Axes by a factor Scaler
+  virtual bool Scale(const double Scaler, const MString Axes = "XYZ");
 
   //! Return a unique position within the volume of the detector (center if possible)
   virtual MVector GetUniquePosition() const;
diff --git a/src/geomega/inc/MDShapeGTRA.h b/src/geomega/inc/MDShapeGTRA.h
index f765bec5f..4c5e11a9f 100644
--- a/src/geomega/inc/MDShapeGTRA.h
+++ b/src/geomega/inc/MDShapeGTRA.h
@@ -58,8 +58,8 @@ class MDShapeGTRA : public MDShape
 
   double GetVolume();
 
-  //! Scale this shape by Factor
-  virtual void Scale(const double Factor);
+  //! Scale the axes given in Axes by a factor Scaler
+  virtual bool Scale(const double Scaler, const MString Axes = "XYZ");
 
   //! Return a unique position within the volume of the detector (center if possible)
   virtual MVector GetUniquePosition() const;
diff --git a/src/geomega/inc/MDShapeIntersection.h b/src/geomega/inc/MDShapeIntersection.h
index 314266d91..6392049c8 100644
--- a/src/geomega/inc/MDShapeIntersection.h
+++ b/src/geomega/inc/MDShapeIntersection.h
@@ -68,10 +68,11 @@ class MDShapeIntersection : public MDShape
   MDOrientation* GetOrientationShapeB() const { return m_Orientation; }
 
   //! Get the volume of this shape
+  //! Attention: For boolean volumes it is sampled thus only correct to >1%
   double GetVolume();
 
-  //! Scale this shape by Factor
-  virtual void Scale(const double Factor);
+  //! Scale the axes given in Axes by a factor Scaler
+  virtual bool Scale(const double Scaler, const MString Axes = "XYZ");
 
   //! Return a unique position within the volume of the detector (center if possible)
   virtual MVector GetUniquePosition() const;
diff --git a/src/geomega/inc/MDShapePCON.h b/src/geomega/inc/MDShapePCON.h
index b0e89f4be..390605b09 100644
--- a/src/geomega/inc/MDShapePCON.h
+++ b/src/geomega/inc/MDShapePCON.h
@@ -69,8 +69,8 @@ class MDShapePCON : public MDShape
 
   double GetVolume();
 
-  //! Scale this shape by Factor
-  virtual void Scale(const double Factor);
+  //! Scale the axes given in Axes by a factor Scaler
+  virtual bool Scale(const double Scaler, const MString Axes = "XYZ");
 
   //! Return a unique position within the volume of the detector (center if possible)
   virtual MVector GetUniquePosition() const;
diff --git a/src/geomega/inc/MDShapePGON.h b/src/geomega/inc/MDShapePGON.h
index 72c3dd0fb..6cd7ed311 100644
--- a/src/geomega/inc/MDShapePGON.h
+++ b/src/geomega/inc/MDShapePGON.h
@@ -70,8 +70,8 @@ class MDShapePGON : public MDShape
 
   double GetVolume();
 
-  //! Scale this shape by Factor
-  virtual void Scale(const double Factor);
+  //! Scale the axes given in Axes by a factor Scaler
+  virtual bool Scale(const double Scaler, const MString Axes = "XYZ");
 
   //! Return a unique position within the volume of the detector (center if possible)
   virtual MVector GetUniquePosition() const;
diff --git a/src/geomega/inc/MDShapeSPHE.h b/src/geomega/inc/MDShapeSPHE.h
index 5ad30db7e..a783c5850 100644
--- a/src/geomega/inc/MDShapeSPHE.h
+++ b/src/geomega/inc/MDShapeSPHE.h
@@ -65,8 +65,8 @@ class MDShapeSPHE : public MDShape
 
   double GetVolume();
 
-  //! Scale this shape by Factor
-  virtual void Scale(const double Factor);
+  //! Scale the axes given in Axes by a factor Scaler
+  virtual bool Scale(const double Scaler, const MString Axes = "XYZ");
 
   //! Return a unique position within the volume of the detector (center if possible)
   virtual MVector GetUniquePosition() const;
diff --git a/src/geomega/inc/MDShapeSubtraction.h b/src/geomega/inc/MDShapeSubtraction.h
index f7998e1ae..248d54d88 100644
--- a/src/geomega/inc/MDShapeSubtraction.h
+++ b/src/geomega/inc/MDShapeSubtraction.h
@@ -69,10 +69,11 @@ class MDShapeSubtraction : public MDShape
   MDOrientation* GetOrientationSubtrahend() const { return m_Orientation; }
 
   //! Get the volume of this shape
+  //! Attention: For boolean volumes it is sampled thus only correct to >1%
   double GetVolume();
 
-  //! Scale this shape by Factor
-  virtual void Scale(const double Factor);
+  //! Scale the axes given in Axes by a factor Scaler
+  virtual bool Scale(const double Scaler, const MString Axes = "XYZ");
 
   //! Return a unique position within the volume of the detector (center if possible)
   virtual MVector GetUniquePosition() const;
diff --git a/src/geomega/inc/MDShapeTRAP.h b/src/geomega/inc/MDShapeTRAP.h
index 86934638b..44d9335d8 100644
--- a/src/geomega/inc/MDShapeTRAP.h
+++ b/src/geomega/inc/MDShapeTRAP.h
@@ -40,7 +40,18 @@ class MDShapeTRAP : public MDShape
   //! Default destructor
   virtual ~MDShapeTRAP();
 
-  //! Set the all parameters of the shape
+  //! Set the all parameters of the shape - The definition is the same as in ROOT
+  //! dz: half-length along the z axis
+  //! theta: polar angle of the line joining the centre of the face at -DZ to the centre of the one at +DZ
+  //! phi: azimuthal angle of the line joining the centre of the face at -DZ to the centre of the one at +DZ
+  //! h1: half-length along y of the face at -DZ
+  //! bl1: half-length along x of the side at -H1 in y of the face at -DZ in z
+  //! tl1: half-length along x of the side at +H1 in y of the face at -DZ in z
+  //! alpha1: angle with respect to the y axis from the centre of the side at -H1 in y to the centre of the side at +H1 in y of the face at -DZ in z
+  //! h2: half-length along y of the face at +DZ
+  //! bl2: half-length along x of the side at -H2 in y of the face at +DZ in z
+  //! tl2: half-length along x of the side at +H2 in y of the face at +DZ in z
+  //! alpha2: angle with respect to the y axis from the centre of the side at -H2 in y to the centre of the side at +H2 in y of the face at +DZ in z
   bool Set(double Dz, double Theta, double Phi, 
            double H1, double Bl1, double Tl1, double Alpha1, 
            double H2, double Bl2, double Tl2, double Alpha2);
@@ -70,8 +81,8 @@ class MDShapeTRAP : public MDShape
 
   double GetVolume();
 
-  //! Scale this shape by Factor
-  virtual void Scale(const double Factor);
+  //! Scale the axes given in Axes by a factor Scaler
+  virtual bool Scale(const double Scaler, const MString Axes = "XYZ");
 
   //! Return a unique position within the volume of the detector (center if possible)
   virtual MVector GetUniquePosition() const;
diff --git a/src/geomega/inc/MDShapeTRD1.h b/src/geomega/inc/MDShapeTRD1.h
index 118454ce1..6c7e7bf2e 100644
--- a/src/geomega/inc/MDShapeTRD1.h
+++ b/src/geomega/inc/MDShapeTRD1.h
@@ -61,8 +61,8 @@ class MDShapeTRD1 : public MDShape
 
   double GetVolume();
 
-  //! Scale this shape by Factor
-  virtual void Scale(const double Factor);
+  //! Scale the axes given in Axes by a factor Scaler
+  virtual bool Scale(const double Scaler, const MString Axes = "XYZ");
 
   //! Return a unique position within the volume of the detector (center if possible)
   virtual MVector GetUniquePosition() const;
diff --git a/src/geomega/inc/MDShapeTRD2.h b/src/geomega/inc/MDShapeTRD2.h
index 598f49321..6437e0a39 100644
--- a/src/geomega/inc/MDShapeTRD2.h
+++ b/src/geomega/inc/MDShapeTRD2.h
@@ -62,8 +62,8 @@ class MDShapeTRD2 : public MDShape
 
   double GetVolume();
 
-  //! Scale this shape by Factor
-  virtual void Scale(const double Factor);
+  //! Scale the axes given in Axes by a factor Scaler
+  virtual bool Scale(const double Scaler, const MString Axes = "XYZ");
 
   //! Return a unique position within the volume of the detector (center if possible)
   virtual MVector GetUniquePosition() const;
diff --git a/src/geomega/inc/MDShapeTUBS.h b/src/geomega/inc/MDShapeTUBS.h
index 1b26fd613..c9acfa3ef 100644
--- a/src/geomega/inc/MDShapeTUBS.h
+++ b/src/geomega/inc/MDShapeTUBS.h
@@ -62,8 +62,8 @@ class MDShapeTUBS : public MDShape
 
   double GetVolume();
 
-  //! Scale this shape by Factor
-  virtual void Scale(const double Factor);
+  //! Scale the axes given in Axes by a factor Scaler
+  virtual bool Scale(const double Scaler, const MString Axes = "XYZ");
 
   //! Return a unique position within the volume of the detector (center if possible)
   virtual MVector GetUniquePosition() const;
diff --git a/src/geomega/inc/MDShapeUnion.h b/src/geomega/inc/MDShapeUnion.h
index 3da7947e6..0c28bff01 100644
--- a/src/geomega/inc/MDShapeUnion.h
+++ b/src/geomega/inc/MDShapeUnion.h
@@ -51,7 +51,7 @@ class MDShapeUnion : public MDShape
   //! Parse some tokenized text
   bool Parse(const MTokenizer& Tokenizer, const MDDebugInfo& Info);
 
-  //!
+  //! Not implemented
   MVector GetSize() { return MVector(); }
 
   //! Dump the content as a string
@@ -68,10 +68,11 @@ class MDShapeUnion : public MDShape
   MDOrientation* GetOrientationAddend() const { return m_Orientation; }
 
   //! Get the volume of this shape
+  //! Attention: For boolean volumes it is sampled thus only correct to >1%
   double GetVolume();
 
-  //! Scale this shape by Factor
-  virtual void Scale(const double Factor);
+  //! Scale the axes given in Axes by a factor Scaler
+  virtual bool Scale(const double Scaler, const MString Axes = "XYZ");
 
   //! Return a unique position within the volume of the detector (center if possible)
   virtual MVector GetUniquePosition() const;
diff --git a/src/geomega/inc/MDVolume.h b/src/geomega/inc/MDVolume.h
index 25ec5562e..9b4fa3fa1 100644
--- a/src/geomega/inc/MDVolume.h
+++ b/src/geomega/inc/MDVolume.h
@@ -203,9 +203,10 @@ class MDVolume
   //! Finds all DEEPEST volumes Pos is in...
   //! The return value is for internal purposes only!
   bool FindOverlaps(MVector Pos, vector<MDVolume*>& OverlappingVolumes);
-  //! Scale this volume
+  //! Scale this volume, scalingaxes is "X", "Y", "Z" or any combination thereof
+  //! However, not all volumes support all scalings.
   //! The return value is for internal purposes only!
-  bool Scale(const double Scale);
+  bool Scale(const double Scale, const MString ScalingAxes);
   //! Correctly remove all virtual volumes from the volume tree
   //! The return value is for internal purposes only!
   //! The vector contains a list of all newly generated volumes
diff --git a/src/geomega/src/MDGeometry.cxx b/src/geomega/src/MDGeometry.cxx
index d8810d48d..0e2d3337a 100644
--- a/src/geomega/src/MDGeometry.cxx
+++ b/src/geomega/src/MDGeometry.cxx
@@ -384,7 +384,8 @@ bool MDGeometry::ScanSetupFile(MString FileName, bool CreateNodes, bool Virtuali
   MDOrientation* Orientation = 0;
 
   // For scaling some volumes:
-  map<MDVolume*, double> ScaledVolumes;
+  map<MDVolume*, double> ScaledVolumesScaler;
+  map<MDVolume*, MString> ScaledVolumesScalingAxes;
 
   // Since the geometry-file can include other geometry files,
   // we have to store the whole file in memory
@@ -2508,16 +2509,21 @@ bool MDGeometry::ScanSetupFile(MString FileName, bool CreateNodes, bool Virtuali
         }
         V->SetLineWidth(Tokenizer.GetTokenAtAsInt(2));
       } else if (Tokenizer.IsTokenAt(1, "Scale") == true) {
-        if (Tokenizer.GetNTokens() != 3) {
-          Typo("Line must contain two strings and one integer"
-               " e.g. \"Triangle.Scale 2.0\"");
+        if (Tokenizer.GetNTokens() < 3 || Tokenizer.GetNTokens() > 4) {
+          Typo("Line must contain two strings, one double, and one optional scaling axes"
+               " e.g. \"Triangle.Scale 2.0 XY\"");
           return false;
         }
         if (Tokenizer.GetTokenAtAsDouble(2) <= 0) {
           Typo("The color value needs to be positive");
           return false;
         }
-        ScaledVolumes[V] = Tokenizer.GetTokenAtAsDouble(2);
+        ScaledVolumesScaler[V] = Tokenizer.GetTokenAtAsDouble(2);
+        if (Tokenizer.GetNTokens() == 4) {
+          ScaledVolumesScalingAxes[V] = Tokenizer.GetTokenAtAsString(3);
+        } else {
+          ScaledVolumesScalingAxes[V] = "XYZ";
+        }
       } else if (Tokenizer.IsTokenAt(1, "Virtual") == true) {
         if (Tokenizer.GetNTokens() != 3) {
           Typo("Line must contain two strings and one boolean"
@@ -3668,16 +3674,25 @@ bool MDGeometry::ScanSetupFile(MString FileName, bool CreateNodes, bool Virtuali
   }
 
   // Scale some volumes:
-  map<MDVolume*, double>::iterator ScaleIter;
-  for (ScaleIter = ScaledVolumes.begin();
-       ScaleIter != ScaledVolumes.end(); ++ScaleIter) {
-    if ((*ScaleIter).first->IsClone() == false) {
-      (*ScaleIter).first->Scale((*ScaleIter).second);
+  auto ScaleIter = ScaledVolumesScaler.begin();
+  auto AxesIter = ScaledVolumesScalingAxes.begin();
+
+  while (ScaleIter != ScaledVolumesScaler.end() && AxesIter != ScaledVolumesScalingAxes.end()) {
+    if (ScaleIter->first == AxesIter->first) {  // Make sure the keys match
+      if ((*ScaleIter).first->IsClone() == false) {
+        (*ScaleIter).first->Scale((*ScaleIter).second, (*AxesIter).second);
+      } else {
+        mout<<"   ***  Error  ***  Scaling is not applicable to clones/copies"<<endl;
+        Reset();
+        return false;
+      }
     } else {
-      mout<<"   ***  Error  ***  Scaling is not applicable to clones/copies"<<endl;
+      mout<<"   ***  Internal Fatal Error  ***  The axes and the scaler iterators for scaled volumes are not in sync."<<endl;
       Reset();
       return false;
     }
+    ++ScaleIter;
+    ++AxesIter;
   }
   m_WorldVolume->ResetCloneTemplateFlags();
 
@@ -4669,12 +4684,18 @@ void MDGeometry::CalculateMasses()
   out<<endl;
   out<<setw(NameWidth+2)<<"Total"<<" :  "<<setw(12)<<Total<<" g"<<endl;
   out<<endl;
-  out<<"No warranty for this information!"<<endl;
   out<<"This information is only valid, if "<<endl;
   out<<"(a) No volume intersects any volume which is not either its mother or daughter."<<endl;
   out<<"(b) All daughters lie completely inside their mothers"<<endl;
   out<<"(c) The material information is correct"<<endl;
-  out<<"(d) tbd."<<endl;
+  out<<"(d) and more"<<endl;
+  out<<endl;
+  out<<"Attention:"<<endl;
+  out<<"If you have boolean volumes, ROOT determines the volume via random samples."<<endl;
+  out<<"This is a ROOT limitation. The accuracy is >1% (= 10,000 samples)."<<endl;
+  out<<"If you have other volumes in the boolean volume, then the accuracy is before the subtraction."<<endl;
+  out<<"In rare cases of very small volumes, this can lead to negative masses..."<<endl;
+  out<<endl;
 
   mout<<out.str()<<endl;
 }
diff --git a/src/geomega/src/MDOrientation.cxx b/src/geomega/src/MDOrientation.cxx
index 87e72d630..bc568f083 100644
--- a/src/geomega/src/MDOrientation.cxx
+++ b/src/geomega/src/MDOrientation.cxx
@@ -379,6 +379,57 @@ void MDOrientation::SetRotation(MRotation RotationMatrix, int RotID)
 ////////////////////////////////////////////////////////////////////////////////
 
 
+bool MDOrientation::Scale(const double Scale, const MString Axes)
+{
+  // Scale this shape by a factor of Scale
+
+  if (IsScaled() == true) {
+    mout<<"   ***  Error  ***  in shape "<<m_Name<<endl;
+    mout<<"The shape is already scaled."<<endl;
+    return false;
+  }
+
+  for (unsigned int c = 0; c < Axes.Length(); ++c) {
+    char C = Axes[c];
+    if (C != 'X' && C != 'Y' && C != 'Z') {
+      mout<<"   ***  Error  ***  in shape "<<m_Name<<endl;
+      mout<<"The scaling axis can only contaion X, Y, or Z, and not "<<C<<"."<<endl;
+      return false;
+    }
+  }
+
+  if (Scale == 1.0) return true;
+
+  if (IsRotated() == true && Axes != "XYZ") {
+    mout<<"   ***  Error  ***  in shape "<<m_Name<<endl;
+    mout<<"This is a rotated volumes. The only allowed scaling is \"XYZ\"."<<endl;
+    return false;
+  }
+
+  m_Scaler = Scale;
+  m_ScalingAxis = Axes;
+
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! True if we are scaled
+bool MDOrientation::IsScaled() const
+{
+  if (m_ScalingAxis != "") {
+    return true;
+  }
+
+  return false;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
 MString MDOrientation::ToString() const
 {
   //! Dump content into a string
diff --git a/src/geomega/src/MDShape.cxx b/src/geomega/src/MDShape.cxx
index 94676d0fd..d0af7af84 100644
--- a/src/geomega/src/MDShape.cxx
+++ b/src/geomega/src/MDShape.cxx
@@ -68,6 +68,9 @@ MDShape::MDShape(const MString& Name)
   m_Name = Name;
   m_Geo = nullptr;
   m_IsValidated = false;
+
+  m_Scaler = 1.0;
+  m_ScalingAxis = "";
 }
 
 
@@ -219,19 +222,27 @@ MVector MDShape::GetRandomPositionInside()
   TGeoBBox* BBox = (TGeoBBox*) m_Geo; // All geometries are derived from TGeoBBox!
   
   MVector R;
-  
-  int Counter = 0;
+
+  unsigned long Counter = 0;
   do {
     R.SetX((2.0*gRandom->Rndm()-1.0)*BBox->GetDX() + BBox->GetOrigin()[0]);
     R.SetY((2.0*gRandom->Rndm()-1.0)*BBox->GetDY() + BBox->GetOrigin()[1]);
     R.SetZ((2.0*gRandom->Rndm()-1.0)*BBox->GetDZ() + BBox->GetOrigin()[2]);
 
     Counter++;
+
+    if (Counter > 10000000) {
+      mout<<"   ***  FATAL ERROR  ***  in shape "<<m_Type<<endl;
+      mout<<"GetRandomPositionInside() required more than "<<Counter<<" trials."<<endl;
+      mout<<"There is likely something wrong with your shape, especially when it is a boolean one. You have: "<<m_Type<<endl;
+      abort();
+      return g_VectorNotDefined;
+    }
   } while (IsInside(R) == false);
 
-  if (Counter > 100) {
-    mout<<"   ***  Warning  ***  in shape "<<m_Name<<endl;
-    mout<<"GetRandomPositionInside() required "<<Counter<<" trials."<<endl;
+  if (Counter > 10000) {
+    mout<<"   ***  Warning  ***  in shape "<<m_Type<<endl;
+    mout<<"GetRandomPositionInside() required more than "<<Counter<<" trials."<<endl;
     mout<<"You might want to ask the developers to write an optimized version of GetRandomPositionInside() for type "<<m_Type<<endl;
   }
 
@@ -242,12 +253,46 @@ MVector MDShape::GetRandomPositionInside()
 ////////////////////////////////////////////////////////////////////////////////
 
 
-void MDShape::Scale(const double Scale)
+bool MDShape::Scale(const double Scale, const MString Axes)
 {
-  // Scale this shape by a factor of Scale
+  // Base class: Call this one first in derived classed
+  // Performs sanity checks on scaling, and saves data
+
+  if (IsScaled() == true) {
+    mout<<"   ***  Error  ***  in shape "<<m_Name<<endl;
+    mout<<"The shape is already scaled."<<endl;
+    return false;
+  }
+
+  for (unsigned int c = 0; c < Axes.Length(); ++c) {
+    char C = Axes[c];
+    if (C != 'X' && C != 'Y' && C != 'Z') {
+      mout<<"   ***  Error  ***  in shape "<<m_Name<<endl;
+      mout<<"The scaling axis can only contain X, Y, or Z, and not \""<<C<<"\"."<<endl;
+      return false;
+    }
+  }
+
+  if (Scale == 1.0) return true;
 
   m_Scaler = Scale;
-  Validate();
+  m_ScalingAxis = Axes;
+
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! True if we are scaled
+bool MDShape::IsScaled() const
+{
+  if (m_ScalingAxis != "") {
+    return true;
+  }
+
+  return false;
 }
 
 
diff --git a/src/geomega/src/MDShapeBRIK.cxx b/src/geomega/src/MDShapeBRIK.cxx
index 8495b0961..4384db803 100644
--- a/src/geomega/src/MDShapeBRIK.cxx
+++ b/src/geomega/src/MDShapeBRIK.cxx
@@ -229,17 +229,33 @@ double MDShapeBRIK::GetVolume()
 ////////////////////////////////////////////////////////////////////////////////
 
 
-void MDShapeBRIK::Scale(const double Factor)
+bool MDShapeBRIK::Scale(const double Factor, const MString Axes)
 {
-  // Scale this shape by Factor
 
-  m_Dx *= Factor;
-  m_Dy *= Factor;
-  m_Dz *= Factor;
+  // Don't do anything if the scaling has already been applied
+  if (Factor == m_Scaler && Axes == m_ScalingAxis) return true;
+
+  // Base class handles sanity checks and storing data
+  if (MDShape::Scale(Factor, Axes) == false) return false;
+  // If there was no scaling return true;
+  if (IsScaled() == false) return true;
+
+
+  // Now scale
+  if (m_ScalingAxis.Contains("X") == true) {
+    m_Dx *= m_Scaler;
+  }
+  if (m_ScalingAxis.Contains("Y") == true) {
+    m_Dy *= m_Scaler;
+  }
+  if (m_ScalingAxis.Contains("Z") == true) {
+    m_Dz *= m_Scaler;
+  }
   
+
+  // And validate
   m_IsValidated = false;
-  
-  Validate();
+  return Validate();
 }
 
 
diff --git a/src/geomega/src/MDShapeCONE.cxx b/src/geomega/src/MDShapeCONE.cxx
index aaa2c35cc..0d49c7b65 100644
--- a/src/geomega/src/MDShapeCONE.cxx
+++ b/src/geomega/src/MDShapeCONE.cxx
@@ -258,19 +258,40 @@ double MDShapeCONE::GetVolume()
 ////////////////////////////////////////////////////////////////////////////////
 
 
-void MDShapeCONE::Scale(const double Factor)
+bool MDShapeCONE::Scale(const double Factor, const MString Axes)
 {
-  // Scale this shape by Factor
+  //! Scale the axes given in Axes by a factor Scaler
 
-  m_RminBottom *= Factor;
-  m_RmaxBottom *= Factor;
-  m_RminTop *= Factor;
-  m_RmaxTop *= Factor;
-  m_HalfHeight *= Factor;
-  
+  // Don't do anything if the scaling has already been applied
+  if (Factor == m_Scaler && Axes == m_ScalingAxis) return true;
+
+  // Base class handles sanity checks and storing data
+  if (MDShape::Scale(Factor, Axes) == false) return false;
+  // If there was no scaling return true;
+  if (IsScaled() == false) return true;
+
+  if ((m_ScalingAxis.Contains("X") == true && m_ScalingAxis.Contains("Y") == false) || (m_ScalingAxis.Contains("X") == false && m_ScalingAxis.Contains("Y") == true)) {
+    mout<<"   ***  Error  ***  in shape "<<m_Name<<endl;
+    mout<<"This volume can only be scaled the same way in X as in Y axis, i.e., the axis string must contain \"XY\"."<<endl;
+    return false;
+  }
+
+
+  // Scale
+  if (m_ScalingAxis.Contains("X") == true && m_ScalingAxis.Contains("Y") == true) {
+    m_RminBottom *= m_Scaler;
+    m_RmaxBottom *= m_Scaler;
+    m_RminTop *= m_Scaler;
+    m_RmaxTop *= m_Scaler;
+  }
+  if (m_ScalingAxis.Contains("Z") == true) {
+    m_HalfHeight *= m_Scaler;
+  }
+
+
+  // Validate
   m_IsValidated = false;
-  
-  Validate();
+  return Validate();
 }
 
 
diff --git a/src/geomega/src/MDShapeCONS.cxx b/src/geomega/src/MDShapeCONS.cxx
index be084b3da..d4e199ae4 100644
--- a/src/geomega/src/MDShapeCONS.cxx
+++ b/src/geomega/src/MDShapeCONS.cxx
@@ -318,18 +318,39 @@ double MDShapeCONS::GetVolume()
 ////////////////////////////////////////////////////////////////////////////////
 
 
-void MDShapeCONS::Scale(const double Factor)
+bool MDShapeCONS::Scale(const double Factor, const MString Axes)
 {
-  // Scale this shape by Factor
+  //! Scale the axes given in Axes by a factor Scaler
 
-  m_RminBottom *= Factor;
-  m_RmaxBottom *= Factor;
-  m_RminTop *= Factor;
-  m_RmaxTop *= Factor;
-  m_HalfHeight *= Factor;
-  
+  // Don't do anything if the scaling has already been applied
+  if (Factor == m_Scaler && Axes == m_ScalingAxis) return true;
+
+  // Base class handles sanity checks and storing data
+  if (MDShape::Scale(Factor, Axes) == false) return false;
+  // If there was no scaling return true;
+  if (IsScaled() == false) return true;
+
+  if ((m_ScalingAxis.Contains("X") == true && m_ScalingAxis.Contains("Y") == false) || (m_ScalingAxis.Contains("X") == false && m_ScalingAxis.Contains("Y") == true)) {
+    mout<<"   ***  Error  ***  in shape "<<m_Name<<endl;
+    mout<<"This volume can only be scaled the same way in X as in Y axis, i.e., the axis string must contain \"XY\"."<<endl;
+    return false;
+  }
+
+
+  // Scale
+  if (m_ScalingAxis.Contains("X") == true && m_ScalingAxis.Contains("Y") == true) {
+    m_RminBottom *= m_Scaler;
+    m_RmaxBottom *= m_Scaler;
+    m_RminTop *= m_Scaler;
+    m_RmaxTop *= m_Scaler;
+  }
+  if (m_ScalingAxis.Contains("Z") == true) {
+    m_HalfHeight *= m_Scaler;
+  }
+
+
+  // Validate
   m_IsValidated = false;
-  
   Validate();
 }
 
diff --git a/src/geomega/src/MDShapeGTRA.cxx b/src/geomega/src/MDShapeGTRA.cxx
index 69c504eb4..ce65df46a 100644
--- a/src/geomega/src/MDShapeGTRA.cxx
+++ b/src/geomega/src/MDShapeGTRA.cxx
@@ -305,26 +305,38 @@ double MDShapeGTRA::GetVolume()
 ////////////////////////////////////////////////////////////////////////////////
 
 
-void MDShapeGTRA::Scale(const double Factor)
+bool MDShapeGTRA::Scale(const double Factor, const MString Axes)
 {
-  // Scale this shape by Factor
-
-  m_Dz *= Factor;
-  // m_Theta *= Factor;
-  // m_Phi *= Factor;
-  // m_Twist *= Factor;
-  m_H1 *= Factor;
-  m_H2 *= Factor;
-  m_Bl1 *= Factor;
-  m_Bl2 *= Factor;
-  m_Tl1 *= Factor;
-  m_Tl2 *= Factor;
-  // m_Alpha1 *= Factor;
-  // m_Alpha2 *= Factor;
-  
+  //! Scale the axes given in Axes by a factor Scaler
+
+  // Don't do anything if the scaling has already been applied
+  if (Factor == m_Scaler && Axes == m_ScalingAxis) return true;
+
+  // Base class handles sanity checks and storing data
+  if (MDShape::Scale(Factor, Axes) == false) return false;
+  // If there was no scaling return true;
+  if (IsScaled() == false) return true;
+
+
+  // Now scale
+  if (m_ScalingAxis.Contains("X") == true) {
+    m_Bl1 *= m_Scaler;
+    m_Bl2 *= m_Scaler;
+    m_Tl1 *= m_Scaler;
+    m_Tl2 *= m_Scaler;
+  }
+  if (m_ScalingAxis.Contains("Y") == true) {
+    m_H1 *= m_Scaler;
+    m_H2 *= m_Scaler;
+  }
+  if (m_ScalingAxis.Contains("Z") == true) {
+    m_Dz *= m_Scaler;
+  }
+
+
+  // Now validate
   m_IsValidated = false;
-  
-  Validate();
+  return Validate();
 }
 
 
diff --git a/src/geomega/src/MDShapeIntersection.cxx b/src/geomega/src/MDShapeIntersection.cxx
index ce8036511..f66d53f27 100644
--- a/src/geomega/src/MDShapeIntersection.cxx
+++ b/src/geomega/src/MDShapeIntersection.cxx
@@ -171,22 +171,60 @@ double MDShapeIntersection::GetVolume()
 {
   // Return the volume of this cylinder
 
-  return m_Geo->Capacity();
+  // Since the accuracy is only 1%, run it 16 times to get 4 times better precision
+  const unsigned int Runs = 16;
+  double Sum = 0.0;
+  for (unsigned int i = 0; i < Runs; ++i) {
+    Sum += m_Geo->Capacity();
+  }
+
+  return Sum / Runs;
 }
 
 
 ////////////////////////////////////////////////////////////////////////////////
 
 
-void MDShapeIntersection::Scale(const double Factor)
+bool MDShapeIntersection::Scale(const double Factor, const MString Axes)
 {
-  // Scale this shape by Factor
+  //! Scale the axes given in Axes by a factor Scaler
 
-  m_Scaler = Factor;
-  
+  // Don't do anything if the scaling has already been applied
+  if (Factor == m_Scaler && Axes == m_ScalingAxis) return true;
+
+  // Base class handles sanity checks and storing data
+  if (MDShape::Scale(Factor, Axes) == false) return false;
+  // If there was no scaling return true;
+  if (IsScaled() == false) return true;
+
+
+  // Scale
+  if (m_SubShapes[0]->IsScaled() == true) {
+    mout<<"   ***  Error  ***  in shape "<<m_Name<<endl;
+    mout<<"Trying to scale already scaled first shape: "<<m_SubShapes[0]->GetName()<<endl;
+    return false;
+  }
+
+  if (m_SubShapes[1]->IsScaled() == true) {
+    mout<<"   ***  Error  ***  in shape "<<m_Name<<endl;
+    mout<<"Trying to scale already scaled second shape: "<<m_SubShapes[1]->GetName()<<endl;
+    return false;
+  }
+
+  if (m_Orientation->IsScaled() == true) {
+    mout<<"   ***  Error  ***  in shape "<<m_Name<<endl;
+    mout<<"Trying to scale already scaled orientation: "<<m_Orientation->GetName()<<endl;
+    return false;
+  }
+
+  m_SubShapes[0]->Scale(m_Scaler, m_ScalingAxis);
+  m_SubShapes[1]->Scale(m_Scaler, m_ScalingAxis);
+  m_Orientation->Scale(m_Scaler, m_ScalingAxis);
+
+
+  // Validate
   m_IsValidated = false;
-  
-  Validate();
+  return Validate();
 }
 
 
diff --git a/src/geomega/src/MDShapePCON.cxx b/src/geomega/src/MDShapePCON.cxx
index a52d7450b..4eb007f29 100644
--- a/src/geomega/src/MDShapePCON.cxx
+++ b/src/geomega/src/MDShapePCON.cxx
@@ -366,19 +366,38 @@ double MDShapePCON::GetVolume()
 ////////////////////////////////////////////////////////////////////////////////
 
 
-void MDShapePCON::Scale(const double Factor)
+bool MDShapePCON::Scale(const double Factor, const MString Axes)
 {
-  // Scale this shape by Factor
+  //! Scale the axes given in Axes by a factor Scaler
 
+  // Don't do anything if the scaling has already been applied
+  if (Factor == m_Scaler && Axes == m_ScalingAxis) return true;
+
+  // Base class handles sanity checks and storing data
+  if (MDShape::Scale(Factor, Axes) == false) return false;
+  // If there was no scaling return true;
+  if (IsScaled() == false) return true;
+
+  if ((m_ScalingAxis.Contains("X") == true && m_ScalingAxis.Contains("Y") == false) || (m_ScalingAxis.Contains("X") == false && m_ScalingAxis.Contains("Y") == true)) {
+    mout<<"   ***  Error  ***  in shape "<<m_Name<<endl;
+    mout<<"This volume can only be scaled the same way in X as in Y axis, i.e., the axis string must contain \"XY\"."<<endl;
+    return false;
+  }
+
+  // Scale
   for (unsigned int i = 0; i < m_NSections; ++i) {
-    m_Rmin[i] *= Factor;
-    m_Rmax[i] *= Factor;
-    m_Z[i] *= Factor;  
+    if (m_ScalingAxis.Contains("X") == true && m_ScalingAxis.Contains("Y") == true) {
+      m_Rmin[i] *= m_Scaler;
+      m_Rmax[i] *= m_Scaler;
+    }
+    if (m_ScalingAxis.Contains("Z") == true) {
+      m_Z[i] *= m_Scaler;
+    }
   }
-  
+
+  // Validate
   m_IsValidated = false;
-  
-  Validate();
+  return Validate();
 }
 
 
diff --git a/src/geomega/src/MDShapePGON.cxx b/src/geomega/src/MDShapePGON.cxx
index e95319901..fa0888389 100644
--- a/src/geomega/src/MDShapePGON.cxx
+++ b/src/geomega/src/MDShapePGON.cxx
@@ -415,19 +415,38 @@ double MDShapePGON::GetVolume()
 ////////////////////////////////////////////////////////////////////////////////
 
 
-void MDShapePGON::Scale(const double Factor)
+bool MDShapePGON::Scale(const double Factor, const MString Axes)
 {
-  // Scale this shape by Factor
-  
+  //! Scale the axes given in Axes by a factor Scaler
+
+  // Don't do anything if the scaling has already been applied
+  if (Factor == m_Scaler && Axes == m_ScalingAxis) return true;
+
+  // Base class handles sanity checks and storing data
+  if (MDShape::Scale(Factor, Axes) == false) return false;
+  // If there was no scaling return true;
+  if (IsScaled() == false) return true;
+
+  if ((m_ScalingAxis.Contains("X") == true && m_ScalingAxis.Contains("Y") == false) || (m_ScalingAxis.Contains("X") == false && m_ScalingAxis.Contains("Y") == true)) {
+    mout<<"   ***  Error  ***  in shape "<<m_Name<<endl;
+    mout<<"This volume can only be scaled the same way in X as in Y axis, i.e., the axis string must contain \"XY\"."<<endl;
+    return false;
+  }
+
+  // Scale
   for (unsigned int i = 0; i < m_NSections; ++i) {
-    m_Rmin[i] *= Factor;
-    m_Rmax[i] *= Factor;
-    m_Z[i] *= Factor;  
+    if (m_ScalingAxis.Contains("X") == true && m_ScalingAxis.Contains("Y") == true) {
+      m_Rmin[i] *= m_Scaler;
+      m_Rmax[i] *= m_Scaler;
+    }
+    if (m_ScalingAxis.Contains("Z") == true) {
+      m_Z[i] *= m_Scaler;
+    }
   }
   
+  // Validate
   m_IsValidated = false;
-  
-  Validate();
+  return Validate();
 }
 
 
diff --git a/src/geomega/src/MDShapeSPHE.cxx b/src/geomega/src/MDShapeSPHE.cxx
index 8b29b51b4..c076603b2 100644
--- a/src/geomega/src/MDShapeSPHE.cxx
+++ b/src/geomega/src/MDShapeSPHE.cxx
@@ -345,16 +345,33 @@ double MDShapeSPHE::GetVolume()
 ////////////////////////////////////////////////////////////////////////////////
 
 
-void MDShapeSPHE::Scale(const double Factor)
+bool MDShapeSPHE::Scale(const double Factor, const MString Axes)
 {
-  // Scale this shape by Factor
+  //! Scale the axes given in Axes by a factor Scaler
 
-  m_Rmin *= Factor;
-  m_Rmax *= Factor;
+  // Don't do anything if the scaling has already been applied
+  if (Factor == m_Scaler && Axes == m_ScalingAxis) return true;
+
+  // Base class handles sanity checks and storing data
+  if (MDShape::Scale(Factor, Axes) == false) return false;
+  // If there was no scaling return true;
+  if (IsScaled() == false) return true;
+
+  if (!(m_ScalingAxis.Contains("X") == true && m_ScalingAxis.Contains("Y") == true && m_ScalingAxis.Contains("Z") == true)) {
+    mout<<"   ***  Error  ***  in shape "<<m_Name<<endl;
+    mout<<"This volume can only be scaled the same way in X, Y, and Z axis, i.e., the axis string must contain \"XYZ\"."<<endl;
+    return false;
+  }
+
+  // Scale
+  if (m_ScalingAxis.Contains("X") == true && m_ScalingAxis.Contains("Y") == true && m_ScalingAxis.Contains("Z") == true) {
+    m_Rmin *= m_Scaler;
+    m_Rmax *= m_Scaler;
+  }
   
+  // Validate
   m_IsValidated = false;
-  
-  Validate();
+  return Validate();
 }
 
 
diff --git a/src/geomega/src/MDShapeSubtraction.cxx b/src/geomega/src/MDShapeSubtraction.cxx
index 7cf4d8688..cfa6674c0 100644
--- a/src/geomega/src/MDShapeSubtraction.cxx
+++ b/src/geomega/src/MDShapeSubtraction.cxx
@@ -137,7 +137,7 @@ bool MDShapeSubtraction::Validate()
     }
     
     delete m_Geo;
-    cout<<"Creating Node of: "<<m_SubShapes[0]->GetName()<<" & "<<m_SubShapes[1]->GetName()<<endl;
+    //cout<<"Creating Node of: "<<m_SubShapes[0]->GetName()<<" & "<<m_SubShapes[1]->GetName()<<endl;
     TGeoSubtraction* Node = new TGeoSubtraction(m_SubShapes[0]->GetRootShape(), m_SubShapes[1]->GetRootShape(), 0, m_Orientation->GetRootMatrix());
     m_Geo = new TGeoCompositeShape(m_Name, Node);
     
@@ -171,28 +171,62 @@ bool MDShapeSubtraction::Parse(const MTokenizer& Tokenizer, const MDDebugInfo& I
 
 double MDShapeSubtraction::GetVolume()
 {
-  // Return the volume of this cylinder
+  // Return the volume of this subtraction
 
-  return m_Geo->Capacity();
+  // Since the accuracy is only 1%, run it 16 times to get 4 times better precision
+  const unsigned int Runs = 16;
+  double Sum = 0.0;
+  for (unsigned int i = 0; i < Runs; ++i) {
+    Sum += m_Geo->Capacity();
+  }
+
+  return Sum / Runs;
 }
 
 
 ////////////////////////////////////////////////////////////////////////////////
 
 
-void MDShapeSubtraction::Scale(const double Factor)
+bool MDShapeSubtraction::Scale(const double Factor, const MString Axes)
 {
-  // Scale this shape by Factor
+  //! Scale the axes given in Axes by a factor Scaler
 
-  m_Scaler = Factor;
-  
-  //if (m_Minuend->GetScaler() != Factor) m_Minuend->Scale(Factor);
-  //if (m_Subtrahend->GetScaler() != Factor) m_Subtrahend->Scale(Factor);
-  //if (m_Orientation->GetScaler() != Factor) m_Orientation->Scale(Factor);
-  
+  // Don't do anything if the scaling has already been applied
+  if (Factor == m_Scaler && Axes == m_ScalingAxis) return true;
+
+  // Base class handles sanity checks and storing data
+  if (MDShape::Scale(Factor, Axes) == false) return false;
+  // If there was no scaling return true;
+  if (IsScaled() == false) return true;
+
+
+  // Scale
+  if (m_SubShapes[0]->IsScaled() == true) {
+    mout<<"   ***  Error  ***  in shape "<<m_Name<<endl;
+    mout<<"Trying to scale already scaled minuend: "<<m_SubShapes[0]->GetName()<<endl;
+    return false;
+  }
+
+  if (m_SubShapes[1]->IsScaled() == true) {
+    mout<<"   ***  Error  ***  in shape "<<m_Name<<endl;
+    mout<<"Trying to scale already scaled subtrahend: "<<m_SubShapes[1]->GetName()<<endl;
+    return false;
+  }
+
+  if (m_Orientation->IsScaled() == true) {
+    mout<<"   ***  Error  ***  in shape "<<m_Name<<endl;
+    mout<<"Trying to scale already scaled orientation: "<<m_Orientation->GetName()<<endl;
+    return false;
+  }
+
+  m_SubShapes[0]->Scale(m_Scaler, m_ScalingAxis);
+  m_SubShapes[1]->Scale(m_Scaler, m_ScalingAxis);
+  m_Orientation->Scale(m_Scaler, m_ScalingAxis);
+
+
+  // Validate
   m_IsValidated = false;
-  
-  Validate();
+  return Validate();
 }
 
 
diff --git a/src/geomega/src/MDShapeTRAP.cxx b/src/geomega/src/MDShapeTRAP.cxx
index 58c68e96b..b2f1d9dd2 100644
--- a/src/geomega/src/MDShapeTRAP.cxx
+++ b/src/geomega/src/MDShapeTRAP.cxx
@@ -451,21 +451,38 @@ double MDShapeTRAP::GetVolume()
 ////////////////////////////////////////////////////////////////////////////////
 
 
-void MDShapeTRAP::Scale(const double Factor)
+bool MDShapeTRAP::Scale(const double Factor, const MString Axes)
 {
-  // Scale this shape by Factor
-
-  m_Dz *= Factor;
-  m_H1 *= Factor;
-  m_H2 *= Factor;
-  m_Bl1 *= Factor;
-  m_Bl2 *= Factor;
-  m_Tl1 *= Factor;
-  m_Tl2 *= Factor;
-  
+  //! Scale the axes given in Axes by a factor Scaler
+
+  // Don't do anything if the scaling has already been applied
+  if (Factor == m_Scaler && Axes == m_ScalingAxis) return true;
+
+  // Base class handles sanity checks and storing data
+  if (MDShape::Scale(Factor, Axes) == false) return false;
+  // If there was no scaling return true;
+  if (IsScaled() == false) return true;
+
+
+  // Now scale
+  if (m_ScalingAxis.Contains("X") == true) {
+    m_Bl1 *= m_Scaler;
+    m_Bl2 *= m_Scaler;
+    m_Tl1 *= m_Scaler;
+    m_Tl2 *= m_Scaler;
+  }
+  if (m_ScalingAxis.Contains("Y") == true) {
+    m_H1 *= m_Scaler;
+    m_H2 *= m_Scaler;
+  }
+  if (m_ScalingAxis.Contains("Z") == true) {
+    m_Dz *= m_Scaler;
+  }
+
+
+  // Now validate
   m_IsValidated = false;
-  
-  Validate();
+  return Validate();
 }
 
 
diff --git a/src/geomega/src/MDShapeTRD1.cxx b/src/geomega/src/MDShapeTRD1.cxx
index 92b204e5a..7d11fb4da 100644
--- a/src/geomega/src/MDShapeTRD1.cxx
+++ b/src/geomega/src/MDShapeTRD1.cxx
@@ -248,18 +248,33 @@ double MDShapeTRD1::GetVolume()
 ////////////////////////////////////////////////////////////////////////////////
 
 
-void MDShapeTRD1::Scale(const double Factor)
+bool MDShapeTRD1::Scale(const double Factor, const MString Axes)
 {
-  // Scale this shape by Factor
+  //! Scale the axes given in Axes by a factor Scaler
 
-  m_Ddx1 *= Factor;
-  m_Ddx2 *= Factor;
-  m_Dy *= Factor;
-  m_Dz *= Factor;
+  // Don't do anything if the scaling has already been applied
+  if (Factor == m_Scaler && Axes == m_ScalingAxis) return true;
+
+  // Base class handles sanity checks and storing data
+  if (MDShape::Scale(Factor, Axes) == false) return false;
+  // If there was no scaling return true;
+  if (IsScaled() == false) return true;
+
+  // Now scale
+  if (m_ScalingAxis.Contains("X") == true) {
+    m_Ddx1 *= m_Scaler;
+    m_Ddx2 *= m_Scaler;
+  }
+  if (m_ScalingAxis.Contains("Y") == true) {
+    m_Dy *= m_Scaler;
+  }
+  if (m_ScalingAxis.Contains("Z") == true) {
+    m_Dz *= m_Scaler;
+  }
   
+  // Now validate
   m_IsValidated = false;
-  
-  Validate();
+  return Validate();
 }
 
 
diff --git a/src/geomega/src/MDShapeTRD2.cxx b/src/geomega/src/MDShapeTRD2.cxx
index af704e8dc..d4d73cc2f 100644
--- a/src/geomega/src/MDShapeTRD2.cxx
+++ b/src/geomega/src/MDShapeTRD2.cxx
@@ -269,19 +269,36 @@ double MDShapeTRD2::GetVolume()
 ////////////////////////////////////////////////////////////////////////////////
 
 
-void MDShapeTRD2::Scale(const double Factor)
+bool MDShapeTRD2::Scale(const double Factor, const MString Axes)
 {
-  // Scale this shape by Factor
+  //! Scale the axes given in Axes by a factor Scaler
 
-  m_Dx1 *= Factor;
-  m_Dx2 *= Factor;
-  m_Dy1 *= Factor;
-  m_Dy2 *= Factor;
-  m_Z *= Factor;
-  
+  // Don't do anything if the scaling has already been applied
+  if (Factor == m_Scaler && Axes == m_ScalingAxis) return true;
+
+  // Base class handles sanity checks and storing data
+  if (MDShape::Scale(Factor, Axes) == false) return false;
+  // If there was no scaling return true;
+  if (IsScaled() == false) return true;
+
+
+  // Now scale
+  if (m_ScalingAxis.Contains("X") == true) {
+    m_Dx1 *= m_Scaler;
+    m_Dx2 *= m_Scaler;
+  }
+  if (m_ScalingAxis.Contains("Y") == true) {
+    m_Dy1 *= m_Scaler;
+    m_Dy2 *= m_Scaler;
+  }
+  if (m_ScalingAxis.Contains("Z") == true) {
+    m_Z *= m_Scaler;
+  }
+
+
+  // Validate
   m_IsValidated = false;
-  
-  Validate();
+  return Validate();
 }
 
 
diff --git a/src/geomega/src/MDShapeTUBS.cxx b/src/geomega/src/MDShapeTUBS.cxx
index 6197b66e3..d0ee6b323 100644
--- a/src/geomega/src/MDShapeTUBS.cxx
+++ b/src/geomega/src/MDShapeTUBS.cxx
@@ -283,16 +283,37 @@ double MDShapeTUBS::GetVolume()
 ////////////////////////////////////////////////////////////////////////////////
 
 
-void MDShapeTUBS::Scale(const double Factor)
+bool MDShapeTUBS::Scale(const double Factor, const MString Axes)
 {
-  // Scale this shape by Factor
+  //! Scale the axes given in Axes by a factor Scaler
 
-  m_Rmin *= Factor;
-  m_Rmax *= Factor;
-  m_HalfHeight *= Factor;
+  // Don't do anything if the scaling has already been applied
+  if (Factor == m_Scaler && Axes == m_ScalingAxis) return true;
 
+  // Base class handles sanity checks and storing data
+  if (MDShape::Scale(Factor, Axes) == false) return false;
+  // If there was no scaling return true;
+  if (IsScaled() == false) return true;
+
+  if ((m_ScalingAxis.Contains("X") == true && m_ScalingAxis.Contains("Y") == false) || (m_ScalingAxis.Contains("X") == false && m_ScalingAxis.Contains("Y") == true)) {
+    mout<<"   ***  Error  ***  in shape "<<m_Name<<endl;
+    mout<<"This volume can only be scaled the same way in X as in Y axis, i.e., the axis string must contain \"XY\"."<<endl;
+    return false;
+  }
+
+
+  // Scale
+  if (m_ScalingAxis.Contains("X") == true && m_ScalingAxis.Contains("Y") == true) {
+    m_Rmin *= m_Scaler;
+    m_Rmax *= m_Scaler;
+  }
+  if (m_ScalingAxis.Contains("Z") == true) {
+    m_HalfHeight *= m_Scaler;
+  }
+
+
+  // Validate
   m_IsValidated = false;
-  
   Validate();
 }
 
diff --git a/src/geomega/src/MDShapeUnion.cxx b/src/geomega/src/MDShapeUnion.cxx
index 3696469e8..d1aaf0aef 100644
--- a/src/geomega/src/MDShapeUnion.cxx
+++ b/src/geomega/src/MDShapeUnion.cxx
@@ -170,25 +170,63 @@ double MDShapeUnion::GetVolume()
   // Return the volume of this cylinder
 
   return m_Geo->Capacity();
+
+  /* We could do that too, but for unions, it is not so critial than for subtractions and intersections.
+  // Since the accuracy is only 1%, run it 16 times to get 4 times better precision
+  const unsigned int Runs = 16;
+  double Sum = 0.0;
+  for (unsigned int i = 0; i < Runs; ++i) {
+    Sum += m_Geo->Capacity();
+  }
+
+  return Sum / Runs;
+  */
 }
 
 
 ////////////////////////////////////////////////////////////////////////////////
 
 
-void MDShapeUnion::Scale(const double Factor)
+bool MDShapeUnion::Scale(const double Factor, const MString Axes)
 {
-  // Scale this shape by Factor
+  //! Scale the axes given in Axes by a factor Scaler
 
-  m_Scaler = Factor;
-  
-  //if (m_Augend->GetScaler() != Factor) m_Augend->Scale(Factor);
-  //if (m_Addend->GetScaler() != Factor) m_Addend->Scale(Factor);
-  //if (m_Orientation->GetScaler() != Factor) m_Orientation->Scale(Factor);
+  // Don't do anything if the scaling has already been applied
+  if (Factor == m_Scaler && Axes == m_ScalingAxis) return true;
+
+  // Base class handles sanity checks and storing data
+  if (MDShape::Scale(Factor, Axes) == false) return false;
+  // If there was no scaling return true;
+  if (IsScaled() == false) return true;
+
+
+  // Scale
+  if (m_SubShapes[0]->IsScaled() == true) {
+    mout<<"   ***  Error  ***  in shape "<<m_Name<<endl;
+    mout<<"Trying to scale already scaled augend: "<<m_SubShapes[0]->GetName()<<endl;
+    return false;
+  }
+
+  if (m_SubShapes[1]->IsScaled() == true) {
+    mout<<"   ***  Error  ***  in shape "<<m_Name<<endl;
+    mout<<"Trying to scale already scaled addend: "<<m_SubShapes[1]->GetName()<<endl;
+    return false;
+  }
+
+  if (m_Orientation->IsScaled() == true) {
+    mout<<"   ***  Error  ***  in shape "<<m_Name<<endl;
+    mout<<"Trying to scale already scaled orientation: "<<m_Orientation->GetName()<<endl;
+    return false;
+  }
+
+  m_SubShapes[0]->Scale(m_Scaler, m_ScalingAxis);
+  m_SubShapes[1]->Scale(m_Scaler, m_ScalingAxis);
+  m_Orientation->Scale(m_Scaler, m_ScalingAxis);
   
+
+  // Validate
   m_IsValidated = false;
-  
-  Validate();
+  return Validate();
 }
 
 
diff --git a/src/geomega/src/MDVolume.cxx b/src/geomega/src/MDVolume.cxx
index b430368a6..10333deba 100644
--- a/src/geomega/src/MDVolume.cxx
+++ b/src/geomega/src/MDVolume.cxx
@@ -1939,16 +1939,25 @@ bool MDVolume::ApplyPulseShape(double Time, MVector& Pos, double& Energy)
 ////////////////////////////////////////////////////////////////////////////////
 
 
-bool MDVolume::Scale(const double Factor)
+bool MDVolume::Scale(const double Factor, const MString Axes)
 {
   // Scale this volume and all daughter volumes correctly
 
+  if (Factor == 1.0 || Axes == "") return true;
+
   if (m_CloneTemplate != 0 &&
       m_CloneTemplate->IsCloneTemplateVolumeWritten() == false) {
-    m_Shape->Scale(Factor);
-    m_CloneTemplate->SetCloneTemplateVolumeWritten(true);
+    if (m_Shape->Scale(Factor, Axes) == true) {
+      m_CloneTemplate->SetCloneTemplateVolumeWritten(true);
+    } else {
+      // Error message alreday printed
+      return false;
+    }
   } else if (IsClone() == false) {
-    m_Shape->Scale(Factor);
+    if (m_Shape->Scale(Factor, Axes) == false) {
+      // Error message alreday handled
+      return false;
+    }
   }
   // The position of this volume is unchanged!
 
@@ -1956,7 +1965,8 @@ bool MDVolume::Scale(const double Factor)
   vector<MDVolume*>::iterator Daughters;
   for (Daughters = m_Daughters.begin(); Daughters != m_Daughters.end(); ++Daughters) {
     (*Daughters)->SetPosition((*Daughters)->GetPosition()*Factor);
-    if ((*Daughters)->Scale(Factor) == false) {
+    if ((*Daughters)->Scale(Factor, Axes) == false) {
+      // Error message already printed
       return false;
     }
   }
diff --git a/src/sivan/src/MInterfaceSivan.cxx b/src/sivan/src/MInterfaceSivan.cxx
index 0c7c479e2..ec27688a6 100644
--- a/src/sivan/src/MInterfaceSivan.cxx
+++ b/src/sivan/src/MInterfaceSivan.cxx
@@ -5273,23 +5273,28 @@ void MInterfaceSivan::MissingInteractionsStatistics()
   double EscapedEnergy = 0.0;
   double NSEnergy = 0.0;
   map<MString, int> Materials;
+  map<MString, int> MaterialOfFirstMissingInteraction;
   map<MString, double> EnergyInPassiveMaterial;
 
   EventFile.Rewind();
   while ((Event = EventFile.GetNextEvent(false)) != 0) {
+    bool FirstNonStartFound = false;
     for (unsigned int i = 1; i < Event->GetNIAs(); ++i) {
       if (Event->GetIAAt(i)->GetProcess() != "INIT" && 
           Event->GetIAAt(i)->GetProcess() != "ESCP") {
         if (Event->GetIAAt(i)->GetDetectorType() == 0) {
+          MDVolumeSequence* S = m_Geometry->GetVolumeSequencePointer(Event->GetIAAt(i)->GetPosition());
+
           zPosAll->Fill(Event->GetIAAt(i)->GetPosition()[2]);
           xyPosAll->Fill(Event->GetIAAt(i)->GetPosition()[0], Event->GetIAAt(i)->GetPosition()[1]);
           xyzPosAll->Fill(Event->GetIAAt(i)->GetPosition()[0], Event->GetIAAt(i)->GetPosition()[1], Event->GetIAAt(i)->GetPosition()[2]);
-          if (i == 1) {
+          if (FirstNonStartFound == false) {
             zPosStart->Fill(Event->GetIAAt(i)->GetPosition()[2]);
             xyPosStart->Fill(Event->GetIAAt(i)->GetPosition()[0], Event->GetIAAt(i)->GetPosition()[1]);
             xyzPosStart->Fill(Event->GetIAAt(i)->GetPosition()[0], Event->GetIAAt(i)->GetPosition()[1], Event->GetIAAt(i)->GetPosition()[2]);
+            FirstNonStartFound = true;
+            MaterialOfFirstMissingInteraction[S->GetDeepestVolume()->GetMaterial()->GetName()]++;
           }
-          MDVolumeSequence* S = m_Geometry->GetVolumeSequencePointer(Event->GetIAAt(i)->GetPosition());
           Materials[S->GetDeepestVolume()->GetMaterial()->GetName()]++;
           delete S;
         }
@@ -5339,14 +5344,28 @@ void MInterfaceSivan::MissingInteractionsStatistics()
 
   map<MString, int>::iterator MaterialsIter;
   mout<<endl;
-  mout<<"Materials of passive material interaction:"<<endl;
+  mout<<"Materials of passive material of first missing interaction:"<<endl;
 
   int AllHits = 0;
-  for (MaterialsIter = (Materials.begin()); 
+  for (MaterialsIter = (MaterialOfFirstMissingInteraction.begin());
+       MaterialsIter != MaterialOfFirstMissingInteraction.end(); MaterialsIter++) {
+    AllHits += (*MaterialsIter).second;
+  }
+  for (MaterialsIter = (MaterialOfFirstMissingInteraction.begin());
+       MaterialsIter != MaterialOfFirstMissingInteraction.end(); MaterialsIter++) {
+    cout<<setw(24)<<(*MaterialsIter).first<<": "<<setw(10)<<(*MaterialsIter).second
+        <<" ("<<setprecision(4)<<setw(9)<<double((*MaterialsIter).second)/AllHits*100.0<<"%)"<<endl;
+  }
+
+  mout<<endl;
+  mout<<"Materials of passive material any missing interaction:"<<endl;
+
+  AllHits = 0;
+  for (MaterialsIter = (Materials.begin());
        MaterialsIter != Materials.end(); MaterialsIter++) {
     AllHits += (*MaterialsIter).second;
   }
-  for (MaterialsIter = (Materials.begin()); 
+  for (MaterialsIter = (Materials.begin());
        MaterialsIter != Materials.end(); MaterialsIter++) {
     cout<<setw(24)<<(*MaterialsIter).first<<": "<<setw(10)<<(*MaterialsIter).second
         <<" ("<<setprecision(4)<<setw(9)<<double((*MaterialsIter).second)/AllHits*100.0<<"%)"<<endl;

From ed885d7d647ece5996146497a87767670c896d0b Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Wed, 13 Nov 2024 13:10:06 -0800
Subject: [PATCH 103/192] BUG: Missed adding return value

---
 src/geomega/src/MDShapeCONS.cxx | 2 +-
 src/geomega/src/MDShapeTUBS.cxx | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/geomega/src/MDShapeCONS.cxx b/src/geomega/src/MDShapeCONS.cxx
index d4e199ae4..d081083a5 100644
--- a/src/geomega/src/MDShapeCONS.cxx
+++ b/src/geomega/src/MDShapeCONS.cxx
@@ -351,7 +351,7 @@ bool MDShapeCONS::Scale(const double Factor, const MString Axes)
 
   // Validate
   m_IsValidated = false;
-  Validate();
+  return Validate();
 }
 
 
diff --git a/src/geomega/src/MDShapeTUBS.cxx b/src/geomega/src/MDShapeTUBS.cxx
index d0ee6b323..b1c2ebcff 100644
--- a/src/geomega/src/MDShapeTUBS.cxx
+++ b/src/geomega/src/MDShapeTUBS.cxx
@@ -314,7 +314,7 @@ bool MDShapeTUBS::Scale(const double Factor, const MString Axes)
 
   // Validate
   m_IsValidated = false;
-  Validate();
+  return Validate();
 }
 
 

From 9ba45b4a2dd05a0266620578361cde36ff54b44a Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Wed, 13 Nov 2024 15:44:54 -0800
Subject: [PATCH 104/192] FIX: Compiler warnings

---
 src/fretalon/base/src/MCalibrateEnergyFindLines.cxx |  3 ++-
 src/mimrec/src/MARMFitter.cxx                       | 12 ++++++------
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/src/fretalon/base/src/MCalibrateEnergyFindLines.cxx b/src/fretalon/base/src/MCalibrateEnergyFindLines.cxx
index 3248fca7f..bd000e339 100644
--- a/src/fretalon/base/src/MCalibrateEnergyFindLines.cxx
+++ b/src/fretalon/base/src/MCalibrateEnergyFindLines.cxx
@@ -21,6 +21,7 @@
 
 // Standard libs:
 #include <algorithm>
+#include <type_traits>
 using namespace std;
 
 // ROOT libs:
@@ -325,7 +326,7 @@ bool MCalibrateEnergyFindLines::FindPeaks(unsigned int ROGID)
       
       // If this is the first peak it must be at least 3 bins away from the first bin and from any bin with less than 1 counts:
       //if (FirstPeak == true) {
-        if (PeakBin < m_ExcludeFirstNumberOfBins) {
+        if (std::make_unsigned<int>::type(PeakBin) < m_ExcludeFirstNumberOfBins) {
           if (g_Verbosity >= c_Info) cout<<FirstDerivation->GetBinLowEdge(b+1)<<" - Rejected: First peak must be at least "<<m_ExcludeFirstNumberOfBins<<" bins away from start, and not only "<<PeakBin<<endl;
           continue;          
         } else {
diff --git a/src/mimrec/src/MARMFitter.cxx b/src/mimrec/src/MARMFitter.cxx
index ec7719e2b..6b3884a17 100644
--- a/src/mimrec/src/MARMFitter.cxx
+++ b/src/mimrec/src/MARMFitter.cxx
@@ -869,7 +869,7 @@ bool MARMFitter::FitAll()
 {
   unsigned int NFits = 500;
 
-  MARMFitFunctionID Best;
+  MARMFitFunctionID Best = MARMFitFunctionID::c_Gauss;
   double BestBC = 0;
 
   cout<<"Fitting through all functions (except Lorentz) with "<<NFits<<" samples."<<endl;
@@ -974,14 +974,14 @@ void MARMFitter::CalculateBootStrappedMetrics()
 
     // Find the bin with the FWHM closest to the average to choose the best fit parameters
     unsigned int ClosestBin = 0;
-    double ClosestValue = m_BootStrappedFWHMSamples[0];
+    //double ClosestValue = m_BootStrappedFWHMSamples[0];
     double MinDifference = std::abs(m_BootStrappedFWHMSamples[0] - m_FinalFWHM);
 
     for (unsigned int b = 1; b < m_BootStrappedFWHMSamples.size(); ++b) {
       double Difference = std::abs(m_BootStrappedFWHMSamples[b] - m_FinalFWHM);
       if (Difference < MinDifference) {
         MinDifference = Difference;
-        ClosestValue = m_BootStrappedFWHMSamples[b];
+        //ClosestValue = m_BootStrappedFWHMSamples[b];
         ClosestBin = b;
       }
     }
@@ -1009,7 +1009,7 @@ void MARMFitter::CalculateBootStrappedMetrics()
     }
     std::sort(SortedAbs.begin(), SortedAbs.end());
 
-    for (int b = 0; b < SortedAbs.size(); ++b) {
+    for (unsigned int b = 0; b < SortedAbs.size(); ++b) {
       if (m_CountsFWHMWindowMinimum == g_UnsignedIntNotDefined && SortedAbs[b] >= m_FinalFWHM - m_FinalFWHMUncertainty) {
         m_CountsFWHMWindowMinimum = b;
       }
@@ -1051,7 +1051,7 @@ void MARMFitter::CalculateARMMetrics()
   std::sort(SortedAbsSelected.begin(), SortedAbsSelected.end());
 
   double Total = SortedAbsSelected.size();
-  for (int b = 0; b < SortedAbsSelected.size(); ++b) {
+  for (unsigned int b = 0; b < SortedAbsSelected.size(); ++b) {
     if (m_Containment50PercentUsingARMSelection == g_DoubleNotDefined && b >= Sigma0*Total) {
       m_Containment50PercentUsingARMSelection = SortedAbsSelected[b];
     }
@@ -1079,7 +1079,7 @@ void MARMFitter::CalculateARMMetrics()
   std::sort(SortedAbsAll.begin(), SortedAbsAll.end());
 
   Total = SortedAbsAll.size();
-  for (int b = 0; b < SortedAbsAll.size(); ++b) {
+  for (unsigned int b = 0; b < SortedAbsAll.size(); ++b) {
     if (m_Containment50PercentUsingAllData == g_DoubleNotDefined && b >= Sigma0*Total) {
       m_Containment50PercentUsingAllData = SortedAbsAll[b];
     }

From 44aae796b4f6da32c79e9b206c6cc20f6dc42c70 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Wed, 13 Nov 2024 20:05:22 -0800
Subject: [PATCH 105/192] CHG: Fix warnings for Ubuntu 24.04

---
 src/fretalon/base/inc/MCalibrationFit.h       |  2 +-
 .../base/inc/MCalibrationFitGaussLandau.h     |  2 +-
 .../base/inc/MCalibrationFitGaussian.h        |  2 +-
 src/fretalon/base/inc/MCalibrationModel.h     | 30 +++++++++----------
 src/global/misc/inc/MFileResponse.h           |  6 ++++
 5 files changed, 24 insertions(+), 18 deletions(-)

diff --git a/src/fretalon/base/inc/MCalibrationFit.h b/src/fretalon/base/inc/MCalibrationFit.h
index 3a5d7be8f..489460321 100644
--- a/src/fretalon/base/inc/MCalibrationFit.h
+++ b/src/fretalon/base/inc/MCalibrationFit.h
@@ -50,7 +50,7 @@ class MCalibrationFit : public ROOT::Math::IParamFunction
   virtual ~MCalibrationFit();
 
   //! The assignment operator
-  virtual MCalibrationFit& operator= (const MCalibrationFit& CalibrationFit);
+  MCalibrationFit& operator= (const MCalibrationFit& CalibrationFit);
 
   //! Clone this fit - the returned element must be deleted!
   virtual MCalibrationFit* Clone() const;
diff --git a/src/fretalon/base/inc/MCalibrationFitGaussLandau.h b/src/fretalon/base/inc/MCalibrationFitGaussLandau.h
index cd275465d..45c49907b 100644
--- a/src/fretalon/base/inc/MCalibrationFitGaussLandau.h
+++ b/src/fretalon/base/inc/MCalibrationFitGaussLandau.h
@@ -42,7 +42,7 @@ class MCalibrationFitGaussLandau : public MCalibrationFitGaussian
   virtual ~MCalibrationFitGaussLandau();
 
   //! The assignment operator
-  virtual MCalibrationFitGaussLandau& operator= (const MCalibrationFitGaussLandau& Fit);
+  MCalibrationFitGaussLandau& operator= (const MCalibrationFitGaussLandau& Fit);
 
   //! Clone this fit - the returned element must be deleted!
   virtual MCalibrationFitGaussLandau* Clone() const;
diff --git a/src/fretalon/base/inc/MCalibrationFitGaussian.h b/src/fretalon/base/inc/MCalibrationFitGaussian.h
index f37ff4d14..7c14ffc2d 100644
--- a/src/fretalon/base/inc/MCalibrationFitGaussian.h
+++ b/src/fretalon/base/inc/MCalibrationFitGaussian.h
@@ -42,7 +42,7 @@ class MCalibrationFitGaussian : public MCalibrationFit
   virtual ~MCalibrationFitGaussian();
 
   //! The assignment operator
-  virtual MCalibrationFitGaussian& operator= (const MCalibrationFitGaussian& Fit);
+  MCalibrationFitGaussian& operator= (const MCalibrationFitGaussian& Fit);
 
   //! Clone this fit - the returned element must be deleted!
   virtual MCalibrationFitGaussian* Clone() const;
diff --git a/src/fretalon/base/inc/MCalibrationModel.h b/src/fretalon/base/inc/MCalibrationModel.h
index 14f0578de..e6a2b912f 100644
--- a/src/fretalon/base/inc/MCalibrationModel.h
+++ b/src/fretalon/base/inc/MCalibrationModel.h
@@ -64,7 +64,7 @@ class MCalibrationModel : public ROOT::Math::IParamFunction
   virtual ~MCalibrationModel();
 
   //! The assignment operator
-  virtual MCalibrationModel& operator= (const MCalibrationModel& CalibrationModel);
+  MCalibrationModel& operator= (const MCalibrationModel& CalibrationModel);
 
   //! Clone this fit - the returned element must be deleted!
   virtual MCalibrationModel* Clone() const;
@@ -174,7 +174,7 @@ class MCalibrationModelPoly1Zero : public MCalibrationModel
   virtual ~MCalibrationModelPoly1Zero() {}
   
   //! The assignment operator
-  virtual MCalibrationModelPoly1Zero& operator= (const MCalibrationModelPoly1Zero& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
+  MCalibrationModelPoly1Zero& operator= (const MCalibrationModelPoly1Zero& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
   
   //! Clone this fit - the returned element must be deleted!
   virtual MCalibrationModelPoly1Zero* Clone() const { return new MCalibrationModelPoly1Zero(*this); }
@@ -217,7 +217,7 @@ class MCalibrationModelPoly1 : public MCalibrationModel
   virtual ~MCalibrationModelPoly1() {}
   
   //! The assignment operator
-  virtual MCalibrationModelPoly1& operator= (const MCalibrationModelPoly1& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
+  MCalibrationModelPoly1& operator= (const MCalibrationModelPoly1& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
   
   //! Clone this fit - the returned element must be deleted!
   virtual MCalibrationModelPoly1* Clone() const { return new MCalibrationModelPoly1(*this); }
@@ -261,7 +261,7 @@ class MCalibrationModelPoly2 : public MCalibrationModel
   virtual ~MCalibrationModelPoly2() {}
   
   //! The assignment operator
-  virtual MCalibrationModelPoly2& operator= (const MCalibrationModelPoly2& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
+  MCalibrationModelPoly2& operator= (const MCalibrationModelPoly2& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
 
   //! Clone this fit - the returned element must be deleted!
   virtual MCalibrationModelPoly2* Clone() const { return new MCalibrationModelPoly2(*this); }
@@ -307,7 +307,7 @@ class MCalibrationModelPoly3 : public MCalibrationModel
   virtual ~MCalibrationModelPoly3() {}
 
   //! The assignment operator
-  virtual MCalibrationModelPoly3& operator= (const MCalibrationModelPoly3& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
+  MCalibrationModelPoly3& operator= (const MCalibrationModelPoly3& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
 
   //! Clone this fit - the returned element must be deleted!
   virtual MCalibrationModelPoly3* Clone() const { return new MCalibrationModelPoly3(*this); }
@@ -354,7 +354,7 @@ class MCalibrationModelPoly4 : public MCalibrationModel
   virtual ~MCalibrationModelPoly4() {}
 
   //! The assignment operator
-  virtual MCalibrationModelPoly4& operator= (const MCalibrationModelPoly4& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
+  MCalibrationModelPoly4& operator= (const MCalibrationModelPoly4& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
 
   //! Clone this fit - the returned element must be deleted!
   virtual MCalibrationModelPoly4* Clone() const { return new MCalibrationModelPoly4(*this); }
@@ -402,7 +402,7 @@ class MCalibrationModelPoly1Inv1 : public MCalibrationModel
   virtual ~MCalibrationModelPoly1Inv1() {}
   
   //! The assignment operator
-  virtual MCalibrationModelPoly1Inv1& operator= (const MCalibrationModelPoly1Inv1& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
+  MCalibrationModelPoly1Inv1& operator= (const MCalibrationModelPoly1Inv1& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
   
   //! Clone this fit - the returned element must be deleted!
   virtual MCalibrationModelPoly1Inv1* Clone() const { return new MCalibrationModelPoly1Inv1(*this); }
@@ -450,7 +450,7 @@ class MCalibrationModelPoly1Inv1Zero : public MCalibrationModel
   virtual ~MCalibrationModelPoly1Inv1Zero() {}
   
   //! The assignment operator
-  virtual MCalibrationModelPoly1Inv1Zero& operator= (const MCalibrationModelPoly1Inv1Zero& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
+  MCalibrationModelPoly1Inv1Zero& operator= (const MCalibrationModelPoly1Inv1Zero& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
   
   //! Clone this fit - the returned element must be deleted!
   virtual MCalibrationModelPoly1Inv1Zero* Clone() const { return new MCalibrationModelPoly1Inv1Zero(*this); }
@@ -496,7 +496,7 @@ class MCalibrationModelPoly2Inv1 : public MCalibrationModel
   virtual ~MCalibrationModelPoly2Inv1() {}
   
   //! The assignment operator
-  virtual MCalibrationModelPoly2Inv1& operator= (const MCalibrationModelPoly2Inv1& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
+  MCalibrationModelPoly2Inv1& operator= (const MCalibrationModelPoly2Inv1& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
   
   //! Clone this fit - the returned element must be deleted!
   virtual MCalibrationModelPoly2Inv1* Clone() const { return new MCalibrationModelPoly2Inv1(*this); }
@@ -545,7 +545,7 @@ class MCalibrationModelPoly2Inv1Zero : public MCalibrationModel
   virtual ~MCalibrationModelPoly2Inv1Zero() {}
   
   //! The assignment operator
-  virtual MCalibrationModelPoly2Inv1Zero& operator= (const MCalibrationModelPoly2Inv1Zero& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
+  MCalibrationModelPoly2Inv1Zero& operator= (const MCalibrationModelPoly2Inv1Zero& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
   
   //! Clone this fit - the returned element must be deleted!
   virtual MCalibrationModelPoly2Inv1Zero* Clone() const { return new MCalibrationModelPoly2Inv1Zero(*this); }
@@ -592,7 +592,7 @@ class MCalibrationModelPoly1Exp1 : public MCalibrationModel
   virtual ~MCalibrationModelPoly1Exp1() {}
 
   //! The assignment operator
-  virtual MCalibrationModelPoly1Exp1& operator= (const MCalibrationModelPoly1Exp1& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
+  MCalibrationModelPoly1Exp1& operator= (const MCalibrationModelPoly1Exp1& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
 
   //! Clone this fit - the returned element must be deleted!
   virtual MCalibrationModelPoly1Exp1* Clone() const { return new MCalibrationModelPoly1Exp1(*this); }
@@ -644,7 +644,7 @@ class MCalibrationModelPoly1Exp2 : public MCalibrationModel
   virtual ~MCalibrationModelPoly1Exp2() {}
 
   //! The assignment operator
-  virtual MCalibrationModelPoly1Exp2& operator= (const MCalibrationModelPoly1Exp2& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
+  MCalibrationModelPoly1Exp2& operator= (const MCalibrationModelPoly1Exp2& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
 
   //! Clone this fit - the returned element must be deleted!
   virtual MCalibrationModelPoly1Exp2* Clone() const { return new MCalibrationModelPoly1Exp2(*this); }
@@ -696,7 +696,7 @@ class MCalibrationModelPoly1Exp3 : public MCalibrationModel
   virtual ~MCalibrationModelPoly1Exp3() {}
   
   //! The assignment operator
-  virtual MCalibrationModelPoly1Exp3& operator= (const MCalibrationModelPoly1Exp3& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
+  MCalibrationModelPoly1Exp3& operator= (const MCalibrationModelPoly1Exp3& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
   
   //! Clone this fit - the returned element must be deleted!
   virtual MCalibrationModelPoly1Exp3* Clone() const { return new MCalibrationModelPoly1Exp3(*this); }
@@ -748,7 +748,7 @@ class MCalibrationModelPoly1Log1 : public MCalibrationModel
   virtual ~MCalibrationModelPoly1Log1() {}
   
   //! The assignment operator
-  virtual MCalibrationModelPoly1Log1& operator= (const MCalibrationModelPoly1Log1& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
+  MCalibrationModelPoly1Log1& operator= (const MCalibrationModelPoly1Log1& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
   
   //! Clone this fit - the returned element must be deleted!
   virtual MCalibrationModelPoly1Log1* Clone() const { return new MCalibrationModelPoly1Log1(*this); }
@@ -799,7 +799,7 @@ class MCalibrationModelPoly2Log1 : public MCalibrationModel
   virtual ~MCalibrationModelPoly2Log1() {}
   
   //! The assignment operator
-  virtual MCalibrationModelPoly2Log1& operator= (const MCalibrationModelPoly2Log1& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
+  MCalibrationModelPoly2Log1& operator= (const MCalibrationModelPoly2Log1& CalibrationModelLinear) { MCalibrationModel::operator=(CalibrationModelLinear); return *this; }
   
   //! Clone this fit - the returned element must be deleted!
   virtual MCalibrationModelPoly2Log1* Clone() const { return new MCalibrationModelPoly2Log1(*this); }
diff --git a/src/global/misc/inc/MFileResponse.h b/src/global/misc/inc/MFileResponse.h
index 4d2cd9612..f605f3514 100644
--- a/src/global/misc/inc/MFileResponse.h
+++ b/src/global/misc/inc/MFileResponse.h
@@ -35,14 +35,20 @@ class MResponseMatrix;
 ////////////////////////////////////////////////////////////////////////////////
 
 
+//! Class to read response files
 class MFileResponse : public MParser
 {
   // public interface:
  public:
+  //! Default constructor
   explicit MFileResponse();
+  //! Default destructor
   virtual ~MFileResponse();
 
+  //! Read a response matrix
   MResponseMatrix* Read(MString FileName);
+  //! We cannot use the base class version here
+  bool Read(MBinaryStore& Store, unsigned int CharactersToRead) { return false; }
 
   //! Open the file name and read the header
   virtual bool Open(MString FileName, unsigned int Way = 1);

From 53b683a99c48d42bc8291dc018b0e6bd142bd67b Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Wed, 13 Nov 2024 21:26:50 -0800
Subject: [PATCH 106/192] CHG: Fixed a warning. Maybe...

---
 src/revan/src/MEREventClusterizerDistance.cxx | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/revan/src/MEREventClusterizerDistance.cxx b/src/revan/src/MEREventClusterizerDistance.cxx
index 3b9920fc0..b5df6680f 100644
--- a/src/revan/src/MEREventClusterizerDistance.cxx
+++ b/src/revan/src/MEREventClusterizerDistance.cxx
@@ -179,8 +179,10 @@ bool MEREventClusterizerDistance::Analyze(MRawEventIncarnationList* List)
     //  cout<<r<<": "<<RESEs.size()<<endl; 
     //}
     
-    remove_if(RESEs.begin(), RESEs.end(), [](vector<MRESE*> V){return V.size() == 0;});
-    
+    // remove_if(RESEs.begin(), RESEs.end(), [](vector<MRESE*> V){return V.size() == 0;});
+    // AZ 2024-11-13: Fixed a warning that we actually have to use erase to do the erase...
+    RESEs.erase(remove_if(RESEs.begin(), RESEs.end(), [](vector<MRESE*> V){ return V.size() == 0; }), RESEs.end());
+
     //for (unsigned int r = 0; r < RESEs.size(); ++r) {
     //  cout<<r<<": "<<RESEs.size()<<endl; 
     //}

From 9246e529e6511aedcc2479c857f0f82e6f21af93 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Mon, 25 Nov 2024 02:37:20 -0800
Subject: [PATCH 107/192] CHG: Regresssion and bug fixes for Bayesion event
 reconstruction

---
 src/geomega/src/MDStrip2D.cxx                 |   9 +-
 src/response/inc/MResponseBuilder.h           |   2 +-
 .../inc/MResponseMultipleComptonBayes.h       |  16 +-
 src/response/src/MResponseBuilder.cxx         |  21 +-
 .../src/MResponseMultipleComptonBayes.cxx     | 195 +++++++++++-------
 src/revan/inc/MERCSR.h                        |   3 +-
 src/revan/src/MERCSR.cxx                      |  22 +-
 src/revan/src/MERCSRBayesian.cxx              |   4 +-
 src/revan/src/MERHitClusterizer.cxx           |  10 +-
 9 files changed, 186 insertions(+), 96 deletions(-)

diff --git a/src/geomega/src/MDStrip2D.cxx b/src/geomega/src/MDStrip2D.cxx
index 1b12babc9..3813d53db 100644
--- a/src/geomega/src/MDStrip2D.cxx
+++ b/src/geomega/src/MDStrip2D.cxx
@@ -497,19 +497,20 @@ bool MDStrip2D::AreNear(const MVector& Pos1, const MVector& dPos1,
   // --------------------
   // | 5 | 4 | 5 | 8 | 13
 
-  static const double Epsilon = 0.00001; 
+  static const double Epsilon = 0.01; // Needs to be larger than the accuracy in the sim file
 
+  //cout<<"Testing "<<fabs(Pos1[0] - Pos2[0])/m_PitchX*fabs(Pos1[0] - Pos2[0])/m_PitchX<<":"<<fabs(Pos1[1] - Pos2[1])/m_PitchY*fabs(Pos1[1] - Pos2[1])/m_PitchY<<":"<<Level+Epsilon<<endl;
   if (fabs(Pos1[0] - Pos2[0])/m_PitchX*fabs(Pos1[0] - Pos2[0])/m_PitchX +
       fabs(Pos1[1] - Pos2[1])/m_PitchY*fabs(Pos1[1] - Pos2[1])/m_PitchY < Level+Epsilon) {
-    //cout<<"Adjacent!"<<endl;
+    //cout<<"MDStrip2D::AreNear: Adjacent!"<<endl;
     if (Sigma < 0) {
       return true;
     } else if (fabs(Pos1[2] - Pos2[2]) < Sigma*(dPos1[2]+Epsilon) ||
         fabs(Pos1[2] - Pos2[2]) < Sigma*(dPos2[2]+Epsilon) || Sigma < 0) {
-      //cout<<"Within Sigma: "<<Sigma*(dPos2[2]+Epsilon)<<endl;
+      //cout<<"MDStrip2D::AreNear: Within Sigma: "<<Sigma*(dPos2[2]+Epsilon)<<endl;
       return true;
     } else {
-      //cout<<"Outside Sigma: "<<Sigma*(dPos2[2]+Epsilon)<<endl;
+      //cout<<"MDStrip2D::AreNear: Outside Sigma: "<<Sigma*(dPos2[2]+Epsilon)<<"(Sigma: "<<Sigma<<" * Delta zPos2: "<<dPos2[2]<<")"<<endl;
     }
   }
   //cout<<"Not adjacent: "<<fabs(Pos1[0] - Pos2[0])/m_PitchX*fabs(Pos1[0] - Pos2[0])/m_PitchX<<"!"
diff --git a/src/response/inc/MResponseBuilder.h b/src/response/inc/MResponseBuilder.h
index 4a1476aee..9549fe5cf 100644
--- a/src/response/inc/MResponseBuilder.h
+++ b/src/response/inc/MResponseBuilder.h
@@ -212,7 +212,7 @@ class MResponseBuilder
   MSimEvent* m_SiEvent;
   //! The current revan event - if we have multiple, this is just the first one
   MRERawEvent* m_ReEvent;  
-  //! The current revan event
+  //! The current list of revan events
   vector<MRERawEvent*> m_ReEvents;  
   
   //! For read-mode file: The revan reader
diff --git a/src/response/inc/MResponseMultipleComptonBayes.h b/src/response/inc/MResponseMultipleComptonBayes.h
index a5bf91791..cc809e4db 100644
--- a/src/response/inc/MResponseMultipleComptonBayes.h
+++ b/src/response/inc/MResponseMultipleComptonBayes.h
@@ -83,23 +83,20 @@ class MResponseMultipleComptonBayes : public MResponseMultipleCompton
   bool IsTrackStop(MRESE& Central, MRESE& Stop, double Energy);
 
   bool IsComptonStart(MRESE& Start, double Etot, double Eres);
-  bool IsComptonTrack(MRESE& Start, MRESE& Central, int StartPosition, 
-                      double Etot, double Eres);
+  bool IsComptonTrack(MRESE& Start, MRESE& Central, double Etot, double Eres);
   bool IsComptonEnd(MRESE& Stop);
-  bool IsComptonSequence(MRESE& Start, MRESE& Stop,
-                         int StartPosition, double StopEnergy, double Eres);
-  bool IsComptonSequence(MRESE& Start, MRESE& Central, MRESE& Stop,
-                         int StartPosition, double StopEnergy, double Eres);
+  bool IsComptonSequence(MRESE& Start, MRESE& Stop, double StopEnergy, double Eres);
+  bool IsComptonSequence(MRESE& Start, MRESE& Central, MRESE& Stop, double StopEnergy, double Eres);
   bool IsSingleCompton(MRESE& Start);
 
   bool AreInComptonSequence(const vector<int>& StartOriginIds, 
-                            const vector<int>& CentralOriginIds,
-                            int StartPosition);
+                            const vector<int>& CentralOriginIds);
   bool AreReseInSequence(MRESE& Start, MRESE& Central, MRESE& Stop, double Energy);
 
   bool ContainsOnlyComptonDependants(vector<int> AllSimIds);
   bool IsAbsorbed(const vector<int>& AllSimIds, double Energy, double EnergyResolution);
-  bool IsTotalAbsorbed(const vector<int>& AllSimIds, double Energy, double EnergyResolution);
+  //! Check if the sequence composed by AllSimIds is tottaly absorbed given we measure Energy
+  bool IsTotallyAbsorbed(const vector<int>& AllSimIds, double Energy, double EnergyResolution);
   bool IsTrackCompletelyAbsorbed(const vector<int>& Ids, double Energy);
   double GetIdealDepositedEnergy(int MinId);
 
@@ -126,6 +123,7 @@ class MResponseMultipleComptonBayes : public MResponseMultipleCompton
   double CalculateAbsorptionProbabilityPhoto(MRESE& Start, MRESE& Stop, double Etot);
   double CalculateAbsorptionProbabilityCompton(MRESE& Start, MRESE& Stop, double Etot);
   double CalculateAbsorptionProbabilityTotal(MRESE& Start, MRESE& Stop, double Etot);
+  double CalculateReach(MRESE& Start, MRESE& Stop, double Etot);
 
   // private methods:
  private:
diff --git a/src/response/src/MResponseBuilder.cxx b/src/response/src/MResponseBuilder.cxx
index 53d5d18ea..851b1bed3 100644
--- a/src/response/src/MResponseBuilder.cxx
+++ b/src/response/src/MResponseBuilder.cxx
@@ -141,6 +141,9 @@ bool MResponseBuilder::Initialize()
     }
   }
 
+  // We only want the sequences here:
+  m_ReReader->SetCSROnlyCreateSequences(true);
+
   // ... and initialize it
   if (m_ReReader->PreAnalysis() == false) {
     merr<<"Unable to initialize event reconstruction."<<endl;     
@@ -259,10 +262,14 @@ bool MResponseBuilder::SetEvent(const MString String, bool NeedsNoising, int Ver
 {
   // Set and verify the simulation file name
 
+  auto Verbosity = g_Verbosity;
+  g_Verbosity = 0;
+
   m_Mode = MResponseBuilderReadMode::EventByEvent;
 
   if (m_ReReader->AddRawEvent(String, NeedsNoising, Version) == false) {
     cout<<"Unable to add raw event"<<endl;
+    g_Verbosity = Verbosity;
     return false;
   }
   
@@ -282,6 +289,7 @@ bool MResponseBuilder::SetEvent(const MString String, bool NeedsNoising, int Ver
   
   if (m_ReEvent == nullptr) {
     cout<<"We have no good raw event"<<endl;
+    g_Verbosity = Verbosity;
     return false;
   }
   
@@ -291,9 +299,12 @@ bool MResponseBuilder::SetEvent(const MString String, bool NeedsNoising, int Ver
   }
   if (m_SiEvent->ParseEvent(String, Version) == false) {
     cout<<"Unable to add event to sivan"<<endl;
+    g_Verbosity = Verbosity;
     return false;
   }
   
+  g_Verbosity = Verbosity;
+
   return true;
 }
 
@@ -408,6 +419,9 @@ bool MResponseBuilder::InitializeNextMatchingEvent()
 
   if (m_Interrupt == true) return false;
   
+  auto Verbosity = g_Verbosity;
+  g_Verbosity = 0;
+
   unsigned int ERReturnCode;
 
  
@@ -448,8 +462,9 @@ bool MResponseBuilder::InitializeNextMatchingEvent()
       if (m_ReReader->GetRawEventList() != nullptr) {
         MRawEventIncarnationList* REIL = m_ReReader->GetRawEventList();
         for (unsigned int i = 0; i < REIL->Size(); ++i) {
-          if (REIL->Get(i)->GetNRawEvents() > 0) {
-            m_ReEvents.push_back(REIL->Get(i)->GetRawEventAt(0)); // why not the optimum event?
+          // TODO: Test performance if we just pick one random sequence
+          for (unsigned int r = 0; r < REIL->Get(i)->GetNRawEvents(); ++r) {
+            m_ReEvents.push_back(REIL->Get(i)->GetRawEventAt(r));
           }
         }
       }
@@ -536,6 +551,8 @@ bool MResponseBuilder::InitializeNextMatchingEvent()
   }
   //mout<<"Response: Match Sivan ID="<<m_SivanEventID<<"  Revan ID="<<m_RevanEventID<<endl;
   
+  g_Verbosity = Verbosity;
+
   return MoreEvents;  
 }
 
diff --git a/src/response/src/MResponseMultipleComptonBayes.cxx b/src/response/src/MResponseMultipleComptonBayes.cxx
index 90a28a0ee..6315b3d95 100644
--- a/src/response/src/MResponseMultipleComptonBayes.cxx
+++ b/src/response/src/MResponseMultipleComptonBayes.cxx
@@ -219,8 +219,13 @@ bool MResponseMultipleComptonBayes::Initialize()
   MString NameAxisComptonScatterAngleStart = "cos#varphi";
 
   // Scatter probability axis
-  vector<float> AxisScatterProbability = CreateEquiDist(-0.025, 1.025, 42);
-  MString NameAxisScatterProbability = "Scatter probability";
+  // vector<float> AxisScatterProbability = CreateEquiDist(-0.001, 1.001, 42);
+  vector<float> AxisScatterProbability = { -0.001, 0.001, 0.005, 0.01 };
+  vector<float> Middle = CreateEquiDist(0.025, 0.975, 38);
+  AxisScatterProbability.insert(AxisScatterProbability.end(), Middle.begin(), Middle.end());
+  AxisScatterProbability.insert(AxisScatterProbability.end(),{ 0.99, 0.995, 0.999, 1.001 });
+  MString NameAxisScatterProbabilityPhoto = "Scatter probability";
+  MString NameAxisScatterProbabilityCompton = "Reach probability";
 
   // Total energy axis for scatter probabilities
   vector<float> AxisTotalEnergyDistances = CreateLogDist(15, m_EnergyMaximum, 38, 1, 20000);
@@ -241,7 +246,8 @@ bool MResponseMultipleComptonBayes::Initialize()
   MString NameAxisTotalEnergyDual = "Energy [keV]";
 
   // Scatter probability axis
-  vector<float> AxisScatterProbabilityDual = CreateEquiDist(0, 1, 15, -0.025, 1.025);
+  vector<float> AxisScatterProbabilityDual = CreateEquiDist(-0.001, 0.99, 15);
+  AxisScatterProbabilityDual.push_back(1.001);
   MString NameAxisScatterProbabilityDual = "Scatter probability";
   
 
@@ -330,7 +336,7 @@ bool MResponseMultipleComptonBayes::Initialize()
                                         AxisTotalEnergyDistances, 
                                         AxisSequenceLength, 
                                         AxisMaterial);
-  m_PdfComptonScatterProbabilityGood.SetAxisNames(NameAxisScatterProbability, 
+  m_PdfComptonScatterProbabilityGood.SetAxisNames(NameAxisScatterProbabilityCompton,
                                  NameAxisTotalEnergyDistances, 
                                  NameAxisSequenceLength, 
                                  NameAxisMaterial);
@@ -339,7 +345,7 @@ bool MResponseMultipleComptonBayes::Initialize()
                                        AxisTotalEnergyDistances, 
                                        AxisSequenceLength, 
                                        AxisMaterial);
-  m_PdfComptonScatterProbabilityBad.SetAxisNames(NameAxisScatterProbability, 
+  m_PdfComptonScatterProbabilityBad.SetAxisNames(NameAxisScatterProbabilityCompton,
                                 NameAxisTotalEnergyDistances, 
                                 NameAxisSequenceLength, 
                                 NameAxisMaterial);
@@ -351,7 +357,7 @@ bool MResponseMultipleComptonBayes::Initialize()
                                             AxisTotalEnergyDistances, 
                                             AxisSequenceLength, 
                                             AxisMaterial);
-  m_PdfPhotoAbsorptionProbabilityGood.SetAxisNames(NameAxisScatterProbability, 
+  m_PdfPhotoAbsorptionProbabilityGood.SetAxisNames(NameAxisScatterProbabilityPhoto,
                                      NameAxisTotalEnergyDistances, 
                                      NameAxisSequenceLength, 
                                      NameAxisMaterial);
@@ -360,7 +366,7 @@ bool MResponseMultipleComptonBayes::Initialize()
                                            AxisTotalEnergyDistances, 
                                            AxisSequenceLength, 
                                            AxisMaterial);
-  m_PdfPhotoAbsorptionProbabilityBad.SetAxisNames(NameAxisScatterProbability, 
+  m_PdfPhotoAbsorptionProbabilityBad.SetAxisNames(NameAxisScatterProbabilityPhoto,
                                     NameAxisTotalEnergyDistances, 
                                     NameAxisSequenceLength, 
                                     NameAxisMaterial);
@@ -389,7 +395,7 @@ bool MResponseMultipleComptonBayes::Initialize()
   vector<float> AxisDistance = CreateLogDist(0.2, 10, 7, 0.01, 100, 0, false);
   MString NameAxisDistance = "Distance [cm]";
 
-  vector<float> AxisTotalEnergy = CreateLogDist(100, m_EnergyMaximum, 4, 1, 10000, 0, false);
+  vector<float> AxisTotalEnergy = CreateLogDist(100, m_EnergyMaximum, 4, 1, std::max(2*m_EnergyMaximum, 10000.0), 0, false);
   //CreateLogDist(1, 10000, 1); //, 1, 10000, 0, false);
   //mimp<<"No total energy bins!"<<show;
   MString NameAxisTotalEnergy = "E_{tot} [keV]";
@@ -471,7 +477,7 @@ bool MResponseMultipleComptonBayes::Analyze()
   double Etot = 0;
   double Eres = 0;
  
-  
+  //cout<<endl<<endl<<"Analyze: 'ing "<<m_ReEvents.size()<<" sequences"<<endl;
   for (auto RE: m_ReEvents) {
     if (RE == nullptr) continue;
     
@@ -506,11 +512,21 @@ bool MResponseMultipleComptonBayes::Analyze()
       Eres = RE->GetEnergyResolution();
       
       double CosPhiE = CalculateCosPhiE(*Iter.GetCurrent(), Etot);
+      if (CosPhiE <= -10) CosPhiE = -9.99;
       double PhotoDistance = CalculateAbsorptionProbabilityTotal(*Iter.GetCurrent(), *Iter.GetNext(), Iter.GetNext()->GetEnergy());
       
       if (IsComptonStart(*Iter.GetCurrent(), Etot, Eres) == true) {
-        mdebug<<"--------> Found GOOD dual Compton event!"<<endl;
-        m_PdfDualGood.Add(Etot, CosPhiE, PhotoDistance, GetMaterial(*Iter.GetCurrent()));
+        // IsComptonSequence caluculates absorption for the second component only, thus I have to:
+        double Etot2 = Etot - Iter.GetCurrent()->GetEnergy();
+        double Eres2 = sqrt(Eres*Eres - Iter.GetCurrent()->GetEnergyResolution()*Iter.GetCurrent()->GetEnergyResolution());
+        if (IsComptonSequence(*Iter.GetCurrent(), *Iter.GetNext(), Etot2, Eres2) == true) {
+          mdebug<<"--------> Found GOOD dual Compton event!"<<endl;
+          m_PdfDualGood.Add(Etot, CosPhiE, PhotoDistance, GetMaterial(*Iter.GetCurrent()));
+        } else {
+          mdebug<<"--------> Found bad dual Compton event!"<<endl;
+          m_PdfDualBad.Add(Etot, CosPhiE, PhotoDistance, GetMaterial(*Iter.GetCurrent()));
+          SequenceOk = false;
+        }
       } else {
         mdebug<<"--------> Found bad dual Compton event!"<<endl;
         m_PdfDualBad.Add(Etot, CosPhiE, PhotoDistance, GetMaterial(*Iter.GetCurrent()));
@@ -536,7 +552,7 @@ bool MResponseMultipleComptonBayes::Analyze()
       if (Iter.GetCurrent()->GetType() == MRESE::c_Track) {
         double dAlpha = CalculateDCosAlpha(*((MRETrack*) Iter.GetCurrent()), *Iter.GetNext(), Etot);
         double Alpha = CalculateCosAlphaG(*((MRETrack*) Iter.GetCurrent()), *Iter.GetNext(), Etot);
-        if (IsComptonTrack(*Iter.GetCurrent(), *Iter.GetNext(), PreviousPosition, Etot, Eres) == true) {
+        if (IsComptonTrack(*Iter.GetCurrent(), *Iter.GetNext(), Etot, Eres) == true) {
           mdebug<<"--------> Found GOOD Track start!"<<endl;
           m_PdfTrackGood.Add(dAlpha, Alpha, 1, Iter.GetCurrent()->GetEnergy(), SequenceLength, GetMaterial(*Iter.GetCurrent()));
         } else {
@@ -558,9 +574,9 @@ bool MResponseMultipleComptonBayes::Analyze()
         // In the current implementation/simulation the hits have to be in increasing order...
         if (m_DoAbsorptions == true && SequenceLength <= m_MaxAbsorptions) {
           double ComptonDistance = 
-          CalculateAbsorptionProbabilityCompton(*Iter.GetPrevious(), *Iter.GetCurrent(), Etot);
+          CalculateReach(*Iter.GetPrevious(), *Iter.GetCurrent(), Etot);
           mdebug<<"Dist C: "<<ComptonDistance<<": real:"<<(Iter.GetCurrent()->GetPosition() - Iter.GetPrevious()->GetPosition()).Mag()<<endl;
-          if (IsComptonSequence(*Iter.GetPrevious(), *Iter.GetCurrent(), PreviousPosition, Etot, Eres) == true) {
+          if (IsComptonSequence(*Iter.GetPrevious(), *Iter.GetCurrent(), Etot, Eres) == true) {
             mdebug<<"--------> Found GOOD Distance sequence!"<<endl;
             // Retrieve the data:
             m_PdfComptonScatterProbabilityGood.Add(ComptonDistance, Etot, SequenceLength, GetMaterial(*Iter.GetCurrent()));
@@ -579,7 +595,7 @@ bool MResponseMultipleComptonBayes::Analyze()
         double Lever = CalculateMinLeverArm(*Iter.GetPrevious(), *Iter.GetCurrent(), *Iter.GetNext());
         int Material = GetMaterial(*Iter.GetCurrent());
         
-        if (IsComptonSequence(*Iter.GetPrevious(), *Iter.GetCurrent(), *Iter.GetNext(), PreviousPosition, Etot, Eres) == true) {
+        if (IsComptonSequence(*Iter.GetPrevious(), *Iter.GetCurrent(), *Iter.GetNext(), Etot, Eres) == true) {
           mdebug<<"--------> Found GOOD internal Compton sequence!"<<endl;
           // Retrieve the data:
           m_PdfComptonGood.Add(dPhi, PhiE, Lever, Etot, SequenceLength, Material);
@@ -596,7 +612,7 @@ bool MResponseMultipleComptonBayes::Analyze()
           //MRETrack* T = (MRETrack*) Iter.GetCurrent();
           double dAlpha = CalculateDCosAlpha(*((MRETrack*) Iter.GetCurrent()), *Iter.GetNext(), Etot);
           double Alpha = CalculateCosAlphaG(*((MRETrack*) Iter.GetCurrent()), *Iter.GetNext(), Etot);
-          if (IsComptonTrack(*Iter.GetCurrent(), *Iter.GetNext(), PreviousPosition, Etot, Eres) == true) {
+          if (IsComptonTrack(*Iter.GetCurrent(), *Iter.GetNext(), Etot, Eres) == true) {
             mdebug<<"--------> Found GOOD Track start (central)!"<<endl;
             m_PdfTrackGood.Add(dAlpha, Alpha, 1, Iter.GetCurrent()->GetEnergy(), SequenceLength, GetMaterial(*Iter.GetCurrent()));
           } else {
@@ -617,7 +633,7 @@ bool MResponseMultipleComptonBayes::Analyze()
       if (m_DoAbsorptions == true && SequenceLength <= m_MaxAbsorptions) {
         double LastDistance = CalculateAbsorptionProbabilityPhoto(*Iter.GetPrevious(), *Iter.GetCurrent(), Etot);
         mdebug<<"Dist P: "<<LastDistance<<": real:"<<(Iter.GetCurrent()->GetPosition() - Iter.GetPrevious()->GetPosition()).Mag()<<endl;
-        if (IsComptonSequence(*Iter.GetPrevious(), *Iter.GetCurrent(), PreviousPosition, Etot, Eres) == true) {
+        if (IsComptonSequence(*Iter.GetPrevious(), *Iter.GetCurrent(), Etot, Eres) == true) {
           mdebug<<"--------> Found GOOD Lastdistance sequence!"<<endl;
           // Retrieve the data:
           m_PdfPhotoAbsorptionProbabilityGood.Add(CalculateAbsorptionProbabilityPhoto(*Iter.GetPrevious(), *Iter.GetCurrent(), Etot), 
@@ -659,8 +675,7 @@ bool MResponseMultipleComptonBayes::Finalize()
 ////////////////////////////////////////////////////////////////////////////////
 
 
-bool MResponseMultipleComptonBayes::IsComptonTrack(MRESE& Start, MRESE& Center,
-                                       int PreviousPosition, double Etot, double Eres)
+bool MResponseMultipleComptonBayes::IsComptonTrack(MRESE& Start, MRESE& Center, double Etot, double Eres)
 {
   // A good start point of the track consists of the following:
   // (1) Start is a track
@@ -684,7 +699,7 @@ bool MResponseMultipleComptonBayes::IsComptonTrack(MRESE& Start, MRESE& Center,
   }
 
   // (3)
-  if (IsComptonSequence(Start, Center, PreviousPosition, Etot-Start.GetEnergy(), Eres) == false) {
+  if (IsComptonSequence(Start, Center, Etot-Start.GetEnergy(), Eres) == false) {
     // Attention: Eres is a little to large...
     mdebug<<"IsComptonTrack: No Compton sequence!"<<endl;
     return false;        
@@ -1006,7 +1021,7 @@ bool MResponseMultipleComptonBayes::IsComptonStart(MRESE& Start, double Etot, do
   // Return true if the given RESEs are in sequence
   //
   // A good start point for tripple Comptons requires:
-  // (1) An absorption better than 3 sigma energy resolution + 2 keV for the fuirst hitr and the while sequence...
+  // (1) An absorption better than 3 sigma energy resolution + 2 keV for the first hit and the while sequence...
   // (2) The origin is or produced a photon
   // (3) We have exactly one Compton interaction and maybe some other, secondary interaction
 
@@ -1037,8 +1052,8 @@ bool MResponseMultipleComptonBayes::IsComptonStart(MRESE& Start, double Etot, do
       return false;
     }
     // Full sequence
-    if (IsTotalAbsorbed(StartOriginIds, Etot, Eres) == false) {
-      if (g_Verbosity >= c_Chatty) mout<<"IsComptonStart: Not completely absorbed!"<<endl;
+    if (IsTotallyAbsorbed(StartOriginIds, Etot, Eres) == false) {
+      if (g_Verbosity >= c_Chatty) mout<<"IsComptonStart: Remaining sequence not completely absorbed!"<<endl;
       return false;
     }
   }
@@ -1092,9 +1107,7 @@ unsigned int MResponseMultipleComptonBayes::NumberOfComptonInteractions(vector<i
 ////////////////////////////////////////////////////////////////////////////////
 
 
-bool MResponseMultipleComptonBayes::IsComptonSequence(MRESE& Start, MRESE& Central,
-                                          int StartPosition, double Etot, 
-                                          double Eres)
+bool MResponseMultipleComptonBayes::IsComptonSequence(MRESE& Start, MRESE& Central, double Etot, double Eres)
 {
   // Return true if the given RESEs are in sequence
   //
@@ -1126,13 +1139,13 @@ bool MResponseMultipleComptonBayes::IsComptonSequence(MRESE& Start, MRESE& Centr
     mdebug<<"IsComptonSequence2: Central contains not only Compton dependants"<<endl;
     return false;
   }
-  if (AreInComptonSequence(StartOriginIds, CentralOriginIds, StartPosition) == false) {
+  if (AreInComptonSequence(StartOriginIds, CentralOriginIds) == false) {
     mdebug<<"IsComptonSequence2: Not in Compton sequence!"<<endl;
     return false;
   }
 
   if (Etot > 0) {
-    if (IsTotalAbsorbed(CentralOriginIds, Etot, Eres) == false) {
+    if (IsTotallyAbsorbed(CentralOriginIds, Etot, Eres) == false) {
       mdebug<<"IsComptonSequence2: Not completely absorbed!"<<endl;
       return false;
     }
@@ -1145,9 +1158,7 @@ bool MResponseMultipleComptonBayes::IsComptonSequence(MRESE& Start, MRESE& Centr
 ////////////////////////////////////////////////////////////////////////////////
 
 
-bool MResponseMultipleComptonBayes::IsComptonSequence(MRESE& Start, MRESE& Central,
-                                          MRESE& Stop, int StartPosition, 
-                                          double Etot, double Eres)
+bool MResponseMultipleComptonBayes::IsComptonSequence(MRESE& Start, MRESE& Central, MRESE& Stop, double Etot, double Eres)
 {
   // Return true if the given RESEs are in sequence
 
@@ -1213,16 +1224,16 @@ bool MResponseMultipleComptonBayes::IsComptonSequence(MRESE& Start, MRESE& Centr
     mdebug<<"IsComptonSequence3: Stop contains not only Compton dependants"<<endl;
     return false;
   }
-  if (AreInComptonSequence(StartOriginIds, CentralOriginIds, StartPosition) == false) {
+  if (AreInComptonSequence(StartOriginIds, CentralOriginIds) == false) {
     mdebug<<"IsComptonSequence3: Not in Compton sequence!"<<endl;
     return false;
   }
-  if (AreInComptonSequence(CentralOriginIds, StopOriginIds, 0) == false) {
+  if (AreInComptonSequence(CentralOriginIds, StopOriginIds) == false) {
     mdebug<<"IsComptonSequence3: Not in Compton sequence!"<<endl;
     return false;
   }
 
-  if (IsTotalAbsorbed(CentralOriginIds, Etot, Eres) == false) {
+  if (IsTotallyAbsorbed(CentralOriginIds, Etot, Eres) == false) {
     mdebug<<"IsComptonSequence3: Not completely absorbed!"<<endl;
     return false;
   }
@@ -1273,7 +1284,7 @@ bool MResponseMultipleComptonBayes::IsComptonEnd(MRESE& End)
   }
   
   // Absorption:
-  if (IsTotalAbsorbed(EndOriginIds, End.GetEnergy(), End.GetEnergyResolution()) == false) {
+  if (IsTotallyAbsorbed(EndOriginIds, End.GetEnergy(), End.GetEnergyResolution()) == false) {
     mdebug<<"IsComptonEnd: Not completely absorbed!"<<endl;
     return false;
   }
@@ -1385,9 +1396,7 @@ bool MResponseMultipleComptonBayes::IsSingleCompton(MRESE& Start)
 ////////////////////////////////////////////////////////////////////////////////
 
 
-bool MResponseMultipleComptonBayes::AreInComptonSequence(const vector<int>& StartOriginIds,
-                                                    const vector<int>& CentralOriginIds,
-                                                    int StartPosition)
+bool MResponseMultipleComptonBayes::AreInComptonSequence(const vector<int>& StartOriginIds, const vector<int>& CentralOriginIds)
 {
   // They are in good sequence if 
   //  (1) Both smallest IDs originate from 1
@@ -1396,19 +1405,21 @@ bool MResponseMultipleComptonBayes::AreInComptonSequence(const vector<int>& Star
   massert(StartOriginIds.size() > 0);
   massert(CentralOriginIds.size() > 0);
   
+  mdebug<<"AreInComptonSequence: Start origin ID: "<<StartOriginIds[0]<<" Central origin ID: "<<CentralOriginIds[0]<<endl;
+
   if (m_SiEvent->GetIAAt(StartOriginIds[0]-1)->GetProcess() != "COMP") {
-    mdebug<<"CS: No COMP"<<endl;
+    mdebug<<"AreInComptonSequence: No COMP"<<endl;
     return false;
   }
 
   if (m_SiEvent->GetIAAt(StartOriginIds[0]-1)->GetOriginID() != 
       m_SiEvent->GetIAAt(CentralOriginIds[0]-1)->GetOriginID()) {
-    mdebug<<"CS: No common origin"<<endl;
+    mdebug<<"AreInComptonSequence: No common origin"<<endl;
     return false;
   }
 
 //   if (m_SiEvent->GetIAAt(StartOriginIds[0]-1)->GetMotherParticleNumber() != 1) {
-//     mdebug<<"CS: Mother is no photon: "<<m_SiEvent->GetIAAt(StartOriginIds[0]-1)->GetMotherParticleNumber()<<endl;
+//     mdebug<<"AreInComptonSequence: Mother is no photon: "<<m_SiEvent->GetIAAt(StartOriginIds[0]-1)->GetMotherParticleNumber()<<endl;
 //     return false;
 //   }
 
@@ -1421,7 +1432,7 @@ bool MResponseMultipleComptonBayes::AreInComptonSequence(const vector<int>& Star
     }
   }
   if (FoundBehind == false) {
-    mdebug<<"CS: Not behind each other!"<<endl;
+    mdebug<<"AreInComptonSequence: Not behind each other!"<<endl;
     return false;
   }
 
@@ -1434,10 +1445,15 @@ bool MResponseMultipleComptonBayes::AreInComptonSequence(const vector<int>& Star
 
 bool MResponseMultipleComptonBayes::ContainsOnlyComptonDependants(vector<int> AllSimIds)
 {
+  // ?
+
   // We do two checks here, one down the tree and one up the tree
   
   // First check upwards: Is everything in there originating from somewhere else in there or is it an initial process (COMP, INIT, produced a photon)
+  //cout<<"ContainsOnlyComptonDependants: Sim IDs: "; for (auto i: AllSimIds) { cout<<i<<" "; } cout<<endl;
+
   for (unsigned int i = 0; i < AllSimIds.size(); ++i) {
+    //cout<<"ContainsOnlyComptonDependants checking "<<AllSimIds[i]<<endl;
     int ID = AllSimIds[i];
     int HighestOriginID = ID;
     while (true) {
@@ -1457,21 +1473,32 @@ bool MResponseMultipleComptonBayes::ContainsOnlyComptonDependants(vector<int> Al
     
     // We are good if the end point is a Compton scatter or a photo effect which is preceeded by a Compton in the list:
     bool IsGood = false;
+    mdebug<<"ContainsOnlyComptonDependants: Highest ID "<<HighestOriginID<<endl;
     if (m_SiEvent->GetIAAt(HighestOriginID-1)->GetProcess() == "COMP") {
+      mdebug<<"ContainsOnlyComptonDependants: Highest ID "<<HighestOriginID<<" is COMP"<<endl;
       IsGood = true;
     } else if (m_SiEvent->GetIAAt(HighestOriginID-1)->GetProcess() == "PHOT") {
       int Predeccessor = HighestOriginID-1;
       while (true) {
-        if (Predeccessor == 1) break; // we reached init
+        if (Predeccessor == 1) {
+          mdebug<<"ContainsOnlyComptonDependants: Good. "<<Predeccessor<<" is INIT"<<endl;
+          break; // we reached init
+        }
         if (m_SiEvent->GetIAAt(Predeccessor-1)->GetOriginID() == m_SiEvent->GetIAAt(HighestOriginID-1)->GetOriginID()) {
           if (m_SiEvent->GetIAAt(Predeccessor-1)->GetProcess() == "COMP") {
+            /* 2024-11-24: This doesn't make sense: If its a predecessor it will never be in the list
             if (find(AllSimIds.begin(), AllSimIds.end(), Predeccessor) != AllSimIds.end()) {
+              mdebug<<"ContainsOnlyComptonDependants: Good. Preceeding Compton IA "<<Predeccessor<<" is in list"<<endl;
               IsGood = true;
               break;
             } else {
-              mdebug<<"ContainsOnlyComptonDependants: Preceeding Compton IA is missing"<<endl;
+              mdebug<<"ContainsOnlyComptonDependants: Preceeding Compton IA "<<Predeccessor<<" is missing in list"<<endl;
               return false;
             }
+            */
+            // Replacement:
+            IsGood = true;
+            break;
           }
         }
         --Predeccessor;
@@ -1526,11 +1553,10 @@ bool MResponseMultipleComptonBayes::ContainsOnlyComptonDependants(vector<int> Al
 ////////////////////////////////////////////////////////////////////////////////
 
 
-bool MResponseMultipleComptonBayes::IsAbsorbed(const vector<int>& AllSimIds,
-                                          double Energy, double EnergyResolution)
+bool MResponseMultipleComptonBayes::IsAbsorbed(const vector<int>& AllSimIds, double Energy, double EnergyResolution)
 {
   // Rules:
-  // If a Compton scattering is included, the energy of the of the recoild electron plus any instant deposits, bremsstrahlug, etc. must be contained
+  // If a Compton scattering is included, the energy of the of the recoil electron plus any instant deposits, bremsstrahlug, etc. must be contained
   // If a photo is included, the energy of the INCOMING gamma-ray must be contained
   
   EnergyResolution = 3.0*EnergyResolution + 2.0;
@@ -1588,10 +1614,11 @@ bool MResponseMultipleComptonBayes::IsAbsorbed(const vector<int>& AllSimIds,
   
   mdebug<<"SimIDs: "; for (int i: SimIDs) mdebug<<i<<" "; mdebug<<endl;
   
-  // (d) Sanity check - we just should have COMP & PHOT in our list
+  // (d) Sanity check - we just should have COMP & PHOT, RAYL & PAIR in our list
   for (unsigned int i = 0; i < SimIDs.size(); ++i) {
-    if (m_SiEvent->GetIAAt(SimIDs[i]-1)->GetProcess() != "COMP" && m_SiEvent->GetIAAt(SimIDs[i]-1)->GetProcess() != "PHOT") {
-      cout<<"Error: We only should have COMP and PHOT IA's at this point and not \""<<m_SiEvent->GetIAAt(SimIDs[i]-1)->GetProcess()<<"\". Did you use hadronic processes for the simulations?"<<endl;
+    if (m_SiEvent->GetIAAt(SimIDs[i]-1)->GetProcess() != "COMP" && m_SiEvent->GetIAAt(SimIDs[i]-1)->GetProcess() != "PHOT" && m_SiEvent->GetIAAt(SimIDs[i]-1)->GetProcess() != "RAYL") {
+      cout<<"Info: We are ignoreing events that contain any other interaction but COMP, PHOT, RAYL. This one has \""<<m_SiEvent->GetIAAt(SimIDs[i]-1)->GetProcess()<<"\"."<<endl;
+      return false;
     }
   }
   
@@ -1614,7 +1641,7 @@ bool MResponseMultipleComptonBayes::IsAbsorbed(const vector<int>& AllSimIds,
         IdealEnergy += m_SiEvent->GetIAAt(SimIDs[i]-2)->GetSecondaryEnergy();
       }      
     } else {
-      cout<<"Error: We only should have COMP and PHOT IA's at this point. Did you use hadronic processes for the simulations?"<<endl;      
+      cout<<"Error: We only should have COMP, RAYL, and PHOT IA's at this point. Did you use hadronic processes for the simulations?"<<endl;
     }
   }
   
@@ -1632,49 +1659,63 @@ bool MResponseMultipleComptonBayes::IsAbsorbed(const vector<int>& AllSimIds,
 ////////////////////////////////////////////////////////////////////////////////
 
 
-bool MResponseMultipleComptonBayes::IsTotalAbsorbed(const vector<int>& AllSimIds,
-                                               double Energy, double EnergyResolution)
+bool MResponseMultipleComptonBayes::IsTotallyAbsorbed(const vector<int>& AllSimIds, double Energy, double EnergyResolution)
 {
+  // This checks if the sequence is totally absorbed
+
   massert(AllSimIds.size() > 0);
 
   EnergyResolution = 3*EnergyResolution+2;
 
+  // Find the minimum ID, as it will belong to the original Compton
   int MinId = numeric_limits<int>::max();
   for (unsigned int i = 0; i < AllSimIds.size(); ++i) {
     if (MinId > AllSimIds[i] && AllSimIds[i] > 1) MinId = AllSimIds[i];
   }
+  mdebug<<"IsTotallyAbsorbed: Min ID: "<<MinId<<endl;
 
   if (MinId == numeric_limits<int>::max()) return false;
 
-  double Ideal;
+  int CurrentIDInVector = MinId - 1;
+  int MotherIDInVector = MinId - 2;
+
   MSimIA* Top = 0;
-  if (m_SiEvent->GetIAAt(MinId-2)->GetOriginID() == m_SiEvent->GetIAAt(MinId-1)->GetOriginID()) {
-    Top = m_SiEvent->GetIAAt(MinId-2);
-  } else {
-    Top = m_SiEvent->GetIAAt(m_SiEvent->GetIAAt(MinId-1)->GetOriginID()-1);
+  // If Current and mother have same origin ID then we are in a normal sequence, and choose the mother
+  if (m_SiEvent->GetIAAt(MotherIDInVector)->GetOriginID() == m_SiEvent->GetIAAt(CurrentIDInVector)->GetOriginID()) {
+    Top = m_SiEvent->GetIAAt(MotherIDInVector);
+  }
+  // Other wise we have something like Bremsstrahlung and have to find the start this way:
+  else {
+    Top = m_SiEvent->GetIAAt(m_SiEvent->GetIAAt(CurrentIDInVector)->GetOriginID()-1);
   }
 
-  if (m_SiEvent->GetIAAt(MinId-2)->GetProcess() == "COMP") {
+  double Ideal = 0.0;
+  if (m_SiEvent->GetIAAt(MotherIDInVector)->GetProcess() == "COMP") {
     Ideal = Top->GetMotherEnergy();
+    mdebug<<"IsTotallyAbsorbed: GetMother of "<<Top->GetID()<<" with "<<Ideal<<endl;
   } else {
     Ideal = Top->GetSecondaryEnergy();
+    mdebug<<"IsTotallyAbsorbed: GetSecondary of "<<Top->GetID()<<" with "<<Ideal<<endl;
   }
 
-  if (MinId-2 != 0) {
-    Ideal = m_SiEvent->GetIAAt(MinId-2)->GetMotherEnergy();
+  /* Now that was redundant and wrong
+  if (MotherIDInVector != 0) {
+    Ideal = m_SiEvent->GetIAAt(MotherIDInVector)->GetMotherEnergy();
   } else {
-    Ideal = m_SiEvent->GetIAAt(MinId-2)->GetSecondaryEnergy();
+    Ideal = m_SiEvent->GetIAAt(MotherIDInVector)->GetSecondaryEnergy();
   }
+  */
 
   if (fabs(Ideal - Energy) > EnergyResolution) {
-      mdebug<<"Is totally absorbed: Not completely absorbed: Tot abs: i="<<Ideal<<"  r="<<Energy<<"  3*Eres+2="<<EnergyResolution<<endl;
+      mdebug<<"IsTotallyAbsorbed: Not completely absorbed: Tot abs: i="<<Ideal<<"  r="<<Energy<<"  3*Eres+2="<<EnergyResolution<<endl;
     return false;
   } else {
-    mdebug<<"Is totally absorbed: Completely absorbed: Tot abs: i="<<Ideal<<"  r="<<Energy<<"  3*Eres+2="<<EnergyResolution<<endl;
+    mdebug<<"IsTotallyAbsorbed: Completely absorbed: Tot abs: i="<<Ideal<<"  r="<<Energy<<"  3*Eres+2="<<EnergyResolution<<endl;
   }
+
 //   if (fabs((Ideal - Energy)/Ideal) > m_MaxEnergyDifferencePercent &&
 //       fabs(Ideal - Energy) > m_MaxEnergyDifference ) {
-//       mdebug<<"Is totally absorbed: Not completely absorbed: Tot abs: i="<<Ideal<<" r="<<Energy<<endl;
+//       mdebug<<"IsTotallyAbsorbed: Not completely absorbed: Tot abs: i="<<Ideal<<" r="<<Energy<<endl;
 //     return false;
 //   }
 
@@ -1914,13 +1955,11 @@ double MResponseMultipleComptonBayes::CalculateAbsorptionProbabilityTotal(MRESE&
 ////////////////////////////////////////////////////////////////////////////////
 
 
-double MResponseMultipleComptonBayes::CalculateAbsorptionProbabilityCompton(MRESE& Start,
-                                                                       MRESE& Stop, 
-                                                                       double Etot)
+double MResponseMultipleComptonBayes::CalculateAbsorptionProbabilityCompton(MRESE& Start, MRESE& Stop, double Etot)
 {
-  double Distance = 
-    m_ReGeometry->GetComptonAbsorptionProbability(Start.GetPosition(), 
-                                                  Stop.GetPosition(), Etot); 
+  double Distance =
+    m_ReGeometry->GetComptonAbsorptionProbability(Start.GetPosition(),
+                                                  Stop.GetPosition(), Etot);
 
   //cout<<"Distance: "<<Distance<<" E: "<<Etot<<endl;
   //cout<<Start.ToString()<<endl;
@@ -1932,6 +1971,20 @@ double MResponseMultipleComptonBayes::CalculateAbsorptionProbabilityCompton(MRES
 ////////////////////////////////////////////////////////////////////////////////
 
 
+double MResponseMultipleComptonBayes::CalculateReach(MRESE& Start, MRESE& Stop, double Etot)
+{
+  double ReachProbability = 1.0;
+  ReachProbability *= (1 - m_ReGeometry->GetPairAbsorptionProbability(Start.GetPosition(), Stop.GetPosition(), Etot));
+  ReachProbability *= (1 - m_ReGeometry->GetComptonAbsorptionProbability(Start.GetPosition(), Stop.GetPosition(), Etot));
+  ReachProbability *= (1 - m_ReGeometry->GetPhotoAbsorptionProbability(Start.GetPosition(), Stop.GetPosition(), Etot));
+
+  return ReachProbability;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
 double MResponseMultipleComptonBayes::CalculatePhiEInDegree(MRESE& Central, double Etot)
 {
   return MERCSRBayesian::CalculatePhiEInDegree(&Central, Etot);
diff --git a/src/revan/inc/MERCSR.h b/src/revan/inc/MERCSR.h
index 72fd808da..9bc00ee6a 100644
--- a/src/revan/inc/MERCSR.h
+++ b/src/revan/inc/MERCSR.h
@@ -88,7 +88,8 @@ class MERCSR : public MERConstruction
   double CalculatePhotoDistance(const MVector& Start, const MVector& Stop, double Etot);
   double CalculateComptonDistance(const MVector& Start, const MVector& Stop, double Etot);
   double CalculateTotalDistance(const MVector& Start, const MVector& Stop, double Etot);
-  
+  double CalculateReach(const MVector& Start, const MVector& Stop, double Etot);
+
   
   // private methods:
  private:
diff --git a/src/revan/src/MERCSR.cxx b/src/revan/src/MERCSR.cxx
index ed903c047..8fdaeb98a 100644
--- a/src/revan/src/MERCSR.cxx
+++ b/src/revan/src/MERCSR.cxx
@@ -116,7 +116,7 @@ bool MERCSR::Analyze(MRawEventIncarnations* List)
   MERConstruction::Analyze(List);
 
   if (m_CreateOnlyPermutations == true) {
-    m_List->SetOptimumEvent(0);
+    m_List->SetOptimumEvent(nullptr);
 
     int e_max = m_List->GetNRawEvents();
     for (int e = 0; e < e_max; ++e) {
@@ -593,11 +593,11 @@ double MERCSR::CalculatePhotoDistance(const MVector& Start,
 ////////////////////////////////////////////////////////////////////////////////
 
 
-double MERCSR::CalculateComptonDistance(const MVector& Start, 
+double MERCSR::CalculateComptonDistance(const MVector& Start,
                                                 const MVector& Stop, double Etot)
 {
-  double Distance = m_Geometry->GetComptonAbsorptionProbability(Start, Stop, Etot); 
-  
+  double Distance = m_Geometry->GetComptonAbsorptionProbability(Start, Stop, Etot);
+
   return Distance;
 }
 
@@ -605,6 +605,20 @@ double MERCSR::CalculateComptonDistance(const MVector& Start,
 ////////////////////////////////////////////////////////////////////////////////
 
 
+double MERCSR::CalculateReach(const MVector& Start, const MVector& Stop, double Etot)
+{
+  double ReachProbability = 1.0;
+  ReachProbability *= (1 - m_Geometry->GetPairAbsorptionProbability(Start, Stop, Etot));
+  ReachProbability *= (1 - m_Geometry->GetComptonAbsorptionProbability(Start, Stop, Etot));
+  ReachProbability *= (1 - m_Geometry->GetPhotoAbsorptionProbability(Start, Stop, Etot));
+
+  return ReachProbability;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
 double MERCSR::CalculateTotalDistance(const MVector& Start, 
                                               const MVector& Stop, double Etot)
 {
diff --git a/src/revan/src/MERCSRBayesian.cxx b/src/revan/src/MERCSRBayesian.cxx
index eb3a52ede..fe61cf484 100644
--- a/src/revan/src/MERCSRBayesian.cxx
+++ b/src/revan/src/MERCSRBayesian.cxx
@@ -329,9 +329,7 @@ double MERCSRBayesian::ComputeQualityFactor(vector<MRESE*>& Interactions)
     
       // Compton Distance:
       if (Size <= m_UseAbsorptionsUpTo) {
-        double ComptonDistance = 
-          CalculateComptonDistance((*(Iter-1))->GetPosition(), 
-                                   (*Iter)->GetPosition(), Etot);
+        double ComptonDistance = CalculateReach((*(Iter-1))->GetPosition(), (*Iter)->GetPosition(), Etot);
         Material = float(GetMaterial(*Iter));
         EntriesGood = m_GoodComptonDistance.Get(ComptonDistance, Etot, SizeF, Material);
         EntriesBad = m_BadComptonDistance.Get(ComptonDistance, Etot, SizeF, Material);
diff --git a/src/revan/src/MERHitClusterizer.cxx b/src/revan/src/MERHitClusterizer.cxx
index a83736c05..b8564d83c 100644
--- a/src/revan/src/MERHitClusterizer.cxx
+++ b/src/revan/src/MERHitClusterizer.cxx
@@ -188,6 +188,9 @@ bool MERHitClusterizer::Analyze(MRawEventIncarnations* List)
   // Analyze the raw event...
   MERConstruction::Analyze(List);
 
+  //auto V = g_Verbosity;
+  //g_Verbosity = 5;
+
   mdebug<<"Starting cluster search..."<<endl;
   mdebug<<m_List->ToString()<<endl;
 
@@ -215,6 +218,8 @@ bool MERHitClusterizer::Analyze(MRawEventIncarnations* List)
   mdebug<<"Result of cluster search:"<<endl;
   mdebug<<m_List->ToString()<<endl;
   
+  //g_Verbosity = V;
+
   return true;
 }
 
@@ -317,6 +322,7 @@ void MERHitClusterizer::FindClustersInAdjacentVoxels(MRERawEvent* RE, double Sig
   MRESE* RESE = 0;
   MRECluster* Cluster = 0;
 
+
   mdebug<<"FindClustersInAdjacentVoxels for detector "<<Detector<<endl;
 
   // Main subelement loop
@@ -330,8 +336,10 @@ void MERHitClusterizer::FindClustersInAdjacentVoxels(MRERawEvent* RE, double Sig
         continue;
       }
       // if we have a positive cluster-test
+      //mdebug<<"Adjacent: Testing "<<RE->GetRESEAt(h)->GetID()<<" & "<<RE->GetRESEAt(l)->GetID()<<" Sigma: "<<Sigma<<" Level: "<<Level<<endl;
       if (RE->GetRESEAt(h)->AreAdjacent(RE->GetRESEAt(l), Sigma, Level) == true) {
-          
+        //mdebug<<"Adjacent: "<<RE->GetRESEAt(h)->GetID()<<" & "<<RE->GetRESEAt(l)->GetID()<<endl;
+
         // Coalesce 2 hits to a cluster
         if (RE->GetRESEAt(h)->GetType() == MRESE::c_Hit 
             && RE->GetRESEAt(l)->GetType() == MRESE::c_Hit) {

From e77da64c9fb2ffe9b6ca3558d2f7080823f6c761 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Mon, 25 Nov 2024 11:47:06 -0800
Subject: [PATCH 108/192] BUG: Maje sure there are no overflows

---
 .../inc/MResponseMultipleComptonBayes.h       |  3 ++
 .../src/MResponseMultipleComptonBayes.cxx     | 53 +++++++++++++------
 src/revan/inc/MERCSR.h                        |  3 ++
 src/revan/src/MERCSRBayesian.cxx              | 38 +++++++++----
 4 files changed, 72 insertions(+), 25 deletions(-)

diff --git a/src/response/inc/MResponseMultipleComptonBayes.h b/src/response/inc/MResponseMultipleComptonBayes.h
index cc809e4db..2ae85a89c 100644
--- a/src/response/inc/MResponseMultipleComptonBayes.h
+++ b/src/response/inc/MResponseMultipleComptonBayes.h
@@ -137,6 +137,9 @@ class MResponseMultipleComptonBayes : public MResponseMultipleCompton
   //! Maximum energy range
   double m_EnergyMaximum;
 
+  //! The maximum/minimum cos(Compton scatter angle) limit
+  double m_MaxCosineLimit;
+
   //! Do or not to do absorptions
   bool m_DoAbsorptions;
   //! MaximumSequenceLength up to which absorptions are considered
diff --git a/src/response/src/MResponseMultipleComptonBayes.cxx b/src/response/src/MResponseMultipleComptonBayes.cxx
index 6315b3d95..dfcd68779 100644
--- a/src/response/src/MResponseMultipleComptonBayes.cxx
+++ b/src/response/src/MResponseMultipleComptonBayes.cxx
@@ -70,6 +70,9 @@ MResponseMultipleComptonBayes::MResponseMultipleComptonBayes()
 
   m_EnergyMinimum = 100; // keV
   m_EnergyMaximum = 10000; // keV
+
+  // If you change it here, also change it in MResponseMultiComptonBayes
+  m_MaxCosineLimit = 2;
 }
 
 
@@ -197,7 +200,7 @@ bool MResponseMultipleComptonBayes::Initialize()
 
   if (m_ReReader->PreAnalysis() == false) return false;
 
-  double MaxCosineLimit = 10;
+
 
   // Axis representing the sequence length:
   vector<float> AxisSequenceLength;
@@ -215,7 +218,7 @@ bool MResponseMultipleComptonBayes::Initialize()
   // Compton scatter angle axis:
   // Make sure it starts, well below 0 and exceeds (slightly) 1!
   vector<float> AxisComptonScatterAngleStart;
-  AxisComptonScatterAngleStart = CreateEquiDist(-1.5, 1.1, 26, -MaxCosineLimit, +MaxCosineLimit);
+  AxisComptonScatterAngleStart = CreateEquiDist(-1.5, 1.1, 26, -m_MaxCosineLimit, +m_MaxCosineLimit);
   MString NameAxisComptonScatterAngleStart = "cos#varphi";
 
   // Scatter probability axis
@@ -238,7 +241,7 @@ bool MResponseMultipleComptonBayes::Initialize()
 
   // Make sure it starts, well below 0 and exceeds (slightly) 1!
   vector<float> AxisComptonScatterAngleDual;
-  AxisComptonScatterAngleDual = CreateEquiDist(-1.5, 1.1, 26, -MaxCosineLimit, +MaxCosineLimit);
+  AxisComptonScatterAngleDual = CreateEquiDist(-1.5, 1.1, 26, -m_MaxCosineLimit, +m_MaxCosineLimit);
   MString NameAxisComptonScatterAngleDual = "cos#varphi";
 
   // Total energy axis for scatter probabilities
@@ -303,8 +306,8 @@ bool MResponseMultipleComptonBayes::Initialize()
 
   // Track:
   m_PdfTrackGood = MResponseMatrixO6("MC: Track (good)", 
-                                     CreateEquiDist(-0.5, 1.5, 36, c_NoBound, MaxCosineLimit),
-                                     CreateEquiDist(-0.5, 1.5, 1, c_NoBound, MaxCosineLimit),
+                                     CreateEquiDist(-0.5, 1.5, 36, -m_MaxCosineLimit, m_MaxCosineLimit),
+                                     CreateEquiDist(-0.5, 1.5, 1, -m_MaxCosineLimit, m_MaxCosineLimit),
                                      CreateEquiDist(0, 1000000, 1),
                                      CreateLogDist(500, 10000, 10, 0, 100000, 0, false),
                                      AxisSequenceLength, 
@@ -316,8 +319,8 @@ bool MResponseMultipleComptonBayes::Initialize()
                               NameAxisSequenceLength, 
                               NameAxisMaterial);
   m_PdfTrackBad = MResponseMatrixO6("MC: Track (bad)", 
-                                    CreateEquiDist(-0.5, 1.5, 36, c_NoBound, MaxCosineLimit),
-                                    CreateEquiDist(-0.5, 1.5, 1, c_NoBound, MaxCosineLimit),
+                                    CreateEquiDist(-0.5, 1.5, 36, -m_MaxCosineLimit, m_MaxCosineLimit),
+                                    CreateEquiDist(-0.5, 1.5, 1, -m_MaxCosineLimit, m_MaxCosineLimit),
                                     CreateEquiDist(0, 1000000, 1),
                                     CreateLogDist(500, 10000, 10, 0, 100000, 0, false),
                                     AxisSequenceLength, 
@@ -376,9 +379,9 @@ bool MResponseMultipleComptonBayes::Initialize()
   
   // Assymetries would be best handled if -1 .. 1
   //vector<float> AxisDifferenceComptonScatterAngle = 
-  //  CreateLogDist(1E-3, 2, 18, 0.0000001, MaxCosineLimit);
+  //  CreateLogDist(1E-3, 2, 18, 0.0000001, m_MaxCosineLimit);
   vector<float> AxisDifferenceComptonScatterAngle; 
-  vector<float> A = CreateLogDist(0.003, 2, 14, c_NoBound, MaxCosineLimit);
+  vector<float> A = CreateLogDist(0.003, 1.8, 13, c_NoBound, m_MaxCosineLimit);
   for (unsigned int i = A.size()-1; i < A.size(); --i) {
     AxisDifferenceComptonScatterAngle.push_back(-A[i]);
   }
@@ -388,7 +391,7 @@ bool MResponseMultipleComptonBayes::Initialize()
   MString NameAxisDifferenceComptonScatterAngle = "cos#varphi_{E} - cos#varphi_{G}";
 
   vector<float> AxisComptonScatterAngle;
-  AxisComptonScatterAngle = CreateEquiDist(-1.4, 1.2, 13, -MaxCosineLimit, c_NoBound);
+  AxisComptonScatterAngle = CreateEquiDist(-1.4, 1.2, 13, -m_MaxCosineLimit, m_MaxCosineLimit);
   MString NameAxisComptonScatterAngle = NameAxisComptonScatterAngleStart;
 
 
@@ -512,7 +515,8 @@ bool MResponseMultipleComptonBayes::Analyze()
       Eres = RE->GetEnergyResolution();
       
       double CosPhiE = CalculateCosPhiE(*Iter.GetCurrent(), Etot);
-      if (CosPhiE <= -10) CosPhiE = -9.99;
+      if (CosPhiE <= -m_MaxCosineLimit) CosPhiE = -0.99*m_MaxCosineLimit;
+      if (CosPhiE >= +m_MaxCosineLimit) CosPhiE = +0.99*m_MaxCosineLimit;
       double PhotoDistance = CalculateAbsorptionProbabilityTotal(*Iter.GetCurrent(), *Iter.GetNext(), Iter.GetNext()->GetEnergy());
       
       if (IsComptonStart(*Iter.GetCurrent(), Etot, Eres) == true) {
@@ -539,19 +543,29 @@ bool MResponseMultipleComptonBayes::Analyze()
       Iter.GetNextRESE();
       Etot = RE->GetEnergy();
       Eres = RE->GetEnergyResolution();
+
+      double CosPhiE = CalculateCosPhiE(*Iter.GetCurrent(), Etot);
+      if (CosPhiE <= -m_MaxCosineLimit) CosPhiE = -0.99*m_MaxCosineLimit;
+      if (CosPhiE >= +m_MaxCosineLimit) CosPhiE = +0.99*m_MaxCosineLimit;
+
       if (IsComptonStart(*Iter.GetCurrent(), Etot, Eres) == true) {
         mdebug<<"--------> Found GOOD Compton start!"<<endl;
-        m_PdfStartGood.Add(Etot, CalculateCosPhiE(*Iter.GetCurrent(), Etot), SequenceLength, GetMaterial(*Iter.GetCurrent()));
+        m_PdfStartGood.Add(Etot, CosPhiE, SequenceLength, GetMaterial(*Iter.GetCurrent()));
       } else {
         mdebug<<"--------> Found bad Compton start!"<<endl;
-        m_PdfStartBad.Add(Etot, CalculateCosPhiE(*Iter.GetCurrent(), Etot), SequenceLength, GetMaterial(*Iter.GetCurrent()));
+        m_PdfStartBad.Add(Etot, CosPhiE, SequenceLength, GetMaterial(*Iter.GetCurrent()));
         SequenceOk = false;
       }
       
       // Track at start?
       if (Iter.GetCurrent()->GetType() == MRESE::c_Track) {
         double dAlpha = CalculateDCosAlpha(*((MRETrack*) Iter.GetCurrent()), *Iter.GetNext(), Etot);
+        if (dAlpha <= -m_MaxCosineLimit) dAlpha = -0.99*m_MaxCosineLimit;
+        if (dAlpha >= +m_MaxCosineLimit) dAlpha = +0.99*m_MaxCosineLimit;
         double Alpha = CalculateCosAlphaG(*((MRETrack*) Iter.GetCurrent()), *Iter.GetNext(), Etot);
+        if (Alpha <= -m_MaxCosineLimit) Alpha = -0.99*m_MaxCosineLimit;
+        if (Alpha >= +m_MaxCosineLimit) Alpha = +0.99*m_MaxCosineLimit;
+
         if (IsComptonTrack(*Iter.GetCurrent(), *Iter.GetNext(), Etot, Eres) == true) {
           mdebug<<"--------> Found GOOD Track start!"<<endl;
           m_PdfTrackGood.Add(dAlpha, Alpha, 1, Iter.GetCurrent()->GetEnergy(), SequenceLength, GetMaterial(*Iter.GetCurrent()));
@@ -573,8 +587,7 @@ bool MResponseMultipleComptonBayes::Analyze()
         
         // In the current implementation/simulation the hits have to be in increasing order...
         if (m_DoAbsorptions == true && SequenceLength <= m_MaxAbsorptions) {
-          double ComptonDistance = 
-          CalculateReach(*Iter.GetPrevious(), *Iter.GetCurrent(), Etot);
+          double ComptonDistance = CalculateReach(*Iter.GetPrevious(), *Iter.GetCurrent(), Etot);
           mdebug<<"Dist C: "<<ComptonDistance<<": real:"<<(Iter.GetCurrent()->GetPosition() - Iter.GetPrevious()->GetPosition()).Mag()<<endl;
           if (IsComptonSequence(*Iter.GetPrevious(), *Iter.GetCurrent(), Etot, Eres) == true) {
             mdebug<<"--------> Found GOOD Distance sequence!"<<endl;
@@ -591,7 +604,12 @@ bool MResponseMultipleComptonBayes::Analyze()
         // Decide if it is good or bad...
         // In the current implementation/simulation the hits have to be in increasing order...
         double dPhi = CalculateDCosPhi(*Iter.GetPrevious(), *Iter.GetCurrent(), *Iter.GetNext(), Etot);
+        if (dPhi <= -m_MaxCosineLimit) CosPhiE = -0.99*m_MaxCosineLimit;
+        if (dPhi >= +m_MaxCosineLimit) CosPhiE = +0.99*m_MaxCosineLimit;
         double PhiE = CalculateCosPhiE(*Iter.GetCurrent(), Etot);
+        if (PhiE <= -m_MaxCosineLimit) PhiE = -0.99*m_MaxCosineLimit;
+        if (PhiE >= +m_MaxCosineLimit) PhiE = +0.99*m_MaxCosineLimit;
+
         double Lever = CalculateMinLeverArm(*Iter.GetPrevious(), *Iter.GetCurrent(), *Iter.GetNext());
         int Material = GetMaterial(*Iter.GetCurrent());
         
@@ -611,7 +629,12 @@ bool MResponseMultipleComptonBayes::Analyze()
         if (Iter.GetCurrent()->GetType() == MRESE::c_Track) {
           //MRETrack* T = (MRETrack*) Iter.GetCurrent();
           double dAlpha = CalculateDCosAlpha(*((MRETrack*) Iter.GetCurrent()), *Iter.GetNext(), Etot);
+          if (dAlpha <= -m_MaxCosineLimit) dAlpha = -0.99*m_MaxCosineLimit;
+          if (dAlpha >= +m_MaxCosineLimit) dAlpha = +0.99*m_MaxCosineLimit;
           double Alpha = CalculateCosAlphaG(*((MRETrack*) Iter.GetCurrent()), *Iter.GetNext(), Etot);
+          if (Alpha <= -m_MaxCosineLimit) Alpha = -0.99*m_MaxCosineLimit;
+          if (Alpha >= +m_MaxCosineLimit) Alpha = +0.99*m_MaxCosineLimit;
+
           if (IsComptonTrack(*Iter.GetCurrent(), *Iter.GetNext(), Etot, Eres) == true) {
             mdebug<<"--------> Found GOOD Track start (central)!"<<endl;
             m_PdfTrackGood.Add(dAlpha, Alpha, 1, Iter.GetCurrent()->GetEnergy(), SequenceLength, GetMaterial(*Iter.GetCurrent()));
diff --git a/src/revan/inc/MERCSR.h b/src/revan/inc/MERCSR.h
index 9bc00ee6a..59f5f9f9e 100644
--- a/src/revan/inc/MERCSR.h
+++ b/src/revan/inc/MERCSR.h
@@ -105,6 +105,9 @@ class MERCSR : public MERConstruction
   bool m_CreateOnlyPermutations;
   bool m_GuaranteeStartD1;
 
+  //! The maximum/minimum cos(Compton scatter angle) limit
+  double m_MaxCosineLimit;
+
   /// The sorted list of quality factors
   map<double, vector<MRESE*>, less_equal<double> > m_QualityFactors;
   /// An iterator over the sorted list of quality factors
diff --git a/src/revan/src/MERCSRBayesian.cxx b/src/revan/src/MERCSRBayesian.cxx
index fe61cf484..7791ec050 100644
--- a/src/revan/src/MERCSRBayesian.cxx
+++ b/src/revan/src/MERCSRBayesian.cxx
@@ -96,6 +96,9 @@ bool MERCSRBayesian::SetParameters(MString FileName,
 
   m_UseAbsorptionsUpTo = 5;
 
+  // If you change it here, also change it in MResponseMultiComptonBayes
+  m_MaxCosineLimit = 2;
+
   m_FileName = FileName;
 
   if (m_CreateOnlyPermutations == false) {
@@ -221,8 +224,9 @@ double MERCSRBayesian::ComputeQualityFactor(vector<MRESE*>& Interactions)
   if (Size == 2) {
     Material = float(GetMaterial(*Iter));
     double CosPhiE = CalculateCosPhiE((*Iter), Etot);
-    double Distance = 
-      CalculateTotalDistance((*Iter)->GetPosition(), (*(Iter+1))->GetPosition(), (*(Iter+1))->GetEnergy());
+    if (CosPhiE <= -m_MaxCosineLimit) CosPhiE = -0.99*m_MaxCosineLimit;
+    if (CosPhiE >= +m_MaxCosineLimit) CosPhiE = +0.99*m_MaxCosineLimit;
+    double Distance = CalculateTotalDistance((*Iter)->GetPosition(), (*(Iter+1))->GetPosition(), (*(Iter+1))->GetEnergy());
 
     EntriesGood = m_GoodDualDeposit.Get(Etot, CosPhiE, Distance, Material);
     EntriesBad = m_BadDualDeposit.Get(Etot, CosPhiE, Distance, Material);
@@ -256,9 +260,12 @@ double MERCSRBayesian::ComputeQualityFactor(vector<MRESE*>& Interactions)
   } else {
     // Check start:
     Material = float(GetMaterial(*Iter));
-    double PhiE = CalculateCosPhiE((*Iter), Etot);
-    EntriesGood = m_GoodStartDeposit.Get(Etot, PhiE, SizeF, Material);
-    EntriesBad = m_BadStartDeposit.Get(Etot, PhiE, SizeF, Material);
+    double CosPhiE = CalculateCosPhiE((*Iter), Etot);
+    if (CosPhiE <= -m_MaxCosineLimit) CosPhiE = -0.99*m_MaxCosineLimit;
+    if (CosPhiE >= +m_MaxCosineLimit) CosPhiE = +0.99*m_MaxCosineLimit;
+
+    EntriesGood = m_GoodStartDeposit.Get(Etot, CosPhiE, SizeF, Material);
+    EntriesBad = m_BadStartDeposit.Get(Etot, CosPhiE, SizeF, Material);
     SumGood = m_SumGoodStartDeposit.Get(SizeF);
     SumBad = m_SumBadStartDeposit.Get(SizeF);
     VerifyEntries(EntriesGood, EntriesBad);
@@ -266,7 +273,7 @@ double MERCSRBayesian::ComputeQualityFactor(vector<MRESE*>& Interactions)
     if (ShowDebug == true) {
       cout<<"Start:        "
           <<setw(8)<<Etot<<"  "
-          <<setw(8)<<PhiE<<"  "
+          <<setw(8)<<CosPhiE<<"  "
           <<setw(8)<<Size<<"  "
           <<setw(8)<<Material<<"  "
           <<setw(8)<<0.0<<"  "
@@ -289,7 +296,12 @@ double MERCSRBayesian::ComputeQualityFactor(vector<MRESE*>& Interactions)
     // Check initial track:
     if ((*Iter)->GetType() ==  MRESE::c_Track) {
       double dAlpha = CalculateDCosAlpha((MRETrack*) (*Iter), *(Iter+1), Etot);
+      if (dAlpha <= -m_MaxCosineLimit) dAlpha = -0.99*m_MaxCosineLimit;
+      if (dAlpha >= +m_MaxCosineLimit) dAlpha = +0.99*m_MaxCosineLimit;
       double Alpha = CalculateCosAlphaG((MRETrack*) (*Iter), *(Iter+1), Etot);
+      if (Alpha <= -m_MaxCosineLimit) Alpha = -0.99*m_MaxCosineLimit;
+      if (Alpha >= +m_MaxCosineLimit) Alpha = +0.99*m_MaxCosineLimit;
+
       double ElectronEnergy = (*Iter)->GetEnergy();
       EntriesGood = m_GoodTrack.Get(dAlpha, Alpha, 1, ElectronEnergy, SizeF, Material);
       EntriesBad = m_BadTrack.Get(dAlpha, Alpha, 1, ElectronEnergy, SizeF, Material);
@@ -362,10 +374,12 @@ double MERCSRBayesian::ComputeQualityFactor(vector<MRESE*>& Interactions)
       }
 
       // Compton:
-      double dPhi =
-        CalculateDCosPhi((*(Iter-1)), (*Iter), (*(Iter+1)), Etot);
-      double PhiE = 
-        CalculateCosPhiE((*Iter), Etot);
+      double dPhi = CalculateDCosPhi((*(Iter-1)), (*Iter), (*(Iter+1)), Etot);
+      if (dPhi <= -m_MaxCosineLimit) CosPhiE = -0.99*m_MaxCosineLimit;
+      if (dPhi >= +m_MaxCosineLimit) CosPhiE = +0.99*m_MaxCosineLimit;
+      double PhiE = CalculateCosPhiE((*Iter), Etot);
+      if (PhiE <= -m_MaxCosineLimit) PhiE = -0.99*m_MaxCosineLimit;
+      if (PhiE >= +m_MaxCosineLimit) PhiE = +0.99*m_MaxCosineLimit;
       double Lever = CalculateMinLeverArm((*(Iter-1))->GetPosition(), 
                                           (*Iter)->GetPosition(),
                                           (*(Iter+1))->GetPosition());
@@ -402,7 +416,11 @@ double MERCSRBayesian::ComputeQualityFactor(vector<MRESE*>& Interactions)
       // Check central track:
       if ((*Iter)->GetType() ==  MRESE::c_Track) {
         double dAlpha = CalculateDCosAlpha((MRETrack*) (*Iter), *(Iter+1), Etot);
+        if (dAlpha <= -m_MaxCosineLimit) dAlpha = -0.99*m_MaxCosineLimit;
+        if (dAlpha >= +m_MaxCosineLimit) dAlpha = +0.99*m_MaxCosineLimit;
         double Alpha = CalculateCosAlphaG((MRETrack*) (*Iter), *(Iter+1), Etot);
+        if (Alpha <= -m_MaxCosineLimit) Alpha = -0.99*m_MaxCosineLimit;
+        if (Alpha >= +m_MaxCosineLimit) Alpha = +0.99*m_MaxCosineLimit;
         double ElectronEnergy = (*Iter)->GetEnergy();
         EntriesGood = m_GoodTrack.Get(dAlpha, Alpha, 1, ElectronEnergy, SizeF, Material);
         EntriesBad = m_BadTrack.Get(dAlpha, Alpha, 1, ElectronEnergy, SizeF, Material);

From 670fdaabe72be221c272330cb1a6bc553b41ae79 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Fri, 29 Nov 2024 00:37:21 -0800
Subject: [PATCH 109/192] BUG: Wrong variable used

---
 .../src/MResponseMultipleComptonBayes.cxx       | 17 +++++++++++------
 src/revan/src/MERCSRBayesian.cxx                |  4 ++--
 2 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/src/response/src/MResponseMultipleComptonBayes.cxx b/src/response/src/MResponseMultipleComptonBayes.cxx
index dfcd68779..1a1f4eb09 100644
--- a/src/response/src/MResponseMultipleComptonBayes.cxx
+++ b/src/response/src/MResponseMultipleComptonBayes.cxx
@@ -604,8 +604,8 @@ bool MResponseMultipleComptonBayes::Analyze()
         // Decide if it is good or bad...
         // In the current implementation/simulation the hits have to be in increasing order...
         double dPhi = CalculateDCosPhi(*Iter.GetPrevious(), *Iter.GetCurrent(), *Iter.GetNext(), Etot);
-        if (dPhi <= -m_MaxCosineLimit) CosPhiE = -0.99*m_MaxCosineLimit;
-        if (dPhi >= +m_MaxCosineLimit) CosPhiE = +0.99*m_MaxCosineLimit;
+        if (dPhi <= -m_MaxCosineLimit) dPhi = -0.99*m_MaxCosineLimit;
+        if (dPhi >= +m_MaxCosineLimit) dPhi = +0.99*m_MaxCosineLimit;
         double PhiE = CalculateCosPhiE(*Iter.GetCurrent(), Etot);
         if (PhiE <= -m_MaxCosineLimit) PhiE = -0.99*m_MaxCosineLimit;
         if (PhiE >= +m_MaxCosineLimit) PhiE = +0.99*m_MaxCosineLimit;
@@ -621,7 +621,11 @@ bool MResponseMultipleComptonBayes::Analyze()
         } else {
           mdebug<<"--------> Found bad internal Compton sequence!"<<endl;
           // Retrieve the data:
+
           m_PdfComptonBad.Add(dPhi, PhiE, Lever, Etot, SequenceLength, Material);
+          if (fabs(dPhi) < 0.1) {
+            cout<<"Close to good: dPhi="<<dPhi<<" PhiE="<<PhiE<<" PhiG="<<CalculateCosPhiG(*Iter.GetPrevious(), *Iter.GetCurrent(), *Iter.GetNext())<<endl;
+          }
           SequenceOk = false;
         } // Add good / bad
         
@@ -659,13 +663,14 @@ bool MResponseMultipleComptonBayes::Analyze()
         if (IsComptonSequence(*Iter.GetPrevious(), *Iter.GetCurrent(), Etot, Eres) == true) {
           mdebug<<"--------> Found GOOD Lastdistance sequence!"<<endl;
           // Retrieve the data:
-          m_PdfPhotoAbsorptionProbabilityGood.Add(CalculateAbsorptionProbabilityPhoto(*Iter.GetPrevious(), *Iter.GetCurrent(), Etot), 
-                                                  Etot, SequenceLength, GetMaterial(*Iter.GetCurrent()));
+          m_PdfPhotoAbsorptionProbabilityGood.Add(LastDistance, Etot, SequenceLength, GetMaterial(*Iter.GetCurrent()));
         } else {
           mdebug<<"--------> Found bad Lastdistance sequence!"<<endl;
           // Retrieve the data:
-          m_PdfPhotoAbsorptionProbabilityBad.Add(CalculateAbsorptionProbabilityPhoto(*Iter.GetPrevious(), *Iter.GetCurrent(), Etot), 
-                                                 Etot, SequenceLength, GetMaterial(*Iter.GetCurrent()));
+          m_PdfPhotoAbsorptionProbabilityBad.Add(LastDistance, Etot, SequenceLength, GetMaterial(*Iter.GetCurrent()));
+          if (LastDistance > 0.4 && LastDistance < 0.6 && Etot < 200) {
+            cout<<"Close to good: dist="<<LastDistance<<" && Etot="<<Etot<<endl;
+          }
           SequenceOk = false;
         } // Add good / bad
       }
diff --git a/src/revan/src/MERCSRBayesian.cxx b/src/revan/src/MERCSRBayesian.cxx
index 7791ec050..473270ac2 100644
--- a/src/revan/src/MERCSRBayesian.cxx
+++ b/src/revan/src/MERCSRBayesian.cxx
@@ -375,8 +375,8 @@ double MERCSRBayesian::ComputeQualityFactor(vector<MRESE*>& Interactions)
 
       // Compton:
       double dPhi = CalculateDCosPhi((*(Iter-1)), (*Iter), (*(Iter+1)), Etot);
-      if (dPhi <= -m_MaxCosineLimit) CosPhiE = -0.99*m_MaxCosineLimit;
-      if (dPhi >= +m_MaxCosineLimit) CosPhiE = +0.99*m_MaxCosineLimit;
+      if (dPhi <= -m_MaxCosineLimit) dPhi = -0.99*m_MaxCosineLimit;
+      if (dPhi >= +m_MaxCosineLimit) dPhi = +0.99*m_MaxCosineLimit;
       double PhiE = CalculateCosPhiE((*Iter), Etot);
       if (PhiE <= -m_MaxCosineLimit) PhiE = -0.99*m_MaxCosineLimit;
       if (PhiE >= +m_MaxCosineLimit) PhiE = +0.99*m_MaxCosineLimit;

From d6e386525f4ea87ae2efbc5d10a0f2b930691490 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Wed, 8 Jan 2025 11:27:58 -0800
Subject: [PATCH 110/192] CHG: Compatibility updated and hidden --allowroot
 feature

---
 config/build-root.sh |  5 +++--
 setup.sh             | 24 +++++++++++++++++++-----
 2 files changed, 22 insertions(+), 7 deletions(-)

diff --git a/config/build-root.sh b/config/build-root.sh
index ddb1a8789..e8efb7096 100755
--- a/config/build-root.sh
+++ b/config/build-root.sh
@@ -376,8 +376,9 @@ else
   for s in `seq -w 00 2 98`; do
     TESTTARBALL="root_v${WANTEDVERSION}.${s}.source.tar.gz"
     echo "Trying to find ${TESTTARBALL}..."
-    EXISTS=`curl -s --head https://root.cern.ch/download/${TESTTARBALL} | grep gzip`
-    if [[ ${EXISTS} == "" ]]; then # sometimes version 00 does not exist...
+    # old: EXISTS=`curl -s --head https://root.cern.ch/download/${TESTTARBALL} | grep gzip`
+    EXISTS=$(curl -s --head https://root.cern.ch/download/${TESTTARBALL} | head -n 1 )
+    if [[ ${EXISTS} != *OK* ]]; then
       MAX_TRIALS=$(( MAX_TRIALS - 1 ))
       if [[ ${MAX_TRIALS} -eq 0 ]]; then
         break
diff --git a/setup.sh b/setup.sh
index fbb9099a1..283b94d42 100755
--- a/setup.sh
+++ b/setup.sh
@@ -5,8 +5,10 @@
 #
 # Please see the MEGAlib software license and documentation for more informations.
 
-
 # Part 1:
+# Store command line as array
+CMD=( "$@" )
+
 # Helper functions
 
 TIMESTART=$(date +%s)
@@ -77,6 +79,9 @@ confhelp() {
   echo "    Check periodically for updates. Default is off."
   echo "    Even if set to on, update checks will only be performed, if the user has write access to the MEGAlib installation."
   echo " "
+  #echo "--allowroot"
+  #echo "    By default this script does not allow to be installed as ROOT. This option allows it."
+  #echo " " 
   echo "--help or -h"
   echo "    Show this help."
   echo " "
@@ -104,7 +109,15 @@ if [ "$SHELL" != "/bin/bash" ]; then
   echo " "
 fi
 
-if [[ $EUID -eq 0 ]]; then
+# Check if the command line contains "--allowroot"
+ALLOWROOT="off"
+for C in "${CMD[@]}"; do
+  if [[ ${C} == *--allowroot* ]]; then
+    ALLOWROOT="on"
+  fi
+done
+
+if [[ $EUID -eq 0 ]] && [[ ${ALLOWROOT} == off ]]; then
   echo " " 1>&2
   echo "Error: For security reasons, this script is not intended to be run as superuser/root." 1>&2
   echo "       It is intended for a user installation of MEGAlib." 1>&2
@@ -130,9 +143,6 @@ fi
 # Part 3:
 # Upgrade the input options:
 
-# Store command line as array
-CMD=( "$@" )
-
 # Check for help
 for C in "${CMD[@]}"; do
   if [[ ${C} == *-h ]] || [[ ${C} == *-hel* ]]; then
@@ -171,6 +181,7 @@ UPDATES="off"
 PATCH="on"
 CLEANUP="off"
 BRANCH=""
+# ALLOWROOT="off" - initialized in the beginning not here
 
 MAXTHREADS=1;
 if [[ ${OSTYPE} == *arwin* ]]; then
@@ -253,6 +264,9 @@ for C in "${CMD[@]}"; do
   elif [[ ${C} == *-b* ]]; then
     BRANCH=`echo ${C} | awk -F"=" '{ print $2 }'`
     RELEASE="dev"
+  elif [[ ${C} == *--allowroot* ]]; then
+    # Handled above too
+    ALLOWROOT="on"
   elif [[ ${C} == *-h ]] || [[ ${C} == *-hel* ]]; then
     echo ""
     confhelp

From 31e105156432d348261892a01603b7717eadb510 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Thu, 9 Jan 2025 13:44:28 -0800
Subject: [PATCH 111/192] CHG: Switch MFunction to long double, give a warning
 on systems where the accuracy is less than 16 bytes

---
 src/global/misc/inc/MFunction.h   |  66 +++---
 src/global/misc/src/MFunction.cxx | 364 ++++++++++++++----------------
 2 files changed, 200 insertions(+), 230 deletions(-)

diff --git a/src/global/misc/inc/MFunction.h b/src/global/misc/inc/MFunction.h
index 9e1289f68..6745533e6 100644
--- a/src/global/misc/inc/MFunction.h
+++ b/src/global/misc/inc/MFunction.h
@@ -56,50 +56,55 @@ class MFunction
   //! Set the basic data from a 1D ResponseMatrix
   bool Set(const MResponseMatrixO1& Response);
 
-  //! Set the basic data from two vector
+  //! Set the basic data from two vectors
   bool Set(const vector<double>& X, const vector<double>& Y, unsigned int InterpolationType = c_InterpolationLinLin);
 
+  //! Set the basic data from two vectors
+  bool Set(const vector<long double>& X, const vector<long double>& Y, unsigned int InterpolationType = c_InterpolationLinLin);
+
   //! Add a data point
-  bool Add(const double x, const double y);
+  bool Add(const long double x, const long double y);
 
   //! Multiple the x-axis by some value
-  void ScaleX(double Scaler);
+  void ScaleX(long double Scaler);
 
   //! Scale the content by some value
-  void ScaleY(double Scaler);
+  void ScaleY(long double Scaler);
+
+  //! Evaluate the data for a specific x value
+  long double Evaluate(long double x) const;
 
-  //! Evaluate the data for a specific x value 
-  double Evaluate(double x) const; 
-  double Eval(double x) const; // deprecated
+  //! Deprectad - Evaluate the data for a specific x value
+  long double Eval(long double x) const;
 
   //! Integrate all the data from min to max
-  double Integrate() const;
+  long double Integrate() const;
 
   //! Integrate the data from min to max
-  double Integrate(double XMin, double XMax) const;
+  long double Integrate(long double XMin, long double XMax) const;
 
   //! Return a random number distributed as the underlying function
-  double GetRandom();
+  long double GetRandom();
 
   //! Return a random number distributed as the underlying function times the x-value
   //! This is helpfull in case the function is a profile of a radial 2D function
-  double GetRandomTimesX();
+  long double GetRandomTimesX();
 
   //! Return the size of the array
-  double GetSize() const { return m_X.size(); } 
+  long double GetSize() const { return m_X.size(); }
 
   //! Get the minimum x-value
-  double GetXMin() const;
+  long double GetXMin() const;
   //! Get the maximum x-value
-  double GetXMax() const;
+  long double GetXMax() const;
   //! Get the minimum y-value
-  double GetYMin() const;
+  long double GetYMin() const;
   //! Get the maximum y-value
-  double GetYMax() const;
+  long double GetYMax() const;
 
   //! Find the x value starting from Start which would be achieved after integrating until Integral
   //! If we go beyond x_max, x_max is returned if we are not cyclic, otherwise we continue at x_0
-  double FindX(double XStart, double Integral, bool Cyclic);
+  long double FindX(long double XStart, long double Integral, bool Cyclic);
   
   //! ID representing an unknown interpolation
   static const unsigned int c_InterpolationUnknown;
@@ -128,9 +133,9 @@ class MFunction
   //! Get the number of data points
   unsigned int GetNDataPoints() const { return m_X.size(); }
   //! Get the x value of the data point
-  double GetDataPointX(unsigned int n) const { return m_X.at(n); }
+  long double GetDataPointX(unsigned int n) const { return m_X.at(n); }
   //! Get the y value of the data point
-  double GetDataPointY(unsigned int n) const { return m_Y.at(n); }
+  long double GetDataPointY(unsigned int n) const { return m_Y.at(n); }
 
   //! Save the data:
   bool Save(const MString FileName, const MString Keyword = "DP");
@@ -138,14 +143,14 @@ class MFunction
 
   // protected methods:
  protected:
-  //! Create the splines for interpolation
-  void CreateSplines();
-
   //! The interpolation stage of the GetRandom() function
-  double GetRandomInterpolate(double Itot);
+  long double GetRandomInterpolate(long double Itot);
 
   //! Implementation of Lambert's W function branches 0 and -1
-  double LambertW(double x, int Branch);
+  long double LambertW(long double x, int Branch);
+
+  //! Check the dynamic range and give a warning message otherwise
+  void CheckDynamicRange();
 
   // private methods:
  private:
@@ -159,23 +164,16 @@ class MFunction
   unsigned int m_InterpolationType;
 
   //! The x-axis data
-  vector<double> m_X;
-  //! The x-axis data starting at 0
-  vector<double> m_XZero;
+  vector<long double> m_X;
   //! The y-axis data
-  vector<double> m_Y;
+  vector<long double> m_Y;
 
   //! True if the minimum y-value is non-negative
   bool m_YNonNegative;
 
-  //! The 3-spline 
-  TSpline3* m_Spline3;
-  //! The 5-spline
-  TSpline5* m_Spline5;
-
   // For random number generation:
   //! The function as cumulative distribution:
-  vector<double> m_Cumulative;
+  vector<long double> m_Cumulative;
   
 
 #ifdef ___CLING___
diff --git a/src/global/misc/src/MFunction.cxx b/src/global/misc/src/MFunction.cxx
index ece0f8bdc..349c025cc 100644
--- a/src/global/misc/src/MFunction.cxx
+++ b/src/global/misc/src/MFunction.cxx
@@ -29,7 +29,6 @@
 // Standard libs:
 #include <algorithm>
 #include <cmath>
-#include <iomanip>
 using namespace std;
 
 // ROOT libs:
@@ -69,14 +68,10 @@ const unsigned int MFunction::c_InterpolationSpline5  = 8;
 ////////////////////////////////////////////////////////////////////////////////
 
 
-MFunction::MFunction() 
-  : m_InterpolationType(c_InterpolationLinLin)
+MFunction::MFunction() : m_InterpolationType(c_InterpolationLinLin)
 {
   // Construct an instance of MFunction
 
-  m_Spline3 = 0;
-  m_Spline5 = 0;
-
   m_YNonNegative = true;
 }
 
@@ -91,16 +86,9 @@ MFunction::MFunction(const MFunction& F)
   m_InterpolationType = F.m_InterpolationType;
 
   m_X = F.m_X;
-  m_XZero = F.m_XZero;
   m_Y = F.m_Y;
   m_Cumulative = F.m_Cumulative;
   m_YNonNegative = F.m_YNonNegative;
-
-  m_Spline3 = 0;
-  m_Spline5 = 0;
-  if (m_InterpolationType == c_InterpolationSpline3 || m_InterpolationType == c_InterpolationSpline5) { 
-    CreateSplines();
-  }
 }
 
 
@@ -110,9 +98,6 @@ MFunction::MFunction(const MFunction& F)
 MFunction::~MFunction()
 {
   // Delete this instance of MFunction
-
-  delete m_Spline3;
-  delete m_Spline5;
 }
 
 
@@ -126,16 +111,11 @@ const MFunction& MFunction::operator=(const MFunction& F)
   m_InterpolationType = F.m_InterpolationType;
 
   m_X = F.m_X;
-  m_XZero = F.m_XZero;
   m_Y = F.m_Y;
   m_Cumulative = F.m_Cumulative;
   m_YNonNegative = F.m_YNonNegative;
 
-  m_Spline3 = 0;
-  m_Spline5 = 0;
-  if (m_InterpolationType == c_InterpolationSpline3 || m_InterpolationType == c_InterpolationSpline5) { 
-    CreateSplines();
-  }
+  CheckDynamicRange();
 
   return *this;
 }
@@ -233,20 +213,7 @@ bool MFunction::Set(const MString FileName, const MString KeyWord)
     }
   }
 
-  // Determine interapolation type:
-  if (m_InterpolationType == c_InterpolationSpline5 || m_InterpolationType == c_InterpolationSpline3) {
-    mimp<<"Currently spline is no longer supported, thus switch back to linear interpolation"<<endl;
-    m_InterpolationType = c_InterpolationLinLin;
-  }
-
-  if (m_X.size() < 5 && m_InterpolationType == c_InterpolationSpline5) {
-    m_InterpolationType = c_InterpolationSpline3;
-  }
-
-  if (m_X.size() < 3 && m_InterpolationType == c_InterpolationSpline3) {
-    m_InterpolationType = c_InterpolationLinLin;
-  }
-
+  // Determine interpolation type:
   if (m_X.size() > 1 && m_InterpolationType == c_InterpolationConstant) {
     m_InterpolationType = c_InterpolationLinLin;
   } 
@@ -270,13 +237,7 @@ bool MFunction::Set(const MString FileName, const MString KeyWord)
   // Clean up:
   m_Cumulative.clear();
 
-  if (m_InterpolationType == c_InterpolationSpline3 || m_InterpolationType == c_InterpolationSpline5) { 
-    CreateSplines();
-  }
-
-  for (auto x: m_X) {
-    m_XZero.push_back(x - m_X[0]);
-  }
+  CheckDynamicRange();
 
   return true;
 }
@@ -346,9 +307,7 @@ bool MFunction::Set(const MResponseMatrixO1& Response)
   // Clean up:
   m_Cumulative.clear();
 
-  for (auto x: m_X) {
-    m_XZero.push_back(x - m_X[0]);
-  }
+  CheckDynamicRange();
 
   return true;
 }
@@ -357,7 +316,7 @@ bool MFunction::Set(const MResponseMatrixO1& Response)
 ////////////////////////////////////////////////////////////////////////////////
 
 
-bool MFunction::Set(const vector<double>& X, const vector<double>& Y, unsigned int InterpolationType)
+bool MFunction::Set(const vector<long double>& X, const vector<long double>& Y, unsigned int InterpolationType)
 {
   //! Set the basic data from a 1D ResponseMatrix
 
@@ -375,35 +334,58 @@ bool MFunction::Set(const vector<double>& X, const vector<double>& Y, unsigned i
   // Clean up:
   m_Cumulative.clear();
 
-  for (auto x: m_X) {
-    m_XZero.push_back(x - m_X[0]);
-  }
+  CheckDynamicRange();
 
   return true;
 }
 
 
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MFunction::Set(const vector<double>& X, const vector<double>& Y, unsigned int InterpolationType)
+{
+  //! Set the basic data from a 1D ResponseMatrix
+
+  m_X.clear();
+  for (auto& V: X) m_X.push_back(V);
+  m_Y.clear();
+  for (auto& V: Y) m_Y.push_back(V);
+
+  m_InterpolationType = InterpolationType;
+
+  if (GetYMin() < 0) {
+    m_YNonNegative = false;
+  } else {
+    m_YNonNegative = true;
+  }
+
+  // Clean up:
+  m_Cumulative.clear();
+
+  CheckDynamicRange();
+
+  return true;
+}
+
 
 ////////////////////////////////////////////////////////////////////////////////
 
 
-bool MFunction::Add(const double x, const double y)
+bool MFunction::Add(const long double x, const long double y)
 {
   //! Add a data point
 
   if (m_X.size() == 0) {
     m_X.push_back(x);
     m_Y.push_back(y);
-    m_XZero.push_back(x - m_X[0]);
   } else {
     if (x < m_X[0]) {
       m_X.insert(m_X.begin(), x);
       m_Y.insert(m_Y.begin(), y);
-      m_XZero.insert(m_X.begin(), x - m_X[0]);
     } else if (x > m_X.back()) {
       m_X.push_back(x);
       m_Y.push_back(y);
-      m_XZero.push_back(x - m_X[0]);
     } else {
       for (unsigned int i = 0; i < m_X.size(); ++i) {
         if (x == m_X[i]) {
@@ -413,21 +395,51 @@ bool MFunction::Add(const double x, const double y)
         } else if (x < m_X[i]) {
           m_X.insert(m_X.begin()+i, x);
           m_Y.insert(m_Y.begin()+i, y);
-          m_XZero.insert(m_XZero.begin()+i, x - m_X[0]);
           break;
         }
       }
     }
   }
 
+  CheckDynamicRange();
+
   return true;
 }
 
+////////////////////////////////////////////////////////////////////////////////
+
+
+void MFunction::CheckDynamicRange()
+{
+  //! Check the dynamic range and give a warning message if we are too big
+
+  static bool FirstCall = true;
+  if (FirstCall == true) {
+    if (sizeof(long double) < 16) {
+      if (m_X.back() / m_X.front() >= 100000000 && m_X.back() - m_X.front() >= 100000000) { // best guess how to handle zero
+        mout<<endl;
+        mout<<"Attention:"<<endl;
+        mout<<"The size of \"long double\" on this system is just "<<sizeof(long double)<<" bytes."<<endl;
+        mout<<"This can negatively affect analyses / simulations which require an extreme dynamic range, such as"<<endl;
+        mout<<"+ spectra reaching from eV to TeV,"<<endl;
+        mout<<"+ time scales going from nano-seconds to years, or"<<endl;
+        mout<<"+ position accuracies going from detector pixel sizes (mm) to Galactic sizes."<<endl;
+        mout<<"You have a MFunction object (I don't know which one) with a dynamic range from "<<m_X.front()<<" to "<<m_X.back()<<endl;
+        mout<<"Depending on what you are doing exactly, this might impact the accuracy of your results."<<endl;
+        mout<<endl;
+        FirstCall = false;
+      }
+    } else {
+      FirstCall = false;
+    }
+  }
+}
+
 
 ////////////////////////////////////////////////////////////////////////////////
 
 
-void MFunction::ScaleY(double Scaler)
+void MFunction::ScaleY(long double Scaler)
 {
   // Scale the y-content by some value
 
@@ -443,70 +455,29 @@ void MFunction::ScaleY(double Scaler)
 
   // Clean up:
   m_Cumulative.clear();
-
-  if (m_InterpolationType == c_InterpolationSpline3 || m_InterpolationType == c_InterpolationSpline5) { 
-    CreateSplines();
-  }
 }
 
 
 ////////////////////////////////////////////////////////////////////////////////
 
 
-void MFunction::ScaleX(double Scaler)
+void MFunction::ScaleX(long double Scaler)
 {
   // Multiple the x-axis by some value
 
-  for (unsigned int i = 0; i < m_X.size(); ++i) {
+   for (unsigned int i = 0; i < m_X.size(); ++i) {
     m_X[i] *= Scaler;
-    m_XZero[i] = m_X[i] - m_X[0];
-  }
+  }  
 
   // We clear the cumulative function:
   m_Cumulative.clear();
-
-  if (m_InterpolationType == c_InterpolationSpline3 || m_InterpolationType == c_InterpolationSpline5) { 
-    CreateSplines();
-  }
-}
-
-
-////////////////////////////////////////////////////////////////////////////////
-
-
-void MFunction::CreateSplines()
-{
-  // Create the splines for interpolation
-
-    // Generate spline fit:
-  if (m_InterpolationType == c_InterpolationSpline3 || m_InterpolationType == c_InterpolationSpline5) {
-    double* x = new double[m_X.size()];
-    double* y = new double[m_Y.size()];
-    
-    for (unsigned int i = 0; i < m_X.size(); ++i) {
-      x[i] = m_X[i];
-      y[i] = m_Y[i];
-    } 
-
-    if (m_InterpolationType == c_InterpolationSpline3) {
-      delete m_Spline3;
-      m_Spline3 = new TSpline3("", x, y, m_X.size());  
-    } else {
-      delete m_Spline5;
-      m_Spline5 = new TSpline5("", x, y, m_X.size());
-      //m_Spline5->Draw("LP");
-    }
-
-    delete [] x;
-    delete [] y;
-  }
 }
 
 
 ////////////////////////////////////////////////////////////////////////////////
 
 
-double MFunction::Eval(double x) const 
+long double MFunction::Eval(long double x) const
 { 
   mdep<<"MFunction::Eval is deprecated, replace with: MFunction::Evaluate"<<show;
   return Evaluate(x); 
@@ -516,7 +487,7 @@ double MFunction::Eval(double x) const
 ////////////////////////////////////////////////////////////////////////////////
 
 
-double MFunction::Evaluate(double x) const
+long double MFunction::Evaluate(long double x) const
 {
   // Evalute the function considering the different interpolation types
 
@@ -533,10 +504,6 @@ double MFunction::Evaluate(double x) const
 
   if (m_InterpolationType == c_InterpolationConstant || m_X.size() == 1) {
     return m_Y[0];
-  } else if (m_InterpolationType == c_InterpolationSpline3) {
-    return m_Spline3->Eval(x);
-  } else if (m_InterpolationType == c_InterpolationSpline5) {
-    return m_Spline5->Eval(x);
   } else if (m_InterpolationType == c_InterpolationNone) {
 
     // Get Position:
@@ -561,7 +528,7 @@ double MFunction::Evaluate(double x) const
              m_InterpolationType == c_InterpolationLogLin ||
              m_InterpolationType == c_InterpolationLogLog) {
 
-    double y = 0.0;
+    long double y = 0.0;
 
     int Position = -1; 
     for (unsigned int i = 0; i < m_X.size(); ++i) {
@@ -571,7 +538,7 @@ double MFunction::Evaluate(double x) const
       Position = (int) i;
     }
     
-    double x1, x2, y1, y2;
+    long double x1, x2, y1, y2;
     // Position = -1: Extrapolate to lower x
     if (Position == -1) {
       x1 = m_X[0];
@@ -605,8 +572,8 @@ double MFunction::Evaluate(double x) const
       x2 = log(x2);
     }
 
-    double m = (y2-y1)/(x2-x1);
-    double t = y2 - m*x2;
+    long double m = (y2-y1)/(x2-x1);
+    long double t = y2 - m*x2;
 
     if (m_InterpolationType == c_InterpolationLinLog || m_InterpolationType == c_InterpolationLogLog) {
       y = exp(m*x+t);
@@ -629,7 +596,7 @@ double MFunction::Evaluate(double x) const
 ////////////////////////////////////////////////////////////////////////////////
 
 
-double MFunction::Integrate() const
+long double MFunction::Integrate() const
 {
   // Integrate all the data from min to max
 
@@ -639,7 +606,7 @@ double MFunction::Integrate() const
 ////////////////////////////////////////////////////////////////////////////////
 
 
-double MFunction::Integrate(double XMin, double XMax) const
+long double MFunction::Integrate(long double XMin, long double XMax) const
 {
   // Integrate the data from min to max
   
@@ -658,8 +625,8 @@ double MFunction::Integrate(double XMin, double XMax) const
 
   int BinMin = 0;
   if (XMin > m_X.front()) {
-    // BinMin = find_if(m_X.begin(), m_X.end(), bind2nd(greater<double>(), XMin)) - m_X.begin() - 1;
-    BinMin = find_if(m_X.begin(), m_X.end(), bind(greater<double>(), placeholders::_1, XMin)) - m_X.begin() - 1;
+    // BinMin = find_if(m_X.begin(), m_X.end(), bind2nd(greater<long double>(), XMin)) - m_X.begin() - 1;
+    BinMin = find_if(m_X.begin(), m_X.end(), bind(greater<long double>(), placeholders::_1, XMin)) - m_X.begin() - 1;
 //     unsigned int upper = m_Cumulative.size();
 //     unsigned int center = 1;
 //     unsigned int lower = 0;
@@ -679,8 +646,8 @@ double MFunction::Integrate(double XMin, double XMax) const
   }
   int BinMax = m_X.size()-1;
   if (XMax < m_X.back()) {
-    //BinMax = find_if(m_X.begin(), m_X.end(), bind2nd(greater_equal<double>(), XMax)) - m_X.begin();
-    BinMax = find_if(m_X.begin(), m_X.end(), bind(greater_equal<double>(), placeholders::_1, XMax)) - m_X.begin();
+    //BinMax = find_if(m_X.begin(), m_X.end(), bind2nd(greater_equal<long double>(), XMax)) - m_X.begin();
+    BinMax = find_if(m_X.begin(), m_X.end(), bind(greater_equal<long double>(), placeholders::_1, XMax)) - m_X.begin();
 //     unsigned int upper = m_Cumulative.size();
 //     unsigned int center = 1;
 //     unsigned int lower = 0;
@@ -699,14 +666,14 @@ double MFunction::Integrate(double XMin, double XMax) const
 //     BinMax = int(lower)+1;
   }
   
-  double Integral = 0.0;
+  long double Integral = 0.0;
   if (m_InterpolationType == c_InterpolationConstant) {
     Integral = (XMax - XMin) * m_Y[0];
   } else if (m_InterpolationType == c_InterpolationNone) {
     // Just sum rectangular bins:
 
-    double BinCenterMin = m_X[BinMin-1] + 0.5*(m_X[BinMin] - m_X[BinMin-1]);
-    double BinCenterMax = m_X[BinMax-1] + 0.5*(m_X[BinMax] - m_X[BinMax-1]);
+    long double BinCenterMin = m_X[BinMin-1] + 0.5*(m_X[BinMin] - m_X[BinMin-1]);
+    long double BinCenterMax = m_X[BinMax-1] + 0.5*(m_X[BinMax] - m_X[BinMax-1]);
 
     if (BinMin != BinMax) {
       if (XMin < BinCenterMin) {
@@ -740,7 +707,7 @@ double MFunction::Integrate(double XMin, double XMax) const
              m_InterpolationType == c_InterpolationLogLin ||
              m_InterpolationType == c_InterpolationLogLog) {
     
-    double x1, x2, y1, y2;
+    long double x1, x2, y1, y2;
     for (int i = BinMin; i < BinMax; ++i) {
 
       if (i == BinMin) {
@@ -773,8 +740,8 @@ double MFunction::Integrate(double XMin, double XMax) const
       //cout<<x1<<":"<<x2<<endl;
     
       // Calculate m, t of the interpolation "line" (it's always line in the respective mode) 
-      double m = (y2-y1)/(x2-x1);
-      double t = y2 - m*x2;
+      long double m = (y2-y1)/(x2-x1);
+      long double t = y2 - m*x2;
 
       // Switch back
       if (m_InterpolationType == c_InterpolationLinLog || 
@@ -823,7 +790,7 @@ double MFunction::Integrate(double XMin, double XMax) const
 ////////////////////////////////////////////////////////////////////////////////
 
 
-double MFunction::GetRandom()
+long double MFunction::GetRandom()
 {
   // Return a random number distributed as the underlying function
 
@@ -852,7 +819,7 @@ double MFunction::GetRandom()
 ////////////////////////////////////////////////////////////////////////////////
 
 
-double MFunction::GetRandomTimesX()
+long double MFunction::GetRandomTimesX()
 {
   // Return a random number distributed as the underlying function times X
 
@@ -877,15 +844,15 @@ double MFunction::GetRandomTimesX()
 ////////////////////////////////////////////////////////////////////////////////
 
 
-double MFunction::GetRandomInterpolate(double Itot)
+long double MFunction::GetRandomInterpolate(long double Itot)
 {
   // Second stage of the GetRandom function
   // A random number on the total intensity scale, Itot, is already found
   // Now find the correct x-value via interpolation
 
   // Find the correct bin in m_Cumulative
-  //int Bin = find_if(m_Cumulative.begin(), m_Cumulative.end(), bind2nd(greater_equal<double>(), Itot)) - m_Cumulative.begin();
-  int Bin = find_if(m_Cumulative.begin(), m_Cumulative.end(), bind(greater_equal<double>(), placeholders::_1, Itot)) - m_Cumulative.begin();
+  //int Bin = find_if(m_Cumulative.begin(), m_Cumulative.end(), bind2nd(greater_equal<long double>(), Itot)) - m_Cumulative.begin();
+  int Bin = find_if(m_Cumulative.begin(), m_Cumulative.end(), bind(greater_equal<long double>(), placeholders::_1, Itot)) - m_Cumulative.begin();
 
 //   // Binary search:
 //   unsigned int upper = m_Cumulative.size();
@@ -922,9 +889,9 @@ double MFunction::GetRandomInterpolate(double Itot)
   } else if (m_InterpolationType == c_InterpolationNone) {
 
     // Relative intensity in this bin:
-    double I = Itot - m_Cumulative[Bin-1];
+    long double I = Itot - m_Cumulative[Bin-1];
     // Absolute intensity in this bin
-    double A = m_Cumulative[Bin] - m_Cumulative[Bin-1];
+    long double A = m_Cumulative[Bin] - m_Cumulative[Bin-1];
     
     return m_X[Bin-1] + (I/A)*(m_X[Bin] - m_X[Bin-1]);
 
@@ -933,7 +900,7 @@ double MFunction::GetRandomInterpolate(double Itot)
              m_InterpolationType == c_InterpolationLogLin ||
              m_InterpolationType == c_InterpolationLogLog) {
 
-    double x1, x2, y1, y2;
+    long double x1, x2, y1, y2;
     x1 = m_X[Bin-1];
     y1 = m_Y[Bin-1];
     x2 = m_X[Bin];
@@ -950,8 +917,8 @@ double MFunction::GetRandomInterpolate(double Itot)
     }
     
     // Calculate m, t of the interpolation "line" (it's always a line in the respective mode) 
-    double m = (y2-y1)/(x2-x1);
-    double t = y2 - m*x2;
+    long double m = (y2-y1)/(x2-x1);
+    long double t = y2 - m*x2;
     
     // Switch back
     if (m_InterpolationType == c_InterpolationLinLog || m_InterpolationType == c_InterpolationLogLog) {
@@ -964,7 +931,7 @@ double MFunction::GetRandomInterpolate(double Itot)
     }
 
     // Relative intensity in this bin:
-    double I  = Itot - m_Cumulative[Bin-1];
+    long double I  = Itot - m_Cumulative[Bin-1];
 
     if (m_InterpolationType == c_InterpolationLinLin) {
       // We know m, t (from y=m*x+t), as well as I = Itot - I[Bin-1], i.e. the covered area in the given bin
@@ -983,13 +950,13 @@ double MFunction::GetRandomInterpolate(double Itot)
       }
       
       // Standard case
-      double Value = (t+m*x1)*(t+m*x1) + 2*m*I;
+      long double Value = (t+m*x1)*(t+m*x1) + 2*m*I;
   
       // the possible solutions
-      double xs1 = (-t-sqrt(Value))/m;
-      double xs2 = (-t+sqrt(Value))/m;
+      long double xs1 = (-t-sqrt(Value))/m;
+      long double xs2 = (-t+sqrt(Value))/m;
       
-      double x = 0.0;
+      long double x = 0.0;
       if (m >= 0) {
         // Only one positive solution on positive branch of parabola (top is open):
         x = ((xs1 > xs2) ? xs1 : xs2);
@@ -1044,7 +1011,7 @@ double MFunction::GetRandomInterpolate(double Itot)
         }
       }
       
-      double LW = 0.0;
+      long double LW = 0.0;
       // That's just a guess --- not sure is it is not a function of (m*x1*log(x1)-m*x1+t*x1+I)/m*exp(-(m-t)/m
       if (m < 0) {
         LW = LambertW((m*x1*log(x1)-m*x1+t*x1+I)/m*exp(-(m-t)/m), -1);
@@ -1078,7 +1045,7 @@ double MFunction::GetRandomInterpolate(double Itot)
 ////////////////////////////////////////////////////////////////////////////////
 
 
-double MFunction::GetXMin() const
+long double MFunction::GetXMin() const
 {
   //! Get the minimum x-value
 
@@ -1089,7 +1056,7 @@ double MFunction::GetXMin() const
 ////////////////////////////////////////////////////////////////////////////////
 
 
-double MFunction::GetXMax() const
+long double MFunction::GetXMax() const
 {
   //! Get the maximum x-value
 
@@ -1100,11 +1067,11 @@ double MFunction::GetXMax() const
 ////////////////////////////////////////////////////////////////////////////////
 
 
-double MFunction::GetYMin() const
+long double MFunction::GetYMin() const
 {
   //! Get the minimum y-value
 
-  double Min = numeric_limits<double>::max();
+  long double Min = numeric_limits<long double>::max();
   for (unsigned int i = 0; i < m_Y.size(); ++i) {
     if (m_Y[i] < Min) Min = m_Y[i];
   }
@@ -1116,11 +1083,11 @@ double MFunction::GetYMin() const
 ////////////////////////////////////////////////////////////////////////////////
 
 
-double MFunction::GetYMax() const
+long double MFunction::GetYMax() const
 {
   //! Get the maximum y-value
 
-  double Max = -numeric_limits<double>::max();
+  long double Max = -numeric_limits<long double>::max();
   for (unsigned int i = 0; i < m_Y.size(); ++i) {
     if (m_Y[i] > Max) Max = m_Y[i];
   }
@@ -1132,112 +1099,117 @@ double MFunction::GetYMax() const
 ////////////////////////////////////////////////////////////////////////////////
 
 
-double MFunction::FindX(double XStart, double Integral, bool Cyclic)
+long double MFunction::FindX(long double XStart, long double Integral, bool Cyclic)
 {
   //! Find the x value starting from Start which would be achieved after integrating for "Integral"
   //! If we go beyond x_max, x_max is returned if we are not cyclic, otherwise we continue at x_0
 
-  // To reign in larger number rounding issues, use the offset x-values offset everything
-
-  double Modulo = 0;
+  //cout<<"XStart: "<<XStart<<"  Integral: "<<Integral<<endl;
+  
+  long double Modulo = 0;
   if (Cyclic == true) {
     // Project XStart into the frame of this function
-    double Front = m_X.front();
-    double Back = m_X.back();
+    long double Front = m_X.front();
+    long double Back = m_X.back();
     
     if (XStart < Front) {
-      Modulo = double(int((Front - XStart)/(Back-Front)) + 1) * (Back - Front);
+      Modulo = static_cast<long double>(static_cast<int>((Front - XStart)/(Back - Front)) + 1) * (Back - Front);
     } else if (XStart > Back) {
-      Modulo = -double(int((XStart - Back)/(Back-Front)) + 1) * (Back - Front);
+      Modulo = -static_cast<long double>(static_cast<int>((XStart - Back)/(Back - Front)) + 1) * (Back - Front);
     }
   }
 
-  double X = XStart + Modulo - m_X[0]; // To reign in larger number rounding issues, offset everything
+  long double X = XStart + Modulo;
 
   // Find the bin X is in: 
-  if (X < m_XZero.front()) {
+  if (X < m_X.front()) {
     //merr<<"XStart ("<<XStart<<") smaller than minimum x-value ("<<m_X.front()<<") --- starting at minimum x-value"<<endl;
-    X = m_XZero.front();
+    X = m_X.front();
   }
-  if (X > m_XZero.back()) {
+  if (X > m_X.back()) {
     //merr<<"XStart ("<<XStart<<") larger than maximum x-value ("<<m_X.back()<<") --- starting at minimum x-value"<<endl;
-    X = m_XZero.front();
+    X = m_X.front();
   }
 
   // Step 1: Go from bin to bin until we find an upper limit bin, where iIntegral > I
 
   unsigned int BinStart = 0;
-  if (X > m_XZero.front()) {
-    //BinStart = find_if(m_XZero.begin(), m_XZero.end(), bind2nd(greater<double>(), X)) - m_XZero.begin() - 1;
-    BinStart = find_if(m_XZero.begin(), m_XZero.end(), bind(greater<double>(), placeholders::_1, X)) - m_XZero.begin() - 1;
+  if (X > m_X.front()) {
+    //BinStart = find_if(m_X.begin(), m_X.end(), bind2nd(greater<long double>(), X)) - m_X.begin() - 1;
+    BinStart = find_if(m_X.begin(), m_X.end(), bind(greater<long double>(), placeholders::_1, X)) - m_X.begin() - 1;
   }
 
   //cout<<"x: "<<X<<" Bin start: "<<BinStart<<endl;
   
   unsigned int NewUpperBin = BinStart;
-  double tIntegral = 0.0;
-  double iIntegral = 0.0;
+  long double tIntegral = 0.0;
+  long double iIntegral = 0.0;
   do {
     NewUpperBin++;
-    tIntegral = Integrate(X+m_X[0], m_X[NewUpperBin]);
+    tIntegral = Integrate(X, m_X[NewUpperBin]);
     //cout<<"Int from "<<X<<" to "<<m_X[NewUpperBin]<<": "<<tIntegral<<" (total: "<<iIntegral<<")"<<endl;
     if (iIntegral + tIntegral < Integral) {
-      X = m_XZero[NewUpperBin];
+      X = m_X[NewUpperBin];
       iIntegral += tIntegral;
     } else {
       //cout<<"Found it"<<endl;
       break;
     }
-    if (X == m_XZero.back()) {
+    if (X == m_X.back()) {
       if (Cyclic == false) {
         break;
       } else {
         X = 0;
         NewUpperBin = 0;
-        Modulo -= m_XZero.back() - m_XZero.front();
+        Modulo -= m_X.back() - m_X.front();
+        cout<<"New Modulo (while): "<<Modulo<<endl;
       }
     }
   } while (true);
   
   // Non-cyclic exit case
-  if (X == m_XZero.back() && iIntegral < Integral) return numeric_limits<double>::max();
-
+  if (X == m_X.back() && iIntegral < Integral) return numeric_limits<long double>::max();
+  
+  //cout<<"UpperBin: "<<NewUpperBin<<endl;
+  
   // Step 2: Interpolate --- only linear at the moment --- within the given bin to find the right x-value
-
-  double m = (m_Y[NewUpperBin-1] - m_Y[NewUpperBin]) / (m_XZero[NewUpperBin-1] - m_XZero[NewUpperBin]);
-  double t = m_Y[NewUpperBin] - m*m_XZero[NewUpperBin];
   
-  double x1 = 0; 
-  double x2 = 0;
+  long double m = (m_Y[NewUpperBin-1] - m_Y[NewUpperBin]) / (m_X[NewUpperBin-1] - m_X[NewUpperBin]);
+  long double t = m_Y[NewUpperBin] - m*m_X[NewUpperBin];
+  
+  //cout<<"m: "<<m<<" t: "<<t<<endl;
+  
+  long double x1 = 0;
+  long double x2 = 0;
   
   if (m != 0) {
-    double a = 0.5*m;
-    double b = t;
-    double c = -((Integral-iIntegral) + 0.5*m*X*X + t*X);
+    long double a = 0.5*m;
+    long double b = t;
+    long double c = -((Integral-iIntegral) + 0.5*m*X*X + t*X);
   
     x1 = (-b-sqrt(b*b-4*a*c))/(2*a);
     x2 = (-b+sqrt(b*b-4*a*c))/(2*a);
   } else {
     x1 = X + (Integral-iIntegral)/t; // t cannot be null here other wise we would have jumped the bin...
-    x2 = numeric_limits<double>::max();
+    x2 = numeric_limits<long double>::max();
   }
   //cout<<"x1: "<<x1<<" x2: "<<x2<<endl;
   
-  if (x1 >= m_XZero[NewUpperBin-1] && x1 <= m_XZero[NewUpperBin] && (x2 < m_XZero[NewUpperBin-1] || x2 > m_XZero[NewUpperBin])) {
+  if (x1 >= m_X[NewUpperBin-1] && x1 <= m_X[NewUpperBin] && (x2 < m_X[NewUpperBin-1] || x2 > m_X[NewUpperBin])) {
     //mout<<"x="<<x1<<endl;
     X = x1;
-  } else if (x2 >= m_XZero[NewUpperBin-1] && x2 <= m_XZero[NewUpperBin] && (x1 < m_XZero[NewUpperBin-1] || x1 > m_XZero[NewUpperBin])) {
+  } else if (x2 >= m_X[NewUpperBin-1] && x2 <= m_X[NewUpperBin] && (x1 < m_X[NewUpperBin-1] || x1 > m_X[NewUpperBin])) {
     //mout<<"x="<<x2<<endl;
     X = x2; 
-  } else if ((x2 < m_XZero[NewUpperBin-1] || x2 > m_XZero[NewUpperBin]) && (x1 < m_XZero[NewUpperBin-1] || x1 > m_XZero[NewUpperBin])) {
-    merr<<std::setprecision(20)<<"FindX: Both possible results are outside choosen bin ["<<m_XZero[NewUpperBin-1]<<"-"<<m_XZero[NewUpperBin]<<"]: x1="<<x1<<" x2="<<x2<<endl;
+  } else if ((x2 < m_X[NewUpperBin-1] || x2 > m_X[NewUpperBin]) && (x1 < m_X[NewUpperBin-1] || x1 > m_X[NewUpperBin])) {
+    merr<<"FindX: Both possible results are outside choosen bin ["<<m_X[NewUpperBin-1]<<"-"<<m_X[NewUpperBin]<<"]: x1="<<x1<<" x2="<<x2<<endl;
   } else {
-    merr<<std::setprecision(20)<<"FindX: Both possible results are within choosen bin ["<<m_X[NewUpperBin-1]<<"-"<<m_X[NewUpperBin]<<"]: x1="<<x1<<" x2="<<x2<<endl;
+    merr<<"FindX: Both possible results are within choosen bin ["<<m_X[NewUpperBin-1]<<"-"<<m_X[NewUpperBin]<<"]: x1="<<x1<<" x2="<<x2<<endl;    
   }
   
   //cout<<"XStart: "<<XStart<<" X: "<<X<<" modulo: "<<Modulo<<endl;
   
-  return X - Modulo + m_X[0];
+  return X - Modulo;
 }
 
 
@@ -1249,7 +1221,7 @@ void MFunction::Plot()
   // Plot the function in a Canvas (diagnostics only)
   
   if (m_X.size() >= 2) {
-    //double Dist = m_X.back()-m_X.front();
+    //long double Dist = m_X.back()-m_X.front();
     //TH1D* Hist = new TH1D("Diagnostics", "Diagnostics", 10000, m_X.front()-0.1*Dist, m_X.back()+0.1*Dist);
     
     TH1D* Hist = new TH1D("Diagnostics", "Diagnostics", 10000, m_X.front(), m_X.back());
@@ -1277,11 +1249,11 @@ void MFunction::Plot()
 ////////////////////////////////////////////////////////////////////////////////
 
 
-double MFunction::LambertW(double x, int Branch) 
+long double MFunction::LambertW(long double x, int Branch)
 {
   // Implementation of Lambert's W function branches 0 and -1
 
-  double LW = 0.0;
+  long double LW = 0.0;
 
   if (Branch == 0) {
 
@@ -1299,17 +1271,17 @@ double MFunction::LambertW(double x, int Branch)
 
     // Calculate the primary branch:
     if (x <= 20) {
-      double Eta = 2 + 2*TMath::E()*x;
+      long double Eta = 2 + 2*TMath::E()*x;
       
-      double N2 = 4.612634277343749*sqrt(sqrt(sqrt(Eta) + 1.09556884765625)); // eqn. (6) --> Eta -> sqrt(Eta)
-      double N1 = (4 - 3*sqrt(2.0) + N2*(2*sqrt(2.0) - 3))/(sqrt(2.0) - 2); // eqn. above (6)
+      long double N2 = 4.612634277343749*sqrt(sqrt(sqrt(Eta) + 1.09556884765625)); // eqn. (6) --> Eta -> sqrt(Eta)
+      long double N1 = (4 - 3*sqrt(2.0) + N2*(2*sqrt(2.0) - 3))/(sqrt(2.0) - 2); // eqn. above (6)
       
-      double D = N1*sqrt(Eta)/(N2 + sqrt(Eta)); // eqn. below (5)
+      long double D = N1*sqrt(Eta)/(N2 + sqrt(Eta)); // eqn. below (5)
       
       LW = -1.0 + sqrt(Eta)/(1.0 + sqrt(Eta)/(3.0 + D)); // eqn. (5)
     } else {
       // The case x > 20:
-      double h = exp(-1.124491989777808/(0.4225028202459761+log(x))); // eqn. (7)
+      long double h = exp(-1.124491989777808/(0.4225028202459761+log(x))); // eqn. (7)
       LW = log(x/log(x/pow(log(x), h))); // eqn. (8)
     }
     
@@ -1317,8 +1289,8 @@ double MFunction::LambertW(double x, int Branch)
     // Now do some iterations:
     unsigned int NIterations = 2; // if the statements in the paper are correct two passes should be enough
     for (unsigned int i = 0; i < NIterations; ++i) {
-      double zn = log(x/LW) - LW;  // eqn. 13 + 2
-      double en = (zn/(1+LW))*((2*(1 + LW)*(1 + LW + 2.0/3.0*zn) - zn)/(2*(1+LW)*(1 + LW + 2.0/3.0*zn) - 2*zn)); // eqn. 13 + 1
+      long double zn = log(x/LW) - LW;  // eqn. 13 + 2
+      long double en = (zn/(1+LW))*((2*(1 + LW)*(1 + LW + 2.0/3.0*zn) - zn)/(2*(1+LW)*(1 + LW + 2.0/3.0*zn) - 2*zn)); // eqn. 13 + 1
       LW = LW*(1.0 + en); // eqn. 13
     }
   } else if (Branch == -1) {
@@ -1327,13 +1299,13 @@ double MFunction::LambertW(double x, int Branch)
     // Chapeau-Blondeau & Monir, IEEE Transactions on signal processing, v. 50, #9, p. 2160, 2002
 
     if (x >= -1/TMath::E() && x < -0.333) {
-      double p = -sqrt(2*(TMath::E()*x + 1));
+      long double p = -sqrt(2*(TMath::E()*x + 1));
       LW = -1 + p - 1.0/3.0*pow(p, 2) + 11.0/72.0*pow(p, 3) - 43.0/540.0*pow(p, 4) + 769.0/17280.0*pow(p, 5) - 221.0/8505*pow(p, 6);
     } else if (x >= -0.333 && x <= -0.033) {
       LW = (-8.0960+391.0025*x-47.4252*x*x - 4877.6330*pow(x, 3) - 5532.7760*pow(x, 4))/(1 - 82.9423*x + 433.8688*pow(x, 2) + 1515.3060*pow(x, 3));
     } else if (x >= -0.333 && x < 0) {
-      double l1 = log(-x);
-      double l2 = log(-log(-x));
+      long double l1 = log(-x);
+      long double l2 = log(-log(-x));
       LW = l1 -l2 + l2/l1 + (-2 + l2)*l2/(2*l1*l1) + (6 - 9*l2 + 2*l2*l2)*l2/(6*l1*l1*l1) + (-12 + 36*l2 - 22*l2*l2 + 3*l2*l2*l2)*l2/(12*l1*l1*l1*l1) + (60 - 300*l2 + 350*l2*l2 - 125*l2*l2*l2 + 12*l2*l2*l2*l2)*l2/(60*l1*l1*l1*l1*l1);
     } else {
       cout<<"This branch (\"-1\") of the LabertW function is only defined within ["<<-1/TMath::E()<<";0[! Input is "<<x<<". Returning zero..."<<endl;

From 91338f3fa400ca91ffa942def932840bff4b19d2 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Sun, 12 Jan 2025 23:11:56 -0800
Subject: [PATCH 112/192] CHG: Forgot to check for 0

---
 src/global/misc/src/MFunction.cxx | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/src/global/misc/src/MFunction.cxx b/src/global/misc/src/MFunction.cxx
index 349c025cc..625bef5b4 100644
--- a/src/global/misc/src/MFunction.cxx
+++ b/src/global/misc/src/MFunction.cxx
@@ -401,8 +401,6 @@ bool MFunction::Add(const long double x, const long double y)
     }
   }
 
-  CheckDynamicRange();
-
   return true;
 }
 
@@ -414,7 +412,7 @@ void MFunction::CheckDynamicRange()
   //! Check the dynamic range and give a warning message if we are too big
 
   static bool FirstCall = true;
-  if (FirstCall == true) {
+  if (FirstCall == true && m_X.size() > 0) {
     if (sizeof(long double) < 16) {
       if (m_X.back() / m_X.front() >= 100000000 && m_X.back() - m_X.front() >= 100000000) { // best guess how to handle zero
         mout<<endl;

From d840a28e18d6d48d8b3676ce8e391df526890e2e Mon Sep 17 00:00:00 2001
From: GallegoSav <123730578+GallegoSav@users.noreply.github.com>
Date: Thu, 16 Jan 2025 07:31:15 +0100
Subject: [PATCH 113/192] Galactic polarization and EarthOccultation Beam
 profile (#104)

* Update MCSource.cc

* Update MCOrientation.cc

* Update MCParameterFile.cc

* Update MCSource.hh

* Update MCSource.cc

* Update MCParameterFile.cc

* Update MCOrientation.cc

* Update MCParameterFile.cc

* Update MCSource.cc

* Update MCParameterFile.cc

* Update MCSource.hh

* Update MCSource.hh

* Update MCParameterFile.cc

* Update MCParameterFile.cc

* Update MCSource.cc

* Update MCSource.cc

* Create Polarization_IAUconvention

* Delete resource/examples/advanced/Polarization_IAUconvention

* Create Polarized.source

* Update Polarized.source

* Create test.ori

* Rename EarthOccultation.source to EarthOccultation_pointsource.source
---
 ...ce => EarthOccultation_pointsource.source} |   0
 .../Polarized.source                          |  21 ++++
 .../Polarization_IAUconvention/test.ori       |   3 +
 src/cosima/inc/MCSource.hh                    |   2 +
 src/cosima/src/MCParameterFile.cc             |  20 ++-
 src/cosima/src/MCSource.cc                    | 118 +++++++++++++++---
 6 files changed, 144 insertions(+), 20 deletions(-)
 rename resource/examples/advanced/EarthOccultation/{EarthOccultation.source => EarthOccultation_pointsource.source} (100%)
 create mode 100644 resource/examples/advanced/Polarization_IAUconvention/Polarized.source
 create mode 100644 resource/examples/advanced/Polarization_IAUconvention/test.ori

diff --git a/resource/examples/advanced/EarthOccultation/EarthOccultation.source b/resource/examples/advanced/EarthOccultation/EarthOccultation_pointsource.source
similarity index 100%
rename from resource/examples/advanced/EarthOccultation/EarthOccultation.source
rename to resource/examples/advanced/EarthOccultation/EarthOccultation_pointsource.source
diff --git a/resource/examples/advanced/Polarization_IAUconvention/Polarized.source b/resource/examples/advanced/Polarization_IAUconvention/Polarized.source
new file mode 100644
index 000000000..e21514596
--- /dev/null
+++ b/resource/examples/advanced/Polarization_IAUconvention/Polarized.source
@@ -0,0 +1,21 @@
+Geometry  $(MEGALIB)/resource/examples/geomega/cosiballoon/COSIBalloon.9Detector.geo.setup
+StoreSimulationInfo  init-only 
+PhysicsListEM LivermorePol
+
+Run SpaceSim
+SpaceSim.FileName  PolarizedSource
+SpaceSim.Time 10.0
+SpaceSim.OrientationSky Galactic File NoLoop  test.ori
+
+
+SpaceSim.Source AlbedoPhotons
+AlbedoPhotons.ParticleType	       1
+AlbedoPhotons.Beam FarFieldPointSource 0 0
+AlbedoPhotons.Orientation Galactic Fixed -48.90 176.96
+AlbedoPhotons.Spectrum Mono 511
+AlbedoPhotons.Flux	  100
+
+#fst number is the polarization fraction (0 to 1) and the second is the polarization angle (deg)
+#following the IAU convention : https://lambda.gsfc.nasa.gov/product/about/pol_convention.html
+AlbedoPhotons.Polarization galactic 1 45
+
diff --git a/resource/examples/advanced/Polarization_IAUconvention/test.ori b/resource/examples/advanced/Polarization_IAUconvention/test.ori
new file mode 100644
index 000000000..2434eadcc
--- /dev/null
+++ b/resource/examples/advanced/Polarization_IAUconvention/test.ori
@@ -0,0 +1,3 @@
+Type OrientationsGalactic
+OG 0  -60.18 96.33 27.13 122.93
+OG 10 -60.18 96.33  27.13 122.93
diff --git a/src/cosima/inc/MCSource.hh b/src/cosima/inc/MCSource.hh
index 646552668..4aa152171 100644
--- a/src/cosima/inc/MCSource.hh
+++ b/src/cosima/inc/MCSource.hh
@@ -432,6 +432,8 @@ public:
   static const int c_PolarizationRandom;
   /// Id of the polarization being in absolute coordinates
   static const int c_PolarizationAbsolute;
+  /// Id of the polarization being in Galactic coordinates
+  static const int c_PolarizationGalactic;
   /// Id of the polarization being calculated relative to particle direction and x-axis
   static const int c_PolarizationRelativeX;
   /// Id of the polarization being calculated relative to particle direction and y-axis
diff --git a/src/cosima/src/MCParameterFile.cc b/src/cosima/src/MCParameterFile.cc
index 02e9f5306..4cdb2ea60 100644
--- a/src/cosima/src/MCParameterFile.cc
+++ b/src/cosima/src/MCParameterFile.cc
@@ -1449,14 +1449,16 @@ bool MCParameterFile::Parse()
             }
           }
 	  else if (Type == "farfieldearthoccultation" ) {
-            if (T->GetNTokens() >= 3) {
+            if (T->GetNTokens() >= 4) {
               Source->SetBeamType(MCSource::c_FarField,
                                   MCSource::c_FarFieldEarthOccultation);
-              
+	      double Theta = 0.0; // here we don't use theta
+	      bool InverseCut = T->GetTokenAtAsBoolean(3); 			  
+              Source->SetEarthOccultation(Theta,InverseCut);
               mdebug<<"Using beam: "<<Type<<endl;
             } else {
               Typo(i, "Cannot parse token \"Beam - far field file zenith dependent\" correctly:"
-                   " Number of tokens must be larger than 2!");
+                   " Number of tokens must be larger than 4!");
               return false;
             }
           }
@@ -2195,7 +2197,17 @@ bool MCParameterFile::Parse()
               Typo(i, "Cannot parse token \"Polarization absolute\" correctly: Number of tokens is not correct!");
               return false;
             }
-          } else if (Type == "relativex") {
+          } else if (Type == "galactic") {
+            if (T->GetNTokens() == 5) {
+              Source->SetPolarizationType(MCSource::c_PolarizationGalactic);
+              Source->SetPolarizationDegree(T->GetTokenAtAsDouble(3));
+              Source->SetPolarization(T->GetTokenAtAsDouble(4)*deg);
+            } else {
+              Typo(i, "Cannot parse token \"Polarization galactic\" correctly: Number of tokens is not correct!");
+              return false;
+            }
+	  
+	   } else if (Type == "relativex") {
             if (T->GetNTokens() == 5) {
               Source->SetPolarizationType(MCSource::c_PolarizationRelativeX);
               Source->SetPolarizationDegree(T->GetTokenAtAsDouble(3));
diff --git a/src/cosima/src/MCSource.cc b/src/cosima/src/MCSource.cc
index da549e8c9..f17ad6b97 100644
--- a/src/cosima/src/MCSource.cc
+++ b/src/cosima/src/MCSource.cc
@@ -116,7 +116,7 @@ const int MCSource::c_PolarizationAbsolute                         =  3;
 const int MCSource::c_PolarizationRelativeX                        =  4;
 const int MCSource::c_PolarizationRelativeY                        =  5;
 const int MCSource::c_PolarizationRelativeZ                        =  6;
-
+const int MCSource::c_PolarizationGalactic                         =  7;
 
 // Don't change this list because the ID is written to the Sim file
 const int MCSource::c_Gamma                                        = 1;
@@ -271,7 +271,6 @@ void MCSource::Initialize()
   m_PolarizationParam2 = c_Invalid;
   m_PolarizationParam3 = c_Invalid;
   m_PolarizationDegree = 0.0;
-  
   m_UseFarFieldTransmissionProbability = false;
   m_UseEarthOccultation = false;
   m_ThetaMaxEarthOccultation = 0.0;
@@ -441,7 +440,7 @@ bool MCSource::GenerateParticles(G4GeneralParticleSource* ParticleGun)
        
       // convert the Earth galactic l,b coordinate into cartesian representation  
       G4ThreeVector EarthZenith(cos(Lat)*cos(Lon) , cos(Lat)*sin(Lon) , sin(Lat)); 
-     
+        
       //rotate the oriented coordinate system of the event into the local coordinate system
       //Sky.OrientDirectionInvers(m_NextEmission, Dir);
       Sky.OrientDirection(m_NextEmission, Dir);
@@ -452,17 +451,18 @@ bool MCSource::GenerateParticles(G4GeneralParticleSource* ParticleGun)
       //cout<< "particle Dir: "<<Dir[0]<<" " <<Dir[1] <<" "<<Dir[2]<<endl;
       //cout<<"Earth zenith: "<< EarthZenith[0]<<" "<<EarthZenith[1]<<" "<<EarthZenith[2]<<endl;
       //cout<<"Angle between 2 vector : "<<EarthZenith.angle(Dir)/deg<<endl;
+     
       
       
             
       //Do the Theta cut
       if (m_EarthOccultation_InverseCut){
-      if (EarthZenith.angle(Dir)/deg <ThetaMax ){
+      if (abs(EarthZenith.angle(Dir)/deg) <ThetaMax ){
        ParticleGun->GetCurrentSource()->GetEneDist()->SetMonoEnergy(0);
        }
        
       } else {
-       if (EarthZenith.angle(Dir)/deg >=ThetaMax ){
+       if (abs(EarthZenith.angle(Dir)/deg) >=ThetaMax ){
        ParticleGun->GetCurrentSource()->GetEneDist()->SetMonoEnergy(0);
        }
       }
@@ -2256,6 +2256,7 @@ bool MCSource::SetPolarizationType(const int& PolarizationType)
   case c_PolarizationRelativeX:
   case c_PolarizationRelativeY:
   case c_PolarizationRelativeZ:
+  case c_PolarizationGalactic:
     m_PolarizationType = PolarizationType;
     return true;
   default:
@@ -2292,6 +2293,9 @@ string MCSource::GetPolarizationTypeAsString() const
   case c_PolarizationRelativeZ:
     Name = "RelativeZ";
     break;
+  case c_PolarizationGalactic:
+    Name = "Galactic";
+    break;    
   default:
     break;
   }
@@ -3102,28 +3106,67 @@ bool MCSource::GeneratePosition(G4GeneralParticleSource* Gun)
       } else if (m_BeamType == c_FarFieldEarthOccultation) {
         // Determine a random position on the sphere between 
         // theta min and theta max that are computed each time
-	      // according to the pointing of the spacecraft in order
-	      //to take into account the Earth Occultation
+	// according to the pointing of the spacecraft in order
+	//to take into account the Earth Occultation
         
         if (m_StartAreaType == c_StartAreaSphere) {
 	
-	       //determine the theta range 
+	    //determine the theta range 
 	
-	      //get the Earth aspect information from the orientation file
+	    //get the Earth aspect information from the orientation file
             const MCOrientation& Sky = MCRunManager::GetMCRunManager()->GetCurrentRun().GetSkyOrientationReference();
             double Alt,Lat,Lon=0;
+	    
             if (Sky.GetEarthCoordinate(m_NextEmission,  Alt,  Lat, Lon)==true){
-     
-             
+                
+		double R_Earth = 6378; //km
+		
+	        //compute theta max according to the current altitude
+                double ThetaMax =  ( c_Pi - asin( R_Earth/(R_Earth+Alt/km) ) )/deg;
+		
+		// convert the Earth galactic l,b coordinate into cartesian representation  
+                G4ThreeVector EarthZenith(cos(Lat)*cos(Lon) , cos(Lat)*sin(Lon) , sin(Lat));
+		
+		
+              while(true){
+	        //sort theta and phi until it match requirement
+		  
+                // sort random theta and phi
+		Theta = acos(1 - CLHEP::RandFlat::shoot(1)*2);
+                Phi = CLHEP::RandFlat::shoot(1)*360*deg;
+		  
+		// compute xyz of the particle
+		G4ThreeVector Dir(sin(Theta)*cos(Phi),sin(Theta)*sin(Phi),cos(Theta));
+		
+		
+		//rotate the event into the galactic coordinate system
+                Sky.OrientDirection(m_NextEmission, Dir);
+		//Due to the left-handed galactic system used in MEGAlib 
+	        //the Z of particle dir needs to be *-1 #reverseingeniering		
+		Dir[2] = Dir[2]*-1;
+		
+		if (m_EarthOccultation_InverseCut){
+      			if (EarthZenith.angle(Dir)/deg >ThetaMax ){
+			break;
+       		}
+       
+      		} else {
+       			if (EarthZenith.angle(Dir)/deg <=ThetaMax ){
+       		        break;
+       		 	}
+                }
+	      }
+	      
+	      
+	      
+	      
+	      	      
            }
           else{
                 merr<<"the time is not in the ori time range : "<<m_NextEmission<< " ["<<Sky.GetStartTime()<<","<< Sky.GetStopTime() <<"]"<<endl;
            }
 	   
-	    //sort theta and phi 
-        
-            Theta = acos(cos(0*deg) - CLHEP::RandFlat::shoot(1)*(cos(0*deg) - cos(5*deg)));
-            Phi = CLHEP::RandFlat::shoot(1)*360*deg;
+	    
               
         
         } else {
@@ -3582,7 +3625,8 @@ bool MCSource::GeneratePolarization(G4GeneralParticleSource* Gun)
     m_Polarization = m_Direction.orthogonal();
     m_Polarization.rotate(m_Direction, CLHEP::RandFlat::shoot(2*c_Pi));
     m_Polarization = m_Polarization.unit();
-  } else if (m_PolarizationType == c_PolarizationAbsolute || 
+  } else if (m_PolarizationType == c_PolarizationAbsolute ||
+             m_PolarizationType == c_PolarizationGalactic ||
              m_PolarizationType == c_PolarizationRelativeX ||
              m_PolarizationType == c_PolarizationRelativeY ||
              m_PolarizationType == c_PolarizationRelativeZ) {
@@ -3591,6 +3635,48 @@ bool MCSource::GeneratePolarization(G4GeneralParticleSource* Gun)
       if (m_PolarizationType == c_PolarizationAbsolute) {
         m_Polarization.set(m_PolarizationParam1, m_PolarizationParam2, m_PolarizationParam3);
       }
+      if (m_PolarizationType == c_PolarizationGalactic) {
+      
+        //get the Earth aspect information from the orientation file
+        const MCOrientation& Sky = MCRunManager::GetMCRunManager()->GetCurrentRun().GetSkyOrientationReference();
+       
+        //celestial north pole in galactic coordinates l b is 122.93 deg and 27.13 deg
+	//see :https://lambda.gsfc.nasa.gov/product/about/pol_convention.html
+	//because of left handed megalib convention we need to multiply by -1 for Z #reverseingienering
+        G4ThreeVector CelestNorthPole(cos(27.13*deg)*cos(122.93*deg) , cos(27.13*deg)*sin(122.93*deg) , -1*sin(27.13*deg)); 
+	
+	//convert the north pole in local coordinates
+	Sky.OrientDirectionInvers(m_NextEmission, CelestNorthPole);
+	//cout<<"celest vector : "<<CelestNorthPole[0]<<" "<<CelestNorthPole[1]<<" "<<CelestNorthPole[2]<<endl;
+	
+	
+	
+	//compute px and py perpendicular to photon direction
+	G4ThreeVector py = CelestNorthPole.cross(m_Direction);
+	//normalize py
+	py = py.unit();
+	G4ThreeVector px = py.cross(m_Direction);
+	
+        //normalize px
+	px = px.unit();
+	
+       
+        //cout<<"py : "<<py<<endl;
+	//cout<<"px : "<<px<<endl;
+       
+        //define the polarization vector
+	m_Polarization = G4ThreeVector(cos(m_PolarizationParam1)*px[0]+sin(m_PolarizationParam1)*py[0],
+	cos(m_PolarizationParam1)*px[1]+sin(m_PolarizationParam1)*py[1],
+	cos(m_PolarizationParam1)*px[2]+sin(m_PolarizationParam1)*py[2]);
+
+        
+	m_Polarization = m_Polarization.unit();
+	
+	//cout<<"polarization vector : "<<m_Polarization[0]<<" "<<m_Polarization[1]<<" "<<m_Polarization[2]<<endl;
+	//cout<<"photon dir vector : "<<m_Direction[0]<<" "<<m_Direction[1]<<" "<<m_Direction[2]<<endl;
+	//Sky.OrientDirection(m_NextEmission, m_Direction);
+	//cout<<"photon dir (gal) vector : "<<m_Direction[0]<<" "<<m_Direction[1]<<" "<<m_Direction[2]<<endl;
+      }
       // Relative
       else {
         G4ThreeVector Axis;

From be336052df12b1b27167db1f2ab987bd64661fcb Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Wed, 22 Jan 2025 09:35:20 -0800
Subject: [PATCH 114/192] CHG: Replaced locate with pkgconf

---
 configure | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/configure b/configure
index 3bbe40b2f..a12290c4a 100755
--- a/configure
+++ b/configure
@@ -352,8 +352,7 @@ if [[ ${LHEASOFT} != "" ]] && ( [[ -f ${LHEASOFT}/lib/libcfitsio.a ]] || [[ -f $
   echo "Found cfitsio library in ${LHEASOFT}/lib";
   FitsIOFound=0  
 else
-  locate libcfitsio &> /dev/null
-  if [[ "$?" == "0" ]]; then
+  if [[ "$(pkgconf --libs cfitsio)" == *cfitsio* ]]; then
     echo "Found exiting cfitsio in a system path";
     FitsIOFound=0
   fi

From 2d83cdcb7de51bb0deb0f2270a352b30268d8485 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Wed, 22 Jan 2025 09:35:36 -0800
Subject: [PATCH 115/192] CHG: Fixed a warning

---
 src/response/src/MResponseBuilder.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/response/src/MResponseBuilder.cxx b/src/response/src/MResponseBuilder.cxx
index 851b1bed3..dd54ba2bf 100644
--- a/src/response/src/MResponseBuilder.cxx
+++ b/src/response/src/MResponseBuilder.cxx
@@ -463,7 +463,7 @@ bool MResponseBuilder::InitializeNextMatchingEvent()
         MRawEventIncarnationList* REIL = m_ReReader->GetRawEventList();
         for (unsigned int i = 0; i < REIL->Size(); ++i) {
           // TODO: Test performance if we just pick one random sequence
-          for (unsigned int r = 0; r < REIL->Get(i)->GetNRawEvents(); ++r) {
+          for (int r = 0; r < REIL->Get(i)->GetNRawEvents(); ++r) {
             m_ReEvents.push_back(REIL->Get(i)->GetRawEventAt(r));
           }
         }

From 4a6d5855d600243340bf2942d87ab33365751ae4 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Wed, 22 Jan 2025 10:01:15 -0800
Subject: [PATCH 116/192] ADD: long double handling

---
 src/global/misc/inc/MString.h | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/global/misc/inc/MString.h b/src/global/misc/inc/MString.h
index 20eae0270..f05d9458a 100644
--- a/src/global/misc/inc/MString.h
+++ b/src/global/misc/inc/MString.h
@@ -188,6 +188,7 @@ class MString
   MString& operator+=(unsigned long N) { ostringstream out; out<<N; m_String += out.str(); return *this; }
   MString& operator+=(float N) { ostringstream out; out.precision(8); out<<N; m_String += out.str(); return *this; }
   MString& operator+=(double N) { ostringstream out; out.precision(15); out<<N; m_String += out.str(); return *this; }
+  MString& operator+=(long double N) { ostringstream out; (sizeof(long double) == 128) ? out.precision(31) : out.precision(15); out<<N; m_String += out.str(); return *this; }
 
 
   //! Remove all characters from Start to the End

From 184ef3cda45e9aaa8e51e62bb300c04779db3aed Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Tue, 28 Jan 2025 11:29:03 -0800
Subject: [PATCH 117/192] ADD: Example overflow filter

---
 resource/examples/python/OverflowFilter.py | 114 +++++++++++++++++++++
 1 file changed, 114 insertions(+)
 create mode 100644 resource/examples/python/OverflowFilter.py

diff --git a/resource/examples/python/OverflowFilter.py b/resource/examples/python/OverflowFilter.py
new file mode 100644
index 000000000..6d6be0d85
--- /dev/null
+++ b/resource/examples/python/OverflowFilter.py
@@ -0,0 +1,114 @@
+import ROOT as M
+import argparse
+import os
+
+# Load MEGAlib into ROOT
+M.gSystem.Load("$(MEGALIB)/lib/libMEGAlib.so")
+
+# Initialize MEGAlib
+G = M.MGlobal()
+G.Initialize()
+
+# Parse the arguments
+parser = argparse.ArgumentParser(description='Remove part of the overflow contamination')
+parser.add_argument('-f', '--file', default='Isotropic.ContTest.p1.tra.gz', help='The tra file')
+parser.add_argument('-g', '--geometry', default='Ancillary/massmodel/COSISMEX.analysis.geo.setup', help='The geometry')
+
+args = parser.parse_args()
+
+GeometryFileName = args.geometry
+GeometryFileName = os.path.expandvars(GeometryFileName)
+if not os.path.exists(GeometryFileName):
+  print("Unable to read geometry " + GeometryFileName + " - Aborting!")
+  quit()
+
+FileName = args.file
+FileName = os.path.expandvars(FileName)
+if not os.path.exists(FileName):
+  print("Unable to read data file " + FileName + " - Aborting!")
+  quit()
+  
+
+# Load geometry:
+Geometry = M.MDGeometryQuest()
+if Geometry.ScanSetupFile(M.MString(GeometryFileName)) == True:
+  print("Geometry " + GeometryFileName + " loaded!")
+else:
+  print("Unable to load geometry " + GeometryFileName + " - Aborting!")
+  quit()
+
+
+# Load input tra file
+Reader = M.MFileEventsTra()
+if Reader.Open(M.MString(FileName)) == False:
+  print("Unable to open input file " + FileName + ". Aborting!")
+  quit()
+Reader.GetObservationTime()
+
+# Load output tra file
+OutputFileName = FileName
+OutputFileName = OutputFileName.replace('.tra.', '.filtered.tra.')
+Writer = M.MFileEventsTra()
+if Writer.Open(OutputFileName, M.MFile.c_Write) == False:
+  print("Unable to open output file " + OutputFileName + ". Aborting!")
+  quit()
+   
+Writer.TransferInformation(Reader)
+Writer.SetFileType("TRA")
+Writer.WriteHeader()
+
+
+HistBeforeFilter = M.TH1D("Energy Before Filter", "Energy Before Filter", 500, 0, 10000)
+HistAfterFilter = M.TH1D("Energy After Filter", "Energy After Filter", 500, 0, 10000)
+
+
+while True: 
+  Event = Reader.GetNextEvent()
+  if not Event:
+    break
+  M.SetOwnership(Event, True)
+  
+  if Event.GetType() == M.MPhysicalEvent.c_Compton:
+    IsOverflow = False
+    for h in range(0, Event.GetNHits()):
+      HitEnergy = Event.GetHit(h).GetEnergy() 
+      if 1799.999 < HitEnergy < 1800.001:
+        IsOverflow = True
+      elif 3599.999 < HitEnergy < 3600.001:
+         IsOverflow = True
+      elif 5399.999 < HitEnergy < 5400.001:       
+         IsOverflow = True
+      elif 7199.999 < HitEnergy < 7200.001:
+         IsOverflow = True
+      elif 8999.999 < HitEnergy < 9000.001:
+        IsOverflow = True
+
+    HistBeforeFilter.Fill(Event.Ei())
+    if IsOverflow == False:
+      HistAfterFilter.Fill(Event.Ei())
+      Writer.AddEvent(Event)
+
+    if Event.Ei() < 50:
+      print("{}".format(Event.Ei()))
+
+Reader.Close()
+
+Writer.WriteFooter()
+Writer.Close()
+
+CanvasBeforeFilter = M.TCanvas()
+CanvasBeforeFilter.cd()
+HistBeforeFilter.Draw()
+CanvasBeforeFilter.Update()
+
+CanvasAfterFilter = M.TCanvas()
+CanvasAfterFilter.cd()
+HistAfterFilter.Draw()
+CanvasAfterFilter.Update()
+
+
+# Prevent the canvases from being closed
+import os
+print("ATTENTION: Please exit by clicking: File -> Close ROOT! Do not just close the window by clicking \"x\"")
+print("           ... and if you didn't honor this warning, and are stuck, execute the following in a new terminal: kill " + str(os.getpid()))
+M.gApplication.Run()

From de7ba0da29cb0afb0d9be9e68c1c1ad911235476 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Tue, 28 Jan 2025 13:10:22 -0800
Subject: [PATCH 118/192] CHG: Filter updates

---
 resource/examples/python/OverflowFilter.py | 27 ++++++++++++++--------
 1 file changed, 17 insertions(+), 10 deletions(-)

diff --git a/resource/examples/python/OverflowFilter.py b/resource/examples/python/OverflowFilter.py
index 6d6be0d85..dc4e8471a 100644
--- a/resource/examples/python/OverflowFilter.py
+++ b/resource/examples/python/OverflowFilter.py
@@ -43,11 +43,11 @@
 if Reader.Open(M.MString(FileName)) == False:
   print("Unable to open input file " + FileName + ". Aborting!")
   quit()
-Reader.GetObservationTime()
+#Reader.GetObservationTime()
 
 # Load output tra file
 OutputFileName = FileName
-OutputFileName = OutputFileName.replace('.tra.', '.filtered.tra.')
+OutputFileName = OutputFileName.replace('.tra', '.filtered.tra')
 Writer = M.MFileEventsTra()
 if Writer.Open(OutputFileName, M.MFile.c_Write) == False:
   print("Unable to open output file " + OutputFileName + ". Aborting!")
@@ -59,7 +59,12 @@
 
 
 HistBeforeFilter = M.TH1D("Energy Before Filter", "Energy Before Filter", 500, 0, 10000)
+HistBeforeFilter.SetXTitle("Energy [keV]")
+HistBeforeFilter.SetYTitle("counts")
+
 HistAfterFilter = M.TH1D("Energy After Filter", "Energy After Filter", 500, 0, 10000)
+HistAfterFilter.SetXTitle("Energy [keV]")
+HistAfterFilter.SetYTitle("counts")
 
 
 while True: 
@@ -67,9 +72,9 @@
   if not Event:
     break
   M.SetOwnership(Event, True)
-  
+ 
+  IsOverflow = False
   if Event.GetType() == M.MPhysicalEvent.c_Compton:
-    IsOverflow = False
     for h in range(0, Event.GetNHits()):
       HitEnergy = Event.GetHit(h).GetEnergy() 
       if 1799.999 < HitEnergy < 1800.001:
@@ -83,16 +88,18 @@
       elif 8999.999 < HitEnergy < 9000.001:
         IsOverflow = True
 
-    HistBeforeFilter.Fill(Event.Ei())
-    if IsOverflow == False:
-      HistAfterFilter.Fill(Event.Ei())
-      Writer.AddEvent(Event)
+    if Event.Ei() > 0.0: # Events with bad Compton kinematics have 0 here
+      HistBeforeFilter.Fill(Event.Ei())
+      if IsOverflow == False:
+        HistAfterFilter.Fill(Event.Ei())
+
+  if IsOverflow == False:    
+    Writer.AddEvent(Event)
 
-    if Event.Ei() < 50:
-      print("{}".format(Event.Ei()))
 
 Reader.Close()
 
+Writer.TransferInformation(Reader)
 Writer.WriteFooter()
 Writer.Close()
 

From bd1634968fd9f53ab91b9052b938516f80a294b7 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Mon, 10 Feb 2025 19:54:20 -0800
Subject: [PATCH 119/192] CHG: Include libMinuit2 as required library

---
 config/Makefile.linuxclang | 2 +-
 config/Makefile.linuxgcc   | 2 +-
 config/Makefile.linuxicc   | 2 +-
 config/Makefile.macosx     | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/config/Makefile.linuxclang b/config/Makefile.linuxclang
index c601a599c..ff94d778d 100644
--- a/config/Makefile.linuxclang
+++ b/config/Makefile.linuxclang
@@ -24,7 +24,7 @@ DEFINES       := -UHARDWARE
 LD            := clang++
 LDFLAGS       := $(OPT) -D___LINUX___
 SOFLAGS       := -shared  
-LIBS          := $(ROOTLIBS) -lpthread -lThread -lMinuit -lGeom -lSpectrum -lTMVA
+LIBS          := $(ROOTLIBS) -lpthread -lThread -lMinuit -lMinuit2 -lGeom -lSpectrum -lTMVA
 GLIBS         := $(ROOTGLIBS) 
 DEPFLAGS      := -MD -MF
 
diff --git a/config/Makefile.linuxgcc b/config/Makefile.linuxgcc
index a1dcf0d73..ba1c80d19 100644
--- a/config/Makefile.linuxgcc
+++ b/config/Makefile.linuxgcc
@@ -24,7 +24,7 @@ DEFINES       := -UHARDWARE
 LD            := g++
 LDFLAGS       := $(OPT) -D___LINUX___
 SOFLAGS       := -shared  
-LIBS          := $(ROOTLIBS) -lpthread -lThread -lMinuit -lGeom -lSpectrum -lTMVA
+LIBS          := $(ROOTLIBS) -lpthread -lThread -lMinuit -lMinuit2 -lGeom -lSpectrum -lTMVA
 GLIBS         := $(ROOTGLIBS) 
 DEPFLAGS      := -MM
 
diff --git a/config/Makefile.linuxicc b/config/Makefile.linuxicc
index 5cd22386d..22adfe1a5 100644
--- a/config/Makefile.linuxicc
+++ b/config/Makefile.linuxicc
@@ -24,7 +24,7 @@ DEFINES       := -UHARDWARE
 LD            := icc
 LDFLAGS       := $(OPT) -D___LINUX___
 SOFLAGS       := -shared  
-LIBS          := $(ROOTLIBS) -lpthread -lThread -lMinuit -lGeom -lSpectrum -lTMVA
+LIBS          := $(ROOTLIBS) -lpthread -lThread -lMinuit -lMinuit2 -lGeom -lSpectrum -lTMVA
 GLIBS         := $(ROOTGLIBS) 
 DEPFLAGS      := -M
 
diff --git a/config/Makefile.macosx b/config/Makefile.macosx
index 1cd2fa743..7943afe75 100644
--- a/config/Makefile.macosx
+++ b/config/Makefile.macosx
@@ -25,7 +25,7 @@ DEFINES       := -UHARDWARE
 LD            := c++
 LDFLAGS       := $(OPT) -Xlinker -bind_at_load -flat_namespace -D___MACOSX___
 SOFLAGS       := -dynamiclib -flat_namespace -undefined suppress 
-LIBS          := $(ROOTLIBS) -lpthread -lThread -lMinuit -lGeom -lSpectrum -lTMVA
+LIBS          := $(ROOTLIBS) -lpthread -lThread -lMinuit -lMinuit2 -lGeom -lSpectrum -lTMVA
 GLIBS         := $(ROOTGLIBS) 
 DEPFLAGS      := -M
 

From 738d4f3b8699dd5186cc19de7cea8d44c85463ac Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Mon, 17 Mar 2025 15:44:41 -0700
Subject: [PATCH 120/192] ADD: Ability to wait for more than just one program
 and set delay time

---
 bin/mwait | 24 ++++++++++++++++--------
 1 file changed, 16 insertions(+), 8 deletions(-)

diff --git a/bin/mwait b/bin/mwait
index da8c071b1..1fa3c41dd 100755
--- a/bin/mwait
+++ b/bin/mwait
@@ -13,8 +13,9 @@ commandhelp() {
   echo "  --instances=[integer or \"cores\", \"threads\"]: Maximum number of instances or \"cores\"/\"threads\" for the number of available cores or threads (default: 1)"
   echo "  --load=[integer or \"cores\", \"threads\"]: Maximum system load as integer or \"cores\"/\"threads\" for the number of available cores or threads (default: threads + 3)"
   echo "  --program=[name]: The main program to wait for"
-  #echo "  --auxprogram=[name]: Other programs to wait for"
+  echo "  --auxprogram=[name]: Other programs to wait for"
   echo "  --memory: Make sure we have enough free memory, if more than one instance is running"
+  echo "  --delay=[integer]: The delay time"
   echo "  --quiet: No text output"
   echo ""
   echo "Examples:"
@@ -29,10 +30,11 @@ commandhelp() {
 # Defaults
 INSTANCES="cores"
 LOAD="10000"
-PROGAM=""
+PROGRAM=""
 AUXPROGRAMS=()
 MEMORY=false
 QUIET=false
+DELAY=5
 
 # Store command line as array
 CMD=( "$@" )
@@ -54,8 +56,10 @@ for C in "${CMD[@]}"; do
     LOAD=`echo ${C} | awk -F"=" '{ print $2 }'`
   elif [[ ${C} == *-p*=* ]]; then
     PROGRAM=`echo ${C} | awk -F"=" '{ print $2 }'`
-  elif [[ ${C} == *-c*=* ]]; then
+  elif [[ ${C} == *-a*=* ]]; then
     AUXPROGRAMS+=`echo ${C} | awk -F"=" '{ print $2 }'`
+  elif [[ ${C} == *-d*=* ]]; then
+    DELAY=`echo ${C} | awk -F"=" '{ print $2 }'`
   elif [[ ${C} == *-m* ]]; then
     MEMORY=true
   elif [[ ${C} == *-q* ]]; then
@@ -122,7 +126,11 @@ while [[ ${WAIT} == true ]]; do
   # We exclude this process itself in the listing
   # sed -> don't remember
   RUNNINGTHREADS=0
-  RUNNINGTHREADS=$(( RUNNINGTHREADS + $(ps -Af | grep "[ ]${PROGRAM}" | grep -v "mwait ${PROGRAM}" | grep -v "bash -c " | grep -v "timeout " | wc -l | sed 's/^ *//g') ))
+  RUNNINGTHREADS=$(( RUNNINGTHREADS + $(ps -Af | grep -e "[ ]${PROGRAM}" -e "/${PROGRAM}" | grep -v "mwait ${PROGRAM}" | grep -v "bash -c " | grep -v "timeout " | grep -v "grep" | wc -l | sed 's/^ *//g') ))
+  for A in "${AUXPROGRAMS[@]}"; do
+    RUNNINGTHREADS=$(( RUNNINGTHREADS + $(ps -Af | grep -e "[ ]${A}" -e "/${A}" | grep -v "mwait ${A}" | grep -v "bash -c " | grep -v "timeout " | grep -v "grep" | wc -l | sed 's/^ *//g') ))
+  done
+  
   
   #echo "mwait: ${MAXTHREADS} vs. ${RUNNINGTHREADS}"
   
@@ -131,7 +139,7 @@ while [[ ${WAIT} == true ]]; do
     if [[ ${QUIET} == false ]]; then
       echo "Waiting for a free slot: Running ${RUNNINGTHREADS} of ${MAXTHREADS} allowed instances of ${PROGRAM}"
     fi
-    sleep 5
+    sleep ${DELAY}
     continue
   fi
   
@@ -159,7 +167,7 @@ while [[ ${WAIT} == true ]]; do
             echo "Waiting till all programs (n=${RUNNINGTHREADS}) reach memory saturation (now: ${TOTALMEMORY}), last: ${LASTTOTALMEMORY} )..."
           fi
         fi
-        sleep 1
+        sleep ${DELAY}
       else
         break
       fi
@@ -177,7 +185,7 @@ while [[ ${WAIT} == true ]]; do
       if [[ ${QUIET} == false ]]; then
         echo "Waiting until we have enough free memory (required: ${REQUIREDMEMORY}, available: ${AVAILABLEMEMORY})..."
       fi
-      sleep 5
+      sleep ${DELAY}
       continue
     fi
   fi
@@ -195,7 +203,7 @@ while [[ ${WAIT} == true ]]; do
     if [[ ${QUIET} == false ]]; then
       echo "Waiting until the system load falls below the threshold (threshold: ${MAXLOAD}, current:  ${CURRENTLOAD})..."
     fi
-    sleep 5
+    sleep ${DELAY}
     continue  
   fi
   

From f3e87b1353ded29d4a5999d2d25dc7d2d2369c17 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Mon, 17 Mar 2025 23:06:36 -0700
Subject: [PATCH 121/192] BUG: Auxillary programs got merged

---
 bin/mwait | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/mwait b/bin/mwait
index 1fa3c41dd..6888f910c 100755
--- a/bin/mwait
+++ b/bin/mwait
@@ -57,7 +57,7 @@ for C in "${CMD[@]}"; do
   elif [[ ${C} == *-p*=* ]]; then
     PROGRAM=`echo ${C} | awk -F"=" '{ print $2 }'`
   elif [[ ${C} == *-a*=* ]]; then
-    AUXPROGRAMS+=`echo ${C} | awk -F"=" '{ print $2 }'`
+    AUXPROGRAMS+=( `echo ${C} | awk -F"=" '{ print $2 }'` )
   elif [[ ${C} == *-d*=* ]]; then
     DELAY=`echo ${C} | awk -F"=" '{ print $2 }'`
   elif [[ ${C} == *-m* ]]; then

From a8757c27276eeceb9d23f2851b0b2cedc73cd842 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Tue, 18 Mar 2025 22:28:36 -0700
Subject: [PATCH 122/192] ADD: Julia sim parser

---
 resource/examples/julia/SimParser.jl   |  75 +++++++++
 resource/examples/julia/Test.geo.setup | 211 +++++++++++++++++++++++++
 resource/examples/julia/Test.source    |  23 +++
 3 files changed, 309 insertions(+)
 create mode 100644 resource/examples/julia/SimParser.jl
 create mode 100644 resource/examples/julia/Test.geo.setup
 create mode 100644 resource/examples/julia/Test.source

diff --git a/resource/examples/julia/SimParser.jl b/resource/examples/julia/SimParser.jl
new file mode 100644
index 000000000..d37b861ef
--- /dev/null
+++ b/resource/examples/julia/SimParser.jl
@@ -0,0 +1,75 @@
+ #
+ # SimParser.jl
+ #
+ # Copyright (C) by Andreas Zoglauer.
+ # All rights reserved.
+ #
+ # This code implementation is the intellectual property of
+ # Andreas Zoglauer.
+ #
+ # By copying, distributing or modifying the Program (or any work
+ # based on the Program) you indicate your acceptance of this statement,
+ # and all its terms.
+ #
+
+# Define file paths`
+GeometryName = "Test.geo.setup"
+FileName = "Test.inc1.id1.sim.gz"
+
+
+# Load ROOT and integrate MEGAlib
+using PyCall
+M = pyimport("ROOT")
+MEGAlibPath = ENV["MEGALIB"]  # Get the value of the environment variable M
+MEGAlibPath = joinpath(MEGAlibPath, "lib/libMEGAlib.so")  # Safely join the path
+println(MEGAlibPath)
+M.gSystem.Load(MEGAlibPath)
+#M.gSystem.Load("/Users/andreas/Documents/Science/Software/COSItools/megalib/lib/libMEGAlib.so")
+
+
+# Initialize MEGAlib
+G = M.MGlobal()
+G.Initialize()
+
+
+# Load geometry
+Geometry = M.MDGeometryQuest()
+if Geometry.ScanSetupFile(M.MString(GeometryName)) == true
+    println("Geometry ", GeometryName, " loaded!")
+else
+    println("Unable to load geometry ", GeometryName, " - Aborting!")
+    exit()
+end
+# Deactivate noising
+
+
+# Open the sim file
+Reader = M.MFileEventsSim(Geometry)  # Create an instance of MFileEventsSim with the loaded geometry
+if Reader.Open(M.MString(FileName)) == false
+    println("Unable to open file ", FileName, ". Aborting!")
+    exit()
+end
+
+
+# Loop over all events
+while true
+    Event = Reader.GetNextEvent()  # Get the next event from the reader
+    if Event == nothing  # No more events
+        break
+    end
+    M.SetOwnership(Event, true)  # Hold-over from Python - don't know if we need that here
+
+
+    # Retrieve the Hit data
+    for i in 0:Event.GetNHTs()-1
+        Energy = Event.GetHTAt(i).GetEnergy()
+        Position = Event.GetHTAt(i).GetPosition()
+        
+        println("Hit ", i, ": E=", Energy, " P=(", Position.GetX(), "/", Position.GetY(), "/", Position.GetZ(), ")")
+    end
+end
+
+# Clean up
+Reader.Close()
+
+
diff --git a/resource/examples/julia/Test.geo.setup b/resource/examples/julia/Test.geo.setup
new file mode 100644
index 000000000..952cbba25
--- /dev/null
+++ b/resource/examples/julia/Test.geo.setup
@@ -0,0 +1,211 @@
+#---------------------------------------------------------
+# Very simple Germanium ACT - similar to NCT 
+
+
+Name Max
+Version 2.0
+
+SurroundingSphere 10  0.0  0.0  0.0  10.0
+
+# Use this volume, to test the surrounding sphere:
+#Volume Sphere
+#Sphere.Material Vacuum
+#Sphere.Shape SPHE 0.0 10.0 0.0 180.0 0.0 360.
+#Sphere.Position 0.0 0.0 0.0
+#Sphere.Mother WorldVolume
+
+
+Include $(MEGALIB)/resource/examples/geomega/materials/Materials.geo
+
+
+
+#------------------------------------------------------------
+# Volume section:
+
+
+Volume WorldVolume             
+WorldVolume.Material Vacuum
+WorldVolume.Visibility 0   
+WorldVolume.Shape BRIK 5000. 5000. 5000.
+WorldVolume.Mother 0
+
+
+
+//------------------------------------------------------------
+// Define Germanium strip detector:
+
+// One layer of the tracker
+// GeStripDetector is the aluminum cryostat surrounding the 
+// Ge detectors - they are called 'GeWafer' ....
+
+Constant DetectorHalfWidth  4.0
+Constant DetectorHalfHeight 0.75
+Constant GuardRingSize      0.3
+Constant IngotRadius        { 2* 2.54}
+
+Constant CryoThickness  0.1
+Constant CryoOffset     0.5
+
+Constant CryoTotalHeight { 2*(DetectorHalfHeight + CryoOffset + CryoThickness ) } 
+
+Volume GeStripDetector           
+GeStripDetector.Material Aluminium
+GeStripDetector.Visibility 1
+GeStripDetector.Color 2
+GeStripDetector.Shape BRIK  { DetectorHalfWidth + CryoOffset + CryoThickness }  { DetectorHalfWidth + CryoOffset  + CryoThickness }  { DetectorHalfHeight + CryoOffset  + CryoThickness } 
+
+Volume CryoInnerHull 
+CryoInnerHull.Material Vacuum 
+CryoInnerHull.Visibility 1
+CryoInnerHull.Shape BRIK  { DetectorHalfWidth + CryoOffset }  { DetectorHalfWidth + CryoOffset }  { DetectorHalfHeight + CryoOffset } 
+
+
+# Create the whole wafer
+Shape BRIK WaferOuterBox
+WaferOuterBox.Parameters DetectorHalfWidth  DetectorHalfWidth  DetectorHalfHeight
+
+Shape TUBE WaferCutDisk
+WaferCutDisk.Parameters 0.0 IngotRadius DetectorHalfHeight
+
+Shape Intersection WholeWafer
+WholeWafer.Parameters WaferOuterBox WaferCutDisk
+
+# Create the active wafer
+Shape BRIK ActiveWaferOuterBox
+ActiveWaferOuterBox.Parameters { DetectorHalfWidth - GuardRingSize }  { DetectorHalfWidth - GuardRingSize }  DetectorHalfHeight
+
+Shape TUBE ActiveWaferCutDisk
+ActiveWaferCutDisk.Parameters 0.0 { IngotRadius - GuardRingSize } DetectorHalfHeight
+
+Shape Intersection ActiveWafer
+ActiveWafer.Parameters ActiveWaferOuterBox ActiveWaferCutDisk
+
+# Create the guard ring
+Shape Subtraction GuardRing_AlmostThere
+GuardRing_AlmostThere.Parameters WholeWafer ActiveWafer
+
+# A little trick, to get the Strip detector to work: we have to do another intersection, so that the first volume is a box:
+Shape Intersection GuardRing
+GuardRing.Parameters WaferOuterBox GuardRing_AlmostThere
+
+
+Volume GeWafer
+GeWafer.Material Germanium
+GeWafer.Visibility 1
+GeWafer.Color 6
+GeWafer.Shape ActiveWafer
+GeWafer.Position  0.0 0.0 0.0
+GeWafer.Mother CryoInnerHull
+
+Volume GeWaferGuardRing
+GeWaferGuardRing.Material Germanium
+GeWaferGuardRing.Visibility 1
+GeWaferGuardRing.Color 3
+GeWaferGuardRing.Shape GuardRing
+GeWaferGuardRing.Position  0.0 0.0 0.0
+GeWaferGuardRing.Mother CryoInnerHull
+
+CryoInnerHull.Copy Cryo
+Cryo.Position 0.0 0.0 0.0
+Cryo.Mother GeStripDetector
+
+
+
+// Line-Up some Ge-Detector 
+GeStripDetector.Copy GeE1N001
+GeE1N001.Position  0.0  0.0  {  1.5*CryoTotalHeight } 
+GeE1N001.Mother WorldVolume
+
+GeStripDetector.Copy GeE1N002
+GeE1N002.Position  0.0  0.0  {  0.5*CryoTotalHeight } 
+GeE1N002.Mother WorldVolume
+
+GeStripDetector.Copy GeE1N003
+GeE1N003.Position  0.0  0.0  { -0.5*CryoTotalHeight } 
+GeE1N003.Mother WorldVolume
+
+GeStripDetector.Copy GeE1N004
+GeE1N004.Position  0.0  0.0  { -1.5*CryoTotalHeight } 
+GeE1N004.Mother WorldVolume
+
+
+
+
+
+
+#------------------------------------------------------------
+# Detector and trigger section:
+
+
+MDStrip3D                  ActiveDetector
+
+ActiveDetector.DetectorVolume      GeWafer
+ActiveDetector.SensitiveVolume     GeWafer
+
+ActiveDetector.StructuralPitch     0.0   0.0    CryoTotalHeight
+ActiveDetector.StructuralOffset    0.0   0.0    0.0
+
+ActiveDetector.Offset              0.0   0.0
+ActiveDetector.StripNumber         40    40
+
+ActiveDetector.NoiseThreshold      15
+ActiveDetector.TriggerThreshold    30
+
+ActiveDetector.DepthResolution     10  0.02
+ActiveDetector.DepthResolution     100  0.02
+ActiveDetector.DepthResolution     1000  0.02
+
+ActiveDetector.EnergyResolution Gaus 10      10        0.417   
+ActiveDetector.EnergyResolution Gaus 20      20        0.425           
+ActiveDetector.EnergyResolution Gaus 50      50        0.4375    
+ActiveDetector.EnergyResolution Gaus 100     100       0.454     
+ActiveDetector.EnergyResolution Gaus 200     200       0.492     
+ActiveDetector.EnergyResolution Gaus 500     500       0.5875      
+ActiveDetector.EnergyResolution Gaus 1000    1000      0.7217       
+ActiveDetector.EnergyResolution Gaus 2000    2000      0.9317      
+ActiveDetector.EnergyResolution Gaus 5000    5000      1.3819       
+ActiveDetector.EnergyResolution Gaus 10000   10000     1.9094                     
+ActiveDetector.EnergyResolution Gaus 100000  100000    5.907         
+
+ActiveDetector.FailureRate 0.0
+
+ActiveDetector.Named D1
+D1.Assign 0.0  0.0  {  1.5*CryoTotalHeight }
+ActiveDetector.Named D2
+D2.Assign 0.0  0.0  {  0.5*CryoTotalHeight }
+ActiveDetector.Named D3
+D3.Assign  0.0  0.0  { -0.5*CryoTotalHeight }
+ActiveDetector.Named D4  
+D4.Assign 0.0  0.0  { -1.5*CryoTotalHeight }
+
+
+Simple GuardRingDetector
+
+GuardRingDetector.DetectorVolume      GeWaferGuardRing
+GuardRingDetector.SensitiveVolume     GeWaferGuardRing
+
+GuardRingDetector.TriggerThreshold      40
+GuardRingDetector.NoiseThresholdEqualsTriggerThreshold true
+
+GuardRingDetector.EnergyResolution Gaus 10      10        3   
+GuardRingDetector.EnergyResolution Gaus 20      20        3           
+GuardRingDetector.EnergyResolution Gaus 50      50        3    
+GuardRingDetector.EnergyResolution Gaus 100     100       3     
+GuardRingDetector.EnergyResolution Gaus 200     200       3     
+GuardRingDetector.EnergyResolution Gaus 500     500       3      
+GuardRingDetector.EnergyResolution Gaus 1000    1000      3       
+GuardRingDetector.EnergyResolution Gaus 2000    2000      3      
+GuardRingDetector.EnergyResolution Gaus 5000    5000      3       
+
+
+
+// Trigger: at least one hit in one Germanium detector  
+Trigger ActiveDetectorTrigger
+ActiveDetectorTrigger.Veto false
+ActiveDetectorTrigger.TriggerByChannel true
+ActiveDetectorTrigger.Detector ActiveDetector 1
+
+Trigger GuardRingVeto
+GuardRingVeto.Veto true
+GuardRingVeto.TriggerByChannel true
+GuardRingVeto.Detector GuardRingDetector 1
diff --git a/resource/examples/julia/Test.source b/resource/examples/julia/Test.source
new file mode 100644
index 000000000..1061bf796
--- /dev/null
+++ b/resource/examples/julia/Test.source
@@ -0,0 +1,23 @@
+# Example run for Cosima
+
+# Global parameters
+Version         1
+Geometry        Test.geo.setup
+
+# Physics list
+PhysicsListEM               LivermorePol
+
+# Output formats
+StoreSimulationInfo         all
+
+# Run & source parameters
+Run SpaceSim
+SpaceSim.FileName           Test
+SpaceSim.Triggers           20000
+
+SpaceSim.Source Source
+Source.ParticleType           1
+Source.Beam                   FarFieldPointSource 0 0
+Source.Spectrum               Mono 511
+Source.Flux                   1.0
+

From 91cf203afcbe4262119d78deef1208c2b23330e5 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Wed, 19 Mar 2025 09:57:50 -0700
Subject: [PATCH 123/192] CHG: Some modifications plus read me

---
 resource/examples/julia/Readme.md    | 24 ++++++++++++++++++++++++
 resource/examples/julia/SimParser.jl |  4 +---
 2 files changed, 25 insertions(+), 3 deletions(-)
 create mode 100644 resource/examples/julia/Readme.md

diff --git a/resource/examples/julia/Readme.md b/resource/examples/julia/Readme.md
new file mode 100644
index 000000000..503b43fe2
--- /dev/null
+++ b/resource/examples/julia/Readme.md
@@ -0,0 +1,24 @@
+# MEGAlib & Julia
+
+## Setting up Julia
+
+Install Julia from sources as stated here:
+https://julialang.org/downloads/
+
+Then:
+```
+export PYTHON=`which python3`
+julia
+> import Pkg
+> Pkg.build("PyCall")
+> exit()
+```
+
+## Run something:
+
+```
+julia SimParser.jl
+```
+ 
+
+
diff --git a/resource/examples/julia/SimParser.jl b/resource/examples/julia/SimParser.jl
index d37b861ef..424b5bf6f 100644
--- a/resource/examples/julia/SimParser.jl
+++ b/resource/examples/julia/SimParser.jl
@@ -22,9 +22,7 @@ using PyCall
 M = pyimport("ROOT")
 MEGAlibPath = ENV["MEGALIB"]  # Get the value of the environment variable M
 MEGAlibPath = joinpath(MEGAlibPath, "lib/libMEGAlib.so")  # Safely join the path
-println(MEGAlibPath)
 M.gSystem.Load(MEGAlibPath)
-#M.gSystem.Load("/Users/andreas/Documents/Science/Software/COSItools/megalib/lib/libMEGAlib.so")
 
 
 # Initialize MEGAlib
@@ -41,7 +39,7 @@ else
     exit()
 end
 # Deactivate noising
-
+Geometry.ActivateNoising(false)
 
 # Open the sim file
 Reader = M.MFileEventsSim(Geometry)  # Create an instance of MFileEventsSim with the loaded geometry

From 6df23dd572ce649c317d94d05c1049becb6bcf79 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Thu, 27 Mar 2025 08:50:22 -0700
Subject: [PATCH 124/192] ADD: New tool TraMerger

---
 src/addon/Makefile      |   1 +
 src/addon/TraMerger.cxx | 358 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 359 insertions(+)
 create mode 100644 src/addon/TraMerger.cxx

diff --git a/src/addon/Makefile b/src/addon/Makefile
index 61e645080..96b8e25d9 100644
--- a/src/addon/Makefile
+++ b/src/addon/Makefile
@@ -26,6 +26,7 @@ PRGSX := \
 	$(BN)/SimBinaryConverter \
 	$(BN)/SimRandomCoincidence \
 	$(BN)/TraAnalyzer \
+  $(BN)/TraMerger \
 	$(BN)/DecayAnalyzer \
 	$(BN)/BackgroundMixer \
 	$(BN)/SimpleComptonImaging \
diff --git a/src/addon/TraMerger.cxx b/src/addon/TraMerger.cxx
new file mode 100644
index 000000000..d2ccc140d
--- /dev/null
+++ b/src/addon/TraMerger.cxx
@@ -0,0 +1,358 @@
+/* 
+ * TraAnalyzer.cxx
+ *
+ *
+ * Copyright (C) by Andreas Zoglauer.
+ * All rights reserved.
+ *
+ *
+ * This code implementation is the intellectual property of
+ * Andreas Zoglauer.
+ *
+ * By copying, distributing or modifying the Program (or any work
+ * based on the Program) you indicate your acceptance of this statement,
+ * and all its terms.
+ *
+ */
+
+// Standard
+#include <iostream>
+#include <string>
+#include <sstream>
+#include <csignal>
+#include <vector>
+#include <limits>
+#include <map>
+using namespace std;
+
+// ROOT
+#include <TApplication.h>
+#include <TStyle.h>
+#include <TH1.h>
+#include <TCanvas.h>
+#include <MString.h>
+#include <TList.h>
+#include <TSystem.h>
+#include <TSystemFile.h>
+#include <TSystemDirectory.h>
+
+// MEGAlib
+#include "MGlobal.h"
+#include "MStreams.h"
+#include "MDGeometryQuest.h"
+#include "MDDetector.h"
+#include "MFileEventsSim.h"
+#include "MDVolumeSequence.h"
+#include "MPhysicalEvent.h"
+#include "MComptonEvent.h"
+#include "MFileEventsTra.h"
+
+/******************************************************************************/
+
+class TraAnalyzer
+{
+public:
+  //! Default constructor
+  TraAnalyzer();
+  //! Default destructor
+  ~TraAnalyzer();
+  
+  //! Parse the command line
+  bool ParseCommandLine(int argc, char** argv);
+  //! Analyze whatever needs to be analyzed...
+  bool Analyze();
+  //! Interrupt the analysis
+  void Interrupt() { m_Interrupt = true; }
+
+private:
+  //! True, if the analysis needs to be interrupted
+  bool m_Interrupt;
+
+  //! Tra file name prefix
+  MString m_FileNamePrefix;
+  //! Geometry file name
+  MString m_GeometryFileName;
+  //! Output file name
+  MString m_OutputFileName;
+  //! Maximum number of files
+  unsigned int m_MaxFiles;
+};
+
+/******************************************************************************/
+
+
+/******************************************************************************
+ * Default constructor
+ */
+TraAnalyzer::TraAnalyzer() : m_Interrupt(false)
+{
+  m_MaxFiles = numeric_limits<unsigned int>::max();
+}
+
+
+/******************************************************************************
+ * Default destructor
+ */
+TraAnalyzer::~TraAnalyzer()
+{
+  // Intentionally left blank
+}
+
+
+/******************************************************************************
+ * Parse the command line
+ */
+bool TraAnalyzer::ParseCommandLine(int argc, char** argv)
+{
+  ostringstream Usage;
+  Usage<<endl;
+  Usage<<"  Usage: TraAnalyzer <options>"<<endl;
+  Usage<<"    General options:"<<endl;
+  Usage<<"         -p:   tra file name prefix"<<endl;
+  Usage<<"         -o:   output file name"<<endl;
+  Usage<<"         -g:   geometry file name"<<endl;
+  Usage<<"         -m:   maximum number of files"<<endl;
+  Usage<<"         -h:   print this help"<<endl;
+  Usage<<endl;
+
+  string Option;
+
+  // Check for help
+  for (int i = 1; i < argc; i++) {
+    Option = argv[i];
+    if (Option == "-h" || Option == "--help" || Option == "?" || Option == "-?") {
+      cout<<Usage.str()<<endl;
+      return false;
+    }
+  }
+
+  // Now parse the command line options:
+  for (int i = 1; i < argc; i++) {
+    Option = argv[i];
+
+    // First check if each option has sufficient arguments:
+    // Single argument
+    if (Option == "-f" || Option == "-o") {
+      if (!((argc > i+1) && argv[i+1][0] != '-')){
+        cout<<"Error: Option "<<argv[i][1]<<" needs a second argument!"<<endl;
+        cout<<Usage.str()<<endl;
+        return false;
+      }
+    } 
+    // Multiple arguments_
+    //else if (Option == "-??") {
+    //  if (!((argc > i+2) && argv[i+1][0] != '-' && argv[i+2][0] != '-')){
+    //    cout<<"Error: Option "<<argv[i][1]<<" needs two arguments!"<<endl;
+    //    cout<<Usage.str()<<endl;
+    //    return false;
+    //  }
+    //}
+
+    // Then fulfill the options:
+    if (Option == "-p") {
+      m_FileNamePrefix = argv[++i];
+      cout<<"Accepting file name prefix: "<<m_FileNamePrefix<<endl;
+    } else if (Option == "-o") {
+      m_OutputFileName = argv[++i];
+      cout<<"Accepting output file name: "<<m_OutputFileName<<endl;
+    } else if (Option == "-g") {
+      m_GeometryFileName = argv[++i];
+      cout<<"Accepting file name: "<<m_GeometryFileName<<endl;
+    } else if (Option == "-m") {
+      m_MaxFiles = atoi(argv[++i]);
+      cout<<"Accepting maximum number of files: "<<m_MaxFiles<<endl;
+    } else {
+      cout<<"Error: Unknown option \""<<Option<<"\"!"<<endl;
+      cout<<Usage.str()<<endl;
+      return false;
+    }
+  }
+
+  if (m_FileNamePrefix == "") {
+    cout<<"Error: Need a tra file name prefix!"<<endl;
+    cout<<Usage.str()<<endl;
+    return false;
+  }
+
+  if (m_GeometryFileName == "") {
+    cout<<"Error: Need a geometry file name!"<<endl;
+    cout<<Usage.str()<<endl;
+    return false;
+  }
+
+  if (m_OutputFileName == "") {
+    cout<<"Error: Need an output file name!"<<endl;
+    cout<<Usage.str()<<endl;
+    return false;
+  }
+
+  return true;
+}
+
+
+/******************************************************************************
+ * Do whatever analysis is necessary
+ */
+bool TraAnalyzer::Analyze()
+{
+  // Load geometry:
+  MDGeometryQuest* Geometry = new MDGeometryQuest();
+  if (Geometry->ScanSetupFile(m_GeometryFileName) == true) {
+    cout<<"Geometry "<<Geometry->GetName()<<" loaded!"<<endl;
+  } else {
+    cout<<"Unable to load geometry "<<Geometry->GetName()<<" - Aborting!"<<endl;
+    return false;
+  }  
+
+  bool InformationTransfered = false;
+  MFileEventsTra* Writer = new MFileEventsTra();
+  if (Writer->Open(m_OutputFileName, MFile::c_Write) == false) {
+    cout<<"Unable to open output file!"<<endl;
+    return false;
+  }
+
+
+  // Find files:
+  cout<<"Retrieving files..."<<endl;
+  TSystemDirectory D(".", gSystem->pwd());
+  TList* Files = D.GetListOfFiles();
+  if (Files == nullptr) {
+    mout<<"ERROR: Did not find or couldn't get any files!"<<endl;
+    return false;
+  }
+
+
+  // Sort them
+  cout<<"Sorting and eliminating not matching files (current total: "<<Files->LastIndex()<<" files)"<<endl;
+  vector<MString> FileNames;
+                  
+  for (const auto&& Object: *Files) {
+    MString Name = Object->GetName();
+    if (Name.BeginsWith(m_FileNamePrefix) == false) continue;
+    // cout<<"Checking "<<Name<<" for prefix \""<<Prefix<<"\" and suffix \""<<Type<<"\" (+ .gz)... ";
+    if (Name.EndsWith(".tra.gz") == true || Name.EndsWith(".tra") == true) {
+      FileNames.push_back(Name);
+    }
+  }
+  if (FileNames.size() > 0) {
+    cout<<"Considering "<<FileNames.size()<<" files..."<<endl;
+  } else {
+    cout<<"No files found to join..."<<endl;
+    return false;
+  }
+
+  // The vector with the events
+  vector<MPhysicalEvent*> Events;
+
+  unsigned int FileCounter = 0;
+  for (MString FileName: FileNames) {
+    if (++FileCounter > m_MaxFiles) break;
+    
+    MFileEventsTra* Reader = new MFileEventsTra();
+    if (Reader->Open(FileName) == false) {
+      mout<<"Unable to open file "<<FileName<<". Aborting!"<<endl;
+      return false;
+    }
+    if (InformationTransfered == false) {
+      Writer->TransferInformation(Reader);
+      InformationTransfered = true;
+    }
+
+    MPhysicalEvent* Event = nullptr;
+    while ((Event = Reader->GetNextEvent()) != nullptr) { 
+      Events.push_back(Event);    
+      // NO: delete Event;
+    }
+
+    Reader->Close();
+    delete Reader;
+  }
+
+  // Now sort them:
+  cout<<"Starting with sort..."<<endl;
+  sort(Events.begin(), Events.end(), [](MPhysicalEvent* A, MPhysicalEvent* B) { return A->GetTime() < B->GetTime(); });
+
+  // And save:
+  cout<<"Saving"<<endl;
+  Writer->WriteHeader();
+  for (MPhysicalEvent* Event: Events) {
+    Writer->AddEvent(Event);
+  }
+  Writer->WriteFooter();
+  Writer->Close();
+
+  // Some cleanup
+  delete Writer;
+  delete Geometry;
+
+  
+  return true;
+}
+
+
+/******************************************************************************/
+
+TraAnalyzer* g_Prg = 0;
+int g_NInterrupts = 2;
+
+/******************************************************************************/
+
+
+/******************************************************************************
+ * Called when an interrupt signal is flagged
+ * All catched signals lead to a well defined exit of the program
+ */
+void CatchSignal(int a)
+{
+  cout<<"Catched signal Ctrl-C:"<<endl;
+  
+  --g_NInterrupts;
+  if (g_NInterrupts <= 0) {
+    cout<<"Aborting..."<<endl;
+    abort();
+  } else {
+    cout<<"Trying to cancel the analysis..."<<endl;
+    if (g_Prg != 0) {
+      g_Prg->Interrupt();
+    }
+    cout<<"If you hit "<<g_NInterrupts<<" more times, then I will abort immediately!"<<endl;
+  }
+}
+
+
+/******************************************************************************
+ * Main program
+ */
+int main(int argc, char** argv)
+{
+  // Set a default error handler and catch some signals...
+  signal(SIGINT, CatchSignal);
+
+  // Initialize global MEGAlib variables, especially mgui, etc.
+  MGlobal::Initialize();
+
+  TApplication TraAnalyzerApp("TraAnalyzerApp", 0, 0);
+
+  g_Prg = new TraAnalyzer();
+
+  if (g_Prg->ParseCommandLine(argc, argv) == false) {
+    cerr<<"Error during parsing of command line!"<<endl;
+    return -1;
+  } 
+  if (g_Prg->Analyze() == false) {
+    cerr<<"Error during analysis!"<<endl;
+    return -2;
+  } 
+
+  if (gROOT->IsBatch() == false) {
+    TraAnalyzerApp.Run();
+  }
+
+  cout<<"Program exited normally!"<<endl;
+
+  return 0;
+}
+
+/*
+ * Cosima: the end...
+ ******************************************************************************/

From a4428d79aa81f990604fa80c636db854b4699da7 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Thu, 27 Mar 2025 08:50:45 -0700
Subject: [PATCH 125/192] CHG: Make it run on command line

---
 resource/examples/python/OverflowFilter.py | 24 +++++++++++-----------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/resource/examples/python/OverflowFilter.py b/resource/examples/python/OverflowFilter.py
index dc4e8471a..cc8d8ba33 100644
--- a/resource/examples/python/OverflowFilter.py
+++ b/resource/examples/python/OverflowFilter.py
@@ -103,19 +103,19 @@
 Writer.WriteFooter()
 Writer.Close()
 
-CanvasBeforeFilter = M.TCanvas()
-CanvasBeforeFilter.cd()
-HistBeforeFilter.Draw()
-CanvasBeforeFilter.Update()
+#CanvasBeforeFilter = M.TCanvas()
+#CanvasBeforeFilter.cd()
+#HistBeforeFilter.Draw()
+#CanvasBeforeFilter.Update()
 
-CanvasAfterFilter = M.TCanvas()
-CanvasAfterFilter.cd()
-HistAfterFilter.Draw()
-CanvasAfterFilter.Update()
+#CanvasAfterFilter = M.TCanvas()
+#CanvasAfterFilter.cd()
+#HistAfterFilter.Draw()
+#CanvasAfterFilter.Update()
 
 
 # Prevent the canvases from being closed
-import os
-print("ATTENTION: Please exit by clicking: File -> Close ROOT! Do not just close the window by clicking \"x\"")
-print("           ... and if you didn't honor this warning, and are stuck, execute the following in a new terminal: kill " + str(os.getpid()))
-M.gApplication.Run()
+#import os
+#print("ATTENTION: Please exit by clicking: File -> Close ROOT! Do not just close the window by clicking \"x\"")
+#print("           ... and if you didn't honor this warning, and are stuck, execute the following in a new terminal: kill " + str(os.getpid()))
+#M.gApplication.Run()

From a88ad475892785ad0b697c5331c89f329f0e9da4 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Wed, 2 Apr 2025 22:34:34 -0700
Subject: [PATCH 126/192] CHG: Compatibility with MEGAlib 4.0

---
 src/addon/TraMerger.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/addon/TraMerger.cxx b/src/addon/TraMerger.cxx
index d2ccc140d..7ad308d6e 100644
--- a/src/addon/TraMerger.cxx
+++ b/src/addon/TraMerger.cxx
@@ -254,7 +254,7 @@ bool TraAnalyzer::Analyze()
       return false;
     }
     if (InformationTransfered == false) {
-      Writer->TransferInformation(Reader);
+      // Only works in MEGAlib 5.0: Writer->TransferInformation(Reader);
       InformationTransfered = true;
     }
 
@@ -278,7 +278,7 @@ bool TraAnalyzer::Analyze()
   for (MPhysicalEvent* Event: Events) {
     Writer->AddEvent(Event);
   }
-  Writer->WriteFooter();
+  // Only works in MEGAlib 5.0: Writer->WriteFooter();
   Writer->Close();
 
   // Some cleanup

From a77ca4dfbe99a6faf6dfe36096e9377181d65022 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Wed, 30 Apr 2025 09:41:14 -0700
Subject: [PATCH 127/192] BUG: Not sure how that code got checked in...

---
 src/cosima/src/MCParameterFile.cc | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/cosima/src/MCParameterFile.cc b/src/cosima/src/MCParameterFile.cc
index 4cdb2ea60..dbb2f8ce7 100644
--- a/src/cosima/src/MCParameterFile.cc
+++ b/src/cosima/src/MCParameterFile.cc
@@ -801,6 +801,8 @@ bool MCParameterFile::Parse()
                " Number of tokens is not correct!");
           return false;
         }
+      // This comes from a failed merge...
+      /*
       } else if (T->IsTokenAt(1, "Reconstruction", true) == true) {
         if (T->GetNTokens() == 4) {
           Run->SetRevanConfigurationFileName(T->GetTokenAtAsString(2));
@@ -810,6 +812,7 @@ bool MCParameterFile::Parse()
                " Number of tokens is not correct!");
           return false;
         }
+      */
       } else if (T->IsTokenAt(1, "Triggers", true) == true ||
                  T->IsTokenAt(1, "Trigger", true) == true ||
                  T->IsTokenAt(1, "NTrigger", true) == true ||

From 5699872edf9f85778626069e0075a4c1883dd49d Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Wed, 30 Apr 2025 10:08:22 -0700
Subject: [PATCH 128/192] CHG: Merge needs commit

---
 config/AllowedROOTVersions.txt                |   2 +-
 config/build-geant4.sh                        |   2 +-
 config/build-root.sh                          |  31 ++-
 config/configure_packages                     |   6 +-
 resource/patches/geant4_v10.02.p03.patch      | 224 ++++++++++++++++++
 .../framework/src/MGUIMainFretalon.cxx        |   1 +
 src/fretalon/framework/src/MModule.cxx        |   1 +
 .../melinator/src/MGUIMainMelinator.cxx       |   1 +
 src/geomega/src/MDGDMLImport.cxx              |   1 +
 src/geomega/src/MGUIGeomegaMain.cxx           |   3 +-
 src/geomega/src/MInterfaceGeomega.cxx         |   1 +
 src/global/misc/inc/MGlobal.h                 |   3 -
 src/global/misc/src/MBinnerFISBEL.cxx         |   1 +
 src/mimrec/src/MGUIMimrecMain.cxx             |   3 +-
 src/revan/src/MGUIRevanMain.cxx               |   3 +-
 src/sivan/src/MGUISivanMain.cxx               |   5 +-
 16 files changed, 267 insertions(+), 21 deletions(-)

diff --git a/config/AllowedROOTVersions.txt b/config/AllowedROOTVersions.txt
index 6193b76c1..cfee3c9ec 100644
--- a/config/AllowedROOTVersions.txt
+++ b/config/AllowedROOTVersions.txt
@@ -1 +1 @@
-628 
+632 
diff --git a/config/build-geant4.sh b/config/build-geant4.sh
index 6465d1bba..fe393b4ce 100755
--- a/config/build-geant4.sh
+++ b/config/build-geant4.sh
@@ -467,7 +467,7 @@ PATCHAPPLIED="Patch not applied"
 if [[ ${PATCH} == on ]]; then
   echo "Patching..."
   if [ -f "${MEGALIB}/resource/patches/${GEANT4CORE}.patch" ]; then
-    patch -p1 < ${MEGALIB}/resource/patches/${GEANT4CORE}.patch
+    patch -p1 -l < ${MEGALIB}/resource/patches/${GEANT4CORE}.patch
     PATCHMD5=`openssl md5 "${MEGALIB}/resource/patches/${GEANT4CORE}.patch" | awk -F" " '{ print $2 }'`
     PATCHAPPLIED="Patch applied ${PATCHMD5}"
     echo "Applied patch: ${MEGALIB}/resource/patches/${GEANT4CORE}.patch"
diff --git a/config/build-root.sh b/config/build-root.sh
index fe084086a..f0d2c8c47 100755
--- a/config/build-root.sh
+++ b/config/build-root.sh
@@ -24,7 +24,7 @@ CONFIGUREOPTIONS+=" -Dopengl=ON"
 # Mathmore -- needed for fitting, e.g. ARMs"
 CONFIGUREOPTIONS+=" -Dmathmore=ON"
 # Minuit2 -- needed for parallel fitting with melinator
-CONFIGUREOPTIONS+=" -Dminuit2=ON"
+# Minuit 2 is default startin g ROOT 6.30: CONFIGUREOPTIONS+=" -Dminuit2=ON"
 # XFT -- needed for smoothed fonts
 CONFIGUREOPTIONS+=" -Dxft=ON"
 # Afterimage -- support to draw images in pads and save as png, etc.
@@ -333,10 +333,17 @@ if [ "${TARBALL}" != "" ]; then
   fi
 
   # Check if it has the correct version:
-  VER=`tar xfzO ${TARBALL} ${ROOTTOPDIR}/build/version_number | sed 's|/|.|g'`
-  RESULT=$?
-  if [ "${RESULT}" != "0" ]; then
-    echo "ERROR: Something went wrong unpacking the ROOT tarball!"
+  VER=""
+  if tar -tf ${TARBALL} | grep -q "${ROOTTOPDIR}/build/version_number"; then  
+    VER=`tar xfzO ${TARBALL} ${ROOTTOPDIR}/build/version_number | sed 's|/|.|g'`
+  elif tar -tf ${TARBALL} | grep -q "${ROOTTOPDIR}/core/foundation/inc/ROOT/RVersion.hxx"; then
+    VER+=$(tar xfzO ${TARBALL} ${ROOTTOPDIR}/core/foundation/inc/ROOT/RVersion.hxx | grep "ROOT_VERSION_MAJOR" | head -n 1 | awk '{ print $3 }')
+    VER+="."
+    VER+=$(tar xfzO ${TARBALL} ${ROOTTOPDIR}/core/foundation/inc/ROOT/RVersion.hxx | grep "ROOT_VERSION_MINOR" | head -n 1 | awk '{ print $3 }')
+    VER+="."
+    VER+=$(tar xfzO ${TARBALL} ${ROOTTOPDIR}/core/foundation/inc/ROOT/RVersion.hxx | grep "ROOT_VERSION_PATCH" | head -n 1 | awk '{ print $3 }')
+  else
+    echo "ERROR: Cannot find the ROOT version in the tarball!"
     exit 1
   fi
   if echo ${VER} | grep -E '[ "]' >/dev/null; then
@@ -431,9 +438,17 @@ else
     exit 1
   fi
 
-  VER=`tar xfzO ${TARBALL} ${ROOTTOPDIR}/build/version_number | sed 's|/|.|g'`
-  if [ "$?" != "0" ]; then
-    echo "ERROR: Something went wrong unpacking the ROOT tarball!"
+  VER=""
+  if tar -tf ${TARBALL} | grep -q "${ROOTTOPDIR}/build/version_number"; then
+    VER=`tar xfzO ${TARBALL} ${ROOTTOPDIR}/build/version_number | sed 's|/|.|g'`
+  elif tar -tf ${TARBALL} | grep -q "${ROOTTOPDIR}/core/foundation/inc/ROOT/RVersion.hxx"; then
+    VER+=$(tar xfzO ${TARBALL} ${ROOTTOPDIR}/core/foundation/inc/ROOT/RVersion.hxx | grep "ROOT_VERSION_MAJOR" | head -n 1 | awk '{ print $3 }')
+    VER+="."
+    VER+=$(tar xfzO ${TARBALL} ${ROOTTOPDIR}/core/foundation/inc/ROOT/RVersion.hxx | grep "ROOT_VERSION_MINOR" | head -n 1 | awk '{ print $3 }')
+    VER+="."
+    VER+=$(tar xfzO ${TARBALL} ${ROOTTOPDIR}/core/foundation/inc/ROOT/RVersion.hxx | grep "ROOT_VERSION_PATCH" | head -n 1 | awk '{ print $3 }')
+  else
+    echo "ERROR: Cannot find the ROOT version in the tarball!"
     exit 1
   fi
   if echo ${VER} | grep -E '[ "]' >/dev/null; then
diff --git a/config/configure_packages b/config/configure_packages
index 104927c96..b862c4f5f 100755
--- a/config/configure_packages
+++ b/config/configure_packages
@@ -59,9 +59,9 @@ if [[ ${IsDebianClone} -eq 1 ]]; then
     elif [[ ${VERSIONID} == 20.04 ]]; then
       REQUIRED="git gawk dpkg-dev make g++ gcc gfortran gdb valgrind binutils libx11-dev libxpm-dev libxft-dev libxext-dev libssl-dev libpcre3-dev libglu1-mesa-dev libglew-dev libftgl-dev libmysqlclient-dev libfftw3-dev libgraphviz-dev libavahi-compat-libdnssd-dev libldap2-dev python3 python3-dev python3-tk python3-venv libxml2-dev libkrb5-dev libgsl-dev cmake libxmu-dev curl doxygen libblas-dev liblapack-dev expect dos2unix libncurses5-dev libboost-all-dev libcfitsio-dev mlocate"
     elif [[ ${VERSIONID} == 22.04 ]]; then
-      REQUIRED="git gawk dpkg-dev make g++ gcc gfortran gdb valgrind binutils libx11-dev libxpm-dev libxft-dev libxext-dev libssl-dev libpcre3-dev libglu1-mesa-dev libglew-dev libftgl-dev libmysqlclient-dev libfftw3-dev libgraphviz-dev libavahi-compat-libdnssd-dev libldap2-dev python3 python3-dev python3-tk python3-venv libxml2-dev libkrb5-dev libgsl-dev cmake libxmu-dev curl doxygen libblas-dev liblapack-dev expect dos2unix libncurses5-dev libboost-all-dev libcfitsio-dev mlocate"
+      REQUIRED="git gawk dpkg-dev make g++ gcc gfortran gdb valgrind binutils libx11-dev libxpm-dev libxft-dev libxext-dev libssl-dev libpcre3-dev libglu1-mesa-dev libglew-dev libftgl-dev libmysqlclient-dev libfftw3-dev libgraphviz-dev libavahi-compat-libdnssd-dev libldap2-dev python3 python3-dev python3-tk python3-venv libxml2-dev libkrb5-dev libgsl-dev cmake libxmu-dev curl doxygen libblas-dev liblapack-dev expect dos2unix libncurses5-dev libboost-all-dev libcfitsio-dev mlocate libbz2-dev"
     else
-      REQUIRED="git gawk dpkg-dev make g++ gcc gfortran gdb valgrind binutils libx11-dev libxpm-dev libxft-dev libxext-dev libssl-dev libpcre3-dev libglu1-mesa-dev libglew-dev libftgl-dev libmysqlclient-dev libfftw3-dev libgraphviz-dev libavahi-compat-libdnssd-dev libldap2-dev python3 python3-dev python3-tk python3-venv libxml2-dev libkrb5-dev libgsl-dev cmake libxmu-dev curl doxygen libblas-dev liblapack-dev expect dos2unix libncurses5-dev libboost-all-dev libcfitsio-dev mlocate"
+      REQUIRED="git gawk dpkg-dev make g++ gcc gfortran gdb valgrind binutils libx11-dev libxpm-dev libxft-dev libxext-dev libssl-dev libpcre3-dev libglu1-mesa-dev libglew-dev libftgl-dev libmysqlclient-dev libfftw3-dev libgraphviz-dev libavahi-compat-libdnssd-dev libldap2-dev python3 python3-dev python3-tk python3-venv libxml2-dev libkrb5-dev libgsl-dev cmake libxmu-dev curl doxygen libblas-dev liblapack-dev expect dos2unix libncurses5-dev libboost-all-dev libcfitsio-dev mlocate libbz2-dev"
       
       echo "This script has not yet been adapted for your version of Ubuntu: ${VERSIONID}"
       echo "Feel free to write the MEGAlib maintainers an email to update this script and send them the content of the file: /etc/os-release"
@@ -86,7 +86,7 @@ if [[ ${IsDebianClone} -eq 1 ]]; then
       exit 0  
     fi
   else
-    REQUIRED="bc git gawk dpkg-dev make g++ gcc gdb valgrind binutils libx11-dev libxpm-dev libxft-dev libxext-dev libssl-dev libpcre3-dev libglu1-mesa-dev libglew-dev libftgl-dev libfftw3-dev libgraphviz-dev libavahi-compat-libdnssd-dev libldap2-dev python python3-dev python3-tk python3-venv libxml2-dev libkrb5-dev libgsl-dev cmake libxmu-dev curl doxygen libblas-dev liblapack-dev expect dos2unix libncurses5-dev libboost-all-dev libcfitsio-dev"
+    REQUIRED="bc git gawk dpkg-dev make g++ gcc gdb valgrind binutils libx11-dev libxpm-dev libxft-dev libxext-dev libssl-dev libpcre3-dev libglu1-mesa-dev libglew-dev libftgl-dev libfftw3-dev libgraphviz-dev libavahi-compat-libdnssd-dev libldap2-dev python python3-dev python3-tk python3-venv libxml2-dev libkrb5-dev libgsl-dev cmake libxmu-dev curl doxygen libblas-dev liblapack-dev expect dos2unix libncurses5-dev libboost-all-dev libcfitsio-dev libbz2-dev"
  
     echo "This script has not yet been adapted for your version of Linux: Debian-derivative ${OS}"
     echo "Feel free to write the MEGAlib maintainers an email to update this script and send them the content of the file: /etc/os-release"
diff --git a/resource/patches/geant4_v10.02.p03.patch b/resource/patches/geant4_v10.02.p03.patch
index 125c99dc5..e0dca1c56 100644
--- a/resource/patches/geant4_v10.02.p03.patch
+++ b/resource/patches/geant4_v10.02.p03.patch
@@ -1,3 +1,227 @@
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLNNToMultiPionsChannel.cc geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLNNToMultiPionsChannel.cc
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLNNToMultiPionsChannel.cc	2017-01-27 04:24:56
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLNNToMultiPionsChannel.cc	2024-09-24 11:08:46
+@@ -209,7 +209,15 @@ namespace G4INCL {
+             }
+         }
+
+-        std::random_shuffle(isosp,isosp+npion,Random::getAdapter());
++        //std::random_shuffle(isosp,isosp+npion,Random::getAdapter());
++        auto&& r = Random::getAdapter();
++        auto first = isosp;
++        auto last = isosp+npion;
++        for (auto i = last - first - 1; i > 0; --i) {
++            using std::swap;
++            swap(first[i], first[r(i + 1)]);
++        }
++
+         inter2Part(0.5);
+     }
+
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLPhaseSpaceKopylov.cc geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLPhaseSpaceKopylov.cc
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLPhaseSpaceKopylov.cc	2017-01-27 04:24:56
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLPhaseSpaceKopylov.cc	2024-09-24 10:55:25
+@@ -69,7 +69,7 @@ namespace G4INCL {
+     const size_t N = particles.size();
+     masses.resize(N);
+     sumMasses.resize(N);
+-    std::transform(particles.begin(), particles.end(), masses.begin(), std::mem_fun(&Particle::getMass));
++    std::transform(particles.begin(), particles.end(), masses.begin(), std::mem_fn(&Particle::getMass));
+     std::partial_sum(masses.begin(), masses.end(), sumMasses.begin());
+
+     G4double PFragMagCM = 0.0;
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLPhaseSpaceRauboldLynch.cc geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLPhaseSpaceRauboldLynch.cc
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLPhaseSpaceRauboldLynch.cc	2017-01-27 04:24:56
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLPhaseSpaceRauboldLynch.cc	2024-09-24 10:54:24
+@@ -240,7 +240,7 @@ namespace G4INCL {
+     // masses and sum of masses
+     masses.resize(nParticles);
+     sumMasses.resize(nParticles);
+-    std::transform(particles.begin(), particles.end(), masses.begin(), std::mem_fun(&Particle::getMass));
++    std::transform(particles.begin(), particles.end(), masses.begin(), std::mem_fn(&Particle::getMass));
+     std::partial_sum(masses.begin(), masses.end(), sumMasses.begin());
+
+     // sanity check
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLPiNToMultiPionsChannel.cc geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLPiNToMultiPionsChannel.cc
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLPiNToMultiPionsChannel.cc	2017-01-27 04:24:56
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLPiNToMultiPionsChannel.cc	2024-09-24 10:52:09
+@@ -269,7 +269,15 @@ namespace G4INCL {
+             }
+         }
+
+-        std::random_shuffle(isosp,isosp+npion,Random::getAdapter()); // isospin randomly distributed
++        //std::random_shuffle(isosp,isosp+npion,Random::getAdapter()); // isospin randomly distributed
++        auto&& r = Random::getAdapter();
++        auto first = isosp;
++        auto last = isosp+npion;
++        for (auto i = last - first - 1; i > 0; --i) {
++            using std::swap;
++            swap(first[i], first[r(i + 1)]);
++        }
++
+     }
+
+ }
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLCascade.cc geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLCascade.cc
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLCascade.cc	2017-01-27 04:24:56
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLCascade.cc	2024-09-24 10:43:55
+@@ -490,7 +490,15 @@ namespace G4INCL {
+     ParticleList const &initialProjectileComponents = theProjectileRemnant->getParticles();
+     std::vector<Particle *> shuffledComponents(initialProjectileComponents.begin(), initialProjectileComponents.end());
+     // Shuffle the list of potential participants
+-    std::random_shuffle(shuffledComponents.begin(), shuffledComponents.end(), Random::getAdapter());
++    //std::random_shuffle(shuffledComponents.begin(), shuffledComponents.end(), Random::getAdapter());
++    auto&& r = Random::getAdapter();
++    auto first = shuffledComponents.begin();
++    auto last = shuffledComponents.end();
++    for (auto i = last - first - 1; i > 0; --i) {
++      using std::swap;
++      swap(first[i], first[r(i + 1)]);
++    }
++
+
+     G4bool success = true;
+     G4bool atLeastOneNucleonEntering = false;
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLCDPP.cc geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLCDPP.cc
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLCDPP.cc	2017-01-27 04:24:56
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/src/G4INCLCDPP.cc	2024-09-24 10:41:28
+@@ -59,8 +59,12 @@ namespace G4INCL {
+     Sk = 0.0;
+     TbelowTf = 0.0;
+
+-    std::for_each(remnantParticles.begin(), remnantParticles.end(), std::bind1st(std::mem_fun(&G4INCL::CDPP::processOneParticle), this));
+-    std::for_each(created.begin(), created.end(), std::bind1st(std::mem_fun(&G4INCL::CDPP::processOneParticle), this));
++    std::for_each(remnantParticles.begin(), remnantParticles.end(),
++                  [this](Particle const * const p){ this->G4INCL::CDPP::processOneParticle(p); }
++                  );
++    std::for_each(created.begin(), created.end(),
++                  [this](Particle const * const p){ this->G4INCL::CDPP::processOneParticle(p); }
++                  );
+
+     const G4double Tinitial = nucleus->getInitialInternalEnergy();
+     const G4double Eblock = TbelowTf - Tinitial - Sk - S;
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/include/G4INCLProjectileRemnant.hh geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/include/G4INCLProjectileRemnant.hh
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/include/G4INCLProjectileRemnant.hh	2017-01-27 04:24:56
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/incl_physics/include/G4INCLProjectileRemnant.hh	2024-09-23 19:31:52
+@@ -227,7 +227,14 @@ namespace G4INCL {
+     /// \brief Shuffle the list of stored projectile components
+     ParticleList shuffleStoredComponents() {
+       ParticleList pL = getStoredComponents();
+-      std::random_shuffle(pL.begin(), pL.end(), Random::getAdapter());
++      auto&& r = Random::getAdapter();
++      auto first = pL.begin();
++      auto last = pL.end();
++      //std::iterator_traits<ParticleList>::difference_type diff_t;
++      for (auto i = last - first - 1; i > 0; --i) {
++        using std::swap;
++        swap(first[i], first[r(i + 1)]);
++      }
+       return pL;
+     }
+
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/utils/src/G4INCLInterpolationTable.cc geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/utils/src/G4INCLInterpolationTable.cc
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/utils/src/G4INCLInterpolationTable.cc	2017-01-27 04:24:56
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/inclxx/utils/src/G4INCLInterpolationTable.cc	2024-09-23 16:58:22
+@@ -67,14 +67,14 @@ namespace G4INCL {
+   std::vector<G4double> InterpolationTable::getNodeAbscissae() const {
+     std::vector<G4double> x(nodes.size());
+     std::transform(nodes.begin(), nodes.end(), x.begin(),
+-                   std::mem_fun_ref(&InterpolationNode::getX));
++                   std::mem_fn(&InterpolationNode::getX));
+     return x;
+   }
+
+   std::vector<G4double> InterpolationTable::getNodeValues() const {
+     std::vector<G4double> y(nodes.size());
+     std::transform(nodes.begin(), nodes.end(), y.begin(),
+-                   std::mem_fun_ref(&InterpolationNode::getY));
++                   std::mem_fn(&InterpolationNode::getY));
+     return y;
+   }
+
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/de_excitation/multifragmentation/src/G4StatMFChannel.cc geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/de_excitation/multifragmentation/src/G4StatMFChannel.cc
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/de_excitation/multifragmentation/src/G4StatMFChannel.cc	2017-01-27 04:24:56
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/de_excitation/multifragmentation/src/G4StatMFChannel.cc	2024-09-23 16:40:59
+@@ -43,7 +43,7 @@
+ #include "G4Pow.hh"
+ #include "G4Exp.hh"
+
+-class SumCoulombEnergy : public std::binary_function<G4double,G4double,G4double>
++class SumCoulombEnergy
+ {
+ public:
+   SumCoulombEnergy() : total(0.0) {}
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/cascade/cascade/src/G4NucleiModel.cc geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/cascade/cascade/src/G4NucleiModel.cc
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/cascade/cascade/src/G4NucleiModel.cc	2024-09-23 16:21:30
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/cascade/cascade/src/G4NucleiModel.cc	2024-09-23 16:23:47
+@@ -1264,7 +1264,7 @@ void G4NucleiModel::choosePointAlongTraj(G4CascadParti
+
+   // Normalize CDF to unit integral
+   std::transform(wtlen.begin(), wtlen.end(), wtlen.begin(),
+-		 std::bind2nd(std::divides<G4double>(), wtlen.back()));
++		 std::bind(std::divides<G4double>(), std::placeholders::_1, wtlen.back()));
+
+   if (verboseLevel > 3) {
+     G4cout << " weights";
+
+
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/de_excitation/multifragmentation/include/G4StatMFMicroCanonical.hh geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/de_excitation/multifragmentation/include/G4StatMFMicroCanonical.hh
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/processes/hadronic/models/de_excitation/multifragmentation/include/G4StatMFMicroCanonical.hh	2017-01-27 04:24:56
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/processes/hadronic/models/de_excitation/multifragmentation/include/G4StatMFMicroCanonical.hh	2024-09-23 16:02:54
+@@ -110,7 +110,7 @@ class G4StatMFMicroCanonical : public G4VStatMFEnsembl
+     }
+   };
+
+-  class SumProbabilities : public std::binary_function<G4double,G4double,G4double>
++  class SumProbabilities
+   {
+   public:
+     SumProbabilities() : total(0.0) {}
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/geometry/management/include/G4SmartVoxelStat.hh geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/geometry/management/include/G4SmartVoxelStat.hh
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/geometry/management/include/G4SmartVoxelStat.hh	2017-01-27 04:24:59
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/geometry/management/include/G4SmartVoxelStat.hh	2024-09-23 15:56:26
+@@ -106,8 +106,6 @@ class G4SmartVoxelStat
+     // Functor objects for sorting
+     //
+     struct ByCpu
+-      : public std::binary_function< const G4SmartVoxelStat,
+-                                     const G4SmartVoxelStat, G4bool >
+     {
+       G4bool operator()( const G4SmartVoxelStat &a, const G4SmartVoxelStat &b )
+       {
+@@ -116,8 +114,6 @@ class G4SmartVoxelStat
+     };
+
+     struct ByMemory
+-      : public std::binary_function< const G4SmartVoxelStat,
+-                                     const G4SmartVoxelStat, G4bool >
+     {
+       G4bool operator()( const G4SmartVoxelStat &a, const G4SmartVoxelStat &b )
+       {
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/source/externals/clhep/src/mixmax.cc geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/externals/clhep/src/mixmax.cc
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/source/externals/clhep/src/mixmax.cc	2017-01-27 04:24:58
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/source/externals/clhep/src/mixmax.cc	2024-09-23 15:48:28
+@@ -254,7 +254,7 @@ inline myuint fmodmulM61(myuint cum, myuint s, myuint
+
+ inline myuint fmodmulM61(myuint cum, myuint s, myuint a)
+ {
+-    register myuint o,ph,pl,ah,al;
++    myuint o,ph,pl,ah,al;
+     o=(s)*a;
+     ph = ((s)>>32);
+     pl = (s) & MASK32;
+diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/cmake/Modules/Geant4LibraryBuildOptions.cmake geant4_v10.02.p03_patched/geant4_v10.02.p03-source/cmake/Modules/Geant4LibraryBuildOptions.cmake
+--- geant4_v10.02.p03/geant4_v10.02.p03-source/cmake/Modules/Geant4LibraryBuildOptions.cmake	2017-01-27 04:25:00
++++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/cmake/Modules/Geant4LibraryBuildOptions.cmake	2024-09-23 15:35:43
+@@ -76,7 +76,7 @@ enum_option(GEANT4_BUILD_CXXSTD
+ # Mark as advanced because most users will not need it
+ enum_option(GEANT4_BUILD_CXXSTD
+   DOC "C++ Standard to compile against"
+-  VALUES 11 14 c++11 c++14
++  VALUES 11 14 17 c++11 c++14 c++17
+   CASE_INSENSITIVE
+   )
+
 diff -rupN geant4_v10.02.p03/geant4_v10.02.p03-source/cmake/Modules/Geant4InstallData.cmake geant4_v10.02.p03_patched/geant4_v10.02.p03-source/cmake/Modules/Geant4InstallData.cmake
 --- geant4_v10.02.p03/geant4_v10.02.p03-source/cmake/Modules/Geant4InstallData.cmake	2017-01-27 04:25:00.000000000 -0800
 +++ geant4_v10.02.p03_patched/geant4_v10.02.p03-source/cmake/Modules/Geant4InstallData.cmake	2023-02-17 10:38:59.000000000 -0800
diff --git a/src/fretalon/framework/src/MGUIMainFretalon.cxx b/src/fretalon/framework/src/MGUIMainFretalon.cxx
index ea19e5fc6..7a57da05f 100644
--- a/src/fretalon/framework/src/MGUIMainFretalon.cxx
+++ b/src/fretalon/framework/src/MGUIMainFretalon.cxx
@@ -32,6 +32,7 @@
 #include <TGFrame.h>
 #include <TGClient.h>
 #include <TGResourcePool.h>
+#include <TSystem.h>
 
 // MEGAlib libs:
 #include "MStreams.h"
diff --git a/src/fretalon/framework/src/MModule.cxx b/src/fretalon/framework/src/MModule.cxx
index 68f497cf5..abc9145c4 100644
--- a/src/fretalon/framework/src/MModule.cxx
+++ b/src/fretalon/framework/src/MModule.cxx
@@ -29,6 +29,7 @@
 // Standard libs:
 
 // ROOT libs:
+#include "TSystem.h"
 
 // MEGAlib libs:
 #include "MModuleReadOutAssemblyQueues.h"
diff --git a/src/fretalon/melinator/src/MGUIMainMelinator.cxx b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
index af4d56ad9..f1e94ad9b 100644
--- a/src/fretalon/melinator/src/MGUIMainMelinator.cxx
+++ b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
@@ -26,6 +26,7 @@
 using namespace std;
 
 // ROOT libs:
+#include <TSystem.h>
 #include <KeySymbols.h>
 #include <TApplication.h>
 #include <TGPicture.h>
diff --git a/src/geomega/src/MDGDMLImport.cxx b/src/geomega/src/MDGDMLImport.cxx
index f9e9e07b3..3ecb10a87 100644
--- a/src/geomega/src/MDGDMLImport.cxx
+++ b/src/geomega/src/MDGDMLImport.cxx
@@ -22,6 +22,7 @@
 // Standard libs:
 
 // ROOT libs:
+#include "TSystem.h"
 #include "TList.h"
 #include "TGeoBBox.h"
 #include "TGeoNode.h"
diff --git a/src/geomega/src/MGUIGeomegaMain.cxx b/src/geomega/src/MGUIGeomegaMain.cxx
index 86de7efb7..4ee9d11fe 100644
--- a/src/geomega/src/MGUIGeomegaMain.cxx
+++ b/src/geomega/src/MGUIGeomegaMain.cxx
@@ -22,7 +22,8 @@
 // Standard libs:
 
 // ROOT libs:
-#include <TGPicture.h>
+#include "TGPicture.h"
+#include "TSystem.h"
 
 // MEBAlib libs:
 #include "MGUIAbout.h"
diff --git a/src/geomega/src/MInterfaceGeomega.cxx b/src/geomega/src/MInterfaceGeomega.cxx
index 92521c6bb..c5d32097b 100644
--- a/src/geomega/src/MInterfaceGeomega.cxx
+++ b/src/geomega/src/MInterfaceGeomega.cxx
@@ -34,6 +34,7 @@ using namespace std;
 
 // ROOT libs:
 #include "TROOT.h"
+#include "TSystem.h"
 #include "MString.h"
 #include "TCanvas.h"
 #include "TView.h"
diff --git a/src/global/misc/inc/MGlobal.h b/src/global/misc/inc/MGlobal.h
index b26d88d9b..02f0ce5d5 100644
--- a/src/global/misc/inc/MGlobal.h
+++ b/src/global/misc/inc/MGlobal.h
@@ -80,10 +80,7 @@
 #ifndef __MGlobal__
 #define __MGlobal__
 
-#include "TROOT.h"
-#include "TSystem.h"
 #include "TMutex.h"
-#include "TVirtualMutex.h"
 
 #include "MVector.h"
 #include "MString.h"
diff --git a/src/global/misc/src/MBinnerFISBEL.cxx b/src/global/misc/src/MBinnerFISBEL.cxx
index 78c7d2da0..e33e6a349 100644
--- a/src/global/misc/src/MBinnerFISBEL.cxx
+++ b/src/global/misc/src/MBinnerFISBEL.cxx
@@ -29,6 +29,7 @@ using namespace std;
 #include "TMath.h"
 #include "TH2.h"
 #include "TCanvas.h"
+#include "TSystem.h"
 
 // MEGAlib libs:
 #include "MExceptions.h"
diff --git a/src/mimrec/src/MGUIMimrecMain.cxx b/src/mimrec/src/MGUIMimrecMain.cxx
index e4ac6ba75..be10273a1 100644
--- a/src/mimrec/src/MGUIMimrecMain.cxx
+++ b/src/mimrec/src/MGUIMimrecMain.cxx
@@ -22,7 +22,8 @@
 // Standard libs:
 
 // ROOT libs:
-#include <TGPicture.h>
+#include "TSystem.h"
+#include "TGPicture.h"
 
 // MEGAlib libs:
 #include "MStreams.h"
diff --git a/src/revan/src/MGUIRevanMain.cxx b/src/revan/src/MGUIRevanMain.cxx
index a5ae48088..079dd4ebf 100644
--- a/src/revan/src/MGUIRevanMain.cxx
+++ b/src/revan/src/MGUIRevanMain.cxx
@@ -24,7 +24,8 @@
 using namespace std;
 
 // ROOT libs:
-#include <TGPicture.h>
+#include "TSystem.h"
+#include "TGPicture.h"
 
 // MEGAlib libs:
 #include "MGUIAbout.h"
diff --git a/src/sivan/src/MGUISivanMain.cxx b/src/sivan/src/MGUISivanMain.cxx
index 8f6458412..c2029ee8d 100644
--- a/src/sivan/src/MGUISivanMain.cxx
+++ b/src/sivan/src/MGUISivanMain.cxx
@@ -22,8 +22,9 @@
 // Standard libs:
 
 // ROOT libs:
-#include <TGPicture.h>
-#include <TStyle.h>
+#include "TSystem.h"
+#include "TGPicture.h"
+#include "TStyle.h"
 
 // MEGAlib libs:
 #include "MGUIAbout.h"

From 094d35965040367a297d277c4de803b400eca61a Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Wed, 30 Apr 2025 10:09:00 -0700
Subject: [PATCH 129/192] CHG: Require ROOT 6.34

---
 config/AllowedROOTVersions.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/AllowedROOTVersions.txt b/config/AllowedROOTVersions.txt
index cfee3c9ec..d3bead3dc 100644
--- a/config/AllowedROOTVersions.txt
+++ b/config/AllowedROOTVersions.txt
@@ -1 +1 @@
-632 
+634 

From ae0db87c65130e20a5d382d90216b3f7943b9cb2 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Sun, 11 May 2025 04:21:52 -0700
Subject: [PATCH 130/192] ADD: New exception: MExceptionValueNotFound

---
 src/global/misc/inc/MExceptions.h   | 70 ++++++++++++++++++++++++++++-
 src/global/misc/src/MExceptions.cxx |  1 +
 2 files changed, 69 insertions(+), 2 deletions(-)

diff --git a/src/global/misc/inc/MExceptions.h b/src/global/misc/inc/MExceptions.h
index 4f75c0e35..2232e3fd3 100644
--- a/src/global/misc/inc/MExceptions.h
+++ b/src/global/misc/inc/MExceptions.h
@@ -114,8 +114,8 @@ class MExceptionTestFailed : public MException
 ////////////////////////////////////////////////////////////////////////////////
 
 
-//! This exception is thrown when a parmeter is out of range and 
-//! the error cannot be reconvered gracefully
+//! This exception is thrown when a parameter is out of range and
+//! the error cannot be recovered gracefully
 class MExceptionParameterOutOfRange : public MException
 {
 public:
@@ -184,6 +184,72 @@ class MExceptionIndexOutOfBounds : public MException
 ////////////////////////////////////////////////////////////////////////////////
 
 
+//! This exception is thrown when an value cannot be found (e.g. in a map or vector) and
+//! the error cannot be recovered gracefully
+//! This class would ideal for using templeates, but ROOT does not allow that
+class MExceptionValueNotFound : public MException
+{
+public:
+  //! Default constructor
+  MExceptionValueNotFound() : MException() {
+    m_Description = "Value not found!";
+  }
+  //! Constructor giving the not found value and a descriptor where the value cannot be found, e.g. "vector of strip IDs"
+  MExceptionValueNotFound(double& Value, const MString& Where) : MException() {
+    Set(Value, Where);
+  }
+  //! Constructor giving the not found value and a descriptor where the value cannot be found, e.g. "vector of strip IDs"
+  MExceptionValueNotFound(int& Value, const MString& Where) : MException() {
+    Set(Value, Where);
+  }
+  //! Constructor giving the not found value and a descriptor where the value cannot be found, e.g. "vector of strip IDs"
+  MExceptionValueNotFound(unsigned int& Value, const MString& Where) : MException() {
+    Set(Value, Where);
+  }
+  //! Constructor giving the not found value and a descriptor where the value cannot be found, e.g. "vector of strip IDs"
+  MExceptionValueNotFound(MString& Value, const MString& Where) : MException() {
+    Set(Value, Where);
+  }
+  //! Default destructor
+  virtual ~MExceptionValueNotFound() throw() {}
+  //! Set the not found value and a descriptor where the value cannot be found, e.g. "vector of strip IDs"
+  void Set(double& Value, const MString& Where) {
+    ostringstream stream;
+    stream<<"The value \'"<<Value<<"\' cannot be found in "<<Where<<"."<<endl;
+    m_Description = stream.str();
+  }
+  //! Set the not found value and a descriptor where the value cannot be found, e.g. "vector of strip IDs"
+  void Set(unsigned int& Value, const MString& Where) {
+    ostringstream stream;
+    stream<<"The value \'"<<Value<<"\' cannot be found in "<<Where<<"."<<endl;
+    m_Description = stream.str();
+  }
+  //! Set the not found value and a descriptor where the value cannot be found, e.g. "vector of strip IDs"
+  void Set(int& Value, const MString& Where) {
+    ostringstream stream;
+    stream<<"The value \'"<<Value<<"\' cannot be found in "<<Where<<"."<<endl;
+    m_Description = stream.str();
+  }
+  //! Set the not found value and a descriptor where the value cannot be found, e.g. "vector of strip IDs"
+  void Set(MString& Value, const MString& Where) {
+    ostringstream stream;
+    stream<<"The value \'"<<Value<<"\' cannot be found in "<<Where<<"."<<endl;
+    m_Description = stream.str();
+  }
+
+private:
+
+
+#ifdef ___CLING___
+public:
+  ClassDef(MExceptionValueNotFound, 1)
+#endif
+};
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
 //! This exception is thrown when an index is out-of-bounds and 
 //! the error cannot be recovered gracefully
 class MExceptionEmptyArray : public MException
diff --git a/src/global/misc/src/MExceptions.cxx b/src/global/misc/src/MExceptions.cxx
index 7992477c4..a2517b433 100644
--- a/src/global/misc/src/MExceptions.cxx
+++ b/src/global/misc/src/MExceptions.cxx
@@ -41,6 +41,7 @@ ClassImp(MException)
 ClassImp(MExceptionTestFailed)
 ClassImp(MExceptionParameterOutOfRange)
 ClassImp(MExceptionIndexOutOfBounds)
+ClassImp(MExceptionValueNotFound)
 ClassImp(MExceptionEmptyArray)
 ClassImp(MExceptionValueOutOfBounds)
 ClassImp(MExceptionDivisionByZero)

From ab45652eff0e84dd071efcbadf64be3db9bf9aee Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Wed, 30 Apr 2025 20:03:02 -0700
Subject: [PATCH 131/192] ADD: New report feature, fixed Ba-133 only
 calibration

---
 resource/libraries/Calibration.isotopes       |   4 +-
 .../src/MCalibrateEnergyAssignEnergies.cxx    |  43 +++
 .../melinator/inc/MGUIMainMelinator.h         |   3 +
 src/fretalon/melinator/inc/MMelinator.h       |   7 +-
 .../melinator/src/MGUIMainMelinator.cxx       |  37 ++-
 src/fretalon/melinator/src/MMelinator.cxx     | 299 ++++++++++++++++++
 src/global/misc/inc/MIsotope.h                |  16 +-
 src/global/misc/src/MIsotope.cxx              |  46 ++-
 8 files changed, 429 insertions(+), 26 deletions(-)

diff --git a/resource/libraries/Calibration.isotopes b/resource/libraries/Calibration.isotopes
index 39b193d27..803fa5c4a 100644
--- a/resource/libraries/Calibration.isotopes
+++ b/resource/libraries/Calibration.isotopes
@@ -31,10 +31,10 @@ Ba  133    34.987  11.6     E
 Ba  133    35.818   3.58    E
 Ba  133    53.161   2.199   E
 # Ba  133    79.614   2.62    E  this mini line just screws things up in melinator -- we pretend we do not know it...
-Ba  133    80.997  34.06    D 
+Ba  133    80.997  34.06    P 
 Ba  133   276.398   7.164   
 Ba  133   302.853  18.33   
-Ba  133   356.017  62.05    
+Ba  133   356.017  62.05    S
 Ba  133   383.851   8.94
 
 # 137-Cs
diff --git a/src/fretalon/base/src/MCalibrateEnergyAssignEnergies.cxx b/src/fretalon/base/src/MCalibrateEnergyAssignEnergies.cxx
index bb077d8d4..88600eef3 100644
--- a/src/fretalon/base/src/MCalibrateEnergyAssignEnergies.cxx
+++ b/src/fretalon/base/src/MCalibrateEnergyAssignEnergies.cxx
@@ -224,6 +224,7 @@ bool MCalibrateEnergyAssignEnergies::CalibrateLinear()
   if (g_Verbosity >= c_Info) cout<<endl<<"Assigning energies via linear method"<<endl;
   
   // Inventory:
+  unsigned int TotalNumberOfGoodPoints = 0;
   bool NoROGHasMoreThanOneGoodSpectralPoint = true;
   if (g_Verbosity >= c_Info) cout<<"Current line inventory: "<<endl;
   for (unsigned int r = 0; r < m_Results.GetNumberOfReadOutDataGroups(); ++r) {
@@ -234,6 +235,7 @@ bool MCalibrateEnergyAssignEnergies::CalibrateLinear()
       } else {
         if (g_Verbosity >= c_Info) cout<<"Included: "<<m_Results.GetSpectralPoint(r, p)<<endl;
         ++NumberOfGoodPoints;
+        ++TotalNumberOfGoodPoints;
       }
     }
     if (NumberOfGoodPoints > 1) {
@@ -265,6 +267,47 @@ bool MCalibrateEnergyAssignEnergies::CalibrateLinear()
     return true;
   }
   
+  // Special case: We have one ROG with one isotope (which has a primary and secondary line) with two spectral points - this handles Ba-133 only calibrations:
+  if (m_Results.GetNumberOfReadOutDataGroups() == 1 && m_Isotopes[0].size() == 1 && m_Isotopes[0][0].GetPrimaryLine() != -1 && m_Isotopes[0][0].GetSecondaryLine() != -1 && TotalNumberOfGoodPoints == 2) {
+
+    if (g_Verbosity >= c_Info) cout<<"Assign energies: Special case with 1 ROG, 1 isotope with 2 spectral point"<<endl;
+
+    unsigned int r = 0; // our single ROG
+    unsigned int i = 0; // our single Isotope
+    int PrimaryLineID = m_Isotopes[r][i].GetPrimaryLine();
+    int SecondaryLineID = m_Isotopes[r][i].GetSecondaryLine();
+
+    vector<unsigned int> GoodSpectralPointIDs;
+    for (unsigned int p = 0; p < m_Results.GetNumberOfSpectralPoints(r); ++p) {
+      if (m_Results.GetSpectralPoint(r, p).IsGood() == true) {
+        GoodSpectralPointIDs.push_back(p);
+      }
+    }
+
+    unsigned int plow = 0;
+    unsigned int phigh = 0;
+    if (m_Results.GetSpectralPoint(r, GoodSpectralPointIDs[0]).GetPeak() < m_Results.GetSpectralPoint(r, GoodSpectralPointIDs[1]).GetPeak()) {
+      plow = GoodSpectralPointIDs[0];
+      phigh = GoodSpectralPointIDs[1];
+    } else {
+      plow = GoodSpectralPointIDs[1];
+      phigh = GoodSpectralPointIDs[0];
+    }
+
+    if (m_Isotopes[r][0].GetLineEnergy(PrimaryLineID) < m_Isotopes[r][0].GetLineEnergy(SecondaryLineID)) {
+      m_Results.GetSpectralPoint(r, plow).SetIsotope(m_Isotopes[r][0]);
+      m_Results.GetSpectralPoint(r, plow).SetEnergy(m_Isotopes[r][0].GetLineEnergy(PrimaryLineID));
+      m_Results.GetSpectralPoint(r, phigh).SetIsotope(m_Isotopes[r][0]);
+      m_Results.GetSpectralPoint(r, phigh).SetEnergy(m_Isotopes[r][0].GetLineEnergy(SecondaryLineID));
+    } else {
+      m_Results.GetSpectralPoint(r, plow).SetIsotope(m_Isotopes[r][0]);
+      m_Results.GetSpectralPoint(r, plow).SetEnergy(m_Isotopes[r][0].GetLineEnergy(SecondaryLineID));
+      m_Results.GetSpectralPoint(r, phigh).SetIsotope(m_Isotopes[r][0]);
+      m_Results.GetSpectralPoint(r, phigh).SetEnergy(m_Isotopes[r][0].GetLineEnergy(PrimaryLineID));
+    }
+
+    return true;
+  }
   
   
   // Create a list of spectral points
diff --git a/src/fretalon/melinator/inc/MGUIMainMelinator.h b/src/fretalon/melinator/inc/MGUIMainMelinator.h
index 1f7e916b0..e17782606 100644
--- a/src/fretalon/melinator/inc/MGUIMainMelinator.h
+++ b/src/fretalon/melinator/inc/MGUIMainMelinator.h
@@ -111,6 +111,8 @@ class MGUIMainMelinator : public TGMainFrame
   virtual bool OnLoad();
   //! Actions when the save as button has been pressed
   virtual bool OnSaveAs();
+  //! Actions when the show report as button has been pressed
+  virtual bool OnShowReport();
   //! Actions when the next button has been pressed
   virtual bool OnNext();
   //! Actions when the back button has been pressed
@@ -285,6 +287,7 @@ class MGUIMainMelinator : public TGMainFrame
   static const int c_CalibrationModelDeterminationMethodFittingFWHMModel    =  73;
   static const int c_Save                       =  80;
   static const int c_SaveAs                     =  81;
+  static const int c_ShowReport                 =  90;
   static const int c_Remove                     = 400;
   static const int c_Options                    = 500;
   static const int c_Change                     = 600;
diff --git a/src/fretalon/melinator/inc/MMelinator.h b/src/fretalon/melinator/inc/MMelinator.h
index 86685900d..2c41e3559 100644
--- a/src/fretalon/melinator/inc/MMelinator.h
+++ b/src/fretalon/melinator/inc/MMelinator.h
@@ -160,10 +160,13 @@ class MMelinator
   
   //! Remove all collection which don't have positive data entries
   //void RemoveCollectionsWithNoPositiveEntries() { m_Store.RemoveCollectionsWithNoPositiveEntries(); }
- 
+
   //! Save the calibration in e-cal format
   bool Save(MString FileName);
-  
+
+  //! Create a calibration report
+  bool CreateReport();
+
   //! Dump a string
   virtual MString ToString() const;  
   
diff --git a/src/fretalon/melinator/src/MGUIMainMelinator.cxx b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
index af4d56ad9..2da7aa7fc 100644
--- a/src/fretalon/melinator/src/MGUIMainMelinator.cxx
+++ b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
@@ -169,10 +169,6 @@ void MGUIMainMelinator::Create()
   MenuFiles->AddEntry("Choose files and isotopes", c_ChooseCalibrationFiles);
   MenuFiles->AddEntry("Load files", c_LoadLast);
   MenuFiles->AddSeparator();
-  MenuFiles->AddLabel("Calibration result");
-  MenuFiles->AddEntry("Save As...", c_SaveAs);
-  MenuFiles->AddEntry("Save", c_Save);
-  MenuFiles->AddSeparator();
   MenuFiles->AddLabel("Configuration file");
   //MenuFiles->AddEntry("Open", c_LoadConfig);
   MenuFiles->AddEntry("Open -> use command line at launch", c_LoadConfig);
@@ -183,7 +179,18 @@ void MGUIMainMelinator::Create()
   MenuFiles->AddSeparator();
   MenuFiles->AddEntry("Exit", c_Exit);
   MenuFiles->Associate(this);
-  MenuBar->AddPopup("Files", MenuFiles, MenuBarItemLayoutLeft);
+  MenuBar->AddPopup("Input", MenuFiles, MenuBarItemLayoutLeft);
+
+  TGPopupMenu* MenuResults = new TGPopupMenu(gClient->GetRoot());
+  MenuResults->AddLabel("Calibration file");
+  MenuResults->AddEntry("Save As...", c_SaveAs);
+  MenuResults->AddEntry("Save", c_Save);
+  MenuResults->AddSeparator();
+  MenuResults->AddLabel("Calibration report");
+  MenuResults->AddEntry("Create and Show", c_ShowReport);
+  //MenuResults->AddSeparator();
+  MenuResults->Associate(this);
+  MenuBar->AddPopup("Output", MenuResults, MenuBarItemLayoutLeft);
 
   TGPopupMenu* MenuInfo = new TGPopupMenu(fClient->GetRoot());
   MenuInfo->AddEntry("About", c_About);
@@ -932,6 +939,10 @@ bool MGUIMainMelinator::ProcessMessage(long Message, long Parameter1, long Param
         Status = OnSaveAs();
         break;
 
+      case c_ShowReport:
+        Status = OnShowReport();
+        break;
+
       case c_About:
         Status = OnAbout();
         break;
@@ -1442,6 +1453,22 @@ bool MGUIMainMelinator::OnSaveAs()
 ////////////////////////////////////////////////////////////////////////////////
 
 
+//! Actions when the show report button has been pressed
+bool MGUIMainMelinator::OnShowReport()
+{
+  bool Return = m_Melinator.CreateReport();
+
+  if (Return == false) {
+    mgui<<"Unable to create calibration report"<<error;
+  }
+
+  return Return;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
 bool MGUIMainMelinator::OnLoad()
 {  
   return false;
diff --git a/src/fretalon/melinator/src/MMelinator.cxx b/src/fretalon/melinator/src/MMelinator.cxx
index 645ef1424..779d9b2b9 100644
--- a/src/fretalon/melinator/src/MMelinator.cxx
+++ b/src/fretalon/melinator/src/MMelinator.cxx
@@ -27,6 +27,8 @@
 #include "MMelinator.h"
 
 // Standard libs:
+#include <pwd.h>
+#include <unistd.h>
 #include <algorithm>
 #include <new>
 #include <map>
@@ -45,6 +47,11 @@ using namespace std;
 #include "TGaxis.h"
 #include "TGraphErrors.h"
 #include "TSystem.h"
+#include "TH2.h"
+#include "TPaveText.h"
+#include "TPad.h"
+#include "TCanvas.h"
+#include "TLatex.h"
 
 // MEGAlib libs:
 #include "MFile.h"
@@ -1571,6 +1578,298 @@ bool MMelinator::Save(MString FileName)
 ////////////////////////////////////////////////////////////////////////////////
 
 
+//! Create a calibration report
+bool MMelinator::CreateReport()
+{
+  // Create a calibration report
+
+  double MaxADCs = 5000;
+  double MaxEnergy = 500;
+  MString OutputFileName = "MelinatorReport.pdf";
+
+
+  // Section 1: Create histograms
+
+  TH2D* AllFittedEnergies = new TH2D("Fitted", "Fitted", MaxEnergy/2, 0, MaxEnergy, m_CalibrationStore.GetNumberOfElements()+1, -0.5, m_CalibrationStore.GetNumberOfElements() + 0.5);
+  AllFittedEnergies->SetXTitle("Energy [keV]");
+  AllFittedEnergies->SetYTitle("ReadOutUnit ID");
+  AllFittedEnergies->SetContour(99);
+
+
+  TH2D* AllRawADCs = new TH2D("RawADCs", "RawADCs", MaxADCs/4, 0, MaxADCs, m_CalibrationStore.GetNumberOfElements()+1, -0.5, m_CalibrationStore.GetNumberOfElements() + 0.5);
+  AllRawADCs->SetXTitle("ADCs [rou's]");
+  AllRawADCs->SetYTitle("ReadOutUnit ID");
+  AllRawADCs->SetContour(99);
+
+
+  // If we have double-sided strips make one histogram per detector and side
+  map<pair<unsigned int, bool>, MString> TitlesMap;
+  map<pair<unsigned int, bool>, TH2D*> RawADCsMap;
+  map<pair<unsigned int, bool>, TH2D*> FittedEnergiesMap;
+  if (m_CalibrationStore.GetReadOutElement(0).IsOfType("doublesidedstrip") == true) {
+    // Step 1: Maximum strip ID
+    unsigned int MaxStripID = 0;
+    for (unsigned int c = 0; c < m_CalibrationStore.GetNumberOfElements(); ++c) {
+      MReadOutElement& ROE = m_CalibrationStore.GetReadOutElement(c);
+      if (m_CalibrationStore.GetReadOutElement(c).IsOfType("doublesidedstrip") == true) {
+        MReadOutElementDoubleStrip& ROE_DS = static_cast<MReadOutElementDoubleStrip&>(ROE);
+        if (ROE_DS.GetStripID() > MaxStripID) {
+          MaxStripID = ROE_DS.GetStripID();
+        }
+      }
+    }
+    // Step 2: Create histograms
+    for (unsigned int c = 0; c < m_CalibrationStore.GetNumberOfElements(); ++c) {
+      MReadOutElement& ROE = m_CalibrationStore.GetReadOutElement(c);
+      if (m_CalibrationStore.GetReadOutElement(c).IsOfType("doublesidedstrip") == true) {
+        MReadOutElementDoubleStrip& ROE_DS = static_cast<MReadOutElementDoubleStrip&>(ROE);
+        pair<unsigned int, bool> DetectorAndSide = { ROE_DS.GetDetectorID(), ROE_DS.IsLowVoltageStrip() };
+        auto MapIter = RawADCsMap.find(DetectorAndSide);
+        if (MapIter == RawADCsMap.end()) {
+          MString Name = "Detector ";
+          Name += ROE_DS.GetDetectorID();
+          if (ROE_DS.IsLowVoltageStrip() == true) {
+            Name += ", low voltage side";
+          } else {
+            Name += ", high voltage side";
+          }
+
+          TitlesMap[DetectorAndSide] = Name;
+
+          RawADCsMap[DetectorAndSide] = new TH2D("", "ADC spectrum", MaxADCs/2, 0, MaxADCs, MaxStripID+1, -0.5, MaxStripID + 0.5);
+          RawADCsMap[DetectorAndSide]->SetXTitle("ADC units");
+          RawADCsMap[DetectorAndSide]->SetYTitle("Strip ID");
+          RawADCsMap[DetectorAndSide]->SetContour(99);
+
+          FittedEnergiesMap[DetectorAndSide] = new TH2D("", "Energy spectrum", MaxEnergy/2, 0, MaxEnergy, MaxStripID+1, -0.5, MaxStripID + 0.5);
+          FittedEnergiesMap[DetectorAndSide]->SetXTitle("Energy [keV]");
+          FittedEnergiesMap[DetectorAndSide]->SetYTitle("Strip ID");
+          FittedEnergiesMap[DetectorAndSide]->SetContour(99);
+        }
+      }
+    }
+  }
+
+
+
+  // Fill the plots
+
+  for (unsigned int c = 0; c < m_CalibrationStore.GetNumberOfElements(); ++c) {
+    MReadOutElement& ROE = m_CalibrationStore.GetReadOutElement(c);
+    TH2D* CurrentHistEnergy = nullptr;
+    TH2D* CurrentHistADCs = nullptr;
+    unsigned int CurrentStripID = 0;
+    if (m_CalibrationStore.GetReadOutElement(c).IsOfType("doublesidedstrip") == true) {
+      MReadOutElementDoubleStrip& ROE_DS = static_cast<MReadOutElementDoubleStrip&>(ROE);
+      pair<unsigned int, bool> DetectorAndSide = { ROE_DS.GetDetectorID(), ROE_DS.IsLowVoltageStrip() };
+      CurrentHistEnergy = FittedEnergiesMap[DetectorAndSide];
+      CurrentHistADCs = RawADCsMap[DetectorAndSide];
+      CurrentStripID = ROE_DS.GetStripID();
+    }
+    MCalibrationSpectrum* C = dynamic_cast<MCalibrationSpectrum*>(&(m_CalibrationStore.GetCalibration(c)));
+    MCalibrationModel& M = C->GetEnergyModel();
+
+    unsigned int IDofROC = m_Store.FindReadOutCollection(ROE);
+    if (IDofROC == g_UnsignedIntNotDefined) continue;
+    MReadOutCollection& ROC = m_Store.GetReadOutCollection(IDofROC);
+    for (unsigned int g = 0; g < ROC.GetNumberOfReadOutDataGroups(); ++g) {
+      MReadOutDataGroup& RODG = ROC.GetReadOutDataGroup(g);
+      for (unsigned int d = 0; d < RODG.GetNumberOfReadOutDatas(); ++d) {
+        MReadOutData& ROD = RODG.GetReadOutData(d);
+        MReadOutDataADCValue* ROD_ADC = dynamic_cast<MReadOutDataADCValue*>(ROD.Get(MReadOutDataADCValue::m_TypeID));
+        if (ROD_ADC != nullptr) {
+          double ADCs = ROD_ADC->GetADCValue();
+          double Energy = M.GetFitValue(ADCs);
+          AllFittedEnergies->Fill(Energy, c);
+          AllRawADCs->Fill(ADCs, c);
+          if (CurrentHistEnergy != nullptr) {
+            CurrentHistEnergy->Fill(Energy, CurrentStripID);
+            CurrentHistADCs->Fill(ADCs, CurrentStripID);
+          }
+        }
+      }
+    }
+  }
+
+
+  // Create the canvases
+
+  gROOT->SetBatch(true);
+
+  bool FoundHist = false;
+  auto IterTitles = TitlesMap.begin();
+  auto IterEnergy = FittedEnergiesMap.begin();
+  auto IterADCs = RawADCsMap.begin();
+
+  TCanvas* TitleCanvas = new TCanvas("Melinator Calibration Report", "Melinator Calibration Report", 850, 1100);
+  TitleCanvas->cd();
+
+  TPaveText* Title = new TPaveText(0.1, 0.75, 0.9, 0.9, "NDC");
+  Title->AddText("Melinator Calibration Report");
+  Title->SetTextFont(62);
+  Title->SetTextSize(0.05);
+  Title->SetFillColor(0);
+  Title->SetBorderSize(0);
+  Title->SetLineColor(0);
+  Title->Draw();
+
+
+
+  // Align text using TLatex
+  float yStart = 0.70;
+  float yStep = 0.03;
+  float xLabel = 0.195;
+  float xValue = 0.39;
+  unsigned int CurrentStep = 0;
+
+  TLatex* LatexLabel;
+  TLatex* LatexValue;
+
+  unsigned int TextFont = 42;
+  double TextSize = 0.02;
+
+
+  TString UserName = "";
+
+  struct passwd *pw = getpwuid(getuid());
+  if (pw && pw->pw_gecos && strlen(pw->pw_gecos) > 0) {
+    // Some systems use comma-separated GECOS fields: "Full Name,Room,Work Phone,..."
+    UserName = pw->pw_gecos;
+    Ssiz_t commaPos = UserName.First(',');
+    if (commaPos != kNPOS) {
+      UserName.Remove(commaPos);  // Only keep the full name
+    }
+  }
+
+  // Fall backs:
+  if (UserName.IsNull()) UserName = gSystem->Getenv("USER");
+  if (UserName.IsNull()) UserName = gSystem->Getenv("LOGNAME");
+  if (UserName.IsNull()) UserName = "unknown";
+
+  LatexLabel = new TLatex(xLabel, yStart - CurrentStep*yStep, "Created by:");
+  LatexLabel->SetTextFont(TextFont); LatexLabel->SetTextSize(TextSize); LatexLabel->Draw();
+  LatexValue = new TLatex(xValue, yStart - CurrentStep*yStep, UserName.Data());
+  LatexValue->SetTextFont(TextFont); LatexValue->SetTextSize(TextSize); LatexValue->Draw();
+  CurrentStep++;
+
+  TDatime Now;
+  TString DateTime = Form("%04d-%02d-%02d %02d:%02d:%02d", Now.GetYear(), Now.GetMonth(), Now.GetDay(),  Now.GetHour(), Now.GetMinute(), Now.GetSecond());
+
+  LatexLabel = new TLatex(xLabel, yStart - CurrentStep*yStep, "Created on:");
+  LatexLabel->SetTextFont(TextFont); LatexLabel->SetTextSize(TextSize); LatexLabel->Draw();
+  LatexValue = new TLatex(xValue, yStart - CurrentStep*yStep, DateTime);
+  LatexValue->SetTextFont(TextFont); LatexValue->SetTextSize(TextSize); LatexValue->Draw();
+  CurrentStep++;
+
+
+  TString GitHash = gSystem->GetFromPipe("cd $MEGALIB; git rev-parse --short HEAD");
+  if (GitHash.IsNull()) GitHash = "unknown";
+
+  LatexLabel = new TLatex(xLabel, yStart - CurrentStep*yStep, "MEGAlib git commit:");
+  LatexLabel->SetTextFont(TextFont); LatexLabel->SetTextSize(TextSize); LatexLabel->Draw();
+  LatexValue = new TLatex(xValue, yStart - CurrentStep*yStep, GitHash.Data());
+  LatexValue->SetTextFont(TextFont); LatexValue->SetTextSize(TextSize); LatexValue->Draw();
+  CurrentStep++;
+
+
+  LatexLabel = new TLatex(xLabel, yStart - CurrentStep*yStep, "Data sets:");
+  LatexLabel->SetTextFont(TextFont); LatexLabel->SetTextSize(TextSize); LatexLabel->Draw();
+
+  for (unsigned int f = 0; f < m_CalibrationFileNames.size(); ++f) {
+    MString FileName = m_CalibrationFileNames[f];
+    FileName = MFile::GetBaseName(FileName);
+    FileName += " (";
+    for (unsigned int i = 0; i < m_Isotopes[f].size(); ++i) {
+      FileName += m_Isotopes[f][i].GetName();
+      if (i < m_Isotopes[f].size() - 1) {
+        FileName += ", ";
+      }
+    }
+    FileName += ")";
+
+    LatexValue = new TLatex(xValue, yStart - CurrentStep*yStep, FileName.Data());
+    LatexValue->SetTextFont(TextFont); LatexValue->SetTextSize(TextSize); LatexValue->Draw();
+    CurrentStep++;
+  }
+
+
+  TitleCanvas->Print(OutputFileName + "(");
+
+
+  while (IterTitles != TitlesMap.end() && IterEnergy != FittedEnergiesMap.end() && IterADCs != RawADCsMap.end()) {
+    TCanvas* C = new TCanvas("", "", 850, 1100);
+    C->SetLogz();
+    C->cd();
+
+    TPad* TitlePad = new TPad("padTitle", "Title", 0.0, 0.9, 1.0, 1.0);
+    TitlePad->Draw();
+    TitlePad->cd();
+
+    TPaveText* Title = new TPaveText(0.0, 0.0, 1.0, 1.0, "brNDC");
+    Title->AddText(IterTitles->second);
+    Title->SetFillColor(0);     // No background color
+    Title->SetBorderSize(0);    // No border
+    Title->SetLineColor(0);     // Remove outline
+    Title->SetTextFont(TextFont);
+    Title->SetTextSize(0.4);
+    Title->Draw();
+
+    C->cd();
+
+    TPad* ADCPad = new TPad("ADCPad", "ADCPad", 0.0, 0.45, 1.0, 0.9);
+    ADCPad->Draw();
+    ADCPad->cd();
+    ADCPad->SetLogz();
+    IterADCs->second->Draw("colz");
+
+    C->cd();
+
+    TPad* EnergyPad = new TPad("EnergyPad", "EnergyPad", 0.0, 0.0, 1.0, 0.45);
+    EnergyPad->Draw();
+    EnergyPad->cd();
+    EnergyPad->SetLogz();
+    IterEnergy->second->Draw("colz");
+
+    C->cd();
+    C->Update();
+
+    if (next(IterTitles) == TitlesMap.end()) {
+      C->Print(OutputFileName + ")");  // close PDF
+    } else {
+      C->Print(OutputFileName);   // middle pages
+    }
+
+    FoundHist = true;
+
+    ++IterTitles;
+    ++IterEnergy;
+    ++IterADCs;
+  }
+
+  gROOT->SetBatch(false);
+
+
+  int Return = gSystem->Exec(MString("") + "[ -x \"$(command -v xdg-open)\" ] && xdg-open " + OutputFileName + " || { [ -x \"$(command -v open)\" ] && open " + OutputFileName + "; }");
+
+  if (Return != 0) {
+    mgui<<"Failed to open PDF. Return code: "<<Return<<error;
+  }
+
+  if (FoundHist == false) {
+    TCanvas* C = new TCanvas();
+    C->SetLogz();
+    C->cd();
+    AllFittedEnergies->Draw("colz");
+    C->Update();
+  }
+
+
+  return true;
+}
+
+////////////////////////////////////////////////////////////////////////////////
+
+
 //! Dump the content into a string
 MString MMelinator::ToString() const
 {
diff --git a/src/global/misc/inc/MIsotope.h b/src/global/misc/inc/MIsotope.h
index 8fc56f57f..64af5b4f5 100644
--- a/src/global/misc/inc/MIsotope.h
+++ b/src/global/misc/inc/MIsotope.h
@@ -69,8 +69,12 @@ class MIsotope
   bool GetLineExcludeFlag(unsigned int l) const;
   //! Return the default lines (= most commonly seen), either defined by the default flag in the file, or the line with the strongest branching ratio - ignore excluded lines
   //! Return -1 if no default line could be found
-  int GetDefaultLine() const;
-  
+  int GetDefaultLine() const { return GetPrimaryLine(); }
+  //! Return -1 if no primary line could be found
+  int GetPrimaryLine() const;
+  //! Return -1 if no secondary line could be found
+  int GetSecondaryLine() const;
+
   //! Dump a string
   virtual MString ToString() const;
   
@@ -100,9 +104,11 @@ class MIsotope
   vector<double> m_LineBranchingRatios;
   //! The line exclude flags
   vector<bool> m_LineExcludeFlags;
-  //! The line default flags
-  vector<bool> m_LineDefaultFlags;
-  
+  //! The line primary flags
+  vector<bool> m_LinePrimaryFlags;
+  //! The line secondary flags
+  vector<bool> m_LineSecondaryFlags;
+
 
 #ifdef ___CLING___
  public:
diff --git a/src/global/misc/src/MIsotope.cxx b/src/global/misc/src/MIsotope.cxx
index 67aef9c4f..9f09af245 100644
--- a/src/global/misc/src/MIsotope.cxx
+++ b/src/global/misc/src/MIsotope.cxx
@@ -117,9 +117,11 @@ void MIsotope::AddLine(double Energy, double BranchingRatio, const MString& Flag
     m_LineEnergies.push_back(Energy);
     m_LineBranchingRatios.push_back(BranchingRatio);
     m_LineExcludeFlags.push_back(false);
-    m_LineDefaultFlags.push_back(false);
     if (Flags.Contains("E") == true) m_LineExcludeFlags.back() = true;
-    if (Flags.Contains("D") == true) m_LineDefaultFlags.back() = true;
+    m_LinePrimaryFlags.push_back(false);
+    if (Flags.Contains("D") == true || Flags.Contains("P") == true) m_LinePrimaryFlags.back() = true;
+    m_LineSecondaryFlags.push_back(false);
+    if (Flags.Contains("S") == true) m_LineSecondaryFlags.back() = true;
   }
 }
 
@@ -152,18 +154,18 @@ bool MIsotope::GetLineExcludeFlag(unsigned int i) const
 ////////////////////////////////////////////////////////////////////////////////
 
 
-//! Return the default line, or -1 if non could be found
-int MIsotope::GetDefaultLine() const
+//! Return the primary line, or -1 if non could be found
+int MIsotope::GetPrimaryLine() const
 {
-  if (m_LineDefaultFlags.size() == 0) return -1;
-  
-  // If we have defined one , and it is not excluded
-  for (unsigned int l = 0; l < m_LineDefaultFlags.size(); ++l) {
-    if (m_LineDefaultFlags[l] == true && m_LineExcludeFlags[l] == false) {
-      return l; 
+  if (m_LinePrimaryFlags.size() == 0) return -1;
+
+  // If we have defined one, and it is not excluded
+  for (unsigned int l = 0; l < m_LinePrimaryFlags.size(); ++l) {
+    if (m_LinePrimaryFlags[l] == true && m_LineExcludeFlags[l] == false) {
+      return l;
     }
   }
-  
+
   // If not return the line with the strongest branching ratio which is not excluded
   int Line = -1;
   double Strength = -1;
@@ -175,10 +177,30 @@ int MIsotope::GetDefaultLine() const
       }
     }
   }
-  
+
   return Line;
 }
 
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Return the secondary line, or -1 if non could be found
+int MIsotope::GetSecondaryLine() const
+{
+  if (m_LineSecondaryFlags.size() == 0) return -1;
+
+  // If we have defined one, and it is not excluded
+  for (unsigned int l = 0; l < m_LineSecondaryFlags.size(); ++l) {
+    if (m_LineSecondaryFlags[l] == true && m_LineExcludeFlags[l] == false) {
+      return l;
+    }
+  }
+
+  // We have no secondary line defined or available
+  return -1;
+}
+
   
 ////////////////////////////////////////////////////////////////////////////////
 

From 938b3ee6f669f580b50b5e4b39daeb85b21093fd Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Fri, 2 May 2025 14:41:05 -0700
Subject: [PATCH 132/192] ADD: Line FWHM'es and residials

---
 .../src/MCalibrateEnergyDetermineModel.cxx    |   9 +-
 src/fretalon/melinator/src/MMelinator.cxx     | 153 +++++++++++++++---
 2 files changed, 140 insertions(+), 22 deletions(-)

diff --git a/src/fretalon/base/src/MCalibrateEnergyDetermineModel.cxx b/src/fretalon/base/src/MCalibrateEnergyDetermineModel.cxx
index 6f6742a50..ab040dd6e 100644
--- a/src/fretalon/base/src/MCalibrateEnergyDetermineModel.cxx
+++ b/src/fretalon/base/src/MCalibrateEnergyDetermineModel.cxx
@@ -214,7 +214,14 @@ bool MCalibrateEnergyDetermineModel::CalibrateEnergyModel()
     for (unsigned int p = 0; p < m_Results.GetNumberOfSpectralPoints(r); ++p) {
       if (m_Results.GetSpectralPoint(r, p).IsGood() == true) {
         MCalibrationSpectralPoint& P = m_Results.GetSpectralPoint(r, p);
-        P.SetEnergyFWHM(m_Results.GetEnergyModel().GetFitValue(P.GetPeak() + 0.5*P.GetFWHM()) - m_Results.GetEnergyModel().GetFitValue(P.GetPeak() - 0.5*P.GetFWHM()));
+        if (P.HasFit() == true) {
+          MCalibrationFit& Fit = P.GetFit();
+          double FWHM = Fit.GetFWHM();
+          P.SetEnergyFWHM(m_Results.GetEnergyModel().GetFitValue(P.GetPeak() + 0.5*FWHM) - m_Results.GetEnergyModel().GetFitValue(P.GetPeak() - 0.5*FWHM));
+        }
+
+        // We cannot do this, since the old FWHM was estimated and set before the fit
+        //P.SetEnergyFWHM(m_Results.GetEnergyModel().GetFitValue(P.GetPeak() + 0.5*P.GetFWHM()) - m_Results.GetEnergyModel().GetFitValue(P.GetPeak() - 0.5*P.GetFWHM()));
       }
     }
   }
diff --git a/src/fretalon/melinator/src/MMelinator.cxx b/src/fretalon/melinator/src/MMelinator.cxx
index 779d9b2b9..f930e8608 100644
--- a/src/fretalon/melinator/src/MMelinator.cxx
+++ b/src/fretalon/melinator/src/MMelinator.cxx
@@ -1606,6 +1606,10 @@ bool MMelinator::CreateReport()
   map<pair<unsigned int, bool>, MString> TitlesMap;
   map<pair<unsigned int, bool>, TH2D*> RawADCsMap;
   map<pair<unsigned int, bool>, TH2D*> FittedEnergiesMap;
+  // Outer map: detector ID, side; inner map: rog, isotope
+  map<pair<unsigned int, bool>, map<tuple<unsigned int, unsigned int, unsigned int>, TH1D*>> FWHMesMap;
+  map<pair<unsigned int, bool>, map<tuple<unsigned int, unsigned int, unsigned int>, TH1D*>> ResidualsMap;
+
   if (m_CalibrationStore.GetReadOutElement(0).IsOfType("doublesidedstrip") == true) {
     // Step 1: Maximum strip ID
     unsigned int MaxStripID = 0;
@@ -1646,9 +1650,34 @@ bool MMelinator::CreateReport()
           FittedEnergiesMap[DetectorAndSide]->SetYTitle("Strip ID");
           FittedEnergiesMap[DetectorAndSide]->SetContour(99);
         }
-      }
-    }
-  }
+
+        MCalibration& C = m_CalibrationStore.GetCalibration(c);
+        MCalibrationSpectrum& CS = static_cast<MCalibrationSpectrum&>(C);
+        for (unsigned int g = 0; g < CS.GetNumberOfReadOutDataGroups(); ++g) {
+          for (unsigned int i = 0; i < m_Isotopes[g].size(); ++i) {
+            for (unsigned int l = 0; l < m_Isotopes[g][i].GetNLines(); ++l) {
+              if (m_Isotopes[g][i].GetPrimaryLine() == l || m_Isotopes[g][i].GetSecondaryLine() == l)  {
+                tuple<unsigned int, unsigned int, unsigned int> ROGIDAndIsotope = { g, i, l };
+                // Inefficiency: we loop over everything... but avoiding it is a complicated optimization
+                // Use try_emplace to avoid that
+                FWHMesMap.try_emplace(DetectorAndSide, map<tuple<unsigned int, unsigned int, unsigned int>, TH1D*>());
+                FWHMesMap[DetectorAndSide].try_emplace(ROGIDAndIsotope, new TH1D("", "FWHMes", MaxStripID+1, -0.5, MaxStripID + 0.5));
+                FWHMesMap[DetectorAndSide][ROGIDAndIsotope]->SetXTitle("Strip ID");
+                FWHMesMap[DetectorAndSide][ROGIDAndIsotope]->SetYTitle("FWHM [keV]");
+                FWHMesMap[DetectorAndSide][ROGIDAndIsotope]->SetLineWidth(2);
+
+                ResidualsMap.try_emplace(DetectorAndSide, map<tuple<unsigned int, unsigned int, unsigned int>, TH1D*>());
+                ResidualsMap[DetectorAndSide].try_emplace(ROGIDAndIsotope, new TH1D("", "Residuals", MaxStripID+1, -0.5, MaxStripID + 0.5));
+                ResidualsMap[DetectorAndSide][ROGIDAndIsotope]->SetXTitle("Strip ID");
+                ResidualsMap[DetectorAndSide][ROGIDAndIsotope]->SetYTitle("Residuals [keV]");
+                ResidualsMap[DetectorAndSide][ROGIDAndIsotope]->SetLineWidth(2);
+              }
+            }
+          }
+        }
+      } // is // double-sided strip in calibration store
+    } // ROE in calibration store
+  } // double-sided strip
 
 
 
@@ -1666,16 +1695,16 @@ bool MMelinator::CreateReport()
       CurrentHistADCs = RawADCsMap[DetectorAndSide];
       CurrentStripID = ROE_DS.GetStripID();
     }
-    MCalibrationSpectrum* C = dynamic_cast<MCalibrationSpectrum*>(&(m_CalibrationStore.GetCalibration(c)));
-    MCalibrationModel& M = C->GetEnergyModel();
+    MCalibrationSpectrum& CS = dynamic_cast<MCalibrationSpectrum&>(m_CalibrationStore.GetCalibration(c));
+    MCalibrationModel& M = CS.GetEnergyModel();
 
     unsigned int IDofROC = m_Store.FindReadOutCollection(ROE);
     if (IDofROC == g_UnsignedIntNotDefined) continue;
     MReadOutCollection& ROC = m_Store.GetReadOutCollection(IDofROC);
     for (unsigned int g = 0; g < ROC.GetNumberOfReadOutDataGroups(); ++g) {
-      MReadOutDataGroup& RODG = ROC.GetReadOutDataGroup(g);
-      for (unsigned int d = 0; d < RODG.GetNumberOfReadOutDatas(); ++d) {
-        MReadOutData& ROD = RODG.GetReadOutData(d);
+      MReadOutDataGroup& ROG = ROC.GetReadOutDataGroup(g);
+      for (unsigned int d = 0; d < ROG.GetNumberOfReadOutDatas(); ++d) {
+        MReadOutData& ROD = ROG.GetReadOutData(d);
         MReadOutDataADCValue* ROD_ADC = dynamic_cast<MReadOutDataADCValue*>(ROD.Get(MReadOutDataADCValue::m_TypeID));
         if (ROD_ADC != nullptr) {
           double ADCs = ROD_ADC->GetADCValue();
@@ -1689,8 +1718,36 @@ bool MMelinator::CreateReport()
         }
       }
     }
-  }
 
+    if (m_CalibrationStore.GetReadOutElement(c).IsOfType("doublesidedstrip") == true) {
+      MReadOutElementDoubleStrip& ROE_DS = static_cast<MReadOutElementDoubleStrip&>(ROE);
+      pair<unsigned int, bool> DetectorAndSide = { ROE_DS.GetDetectorID(), ROE_DS.IsLowVoltageStrip() };
+
+      for (unsigned int g = 0; g < CS.GetNumberOfReadOutDataGroups(); ++g) {
+        for (unsigned int i = 0; i < m_Isotopes[g].size(); ++i) {
+          for (unsigned int l = 0; l < m_Isotopes[g][i].GetNLines(); ++l) {
+            if (m_Isotopes[g][i].GetPrimaryLine() == l || m_Isotopes[g][i].GetSecondaryLine() == l)  {
+              tuple<unsigned int, unsigned int, unsigned int> ROGIDAndIsotope = { g, i, l };
+
+              // Loop over all spectral point, and find the isotope and the line
+              for (unsigned int ii = 0; ii < CS.GetNumberOfSpectralPoints(g); ++ii) {
+                MCalibrationSpectralPoint& SP = CS.GetSpectralPoint(g, ii);
+                if (SP.GetIsotope() == m_Isotopes[g][i]) {
+                  if (fabs(SP.GetEnergy() - m_Isotopes[g][i].GetLineEnergy(l)) < 0.01 && SP.HasFit() == true) {
+                    FWHMesMap[DetectorAndSide][ROGIDAndIsotope]->SetTitle(MString("FWHM per strip for ") + m_Isotopes[g][i].GetName() + ", " + SP.GetEnergy() + " keV line"); // I know it is set multiple times...
+                    FWHMesMap[DetectorAndSide][ROGIDAndIsotope]->Fill(CurrentStripID, SP.GetEnergyFWHM());
+                    ResidualsMap[DetectorAndSide][ROGIDAndIsotope]->SetTitle(MString("Residuals line/fit per strip for ") + m_Isotopes[g][i].GetName() + ", " + SP.GetEnergy() + " keV line"); // I know it is set multiple times...
+                    double Residual = SP.GetEnergy() - M.GetFitValue(SP.GetPeak());
+                    ResidualsMap[DetectorAndSide][ROGIDAndIsotope]->Fill(CurrentStripID, Residual);
+                  }
+                }
+              }
+            }
+          }
+        }
+      }
+    }
+  }
 
   // Create the canvases
 
@@ -1700,6 +1757,8 @@ bool MMelinator::CreateReport()
   auto IterTitles = TitlesMap.begin();
   auto IterEnergy = FittedEnergiesMap.begin();
   auto IterADCs = RawADCsMap.begin();
+  auto IterFWHMes = FWHMesMap.begin();
+  auto IterResiduals = ResidualsMap.begin();
 
   TCanvas* TitleCanvas = new TCanvas("Melinator Calibration Report", "Melinator Calibration Report", 850, 1100);
   TitleCanvas->cd();
@@ -1796,10 +1855,13 @@ bool MMelinator::CreateReport()
   TitleCanvas->Print(OutputFileName + "(");
 
 
-  while (IterTitles != TitlesMap.end() && IterEnergy != FittedEnergiesMap.end() && IterADCs != RawADCsMap.end()) {
-    TCanvas* C = new TCanvas("", "", 850, 1100);
-    C->SetLogz();
-    C->cd();
+  while (IterTitles != TitlesMap.end() && IterEnergy != FittedEnergiesMap.end() && IterADCs != RawADCsMap.end() && IterFWHMes != FWHMesMap.end() && IterResiduals != ResidualsMap.end()) {
+
+    // Page 1: Spectra
+
+    TCanvas* SpectrumPages = new TCanvas("", "", 850, 1100);
+    SpectrumPages->SetLogz();
+    SpectrumPages->cd();
 
     TPad* TitlePad = new TPad("padTitle", "Title", 0.0, 0.9, 1.0, 1.0);
     TitlePad->Draw();
@@ -1814,7 +1876,7 @@ bool MMelinator::CreateReport()
     Title->SetTextSize(0.4);
     Title->Draw();
 
-    C->cd();
+    SpectrumPages->cd();
 
     TPad* ADCPad = new TPad("ADCPad", "ADCPad", 0.0, 0.45, 1.0, 0.9);
     ADCPad->Draw();
@@ -1822,7 +1884,7 @@ bool MMelinator::CreateReport()
     ADCPad->SetLogz();
     IterADCs->second->Draw("colz");
 
-    C->cd();
+    SpectrumPages->cd();
 
     TPad* EnergyPad = new TPad("EnergyPad", "EnergyPad", 0.0, 0.0, 1.0, 0.45);
     EnergyPad->Draw();
@@ -1830,13 +1892,60 @@ bool MMelinator::CreateReport()
     EnergyPad->SetLogz();
     IterEnergy->second->Draw("colz");
 
-    C->cd();
-    C->Update();
+    SpectrumPages->cd();
+    SpectrumPages->Update();
 
-    if (next(IterTitles) == TitlesMap.end()) {
-      C->Print(OutputFileName + ")");  // close PDF
-    } else {
-      C->Print(OutputFileName);   // middle pages
+    SpectrumPages->Print(OutputFileName);   // middle pages
+
+
+    // Page 2+ is lines:
+
+    auto IterFWHMesInner = IterFWHMes->second.begin();
+    auto IterResidualsInner = IterResiduals->second.begin();
+    while (IterResidualsInner != IterResiduals->second.end() && IterFWHMesInner != IterFWHMes->second.end()) {
+
+      TCanvas* LineFitPages = new TCanvas("", "", 850, 1100);
+      LineFitPages->cd();
+
+      TPad* TitlePadLineFitPages = new TPad("padTitle", "Title", 0.0, 0.9, 1.0, 1.0);
+      TitlePadLineFitPages->Draw();
+      TitlePadLineFitPages->cd();
+
+      TPaveText* TitleLineFitPages = new TPaveText(0.0, 0.0, 1.0, 1.0, "brNDC");
+      TitleLineFitPages->AddText(IterTitles->second);
+      TitleLineFitPages->SetFillColor(0);     // No background color
+      TitleLineFitPages->SetBorderSize(0);    // No border
+      TitleLineFitPages->SetLineColor(0);     // Remove outline
+      TitleLineFitPages->SetTextFont(TextFont);
+      TitleLineFitPages->SetTextSize(0.4);
+      TitleLineFitPages->Draw();
+
+      LineFitPages->cd();
+
+
+      TPad* FWHMPad = new TPad("", "", 0.0, 0.45, 1.0, 0.9);
+      FWHMPad->Draw();
+      FWHMPad->cd();
+      IterFWHMesInner->second->Draw("HIST ");
+
+      LineFitPages->cd();
+
+      TPad* ResidualsPad = new TPad("", "", 0.0, 0.0, 1.0, 0.45);
+      ResidualsPad->Draw();
+      ResidualsPad->cd();
+      IterResidualsInner->second->Draw("HIST ");
+
+      LineFitPages->cd();
+      LineFitPages->Update();
+
+      if (next(IterFWHMesInner) == IterFWHMes->second.end() && next(IterTitles) == TitlesMap.end()) {
+        LineFitPages->Print(OutputFileName + ")");  // close PDF
+      } else {
+        LineFitPages->Print(OutputFileName);   // middle pages
+      }
+
+      ++IterFWHMesInner;
+      ++IterResidualsInner;
     }
 
     FoundHist = true;
@@ -1844,6 +1953,8 @@ bool MMelinator::CreateReport()
     ++IterTitles;
     ++IterEnergy;
     ++IterADCs;
+    ++IterFWHMes;
+    ++IterResiduals;
   }
 
   gROOT->SetBatch(false);

From 24e4c5cb3cb9e4e328187c18b21999bd05e5bc59 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Mon, 5 May 2025 11:27:00 -0700
Subject: [PATCH 133/192] ADD: Threshold and overflow to report

---
 src/fretalon/melinator/src/MMelinator.cxx | 108 +++++++++++++++++-----
 1 file changed, 87 insertions(+), 21 deletions(-)

diff --git a/src/fretalon/melinator/src/MMelinator.cxx b/src/fretalon/melinator/src/MMelinator.cxx
index f930e8608..6c160824d 100644
--- a/src/fretalon/melinator/src/MMelinator.cxx
+++ b/src/fretalon/melinator/src/MMelinator.cxx
@@ -1585,6 +1585,9 @@ bool MMelinator::CreateReport()
 
   double MaxADCs = 5000;
   double MaxEnergy = 500;
+  double ThresholdMaxEnergy = 35;
+  double OverflowMinEnergy = 1750;
+  double OverflowMaxEnergy = 3000;
   MString OutputFileName = "MelinatorReport.pdf";
 
 
@@ -1604,8 +1607,10 @@ bool MMelinator::CreateReport()
 
   // If we have double-sided strips make one histogram per detector and side
   map<pair<unsigned int, bool>, MString> TitlesMap;
-  map<pair<unsigned int, bool>, TH2D*> RawADCsMap;
-  map<pair<unsigned int, bool>, TH2D*> FittedEnergiesMap;
+  map<pair<unsigned int, bool>, TH2D*> ADCsMap;
+  map<pair<unsigned int, bool>, TH2D*> EnergiesMap;
+  map<pair<unsigned int, bool>, TH2D*> ThresholdsMap;
+  map<pair<unsigned int, bool>, TH2D*> OverflowsMap;
   // Outer map: detector ID, side; inner map: rog, isotope
   map<pair<unsigned int, bool>, map<tuple<unsigned int, unsigned int, unsigned int>, TH1D*>> FWHMesMap;
   map<pair<unsigned int, bool>, map<tuple<unsigned int, unsigned int, unsigned int>, TH1D*>> ResidualsMap;
@@ -1628,8 +1633,8 @@ bool MMelinator::CreateReport()
       if (m_CalibrationStore.GetReadOutElement(c).IsOfType("doublesidedstrip") == true) {
         MReadOutElementDoubleStrip& ROE_DS = static_cast<MReadOutElementDoubleStrip&>(ROE);
         pair<unsigned int, bool> DetectorAndSide = { ROE_DS.GetDetectorID(), ROE_DS.IsLowVoltageStrip() };
-        auto MapIter = RawADCsMap.find(DetectorAndSide);
-        if (MapIter == RawADCsMap.end()) {
+        auto MapIter = ADCsMap.find(DetectorAndSide);
+        if (MapIter == ADCsMap.end()) {
           MString Name = "Detector ";
           Name += ROE_DS.GetDetectorID();
           if (ROE_DS.IsLowVoltageStrip() == true) {
@@ -1640,15 +1645,25 @@ bool MMelinator::CreateReport()
 
           TitlesMap[DetectorAndSide] = Name;
 
-          RawADCsMap[DetectorAndSide] = new TH2D("", "ADC spectrum", MaxADCs/2, 0, MaxADCs, MaxStripID+1, -0.5, MaxStripID + 0.5);
-          RawADCsMap[DetectorAndSide]->SetXTitle("ADC units");
-          RawADCsMap[DetectorAndSide]->SetYTitle("Strip ID");
-          RawADCsMap[DetectorAndSide]->SetContour(99);
-
-          FittedEnergiesMap[DetectorAndSide] = new TH2D("", "Energy spectrum", MaxEnergy/2, 0, MaxEnergy, MaxStripID+1, -0.5, MaxStripID + 0.5);
-          FittedEnergiesMap[DetectorAndSide]->SetXTitle("Energy [keV]");
-          FittedEnergiesMap[DetectorAndSide]->SetYTitle("Strip ID");
-          FittedEnergiesMap[DetectorAndSide]->SetContour(99);
+          ADCsMap[DetectorAndSide] = new TH2D("", "ADC spectrum", MaxADCs/2, 0, MaxADCs, MaxStripID+1, -0.5, MaxStripID + 0.5);
+          ADCsMap[DetectorAndSide]->SetXTitle("ADC units");
+          ADCsMap[DetectorAndSide]->SetYTitle("Strip ID");
+          ADCsMap[DetectorAndSide]->SetContour(99);
+
+          EnergiesMap[DetectorAndSide] = new TH2D("", "Energy spectrum", MaxEnergy/2, 0, MaxEnergy, MaxStripID+1, -0.5, MaxStripID + 0.5);
+          EnergiesMap[DetectorAndSide]->SetXTitle("Energy [keV]");
+          EnergiesMap[DetectorAndSide]->SetYTitle("Strip ID");
+          EnergiesMap[DetectorAndSide]->SetContour(99);
+
+          ThresholdsMap[DetectorAndSide] = new TH2D("", "Thresholds", ThresholdMaxEnergy, 0, ThresholdMaxEnergy, MaxStripID+1, -0.5, MaxStripID + 0.5);
+          ThresholdsMap[DetectorAndSide]->SetXTitle("Energy [keV]");
+          ThresholdsMap[DetectorAndSide]->SetYTitle("Strip ID");
+          ThresholdsMap[DetectorAndSide]->SetContour(99);
+
+          OverflowsMap[DetectorAndSide] = new TH2D("", "Overflows", (OverflowMaxEnergy - OverflowMinEnergy)/10, OverflowMinEnergy, OverflowMaxEnergy, MaxStripID+1, -0.5, MaxStripID + 0.5);
+          OverflowsMap[DetectorAndSide]->SetXTitle("Energy [keV]");
+          OverflowsMap[DetectorAndSide]->SetYTitle("Strip ID");
+          OverflowsMap[DetectorAndSide]->SetContour(99);
         }
 
         MCalibration& C = m_CalibrationStore.GetCalibration(c);
@@ -1687,12 +1702,16 @@ bool MMelinator::CreateReport()
     MReadOutElement& ROE = m_CalibrationStore.GetReadOutElement(c);
     TH2D* CurrentHistEnergy = nullptr;
     TH2D* CurrentHistADCs = nullptr;
+    TH2D* CurrentHistThresholds = nullptr;
+    TH2D* CurrentHistOverflows = nullptr;
     unsigned int CurrentStripID = 0;
     if (m_CalibrationStore.GetReadOutElement(c).IsOfType("doublesidedstrip") == true) {
       MReadOutElementDoubleStrip& ROE_DS = static_cast<MReadOutElementDoubleStrip&>(ROE);
       pair<unsigned int, bool> DetectorAndSide = { ROE_DS.GetDetectorID(), ROE_DS.IsLowVoltageStrip() };
-      CurrentHistEnergy = FittedEnergiesMap[DetectorAndSide];
-      CurrentHistADCs = RawADCsMap[DetectorAndSide];
+      CurrentHistEnergy = EnergiesMap[DetectorAndSide];
+      CurrentHistADCs = ADCsMap[DetectorAndSide];
+      CurrentHistThresholds = ThresholdsMap[DetectorAndSide];
+      CurrentHistOverflows = OverflowsMap[DetectorAndSide];
       CurrentStripID = ROE_DS.GetStripID();
     }
     MCalibrationSpectrum& CS = dynamic_cast<MCalibrationSpectrum&>(m_CalibrationStore.GetCalibration(c));
@@ -1713,6 +1732,8 @@ bool MMelinator::CreateReport()
           AllRawADCs->Fill(ADCs, c);
           if (CurrentHistEnergy != nullptr) {
             CurrentHistEnergy->Fill(Energy, CurrentStripID);
+            CurrentHistOverflows->Fill(Energy, CurrentStripID);
+            CurrentHistThresholds->Fill(Energy, CurrentStripID);
             CurrentHistADCs->Fill(ADCs, CurrentStripID);
           }
         }
@@ -1755,8 +1776,10 @@ bool MMelinator::CreateReport()
 
   bool FoundHist = false;
   auto IterTitles = TitlesMap.begin();
-  auto IterEnergy = FittedEnergiesMap.begin();
-  auto IterADCs = RawADCsMap.begin();
+  auto IterEnergies = EnergiesMap.begin();
+  auto IterADCs = ADCsMap.begin();
+  auto IterThresholds = ThresholdsMap.begin();
+  auto IterOverflows = OverflowsMap.begin();
   auto IterFWHMes = FWHMesMap.begin();
   auto IterResiduals = ResidualsMap.begin();
 
@@ -1855,7 +1878,7 @@ bool MMelinator::CreateReport()
   TitleCanvas->Print(OutputFileName + "(");
 
 
-  while (IterTitles != TitlesMap.end() && IterEnergy != FittedEnergiesMap.end() && IterADCs != RawADCsMap.end() && IterFWHMes != FWHMesMap.end() && IterResiduals != ResidualsMap.end()) {
+  while (IterTitles != TitlesMap.end() && IterEnergies != EnergiesMap.end() && IterADCs != ADCsMap.end() && IterThresholds != ThresholdsMap.end() && IterOverflows != OverflowsMap.end() && IterFWHMes != FWHMesMap.end() && IterResiduals != ResidualsMap.end()) {
 
     // Page 1: Spectra
 
@@ -1890,7 +1913,7 @@ bool MMelinator::CreateReport()
     EnergyPad->Draw();
     EnergyPad->cd();
     EnergyPad->SetLogz();
-    IterEnergy->second->Draw("colz");
+    IterEnergies->second->Draw("colz");
 
     SpectrumPages->cd();
     SpectrumPages->Update();
@@ -1898,7 +1921,48 @@ bool MMelinator::CreateReport()
     SpectrumPages->Print(OutputFileName);   // middle pages
 
 
-    // Page 2+ is lines:
+    // Page 2: Thresholds & Overflows
+
+    TCanvas* ThresholdsPages = new TCanvas("", "", 850, 1100);
+    ThresholdsPages->SetLogz();
+    ThresholdsPages->cd();
+
+    TPad* ThresholdsTitlePad = new TPad("padTitle", "Title", 0.0, 0.9, 1.0, 1.0);
+    ThresholdsTitlePad->Draw();
+    ThresholdsTitlePad->cd();
+
+    TPaveText* ThresholdsTitle = new TPaveText(0.0, 0.0, 1.0, 1.0, "brNDC");
+    ThresholdsTitle->AddText(IterTitles->second);
+    ThresholdsTitle->SetFillColor(0);     // No background color
+    ThresholdsTitle->SetBorderSize(0);    // No border
+    ThresholdsTitle->SetLineColor(0);     // Remove outline
+    ThresholdsTitle->SetTextFont(TextFont);
+    ThresholdsTitle->SetTextSize(0.4);
+    ThresholdsTitle->Draw();
+
+    ThresholdsPages->cd();
+
+    TPad* ThresholdsPad = new TPad("ThresholdsPad", "ThresholdsPad", 0.0, 0.45, 1.0, 0.9);
+    ThresholdsPad->Draw();
+    ThresholdsPad->cd();
+    ThresholdsPad->SetLogz();
+    IterThresholds->second->Draw("colz");
+
+    ThresholdsPages->cd();
+
+    TPad* OverflowsPad = new TPad("OverflowsPad", "OverflowsPad", 0.0, 0.0, 1.0, 0.45);
+    OverflowsPad->Draw();
+    OverflowsPad->cd();
+    OverflowsPad->SetLogz();
+    IterOverflows->second->Draw("colz");
+
+    ThresholdsPages->cd();
+    ThresholdsPages->Update();
+
+    ThresholdsPages->Print(OutputFileName);   // middle pages
+
+
+    // Page 3+ is lines:
 
     auto IterFWHMesInner = IterFWHMes->second.begin();
     auto IterResidualsInner = IterResiduals->second.begin();
@@ -1951,8 +2015,10 @@ bool MMelinator::CreateReport()
     FoundHist = true;
 
     ++IterTitles;
-    ++IterEnergy;
+    ++IterEnergies;
     ++IterADCs;
+    ++IterThresholds;
+    ++IterOverflows;
     ++IterFWHMes;
     ++IterResiduals;
   }

From b1bdc4b776af65794d1d18ab25bb4f29fbff9f8b Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Tue, 6 May 2025 08:29:58 -0700
Subject: [PATCH 134/192] ADD: UI to set report parameters

---
 src/fretalon/melinator/Makefile               |   1 +
 .../melinator/inc/MGUIReportCreation.h        | 104 ++++++++
 src/fretalon/melinator/inc/MMelinator.h       |  57 ++++-
 .../melinator/inc/MSettingsMelinator.h        | 110 +++++++-
 .../melinator/src/MGUIMainMelinator.cxx       |  23 ++
 .../melinator/src/MGUIReportCreation.cxx      | 241 ++++++++++++++++++
 src/fretalon/melinator/src/MMelinator.cxx     | 102 ++++++--
 .../melinator/src/MSettingsMelinator.cxx      |  86 +++++++
 8 files changed, 689 insertions(+), 35 deletions(-)
 create mode 100644 src/fretalon/melinator/inc/MGUIReportCreation.h
 create mode 100644 src/fretalon/melinator/src/MGUIReportCreation.cxx

diff --git a/src/fretalon/melinator/Makefile b/src/fretalon/melinator/Makefile
index 61755b9fe..4fcfd41be 100644
--- a/src/fretalon/melinator/Makefile
+++ b/src/fretalon/melinator/Makefile
@@ -29,6 +29,7 @@ FILES_UI := \
 	MGUIEReadOutElementView \
 	MGUIEReadOutUnitsCanvas \
 	MGUILoadCalibration \
+	MGUIReportCreation \
 	MInterfaceMelinator \
 
 LIBRARIES := \
diff --git a/src/fretalon/melinator/inc/MGUIReportCreation.h b/src/fretalon/melinator/inc/MGUIReportCreation.h
new file mode 100644
index 000000000..456b5c934
--- /dev/null
+++ b/src/fretalon/melinator/inc/MGUIReportCreation.h
@@ -0,0 +1,104 @@
+/*
+ * MGUIReportCreation.h
+ *
+ * Copyright (C) by Andreas Zoglauer.
+ * All rights reserved.
+ *
+ * Please see the source-file for the copyright-notice.
+ *
+ */
+
+
+#ifndef __MGUIReportCreation__
+#define __MGUIReportCreation__
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+// ROOT libs:
+#include "TGComboBox.h"
+
+// MEGAlib libs:
+#include "MGlobal.h"
+#include "MGUIDialog.h"
+#include "MSettingsMelinator.h"
+#include "MGUIEFileSelector.h"
+#include "MGUIEEntry.h"
+#include "MGUIEMinMaxEntry.h"
+
+// Forward declarations:
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! GUI dialog showing the options for loading ans classifying the calibration file
+class MGUIReportCreation : public MGUIDialog
+{
+  // Public Interface:
+ public:
+  //! Default constructor
+  MGUIReportCreation(const TGWindow* Parent, const TGWindow* Main, MSettingsMelinator* Settings, bool& OKPressed);
+  //! Default destructor
+  virtual ~MGUIReportCreation();
+
+  
+  // protected methods:
+ protected:
+  //! Create the UI
+  virtual void Create();
+  //! Apply changes
+  virtual bool OnApply();
+  //! Process all messages
+  bool ProcessMessage(long Message, long Parameter1, long Parameter2);
+
+
+
+  // protected members:
+ protected:
+
+
+  // private members:
+ private:
+  //! The return message that OK was pressed
+  bool& m_OkPressed;
+
+  //! The settings file
+  MSettingsMelinator* m_Settings;
+
+  //! The report file name
+  MGUIEFileSelector* m_FileName;
+
+  //! ADC histogram: display min & max
+  MGUIEMinMaxEntry* m_ADCDimension;
+  //! ADC histogram: number of bins
+  MGUIEEntry* m_ADCBins;
+
+  //! Energy histogram: display min & max
+  MGUIEMinMaxEntry* m_EnergyDimension;
+  //! Energy histogram: number of bins
+  MGUIEEntry* m_EnergyBins;
+
+  //! Threshold histogram: display min & max
+  MGUIEMinMaxEntry* m_ThresholdDimension;
+  //! Threshold histogram: number of bins
+  MGUIEEntry* m_ThresholdBins;
+
+  //! Overflow histogram: display min & max
+  MGUIEMinMaxEntry* m_OverflowDimension;
+  //! Overflow histogram: number of bins
+  MGUIEEntry* m_OverflowBins;
+
+
+#ifdef ___CLING___
+ public:
+  ClassDef(MGUIReportCreation, 0)
+#endif
+
+};
+
+#endif
+
+
+////////////////////////////////////////////////////////////////////////////////
diff --git a/src/fretalon/melinator/inc/MMelinator.h b/src/fretalon/melinator/inc/MMelinator.h
index 2c41e3559..5706ff7c3 100644
--- a/src/fretalon/melinator/inc/MMelinator.h
+++ b/src/fretalon/melinator/inc/MMelinator.h
@@ -164,6 +164,27 @@ class MMelinator
   //! Save the calibration in e-cal format
   bool Save(MString FileName);
 
+  //! Set the basic properties of the report
+  void SetReportProperties(MString FileName,
+                           double ADCMinimum, double ADCMaximum, unsigned int ADCBins,
+                           double EnergyMinimum, double EnergyMaximum, unsigned int EnergyBins,
+                           double ThresholdMinimum, double ThresholdMaximum, unsigned int ThresholdBins,
+                           double OverflowMinimum, double OverflowMaximum, unsigned int OverflowBins) {
+    m_ReportFileName = FileName;
+    m_ReportADCHistogramMinimum = ADCMinimum;
+    m_ReportADCHistogramMaximum = ADCMaximum;
+    m_ReportADCHistogramBins = ADCBins;
+    m_ReportEnergyHistogramMinimum = EnergyMinimum;
+    m_ReportEnergyHistogramMaximum = EnergyMaximum;
+    m_ReportEnergyHistogramBins = EnergyBins;
+    m_ReportThresholdHistogramMinimum = ThresholdMinimum;
+    m_ReportThresholdHistogramMaximum = ThresholdMaximum;
+    m_ReportThresholdHistogramBins = ThresholdBins;
+    m_ReportOverflowHistogramMinimum = OverflowMinimum;
+    m_ReportOverflowHistogramMaximum = OverflowMaximum;
+    m_ReportOverflowHistogramBins = OverflowBins;
+  };
+
   //! Create a calibration report
   bool CreateReport();
 
@@ -207,7 +228,7 @@ class MMelinator
   MReadOutStore m_Store;
   //! The storage for all calibrations
   MCalibrationStore m_CalibrationStore;
-  
+
   //! The selected detector ID (negative means all detectors)
   int m_SelectedDetectorID;
   
@@ -295,7 +316,39 @@ class MMelinator
   //! Time to determine model
   double m_TimeToDetermineModel;
   
-  
+
+  //! Set the report file
+  MString m_ReportFileName;
+
+  //! The minimum value of the ADC histogram in the report
+  double m_ReportADCHistogramMinimum;
+  //! The maximum value of the ADC histogram in the report
+  double m_ReportADCHistogramMaximum;
+  //! The number of bins of the ADC histogram in the report
+  unsigned int m_ReportADCHistogramBins;
+
+  //! The minimum value of the Energy histogram in the report
+  double m_ReportEnergyHistogramMinimum;
+  //! The maximum value of the Energy histogram in the report
+  double m_ReportEnergyHistogramMaximum;
+  //! The number of bins of the Energy histogram in the report
+  unsigned int m_ReportEnergyHistogramBins;
+
+  //! The minimum value of the Threshold histogram in the report
+  double m_ReportThresholdHistogramMinimum;
+  //! The maximum value of the Threshold histogram in the report
+  double m_ReportThresholdHistogramMaximum;
+  //! The number of bins of the Threshold histogram in the report
+  unsigned int m_ReportThresholdHistogramBins;
+
+  //! The minimum value of the Overflow histogram in the report
+  double m_ReportOverflowHistogramMinimum;
+  //! The maximum value of the Overflow histogram in the report
+  double m_ReportOverflowHistogramMaximum;
+  //! The number of bins of the Overflow histogram in the report
+  unsigned int m_ReportOverflowHistogramBins;
+
+
   
 #ifdef ___CLING___
  public:
diff --git a/src/fretalon/melinator/inc/MSettingsMelinator.h b/src/fretalon/melinator/inc/MSettingsMelinator.h
index aec6cc4d7..07ba4641c 100644
--- a/src/fretalon/melinator/inc/MSettingsMelinator.h
+++ b/src/fretalon/melinator/inc/MSettingsMelinator.h
@@ -164,13 +164,73 @@ class MSettingsMelinator : public MSettings
 
   //! Set the minimum allowed detector temperature
   void SetMinimumTemperature(double MinimumTemperature) { m_MinimumTemperature = MinimumTemperature; }
-  //! Get the minimum allowed detector temperate
+  //! Get the minimum allowed detector temperature
   double GetMinimumTemperature() const { return m_MinimumTemperature; }
-  //! Set the minimum allowed detector temperature
+  //! Set the maximum allowed detector temperature
   void SetMaximumTemperature(double MaximumTemperature) { m_MaximumTemperature = MaximumTemperature; }
-  //! Get the minimum allowed detector temperate
+  //! Get the maximum allowed detector temperature
   double GetMaximumTemperature() const { return m_MaximumTemperature; }
   
+
+  //! Set the report file name
+  void SetReportFileName(const MString& ReportFileName) { m_ReportFileName = ReportFileName; }
+  //! Get the report file name
+  MString GetReportFileName() const { return m_ReportFileName; }
+
+  //! Set the minimum value of the ADC histogram in the report
+  void SetReportADCHistogramMinimum(double ReportADCHistogramMinimum) { m_ReportADCHistogramMinimum = ReportADCHistogramMinimum; }
+  //! Get the minimum value of the ADC histogram in the report
+  double GetReportADCHistogramMinimum() const { return m_ReportADCHistogramMinimum; }
+  //! Set the maximum value of the ADC histogram in the report
+  void SetReportADCHistogramMaximum(double ReportADCHistogramMaximum) { m_ReportADCHistogramMaximum = ReportADCHistogramMaximum; }
+  //! Get the maximum value of the ADC histogram in the report
+  double GetReportADCHistogramMaximum() const { return m_ReportADCHistogramMaximum; }
+  //! Set the number of bins of the ADC histogram in the report
+  void SetReportADCHistogramBins(unsigned int ReportADCHistogramBins) { m_ReportADCHistogramBins = ReportADCHistogramBins; }
+  //! Get the number of bins of the ADC histogram in the report
+  unsigned int GetReportADCHistogramBins() const { return m_ReportADCHistogramBins; }
+
+  //! Set the minimum value of the Energy histogram in the report
+  void SetReportEnergyHistogramMinimum(double ReportEnergyHistogramMinimum) { m_ReportEnergyHistogramMinimum = ReportEnergyHistogramMinimum; }
+  //! Get the minimum value of the Energy histogram in the report
+  double GetReportEnergyHistogramMinimum() const { return m_ReportEnergyHistogramMinimum; }
+  //! Set the maximum value of the Energy histogram in the report
+  void SetReportEnergyHistogramMaximum(double ReportEnergyHistogramMaximum) { m_ReportEnergyHistogramMaximum = ReportEnergyHistogramMaximum; }
+  //! Get the maximum value of the Energy histogram in the report
+  double GetReportEnergyHistogramMaximum() const { return m_ReportEnergyHistogramMaximum; }
+  //! Set the number of bins of the Energy histogram in the report
+  void SetReportEnergyHistogramBins(unsigned int ReportEnergyHistogramBins) { m_ReportEnergyHistogramBins = ReportEnergyHistogramBins; }
+  //! Get the number of bins of the Energy histogram in the report
+  unsigned int GetReportEnergyHistogramBins() const { return m_ReportEnergyHistogramBins; }
+
+  //! Set the minimum value of the Threshold histogram in the report
+  void SetReportThresholdHistogramMinimum(double ReportThresholdHistogramMinimum) { m_ReportThresholdHistogramMinimum = ReportThresholdHistogramMinimum; }
+  //! Get the minimum value of the Threshold histogram in the report
+  double GetReportThresholdHistogramMinimum() const { return m_ReportThresholdHistogramMinimum; }
+  //! Set the maximum value of the Threshold histogram in the report
+  void SetReportThresholdHistogramMaximum(double ReportThresholdHistogramMaximum) { m_ReportThresholdHistogramMaximum = ReportThresholdHistogramMaximum; }
+  //! Get the maximum value of the Threshold histogram in the report
+  double GetReportThresholdHistogramMaximum() const { return m_ReportThresholdHistogramMaximum; }
+  //! Set the number of bins of the Threshold histogram in the report
+  void SetReportThresholdHistogramBins(unsigned int ReportThresholdHistogramBins) { m_ReportThresholdHistogramBins = ReportThresholdHistogramBins; }
+  //! Get the number of bins of the Threshold histogram in the report
+  unsigned int GetReportThresholdHistogramBins() const { return m_ReportThresholdHistogramBins; }
+
+  //! Set the minimum value of the Overflow histogram in the report
+  void SetReportOverflowHistogramMinimum(double ReportOverflowHistogramMinimum) { m_ReportOverflowHistogramMinimum = ReportOverflowHistogramMinimum; }
+  //! Get the minimum value of the Overflow histogram in the report
+  double GetReportOverflowHistogramMinimum() const { return m_ReportOverflowHistogramMinimum; }
+  //! Set the maximum value of the Overflow histogram in the report
+  void SetReportOverflowHistogramMaximum(double ReportOverflowHistogramMaximum) { m_ReportOverflowHistogramMaximum = ReportOverflowHistogramMaximum; }
+  //! Get the maximum value of the Overflow histogram in the report
+  double GetReportOverflowHistogramMaximum() const { return m_ReportOverflowHistogramMaximum; }
+  //! Set the number of bins of the Overflow histogram in the report
+  void SetReportOverflowHistogramBins(unsigned int ReportOverflowHistogramBins) { m_ReportOverflowHistogramBins = ReportOverflowHistogramBins; }
+  //! Get the number of bins of the Overflow histogram in the report
+  unsigned int GetReportOverflowHistogramBins() const { return m_ReportOverflowHistogramBins; }
+
+
+
   
 // protected members:
  protected:
@@ -231,20 +291,52 @@ class MSettingsMelinator : public MSettings
   //! Fitting model of the FWHM calibration model determination method
   unsigned int m_CalibrationModelDeterminationMethodFittingFWHMModel;
   
-  //! Set the save as file
+  //! Set the save as file name
   MString m_SaveAsFileName;
   
-  //! Set the single detector to use (negative means use all)
+  //! The single detector to use (negative means use all)
   int m_SelectedDetectorID;
-  //! Set the detector side to use (< 0: all, 0: negative side, 1: positive side, >=2: all)
+  //! The detector side to use (< 0: all, 0: negative side, 1: positive side, >=2: all)
   int m_SelectedDetectorSide;
 
-  //! Set the minimum allowed detector temperature
+  //! The minimum allowed detector temperature
   double m_MinimumTemperature;
-  //! Set the maximum allowed detector temperature
+  //! The maximum allowed detector temperature
   double m_MaximumTemperature;
   
-  
+
+  //! Set the report file
+  MString m_ReportFileName;
+
+  //! The minimum value of the ADC histogram in the report
+  double m_ReportADCHistogramMinimum;
+  //! The maximum value of the ADC histogram in the report
+  double m_ReportADCHistogramMaximum;
+  //! The number of bins of the ADC histogram in the report
+  unsigned int m_ReportADCHistogramBins;
+
+  //! The minimum value of the Energy histogram in the report
+  double m_ReportEnergyHistogramMinimum;
+  //! The maximum value of the Energy histogram in the report
+  double m_ReportEnergyHistogramMaximum;
+  //! The number of bins of the Energy histogram in the report
+  unsigned int m_ReportEnergyHistogramBins;
+
+  //! The minimum value of the Threshold histogram in the report
+  double m_ReportThresholdHistogramMinimum;
+  //! The maximum value of the Threshold histogram in the report
+  double m_ReportThresholdHistogramMaximum;
+  //! The number of bins of the Threshold histogram in the report
+  unsigned int m_ReportThresholdHistogramBins;
+
+  //! The minimum value of the Overflow histogram in the report
+  double m_ReportOverflowHistogramMinimum;
+  //! The maximum value of the Overflow histogram in the report
+  double m_ReportOverflowHistogramMaximum;
+  //! The number of bins of the Overflow histogram in the report
+  unsigned int m_ReportOverflowHistogramBins;
+
+
 #ifdef ___CLING___
  public:
   ClassDef(MSettingsMelinator, 0) // no description
diff --git a/src/fretalon/melinator/src/MGUIMainMelinator.cxx b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
index 2da7aa7fc..9f3d9fe85 100644
--- a/src/fretalon/melinator/src/MGUIMainMelinator.cxx
+++ b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
@@ -49,6 +49,7 @@ using namespace std;
 #include "MGUIAbout.h"
 #include "MGUIGeometry.h"
 #include "MGUILoadCalibration.h"
+#include "MGUIReportCreation.h"
 #include "MGUIEFileSelector.h"
 #include "MIsotope.h"
 #include "MIsotopeStore.h"
@@ -1456,6 +1457,28 @@ bool MGUIMainMelinator::OnSaveAs()
 //! Actions when the show report button has been pressed
 bool MGUIMainMelinator::OnShowReport()
 {
+  bool OKPressed = false;
+  new MGUIReportCreation(gClient->GetRoot(), this, m_Settings, OKPressed);
+  if (OKPressed == false) {
+    return false;
+  }
+
+  m_Melinator.SetReportProperties(
+    m_Settings->GetReportFileName(),
+    m_Settings->GetReportADCHistogramMinimum(),
+    m_Settings->GetReportADCHistogramMaximum(),
+    m_Settings->GetReportADCHistogramBins(),
+    m_Settings->GetReportEnergyHistogramMinimum(),
+    m_Settings->GetReportEnergyHistogramMaximum(),
+    m_Settings->GetReportEnergyHistogramBins(),
+    m_Settings->GetReportThresholdHistogramMinimum(),
+    m_Settings->GetReportThresholdHistogramMaximum(),
+    m_Settings->GetReportThresholdHistogramBins(),
+    m_Settings->GetReportOverflowHistogramMinimum(),
+    m_Settings->GetReportOverflowHistogramMaximum(),
+    m_Settings->GetReportOverflowHistogramBins()
+  );
+
   bool Return = m_Melinator.CreateReport();
 
   if (Return == false) {
diff --git a/src/fretalon/melinator/src/MGUIReportCreation.cxx b/src/fretalon/melinator/src/MGUIReportCreation.cxx
new file mode 100644
index 000000000..08fef68ec
--- /dev/null
+++ b/src/fretalon/melinator/src/MGUIReportCreation.cxx
@@ -0,0 +1,241 @@
+/*
+ * MGUIReportCreation.cxx
+ *
+ *
+ * Copyright (C) by Andreas Zoglauer.
+ * All rights reserved.
+ *
+ *
+ * This code implementation is the intellectual property of
+ * Andreas Zoglauer.
+ *
+ * By copying, distributing or modifying the Program (or any work
+ * based on the Program) you indicate your acceptance of this statement,
+ * and all its terms.
+ *
+ */
+
+
+////////////////////////////////////////////////////////////////////////////////
+//
+// MGUIReportCreation
+//
+////////////////////////////////////////////////////////////////////////////////
+
+
+// Include the header:
+#include "MGUIReportCreation.h"
+
+// Standard libs:
+
+// ROOT libs:
+
+// MEGAlib libs:
+#include "MStreams.h"
+#include "MFile.h"
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+#ifdef ___CLING___
+ClassImp(MGUIReportCreation)
+#endif
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+MGUIReportCreation::MGUIReportCreation(const TGWindow* Parent, const TGWindow* Main, MSettingsMelinator* Settings, bool& OkPressed)
+  : MGUIDialog(Parent, Main), m_OkPressed(OkPressed)
+{
+  // Construct an instance of MGUIReportCreation and bring it to the screen
+
+  m_Settings = Settings;
+  m_OkPressed = false;
+
+  // use hierarchical cleaning
+  SetCleanup(kDeepCleanup);
+
+  Create();
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+MGUIReportCreation::~MGUIReportCreation()
+{
+  // Delete an instance of MGUIReportCreation
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+void MGUIReportCreation::Create()
+{
+  // Create the main window
+
+  // We start with a name and an icon...
+  SetWindowName("Calibration report");
+
+  AddSubTitle("Choose the options for the calibration report:");
+
+  TGLayoutHints* FirstLayout = new TGLayoutHints(kLHintsCenterX | kLHintsTop | kLHintsExpandX, 20*m_FontScaler, 20*m_FontScaler, 0*m_FontScaler, 20*m_FontScaler);
+  TGLayoutHints* DimensionLayout = new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, 20*m_FontScaler, 20*m_FontScaler, 0*m_FontScaler, 0*m_FontScaler);
+  TGLayoutHints* BinLayout = new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, 40*m_FontScaler, 20*m_FontScaler, 0*m_FontScaler, 20*m_FontScaler);
+
+
+  m_FileName = new MGUIEFileSelector(this, "Save report as...", m_Settings->GetReportFileName());
+  m_FileName->SetFileType("Report file", "*.pdf");
+  //FileName->ChangeOptions(kFixedWidth);
+  //FileName->SetWidth(m_FontScaler*500);
+  AddFrame(m_FileName, FirstLayout);
+  
+
+
+  m_ADCDimension = new MGUIEMinMaxEntry(this,
+                                        MString("ADC histogram:"),
+                                        false,
+                                        MString("Minimum [ADC units]: "),
+                                        MString("Maximum [ADC units]: "),
+                                        m_Settings->GetReportADCHistogramMinimum(),
+                                        m_Settings->GetReportADCHistogramMaximum(),
+                                        true,
+                                        0.0);
+  AddFrame(m_ADCDimension, DimensionLayout);
+
+  m_ADCBins = new MGUIEEntry(this, "Number of Bins:", false, m_Settings->GetReportADCHistogramBins(), true, 1);
+  AddFrame(m_ADCBins, BinLayout);
+
+
+  m_EnergyDimension = new MGUIEMinMaxEntry(this,
+                                        MString("Energy histogram:"),
+                                        false,
+                                        MString("Minimum [keV]: "),
+                                        MString("Maximum [keV]: "),
+                                        m_Settings->GetReportEnergyHistogramMinimum(),
+                                        m_Settings->GetReportEnergyHistogramMaximum(),
+                                        true,
+                                        0.0);
+  AddFrame(m_EnergyDimension, DimensionLayout);
+
+  m_EnergyBins = new MGUIEEntry(this, "Number of Bins:", false, m_Settings->GetReportEnergyHistogramBins(), true, 1);
+  AddFrame(m_EnergyBins, BinLayout);
+
+
+
+  m_ThresholdDimension = new MGUIEMinMaxEntry(this,
+                                        MString("Threshold histogram:"),
+                                        false,
+                                        MString("Minimum [keV]: "),
+                                        MString("Maximum [keV]: "),
+                                        m_Settings->GetReportThresholdHistogramMinimum(),
+                                        m_Settings->GetReportThresholdHistogramMaximum(),
+                                        true,
+                                        0.0);
+  AddFrame(m_ThresholdDimension, DimensionLayout);
+
+  m_ThresholdBins = new MGUIEEntry(this, "Number of Bins:", false, m_Settings->GetReportThresholdHistogramBins(), true, 1);
+  AddFrame(m_ThresholdBins, BinLayout);
+
+
+
+  m_OverflowDimension = new MGUIEMinMaxEntry(this,
+                                        MString("Overflow histogram:"),
+                                        false,
+                                        MString("Minimum [keV]: "),
+                                        MString("Maximum [keV]: "),
+                                        m_Settings->GetReportOverflowHistogramMinimum(),
+                                        m_Settings->GetReportOverflowHistogramMaximum(),
+                                        true,
+                                        0.0);
+  AddFrame(m_OverflowDimension, DimensionLayout);
+
+  m_OverflowBins = new MGUIEEntry(this, "Number of Bins:", false, m_Settings->GetReportOverflowHistogramBins(), true, 1);
+  AddFrame(m_OverflowBins, BinLayout);
+
+
+
+  AddOKCancelButtons();
+
+  PositionWindow(GetDefaultWidth(), GetDefaultHeight(), true);
+
+  // and bring it to the screen.
+  MapSubwindows();
+  MapWindow();  
+
+  Layout();
+
+  fClient->WaitFor(this);
+ 
+  return;
+}
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MGUIReportCreation::ProcessMessage(long Message, long Parameter1, long Parameter2)
+{
+  // Process the messages for this application
+
+  switch (GET_MSG(Message)) {
+  case kC_COMMAND:
+    switch (GET_SUBMSG(Message)) {
+    case kCM_BUTTON:
+      break;
+    default:
+      break;
+    }
+  default:
+    break;
+  }
+
+  return MGUIDialog::ProcessMessage(Message, Parameter1, Parameter2);
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+//! Action after the Apply or OK button has been pressed.
+bool MGUIReportCreation::OnApply()
+{
+  if (m_ADCDimension->CheckRange(0.0, 100000.0, 0.0, 100000.0, true) == false) return false;
+  if (m_ADCBins->IsInt(1, 100000) == false) return false;
+
+  if (m_EnergyDimension->CheckRange(0.0, 100000.0, 0.0, 100000.0, true) == false) return false;
+  if (m_EnergyBins->IsInt(1, 100000) == false) return false;
+
+  if (m_ThresholdDimension->CheckRange(0.0, 100000.0, 0.0, 100000.0, true) == false) return false;
+  if (m_ThresholdBins->IsInt(1, 100000) == false) return false;
+
+  if (m_OverflowDimension->CheckRange(0.0, 100000.0, 0.0, 100000.0, true) == false) return false;
+  if (m_OverflowBins->IsInt(1, 100000) == false) return false;
+
+  m_Settings->SetReportFileName(m_FileName->GetFileName());
+
+  m_Settings->SetReportADCHistogramMinimum(m_ADCDimension->GetMinValue());
+  m_Settings->SetReportADCHistogramMaximum(m_ADCDimension->GetMaxValue());
+  m_Settings->SetReportADCHistogramBins(m_ADCBins->GetAsInt());
+
+  m_Settings->SetReportEnergyHistogramMinimum(m_EnergyDimension->GetMinValue());
+  m_Settings->SetReportEnergyHistogramMaximum(m_EnergyDimension->GetMaxValue());
+  m_Settings->SetReportEnergyHistogramBins(m_EnergyBins->GetAsInt());
+
+  m_Settings->SetReportThresholdHistogramMinimum(m_ThresholdDimension->GetMinValue());
+  m_Settings->SetReportThresholdHistogramMaximum(m_ThresholdDimension->GetMaxValue());
+  m_Settings->SetReportThresholdHistogramBins(m_ThresholdBins->GetAsInt());
+
+  m_Settings->SetReportOverflowHistogramMinimum(m_OverflowDimension->GetMinValue());
+  m_Settings->SetReportOverflowHistogramMaximum(m_OverflowDimension->GetMaxValue());
+  m_Settings->SetReportOverflowHistogramBins(m_OverflowBins->GetAsInt());
+
+  m_OkPressed = true;
+
+  return true;
+}
+
+
+// MGUIReportCreation: the end...
+////////////////////////////////////////////////////////////////////////////////
diff --git a/src/fretalon/melinator/src/MMelinator.cxx b/src/fretalon/melinator/src/MMelinator.cxx
index 6c160824d..e2f4cb76d 100644
--- a/src/fretalon/melinator/src/MMelinator.cxx
+++ b/src/fretalon/melinator/src/MMelinator.cxx
@@ -122,6 +122,24 @@ MMelinator::MMelinator()
   m_CalibrationModelEnergyAssignmentMethod = MCalibrateEnergyAssignEnergyModes::e_LinearZeroCrossing;
   m_CalibrationModelDeterminationMethod = MCalibrateEnergyDetermineModel::c_CalibrationModelStepWise;
   
+  m_ReportFileName = "MelinatorReport.pdf";
+
+  m_ReportADCHistogramMinimum = 0;
+  m_ReportADCHistogramMaximum = 10000;
+  m_ReportADCHistogramBins = 1000;
+
+  m_ReportEnergyHistogramMinimum = 0;
+  m_ReportEnergyHistogramMaximum = 2000;
+  m_ReportEnergyHistogramBins = 500;
+
+  m_ReportThresholdHistogramMinimum = 0;
+  m_ReportThresholdHistogramMaximum = 40;
+  m_ReportThresholdHistogramBins = 40;
+
+  m_ReportOverflowHistogramMinimum = 1500;
+  m_ReportOverflowHistogramMaximum = 2500;
+  m_ReportOverflowHistogramBins = 100;
+
   m_NThreads = thread::hardware_concurrency();
   if (m_NThreads < 1) m_NThreads = 1;
   
@@ -1527,6 +1545,23 @@ bool MMelinator::ReCalibrateModel(unsigned int Collection)
 //! Save the calibration in e-cal format
 bool MMelinator::Save(MString FileName)
 {
+  if (m_CalibrationStore.GetNumberOfElements() == 0) {
+    mgui<<"You need to run the calibration first, before saving the results."<<error;
+    return true; // True: No subsequent error messages required
+  } else {
+    bool FoundOne = false;
+    for (unsigned int c = 0; c < m_CalibrationStore.GetNumberOfElements(); ++c) {
+      if (dynamic_cast<MCalibrationSpectrum*>(&(m_CalibrationStore.GetCalibration(c))) != nullptr) {
+        FoundOne = true;
+        break;
+      }
+    }
+    if (FoundOne == false) {
+      mgui<<"You need to run the calibration first, before saving the results."<<error;
+      return true; // True: No subsequent error messages required
+    }
+  }
+
   ofstream out;
   out.open(FileName);
   if (out.is_open() == false) {
@@ -1581,25 +1616,32 @@ bool MMelinator::Save(MString FileName)
 //! Create a calibration report
 bool MMelinator::CreateReport()
 {
-  // Create a calibration report
-
-  double MaxADCs = 5000;
-  double MaxEnergy = 500;
-  double ThresholdMaxEnergy = 35;
-  double OverflowMinEnergy = 1750;
-  double OverflowMaxEnergy = 3000;
-  MString OutputFileName = "MelinatorReport.pdf";
-
+  if (m_CalibrationStore.GetNumberOfElements() == 0) {
+    mgui<<"You need to run the calibration first, before creating a report."<<error;
+    return true; // True: No subsequent error messages required
+  } else {
+    bool FoundOne = false;
+    for (unsigned int c = 0; c < m_CalibrationStore.GetNumberOfElements(); ++c) {
+      if (dynamic_cast<MCalibrationSpectrum*>(&(m_CalibrationStore.GetCalibration(c))) != nullptr) {
+        FoundOne = true;
+        break;
+      }
+    }
+    if (FoundOne == false) {
+      mgui<<"You need to run the calibration first, before creating a report."<<error;
+      return true; // True: No subsequent error messages required
+    }
+  }
 
   // Section 1: Create histograms
 
-  TH2D* AllFittedEnergies = new TH2D("Fitted", "Fitted", MaxEnergy/2, 0, MaxEnergy, m_CalibrationStore.GetNumberOfElements()+1, -0.5, m_CalibrationStore.GetNumberOfElements() + 0.5);
+  TH2D* AllFittedEnergies = new TH2D("Fitted", "Fitted", m_ReportEnergyHistogramBins, m_ReportEnergyHistogramMinimum, m_ReportEnergyHistogramMaximum, m_CalibrationStore.GetNumberOfElements()+1, -0.5, m_CalibrationStore.GetNumberOfElements() + 0.5);
   AllFittedEnergies->SetXTitle("Energy [keV]");
   AllFittedEnergies->SetYTitle("ReadOutUnit ID");
   AllFittedEnergies->SetContour(99);
 
 
-  TH2D* AllRawADCs = new TH2D("RawADCs", "RawADCs", MaxADCs/4, 0, MaxADCs, m_CalibrationStore.GetNumberOfElements()+1, -0.5, m_CalibrationStore.GetNumberOfElements() + 0.5);
+  TH2D* AllRawADCs = new TH2D("RawADCs", "RawADCs", m_ReportADCHistogramBins, m_ReportADCHistogramMinimum, m_ReportADCHistogramMaximum, m_CalibrationStore.GetNumberOfElements()+1, -0.5, m_CalibrationStore.GetNumberOfElements() + 0.5);
   AllRawADCs->SetXTitle("ADCs [rou's]");
   AllRawADCs->SetYTitle("ReadOutUnit ID");
   AllRawADCs->SetContour(99);
@@ -1645,28 +1687,29 @@ bool MMelinator::CreateReport()
 
           TitlesMap[DetectorAndSide] = Name;
 
-          ADCsMap[DetectorAndSide] = new TH2D("", "ADC spectrum", MaxADCs/2, 0, MaxADCs, MaxStripID+1, -0.5, MaxStripID + 0.5);
+          ADCsMap[DetectorAndSide] = new TH2D("", "ADC spectrum", m_ReportADCHistogramBins, m_ReportADCHistogramMinimum, m_ReportADCHistogramMaximum, MaxStripID+1, -0.5, MaxStripID + 0.5);
           ADCsMap[DetectorAndSide]->SetXTitle("ADC units");
           ADCsMap[DetectorAndSide]->SetYTitle("Strip ID");
           ADCsMap[DetectorAndSide]->SetContour(99);
 
-          EnergiesMap[DetectorAndSide] = new TH2D("", "Energy spectrum", MaxEnergy/2, 0, MaxEnergy, MaxStripID+1, -0.5, MaxStripID + 0.5);
+          EnergiesMap[DetectorAndSide] = new TH2D("", "Energy spectrum", m_ReportEnergyHistogramBins, m_ReportEnergyHistogramMinimum, m_ReportEnergyHistogramMaximum, MaxStripID+1, -0.5, MaxStripID + 0.5);
           EnergiesMap[DetectorAndSide]->SetXTitle("Energy [keV]");
           EnergiesMap[DetectorAndSide]->SetYTitle("Strip ID");
           EnergiesMap[DetectorAndSide]->SetContour(99);
 
-          ThresholdsMap[DetectorAndSide] = new TH2D("", "Thresholds", ThresholdMaxEnergy, 0, ThresholdMaxEnergy, MaxStripID+1, -0.5, MaxStripID + 0.5);
+          ThresholdsMap[DetectorAndSide] = new TH2D("", "Thresholds", m_ReportThresholdHistogramBins, m_ReportThresholdHistogramMinimum, m_ReportThresholdHistogramMaximum, MaxStripID+1, -0.5, MaxStripID + 0.5);
           ThresholdsMap[DetectorAndSide]->SetXTitle("Energy [keV]");
           ThresholdsMap[DetectorAndSide]->SetYTitle("Strip ID");
           ThresholdsMap[DetectorAndSide]->SetContour(99);
 
-          OverflowsMap[DetectorAndSide] = new TH2D("", "Overflows", (OverflowMaxEnergy - OverflowMinEnergy)/10, OverflowMinEnergy, OverflowMaxEnergy, MaxStripID+1, -0.5, MaxStripID + 0.5);
+          OverflowsMap[DetectorAndSide] = new TH2D("", "Overflows", m_ReportOverflowHistogramBins, m_ReportOverflowHistogramMinimum, m_ReportOverflowHistogramMaximum, MaxStripID+1, -0.5, MaxStripID + 0.5);
           OverflowsMap[DetectorAndSide]->SetXTitle("Energy [keV]");
           OverflowsMap[DetectorAndSide]->SetYTitle("Strip ID");
           OverflowsMap[DetectorAndSide]->SetContour(99);
         }
 
         MCalibration& C = m_CalibrationStore.GetCalibration(c);
+        if (dynamic_cast<MCalibrationSpectrum*>(&C) == nullptr) continue;
         MCalibrationSpectrum& CS = static_cast<MCalibrationSpectrum&>(C);
         for (unsigned int g = 0; g < CS.GetNumberOfReadOutDataGroups(); ++g) {
           for (unsigned int i = 0; i < m_Isotopes[g].size(); ++i) {
@@ -1714,6 +1757,7 @@ bool MMelinator::CreateReport()
       CurrentHistOverflows = OverflowsMap[DetectorAndSide];
       CurrentStripID = ROE_DS.GetStripID();
     }
+    if (dynamic_cast<MCalibrationSpectrum*>(&(m_CalibrationStore.GetCalibration(c))) == nullptr) continue;
     MCalibrationSpectrum& CS = dynamic_cast<MCalibrationSpectrum&>(m_CalibrationStore.GetCalibration(c));
     MCalibrationModel& M = CS.GetEnergyModel();
 
@@ -1875,7 +1919,7 @@ bool MMelinator::CreateReport()
   }
 
 
-  TitleCanvas->Print(OutputFileName + "(");
+  TitleCanvas->Print(m_ReportFileName + "(");
 
 
   while (IterTitles != TitlesMap.end() && IterEnergies != EnergiesMap.end() && IterADCs != ADCsMap.end() && IterThresholds != ThresholdsMap.end() && IterOverflows != OverflowsMap.end() && IterFWHMes != FWHMesMap.end() && IterResiduals != ResidualsMap.end()) {
@@ -1918,7 +1962,7 @@ bool MMelinator::CreateReport()
     SpectrumPages->cd();
     SpectrumPages->Update();
 
-    SpectrumPages->Print(OutputFileName);   // middle pages
+    SpectrumPages->Print(m_ReportFileName);   // middle pages
 
 
     // Page 2: Thresholds & Overflows
@@ -1959,7 +2003,7 @@ bool MMelinator::CreateReport()
     ThresholdsPages->cd();
     ThresholdsPages->Update();
 
-    ThresholdsPages->Print(OutputFileName);   // middle pages
+    ThresholdsPages->Print(m_ReportFileName);   // middle pages
 
 
     // Page 3+ is lines:
@@ -2002,11 +2046,7 @@ bool MMelinator::CreateReport()
       LineFitPages->cd();
       LineFitPages->Update();
 
-      if (next(IterFWHMesInner) == IterFWHMes->second.end() && next(IterTitles) == TitlesMap.end()) {
-        LineFitPages->Print(OutputFileName + ")");  // close PDF
-      } else {
-        LineFitPages->Print(OutputFileName);   // middle pages
-      }
+      LineFitPages->Print(m_ReportFileName);   // middle pages
 
       ++IterFWHMesInner;
       ++IterResidualsInner;
@@ -2023,10 +2063,24 @@ bool MMelinator::CreateReport()
     ++IterResiduals;
   }
 
+  TCanvas* EndPageCanvas = new TCanvas("EndPage", "EndPage", 850, 1100);
+  EndPageCanvas->cd();
+
+  TPaveText* TheEnd = new TPaveText(0.1, 0.75, 0.9, 0.9, "NDC");
+  TheEnd->AddText("The End");
+  TheEnd->SetTextFont(62);
+  TheEnd->SetTextSize(0.02);
+  TheEnd->SetFillColor(0);
+  TheEnd->SetBorderSize(0);
+  TheEnd->SetLineColor(0);
+  TheEnd->Draw();
+
+  EndPageCanvas->Print(m_ReportFileName + ")");  // close PDF
+
   gROOT->SetBatch(false);
 
 
-  int Return = gSystem->Exec(MString("") + "[ -x \"$(command -v xdg-open)\" ] && xdg-open " + OutputFileName + " || { [ -x \"$(command -v open)\" ] && open " + OutputFileName + "; }");
+  int Return = gSystem->Exec(MString("") + "[ -x \"$(command -v xdg-open)\" ] && xdg-open " + m_ReportFileName + " || { [ -x \"$(command -v open)\" ] && open " + m_ReportFileName + "; }");
 
   if (Return != 0) {
     mgui<<"Failed to open PDF. Return code: "<<Return<<error;
diff --git a/src/fretalon/melinator/src/MSettingsMelinator.cxx b/src/fretalon/melinator/src/MSettingsMelinator.cxx
index b64697542..e89b5aa4d 100644
--- a/src/fretalon/melinator/src/MSettingsMelinator.cxx
+++ b/src/fretalon/melinator/src/MSettingsMelinator.cxx
@@ -86,6 +86,25 @@ MSettingsMelinator::MSettingsMelinator(bool AutoLoad) : MSettings("MelinatorConf
   m_MinimumTemperature = -numeric_limits<double>::max();
   m_MaximumTemperature = +numeric_limits<double>::max();
   
+  m_ReportFileName = "MelinatorReport.pdf";
+
+  m_ReportADCHistogramMinimum = 0;
+  m_ReportADCHistogramMaximum = 10000;
+  m_ReportADCHistogramBins = 1000;
+
+  m_ReportEnergyHistogramMinimum = 0;
+  m_ReportEnergyHistogramMaximum = 2000;
+  m_ReportEnergyHistogramBins = 500;
+
+  m_ReportThresholdHistogramMinimum = 0;
+  m_ReportThresholdHistogramMaximum = 40;
+  m_ReportThresholdHistogramBins = 40;
+
+  m_ReportOverflowHistogramMinimum = 1500;
+  m_ReportOverflowHistogramMaximum = 2500;
+  m_ReportOverflowHistogramBins = 100;
+
+
   if (AutoLoad == true) {
     Read();
   }
@@ -178,6 +197,25 @@ bool MSettingsMelinator::WriteXml(MXmlNode* Node)
   
   new MXmlNode(Node, "SaveAsFileName", m_SaveAsFileName);
   
+  new MXmlNode(Node, "ReportFileName", m_ReportFileName);
+
+  new MXmlNode(Node, "ReportADCHistogramMinimum", m_ReportADCHistogramMinimum);
+  new MXmlNode(Node, "ReportADCHistogramMaximum", m_ReportADCHistogramMaximum);
+  new MXmlNode(Node, "ReportADCHistogramBins", m_ReportADCHistogramBins);
+
+  new MXmlNode(Node, "ReportEnergyHistogramMinimum", m_ReportEnergyHistogramMinimum);
+  new MXmlNode(Node, "ReportEnergyHistogramMaximum", m_ReportEnergyHistogramMaximum);
+  new MXmlNode(Node, "ReportEnergyHistogramBins", m_ReportEnergyHistogramBins);
+
+  new MXmlNode(Node, "ReportThresholdHistogramMinimum", m_ReportThresholdHistogramMinimum);
+  new MXmlNode(Node, "ReportThresholdHistogramMaximum", m_ReportThresholdHistogramMaximum);
+  new MXmlNode(Node, "ReportThresholdHistogramBins", m_ReportThresholdHistogramBins);
+
+  new MXmlNode(Node, "ReportOverflowHistogramMinimum", m_ReportOverflowHistogramMinimum);
+  new MXmlNode(Node, "ReportOverflowHistogramMaximum", m_ReportOverflowHistogramMaximum);
+  new MXmlNode(Node, "ReportOverflowHistogramBins", m_ReportOverflowHistogramBins);
+
+
   // Not stored, since command line options:
   // new MXmlNode(Node, "SelectedDetectorID", m_SelectedDetectorID);
   // new MXmlNode(Node, "SelectedDetectorSide", m_SelectedDetectorSide);
@@ -298,6 +336,54 @@ bool MSettingsMelinator::ReadXml(MXmlNode* Node)
   if ((aNode = Node->GetNode("SaveAsFileName")) != 0) {
     m_SaveAsFileName = aNode->GetValueAsString();
   }
+
+
+  if ((aNode = Node->GetNode("ReportFileName")) != 0) {
+    m_ReportFileName = aNode->GetValueAsString();
+  }
+
+  if ((aNode = Node->GetNode("ReportADCHistogramMinimum")) != 0) {
+    m_ReportADCHistogramMinimum = aNode->GetValueAsDouble();
+  }
+  if ((aNode = Node->GetNode("ReportADCHistogramMaximum")) != 0) {
+    m_ReportADCHistogramMaximum = aNode->GetValueAsDouble();
+  }
+  if ((aNode = Node->GetNode("ReportADCHistogramBins")) != 0) {
+    m_ReportADCHistogramBins = aNode->GetValueAsUnsignedInt();
+  }
+
+  if ((aNode = Node->GetNode("ReportEnergyHistogramMinimum")) != 0) {
+    m_ReportEnergyHistogramMinimum = aNode->GetValueAsDouble();
+  }
+  if ((aNode = Node->GetNode("ReportEnergyHistogramMaximum")) != 0) {
+    m_ReportEnergyHistogramMaximum = aNode->GetValueAsDouble();
+  }
+  if ((aNode = Node->GetNode("ReportEnergyHistogramBins")) != 0) {
+    m_ReportEnergyHistogramBins = aNode->GetValueAsUnsignedInt();
+  }
+
+  if ((aNode = Node->GetNode("ReportThresholdHistogramMinimum")) != 0) {
+    m_ReportThresholdHistogramMinimum = aNode->GetValueAsDouble();
+  }
+  if ((aNode = Node->GetNode("ReportThresholdHistogramMaximum")) != 0) {
+    m_ReportThresholdHistogramMaximum = aNode->GetValueAsDouble();
+  }
+  if ((aNode = Node->GetNode("ReportThresholdHistogramBins")) != 0) {
+    m_ReportThresholdHistogramBins = aNode->GetValueAsUnsignedInt();
+  }
+
+  if ((aNode = Node->GetNode("ReportOverflowHistogramMinimum")) != 0) {
+    m_ReportOverflowHistogramMinimum = aNode->GetValueAsDouble();
+  }
+  if ((aNode = Node->GetNode("ReportOverflowHistogramMaximum")) != 0) {
+    m_ReportOverflowHistogramMaximum = aNode->GetValueAsDouble();
+  }
+  if ((aNode = Node->GetNode("ReportOverflowHistogramBins")) != 0) {
+    m_ReportOverflowHistogramBins = aNode->GetValueAsUnsignedInt();
+  }
+
+
+
  
   /*
   // Not stored since command line options

From 1f9c4fd9bcc9875ddfad25657d10d68599b61dea Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Wed, 21 May 2025 20:50:38 -0700
Subject: [PATCH 135/192] BUG: Revert "ADD: New exception:
 MExceptionValueNotFound"

This reverts commit ae0db87c65130e20a5d382d90216b3f7943b9cb2.
---
 src/global/misc/inc/MExceptions.h   | 70 +----------------------------
 src/global/misc/src/MExceptions.cxx |  1 -
 2 files changed, 2 insertions(+), 69 deletions(-)

diff --git a/src/global/misc/inc/MExceptions.h b/src/global/misc/inc/MExceptions.h
index 2232e3fd3..4f75c0e35 100644
--- a/src/global/misc/inc/MExceptions.h
+++ b/src/global/misc/inc/MExceptions.h
@@ -114,8 +114,8 @@ class MExceptionTestFailed : public MException
 ////////////////////////////////////////////////////////////////////////////////
 
 
-//! This exception is thrown when a parameter is out of range and
-//! the error cannot be recovered gracefully
+//! This exception is thrown when a parmeter is out of range and 
+//! the error cannot be reconvered gracefully
 class MExceptionParameterOutOfRange : public MException
 {
 public:
@@ -184,72 +184,6 @@ class MExceptionIndexOutOfBounds : public MException
 ////////////////////////////////////////////////////////////////////////////////
 
 
-//! This exception is thrown when an value cannot be found (e.g. in a map or vector) and
-//! the error cannot be recovered gracefully
-//! This class would ideal for using templeates, but ROOT does not allow that
-class MExceptionValueNotFound : public MException
-{
-public:
-  //! Default constructor
-  MExceptionValueNotFound() : MException() {
-    m_Description = "Value not found!";
-  }
-  //! Constructor giving the not found value and a descriptor where the value cannot be found, e.g. "vector of strip IDs"
-  MExceptionValueNotFound(double& Value, const MString& Where) : MException() {
-    Set(Value, Where);
-  }
-  //! Constructor giving the not found value and a descriptor where the value cannot be found, e.g. "vector of strip IDs"
-  MExceptionValueNotFound(int& Value, const MString& Where) : MException() {
-    Set(Value, Where);
-  }
-  //! Constructor giving the not found value and a descriptor where the value cannot be found, e.g. "vector of strip IDs"
-  MExceptionValueNotFound(unsigned int& Value, const MString& Where) : MException() {
-    Set(Value, Where);
-  }
-  //! Constructor giving the not found value and a descriptor where the value cannot be found, e.g. "vector of strip IDs"
-  MExceptionValueNotFound(MString& Value, const MString& Where) : MException() {
-    Set(Value, Where);
-  }
-  //! Default destructor
-  virtual ~MExceptionValueNotFound() throw() {}
-  //! Set the not found value and a descriptor where the value cannot be found, e.g. "vector of strip IDs"
-  void Set(double& Value, const MString& Where) {
-    ostringstream stream;
-    stream<<"The value \'"<<Value<<"\' cannot be found in "<<Where<<"."<<endl;
-    m_Description = stream.str();
-  }
-  //! Set the not found value and a descriptor where the value cannot be found, e.g. "vector of strip IDs"
-  void Set(unsigned int& Value, const MString& Where) {
-    ostringstream stream;
-    stream<<"The value \'"<<Value<<"\' cannot be found in "<<Where<<"."<<endl;
-    m_Description = stream.str();
-  }
-  //! Set the not found value and a descriptor where the value cannot be found, e.g. "vector of strip IDs"
-  void Set(int& Value, const MString& Where) {
-    ostringstream stream;
-    stream<<"The value \'"<<Value<<"\' cannot be found in "<<Where<<"."<<endl;
-    m_Description = stream.str();
-  }
-  //! Set the not found value and a descriptor where the value cannot be found, e.g. "vector of strip IDs"
-  void Set(MString& Value, const MString& Where) {
-    ostringstream stream;
-    stream<<"The value \'"<<Value<<"\' cannot be found in "<<Where<<"."<<endl;
-    m_Description = stream.str();
-  }
-
-private:
-
-
-#ifdef ___CLING___
-public:
-  ClassDef(MExceptionValueNotFound, 1)
-#endif
-};
-
-
-////////////////////////////////////////////////////////////////////////////////
-
-
 //! This exception is thrown when an index is out-of-bounds and 
 //! the error cannot be recovered gracefully
 class MExceptionEmptyArray : public MException
diff --git a/src/global/misc/src/MExceptions.cxx b/src/global/misc/src/MExceptions.cxx
index a2517b433..7992477c4 100644
--- a/src/global/misc/src/MExceptions.cxx
+++ b/src/global/misc/src/MExceptions.cxx
@@ -41,7 +41,6 @@ ClassImp(MException)
 ClassImp(MExceptionTestFailed)
 ClassImp(MExceptionParameterOutOfRange)
 ClassImp(MExceptionIndexOutOfBounds)
-ClassImp(MExceptionValueNotFound)
 ClassImp(MExceptionEmptyArray)
 ClassImp(MExceptionValueOutOfBounds)
 ClassImp(MExceptionDivisionByZero)

From e4c47101a1ffca6ed6249dcb4ea244662c0602f7 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Wed, 21 May 2025 20:59:45 -0700
Subject: [PATCH 136/192] Revert "BUG: Revert "ADD: New exception:
 MExceptionValueNotFound""

This reverts commit 1f9c4fd9bcc9875ddfad25657d10d68599b61dea.
---
 src/global/misc/inc/MExceptions.h   | 70 ++++++++++++++++++++++++++++-
 src/global/misc/src/MExceptions.cxx |  1 +
 2 files changed, 69 insertions(+), 2 deletions(-)

diff --git a/src/global/misc/inc/MExceptions.h b/src/global/misc/inc/MExceptions.h
index 4f75c0e35..2232e3fd3 100644
--- a/src/global/misc/inc/MExceptions.h
+++ b/src/global/misc/inc/MExceptions.h
@@ -114,8 +114,8 @@ class MExceptionTestFailed : public MException
 ////////////////////////////////////////////////////////////////////////////////
 
 
-//! This exception is thrown when a parmeter is out of range and 
-//! the error cannot be reconvered gracefully
+//! This exception is thrown when a parameter is out of range and
+//! the error cannot be recovered gracefully
 class MExceptionParameterOutOfRange : public MException
 {
 public:
@@ -184,6 +184,72 @@ class MExceptionIndexOutOfBounds : public MException
 ////////////////////////////////////////////////////////////////////////////////
 
 
+//! This exception is thrown when an value cannot be found (e.g. in a map or vector) and
+//! the error cannot be recovered gracefully
+//! This class would ideal for using templeates, but ROOT does not allow that
+class MExceptionValueNotFound : public MException
+{
+public:
+  //! Default constructor
+  MExceptionValueNotFound() : MException() {
+    m_Description = "Value not found!";
+  }
+  //! Constructor giving the not found value and a descriptor where the value cannot be found, e.g. "vector of strip IDs"
+  MExceptionValueNotFound(double& Value, const MString& Where) : MException() {
+    Set(Value, Where);
+  }
+  //! Constructor giving the not found value and a descriptor where the value cannot be found, e.g. "vector of strip IDs"
+  MExceptionValueNotFound(int& Value, const MString& Where) : MException() {
+    Set(Value, Where);
+  }
+  //! Constructor giving the not found value and a descriptor where the value cannot be found, e.g. "vector of strip IDs"
+  MExceptionValueNotFound(unsigned int& Value, const MString& Where) : MException() {
+    Set(Value, Where);
+  }
+  //! Constructor giving the not found value and a descriptor where the value cannot be found, e.g. "vector of strip IDs"
+  MExceptionValueNotFound(MString& Value, const MString& Where) : MException() {
+    Set(Value, Where);
+  }
+  //! Default destructor
+  virtual ~MExceptionValueNotFound() throw() {}
+  //! Set the not found value and a descriptor where the value cannot be found, e.g. "vector of strip IDs"
+  void Set(double& Value, const MString& Where) {
+    ostringstream stream;
+    stream<<"The value \'"<<Value<<"\' cannot be found in "<<Where<<"."<<endl;
+    m_Description = stream.str();
+  }
+  //! Set the not found value and a descriptor where the value cannot be found, e.g. "vector of strip IDs"
+  void Set(unsigned int& Value, const MString& Where) {
+    ostringstream stream;
+    stream<<"The value \'"<<Value<<"\' cannot be found in "<<Where<<"."<<endl;
+    m_Description = stream.str();
+  }
+  //! Set the not found value and a descriptor where the value cannot be found, e.g. "vector of strip IDs"
+  void Set(int& Value, const MString& Where) {
+    ostringstream stream;
+    stream<<"The value \'"<<Value<<"\' cannot be found in "<<Where<<"."<<endl;
+    m_Description = stream.str();
+  }
+  //! Set the not found value and a descriptor where the value cannot be found, e.g. "vector of strip IDs"
+  void Set(MString& Value, const MString& Where) {
+    ostringstream stream;
+    stream<<"The value \'"<<Value<<"\' cannot be found in "<<Where<<"."<<endl;
+    m_Description = stream.str();
+  }
+
+private:
+
+
+#ifdef ___CLING___
+public:
+  ClassDef(MExceptionValueNotFound, 1)
+#endif
+};
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
 //! This exception is thrown when an index is out-of-bounds and 
 //! the error cannot be recovered gracefully
 class MExceptionEmptyArray : public MException
diff --git a/src/global/misc/src/MExceptions.cxx b/src/global/misc/src/MExceptions.cxx
index 7992477c4..a2517b433 100644
--- a/src/global/misc/src/MExceptions.cxx
+++ b/src/global/misc/src/MExceptions.cxx
@@ -41,6 +41,7 @@ ClassImp(MException)
 ClassImp(MExceptionTestFailed)
 ClassImp(MExceptionParameterOutOfRange)
 ClassImp(MExceptionIndexOutOfBounds)
+ClassImp(MExceptionValueNotFound)
 ClassImp(MExceptionEmptyArray)
 ClassImp(MExceptionValueOutOfBounds)
 ClassImp(MExceptionDivisionByZero)

From cf3d78b4a66ded151e43fe74be155193821eeaef Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Wed, 21 May 2025 20:59:45 -0700
Subject: [PATCH 137/192] Revert "ADD: UI to set report parameters"

This reverts commit b1bdc4b776af65794d1d18ab25bb4f29fbff9f8b.
---
 src/fretalon/melinator/Makefile               |   1 -
 .../melinator/inc/MGUIReportCreation.h        | 104 --------
 src/fretalon/melinator/inc/MMelinator.h       |  57 +----
 .../melinator/inc/MSettingsMelinator.h        | 110 +-------
 .../melinator/src/MGUIMainMelinator.cxx       |  23 --
 .../melinator/src/MGUIReportCreation.cxx      | 241 ------------------
 src/fretalon/melinator/src/MMelinator.cxx     | 102 ++------
 .../melinator/src/MSettingsMelinator.cxx      |  86 -------
 8 files changed, 35 insertions(+), 689 deletions(-)
 delete mode 100644 src/fretalon/melinator/inc/MGUIReportCreation.h
 delete mode 100644 src/fretalon/melinator/src/MGUIReportCreation.cxx

diff --git a/src/fretalon/melinator/Makefile b/src/fretalon/melinator/Makefile
index 4fcfd41be..61755b9fe 100644
--- a/src/fretalon/melinator/Makefile
+++ b/src/fretalon/melinator/Makefile
@@ -29,7 +29,6 @@ FILES_UI := \
 	MGUIEReadOutElementView \
 	MGUIEReadOutUnitsCanvas \
 	MGUILoadCalibration \
-	MGUIReportCreation \
 	MInterfaceMelinator \
 
 LIBRARIES := \
diff --git a/src/fretalon/melinator/inc/MGUIReportCreation.h b/src/fretalon/melinator/inc/MGUIReportCreation.h
deleted file mode 100644
index 456b5c934..000000000
--- a/src/fretalon/melinator/inc/MGUIReportCreation.h
+++ /dev/null
@@ -1,104 +0,0 @@
-/*
- * MGUIReportCreation.h
- *
- * Copyright (C) by Andreas Zoglauer.
- * All rights reserved.
- *
- * Please see the source-file for the copyright-notice.
- *
- */
-
-
-#ifndef __MGUIReportCreation__
-#define __MGUIReportCreation__
-
-
-////////////////////////////////////////////////////////////////////////////////
-
-
-// ROOT libs:
-#include "TGComboBox.h"
-
-// MEGAlib libs:
-#include "MGlobal.h"
-#include "MGUIDialog.h"
-#include "MSettingsMelinator.h"
-#include "MGUIEFileSelector.h"
-#include "MGUIEEntry.h"
-#include "MGUIEMinMaxEntry.h"
-
-// Forward declarations:
-
-
-////////////////////////////////////////////////////////////////////////////////
-
-
-//! GUI dialog showing the options for loading ans classifying the calibration file
-class MGUIReportCreation : public MGUIDialog
-{
-  // Public Interface:
- public:
-  //! Default constructor
-  MGUIReportCreation(const TGWindow* Parent, const TGWindow* Main, MSettingsMelinator* Settings, bool& OKPressed);
-  //! Default destructor
-  virtual ~MGUIReportCreation();
-
-  
-  // protected methods:
- protected:
-  //! Create the UI
-  virtual void Create();
-  //! Apply changes
-  virtual bool OnApply();
-  //! Process all messages
-  bool ProcessMessage(long Message, long Parameter1, long Parameter2);
-
-
-
-  // protected members:
- protected:
-
-
-  // private members:
- private:
-  //! The return message that OK was pressed
-  bool& m_OkPressed;
-
-  //! The settings file
-  MSettingsMelinator* m_Settings;
-
-  //! The report file name
-  MGUIEFileSelector* m_FileName;
-
-  //! ADC histogram: display min & max
-  MGUIEMinMaxEntry* m_ADCDimension;
-  //! ADC histogram: number of bins
-  MGUIEEntry* m_ADCBins;
-
-  //! Energy histogram: display min & max
-  MGUIEMinMaxEntry* m_EnergyDimension;
-  //! Energy histogram: number of bins
-  MGUIEEntry* m_EnergyBins;
-
-  //! Threshold histogram: display min & max
-  MGUIEMinMaxEntry* m_ThresholdDimension;
-  //! Threshold histogram: number of bins
-  MGUIEEntry* m_ThresholdBins;
-
-  //! Overflow histogram: display min & max
-  MGUIEMinMaxEntry* m_OverflowDimension;
-  //! Overflow histogram: number of bins
-  MGUIEEntry* m_OverflowBins;
-
-
-#ifdef ___CLING___
- public:
-  ClassDef(MGUIReportCreation, 0)
-#endif
-
-};
-
-#endif
-
-
-////////////////////////////////////////////////////////////////////////////////
diff --git a/src/fretalon/melinator/inc/MMelinator.h b/src/fretalon/melinator/inc/MMelinator.h
index 5706ff7c3..2c41e3559 100644
--- a/src/fretalon/melinator/inc/MMelinator.h
+++ b/src/fretalon/melinator/inc/MMelinator.h
@@ -164,27 +164,6 @@ class MMelinator
   //! Save the calibration in e-cal format
   bool Save(MString FileName);
 
-  //! Set the basic properties of the report
-  void SetReportProperties(MString FileName,
-                           double ADCMinimum, double ADCMaximum, unsigned int ADCBins,
-                           double EnergyMinimum, double EnergyMaximum, unsigned int EnergyBins,
-                           double ThresholdMinimum, double ThresholdMaximum, unsigned int ThresholdBins,
-                           double OverflowMinimum, double OverflowMaximum, unsigned int OverflowBins) {
-    m_ReportFileName = FileName;
-    m_ReportADCHistogramMinimum = ADCMinimum;
-    m_ReportADCHistogramMaximum = ADCMaximum;
-    m_ReportADCHistogramBins = ADCBins;
-    m_ReportEnergyHistogramMinimum = EnergyMinimum;
-    m_ReportEnergyHistogramMaximum = EnergyMaximum;
-    m_ReportEnergyHistogramBins = EnergyBins;
-    m_ReportThresholdHistogramMinimum = ThresholdMinimum;
-    m_ReportThresholdHistogramMaximum = ThresholdMaximum;
-    m_ReportThresholdHistogramBins = ThresholdBins;
-    m_ReportOverflowHistogramMinimum = OverflowMinimum;
-    m_ReportOverflowHistogramMaximum = OverflowMaximum;
-    m_ReportOverflowHistogramBins = OverflowBins;
-  };
-
   //! Create a calibration report
   bool CreateReport();
 
@@ -228,7 +207,7 @@ class MMelinator
   MReadOutStore m_Store;
   //! The storage for all calibrations
   MCalibrationStore m_CalibrationStore;
-
+  
   //! The selected detector ID (negative means all detectors)
   int m_SelectedDetectorID;
   
@@ -316,39 +295,7 @@ class MMelinator
   //! Time to determine model
   double m_TimeToDetermineModel;
   
-
-  //! Set the report file
-  MString m_ReportFileName;
-
-  //! The minimum value of the ADC histogram in the report
-  double m_ReportADCHistogramMinimum;
-  //! The maximum value of the ADC histogram in the report
-  double m_ReportADCHistogramMaximum;
-  //! The number of bins of the ADC histogram in the report
-  unsigned int m_ReportADCHistogramBins;
-
-  //! The minimum value of the Energy histogram in the report
-  double m_ReportEnergyHistogramMinimum;
-  //! The maximum value of the Energy histogram in the report
-  double m_ReportEnergyHistogramMaximum;
-  //! The number of bins of the Energy histogram in the report
-  unsigned int m_ReportEnergyHistogramBins;
-
-  //! The minimum value of the Threshold histogram in the report
-  double m_ReportThresholdHistogramMinimum;
-  //! The maximum value of the Threshold histogram in the report
-  double m_ReportThresholdHistogramMaximum;
-  //! The number of bins of the Threshold histogram in the report
-  unsigned int m_ReportThresholdHistogramBins;
-
-  //! The minimum value of the Overflow histogram in the report
-  double m_ReportOverflowHistogramMinimum;
-  //! The maximum value of the Overflow histogram in the report
-  double m_ReportOverflowHistogramMaximum;
-  //! The number of bins of the Overflow histogram in the report
-  unsigned int m_ReportOverflowHistogramBins;
-
-
+  
   
 #ifdef ___CLING___
  public:
diff --git a/src/fretalon/melinator/inc/MSettingsMelinator.h b/src/fretalon/melinator/inc/MSettingsMelinator.h
index 07ba4641c..aec6cc4d7 100644
--- a/src/fretalon/melinator/inc/MSettingsMelinator.h
+++ b/src/fretalon/melinator/inc/MSettingsMelinator.h
@@ -164,73 +164,13 @@ class MSettingsMelinator : public MSettings
 
   //! Set the minimum allowed detector temperature
   void SetMinimumTemperature(double MinimumTemperature) { m_MinimumTemperature = MinimumTemperature; }
-  //! Get the minimum allowed detector temperature
+  //! Get the minimum allowed detector temperate
   double GetMinimumTemperature() const { return m_MinimumTemperature; }
-  //! Set the maximum allowed detector temperature
+  //! Set the minimum allowed detector temperature
   void SetMaximumTemperature(double MaximumTemperature) { m_MaximumTemperature = MaximumTemperature; }
-  //! Get the maximum allowed detector temperature
+  //! Get the minimum allowed detector temperate
   double GetMaximumTemperature() const { return m_MaximumTemperature; }
   
-
-  //! Set the report file name
-  void SetReportFileName(const MString& ReportFileName) { m_ReportFileName = ReportFileName; }
-  //! Get the report file name
-  MString GetReportFileName() const { return m_ReportFileName; }
-
-  //! Set the minimum value of the ADC histogram in the report
-  void SetReportADCHistogramMinimum(double ReportADCHistogramMinimum) { m_ReportADCHistogramMinimum = ReportADCHistogramMinimum; }
-  //! Get the minimum value of the ADC histogram in the report
-  double GetReportADCHistogramMinimum() const { return m_ReportADCHistogramMinimum; }
-  //! Set the maximum value of the ADC histogram in the report
-  void SetReportADCHistogramMaximum(double ReportADCHistogramMaximum) { m_ReportADCHistogramMaximum = ReportADCHistogramMaximum; }
-  //! Get the maximum value of the ADC histogram in the report
-  double GetReportADCHistogramMaximum() const { return m_ReportADCHistogramMaximum; }
-  //! Set the number of bins of the ADC histogram in the report
-  void SetReportADCHistogramBins(unsigned int ReportADCHistogramBins) { m_ReportADCHistogramBins = ReportADCHistogramBins; }
-  //! Get the number of bins of the ADC histogram in the report
-  unsigned int GetReportADCHistogramBins() const { return m_ReportADCHistogramBins; }
-
-  //! Set the minimum value of the Energy histogram in the report
-  void SetReportEnergyHistogramMinimum(double ReportEnergyHistogramMinimum) { m_ReportEnergyHistogramMinimum = ReportEnergyHistogramMinimum; }
-  //! Get the minimum value of the Energy histogram in the report
-  double GetReportEnergyHistogramMinimum() const { return m_ReportEnergyHistogramMinimum; }
-  //! Set the maximum value of the Energy histogram in the report
-  void SetReportEnergyHistogramMaximum(double ReportEnergyHistogramMaximum) { m_ReportEnergyHistogramMaximum = ReportEnergyHistogramMaximum; }
-  //! Get the maximum value of the Energy histogram in the report
-  double GetReportEnergyHistogramMaximum() const { return m_ReportEnergyHistogramMaximum; }
-  //! Set the number of bins of the Energy histogram in the report
-  void SetReportEnergyHistogramBins(unsigned int ReportEnergyHistogramBins) { m_ReportEnergyHistogramBins = ReportEnergyHistogramBins; }
-  //! Get the number of bins of the Energy histogram in the report
-  unsigned int GetReportEnergyHistogramBins() const { return m_ReportEnergyHistogramBins; }
-
-  //! Set the minimum value of the Threshold histogram in the report
-  void SetReportThresholdHistogramMinimum(double ReportThresholdHistogramMinimum) { m_ReportThresholdHistogramMinimum = ReportThresholdHistogramMinimum; }
-  //! Get the minimum value of the Threshold histogram in the report
-  double GetReportThresholdHistogramMinimum() const { return m_ReportThresholdHistogramMinimum; }
-  //! Set the maximum value of the Threshold histogram in the report
-  void SetReportThresholdHistogramMaximum(double ReportThresholdHistogramMaximum) { m_ReportThresholdHistogramMaximum = ReportThresholdHistogramMaximum; }
-  //! Get the maximum value of the Threshold histogram in the report
-  double GetReportThresholdHistogramMaximum() const { return m_ReportThresholdHistogramMaximum; }
-  //! Set the number of bins of the Threshold histogram in the report
-  void SetReportThresholdHistogramBins(unsigned int ReportThresholdHistogramBins) { m_ReportThresholdHistogramBins = ReportThresholdHistogramBins; }
-  //! Get the number of bins of the Threshold histogram in the report
-  unsigned int GetReportThresholdHistogramBins() const { return m_ReportThresholdHistogramBins; }
-
-  //! Set the minimum value of the Overflow histogram in the report
-  void SetReportOverflowHistogramMinimum(double ReportOverflowHistogramMinimum) { m_ReportOverflowHistogramMinimum = ReportOverflowHistogramMinimum; }
-  //! Get the minimum value of the Overflow histogram in the report
-  double GetReportOverflowHistogramMinimum() const { return m_ReportOverflowHistogramMinimum; }
-  //! Set the maximum value of the Overflow histogram in the report
-  void SetReportOverflowHistogramMaximum(double ReportOverflowHistogramMaximum) { m_ReportOverflowHistogramMaximum = ReportOverflowHistogramMaximum; }
-  //! Get the maximum value of the Overflow histogram in the report
-  double GetReportOverflowHistogramMaximum() const { return m_ReportOverflowHistogramMaximum; }
-  //! Set the number of bins of the Overflow histogram in the report
-  void SetReportOverflowHistogramBins(unsigned int ReportOverflowHistogramBins) { m_ReportOverflowHistogramBins = ReportOverflowHistogramBins; }
-  //! Get the number of bins of the Overflow histogram in the report
-  unsigned int GetReportOverflowHistogramBins() const { return m_ReportOverflowHistogramBins; }
-
-
-
   
 // protected members:
  protected:
@@ -291,52 +231,20 @@ class MSettingsMelinator : public MSettings
   //! Fitting model of the FWHM calibration model determination method
   unsigned int m_CalibrationModelDeterminationMethodFittingFWHMModel;
   
-  //! Set the save as file name
+  //! Set the save as file
   MString m_SaveAsFileName;
   
-  //! The single detector to use (negative means use all)
+  //! Set the single detector to use (negative means use all)
   int m_SelectedDetectorID;
-  //! The detector side to use (< 0: all, 0: negative side, 1: positive side, >=2: all)
+  //! Set the detector side to use (< 0: all, 0: negative side, 1: positive side, >=2: all)
   int m_SelectedDetectorSide;
 
-  //! The minimum allowed detector temperature
+  //! Set the minimum allowed detector temperature
   double m_MinimumTemperature;
-  //! The maximum allowed detector temperature
+  //! Set the maximum allowed detector temperature
   double m_MaximumTemperature;
   
-
-  //! Set the report file
-  MString m_ReportFileName;
-
-  //! The minimum value of the ADC histogram in the report
-  double m_ReportADCHistogramMinimum;
-  //! The maximum value of the ADC histogram in the report
-  double m_ReportADCHistogramMaximum;
-  //! The number of bins of the ADC histogram in the report
-  unsigned int m_ReportADCHistogramBins;
-
-  //! The minimum value of the Energy histogram in the report
-  double m_ReportEnergyHistogramMinimum;
-  //! The maximum value of the Energy histogram in the report
-  double m_ReportEnergyHistogramMaximum;
-  //! The number of bins of the Energy histogram in the report
-  unsigned int m_ReportEnergyHistogramBins;
-
-  //! The minimum value of the Threshold histogram in the report
-  double m_ReportThresholdHistogramMinimum;
-  //! The maximum value of the Threshold histogram in the report
-  double m_ReportThresholdHistogramMaximum;
-  //! The number of bins of the Threshold histogram in the report
-  unsigned int m_ReportThresholdHistogramBins;
-
-  //! The minimum value of the Overflow histogram in the report
-  double m_ReportOverflowHistogramMinimum;
-  //! The maximum value of the Overflow histogram in the report
-  double m_ReportOverflowHistogramMaximum;
-  //! The number of bins of the Overflow histogram in the report
-  unsigned int m_ReportOverflowHistogramBins;
-
-
+  
 #ifdef ___CLING___
  public:
   ClassDef(MSettingsMelinator, 0) // no description
diff --git a/src/fretalon/melinator/src/MGUIMainMelinator.cxx b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
index 9f3d9fe85..2da7aa7fc 100644
--- a/src/fretalon/melinator/src/MGUIMainMelinator.cxx
+++ b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
@@ -49,7 +49,6 @@ using namespace std;
 #include "MGUIAbout.h"
 #include "MGUIGeometry.h"
 #include "MGUILoadCalibration.h"
-#include "MGUIReportCreation.h"
 #include "MGUIEFileSelector.h"
 #include "MIsotope.h"
 #include "MIsotopeStore.h"
@@ -1457,28 +1456,6 @@ bool MGUIMainMelinator::OnSaveAs()
 //! Actions when the show report button has been pressed
 bool MGUIMainMelinator::OnShowReport()
 {
-  bool OKPressed = false;
-  new MGUIReportCreation(gClient->GetRoot(), this, m_Settings, OKPressed);
-  if (OKPressed == false) {
-    return false;
-  }
-
-  m_Melinator.SetReportProperties(
-    m_Settings->GetReportFileName(),
-    m_Settings->GetReportADCHistogramMinimum(),
-    m_Settings->GetReportADCHistogramMaximum(),
-    m_Settings->GetReportADCHistogramBins(),
-    m_Settings->GetReportEnergyHistogramMinimum(),
-    m_Settings->GetReportEnergyHistogramMaximum(),
-    m_Settings->GetReportEnergyHistogramBins(),
-    m_Settings->GetReportThresholdHistogramMinimum(),
-    m_Settings->GetReportThresholdHistogramMaximum(),
-    m_Settings->GetReportThresholdHistogramBins(),
-    m_Settings->GetReportOverflowHistogramMinimum(),
-    m_Settings->GetReportOverflowHistogramMaximum(),
-    m_Settings->GetReportOverflowHistogramBins()
-  );
-
   bool Return = m_Melinator.CreateReport();
 
   if (Return == false) {
diff --git a/src/fretalon/melinator/src/MGUIReportCreation.cxx b/src/fretalon/melinator/src/MGUIReportCreation.cxx
deleted file mode 100644
index 08fef68ec..000000000
--- a/src/fretalon/melinator/src/MGUIReportCreation.cxx
+++ /dev/null
@@ -1,241 +0,0 @@
-/*
- * MGUIReportCreation.cxx
- *
- *
- * Copyright (C) by Andreas Zoglauer.
- * All rights reserved.
- *
- *
- * This code implementation is the intellectual property of
- * Andreas Zoglauer.
- *
- * By copying, distributing or modifying the Program (or any work
- * based on the Program) you indicate your acceptance of this statement,
- * and all its terms.
- *
- */
-
-
-////////////////////////////////////////////////////////////////////////////////
-//
-// MGUIReportCreation
-//
-////////////////////////////////////////////////////////////////////////////////
-
-
-// Include the header:
-#include "MGUIReportCreation.h"
-
-// Standard libs:
-
-// ROOT libs:
-
-// MEGAlib libs:
-#include "MStreams.h"
-#include "MFile.h"
-
-////////////////////////////////////////////////////////////////////////////////
-
-
-#ifdef ___CLING___
-ClassImp(MGUIReportCreation)
-#endif
-
-
-////////////////////////////////////////////////////////////////////////////////
-
-
-MGUIReportCreation::MGUIReportCreation(const TGWindow* Parent, const TGWindow* Main, MSettingsMelinator* Settings, bool& OkPressed)
-  : MGUIDialog(Parent, Main), m_OkPressed(OkPressed)
-{
-  // Construct an instance of MGUIReportCreation and bring it to the screen
-
-  m_Settings = Settings;
-  m_OkPressed = false;
-
-  // use hierarchical cleaning
-  SetCleanup(kDeepCleanup);
-
-  Create();
-}
-
-
-////////////////////////////////////////////////////////////////////////////////
-
-
-MGUIReportCreation::~MGUIReportCreation()
-{
-  // Delete an instance of MGUIReportCreation
-}
-
-
-////////////////////////////////////////////////////////////////////////////////
-
-
-void MGUIReportCreation::Create()
-{
-  // Create the main window
-
-  // We start with a name and an icon...
-  SetWindowName("Calibration report");
-
-  AddSubTitle("Choose the options for the calibration report:");
-
-  TGLayoutHints* FirstLayout = new TGLayoutHints(kLHintsCenterX | kLHintsTop | kLHintsExpandX, 20*m_FontScaler, 20*m_FontScaler, 0*m_FontScaler, 20*m_FontScaler);
-  TGLayoutHints* DimensionLayout = new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, 20*m_FontScaler, 20*m_FontScaler, 0*m_FontScaler, 0*m_FontScaler);
-  TGLayoutHints* BinLayout = new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, 40*m_FontScaler, 20*m_FontScaler, 0*m_FontScaler, 20*m_FontScaler);
-
-
-  m_FileName = new MGUIEFileSelector(this, "Save report as...", m_Settings->GetReportFileName());
-  m_FileName->SetFileType("Report file", "*.pdf");
-  //FileName->ChangeOptions(kFixedWidth);
-  //FileName->SetWidth(m_FontScaler*500);
-  AddFrame(m_FileName, FirstLayout);
-  
-
-
-  m_ADCDimension = new MGUIEMinMaxEntry(this,
-                                        MString("ADC histogram:"),
-                                        false,
-                                        MString("Minimum [ADC units]: "),
-                                        MString("Maximum [ADC units]: "),
-                                        m_Settings->GetReportADCHistogramMinimum(),
-                                        m_Settings->GetReportADCHistogramMaximum(),
-                                        true,
-                                        0.0);
-  AddFrame(m_ADCDimension, DimensionLayout);
-
-  m_ADCBins = new MGUIEEntry(this, "Number of Bins:", false, m_Settings->GetReportADCHistogramBins(), true, 1);
-  AddFrame(m_ADCBins, BinLayout);
-
-
-  m_EnergyDimension = new MGUIEMinMaxEntry(this,
-                                        MString("Energy histogram:"),
-                                        false,
-                                        MString("Minimum [keV]: "),
-                                        MString("Maximum [keV]: "),
-                                        m_Settings->GetReportEnergyHistogramMinimum(),
-                                        m_Settings->GetReportEnergyHistogramMaximum(),
-                                        true,
-                                        0.0);
-  AddFrame(m_EnergyDimension, DimensionLayout);
-
-  m_EnergyBins = new MGUIEEntry(this, "Number of Bins:", false, m_Settings->GetReportEnergyHistogramBins(), true, 1);
-  AddFrame(m_EnergyBins, BinLayout);
-
-
-
-  m_ThresholdDimension = new MGUIEMinMaxEntry(this,
-                                        MString("Threshold histogram:"),
-                                        false,
-                                        MString("Minimum [keV]: "),
-                                        MString("Maximum [keV]: "),
-                                        m_Settings->GetReportThresholdHistogramMinimum(),
-                                        m_Settings->GetReportThresholdHistogramMaximum(),
-                                        true,
-                                        0.0);
-  AddFrame(m_ThresholdDimension, DimensionLayout);
-
-  m_ThresholdBins = new MGUIEEntry(this, "Number of Bins:", false, m_Settings->GetReportThresholdHistogramBins(), true, 1);
-  AddFrame(m_ThresholdBins, BinLayout);
-
-
-
-  m_OverflowDimension = new MGUIEMinMaxEntry(this,
-                                        MString("Overflow histogram:"),
-                                        false,
-                                        MString("Minimum [keV]: "),
-                                        MString("Maximum [keV]: "),
-                                        m_Settings->GetReportOverflowHistogramMinimum(),
-                                        m_Settings->GetReportOverflowHistogramMaximum(),
-                                        true,
-                                        0.0);
-  AddFrame(m_OverflowDimension, DimensionLayout);
-
-  m_OverflowBins = new MGUIEEntry(this, "Number of Bins:", false, m_Settings->GetReportOverflowHistogramBins(), true, 1);
-  AddFrame(m_OverflowBins, BinLayout);
-
-
-
-  AddOKCancelButtons();
-
-  PositionWindow(GetDefaultWidth(), GetDefaultHeight(), true);
-
-  // and bring it to the screen.
-  MapSubwindows();
-  MapWindow();  
-
-  Layout();
-
-  fClient->WaitFor(this);
- 
-  return;
-}
-
-////////////////////////////////////////////////////////////////////////////////
-
-
-bool MGUIReportCreation::ProcessMessage(long Message, long Parameter1, long Parameter2)
-{
-  // Process the messages for this application
-
-  switch (GET_MSG(Message)) {
-  case kC_COMMAND:
-    switch (GET_SUBMSG(Message)) {
-    case kCM_BUTTON:
-      break;
-    default:
-      break;
-    }
-  default:
-    break;
-  }
-
-  return MGUIDialog::ProcessMessage(Message, Parameter1, Parameter2);
-}
-
-
-////////////////////////////////////////////////////////////////////////////////
-
-
-//! Action after the Apply or OK button has been pressed.
-bool MGUIReportCreation::OnApply()
-{
-  if (m_ADCDimension->CheckRange(0.0, 100000.0, 0.0, 100000.0, true) == false) return false;
-  if (m_ADCBins->IsInt(1, 100000) == false) return false;
-
-  if (m_EnergyDimension->CheckRange(0.0, 100000.0, 0.0, 100000.0, true) == false) return false;
-  if (m_EnergyBins->IsInt(1, 100000) == false) return false;
-
-  if (m_ThresholdDimension->CheckRange(0.0, 100000.0, 0.0, 100000.0, true) == false) return false;
-  if (m_ThresholdBins->IsInt(1, 100000) == false) return false;
-
-  if (m_OverflowDimension->CheckRange(0.0, 100000.0, 0.0, 100000.0, true) == false) return false;
-  if (m_OverflowBins->IsInt(1, 100000) == false) return false;
-
-  m_Settings->SetReportFileName(m_FileName->GetFileName());
-
-  m_Settings->SetReportADCHistogramMinimum(m_ADCDimension->GetMinValue());
-  m_Settings->SetReportADCHistogramMaximum(m_ADCDimension->GetMaxValue());
-  m_Settings->SetReportADCHistogramBins(m_ADCBins->GetAsInt());
-
-  m_Settings->SetReportEnergyHistogramMinimum(m_EnergyDimension->GetMinValue());
-  m_Settings->SetReportEnergyHistogramMaximum(m_EnergyDimension->GetMaxValue());
-  m_Settings->SetReportEnergyHistogramBins(m_EnergyBins->GetAsInt());
-
-  m_Settings->SetReportThresholdHistogramMinimum(m_ThresholdDimension->GetMinValue());
-  m_Settings->SetReportThresholdHistogramMaximum(m_ThresholdDimension->GetMaxValue());
-  m_Settings->SetReportThresholdHistogramBins(m_ThresholdBins->GetAsInt());
-
-  m_Settings->SetReportOverflowHistogramMinimum(m_OverflowDimension->GetMinValue());
-  m_Settings->SetReportOverflowHistogramMaximum(m_OverflowDimension->GetMaxValue());
-  m_Settings->SetReportOverflowHistogramBins(m_OverflowBins->GetAsInt());
-
-  m_OkPressed = true;
-
-  return true;
-}
-
-
-// MGUIReportCreation: the end...
-////////////////////////////////////////////////////////////////////////////////
diff --git a/src/fretalon/melinator/src/MMelinator.cxx b/src/fretalon/melinator/src/MMelinator.cxx
index e2f4cb76d..6c160824d 100644
--- a/src/fretalon/melinator/src/MMelinator.cxx
+++ b/src/fretalon/melinator/src/MMelinator.cxx
@@ -122,24 +122,6 @@ MMelinator::MMelinator()
   m_CalibrationModelEnergyAssignmentMethod = MCalibrateEnergyAssignEnergyModes::e_LinearZeroCrossing;
   m_CalibrationModelDeterminationMethod = MCalibrateEnergyDetermineModel::c_CalibrationModelStepWise;
   
-  m_ReportFileName = "MelinatorReport.pdf";
-
-  m_ReportADCHistogramMinimum = 0;
-  m_ReportADCHistogramMaximum = 10000;
-  m_ReportADCHistogramBins = 1000;
-
-  m_ReportEnergyHistogramMinimum = 0;
-  m_ReportEnergyHistogramMaximum = 2000;
-  m_ReportEnergyHistogramBins = 500;
-
-  m_ReportThresholdHistogramMinimum = 0;
-  m_ReportThresholdHistogramMaximum = 40;
-  m_ReportThresholdHistogramBins = 40;
-
-  m_ReportOverflowHistogramMinimum = 1500;
-  m_ReportOverflowHistogramMaximum = 2500;
-  m_ReportOverflowHistogramBins = 100;
-
   m_NThreads = thread::hardware_concurrency();
   if (m_NThreads < 1) m_NThreads = 1;
   
@@ -1545,23 +1527,6 @@ bool MMelinator::ReCalibrateModel(unsigned int Collection)
 //! Save the calibration in e-cal format
 bool MMelinator::Save(MString FileName)
 {
-  if (m_CalibrationStore.GetNumberOfElements() == 0) {
-    mgui<<"You need to run the calibration first, before saving the results."<<error;
-    return true; // True: No subsequent error messages required
-  } else {
-    bool FoundOne = false;
-    for (unsigned int c = 0; c < m_CalibrationStore.GetNumberOfElements(); ++c) {
-      if (dynamic_cast<MCalibrationSpectrum*>(&(m_CalibrationStore.GetCalibration(c))) != nullptr) {
-        FoundOne = true;
-        break;
-      }
-    }
-    if (FoundOne == false) {
-      mgui<<"You need to run the calibration first, before saving the results."<<error;
-      return true; // True: No subsequent error messages required
-    }
-  }
-
   ofstream out;
   out.open(FileName);
   if (out.is_open() == false) {
@@ -1616,32 +1581,25 @@ bool MMelinator::Save(MString FileName)
 //! Create a calibration report
 bool MMelinator::CreateReport()
 {
-  if (m_CalibrationStore.GetNumberOfElements() == 0) {
-    mgui<<"You need to run the calibration first, before creating a report."<<error;
-    return true; // True: No subsequent error messages required
-  } else {
-    bool FoundOne = false;
-    for (unsigned int c = 0; c < m_CalibrationStore.GetNumberOfElements(); ++c) {
-      if (dynamic_cast<MCalibrationSpectrum*>(&(m_CalibrationStore.GetCalibration(c))) != nullptr) {
-        FoundOne = true;
-        break;
-      }
-    }
-    if (FoundOne == false) {
-      mgui<<"You need to run the calibration first, before creating a report."<<error;
-      return true; // True: No subsequent error messages required
-    }
-  }
+  // Create a calibration report
+
+  double MaxADCs = 5000;
+  double MaxEnergy = 500;
+  double ThresholdMaxEnergy = 35;
+  double OverflowMinEnergy = 1750;
+  double OverflowMaxEnergy = 3000;
+  MString OutputFileName = "MelinatorReport.pdf";
+
 
   // Section 1: Create histograms
 
-  TH2D* AllFittedEnergies = new TH2D("Fitted", "Fitted", m_ReportEnergyHistogramBins, m_ReportEnergyHistogramMinimum, m_ReportEnergyHistogramMaximum, m_CalibrationStore.GetNumberOfElements()+1, -0.5, m_CalibrationStore.GetNumberOfElements() + 0.5);
+  TH2D* AllFittedEnergies = new TH2D("Fitted", "Fitted", MaxEnergy/2, 0, MaxEnergy, m_CalibrationStore.GetNumberOfElements()+1, -0.5, m_CalibrationStore.GetNumberOfElements() + 0.5);
   AllFittedEnergies->SetXTitle("Energy [keV]");
   AllFittedEnergies->SetYTitle("ReadOutUnit ID");
   AllFittedEnergies->SetContour(99);
 
 
-  TH2D* AllRawADCs = new TH2D("RawADCs", "RawADCs", m_ReportADCHistogramBins, m_ReportADCHistogramMinimum, m_ReportADCHistogramMaximum, m_CalibrationStore.GetNumberOfElements()+1, -0.5, m_CalibrationStore.GetNumberOfElements() + 0.5);
+  TH2D* AllRawADCs = new TH2D("RawADCs", "RawADCs", MaxADCs/4, 0, MaxADCs, m_CalibrationStore.GetNumberOfElements()+1, -0.5, m_CalibrationStore.GetNumberOfElements() + 0.5);
   AllRawADCs->SetXTitle("ADCs [rou's]");
   AllRawADCs->SetYTitle("ReadOutUnit ID");
   AllRawADCs->SetContour(99);
@@ -1687,29 +1645,28 @@ bool MMelinator::CreateReport()
 
           TitlesMap[DetectorAndSide] = Name;
 
-          ADCsMap[DetectorAndSide] = new TH2D("", "ADC spectrum", m_ReportADCHistogramBins, m_ReportADCHistogramMinimum, m_ReportADCHistogramMaximum, MaxStripID+1, -0.5, MaxStripID + 0.5);
+          ADCsMap[DetectorAndSide] = new TH2D("", "ADC spectrum", MaxADCs/2, 0, MaxADCs, MaxStripID+1, -0.5, MaxStripID + 0.5);
           ADCsMap[DetectorAndSide]->SetXTitle("ADC units");
           ADCsMap[DetectorAndSide]->SetYTitle("Strip ID");
           ADCsMap[DetectorAndSide]->SetContour(99);
 
-          EnergiesMap[DetectorAndSide] = new TH2D("", "Energy spectrum", m_ReportEnergyHistogramBins, m_ReportEnergyHistogramMinimum, m_ReportEnergyHistogramMaximum, MaxStripID+1, -0.5, MaxStripID + 0.5);
+          EnergiesMap[DetectorAndSide] = new TH2D("", "Energy spectrum", MaxEnergy/2, 0, MaxEnergy, MaxStripID+1, -0.5, MaxStripID + 0.5);
           EnergiesMap[DetectorAndSide]->SetXTitle("Energy [keV]");
           EnergiesMap[DetectorAndSide]->SetYTitle("Strip ID");
           EnergiesMap[DetectorAndSide]->SetContour(99);
 
-          ThresholdsMap[DetectorAndSide] = new TH2D("", "Thresholds", m_ReportThresholdHistogramBins, m_ReportThresholdHistogramMinimum, m_ReportThresholdHistogramMaximum, MaxStripID+1, -0.5, MaxStripID + 0.5);
+          ThresholdsMap[DetectorAndSide] = new TH2D("", "Thresholds", ThresholdMaxEnergy, 0, ThresholdMaxEnergy, MaxStripID+1, -0.5, MaxStripID + 0.5);
           ThresholdsMap[DetectorAndSide]->SetXTitle("Energy [keV]");
           ThresholdsMap[DetectorAndSide]->SetYTitle("Strip ID");
           ThresholdsMap[DetectorAndSide]->SetContour(99);
 
-          OverflowsMap[DetectorAndSide] = new TH2D("", "Overflows", m_ReportOverflowHistogramBins, m_ReportOverflowHistogramMinimum, m_ReportOverflowHistogramMaximum, MaxStripID+1, -0.5, MaxStripID + 0.5);
+          OverflowsMap[DetectorAndSide] = new TH2D("", "Overflows", (OverflowMaxEnergy - OverflowMinEnergy)/10, OverflowMinEnergy, OverflowMaxEnergy, MaxStripID+1, -0.5, MaxStripID + 0.5);
           OverflowsMap[DetectorAndSide]->SetXTitle("Energy [keV]");
           OverflowsMap[DetectorAndSide]->SetYTitle("Strip ID");
           OverflowsMap[DetectorAndSide]->SetContour(99);
         }
 
         MCalibration& C = m_CalibrationStore.GetCalibration(c);
-        if (dynamic_cast<MCalibrationSpectrum*>(&C) == nullptr) continue;
         MCalibrationSpectrum& CS = static_cast<MCalibrationSpectrum&>(C);
         for (unsigned int g = 0; g < CS.GetNumberOfReadOutDataGroups(); ++g) {
           for (unsigned int i = 0; i < m_Isotopes[g].size(); ++i) {
@@ -1757,7 +1714,6 @@ bool MMelinator::CreateReport()
       CurrentHistOverflows = OverflowsMap[DetectorAndSide];
       CurrentStripID = ROE_DS.GetStripID();
     }
-    if (dynamic_cast<MCalibrationSpectrum*>(&(m_CalibrationStore.GetCalibration(c))) == nullptr) continue;
     MCalibrationSpectrum& CS = dynamic_cast<MCalibrationSpectrum&>(m_CalibrationStore.GetCalibration(c));
     MCalibrationModel& M = CS.GetEnergyModel();
 
@@ -1919,7 +1875,7 @@ bool MMelinator::CreateReport()
   }
 
 
-  TitleCanvas->Print(m_ReportFileName + "(");
+  TitleCanvas->Print(OutputFileName + "(");
 
 
   while (IterTitles != TitlesMap.end() && IterEnergies != EnergiesMap.end() && IterADCs != ADCsMap.end() && IterThresholds != ThresholdsMap.end() && IterOverflows != OverflowsMap.end() && IterFWHMes != FWHMesMap.end() && IterResiduals != ResidualsMap.end()) {
@@ -1962,7 +1918,7 @@ bool MMelinator::CreateReport()
     SpectrumPages->cd();
     SpectrumPages->Update();
 
-    SpectrumPages->Print(m_ReportFileName);   // middle pages
+    SpectrumPages->Print(OutputFileName);   // middle pages
 
 
     // Page 2: Thresholds & Overflows
@@ -2003,7 +1959,7 @@ bool MMelinator::CreateReport()
     ThresholdsPages->cd();
     ThresholdsPages->Update();
 
-    ThresholdsPages->Print(m_ReportFileName);   // middle pages
+    ThresholdsPages->Print(OutputFileName);   // middle pages
 
 
     // Page 3+ is lines:
@@ -2046,7 +2002,11 @@ bool MMelinator::CreateReport()
       LineFitPages->cd();
       LineFitPages->Update();
 
-      LineFitPages->Print(m_ReportFileName);   // middle pages
+      if (next(IterFWHMesInner) == IterFWHMes->second.end() && next(IterTitles) == TitlesMap.end()) {
+        LineFitPages->Print(OutputFileName + ")");  // close PDF
+      } else {
+        LineFitPages->Print(OutputFileName);   // middle pages
+      }
 
       ++IterFWHMesInner;
       ++IterResidualsInner;
@@ -2063,24 +2023,10 @@ bool MMelinator::CreateReport()
     ++IterResiduals;
   }
 
-  TCanvas* EndPageCanvas = new TCanvas("EndPage", "EndPage", 850, 1100);
-  EndPageCanvas->cd();
-
-  TPaveText* TheEnd = new TPaveText(0.1, 0.75, 0.9, 0.9, "NDC");
-  TheEnd->AddText("The End");
-  TheEnd->SetTextFont(62);
-  TheEnd->SetTextSize(0.02);
-  TheEnd->SetFillColor(0);
-  TheEnd->SetBorderSize(0);
-  TheEnd->SetLineColor(0);
-  TheEnd->Draw();
-
-  EndPageCanvas->Print(m_ReportFileName + ")");  // close PDF
-
   gROOT->SetBatch(false);
 
 
-  int Return = gSystem->Exec(MString("") + "[ -x \"$(command -v xdg-open)\" ] && xdg-open " + m_ReportFileName + " || { [ -x \"$(command -v open)\" ] && open " + m_ReportFileName + "; }");
+  int Return = gSystem->Exec(MString("") + "[ -x \"$(command -v xdg-open)\" ] && xdg-open " + OutputFileName + " || { [ -x \"$(command -v open)\" ] && open " + OutputFileName + "; }");
 
   if (Return != 0) {
     mgui<<"Failed to open PDF. Return code: "<<Return<<error;
diff --git a/src/fretalon/melinator/src/MSettingsMelinator.cxx b/src/fretalon/melinator/src/MSettingsMelinator.cxx
index e89b5aa4d..b64697542 100644
--- a/src/fretalon/melinator/src/MSettingsMelinator.cxx
+++ b/src/fretalon/melinator/src/MSettingsMelinator.cxx
@@ -86,25 +86,6 @@ MSettingsMelinator::MSettingsMelinator(bool AutoLoad) : MSettings("MelinatorConf
   m_MinimumTemperature = -numeric_limits<double>::max();
   m_MaximumTemperature = +numeric_limits<double>::max();
   
-  m_ReportFileName = "MelinatorReport.pdf";
-
-  m_ReportADCHistogramMinimum = 0;
-  m_ReportADCHistogramMaximum = 10000;
-  m_ReportADCHistogramBins = 1000;
-
-  m_ReportEnergyHistogramMinimum = 0;
-  m_ReportEnergyHistogramMaximum = 2000;
-  m_ReportEnergyHistogramBins = 500;
-
-  m_ReportThresholdHistogramMinimum = 0;
-  m_ReportThresholdHistogramMaximum = 40;
-  m_ReportThresholdHistogramBins = 40;
-
-  m_ReportOverflowHistogramMinimum = 1500;
-  m_ReportOverflowHistogramMaximum = 2500;
-  m_ReportOverflowHistogramBins = 100;
-
-
   if (AutoLoad == true) {
     Read();
   }
@@ -197,25 +178,6 @@ bool MSettingsMelinator::WriteXml(MXmlNode* Node)
   
   new MXmlNode(Node, "SaveAsFileName", m_SaveAsFileName);
   
-  new MXmlNode(Node, "ReportFileName", m_ReportFileName);
-
-  new MXmlNode(Node, "ReportADCHistogramMinimum", m_ReportADCHistogramMinimum);
-  new MXmlNode(Node, "ReportADCHistogramMaximum", m_ReportADCHistogramMaximum);
-  new MXmlNode(Node, "ReportADCHistogramBins", m_ReportADCHistogramBins);
-
-  new MXmlNode(Node, "ReportEnergyHistogramMinimum", m_ReportEnergyHistogramMinimum);
-  new MXmlNode(Node, "ReportEnergyHistogramMaximum", m_ReportEnergyHistogramMaximum);
-  new MXmlNode(Node, "ReportEnergyHistogramBins", m_ReportEnergyHistogramBins);
-
-  new MXmlNode(Node, "ReportThresholdHistogramMinimum", m_ReportThresholdHistogramMinimum);
-  new MXmlNode(Node, "ReportThresholdHistogramMaximum", m_ReportThresholdHistogramMaximum);
-  new MXmlNode(Node, "ReportThresholdHistogramBins", m_ReportThresholdHistogramBins);
-
-  new MXmlNode(Node, "ReportOverflowHistogramMinimum", m_ReportOverflowHistogramMinimum);
-  new MXmlNode(Node, "ReportOverflowHistogramMaximum", m_ReportOverflowHistogramMaximum);
-  new MXmlNode(Node, "ReportOverflowHistogramBins", m_ReportOverflowHistogramBins);
-
-
   // Not stored, since command line options:
   // new MXmlNode(Node, "SelectedDetectorID", m_SelectedDetectorID);
   // new MXmlNode(Node, "SelectedDetectorSide", m_SelectedDetectorSide);
@@ -336,54 +298,6 @@ bool MSettingsMelinator::ReadXml(MXmlNode* Node)
   if ((aNode = Node->GetNode("SaveAsFileName")) != 0) {
     m_SaveAsFileName = aNode->GetValueAsString();
   }
-
-
-  if ((aNode = Node->GetNode("ReportFileName")) != 0) {
-    m_ReportFileName = aNode->GetValueAsString();
-  }
-
-  if ((aNode = Node->GetNode("ReportADCHistogramMinimum")) != 0) {
-    m_ReportADCHistogramMinimum = aNode->GetValueAsDouble();
-  }
-  if ((aNode = Node->GetNode("ReportADCHistogramMaximum")) != 0) {
-    m_ReportADCHistogramMaximum = aNode->GetValueAsDouble();
-  }
-  if ((aNode = Node->GetNode("ReportADCHistogramBins")) != 0) {
-    m_ReportADCHistogramBins = aNode->GetValueAsUnsignedInt();
-  }
-
-  if ((aNode = Node->GetNode("ReportEnergyHistogramMinimum")) != 0) {
-    m_ReportEnergyHistogramMinimum = aNode->GetValueAsDouble();
-  }
-  if ((aNode = Node->GetNode("ReportEnergyHistogramMaximum")) != 0) {
-    m_ReportEnergyHistogramMaximum = aNode->GetValueAsDouble();
-  }
-  if ((aNode = Node->GetNode("ReportEnergyHistogramBins")) != 0) {
-    m_ReportEnergyHistogramBins = aNode->GetValueAsUnsignedInt();
-  }
-
-  if ((aNode = Node->GetNode("ReportThresholdHistogramMinimum")) != 0) {
-    m_ReportThresholdHistogramMinimum = aNode->GetValueAsDouble();
-  }
-  if ((aNode = Node->GetNode("ReportThresholdHistogramMaximum")) != 0) {
-    m_ReportThresholdHistogramMaximum = aNode->GetValueAsDouble();
-  }
-  if ((aNode = Node->GetNode("ReportThresholdHistogramBins")) != 0) {
-    m_ReportThresholdHistogramBins = aNode->GetValueAsUnsignedInt();
-  }
-
-  if ((aNode = Node->GetNode("ReportOverflowHistogramMinimum")) != 0) {
-    m_ReportOverflowHistogramMinimum = aNode->GetValueAsDouble();
-  }
-  if ((aNode = Node->GetNode("ReportOverflowHistogramMaximum")) != 0) {
-    m_ReportOverflowHistogramMaximum = aNode->GetValueAsDouble();
-  }
-  if ((aNode = Node->GetNode("ReportOverflowHistogramBins")) != 0) {
-    m_ReportOverflowHistogramBins = aNode->GetValueAsUnsignedInt();
-  }
-
-
-
  
   /*
   // Not stored since command line options

From 2c6584b178d449d12117a0605c35d34b92736030 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Wed, 21 May 2025 20:59:45 -0700
Subject: [PATCH 138/192] Revert "ADD: Threshold and overflow to report"

This reverts commit 24e4c5cb3cb9e4e328187c18b21999bd05e5bc59.
---
 src/fretalon/melinator/src/MMelinator.cxx | 108 +++++-----------------
 1 file changed, 21 insertions(+), 87 deletions(-)

diff --git a/src/fretalon/melinator/src/MMelinator.cxx b/src/fretalon/melinator/src/MMelinator.cxx
index 6c160824d..f930e8608 100644
--- a/src/fretalon/melinator/src/MMelinator.cxx
+++ b/src/fretalon/melinator/src/MMelinator.cxx
@@ -1585,9 +1585,6 @@ bool MMelinator::CreateReport()
 
   double MaxADCs = 5000;
   double MaxEnergy = 500;
-  double ThresholdMaxEnergy = 35;
-  double OverflowMinEnergy = 1750;
-  double OverflowMaxEnergy = 3000;
   MString OutputFileName = "MelinatorReport.pdf";
 
 
@@ -1607,10 +1604,8 @@ bool MMelinator::CreateReport()
 
   // If we have double-sided strips make one histogram per detector and side
   map<pair<unsigned int, bool>, MString> TitlesMap;
-  map<pair<unsigned int, bool>, TH2D*> ADCsMap;
-  map<pair<unsigned int, bool>, TH2D*> EnergiesMap;
-  map<pair<unsigned int, bool>, TH2D*> ThresholdsMap;
-  map<pair<unsigned int, bool>, TH2D*> OverflowsMap;
+  map<pair<unsigned int, bool>, TH2D*> RawADCsMap;
+  map<pair<unsigned int, bool>, TH2D*> FittedEnergiesMap;
   // Outer map: detector ID, side; inner map: rog, isotope
   map<pair<unsigned int, bool>, map<tuple<unsigned int, unsigned int, unsigned int>, TH1D*>> FWHMesMap;
   map<pair<unsigned int, bool>, map<tuple<unsigned int, unsigned int, unsigned int>, TH1D*>> ResidualsMap;
@@ -1633,8 +1628,8 @@ bool MMelinator::CreateReport()
       if (m_CalibrationStore.GetReadOutElement(c).IsOfType("doublesidedstrip") == true) {
         MReadOutElementDoubleStrip& ROE_DS = static_cast<MReadOutElementDoubleStrip&>(ROE);
         pair<unsigned int, bool> DetectorAndSide = { ROE_DS.GetDetectorID(), ROE_DS.IsLowVoltageStrip() };
-        auto MapIter = ADCsMap.find(DetectorAndSide);
-        if (MapIter == ADCsMap.end()) {
+        auto MapIter = RawADCsMap.find(DetectorAndSide);
+        if (MapIter == RawADCsMap.end()) {
           MString Name = "Detector ";
           Name += ROE_DS.GetDetectorID();
           if (ROE_DS.IsLowVoltageStrip() == true) {
@@ -1645,25 +1640,15 @@ bool MMelinator::CreateReport()
 
           TitlesMap[DetectorAndSide] = Name;
 
-          ADCsMap[DetectorAndSide] = new TH2D("", "ADC spectrum", MaxADCs/2, 0, MaxADCs, MaxStripID+1, -0.5, MaxStripID + 0.5);
-          ADCsMap[DetectorAndSide]->SetXTitle("ADC units");
-          ADCsMap[DetectorAndSide]->SetYTitle("Strip ID");
-          ADCsMap[DetectorAndSide]->SetContour(99);
-
-          EnergiesMap[DetectorAndSide] = new TH2D("", "Energy spectrum", MaxEnergy/2, 0, MaxEnergy, MaxStripID+1, -0.5, MaxStripID + 0.5);
-          EnergiesMap[DetectorAndSide]->SetXTitle("Energy [keV]");
-          EnergiesMap[DetectorAndSide]->SetYTitle("Strip ID");
-          EnergiesMap[DetectorAndSide]->SetContour(99);
-
-          ThresholdsMap[DetectorAndSide] = new TH2D("", "Thresholds", ThresholdMaxEnergy, 0, ThresholdMaxEnergy, MaxStripID+1, -0.5, MaxStripID + 0.5);
-          ThresholdsMap[DetectorAndSide]->SetXTitle("Energy [keV]");
-          ThresholdsMap[DetectorAndSide]->SetYTitle("Strip ID");
-          ThresholdsMap[DetectorAndSide]->SetContour(99);
-
-          OverflowsMap[DetectorAndSide] = new TH2D("", "Overflows", (OverflowMaxEnergy - OverflowMinEnergy)/10, OverflowMinEnergy, OverflowMaxEnergy, MaxStripID+1, -0.5, MaxStripID + 0.5);
-          OverflowsMap[DetectorAndSide]->SetXTitle("Energy [keV]");
-          OverflowsMap[DetectorAndSide]->SetYTitle("Strip ID");
-          OverflowsMap[DetectorAndSide]->SetContour(99);
+          RawADCsMap[DetectorAndSide] = new TH2D("", "ADC spectrum", MaxADCs/2, 0, MaxADCs, MaxStripID+1, -0.5, MaxStripID + 0.5);
+          RawADCsMap[DetectorAndSide]->SetXTitle("ADC units");
+          RawADCsMap[DetectorAndSide]->SetYTitle("Strip ID");
+          RawADCsMap[DetectorAndSide]->SetContour(99);
+
+          FittedEnergiesMap[DetectorAndSide] = new TH2D("", "Energy spectrum", MaxEnergy/2, 0, MaxEnergy, MaxStripID+1, -0.5, MaxStripID + 0.5);
+          FittedEnergiesMap[DetectorAndSide]->SetXTitle("Energy [keV]");
+          FittedEnergiesMap[DetectorAndSide]->SetYTitle("Strip ID");
+          FittedEnergiesMap[DetectorAndSide]->SetContour(99);
         }
 
         MCalibration& C = m_CalibrationStore.GetCalibration(c);
@@ -1702,16 +1687,12 @@ bool MMelinator::CreateReport()
     MReadOutElement& ROE = m_CalibrationStore.GetReadOutElement(c);
     TH2D* CurrentHistEnergy = nullptr;
     TH2D* CurrentHistADCs = nullptr;
-    TH2D* CurrentHistThresholds = nullptr;
-    TH2D* CurrentHistOverflows = nullptr;
     unsigned int CurrentStripID = 0;
     if (m_CalibrationStore.GetReadOutElement(c).IsOfType("doublesidedstrip") == true) {
       MReadOutElementDoubleStrip& ROE_DS = static_cast<MReadOutElementDoubleStrip&>(ROE);
       pair<unsigned int, bool> DetectorAndSide = { ROE_DS.GetDetectorID(), ROE_DS.IsLowVoltageStrip() };
-      CurrentHistEnergy = EnergiesMap[DetectorAndSide];
-      CurrentHistADCs = ADCsMap[DetectorAndSide];
-      CurrentHistThresholds = ThresholdsMap[DetectorAndSide];
-      CurrentHistOverflows = OverflowsMap[DetectorAndSide];
+      CurrentHistEnergy = FittedEnergiesMap[DetectorAndSide];
+      CurrentHistADCs = RawADCsMap[DetectorAndSide];
       CurrentStripID = ROE_DS.GetStripID();
     }
     MCalibrationSpectrum& CS = dynamic_cast<MCalibrationSpectrum&>(m_CalibrationStore.GetCalibration(c));
@@ -1732,8 +1713,6 @@ bool MMelinator::CreateReport()
           AllRawADCs->Fill(ADCs, c);
           if (CurrentHistEnergy != nullptr) {
             CurrentHistEnergy->Fill(Energy, CurrentStripID);
-            CurrentHistOverflows->Fill(Energy, CurrentStripID);
-            CurrentHistThresholds->Fill(Energy, CurrentStripID);
             CurrentHistADCs->Fill(ADCs, CurrentStripID);
           }
         }
@@ -1776,10 +1755,8 @@ bool MMelinator::CreateReport()
 
   bool FoundHist = false;
   auto IterTitles = TitlesMap.begin();
-  auto IterEnergies = EnergiesMap.begin();
-  auto IterADCs = ADCsMap.begin();
-  auto IterThresholds = ThresholdsMap.begin();
-  auto IterOverflows = OverflowsMap.begin();
+  auto IterEnergy = FittedEnergiesMap.begin();
+  auto IterADCs = RawADCsMap.begin();
   auto IterFWHMes = FWHMesMap.begin();
   auto IterResiduals = ResidualsMap.begin();
 
@@ -1878,7 +1855,7 @@ bool MMelinator::CreateReport()
   TitleCanvas->Print(OutputFileName + "(");
 
 
-  while (IterTitles != TitlesMap.end() && IterEnergies != EnergiesMap.end() && IterADCs != ADCsMap.end() && IterThresholds != ThresholdsMap.end() && IterOverflows != OverflowsMap.end() && IterFWHMes != FWHMesMap.end() && IterResiduals != ResidualsMap.end()) {
+  while (IterTitles != TitlesMap.end() && IterEnergy != FittedEnergiesMap.end() && IterADCs != RawADCsMap.end() && IterFWHMes != FWHMesMap.end() && IterResiduals != ResidualsMap.end()) {
 
     // Page 1: Spectra
 
@@ -1913,7 +1890,7 @@ bool MMelinator::CreateReport()
     EnergyPad->Draw();
     EnergyPad->cd();
     EnergyPad->SetLogz();
-    IterEnergies->second->Draw("colz");
+    IterEnergy->second->Draw("colz");
 
     SpectrumPages->cd();
     SpectrumPages->Update();
@@ -1921,48 +1898,7 @@ bool MMelinator::CreateReport()
     SpectrumPages->Print(OutputFileName);   // middle pages
 
 
-    // Page 2: Thresholds & Overflows
-
-    TCanvas* ThresholdsPages = new TCanvas("", "", 850, 1100);
-    ThresholdsPages->SetLogz();
-    ThresholdsPages->cd();
-
-    TPad* ThresholdsTitlePad = new TPad("padTitle", "Title", 0.0, 0.9, 1.0, 1.0);
-    ThresholdsTitlePad->Draw();
-    ThresholdsTitlePad->cd();
-
-    TPaveText* ThresholdsTitle = new TPaveText(0.0, 0.0, 1.0, 1.0, "brNDC");
-    ThresholdsTitle->AddText(IterTitles->second);
-    ThresholdsTitle->SetFillColor(0);     // No background color
-    ThresholdsTitle->SetBorderSize(0);    // No border
-    ThresholdsTitle->SetLineColor(0);     // Remove outline
-    ThresholdsTitle->SetTextFont(TextFont);
-    ThresholdsTitle->SetTextSize(0.4);
-    ThresholdsTitle->Draw();
-
-    ThresholdsPages->cd();
-
-    TPad* ThresholdsPad = new TPad("ThresholdsPad", "ThresholdsPad", 0.0, 0.45, 1.0, 0.9);
-    ThresholdsPad->Draw();
-    ThresholdsPad->cd();
-    ThresholdsPad->SetLogz();
-    IterThresholds->second->Draw("colz");
-
-    ThresholdsPages->cd();
-
-    TPad* OverflowsPad = new TPad("OverflowsPad", "OverflowsPad", 0.0, 0.0, 1.0, 0.45);
-    OverflowsPad->Draw();
-    OverflowsPad->cd();
-    OverflowsPad->SetLogz();
-    IterOverflows->second->Draw("colz");
-
-    ThresholdsPages->cd();
-    ThresholdsPages->Update();
-
-    ThresholdsPages->Print(OutputFileName);   // middle pages
-
-
-    // Page 3+ is lines:
+    // Page 2+ is lines:
 
     auto IterFWHMesInner = IterFWHMes->second.begin();
     auto IterResidualsInner = IterResiduals->second.begin();
@@ -2015,10 +1951,8 @@ bool MMelinator::CreateReport()
     FoundHist = true;
 
     ++IterTitles;
-    ++IterEnergies;
+    ++IterEnergy;
     ++IterADCs;
-    ++IterThresholds;
-    ++IterOverflows;
     ++IterFWHMes;
     ++IterResiduals;
   }

From 75217f43342ae2e4be03d284e3d16d1825633716 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Wed, 21 May 2025 20:59:45 -0700
Subject: [PATCH 139/192] Revert "ADD: Line FWHM'es and residials"

This reverts commit 938b3ee6f669f580b50b5e4b39daeb85b21093fd.
---
 .../src/MCalibrateEnergyDetermineModel.cxx    |   9 +-
 src/fretalon/melinator/src/MMelinator.cxx     | 153 +++---------------
 2 files changed, 22 insertions(+), 140 deletions(-)

diff --git a/src/fretalon/base/src/MCalibrateEnergyDetermineModel.cxx b/src/fretalon/base/src/MCalibrateEnergyDetermineModel.cxx
index ab040dd6e..6f6742a50 100644
--- a/src/fretalon/base/src/MCalibrateEnergyDetermineModel.cxx
+++ b/src/fretalon/base/src/MCalibrateEnergyDetermineModel.cxx
@@ -214,14 +214,7 @@ bool MCalibrateEnergyDetermineModel::CalibrateEnergyModel()
     for (unsigned int p = 0; p < m_Results.GetNumberOfSpectralPoints(r); ++p) {
       if (m_Results.GetSpectralPoint(r, p).IsGood() == true) {
         MCalibrationSpectralPoint& P = m_Results.GetSpectralPoint(r, p);
-        if (P.HasFit() == true) {
-          MCalibrationFit& Fit = P.GetFit();
-          double FWHM = Fit.GetFWHM();
-          P.SetEnergyFWHM(m_Results.GetEnergyModel().GetFitValue(P.GetPeak() + 0.5*FWHM) - m_Results.GetEnergyModel().GetFitValue(P.GetPeak() - 0.5*FWHM));
-        }
-
-        // We cannot do this, since the old FWHM was estimated and set before the fit
-        //P.SetEnergyFWHM(m_Results.GetEnergyModel().GetFitValue(P.GetPeak() + 0.5*P.GetFWHM()) - m_Results.GetEnergyModel().GetFitValue(P.GetPeak() - 0.5*P.GetFWHM()));
+        P.SetEnergyFWHM(m_Results.GetEnergyModel().GetFitValue(P.GetPeak() + 0.5*P.GetFWHM()) - m_Results.GetEnergyModel().GetFitValue(P.GetPeak() - 0.5*P.GetFWHM()));
       }
     }
   }
diff --git a/src/fretalon/melinator/src/MMelinator.cxx b/src/fretalon/melinator/src/MMelinator.cxx
index f930e8608..779d9b2b9 100644
--- a/src/fretalon/melinator/src/MMelinator.cxx
+++ b/src/fretalon/melinator/src/MMelinator.cxx
@@ -1606,10 +1606,6 @@ bool MMelinator::CreateReport()
   map<pair<unsigned int, bool>, MString> TitlesMap;
   map<pair<unsigned int, bool>, TH2D*> RawADCsMap;
   map<pair<unsigned int, bool>, TH2D*> FittedEnergiesMap;
-  // Outer map: detector ID, side; inner map: rog, isotope
-  map<pair<unsigned int, bool>, map<tuple<unsigned int, unsigned int, unsigned int>, TH1D*>> FWHMesMap;
-  map<pair<unsigned int, bool>, map<tuple<unsigned int, unsigned int, unsigned int>, TH1D*>> ResidualsMap;
-
   if (m_CalibrationStore.GetReadOutElement(0).IsOfType("doublesidedstrip") == true) {
     // Step 1: Maximum strip ID
     unsigned int MaxStripID = 0;
@@ -1650,34 +1646,9 @@ bool MMelinator::CreateReport()
           FittedEnergiesMap[DetectorAndSide]->SetYTitle("Strip ID");
           FittedEnergiesMap[DetectorAndSide]->SetContour(99);
         }
-
-        MCalibration& C = m_CalibrationStore.GetCalibration(c);
-        MCalibrationSpectrum& CS = static_cast<MCalibrationSpectrum&>(C);
-        for (unsigned int g = 0; g < CS.GetNumberOfReadOutDataGroups(); ++g) {
-          for (unsigned int i = 0; i < m_Isotopes[g].size(); ++i) {
-            for (unsigned int l = 0; l < m_Isotopes[g][i].GetNLines(); ++l) {
-              if (m_Isotopes[g][i].GetPrimaryLine() == l || m_Isotopes[g][i].GetSecondaryLine() == l)  {
-                tuple<unsigned int, unsigned int, unsigned int> ROGIDAndIsotope = { g, i, l };
-                // Inefficiency: we loop over everything... but avoiding it is a complicated optimization
-                // Use try_emplace to avoid that
-                FWHMesMap.try_emplace(DetectorAndSide, map<tuple<unsigned int, unsigned int, unsigned int>, TH1D*>());
-                FWHMesMap[DetectorAndSide].try_emplace(ROGIDAndIsotope, new TH1D("", "FWHMes", MaxStripID+1, -0.5, MaxStripID + 0.5));
-                FWHMesMap[DetectorAndSide][ROGIDAndIsotope]->SetXTitle("Strip ID");
-                FWHMesMap[DetectorAndSide][ROGIDAndIsotope]->SetYTitle("FWHM [keV]");
-                FWHMesMap[DetectorAndSide][ROGIDAndIsotope]->SetLineWidth(2);
-
-                ResidualsMap.try_emplace(DetectorAndSide, map<tuple<unsigned int, unsigned int, unsigned int>, TH1D*>());
-                ResidualsMap[DetectorAndSide].try_emplace(ROGIDAndIsotope, new TH1D("", "Residuals", MaxStripID+1, -0.5, MaxStripID + 0.5));
-                ResidualsMap[DetectorAndSide][ROGIDAndIsotope]->SetXTitle("Strip ID");
-                ResidualsMap[DetectorAndSide][ROGIDAndIsotope]->SetYTitle("Residuals [keV]");
-                ResidualsMap[DetectorAndSide][ROGIDAndIsotope]->SetLineWidth(2);
-              }
-            }
-          }
-        }
-      } // is // double-sided strip in calibration store
-    } // ROE in calibration store
-  } // double-sided strip
+      }
+    }
+  }
 
 
 
@@ -1695,16 +1666,16 @@ bool MMelinator::CreateReport()
       CurrentHistADCs = RawADCsMap[DetectorAndSide];
       CurrentStripID = ROE_DS.GetStripID();
     }
-    MCalibrationSpectrum& CS = dynamic_cast<MCalibrationSpectrum&>(m_CalibrationStore.GetCalibration(c));
-    MCalibrationModel& M = CS.GetEnergyModel();
+    MCalibrationSpectrum* C = dynamic_cast<MCalibrationSpectrum*>(&(m_CalibrationStore.GetCalibration(c)));
+    MCalibrationModel& M = C->GetEnergyModel();
 
     unsigned int IDofROC = m_Store.FindReadOutCollection(ROE);
     if (IDofROC == g_UnsignedIntNotDefined) continue;
     MReadOutCollection& ROC = m_Store.GetReadOutCollection(IDofROC);
     for (unsigned int g = 0; g < ROC.GetNumberOfReadOutDataGroups(); ++g) {
-      MReadOutDataGroup& ROG = ROC.GetReadOutDataGroup(g);
-      for (unsigned int d = 0; d < ROG.GetNumberOfReadOutDatas(); ++d) {
-        MReadOutData& ROD = ROG.GetReadOutData(d);
+      MReadOutDataGroup& RODG = ROC.GetReadOutDataGroup(g);
+      for (unsigned int d = 0; d < RODG.GetNumberOfReadOutDatas(); ++d) {
+        MReadOutData& ROD = RODG.GetReadOutData(d);
         MReadOutDataADCValue* ROD_ADC = dynamic_cast<MReadOutDataADCValue*>(ROD.Get(MReadOutDataADCValue::m_TypeID));
         if (ROD_ADC != nullptr) {
           double ADCs = ROD_ADC->GetADCValue();
@@ -1718,37 +1689,9 @@ bool MMelinator::CreateReport()
         }
       }
     }
-
-    if (m_CalibrationStore.GetReadOutElement(c).IsOfType("doublesidedstrip") == true) {
-      MReadOutElementDoubleStrip& ROE_DS = static_cast<MReadOutElementDoubleStrip&>(ROE);
-      pair<unsigned int, bool> DetectorAndSide = { ROE_DS.GetDetectorID(), ROE_DS.IsLowVoltageStrip() };
-
-      for (unsigned int g = 0; g < CS.GetNumberOfReadOutDataGroups(); ++g) {
-        for (unsigned int i = 0; i < m_Isotopes[g].size(); ++i) {
-          for (unsigned int l = 0; l < m_Isotopes[g][i].GetNLines(); ++l) {
-            if (m_Isotopes[g][i].GetPrimaryLine() == l || m_Isotopes[g][i].GetSecondaryLine() == l)  {
-              tuple<unsigned int, unsigned int, unsigned int> ROGIDAndIsotope = { g, i, l };
-
-              // Loop over all spectral point, and find the isotope and the line
-              for (unsigned int ii = 0; ii < CS.GetNumberOfSpectralPoints(g); ++ii) {
-                MCalibrationSpectralPoint& SP = CS.GetSpectralPoint(g, ii);
-                if (SP.GetIsotope() == m_Isotopes[g][i]) {
-                  if (fabs(SP.GetEnergy() - m_Isotopes[g][i].GetLineEnergy(l)) < 0.01 && SP.HasFit() == true) {
-                    FWHMesMap[DetectorAndSide][ROGIDAndIsotope]->SetTitle(MString("FWHM per strip for ") + m_Isotopes[g][i].GetName() + ", " + SP.GetEnergy() + " keV line"); // I know it is set multiple times...
-                    FWHMesMap[DetectorAndSide][ROGIDAndIsotope]->Fill(CurrentStripID, SP.GetEnergyFWHM());
-                    ResidualsMap[DetectorAndSide][ROGIDAndIsotope]->SetTitle(MString("Residuals line/fit per strip for ") + m_Isotopes[g][i].GetName() + ", " + SP.GetEnergy() + " keV line"); // I know it is set multiple times...
-                    double Residual = SP.GetEnergy() - M.GetFitValue(SP.GetPeak());
-                    ResidualsMap[DetectorAndSide][ROGIDAndIsotope]->Fill(CurrentStripID, Residual);
-                  }
-                }
-              }
-            }
-          }
-        }
-      }
-    }
   }
 
+
   // Create the canvases
 
   gROOT->SetBatch(true);
@@ -1757,8 +1700,6 @@ bool MMelinator::CreateReport()
   auto IterTitles = TitlesMap.begin();
   auto IterEnergy = FittedEnergiesMap.begin();
   auto IterADCs = RawADCsMap.begin();
-  auto IterFWHMes = FWHMesMap.begin();
-  auto IterResiduals = ResidualsMap.begin();
 
   TCanvas* TitleCanvas = new TCanvas("Melinator Calibration Report", "Melinator Calibration Report", 850, 1100);
   TitleCanvas->cd();
@@ -1855,13 +1796,10 @@ bool MMelinator::CreateReport()
   TitleCanvas->Print(OutputFileName + "(");
 
 
-  while (IterTitles != TitlesMap.end() && IterEnergy != FittedEnergiesMap.end() && IterADCs != RawADCsMap.end() && IterFWHMes != FWHMesMap.end() && IterResiduals != ResidualsMap.end()) {
-
-    // Page 1: Spectra
-
-    TCanvas* SpectrumPages = new TCanvas("", "", 850, 1100);
-    SpectrumPages->SetLogz();
-    SpectrumPages->cd();
+  while (IterTitles != TitlesMap.end() && IterEnergy != FittedEnergiesMap.end() && IterADCs != RawADCsMap.end()) {
+    TCanvas* C = new TCanvas("", "", 850, 1100);
+    C->SetLogz();
+    C->cd();
 
     TPad* TitlePad = new TPad("padTitle", "Title", 0.0, 0.9, 1.0, 1.0);
     TitlePad->Draw();
@@ -1876,7 +1814,7 @@ bool MMelinator::CreateReport()
     Title->SetTextSize(0.4);
     Title->Draw();
 
-    SpectrumPages->cd();
+    C->cd();
 
     TPad* ADCPad = new TPad("ADCPad", "ADCPad", 0.0, 0.45, 1.0, 0.9);
     ADCPad->Draw();
@@ -1884,7 +1822,7 @@ bool MMelinator::CreateReport()
     ADCPad->SetLogz();
     IterADCs->second->Draw("colz");
 
-    SpectrumPages->cd();
+    C->cd();
 
     TPad* EnergyPad = new TPad("EnergyPad", "EnergyPad", 0.0, 0.0, 1.0, 0.45);
     EnergyPad->Draw();
@@ -1892,60 +1830,13 @@ bool MMelinator::CreateReport()
     EnergyPad->SetLogz();
     IterEnergy->second->Draw("colz");
 
-    SpectrumPages->cd();
-    SpectrumPages->Update();
-
-    SpectrumPages->Print(OutputFileName);   // middle pages
-
-
-    // Page 2+ is lines:
-
-    auto IterFWHMesInner = IterFWHMes->second.begin();
-    auto IterResidualsInner = IterResiduals->second.begin();
-    while (IterResidualsInner != IterResiduals->second.end() && IterFWHMesInner != IterFWHMes->second.end()) {
-
-      TCanvas* LineFitPages = new TCanvas("", "", 850, 1100);
-      LineFitPages->cd();
-
-      TPad* TitlePadLineFitPages = new TPad("padTitle", "Title", 0.0, 0.9, 1.0, 1.0);
-      TitlePadLineFitPages->Draw();
-      TitlePadLineFitPages->cd();
-
-      TPaveText* TitleLineFitPages = new TPaveText(0.0, 0.0, 1.0, 1.0, "brNDC");
-      TitleLineFitPages->AddText(IterTitles->second);
-      TitleLineFitPages->SetFillColor(0);     // No background color
-      TitleLineFitPages->SetBorderSize(0);    // No border
-      TitleLineFitPages->SetLineColor(0);     // Remove outline
-      TitleLineFitPages->SetTextFont(TextFont);
-      TitleLineFitPages->SetTextSize(0.4);
-      TitleLineFitPages->Draw();
-
-      LineFitPages->cd();
-
-
-      TPad* FWHMPad = new TPad("", "", 0.0, 0.45, 1.0, 0.9);
-      FWHMPad->Draw();
-      FWHMPad->cd();
-      IterFWHMesInner->second->Draw("HIST ");
-
-      LineFitPages->cd();
-
-      TPad* ResidualsPad = new TPad("", "", 0.0, 0.0, 1.0, 0.45);
-      ResidualsPad->Draw();
-      ResidualsPad->cd();
-      IterResidualsInner->second->Draw("HIST ");
-
-      LineFitPages->cd();
-      LineFitPages->Update();
-
-      if (next(IterFWHMesInner) == IterFWHMes->second.end() && next(IterTitles) == TitlesMap.end()) {
-        LineFitPages->Print(OutputFileName + ")");  // close PDF
-      } else {
-        LineFitPages->Print(OutputFileName);   // middle pages
-      }
+    C->cd();
+    C->Update();
 
-      ++IterFWHMesInner;
-      ++IterResidualsInner;
+    if (next(IterTitles) == TitlesMap.end()) {
+      C->Print(OutputFileName + ")");  // close PDF
+    } else {
+      C->Print(OutputFileName);   // middle pages
     }
 
     FoundHist = true;
@@ -1953,8 +1844,6 @@ bool MMelinator::CreateReport()
     ++IterTitles;
     ++IterEnergy;
     ++IterADCs;
-    ++IterFWHMes;
-    ++IterResiduals;
   }
 
   gROOT->SetBatch(false);

From 9578d500783f9b95a66d214e77e6cee60b5866c1 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Wed, 21 May 2025 20:59:45 -0700
Subject: [PATCH 140/192] Revert "ADD: New report feature, fixed Ba-133 only
 calibration"

This reverts commit ab45652eff0e84dd071efcbadf64be3db9bf9aee.
---
 resource/libraries/Calibration.isotopes       |   4 +-
 .../src/MCalibrateEnergyAssignEnergies.cxx    |  43 ---
 .../melinator/inc/MGUIMainMelinator.h         |   3 -
 src/fretalon/melinator/inc/MMelinator.h       |   7 +-
 .../melinator/src/MGUIMainMelinator.cxx       |  37 +--
 src/fretalon/melinator/src/MMelinator.cxx     | 299 ------------------
 src/global/misc/inc/MIsotope.h                |  16 +-
 src/global/misc/src/MIsotope.cxx              |  46 +--
 8 files changed, 26 insertions(+), 429 deletions(-)

diff --git a/resource/libraries/Calibration.isotopes b/resource/libraries/Calibration.isotopes
index 803fa5c4a..39b193d27 100644
--- a/resource/libraries/Calibration.isotopes
+++ b/resource/libraries/Calibration.isotopes
@@ -31,10 +31,10 @@ Ba  133    34.987  11.6     E
 Ba  133    35.818   3.58    E
 Ba  133    53.161   2.199   E
 # Ba  133    79.614   2.62    E  this mini line just screws things up in melinator -- we pretend we do not know it...
-Ba  133    80.997  34.06    P 
+Ba  133    80.997  34.06    D 
 Ba  133   276.398   7.164   
 Ba  133   302.853  18.33   
-Ba  133   356.017  62.05    S
+Ba  133   356.017  62.05    
 Ba  133   383.851   8.94
 
 # 137-Cs
diff --git a/src/fretalon/base/src/MCalibrateEnergyAssignEnergies.cxx b/src/fretalon/base/src/MCalibrateEnergyAssignEnergies.cxx
index 88600eef3..bb077d8d4 100644
--- a/src/fretalon/base/src/MCalibrateEnergyAssignEnergies.cxx
+++ b/src/fretalon/base/src/MCalibrateEnergyAssignEnergies.cxx
@@ -224,7 +224,6 @@ bool MCalibrateEnergyAssignEnergies::CalibrateLinear()
   if (g_Verbosity >= c_Info) cout<<endl<<"Assigning energies via linear method"<<endl;
   
   // Inventory:
-  unsigned int TotalNumberOfGoodPoints = 0;
   bool NoROGHasMoreThanOneGoodSpectralPoint = true;
   if (g_Verbosity >= c_Info) cout<<"Current line inventory: "<<endl;
   for (unsigned int r = 0; r < m_Results.GetNumberOfReadOutDataGroups(); ++r) {
@@ -235,7 +234,6 @@ bool MCalibrateEnergyAssignEnergies::CalibrateLinear()
       } else {
         if (g_Verbosity >= c_Info) cout<<"Included: "<<m_Results.GetSpectralPoint(r, p)<<endl;
         ++NumberOfGoodPoints;
-        ++TotalNumberOfGoodPoints;
       }
     }
     if (NumberOfGoodPoints > 1) {
@@ -267,47 +265,6 @@ bool MCalibrateEnergyAssignEnergies::CalibrateLinear()
     return true;
   }
   
-  // Special case: We have one ROG with one isotope (which has a primary and secondary line) with two spectral points - this handles Ba-133 only calibrations:
-  if (m_Results.GetNumberOfReadOutDataGroups() == 1 && m_Isotopes[0].size() == 1 && m_Isotopes[0][0].GetPrimaryLine() != -1 && m_Isotopes[0][0].GetSecondaryLine() != -1 && TotalNumberOfGoodPoints == 2) {
-
-    if (g_Verbosity >= c_Info) cout<<"Assign energies: Special case with 1 ROG, 1 isotope with 2 spectral point"<<endl;
-
-    unsigned int r = 0; // our single ROG
-    unsigned int i = 0; // our single Isotope
-    int PrimaryLineID = m_Isotopes[r][i].GetPrimaryLine();
-    int SecondaryLineID = m_Isotopes[r][i].GetSecondaryLine();
-
-    vector<unsigned int> GoodSpectralPointIDs;
-    for (unsigned int p = 0; p < m_Results.GetNumberOfSpectralPoints(r); ++p) {
-      if (m_Results.GetSpectralPoint(r, p).IsGood() == true) {
-        GoodSpectralPointIDs.push_back(p);
-      }
-    }
-
-    unsigned int plow = 0;
-    unsigned int phigh = 0;
-    if (m_Results.GetSpectralPoint(r, GoodSpectralPointIDs[0]).GetPeak() < m_Results.GetSpectralPoint(r, GoodSpectralPointIDs[1]).GetPeak()) {
-      plow = GoodSpectralPointIDs[0];
-      phigh = GoodSpectralPointIDs[1];
-    } else {
-      plow = GoodSpectralPointIDs[1];
-      phigh = GoodSpectralPointIDs[0];
-    }
-
-    if (m_Isotopes[r][0].GetLineEnergy(PrimaryLineID) < m_Isotopes[r][0].GetLineEnergy(SecondaryLineID)) {
-      m_Results.GetSpectralPoint(r, plow).SetIsotope(m_Isotopes[r][0]);
-      m_Results.GetSpectralPoint(r, plow).SetEnergy(m_Isotopes[r][0].GetLineEnergy(PrimaryLineID));
-      m_Results.GetSpectralPoint(r, phigh).SetIsotope(m_Isotopes[r][0]);
-      m_Results.GetSpectralPoint(r, phigh).SetEnergy(m_Isotopes[r][0].GetLineEnergy(SecondaryLineID));
-    } else {
-      m_Results.GetSpectralPoint(r, plow).SetIsotope(m_Isotopes[r][0]);
-      m_Results.GetSpectralPoint(r, plow).SetEnergy(m_Isotopes[r][0].GetLineEnergy(SecondaryLineID));
-      m_Results.GetSpectralPoint(r, phigh).SetIsotope(m_Isotopes[r][0]);
-      m_Results.GetSpectralPoint(r, phigh).SetEnergy(m_Isotopes[r][0].GetLineEnergy(PrimaryLineID));
-    }
-
-    return true;
-  }
   
   
   // Create a list of spectral points
diff --git a/src/fretalon/melinator/inc/MGUIMainMelinator.h b/src/fretalon/melinator/inc/MGUIMainMelinator.h
index e17782606..1f7e916b0 100644
--- a/src/fretalon/melinator/inc/MGUIMainMelinator.h
+++ b/src/fretalon/melinator/inc/MGUIMainMelinator.h
@@ -111,8 +111,6 @@ class MGUIMainMelinator : public TGMainFrame
   virtual bool OnLoad();
   //! Actions when the save as button has been pressed
   virtual bool OnSaveAs();
-  //! Actions when the show report as button has been pressed
-  virtual bool OnShowReport();
   //! Actions when the next button has been pressed
   virtual bool OnNext();
   //! Actions when the back button has been pressed
@@ -287,7 +285,6 @@ class MGUIMainMelinator : public TGMainFrame
   static const int c_CalibrationModelDeterminationMethodFittingFWHMModel    =  73;
   static const int c_Save                       =  80;
   static const int c_SaveAs                     =  81;
-  static const int c_ShowReport                 =  90;
   static const int c_Remove                     = 400;
   static const int c_Options                    = 500;
   static const int c_Change                     = 600;
diff --git a/src/fretalon/melinator/inc/MMelinator.h b/src/fretalon/melinator/inc/MMelinator.h
index 2c41e3559..86685900d 100644
--- a/src/fretalon/melinator/inc/MMelinator.h
+++ b/src/fretalon/melinator/inc/MMelinator.h
@@ -160,13 +160,10 @@ class MMelinator
   
   //! Remove all collection which don't have positive data entries
   //void RemoveCollectionsWithNoPositiveEntries() { m_Store.RemoveCollectionsWithNoPositiveEntries(); }
-
+ 
   //! Save the calibration in e-cal format
   bool Save(MString FileName);
-
-  //! Create a calibration report
-  bool CreateReport();
-
+  
   //! Dump a string
   virtual MString ToString() const;  
   
diff --git a/src/fretalon/melinator/src/MGUIMainMelinator.cxx b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
index 2da7aa7fc..af4d56ad9 100644
--- a/src/fretalon/melinator/src/MGUIMainMelinator.cxx
+++ b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
@@ -169,6 +169,10 @@ void MGUIMainMelinator::Create()
   MenuFiles->AddEntry("Choose files and isotopes", c_ChooseCalibrationFiles);
   MenuFiles->AddEntry("Load files", c_LoadLast);
   MenuFiles->AddSeparator();
+  MenuFiles->AddLabel("Calibration result");
+  MenuFiles->AddEntry("Save As...", c_SaveAs);
+  MenuFiles->AddEntry("Save", c_Save);
+  MenuFiles->AddSeparator();
   MenuFiles->AddLabel("Configuration file");
   //MenuFiles->AddEntry("Open", c_LoadConfig);
   MenuFiles->AddEntry("Open -> use command line at launch", c_LoadConfig);
@@ -179,18 +183,7 @@ void MGUIMainMelinator::Create()
   MenuFiles->AddSeparator();
   MenuFiles->AddEntry("Exit", c_Exit);
   MenuFiles->Associate(this);
-  MenuBar->AddPopup("Input", MenuFiles, MenuBarItemLayoutLeft);
-
-  TGPopupMenu* MenuResults = new TGPopupMenu(gClient->GetRoot());
-  MenuResults->AddLabel("Calibration file");
-  MenuResults->AddEntry("Save As...", c_SaveAs);
-  MenuResults->AddEntry("Save", c_Save);
-  MenuResults->AddSeparator();
-  MenuResults->AddLabel("Calibration report");
-  MenuResults->AddEntry("Create and Show", c_ShowReport);
-  //MenuResults->AddSeparator();
-  MenuResults->Associate(this);
-  MenuBar->AddPopup("Output", MenuResults, MenuBarItemLayoutLeft);
+  MenuBar->AddPopup("Files", MenuFiles, MenuBarItemLayoutLeft);
 
   TGPopupMenu* MenuInfo = new TGPopupMenu(fClient->GetRoot());
   MenuInfo->AddEntry("About", c_About);
@@ -939,10 +932,6 @@ bool MGUIMainMelinator::ProcessMessage(long Message, long Parameter1, long Param
         Status = OnSaveAs();
         break;
 
-      case c_ShowReport:
-        Status = OnShowReport();
-        break;
-
       case c_About:
         Status = OnAbout();
         break;
@@ -1453,22 +1442,6 @@ bool MGUIMainMelinator::OnSaveAs()
 ////////////////////////////////////////////////////////////////////////////////
 
 
-//! Actions when the show report button has been pressed
-bool MGUIMainMelinator::OnShowReport()
-{
-  bool Return = m_Melinator.CreateReport();
-
-  if (Return == false) {
-    mgui<<"Unable to create calibration report"<<error;
-  }
-
-  return Return;
-}
-
-
-////////////////////////////////////////////////////////////////////////////////
-
-
 bool MGUIMainMelinator::OnLoad()
 {  
   return false;
diff --git a/src/fretalon/melinator/src/MMelinator.cxx b/src/fretalon/melinator/src/MMelinator.cxx
index 779d9b2b9..645ef1424 100644
--- a/src/fretalon/melinator/src/MMelinator.cxx
+++ b/src/fretalon/melinator/src/MMelinator.cxx
@@ -27,8 +27,6 @@
 #include "MMelinator.h"
 
 // Standard libs:
-#include <pwd.h>
-#include <unistd.h>
 #include <algorithm>
 #include <new>
 #include <map>
@@ -47,11 +45,6 @@ using namespace std;
 #include "TGaxis.h"
 #include "TGraphErrors.h"
 #include "TSystem.h"
-#include "TH2.h"
-#include "TPaveText.h"
-#include "TPad.h"
-#include "TCanvas.h"
-#include "TLatex.h"
 
 // MEGAlib libs:
 #include "MFile.h"
@@ -1578,298 +1571,6 @@ bool MMelinator::Save(MString FileName)
 ////////////////////////////////////////////////////////////////////////////////
 
 
-//! Create a calibration report
-bool MMelinator::CreateReport()
-{
-  // Create a calibration report
-
-  double MaxADCs = 5000;
-  double MaxEnergy = 500;
-  MString OutputFileName = "MelinatorReport.pdf";
-
-
-  // Section 1: Create histograms
-
-  TH2D* AllFittedEnergies = new TH2D("Fitted", "Fitted", MaxEnergy/2, 0, MaxEnergy, m_CalibrationStore.GetNumberOfElements()+1, -0.5, m_CalibrationStore.GetNumberOfElements() + 0.5);
-  AllFittedEnergies->SetXTitle("Energy [keV]");
-  AllFittedEnergies->SetYTitle("ReadOutUnit ID");
-  AllFittedEnergies->SetContour(99);
-
-
-  TH2D* AllRawADCs = new TH2D("RawADCs", "RawADCs", MaxADCs/4, 0, MaxADCs, m_CalibrationStore.GetNumberOfElements()+1, -0.5, m_CalibrationStore.GetNumberOfElements() + 0.5);
-  AllRawADCs->SetXTitle("ADCs [rou's]");
-  AllRawADCs->SetYTitle("ReadOutUnit ID");
-  AllRawADCs->SetContour(99);
-
-
-  // If we have double-sided strips make one histogram per detector and side
-  map<pair<unsigned int, bool>, MString> TitlesMap;
-  map<pair<unsigned int, bool>, TH2D*> RawADCsMap;
-  map<pair<unsigned int, bool>, TH2D*> FittedEnergiesMap;
-  if (m_CalibrationStore.GetReadOutElement(0).IsOfType("doublesidedstrip") == true) {
-    // Step 1: Maximum strip ID
-    unsigned int MaxStripID = 0;
-    for (unsigned int c = 0; c < m_CalibrationStore.GetNumberOfElements(); ++c) {
-      MReadOutElement& ROE = m_CalibrationStore.GetReadOutElement(c);
-      if (m_CalibrationStore.GetReadOutElement(c).IsOfType("doublesidedstrip") == true) {
-        MReadOutElementDoubleStrip& ROE_DS = static_cast<MReadOutElementDoubleStrip&>(ROE);
-        if (ROE_DS.GetStripID() > MaxStripID) {
-          MaxStripID = ROE_DS.GetStripID();
-        }
-      }
-    }
-    // Step 2: Create histograms
-    for (unsigned int c = 0; c < m_CalibrationStore.GetNumberOfElements(); ++c) {
-      MReadOutElement& ROE = m_CalibrationStore.GetReadOutElement(c);
-      if (m_CalibrationStore.GetReadOutElement(c).IsOfType("doublesidedstrip") == true) {
-        MReadOutElementDoubleStrip& ROE_DS = static_cast<MReadOutElementDoubleStrip&>(ROE);
-        pair<unsigned int, bool> DetectorAndSide = { ROE_DS.GetDetectorID(), ROE_DS.IsLowVoltageStrip() };
-        auto MapIter = RawADCsMap.find(DetectorAndSide);
-        if (MapIter == RawADCsMap.end()) {
-          MString Name = "Detector ";
-          Name += ROE_DS.GetDetectorID();
-          if (ROE_DS.IsLowVoltageStrip() == true) {
-            Name += ", low voltage side";
-          } else {
-            Name += ", high voltage side";
-          }
-
-          TitlesMap[DetectorAndSide] = Name;
-
-          RawADCsMap[DetectorAndSide] = new TH2D("", "ADC spectrum", MaxADCs/2, 0, MaxADCs, MaxStripID+1, -0.5, MaxStripID + 0.5);
-          RawADCsMap[DetectorAndSide]->SetXTitle("ADC units");
-          RawADCsMap[DetectorAndSide]->SetYTitle("Strip ID");
-          RawADCsMap[DetectorAndSide]->SetContour(99);
-
-          FittedEnergiesMap[DetectorAndSide] = new TH2D("", "Energy spectrum", MaxEnergy/2, 0, MaxEnergy, MaxStripID+1, -0.5, MaxStripID + 0.5);
-          FittedEnergiesMap[DetectorAndSide]->SetXTitle("Energy [keV]");
-          FittedEnergiesMap[DetectorAndSide]->SetYTitle("Strip ID");
-          FittedEnergiesMap[DetectorAndSide]->SetContour(99);
-        }
-      }
-    }
-  }
-
-
-
-  // Fill the plots
-
-  for (unsigned int c = 0; c < m_CalibrationStore.GetNumberOfElements(); ++c) {
-    MReadOutElement& ROE = m_CalibrationStore.GetReadOutElement(c);
-    TH2D* CurrentHistEnergy = nullptr;
-    TH2D* CurrentHistADCs = nullptr;
-    unsigned int CurrentStripID = 0;
-    if (m_CalibrationStore.GetReadOutElement(c).IsOfType("doublesidedstrip") == true) {
-      MReadOutElementDoubleStrip& ROE_DS = static_cast<MReadOutElementDoubleStrip&>(ROE);
-      pair<unsigned int, bool> DetectorAndSide = { ROE_DS.GetDetectorID(), ROE_DS.IsLowVoltageStrip() };
-      CurrentHistEnergy = FittedEnergiesMap[DetectorAndSide];
-      CurrentHistADCs = RawADCsMap[DetectorAndSide];
-      CurrentStripID = ROE_DS.GetStripID();
-    }
-    MCalibrationSpectrum* C = dynamic_cast<MCalibrationSpectrum*>(&(m_CalibrationStore.GetCalibration(c)));
-    MCalibrationModel& M = C->GetEnergyModel();
-
-    unsigned int IDofROC = m_Store.FindReadOutCollection(ROE);
-    if (IDofROC == g_UnsignedIntNotDefined) continue;
-    MReadOutCollection& ROC = m_Store.GetReadOutCollection(IDofROC);
-    for (unsigned int g = 0; g < ROC.GetNumberOfReadOutDataGroups(); ++g) {
-      MReadOutDataGroup& RODG = ROC.GetReadOutDataGroup(g);
-      for (unsigned int d = 0; d < RODG.GetNumberOfReadOutDatas(); ++d) {
-        MReadOutData& ROD = RODG.GetReadOutData(d);
-        MReadOutDataADCValue* ROD_ADC = dynamic_cast<MReadOutDataADCValue*>(ROD.Get(MReadOutDataADCValue::m_TypeID));
-        if (ROD_ADC != nullptr) {
-          double ADCs = ROD_ADC->GetADCValue();
-          double Energy = M.GetFitValue(ADCs);
-          AllFittedEnergies->Fill(Energy, c);
-          AllRawADCs->Fill(ADCs, c);
-          if (CurrentHistEnergy != nullptr) {
-            CurrentHistEnergy->Fill(Energy, CurrentStripID);
-            CurrentHistADCs->Fill(ADCs, CurrentStripID);
-          }
-        }
-      }
-    }
-  }
-
-
-  // Create the canvases
-
-  gROOT->SetBatch(true);
-
-  bool FoundHist = false;
-  auto IterTitles = TitlesMap.begin();
-  auto IterEnergy = FittedEnergiesMap.begin();
-  auto IterADCs = RawADCsMap.begin();
-
-  TCanvas* TitleCanvas = new TCanvas("Melinator Calibration Report", "Melinator Calibration Report", 850, 1100);
-  TitleCanvas->cd();
-
-  TPaveText* Title = new TPaveText(0.1, 0.75, 0.9, 0.9, "NDC");
-  Title->AddText("Melinator Calibration Report");
-  Title->SetTextFont(62);
-  Title->SetTextSize(0.05);
-  Title->SetFillColor(0);
-  Title->SetBorderSize(0);
-  Title->SetLineColor(0);
-  Title->Draw();
-
-
-
-  // Align text using TLatex
-  float yStart = 0.70;
-  float yStep = 0.03;
-  float xLabel = 0.195;
-  float xValue = 0.39;
-  unsigned int CurrentStep = 0;
-
-  TLatex* LatexLabel;
-  TLatex* LatexValue;
-
-  unsigned int TextFont = 42;
-  double TextSize = 0.02;
-
-
-  TString UserName = "";
-
-  struct passwd *pw = getpwuid(getuid());
-  if (pw && pw->pw_gecos && strlen(pw->pw_gecos) > 0) {
-    // Some systems use comma-separated GECOS fields: "Full Name,Room,Work Phone,..."
-    UserName = pw->pw_gecos;
-    Ssiz_t commaPos = UserName.First(',');
-    if (commaPos != kNPOS) {
-      UserName.Remove(commaPos);  // Only keep the full name
-    }
-  }
-
-  // Fall backs:
-  if (UserName.IsNull()) UserName = gSystem->Getenv("USER");
-  if (UserName.IsNull()) UserName = gSystem->Getenv("LOGNAME");
-  if (UserName.IsNull()) UserName = "unknown";
-
-  LatexLabel = new TLatex(xLabel, yStart - CurrentStep*yStep, "Created by:");
-  LatexLabel->SetTextFont(TextFont); LatexLabel->SetTextSize(TextSize); LatexLabel->Draw();
-  LatexValue = new TLatex(xValue, yStart - CurrentStep*yStep, UserName.Data());
-  LatexValue->SetTextFont(TextFont); LatexValue->SetTextSize(TextSize); LatexValue->Draw();
-  CurrentStep++;
-
-  TDatime Now;
-  TString DateTime = Form("%04d-%02d-%02d %02d:%02d:%02d", Now.GetYear(), Now.GetMonth(), Now.GetDay(),  Now.GetHour(), Now.GetMinute(), Now.GetSecond());
-
-  LatexLabel = new TLatex(xLabel, yStart - CurrentStep*yStep, "Created on:");
-  LatexLabel->SetTextFont(TextFont); LatexLabel->SetTextSize(TextSize); LatexLabel->Draw();
-  LatexValue = new TLatex(xValue, yStart - CurrentStep*yStep, DateTime);
-  LatexValue->SetTextFont(TextFont); LatexValue->SetTextSize(TextSize); LatexValue->Draw();
-  CurrentStep++;
-
-
-  TString GitHash = gSystem->GetFromPipe("cd $MEGALIB; git rev-parse --short HEAD");
-  if (GitHash.IsNull()) GitHash = "unknown";
-
-  LatexLabel = new TLatex(xLabel, yStart - CurrentStep*yStep, "MEGAlib git commit:");
-  LatexLabel->SetTextFont(TextFont); LatexLabel->SetTextSize(TextSize); LatexLabel->Draw();
-  LatexValue = new TLatex(xValue, yStart - CurrentStep*yStep, GitHash.Data());
-  LatexValue->SetTextFont(TextFont); LatexValue->SetTextSize(TextSize); LatexValue->Draw();
-  CurrentStep++;
-
-
-  LatexLabel = new TLatex(xLabel, yStart - CurrentStep*yStep, "Data sets:");
-  LatexLabel->SetTextFont(TextFont); LatexLabel->SetTextSize(TextSize); LatexLabel->Draw();
-
-  for (unsigned int f = 0; f < m_CalibrationFileNames.size(); ++f) {
-    MString FileName = m_CalibrationFileNames[f];
-    FileName = MFile::GetBaseName(FileName);
-    FileName += " (";
-    for (unsigned int i = 0; i < m_Isotopes[f].size(); ++i) {
-      FileName += m_Isotopes[f][i].GetName();
-      if (i < m_Isotopes[f].size() - 1) {
-        FileName += ", ";
-      }
-    }
-    FileName += ")";
-
-    LatexValue = new TLatex(xValue, yStart - CurrentStep*yStep, FileName.Data());
-    LatexValue->SetTextFont(TextFont); LatexValue->SetTextSize(TextSize); LatexValue->Draw();
-    CurrentStep++;
-  }
-
-
-  TitleCanvas->Print(OutputFileName + "(");
-
-
-  while (IterTitles != TitlesMap.end() && IterEnergy != FittedEnergiesMap.end() && IterADCs != RawADCsMap.end()) {
-    TCanvas* C = new TCanvas("", "", 850, 1100);
-    C->SetLogz();
-    C->cd();
-
-    TPad* TitlePad = new TPad("padTitle", "Title", 0.0, 0.9, 1.0, 1.0);
-    TitlePad->Draw();
-    TitlePad->cd();
-
-    TPaveText* Title = new TPaveText(0.0, 0.0, 1.0, 1.0, "brNDC");
-    Title->AddText(IterTitles->second);
-    Title->SetFillColor(0);     // No background color
-    Title->SetBorderSize(0);    // No border
-    Title->SetLineColor(0);     // Remove outline
-    Title->SetTextFont(TextFont);
-    Title->SetTextSize(0.4);
-    Title->Draw();
-
-    C->cd();
-
-    TPad* ADCPad = new TPad("ADCPad", "ADCPad", 0.0, 0.45, 1.0, 0.9);
-    ADCPad->Draw();
-    ADCPad->cd();
-    ADCPad->SetLogz();
-    IterADCs->second->Draw("colz");
-
-    C->cd();
-
-    TPad* EnergyPad = new TPad("EnergyPad", "EnergyPad", 0.0, 0.0, 1.0, 0.45);
-    EnergyPad->Draw();
-    EnergyPad->cd();
-    EnergyPad->SetLogz();
-    IterEnergy->second->Draw("colz");
-
-    C->cd();
-    C->Update();
-
-    if (next(IterTitles) == TitlesMap.end()) {
-      C->Print(OutputFileName + ")");  // close PDF
-    } else {
-      C->Print(OutputFileName);   // middle pages
-    }
-
-    FoundHist = true;
-
-    ++IterTitles;
-    ++IterEnergy;
-    ++IterADCs;
-  }
-
-  gROOT->SetBatch(false);
-
-
-  int Return = gSystem->Exec(MString("") + "[ -x \"$(command -v xdg-open)\" ] && xdg-open " + OutputFileName + " || { [ -x \"$(command -v open)\" ] && open " + OutputFileName + "; }");
-
-  if (Return != 0) {
-    mgui<<"Failed to open PDF. Return code: "<<Return<<error;
-  }
-
-  if (FoundHist == false) {
-    TCanvas* C = new TCanvas();
-    C->SetLogz();
-    C->cd();
-    AllFittedEnergies->Draw("colz");
-    C->Update();
-  }
-
-
-  return true;
-}
-
-////////////////////////////////////////////////////////////////////////////////
-
-
 //! Dump the content into a string
 MString MMelinator::ToString() const
 {
diff --git a/src/global/misc/inc/MIsotope.h b/src/global/misc/inc/MIsotope.h
index 64af5b4f5..8fc56f57f 100644
--- a/src/global/misc/inc/MIsotope.h
+++ b/src/global/misc/inc/MIsotope.h
@@ -69,12 +69,8 @@ class MIsotope
   bool GetLineExcludeFlag(unsigned int l) const;
   //! Return the default lines (= most commonly seen), either defined by the default flag in the file, or the line with the strongest branching ratio - ignore excluded lines
   //! Return -1 if no default line could be found
-  int GetDefaultLine() const { return GetPrimaryLine(); }
-  //! Return -1 if no primary line could be found
-  int GetPrimaryLine() const;
-  //! Return -1 if no secondary line could be found
-  int GetSecondaryLine() const;
-
+  int GetDefaultLine() const;
+  
   //! Dump a string
   virtual MString ToString() const;
   
@@ -104,11 +100,9 @@ class MIsotope
   vector<double> m_LineBranchingRatios;
   //! The line exclude flags
   vector<bool> m_LineExcludeFlags;
-  //! The line primary flags
-  vector<bool> m_LinePrimaryFlags;
-  //! The line secondary flags
-  vector<bool> m_LineSecondaryFlags;
-
+  //! The line default flags
+  vector<bool> m_LineDefaultFlags;
+  
 
 #ifdef ___CLING___
  public:
diff --git a/src/global/misc/src/MIsotope.cxx b/src/global/misc/src/MIsotope.cxx
index 9f09af245..67aef9c4f 100644
--- a/src/global/misc/src/MIsotope.cxx
+++ b/src/global/misc/src/MIsotope.cxx
@@ -117,11 +117,9 @@ void MIsotope::AddLine(double Energy, double BranchingRatio, const MString& Flag
     m_LineEnergies.push_back(Energy);
     m_LineBranchingRatios.push_back(BranchingRatio);
     m_LineExcludeFlags.push_back(false);
+    m_LineDefaultFlags.push_back(false);
     if (Flags.Contains("E") == true) m_LineExcludeFlags.back() = true;
-    m_LinePrimaryFlags.push_back(false);
-    if (Flags.Contains("D") == true || Flags.Contains("P") == true) m_LinePrimaryFlags.back() = true;
-    m_LineSecondaryFlags.push_back(false);
-    if (Flags.Contains("S") == true) m_LineSecondaryFlags.back() = true;
+    if (Flags.Contains("D") == true) m_LineDefaultFlags.back() = true;
   }
 }
 
@@ -154,18 +152,18 @@ bool MIsotope::GetLineExcludeFlag(unsigned int i) const
 ////////////////////////////////////////////////////////////////////////////////
 
 
-//! Return the primary line, or -1 if non could be found
-int MIsotope::GetPrimaryLine() const
+//! Return the default line, or -1 if non could be found
+int MIsotope::GetDefaultLine() const
 {
-  if (m_LinePrimaryFlags.size() == 0) return -1;
-
-  // If we have defined one, and it is not excluded
-  for (unsigned int l = 0; l < m_LinePrimaryFlags.size(); ++l) {
-    if (m_LinePrimaryFlags[l] == true && m_LineExcludeFlags[l] == false) {
-      return l;
+  if (m_LineDefaultFlags.size() == 0) return -1;
+  
+  // If we have defined one , and it is not excluded
+  for (unsigned int l = 0; l < m_LineDefaultFlags.size(); ++l) {
+    if (m_LineDefaultFlags[l] == true && m_LineExcludeFlags[l] == false) {
+      return l; 
     }
   }
-
+  
   // If not return the line with the strongest branching ratio which is not excluded
   int Line = -1;
   double Strength = -1;
@@ -177,30 +175,10 @@ int MIsotope::GetPrimaryLine() const
       }
     }
   }
-
+  
   return Line;
 }
 
-
-////////////////////////////////////////////////////////////////////////////////
-
-
-//! Return the secondary line, or -1 if non could be found
-int MIsotope::GetSecondaryLine() const
-{
-  if (m_LineSecondaryFlags.size() == 0) return -1;
-
-  // If we have defined one, and it is not excluded
-  for (unsigned int l = 0; l < m_LineSecondaryFlags.size(); ++l) {
-    if (m_LineSecondaryFlags[l] == true && m_LineExcludeFlags[l] == false) {
-      return l;
-    }
-  }
-
-  // We have no secondary line defined or available
-  return -1;
-}
-
   
 ////////////////////////////////////////////////////////////////////////////////
 

From 0d2d2f54c0b3d7a590110fd84aa3011a3ec2b932 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Mon, 26 May 2025 14:35:25 -0700
Subject: [PATCH 141/192] CHG: Reintroduce break on exception durign debug

---
 src/global/misc/src/MGlobal.cxx | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/global/misc/src/MGlobal.cxx b/src/global/misc/src/MGlobal.cxx
index a9eb7e937..346c8e0aa 100644
--- a/src/global/misc/src/MGlobal.cxx
+++ b/src/global/misc/src/MGlobal.cxx
@@ -44,6 +44,7 @@ using namespace std;
 
 // MEGAlib libs:
 #include "MGUIDefaults.h"
+#include "MExceptions.h"
 #include "MStreams.h"
 #include "MFile.h"
 
@@ -152,6 +153,9 @@ bool MGlobal::Initialize(MString ProgramName, MString ProgramDescription)
   g_OSType = "Unknown";
 #endif
 
+#ifndef NDEBUG
+  MException::UseAbort();
+#endif
 
   // Load the GUI defaults by initializing the singleton
   MGUIDefaults::GetInstance();

From 0baaf81a30dd7d98acffb273a1292b736a1ca2a5 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Wed, 28 May 2025 14:08:16 -0700
Subject: [PATCH 142/192] ADD: distcc option for the ROOT compile

---
 config/build-root.sh | 57 +++++++++++++++++++++++++++++++----
 setup.sh             | 72 ++++++++++++++++++++++++++++++++++++--------
 2 files changed, 110 insertions(+), 19 deletions(-)

diff --git a/config/build-root.sh b/config/build-root.sh
index e8efb7096..4e4e72f7d 100755
--- a/config/build-root.sh
+++ b/config/build-root.sh
@@ -137,6 +137,9 @@ confhelp() {
   echo "--cleanup=[off/no, on/yes - default: off]"
   echo "    Remove intermediate build files"
   echo " "
+  echo "--distcc=[off/no, on/yes]"
+  echo "    If this flag is set and distcc is setup, we will use distcc"
+  echo " "
   echo "--help or -h"
   echo "    Show this help."
   echo " "
@@ -167,6 +170,7 @@ DEBUGSTRING=""
 DEBUGOPTIONS=""
 PATCH="off"
 CLEANUP="off"
+DISTCC="off"
 KEEPENVASIS="off"
 WANTEDVERSION=""
 
@@ -178,7 +182,7 @@ for C in ${CMD}; do
     ENVFILE=`echo ${C} | awk -F"=" '{ print $2 }'`
   elif [[ ${C} == *-m*=* ]]; then
     MAXTHREADS=`echo ${C} | awk -F"=" '{ print $2 }'`
-  elif [[ ${C} == *-d*=* ]]; then
+  elif [[ ${C} == *-de*=* ]]; then
     DEBUG=`echo ${C} | awk -F"=" '{ print $2 }'`
   elif [[ ${C} == *-p*=* ]]; then
     PATCH=`echo ${C} | awk -F"=" '{ print $2 }'`
@@ -188,6 +192,8 @@ for C in ${CMD}; do
     WANTEDVERSION=`echo ${C} | awk -F"=" '{ print $2 }'`
   elif [[ ${C} == *-k*=* ]]; then
     KEEPENVASIS=`echo ${C} | awk -F"=" '{ print $2 }'`
+  elif [[ ${C} == *-di*=* ]]; then
+    DISTCC=`echo ${C} | awk -F"=" '{ print $2 }'`
   elif [[ ${C} == *-h* ]]; then
     echo ""
     confhelp
@@ -291,6 +297,34 @@ else
 fi
 
 
+DISTCC=`echo ${DISTCC} | tr '[:upper:]' '[:lower:]'`
+if ( [[ ${DISTCC} == of* ]] || [[ ${DISTCC} == n* ]] ); then
+  DISTCC="off"
+  echo " * Don't use distcc"
+elif ( [[ ${DISTCC} == on ]] || [[ ${DISTCC} == y* ]] ); then
+  type distcc >/dev/null 2>&1
+  if [ $? -ne 0 ]; then
+    echo " * Distcc requested, but not installed. Performing local compile."
+    DISTCC="off"
+  else
+    if [ -n "${DISTCC_HOSTS}" ]; then
+      DISTCC="on"
+      export CC="distcc $(which gcc)"
+      export CXX="distcc $(which g++)"
+      echo " * Using distcc with the following host: ${DISTCC_HOSTS}."
+    else 
+      DISTCC="off"
+      echo " * Distcc requested, but not setup. Performing local compile."
+    fi
+  fi
+else
+  echo " "
+  echo "ERROR: Unknown option for distcc: ${DISTCC}"
+  confhelp
+  exit 1
+fi
+
+
 KEEPENVASIS=`echo ${KEEPENVASIS} | tr '[:upper:]' '[:lower:]'`
 if ( [[ ${KEEPENVASIS} == of* ]] || [[ ${KEEPENVASIS} == n* ]] ); then
   KEEPENVASIS="off"
@@ -568,17 +602,28 @@ fi
 
 
 CORES=1;
-if [[ ${OSTYPE} == darwin* ]]; then
-  CORES=`sysctl -n hw.logicalcpu_max`
-elif [[ ${OSTYPE} == linux* ]]; then
-  CORES=`grep processor /proc/cpuinfo | wc -l`
+if [[ ${DISTCC} == "on" ]]; then
+  DISTCC_JOBS_OUTPUT=$(distcc -j 2>/dev/null)
+  if [[ $? -eq 0 && -n "$DISTCC_JOBS_OUTPUT" && "$DISTCC_JOBS_OUTPUT" -gt 0 ]]; then
+    CORES=$(( DISTCC_JOBS_OUTPUT )) # Ensure it's treated as a number
+  fi
+else
+  if [[ ${OSTYPE} == darwin* ]]; then
+    CORES=`sysctl -n hw.logicalcpu_max`
+  elif [[ ${OSTYPE} == linux* ]]; then
+    CORES=`grep processor /proc/cpuinfo | wc -l`
+  fi
 fi
-if [ "$?" != "0" ]; then
+if [ "$?" != "0" ] || [ -z "$CORES" ] || [ "$CORES" -le 0 ]; then # Check if CORES is empty or non-positive
   CORES=1
 fi
 if [ "${CORES}" -gt "${MAXTHREADS}" ]; then
   CORES=${MAXTHREADS}
 fi
+# Final check to ensure CORES is at least 1
+if [ "${CORES}" -le "0" ]; then
+    CORES=1
+fi
 echo "Using this number of cores for compilation: ${CORES}"
 
 
diff --git a/setup.sh b/setup.sh
index 283b94d42..d0b8cbc40 100755
--- a/setup.sh
+++ b/setup.sh
@@ -75,6 +75,11 @@ confhelp() {
   echo "--optimization=[off/no, normal/on/yes, strong/hard (requires gcc 4.2 or higher) - first launch default: on]"
   echo "    Compilation optimization for MEGAlib ONLY (Default is normal)"
   echo " "
+  echo "--distcc=[off/no, on/yes]"
+  echo "    If this flag is set and distcc is setup, we will use distcc"
+  echo "    To setup distcc, install it and make sure the following environment variable is exported, e.g.:"
+  echo "    export DISTCC_HOSTS='@remote1/16 @remote2/8 localhost'"
+  echo " "
   echo "--updates=[off/no, on/yes - first launch default: off]"
   echo "    Check periodically for updates. Default is off."
   echo "    Even if set to on, update checks will only be performed, if the user has write access to the MEGAlib installation."
@@ -181,17 +186,9 @@ UPDATES="off"
 PATCH="on"
 CLEANUP="off"
 BRANCH=""
+DISTCC="off"
 # ALLOWROOT="off" - initialized in the beginning not here
-
-MAXTHREADS=1;
-if [[ ${OSTYPE} == *arwin* ]]; then
-  MAXTHREADS=`sysctl -n hw.logicalcpu_max`
-elif [[ ${OSTYPE} == *inux* ]]; then
-  MAXTHREADS=`grep processor /proc/cpuinfo | wc -l`
-fi
-if [ "$?" != "0" ]; then
-  MAXTHREADS=1
-fi
+MAXTHREADS=0
 
 
 # Prelude - Find an old configuration
@@ -245,7 +242,7 @@ for C in "${CMD[@]}"; do
     HEASOFTPATH=`echo ${C} | awk -F"=" '{ print $2 }'`
   elif [[ ${C} == *-o*=* ]]; then
     OPT=`echo ${C} | awk -F"=" '{ print $2 }'`
-  elif [[ ${C} == *-d*=* ]]; then
+  elif [[ ${C} == *-de*=* ]]; then
     DEBUG=`echo ${C} | awk -F"=" '{ print $2 }'`
   elif [[ ${C} == *-u*=* ]]; then
     UPDATES=`echo ${C} | awk -F"=" '{ print $2 }'`
@@ -261,6 +258,8 @@ for C in "${CMD[@]}"; do
     KEEPMEGALIBASIS=`echo ${C} | awk -F"=" '{ print $2 }'`
   elif [[ ${C} == *-keepe* ]]; then
     KEEPENVASIS=`echo ${C} | awk -F"=" '{ print $2 }'`
+  elif [[ ${C} == *-di* ]]; then
+    DISTCC=`echo ${C} | awk -F"=" '{ print $2 }'`
   elif [[ ${C} == *-b* ]]; then
     BRANCH=`echo ${C} | awk -F"=" '{ print $2 }'`
     RELEASE="dev"
@@ -292,6 +291,7 @@ PATCH=`echo ${PATCH} | tr '[:upper:]' '[:lower:]'`
 CLEANUP=`echo ${CLEANUP} | tr '[:upper:]' '[:lower:]'`
 KEEPMEGALIBASIS=`echo ${KEEPMEGALIBASIS} | tr '[:upper:]' '[:lower:]'`
 KEEPENVASIS=`echo ${KEEPENVASIS} | tr '[:upper:]' '[:lower:]'`
+DISTCC=`echo ${DISTCC} | tr '[:upper:]' '[:lower:]'`
 
 
 
@@ -330,6 +330,52 @@ else
 fi
 
 
+if ( [[ ${DISTCC} == of* ]] || [[ ${DISTCC} == n* ]] ); then
+  DISTCC="off"
+  echo " * Do not use distcc"
+elif ( [[ ${DISTCC} == on ]] || [[ ${DISTCC} == y* ]] ); then
+  if [ -n "${DISTCC_HOSTS}" ]; then
+    DISTCC="on"
+    echo " * Using distcc with the following host: ${DISTCC_HOSTS}."
+  else 
+    DISTCC="off"
+    echo " * Distcc requested, but cannot use distcc since it is not installed or not setup."
+  fi
+else
+  echo " "
+  echo "ERROR: Unknown option for distcc: ${DISTCC}"
+  confhelp
+  exit 1
+fi
+
+
+if [ ! -z "${MAXTHREADS##[0-9]*}" ] 2>/dev/null; then
+  echo "ERROR: The maximum number of threads must be a number and not ${MAXTHREADS}!"
+  exit 1
+fi
+if [[ ${MAXTHREADS} == "0" ]]; then
+  if [[ ${DISTCC} == "on" ]]; then
+    DISTCC_JOBS_OUTPUT=$(distcc -j 2>/dev/null)
+    if [[ $? -eq 0 && -n "$DISTCC_JOBS_OUTPUT" && "$DISTCC_JOBS_OUTPUT" -gt 0 ]]; then
+      MAXTHREADS=$(( DISTCC_JOBS_OUTPUT ))
+    fi
+  else 
+    if [[ ${OSTYPE} == *arwin* ]]; then
+      MAXTHREADS=`sysctl -n hw.logicalcpu_max`
+    elif [[ ${OSTYPE} == *inux* ]]; then
+      MAXTHREADS=`grep processor /proc/cpuinfo | wc -l`
+    fi
+    if [ "$?" != "0" ]; then
+      MAXTHREADS=1
+    fi
+  fi
+fi
+if [ ! -z "${MAXTHREADS##[0-9]*}" ] || [ "${MAXTHREADS}" -le 0 ]; then 
+  MAXTHREADS=1
+fi
+echo " * Using this maximum number of threads: ${MAXTHREADS}"
+
+
 if [[ ${BRANCH} != "" ]]; then
   echo " * Using MEGAlib branch ${BRANCH}"
 else
@@ -749,7 +795,7 @@ else
   fi
   cd ${EXTERNALPATH}
   echo "Switching to build-root.sh script..."
-  bash ${MEGALIBDIR}/config/build-root.sh -source=${ENVFILE} -patch=${PATCH} --debug=${DEBUG} --maxthreads=${MAXTHREADS} --cleanup=${CLEANUP} --keepenvironmentasis=${KEEPENVASIS} 2>&1 | tee RootBuildLog.txt
+  bash ${MEGALIBDIR}/config/build-root.sh -source=${ENVFILE} -patch=${PATCH} --debug=${DEBUG} --maxthreads=${MAXTHREADS} --cleanup=${CLEANUP} --keepenvironmentasis=${KEEPENVASIS} --distcc=${DISTCC} 2>&1 | tee RootBuildLog.txt
   RESULT=${PIPESTATUS[0]}
 
   # If we have a new ROOT dir, copy the build log there
@@ -971,7 +1017,7 @@ mv ${ENVFILE} bin/source-megalib.sh
 
 echo "Storing last good options..."
 rm -f ${MEGALIBDIR}/config/SetupOptions.txt
-SETUP="--external-path=${EXTERNALPATH} --root=${ROOTPATH} --geant4=${GEANT4PATH} --release=${RELEASE} --repository=${REPOSITORY} --optimization=${OPT} --debug=${DEBUG} --updates=${UPDATES} --patch=${PATCH} --cleanup=${CLEANUP} --keepmegalibasis=${KEEPMEGALIBASIS} --keepenvironmentasis=${KEEPENVASIS} --maxthreads=${MAXTHREADS}"
+SETUP="--external-path=${EXTERNALPATH} --root=${ROOTPATH} --geant4=${GEANT4PATH} --release=${RELEASE} --repository=${REPOSITORY} --optimization=${OPT} --debug=${DEBUG} --updates=${UPDATES} --patch=${PATCH} --cleanup=${CLEANUP} --keepmegalibasis=${KEEPMEGALIBASIS} --keepenvironmentasis=${KEEPENVASIS} --maxthreads=${MAXTHREADS} --distcc=${DISTCC}"
 if [[ ${BRANCH} != "" ]]; then
   SETUP+=" --branch=${BRANCH}"
 fi

From 2d4be017ab49d57fcbc7ad8bfbc1bffc957de963 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Fri, 20 Jun 2025 10:55:29 -0700
Subject: [PATCH 143/192] ADD: Memory monitoring script

---
 bin/mmaxmem | 77 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 77 insertions(+)
 create mode 100755 bin/mmaxmem

diff --git a/bin/mmaxmem b/bin/mmaxmem
new file mode 100755
index 000000000..17ba86d6e
--- /dev/null
+++ b/bin/mmaxmem
@@ -0,0 +1,77 @@
+#! /bin/bash
+
+echo ""
+echo "mmaxmem - MEGAlib's memory monitor"
+echo ""
+
+
+
+help() {
+  echo ""
+  echo "mmaxmem - script for MEGAlib";
+  echo "(C) by Andreas Zoglauer"
+  echo "";
+  echo "This script keeps track of the maximum memory used by a process."
+  echo "";
+  echo "Usage:";
+  echo "    mmaxmem [program name] [optional command line arguments]";
+  echo "";
+  echo "Example:";
+  echo "    mmaxmem mimrec";
+  echo "";
+}
+
+
+# Make sure there's at least one argument
+if [ $# -lt 1 ]; then
+  help
+  exit 1
+fi
+
+# Check for help flag
+if [[ "$1" == "*-h*" ]]; then
+  help
+  exit 0
+fi
+
+OS=$(uname)
+
+RSS_KB=0
+MAX_RSS_KB=0
+
+# Start the command in the background
+"$@" &> /dev/null &
+APPPID=$!
+APPNAME=$*
+sleep 0.2
+
+echo "Monitoring memory usage of program ${APPNAME} with ${APPPID} ..."
+echo ""
+
+while true; do
+  if ps -p "${APPPID}" > /dev/null 2>&1; then
+    if [[ "${OS}" == *inux* ]]; then
+      RSS_KB=$(awk '/VmRSS/ {print $2}' /proc/${APPPID}/status 2>/dev/null)
+    elif [[ "${OS}" == *arwin* ]]; then
+      RSS_KB=$(ps -o rss= -p "${APPPID}" | awk '{print $1}')
+    else
+      echo "Unsupported OS: \"${OS}\""
+      exit 1
+    fi
+
+    if [[ "${RSS_KB}" =~ ^[0-9]+$ ]]; then
+      if [ "${RSS_KB}" -gt "${MAX_RSS_KB}" ]; then
+        MAX_RSS_KB=${RSS_KB}
+      fi
+      CURRENT_MB=$(awk "BEGIN {printf \"%.2f\", ${RSS_KB}/1024}")
+      MAX_MB=$(awk "BEGIN {printf \"%.2f\", ${MAX_RSS_KB}/1024}")
+      echo -ne "Current: ${CURRENT_MB} MB\tMax: ${MAX_MB} MB\r"
+    fi
+    sleep 1.0
+  else
+    echo -e "\nProcess ${APPPID} has exited."
+    MAX_MB=$(awk "BEGIN {printf \"%.2f\", ${MAX_RSS_KB}/1024}")
+    echo "Maximum RSS memory used: ${MAX_MB} MB"
+    break
+  fi
+done

From 60875bd4e12912090ea6392952d3591c1b367970 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Fri, 20 Jun 2025 15:35:49 -0700
Subject: [PATCH 144/192] CHG: Include Fretalon base

---
 resource/standalone/Makefile.StandAlone | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/resource/standalone/Makefile.StandAlone b/resource/standalone/Makefile.StandAlone
index ce5a1330c..9d51dd54e 100644
--- a/resource/standalone/Makefile.StandAlone
+++ b/resource/standalone/Makefile.StandAlone
@@ -42,7 +42,7 @@ CT  = $(TOP)/cint
 
 MPRG=$(subst .cxx,,$(PRG))
 
-MLIBS = -L$(LB) -lMimrecGui -lMimrec -lRevanGui -lRevan -lSivanGui -lSivan -lSpectralyzeGui -lSpectralyze -lGeomegaGui -lGeomega -lCommonMisc -lCommonGui  
+MLIBS = -L$(LB) -lMimrecGui -lMimrec -lRevanGui -lRevan -lSivanGui -lFretalonBase -lSivan -lSpectralyzeGui -lSpectralyze -lGeomegaGui -lGeomega -lCommonMisc -lCommonGui  
 
 
 #-------------------------------------------------------------------------------

From eba2dffbc63588a4113aeec96a13bc09a88aaa16 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Fri, 20 Jun 2025 15:36:30 -0700
Subject: [PATCH 145/192] BUG: Prevent UI clicks when analysis is running

---
 src/fretalon/melinator/inc/MGUIMainMelinator.h   |  2 ++
 src/fretalon/melinator/src/MGUIMainMelinator.cxx | 14 ++++++++++++--
 2 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/src/fretalon/melinator/inc/MGUIMainMelinator.h b/src/fretalon/melinator/inc/MGUIMainMelinator.h
index 1f7e916b0..373ead27c 100644
--- a/src/fretalon/melinator/inc/MGUIMainMelinator.h
+++ b/src/fretalon/melinator/inc/MGUIMainMelinator.h
@@ -163,6 +163,8 @@ class MGUIMainMelinator : public TGMainFrame
   unsigned int m_ActiveLineFit;
   //! The active results view
   bool m_ActiveResultIsEnergy;
+  //! True if any analysis is ongoing
+  bool m_AnalysisRunning;
   
   //! The label of the main histogram
   TGLabel* m_MainHistogramLabel;
diff --git a/src/fretalon/melinator/src/MGUIMainMelinator.cxx b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
index af4d56ad9..0ca8591bb 100644
--- a/src/fretalon/melinator/src/MGUIMainMelinator.cxx
+++ b/src/fretalon/melinator/src/MGUIMainMelinator.cxx
@@ -87,6 +87,7 @@ MGUIMainMelinator::MGUIMainMelinator(MInterfaceMelinator* Interface,
   m_ActiveCollection = 0;
   m_ActiveLineFit = 0;
   m_ActiveResultIsEnergy = true;
+  m_AnalysisRunning = false;
 }
 
 
@@ -793,6 +794,13 @@ bool MGUIMainMelinator::ProcessMessage(long Message, long Parameter1, long Param
   
   bool Status = true;
 
+  // Protection against reentering running analysis:
+  if (m_AnalysisRunning == true) {
+    mout<<"Please wait until the current analysis is done"<<endl;
+    return true;
+  }
+  m_AnalysisRunning = true;
+  
   switch (GET_MSG(Message)) {
   case kC_COMMAND:
     switch (GET_SUBMSG(Message)) {
@@ -946,6 +954,8 @@ bool MGUIMainMelinator::ProcessMessage(long Message, long Parameter1, long Param
     break;
   }
   
+  m_AnalysisRunning = false;  
+  
   return Status;
 }
 
@@ -1030,7 +1040,7 @@ bool MGUIMainMelinator::OnExit()
 
 //! Switch the histogram binning mode
 bool MGUIMainMelinator::OnSwitchHistogramBinningMode(unsigned int ID)
-{  
+{ 
   if (ID == MMelinator::c_HistogramBinningModeFixedNumberOfBins) {
     m_HistogramBinningModeValueLabel->SetText("  bins");
   } else if (ID == MMelinator::c_HistogramBinningModeFixedCountsPerBin) {
@@ -1054,7 +1064,7 @@ bool MGUIMainMelinator::OnSwitchHistogramBinningMode(unsigned int ID)
 
 //! Switch the histogram binning mode
 bool MGUIMainMelinator::OnSwitchPeakParametrizationMode(unsigned int ID)
-{    
+{
   if (ID == MCalibrateEnergyFindLines::c_PeakParametrizationMethodBayesianBlockPeak) {
     m_PeakParametrizationOptions->RemoveAll(); // Deletes everyting too 
   } else if (ID == MCalibrateEnergyFindLines::c_PeakParametrizationMethodSmoothedPeak) {

From 2bacbc4eff35aa1363642e8221fdd3e59a52769a Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Mon, 7 Jul 2025 10:52:45 -0700
Subject: [PATCH 146/192] ADD: Command line option to show the location of the
 first interaction

---
 src/mimrec/src/MInterfaceMimrec.cxx | 48 ++++++++++++++++-------------
 1 file changed, 27 insertions(+), 21 deletions(-)

diff --git a/src/mimrec/src/MInterfaceMimrec.cxx b/src/mimrec/src/MInterfaceMimrec.cxx
index eab35716e..9032b7dcf 100644
--- a/src/mimrec/src/MInterfaceMimrec.cxx
+++ b/src/mimrec/src/MInterfaceMimrec.cxx
@@ -166,6 +166,8 @@ bool MInterfaceMimrec::ParseCommandLine(int argc, char** argv)
   Usage<<"             Create the scatter-angle distributions. If the -o option is given then the image is saved to this file."<<endl;
   Usage<<"         --sequence-length:"<<endl;
   Usage<<"             Create the sequence length plots. If the -o option is given then the image is saved to this file."<<endl;
+  Usage<<"         --location-first-interaction:"<<endl;
+  Usage<<"             Create histograms on the detector locations of the first interaction."<<endl;
   Usage<<"      -x --extract:"<<endl;
   Usage<<"             Extract events using the given event selection to the file given by -o"<<endl;
   Usage<<"      -e --event-selections:"<<endl;
@@ -364,9 +366,13 @@ bool MInterfaceMimrec::ParseCommandLine(int argc, char** argv)
       DistanceDistribution();
       return KeepAlive;
     } else if (Option == "--sequence-length") {
-      cout<<"Command-line parser: Generating Compton-sequence length plot..."<<endl;  
+      cout<<"Command-line parser: Generating Compton-sequence length plot..."<<endl;
       SequenceLengths();
       return KeepAlive;
+    } else if (Option == "--location-first-interaction") {
+      cout<<"Command-line parser: Generating Compton-sequence length plot..."<<endl;
+      LocationOfInitialInteraction();
+      return KeepAlive;
     } else if (Option == "--extract" || Option == "-x") {
       cout<<"Command-line parser: Extracting events..."<<endl;  
       ExtractEvents();
@@ -6184,8 +6190,8 @@ void MInterfaceMimrec::LocationOfInitialInteraction()
   // Step 2: Create the histograms
   DetermineAxis(xMin, xMax, yMin, yMax, zMin, zMax, Positions);
   
-  TH3D* xyzHist = new TH3D("SpacialHitDistributionXYZ", 
-                        "Spacial hit distribution xyz", 
+  TH3D* xyzHist = new TH3D("SpatialHitDistributionXYZ",
+                        "Spatial hit distribution xyz",
                         MaxNBins, xMin, +xMax,
                         MaxNBins, yMin, +yMax, 
                         MaxNBins, zMin, +zMax);
@@ -6194,22 +6200,22 @@ void MInterfaceMimrec::LocationOfInitialInteraction()
   xyzHist->GetYaxis()->SetTitle("y [cm]");
   xyzHist->GetZaxis()->SetTitle("z [cm]");
 
-  TH1D* xHist = new TH1D("SpacialHitDistributionX", 
-       "Spacial hit distribution x", 
+  TH1D* xHist = new TH1D("SpatialHitDistributionX",
+       "Spatial hit distribution x",
        MaxNBins, xMin, +xMax);
   xHist->SetBit(kCanDelete);
   xHist->GetXaxis()->SetTitle("x [cm]");
   xHist->GetYaxis()->SetTitle("counts");
 
-  TH1D* yHist = new TH1D("SpacialHitDistributionY", 
-       "Spacial hit distribution y", 
+  TH1D* yHist = new TH1D("SpatialHitDistributionY",
+       "Spatial hit distribution y",
        MaxNBins, yMin, +yMax);
   yHist->SetBit(kCanDelete);
   yHist->GetXaxis()->SetTitle("y [cm]");
   yHist->GetYaxis()->SetTitle("counts");
 
-  TH1D* zHist = new TH1D("SpacialHitDistributionZ", 
-       "Spacial hit distribution z", 
+  TH1D* zHist = new TH1D("SpatialHitDistributionZ",
+       "Spatial hit distribution z",
        MaxNBins, zMin, +zMax);
   zHist->SetBit(kCanDelete);
   zHist->GetXaxis()->SetTitle("z [cm]");
@@ -6259,25 +6265,25 @@ void MInterfaceMimrec::LocationOfInitialInteraction()
 
   // Step 5: Show the histograms
 
-  TCanvas* xyzCanvas = new TCanvas();
-  xyzCanvas->cd();
+  TCanvas* Canvas = new TCanvas();
+  Canvas->Divide(2, 2);
+
+  Canvas->cd(4);
   xyzHist->Draw();
-  xyzCanvas->Update();
 
-  TCanvas* xCanvas = new TCanvas();
-  xCanvas->cd();
+  Canvas->cd(1);
   xHist->Draw();
-  xCanvas->Update();
 
-  TCanvas* yCanvas = new TCanvas();
-  yCanvas->cd();
+  Canvas->cd(2);
   yHist->Draw();
-  yCanvas->Update();
 
-  TCanvas* zCanvas = new TCanvas();
-  zCanvas->cd();
+  Canvas->cd(3);
   zHist->Draw();
-  zCanvas->Update();
+
+  Canvas->Update();
+  if (m_OutputFileName.IsEmpty() == false) {
+    Canvas->SaveAs(m_OutputFileName);
+  }
 
   // Dump the info:
   map<MString, int>::iterator Iter;

From ff1f9167597e0f5c2d46ec3a693c364d33d00437 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Wed, 17 Sep 2025 12:18:53 -0700
Subject: [PATCH 147/192] CHG: Increase ROOT version to 6.36

---
 config/AllowedROOTVersions.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/AllowedROOTVersions.txt b/config/AllowedROOTVersions.txt
index cfee3c9ec..ad5788043 100644
--- a/config/AllowedROOTVersions.txt
+++ b/config/AllowedROOTVersions.txt
@@ -1 +1 @@
-632 
+632 636 

From 55cd3a43e1d51aaff0a03c9f6376182e948773d8 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Wed, 17 Sep 2025 12:19:23 -0700
Subject: [PATCH 148/192] CHG: Compatibility with macOS 26 Tahoe

---
 config/build-root.sh | 56 +++++++++++++++++++++++++-------------------
 1 file changed, 32 insertions(+), 24 deletions(-)

diff --git a/config/build-root.sh b/config/build-root.sh
index f0d2c8c47..e626b87ab 100755
--- a/config/build-root.sh
+++ b/config/build-root.sh
@@ -5,43 +5,51 @@
 #
 # Please see the MEGAlib software license and documentation for more informations.
 
-CONFIGUREOPTIONS=" "
+# Need an array here
+CONFIGUREOPTIONS=( )
 # Install path relative to the build path --- simply one up in this script
-CONFIGUREOPTIONS+=" -DCMAKE_INSTALL_PREFIX=.."
+CONFIGUREOPTIONS+=("-DCMAKE_INSTALL_PREFIX=..")
 # Make sure we ignore some default paths of macport.
 type port >/dev/null 2>&1
 if [[ $? -eq 0 ]]; then
   PORTPATH=$(which port)
   PORTPATH=${PORTPATH%/bin/port}
-  CONFIGUREOPTIONS+=" -DCMAKE_IGNORE_PATH=${PORTPATH};${PORTPATH}/bin;${PORTPATH}/include;${PORTPATH}/include/libxml2;${PORTPATH}/include/unicode"
+  CONFIGUREOPTIONS+=("-DCMAKE_IGNORE_PATH=${PORTPATH};${PORTPATH}/bin;${PORTPATH}/include;${PORTPATH}/include/libxml2;${PORTPATH}/include/unicode")
 fi
 # Until ROOT 6.24: C++ 11
-CONFIGUREOPTIONS+=" -DCMAKE_CXX_STANDARD=17"
+CONFIGUREOPTIONS+=("-DCMAKE_CXX_STANDARD=17")
 # We want a minimal system and enable what we really need:
-#CONFIGUREOPTIONS+=" -Dgminimal=ON"
+# No, not any longer true: CONFIGUREOPTIONS+=("-Dgminimal=ON")
 # Open GL -- needed by geomega
-CONFIGUREOPTIONS+=" -Dopengl=ON"
-# Mathmore -- needed for fitting, e.g. ARMs"
-CONFIGUREOPTIONS+=" -Dmathmore=ON"
+CONFIGUREOPTIONS+=("-Dopengl=ON")
+# Mathmore -- needed for fitting, e.g. ARMs
+CONFIGUREOPTIONS+=("-Dmathmore=ON")
 # Minuit2 -- needed for parallel fitting with melinator
-# Minuit 2 is default startin g ROOT 6.30: CONFIGUREOPTIONS+=" -Dminuit2=ON"
+# Minuit 2 is default starting ROOT 6.30: CONFIGUREOPTIONS+=("-Dminuit2=ON")
 # XFT -- needed for smoothed fonts
-CONFIGUREOPTIONS+=" -Dxft=ON"
+CONFIGUREOPTIONS+=("-Dxft=ON")
 # Afterimage -- support to draw images in pads and save as png, etc.
-CONFIGUREOPTIONS+=" -Dasimage=ON"
+CONFIGUREOPTIONS+=("-Dasimage=ON")
 # Stuff for linking, paths in so files, versioning etc
-CONFIGUREOPTIONS+=" -Dexplicitlink=ON -Drpath=ON -Dsoversion=ON"
+CONFIGUREOPTIONS+=("-Dexplicitlink=ON" "-Drpath=ON" "-Dsoversion=ON")
 # enable builtin glew
-CONFIGUREOPTIONS+=" -Dbuiltin_glew=ON"
+CONFIGUREOPTIONS+=("-Dbuiltin_glew=ON")
+# Stick with ROOT 6 for the time being
+CONFIGUREOPTIONS+=("-Droot7=OFF")
+# macOS specific fixes:
+if [[ $(uname -s) == *arwin ]]; then
+  SDKPATH=$(xcrun --show-sdk-path)
+  CONFIGUREOPTIONS+=("-DCMAKE_OSX_SYSROOT=${SDKPATH}" "-DCMAKE_CXX_FLAGS=-isysroot ${SDKPATH}")
+fi
 
 # In case you have trouble with anything related to freetype, try to comment in this option
-# CONFIGUREOPTIONS+=" -Dbuiltin-freetype=ON"
+# CONFIGUREOPTIONS+=("-Dbuiltin-freetype=ON")
 
 # In case you get strange error messages concerning jpeg, png, tiff
-# CONFIGUREOPTIONS+=" -Dasimage=OFF -Dastiff=OFF -Dbuiltin_afterimage=OFF"
+# CONFIGUREOPTIONS+=("-Dasimage=OFF" "-Dastiff=OFF" "-Dbuiltin_afterimage=OFF")
 
 # In case you have trouble with zlib (gz... something error messages)
-# CONFIGUREOPTIONS+=" -Dbuiltin_zlib=ON -Dbuiltin_lzma=ON"
+# CONFIGUREOPTIONS+=("-Dbuiltin_zlib=ON" "-Dbuiltin_lzma=ON")
 
 # By default we build with python 3:
 type python3 >/dev/null 2>&1
@@ -52,7 +60,7 @@ if [[ $? -eq 0 ]]; then
       echo "ERROR: You cannot use a python version installed via (ana)conda with ROOT."
       exit 1
     else
-      CONFIGUREOPTIONS+=" -DPYTHON_EXECUTABLE:FILEPATH=${PPATH} -Dpython3=ON"
+      CONFIGUREOPTIONS+=("-DPYTHON_EXECUTABLE:FILEPATH=${PPATH}" "-Dpython3=ON")
     fi
   fi
 fi
@@ -60,18 +68,18 @@ fi
 # Enable cuda if available
 type nvcc >/dev/null 2>&1
 if [[ $? -eq 0 ]]; then
-  CONFIGUREOPTIONS+=" -Dcuda=ON"
+  CONFIGUREOPTIONS+=("-Dcuda=ON")
 fi
 
 # In case ROOT complains about your python version
-# CONFIGUREOPTIONS+=" -Dpython=OFF"
-# CONFIGUREOPTIONS+=" -Dpython3=OFF"
+# CONFIGUREOPTIONS+=("-Dpython=OFF")
+# CONFIGUREOPTIONS+=("-Dpython3=OFF")
 
 # Switching off things we do not need right now but which are on by default
-CONFIGUREOPTIONS+=" -Dalien=OFF -Dbonjour=OFF -Dcastor=OFF -Ddavix=OFF -Dfortran=OFF -Dfitsio=OFF -Dchirp=OFF -Ddcache=OFF -Dgfal=OFF -Dglite=off -Dhdfs=OFF -Dkerb5=OFF -Dldap=OFF -Dmonalisa=OFF -Dodbc=OFF -Doracle=OFF -Dpch=OFF -Dpgsql=OFF -Dpythia6=OFF -Dpythia8=OFF -Drfio=OFF -Dsapdb=OFF -Dshadowpw=OFF -Dsqlite=OFF -Dsrp=OFF -Dssl=OFF -Dxrootd=OFF"
+CONFIGUREOPTIONS+=("-Dalien=OFF" "-Dbonjour=OFF" "-Dcastor=OFF" "-Ddavix=OFF" "-Dfortran=OFF" "-Dfitsio=OFF" "-Dchirp=OFF" "-Ddcache=OFF" "-Dgfal=OFF" "-Dglite=off" "-Dhdfs=OFF" "-Dkerb5=OFF" "-Dldap=OFF" "-Dmonalisa=OFF" "-Dodbc=OFF" "-Doracle=OFF" "-Dpch=OFF" "-Dpgsql=OFF" "-Dpythia6=OFF" "-Dpythia8=OFF" "-Drfio=OFF" "-Dsapdb=OFF" "-Dshadowpw=OFF" "-Dsqlite=OFF" "-Dsrp=OFF" "-Dssl=OFF" "-Dxrootd=OFF")
 
 # Explictly add gcc -- cmake seems to sometimes digg up other compilers on the system, not the default one...
-# CONFIGUREOPTIONS+=" -DCMAKE_C_COMPILER=$(which gcc) -DCMAKE_CXX_COMPILER=$(which g++)"
+# CONFIGUREOPTIONS+=("-DCMAKE_C_COMPILER=$(which gcc)" "-DCMAKE_CXX_COMPILER=$(which g++)")
 
 # The compiler
 COMPILEROPTIONS=`gcc --version | head -n 1`
@@ -573,8 +581,8 @@ export ROOTSYS=${ROOTDIR}
 #  export CPLUS_INCLUDE_PATH=`xcrun --show-sdk-path`/usr/include
 #  export LIBRARY_PATH=$LIBRARY_PATH:`xcrun --show-sdk-path`/usr/lib
 #fi
-echo "Configure command: cmake ${CONFIGUREOPTIONS} ${DEBUGOPTIONS} ../${ROOTSOURCEDIR}"
-cmake ${CONFIGUREOPTIONS} ${DEBUGOPTIONS} ../${ROOTSOURCEDIR}
+echo "Configure command: cmake ${CONFIGUREOPTIONS[@]} ${DEBUGOPTIONS} ../${ROOTSOURCEDIR}"
+cmake "${CONFIGUREOPTIONS[@]}" ${DEBUGOPTIONS} ../${ROOTSOURCEDIR}
 if [ "$?" != "0" ]; then
   echo "ERROR: Something went wrong configuring (cmake'ing) ROOT!"
   exit 1

From 4716deb01c6e869049c4997aeefaa9c0a82f3863 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Wed, 17 Sep 2025 13:42:36 -0700
Subject: [PATCH 149/192] CHG: Fix some warnings on macOS

---
 config/Makefile.macosx | 13 ++++++-------
 src/addon/Makefile     |  2 +-
 2 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/config/Makefile.macosx b/config/Makefile.macosx
index 7943afe75..b8393f419 100644
--- a/config/Makefile.macosx
+++ b/config/Makefile.macosx
@@ -15,7 +15,6 @@ DLL           := so
 
 # Basic flags generated by ROOT
 ROOTCFLAGS    := $(shell root-config --cflags)
-ROOTLIBS      := $(shell root-config --libs)
 ROOTGLIBS     := $(shell root-config --glibs)
 
 # Compiler & linker options:
@@ -23,10 +22,10 @@ CXX           := c++
 CXXFLAGS      := $(OPT) -std=c++14 -pipe -Wall -fPIC -D_REENTRANT -I$(IN) -I$(CT) -I. $(ROOTCFLAGS) -D___MACOSX___ -D___CLING___ -Wno-unused-but-set-variable -Wno-overloaded-virtual -Wno-tautological-undefined-compare -Wno-deprecated-declarations
 DEFINES       := -UHARDWARE
 LD            := c++
-LDFLAGS       := $(OPT) -Xlinker -bind_at_load -flat_namespace -D___MACOSX___
-SOFLAGS       := -dynamiclib -flat_namespace -undefined suppress 
-LIBS          := $(ROOTLIBS) -lpthread -lThread -lMinuit -lMinuit2 -lGeom -lSpectrum -lTMVA
-GLIBS         := $(ROOTGLIBS) 
+LDFLAGS       := $(OPT) -Xlinker -flat_namespace -D___MACOSX___
+SOFLAGS       := -dynamiclib -undefined dynamic_lookup
+LIBS          := $(ROOTGLIBS) -lMinuit -lMinuit2 -lGeom -lSpectrum -lTMVA
+GLIBS         := 
 DEPFLAGS      := -M
 
 LINK          := ln -s -f
@@ -36,10 +35,10 @@ HEACFLAGS     :=
 HEALIBS       :=
 ifeq ("$(shell PKG_CONFIG_PATH=$(LHEASOFT)/lib/pkgconfig pkg-config --exists cfitsio 1>&2 2> /dev/null; echo $$?)", "0")
         HEACFLAGS += $(shell PKG_CONFIG_PATH=$(LHEASOFT)/lib/pkgconfig pkg-config --cflags cfitsio)
-        HEALIBS += $(shell PKG_CONFIG_PATH=$(LHEASOFT)/lib/pkgconfig pkg-config --libs cfitsio --static)
+	HEALIBS += $(filter-out -lm, $(shell PKG_CONFIG_PATH=$(LHEASOFT)/lib/pkgconfig pkg-config --libs cfitsio --static))
 else ifeq ("$(shell pkg-config --exists cfitsio 1>&2 2> /dev/null; echo $$?)", "0")
         HEACFLAGS += $(shell pkg-config --cflags cfitsio)
-        HEALIBS += $(shell pkg-config --libs cfitsio)
+	HEALIBS = $(filter-out -lm, $(shell pkg-config --libs cfitsio))
 endif
 
 
diff --git a/src/addon/Makefile b/src/addon/Makefile
index 96b8e25d9..1103bcf1d 100644
--- a/src/addon/Makefile
+++ b/src/addon/Makefile
@@ -80,7 +80,7 @@ clean:
 $(FITS): $(BN)/%: %.cxx
 ifeq "$(strip $(HEASOFTINSTALLED))" "0"
 	@echo "Compiling and linking $(subst $(BN)/,,$@) ..."
-	$(LD) $(LDFLAGS) $(CXXFLAGS) $(HEACFLAGS) $(DEFINES) $< $(MLIBS) -lcfitsio -lm $(GLIBS) $(LIBS) $(HEALIBS) -o $@
+	$(LD) $(LDFLAGS) $(CXXFLAGS) $(HEACFLAGS) $(DEFINES) $< $(MLIBS) $(GLIBS) $(LIBS) $(HEALIBS) -o $@
 endif
 
 $(MPI): $(BN)/%: %.cxx

From 6274a3612177d36072cdfd6cd2706f34198ced82 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Wed, 17 Sep 2025 14:42:01 -0700
Subject: [PATCH 150/192] CHG: Sort the element list

---
 src/cosima/src/MCRun.cc | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/src/cosima/src/MCRun.cc b/src/cosima/src/MCRun.cc
index 8bd7a38ae..557f7cc40 100644
--- a/src/cosima/src/MCRun.cc
+++ b/src/cosima/src/MCRun.cc
@@ -502,11 +502,18 @@ void MCRun::DumpRunStatistics(double CPUTime)
   cout<<"Summary for run "<<m_Name<<endl;
   cout<<endl;
   cout<<"Total number of generated particles:     "<<m_NGeneratedParticles<<endl;
-  for (unsigned int i = 0; i < m_SourceList.size(); ++i) {
-    int Length = m_SourceList[i]->GetName().Length();
-    cout<<"  Source "<<m_SourceList[i]->GetName()<<": ";
+  vector<MCSource*> SortedSourceList = m_SourceList;
+  sort(SortedSourceList.begin(), SortedSourceList.end(), [](MCSource* A, MCSource* B) {
+    if (A->GetNGeneratedParticles() == B->GetNGeneratedParticles()) {
+      return A->GetName() < B->GetName();
+    }
+    return A->GetNGeneratedParticles() > B->GetNGeneratedParticles();
+  });
+  for (unsigned int i = 0; i < SortedSourceList.size(); ++i) {
+    int Length = SortedSourceList[i]->GetName().Length();
+    cout<<"  Source "<<SortedSourceList[i]->GetName()<<": ";
     for (int l = Length+11; l < 41; ++l) cout<<" ";
-    cout<<m_SourceList[i]->GetNGeneratedParticles()<<endl;
+    cout<<SortedSourceList[i]->GetNGeneratedParticles()<<endl;
   }
   cout<<endl;
   cout<<"Total CPU time spent in run:             "<<CPUTime<<" sec"<<endl;

From b63985a32873a7b34282c83f2d20b4831023f5d5 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Wed, 17 Sep 2025 15:15:27 -0700
Subject: [PATCH 151/192] VER: 4.02

---
 config/Version.txt |  2 +-
 doc/ChangeLog.txt  | 19 +++++++++++++++++++
 2 files changed, 20 insertions(+), 1 deletion(-)

diff --git a/config/Version.txt b/config/Version.txt
index 4e7283627..283e0089a 100644
--- a/config/Version.txt
+++ b/config/Version.txt
@@ -1 +1 @@
-4.00.00
+4.02.00
diff --git a/doc/ChangeLog.txt b/doc/ChangeLog.txt
index f8cab2c45..62d7a4b2d 100644
--- a/doc/ChangeLog.txt
+++ b/doc/ChangeLog.txt
@@ -7,6 +7,25 @@
 
 
 
+Version 4.01/4.02
+=================
+
+This is mostly a compatibility, bug fix, and minor updates release.
+The main development towards MEGAlib 5.0 is happening in the branch develop-cosi.
+However, as of Septmeber 2025, this branch contains a few features which only work with COSI.
+
+General:
++ Default ROOT version is 6.36
++ Updates to run on all the latest OS'es
+
+Mimrec:
++ New ARM fitting tool
+
+Fretalon / Melinator:
++ Many updates to Melinator to improve the energy calibration
+
+
+
 Version 4.00
 ============
 

From 08d124a8f8556b83e5c15b4bfa748d8afe41ec32 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Thu, 18 Sep 2025 15:04:27 -0700
Subject: [PATCH 152/192] CHG: Compatibility with brew on macOS Sequoia & Tahoe

---
 config/build-geant4.sh | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/config/build-geant4.sh b/config/build-geant4.sh
index c603a9c54..b2ffb149e 100755
--- a/config/build-geant4.sh
+++ b/config/build-geant4.sh
@@ -7,11 +7,15 @@ if [[ $(uname -a) != *arwin* ]]; then
   type g++ >/dev/null 2>&1
   if [ $? -eq 0 ]; then
     # echo "g++ compiler found - using it as default!";
-    CONFIGUREOPTIONS="-DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++"
+    CONFIGUREOPTIONS+=" -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++"
   fi
 fi
-CONFIGUREOPTIONS="${CONFIGUREOPTIONS} -DCMAKE_INSTALL_PREFIX=.. -DGEANT4_INSTALL_DATA=ON -DGEANT4_USE_OPENGL_X11=OFF -DGEANT4_INSTALL_DATA_TIMEOUT=14400 -DGEANT4_USE_SYSTEM_EXPAT=OFF -DGEANT4_BUILD_CXXSTD=c++17"
-#CONFIGUREOPTIONS="${CONFIGUREOPTIONS} -DCMAKE_CXX_FLAGS=-D_GLIBCXX_USE_CXX11_ABI=0"
+
+# Standard options:
+CONFIGUREOPTIONS+=" -DCMAKE_INSTALL_PREFIX=.. -DGEANT4_INSTALL_DATA=ON -DGEANT4_USE_OPENGL_X11=OFF -DGEANT4_INSTALL_DATA_TIMEOUT=14400 -DGEANT4_USE_SYSTEM_EXPAT=OFF -DGEANT4_BUILD_CXXSTD=c++17"
+# To make old Geant4 versions run with the latest cmake
+CONFIGUREOPTIONS+=" -DCMAKE_POLICY_VERSION_MINIMUM=3.5"
+
 # Reduce the warning messages:
 WARNINGS="-Wno-shadow -Wno-implicit-fallthrough -Wno-overloaded-virtual -Wno-deprecated-copy -Wno-unused-result -Wno-format-overflow="
 

From 08b9f59c3aebf971526894285eacf36f8bfc0fc9 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <andreas@megalibtoolkit.com>
Date: Thu, 18 Sep 2025 23:58:37 -0700
Subject: [PATCH 153/192] CHG: Require C++ 17

---
 config/configure_compilertest | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/configure_compilertest b/config/configure_compilertest
index c9b0c2783..91756159f 100755
--- a/config/configure_compilertest
+++ b/config/configure_compilertest
@@ -69,7 +69,7 @@ int main()
 
 #echo "${CODE}"
 
-echo "${CODE}" | ${COMPILER} -o compilertest -x c++ -
+echo "${CODE}" | ${COMPILER} -std=c++17 -o compilertest -x c++ -
 STATUS=""
 if [[ -f compilertest ]]; then
   STATUS=`./compilertest`

From 74589d6265113290ab5e6d247bd9795070893807 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Tue, 30 Sep 2025 11:12:14 -0700
Subject: [PATCH 154/192] CHG: More Geant4 install fixes

---
 config/build-geant4.sh                |  6 ++++++
 resource/patches/geant4_v11.2.2.patch | 11 +++++++++++
 2 files changed, 17 insertions(+)
 create mode 100644 resource/patches/geant4_v11.2.2.patch

diff --git a/config/build-geant4.sh b/config/build-geant4.sh
index b2ffb149e..45a7f49fa 100755
--- a/config/build-geant4.sh
+++ b/config/build-geant4.sh
@@ -15,6 +15,7 @@ fi
 CONFIGUREOPTIONS+=" -DCMAKE_INSTALL_PREFIX=.. -DGEANT4_INSTALL_DATA=ON -DGEANT4_USE_OPENGL_X11=OFF -DGEANT4_INSTALL_DATA_TIMEOUT=14400 -DGEANT4_USE_SYSTEM_EXPAT=OFF -DGEANT4_BUILD_CXXSTD=c++17"
 # To make old Geant4 versions run with the latest cmake
 CONFIGUREOPTIONS+=" -DCMAKE_POLICY_VERSION_MINIMUM=3.5"
+CONFIGUREOPTIONS+=" -DGEANT4_USE_SYSTEM_ZLIB=ON"
 
 # Reduce the warning messages:
 WARNINGS="-Wno-shadow -Wno-implicit-fallthrough -Wno-overloaded-virtual -Wno-deprecated-copy -Wno-unused-result -Wno-format-overflow="
@@ -368,6 +369,11 @@ if [[ ${GEANT4CORE} == "geant4_v10.02.p03" ]]; then
   PATCH="on"
   echo "This version of Geant4 requires a mandatory patch"
 fi
+if [[ ${GEANT4CORE} == "geant4_v11.02.p02" ]]; then
+  PATCH="on"
+  echo "This version of Geant4 requires a mandatory patch"
+fi
+
 
 echo "Checking for old installation..."
 if [ -d ${GEANT4DIR} ]; then
diff --git a/resource/patches/geant4_v11.2.2.patch b/resource/patches/geant4_v11.2.2.patch
new file mode 100644
index 000000000..cb415087e
--- /dev/null
+++ b/resource/patches/geant4_v11.2.2.patch
@@ -0,0 +1,11 @@
+--- a/geant4_v11.2.2-source/source/externals/g4tools/include/tools/wroot/columns.icc	2025-09-25 15:33:21
++++ b/geant4_v11.2.2-source/source/externals/g4tools/include/tools/wroot/columns.icc	2025-09-25 15:34:48
+@@ -399,7 +399,7 @@
+   protected:
+     std_vector_column_ref(const std_vector_column_ref& a_from)
+     :icol(a_from)
+-    ,m_branch(a_from.m_barnch)
++    ,m_branch(a_from.m_branch)
+     ,m_ref(a_from.m_ref)
+     ,m_leaf(0)
+     ,m_leaf_count(0)

From ed1b7075354618bd9a2f98d46f52e9a0eacf5992 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Tue, 30 Sep 2025 11:14:34 -0700
Subject: [PATCH 155/192] ADD: Fretaloin framework submodules

---
 src/fretalon/framework/inc/MModule.h      |  11 ++-
 src/fretalon/framework/inc/MSubModule.h   | 105 ++++++++++++++++++++
 src/fretalon/framework/src/MSubModule.cxx | 115 ++++++++++++++++++++++
 3 files changed, 229 insertions(+), 2 deletions(-)
 create mode 100644 src/fretalon/framework/inc/MSubModule.h
 create mode 100644 src/fretalon/framework/src/MSubModule.cxx

diff --git a/src/fretalon/framework/inc/MModule.h b/src/fretalon/framework/inc/MModule.h
index 552b460f8..f083989ca 100644
--- a/src/fretalon/framework/inc/MModule.h
+++ b/src/fretalon/framework/inc/MModule.h
@@ -47,7 +47,14 @@ void* MModuleKickstartThread(void* ClassDerivedFromMModule);
 
 ////////////////////////////////////////////////////////////////////////////////
 
-
+//! This is the base class for all modules. It provides
+//! + Logic to determine which services it provides
+//! + Which modules must preceed it
+//! + Multi-threading capabilities
+//! + Read-out assembly handling and queuing
+//! + Xml reading and writing of the configuration files
+//! + Expo generation and handling
+//! + and general analysis task management features
 class MModule
 {
   // public interface:
@@ -115,7 +122,7 @@ class MModule
   //! Initialize the module
   //! When overwritten, the base-class'es Initialize() has to be called *at the very end* of the 
   //! Initilize() function of the derived class, since in multi-threaded mode it 
-  //! starts the thraeds
+  //! starts the threads
   virtual bool Initialize();
 
   //! Finalize the module
diff --git a/src/fretalon/framework/inc/MSubModule.h b/src/fretalon/framework/inc/MSubModule.h
new file mode 100644
index 000000000..14daaf055
--- /dev/null
+++ b/src/fretalon/framework/inc/MSubModule.h
@@ -0,0 +1,105 @@
+/*
+ * MSubModule.h
+ *
+ * Copyright (C) by Andreas Zoglauer.
+ * All rights reserved.
+ *
+ * Please see the source-file for the copyright-notice.
+ *
+ */
+
+
+#ifndef __MSubModule__
+#define __MSubModule__
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+// Standard libs:
+#include <vector>
+using namespace std;
+
+// ROOT libs:
+
+// MEGAlib libs:
+#include "MGlobal.h"
+#include "MXmlNode.h"
+#include "MReadOutAssembly.h"
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+//! This is the base class for all sub modules. It provides
+//! + Read-out assembly handling
+//! + and general analysis task management features
+class MSubModule
+{
+  // public interface:
+ public:
+  //! Default constructor
+  MSubModule();
+
+  //! No copy constructor
+  MSubModule(const MSubModule&) = delete;
+  //! No copy assignment
+  MSubModule& operator=(const MSubModule&) = delete;
+  //! No move constructors
+  MSubModule(MSubModule&&) = delete;
+  //! No move MSubModule
+  MSubModule& operator=(MSubModule&&) = delete;
+
+  //! Default destructor
+  virtual ~MSubModule();
+  //! Initialize the module
+  //! When overwritten, the base-class'es Initialize() has to be called *at the very end* of the 
+  //! Initilize() function of the derived class, since in multi-threaded mode it 
+  //! starts the thraeds
+  virtual bool Initialize();
+
+  //! Clear event data
+  virtual void Clear();
+
+  //! Main data analysis routine, which updates the event to a new level 
+  //! Has to be overwritten in derived class
+  virtual bool AnalyzeEvent(MReadOutAssembly* Event) = 0;
+
+  //! Finalize the module
+  //! When overwritten, the base-class'es Finalize() has to be called *at the very beginning* of the
+  //! Finalize() function of the derived class, since in multi-threaded mode it
+  //! ends the threads
+  virtual void Finalize();
+
+  //! Read the configuration data from an XML node
+  virtual bool ReadXmlConfiguration(MXmlNode* Node);
+  //! Create an XML node tree from the configuration
+  virtual MXmlNode* CreateXmlConfiguration(MXmlNode* Node);
+  
+  // protected methods:
+ protected:
+  
+
+  // private methods:
+ private:
+
+  
+  // protected members:
+ protected:
+
+
+  
+  // private members:
+ private:
+
+
+#ifdef ___CLING___
+ public:
+  ClassDef(MSubModule, 0) // no description
+#endif
+
+};
+
+#endif
+
+
+////////////////////////////////////////////////////////////////////////////////
diff --git a/src/fretalon/framework/src/MSubModule.cxx b/src/fretalon/framework/src/MSubModule.cxx
new file mode 100644
index 000000000..46bec9d40
--- /dev/null
+++ b/src/fretalon/framework/src/MSubModule.cxx
@@ -0,0 +1,115 @@
+/*
+ * MSubModule.cxx
+ *
+ *
+ * Copyright (C) by Andreas Zoglauer.
+ * All rights reserved.
+ *
+ *
+ * This code implementation is the intellectual property of
+ * Andreas Zoglauer.
+ *
+ * By copying, distributing or modifying the Program (or any work
+ * based on the Program) you indicate your acceptance of this statement,
+ * and all its terms.
+ *
+ */
+
+
+////////////////////////////////////////////////////////////////////////////////
+//
+// MSubModule
+//
+////////////////////////////////////////////////////////////////////////////////
+
+
+// Include the header:
+#include "MSubModule.h"
+
+// Standard libs:
+
+// ROOT libs:
+#include "TSystem.h"
+
+// MEGAlib libs:
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+#ifdef ___CLING___
+ClassImp(MSubModule)
+#endif
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+MSubModule::MSubModule()
+{
+  // Construct an instance of MSubModule
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+MSubModule::~MSubModule()
+{
+  // Delete this instance of MSubModule
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MSubModule::Initialize()
+{
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+void MSubModule::Clear()
+{
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+void MSubModule::Finalize()
+{
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MSubModule::ReadXmlConfiguration(MXmlNode* Node)
+{
+  //! Read the configuration data from an XML node
+
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+MXmlNode* MSubModule::CreateXmlConfiguration(MXmlNode* Node)
+{
+  //! Create an XML node tree from the configuration
+
+  /*
+  MXmlNode* SomeTagNode = new MXmlNode(Node, "SomeTag", "SomeValue");
+  */
+
+  return Node;
+}
+
+
+// MSubModule.cxx: the end...
+////////////////////////////////////////////////////////////////////////////////

From 507ef0892c621c8e3c34295ee39d44157e5a69c4 Mon Sep 17 00:00:00 2001
From: Andreas Zoglauer <zoglauer@berkeley.edu>
Date: Wed, 15 Oct 2025 11:43:46 -0500
Subject: [PATCH 156/192] ADD: Names for sub module

---
 src/fretalon/framework/inc/MSubModule.h   | 3 ++-
 src/fretalon/framework/src/MSubModule.cxx | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/fretalon/framework/inc/MSubModule.h b/src/fretalon/framework/inc/MSubModule.h
index 14daaf055..04e9bd9b9 100644
--- a/src/fretalon/framework/inc/MSubModule.h
+++ b/src/fretalon/framework/inc/MSubModule.h
@@ -85,7 +85,8 @@ class MSubModule
   
   // protected members:
  protected:
-
+  //! A name of the module
+  MString m_Name;
 
   
   // private members:
diff --git a/src/fretalon/framework/src/MSubModule.cxx b/src/fretalon/framework/src/MSubModule.cxx
index 46bec9d40..0fc4fcb4c 100644
--- a/src/fretalon/framework/src/MSubModule.cxx
+++ b/src/fretalon/framework/src/MSubModule.cxx
@@ -45,7 +45,7 @@ ClassImp(MSubModule)
 ////////////////////////////////////////////////////////////////////////////////
 
 
-MSubModule::MSubModule()
+MSubModule::MSubModule() : m_Name("Unnamed sub-module")
 {
   // Construct an instance of MSubModule
 }

From 7c37ec9ce57e2a8df42b4f808f422c52831ead8e Mon Sep 17 00:00:00 2001
From: Rhea Senthil Kumar <rheask@berkeley.edu>
Date: Tue, 13 Jul 2021 14:37:36 -0400
Subject: [PATCH 157/192] Energy edits and comments added to Kalman 3D code.

---
 src/revan/src/MERTrackKalman3D.cxx | 1220 ++++++++++++++++++++++++++++
 1 file changed, 1220 insertions(+)
 create mode 100644 src/revan/src/MERTrackKalman3D.cxx

diff --git a/src/revan/src/MERTrackKalman3D.cxx b/src/revan/src/MERTrackKalman3D.cxx
new file mode 100644
index 000000000..18c561714
--- /dev/null
+++ b/src/revan/src/MERTrackKalman3D.cxx
@@ -0,0 +1,1220 @@
+/*
+* MERTrackKalman3D.cxx
+*
+*
+* Copyright (C) by Paolo Cumani & Andreas Zoglauer.
+* All rights reserved.
+*
+*
+* This code implementation is the intellectual property of
+* Andreas Zoglauer.
+*
+* By copying, distributing or modifying the Program (or any work
+* based on the Program) you indicate your acceptance of this statement,
+* and all its terms.
+*
+*/
+
+
+////////////////////////////////////////////////////////////////////////////////
+//
+// MERTrackKalman3D
+//
+// Base class for event reconstruction tasks, e.g. find clusters, tracks,
+// Compton sequence
+//
+////////////////////////////////////////////////////////////////////////////////
+
+
+// Include the header:
+#include "MERTrackKalman3D.h"
+
+// Standard libs:
+#include <list>
+#include <algorithm>
+#include <iomanip>
+#include <iostream>
+#include <functional>
+using namespace std;
+
+// ROOT libs:
+#include "TMath.h"
+#include "TH1F.h"
+
+
+// MEGAlib libs:
+#include "MAssert.h"
+#include "MStreams.h"
+#include "MRESE.h"
+#include "MRESEIterator.h"
+#include "MRETrack.h"
+#include "MREHit.h"
+#include "MMuonEvent.h"
+#include "MTimer.h"
+#include "MFile.h"
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+#ifdef ___CINT___
+ClassImp(MERTrackKalman3D)
+#endif
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+Float_t MERTrackKalman3D::accumulate(vector<Float_t>::const_iterator start,
+				   vector<Float_t>::const_iterator stop,
+				   Float_t init_value)
+{
+  // Use a double to store the running sum, since we might be 
+  // adding together a lot of things
+  double sum(init_value);
+  for ( std::vector<float>::const_iterator itr = start;
+	itr != stop; itr++ ) {
+    sum += *itr;
+  }
+  return (Float_t)sum;
+}
+
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+MERTrackKalman3D::MERTrackKalman3D() : MERTrack()
+{
+  // Construct an instance of MERTrackKalman3D
+  w=pow(tan(60*(TMath::Pi())/180.),2);
+  sfg_factor=24;//1.5/sigma;
+  max_offset=30.;
+  start_nrg_fit=20;
+  n_fit = 7;
+
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+MERTrackKalman3D::~MERTrackKalman3D()
+{
+  // Delete this instance of MERTrackKalman3D
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+/*bool MERTrackKalman3D::EvaluateTracks(MRERawEvent* RE)
+{
+  // Evaluate the given tracks...
+
+  if (RE->GetVertex() != 0) {
+    return EvaluatePairs(RE);
+    //return RE->IsGoodEvent();
+  }
+
+  // Mark: Add you evaluations here:
+  mout<<"MRawEventIncarnations* MERTrackKalman3D::EvaluateTracks(MRERawEvent* ER): nyi!"<<endl;
+  //return MERTrack::EvaluateTracks(RE);
+  //this->TrackPairs(RE);
+
+  //return RE->IsGoodEvent();
+  // Store your results:
+  RE->SetTrackQualityFactor(MRERawEvent::c_NoQualityFactor);
+  RE->SetPairQualityFactor(MRERawEvent::c_NoQualityFactor);
+
+  return true;
+}*/
+
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MERTrackKalman3D::SetSpecialParameters(double SigmaHitPos, unsigned int NLayersForVertexSearch)
+{
+  m_NLayersForVertexSearch = NLayersForVertexSearch;
+  m_sigma = SigmaHitPos;
+
+  if (m_NLayersForVertexSearch < 4) {
+    merr<<"Error: Revan (tracking): NLayersForVertexSearch (="<<m_NLayersForVertexSearch<<") must be >= 4. Setting it to 4."<<show;
+    m_NLayersForVertexSearch = 4;
+  }
+  return true;
+}
+
+
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+MString MERTrackKalman3D::ToString(bool CoreOnly) const
+{
+  // Dump an options string gor the tra file:
+
+  ostringstream out;
+
+  if (CoreOnly == false) {
+    out<<"# Tracking - Kalman options:"<<endl;
+    out<<"# "<<endl;
+  }
+  out<<MERTrack::ToString(true);
+  if (CoreOnly == false) {
+    out<<"# "<<endl;
+  }
+
+  return out.str().c_str();
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+MRawEventIncarnations* MERTrackKalman3D::CheckForPair(MRERawEvent* RE)
+{
+  // Check if this event could be a pair:
+  //
+  // The typical pattern of a pair is:
+  // (a) There is a vertex
+  // (b) In N layers above/below are at least two hits
+
+  // Search the vertex:
+  // The vertex is at this point a (non-ambiguous) track or a single (clustered)
+  // hit followed by at least N layers with two hits per layer:
+
+  mdebug<<"Searching for a pair vertex"<<endl;
+  MRESE* Vertex = 0;
+  MRawEventIncarnations *List = 0;
+  bool OnlyHitInLayer = false;
+  //unsigned int MaximumLayerJump = 2;
+  //MRESE* RESE = 0;
+  unsigned int SearchRange = 30;
+  //int MinPairLength = m_NLayersForVertexSearch;
+
+  // Create a list of RESEs sorted by depth in tracker
+  vector<MRESE*> ReseList;
+  for (int h = 0; h < RE->GetNRESEs(); h++) {
+    if (IsInTracker(RE->GetRESEAt(h)) == false) continue;
+    // Everthing below 90 has to go -- eliminate Bremsstrahlung
+    //if (RE->GetRESEAt(h)->GetEnergy() < 90) continue;
+
+    ReseList.push_back(RE->GetRESEAt(h));
+  }
+  sort(ReseList.begin(), ReseList.end(), CompareRESEByZ());
+
+  mdebug<<"RESE's sorted by depth: "<<endl;
+  vector<MRESE*>::iterator Iterator1;
+  vector<MRESE*>::iterator Iterator2;
+  for (Iterator1 = ReseList.begin(); Iterator1 != ReseList.end(); Iterator1++) {
+    mdebug<<(*Iterator1)->GetID()<<": "<<(*Iterator1)->GetPosition().Z()<<endl;
+  }
+
+  // For each of the RESE's in the list check if it could be the first of the vertex
+  for (Iterator1 = ReseList.begin(); Iterator1 != ReseList.end(); Iterator1++) {
+
+    // If it is a single hit, and if it is the only one in its layer:
+    OnlyHitInLayer = true;
+    for (Iterator2 = ReseList.begin(); Iterator2 != ReseList.end(); Iterator2++) {
+      if ((*Iterator1) == (*Iterator2)) continue;
+      if (m_Geometry->AreInSameLayer((*Iterator1), (*Iterator2)) == true) {
+        OnlyHitInLayer = false;
+        break;
+      }
+    }
+    if (OnlyHitInLayer == false) continue;
+    mdebug<<"Search vertex: Only hit in layer:"<<endl;
+    mdebug<<(*Iterator1)->ToString()<<endl;
+
+    // We only have one hit:
+    vector<int> NBelow(SearchRange, 0);
+    vector<int> NAbove(SearchRange, 0);
+
+    int Distance;
+    for (Iterator2 = ReseList.begin(); Iterator2 != ReseList.end(); Iterator2++) {
+      if ((*Iterator1) == (*Iterator2)) continue;
+      // Ignore small energy deposits equivalent to bremsstrahlung
+      //if ((*Iterator2)->GetEnergy() < 90) continue;
+
+      Distance = m_Geometry->GetLayerDistance((*Iterator1), (*Iterator2));
+      if (Distance > 0 && Distance < int(SearchRange)) NAbove[Distance]++;
+      if (Distance < 0 && abs(Distance) < int(SearchRange)) NBelow[abs(Distance)]++;
+      massert(Distance != 0); // In this case the algorithm is broken...
+      //mdebug<<"Distance "<<(*Iterator1)->GetID()<<" - "<<(*Iterator2)->GetID()<<": "<<Distance<<endl;
+    }
+
+
+    // Under the following conditions we do have a pair:
+
+    // Check for vertex below
+    if (NAbove[1] == 0) {
+      int StartIndex = 0; // We start when we have 2 hits for the first time
+      int StopIndex = 0; // We stop when we skip 2 layers for the first time
+      int LayersWithAtLeastTwoHitsBetweenStartAndStop = 0;
+
+
+      for (unsigned int d = 1; d < SearchRange-1; ++d) {
+        // We stop when we skip 2 layers for the first time
+        if (NBelow[d] == 0 && NBelow[d+1] == 0) break;
+        StopIndex = d;
+        // Store the index where we have 2 hits for the first time, twice
+        if (StartIndex == 0 && NBelow[d] > 1 && NBelow[d+2] > 1) StartIndex = d;
+
+        if (StartIndex != 0) {
+          if (NBelow[d] >= 2) ++LayersWithAtLeastTwoHitsBetweenStartAndStop;
+        }
+      }
+
+      // Since we can have just a single track at the end, move upward until we have at least two hits in a row
+      for (unsigned int d = StopIndex; d > 2; --d) {
+        if (NBelow[d-1] >= 2 && NBelow[d-2] >= 2) break;
+        StopIndex = d;
+      }
+
+      mdebug<<"Search vertex ("<<(*Iterator1)->GetPosition().Z()<<"): Above: ";
+      for (int i: NAbove) mdebug<<i<<" ";
+      mdebug<<endl;
+      mdebug<<"Search vertex ("<<(*Iterator1)->GetPosition().Z()<<"): Below: ";
+      for (int i: NBelow) mdebug<<i<<" ";
+      mdebug<<endl;
+
+      mdebug<<"Vertex statistics (max: "<<SearchRange<<"): layers used: "<<StopIndex<<", start of 2+ hits: "<<StartIndex<<"  layers with 2+ hits between start and stop: "<<LayersWithAtLeastTwoHitsBetweenStartAndStop<<" ("<<((StopIndex-StartIndex > 0) ? 100.0*LayersWithAtLeastTwoHitsBetweenStartAndStop/(StopIndex-StartIndex) : 0)<<"%)"<<endl;
+
+      if (LayersWithAtLeastTwoHitsBetweenStartAndStop > 4 && double (LayersWithAtLeastTwoHitsBetweenStartAndStop)/(StopIndex-StartIndex) > 0.5) {
+        Vertex = (*Iterator1);
+      }
+    }
+
+    if (Vertex != 0) {
+      if (List == 0) List = new MRawEventIncarnations();
+      RE->SetVertex(Vertex);
+      RE->SetVertexDirection(-1);
+      MRERawEvent *New = RE->Duplicate();
+      RE->SetVertex(0);
+      List->AddRawEvent(New);
+      mdebug<<"Search vertex: Found vertex: "<<Vertex->GetID()<<endl;
+      return List; // Only take first right now
+    }
+  }
+
+  if (Vertex == 0){
+    vector < Float_t > Chi2;
+    vector < Int_t > ID;
+
+    Int_t nplanes = 0;
+    Double_t PlaneZ = (*ReseList.begin())->GetPosition().Z();
+
+    // Pair starting from top
+
+    int VertexDirection = 0;
+
+    for (Iterator1 = ReseList.begin(); Iterator1 != ReseList.end() && nplanes<2; Iterator1++) {
+      if (IsInTracker(*Iterator1) == false) continue;
+
+      if (abs(PlaneZ - (*Iterator1)->GetPosition().Z())>  + 0.0001){
+        nplanes++;
+        PlaneZ = (*Iterator1)->GetPosition().Z();
+      }
+      Float_t ChiT1=0.;
+      Float_t ChiT2=0.;
+
+      vector < TMatrix > Track1;
+      vector < TMatrix > Track2;
+
+      Float_t E1=0.;
+      Float_t E2=0.;
+
+      MRESEList Chosen1;
+      MRESEList Chosen2;
+
+      RE->SetVertex(*Iterator1);
+
+      tie(Track1, E1, ChiT1, Track2, E2, ChiT2, Chosen1, Chosen2) = SearchTracks(RE);
+      RE->SetVertex(0);
+
+      if ((ChiT1==0. && ChiT2==0.) || !(Chosen1.GetNRESEs()>2 && Chosen2.GetNRESEs()>2)) continue;
+      Chi2.push_back(ChiT1+ChiT2);
+      ID.push_back((*Iterator1)->GetID());
+    }
+
+    if (Chi2.size()==0) return List;
+
+    if (*min_element(Chi2.begin(), Chi2.end())<=50){
+      for (UInt_t i = 0; i < Chi2.size(); i++) {
+        if(Chi2[i]==*min_element(Chi2.begin(), Chi2.end())) {
+          Vertex=RE->GetRESE(ID[i]);
+        }
+      }
+    }
+
+    if (Vertex != 0 ) {
+      if (List == 0) List = new MRawEventIncarnations();
+      VertexDirection = -1;
+      RE->SetVertex(Vertex);
+      RE->SetVertexDirection(VertexDirection);
+      MRERawEvent *New = RE->Duplicate();
+      RE->SetVertex(0);
+      List->AddRawEvent(New);
+
+      mdebug<<"Vertex: "<<Vertex->GetPosition().X()<<" "<<Vertex->GetPosition().Y()<<" "<<Vertex->GetPosition().Z()<<" "<<*min_element(Chi2.begin(), Chi2.end())<<endl;
+      mdebug<<"Search vertex: Found vertex: "<<Vertex->GetID()<<endl;
+    }
+    //}
+  }
+  return List;
+}
+
+
+/*MRawEventIncarnations* MERTrackKalman3D::CheckForPair(MRERawEvent* RE)
+{
+// Check if this event could be a pair:
+//
+// The typical pattern of a pair is:
+// (a) There is a vertex
+// (b) In N layers above/below are at least two hits
+
+// Search the vertex:
+// The vertex is at this point a (non-ambiguous) track or a single (clustered)
+// hit followed by at least N layers with two hits per layer:
+
+mdebug<<"Searching for a pair vertex"<<endl;
+MRESE* Vertex = 0;
+MRawEventIncarnations *List = 0;
+bool OnlyHitInLayer = false;
+//unsigned int MaximumLayerJump = 2;
+//MRESE* RESE = 0;
+unsigned int SearchRange = 30;
+//int MinPairLength = m_NLayersForVertexSearch;
+
+// Create a list of RESEs sorted by depth in tracker
+vector<MRESE*> ReseList;
+for (int h = 0; h < RE->GetNRESEs(); h++) {
+if (IsInTracker(RE->GetRESEAt(h)) == false) continue;
+// Everthing below 90 has to go -- eliminate Bremsstrahlung
+//if (RE->GetRESEAt(h)->GetEnergy() < 90) continue;
+
+ReseList.push_back(RE->GetRESEAt(h));
+}
+sort(ReseList.begin(), ReseList.end(), CompareRESEByZ());
+
+mdebug<<"RESE's sorted by depth: "<<endl;
+vector<MRESE*>::iterator Iterator1;
+vector<MRESE*>::iterator Iterator2;
+for (Iterator1 = ReseList.begin(); Iterator1 != ReseList.end(); Iterator1++) {
+mdebug<<(*Iterator1)->GetID()<<": "<<(*Iterator1)->GetPosition().Z()<<endl;
+}
+
+// For each of the RESE's in the list check if it could be the first of the vertex
+for (Iterator1 = ReseList.begin(); Iterator1 != ReseList.end(); Iterator1++) {
+
+// If it is a single hit, and if it is the only one in its layer:
+OnlyHitInLayer = true;
+for (Iterator2 = ReseList.begin(); Iterator2 != ReseList.end(); Iterator2++) {
+if ((*Iterator1) == (*Iterator2)) continue;
+if (m_Geometry->AreInSameLayer((*Iterator1), (*Iterator2)) == true) {
+OnlyHitInLayer = false;
+break;
+}
+}
+if (OnlyHitInLayer == false) continue;
+mdebug<<"Search vertex: Only hit in layer:"<<endl;
+mdebug<<(*Iterator1)->ToString()<<endl;
+
+// We only have one hit:
+vector<int> NBelow(SearchRange, 0);
+vector<int> NAbove(SearchRange, 0);
+
+int Distance;
+for (Iterator2 = ReseList.begin(); Iterator2 != ReseList.end(); Iterator2++) {
+if ((*Iterator1) == (*Iterator2)) continue;
+// Ignore small energy deposits equivalent to bremsstrahlung
+//if ((*Iterator2)->GetEnergy() < 90) continue;
+
+Distance = m_Geometry->GetLayerDistance((*Iterator1), (*Iterator2));
+if (Distance > 0 && Distance < int(SearchRange)) NAbove[Distance]++;
+if (Distance < 0 && abs(Distance) < int(SearchRange)) NBelow[abs(Distance)]++;
+massert(Distance != 0); // In this case the algorithm is broken...
+//mdebug<<"Distance "<<(*Iterator1)->GetID()<<" - "<<(*Iterator2)->GetID()<<": "<<Distance<<endl;
+}
+
+
+// Under the following conditions we do have a pair:
+
+// Check for vertex below
+if (NAbove[1] == 0) {
+int StartIndex = 0; // We start when we have 2 hits for the first time
+int StopIndex = 0; // We stop when we skip 2 layers for the first time
+int LayersWithAtLeastTwoHitsBetweenStartAndStop = 0;
+
+
+for (unsigned int d = 1; d < SearchRange-1; ++d) {
+// We stop when we skip 2 layers for the first time
+if (NBelow[d] == 0 && NBelow[d+1] == 0) break;
+StopIndex = d;
+// Store the index where we have 2 hits for the first time, twice
+if (StartIndex == 0 && NBelow[d] > 1 && NBelow[d+2] > 1) StartIndex = d;
+
+if (StartIndex != 0) {
+if (NBelow[d] >= 2) ++LayersWithAtLeastTwoHitsBetweenStartAndStop;
+}
+}
+
+// Since we can have just a single track at the end, move upward until we have at least two hits in a row
+for (unsigned int d = StopIndex; d > 2; --d) {
+if (NBelow[d-1] >= 2 && NBelow[d-2] >= 2) break;
+StopIndex = d;
+}
+
+mdebug<<"Search vertex ("<<(*Iterator1)->GetPosition().Z()<<"): Above: ";
+for (int i: NAbove) mdebug<<i<<" ";
+mdebug<<endl;
+mdebug<<"Search vertex ("<<(*Iterator1)->GetPosition().Z()<<"): Below: ";
+for (int i: NBelow) mdebug<<i<<" ";
+mdebug<<endl;
+
+mdebug<<"Vertex statistics (max: "<<SearchRange<<"): layers used: "<<StopIndex<<", start of 2+ hits: "<<StartIndex<<"  layers with 2+ hits between start and stop: "<<LayersWithAtLeastTwoHitsBetweenStartAndStop<<" ("<<((StopIndex-StartIndex > 0) ? 100.0*LayersWithAtLeastTwoHitsBetweenStartAndStop/(StopIndex-StartIndex) : 0)<<"%)"<<endl;
+
+if (LayersWithAtLeastTwoHitsBetweenStartAndStop > 4 && double (LayersWithAtLeastTwoHitsBetweenStartAndStop)/(StopIndex-StartIndex) > 0.5) {
+Vertex = (*Iterator1);
+}
+}
+
+if (Vertex != 0) {
+if (List == 0) List = new MRawEventIncarnations();
+break; // Only take first right now
+}
+}
+
+if (Vertex != 0){
+MRESE* PrelVertex = Vertex;
+vector < Float_t > Chi2;
+vector < Int_t > ID;
+
+Int_t nplanes = 0;
+Double_t PlaneZ = (*ReseList.begin())->GetPosition().Z();
+
+// Pair starting from top
+
+int VertexDirection = 0;
+
+for (Iterator1 = ReseList.begin(); Iterator1 != ReseList.end() && nplanes<2; Iterator1++) {
+if (IsInTracker(*Iterator1) == false) continue;
+
+if (abs(PlaneZ - (*Iterator1)->GetPosition().Z())>  + 0.0001){
+nplanes++;
+PlaneZ = (*Iterator1)->GetPosition().Z();
+}
+Float_t ChiT1=0.;
+Float_t ChiT2=0.;
+
+vector < TMatrix > Track1;
+vector < TMatrix > Track2;
+
+Float_t E1=0.;
+Float_t E2=0.;
+
+MRESEList Chosen1;
+MRESEList Chosen2;
+
+RE->SetVertex(*Iterator1);
+
+tie(Track1, E1, ChiT1, Track2, E2, ChiT2, Chosen1, Chosen2) = SearchTracks(RE);
+
+if ((ChiT1==0. && ChiT2==0.) || !(Chosen1.GetNRESEs()>2 && Chosen2.GetNRESEs()>2)) continue;
+if((*Iterator1)==PrelVertex) Chi2.push_back(ChiT1+ChiT2-sfg_factor);
+else Chi2.push_back(ChiT1+ChiT2);
+ID.push_back((*Iterator1)->GetID());
+}
+
+for (UInt_t i = 0; i < Chi2.size(); i++) {
+if(Chi2[i]==*min_element(Chi2.begin(), Chi2.end())) {
+Vertex=RE->GetRESE(ID[i]);
+}
+}
+
+if (Vertex != 0 ) {
+if (List == 0) List = new MRawEventIncarnations();
+VertexDirection = -1;
+RE->SetVertex(PrelVertex);
+RE->SetVertexDirection(VertexDirection);
+MRERawEvent *New = RE->Duplicate();
+//RE->SetVertex(0);
+List->AddRawEvent(New);
+if (Vertex != PrelVertex && PrelVertex->GetPosition().Z()<Vertex->GetPosition().Z()) {
+cout<<"Original vertex: "<<PrelVertex->GetPosition().X()<<" "<<PrelVertex->GetPosition().Y()<<" "<<PrelVertex->GetPosition().Z()<<endl;
+cout<<"New vertex: "<<Vertex->GetPosition().X()<<" "<<Vertex->GetPosition().Y()<<" "<<Vertex->GetPosition().Z()<<endl;
+//print=true;
+}
+mdebug<<"Search vertex: Found vertex: "<<Vertex->GetID()<<endl;
+}
+//}
+}
+return List;
+}
+
+*/
+////////////////////////////////////////////////////////////////////////////////
+
+// This function does the filtering and smoothing of the Kalman algorithm.
+
+Float_t MERTrackKalman3D::Kalman(MRERawEvent* RE, Int_t n, Float_t en, MRESEList Previous, vector < TMatrix > &trk, MRESEList &Chosen)
+{
+
+  vector < TMatrix > Ck;
+  vector < TMatrix > Csmoothk;
+  vector < TMatrix > Fk;
+  vector < TMatrix > FTk;
+  vector < TMatrix > Cprojk;
+  vector < TMatrix > CprojInvk;
+  //vector < TMatrix > Qk;
+  vector < TMatrix > xk;
+  vector < TMatrix > xprojk;
+  vector < TMatrix > xsmoothk;
+
+  Float_t _planedistance = 0.;
+
+
+  TMatrix C(4,4);
+  TMatrix C_proj(4,4);
+  Cprojk.push_back(C_proj);
+  CprojInvk.push_back(C_proj);
+  TMatrix F(4,4);
+  TMatrix Q(4,4);
+
+  Chosen.RemoveAllRESEs();
+  Chosen.Compress();
+
+  Float_t chi2 = 0.;
+  MRESE vertex = RE->GetVertex();
+  Chosen.AddRESE(RE->GetVertex());
+
+  Float_t height = 2*vertex.GetVolumeSequence()->GetDetector()->GetStructuralSize().GetZ();
+  m_heightX0 = height/vertex.GetVolumeSequence()->GetDetector()->GetSensitiveVolume(0)->GetMaterial()->GetRadiationLength();
+
+// as of now, not known what units radiation length is in
+
+  //Filtering
+  Float_t t;// tan of the RMS of the scattering angle
+
+  Float_t V = (m_sigma*m_sigma);  //Weight Matrix
+
+  TMatrix G(3,3);
+  G(0,0)=1/(m_sigma*m_sigma);
+  G(0,1)=0.;
+  G(0,2)=0.;
+  G(1,0)=0.;
+  G(1,1)=0.;
+  G(1,2)=0.;
+  G(2,0)=0.;
+  G(2,1)=0.;
+  G(2,2)=1/(m_sigma*m_sigma);
+
+
+  C(0,0)=m_sigma*m_sigma;
+  C(0,1)=0.;
+  C(1,0)=0.;
+  C(0,2)=0.;
+  C(0,3)=0.;
+  C(1,1)=w;
+  C(1,2)=0.;
+  C(1,3)=0.;
+  C(2,0)=0.;
+  C(2,1)=0.;
+  C(3,0)=0.;
+  C(3,1)=0.;
+  C(2,2)=m_sigma*m_sigma;
+  C(3,3)=w;
+  C(3,2)=0.;
+  C(2,3)=0.;
+
+  Ck.push_back(C);
+
+  TMatrix x(4,1);
+  x(0,0)=vertex.GetPositionX();
+  x(1,0)=0.;
+  x(2,0)=vertex.GetPositionY();
+  x(3,0)=0.;
+
+  xk.push_back(x);
+
+  vector < TMatrix > mk;
+
+  TMatrix m_temp(3,1);
+  m_temp(0,0) = x(0,0);
+  m_temp(1,0) = 0.;
+  m_temp(2,0) = x(2,0);
+
+  mk.push_back(m_temp);
+
+  TMatrix x_proj(4,1);
+  xprojk.push_back(x_proj);
+
+  Int_t i=0;
+
+  MRESEList List;
+  List.RemoveAllRESEs();
+  List.Compress();
+
+  // Create a list of RESEs sorted by depth in tracker
+  vector<MRESE*> ReseList;
+  for (int h = 0; h < RE->GetNRESEs(); h++) {
+    ReseList.push_back(RE->GetRESEAt(h));
+  }
+  sort(ReseList.begin(), ReseList.end(), CompareRESEByZ());
+
+  //mdebug<<"RESE's sorted by depth: "<<endl;
+  vector<MRESE*>::iterator Iterator1;
+  for (Iterator1 = ReseList.begin(); Iterator1 != ReseList.end(); Iterator1++) {
+    if (IsInTracker(*Iterator1) == false) continue;
+    List.AddRESE(*Iterator1);
+  }
+  ReseList.clear();
+
+  Float_t PlaneZ = vertex.GetPosition().Z();
+
+  Float_t LayerDistance = vertex.GetVolumeSequence()->GetDetector()->GetStructuralPitch().GetZ();
+
+  for (int r = 0; r < List.GetNRESEs() && i<n-1; r++) {
+
+    if (PlaneZ <= (List.GetRESEAt(r)->GetPosition().Z() + 0.0001)) continue;
+
+    PlaneZ = List.GetRESEAt(r)->GetPosition().Z();
+
+    for (int k = 0; k < r; k++) {
+      if(List.GetRESEAt(k)->GetPosition().Z()-PlaneZ < 0.0001) break;
+      _planedistance = List.GetRESEAt(k)->GetPosition().Z()-PlaneZ;
+    }
+
+    if(_planedistance>1.5*LayerDistance) break; // we accept only hits on subsequent planes
+    t=(13.6/en)*sqrt(m_heightX0)*(1+0.038*log(m_heightX0));
+
+    F(0,0)=1.;
+    F(0,1)=_planedistance;
+    F(0,2)=0.;
+    F(0,3)=0.;
+    F(1,0)=0.;
+    F(1,1)=1.;
+    F(1,2)=0.;
+    F(1,3)=0.;
+    F(2,0)=0.;
+    F(2,1)=0.;
+    F(2,2)=1.;
+    F(2,3)=_planedistance;
+    F(3,0)=0.;
+    F(3,1)=0.;
+    F(3,2)=0.;
+    F(3,3)=1.;
+
+    Fk.push_back(F);
+
+    Q(0,0)=(t*t*height*height)/3.;
+    Q(2,2)=(t*t*height*height)/3.;
+    Q(0,1)=t*t*height/2.;
+    Q(1,0)=t*t*height/2.;
+    Q(2,3)=t*t*height/2.;
+    Q(3,2)=t*t*height/2.;
+    Q(1,1)=t*t;
+    Q(3,3)=t*t;
+    Q(0,2)=0.;
+    Q(0,3)=0.;
+    Q(1,2)=0.;
+    Q(1,3)=0.;
+    Q(2,0)=0.;
+    Q(2,1)=0.;
+    Q(3,0)=0.;
+    Q(3,1)=0.;
+
+    //Qk.push_back(Q);
+
+    TMatrix H(3,4);
+    H(0,0)=1.;
+    H(0,1)=0.;
+    H(0,2)=0.;
+    H(0,3)=0.;
+    H(1,0)=0.;
+    H(1,1)=0.;
+    H(1,2)=0.;
+    H(1,3)=0.;
+    H(2,0)=0.;
+    H(2,1)=0.;
+    H(2,2)=1.;
+    H(2,3)=0.;
+
+    TMatrix HT=H;
+    HT.T();
+
+    x_proj = (F*x);
+
+    xprojk.push_back(x_proj);
+
+    TMatrix FT = F;
+    FT.T();
+    FTk.push_back(FT);
+
+    C_proj = F*C*FT + Q;
+
+    Cprojk.push_back(C_proj);
+
+    TMatrix C_projInv=C_proj;
+
+    C_projInv.Invert();
+
+    CprojInvk.push_back(C_projInv);
+
+    C = C_projInv;
+
+    C+=HT*G*H;
+
+    C.Invert();
+
+    Ck.push_back(C);
+
+    vector < Float_t > weight;
+
+    for (int k = 0; k < List.GetNRESEs(); k++) {
+
+      if(abs(List.GetRESEAt(k)->GetPosition().Z()-PlaneZ) > 0.0001) continue;
+
+      Bool_t previous = false;
+
+      for (int j = 0; j < Previous.GetNRESEs(); j++) {
+        if(abs(Previous.GetRESEAt(j)->GetPosition().Z()-PlaneZ)  > 0.0001) continue;
+
+        if(Previous.GetRESEAt(j)->ComputeMinDistance(List.GetRESEAt(k)) <0.001) previous = true;
+      }
+      Float_t distx = (List.GetRESEAt(k)->GetPosition().X()-x_proj(0,0));
+      Float_t disty = (List.GetRESEAt(k)->GetPosition().Y()-x_proj(2,0));
+      Float_t dist = distx*distx + disty * disty;
+      if (previous) weight.push_back(sfg_factor+sqrt(dist/C_proj(0,0)));
+      else weight.push_back(sqrt(dist/C_proj(0,0)));
+    }
+
+    Int_t kmin=0;
+
+    for(int kk=0; kk<(int) weight.size(); kk++){
+      if(weight[kk]==*min_element(weight.begin(), weight.end())) kmin=kk;
+      if(*min_element(weight.begin(), weight.end())>max_offset && i>2) kmin=-1;
+    }
+
+    if (kmin>=0)
+    {
+      Int_t kind=0;
+      for (int kk = 0; kk < List.GetNRESEs(); kk++) {
+        if(abs(List.GetRESEAt(kk)->GetPosition().Z()-PlaneZ) > 0.0001) continue;
+        else {
+          if (kind==kmin){
+            m_temp(0,0)=List.GetRESEAt(kk)->GetPosition().X();
+            m_temp(1,0)=0.;
+            m_temp(2,0)=List.GetRESEAt(kk)->GetPosition().Y();
+
+            Chosen.AddRESE(List.GetRESEAt(kk));
+            break;
+          }
+          kind ++;
+        }
+      }
+    } else {
+      m_temp(0,0)=x_proj(0,0);
+      m_temp(1,0)=0.;
+      m_temp(2,0)=x_proj(2,0);
+    }
+
+    mk.push_back(m_temp);
+    x = C * (C_projInv*x_proj+HT*G*m_temp);
+    xk.push_back(x);
+
+    i++;
+  }
+
+
+  if ((Int_t)xk.size()< n) n = xk.size();
+  if (n<2) return chi2;
+  //Smoothing
+
+  TMatrix xsmooth(4,1);
+
+  xsmoothk.resize(xk.size(), xsmooth);
+  xsmoothk[xsmoothk.size()-1] = xk[xk.size()-1];
+  trk.push_back(xsmoothk[xsmoothk.size()-1]);
+
+  TMatrix Csmooth(4,4);
+  Csmoothk.resize(Ck.size(), Csmooth);
+  Csmoothk[Ck.size()-1] = C;
+
+
+  for (Int_t i = n-2; i >= 0; i--) {
+
+    TMatrix A(4,4);
+
+    A = Ck[i]*FTk[i]*CprojInvk[i+1];
+
+    TMatrix AT = A;
+    AT.T();
+
+    xsmoothk[i] = xk[i] + A * (xsmoothk[i+1] - xprojk[i+1]);
+
+    trk.push_back(xsmoothk[i]);
+
+    Csmooth = Ck[i] + A*(Csmoothk[i+1] - Cprojk[i+1])*AT;
+    Csmoothk[i] = Csmooth;
+
+    Float_t rkx = mk[i](0,0) - xsmoothk[i](0,0);
+    Float_t rky = mk[i](2,0) - xsmoothk[i](2,0);
+    Float_t rk = sqrt(rkx*rkx+rky*rky);
+
+    Float_t Rkx = V -  Csmoothk[i](0,0);
+    Float_t Rky = V -  Csmoothk[i](2,2);
+    Float_t Rk = sqrt(Rkx*Rkx+Rky*Rky);
+
+    chi2 += rk * rk / Rk;
+  }
+
+  chi2 /= n-3;
+  reverse(trk.begin(),trk.end());
+
+  return chi2;
+}
+
+tuple<vector < TMatrix >, Float_t, Float_t, vector < TMatrix >, Float_t, Float_t, MRESEList, MRESEList> MERTrackKalman3D::SearchTracks(MRERawEvent* RE)
+{
+  MRESEList PrevChoice;
+  Float_t en = start_nrg_fit;
+  Float_t nrg_est1;
+  Float_t nrg_est2;
+  Float_t chi1=0.;
+  Float_t chi2=0.;
+  Int_t loop1=0;
+  Bool_t stop=false;
+  Int_t n = n_fit;
+
+  MRESEList Chosen1;
+  MRESEList Chosen2;
+
+  vector < TMatrix > trk1;
+  vector < TMatrix > trk2;
+
+  PrevChoice.RemoveAllRESEs();
+  PrevChoice.Compress();
+
+  //track 1
+  while(!stop){
+
+    chi1 = Kalman(RE, n, en, PrevChoice, trk1, Chosen1);
+    
+    if (trk1.size()<3){
+      return std::make_tuple(trk1, 0, 0, trk2, 0, 0, Chosen1, Chosen2);
+    }
+
+    nrg_est1=0.;
+
+    //Energy Estimation
+
+    nrg_est1 = MultipleScattering(trk1);
+    //nrg_est1 = EnergyEst3D(trk1);
+
+//not sure why the part below is being done
+
+    if (nrg_est1> 50000.) nrg_est1=50000.;
+    if ((nrg_est1/en)<1/3){
+      //loop1++;
+      en=en/3.;
+      trk1.clear();
+    } else if ((nrg_est1/en)>3. && loop1<9){
+      loop1++;
+      en=en*3.;
+      trk1.clear();
+    } else stop=true;
+  }
+
+  for (size_t i = 0; i < trk1.size(); i++) {
+    mdebug<<"Track1 after Kalman "<<trk1.size()<<" "<<trk1[i](0,0)<<" "<<trk1[i](1,0)<<endl;
+  }
+  stop=false;
+  en = start_nrg_fit;
+  Int_t loop2=0;
+
+  while(!stop){
+    chi2 = Kalman(RE, n, en, Chosen1, trk2, Chosen2);
+    
+    if (trk2.size()<3){
+      return std::make_tuple(trk1, 0, 0, trk2, 0, 0, Chosen1, Chosen2);
+    }
+
+
+    nrg_est2=0;
+
+    //Energy Estimation
+    nrg_est2 = MultipleScattering(trk2);
+    //nrg_est2 = EnergyEst3D(trk2);
+    
+    if (nrg_est2> 50000.) nrg_est2=50000.;
+    if ((nrg_est2/en)<1/3){
+      //loop1++;
+      en=en/3.;
+      trk2.clear();
+    } else if ((nrg_est2/en)>3. && loop2<9){
+      loop2++;
+      en=en*3.;
+      trk2.clear();
+    } else stop=true;
+  }
+  
+  for (size_t i = 0; i < trk2.size(); i++) {
+    mdebug<<"Track2 after Kalman "<<trk2.size()<<" "<<trk2[i](0,0)<<" "<<trk2[i](1,0)<<endl;
+  }
+  return std::make_tuple(trk1, nrg_est1, chi1, trk2, nrg_est2, chi2, Chosen1, Chosen2);
+}
+
+
+//returns an energy estimate. As of now, not sure whether the average of energies is being calculated correctly.
+Float_t MERTrackKalman3D::MultipleScattering(vector < TMatrix > trk)
+{
+  Int_t n = trk.size();
+  TVector3 vi0(1,0,0);
+  TVector3 vi1(1,0,0);
+
+  Float_t var = 0;
+  Float_t sum = 0;
+  vector < Float_t > E;
+
+  for (Int_t i = 0; i < n; i++) {
+
+//not known why these equations are used to set theta and phi
+    vi0.SetTheta(acos(1/(pow(trk[i](3,0),2)+pow(trk[i](1,0),2)+1)));
+    vi0.SetPhi(atan2(trk[i](3,0),trk[i](1,0)));
+
+    if (i != 0) {
+      Float_t angle = vi0.Angle(vi1);
+      //Ei below seems to be from equation 34.16 from Particle Data Group: https://pdg.lbl.gov/2021/reviews/rpp2020-rev-passage-particles-matter.pdf
+      Float_t Ei = (13.6/angle)*sqrt(m_heightX0/cos(vi0.Theta()))*(1+0.038*log(m_heightX0/cos(vi0.Theta())));
+      if (isfinite(Ei)){
+        E.push_back(Ei);
+      } else{
+        E.push_back(1e+6);
+      }
+      //break;
+    }
+    vi1=vi0;
+  }
+
+  sort(E.begin(), E.end());
+  E.pop_back();
+  E.erase(E.begin());
+
+  Float_t average = accumulate( E.begin(), E.end(), 0.0)/E.size();
+
+  for ( uint j =0; j < E.size(); j++) {
+    Float_t temp = pow((E[j] - average),2);
+    sum += temp;
+  }
+
+  var = sqrt(sum /E.size());
+
+  return E[lower_bound (E.begin(), E.end(), average-var)- E.begin()];
+}
+
+//not used
+Float_t MERTrackKalman3D::MultipleScattering3D(vector < TMatrix > trk, Double_t e0)
+{
+  Double_t epsilon = 1.5;
+  Int_t n = trk.size();
+  TVector3 vi0(1,0,0);
+  TVector3 vi1(1,0,0);
+
+  vector< Float_t > theta(n);
+  vector< Float_t > thickness;
+  vector< Float_t > en;
+  vector< Float_t > angle;
+
+  for (Int_t i = 0; i < n-1; i++) {
+
+    if(trk[i](3,0) == 0) vi0.SetTheta(0.);
+    else vi0.SetTheta(atan(trk[i](3,0)/sin(atan2(trk[i](3,0),trk[i](1,0)))));
+    vi0.SetPhi(atan2(trk[i](3,0),trk[i](1,0)));
+
+    theta[i] = vi0.Theta();
+
+    if (i != 0) {
+      angle.push_back(vi0.Angle(vi1));
+
+    }
+    vi1=vi0;
+  }
+  Double_t sigma = 0;
+  Double_t chi = 0;
+
+  for (Int_t i = 0; i < n-1; i++) {
+    thickness.push_back(m_heightX0/cos(theta[i]));
+    if ((e0 - (i + 1) * epsilon * cos(theta[i])) > 1) en.push_back(e0 - (i + 1) * epsilon * cos( theta[i]));
+    else en.push_back(1);
+  }
+
+  for (Int_t i = 0; i < n - 1; i++) {
+    sigma = 13.6 / en[i] * sqrt(2*thickness[i]);
+    chi += (angle[i] / sigma) * (angle[i] / sigma);
+  }
+  chi /= n - 1;
+
+  return chi;
+}
+
+//not used
+Float_t MERTrackKalman3D::EnergyEst3D(vector < TMatrix > trk)
+{
+  Int_t jjmax = 13;
+  Int_t jjmin = 1;
+  Int_t jmin = 0;
+  Double_t ejmin = pow(2., jjmax);
+  Double_t ej;
+
+  Double_t absm[5];
+  for (Int_t i = jjmax; i >= jjmin; i--) {
+    Double_t m[5] = {10000, 10000, 10000, 10000, 10000};
+
+    for (Int_t j = 0; j < 5; j++) {
+      ej = ejmin - pow(2., i) + j * pow(2., (i - 1));
+      m[j] = MultipleScattering3D(trk, ej);
+      absm[j] = abs(m[j] - 1);
+    }
+
+    for (Int_t j = 0; j < 5; j++) {
+      if (absm[j] == *min_element(absm, absm+5)) jmin = j;
+    }
+    if (ejmin > (pow(2., i) - jmin * pow(2., (i - 1)))) {
+      ejmin = ejmin - pow(2., i) + jmin * pow(2., (i - 1));
+    } else {
+      ejmin = 0;
+    }
+
+  }
+  Double_t energy = ejmin;
+  return energy;
+}
+
+void MERTrackKalman3D::TrackPairs(MRERawEvent* RE)
+{
+  if (RE->GetVertex() == 0) {
+    /*Fatal("void MRERawEvent::TrackPairs()",
+    "No vertex found!");*/
+    if (CheckForPair(RE) == 0) return;
+  }
+
+  Float_t ChiT1=0.;
+  Float_t ChiT2=0.;
+
+  vector < TMatrix > Track1;
+  vector < TMatrix > Track2;
+
+  Float_t E1=0.;
+  Float_t E2=0.;
+  Float_t Egamma=0.;
+
+
+  MRESEList Chosen1;
+  MRESEList Chosen2;
+
+  MRETrack* Electron = new MRETrack();
+  MRETrack* Positron = new MRETrack();
+
+  // Now create the vertex:
+  Electron->AddRESE(RE->GetVertex());
+  Electron->SetStartPoint(RE->GetVertex());
+//commented out the below line since in the standard case, only the electron has the vertex added to it. Further work may need to be done to avoid any overcounting of hits.
+//  Positron->AddRESE(RE->GetVertex());
+  Positron->SetStartPoint(RE->GetVertex());
+
+  mdebug<<"Vertex : "<<" "<<RE->GetVertex()->GetPosition().X()<<" "<<RE->GetVertex()->GetPosition().Y()<<" "<<RE->GetVertex()->GetPosition().Z()<<endl;
+
+  tie(Track1, E1, ChiT1, Track2, E2, ChiT2, Chosen1, Chosen2) = SearchTracks(RE);
+
+  if (isinf(ChiT1+ChiT2) || (ChiT1==0. && ChiT2==0.) || !(Chosen1.GetNRESEs()>2 && Chosen2.GetNRESEs()>2)) return;
+
+  for (int r = 0; r < Chosen1.GetNRESEs(); r++) {
+    Electron->AddRESE(Chosen1.GetRESEAt(r));
+
+  }
+
+  for (int r = 0; r < Chosen2.GetNRESEs(); r++) {
+    Positron->AddRESE(Chosen2.GetRESEAt(r));
+  }
+
+// add RESEs for hits not included in Chosen1 and Chosen2 tracks (aka all other hits + calorimeter)
+
+  for (int r = 0; r < RE->GetNRESEs(); r++) {
+    if (Chosen1.ContainsRESE(RE->GetRESEAt(r)) == false && Chosen2.ContainsRESE(RE->GetRESEAt(r)) == false) {
+      if (Electron->ComputeMinDistance(RE->GetRESEAt(r)) < Positron->ComputeMinDistance(RE->GetRESEAt(r))) {
+        Electron->AddRESE(RE->GetRESEAt(r));
+      } else {
+	Positron->AddRESE(RE->GetRESEAt(r));
+	}
+    }
+  }
+
+// end of inserted code
+
+  Egamma= E1+E2;
+
+  Float_t theta1x=Track1[0](1,0);
+  Float_t theta1y=Track1[0](3,0);
+
+  Float_t theta2x=Track2[0](1,0);
+  Float_t theta2y=Track2[0](3,0);
+
+  Float_t phi1 = atan2(theta1y,theta1x);
+  Float_t theta1 = atan(theta1y/sin(phi1));
+  if(theta1y == 0) theta1 =0.;
+  else theta1 = atan(theta1y/sin(phi1));
+  Float_t phi2 = atan2(theta2y,theta2x);
+  Float_t theta2 = atan(theta2y/sin(phi2));
+  if(theta2y == 0) theta2 =0.;
+  else theta2 = atan(theta2y/sin(phi2));
+
+  Float_t x1= sin(theta1)*cos(phi1);
+  Float_t y1= sin(theta1)*sin(phi1);
+  Float_t z1= cos(theta1);
+
+  Float_t x2= sin(theta2)*cos(phi2);
+  Float_t y2= sin(theta2)*sin(phi2);
+  Float_t z2= cos(theta2);
+
+  Float_t x= (x1*E1+x2*E2)/Egamma;
+  Float_t y= (y1*E1+y2*E2)/Egamma;
+  Float_t z= (z1*E1+z2*E2)/Egamma;
+
+  Float_t mag=sqrt(x*x+y*y+z*z);
+  Float_t mag1=sqrt(x1*x1+y1*y1+z1*z1);
+  Float_t mag2=sqrt(x2*x2+y2*y2+z2*z2);
+
+  MVector direction(x/mag,y/mag,-z/mag);
+  MVector direction1(x1/mag1,y1/mag1,-z1/mag1);
+  MVector direction2(x2/mag2,y2/mag2,-z2/mag2);
+
+  Electron->SetFixedDirection(direction1);
+  Positron->SetFixedDirection(direction2);
+
+//Commented the below lines as they'd overwrite the energy with scattering angle values. We only use energies from the hits.
+//  Electron->SetEnergy(E1*1000); //So far the energy was calculated in MeV, MEGAlib works in keV
+//  Positron->SetEnergy(E2*1000);
+
+  Electron->SetQualityFactor(ChiT1);
+  Positron->SetQualityFactor(ChiT2);
+
+  mdebug<<"Energy of the two particles: "<<E1<<" "<<E2<<endl;
+  mdebug<<"Reconstructed theta, phi and energy of the gamma: "<<c_Deg*direction.Theta()<<" "<<c_Deg*direction.Phi()<<" "<<Egamma<<endl;
+
+
+  MVector origin(0.5, 0., -0.866025);
+  mdebug<<"Event "<<RE->GetEventID()<<endl;
+  //" ERROR wrt 30 "<<c_Deg*origin.Angle(direction)<<endl;
+
+  RE->SetElectronTrack(Electron);
+  RE->SetPositronTrack(Positron);
+
+  //RE->SetTrackQualityFactor(ChiT1+ChiT2);
+  RE->SetPairQualityFactor(ChiT1+ChiT2);
+  RE->SetGoodEvent(true);
+  RE->SetEventType(MRERawEvent::c_PairEvent);
+
+}
+// MERTrackKalman3D.cxx: the end...
+////////////////////////////////////////////////////////////////////////////////

From a8d0761d76357a45ed24b892a644bfedad8880f5 Mon Sep 17 00:00:00 2001
From: Eric Charles <echarles@gmail.com>
Date: Tue, 2 Feb 2021 10:40:35 -0800
Subject: [PATCH 158/192] Pair dev (#2)

* ADD: Kalman Filter to pair reconstruction algorithm and to revan GUI
BUG: solved some memory usage issue in declaration GUI

* BUG: there were no memory problems in the GUI declaration, fix
ADD: Pair quality factor to Kalman
Fix copyright line

* ADD Set Pair Quality factor min/max in mimrec GUI and in event selection

* CHG: - Default vertex finder algorithm used also in Kalman3D
- Run not stopping at the first plane skipped

* BUG: Polarization needs to be oriented to!

* DOC: Improved comments

* BUG: Horizon angle calculation was wrong - difference for the default NUSTAR orbit: new: 113 vs old: 126 degree cutoff

* BUG: Alpha paerticle flux was a factor 4 too high - reported by Paolo

* ADD: Assymetric Gausssian for Galactic disc simulations:

* CHG: Overflow considered in Duke data. Path not applied for Activation Simulations

* ADD: different models of some of the background components (used by adding -pb)

* ADD file containing AMS data to model the Background

* BUG: solved bug in the vertex finding algorithm

* CHG default value for the pair quality cut

* CHG MRawEventList to MRawEventIncarnations, BUG in particles direction storage for Kalman

* merge in master

* remove background files

* resources/examples with master

Co-authored-by: Paolo Cumani <cumani@ice.csic.es>
Co-authored-by: pcumani <pcumani@ifae.es>
Co-authored-by: Paolo Cumani <cumani@cumani-megalib.lal.in2p3.fr>
Co-authored-by: Andreas Zoglauer <andreas@megalibtoolkit.com>
Co-authored-by: Paolo Cumani <17795491+pcumani@users.noreply.github.com>
Co-authored-by: Eric Charles <badass@stanford.edu>
---
 doc/ChangeLog.txt                             |    6 +-
 src/mimrec/inc/MGUIEventSelection.h           |   21 +-
 src/mimrec/inc/MSettingsEventSelections.h     |   52 +-
 src/mimrec/src/MEventSelector.cxx             |  298 ++--
 src/mimrec/src/MGUIEventSelection.cxx         |  317 ++--
 src/mimrec/src/MInterfaceMimrec.cxx           | 1381 +++++++++--------
 src/mimrec/src/MSettingsEventSelections.cxx   |   75 +-
 src/revan/Makefile                            |    5 +-
 src/revan/inc/MERTrackKalman2D.h              |   84 +
 src/revan/inc/MERTrackKalman3D.h              |   96 ++
 src/revan/inc/MGUIERAlgorithm.h               |    5 +-
 src/revan/inc/MGUIOptionsTracking.h           |    7 +-
 src/revan/inc/MRawEventAnalyzer.h             |   69 +-
 src/revan/inc/MSettingsEventReconstruction.h  |   40 +-
 src/revan/src/MERTrack.cxx                    |  255 +--
 src/revan/src/MERTrackKalman2D.cxx            |  715 +++++++++
 src/revan/src/MERTrackKalman3D.cxx            |    7 +-
 src/revan/src/MGUIERAlgorithm.cxx             |   21 +-
 src/revan/src/MGUIOptionsTracking.cxx         |   86 +-
 src/revan/src/MGUIRevanMain.cxx               |   34 +-
 src/revan/src/MInterfaceRevan.cxx             |  430 ++---
 src/revan/src/MREHit.cxx                      |   84 +-
 src/revan/src/MRawEventAnalyzer.cxx           |  237 +--
 .../src/MSettingsEventReconstruction.cxx      |   35 +-
 24 files changed, 2690 insertions(+), 1670 deletions(-)
 create mode 100644 src/revan/inc/MERTrackKalman2D.h
 create mode 100644 src/revan/inc/MERTrackKalman3D.h
 create mode 100644 src/revan/src/MERTrackKalman2D.cxx

diff --git a/doc/ChangeLog.txt b/doc/ChangeLog.txt
index 62d7a4b2d..6de32471b 100644
--- a/doc/ChangeLog.txt
+++ b/doc/ChangeLog.txt
@@ -153,6 +153,10 @@ Version 2.99/3.00
 + The performance of activation simulations is still not the best...
   
   
+*** Critcal bug fixes
++ Powerlaws with an index of alpha=1.0 were not simulated correctly in cosima
++ When simulating guard rings for voxel detectors, the Y offset was used as Z offset
+
 *** Significant new features & improvements:
 
 General:
@@ -237,7 +241,7 @@ Examples:
   basically allowing any arbitrary beam/spectrum/polarization input
 + GRB sampling based on BATSE catalog
 
-  
+
 ... plus many, many smaller things I already forgot about :)
 
 
diff --git a/src/mimrec/inc/MGUIEventSelection.h b/src/mimrec/inc/MGUIEventSelection.h
index f2e2b29be..0f6df2f85 100644
--- a/src/mimrec/inc/MGUIEventSelection.h
+++ b/src/mimrec/inc/MGUIEventSelection.h
@@ -48,7 +48,7 @@ class MGUIEventSelection : public MGUIDialog
 {
   // Public Interface:
  public:
-  MGUIEventSelection(const TGWindow* p, const TGWindow* main, 
+  MGUIEventSelection(const TGWindow* p, const TGWindow* main,
                      MSettingsEventSelections* Data, MDGeometryQuest* Geometry);
   virtual ~MGUIEventSelection();
 
@@ -92,11 +92,11 @@ class MGUIEventSelection : public MGUIDialog
   TGCheckButton* m_BadCB;
 
   MGUIEMinMaxEntry* m_EventId;
-  
+
   TGRadioButton* m_GTIAllRB;
   TGRadioButton* m_GTIEntryRB;
-  MGUIEEntry* m_MinTimeEntry; 
-  MGUIEEntry* m_MaxTimeEntry; 
+  MGUIEEntry* m_MinTimeEntry;
+  MGUIEEntry* m_MaxTimeEntry;
   TGRadioButton* m_GTIFileRB;
   MGUIEFileSelector* m_GTIFile;
   
@@ -122,6 +122,7 @@ class MGUIEventSelection : public MGUIDialog
   MGUIEMinMaxEntry* m_TimeWalk;
   MGUIEMinMaxEntry* m_OpeningAnglePair;
   MGUIEMinMaxEntry* m_InitialEnergyDepositPair;
+  MGUIEMinMaxEntry* m_QualityFactorPair;
 
   MGUIEEntry* m_ThetaDeviationMax;
 
@@ -145,7 +146,6 @@ class MGUIEventSelection : public MGUIDialog
   MGUIEMinMaxEntry* m_SPD;
   int m_CoordinatesSelected;
 
-  
   // Pointing frame
   TGRadioButton* m_UsePointingSelectionNone;
   TGRadioButton* m_UsePointingSelectionPointSource;
@@ -156,7 +156,6 @@ class MGUIEventSelection : public MGUIDialog
   MGUIEEntry* m_PointingBoxExtentLatitude;
   MGUIEEntry* m_PointingBoxExtentLongitude;
   
-  
   // Beam/Box frame
   TGCheckButton* m_UseBeam;
   MGUIEEntryList* m_BeamStart;
@@ -172,22 +171,22 @@ class MGUIEventSelection : public MGUIDialog
 
 
 
-  enum ButtonIDs { c_Compton = 140, 
+  enum ButtonIDs { c_Compton = 140,
                    c_ComptonUntracked,
                    c_ComptonTracked, 
                    c_Pair, 
                    c_Photo, 
                    c_PET, 
                    c_Multi, 
-                   c_Unidentifiable, 
+                   c_Unidentifiable,
                    c_Decay,
                    c_Bad,
                    c_GTIAll,
                    c_GTIEntry,
                    c_GTIFile,
-                   c_Detectors, 
-                   c_EHCNone, 
-                   c_EHCIntersection, 
+                   c_Detectors,
+                   c_EHCNone,
+                   c_EHCIntersection,
                    c_EHCProbability,
                    c_UsePointSource,
                    c_UseGalacticPointSource,
diff --git a/src/mimrec/inc/MSettingsEventSelections.h b/src/mimrec/inc/MSettingsEventSelections.h
index 4a3905210..ee5cc1040 100644
--- a/src/mimrec/inc/MSettingsEventSelections.h
+++ b/src/mimrec/inc/MSettingsEventSelections.h
@@ -176,8 +176,8 @@ class MSettingsEventSelections : public MSettingsInterface
   double GetComptonAngleRangeMax() const { return m_ComptonAngleRangeMax; }
   void SetComptonAngleRangeMax(double ComptonAngleRangeMax) { m_ComptonAngleRangeMax = ComptonAngleRangeMax; m_EventSelectionModified = true; }
 
-  
-  
+
+
   double GetEHCAngle() const { return m_EHCAngle; }
   void SetEHCAngle(double EHCAngle) { m_EHCAngle = EHCAngle; m_EventSelectionModified = true; }
 
@@ -196,20 +196,20 @@ class MSettingsEventSelections : public MSettingsInterface
   int GetEHCType() const { return m_EHCType; }
   void SetEHCType(int EHCType) { m_EHCType = EHCType; m_EventSelectionModified = true; }
 
-  
-  
+
+
   bool GetSourceUsePointSource() const { return m_SourceUsePointSource; }
   void SetSourceUsePointSource(bool SourceUsePointSource) { m_SourceUsePointSource = SourceUsePointSource; m_EventSelectionModified = true; }
 
   MCoordinateSystem GetSourceCoordinates() const { return m_SourceCoordinates; }
   void SetSourceCoordinates(MCoordinateSystem SourceCoordinates) { m_SourceCoordinates = SourceCoordinates; m_EventSelectionModified = true; }
-  
+
   double GetSourcePhi() const { return m_SourcePhi; }
   void SetSourcePhi(double SourcePhi) { m_SourcePhi = SourcePhi; m_EventSelectionModified = true; }
 
   double GetSourceTheta() const { return m_SourceTheta; }
   void SetSourceTheta(double SourceTheta) { m_SourceTheta = SourceTheta; m_EventSelectionModified = true; }
-  
+
   double GetSourceLongitude() const { return m_SourceLongitude; }
   void SetSourceLongitude(double SourceLongitude) { m_SourceLongitude = SourceLongitude; m_EventSelectionModified = true; }
 
@@ -236,8 +236,8 @@ class MSettingsEventSelections : public MSettingsInterface
 
   double GetSourceSPDMax() const { return m_SourceSPDMax; }
   void SetSourceSPDMax(double SourceSPDMax) { m_SourceSPDMax = SourceSPDMax; m_EventSelectionModified = true; }
-  
-  
+
+
   unsigned int GetPointingSelectionType() const {  return m_PointingSelectionType; }
   void SetPointingSelectionType(unsigned int PointingSelectionType) { m_PointingSelectionType = PointingSelectionType; m_EventSelectionModified = true; }
 
@@ -261,13 +261,10 @@ class MSettingsEventSelections : public MSettingsInterface
 
   double GetPointingBoxExtentLatitude() const { return m_PointingBoxExtentLatitude; }
   void SetPointingBoxExtentLatitude(double PointingBoxExtentLatitude) { m_PointingBoxExtentLatitude = PointingBoxExtentLatitude; m_EventSelectionModified = true; }
-  
-  
-  // Beam selection
-  
+
   bool GetBeamUse() const { return m_BeamUse; }
   void SetBeamUse(bool BeamUse) { m_BeamUse = BeamUse; m_EventSelectionModified = true; }
-  
+
   double GetBeamStartX() const {  return m_BeamStartX; }
   void SetBeamStartX(double BeamStartX) { m_BeamStartX = BeamStartX; m_EventSelectionModified = true; }
 
@@ -285,7 +282,7 @@ class MSettingsEventSelections : public MSettingsInterface
 
   double GetBeamFocalSpotZ() const { return m_BeamFocalSpotZ; }
   void SetBeamFocalSpotZ(double BeamFocalSpotZ) { m_BeamFocalSpotZ = BeamFocalSpotZ; m_EventSelectionModified = true; }
-  
+
   double GetBeamRadius() const { return m_BeamRadius; }
   void SetBeamRadius(double BeamRadius) { m_BeamRadius = BeamRadius; m_EventSelectionModified = true; }
 
@@ -364,8 +361,8 @@ class MSettingsEventSelections : public MSettingsInterface
 
   MString GetTimeFile() const { return m_TimeFile; }
   void SetTimeFile(MString TimeFile) { m_TimeFile = TimeFile; m_EventSelectionModified = true; }
-  
-  
+
+
   double GetTimeWalkRangeMin() const { return m_TimeWalkRangeMin; }
   void SetTimeWalkRangeMin(double TimeWalkRangeMin) { m_TimeWalkRangeMin = TimeWalkRangeMin; m_EventSelectionModified = true; }
 
@@ -390,6 +387,12 @@ class MSettingsEventSelections : public MSettingsInterface
   double GetInitialEnergyDepositPairMax() const { return m_InitialEnergyDepositPairMax; }
   void SetInitialEnergyDepositPairMax(double InitialEnergyDepositPairMax) { m_InitialEnergyDepositPairMax = InitialEnergyDepositPairMax; m_EventSelectionModified = true; }
 
+  double GetQualityFactorPairMin() const { return m_QualityFactorPairMin; }
+  void SetQualityFactorPairMin(double QualityFactorPairMin) { m_QualityFactorPairMin = QualityFactorPairMin; m_EventSelectionModified = true; }
+
+  double GetQualityFactorPairMax() const { return m_QualityFactorPairMax; }
+  void SetQualityFactorPairMax(double QualityFactorPairMax) { m_QualityFactorPairMax = QualityFactorPairMax; m_EventSelectionModified = true; }
+
 
   //! Set the special GUI mode (this is not saved to file!)
   void SetSpecialMode(const bool SpecialMode) { m_SpecialMode = SpecialMode; }
@@ -419,7 +422,7 @@ class MSettingsEventSelections : public MSettingsInterface
   MTime m_TimeRangeMin;
   MTime m_TimeRangeMax;
   MString m_TimeFile;
-  
+
   int m_EventSelectorTab;
 
   int m_TrackLengthRangeMin;
@@ -478,6 +481,9 @@ class MSettingsEventSelections : public MSettingsInterface
   double m_InitialEnergyDepositPairMin;
   double m_InitialEnergyDepositPairMax;
 
+  double m_QualityFactorPairMin;
+  double m_QualityFactorPairMax;
+
   int m_EventTypeCompton;
   int m_EventTypeDoubleCompton;
   int m_EventTypeComptonNotTracked;
@@ -508,14 +514,14 @@ class MSettingsEventSelections : public MSettingsInterface
   double m_SourceLongitude;
   double m_SourceLatitude;
   double m_SourceX;
-  double m_SourceY; 
+  double m_SourceY;
   double m_SourceZ;
   double m_SourceARMMin;
   double m_SourceARMMax;
   double m_SourceSPDMin;
   double m_SourceSPDMax;
 
-  
+
   unsigned int m_PointingSelectionType;
   double m_PointingPointSourceLatitude;
   double m_PointingPointSourceLongitude;
@@ -524,14 +530,14 @@ class MSettingsEventSelections : public MSettingsInterface
   double m_PointingBoxLongitude;
   double m_PointingBoxExtentLatitude;
   double m_PointingBoxExtentLongitude;
-  
-  
+
+
   bool m_BeamUse;
   double m_BeamStartX;
-  double m_BeamStartY; 
+  double m_BeamStartY;
   double m_BeamStartZ;
   double m_BeamFocalSpotX;
-  double m_BeamFocalSpotY; 
+  double m_BeamFocalSpotY;
   double m_BeamFocalSpotZ;
   double m_BeamRadius;
   double m_BeamDepth;
diff --git a/src/mimrec/src/MEventSelector.cxx b/src/mimrec/src/MEventSelector.cxx
index ecba07ff7..59613f3fb 100644
--- a/src/mimrec/src/MEventSelector.cxx
+++ b/src/mimrec/src/MEventSelector.cxx
@@ -70,12 +70,12 @@ MEventSelector::MEventSelector()
   m_ThirdTotalEnergyMax = 0;
   m_FourthTotalEnergyMin = 0;
   m_FourthTotalEnergyMax = 0;
-  
+
   m_TimeMode = 0;
   m_TimeMin.Set(0);
   m_TimeMax.Set(2000000000);
   m_TimeFile = "";
-  
+
   m_TimeWalkMin = -numeric_limits<double>::max();
   m_TimeWalkMax = numeric_limits<double>::max();
 
@@ -92,27 +92,27 @@ MEventSelector::MEventSelector()
   m_FirstLeverArmMin = 0; //cm
   m_FirstLeverArmMax = numeric_limits<double>::max();
 
-  m_SequenceLengthMin = 2; 
+  m_SequenceLengthMin = 2;
   m_SequenceLengthMax = numeric_limits<int>::max();
 
-  m_TrackLengthMin = 1; 
+  m_TrackLengthMin = 1;
   m_TrackLengthMax = numeric_limits<int>::max();
 
-  m_ClusteringQualityFactorMin = 0; 
+  m_ClusteringQualityFactorMin = 0;
   m_ClusteringQualityFactorMax = numeric_limits<double>::max();
 
-  m_ComptonQualityFactorMin = -numeric_limits<double>::max(); 
+  m_ComptonQualityFactorMin = -numeric_limits<double>::max();
   m_ComptonQualityFactorMax = numeric_limits<double>::max();
 
-  m_TrackQualityFactorMin = 0; 
+  m_TrackQualityFactorMin = 0;
   m_TrackQualityFactorMax = numeric_limits<double>::max();
 
-  m_CoincidenceWindowMin = 0; 
+  m_CoincidenceWindowMin = 0;
   m_CoincidenceWindowMax = numeric_limits<double>::max();
 
   m_ThetaDeviationMax = 180;
 
-  m_EventIdMin = 0; 
+  m_EventIdMin = 0;
   m_EventIdMax = numeric_limits<long>::max();
 
   m_UseSource = false;
@@ -161,7 +161,7 @@ MEventSelector::MEventSelector()
   m_InitialEnergyDepositPairMin = 0; // keV
   m_InitialEnergyDepositPairMax = numeric_limits<double>::max();
 
-  m_PairQualityFactorMin = 0; 
+  m_PairQualityFactorMin = 0;
   m_PairQualityFactorMax = numeric_limits<double>::max();
 
   Reset();
@@ -174,7 +174,7 @@ MEventSelector::MEventSelector()
 MEventSelector::MEventSelector(const MEventSelector& EventSelector)
 {
   // Default copy constructor
- 
+
   (*this) = EventSelector;
 }
 
@@ -208,48 +208,48 @@ const MEventSelector& MEventSelector::operator=(const MEventSelector& EventSelec
   m_FourthTotalEnergyMax = EventSelector.m_FourthTotalEnergyMax;              
   
   m_TimeMode = EventSelector.m_TimeMode;
-  m_TimeMin = EventSelector.m_TimeMin;                           
+  m_TimeMin = EventSelector.m_TimeMin;
   m_TimeMax = EventSelector.m_TimeMax;
   m_TimeFile = EventSelector.m_TimeFile;
   m_TimeGTI = EventSelector.m_TimeGTI;
-  
-  m_TimeWalkMin = EventSelector.m_TimeWalkMin;                       
-  m_TimeWalkMax = EventSelector.m_TimeWalkMax;                       
-                                                                               
-  m_ElectronEnergyMin = EventSelector.m_ElectronEnergyMin;                 
-  m_ElectronEnergyMax = EventSelector.m_ElectronEnergyMax;                 
-  m_GammaEnergyMin = EventSelector.m_GammaEnergyMin;                    
-  m_GammaEnergyMax = EventSelector.m_GammaEnergyMax;                    
-  m_ComptonAngleMin = EventSelector.m_ComptonAngleMin;                   
-  m_ComptonAngleMax = EventSelector.m_ComptonAngleMax;                   
-  m_LeverArmMin = EventSelector.m_LeverArmMin;                       
-  m_LeverArmMax = EventSelector.m_LeverArmMax;                       
-  m_FirstLeverArmMin = EventSelector.m_FirstLeverArmMin;                  
-  m_FirstLeverArmMax = EventSelector.m_FirstLeverArmMax;                  
-  m_SequenceLengthMin = EventSelector.m_SequenceLengthMin;                 
-  m_SequenceLengthMax = EventSelector.m_SequenceLengthMax;                 
-  m_TrackLengthMin = EventSelector.m_TrackLengthMin;                    
-  m_TrackLengthMax = EventSelector.m_TrackLengthMax;                    
-  m_ClusteringQualityFactorMin = EventSelector.m_ClusteringQualityFactorMin;              
-  m_ClusteringQualityFactorMax = EventSelector.m_ClusteringQualityFactorMax;              
-  m_ComptonQualityFactorMin = EventSelector.m_ComptonQualityFactorMin;              
-  m_ComptonQualityFactorMax = EventSelector.m_ComptonQualityFactorMax;              
-  m_TrackQualityFactorMin = EventSelector.m_TrackQualityFactorMin;              
-  m_TrackQualityFactorMax = EventSelector.m_TrackQualityFactorMax;              
-  m_CoincidenceWindowMin = EventSelector.m_CoincidenceWindowMin;              
-  m_CoincidenceWindowMax = EventSelector.m_CoincidenceWindowMax;              
-  m_EventIdMin = EventSelector.m_EventIdMin;                        
-  m_EventIdMax = EventSelector.m_EventIdMax;                        
-  m_ThetaDeviationMax = EventSelector.m_ThetaDeviationMax;              
+
+  m_TimeWalkMin = EventSelector.m_TimeWalkMin;
+  m_TimeWalkMax = EventSelector.m_TimeWalkMax;
+
+  m_ElectronEnergyMin = EventSelector.m_ElectronEnergyMin;
+  m_ElectronEnergyMax = EventSelector.m_ElectronEnergyMax;
+  m_GammaEnergyMin = EventSelector.m_GammaEnergyMin;
+  m_GammaEnergyMax = EventSelector.m_GammaEnergyMax;
+  m_ComptonAngleMin = EventSelector.m_ComptonAngleMin;
+  m_ComptonAngleMax = EventSelector.m_ComptonAngleMax;
+  m_LeverArmMin = EventSelector.m_LeverArmMin;
+  m_LeverArmMax = EventSelector.m_LeverArmMax;
+  m_FirstLeverArmMin = EventSelector.m_FirstLeverArmMin;
+  m_FirstLeverArmMax = EventSelector.m_FirstLeverArmMax;
+  m_SequenceLengthMin = EventSelector.m_SequenceLengthMin;
+  m_SequenceLengthMax = EventSelector.m_SequenceLengthMax;
+  m_TrackLengthMin = EventSelector.m_TrackLengthMin;
+  m_TrackLengthMax = EventSelector.m_TrackLengthMax;
+  m_ClusteringQualityFactorMin = EventSelector.m_ClusteringQualityFactorMin;
+  m_ClusteringQualityFactorMax = EventSelector.m_ClusteringQualityFactorMax;
+  m_ComptonQualityFactorMin = EventSelector.m_ComptonQualityFactorMin;
+  m_ComptonQualityFactorMax = EventSelector.m_ComptonQualityFactorMax;
+  m_TrackQualityFactorMin = EventSelector.m_TrackQualityFactorMin;
+  m_TrackQualityFactorMax = EventSelector.m_TrackQualityFactorMax;
+  m_CoincidenceWindowMin = EventSelector.m_CoincidenceWindowMin;
+  m_CoincidenceWindowMax = EventSelector.m_CoincidenceWindowMax;
+  m_EventIdMin = EventSelector.m_EventIdMin;
+  m_EventIdMax = EventSelector.m_EventIdMax;
+  m_ThetaDeviationMax = EventSelector.m_ThetaDeviationMax;
   m_EarthHorizon = EventSelector.m_EarthHorizon;
-                                                                               
-  m_InitialEnergyDepositPairMin = EventSelector.m_InitialEnergyDepositPairMin;              
-  m_InitialEnergyDepositPairMax = EventSelector.m_InitialEnergyDepositPairMax;              
-  m_OpeningAnglePairMin = EventSelector.m_OpeningAnglePairMin;               
-  m_OpeningAnglePairMax = EventSelector.m_OpeningAnglePairMax;               
-  m_PairQualityFactorMin = EventSelector.m_PairQualityFactorMin;              
-  m_PairQualityFactorMax = EventSelector.m_PairQualityFactorMax;              
-                 
+
+  m_InitialEnergyDepositPairMin = EventSelector.m_InitialEnergyDepositPairMin;
+  m_InitialEnergyDepositPairMax = EventSelector.m_InitialEnergyDepositPairMax;
+  m_OpeningAnglePairMin = EventSelector.m_OpeningAnglePairMin;
+  m_OpeningAnglePairMax = EventSelector.m_OpeningAnglePairMax;
+  m_PairQualityFactorMin = EventSelector.m_PairQualityFactorMin;
+  m_PairQualityFactorMax = EventSelector.m_PairQualityFactorMax;
+
   m_UseSource = EventSelector.m_UseSource;
   m_SourcePosition = EventSelector.m_SourcePosition;
   m_SourceCoordinateSystem = EventSelector.m_SourceCoordinateSystem;
@@ -279,7 +279,6 @@ const MEventSelector& MEventSelector::operator=(const MEventSelector& EventSelec
   m_PointingSelectionBoxLatitudeExtent = EventSelector.m_PointingSelectionBoxLatitudeExtent;
   m_PointingSelectionBoxLongitudeExtent = EventSelector.m_PointingSelectionBoxLongitudeExtent;
   
-  
   m_UsePhotos = EventSelector.m_UsePhotos;                         
   m_UsePairs = EventSelector.m_UsePairs;                          
   m_UseComptons = EventSelector.m_UseComptons;                       
@@ -328,6 +327,7 @@ const MEventSelector& MEventSelector::operator=(const MEventSelector& EventSelec
   m_NRejectedOpeningAnglePair = EventSelector.m_NRejectedOpeningAnglePair;              
   m_NRejectedInitialEnergyDepositPair = EventSelector.m_NRejectedInitialEnergyDepositPair;              
   m_NRejectedPairQualityFactor = EventSelector.m_NRejectedPairQualityFactor;              
+
   m_NRejectedPointing = EventSelector.m_NRejectedPointing;
   m_NRejectedARM = EventSelector.m_NRejectedARM;
   m_NRejectedSPD = EventSelector.m_NRejectedSPD;
@@ -388,7 +388,7 @@ void MEventSelector::Reset()
   m_NRejectedQuickHack = 0;
 }
 
- 
+
 ////////////////////////////////////////////////////////////////////////////////
 
 
@@ -400,11 +400,11 @@ void MEventSelector::SetSettings(MSettingsEventSelections* S)
   SetSecondTotalEnergy(S->GetSecondEnergyRangeMin(), S->GetSecondEnergyRangeMax());
   SetThirdTotalEnergy(S->GetThirdEnergyRangeMin(), S->GetThirdEnergyRangeMax());
   SetFourthTotalEnergy(S->GetFourthEnergyRangeMin(), S->GetFourthEnergyRangeMax());
-  
+
   SetTimeMode(S->GetTimeMode());
   SetTime(S->GetTimeRangeMin(), S->GetTimeRangeMax());
   SetTimeFile(S->GetTimeFile());
-  
+
   SetTimeWalk(S->GetTimeWalkRangeMin(), S->GetTimeWalkRangeMax());
 
   UsePhotos(S->GetEventTypePhoto());
@@ -445,8 +445,8 @@ void MEventSelector::SetSettings(MSettingsEventSelections* S)
   SetPointingSelectionType(S->GetPointingSelectionType());
   SetPointingSelectionPointSource(S->GetPointingPointSourceLatitude(), S->GetPointingPointSourceLongitude(), S->GetPointingPointSourceRadius());
   SetPointingSelectionBox(S->GetPointingBoxLatitude(), S->GetPointingBoxLongitude(), S->GetPointingBoxExtentLatitude(), S->GetPointingBoxExtentLongitude());
-  
-  
+
+
   // Set the source:
   if (S->GetSourceUsePointSource() == true) {
     MVector Pos;
@@ -464,7 +464,7 @@ void MEventSelector::SetSettings(MSettingsEventSelections* S)
     SetSourceWindow(false);
   }
 
-  SetBeam(S->GetBeamUse(), 
+  SetBeam(S->GetBeamUse(),
           MVector(S->GetBeamStartX(), S->GetBeamStartY(), S->GetBeamStartZ()),
           MVector(S->GetBeamFocalSpotX(), S->GetBeamFocalSpotY(), S->GetBeamFocalSpotZ()));
   SetBeamRadius(S->GetBeamRadius());
@@ -478,6 +478,7 @@ void MEventSelector::SetSettings(MSettingsEventSelections* S)
   
   SetThetaDeviationMax(S->GetThetaDeviationMax());
   SetInitialEnergyDepositPair(S->GetInitialEnergyDepositPairMin(), S->GetInitialEnergyDepositPairMax());
+  SetPairQualityFactor(S->GetQualityFactorPairMin(), S->GetQualityFactorPairMax());
   SetOpeningAnglePair(S->GetOpeningAnglePairMin(), S->GetOpeningAnglePairMax());
   SetDistance(S->GetDistanceRangeMin(), S->GetDistanceRangeMax());
   SetFirstDistance(S->GetFirstDistanceRangeMin(), S->GetFirstDistanceRangeMax());
@@ -496,13 +497,13 @@ void MEventSelector::SetSettings(MSettingsEventSelections* S)
 bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
 {
   // Check if the event fullfills all event selection criteria
-  // This is the detailed version which is output capable and stores 
+  // This is the detailed version which is output capable and stores
   // which criteria trigger on the event
 
   // ATTENTION: PUT ALL CHANGES HERE INTO BOTH (FAST & DETAILED) VERSION OF THIS FUNCTION
 
   m_NAnalyzed++;
-  
+
   if (g_Verbosity > 1) DumpOutput = true;
 
   bool Return = true;
@@ -558,17 +559,17 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
 //       //cout<<"Outside beam: "<<Pos[0]<<"!"<<Pos[1]<<"!"<<Pos[2]<<endl;
 //       Return = false;
 //     }
-//   } 
+//   }
 
   /*
   MVector GalacticCenter;
   GalacticCenter.SetMagThetaPhi(1.0, 90*c_Rad, 0*c_Rad);
   if (GalacticCenter.Angle(Event->GetGalacticPointingZAxis()) > 50*c_Rad) {
     m_NRejectedQuickHack++;
-    Return = false; 
+    Return = false;
   }
   */
-  
+
 //   bool UseSideD2 = true;
 //   bool UseBottomD2 = true;
 //   // Second hit has to be in bottom calorimeters:
@@ -582,7 +583,7 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
 //         Pos = ((MComptonEvent *) Event)->C2();
 //         //cout<<"Deselecting side calor: "<<Pos[0]<<"!"<<Pos[1]<<"!"<<Pos[2]<<endl;
 //         Return = false;
-//       } 
+//       }
 //    } else {
 //       if (UseBottomD2 == false) {
 //         Pos = ((MComptonEvent *) Event)->C2();
@@ -650,13 +651,13 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
 
 
   // First test everything common to pairs and comptons:
-  if (!(Event->Ei() >= m_FirstTotalEnergyMin && 
+  if (!(Event->Ei() >= m_FirstTotalEnergyMin &&
         Event->Ei() <= m_FirstTotalEnergyMax) &&
-      !(Event->Ei() >= m_SecondTotalEnergyMin && 
+      !(Event->Ei() >= m_SecondTotalEnergyMin &&
         Event->Ei() <= m_SecondTotalEnergyMax) &&
-      !(Event->Ei() >= m_ThirdTotalEnergyMin && 
+      !(Event->Ei() >= m_ThirdTotalEnergyMin &&
         Event->Ei() <= m_ThirdTotalEnergyMax) &&
-      !(Event->Ei() >= m_FourthTotalEnergyMin && 
+      !(Event->Ei() >= m_FourthTotalEnergyMin &&
         Event->Ei() <= m_FourthTotalEnergyMax)) {
     if (DumpOutput == true) {
       cout<<"ID "<<Event->GetId()<<": Total energy out of range: "
@@ -668,7 +669,7 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
     m_NRejectedTotalEnergy++;
     Return = false;
   }
-  
+
   if (m_TimeMode == 2) {
     if (m_TimeGTI.IsGood(Event->GetTime()) == false) {
       if (DumpOutput == true) {
@@ -686,8 +687,8 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
       Return = false;
     }
   }
-  
-  if (Event->GetTimeWalk() < m_TimeWalkMin || 
+
+  if (Event->GetTimeWalk() < m_TimeWalkMin ||
       Event->GetTimeWalk() > m_TimeWalkMax) {
     if (DumpOutput == true) {
       cout<<"ID "<<Event->GetId()<<": Time-walk out of range: "
@@ -696,43 +697,43 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
     m_NRejectedTimeWalk++;
     Return = false;
   }
-  if (Event->GetId() < m_EventIdMin || 
+  if (Event->GetId() < m_EventIdMin ||
       Event->GetId() > m_EventIdMax) {
     if (DumpOutput == true) {
       cout<<"ID "<<Event->GetId()<<": Not within event ID selection: "
           <<m_EventIdMin<<"<"<<Event->GetId()<<"<"<<m_EventIdMax<<"!"<<endl;
-    }      
+    }
     m_NRejectedEventId++;
     Return = false;
   }
   if (Event->IsDecay() == true && m_UseDecays == false) {
     if (DumpOutput == true) {
       cout<<"ID "<<Event->GetId()<<": Decay!"<<endl;
-    }      
+    }
     m_NRejectedUseDecays++;
     Return = false;
   }
   if (Event->IsBad() == true && m_UseFlaggedAsBad == false) {
     if (DumpOutput == true) {
       cout<<"ID "<<Event->GetId()<<": Flagged as bad!"<<endl;
-    }      
+    }
     m_NRejectedUseFlaggedAsBad++;
     Return = false;
   }
   if (m_UseBeam == true) {
     if (Event->GetType() == MPhysicalEvent::c_Photo ||
-        Event->GetType() == MPhysicalEvent::c_Compton || 
+        Event->GetType() == MPhysicalEvent::c_Compton ||
         Event->GetType() == MPhysicalEvent::c_Pair) {
       MVector Position = Event->GetPosition();
       // The same equations appear in MResponseMultipleComptonLens
       double Radius = (Position - m_BeamFocalSpot).Cross(m_BeamStart - m_BeamFocalSpot).Mag()/(m_BeamStart - m_BeamFocalSpot).Mag();
       double Depth = (Position - m_BeamFocalSpot).Dot(m_BeamFocalSpot - m_BeamStart)/(m_BeamFocalSpot - m_BeamStart).Mag();
-      
+
       if (Radius > m_BeamRadius || Depth > m_BeamDepth) {
         if (DumpOutput == true) {
           cout<<"ID "<<Event->GetId()<<": Not within beam selection: "
               <<0<<"<"<<Radius<<"<"<<m_BeamRadius<<" or "<<0<<"<"<<Depth<<"<"<<m_BeamDepth<<endl;
-        }      
+        }
         m_NRejectedBeam++;
         Return = false;
       }
@@ -777,41 +778,41 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
         cout<<"ID "<<Event->GetId()<<": Not within pointing range: Radius "<<Location.Angle(Event->GetGalacticPointingZAxis())*c_Deg<<" > "<<m_PointingSelectionPointSourceRadius<<" deg from lat/long: "<<m_PointingSelectionPointSourceLatitude<<"/"<<m_PointingSelectionPointSourceLongitude<<endl;
       }
       m_NRejectedPointing++;
-      Return = false; 
+      Return = false;
     }
   } else if (m_PointingSelectionType == 2) {
     double LatMin = m_PointingSelectionBoxLatitude - m_PointingSelectionBoxLatitudeExtent;
-    if (LatMin < -90) LatMin = -90; 
+    if (LatMin < -90) LatMin = -90;
     double LatMax = m_PointingSelectionBoxLatitude + m_PointingSelectionBoxLatitudeExtent;
-    if (LatMax > 90) LatMax = 90; 
+    if (LatMax > 90) LatMax = 90;
 
     double LongMin = m_PointingSelectionBoxLongitude - m_PointingSelectionBoxLongitudeExtent;
     double LongMax = m_PointingSelectionBoxLongitude + m_PointingSelectionBoxLongitudeExtent;
-    
+
     double Lat = Event->GetGalacticPointingZAxis().Theta()*c_Deg - 90;
     double Long = Event->GetGalacticPointingZAxis().Phi()*c_Deg;
-    
+
     // Get it into the right range:
     while (Long < LongMin) Long += 360;
     while (Long > LongMax) Long -= 360;
-    
+
     if (Lat < LatMin || Lat > LatMax || Long < LongMin || Long > LongMax) {
       if (DumpOutput == true) {
         cout<<"ID "<<Event->GetId()<<": Not within pointing range: Lat: "<<LatMin<<"<="<<Lat<<"<="<<LatMax<<" && "<<LongMin<<"<="<<Long<<"<="<<LongMax<<endl;
       }
       m_NRejectedPointing++;
-      Return = false;       
+      Return = false;
     }
   }
-  
-  
+
+
 
   // ATTENTION: PUT ALL CHANGES HERE INTO BOTH (FAST & DETAILED) VERSION OF THIS FUNCTION
 
   // Compton events:
   if (Event->GetType() == MPhysicalEvent::c_Compton) {
     MComptonEvent *C = (MComptonEvent *) Event;
-    
+
     // Deselect bottom calorimeters in MPE prototype
     //MVector Pos = C->C2();
     //if (fabs(Pos.X()) < 9.5 && fabs(Pos.Y()) < 9.5) {
@@ -842,7 +843,7 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
     if (C->HasTrack() == false && m_UseNotTrackedComptons == false) {
       if (DumpOutput == true) {
         cout<<"ID "<<Event->GetId()<<": Unwanted not tracked Compton"<<endl;
-      }      
+      }
       m_NRejectedUseNotTrackedComptons++;
       Return = false;
     }
@@ -862,49 +863,49 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
       m_NRejectedElectronEnergy++;
       Return = false;
     }
-    if (C->Phi()*c_Deg < m_ComptonAngleMin || 
+    if (C->Phi()*c_Deg < m_ComptonAngleMin ||
         C->Phi()*c_Deg > m_ComptonAngleMax) {
       if (DumpOutput == true) {
         cout<<"ID "<<Event->GetId()<<": Compton angle out of range: "
             <<m_ComptonAngleMin<<"<"<<C->Phi()*c_Deg<<"<"
             <<m_ComptonAngleMax<<endl;
-      }      
+      }
       m_NRejectedComptonAngle++;
       Return = false;
     }
-    if (C->LeverArm() < m_LeverArmMin || 
+    if (C->LeverArm() < m_LeverArmMin ||
         C->LeverArm() > m_LeverArmMax) {
       if (DumpOutput == true) {
         cout<<"ID "<<Event->GetId()<<": Not within lever arm selection: "
             <<C->LeverArm()<<" cm!"<<endl;
-      }      
+      }
       m_NRejectedLeverArm++;
       Return = false;
     }
-    if ((C->C1() - C->C2()).Mag() < m_FirstLeverArmMin || 
+    if ((C->C1() - C->C2()).Mag() < m_FirstLeverArmMin ||
         (C->C1() - C->C2()).Mag() > m_FirstLeverArmMax) {
       if (DumpOutput == true) {
         cout<<"ID "<<Event->GetId()<<": Not within first lever arm selection: "
             <<(C->C1() - C->C2()).Mag()<<" cm!"<<endl;
-      }      
+      }
       m_NRejectedFirstLeverArm++;
       Return = false;
     }
-    if (C->SequenceLength() < m_SequenceLengthMin || 
+    if (C->SequenceLength() < m_SequenceLengthMin ||
         C->SequenceLength() > m_SequenceLengthMax) {
       if (DumpOutput == true) {
         cout<<"ID "<<Event->GetId()<<": Not within Compton sequence length selection: "
             <<m_SequenceLengthMin<<" !< "<<C->SequenceLength()<<" !< "<<m_SequenceLengthMax<<" Compton interactions!"<<endl;
-      }      
+      }
       m_NRejectedSequenceLength++;
       Return = false;
     }
-    if (C->TrackLength() < m_TrackLengthMin || 
+    if (C->TrackLength() < m_TrackLengthMin ||
         C->TrackLength() > m_TrackLengthMax) {
       if (DumpOutput == true) {
         cout<<"ID "<<Event->GetId()<<": Not within Track sequence length selection: "
             <<m_TrackLengthMin<<" !< "<<C->TrackLength()<<" !< "<<m_TrackLengthMax<<" Compton interactions!"<<endl;
-      }      
+      }
       m_NRejectedTrackLength++;
       Return = false;
     }
@@ -913,7 +914,7 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
       if (DumpOutput == true) {
         cout<<"ID "<<Event->GetId()<<": Not within Clustering quality factor selection: "
             <<m_ClusteringQualityFactorMin<<"<"<<C->ClusteringQualityFactor()<<"<"<<m_ClusteringQualityFactorMax<<endl;
-      }      
+      }
       m_NRejectedClusteringQualityFactor++;
       Return = false;
     }
@@ -922,26 +923,26 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
       if (DumpOutput == true) {
         cout<<"ID "<<Event->GetId()<<": Not within Compton quality factor selection: "
             <<m_ComptonQualityFactorMin<<"<"<<C->ComptonQualityFactor1()<<"<"<<m_ComptonQualityFactorMax<<endl;
-      }      
+      }
       m_NRejectedComptonQualityFactor++;
       Return = false;
     }
-    if (C->TrackQualityFactor1() < m_TrackQualityFactorMin || 
+    if (C->TrackQualityFactor1() < m_TrackQualityFactorMin ||
         C->TrackQualityFactor1() > m_TrackQualityFactorMax) {
       if (DumpOutput == true) {
         cout<<"ID "<<Event->GetId()<<": Not within track quality factor selection: "
             <<m_TrackQualityFactorMin<<"<"<<C->TrackQualityFactor1()<<"<"<<m_TrackQualityFactorMax<<endl;
-      }      
+      }
       m_NRejectedTrackQualityFactor++;
       Return = false;
     }
 
-    if (C->CoincidenceWindow() < m_CoincidenceWindowMin || 
+    if (C->CoincidenceWindow() < m_CoincidenceWindowMin ||
         C->CoincidenceWindow() > m_CoincidenceWindowMax) {
       if (DumpOutput == true) {
         cout<<"ID "<<Event->GetId()<<": Not within coincidence window selection: "
             <<m_CoincidenceWindowMin<<"<"<<C->CoincidenceWindow()<<"<"<<m_CoincidenceWindowMax<<endl;
-      }      
+      }
       m_NRejectedCoincidenceWindow++;
       Return = false;
     }
@@ -961,7 +962,7 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
       if (m_EarthHorizon.IsEventFromEarth(Event, DumpOutput) == true) {
         if (DumpOutput == true) {
           cout<<"ID "<<Event->GetId()<<": Not within earth horizon cut "<<endl;
-        }      
+        }
         m_NRejectedEarthHorizonCut++;
         Return = false;
       }
@@ -970,22 +971,22 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
     if (m_UseSource == true) {
       //m_SourcePosition.SetMagThetaPhi(c_FarAway, (-5.78 + 90)*c_Rad, (184.56)*c_Rad);
 
-      if (fabs(C->GetARMGamma(m_SourcePosition, m_SourceCoordinateSystem)*c_Deg) < m_ARMMin || 
+      if (fabs(C->GetARMGamma(m_SourcePosition, m_SourceCoordinateSystem)*c_Deg) < m_ARMMin ||
           fabs(C->GetARMGamma(m_SourcePosition, m_SourceCoordinateSystem)*c_Deg) > m_ARMMax) {
         if (DumpOutput == true) {
           cout<<"ID "<<Event->GetId()<<": Not within ARM cut around "<<m_SourcePosition<<" (Coordinate system: "<<m_SourceCoordinateSystem<<"): "
               <<m_ARMMin<<" < "<<fabs(C->GetARMGamma(m_SourcePosition, m_SourceCoordinateSystem))*c_Deg<<" < "<<m_ARMMax<<endl;
-        }      
+        }
         m_NRejectedARM++;
         Return = false;
       }
       if (C->TrackLength() > 1) {
-        if (fabs(C->GetSPDElectron(m_SourcePosition, m_SourceCoordinateSystem))*c_Deg < m_SPDMin || 
+        if (fabs(C->GetSPDElectron(m_SourcePosition, m_SourceCoordinateSystem))*c_Deg < m_SPDMin ||
             fabs(C->GetSPDElectron(m_SourcePosition, m_SourceCoordinateSystem))*c_Deg > m_SPDMax) {
           if (DumpOutput == true) {
             cout<<"ID "<<Event->GetId()<<": Not within SPD cut around "<<m_SourcePosition<<": "
                 <<m_SPDMax<<" < "<<fabs(C->GetSPDElectron(m_SourcePosition, m_SourceCoordinateSystem))*c_Deg<<" < "<<m_SPDMax<<endl;
-          }      
+          }
           m_NRejectedSPD++;
           Return = false;
         }
@@ -1004,7 +1005,7 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
       m_NRejectedUsePairs++;
       Return = false;
     }
-    if (Pair->GetOpeningAngle()*c_Deg < m_OpeningAnglePairMin || 
+    if (Pair->GetOpeningAngle()*c_Deg < m_OpeningAnglePairMin ||
         Pair->GetOpeningAngle()*c_Deg > m_OpeningAnglePairMax) {
       if (DumpOutput == true) {
         cout<<"ID "<<Event->GetId()
@@ -1014,7 +1015,7 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
       m_NRejectedOpeningAnglePair++;
       Return = false;
     }
-    if (Pair->GetInitialEnergyDeposit() < m_InitialEnergyDepositPairMin || 
+    if (Pair->GetInitialEnergyDeposit() < m_InitialEnergyDepositPairMin ||
         Pair->GetInitialEnergyDeposit() > m_InitialEnergyDepositPairMax) {
       if (DumpOutput == true) {
         cout<<"ID "<<Event->GetId()
@@ -1024,7 +1025,7 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
       m_NRejectedInitialEnergyDepositPair++;
       Return = false;
     }
-    if (Pair->GetTrackQualityFactor() < m_PairQualityFactorMin || 
+    if (Pair->GetTrackQualityFactor() < m_PairQualityFactorMin ||
         Pair->GetTrackQualityFactor() > m_PairQualityFactorMax) {
       if (DumpOutput == true) {
         cout<<"ID "<<Event->GetId()
@@ -1038,18 +1039,18 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
       if (m_EarthHorizon.IsEventFromEarth(Event, DumpOutput) == true) {
         if (DumpOutput == true) {
           cout<<"ID "<<Event->GetId()<<": Not within earth horizon cut "<<endl;
-        }      
+        }
         m_NRejectedEarthHorizonCut++;
         Return = false;
       }
     }
     if (m_UseSource == true) {
-      if (fabs(Pair->GetARMGamma(m_SourcePosition, m_SourceCoordinateSystem)*c_Deg) < m_ARMMin || 
+      if (fabs(Pair->GetARMGamma(m_SourcePosition, m_SourceCoordinateSystem)*c_Deg) < m_ARMMin ||
           fabs(Pair->GetARMGamma(m_SourcePosition, m_SourceCoordinateSystem)*c_Deg) > m_ARMMax) {
         if (DumpOutput == true) {
           cout<<"ID "<<Event->GetId()<<": Not within ARM cut around "<<m_SourcePosition<<": "
               <<m_ARMMin<<" < "<<fabs(Pair->GetARMGamma(m_SourcePosition, m_SourceCoordinateSystem))<<" < "<<m_ARMMax<<endl;
-        }      
+        }
         m_NRejectedARM++;
         Return = false;
       }
@@ -1137,13 +1138,13 @@ bool MEventSelector::IsQualifiedEventFast(MPhysicalEvent* Event)
 
 
   // First test everything common to pairs and comptons:
-  if (!(Event->Ei() >= m_FirstTotalEnergyMin && 
+  if (!(Event->Ei() >= m_FirstTotalEnergyMin &&
         Event->Ei() <= m_FirstTotalEnergyMax) &&
-      !(Event->Ei() >= m_SecondTotalEnergyMin && 
+      !(Event->Ei() >= m_SecondTotalEnergyMin &&
         Event->Ei() <= m_SecondTotalEnergyMax) &&
-      !(Event->Ei() >= m_ThirdTotalEnergyMin && 
+      !(Event->Ei() >= m_ThirdTotalEnergyMin &&
         Event->Ei() <= m_ThirdTotalEnergyMax) &&
-      !(Event->Ei() >= m_FourthTotalEnergyMin && 
+      !(Event->Ei() >= m_FourthTotalEnergyMin &&
         Event->Ei() <= m_FourthTotalEnergyMax)) {
     return false;
   }
@@ -1152,7 +1153,7 @@ bool MEventSelector::IsQualifiedEventFast(MPhysicalEvent* Event)
   // Compton events:
   if (Event->GetType() == MPhysicalEvent::c_Compton) {
     MComptonEvent *C = (MComptonEvent *) Event;
-    
+
 
     if (C->IsKinematicsOK() == false) {
       // no counting here!
@@ -1167,7 +1168,7 @@ bool MEventSelector::IsQualifiedEventFast(MPhysicalEvent* Event)
     if (C->HasTrack() == false && m_UseNotTrackedComptons == false) {
       return false;
     }
-    if (C->Phi()*c_Deg < m_ComptonAngleMin || 
+    if (C->Phi()*c_Deg < m_ComptonAngleMin ||
         C->Phi()*c_Deg > m_ComptonAngleMax) {
       return false;
     }
@@ -1177,19 +1178,19 @@ bool MEventSelector::IsQualifiedEventFast(MPhysicalEvent* Event)
     if (C->Ee() < m_ElectronEnergyMin || C->Ee() > m_ElectronEnergyMax) {
       return false;
     }
-    if (C->LeverArm() < m_LeverArmMin || 
+    if (C->LeverArm() < m_LeverArmMin ||
         C->LeverArm() > m_LeverArmMax) {
       return false;
     }
-    if ((C->C1() - C->C2()).Mag() < m_FirstLeverArmMin || 
+    if ((C->C1() - C->C2()).Mag() < m_FirstLeverArmMin ||
         (C->C1() - C->C2()).Mag() > m_FirstLeverArmMax) {
       return false;
     }
-    if (C->SequenceLength() < m_SequenceLengthMin || 
+    if (C->SequenceLength() < m_SequenceLengthMin ||
         C->SequenceLength() > m_SequenceLengthMax) {
       return false;
     }
-    if (C->TrackLength() < m_TrackLengthMin || 
+    if (C->TrackLength() < m_TrackLengthMin ||
         C->TrackLength() > m_TrackLengthMax) {
       return false;
     }
@@ -1201,12 +1202,12 @@ bool MEventSelector::IsQualifiedEventFast(MPhysicalEvent* Event)
         C->ComptonQualityFactor1() > m_ComptonQualityFactorMax) {
       return false;
     }
-    if (C->TrackQualityFactor1() < m_TrackQualityFactorMin || 
+    if (C->TrackQualityFactor1() < m_TrackQualityFactorMin ||
         C->TrackQualityFactor1() > m_TrackQualityFactorMax) {
       return false;
     }
 
-    if (C->CoincidenceWindow() < m_CoincidenceWindowMin || 
+    if (C->CoincidenceWindow() < m_CoincidenceWindowMin ||
         C->CoincidenceWindow() > m_CoincidenceWindowMax) {
       return false;
     }
@@ -1224,12 +1225,12 @@ bool MEventSelector::IsQualifiedEventFast(MPhysicalEvent* Event)
     }
 
     if (m_UseSource == true) {
-      if (fabs(C->GetARMGamma(m_SourcePosition, m_SourceCoordinateSystem)*c_Deg) < m_ARMMin || 
+      if (fabs(C->GetARMGamma(m_SourcePosition, m_SourceCoordinateSystem)*c_Deg) < m_ARMMin ||
           fabs(C->GetARMGamma(m_SourcePosition, m_SourceCoordinateSystem)*c_Deg) > m_ARMMax) {
         return false;
       }
       if (C->TrackLength() > 1) {
-        if (fabs(C->GetSPDElectron(m_SourcePosition, m_SourceCoordinateSystem))*c_Deg < m_SPDMin || 
+        if (fabs(C->GetSPDElectron(m_SourcePosition, m_SourceCoordinateSystem))*c_Deg < m_SPDMin ||
             fabs(C->GetSPDElectron(m_SourcePosition, m_SourceCoordinateSystem))*c_Deg > m_SPDMax) {
           return false;
         }
@@ -1244,15 +1245,15 @@ bool MEventSelector::IsQualifiedEventFast(MPhysicalEvent* Event)
     if (m_UsePairs == false) {
       return false;
     }
-    if (Pair->GetOpeningAngle()*c_Deg < m_OpeningAnglePairMin || 
+    if (Pair->GetOpeningAngle()*c_Deg < m_OpeningAnglePairMin ||
         Pair->GetOpeningAngle()*c_Deg > m_OpeningAnglePairMax) {
       return false;
     }
-    if (Pair->GetInitialEnergyDeposit() < m_InitialEnergyDepositPairMin || 
+    if (Pair->GetInitialEnergyDeposit() < m_InitialEnergyDepositPairMin ||
         Pair->GetInitialEnergyDeposit() > m_InitialEnergyDepositPairMax) {
       return false;
     }
-    if (Pair->GetTrackQualityFactor() < m_PairQualityFactorMin || 
+    if (Pair->GetTrackQualityFactor() < m_PairQualityFactorMin ||
         Pair->GetTrackQualityFactor() > m_PairQualityFactorMax) {
       return false;
     }
@@ -1262,7 +1263,7 @@ bool MEventSelector::IsQualifiedEventFast(MPhysicalEvent* Event)
       }
     }
     if (m_UseSource == true) {
-      if (fabs(Pair->GetARMGamma(m_SourcePosition, m_SourceCoordinateSystem)*c_Deg) < m_ARMMin || 
+      if (fabs(Pair->GetARMGamma(m_SourcePosition, m_SourceCoordinateSystem)*c_Deg) < m_ARMMin ||
           fabs(Pair->GetARMGamma(m_SourcePosition, m_SourceCoordinateSystem)*c_Deg) > m_ARMMax) {
         return false;
       }
@@ -1296,7 +1297,6 @@ bool MEventSelector::IsQualifiedEventFast(MPhysicalEvent* Event)
     cout<<"Unknown event type: "<<Event->GetType()<<endl;
     return false;
   }
-  
   if (m_TimeMode == 2) {
     if (m_TimeGTI.IsGood(Event->GetTime()) == false) {
       return false;
@@ -1311,7 +1311,7 @@ bool MEventSelector::IsQualifiedEventFast(MPhysicalEvent* Event)
       Event->GetTimeWalk() > m_TimeWalkMax) {
     return false;
   }
-  if (Event->GetId() < m_EventIdMin || 
+  if (Event->GetId() < m_EventIdMin ||
       Event->GetId() > m_EventIdMax) {
     return false;
   }
@@ -1327,13 +1327,13 @@ bool MEventSelector::IsQualifiedEventFast(MPhysicalEvent* Event)
 
   if (m_UseBeam == true) {
     if (Event->GetType() == MPhysicalEvent::c_Photo ||
-        Event->GetType() == MPhysicalEvent::c_Compton || 
+        Event->GetType() == MPhysicalEvent::c_Compton ||
         Event->GetType() == MPhysicalEvent::c_Pair) {
       MVector Position = Event->GetPosition();
       // The same equations appear in MResponseMultipleComptonLens
       double Radius = (Position - m_BeamFocalSpot).Cross(m_BeamStart - m_BeamFocalSpot).Mag()/(m_BeamStart - m_BeamFocalSpot).Mag();
       double Depth = (Position - m_BeamFocalSpot).Dot(m_BeamFocalSpot - m_BeamStart)/(m_BeamFocalSpot - m_BeamStart).Mag();
-      
+
       if (Radius > m_BeamRadius || Depth > m_BeamDepth) {
         return false;
       }
@@ -1368,20 +1368,20 @@ bool MEventSelector::IsQualifiedEventFast(MPhysicalEvent* Event)
     }
   } else if (m_PointingSelectionType == 2) {
     double LatMin = m_PointingSelectionBoxLatitude - m_PointingSelectionBoxLatitudeExtent;
-    if (LatMin < -90) LatMin = -90; 
+    if (LatMin < -90) LatMin = -90;
     double LatMax = m_PointingSelectionBoxLatitude + m_PointingSelectionBoxLatitudeExtent;
-    if (LatMax > 90) LatMax = 90; 
+    if (LatMax > 90) LatMax = 90;
 
     double LongMin = m_PointingSelectionBoxLongitude - m_PointingSelectionBoxLongitudeExtent;
     double LongMax = m_PointingSelectionBoxLongitude + m_PointingSelectionBoxLongitudeExtent;
-    
+
     double Lat = Event->GetGalacticPointingZAxis().Theta()*c_Deg - 90.0;
     double Long = Event->GetGalacticPointingZAxis().Phi()*c_Deg;
-    
+
     // Get it into the right range:
     while (Long < LongMin) Long += 360;
     while (Long > LongMax) Long -= 360;
-     
+
     if (Lat < LatMin || Lat > LatMax || Long < LongMin || Long > LongMax) {
       return false;
     }
@@ -1433,7 +1433,7 @@ bool MEventSelector::IsQualifiedEventFast(MPhysicalEvent* Event)
 bool MEventSelector::IsDirectionWithinARMWindow(MVector Direction)
 {
   // Just do a little test if the direction is within a selected ARM window
-  // This has nothing to do with the current event, just for testing of the 
+  // This has nothing to do with the current event, just for testing of the
   // event selection... (required by SensitivityOptimizer)
 
   if (m_UseSource == true) {
@@ -1476,6 +1476,7 @@ void MEventSelector::SetExcludedFirstIADetectors(vector<MString> ExcludedFirstIA
 void MEventSelector::SetExcludedSecondIADetectors(vector<MString> ExcludedSecondIADetectors)
 {
   // Set the detectors in which the events are not allowed to start:
+
   
   m_ExcludedSecondIADetectors = ExcludedSecondIADetectors;
 }
@@ -1617,15 +1618,20 @@ void MEventSelector::SetTimeMode(unsigned int TimeMode)
 void MEventSelector::SetTimeFile(MString TimeFile)
 {
   m_TimeFile = TimeFile;
-  
+
   m_TimeGTI.Reset(true);
 
+//<<<<<<< HEAD
   if (m_TimeMode == 2) {  
     if (MFile::Exists(m_TimeFile) == true) {
       if (m_TimeGTI.Load(m_TimeFile) == false) {
         cout<<"Error: Unable to load GTI file! Using all open one!"<<endl;
       }
     } else {
+//=======
+//  if (MFile::Exists(m_TimeFile) == true) {
+//    if (m_TimeGTI.Load(m_TimeFile) == false) {
+//>>>>>>> 683f76f6 (Pair dev (#2))
       cout<<"Error: Unable to load GTI file! Using all open one!"<<endl;
     }
   }
@@ -1751,9 +1757,9 @@ void MEventSelector::SetEarthHorizonCut(const MEarthHorizon& EH)
 ////////////////////////////////////////////////////////////////////////////////
 
 
-void MEventSelector::SetEarthHorizonCutAngle(double Angle) 
-{ 
-  m_EarthHorizon.SetEarthHorizon(MVector(0, 0, -1E20), Angle*c_Rad); 
+void MEventSelector::SetEarthHorizonCutAngle(double Angle)
+{
+  m_EarthHorizon.SetEarthHorizon(MVector(0, 0, -1E20), Angle*c_Rad);
 }
 
 
diff --git a/src/mimrec/src/MGUIEventSelection.cxx b/src/mimrec/src/MGUIEventSelection.cxx
index 4c642b83e..2cf55599b 100644
--- a/src/mimrec/src/MGUIEventSelection.cxx
+++ b/src/mimrec/src/MGUIEventSelection.cxx
@@ -46,7 +46,7 @@ ClassImp(MGUIEventSelection)
 ////////////////////////////////////////////////////////////////////////////////
 
 
-MGUIEventSelection::MGUIEventSelection(const TGWindow* p, const TGWindow* main, 
+MGUIEventSelection::MGUIEventSelection(const TGWindow* p, const TGWindow* main,
                                        MSettingsEventSelections* Data, MDGeometryQuest* Geo)
   : MGUIDialog(p, main)
 {
@@ -85,8 +85,8 @@ void MGUIEventSelection::Create()
   int TopGap = m_FontScaler*20;
 
   // We start with a name and an icon...
-  SetWindowName("Event selector");  
- 
+  SetWindowName("Event selector");
+
   // The subtitle
   SetSubTitleText("Please set all the cuts on the data for the analysis");
 
@@ -119,9 +119,9 @@ void MGUIEventSelection::Create()
 
   m_MainTab->SetTab(m_Settings->GetEventSelectorTab());
 
-  
+
   // Event type frame
-  
+
   // Event and detector type frame:
   TGLabel* LabelEventSelection = new TGLabel(EventTypeFrame, new TGString("Choose from the following event types:"));
   TGLayoutHints* LabelEventSelectionLayout =
@@ -178,8 +178,8 @@ void MGUIEventSelection::Create()
   TGLayoutHints* UnidentifiableCBLayout = new TGLayoutHints(kLHintsLeft, LeftGap+10, RightGap, 5, 0);
   EventTypeFrame->AddFrame(m_UnidentifiableCB, UnidentifiableCBLayout);
   m_UnidentifiableCB->SetState((m_Settings->GetEventTypeUnidentifiable() == 1) ?  kButtonDown : kButtonUp);
-  
-  
+
+
   TGLabel* LabelSpecialEvents = new TGLabel(EventTypeFrame, new TGString("Choose, if events with these special flags should be used:"));
   EventTypeFrame->AddFrame(LabelSpecialEvents, LabelEventSelectionLayout);
 
@@ -200,8 +200,8 @@ void MGUIEventSelection::Create()
                                    false,
                                    MString("Minimum ID: "),
                                    MString("Maximum ID: "),
-                                   m_Settings->GetEventIdRangeMin(), 
-                                   m_Settings->GetEventIdRangeMax(), 
+                                   m_Settings->GetEventIdRangeMin(),
+                                   m_Settings->GetEventIdRangeMax(),
                                    true, 0l);
   m_EventId->SetEntryFieldSize(FieldSize);
   EventTypeFrame->AddFrame(m_EventId, MinMaxFirstLayout);
@@ -210,23 +210,23 @@ void MGUIEventSelection::Create()
 
   // General Frame
 
-  
+
   // GTI
   TGLabel* LabelTimes = new TGLabel(GeneralFrame, "Good time interval");
   TGLayoutHints* LabelTimesLayout =
-    new TGLayoutHints(kLHintsLeft | kLHintsTop, LeftGap, RightGap, TopGap, 0);  
+    new TGLayoutHints(kLHintsLeft | kLHintsTop, LeftGap, RightGap, TopGap, 0);
   GeneralFrame->AddFrame(LabelTimes, LabelTimesLayout);
-    
+
   TGLayoutHints* GTIRBLayout = new TGLayoutHints(kLHintsLeft, LeftGap + 10*m_FontScaler, RightGap, 5*m_FontScaler, 2*m_FontScaler);
 
   m_GTIAllRB = new TGRadioButton(GeneralFrame, "Use all times", c_GTIAll);
   m_GTIAllRB->Associate(this);
   GeneralFrame->AddFrame(m_GTIAllRB, GTIRBLayout);
-    
+
   m_GTIEntryRB = new TGRadioButton(GeneralFrame, "Set a single GTI directly", c_GTIEntry);
   m_GTIEntryRB->Associate(this);
   GeneralFrame->AddFrame(m_GTIEntryRB, GTIRBLayout);
-  
+
   m_MinTimeEntry = new MGUIEEntry(GeneralFrame, "Minimum [sec]:", false, m_Settings->GetTimeRangeMin().GetLongIntsString());
   m_MinTimeEntry->SetEntryFieldSize(LargeFieldSize);
   TGLayoutHints* TimeEntryLayout = new TGLayoutHints(kLHintsTop | kLHintsExpandX, LeftGap + 21*m_FontScaler, RightGap, 0, 2*m_FontScaler);
@@ -234,11 +234,11 @@ void MGUIEventSelection::Create()
   m_MaxTimeEntry = new MGUIEEntry(GeneralFrame, "Maximum [sec]:", false, m_Settings->GetTimeRangeMax().GetLongIntsString());
   m_MaxTimeEntry->SetEntryFieldSize(LargeFieldSize);
   GeneralFrame->AddFrame(m_MaxTimeEntry, TimeEntryLayout);
-  
+
   m_GTIFileRB = new TGRadioButton(GeneralFrame, "Read the GTIs from file", c_GTIFile);
   m_GTIFileRB->Associate(this);
   GeneralFrame->AddFrame(m_GTIFileRB, GTIRBLayout);
-  
+
   m_GTIFile = new MGUIEFileSelector(GeneralFrame, "", m_Settings->GetTimeFile());
   m_GTIFile->SetFileType("GTI file", "*.gti");
   GeneralFrame->AddFrame(m_GTIFile, TimeEntryLayout);
@@ -263,11 +263,22 @@ void MGUIEventSelection::Create()
     m_GTIFileRB->SetState(kButtonUp);
     m_MinTimeEntry->SetEnabled(false);
     m_MaxTimeEntry->SetEnabled(false);
-    m_GTIFile->SetEnabled(false);    
+    m_GTIFile->SetEnabled(false);
   }
-  
+
 
   // Detectors
+  TGLabel* LabelDetectors =
+    new TGLabel(GeneralFrame, new TGString("Select detectors in which the first interaction is *NOT* allowed to have happend:"));
+  TGLayoutHints* LabelDetectorsLayout =
+    new TGLayoutHints(kLHintsLeft | kLHintsTop, LeftGap, RightGap, 20, 0);
+  GeneralFrame->AddFrame(LabelDetectors, LabelDetectorsLayout);
+
+  //m_DetectorList = new TGListBox(GeneralFrame, c_Detectors);
+  //m_DetectorList->SetMultipleSelections(true);
+  //TGLayoutHints* DetectorListLayout =
+  //  new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, LeftGap, RightGap, 5, 0);
+  //GeneralFrame->AddFrame(m_DetectorList, DetectorListLayout);
 
   m_FirstIADetectorList = new TGListBox(GeneralFrame, c_Detectors);
   m_FirstIADetectorList->SetMultipleSelections(true);
@@ -316,56 +327,56 @@ void MGUIEventSelection::Create()
   m_SecondIADetectorList->Resize(m_FontScaler*200, m_FontScaler*100);
   
 
-  
-  
+
+
   // Energies Frame
 
   m_FirstTotalEnergy = new MGUIEMinMaxEntry(EnergiesFrame,
-                                            MString("First energy window on total energy of incident gamma ray:"), 
+                                            MString("First energy window on total energy of incident gamma ray:"),
                                             false,
                                             MString("Minimum energy [keV]: "),
                                             MString("Maximum energy [keV]: "),
-                                            m_Settings->GetFirstEnergyRangeMin(), 
+                                            m_Settings->GetFirstEnergyRangeMin(),
                                             m_Settings->GetFirstEnergyRangeMax(),
                                             true, 0.0);
   m_FirstTotalEnergy->SetEntryFieldSize(FieldSize);
   EnergiesFrame->AddFrame(m_FirstTotalEnergy, MinMaxFirstLayout);
 
   m_SecondTotalEnergy = new MGUIEMinMaxEntry(EnergiesFrame,
-                                             MString("Second energy window on total energy of incident gamma ray:"), 
+                                             MString("Second energy window on total energy of incident gamma ray:"),
                                              false,
                                              MString("Minimum energy [keV]: "),
                                              MString("Maximum energy [keV]: "),
-                                             m_Settings->GetSecondEnergyRangeMin(), 
-                                             m_Settings->GetSecondEnergyRangeMax(), 
+                                             m_Settings->GetSecondEnergyRangeMin(),
+                                             m_Settings->GetSecondEnergyRangeMax(),
                                              true, 0.0);
   m_SecondTotalEnergy->SetEntryFieldSize(FieldSize);
   EnergiesFrame->AddFrame(m_SecondTotalEnergy, MinMaxLayout);
 
   m_ThirdTotalEnergy = new MGUIEMinMaxEntry(EnergiesFrame,
-                                            MString("Third energy window on total energy of incident gamma ray:"), 
+                                            MString("Third energy window on total energy of incident gamma ray:"),
                                             false,
                                             MString("Minimum energy [keV]: "),
                                             MString("Maximum energy [keV]: "),
-                                            m_Settings->GetThirdEnergyRangeMin(), 
-                                            m_Settings->GetThirdEnergyRangeMax(), 
+                                            m_Settings->GetThirdEnergyRangeMin(),
+                                            m_Settings->GetThirdEnergyRangeMax(),
                                             true, 0.0);
   m_ThirdTotalEnergy->SetEntryFieldSize(FieldSize);
   EnergiesFrame->AddFrame(m_ThirdTotalEnergy, MinMaxLayout);
 
   m_FourthTotalEnergy = new MGUIEMinMaxEntry(EnergiesFrame,
-                                             MString("Fourth energy window on total energy of incident gamma ray:"), 
+                                             MString("Fourth energy window on total energy of incident gamma ray:"),
                                              false,
                                              MString("Minimum energy [keV]: "),
                                              MString("Maximum energy [keV]: "),
-                                             m_Settings->GetFourthEnergyRangeMin(), 
-                                             m_Settings->GetFourthEnergyRangeMax(), 
+                                             m_Settings->GetFourthEnergyRangeMin(),
+                                             m_Settings->GetFourthEnergyRangeMax(),
                                              true, 0.0);
   m_FourthTotalEnergy->SetEntryFieldSize(FieldSize);
   EnergiesFrame->AddFrame(m_FourthTotalEnergy, MinMaxLayout);
 
 
-  
+
   // Compton frame:
 
   m_ComptonAngle = new MGUIEMinMaxEntry(ComptonEAFrame,
@@ -373,13 +384,13 @@ void MGUIEventSelection::Create()
                                         false,
                                         MString("Minimum angle [deg]: "),
                                         MString("Maximum angle [deg]: "),
-                                        m_Settings->GetComptonAngleRangeMin(), 
-                                        m_Settings->GetComptonAngleRangeMax(), 
+                                        m_Settings->GetComptonAngleRangeMin(),
+                                        m_Settings->GetComptonAngleRangeMax(),
                                         true, 0.0, 180.0);
   m_ComptonAngle->SetEntryFieldSize(FieldSize);
   ComptonEAFrame->AddFrame(m_ComptonAngle, MinMaxFirstLayout);
 
-  m_ThetaDeviationMax = 
+  m_ThetaDeviationMax =
     new MGUIEEntry(ComptonEAFrame,
                    MString("Maximum deviation of total scatter angles (energy vs. geo) [deg]:"),
                    false,
@@ -388,14 +399,14 @@ void MGUIEventSelection::Create()
   m_ThetaDeviationMax->SetEntryFieldSize(FieldSize);
   ComptonEAFrame->AddFrame(m_ThetaDeviationMax, SingleLayout);
 
-  
+
   m_GammaEnergy = new MGUIEMinMaxEntry(ComptonEAFrame,
                                        MString("Energy range of scattered gamma ray:"),
                                        false,
                                        MString("Minimum energy [keV]: "),
                                        MString("Maximum energy [keV]: "),
-                                       m_Settings->GetEnergyRangeGammaMin(), 
-                                       m_Settings->GetEnergyRangeGammaMax(), 
+                                       m_Settings->GetEnergyRangeGammaMin(),
+                                       m_Settings->GetEnergyRangeGammaMax(),
                                        true, 0.0);
   m_GammaEnergy->SetEntryFieldSize(FieldSize);
   ComptonEAFrame->AddFrame(m_GammaEnergy, MinMaxFirstLayout);
@@ -405,14 +416,14 @@ void MGUIEventSelection::Create()
                                           false,
                                           MString("Minimum energy [keV]: "),
                                           MString("Maximum energy [keV]: "),
-                                          m_Settings->GetEnergyRangeElectronMin(), 
-                                          m_Settings->GetEnergyRangeElectronMax(), 
+                                          m_Settings->GetEnergyRangeElectronMin(),
+                                          m_Settings->GetEnergyRangeElectronMax(),
                                           true, 0.0);
   m_ElectronEnergy->SetEntryFieldSize(FieldSize);
   ComptonEAFrame->AddFrame(m_ElectronEnergy, MinMaxLayout);
 
-  
-  
+
+
 
   // Compton 2 frame:
 
@@ -421,8 +432,8 @@ void MGUIEventSelection::Create()
                                            false,
                                            MString("Minimum distance [cm]: "),
                                            MString("Maximum distance [cm]: "),
-                                           m_Settings->GetFirstDistanceRangeMin(), 
-                                           m_Settings->GetFirstDistanceRangeMax(), 
+                                           m_Settings->GetFirstDistanceRangeMin(),
+                                           m_Settings->GetFirstDistanceRangeMax(),
                                            true, 0.0);
   m_FirstIADistance->SetEntryFieldSize(FieldSize);
   ComptonDLFrame->AddFrame(m_FirstIADistance, MinMaxFirstLayout);
@@ -432,7 +443,7 @@ void MGUIEventSelection::Create()
                                        false,
                                       MString("Minimum distance [cm]: "),
                                       MString("Maximum distance [cm]: "),
-                                      m_Settings->GetDistanceRangeMin(), 
+                                      m_Settings->GetDistanceRangeMin(),
                                       m_Settings->GetDistanceRangeMax(),
                                       true, 0.0);
   m_IADistance->SetEntryFieldSize(FieldSize);
@@ -443,8 +454,8 @@ void MGUIEventSelection::Create()
                                           false,
                                           MString("Minimum: "),
                                           MString("Maximum: "),
-                                          m_Settings->GetSequenceLengthRangeMin(), 
-                                          m_Settings->GetSequenceLengthRangeMax(), 
+                                          m_Settings->GetSequenceLengthRangeMin(),
+                                          m_Settings->GetSequenceLengthRangeMax(),
                                           true, 1);
   m_SequenceLength->SetEntryFieldSize(FieldSize);
   ComptonDLFrame->AddFrame(m_SequenceLength, MinMaxLayout);
@@ -454,7 +465,7 @@ void MGUIEventSelection::Create()
                                        false,
                                        MString("Minimum: "),
                                        MString("Maximum: "),
-                                       m_Settings->GetTrackLengthRangeMin(), 
+                                       m_Settings->GetTrackLengthRangeMin(),
                                        m_Settings->GetTrackLengthRangeMax(),
                                        true, 0);
   m_TrackLength->SetEntryFieldSize(FieldSize);
@@ -468,8 +479,9 @@ void MGUIEventSelection::Create()
                                              false,
                                              MString("Minimum: "),
                                              MString("Maximum: "),
-                                             m_Settings->GetComptonQualityFactorRangeMin(), 
+                                             m_Settings->GetComptonQualityFactorRangeMin(),
                                              m_Settings->GetComptonQualityFactorRangeMax());
+
   m_ComptonQualityFactor->SetEntryFieldSize(FieldSize);
   ComptonQFrame->AddFrame(m_ComptonQualityFactor, MinMaxFirstLayout);
 
@@ -478,8 +490,8 @@ void MGUIEventSelection::Create()
                                              false,
                                              MString("Minimum: "),
                                              MString("Maximum: "),
-                                             m_Settings->GetTrackQualityFactorRangeMin(), 
-                                             m_Settings->GetTrackQualityFactorRangeMax(), 
+                                             m_Settings->GetTrackQualityFactorRangeMin(),
+                                             m_Settings->GetTrackQualityFactorRangeMax(),
                                              true, 0.0);
   m_TrackQualityFactor->SetEntryFieldSize(FieldSize);
   ComptonQFrame->AddFrame(m_TrackQualityFactor, MinMaxLayout);
@@ -488,8 +500,8 @@ void MGUIEventSelection::Create()
                                                    MString("Clustering quality factor:"),
                                                    false,
                                                    MString("Minimum: "),
-                                                   MString("Maximum: "),                                                     m_Settings->GetClusteringQualityFactorRangeMin(), 
-                                                   m_Settings->GetClusteringQualityFactorRangeMax(), 
+                                                   MString("Maximum: "),                                                     m_Settings->GetClusteringQualityFactorRangeMin(),
+                                                   m_Settings->GetClusteringQualityFactorRangeMax(),
                                                    true, 0.0);
   m_ClusteringQualityFactor->SetEntryFieldSize(FieldSize);
   ComptonQFrame->AddFrame(m_ClusteringQualityFactor, MinMaxLayout);
@@ -499,8 +511,8 @@ void MGUIEventSelection::Create()
                                              false,
                                              MString("Minimum (should be zero): "),
                                              MString("Maximum: "),
-                                             m_Settings->GetCoincidenceWindowRangeMin(), 
-                                             m_Settings->GetCoincidenceWindowRangeMax(), 
+                                             m_Settings->GetCoincidenceWindowRangeMin(),
+                                             m_Settings->GetCoincidenceWindowRangeMax(),
                                              true, 0.0);
   m_CoincidenceWindow->SetEntryFieldSize(FieldSize);
   ComptonQFrame->AddFrame(m_CoincidenceWindow, MinMaxLayout);
@@ -535,7 +547,7 @@ void MGUIEventSelection::Create()
   TGLayoutHints* EHCSingleLayout =
     new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, LeftGap+30, RightGap, 5, 5);
 
-  m_EHCProbability = 
+  m_EHCProbability =
     new MGUIEEntry(ComptonEHCFrame,
                    MString("Maximum Earth probability [0..1]:"),
                    false,
@@ -544,7 +556,7 @@ void MGUIEventSelection::Create()
   m_EHCProbability->SetEntryFieldSize(FieldSize);
   ComptonEHCFrame->AddFrame(m_EHCProbability, EHCSingleLayout);
 
-  m_EHCProbabilityFile = 
+  m_EHCProbabilityFile =
     new MGUIEFileSelector(ComptonEHCFrame,
                           MString("EHC Compton probability response file (*.compton.ehc.rsp):"),
                           m_Settings->GetEHCComptonProbabilityFileName());
@@ -557,7 +569,7 @@ void MGUIEventSelection::Create()
     m_EHCProbabilityFile->SetEnabled(false);
   }
 
-  m_EHCAngle = 
+  m_EHCAngle =
     new MGUIEEntry(ComptonEHCFrame,
                    MString("Angle between direction to Earth's center and horizon (0 = nadir) [deg]:"),
                    false,
@@ -580,7 +592,7 @@ void MGUIEventSelection::Create()
                                             false,
                                             MString("Minimum angle [deg]: "),
                                             MString("Maximum angle [deg]: "),
-                                            m_Settings->GetOpeningAnglePairMin(), 
+                                            m_Settings->GetOpeningAnglePairMin(),
                                             m_Settings->GetOpeningAnglePairMax(),
                                             true, 0.0, 180.0);
   m_OpeningAnglePair->SetEntryFieldSize(FieldSize);
@@ -591,17 +603,28 @@ void MGUIEventSelection::Create()
                                                     false,
                                                     MString("Minimum [keV]: "),
                                                     MString("Maximum [keV]: "),
-                                                    m_Settings->GetInitialEnergyDepositPairMin(), 
+                                                    m_Settings->GetInitialEnergyDepositPairMin(),
                                                     m_Settings->GetInitialEnergyDepositPairMax(),
                                                     true, 0.0);
   m_InitialEnergyDepositPair->SetEntryFieldSize(FieldSize);
   PairFrame->AddFrame(m_InitialEnergyDepositPair, MinMaxLayout);
 
+  m_QualityFactorPair = new MGUIEMinMaxEntry(PairFrame,
+                                                    MString("Pair quality factor:"),
+                                                    false,
+                                                    MString("Minimum: "),
+                                                    MString("Maximum: "),
+                                                    m_Settings->GetQualityFactorPairMin(),
+                                                    m_Settings->GetQualityFactorPairMax(),
+                                                    true, -10.);
+  m_QualityFactorPair->SetEntryFieldSize(FieldSize);
+  PairFrame->AddFrame(m_QualityFactorPair, MinMaxLayout);
+
 
 
   // Source frame:
-  
-  
+
+
   m_UsePointSource = new TGCheckButton(SourceFrame, "Use selection on point source:", c_UsePointSource);
   SourceFrame->AddFrame(m_UsePointSource, MinMaxFirstLayout);
   m_UsePointSource->Associate(this);
@@ -652,8 +675,8 @@ void MGUIEventSelection::Create()
                                false,
                                MString("Minimum [deg]: "),
                                MString("Maximum [deg]: "),
-                               m_Settings->GetSourceARMMin(), 
-                               m_Settings->GetSourceARMMax(), 
+                               m_Settings->GetSourceARMMin(),
+                               m_Settings->GetSourceARMMax(),
                                true, 0.0, 180.0);
   m_ARM->SetEntryFieldSize(FieldSize);
   SourceFrame->AddFrame(m_ARM, CoordinatesLayout);
@@ -663,8 +686,8 @@ void MGUIEventSelection::Create()
                                false,
                                MString("Minimum [deg]: "),
                                MString("Maximum [deg]: "),
-                               m_Settings->GetSourceSPDMin(), 
-                               m_Settings->GetSourceSPDMax(), 
+                               m_Settings->GetSourceSPDMin(),
+                               m_Settings->GetSourceSPDMax(),
                                true, 0.0, 180.0);
   m_SPD->SetEntryFieldSize(FieldSize);
   SourceFrame->AddFrame(m_SPD, CoordinatesLayout);
@@ -676,7 +699,7 @@ void MGUIEventSelection::Create()
       m_CoordinatesSelected = c_UseSphericPointSource;
     } else {
       m_CoordinatesSelected = c_UseCartesianPointSource;
-    }           
+    }
     m_ARM->SetEnabled(true);
     m_SPD->SetEnabled(true);
     if (m_CoordinatesSelected == c_UseGalacticPointSource) {
@@ -708,7 +731,7 @@ void MGUIEventSelection::Create()
       m_CoordinatesSelected = c_UseSphericPointSource;
     } else {
       m_CoordinatesSelected = c_UseCartesianPointSource;
-    }           
+    }
     m_UseGalacticPointSource->SetState(kButtonUp);
     m_SourceGalactic->SetEnabled(false);
     m_UseSphericPointSource->SetState(kButtonUp);
@@ -719,13 +742,13 @@ void MGUIEventSelection::Create()
     m_SPD->SetEnabled(false);
   }
 
-  
+
   // Pointing frame
-  
+
   TGLabel* PointingSelectionLabel = new TGLabel(PointingFrame, "Use only pointings which are within the following selection:");
   TGLayoutHints* PointingSelectionLabelLayout = new TGLayoutHints(kLHintsTop | kLHintsLeft, LeftGap, RightGap, TopGap, 5);
   PointingFrame->AddFrame(PointingSelectionLabel, PointingSelectionLabelLayout);
-  
+
   m_UsePointingSelectionNone = new TGRadioButton(PointingFrame, "Do NOT use a pointing selection", c_UsePointingSelectionNone);
   m_UsePointingSelectionNone->Associate(this);
   PointingFrame->AddFrame(m_UsePointingSelectionNone, CoordinatesLayout);
@@ -741,7 +764,7 @@ void MGUIEventSelection::Create()
   m_PointingPointSourceLocation->Create();
   PointingFrame->AddFrame(m_PointingPointSourceLocation, SourceLayout);
 
-  m_PointingPointSourceRadius = 
+  m_PointingPointSourceRadius =
     new MGUIEEntry(PointingFrame,
                    MString("Radius of disk [deg]:"),
                    false,
@@ -761,7 +784,7 @@ void MGUIEventSelection::Create()
   m_PointingBoxLocation->Create();
   PointingFrame->AddFrame(m_PointingBoxLocation, SourceLayout);
 
-  m_PointingBoxExtentLatitude = 
+  m_PointingBoxExtentLatitude =
     new MGUIEEntry(PointingFrame,
                    MString("Extent in latitude (half) [deg]:"),
                    false,
@@ -770,7 +793,7 @@ void MGUIEventSelection::Create()
   m_PointingBoxExtentLatitude->SetEntryFieldSize(FieldSize);
   PointingFrame->AddFrame(m_PointingBoxExtentLatitude, SourceLayout);
 
-  m_PointingBoxExtentLongitude = 
+  m_PointingBoxExtentLongitude =
     new MGUIEEntry(PointingFrame,
                    MString("Extent in longitude (half) [deg]:"),
                    false,
@@ -778,7 +801,7 @@ void MGUIEventSelection::Create()
                    true, 0.0, 180.0);
   m_PointingBoxExtentLongitude->SetEntryFieldSize(FieldSize);
   PointingFrame->AddFrame(m_PointingBoxExtentLongitude, SourceLayout);
-  
+
   if (m_Settings->GetPointingSelectionType() == 1) {
     m_UsePointingSelectionNone->SetState(kButtonUp);
     m_UsePointingSelectionPointSource->SetState(kButtonDown);
@@ -807,12 +830,10 @@ void MGUIEventSelection::Create()
     m_PointingBoxExtentLatitude->SetEnabled(false);
     m_PointingBoxExtentLongitude->SetEnabled(false);
   }
-  
 
-  // Beam/Box frame
-  
-  
-  m_UseBeam = new TGCheckButton(BeamFrame, "Use beam to select on the first interaction in the detector:", c_UseBeam);
+
+  // Beam frame
+  m_UseBeam = new TGCheckButton(BeamFrame, "Use beam selection:", c_UseBeam);
   BeamFrame->AddFrame(m_UseBeam, MinMaxFirstLayout);
   m_UseBeam->Associate(this);
   m_UseBeam->SetState((m_Settings->GetBeamUse() == true) ?  kButtonDown : kButtonUp);
@@ -835,7 +856,7 @@ void MGUIEventSelection::Create()
   m_BeamFocalSpot->Create();
   BeamFrame->AddFrame(m_BeamFocalSpot, BeamLayout);
 
-  m_BeamRadius = 
+  m_BeamRadius =
     new MGUIEEntry(BeamFrame,
                    "Selected radius around beam center [cm]:",
                    false,
@@ -844,7 +865,7 @@ void MGUIEventSelection::Create()
   m_BeamRadius->SetEntryFieldSize(FieldSize);
   BeamFrame->AddFrame(m_BeamRadius, BeamLayout);
 
-  m_BeamDepth = 
+  m_BeamDepth =
     new MGUIEEntry(BeamFrame,
                    "Selected maximum (fist) interaction depth [cm]:",
                    false,
@@ -941,11 +962,11 @@ void MGUIEventSelection::Create()
                                       false,
                                       MString("Minimum [ns]: "),
                                       MString("Maximum [ns]: "),
-                                      m_Settings->GetTimeWalkRangeMin(), 
+                                      m_Settings->GetTimeWalkRangeMin(),
                                       m_Settings->GetTimeWalkRangeMax());
     SpecialFrame->AddFrame(m_TimeWalk, MinMaxFirstLayout);
   }
-  
+
 
   // Finally bring it to the screen
   FinalizeCreate(GetDefaultWidth(), GetDefaultHeight()+40, false);
@@ -957,7 +978,7 @@ void MGUIEventSelection::Create()
 ////////////////////////////////////////////////////////////////////////////////
 
 
-bool MGUIEventSelection::ProcessMessage(long Message, long Parameter1, 
+bool MGUIEventSelection::ProcessMessage(long Message, long Parameter1,
                                         long Parameter2)
 {
   // Process the messages for this application
@@ -971,7 +992,7 @@ bool MGUIEventSelection::ProcessMessage(long Message, long Parameter1,
     case kCM_RADIOBUTTON:
       if (Parameter1 == c_GTIAll) {
         if (m_GTIAllRB->GetState() == kButtonUp) {
-          m_GTIAllRB->SetState(kButtonDown); 
+          m_GTIAllRB->SetState(kButtonDown);
         } else {
           m_GTIEntryRB->SetState(kButtonUp);
           m_GTIFileRB->SetState(kButtonUp);
@@ -981,7 +1002,7 @@ bool MGUIEventSelection::ProcessMessage(long Message, long Parameter1,
         }
       } else if (Parameter1 == c_GTIEntry) {
         if (m_GTIEntryRB->GetState() == kButtonUp) {
-          m_GTIEntryRB->SetState(kButtonDown); 
+          m_GTIEntryRB->SetState(kButtonDown);
         } else {
           m_GTIAllRB->SetState(kButtonUp);
           m_GTIFileRB->SetState(kButtonUp);
@@ -991,7 +1012,7 @@ bool MGUIEventSelection::ProcessMessage(long Message, long Parameter1,
         }
       } else if (Parameter1 == c_GTIFile) {
         if (m_GTIFileRB->GetState() == kButtonUp) {
-          m_GTIFileRB->SetState(kButtonDown); 
+          m_GTIFileRB->SetState(kButtonDown);
         } else {
           m_GTIAllRB->SetState(kButtonUp);
           m_GTIEntryRB->SetState(kButtonUp);
@@ -1029,47 +1050,47 @@ bool MGUIEventSelection::ProcessMessage(long Message, long Parameter1,
           m_EHCProbability->SetEnabled(false);
           m_EHCProbabilityFile->SetEnabled(false);
         }
-        
+
       } else if (Parameter1 == c_UsePointingSelectionNone) {
         if (m_UsePointingSelectionNone->GetState() == kButtonUp) {
-          m_UsePointingSelectionNone->SetState(kButtonDown); 
+          m_UsePointingSelectionNone->SetState(kButtonDown);
         } else {
-          m_UsePointingSelectionPointSource->SetState(kButtonUp); 
-          m_UsePointingSelectionBox->SetState(kButtonUp); 
+          m_UsePointingSelectionPointSource->SetState(kButtonUp);
+          m_UsePointingSelectionBox->SetState(kButtonUp);
           m_PointingPointSourceLocation->SetEnabled(false);
           m_PointingPointSourceRadius->SetEnabled(false);
           m_PointingBoxLocation->SetEnabled(false);
           m_PointingBoxExtentLatitude->SetEnabled(false);
           m_PointingBoxExtentLongitude->SetEnabled(false);
         }
-        
+
       } else if (Parameter1 == c_UsePointingSelectionPointSource) {
         if (m_UsePointingSelectionPointSource->GetState() == kButtonUp) {
-          m_UsePointingSelectionPointSource->SetState(kButtonDown); 
+          m_UsePointingSelectionPointSource->SetState(kButtonDown);
         } else {
-          m_UsePointingSelectionNone->SetState(kButtonUp); 
-          m_UsePointingSelectionBox->SetState(kButtonUp); 
+          m_UsePointingSelectionNone->SetState(kButtonUp);
+          m_UsePointingSelectionBox->SetState(kButtonUp);
           m_PointingPointSourceLocation->SetEnabled(true);
           m_PointingPointSourceRadius->SetEnabled(true);
           m_PointingBoxLocation->SetEnabled(false);
           m_PointingBoxExtentLatitude->SetEnabled(false);
           m_PointingBoxExtentLongitude->SetEnabled(false);
         }
-        
+
       } else if (Parameter1 == c_UsePointingSelectionBox) {
         if (m_UsePointingSelectionBox->GetState() == kButtonUp) {
-          m_UsePointingSelectionBox->SetState(kButtonDown); 
+          m_UsePointingSelectionBox->SetState(kButtonDown);
         } else {
-          m_UsePointingSelectionNone->SetState(kButtonUp); 
-          m_UsePointingSelectionPointSource->SetState(kButtonUp); 
+          m_UsePointingSelectionNone->SetState(kButtonUp);
+          m_UsePointingSelectionPointSource->SetState(kButtonUp);
           m_PointingPointSourceLocation->SetEnabled(false);
           m_PointingPointSourceRadius->SetEnabled(false);
           m_PointingBoxLocation->SetEnabled(true);
           m_PointingBoxExtentLatitude->SetEnabled(true);
           m_PointingBoxExtentLongitude->SetEnabled(true);
         }
-        
-      } else if (Parameter1 >= c_UseGalacticPointSource && 
+
+      } else if (Parameter1 >= c_UseGalacticPointSource &&
                  Parameter1 <= c_UseCartesianPointSource) {
         if (m_UsePointSource->GetState() == kButtonUp) {
           m_UsePointSource->SetState(kButtonUp);
@@ -1083,21 +1104,21 @@ bool MGUIEventSelection::ProcessMessage(long Message, long Parameter1,
           } else {
             m_UseGalacticPointSource->SetState(kButtonUp);
             m_SourceGalactic->SetEnabled(false);
-          }     
+          }
           if (c_UseSphericPointSource == Parameter1) {
             m_UseSphericPointSource->SetState(kButtonDown);
             m_SourceSpheric->SetEnabled(true);
           } else {
             m_UseSphericPointSource->SetState(kButtonUp);
             m_SourceSpheric->SetEnabled(false);
-          }     
+          }
           if (c_UseCartesianPointSource == Parameter1) {
             m_UseCartesianPointSource->SetState(kButtonDown);
             m_SourceCartesian->SetEnabled(true);
           } else {
             m_UseCartesianPointSource->SetState(kButtonUp);
             m_SourceCartesian->SetEnabled(false);
-          }     
+          }
         }
       }
       break;
@@ -1121,7 +1142,7 @@ bool MGUIEventSelection::ProcessMessage(long Message, long Parameter1,
           } else {
             m_ComptonTrackedCB->SetState(kButtonUp);
           }
-        } 
+        }
         break;
 
       case c_ComptonTracked:
@@ -1207,7 +1228,7 @@ bool MGUIEventSelection::ProcessMessage(long Message, long Parameter1,
         break;
 
      default:
-        break; 
+        break;
       }
       break;
 
@@ -1219,15 +1240,15 @@ bool MGUIEventSelection::ProcessMessage(long Message, long Parameter1,
 
       case e_Cancel:
         Status = OnCancel();
-        break;  
-        
+        break;
+
       default:
         break;
       }
-      
+
     case kCM_MENUSELECT:
       break;
-      
+
     case kCM_MENU:
       switch (Parameter1) {
       default:
@@ -1239,7 +1260,7 @@ bool MGUIEventSelection::ProcessMessage(long Message, long Parameter1,
   default:
     break;
   }
-  
+
   return Status;
 }
 
@@ -1262,68 +1283,67 @@ bool MGUIEventSelection::OnApply()
                  " Compton / pair / photo / PET / multi / unidentifiable", kMBIconStop, kMBOk);
     return false;
   }
-  if (m_ComptonCB->GetState() == kButtonDown && 
+  if (m_ComptonCB->GetState() == kButtonDown &&
       m_ComptonNotTrackedCB->GetState() == kButtonUp &&
       m_ComptonTrackedCB->GetState() == kButtonUp) {
-    new TGMsgBox(gClient->GetRoot(), this, "Type error", 
+    new TGMsgBox(gClient->GetRoot(), this, "Type error",
                        "You have to selected Compton-events. So you have also to select: \n"
                  "Tracked and/or not-tracked Compton-events", kMBIconStop, kMBOk);
     return false;
   }
-  if (m_EventId->CheckRange(0l, numeric_limits<long>::max(), 
+  if (m_EventId->CheckRange(0l, numeric_limits<long>::max(),
                             0l, numeric_limits<long>::max(), false) == false) return false;
-  if (m_TrackLength->CheckRange(1, numeric_limits<int>::max(), 
+  if (m_TrackLength->CheckRange(1, numeric_limits<int>::max(),
                                 1, numeric_limits<int>::max(), false) == false) return false;
-  if (m_SequenceLength->CheckRange(2, numeric_limits<int>::max(), 
+  if (m_SequenceLength->CheckRange(2, numeric_limits<int>::max(),
                                    2, numeric_limits<int>::max(), false) == false) return false;
-  if (m_ClusteringQualityFactor->CheckRange(0.0, numeric_limits<double>::max(), 
+  if (m_ClusteringQualityFactor->CheckRange(0.0, numeric_limits<double>::max(),
                                             0.0, numeric_limits<double>::max(), true) == false) return false;
-  //if (m_ComptonQualityFactor->CheckRange(0.0, numeric_limits<double>::max(), 
+  //if (m_ComptonQualityFactor->CheckRange(0.0, numeric_limits<double>::max(),
   //                                       0.0, numeric_limits<double>::max(), true) == false) return false;
-  if (m_TrackQualityFactor->CheckRange(0.0, numeric_limits<double>::max(), 
+  if (m_TrackQualityFactor->CheckRange(0.0, numeric_limits<double>::max(),
                                        0.0, numeric_limits<double>::max(), true) == false) return false;
-  if (m_CoincidenceWindow->CheckRange(0.0, numeric_limits<double>::max(), 
+  if (m_CoincidenceWindow->CheckRange(0.0, numeric_limits<double>::max(),
                                       0.0, numeric_limits<double>::max(), true) == false) return false;
-  if (m_FirstTotalEnergy->CheckRange(0.0, numeric_limits<double>::max(), 
+  if (m_FirstTotalEnergy->CheckRange(0.0, numeric_limits<double>::max(),
                                      0.0, numeric_limits<double>::max(), false) == false) return false;
-  if (m_SecondTotalEnergy->CheckRange(0.0, numeric_limits<double>::max(), 
+  if (m_SecondTotalEnergy->CheckRange(0.0, numeric_limits<double>::max(),
                                       0.0, numeric_limits<double>::max(), false) == false) return false;
-  if (m_ThirdTotalEnergy->CheckRange(0.0, numeric_limits<double>::max(), 
+  if (m_ThirdTotalEnergy->CheckRange(0.0, numeric_limits<double>::max(),
                                       0.0, numeric_limits<double>::max(), false) == false) return false;
-  if (m_FourthTotalEnergy->CheckRange(0.0, numeric_limits<double>::max(), 
+  if (m_FourthTotalEnergy->CheckRange(0.0, numeric_limits<double>::max(),
                                       0.0, numeric_limits<double>::max(), false) == false) return false;
-  if (m_GammaEnergy->CheckRange(0.0, numeric_limits<double>::max(), 
+  if (m_GammaEnergy->CheckRange(0.0, numeric_limits<double>::max(),
                                       0.0, numeric_limits<double>::max(), true) == false) return false;
-  if (m_ElectronEnergy->CheckRange(0.0, numeric_limits<double>::max(), 
+  if (m_ElectronEnergy->CheckRange(0.0, numeric_limits<double>::max(),
                                    0.0, numeric_limits<double>::max(), true) == false) return false;
   if (m_ComptonAngle->CheckRange(0.0, 180.0, 0.0, 180.0, true) == false) return false;
-  if (m_FirstIADistance->CheckRange(0.0, numeric_limits<double>::max(), 
+  if (m_FirstIADistance->CheckRange(0.0, numeric_limits<double>::max(),
                                     0.0, numeric_limits<double>::max(), true) == false) return false;
-  if (m_IADistance->CheckRange(0.0, numeric_limits<double>::max(), 
+  if (m_IADistance->CheckRange(0.0, numeric_limits<double>::max(),
                                0.0, numeric_limits<double>::max(), true) == false) return false;
   double MinTime = m_MinTimeEntry->GetAsString().ToDouble();
   double MaxTime = m_MaxTimeEntry->GetAsString().ToDouble();
   if (MinTime >= MaxTime) {
-    mgui<<"The minimum time is larger or equal the maximum time"<<error;     
+    mgui<<"The minimum time is larger or equal the maximum time"<<error;
     return false;
   }
   if (MinTime < 0) {
-    mgui<<"The minimum time is smaller than zero!"<<error;     
-    return false;    
+    mgui<<"The minimum time is smaller than zero!"<<error;
+    return false;
   }
   if (m_Settings->GetSpecialMode() == true) {
-    if (m_TimeWalk->CheckRange(-numeric_limits<double>::max(), numeric_limits<double>::max(), 
+    if (m_TimeWalk->CheckRange(-numeric_limits<double>::max(), numeric_limits<double>::max(),
                                -numeric_limits<double>::max(), numeric_limits<double>::max(), true) == false) return false;
   }
   if (m_OpeningAnglePair->CheckRange(0.0, 180.0, 0.0, 180.0, true) == false) return false;
   if (m_InitialEnergyDepositPair->CheckRange(0.0, 100000.0, 0.0, 100000.0, true) == false) return false;
   
-  
   if (m_FirstTotalEnergy->GetMaxValue() == 0 && 
       m_SecondTotalEnergy->GetMaxValue() == 0 && 
       m_ThirdTotalEnergy->GetMaxValue() == 0 && 
       m_FourthTotalEnergy->GetMaxValue() == 0) {
-    mgui<<"At least one total energy window must be open."<<error; 
+    mgui<<"At least one total energy window must be open."<<error;
     return false;
   }
 
@@ -1353,7 +1373,7 @@ bool MGUIEventSelection::OnApply()
   if (m_Settings->GetEventTypeUnidentifiable() != ((m_UnidentifiableCB->GetState() == kButtonDown) ? 1 : 0)) m_Settings->SetEventTypeUnidentifiable((m_UnidentifiableCB->GetState() == kButtonDown) ? 1 : 0);
   if (m_Settings->GetEventTypeDecay() != ((m_DecayCB->GetState() == kButtonDown) ? 1 : 0)) m_Settings->SetEventTypeDecay((m_DecayCB->GetState() == kButtonDown) ? 1 : 0);
 
-  if (m_Settings->GetFlaggedAsBad() != ((m_BadCB->GetState() == kButtonDown) ? true : false)) m_Settings->SetFlaggedAsBad((m_BadCB->GetState() == kButtonDown) ? true : false);  
+  if (m_Settings->GetFlaggedAsBad() != ((m_BadCB->GetState() == kButtonDown) ? true : false)) m_Settings->SetFlaggedAsBad((m_BadCB->GetState() == kButtonDown) ? true : false);
 
   if (m_EventId->IsModified() == true) {
     m_Settings->SetEventIdRangeMin(long(m_EventId->GetMinValueInt()));
@@ -1374,19 +1394,19 @@ bool MGUIEventSelection::OnApply()
       m_Settings->SetTimeMode(0);
     }
   }
-  
+
   if (m_MinTimeEntry->IsModified() == true) {
     m_Settings->SetTimeRangeMin(m_MinTimeEntry->GetAsString().ToDouble());
   }
   if (m_MaxTimeEntry->IsModified() == true) {
     m_Settings->SetTimeRangeMax(m_MaxTimeEntry->GetAsString().ToDouble());
-  }  
+  }
   if (m_GTIFile->GetFileName() != m_Settings->GetTimeFile()) {
     m_Settings->SetTimeFile(m_GTIFile->GetFileName());
   }
-  
-  
-  
+
+
+
   if (m_TrackLength->IsModified() == true) {
     m_Settings->SetTrackLengthRangeMin(m_TrackLength->GetMinValueInt());
     m_Settings->SetTrackLengthRangeMax(m_TrackLength->GetMaxValueInt());
@@ -1468,7 +1488,7 @@ bool MGUIEventSelection::OnApply()
     m_Settings->SetThetaDeviationMax(m_ThetaDeviationMax->GetAsDouble());
   }
 
-  
+
   if (((m_UsePointSource->GetState() == kButtonDown) ? true : false) != m_Settings->GetSourceUsePointSource()) {
     m_Settings->SetSourceUsePointSource((m_UsePointSource->GetState() == kButtonDown) ? true : false);
   }
@@ -1518,7 +1538,7 @@ bool MGUIEventSelection::OnApply()
       m_Settings->SetPointingSelectionType(0);
     }
   }
-  
+
   if (m_PointingPointSourceLocation->IsModified() == true) {
     m_Settings->SetPointingPointSourceLatitude(m_PointingPointSourceLocation->GetAsDouble(0));
     m_Settings->SetPointingPointSourceLongitude(m_PointingPointSourceLocation->GetAsDouble(1));
@@ -1536,10 +1556,6 @@ bool MGUIEventSelection::OnApply()
   if (m_PointingBoxExtentLongitude->IsModified() == true) {
     m_Settings->SetPointingBoxExtentLongitude(m_PointingBoxExtentLongitude->GetAsDouble());
   }
-  
-  
-  // Beam
-  
   if (m_Settings->GetBeamUse() != ((m_UseBeam->GetState() == kButtonDown) ? true : false)) {
     m_Settings->SetBeamUse((m_UseBeam->GetState() == kButtonDown) ? true : false);
   }
@@ -1616,6 +1632,11 @@ bool MGUIEventSelection::OnApply()
     m_Settings->SetOpeningAnglePairMax(m_OpeningAnglePair->GetMaxValue());
   }
 
+  if (m_QualityFactorPair->IsModified() == true) {
+    m_Settings->SetQualityFactorPairMin(m_QualityFactorPair->GetMinValue());
+    m_Settings->SetQualityFactorPairMax(m_QualityFactorPair->GetMaxValue());
+  }
+
   if (m_InitialEnergyDepositPair->IsModified() == true) {
     m_Settings->SetInitialEnergyDepositPairMin(m_InitialEnergyDepositPair->GetMinValue());
     m_Settings->SetInitialEnergyDepositPairMax(m_InitialEnergyDepositPair->GetMaxValue());
@@ -1690,7 +1711,7 @@ bool MGUIEventSelection::OnApply()
   m_Settings->SetEventSelectorTab(m_MainTab->GetCurrent());
 
   dynamic_cast<MSettings*>(m_Settings)->Write();
-  
+
   return true;
 }
 
diff --git a/src/mimrec/src/MInterfaceMimrec.cxx b/src/mimrec/src/MInterfaceMimrec.cxx
index 9032b7dcf..0aab0aa16 100644
--- a/src/mimrec/src/MInterfaceMimrec.cxx
+++ b/src/mimrec/src/MInterfaceMimrec.cxx
@@ -145,7 +145,7 @@ bool MInterfaceMimrec::ParseCommandLine(int argc, char** argv)
   Usage<<"      -o --output:"<<endl;
   Usage<<"             For --image, --spectrum, --light-curve, --distances, --scatter-angles, --sequence-length, and --arm-gamma: Save the generated histogram."<<endl;
   Usage<<"             For -x: Save the extracted events"<<endl;
-  Usage<<"             If multiple histograms are generated, additional modifiers will be added to the file name"<<endl; 
+  Usage<<"             If multiple histograms are generated, additional modifiers will be added to the file name"<<endl;
   Usage<<"      -i --image:"<<endl;
   Usage<<"             Create an image. If the -o option is given then the image is saved to this file."<<endl;
   Usage<<"      -s --spectrum:"<<endl;
@@ -206,7 +206,7 @@ bool MInterfaceMimrec::ParseCommandLine(int argc, char** argv)
     Option = argv[i];
 
     // Single argument
-    if (Option == "-g" || Option == "--geometry" || 
+    if (Option == "-g" || Option == "--geometry" ||
         Option == "-c" || Option == "--configuration" ||
         Option == "-o" || Option == "--output" ||
         Option == "-f" || Option == "--filename") {
@@ -225,7 +225,7 @@ bool MInterfaceMimrec::ParseCommandLine(int argc, char** argv)
       }
     }
   }
-  
+
   // Now parse all first level options
   for (int i = 1; i < argc; i++) {
     Option = argv[i];
@@ -256,19 +256,19 @@ bool MInterfaceMimrec::ParseCommandLine(int argc, char** argv)
       cout<<"Command-line parser: Use this output file name "<<m_OutputFileName<<endl;
     }
   }
-  
+
   // Look if we need to change the configuration
   for (int i = 1; i < argc; i++) {
     Option = argv[i];
     if (Option == "--change-configuration" || Option == "-C") {
       if (m_Settings->Change(argv[++i]) == false) {
-        cout<<"ERROR: Command-line parser: Unable to change this configuration value: "<<argv[i]<<endl;        
+        cout<<"ERROR: Command-line parser: Unable to change this configuration value: "<<argv[i]<<endl;
       } else {
         cout<<"Command-line parser: Changing this configuration value: "<<argv[i]<<endl;
       }
     }
   }
-  
+
   // Do we have a X up and running?
   if (gClient == 0 || gClient->GetRoot() == 0 || gROOT->IsBatch() == true) {
     cout<<"Command-line parser: No X-client or ROOT in batch mode: Using batch mode"<<endl;
@@ -334,7 +334,7 @@ bool MInterfaceMimrec::ParseCommandLine(int argc, char** argv)
   for (int i = 1; i < argc; i++) {
     Option = argv[i];
     if (Option == "--spectrum" || Option == "-s") {
-      cout<<"Command-line parser: Generating spectrum..."<<endl;  
+      cout<<"Command-line parser: Generating spectrum..."<<endl;
       EnergySpectra();
       return KeepAlive;
     } else if (Option == "--arm-gamma" || Option == "-a") {
@@ -346,11 +346,11 @@ bool MInterfaceMimrec::ParseCommandLine(int argc, char** argv)
       SPDElectron();
       return KeepAlive;
     } else if (Option == "--light-curve" || Option == "-l") {
-      cout<<"Command-line parser: Generating light curve..."<<endl;  
+      cout<<"Command-line parser: Generating light curve..."<<endl;
       LightCurve();
       return KeepAlive;
     } else if (Option == "--polarization" || Option == "-p") {
-      cout<<"Command-line parser: Performing polarization analysis..."<<endl;  
+      cout<<"Command-line parser: Performing polarization analysis..."<<endl;
       Polarization();
       return KeepAlive;
     } else if (Option == "--scatter-angles") {
@@ -362,7 +362,7 @@ bool MInterfaceMimrec::ParseCommandLine(int argc, char** argv)
       SaveConfiguration(m_OutputFileName != "" ? m_OutputFileName : "NewConfiguration.cfg");
       return KeepAlive;
     } else if (Option == "--interaction-distance") {
-      cout<<"Command-line parser: Generating interaction-distance plot..."<<endl;  
+      cout<<"Command-line parser: Generating interaction-distance plot..."<<endl;
       DistanceDistribution();
       return KeepAlive;
     } else if (Option == "--sequence-length") {
@@ -374,7 +374,7 @@ bool MInterfaceMimrec::ParseCommandLine(int argc, char** argv)
       LocationOfInitialInteraction();
       return KeepAlive;
     } else if (Option == "--extract" || Option == "-x") {
-      cout<<"Command-line parser: Extracting events..."<<endl;  
+      cout<<"Command-line parser: Extracting events..."<<endl;
       ExtractEvents();
       return KeepAlive;
     } else if (Option == "--standard-analysis-spherical") {
@@ -383,23 +383,23 @@ bool MInterfaceMimrec::ParseCommandLine(int argc, char** argv)
       double Phi = atof(argv[++i])*c_Rad;
       MVector Position;
       Position.SetMagThetaPhi(c_FarAway, Theta, Phi);
-      cout<<"Command-line parser: Performing standard analysis..."<<endl;  
+      cout<<"Command-line parser: Performing standard analysis..."<<endl;
       StandardAnalysis(Energy, Position);
       return KeepAlive;
     } else if (Option == "--event-selections" || Option == "-e") {
-      cout<<"Command-line parser: Dumping event selections..."<<endl;  
+      cout<<"Command-line parser: Dumping event selections..."<<endl;
       // m_Settings->SetStoreImages(true);
       ShowEventSelections();
       return KeepAlive;
     } else if (Option == "--image" || Option == "-i") {
-      cout<<"Command-line parser: Generating image..."<<endl;  
+      cout<<"Command-line parser: Generating image..."<<endl;
       // m_Settings->SetStoreImages(true);
       Reconstruct();
       return KeepAlive;
     }
   }
 
-   
+
   // Execute some low level commands
   if (m_UseGui == true) {
     m_Gui = new MGUIMimrecMain(this, m_Settings);
@@ -411,7 +411,7 @@ bool MInterfaceMimrec::ParseCommandLine(int argc, char** argv)
   // Show change log / license if changed:
   MPrelude P;
   if (P.Play() == false) return false; // license was not accepted
-  
+
   return true;
 }
 
@@ -435,7 +435,7 @@ bool MInterfaceMimrec::ParseCommandLine(int argc, char** argv)
 
 
 bool MInterfaceMimrec::LoadConfiguration(MString FileName)
-{  
+{
   // Load the configuration file
 
   if (m_Settings == 0) {
@@ -445,7 +445,7 @@ bool MInterfaceMimrec::LoadConfiguration(MString FileName)
       m_Gui->SetConfiguration(m_Settings);
     }
   }
-  
+
   m_Settings->Read(FileName);
 
   return true;
@@ -498,7 +498,7 @@ bool MInterfaceMimrec::SetGeometry(MString FileName, bool UpdateGui)
     delete m_Geometry;
     m_Geometry = 0;
     m_BasicGuiData->SetGeometryFileName(g_StringNotDefined);
-  } 
+  }
 
   if (m_UseGui == true && UpdateGui == true) {
     m_Gui->UpdateConfiguration();
@@ -515,7 +515,7 @@ MVector MInterfaceMimrec::GetTestPosition()
 {
   // Determine the test position of ARM, etc. cuts in various coordinate system
 
-  MVector Test(0.0, 0.0, 1.0); 
+  MVector Test(0.0, 0.0, 1.0);
 
   // Get the data of the ARM-"Test"-Position
   if (m_Settings->GetCoordinateSystem() == MCoordinateSystem::c_Spheric) {
@@ -540,7 +540,7 @@ double MInterfaceMimrec::GetTotalEnergyMin()
 {
   // Determine the test position of ARM, etc. cuts in various coordinate system
 
-  double Min = numeric_limits<double>::max(); 
+  double Min = numeric_limits<double>::max();
 
   if (m_Settings->GetFirstEnergyRangeMax() > 0) {
     if (m_Settings->GetFirstEnergyRangeMin() < Min) Min = m_Settings->GetFirstEnergyRangeMin();
@@ -566,7 +566,7 @@ double MInterfaceMimrec::GetTotalEnergyMax()
 {
   // Determine the test position of ARM, etc. cuts in various coordinate system
 
-  double Max = 0; 
+  double Max = 0;
 
   if (m_Settings->GetFirstEnergyRangeMax() > 0) {
     if (m_Settings->GetFirstEnergyRangeMax() > Max) Max = m_Settings->GetFirstEnergyRangeMax();
@@ -600,16 +600,16 @@ void MInterfaceMimrec::Reconstruct(bool Animate)
       m_Settings->IsBackprojectionModified() == false) {
     if (m_Settings->IsLikelihoodModified() == true) {
       int Return = 0;
-      new TGMsgBox(gClient->GetRoot(), gClient->GetRoot(), "Info", 
-                   "Only data concerning the deconvolution has been modified.\nDo you wish to just perform deconvolution?\nOtherwise also the response is redetermined, too.", 
+      new TGMsgBox(gClient->GetRoot(), gClient->GetRoot(), "Info",
+                   "Only data concerning the deconvolution has been modified.\nDo you wish to just perform deconvolution?\nOtherwise also the response is redetermined, too.",
                    kMBIconQuestion, kMBYes | kMBNo, &Return);
       if (Return == 1) {
         JustDeconvolve = true;
       }
     } else {
       int Return = 0;
-      new TGMsgBox(gClient->GetRoot(), gClient->GetRoot(), "Info", 
-                   "No data has been modified.\nDo you just want to see the last image again?\nIf not, the image will be recomputed.", 
+      new TGMsgBox(gClient->GetRoot(), gClient->GetRoot(), "Info",
+                   "No data has been modified.\nDo you just want to see the last image again?\nIf not, the image will be recomputed.",
                    kMBIconQuestion, kMBYes | kMBNo | kMBCancel, &Return);
       if (Return == 1) {
         JustShowImage = true;
@@ -623,16 +623,16 @@ void MInterfaceMimrec::Reconstruct(bool Animate)
     if (m_Imager != 0) {
       delete m_Imager;
     }
-    
+
     // Initialize:
     m_Imager = new MImager(m_Settings->GetCoordinateSystem());
     m_Imager->SetGeometry(m_Geometry);
-    
+
     if (m_Imager->SetImagingSettings(m_Settings) == false) {
       mgui<<"Unable to set all imaging settings"<<error;
       return;
     }
- 
+
     // Animations are OFF by default when set via SetImageSettings
     if (Animate == true) {
       m_Imager->SetAnimationMode(m_Settings->GetAnimationMode());
@@ -658,7 +658,7 @@ void MInterfaceMimrec::Reconstruct(bool Animate)
       mgui<<"Unable to set all deconvolution settings"<<error;
       return;
     }
-    
+
     // Analyze... do the reconstruction
     m_Imager->Analyze(!JustDeconvolve);
 
@@ -689,7 +689,7 @@ void MInterfaceMimrec::Reconstruct(bool Animate)
 
 ////////////////////////////////////////////////////////////////////////////////
 
-  
+
 void MInterfaceMimrec::SpectralAnalyzer()
 {
   //! The spectral analyzer
@@ -699,8 +699,8 @@ void MInterfaceMimrec::SpectralAnalyzer()
 
 
   MSpectralAnalyzer S;
-  
-  
+
+
   // Fill the initial histogram:
   S.SetGeometry(m_Geometry);
   S.SetSpectrum(1000, GetTotalEnergyMin(), GetTotalEnergyMax());
@@ -715,24 +715,24 @@ void MInterfaceMimrec::SpectralAnalyzer()
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
       S.FillSpectrum(Event->GetEnergy());
     }
-    
+
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
-  
+
   // Set the GUI options
- 
+
   // peak search
 
   S.SetSignaltoNoiseRatio(m_Settings->GetSpectralSignaltoNoiseRatio());
   S.SetPoissonLimit(m_Settings->GetSpectralPoissonLimit());
-  
+
   // Isotope Selection
   S.SetIsotopeFileName(m_Settings->GetSpectralIsotopeFileName());
   S.SetEnergyRange(m_Settings->GetSpectralEnergyRange());
-  
+
   // Do the analysis
   if (S.FindIsotopes() == true) {
 //    cout<<"Found "<<S.GetNIsotopes()<<" isotopes."<<endl;
@@ -742,7 +742,7 @@ void MInterfaceMimrec::SpectralAnalyzer()
 
 ////////////////////////////////////////////////////////////////////////////////
 
-  
+
 bool MInterfaceMimrec::InitializeEventLoader(MString File)
 {
   // Start the event loader...
@@ -750,17 +750,17 @@ bool MInterfaceMimrec::InitializeEventLoader(MString File)
   if (File.IsEmpty() == true) {
     File = m_Settings->GetCurrentFileName();
   }
-  
+
   if (m_EventFile != nullptr) delete m_EventFile;
   m_EventFile = new MFileEventsTra();
-  
+
   m_EventFile->SetFastFileParsing(m_Settings->GetFastFileParsing());
   if (m_EventFile->Open(File) == false) return false;
   m_EventFile->ShowProgress(m_UseGui);
   if (m_Settings->GetNThreads() > 1) {
     m_EventFile->StartThread();
   }
-  
+
   m_Selector->Reset();
   m_Selector->SetGeometry(m_Geometry);
   m_Selector->SetSettings(m_Settings);
@@ -770,7 +770,7 @@ bool MInterfaceMimrec::InitializeEventLoader(MString File)
 
 ////////////////////////////////////////////////////////////////////////////////
 
-    
+
 MPhysicalEvent* MInterfaceMimrec::GetNextEvent(bool Checks)
 {
   // Get the next event
@@ -779,14 +779,14 @@ MPhysicalEvent* MInterfaceMimrec::GetNextEvent(bool Checks)
     if (m_EventFile == nullptr) return nullptr;
     if (m_EventFile->IsOpen() == false) return nullptr;
   }
-  
+
   return m_EventFile->GetNextEvent();
 }
 
 
 ////////////////////////////////////////////////////////////////////////////////
 
-    
+
 void MInterfaceMimrec::FinalizeEventLoader()
 {
   // Close the event loader
@@ -803,14 +803,14 @@ void MInterfaceMimrec::FinalizeEventLoader()
 
 ////////////////////////////////////////////////////////////////////////////////
 
-  
+
 void MInterfaceMimrec::ShowEventSelections()
 {
   // Show how many events pass the event selections
 
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
-  
+
   int NEvents = 0;
   int NGoodEvents = 0;
 
@@ -821,13 +821,13 @@ void MInterfaceMimrec::ShowEventSelections()
     if (m_Selector->IsQualifiedEvent(Event, true) == true) {
       NGoodEvents++;
     }
-    
+
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
-  
+
   cout<<endl;
   cout<<endl;
   cout<<"Event selections:"<<endl;
@@ -835,18 +835,18 @@ void MInterfaceMimrec::ShowEventSelections()
   cout<<"All events  .................... "<<NEvents<<endl;
   cout<<"Not rejected events  ........... "<<NGoodEvents<<endl;
   cout<<endl;
-  
+
   cout<<m_Selector->ToString()<<endl;
 }
 
 
 ////////////////////////////////////////////////////////////////////////////////
 
-  
+
 void MInterfaceMimrec::ShowEventSelectionsStepwise()
 {
   // Show how many events pass the event selections
-  
+
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
@@ -976,8 +976,8 @@ void MInterfaceMimrec::ShowEventSelectionsStepwise()
       NRestrictSPD++;
     }
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -1007,11 +1007,11 @@ void MInterfaceMimrec::ShowEventSelectionsStepwise()
 
 ////////////////////////////////////////////////////////////////////////////////
 
-  
+
 void MInterfaceMimrec::ExtractEvents()
 {
   // Show how many events pass the event selections
-    
+
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
@@ -1025,8 +1025,8 @@ void MInterfaceMimrec::ExtractEvents()
       FileName = FileName.Remove(FileName.Length()-7, 7); // remove final tra
     }
     FileName += ".extracted.tra";
-  } 
-  
+  }
+
   MFileEventsTra* OutFile = new MFileEventsTra();
   OutFile->Open(FileName, MFile::c_Write);
   if (OutFile->IsOpen() == false) {
@@ -1034,17 +1034,17 @@ void MInterfaceMimrec::ExtractEvents()
     mgui<<"Aborting event extraction"<<show;
     return;
   }
-  
+
 
   MPhysicalEvent* Event = nullptr;
   while ((Event = GetNextEvent()) != 0) {
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
       OutFile->AddEvent(Event);
     }
-    
+
     delete Event;
   }
-  
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -1056,15 +1056,15 @@ void MInterfaceMimrec::ExtractEvents()
 
 ////////////////////////////////////////////////////////////////////////////////
 
-  
+
 void MInterfaceMimrec::ThetaOriginDistribution()
 {
   // Show how many events pass the event selections
-  
+
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  TH1D* Hist = new TH1D("ThetaOriginDistribution", 
+  TH1D* Hist = new TH1D("ThetaOriginDistribution",
                         "Theta Origin Distribution", 90, 0, 180);
   Hist->SetBit(kCanDelete);
   Hist->SetDirectory(0);
@@ -1076,12 +1076,12 @@ void MInterfaceMimrec::ThetaOriginDistribution()
 
   MPhysicalEvent* Event = nullptr;
   while ((Event = GetNextEvent()) != 0) {
-    
+
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
       if (Event->GetOrigin() != g_VectorNotDefined) {
         if (Event->GetType() == MPhysicalEvent::c_Compton) {
-          Hist->Fill(dynamic_cast<MComptonEvent*>(Event)->Di().Theta()*c_Deg);          
+          Hist->Fill(dynamic_cast<MComptonEvent*>(Event)->Di().Theta()*c_Deg);
         } else {
           Hist->Fill(Event->GetOrigin().Theta()*c_Deg);
         }
@@ -1089,12 +1089,12 @@ void MInterfaceMimrec::ThetaOriginDistribution()
     }
 
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
-  TCanvas* Canvas = new TCanvas("ThetaOriginDistributionCanvas", 
+  TCanvas* Canvas = new TCanvas("ThetaOriginDistributionCanvas",
                                 "Theta Origin Distribution Canvas", 800, 600);
   Canvas->SetFillColor(0);
   Canvas->SetFrameBorderSize(0);
@@ -1111,12 +1111,12 @@ void MInterfaceMimrec::ThetaOriginDistribution()
 
 ////////////////////////////////////////////////////////////////////////////////
 
-  
+
 void MInterfaceMimrec::ARMGamma()
 {
   // Display the angular resolution measurement for the gamma-ray
-  // The ARM value for the scattered gamma-ray is the minimum angle between 
-  // the gamma-cone-surface and the line connecting the cone-apex with the 
+  // The ARM value for the scattered gamma-ray is the minimum angle between
+  // the gamma-cone-surface and the line connecting the cone-apex with the
   // (Test-)position
 
   // Start with the event file loader first (just in case something goes wrong here)
@@ -1579,12 +1579,12 @@ void MInterfaceMimrec::ARMGammaClassic()
 
 ////////////////////////////////////////////////////////////////////////////////
 
-  
+
 void MInterfaceMimrec::DualARM()
 {
   // Display the angular resolution measurement for the gamma-ray
-  // The ARM value for the scattered gamma-ray is the minimum angle between 
-  // the gamma-cone-surface and the line connecting the cone-apex with the 
+  // The ARM value for the scattered gamma-ray is the minimum angle between
+  // the gamma-cone-surface and the line connecting the cone-apex with the
   // (Test-)position
 
   // Start with the event file loader first (just in case something goes wrong here)
@@ -1592,9 +1592,9 @@ void MInterfaceMimrec::DualARM()
 
   int NEvents = 0;
   int NEventsInside = 0;
-  
+
   MVector TestPosition = GetTestPosition();
-  
+
   double x1Max = m_Settings->GetTPDistanceTrans();
   int x1Bins = m_Settings->GetHistBinsARMGamma();
 
@@ -1613,7 +1613,7 @@ void MInterfaceMimrec::DualARM()
   Hist->SetContour(50);
 
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* ComptonEvent = nullptr; 
+  MComptonEvent* ComptonEvent = nullptr;
   double xValue = 0;
   double yValue = 0;
   // ... loop over all events and save a count in the belonging bin ...
@@ -1632,12 +1632,12 @@ void MInterfaceMimrec::DualARM()
         }
         Hist->Fill(xValue*c_Deg, yValue*c_Deg, 1);
         NEvents++;
-      } 
+      }
     }
 
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -1668,13 +1668,13 @@ void MInterfaceMimrec::DualARM()
   mout<<"Analyzed Compton and pair events:        "<<NEvents<<endl;
   mout<<"Compton and pair events in histogram:    "<<NEventsInside
       <<" ("<<((NEvents > 0) ? 100.0*NEventsInside/NEvents : 0.0)<<"%)"<<endl;
- 
+
   return;
 }
 
 ////////////////////////////////////////////////////////////////////////////////
 
-  
+
 void MInterfaceMimrec::ARMResponseComparison()
 {
   // Compare the ARM with the imaging response
@@ -1682,20 +1682,20 @@ void MInterfaceMimrec::ARMResponseComparison()
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   MVector TestPosition = GetTestPosition();
-  
+
   double ARMMax = m_Settings->GetTPDistanceTrans();
   int ARMBins = m_Settings->GetHistBinsARMGamma();
-  
+
   MResponse* Response = 0;
   if (m_Settings->GetResponseType() == MResponseType::Gauss1D) {
-    Response = new MResponseGaussian(m_Settings->GetFitParameterComptonTransSphere(), 
+    Response = new MResponseGaussian(m_Settings->GetFitParameterComptonTransSphere(),
                                      m_Settings->GetFitParameterComptonLongSphere(),
                                      m_Settings->GetFitParameterPair(),
                                      m_Settings->GetFitParameterPET());
   } else if (m_Settings->GetResponseType() == MResponseType::GaussByEnergyLeakage) {
-    Response = new MResponseEnergyLeakage(m_Settings->GetFitParameterComptonTransSphere(), 
+    Response = new MResponseEnergyLeakage(m_Settings->GetFitParameterComptonTransSphere(),
                                        m_Settings->GetFitParameterComptonLongSphere());
   } else if (m_Settings->GetResponseType() == MResponseType::GaussByUncertainties) {
     Response = new MResponseGaussianByUncertainties();
@@ -1719,7 +1719,7 @@ void MInterfaceMimrec::ARMResponseComparison()
     merr<<"Unknown response type: "<<m_Settings->GetResponseType()<<show;
     return;
   }
-  
+
   // Initalize the ARM histogram
   TH1D* ARMHist = new TH1D("ARMHist", "ARM (coarsly binned) vs. Response (smoothly binned)", ARMBins, -ARMMax, ARMMax);
   ARMHist->SetBit(kCanDelete);
@@ -1737,10 +1737,10 @@ void MInterfaceMimrec::ARMResponseComparison()
   ResponseHist->SetYTitle("normalized counts");
   ResponseHist->SetStats(false);
   ResponseHist->SetContour(50);
-  
+
 
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* ComptonEvent = nullptr; 
+  MComptonEvent* ComptonEvent = nullptr;
   // ... loop over all events and save a count in the belonging bin ...
   while ((Event = GetNextEvent()) != 0) {
 
@@ -1752,14 +1752,14 @@ void MInterfaceMimrec::ARMResponseComparison()
         ARMHist->Fill(ARM, 1);
         Response->AnalyzeEvent(ComptonEvent);
         for (int b = 1; b <= ResponseHist->GetNbinsX(); ++b) {
-          ResponseHist->SetBinContent(b, ResponseHist->GetBinContent(b) + Response->GetComptonResponse((ResponseHist->GetBinCenter(b) - ARM)*c_Rad)); 
+          ResponseHist->SetBinContent(b, ResponseHist->GetBinContent(b) + Response->GetComptonResponse((ResponseHist->GetBinCenter(b) - ARM)*c_Rad));
         }
-      } 
+      }
     }
 
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -1779,21 +1779,21 @@ void MInterfaceMimrec::ARMResponseComparison()
   Canvas->Update();
 }
 
-  
+
 ////////////////////////////////////////////////////////////////////////////////
 
-  
+
 void MInterfaceMimrec::AngularResolutionPairs()
 {
   // Display the angular resolution measurement for the gamma-ray
-  // The ARM value for the scattered gamma-ray is the minimum angle between 
-  // the gamma-cone-surface and the line connecting the cone-apex with the 
+  // The ARM value for the scattered gamma-ray is the minimum angle between
+  // the gamma-cone-surface and the line connecting the cone-apex with the
   // (Test-)position
 
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   int NEvents = 0;
   double Value = 0;
   int Inside = 0;
@@ -1801,7 +1801,7 @@ void MInterfaceMimrec::AngularResolutionPairs()
   int NBins = m_Settings->GetHistBinsARMGamma();
   double Disk = m_Settings->GetTPDistanceTrans();
   MVector TestPosition = GetTestPosition();
-  
+
   // Initalize the image size (x-axis)
   //BinWidth = 2*Disk/NBins;
   TH1D* Hist = new TH1D("AngularResolutionPairs", "Angular resolution pairs", NBins, 0, Disk);
@@ -1825,7 +1825,7 @@ void MInterfaceMimrec::AngularResolutionPairs()
 
 
   MPhysicalEvent* Event = nullptr;
-  MPairEvent* PairEvent = 0; 
+  MPairEvent* PairEvent = 0;
   // ... loop over all events and save a count in the belonging bin ...
   while ((Event = GetNextEvent()) != 0) {
 
@@ -1843,8 +1843,8 @@ void MInterfaceMimrec::AngularResolutionPairs()
     }
 
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -1853,7 +1853,7 @@ void MInterfaceMimrec::AngularResolutionPairs()
     return;
   }
 
-    
+
   TCanvas *Canvas = new TCanvas("Canvas angular resolution pairs", "Canvas angular resolution pairs", 800, 600);
   Canvas->SetFillColor(0);
   Canvas->SetFrameBorderSize(0);
@@ -1878,9 +1878,9 @@ void MInterfaceMimrec::AngularResolutionPairs()
 
   //   TF1* AsymGausFunction = new TF1("AGF", AsymGaus, -Disk*0.99, Disk*0.99, 5);
   //   AsymGausFunction->SetParNames("Offset", "Gaus Height", "Gaus Mean", "Gaus Sigma 1", "Gaus Sigma 2");
-  //   AsymGausFunction->SetParameters(L->GetParameter(3), L->GetParameter(4), 
+  //   AsymGausFunction->SetParameters(L->GetParameter(3), L->GetParameter(4),
   //                                   L->GetParameter(5), L->GetParameter(6), L->GetParameter(7));
-  
+
 
   Canvas->cd();
   Hist->Draw();
@@ -1906,11 +1906,11 @@ void MInterfaceMimrec::AngularResolutionPairs()
   for (int b = 1; b <= NBins; b++) {
     Content += Hist->GetBinContent(b);
     if (Content >= Containment*All) {
-      cout<<Containment<<"% containment: "<<Hist->GetBinCenter(b)<<endl;
+      cout<<100*Containment<<"% containment: "<<Hist->GetBinCenter(b)<<endl;
       break;
     }
   }
-    
+
   TCanvas* Canvas2 = new TCanvas("CanvasAngularResolutionPairsVsOpeningAngle", "Canvas angular resolution pairs vs. opening angle", 800, 600);
   Canvas2->cd();
   Hist2->Draw("colz");
@@ -2030,94 +2030,95 @@ void MInterfaceMimrec::ResolutionMeasurePET()
 void MInterfaceMimrec::PhiKinVsPhiGeo()
 {
   // Display a 2D histogram of the Compton scatter angle Phi calculated via kinematics and via geometry
-  
+
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
-  
-  
+
+
   int NBins = m_Settings->GetHistBinsARMGamma();
   double Disk = m_Settings->GetTPDistanceTrans();
   MVector TestPosition = GetTestPosition();
-  
+
   // Initalize the image size (x-axis)
-  TH2D* Hist = new TH2D("PhiKinVsPhiGeo", "Compton scatter angle: Kienmatics vs. geometry", 
+  TH2D* Hist = new TH2D("PhiKinVsPhiGeo", "Compton scatter angle: Kienmatics vs. geometry",
                         NBins, 0, Disk, NBins, 0, Disk);
   Hist->SetBit(kCanDelete);
   Hist->SetXTitle("Compton scatter angle via geometry [deg]");
   Hist->SetYTitle("Compton scatter angle via kinematics [deg]");
-  
-  
+
+
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* ComptonEvent = nullptr; 
+  MComptonEvent* ComptonEvent = nullptr;
   // ... loop over all events and save a count in the belonging bin ...
   while ((Event = GetNextEvent()) != 0) {
-    
+
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
       if (Event->GetType() == MPhysicalEvent::c_Compton) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
-        
+
         // Comtpon scatter angle via geometry - take care of coordinate systems:
         MVector RotPosition = TestPosition;
         if (ComptonEvent->HasDetectorRotation() == true) RotPosition = ComptonEvent->GetDetectorInverseRotationMatrix()*RotPosition;
         if (m_Settings->GetCoordinateSystem() == MCoordinateSystem::c_Galactic && ComptonEvent->HasGalacticPointing() == true) RotPosition = ComptonEvent->GetGalacticPointingInverseRotationMatrix()*RotPosition;
-        
+
         if ((ComptonEvent->C1() - ComptonEvent->C2()).Angle(RotPosition - ComptonEvent->C1())*c_Deg > 89 && (ComptonEvent->C1() - ComptonEvent->C2()).Angle(RotPosition - ComptonEvent->C1())*c_Deg < 91) {
           cout<<ComptonEvent->GetId()<<": "<<(ComptonEvent->C1() - ComptonEvent->C2()).Angle(RotPosition - ComptonEvent->C1())*c_Deg*c_Deg<<endl;
         }
-        
-        Hist->Fill((ComptonEvent->C1() - ComptonEvent->C2()).Angle(RotPosition - ComptonEvent->C1())*c_Deg, 
+
+        Hist->Fill((ComptonEvent->C1() - ComptonEvent->C2()).Angle(RotPosition - ComptonEvent->C1())*c_Deg,
                    ComptonEvent->Phi()*c_Deg);
-      } 
+      }
     }
-    
+
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
-  
+
   if (Hist->GetMaximum() == 0) {
     Error("ARMGamma()", "No events passed the event selections or file is empty!");
     return;
   }
-  
+
   TCanvas* Canvas = new TCanvas();
   Canvas->SetTitle("Compton scatter angle: Kienmatics vs. geometry");
   Canvas->cd();
   Hist->Draw("COLZ");
   Canvas->Update();
-  
+
   return;
 }
 
 
 ////////////////////////////////////////////////////////////////////////////////
 
-  
+
 void MInterfaceMimrec::ARMGammaVsComptonScatterAngle()
 {
   // Display the angular resolution measurement for the gamma-ray as function of
   // the Compton scatter angle
-  // The ARM value for the scattered gamma-ray is the minimum angle between 
-  // the gamma-cone-surface and the line connecting the cone-apex with the 
+  // The ARM value for the scattered gamma-ray is the minimum angle between
+  // the gamma-cone-surface and the line connecting the cone-apex with the
   // (Test-)position
 
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   int NBins = m_Settings->GetHistBinsARMGamma();
   double Disk = m_Settings->GetTPDistanceTrans();
   MVector TestPosition = GetTestPosition();
-  
+
   // Initalize the image size (x-axis)
   //BinWidth = 2*Disk/NBins;
   int NBinsArm = NBins;
   int NBinsAngle = NBins;
-  TH2D* Hist = new TH2D("ARMvsComptonScatterAngle", "ARM vs. Compton scatter angle", 
-                        NBinsArm, -Disk, Disk, NBinsAngle, 
-                        m_Settings->GetComptonAngleRangeMin(), 
+
+  TH2D* Hist = new TH2D("ARMvsComptonScatterAngle", "ARM vs. Compton scatter angle",
+                        NBinsArm, -Disk, Disk, NBinsAngle,
+                        m_Settings->GetComptonAngleRangeMin(),
                         m_Settings->GetComptonAngleRangeMax());
   Hist->SetBit(kCanDelete);
   Hist->SetXTitle("ARM [deg]");
@@ -2125,7 +2126,7 @@ void MInterfaceMimrec::ARMGammaVsComptonScatterAngle()
 
 
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* ComptonEvent = nullptr; 
+  MComptonEvent* ComptonEvent = nullptr;
   // ... loop over all events and save a count in the belonging bin ...
   while ((Event = GetNextEvent()) != 0) {
 
@@ -2134,14 +2135,14 @@ void MInterfaceMimrec::ARMGammaVsComptonScatterAngle()
       if (Event->GetType() == MPhysicalEvent::c_Compton) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
-        Hist->Fill(ComptonEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem())*c_Deg, 
+        Hist->Fill(ComptonEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem())*c_Deg,
                    ComptonEvent->Phi()*c_Deg);
-      } 
+      }
     }
 
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -2164,7 +2165,7 @@ void MInterfaceMimrec::ARMGammaVsComptonScatterAngle()
     }
   }
   */
-    
+
   TCanvas* Canvas = new TCanvas();
   Canvas->SetTitle("ARM vs. Compton scatter angle");
   Canvas->cd();
@@ -2177,30 +2178,30 @@ void MInterfaceMimrec::ARMGammaVsComptonScatterAngle()
 
 ////////////////////////////////////////////////////////////////////////////////
 
-  
+
 void MInterfaceMimrec::ARMGammaVsDistance()
 {
   // Display the angular resolution measurement for the gamma-ray as function of
   // the Compton scatter angle
-  // The ARM value for the scattered gamma-ray is the minimum angle between 
-  // the gamma-cone-surface and the line connecting the cone-apex with the 
+  // The ARM value for the scattered gamma-ray is the minimum angle between
+  // the gamma-cone-surface and the line connecting the cone-apex with the
   // (Test-)position
 
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   int NBins = m_Settings->GetHistBinsARMGamma();
   double Disk = m_Settings->GetTPDistanceTrans();
   MVector TestPosition = GetTestPosition();
-  
+
   // Initalize the image size (x-axis)
   //BinWidth = 2*Disk/NBins;
   int NBinsArm = NBins;
   int NBinsDistance = 20;
-  TH2D* Hist = new TH2D("ARMVsDistance", "ARM vs. distance", 
-                        NBinsArm, -Disk, Disk, NBinsDistance, 
-                        m_Settings->GetFirstDistanceRangeMin(), 
+  TH2D* Hist = new TH2D("ARMVsDistance", "ARM vs. distance",
+                        NBinsArm, -Disk, Disk, NBinsDistance,
+                        m_Settings->GetFirstDistanceRangeMin(),
                         m_Settings->GetFirstDistanceRangeMax());
   Hist->SetBit(kCanDelete);
   Hist->SetXTitle("ARM [#circ]");
@@ -2210,7 +2211,7 @@ void MInterfaceMimrec::ARMGammaVsDistance()
 
 
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* ComptonEvent = nullptr; 
+  MComptonEvent* ComptonEvent = nullptr;
   // ... loop over all events and save a count in the belonging bin ...
   while ((Event = GetNextEvent()) != 0) {
 
@@ -2219,14 +2220,14 @@ void MInterfaceMimrec::ARMGammaVsDistance()
       if (Event->GetType() == MPhysicalEvent::c_Compton) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
-        Hist->Fill(ComptonEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem())*c_Deg, 
+        Hist->Fill(ComptonEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem())*c_Deg,
                    (ComptonEvent->C2() - ComptonEvent->C1()).Mag());
-      } 
+      }
     }
 
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -2247,9 +2248,9 @@ void MInterfaceMimrec::ARMGammaVsDistance()
 //       }
 //     }
 //   }
-    
-  TCanvas* ARMvsComptonCanvas = 
-    new TCanvas("CanvasARMVSDistance", 
+
+  TCanvas* ARMvsComptonCanvas =
+    new TCanvas("CanvasARMVSDistance",
                 "Canvas ARM vs Distance", 800, 600);
   ARMvsComptonCanvas->cd();
   //Nicen(Hist, ARMvsComptonCanvas);
@@ -2262,19 +2263,19 @@ void MInterfaceMimrec::ARMGammaVsDistance()
 
 ////////////////////////////////////////////////////////////////////////////////
 
-  
+
 void MInterfaceMimrec::SignificanceMap()
 {
   // Display the angular resolution measurement for the gamma-ray as function of
   // the Compton scatter angle
-  // The ARM value for the scattered gamma-ray is the minimum angle between 
-  // the gamma-cone-surface and the line connecting the cone-apex with the 
+  // The ARM value for the scattered gamma-ray is the minimum angle between
+  // the gamma-cone-surface and the line connecting the cone-apex with the
   // (Test-)position
 
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   double XMin = m_Settings->GetGalLongitudeMin();
   double XMax = m_Settings->GetGalLongitudeMax();
   int NBinsXAngle = m_Settings->GetBinsGalLongitude();
@@ -2286,9 +2287,9 @@ void MInterfaceMimrec::SignificanceMap()
 
   double dX = (XMax-XMin)/((double)NBinsXAngle);
   double dY = (YMax-YMin)/((double)NBinsYAngle);
-  
+
   // Initalize the image size (x-axis)
-  TH2D* Hist_CenterCounts = new TH2D("SignificanceMap_C", "Counts at each point within ARM cut", 
+  TH2D* Hist_CenterCounts = new TH2D("SignificanceMap_C", "Counts at each point within ARM cut",
       NBinsXAngle, XMin, XMax,
       NBinsYAngle, YMin, YMax);
   Hist_CenterCounts->SetBit(kCanDelete);
@@ -2296,94 +2297,94 @@ void MInterfaceMimrec::SignificanceMap()
   Hist_CenterCounts->SetYTitle("Galactic Latitude [#circ]");
   // Other histograms for counting
   // Center point and K test points
-  TH2D* Hist_Center_0 = new TH2D("SignificanceMap_C_0", "Counts at center and 0 test points", 
+  TH2D* Hist_Center_0 = new TH2D("SignificanceMap_C_0", "Counts at center and 0 test points",
          NBinsXAngle, XMin, XMax,
          NBinsYAngle, YMin, YMax);
-  TH2D* Hist_Center_1 = new TH2D("SignificanceMap_C_1", "Counts at center and 1 test point", 
+  TH2D* Hist_Center_1 = new TH2D("SignificanceMap_C_1", "Counts at center and 1 test point",
          NBinsXAngle, XMin, XMax,
          NBinsYAngle, YMin, YMax);
-  TH2D* Hist_Center_2 = new TH2D("SignificanceMap_C_2", "Counts at center and 2 test points", 
+  TH2D* Hist_Center_2 = new TH2D("SignificanceMap_C_2", "Counts at center and 2 test points",
          NBinsXAngle, XMin, XMax,
          NBinsYAngle, YMin, YMax);
-  TH2D* Hist_Center_3 = new TH2D("SignificanceMap_C_3", "Counts at center and 3 test points", 
+  TH2D* Hist_Center_3 = new TH2D("SignificanceMap_C_3", "Counts at center and 3 test points",
          NBinsXAngle, XMin, XMax,
          NBinsYAngle, YMin, YMax);
-  TH2D* Hist_Center_4 = new TH2D("SignificanceMap_C_4", "Counts at center and 4 test points", 
+  TH2D* Hist_Center_4 = new TH2D("SignificanceMap_C_4", "Counts at center and 4 test points",
          NBinsXAngle, XMin, XMax,
          NBinsYAngle, YMin, YMax);
-  TH2D* Hist_Center_5 = new TH2D("SignificanceMap_C_5", "Counts at center and 5 test points", 
+  TH2D* Hist_Center_5 = new TH2D("SignificanceMap_C_5", "Counts at center and 5 test points",
          NBinsXAngle, XMin, XMax,
          NBinsYAngle, YMin, YMax);
-  TH2D* Hist_Center_6 = new TH2D("SignificanceMap_C_6", "Counts at center and 6 test points", 
+  TH2D* Hist_Center_6 = new TH2D("SignificanceMap_C_6", "Counts at center and 6 test points",
          NBinsXAngle, XMin, XMax,
          NBinsYAngle, YMin, YMax);
-  TH2D* Hist_Center_7 = new TH2D("SignificanceMap_C_7", "Counts at center and 7 test points", 
+  TH2D* Hist_Center_7 = new TH2D("SignificanceMap_C_7", "Counts at center and 7 test points",
          NBinsXAngle, XMin, XMax,
          NBinsYAngle, YMin, YMax);
-  TH2D* Hist_Center_8 = new TH2D("SignificanceMap_C_8", "Counts at center and 8 test points", 
+  TH2D* Hist_Center_8 = new TH2D("SignificanceMap_C_8", "Counts at center and 8 test points",
          NBinsXAngle, XMin, XMax,
          NBinsYAngle, YMin, YMax);
   // No center point, but at K test points
-  TH2D* Hist_NoCenter_1 = new TH2D("SignificanceMap_NC_1", "Counts at 1 test point, not at center", 
+  TH2D* Hist_NoCenter_1 = new TH2D("SignificanceMap_NC_1", "Counts at 1 test point, not at center",
            NBinsXAngle, XMin, XMax,
            NBinsYAngle, YMin, YMax);
-  TH2D* Hist_NoCenter_2 = new TH2D("SignificanceMap_NC_2", "Counts at 2 test points, not at center", 
+  TH2D* Hist_NoCenter_2 = new TH2D("SignificanceMap_NC_2", "Counts at 2 test points, not at center",
            NBinsXAngle, XMin, XMax,
            NBinsYAngle, YMin, YMax);
-  TH2D* Hist_NoCenter_3 = new TH2D("SignificanceMap_NC_3", "Counts at 3 test points, not at center", 
+  TH2D* Hist_NoCenter_3 = new TH2D("SignificanceMap_NC_3", "Counts at 3 test points, not at center",
            NBinsXAngle, XMin, XMax,
            NBinsYAngle, YMin, YMax);
-  TH2D* Hist_NoCenter_4 = new TH2D("SignificanceMap_NC_4", "Counts at 4 test points, not at center", 
+  TH2D* Hist_NoCenter_4 = new TH2D("SignificanceMap_NC_4", "Counts at 4 test points, not at center",
            NBinsXAngle, XMin, XMax,
            NBinsYAngle, YMin, YMax);
-  TH2D* Hist_NoCenter_5 = new TH2D("SignificanceMap_NC_5", "Counts at 5 test points, not at center", 
+  TH2D* Hist_NoCenter_5 = new TH2D("SignificanceMap_NC_5", "Counts at 5 test points, not at center",
            NBinsXAngle, XMin, XMax,
            NBinsYAngle, YMin, YMax);
-  TH2D* Hist_NoCenter_6 = new TH2D("SignificanceMap_NC_6", "Counts at 6 test points, not at center", 
+  TH2D* Hist_NoCenter_6 = new TH2D("SignificanceMap_NC_6", "Counts at 6 test points, not at center",
            NBinsXAngle, XMin, XMax,
            NBinsYAngle, YMin, YMax);
-  TH2D* Hist_NoCenter_7 = new TH2D("SignificanceMap_NC_7", "Counts at 7 test points, not at center", 
+  TH2D* Hist_NoCenter_7 = new TH2D("SignificanceMap_NC_7", "Counts at 7 test points, not at center",
            NBinsXAngle, XMin, XMax,
            NBinsYAngle, YMin, YMax);
-  TH2D* Hist_NoCenter_8 = new TH2D("SignificanceMap_NC_8", "Counts at 8 test points, not at center", 
+  TH2D* Hist_NoCenter_8 = new TH2D("SignificanceMap_NC_8", "Counts at 8 test points, not at center",
            NBinsXAngle, XMin, XMax,
            NBinsYAngle, YMin, YMax);
   // Counts at each test point
-  TH2D* Hist_Counts1 = new TH2D("SignificanceMap_Counts1", "Counts at test point 1", 
+  TH2D* Hist_Counts1 = new TH2D("SignificanceMap_Counts1", "Counts at test point 1",
            NBinsXAngle, XMin, XMax,
            NBinsYAngle, YMin, YMax);
-  TH2D* Hist_Counts2 = new TH2D("SignificanceMap_Counts2", "Counts at test point 2", 
+  TH2D* Hist_Counts2 = new TH2D("SignificanceMap_Counts2", "Counts at test point 2",
            NBinsXAngle, XMin, XMax,
            NBinsYAngle, YMin, YMax);
-  TH2D* Hist_Counts3 = new TH2D("SignificanceMap_Counts3", "Counts at test point 3", 
+  TH2D* Hist_Counts3 = new TH2D("SignificanceMap_Counts3", "Counts at test point 3",
            NBinsXAngle, XMin, XMax,
            NBinsYAngle, YMin, YMax);
-  TH2D* Hist_Counts4 = new TH2D("SignificanceMap_Counts4", "Counts at test point 4", 
+  TH2D* Hist_Counts4 = new TH2D("SignificanceMap_Counts4", "Counts at test point 4",
            NBinsXAngle, XMin, XMax,
            NBinsYAngle, YMin, YMax);
-  TH2D* Hist_Counts5 = new TH2D("SignificanceMap_Counts5", "Counts at test point 5", 
+  TH2D* Hist_Counts5 = new TH2D("SignificanceMap_Counts5", "Counts at test point 5",
            NBinsXAngle, XMin, XMax,
            NBinsYAngle, YMin, YMax);
-  TH2D* Hist_Counts6 = new TH2D("SignificanceMap_Counts6", "Counts at test point 6", 
+  TH2D* Hist_Counts6 = new TH2D("SignificanceMap_Counts6", "Counts at test point 6",
            NBinsXAngle, XMin, XMax,
            NBinsYAngle, YMin, YMax);
-  TH2D* Hist_Counts7 = new TH2D("SignificanceMap_Counts7", "Counts at test point 7", 
+  TH2D* Hist_Counts7 = new TH2D("SignificanceMap_Counts7", "Counts at test point 7",
            NBinsXAngle, XMin, XMax,
            NBinsYAngle, YMin, YMax);
-  TH2D* Hist_Counts8 = new TH2D("SignificanceMap_Counts8", "Counts at test point 8", 
+  TH2D* Hist_Counts8 = new TH2D("SignificanceMap_Counts8", "Counts at test point 8",
            NBinsXAngle, XMin, XMax,
            NBinsYAngle, YMin, YMax);
   // Histograms for SNR calculation
-  TH2D* Hist_Average = new TH2D("SignificanceMap_Average", "Average", 
+  TH2D* Hist_Average = new TH2D("SignificanceMap_Average", "Average",
            NBinsXAngle, XMin, XMax,
            NBinsYAngle, YMin, YMax);
-  TH2D* Hist_Excess = new TH2D("SignificanceMap_Excess", "Excess", 
+  TH2D* Hist_Excess = new TH2D("SignificanceMap_Excess", "Excess",
            NBinsXAngle, XMin, XMax,
            NBinsYAngle, YMin, YMax);
-  TH2D* Hist_Sigma = new TH2D("SignificanceMap_Sigma", "Sigma", 
+  TH2D* Hist_Sigma = new TH2D("SignificanceMap_Sigma", "Sigma",
            NBinsXAngle, XMin, XMax,
            NBinsYAngle, YMin, YMax);
-  TH2D* Hist_SNR = new TH2D("SignificanceMap_SNR", "Signal-to-noise ratio", 
+  TH2D* Hist_SNR = new TH2D("SignificanceMap_SNR", "Signal-to-noise ratio",
           NBinsXAngle, XMin, XMax,
           NBinsYAngle, YMin, YMax);
 
@@ -2395,10 +2396,10 @@ void MInterfaceMimrec::SignificanceMap()
   mout << "  Radius:   " << Radius << endl;
 
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* ComptonEvent = nullptr; 
+  MComptonEvent* ComptonEvent = nullptr;
   // ... loop over all events and save a count in the belonging bin ...
   while ((Event = GetNextEvent()) != 0) {
-    
+
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
       if (Event->GetType() == MPhysicalEvent::c_Compton) {
@@ -2520,12 +2521,12 @@ void MInterfaceMimrec::SignificanceMap()
             }
           }
         }
-      } 
+      }
     }
-    
+
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -2625,8 +2626,8 @@ void MInterfaceMimrec::SignificanceMap()
 
   /*
   // Counts consistent with central bin
-  TCanvas* Sig_CenterCounts_Canvas = 
-    new TCanvas("SignificanceMap", 
+  TCanvas* Sig_CenterCounts_Canvas =
+    new TCanvas("SignificanceMap",
                 "Counts at each point within ARM cut", 800, 600);
   Sig_CenterCounts_Canvas->cd();
   // do a trick to reverse the x axis
@@ -2639,8 +2640,8 @@ void MInterfaceMimrec::SignificanceMap()
   Sig_CenterCounts_Canvas->Update();
 
   // Counts consistent with test point 1
-  TCanvas* Sig_Counts1_Canvas = 
-    new TCanvas("SignificanceMap_TestPoint1", 
+  TCanvas* Sig_Counts1_Canvas =
+    new TCanvas("SignificanceMap_TestPoint1",
                 "Counts at test point 1 within ARM cut", 800, 600);
   Sig_Counts1_Canvas->cd();
   // do a trick to reverse the x axis
@@ -2653,8 +2654,8 @@ void MInterfaceMimrec::SignificanceMap()
   Sig_Counts1_Canvas->Update();
 
   // Counts consistent with test point 2
-  TCanvas* Sig_Counts2_Canvas = 
-    new TCanvas("SignificanceMap_TestPoint2", 
+  TCanvas* Sig_Counts2_Canvas =
+    new TCanvas("SignificanceMap_TestPoint2",
                 "Counts at test point 2 within ARM cut", 800, 600);
   Sig_Counts2_Canvas->cd();
   // do a trick to reverse the x axis
@@ -2667,8 +2668,8 @@ void MInterfaceMimrec::SignificanceMap()
   Sig_Counts2_Canvas->Update();
 
   // Counts consistent with test point 3
-  TCanvas* Sig_Counts3_Canvas = 
-    new TCanvas("SignificanceMap_TestPoint3", 
+  TCanvas* Sig_Counts3_Canvas =
+    new TCanvas("SignificanceMap_TestPoint3",
                 "Counts at test point 3 within ARM cut", 800, 600);
   Sig_Counts3_Canvas->cd();
   // do a trick to reverse the x axis
@@ -2681,8 +2682,8 @@ void MInterfaceMimrec::SignificanceMap()
   Sig_Counts3_Canvas->Update();
 
   // Counts consistent with test point 4
-  TCanvas* Sig_Counts4_Canvas = 
-    new TCanvas("SignificanceMap_TestPoint4", 
+  TCanvas* Sig_Counts4_Canvas =
+    new TCanvas("SignificanceMap_TestPoint4",
                 "Counts at test point 4 within ARM cut", 800, 600);
   Sig_Counts4_Canvas->cd();
   // do a trick to reverse the x axis
@@ -2695,8 +2696,8 @@ void MInterfaceMimrec::SignificanceMap()
   Sig_Counts4_Canvas->Update();
 
   // Counts consistent with test point 5
-  TCanvas* Sig_Counts5_Canvas = 
-    new TCanvas("SignificanceMap_TestPoint5", 
+  TCanvas* Sig_Counts5_Canvas =
+    new TCanvas("SignificanceMap_TestPoint5",
                 "Counts at test point 5 within ARM cut", 800, 600);
   Sig_Counts5_Canvas->cd();
   // do a trick to reverse the x axis
@@ -2709,8 +2710,8 @@ void MInterfaceMimrec::SignificanceMap()
   Sig_Counts5_Canvas->Update();
 
   // Counts consistent with test point 6
-  TCanvas* Sig_Counts6_Canvas = 
-    new TCanvas("SignificanceMap_TestPoint6", 
+  TCanvas* Sig_Counts6_Canvas =
+    new TCanvas("SignificanceMap_TestPoint6",
                 "Counts at test point 6 within ARM cut", 800, 600);
   Sig_Counts6_Canvas->cd();
   // do a trick to reverse the x axis
@@ -2723,8 +2724,8 @@ void MInterfaceMimrec::SignificanceMap()
   Sig_Counts6_Canvas->Update();
 
   // Counts consistent with test point 7
-  TCanvas* Sig_Counts7_Canvas = 
-    new TCanvas("SignificanceMap_TestPoint7", 
+  TCanvas* Sig_Counts7_Canvas =
+    new TCanvas("SignificanceMap_TestPoint7",
                 "Counts at test point 7 within ARM cut", 800, 600);
   Sig_Counts7_Canvas->cd();
   // do a trick to reverse the x axis
@@ -2737,8 +2738,8 @@ void MInterfaceMimrec::SignificanceMap()
   Sig_Counts7_Canvas->Update();
 
   // Counts consistent with test point 8
-  TCanvas* Sig_Counts8_Canvas = 
-    new TCanvas("SignificanceMap_TestPoint8", 
+  TCanvas* Sig_Counts8_Canvas =
+    new TCanvas("SignificanceMap_TestPoint8",
                 "Counts at test point 8 within ARM cut", 800, 600);
   Sig_Counts8_Canvas->cd();
   // do a trick to reverse the x axis
@@ -2753,8 +2754,8 @@ void MInterfaceMimrec::SignificanceMap()
   mout << "Max of 8:             " << Hist_Counts8->GetMaximum() << endl;
 
   // Average counts
-  TCanvas* Sig_Average_Canvas = 
-    new TCanvas("SignificanceMap_Average", 
+  TCanvas* Sig_Average_Canvas =
+    new TCanvas("SignificanceMap_Average",
                 "Background estimate (average of four test points)", 800, 600);
   Sig_Average_Canvas->cd();
   // do a trick to reverse the x axis
@@ -2769,8 +2770,8 @@ void MInterfaceMimrec::SignificanceMap()
   Sig_Average_Canvas->Update();
 
   // Excess counts
-  TCanvas* Sig_Excess_Canvas = 
-    new TCanvas("SignificanceMap_Excess", 
+  TCanvas* Sig_Excess_Canvas =
+    new TCanvas("SignificanceMap_Excess",
                 "Excess counts above background", 800, 600);
   Sig_Excess_Canvas->cd();
   // do a trick to reverse the x axis
@@ -2779,10 +2780,10 @@ void MInterfaceMimrec::SignificanceMap()
   Hist_Excess->Draw("SURF2Z");
   //Hist_Excess->Draw("COLZ");
   Sig_Excess_Canvas->Update();
-  
+
   // SNR
-  TCanvas* Sig_SNR_Canvas = 
-    new TCanvas("SignificanceMap_SNR", 
+  TCanvas* Sig_SNR_Canvas =
+    new TCanvas("SignificanceMap_SNR",
                 "Signal-to-noise ratio", 800, 600);
   Sig_SNR_Canvas->cd();
   // do a trick to reverse the x axis
@@ -2792,7 +2793,7 @@ void MInterfaceMimrec::SignificanceMap()
   //Hist_SNR->Draw("COLZ");
   Sig_SNR_Canvas->Update();
   */
-  
+
   // Convert to MImage*
   double* Array = new double[NBinsXAngle*NBinsYAngle];
   for (int x = 0; x < NBinsXAngle; ++x) {
@@ -2801,55 +2802,55 @@ void MInterfaceMimrec::SignificanceMap()
     }
   }
 
-  MImageGalactic* Image = new MImageGalactic("Significance map", 
-                               Array, 
-                               "Longitude [deg]", 
+  MImageGalactic* Image = new MImageGalactic("Significance map",
+                               Array,
+                               "Longitude [deg]",
                                XMin,
-                               XMax, 
+                               XMax,
                                NBinsXAngle,
-                               "Latitude [deg]", 
-                               YMin, 
-                               YMax, 
-                               NBinsYAngle, 
+                               "Latitude [deg]",
+                               YMin,
+                               YMax,
+                               NBinsYAngle,
                                "Significance",
-                               m_Settings->GetImagePalette(), 
+                               m_Settings->GetImagePalette(),
                                m_Settings->GetImageDrawMode(),
                                m_Settings->GetImageSourceCatalog());
   Image->Display();
-  
+
   delete [] Array;
   // Image: memory leak, but who cares...
-  
+
   return;
 }
 
 
 ////////////////////////////////////////////////////////////////////////////////
 
-  
+
 void MInterfaceMimrec::SPDElectronVsCompton()
 {
   // Display the angular resolution measurement for the gamma-ray as function of
   // the Compton scatter angle
-  // The ARM value for the scattered gamma-ray is the minimum angle between 
-  // the gamma-cone-surface and the line connecting the cone-apex with the 
+  // The ARM value for the scattered gamma-ray is the minimum angle between
+  // the gamma-cone-surface and the line connecting the cone-apex with the
   // (Test-)position
 
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   int NBins = m_Settings->GetHistBinsARMElectron();
   double Disk = m_Settings->GetTPDistanceLong();
   MVector TestPosition = GetTestPosition();
-  
+
   // Initalize the image size (x-axis)
   //BinWidth = 2*Disk/NBins;
   int NBinsArm = NBins;
   int NBinsAngle = NBins/3;
-  TH2D* Hist = new TH2D("SPD vs. Compton Scatter Angle", "SPD vs. Compton Scatter Angle", 
-                        NBinsArm, 0, Disk, NBinsAngle, 
-                        m_Settings->GetComptonAngleRangeMin(), 
+  TH2D* Hist = new TH2D("SPD vs. Compton Scatter Angle", "SPD vs. Compton Scatter Angle",
+                        NBinsArm, 0, Disk, NBinsAngle,
+                        m_Settings->GetComptonAngleRangeMin(),
                         m_Settings->GetComptonAngleRangeMax());
   Hist->SetBit(kCanDelete);
   Hist->SetXTitle("SPD [#circ]");
@@ -2857,7 +2858,7 @@ void MInterfaceMimrec::SPDElectronVsCompton()
 
 
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* ComptonEvent = nullptr; 
+  MComptonEvent* ComptonEvent = nullptr;
   // ... loop over all events and save a count in the belonging bin ...
   while ((Event = GetNextEvent()) != 0) {
 
@@ -2866,14 +2867,14 @@ void MInterfaceMimrec::SPDElectronVsCompton()
       if (Event->GetType() == MPhysicalEvent::c_Compton) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
-        Hist->Fill(ComptonEvent->GetSPDElectron(TestPosition)*c_Deg, 
+        Hist->Fill(ComptonEvent->GetSPDElectron(TestPosition)*c_Deg,
                    ComptonEvent->Phi()*c_Deg);
-      } 
+      }
     }
 
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -2882,7 +2883,7 @@ void MInterfaceMimrec::SPDElectronVsCompton()
     return;
   }
 
-  
+
 
 
   // Normalize:
@@ -2897,7 +2898,7 @@ void MInterfaceMimrec::SPDElectronVsCompton()
       }
     }
   }
-    
+
   // Fill empty bins with something extremely small:
   mimp<<"HACK!"<<endl;
   for (int by = 1; by <= Hist->GetNbinsY(); ++by) {
@@ -2908,8 +2909,8 @@ void MInterfaceMimrec::SPDElectronVsCompton()
     }
   }
 
-  TCanvas* ARMvsComptonCanvas = 
-    new TCanvas("Canvas ARM vs Compton", 
+  TCanvas* ARMvsComptonCanvas =
+    new TCanvas("Canvas ARM vs Compton",
                 "Canvas ARM vs Compton", 800, 600);
   ARMvsComptonCanvas->cd();
   //Nicen(Hist, ARMvsComptonCanvas);
@@ -2933,7 +2934,7 @@ void MInterfaceMimrec::SPDElectronVsCompton()
 
   for (unsigned int i = 1; i < X.size(); ++i) {
     if (X[i-1] != 0 && X[i] != 0) {
-      TLine* line = new TLine(X[i-1], Hist->GetYaxis()->GetBinCenter(i), 
+      TLine* line = new TLine(X[i-1], Hist->GetYaxis()->GetBinCenter(i),
                               X[i], Hist->GetYaxis()->GetBinCenter(i+1));
       line->SetLineWidth(3);
       line->Draw();
@@ -2952,14 +2953,14 @@ void MInterfaceMimrec::ComptonProbabilityWithARMSelection()
 {
   // Display the angular resolution measurement for the gamma-ray as function of
   // the Compton scatter angle
-  // The ARM value for the scattered gamma-ray is the minimum angle between 
-  // the gamma-cone-surface and the line connecting the cone-apex with the 
+  // The ARM value for the scattered gamma-ray is the minimum angle between
+  // the gamma-cone-surface and the line connecting the cone-apex with the
   // (Test-)position
 
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-    
+
   double Disk = m_Settings->GetTPDistanceTrans();
   MVector TestPosition = GetTestPosition();
 
@@ -2969,8 +2970,8 @@ void MInterfaceMimrec::ComptonProbabilityWithARMSelection()
 
 
 
-  TH1D* HistGood = new TH1D("Compton Quality Factor in and outside ARM Selection", 
-                            "Compton Quality Factor in and outside ARM Selection", 
+  TH1D* HistGood = new TH1D("Compton Quality Factor in and outside ARM Selection",
+                            "Compton Quality Factor in and outside ARM Selection",
                             xNBins, xBins);
   HistGood->SetBit(kCanDelete);
   HistGood->SetXTitle("Compton Quality Factor");
@@ -2978,8 +2979,8 @@ void MInterfaceMimrec::ComptonProbabilityWithARMSelection()
   HistGood->SetFillColor(8);
   //HistGood->SetMinimum(0);
 
-  TH1D* HistBad = new TH1D("Compton Quality Factor inside (green) and outside (red) ARM Selection", 
-                           "Compton Quality Factor inside (green) and outside (red) ARM Selection", 
+  TH1D* HistBad = new TH1D("Compton Quality Factor inside (green) and outside (red) ARM Selection",
+                           "Compton Quality Factor inside (green) and outside (red) ARM Selection",
                            xNBins, xBins);
   HistBad->SetBit(kCanDelete);
   HistBad->SetXTitle("Compton Quality Factor");
@@ -2990,7 +2991,7 @@ void MInterfaceMimrec::ComptonProbabilityWithARMSelection()
 
   double ArmValue;
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* ComptonEvent = nullptr; 
+  MComptonEvent* ComptonEvent = nullptr;
   // ... loop over all events and save a count in the belonging bin ...
   while ((Event = GetNextEvent()) != 0) {
 
@@ -3005,12 +3006,12 @@ void MInterfaceMimrec::ComptonProbabilityWithARMSelection()
         } else {
           HistBad->Fill(ComptonEvent->ComptonQualityFactor1());
         }
-      } 
+      }
     }
 
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -3019,16 +3020,16 @@ void MInterfaceMimrec::ComptonProbabilityWithARMSelection()
     return;
   }
 
-    
-  TCanvas* CanvasHistGood = 
+
+  TCanvas* CanvasHistGood =
     new TCanvas("Compton Quality Factor in and outside ARM Selection",
                 "Compton Quality Factor in and outside ARM Selection", 800, 600);
   CanvasHistGood->cd();
   HistBad->Draw();
   HistGood->Draw("SAME");
-  CanvasHistGood->SetLogx();  
+  CanvasHistGood->SetLogx();
   CanvasHistGood->Update();
-    
+
   delete [] xBins;
 
   return;
@@ -3037,26 +3038,25 @@ void MInterfaceMimrec::ComptonProbabilityWithARMSelection()
 
 ////////////////////////////////////////////////////////////////////////////////
 
-  
+
 void MInterfaceMimrec::ARMGammaVsComptonProbability()
 {
   // Display the angular resolution measurement for the gamma-ray as function of
   // the Compton scatter angle
-  // The ARM value for the scattered gamma-ray is the minimum angle between 
-  // the gamma-cone-surface and the line connecting the cone-apex with the 
+  // The ARM value for the scattered gamma-ray is the minimum angle between
+  // the gamma-cone-surface and the line connecting the cone-apex with the
   // (Test-)position
 
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   int NBins = m_Settings->GetHistBinsARMGamma();
   double Disk = m_Settings->GetTPDistanceTrans();
   MVector TestPosition = GetTestPosition();
 
-
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* ComptonEvent = nullptr; 
+  MComptonEvent* ComptonEvent = nullptr;
   // ... loop over all events and save a count in the belonging bin ...
   vector<double> ARMValues;
   vector<double> CQFs;
@@ -3069,46 +3069,46 @@ void MInterfaceMimrec::ARMGammaVsComptonProbability()
 
         ARMValues.push_back(ComptonEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem())*c_Deg);
         CQFs.push_back(ComptonEvent->ComptonQualityFactor1());
-      } 
+      }
     }
 
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
   if (ARMValues.size() == 0) {
     merr<<"No events passed the event selections or file is empty!"<<endl;
-    return; 
+    return;
   }
-  
+
   // Initialize the image size (x-axis)
   double CQFMax = *max_element(CQFs.begin(), CQFs.end());
   double CQFMin = *min_element(CQFs.begin(), CQFs.end());
-  
+
   if (CQFMax > m_Settings->GetComptonQualityFactorRangeMax()) {
     CQFMax = m_Settings->GetComptonQualityFactorRangeMax();
   }
   if (CQFMin < m_Settings->GetComptonQualityFactorRangeMin()) {
     CQFMin = m_Settings->GetComptonQualityFactorRangeMin();
   }
-  
-  TH2D* Hist = new TH2D("ARM vs. Compton Quality Factor", "ARM vs. Compton Quality Factor", 
+
+  TH2D* Hist = new TH2D("ARM vs. Compton Quality Factor", "ARM vs. Compton Quality Factor",
                         NBins, -Disk, +Disk, NBins, CQFMin, CQFMax);
   Hist->SetBit(kCanDelete);
   Hist->SetXTitle("ARM [#circ]");
-  Hist->SetYTitle("Compton quality factor");  
-  
+  Hist->SetYTitle("Compton quality factor");
+
   for (unsigned int i = 0; i < ARMValues.size(); ++i) {
     Hist->Fill(ARMValues[i], CQFs[i]);
   }
 
-    
-  TCanvas* ARMvsComptonCanvas = 
+  TCanvas* ARMvsComptonCanvas =
     new TCanvas("Canvas ARM vs Compton quality factor",
                 "Canvas ARM vs Compton quality factor", 800, 600);
   ARMvsComptonCanvas->cd();
+
   Hist->Draw("COLZ");
   ARMvsComptonCanvas->Update();
 
@@ -3123,14 +3123,14 @@ void MInterfaceMimrec::ARMGammaVsClusteringProbability()
 {
   // Display the angular resolution measurement for the gamma-ray as function of
   // the Compton scatter angle
-  // The ARM value for the scattered gamma-ray is the minimum angle between 
-  // the gamma-cone-surface and the line connecting the cone-apex with the 
+  // The ARM value for the scattered gamma-ray is the minimum angle between
+  // the gamma-cone-surface and the line connecting the cone-apex with the
   // (Test-)position
 
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   int NBins = m_Settings->GetHistBinsARMGamma();
   double Disk = m_Settings->GetTPDistanceTrans();
   MVector TestPosition = GetTestPosition();
@@ -3144,7 +3144,7 @@ void MInterfaceMimrec::ARMGammaVsClusteringProbability()
   double* x2Bins = CreateAxisBins(m_Settings->GetClusteringQualityFactorRangeMin(), m_Settings->GetClusteringQualityFactorRangeMax(), x2NBins, logx2);
 
 
-  TH2D* Hist = new TH2D("ARMVsClusteringQualityFactor", "ARM vs. Clustering Quality Factor", 
+  TH2D* Hist = new TH2D("ARMVsClusteringQualityFactor", "ARM vs. Clustering Quality Factor",
                         x1NBins, x1Bins, x2NBins, x2Bins);
   Hist->SetBit(kCanDelete);
   Hist->SetXTitle("ARM [#circ]");
@@ -3152,7 +3152,7 @@ void MInterfaceMimrec::ARMGammaVsClusteringProbability()
 
 
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* ComptonEvent = nullptr; 
+  MComptonEvent* ComptonEvent = nullptr;
   // ... loop over all events and save a count in the belonging bin ...
   while ((Event = GetNextEvent()) != 0) {
 
@@ -3161,14 +3161,14 @@ void MInterfaceMimrec::ARMGammaVsClusteringProbability()
       if (Event->GetType() == MPhysicalEvent::c_Compton) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
-        Hist->Fill(ComptonEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem())*c_Deg, 
+        Hist->Fill(ComptonEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem())*c_Deg,
                    ComptonEvent->ClusteringQualityFactor());
-      } 
+      }
     }
 
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -3177,12 +3177,12 @@ void MInterfaceMimrec::ARMGammaVsClusteringProbability()
     return;
   }
 
-    
-  TCanvas* ARMvsClusteringCanvas = 
+
+  TCanvas* ARMvsClusteringCanvas =
     new TCanvas("CanvasARMVsClusteringProbability",
                 "Canvas ARM vs Clustering Probability", 800, 600);
   ARMvsClusteringCanvas->cd();
-  ARMvsClusteringCanvas->SetLogy();  
+  ARMvsClusteringCanvas->SetLogy();
   //Nicen(Hist, ARMvsClusteringCanvas);
   Hist->Draw("COLZ");
   ARMvsClusteringCanvas->Update();
@@ -3196,23 +3196,23 @@ void MInterfaceMimrec::ARMGammaVsClusteringProbability()
 
 ////////////////////////////////////////////////////////////////////////////////
 
-  
+
 void MInterfaceMimrec::SPDVsTrackQualityFactor()
 {
   // Display the angular resolution measurement for the gamma-ray as function of
   // the Compton scatter angle
-  // The ARM value for the scattered gamma-ray is the minimum angle between 
-  // the gamma-cone-surface and the line connecting the cone-apex with the 
+  // The ARM value for the scattered gamma-ray is the minimum angle between
+  // the gamma-cone-surface and the line connecting the cone-apex with the
   // (Test-)position
 
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   int NBins = m_Settings->GetHistBinsARMElectron();
   double Disk = m_Settings->GetTPDistanceLong();
   MVector TestPosition = GetTestPosition();
-  
+
   // Initalize the image size (x-axis)
   int xNBins = NBins;
   double* xBins = CreateAxisBins(0, +Disk, xNBins, false);
@@ -3228,7 +3228,7 @@ void MInterfaceMimrec::SPDVsTrackQualityFactor()
 
 
   // Create the histogram
-  TH2D* Hist = new TH2D("SPD vs. Track Quality Factor", "SPD vs. Track Quality Factor", 
+  TH2D* Hist = new TH2D("SPD vs. Track Quality Factor", "SPD vs. Track Quality Factor",
                         xNBins, xBins, yNBins, yBins);
   Hist->SetBit(kCanDelete);
   Hist->SetXTitle("SPD [#circ]");
@@ -3239,7 +3239,7 @@ void MInterfaceMimrec::SPDVsTrackQualityFactor()
   int NQFZero = 0;
 
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* ComptonEvent = nullptr; 
+  MComptonEvent* ComptonEvent = nullptr;
   // ... loop over all events and save a count in the belonging bin ...
   while ((Event = GetNextEvent()) != 0) {
 
@@ -3248,15 +3248,15 @@ void MInterfaceMimrec::SPDVsTrackQualityFactor()
       if (Event->GetType() == MPhysicalEvent::c_Compton) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
-        Hist->Fill(ComptonEvent->GetSPDElectron(TestPosition)*c_Deg, 
+        Hist->Fill(ComptonEvent->GetSPDElectron(TestPosition)*c_Deg,
                    ComptonEvent->TrackQualityFactor1());
         if (ComptonEvent->TrackQualityFactor1() == 0) NQFZero++;
-      } 
+      }
     }
 
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -3266,14 +3266,14 @@ void MInterfaceMimrec::SPDVsTrackQualityFactor()
     return;
   }
 
-    
-  TCanvas* Canvas = 
+
+  TCanvas* Canvas =
     new TCanvas("SPDVsTrackQualityFactorCanvas",
                 "SPD vs Track Quality Factor Canvas", 800, 600);
   Canvas->cd();
   if (yLog == true) {
-    Canvas->SetLogy(); 
-  } 
+    Canvas->SetLogy();
+  }
   Hist->Draw("COLZ");
   Canvas->Update();
 
@@ -3286,26 +3286,26 @@ void MInterfaceMimrec::SPDVsTrackQualityFactor()
 
 ////////////////////////////////////////////////////////////////////////////////
 
-  
+
 void MInterfaceMimrec::SPDVsTotalScatterAngleDeviation()
 {
   // Display the angular resolution measurement for the gamma-ray as function of
   // the Compton scatter angle
-  // The ARM value for the scattered gamma-ray is the minimum angle between 
-  // the gamma-cone-surface and the line connecting the cone-apex with the 
+  // The ARM value for the scattered gamma-ray is the minimum angle between
+  // the gamma-cone-surface and the line connecting the cone-apex with the
   // (Test-)position
 
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   int NBins = m_Settings->GetHistBinsARMElectron();
   double Disk = m_Settings->GetTPDistanceLong();
   MVector TestPosition = GetTestPosition();
-  
 
-  TH2D* Hist = new TH2D("SPD vs. Total Scatter Angle Deviation", 
-                        "SPD vs. Total Scatter Angle Deviation", 
+
+  TH2D* Hist = new TH2D("SPD vs. Total Scatter Angle Deviation",
+                        "SPD vs. Total Scatter Angle Deviation",
                         NBins, 0, Disk, NBins, 0, m_Settings->GetThetaDeviationMax());
   Hist->SetBit(kCanDelete);
   Hist->SetXTitle("SPD [#circ]");
@@ -3314,7 +3314,7 @@ void MInterfaceMimrec::SPDVsTotalScatterAngleDeviation()
 
 
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* ComptonEvent = nullptr; 
+  MComptonEvent* ComptonEvent = nullptr;
   // ... loop over all events and save a count in the belonging bin ...
   while ((Event = GetNextEvent()) != 0) {
 
@@ -3323,14 +3323,14 @@ void MInterfaceMimrec::SPDVsTotalScatterAngleDeviation()
       if (Event->GetType() == MPhysicalEvent::c_Compton) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
-        Hist->Fill(ComptonEvent->GetSPDElectron(TestPosition)*c_Deg, 
+        Hist->Fill(ComptonEvent->GetSPDElectron(TestPosition)*c_Deg,
                    ComptonEvent->DeltaTheta()*c_Deg);
-      } 
+      }
     }
 
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -3339,8 +3339,8 @@ void MInterfaceMimrec::SPDVsTotalScatterAngleDeviation()
     return;
   }
 
-    
-  TCanvas* Canvas = 
+
+  TCanvas* Canvas =
     new TCanvas("SPDVsTotalScatterAngleDeviationCanvas",
                 "SPD vs Total Scatter Angle Deviation Canvas", 800, 600);
   Canvas->cd();
@@ -3353,23 +3353,23 @@ void MInterfaceMimrec::SPDVsTotalScatterAngleDeviation()
 
 ////////////////////////////////////////////////////////////////////////////////
 
-  
+
 void MInterfaceMimrec::EnergyVsComptonProbability()
 {
   // Display the angular resolution measurement for the gamma-ray as function of
   // the Compton scatter angle
-  // The ARM value for the scattered gamma-ray is the minimum angle between 
-  // the gamma-cone-surface and the line connecting the cone-apex with the 
+  // The ARM value for the scattered gamma-ray is the minimum angle between
+  // the gamma-cone-surface and the line connecting the cone-apex with the
   // (Test-)position
 
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   double x, y, z = 10000000.0;
-  
+
   // Get the data of the ARM-"Test"-Position
-  if (m_Settings->GetCoordinateSystem() == MCoordinateSystem::c_Spheric) {  // spheric 
+  if (m_Settings->GetCoordinateSystem() == MCoordinateSystem::c_Spheric) {  // spheric
     x = m_Settings->GetTPTheta();
     y = m_Settings->GetTPPhi();
 
@@ -3386,7 +3386,7 @@ void MInterfaceMimrec::EnergyVsComptonProbability()
     merr<<"Unknown coordinate system ID: "<<m_Settings->GetCoordinateSystem()<<fatal;
   }
 
-  
+
   // Initialize the histogram size
   int x1NBins = 50;
   double* x1Bins = CreateAxisBins(GetTotalEnergyMin(), GetTotalEnergyMax(), x1NBins, false);
@@ -3396,7 +3396,7 @@ void MInterfaceMimrec::EnergyVsComptonProbability()
 
 
   // Create the histogram
-  TH2D* Hist = new TH2D("Energy vs. Compton Quality Factor", "Energy vs. Compton Quality Factor", 
+  TH2D* Hist = new TH2D("Energy vs. Compton Quality Factor", "Energy vs. Compton Quality Factor",
                         x1NBins, x1Bins, x2NBins, x2Bins);
   Hist->SetBit(kCanDelete);
   Hist->SetXTitle("Energy [keV]");
@@ -3404,7 +3404,7 @@ void MInterfaceMimrec::EnergyVsComptonProbability()
 
 
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* ComptonEvent = nullptr; 
+  MComptonEvent* ComptonEvent = nullptr;
   // ... loop over all events and save a count in the belonging bin ...
   while ((Event = GetNextEvent()) != 0) {
 
@@ -3413,14 +3413,14 @@ void MInterfaceMimrec::EnergyVsComptonProbability()
       if (Event->GetType() == MPhysicalEvent::c_Compton) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
-        Hist->Fill(ComptonEvent->Ei(), 
+        Hist->Fill(ComptonEvent->Ei(),
                    ComptonEvent->ComptonQualityFactor1());
-      } 
+      }
     }
 
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -3429,12 +3429,12 @@ void MInterfaceMimrec::EnergyVsComptonProbability()
     return;
   }
 
-    
-  TCanvas* EnergyvsComptonCanvas = 
+
+  TCanvas* EnergyvsComptonCanvas =
     new TCanvas("Canvas Energy vs Compton Probability",
                 "Canvas Energy vs Compton Probability", 800, 600);
   EnergyvsComptonCanvas->cd();
-  EnergyvsComptonCanvas->SetLogy();  
+  EnergyvsComptonCanvas->SetLogy();
   //Nicen(Hist, EnergyvsComptonCanvas);
   Hist->Draw("COLZ");
   EnergyvsComptonCanvas->Update();
@@ -3448,7 +3448,7 @@ void MInterfaceMimrec::EnergyVsComptonProbability()
 
 ////////////////////////////////////////////////////////////////////////////////
 
-  
+
 void MInterfaceMimrec::ComptonSequenceLengthVsComptonProbability()
 {
   // Compton Sequence Length vs. Compton Quality Factor
@@ -3456,9 +3456,9 @@ void MInterfaceMimrec::ComptonSequenceLengthVsComptonProbability()
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   unsigned int MaxSequenceLength = 3;
-  
+
   // Initialize the image size
   int xNBins = 100;
   double* xBins = CreateAxisBins(0.5, 100.5, xNBins, false);
@@ -3467,8 +3467,8 @@ void MInterfaceMimrec::ComptonSequenceLengthVsComptonProbability()
   double* yBins = CreateAxisBins(m_Settings->GetComptonQualityFactorRangeMin(), m_Settings->GetComptonQualityFactorRangeMax(), yNBins, true);
 
 
-  TH2D* Hist = new TH2D("ComptonSequenceLengthVsComptonQualityFactor", 
-                        "Compton Sequence Length vs. Compton Quality Factor", 
+  TH2D* Hist = new TH2D("ComptonSequenceLengthVsComptonQualityFactor",
+                        "Compton Sequence Length vs. Compton Quality Factor",
                         xNBins, xBins, yNBins, yBins);
   Hist->SetBit(kCanDelete);
   Hist->SetContour(50);
@@ -3477,7 +3477,7 @@ void MInterfaceMimrec::ComptonSequenceLengthVsComptonProbability()
 
 
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* Compton = 0; 
+  MComptonEvent* Compton = 0;
   // ... loop over all events and save a count in the belonging bin ...
   while ((Event = GetNextEvent()) != 0) {
 
@@ -3488,12 +3488,12 @@ void MInterfaceMimrec::ComptonSequenceLengthVsComptonProbability()
 
         if (Compton->SequenceLength() > MaxSequenceLength) MaxSequenceLength = Compton->SequenceLength();
         Hist->Fill(Compton->SequenceLength(), Compton->ComptonQualityFactor1());
-      } 
+      }
     }
 
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -3502,12 +3502,12 @@ void MInterfaceMimrec::ComptonSequenceLengthVsComptonProbability()
     return;
   }
 
-    
-  TCanvas* Canvas = 
+
+  TCanvas* Canvas =
     new TCanvas("CanvasComptonSequenceLengthVsComptonQualityFactor",
                 "Canvas Compton Sequence Length vs. Compton Quality Factor", 800, 600);
   Canvas->cd();
-  Canvas->SetLogy();  
+  Canvas->SetLogy();
   Hist->SetAxisRange(2, MaxSequenceLength);
   Hist->Draw("COLZ");
   Canvas->Update();
@@ -3521,18 +3521,18 @@ void MInterfaceMimrec::ComptonSequenceLengthVsComptonProbability()
 
 ////////////////////////////////////////////////////////////////////////////////
 
-  
+
 void MInterfaceMimrec::SPDElectron()
 {
   // Display the angular resolution measurement for the recoil electron
-  // The ARM value for the recoil electron is the minimum angle between 
-  // the electron-cone-surface and the line connecting the cone-apex with the 
+  // The ARM value for the recoil electron is the minimum angle between
+  // the electron-cone-surface and the line connecting the cone-apex with the
   // (Test-) position
-  
+
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   int NEvents = 0;
   double Value = 0;
   int NAverages = 0;
@@ -3548,7 +3548,7 @@ void MInterfaceMimrec::SPDElectron()
   double Disk = m_Settings->GetTPDistanceLong();
   MVector TestPosition = GetTestPosition();
 
-  
+
   // Initalize the image size (x-axis)
   //BinWidth = 2*Disk/NBins;
   TH1D* Hist = new TH1D("Scatter Plane Deviation",
@@ -3564,7 +3564,7 @@ void MInterfaceMimrec::SPDElectron()
   // And fill the ARM-vector:
 
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* ComptonEvent = nullptr; 
+  MComptonEvent* ComptonEvent = nullptr;
   // ... loop over all events and save a count in the belonging bin ...
   while ((Event = GetNextEvent()) != 0) {
 
@@ -3610,8 +3610,8 @@ void MInterfaceMimrec::SPDElectron()
     NEvents++;
 
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -3620,7 +3620,7 @@ void MInterfaceMimrec::SPDElectron()
     return;
   }
 
-    
+
   TCanvas *Canvas = new TCanvas("Canvas SPD Gamma", "Canvas SPD Gamma", 800, 600);
   Canvas->SetFillColor(0);
   Canvas->SetFrameBorderSize(0);
@@ -3645,7 +3645,7 @@ void MInterfaceMimrec::SPDElectron()
   //L->SetParLimits(2, 0, 99999);
   L->SetParLimits(0, 0, 99999);
   //L->FixParameter(1, 0);
-  L->SetParNames("Offset", "Sigma1", "Height1", 
+  L->SetParNames("Offset", "Sigma1", "Height1",
                  "Sigma2", "Height2");
   Hist->Fit("LorentzGaussSPD", "Rw");
 
@@ -3657,7 +3657,6 @@ void MInterfaceMimrec::SPDElectron()
     Canvas->SaveAs(m_OutputFileName);
   }
 
-
   cout<<endl;
   cout<<"SPD - Characteristics:"<<endl;
   cout<<endl;
@@ -3686,18 +3685,18 @@ void MInterfaceMimrec::SPDElectron()
 
 ////////////////////////////////////////////////////////////////////////////////
 
-  
+
 void MInterfaceMimrec::ARMElectron()
 {
   // Display the angular resolution measurement for the recoil electron
-  // The ARM value for the recoil electron is the minimum angle between 
-  // the electron-cone-surface and the line connecting the cone-apex with the 
+  // The ARM value for the recoil electron is the minimum angle between
+  // the electron-cone-surface and the line connecting the cone-apex with the
   // (Test-) position
 
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   int NEvents = 0;
   double Value = 0;
   int NAverages = 0;
@@ -3713,7 +3712,7 @@ void MInterfaceMimrec::ARMElectron()
 
   // Initalize the image size (x-axis)
   //BinWidth = 2*Disk/NBins;
-  TH1D* Hist = new TH1D("ARM - electron cone", 
+  TH1D* Hist = new TH1D("ARM - electron cone",
                         "ARM - electron cone", NBins, -Disk, Disk);
   Hist->SetXTitle("ARM - electron cone [#circ]");
   Hist->SetYTitle("counts/degree");
@@ -3726,7 +3725,7 @@ void MInterfaceMimrec::ARMElectron()
   // And fill the ARM-vector:
 
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* ComptonEvent = nullptr; 
+  MComptonEvent* ComptonEvent = nullptr;
   // ... loop over all events and save a count in the belonging bin ...
   while ((Event = GetNextEvent()) != 0) {
 
@@ -3766,8 +3765,8 @@ void MInterfaceMimrec::ARMElectron()
     NEvents++;
 
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -3812,10 +3811,10 @@ void MInterfaceMimrec::ARMElectron()
       cout<<100*Sigma3<<"% containment: "<<Hist->GetBinCenter(CentralBin + b)<<endl;
       Sigma3Found = true;
     }
-    
+
   }
 
-    
+
   TCanvas *Canvas = new TCanvas("Canvas ARM Electron", "Canvas ARM Electron", 800, 600);
   Canvas->SetFillColor(0);
   Canvas->SetFrameBorderSize(0);
@@ -3825,10 +3824,10 @@ void MInterfaceMimrec::ARMElectron()
 
 
   TF1* Fit = 0;
-  Fit = new TF1("DoubleLorentzAsymGausArm", DoubleLorentzAsymGausArm, 
+  Fit = new TF1("DoubleLorentzAsymGausArm", DoubleLorentzAsymGausArm,
                 -Disk*0.99, TMath::Min(40.0, Disk*0.99), 9);
   Fit->SetBit(kCanDelete);
-  Fit->SetParNames("Offset", "Mean", 
+  Fit->SetParNames("Offset", "Mean",
                    "Lorentz Width1", "Lorentz Height1",
                    "Lorentz Width2", "Lorentz Height2",
                    "Gaus Height", "Gaus Sigma 1", "Gaus Sigma 2");
@@ -3836,14 +3835,14 @@ void MInterfaceMimrec::ARMElectron()
   Fit->SetParLimits(1, -Disk*0.99, Disk*0.99);
 
 
-  
+
   Canvas->cd();
   Hist->Fit(Fit, "RQI");
   Hist->Draw("HIST");
   Fit->Draw("SAME");
   Canvas->Modified();
   Canvas->Update();
-  
+
   cout<<endl;
   cout<<"ARM - Characteristics:"<<endl;
   cout<<endl;
@@ -3864,20 +3863,20 @@ void MInterfaceMimrec::ARMElectron()
 
 void MInterfaceMimrec::EnergySpectra()
 {
-  // Display the energy-spectrum of all acceptable events 
+  // Display the energy-spectrum of all acceptable events
 
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   bool xLog = m_Settings->GetLogBinningSpectrum();
   double xMin = GetTotalEnergyMin();
   double xMax = GetTotalEnergyMax();
 
   if (xLog == true) {
-    if (xMin <= 0) xMin = 1; 
+    if (xMin <= 0) xMin = 1;
   }
-  
+
   if (m_Settings->GetSecondEnergyRangeMax() > 0) {
     if (m_Settings->GetSecondEnergyRangeMax() > xMax) xMax = m_Settings->GetSecondEnergyRangeMax();
     if (m_Settings->GetSecondEnergyRangeMin() < xMin) xMin = m_Settings->GetSecondEnergyRangeMin();
@@ -3890,7 +3889,7 @@ void MInterfaceMimrec::EnergySpectra()
     if (m_Settings->GetFourthEnergyRangeMax() > xMax) xMax = m_Settings->GetFourthEnergyRangeMax();
     if (m_Settings->GetFourthEnergyRangeMin() < xMin) xMin = m_Settings->GetFourthEnergyRangeMin();
   }
-  
+
 
   int NBins = m_Settings->GetHistBinsSpectrum();
   double Disk = m_Settings->GetTPDistanceTrans();
@@ -3921,13 +3920,14 @@ void MInterfaceMimrec::EnergySpectra()
   MBinnerBayesianBlocks Bayes;
   Bayes.SetMinMax(xMin, xMax);
   Bayes.SetMinimumBinWidth((xMax-xMin)/NBins);
-  Bayes.SetPrior(3); 
+  Bayes.SetPrior(3);
+
 
- 
   // ... loop over all events and save a count in the belonging bin ...
   MPhysicalEvent* Event = nullptr;
   while ((Event = GetNextEvent()) != 0) {
 
+
     if (m_Selector->IsQualifiedEventFast(Event) == false) {
       delete Event;
       continue;
@@ -3961,11 +3961,11 @@ void MInterfaceMimrec::EnergySpectra()
     }
 
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
-  
+
 //   // %%%%%%%%%%%%%%%%%%%%%%%% Write Spectra as ASCII %%%%%%%%%%
 
 //   // Get the base file name of the tra file:
@@ -3975,25 +3975,25 @@ void MInterfaceMimrec::EnergySpectra()
 
 //   AsciiSpectrumName.Remove(AsciiSpectrumName.Length()-4, 4);
 //   AsciiSpectrumName.Append(".ASCIIspectrum.dat");
-  
+
 //   std::ofstream ASCIIout(AsciiSpectrumName, ios::out);
-  
+
 //   for (int b = 1; b <= (Hist->GetNbinsX() + 1); ++b)
 //     {
 //       ASCIIout << (Hist->GetBinLowEdge(b)) << " \t" ;
-//       if (b <= Hist->GetNbinsX()) 
+//       if (b <= Hist->GetNbinsX())
 //  {
 //    ASCIIout << (Hist->GetBinContent(b)) << endl;
-//  } 
-//       else 
+//  }
+//       else
 //  {
 //    ASCIIout << "0.0 \n";
 //  }
-      
+
 //     }
-  
+
 //   ASCIIout.close();
-  
+
 //   cout << "Wrote ASCII spectrum to " <<  AsciiSpectrumName << endl;
 
 //   // %%%%%%%%% End Write spectra as ASCII %%%%%%%%%%%%%%%%%%%%%
@@ -4003,7 +4003,7 @@ void MInterfaceMimrec::EnergySpectra()
 //   for (int b = 1; b <= Hist->GetNbinsX(); ++b) {
 //     Hist->SetBinContent(b, Hist->GetBinContent(b)/Hist->GetBinWidth(b));
 //   }
-  
+
   /*
   TCanvas* Canvas2 = new TCanvas();
   Canvas2->cd();
@@ -4011,7 +4011,7 @@ void MInterfaceMimrec::EnergySpectra()
   HistBayes->Draw();
   Canvas2->Update();
   */
-  
+
   // Normalize
   for (int b = 1; b <= Hist->GetNbinsX(); ++b) {
     Hist->SetBinContent(b, Hist->GetBinContent(b)/Hist->GetBinWidth(b));
@@ -4026,22 +4026,22 @@ void MInterfaceMimrec::EnergySpectra()
   Hist->Draw();
   Canvas->Update();
 
- 
+
   //TF1 *L = new TF1("TrippleGauss", TrippleGauss, 0.01*xMin, 0.99*xMax, 10);
 //   TF1 *L = new TF1("TrippleGauss", TrippleGauss, 300, 900, 10);
 
 //   L->SetParameters(1, 1, 1, 1, 1, 1, 1, 1, 1, 1);
 
-//   L->SetParNames("Offset", "Sigma1", "Mean1", "Height1", 
+//   L->SetParNames("Offset", "Sigma1", "Mean1", "Height1",
 //                  "Sigma2", "Mean2", "Height2",
 //                  "Sigma3", "Mean3", "Height3");
 //   Hist->Fit("TrippleGauss", "Rw");
-  
+
   //Hist->SetStats(false);
   //Canvas->cd();
   //Hist->SetMinimum(0);
   //Hist->Draw();
-  Canvas->Update(); 
+  Canvas->Update();
   if (m_OutputFileName.IsEmpty() == false) {
     Canvas->SaveAs(m_OutputFileName);
   }
@@ -4077,13 +4077,13 @@ void MInterfaceMimrec::EnergySpectra()
 
 void MInterfaceMimrec::InitialEnergyDeposit()
 {
-  // Display the energy-spectrum of all acceptable events 
+  // Display the energy-spectrum of all acceptable events
   // (remember: not all of them will be reconstructable)
 
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   double EnergyMin = m_Settings->GetInitialEnergyDepositPairMin();
   double EnergyMax = m_Settings->GetInitialEnergyDepositPairMax();
 
@@ -4100,7 +4100,7 @@ void MInterfaceMimrec::InitialEnergyDeposit()
   MPhysicalEvent* Event = nullptr;
   while ((Event = GetNextEvent()) != 0) {
 
-    // Only accept Comptons within the selected ranges... 
+    // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == false) {
       delete Event;
       continue;
@@ -4108,11 +4108,11 @@ void MInterfaceMimrec::InitialEnergyDeposit()
 
     if (Event->GetType() == MPhysicalEvent::c_Pair) {
       Hist->Fill(((MPairEvent*) Event)->GetInitialEnergyDeposit());
-    } 
+    }
 
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -4130,7 +4130,7 @@ void MInterfaceMimrec::InitialEnergyDeposit()
 
 void MInterfaceMimrec::EnergyDistributionElectronPhoton()
 {
-  // Display the energy-spectrum of all acceptable events 
+  // Display the energy-spectrum of all acceptable events
   // (remember: not all of them will be reconstructable)
 
   // Start with the event file loader first (just in case something goes wrong here)
@@ -4171,7 +4171,7 @@ void MInterfaceMimrec::EnergyDistributionElectronPhoton()
   TH2D* ScatterPlot = new TH2D("Energy Distribution", "Energy Distribution", NBins, xBins, NBins, xBins);
   delete [] xBins;
   
-  
+
   ScatterPlot->SetBit(kCanDelete);
   ScatterPlot->SetXTitle("Energy scattered gamma ray [keV]");
   ScatterPlot->SetYTitle("Energy recoil electron [keV]");
@@ -4183,7 +4183,7 @@ void MInterfaceMimrec::EnergyDistributionElectronPhoton()
   MPhysicalEvent* Event = nullptr;
   while ((Event = GetNextEvent()) != 0) {
 
-    // Only accept Comptons within the selected ranges... 
+    // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
       if (Event->GetType() == MPhysicalEvent::c_Compton) {
         Compton = dynamic_cast<MComptonEvent*>(Event);
@@ -4198,8 +4198,8 @@ void MInterfaceMimrec::EnergyDistributionElectronPhoton()
     }
 
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -4222,8 +4222,8 @@ void MInterfaceMimrec::TimeWalkDistribution()
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
-  TH1D* TWHist = new TH1D("Time walk Distribution", "Time walk Distribution", 
+
+  TH1D* TWHist = new TH1D("Time walk Distribution", "Time walk Distribution",
                           100, m_Settings->GetTimeWalkRangeMin(), m_Settings->GetTimeWalkRangeMax());
   TWHist->SetBit(kCanDelete);
   TWHist->SetXTitle("Time walk [ns]");
@@ -4231,19 +4231,19 @@ void MInterfaceMimrec::TimeWalkDistribution()
   TWHist->SetStats(false);
   TWHist->SetFillColor(8);
 
-  
+
   // ... loop over all events and save a count in the belonging bin ...
   MPhysicalEvent* Event = nullptr;
   while ((Event = GetNextEvent()) != 0) {
 
-    // Only accept Comptons within the selected ranges... 
+    // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
       TWHist->Fill(Event->GetTimeWalk());
     }
 
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -4266,14 +4266,14 @@ void MInterfaceMimrec::TimeWalkArmDistribution()
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   MImage Image;
   Image.SetSpectrum(MImage::c_WhiteBlack);
 
   MVector TestPosition = GetTestPosition();
 
-  TH2D* TWHist = new TH2D("Time walk ARM Distribution", "Time walk ARM Distribution", 
-                          int(m_Settings->GetTimeWalkRangeMax() - m_Settings->GetTimeWalkRangeMin())/100, m_Settings->GetTimeWalkRangeMin(), m_Settings->GetTimeWalkRangeMax(), 
+  TH2D* TWHist = new TH2D("Time walk ARM Distribution", "Time walk ARM Distribution",
+                          int(m_Settings->GetTimeWalkRangeMax() - m_Settings->GetTimeWalkRangeMin())/100, m_Settings->GetTimeWalkRangeMin(), m_Settings->GetTimeWalkRangeMax(),
                           100, m_Settings->GetComptonAngleRangeMin(), m_Settings->GetComptonAngleRangeMax());
   TWHist->SetBit(kCanDelete);
   TWHist->SetXTitle("Time walk [ns]");
@@ -4283,11 +4283,11 @@ void MInterfaceMimrec::TimeWalkArmDistribution()
 
   // ... loop over all events and save a count in the belonging bin ...
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* ComptonEvent = nullptr; 
-  MPairEvent* PairEvent = 0; 
+  MComptonEvent* ComptonEvent = nullptr;
+  MPairEvent* PairEvent = 0;
   while ((Event = GetNextEvent()) != 0) {
 
-    // Only accept Comptons within the selected ranges... 
+    // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
       if (Event->GetType() == MPhysicalEvent::c_Compton) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
@@ -4299,8 +4299,8 @@ void MInterfaceMimrec::TimeWalkArmDistribution()
     }
 
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -4323,7 +4323,7 @@ void MInterfaceMimrec::ScatterAnglesDistribution()
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   int NBins = 90;
 
   //double Phi;
@@ -4332,7 +4332,7 @@ void MInterfaceMimrec::ScatterAnglesDistribution()
   double AvgSinPhi = 0;
   double PhiMin = m_Settings->GetComptonAngleRangeMin();
   double PhiMax = m_Settings->GetComptonAngleRangeMax();
-  TH1D* PhiHist = new TH1D("PhiDistribution", "Compton scatter angle (phi) distribution", 
+  TH1D* PhiHist = new TH1D("PhiDistribution", "Compton scatter angle (phi) distribution",
                            NBins, PhiMin, PhiMax);
   PhiHist->SetBit(kCanDelete);
   PhiHist->SetStats(false);
@@ -4346,7 +4346,7 @@ void MInterfaceMimrec::ScatterAnglesDistribution()
   double AvgEpsilon = 0;
   double EpsilonMin = 0;
   double EpsilonMax = 90;
-  TH1D* EpsilonHist = new TH1D("EpsilonDistribution", "Electron scatter angle (epsilon) distribution", 
+  TH1D* EpsilonHist = new TH1D("EpsilonDistribution", "Electron scatter angle (epsilon) distribution",
                                NBins, EpsilonMin, EpsilonMax);
   EpsilonHist->SetBit(kCanDelete);
   EpsilonHist->SetStats(false);
@@ -4375,24 +4375,24 @@ void MInterfaceMimrec::ScatterAnglesDistribution()
   ThetaGeoHist->SetFillColor(8);
   ThetaGeoHist->SetXTitle("[degree]");
   ThetaGeoHist->SetYTitle("#");
-  
+
   TH1D* ThetaDiffHist = new TH1D("ThetaDiffDistribution", "Total scatter angle (theta): difference between geometric and kinetic angle", NBins, -180, 180);
   ThetaDiffHist->SetBit(kCanDelete);
   ThetaDiffHist->SetStats(false);
   ThetaDiffHist->SetFillColor(8);
   ThetaDiffHist->SetXTitle("#theta_{kin} - #theta_{geo} [degree]");
   ThetaDiffHist->SetYTitle("#");
-  
+
 
 
   MPhysicalEvent* Event = nullptr;
 
   bool FoundTrack = false;
-  MComptonEvent* ComptonEvent = nullptr; 
+  MComptonEvent* ComptonEvent = nullptr;
   // ... loop over all events and save a count in the belonging bin ...
   while ((Event = GetNextEvent()) != 0) {
 
-    // Only accept Comptons within the selected ranges... 
+    // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == false) {
       delete Event;
       continue;
@@ -4428,7 +4428,7 @@ void MInterfaceMimrec::ScatterAnglesDistribution()
 
     delete Event;
   }
-  
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -4471,7 +4471,7 @@ void MInterfaceMimrec::ScatterAnglesDistribution()
         }
         EpsilonCanvas->SaveAs(Name);
       }
-    
+
       TCanvas* ThetaCanvas = new TCanvas("CanvasThetaViaEnergy", "Canvas of total scatter angle distribution (kin)", 800, 600);
       ThetaHist->SetStats(false);
       ThetaCanvas->cd();
@@ -4485,12 +4485,12 @@ void MInterfaceMimrec::ScatterAnglesDistribution()
         }
         ThetaCanvas->SaveAs(Name);
       }
-      
+
       TCanvas* ThetaGeoCanvas = new TCanvas("CanvasThetaViaGeo", "Canvas of total scatter angle distribution (geo)", 800, 600);
       ThetaGeoHist->SetStats(false);
       ThetaGeoCanvas->cd();
       ThetaGeoHist->Draw();
-      
+
       TCanvas* ThetaDiffCanvas = new TCanvas("CanvasThetaDiff", "Canvas of total scatter angle distribution: kin - geo", 800, 600);
       ThetaDiffHist->SetStats(false);
       ThetaDiffCanvas->cd();
@@ -4520,7 +4520,7 @@ void MInterfaceMimrec::ClusteringQualityFactor()
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   bool xLog;
   if (m_Settings->GetClusteringQualityFactorRangeMin() > 0 && m_Settings->GetClusteringQualityFactorRangeMin() < 0.01) {
     xLog = true;
@@ -4531,7 +4531,7 @@ void MInterfaceMimrec::ClusteringQualityFactor()
   double* xBins = CreateAxisBins(m_Settings->GetClusteringQualityFactorRangeMin(), m_Settings->GetClusteringQualityFactorRangeMax(), xNBins, xLog);
 
 
-  TH1D* Hist = new TH1D("ClusteringQualityFactor", "Clustering Quality Factor", 
+  TH1D* Hist = new TH1D("ClusteringQualityFactor", "Clustering Quality Factor",
                         xNBins, xBins);
   Hist->SetBit(kCanDelete);
   Hist->SetXTitle("Clustering Quality Factor");
@@ -4542,11 +4542,11 @@ void MInterfaceMimrec::ClusteringQualityFactor()
 
 
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* ComptonEvent = nullptr; 
+  MComptonEvent* ComptonEvent = nullptr;
   // ... loop over all events and save a count in the belonging bin ...
   while ((Event = GetNextEvent()) != 0) {
 
-    // Only accept Comptons within the selected ranges... 
+    // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == false) {
       delete Event;
       continue;
@@ -4558,10 +4558,10 @@ void MInterfaceMimrec::ClusteringQualityFactor()
     ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
     Hist->Fill(ComptonEvent->ClusteringQualityFactor());
-    
+
     delete Event;
   }
-  
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -4589,7 +4589,7 @@ void MInterfaceMimrec::ComptonQualityFactor()
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   bool xLog;
   if (m_Settings->GetComptonQualityFactorRangeMin() > 0 && m_Settings->GetComptonQualityFactorRangeMin() < 0.01) {
     xLog = true;
@@ -4600,7 +4600,7 @@ void MInterfaceMimrec::ComptonQualityFactor()
   double* xBins = CreateAxisBins(m_Settings->GetComptonQualityFactorRangeMin(), m_Settings->GetComptonQualityFactorRangeMax(), xNBins, xLog);
 
 
-  TH1D* Hist = new TH1D("Compton Quality Factor", "Compton Quality Factor", 
+  TH1D* Hist = new TH1D("Compton Quality Factor", "Compton Quality Factor",
                         xNBins, xBins);
   Hist->SetBit(kCanDelete);
   Hist->SetXTitle("Compton Quality Factor");
@@ -4611,11 +4611,11 @@ void MInterfaceMimrec::ComptonQualityFactor()
 
 
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* ComptonEvent = nullptr; 
+  MComptonEvent* ComptonEvent = nullptr;
   // ... loop over all events and save a count in the belonging bin ...
   while ((Event = GetNextEvent()) != 0) {
 
-    // Only accept Comptons within the selected ranges... 
+    // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == false) {
       delete Event;
       continue;
@@ -4627,10 +4627,10 @@ void MInterfaceMimrec::ComptonQualityFactor()
     ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
     Hist->Fill(ComptonEvent->ComptonQualityFactor1());
-    
+
     delete Event;
   }
-  
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -4658,7 +4658,7 @@ void MInterfaceMimrec::TrackQualityFactor()
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   bool xLog;
   if (m_Settings->GetTrackQualityFactorRangeMin() > 0 && m_Settings->GetTrackQualityFactorRangeMin() < 0.01) {
     xLog = true;
@@ -4669,7 +4669,7 @@ void MInterfaceMimrec::TrackQualityFactor()
   double* xBins = CreateAxisBins(m_Settings->GetTrackQualityFactorRangeMin(), m_Settings->GetTrackQualityFactorRangeMax(), xNBins, xLog);
 
 
-  TH1D* Hist = new TH1D("Track Quality Factor", "Track Quality Factor", 
+  TH1D* Hist = new TH1D("Track Quality Factor", "Track Quality Factor",
                         xNBins, xBins);
   Hist->SetBit(kCanDelete);
   Hist->SetXTitle("Track Quality Factor");
@@ -4680,11 +4680,11 @@ void MInterfaceMimrec::TrackQualityFactor()
 
 
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* ComptonEvent = nullptr; 
+  MComptonEvent* ComptonEvent = nullptr;
   // ... loop over all events and save a count in the belonging bin ...
   while ((Event = GetNextEvent()) != 0) {
 
-    // Only accept Comptons within the selected ranges... 
+    // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == false) {
       delete Event;
       continue;
@@ -4696,10 +4696,10 @@ void MInterfaceMimrec::TrackQualityFactor()
     ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
     Hist->Fill(ComptonEvent->TrackQualityFactor1());
-    
+
     delete Event;
   }
-  
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -4726,7 +4726,7 @@ void MInterfaceMimrec::EarthCenterDistance()
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   mimp<<"Fixed earth position at (0, 0, -1e20) = 180 deg"<<endl;
 
   MVector Position(0, 0, -c_FarAway);
@@ -4736,10 +4736,10 @@ void MInterfaceMimrec::EarthCenterDistance()
 
   int NEvents = 0;
   int NBins = 100;
-  
-  TH1D* Hist = 
-    new TH1D("EarthCenterDistance", 
-             "Distance between cone circle and earth center", NBins, 
+
+  TH1D* Hist =
+    new TH1D("EarthCenterDistance",
+             "Distance between cone circle and earth center", NBins,
              0.0, 180.0);
   Hist->SetBit(kCanDelete);
   Hist->SetXTitle("Distance between cone circle and earth center [deg]");
@@ -4751,16 +4751,16 @@ void MInterfaceMimrec::EarthCenterDistance()
  // First check on the size of the histogram:
   while ((Event = GetNextEvent()) != 0) {
 
-    // Only accept Comptons within the selected ranges... 
+    // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true &&
         Event->GetType() == MPhysicalEvent::c_Compton) {
       Compton = (MComptonEvent*) Event;
       Hist->Fill(Compton->GetARMGamma(Position, m_Settings->GetCoordinateSystem())*c_Deg);
       NEvents++;
-    }    
+    }
     delete Event;
   }
-  
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -4791,15 +4791,15 @@ void MInterfaceMimrec::DistanceDistribution()
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   int NBins = 100;
 
   MComptonEvent* Compton = 0;
   MPhysicalEvent* Event = nullptr;
 
-  TH1D* FirstHist = 
-    new TH1D("FirstDistance", 
-             "Distance between first and second hit", NBins, 
+  TH1D* FirstHist =
+    new TH1D("FirstDistance",
+             "Distance between first and second hit", NBins,
              m_Settings->GetFirstDistanceRangeMin(), m_Settings->GetFirstDistanceRangeMax());
   FirstHist->SetBit(kCanDelete);
   FirstHist->SetXTitle("distance [cm]");
@@ -4808,7 +4808,7 @@ void MInterfaceMimrec::DistanceDistribution()
   FirstHist->SetFillColor(8);
   FirstHist->SetMinimum(0);
 
-  TH1D* AnyHist = new TH1D("AnyDistance", "Minimum distance between any hit", NBins, 
+  TH1D* AnyHist = new TH1D("AnyDistance", "Minimum distance between any hit", NBins,
                            m_Settings->GetDistanceRangeMin(), m_Settings->GetDistanceRangeMax());
   AnyHist->SetBit(kCanDelete);
   AnyHist->SetXTitle("distance [cm]");
@@ -4823,17 +4823,17 @@ void MInterfaceMimrec::DistanceDistribution()
   // First check on the size of the histogram:
   while ((Event = GetNextEvent()) != 0) {
 
-    // Only accept Comptons within the selected ranges... 
+    // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true &&
         Event->GetType() == MPhysicalEvent::c_Compton) {
       Compton = (MComptonEvent*) Event;
       FirstHist->Fill((Compton->C2()-Compton->C1()).Mag());
       AnyHist->Fill(Compton->LeverArm());
       NEvents++;
-    }    
+    }
     delete Event;
   }
-  
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -4892,7 +4892,7 @@ void MInterfaceMimrec::SequenceLengths()
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   unsigned int MaxTrackLength = 3;
   unsigned int MaxSequenceLength = 3;
   int NBins = 100;
@@ -4900,9 +4900,9 @@ void MInterfaceMimrec::SequenceLengths()
   MComptonEvent* Compton = 0;
   MPhysicalEvent* Event = nullptr;
 
-  TH1D* TrackHist = 
-    new TH1D("LengthFirstTrack", 
-             "Length of first Compton electron track", NBins, 
+  TH1D* TrackHist =
+    new TH1D("LengthFirstTrack",
+             "Length of first Compton electron track", NBins,
              0.5, NBins+0.5);
   TrackHist->SetBit(kCanDelete);
   TrackHist->SetXTitle("Reconstructed electron track length");
@@ -4911,8 +4911,8 @@ void MInterfaceMimrec::SequenceLengths()
   TrackHist->SetFillColor(8);
   TrackHist->SetMinimum(0);
 
-  TH1D* ComptonHist = new TH1D("LengthComptonSequence", 
-                               "Length of reconstructed Compton sequence", NBins, 
+  TH1D* ComptonHist = new TH1D("LengthComptonSequence",
+                               "Length of reconstructed Compton sequence", NBins,
                            0.5, NBins+0.5);
   ComptonHist->SetBit(kCanDelete);
   ComptonHist->SetXTitle("Reconstructed sequence length");
@@ -4930,7 +4930,7 @@ void MInterfaceMimrec::SequenceLengths()
   // First check on the size of the histogram:
   while ((Event = GetNextEvent()) != 0) {
 
-    // Only accept Comptons within the selected ranges... 
+    // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true &&
         Event->GetType() == MPhysicalEvent::c_Compton) {
       Compton = (MComptonEvent*) Event;
@@ -4943,10 +4943,10 @@ void MInterfaceMimrec::SequenceLengths()
       if (Compton->SequenceLength() > MaxSequenceLength) MaxSequenceLength = Compton->SequenceLength();
       ComptonHist->Fill(Compton->SequenceLength());
       NEvents++;
-    }    
+    }
     delete Event;
   }
-  
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -4956,8 +4956,8 @@ void MInterfaceMimrec::SequenceLengths()
     return;
   }
 
-  TCanvas* TrackCanvas = 
-    new TCanvas("CanvasLengthFirstTrack", 
+  TCanvas* TrackCanvas =
+    new TCanvas("CanvasLengthFirstTrack",
                 "Canvas of length of first Compton electron track", 800, 600);
   TrackCanvas->cd();
   TrackHist->SetAxisRange(0, MaxTrackLength);
@@ -4971,10 +4971,10 @@ void MInterfaceMimrec::SequenceLengths()
       Name += MString(".firsttrack") + Suffix;
     }
     TrackCanvas->SaveAs(Name);
-  } 
+  }
 
-  TCanvas* ComptonCanvas = 
-    new TCanvas("CanvasLengthComptonSequence", 
+  TCanvas* ComptonCanvas =
+    new TCanvas("CanvasLengthComptonSequence",
                 "Canvas of length of reconstructed Compton sequence", 800, 600);
   ComptonCanvas->cd();
   ComptonHist->SetAxisRange(0, MaxSequenceLength);
@@ -4989,7 +4989,7 @@ void MInterfaceMimrec::SequenceLengths()
     }
     ComptonCanvas->SaveAs(Name);
   }
-  
+
   mout<<"Track lengths:"<<endl;
   int All = 0;
   for (int b = 1; b <= TrackHist->GetNbinsX() && b <= 15; ++b) {
@@ -5025,7 +5025,7 @@ void MInterfaceMimrec::LightCurve()
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   unsigned int NBins = 1000;
 
   MPhysicalEvent* Event = nullptr;
@@ -5037,60 +5037,60 @@ void MInterfaceMimrec::LightCurve()
   MEventSelector NoTimeWindowSelector = *m_Selector;
   NoTimeWindowSelector.SetTime(0, numeric_limits<double>::max());
 
-  
+
   // First check on the size of the histogram:
   unsigned long NEvents = 0;
   while ((Event = GetNextEvent()) != 0) {
 
-    // Only accept Comptons within the selected ranges... 
+    // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
       if (Event->GetTime().GetAsDouble() == 0) {
-        mout<<"Info - light curve: Ignoring all events with time zero"<<endl; 
+        mout<<"Info - light curve: Ignoring all events with time zero"<<endl;
       } else {
         if (Event->GetTime().GetAsDouble() < MinTime) MinTime = Event->GetTime().GetAsDouble();
         if (Event->GetTime().GetAsDouble() > MaxTime) MaxTime = Event->GetTime().GetAsDouble();
         if (NEvents > 0) {
           if (TimeList.back() > Event->GetTime().GetAsDouble()) {
-            cout<<"Backwards time jump detected: "<<setprecision(20)<<TimeList.back()<<" --> "<<Event->GetTime().GetAsDouble()<<endl; 
+            cout<<"Backwards time jump detected: "<<setprecision(20)<<TimeList.back()<<" --> "<<Event->GetTime().GetAsDouble()<<endl;
           }
         }
         TimeList.push_back(Event->GetTime().GetAsDouble());
         NEvents++;
       }
-    }    
+    }
 
     delete Event;
   }
-  
+
   // Close the event loader
   FinalizeEventLoader();
 
   if (TimeList.empty() == true) {
-    mgui<<"Light curve: No events passed the event selections!"<<show; 
+    mgui<<"Light curve: No events passed the event selections!"<<show;
     return;
   }
-  
+
   mout<<"Minimum time: "<<setprecision(20)<<MinTime<<endl;
   mout<<"Maximum time: "<<setprecision(20)<<MaxTime<<setprecision(6)<<endl;
 
   if (NEvents/10 < NBins) NBins = NEvents/10;
   if (NBins < 10) NBins = 10;
-  
+
   //NBins = (int) (MaxTime - MinTime);
-  
+
   // Find the common time between min and max
   long min = (long) MinTime;
   long max = (long) MaxTime;
-  
+
   int Counter = 0;
   do {
     min /= 10;
     max /= 10;
     Counter++;
   } while (min != max);
-  
+
   int Subtract = min * pow(10, Counter);
-  
+
   TH1D* HistOptimized = new TH1D("TimeOptimized", "Light curve", NBins, MinTime - Subtract, MaxTime - Subtract);
   HistOptimized->SetBit(kCanDelete);
   HistOptimized->SetXTitle(MString("Time [s] + ") + MString(Subtract) + " seconds");
@@ -5100,7 +5100,7 @@ void MInterfaceMimrec::LightCurve()
   HistOptimized->SetFillColor(8);
   HistOptimized->SetMinimum(0);
   HistOptimized->GetXaxis()->SetNdivisions(509);
-  
+
   for (unsigned int i = 0; i < TimeList.size(); ++i) {
     HistOptimized->Fill(TimeList[i] - Subtract);
   }
@@ -5115,8 +5115,8 @@ void MInterfaceMimrec::LightCurve()
   MBinnerBayesianBlocks Bayes;
   Bayes.SetMinMax(MinTime - Subtract, MaxTime - Subtract);
   Bayes.SetMinimumBinWidth((int) (std::max(1.0, 0.5*HistOptimized->GetBinWidth(1)) + 0.5));
-  Bayes.SetPrior(5); 
-    
+  Bayes.SetPrior(5);
+
   for (unsigned int i = 0; i < TimeList.size(); ++i) {
     Bayes.Add(TimeList[i] - Subtract, 1);
   }
@@ -5130,13 +5130,13 @@ void MInterfaceMimrec::LightCurve()
   HistBayes->Draw("SAME");
   CanvasOptimized->Update();
   */
-  
+
   if (m_OutputFileName.IsEmpty() == false) {
     CanvasOptimized->SaveAs(m_OutputFileName);
   }
-  
-  
-  return; 
+
+
+  return;
 }
 
 
@@ -5150,13 +5150,13 @@ void MInterfaceMimrec::CoincidenceWindowDistribution()
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   int NBins = 100;
 
   MPhysicalEvent* Event = nullptr;
 
-  TH1D* Hist = 
-    new TH1D("CoincidenceWindow", "Coincidence window", NBins, 
+  TH1D* Hist =
+    new TH1D("CoincidenceWindow", "Coincidence window", NBins,
              m_Settings->GetCoincidenceWindowRangeMin(), m_Settings->GetCoincidenceWindowRangeMax());
   Hist->SetBit(kCanDelete);
   Hist->SetXTitle("time [s]");
@@ -5182,18 +5182,18 @@ void MInterfaceMimrec::CoincidenceWindowDistribution()
       if (ComptonEvent->CoincidenceWindow().GetAsDouble() < MinTime) MinTime = ComptonEvent->CoincidenceWindow().GetAsDouble();
       if (ComptonEvent->CoincidenceWindow().GetAsDouble() > MaxTime) MaxTime = ComptonEvent->CoincidenceWindow().GetAsDouble();
 
-      // Only accept Comptons within the selected ranges... 
+      // Only accept Comptons within the selected ranges...
       if (m_Selector->IsQualifiedEventFast(ComptonEvent) == true) {
         Hist->Fill(ComptonEvent->CoincidenceWindow().GetAsDouble());
-      }    
-      // Only accept Comptons within the selected ranges... 
+      }
+      // Only accept Comptons within the selected ranges...
       if (NoTimeWindowSelector.IsQualifiedEventFast(ComptonEvent) == true) {
         TimeList.push_back(ComptonEvent->CoincidenceWindow().GetAsDouble());
       }
     }
     delete Event;
   }
-  
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -5211,7 +5211,7 @@ void MInterfaceMimrec::CoincidenceWindowDistribution()
   Canvas->Update();
 
 
-  TH1D* HistOptimized = 
+  TH1D* HistOptimized =
     new TH1D("OptimizedCoincidenceWindow", "Coincidence window (optimized window without the cuts in the event selector)", NBins, MinTime, MaxTime);
   HistOptimized->SetBit(kCanDelete);
   HistOptimized->SetXTitle("time [s]");
@@ -5230,7 +5230,7 @@ void MInterfaceMimrec::CoincidenceWindowDistribution()
   CanvasOptimized->Update();
 
 
-  return; 
+  return;
 }
 
 
@@ -5244,7 +5244,7 @@ void MInterfaceMimrec::LocationOfFirstIA()
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   int x, y;
   int x1NBins = 100;
   int x2NBins = 100;
@@ -5255,7 +5255,7 @@ void MInterfaceMimrec::LocationOfFirstIA()
 
   double* Array = new double[x1NBins*x2NBins];
   for (x = 0; x < x1NBins*x2NBins; x++) Array[x] = 0.0;
-  
+
   // ... loop over all events and save a count in the belonging bin ...
   MPhysicalEvent* Event;
   MComptonEvent Compton;
@@ -5278,13 +5278,13 @@ void MInterfaceMimrec::LocationOfFirstIA()
     }
 
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
 
-  MImage2D* Image = 
+  MImage2D* Image =
     new MImage2D("Location of Second Interaction", Array,
                  "x [m]", x1Min, x1Max, x1NBins,
                  "y [m]", x2Min, x2Max, x2NBins, "counts");
@@ -5309,7 +5309,7 @@ void MInterfaceMimrec::Polarization()
 
   double Min = -180.000001;
   double Max = +180.000001;
-  
+
   TH1D* Background = new TH1D("Background", "Not polarized source", NBins, Min, Max);
   Background->SetBit(kCanDelete);
   Background->SetXTitle("[degree]");
@@ -5337,10 +5337,10 @@ void MInterfaceMimrec::Polarization()
   Corrected->SetMinimum(0.0);
   Corrected->SetNdivisions(-508, "X");
   Corrected->SetFillColor(0);
-  
+
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* ComptonEvent = nullptr; 
-  MPairEvent* PairEvent = nullptr; 
+  MComptonEvent* ComptonEvent = nullptr;
+  MPairEvent* PairEvent = nullptr;
 
   // Test position for ARM:
   MVector TestPosition = GetTestPosition();
@@ -5387,6 +5387,7 @@ void MInterfaceMimrec::Polarization()
 
         if (fabs(PairEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem()))*c_Deg < ArmCut) {
           /*
+        if (fabs(PairEvent->GetARMGamma(Origin, m_Settings->GetCoordinateSystem()))*c_Deg < ArmCut) {
           MVector Plain = PairEvent->GetElectronDirection() + PairEvent->GetPositronDirection();
           Plain.RotateZ(-Phi);
           Plain.RotateY(-Theta);
@@ -5406,11 +5407,11 @@ void MInterfaceMimrec::Polarization()
     }
 
     delete Event;
-  }   
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
- 
+
   if (Polarization->Integral() == 0) {
     mgui<<"No events passed the event selections for the polarized data file"<<show;
     return;
@@ -5427,10 +5428,10 @@ void MInterfaceMimrec::Polarization()
   // Now restart the event-loader with the background file:
   if (InitializeEventLoader(m_Settings->GetPolarizationBackgroundFileName()) == false) return;
 
-  
+
   MEventSelector SecondSelector(*m_Selector);
   SecondSelector.SetTimeMode(0); // Since the background file is likely simulation, we do not use a time cut -- this is noted in the GUI
-  
+
   // ... loop over all events and save a count in the belonging bin ...
   while ((Event = GetNextEvent()) != nullptr) {
 
@@ -5463,7 +5464,7 @@ void MInterfaceMimrec::Polarization()
           MVector Plain = PairEvent->GetElectronDirection() + PairEvent->GetPositronDirection();
           Plain.RotateZ(-Phi);
           Plain.RotateY(-Theta);
-          
+
           double Angle = Plain.Phi();
           Background->Fill(Angle*c_Deg);
           */
@@ -5479,8 +5480,8 @@ void MInterfaceMimrec::Polarization()
     }
 
     delete Event;
-  }   
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -5499,21 +5500,21 @@ void MInterfaceMimrec::Polarization()
 
 
   // Correct the modulation signature with the zero modulation
-  
+
   // The correction is
-  // C[i] = P[i]/B[i] * SUM_j( B[j] ) / NBins 
-  
+  // C[i] = P[i]/B[i] * SUM_j( B[j] ) / NBins
+
   // Why do we do this?
   // The measurement counts is basically the perfect polarization signature multiplied with the probability that we detect something in this direction:
   // Now to get the polarization signature we have to divide by this probability.
   // We don't need anything absolute since we are only interested in the polarization angle and modulation.
   // Thus a proxy for the polarization is the normalized background, i.e. background divided by its mean.
-  
-  
-  // Its uncertainty is 
-  // dC[i] = 
-  //  
-  
+
+
+  // Its uncertainty is
+  // dC[i] =
+  //
+
 
   // Since we correcting with background, we have to multiply with its mean
   double Mean = Background->Integral()/NBins;
@@ -5521,42 +5522,42 @@ void MInterfaceMimrec::Polarization()
   for (int i = 1; i <= NBins; ++i) {
     Corrected->SetBinContent(i, Polarization->GetBinContent(i)/Background->GetBinContent(i)*Mean);
     double Uncertainty = 0.0;
-    
+
     // Mean part
     for (int j = 1; j <= NBins; ++j) {
       Uncertainty += pow(Polarization->GetBinContent(i)/Background->GetBinContent(i)/NBins * sqrt(Background->GetBinContent(j)), 2);
     }
-    
+
     // Background part:
     Uncertainty += pow(Polarization->GetBinContent(i)/Background->GetBinContent(i)/Background->GetBinContent(i) * Mean * sqrt(Background->GetBinContent(i)), 2);
     // REMARK:
     // In theory the above case would never the uncertainty equation, since when i look at the mean
     // part: P[i]/B[i] * B[i] cancels out
     // However, since significantly underestimates the uncertainty, thus cannot be right...
-    
-    
+
+
     // Polarization part:
     Uncertainty += pow(Mean/Background->GetBinContent(i) * sqrt(Polarization->GetBinContent(i)), 2);
 
     Corrected->SetBinError(i, sqrt(Uncertainty));
   }
-    
-  // Normalize before we do anything else  
-  
+
+  // Normalize before we do anything else
+
   for (int b = 1; b <= NBins; ++b) {
     Polarization->SetBinContent(b, Polarization->GetBinContent(b)/Polarization->GetBinWidth(b));
   }
 
   for (int b = 1; b <= NBins; ++b) {
     Background->SetBinContent(b, Background->GetBinContent(b)/Background->GetBinWidth(b));
-  }    
-    
+  }
+
   for (int b = 1; b <= NBins; ++b) {
     Corrected->SetBinContent(b, Corrected->GetBinContent(b)/Corrected->GetBinWidth(b));
     Corrected->SetBinError(b, Corrected->GetBinError(b)/Corrected->GetBinWidth(b));
   }
-  
-    
+
+
   // Try to fit a cosine
   TF1* Lin = new TF1("LinearModulation", "pol0", -180*0.99, 180*0.99);
   Corrected->Fit(Lin, "RQFI");
@@ -5571,7 +5572,7 @@ void MInterfaceMimrec::Polarization()
   Corrected->Fit(Mod, "RQ");
 
   double Modulation = fabs(Mod->GetParameter(1)/Mod->GetParameter(0));
-  double ModulationError = sqrt((Mod->GetParError(1)*Mod->GetParError(1))/(Mod->GetParameter(0)*Mod->GetParameter(0)) + 
+  double ModulationError = sqrt((Mod->GetParError(1)*Mod->GetParError(1))/(Mod->GetParameter(0)*Mod->GetParameter(0)) +
                         (Mod->GetParError(0)*Mod->GetParError(0)*Mod->GetParameter(1)*Mod->GetParameter(1))/
                         (Mod->GetParameter(0)*Mod->GetParameter(0)*Mod->GetParameter(0)*Mod->GetParameter(0)));
 
@@ -5605,29 +5606,29 @@ void MInterfaceMimrec::Polarization()
   mout<<"  Outside ARM cut (bkg): "<<OutsideArmCutBackground<<endl;
   mout<<endl;
 
-  
-  
+
+
   // Now normalize to counts/deg & draw everything on screen:
 
   TCanvas* PolarizationCanvas = new TCanvas("PolarizationCanvas", "Polarized source", 800, 600);
   PolarizationCanvas->cd();
   Polarization->Draw();
-  PolarizationCanvas->Update(); 
-  
+  PolarizationCanvas->Update();
+
 
   TCanvas* BackgroundCanvas = new TCanvas("BackgroundCanvas", "Not polarized source", 800, 600);
   BackgroundCanvas->cd();
   Background->Draw();
   BackgroundCanvas->Update();
 
-  
+
   TCanvas* CorrectedCanvas = new TCanvas("CorrectedCanvas", "Background corrected polarization signature", 800, 600);
   CorrectedCanvas->cd();
   Corrected->Draw(); //"EHIST");
   Mod->Draw("SAME");
   CorrectedCanvas->Update();
 
-  
+
   // Safe
   if (m_OutputFileName.IsEmpty() == false) {
     MString Name;
@@ -5656,7 +5657,7 @@ void MInterfaceMimrec::Polarization()
     }
     CorrectedCanvas->SaveAs(Name);
   }
-  
+
   delete Lin;
   delete Mod;
 
@@ -5673,7 +5674,7 @@ void MInterfaceMimrec::AzimuthalComptonScatterAngle()
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   // Initalize the image size (x-axis)
   int NBins = m_Settings->GetHistBinsARMGamma();
   double Disk = m_Settings->GetTPDistanceTrans();
@@ -5689,7 +5690,7 @@ void MInterfaceMimrec::AzimuthalComptonScatterAngle()
   Hist->SetNdivisions(-508, "X");
 
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* ComptonEvent = nullptr; 
+  MComptonEvent* ComptonEvent = nullptr;
 
   // Some statistics:
   int InsideArmCutSource = 0;
@@ -5716,7 +5717,7 @@ void MInterfaceMimrec::AzimuthalComptonScatterAngle()
     }
 
     delete Event;
-  }   
+  }
 
   // Close the event loader
   FinalizeEventLoader();
@@ -5731,8 +5732,8 @@ void MInterfaceMimrec::AzimuthalComptonScatterAngle()
     return;
   }
 
-  TCanvas* Canvas = 
-    new TCanvas("AzimuthalComptonScatterAngleCanvas", 
+  TCanvas* Canvas =
+    new TCanvas("AzimuthalComptonScatterAngleCanvas",
                 "Azimuthal Compton Scatter Angle Canvas", 800, 600);
   Canvas->cd();
   Hist->Draw();
@@ -5748,7 +5749,7 @@ void MInterfaceMimrec::AzimuthalElectronScatterAngle()
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   // Initalize the image size (x-axis)
   int NBins = m_Settings->GetHistBinsARMElectron();
 
@@ -5763,7 +5764,7 @@ void MInterfaceMimrec::AzimuthalElectronScatterAngle()
 
 
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* ComptonEvent = nullptr; 
+  MComptonEvent* ComptonEvent = nullptr;
 
   // Origin in spherical coordinates:
   double Theta = m_Settings->GetTPTheta()*c_Rad;
@@ -5791,10 +5792,10 @@ void MInterfaceMimrec::AzimuthalElectronScatterAngle()
             MVector Plain = ComptonEvent->De();
             Plain.RotateZ(-Phi);
             Plain.RotateY(-Theta);
-          
+
             double Angle = Plain.Phi();
             Hist->Fill(Angle*c_Deg);
-            
+
             InsideArmCutSource++;
           } else {
             OutsideArmCutSource++;
@@ -5804,8 +5805,8 @@ void MInterfaceMimrec::AzimuthalElectronScatterAngle()
     }
 
     delete Event;
-  }   
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -5819,8 +5820,8 @@ void MInterfaceMimrec::AzimuthalElectronScatterAngle()
     return;
   }
 
-  TCanvas* Canvas = 
-    new TCanvas("AzimuthalElectronScatterAngleCanvas", 
+  TCanvas* Canvas =
+    new TCanvas("AzimuthalElectronScatterAngleCanvas",
                 "Azimuthal Electron Scatter Angle Canvas", 800, 600);
   Canvas->cd();
   Hist->Draw();
@@ -5838,10 +5839,10 @@ void MInterfaceMimrec::OpeningAnglePair()
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   // Initalize the image size (x-axis)
   int NBins = 100;
-  TH1D* Hist = new TH1D("OpeningAnglePair", "Opening Angle Pair", NBins, 
+  TH1D* Hist = new TH1D("OpeningAnglePair", "Opening Angle Pair", NBins,
                         m_Settings->GetOpeningAnglePairMin(), m_Settings->GetOpeningAnglePairMax());
   Hist->SetBit(kCanDelete);
   Hist->SetXTitle("Opening angle [#circ]");
@@ -5851,7 +5852,7 @@ void MInterfaceMimrec::OpeningAnglePair()
 
 
   MPhysicalEvent* Event = nullptr;
-  MPairEvent* PairEvent = 0; 
+  MPairEvent* PairEvent = 0;
   // ... loop over all events and save a count in the belonging bin ...
   while ((Event = GetNextEvent()) != 0) {
 
@@ -5864,8 +5865,8 @@ void MInterfaceMimrec::OpeningAnglePair()
     }
 
     delete Event;
-  }   
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -5882,25 +5883,25 @@ void MInterfaceMimrec::OpeningAnglePair()
 void MInterfaceMimrec::AngularResolutionVsQualityFactorPair()
 {
   // Display the angular resolution measurement for the gamma-ray
-  // The ARM value for the scattered gamma-ray is the minimum angle between 
-  // the gamma-cone-surface and the line connecting the cone-apex with the 
+  // The ARM value for the scattered gamma-ray is the minimum angle between
+  // the gamma-cone-surface and the line connecting the cone-apex with the
   // (Test-)position
 
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   int NEvents = 0;
   double Value = 0;
   int Inside = 0;
-  
+
   int NBins = m_Settings->GetHistBinsARMGamma();
   double Disk = m_Settings->GetTPDistanceTrans();
   MVector TestPosition = GetTestPosition();
 
   // Initalize the image size (x-axis)
   //BinWidth = 2*Disk/NBins;
-  TH2D* Hist = new TH2D("Angular resolution pairs", "Angular resolution pairs", NBins, 0, Disk, 100, 0, 1);
+  TH2D* Hist = new TH2D("Angular resolution pairs", "Angular resolution pairs", NBins, 0, Disk, 10000, 0, 10000);
   Hist->SetBit(kCanDelete);
   Hist->SetDirectory(0);
   Hist->SetXTitle("Angular resolution pairs [#circ]");
@@ -5911,7 +5912,7 @@ void MInterfaceMimrec::AngularResolutionVsQualityFactorPair()
 
 
   MPhysicalEvent* Event = nullptr;
-  MPairEvent* PairEvent = 0; 
+  MPairEvent* PairEvent = 0;
   // ... loop over all events and save a count in the belonging bin ...
   while ((Event = GetNextEvent()) != 0) {
 
@@ -5928,8 +5929,8 @@ void MInterfaceMimrec::AngularResolutionVsQualityFactorPair()
     }
 
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -5938,7 +5939,7 @@ void MInterfaceMimrec::AngularResolutionVsQualityFactorPair()
     return;
   }
 
-    
+
   TCanvas *Canvas = new TCanvas("Canvas angular resolution pairs vs quality factor", "Canvas angular resolution pairs vs quality factor", 800, 600);
   Canvas->SetFillColor(0);
   Canvas->SetFrameBorderSize(0);
@@ -5959,12 +5960,12 @@ void MInterfaceMimrec::AngularResolutionVsQualityFactorPair()
 
 void MInterfaceMimrec::DirectionScatteredGammaRay()
 {
-  
+
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
-  
-  
-  
+
+
+
   // Initalize the image size (x-axis)
   //BinWidth = 2*Disk/NBins;
   TH2D* Hist = new TH2D("Direction scattered gamma ray", "Direction scattered gamma ray", 90, -180, 180, 45, 0, 180);
@@ -5975,45 +5976,45 @@ void MInterfaceMimrec::DirectionScatteredGammaRay()
   Hist->SetStats(false);
   Hist->SetFillColor(8);
   //double BinWidth = 2*Disk/NBins;
-  
-  
+
+
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* ComptonEvent = 0; 
+  MComptonEvent* ComptonEvent = 0;
   // ... loop over all events and save a count in the belonging bin ...
   while ((Event = GetNextEvent()) != 0) {
-    
+
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
       if (Event->GetType() == MPhysicalEvent::c_Compton) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
-        
+
         Hist->Fill(ComptonEvent->Dg().Phi()*c_Deg, ComptonEvent->Dg().Theta()*c_Deg);
       }
     }
-    
+
     delete Event;
-  } 
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
-  
+
   if (Hist->GetMaximum() == 0) {
     mgui<<"No events passed the event selections or file is empty!"<<endl;
     return;
   }
-  
-  
+
+
   TCanvas *Canvas = new TCanvas("Canvas direction scattered gamma ray", "Canvas direction scattered gamma ray", 800, 600);
   Canvas->SetFillColor(0);
   Canvas->SetFrameBorderSize(0);
   Canvas->SetFrameBorderMode(0);
   Canvas->SetBorderSize(0);
   Canvas->SetBorderMode(0);
-  
+
   Canvas->cd();
   Hist->Draw("colz");
   Canvas->Update();
-  
+
   return;
 }
 
@@ -6028,7 +6029,7 @@ void MInterfaceMimrec::SelectIds()
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   MString Name = m_EventFile->GetFileName();
   Name.Replace(Name.Length()-4, 4, ".ids");
 
@@ -6048,8 +6049,8 @@ void MInterfaceMimrec::SelectIds()
     }
 
     delete Event;
-  }   
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -6067,7 +6068,7 @@ void MInterfaceMimrec::InteractionDepth()
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   TH1D* D1 = new TH1D("D1", "D1", 50, 15, 26);
   D1->SetBit(kCanDelete);
   D1->SetXTitle("[cm]");
@@ -6089,7 +6090,7 @@ void MInterfaceMimrec::InteractionDepth()
 
 
   MPhysicalEvent* Event = nullptr;
-  MComptonEvent* ComptonEvent = nullptr; 
+  MComptonEvent* ComptonEvent = nullptr;
   // ... loop over all events and save a count in the belonging bin ...
   while ((Event = GetNextEvent()) != 0) {
 
@@ -6107,8 +6108,8 @@ void MInterfaceMimrec::InteractionDepth()
     }
 
     delete Event;
-  }   
-  
+  }
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -6141,7 +6142,7 @@ void MInterfaceMimrec::LocationOfInitialInteraction()
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-  
+
   double xMin = -100;
   double xMax = +100;
   double yMin = -100;
@@ -6158,8 +6159,8 @@ void MInterfaceMimrec::LocationOfInitialInteraction()
 
   long NMeanDepths = 0;
   double MeanDepth = 0.0;
-  
-  
+
+
   // Step 1: Accumulate many, many hits:
 
   MVector Pos;
@@ -6178,7 +6179,7 @@ void MInterfaceMimrec::LocationOfInitialInteraction()
         merr<<"We have a event without a valid position. ID = "<<Event->GetId()<<". Ignoring it..."<<endl;
       }
     }
-    
+
     delete Event;
 
     if (Positions.size() > MaxNPositions) {
@@ -6190,32 +6191,32 @@ void MInterfaceMimrec::LocationOfInitialInteraction()
   // Step 2: Create the histograms
   DetermineAxis(xMin, xMax, yMin, yMax, zMin, zMax, Positions);
   
-  TH3D* xyzHist = new TH3D("SpatialHitDistributionXYZ",
-                        "Spatial hit distribution xyz",
+  TH3D* xyzHist = new TH3D("SpacialHitDistributionXYZ",
+                        "Spacial hit distribution xyz",
                         MaxNBins, xMin, +xMax,
-                        MaxNBins, yMin, +yMax, 
+                        MaxNBins, yMin, +yMax,
                         MaxNBins, zMin, +zMax);
   xyzHist->SetBit(kCanDelete);
   xyzHist->GetXaxis()->SetTitle("x [cm]");
   xyzHist->GetYaxis()->SetTitle("y [cm]");
   xyzHist->GetZaxis()->SetTitle("z [cm]");
 
-  TH1D* xHist = new TH1D("SpatialHitDistributionX",
-       "Spatial hit distribution x",
+  TH1D* xHist = new TH1D("SpacialHitDistributionX",
+       "Spacial hit distribution x",
        MaxNBins, xMin, +xMax);
   xHist->SetBit(kCanDelete);
   xHist->GetXaxis()->SetTitle("x [cm]");
   xHist->GetYaxis()->SetTitle("counts");
 
-  TH1D* yHist = new TH1D("SpatialHitDistributionY",
-       "Spatial hit distribution y",
+  TH1D* yHist = new TH1D("SpacialHitDistributionY",
+       "Spacial hit distribution y",
        MaxNBins, yMin, +yMax);
   yHist->SetBit(kCanDelete);
   yHist->GetXaxis()->SetTitle("y [cm]");
   yHist->GetYaxis()->SetTitle("counts");
 
-  TH1D* zHist = new TH1D("SpatialHitDistributionZ",
-       "Spatial hit distribution z",
+  TH1D* zHist = new TH1D("SpacialHitDistributionZ",
+       "Spacial hit distribution z",
        MaxNBins, zMin, +zMax);
   zHist->SetBit(kCanDelete);
   zHist->GetXaxis()->SetTitle("z [cm]");
@@ -6231,7 +6232,7 @@ void MInterfaceMimrec::LocationOfInitialInteraction()
     xHist->Fill(Pos[0]);
     yHist->Fill(Pos[1]);
     zHist->Fill(Pos[2]);
-    
+
     NMeanDepths++;
     MeanDepth += Pos[2];
   }
@@ -6252,12 +6253,12 @@ void MInterfaceMimrec::LocationOfInitialInteraction()
           xHist->Fill(Pos[0]);
           yHist->Fill(Pos[1]);
           zHist->Fill(Pos[2]);
-          
+
           NMeanDepths++;
           MeanDepth += Pos[2];
         }
       }
-    } 
+    }
 
     delete Event;
   }
@@ -6298,7 +6299,7 @@ void MInterfaceMimrec::LocationOfInitialInteraction()
     mout<<"Mean depth: "<<MeanDepth/NMeanDepths<<" cm"<<endl;
     mout<<endl;
   }
-  
+
   // Close the event loader
   FinalizeEventLoader();
 }
@@ -6310,63 +6311,63 @@ void MInterfaceMimrec::LocationOfInitialInteraction()
 void MInterfaceMimrec::CreateExposureMap()
 {
   // Create an exposure map
-  
+
   if (m_Settings->GetExposureMode() == MExposureMode::Flat) {
     mgui<<"ERROR: You need to set an exposure mode other than \"flat\" in order to create a useful exposure"<<show;
-    return;    
+    return;
   }
-  
+
   // Check if the exposure efficiency file is there:
   if (MFile::Exists(m_Settings->GetExposureEfficiencyFile()) == false) {
     mgui<<"ERROR: Unable to find exposure efficiency file: \""<<m_Settings->GetExposureEfficiencyFile()<<"\""<<show;
     return;
   }
-  
+
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
-  
+
   MExposure Exposure;
   if (Exposure.SetEfficiencyFile(m_Settings->GetExposureEfficiencyFile()) == false) {
     mgui<<"ERROR: Unable to load exposure efficiency file: \""<<m_Settings->GetExposureEfficiencyFile()<<"\""<<show;
-    return;    
+    return;
   }
-  Exposure.SetDimensions(m_Settings->GetGalLongitudeMin()*c_Rad, 
-                        m_Settings->GetGalLongitudeMax()*c_Rad, 
+  Exposure.SetDimensions(m_Settings->GetGalLongitudeMin()*c_Rad,
+                        m_Settings->GetGalLongitudeMax()*c_Rad,
                         m_Settings->GetBinsGalLongitude(),
                         (m_Settings->GetGalLatitudeMin()+90)*c_Rad,
                         (m_Settings->GetGalLatitudeMax()+90)*c_Rad,
                         m_Settings->GetBinsGalLatitude(),
-                        c_FarAway/10, 
-                        c_FarAway, 
+                        c_FarAway/10,
+                        c_FarAway,
                         1);
-  
-  
+
+
   MPhysicalEvent* Event;
-  while ((Event = GetNextEvent()) != 0) { 
-    
+  while ((Event = GetNextEvent()) != 0) {
+
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
       Exposure.Expose(Event);
     }
     delete Event;
   }
-  
+
   // Close the event loader
   FinalizeEventLoader();
-  
+
   double* ExposureImage = Exposure.GetExposure();
-  
-  MImageGalactic* Galactic = 
-    new MImageGalactic("Exposure in Galactic coordinates", ExposureImage, 
+
+  MImageGalactic* Galactic =
+    new MImageGalactic("Exposure in Galactic coordinates", ExposureImage,
                        "Longitude [deg]", m_Settings->GetGalLongitudeMin(), m_Settings->GetGalLongitudeMax(), m_Settings->GetBinsGalLongitude(),
                        "Latitude [deg]", m_Settings->GetGalLatitudeMin(), m_Settings->GetGalLatitudeMax(), m_Settings->GetBinsGalLatitude(), "Exposure [cm^{2} s]");
   Galactic->Display(nullptr);
 
   delete [] ExposureImage;
-  
+
   return;
 }
-  
-  
+
+
 ////////////////////////////////////////////////////////////////////////////////
 
 
@@ -6377,8 +6378,8 @@ void MInterfaceMimrec::PointingInGalacticCoordinates()
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-    
-  double LatMin = 0;   // -90 
+
+  double LatMin = 0;   // -90
   double LatMax = 180; // -90
   unsigned int LatBins = 360;
   double LatBinSize = (LatMax - LatMin)/LatBins;
@@ -6402,17 +6403,17 @@ void MInterfaceMimrec::PointingInGalacticCoordinates()
       int LatBin = int((Event->GetGalacticPointingZAxisLatitude()*c_Deg + 90 - LatMin)/LatBinSize);
       Array[LongBin + LatBin*LongBins] += 1.0;
     }
-    
+
     delete Event;
   }
-  
+
   // Close the event loader
   FinalizeEventLoader();
 
   // Prepare an MImageGalactic class:
-  MImageGalactic* Galactic = 
+  MImageGalactic* Galactic =
     new MImageGalactic("Pointing in galactic coordinates", Array,
-                       "Longitude", LongMin, LongMax, LongBins, 
+                       "Longitude", LongMin, LongMax, LongBins,
                        "Latitude", LatMin-90, LatMax-90, LatBins,
                        "propotional to time spent [a.u.]",
                        m_Settings->GetImagePalette(), m_Settings->GetImageDrawMode());
@@ -6436,8 +6437,8 @@ void MInterfaceMimrec::HorizonInSphericalDetectorCoordinates()
   // Start with the event file loader first (just in case something goes wrong here)
   if (InitializeEventLoader() == false) return;
 
-    
-  double PhiMin = 0;   // -90 
+
+  double PhiMin = 0;   // -90
   double PhiMax = 360; // -90
   unsigned int PhiBins = 360;
 
@@ -6462,14 +6463,14 @@ void MInterfaceMimrec::HorizonInSphericalDetectorCoordinates()
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
       MVector Z = Event->GetHorizonPointingZAxis();
       double phi = Z.Phi()*c_Deg;
-      while (phi < 0) phi += 360; 
-      while (phi > 360) phi -= 360; 
+      while (phi < 0) phi += 360;
+      while (phi > 360) phi -= 360;
       Spherical->Fill(phi, Z.Theta()*c_Deg);
     }
-    
+
     delete Event;
   }
-  
+
   // Close the event loader
   FinalizeEventLoader();
 
@@ -6494,7 +6495,7 @@ void MInterfaceMimrec::CreateCosimaOrientationFile()
   MString FileName = m_Settings->GetCurrentFileName();
   FileName.ReplaceAtEnd(".tra.gz", ".ori");
   FileName.ReplaceAtEnd(".tra", ".ori");
-  
+
   ofstream out;
   out.open(FileName);
   out<<endl;
@@ -6503,11 +6504,11 @@ void MInterfaceMimrec::CreateCosimaOrientationFile()
   out.setf(ios::fixed);
   out.precision(6);
   // First check on the size of the histogram:
-  
+
   FileName = m_Settings->GetCurrentFileName();
   FileName.ReplaceAtEnd(".tra.gz", ".onoff");
   FileName.ReplaceAtEnd(".tra", ".onoff");
-  
+
   ofstream lout;
   lout.open(FileName);
   lout<<endl;
@@ -6516,16 +6517,16 @@ void MInterfaceMimrec::CreateCosimaOrientationFile()
   lout.setf(ios::fixed);
   lout.precision(6);
   // First check on the size of the histogram:
-  
+
   double LastXAxisLongitude = -1000;
   double LastXAxisLatitude = -1000;
   double LastZAxisLongitude = -1000;
   double LastZAxisLatitude = -1000;
-  
+
   bool First = true;
   MTime LastTime(0);
-  MTime Gap(5.0); 
-  
+  MTime Gap(5.0);
+
   bool IsOn = false;
   MPhysicalEvent* Event = nullptr;
   while ((Event = GetNextEvent()) != 0) {
@@ -6539,7 +6540,7 @@ void MInterfaceMimrec::CreateCosimaOrientationFile()
           <<" "<<Event->GetGalacticPointingXAxisLongitude()*c_Deg
           <<" "<<Event->GetGalacticPointingZAxisLatitude()*c_Deg
           <<" "<<Event->GetGalacticPointingZAxisLongitude()*c_Deg<<endl;
-         
+
         LastXAxisLongitude = Event->GetGalacticPointingXAxisLongitude();
         LastXAxisLatitude = Event->GetGalacticPointingXAxisLatitude();
         LastZAxisLongitude = Event->GetGalacticPointingZAxisLongitude();
@@ -6552,7 +6553,7 @@ void MInterfaceMimrec::CreateCosimaOrientationFile()
             lout<<"DP "<<LastTime<<" off"<<endl;
             IsOn = false;
           }
-        } else {  
+        } else {
           if (Event->GetTime() - LastTime > Gap) {
             if (IsOn == true) {
               cout<<"Forward Jump: Off: "<<Event->GetTime()<<":"<<LastTime<<endl;
@@ -6584,18 +6585,18 @@ void MInterfaceMimrec::CreateCosimaOrientationFile()
     //cout<<"Off: "<<LastTime<<endl;
     lout<<"DP "<<LastTime<<" off"<<endl;
   }
-  
+
   // Close the event loader
   FinalizeEventLoader();
-  
+
   out<<"EN"<<endl;
   out<<endl;
   out.close();
-  
+
   lout<<"EN"<<endl;
   lout<<endl;
   lout.close();
-  
+
   return;
 }
 
@@ -6605,17 +6606,17 @@ void MInterfaceMimrec::CreateCosimaOrientationFile()
 
 void MInterfaceMimrec::StandardAnalysis(double Energy, MVector Position)
 {
-  cout<<"Standard analysis started"<<endl; 
+  cout<<"Standard analysis started"<<endl;
 
   MStandardAnalysis A;
-  
+
   A.SetEventSelector(*m_Selector);
   A.SetGeometry(m_Geometry);
   A.SetFileName(m_Settings->GetCurrentFileName());
-   
+
   A.SetPosition(Position);
   A.SetEnergy(Energy);
-  
+
   if (A.Analyze() == false) {
     cout<<"Analysis failed"<<endl;
   }
diff --git a/src/mimrec/src/MSettingsEventSelections.cxx b/src/mimrec/src/MSettingsEventSelections.cxx
index ff755aadb..9dfb57805 100644
--- a/src/mimrec/src/MSettingsEventSelections.cxx
+++ b/src/mimrec/src/MSettingsEventSelections.cxx
@@ -114,7 +114,7 @@ MSettingsEventSelections::MSettingsEventSelections() : MSettingsInterface()
   m_SourceLongitude = 184.56;
   m_SourceLatitude = -5.78;
   m_SourceX = 0.0;
-  m_SourceY = 0.0; 
+  m_SourceY = 0.0;
   m_SourceZ = 100.0;
   m_SourceARMMin = 0.0;
   m_SourceARMMax = 180.0;
@@ -129,13 +129,13 @@ MSettingsEventSelections::MSettingsEventSelections() : MSettingsInterface()
   m_PointingBoxLongitude = 0;
   m_PointingBoxExtentLatitude = 0;
   m_PointingBoxExtentLongitude = 0;
-  
+
   m_BeamUse = false;
   m_BeamStartX = 0.0;
-  m_BeamStartY = 0.0; 
+  m_BeamStartY = 0.0;
   m_BeamStartZ = 10000.0;
   m_BeamFocalSpotX = 0.0;
-  m_BeamFocalSpotY = 0.0; 
+  m_BeamFocalSpotY = 0.0;
   m_BeamFocalSpotZ = 0.0;
   m_BeamRadius = 1000.0;
   m_BeamDepth = 1000.0;
@@ -166,7 +166,7 @@ MSettingsEventSelections::MSettingsEventSelections() : MSettingsInterface()
   m_TimeRangeMin.Set(0.0);
   m_TimeRangeMax.Set(2000000000.0);
   m_TimeFile = "";
-  
+
   m_TimeWalkRangeMin = -1000;
   m_TimeWalkRangeMax = numeric_limits<int>::max();
 
@@ -179,6 +179,9 @@ MSettingsEventSelections::MSettingsEventSelections() : MSettingsInterface()
   m_InitialEnergyDepositPairMin = 0;
   m_InitialEnergyDepositPairMax = 10000;
 
+  m_QualityFactorPairMin = -1;
+  m_QualityFactorPairMax = numeric_limits<double>::max();
+
   m_EventTypeCompton = 1;
   m_EventTypeDoubleCompton = 1;
   m_EventTypeComptonNotTracked = 1;
@@ -227,6 +230,8 @@ bool MSettingsEventSelections::WriteXml(MXmlNode* Node)
   new MXmlNode(aNode, "UseEventTypeComptonNotTracked", m_EventTypeComptonNotTracked);
   new MXmlNode(aNode, "UseEventTypeComptonTracked", m_EventTypeComptonTracked);
   new MXmlNode(aNode, "UseEventTypePair", m_EventTypePair);
+  new MXmlNode(aNode, "UseEventTypePhoto", m_EventTypePhoto);
+  new MXmlNode(aNode, "UseEventTypeUnidentifiable", m_EventTypeUnidentifiable);
   new MXmlNode(aNode, "UseEventTypePhoto", m_EventTypePhoto); 
   new MXmlNode(aNode, "UseEventTypePET", m_EventTypePET); 
   new MXmlNode(aNode, "UseEventTypeMulti", m_EventTypeMulti); 
@@ -260,29 +265,29 @@ bool MSettingsEventSelections::WriteXml(MXmlNode* Node)
   new MXmlNode(aNode, "CoincidenceWindow", m_CoincidenceWindowRangeMin, m_CoincidenceWindowRangeMax);
   new MXmlNode(aNode, "OpeningAnglePair", m_OpeningAnglePairMin, m_OpeningAnglePairMax);
   new MXmlNode(aNode, "InitialEnergyDepositPair", m_InitialEnergyDepositPairMin, m_InitialEnergyDepositPairMax);
-  
+
   bNode = new MXmlNode(aNode, "EarthHorizonCut");
-  new MXmlNode(bNode, "Type", m_EHCType); 
+  new MXmlNode(bNode, "Type", m_EHCType);
   new MXmlNode(bNode, "Probability", m_EHCProbability);
-  new MXmlNode(bNode, "ComptonProbabilityFile", m_EHCComptonProbabilityFileName); 
+  new MXmlNode(bNode, "ComptonProbabilityFile", m_EHCComptonProbabilityFileName);
   new MXmlNode(bNode, "PairProbabilityFile", m_EHCPairProbabilityFileName);
   new MXmlNode(bNode, "Angle", m_EHCAngle);
-  new MXmlNode(bNode, "EarthPosition", m_EHCEarthPosition); 
+  new MXmlNode(bNode, "EarthPosition", m_EHCEarthPosition);
 
-  bNode = new MXmlNode(aNode, "Source");  
+  bNode = new MXmlNode(aNode, "Source");
   new MXmlNode(bNode, "UsePointSource", m_SourceUsePointSource);
   new MXmlNode(bNode, "Coordinates", static_cast<int>(m_SourceCoordinates));
-  new MXmlNode(bNode, "Phi", m_SourcePhi); 
+  new MXmlNode(bNode, "Phi", m_SourcePhi);
   new MXmlNode(bNode, "Theta", m_SourceTheta);
-  new MXmlNode(bNode, "Longitude", m_SourceLongitude); 
+  new MXmlNode(bNode, "Longitude", m_SourceLongitude);
   new MXmlNode(bNode, "Latitude", m_SourceLatitude);
-  new MXmlNode(bNode, "X", m_SourceX); 
-  new MXmlNode(bNode, "Y", m_SourceY); 
-  new MXmlNode(bNode, "Z", m_SourceZ); 
-  new MXmlNode(bNode, "ARM", m_SourceARMMin, m_SourceARMMax); 
+  new MXmlNode(bNode, "X", m_SourceX);
+  new MXmlNode(bNode, "Y", m_SourceY);
+  new MXmlNode(bNode, "Z", m_SourceZ);
+  new MXmlNode(bNode, "ARM", m_SourceARMMin, m_SourceARMMax);
   new MXmlNode(bNode, "SPD", m_SourceSPDMin, m_SourceSPDMax);
 
-  bNode = new MXmlNode(aNode, "Pointing");  
+  bNode = new MXmlNode(aNode, "Pointing");
   new MXmlNode(bNode, "PointingSelectionType", m_PointingSelectionType);
   new MXmlNode(bNode, "PointingPointSourceLatitude", m_PointingPointSourceLatitude);
   new MXmlNode(bNode, "PointingPointSourceLongitude", m_PointingPointSourceLongitude);
@@ -291,16 +296,16 @@ bool MSettingsEventSelections::WriteXml(MXmlNode* Node)
   new MXmlNode(bNode, "PointingBoxLongitude", m_PointingBoxLongitude);
   new MXmlNode(bNode, "PointingBoxExtentLatitude", m_PointingBoxExtentLatitude);
   new MXmlNode(bNode, "PointingBoxExtentLongitude", m_PointingBoxExtentLongitude);
-  
+
   bNode = new MXmlNode(aNode, "Beam");
   new MXmlNode(bNode, "UseBeam", m_BeamUse);
-  new MXmlNode(bNode, "StartX", m_BeamStartX); 
-  new MXmlNode(bNode, "StartY", m_BeamStartY); 
-  new MXmlNode(bNode, "StartZ", m_BeamStartZ); 
-  new MXmlNode(bNode, "FocalSpotX", m_BeamFocalSpotX); 
-  new MXmlNode(bNode, "FocalSpotY", m_BeamFocalSpotY); 
-  new MXmlNode(bNode, "FocalSpotZ", m_BeamFocalSpotZ); 
-  new MXmlNode(bNode, "Radius", m_BeamRadius); 
+  new MXmlNode(bNode, "StartX", m_BeamStartX);
+  new MXmlNode(bNode, "StartY", m_BeamStartY);
+  new MXmlNode(bNode, "StartZ", m_BeamStartZ);
+  new MXmlNode(bNode, "FocalSpotX", m_BeamFocalSpotX);
+  new MXmlNode(bNode, "FocalSpotY", m_BeamFocalSpotY);
+  new MXmlNode(bNode, "FocalSpotZ", m_BeamFocalSpotZ);
+  new MXmlNode(bNode, "Radius", m_BeamRadius);
   new MXmlNode(bNode, "BeamDepth", m_BeamDepth);
   
   bNode = new MXmlNode(aNode, "Box");
@@ -339,12 +344,12 @@ bool MSettingsEventSelections::WriteXml(MXmlNode* Node)
 bool MSettingsEventSelections::ReadXml(MXmlNode* Node)
 {
   // Retrieve the content from an XML tree
-  
+
   MXmlNode* aNode = 0;
   MXmlNode* bNode = 0;
   MXmlNode* cNode = 0;
- 
- 
+
+
   if ((aNode = Node->GetNode("EventSelections")) != 0) {
     if ((bNode = aNode->GetNode("EventSelectorTab")) != 0) {
       m_EventSelectorTab = bNode->GetValueAsInt();
@@ -379,12 +384,12 @@ bool MSettingsEventSelections::ReadXml(MXmlNode* Node)
     if ((bNode = aNode->GetNode("FlaggedAsBad")) != 0) {
       m_FlaggedAsBad = bNode->GetValueAsInt();
     }
-    
+
     if ((bNode = aNode->GetNode("EventID")) != 0) {
       m_EventIdRangeMin = bNode->GetMinValueAsLong();
       m_EventIdRangeMax = bNode->GetMaxValueAsLong();
     }
-    
+
     if ((bNode = aNode->GetNode("TimeMode")) != 0) {
       m_TimeMode = bNode->GetValueAsUnsignedInt();
     }
@@ -395,7 +400,7 @@ bool MSettingsEventSelections::ReadXml(MXmlNode* Node)
     if ((bNode = aNode->GetNode("TimeFile")) != 0) {
       m_TimeFile = bNode->GetValueAsString();
     }
-    
+
     if ((bNode = aNode->GetNode("TrackLength")) != 0) {
       m_TrackLengthRangeMin = bNode->GetMinValueAsInt();
       m_TrackLengthRangeMax = bNode->GetMaxValueAsInt();
@@ -522,15 +527,15 @@ bool MSettingsEventSelections::ReadXml(MXmlNode* Node)
         m_SourceZ = cNode->GetValueAsDouble();
       }
       if ((cNode = bNode->GetNode("ARM")) != 0) {
-        m_SourceARMMin = cNode->GetMinValueAsDouble(); 
+        m_SourceARMMin = cNode->GetMinValueAsDouble();
         m_SourceARMMax = cNode->GetMaxValueAsDouble();
       }
       if ((cNode = bNode->GetNode("SPD")) != 0) {
-        m_SourceSPDMin = cNode->GetMinValueAsDouble(); 
+        m_SourceSPDMin = cNode->GetMinValueAsDouble();
         m_SourceSPDMax = cNode->GetMaxValueAsDouble();
       }
     }
-  
+
     if ((bNode = aNode->GetNode("Pointing")) != 0) {
       if ((cNode = bNode->GetNode("PointingSelectionType")) != 0) {
         m_PointingSelectionType = cNode->GetValueAsUnsignedInt();
@@ -557,7 +562,7 @@ bool MSettingsEventSelections::ReadXml(MXmlNode* Node)
         m_PointingBoxExtentLongitude = cNode->GetValueAsDouble();
       }
     }
-      
+
     if ((bNode = aNode->GetNode("Beam")) != 0) {
       if ((cNode = bNode->GetNode("UseBeam")) != 0) {
         m_BeamUse = cNode->GetValueAsBoolean();
diff --git a/src/revan/Makefile b/src/revan/Makefile
index bc1f16049..2ef84eb01 100644
--- a/src/revan/Makefile
+++ b/src/revan/Makefile
@@ -40,6 +40,8 @@ FILES := MGeometryRevan \
 	MERTrackGas \
 	MERTrackDirectional \
 	MERTrackChiSquare \
+	MERTrackKalman3D \
+	MERTrackKalman2D \
 	MERCSR \
 	MERCSRChiSquare \
 	MERCSREnergyRecovery \
@@ -207,6 +209,3 @@ $(EXECUTABLE): $(SHAREDLIB_UI) $(SHAREDLIB) $(OBJECT_MAIN)
 	
 #
 #----------------------------------------------------------------
-
-
-
diff --git a/src/revan/inc/MERTrackKalman2D.h b/src/revan/inc/MERTrackKalman2D.h
new file mode 100644
index 000000000..36aa17087
--- /dev/null
+++ b/src/revan/inc/MERTrackKalman2D.h
@@ -0,0 +1,84 @@
+/*
+ * MERTrackKalman2D.h
+ *
+ * Copyright (C) by Paolo Cumani & Andreas Zoglauer.
+ * All rights reserved.
+ *
+ * Please see the source-file for the copyright-notice.
+ *
+ */
+
+
+#ifndef __MERTrackKalman2D__
+#define __MERTrackKalman2D__
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+// ROOT libs:
+
+// MEGAlib libs:
+#include "MGlobal.h"
+#include "MGeometryRevan.h"
+#include "MERTrack.h"
+
+
+// Forward declarations:
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+class MERTrackKalman2D : public MERTrack
+{
+  // public interface:
+ public:
+  MERTrackKalman2D();
+  virtual ~MERTrackKalman2D();
+
+  //! Set all special parameters - this function should not rely on a previous
+  //! call to SetParameters()
+  virtual bool SetSpecialParameters(double SigmaHitPos, unsigned int NLayersForVertexSearch);
+
+  virtual MString ToString(bool CoreOnly = false) const;
+
+  // protected methods:
+ protected:
+
+  //bool EvaluateTracks(MRERawEvent* ER);
+  Float_t Kalman(MRERawEvent* RE, Int_t n, Float_t en, MRESEList Previous, vector < TMatrix > &trk, Int_t view, MRESEList &Chosen);
+  tuple<vector < TMatrix >, Float_t, Float_t, vector < TMatrix >, Float_t, Float_t, MRESEList, MRESEList> SearchTracks(MRERawEvent* RE, Int_t view);
+  Float_t MultipleScattering2D(vector < TMatrix > trk);
+  Float_t MultipleScattering3D(MRESEList trkx, MRESEList trky);
+  void TrackPairs(MRERawEvent* RE);
+
+  // private methods:
+ private:
+
+  // protected members:
+ protected:
+
+  Float_t m_sigma;
+  Float_t w;
+  Float_t m_heightX0;
+  Float_t sfg_factor;
+
+  Float_t start_nrg_fit;        //Energy used in Kalman matrix (keV)
+  Int_t n_fit;
+
+  // private members:
+ private:
+
+
+#ifdef ___CINT___
+ public:
+  ClassDef(MERTrackKalman2D, 0) // no description
+#endif
+
+};
+
+#endif
+
+
+////////////////////////////////////////////////////////////////////////////////
diff --git a/src/revan/inc/MERTrackKalman3D.h b/src/revan/inc/MERTrackKalman3D.h
new file mode 100644
index 000000000..c36cd0050
--- /dev/null
+++ b/src/revan/inc/MERTrackKalman3D.h
@@ -0,0 +1,96 @@
+/*
+ * MERTrackKalman3D.h
+ *
+ * Copyright (C) by Paolo Cumani & Andreas Zoglauer.
+ * All rights reserved.
+ *
+ * Please see the source-file for the copyright-notice.
+ *
+ */
+
+
+#ifndef __MERTrackKalman3D__
+#define __MERTrackKalman3D__
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+// ROOT libs:
+
+// MEGAlib libs:
+#include "MGlobal.h"
+#include "MGeometryRevan.h"
+#include "MERTrack.h"
+
+#include "TTree.h"
+// Forward declarations:
+
+#include <vector>
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+class MERTrackKalman3D : public MERTrack
+{
+
+  // Utility fucnciton
+  static Float_t accumulate(vector<Float_t>::const_iterator start,
+			    vector<Float_t>::const_iterator stop,
+			    Float_t init_value);
+  
+  // public interface:
+ public:
+  MERTrackKalman3D();
+  virtual ~MERTrackKalman3D();
+
+  //! Set all special parameters - this function should not rely on a previous
+  //! call to SetParameters()
+  virtual bool SetSpecialParameters(double SigmaHitPos, unsigned int NLayersForVertexSearch);
+
+  virtual MString ToString(bool CoreOnly = false) const;
+
+  // protected methods:
+ protected:
+
+  //bool EvaluateTracks(MRERawEvent* ER);
+  Float_t Kalman(MRERawEvent* RE, Int_t n, Float_t en, MRESEList Previous, vector < TMatrix > &trk, MRESEList &Chosen);
+  tuple<vector < TMatrix >, Float_t, Float_t, vector < TMatrix >, Float_t, Float_t, MRESEList, MRESEList> SearchTracks(MRERawEvent* RE);
+  Float_t MultipleScattering(vector < TMatrix > trk);
+  void TrackPairs(MRERawEvent* RE);
+  MRawEventIncarnations* CheckForPair(MRERawEvent* RE);
+
+  //These functions are not used, they are kept for record-keeping
+  Float_t EnergyEst3D(vector < TMatrix > trk);
+  Float_t MultipleScattering3D(vector < TMatrix > trk, Double_t e0);
+
+  // private methods:
+ private:
+
+  // protected members:
+ protected:
+
+  Float_t m_sigma;
+  Float_t w;
+  Float_t m_heightX0;
+  Float_t sfg_factor;
+  Float_t max_offset;
+
+  Float_t start_nrg_fit;        //Energy used in Kalman matrix (keV)
+  Int_t n_fit;
+
+  // private members:
+ private:
+
+
+#ifdef ___CINT___
+ public:
+  ClassDef(MERTrackKalman3D, 0) // no description
+#endif
+
+};
+
+#endif
+
+
+////////////////////////////////////////////////////////////////////////////////
diff --git a/src/revan/inc/MGUIERAlgorithm.h b/src/revan/inc/MGUIERAlgorithm.h
index 4e985893e..87db721f8 100644
--- a/src/revan/inc/MGUIERAlgorithm.h
+++ b/src/revan/inc/MGUIERAlgorithm.h
@@ -34,7 +34,7 @@ class MGUIERAlgorithm : public MGUIDialog
 {
   // Public Interface:
  public:
-  MGUIERAlgorithm(const TGWindow* Parent, const TGWindow* Main, 
+  MGUIERAlgorithm(const TGWindow* Parent, const TGWindow* Main,
                   MSettingsEventReconstruction* Data);
   virtual ~MGUIERAlgorithm();
 
@@ -62,8 +62,9 @@ class MGUIERAlgorithm : public MGUIDialog
   MGUIERBList* m_HitClusteringList;
   MGUIERBList* m_TrackingList;
   MGUIERBList* m_CSRList;
+  MGUIERBList* m_PairList;
   //MGUIERBList* m_DecayList;
- 
+
 
 
 #ifdef ___CLING___
diff --git a/src/revan/inc/MGUIOptionsTracking.h b/src/revan/inc/MGUIOptionsTracking.h
index 3305d9763..c87d0daef 100644
--- a/src/revan/inc/MGUIOptionsTracking.h
+++ b/src/revan/inc/MGUIOptionsTracking.h
@@ -38,7 +38,7 @@ class MGUIOptionsTracking : public MGUIDialog
 {
   // Public Interface:
  public:
-  MGUIOptionsTracking(const TGWindow* Parent, const TGWindow* Main, 
+  MGUIOptionsTracking(const TGWindow* Parent, const TGWindow* Main,
                       MSettingsEventReconstruction* Data,
                       MDGeometryQuest* Geometry);
   virtual ~MGUIOptionsTracking();
@@ -60,16 +60,17 @@ class MGUIOptionsTracking : public MGUIDialog
  private:
   MSettingsEventReconstruction* m_Data;
   MDGeometryQuest* m_Geometry;
-  
+
   MGUIECBList* m_CBList;
   MGUIEEntry* m_MaxComptonJump;
   MGUIEEntry* m_NSequencesToKeep;
   TGCheckButton* m_RejectPurelyAmbiguousSequences;
   MGUIEFileSelector* m_FileSelector;
   MGUIEEntry* m_NLayersForVertexSearch;
+  MGUIEEntry* m_SigmaHitPos;
 
   TGListBox* m_DetectorList;
-  
+
   enum ButtonCodes { e_DoTracking = 100, e_RejectPurelyAmbiguousSequences, e_Detectors };
 
 #ifdef ___CLING___
diff --git a/src/revan/inc/MRawEventAnalyzer.h b/src/revan/inc/MRawEventAnalyzer.h
index ba5bf31d1..aa2b70733 100644
--- a/src/revan/inc/MRawEventAnalyzer.h
+++ b/src/revan/inc/MRawEventAnalyzer.h
@@ -46,7 +46,7 @@ class MERDecay;
 ////////////////////////////////////////////////////////////////////////////////
 
 //! How to use guide:
-//! 
+//!
 //! First create the analyzer:
 //! > MRawEventAnalyzer Analyzer;
 //! Then set the event mode (default is "Add")
@@ -64,7 +64,7 @@ class MRawEventAnalyzer
 
   //! Set all options from a settings file
   void SetSettings(MSettingsEventReconstruction* Setting);
-  
+
   //! If events are read from file set it here
   bool SetInputModeFile(MString Filename);
   //! If events are written to a file, set it with this function
@@ -72,19 +72,19 @@ class MRawEventAnalyzer
 
   //! Do not use any GUI functions
   void SetBatch(bool IsBatch) { m_IsBatch = IsBatch; }
-  
+
   //! Call this function just before the event reconstruction starts
   bool PreAnalysis();
-  
+
   //! In case the events are not read from file,
   //! add an event to the back of the temporary event store.
   //! The raw event will be deleted by this class!
   bool AddRawEvent(MRERawEvent* RE);
-  
+
   //! In case the events are not read from file,
   //! create the event from a string containing ALL event data
   bool AddRawEvent(const MString& RE, bool NeedsNoising = true, int Version = 25);
-  
+
   //! Analyze one event
   //! The event can then be retrieved via GetOptimumEvent() or GetBestTryEvent()
   //! Return codes:
@@ -93,10 +93,10 @@ class MRawEventAnalyzer
   //! c_AnalysisNoEventsInStore
   //! c_AnalysisNoEventsLeftInFile
   unsigned int AnalyzeEvent();
-  
-  //! Save the OI 
+
+  //! Save the OI
   void SetSaveOI(bool SaveOI);
-  
+
   // The return codes of AnalyzeEvent()
   static const unsigned int c_AnalysisSucess;
   static const unsigned int c_AnalysisCoincidenceWindowWait;
@@ -105,14 +105,14 @@ class MRawEventAnalyzer
   static const unsigned int c_AnalysisNoEventsLeftInFile;
   static const unsigned int c_AnalysisSavingEventFailed;
   static const unsigned int c_AnalysisUndefinedError;
-  
+
   //! Return the next initial raw event from file
   //! Return zero if the input mode is not file or if the ened of the file has been reached
   MRERawEvent* GetNextInitialRawEventFromFile();
 
-  
+
   // The results:
-  
+
   //! The returns the best found event
   vector<MRERawEvent*> GetOptimumEvents();
   //! Return the single best event -- if we have multiple events it will just return the first one
@@ -134,11 +134,11 @@ class MRawEventAnalyzer
 
   //! Optional: Call this function at the end of the event reconstruction to gather some statistics
   bool PostAnalysis();
-  
+
   //! If multiple raw event analyzer have been started, e.g. for multi threading, the analysis statistics can be joinded with this function
   void JoinStatistics(const MRawEventAnalyzer& A);
 
-  
+
   // Interface for the basic reconstruction algorithms
   
   static const int c_CoincidenceAlgoNone;
@@ -171,18 +171,27 @@ class MRawEventAnalyzer
   static const int c_TrackingAlgoBayesian;
   static const int c_TrackingAlgoRank;
 
-  //! Set the electron tracking algorithm: One of c_TrackingAlgoNone, c_TrackingAlgoModifiedPearson, c_TrackingAlgoPearson, 
-  //! c_TrackingAlgoChiSquare, c_TrackingAlgoGas, c_TrackingAlgoDirectional, c_TrackingAlgoBayesian, c_TrackingAlgoRank 
+  //! Set the electron tracking algorithm: One of c_TrackingAlgoNone, c_TrackingAlgoModifiedPearson, c_TrackingAlgoPearson,
+  //! c_TrackingAlgoChiSquare, c_TrackingAlgoGas, c_TrackingAlgoDirectional, c_TrackingAlgoBayesian, c_TrackingAlgoRank
   void SetTrackingAlgorithm(int ID) { m_TrackingAlgorithm = ID; }
 
+  static const int c_PairDefault;
+  static const int c_PairKalman3D;
+  static const int c_PairKalman2D;
+
+  //! Set the pair reconstruction algorithm: One of c_PairDefault, c_PairKalman3D or c_PairKalman2D
+  void SetPairAlgorithm(int ID) { m_PairAlgorithm = ID; }
+
+
   static const int c_CSRAlgoNone;
   static const int c_CSRAlgoFoM;
   static const int c_CSRAlgoFoME;
   static const int c_CSRAlgoFoMToF;
   static const int c_CSRAlgoFoMToFAndE;
   static const int c_CSRAlgoBayesian;
+
   static const int c_CSRAlgoTMVA;
-  
+
   //! Set the Compton photon tracking algorithm: One of c_CSRAlgoNone, c_CSRAlgoFoM, c_CSRAlgoFoME, c_CSRAlgoFoMToF, c_CSRAlgoBayesian
   void SetCSRAlgorithm(int ID) { m_CSRAlgorithm = ID; }
 
@@ -242,7 +251,7 @@ class MRawEventAnalyzer
   void SetPDFClusterizer(MString BaseFileName) {
     m_PDFClusterizerBaseFileName = BaseFileName;
   }
-  
+
   // Options electron tracking:
   void SetDoTracking(bool Do) { m_DoTracking = Do; if (Do == false) m_TrackingAlgorithm = c_TrackingAlgoNone; }
   void SetSearchPairTracks(bool Search) { m_SearchPairTracks = Search; }
@@ -256,27 +265,30 @@ class MRawEventAnalyzer
   void SetRejectPurelyAmbiguousTrackSequences(bool Flag) { m_RejectPurelyAmbiguousTrackSequences = Flag; }
   void SetNLayersForVertexSearch(unsigned int NLayersForVertexSearch) { m_NLayersForVertexSearch = NLayersForVertexSearch; }
   void SetElectronTrackingDetectorList(vector<MString> DetectorList) { m_ElectronTrackingDetectorList = DetectorList; }
-  
+
+  // Options Kalman Filter
+  void SetSigmaHitPos(double SigmaHitPos) { m_SigmaHitPos = SigmaHitPos; }
+
   // Option Compton tracking:
   void SetClassicUndecidedHandling(int Flag) { m_ClassicUndecidedHandling = Flag; }
   void SetAssumeD1First(bool Flag) { m_AssumeD1First = Flag; }
   void SetUseComptelTypeEvents(bool Flag) { m_UseComptelTypeEvents = Flag; }
   void SetGuaranteeStartD1(bool Flag) { m_GuaranteeStartD1 = Flag; }
   void SetRejectOneDetectorTypeOnlyEvents(bool Flag) { m_RejectOneDetectorTypeOnlyEvents = Flag; }
-  
+
   void SetCSRThresholdMin(double Value) { m_CSRThresholdMin = Value; }
   void SetCSRThresholdMax(double Value) { m_CSRThresholdMax = Value; }
 
   void SetCSRMaxNHits(int Value) { m_CSRMaxNHits = Value; }
   void SetCSROnlyCreateSequences(bool Flag) { m_CSROnlyCreateSequences = Flag; }
   void SetOriginObjectsFileName(MString Name) { m_OriginObjectsFileName = Name; }
-  
+
   void SetBCTFileName(MString FileName) { m_BCTFileName = FileName; }
   
   void SetCSRTMVAFileName(MString FileName) { m_CSRTMVAFileName = FileName; }
   void SetCSRTMVAMethods(MERCSRTMVAMethods Methods) { m_CSRTMVAMethods = Methods; }
   
-  
+
   void SetFocalSpotCenter(MVector FocalSpotCenter) { m_FocalSpotCenter = FocalSpotCenter; }
   void SetLensCenter(MVector LensCenter) { m_LensCenter = LensCenter; }
 
@@ -294,6 +306,7 @@ class MRawEventAnalyzer
 
   // Decay options
   void SetDecayFileName(MString FileName) { m_DecayFileName = FileName; }
+
   void AddDecayEnergy(double Energy, double Error) { m_DecayEnergy.push_back(Energy); m_DecayEnergyError.push_back(Error); }
 
 
@@ -350,7 +363,7 @@ class MRawEventAnalyzer
   //! Provides functionality for noising simulation data
   //! This one is independent of the one used in MFileEventsEvta
   MERNoising* m_Noising;
-  
+
   MString m_Filename;
   MString m_FilenameOut;
 
@@ -380,6 +393,7 @@ class MRawEventAnalyzer
   int m_EventClusteringAlgorithm;
   int m_HitClusteringAlgorithm;
   int m_TrackingAlgorithm;
+  int m_PairAlgorithm;
   int m_CSRAlgorithm;
   int m_DecayAlgorithm;
 
@@ -422,7 +436,10 @@ class MRawEventAnalyzer
   unsigned int m_NLayersForVertexSearch;
 
   vector<MString> m_ElectronTrackingDetectorList;
-  
+
+  //Kalman Filter:
+  double m_SigmaHitPos;
+
   // Compton tracking:
   bool m_AssumeD1First;
   bool m_UseComptelTypeEvents;
@@ -430,7 +447,7 @@ class MRawEventAnalyzer
   bool m_GuaranteeStartD1;
   bool m_RejectOneDetectorTypeOnlyEvents;
   bool m_CSROnlyCreateSequences;
-  
+
   double m_CSRThresholdMin;
   double m_CSRThresholdMax;
 
@@ -438,7 +455,7 @@ class MRawEventAnalyzer
 
   MString m_OriginObjectsFileName;
   MString m_BCTFileName;
-  
+
   MString m_CSRTMVAFileName;
   MERCSRTMVAMethods m_CSRTMVAMethods;
   
diff --git a/src/revan/inc/MSettingsEventReconstruction.h b/src/revan/inc/MSettingsEventReconstruction.h
index 9e9f865e0..3496966ad 100644
--- a/src/revan/inc/MSettingsEventReconstruction.h
+++ b/src/revan/inc/MSettingsEventReconstruction.h
@@ -38,7 +38,7 @@ class MSettingsEventReconstruction : public MSettingsInterface
 
   void SetSaveOI(bool SaveOI) { m_SaveOI = SaveOI; }
   bool GetSaveOI() const { return m_SaveOI; }
-  
+
   void SetNJobs(unsigned int ID) { m_NJobs = ID; }
   unsigned int GetNJobs() { return m_NJobs; }
 
@@ -54,12 +54,15 @@ class MSettingsEventReconstruction : public MSettingsInterface
   void SetTrackingAlgorithm(int ID) { m_TrackingAlgorithm = ID; }
   int GetTrackingAlgorithm() { return m_TrackingAlgorithm; }
 
+  void SetPairAlgorithm(int ID) { m_PairAlgorithm = ID; }
+  int GetPairAlgorithm() { return m_PairAlgorithm; }
+
   void SetCSRAlgorithm(int ID) { m_CSRAlgorithm = ID; }
   int GetCSRAlgorithm() { return m_CSRAlgorithm; }
 
   void SetDecayAlgorithm(int ID) { m_DecayAlgorithm = ID; }
   int GetDecayAlgorithm() { return m_DecayAlgorithm; }
-  
+
   void SetCoincidenceWindow(double Time) {
     m_CoincidenceWindow = Time;
   }
@@ -156,7 +159,7 @@ class MSettingsEventReconstruction : public MSettingsInterface
   int GetAdjacentLevel() const {
     return m_AdjacentLevel;
   }
-  
+
   void SetPDFClusterizerBaseFileName(MString BaseFileName) {
     m_PDFClusterizerBaseFileName = BaseFileName;
   }
@@ -186,6 +189,11 @@ class MSettingsEventReconstruction : public MSettingsInterface
   void SetNLayersForVertexSearch(int Value) { m_NLayersForVertexSearch = Value; }
   int GetNLayersForVertexSearch() { return m_NLayersForVertexSearch; }
 
+  void SetHeightX0(double Value) { m_HeightX0 = Value; }
+  double GetHeightX0() { return m_HeightX0; }
+  void SetSigmaHitPos(double Value) { m_SigmaHitPos = Value; }
+  double GetSigmaHitPos() { return m_SigmaHitPos; }
+
 
   void RemoveAllElectronTrackingDetectors() { m_ElectronTrackingDetectors.clear(); }
   void AddElectronTrackingDetector(const MString& ElectronTracking) { m_ElectronTrackingDetectors.push_back(ElectronTracking); }
@@ -207,10 +215,10 @@ class MSettingsEventReconstruction : public MSettingsInterface
   bool GetGuaranteeStartD1() { return m_GuaranteeStartD1; }
   void SetRejectOneDetectorTypeOnlyEvents(bool Flag) { m_RejectOneDetectorTypeOnlyEvents = Flag; }
   bool GetRejectOneDetectorTypeOnlyEvents() { return m_RejectOneDetectorTypeOnlyEvents; }
-  
+
   void SetCSRThresholdMin(double Value) { m_CSRThresholdMin = Value; }
   double GetCSRThresholdMin() { return m_CSRThresholdMin; }
-  
+
   void SetCSRThresholdMax(double Value) { m_CSRThresholdMax = Value; }
   double GetCSRThresholdMax() { return m_CSRThresholdMax; }
 
@@ -219,7 +227,7 @@ class MSettingsEventReconstruction : public MSettingsInterface
 
   void SetBayesianElectronFileName(MString Name) { m_BayesianElectronFileName = Name; }
   MString GetBayesianElectronFileName() { return m_BayesianElectronFileName; }
-  
+
   void SetBayesianComptonFileName(MString Name) { m_BayesianComptonFileName = Name; }
   MString GetBayesianComptonFileName() { return m_BayesianComptonFileName; }
   
@@ -246,12 +254,12 @@ class MSettingsEventReconstruction : public MSettingsInterface
   double GetTotalEnergyMax() { return m_TotalEnergyMax; }
   void SetTotalEnergyMin(double Value) { m_TotalEnergyMin = Value; }
   double GetTotalEnergyMin() { return m_TotalEnergyMin; }
-  
+
   void SetLeverArmMax(double Value) { m_LeverArmMax = Value; }
   double GetLeverArmMax() { return m_LeverArmMax; }
   void SetLeverArmMin(double Value) { m_LeverArmMin = Value; }
   double GetLeverArmMin() { return m_LeverArmMin; }
-  
+
   void SetEventIdMax(long Value) { m_EventIdMax = Value; }
   long GetEventIdMax() { return m_EventIdMax; }
   void SetEventIdMin(long Value) { m_EventIdMin = Value; }
@@ -281,12 +289,13 @@ class MSettingsEventReconstruction : public MSettingsInterface
 
   //! Save the OI information
   bool m_SaveOI;
-  
+
   // Reconstruction options:
   int m_CoincidenceAlgorithm;
   int m_EventClusteringAlgorithm;
   int m_HitClusteringAlgorithm;
   int m_TrackingAlgorithm;
+  int m_PairAlgorithm;
   int m_CSRAlgorithm;
   int m_DecayAlgorithm;
 
@@ -330,11 +339,13 @@ class MSettingsEventReconstruction : public MSettingsInterface
   int m_NTrackSequencesToKeep;
   bool m_RejectPurelyAmbiguousTrackSequences;
   int m_NLayersForVertexSearch;
+  double m_HeightX0;
+  double m_SigmaHitPos;
 
   MString m_BayesianElectronFileName;
 
   vector<MString> m_ElectronTrackingDetectors;
-  
+
   // Compton tracking:
   bool m_AssumeD1First;
   int m_ClassicUndecidedHandling;
@@ -342,18 +353,19 @@ class MSettingsEventReconstruction : public MSettingsInterface
   bool m_UseComptelTypeEvents;
   bool m_GuaranteeStartD1;
   bool m_RejectOneDetectorTypeOnlyEvents;
-  
+
   double m_CSRThresholdMin;
   double m_CSRThresholdMax;
   int m_CSRMaxNHits;
-  
+
   MString m_BayesianComptonFileName;
-  
+
   //! The TMVA file name
   MString m_CSRTMVAFileName;
   //! The TMVA methods
+
   MERCSRTMVAMethods m_CSRTMVAMethods;
-  
+
   MVector m_LensCenter;
   MVector m_FocalSpotCenter;
   MString m_OriginObjectsFileName;
diff --git a/src/revan/src/MERTrack.cxx b/src/revan/src/MERTrack.cxx
index 1fba6a722..bad18e75d 100644
--- a/src/revan/src/MERTrack.cxx
+++ b/src/revan/src/MERTrack.cxx
@@ -75,7 +75,7 @@ bool MRESEDistCompare(const MRESEDist& a, const MRESEDist& b) {
 ///
 
 struct MRESETrackCont {
-  MRESETrackCont(MRETrack* T, int e1, MRESE* R, int e2, double A) { 
+  MRESETrackCont(MRETrack* T, int e1, MRESE* R, int e2, double A) {
     massert(T!=0); massert(R!=0); m_Track=T; m_EndPoint1 = e1; m_Next=R; m_EndPoint2 = e2; m_Angle=A; }
 
   MRETrack* m_Track;
@@ -111,7 +111,7 @@ MERTrack::MERTrack()
   m_TimeMips = 0;
   m_TimeComptonSequences = 0;
   m_TimeComptonDirections = 0;
-  
+
   m_NLayersForVertexSearch = 5;
 }
 
@@ -128,11 +128,11 @@ MERTrack::~MERTrack()
 ////////////////////////////////////////////////////////////////////////////////
 
 
-bool MERTrack::SetParameters(bool SearchMIPs, 
-                             bool SearchPairs, 
-                             bool SearchComptons, 
-                             unsigned int MaxLayerJump, 
-                             unsigned int NSequencesToKeep, 
+bool MERTrack::SetParameters(bool SearchMIPs,
+                             bool SearchPairs,
+                             bool SearchComptons,
+                             unsigned int MaxLayerJump,
+                             unsigned int NSequencesToKeep,
                              bool RejectPureAmbiguities,
                              unsigned int NLayersForVertexSearch,
                              vector<MString> DetectorList)
@@ -144,22 +144,22 @@ bool MERTrack::SetParameters(bool SearchMIPs,
   m_NSequencesToKeep = NSequencesToKeep;
   m_RejectPureAmbiguities = RejectPureAmbiguities;
   m_NLayersForVertexSearch = NLayersForVertexSearch;
- 
+
   if (m_NLayersForVertexSearch < 4) {
     merr<<"Error: Revan (tracking): NLayersForVertexSearch (="<<m_NLayersForVertexSearch<<") must be >= 4. Setting it to 4."<<show;
     m_NLayersForVertexSearch = 4;
   }
-  
+
   if (m_ComptonMaxLayerJump < 1) {
-    merr<<"Error: Revan (tracking): MaxLayerJump must be >= 1. Setting it to 1."<<show;   
+    merr<<"Error: Revan (tracking): MaxLayerJump must be >= 1. Setting it to 1."<<show;
     m_ComptonMaxLayerJump = 1;
   }
 
   if (m_NSequencesToKeep < 1) {
-    merr<<"Error: Revan (tracking): NSequencesToKeep must be >= 1. Setting it to 1."<<show;   
+    merr<<"Error: Revan (tracking): NSequencesToKeep must be >= 1. Setting it to 1."<<show;
     m_NSequencesToKeep = 1;
   }
-  
+
   // Check if for the tracking detector names real detectors exist
   if (DetectorList.size() == 0) {
     merr<<"Error: Revan (tracking): You did not give *any* detectors for electron tracking."<<endl;
@@ -262,7 +262,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
       }
     }
     if (HasVertices == true) {
-      // Let's analyze pairs: 
+      // Let's analyze pairs:
       mdebug<<"* Step: Pair tracking"<<endl;
       mdebug<<m_List->ToString()<<endl;
       int e_max = m_List->GetNRawEvents();
@@ -340,7 +340,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
     m_TimeComptonSequences += Timer.ElapsedTime();
 
 
-    // We now accept only events with the maximum possible number of tracks, 
+    // We now accept only events with the maximum possible number of tracks,
     // if the flag is set
     if (m_AllowOnlyMinNumberOfRESEsD1 == true) {
       mdebug<<"Allowing only events with the maximum number of elements in the tracks. Starting with this amount: "<<m_List->GetNRawEvents()<<endl;
@@ -384,7 +384,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
 
     for (int e = 0; e < m_List->GetNRawEvents(); e++) {
       RE = m_List->GetRawEventAt(e);
-        
+
       for (int r = 0; r < RE->GetNRESEs(); r++) {
         RESE = RE->GetRESEAt(r);
         IDRESE = RESE->GetID();
@@ -397,7 +397,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
             REdup = RE->Duplicate();
             ((MRETrack *) (REdup->GetRESE(IDRESE)))->SetStartPoint(((MRETrack *) (REdup->GetRESE(IDRESE)))->GetRESE(IDEP));
             m_List->AddRawEvent(REdup);
-            
+
             Track->SetStartPoint(Track->GetEndPointAt(1));
           }
         }
@@ -424,7 +424,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
 
     //m_List->SetValidEvent(m_List->GetRawEventAt(m_List->GetNRawEvents()-1));
     m_List->SetBestTryEvent(m_List->GetRawEventAt(0));
-       
+
 
     // Remove all not-so-good sequences:
     for (int e = m_NSequencesToKeep; e < m_List->GetNRawEvents(); ++e) {
@@ -432,13 +432,13 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
       m_List->DeleteRawEvent(RE);
       e--;
     }
-    
+
     m_TimeComptonDirections += Timer.ElapsedTime();
   }
 
 
   // Step E: Epilog
-  
+
   mdebug<<"Result of tracking:"<<endl;
   mdebug<<m_List->ToString()<<endl;
 
@@ -458,7 +458,7 @@ bool MERTrack::IsInTracker(MRESE* R)
   // While building tracks their volume sequence might not be correct
   // But, if we have a track, it is in the tracker... so:
   if (R->GetType() == MRESE::c_Track) return true;
-  
+
   MDVolumeSequence* VS = R->GetVolumeSequence();
   for (unsigned int d = 0; d < m_DetectorList.size(); ++d) {
     if (VS->GetDetector() == m_DetectorList[d]) {
@@ -467,8 +467,8 @@ bool MERTrack::IsInTracker(MRESE* R)
   }
   return false;
 }
-  
-  
+
+
 ////////////////////////////////////////////////////////////////////////////////
 
 
@@ -490,7 +490,7 @@ MRawEventIncarnations* MERTrack::CheckForPair(MRERawEvent* RE)
   // (b) In N layers above/below are at least two hits
 
   // Search the vertex:
-  // The vertex is at this point a (non-ambiguous) track or a single (clustered) 
+  // The vertex is at this point a (non-ambiguous) track or a single (clustered)
   // hit followed by at least N layers with two hits per layer:
 
   mdebug<<"Searching for a pair vertex"<<endl;
@@ -499,16 +499,16 @@ MRawEventIncarnations* MERTrack::CheckForPair(MRERawEvent* RE)
   bool OnlyHitInLayer = false;
   //unsigned int MaximumLayerJump = 2;
   //MRESE* RESE = 0;
-  unsigned int SearchRange = 30; 
+  unsigned int SearchRange = 30;
   //int MinPairLength = m_NLayersForVertexSearch;
-  
+
   // Create a list of RESEs sorted by depth in tracker
   vector<MRESE*> ReseList;
   for (int h = 0; h < RE->GetNRESEs(); h++) {
     if (IsInTracker(RE->GetRESEAt(h)) == false) continue;
     // Everthing below 90 has to go -- eliminate Bremsstrahlung
     //if (RE->GetRESEAt(h)->GetEnergy() < 90) continue;
-    
+
     ReseList.push_back(RE->GetRESEAt(h));
   }
   sort(ReseList.begin(), ReseList.end(), CompareRESEByZ());
@@ -522,7 +522,7 @@ MRawEventIncarnations* MERTrack::CheckForPair(MRERawEvent* RE)
 
   // For each of the RESE's in the list check if it could be the first of the vertex
   for (Iterator1 = ReseList.begin(); Iterator1 != ReseList.end(); Iterator1++) {
- 
+
     // If it is a single hit, and if it is the only one in its layer:
     OnlyHitInLayer = true;
     for (Iterator2 = ReseList.begin(); Iterator2 != ReseList.end(); Iterator2++) {
@@ -555,47 +555,47 @@ MRawEventIncarnations* MERTrack::CheckForPair(MRERawEvent* RE)
 
 
     // Under the following conditions we do have a pair:
-    
+
     // Pair starting from top
     MRESE* Vertex = 0;
     int VertexDirection = 0;
 
-    
+
     // Check for vertex below
     if (NAbove[1] == 0) {
       int StartIndex = 0; // We start when we have 2 hits for the first time
       int StopIndex = 0; // We stop when we skip 2 layers for the first time
       int LayersWithAtLeastTwoHitsBetweenStartAndStop = 0;
 
-      
+
       for (unsigned int d = 1; d < SearchRange-1; ++d) {
         // We stop when we skip 2 layers for the first time
         if (NBelow[d] == 0 && NBelow[d+1] == 0) break;
         StopIndex = d;
         // Store the index where we have 2 hits for the first time, twice
         if (StartIndex == 0 && NBelow[d] > 1 && NBelow[d+1] > 1) StartIndex = d;
-        
+
         if (StartIndex != 0) {
           if (NBelow[d] >= 2) ++LayersWithAtLeastTwoHitsBetweenStartAndStop;
         }
       }
-      
+
       // Since we can have just a single track at the end, move upward until we have at least two hits in a row
       for (unsigned int d = StopIndex; d > 2; --d) {
         if (NBelow[d-1] >= 2 && NBelow[d-2] >= 2) break;
         StopIndex = d;
       }
-      
+
       mdebug<<"Search vertex ("<<(*Iterator1)->GetPosition().Z()<<"): Above: ";
       for (int i: NAbove) mdebug<<i<<" ";
       mdebug<<endl;
       mdebug<<"Search vertex ("<<(*Iterator1)->GetPosition().Z()<<"): Below: ";
       for (int i: NBelow) mdebug<<i<<" ";
       mdebug<<endl;
-     
-      mdebug<<"Vertex statistics (max: "<<SearchRange<<"): layers used: "<<StopIndex<<", start of 2+ hits: "<<StartIndex<<"  layers with 2+ hits between start and stop: "<<LayersWithAtLeastTwoHitsBetweenStartAndStop<<" ("<<((StopIndex-StartIndex > 0) ? 100.0*LayersWithAtLeastTwoHitsBetweenStartAndStop/(StopIndex-StartIndex) : 0)<<"%)"<<endl; 
-      
-      if (LayersWithAtLeastTwoHitsBetweenStartAndStop > 4 && double (LayersWithAtLeastTwoHitsBetweenStartAndStop)/(StopIndex-StartIndex) > 0.5) {  
+
+      mdebug<<"Vertex statistics (max: "<<SearchRange<<"): layers used: "<<StopIndex<<", start of 2+ hits: "<<StartIndex<<"  layers with 2+ hits between start and stop: "<<LayersWithAtLeastTwoHitsBetweenStartAndStop<<" ("<<((StopIndex-StartIndex > 0) ? 100.0*LayersWithAtLeastTwoHitsBetweenStartAndStop/(StopIndex-StartIndex) : 0)<<"%)"<<endl;
+
+      if (LayersWithAtLeastTwoHitsBetweenStartAndStop > 4 && double (LayersWithAtLeastTwoHitsBetweenStartAndStop)/(StopIndex-StartIndex) > 0.5) {
         Vertex = (*Iterator1);
         VertexDirection = -1;
       }
@@ -632,20 +632,20 @@ void MERTrack::TrackPairs(MRERawEvent* RE)
   }
 
   mdebug<<"Vertex: "<<RE->GetVertex()->GetPosition().Z()<<endl;
-  
+
   MRETrack* Electron = new MRETrack();
   MRETrack* Positron = new MRETrack();
 
   // Now figure out if we have to go up or down:
   int Direction = RE->GetVertexDirection();
-  
+
   // Now create the vertex:
   Electron->AddRESE(RE->GetVertex());
   Electron->SetStartPoint(RE->GetVertex());
 
   // TODO: Problem virtual is not deleted!!!!
   MRESE* Virtual = RE->GetVertex()->Duplicate();
-  Virtual->SetEnergy(0); // TODO: the energies should be split evenly, between electron and positron 
+  Virtual->SetEnergy(0); // TODO: the energies should be split evenly, between electron and positron
 
   Positron->AddRESE(Virtual);
   Positron->SetStartPoint(Virtual);
@@ -653,9 +653,9 @@ void MERTrack::TrackPairs(MRERawEvent* RE)
 
   bool HaveElectronDirection = false;
   bool HavePositronDirection = false;
-  
+
   // Now we have the vertex
-  // Go up/down the track until we do not find hits any more and assign them 
+  // Go up/down the track until we do not find hits any more and assign them
   // to the tracks
   int NTrials = 0;
   MRESEList List;
@@ -665,7 +665,7 @@ void MERTrack::TrackPairs(MRERawEvent* RE)
     List.Compress();
 
     NTrials = 0;
-    while (List.GetNRESEs() == 0 && NTrials < 10) { 
+    while (List.GetNRESEs() == 0 && NTrials < 10) {
       mdebug<<"Testing direction: "<<Direction<<endl;
       NTrials++;
       for (int r = 0; r < RE->GetNRESEs(); r++) {
@@ -673,7 +673,7 @@ void MERTrack::TrackPairs(MRERawEvent* RE)
 
         if (m_Geometry->IsAbove(RE->GetVertex(), RE->GetRESEAt(r), Direction) == true) {
           List.AddRESE(RE->GetRESEAt(r));
-        }      
+        }
       }
       mdebug<<"Distance: "<<abs(Direction)<<"  Entries: "<<List.GetNRESEs();
       if (List.GetNRESEs() > 0) {
@@ -688,7 +688,7 @@ void MERTrack::TrackPairs(MRERawEvent* RE)
     int BestPos = -1;
     double BestScore = 1E10;
     double NewScore = 0;
-    
+
     // If we have only one hit:
     if (List.GetNRESEs() == 0) {
       break;
@@ -700,11 +700,11 @@ void MERTrack::TrackPairs(MRERawEvent* RE)
         BestPos = 0;
       } else {
         mdebug<<"Pair tracking: One hit: e-angle: "
-            <<Electron->GetFinalDirection().Angle(List.GetRESEAt(0)->GetPosition() - 
+            <<Electron->GetFinalDirection().Angle(List.GetRESEAt(0)->GetPosition() -
                                                   Electron->GetStopPoint()->GetPosition())*c_Deg
-            <<" p-angle: "<<Positron->GetFinalDirection().Angle(List.GetRESEAt(0)->GetPosition() - 
+            <<" p-angle: "<<Positron->GetFinalDirection().Angle(List.GetRESEAt(0)->GetPosition() -
                                                                 Positron->GetStopPoint()->GetPosition())*c_Deg<<endl;
-        
+
         if (Electron->GetFinalDirection().Angle(List.GetRESEAt(0)->GetPosition() - Electron->GetStopPoint()->GetPosition()) <
             Positron->GetFinalDirection().Angle(List.GetRESEAt(0)->GetPosition() - Positron->GetStopPoint()->GetPosition())) {
           BestEl = 0;
@@ -746,7 +746,7 @@ void MERTrack::TrackPairs(MRERawEvent* RE)
 
         // Search the straightest continuation for the positron:
         for (int r = 0; r < List.GetNRESEs(); r++) {
-          NewScore = Positron->GetFinalDirection().Angle(List.GetRESEAt(r)->GetPosition() - 
+          NewScore = Positron->GetFinalDirection().Angle(List.GetRESEAt(r)->GetPosition() -
                                                          Positron->GetStopPoint()->GetPosition());
           if (NewScore < BestScore) {
             BestScore = NewScore;
@@ -767,9 +767,9 @@ void MERTrack::TrackPairs(MRERawEvent* RE)
         for (int r = 0; r < List.GetNRESEs(); r++) {
           for (int s = r+1; s < List.GetNRESEs(); s++) {
             // Direction One:
-            NewScore = 
+            NewScore =
               Electron->GetFinalDirection().Angle(List.GetRESEAt(r)->GetPosition() - Electron->GetStopPoint()->GetPosition())*
-              Electron->GetFinalDirection().Angle(List.GetRESEAt(r)->GetPosition() - Electron->GetStopPoint()->GetPosition()) + 
+              Electron->GetFinalDirection().Angle(List.GetRESEAt(r)->GetPosition() - Electron->GetStopPoint()->GetPosition()) +
               Positron->GetFinalDirection().Angle(List.GetRESEAt(s)->GetPosition() - Positron->GetStopPoint()->GetPosition())*
               Positron->GetFinalDirection().Angle(List.GetRESEAt(s)->GetPosition() - Positron->GetStopPoint()->GetPosition());
             if (NewScore < BestScore) {
@@ -777,14 +777,14 @@ void MERTrack::TrackPairs(MRERawEvent* RE)
               BestEl = r;
               BestPos = s;
             }
-            
+
             // Direction Two:
-            NewScore = 
+            NewScore =
               Electron->GetFinalDirection().Angle(List.GetRESEAt(s)->GetPosition() - Electron->GetStopPoint()->GetPosition())*
-              Electron->GetFinalDirection().Angle(List.GetRESEAt(s)->GetPosition() - Electron->GetStopPoint()->GetPosition()) + 
+              Electron->GetFinalDirection().Angle(List.GetRESEAt(s)->GetPosition() - Electron->GetStopPoint()->GetPosition()) +
               Positron->GetFinalDirection().Angle(List.GetRESEAt(r)->GetPosition() - Positron->GetStopPoint()->GetPosition())*
               Positron->GetFinalDirection().Angle(List.GetRESEAt(r)->GetPosition() - Positron->GetStopPoint()->GetPosition());
-            
+
             if (NewScore < BestScore) {
               BestScore = NewScore;
               BestEl = s;
@@ -812,12 +812,12 @@ void MERTrack::TrackPairs(MRERawEvent* RE)
 
   } while (true);
 
-  
+
   // For the electron and positron track walk down the track and determine the straightness from the 5 straigtest segments
   // Hits with deviate more than X% from this straightness are tossed out of the track
   EliminatePairDeviations(RE, Electron);
   EliminatePairDeviations(RE, Positron);
-  
+
   // Clean up
   RE->RemoveRESE(RE->GetVertex());
   RE->CompressRESEs();
@@ -825,7 +825,7 @@ void MERTrack::TrackPairs(MRERawEvent* RE)
   // We now might have a new start point, thus make sure we fix the vertex
   MRESE* NewStartElectron = Electron->GetStartPoint();
   MRESE* NewStartPositron = Positron->GetStartPoint();
-  
+
   if (NewStartElectron->GetPosition().GetZ() < NewStartPositron->GetPosition().GetZ()) {
     MRESE* NewStart = NewStartPositron->Duplicate();
     NewStartElectron->AddLink(NewStart);
@@ -839,12 +839,12 @@ void MERTrack::TrackPairs(MRERawEvent* RE)
     NewStart->AddLink(NewStartPositron);
     Positron->AddRESE(NewStart);
     Positron->SetStartPoint(NewStart);
-    RE->SetVertex(NewStart);    
+    RE->SetVertex(NewStart);
   } else {
-    RE->SetVertex(NewStartElectron);   
+    RE->SetVertex(NewStartElectron);
   }
-  
-  
+
+
   // Now add (not append) the remaining hits to the nearest track
 
   for (int r = 0; r < RE->GetNRESEs(); r++) {
@@ -855,7 +855,7 @@ void MERTrack::TrackPairs(MRERawEvent* RE)
     }
     RE->RemoveRESE(RE->GetRESEAt(r));
   }
-  
+
   RE->CompressRESEs();
 
 
@@ -893,9 +893,9 @@ void MERTrack::EliminatePairDeviations(MRERawEvent* RE, MRETrack* Track)
   const int NEvaluations = 4;
   const double FactorAboveMaxDeviation = 1.3;
   const double MinDeviation = 8.0*c_Rad;
-  
+
   vector<double> Deviations;
-  
+
   MRESE* Start = Track->GetStartPoint();
   if (Start == nullptr) return;
   if (Start->GetNLinks() != 1) return;
@@ -904,26 +904,26 @@ void MERTrack::EliminatePairDeviations(MRERawEvent* RE, MRETrack* Track)
   MRESE* End = Middle->GetOtherLink(Start);
   while (true) {
     Deviations.push_back((Middle->GetPosition() - Start->GetPosition()).Angle(End->GetPosition() - Middle->GetPosition()));
-    
+
     Start = Middle;
     Middle = End;
     if (Middle->GetNLinks() != 2) break;
     End = Middle->GetOtherLink(Start);
   }
-  
+
   // If we have less or equal than "NEvaluations" values, we do nothing
   if (Deviations.size() <= NEvaluations) return;
-  
+
   // Sort increasing
   sort(Deviations.begin(), Deviations.end(), std::less<double>());
-  
+
   // Create the average of the first NEvaluations
   double AverageDeviation = 0.0;
   for (unsigned int i = 0; i < NEvaluations; ++i) {
     AverageDeviation += Deviations[i];
   }
   AverageDeviation /= NEvaluations;
-  
+
   // Find the largest deviation
   double MaxDeviation = 0.0;
   for (unsigned int i = 0; i < NEvaluations; ++i) {
@@ -933,18 +933,18 @@ void MERTrack::EliminatePairDeviations(MRERawEvent* RE, MRETrack* Track)
   }
   MaxDeviation *= FactorAboveMaxDeviation;
   if (MaxDeviation < MinDeviation) MaxDeviation = MinDeviation;
-  
+
   mdebug<<"Maximum deviation: "<<MaxDeviation*c_Deg<<" degrees"<<endl;
-  
+
   // Find the first segment which is below the average deviation:
   Start = Track->GetStartPoint();
   Middle = Start->GetLinkAt(0);
   End = Middle->GetOtherLink(Start);
   while (true) {
     double Deviation = (Middle->GetPosition() - Start->GetPosition()).Angle(End->GetPosition() - Middle->GetPosition());
-    
+
     if (Deviation <= AverageDeviation) break;
-    
+
     Start = Middle;
     Middle = End;
     if (Middle->GetNLinks() != 2) break;
@@ -958,29 +958,29 @@ void MERTrack::EliminatePairDeviations(MRERawEvent* RE, MRETrack* Track)
     Middle = Start;
     Start = Middle->GetOtherLink(End);
     MRESE* StartOldOtherLink = Middle;
-    
+
     double Deviation = (Middle->GetPosition() - Start->GetPosition()).Angle(End->GetPosition() - Middle->GetPosition());
-    mdebug<<"Deviation: "<<Start->GetID()<<"->"<<Middle->GetID()<<"->"<<End->GetID()<<": "<<Deviation*c_Deg<<" deg"<<endl; 
+    mdebug<<"Deviation: "<<Start->GetID()<<"->"<<Middle->GetID()<<"->"<<End->GetID()<<": "<<Deviation*c_Deg<<" deg"<<endl;
 
     while (Deviation > MaxDeviation && Start->GetNLinks() == 2) {
       MRESE* ThrowOut = Start;
       Start = Start->GetOtherLink(StartOldOtherLink);
       StartOldOtherLink = ThrowOut;
-      
+
       // Remove the RESE
       Track->RemoveRESE(ThrowOut);
       mdebug<<"Removing RESE: "<<ThrowOut->GetID()<<" from track due to a deviation of "<<Deviation*c_Deg<<" deg (max allowed: "<<MaxDeviation*c_Deg<<" deg)"<<endl;
       RE->AddRESE(ThrowOut);
-        
+
       // Relink the others
       ThrowOut->RemoveAllLinks();
       Start->RemoveLink(ThrowOut);
       Middle->RemoveLink(ThrowOut);
       Start->AddLink(Middle);
       Middle->AddLink(Start);
-      
+
       Deviation = (Middle->GetPosition() - Start->GetPosition()).Angle(End->GetPosition() - Middle->GetPosition());
-      mdebug<<"Deviation: "<<Start->GetID()<<"->"<<Middle->GetID()<<"->"<<End->GetID()<<": "<<Deviation*c_Deg<<" deg "<<endl; 
+      mdebug<<"Deviation: "<<Start->GetID()<<"->"<<Middle->GetID()<<"->"<<End->GetID()<<": "<<Deviation*c_Deg<<" deg "<<endl;
     }
 
     if (Deviation < MaxDeviation) {
@@ -992,7 +992,7 @@ void MERTrack::EliminatePairDeviations(MRERawEvent* RE, MRETrack* Track)
       Track->RemoveRESE(Start);
     }
   }
-  
+
   Track->SetStartPoint(BestNewStartPoint);
   Track->CompressRESEs();
 }
@@ -1009,7 +1009,7 @@ void MERTrack::CheckForMips(MRERawEvent* RE)
   // The typical pattern of a MIP is:
   // We have a straight track with serveral hits which, do not belong to the
   // original MIP, but to its secondaries, bremsstrahlung etc.
-  
+
   mdebug<<"Checking for Mips..."<<endl;
 
   const int MinElements = 4;
@@ -1025,7 +1025,7 @@ void MERTrack::CheckForMips(MRERawEvent* RE)
     }
   }
 
-  // Sort the array for decreasing z: 
+  // Sort the array for decreasing z:
   MRESE* Temp = 0;
   unsigned int HighestPos = 0;
   double HighestValue = -1;
@@ -1064,7 +1064,7 @@ void MERTrack::CheckForMips(MRERawEvent* RE)
       jRESE = D1Hits[j];
       //mdebug<<"j:"<<jRESE->ToString()<<endl;
       Direction1 = jRESE->GetPosition() - iRESE->GetPosition();
-      
+
       Track = 0; // No memory leak!
 
       for (unsigned int k = j+1; k < max; ++k) {
@@ -1072,7 +1072,7 @@ void MERTrack::CheckForMips(MRERawEvent* RE)
         kRESE = D1Hits[k];
         //mdebug<<"k:"<<kRESE->ToString()<<endl;
         Direction2 = kRESE->GetPosition() - jRESE->GetPosition();
-        
+
         // Check the straightness:
         //mdebug<<"Angle: "<<Direction1.Angle(Direction2)<<endl;
         if (Direction1.Angle(Direction2) < MinStraightness) {
@@ -1090,8 +1090,8 @@ void MERTrack::CheckForMips(MRERawEvent* RE)
           } else {
             Track->AddRESE(kRESE);
             D1Hits[k] = 0;
-          }            
-          
+          }
+
           Direction1 = Direction2;
         }
       } // end k
@@ -1102,7 +1102,7 @@ void MERTrack::CheckForMips(MRERawEvent* RE)
   } // end i
 
   // We need at least one track with at least MinElements hits:
-  // For now: Search for the largest track: 
+  // For now: Search for the largest track:
   HighestPos = 0;
   HighestValue = -1;
   for (unsigned int i = 0; i < TrackArray.size(); ++i) {
@@ -1127,7 +1127,7 @@ void MERTrack::CheckForMips(MRERawEvent* RE)
     EvaluateTrack(TrackArray[HighestPos]);
     RE->AddRESE(TrackArray[HighestPos]);
     RE->CompressRESEs();
-    
+
     // b. Store the new event:
     MMuonEvent* Muon = new MMuonEvent(); // is later stored as m_Event!
     Muon->SetEnergy(RE->GetEnergy());
@@ -1143,7 +1143,7 @@ void MERTrack::CheckForMips(MRERawEvent* RE)
     RE->SetPhysicalEvent(Muon);
     RE->SetEventType(MRERawEvent::c_MipEvent);
     RE->SetGoodEvent(true);
-  } 
+  }
   // b. A shower
   else if (TrackArray.size() > 1) {
     mdebug<<"==> Found a shower!"<<endl;
@@ -1191,7 +1191,7 @@ MRawEventIncarnations* MERTrack::TrackComptons(MRERawEvent* RE)
 
     // if it's not in D1 reject it
     if (IsInTracker(RESE) == false) {
-      continue; 
+      continue;
     }
 
     Added = false;
@@ -1208,7 +1208,7 @@ MRawEventIncarnations* MERTrack::TrackComptons(MRERawEvent* RE)
       MasterRESEs.push_back(RESE);
       DistList.resize(MasterRESEs.size());
       MRESEDist RD(RESE, 0);
-      DistList[DistList.size()-1].push_back(RD);        
+      DistList[DistList.size()-1].push_back(RD);
     }
   }
 
@@ -1265,11 +1265,12 @@ MRawEventIncarnations* MERTrack::TrackComptons(MRERawEvent* RE)
           }
         }
         LastRESE = RESE;
-        LastDist = (*DistListIter).Distance;     
+        LastDist = (*DistListIter).Distance;
       }
     }
   }
 
+
   MRawEventIncarnations* List = new MRawEventIncarnations(); 
 
   if (IsPureAmbiguity == true && m_RejectPureAmbiguities == true) {
@@ -1279,11 +1280,11 @@ MRawEventIncarnations* MERTrack::TrackComptons(MRERawEvent* RE)
   }
 
   if (NAmbiguities <= m_MaxNAmbiguities) {
-    // Find ambiguous sequences 
+    // Find ambiguous sequences
     mdebug<<"Testing ambiguous sequences"<<endl;
 
     List->AddRawEvent(RE->Duplicate());
-    
+
     MRESE* RESEmain = 0;
     MRESE* RESEp1 = 0;
     MRESE* RESEp2 = 0;
@@ -1291,22 +1292,22 @@ MRawEventIncarnations* MERTrack::TrackComptons(MRERawEvent* RE)
     vector<MRESEDist> Partners;
     vector<MRESEDist>::iterator SecDistListIter;
     vector<MRESEDist>::iterator TerDistListIter;
-    
+
     int NNewREs;
     MRERawEvent* NewRE = 0;
     MRERawEvent* NewREdup = 0;
-    
+
     // Find a list of all possible combinations:
     for (unsigned int m = 0; m < DistList.size(); ++m) {
       for (DistListIter = DistList[m].begin();
            DistListIter != DistList[m].end(); DistListIter++) {
-        
+
         RESEmain = (*DistListIter).RESE;
-        
+
         if (RESEmain->GetNLinks() >= 2) {
           continue;
         }
-        
+
         // Find all possible partners:
         int Diff = 0;
         Partners.clear();
@@ -1325,34 +1326,34 @@ MRawEventIncarnations* MERTrack::TrackComptons(MRERawEvent* RE)
           }
           Partners.push_back((*SecDistListIter));
         }
-        
+
         mdebug<<"New partners for "<<RESEmain->GetID()<<": ";
         for (SecDistListIter = Partners.begin();
              SecDistListIter != Partners.end(); SecDistListIter++) {
           mdebug<<(*SecDistListIter).RESE->GetID()<<" ";
         }
         mdebug<<endl;
-        
+
 
         // Now generate the links:
         NNewREs = List->GetNRawEvents();
         for (int t = 0; t < NNewREs; ++t) {
           NewRE = List->GetRawEventAt(t);
-                    
+
           if (NewRE->GetRESE(RESEmain->GetID())->GetNLinks() == 2) {
-            continue; 
+            continue;
           }
-          
+
           // Single partners
           mdebug<<"Searching single partners for "<<RESEmain->GetID()<<endl;
           for (SecDistListIter = Partners.begin();
                SecDistListIter != Partners.end(); SecDistListIter++) {
             RESEp1 = (*SecDistListIter).RESE;
-            
+
             if (NewRE->GetRESE(RESEmain->GetID())->IsLink(NewRE->GetRESE(RESEp1->GetID())) == true) {
               continue;
             }
-            
+
             if (NewRE->GetRESE(RESEp1->GetID())->GetNLinks() <= 1) {
               mdebug<<"Linking: "<<RESEmain->GetID()<<" with "<<RESEp1->GetID()<<endl;
               NewREdup = NewRE->Duplicate();
@@ -1365,7 +1366,7 @@ MRawEventIncarnations* MERTrack::TrackComptons(MRERawEvent* RE)
           } // end single partner loop
 
           if (NewRE->GetRESE(RESEmain->GetID())->GetNLinks() > 0) {
-            continue; 
+            continue;
           }
 
           // Double partners:
@@ -1405,16 +1406,16 @@ MRawEventIncarnations* MERTrack::TrackComptons(MRERawEvent* RE)
             }
           } // end double partner loop
 
-        } // end loop over List      
+        } // end loop over List
       }
     }
-  
+
     // Create tracks in the list:
     mdebug<<"Newly tracked events: "<<List->GetNRawEvents()<<endl;
     for (int i = 0; i < List->GetNRawEvents(); i++) {
       mdebug<<List->GetRawEventAt(i)->ToString()<<endl;;
-    }   
-    
+    }
+
     // Create tracks in the list:
     for (int i = 0; i < List->GetNRawEvents(); i++) {
       if (List->GetRawEventAt(i)->CreateTracks() == false) {
@@ -1432,7 +1433,7 @@ MRawEventIncarnations* MERTrack::TrackComptons(MRERawEvent* RE)
 
     // Only continue if we already have a track segment, from which we can start:
 
-    // Upgrade links to tracks... 
+    // Upgrade links to tracks...
     if (RE->CreateTracks() == false) {
       mout<<"No crystallization point! --> Add rejection for this..."<<endl;
       for (int r = 0; r < RE->GetNRESEs(); ++r) {
@@ -1442,7 +1443,7 @@ MRawEventIncarnations* MERTrack::TrackComptons(MRERawEvent* RE)
     }
 
     bool ThereWasAChange = true;
-    list<MRESETrackCont> Neighbors; 
+    list<MRESETrackCont> Neighbors;
     do {
       Neighbors.clear();
       // For each track search all possible continuation (within layer jump)
@@ -1483,29 +1484,29 @@ MRawEventIncarnations* MERTrack::TrackComptons(MRERawEvent* RE)
           }
         }
       }
-      
+
       if (Neighbors.size() == 0) {
         break;
       }
 
       // Only append the best one!
       Neighbors.sort(MRESETrackContCompare);
-      
+
       if (Neighbors.front().m_EndPoint2 < 0) {
-        Neighbors.front().m_Track->AddEndPoint(Neighbors.front().m_Next, 
+        Neighbors.front().m_Track->AddEndPoint(Neighbors.front().m_Next,
                                                Neighbors.front().m_Track->GetEndPointAt(Neighbors.front().m_EndPoint1));
         RE->RemoveRESE(Neighbors.front().m_Next);
       } else {
-        Neighbors.front().m_Track->AddEndPoint(dynamic_cast<MRETrack*>(Neighbors.front().m_Next), 
+        Neighbors.front().m_Track->AddEndPoint(dynamic_cast<MRETrack*>(Neighbors.front().m_Next),
                                                dynamic_cast<MRETrack*>(Neighbors.front().m_Next)->GetEndPointAt(Neighbors.front().m_EndPoint2),
-                                               Neighbors.front().m_Track->GetEndPointAt(Neighbors.front().m_EndPoint1));        
+                                               Neighbors.front().m_Track->GetEndPointAt(Neighbors.front().m_EndPoint1));
         RE->RemoveRESE(Neighbors.front().m_Next);
         delete Neighbors.front().m_Next;
       }
       RE->CompressRESEs();
 
       // Search for new non ambiguous sequences:
-      
+
     } while (ThereWasAChange == true);
 
     // Add the only raw event...
@@ -1518,9 +1519,9 @@ MRawEventIncarnations* MERTrack::TrackComptons(MRERawEvent* RE)
 
 
   // Let's do some sanity checks:
-  
+
   // Append straight (long) tracks:
-  
+
 
   return List;
 }
@@ -1539,7 +1540,7 @@ bool MERTrack::PostAnalysis()
   mout<<"Time Comptons - directions: "<<m_TimeComptonDirections<<endl;
   mout<<endl;
   */
-  
+
   return true;
 }
 
@@ -1562,7 +1563,7 @@ bool MERTrack::EvaluateTracks(MRERawEvent* RE)
   //     Score = 1 / (# tracks + # remaining hits in D1)
 
   int NTracks = 0, NRemainingHits = 0;
-  
+
   MRESE* RESE = 0;
   for (int i = 0; i < RE->GetNRESEs(); i++) {
     RESE = RE->GetRESEAt(i);
@@ -1570,7 +1571,7 @@ bool MERTrack::EvaluateTracks(MRERawEvent* RE)
       //mdebug<<"Detecor"<<RESE->GetDetector()<<endl;
       if (RESE->GetType() == MRESE::c_Track) {
         NTracks++;
-      } else if (RESE->GetType() == MRESE::c_Hit || 
+      } else if (RESE->GetType() == MRESE::c_Hit ||
                  RESE->GetType() == MRESE::c_Cluster) {
         NRemainingHits++;
       } else {
@@ -1616,7 +1617,7 @@ bool MERTrack::EvaluateTracks(MRERawEvent* RE)
 
 bool MERTrack::EvaluateTrack(MRETrack* Track)
 {
-  double QF = 0; 
+  double QF = 0;
   QF = Track->CalculatePearsonCorrelation();
   Track->SetQualityFactor(QF);
 
@@ -1639,7 +1640,7 @@ bool MERTrack::EvaluatePairs(MRERawEvent* RE)
     Score = ((MRETrack*) RE->GetPositronTrack())->CalculatePearsonCorrelation();
     ((MRETrack*) RE->GetPositronTrack())->SetQualityFactor(Score);
 
-    ScorePair = ((MRETrack*) RE->GetElectronTrack())->GetQualityFactor() + 
+    ScorePair = ((MRETrack*) RE->GetElectronTrack())->GetQualityFactor() +
       ((MRETrack *) RE->GetPositronTrack())->GetQualityFactor();
     mdebug<<"Best score = "<<ScorePair<<endl;
   }
diff --git a/src/revan/src/MERTrackKalman2D.cxx b/src/revan/src/MERTrackKalman2D.cxx
new file mode 100644
index 000000000..d984fd90c
--- /dev/null
+++ b/src/revan/src/MERTrackKalman2D.cxx
@@ -0,0 +1,715 @@
+/*
+* MERTrackKalman2D.cxx
+*
+*
+* Copyright (C) by Paolo Cumani & Andreas Zoglauer.
+* All rights reserved.
+*
+*
+* This code implementation is the intellectual property of
+* Andreas Zoglauer.
+*
+* By copying, distributing or modifying the Program (or any work
+* based on the Program) you indicate your acceptance of this statement,
+* and all its terms.
+*
+*/
+
+
+////////////////////////////////////////////////////////////////////////////////
+//
+// MERTrackKalman2D
+//
+// Base class for event reconstruction tasks, e.g. find clusters, tracks,
+// Compton sequence
+//
+////////////////////////////////////////////////////////////////////////////////
+
+
+// Include the header:
+#include "MERTrackKalman2D.h"
+
+// Standard libs:
+#include <list>
+#include <algorithm>
+#include <iomanip>
+#include <iostream>
+#include <functional>
+using namespace std;
+
+// ROOT libs:
+#include "TMath.h"
+
+// MEGAlib libs:
+#include "MAssert.h"
+#include "MStreams.h"
+#include "MRESE.h"
+#include "MRESEIterator.h"
+#include "MRETrack.h"
+#include "MREHit.h"
+#include "MMuonEvent.h"
+#include "MTimer.h"
+#include "MFile.h"
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+#ifdef ___CINT___
+ClassImp(MERTrackKalman2D)
+#endif
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+MERTrackKalman2D::MERTrackKalman2D() : MERTrack()
+{
+  // Construct an instance of MERTrackKalman2D
+  w=pow(tan(60*(TMath::Pi())/180.),2);
+  sfg_factor=24;
+  start_nrg_fit=20;
+  n_fit = 7;
+
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MERTrackKalman2D::SetSpecialParameters(double SigmaHitPos, unsigned int NLayersForVertexSearch)
+  {
+    m_NLayersForVertexSearch = NLayersForVertexSearch;
+    m_sigma = SigmaHitPos;
+
+    if (m_NLayersForVertexSearch < 4) {
+      merr<<"Error: Revan (tracking): NLayersForVertexSearch (="<<m_NLayersForVertexSearch<<") must be >= 4. Setting it to 4."<<show;
+      m_NLayersForVertexSearch = 4;
+    }
+
+    return true;
+  }
+
+
+  ////////////////////////////////////////////////////////////////////////////////
+
+
+  MERTrackKalman2D::~MERTrackKalman2D()
+  {
+    // Delete this instance of MERTrackKalman2D
+  }
+
+
+  ////////////////////////////////////////////////////////////////////////////////
+
+
+  /*bool MERTrackKalman2D::EvaluateTracks(MRERawEvent* RE)
+  {
+    // Evaluate the given tracks...
+
+    if (RE->GetVertex() != 0) {
+      return EvaluatePairs(RE);
+    }
+
+    // Mark: Add you evaluations here:
+    mout<<"MRawEventIncarnationList* MERTrackKalman2D::EvaluateTracks(MRERawEvent* ER): nyi!"<<endl;
+    //return MERTrack::EvaluateTracks(RE);
+
+    // Store your results:
+    RE->SetTrackQualityFactor(MRERawEvent::c_NoQualityFactor);
+    RE->SetPairQualityFactor(MRERawEvent::c_NoQualityFactor);
+
+    return true;
+  }*/
+
+
+  ////////////////////////////////////////////////////////////////////////////////
+
+
+  MString MERTrackKalman2D::ToString(bool CoreOnly) const
+  {
+    // Dump an options string gor the tra file:
+
+    ostringstream out;
+
+    if (CoreOnly == false) {
+      out<<"# Tracking - Kalman options:"<<endl;
+      out<<"# "<<endl;
+    }
+    out<<MERTrack::ToString(true);
+    if (CoreOnly == false) {
+      out<<"# "<<endl;
+    }
+
+    return out.str().c_str();
+  }
+
+  ////////////////////////////////////////////////////////////////////////////////
+
+  Float_t MERTrackKalman2D::Kalman(MRERawEvent* RE, Int_t n, Float_t en, MRESEList Previous, vector < TMatrix > &trk, Int_t view, MRESEList &Chosen)
+  {
+    vector < TMatrix > Ck;
+    vector < TMatrix > Csmoothk;
+    vector < TMatrix > Fk;
+    vector < TMatrix > FTk;
+    vector < TMatrix > Cprojk;
+    vector < TMatrix > CprojInvk;
+    vector < TMatrix > Qk;
+    vector < TMatrix > xk;
+    vector < TMatrix > xprojk;
+    vector < TMatrix > xsmoothk;
+
+    Float_t _planedistance = 0.;
+    Float_t m = 1000.;
+
+    TMatrix C(2,2);
+    TMatrix C_proj(2,2);
+    Cprojk.push_back(C_proj);
+    CprojInvk.push_back(C_proj);
+    TMatrix F(2,2);
+    TMatrix Q(2,2);
+
+    Chosen.RemoveAllRESEs();
+    Chosen.Compress();
+
+    Float_t chi2 = 0.;
+    MRESE vertex = RE->GetVertex();
+    Chosen.AddRESE(RE->GetVertex());
+
+    Float_t height = 2*vertex.GetVolumeSequence()->GetDetector()->GetStructuralSize().GetZ();
+    m_heightX0 = height/vertex.GetVolumeSequence()->GetDetector()->GetSensitiveVolume(0)->GetMaterial()->GetRadiationLength();
+
+    //Filtering
+    Float_t t; // tan of the RMS of the scattering angle
+
+    Float_t V = (m_sigma*m_sigma);  //Weight Matrix
+
+    Float_t G = 1./(m_sigma*m_sigma); //(Weight Matrix)^-1
+
+    C(0,0)=m_sigma*m_sigma;
+    C(0,1)=0.;
+    C(1,0)=0.;
+    C(1,1)=w;
+
+    Ck.push_back(C);
+
+    vector < Float_t > mk;
+
+    TMatrix x(2,1);
+    if(view==0)  x(0,0)=vertex.GetPositionX();
+    else if(view==1)  x(0,0)=vertex.GetPositionY();
+    x(1,0)=0;
+
+    xk.push_back(x);
+
+    mk.push_back(x(0,0));
+
+    TMatrix x_proj(2,1);
+    xprojk.push_back(x_proj);
+
+    Int_t i=0;
+
+    MRESEList List;
+    List.RemoveAllRESEs();
+    List.Compress();
+
+    // Create a list of RESEs sorted by depth in tracker
+    vector<MRESE*> ReseList;
+    for (int h = 0; h < RE->GetNRESEs(); h++) {
+      if (m_Geometry->IsAbove(RE->GetVertex(), RE->GetRESEAt(h)) == false) {
+        ReseList.push_back(RE->GetRESEAt(h));
+      }
+    }
+    sort(ReseList.begin(), ReseList.end(), CompareRESEByZ());
+
+    vector<MRESE*>::iterator Iterator1;
+    for (Iterator1 = ReseList.begin(); Iterator1 != ReseList.end(); Iterator1++) {
+      if (IsInTracker(*Iterator1) == false) continue;
+      List.AddRESE(*Iterator1);
+    }
+    ReseList.clear();
+
+    Float_t PlaneZ = vertex.GetPosition().Z();
+    mdebug<<"Vertex : "<<vertex.GetPosition().X()<<" "<<vertex.GetPosition().Y()<<" "<<vertex.GetPosition().Z()<<endl;
+    Float_t LayerDistance = vertex.GetVolumeSequence()->GetDetector()->GetStructuralPitch().GetZ();
+
+    for (int r = 0; r < List.GetNRESEs() && i<n-1; r++) {
+
+      if (PlaneZ <= (List.GetRESEAt(r)->GetPosition().Z() + 0.0001)) continue;
+      PlaneZ = List.GetRESEAt(r)->GetPosition().Z();
+
+      for (int k = 0; k < r; k++) {
+        if(List.GetRESEAt(k)->GetPosition().Z()-PlaneZ < 0.0001) break;
+        _planedistance = List.GetRESEAt(k)->GetPosition().Z()-PlaneZ;
+      }
+
+      if(_planedistance>1.5*LayerDistance) break; // we accept only hits on subsequent planes
+
+      t=(13.6/en)*sqrt(m_heightX0)*(1+0.038*log(m_heightX0));
+
+      F(0,0)=1.;
+      F(0,1)=_planedistance;
+      F(1,0)=0.;
+      F(1,1)=1.;
+
+      Fk.push_back(F);
+
+      Q(0,0)=(t*t*height*height)/3.;
+      Q(0,1)=t*t*height/2.;
+      Q(1,0)=t*t*height/2.;
+      Q(1,1)=t*t;
+      Qk.push_back(Q);
+
+      TMatrix H(2,1);
+      H(0,0)=1;
+      H(1,0)=0;
+
+      x_proj = (F*x);
+
+      xprojk.push_back(x_proj);
+
+      TMatrix FT = F;
+      FT.T();
+      FTk.push_back(FT);
+
+      C_proj = (F*C)*FT + Q;
+
+      Cprojk.push_back(C_proj);
+
+      TMatrix C_projInv=C_proj;
+
+      C_projInv.Invert();
+
+      CprojInvk.push_back(C_projInv);
+
+      C = C_projInv;
+      C(0,0)+=G;
+      C.Invert();
+
+      Ck.push_back(C);
+      //Fk.push_back(F);
+      Qk.push_back(Q);
+
+      vector < Float_t > weight;
+
+      for (int k = 0; k < List.GetNRESEs(); k++) {
+
+        if(abs(List.GetRESEAt(k)->GetPosition().Z()-PlaneZ) > 0.0001) continue;
+
+        Bool_t previous = false;
+
+        for (int j = 0; j < Previous.GetNRESEs(); j++) {
+          if(abs(Previous.GetRESEAt(j)->GetPosition().Z()-PlaneZ)  > 0.0001) continue;
+          if(view==0){
+            if(Previous.GetRESEAt(j)->GetPosition().X()-List.GetRESEAt(k)->GetPosition().X() ==0) previous = true;
+          } else if(view==1){
+            if(Previous.GetRESEAt(j)->GetPosition().Y()-List.GetRESEAt(k)->GetPosition().Y() ==0) previous = true;
+          }
+        }
+
+        if(view==0){
+          if (previous) weight.push_back(sfg_factor+abs(List.GetRESEAt(k)->GetPosition().X()-x_proj(0,0))/(sqrt(C_proj(0,0))));
+          else weight.push_back(abs(List.GetRESEAt(k)->GetPosition().X()-x_proj(0,0))/(sqrt(C_proj(0,0))));
+        } else if(view==1){
+          if (previous) weight.push_back(sfg_factor+abs(List.GetRESEAt(k)->GetPosition().Y()-x_proj(0,0))/(sqrt(C_proj(0,0))));
+          else weight.push_back(abs(List.GetRESEAt(k)->GetPosition().Y()-x_proj(0,0))/(sqrt(C_proj(0,0))));
+        }
+
+      }
+      Int_t kmin=0;
+      for(int kk=0; kk<(int) weight.size(); kk++){
+        if(weight[kk]==*min_element(weight.begin(), weight.end())) kmin=kk;
+      }
+
+      Int_t kind=0;
+      for (int kk = 0; kk < List.GetNRESEs(); kk++) {
+        if(abs(List.GetRESEAt(kk)->GetPosition().Z()-PlaneZ) > 0.0001) continue;
+        else {
+          if (kind==kmin){
+            if(view==0){
+              m=List.GetRESEAt(kk)->GetPosition().X();
+            } else if(view==1){
+              m=List.GetRESEAt(kk)->GetPosition().Y();
+            }
+
+            Chosen.AddRESE(List.GetRESEAt(kk));
+            break;
+          }
+          kind ++;
+        }
+      }
+
+      mk.push_back(m);
+      x = C * (C_projInv*x_proj+(H*(G*m)));
+      xk.push_back(x);
+      i++;
+    }
+
+    if ((Int_t) xk.size()<n) n = xk.size();
+    if (n<2) return chi2;
+
+    //Smoothing
+
+    TMatrix xsmooth(2,1);
+
+    xsmoothk.resize(xk.size(), xsmooth);
+    xsmoothk[xsmoothk.size()-1] = xk[xk.size()-1];
+    trk.push_back(xsmoothk[xsmoothk.size()-1]);
+
+    TMatrix Csmooth(2,2);
+    Csmoothk.resize(Ck.size(), Csmooth);
+    Csmoothk[Ck.size()-1] = C;
+
+    for (Int_t i = n-2; i >= 0; i--) {
+      TMatrix A(2,2);
+
+      A = Ck[i]*FTk[i]*CprojInvk[i+1];
+
+      TMatrix AT = A;
+      AT.T();
+
+      xsmoothk[i] = xk[i] + A * (xsmoothk[i+1] - xprojk[i+1]);
+
+      trk.push_back(xsmoothk[i]);
+
+      Csmooth = Ck[i] + A*(Csmoothk[i+1] - Cprojk[i+1])*AT;
+      Csmoothk[i] = Csmooth;
+      Float_t rk = mk[i] - xsmoothk[i](0,0);
+      Float_t Rk = V -  Csmoothk[i](0,0);
+
+      chi2 += rk * rk / Rk;
+    }
+    reverse(trk.begin(),trk.end());
+    return chi2;
+  }
+
+  tuple<vector < TMatrix >, Float_t, Float_t, vector < TMatrix >, Float_t, Float_t, MRESEList, MRESEList> MERTrackKalman2D::SearchTracks(MRERawEvent* RE, Int_t view)
+  {
+    MRESEList PrevChoice;
+    Float_t en = start_nrg_fit;
+    Float_t nrg_est1;
+    Float_t nrg_est2;
+    Float_t chi1=0.;
+    Float_t chi2=0.;
+    Int_t loop1=0;
+    Bool_t stop=false;
+    Int_t n = n_fit;
+
+    MRESEList Chosen1;
+    MRESEList Chosen2;
+
+    vector < TMatrix > trk1;
+    vector < TMatrix > trk2;
+    mdebug<<"First track "<<endl;
+    PrevChoice.RemoveAllRESEs();
+    PrevChoice.Compress();
+
+    //track 1
+    while(!stop){
+
+      chi1 = Kalman(RE, n, en, PrevChoice, trk1, view, Chosen1);
+
+      if (trk1.size()<2){
+        return std::make_tuple(trk1, 0, 0, trk2, 0, 0, Chosen1, Chosen2);
+      }
+
+      nrg_est1=0.;
+
+      //Energy Estimation
+      nrg_est1 = MultipleScattering2D(trk1);
+
+      if (nrg_est1> 500000.) nrg_est1=500000.;
+      if ((nrg_est1/en)<1/3){
+        //loop1++;
+        en=en/3.;
+        trk1.clear();
+      } else if ((nrg_est1/en)>3. && loop1<9){
+        loop1++;
+        en=en*3.;
+        trk1.clear();
+      } else stop=true;
+    }
+
+    for (size_t i = 0; i < trk1.size(); i++) {
+      mdebug<<"Track1 after Kalman "<<trk1.size()<<" "<<trk1[i](0,0)<<" "<<trk1[i](1,0)<<endl;
+    }
+
+    stop=false;
+    en = start_nrg_fit;
+    Int_t loop2=0;
+    mdebug<<"Second track "<<endl;
+    //track 2
+    while(!stop){
+      Chosen2.RemoveAllRESEs();
+      Chosen2.Compress();
+
+      chi2 = Kalman(RE, n, en, Chosen1, trk2, view, Chosen2);
+
+      if (trk2.size()<2){
+        return std::make_tuple(trk1, 0, 0, trk2, 0, 0, Chosen1, Chosen2);
+      }
+
+      nrg_est2=0;
+
+      //Energy Estimation
+      nrg_est2 = MultipleScattering2D(trk2);
+
+      if (nrg_est2> 500000.) nrg_est2=500000.;
+      if ((nrg_est2/en)<1/3){
+        //loop1++;
+        en=en/3.;
+        trk2.clear();
+      } else if ((nrg_est2/en)>3. && loop2<9){
+        loop2++;
+        en=en*3.;
+        trk2.clear();
+      } else stop=true;
+    }
+    for (size_t i = 0; i < trk2.size(); i++) {
+      mdebug<<"Track2 after Kalman "<<trk2.size()<<" "<<trk2[i](0,0)<<" "<<trk2[i](1,0)<<endl;
+    }
+    return std::make_tuple(trk1, nrg_est1, chi1, trk2, nrg_est2, chi2, Chosen1, Chosen2);
+  }
+
+  Float_t MERTrackKalman2D::MultipleScattering2D(vector < TMatrix > trk)
+  {
+    vector < Float_t > angles;
+    UInt_t i;
+
+    for (i = 0; i < trk.size(); i++) {
+      angles.push_back(TMath::ATan( trk[i](1,0)));
+    }
+
+    vector < Float_t > dtheta1;
+    vector < Float_t > absdtheta1;
+    Float_t dt1;
+    for (i = 1; i < angles.size(); i++) {
+      dtheta1.push_back((Float_t) (angles[i] - angles[i - 1]));
+    }
+
+    dtheta1.erase(dtheta1.end() - 1, dtheta1.end());
+
+    Float_t   heightX0tot = 0;
+    vector < Float_t > planes;
+    Float_t meanX0 = 0;
+
+    for(i=0; i< dtheta1.size(); i++){
+      heightX0tot +=  m_heightX0;
+      dtheta1[i]/= exp(m_heightX0/cos(atan2(trk[1](1,0),1)));    //Energy correction
+    }
+
+    bool stop = false;
+    meanX0 = heightX0tot/dtheta1.size();
+
+    while (!stop) {
+      Float_t maxdt =0.;
+      dt1 = 0.;
+      absdtheta1.clear();
+
+      for (i = 0; i < dtheta1.size(); i++) {
+        dt1 += dtheta1[i] * dtheta1[i];
+        absdtheta1.push_back(TMath::Abs( dtheta1[i]));
+        if(TMath::Abs( dtheta1[i])>maxdt) maxdt=TMath::Abs( dtheta1[i]);
+      }
+      dt1 = sqrt((dt1 / dtheta1.size()));
+
+      if (maxdt / dt1 > 3.) {
+        for (i = 0; i < absdtheta1.size(); i++) {
+
+          if (absdtheta1[i] == maxdt) {
+            absdtheta1.erase(absdtheta1.begin() + i);
+            dtheta1.erase(dtheta1.begin() + i);
+            i--;
+          }
+        }
+      } else {
+        stop = true;
+      }
+    }
+
+    Float_t energy=13.6*sqrt(meanX0)*(1.+0.038*log(meanX0))/(dt1*sqrt(cos(atan2(trk[1](1,0), 1.))));
+    dtheta1.clear();
+    absdtheta1.clear();
+    angles.clear();
+    return energy;
+
+  }   //MultipleScattering2D
+
+  Float_t MERTrackKalman2D::MultipleScattering3D(MRESEList trkx, MRESEList trky)
+  {
+    Int_t n = min((trkx.GetNRESEs()),(trky.GetNRESEs()));
+    Float_t vi[3];
+    TVector3 vi0;
+    TVector3 vi1;
+
+    vector < Float_t > theta(n);
+
+    Float_t E = 0;
+
+    for (Int_t i = 0; i < n-1; i++) {
+
+      vi[0] = trkx.GetRESEAt(i+1)->GetPosition().X() - trkx.GetRESEAt(i)->GetPosition().X();
+      vi[1] = trky.GetRESEAt(i+1)->GetPosition().Y() - trky.GetRESEAt(i)->GetPosition().Y();
+      vi[2]= trkx.GetRESEAt(i+1)->GetPosition().Z() - trkx.GetRESEAt(i)->GetPosition().Z();
+      vi0.SetXYZ(vi[0], vi[1], vi[2]);
+      vi0.SetMag(1.);
+
+      theta[i] = vi0.Theta();
+
+      if (i != 0) {
+        Float_t angle = vi0.Angle(vi1);
+        E = (13.6/angle)*sqrt(m_heightX0/cos(TMath::Pi()-vi0.Theta()))*(1+0.038*log(m_heightX0/cos(TMath::Pi()-vi0.Theta())));
+
+        break;
+      }
+      vi1=vi0;
+    }
+    return E;
+  }
+
+  void MERTrackKalman2D::TrackPairs(MRERawEvent* RE)
+  {
+    if (RE->GetVertex() == 0) {
+      Fatal("void MRERawEvent::TrackPairs()",
+      "No vertex found!");
+    }
+
+    Float_t E1x=0.;
+    Float_t E2x=0.;
+    Float_t ChiT1x=0.;
+    Float_t ChiT2x=0.;
+
+    vector < TMatrix > Track1x;
+    vector < TMatrix > Track2x;
+
+    Float_t E1y=0.;
+    Float_t E2y=0.;
+    Float_t ChiT1y=0.;
+    Float_t ChiT2y=0.;
+
+    Float_t E1=0.;
+    Float_t E2=0.;
+    Float_t Egamma=0.;
+
+    vector < TMatrix > Track1y;
+    vector < TMatrix > Track2y;
+
+    MRESEList Chosen1x;
+    MRESEList Chosen2x;
+
+    MRESEList Chosen1y;
+    MRESEList Chosen2y;
+
+    MRETrack* Electron = new MRETrack();
+    MRETrack* Positron = new MRETrack();
+
+    // Now create the vertex:
+    Electron->AddRESE(RE->GetVertex());
+    Electron->SetStartPoint(RE->GetVertex());
+    Positron->AddRESE(RE->GetVertex());
+    Positron->SetStartPoint(RE->GetVertex());
+
+    // View X
+    tie(Track1x, E1x, ChiT1x, Track2x, E2x, ChiT2x, Chosen1x, Chosen2x) = SearchTracks(RE, 0);
+    if (ChiT1x==0. && ChiT2x==0.) return;
+
+    //View Y
+    tie(Track1y, E1y, ChiT1y, Track2y, E2y, ChiT2y, Chosen1y, Chosen2y) = SearchTracks(RE, 1);
+
+    if (ChiT1y==0. && ChiT2y==0.) return;
+
+    if((E1x-E2x)*(E1y-E2y)<0.){
+      Float_t E1ytemp=E1y;
+      E1y=E2y;
+      E2y=E1ytemp;
+
+      Float_t ChiT1ytemp=ChiT1y;
+      ChiT1y=ChiT2y;
+      ChiT2y=ChiT1ytemp;
+
+      Track1y.swap(Track2y);
+
+      MRESEList Chosen1ytemp(Chosen1y);
+      Chosen1y=Chosen2y;
+      Chosen2y=Chosen1ytemp;
+    }
+
+    if (Chosen1x.GetNRESEs()>2 && Chosen1y.GetNRESEs()>2){
+      E1= MultipleScattering3D(Chosen1x, Chosen1y);
+      if (Chosen2x.GetNRESEs()>2 && Chosen2y.GetNRESEs()>2){
+        E2= MultipleScattering3D(Chosen2x, Chosen2y);
+      } else E2= 0.;
+      Egamma= E1+E2;
+
+      for (int r = 0; r < Chosen1x.GetNRESEs(); r++) {
+        Electron->AddRESE(Chosen1x.GetRESEAt(r));
+      }
+
+      for (int r = 0; r < Chosen1y.GetNRESEs(); r++) {
+        Electron->AddRESE(Chosen1y.GetRESEAt(r));
+      }
+
+      for (int r = 0; r < Chosen2x.GetNRESEs(); r++) {
+        Positron->AddRESE(Chosen2x.GetRESEAt(r));
+      }
+
+      for (int r = 0; r < Chosen2y.GetNRESEs(); r++) {
+        Positron->AddRESE(Chosen2y.GetRESEAt(r));
+      }
+
+      Float_t thetax1=Track1x[0](1,0);
+      Float_t thetay1=Track1y[0](1,0);
+
+      Float_t thetax2=Track2x[0](1,0);
+      Float_t thetay2=Track2y[0](1,0);
+
+      mdebug<<"Theta of the four tracks: "<<c_Deg*atan(thetax1)<<" "<<c_Deg*atan(thetay1)<<" "<<c_Deg*atan(thetax2)<<" "<<c_Deg*atan(thetay2)<<" "<<endl;
+
+      Float_t x1= thetax1/sqrt(pow(thetax1,2.)+pow(thetay1,2.)+1);
+      Float_t y1= thetay1/sqrt(pow(thetax1,2.)+pow(thetay1,2.)+1);
+      Float_t z1= 1./sqrt(pow(thetax1,2.)+pow(thetay1,2.)+1);
+
+      Float_t x2= thetax2/sqrt(pow(thetax2,2.)+pow(thetay2,2.)+1);
+      Float_t y2= thetay2/sqrt(pow(thetax2,2.)+pow(thetay2,2.)+1);
+      Float_t z2= 1./sqrt(pow(thetax2,2.)+pow(thetay2,2.)+1);
+
+      Float_t x= x1*E1+x2*E2/Egamma;
+      Float_t y= y1*E1+y2*E2/Egamma;
+      Float_t z= z1*E1+z2*E2/Egamma;
+
+      Float_t mag=sqrt(x*x+y*y+z*z);
+      Float_t mag1=sqrt(x1*x1+y1*y1+z1*z1);
+      Float_t mag2=sqrt(x2*x2+y2*y2+z2*z2);
+
+
+      MVector direction(x/mag,y/mag,-z/mag);
+      MVector direction1(x1/mag1,y1/mag1,-z1/mag1);
+      MVector direction2(x2/mag2,y2/mag2,-z2/mag2);
+
+      Electron->SetFixedDirection(direction1);
+      Positron->SetFixedDirection(direction2);
+
+      Electron->SetEnergy(E1*1000); //So far the energy was calculated in MeV, MEGAlib works in keV
+      Positron->SetEnergy(E2*1000);
+
+      Electron->SetQualityFactor(ChiT1x+ChiT2x);
+      Positron->SetQualityFactor(ChiT1y+ChiT2y);
+
+      mdebug<<"Energy of the two particles: "<<E1<<" "<<E2<<endl;
+      mdebug<<"Reconstructed theta, phi and energy of the gamma: "<<c_Deg*direction.Theta()<<" "<<c_Deg*direction.Phi()<<" "<<Egamma<<endl;
+      RE->SetElectronTrack(Electron);
+      RE->SetPositronTrack(Positron);
+
+      //RE->SetTrackQualityFactor((ChiT1y+ChiT2y)/100);
+      RE->SetPairQualityFactor((ChiT1y+ChiT2y));
+      RE->SetGoodEvent(true);
+      RE->SetEventType(MRERawEvent::c_PairEvent);
+
+    } else{
+      Egamma= -1.;
+      E1= 1.;
+      E2= 1.;
+    }
+
+  }
+  // MERTrackKalman2D.cxx: the end...
+  ////////////////////////////////////////////////////////////////////////////////
diff --git a/src/revan/src/MERTrackKalman3D.cxx b/src/revan/src/MERTrackKalman3D.cxx
index 18c561714..cb11f47f8 100644
--- a/src/revan/src/MERTrackKalman3D.cxx
+++ b/src/revan/src/MERTrackKalman3D.cxx
@@ -556,7 +556,6 @@ return List;
 ////////////////////////////////////////////////////////////////////////////////
 
 // This function does the filtering and smoothing of the Kalman algorithm.
-
 Float_t MERTrackKalman3D::Kalman(MRERawEvent* RE, Int_t n, Float_t en, MRESEList Previous, vector < TMatrix > &trk, MRESEList &Chosen)
 {
 
@@ -900,7 +899,7 @@ tuple<vector < TMatrix >, Float_t, Float_t, vector < TMatrix >, Float_t, Float_t
   while(!stop){
 
     chi1 = Kalman(RE, n, en, PrevChoice, trk1, Chosen1);
-    
+
     if (trk1.size()<3){
       return std::make_tuple(trk1, 0, 0, trk2, 0, 0, Chosen1, Chosen2);
     }
@@ -925,7 +924,6 @@ tuple<vector < TMatrix >, Float_t, Float_t, vector < TMatrix >, Float_t, Float_t
       trk1.clear();
     } else stop=true;
   }
-
   for (size_t i = 0; i < trk1.size(); i++) {
     mdebug<<"Track1 after Kalman "<<trk1.size()<<" "<<trk1[i](0,0)<<" "<<trk1[i](1,0)<<endl;
   }
@@ -935,7 +933,6 @@ tuple<vector < TMatrix >, Float_t, Float_t, vector < TMatrix >, Float_t, Float_t
 
   while(!stop){
     chi2 = Kalman(RE, n, en, Chosen1, trk2, Chosen2);
-    
     if (trk2.size()<3){
       return std::make_tuple(trk1, 0, 0, trk2, 0, 0, Chosen1, Chosen2);
     }
@@ -946,7 +943,6 @@ tuple<vector < TMatrix >, Float_t, Float_t, vector < TMatrix >, Float_t, Float_t
     //Energy Estimation
     nrg_est2 = MultipleScattering(trk2);
     //nrg_est2 = EnergyEst3D(trk2);
-    
     if (nrg_est2> 50000.) nrg_est2=50000.;
     if ((nrg_est2/en)<1/3){
       //loop1++;
@@ -958,7 +954,6 @@ tuple<vector < TMatrix >, Float_t, Float_t, vector < TMatrix >, Float_t, Float_t
       trk2.clear();
     } else stop=true;
   }
-  
   for (size_t i = 0; i < trk2.size(); i++) {
     mdebug<<"Track2 after Kalman "<<trk2.size()<<" "<<trk2[i](0,0)<<" "<<trk2[i](1,0)<<endl;
   }
diff --git a/src/revan/src/MGUIERAlgorithm.cxx b/src/revan/src/MGUIERAlgorithm.cxx
index bed52e250..c4173b070 100644
--- a/src/revan/src/MGUIERAlgorithm.cxx
+++ b/src/revan/src/MGUIERAlgorithm.cxx
@@ -45,10 +45,10 @@ ClassImp(MGUIERAlgorithm)
 ////////////////////////////////////////////////////////////////////////////////
 
 
+
 MGUIERAlgorithm::MGUIERAlgorithm(const TGWindow* Parent, const TGWindow* Main, MSettingsEventReconstruction* Data) : MGUIDialog(Parent, Main)
 {
   // Construct an instance of MGUIERAlgorithm and bring it to the screen
-
   m_Data = Data;
 
   Create();
@@ -67,6 +67,7 @@ MGUIERAlgorithm::~MGUIERAlgorithm()
   delete m_HitClusteringList;
   delete m_TrackingList;
   delete m_CSRList;
+  delete m_PairList;
   //delete m_DecayList;
   delete m_ListLayout;
 }
@@ -80,8 +81,8 @@ void MGUIERAlgorithm::Create()
   // Create the main window
 
   // We start with a name and an icon...
-  SetWindowName("ER algorithms");  
-  AddSubTitle("Choose the reconstruction algorithms"); 
+  SetWindowName("ER algorithms");
+  AddSubTitle("Choose the reconstruction algorithms");
 
   m_ListLayout = new TGLayoutHints(kLHintsExpandX | kLHintsTop, 20, 20, 10, 10);
 
@@ -148,6 +149,14 @@ void MGUIERAlgorithm::Create()
   m_TrackingList->Create();
   AddFrame(m_TrackingList, m_ListLayout);
 
+  m_PairList = new MGUIERBList(this, "Pair reconstruction", true);
+  m_PairList->Add("Default algorithm");  // 0
+  m_PairList->Add("Kalman Filter 3D (work in progress)"); // 1
+  m_PairList->Add("Kalman Filter 2D (work in progress)"); // 2
+  m_PairList->SetSelected(m_Data->GetPairAlgorithm());
+  m_PairList->Create();
+  AddFrame(m_PairList, m_ListLayout);
+
   m_CSRList = new MGUIERBList(this, "Compton tracking", true);
   m_CSRList->Add("No Compton tracking");
   m_CSRList->Add("Classic Compton Sequence Reconstruction without Energy Recovery (Chi-square approach via angles)");
@@ -176,10 +185,10 @@ void MGUIERAlgorithm::Create()
 
   // and bring it to the screen.
   MapSubwindows();
-  MapWindow();  
+  MapWindow();
 
   Layout();
- 
+
   return;
 }
 
@@ -220,7 +229,7 @@ bool MGUIERAlgorithm::OnApply()
   } else if (m_TrackingList->GetSelected() == 7) {
     m_Data->SetTrackingAlgorithm(MRawEventAnalyzer::c_TrackingAlgoBayesian);
   }
-  
+  m_Data->SetPairAlgorithm(m_PairList->GetSelected());
   m_Data->SetCSRAlgorithm(m_CSRList->GetSelected());
   
   //m_Data->SetDecayAlgorithm(m_DecayList->GetSelected());
diff --git a/src/revan/src/MGUIOptionsTracking.cxx b/src/revan/src/MGUIOptionsTracking.cxx
index 668590209..1cfcaf989 100644
--- a/src/revan/src/MGUIOptionsTracking.cxx
+++ b/src/revan/src/MGUIOptionsTracking.cxx
@@ -46,14 +46,13 @@ ClassImp(MGUIOptionsTracking)
 ////////////////////////////////////////////////////////////////////////////////
 
 
-MGUIOptionsTracking::MGUIOptionsTracking(const TGWindow* Parent, 
-                                         const TGWindow* Main, 
+MGUIOptionsTracking::MGUIOptionsTracking(const TGWindow* Parent,
+                                         const TGWindow* Main,
                                          MSettingsEventReconstruction* Data,
                                          MDGeometryQuest* Geometry)
   : MGUIDialog(Parent, Main)
 {
   // Construct an instance of MGUIOptionsTracking and bring it to the screen
-
   m_Data = Data;
   m_Geometry = Geometry;
 
@@ -81,53 +80,53 @@ void MGUIOptionsTracking::Create()
   // Create the main window
 
   // We start with a name and an icon...
-  SetWindowName("Tracking");  
+  SetWindowName("Tracking");
 
   if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoModifiedPearson) {
-    AddSubTitle("Tracking options for Modified Pearson correlation:"); 
+    AddSubTitle("Tracking options for Modified Pearson correlation:");
   } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoPearson) {
-    AddSubTitle("Tracking options for Pearson correlation:"); 
+    AddSubTitle("Tracking options for Pearson correlation:");
   } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoRank) {
-    AddSubTitle("Tracking options for Rank correlation:"); 
+    AddSubTitle("Tracking options for Rank correlation:");
   } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoChiSquare) {
-    AddSubTitle("Tracking options for Chi-Square method:"); 
+    AddSubTitle("Tracking options for Chi-Square method:");
   } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoGas) {
-    AddSubTitle("Tracking options for gas detectors:"); 
+    AddSubTitle("Tracking options for gas detectors:");
   } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoDirectional) {
-    AddSubTitle("Tracking options for intrinsic electron tracking detectors - no options!"); 
+    AddSubTitle("Tracking options for intrinsic electron tracking detectors - no options!");
   } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoBayesian) {
-    AddSubTitle("Tracking options for Bayesian electron tracking:"); 
+    AddSubTitle("Tracking options for Bayesian electron tracking:");
   } else {
-    AddSubTitle("You deselected electron tracking!");     
+    AddSubTitle("You deselected electron tracking!");
   }
 
-  if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoModifiedPearson || 
+  if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoModifiedPearson ||
       m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoPearson ||
       m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoRank ||
       m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoChiSquare ||
       m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoGas ||
       m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoBayesian) {
     m_CBList = new MGUIECBList(this, "Search for the following event types:");
-    m_CBList->Add("Search for MIPS");              
+    m_CBList->Add("Search for MIPS");
     m_CBList->SetSelected(0, m_Data->GetSearchMIPs());
-    m_CBList->Add("Search for pairs");  
+    m_CBList->Add("Search for pairs");
     m_CBList->SetSelected(1, m_Data->GetSearchPairs());
-    m_CBList->Add("Search for Compton tracks");          
+    m_CBList->Add("Search for Compton tracks");
     m_CBList->SetSelected(2, m_Data->GetSearchComptons());
 //     if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoPearson) {
 //       m_CBList->Add("Cheating: Assume Compton tracks go from top to bottom");
 //       m_CBList->SetSelected(3, m_Data->GetAssumeTrackTopBottom());
-//     }          
+//     }
     m_CBList->Create();
-    TGLayoutHints* CBListLayout = 
+    TGLayoutHints* CBListLayout =
       new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, 20, 20, 0, 0);
     AddFrame(m_CBList, CBListLayout);
 
-    
+
     TGLayoutHints* SubLabel = new TGLayoutHints(kLHintsLeft | kLHintsTop, 20, 20, 20, 5);
     TGLabel* ComptonLabel = new TGLabel(this, "Compton options:");
     AddFrame(ComptonLabel, SubLabel);
-    
+
     TGLayoutHints* SubOptions = new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, 40, 20, 0, 5);
     m_MaxComptonJump = new MGUIEEntry(this,
                                       "Maximum number of layers a Compton track can skip (e.g. due to hits in passive material):",
@@ -150,7 +149,7 @@ void MGUIOptionsTracking::Create()
     } else {
       m_RejectPurelyAmbiguousSequences->SetState(kButtonUp);
     }
-    
+
 
     TGLabel* PairLabel = new TGLabel(this, "Pair options:");
     AddFrame(PairLabel, SubLabel);
@@ -161,19 +160,25 @@ void MGUIOptionsTracking::Create()
                                       m_Data->GetNLayersForVertexSearch(), true, 4);
     AddFrame(m_NLayersForVertexSearch, SubOptions);
 
+    m_SigmaHitPos = new MGUIEEntry(this,
+                                  "Error in the position of the hit in the tracker (used by the Kalman filter) [cm]:",
+                                  false,
+                                  m_Data->GetSigmaHitPos(), true, 0.00693);
+    AddFrame(m_SigmaHitPos, SubOptions);
+
 
     if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoBayesian) {
       TGLabel* GeneralLabel = new TGLabel(this, "General options:");
       AddFrame(GeneralLabel, SubLabel);
 
-      m_FileSelector = 
-        new MGUIEFileSelector(this, "File containing the Bayesian tracking data:", 
+      m_FileSelector =
+        new MGUIEFileSelector(this, "File containing the Bayesian tracking data:",
                               m_Data->GetBayesianElectronFileName());
       m_FileSelector->SetFileType("Response file", "*.rsp");
-      AddFrame(m_FileSelector, SubOptions);      
+      AddFrame(m_FileSelector, SubOptions);
     }
 
-    
+
     TGLabel* LabelDetectors = new TGLabel(this, "Select the tracking detector(s):");
     TGLayoutHints* LabelDetectorsLayout = new TGLayoutHints(kLHintsLeft | kLHintsTop, 20, 20, 20, 0);
     AddFrame(LabelDetectors, LabelDetectorsLayout);
@@ -197,10 +202,10 @@ void MGUIOptionsTracking::Create()
         }
       }
     } else {
-      merr<<"No geometry!"<<show; 
+      merr<<"No geometry!"<<show;
     }
     m_DetectorList->Resize(200, 100);
-    
+
   } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoDirectional) {
     // no options...
   }
@@ -210,10 +215,10 @@ void MGUIOptionsTracking::Create()
 
   // and bring it to the screen.
   MapSubwindows();
-  MapWindow();  
+  MapWindow();
 
   Layout();
- 
+
   return;
 }
 
@@ -223,9 +228,9 @@ void MGUIOptionsTracking::Create()
 
 bool MGUIOptionsTracking::OnApply()
 {
-  // The Apply button has been pressed
+	// The Apply button has been pressed
 
-  if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoModifiedPearson || 
+  if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoModifiedPearson ||
       m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoPearson ||
       m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoRank ||
       m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoChiSquare ||
@@ -236,13 +241,14 @@ bool MGUIOptionsTracking::OnApply()
     m_Data->SetSearchComptons(m_CBList->GetSelected(2));
     m_Data->SetMaxComptonJump(m_MaxComptonJump->GetAsInt());
     m_Data->SetNTrackSequencesToKeep(m_NSequencesToKeep->GetAsInt());
-    m_Data->SetNLayersForVertexSearch(m_NLayersForVertexSearch->GetAsInt());  
+    m_Data->SetNLayersForVertexSearch(m_NLayersForVertexSearch->GetAsInt());
+    m_Data->SetSigmaHitPos(m_SigmaHitPos->GetAsDouble());
     if (m_RejectPurelyAmbiguousSequences->GetState() == kButtonDown) {
       m_Data->SetRejectPurelyAmbiguousTrackSequences(true);
     } else {
       m_Data->SetRejectPurelyAmbiguousTrackSequences(false);
     }
-    
+
     m_Data->RemoveAllElectronTrackingDetectors();
     for (int d = 0; d < m_DetectorList->GetNumberOfEntries(); ++d) {
       if (m_DetectorList->GetSelection(d) == true) {
@@ -253,19 +259,19 @@ bool MGUIOptionsTracking::OnApply()
     // no options...
   }
 
-   
-//   if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoPearson || 
+
+//   if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoPearson ||
 //       m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoRank) {
 //     m_Data->SetAssumeTrackTopBottom(m_CBList->GetSelected(3));
-//   } 
-  
+//   }
+
   if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoBayesian) {
     m_Data->SetBayesianElectronFileName(m_FileSelector->GetFileName());
   }
 
-  
-  
-  return true;
+
+
+	return true;
 }
 
 
diff --git a/src/revan/src/MGUIRevanMain.cxx b/src/revan/src/MGUIRevanMain.cxx
index 079dd4ebf..ccd74444c 100644
--- a/src/revan/src/MGUIRevanMain.cxx
+++ b/src/revan/src/MGUIRevanMain.cxx
@@ -70,7 +70,7 @@ MGUIRevanMain::MGUIRevanMain(MInterfaceRevan* Interface, MSettingsRevan* Data)
 
 MGUIRevanMain::~MGUIRevanMain()
 {
-  // Standard destructor - in all normal exit cases the session have already 
+  // Standard destructor - in all normal exit cases the session have already
   // been deleted in CloseWindow
 }
 
@@ -81,11 +81,11 @@ MGUIRevanMain::~MGUIRevanMain()
 void MGUIRevanMain::Create()
 {
   // Create the main window
-  
+
   MGUIMain::Create();
 
   // We start with a name and an icon...
-  SetWindowName("Revan - Real event analyzer");  
+  SetWindowName("Revan - Real event analyzer");
 
   m_MenuReconstruction = new TGPopupMenu(fClient->GetRoot());
   m_MenuReconstruction->AddLabel("Analysis");
@@ -149,7 +149,7 @@ void MGUIRevanMain::Create()
   // Title:
   MString TitleIcon(g_MEGAlibPath + "/resource/icons/revan/Large.xpm");
   MFile::ExpandFileName(TitleIcon);
-  
+
   m_TitlePicture = fClient->GetPicture(TitleIcon);
   if (m_TitlePicture == 0) {
     mgui<<"Can't find picture "<<TitleIcon<<"! Aborting!"<<error;
@@ -159,7 +159,7 @@ void MGUIRevanMain::Create()
   m_TitleIconLayout = new TGLayoutHints(kLHintsCenterY | kLHintsCenterX, 0, 0, 10, 10);
   AddFrame(m_TitleIcon, m_TitleIconLayout);
 
-  // The status bars  
+  // The status bars
   m_StatusBarGeo->SetContent("Active:", MFile::GetBaseName(m_Data->GetGeometryFileName()));
   m_StatusBarGeo->Create();
   AddFrame(m_StatusBarGeo, m_StatusBarLayout);
@@ -170,7 +170,7 @@ void MGUIRevanMain::Create()
 
 
   MapSubwindows();
-  MapWindow();  
+  MapWindow();
   Layout();
 
   gSystem->ProcessEvents();
@@ -190,7 +190,7 @@ void MGUIRevanMain::Create()
 ////////////////////////////////////////////////////////////////////////////////
 
 
-bool MGUIRevanMain::ProcessMessage(long Message, long Parameter1, 
+bool MGUIRevanMain::ProcessMessage(long Message, long Parameter1,
                                      long Parameter2)
 {
   // Process the messages for this application
@@ -241,7 +241,7 @@ bool MGUIRevanMain::ProcessMessage(long Message, long Parameter1,
       case c_OptionsDecay:
         new MGUIOptionsDecay(gClient->GetRoot(), this, m_Data);
         break;
-        
+
       case c_Test:
         m_Interface->Test();
         //m_Interface->InitializeEventView();
@@ -253,14 +253,14 @@ bool MGUIRevanMain::ProcessMessage(long Message, long Parameter1,
         break;
 
       case c_Spectrum:
-        new MGUIReconstructedSpectrum(gClient->GetRoot(), this, m_Data, OKPressed);        
+        new MGUIReconstructedSpectrum(gClient->GetRoot(), this, m_Data, OKPressed);
         if (OKPressed == true) {
           m_Interface->GenerateSpectra();
         }
         break;
 
       case c_ExportSpectrum:
-        new MGUIExportSpectrum(gClient->GetRoot(), this, m_Data, OKPressed);        
+        new MGUIExportSpectrum(gClient->GetRoot(), this, m_Data, OKPressed);
         if (OKPressed == true) {
           m_Interface->ExportSpectrum();
         }
@@ -354,7 +354,7 @@ bool MGUIRevanMain::ProcessMessage(long Message, long Parameter1,
   default:
     break;
   }
-  
+
   return true;
 }
 
@@ -404,14 +404,14 @@ void MGUIRevanMain::Open()
   Info.fFileTypes = (const char **) Types;
   Info.fIniDir = StrDup(gSystem->DirName(m_Data->GetCurrentFileName()));
   new TGFileDialog(gClient->GetRoot(), this, kFDOpen, &Info);
-  
+
   delete [] Types;
-  
+
   // Get the filename ...
   if ((char *) Info.fFilename != 0) {
     m_Data->SetCurrentFileName(MString(Info.fFilename));
     UpdateConfiguration();
-  } 
+  }
   // ... or return when cancel has been pressed
   else {
     return;
@@ -450,13 +450,13 @@ void MGUIRevanMain::About()
 
 void MGUIRevanMain::Launch()
 {
-  // This method is called after pressing the MEGA-button in the 
+  // This method is called after pressing the MEGA-button in the
   // M.I.Works main GUI:
   // The reconstruction is started.
-  
+
   MString Name = m_Data->GetCurrentFileName();
 
-  if (Name.EndsWith("sim") == false && Name.EndsWith("evta") == false && 
+  if (Name.EndsWith("sim") == false && Name.EndsWith("evta") == false &&
       Name.EndsWith("sim.gz") == false && Name.EndsWith("evta.gz") == false) {
     mgui<<"The input file of Revan needs to have the suffix \"sim\", \"sim.gz\", \"evta\", or \"evta.gz\"!"<<error;
     return;
diff --git a/src/revan/src/MInterfaceRevan.cxx b/src/revan/src/MInterfaceRevan.cxx
index 122aa8c27..040537cbb 100644
--- a/src/revan/src/MInterfaceRevan.cxx
+++ b/src/revan/src/MInterfaceRevan.cxx
@@ -182,7 +182,7 @@ bool MInterfaceRevan::ParseCommandLine(int argc, char** argv)
         cout<<Usage.str()<<endl;
         return false;
       }
-    }   
+    }
     // Double argument
     //     if (Option == "-c" || Option == "--calibrate") {
     //      if (!((argc > i+2) && argv[i+1][0] != '-' && argv[i+2][0] != '-')){
@@ -193,7 +193,7 @@ bool MInterfaceRevan::ParseCommandLine(int argc, char** argv)
     //    }
 
   }
-    
+
   // Now parse all low level options
   for (int i = 1; i < argc; i++) {
     Option = argv[i];
@@ -212,13 +212,13 @@ bool MInterfaceRevan::ParseCommandLine(int argc, char** argv)
       cout<<"Command-line parser: Use configuration file "<<m_Data->GetSettingsFileName()<<endl;
     }
   }
-  
+
   // Look if we need to change the configuration
   for (int i = 1; i < argc; i++) {
     Option = argv[i];
     if (Option == "--change-configuration" || Option == "-C") {
       if (m_Data->Change(argv[++i]) == false) {
-        cout<<"ERROR: Command-line parser: Unable to change this configuration value: "<<argv[i]<<endl;        
+        cout<<"ERROR: Command-line parser: Unable to change this configuration value: "<<argv[i]<<endl;
       } else {
         cout<<"Command-line parser: Changing this configuration value: "<<argv[i]<<endl;
       }
@@ -303,7 +303,7 @@ bool MInterfaceRevan::ParseCommandLine(int argc, char** argv)
       return true;
     }
   }
-   
+
   // Execute some low level commands
   if (m_UseGui == true) {
     m_Gui = new MGUIRevanMain(this, m_Data);
@@ -324,7 +324,7 @@ bool MInterfaceRevan::ParseCommandLine(int argc, char** argv)
 
 
 bool MInterfaceRevan::LoadConfiguration(MString FileName)
-{  
+{
   // Load the configuration file
 
   if (m_Data == 0) {
@@ -389,7 +389,7 @@ bool MInterfaceRevan::SetGeometry(MString FileName, bool UpdateGui)
 
   m_Data->SetGeometryFileName(FileName);
   mout<<"Geometry "<<m_Geometry->GetName()<<" loaded!"<<endl;
-  
+
   if (m_UseGui == true && UpdateGui == true) {
     m_Gui->UpdateConfiguration();
   }
@@ -400,7 +400,7 @@ bool MInterfaceRevan::SetGeometry(MString FileName, bool UpdateGui)
 
 ////////////////////////////////////////////////////////////////////////////////
 
-  
+
 bool MInterfaceRevan::IsInitialized()
 {
   if (m_Geometry == 0) {
@@ -414,7 +414,7 @@ bool MInterfaceRevan::IsInitialized()
 
 ////////////////////////////////////////////////////////////////////////////////
 
-  
+
 void MInterfaceRevan::SetGuiData(MRawEventAnalyzer& REA)
 {
   // Transfer Gui data to the analyzer
@@ -430,7 +430,7 @@ void MInterfaceRevan::SetGuiData(MRawEventAnalyzer& REA)
 
 ////////////////////////////////////////////////////////////////////////////////
 
-  
+
 void MInterfaceRevan::AnalyzeEvents()
 {
   // Start Revan main program and analyze all events...
@@ -460,7 +460,7 @@ void MInterfaceRevan::AnalyzeEvents()
   if (Analyzer.SetInputModeFile(m_Data->GetCurrentFileName()) == false) return;
   if (Analyzer.SetOutputModeFile(FilenameOut) == false) return;
   SetGuiData(Analyzer);
-  
+
   if (Analyzer.PreAnalysis() == false) {
     mout<<"Event reconstruction: Initialization failed."<<endl;
     return;
@@ -477,7 +477,7 @@ void MInterfaceRevan::AnalyzeEvents()
   } while (ReturnCode != MRawEventAnalyzer::c_AnalysisNoEventsLeftInFile && ReturnCode != MRawEventAnalyzer::c_AnalysisSavingEventFailed);
   if (Analyzer.PostAnalysis() == false) {
     mout<<"Event reconstruction: Postprocessing failed"<<endl;
-    return;   
+    return;
   }
 
   mout<<"Event reconstruction finished in "<<Timer.ElapsedTime()<<" sec."<<endl;
@@ -502,20 +502,20 @@ void MInterfaceRevan::GenerateSpectra()
 
   bool BeforeReconstruction = m_Data->GetSpectrumBefore();
   bool AfterReconstruction = m_Data->GetSpectrumAfter();
-  
+
   bool ByInstrument = m_Data->GetSpectrumSortByInstrument();
   bool ByDetectorType = m_Data->GetSpectrumSortByDetectorType();
   bool ByNamedDetector = m_Data->GetSpectrumSortByNamedDetector();
   bool ByDetector = m_Data->GetSpectrumSortByDetector();
-  
+
   bool Combine = m_Data->GetSpectrumCombine();
-  
+
   bool OutputScreen = m_Data->GetSpectrumOutputToScreen();
   bool OutputFile = m_Data->GetSpectrumOutputToFile();
-  
+
   vector<TH1D*> AllSpectra;
-  
-  
+
+
   // Step 1: Let's create all the histograms:
   TH1D* SpectrumBeforeByInstrument = nullptr;
   map<int, TH1D*> SpectrumBeforeByDetectorType;
@@ -526,7 +526,7 @@ void MInterfaceRevan::GenerateSpectra()
       if (Combine == true) {
         SpectrumBeforeByInstrument = new TH1D("SpectrumCombinedBeforeByInstrument", "Event spectrum before reconstruction for the whole instrument", xNBins, xBins);
       } else {
-        SpectrumBeforeByInstrument = new TH1D("HitSpectrumBeforeByInstrument", "Hit spectrum before reconstruction for the whole instrument", xNBins, xBins);        
+        SpectrumBeforeByInstrument = new TH1D("HitSpectrumBeforeByInstrument", "Hit spectrum before reconstruction for the whole instrument", xNBins, xBins);
       }
       AllSpectra.push_back(SpectrumBeforeByInstrument);
     }
@@ -534,10 +534,10 @@ void MInterfaceRevan::GenerateSpectra()
       // Generated on the fly
     }
     if (ByDetector == true) {
-      // Generated on the fly      
+      // Generated on the fly
     }
   }
-  
+
   TH1D* SpectrumAfterByInstrument = nullptr;
   map<int, TH1D*> SpectrumAfterByDetectorType;
   map<MString, TH1D*> SpectrumAfterByNamedDetector;
@@ -547,27 +547,27 @@ void MInterfaceRevan::GenerateSpectra()
       if (Combine == true) {
         SpectrumAfterByInstrument = new TH1D("SpectrumCombinedAfterByInstrument", "Event spectrum after reconstruction for the whole instrument", xNBins, xBins);
       } else {
-        SpectrumAfterByInstrument = new TH1D("HitSpectrumAfterByInstrument", "Hit spectrum after reconstruction for the whole instrument", xNBins, xBins);        
+        SpectrumAfterByInstrument = new TH1D("HitSpectrumAfterByInstrument", "Hit spectrum after reconstruction for the whole instrument", xNBins, xBins);
       }
       AllSpectra.push_back(SpectrumAfterByInstrument);
     }
     if (ByDetectorType == true) {
-      // Generated on the fly      
+      // Generated on the fly
     }
     if (ByNamedDetector == true) {
       // Generated on the fly
-    }    
+    }
     if (ByDetector == true) {
       // Generated on the fly
-    }    
+    }
   }
-  
-  
+
+
   // Step 2: Let's fill all the histograms:
   MRawEventAnalyzer Analyzer;
   Analyzer.SetGeometry(m_Geometry);
   if (Analyzer.SetInputModeFile(m_Data->GetCurrentFileName()) == false) return;
-  
+
   SetGuiData(Analyzer);
   Analyzer.SetTotalEnergyMin(xMin);
   Analyzer.SetTotalEnergyMax(xMax);
@@ -576,16 +576,16 @@ void MInterfaceRevan::GenerateSpectra()
   unsigned int ReturnCode;
   do {
     ReturnCode = Analyzer.AnalyzeEvent();
-    
-    if (ReturnCode == MRawEventAnalyzer::c_AnalysisNoEventsLeftInFile || 
+
+    if (ReturnCode == MRawEventAnalyzer::c_AnalysisNoEventsLeftInFile ||
         ReturnCode == MRawEventAnalyzer::c_AnalysisSavingEventFailed) break;
-    
+
     MRERawEvent* Before = Analyzer.GetInitialRawEvent();
     vector<MRERawEvent*> AfterRecon = Analyzer.GetOptimumEvents();
     
     // BEFORE :
     if (BeforeReconstruction == true && Before != nullptr) {
-      
+
       if (ByInstrument == true) {
         if (Combine == true) {
           SpectrumBeforeByInstrument->Fill(Before->GetEnergy());
@@ -595,7 +595,7 @@ void MInterfaceRevan::GenerateSpectra()
           }
         }
       }
-      
+
       if (ByDetectorType == true) {
         if (Combine == true) {
           map<int, double> EnergyBeforeByDetectorType;
@@ -604,18 +604,18 @@ void MInterfaceRevan::GenerateSpectra()
           }
           for (auto E: EnergyBeforeByDetectorType) {
             if (SpectrumBeforeByDetectorType[E.first] == nullptr) {
-              TH1D* H = new TH1D(MString("SpectrumBeforeCombinedByDetectorType_") + E.first, 
+              TH1D* H = new TH1D(MString("SpectrumBeforeCombinedByDetectorType_") + E.first,
                                  MString("Spectrum before reconstruction for detector type ") + E.first + MString(" (individual hits of the events have been combined)"), xNBins, xBins);
               SpectrumBeforeByDetectorType[E.first] = H;
               AllSpectra.push_back(H);
             }
             SpectrumBeforeByDetectorType[E.first]->Fill(E.second);
-          }        
+          }
         } else {
           for (int r = 0; r < Before->GetNRESEs(); ++r) {
             int DetectorType = Before->GetRESEAt(r)->GetDetector();
             if (SpectrumBeforeByDetectorType[DetectorType] == nullptr) {
-              TH1D* H = new TH1D(MString("HitSpectrumBeforeByDetectorType_") + DetectorType, 
+              TH1D* H = new TH1D(MString("HitSpectrumBeforeByDetectorType_") + DetectorType,
                                  MString("Spectrum for individual hits before reconstruction for detector type ") + DetectorType, xNBins, xBins);
               SpectrumBeforeByDetectorType[DetectorType] = H;
               AllSpectra.push_back(H);
@@ -624,7 +624,7 @@ void MInterfaceRevan::GenerateSpectra()
           }
         }
       }
-      
+
       if (ByNamedDetector == true) {
         if (Combine == true) {
           map<MString, double> EnergyBeforeByNamedDetector;
@@ -634,7 +634,7 @@ void MInterfaceRevan::GenerateSpectra()
           }
           for (auto E: EnergyBeforeByNamedDetector) {
             if (SpectrumBeforeByNamedDetector[E.first] == nullptr) {
-              TH1D* H = new TH1D(MString("SpectrumBeforeCombinedByNamedDetector_") + E.first, 
+              TH1D* H = new TH1D(MString("SpectrumBeforeCombinedByNamedDetector_") + E.first,
                                  MString("Spectrum before reconstruction for detector ") + E.first + MString(" (individual hits of the events have been combined)"),  xNBins, xBins);
               SpectrumBeforeByNamedDetector[E.first] = H;
               AllSpectra.push_back(H);
@@ -654,8 +654,8 @@ void MInterfaceRevan::GenerateSpectra()
           }
         }
       } // By named detector
-      
-      
+
+
       if (ByDetector == true) {
         if (Combine == true) {
           map<MVector, double> EnergyBeforeByDetector;
@@ -668,7 +668,7 @@ void MInterfaceRevan::GenerateSpectra()
           for (auto E: EnergyBeforeByDetector) {
             MVector Pos = E.first;
             if (SpectrumBeforeByDetector[E.first] == nullptr) {
-              TH1D* H = new TH1D(MString("SpectrumBeforeCombinedByDetector_") + Name + "_" + Pos.ToString(), 
+              TH1D* H = new TH1D(MString("SpectrumBeforeCombinedByDetector_") + Name + "_" + Pos.ToString(),
                                  MString("Spectrum before reconstruction for detector ") + Name + " at position " + Pos.ToString() + MString(" (individual hits of the events have been combined)"),  xNBins, xBins);
               SpectrumBeforeByDetector[E.first] = H;
               AllSpectra.push_back(H);
@@ -681,7 +681,7 @@ void MInterfaceRevan::GenerateSpectra()
             Position = Before->GetRESEAt(r)->GetVolumeSequence()->GetPositionInFirstVolume(Position, Before->GetRESEAt(r)->GetVolumeSequence()->GetDeepestVolume());
             MString Name = Before->GetRESEAt(r)->GetVolumeSequence()->GetDeepestVolume()->GetName();
             if (SpectrumBeforeByDetector[Position] == nullptr) {
-              TH1D* H = new TH1D(MString("HitSpectrumBeforeByDetector_") + Name + "_" + Position.ToString(), 
+              TH1D* H = new TH1D(MString("HitSpectrumBeforeByDetector_") + Name + "_" + Position.ToString(),
                                  MString("Spectrum for individual hits before reconstruction for detector ") + Name + " at position " + Position.ToString(),  xNBins, xBins);
               SpectrumBeforeByDetector[Position] = H;
               AllSpectra.push_back(H);
@@ -691,9 +691,9 @@ void MInterfaceRevan::GenerateSpectra()
         }
       } // By detector
     } // BEFORE
-    
-    
-    
+
+
+
     // AFTER
     if (AfterReconstruction == true) {
       
@@ -809,41 +809,41 @@ void MInterfaceRevan::GenerateSpectra()
         } // By detector
       } // each after event
     } // AFTER
-    
+
   } while (true);
 
   if (Analyzer.PostAnalysis() == false) return;
-  
-  
+
+
   // Step 3: Nicen it!
-  
+
   for (TH1D* Hist: AllSpectra) {
     Hist->SetBit(kCanDelete);
     Hist->SetStats(false);
     Hist->SetFillColor(8);
     Hist->GetXaxis()->SetTitle("Energy [keV]");
-    Hist->GetYaxis()->SetTitle("counts/keV"); 
+    Hist->GetYaxis()->SetTitle("counts/keV");
   }
-  
-   
+
+
   // Step 4: Dump it!
-  
+
   if (OutputFile == true) {
     for (TH1D* Hist: AllSpectra) {
       MString FileName = m_Data->GetCurrentFileName();
       if (FileName.EndsWith(".gz")) {
-        FileName.RemoveLast(3); 
+        FileName.RemoveLast(3);
       }
       if (FileName.EndsWith(".sim")) {
-        FileName.RemoveLast(4); 
+        FileName.RemoveLast(4);
       }
       if (FileName.EndsWith(".evta")) {
-        FileName.RemoveLast(5); 
+        FileName.RemoveLast(5);
       }
       FileName += "_";
       FileName += Hist->GetName();
       FileName += ".dat";
-      
+
       ofstream out(FileName);
       out<<"# "<<Hist->GetTitle()<<endl;
       out<<"# File: "<<m_Data->GetCurrentFileName()<<endl;
@@ -874,23 +874,23 @@ void MInterfaceRevan::GenerateSpectra()
         mgui<<"We only display up to "<<MaxCanvases<<" individual spectra"<<info;
         break;
       }
-      
+
       // Convert to cts/keV
       for (int b = 1; b <= Hist->GetXaxis()->GetNbins(); ++b) {
         if (Hist->GetBinContent(b) > 0) {
           Hist->SetBinContent(b, Hist->GetBinContent(b)/Hist->GetBinWidth(b));
         }
       }
-      
+
       TCanvas* C = new TCanvas();
       C->cd();
       if (xLog == true) C->SetLogx();
       Hist->Draw();
       C->Update();
     }
-  }  
-  
-  
+  }
+
+
   delete [] xBins;
 }
 
@@ -913,7 +913,7 @@ void MInterfaceRevan::ExportSpectrum()
 
   TH1D* Hist = new TH1D("InitialEnergySpectrum", "Initial energy spectrum",  xNBins, xBins);
   Hist->SetBit(kCanDelete);
-  
+
   MRawEventAnalyzer Analyzer;
   Analyzer.SetGeometry(m_Geometry);
   if (Analyzer.SetInputModeFile(m_Data->GetCurrentFileName()) == false) return;
@@ -973,7 +973,7 @@ void MInterfaceRevan::InitialEnergySpectrum()
   Hist->GetXaxis()->SetTitle("Energy [keV]");
   Hist->GetYaxis()->SetTitle("counts/keV");
   //Hist->GetYaxis()->SetTitle("counts/keV/s");
-  
+
   MRawEventAnalyzer Analyzer;
   Analyzer.SetGeometry(m_Geometry);
   if (Analyzer.SetInputModeFile(m_Data->GetCurrentFileName()) == false) return;
@@ -1096,11 +1096,11 @@ void MInterfaceRevan::Coincidence()
   Hist->GetXaxis()->SetTitle("Time [s]");
   Hist->GetYaxis()->SetTitle("counts");
   //Hist->GetYaxis()->SetTitle("counts/keV/s");
-  
+
   MRawEventAnalyzer Analyzer;
   Analyzer.SetGeometry(m_Geometry);
   if (Analyzer.SetInputModeFile(m_Data->GetCurrentFileName()) == false) return;
-  
+
   SetGuiData(Analyzer);
   if (Analyzer.PreAnalysis() == false) return;
 
@@ -1112,7 +1112,7 @@ void MInterfaceRevan::Coincidence()
       continue;
     }
     Hist->Fill(fabs((This->GetEventTime() - Last->GetEventTime()).GetAsSeconds()));
-    
+
     delete Last;
     Last = This;
   }
@@ -1144,14 +1144,14 @@ void MInterfaceRevan::TriggerStatistics()
   Reader->ShowProgress();
 
   MRERawEvent* RE = 0;
-  while ((RE = Reader->GetNextEvent()) != 0) { 
+  while ((RE = Reader->GetNextEvent()) != 0) {
     delete RE;
   }
   mout<<Reader->GetERNoising()->ToString()<<endl;
 
   delete Reader;
 
-  return; 
+  return;
 }
 
 
@@ -1167,12 +1167,12 @@ void MInterfaceRevan::TriggerStatistics()
 //   if (Analyzer.PreAnalysis() == false) return;
 
 
-//   TH1D* CSRGood = new TH1D("CSR Good Test Statistics", "CSR Good Test Statistics", 
+//   TH1D* CSRGood = new TH1D("CSR Good Test Statistics", "CSR Good Test Statistics",
 //         50, m_Data->GetCSRThresholdMin(), m_Data->GetCSRThresholdMax());
 //   CSRGood->SetBit(kCanDelete);
 //   CSRGood->SetFillColor(8);
 
-//   TH1D* CSRAll = new TH1D("CSR All Test Statistics", "CSR All Test Statistics", 
+//   TH1D* CSRAll = new TH1D("CSR All Test Statistics", "CSR All Test Statistics",
 //        50, m_Data->GetCSRThresholdMin(), m_Data->GetCSRThresholdMax());
 //   CSRAll->SetBit(kCanDelete);
 //   CSRAll->SetFillColor(8);
@@ -1188,27 +1188,27 @@ void MInterfaceRevan::TriggerStatistics()
 //         CSRGood->Fill(Analyzer.GetRawEvent()->GetScoreComptonQualityFactor1());
 //       }
 
-//       map<double, vector<MRESE*>, greater_equal<double> >& TestStatistics = 
+//       map<double, vector<MRESE*>, greater_equal<double> >& TestStatistics =
 //         CSR.GetTestStatistics();
 
 //       map<double, vector<MRESE*>, greater_equal<double> >::iterator TestStatisticsIterator;
 
-//       for (TestStatisticsIterator = TestStatistics.begin(); 
-//            TestStatisticsIterator != TestStatistics.end(); 
+//       for (TestStatisticsIterator = TestStatistics.begin();
+//            TestStatisticsIterator != TestStatistics.end();
 //            TestStatisticsIterator++) {
 //         CSRAll->Fill((*TestStatisticsIterator).first);
 //       }
-      
-//     }  
+
+//     }
 //   }
 
-//   TCanvas* CSRGoodCanvas = 
+//   TCanvas* CSRGoodCanvas =
 //     new TCanvas("CSR Test Good Statistics Canvas", "CSR Test Good Statistics Canvas", 640, 480);
 //   CSRGoodCanvas->cd();
 //   CSRGood->Draw();
 //   CSRGoodCanvas->Update();
 
-//   TCanvas* CSRAllCanvas = 
+//   TCanvas* CSRAllCanvas =
 //     new TCanvas("CSR Test All Statistics Canvas", "CSR Test All Statistics Canvas", 640, 480);
 //   CSRAllCanvas->cd();
 //   CSRAll->Draw();
@@ -1231,16 +1231,16 @@ void MInterfaceRevan::EnergyDistribution()
   double EMax = m_Data->GetTotalEnergyMax();
   double EMin = m_Data->GetTotalEnergyMin();
 
-  TH1D* Before = new TH1D("InitialEnergySpectrum", 
-        "Energy spectrum BEFORE reconstruction", 
+  TH1D* Before = new TH1D("InitialEnergySpectrum",
+        "Energy spectrum BEFORE reconstruction",
         NBins, EMin, EMax);
   Before->SetBit(kCanDelete);
   Before->SetFillColor(8);
   Before->GetXaxis()->SetTitle("Energy [keV]");
   Before->GetYaxis()->SetTitle("counts");
 
-  TH1D* After = new TH1D("InitialEnergySpectrum", 
-       "Energy spectrum AFTER reconstruction", 
+  TH1D* After = new TH1D("InitialEnergySpectrum",
+       "Energy spectrum AFTER reconstruction",
        NBins, EMin, EMax);
   After->SetBit(kCanDelete);
   After->SetFillColor(8);
@@ -1250,36 +1250,36 @@ void MInterfaceRevan::EnergyDistribution()
   MRawEventAnalyzer Analyzer;
   Analyzer.SetGeometry(m_Geometry);
   if (Analyzer.SetInputModeFile(m_Data->GetCurrentFileName()) == false) return;
-  
+
   SetGuiData(Analyzer);
   if (Analyzer.PreAnalysis() == false) return;
 
   unsigned int ReturnCode;
   do {
     ReturnCode = Analyzer.AnalyzeEvent();
-    
-    if (ReturnCode == MRawEventAnalyzer::c_AnalysisNoEventsLeftInFile || 
+
+    if (ReturnCode == MRawEventAnalyzer::c_AnalysisNoEventsLeftInFile ||
         ReturnCode == MRawEventAnalyzer::c_AnalysisSavingEventFailed) break;
-    
+
     if (Analyzer.GetInitialRawEvent() != 0) {
       Before->Fill(Analyzer.GetInitialRawEvent()->GetEnergy());
-    } 
+    }
 
     vector<MRERawEvent*> REs = Analyzer.GetOptimumEvents();
     for (auto RE: REs) {
       if (RE == nullptr) continue;
       After->Fill(RE->GetEnergy());
     }
-    
+
   } while (true);
 
   if (Analyzer.PostAnalysis() == false) return;
-  
+
   TCanvas* BeforeCanvas = new TCanvas("Before", "Before", 640, 480);
   BeforeCanvas->cd();
   Before->Draw();
   BeforeCanvas->Update();
-  
+
   TCanvas* AfterCanvas = new TCanvas("After", "After", 640, 480);
   AfterCanvas->cd();
   After->Draw();
@@ -1337,8 +1337,8 @@ void MInterfaceRevan::InitialEventStatistics()
     unsigned int NHits = RE->GetNRESEs();
     if (NHits < MaxHits) {
       if (MaxFoundHits < NHits) MaxFoundHits = NHits;
-      Hits[NHits]++;    
-    }    
+      Hits[NHits]++;
+    }
     ++NEvents;
     AverageEnergy += RE->GetEnergy();
 
@@ -1350,7 +1350,7 @@ void MInterfaceRevan::InitialEventStatistics()
       if (MaxFoundSeparatedHits < NSeparatedHits) MaxFoundSeparatedHits = NSeparatedHits;
       SeparatedHits[NSeparatedHits]++;
       NSeparatedHitsEvents++;
-    }    
+    }
 
     // delete RE; --> delete by RawEvents
   }
@@ -1421,7 +1421,7 @@ void MInterfaceRevan::HitStatistics()
 
    unsigned int ind = 0;
 
-//   while ((RE = Reader->GetNextEvent()) != 0) { 
+//   while ((RE = Reader->GetNextEvent()) != 0) {
 
   MERHitClusterizer HitClusterizer;
   if (m_Data->GetHitClusteringAlgorithm() == MRawEventAnalyzer::c_HitClusteringAlgoDistance) {
@@ -1441,18 +1441,18 @@ void MInterfaceRevan::HitStatistics()
   MRERawEvent* RE = 0;
   MRawEventIncarnations* RawEvents = new MRawEventIncarnations(0);
 
-  while ((RE = Reader->GetNextEvent()) != 0) { 
+  while ((RE = Reader->GetNextEvent()) != 0) {
     RawEvents->SetInitialRawEvent(RE);
     HitClusterizer.Analyze(RawEvents);
   
     massert(RawEvents->GetNRawEvents() == 1);
-    
+
     MRERawEvent* RW = RawEvents->GetRawEventAt(0);
 
     for (int i = 0; i < RW->GetNRESEs(); ++i) {
       RESE = RW->GetRESEAt(i);
       Detector = RESE->GetVolumeSequence()->GetDetector()->GetName();
-      
+
       for (ind = 0; ind < DetectorNames.size(); ++ind) {
         if (DetectorNames[ind] == Detector) break;
       }
@@ -1502,7 +1502,7 @@ void MInterfaceRevan::HitStatistics()
   map<MString, int>::iterator Iter;
   map<MString, double> DetectorEfficiency;
   map<MString, double>::iterator EIter;
-  
+
   MFileEventsEvta* Reader = new MFileEventsEvta(m_Geometry);
   if (Reader->Open(m_Data->GetCurrentFileName()) == false) {
     mout<<"Unable to open file "<<m_Data->GetCurrentFileName()<<". Aborting!"<<endl;
@@ -1515,7 +1515,7 @@ void MInterfaceRevan::HitStatistics()
   MRERawEvent* RE = 0;
   MString Detector;
 
-  while ((RE = Reader->GetNextEvent()) != 0) { 
+  while ((RE = Reader->GetNextEvent()) != 0) {
     if (RE->GetNRESEs() != 1) continue;
     for (int i = 0; i < RE->GetNRESEs(); ++i) {
       RESE = RE->GetRESEAt(i);
@@ -1523,7 +1523,7 @@ void MInterfaceRevan::HitStatistics()
       if (RESE->GetEnergy() < MaxEnergy && RESE->GetEnergy() > MinEnergy) {
         Detector = m_Geometry->GetDetectorName(Pos);
         DetectorHits[Detector]++;
-      }    
+      }
     }
     delete RE;
   }
@@ -1531,7 +1531,7 @@ void MInterfaceRevan::HitStatistics()
   cout<<"Hits per detector up to "<<setw(6)<<MaxEnergy<<"keV:"<<endl;
   for (Iter = DetectorHits.begin(); Iter != DetectorHits.end(); Iter++) {
     cout<<setw(13)<<(*Iter).first<<": "<<setw(6)<<(*Iter).second<<" hits"<<endl;
-  }  
+  }
 
   int SumD1 = 0;
   int SumD22 = 0;
@@ -1539,13 +1539,13 @@ void MInterfaceRevan::HitStatistics()
   int SumD28 = 0;
   for (Iter = DetectorHits.begin(); Iter != DetectorHits.end(); Iter++) {
     MString Name = (*Iter).first;
-    if (Name == "athene" || Name == "daphne" || 
+    if (Name == "athene" || Name == "daphne" ||
         Name == "xantippe" || Name == "aphrodite") {
       SumD28 += (*Iter).second;
     } else if (Name == "medusa" || Name == "fortuna" || Name == "penelope" || Name == "venus" ||
          Name == "hydra" || Name == "aetna" || Name == "ariadne" || Name == "helena") {
       SumD24 += (*Iter).second;
-    } else if (Name == "antigone" || Name == "diane" || Name == "persephone" || Name == "minerva" || 
+    } else if (Name == "antigone" || Name == "diane" || Name == "persephone" || Name == "minerva" ||
          Name == "pallas" || Name == "thetis" || Name == "circe" || Name == "europa") {
       SumD22 += (*Iter).second;
     } else {
@@ -1555,25 +1555,25 @@ void MInterfaceRevan::HitStatistics()
 
   for (Iter = DetectorHits.begin(); Iter != DetectorHits.end(); Iter++) {
     MString Name = (*Iter).first;
-    if (Name == "athene" || Name == "daphne" || 
+    if (Name == "athene" || Name == "daphne" ||
         Name == "xantippe" || Name == "aphrodite") {
       DetectorEfficiency[Name] = 4.0*(*Iter).second/SumD28;
     } else if (Name == "medusa" || Name == "fortuna" || Name == "penelope" || Name == "venus" ||
          Name == "hydra" || Name == "aetna" || Name == "ariadne" || Name == "helena") {
       DetectorEfficiency[Name] = 8.0*(*Iter).second/SumD24;
-    } else if (Name == "antigone" || Name == "diane" || Name == "persephone" || Name == "minerva" || 
+    } else if (Name == "antigone" || Name == "diane" || Name == "persephone" || Name == "minerva" ||
          Name == "pallas" || Name == "thetis" || Name == "circe" || Name == "europa") {
       DetectorEfficiency[Name] = 8.0*(*Iter).second/SumD22;
     } else {
       DetectorEfficiency[Name] = 11.0*(*Iter).second/SumD1;
     }
-  }  
+  }
 
   cout<<"  // Efficiency between "<<MinEnergy<<"keV and "<<MaxEnergy<<"keV:"<<endl;
   for (EIter = DetectorEfficiency.begin(); EIter != DetectorEfficiency.end(); EIter++) {
     //cout<<setw(13)<<(*EIter).first<<": "<<setw(6)<<(*EIter).second<<endl;
     cout<<"  m_Efficiency[\""<<(*EIter).first<<"\"] = "<<(*EIter).second<<";"<<endl;
-  }  
+  }
 }
 */
 
@@ -1597,6 +1597,7 @@ void MInterfaceRevan::DetectorTypeClusterDistribution(bool Before)
   SetGuiData(Analyzer);
   if (Before == true) {
     Analyzer.SetTrackingAlgorithm(MRawEventAnalyzer::c_TrackingAlgoNone);
+    Analyzer.SetPairAlgorithm(MRawEventAnalyzer::c_PairKalman2D);
     Analyzer.SetCSRAlgorithm(MRawEventAnalyzer::c_CSRAlgoNone);
     Analyzer.SetDecayAlgorithm(MRawEventAnalyzer::c_DecayAlgoNone);
   }
@@ -1610,10 +1611,10 @@ void MInterfaceRevan::DetectorTypeClusterDistribution(bool Before)
   unsigned int ReturnCode;
   do {
     ReturnCode = Analyzer.AnalyzeEvent();
-    
-    if (ReturnCode == MRawEventAnalyzer::c_AnalysisNoEventsLeftInFile || 
+
+    if (ReturnCode == MRawEventAnalyzer::c_AnalysisNoEventsLeftInFile ||
         ReturnCode == MRawEventAnalyzer::c_AnalysisSavingEventFailed) break;
-    
+
     if (Before == true) {
       REs = Analyzer.GetInitialRawEvents();
     } else {
@@ -1630,7 +1631,7 @@ void MInterfaceRevan::DetectorTypeClusterDistribution(bool Before)
           // Split top-level tracks:
           Track = dynamic_cast<MRETrack*>(RESE);
           for (int h = 0; h < Track->GetNRESEs(); ++h) {
-            Hits[Track->GetRESEAt(h)->GetDetector()]++;            
+            Hits[Track->GetRESEAt(h)->GetDetector()]++;
           }
         } else {
           Hits[RESE->GetDetector()]++;
@@ -1668,9 +1669,9 @@ void MInterfaceRevan::DetectorTypeClusterDistribution(bool Before)
   // To screen...
   for (map<int, vector<unsigned int> >::iterator Iter = ClusterDistribution.begin();
        Iter != ClusterDistribution.end(); ++Iter) {
-    TH1D* Clusters = new TH1D(MString("ClusterDistribution") + 
+    TH1D* Clusters = new TH1D(MString("ClusterDistribution") +
                               MDDetector::GetDetectorTypeName((*Iter).first) + SuffixName,
-                              MString("Cluster Distribution in Detector Type ") + 
+                              MString("Cluster Distribution in Detector Type ") +
                               MDDetector::GetDetectorTypeName((*Iter).first) + SuffixTitle,
                               (*Iter).second.size(), 0.5, (*Iter).second.size()+0.5);
     Clusters->SetBit(kCanDelete);
@@ -1682,10 +1683,10 @@ void MInterfaceRevan::DetectorTypeClusterDistribution(bool Before)
       Clusters->SetBinContent(b, (*Iter).second[b]);
     }
 
-    TCanvas* ClustersCanvas = 
-      new TCanvas(MString("CanvasClusterDistribution") + 
+    TCanvas* ClustersCanvas =
+      new TCanvas(MString("CanvasClusterDistribution") +
                   MDDetector::GetDetectorTypeName((*Iter).first) + SuffixName,
-                  MString("Canvas for Cluster Distribution in Detector Type ") + 
+                  MString("Canvas for Cluster Distribution in Detector Type ") +
                   MDDetector::GetDetectorTypeName((*Iter).first) + SuffixTitle);
     ClustersCanvas->cd();
     Clusters->Draw();
@@ -1717,6 +1718,7 @@ void MInterfaceRevan::DetectorTypeHitDistribution(bool Before)
   SetGuiData(Analyzer);
   if (Before == true) {
     Analyzer.SetTrackingAlgorithm(MRawEventAnalyzer::c_TrackingAlgoNone);
+    Analyzer.SetPairAlgorithm(MRawEventAnalyzer::c_PairKalman2D);
     Analyzer.SetCSRAlgorithm(MRawEventAnalyzer::c_CSRAlgoNone);
     Analyzer.SetDecayAlgorithm(MRawEventAnalyzer::c_DecayAlgoNone);
   }
@@ -1731,10 +1733,10 @@ void MInterfaceRevan::DetectorTypeHitDistribution(bool Before)
   unsigned int ReturnCode;
   do {
     ReturnCode = Analyzer.AnalyzeEvent();
-    
-    if (ReturnCode == MRawEventAnalyzer::c_AnalysisNoEventsLeftInFile || 
+
+    if (ReturnCode == MRawEventAnalyzer::c_AnalysisNoEventsLeftInFile ||
         ReturnCode == MRawEventAnalyzer::c_AnalysisSavingEventFailed) break;
-    
+
     if (Before == true) {
       REs = Analyzer.GetBestTryEvents();
     } else {
@@ -1755,17 +1757,17 @@ void MInterfaceRevan::DetectorTypeHitDistribution(bool Before)
               // Split second-level clusters:
               Cluster = dynamic_cast<MRECluster*>(RESE);
               for (int h = 0; h < Cluster->GetNRESEs(); ++h) {
-                Hits[Cluster->GetRESEAt(h)->GetDetector()]++;            
+                Hits[Cluster->GetRESEAt(h)->GetDetector()]++;
               }
             } else {
-              Hits[Track->GetRESEAt(h)->GetDetector()]++;  
+              Hits[Track->GetRESEAt(h)->GetDetector()]++;
             }
           }
         } else if (RESE->GetType() == MRESE::c_Cluster) {
           // Split top-level clusters:
           Cluster = dynamic_cast<MRECluster*>(RESE);
           for (int h = 0; h < Cluster->GetNRESEs(); ++h) {
-            Hits[Cluster->GetRESEAt(h)->GetDetector()]++;            
+            Hits[Cluster->GetRESEAt(h)->GetDetector()]++;
           }
         } else {
           Hits[RESE->GetDetector()]++;
@@ -1789,7 +1791,7 @@ void MInterfaceRevan::DetectorTypeHitDistribution(bool Before)
       if (Added == true) {
         NEvents++;
         if (IsTwoPlus == true) {
-          NTwoPlusEvents++; 
+          NTwoPlusEvents++;
         }
       }
     }
@@ -1810,9 +1812,9 @@ void MInterfaceRevan::DetectorTypeHitDistribution(bool Before)
   // To screen...
   for (map<int, vector<unsigned int> >::iterator Iter = HitDistribution.begin();
        Iter != HitDistribution.end(); ++Iter) {
-    TH1D* Hits = new TH1D(MString("HitDistribution") + 
+    TH1D* Hits = new TH1D(MString("HitDistribution") +
                               MDDetector::GetDetectorTypeName((*Iter).first) + SuffixName,
-                              MString("Hit Distribution in Detector Type ") + 
+                              MString("Hit Distribution in Detector Type ") +
                               MDDetector::GetDetectorTypeName((*Iter).first) + SuffixTitle,
                               (*Iter).second.size(), 0.5, (*Iter).second.size()+0.5);
     Hits->SetBit(kCanDelete);
@@ -1824,10 +1826,10 @@ void MInterfaceRevan::DetectorTypeHitDistribution(bool Before)
       Hits->SetBinContent(b, (*Iter).second[b]);
     }
 
-    TCanvas* HitsCanvas = 
-      new TCanvas(MString("CanvasHitDistribution") + 
+    TCanvas* HitsCanvas =
+      new TCanvas(MString("CanvasHitDistribution") +
                   MDDetector::GetDetectorTypeName((*Iter).first) + SuffixName,
-                  MString("Canvas for Hit Distribution in Detector Type ") + 
+                  MString("Canvas for Hit Distribution in Detector Type ") +
                   MDDetector::GetDetectorTypeName((*Iter).first) + SuffixTitle);
     HitsCanvas->cd();
     Hits->Draw();
@@ -1860,21 +1862,21 @@ void MInterfaceRevan::DepthProfileByDetector()
   double MaxTotalEnergy = m_Data->GetTotalEnergyMax();
 
   // Since we do not know anything about the detectors we have to store the events by detector first:
-  
+
   // Map the detector center to a vector of depths
   map<MVector, vector<double>> Depths;
-  
+
   // Step 1: Accumulate all hits:
 
   MRERawEvent* RE = 0;
   while ((RE = Reader->GetNextEvent()) != 0) {
-    
+
     // Make sure the total energy is right:
     double Total = 0;
     for (int i = 0; i < RE->GetNRESEs(); ++i) {
       Total += RE->GetRESEAt(i)->GetEnergy();
     }
-    if (Total >= MinTotalEnergy && Total <= MaxTotalEnergy) { 
+    if (Total >= MinTotalEnergy && Total <= MaxTotalEnergy) {
       // Save positions and energies
       for (int i = 0; i < RE->GetNRESEs(); ++i) {
         MDVolumeSequence* V = RE->GetRESEAt(i)->GetVolumeSequence();
@@ -1885,10 +1887,10 @@ void MInterfaceRevan::DepthProfileByDetector()
         }
       }
     }
-    
+
     delete RE;
   }
-  
+
   // Step 2: Show everything:
   for (auto& Pair: Depths) {
     MString Title;
@@ -1905,7 +1907,7 @@ void MInterfaceRevan::DepthProfileByDetector()
         for (double N: Pair.second) {
           if (N < Min) Min = N;
           if (N > Max) Max = N;
-        }         
+        }
       }
     } else {
       Title = Pair.first.ToString();
@@ -1914,21 +1916,21 @@ void MInterfaceRevan::DepthProfileByDetector()
         if (N > Max) Max = N;
       }
     }
-    
+
     TH1D* Hist = new TH1D(Title, Title, 100, Min, Max);
     Hist->SetXTitle("Interaction depth [cm]");
     Hist->SetYTitle("counts");
     for (double N: Pair.second) {
-      Hist->Fill(N);    
+      Hist->Fill(N);
     }
-    
+
     TCanvas* Canvas = new TCanvas();
     Canvas->cd();
     Hist->Draw();
     Canvas->Update();
   }
-  
-  
+
+
 }
 
 
@@ -1954,26 +1956,26 @@ void MInterfaceRevan::SpatialDistribution(bool UseEnergy)
 
   double MinTotalEnergy = m_Data->GetTotalEnergyMin();
   double MaxTotalEnergy = m_Data->GetTotalEnergyMax();
-  
+
   // Step 1: Accumulate many, many hits:
 
   MRESE* RESE = 0;
   MRERawEvent* RE = 0;
   while ((RE = Reader->GetNextEvent()) != 0) {
-    
+
     // Make sure the total energy is right:
     double Total = 0;
     for (int i = 0; i < RE->GetNRESEs(); ++i) {
       Total += RE->GetRESEAt(i)->GetEnergy();
     }
-    if (Total >= MinTotalEnergy && Total <= MaxTotalEnergy) { 
+    if (Total >= MinTotalEnergy && Total <= MaxTotalEnergy) {
       // Save positions and energies
       for (int i = 0; i < RE->GetNRESEs(); ++i) {
         Positions.push_back(RE->GetRESEAt(i)->GetPosition());
         Energies.push_back(RE->GetRESEAt(i)->GetEnergy());
       }
     }
-    
+
     delete RE;
 
     if (Positions.size() > MaxNPositions) {
@@ -2006,18 +2008,18 @@ void MInterfaceRevan::SpatialDistribution(bool UseEnergy)
     ValueAxisTitle = "Counts per bin";
   }
 
-  TH3D* xyzHist = new TH3D(HistName + "xyz", 
-                           HistTitle + "xyz", 
+  TH3D* xyzHist = new TH3D(HistName + "xyz",
+                           HistTitle + "xyz",
                            MaxNBins, xMin, xMax,
-                           MaxNBins, yMin, yMax, 
+                           MaxNBins, yMin, yMax,
                            MaxNBins, zMin, zMax);
   xyzHist->SetBit(kCanDelete);
   xyzHist->GetXaxis()->SetTitle("x [cm]");
   xyzHist->GetYaxis()->SetTitle("y [cm]");
   xyzHist->GetZaxis()->SetTitle("z [cm]");
 
-  TH2D* xyHist = new TH2D(HistName + "xy", 
-                          HistTitle + "xy", 
+  TH2D* xyHist = new TH2D(HistName + "xy",
+                          HistTitle + "xy",
                           MaxNBins, xMin, xMax,
                           MaxNBins, yMin, yMax);
   xyHist->SetBit(kCanDelete);
@@ -2025,8 +2027,8 @@ void MInterfaceRevan::SpatialDistribution(bool UseEnergy)
   xyHist->GetYaxis()->SetTitle("y [cm]");
   xyHist->GetZaxis()->SetTitle(ValueAxisTitle);
 
-  TH2D* xzHist = new TH2D(HistName + "xz", 
-                          HistTitle + "xz", 
+  TH2D* xzHist = new TH2D(HistName + "xz",
+                          HistTitle + "xz",
                           MaxNBins, xMin, xMax,
                           MaxNBins, zMin, zMax);
   xzHist->SetBit(kCanDelete);
@@ -2034,8 +2036,8 @@ void MInterfaceRevan::SpatialDistribution(bool UseEnergy)
   xzHist->GetYaxis()->SetTitle("z [cm]");
   xzHist->GetZaxis()->SetTitle(ValueAxisTitle);
 
-  TH2D* yzHist = new TH2D(HistName + "yz", 
-                          HistTitle + "yz", 
+  TH2D* yzHist = new TH2D(HistName + "yz",
+                          HistTitle + "yz",
                           MaxNBins, yMin, yMax,
                           MaxNBins, zMin, zMax);
   yzHist->SetBit(kCanDelete);
@@ -2043,22 +2045,22 @@ void MInterfaceRevan::SpatialDistribution(bool UseEnergy)
   yzHist->GetYaxis()->SetTitle("z [cm]");
   yzHist->GetZaxis()->SetTitle(ValueAxisTitle);
 
-  TH1D* xHist = new TH1D(HistName + "x", 
-                         HistTitle + "x", 
+  TH1D* xHist = new TH1D(HistName + "x",
+                         HistTitle + "x",
                          MaxNBins, xMin, xMax);
   xHist->SetBit(kCanDelete);
   xHist->GetXaxis()->SetTitle("x [cm]");
   xHist->GetYaxis()->SetTitle(ValueAxisTitle);
 
-  TH1D* yHist = new TH1D(HistName + "y", 
-                         HistTitle + "y", 
+  TH1D* yHist = new TH1D(HistName + "y",
+                         HistTitle + "y",
                          MaxNBins, yMin, yMax);
   yHist->SetBit(kCanDelete);
   yHist->GetXaxis()->SetTitle("y [cm]");
   yHist->GetYaxis()->SetTitle(ValueAxisTitle);
 
-  TH1D* zHist = new TH1D(HistName + "z", 
-                         HistTitle + "z", 
+  TH1D* zHist = new TH1D(HistName + "z",
+                         HistTitle + "z",
                          MaxNBins, zMin, zMax);
   zHist->SetBit(kCanDelete);
   zHist->GetXaxis()->SetTitle("z [cm]");
@@ -2085,7 +2087,7 @@ void MInterfaceRevan::SpatialDistribution(bool UseEnergy)
 
   // Step 4: Continue filling from file:
 
-  while ((RE = Reader->GetNextEvent()) != 0) { 
+  while ((RE = Reader->GetNextEvent()) != 0) {
     for (int i = 0; i < RE->GetNRESEs(); ++i) {
       RESE = RE->GetRESEAt(i);
       Pos = RESE->GetPosition();
@@ -2191,7 +2193,7 @@ void MInterfaceRevan::EnergyPerDetector()
   MVector Pos;
   MRESE* RESE = 0;
   MRERawEvent* RE = 0;
-  while ((RE = Reader->GetNextEvent()) != 0) { 
+  while ((RE = Reader->GetNextEvent()) != 0) {
     // categorize the beam into layers:
 
     int NHitsD1 = 0;
@@ -2205,7 +2207,7 @@ void MInterfaceRevan::EnergyPerDetector()
       }
     }
 
-    if (RE->GetEnergy() > Emax || 
+    if (RE->GetEnergy() > Emax ||
   //if (RE->GetEnergy() > 1.1*Emax || RE->GetEnergy() < 0.9*Emax ||
         NHitsD1 == 0 || NHitsD2 == 0) {
       delete RE;
@@ -2223,12 +2225,12 @@ void MInterfaceRevan::EnergyPerDetector()
         AvgEnergyD2 += RESE->GetEnergy();
       }
     }
-    
+
 
     bool HitD2side = false;
     bool HitD2bottom = false;
     for (int i = 0; i < RE->GetNRESEs(); ++i) {
-      RESE = RE->GetRESEAt(i); 
+      RESE = RE->GetRESEAt(i);
       if (RESE->GetDetector() == 1) {
         D1Hist->Fill(RESE->GetEnergy());
       } else if (RESE->GetDetector() == 2) {
@@ -2331,48 +2333,48 @@ void MInterfaceRevan::EnergyPerCentralTrackElement()
   double EMin = 100;
   double EMax = 1000;
 
-  TH1D* StartEnergy = new TH1D("StartEnergySpectrum", 
-                                 "Energy of start track element", 
+  TH1D* StartEnergy = new TH1D("StartEnergySpectrum",
+                                 "Energy of start track element",
                                  NBins/2, EMin, EMax);
   StartEnergy->SetBit(kCanDelete);
   StartEnergy->SetFillColor(8);
   StartEnergy->GetXaxis()->SetTitle("Energy [keV]");
   StartEnergy->GetYaxis()->SetTitle("counts");
 
-  TH1D* StartAngle = new TH1D("StartAngleDstribution", 
-                                "Angle of start track element", 
+  TH1D* StartAngle = new TH1D("StartAngleDstribution",
+                                "Angle of start track element",
                                 90, 0, 180);
   StartAngle->SetBit(kCanDelete);
   StartAngle->SetFillColor(8);
   StartAngle->GetXaxis()->SetTitle("Angle [#circ]");
   StartAngle->GetYaxis()->SetTitle("counts");
 
-  TH1D* CentralEnergy = new TH1D("CentralEnergySpectrum", 
-                                 "Energy of central track element", 
+  TH1D* CentralEnergy = new TH1D("CentralEnergySpectrum",
+                                 "Energy of central track element",
                                  NBins, EMin, EMax);
   CentralEnergy->SetBit(kCanDelete);
   CentralEnergy->SetFillColor(8);
   CentralEnergy->GetXaxis()->SetTitle("Energy [keV]");
   CentralEnergy->GetYaxis()->SetTitle("counts");
 
-  TH1D* CentralAngle = new TH1D("CentralAngleDstribution", 
-                                "Angle of central track element", 
+  TH1D* CentralAngle = new TH1D("CentralAngleDstribution",
+                                "Angle of central track element",
                                 90, 0, 180);
   CentralAngle->SetBit(kCanDelete);
   CentralAngle->SetFillColor(8);
   CentralAngle->GetXaxis()->SetTitle("Angle [#circ]");
   CentralAngle->GetYaxis()->SetTitle("counts");
 
-  TH1D* StopEnergy = new TH1D("StopEnergySpectrum", 
-                                 "Energy of stop track element", 
+  TH1D* StopEnergy = new TH1D("StopEnergySpectrum",
+                                 "Energy of stop track element",
                                  NBins, EMin, EMax);
   StopEnergy->SetBit(kCanDelete);
   StopEnergy->SetFillColor(8);
   StopEnergy->GetXaxis()->SetTitle("Energy [keV]");
   StopEnergy->GetYaxis()->SetTitle("counts");
 
-  TH1D* StopAngle = new TH1D("StopAngleDstribution", 
-                                "Angle of stop track element", 
+  TH1D* StopAngle = new TH1D("StopAngleDstribution",
+                                "Angle of stop track element",
                                 90, 0, 180);
   StopAngle->SetBit(kCanDelete);
   StopAngle->SetFillColor(8);
@@ -2390,8 +2392,8 @@ void MInterfaceRevan::EnergyPerCentralTrackElement()
   unsigned int ReturnCode;
   do {
     ReturnCode = Analyzer.AnalyzeEvent();
-    
-    if (ReturnCode == MRawEventAnalyzer::c_AnalysisNoEventsLeftInFile || 
+
+    if (ReturnCode == MRawEventAnalyzer::c_AnalysisNoEventsLeftInFile ||
         ReturnCode == MRawEventAnalyzer::c_AnalysisSavingEventFailed) break;
     
     vector<MRERawEvent*> REs = Analyzer.GetOptimumEvents();
@@ -2418,32 +2420,32 @@ void MInterfaceRevan::EnergyPerCentralTrackElement()
   } while (true);
 
   if (Analyzer.PostAnalysis() == false) return;
-  
+
   TCanvas* StartEnergyCanvas = new TCanvas("StartEnergy", "StartEnergy", 640, 480);
   StartEnergyCanvas->cd();
   StartEnergy->Draw();
   StartEnergyCanvas->Update();
-  
+
   TCanvas* StartAngleCanvas = new TCanvas("StartAngle", "StartAngle", 640, 480);
   StartAngleCanvas->cd();
   StartAngle->Draw();
   StartAngleCanvas->Update();
-  
+
   TCanvas* CentralEnergyCanvas = new TCanvas("CentralEnergy", "CentralEnergy", 640, 480);
   CentralEnergyCanvas->cd();
   CentralEnergy->Draw();
   CentralEnergyCanvas->Update();
-  
+
   TCanvas* CentralAngleCanvas = new TCanvas("CentralAngle", "CentralAngle", 640, 480);
   CentralAngleCanvas->cd();
   CentralAngle->Draw();
   CentralAngleCanvas->Update();
-  
+
   TCanvas* StopEnergyCanvas = new TCanvas("StopEnergy", "StopEnergy", 640, 480);
   StopEnergyCanvas->cd();
   StopEnergy->Draw();
   StopEnergyCanvas->Update();
-  
+
   TCanvas* StopAngleCanvas = new TCanvas("StopAngle", "StopAngle", 640, 480);
   StopAngleCanvas->cd();
   StopAngle->Draw();
@@ -2493,7 +2495,7 @@ void MInterfaceRevan::FindPolarization()
   double MaxGammaEnergy = 100000;
 
 
-  while ((RE = Reader->GetNextEvent()) != 0) { 
+  while ((RE = Reader->GetNextEvent()) != 0) {
     // categorize the beam into layers:
 
     NEvents++;
@@ -2518,7 +2520,7 @@ void MInterfaceRevan::FindPolarization()
       } // Energy
     } // Number of RESE
     delete RE;
-  }  
+  }
 
   TCanvas* Canvas = new TCanvas();
   Hist->Draw("lego2");
@@ -2555,19 +2557,19 @@ void MInterfaceRevan::StartDistribution()
   double eMin = 0;
   double eMax = 700;
 
-  TH1D* DOM = new TH1D("DOM", "DOM", NBins, 0, 180); 
+  TH1D* DOM = new TH1D("DOM", "DOM", NBins, 0, 180);
   DOM->SetBit(kCanDelete);
 
-  TH1D* EFirst = new TH1D("EFirst", "EFirst", NBins, eMin, eMax); 
+  TH1D* EFirst = new TH1D("EFirst", "EFirst", NBins, eMin, eMax);
   EFirst->SetBit(kCanDelete);
   TH1D* ESecond = new TH1D("ESecond", "ESecond", NBins, eMin, eMax);
   ESecond->SetBit(kCanDelete);
   TH1D* EThird = new TH1D("EThird", "EThird", NBins, eMin, eMax);
   EThird->SetBit(kCanDelete);
 
-  TH2D* Double = new TH2D("Double", "Double", NBins, xMin, xMax, NBins, yMin, yMax); 
+  TH2D* Double = new TH2D("Double", "Double", NBins, xMin, xMax, NBins, yMin, yMax);
   Double->SetBit(kCanDelete);
-  TH2D* Triple = new TH2D("Triple+", "Triple+", NBins, xMin, xMax, NBins, yMin, yMax); 
+  TH2D* Triple = new TH2D("Triple+", "Triple+", NBins, xMin, xMax, NBins, yMin, yMax);
   Triple->SetBit(kCanDelete);
 
 
@@ -2575,12 +2577,12 @@ void MInterfaceRevan::StartDistribution()
   unsigned int ReturnCode;
   do {
     ReturnCode = Analyzer.AnalyzeEvent();
-    
-    if (ReturnCode == MRawEventAnalyzer::c_AnalysisNoEventsLeftInFile || 
+
+    if (ReturnCode == MRawEventAnalyzer::c_AnalysisNoEventsLeftInFile ||
         ReturnCode == MRawEventAnalyzer::c_AnalysisSavingEventFailed) break;
 
     if ((RE = Analyzer.GetInitialRawEvent()) != 0) {
-      
+
       cout<<"Number: "<<RE->GetNRESEs()<<endl;
       if (RE->GetNRESEs() == 2) {
         if (RE->GetRESEAt(0)->GetPosition().Z() == 24.720 &&
@@ -2593,9 +2595,9 @@ void MInterfaceRevan::StartDistribution()
         if (RE->GetRESEAt(0)->GetPosition().Z() == 24.720 &&
             RE->GetRESEAt(1)->GetPosition().Z() == 23.720 &&
             RE->GetRESEAt(2)->GetPosition().Z() == 22.720 &&
-            RE->GetRESEAt(0)->GetPosition().X() > -3 && 
-            RE->GetRESEAt(0)->GetPosition().X() < 3 && 
-            RE->GetRESEAt(0)->GetPosition().Y() > -3 && 
+            RE->GetRESEAt(0)->GetPosition().X() > -3 &&
+            RE->GetRESEAt(0)->GetPosition().X() < 3 &&
+            RE->GetRESEAt(0)->GetPosition().Y() > -3 &&
             RE->GetRESEAt(0)->GetPosition().Y() < 3 ) {
           Triple->Fill(RE->GetRESEAt(0)->GetPosition().X(), RE->GetRESEAt(0)->GetPosition().Y(), 1);
         
@@ -2626,7 +2628,7 @@ void MInterfaceRevan::StartDistribution()
   DOMCanvas->cd();
   DOM->Draw();
   cout<<" < 90: "<<DOM->Integral(0, NBins/2)<<"   > 90: "<<DOM->Integral(NBins/2+1, NBins)<<endl;
-   
+
   //   TCanvas* DoubleCanvas = new TCanvas();
   //   Double->Draw();
 
@@ -2634,17 +2636,17 @@ void MInterfaceRevan::StartDistribution()
   //   Triple->Draw();
 
   TCanvas* EFirstCanvas = new TCanvas();
-  EFirstCanvas->cd();  
+  EFirstCanvas->cd();
   EFirst->Draw();
 
   TCanvas* ESecondCanvas = new TCanvas();
-  ESecondCanvas->cd();  
+  ESecondCanvas->cd();
   ESecond->Draw();
 
   TCanvas* EThirdCanvas = new TCanvas();
-  EThirdCanvas->cd();  
+  EThirdCanvas->cd();
   EThird->Draw();
-  
+
   return;
 }
 
@@ -2656,7 +2658,7 @@ void MInterfaceRevan::FindBeamPath()
 {
   if (IsInitialized() == false) return;
 
-  // 
+  //
 
   int Number = 3;
   double Stops[3] = { 0.00, 0.50, 1.00 };
@@ -2673,7 +2675,7 @@ void MInterfaceRevan::FindBeamPath()
   Reader->ShowProgress(m_UseGui);
 
   // Create a list of histograms:
-  vector<double> zValues; 
+  vector<double> zValues;
   vector<TH2D*> Histos;
   vector<TCanvas*> Canvases;
 
@@ -2695,7 +2697,7 @@ void MInterfaceRevan::FindBeamPath()
   int NEvents = 0;
   MRESE* R;
   MRERawEvent* RE = 0;
-  while ((RE = Reader->GetNextEvent()) != 0) { 
+  while ((RE = Reader->GetNextEvent()) != 0) {
     EventUsed = false;
     // categorize the beam into layers:
     for (int r = 0; r < RE->GetNRESEs(); ++r) {
@@ -2711,7 +2713,7 @@ void MInterfaceRevan::FindBeamPath()
     }
     if (EventUsed == true) NEvents++;
     delete RE;
-  }  
+  }
 
 
   // Show the histograms:
@@ -2720,7 +2722,7 @@ void MInterfaceRevan::FindBeamPath()
     Histos[l]->Draw("colz");
     Canvases [l]->Update();
   }
-  
+
   // Now do a fit to determine the path
   TGraph* PathX = new TGraph(Layers);
   for (unsigned int l = 0; l < Layers; ++l) {
@@ -2733,7 +2735,7 @@ void MInterfaceRevan::FindBeamPath()
   PathX->SetMarkerStyle(3);
   PathX->Draw("AP");
   PathXCanvas->Update();
-  
+
   TGraph* PathY = new TGraph(Layers);
   for (unsigned int l = 0; l < Layers; ++l) {
     PathY->SetPoint(l, zValues[l], Histos[l]->GetMean(2));
@@ -2761,7 +2763,7 @@ void MInterfaceRevan::FindBeamPath()
   ProfileCanvas->cd();
   Profile->Draw();
   ProfileCanvas->Update();
-  
+
   cout<<"Number of used events: "<<NEvents<<endl;
 
 
@@ -2794,16 +2796,16 @@ void MInterfaceRevan::NumberOfClusters()
   if (Analyzer.SetInputModeFile(m_Data->GetCurrentFileName()) == false) return;
   SetGuiData(Analyzer);
   Analyzer.SetTrackingAlgorithm(MRawEventAnalyzer::c_TrackingAlgoNone);
+  Analyzer.SetPairAlgorithm(MRawEventAnalyzer::c_PairKalman2D);
   Analyzer.SetCSRAlgorithm(MRawEventAnalyzer::c_CSRAlgoNone);
   Analyzer.SetDecayAlgorithm(MRawEventAnalyzer::c_DecayAlgoNone);
 
   if (Analyzer.PreAnalysis() == false) return;
-  
   unsigned int ReturnCode;
   do {
     ReturnCode = Analyzer.AnalyzeEvent();
-    
-    if (ReturnCode == MRawEventAnalyzer::c_AnalysisNoEventsLeftInFile || 
+
+    if (ReturnCode == MRawEventAnalyzer::c_AnalysisNoEventsLeftInFile ||
         ReturnCode == MRawEventAnalyzer::c_AnalysisSavingEventFailed) break;
 
     vector<MRERawEvent*> REs = Analyzer.GetBestTryEvents();
@@ -2817,7 +2819,7 @@ void MInterfaceRevan::NumberOfClusters()
     // delete RE; // ?????
   } while (true);
 
-  TH1D* ClustersHist = 
+  TH1D* ClustersHist =
     new TH1D("NumberOfClustersPerEvent",
              "Number of Cluster per Event",
              Clusters.size(), 0.5, Clusters.size()+0.5);
@@ -2829,8 +2831,8 @@ void MInterfaceRevan::NumberOfClusters()
   for (int b = 0; b < ClustersHist->GetNbinsX(); ++b) {
     ClustersHist->SetBinContent(b, Clusters[b]);
   }
-  
-  TCanvas* ClustersCanvas = 
+
+  TCanvas* ClustersCanvas =
     new TCanvas("CanvasNumberOfClustersPerEvent",
                 "Canvas for Number of Cluster per event");
   ClustersCanvas->cd();
diff --git a/src/revan/src/MREHit.cxx b/src/revan/src/MREHit.cxx
index ad2b90b76..e0c327723 100644
--- a/src/revan/src/MREHit.cxx
+++ b/src/revan/src/MREHit.cxx
@@ -69,24 +69,24 @@ bool MREHit::ParseLine(MString HitString, int Version)
   // m_IsValid = false
 
   Reset();
-  
+
   // Handle the most common MEGAlib 2.x sim / evta file versions
   if (Version == 25 && HitString.BeginsWith("HTsim ")) {
     Version = 101;
   } else if (Version == 21 && HitString.BeginsWith("HT ")) {
     Version = 200;
-  }
-  
+  } else if (Version == -1 && !HitString.BeginsWith("HTsim ")) Version = 4;
+
   m_IsValid = true;
   m_FixedResolutions = false;
 
 
   if (Version == 100) {
-    if (sscanf(HitString, "HTsim %d;%lf;%lf;%lf;%lf\n", 
-               &m_Detector, 
-               &m_Position[0], 
-               &m_Position[1], 
-               &m_Position[2], 
+    if (sscanf(HitString, "HTsim %d;%lf;%lf;%lf;%lf\n",
+               &m_Detector,
+               &m_Position[0],
+               &m_Position[1],
+               &m_Position[2],
                &m_Energy) == 5) {
       m_Time = 0;
       m_PositionResolution.SetXYZ(0.0, 0.0, 0.0);
@@ -95,28 +95,28 @@ bool MREHit::ParseLine(MString HitString, int Version)
       m_IsValid = true;
     }
   } else if (Version == 101) {
-    if (sscanf(HitString, "HTsim %d;%lf;%lf;%lf;%lf;%lf\n", 
-               &m_Detector, 
-               &m_Position[0], 
-               &m_Position[1], 
-               &m_Position[2], 
-               &m_Energy, 
+    if (sscanf(HitString, "HTsim %d;%lf;%lf;%lf;%lf;%lf\n",
+               &m_Detector,
+               &m_Position[0],
+               &m_Position[1],
+               &m_Position[2],
+               &m_Energy,
                &m_Time) == 6) {
       m_PositionResolution.SetXYZ(0.0, 0.0, 0.0);
       m_EnergyResolution = 0.0;
       m_TimeResolution = 0.0;
       m_IsValid = true;
-    }    
+    }
   } else if (Version == 200) {
     if (sscanf(HitString, "HT %d;%lf;%lf;%lf;%lf;%lf;%lf;%lf;%lf\n",
                &m_Detector,
-               &m_Position[0], 
-               &m_Position[1], 
-               &m_Position[2], 
-               &m_Energy, 
-               &m_PositionResolution[0], 
-               &m_PositionResolution[1], 
-               &m_PositionResolution[2], 
+               &m_Position[0],
+               &m_Position[1],
+               &m_Position[2],
+               &m_Energy,
+               &m_PositionResolution[0],
+               &m_PositionResolution[1],
+               &m_PositionResolution[2],
                &m_EnergyResolution) == 9) {
       m_Time = 0;
       m_TimeResolution = 0;
@@ -126,14 +126,14 @@ bool MREHit::ParseLine(MString HitString, int Version)
   } else if (Version == 201) {
     if (sscanf(HitString, "HT %d;%lf;%lf;%lf;%lf;%lf;%lf;%lf;%lf;%lf;%lf\n",
                &m_Detector,
-               &m_Position[0], 
-               &m_Position[1], 
-               &m_Position[2], 
+               &m_Position[0],
+               &m_Position[1],
+               &m_Position[2],
                &m_Energy,
                &m_Time,
-               &m_PositionResolution[0], 
-               &m_PositionResolution[1], 
-               &m_PositionResolution[2], 
+               &m_PositionResolution[0],
+               &m_PositionResolution[1],
+               &m_PositionResolution[2],
                &m_EnergyResolution,
                &m_TimeResolution
               ) == 11) {
@@ -180,7 +180,7 @@ MREHit::MREHit(MREHit *Hit) : MRESE((MRESE *) Hit)
   m_IsValid = Hit->m_IsValid; 
   m_SubElementType = MRESE::c_Hit;
   m_FixedResolutions = Hit->m_FixedResolutions;
-} 
+}
 
 
 ////////////////////////////////////////////////////////////////////////////////
@@ -188,7 +188,7 @@ MREHit::MREHit(MREHit *Hit) : MRESE((MRESE *) Hit)
 
 MREHit::~MREHit()
 {
-  // Delete this object, but do not delete its links and RESEs 
+  // Delete this object, but do not delete its links and RESEs
 }
 
 
@@ -287,7 +287,7 @@ MString MREHit::ToString(bool WithLink, int Level)
     for (int i = 0; i < Level+1; i++) {
       String += MString("   ");
     }
-    String += MString("Linked with: ");   
+    String += MString("Linked with: ");
     for (int a = 0; a < GetNLinks(); a++) {
       snprintf(Text, Length, "  (%d)", GetLinkAt(a)->GetID());
       String += MString(Text);
@@ -303,7 +303,7 @@ MString MREHit::ToString(bool WithLink, int Level)
 
 
 MString MREHit::ToEvtaString(const int ScientificPrecision, const int Version)
-{  
+{
   //! Convert to a string in the evta file
 
   ostringstream S;
@@ -369,13 +369,13 @@ MREHit* MREHit::Duplicate()
 bool MREHit::UpdateVolumeSequence(MDGeometryQuest* Geometry)
 {
   /* This optimization is for another day...
-  if (m_VolumeSequence != nullptr && 
+  if (m_VolumeSequence != nullptr &&
       m_VolumeSequence->GetNVolumes() > 0 &&
       m_VolumeSequence->GetPosition(0) == m_Position) {
-    return true; 
+    return true;
   }
   */
-  
+
   MDVolumeSequence* V = Geometry->GetVolumeSequencePointer(m_Position, true, true);
 
   // Check if we do have a resonable volume sequence:
@@ -387,7 +387,7 @@ bool MREHit::UpdateVolumeSequence(MDGeometryQuest* Geometry)
     delete m_VolumeSequence;
     m_VolumeSequence = V;
   }
-  
+
   return true;
 }
 
@@ -399,15 +399,15 @@ bool MREHit::RetrieveResolutions(MDGeometryQuest* Geometry)
 {
   // Do not do anything if we have fixed resolutions
   if (m_FixedResolutions == true) return true;
-  
+
   if (UpdateVolumeSequence(Geometry) == false) return false;
-  
+
   Geometry->GetResolutions(m_Position, m_Energy, m_Time, *m_VolumeSequence, m_PositionResolution, m_EnergyResolution, m_TimeResolution);
-  
+
   return true;
 }
-  
-  
+
+
 ////////////////////////////////////////////////////////////////////////////////
 
 
@@ -422,7 +422,7 @@ bool MREHit::Noise(MDGeometryQuest* Geometry)
   }
   //cout<<"Pos after: "<<m_Position[0]<<"!"<<m_Position[1]<<"!"<<m_Position[2]<<endl;
 
-  if (m_Detector < MDDetector::c_MinDetector || 
+  if (m_Detector < MDDetector::c_MinDetector ||
       m_Detector > MDDetector::c_MaxDetector) {
     merr<<"Unknown detector ID: "<<m_Detector<<show;
     return false;
diff --git a/src/revan/src/MRawEventAnalyzer.cxx b/src/revan/src/MRawEventAnalyzer.cxx
index 205eb1e9e..f8720497f 100644
--- a/src/revan/src/MRawEventAnalyzer.cxx
+++ b/src/revan/src/MRawEventAnalyzer.cxx
@@ -23,13 +23,13 @@
 //
 // This class analyzes raw events.
 //
-// During the analysis of one event, different ordering possibilties are stored 
+// During the analysis of one event, different ordering possibilties are stored
 // in the m_RawEvents member. After loading the event it contains only one
-// expression of the event: only single hits. After the track analysis also the 
-// possibilties for different tracks in the one raw event are stored as 
+// expression of the event: only single hits. After the track analysis also the
+// possibilties for different tracks in the one raw event are stored as
 // different expressions in the m_RawEvents member.
 //
-// After all analysis is done the most likely expression is the chosen one. 
+// After all analysis is done the most likely expression is the chosen one.
 //
 //
 ////////////////////////////////////////////////////////////////////////////////
@@ -62,6 +62,8 @@ using namespace std;
 #include "MERTrackGas.h"
 #include "MERTrackDirectional.h"
 #include "MERTrackChiSquare.h"
+#include "MERTrackKalman3D.h"
+#include "MERTrackKalman2D.h"
 #include "MERCSRChiSquare.h"
 #include "MERCSRToF.h"
 #include "MERCSREnergyRecovery.h"
@@ -101,6 +103,10 @@ const int MRawEventAnalyzer::c_TrackingAlgoBayesian        = 5;
 const int MRawEventAnalyzer::c_TrackingAlgoRank            = 6;
 const int MRawEventAnalyzer::c_TrackingAlgoPearson         = 7;
 
+const int MRawEventAnalyzer::c_PairDefault   = 0;
+const int MRawEventAnalyzer::c_PairKalman3D = 1;
+const int MRawEventAnalyzer::c_PairKalman2D = 2;
+
 const int MRawEventAnalyzer::c_CSRAlgoNone          = 0;
 const int MRawEventAnalyzer::c_CSRAlgoFoM           = 1;
 const int MRawEventAnalyzer::c_CSRAlgoFoME          = 2;
@@ -134,7 +140,7 @@ MRawEventAnalyzer::MRawEventAnalyzer()
   m_Filename = "";
   m_Reader = nullptr;
   m_SaveOI = false;
-  
+
   m_FilenameOut = "";
   m_PhysFile = nullptr;
 
@@ -163,6 +169,7 @@ MRawEventAnalyzer::MRawEventAnalyzer()
   m_EventClusteringAlgorithm = c_EventClusteringAlgoNone;
   m_HitClusteringAlgorithm = c_HitClusteringAlgoAdjacent;
   m_TrackingAlgorithm = c_TrackingAlgoNone;
+  m_PairAlgorithm = c_PairDefault;
   m_CSRAlgorithm = c_CSRAlgoFoM;
   m_DecayAlgorithm = c_DecayAlgoNone;
 
@@ -190,13 +197,14 @@ MRawEventAnalyzer::MRawEventAnalyzer()
   m_NTrackSequencesToKeep = 1;
   m_RejectPurelyAmbiguousTrackSequences = false;
   m_NLayersForVertexSearch = 4;
+  m_SigmaHitPos = 0.00693;
 
   m_AssumeD1First = false;
   m_ClassicUndecidedHandling = false;
   m_UseComptelTypeEvents = true;
   m_GuaranteeStartD1 = true;
   m_RejectOneDetectorTypeOnlyEvents = true;
-  
+
   m_CSRThresholdMin = 0;
   m_CSRThresholdMax = 1;
   m_CSRMaxNHits = 4;
@@ -257,7 +265,7 @@ MRawEventAnalyzer::~MRawEventAnalyzer()
   delete m_InitialRawEvent;
 
   delete m_EventStore;
-  
+
   delete m_Coincidence;
   delete m_EventClusterizer;
   delete m_HitClusterizer;
@@ -274,10 +282,10 @@ MRawEventAnalyzer::~MRawEventAnalyzer()
 void MRawEventAnalyzer::SetGeometry(MGeometryRevan* Geometry)
 {
   // Set the geometry
-  
+
   massert(Geometry != nullptr);
   m_Geometry = Geometry;
-  
+
   // The noising is based on the geometry data, thus set here
   delete m_Noising;
   m_Noising = new MERNoising();
@@ -285,7 +293,7 @@ void MRawEventAnalyzer::SetGeometry(MGeometryRevan* Geometry)
   m_Noising->PreAnalysis();
 }
 
- 
+
 ////////////////////////////////////////////////////////////////////////////////
 
 
@@ -293,10 +301,11 @@ void MRawEventAnalyzer::SetSettings(MSettingsEventReconstruction* S)
 {
   // Transfer all necessary data to the analyzer...
 
-  SetCoincidenceAlgorithm(S->GetCoincidenceAlgorithm()); 
-  SetEventClusteringAlgorithm(S->GetEventClusteringAlgorithm()); 
-  SetHitClusteringAlgorithm(S->GetHitClusteringAlgorithm()); 
-  SetTrackingAlgorithm(S->GetTrackingAlgorithm()); 
+  SetCoincidenceAlgorithm(S->GetCoincidenceAlgorithm());
+  SetEventClusteringAlgorithm(S->GetEventClusteringAlgorithm());
+  SetHitClusteringAlgorithm(S->GetHitClusteringAlgorithm());
+  SetTrackingAlgorithm(S->GetTrackingAlgorithm());
+  SetPairAlgorithm(S->GetPairAlgorithm());
   SetCSRAlgorithm(S->GetCSRAlgorithm());
   SetDecayAlgorithm(S->GetDecayAlgorithm());
 
@@ -319,12 +328,12 @@ void MRawEventAnalyzer::SetSettings(MSettingsEventReconstruction* S)
   SetStandardClusterizerMinDistanceD7(S->GetStandardClusterizerMinDistanceD7());
   SetStandardClusterizerMinDistanceD8(S->GetStandardClusterizerMinDistanceD8());
   SetStandardClusterizerCenterIsReference(S->GetStandardClusterizerCenterIsReference());
-   
+
   SetAdjacentLevel(S->GetAdjacentLevel());
   SetAdjacentSigma(S->GetAdjacentSigma());
 
   SetPDFClusterizer(S->GetPDFClusterizerBaseFileName());
-  
+
   // electron tracking
   SetSearchPairTracks(S->GetSearchPairs());
   SetSearchMIPTracks(S->GetSearchMIPs());
@@ -336,9 +345,12 @@ void MRawEventAnalyzer::SetSettings(MSettingsEventReconstruction* S)
   SetNTrackSequencesToKeep(S->GetNTrackSequencesToKeep());
   SetRejectPurelyAmbiguousTrackSequences(S->GetRejectPurelyAmbiguousTrackSequences());
   SetNLayersForVertexSearch(S->GetNLayersForVertexSearch());
-  
+
   SetElectronTrackingDetectorList(S->GetElectronTrackingDetectors());
-  
+
+  // Kalman Filter
+  SetSigmaHitPos(S->GetSigmaHitPos());
+
   // compton tracking:
   SetAssumeD1First(S->GetAssumeD1First());
   SetClassicUndecidedHandling(S->GetClassicUndecidedHandling());
@@ -353,7 +365,7 @@ void MRawEventAnalyzer::SetSettings(MSettingsEventReconstruction* S)
   SetCSRMaxNHits(S->GetCSRMaxNHits());
 
   SetOriginObjectsFileName(S->GetOriginObjectsFileName());
-  
+
   SetBCTFileName(S->GetBayesianComptonFileName());
   
   SetCSRTMVAFileName(S->GetCSRTMVAFileName());
@@ -376,7 +388,7 @@ void MRawEventAnalyzer::SetSettings(MSettingsEventReconstruction* S)
   SetEventIdMin(S->GetEventIdMin());
 
   SetRejectAllBadEvents(S->GetRejectAllBadEvents());
-  
+
   SetSaveOI(S->GetSaveOI());
 }
 
@@ -384,13 +396,13 @@ void MRawEventAnalyzer::SetSettings(MSettingsEventReconstruction* S)
 ////////////////////////////////////////////////////////////////////////////////
 
 
-void MRawEventAnalyzer::SetSaveOI(bool SaveOI) 
-{ 
-  //! Save the OI 
+void MRawEventAnalyzer::SetSaveOI(bool SaveOI)
+{
+  //! Save the OI
 
-  m_SaveOI = SaveOI; 
+  m_SaveOI = SaveOI;
   if (m_Reader != nullptr) {
-    m_Reader->SaveOI(m_SaveOI); 
+    m_Reader->SaveOI(m_SaveOI);
   }
 }
 
@@ -402,13 +414,13 @@ bool MRawEventAnalyzer::SetInputModeFile(MString Filename)
 {
   delete m_Reader;
   m_Reader = nullptr;
-  
+
   if (MFile::Exists(Filename) == false) {
     mout<<"MRawEventAnalyzer: Input file: \""<<Filename<<"\" does not exist!"<<endl;
     return false;
   }
   m_Filename = Filename;
-  
+
   m_Reader = new MFileEventsEvta(m_Geometry);
   if (m_Reader->Open(m_Filename) == false) {
     mout<<"MRawEventAnalyzer: Unable to open input file \""<<m_Filename<<"\""<<endl;
@@ -417,11 +429,11 @@ bool MRawEventAnalyzer::SetInputModeFile(MString Filename)
     return false;
   }
   m_Reader->SaveOI(m_SaveOI);
-  
+
   return true;
 }
 
-  
+
 ////////////////////////////////////////////////////////////////////////////////
 
 
@@ -429,13 +441,13 @@ bool MRawEventAnalyzer::SetOutputModeFile(MString Filename)
 {
   delete m_PhysFile;
   m_PhysFile = nullptr;
-  
+
   if (Filename == "") {
     mout<<"MRawEventAnalyzer: No output file name given!"<<endl;
     return false;
   }
   m_FilenameOut = Filename;
-  
+
   m_PhysFile = new MFileEventsTra();
   if (m_PhysFile->Open(m_FilenameOut, MFile::c_Write) == false) {
     mout<<"MRawEventAnalyzer: Unable to open output file \""<<m_FilenameOut<<"\""<<endl;
@@ -447,29 +459,29 @@ bool MRawEventAnalyzer::SetOutputModeFile(MString Filename)
   return true;
 }
 
-  
+
 ////////////////////////////////////////////////////////////////////////////////
 
 
 bool MRawEventAnalyzer::AddRawEvent(const MString& String, bool NeedsNoising, int Version)
 {
   // Add a raw event to the store
-  
+
   if (m_Reader != nullptr) {
     merr<<"You can only add events if you don't read them from file!"<<show;
     return false;
   }
-  
+
   vector<MString> Lines = String.Tokenize("\n");
 
   MRESE::ResetIDCounter();
   MRERawEvent* RE = new MRERawEvent(m_Geometry);
-  
+
   for (MString L: Lines) {
     if (RE->ParseLine(L, Version) == 1) {
       delete RE;
       cout<<"Parsing of line failed: "<<L<<endl;
-      return false; 
+      return false;
     }
   }
 
@@ -477,29 +489,29 @@ bool MRawEventAnalyzer::AddRawEvent(const MString& String, bool NeedsNoising, in
     m_Noising->Analyze(RE);
   }
   m_EventStore->AddRawEvent(RE);
-  
+
   return true;
 }
 
-  
+
 ////////////////////////////////////////////////////////////////////////////////
 
 
 bool MRawEventAnalyzer::AddRawEvent(MRERawEvent* RE)
 {
   // Add a raw event to the store
-  
+
   if (m_Reader != nullptr) {
     merr<<"You can only add events if you don't read them from file!"<<show;
     return false;
   }
-  
+
   m_EventStore->AddRawEvent(RE);
-  
+
   return true;
 }
 
- 
+
 ////////////////////////////////////////////////////////////////////////////////
 
 
@@ -507,13 +519,13 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
 {
   // A event timer...
   MTimer Timer;
-  
+
   // this flag indicates that we have no more events in file, and the coincidence search has to "clear the store"
   bool ClearStore = false;
-  
+
   // A temporary raw event...
   MRERawEvent* RE = nullptr;
-  
+
   // Read events if we have reader
   if (m_Reader != nullptr) {
     RE = m_Reader->GetNextEvent();
@@ -525,41 +537,41 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
     } else {
       m_EventStore->AddRawEvent(RE);
     }
-    
+
     // Event timing...
     m_TimeLoad += Timer.ElapsedTime();
     Timer.Start();
   }
-  
+
   if (m_EventStore->GetNRawEvents() == 0) {
     return c_AnalysisNoEventsInStore;
   }
-  
+
   // We have events, we can start the analysis:
-  
+
   // Section A: Coincidence search
   if (m_CoincidenceAlgorithm != c_CoincidenceAlgoNone) {
     if (m_Coincidence == nullptr) {
       merr<<"Coincidence pointer is zero. You changed the event reconstruction setup without calling PreAnalysis()!"<<show;
       return c_AnalysisUndefinedError;
     }
-    
+
     RE = nullptr;
-    
+
     // Search for coincidences
     if (ClearStore == true || m_EventStore->GetNRawEvents() >= 2) {
       RE = m_Coincidence->Search(m_EventStore, ClearStore);
     }
-    
+
     // When does this case happen???
     if (RE == nullptr && m_EventStore->GetNRawEvents() == 0) {
       return c_AnalysisNoEventsInStore;
     }
-    
+
     if (RE == nullptr) {
       return c_AnalysisCoincidenceWindowWait;
     }
-    
+
     // Handle coincidences in the same voxel due to coincidence search - this should only happen in the simulation...
     if (RE != nullptr && m_CoincidenceAlgorithm != c_CoincidenceAlgoNone) {
       for (int r1 = 0; r1 < RE->GetNRESEs(); ++r1) {
@@ -582,17 +594,18 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
     RE = m_EventStore->GetRawEventAt(0);
     m_EventStore->RemoveRawEvent(RE);
   }
-  
+
   if (RE == nullptr) {
     merr<<"We don't have a raw event..."<<fatal;
     return c_AnalysisUndefinedError;
   }
-  
+
   mdebug<<endl;
   mdebug<<endl;
   mdebug<<endl;
   mdebug<<"ER - Event: "<<RE->GetEventID()<<endl;
   mdebug<<endl;
+
   
   
   // Store the inital coincident event:
@@ -631,7 +644,7 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
       mout<<"ER - Event ID above limit!"<<endl;
       return c_AnalysisUndefinedError;
     }
-    SelectionsPassed = false;      
+    SelectionsPassed = false;
   }
   
   if (SelectionsPassed == true && (RE->GetEnergy() < m_TotalEnergyMin || RE->GetEnergy() > m_TotalEnergyMax)) {
@@ -827,7 +840,7 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
   
   m_NEvents++;
   if (SelectionsPassed == true) {
-    m_NPassedEventSelection++;  
+    m_NPassedEventSelection++;
   }
   
   m_TimeFinalize += Timer.ElapsedTime();
@@ -938,7 +951,7 @@ void MRawEventAnalyzer::JoinStatistics(const MRawEventAnalyzer& A)
   m_NEvents += A.m_NEvents;
   m_NPassedEventSelection += A.m_NPassedEventSelection;
   m_NGoodEvents += A.m_NGoodEvents;
-  
+
   m_NPhotoEvents += A.m_NPhotoEvents;
   m_NComptonEvents += A.m_NComptonEvents;
   m_NPairEvents += A.m_NPairEvents;
@@ -961,12 +974,11 @@ void MRawEventAnalyzer::JoinStatistics(const MRawEventAnalyzer& A)
 bool MRawEventAnalyzer::PostAnalysis()
 {
   // No more events available
-  
   if (m_PhysFile != nullptr) {
     m_PhysFile->SetObservationTime(m_Reader->GetObservationTime());
-  } 
-  
-  
+  }
+
+
   ostringstream out;
 
   out<<endl;
@@ -1000,7 +1012,7 @@ bool MRawEventAnalyzer::PostAnalysis()
   int Width = 6;
   int WidthPercent = 7;
   int Precision = 3;
-  
+
   out<<endl;
   out<<"----------------------------------------------------------------------------"<<endl;
   if (m_Reader != nullptr) {
@@ -1109,13 +1121,13 @@ bool MRawEventAnalyzer::PostAnalysis()
 
 bool MRawEventAnalyzer::PreAnalysis()
 {
-  // 
+  //
 
   bool Return = false;
 
   m_NEvents = 0;
   m_NGoodEvents = 0;
-  
+
   if (m_OriginObjectsFileName != "") {
     if (MFile::FileExists(m_OriginObjectsFileName) == true) {
       delete m_OriginGeometry;
@@ -1160,8 +1172,9 @@ bool MRawEventAnalyzer::PreAnalysis()
       Return = false;
     }
   }
-  
-  
+
+
+
   // Coincidence
   if (Return == true) {
     delete m_Coincidence;
@@ -1241,56 +1254,56 @@ bool MRawEventAnalyzer::PreAnalysis()
     m_CSR = nullptr;
     if (m_CSRAlgorithm == c_CSRAlgoFoM) {
       m_CSR = new MERCSRChiSquare();
-      if (dynamic_cast<MERCSRChiSquare*>(m_CSR)->SetParameters(m_Geometry, 
-                                                               m_CSRThresholdMin, 
-                                                               m_CSRThresholdMax, 
-                                                               m_CSRMaxNHits, 
-                                                               m_GuaranteeStartD1, 
-                                                               m_CSROnlyCreateSequences, 
-                                                               m_UseComptelTypeEvents, 
-                                                               m_ClassicUndecidedHandling, 
-                                                               m_RejectOneDetectorTypeOnlyEvents, 
+      if (dynamic_cast<MERCSRChiSquare*>(m_CSR)->SetParameters(m_Geometry,
+                                                               m_CSRThresholdMin,
+                                                               m_CSRThresholdMax,
+                                                               m_CSRMaxNHits,
+                                                               m_GuaranteeStartD1,
+                                                               m_CSROnlyCreateSequences,
+                                                               m_UseComptelTypeEvents,
+                                                               m_ClassicUndecidedHandling,
+                                                               m_RejectOneDetectorTypeOnlyEvents,
                                                                m_OriginGeometry) == false) {
         Return = false;
       }
     } else if (m_CSRAlgorithm == c_CSRAlgoFoME) {
       m_CSR = new MERCSREnergyRecovery();
-      if (dynamic_cast<MERCSREnergyRecovery*>(m_CSR)->SetParameters(m_Geometry, 
-                                 m_CSRThresholdMin, 
-                                 m_CSRThresholdMax, 
-                                 m_CSRMaxNHits, 
-                                 m_GuaranteeStartD1, 
+      if (dynamic_cast<MERCSREnergyRecovery*>(m_CSR)->SetParameters(m_Geometry,
+                                 m_CSRThresholdMin,
+                                 m_CSRThresholdMax,
+                                 m_CSRMaxNHits,
+                                 m_GuaranteeStartD1,
                                  m_CSROnlyCreateSequences) == false) {
         Return = false;
       }
     } else if (m_CSRAlgorithm == c_CSRAlgoFoMToF) {
       m_CSR = new MERCSRToF();
-      if (dynamic_cast<MERCSRToF*>(m_CSR)->SetParameters(m_Geometry, 
-                                    m_CSRThresholdMin, 
-                                    m_CSRThresholdMax, 
-                                    m_CSRMaxNHits, 
-                                    m_GuaranteeStartD1, 
+      if (dynamic_cast<MERCSRToF*>(m_CSR)->SetParameters(m_Geometry,
+                                    m_CSRThresholdMin,
+                                    m_CSRThresholdMax,
+                                    m_CSRMaxNHits,
+                                    m_GuaranteeStartD1,
                                     m_CSROnlyCreateSequences) == false) {
         Return = false;
       }
     } else if (m_CSRAlgorithm == c_CSRAlgoFoMToFAndE) {
       m_CSR = new MERCSRToFWithEnergyRecovery();
-      if (dynamic_cast<MERCSRToFWithEnergyRecovery*>(m_CSR)->SetParameters(m_Geometry, 
-                                    m_CSRThresholdMin, 
-                                    m_CSRThresholdMax, 
-                                    m_CSRMaxNHits, 
-                                    m_GuaranteeStartD1, 
+      if (dynamic_cast<MERCSRToFWithEnergyRecovery*>(m_CSR)->SetParameters(m_Geometry,
+                                    m_CSRThresholdMin,
+                                    m_CSRThresholdMax,
+                                    m_CSRMaxNHits,
+                                    m_GuaranteeStartD1,
                                     m_CSROnlyCreateSequences) == false) {
         Return = false;
       }
     } else if (m_CSRAlgorithm == c_CSRAlgoBayesian) {
       m_CSR = new MERCSRBayesian();
-      if (dynamic_cast<MERCSRBayesian*>(m_CSR)->SetParameters(m_BCTFileName, 
-                                      m_Geometry, 
-                                      m_CSRThresholdMin, 
-                                      m_CSRThresholdMax, 
-                                      m_CSRMaxNHits, 
-                                      m_GuaranteeStartD1, 
+      if (dynamic_cast<MERCSRBayesian*>(m_CSR)->SetParameters(m_BCTFileName,
+                                      m_Geometry,
+                                      m_CSRThresholdMin,
+                                      m_CSRThresholdMax,
+                                      m_CSRMaxNHits,
+                                      m_GuaranteeStartD1,
                                       m_CSROnlyCreateSequences) == false) {
         Return = false;
       }
@@ -1313,7 +1326,6 @@ bool MRawEventAnalyzer::PreAnalysis()
       Return = false;
     }
 
-    
     // Electron tracking
     delete m_Tracker;
     m_Tracker = nullptr;
@@ -1342,19 +1354,32 @@ bool MRawEventAnalyzer::PreAnalysis()
       Return = false;
     }
 
+    // Pair Algorithm
+    if (m_PairAlgorithm == c_PairKalman3D) {
+      m_Tracker = new MERTrackKalman3D();
+      dynamic_cast<MERTrackKalman3D*>(m_Tracker)->SetSpecialParameters(m_SigmaHitPos, m_NLayersForVertexSearch);
+    } else if (m_PairAlgorithm == c_PairKalman2D) {
+      m_Tracker = new MERTrackKalman2D();
+      dynamic_cast<MERTrackKalman2D*>(m_Tracker)->SetSpecialParameters(m_SigmaHitPos, m_NLayersForVertexSearch);
+    }else if (m_PairAlgorithm == c_PairDefault) {
+      m_Tracker = new MERTrack();
+    } else {
+      Return = false;
+    }
+
     if (m_Tracker != nullptr) {
       m_Tracker->SetGeometry(m_Geometry);
-      m_Tracker->SetParameters(m_SearchMIPTracks, 
-                               m_SearchPairTracks, 
-                               m_SearchComptonTracks, 
-                               m_MaxComptonJump, 
-                               m_NTrackSequencesToKeep, 
-                               m_RejectPurelyAmbiguousTrackSequences, 
+      m_Tracker->SetParameters(m_SearchMIPTracks,
+                               m_SearchPairTracks,
+                               m_SearchComptonTracks,
+                               m_MaxComptonJump,
+                               m_NTrackSequencesToKeep,
+                               m_RejectPurelyAmbiguousTrackSequences,
                                m_NLayersForVertexSearch,
                                m_ElectronTrackingDetectorList);
     }
 
-    
+
     // Initialize the Decay searcher:
     delete m_Decay;
     m_Decay = nullptr;
diff --git a/src/revan/src/MSettingsEventReconstruction.cxx b/src/revan/src/MSettingsEventReconstruction.cxx
index 085d2a960..c5305d62d 100644
--- a/src/revan/src/MSettingsEventReconstruction.cxx
+++ b/src/revan/src/MSettingsEventReconstruction.cxx
@@ -51,6 +51,7 @@ MSettingsEventReconstruction::MSettingsEventReconstruction() : MSettingsInterfac
   m_EventClusteringAlgorithm = 0;
   m_HitClusteringAlgorithm = 1;
   m_TrackingAlgorithm = 0;
+  m_PairAlgorithm = 0;
   m_CSRAlgorithm = 1;
   m_DecayAlgorithm = 0;
 
@@ -86,17 +87,21 @@ MSettingsEventReconstruction::MSettingsEventReconstruction() : MSettingsInterfac
   m_NLayersForVertexSearch = 6;
 
   m_ElectronTrackingDetectors.clear();
-  
+
+  // Kalman Filter
+  m_SigmaHitPos = 0.00693;
+  m_HeightX0 = 0.005336179;
+
   // Compton tracking
   m_RejectOneDetectorTypeOnlyEvents = false;
   m_GuaranteeStartD1 = false;
   m_UseComptelTypeEvents = true;
 
-  m_ClassicUndecidedHandling = 0; 
+  m_ClassicUndecidedHandling = 0;
 
   m_AssumeD1First = false;
   m_AssumeTrackTopBottom = false;
-  
+
   m_CSRThresholdMin = 0;
   m_CSRThresholdMax = 1000;
 
@@ -134,7 +139,6 @@ MSettingsEventReconstruction::MSettingsEventReconstruction() : MSettingsInterfac
   m_SaveOI = false;
 
   m_SpecialMode = false;
-  
 }
 
 ////////////////////////////////////////////////////////////////////////////////
@@ -158,6 +162,7 @@ bool MSettingsEventReconstruction::WriteXml(MXmlNode* Node)
   new MXmlNode(Node, "EventClusteringAlgorithm", m_EventClusteringAlgorithm);
   new MXmlNode(Node, "HitClusteringAlgorithm", m_HitClusteringAlgorithm);
   new MXmlNode(Node, "TrackingAlgorithm", m_TrackingAlgorithm);
+  new MXmlNode(Node, "PairAlgorithm", m_PairAlgorithm);
   new MXmlNode(Node, "CSRAlgorithm", m_CSRAlgorithm);
   new MXmlNode(Node, "DecayAlgorithm", m_DecayAlgorithm);
   new MXmlNode(Node, "CoincidenceWindow", m_CoincidenceWindow);
@@ -187,13 +192,15 @@ bool MSettingsEventReconstruction::WriteXml(MXmlNode* Node)
   new MXmlNode(Node, "NTrackSequencesToKeep", m_NTrackSequencesToKeep);
   new MXmlNode(Node, "RejectPurelyAmbiguousTrackSequences", m_RejectPurelyAmbiguousTrackSequences);
   new MXmlNode(Node, "NLayersForVertexSearch", m_NLayersForVertexSearch);
-  
+  new MXmlNode(Node, "SigmaHitPos", m_SigmaHitPos);
+  new MXmlNode(Node, "HeightX0", m_HeightX0);
+
   MXmlNode* aNode = new MXmlNode(Node, "ElectronTrackingDetectors");
   for (unsigned int i = 0; i < m_ElectronTrackingDetectors.size(); ++i) {
     new MXmlNode(aNode, "ElectronTrackingDetector",  m_ElectronTrackingDetectors[i]);
   }
 
-  
+
   new MXmlNode(Node, "AssumeD1First", m_AssumeD1First);
   new MXmlNode(Node, "ClassicUndecidedHandling", m_ClassicUndecidedHandling);
   new MXmlNode(Node, "AssumeTrackTopBottom", m_AssumeTrackTopBottom);
@@ -207,7 +214,7 @@ bool MSettingsEventReconstruction::WriteXml(MXmlNode* Node)
   new MXmlNode(Node, "FocalSpotCenter", m_FocalSpotCenter);
   new MXmlNode(Node, "OriginObjectsFile", CleanPath(m_OriginObjectsFileName));
   new MXmlNode(Node, "DecayFile", CleanPath(m_DecayFileName));
-  
+
   new MXmlNode(Node, "BayesianComptonFile", CleanPath(m_BayesianComptonFileName));
   new MXmlNode(Node, "BayesianElectronFile", CleanPath(m_BayesianElectronFileName));
   
@@ -227,7 +234,7 @@ bool MSettingsEventReconstruction::WriteXml(MXmlNode* Node)
 
 
 bool MSettingsEventReconstruction::ReadXml(MXmlNode* Node)
-{  
+{
   MXmlNode* aNode = 0;
   MXmlNode* bNode = 0;
 
@@ -239,7 +246,6 @@ bool MSettingsEventReconstruction::ReadXml(MXmlNode* Node)
     m_Save = aNode->GetValueAsBoolean();
   }
   */
-  
   if ((aNode = Node->GetNode("CoincidenceAlgorithm")) != 0) {
     m_CoincidenceAlgorithm = aNode->GetValueAsInt();
   }
@@ -255,6 +261,9 @@ bool MSettingsEventReconstruction::ReadXml(MXmlNode* Node)
   if ((aNode = Node->GetNode("TrackingAlgorithm")) != 0) {
     m_TrackingAlgorithm = aNode->GetValueAsInt();
   }
+  if ((aNode = Node->GetNode("PairAlgorithm")) != 0) {
+    m_PairAlgorithm = aNode->GetValueAsInt();
+  }
   if ((aNode = Node->GetNode("CSRAlgorithm")) != 0) {
     m_CSRAlgorithm = aNode->GetValueAsInt();
   }
@@ -338,6 +347,12 @@ bool MSettingsEventReconstruction::ReadXml(MXmlNode* Node)
   if ((aNode = Node->GetNode("NLayersForVertexSearch")) != 0) {
     m_NLayersForVertexSearch = aNode->GetValueAsInt();
   }
+  if ((aNode = Node->GetNode("SigmaHitPos")) != 0) {
+    m_SigmaHitPos = aNode->GetValueAsDouble();
+  }
+  if ((aNode = Node->GetNode("HeightX0")) != 0) {
+    m_HeightX0 = aNode->GetValueAsDouble();
+  }
   if ((aNode = Node->GetNode("ElectronTrackingDetectors")) != 0) {
     m_ElectronTrackingDetectors.clear();
     for (unsigned int n = 0; n < aNode->GetNNodes(); ++n) {
@@ -415,7 +430,7 @@ bool MSettingsEventReconstruction::ReadXml(MXmlNode* Node)
 
   return true;
 }
-  
+
 
 // MSettingsEventReconstruction.cxx: the end...
 ////////////////////////////////////////////////////////////////////////////////

From 5ade794667a58fb469a6dfd8bf00822fa33134d2 Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Fri, 9 May 2025 09:55:14 -0400
Subject: [PATCH 159/192] CHG: Ignore *.rsp files

---
 .../materials/Xsection.Compton.ACSPaper.rsp   | 414 ------------------
 .../materials/Xsection.Compton.Air.rsp        | 414 ------------------
 .../materials/Xsection.Compton.Alu6061.rsp    | 414 ------------------
 .../materials/Xsection.Compton.Aluminium.rsp  | 414 ------------------
 .../materials/Xsection.Compton.BGO.rsp        | 414 ------------------
 .../materials/Xsection.Compton.CZT.rsp        | 414 ------------------
 .../Xsection.Compton.CarbonCyanateEster.rsp   | 414 ------------------
 .../materials/Xsection.Compton.CdTe.rsp       | 414 ------------------
 .../Xsection.Compton.CircuitBoard.rsp         | 414 ------------------
 .../materials/Xsection.Compton.Copper.rsp     | 414 ------------------
 .../materials/Xsection.Compton.CsI.rsp        | 414 ------------------
 .../Xsection.Compton.Densimet180.rsp          | 414 ------------------
 .../materials/Xsection.Compton.Diamant.rsp    | 414 ------------------
 .../materials/Xsection.Compton.GePassive.rsp  | 414 ------------------
 .../materials/Xsection.Compton.Germanium.rsp  | 414 ------------------
 .../materials/Xsection.Compton.Glass.rsp      | 414 ------------------
 .../materials/Xsection.Compton.Indium.rsp     | 414 ------------------
 .../materials/Xsection.Compton.Iron.rsp       | 414 ------------------
 .../materials/Xsection.Compton.LaBr3.rsp      | 414 ------------------
 .../materials/Xsection.Compton.MLI.rsp        | 414 ------------------
 .../materials/Xsection.Compton.MgS.rsp        | 414 ------------------
 .../materials/Xsection.Compton.Millipore.rsp  | 414 ------------------
 .../materials/Xsection.Compton.NE110.rsp      | 414 ------------------
 .../materials/Xsection.Compton.NE213.rsp      | 414 ------------------
 .../materials/Xsection.Compton.NaI.rsp        | 414 ------------------
 .../materials/Xsection.Compton.Nylon.rsp      | 414 ------------------
 .../materials/Xsection.Compton.PCB.rsp        | 414 ------------------
 .../materials/Xsection.Compton.PMTPlastic.rsp | 414 ------------------
 .../geomega/materials/Xsection.Compton.Pb.rsp | 414 ------------------
 .../materials/Xsection.Compton.Peek.rsp       | 414 ------------------
 .../Xsection.Compton.Plastic_Isolation.rsp    | 414 ------------------
 .../materials/Xsection.Compton.Plywood.rsp    | 414 ------------------
 .../Xsection.Compton.PressurizedAir.rsp       | 414 ------------------
 .../materials/Xsection.Compton.Silicon.rsp    | 414 ------------------
 .../materials/Xsection.Compton.SiliconPIN.rsp | 414 ------------------
 .../materials/Xsection.Compton.Steel.rsp      | 414 ------------------
 .../materials/Xsection.Compton.Steel_18_8.rsp | 414 ------------------
 ...ompton.SurroundingSphereVolumeMaterial.rsp | 414 ------------------
 .../materials/Xsection.Compton.Tin.rsp        | 414 ------------------
 .../materials/Xsection.Compton.Vacuum.rsp     | 414 ------------------
 .../materials/Xsection.Compton.Xenon.rsp      | 414 ------------------
 .../Xsection.Compton.XenonLXeGRIT.rsp         | 414 ------------------
 .../materials/Xsection.Compton.ro3003.rsp     | 414 ------------------
 .../materials/Xsection.Compton.ro3006.rsp     | 414 ------------------
 .../materials/Xsection.Compton.ro3010.rsp     | 414 ------------------
 .../materials/Xsection.Compton.ro4003.rsp     | 414 ------------------
 .../materials/Xsection.Compton.roTMM3.rsp     | 414 ------------------
 .../materials/Xsection.Pair.ACSPaper.rsp      | 414 ------------------
 .../geomega/materials/Xsection.Pair.Air.rsp   | 414 ------------------
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 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.Indium.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.Iron.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.LaBr3.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.MLI.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.MgS.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.Millipore.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.NE110.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.NE213.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.NaI.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.Nylon.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.PCB.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.PMTPlastic.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.Pb.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.Peek.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.Plastic_Isolation.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.Plywood.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.PressurizedAir.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.Silicon.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.SiliconPIN.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.Steel.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.Steel_18_8.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.SurroundingSphereVolumeMaterial.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.Tin.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.Vacuum.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.Xenon.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.XenonLXeGRIT.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.ro3003.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.ro3006.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.ro3010.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.ro4003.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Rayleigh.roTMM3.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.ACSPaper.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.Air.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.Alu6061.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.Aluminium.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.BGO.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.CZT.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.CarbonCyanateEster.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.CdTe.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.CircuitBoard.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.Copper.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.CsI.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.Densimet180.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.Diamant.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.GePassive.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.Germanium.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.Glass.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.Indium.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.Iron.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.LaBr3.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.MLI.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.MgS.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.Millipore.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.NE110.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.NE213.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.NaI.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.Nylon.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.PCB.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.PMTPlastic.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.Pb.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.Peek.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.Plastic_Isolation.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.Plywood.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.PressurizedAir.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.Silicon.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.SiliconPIN.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.Steel.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.Steel_18_8.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.SurroundingSphereVolumeMaterial.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.Tin.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.Vacuum.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.Xenon.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.XenonLXeGRIT.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.ro3003.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.ro3006.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.ro3010.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.ro4003.rsp
 delete mode 100644 resource/examples/geomega/materials/Xsection.Total.roTMM3.rsp

diff --git a/resource/examples/geomega/materials/Xsection.Compton.ACSPaper.rsp b/resource/examples/geomega/materials/Xsection.Compton.ACSPaper.rsp
deleted file mode 100644
index e6cea73c8..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.ACSPaper.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for ACSPaper
-CE false
-HA 869331804
-
-R1         1.000000 1.296247e-02
-R1         1.047129 1.405924e-02
-R1         1.096478 1.524890e-02
-R1         1.148154 1.653930e-02
-R1         1.202264 1.793901e-02
-R1         1.258925 1.945723e-02
-R1         1.318257 2.099369e-02
-R1         1.380384 2.265175e-02
-R1         1.445440 2.444103e-02
-R1         1.513561 2.637195e-02
-R1         1.584893 2.845575e-02
-R1         1.659587 3.051668e-02
-R1         1.737801 3.272750e-02
-R1         1.819701 3.509918e-02
-R1         1.905461 3.764349e-02
-R1         1.995262 4.037303e-02
-R1         2.089296 4.296206e-02
-R1         2.187762 4.571852e-02
-R1         2.290868 4.865348e-02
-R1         2.398833 5.177862e-02
-R1         2.511886 5.510635e-02
-R1         2.630268 5.812638e-02
-R1         2.754229 6.131492e-02
-R1         2.884032 6.468157e-02
-R1         3.019952 6.823646e-02
-R1         3.162278 7.199029e-02
-R1         3.311311 7.523792e-02
-R1         3.467369 7.863678e-02
-R1         3.630781 8.219421e-02
-R1         3.801894 8.591782e-02
-R1         3.981072 8.981555e-02
-R1         4.168694 9.301722e-02
-R1         4.365158 9.633874e-02
-R1         4.570882 9.978493e-02
-R1         4.786301 1.033606e-01
-R1         5.011872 1.070709e-01
-R1         5.248075 1.099679e-01
-R1         5.495409 1.129487e-01
-R1         5.754399 1.160161e-01
-R1         6.025596 1.191725e-01
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-R1         6.918310 1.274456e-01
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-R1         7.943282 1.354064e-01
-R1         8.317638 1.375130e-01
-R1         8.709636 1.396558e-01
-R1         9.120108 1.418354e-01
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-R1        10.000000 1.463079e-01
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-R1        12.022644 1.535684e-01
-R1        12.589254 1.554432e-01
-R1        13.182567 1.570502e-01
-R1        13.803843 1.586764e-01
-R1        14.454398 1.603218e-01
-R1        15.135612 1.619869e-01
-R1        15.848932 1.636718e-01
-R1        16.595869 1.648750e-01
-R1        17.378008 1.660889e-01
-R1        18.197009 1.673135e-01
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-R1        19.952623 1.697953e-01
-R1        20.892961 1.706045e-01
-R1        21.877616 1.714187e-01
-R1        22.908677 1.722382e-01
-R1        23.988329 1.730628e-01
-R1        25.118864 1.738928e-01
-R1        26.302680 1.742424e-01
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-R1        28.840315 1.749461e-01
-R1        30.199517 1.753002e-01
-R1        31.622777 1.756559e-01
-R1        33.113112 1.755535e-01
-R1        34.673685 1.754515e-01
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-R1        38.018940 1.752491e-01
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-R1        47.863009 1.731307e-01
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-R1        57.543994 1.700312e-01
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.Air.rsp b/resource/examples/geomega/materials/Xsection.Compton.Air.rsp
deleted file mode 100644
index 7cbff774a..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.Air.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for Air
-CE false
-HA 230661740
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.Alu6061.rsp b/resource/examples/geomega/materials/Xsection.Compton.Alu6061.rsp
deleted file mode 100644
index 6822b8357..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.Alu6061.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for Alu6061
-CE false
-HA 203757245
-
-R1         1.000000 3.827112e-02
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.Aluminium.rsp b/resource/examples/geomega/materials/Xsection.Compton.Aluminium.rsp
deleted file mode 100644
index 54ff7c8cb..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.Aluminium.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for Aluminium
-CE false
-HA 825250182
-
-R1         1.000000 3.855789e-02
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.BGO.rsp b/resource/examples/geomega/materials/Xsection.Compton.BGO.rsp
deleted file mode 100644
index 50c8cfbf8..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.BGO.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for BGO
-CE false
-HA 1061301671
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.CZT.rsp b/resource/examples/geomega/materials/Xsection.Compton.CZT.rsp
deleted file mode 100644
index 622c079fa..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.CZT.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for CZT
-CE false
-HA 3645592918
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.CarbonCyanateEster.rsp b/resource/examples/geomega/materials/Xsection.Compton.CarbonCyanateEster.rsp
deleted file mode 100644
index 9caf91299..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.CarbonCyanateEster.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for CarbonCyanateEster
-CE false
-HA 3197857782
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.CdTe.rsp b/resource/examples/geomega/materials/Xsection.Compton.CdTe.rsp
deleted file mode 100644
index 7c910bfc9..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.CdTe.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for CdTe
-CE false
-HA 2408428372
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.CircuitBoard.rsp b/resource/examples/geomega/materials/Xsection.Compton.CircuitBoard.rsp
deleted file mode 100644
index a4c76ae37..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.CircuitBoard.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for CircuitBoard
-CE false
-HA 790253057
-
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-R1  95499258.602144 9.816249e-06
-R1 100000000.000000 9.407019e-06
-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.Copper.rsp b/resource/examples/geomega/materials/Xsection.Compton.Copper.rsp
deleted file mode 100644
index 9bc8f7070..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.Copper.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for Copper
-CE false
-HA 3193575607
-
-R1         1.000000 5.302563e-02
-R1         1.047129 5.694522e-02
-R1         1.096478 6.115454e-02
-R1         1.148154 6.567501e-02
-R1         1.202264 7.052962e-02
-R1         1.258925 7.574290e-02
-R1         1.318257 8.087806e-02
-R1         1.380384 8.636137e-02
-R1         1.445440 9.221644e-02
-R1         1.513561 9.846846e-02
-R1         1.584893 1.051444e-01
-R1         1.659587 1.117176e-01
-R1         1.737801 1.187017e-01
-R1         1.819701 1.261225e-01
-R1         1.905461 1.340072e-01
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.CsI.rsp b/resource/examples/geomega/materials/Xsection.Compton.CsI.rsp
deleted file mode 100644
index 01f5c5d09..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.CsI.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for CsI
-CE false
-HA 3350302246
-
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diff --git a/resource/examples/geomega/materials/Xsection.Compton.Densimet180.rsp b/resource/examples/geomega/materials/Xsection.Compton.Densimet180.rsp
deleted file mode 100644
index f2be25203..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.Densimet180.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for Densimet180
-CE false
-HA 2913098225
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.Diamant.rsp b/resource/examples/geomega/materials/Xsection.Compton.Diamant.rsp
deleted file mode 100644
index 7b065657b..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.Diamant.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for Diamant
-CE false
-HA 289970476
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.GePassive.rsp b/resource/examples/geomega/materials/Xsection.Compton.GePassive.rsp
deleted file mode 100644
index f35bc130a..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.GePassive.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for GePassive
-CE false
-HA 359300401
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.Germanium.rsp b/resource/examples/geomega/materials/Xsection.Compton.Germanium.rsp
deleted file mode 100644
index c24e21a64..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.Germanium.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for Germanium
-CE false
-HA 359300401
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.Glass.rsp b/resource/examples/geomega/materials/Xsection.Compton.Glass.rsp
deleted file mode 100644
index 71e4b3392..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.Glass.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for Glass
-CE false
-HA 4029087792
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.Indium.rsp b/resource/examples/geomega/materials/Xsection.Compton.Indium.rsp
deleted file mode 100644
index 09150bbdc..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.Indium.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for Indium
-CE false
-HA 3903719287
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.Iron.rsp b/resource/examples/geomega/materials/Xsection.Compton.Iron.rsp
deleted file mode 100644
index 66fae23bd..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.Iron.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for Iron
-CE false
-HA 4094812641
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.LaBr3.rsp b/resource/examples/geomega/materials/Xsection.Compton.LaBr3.rsp
deleted file mode 100644
index 7007d4b79..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.LaBr3.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for LaBr3
-CE false
-HA 3587683841
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.MLI.rsp b/resource/examples/geomega/materials/Xsection.Compton.MLI.rsp
deleted file mode 100644
index 9768892b9..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.MLI.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for MLI
-CE false
-HA 1447136272
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.MgS.rsp b/resource/examples/geomega/materials/Xsection.Compton.MgS.rsp
deleted file mode 100644
index e076e1caa..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.MgS.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for MgS
-CE false
-HA 2183886950
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.Millipore.rsp b/resource/examples/geomega/materials/Xsection.Compton.Millipore.rsp
deleted file mode 100644
index 3e2e5beff..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.Millipore.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for Millipore
-CE false
-HA 869331804
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.NE110.rsp b/resource/examples/geomega/materials/Xsection.Compton.NE110.rsp
deleted file mode 100644
index 143519528..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.NE110.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for NE110
-CE false
-HA 917272579
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.NE213.rsp b/resource/examples/geomega/materials/Xsection.Compton.NE213.rsp
deleted file mode 100644
index fc8a2234a..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.NE213.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for NE213
-CE false
-HA 2640400524
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.NaI.rsp b/resource/examples/geomega/materials/Xsection.Compton.NaI.rsp
deleted file mode 100644
index 7d5f91ae9..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.NaI.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for NaI
-CE false
-HA 1958776091
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.Nylon.rsp b/resource/examples/geomega/materials/Xsection.Compton.Nylon.rsp
deleted file mode 100644
index fe9a187f6..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.Nylon.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for Nylon
-CE false
-HA 3741285600
-
-R1         1.000000 1.722110e-02
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.PCB.rsp b/resource/examples/geomega/materials/Xsection.Compton.PCB.rsp
deleted file mode 100644
index bc43900a5..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.PCB.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for PCB
-CE false
-HA 480612584
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.PMTPlastic.rsp b/resource/examples/geomega/materials/Xsection.Compton.PMTPlastic.rsp
deleted file mode 100644
index cd58f83b7..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.PMTPlastic.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for PMTPlastic
-CE false
-HA 1684120221
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.Pb.rsp b/resource/examples/geomega/materials/Xsection.Compton.Pb.rsp
deleted file mode 100644
index 22eab082b..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.Pb.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for Pb
-CE false
-HA 2559858824
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.Peek.rsp b/resource/examples/geomega/materials/Xsection.Compton.Peek.rsp
deleted file mode 100644
index 4fba79256..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.Peek.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for Peek
-CE false
-HA 3912604896
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.Plastic_Isolation.rsp b/resource/examples/geomega/materials/Xsection.Compton.Plastic_Isolation.rsp
deleted file mode 100644
index b0b373f9e..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.Plastic_Isolation.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for Plastic_Isolation
-CE false
-HA 2914733143
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.Plywood.rsp b/resource/examples/geomega/materials/Xsection.Compton.Plywood.rsp
deleted file mode 100644
index 2089bf430..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.Plywood.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for Plywood
-CE false
-HA 2593954094
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.PressurizedAir.rsp b/resource/examples/geomega/materials/Xsection.Compton.PressurizedAir.rsp
deleted file mode 100644
index d1f81253d..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.PressurizedAir.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for PressurizedAir
-CE false
-HA 3401473699
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.Silicon.rsp b/resource/examples/geomega/materials/Xsection.Compton.Silicon.rsp
deleted file mode 100644
index 49b9ed773..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.Silicon.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for Silicon
-CE false
-HA 3884499373
-
-R1         1.000000 3.071522e-02
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.SiliconPIN.rsp b/resource/examples/geomega/materials/Xsection.Compton.SiliconPIN.rsp
deleted file mode 100644
index b6bf6b00d..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.SiliconPIN.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for SiliconPIN
-CE false
-HA 3884499373
-
-R1         1.000000 3.071522e-02
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.Steel.rsp b/resource/examples/geomega/materials/Xsection.Compton.Steel.rsp
deleted file mode 100644
index 2d82d524c..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.Steel.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for Steel
-CE false
-HA 619348587
-
-R1         1.000000 6.843351e-02
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.Steel_18_8.rsp b/resource/examples/geomega/materials/Xsection.Compton.Steel_18_8.rsp
deleted file mode 100644
index 6306f73c3..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.Steel_18_8.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for Steel_18_8
-CE false
-HA 1429918153
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.SurroundingSphereVolumeMaterial.rsp b/resource/examples/geomega/materials/Xsection.Compton.SurroundingSphereVolumeMaterial.rsp
deleted file mode 100644
index 290337146..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.SurroundingSphereVolumeMaterial.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for SurroundingSphereVolumeMaterial
-CE false
-HA 1487652151
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.Tin.rsp b/resource/examples/geomega/materials/Xsection.Compton.Tin.rsp
deleted file mode 100644
index f41d74251..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.Tin.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for Tin
-CE false
-HA 1304486184
-
-R1         1.000000 3.847980e-02
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.Vacuum.rsp b/resource/examples/geomega/materials/Xsection.Compton.Vacuum.rsp
deleted file mode 100644
index 68bcc71d0..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.Vacuum.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for Vacuum
-CE false
-HA 3622691594
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.Xenon.rsp b/resource/examples/geomega/materials/Xsection.Compton.Xenon.rsp
deleted file mode 100644
index cd0f393ca..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.Xenon.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for Xenon
-CE false
-HA 3026073170
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.XenonLXeGRIT.rsp b/resource/examples/geomega/materials/Xsection.Compton.XenonLXeGRIT.rsp
deleted file mode 100644
index 9cbbf539f..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.XenonLXeGRIT.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for XenonLXeGRIT
-CE false
-HA 3741687031
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.ro3003.rsp b/resource/examples/geomega/materials/Xsection.Compton.ro3003.rsp
deleted file mode 100644
index 2fc6e2f63..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.ro3003.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for ro3003
-CE false
-HA 3212075832
-
-R1         1.000000 2.037305e-02
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.ro3006.rsp b/resource/examples/geomega/materials/Xsection.Compton.ro3006.rsp
deleted file mode 100644
index a346404e9..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.ro3006.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for ro3006
-CE false
-HA 1294534288
-
-R1         1.000000 2.042459e-02
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-R1  95499258.602144 1.301449e-05
-R1 100000000.000000 1.247190e-05
-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.ro3010.rsp b/resource/examples/geomega/materials/Xsection.Compton.ro3010.rsp
deleted file mode 100644
index d8ca03977..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.ro3010.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for ro3010
-CE false
-HA 404016241
-
-R1         1.000000 2.072476e-02
-R1         1.047129 2.245084e-02
-R1         1.096478 2.432159e-02
-R1         1.148154 2.634921e-02
-R1         1.202264 2.854694e-02
-R1         1.258925 3.092905e-02
-R1         1.318257 3.335070e-02
-R1         1.380384 3.596389e-02
-R1         1.445440 3.878391e-02
-R1         1.513561 4.182730e-02
-R1         1.584893 4.511189e-02
-R1         1.659587 4.839348e-02
-R1         1.737801 5.191712e-02
-R1         1.819701 5.570090e-02
-R1         1.905461 5.976426e-02
-R1         1.995262 6.412812e-02
-R1         2.089296 6.837340e-02
-R1         2.187762 7.290420e-02
-R1         2.290868 7.774021e-02
-R1         2.398833 8.290225e-02
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-R1         2.754229 9.914026e-02
-R1         2.884032 1.049909e-01
-R1         3.019952 1.111924e-01
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-R1         5.011872 1.866539e-01
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-R1        10.000000 2.860988e-01
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-R1        19.952623 3.603707e-01
-R1        20.892961 3.639481e-01
-R1        21.877616 3.675756e-01
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-R1        25.118864 3.787710e-01
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-R1        30.199517 3.896562e-01
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-R1        83.176377 3.904756e-01
-R1        87.096359 3.880654e-01
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-R1        95.499259 3.833040e-01
-R1       100.000000 3.809526e-01
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-R1       138.038426 3.577087e-01
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-R1       151.356125 3.502851e-01
-R1       158.489319 3.466341e-01
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-R1       173.780083 3.381556e-01
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.ro4003.rsp b/resource/examples/geomega/materials/Xsection.Compton.ro4003.rsp
deleted file mode 100644
index 92cd88258..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.ro4003.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for ro4003
-CE false
-HA 3349552005
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-
diff --git a/resource/examples/geomega/materials/Xsection.Compton.roTMM3.rsp b/resource/examples/geomega/materials/Xsection.Compton.roTMM3.rsp
deleted file mode 100644
index bc638d1c9..000000000
--- a/resource/examples/geomega/materials/Xsection.Compton.roTMM3.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Compton scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Compton scattering cross section for roTMM3
-CE false
-HA 3816565079
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.ACSPaper.rsp b/resource/examples/geomega/materials/Xsection.Pair.ACSPaper.rsp
deleted file mode 100644
index d4bd40106..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.ACSPaper.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for ACSPaper
-CE false
-HA 869331804
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.Air.rsp b/resource/examples/geomega/materials/Xsection.Pair.Air.rsp
deleted file mode 100644
index afe5a8e16..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.Air.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for Air
-CE false
-HA 230661740
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.Alu6061.rsp b/resource/examples/geomega/materials/Xsection.Pair.Alu6061.rsp
deleted file mode 100644
index fde621f0a..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.Alu6061.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for Alu6061
-CE false
-HA 203757245
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.Aluminium.rsp b/resource/examples/geomega/materials/Xsection.Pair.Aluminium.rsp
deleted file mode 100644
index 8a237d010..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.Aluminium.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for Aluminium
-CE false
-HA 825250182
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.BGO.rsp b/resource/examples/geomega/materials/Xsection.Pair.BGO.rsp
deleted file mode 100644
index ac956c43e..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.BGO.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for BGO
-CE false
-HA 1061301671
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.CZT.rsp b/resource/examples/geomega/materials/Xsection.Pair.CZT.rsp
deleted file mode 100644
index 1c7b93328..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.CZT.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for CZT
-CE false
-HA 3645592918
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.CarbonCyanateEster.rsp b/resource/examples/geomega/materials/Xsection.Pair.CarbonCyanateEster.rsp
deleted file mode 100644
index 9ddbfb453..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.CarbonCyanateEster.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for CarbonCyanateEster
-CE false
-HA 3197857782
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.CdTe.rsp b/resource/examples/geomega/materials/Xsection.Pair.CdTe.rsp
deleted file mode 100644
index c1ed3ac78..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.CdTe.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for CdTe
-CE false
-HA 2408428372
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.CircuitBoard.rsp b/resource/examples/geomega/materials/Xsection.Pair.CircuitBoard.rsp
deleted file mode 100644
index d3e500a22..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.CircuitBoard.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for CircuitBoard
-CE false
-HA 790253057
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.Copper.rsp b/resource/examples/geomega/materials/Xsection.Pair.Copper.rsp
deleted file mode 100644
index baca09a1d..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.Copper.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for Copper
-CE false
-HA 3193575607
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.CsI.rsp b/resource/examples/geomega/materials/Xsection.Pair.CsI.rsp
deleted file mode 100644
index e2279bff0..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.CsI.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for CsI
-CE false
-HA 3350302246
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.Densimet180.rsp b/resource/examples/geomega/materials/Xsection.Pair.Densimet180.rsp
deleted file mode 100644
index 01c15df32..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.Densimet180.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for Densimet180
-CE false
-HA 2913098225
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.Diamant.rsp b/resource/examples/geomega/materials/Xsection.Pair.Diamant.rsp
deleted file mode 100644
index 3e30f5102..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.Diamant.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for Diamant
-CE false
-HA 289970476
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.GePassive.rsp b/resource/examples/geomega/materials/Xsection.Pair.GePassive.rsp
deleted file mode 100644
index 936d3a151..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.GePassive.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for GePassive
-CE false
-HA 359300401
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.Germanium.rsp b/resource/examples/geomega/materials/Xsection.Pair.Germanium.rsp
deleted file mode 100644
index 54f005e93..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.Germanium.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for Germanium
-CE false
-HA 359300401
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.Glass.rsp b/resource/examples/geomega/materials/Xsection.Pair.Glass.rsp
deleted file mode 100644
index baea41512..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.Glass.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for Glass
-CE false
-HA 4029087792
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.Indium.rsp b/resource/examples/geomega/materials/Xsection.Pair.Indium.rsp
deleted file mode 100644
index 230b17885..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.Indium.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for Indium
-CE false
-HA 3903719287
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.Iron.rsp b/resource/examples/geomega/materials/Xsection.Pair.Iron.rsp
deleted file mode 100644
index 9e5b4f9cf..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.Iron.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for Iron
-CE false
-HA 4094812641
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.LaBr3.rsp b/resource/examples/geomega/materials/Xsection.Pair.LaBr3.rsp
deleted file mode 100644
index 1b8f38f98..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.LaBr3.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for LaBr3
-CE false
-HA 3587683841
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.MLI.rsp b/resource/examples/geomega/materials/Xsection.Pair.MLI.rsp
deleted file mode 100644
index 505ec4a65..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.MLI.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for MLI
-CE false
-HA 1447136272
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.MgS.rsp b/resource/examples/geomega/materials/Xsection.Pair.MgS.rsp
deleted file mode 100644
index 6641eda78..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.MgS.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for MgS
-CE false
-HA 2183886950
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.Millipore.rsp b/resource/examples/geomega/materials/Xsection.Pair.Millipore.rsp
deleted file mode 100644
index d432ca507..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.Millipore.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for Millipore
-CE false
-HA 869331804
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.NE110.rsp b/resource/examples/geomega/materials/Xsection.Pair.NE110.rsp
deleted file mode 100644
index 93a231790..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.NE110.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for NE110
-CE false
-HA 917272579
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.NE213.rsp b/resource/examples/geomega/materials/Xsection.Pair.NE213.rsp
deleted file mode 100644
index d2f05a9a5..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.NE213.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for NE213
-CE false
-HA 2640400524
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.NaI.rsp b/resource/examples/geomega/materials/Xsection.Pair.NaI.rsp
deleted file mode 100644
index 6cfdd0ab6..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.NaI.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for NaI
-CE false
-HA 1958776091
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.Nylon.rsp b/resource/examples/geomega/materials/Xsection.Pair.Nylon.rsp
deleted file mode 100644
index ddf481ec9..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.Nylon.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for Nylon
-CE false
-HA 3741285600
-
-R1         1.000000 1.127773e-301
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.PCB.rsp b/resource/examples/geomega/materials/Xsection.Pair.PCB.rsp
deleted file mode 100644
index cd0994704..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.PCB.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for PCB
-CE false
-HA 480612584
-
-R1         1.000000 1.069879e-301
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.PMTPlastic.rsp b/resource/examples/geomega/materials/Xsection.Pair.PMTPlastic.rsp
deleted file mode 100644
index b49eb433e..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.PMTPlastic.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for PMTPlastic
-CE false
-HA 1684120221
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.Pb.rsp b/resource/examples/geomega/materials/Xsection.Pair.Pb.rsp
deleted file mode 100644
index f749fba19..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.Pb.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for Pb
-CE false
-HA 2559858824
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.Peek.rsp b/resource/examples/geomega/materials/Xsection.Pair.Peek.rsp
deleted file mode 100644
index f03def273..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.Peek.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for Peek
-CE false
-HA 3912604896
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.Plastic_Isolation.rsp b/resource/examples/geomega/materials/Xsection.Pair.Plastic_Isolation.rsp
deleted file mode 100644
index 3828b6ef0..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.Plastic_Isolation.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for Plastic_Isolation
-CE false
-HA 2914733143
-
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-R1  91201083.935591 2.481714e-02
-R1  95499258.602144 2.481919e-02
-R1 100000000.000000 2.482125e-02
-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.Plywood.rsp b/resource/examples/geomega/materials/Xsection.Pair.Plywood.rsp
deleted file mode 100644
index 4717ca8d1..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.Plywood.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for Plywood
-CE false
-HA 2593954094
-
-R1         1.000000 5.349395e-302
-R1         1.047129 5.349395e-302
-R1         1.096478 5.349395e-302
-R1         1.148154 5.349395e-302
-R1         1.202264 5.349395e-302
-R1         1.258925 5.349395e-302
-R1         1.318257 5.349395e-302
-R1         1.380384 5.349395e-302
-R1         1.445440 5.349395e-302
-R1         1.513561 5.349395e-302
-R1         1.584893 5.349395e-302
-R1         1.659587 5.349395e-302
-R1         1.737801 5.349395e-302
-R1         1.819701 5.349395e-302
-R1         1.905461 5.349395e-302
-R1         1.995262 5.349395e-302
-R1         2.089296 5.349395e-302
-R1         2.187762 5.349395e-302
-R1         2.290868 5.349395e-302
-R1         2.398833 5.349395e-302
-R1         2.511886 5.349395e-302
-R1         2.630268 5.349395e-302
-R1         2.754229 5.349395e-302
-R1         2.884032 5.349395e-302
-R1         3.019952 5.349395e-302
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-R1         3.311311 5.349395e-302
-R1         3.467369 5.349395e-302
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-R1         3.801894 5.349395e-302
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-R1         4.168694 5.349395e-302
-R1         4.365158 5.349395e-302
-R1         4.570882 5.349395e-302
-R1         4.786301 5.349395e-302
-R1         5.011872 5.349395e-302
-R1         5.248075 5.349395e-302
-R1         5.495409 5.349395e-302
-R1         5.754399 5.349395e-302
-R1         6.025596 5.349395e-302
-R1         6.309573 5.349395e-302
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-R1         8.709636 5.349395e-302
-R1         9.120108 5.349395e-302
-R1         9.549926 5.349395e-302
-R1        10.000000 5.349395e-302
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-R1        20.892961 5.349395e-302
-R1        21.877616 5.349395e-302
-R1        22.908677 5.349395e-302
-R1        23.988329 5.349395e-302
-R1        25.118864 5.349395e-302
-R1        26.302680 5.349395e-302
-R1        27.542287 5.349395e-302
-R1        28.840315 5.349395e-302
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-R1        31.622777 5.349395e-302
-R1        33.113112 5.349395e-302
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-R1        36.307805 5.349395e-302
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-R1        60.255959 5.349395e-302
-R1        63.095734 5.349395e-302
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-R1        83.176377 5.349395e-302
-R1        87.096359 5.349395e-302
-R1        91.201084 5.349395e-302
-R1        95.499259 5.349395e-302
-R1       100.000000 5.349395e-302
-R1       104.712855 5.349395e-302
-R1       109.647820 5.349395e-302
-R1       114.815362 5.349395e-302
-R1       120.226443 5.349395e-302
-R1       125.892541 5.349395e-302
-R1       131.825674 5.349395e-302
-R1       138.038426 5.349395e-302
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-R1       151.356125 5.349395e-302
-R1       158.489319 5.349395e-302
-R1       165.958691 5.349395e-302
-R1       173.780083 5.349395e-302
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-R1       208.929613 5.349395e-302
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-R1       275.422870 5.349395e-302
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-R1       416.869383 5.349395e-302
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-R1       660.693448 5.349395e-302
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-R1       954.992586 5.349395e-302
-R1      1000.000000 5.349395e-302
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-R1      1584.893192 7.104845e-05
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.PressurizedAir.rsp b/resource/examples/geomega/materials/Xsection.Pair.PressurizedAir.rsp
deleted file mode 100644
index 22d9265ee..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.PressurizedAir.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for PressurizedAir
-CE false
-HA 3401473699
-
-R1         1.000000 1.032722e-301
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.Silicon.rsp b/resource/examples/geomega/materials/Xsection.Pair.Silicon.rsp
deleted file mode 100644
index 40f162883..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.Silicon.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for Silicon
-CE false
-HA 3884499373
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.SiliconPIN.rsp b/resource/examples/geomega/materials/Xsection.Pair.SiliconPIN.rsp
deleted file mode 100644
index e4c5bc538..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.SiliconPIN.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for SiliconPIN
-CE false
-HA 3884499373
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.Steel.rsp b/resource/examples/geomega/materials/Xsection.Pair.Steel.rsp
deleted file mode 100644
index fb09e479a..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.Steel.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for Steel
-CE false
-HA 619348587
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.Steel_18_8.rsp b/resource/examples/geomega/materials/Xsection.Pair.Steel_18_8.rsp
deleted file mode 100644
index 12d72855d..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.Steel_18_8.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for Steel_18_8
-CE false
-HA 1429918153
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.SurroundingSphereVolumeMaterial.rsp b/resource/examples/geomega/materials/Xsection.Pair.SurroundingSphereVolumeMaterial.rsp
deleted file mode 100644
index 5a50bdc0b..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.SurroundingSphereVolumeMaterial.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for SurroundingSphereVolumeMaterial
-CE false
-HA 1487652151
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.Tin.rsp b/resource/examples/geomega/materials/Xsection.Pair.Tin.rsp
deleted file mode 100644
index b07d62db8..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.Tin.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for Tin
-CE false
-HA 1304486184
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.Vacuum.rsp b/resource/examples/geomega/materials/Xsection.Pair.Vacuum.rsp
deleted file mode 100644
index ed1c155ee..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.Vacuum.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for Vacuum
-CE false
-HA 3622691594
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.Xenon.rsp b/resource/examples/geomega/materials/Xsection.Pair.Xenon.rsp
deleted file mode 100644
index f8ae01bee..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.Xenon.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for Xenon
-CE false
-HA 3026073170
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.XenonLXeGRIT.rsp b/resource/examples/geomega/materials/Xsection.Pair.XenonLXeGRIT.rsp
deleted file mode 100644
index e95e1510d..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.XenonLXeGRIT.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for XenonLXeGRIT
-CE false
-HA 3741687031
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.ro3003.rsp b/resource/examples/geomega/materials/Xsection.Pair.ro3003.rsp
deleted file mode 100644
index 6ce4f1fa0..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.ro3003.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for ro3003
-CE false
-HA 3212075832
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.ro3006.rsp b/resource/examples/geomega/materials/Xsection.Pair.ro3006.rsp
deleted file mode 100644
index 30073c366..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.ro3006.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for ro3006
-CE false
-HA 1294534288
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.ro3010.rsp b/resource/examples/geomega/materials/Xsection.Pair.ro3010.rsp
deleted file mode 100644
index 72f781d02..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.ro3010.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for ro3010
-CE false
-HA 404016241
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.ro4003.rsp b/resource/examples/geomega/materials/Xsection.Pair.ro4003.rsp
deleted file mode 100644
index d721d7d85..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.ro4003.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for ro4003
-CE false
-HA 3349552005
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-
diff --git a/resource/examples/geomega/materials/Xsection.Pair.roTMM3.rsp b/resource/examples/geomega/materials/Xsection.Pair.roTMM3.rsp
deleted file mode 100644
index d41637b17..000000000
--- a/resource/examples/geomega/materials/Xsection.Pair.roTMM3.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for pair creation
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Pair creation cross section for roTMM3
-CE false
-HA 3816565079
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.ACSPaper.rsp b/resource/examples/geomega/materials/Xsection.Photo.ACSPaper.rsp
deleted file mode 100644
index a4d9c19af..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.ACSPaper.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for ACSPaper
-CE false
-HA 869331804
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.Air.rsp b/resource/examples/geomega/materials/Xsection.Photo.Air.rsp
deleted file mode 100644
index ad1b82aca..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.Air.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for Air
-CE false
-HA 230661740
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.Alu6061.rsp b/resource/examples/geomega/materials/Xsection.Photo.Alu6061.rsp
deleted file mode 100644
index 95a5980b2..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.Alu6061.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for Alu6061
-CE false
-HA 203757245
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.Aluminium.rsp b/resource/examples/geomega/materials/Xsection.Photo.Aluminium.rsp
deleted file mode 100644
index 12c188ee0..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.Aluminium.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for Aluminium
-CE false
-HA 825250182
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.BGO.rsp b/resource/examples/geomega/materials/Xsection.Photo.BGO.rsp
deleted file mode 100644
index 92e6c5cb2..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.BGO.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for BGO
-CE false
-HA 1061301671
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.CZT.rsp b/resource/examples/geomega/materials/Xsection.Photo.CZT.rsp
deleted file mode 100644
index 4739be63f..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.CZT.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for CZT
-CE false
-HA 3645592918
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.CarbonCyanateEster.rsp b/resource/examples/geomega/materials/Xsection.Photo.CarbonCyanateEster.rsp
deleted file mode 100644
index 7bac1a8e2..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.CarbonCyanateEster.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for CarbonCyanateEster
-CE false
-HA 3197857782
-
-R1         1.000000 2.753094e+03
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.CdTe.rsp b/resource/examples/geomega/materials/Xsection.Photo.CdTe.rsp
deleted file mode 100644
index f76e701b8..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.CdTe.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for CdTe
-CE false
-HA 2408428372
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.CircuitBoard.rsp b/resource/examples/geomega/materials/Xsection.Photo.CircuitBoard.rsp
deleted file mode 100644
index c942498e7..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.CircuitBoard.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for CircuitBoard
-CE false
-HA 790253057
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.Copper.rsp b/resource/examples/geomega/materials/Xsection.Photo.Copper.rsp
deleted file mode 100644
index a69b46526..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.Copper.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for Copper
-CE false
-HA 3193575607
-
-R1         1.000000 9.451510e+04
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.CsI.rsp b/resource/examples/geomega/materials/Xsection.Photo.CsI.rsp
deleted file mode 100644
index cf0c883a2..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.CsI.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for CsI
-CE false
-HA 3350302246
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.Densimet180.rsp b/resource/examples/geomega/materials/Xsection.Photo.Densimet180.rsp
deleted file mode 100644
index 20e8681db..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.Densimet180.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for Densimet180
-CE false
-HA 2913098225
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.Diamant.rsp b/resource/examples/geomega/materials/Xsection.Photo.Diamant.rsp
deleted file mode 100644
index b6e8e015a..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.Diamant.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for Diamant
-CE false
-HA 289970476
-
-R1         1.000000 7.749631e+03
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.GePassive.rsp b/resource/examples/geomega/materials/Xsection.Photo.GePassive.rsp
deleted file mode 100644
index 57f7efa1f..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.GePassive.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for GePassive
-CE false
-HA 359300401
-
-R1         1.000000 1.003975e+04
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.Germanium.rsp b/resource/examples/geomega/materials/Xsection.Photo.Germanium.rsp
deleted file mode 100644
index ffacb3229..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.Germanium.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for Germanium
-CE false
-HA 359300401
-
-R1         1.000000 1.003975e+04
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.Glass.rsp b/resource/examples/geomega/materials/Xsection.Photo.Glass.rsp
deleted file mode 100644
index 1c5ef91ef..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.Glass.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for Glass
-CE false
-HA 4029087792
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.Indium.rsp b/resource/examples/geomega/materials/Xsection.Photo.Indium.rsp
deleted file mode 100644
index 0c600771d..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.Indium.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for Indium
-CE false
-HA 3903719287
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.Iron.rsp b/resource/examples/geomega/materials/Xsection.Photo.Iron.rsp
deleted file mode 100644
index e7e59c177..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.Iron.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for Iron
-CE false
-HA 4094812641
-
-R1         1.000000 7.171723e+04
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-R1         1.096478 5.772368e+04
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.LaBr3.rsp b/resource/examples/geomega/materials/Xsection.Photo.LaBr3.rsp
deleted file mode 100644
index 350a42d9f..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.LaBr3.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for LaBr3
-CE false
-HA 3587683841
-
-R1         1.000000 2.645106e+04
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.MLI.rsp b/resource/examples/geomega/materials/Xsection.Photo.MLI.rsp
deleted file mode 100644
index f7644f663..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.MLI.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for MLI
-CE false
-HA 1447136272
-
-R1         1.000000 3.958234e+03
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-R1  95499258.602144 1.042259e-11
-R1 100000000.000000 9.953416e-12
-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.MgS.rsp b/resource/examples/geomega/materials/Xsection.Photo.MgS.rsp
deleted file mode 100644
index cfc649a1a..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.MgS.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for MgS
-CE false
-HA 2183886950
-
-R1         1.000000 1.775592e+03
-R1         1.047129 1.573704e+03
-R1         1.096478 1.394756e+03
-R1         1.148154 1.234785e+03
-R1         1.202264 1.093078e+03
-R1         1.258925 9.678007e+02
-R1         1.318257 3.022755e+03
-R1         1.380384 2.725457e+03
-R1         1.445440 2.416533e+03
-R1         1.513561 2.145313e+03
-R1         1.584893 1.907453e+03
-R1         1.659587 1.696006e+03
-R1         1.737801 1.507594e+03
-R1         1.819701 1.340139e+03
-R1         1.905461 1.189602e+03
-R1         1.995262 1.055766e+03
-R1         2.089296 9.369644e+02
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-R1         2.290868 7.338501e+02
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-R1        10.000000 3.682739e+01
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-R1        21.877616 3.511804e+00
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-R1        25.118864 2.293933e+00
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.Millipore.rsp b/resource/examples/geomega/materials/Xsection.Photo.Millipore.rsp
deleted file mode 100644
index af3414cc4..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.Millipore.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for Millipore
-CE false
-HA 869331804
-
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diff --git a/resource/examples/geomega/materials/Xsection.Photo.NE110.rsp b/resource/examples/geomega/materials/Xsection.Photo.NE110.rsp
deleted file mode 100644
index a7792fef4..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.NE110.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for NE110
-CE false
-HA 917272579
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.NE213.rsp b/resource/examples/geomega/materials/Xsection.Photo.NE213.rsp
deleted file mode 100644
index a08b09b1f..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.NE213.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for NE213
-CE false
-HA 2640400524
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.NaI.rsp b/resource/examples/geomega/materials/Xsection.Photo.NaI.rsp
deleted file mode 100644
index 7b3c2fe3b..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.NaI.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for NaI
-CE false
-HA 1958776091
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.Nylon.rsp b/resource/examples/geomega/materials/Xsection.Photo.Nylon.rsp
deleted file mode 100644
index 86689300b..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.Nylon.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for Nylon
-CE false
-HA 3741285600
-
-R1         1.000000 3.034793e+03
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.PCB.rsp b/resource/examples/geomega/materials/Xsection.Photo.PCB.rsp
deleted file mode 100644
index 5b97c4d1f..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.PCB.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for PCB
-CE false
-HA 480612584
-
-R1         1.000000 3.349009e+03
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.PMTPlastic.rsp b/resource/examples/geomega/materials/Xsection.Photo.PMTPlastic.rsp
deleted file mode 100644
index 469d68011..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.PMTPlastic.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for PMTPlastic
-CE false
-HA 1684120221
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.Pb.rsp b/resource/examples/geomega/materials/Xsection.Photo.Pb.rsp
deleted file mode 100644
index cccab5b35..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.Pb.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for Pb
-CE false
-HA 2559858824
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.Peek.rsp b/resource/examples/geomega/materials/Xsection.Photo.Peek.rsp
deleted file mode 100644
index 8672094c8..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.Peek.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for Peek
-CE false
-HA 3912604896
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.Plastic_Isolation.rsp b/resource/examples/geomega/materials/Xsection.Photo.Plastic_Isolation.rsp
deleted file mode 100644
index 212f72d11..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.Plastic_Isolation.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for Plastic_Isolation
-CE false
-HA 2914733143
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.Plywood.rsp b/resource/examples/geomega/materials/Xsection.Photo.Plywood.rsp
deleted file mode 100644
index 979251976..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.Plywood.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for Plywood
-CE false
-HA 2593954094
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.PressurizedAir.rsp b/resource/examples/geomega/materials/Xsection.Photo.PressurizedAir.rsp
deleted file mode 100644
index 9e1372435..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.PressurizedAir.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for PressurizedAir
-CE false
-HA 3401473699
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.Silicon.rsp b/resource/examples/geomega/materials/Xsection.Photo.Silicon.rsp
deleted file mode 100644
index d9e627d96..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.Silicon.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for Silicon
-CE false
-HA 3884499373
-
-R1         1.000000 3.648911e+03
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.SiliconPIN.rsp b/resource/examples/geomega/materials/Xsection.Photo.SiliconPIN.rsp
deleted file mode 100644
index ec1a00e3b..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.SiliconPIN.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for SiliconPIN
-CE false
-HA 3884499373
-
-R1         1.000000 3.648911e+03
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.Steel.rsp b/resource/examples/geomega/materials/Xsection.Photo.Steel.rsp
deleted file mode 100644
index 44bc37375..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.Steel.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for Steel
-CE false
-HA 619348587
-
-R1         1.000000 6.949452e+04
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.Steel_18_8.rsp b/resource/examples/geomega/materials/Xsection.Photo.Steel_18_8.rsp
deleted file mode 100644
index 08d2d8176..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.Steel_18_8.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for Steel_18_8
-CE false
-HA 1429918153
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.SurroundingSphereVolumeMaterial.rsp b/resource/examples/geomega/materials/Xsection.Photo.SurroundingSphereVolumeMaterial.rsp
deleted file mode 100644
index 3c2e755c4..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.SurroundingSphereVolumeMaterial.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for SurroundingSphereVolumeMaterial
-CE false
-HA 1487652151
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.Tin.rsp b/resource/examples/geomega/materials/Xsection.Photo.Tin.rsp
deleted file mode 100644
index c5dee125c..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.Tin.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for Tin
-CE false
-HA 1304486184
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.Vacuum.rsp b/resource/examples/geomega/materials/Xsection.Photo.Vacuum.rsp
deleted file mode 100644
index d7ff00aa1..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.Vacuum.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for Vacuum
-CE false
-HA 3622691594
-
-R1         1.000000 6.816138e-12
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.Xenon.rsp b/resource/examples/geomega/materials/Xsection.Photo.Xenon.rsp
deleted file mode 100644
index 57ddc49f0..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.Xenon.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for Xenon
-CE false
-HA 3026073170
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.XenonLXeGRIT.rsp b/resource/examples/geomega/materials/Xsection.Photo.XenonLXeGRIT.rsp
deleted file mode 100644
index 7d609a0bb..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.XenonLXeGRIT.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for XenonLXeGRIT
-CE false
-HA 3741687031
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.ro3003.rsp b/resource/examples/geomega/materials/Xsection.Photo.ro3003.rsp
deleted file mode 100644
index 84b017af1..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.ro3003.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for ro3003
-CE false
-HA 3212075832
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.ro3006.rsp b/resource/examples/geomega/materials/Xsection.Photo.ro3006.rsp
deleted file mode 100644
index 9500e64f7..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.ro3006.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for ro3006
-CE false
-HA 1294534288
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.ro3010.rsp b/resource/examples/geomega/materials/Xsection.Photo.ro3010.rsp
deleted file mode 100644
index bddf3a044..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.ro3010.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for ro3010
-CE false
-HA 404016241
-
-R1         1.000000 1.366150e+04
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.ro4003.rsp b/resource/examples/geomega/materials/Xsection.Photo.ro4003.rsp
deleted file mode 100644
index 834c9779f..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.ro4003.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for ro4003
-CE false
-HA 3349552005
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Photo.roTMM3.rsp b/resource/examples/geomega/materials/Xsection.Photo.roTMM3.rsp
deleted file mode 100644
index 2e807738f..000000000
--- a/resource/examples/geomega/materials/Xsection.Photo.roTMM3.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Photo absorption
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Photo absorption cross section for roTMM3
-CE false
-HA 3816565079
-
-R1         1.000000 5.532566e+03
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.ACSPaper.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.ACSPaper.rsp
deleted file mode 100644
index abfeb6ac2..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.ACSPaper.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for ACSPaper
-CE false
-HA 869331804
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.Air.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.Air.rsp
deleted file mode 100644
index c7ebc8389..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.Air.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for Air
-CE false
-HA 230661740
-
-R1         1.000000 1.861559e-03
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.Alu6061.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.Alu6061.rsp
deleted file mode 100644
index af9989772..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.Alu6061.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for Alu6061
-CE false
-HA 203757245
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.Aluminium.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.Aluminium.rsp
deleted file mode 100644
index 27c96cce4..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.Aluminium.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for Aluminium
-CE false
-HA 825250182
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.BGO.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.BGO.rsp
deleted file mode 100644
index 4832b27c2..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.BGO.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for BGO
-CE false
-HA 1061301671
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.CZT.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.CZT.rsp
deleted file mode 100644
index 3ac03b2a3..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.CZT.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for CZT
-CE false
-HA 3645592918
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.CarbonCyanateEster.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.CarbonCyanateEster.rsp
deleted file mode 100644
index 0d5d054f7..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.CarbonCyanateEster.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for CarbonCyanateEster
-CE false
-HA 3197857782
-
-R1         1.000000 1.490838e+00
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.CdTe.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.CdTe.rsp
deleted file mode 100644
index 0693fc18d..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.CdTe.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for CdTe
-CE false
-HA 2408428372
-
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-R1  95499258.602144 7.653033e-13
-R1 100000000.000000 6.979648e-13
-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.CircuitBoard.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.CircuitBoard.rsp
deleted file mode 100644
index 5d583ba76..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.CircuitBoard.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for CircuitBoard
-CE false
-HA 790253057
-
-R1         1.000000 3.323073e+00
-R1         1.047129 3.314481e+00
-R1         1.096478 3.304486e+00
-R1         1.148154 3.289678e+00
-R1         1.202264 3.252705e+00
-R1         1.258925 3.204296e+00
-R1         1.318257 3.149073e+00
-R1         1.380384 3.084647e+00
-R1         1.445440 3.006120e+00
-R1         1.513561 2.886708e+00
-R1         1.584893 2.859500e+00
-R1         1.659587 2.842161e+00
-R1         1.737801 2.749697e+00
-R1         1.819701 2.556785e+00
-R1         1.905461 2.780975e+00
-R1         1.995262 2.853311e+00
-R1         2.089296 2.861165e+00
-R1         2.187762 2.840984e+00
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-R1         4.168694 2.029014e+00
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-R1         4.570882 1.904897e+00
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-R1         5.248075 1.699078e+00
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-R1         8.317638 1.045918e+00
-R1         8.709636 9.827366e-01
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.Copper.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.Copper.rsp
deleted file mode 100644
index a63ff0e42..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.Copper.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for Copper
-CE false
-HA 3193575607
-
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diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.CsI.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.CsI.rsp
deleted file mode 100644
index 4263446be..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.CsI.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for CsI
-CE false
-HA 3350302246
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.Densimet180.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.Densimet180.rsp
deleted file mode 100644
index 49f6c874d..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.Densimet180.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for Densimet180
-CE false
-HA 2913098225
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.Diamant.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.Diamant.rsp
deleted file mode 100644
index db63ce4b6..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.Diamant.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for Diamant
-CE false
-HA 289970476
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.GePassive.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.GePassive.rsp
deleted file mode 100644
index d8c2afe73..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.GePassive.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for GePassive
-CE false
-HA 359300401
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.Germanium.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.Germanium.rsp
deleted file mode 100644
index 392edeeca..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.Germanium.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for Germanium
-CE false
-HA 359300401
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.Glass.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.Glass.rsp
deleted file mode 100644
index dd4f1f612..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.Glass.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for Glass
-CE false
-HA 4029087792
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.Indium.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.Indium.rsp
deleted file mode 100644
index f42b63a48..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.Indium.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for Indium
-CE false
-HA 3903719287
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.Iron.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.Iron.rsp
deleted file mode 100644
index ee6190cca..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.Iron.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for Iron
-CE false
-HA 4094812641
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.LaBr3.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.LaBr3.rsp
deleted file mode 100644
index 06e35bbbd..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.LaBr3.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for LaBr3
-CE false
-HA 3587683841
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.MLI.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.MLI.rsp
deleted file mode 100644
index 96a92cd5c..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.MLI.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for MLI
-CE false
-HA 1447136272
-
-R1         1.000000 1.870982e+00
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.MgS.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.MgS.rsp
deleted file mode 100644
index 25a930019..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.MgS.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for MgS
-CE false
-HA 2183886950
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.Millipore.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.Millipore.rsp
deleted file mode 100644
index 1634ca617..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.Millipore.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for Millipore
-CE false
-HA 869331804
-
-R1         1.000000 1.400747e+00
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.NE110.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.NE110.rsp
deleted file mode 100644
index 73058cc1c..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.NE110.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for NE110
-CE false
-HA 917272579
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.NE213.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.NE213.rsp
deleted file mode 100644
index 51eab873e..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.NE213.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for NE213
-CE false
-HA 2640400524
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.NaI.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.NaI.rsp
deleted file mode 100644
index adb6974c2..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.NaI.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for NaI
-CE false
-HA 1958776091
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.Nylon.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.Nylon.rsp
deleted file mode 100644
index fa12d5a9e..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.Nylon.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for Nylon
-CE false
-HA 3741285600
-
-R1         1.000000 1.446857e+00
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-R1         1.258925 1.363230e+00
-R1         1.318257 1.341576e+00
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-R1         1.445440 1.296757e+00
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.PCB.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.PCB.rsp
deleted file mode 100644
index efebf66b7..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.PCB.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for PCB
-CE false
-HA 480612584
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.PMTPlastic.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.PMTPlastic.rsp
deleted file mode 100644
index de875c012..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.PMTPlastic.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for PMTPlastic
-CE false
-HA 1684120221
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.Pb.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.Pb.rsp
deleted file mode 100644
index a2345fb5e..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.Pb.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for Pb
-CE false
-HA 2559858824
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.Peek.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.Peek.rsp
deleted file mode 100644
index 62ea16a59..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.Peek.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for Peek
-CE false
-HA 3912604896
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.Plastic_Isolation.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.Plastic_Isolation.rsp
deleted file mode 100644
index 11d509346..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.Plastic_Isolation.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for Plastic_Isolation
-CE false
-HA 2914733143
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.Plywood.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.Plywood.rsp
deleted file mode 100644
index ae958d5ce..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.Plywood.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for Plywood
-CE false
-HA 2593954094
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.PressurizedAir.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.PressurizedAir.rsp
deleted file mode 100644
index 3bb60c82c..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.PressurizedAir.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for PressurizedAir
-CE false
-HA 3401473699
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.Silicon.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.Silicon.rsp
deleted file mode 100644
index d07c982fe..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.Silicon.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for Silicon
-CE false
-HA 3884499373
-
-R1         1.000000 4.994248e+00
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-R1         1.258925 4.437268e+00
-R1         1.318257 4.305893e+00
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-R1        30.199517 2.928251e-01
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-R1        33.113112 2.524842e-01
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.SiliconPIN.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.SiliconPIN.rsp
deleted file mode 100644
index 3fd469d70..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.SiliconPIN.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for SiliconPIN
-CE false
-HA 3884499373
-
-R1         1.000000 4.994248e+00
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.Steel.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.Steel.rsp
deleted file mode 100644
index 2bdf85623..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.Steel.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for Steel
-CE false
-HA 619348587
-
-R1         1.000000 3.363907e+01
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.Steel_18_8.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.Steel_18_8.rsp
deleted file mode 100644
index fd51f6904..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.Steel_18_8.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for Steel_18_8
-CE false
-HA 1429918153
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.SurroundingSphereVolumeMaterial.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.SurroundingSphereVolumeMaterial.rsp
deleted file mode 100644
index e8e3f67f8..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.SurroundingSphereVolumeMaterial.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for SurroundingSphereVolumeMaterial
-CE false
-HA 1487652151
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.Tin.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.Tin.rsp
deleted file mode 100644
index 7b5de8f4f..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.Tin.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for Tin
-CE false
-HA 1304486184
-
-R1         1.000000 4.782969e+01
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.Vacuum.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.Vacuum.rsp
deleted file mode 100644
index 2d1a9a976..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.Vacuum.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for Vacuum
-CE false
-HA 3622691594
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.Xenon.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.Xenon.rsp
deleted file mode 100644
index 8e85fb43d..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.Xenon.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for Xenon
-CE false
-HA 3026073170
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.XenonLXeGRIT.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.XenonLXeGRIT.rsp
deleted file mode 100644
index 5867826d0..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.XenonLXeGRIT.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for XenonLXeGRIT
-CE false
-HA 3741687031
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.ro3003.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.ro3003.rsp
deleted file mode 100644
index baea4cb00..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.ro3003.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for ro3003
-CE false
-HA 3212075832
-
-R1         1.000000 3.905193e+00
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-R1  83176377.110267 4.805543e-14
-R1  87096358.995608 4.382706e-14
-R1  91201083.935591 3.997075e-14
-R1  95499258.602144 3.645375e-14
-R1 100000000.000000 3.324621e-14
-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.ro3006.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.ro3006.rsp
deleted file mode 100644
index c44fc6aae..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.ro3006.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for ro3006
-CE false
-HA 1294534288
-
-R1         1.000000 7.674657e+00
-R1         1.047129 7.698864e+00
-R1         1.096478 7.704934e+00
-R1         1.148154 7.690788e+00
-R1         1.202264 7.650735e+00
-R1         1.258925 7.593335e+00
-R1         1.318257 7.521930e+00
-R1         1.380384 7.439926e+00
-R1         1.445440 7.344326e+00
-R1         1.513561 7.221803e+00
-R1         1.584893 7.079864e+00
-R1         1.659587 6.913880e+00
-R1         1.737801 6.708252e+00
-R1         1.819701 6.426626e+00
-R1         1.905461 6.395231e+00
-R1         1.995262 6.221990e+00
-R1         2.089296 5.960834e+00
-R1         2.187762 5.600292e+00
-R1         2.290868 5.027446e+00
-R1         2.398833 4.250977e+00
-R1         2.511886 5.309807e+00
-R1         2.630268 6.315363e+00
-R1         2.754229 6.764657e+00
-R1         2.884032 6.774742e+00
-R1         3.019952 7.214530e+00
-R1         3.162278 7.426995e+00
-R1         3.311311 7.395305e+00
-R1         3.467369 7.398186e+00
-R1         3.630781 7.399887e+00
-R1         3.801894 7.454396e+00
-R1         3.981072 7.399216e+00
-R1         4.168694 7.292038e+00
-R1         4.365158 7.156829e+00
-R1         4.570882 6.999727e+00
-R1         4.786301 6.826682e+00
-R1         5.011872 6.640416e+00
-R1         5.248075 6.445400e+00
-R1         5.495409 6.241214e+00
-R1         5.754399 6.031380e+00
-R1         6.025596 5.821365e+00
-R1         6.309573 5.606050e+00
-R1         6.606934 5.392344e+00
-R1         6.918310 5.173898e+00
-R1         7.244360 4.958587e+00
-R1         7.585776 4.743459e+00
-R1         7.943282 4.529189e+00
-R1         8.317638 4.318731e+00
-R1         8.709636 4.111289e+00
-R1         9.120108 3.899453e+00
-R1         9.549926 3.695081e+00
-R1        10.000000 3.489086e+00
-R1        10.471285 3.280645e+00
-R1        10.964782 3.069376e+00
-R1        11.481536 2.845778e+00
-R1        12.022644 2.587782e+00
-R1        12.589254 2.170287e+00
-R1        13.182567 2.360662e+00
-R1        13.803843 2.317204e+00
-R1        14.454398 2.141647e+00
-R1        15.135612 2.086718e+00
-R1        15.848932 2.151718e+00
-R1        16.595869 2.121063e+00
-R1        17.378008 2.052140e+00
-R1        18.197009 1.968990e+00
-R1        19.054607 1.878816e+00
-R1        19.952623 1.787014e+00
-R1        20.892961 1.692765e+00
-R1        21.877616 1.601618e+00
-R1        22.908677 1.510988e+00
-R1        23.988329 1.424306e+00
-R1        25.118864 1.339572e+00
-R1        26.302680 1.259608e+00
-R1        27.542287 1.181060e+00
-R1        28.840315 1.107336e+00
-R1        30.199517 1.037050e+00
-R1        31.622777 9.697874e-01
-R1        33.113112 9.068974e-01
-R1        34.673685 8.466684e-01
-R1        36.307805 7.895596e-01
-R1        38.018940 7.347563e-01
-R1        39.810717 6.830059e-01
-R1        41.686938 6.335830e-01
-R1        43.651583 5.870877e-01
-R1        45.708819 5.435737e-01
-R1        47.863009 5.032786e-01
-R1        50.118723 4.659314e-01
-R1        52.480746 4.303692e-01
-R1        54.954087 3.974519e-01
-R1        57.543994 3.666930e-01
-R1        60.255959 3.377000e-01
-R1        63.095734 3.105699e-01
-R1        66.069345 2.853793e-01
-R1        69.183097 2.615741e-01
-R1        72.443596 2.393512e-01
-R1        75.857758 2.180826e-01
-R1        79.432823 1.970263e-01
-R1        83.176377 1.731708e-01
-R1        87.096359 1.564848e-01
-R1        91.201084 1.595740e-01
-R1        95.499259 1.523770e-01
-R1       100.000000 1.434858e-01
-R1       104.712855 1.342334e-01
-R1       109.647820 1.250033e-01
-R1       114.815362 1.160667e-01
-R1       120.226443 1.074388e-01
-R1       125.892541 9.937019e-02
-R1       131.825674 9.169253e-02
-R1       138.038426 8.460654e-02
-R1       144.543977 7.793392e-02
-R1       151.356125 7.176889e-02
-R1       158.489319 6.609189e-02
-R1       165.958691 6.085785e-02
-R1       173.780083 5.595865e-02
-R1       181.970086 5.145347e-02
-R1       190.546072 4.730900e-02
-R1       199.526231 4.349816e-02
-R1       208.929613 3.994261e-02
-R1       218.776162 3.666792e-02
-R1       229.086765 3.366179e-02
-R1       239.883292 3.090218e-02
-R1       251.188643 2.834056e-02
-R1       263.026799 2.597971e-02
-R1       275.422870 2.381543e-02
-R1       288.403150 2.183122e-02
-R1       301.995172 2.000038e-02
-R1       316.227766 1.831176e-02
-R1       331.131121 1.676547e-02
-R1       346.736850 1.534976e-02
-R1       363.078055 1.405360e-02
-R1       380.189396 1.286315e-02
-R1       398.107171 1.176438e-02
-R1       416.869383 1.075947e-02
-R1       436.515832 9.840401e-03
-R1       457.088190 8.999846e-03
-R1       478.630092 8.231094e-03
-R1       501.187234 7.527997e-03
-R1       524.807460 6.883816e-03
-R1       549.540874 6.290311e-03
-R1       575.439937 5.747979e-03
-R1       602.559586 5.252406e-03
-R1       630.957344 4.799561e-03
-R1       660.693448 4.385760e-03
-R1       691.830971 4.007636e-03
-R1       724.435960 3.662084e-03
-R1       758.577575 3.346322e-03
-R1       794.328235 3.057771e-03
-R1       831.763771 2.792785e-03
-R1       870.963590 2.550242e-03
-R1       912.010839 2.328763e-03
-R1       954.992586 2.126519e-03
-R1      1000.000000 1.941840e-03
-R1      1047.128548 1.773199e-03
-R1      1096.478196 1.619204e-03
-R1      1148.153621 1.478583e-03
-R1      1202.264435 1.350175e-03
-R1      1258.925412 1.232918e-03
-R1      1318.256739 1.125454e-03
-R1      1380.384265 1.027038e-03
-R1      1445.439771 9.372277e-04
-R1      1513.561248 8.552709e-04
-R1      1584.893192 7.804803e-04
-R1      1659.586907 7.122292e-04
-R1      1737.800829 6.499466e-04
-R1      1819.700859 5.931104e-04
-R1      1905.460718 5.412444e-04
-R1      1995.262315 4.939140e-04
-R1      2089.296131 4.507225e-04
-R1      2187.761624 4.113075e-04
-R1      2290.867653 3.753390e-04
-R1      2398.832919 3.424340e-04
-R1      2511.886432 3.123469e-04
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-R1      2754.228703 2.598710e-04
-R1      2884.031503 2.370380e-04
-R1      3019.951720 2.162113e-04
-R1      3162.277660 1.972144e-04
-R1      3311.311215 1.798866e-04
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-R1      3630.780548 1.496647e-04
-R1      3801.893963 1.365148e-04
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-R1      4365.158322 1.036002e-04
-R1      4570.881896 9.449764e-05
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-R1      6606.934480 4.527961e-05
-R1      6918.309709 4.130121e-05
-R1      7244.359601 3.766982e-05
-R1      7585.775750 3.435564e-05
-R1      7943.282347 3.133303e-05
-R1      8317.637711 2.857636e-05
-R1      8709.635900 2.606222e-05
-R1      9120.108394 2.376927e-05
-R1      9549.925860 2.167805e-05
-R1     10000.000000 1.977082e-05
-R1     10471.285481 1.803139e-05
-R1     10964.781961 1.644499e-05
-R1     11481.536215 1.499816e-05
-R1     12022.644346 1.367863e-05
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-R1     13182.567386 1.137762e-05
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-R1    100000.000000 1.977471e-07
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-R1    144543.977075 9.464782e-08
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.ro3010.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.ro3010.rsp
deleted file mode 100644
index 902fef736..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.ro3010.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for ro3010
-CE false
-HA 404016241
-
-R1         1.000000 1.051182e+01
-R1         1.047129 1.056631e+01
-R1         1.096478 1.059373e+01
-R1         1.148154 1.059111e+01
-R1         1.202264 1.055240e+01
-R1         1.258925 1.049009e+01
-R1         1.318257 1.040819e+01
-R1         1.380384 1.031089e+01
-R1         1.445440 1.019500e+01
-R1         1.513561 1.004001e+01
-R1         1.584893 9.858964e+00
-R1         1.659587 9.651156e+00
-R1         1.737801 9.405380e+00
-R1         1.819701 9.105538e+00
-R1         1.905461 8.863539e+00
-R1         1.995262 8.509705e+00
-R1         2.089296 8.059289e+00
-R1         2.187762 7.461992e+00
-R1         2.290868 6.520957e+00
-R1         2.398833 5.246319e+00
-R1         2.511886 7.060251e+00
-R1         2.630268 8.789516e+00
-R1         2.754229 9.586791e+00
-R1         2.884032 9.649440e+00
-R1         3.019952 1.043689e+01
-R1         3.162278 1.084330e+01
-R1         3.311311 1.084204e+01
-R1         3.467369 1.089884e+01
-R1         3.630781 1.095505e+01
-R1         3.801894 1.109895e+01
-R1         3.981072 1.106046e+01
-R1         4.168694 1.093305e+01
-R1         4.365158 1.075872e+01
-R1         4.570882 1.054677e+01
-R1         4.786301 1.030708e+01
-R1         5.011872 1.004456e+01
-R1         5.248075 9.766543e+00
-R1         5.495409 9.471968e+00
-R1         5.754399 9.166414e+00
-R1         6.025596 8.859797e+00
-R1         6.309573 8.543056e+00
-R1         6.606934 8.227727e+00
-R1         6.918310 7.903258e+00
-R1         7.244360 7.582230e+00
-R1         7.585776 7.260647e+00
-R1         7.943282 6.938802e+00
-R1         8.317638 6.622016e+00
-R1         8.709636 6.308842e+00
-R1         9.120108 5.987120e+00
-R1         9.549926 5.676226e+00
-R1        10.000000 5.361434e+00
-R1        10.471285 5.040690e+00
-R1        10.964782 4.714185e+00
-R1        11.481536 4.365379e+00
-R1        12.022644 3.957561e+00
-R1        12.589254 3.280392e+00
-R1        13.182567 3.622953e+00
-R1        13.803843 3.571667e+00
-R1        14.454398 3.297163e+00
-R1        15.135612 3.224089e+00
-R1        15.848932 3.351541e+00
-R1        16.595869 3.317190e+00
-R1        17.378008 3.217567e+00
-R1        18.197009 3.093005e+00
-R1        19.054607 2.955804e+00
-R1        19.952623 2.815058e+00
-R1        20.892961 2.669380e+00
-R1        21.877616 2.528070e+00
-R1        22.908677 2.386952e+00
-R1        23.988329 2.251773e+00
-R1        25.118864 2.119261e+00
-R1        26.302680 1.994229e+00
-R1        27.542287 1.870928e+00
-R1        28.840315 1.755167e+00
-R1        30.199517 1.644719e+00
-R1        31.622777 1.538828e+00
-R1        33.113112 1.439763e+00
-R1        34.673685 1.344699e+00
-R1        36.307805 1.254503e+00
-R1        38.018940 1.167815e+00
-R1        39.810717 1.085875e+00
-R1        41.686938 1.007547e+00
-R1        43.651583 9.338100e-01
-R1        45.708819 8.647454e-01
-R1        47.863009 8.007827e-01
-R1        50.118723 7.415184e-01
-R1        52.480746 6.850106e-01
-R1        54.954087 6.326954e-01
-R1        57.543994 5.838109e-01
-R1        60.255959 5.376883e-01
-R1        63.095734 4.944941e-01
-R1        66.069345 4.543668e-01
-R1        69.183097 4.164154e-01
-R1        72.443596 3.809589e-01
-R1        75.857758 3.469581e-01
-R1        79.432823 3.131731e-01
-R1        83.176377 2.745591e-01
-R1        87.096359 2.478811e-01
-R1        91.201084 2.543170e-01
-R1        95.499259 2.433700e-01
-R1       100.000000 2.294820e-01
-R1       104.712855 2.148999e-01
-R1       109.647820 2.002811e-01
-R1       114.815362 1.860885e-01
-R1       120.226443 1.723453e-01
-R1       125.892541 1.594788e-01
-R1       131.825674 1.472109e-01
-R1       138.038426 1.358857e-01
-R1       144.543977 1.252096e-01
-R1       151.356125 1.153416e-01
-R1       158.489319 1.062516e-01
-R1       165.958691 9.786749e-02
-R1       173.780083 9.001109e-02
-R1       181.970086 8.278526e-02
-R1       190.546072 7.613820e-02
-R1       199.526231 7.002460e-02
-R1       208.929613 6.431536e-02
-R1       218.776162 5.905510e-02
-R1       229.086765 5.422515e-02
-R1       239.883292 4.979030e-02
-R1       251.188643 4.567115e-02
-R1       263.026799 4.187374e-02
-R1       275.422870 3.839198e-02
-R1       288.403150 3.519949e-02
-R1       301.995172 3.225241e-02
-R1       316.227766 2.953304e-02
-R1       331.131121 2.704267e-02
-R1       346.736850 2.476231e-02
-R1       363.078055 2.267425e-02
-R1       380.189396 2.075618e-02
-R1       398.107171 1.898506e-02
-R1       416.869383 1.736507e-02
-R1       436.515832 1.588332e-02
-R1       457.088190 1.452801e-02
-R1       478.630092 1.328835e-02
-R1       501.187234 1.215446e-02
-R1       524.807460 1.111543e-02
-R1       549.540874 1.015774e-02
-R1       575.439937 9.282577e-03
-R1       602.559586 8.482812e-03
-R1       630.957344 7.751954e-03
-R1       660.693448 7.084067e-03
-R1       691.830971 6.473723e-03
-R1       724.435960 5.915954e-03
-R1       758.577575 5.406240e-03
-R1       794.328235 4.940425e-03
-R1       831.763771 4.512536e-03
-R1       870.963590 4.120831e-03
-R1       912.010839 3.763127e-03
-R1       954.992586 3.436474e-03
-R1      1000.000000 3.138176e-03
-R1      1047.128548 2.865771e-03
-R1      1096.478196 2.617012e-03
-R1      1148.153621 2.389846e-03
-R1      1202.264435 2.182400e-03
-R1      1258.925412 1.992960e-03
-R1      1318.256739 1.819308e-03
-R1      1380.384265 1.660251e-03
-R1      1445.439771 1.515099e-03
-R1      1513.561248 1.382638e-03
-R1      1584.893192 1.261757e-03
-R1      1659.586907 1.151443e-03
-R1      1737.800829 1.050774e-03
-R1      1819.700859 9.589067e-04
-R1      1905.460718 8.750710e-04
-R1      1995.262315 7.985649e-04
-R1      2089.296131 7.287477e-04
-R1      2187.761624 6.650343e-04
-R1      2290.867653 6.068911e-04
-R1      2398.832919 5.536939e-04
-R1      2511.886432 5.050475e-04
-R1      2630.267992 4.606751e-04
-R1      2754.228703 4.202011e-04
-R1      2884.031503 3.832831e-04
-R1      3019.951720 3.496087e-04
-R1      3162.277660 3.188928e-04
-R1      3311.311215 2.908755e-04
-R1      3467.368505 2.653198e-04
-R1      3630.780548 2.420094e-04
-R1      3801.893963 2.207469e-04
-R1      3981.071706 2.013526e-04
-R1      4168.693835 1.836621e-04
-R1      4365.158322 1.675260e-04
-R1      4570.881896 1.528075e-04
-R1      4786.300923 1.393821e-04
-R1      5011.872336 1.271363e-04
-R1      5248.074602 1.159664e-04
-R1      5495.408739 1.057778e-04
-R1      5754.399373 9.648435e-05
-R1      6025.595861 8.800743e-05
-R1      6309.573445 8.027527e-05
-R1      6606.934480 7.322244e-05
-R1      6918.309709 6.678926e-05
-R1      7244.359601 6.091701e-05
-R1      7585.775750 5.555756e-05
-R1      7943.282347 5.066964e-05
-R1      8317.637711 4.621175e-05
-R1      8709.635900 4.214606e-05
-R1      9120.108394 3.843808e-05
-R1      9549.925860 3.505631e-05
-R1     10000.000000 3.197208e-05
-R1     10471.285481 2.915919e-05
-R1     10964.781961 2.659378e-05
-R1     11481.536215 2.425407e-05
-R1     12022.644346 2.212021e-05
-R1     12589.254118 2.017409e-05
-R1     13182.567386 1.839918e-05
-R1     13803.842646 1.678043e-05
-R1     14454.397707 1.530410e-05
-R1     15135.612484 1.395765e-05
-R1     15848.931925 1.272966e-05
-R1     16595.869074 1.160971e-05
-R1     17378.008287 1.058830e-05
-R1     18197.008586 9.656745e-06
-R1     19054.607180 8.807150e-06
-R1     19952.623150 8.032301e-06
-R1     20892.961309 7.325623e-06
-R1     21877.616239 6.681085e-06
-R1     22908.676528 6.093229e-06
-R1     23988.329190 5.557098e-06
-R1     25118.864315 5.068139e-06
-R1     26302.679919 4.622203e-06
-R1     27542.287033 4.215504e-06
-R1     28840.315031 3.844590e-06
-R1     30199.517204 3.506312e-06
-R1     31622.776602 3.197798e-06
-R1     33113.112148 2.916430e-06
-R1     34673.685045 2.659819e-06
-R1     36307.805477 2.425787e-06
-R1     38018.939632 2.212346e-06
-R1     39810.717055 2.017686e-06
-R1     41686.938347 1.840154e-06
-R1     43651.583224 1.678242e-06
-R1     45708.818961 1.530577e-06
-R1     47863.009232 1.395904e-06
-R1     50118.723363 1.273081e-06
-R1     52480.746025 1.161065e-06
-R1     54954.087386 1.058905e-06
-R1     57543.993734 9.657343e-07
-R1     60255.958607 8.807611e-07
-R1     63095.734448 8.032646e-07
-R1     66069.344801 7.325865e-07
-R1     69183.097092 6.681269e-07
-R1     72443.596007 6.093391e-07
-R1     75857.757503 5.557239e-07
-R1     79432.823472 5.068263e-07
-R1     83176.377110 4.622311e-07
-R1     87096.358996 4.215599e-07
-R1     91201.083936 3.844672e-07
-R1     95499.258602 3.506383e-07
-R1    100000.000000 3.197860e-07
-R1    104712.854805 2.916483e-07
-R1    109647.819614 2.659865e-07
-R1    114815.362150 2.425826e-07
-R1    120226.443462 2.212380e-07
-R1    125892.541179 2.017714e-07
-R1    131825.673856 1.840178e-07
-R1    138038.426460 1.678262e-07
-R1    144543.977075 1.530593e-07
-R1    151356.124844 1.395918e-07
-R1    158489.319246 1.273093e-07
-R1    165958.690744 1.161074e-07
-R1    173780.082875 1.058912e-07
-R1    181970.085861 9.657398e-08
-R1    190546.071796 8.807653e-08
-R1    199526.231497 8.032675e-08
-R1    208929.613085 7.325887e-08
-R1    218776.162395 6.681288e-08
-R1    229086.765277 6.093407e-08
-R1    239883.291902 5.557254e-08
-R1    251188.643151 5.068275e-08
-R1    263026.799190 4.622322e-08
-R1    275422.870334 4.215608e-08
-R1    288403.150313 3.844680e-08
-R1    301995.172040 3.506390e-08
-R1    316227.766017 3.197866e-08
-R1    331131.121483 2.916488e-08
-R1    346736.850453 2.659869e-08
-R1    363078.054770 2.425829e-08
-R1    380189.396321 2.212383e-08
-R1    398107.170553 2.017717e-08
-R1    416869.383470 1.840180e-08
-R1    436515.832240 1.678264e-08
-R1    457088.189615 1.530595e-08
-R1    478630.092323 1.395919e-08
-R1    501187.233627 1.273093e-08
-R1    524807.460250 1.161075e-08
-R1    549540.873858 1.058913e-08
-R1    575439.937337 9.657400e-09
-R1    602559.586074 8.807653e-09
-R1    630957.344480 8.032675e-09
-R1    660693.448008 7.325887e-09
-R1    691830.970919 6.681288e-09
-R1    724435.960075 6.093407e-09
-R1    758577.575029 5.557253e-09
-R1    794328.234724 5.068275e-09
-R1    831763.771103 4.622322e-09
-R1    870963.589956 4.215608e-09
-R1    912010.839356 3.844680e-09
-R1    954992.586021 3.506390e-09
-R1   1000000.000000 3.197865e-09
-R1   1047128.548051 2.916488e-09
-R1   1096478.196143 2.659869e-09
-R1   1148153.621497 2.425829e-09
-R1   1202264.434617 2.212382e-09
-R1   1258925.411794 2.017717e-09
-R1   1318256.738556 1.840179e-09
-R1   1380384.264603 1.678264e-09
-R1   1445439.770746 1.530595e-09
-R1   1513561.248436 1.395919e-09
-R1   1584893.192461 1.273093e-09
-R1   1659586.907438 1.161075e-09
-R1   1737800.828749 1.058913e-09
-R1   1819700.858610 9.657398e-10
-R1   1905460.717963 8.807652e-10
-R1   1995262.314969 8.032674e-10
-R1   2089296.130854 7.325886e-10
-R1   2187761.623950 6.681287e-10
-R1   2290867.652768 6.093406e-10
-R1   2398832.919019 5.557253e-10
-R1   2511886.431510 5.068275e-10
-R1   2630267.991895 4.622322e-10
-R1   2754228.703338 4.215607e-10
-R1   2884031.503127 3.844680e-10
-R1   3019951.720402 3.506390e-10
-R1   3162277.660168 3.197865e-10
-R1   3311311.214826 2.916488e-10
-R1   3467368.504525 2.659869e-10
-R1   3630780.547701 2.425829e-10
-R1   3801893.963206 2.212382e-10
-R1   3981071.705535 2.017717e-10
-R1   4168693.834703 1.840180e-10
-R1   4365158.322402 1.678264e-10
-R1   4570881.896149 1.530595e-10
-R1   4786300.923226 1.395919e-10
-R1   5011872.336273 1.273093e-10
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-R1   5754399.373372 9.657400e-11
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-R1   6309573.444802 8.032675e-11
-R1   6606934.480076 7.325887e-11
-R1   6918309.709189 6.681288e-11
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-R1   8317637.711027 4.622322e-11
-R1   8709635.899561 4.215608e-11
-R1   9120108.393559 3.844680e-11
-R1   9549925.860214 3.506390e-11
-R1  10000000.000000 3.197865e-11
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-R1  11481536.214969 2.425829e-11
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-R1  12589254.117942 2.017717e-11
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-R1  87096358.995608 4.215609e-13
-R1  91201083.935591 3.844681e-13
-R1  95499258.602144 3.506390e-13
-R1 100000000.000000 3.197865e-13
-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.ro4003.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.ro4003.rsp
deleted file mode 100644
index 3b63891bc..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.ro4003.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for ro4003
-CE false
-HA 3349552005
-
-R1         1.000000 3.244959e+00
-R1         1.047129 3.207025e+00
-R1         1.096478 3.166341e+00
-R1         1.148154 3.122212e+00
-R1         1.202264 3.067916e+00
-R1         1.258925 3.005465e+00
-R1         1.318257 2.945416e+00
-R1         1.380384 2.883156e+00
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-
diff --git a/resource/examples/geomega/materials/Xsection.Rayleigh.roTMM3.rsp b/resource/examples/geomega/materials/Xsection.Rayleigh.roTMM3.rsp
deleted file mode 100644
index 6929b24b8..000000000
--- a/resource/examples/geomega/materials/Xsection.Rayleigh.roTMM3.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section for Rayleigh scattering
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Rayleigh scattering cross section for roTMM3
-CE false
-HA 3816565079
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.ACSPaper.rsp b/resource/examples/geomega/materials/Xsection.Total.ACSPaper.rsp
deleted file mode 100644
index 60e082593..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.ACSPaper.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for ACSPaper
-CE false
-HA 869331804
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.Air.rsp b/resource/examples/geomega/materials/Xsection.Total.Air.rsp
deleted file mode 100644
index 2d0f1c9f8..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.Air.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for Air
-CE false
-HA 230661740
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.Alu6061.rsp b/resource/examples/geomega/materials/Xsection.Total.Alu6061.rsp
deleted file mode 100644
index c37bbc3c0..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.Alu6061.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for Alu6061
-CE false
-HA 203757245
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.Aluminium.rsp b/resource/examples/geomega/materials/Xsection.Total.Aluminium.rsp
deleted file mode 100644
index c8a971b4f..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.Aluminium.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for Aluminium
-CE false
-HA 825250182
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.BGO.rsp b/resource/examples/geomega/materials/Xsection.Total.BGO.rsp
deleted file mode 100644
index 1b5848223..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.BGO.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for BGO
-CE false
-HA 1061301671
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.CZT.rsp b/resource/examples/geomega/materials/Xsection.Total.CZT.rsp
deleted file mode 100644
index 5a251a2c5..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.CZT.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for CZT
-CE false
-HA 3645592918
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.CarbonCyanateEster.rsp b/resource/examples/geomega/materials/Xsection.Total.CarbonCyanateEster.rsp
deleted file mode 100644
index 962c864ba..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.CarbonCyanateEster.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for CarbonCyanateEster
-CE false
-HA 3197857782
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.CdTe.rsp b/resource/examples/geomega/materials/Xsection.Total.CdTe.rsp
deleted file mode 100644
index 820b8ab3e..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.CdTe.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for CdTe
-CE false
-HA 2408428372
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.CircuitBoard.rsp b/resource/examples/geomega/materials/Xsection.Total.CircuitBoard.rsp
deleted file mode 100644
index 9c650b23b..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.CircuitBoard.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for CircuitBoard
-CE false
-HA 790253057
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.Copper.rsp b/resource/examples/geomega/materials/Xsection.Total.Copper.rsp
deleted file mode 100644
index ec12e7062..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.Copper.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for Copper
-CE false
-HA 3193575607
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.CsI.rsp b/resource/examples/geomega/materials/Xsection.Total.CsI.rsp
deleted file mode 100644
index 53b0f8989..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.CsI.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for CsI
-CE false
-HA 3350302246
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.Densimet180.rsp b/resource/examples/geomega/materials/Xsection.Total.Densimet180.rsp
deleted file mode 100644
index 55650d6f8..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.Densimet180.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for Densimet180
-CE false
-HA 2913098225
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.Diamant.rsp b/resource/examples/geomega/materials/Xsection.Total.Diamant.rsp
deleted file mode 100644
index cf6223405..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.Diamant.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for Diamant
-CE false
-HA 289970476
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.GePassive.rsp b/resource/examples/geomega/materials/Xsection.Total.GePassive.rsp
deleted file mode 100644
index 39e7f1c88..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.GePassive.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for GePassive
-CE false
-HA 359300401
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.Germanium.rsp b/resource/examples/geomega/materials/Xsection.Total.Germanium.rsp
deleted file mode 100644
index f18cf0e87..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.Germanium.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for Germanium
-CE false
-HA 359300401
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.Glass.rsp b/resource/examples/geomega/materials/Xsection.Total.Glass.rsp
deleted file mode 100644
index abbb70177..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.Glass.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for Glass
-CE false
-HA 4029087792
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.Indium.rsp b/resource/examples/geomega/materials/Xsection.Total.Indium.rsp
deleted file mode 100644
index 51889fd78..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.Indium.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for Indium
-CE false
-HA 3903719287
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.Iron.rsp b/resource/examples/geomega/materials/Xsection.Total.Iron.rsp
deleted file mode 100644
index ae9c2e149..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.Iron.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for Iron
-CE false
-HA 4094812641
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.LaBr3.rsp b/resource/examples/geomega/materials/Xsection.Total.LaBr3.rsp
deleted file mode 100644
index ef409ec64..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.LaBr3.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for LaBr3
-CE false
-HA 3587683841
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.MLI.rsp b/resource/examples/geomega/materials/Xsection.Total.MLI.rsp
deleted file mode 100644
index f3619927a..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.MLI.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for MLI
-CE false
-HA 1447136272
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.MgS.rsp b/resource/examples/geomega/materials/Xsection.Total.MgS.rsp
deleted file mode 100644
index 787173f35..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.MgS.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for MgS
-CE false
-HA 2183886950
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.Millipore.rsp b/resource/examples/geomega/materials/Xsection.Total.Millipore.rsp
deleted file mode 100644
index 1143fd4b9..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.Millipore.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for Millipore
-CE false
-HA 869331804
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.NE110.rsp b/resource/examples/geomega/materials/Xsection.Total.NE110.rsp
deleted file mode 100644
index 4f1f62728..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.NE110.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for NE110
-CE false
-HA 917272579
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.NE213.rsp b/resource/examples/geomega/materials/Xsection.Total.NE213.rsp
deleted file mode 100644
index a2d0b25f2..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.NE213.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for NE213
-CE false
-HA 2640400524
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.NaI.rsp b/resource/examples/geomega/materials/Xsection.Total.NaI.rsp
deleted file mode 100644
index b3c847db3..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.NaI.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for NaI
-CE false
-HA 1958776091
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.Nylon.rsp b/resource/examples/geomega/materials/Xsection.Total.Nylon.rsp
deleted file mode 100644
index d449300a5..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.Nylon.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for Nylon
-CE false
-HA 3741285600
-
-R1         1.000000 3.036257e+03
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-R1         1.318257 1.423712e+03
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-R1         1.513561 9.674442e+02
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.PCB.rsp b/resource/examples/geomega/materials/Xsection.Total.PCB.rsp
deleted file mode 100644
index 8a518cca6..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.PCB.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for PCB
-CE false
-HA 480612584
-
-R1         1.000000 3.350593e+03
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-R1         1.096478 2.612302e+03
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-R1         1.202264 2.030127e+03
-R1         1.258925 1.788387e+03
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-R1         1.380384 1.385355e+03
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-R1         4.365158 4.840288e+01
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.PMTPlastic.rsp b/resource/examples/geomega/materials/Xsection.Total.PMTPlastic.rsp
deleted file mode 100644
index 018aedfa7..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.PMTPlastic.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for PMTPlastic
-CE false
-HA 1684120221
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.Pb.rsp b/resource/examples/geomega/materials/Xsection.Total.Pb.rsp
deleted file mode 100644
index 6d8a5b88f..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.Pb.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for Pb
-CE false
-HA 2559858824
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.Peek.rsp b/resource/examples/geomega/materials/Xsection.Total.Peek.rsp
deleted file mode 100644
index fed9ea912..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.Peek.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for Peek
-CE false
-HA 3912604896
-
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-R1 100000000.000000 2.423145e-02
-
diff --git a/resource/examples/geomega/materials/Xsection.Total.Plastic_Isolation.rsp b/resource/examples/geomega/materials/Xsection.Total.Plastic_Isolation.rsp
deleted file mode 100644
index 25e6065b4..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.Plastic_Isolation.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for Plastic_Isolation
-CE false
-HA 2914733143
-
-R1         1.000000 3.657731e+03
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.Plywood.rsp b/resource/examples/geomega/materials/Xsection.Total.Plywood.rsp
deleted file mode 100644
index 1c27ad77a..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.Plywood.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for Plywood
-CE false
-HA 2593954094
-
-R1         1.000000 1.675297e+03
-R1         1.047129 1.480333e+03
-R1         1.096478 1.306151e+03
-R1         1.148154 1.151939e+03
-R1         1.202264 1.015064e+03
-R1         1.258925 8.941933e+02
-R1         1.318257 7.871295e+02
-R1         1.380384 6.926773e+02
-R1         1.445440 6.089427e+02
-R1         1.513561 5.353052e+02
-R1         1.584893 4.700456e+02
-R1         1.659587 4.124471e+02
-R1         1.737801 3.618846e+02
-R1         1.819701 3.175343e+02
-R1         1.905461 2.782475e+02
-R1         1.995262 2.436700e+02
-R1         2.089296 2.133897e+02
-R1         2.187762 1.868792e+02
-R1         2.290868 1.634621e+02
-R1         2.398833 1.429006e+02
-R1         2.511886 1.249298e+02
-R1         2.630268 1.092240e+02
-R1         2.754229 9.537658e+01
-R1         2.884032 8.325051e+01
-R1         3.019952 7.267173e+01
-R1         3.162278 6.344170e+01
-R1         3.311311 5.532258e+01
-R1         3.467369 4.822139e+01
-R1         3.630781 4.203593e+01
-R1         3.801894 3.664810e+01
-R1         3.981072 3.192266e+01
-R1         4.168694 2.779549e+01
-R1         4.365158 2.420144e+01
-R1         4.570882 2.107487e+01
-R1         4.786301 1.834328e+01
-R1         5.011872 1.596518e+01
-R1         5.248075 1.388913e+01
-R1         5.495409 1.208592e+01
-R1         5.754399 1.051521e+01
-R1         6.025596 9.147973e+00
-R1         6.309573 7.960042e+00
-R1         6.606934 6.925664e+00
-R1         6.918310 6.028482e+00
-R1         7.244360 5.246067e+00
-R1         7.585776 4.567938e+00
-R1         7.943282 3.979621e+00
-R1         8.317638 3.467854e+00
-R1         8.709636 3.023929e+00
-R1         9.120108 2.637822e+00
-R1         9.549926 2.303561e+00
-R1        10.000000 2.014177e+00
-R1        10.471285 1.762469e+00
-R1        10.964782 1.544298e+00
-R1        11.481536 1.354710e+00
-R1        12.022644 1.190746e+00
-R1        12.589254 1.048826e+00
-R1        13.182567 9.257025e-01
-R1        13.803843 8.190044e-01
-R1        14.454398 7.262846e-01
-R1        15.135612 6.460882e-01
-R1        15.848932 5.766965e-01
-R1        16.595869 5.163760e-01
-R1        17.378008 4.639468e-01
-R1        18.197009 4.183663e-01
-R1        19.054607 3.789020e-01
-R1        19.952623 3.447698e-01
-R1        20.892961 3.149099e-01
-R1        21.877616 2.890422e-01
-R1        22.908677 2.665649e-01
-R1        23.988329 2.469742e-01
-R1        25.118864 2.300119e-01
-R1        26.302680 2.149784e-01
-R1        27.542287 2.019115e-01
-R1        28.840315 1.905470e-01
-R1        30.199517 1.806326e-01
-R1        31.622777 1.719898e-01
-R1        33.113112 1.641977e-01
-R1        34.673685 1.573771e-01
-R1        36.307805 1.513865e-01
-R1        38.018940 1.461380e-01
-R1        39.810717 1.415362e-01
-R1        41.686938 1.372437e-01
-R1        43.651583 1.334237e-01
-R1        45.708819 1.300336e-01
-R1        47.863009 1.270192e-01
-R1        50.118723 1.243256e-01
-R1        52.480746 1.216890e-01
-R1        54.954087 1.193054e-01
-R1        57.543994 1.171426e-01
-R1        60.255959 1.151698e-01
-R1        63.095734 1.133605e-01
-R1        66.069345 1.115025e-01
-R1        69.183097 1.097795e-01
-R1        72.443596 1.081743e-01
-R1        75.857758 1.066699e-01
-R1        79.432823 1.052583e-01
-R1        83.176377 1.037529e-01
-R1        87.096359 1.023242e-01
-R1        91.201084 1.009622e-01
-R1        95.499259 9.966012e-02
-R1       100.000000 9.841333e-02
-R1       104.712855 9.705615e-02
-R1       109.647820 9.574675e-02
-R1       114.815362 9.448003e-02
-R1       120.226443 9.325340e-02
-R1       125.892541 9.206245e-02
-R1       131.825674 9.076013e-02
-R1       138.038426 8.949207e-02
-R1       144.543977 8.825559e-02
-R1       151.356125 8.704859e-02
-R1       158.489319 8.586933e-02
-R1       165.958691 8.459066e-02
-R1       173.780083 8.333936e-02
-R1       181.970086 8.211435e-02
-R1       190.546072 8.091428e-02
-R1       199.526231 7.973790e-02
-R1       208.929613 7.847626e-02
-R1       218.776162 7.723943e-02
-R1       229.086765 7.602646e-02
-R1       239.883292 7.483643e-02
-R1       251.188643 7.366859e-02
-R1       263.026799 7.243245e-02
-R1       275.422870 7.121979e-02
-R1       288.403150 7.002985e-02
-R1       301.995172 6.886200e-02
-R1       316.227766 6.771564e-02
-R1       331.131121 6.651354e-02
-R1       346.736850 6.533437e-02
-R1       363.078055 6.417755e-02
-R1       380.189396 6.304251e-02
-R1       398.107171 6.192873e-02
-R1       416.869383 6.077069e-02
-R1       436.515832 5.963522e-02
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-R1       501.187234 5.635918e-02
-R1       524.807460 5.524948e-02
-R1       549.540874 5.416218e-02
-R1       575.439937 5.309677e-02
-R1       602.559586 5.205278e-02
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-R1       660.693448 4.997346e-02
-R1       691.830971 4.893939e-02
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-R1       912.010839 4.302743e-02
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-R1      1000.000000 4.117465e-02
-R1      1047.128548 4.023120e-02
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-R1      1202.264435 3.753419e-02
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.PressurizedAir.rsp b/resource/examples/geomega/materials/Xsection.Total.PressurizedAir.rsp
deleted file mode 100644
index 785600de7..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.PressurizedAir.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for PressurizedAir
-CE false
-HA 3401473699
-
-R1         1.000000 8.982653e+03
-R1         1.047129 7.943923e+03
-R1         1.096478 7.019299e+03
-R1         1.148154 6.193869e+03
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.Silicon.rsp b/resource/examples/geomega/materials/Xsection.Total.Silicon.rsp
deleted file mode 100644
index c26778d4d..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.Silicon.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for Silicon
-CE false
-HA 3884499373
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.SiliconPIN.rsp b/resource/examples/geomega/materials/Xsection.Total.SiliconPIN.rsp
deleted file mode 100644
index fbfa3e463..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.SiliconPIN.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for SiliconPIN
-CE false
-HA 3884499373
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.Steel.rsp b/resource/examples/geomega/materials/Xsection.Total.Steel.rsp
deleted file mode 100644
index da2e2b36a..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.Steel.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for Steel
-CE false
-HA 619348587
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.Steel_18_8.rsp b/resource/examples/geomega/materials/Xsection.Total.Steel_18_8.rsp
deleted file mode 100644
index f58889c3a..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.Steel_18_8.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for Steel_18_8
-CE false
-HA 1429918153
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.SurroundingSphereVolumeMaterial.rsp b/resource/examples/geomega/materials/Xsection.Total.SurroundingSphereVolumeMaterial.rsp
deleted file mode 100644
index fef664d1e..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.SurroundingSphereVolumeMaterial.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for SurroundingSphereVolumeMaterial
-CE false
-HA 1487652151
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.Tin.rsp b/resource/examples/geomega/materials/Xsection.Total.Tin.rsp
deleted file mode 100644
index 472976724..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.Tin.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for Tin
-CE false
-HA 1304486184
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.Vacuum.rsp b/resource/examples/geomega/materials/Xsection.Total.Vacuum.rsp
deleted file mode 100644
index a7a9d0d65..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.Vacuum.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for Vacuum
-CE false
-HA 3622691594
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.Xenon.rsp b/resource/examples/geomega/materials/Xsection.Total.Xenon.rsp
deleted file mode 100644
index 67348a4ba..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.Xenon.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for Xenon
-CE false
-HA 3026073170
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.XenonLXeGRIT.rsp b/resource/examples/geomega/materials/Xsection.Total.XenonLXeGRIT.rsp
deleted file mode 100644
index 31ca000ac..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.XenonLXeGRIT.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for XenonLXeGRIT
-CE false
-HA 3741687031
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.ro3003.rsp b/resource/examples/geomega/materials/Xsection.Total.ro3003.rsp
deleted file mode 100644
index b8124e462..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.ro3003.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for ro3003
-CE false
-HA 3212075832
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.ro3006.rsp b/resource/examples/geomega/materials/Xsection.Total.ro3006.rsp
deleted file mode 100644
index ab76b377d..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.ro3006.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for ro3006
-CE false
-HA 1294534288
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.ro3010.rsp b/resource/examples/geomega/materials/Xsection.Total.ro3010.rsp
deleted file mode 100644
index 9ac97a52c..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.ro3010.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for ro3010
-CE false
-HA 404016241
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.ro4003.rsp b/resource/examples/geomega/materials/Xsection.Total.ro4003.rsp
deleted file mode 100644
index 9875d04d2..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.ro4003.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for ro4003
-CE false
-HA 3349552005
-
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-
diff --git a/resource/examples/geomega/materials/Xsection.Total.roTMM3.rsp b/resource/examples/geomega/materials/Xsection.Total.roTMM3.rsp
deleted file mode 100644
index 644279393..000000000
--- a/resource/examples/geomega/materials/Xsection.Total.roTMM3.rsp
+++ /dev/null
@@ -1,414 +0,0 @@
-# Macroscopic cross section (total)
-# Derived from Geant4 version 1023
-# X: Energy in keV
-# Y: Macroscopic cross section in 1/cm
-
-Type    ResponseMatrixO1
-Version 1
-
-NM Total cross section for roTMM3
-CE false
-HA 3816565079
-
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-R1    229086.765277 4.250038e-02
-R1    239883.291902 4.267158e-02
-R1    251188.643151 4.284776e-02
-R1    263026.799190 4.302837e-02
-R1    275422.870334 4.321376e-02
-R1    288403.150313 4.340382e-02
-R1    301995.172040 4.359055e-02
-R1    316227.766017 4.373455e-02
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-R1    416869.383470 4.463994e-02
-R1    436515.832240 4.477197e-02
-R1    457088.189615 4.490683e-02
-R1    478630.092323 4.504444e-02
-R1    501187.233627 4.518350e-02
-R1    524807.460250 4.530237e-02
-R1    549540.873858 4.542360e-02
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-R1    602559.586074 4.567060e-02
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-R1    724435.960075 4.609438e-02
-R1    758577.575029 4.620488e-02
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-R1    831763.771103 4.640988e-02
-R1    870963.589956 4.650032e-02
-R1    912010.839356 4.659221e-02
-R1    954992.586021 4.668550e-02
-R1   1000000.000000 4.678016e-02
-R1   1047128.548051 4.685081e-02
-R1   1096478.196143 4.692263e-02
-R1   1148153.621497 4.699558e-02
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-R1   1258925.411794 4.714475e-02
-R1   1318256.738556 4.722083e-02
-R1   1380384.264603 4.729790e-02
-R1   1445439.770746 4.737595e-02
-R1   1513561.248436 4.745025e-02
-R1   1584893.192461 4.750614e-02
-R1   1659586.907438 4.756277e-02
-R1   1737800.828749 4.762018e-02
-R1   1819700.858610 4.767832e-02
-R1   1905460.717963 4.773719e-02
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-R1   2089296.130854 4.784203e-02
-R1   2187761.623950 4.788711e-02
-R1   2290867.652768 4.793279e-02
-R1   2398832.919019 4.797902e-02
-R1   2511886.431510 4.802580e-02
-R1   2630267.991895 4.807308e-02
-R1   2754228.703338 4.812088e-02
-R1   2884031.503127 4.816916e-02
-R1   3019951.720402 4.821605e-02
-R1   3162277.660168 4.825230e-02
-R1   3311311.214826 4.828894e-02
-R1   3467368.504525 4.832597e-02
-R1   3630780.547701 4.836340e-02
-R1   3801893.963206 4.840120e-02
-R1   3981071.705535 4.843937e-02
-R1   4168693.834703 4.846730e-02
-R1   4365158.322402 4.849434e-02
-R1   4570881.896149 4.852169e-02
-R1   4786300.923226 4.854933e-02
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-R1   5248074.602498 4.860547e-02
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-R1   5754399.373372 4.866266e-02
-R1   6025595.860744 4.869075e-02
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-R1   6606934.480076 4.873031e-02
-R1   6918309.709189 4.875040e-02
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-R1   7585775.750292 4.879117e-02
-R1   7943282.347243 4.881184e-02
-R1   8317637.711027 4.883016e-02
-R1   8709635.899561 4.884819e-02
-R1   9120108.393559 4.886639e-02
-R1   9549925.860214 4.888474e-02
-R1  10000000.000000 4.890325e-02
-R1  10471285.480509 4.891494e-02
-R1  10964781.961432 4.892677e-02
-R1  11481536.214969 4.893874e-02
-R1  12022644.346174 4.895082e-02
-R1  12589254.117942 4.896302e-02
-R1  13182567.385564 4.897534e-02
-R1  13803842.646029 4.898776e-02
-R1  14454397.707459 4.900029e-02
-R1  15135612.484362 4.901241e-02
-R1  15848931.924611 4.902253e-02
-R1  16595869.074376 4.903274e-02
-R1  17378008.287494 4.904304e-02
-R1  18197008.586100 4.905342e-02
-R1  19054607.179633 4.906389e-02
-R1  19952623.149689 4.907443e-02
-R1  20892961.308540 4.908327e-02
-R1  21877616.239496 4.909209e-02
-R1  22908676.527678 4.910098e-02
-R1  23988329.190195 4.910994e-02
-R1  25118864.315096 4.911896e-02
-R1  26302679.918954 4.912804e-02
-R1  27542287.033382 4.913717e-02
-R1  28840315.031266 4.914637e-02
-R1  30199517.204020 4.915512e-02
-R1  31622776.601684 4.916095e-02
-R1  33113112.148259 4.916682e-02
-R1  34673685.045253 4.917275e-02
-R1  36307805.477010 4.917872e-02
-R1  38018939.632056 4.918473e-02
-R1  39810717.055350 4.919078e-02
-R1  41686938.347034 4.919315e-02
-R1  43651583.224017 4.919512e-02
-R1  45708818.961488 4.919713e-02
-R1  47863009.232264 4.919918e-02
-R1  50118723.362727 4.920147e-02
-R1  52480746.024977 4.920758e-02
-R1  54954087.385763 4.921373e-02
-R1  57543993.733716 4.921991e-02
-R1  60255958.607436 4.922567e-02
-R1  63095734.448019 4.922704e-02
-R1  66069344.800760 4.922843e-02
-R1  69183097.091894 4.922984e-02
-R1  72443596.007499 4.923128e-02
-R1  75857757.502919 4.923275e-02
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-R1  83176377.110267 4.923851e-02
-R1  87096358.995608 4.924331e-02
-R1  91201083.935591 4.924813e-02
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-R1 100000000.000000 4.925784e-02
-

From 2e5e542eb78174b1e3ea5dee8ec42ff963c32d77 Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Fri, 9 May 2025 10:31:35 -0400
Subject: [PATCH 160/192] CHG: Ignore a few more executables

---
 .gitignore                              | 12 ++++++++++++
 src/global/misc/inc/MResponseMatrixO1.h |  8 ++++----
 2 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/.gitignore b/.gitignore
index 40e4e6051..f685fbff0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,6 +10,17 @@ bin/realta
 bin/revan
 bin/sivan
 bin/spectralyze
+bin/AspectOptimizerStep1
+bin/CompareHistograms
+bin/DistanceOptimizerForEventClusterizer
+bin/SimBinaryConverter
+bin/TH1_summer_cpp
+bin/ThresholdCalculation
+bin/TraMerger
+bin/UTARMFitter
+bin/UTCosimaInputSpectra
+bin/photopeak_depth_distribution
+bin/xyscanner
 
 BackgroundMixer
 ConvertACTtools
@@ -75,6 +86,7 @@ configure_lastgoodoptions
 source-megalib.sh
 SetupOptions.txt
 new-source-megalib.sh
+config/Configuration.txt
 
 # doc directory:
 Peoples.txt
diff --git a/src/global/misc/inc/MResponseMatrixO1.h b/src/global/misc/inc/MResponseMatrixO1.h
index 580ce8bd7..4510c4748 100644
--- a/src/global/misc/inc/MResponseMatrixO1.h
+++ b/src/global/misc/inc/MResponseMatrixO1.h
@@ -60,10 +60,10 @@ class MResponseMatrixO1 : public MResponseMatrixOx
 
   void Init();
 
-  bool operator==(const MResponseMatrixO1& ResponseMatrixO1);  
-  MResponseMatrixO1& operator+=(const MResponseMatrixO1& ResponseMatrixO1);  
-  MResponseMatrixO1& operator-=(const MResponseMatrixO1& ResponseMatrixO1);  
-  MResponseMatrixO1& operator/=(const MResponseMatrixO1& ResponseMatrixO1);  
+  bool operator==(const MResponseMatrixO1& ResponseMatrixO1);
+  MResponseMatrixO1& operator+=(const MResponseMatrixO1& ResponseMatrixO1);
+  MResponseMatrixO1& operator-=(const MResponseMatrixO1& ResponseMatrixO1);
+  MResponseMatrixO1& operator/=(const MResponseMatrixO1& ResponseMatrixO1);
 
   MResponseMatrixO1& operator+=(const float& Value);  
   MResponseMatrixO1& operator*=(const float& Value);  

From 629fa7bf8dd8829546f5b2bae811211ca5468c35 Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Fri, 9 May 2025 13:24:41 -0400
Subject: [PATCH 161/192] CHG: Minor code clean-ups

---
 src/mimrec/src/MEventSelector.cxx   | 5 -----
 src/mimrec/src/MInterfaceMimrec.cxx | 1 -
 src/revan/Makefile                  | 1 -
 3 files changed, 7 deletions(-)

diff --git a/src/mimrec/src/MEventSelector.cxx b/src/mimrec/src/MEventSelector.cxx
index 59613f3fb..5e6709cb9 100644
--- a/src/mimrec/src/MEventSelector.cxx
+++ b/src/mimrec/src/MEventSelector.cxx
@@ -1621,17 +1621,12 @@ void MEventSelector::SetTimeFile(MString TimeFile)
 
   m_TimeGTI.Reset(true);
 
-//<<<<<<< HEAD
   if (m_TimeMode == 2) {  
     if (MFile::Exists(m_TimeFile) == true) {
       if (m_TimeGTI.Load(m_TimeFile) == false) {
         cout<<"Error: Unable to load GTI file! Using all open one!"<<endl;
       }
     } else {
-//=======
-//  if (MFile::Exists(m_TimeFile) == true) {
-//    if (m_TimeGTI.Load(m_TimeFile) == false) {
-//>>>>>>> 683f76f6 (Pair dev (#2))
       cout<<"Error: Unable to load GTI file! Using all open one!"<<endl;
     }
   }
diff --git a/src/mimrec/src/MInterfaceMimrec.cxx b/src/mimrec/src/MInterfaceMimrec.cxx
index 0aab0aa16..0ac8d6508 100644
--- a/src/mimrec/src/MInterfaceMimrec.cxx
+++ b/src/mimrec/src/MInterfaceMimrec.cxx
@@ -5387,7 +5387,6 @@ void MInterfaceMimrec::Polarization()
 
         if (fabs(PairEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem()))*c_Deg < ArmCut) {
           /*
-        if (fabs(PairEvent->GetARMGamma(Origin, m_Settings->GetCoordinateSystem()))*c_Deg < ArmCut) {
           MVector Plain = PairEvent->GetElectronDirection() + PairEvent->GetPositronDirection();
           Plain.RotateZ(-Phi);
           Plain.RotateY(-Theta);
diff --git a/src/revan/Makefile b/src/revan/Makefile
index 2ef84eb01..1e679ec43 100644
--- a/src/revan/Makefile
+++ b/src/revan/Makefile
@@ -12,7 +12,6 @@
 # Base definitions:
 #
 
-
 PROGRAM := revan
 
 MAIN  := MRevanMain

From aa02b49d80cd27ec0838baceb22f5fc6eab4d18b Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Tue, 27 May 2025 16:25:48 -0400
Subject: [PATCH 162/192] CHG: UI only, set Kalman as electron tracking and add
 external event id (for future python-based NN)

---
 src/revan/inc/MGUIERAlgorithm.h               |  1 +
 src/revan/inc/MRawEventAnalyzer.h             | 43 +++++++++----
 src/revan/inc/MSettingsEventReconstruction.h  |  4 ++
 src/revan/src/MGUIERAlgorithm.cxx             | 60 ++++++++++++-------
 src/revan/src/MInterfaceRevan.cxx             |  6 +-
 src/revan/src/MRawEventAnalyzer.cxx           | 55 +++++++++++------
 .../src/MSettingsEventReconstruction.cxx      |  9 ++-
 7 files changed, 124 insertions(+), 54 deletions(-)

diff --git a/src/revan/inc/MGUIERAlgorithm.h b/src/revan/inc/MGUIERAlgorithm.h
index 87db721f8..e69b91a95 100644
--- a/src/revan/inc/MGUIERAlgorithm.h
+++ b/src/revan/inc/MGUIERAlgorithm.h
@@ -60,6 +60,7 @@ class MGUIERAlgorithm : public MGUIDialog
   MGUIERBList* m_CoincidenceList;
   MGUIERBList* m_EventClusteringList;
   MGUIERBList* m_HitClusteringList;
+  MGUIERBList* m_EventIdList;
   MGUIERBList* m_TrackingList;
   MGUIERBList* m_CSRList;
   MGUIERBList* m_PairList;
diff --git a/src/revan/inc/MRawEventAnalyzer.h b/src/revan/inc/MRawEventAnalyzer.h
index aa2b70733..2f407cf11 100644
--- a/src/revan/inc/MRawEventAnalyzer.h
+++ b/src/revan/inc/MRawEventAnalyzer.h
@@ -162,22 +162,44 @@ class MRawEventAnalyzer
   //! Set the clustering algorithm: One of c_ClusteringAlgoNone, c_ClusteringAlgoDistance, c_ClusteringAlgoAdjacent;
   void SetHitClusteringAlgorithm(int ID) { m_HitClusteringAlgorithm = ID; }
 
-  static const int c_TrackingAlgoNone;
-  static const int c_TrackingAlgoModifiedPearson;
-  static const int c_TrackingAlgoPearson;
-  static const int c_TrackingAlgoChiSquare;
-  static const int c_TrackingAlgoGas;
-  static const int c_TrackingAlgoDirectional;
-  static const int c_TrackingAlgoBayesian;
-  static const int c_TrackingAlgoRank;
+  enum c_EventIdAlgo {
+    c_EventIdDefault, c_EventIdExternal
+  };
+  //! Set the Event tyep identification algorithm
+  void SetEventIdAlgorithm(int ID) { m_EventIdAlgorithm = ID; }
+
+
+//  static const int c_TrackingAlgoNone;
+//  static const int c_TrackingAlgoModifiedPearson;
+//  static const int c_TrackingAlgoPearson;
+//  static const int c_TrackingAlgoChiSquare;
+//  static const int c_TrackingAlgoGas;
+//  static const int c_TrackingAlgoDirectional;
+//  static const int c_TrackingAlgoBayesian;
+//  static const int c_TrackingAlgoRank;
+//  static const int c_PairKalman3D;
+//  static const int c_PairKalman2D;
+// static const int c_Trackingfirstlayers --
+
+  enum c_TrackingAlgo {
+    c_TrackingAlgoNone,
+    c_TrackingAlgoModifiedPearson,
+    c_TrackingAlgoChiSquare,
+    c_TrackingAlgoGas,
+    c_TrackingAlgoDirectional,
+    c_TrackingAlgoBayesian,
+    c_TrackingAlgoRank,
+    c_TrackingAlgoPearson,
+    c_TrackingAlgoKalman2D,
+    c_TrackingAlgoKalman3D,
+    c_TrackingAlgoFirstLayer
+  };
 
   //! Set the electron tracking algorithm: One of c_TrackingAlgoNone, c_TrackingAlgoModifiedPearson, c_TrackingAlgoPearson,
   //! c_TrackingAlgoChiSquare, c_TrackingAlgoGas, c_TrackingAlgoDirectional, c_TrackingAlgoBayesian, c_TrackingAlgoRank
   void SetTrackingAlgorithm(int ID) { m_TrackingAlgorithm = ID; }
 
   static const int c_PairDefault;
-  static const int c_PairKalman3D;
-  static const int c_PairKalman2D;
 
   //! Set the pair reconstruction algorithm: One of c_PairDefault, c_PairKalman3D or c_PairKalman2D
   void SetPairAlgorithm(int ID) { m_PairAlgorithm = ID; }
@@ -392,6 +414,7 @@ class MRawEventAnalyzer
   int m_CoincidenceAlgorithm;
   int m_EventClusteringAlgorithm;
   int m_HitClusteringAlgorithm;
+  int m_EventIdAlgorithm;
   int m_TrackingAlgorithm;
   int m_PairAlgorithm;
   int m_CSRAlgorithm;
diff --git a/src/revan/inc/MSettingsEventReconstruction.h b/src/revan/inc/MSettingsEventReconstruction.h
index 3496966ad..07889e1a9 100644
--- a/src/revan/inc/MSettingsEventReconstruction.h
+++ b/src/revan/inc/MSettingsEventReconstruction.h
@@ -50,6 +50,9 @@ class MSettingsEventReconstruction : public MSettingsInterface
   
   void SetHitClusteringAlgorithm(int ID) { m_HitClusteringAlgorithm = ID; }
   int GetHitClusteringAlgorithm() { return m_HitClusteringAlgorithm; }
+
+  void SetEventIdAlgorithm(int ID) {m_EventIdAlgorithm = ID; }
+  int GetEventIdAlgorithm() { return m_EventIdAlgorithm; }
   
   void SetTrackingAlgorithm(int ID) { m_TrackingAlgorithm = ID; }
   int GetTrackingAlgorithm() { return m_TrackingAlgorithm; }
@@ -294,6 +297,7 @@ class MSettingsEventReconstruction : public MSettingsInterface
   int m_CoincidenceAlgorithm;
   int m_EventClusteringAlgorithm;
   int m_HitClusteringAlgorithm;
+  int m_EventIdAlgorithm;
   int m_TrackingAlgorithm;
   int m_PairAlgorithm;
   int m_CSRAlgorithm;
diff --git a/src/revan/src/MGUIERAlgorithm.cxx b/src/revan/src/MGUIERAlgorithm.cxx
index c4173b070..dd2d0b3f3 100644
--- a/src/revan/src/MGUIERAlgorithm.cxx
+++ b/src/revan/src/MGUIERAlgorithm.cxx
@@ -86,6 +86,7 @@ void MGUIERAlgorithm::Create()
 
   m_ListLayout = new TGLayoutHints(kLHintsExpandX | kLHintsTop, 20, 20, 10, 10);
 
+  // Coincidence search
   m_CoincidenceList = new MGUIERBList(this, "Coincidence search", true);
   m_CoincidenceList->Add("No coincidence or coincident hits already merged in simulation or hardware (DEFAULT)");
   m_CoincidenceList->Add("Coincidence window");
@@ -93,6 +94,7 @@ void MGUIERAlgorithm::Create()
   m_CoincidenceList->Create();
   AddFrame(m_CoincidenceList, m_ListLayout);
   
+  // Event clustering
   m_EventClusteringList = new MGUIERBList(this, "Find multiple, coincident gamma rays in one event", true);
   m_EventClusteringList->Add("No event clustering (DEFAULT - unless you have the very rare case of pile up)");
   m_EventClusteringList->Add("Event clustering using using interaction distances (alpha)");
@@ -109,6 +111,7 @@ void MGUIERAlgorithm::Create()
   m_EventClusteringList->Create();
   AddFrame(m_EventClusteringList, m_ListLayout);
   
+  // Hit clustering
   m_HitClusteringList = new MGUIERBList(this, "Clustering of neighboring hits", true);
   m_HitClusteringList->Add("No clustering");
   m_HitClusteringList->Add("Clustering by Distance");
@@ -117,7 +120,16 @@ void MGUIERAlgorithm::Create()
   m_HitClusteringList->SetSelected(m_Data->GetHitClusteringAlgorithm());
   m_HitClusteringList->Create();
   AddFrame(m_HitClusteringList, m_ListLayout);
-
+  
+  // Event identification
+  m_EventIdList = new MGUIERBList(this, "Event type identification", true);
+  m_EventIdList->Add("Default algorithm"); // 0
+  m_EventIdList->Add("External from file (not implemented)"); // 1
+  m_EventIdList->SetSelected(m_Data->GetEventIdAlgorithm());
+  m_EventIdList->Create();
+  AddFrame(m_EventIdList, m_ListLayout);
+
+  // Electron tracking
   m_TrackingList = new MGUIERBList(this, "Electron tracking", true);
   m_TrackingList->Add("No electron tracking"); // 0
   m_TrackingList->Add("Modified Pearson correlation (Figure-of-merit approach)"); // 1
@@ -127,32 +139,36 @@ void MGUIERAlgorithm::Create()
   m_TrackingList->Add("Tracking in gas detector (Figure-of-merit approach)"); // 5
   m_TrackingList->Add("Tracking in direction sensitive strip detector (Figure-of-merit approach)"); // 6
   m_TrackingList->Add("Bayesian electron tracking (Bayesian model selection)"); // 7
-  if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoNone) {
-    m_TrackingList->SetSelected(0);
-  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoModifiedPearson) {
-    m_TrackingList->SetSelected(1);
-  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoPearson) {
-    m_TrackingList->SetSelected(2);
-  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoRank) {
-    m_TrackingList->SetSelected(3);
-  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoChiSquare) {
-    m_TrackingList->SetSelected(4);
-  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoGas) {
-    m_TrackingList->SetSelected(5);
-  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoDirectional) {
-    m_TrackingList->SetSelected(6);
-  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoBayesian) {
-    m_TrackingList->SetSelected(7);
-  } else {
-    m_TrackingList->SetSelected(0);
-  }
+  m_TrackingList->Add("Kalman Filter 2D (work in progress)"); // 8
+  m_TrackingList->Add("Kalman Filter 3D (work in progress)"); // 9
+  m_TrackingList->Add("First two layers (to be implemented)"); // 10
+  m_TrackingList->SetSelected(m_Data->GetTrackingAlgorithm());
+//  if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoNone) {
+//    m_TrackingList->SetSelected(0);
+//  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoModifiedPearson) {
+//    m_TrackingList->SetSelected(1);
+//  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoPearson) {
+//    m_TrackingList->SetSelected(2);
+//  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoRank) {
+//    m_TrackingList->SetSelected(3);
+//  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoChiSquare) {
+//    m_TrackingList->SetSelected(4);
+//  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoGas) {
+//    m_TrackingList->SetSelected(5);
+//  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoDirectional) {
+//    m_TrackingList->SetSelected(6);
+//  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoBayesian) {
+//    m_TrackingList->SetSelected(7);
+//  } else {
+//    m_TrackingList->SetSelected(0);
+//  }
   m_TrackingList->Create();
   AddFrame(m_TrackingList, m_ListLayout);
 
   m_PairList = new MGUIERBList(this, "Pair reconstruction", true);
   m_PairList->Add("Default algorithm");  // 0
-  m_PairList->Add("Kalman Filter 3D (work in progress)"); // 1
-  m_PairList->Add("Kalman Filter 2D (work in progress)"); // 2
+  //m_PairList->Add("Kalman Filter 3D (work in progress)"); // 1
+  //m_PairList->Add("Kalman Filter 2D (work in progress)"); // 2
   m_PairList->SetSelected(m_Data->GetPairAlgorithm());
   m_PairList->Create();
   AddFrame(m_PairList, m_ListLayout);
diff --git a/src/revan/src/MInterfaceRevan.cxx b/src/revan/src/MInterfaceRevan.cxx
index 040537cbb..23edc66f2 100644
--- a/src/revan/src/MInterfaceRevan.cxx
+++ b/src/revan/src/MInterfaceRevan.cxx
@@ -1597,7 +1597,7 @@ void MInterfaceRevan::DetectorTypeClusterDistribution(bool Before)
   SetGuiData(Analyzer);
   if (Before == true) {
     Analyzer.SetTrackingAlgorithm(MRawEventAnalyzer::c_TrackingAlgoNone);
-    Analyzer.SetPairAlgorithm(MRawEventAnalyzer::c_PairKalman2D);
+    Analyzer.SetPairAlgorithm(MRawEventAnalyzer::c_PairDefault);
     Analyzer.SetCSRAlgorithm(MRawEventAnalyzer::c_CSRAlgoNone);
     Analyzer.SetDecayAlgorithm(MRawEventAnalyzer::c_DecayAlgoNone);
   }
@@ -1718,7 +1718,7 @@ void MInterfaceRevan::DetectorTypeHitDistribution(bool Before)
   SetGuiData(Analyzer);
   if (Before == true) {
     Analyzer.SetTrackingAlgorithm(MRawEventAnalyzer::c_TrackingAlgoNone);
-    Analyzer.SetPairAlgorithm(MRawEventAnalyzer::c_PairKalman2D);
+    Analyzer.SetPairAlgorithm(MRawEventAnalyzer::c_PairDefault);
     Analyzer.SetCSRAlgorithm(MRawEventAnalyzer::c_CSRAlgoNone);
     Analyzer.SetDecayAlgorithm(MRawEventAnalyzer::c_DecayAlgoNone);
   }
@@ -2796,7 +2796,7 @@ void MInterfaceRevan::NumberOfClusters()
   if (Analyzer.SetInputModeFile(m_Data->GetCurrentFileName()) == false) return;
   SetGuiData(Analyzer);
   Analyzer.SetTrackingAlgorithm(MRawEventAnalyzer::c_TrackingAlgoNone);
-  Analyzer.SetPairAlgorithm(MRawEventAnalyzer::c_PairKalman2D);
+  Analyzer.SetPairAlgorithm(MRawEventAnalyzer::c_PairDefault);
   Analyzer.SetCSRAlgorithm(MRawEventAnalyzer::c_CSRAlgoNone);
   Analyzer.SetDecayAlgorithm(MRawEventAnalyzer::c_DecayAlgoNone);
 
diff --git a/src/revan/src/MRawEventAnalyzer.cxx b/src/revan/src/MRawEventAnalyzer.cxx
index f8720497f..3d677dec0 100644
--- a/src/revan/src/MRawEventAnalyzer.cxx
+++ b/src/revan/src/MRawEventAnalyzer.cxx
@@ -94,18 +94,39 @@ const int MRawEventAnalyzer::c_HitClusteringAlgoDistance = 1;
 const int MRawEventAnalyzer::c_HitClusteringAlgoAdjacent = 2;
 const int MRawEventAnalyzer::c_HitClusteringAlgoPDF      = 3;
 
-const int MRawEventAnalyzer::c_TrackingAlgoNone            = 0;
-const int MRawEventAnalyzer::c_TrackingAlgoModifiedPearson = 1;
-const int MRawEventAnalyzer::c_TrackingAlgoChiSquare       = 2;
-const int MRawEventAnalyzer::c_TrackingAlgoGas             = 3;
-const int MRawEventAnalyzer::c_TrackingAlgoDirectional     = 4;
-const int MRawEventAnalyzer::c_TrackingAlgoBayesian        = 5;
-const int MRawEventAnalyzer::c_TrackingAlgoRank            = 6;
-const int MRawEventAnalyzer::c_TrackingAlgoPearson         = 7;
+//const int MRawEventAnalyzer::c_TrackingAlgoNone            = 0;
+//const int MRawEventAnalyzer::c_TrackingAlgoModifiedPearson = 1;
+//const int MRawEventAnalyzer::c_TrackingAlgoChiSquare       = 2;
+//const int MRawEventAnalyzer::c_TrackingAlgoGas             = 3;
+//const int MRawEventAnalyzer::c_TrackingAlgoDirectional     = 4;
+//const int MRawEventAnalyzer::c_TrackingAlgoBayesian        = 5;
+//const int MRawEventAnalyzer::c_TrackingAlgoRank            = 6;
+//const int MRawEventAnalyzer::c_TrackingAlgoPearson         = 7;
+
+//namespace MRawEventAnalyzer {
+//Push the "do not change the numbers" constraint to the compiler with enum
+//  enum MRawEventAnalyzer::c_TrackingAlgo { // Also pushed to the header file.
+//    c_TrackingAlgoNone,
+//    c_TrackingAlgoModifiedPearson,
+//    c_TrackingAlgoChiSquare,
+//    c_TrackingAlgoGas,
+//    c_TrackingAlgoDirectional,
+//    c_TrackingAlgoBayesian,
+//    c_TrackingAlgoRank,
+//    c_TrackingAlgoPearson,
+//    c_TrackingAlgoKalman2D,
+//    c_TrackingAlgoKalman3D,
+//    c_TrackingAlgoFirstLayer
+//  };
+
+//  enum c_EventIdAlgo {
+//    c_EventIdDefault, c_EventIdExternal
+//  };
+//}
 
 const int MRawEventAnalyzer::c_PairDefault   = 0;
-const int MRawEventAnalyzer::c_PairKalman3D = 1;
-const int MRawEventAnalyzer::c_PairKalman2D = 2;
+//const int MRawEventAnalyzer::c_PairKalman3D = 1;
+//const int MRawEventAnalyzer::c_PairKalman2D = 2;
 
 const int MRawEventAnalyzer::c_CSRAlgoNone          = 0;
 const int MRawEventAnalyzer::c_CSRAlgoFoM           = 1;
@@ -1347,6 +1368,12 @@ bool MRawEventAnalyzer::PreAnalysis()
           SetSpecialParameters(m_BETFileName) == false) {
         Return = false;
       }
+    } else if (m_TrackingAlgorithm == c_TrackingAlgoKalman3D) {
+      m_Tracker = new MERTrackKalman3D();
+      dynamic_cast<MERTrackKalman3D*>(m_Tracker)->SetSpecialParameters(m_SigmaHitPos, m_NLayersForVertexSearch);
+    } else if (m_TrackingAlgorithm == c_TrackingAlgoKalman2D) {
+      m_Tracker = new MERTrackKalman2D();
+      dynamic_cast<MERTrackKalman2D*>(m_Tracker)->SetSpecialParameters(m_SigmaHitPos, m_NLayersForVertexSearch);
     } else if (m_TrackingAlgorithm == c_TrackingAlgoNone) {
       // Nothing
     } else {
@@ -1355,13 +1382,7 @@ bool MRawEventAnalyzer::PreAnalysis()
     }
 
     // Pair Algorithm
-    if (m_PairAlgorithm == c_PairKalman3D) {
-      m_Tracker = new MERTrackKalman3D();
-      dynamic_cast<MERTrackKalman3D*>(m_Tracker)->SetSpecialParameters(m_SigmaHitPos, m_NLayersForVertexSearch);
-    } else if (m_PairAlgorithm == c_PairKalman2D) {
-      m_Tracker = new MERTrackKalman2D();
-      dynamic_cast<MERTrackKalman2D*>(m_Tracker)->SetSpecialParameters(m_SigmaHitPos, m_NLayersForVertexSearch);
-    }else if (m_PairAlgorithm == c_PairDefault) {
+    if (m_PairAlgorithm == c_PairDefault) {
       m_Tracker = new MERTrack();
     } else {
       Return = false;
diff --git a/src/revan/src/MSettingsEventReconstruction.cxx b/src/revan/src/MSettingsEventReconstruction.cxx
index c5305d62d..45401c57c 100644
--- a/src/revan/src/MSettingsEventReconstruction.cxx
+++ b/src/revan/src/MSettingsEventReconstruction.cxx
@@ -50,6 +50,7 @@ MSettingsEventReconstruction::MSettingsEventReconstruction() : MSettingsInterfac
   m_CoincidenceAlgorithm = 0;
   m_EventClusteringAlgorithm = 0;
   m_HitClusteringAlgorithm = 1;
+  m_EventIdAlgorithm = 0;
   m_TrackingAlgorithm = 0;
   m_PairAlgorithm = 0;
   m_CSRAlgorithm = 1;
@@ -161,6 +162,7 @@ bool MSettingsEventReconstruction::WriteXml(MXmlNode* Node)
   new MXmlNode(Node, "CoincidenceAlgorithm", m_CoincidenceAlgorithm);
   new MXmlNode(Node, "EventClusteringAlgorithm", m_EventClusteringAlgorithm);
   new MXmlNode(Node, "HitClusteringAlgorithm", m_HitClusteringAlgorithm);
+  new MXmlNode(Node, "EventIdAlgorithm", m_EventIdAlgorithm);
   new MXmlNode(Node, "TrackingAlgorithm", m_TrackingAlgorithm);
   new MXmlNode(Node, "PairAlgorithm", m_PairAlgorithm);
   new MXmlNode(Node, "CSRAlgorithm", m_CSRAlgorithm);
@@ -255,8 +257,11 @@ bool MSettingsEventReconstruction::ReadXml(MXmlNode* Node)
   if ((aNode = Node->GetNode("HitClusteringAlgorithm")) != 0) {
     m_HitClusteringAlgorithm = aNode->GetValueAsInt();
   }
-  if ((aNode = Node->GetNode("ClusteringAlgorithm")) != 0) {  // TODO: Delete in 2020
-    m_HitClusteringAlgorithm = aNode->GetValueAsInt();
+//  if ((aNode = Node->GetNode("ClusteringAlgorithm")) != 0) {  // TODO: Delete in 2020
+//    m_HitClusteringAlgorithm = aNode->GetValueAsInt();
+//  }
+  if ((aNode = Node->GetNode("EventIdAlgorithm")) != 0) {
+    m_EventIdAlgorithm = aNode->GetValueAsInt();
   }
   if ((aNode = Node->GetNode("TrackingAlgorithm")) != 0) {
     m_TrackingAlgorithm = aNode->GetValueAsInt();

From ec36343fd5fa0986d6297f0ecb5bde3cf29433c0 Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Fri, 30 May 2025 13:34:37 -0400
Subject: [PATCH 163/192] CHG: Add vim temp *.swp files to gitignore

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index f685fbff0..3d1245a09 100644
--- a/.gitignore
+++ b/.gitignore
@@ -114,4 +114,5 @@ External
 callgrind.*
 *.rsp
 *.erm
+*.swp
 

From 04cb0e529d2e9ca5fe2b51bb3c443cd0fa6a0956 Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Fri, 30 May 2025 13:37:10 -0400
Subject: [PATCH 164/192] CHG: Minor typos and spurious indents

---
 src/revan/src/MERTrack.cxx          |   3 +-
 src/revan/src/MERTrackKalman2D.cxx  | 946 ++++++++++++++--------------
 src/revan/src/MRawEventAnalyzer.cxx |  12 +-
 3 files changed, 481 insertions(+), 480 deletions(-)

diff --git a/src/revan/src/MERTrack.cxx b/src/revan/src/MERTrack.cxx
index bad18e75d..2f920ae81 100644
--- a/src/revan/src/MERTrack.cxx
+++ b/src/revan/src/MERTrack.cxx
@@ -322,7 +322,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
 
     Timer.Start();
     // Generate a list of possible Compton tracks -
-    // we only want to have sequences now and do not yet care aboput directions!
+    // we only want to have sequences now and do not yet care about directions!
     int e_max = m_List->GetNRawEvents();
     for (int e = 0; e < e_max; e++) {
       RE = m_List->GetRawEventAt(e);
@@ -596,6 +596,7 @@ MRawEventIncarnations* MERTrack::CheckForPair(MRERawEvent* RE)
       mdebug<<"Vertex statistics (max: "<<SearchRange<<"): layers used: "<<StopIndex<<", start of 2+ hits: "<<StartIndex<<"  layers with 2+ hits between start and stop: "<<LayersWithAtLeastTwoHitsBetweenStartAndStop<<" ("<<((StopIndex-StartIndex > 0) ? 100.0*LayersWithAtLeastTwoHitsBetweenStartAndStop/(StopIndex-StartIndex) : 0)<<"%)"<<endl;
 
       if (LayersWithAtLeastTwoHitsBetweenStartAndStop > 4 && double (LayersWithAtLeastTwoHitsBetweenStartAndStop)/(StopIndex-StartIndex) > 0.5) {
+        // A.L. Why require that at least half the layers should have two hits?
         Vertex = (*Iterator1);
         VertexDirection = -1;
       }
diff --git a/src/revan/src/MERTrackKalman2D.cxx b/src/revan/src/MERTrackKalman2D.cxx
index d984fd90c..c0219058f 100644
--- a/src/revan/src/MERTrackKalman2D.cxx
+++ b/src/revan/src/MERTrackKalman2D.cxx
@@ -77,639 +77,639 @@ MERTrackKalman2D::MERTrackKalman2D() : MERTrack()
 
 
 bool MERTrackKalman2D::SetSpecialParameters(double SigmaHitPos, unsigned int NLayersForVertexSearch)
-  {
-    m_NLayersForVertexSearch = NLayersForVertexSearch;
-    m_sigma = SigmaHitPos;
-
-    if (m_NLayersForVertexSearch < 4) {
-      merr<<"Error: Revan (tracking): NLayersForVertexSearch (="<<m_NLayersForVertexSearch<<") must be >= 4. Setting it to 4."<<show;
-      m_NLayersForVertexSearch = 4;
-    }
+{
+  m_NLayersForVertexSearch = NLayersForVertexSearch;
+  m_sigma = SigmaHitPos;
 
-    return true;
+  if (m_NLayersForVertexSearch < 4) {
+    merr<<"Error: Revan (tracking): NLayersForVertexSearch (="<<m_NLayersForVertexSearch<<") must be >= 4. Setting it to 4."<<show;
+    m_NLayersForVertexSearch = 4;
   }
 
+  return true;
+}
 
-  ////////////////////////////////////////////////////////////////////////////////
 
+////////////////////////////////////////////////////////////////////////////////
 
-  MERTrackKalman2D::~MERTrackKalman2D()
-  {
-    // Delete this instance of MERTrackKalman2D
-  }
 
+MERTrackKalman2D::~MERTrackKalman2D()
+{
+  // Delete this instance of MERTrackKalman2D
+}
 
-  ////////////////////////////////////////////////////////////////////////////////
 
+////////////////////////////////////////////////////////////////////////////////
 
-  /*bool MERTrackKalman2D::EvaluateTracks(MRERawEvent* RE)
-  {
-    // Evaluate the given tracks...
 
-    if (RE->GetVertex() != 0) {
-      return EvaluatePairs(RE);
-    }
+/*bool MERTrackKalman2D::EvaluateTracks(MRERawEvent* RE)
+{
+  // Evaluate the given tracks...
 
-    // Mark: Add you evaluations here:
-    mout<<"MRawEventIncarnationList* MERTrackKalman2D::EvaluateTracks(MRERawEvent* ER): nyi!"<<endl;
-    //return MERTrack::EvaluateTracks(RE);
+  if (RE->GetVertex() != 0) {
+    return EvaluatePairs(RE);
+  }
 
-    // Store your results:
-    RE->SetTrackQualityFactor(MRERawEvent::c_NoQualityFactor);
-    RE->SetPairQualityFactor(MRERawEvent::c_NoQualityFactor);
+  // Mark: Add you evaluations here:
+  mout<<"MRawEventIncarnationList* MERTrackKalman2D::EvaluateTracks(MRERawEvent* ER): nyi!"<<endl;
+  //return MERTrack::EvaluateTracks(RE);
 
-    return true;
-  }*/
+  // Store your results:
+  RE->SetTrackQualityFactor(MRERawEvent::c_NoQualityFactor);
+  RE->SetPairQualityFactor(MRERawEvent::c_NoQualityFactor);
 
+  return true;
+}*/
 
-  ////////////////////////////////////////////////////////////////////////////////
 
+////////////////////////////////////////////////////////////////////////////////
 
-  MString MERTrackKalman2D::ToString(bool CoreOnly) const
-  {
-    // Dump an options string gor the tra file:
 
-    ostringstream out;
+MString MERTrackKalman2D::ToString(bool CoreOnly) const
+{
+  // Dump an options string gor the tra file:
 
-    if (CoreOnly == false) {
-      out<<"# Tracking - Kalman options:"<<endl;
-      out<<"# "<<endl;
-    }
-    out<<MERTrack::ToString(true);
-    if (CoreOnly == false) {
-      out<<"# "<<endl;
-    }
+  ostringstream out;
 
-    return out.str().c_str();
+  if (CoreOnly == false) {
+    out<<"# Tracking - Kalman options:"<<endl;
+    out<<"# "<<endl;
+  }
+  out<<MERTrack::ToString(true);
+  if (CoreOnly == false) {
+    out<<"# "<<endl;
   }
 
-  ////////////////////////////////////////////////////////////////////////////////
-
-  Float_t MERTrackKalman2D::Kalman(MRERawEvent* RE, Int_t n, Float_t en, MRESEList Previous, vector < TMatrix > &trk, Int_t view, MRESEList &Chosen)
-  {
-    vector < TMatrix > Ck;
-    vector < TMatrix > Csmoothk;
-    vector < TMatrix > Fk;
-    vector < TMatrix > FTk;
-    vector < TMatrix > Cprojk;
-    vector < TMatrix > CprojInvk;
-    vector < TMatrix > Qk;
-    vector < TMatrix > xk;
-    vector < TMatrix > xprojk;
-    vector < TMatrix > xsmoothk;
-
-    Float_t _planedistance = 0.;
-    Float_t m = 1000.;
-
-    TMatrix C(2,2);
-    TMatrix C_proj(2,2);
-    Cprojk.push_back(C_proj);
-    CprojInvk.push_back(C_proj);
-    TMatrix F(2,2);
-    TMatrix Q(2,2);
+  return out.str().c_str();
+}
 
-    Chosen.RemoveAllRESEs();
-    Chosen.Compress();
+////////////////////////////////////////////////////////////////////////////////
 
-    Float_t chi2 = 0.;
-    MRESE vertex = RE->GetVertex();
-    Chosen.AddRESE(RE->GetVertex());
+Float_t MERTrackKalman2D::Kalman(MRERawEvent* RE, Int_t n, Float_t en, MRESEList Previous, vector < TMatrix > &trk, Int_t view, MRESEList &Chosen)
+{
+  vector < TMatrix > Ck;
+  vector < TMatrix > Csmoothk;
+  vector < TMatrix > Fk;
+  vector < TMatrix > FTk;
+  vector < TMatrix > Cprojk;
+  vector < TMatrix > CprojInvk;
+  vector < TMatrix > Qk;
+  vector < TMatrix > xk;
+  vector < TMatrix > xprojk;
+  vector < TMatrix > xsmoothk;
 
-    Float_t height = 2*vertex.GetVolumeSequence()->GetDetector()->GetStructuralSize().GetZ();
-    m_heightX0 = height/vertex.GetVolumeSequence()->GetDetector()->GetSensitiveVolume(0)->GetMaterial()->GetRadiationLength();
+  Float_t _planedistance = 0.;
+  Float_t m = 1000.;
 
-    //Filtering
-    Float_t t; // tan of the RMS of the scattering angle
+  TMatrix C(2,2);
+  TMatrix C_proj(2,2);
+  Cprojk.push_back(C_proj);
+  CprojInvk.push_back(C_proj);
+  TMatrix F(2,2);
+  TMatrix Q(2,2);
 
-    Float_t V = (m_sigma*m_sigma);  //Weight Matrix
+  Chosen.RemoveAllRESEs();
+  Chosen.Compress();
 
-    Float_t G = 1./(m_sigma*m_sigma); //(Weight Matrix)^-1
+  Float_t chi2 = 0.;
+  MRESE vertex = RE->GetVertex();
+  Chosen.AddRESE(RE->GetVertex());
 
-    C(0,0)=m_sigma*m_sigma;
-    C(0,1)=0.;
-    C(1,0)=0.;
-    C(1,1)=w;
+  Float_t height = 2*vertex.GetVolumeSequence()->GetDetector()->GetStructuralSize().GetZ();
+  m_heightX0 = height/vertex.GetVolumeSequence()->GetDetector()->GetSensitiveVolume(0)->GetMaterial()->GetRadiationLength();
 
-    Ck.push_back(C);
+  //Filtering
+  Float_t t; // tan of the RMS of the scattering angle
 
-    vector < Float_t > mk;
+  Float_t V = (m_sigma*m_sigma);  //Weight Matrix
 
-    TMatrix x(2,1);
-    if(view==0)  x(0,0)=vertex.GetPositionX();
-    else if(view==1)  x(0,0)=vertex.GetPositionY();
-    x(1,0)=0;
+  Float_t G = 1./(m_sigma*m_sigma); //(Weight Matrix)^-1
 
-    xk.push_back(x);
+  C(0,0)=m_sigma*m_sigma;
+  C(0,1)=0.;
+  C(1,0)=0.;
+  C(1,1)=w;
 
-    mk.push_back(x(0,0));
+  Ck.push_back(C);
 
-    TMatrix x_proj(2,1);
-    xprojk.push_back(x_proj);
+  vector < Float_t > mk;
 
-    Int_t i=0;
+  TMatrix x(2,1);
+  if(view==0)  x(0,0)=vertex.GetPositionX();
+  else if(view==1)  x(0,0)=vertex.GetPositionY();
+  x(1,0)=0;
 
-    MRESEList List;
-    List.RemoveAllRESEs();
-    List.Compress();
+  xk.push_back(x);
 
-    // Create a list of RESEs sorted by depth in tracker
-    vector<MRESE*> ReseList;
-    for (int h = 0; h < RE->GetNRESEs(); h++) {
-      if (m_Geometry->IsAbove(RE->GetVertex(), RE->GetRESEAt(h)) == false) {
-        ReseList.push_back(RE->GetRESEAt(h));
-      }
-    }
-    sort(ReseList.begin(), ReseList.end(), CompareRESEByZ());
+  mk.push_back(x(0,0));
+
+  TMatrix x_proj(2,1);
+  xprojk.push_back(x_proj);
+
+  Int_t i=0;
+
+  MRESEList List;
+  List.RemoveAllRESEs();
+  List.Compress();
 
-    vector<MRESE*>::iterator Iterator1;
-    for (Iterator1 = ReseList.begin(); Iterator1 != ReseList.end(); Iterator1++) {
-      if (IsInTracker(*Iterator1) == false) continue;
-      List.AddRESE(*Iterator1);
+  // Create a list of RESEs sorted by depth in tracker
+  vector<MRESE*> ReseList;
+  for (int h = 0; h < RE->GetNRESEs(); h++) {
+    if (m_Geometry->IsAbove(RE->GetVertex(), RE->GetRESEAt(h)) == false) {
+      ReseList.push_back(RE->GetRESEAt(h));
     }
-    ReseList.clear();
+  }
+  sort(ReseList.begin(), ReseList.end(), CompareRESEByZ());
 
-    Float_t PlaneZ = vertex.GetPosition().Z();
-    mdebug<<"Vertex : "<<vertex.GetPosition().X()<<" "<<vertex.GetPosition().Y()<<" "<<vertex.GetPosition().Z()<<endl;
-    Float_t LayerDistance = vertex.GetVolumeSequence()->GetDetector()->GetStructuralPitch().GetZ();
+  vector<MRESE*>::iterator Iterator1;
+  for (Iterator1 = ReseList.begin(); Iterator1 != ReseList.end(); Iterator1++) {
+    if (IsInTracker(*Iterator1) == false) continue;
+    List.AddRESE(*Iterator1);
+  }
+  ReseList.clear();
 
-    for (int r = 0; r < List.GetNRESEs() && i<n-1; r++) {
+  Float_t PlaneZ = vertex.GetPosition().Z();
+  mdebug<<"Vertex : "<<vertex.GetPosition().X()<<" "<<vertex.GetPosition().Y()<<" "<<vertex.GetPosition().Z()<<endl;
+  Float_t LayerDistance = vertex.GetVolumeSequence()->GetDetector()->GetStructuralPitch().GetZ();
 
-      if (PlaneZ <= (List.GetRESEAt(r)->GetPosition().Z() + 0.0001)) continue;
-      PlaneZ = List.GetRESEAt(r)->GetPosition().Z();
+  for (int r = 0; r < List.GetNRESEs() && i<n-1; r++) {
 
-      for (int k = 0; k < r; k++) {
-        if(List.GetRESEAt(k)->GetPosition().Z()-PlaneZ < 0.0001) break;
-        _planedistance = List.GetRESEAt(k)->GetPosition().Z()-PlaneZ;
-      }
+    if (PlaneZ <= (List.GetRESEAt(r)->GetPosition().Z() + 0.0001)) continue;
+    PlaneZ = List.GetRESEAt(r)->GetPosition().Z();
 
-      if(_planedistance>1.5*LayerDistance) break; // we accept only hits on subsequent planes
+    for (int k = 0; k < r; k++) {
+      if(List.GetRESEAt(k)->GetPosition().Z()-PlaneZ < 0.0001) break;
+      _planedistance = List.GetRESEAt(k)->GetPosition().Z()-PlaneZ;
+    }
 
-      t=(13.6/en)*sqrt(m_heightX0)*(1+0.038*log(m_heightX0));
+    if(_planedistance>1.5*LayerDistance) break; // we accept only hits on subsequent planes
 
-      F(0,0)=1.;
-      F(0,1)=_planedistance;
-      F(1,0)=0.;
-      F(1,1)=1.;
+    t=(13.6/en)*sqrt(m_heightX0)*(1+0.038*log(m_heightX0));
 
-      Fk.push_back(F);
+    F(0,0)=1.;
+    F(0,1)=_planedistance;
+    F(1,0)=0.;
+    F(1,1)=1.;
 
-      Q(0,0)=(t*t*height*height)/3.;
-      Q(0,1)=t*t*height/2.;
-      Q(1,0)=t*t*height/2.;
-      Q(1,1)=t*t;
-      Qk.push_back(Q);
+    Fk.push_back(F);
 
-      TMatrix H(2,1);
-      H(0,0)=1;
-      H(1,0)=0;
+    Q(0,0)=(t*t*height*height)/3.;
+    Q(0,1)=t*t*height/2.;
+    Q(1,0)=t*t*height/2.;
+    Q(1,1)=t*t;
+    Qk.push_back(Q);
 
-      x_proj = (F*x);
+    TMatrix H(2,1);
+    H(0,0)=1;
+    H(1,0)=0;
 
-      xprojk.push_back(x_proj);
+    x_proj = (F*x);
 
-      TMatrix FT = F;
-      FT.T();
-      FTk.push_back(FT);
+    xprojk.push_back(x_proj);
 
-      C_proj = (F*C)*FT + Q;
+    TMatrix FT = F;
+    FT.T();
+    FTk.push_back(FT);
 
-      Cprojk.push_back(C_proj);
+    C_proj = (F*C)*FT + Q;
 
-      TMatrix C_projInv=C_proj;
+    Cprojk.push_back(C_proj);
 
-      C_projInv.Invert();
+    TMatrix C_projInv=C_proj;
 
-      CprojInvk.push_back(C_projInv);
+    C_projInv.Invert();
 
-      C = C_projInv;
-      C(0,0)+=G;
-      C.Invert();
+    CprojInvk.push_back(C_projInv);
 
-      Ck.push_back(C);
-      //Fk.push_back(F);
-      Qk.push_back(Q);
+    C = C_projInv;
+    C(0,0)+=G;
+    C.Invert();
 
-      vector < Float_t > weight;
+    Ck.push_back(C);
+    //Fk.push_back(F);
+    Qk.push_back(Q);
 
-      for (int k = 0; k < List.GetNRESEs(); k++) {
+    vector < Float_t > weight;
 
-        if(abs(List.GetRESEAt(k)->GetPosition().Z()-PlaneZ) > 0.0001) continue;
+    for (int k = 0; k < List.GetNRESEs(); k++) {
 
-        Bool_t previous = false;
+      if(abs(List.GetRESEAt(k)->GetPosition().Z()-PlaneZ) > 0.0001) continue;
 
-        for (int j = 0; j < Previous.GetNRESEs(); j++) {
-          if(abs(Previous.GetRESEAt(j)->GetPosition().Z()-PlaneZ)  > 0.0001) continue;
-          if(view==0){
-            if(Previous.GetRESEAt(j)->GetPosition().X()-List.GetRESEAt(k)->GetPosition().X() ==0) previous = true;
-          } else if(view==1){
-            if(Previous.GetRESEAt(j)->GetPosition().Y()-List.GetRESEAt(k)->GetPosition().Y() ==0) previous = true;
-          }
-        }
+      Bool_t previous = false;
 
+      for (int j = 0; j < Previous.GetNRESEs(); j++) {
+        if(abs(Previous.GetRESEAt(j)->GetPosition().Z()-PlaneZ)  > 0.0001) continue;
         if(view==0){
-          if (previous) weight.push_back(sfg_factor+abs(List.GetRESEAt(k)->GetPosition().X()-x_proj(0,0))/(sqrt(C_proj(0,0))));
-          else weight.push_back(abs(List.GetRESEAt(k)->GetPosition().X()-x_proj(0,0))/(sqrt(C_proj(0,0))));
+          if(Previous.GetRESEAt(j)->GetPosition().X()-List.GetRESEAt(k)->GetPosition().X() ==0) previous = true;
         } else if(view==1){
-          if (previous) weight.push_back(sfg_factor+abs(List.GetRESEAt(k)->GetPosition().Y()-x_proj(0,0))/(sqrt(C_proj(0,0))));
-          else weight.push_back(abs(List.GetRESEAt(k)->GetPosition().Y()-x_proj(0,0))/(sqrt(C_proj(0,0))));
+          if(Previous.GetRESEAt(j)->GetPosition().Y()-List.GetRESEAt(k)->GetPosition().Y() ==0) previous = true;
         }
-
       }
-      Int_t kmin=0;
-      for(int kk=0; kk<(int) weight.size(); kk++){
-        if(weight[kk]==*min_element(weight.begin(), weight.end())) kmin=kk;
+
+      if(view==0){
+        if (previous) weight.push_back(sfg_factor+abs(List.GetRESEAt(k)->GetPosition().X()-x_proj(0,0))/(sqrt(C_proj(0,0))));
+        else weight.push_back(abs(List.GetRESEAt(k)->GetPosition().X()-x_proj(0,0))/(sqrt(C_proj(0,0))));
+      } else if(view==1){
+        if (previous) weight.push_back(sfg_factor+abs(List.GetRESEAt(k)->GetPosition().Y()-x_proj(0,0))/(sqrt(C_proj(0,0))));
+        else weight.push_back(abs(List.GetRESEAt(k)->GetPosition().Y()-x_proj(0,0))/(sqrt(C_proj(0,0))));
       }
 
-      Int_t kind=0;
-      for (int kk = 0; kk < List.GetNRESEs(); kk++) {
-        if(abs(List.GetRESEAt(kk)->GetPosition().Z()-PlaneZ) > 0.0001) continue;
-        else {
-          if (kind==kmin){
-            if(view==0){
-              m=List.GetRESEAt(kk)->GetPosition().X();
-            } else if(view==1){
-              m=List.GetRESEAt(kk)->GetPosition().Y();
-            }
-
-            Chosen.AddRESE(List.GetRESEAt(kk));
-            break;
+    }
+    Int_t kmin=0;
+    for(int kk=0; kk<(int) weight.size(); kk++){
+      if(weight[kk]==*min_element(weight.begin(), weight.end())) kmin=kk;
+    }
+
+    Int_t kind=0;
+    for (int kk = 0; kk < List.GetNRESEs(); kk++) {
+      if(abs(List.GetRESEAt(kk)->GetPosition().Z()-PlaneZ) > 0.0001) continue;
+      else {
+        if (kind==kmin){
+          if(view==0){
+            m=List.GetRESEAt(kk)->GetPosition().X();
+          } else if(view==1){
+            m=List.GetRESEAt(kk)->GetPosition().Y();
           }
-          kind ++;
+
+          Chosen.AddRESE(List.GetRESEAt(kk));
+          break;
         }
+        kind ++;
       }
-
-      mk.push_back(m);
-      x = C * (C_projInv*x_proj+(H*(G*m)));
-      xk.push_back(x);
-      i++;
     }
 
-    if ((Int_t) xk.size()<n) n = xk.size();
-    if (n<2) return chi2;
+    mk.push_back(m);
+    x = C * (C_projInv*x_proj+(H*(G*m)));
+    xk.push_back(x);
+    i++;
+  }
 
-    //Smoothing
+  if ((Int_t) xk.size()<n) n = xk.size();
+  if (n<2) return chi2;
 
-    TMatrix xsmooth(2,1);
+  //Smoothing
 
-    xsmoothk.resize(xk.size(), xsmooth);
-    xsmoothk[xsmoothk.size()-1] = xk[xk.size()-1];
-    trk.push_back(xsmoothk[xsmoothk.size()-1]);
+  TMatrix xsmooth(2,1);
 
-    TMatrix Csmooth(2,2);
-    Csmoothk.resize(Ck.size(), Csmooth);
-    Csmoothk[Ck.size()-1] = C;
+  xsmoothk.resize(xk.size(), xsmooth);
+  xsmoothk[xsmoothk.size()-1] = xk[xk.size()-1];
+  trk.push_back(xsmoothk[xsmoothk.size()-1]);
 
-    for (Int_t i = n-2; i >= 0; i--) {
-      TMatrix A(2,2);
+  TMatrix Csmooth(2,2);
+  Csmoothk.resize(Ck.size(), Csmooth);
+  Csmoothk[Ck.size()-1] = C;
 
-      A = Ck[i]*FTk[i]*CprojInvk[i+1];
+  for (Int_t i = n-2; i >= 0; i--) {
+    TMatrix A(2,2);
 
-      TMatrix AT = A;
-      AT.T();
+    A = Ck[i]*FTk[i]*CprojInvk[i+1];
 
-      xsmoothk[i] = xk[i] + A * (xsmoothk[i+1] - xprojk[i+1]);
+    TMatrix AT = A;
+    AT.T();
 
-      trk.push_back(xsmoothk[i]);
+    xsmoothk[i] = xk[i] + A * (xsmoothk[i+1] - xprojk[i+1]);
 
-      Csmooth = Ck[i] + A*(Csmoothk[i+1] - Cprojk[i+1])*AT;
-      Csmoothk[i] = Csmooth;
-      Float_t rk = mk[i] - xsmoothk[i](0,0);
-      Float_t Rk = V -  Csmoothk[i](0,0);
+    trk.push_back(xsmoothk[i]);
 
-      chi2 += rk * rk / Rk;
-    }
-    reverse(trk.begin(),trk.end());
-    return chi2;
-  }
+    Csmooth = Ck[i] + A*(Csmoothk[i+1] - Cprojk[i+1])*AT;
+    Csmoothk[i] = Csmooth;
+    Float_t rk = mk[i] - xsmoothk[i](0,0);
+    Float_t Rk = V -  Csmoothk[i](0,0);
 
-  tuple<vector < TMatrix >, Float_t, Float_t, vector < TMatrix >, Float_t, Float_t, MRESEList, MRESEList> MERTrackKalman2D::SearchTracks(MRERawEvent* RE, Int_t view)
-  {
-    MRESEList PrevChoice;
-    Float_t en = start_nrg_fit;
-    Float_t nrg_est1;
-    Float_t nrg_est2;
-    Float_t chi1=0.;
-    Float_t chi2=0.;
-    Int_t loop1=0;
-    Bool_t stop=false;
-    Int_t n = n_fit;
-
-    MRESEList Chosen1;
-    MRESEList Chosen2;
-
-    vector < TMatrix > trk1;
-    vector < TMatrix > trk2;
-    mdebug<<"First track "<<endl;
-    PrevChoice.RemoveAllRESEs();
-    PrevChoice.Compress();
-
-    //track 1
-    while(!stop){
-
-      chi1 = Kalman(RE, n, en, PrevChoice, trk1, view, Chosen1);
-
-      if (trk1.size()<2){
-        return std::make_tuple(trk1, 0, 0, trk2, 0, 0, Chosen1, Chosen2);
-      }
+    chi2 += rk * rk / Rk;
+  }
+  reverse(trk.begin(),trk.end());
+  return chi2;
+}
 
-      nrg_est1=0.;
-
-      //Energy Estimation
-      nrg_est1 = MultipleScattering2D(trk1);
-
-      if (nrg_est1> 500000.) nrg_est1=500000.;
-      if ((nrg_est1/en)<1/3){
-        //loop1++;
-        en=en/3.;
-        trk1.clear();
-      } else if ((nrg_est1/en)>3. && loop1<9){
-        loop1++;
-        en=en*3.;
-        trk1.clear();
-      } else stop=true;
+tuple<vector < TMatrix >, Float_t, Float_t, vector < TMatrix >, Float_t, Float_t, MRESEList, MRESEList> MERTrackKalman2D::SearchTracks(MRERawEvent* RE, Int_t view)
+{
+  MRESEList PrevChoice;
+  Float_t en = start_nrg_fit;
+  Float_t nrg_est1;
+  Float_t nrg_est2;
+  Float_t chi1=0.;
+  Float_t chi2=0.;
+  Int_t loop1=0;
+  Bool_t stop=false;
+  Int_t n = n_fit;
+
+  MRESEList Chosen1;
+  MRESEList Chosen2;
+
+  vector < TMatrix > trk1;
+  vector < TMatrix > trk2;
+  mdebug<<"First track "<<endl;
+  PrevChoice.RemoveAllRESEs();
+  PrevChoice.Compress();
+
+  //track 1
+  while(!stop){
+
+    chi1 = Kalman(RE, n, en, PrevChoice, trk1, view, Chosen1);
+
+    if (trk1.size()<2){
+      return std::make_tuple(trk1, 0, 0, trk2, 0, 0, Chosen1, Chosen2);
     }
 
-    for (size_t i = 0; i < trk1.size(); i++) {
-      mdebug<<"Track1 after Kalman "<<trk1.size()<<" "<<trk1[i](0,0)<<" "<<trk1[i](1,0)<<endl;
-    }
+    nrg_est1=0.;
+
+    //Energy Estimation
+    nrg_est1 = MultipleScattering2D(trk1);
+
+    if (nrg_est1> 500000.) nrg_est1=500000.;
+    if ((nrg_est1/en)<1/3){
+      //loop1++;
+      en=en/3.;
+      trk1.clear();
+    } else if ((nrg_est1/en)>3. && loop1<9){
+      loop1++;
+      en=en*3.;
+      trk1.clear();
+    } else stop=true;
+  }
 
-    stop=false;
-    en = start_nrg_fit;
-    Int_t loop2=0;
-    mdebug<<"Second track "<<endl;
-    //track 2
-    while(!stop){
-      Chosen2.RemoveAllRESEs();
-      Chosen2.Compress();
+  for (size_t i = 0; i < trk1.size(); i++) {
+    mdebug<<"Track1 after Kalman "<<trk1.size()<<" "<<trk1[i](0,0)<<" "<<trk1[i](1,0)<<endl;
+  }
 
-      chi2 = Kalman(RE, n, en, Chosen1, trk2, view, Chosen2);
+  stop=false;
+  en = start_nrg_fit;
+  Int_t loop2=0;
+  mdebug<<"Second track "<<endl;
+  //track 2
+  while(!stop){
+    Chosen2.RemoveAllRESEs();
+    Chosen2.Compress();
 
-      if (trk2.size()<2){
-        return std::make_tuple(trk1, 0, 0, trk2, 0, 0, Chosen1, Chosen2);
-      }
+    chi2 = Kalman(RE, n, en, Chosen1, trk2, view, Chosen2);
 
-      nrg_est2=0;
-
-      //Energy Estimation
-      nrg_est2 = MultipleScattering2D(trk2);
-
-      if (nrg_est2> 500000.) nrg_est2=500000.;
-      if ((nrg_est2/en)<1/3){
-        //loop1++;
-        en=en/3.;
-        trk2.clear();
-      } else if ((nrg_est2/en)>3. && loop2<9){
-        loop2++;
-        en=en*3.;
-        trk2.clear();
-      } else stop=true;
-    }
-    for (size_t i = 0; i < trk2.size(); i++) {
-      mdebug<<"Track2 after Kalman "<<trk2.size()<<" "<<trk2[i](0,0)<<" "<<trk2[i](1,0)<<endl;
+    if (trk2.size()<2){
+      return std::make_tuple(trk1, 0, 0, trk2, 0, 0, Chosen1, Chosen2);
     }
-    return std::make_tuple(trk1, nrg_est1, chi1, trk2, nrg_est2, chi2, Chosen1, Chosen2);
+
+    nrg_est2=0;
+
+    //Energy Estimation
+    nrg_est2 = MultipleScattering2D(trk2);
+
+    if (nrg_est2> 500000.) nrg_est2=500000.;
+    if ((nrg_est2/en)<1/3){
+      //loop1++;
+      en=en/3.;
+      trk2.clear();
+    } else if ((nrg_est2/en)>3. && loop2<9){
+      loop2++;
+      en=en*3.;
+      trk2.clear();
+    } else stop=true;
   }
+  for (size_t i = 0; i < trk2.size(); i++) {
+    mdebug<<"Track2 after Kalman "<<trk2.size()<<" "<<trk2[i](0,0)<<" "<<trk2[i](1,0)<<endl;
+  }
+  return std::make_tuple(trk1, nrg_est1, chi1, trk2, nrg_est2, chi2, Chosen1, Chosen2);
+}
 
-  Float_t MERTrackKalman2D::MultipleScattering2D(vector < TMatrix > trk)
-  {
-    vector < Float_t > angles;
-    UInt_t i;
+Float_t MERTrackKalman2D::MultipleScattering2D(vector < TMatrix > trk)
+{
+  vector < Float_t > angles;
+  UInt_t i;
 
-    for (i = 0; i < trk.size(); i++) {
-      angles.push_back(TMath::ATan( trk[i](1,0)));
-    }
+  for (i = 0; i < trk.size(); i++) {
+    angles.push_back(TMath::ATan( trk[i](1,0)));
+  }
 
-    vector < Float_t > dtheta1;
-    vector < Float_t > absdtheta1;
-    Float_t dt1;
-    for (i = 1; i < angles.size(); i++) {
-      dtheta1.push_back((Float_t) (angles[i] - angles[i - 1]));
-    }
+  vector < Float_t > dtheta1;
+  vector < Float_t > absdtheta1;
+  Float_t dt1;
+  for (i = 1; i < angles.size(); i++) {
+    dtheta1.push_back((Float_t) (angles[i] - angles[i - 1]));
+  }
 
-    dtheta1.erase(dtheta1.end() - 1, dtheta1.end());
+  dtheta1.erase(dtheta1.end() - 1, dtheta1.end());
 
-    Float_t   heightX0tot = 0;
-    vector < Float_t > planes;
-    Float_t meanX0 = 0;
+  Float_t   heightX0tot = 0;
+  vector < Float_t > planes;
+  Float_t meanX0 = 0;
 
-    for(i=0; i< dtheta1.size(); i++){
-      heightX0tot +=  m_heightX0;
-      dtheta1[i]/= exp(m_heightX0/cos(atan2(trk[1](1,0),1)));    //Energy correction
-    }
+  for(i=0; i< dtheta1.size(); i++){
+    heightX0tot +=  m_heightX0;
+    dtheta1[i]/= exp(m_heightX0/cos(atan2(trk[1](1,0),1)));    //Energy correction
+  }
 
-    bool stop = false;
-    meanX0 = heightX0tot/dtheta1.size();
+  bool stop = false;
+  meanX0 = heightX0tot/dtheta1.size();
 
-    while (!stop) {
-      Float_t maxdt =0.;
-      dt1 = 0.;
-      absdtheta1.clear();
+  while (!stop) {
+    Float_t maxdt =0.;
+    dt1 = 0.;
+    absdtheta1.clear();
 
-      for (i = 0; i < dtheta1.size(); i++) {
-        dt1 += dtheta1[i] * dtheta1[i];
-        absdtheta1.push_back(TMath::Abs( dtheta1[i]));
-        if(TMath::Abs( dtheta1[i])>maxdt) maxdt=TMath::Abs( dtheta1[i]);
-      }
-      dt1 = sqrt((dt1 / dtheta1.size()));
+    for (i = 0; i < dtheta1.size(); i++) {
+      dt1 += dtheta1[i] * dtheta1[i];
+      absdtheta1.push_back(TMath::Abs( dtheta1[i]));
+      if(TMath::Abs( dtheta1[i])>maxdt) maxdt=TMath::Abs( dtheta1[i]);
+    }
+    dt1 = sqrt((dt1 / dtheta1.size()));
 
-      if (maxdt / dt1 > 3.) {
-        for (i = 0; i < absdtheta1.size(); i++) {
+    if (maxdt / dt1 > 3.) {
+      for (i = 0; i < absdtheta1.size(); i++) {
 
-          if (absdtheta1[i] == maxdt) {
-            absdtheta1.erase(absdtheta1.begin() + i);
-            dtheta1.erase(dtheta1.begin() + i);
-            i--;
-          }
+        if (absdtheta1[i] == maxdt) {
+          absdtheta1.erase(absdtheta1.begin() + i);
+          dtheta1.erase(dtheta1.begin() + i);
+          i--;
         }
-      } else {
-        stop = true;
       }
+    } else {
+      stop = true;
     }
+  }
 
-    Float_t energy=13.6*sqrt(meanX0)*(1.+0.038*log(meanX0))/(dt1*sqrt(cos(atan2(trk[1](1,0), 1.))));
-    dtheta1.clear();
-    absdtheta1.clear();
-    angles.clear();
-    return energy;
+  Float_t energy=13.6*sqrt(meanX0)*(1.+0.038*log(meanX0))/(dt1*sqrt(cos(atan2(trk[1](1,0), 1.))));
+  dtheta1.clear();
+  absdtheta1.clear();
+  angles.clear();
+  return energy;
 
-  }   //MultipleScattering2D
+}   //MultipleScattering2D
 
-  Float_t MERTrackKalman2D::MultipleScattering3D(MRESEList trkx, MRESEList trky)
-  {
-    Int_t n = min((trkx.GetNRESEs()),(trky.GetNRESEs()));
-    Float_t vi[3];
-    TVector3 vi0;
-    TVector3 vi1;
+Float_t MERTrackKalman2D::MultipleScattering3D(MRESEList trkx, MRESEList trky)
+{
+  Int_t n = min((trkx.GetNRESEs()),(trky.GetNRESEs()));
+  Float_t vi[3];
+  TVector3 vi0;
+  TVector3 vi1;
 
-    vector < Float_t > theta(n);
+  vector < Float_t > theta(n);
 
-    Float_t E = 0;
+  Float_t E = 0;
 
-    for (Int_t i = 0; i < n-1; i++) {
+  for (Int_t i = 0; i < n-1; i++) {
 
-      vi[0] = trkx.GetRESEAt(i+1)->GetPosition().X() - trkx.GetRESEAt(i)->GetPosition().X();
-      vi[1] = trky.GetRESEAt(i+1)->GetPosition().Y() - trky.GetRESEAt(i)->GetPosition().Y();
-      vi[2]= trkx.GetRESEAt(i+1)->GetPosition().Z() - trkx.GetRESEAt(i)->GetPosition().Z();
-      vi0.SetXYZ(vi[0], vi[1], vi[2]);
-      vi0.SetMag(1.);
+    vi[0] = trkx.GetRESEAt(i+1)->GetPosition().X() - trkx.GetRESEAt(i)->GetPosition().X();
+    vi[1] = trky.GetRESEAt(i+1)->GetPosition().Y() - trky.GetRESEAt(i)->GetPosition().Y();
+    vi[2]= trkx.GetRESEAt(i+1)->GetPosition().Z() - trkx.GetRESEAt(i)->GetPosition().Z();
+    vi0.SetXYZ(vi[0], vi[1], vi[2]);
+    vi0.SetMag(1.);
 
-      theta[i] = vi0.Theta();
+    theta[i] = vi0.Theta();
 
-      if (i != 0) {
-        Float_t angle = vi0.Angle(vi1);
-        E = (13.6/angle)*sqrt(m_heightX0/cos(TMath::Pi()-vi0.Theta()))*(1+0.038*log(m_heightX0/cos(TMath::Pi()-vi0.Theta())));
+    if (i != 0) {
+      Float_t angle = vi0.Angle(vi1);
+      E = (13.6/angle)*sqrt(m_heightX0/cos(TMath::Pi()-vi0.Theta()))*(1+0.038*log(m_heightX0/cos(TMath::Pi()-vi0.Theta())));
 
-        break;
-      }
-      vi1=vi0;
+      break;
     }
-    return E;
+    vi1=vi0;
   }
+  return E;
+}
 
-  void MERTrackKalman2D::TrackPairs(MRERawEvent* RE)
-  {
-    if (RE->GetVertex() == 0) {
-      Fatal("void MRERawEvent::TrackPairs()",
-      "No vertex found!");
-    }
-
-    Float_t E1x=0.;
-    Float_t E2x=0.;
-    Float_t ChiT1x=0.;
-    Float_t ChiT2x=0.;
+void MERTrackKalman2D::TrackPairs(MRERawEvent* RE)
+{
+  if (RE->GetVertex() == 0) {
+    Fatal("void MRERawEvent::TrackPairs()",
+    "No vertex found!");
+  }
 
-    vector < TMatrix > Track1x;
-    vector < TMatrix > Track2x;
+  Float_t E1x=0.;
+  Float_t E2x=0.;
+  Float_t ChiT1x=0.;
+  Float_t ChiT2x=0.;
 
-    Float_t E1y=0.;
-    Float_t E2y=0.;
-    Float_t ChiT1y=0.;
-    Float_t ChiT2y=0.;
+  vector < TMatrix > Track1x;
+  vector < TMatrix > Track2x;
 
-    Float_t E1=0.;
-    Float_t E2=0.;
-    Float_t Egamma=0.;
+  Float_t E1y=0.;
+  Float_t E2y=0.;
+  Float_t ChiT1y=0.;
+  Float_t ChiT2y=0.;
 
-    vector < TMatrix > Track1y;
-    vector < TMatrix > Track2y;
+  Float_t E1=0.;
+  Float_t E2=0.;
+  Float_t Egamma=0.;
 
-    MRESEList Chosen1x;
-    MRESEList Chosen2x;
+  vector < TMatrix > Track1y;
+  vector < TMatrix > Track2y;
 
-    MRESEList Chosen1y;
-    MRESEList Chosen2y;
+  MRESEList Chosen1x;
+  MRESEList Chosen2x;
 
-    MRETrack* Electron = new MRETrack();
-    MRETrack* Positron = new MRETrack();
+  MRESEList Chosen1y;
+  MRESEList Chosen2y;
 
-    // Now create the vertex:
-    Electron->AddRESE(RE->GetVertex());
-    Electron->SetStartPoint(RE->GetVertex());
-    Positron->AddRESE(RE->GetVertex());
-    Positron->SetStartPoint(RE->GetVertex());
+  MRETrack* Electron = new MRETrack();
+  MRETrack* Positron = new MRETrack();
 
-    // View X
-    tie(Track1x, E1x, ChiT1x, Track2x, E2x, ChiT2x, Chosen1x, Chosen2x) = SearchTracks(RE, 0);
-    if (ChiT1x==0. && ChiT2x==0.) return;
+  // Now create the vertex:
+  Electron->AddRESE(RE->GetVertex());
+  Electron->SetStartPoint(RE->GetVertex());
+  Positron->AddRESE(RE->GetVertex());
+  Positron->SetStartPoint(RE->GetVertex());
 
-    //View Y
-    tie(Track1y, E1y, ChiT1y, Track2y, E2y, ChiT2y, Chosen1y, Chosen2y) = SearchTracks(RE, 1);
+  // View X
+  tie(Track1x, E1x, ChiT1x, Track2x, E2x, ChiT2x, Chosen1x, Chosen2x) = SearchTracks(RE, 0);
+  if (ChiT1x==0. && ChiT2x==0.) return;
 
-    if (ChiT1y==0. && ChiT2y==0.) return;
+  //View Y
+  tie(Track1y, E1y, ChiT1y, Track2y, E2y, ChiT2y, Chosen1y, Chosen2y) = SearchTracks(RE, 1);
 
-    if((E1x-E2x)*(E1y-E2y)<0.){
-      Float_t E1ytemp=E1y;
-      E1y=E2y;
-      E2y=E1ytemp;
+  if (ChiT1y==0. && ChiT2y==0.) return;
 
-      Float_t ChiT1ytemp=ChiT1y;
-      ChiT1y=ChiT2y;
-      ChiT2y=ChiT1ytemp;
+  if((E1x-E2x)*(E1y-E2y)<0.){
+    Float_t E1ytemp=E1y;
+    E1y=E2y;
+    E2y=E1ytemp;
 
-      Track1y.swap(Track2y);
+    Float_t ChiT1ytemp=ChiT1y;
+    ChiT1y=ChiT2y;
+    ChiT2y=ChiT1ytemp;
 
-      MRESEList Chosen1ytemp(Chosen1y);
-      Chosen1y=Chosen2y;
-      Chosen2y=Chosen1ytemp;
-    }
+    Track1y.swap(Track2y);
 
-    if (Chosen1x.GetNRESEs()>2 && Chosen1y.GetNRESEs()>2){
-      E1= MultipleScattering3D(Chosen1x, Chosen1y);
-      if (Chosen2x.GetNRESEs()>2 && Chosen2y.GetNRESEs()>2){
-        E2= MultipleScattering3D(Chosen2x, Chosen2y);
-      } else E2= 0.;
-      Egamma= E1+E2;
+    MRESEList Chosen1ytemp(Chosen1y);
+    Chosen1y=Chosen2y;
+    Chosen2y=Chosen1ytemp;
+  }
 
-      for (int r = 0; r < Chosen1x.GetNRESEs(); r++) {
-        Electron->AddRESE(Chosen1x.GetRESEAt(r));
-      }
+  if (Chosen1x.GetNRESEs()>2 && Chosen1y.GetNRESEs()>2){
+    E1= MultipleScattering3D(Chosen1x, Chosen1y);
+    if (Chosen2x.GetNRESEs()>2 && Chosen2y.GetNRESEs()>2){
+      E2= MultipleScattering3D(Chosen2x, Chosen2y);
+    } else E2= 0.;
+    Egamma= E1+E2;
 
-      for (int r = 0; r < Chosen1y.GetNRESEs(); r++) {
-        Electron->AddRESE(Chosen1y.GetRESEAt(r));
-      }
+    for (int r = 0; r < Chosen1x.GetNRESEs(); r++) {
+      Electron->AddRESE(Chosen1x.GetRESEAt(r));
+    }
 
-      for (int r = 0; r < Chosen2x.GetNRESEs(); r++) {
-        Positron->AddRESE(Chosen2x.GetRESEAt(r));
-      }
+    for (int r = 0; r < Chosen1y.GetNRESEs(); r++) {
+      Electron->AddRESE(Chosen1y.GetRESEAt(r));
+    }
 
-      for (int r = 0; r < Chosen2y.GetNRESEs(); r++) {
-        Positron->AddRESE(Chosen2y.GetRESEAt(r));
-      }
+    for (int r = 0; r < Chosen2x.GetNRESEs(); r++) {
+      Positron->AddRESE(Chosen2x.GetRESEAt(r));
+    }
 
-      Float_t thetax1=Track1x[0](1,0);
-      Float_t thetay1=Track1y[0](1,0);
+    for (int r = 0; r < Chosen2y.GetNRESEs(); r++) {
+      Positron->AddRESE(Chosen2y.GetRESEAt(r));
+    }
 
-      Float_t thetax2=Track2x[0](1,0);
-      Float_t thetay2=Track2y[0](1,0);
+    Float_t thetax1=Track1x[0](1,0);
+    Float_t thetay1=Track1y[0](1,0);
 
-      mdebug<<"Theta of the four tracks: "<<c_Deg*atan(thetax1)<<" "<<c_Deg*atan(thetay1)<<" "<<c_Deg*atan(thetax2)<<" "<<c_Deg*atan(thetay2)<<" "<<endl;
+    Float_t thetax2=Track2x[0](1,0);
+    Float_t thetay2=Track2y[0](1,0);
 
-      Float_t x1= thetax1/sqrt(pow(thetax1,2.)+pow(thetay1,2.)+1);
-      Float_t y1= thetay1/sqrt(pow(thetax1,2.)+pow(thetay1,2.)+1);
-      Float_t z1= 1./sqrt(pow(thetax1,2.)+pow(thetay1,2.)+1);
+    mdebug<<"Theta of the four tracks: "<<c_Deg*atan(thetax1)<<" "<<c_Deg*atan(thetay1)<<" "<<c_Deg*atan(thetax2)<<" "<<c_Deg*atan(thetay2)<<" "<<endl;
 
-      Float_t x2= thetax2/sqrt(pow(thetax2,2.)+pow(thetay2,2.)+1);
-      Float_t y2= thetay2/sqrt(pow(thetax2,2.)+pow(thetay2,2.)+1);
-      Float_t z2= 1./sqrt(pow(thetax2,2.)+pow(thetay2,2.)+1);
+    Float_t x1= thetax1/sqrt(pow(thetax1,2.)+pow(thetay1,2.)+1);
+    Float_t y1= thetay1/sqrt(pow(thetax1,2.)+pow(thetay1,2.)+1);
+    Float_t z1= 1./sqrt(pow(thetax1,2.)+pow(thetay1,2.)+1);
 
-      Float_t x= x1*E1+x2*E2/Egamma;
-      Float_t y= y1*E1+y2*E2/Egamma;
-      Float_t z= z1*E1+z2*E2/Egamma;
+    Float_t x2= thetax2/sqrt(pow(thetax2,2.)+pow(thetay2,2.)+1);
+    Float_t y2= thetay2/sqrt(pow(thetax2,2.)+pow(thetay2,2.)+1);
+    Float_t z2= 1./sqrt(pow(thetax2,2.)+pow(thetay2,2.)+1);
 
-      Float_t mag=sqrt(x*x+y*y+z*z);
-      Float_t mag1=sqrt(x1*x1+y1*y1+z1*z1);
-      Float_t mag2=sqrt(x2*x2+y2*y2+z2*z2);
+    Float_t x= x1*E1+x2*E2/Egamma;
+    Float_t y= y1*E1+y2*E2/Egamma;
+    Float_t z= z1*E1+z2*E2/Egamma;
 
+    Float_t mag=sqrt(x*x+y*y+z*z);
+    Float_t mag1=sqrt(x1*x1+y1*y1+z1*z1);
+    Float_t mag2=sqrt(x2*x2+y2*y2+z2*z2);
 
-      MVector direction(x/mag,y/mag,-z/mag);
-      MVector direction1(x1/mag1,y1/mag1,-z1/mag1);
-      MVector direction2(x2/mag2,y2/mag2,-z2/mag2);
 
-      Electron->SetFixedDirection(direction1);
-      Positron->SetFixedDirection(direction2);
+    MVector direction(x/mag,y/mag,-z/mag);
+    MVector direction1(x1/mag1,y1/mag1,-z1/mag1);
+    MVector direction2(x2/mag2,y2/mag2,-z2/mag2);
 
-      Electron->SetEnergy(E1*1000); //So far the energy was calculated in MeV, MEGAlib works in keV
-      Positron->SetEnergy(E2*1000);
+    Electron->SetFixedDirection(direction1);
+    Positron->SetFixedDirection(direction2);
 
-      Electron->SetQualityFactor(ChiT1x+ChiT2x);
-      Positron->SetQualityFactor(ChiT1y+ChiT2y);
+    Electron->SetEnergy(E1*1000); //So far the energy was calculated in MeV, MEGAlib works in keV
+    Positron->SetEnergy(E2*1000);
 
-      mdebug<<"Energy of the two particles: "<<E1<<" "<<E2<<endl;
-      mdebug<<"Reconstructed theta, phi and energy of the gamma: "<<c_Deg*direction.Theta()<<" "<<c_Deg*direction.Phi()<<" "<<Egamma<<endl;
-      RE->SetElectronTrack(Electron);
-      RE->SetPositronTrack(Positron);
+    Electron->SetQualityFactor(ChiT1x+ChiT2x);
+    Positron->SetQualityFactor(ChiT1y+ChiT2y);
 
-      //RE->SetTrackQualityFactor((ChiT1y+ChiT2y)/100);
-      RE->SetPairQualityFactor((ChiT1y+ChiT2y));
-      RE->SetGoodEvent(true);
-      RE->SetEventType(MRERawEvent::c_PairEvent);
+    mdebug<<"Energy of the two particles: "<<E1<<" "<<E2<<endl;
+    mdebug<<"Reconstructed theta, phi and energy of the gamma: "<<c_Deg*direction.Theta()<<" "<<c_Deg*direction.Phi()<<" "<<Egamma<<endl;
+    RE->SetElectronTrack(Electron);
+    RE->SetPositronTrack(Positron);
 
-    } else{
-      Egamma= -1.;
-      E1= 1.;
-      E2= 1.;
-    }
+    //RE->SetTrackQualityFactor((ChiT1y+ChiT2y)/100);
+    RE->SetPairQualityFactor((ChiT1y+ChiT2y));
+    RE->SetGoodEvent(true);
+    RE->SetEventType(MRERawEvent::c_PairEvent);
 
+  } else{
+    Egamma= -1.;
+    E1= 1.;
+    E2= 1.;
   }
-  // MERTrackKalman2D.cxx: the end...
-  ////////////////////////////////////////////////////////////////////////////////
+
+}
+// MERTrackKalman2D.cxx: the end...
+////////////////////////////////////////////////////////////////////////////////
diff --git a/src/revan/src/MRawEventAnalyzer.cxx b/src/revan/src/MRawEventAnalyzer.cxx
index 3d677dec0..3791cf720 100644
--- a/src/revan/src/MRawEventAnalyzer.cxx
+++ b/src/revan/src/MRawEventAnalyzer.cxx
@@ -571,7 +571,7 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
   // We have events, we can start the analysis:
 
   // Section A: Coincidence search
-  if (m_CoincidenceAlgorithm != c_CoincidenceAlgoNone) {
+  if (m_CoincidenceAlgorithm == c_CoincidenceAlgoWindow) {
     if (m_Coincidence == nullptr) {
       merr<<"Coincidence pointer is zero. You changed the event reconstruction setup without calling PreAnalysis()!"<<show;
       return c_AnalysisUndefinedError;
@@ -594,7 +594,7 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
     }
 
     // Handle coincidences in the same voxel due to coincidence search - this should only happen in the simulation...
-    if (RE != nullptr && m_CoincidenceAlgorithm != c_CoincidenceAlgoNone) {
+    if (RE != nullptr/* && m_CoincidenceAlgorithm == c_CoincidenceAlgoWindow*/) {
       for (int r1 = 0; r1 < RE->GetNRESEs(); ++r1) {
         for (int r2 = r1+1; r2 < RE->GetNRESEs(); ++r2) {
           if (RE->GetRESEAt(r1)->GetPosition().AreEqual(RE->GetRESEAt(r2)->GetPosition(), 0.0000001) == true) {
@@ -610,8 +610,7 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
         }
       }
     }
-  } // no coincidence search
-  else {
+  } else { // no coincidence search
     RE = m_EventStore->GetRawEventAt(0);
     m_EventStore->RemoveRawEvent(RE);
   }
@@ -804,7 +803,7 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
     
     Event = m_RawEvents->GetOptimumPhysicalEvent();
   } else {
-    mdebug<<"We have a best rey events..."<<endl;
+    mdebug<<"We have a best try event ..."<<endl;
     
     Event = m_RawEvents->GetBestTryPhysicalEvent();
     
@@ -1199,8 +1198,9 @@ bool MRawEventAnalyzer::PreAnalysis()
   // Coincidence
   if (Return == true) {
     delete m_Coincidence;
-    m_Coincidence = new MERCoincidence();
+    m_Coincidence = nullptr;
     if (m_CoincidenceAlgorithm == c_CoincidenceAlgoWindow) {
+      m_Coincidence = new MERCoincidence();
       m_Coincidence->SetCoincidenceWindow(m_CoincidenceWindow);
     } else if (m_CoincidenceAlgorithm == c_CoincidenceAlgoNone) {
       // Nothing

From e406086ba85cd5da35677e4ad5483dc9b11bc1b3 Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Fri, 30 May 2025 14:01:26 -0400
Subject: [PATCH 165/192] CHG: Changed lists of 'static const' variables for
 reconstruction algorithms and analysis return codes into enum-based
 variables.

---
 src/revan/inc/MRawEventAnalyzer.h   | 137 ++++++++++++----------------
 src/revan/src/MRawEventAnalyzer.cxx |  79 ++++++----------
 2 files changed, 87 insertions(+), 129 deletions(-)

diff --git a/src/revan/inc/MRawEventAnalyzer.h b/src/revan/inc/MRawEventAnalyzer.h
index 2f407cf11..651ef4b42 100644
--- a/src/revan/inc/MRawEventAnalyzer.h
+++ b/src/revan/inc/MRawEventAnalyzer.h
@@ -98,13 +98,22 @@ class MRawEventAnalyzer
   void SetSaveOI(bool SaveOI);
 
   // The return codes of AnalyzeEvent()
-  static const unsigned int c_AnalysisSucess;
-  static const unsigned int c_AnalysisCoincidenceWindowWait;
-  static const unsigned int c_AnalysisEventClusteringFailed;
-  static const unsigned int c_AnalysisNoEventsInStore;
-  static const unsigned int c_AnalysisNoEventsLeftInFile;
-  static const unsigned int c_AnalysisSavingEventFailed;
-  static const unsigned int c_AnalysisUndefinedError;
+  enum c_AnalysisReturn {
+    c_AnalysisSucess,
+    c_AnalysisCoincidenceWindowWait,
+    c_AnalysisEventClusteringFailed,
+    c_AnalysisNoEventsInStore,
+    c_AnalysisNoEventsLeftInFile,
+    c_AnalysisSavingEventFailed,
+    c_AnalysisUndefinedError
+  };
+//  static const unsigned int c_AnalysisSucess;
+//  static const unsigned int c_AnalysisCoincidenceWindowWait;
+//  static const unsigned int c_AnalysisEventClusteringFailed;
+//  static const unsigned int c_AnalysisNoEventsInStore;
+//  static const unsigned int c_AnalysisNoEventsLeftInFile;
+//  static const unsigned int c_AnalysisSavingEventFailed;
+//  static const unsigned int c_AnalysisUndefinedError;
 
   //! Return the next initial raw event from file
   //! Return zero if the input mode is not file or if the ened of the file has been reached
@@ -140,46 +149,37 @@ class MRawEventAnalyzer
 
 
   // Interface for the basic reconstruction algorithms
-  
-  static const int c_CoincidenceAlgoNone;
-  static const int c_CoincidenceAlgoWindow;
+
+  enum c_CoincidenceAlgo {
+    c_CoincidenceAlgoNone,
+    c_CoincidenceAlgoWindow };
   
   //! Set the coincidence algorithm. One of: c_CoincidenceAlgoNone, c_CoincidenceAlgoWindow
   void SetCoincidenceAlgorithm(int ID) { m_CoincidenceAlgorithm = ID; }
-  
-  static const int c_EventClusteringAlgoNone;
-  static const int c_EventClusteringAlgoTMVA;
-  static const int c_EventClusteringAlgoDistance;
+
+  enum c_EventClusteringAlgo {
+    c_EventClusteringAlgoNone,
+    c_EventClusteringAlgoTMVA,
+    c_EventClusteringAlgoDistance };
   
   //! Set the coincidence algorithm. One of: c_EventClusteringAlgoNone, c_EventClusteringAlgoDistance, c_EventClusteringAlgoTMVA
   void SetEventClusteringAlgorithm(int ID) { m_EventClusteringAlgorithm = ID; }
-  
-  static const int c_HitClusteringAlgoNone;
-  static const int c_HitClusteringAlgoDistance;
-  static const int c_HitClusteringAlgoAdjacent;
-  static const int c_HitClusteringAlgoPDF;
+
+  enum c_HitClusteringAlgo {
+    c_HitClusteringAlgoNone,
+    c_HitClusteringAlgoDistance,
+    c_HitClusteringAlgoAdjacent,
+    c_HitClusteringAlgoPDF };
 
   //! Set the clustering algorithm: One of c_ClusteringAlgoNone, c_ClusteringAlgoDistance, c_ClusteringAlgoAdjacent;
   void SetHitClusteringAlgorithm(int ID) { m_HitClusteringAlgorithm = ID; }
 
   enum c_EventIdAlgo {
-    c_EventIdDefault, c_EventIdExternal
-  };
-  //! Set the Event tyep identification algorithm
-  void SetEventIdAlgorithm(int ID) { m_EventIdAlgorithm = ID; }
-
+    c_EventIdDefault,
+    c_EventIdExternal };
 
-//  static const int c_TrackingAlgoNone;
-//  static const int c_TrackingAlgoModifiedPearson;
-//  static const int c_TrackingAlgoPearson;
-//  static const int c_TrackingAlgoChiSquare;
-//  static const int c_TrackingAlgoGas;
-//  static const int c_TrackingAlgoDirectional;
-//  static const int c_TrackingAlgoBayesian;
-//  static const int c_TrackingAlgoRank;
-//  static const int c_PairKalman3D;
-//  static const int c_PairKalman2D;
-// static const int c_Trackingfirstlayers --
+  //! Set the Event type identification algorithm
+  void SetEventIdAlgorithm(int ID) { m_EventIdAlgorithm = ID; }
 
   enum c_TrackingAlgo {
     c_TrackingAlgoNone,
@@ -199,26 +199,28 @@ class MRawEventAnalyzer
   //! c_TrackingAlgoChiSquare, c_TrackingAlgoGas, c_TrackingAlgoDirectional, c_TrackingAlgoBayesian, c_TrackingAlgoRank
   void SetTrackingAlgorithm(int ID) { m_TrackingAlgorithm = ID; }
 
-  static const int c_PairDefault;
+  enum c_PairAlgo {
+    c_PairDefault };
 
   //! Set the pair reconstruction algorithm: One of c_PairDefault, c_PairKalman3D or c_PairKalman2D
   void SetPairAlgorithm(int ID) { m_PairAlgorithm = ID; }
 
-
-  static const int c_CSRAlgoNone;
-  static const int c_CSRAlgoFoM;
-  static const int c_CSRAlgoFoME;
-  static const int c_CSRAlgoFoMToF;
-  static const int c_CSRAlgoFoMToFAndE;
-  static const int c_CSRAlgoBayesian;
+  enum c_CSRAlgo {
+    c_CSRAlgoNone,
+    c_CSRAlgoFoM,
+    c_CSRAlgoFoME,
+    c_CSRAlgoFoMToF,
+    c_CSRAlgoFoMToFAndE,
+    c_CSRAlgoBayesian };
 
   static const int c_CSRAlgoTMVA;
 
   //! Set the Compton photon tracking algorithm: One of c_CSRAlgoNone, c_CSRAlgoFoM, c_CSRAlgoFoME, c_CSRAlgoFoMToF, c_CSRAlgoBayesian
   void SetCSRAlgorithm(int ID) { m_CSRAlgorithm = ID; }
 
-  static const int c_DecayAlgoNone;
-  static const int c_DecayAlgoStandard;
+  enum c_DecayAlgo {
+    c_DecayAlgoNone,
+    c_DecayAlgoStandard };
 
   //! Set the radioactive decay detection algorithm: One of c_DecayAlgoNone, c_DecayAlgoStandard
   void SetDecayAlgorithm(int ID) { m_DecayAlgorithm = ID; }
@@ -227,9 +229,7 @@ class MRawEventAnalyzer
   // Section: Interface to set all reconstruction options:
   
   // Options coincidence:
-  void SetCoincidenceWindow(double CoincidenceWindow) {
-    m_CoincidenceWindow = CoincidenceWindow;
-  }
+  void SetCoincidenceWindow(double CoincidenceWindow) { m_CoincidenceWindow = CoincidenceWindow; }
 
   // Options for event clustering
   void SetEventClusteringDistanceCutOff(double DistanceCutOff) { m_EventClusteringDistanceCutOff = DistanceCutOff; }
@@ -240,39 +240,18 @@ class MRawEventAnalyzer
   
   
   // Options hit clustering:
-  void SetStandardClusterizerMinDistanceD1(double MinDistance) {
-    m_StandardClusterizerMinDistanceD1 = MinDistance;
-  }
-  void SetStandardClusterizerMinDistanceD2(double MinDistance) {
-    m_StandardClusterizerMinDistanceD2 = MinDistance;
-  }
-  void SetStandardClusterizerMinDistanceD3(double MinDistance) {
-    m_StandardClusterizerMinDistanceD3 = MinDistance;
-  }
-  void SetStandardClusterizerMinDistanceD4(double MinDistance) {
-    m_StandardClusterizerMinDistanceD4 = MinDistance;
-  }
-  void SetStandardClusterizerMinDistanceD5(double MinDistance) {
-    m_StandardClusterizerMinDistanceD5 = MinDistance;
-  }
-  void SetStandardClusterizerMinDistanceD6(double MinDistance) {
-    m_StandardClusterizerMinDistanceD6 = MinDistance;
-  }
-  void SetStandardClusterizerMinDistanceD7(double MinDistance) {
-    m_StandardClusterizerMinDistanceD7 = MinDistance;
-  }
-  void SetStandardClusterizerMinDistanceD8(double MinDistance) {
-    m_StandardClusterizerMinDistanceD8 = MinDistance;
-  }
-  void SetStandardClusterizerCenterIsReference(bool CenterIsReference) {
-    m_StandardClusterizerCenterIsReference = CenterIsReference;
-  }
+  void SetStandardClusterizerMinDistanceD1(double MinDistance) { m_StandardClusterizerMinDistanceD1 = MinDistance; }
+  void SetStandardClusterizerMinDistanceD2(double MinDistance) { m_StandardClusterizerMinDistanceD2 = MinDistance; }
+  void SetStandardClusterizerMinDistanceD3(double MinDistance) { m_StandardClusterizerMinDistanceD3 = MinDistance; }
+  void SetStandardClusterizerMinDistanceD4(double MinDistance) { m_StandardClusterizerMinDistanceD4 = MinDistance; }
+  void SetStandardClusterizerMinDistanceD5(double MinDistance) { m_StandardClusterizerMinDistanceD5 = MinDistance; }
+  void SetStandardClusterizerMinDistanceD6(double MinDistance) { m_StandardClusterizerMinDistanceD6 = MinDistance; }
+  void SetStandardClusterizerMinDistanceD7(double MinDistance) { m_StandardClusterizerMinDistanceD7 = MinDistance; }
+  void SetStandardClusterizerMinDistanceD8(double MinDistance) { m_StandardClusterizerMinDistanceD8 = MinDistance; }
+  void SetStandardClusterizerCenterIsReference(bool CenterIsReference) { m_StandardClusterizerCenterIsReference = CenterIsReference; }
   void SetAdjacentLevel(const int Value) { m_AdjacentLevel = Value; }
   void SetAdjacentSigma(const double Value) { m_AdjacentSigma = Value; }
-
-  void SetPDFClusterizer(MString BaseFileName) {
-    m_PDFClusterizerBaseFileName = BaseFileName;
-  }
+  void SetPDFClusterizer(MString BaseFileName) { m_PDFClusterizerBaseFileName = BaseFileName; }
 
   // Options electron tracking:
   void SetDoTracking(bool Do) { m_DoTracking = Do; if (Do == false) m_TrackingAlgorithm = c_TrackingAlgoNone; }
diff --git a/src/revan/src/MRawEventAnalyzer.cxx b/src/revan/src/MRawEventAnalyzer.cxx
index 3791cf720..02c68f024 100644
--- a/src/revan/src/MRawEventAnalyzer.cxx
+++ b/src/revan/src/MRawEventAnalyzer.cxx
@@ -82,17 +82,17 @@ ClassImp(MRawEventAnalyzer)
 
 // DONT'T CHANGE THE NUMBERS!!
 
-const int MRawEventAnalyzer::c_CoincidenceAlgoNone   = 0;
-const int MRawEventAnalyzer::c_CoincidenceAlgoWindow = 1;
-
-const int MRawEventAnalyzer::c_EventClusteringAlgoNone     = 0;
-const int MRawEventAnalyzer::c_EventClusteringAlgoTMVA     = 1;
-const int MRawEventAnalyzer::c_EventClusteringAlgoDistance = 2;
-
-const int MRawEventAnalyzer::c_HitClusteringAlgoNone     = 0;
-const int MRawEventAnalyzer::c_HitClusteringAlgoDistance = 1;
-const int MRawEventAnalyzer::c_HitClusteringAlgoAdjacent = 2;
-const int MRawEventAnalyzer::c_HitClusteringAlgoPDF      = 3;
+//const int MRawEventAnalyzer::c_CoincidenceAlgoNone   = 0;
+//const int MRawEventAnalyzer::c_CoincidenceAlgoWindow = 1;
+//
+//const int MRawEventAnalyzer::c_EventClusteringAlgoNone     = 0;
+//const int MRawEventAnalyzer::c_EventClusteringAlgoTMVA     = 1;
+//const int MRawEventAnalyzer::c_EventClusteringAlgoDistance = 2;
+//
+//const int MRawEventAnalyzer::c_HitClusteringAlgoNone     = 0;
+//const int MRawEventAnalyzer::c_HitClusteringAlgoDistance = 1;
+//const int MRawEventAnalyzer::c_HitClusteringAlgoAdjacent = 2;
+//const int MRawEventAnalyzer::c_HitClusteringAlgoPDF      = 3;
 
 //const int MRawEventAnalyzer::c_TrackingAlgoNone            = 0;
 //const int MRawEventAnalyzer::c_TrackingAlgoModifiedPearson = 1;
@@ -103,51 +103,30 @@ const int MRawEventAnalyzer::c_HitClusteringAlgoPDF      = 3;
 //const int MRawEventAnalyzer::c_TrackingAlgoRank            = 6;
 //const int MRawEventAnalyzer::c_TrackingAlgoPearson         = 7;
 
-//namespace MRawEventAnalyzer {
-//Push the "do not change the numbers" constraint to the compiler with enum
-//  enum MRawEventAnalyzer::c_TrackingAlgo { // Also pushed to the header file.
-//    c_TrackingAlgoNone,
-//    c_TrackingAlgoModifiedPearson,
-//    c_TrackingAlgoChiSquare,
-//    c_TrackingAlgoGas,
-//    c_TrackingAlgoDirectional,
-//    c_TrackingAlgoBayesian,
-//    c_TrackingAlgoRank,
-//    c_TrackingAlgoPearson,
-//    c_TrackingAlgoKalman2D,
-//    c_TrackingAlgoKalman3D,
-//    c_TrackingAlgoFirstLayer
-//  };
-
-//  enum c_EventIdAlgo {
-//    c_EventIdDefault, c_EventIdExternal
-//  };
-//}
-
-const int MRawEventAnalyzer::c_PairDefault   = 0;
+//const int MRawEventAnalyzer::c_PairDefault   = 0;
 //const int MRawEventAnalyzer::c_PairKalman3D = 1;
 //const int MRawEventAnalyzer::c_PairKalman2D = 2;
 
-const int MRawEventAnalyzer::c_CSRAlgoNone          = 0;
-const int MRawEventAnalyzer::c_CSRAlgoFoM           = 1;
-const int MRawEventAnalyzer::c_CSRAlgoFoME          = 2;
-const int MRawEventAnalyzer::c_CSRAlgoFoMToF        = 3;
-const int MRawEventAnalyzer::c_CSRAlgoBayesian      = 4;
-const int MRawEventAnalyzer::c_CSRAlgoTMVA          = 5;
-const int MRawEventAnalyzer::c_CSRAlgoFoMToFAndE    = 6;
-
-const int MRawEventAnalyzer::c_DecayAlgoNone     = 0;
-const int MRawEventAnalyzer::c_DecayAlgoStandard = 1;
+//const int MRawEventAnalyzer::c_CSRAlgoNone          = 0;
+//const int MRawEventAnalyzer::c_CSRAlgoFoM           = 1;
+//const int MRawEventAnalyzer::c_CSRAlgoFoME          = 2;
+//const int MRawEventAnalyzer::c_CSRAlgoFoMToF        = 3;
+//const int MRawEventAnalyzer::c_CSRAlgoBayesian      = 4;
+//const int MRawEventAnalyzer::c_CSRAlgoTMVA          = 5;
+//const int MRawEventAnalyzer::c_CSRAlgoFoMToFAndE    = 6;
+//
+//const int MRawEventAnalyzer::c_DecayAlgoNone     = 0;
+//const int MRawEventAnalyzer::c_DecayAlgoStandard = 1;
 
 // DONT'T CHANGE THE NUMBERS!!
 
-const unsigned int MRawEventAnalyzer::c_AnalysisSucess                 = 0;
-const unsigned int MRawEventAnalyzer::c_AnalysisCoincidenceWindowWait  = 1;
-const unsigned int MRawEventAnalyzer::c_AnalysisEventClusteringFailed  = 2;
-const unsigned int MRawEventAnalyzer::c_AnalysisNoEventsInStore        = 3;
-const unsigned int MRawEventAnalyzer::c_AnalysisNoEventsLeftInFile     = 4;
-const unsigned int MRawEventAnalyzer::c_AnalysisSavingEventFailed      = 5;
-const unsigned int MRawEventAnalyzer::c_AnalysisUndefinedError         = 6;
+//const unsigned int MRawEventAnalyzer::c_AnalysisSucess                 = 0;
+//const unsigned int MRawEventAnalyzer::c_AnalysisCoincidenceWindowWait  = 1;
+//const unsigned int MRawEventAnalyzer::c_AnalysisEventClusteringFailed  = 2;
+//const unsigned int MRawEventAnalyzer::c_AnalysisNoEventsInStore        = 3;
+//const unsigned int MRawEventAnalyzer::c_AnalysisNoEventsLeftInFile     = 4;
+//const unsigned int MRawEventAnalyzer::c_AnalysisSavingEventFailed      = 5;
+//const unsigned int MRawEventAnalyzer::c_AnalysisUndefinedError         = 6;
 
 
 

From 08b8717eda7066e32dca4740d8bef126a49c7f83 Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Sat, 31 May 2025 13:53:10 -0400
Subject: [PATCH 166/192] FIX: bug in CSR algo enum

---
 src/revan/inc/MRawEventAnalyzer.h | 5 ++---
 src/revan/src/MGUIERAlgorithm.cxx | 1 +
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/revan/inc/MRawEventAnalyzer.h b/src/revan/inc/MRawEventAnalyzer.h
index 651ef4b42..184f99e97 100644
--- a/src/revan/inc/MRawEventAnalyzer.h
+++ b/src/revan/inc/MRawEventAnalyzer.h
@@ -211,9 +211,8 @@ class MRawEventAnalyzer
     c_CSRAlgoFoME,
     c_CSRAlgoFoMToF,
     c_CSRAlgoFoMToFAndE,
-    c_CSRAlgoBayesian };
-
-  static const int c_CSRAlgoTMVA;
+    c_CSRAlgoBayesian,
+    c_CSRAlgoTMVA };
 
   //! Set the Compton photon tracking algorithm: One of c_CSRAlgoNone, c_CSRAlgoFoM, c_CSRAlgoFoME, c_CSRAlgoFoMToF, c_CSRAlgoBayesian
   void SetCSRAlgorithm(int ID) { m_CSRAlgorithm = ID; }
diff --git a/src/revan/src/MGUIERAlgorithm.cxx b/src/revan/src/MGUIERAlgorithm.cxx
index dd2d0b3f3..3a71bc459 100644
--- a/src/revan/src/MGUIERAlgorithm.cxx
+++ b/src/revan/src/MGUIERAlgorithm.cxx
@@ -66,6 +66,7 @@ MGUIERAlgorithm::~MGUIERAlgorithm()
   delete m_EventClusteringList;
   delete m_HitClusteringList;
   delete m_TrackingList;
+  delete m_EventIdList;
   delete m_CSRList;
   delete m_PairList;
   //delete m_DecayList;

From 9fd3964bd4ef28a3c85e67ad6e3029cfc2465931 Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Thu, 5 Jun 2025 09:20:18 -0400
Subject: [PATCH 167/192] ADD: (red) Event type identification class

---
 src/revan/inc/MEREventId.h          |  122 +++
 src/revan/inc/MRawEventAnalyzer.h   |   11 +-
 src/revan/src/MEREventId.cxx        | 1176 +++++++++++++++++++++++++++
 src/revan/src/MRawEventAnalyzer.cxx |   33 +-
 4 files changed, 1332 insertions(+), 10 deletions(-)
 create mode 100644 src/revan/inc/MEREventId.h
 create mode 100644 src/revan/src/MEREventId.cxx

diff --git a/src/revan/inc/MEREventId.h b/src/revan/inc/MEREventId.h
new file mode 100644
index 000000000..2bfe5e69b
--- /dev/null
+++ b/src/revan/inc/MEREventId.h
@@ -0,0 +1,122 @@
+/*
+ * MEREventId.h
+ *
+ * Copyright (C) by Andreas Zoglauer.
+ * All rights reserved.
+ *
+ * Please see the source-file for the copyright-notice.
+ *
+ */
+
+
+#ifndef __MEREventId__
+#define __MEREventId__
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+// ROOT libs:
+#include <TROOT.h>
+
+// MEGAlib libs:
+#include "MGlobal.h"
+#include "MERConstruction.h"
+#include "MRawEventIncarnations.h"
+#include "MGeometryRevan.h"
+#include "MDDetector.h"
+
+// Forward declarations:
+class MRETrack;
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+class MEREventId : public MERConstruction
+{
+  // public interface:
+ public:
+  MEREventId();
+  virtual ~MEREventId();
+
+  //! Global parameters used by all electron tracking algorithms
+  virtual bool SetParameters(bool SearchMIPS, 
+                             bool SearchPairs,  
+                             bool SearchComptons,
+                             bool SearchPhoto,
+                             unsigned int NLayersForVertexSearch,
+                             vector<MString> DetectorList);
+  virtual bool Analyze(MRawEventIncarnations* List);
+
+  virtual bool PostAnalysis();
+  virtual MString ToString(bool CoreOnly = false) const;
+
+
+  // protected methods:
+ protected:
+  virtual void CheckForPair(MRERawEvent* RE);
+  virtual void CheckForMips(MRERawEvent* RE);
+  virtual void CheckForPhoto(MRERawEvent* RE);
+  virtual void CheckForCompton(MRERawEvent* RE);
+
+  //virtual MRawEventIncarnations* TrackComptons(MRERawEvent* ER);
+
+  //! Return true, if the RESE happened in a detector in our list
+  bool IsInTracker(MRESE* R);
+
+  // private methods:
+ private:
+
+
+
+  // protected members:
+ protected:
+  //! True, if we should look for minimum ionizing particles (muons)
+  bool m_SearchMIPs;
+  //! True, if we should look for electron/positron-pair creation events
+  bool m_SearchPairs;
+  //! Search for Compton events
+  bool m_SearchCompton;
+  //! Search for Single-site events
+  bool m_SearchPhoto;
+  
+  //! The maximum allowed layer jump (1: do not skip one single layer)
+//  unsigned int m_ComptonMaxLayerJump;
+  //! Reject all ping-pong/curl events
+//  bool m_RejectPureAmbiguities;
+  //! The best N sequenecs are passed on to the next reconstruction stage
+//  unsigned int m_NSequencesToKeep;
+
+  //! maximum number of ambiguities of Compton events before switching to high energy tracking
+//  unsigned int m_MaxNAmbiguities; 
+
+  //! If there are multiple possible Compton tracks - consider only those with a maximum number of tracks - i.e. the minimum number of object sin D1
+//  bool m_AllowOnlyMinNumberOfRESEsD1;
+
+  //! The number of layers used for vertex search
+  unsigned int m_NLayersForVertexSearch;
+
+  //! List of detectors in which the electron tracking is performed
+  vector<MDDetector*> m_DetectorList;
+  
+  double m_TimePhoto;
+  double m_TimePairs;
+  double m_TimeMips;
+  double m_TimeCompton;
+
+
+#ifdef ___CLING___
+ public:
+  ClassDef(MEREventId, 0) // no description
+#endif
+
+};
+
+#endif
+
+
+////////////////////////////////////////////////////////////////////////////////
diff --git a/src/revan/inc/MRawEventAnalyzer.h b/src/revan/inc/MRawEventAnalyzer.h
index 184f99e97..5805753dd 100644
--- a/src/revan/inc/MRawEventAnalyzer.h
+++ b/src/revan/inc/MRawEventAnalyzer.h
@@ -39,6 +39,7 @@ class MDGeometryQuest;
 class MERCoincidence;
 class MEREventClusterizer;
 class MERHitClusterizer;
+class MEREventId;
 class MERTrack;
 class MERCSR;
 class MERDecay;
@@ -107,13 +108,6 @@ class MRawEventAnalyzer
     c_AnalysisSavingEventFailed,
     c_AnalysisUndefinedError
   };
-//  static const unsigned int c_AnalysisSucess;
-//  static const unsigned int c_AnalysisCoincidenceWindowWait;
-//  static const unsigned int c_AnalysisEventClusteringFailed;
-//  static const unsigned int c_AnalysisNoEventsInStore;
-//  static const unsigned int c_AnalysisNoEventsLeftInFile;
-//  static const unsigned int c_AnalysisSavingEventFailed;
-//  static const unsigned int c_AnalysisUndefinedError;
 
   //! Return the next initial raw event from file
   //! Return zero if the input mode is not file or if the ened of the file has been reached
@@ -354,6 +348,8 @@ class MRawEventAnalyzer
   MEREventClusterizer* m_EventClusterizer;
   //! Hit clustering
   MERHitClusterizer* m_HitClusterizer;
+  //! Event type identification
+  MEREventId* m_EventId;
   //! Electron tracking
   MERTrack* m_Tracker;
   //! Compton sequence reconstruction
@@ -486,6 +482,7 @@ class MRawEventAnalyzer
   double m_TimeLoad;
   double m_TimeEventClusterize;
   double m_TimeHitClusterize;
+  double m_TimeEventId;
   double m_TimeTrack;
   double m_TimeCSR;
   double m_TimeFinalize;
diff --git a/src/revan/src/MEREventId.cxx b/src/revan/src/MEREventId.cxx
new file mode 100644
index 000000000..8d56abd7a
--- /dev/null
+++ b/src/revan/src/MEREventId.cxx
@@ -0,0 +1,1176 @@
+/*
+ * MEREventId.cxx
+ *
+ *
+ * Copyright (C) by Andreas Zoglauer.
+ * All rights reserved.
+ *
+ *
+ * This code implementation is the intellectual property of
+ * Andreas Zoglauer.
+ *
+ * By copying, distributing or modifying the Program (or any work
+ * based on the Program) you indicate your acceptance of this statement,
+ * and all its terms.
+ *
+ */
+
+
+////////////////////////////////////////////////////////////////////////////////
+//
+// MEREventId
+//
+// Base class for event reconstruction tasks, e.g. find clusters, tracks,
+// Compton sequence
+//
+////////////////////////////////////////////////////////////////////////////////
+
+
+// Include the header:
+#include "MEREventId.h"
+
+// Standard libs:
+#include <list>
+#include <algorithm>
+#include <functional>
+#include <limits>
+#include <cfloat>
+using namespace std;
+
+// ROOT libs:
+
+// MEGAlib libs:
+#include "MAssert.h"
+#include "MStreams.h"
+#include "MRESE.h"
+#include "MRETrack.h"
+#include "MREHit.h"
+#include "MMuonEvent.h"
+#include "MTimer.h"
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+#ifdef ___CLING___
+ClassImp(MEREventId)
+#endif
+
+
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+MEREventId::MEREventId()
+{
+  // Construct an instance of MEREventId
+
+  m_SearchPairs = true;
+  m_SearchMIPs = true;
+  m_SearchCompton = true;
+  m_SearchPhoto = true;
+
+  //m_MaxNAmbiguities = 5;
+  //m_AllowOnlyMinNumberOfRESEsD1 = false;
+
+  //m_ComptonMaxLayerJump = 2;
+  //m_RejectPureAmbiguities = false;
+
+  m_TimePairs = 0;
+  m_TimeMips = 0;
+  m_TimePhoto = 0;
+  m_TimeCompton = 0;
+
+  m_NLayersForVertexSearch = 5;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+MEREventId::~MEREventId()
+{
+  // Delete this instance of MEREventId
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MEREventId::SetParameters(bool SearchMIPs,
+                             bool SearchPairs,
+                             bool SearchCompton,
+                             bool SearchPhoto,
+                             unsigned int NLayersForVertexSearch,
+                             vector<MString> DetectorList)
+{
+  m_SearchMIPs = SearchMIPs;
+  m_SearchPairs = SearchPairs;
+  m_SearchPhoto = SearchPhoto;
+  m_SearchCompton = SearchCompton;
+  m_NLayersForVertexSearch = NLayersForVertexSearch;
+
+  if (m_NLayersForVertexSearch < 4) {
+    merr<<"Error: Revan (tracking): NLayersForVertexSearch (="<<m_NLayersForVertexSearch<<") must be >= 4. Setting it to 4."<<show;
+    m_NLayersForVertexSearch = 4;
+  }
+/*
+  if (m_ComptonMaxLayerJump < 1) {
+    merr<<"Error: Revan (tracking): MaxLayerJump must be >= 1. Setting it to 1."<<show;
+    m_ComptonMaxLayerJump = 1;
+  }
+
+  if (m_NSequencesToKeep < 1) {
+    merr<<"Error: Revan (tracking): NSequencesToKeep must be >= 1. Setting it to 1."<<show;
+    m_NSequencesToKeep = 1;
+  }
+*/
+  // Check if for the tracking detector names real detectors exist
+//  if (DetectorList.size() == 0) {
+//    merr<<"Error: Revan (tracking): You did not give *any* detectors for electron tracking."<<endl;
+//    merr<<"No electron tracking will be performed!"<<show;
+//  } else {
+  for (unsigned int n = 0; n < DetectorList.size(); ++n) {//Ignored if no detector used for tracking
+    bool Found = false;
+    for (unsigned int d = 0; d < m_Geometry->GetNDetectors(); ++d) {
+      if (m_Geometry->GetDetectorAt(d)->GetName() == DetectorList[n]) {
+        m_DetectorList.push_back(m_Geometry->GetDetectorAt(d));
+        Found = true;
+      }
+    }
+    if (Found == false) {
+      merr<<"Error: Revan (tracking): Did not find detector "<<DetectorList[n]<<" in geometry."<<endl;
+      merr<<"No electron tracking will be performed in this detector!"<<show;
+    }
+  }
+  if (m_DetectorList.size() == 0 && (m_SearchMIPs || m_SearchPairs) ) {
+    merr<<"Error: Revan (tracking): I could not find *any* detectors for electron tracking."<<endl;
+    merr<<"No electron tracking will be performed!"<<show;
+  }
+//  }
+
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MEREventId::Analyze(MRawEventIncarnations* REList)
+{
+  // Analyze the raw event...
+
+  massert(m_Geometry != 0);
+
+  MERConstruction::Analyze(REList);
+
+  // mdebug<<m_List->ToString()<<endl;
+
+  mdebug<<"Starting tracking"<<endl;
+
+
+  bool Identified = false;
+  MRERawEvent* RE = 0;
+  MRawEventIncarnations* List = 0;
+  MRESE* RESE = 0;
+  MRETrack* Track = 0;
+  MTimer Timer;
+
+  // Step A: Preparation:
+
+  // Step A (bis): Single-site events
+/*
+  Timer.Start();
+  if (Identified == false && m_SearchPhoto == true) {
+    mdebug <<"* Search for single-site events"<<endl;
+    for (int e = 0; e < m_List ///////////////
+    if (RE->GetNRESE() == 1) {
+      if (RE->GetRESEAt(0)->GetType() == MRESE::c_Hit || 
+        RE->GetRESEAt(0)->GetType() == MRESE::c_Cluster) {
+        RE->SetEventType(MRERawEvent::c_PhotoEvent);
+        RE->SetGoodEvent(true);
+      }
+    }
+  }
+  m_TimePhoto += Timer.ElapsedTime();
+*/
+
+  // Before we do anything we check if we have at least two hits in one of the defines electron trackers
+  bool StartTracking = false;
+  for (int e = 0; e < m_List->GetNRawEvents(); e++) {
+    RE = m_List->GetRawEventAt(e);
+    unsigned int NHits = 0;
+    for (int h = 0; h < RE->GetNRESEs(); ++h) {
+      if (IsInTracker(RE->GetRESEAt(h)) == true) {
+        ++NHits;
+      }
+    }
+    //if (NHits > 50) {
+    //  mout<<"Too many hits for tracking: "<<NHits<<endl;
+    //  return true;
+    //}
+    if (NHits >= 2) {
+      StartTracking = true;
+      break;
+    }
+  }
+/*
+  if (StartTracking == false) {
+    mdebug<<"Not enough hits in tracker!"<<endl;
+    return true;
+  }
+*/
+
+  // Step B: Pairs
+
+  Timer.Start();
+  if (StartTracking && !Identified && m_SearchPairs) {
+    mdebug<<"* Search for pairs: Vertex"<<endl;
+    bool HasVertices = false;
+    int e_max = m_List->GetNRawEvents();
+    for (int e = 0; e < e_max; e++) {
+      RE = m_List->GetRawEventAt(e);
+      List = CheckForPair(RE);
+      if (List != 0) {
+        mdebug<<"List: "<<List->GetNRawEvents()<<endl;
+        HasVertices = true;
+        m_List->DeleteRawEvent(RE);
+        e--;
+        e_max--;
+        for (int i = 0; i < List->GetNRawEvents(); i++) {
+          m_List->AddRawEvent(List->GetRawEventAt(i));
+        }
+        delete List;
+        mdebug<<"Tracking: Event has vertex!"<<endl;
+      }
+    }
+    /*
+    if (HasVertices == true) {
+      // Let's analyze pairs:
+      mdebug<<"* Step: Pair tracking"<<endl;
+      mdebug<<m_List->ToString()<<endl;
+      int e_max = m_List->GetNRawEvents();
+      for (int e = 0; e < e_max; e++) {
+        RE = m_List->GetRawEventAt(e);
+        if (RE->GetVertex() != 0) {
+          TrackPairs(RE);
+        }
+      }
+      mdebug<<"Tracking:  Successful identification: Pair event!"<<endl;
+      mdebug<<"        Pair results:"<<endl;
+      mdebug<<m_List->ToString()<<endl;
+      mdebug<<endl;
+      Identified = true;
+      m_List->SetOptimumEvent(RE);
+      m_List->SetBestTryEvent(RE);
+    } // pair...
+  }*/
+  m_TimePairs += Timer.ElapsedTime();
+
+
+  // Step C: Mips
+
+  Timer.Start();
+  if (StartTracking && !Identified && m_SearchMIPs) {
+    mdebug<<"* Search for MIPs"<<endl;
+    for (int e = 0; e < m_List->GetNRawEvents(); e++) {
+      RE = m_List->GetRawEventAt(e);
+      CheckForMips(RE);
+      // If we have found a MIP then we are done!
+      if (RE->GetEventType() == MRERawEvent::c_MipEvent) {
+        mdebug<<"Tracking: Successful identification: MIP (probably muon)"<<endl;
+        Identified = true;
+        m_List->SetOptimumEvent(RE);
+        m_List->SetBestTryEvent(RE);
+      }
+      if (RE->GetEventType() == MRERawEvent::c_ShowerEvent) {
+        mdebug<<"Tracking: Successful identification: Shower"<<endl;
+        Identified = true;
+        m_List->SetOptimumEvent(RE);
+        m_List->SetBestTryEvent(RE);
+      }
+    }
+    mdebug<<"        MIP results:"<<endl;
+    mdebug<<m_List->ToString()<<endl;
+    mdebug<<endl;
+  }
+  m_TimeMips += Timer.ElapsedTime();
+
+
+  // Step C: Compton tracks
+
+  // implement smtg here
+
+/*
+  if (Identified == false && m_SearchComptons == true) {
+    mdebug<<"* Search for Comptons"<<endl;
+
+    // Step C.1: Generate the links
+
+    Timer.Start();
+    // Generate a list of possible Compton tracks -
+    // we only want to have sequences now and do not yet care about directions!
+    int e_max = m_List->GetNRawEvents();
+    for (int e = 0; e < e_max; e++) {
+      RE = m_List->GetRawEventAt(e);
+      List = TrackComptons(RE);
+      if (List != 0) {
+        m_List->DeleteRawEvent(RE);
+        e--;
+        e_max--;
+        for (int i = 0; i < List->GetNRawEvents(); i++) {
+          m_List->AddRawEvent(List->GetRawEventAt(i));
+        }
+        delete List;
+      }
+    }
+    m_TimeComptonSequences += Timer.ElapsedTime();
+
+
+    // We now accept only events with the maximum possible number of tracks,
+    // if the flag is set
+    if (m_AllowOnlyMinNumberOfRESEsD1 == true) {
+      mdebug<<"Allowing only events with the maximum number of elements in the tracks. Starting with this amount: "<<m_List->GetNRawEvents()<<endl;
+      int MinN = numeric_limits<int>::max();
+      for (int e = 0; e < m_List->GetNRawEvents(); e++) {
+        int CurrentN = 0;
+        RE = m_List->GetRawEventAt(e);
+        for (int r = 0; r < RE->GetNRESEs(); r++) {
+          RESE = RE->GetRESEAt(r);
+          if (IsInTracker(RESE) == true) {
+            CurrentN++;
+          }
+        }
+        if (CurrentN < MinN) MinN = CurrentN;
+      }
+
+      for (int e = 0; e < m_List->GetNRawEvents(); e++) {
+        int CurrentN = 0;
+        RE = m_List->GetRawEventAt(e);
+        for (int r = 0; r < RE->GetNRESEs(); r++) {
+          RESE = RE->GetRESEAt(r);
+          if (IsInTracker(RESE) == true) CurrentN++;
+        }
+        if (CurrentN > MinN) {
+          m_List->DeleteRawEvent(RE);
+          e--;
+        }
+      }
+      mdebug<<"Keeping "<<m_List->GetNRawEvents()<<" possibilities for further processing."<<endl;
+    }
+
+
+    // Step C.2: Duplicate each track and assign the two possible start positions
+
+    Timer.Start();
+    mdebug<<"Checking for track directions..."<<endl;
+
+    int IDRESE = 0;
+    int IDEP = 0;
+    MRERawEvent* REdup = 0;
+
+    for (int e = 0; e < m_List->GetNRawEvents(); e++) {
+      RE = m_List->GetRawEventAt(e);
+
+      for (int r = 0; r < RE->GetNRESEs(); r++) {
+        RESE = RE->GetRESEAt(r);
+        IDRESE = RESE->GetID();
+        if (RESE->GetType() == MRESE::c_Track) {
+          Track = (MRETrack *) RESE;
+          if (Track->GetStartPoint() == 0) {
+            massert(Track->GetNEndPoints() == 2);
+
+            IDEP = Track->GetEndPointAt(0)->GetID();
+            REdup = RE->Duplicate();
+            ((MRETrack *) (REdup->GetRESE(IDRESE)))->SetStartPoint(((MRETrack *) (REdup->GetRESE(IDRESE)))->GetRESE(IDEP));
+            m_List->AddRawEvent(REdup);
+
+            Track->SetStartPoint(Track->GetEndPointAt(1));
+          }
+        }
+      }
+    }
+
+    // Step C.3:  Find the most probable combination
+
+    for (int e = 0; e < m_List->GetNRawEvents(); e++) {
+      RE = m_List->GetRawEventAt(e);
+      EvaluateTracks(RE);
+    }
+    SortByTrackQualityFactor(m_List);
+
+    // We always have 1 raw event - the original one!
+    massert(m_List->GetNRawEvents() >= 1);
+
+    mdebug<<m_List->ToString()<<endl;
+
+    mdebug<<"Step 5: Best track solution out of "<<m_List->GetNRawEvents()<<": "<<endl
+          <<m_List->GetRawEventAt(0)->ToString()<<endl;
+
+    mdebug<<"Tracking: Best Compton track: "<<m_List->GetRawEventAt(0)->GetTrackQualityFactor()<<endl;
+
+    //m_List->SetValidEvent(m_List->GetRawEventAt(m_List->GetNRawEvents()-1));
+    m_List->SetBestTryEvent(m_List->GetRawEventAt(0));
+
+
+    // Remove all not-so-good sequences:
+    for (int e = m_NSequencesToKeep; e < m_List->GetNRawEvents(); ++e) {
+      RE = m_List->GetRawEventAt(e);
+      m_List->DeleteRawEvent(RE);
+      e--;
+    }
+
+    m_TimeComptonDirections += Timer.ElapsedTime();
+  }*/
+
+
+  // Step E: Epilog
+
+  mdebug<<"Result of tracking:"<<endl;
+  mdebug<<m_List->ToString()<<endl;
+
+
+  return true;
+}
+
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MEREventId::IsInTracker(MRESE* R)
+{
+  //! Return true, if the RESE happened in a detector in our list
+
+  // While building tracks their volume sequence might not be correct
+  // But, if we have a track, it is in the tracker... so:
+  if (R->GetType() == MRESE::c_Track) return true;
+
+  MDVolumeSequence* VS = R->GetVolumeSequence();
+  for (unsigned int d = 0; d < m_DetectorList.size(); ++d) {
+    if (VS->GetDetector() == m_DetectorList[d]) {
+      return true;
+    }
+  }
+  return false;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+void MEREventId::CheckForPair(MRERawEvent* RE)
+{
+  // Check if this event could be a pair:
+  //
+  // The typical pattern of a pair is:
+  // (a) There is a vertex
+  // (b) In N layers above/below are at least two hits
+
+  // Search the vertex:
+  // The vertex is at this point a (non-ambiguous) track or a single (clustered)
+  // hit followed by at least N layers with two hits per layer:
+
+  mdebug<<"Searching for a pair vertex"<<endl;
+
+  MRawEventIncarnations *List = 0;
+  bool OnlyHitInLayer = false;
+  //unsigned int MaximumLayerJump = 2;
+  //MRESE* RESE = 0;
+  unsigned int SearchRange = 30;
+  //int MinPairLength = m_NLayersForVertexSearch;
+
+  // Create a list of RESEs sorted by depth in tracker
+  vector<MRESE*> ReseList;
+  for (int h = 0; h < RE->GetNRESEs(); h++) {
+    if (IsInTracker(RE->GetRESEAt(h)) == false) continue;
+    // Everthing below 90 has to go -- eliminate Bremsstrahlung
+    //if (RE->GetRESEAt(h)->GetEnergy() < 90) continue;
+
+    ReseList.push_back(RE->GetRESEAt(h));
+  }
+  sort(ReseList.begin(), ReseList.end(), CompareRESEByZ());
+
+  mdebug<<"RESE's sorted by depth: "<<endl;
+  vector<MRESE*>::iterator Iterator1;
+  vector<MRESE*>::iterator Iterator2;
+  for (Iterator1 = ReseList.begin(); Iterator1 != ReseList.end(); Iterator1++) {
+    mdebug<<(*Iterator1)->GetID()<<": "<<(*Iterator1)->GetPosition().Z()<<endl;
+  }
+
+  // For each of the RESE's in the list check if it could be the first of the vertex
+  for (Iterator1 = ReseList.begin(); Iterator1 != ReseList.end(); Iterator1++) {
+
+    // If it is a single hit, and if it is the only one in its layer:
+    OnlyHitInLayer = true;
+    for (Iterator2 = ReseList.begin(); Iterator2 != ReseList.end(); Iterator2++) {
+      if ((*Iterator1) == (*Iterator2)) continue;
+      if (m_Geometry->AreInSameLayer((*Iterator1), (*Iterator2)) == true) {
+        OnlyHitInLayer = false;
+        break;
+      }
+    }
+    if (OnlyHitInLayer == false) continue;
+    mdebug<<"Search vertex: Only hit in layer:"<<endl;
+    mdebug<<(*Iterator1)->ToString()<<endl;
+
+    // We only have one hit:
+    vector<int> NBelow(SearchRange, 0);
+    vector<int> NAbove(SearchRange, 0);
+
+    int Distance;
+    for (Iterator2 = ReseList.begin(); Iterator2 != ReseList.end(); Iterator2++) {
+      if ((*Iterator1) == (*Iterator2)) continue;
+      // Ignore small energy deposits equivalent to bremsstrahlung
+      //if ((*Iterator2)->GetEnergy() < 90) continue;
+
+      Distance = m_Geometry->GetLayerDistance((*Iterator1), (*Iterator2));
+      if (Distance > 0 && Distance < int(SearchRange)) NAbove[Distance]++;
+      if (Distance < 0 && abs(Distance) < int(SearchRange)) NBelow[abs(Distance)]++;
+      massert(Distance != 0); // In this case the algorithm is broken...
+      //mdebug<<"Distance "<<(*Iterator1)->GetID()<<" - "<<(*Iterator2)->GetID()<<": "<<Distance<<endl;
+    }
+
+
+    // Under the following conditions we do have a pair:
+
+    // Pair starting from top
+    MRESE* Vertex = 0;
+    int VertexDirection = 0;
+
+
+    // Check for vertex below
+    if (NAbove[1] == 0) {
+      int StartIndex = 0; // We start when we have 2 hits for the first time
+      int StopIndex = 0; // We stop when we skip 2 layers for the first time
+      int LayersWithAtLeastTwoHitsBetweenStartAndStop = 0;
+
+
+      for (unsigned int d = 1; d < SearchRange-1; ++d) {
+        // We stop when we skip 2 layers for the first time
+        if (NBelow[d] == 0 && NBelow[d+1] == 0) break;
+        StopIndex = d;
+        // Store the index where we have 2 hits for the first time, twice
+        if (StartIndex == 0 && NBelow[d] > 1 && NBelow[d+1] > 1) StartIndex = d;
+
+        if (StartIndex != 0) {
+          if (NBelow[d] >= 2) ++LayersWithAtLeastTwoHitsBetweenStartAndStop;
+        }
+      }
+
+      // Since we can have just a single track at the end, move upward until we have at least two hits in a row
+      for (unsigned int d = StopIndex; d > 2; --d) {
+        if (NBelow[d-1] >= 2 && NBelow[d-2] >= 2) break;
+        StopIndex = d;
+      }
+
+      mdebug<<"Search vertex ("<<(*Iterator1)->GetPosition().Z()<<"): Above: ";
+      for (int i: NAbove) mdebug<<i<<" ";
+      mdebug<<endl;
+      mdebug<<"Search vertex ("<<(*Iterator1)->GetPosition().Z()<<"): Below: ";
+      for (int i: NBelow) mdebug<<i<<" ";
+      mdebug<<endl;
+
+      mdebug<<"Vertex statistics (max: "<<SearchRange<<"): layers used: "<<StopIndex<<", start of 2+ hits: "<<StartIndex<<"  layers with 2+ hits between start and stop: "<<LayersWithAtLeastTwoHitsBetweenStartAndStop<<" ("<<((StopIndex-StartIndex > 0) ? 100.0*LayersWithAtLeastTwoHitsBetweenStartAndStop/(StopIndex-StartIndex) : 0)<<"%)"<<endl;
+
+      if (LayersWithAtLeastTwoHitsBetweenStartAndStop > 4 && double (LayersWithAtLeastTwoHitsBetweenStartAndStop)/(StopIndex-StartIndex) > 0.5) {
+        // A.L. Why require that at least half the layers should have two hits?
+        Vertex = (*Iterator1);
+        VertexDirection = -1;
+      }
+    }
+
+    if (Vertex != 0) {
+      if (List == 0) List = new MRawEventIncarnations();
+      RE->SetVertex(Vertex);
+      RE->SetVertexDirection(VertexDirection);
+      MRERawEvent *New = RE->Duplicate();
+      RE->SetVertex(0);
+      List->AddRawEvent(New);
+      mdebug<<"Search vertex: Found vertex: "<<Vertex->GetID()<<endl;
+      break; // Only take first right now
+    }
+  }
+
+  //return List;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+void MEREventId::CheckForMips(MRERawEvent* RE)
+{
+  // Check if the events structure can be created by a massive interacting
+  // particle like myons:
+  //
+  // The typical pattern of a MIP is:
+  // We have a straight track with serveral hits which, do not belong to the
+  // original MIP, but to its secondaries, bremsstrahlung etc.
+
+  mdebug<<"Checking for Mips..."<<endl;
+
+  const int MinElements = 4;
+  const double MinStraightness = 0.05;
+
+  // a. Check all hit combinations in D1 for their straightness
+  vector<MRETrack*> TrackArray; // Array of Tracks
+
+  vector<MRESE*> D1Hits;
+  for (int i = 0; i < RE->GetNRESEs(); ++i) {
+    if (IsInTracker(RE->GetRESEAt(i)) == true) {
+      D1Hits.push_back(RE->GetRESEAt(i));
+    }
+  }
+
+  // Sort the array for decreasing z:
+  MRESE* Temp = 0;
+  unsigned int HighestPos = 0;
+  double HighestValue = -1;
+  for (unsigned int i = 0; i < D1Hits.size(); ++i) {
+    HighestPos = i;
+    HighestValue = D1Hits[i]->GetPosition().Z();
+    for (unsigned int j = i; j < D1Hits.size(); ++j) {
+      if (D1Hits[j]->GetPosition().Z() > HighestValue) {
+        HighestValue = D1Hits[j]->GetPosition().Z();
+        HighestPos = j;
+      }
+    }
+    // Change Position
+    if (HighestPos != i) {
+      Temp = D1Hits[i];
+      D1Hits[i] = D1Hits[HighestPos];
+      D1Hits[HighestPos] = Temp;
+    }
+  }
+
+
+  // We look for straight tripple combinations:
+  unsigned int max = D1Hits.size();
+  MRESE* iRESE;
+  MRESE* jRESE;
+  MRESE* kRESE;
+  MRETrack* Track = 0;
+  MVector Direction1, Direction2;
+  for (unsigned int i = 0; i < max; ++i) {
+    if (D1Hits[i] == 0) continue;
+    iRESE = D1Hits[i];
+    //mdebug<<"i:"<<iRESE->ToString()<<endl;
+
+    for (unsigned int j = i+1; j < max; ++j) {
+      if (D1Hits[j] == 0) continue;
+      jRESE = D1Hits[j];
+      //mdebug<<"j:"<<jRESE->ToString()<<endl;
+      Direction1 = jRESE->GetPosition() - iRESE->GetPosition();
+
+      Track = 0; // No memory leak!
+
+      for (unsigned int k = j+1; k < max; ++k) {
+        if (D1Hits[k] == 0) continue;
+        kRESE = D1Hits[k];
+        //mdebug<<"k:"<<kRESE->ToString()<<endl;
+        Direction2 = kRESE->GetPosition() - jRESE->GetPosition();
+
+        // Check the straightness:
+        //mdebug<<"Angle: "<<Direction1.Angle(Direction2)<<endl;
+        if (Direction1.Angle(Direction2) < MinStraightness) {
+          //mdebug<<"Found some straight track!!!!"<<endl;
+          if (Track == 0) {
+            //mdebug<<"Creating new track!!!!"<<endl;
+            Track = new MRETrack();
+            TrackArray.push_back(Track);
+            Track->AddRESE(iRESE);
+            Track->AddRESE(jRESE);
+            Track->AddRESE(kRESE);
+            D1Hits[i] = 0;
+            D1Hits[j] = 0;
+            D1Hits[k] = 0;
+          } else {
+            Track->AddRESE(kRESE);
+            D1Hits[k] = 0;
+          }
+
+          Direction1 = Direction2;
+        }
+      } // end k
+
+      if (Track != 0) break;
+
+    } // end j
+  } // end i
+
+  // We need at least one track with at least MinElements hits:
+  // For now: Search for the largest track:
+  HighestPos = 0;
+  HighestValue = -1;
+  for (unsigned int i = 0; i < TrackArray.size(); ++i) {
+    if (TrackArray[i]->GetNRESEs() > MinElements) {
+      HighestValue = TrackArray[i]->GetNRESEs();
+      HighestPos = i;
+    }
+  }
+
+
+  // Now the result:
+
+  // a. Definitely a muon
+  if (TrackArray.size() == 1) {
+    mdebug<<"==> This was fucking easy! Found a muon!"<<endl;
+
+    // a. Integrate the track into this raw event:
+    TrackArray[HighestPos]->LinkSequential();
+    for (unsigned int i = 0; i < (unsigned int) TrackArray[HighestPos]->GetNRESEs(); ++i) {
+      RE->RemoveRESE(TrackArray[HighestPos]->GetRESEAt(i));
+    }
+    EvaluateTrack(TrackArray[HighestPos]);
+    RE->AddRESE(TrackArray[HighestPos]);
+    RE->CompressRESEs();
+
+    // b. Store the new event:
+    MMuonEvent* Muon = new MMuonEvent(); // is later stored as m_Event!
+    Muon->SetEnergy(RE->GetEnergy());
+    Muon->SetDirection(TrackArray[HighestPos]->GetAverageDirection());
+    Muon->SetCenterOfGravity(TrackArray[HighestPos]->GetCenterOfGravity());
+
+    // c. Remove the track from the array
+    for (unsigned int i = 0; i < TrackArray.size(); ++i) {
+      if (i != HighestPos) delete TrackArray[i];
+    }
+
+    // d. This is a good event...
+    RE->SetPhysicalEvent(Muon);
+    RE->SetEventType(MRERawEvent::c_MipEvent);
+    RE->SetGoodEvent(true);
+  }
+  // b. A shower
+  else if (TrackArray.size() > 1) {
+    mdebug<<"==> Found a shower!"<<endl;
+    RE->SetEventType(MRERawEvent::c_ShowerEvent);
+
+    // b. Integrate all tracks into this raw event:
+    for (unsigned int i = 0; i < TrackArray.size(); ++i) {
+      TrackArray[i]->LinkSequential();
+      for (unsigned int j = 0; j < (unsigned int) TrackArray[i]->GetNRESEs(); ++j) {
+        RE->RemoveRESE(TrackArray[i]->GetRESEAt(j));
+      }
+      EvaluateTrack(TrackArray[i]);
+      RE->CompressRESEs();
+      RE->AddRESE(TrackArray[i]);
+      RE->SetGoodEvent(true);
+    }
+  }
+
+  // return;
+}
+
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+/*
+MRawEventIncarnations* MEREventId::TrackComptons(MRERawEvent* RE)
+{
+  mdebug<<"Track Compton events..."<<endl;
+
+  MRESE* RESE = 0;
+
+  mdebug<<"Create list:"<<endl;
+
+  // Create a list consisting of the RESEs and their distance:
+  int Dist = 0;
+  bool Added = false;
+  vector<MRESE*> MasterRESEs;
+  vector<vector<MRESEDist> > DistList;
+  vector<MRESEDist>::iterator DistListIter;
+
+  int i_max = RE->GetNRESEs();
+  for (int i = 0; i < i_max; i++) {
+    RESE = RE->GetRESEAt(i);
+
+    // if it's not in D1 reject it
+    if (IsInTracker(RESE) == false) {
+      continue;
+    }
+
+    Added = false;
+    for (unsigned int m = 0; m < MasterRESEs.size(); ++m) {
+      Dist = m_Geometry->GetLayerDistance(MasterRESEs[m], RESE);
+      if (Dist == MGeometryRevan::c_DifferentTracker) {
+        continue;
+      }
+      MRESEDist RD(RESE, Dist);
+      DistList[m].push_back(RD);
+      Added = true;
+    }
+    if (Added == false) {
+      MasterRESEs.push_back(RESE);
+      DistList.resize(MasterRESEs.size());
+      MRESEDist RD(RESE, 0);
+      DistList[DistList.size()-1].push_back(RD);
+    }
+  }
+
+  // Sort the list:
+  for (unsigned int m = 0; m < MasterRESEs.size(); ++m) {
+    sort(DistList[m].begin(), DistList[m].end(), MRESEDistCompare);
+  }
+
+  // Create the layer occupation:
+  vector<map<int, int> > OccupationList;
+  OccupationList.resize(DistList.size());
+
+  for (unsigned int m = 0; m < DistList.size(); ++m) {
+    for (DistListIter = DistList[m].begin();
+         DistListIter != DistList[m].end(); DistListIter++) {
+      OccupationList[m][(*DistListIter).Distance]++;
+    }
+  }
+
+  // Dump the list:
+  for (unsigned int m = 0; m < DistList.size(); ++m) {
+    mdebug<<"MasterRESE: "<<MasterRESEs[m]->GetID()<<endl;
+    for (DistListIter = DistList[m].begin();
+         DistListIter != DistList[m].end(); DistListIter++) {
+      mdebug<<"  ID "<<(*DistListIter).RESE->GetID()<<": Distance="
+            <<(*DistListIter).Distance<<" ("
+            <<OccupationList[m][(*DistListIter).Distance]<<")"<<endl;
+    }
+  }
+
+  // Augment everything non-ambiguous to linked RESEs:
+  unsigned int NAmbiguities = 0;
+  bool IsPureAmbiguity = true;
+  const int NoDist = numeric_limits<int>::max();
+  int LastDist = NoDist;
+  MRESE* LastRESE = 0;
+  for (unsigned int m = 0; m < DistList.size(); ++m) {
+    NAmbiguities += DistList[m].size();
+    for (DistListIter = DistList[m].begin();
+         DistListIter != DistList[m].end(); DistListIter++) {
+      if (OccupationList[m][(*DistListIter).Distance] != 1) {
+        LastRESE = 0;
+        LastDist = NoDist;
+        continue;
+      } else {
+        RESE = (*DistListIter).RESE;
+        if (LastRESE != 0) {
+          if ((unsigned int) abs(LastDist - (*DistListIter).Distance) <= m_ComptonMaxLayerJump) {
+            RESE->AddLink(LastRESE);
+            LastRESE->AddLink(RESE);
+            LastDist = (*DistListIter).Distance;
+            NAmbiguities--;
+            IsPureAmbiguity = false;
+          }
+        }
+        LastRESE = RESE;
+        LastDist = (*DistListIter).Distance;
+      }
+    }
+  }
+
+
+  MRawEventIncarnations* List = new MRawEventIncarnations(); 
+
+  if (IsPureAmbiguity == true && m_RejectPureAmbiguities == true) {
+    mout<<"Tracking: Rejecting purely ambiguous event!"<<endl;
+    List->AddRawEvent(RE->Duplicate());
+    return List;
+  }
+
+  if (NAmbiguities <= m_MaxNAmbiguities) {
+    // Find ambiguous sequences
+    mdebug<<"Testing ambiguous sequences"<<endl;
+
+    List->AddRawEvent(RE->Duplicate());
+
+    MRESE* RESEmain = 0;
+    MRESE* RESEp1 = 0;
+    MRESE* RESEp2 = 0;
+
+    vector<MRESEDist> Partners;
+    vector<MRESEDist>::iterator SecDistListIter;
+    vector<MRESEDist>::iterator TerDistListIter;
+
+    int NNewREs;
+    MRERawEvent* NewRE = 0;
+    MRERawEvent* NewREdup = 0;
+
+    // Find a list of all possible combinations:
+    for (unsigned int m = 0; m < DistList.size(); ++m) {
+      for (DistListIter = DistList[m].begin();
+           DistListIter != DistList[m].end(); DistListIter++) {
+
+        RESEmain = (*DistListIter).RESE;
+
+        if (RESEmain->GetNLinks() >= 2) {
+          continue;
+        }
+
+        // Find all possible partners:
+        int Diff = 0;
+        Partners.clear();
+        for (SecDistListIter = DistListIter+1;
+             SecDistListIter != DistList[m].end(); SecDistListIter++) {
+          if ((*SecDistListIter).Distance == (*DistListIter).Distance) {
+            continue;
+          }
+          if (Diff == 0) {
+            Diff = (*SecDistListIter).Distance - (*DistListIter).Distance;
+          }
+          // Only use the nearest neighbor:
+          if (Diff != (*SecDistListIter).Distance - (*DistListIter).Distance ||
+              (unsigned int) abs(Diff) > m_ComptonMaxLayerJump) {
+            break;
+          }
+          Partners.push_back((*SecDistListIter));
+        }
+
+        mdebug<<"New partners for "<<RESEmain->GetID()<<": ";
+        for (SecDistListIter = Partners.begin();
+             SecDistListIter != Partners.end(); SecDistListIter++) {
+          mdebug<<(*SecDistListIter).RESE->GetID()<<" ";
+        }
+        mdebug<<endl;
+
+
+        // Now generate the links:
+        NNewREs = List->GetNRawEvents();
+        for (int t = 0; t < NNewREs; ++t) {
+          NewRE = List->GetRawEventAt(t);
+
+          if (NewRE->GetRESE(RESEmain->GetID())->GetNLinks() == 2) {
+            continue;
+          }
+
+          // Single partners
+          mdebug<<"Searching single partners for "<<RESEmain->GetID()<<endl;
+          for (SecDistListIter = Partners.begin();
+               SecDistListIter != Partners.end(); SecDistListIter++) {
+            RESEp1 = (*SecDistListIter).RESE;
+
+            if (NewRE->GetRESE(RESEmain->GetID())->IsLink(NewRE->GetRESE(RESEp1->GetID())) == true) {
+              continue;
+            }
+
+            if (NewRE->GetRESE(RESEp1->GetID())->GetNLinks() <= 1) {
+              mdebug<<"Linking: "<<RESEmain->GetID()<<" with "<<RESEp1->GetID()<<endl;
+              NewREdup = NewRE->Duplicate();
+              NewREdup->GetRESE(RESEmain->GetID())->
+                AddLink(NewREdup->GetRESE(RESEp1->GetID()));
+              NewREdup->GetRESE(RESEp1->GetID())->
+                AddLink(NewREdup->GetRESE(RESEmain->GetID()));
+              List->AddRawEvent(NewREdup);
+            }
+          } // end single partner loop
+
+          if (NewRE->GetRESE(RESEmain->GetID())->GetNLinks() > 0) {
+            continue;
+          }
+
+          // Double partners:
+          mdebug<<"Searching double partners for "<<RESEmain->GetID()<<endl;
+          for (SecDistListIter = Partners.begin();
+               SecDistListIter != Partners.end(); SecDistListIter++) {
+
+            RESEp1 = (*SecDistListIter).RESE;
+            if (NewRE->GetRESE(RESEp1->GetID())->GetNLinks() > 1) {
+              continue;
+            }
+            if (NewRE->GetRESE(RESEmain->GetID())
+                ->IsLink(NewRE->GetRESE(RESEp1->GetID())) == true) {
+              continue;
+            }
+            for (TerDistListIter = SecDistListIter+1;
+                 TerDistListIter != Partners.end(); TerDistListIter++) {
+              RESEp2 = (*TerDistListIter).RESE;
+              if (NewRE->GetRESE(RESEp2->GetID())->GetNLinks() > 1) {
+                continue;
+              }
+              if (NewRE->GetRESE(RESEmain->GetID())->IsLink(NewRE->GetRESE(RESEp2->GetID())) == true) {
+                continue;
+              }
+              mdebug<<"Double link: "<<RESEmain->GetID()<<" with "<<RESEp1->GetID()<<" and "<<RESEp2->GetID()<<endl;
+              NewREdup = NewRE->Duplicate();
+              NewREdup->GetRESE(RESEmain->GetID())->
+                AddLink(NewREdup->GetRESE(RESEp1->GetID()));
+              NewREdup->GetRESE(RESEp1->GetID())->
+                AddLink(NewREdup->GetRESE(RESEmain->GetID()));
+              NewREdup->GetRESE(RESEmain->GetID())->
+                AddLink(NewREdup->GetRESE(RESEp2->GetID()));
+              NewREdup->GetRESE(RESEp2->GetID())->
+                AddLink(NewREdup->GetRESE(RESEmain->GetID()));
+              //mdebug<<"NewREdup: "<<endl<<NewREdup->ToString()<<endl;
+              List->AddRawEvent(NewREdup);
+            }
+          } // end double partner loop
+
+        } // end loop over List
+      }
+    }
+
+    // Create tracks in the list:
+    mdebug<<"Newly tracked events: "<<List->GetNRawEvents()<<endl;
+    for (int i = 0; i < List->GetNRawEvents(); i++) {
+      mdebug<<List->GetRawEventAt(i)->ToString()<<endl;;
+    }
+
+    // Create tracks in the list:
+    for (int i = 0; i < List->GetNRawEvents(); i++) {
+      if (List->GetRawEventAt(i)->CreateTracks() == false) {
+        List->DeleteRawEvent(List->GetRawEventAt(i));
+        i--;
+        continue;
+      }
+    }
+
+  } else {
+    // High energy Compton tracking - very similar to that of pairs:
+    // We do NOT generate multiple raw events here!
+
+    mdebug<<"Doing high energy electron tracking..."<<endl;
+
+    // Only continue if we already have a track segment, from which we can start:
+
+    // Upgrade links to tracks...
+    if (RE->CreateTracks() == false) {
+      mout<<"No crystallization point! --> Add rejection for this..."<<endl;
+      for (int r = 0; r < RE->GetNRESEs(); ++r) {
+        RE->GetRESEAt(r)->RemoveAllLinks();
+      }
+      return 0;
+    }
+
+    bool ThereWasAChange = true;
+    list<MRESETrackCont> Neighbors;
+    do {
+      Neighbors.clear();
+      // For each track search all possible continuation (within layer jump)
+      for (int r = 0; r < RE->GetNRESEs(); ++r) {
+        if (RE->GetRESEAt(r)->GetType() == MRESE::c_Track) {
+          MRETrack* Track = dynamic_cast<MRETrack*>(RE->GetRESEAt(r));
+          for (int e = 0; e < Track->GetNEndPoints(); ++e) {
+            for (int c = 0; c < RE->GetNRESEs(); ++c) {
+              if (RE->GetRESEAt(r)->GetID() == RE->GetRESEAt(c)->GetID()) continue;
+              if (RE->GetRESEAt(c)->GetType() == MRESE::c_Cluster ||
+                  RE->GetRESEAt(c)->GetType() == MRESE::c_Hit) {
+                int Dist = m_Geometry->GetLayerDistance(Track->GetEndPointAt(e), RE->GetRESEAt(c));
+                if (Dist == MGeometryRevan::c_DifferentTracker) {
+                  continue;
+                }
+                if ((unsigned int) abs(Dist) <= m_ComptonMaxLayerJump && abs(Dist) > 0) {
+                  double Angle = Track->GetDirectionOfEndPoint(Track->GetEndPointAt(e)).
+                    Angle(RE->GetRESEAt(c)->GetPosition()-Track->GetEndPointAt(e)->GetPosition());
+                  MRESETrackCont C(Track, e, RE->GetRESEAt(c), -1, Angle);
+                  Neighbors.push_back(C);
+                }
+              } else if (RE->GetRESEAt(c)->GetType() == MRESE::c_Track) {
+                MRETrack* Track2 = dynamic_cast<MRETrack*>(RE->GetRESEAt(c));
+                for (int e2 = 0; e2 < Track2->GetNEndPoints(); ++e2) {
+                  int Dist = m_Geometry->GetLayerDistance(Track->GetEndPointAt(e), Track2->GetEndPointAt(e2));
+                  if (Dist == MGeometryRevan::c_DifferentTracker) {
+                    continue;
+                  }
+                  if ((unsigned int) abs(Dist) <= m_ComptonMaxLayerJump && abs(Dist) > 0) {
+                    double Angle = Track->GetDirectionOfEndPoint(Track->GetEndPointAt(e)).
+                      Angle(Track2->GetEndPointAt(e2)->GetPosition()-Track->GetEndPointAt(e)->GetPosition());
+                    MRESETrackCont C(Track, e, RE->GetRESEAt(c), e2, Angle);
+                    Neighbors.push_back(C);
+                  }
+                }
+              }
+            }
+          }
+        }
+      }
+
+      if (Neighbors.size() == 0) {
+        break;
+      }
+
+      // Only append the best one!
+      Neighbors.sort(MRESETrackContCompare);
+
+      if (Neighbors.front().m_EndPoint2 < 0) {
+        Neighbors.front().m_Track->AddEndPoint(Neighbors.front().m_Next,
+                                               Neighbors.front().m_Track->GetEndPointAt(Neighbors.front().m_EndPoint1));
+        RE->RemoveRESE(Neighbors.front().m_Next);
+      } else {
+        Neighbors.front().m_Track->AddEndPoint(dynamic_cast<MRETrack*>(Neighbors.front().m_Next),
+                                               dynamic_cast<MRETrack*>(Neighbors.front().m_Next)->GetEndPointAt(Neighbors.front().m_EndPoint2),
+                                               Neighbors.front().m_Track->GetEndPointAt(Neighbors.front().m_EndPoint1));
+        RE->RemoveRESE(Neighbors.front().m_Next);
+        delete Neighbors.front().m_Next;
+      }
+      RE->CompressRESEs();
+
+      // Search for new non ambiguous sequences:
+
+    } while (ThereWasAChange == true);
+
+    // Add the only raw event...
+    List->AddRawEvent(RE->Duplicate());
+  }
+
+  for (int r = 0; r < RE->GetNRESEs(); ++r) {
+    RE->GetRESEAt(r)->RemoveAllLinks();
+  }
+
+
+  // Let's do some sanity checks:
+
+  // Append straight (long) tracks:
+
+
+  return List;
+}
+*/
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MEREventId::PostAnalysis()
+{
+  /*
+  mout<<"Timings of tracking:"<<endl;
+  mout<<"Time Pairs:                 "<<m_TimePairs<<endl;
+  mout<<"Time Mips:                  "<<m_TimeMips<<endl;
+  mout<<"Time Comptons - sequence:   "<<m_TimeComptonSequences<<endl;
+  mout<<"Time Comptons - directions: "<<m_TimeComptonDirections<<endl;
+  mout<<endl;
+  */
+
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+MString MEREventId::ToString(bool CoreOnly) const
+{
+  // Dump an options string gor the tra file:
+
+  ostringstream out;
+
+  if (CoreOnly == false) {
+    out<<"# Tracking - FoM options:"<<endl;
+    out<<"# "<<endl;
+  }
+  out<<"# Search MIPs:                  "<<m_SearchMIPs<<endl;
+  out<<"# Search Pairs:                 "<<m_SearchPairs<<endl;
+  out<<"# Search Photos:              "<<m_SearchPhoto<<endl;
+  //out<<"# Max. number of ambiguities:   "<<m_MaxNAmbiguities<<endl;
+  //out<<"# Max. layer jump Compton:      "<<m_ComptonMaxLayerJump<<endl;
+  out<<"# Number of sequences to keep:  "<<m_NSequencesToKeep<<endl;
+  //out<<"# Reject pure ambiguities:      "<<m_RejectPureAmbiguities<<endl;
+  if (CoreOnly == false) {
+    out<<"# "<<endl;
+  }
+
+  return out.str().c_str();
+}
+
+
+
+// MEREventId.cxx: the end...
+////////////////////////////////////////////////////////////////////////////////
diff --git a/src/revan/src/MRawEventAnalyzer.cxx b/src/revan/src/MRawEventAnalyzer.cxx
index 02c68f024..e016a2fd2 100644
--- a/src/revan/src/MRawEventAnalyzer.cxx
+++ b/src/revan/src/MRawEventAnalyzer.cxx
@@ -55,6 +55,7 @@ using namespace std;
 #include "MEREventClusterizer.h"
 #include "MEREventClusterizerDistance.h"
 #include "MEREventClusterizerTMVA.h"
+#include "MEREventId.h"
 #include "MERTrack.h"
 #include "MERTrackPearson.h"
 #include "MERTrackRank.h"
@@ -529,6 +530,7 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
   // Read events if we have reader
   if (m_Reader != nullptr) {
     RE = m_Reader->GetNextEvent();
+    mout << "AL " << RE << show;
     if (RE == nullptr) { // No more events left in file
       ClearStore = true;
       if (m_EventStore->GetNRawEvents() == 0) {
@@ -696,8 +698,30 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
     
     m_TimeHitClusterize += Timer.ElapsedTime();  
   }
-  
-  
+
+
+  // Section I: Event type identification
+
+  if (SelectionsPassed) {
+    Timer.Start();
+
+    if (m_EventId == nullptr) {
+      merr << "Event identification pointer is zero. You changed the event reconstruction setup without calling PreAnalysis()!" << show;
+      return c_AnalysisUndefinedError;
+    }
+
+    for (unsigned int i = 0; i < m_RawEvents->Size(); ++i) {
+      MRawEventIncarnations* REI = m_RawEvents->Get(i);
+      m_EventId->Analyze(REI);
+    }
+
+    if (m_RawEvents->IsAnyEventValid() == false) SelectionsPassed = false;
+
+    m_TimeEventId += Timer.ElapsedTime();
+
+  }
+
+
   // Section D: Tracking:
   
   if (SelectionsPassed == true && m_TrackingAlgorithm > c_TrackingAlgoNone) {
@@ -741,7 +765,9 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
       }
     }
     
-    if (m_RawEvents->IsAnyEventValid() == false) SelectionsPassed = false;    
+    if (m_RawEvents->IsAnyEventValid() == false) SelectionsPassed = false;
+
+    m_TimeCSR += Timer.ElapsedTime();
     
   } else {
     mdebug<<"I am not doing CSR!"<<endl;
@@ -1091,6 +1117,7 @@ bool MRawEventAnalyzer::PostAnalysis()
   mout<<"General timings:"<<endl;
   mout<<"Timer Load     "<<m_TimeLoad<<endl;
   mout<<"Timer Cluster  "<<m_TimeClusterize<<endl;
+  mout<<"Timer EventId    "<<m_TimeEventId<<endl;
   mout<<"Timer Track    "<<m_TimeTrack<<endl;
   mout<<"Timer CSR      "<<m_TimeCSR<<endl;
   mout<<"Timer Finalize "<<m_TimeFinalize<<endl;

From f1bed10416c7b383393fbbd6120f0b0232b21811 Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Wed, 11 Jun 2025 15:03:36 -0400
Subject: [PATCH 168/192] ADD: Event type identification algorithm and
 accompanying GUI options

---
 src/revan/Makefile                            |   2 +
 .../inc/{MEREventId.h => MEREventType.h}      |  14 +-
 src/revan/inc/MGUIOptionsEventType.h          |  86 +++++
 .../src/{MEREventId.cxx => MEREventType.cxx}  | 189 ++++++----
 src/revan/src/MGUIOptionsEventType.cxx        | 340 ++++++++++++++++++
 5 files changed, 553 insertions(+), 78 deletions(-)
 rename src/revan/inc/{MEREventId.h => MEREventType.h} (93%)
 create mode 100644 src/revan/inc/MGUIOptionsEventType.h
 rename src/revan/src/{MEREventId.cxx => MEREventType.cxx} (91%)
 create mode 100644 src/revan/src/MGUIOptionsEventType.cxx

diff --git a/src/revan/Makefile b/src/revan/Makefile
index 1e679ec43..f6a7f75b5 100644
--- a/src/revan/Makefile
+++ b/src/revan/Makefile
@@ -32,6 +32,7 @@ FILES := MGeometryRevan \
 	MEREventClusterizerTMVA \
 	MEREventClusterizerDataSet \
 	MERHitClusterizer \
+  MEREventType \
 	MERTrack \
 	MERTrackPearson \
 	MERTrackRank \
@@ -79,6 +80,7 @@ FILES_UI := \
 	MGUIOptionsCoincidence \
 	MGUIOptionsHitClustering \
 	MGUIOptionsEventClustering \
+  MGUIOptionsEventType \
 	MGUIOptionsTracking \
 	MGUIOptionsCSR \
 	MGUIOptionsDecay \
diff --git a/src/revan/inc/MEREventId.h b/src/revan/inc/MEREventType.h
similarity index 93%
rename from src/revan/inc/MEREventId.h
rename to src/revan/inc/MEREventType.h
index 2bfe5e69b..1a87f064d 100644
--- a/src/revan/inc/MEREventId.h
+++ b/src/revan/inc/MEREventType.h
@@ -1,5 +1,5 @@
 /*
- * MEREventId.h
+ * MEREventType.h
  *
  * Copyright (C) by Andreas Zoglauer.
  * All rights reserved.
@@ -9,8 +9,8 @@
  */
 
 
-#ifndef __MEREventId__
-#define __MEREventId__
+#ifndef __MEREventType__
+#define __MEREventType__
 
 
 ////////////////////////////////////////////////////////////////////////////////
@@ -36,12 +36,12 @@ class MRETrack;
 ////////////////////////////////////////////////////////////////////////////////
 
 
-class MEREventId : public MERConstruction
+class MEREventType : public MERConstruction
 {
   // public interface:
  public:
-  MEREventId();
-  virtual ~MEREventId();
+  MEREventType();
+  virtual ~MEREventType();
 
   //! Global parameters used by all electron tracking algorithms
   virtual bool SetParameters(bool SearchMIPS, 
@@ -111,7 +111,7 @@ class MEREventId : public MERConstruction
 
 #ifdef ___CLING___
  public:
-  ClassDef(MEREventId, 0) // no description
+  ClassDef(MEREventType, 0) // no description
 #endif
 
 };
diff --git a/src/revan/inc/MGUIOptionsEventType.h b/src/revan/inc/MGUIOptionsEventType.h
new file mode 100644
index 000000000..def3ba5ab
--- /dev/null
+++ b/src/revan/inc/MGUIOptionsEventType.h
@@ -0,0 +1,86 @@
+/*
+ * MGUIOptionsEventType.h
+ *
+ * Copyright (C) by Andreas Zoglauer.
+ * All rights reserved.
+ *
+ * Please see the source-file for the copyright-notice.
+ *
+ */
+
+
+#ifndef __MGUIOptionsEventType__
+#define __MGUIOptionsEventType__
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+// ROOT libs:
+#include "TGListBox.h"
+
+// MEGAlib libs:
+#include "MGlobal.h"
+#include "MGUIDialog.h"
+#include "MDGeometryQuest.h"
+#include "MSettingsEventReconstruction.h"
+#include "MGUIECBList.h"
+#include "MGUIEFileSelector.h"
+#include "MGUIEEntry.h"
+
+// Forward declarations:
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+class MGUIOptionsEventType : public MGUIDialog
+{
+  // Public Interface:
+ public:
+  MGUIOptionsEventType(const TGWindow* Parent, const TGWindow* Main,
+                      MSettingsEventReconstruction* Data,
+                      MDGeometryQuest* Geometry);
+  virtual ~MGUIOptionsEventType();
+
+
+  // protected methods:
+ protected:
+  virtual void Create();
+  virtual bool OnApply();
+
+  // private methods:
+ private:
+
+  // protected members:
+ protected:
+
+
+  // private members:
+ private:
+  MSettingsEventReconstruction* m_Data;
+  MDGeometryQuest* m_Geometry;
+
+  MGUIECBList* m_CBList;
+  //MGUIEEntry* m_MaxComptonJump;
+  //MGUIEEntry* m_NSequencesToKeep;
+  //TGCheckButton* m_RejectPurelyAmbiguousSequences;
+  MGUIEFileSelector* m_FileSelector;
+  MGUIEEntry* m_NLayersForVertexSearch;
+  //MGUIEEntry* m_SigmaHitPos;
+
+  TGListBox* m_DetectorList;
+
+  enum ButtonCodes { e_DoTracking = 100, e_RejectPurelyAmbiguousSequences, e_Detectors };
+
+#ifdef ___CLING___
+ public:
+  ClassDef(MGUIOptionsEventType, 0)
+#endif
+
+};
+
+#endif
+
+
+////////////////////////////////////////////////////////////////////////////////
diff --git a/src/revan/src/MEREventId.cxx b/src/revan/src/MEREventType.cxx
similarity index 91%
rename from src/revan/src/MEREventId.cxx
rename to src/revan/src/MEREventType.cxx
index 8d56abd7a..f9528bd45 100644
--- a/src/revan/src/MEREventId.cxx
+++ b/src/revan/src/MEREventType.cxx
@@ -1,5 +1,5 @@
 /*
- * MEREventId.cxx
+ * MEREventType.cxx
  *
  *
  * Copyright (C) by Andreas Zoglauer.
@@ -18,7 +18,7 @@
 
 ////////////////////////////////////////////////////////////////////////////////
 //
-// MEREventId
+// MEREventType
 //
 // Base class for event reconstruction tasks, e.g. find clusters, tracks,
 // Compton sequence
@@ -27,7 +27,7 @@
 
 
 // Include the header:
-#include "MEREventId.h"
+#include "MEREventType.h"
 
 // Standard libs:
 #include <list>
@@ -52,7 +52,7 @@ using namespace std;
 
 
 #ifdef ___CLING___
-ClassImp(MEREventId)
+ClassImp(MEREventType)
 #endif
 
 
@@ -61,9 +61,9 @@ ClassImp(MEREventId)
 ////////////////////////////////////////////////////////////////////////////////
 
 
-MEREventId::MEREventId()
+MEREventType::MEREventType()
 {
-  // Construct an instance of MEREventId
+  // Construct an instance of MEREventType
 
   m_SearchPairs = true;
   m_SearchMIPs = true;
@@ -88,16 +88,16 @@ MEREventId::MEREventId()
 ////////////////////////////////////////////////////////////////////////////////
 
 
-MEREventId::~MEREventId()
+MEREventType::~MEREventType()
 {
-  // Delete this instance of MEREventId
+  // Delete this instance of MEREventType
 }
 
 
 ////////////////////////////////////////////////////////////////////////////////
 
 
-bool MEREventId::SetParameters(bool SearchMIPs,
+bool MEREventType::SetParameters(bool SearchMIPs,
                              bool SearchPairs,
                              bool SearchCompton,
                              bool SearchPhoto,
@@ -156,13 +156,13 @@ bool MEREventId::SetParameters(bool SearchMIPs,
 ////////////////////////////////////////////////////////////////////////////////
 
 
-bool MEREventId::Analyze(MRawEventIncarnations* REList)
+bool MEREventType::Analyze(MRawEventIncarnations* REList)
 {
   // Analyze the raw event...
 
   massert(m_Geometry != 0);
 
-  MERConstruction::Analyze(REList);
+  MERConstruction::Analyze(REList);//Set m_List to REList
 
   // mdebug<<m_List->ToString()<<endl;
 
@@ -171,47 +171,46 @@ bool MEREventId::Analyze(MRawEventIncarnations* REList)
 
   bool Identified = false;
   MRERawEvent* RE = 0;
-  MRawEventIncarnations* List = 0;
-  MRESE* RESE = 0;
-  MRETrack* Track = 0;
+  //MRawEventIncarnations* List = 0;
+  //MRESE* RESE = 0;
+  //MRETrack* Track = 0;
   MTimer Timer;
 
   // Step A: Preparation:
 
   // Step A (bis): Single-site events
-/*
+
   Timer.Start();
-  if (Identified == false && m_SearchPhoto == true) {
+  if (!Identified && m_SearchPhoto) {
     mdebug <<"* Search for single-site events"<<endl;
-    for (int e = 0; e < m_List ///////////////
-    if (RE->GetNRESE() == 1) {
-      if (RE->GetRESEAt(0)->GetType() == MRESE::c_Hit || 
-        RE->GetRESEAt(0)->GetType() == MRESE::c_Cluster) {
-        RE->SetEventType(MRERawEvent::c_PhotoEvent);
-        RE->SetGoodEvent(true);
-      }
+    for (int e = 0; e < m_List->GetNRawEvents(); e++) {
+      RE = m_List->GetRawEventAt(e);
+      CheckForPhoto(RE);
+      Identified = RE->GetEventType() == MRERawEvent::c_PhotoEvent;
     }
   }
   m_TimePhoto += Timer.ElapsedTime();
-*/
+
 
   // Before we do anything we check if we have at least two hits in one of the defines electron trackers
   bool StartTracking = false;
-  for (int e = 0; e < m_List->GetNRawEvents(); e++) {
-    RE = m_List->GetRawEventAt(e);
-    unsigned int NHits = 0;
-    for (int h = 0; h < RE->GetNRESEs(); ++h) {
-      if (IsInTracker(RE->GetRESEAt(h)) == true) {
-        ++NHits;
+  if (!Identified) {
+    for (int e = 0; e < m_List->GetNRawEvents(); e++) {
+      RE = m_List->GetRawEventAt(e);
+      unsigned int NHits = 0;
+      for (int h = 0; h < RE->GetNRESEs(); ++h) {
+        if (IsInTracker(RE->GetRESEAt(h)) == true) {
+          ++NHits;
+        }
+      }
+      //if (NHits > 50) {
+      //  mout<<"Too many hits for tracking: "<<NHits<<endl;
+      //  return true;
+      //}
+      if (NHits >= 2) {
+        StartTracking = true;
+        break;
       }
-    }
-    //if (NHits > 50) {
-    //  mout<<"Too many hits for tracking: "<<NHits<<endl;
-    //  return true;
-    //}
-    if (NHits >= 2) {
-      StartTracking = true;
-      break;
     }
   }
 /*
@@ -226,14 +225,13 @@ bool MEREventId::Analyze(MRawEventIncarnations* REList)
   Timer.Start();
   if (StartTracking && !Identified && m_SearchPairs) {
     mdebug<<"* Search for pairs: Vertex"<<endl;
-    bool HasVertices = false;
     int e_max = m_List->GetNRawEvents();
     for (int e = 0; e < e_max; e++) {
       RE = m_List->GetRawEventAt(e);
-      List = CheckForPair(RE);
-      if (List != 0) {
-        mdebug<<"List: "<<List->GetNRawEvents()<<endl;
-        HasVertices = true;
+      CheckForPair(RE);
+      Identified = RE->GetEventType() == MRERawEvent::c_PairEvent;
+      /*
+      if () {
         m_List->DeleteRawEvent(RE);
         e--;
         e_max--;
@@ -242,7 +240,7 @@ bool MEREventId::Analyze(MRawEventIncarnations* REList)
         }
         delete List;
         mdebug<<"Tracking: Event has vertex!"<<endl;
-      }
+      }*/
     }
     /*
     if (HasVertices == true) {
@@ -263,8 +261,8 @@ bool MEREventId::Analyze(MRawEventIncarnations* REList)
       Identified = true;
       m_List->SetOptimumEvent(RE);
       m_List->SetBestTryEvent(RE);
-    } // pair...
-  }*/
+    } // pair...*/
+  }
   m_TimePairs += Timer.ElapsedTime();
 
 
@@ -276,18 +274,19 @@ bool MEREventId::Analyze(MRawEventIncarnations* REList)
     for (int e = 0; e < m_List->GetNRawEvents(); e++) {
       RE = m_List->GetRawEventAt(e);
       CheckForMips(RE);
+      //Identified = RE->IsGoodEvent();
       // If we have found a MIP then we are done!
       if (RE->GetEventType() == MRERawEvent::c_MipEvent) {
         mdebug<<"Tracking: Successful identification: MIP (probably muon)"<<endl;
         Identified = true;
-        m_List->SetOptimumEvent(RE);
-        m_List->SetBestTryEvent(RE);
+        //m_List->SetOptimumEvent(RE);
+        //m_List->SetBestTryEvent(RE);
       }
       if (RE->GetEventType() == MRERawEvent::c_ShowerEvent) {
         mdebug<<"Tracking: Successful identification: Shower"<<endl;
         Identified = true;
-        m_List->SetOptimumEvent(RE);
-        m_List->SetBestTryEvent(RE);
+        //m_List->SetOptimumEvent(RE);
+        //m_List->SetBestTryEvent(RE);
       }
     }
     mdebug<<"        MIP results:"<<endl;
@@ -297,7 +296,24 @@ bool MEREventId::Analyze(MRawEventIncarnations* REList)
   m_TimeMips += Timer.ElapsedTime();
 
 
-  // Step C: Compton tracks
+  // Step C: Compton events
+  Timer.Start();
+  if (!Identified && m_SearchCompton) {
+    for (int e = 0; e < m_List->GetNRawEvents(); e++) {
+      RE = m_List->GetRawEventAt(e);
+      CheckForCompton(RE);
+      Identified = RE->GetEventType() == MRERawEvent::c_ComptonEvent;
+    }
+  }
+
+  // Step U: unknown
+  if (!Identified) {
+    // Set all to unknown
+    for (int e = 0; e < m_List->GetNRawEvents(); e++) {
+      RE = m_List->GetRawEventAt(e);
+      RE->SetEventType(MRERawEvent::c_UnknownEvent);
+    }
+  }
 
   // implement smtg here
 
@@ -425,10 +441,10 @@ bool MEREventId::Analyze(MRawEventIncarnations* REList)
 
 
   // Step E: Epilog
-
+/*
   mdebug<<"Result of tracking:"<<endl;
   mdebug<<m_List->ToString()<<endl;
-
+*/
 
   return true;
 }
@@ -438,7 +454,7 @@ bool MEREventId::Analyze(MRawEventIncarnations* REList)
 ////////////////////////////////////////////////////////////////////////////////
 
 
-bool MEREventId::IsInTracker(MRESE* R)
+bool MEREventType::IsInTracker(MRESE* R)
 {
   //! Return true, if the RESE happened in a detector in our list
 
@@ -459,7 +475,33 @@ bool MEREventId::IsInTracker(MRESE* R)
 ////////////////////////////////////////////////////////////////////////////////
 
 
-void MEREventId::CheckForPair(MRERawEvent* RE)
+void MEREventType::CheckForPhoto(MRERawEvent* RE)
+{
+  if (RE->GetNRESEs() == 1) {
+    if (RE->GetRESEAt(0)->GetType() == MRESE::c_Hit || 
+      RE->GetRESEAt(0)->GetType() == MRESE::c_Cluster) {
+      RE->SetEventType(MRERawEvent::c_PhotoEvent);
+      //RE->SetGoodEvent(true);
+    }
+  }
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+void MEREventType::CheckForCompton(MRERawEvent* RE)
+{
+  // If we get there, this is a Compton event by default
+  RE->SetEventType(MRERawEvent::c_ComptonEvent);
+  //RE->SetGoodEvent(true);
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+void MEREventType::CheckForPair(MRERawEvent* RE)
 {
   // Check if this event could be a pair:
   //
@@ -473,7 +515,7 @@ void MEREventId::CheckForPair(MRERawEvent* RE)
 
   mdebug<<"Searching for a pair vertex"<<endl;
 
-  MRawEventIncarnations *List = 0;
+//  MRawEventIncarnations *List = 0;
   bool OnlyHitInLayer = false;
   //unsigned int MaximumLayerJump = 2;
   //MRESE* RESE = 0;
@@ -579,15 +621,18 @@ void MEREventId::CheckForPair(MRERawEvent* RE)
         VertexDirection = -1;
       }
     }
-
+    
     if (Vertex != 0) {
+      /*
       if (List == 0) List = new MRawEventIncarnations();
       RE->SetVertex(Vertex);
       RE->SetVertexDirection(VertexDirection);
       MRERawEvent *New = RE->Duplicate();
       RE->SetVertex(0);
       List->AddRawEvent(New);
-      mdebug<<"Search vertex: Found vertex: "<<Vertex->GetID()<<endl;
+      mdebug<<"Search vertex: Found vertex: "<<Vertex->GetID()<<endl;*/
+      RE->SetEventType(MRERawEvent::c_PairEvent);
+      //RE->SetGoodEvent(true);
       break; // Only take first right now
     }
   }
@@ -599,7 +644,7 @@ void MEREventId::CheckForPair(MRERawEvent* RE)
 ////////////////////////////////////////////////////////////////////////////////
 
 
-void MEREventId::CheckForMips(MRERawEvent* RE)
+void MEREventType::CheckForMips(MRERawEvent* RE)
 {
   // Check if the events structure can be created by a massive interacting
   // particle like myons:
@@ -716,7 +761,7 @@ void MEREventId::CheckForMips(MRERawEvent* RE)
   // a. Definitely a muon
   if (TrackArray.size() == 1) {
     mdebug<<"==> This was fucking easy! Found a muon!"<<endl;
-
+/*
     // a. Integrate the track into this raw event:
     TrackArray[HighestPos]->LinkSequential();
     for (unsigned int i = 0; i < (unsigned int) TrackArray[HighestPos]->GetNRESEs(); ++i) {
@@ -738,15 +783,16 @@ void MEREventId::CheckForMips(MRERawEvent* RE)
     }
 
     // d. This is a good event...
-    RE->SetPhysicalEvent(Muon);
+    RE->SetPhysicalEvent(Muon);*/
     RE->SetEventType(MRERawEvent::c_MipEvent);
-    RE->SetGoodEvent(true);
+    //RE->SetGoodEvent(true);
   }
   // b. A shower
   else if (TrackArray.size() > 1) {
     mdebug<<"==> Found a shower!"<<endl;
     RE->SetEventType(MRERawEvent::c_ShowerEvent);
-
+    //RE->SetGoodEvent(true);
+/*
     // b. Integrate all tracks into this raw event:
     for (unsigned int i = 0; i < TrackArray.size(); ++i) {
       TrackArray[i]->LinkSequential();
@@ -757,7 +803,7 @@ void MEREventId::CheckForMips(MRERawEvent* RE)
       RE->CompressRESEs();
       RE->AddRESE(TrackArray[i]);
       RE->SetGoodEvent(true);
-    }
+    }*/
   }
 
   // return;
@@ -768,7 +814,7 @@ void MEREventId::CheckForMips(MRERawEvent* RE)
 ////////////////////////////////////////////////////////////////////////////////
 
 /*
-MRawEventIncarnations* MEREventId::TrackComptons(MRERawEvent* RE)
+MRawEventIncarnations* MEREventType::TrackComptons(MRERawEvent* RE)
 {
   mdebug<<"Track Compton events..."<<endl;
 
@@ -1128,7 +1174,7 @@ MRawEventIncarnations* MEREventId::TrackComptons(MRERawEvent* RE)
 ////////////////////////////////////////////////////////////////////////////////
 
 
-bool MEREventId::PostAnalysis()
+bool MEREventType::PostAnalysis()
 {
   /*
   mout<<"Timings of tracking:"<<endl;
@@ -1146,7 +1192,7 @@ bool MEREventId::PostAnalysis()
 ////////////////////////////////////////////////////////////////////////////////
 
 
-MString MEREventId::ToString(bool CoreOnly) const
+MString MEREventType::ToString(bool CoreOnly) const
 {
   // Dump an options string gor the tra file:
 
@@ -1156,12 +1202,13 @@ MString MEREventId::ToString(bool CoreOnly) const
     out<<"# Tracking - FoM options:"<<endl;
     out<<"# "<<endl;
   }
-  out<<"# Search MIPs:                  "<<m_SearchMIPs<<endl;
-  out<<"# Search Pairs:                 "<<m_SearchPairs<<endl;
   out<<"# Search Photos:              "<<m_SearchPhoto<<endl;
+  out<<"# Search Pairs:                 "<<m_SearchPairs<<endl;
+  out<<"# Search MIPs:                  "<<m_SearchMIPs<<endl;
+  out<<"# Search Compton:              "<<m_SearchCompton<<endl;
   //out<<"# Max. number of ambiguities:   "<<m_MaxNAmbiguities<<endl;
   //out<<"# Max. layer jump Compton:      "<<m_ComptonMaxLayerJump<<endl;
-  out<<"# Number of sequences to keep:  "<<m_NSequencesToKeep<<endl;
+  //out<<"# Number of sequences to keep:  "<<m_NSequencesToKeep<<endl;
   //out<<"# Reject pure ambiguities:      "<<m_RejectPureAmbiguities<<endl;
   if (CoreOnly == false) {
     out<<"# "<<endl;
@@ -1172,5 +1219,5 @@ MString MEREventId::ToString(bool CoreOnly) const
 
 
 
-// MEREventId.cxx: the end...
+// MEREventType.cxx: the end...
 ////////////////////////////////////////////////////////////////////////////////
diff --git a/src/revan/src/MGUIOptionsEventType.cxx b/src/revan/src/MGUIOptionsEventType.cxx
new file mode 100644
index 000000000..e0d0750c9
--- /dev/null
+++ b/src/revan/src/MGUIOptionsEventType.cxx
@@ -0,0 +1,340 @@
+/*
+ * MGUIOptionsEventType.cxx
+ *
+ *
+ * Copyright (C) by Andreas Zoglauer.
+ * All rights reserved.
+ *
+ *
+ * This code implementation is the intellectual property of
+ * Andreas Zoglauer.
+ *
+ * By copying, distributing or modifying the Program (or any work
+ * based on the Program) you indicate your acceptance of this statement,
+ * and all its terms.
+ *
+ */
+
+
+////////////////////////////////////////////////////////////////////////////////
+//
+// MGUIOptionsEventType
+//
+////////////////////////////////////////////////////////////////////////////////
+
+
+// Include the header:
+#include "MGUIOptionsEventType.h"
+
+// Standard libs:
+#include <iostream>
+using namespace std;
+
+// ROOT libs:
+
+// MEGAlib libs:
+#include "MRawEventAnalyzer.h"
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+#ifdef ___CLING___
+ClassImp(MGUIOptionsEventType)
+#endif
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+MGUIOptionsEventType::MGUIOptionsEventType(const TGWindow* Parent,
+                                         const TGWindow* Main,
+                                         MSettingsEventReconstruction* Data,
+                                         MDGeometryQuest* Geometry)
+  : MGUIDialog(Parent, Main)
+{
+  // Construct an instance of MGUIOptionsEventType and bring it to the screen
+  m_Data = Data;
+  m_Geometry = Geometry;
+
+  // use hierarchical cleaning
+  SetCleanup(kDeepCleanup);
+
+  Create();
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+MGUIOptionsEventType::~MGUIOptionsEventType()
+{
+  // kDeepCleanup is activated
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+void MGUIOptionsEventType::Create()
+{
+  // Create the main window
+
+  // We start with a name and an icon...
+  SetWindowName("Event Type Identification");
+
+  if (m_Data->GetEventTypeAlgorithm() == MRawEventAnalyzer::c_EventTypeDefault) {
+    // Which event types to search
+    AddSubTitle("Options for default algorithm");
+    m_CBList = new MGUIECBList(this, "Search for the following event types:");
+    m_CBList->Add("Search for single-site");
+    m_CBList->SetSelected(0, m_Data->GetSearchPhoto());
+    m_CBList->Add("Search for pairs");
+    m_CBList->SetSelected(1, m_Data->GetSearchPairs());
+    m_CBList->Add("Search for MIPS");
+    m_CBList->SetSelected(2, m_Data->GetSearchMIPs());
+    m_CBList->Add("Search for Compton tracks");
+    m_CBList->SetSelected(3, m_Data->GetSearchComptons());
+//     if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoPearson) {
+//       m_CBList->Add("Cheating: Assume Compton tracks go from top to bottom");
+//       m_CBList->SetSelected(3, m_Data->GetAssumeTrackTopBottom());
+//     }
+    m_CBList->Create();
+    TGLayoutHints* CBListLayout =
+      new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, 20, 20, 0, 0);
+    AddFrame(m_CBList, CBListLayout);
+
+    // Number of layers for vertex
+    TGLayoutHints* SubLabel = new TGLayoutHints(kLHintsLeft | kLHintsTop, 20, 20, 20, 5);
+    TGLabel* PairLabel = new TGLabel(this, "Pair options:");
+    AddFrame(PairLabel, SubLabel);
+
+    TGLayoutHints* SubOptions = new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, 40, 20, 0, 5);
+    m_NLayersForVertexSearch = new MGUIEEntry(this,
+                                      "Search for a pair vertex within this amount of layers (min 4):",
+                                      false,
+                                      m_Data->GetNLayersForVertexSearch(), true, 4);
+    AddFrame(m_NLayersForVertexSearch, SubOptions);
+
+    // Select tracking detectors
+    TGLabel* LabelDetectors = new TGLabel(this, "Select the tracking detector(s):");
+    TGLayoutHints* LabelDetectorsLayout = new TGLayoutHints(kLHintsLeft | kLHintsTop, 20, 20, 20, 0);
+    AddFrame(LabelDetectors, LabelDetectorsLayout);
+
+    m_DetectorList = new TGListBox(this, e_Detectors);
+    m_DetectorList->SetMultipleSelections(true);
+    TGLayoutHints* DetectorListLayout = new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, 20, 20, 5, 0);
+    AddFrame(m_DetectorList, DetectorListLayout);
+
+    if (m_Geometry != 0) {
+      for (unsigned int d = 0; d < m_Geometry->GetNDetectors(); ++d) {
+        MString Name = m_Geometry->GetDetectorAt(d)->GetName() + " (" + m_Geometry->GetDetectorAt(d)->GetTypeName() + ")";
+        m_DetectorList->AddEntry(Name, d);
+
+        // Highlight those detectors which are already in the list:
+        for (unsigned int e = 0; e < m_Data->GetNElectronTrackingDetectors(); ++e) {
+          if (m_Data->GetElectronTrackingDetector(e) == m_Geometry->GetDetectorAt(d)->GetName()) {
+            m_DetectorList->Select(d);
+            break;
+          }
+        }
+      }
+    } else {
+      merr<<"No geometry!"<<show;
+    }
+    m_DetectorList->Resize(200, 100);
+
+  } else if (m_Data->GetEventTypeAlgorithm() == MRawEventAnalyzer::c_EventTypeExternal) {
+/*    AddSubTitle("Options for external input");
+    TGLayoutHints* SubLabel = new TGLayoutHints(kLHintsLeft | kLHintsTop, 20, 20, 20, 5);
+    TGLabel* ComptonLabel = new TGLabel(this, "Compton options: where2");
+    AddFrame(ComptonLabel, SubLabel);
+
+    TGLayoutHints* SubOptions = new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, 40, 20, 0, 5);
+    TGLabel* GeneralLabel = new TGLabel(this, "General options: whereisthisprinted?");
+    AddFrame(GeneralLabel, SubLabel);
+
+    m_FileSelector =
+      new MGUIEFileSelector(this, "File containing the event type data:",
+                            m_Data->GetEventTypeFileName());//To be implemented
+    m_FileSelector->SetFileType("file to be implemented", "*.dodo");// implementation in progress
+    AddFrame(m_FileSelector, SubOptions);*/
+  } else {
+    AddSubTitle("Unknown Event Type identification algorithm!");
+  }
+
+/*
+if(false) { // FAKE COMMENT
+  if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoModifiedPearson) {
+    AddSubTitle("Tracking options for Modified Pearson correlation:");
+  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoPearson) {
+    AddSubTitle("Tracking options for Pearson correlation:");
+  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoRank) {
+    AddSubTitle("Tracking options for Rank correlation:");
+  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoChiSquare) {
+    AddSubTitle("Tracking options for Chi-Square method:");
+  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoGas) {
+    AddSubTitle("Tracking options for gas detectors:");
+  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoDirectional) {
+    AddSubTitle("Tracking options for intrinsic electron tracking detectors - no options!");
+  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoBayesian) {
+    AddSubTitle("Tracking options for Bayesian electron tracking:");
+  } else {
+    AddSubTitle("You deselected electron tracking!");
+  }
+
+  if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoModifiedPearson ||
+      m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoPearson ||
+      m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoRank ||
+      m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoChiSquare ||
+      m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoGas ||
+      m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoBayesian) {
+    m_CBList = new MGUIECBList(this, "Search for the following event types:");
+    m_CBList->Add("Search for MIPS");
+    m_CBList->SetSelected(0, m_Data->GetSearchMIPs());
+    m_CBList->Add("Search for pairs");
+    m_CBList->SetSelected(1, m_Data->GetSearchPairs());
+    m_CBList->Add("Search for Compton tracks");
+    m_CBList->SetSelected(2, m_Data->GetSearchComptons());
+//     if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoPearson) {
+//       m_CBList->Add("Cheating: Assume Compton tracks go from top to bottom");
+//       m_CBList->SetSelected(3, m_Data->GetAssumeTrackTopBottom());
+//     }
+    m_CBList->Create();
+    TGLayoutHints* CBListLayout =
+      new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, 20, 20, 0, 0);
+    AddFrame(m_CBList, CBListLayout);
+
+
+    TGLayoutHints* SubLabel = new TGLayoutHints(kLHintsLeft | kLHintsTop, 20, 20, 20, 5);
+    TGLabel* ComptonLabel = new TGLabel(this, "Compton options:");
+    AddFrame(ComptonLabel, SubLabel);
+
+    TGLayoutHints* SubOptions = new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, 40, 20, 0, 5);
+    m_MaxComptonJump = new MGUIEEntry(this,
+                                      "Maximum number of layers a Compton track can skip (e.g. due to hits in passive material):",
+                                      false,
+                                      m_Data->GetMaxComptonJump(), true, 1);
+    AddFrame(m_MaxComptonJump, SubOptions);
+
+    m_NSequencesToKeep = new MGUIEEntry(this,
+                                      "Maximum number of different possible track sequences to keep in the initial analysis:",
+                                      false,
+                                      m_Data->GetNTrackSequencesToKeep(), true, 1);
+    AddFrame(m_NSequencesToKeep, SubOptions);
+
+    m_RejectPurelyAmbiguousSequences = new TGCheckButton(this,
+                                                         "Reject purely ambiguous sequences",
+                                                         e_RejectPurelyAmbiguousSequences);
+    AddFrame(m_RejectPurelyAmbiguousSequences, SubOptions);
+    if (m_Data->GetRejectPurelyAmbiguousTrackSequences() == true) {
+      m_RejectPurelyAmbiguousSequences->SetState(kButtonDown);
+    } else {
+      m_RejectPurelyAmbiguousSequences->SetState(kButtonUp);
+    }
+
+
+    TGLabel* PairLabel = new TGLabel(this, "Pair options:");
+    AddFrame(PairLabel, SubLabel);
+
+    m_NLayersForVertexSearch = new MGUIEEntry(this,
+                                      "Search for a pair vertex within this amount of layers (min 4):",
+                                      false,
+                                      m_Data->GetNLayersForVertexSearch(), true, 4);
+    AddFrame(m_NLayersForVertexSearch, SubOptions);
+
+    m_SigmaHitPos = new MGUIEEntry(this,
+                                  "Error in the position of the hit in the tracker (used by the Kalman filter) [cm]:",
+                                  false,
+                                  m_Data->GetSigmaHitPos(), true, 0.00693);
+    AddFrame(m_SigmaHitPos, SubOptions);
+
+
+    if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoBayesian) {
+      TGLabel* GeneralLabel = new TGLabel(this, "General options:");
+      AddFrame(GeneralLabel, SubLabel);
+
+      m_FileSelector =
+        new MGUIEFileSelector(this, "File containing the Bayesian tracking data:",
+                              m_Data->GetBayesianElectronFileName());
+      m_FileSelector->SetFileType("Response file", "*.rsp");
+      AddFrame(m_FileSelector, SubOptions);
+    }
+
+
+    TGLabel* LabelDetectors = new TGLabel(this, "Select the tracking detector(s):");
+    TGLayoutHints* LabelDetectorsLayout = new TGLayoutHints(kLHintsLeft | kLHintsTop, 20, 20, 20, 0);
+    AddFrame(LabelDetectors, LabelDetectorsLayout);
+
+    m_DetectorList = new TGListBox(this, e_Detectors);
+    m_DetectorList->SetMultipleSelections(true);
+    TGLayoutHints* DetectorListLayout = new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, 20, 20, 5, 0);
+    AddFrame(m_DetectorList, DetectorListLayout);
+
+    if (m_Geometry != 0) {
+      for (unsigned int d = 0; d < m_Geometry->GetNDetectors(); ++d) {
+        MString Name = m_Geometry->GetDetectorAt(d)->GetName() + " (" + m_Geometry->GetDetectorAt(d)->GetTypeName() + ")";
+        m_DetectorList->AddEntry(Name, d);
+
+        // Highlight those detectors which are already in the list:
+        for (unsigned int e = 0; e < m_Data->GetNElectronTrackingDetectors(); ++e) {
+          if (m_Data->GetElectronTrackingDetector(e) == m_Geometry->GetDetectorAt(d)->GetName()) {
+            m_DetectorList->Select(d);
+            break;
+          }
+        }
+      }
+    } else {
+      merr<<"No geometry!"<<show;
+    }
+    m_DetectorList->Resize(200, 100);
+
+  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoDirectional) {
+    // no options...
+  }
+
+} // FAKE COMMENT END*/
+
+  AddButtons();
+  PositionWindow(GetDefaultWidth()+30, GetDefaultHeight()+30, false);
+
+  // and bring it to the screen.
+  MapSubwindows();
+  MapWindow();
+
+  Layout();
+
+  return;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MGUIOptionsEventType::OnApply()
+{
+	// The Apply button has been pressed
+
+  if (m_Data->GetEventTypeAlgorithm() == MRawEventAnalyzer::c_EventTypeDefault) {
+    m_Data->SetSearchPhoto(m_CBList->GetSelected(0));
+    m_Data->SetSearchPairs(m_CBList->GetSelected(1));
+    m_Data->SetSearchMIPs(m_CBList->GetSelected(2));
+    m_Data->SetSearchComptons(m_CBList->GetSelected(3));
+    m_Data->SetNLayersForVertexSearch(m_NLayersForVertexSearch->GetAsInt());
+
+    m_Data->RemoveAllElectronTrackingDetectors();
+    for (int d = 0; d < m_DetectorList->GetNumberOfEntries(); ++d) {
+      if (m_DetectorList->GetSelection(d) == true) {
+        m_Data->AddElectronTrackingDetector(m_Geometry->GetDetectorAt(d)->GetName());
+      }
+    }
+  } else if (m_Data->GetEventTypeAlgorithm() == MRawEventAnalyzer::c_EventTypeExternal) {
+    m_Data->SetBayesianElectronFileName(m_FileSelector->GetFileName());
+  }
+
+	return true;
+}
+
+
+
+// MGUIOptionsEventType: the end...
+////////////////////////////////////////////////////////////////////////////////

From b80dbc4d1cf21bfae1ff6041bfe5a6014f3d2e2c Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Thu, 12 Jun 2025 15:05:36 -0400
Subject: [PATCH 169/192] CHG: finish implementing separate Event Type
 Identification - to be tested

---
 src/revan/inc/MERTrack.h                      |   3 +
 src/revan/inc/MGUIERAlgorithm.h               |   4 +-
 src/revan/inc/MGUIRevanMain.h                 |   4 +-
 src/revan/inc/MRawEventAnalyzer.h             |  36 ++--
 src/revan/inc/MSettingsEventReconstruction.h  |  16 +-
 src/revan/src/MEREventType.cxx                |   2 +-
 src/revan/src/MERTrack.cxx                    | 192 ++++++++++--------
 src/revan/src/MGUIERAlgorithm.cxx             |  24 +--
 src/revan/src/MGUIRevanMain.cxx               |  16 +-
 src/revan/src/MRERawEvent.cxx                 |  54 +++--
 src/revan/src/MRawEventAnalyzer.cxx           | 162 +++++++++------
 .../src/MSettingsEventReconstruction.cxx      |   8 +-
 12 files changed, 300 insertions(+), 221 deletions(-)

diff --git a/src/revan/inc/MERTrack.h b/src/revan/inc/MERTrack.h
index 649e304c6..a0521da86 100644
--- a/src/revan/inc/MERTrack.h
+++ b/src/revan/inc/MERTrack.h
@@ -78,6 +78,9 @@ class MERTrack : public MERConstruction
   //! Return true, if the RESE happened in a detector in our list
   bool IsInTracker(MRESE* R);
 
+  //! Return true if one Raw Event of m_List is of type EventType
+  bool HasOneREOfType(int EventType);
+
   // private methods:
  private:
 
diff --git a/src/revan/inc/MGUIERAlgorithm.h b/src/revan/inc/MGUIERAlgorithm.h
index e69b91a95..e68ff180c 100644
--- a/src/revan/inc/MGUIERAlgorithm.h
+++ b/src/revan/inc/MGUIERAlgorithm.h
@@ -60,10 +60,10 @@ class MGUIERAlgorithm : public MGUIDialog
   MGUIERBList* m_CoincidenceList;
   MGUIERBList* m_EventClusteringList;
   MGUIERBList* m_HitClusteringList;
-  MGUIERBList* m_EventIdList;
+  MGUIERBList* m_EventTypeList;
   MGUIERBList* m_TrackingList;
   MGUIERBList* m_CSRList;
-  MGUIERBList* m_PairList;
+//  MGUIERBList* m_PairList;
   //MGUIERBList* m_DecayList;
 
 
diff --git a/src/revan/inc/MGUIRevanMain.h b/src/revan/inc/MGUIRevanMain.h
index 05c902db3..f49792e2f 100644
--- a/src/revan/inc/MGUIRevanMain.h
+++ b/src/revan/inc/MGUIRevanMain.h
@@ -35,8 +35,9 @@
 #include "MSettingsSpectralOptions.h"
 #include "MGUISpectralAnalyzer.h"
 
-class MInterfaceRevan;
+#include "MGUIOptionsEventType.h"
 
+class MInterfaceRevan;
 
 ////////////////////////////////////////////////////////////////////////////////
 
@@ -78,6 +79,7 @@ class MGUIRevanMain : public MGUIMain
     c_OptionsCoincidence, 
     c_OptionsEventClustering, 
     c_OptionsHitClustering, 
+    c_OptionsEventType, 
     c_OptionsTracking, 
     c_OptionsSequencing, 
     c_OptionsDecay, 
diff --git a/src/revan/inc/MRawEventAnalyzer.h b/src/revan/inc/MRawEventAnalyzer.h
index 5805753dd..e55dce737 100644
--- a/src/revan/inc/MRawEventAnalyzer.h
+++ b/src/revan/inc/MRawEventAnalyzer.h
@@ -39,7 +39,7 @@ class MDGeometryQuest;
 class MERCoincidence;
 class MEREventClusterizer;
 class MERHitClusterizer;
-class MEREventId;
+class MEREventType;
 class MERTrack;
 class MERCSR;
 class MERDecay;
@@ -168,12 +168,12 @@ class MRawEventAnalyzer
   //! Set the clustering algorithm: One of c_ClusteringAlgoNone, c_ClusteringAlgoDistance, c_ClusteringAlgoAdjacent;
   void SetHitClusteringAlgorithm(int ID) { m_HitClusteringAlgorithm = ID; }
 
-  enum c_EventIdAlgo {
-    c_EventIdDefault,
-    c_EventIdExternal };
+  enum c_EventTypeAlgo {
+    c_EventTypeDefault,
+    c_EventTypeExternal };
 
   //! Set the Event type identification algorithm
-  void SetEventIdAlgorithm(int ID) { m_EventIdAlgorithm = ID; }
+  void SetEventTypeAlgorithm(int ID) { m_EventTypeAlgorithm = ID; }
 
   enum c_TrackingAlgo {
     c_TrackingAlgoNone,
@@ -246,18 +246,21 @@ class MRawEventAnalyzer
   void SetAdjacentSigma(const double Value) { m_AdjacentSigma = Value; }
   void SetPDFClusterizer(MString BaseFileName) { m_PDFClusterizerBaseFileName = BaseFileName; }
 
-  // Options electron tracking:
-  void SetDoTracking(bool Do) { m_DoTracking = Do; if (Do == false) m_TrackingAlgorithm = c_TrackingAlgoNone; }
+  // Event type identification:
   void SetSearchPairTracks(bool Search) { m_SearchPairTracks = Search; }
   void SetSearchMIPTracks(bool Search) { m_SearchMIPTracks = Search; }
+  void SetSearchPhotoEvent(bool Search) { m_SearchPhotoEvent = Search; }
   void SetSearchComptonTracks(bool Search) { m_SearchComptonTracks = Search; }
+  void SetNLayersForVertexSearch(unsigned int NLayersForVertexSearch) { m_NLayersForVertexSearch = NLayersForVertexSearch; }
+
+  // Options electron tracking:
+  void SetDoTracking(bool Do) { m_DoTracking = Do; if (Do == false) m_TrackingAlgorithm = c_TrackingAlgoNone; }
   void SetKeepAllComptonTracks(bool Keep) { m_KeepAllComptonTracks = Keep; }
   void SetAssumeTrackTopBottom(bool Flag) { m_AssumeTrackTopBottom = Flag; }
   void SetBETFileName(MString FileName) { m_BETFileName = FileName; }
   void SetMaxComptonJump(unsigned int Jump) { m_MaxComptonJump = Jump; }
   void SetNTrackSequencesToKeep(unsigned int Jump) { m_NTrackSequencesToKeep = Jump; }
   void SetRejectPurelyAmbiguousTrackSequences(bool Flag) { m_RejectPurelyAmbiguousTrackSequences = Flag; }
-  void SetNLayersForVertexSearch(unsigned int NLayersForVertexSearch) { m_NLayersForVertexSearch = NLayersForVertexSearch; }
   void SetElectronTrackingDetectorList(vector<MString> DetectorList) { m_ElectronTrackingDetectorList = DetectorList; }
 
   // Options Kalman Filter
@@ -349,9 +352,11 @@ class MRawEventAnalyzer
   //! Hit clustering
   MERHitClusterizer* m_HitClusterizer;
   //! Event type identification
-  MEREventId* m_EventId;
+  MEREventType* m_EventType;
   //! Electron tracking
   MERTrack* m_Tracker;
+  //! Pair reconstruction
+//  MERPair* m_Pair;
   //! Compton sequence reconstruction
   MERCSR* m_CSR;
   //! Decay search
@@ -388,7 +393,7 @@ class MRawEventAnalyzer
   int m_CoincidenceAlgorithm;
   int m_EventClusteringAlgorithm;
   int m_HitClusteringAlgorithm;
-  int m_EventIdAlgorithm;
+  int m_EventTypeAlgorithm;
   int m_TrackingAlgorithm;
   int m_PairAlgorithm;
   int m_CSRAlgorithm;
@@ -418,11 +423,15 @@ class MRawEventAnalyzer
 
   MString m_PDFClusterizerBaseFileName;
 
-  // Electron tracking:
-  bool m_DoTracking;
+  // Event type identification
+  bool m_SearchPhotoEvent;
   bool m_SearchPairTracks;
   bool m_SearchMIPTracks;
   bool m_SearchComptonTracks;
+  unsigned int m_NLayersForVertexSearch;
+  
+  // Electron tracking:
+  bool m_DoTracking;
   bool m_KeepAllComptonTracks;
   bool m_AssumeTrackTopBottom;
   MString m_BETFileName;
@@ -430,7 +439,6 @@ class MRawEventAnalyzer
   unsigned int m_MaxComptonJump;
   unsigned int m_NTrackSequencesToKeep;
   bool m_RejectPurelyAmbiguousTrackSequences;
-  unsigned int m_NLayersForVertexSearch;
 
   vector<MString> m_ElectronTrackingDetectorList;
 
@@ -482,7 +490,7 @@ class MRawEventAnalyzer
   double m_TimeLoad;
   double m_TimeEventClusterize;
   double m_TimeHitClusterize;
-  double m_TimeEventId;
+  double m_TimeEventType;
   double m_TimeTrack;
   double m_TimeCSR;
   double m_TimeFinalize;
diff --git a/src/revan/inc/MSettingsEventReconstruction.h b/src/revan/inc/MSettingsEventReconstruction.h
index 07889e1a9..c722ebc06 100644
--- a/src/revan/inc/MSettingsEventReconstruction.h
+++ b/src/revan/inc/MSettingsEventReconstruction.h
@@ -51,8 +51,8 @@ class MSettingsEventReconstruction : public MSettingsInterface
   void SetHitClusteringAlgorithm(int ID) { m_HitClusteringAlgorithm = ID; }
   int GetHitClusteringAlgorithm() { return m_HitClusteringAlgorithm; }
 
-  void SetEventIdAlgorithm(int ID) {m_EventIdAlgorithm = ID; }
-  int GetEventIdAlgorithm() { return m_EventIdAlgorithm; }
+  void SetEventTypeAlgorithm(int ID) {m_EventTypeAlgorithm = ID; }
+  int GetEventTypeAlgorithm() { return m_EventTypeAlgorithm; }
   
   void SetTrackingAlgorithm(int ID) { m_TrackingAlgorithm = ID; }
   int GetTrackingAlgorithm() { return m_TrackingAlgorithm; }
@@ -173,6 +173,8 @@ class MSettingsEventReconstruction : public MSettingsInterface
   void SetDoTracking(bool Do) { m_DoTracking = Do; }
   bool GetDoTracking() { return m_DoTracking; }
 
+  void SetSearchPhoto(bool Search) { m_SearchPhoto = Search; }
+  bool GetSearchPhoto() { return m_SearchPhoto; }
   void SetSearchPairs(bool Search) { m_SearchPairs = Search; }
   bool GetSearchPairs() { return m_SearchPairs; }
   void SetSearchMIPs(bool Search) { m_SearchMIPs = Search; }
@@ -297,7 +299,7 @@ class MSettingsEventReconstruction : public MSettingsInterface
   int m_CoincidenceAlgorithm;
   int m_EventClusteringAlgorithm;
   int m_HitClusteringAlgorithm;
-  int m_EventIdAlgorithm;
+  int m_EventTypeAlgorithm;
   int m_TrackingAlgorithm;
   int m_PairAlgorithm;
   int m_CSRAlgorithm;
@@ -333,16 +335,18 @@ class MSettingsEventReconstruction : public MSettingsInterface
 
   MString m_PDFClusterizerBaseFileName;
 
-  // Electron tracking:
-  bool m_DoTracking;
+  // Event type identification
   bool m_SearchPairs;
   bool m_SearchMIPs;
   bool m_SearchComptons;
+  bool m_SearchPhoto;
+  int m_NLayersForVertexSearch;
 
+  // Electron tracking:
+  bool m_DoTracking;
   int m_MaxComptonJump;
   int m_NTrackSequencesToKeep;
   bool m_RejectPurelyAmbiguousTrackSequences;
-  int m_NLayersForVertexSearch;
   double m_HeightX0;
   double m_SigmaHitPos;
 
diff --git a/src/revan/src/MEREventType.cxx b/src/revan/src/MEREventType.cxx
index f9528bd45..6a4012b0c 100644
--- a/src/revan/src/MEREventType.cxx
+++ b/src/revan/src/MEREventType.cxx
@@ -1199,7 +1199,7 @@ MString MEREventType::ToString(bool CoreOnly) const
   ostringstream out;
 
   if (CoreOnly == false) {
-    out<<"# Tracking - FoM options:"<<endl;
+    out<<"# Event type - options:"<<endl;
     out<<"# "<<endl;
   }
   out<<"# Search Photos:              "<<m_SearchPhoto<<endl;
diff --git a/src/revan/src/MERTrack.cxx b/src/revan/src/MERTrack.cxx
index 2f920ae81..57bfe6cb3 100644
--- a/src/revan/src/MERTrack.cxx
+++ b/src/revan/src/MERTrack.cxx
@@ -191,6 +191,21 @@ bool MERTrack::SetParameters(bool SearchMIPs,
 ////////////////////////////////////////////////////////////////////////////////
 
 
+bool MERTrack::HasOneREOfType(int EventType) {
+  MRERawEvent* RE = nullptr;
+  for (int e = 0; e < m_List->GetNRawEvents(); e++) {
+    RE = m_List->GetRawEventAt(e);
+    if (RE->GetEventType() == EventType) {
+      return true;
+    }
+  }
+  return false;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
 bool MERTrack::Analyze(MRawEventIncarnations* REList)
 {
   // Analyze the raw event...
@@ -204,7 +219,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
   mdebug<<"Starting tracking"<<endl;
 
 
-  bool Identified = false;
+  //bool Identified = false;
   MRERawEvent* RE = 0;
   MRawEventIncarnations* List = 0;
   MRESE* RESE = 0;
@@ -239,47 +254,51 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
   }
 
   // Step B: Pairs
-
   Timer.Start();
-  if (m_SearchPairs == true) {
+  if (HasOneREOfType(MRERawEvent::c_PairEvent)) {
     mdebug<<"* Search for pairs: Vertex"<<endl;
     bool HasVertices = false;
     int e_max = m_List->GetNRawEvents();
     for (int e = 0; e < e_max; e++) {
       RE = m_List->GetRawEventAt(e);
-      List = CheckForPair(RE);
-      if (List != 0) {
-        mdebug<<"List: "<<List->GetNRawEvents()<<endl;
-        HasVertices = true;
-        m_List->DeleteRawEvent(RE);
-        e--;
-        e_max--;
-        for (int i = 0; i < List->GetNRawEvents(); i++) {
-          m_List->AddRawEvent(List->GetRawEventAt(i));
+      if (RE->GetEventType() == MRERawEvent::c_PairEvent) {// Iterate only over pair events
+        List = CheckForPair(RE);//Check for vertices
+        if (List) { // if vertices
+          mdebug<<"List: "<<List->GetNRawEvents()<<endl;
+          HasVertices = true;
+          m_List->DeleteRawEvent(RE);
+          e--;
+          e_max--;
+          for (int i = 0; i < List->GetNRawEvents(); i++) {
+            m_List->AddRawEvent(List->GetRawEventAt(i));
+          }
+          delete List;
+          List = nullptr;
+          mdebug<<"Tracking: Event has vertex!"<<endl;
         }
-        delete List;
-        mdebug<<"Tracking: Event has vertex!"<<endl;
-      }
-    }
-    if (HasVertices == true) {
-      // Let's analyze pairs:
-      mdebug<<"* Step: Pair tracking"<<endl;
-      mdebug<<m_List->ToString()<<endl;
-      int e_max = m_List->GetNRawEvents();
-      for (int e = 0; e < e_max; e++) {
-        RE = m_List->GetRawEventAt(e);
-        if (RE->GetVertex() != 0) {
-          TrackPairs(RE);
+        if (HasVertices == true) {
+          // Let's analyze pairs:
+          mdebug<<"* Step: Pair tracking"<<endl;
+          mdebug<<m_List->ToString()<<endl;
+          int e_max = m_List->GetNRawEvents();
+          for (int e = 0; e < e_max; e++) {
+            RE = m_List->GetRawEventAt(e);
+            if (RE->GetVertex() != 0) {
+              TrackPairs(RE);
+            }
+          }
+          mdebug<<"Tracking:  Successful identification: Pair event!"<<endl;
+          mdebug<<"        Pair results:"<<endl;
+          mdebug<<m_List->ToString()<<endl;
+          mdebug<<endl;
+          //Identified = true;
+          m_List->SetOptimumEvent(RE);
+          m_List->SetBestTryEvent(RE);
+        } else { // if no vertices
+          RE->SetEventType(MRERawEvent::c_UnknownEvent); // discard
         }
       }
-      mdebug<<"Tracking:  Successful identification: Pair event!"<<endl;
-      mdebug<<"        Pair results:"<<endl;
-      mdebug<<m_List->ToString()<<endl;
-      mdebug<<endl;
-      Identified = true;
-      m_List->SetOptimumEvent(RE);
-      m_List->SetBestTryEvent(RE);
-    } // pair...
+    } // end for
   }
   m_TimePairs += Timer.ElapsedTime();
 
@@ -287,23 +306,27 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
   // Step C: Mips
 
   Timer.Start();
-  if (Identified == false && m_SearchMIPs == true) {
+  if (HasOneREOfType(MRERawEvent::c_MipEvent) || HasOneREOfType(MRERawEvent::c_ShowerEvent)) {
+  //if (m_SearchMIPs == true) {
     mdebug<<"* Search for MIPs"<<endl;
     for (int e = 0; e < m_List->GetNRawEvents(); e++) {
       RE = m_List->GetRawEventAt(e);
-      CheckForMips(RE);
-      // If we have found a MIP then we are done!
-      if (RE->GetEventType() == MRERawEvent::c_MipEvent) {
-        mdebug<<"Tracking: Successful identification: MIP (probably muon)"<<endl;
-        Identified = true;
-        m_List->SetOptimumEvent(RE);
-        m_List->SetBestTryEvent(RE);
-      }
-      if (RE->GetEventType() == MRERawEvent::c_ShowerEvent) {
-        mdebug<<"Tracking: Successful identification: Shower"<<endl;
-        Identified = true;
-        m_List->SetOptimumEvent(RE);
-        m_List->SetBestTryEvent(RE);
+      if (RE->GetEventType() == MRERawEvent::c_MipEvent || RE->GetEventType() == MRERawEvent::c_ShowerEvent) {// Iterate only over MIP/shower events
+        CheckForMips(RE);
+        // If we have found a MIP then we are done!
+        if (RE->GetEventType() == MRERawEvent::c_MipEvent) {
+          mdebug<<"Tracking: Successful identification: MIP (probably muon)"<<endl;
+          //Identified = true;
+          m_List->SetOptimumEvent(RE);
+          m_List->SetBestTryEvent(RE);
+        } else if (RE->GetEventType() == MRERawEvent::c_ShowerEvent) {
+          mdebug<<"Tracking: Successful identification: Shower"<<endl;
+          //Identified = true;
+          m_List->SetOptimumEvent(RE);
+          m_List->SetBestTryEvent(RE);
+        } else {
+          RE->SetEventType(MRERawEvent::c_UnknownEvent); // discard
+        }
       }
     }
     mdebug<<"        MIP results:"<<endl;
@@ -315,7 +338,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
 
   // Step C: Compton tracks:
 
-  if (Identified == false && m_SearchComptons == true) {
+  if (HasOneREOfType(MRERawEvent::c_ComptonEvent)) {
     mdebug<<"* Search for Comptons"<<endl;
 
     // Step C.1: Generate the links
@@ -326,20 +349,22 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
     int e_max = m_List->GetNRawEvents();
     for (int e = 0; e < e_max; e++) {
       RE = m_List->GetRawEventAt(e);
-      List = TrackComptons(RE);
-      if (List != 0) {
-        m_List->DeleteRawEvent(RE);
-        e--;
-        e_max--;
-        for (int i = 0; i < List->GetNRawEvents(); i++) {
-          m_List->AddRawEvent(List->GetRawEventAt(i));
+      if (RE->GetEventType() == MRERawEvent::c_ComptonEvent) {
+        List = TrackComptons(RE);
+        if (List != 0) {
+          m_List->DeleteRawEvent(RE);
+          e--;
+          e_max--;
+          for (int i = 0; i < List->GetNRawEvents(); i++) {
+            m_List->AddRawEvent(List->GetRawEventAt(i));
+          }
+          delete List;
+          List = nullptr;
         }
-        delete List;
       }
     }
     m_TimeComptonSequences += Timer.ElapsedTime();
 
-
     // We now accept only events with the maximum possible number of tracks,
     // if the flag is set
     if (m_AllowOnlyMinNumberOfRESEsD1 == true) {
@@ -348,10 +373,10 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
       for (int e = 0; e < m_List->GetNRawEvents(); e++) {
         int CurrentN = 0;
         RE = m_List->GetRawEventAt(e);
-        for (int r = 0; r < RE->GetNRESEs(); r++) {
-          RESE = RE->GetRESEAt(r);
-          if (IsInTracker(RESE) == true) {
-            CurrentN++;
+        if (RE->GetEventType() == MRERawEvent::c_ComptonEvent) {
+          for (int r = 0; r < RE->GetNRESEs(); r++) {
+            RESE = RE->GetRESEAt(r);
+            if (IsInTracker(RESE) == true) CurrentN++;
           }
         }
         if (CurrentN < MinN) MinN = CurrentN;
@@ -360,9 +385,11 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
       for (int e = 0; e < m_List->GetNRawEvents(); e++) {
         int CurrentN = 0;
         RE = m_List->GetRawEventAt(e);
-        for (int r = 0; r < RE->GetNRESEs(); r++) {
-          RESE = RE->GetRESEAt(r);
-          if (IsInTracker(RESE) == true) CurrentN++;
+        if (RE->GetEventType() == MRERawEvent::c_ComptonEvent) {
+          for (int r = 0; r < RE->GetNRESEs(); r++) {
+            RESE = RE->GetRESEAt(r);
+            if (IsInTracker(RESE) == true) CurrentN++;
+          }
         }
         if (CurrentN > MinN) {
           m_List->DeleteRawEvent(RE);
@@ -384,21 +411,23 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
 
     for (int e = 0; e < m_List->GetNRawEvents(); e++) {
       RE = m_List->GetRawEventAt(e);
+      if (RE->GetEventType() == MRERawEvent::c_ComptonEvent) {
 
-      for (int r = 0; r < RE->GetNRESEs(); r++) {
-        RESE = RE->GetRESEAt(r);
-        IDRESE = RESE->GetID();
-        if (RESE->GetType() == MRESE::c_Track) {
-          Track = (MRETrack *) RESE;
-          if (Track->GetStartPoint() == 0) {
-            massert(Track->GetNEndPoints() == 2);
-
-            IDEP = Track->GetEndPointAt(0)->GetID();
-            REdup = RE->Duplicate();
-            ((MRETrack *) (REdup->GetRESE(IDRESE)))->SetStartPoint(((MRETrack *) (REdup->GetRESE(IDRESE)))->GetRESE(IDEP));
-            m_List->AddRawEvent(REdup);
-
-            Track->SetStartPoint(Track->GetEndPointAt(1));
+        for (int r = 0; r < RE->GetNRESEs(); r++) {
+          RESE = RE->GetRESEAt(r);
+          IDRESE = RESE->GetID();
+          if (RESE->GetType() == MRESE::c_Track) {
+            Track = (MRETrack *) RESE;
+            if (Track->GetStartPoint() == 0) {
+              massert(Track->GetNEndPoints() == 2);
+
+              IDEP = Track->GetEndPointAt(0)->GetID();
+              REdup = RE->Duplicate();
+              ((MRETrack *) (REdup->GetRESE(IDRESE)))->SetStartPoint(((MRETrack *) (REdup->GetRESE(IDRESE)))->GetRESE(IDEP));
+              m_List->AddRawEvent(REdup);
+
+              Track->SetStartPoint(Track->GetEndPointAt(1));
+            }
           }
         }
       }
@@ -408,7 +437,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
 
     for (int e = 0; e < m_List->GetNRawEvents(); e++) {
       RE = m_List->GetRawEventAt(e);
-      EvaluateTracks(RE);
+      if (RE->GetEventType() == MRERawEvent::c_ComptonEvent) EvaluateTracks(RE);
     }
     SortByTrackQualityFactor(m_List);
 
@@ -1005,7 +1034,7 @@ void MERTrack::EliminatePairDeviations(MRERawEvent* RE, MRETrack* Track)
 void MERTrack::CheckForMips(MRERawEvent* RE)
 {
   // Check if the events structure can be created by a massive interacting
-  // particle like myons:
+  // particle like muons:
   //
   // The typical pattern of a MIP is:
   // We have a straight track with serveral hits which, do not belong to the
@@ -1048,7 +1077,7 @@ void MERTrack::CheckForMips(MRERawEvent* RE)
   }
 
 
-  // We look for straight tripple combinations:
+  // We look for straight triple combinations:
   unsigned int max = D1Hits.size();
   MRESE* iRESE;
   MRESE* jRESE;
@@ -1283,7 +1312,6 @@ MRawEventIncarnations* MERTrack::TrackComptons(MRERawEvent* RE)
   if (NAmbiguities <= m_MaxNAmbiguities) {
     // Find ambiguous sequences
     mdebug<<"Testing ambiguous sequences"<<endl;
-
     List->AddRawEvent(RE->Duplicate());
 
     MRESE* RESEmain = 0;
diff --git a/src/revan/src/MGUIERAlgorithm.cxx b/src/revan/src/MGUIERAlgorithm.cxx
index 3a71bc459..976655d3e 100644
--- a/src/revan/src/MGUIERAlgorithm.cxx
+++ b/src/revan/src/MGUIERAlgorithm.cxx
@@ -66,9 +66,9 @@ MGUIERAlgorithm::~MGUIERAlgorithm()
   delete m_EventClusteringList;
   delete m_HitClusteringList;
   delete m_TrackingList;
-  delete m_EventIdList;
+  delete m_EventTypeList;
   delete m_CSRList;
-  delete m_PairList;
+//  delete m_PairList;
   //delete m_DecayList;
   delete m_ListLayout;
 }
@@ -83,7 +83,7 @@ void MGUIERAlgorithm::Create()
 
   // We start with a name and an icon...
   SetWindowName("ER algorithms");
-  AddSubTitle("Choose the reconstruction algorithms");
+  //AddSubTitle("Choose the reconstruction algorithms");
 
   m_ListLayout = new TGLayoutHints(kLHintsExpandX | kLHintsTop, 20, 20, 10, 10);
 
@@ -123,12 +123,12 @@ void MGUIERAlgorithm::Create()
   AddFrame(m_HitClusteringList, m_ListLayout);
   
   // Event identification
-  m_EventIdList = new MGUIERBList(this, "Event type identification", true);
-  m_EventIdList->Add("Default algorithm"); // 0
-  m_EventIdList->Add("External from file (not implemented)"); // 1
-  m_EventIdList->SetSelected(m_Data->GetEventIdAlgorithm());
-  m_EventIdList->Create();
-  AddFrame(m_EventIdList, m_ListLayout);
+  m_EventTypeList = new MGUIERBList(this, "Event type identification", true);
+  m_EventTypeList->Add("Default algorithm"); // 0
+  m_EventTypeList->Add("External from file (not implemented)"); // 1
+  m_EventTypeList->SetSelected(m_Data->GetEventTypeAlgorithm());
+  m_EventTypeList->Create();
+  AddFrame(m_EventTypeList, m_ListLayout);
 
   // Electron tracking
   m_TrackingList = new MGUIERBList(this, "Electron tracking", true);
@@ -165,7 +165,7 @@ void MGUIERAlgorithm::Create()
 //  }
   m_TrackingList->Create();
   AddFrame(m_TrackingList, m_ListLayout);
-
+/*
   m_PairList = new MGUIERBList(this, "Pair reconstruction", true);
   m_PairList->Add("Default algorithm");  // 0
   //m_PairList->Add("Kalman Filter 3D (work in progress)"); // 1
@@ -173,7 +173,7 @@ void MGUIERAlgorithm::Create()
   m_PairList->SetSelected(m_Data->GetPairAlgorithm());
   m_PairList->Create();
   AddFrame(m_PairList, m_ListLayout);
-
+*/
   m_CSRList = new MGUIERBList(this, "Compton tracking", true);
   m_CSRList->Add("No Compton tracking");
   m_CSRList->Add("Classic Compton Sequence Reconstruction without Energy Recovery (Chi-square approach via angles)");
@@ -246,7 +246,7 @@ bool MGUIERAlgorithm::OnApply()
   } else if (m_TrackingList->GetSelected() == 7) {
     m_Data->SetTrackingAlgorithm(MRawEventAnalyzer::c_TrackingAlgoBayesian);
   }
-  m_Data->SetPairAlgorithm(m_PairList->GetSelected());
+  //m_Data->SetPairAlgorithm(m_PairList->GetSelected());
   m_Data->SetCSRAlgorithm(m_CSRList->GetSelected());
   
   //m_Data->SetDecayAlgorithm(m_DecayList->GetSelected());
diff --git a/src/revan/src/MGUIRevanMain.cxx b/src/revan/src/MGUIRevanMain.cxx
index ccd74444c..ce69c2f2d 100644
--- a/src/revan/src/MGUIRevanMain.cxx
+++ b/src/revan/src/MGUIRevanMain.cxx
@@ -38,6 +38,7 @@ using namespace std;
 #include "MGUIOptionsCoincidence.h"
 #include "MGUIOptionsEventClustering.h"
 #include "MGUIOptionsHitClustering.h"
+#include "MGUIOptionsEventType.h"
 #include "MGUIOptionsTracking.h"
 #include "MGUIOptionsCSR.h"
 #include "MGUIOptionsDecay.h"
@@ -99,6 +100,7 @@ void MGUIRevanMain::Create()
   m_MenuReconstruction->AddEntry("Coincidence options", c_OptionsCoincidence);
   m_MenuReconstruction->AddEntry("Event clustering options", c_OptionsEventClustering);
   m_MenuReconstruction->AddEntry("Hit clustering options", c_OptionsHitClustering);
+  m_MenuReconstruction->AddEntry("Event type identification", c_OptionsEventType);
   m_MenuReconstruction->AddEntry("Electron tracking options", c_OptionsTracking);
   m_MenuReconstruction->AddEntry("Compton sequencing options", c_OptionsSequencing);
   //m_MenuReconstruction->AddEntry("Decay options", c_OptionsDecay);
@@ -218,10 +220,6 @@ bool MGUIRevanMain::ProcessMessage(long Message, long Parameter1,
         new MGUIOptionsGeneral(gClient->GetRoot(), this, m_Data);
         break;
 
-      case c_OptionsTracking:
-        new MGUIOptionsTracking(gClient->GetRoot(), this, m_Data, m_Interface->GetGeometry());
-        break;
-
       case c_OptionsCoincidence:
         new MGUIOptionsCoincidence(gClient->GetRoot(), this, m_Data);
         break;
@@ -233,6 +231,14 @@ bool MGUIRevanMain::ProcessMessage(long Message, long Parameter1,
       case c_OptionsHitClustering:
         new MGUIOptionsHitClustering(gClient->GetRoot(), this, m_Data);
         break;
+
+      case c_OptionsEventType:
+        new MGUIOptionsEventType(gClient->GetRoot(), this, m_Data, m_Interface->GetGeometry());
+        break;
+
+      case c_OptionsTracking:
+        new MGUIOptionsTracking(gClient->GetRoot(), this, m_Data, m_Interface->GetGeometry());
+        break;
         
       case c_OptionsSequencing:
         new MGUIOptionsCSR(gClient->GetRoot(), this, m_Data);
@@ -384,7 +390,7 @@ void MGUIRevanMain::Open()
     Types[8] = "All files";
     Types[9] = "*";
     Types[10] = 0;
-    Types[1] = 0;
+    Types[11] = 0;
   } else {
     Types[0] = "Analyzed events";
     Types[1] = "*.evta";
diff --git a/src/revan/src/MRERawEvent.cxx b/src/revan/src/MRERawEvent.cxx
index 468df196c..84c4f6a44 100644
--- a/src/revan/src/MRERawEvent.cxx
+++ b/src/revan/src/MRERawEvent.cxx
@@ -124,7 +124,6 @@ MRERawEvent::MRERawEvent(MRERawEvent* RE) : MRESE((MRESE *) RE)
   // Some kind of copy constructor
 
   Init();
-
   SetGeometry(RE->GetGeometry());
   SetGoodEvent(RE->IsGoodEvent());
 
@@ -1011,7 +1010,6 @@ MPhysicalEvent* MRERawEvent::GetPhysicalEvent()
 
   // This is only an experimental flag --- don't activate it unless you know what you are doing...
   bool UseCenterD2 = false;
-
   if (m_Event != nullptr && m_Event->GetType() != m_EventType) {
     // We had an upgrade...
     delete m_Event;
@@ -1019,7 +1017,7 @@ MPhysicalEvent* MRERawEvent::GetPhysicalEvent()
   }
 
   if (m_Event == nullptr) {
-    if (m_EventType == c_ComptonEvent) {
+    if (m_EventType == c_ComptonEvent && m_Start != nullptr) {
       MComptonEvent* CE = new MComptonEvent();
       double ED1 = 0.0;
       double ED2 = 0.0;
@@ -1115,10 +1113,10 @@ MPhysicalEvent* MRERawEvent::GetPhysicalEvent()
       }
       
       m_Event = (MPhysicalEvent*) CE;
-    } else if (m_EventType == c_PairEvent) {
+    } else if (m_EventType == c_PairEvent && m_ElectronTrack && m_PositronTrack) {
       // We need to have two tracks:
-      massert(m_ElectronTrack != 0);
-      massert(m_PositronTrack != 0);
+      //massert(m_ElectronTrack != 0);
+      //massert(m_PositronTrack != 0); now in the condition above
 
       MPairEvent* Pair = new MPairEvent();
       
@@ -1153,31 +1151,31 @@ MPhysicalEvent* MRERawEvent::GetPhysicalEvent()
       m_Event = (MPhysicalEvent*) U;
       m_Event->SetBad(true, GetRejectionReasonAsString(true));
     }
-  }
 
-  m_Event->Set(*dynamic_cast<MRotationInterface*>(this));
-  
-  m_Event->SetAllHitsGood(IsValid());
-  m_Event->SetTime(m_EventTime);
-  m_Event->SetId(m_EventID);
-  m_Event->SetTimeWalk(m_TimeWalk);
-  m_Event->SetDecay(m_Decay);
-  if (m_ExternalBadEventFlag == true) {
-    m_Event->SetBad(m_ExternalBadEventFlag, m_ExternalBadEventString);
-  }
-
-  for (unsigned int m = 0; m < m_Measurements.size(); ++m) {
-    if (m_Measurements[m]->GetType() == MREAM::c_StartInformation) {
-      MREAMStartInformation* Start = dynamic_cast<MREAMStartInformation*>(m_Measurements[m]);
-      m_Event->SetOIInformation(Start->GetPosition(), Start->GetDirection(), Start->GetPolarization(), Start->GetEnergy());
+    m_Event->Set(*dynamic_cast<MRotationInterface*>(this));
+    
+    m_Event->SetAllHitsGood(IsValid());
+    m_Event->SetTime(m_EventTime);
+    m_Event->SetId(m_EventID);
+    m_Event->SetTimeWalk(m_TimeWalk);
+    m_Event->SetDecay(m_Decay);
+    if (m_ExternalBadEventFlag == true) {
+      m_Event->SetBad(m_ExternalBadEventFlag, m_ExternalBadEventString);
+    }
+
+    for (unsigned int m = 0; m < m_Measurements.size(); ++m) {
+      if (m_Measurements[m]->GetType() == MREAM::c_StartInformation) {
+        MREAMStartInformation* Start = dynamic_cast<MREAMStartInformation*>(m_Measurements[m]);
+        m_Event->SetOIInformation(Start->GetPosition(), Start->GetDirection(), Start->GetPolarization(), Start->GetEnergy());
+      }
+    }
+    m_Event->ClearComments(); // Since this info might be added multiple times.
+    for (unsigned int c = 0; c < m_Comments.size(); ++c) {
+      m_Event->AddComment(m_Comments[c]);
     }
-  }
-  m_Event->ClearComments(); // Since this info might be added multiple times.
-  for (unsigned int c = 0; c < m_Comments.size(); ++c) {
-    m_Event->AddComment(m_Comments[c]);
-  }
 
-  m_Event->Validate();
+    m_Event->Validate();
+  }
 
   return m_Event;
 }
diff --git a/src/revan/src/MRawEventAnalyzer.cxx b/src/revan/src/MRawEventAnalyzer.cxx
index e016a2fd2..e7c1acb0c 100644
--- a/src/revan/src/MRawEventAnalyzer.cxx
+++ b/src/revan/src/MRawEventAnalyzer.cxx
@@ -55,7 +55,7 @@ using namespace std;
 #include "MEREventClusterizer.h"
 #include "MEREventClusterizerDistance.h"
 #include "MEREventClusterizerTMVA.h"
-#include "MEREventId.h"
+#include "MEREventType.h"
 #include "MERTrack.h"
 #include "MERTrackPearson.h"
 #include "MERTrackRank.h"
@@ -169,6 +169,7 @@ MRawEventAnalyzer::MRawEventAnalyzer()
   m_CoincidenceAlgorithm = c_CoincidenceAlgoNone;
   m_EventClusteringAlgorithm = c_EventClusteringAlgoNone;
   m_HitClusteringAlgorithm = c_HitClusteringAlgoAdjacent;
+  m_EventTypeAlgorithm = c_EventTypeDefault;
   m_TrackingAlgorithm = c_TrackingAlgoNone;
   m_PairAlgorithm = c_PairDefault;
   m_CSRAlgorithm = c_CSRAlgoFoM;
@@ -186,11 +187,13 @@ MRawEventAnalyzer::MRawEventAnalyzer()
 
   m_AdjacentLevel = 2;
   m_AdjacentSigma = 0.0;
-
-  m_DoTracking = true;
+  
+  m_SearchPhotoEvent = true;
   m_SearchPairTracks = true;
   m_SearchMIPTracks = false;
   m_SearchComptonTracks = true;
+
+  m_DoTracking = true;
   m_KeepAllComptonTracks = false;
   m_AssumeTrackTopBottom = false;
 
@@ -239,6 +242,7 @@ MRawEventAnalyzer::MRawEventAnalyzer()
   m_Coincidence = nullptr;
   m_EventClusterizer = nullptr;
   m_HitClusterizer = nullptr;
+  m_EventType = nullptr;
   m_Tracker = nullptr;
   m_CSR = nullptr;
   m_Decay = nullptr;
@@ -270,6 +274,7 @@ MRawEventAnalyzer::~MRawEventAnalyzer()
   delete m_Coincidence;
   delete m_EventClusterizer;
   delete m_HitClusterizer;
+  delete m_EventType;
   delete m_Tracker;
   delete m_CSR;
   delete m_Decay;
@@ -530,7 +535,6 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
   // Read events if we have reader
   if (m_Reader != nullptr) {
     RE = m_Reader->GetNextEvent();
-    mout << "AL " << RE << show;
     if (RE == nullptr) { // No more events left in file
       ClearStore = true;
       if (m_EventStore->GetNRawEvents() == 0) {
@@ -595,7 +599,6 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
     RE = m_EventStore->GetRawEventAt(0);
     m_EventStore->RemoveRawEvent(RE);
   }
-
   if (RE == nullptr) {
     merr<<"We don't have a raw event..."<<fatal;
     return c_AnalysisUndefinedError;
@@ -657,7 +660,6 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
   
   
   // Section B: Event clustering:
-  
   if (SelectionsPassed == true && m_EventClusteringAlgorithm > c_EventClusteringAlgoNone) {
     Timer.Start();
     
@@ -675,7 +677,6 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
   
   
   // Section C: Hit Clustering:
-  
   if (SelectionsPassed == true && m_HitClusteringAlgorithm > c_HitClusteringAlgoNone) {
     Timer.Start();
     
@@ -701,23 +702,22 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
 
 
   // Section I: Event type identification
-
   if (SelectionsPassed) {
     Timer.Start();
 
-    if (m_EventId == nullptr) {
+    if (m_EventType == nullptr) {
       merr << "Event identification pointer is zero. You changed the event reconstruction setup without calling PreAnalysis()!" << show;
       return c_AnalysisUndefinedError;
     }
 
     for (unsigned int i = 0; i < m_RawEvents->Size(); ++i) {
       MRawEventIncarnations* REI = m_RawEvents->Get(i);
-      m_EventId->Analyze(REI);
+      m_EventType->Analyze(REI);
     }
 
     if (m_RawEvents->IsAnyEventValid() == false) SelectionsPassed = false;
 
-    m_TimeEventId += Timer.ElapsedTime();
+    m_TimeEventType += Timer.ElapsedTime();
 
   }
 
@@ -1021,6 +1021,10 @@ bool MRawEventAnalyzer::PostAnalysis()
     out<<"# "<<endl;
     out<<m_HitClusterizer->ToString();
   }
+  if (m_EventType != nullptr) {
+    out<<"# "<<endl;
+    out<<m_EventType->ToString();
+  }
   if (m_Tracker != nullptr) {
     out<<"# "<<endl;
     out<<m_Tracker->ToString();
@@ -1117,7 +1121,7 @@ bool MRawEventAnalyzer::PostAnalysis()
   mout<<"General timings:"<<endl;
   mout<<"Timer Load     "<<m_TimeLoad<<endl;
   mout<<"Timer Cluster  "<<m_TimeClusterize<<endl;
-  mout<<"Timer EventId    "<<m_TimeEventId<<endl;
+  mout<<"Timer EventType"<<m_TimeEventType<<endl;
   mout<<"Timer Track    "<<m_TimeTrack<<endl;
   mout<<"Timer CSR      "<<m_TimeCSR<<endl;
   mout<<"Timer Finalize "<<m_TimeFinalize<<endl;
@@ -1127,6 +1131,9 @@ bool MRawEventAnalyzer::PostAnalysis()
   if (m_HitClusterizer != nullptr) {
     m_HitClusterizer->PostAnalysis();
   }
+  if (m_EventType != nullptr) {
+    m_EventType->PostAnalysis();
+  }
   if (m_Tracker != nullptr) {
     m_Tracker->PostAnalysis();
   }
@@ -1276,6 +1283,83 @@ bool MRawEventAnalyzer::PreAnalysis()
       Return = false;
     }
 
+    // Event type identification
+    delete m_EventType;
+    m_EventType = nullptr;
+    if (m_EventTypeAlgorithm == c_EventTypeDefault) {
+      m_EventType = new MEREventType();
+    } else if (m_EventTypeAlgorithm == c_EventTypeExternal) {
+      merr << "External event type identification not implemented yet!" << show;
+      Return = false;
+    } else {
+      merr<<"Unknown event type algorithm: "<<m_EventTypeAlgorithm<<endl;
+      Return = false;
+    }
+    if (m_EventType) {
+      m_EventType->SetGeometry(m_Geometry);
+      m_EventType->SetParameters( m_SearchMIPTracks,
+                                  m_SearchPairTracks,
+                                  m_SearchComptonTracks,
+                                  m_SearchPhotoEvent,
+                                  m_NLayersForVertexSearch,
+                                  m_ElectronTrackingDetectorList);
+    }
+
+    // Electron tracking
+    delete m_Tracker;
+    m_Tracker = nullptr;
+    if (m_TrackingAlgorithm == c_TrackingAlgoModifiedPearson) {
+      m_Tracker = new MERTrack();
+    } else if (m_TrackingAlgorithm == c_TrackingAlgoPearson) {
+      m_Tracker = new MERTrackPearson();
+    } else if (m_TrackingAlgorithm == c_TrackingAlgoRank) {
+      m_Tracker = new MERTrackRank();
+    } else if (m_TrackingAlgorithm == c_TrackingAlgoChiSquare) {
+      m_Tracker = new MERTrackChiSquare();
+    } else if (m_TrackingAlgorithm == c_TrackingAlgoGas) {
+      m_Tracker = new MERTrackGas();
+    } else if (m_TrackingAlgorithm == c_TrackingAlgoDirectional) {
+      m_Tracker = new MERTrackDirectional();
+    } else if (m_TrackingAlgorithm == c_TrackingAlgoBayesian) {
+      m_Tracker = new MERTrackBayesian();
+      if (dynamic_cast<MERTrackBayesian*>(m_Tracker)->
+          SetSpecialParameters(m_BETFileName) == false) {
+        Return = false;
+      }
+    } else if (m_TrackingAlgorithm == c_TrackingAlgoKalman3D) {
+      m_Tracker = new MERTrackKalman3D();
+      dynamic_cast<MERTrackKalman3D*>(m_Tracker)->SetSpecialParameters(m_SigmaHitPos, m_NLayersForVertexSearch);
+    } else if (m_TrackingAlgorithm == c_TrackingAlgoKalman2D) {
+      m_Tracker = new MERTrackKalman2D();
+      dynamic_cast<MERTrackKalman2D*>(m_Tracker)->SetSpecialParameters(m_SigmaHitPos, m_NLayersForVertexSearch);
+    } else if (m_TrackingAlgorithm == c_TrackingAlgoNone) {
+      // Nothing
+    } else {
+      merr<<"Unknown electron tracking algorithm: "<<m_TrackingAlgorithm<<endl;
+      Return = false;
+    }
+
+    if (m_Tracker != nullptr) {
+      m_Tracker->SetGeometry(m_Geometry);
+      m_Tracker->SetParameters(m_SearchMIPTracks,
+                               m_SearchPairTracks,
+                               m_SearchComptonTracks,
+                               m_MaxComptonJump,
+                               m_NTrackSequencesToKeep,
+                               m_RejectPurelyAmbiguousTrackSequences,
+                               m_NLayersForVertexSearch,
+                               m_ElectronTrackingDetectorList);
+    }
+
+/*
+    // Pair Algorithm
+    if (m_PairAlgorithm == c_PairDefault) {
+      m_Tracker = new MERTrack();
+    } else {
+      Return = false;
+    }*/
+
+
     // Compton sequence reconstruction
     delete m_CSR;
     m_CSR = nullptr;
@@ -1353,60 +1437,6 @@ bool MRawEventAnalyzer::PreAnalysis()
       Return = false;
     }
 
-    // Electron tracking
-    delete m_Tracker;
-    m_Tracker = nullptr;
-    if (m_TrackingAlgorithm == c_TrackingAlgoModifiedPearson) {
-      m_Tracker = new MERTrack();
-    } else if (m_TrackingAlgorithm == c_TrackingAlgoPearson) {
-      m_Tracker = new MERTrackPearson();
-    } else if (m_TrackingAlgorithm == c_TrackingAlgoRank) {
-      m_Tracker = new MERTrackRank();
-    } else if (m_TrackingAlgorithm == c_TrackingAlgoChiSquare) {
-      m_Tracker = new MERTrackChiSquare();
-    } else if (m_TrackingAlgorithm == c_TrackingAlgoGas) {
-      m_Tracker = new MERTrackGas();
-    } else if (m_TrackingAlgorithm == c_TrackingAlgoDirectional) {
-      m_Tracker = new MERTrackDirectional();
-    } else if (m_TrackingAlgorithm == c_TrackingAlgoBayesian) {
-      m_Tracker = new MERTrackBayesian();
-      if (dynamic_cast<MERTrackBayesian*>(m_Tracker)->
-          SetSpecialParameters(m_BETFileName) == false) {
-        Return = false;
-      }
-    } else if (m_TrackingAlgorithm == c_TrackingAlgoKalman3D) {
-      m_Tracker = new MERTrackKalman3D();
-      dynamic_cast<MERTrackKalman3D*>(m_Tracker)->SetSpecialParameters(m_SigmaHitPos, m_NLayersForVertexSearch);
-    } else if (m_TrackingAlgorithm == c_TrackingAlgoKalman2D) {
-      m_Tracker = new MERTrackKalman2D();
-      dynamic_cast<MERTrackKalman2D*>(m_Tracker)->SetSpecialParameters(m_SigmaHitPos, m_NLayersForVertexSearch);
-    } else if (m_TrackingAlgorithm == c_TrackingAlgoNone) {
-      // Nothing
-    } else {
-      merr<<"Unknown electron tracking algorithm: "<<m_TrackingAlgorithm<<endl;
-      Return = false;
-    }
-
-    // Pair Algorithm
-    if (m_PairAlgorithm == c_PairDefault) {
-      m_Tracker = new MERTrack();
-    } else {
-      Return = false;
-    }
-
-    if (m_Tracker != nullptr) {
-      m_Tracker->SetGeometry(m_Geometry);
-      m_Tracker->SetParameters(m_SearchMIPTracks,
-                               m_SearchPairTracks,
-                               m_SearchComptonTracks,
-                               m_MaxComptonJump,
-                               m_NTrackSequencesToKeep,
-                               m_RejectPurelyAmbiguousTrackSequences,
-                               m_NLayersForVertexSearch,
-                               m_ElectronTrackingDetectorList);
-    }
-
-
     // Initialize the Decay searcher:
     delete m_Decay;
     m_Decay = nullptr;
diff --git a/src/revan/src/MSettingsEventReconstruction.cxx b/src/revan/src/MSettingsEventReconstruction.cxx
index 45401c57c..2f041f07a 100644
--- a/src/revan/src/MSettingsEventReconstruction.cxx
+++ b/src/revan/src/MSettingsEventReconstruction.cxx
@@ -50,7 +50,7 @@ MSettingsEventReconstruction::MSettingsEventReconstruction() : MSettingsInterfac
   m_CoincidenceAlgorithm = 0;
   m_EventClusteringAlgorithm = 0;
   m_HitClusteringAlgorithm = 1;
-  m_EventIdAlgorithm = 0;
+  m_EventTypeAlgorithm = 0;
   m_TrackingAlgorithm = 0;
   m_PairAlgorithm = 0;
   m_CSRAlgorithm = 1;
@@ -162,7 +162,7 @@ bool MSettingsEventReconstruction::WriteXml(MXmlNode* Node)
   new MXmlNode(Node, "CoincidenceAlgorithm", m_CoincidenceAlgorithm);
   new MXmlNode(Node, "EventClusteringAlgorithm", m_EventClusteringAlgorithm);
   new MXmlNode(Node, "HitClusteringAlgorithm", m_HitClusteringAlgorithm);
-  new MXmlNode(Node, "EventIdAlgorithm", m_EventIdAlgorithm);
+  new MXmlNode(Node, "EventTypeAlgorithm", m_EventTypeAlgorithm);
   new MXmlNode(Node, "TrackingAlgorithm", m_TrackingAlgorithm);
   new MXmlNode(Node, "PairAlgorithm", m_PairAlgorithm);
   new MXmlNode(Node, "CSRAlgorithm", m_CSRAlgorithm);
@@ -260,8 +260,8 @@ bool MSettingsEventReconstruction::ReadXml(MXmlNode* Node)
 //  if ((aNode = Node->GetNode("ClusteringAlgorithm")) != 0) {  // TODO: Delete in 2020
 //    m_HitClusteringAlgorithm = aNode->GetValueAsInt();
 //  }
-  if ((aNode = Node->GetNode("EventIdAlgorithm")) != 0) {
-    m_EventIdAlgorithm = aNode->GetValueAsInt();
+  if ((aNode = Node->GetNode("EventTypeAlgorithm")) != 0) {
+    m_EventTypeAlgorithm = aNode->GetValueAsInt();
   }
   if ((aNode = Node->GetNode("TrackingAlgorithm")) != 0) {
     m_TrackingAlgorithm = aNode->GetValueAsInt();

From df9129d1bc2c2f73c7c7fe49c958374669d5d73d Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Fri, 27 Jun 2025 15:07:14 -0400
Subject: [PATCH 170/192] ADD: (red) MRERawEvent member to state whether this
 event has been reconstructed (since having a type is not enough anymore)

---
 src/revan/inc/MRERawEvent.h   | 15 ++++++++------
 src/revan/src/MRERawEvent.cxx | 39 ++++++++++++++++++++++++++++-------
 2 files changed, 41 insertions(+), 13 deletions(-)

diff --git a/src/revan/inc/MRERawEvent.h b/src/revan/inc/MRERawEvent.h
index 514a9875e..9da8ea4a3 100644
--- a/src/revan/inc/MRERawEvent.h
+++ b/src/revan/inc/MRERawEvent.h
@@ -113,7 +113,7 @@ class MRERawEvent : public MRESE, public MRotationInterface
   //! Restart the iterator
   bool ResetIterator(MRESE *RESE = 0);
   //! Return the next RESE in the iterator, nullptr when done
-  MRESE* GetNextRESE();;
+  MRESE* GetNextRESE();
   
   
   //! Set the start point of the event
@@ -172,19 +172,19 @@ class MRERawEvent : public MRESE, public MRotationInterface
 
 
   // Interface to the event quality
-
-  
-  
   void SetGoodEvent(bool GoodEvent = true);
   bool IsGoodEvent();
   
-  bool IsValid();
-  
   void SetRejectionReason(int Reason);
   int GetRejectionReason();
   static MString GetRejectionReasonAsString(int r, bool Short = false);
   MString GetRejectionReasonAsString(bool Short = false);
+
+  bool IsValid();
   
+  // Interface to the event reconstruction status
+  void SetEventReconstructed(bool ReconstructedEvent = true);
+  bool IsEventReconstructed();
   
   //! Return the clustering quality factor
   double GetClusteringQualityFactor() const { return m_ClusteringQualityFactor; }
@@ -315,6 +315,9 @@ class MRERawEvent : public MRESE, public MRotationInterface
   //! True if this is a good event
   bool m_GoodEvent;
 
+  //! True if this event went through an event reconstruction algorithm
+  bool m_EventReconstructed;
+
   //! The time this event happened
   MTime m_EventTime;
   //! The clock time this event happened
diff --git a/src/revan/src/MRERawEvent.cxx b/src/revan/src/MRERawEvent.cxx
index 84c4f6a44..0c8447668 100644
--- a/src/revan/src/MRERawEvent.cxx
+++ b/src/revan/src/MRERawEvent.cxx
@@ -126,6 +126,7 @@ MRERawEvent::MRERawEvent(MRERawEvent* RE) : MRESE((MRESE *) RE)
   Init();
   SetGeometry(RE->GetGeometry());
   SetGoodEvent(RE->IsGoodEvent());
+  SetEventReconstructed(RE->IsEventReconstructed());
 
   if (RE->GetStartPoint() != 0) {
     int id = RE->GetStartPoint()->GetID();
@@ -213,8 +214,6 @@ MRERawEvent::MRERawEvent(MRERawEvent* RE) : MRESE((MRESE *) RE)
   m_TrackQualityFactor = RE->m_TrackQualityFactor;
 
   m_PairQualityFactor = RE->m_PairQualityFactor;
-
-  m_GoodEvent = RE->m_GoodEvent;
   
   m_CoincidenceWindow = RE->m_CoincidenceWindow;
   
@@ -281,8 +280,10 @@ void MRERawEvent::Init()
   m_VertexDirection = 0;
   
   m_SubElementType = MRESE::c_Event;
-  m_GoodEvent = false;
 
+  m_EventReconstructed = false;
+
+  m_GoodEvent = false;
   m_ExternalBadEventFlag = false;
   m_ExternalBadEventString = "";
 
@@ -463,6 +464,7 @@ void MRERawEvent::SetOriginInformation(MVector Position, MVector Direction, MVec
 MString MRERawEvent::ToString(bool WithLink, int Level)
 {
   //
+  massert(m_EventReconstructed);
 
   const int Length = 5000;
   char *Text = new char[Length];
@@ -551,6 +553,24 @@ bool MRERawEvent::IsValid()
 ////////////////////////////////////////////////////////////////////////////////
 
 
+void MRERawEvent::SetEventReconstructed(bool ReconstructedEvent)
+{
+  m_EventReconstructed = ReconstructedEvent;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MRERawEvent::IsEventReconstructed()
+{
+  return m_EventReconstructed;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
 void MRERawEvent::SetGoodEvent(bool IsGoodEvent)
 {
   m_GoodEvent = IsGoodEvent;
@@ -998,6 +1018,7 @@ void MRERawEvent::SetPhysicalEvent(MPhysicalEvent* Event)
   m_GoodEvent = true;
   delete m_Event;
   m_Event = Event;
+  m_EventReconstructed = true;
 }
 
 
@@ -1007,6 +1028,7 @@ void MRERawEvent::SetPhysicalEvent(MPhysicalEvent* Event)
 MPhysicalEvent* MRERawEvent::GetPhysicalEvent()
 {
   // Return a pointer to the physical event...
+  if (!m_EventReconstructed) return nullptr;
 
   // This is only an experimental flag --- don't activate it unless you know what you are doing...
   bool UseCenterD2 = false;
@@ -1017,7 +1039,7 @@ MPhysicalEvent* MRERawEvent::GetPhysicalEvent()
   }
 
   if (m_Event == nullptr) {
-    if (m_EventType == c_ComptonEvent && m_Start != nullptr) {
+    if (m_EventType == c_ComptonEvent) {
       MComptonEvent* CE = new MComptonEvent();
       double ED1 = 0.0;
       double ED2 = 0.0;
@@ -1113,7 +1135,7 @@ MPhysicalEvent* MRERawEvent::GetPhysicalEvent()
       }
       
       m_Event = (MPhysicalEvent*) CE;
-    } else if (m_EventType == c_PairEvent && m_ElectronTrack && m_PositronTrack) {
+    } else if (m_EventType == c_PairEvent) {
       // We need to have two tracks:
       //massert(m_ElectronTrack != 0);
       //massert(m_PositronTrack != 0); now in the condition above
@@ -1155,8 +1177,10 @@ MPhysicalEvent* MRERawEvent::GetPhysicalEvent()
     m_Event->Set(*dynamic_cast<MRotationInterface*>(this));
     
     m_Event->SetAllHitsGood(IsValid());
-    m_Event->SetTime(m_EventTime);
     m_Event->SetId(m_EventID);
+    mout << "AL settime2" << show;
+    m_Event->SetTime(m_EventTime);
+    mout << "AL settime2=" << m_Event->GetTime() << show;
     m_Event->SetTimeWalk(m_TimeWalk);
     m_Event->SetDecay(m_Decay);
     if (m_ExternalBadEventFlag == true) {
@@ -1176,6 +1200,7 @@ MPhysicalEvent* MRERawEvent::GetPhysicalEvent()
 
     m_Event->Validate();
   }
+  mout << "AL GPE addr=" << m_Event << " evtid=" << m_EventID << " time=" << m_EventTime << " type=" << GetEventTypeAsString() << " rec=" << IsEventReconstructed() << "/ ";
 
   return m_Event;
 }
@@ -1214,7 +1239,7 @@ MString MRERawEvent::ToEvtaString(const int Precision, const int Version)
 MString MRERawEvent::ToCompactString()
 {
   //
-
+  massert(m_EventReconstructed);
   if (IsGoodEvent() == false) {
     return MString("");
   }

From a5c9455cb45feaa23f5cccd602fefb77ddedb945 Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Fri, 27 Jun 2025 15:13:41 -0400
Subject: [PATCH 171/192] ADD: (red) State when event is reconstructed

---
 src/revan/src/MERTrack.cxx | 30 +++++++++++++++++++++++++++---
 1 file changed, 27 insertions(+), 3 deletions(-)

diff --git a/src/revan/src/MERTrack.cxx b/src/revan/src/MERTrack.cxx
index 57bfe6cb3..ee03b425a 100644
--- a/src/revan/src/MERTrack.cxx
+++ b/src/revan/src/MERTrack.cxx
@@ -252,6 +252,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
     mdebug<<"Not enough hits in tracker!"<<endl;
     return true;
   }
+  //mout << "AL cktime e=" << e << " id=" << ->GetEventId() << " time=" << RE->GetTime() << show;
 
   // Step B: Pairs
   Timer.Start();
@@ -297,10 +298,12 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
         } else { // if no vertices
           RE->SetEventType(MRERawEvent::c_UnknownEvent); // discard
         }
+        RE->SetEventReconstructed(true);
       }
     } // end for
   }
   m_TimePairs += Timer.ElapsedTime();
+  mout << "AL endPA" << show;
 
 
   // Step C: Mips
@@ -311,6 +314,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
     mdebug<<"* Search for MIPs"<<endl;
     for (int e = 0; e < m_List->GetNRawEvents(); e++) {
       RE = m_List->GetRawEventAt(e);
+      mout << "AL cfmtm=" << RE->GetTime() << show;
       if (RE->GetEventType() == MRERawEvent::c_MipEvent || RE->GetEventType() == MRERawEvent::c_ShowerEvent) {// Iterate only over MIP/shower events
         CheckForMips(RE);
         // If we have found a MIP then we are done!
@@ -327,6 +331,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
         } else {
           RE->SetEventType(MRERawEvent::c_UnknownEvent); // discard
         }
+        RE->SetEventReconstructed(true);
       }
     }
     mdebug<<"        MIP results:"<<endl;
@@ -334,10 +339,11 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
     mdebug<<endl;
   }
   m_TimeMips += Timer.ElapsedTime();
+  if(m_List->HasOptimumEvent()) mout << "AL endMU pid=" <<  m_List->GetOptimumEvent()->GetPhysicalEvent()->GetId() << " ptype=" << m_List->GetOptimumEvent()->GetPhysicalEvent()->GetTypeString() << show;
 
 
   // Step C: Compton tracks:
-
+  // IsEventReconstructed stays false until CSR is performed
   if (HasOneREOfType(MRERawEvent::c_ComptonEvent)) {
     mdebug<<"* Search for Comptons"<<endl;
 
@@ -350,7 +356,11 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
     for (int e = 0; e < e_max; e++) {
       RE = m_List->GetRawEventAt(e);
       if (RE->GetEventType() == MRERawEvent::c_ComptonEvent) {
+        //RE->SetEventType(MRERawEvent::c_UnknownEvent);
+        mout << "AL -a" << show;
         List = TrackComptons(RE);
+        mout << "AL -b" << show;
+        //RE->SetEventType(MRERawEvent::c_ComptonEvent);
         if (List != 0) {
           m_List->DeleteRawEvent(RE);
           e--;
@@ -361,6 +371,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
           delete List;
           List = nullptr;
         }
+        mout << "AL -c" << show;
       }
     }
     m_TimeComptonSequences += Timer.ElapsedTime();
@@ -381,6 +392,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
         }
         if (CurrentN < MinN) MinN = CurrentN;
       }
+      mout << "AL -d" << show;
 
       for (int e = 0; e < m_List->GetNRawEvents(); e++) {
         int CurrentN = 0;
@@ -396,6 +408,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
           e--;
         }
       }
+      mout << "AL -e" << show;
       mdebug<<"Keeping "<<m_List->GetNRawEvents()<<" possibilities for further processing."<<endl;
     }
 
@@ -412,7 +425,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
     for (int e = 0; e < m_List->GetNRawEvents(); e++) {
       RE = m_List->GetRawEventAt(e);
       if (RE->GetEventType() == MRERawEvent::c_ComptonEvent) {
-
+        mout << "AL -f" << show;
         for (int r = 0; r < RE->GetNRESEs(); r++) {
           RESE = RE->GetRESEAt(r);
           IDRESE = RESE->GetID();
@@ -430,6 +443,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
             }
           }
         }
+        mout << "AL -g" << show;
       }
     }
 
@@ -437,7 +451,9 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
 
     for (int e = 0; e < m_List->GetNRawEvents(); e++) {
       RE = m_List->GetRawEventAt(e);
+      mout << "AL -h" << show;
       if (RE->GetEventType() == MRERawEvent::c_ComptonEvent) EvaluateTracks(RE);
+      mout << "AL -i" << show;
     }
     SortByTrackQualityFactor(m_List);
 
@@ -455,15 +471,18 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
     m_List->SetBestTryEvent(m_List->GetRawEventAt(0));
 
 
+
     // Remove all not-so-good sequences:
     for (int e = m_NSequencesToKeep; e < m_List->GetNRawEvents(); ++e) {
       RE = m_List->GetRawEventAt(e);
       m_List->DeleteRawEvent(RE);
       e--;
     }
+    mout << "AL nRE=" << m_List->GetNRawEvents() << show;
 
     m_TimeComptonDirections += Timer.ElapsedTime();
   }
+  mout << "AL tr=" << StartTracking << " type=" << m_List->GetRawEventAt(0)->GetEventTypeAsString() << " rec=" << m_List->GetRawEventAt(0)->IsEventReconstructed() /*<< " ptype=" << m_List->GetRawEventAt(0)->GetPhysicalEvent()->GetTypeString()*/ << show;
 
 
   // Step E: Epilog
@@ -1160,6 +1179,10 @@ void MERTrack::CheckForMips(MRERawEvent* RE)
 
     // b. Store the new event:
     MMuonEvent* Muon = new MMuonEvent(); // is later stored as m_Event!
+    Muon->SetId(RE->GetEventId());
+    //mout << "AL settime" << show;
+    Muon->SetTime(RE->GetEventTime());
+    //mout << "AL settime=" << Muon->GetTime() << show;
     Muon->SetEnergy(RE->GetEnergy());
     Muon->SetDirection(TrackArray[HighestPos]->GetAverageDirection());
     Muon->SetCenterOfGravity(TrackArray[HighestPos]->GetCenterOfGravity());
@@ -1171,8 +1194,9 @@ void MERTrack::CheckForMips(MRERawEvent* RE)
 
     // d. This is a good event...
     RE->SetPhysicalEvent(Muon);
-    RE->SetEventType(MRERawEvent::c_MipEvent);
+    //RE->SetEventType(MRERawEvent::c_MipEvent);
     RE->SetGoodEvent(true);
+    mout << "AL muon id=" << Muon->GetId() << " time=" << Muon->GetTime() << " type=" << Muon->GetType() << show;
   }
   // b. A shower
   else if (TrackArray.size() > 1) {

From bba21470cbbcc2bef722b8d8a98811baf4a12cb9 Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Fri, 27 Jun 2025 15:14:11 -0400
Subject: [PATCH 172/192] ADD: (red) State when event is reconstructed, minor
 code refactor

---
 src/revan/src/MERCSR.cxx | 82 +++++++++++++++++++++++++++-------------
 1 file changed, 56 insertions(+), 26 deletions(-)

diff --git a/src/revan/src/MERCSR.cxx b/src/revan/src/MERCSR.cxx
index 8fdaeb98a..a86bab476 100644
--- a/src/revan/src/MERCSR.cxx
+++ b/src/revan/src/MERCSR.cxx
@@ -115,44 +115,52 @@ bool MERCSR::Analyze(MRawEventIncarnations* List)
 
   MERConstruction::Analyze(List);
 
+  int e_max = m_List->GetNRawEvents();
+  MRERawEvent* RE = nullptr;
+  mout << "AL t" << m_CreateOnlyPermutations << show;
   if (m_CreateOnlyPermutations == true) {
     m_List->SetOptimumEvent(nullptr);
 
-    int e_max = m_List->GetNRawEvents();
     for (int e = 0; e < e_max; ++e) {
-      MRERawEvent* RE = m_List->GetRawEventAt(e);
-      MRawEventIncarnations* NewList = CreateOnlyPermutations(RE);
-      if (NewList != 0) {
-        m_List->DeleteRawEvent(RE);
-        e--;
-        e_max--;
-        for (int i = 0; i < NewList->GetNRawEvents(); ++i) {
-          m_List->AddRawEvent(NewList->GetRawEventAt(i));
+      RE = m_List->GetRawEventAt(e);
+      if (RE->GetEventType() == MRERawEvent::c_ComptonEvent) {// Iterate only over Compton events
+        MRawEventIncarnations* NewList = CreateOnlyPermutations(RE);
+        if (NewList != 0) {
+          m_List->DeleteRawEvent(RE);
+          e--;
+          e_max--;
+          for (int i = 0; i < NewList->GetNRawEvents(); ++i) {
+            m_List->AddRawEvent(NewList->GetRawEventAt(i));
+          }
+          delete NewList;
         }
-        delete NewList;
-      }        
+      }
     }
   } else {
     // Loop over all raw events and calculate all sequences:
-    int e_max = m_List->GetNRawEvents();
+    //int e_max = m_List->GetNRawEvents();
     for (int e = 0; e < e_max; ++e) {
-      FindComptonSequence(m_List->GetRawEventAt(e));
+      RE = m_List->GetRawEventAt(e);
+      if (RE->GetEventType() == MRERawEvent::c_ComptonEvent) {// Iterate only over Compton events
+        FindComptonSequence(RE);
+      }
     }
     
     // Select the raw event with the best quality factor as the good one:
     int NGoodEvents = 0;
     double BestQualityFactor = c_CSRFailed;
     for (int e = m_List->GetNRawEvents()-1; e >= 0; e--) {
-      if (m_List->GetRawEventAt(e)->IsGoodEvent() == true) {
-        if (m_List->GetRawEventAt(e)->GetEventType() == MRERawEvent::c_ComptonEvent) {
-          if (m_List->GetRawEventAt(e)->GetComptonQualityFactor() < BestQualityFactor) {
-            BestQualityFactor = m_List->GetRawEventAt(e)->GetComptonQualityFactor();
-            m_List->SetOptimumEvent(m_List->GetRawEventAt(e));
-            m_List->SetBestTryEvent(m_List->GetRawEventAt(e));
+      RE = m_List->GetRawEventAt(e);
+      if (RE->GetEventType() == MRERawEvent::c_ComptonEvent) {
+        if (RE->IsGoodEvent() == true) {
+          if (RE->GetComptonQualityFactor() < BestQualityFactor) {
+            BestQualityFactor = RE->GetComptonQualityFactor();
+            m_List->SetOptimumEvent(RE);
+            m_List->SetBestTryEvent(RE);
           }
-        } else if (m_List->GetRawEventAt(e)->GetEventType() == MRERawEvent::c_PhotoEvent) {
-          m_List->SetOptimumEvent(m_List->GetRawEventAt(e));
-          m_List->SetBestTryEvent(m_List->GetRawEventAt(e));
+        } else if (RE->GetEventType() == MRERawEvent::c_PhotoEvent) {//A.L. This doesn’t happen anymore - need to reimplement somewhere else
+          m_List->SetOptimumEvent(RE);
+          m_List->SetBestTryEvent(RE);
         }
         NGoodEvents++;
       }
@@ -189,10 +197,14 @@ MRawEventIncarnations* MERCSR::CreateOnlyPermutations(MRERawEvent* RE)
   if (RE->GetNRESEs() > m_MaxNInteractions) {
     mout<<"BCT - Sequence: Too Many hits: "<<RE->GetNRESEs()<<" > "<<m_MaxNInteractions<<endl;
     RE->SetRejectionReason(MRERawEvent::c_RejectionTooManyHitsCSR);
+    RE->SetEventType(MRERawEvent::c_UnknownEvent);
+    RE->SetEventReconstructed(true);
     return 0;
   } else if (RE->GetNRESEs() == 0) {
     mout<<"BCT - Sequence: Event without hits"<<endl;
     RE->SetRejectionReason(MRERawEvent::c_RejectionNoHits);
+    RE->SetEventType(MRERawEvent::c_UnknownEvent);
+    RE->SetEventReconstructed(true);
     return 0; 
   }
 
@@ -246,6 +258,8 @@ void MERCSR::FindComptonSequence(MRERawEvent* RE)
   if (RE->GetNRESEs() > m_MaxNInteractions) {
     mout<<"CSR - Sequence: Too Many hits: "<<RE->GetNRESEs()<<" > "<<m_MaxNInteractions<<endl;
     RE->SetRejectionReason(MRERawEvent::c_RejectionTooManyHitsCSR);
+    RE->SetEventType(MRERawEvent::c_UnknownEvent);
+    RE->SetEventReconstructed(true);
     return;
   } else if (RE->GetNRESEs() == 1) {
     mout<<"CSR - Sequence: Only single hit event!"<<endl;
@@ -254,13 +268,18 @@ void MERCSR::FindComptonSequence(MRERawEvent* RE)
         RE->GetRESEAt(0)->GetType() == MRESE::c_Cluster) {
       RE->SetEventType(MRERawEvent::c_PhotoEvent);
       RE->SetGoodEvent(true);
+      RE->SetEventReconstructed(true);
     } else {
       RE->SetRejectionReason(MRERawEvent::c_RejectionOneTrackOnly);
+      RE->SetEventType(MRERawEvent::c_UnknownEvent);
+      RE->SetEventReconstructed(true);
     }
     return; 
   } else if (RE->GetNRESEs() == 0) {
     mout<<"CSR - Sequence: Event without hits"<<endl;
     RE->SetRejectionReason(MRERawEvent::c_RejectionNoHits);
+    RE->SetEventType(MRERawEvent::c_UnknownEvent);
+    RE->SetEventReconstructed(true);
     return; 
   }
 
@@ -287,8 +306,10 @@ void MERCSR::FindComptonSequence(MRERawEvent* RE)
   }
 
   if (NGoodSequences == 0) {
-    RE->SetRejectionReason(MRERawEvent::c_RejectionCSRNoGoodCombination);
     mout<<"CSR - Sequence: None of the sequences is valid!"<<endl;
+    RE->SetRejectionReason(MRERawEvent::c_RejectionCSRNoGoodCombination);
+    RE->SetEventType(MRERawEvent::c_UnknownEvent);
+    RE->SetEventReconstructed(true);
     return;    
   }
 
@@ -308,8 +329,10 @@ void MERCSR::FindComptonSequence(MRERawEvent* RE)
 
   // Test if we have at least one good sequence:
   if (BestQualityFactor == c_CSRFailed) {
-    RE->SetRejectionReason(MRERawEvent::c_RejectionCSRNoGoodCombination);
     mout<<"CSR - Sequence: None of the sequences is valid!"<<endl;
+    RE->SetRejectionReason(MRERawEvent::c_RejectionCSRNoGoodCombination);
+    RE->SetEventType(MRERawEvent::c_UnknownEvent);
+    RE->SetEventReconstructed(true);
     return;    
   }
 
@@ -327,7 +350,7 @@ void MERCSR::FindComptonSequence(MRERawEvent* RE)
       BestSequence[i]->AddLink(BestSequence[i+1]);
     }
   }
-  // m_List->SetBestEvent(RE); // Problem wenn mehrere RE zu vergleichen sind...
+  // m_List->SetBestEvent(RE); // Problem wenn mehrere RE zu vergleichen sind... (Problem when several REs are to be compared...)
 
 
   // Check if the threshold is ok:
@@ -336,6 +359,8 @@ void MERCSR::FindComptonSequence(MRERawEvent* RE)
     RE->SetRejectionReason(MRERawEvent::c_RejectionCSRThreshold);
     mout<<"CSR - Sequence: Teststatistics ("<<BestQualityFactor
         <<") out of threshold ("<<m_QualityFactorMin<<" - "<<m_QualityFactorMax<<")"<<endl;
+    RE->SetEventType(MRERawEvent::c_UnknownEvent);
+    RE->SetEventReconstructed(true);
     return;
   }
 
@@ -346,6 +371,8 @@ void MERCSR::FindComptonSequence(MRERawEvent* RE)
     RE->SetRejectionReason(MRERawEvent::c_RejectionEventStartNotD1);
     mout<<"CSR - Sequence: Event starts in not in D1/D5 but in "<<BestSequence[0]->GetDetector()<<endl;
     mout<<"CSR - Sequence: Good event with TS: "<<BestQualityFactor<<endl;
+    RE->SetEventType(MRERawEvent::c_UnknownEvent);
+    RE->SetEventReconstructed(true);
     return;
   }
  
@@ -361,14 +388,17 @@ void MERCSR::FindComptonSequence(MRERawEvent* RE)
     RE->SetRejectionReason(MRERawEvent::c_RejectionElectronDirectionBad);
     mout<<"CSR - Sequence: Electron direction test failed!"<<endl;
     mout<<"CSR - Sequence: Good event with TS: "<<BestQualityFactor<<endl;
+    RE->SetEventType(MRERawEvent::c_UnknownEvent);
+    RE->SetEventReconstructed(true);
     return;
   }
 
   mout<<"CSR - Sequence: Good event with TS: "<<BestQualityFactor<<endl;
     
   RE->SetComptonQualityFactors(BestQualityFactor, SecondBestQualityFactor);
-  RE->SetEventType(MRERawEvent::c_ComptonEvent);
+  //RE->SetEventType(MRERawEvent::c_ComptonEvent);
   RE->SetGoodEvent(true);      
+  RE->SetEventReconstructed(true);
 }
 
 

From 419f0c7ce29ec85cb9e77e07f5668fe7a97c7889 Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Fri, 27 Jun 2025 15:18:24 -0400
Subject: [PATCH 173/192] FIX: Minor fix

---
 src/revan/src/MRawEventAnalyzer.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/revan/src/MRawEventAnalyzer.cxx b/src/revan/src/MRawEventAnalyzer.cxx
index e7c1acb0c..9178ee45e 100644
--- a/src/revan/src/MRawEventAnalyzer.cxx
+++ b/src/revan/src/MRawEventAnalyzer.cxx
@@ -749,7 +749,7 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
   
   // Section E: Compton sequence reconstruction       
   
-  if (SelectionsPassed == true && m_CSRAlgorithm > c_CSRAlgoNone && m_RawEvents->HasOnlyOptimumEvents() == false) { // Only continue if we have not yet found a good event
+  if (SelectionsPassed == true && m_CSRAlgorithm > c_CSRAlgoNone) {
     
     Timer.Start();
     

From 729a379850c52d1f805a9020785b099efcfa3c80 Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Fri, 27 Jun 2025 23:42:02 -0400
Subject: [PATCH 174/192] ADD: (red) Compatibility of other Pair and Compton
 event reconstruction classes with new event type identification

---
 src/revan/src/MERCSR.cxx           | 22 +---------------------
 src/revan/src/MERCSRChiSquare.cxx  | 16 +++++++++++-----
 src/revan/src/MERTrackKalman2D.cxx |  3 ++-
 src/revan/src/MERTrackKalman3D.cxx |  3 ++-
 src/revan/src/MRERawEvent.cxx      |  3 +++
 5 files changed, 19 insertions(+), 28 deletions(-)

diff --git a/src/revan/src/MERCSR.cxx b/src/revan/src/MERCSR.cxx
index a86bab476..c0755fca8 100644
--- a/src/revan/src/MERCSR.cxx
+++ b/src/revan/src/MERCSR.cxx
@@ -197,14 +197,10 @@ MRawEventIncarnations* MERCSR::CreateOnlyPermutations(MRERawEvent* RE)
   if (RE->GetNRESEs() > m_MaxNInteractions) {
     mout<<"BCT - Sequence: Too Many hits: "<<RE->GetNRESEs()<<" > "<<m_MaxNInteractions<<endl;
     RE->SetRejectionReason(MRERawEvent::c_RejectionTooManyHitsCSR);
-    RE->SetEventType(MRERawEvent::c_UnknownEvent);
-    RE->SetEventReconstructed(true);
     return 0;
   } else if (RE->GetNRESEs() == 0) {
     mout<<"BCT - Sequence: Event without hits"<<endl;
     RE->SetRejectionReason(MRERawEvent::c_RejectionNoHits);
-    RE->SetEventType(MRERawEvent::c_UnknownEvent);
-    RE->SetEventReconstructed(true);
     return 0; 
   }
 
@@ -258,12 +254,10 @@ void MERCSR::FindComptonSequence(MRERawEvent* RE)
   if (RE->GetNRESEs() > m_MaxNInteractions) {
     mout<<"CSR - Sequence: Too Many hits: "<<RE->GetNRESEs()<<" > "<<m_MaxNInteractions<<endl;
     RE->SetRejectionReason(MRERawEvent::c_RejectionTooManyHitsCSR);
-    RE->SetEventType(MRERawEvent::c_UnknownEvent);
-    RE->SetEventReconstructed(true);
     return;
   } else if (RE->GetNRESEs() == 1) {
     mout<<"CSR - Sequence: Only single hit event!"<<endl;
-    //RE->SetRejectionReason(MRERawEvent::c_RejectionSingleSiteEvent);
+    //RE->SetRejectionReason(MRERawEvent::c_RejectionSingleSiteEvent); // We could use that after event type identification?
     if (RE->GetRESEAt(0)->GetType() == MRESE::c_Hit || 
         RE->GetRESEAt(0)->GetType() == MRESE::c_Cluster) {
       RE->SetEventType(MRERawEvent::c_PhotoEvent);
@@ -271,15 +265,11 @@ void MERCSR::FindComptonSequence(MRERawEvent* RE)
       RE->SetEventReconstructed(true);
     } else {
       RE->SetRejectionReason(MRERawEvent::c_RejectionOneTrackOnly);
-      RE->SetEventType(MRERawEvent::c_UnknownEvent);
-      RE->SetEventReconstructed(true);
     }
     return; 
   } else if (RE->GetNRESEs() == 0) {
     mout<<"CSR - Sequence: Event without hits"<<endl;
     RE->SetRejectionReason(MRERawEvent::c_RejectionNoHits);
-    RE->SetEventType(MRERawEvent::c_UnknownEvent);
-    RE->SetEventReconstructed(true);
     return; 
   }
 
@@ -308,8 +298,6 @@ void MERCSR::FindComptonSequence(MRERawEvent* RE)
   if (NGoodSequences == 0) {
     mout<<"CSR - Sequence: None of the sequences is valid!"<<endl;
     RE->SetRejectionReason(MRERawEvent::c_RejectionCSRNoGoodCombination);
-    RE->SetEventType(MRERawEvent::c_UnknownEvent);
-    RE->SetEventReconstructed(true);
     return;    
   }
 
@@ -331,8 +319,6 @@ void MERCSR::FindComptonSequence(MRERawEvent* RE)
   if (BestQualityFactor == c_CSRFailed) {
     mout<<"CSR - Sequence: None of the sequences is valid!"<<endl;
     RE->SetRejectionReason(MRERawEvent::c_RejectionCSRNoGoodCombination);
-    RE->SetEventType(MRERawEvent::c_UnknownEvent);
-    RE->SetEventReconstructed(true);
     return;    
   }
 
@@ -359,8 +345,6 @@ void MERCSR::FindComptonSequence(MRERawEvent* RE)
     RE->SetRejectionReason(MRERawEvent::c_RejectionCSRThreshold);
     mout<<"CSR - Sequence: Teststatistics ("<<BestQualityFactor
         <<") out of threshold ("<<m_QualityFactorMin<<" - "<<m_QualityFactorMax<<")"<<endl;
-    RE->SetEventType(MRERawEvent::c_UnknownEvent);
-    RE->SetEventReconstructed(true);
     return;
   }
 
@@ -371,8 +355,6 @@ void MERCSR::FindComptonSequence(MRERawEvent* RE)
     RE->SetRejectionReason(MRERawEvent::c_RejectionEventStartNotD1);
     mout<<"CSR - Sequence: Event starts in not in D1/D5 but in "<<BestSequence[0]->GetDetector()<<endl;
     mout<<"CSR - Sequence: Good event with TS: "<<BestQualityFactor<<endl;
-    RE->SetEventType(MRERawEvent::c_UnknownEvent);
-    RE->SetEventReconstructed(true);
     return;
   }
  
@@ -388,8 +370,6 @@ void MERCSR::FindComptonSequence(MRERawEvent* RE)
     RE->SetRejectionReason(MRERawEvent::c_RejectionElectronDirectionBad);
     mout<<"CSR - Sequence: Electron direction test failed!"<<endl;
     mout<<"CSR - Sequence: Good event with TS: "<<BestQualityFactor<<endl;
-    RE->SetEventType(MRERawEvent::c_UnknownEvent);
-    RE->SetEventReconstructed(true);
     return;
   }
 
diff --git a/src/revan/src/MERCSRChiSquare.cxx b/src/revan/src/MERCSRChiSquare.cxx
index 3fa97b407..53c1cc397 100644
--- a/src/revan/src/MERCSRChiSquare.cxx
+++ b/src/revan/src/MERCSRChiSquare.cxx
@@ -145,6 +145,8 @@ void MERCSRChiSquare::FindComptonSequenceDualHitEvent(MRERawEvent* RE)
   
   if (RE->GetNRESEs() != 2) {
     merr<<"FindComptonSequenceDualHitEvent called with "<<RE->GetNRESEs()<<" hits instead of exactly 2!"<<endl;
+    RE->SetEventType(MRERawEvent::c_UnknownEvent);
+    RE->SetEventReconstructed(true);
     return;
   }
   
@@ -479,6 +481,8 @@ void MERCSRChiSquare::FindComptonSequenceDualHitEvent(MRERawEvent* RE)
   if (IsGood == true) {
     if (EstimatedFirst < 0) {
       merr<<"ERROR: We missed some condition during handling of two-site events... Bug!"<<endl;
+      RE->SetEventType(MRERawEvent::c_UnknownEvent);
+      RE->SetReconstructedEvent(true);
       return;
     }
     
@@ -536,7 +540,7 @@ void MERCSRChiSquare::FindComptonSequenceDualHitEvent(MRERawEvent* RE)
   if (IsGood == false) {
     mdebug<<"CSR-CS - Dual hit: Bad Compton event"<<endl;				
   }
-  
+  RE->SetReconstructedEvent(true);
   return;
 }
 
@@ -560,14 +564,15 @@ void MERCSRChiSquare::FindComptonSequence(MRERawEvent* RE)
     RE->SetRejectionReason(MRERawEvent::c_RejectionTooManyHitsCSR);
     return;
   } else if (RE->GetNRESEs() == 2) {
-    FindComptonSequenceDualHitEvent(RE);
+    FindComptonSequenceDualHitEvent(RE);//Sets ReconstructedEvent to true
     return;
   } else if (RE->GetNRESEs() == 1) {
     mdebug<<"CSR-CS - Sequence: Only single hit event!"<<endl;
     //RE->SetRejectionReason(MRERawEvent::c_RejectionSingleSiteEvent);
     if (RE->GetRESEAt(0)->GetType() == MRESE::c_Hit || RE->GetRESEAt(0)->GetType() == MRESE::c_Cluster) {
       RE->SetEventType(MRERawEvent::c_PhotoEvent);
-      RE->SetGoodEvent(true);      
+      RE->SetGoodEvent(true);
+      RE->SetReconstructedEvent(true);
     } else {
       RE->SetRejectionReason(MRERawEvent::c_RejectionOneTrackOnly);
     }
@@ -673,8 +678,9 @@ void MERCSRChiSquare::FindComptonSequence(MRERawEvent* RE)
   mdebug<<"CSR-CS - Sequence: Good event with TS: "<<BestQualityFactor<<endl;
   
   RE->SetComptonQualityFactors(BestQualityFactor, SecondBestQualityFactor);
-  RE->SetEventType(MRERawEvent::c_ComptonEvent);
-  RE->SetGoodEvent(true);      
+  //RE->SetEventType(MRERawEvent::c_ComptonEvent);
+  RE->SetGoodEvent(true);
+  RE->SetReconstructedEvent(true);
 }
 
 
diff --git a/src/revan/src/MERTrackKalman2D.cxx b/src/revan/src/MERTrackKalman2D.cxx
index c0219058f..b3098ddce 100644
--- a/src/revan/src/MERTrackKalman2D.cxx
+++ b/src/revan/src/MERTrackKalman2D.cxx
@@ -702,7 +702,8 @@ void MERTrackKalman2D::TrackPairs(MRERawEvent* RE)
     //RE->SetTrackQualityFactor((ChiT1y+ChiT2y)/100);
     RE->SetPairQualityFactor((ChiT1y+ChiT2y));
     RE->SetGoodEvent(true);
-    RE->SetEventType(MRERawEvent::c_PairEvent);
+    //RE->SetEventType(MRERawEvent::c_PairEvent);
+    RE->SetEventReconstructed(true);
 
   } else{
     Egamma= -1.;
diff --git a/src/revan/src/MERTrackKalman3D.cxx b/src/revan/src/MERTrackKalman3D.cxx
index cb11f47f8..1259f7ea2 100644
--- a/src/revan/src/MERTrackKalman3D.cxx
+++ b/src/revan/src/MERTrackKalman3D.cxx
@@ -1208,7 +1208,8 @@ void MERTrackKalman3D::TrackPairs(MRERawEvent* RE)
   //RE->SetTrackQualityFactor(ChiT1+ChiT2);
   RE->SetPairQualityFactor(ChiT1+ChiT2);
   RE->SetGoodEvent(true);
-  RE->SetEventType(MRERawEvent::c_PairEvent);
+  //RE->SetEventType(MRERawEvent::c_PairEvent);
+  RE->SetEventReconstructed(true);
 
 }
 // MERTrackKalman3D.cxx: the end...
diff --git a/src/revan/src/MRERawEvent.cxx b/src/revan/src/MRERawEvent.cxx
index 0c8447668..c42ea69f7 100644
--- a/src/revan/src/MRERawEvent.cxx
+++ b/src/revan/src/MRERawEvent.cxx
@@ -715,6 +715,9 @@ void MRERawEvent::SetRejectionReason(int Reason)
   if (m_RejectionReason != c_RejectionNone) {
     m_IsValid = false;
   }
+  // If rejected after event type identification
+  m_EventType = c_UnknownEvent;
+  m_EventReconstructed = true;
 }
 
 

From 466b86a3b5380ad0e1ab48d1e65286a09d5a1c84 Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Sun, 29 Jun 2025 19:27:48 -0400
Subject: [PATCH 175/192] Fix: Photo events and typo in CSRchisquare

---
 src/revan/src/MERCSRChiSquare.cxx   | 10 +++++-----
 src/revan/src/MRawEventAnalyzer.cxx | 15 +++++++++++++++
 2 files changed, 20 insertions(+), 5 deletions(-)

diff --git a/src/revan/src/MERCSRChiSquare.cxx b/src/revan/src/MERCSRChiSquare.cxx
index 53c1cc397..942c158b5 100644
--- a/src/revan/src/MERCSRChiSquare.cxx
+++ b/src/revan/src/MERCSRChiSquare.cxx
@@ -482,7 +482,7 @@ void MERCSRChiSquare::FindComptonSequenceDualHitEvent(MRERawEvent* RE)
     if (EstimatedFirst < 0) {
       merr<<"ERROR: We missed some condition during handling of two-site events... Bug!"<<endl;
       RE->SetEventType(MRERawEvent::c_UnknownEvent);
-      RE->SetReconstructedEvent(true);
+      RE->SetEventReconstructed(true);
       return;
     }
     
@@ -540,7 +540,7 @@ void MERCSRChiSquare::FindComptonSequenceDualHitEvent(MRERawEvent* RE)
   if (IsGood == false) {
     mdebug<<"CSR-CS - Dual hit: Bad Compton event"<<endl;				
   }
-  RE->SetReconstructedEvent(true);
+  RE->SetEventReconstructed(true);
   return;
 }
 
@@ -564,7 +564,7 @@ void MERCSRChiSquare::FindComptonSequence(MRERawEvent* RE)
     RE->SetRejectionReason(MRERawEvent::c_RejectionTooManyHitsCSR);
     return;
   } else if (RE->GetNRESEs() == 2) {
-    FindComptonSequenceDualHitEvent(RE);//Sets ReconstructedEvent to true
+    FindComptonSequenceDualHitEvent(RE);//Sets Event Reconstructed to true
     return;
   } else if (RE->GetNRESEs() == 1) {
     mdebug<<"CSR-CS - Sequence: Only single hit event!"<<endl;
@@ -572,7 +572,7 @@ void MERCSRChiSquare::FindComptonSequence(MRERawEvent* RE)
     if (RE->GetRESEAt(0)->GetType() == MRESE::c_Hit || RE->GetRESEAt(0)->GetType() == MRESE::c_Cluster) {
       RE->SetEventType(MRERawEvent::c_PhotoEvent);
       RE->SetGoodEvent(true);
-      RE->SetReconstructedEvent(true);
+      RE->SetEventReconstructed(true);
     } else {
       RE->SetRejectionReason(MRERawEvent::c_RejectionOneTrackOnly);
     }
@@ -680,7 +680,7 @@ void MERCSRChiSquare::FindComptonSequence(MRERawEvent* RE)
   RE->SetComptonQualityFactors(BestQualityFactor, SecondBestQualityFactor);
   //RE->SetEventType(MRERawEvent::c_ComptonEvent);
   RE->SetGoodEvent(true);
-  RE->SetReconstructedEvent(true);
+  RE->SetEventReconstructed(true);
 }
 
 
diff --git a/src/revan/src/MRawEventAnalyzer.cxx b/src/revan/src/MRawEventAnalyzer.cxx
index 9178ee45e..a1b03f193 100644
--- a/src/revan/src/MRawEventAnalyzer.cxx
+++ b/src/revan/src/MRawEventAnalyzer.cxx
@@ -722,6 +722,21 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
   }
 
 
+  // Section P: Photo events
+
+  if (SelectionsPassed) {
+    for (unsigned int i = 0; i < m_RawEvents->Size(); i++) {
+      MRawEventIncarnations* REI = m_RawEvents->Get(i);
+      for (int e = 0; e < REI->GetNRawEvents(); e++) {
+        MRERawEvent* RE = REI->GetRawEventAt(e);
+        if (RE->GetEventType() == MRERawEvent::c_PhotoEvent) {
+          RE->SetEventReconstructed(true);
+        }
+      }
+    }
+  }
+
+
   // Section D: Tracking:
   
   if (SelectionsPassed == true && m_TrackingAlgorithm > c_TrackingAlgoNone) {

From 8fe4779b6fba25c9b808772c6d0eb305b2b07f12 Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Thu, 10 Jul 2025 13:51:53 -0400
Subject: [PATCH 176/192] Feat: Add the MFileEventsType class to handle (rw)
 the *.etp files containing external event types and associated probabilities

---
 src/global/misc/Makefile                |   1 +
 src/global/misc/inc/MFileEventsType.h   |  78 ++++++++
 src/global/misc/inc/MPhysicalEvent.h    |   2 +
 src/global/misc/src/MFileEventsType.cxx | 234 ++++++++++++++++++++++++
 src/global/misc/src/MPhysicalEvent.cxx  |  58 +++++-
 5 files changed, 367 insertions(+), 6 deletions(-)
 create mode 100644 src/global/misc/inc/MFileEventsType.h
 create mode 100644 src/global/misc/src/MFileEventsType.cxx

diff --git a/src/global/misc/Makefile b/src/global/misc/Makefile
index 64eb5489b..40c33c335 100644
--- a/src/global/misc/Makefile
+++ b/src/global/misc/Makefile
@@ -52,6 +52,7 @@ FILES := MGlobal \
 	MFileEvents \
 	MFileEventsRawa \
 	MFileEventsTra \
+  MFileEventsType \
 	MFileManager \
 	MFileResponse \
 	MFileInfo \
diff --git a/src/global/misc/inc/MFileEventsType.h b/src/global/misc/inc/MFileEventsType.h
new file mode 100644
index 000000000..fa878be49
--- /dev/null
+++ b/src/global/misc/inc/MFileEventsType.h
@@ -0,0 +1,78 @@
+/*
+ * MFileEventsType.h
+ *
+ * Copyright (C) by Andreas Zoglauer.
+ * All rights reserved.
+ *
+ * Please see the source-file for the copyright-notice.
+ *
+ */
+
+
+#ifndef __MFileEventsType__
+#define __MFileEventsType__
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+// Standard libs:
+#include <map>
+using namespace std;
+
+// MEGAlib libs:
+#include "MGlobal.h"
+#include "MFileEvents.h"
+#include "MRERawEvent.h"
+
+// Forward declarations:
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+class MFileEventsType : public MFileEvents
+{
+  // public interface:
+ public:
+  MFileEventsType();
+  virtual ~MFileEventsType();
+
+  virtual bool Open(MString FileName, unsigned int Way = MFile::c_Read, bool IsBinary = false);
+  virtual bool Close();
+
+  bool AddEvent(long EventId, int EventType, double EventTypeProbability);
+  bool GetNextEvent();// fills private members with file content
+
+  // Access private members
+  long GetEventId();
+  int GetEventType();
+  double GetEventTypeProbability();
+  // private methods:
+ private:
+  void Reset();
+
+  // private members:
+ private:
+  MGeometryRevan* m_Geometry;
+  MString m_GeometryFileName;
+
+  long m_EventId;
+  int m_EventType;
+  double m_EventTypeProbability;
+
+  static const long c_NoId;
+  bool m_IsFirstEvent;
+
+
+#ifdef ___CLING___
+ public:
+  ClassDef(MFileEventsType, 0) // no description
+#endif
+
+};
+
+#endif
+
+
+////////////////////////////////////////////////////////////////////////////////
diff --git a/src/global/misc/inc/MPhysicalEvent.h b/src/global/misc/inc/MPhysicalEvent.h
index f9b941cbc..f30364917 100644
--- a/src/global/misc/inc/MPhysicalEvent.h
+++ b/src/global/misc/inc/MPhysicalEvent.h
@@ -57,6 +57,7 @@ class MPhysicalEvent : public MRotationInterface
   virtual MString ToTraString() const;
   //! Parse the content of the stream
   virtual int ParseLine(const char* Line, bool Fast = false);
+  static int ParseET(const char* type);
   //! Parse the content of the stream
   virtual bool ParseDelayed(bool Fast = false);
 
@@ -72,6 +73,7 @@ class MPhysicalEvent : public MRotationInterface
   int GetEventType() const { return m_EventType; }
   //! Return the type of this event as string 
   MString GetTypeString() const;
+  static MString GetTypeStringCode(int evtype);
   
   void SetTime(const MTime Time) { m_Time = Time; }
   MTime GetTime() const { return m_Time; }
diff --git a/src/global/misc/src/MFileEventsType.cxx b/src/global/misc/src/MFileEventsType.cxx
new file mode 100644
index 000000000..75f74c966
--- /dev/null
+++ b/src/global/misc/src/MFileEventsType.cxx
@@ -0,0 +1,234 @@
+/*
+ * MFileEventsType.cxx
+ *
+ *
+ * Copyright (C) by Andreas Zoglauer.
+ * All rights reserved.
+ *
+ *
+ * This code implementation is the intellectual property of
+ * Andreas Zoglauer.
+ *
+ * By copying, distributing or modifying the Program (or any work
+ * based on the Program) you indicate your acceptance of this statement,
+ * and all its terms.
+ *
+ */
+
+
+////////////////////////////////////////////////////////////////////////////////
+//
+// MFileEventsType
+//
+////////////////////////////////////////////////////////////////////////////////
+
+
+// Include the header:
+#include "MFileEventsType.h"
+
+// Standard libs:
+
+// ROOT libs:
+
+// MEGAlib:
+#include "MAssert.h"
+#include "MFileEvents.h"
+#include "MPhysicalEvent.h"
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+#ifdef ___CLING___
+ClassImp(MFileEventsType)
+#endif
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+const long MFileEventsType::c_NoId = -1;
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+MFileEventsType::MFileEventsType() : MFileEvents()
+{
+  // Construct an instance of MFileEventsType
+  m_Geometry = nullptr;
+  m_GeometryFileName = MString("None");
+  m_Version = 0;
+/*
+  m_Geometry = Geometry;
+  if (Geometry == 0) {
+    merr<<"Geometry pointer is zero! Aborting!"<<fatal;
+  }*/
+  Reset();
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+MFileEventsType::~MFileEventsType() {}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+bool MFileEventsType::Open(MString FileName, unsigned int Way, bool IsBinary)
+{
+  // Open the file, check if the type is correct
+
+  m_IncludeFileUsed = false;
+  m_IncludeFile = new MFileEventsType();
+  m_IncludeFile->SetIsIncludeFile(true);
+  
+  if (FileName.EndsWith("etp") == false) {
+    merr<<"This file is not an event type (.etp) file: "<<FileName<<endl;
+    return false;    
+  } else {
+    m_FileType = MString("etp");
+  }
+  
+  if (MFileEvents::Open(FileName, Way, IsBinary) == false) {
+    return false;
+  }
+  /* We don’t really use Geometry I think - to be removed?
+  if (m_Geometry->IsScanned() == false) {
+    merr<<"We do not have a properly initialized geometry!"<<endl;
+    return false;
+  }*/
+  
+  Reset();
+  return true;
+}
+
+////////////////////////////////////////////////////////////////////////////////
+void MFileEventsType::Reset()
+{
+  m_EventId = -1;
+  m_EventType = MRERawEvent::c_UnknownEvent;
+  m_EventTypeProbability = 0.;
+
+  m_IsFirstEvent = true;
+}
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+bool MFileEventsType::Close()
+{
+  // Close the file
+  if (m_Way == c_Write || m_Way == c_Create) Write(MString("\n\nEN\n\n"));
+
+  return MFileEvents::Close();
+}
+
+long MFileEventsType::GetEventId()
+{
+  return m_EventId;
+}
+
+int MFileEventsType::GetEventType()
+{
+  return m_EventType;
+}
+
+double MFileEventsType::GetEventTypeProbability()
+{
+  return m_EventTypeProbability;
+}
+
+////////////////////////////////////////////////////////////////////////////////
+
+bool MFileEventsType::GetNextEvent()
+{
+  // Recursive call if included file is in use
+  if (m_IncludeFileUsed) {
+    if (! dynamic_cast<MFileEventsType*>(m_IncludeFile)->GetNextEvent()) {
+      if (m_IncludeFile->IsCanceled()) m_Canceled = true;
+      m_IncludeFile->Close();
+      m_IncludeFileUsed = false;
+      if (m_Canceled) return false;
+    } else {
+      return true;
+    }
+  }
+  
+  MString Line;
+  // Reset data fields
+  unsigned int status = 0; //3 LSB for id, et, tp
+  m_EventId = c_NoId;
+  m_EventType = MRERawEvent::c_UnknownEvent;
+  m_EventTypeProbability = 0.;
+
+  // Resume reading file
+  while (IsGood() && ReadLine(Line)) {
+    if (Line.Length() < 2) continue;
+
+    // Include another file:
+    if (Line[0] == 'I' && Line[1] == 'N') {
+      if (OpenIncludeFile(Line)) {
+        return GetNextEvent();//now that m_IncludeFileUsed is true
+      } else {
+        m_IncludeFile->Close();
+        m_IncludeFileUsed = false;
+      }
+
+    // New event
+    } else if (Line[0] == 'S' && Line[1] == 'E') {
+      if (status) return true; // Even if incomplete event - allows to skip TP
+    } else if (Line[0] == 'I' && Line[1] == 'D') {
+      sscanf(Line.Data(), "ID %lu", &m_EventId);
+      status |= 0b001;
+    } else if (Line[0] == 'E' && Line[1] == 'T' && Line.Length() > 4) {
+      m_EventType = MPhysicalEvent::ParseET(&Line[3]);
+      status |= 0b010;
+    } else if (Line[0] == 'T' && Line[1] == 'P') {
+      sscanf(Line.Data(), "TP %lf", &m_EventTypeProbability);
+      status |= 0b100;
+    // Next file
+    } else if (Line[0] == 'N' && Line[1] == 'F') {
+      if (! OpenNextFile(Line) ) {
+        mout<<"Did not find a valid continuation file..."<<endl;
+        return false;
+      }
+    // End of file
+    } else if (Line[0] == 'E' && Line[1] == 'N') {
+      ReadFooter(true);
+      if (status) return true; // Even if incomplete event - allows to skip TP
+    }
+    if (status == 0b111) return true;
+  }
+
+  return false;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+bool MFileEventsType::AddEvent(long EventId, int EventType, double EventTypeProbability)
+{
+  if (m_Way == c_Read)
+  {
+    merr << "Only valid if file is in write-mode!" << endl;
+    massert(false);
+    return false;
+  }
+  if (!m_IsOpen) return false;
+
+  if (m_IsFirstEvent) {
+    WriteHeader();
+    m_IsFirstEvent = false;
+  }
+
+  ostringstream S;
+  S << "SE" << endl;
+  S << "ID " << EventId << endl;
+  S << "ET " << MPhysicalEvent::GetTypeStringCode(EventType) << endl;
+  S << "TP " << EventTypeProbability << endl;
+
+  Write(S);
+
+  return true;
+}
+
diff --git a/src/global/misc/src/MPhysicalEvent.cxx b/src/global/misc/src/MPhysicalEvent.cxx
index 60b685a7d..c3cfef2d9 100644
--- a/src/global/misc/src/MPhysicalEvent.cxx
+++ b/src/global/misc/src/MPhysicalEvent.cxx
@@ -263,14 +263,37 @@ const MPhysicalEventHit& MPhysicalEvent::GetHit(unsigned int i) const
 
 
 ////////////////////////////////////////////////////////////////////////////////
-
+MString MPhysicalEvent::GetTypeStringCode(int evtype)
+{
+  switch (evtype) {
+    case c_Compton:
+      return MString("CO");
+    case c_Pair:
+      return MString("PA");
+    case c_Photo:
+      return MString("PH");
+    case c_Muon:
+      return MString("MU");
+    case c_Decay:
+      return MString("DY");
+    case c_PET:
+      return MString("PT");
+    case c_Multi:
+      return MString("MT");
+    case c_Unidentifiable:
+      return MString("UN");
+    default:
+      massert(false);
+      return MString("Unkown");
+  }
+}
 
 MString MPhysicalEvent::ToTraString() const
 {
   //! Stream the content into a tra-file compatible string
 
   ostringstream S;
-  switch (m_EventType) {
+/*  switch (m_EventType) {
   case c_Compton:
     S<<"ET CO"<<endl;
     break;
@@ -299,7 +322,8 @@ MString MPhysicalEvent::ToTraString() const
     massert(false);
     S<<"ET Unkown"<<endl;
     break;
-  }
+  }*/
+  S<<"ET "<<GetTypeStringCode(m_EventType)<<endl;
   S<<"ID "<<m_Id<<endl;
   S<<"TI "<<m_Time.GetLongIntsString()<<endl;
   if (m_TimeWalk != -1) {
@@ -391,7 +415,22 @@ bool MPhysicalEvent::ParseDelayed(bool Fast)
 
 
 ////////////////////////////////////////////////////////////////////////////////
-
+int MPhysicalEvent::ParseET(const char* type)
+{
+  if (type[0] == 'C' && type[1] == 'O') return c_Compton;
+  else if (type[0] == 'C' && type[1] == 'O') return c_Compton;
+  else if (type[0] == 'P' && type[1] == 'A') return c_Pair;
+  else if (type[0] == 'P' && type[1] == 'H') return c_Photo;
+  else if (type[0] == 'M' && type[1] == 'U') return c_Muon;
+  else if (type[0] == 'D' && type[1] == 'Y') return c_Decay;
+  else if (type[0] == 'P' && type[1] == 'T') return c_PET;
+  else if (type[0] == 'M' && type[1] == 'T') return c_Multi;
+  else if (type[0] == 'U' && type[1] == 'N') return c_Unidentifiable;
+  else {
+    mout<<"int MPhysicalEvent::ParseET: Unkown event type..."<<endl;
+    return c_Unknown;
+  }
+}
 
 int MPhysicalEvent::ParseLine(const char* Line, bool Fast)
 {
@@ -403,7 +442,14 @@ int MPhysicalEvent::ParseLine(const char* Line, bool Fast)
   int Ret = 0;
   
   if (Line[0] == 'E' && Line[1] == 'T') {
-    if (Line[3] == 'C' && Line[4] == 'O') {
+    int type = ParseET(&Line[3]);//skips "ET "
+    if (m_EventType != type) {
+      mout << "int MPhysicalEvent::ParseLine: Event is no "
+            << GetTypeStringCode(type) << " as suggested but a "
+            << GetTypeString() << "!" << endl;
+      Ret = 1;
+    }
+/*    if (Line[3] == 'C' && Line[4] == 'O') {
       if (m_EventType != c_Compton) {
         cout<<"int MPhysicalEvent::ParseLine: Event is no Compton event as suggested but a "<<GetTypeString()<<"!"<<endl;
         Ret = 1;
@@ -446,7 +492,7 @@ int MPhysicalEvent::ParseLine(const char* Line, bool Fast)
     } else {
       cout<<"int MPhysicalEvent::ParseLine: Unkown event type..."<<endl;
       Ret = 1;
-    }
+    }*/
   } else if (Line[0] == 'T' && Line[1] == 'I') {
     if (Fast == true) {
       if (m_Time.Set(Line) == false) {

From 7a5af768a1f0e5f7b3f65b3940aa95caa66566f0 Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Fri, 11 Jul 2025 09:41:32 -0400
Subject: [PATCH 177/192] FIX: Remove one extraneous line

---
 src/global/misc/src/MPhysicalEvent.cxx | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/global/misc/src/MPhysicalEvent.cxx b/src/global/misc/src/MPhysicalEvent.cxx
index c3cfef2d9..a43c7d65d 100644
--- a/src/global/misc/src/MPhysicalEvent.cxx
+++ b/src/global/misc/src/MPhysicalEvent.cxx
@@ -418,7 +418,6 @@ bool MPhysicalEvent::ParseDelayed(bool Fast)
 int MPhysicalEvent::ParseET(const char* type)
 {
   if (type[0] == 'C' && type[1] == 'O') return c_Compton;
-  else if (type[0] == 'C' && type[1] == 'O') return c_Compton;
   else if (type[0] == 'P' && type[1] == 'A') return c_Pair;
   else if (type[0] == 'P' && type[1] == 'H') return c_Photo;
   else if (type[0] == 'M' && type[1] == 'U') return c_Muon;

From 22f4a541e6ba1ee02ac90b336e26e64b16d2ddd1 Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Fri, 11 Jul 2025 10:03:05 -0400
Subject: [PATCH 178/192] REF: Remove debugging prints

---
 src/revan/src/MERCSR.cxx      |  1 -
 src/revan/src/MERTrack.cxx    | 18 ------------------
 src/revan/src/MRERawEvent.cxx |  3 ---
 3 files changed, 22 deletions(-)

diff --git a/src/revan/src/MERCSR.cxx b/src/revan/src/MERCSR.cxx
index c0755fca8..910ebc4cd 100644
--- a/src/revan/src/MERCSR.cxx
+++ b/src/revan/src/MERCSR.cxx
@@ -117,7 +117,6 @@ bool MERCSR::Analyze(MRawEventIncarnations* List)
 
   int e_max = m_List->GetNRawEvents();
   MRERawEvent* RE = nullptr;
-  mout << "AL t" << m_CreateOnlyPermutations << show;
   if (m_CreateOnlyPermutations == true) {
     m_List->SetOptimumEvent(nullptr);
 
diff --git a/src/revan/src/MERTrack.cxx b/src/revan/src/MERTrack.cxx
index ee03b425a..c27f2edbb 100644
--- a/src/revan/src/MERTrack.cxx
+++ b/src/revan/src/MERTrack.cxx
@@ -252,7 +252,6 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
     mdebug<<"Not enough hits in tracker!"<<endl;
     return true;
   }
-  //mout << "AL cktime e=" << e << " id=" << ->GetEventId() << " time=" << RE->GetTime() << show;
 
   // Step B: Pairs
   Timer.Start();
@@ -303,7 +302,6 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
     } // end for
   }
   m_TimePairs += Timer.ElapsedTime();
-  mout << "AL endPA" << show;
 
 
   // Step C: Mips
@@ -314,7 +312,6 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
     mdebug<<"* Search for MIPs"<<endl;
     for (int e = 0; e < m_List->GetNRawEvents(); e++) {
       RE = m_List->GetRawEventAt(e);
-      mout << "AL cfmtm=" << RE->GetTime() << show;
       if (RE->GetEventType() == MRERawEvent::c_MipEvent || RE->GetEventType() == MRERawEvent::c_ShowerEvent) {// Iterate only over MIP/shower events
         CheckForMips(RE);
         // If we have found a MIP then we are done!
@@ -339,7 +336,6 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
     mdebug<<endl;
   }
   m_TimeMips += Timer.ElapsedTime();
-  if(m_List->HasOptimumEvent()) mout << "AL endMU pid=" <<  m_List->GetOptimumEvent()->GetPhysicalEvent()->GetId() << " ptype=" << m_List->GetOptimumEvent()->GetPhysicalEvent()->GetTypeString() << show;
 
 
   // Step C: Compton tracks:
@@ -357,9 +353,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
       RE = m_List->GetRawEventAt(e);
       if (RE->GetEventType() == MRERawEvent::c_ComptonEvent) {
         //RE->SetEventType(MRERawEvent::c_UnknownEvent);
-        mout << "AL -a" << show;
         List = TrackComptons(RE);
-        mout << "AL -b" << show;
         //RE->SetEventType(MRERawEvent::c_ComptonEvent);
         if (List != 0) {
           m_List->DeleteRawEvent(RE);
@@ -371,7 +365,6 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
           delete List;
           List = nullptr;
         }
-        mout << "AL -c" << show;
       }
     }
     m_TimeComptonSequences += Timer.ElapsedTime();
@@ -392,7 +385,6 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
         }
         if (CurrentN < MinN) MinN = CurrentN;
       }
-      mout << "AL -d" << show;
 
       for (int e = 0; e < m_List->GetNRawEvents(); e++) {
         int CurrentN = 0;
@@ -408,7 +400,6 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
           e--;
         }
       }
-      mout << "AL -e" << show;
       mdebug<<"Keeping "<<m_List->GetNRawEvents()<<" possibilities for further processing."<<endl;
     }
 
@@ -425,7 +416,6 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
     for (int e = 0; e < m_List->GetNRawEvents(); e++) {
       RE = m_List->GetRawEventAt(e);
       if (RE->GetEventType() == MRERawEvent::c_ComptonEvent) {
-        mout << "AL -f" << show;
         for (int r = 0; r < RE->GetNRESEs(); r++) {
           RESE = RE->GetRESEAt(r);
           IDRESE = RESE->GetID();
@@ -443,7 +433,6 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
             }
           }
         }
-        mout << "AL -g" << show;
       }
     }
 
@@ -451,9 +440,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
 
     for (int e = 0; e < m_List->GetNRawEvents(); e++) {
       RE = m_List->GetRawEventAt(e);
-      mout << "AL -h" << show;
       if (RE->GetEventType() == MRERawEvent::c_ComptonEvent) EvaluateTracks(RE);
-      mout << "AL -i" << show;
     }
     SortByTrackQualityFactor(m_List);
 
@@ -478,11 +465,9 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
       m_List->DeleteRawEvent(RE);
       e--;
     }
-    mout << "AL nRE=" << m_List->GetNRawEvents() << show;
 
     m_TimeComptonDirections += Timer.ElapsedTime();
   }
-  mout << "AL tr=" << StartTracking << " type=" << m_List->GetRawEventAt(0)->GetEventTypeAsString() << " rec=" << m_List->GetRawEventAt(0)->IsEventReconstructed() /*<< " ptype=" << m_List->GetRawEventAt(0)->GetPhysicalEvent()->GetTypeString()*/ << show;
 
 
   // Step E: Epilog
@@ -1180,9 +1165,7 @@ void MERTrack::CheckForMips(MRERawEvent* RE)
     // b. Store the new event:
     MMuonEvent* Muon = new MMuonEvent(); // is later stored as m_Event!
     Muon->SetId(RE->GetEventId());
-    //mout << "AL settime" << show;
     Muon->SetTime(RE->GetEventTime());
-    //mout << "AL settime=" << Muon->GetTime() << show;
     Muon->SetEnergy(RE->GetEnergy());
     Muon->SetDirection(TrackArray[HighestPos]->GetAverageDirection());
     Muon->SetCenterOfGravity(TrackArray[HighestPos]->GetCenterOfGravity());
@@ -1196,7 +1179,6 @@ void MERTrack::CheckForMips(MRERawEvent* RE)
     RE->SetPhysicalEvent(Muon);
     //RE->SetEventType(MRERawEvent::c_MipEvent);
     RE->SetGoodEvent(true);
-    mout << "AL muon id=" << Muon->GetId() << " time=" << Muon->GetTime() << " type=" << Muon->GetType() << show;
   }
   // b. A shower
   else if (TrackArray.size() > 1) {
diff --git a/src/revan/src/MRERawEvent.cxx b/src/revan/src/MRERawEvent.cxx
index c42ea69f7..9cf3b901a 100644
--- a/src/revan/src/MRERawEvent.cxx
+++ b/src/revan/src/MRERawEvent.cxx
@@ -1181,9 +1181,7 @@ MPhysicalEvent* MRERawEvent::GetPhysicalEvent()
     
     m_Event->SetAllHitsGood(IsValid());
     m_Event->SetId(m_EventID);
-    mout << "AL settime2" << show;
     m_Event->SetTime(m_EventTime);
-    mout << "AL settime2=" << m_Event->GetTime() << show;
     m_Event->SetTimeWalk(m_TimeWalk);
     m_Event->SetDecay(m_Decay);
     if (m_ExternalBadEventFlag == true) {
@@ -1203,7 +1201,6 @@ MPhysicalEvent* MRERawEvent::GetPhysicalEvent()
 
     m_Event->Validate();
   }
-  mout << "AL GPE addr=" << m_Event << " evtid=" << m_EventID << " time=" << m_EventTime << " type=" << GetEventTypeAsString() << " rec=" << IsEventReconstructed() << "/ ";
 
   return m_Event;
 }

From 955d195becd93f7460b8f52cfcdf6ae8173dbfa8 Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Sat, 12 Jul 2025 00:00:20 -0400
Subject: [PATCH 179/192] Feat: Implement external event type identification
 from event type *.etp file

---
 src/global/misc/inc/MPhysicalEvent.h          |   6 +
 src/global/misc/src/MFileEventsType.cxx       |   3 +-
 src/revan/Makefile                            |   1 +
 src/revan/inc/MEREventType.h                  |   2 +-
 src/revan/inc/MEREventTypeExternal.h          |  66 ++++++++++
 src/revan/inc/MRERawEvent.h                   |   7 ++
 src/revan/inc/MRawEventAnalyzer.h             |   2 +
 src/revan/inc/MSettingsEventReconstruction.h  |   5 +
 src/revan/src/MEREventType.cxx                |   2 +-
 src/revan/src/MEREventTypeExternal.cxx        | 115 ++++++++++++++++++
 src/revan/src/MRERawEvent.cxx                 |  27 +++-
 src/revan/src/MRawEventAnalyzer.cxx           |  22 ++--
 .../src/MSettingsEventReconstruction.cxx      |   8 +-
 13 files changed, 251 insertions(+), 15 deletions(-)
 create mode 100644 src/revan/inc/MEREventTypeExternal.h
 create mode 100644 src/revan/src/MEREventTypeExternal.cxx

diff --git a/src/global/misc/inc/MPhysicalEvent.h b/src/global/misc/inc/MPhysicalEvent.h
index f30364917..c94afc1bb 100644
--- a/src/global/misc/inc/MPhysicalEvent.h
+++ b/src/global/misc/inc/MPhysicalEvent.h
@@ -74,6 +74,11 @@ class MPhysicalEvent : public MRotationInterface
   //! Return the type of this event as string 
   MString GetTypeString() const;
   static MString GetTypeStringCode(int evtype);
+  //! Set event type probability
+  void SetTypeProbability(double evtTypeProbability)
+        { m_EventTypeProbability = evtTypeProbability; }
+  //! Get event type probability
+  double GetTypeProbability() { return m_EventTypeProbability; }
   
   void SetTime(const MTime Time) { m_Time = Time; }
   MTime GetTime() const { return m_Time; }
@@ -167,6 +172,7 @@ class MPhysicalEvent : public MRotationInterface
  protected:
   //! Type of the event 
   int m_EventType;
+  double m_EventTypeProbability;
 
   //! The time this event occurred
   MTime m_Time;
diff --git a/src/global/misc/src/MFileEventsType.cxx b/src/global/misc/src/MFileEventsType.cxx
index 75f74c966..2f8b39f2c 100644
--- a/src/global/misc/src/MFileEventsType.cxx
+++ b/src/global/misc/src/MFileEventsType.cxx
@@ -55,7 +55,6 @@ MFileEventsType::MFileEventsType() : MFileEvents()
 {
   // Construct an instance of MFileEventsType
   m_Geometry = nullptr;
-  m_GeometryFileName = MString("None");
   m_Version = 0;
 /*
   m_Geometry = Geometry;
@@ -105,7 +104,7 @@ bool MFileEventsType::Open(MString FileName, unsigned int Way, bool IsBinary)
 ////////////////////////////////////////////////////////////////////////////////
 void MFileEventsType::Reset()
 {
-  m_EventId = -1;
+  m_EventId = c_NoId;
   m_EventType = MRERawEvent::c_UnknownEvent;
   m_EventTypeProbability = 0.;
 
diff --git a/src/revan/Makefile b/src/revan/Makefile
index f6a7f75b5..75314c309 100644
--- a/src/revan/Makefile
+++ b/src/revan/Makefile
@@ -33,6 +33,7 @@ FILES := MGeometryRevan \
 	MEREventClusterizerDataSet \
 	MERHitClusterizer \
   MEREventType \
+  MEREventTypeExternal \
 	MERTrack \
 	MERTrackPearson \
 	MERTrackRank \
diff --git a/src/revan/inc/MEREventType.h b/src/revan/inc/MEREventType.h
index 1a87f064d..a721bd096 100644
--- a/src/revan/inc/MEREventType.h
+++ b/src/revan/inc/MEREventType.h
@@ -27,7 +27,7 @@
 #include "MDDetector.h"
 
 // Forward declarations:
-class MRETrack;
+//class MRETrack;
 
 ////////////////////////////////////////////////////////////////////////////////
 
diff --git a/src/revan/inc/MEREventTypeExternal.h b/src/revan/inc/MEREventTypeExternal.h
new file mode 100644
index 000000000..7812bb452
--- /dev/null
+++ b/src/revan/inc/MEREventTypeExternal.h
@@ -0,0 +1,66 @@
+/*
+ * MEREventTypeExternal.h
+ *
+ * Copyright (C) by Andreas Zoglauer.
+ * All rights reserved.
+ *
+ * Please see the source-file for the copyright-notice.
+ *
+ */
+
+
+#ifndef __MEREventTypeExternal__
+#define __MEREventTypeExternal__
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+// ROOT libs:
+#include <TROOT.h>
+
+// MEGAlib libs:
+#include "MGlobal.h"
+#include "MEREventType.h"
+#include "MFileEventsType.h"
+#include "MRawEventIncarnations.h"
+
+// Forward declarations:
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+class MEREventTypeExternal : public MEREventType
+{
+  // public interface:
+ public:
+  MEREventTypeExternal();
+  virtual ~MEREventTypeExternal();
+
+  //! Global parameters used by all electron tracking algorithms
+  virtual void SetParameters(MString EventTypeFileName);
+  bool Analyze(MRawEventIncarnations* List);
+
+  bool PostAnalysis();
+  MString ToString(bool CoreOnly = false) const;
+
+
+  // protected members:
+ protected:
+  MString m_EventTypeFileName;
+  MFileEventsType* m_FileEventsType;
+
+
+#ifdef ___CLING___
+ public:
+  ClassDef(MEREventTypeExternal, 0) // no description
+#endif
+
+};
+
+#endif
+
+
+
+
diff --git a/src/revan/inc/MRERawEvent.h b/src/revan/inc/MRERawEvent.h
index 9da8ea4a3..a0de2fee6 100644
--- a/src/revan/inc/MRERawEvent.h
+++ b/src/revan/inc/MRERawEvent.h
@@ -85,6 +85,10 @@ class MRERawEvent : public MRESE, public MRotationInterface
   void SetEventType(int Type);
   //! Get the event type as string
   MString GetEventTypeAsString();
+
+  //! Event type probability
+  double GetEventTypeProbability();
+  void SetEventTypeProbability(double typeProbability);
   
   //! Set origin information
   void SetOriginInformation(MVector Position, MVector Direction, MVector Polarization, double Energy);
@@ -290,6 +294,7 @@ class MRERawEvent : public MRESE, public MRotationInterface
   static const int c_RejectionEventClusteringUnresolvedHits      = 33;
   static const int c_RejectionEventClusteringNoOrigins           = 34;
   static const int c_RejectionEventClusteringEnergyOutOfBounds   = 35;
+  static const int c_RejectionNotEnoughHitsInTracker             = 36;
 
   
   static const double c_NoQualityFactor;
@@ -326,6 +331,8 @@ class MRERawEvent : public MRESE, public MRotationInterface
   unsigned long m_EventID;
   //! The type (Compton, etc.)
   int m_EventType;
+  //! Probability this type is the right one
+  double m_EventTypeProbability;
   //! The rejection reason, if any
   int m_RejectionReason;
 
diff --git a/src/revan/inc/MRawEventAnalyzer.h b/src/revan/inc/MRawEventAnalyzer.h
index e55dce737..bc3c019d2 100644
--- a/src/revan/inc/MRawEventAnalyzer.h
+++ b/src/revan/inc/MRawEventAnalyzer.h
@@ -252,6 +252,7 @@ class MRawEventAnalyzer
   void SetSearchPhotoEvent(bool Search) { m_SearchPhotoEvent = Search; }
   void SetSearchComptonTracks(bool Search) { m_SearchComptonTracks = Search; }
   void SetNLayersForVertexSearch(unsigned int NLayersForVertexSearch) { m_NLayersForVertexSearch = NLayersForVertexSearch; }
+  void SetEventTypeFileName(MString etpFileName) { m_EventTypeFileName = etpFileName; }
 
   // Options electron tracking:
   void SetDoTracking(bool Do) { m_DoTracking = Do; if (Do == false) m_TrackingAlgorithm = c_TrackingAlgoNone; }
@@ -429,6 +430,7 @@ class MRawEventAnalyzer
   bool m_SearchMIPTracks;
   bool m_SearchComptonTracks;
   unsigned int m_NLayersForVertexSearch;
+  MString m_EventTypeFileName;
   
   // Electron tracking:
   bool m_DoTracking;
diff --git a/src/revan/inc/MSettingsEventReconstruction.h b/src/revan/inc/MSettingsEventReconstruction.h
index c722ebc06..de5b9ce24 100644
--- a/src/revan/inc/MSettingsEventReconstruction.h
+++ b/src/revan/inc/MSettingsEventReconstruction.h
@@ -170,6 +170,9 @@ class MSettingsEventReconstruction : public MSettingsInterface
     return m_PDFClusterizerBaseFileName;
   }
 
+  void SetEventTypeFileName(MString etpFileName) { m_EventTypeFileName = etpFileName; }
+  MString GetEventTypeFileName() const { return m_EventTypeFileName; }
+
   void SetDoTracking(bool Do) { m_DoTracking = Do; }
   bool GetDoTracking() { return m_DoTracking; }
 
@@ -342,6 +345,8 @@ class MSettingsEventReconstruction : public MSettingsInterface
   bool m_SearchPhoto;
   int m_NLayersForVertexSearch;
 
+  MString m_EventTypeFileName;
+
   // Electron tracking:
   bool m_DoTracking;
   int m_MaxComptonJump;
diff --git a/src/revan/src/MEREventType.cxx b/src/revan/src/MEREventType.cxx
index 6a4012b0c..cc22ebf15 100644
--- a/src/revan/src/MEREventType.cxx
+++ b/src/revan/src/MEREventType.cxx
@@ -170,7 +170,7 @@ bool MEREventType::Analyze(MRawEventIncarnations* REList)
 
 
   bool Identified = false;
-  MRERawEvent* RE = 0;
+  MRERawEvent* RE = nullptr;
   //MRawEventIncarnations* List = 0;
   //MRESE* RESE = 0;
   //MRETrack* Track = 0;
diff --git a/src/revan/src/MEREventTypeExternal.cxx b/src/revan/src/MEREventTypeExternal.cxx
new file mode 100644
index 000000000..d26ef01d4
--- /dev/null
+++ b/src/revan/src/MEREventTypeExternal.cxx
@@ -0,0 +1,115 @@
+/*
+ * MEREventTypeExternal.cxx
+ *
+ *
+ * Copyright (C) by Andreas Zoglauer.
+ * All rights reserved.
+ *
+ *
+ * This code implementation is the intellectual property of
+ * Andreas Zoglauer.
+ *
+ * By copying, distributing or modifying the Program (or any work
+ * based on the Program) you indicate your acceptance of this statement,
+ * and all its terms.
+ *
+ */
+
+
+// Include the header:
+#include "MEREventTypeExternal.h"
+
+
+// MEGAlib libs:
+#include "MAssert.h"
+#include "MFileEventsType.h"
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+#ifdef ___CLING___
+ClassImp(MEREventTypeExternal)
+#endif
+
+
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
+MEREventTypeExternal::MEREventTypeExternal() : MEREventType()
+{
+  m_EventTypeFileName = "";
+  m_FileEventsType = new MFileEventsType();
+}
+
+MEREventTypeExternal::~MEREventTypeExternal()
+{
+  delete m_FileEventsType;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+void MEREventTypeExternal::SetParameters(MString EventTypeFileName)
+{
+  m_EventTypeFileName = EventTypeFileName;
+}
+
+bool MEREventTypeExternal::PostAnalysis()
+{
+  return m_FileEventsType->Close();
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+bool MEREventTypeExternal::Analyze(MRawEventIncarnations* List)
+{
+  massert(m_FileEventsType);
+  MERConstruction::Analyze(List);
+
+  if (! m_FileEventsType->IsOpen() ) {//First event
+    m_FileEventsType->Open(m_EventTypeFileName); //Read-mode
+  }
+
+  // Read file
+  streampos filePos = m_FileEventsType->GetFilePosition(); // Position at start of REI
+  MRERawEvent* RE = nullptr;  
+  for (int e = 0; e < m_List->GetNRawEvents(); e++) {
+    m_FileEventsType->Seek(filePos);// Rewind to position at start of REI
+    RE = m_List->GetRawEventAt(e);
+    while(m_FileEventsType->GetNextEvent() && m_FileEventsType->GetEventId() != RE->GetEventId()) {}
+    mout << "evtid=" << m_FileEventsType->GetEventId() << endl;
+    if (m_FileEventsType->GetEventId() == RE->GetEventId()) { // if found matching ID
+      RE->SetEventType( m_FileEventsType->GetEventType() );
+      RE->SetEventTypeProbability( m_FileEventsType->GetEventTypeProbability() );
+    } else {
+      merr << "MEREventTypeExternal: No event type found for event ID " << RE->GetEventId() << endl;
+      RE->SetEventType( MRERawEvent::c_UnknownEvent );
+      RE->SetEventTypeProbability( 0. );
+    }
+  }
+  return true;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+MString MEREventTypeExternal::ToString(bool CoreOnly) const
+{
+  // Dump an options string gor the tra file:
+  ostringstream out;
+
+  if (CoreOnly == false) {
+    out<<"# Event type - options:"<<endl;
+    out<<"# "<<endl;
+  }
+  out<<"# Event Type file name:         "<<m_EventTypeFileName<<endl;
+  if (CoreOnly == false) {
+    out<<"# "<<endl;
+  }
+
+  return out.str().c_str();
+}
+
diff --git a/src/revan/src/MRERawEvent.cxx b/src/revan/src/MRERawEvent.cxx
index 9cf3b901a..5010d22ae 100644
--- a/src/revan/src/MRERawEvent.cxx
+++ b/src/revan/src/MRERawEvent.cxx
@@ -708,6 +708,24 @@ MString MRERawEvent::GetEventTypeAsString()
 ////////////////////////////////////////////////////////////////////////////////
 
 
+double MRERawEvent::GetEventTypeProbability()
+{
+  return m_EventTypeProbability;
+}  
+
+ 
+////////////////////////////////////////////////////////////////////////////////
+
+
+void MRERawEvent::SetEventTypeProbability(double typeProbability)
+{
+  m_EventTypeProbability = typeProbability;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////
+
+
 void MRERawEvent::SetRejectionReason(int Reason)
 {
   m_RejectionReason = Reason;
@@ -992,6 +1010,13 @@ MString MRERawEvent::GetRejectionReasonAsString(int r, bool Short)
       out<<"The energy is outside of what the event clustering was trained for";
     }
     break;
+  case c_RejectionNotEnoughHitsInTracker:
+    if (Short == true) {
+      out<<"NotEnoughHitsTracker";
+    } else {
+      out<<"Not enough hits in tracker";
+    }
+    break;
   default:
     if (Short == true) {
       out<<"";
@@ -1198,7 +1223,7 @@ MPhysicalEvent* MRERawEvent::GetPhysicalEvent()
     for (unsigned int c = 0; c < m_Comments.size(); ++c) {
       m_Event->AddComment(m_Comments[c]);
     }
-
+    m_Event->SetTypeProbability(m_EventTypeProbability);
     m_Event->Validate();
   }
 
diff --git a/src/revan/src/MRawEventAnalyzer.cxx b/src/revan/src/MRawEventAnalyzer.cxx
index a1b03f193..fc4319edd 100644
--- a/src/revan/src/MRawEventAnalyzer.cxx
+++ b/src/revan/src/MRawEventAnalyzer.cxx
@@ -56,6 +56,7 @@ using namespace std;
 #include "MEREventClusterizerDistance.h"
 #include "MEREventClusterizerTMVA.h"
 #include "MEREventType.h"
+#include "MEREventTypeExternal.h"
 #include "MERTrack.h"
 #include "MERTrackPearson.h"
 #include "MERTrackRank.h"
@@ -310,6 +311,7 @@ void MRawEventAnalyzer::SetSettings(MSettingsEventReconstruction* S)
   SetCoincidenceAlgorithm(S->GetCoincidenceAlgorithm());
   SetEventClusteringAlgorithm(S->GetEventClusteringAlgorithm());
   SetHitClusteringAlgorithm(S->GetHitClusteringAlgorithm());
+  SetEventTypeAlgorithm(S->GetEventTypeAlgorithm());
   SetTrackingAlgorithm(S->GetTrackingAlgorithm());
   SetPairAlgorithm(S->GetPairAlgorithm());
   SetCSRAlgorithm(S->GetCSRAlgorithm());
@@ -340,8 +342,12 @@ void MRawEventAnalyzer::SetSettings(MSettingsEventReconstruction* S)
 
   SetPDFClusterizer(S->GetPDFClusterizerBaseFileName());
 
+  // Event type identification
+  SetSearchPhotoEvent(S->GetSearchPhoto());
+  SetEventTypeFileName(S->GetEventTypeFileName());
+
   // electron tracking
-  SetSearchPairTracks(S->GetSearchPairs());
+  SetSearchPairTracks(S->GetSearchPairs());//also in use in default event type identification
   SetSearchMIPTracks(S->GetSearchMIPs());
   SetSearchComptonTracks(S->GetSearchComptons());
 
@@ -1303,14 +1309,6 @@ bool MRawEventAnalyzer::PreAnalysis()
     m_EventType = nullptr;
     if (m_EventTypeAlgorithm == c_EventTypeDefault) {
       m_EventType = new MEREventType();
-    } else if (m_EventTypeAlgorithm == c_EventTypeExternal) {
-      merr << "External event type identification not implemented yet!" << show;
-      Return = false;
-    } else {
-      merr<<"Unknown event type algorithm: "<<m_EventTypeAlgorithm<<endl;
-      Return = false;
-    }
-    if (m_EventType) {
       m_EventType->SetGeometry(m_Geometry);
       m_EventType->SetParameters( m_SearchMIPTracks,
                                   m_SearchPairTracks,
@@ -1318,6 +1316,12 @@ bool MRawEventAnalyzer::PreAnalysis()
                                   m_SearchPhotoEvent,
                                   m_NLayersForVertexSearch,
                                   m_ElectronTrackingDetectorList);
+    } else if (m_EventTypeAlgorithm == c_EventTypeExternal) {
+      m_EventType = new MEREventTypeExternal();
+      dynamic_cast<MEREventTypeExternal*>(m_EventType)->SetParameters( m_EventTypeFileName );
+    } else {
+      merr<<"Unknown event type algorithm: "<<m_EventTypeAlgorithm<<endl;
+      Return = false;
     }
 
     // Electron tracking
diff --git a/src/revan/src/MSettingsEventReconstruction.cxx b/src/revan/src/MSettingsEventReconstruction.cxx
index 2f041f07a..fc98323cb 100644
--- a/src/revan/src/MSettingsEventReconstruction.cxx
+++ b/src/revan/src/MSettingsEventReconstruction.cxx
@@ -76,12 +76,14 @@ MSettingsEventReconstruction::MSettingsEventReconstruction() : MSettingsInterfac
 
   m_PDFClusterizerBaseFileName = "";
 
-  // Electron tracking
+  // Event type identification
   m_DoTracking = true;
   m_SearchPairs = true;
   m_SearchMIPs = true;
   m_SearchComptons = true;
+  m_EventTypeFileName = "";
 
+  // Electron tracking
   m_MaxComptonJump = 2;
   m_NTrackSequencesToKeep = 1;
   m_RejectPurelyAmbiguousTrackSequences = false;
@@ -190,6 +192,7 @@ bool MSettingsEventReconstruction::WriteXml(MXmlNode* Node)
   new MXmlNode(Node, "SearchPairs", m_SearchPairs);
   new MXmlNode(Node, "SearchMIPs", m_SearchMIPs);
   new MXmlNode(Node, "SearchComptons", m_SearchComptons);
+  new MXmlNode(Node, "EventTypeFileName", m_EventTypeFileName);
   new MXmlNode(Node, "MaxComptonJump", m_MaxComptonJump);
   new MXmlNode(Node, "NTrackSequencesToKeep", m_NTrackSequencesToKeep);
   new MXmlNode(Node, "RejectPurelyAmbiguousTrackSequences", m_RejectPurelyAmbiguousTrackSequences);
@@ -328,6 +331,9 @@ bool MSettingsEventReconstruction::ReadXml(MXmlNode* Node)
   if ((aNode = Node->GetNode("PDFClusterizerBaseFileName")) != 0) {
     m_PDFClusterizerBaseFileName = aNode->GetValueAsString();
   }
+  if ((aNode = Node->GetNode("EventTypeFileName")) != 0) {
+    m_EventTypeFileName = aNode->GetValueAsString();
+  }
   if ((aNode = Node->GetNode("DoTracking")) != 0) {
     m_DoTracking = aNode->GetValueAsBoolean();
   }

From ada415071f37eaa696b2eff3f958116ff1954fea Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Sat, 12 Jul 2025 00:01:03 -0400
Subject: [PATCH 180/192] Feat: GUI modifications for external event type
 identification

---
 src/revan/src/MGUIERAlgorithm.cxx      |  22 ++--
 src/revan/src/MGUIOptionsEventType.cxx | 150 +------------------------
 2 files changed, 20 insertions(+), 152 deletions(-)

diff --git a/src/revan/src/MGUIERAlgorithm.cxx b/src/revan/src/MGUIERAlgorithm.cxx
index 976655d3e..d32b810d9 100644
--- a/src/revan/src/MGUIERAlgorithm.cxx
+++ b/src/revan/src/MGUIERAlgorithm.cxx
@@ -122,10 +122,10 @@ void MGUIERAlgorithm::Create()
   m_HitClusteringList->Create();
   AddFrame(m_HitClusteringList, m_ListLayout);
   
-  // Event identification
+  // Event type identification
   m_EventTypeList = new MGUIERBList(this, "Event type identification", true);
   m_EventTypeList->Add("Default algorithm"); // 0
-  m_EventTypeList->Add("External from file (not implemented)"); // 1
+  m_EventTypeList->Add("External from file"); // 1
   m_EventTypeList->SetSelected(m_Data->GetEventTypeAlgorithm());
   m_EventTypeList->Create();
   AddFrame(m_EventTypeList, m_ListLayout);
@@ -217,8 +217,9 @@ bool MGUIERAlgorithm::OnApply()
 {
   // The Apply button has been pressed
 
+  // Coincidences
   m_Data->SetCoincidenceAlgorithm(m_CoincidenceList->GetSelected());
-  
+  // Event clustering
   if (m_EventClusteringList->GetSelected() == 0) {
     m_Data->SetEventClusteringAlgorithm(MRawEventAnalyzer::c_EventClusteringAlgoNone);
   } else if (m_EventClusteringList->GetSelected() == 1) {
@@ -226,9 +227,15 @@ bool MGUIERAlgorithm::OnApply()
   } else if (m_EventClusteringList->GetSelected() == 2) {
     m_Data->SetEventClusteringAlgorithm(MRawEventAnalyzer::c_EventClusteringAlgoTMVA);
   }
-    
+  // Hit clustering
   m_Data->SetHitClusteringAlgorithm(m_HitClusteringList->GetSelected());
-  
+  // Event type identification
+  if (m_EventTypeList->GetSelected() == 0) {
+    m_Data->SetEventTypeAlgorithm(MRawEventAnalyzer::c_EventTypeDefault);
+  } else if (m_EventTypeList->GetSelected() == 1) {
+    m_Data->SetEventTypeAlgorithm(MRawEventAnalyzer::c_EventTypeExternal);
+  }
+  // Tracking
   if (m_TrackingList->GetSelected() == 0) {
     m_Data->SetTrackingAlgorithm(MRawEventAnalyzer::c_TrackingAlgoNone);
   } else if (m_TrackingList->GetSelected() == 1) {
@@ -246,11 +253,12 @@ bool MGUIERAlgorithm::OnApply()
   } else if (m_TrackingList->GetSelected() == 7) {
     m_Data->SetTrackingAlgorithm(MRawEventAnalyzer::c_TrackingAlgoBayesian);
   }
+  // Pair
   //m_Data->SetPairAlgorithm(m_PairList->GetSelected());
+  // Compton
   m_Data->SetCSRAlgorithm(m_CSRList->GetSelected());
-  
+  // Decay
   //m_Data->SetDecayAlgorithm(m_DecayList->GetSelected());
-  
   m_Data->SetDecayAlgorithm(0);
 
   return true;
diff --git a/src/revan/src/MGUIOptionsEventType.cxx b/src/revan/src/MGUIOptionsEventType.cxx
index e0d0750c9..6f498e9ed 100644
--- a/src/revan/src/MGUIOptionsEventType.cxx
+++ b/src/revan/src/MGUIOptionsEventType.cxx
@@ -94,10 +94,6 @@ void MGUIOptionsEventType::Create()
     m_CBList->SetSelected(2, m_Data->GetSearchMIPs());
     m_CBList->Add("Search for Compton tracks");
     m_CBList->SetSelected(3, m_Data->GetSearchComptons());
-//     if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoPearson) {
-//       m_CBList->Add("Cheating: Assume Compton tracks go from top to bottom");
-//       m_CBList->SetSelected(3, m_Data->GetAssumeTrackTopBottom());
-//     }
     m_CBList->Create();
     TGLayoutHints* CBListLayout =
       new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, 20, 20, 0, 0);
@@ -144,155 +140,19 @@ void MGUIOptionsEventType::Create()
     m_DetectorList->Resize(200, 100);
 
   } else if (m_Data->GetEventTypeAlgorithm() == MRawEventAnalyzer::c_EventTypeExternal) {
-/*    AddSubTitle("Options for external input");
-    TGLayoutHints* SubLabel = new TGLayoutHints(kLHintsLeft | kLHintsTop, 20, 20, 20, 5);
-    TGLabel* ComptonLabel = new TGLabel(this, "Compton options: where2");
-    AddFrame(ComptonLabel, SubLabel);
+    AddSubTitle("Options for external input");
 
     TGLayoutHints* SubOptions = new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, 40, 20, 0, 5);
-    TGLabel* GeneralLabel = new TGLabel(this, "General options: whereisthisprinted?");
-    AddFrame(GeneralLabel, SubLabel);
 
     m_FileSelector =
       new MGUIEFileSelector(this, "File containing the event type data:",
-                            m_Data->GetEventTypeFileName());//To be implemented
-    m_FileSelector->SetFileType("file to be implemented", "*.dodo");// implementation in progress
-    AddFrame(m_FileSelector, SubOptions);*/
+                            m_Data->GetEventTypeFileName());
+    m_FileSelector->SetFileType("file to be implemented", "*.etp");
+    AddFrame(m_FileSelector, SubOptions);
   } else {
     AddSubTitle("Unknown Event Type identification algorithm!");
   }
 
-/*
-if(false) { // FAKE COMMENT
-  if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoModifiedPearson) {
-    AddSubTitle("Tracking options for Modified Pearson correlation:");
-  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoPearson) {
-    AddSubTitle("Tracking options for Pearson correlation:");
-  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoRank) {
-    AddSubTitle("Tracking options for Rank correlation:");
-  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoChiSquare) {
-    AddSubTitle("Tracking options for Chi-Square method:");
-  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoGas) {
-    AddSubTitle("Tracking options for gas detectors:");
-  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoDirectional) {
-    AddSubTitle("Tracking options for intrinsic electron tracking detectors - no options!");
-  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoBayesian) {
-    AddSubTitle("Tracking options for Bayesian electron tracking:");
-  } else {
-    AddSubTitle("You deselected electron tracking!");
-  }
-
-  if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoModifiedPearson ||
-      m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoPearson ||
-      m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoRank ||
-      m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoChiSquare ||
-      m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoGas ||
-      m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoBayesian) {
-    m_CBList = new MGUIECBList(this, "Search for the following event types:");
-    m_CBList->Add("Search for MIPS");
-    m_CBList->SetSelected(0, m_Data->GetSearchMIPs());
-    m_CBList->Add("Search for pairs");
-    m_CBList->SetSelected(1, m_Data->GetSearchPairs());
-    m_CBList->Add("Search for Compton tracks");
-    m_CBList->SetSelected(2, m_Data->GetSearchComptons());
-//     if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoPearson) {
-//       m_CBList->Add("Cheating: Assume Compton tracks go from top to bottom");
-//       m_CBList->SetSelected(3, m_Data->GetAssumeTrackTopBottom());
-//     }
-    m_CBList->Create();
-    TGLayoutHints* CBListLayout =
-      new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, 20, 20, 0, 0);
-    AddFrame(m_CBList, CBListLayout);
-
-
-    TGLayoutHints* SubLabel = new TGLayoutHints(kLHintsLeft | kLHintsTop, 20, 20, 20, 5);
-    TGLabel* ComptonLabel = new TGLabel(this, "Compton options:");
-    AddFrame(ComptonLabel, SubLabel);
-
-    TGLayoutHints* SubOptions = new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, 40, 20, 0, 5);
-    m_MaxComptonJump = new MGUIEEntry(this,
-                                      "Maximum number of layers a Compton track can skip (e.g. due to hits in passive material):",
-                                      false,
-                                      m_Data->GetMaxComptonJump(), true, 1);
-    AddFrame(m_MaxComptonJump, SubOptions);
-
-    m_NSequencesToKeep = new MGUIEEntry(this,
-                                      "Maximum number of different possible track sequences to keep in the initial analysis:",
-                                      false,
-                                      m_Data->GetNTrackSequencesToKeep(), true, 1);
-    AddFrame(m_NSequencesToKeep, SubOptions);
-
-    m_RejectPurelyAmbiguousSequences = new TGCheckButton(this,
-                                                         "Reject purely ambiguous sequences",
-                                                         e_RejectPurelyAmbiguousSequences);
-    AddFrame(m_RejectPurelyAmbiguousSequences, SubOptions);
-    if (m_Data->GetRejectPurelyAmbiguousTrackSequences() == true) {
-      m_RejectPurelyAmbiguousSequences->SetState(kButtonDown);
-    } else {
-      m_RejectPurelyAmbiguousSequences->SetState(kButtonUp);
-    }
-
-
-    TGLabel* PairLabel = new TGLabel(this, "Pair options:");
-    AddFrame(PairLabel, SubLabel);
-
-    m_NLayersForVertexSearch = new MGUIEEntry(this,
-                                      "Search for a pair vertex within this amount of layers (min 4):",
-                                      false,
-                                      m_Data->GetNLayersForVertexSearch(), true, 4);
-    AddFrame(m_NLayersForVertexSearch, SubOptions);
-
-    m_SigmaHitPos = new MGUIEEntry(this,
-                                  "Error in the position of the hit in the tracker (used by the Kalman filter) [cm]:",
-                                  false,
-                                  m_Data->GetSigmaHitPos(), true, 0.00693);
-    AddFrame(m_SigmaHitPos, SubOptions);
-
-
-    if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoBayesian) {
-      TGLabel* GeneralLabel = new TGLabel(this, "General options:");
-      AddFrame(GeneralLabel, SubLabel);
-
-      m_FileSelector =
-        new MGUIEFileSelector(this, "File containing the Bayesian tracking data:",
-                              m_Data->GetBayesianElectronFileName());
-      m_FileSelector->SetFileType("Response file", "*.rsp");
-      AddFrame(m_FileSelector, SubOptions);
-    }
-
-
-    TGLabel* LabelDetectors = new TGLabel(this, "Select the tracking detector(s):");
-    TGLayoutHints* LabelDetectorsLayout = new TGLayoutHints(kLHintsLeft | kLHintsTop, 20, 20, 20, 0);
-    AddFrame(LabelDetectors, LabelDetectorsLayout);
-
-    m_DetectorList = new TGListBox(this, e_Detectors);
-    m_DetectorList->SetMultipleSelections(true);
-    TGLayoutHints* DetectorListLayout = new TGLayoutHints(kLHintsLeft | kLHintsTop | kLHintsExpandX, 20, 20, 5, 0);
-    AddFrame(m_DetectorList, DetectorListLayout);
-
-    if (m_Geometry != 0) {
-      for (unsigned int d = 0; d < m_Geometry->GetNDetectors(); ++d) {
-        MString Name = m_Geometry->GetDetectorAt(d)->GetName() + " (" + m_Geometry->GetDetectorAt(d)->GetTypeName() + ")";
-        m_DetectorList->AddEntry(Name, d);
-
-        // Highlight those detectors which are already in the list:
-        for (unsigned int e = 0; e < m_Data->GetNElectronTrackingDetectors(); ++e) {
-          if (m_Data->GetElectronTrackingDetector(e) == m_Geometry->GetDetectorAt(d)->GetName()) {
-            m_DetectorList->Select(d);
-            break;
-          }
-        }
-      }
-    } else {
-      merr<<"No geometry!"<<show;
-    }
-    m_DetectorList->Resize(200, 100);
-
-  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoDirectional) {
-    // no options...
-  }
-
-} // FAKE COMMENT END*/
 
   AddButtons();
   PositionWindow(GetDefaultWidth()+30, GetDefaultHeight()+30, false);
@@ -328,7 +188,7 @@ bool MGUIOptionsEventType::OnApply()
       }
     }
   } else if (m_Data->GetEventTypeAlgorithm() == MRawEventAnalyzer::c_EventTypeExternal) {
-    m_Data->SetBayesianElectronFileName(m_FileSelector->GetFileName());
+    m_Data->SetEventTypeFileName(m_FileSelector->GetFileName());
   }
 
 	return true;

From bb7ddf2508987da000ac4b32b938b16e4826704e Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Sat, 12 Jul 2025 00:01:33 -0400
Subject: [PATCH 181/192] Fix: Pair events with not enough hits in tracker are
 properly rejected

---
 src/revan/src/MERTrack.cxx | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/revan/src/MERTrack.cxx b/src/revan/src/MERTrack.cxx
index c27f2edbb..90ad47cb4 100644
--- a/src/revan/src/MERTrack.cxx
+++ b/src/revan/src/MERTrack.cxx
@@ -250,6 +250,9 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
 
   if (StartTracking == false) {
     mdebug<<"Not enough hits in tracker!"<<endl;
+    RE->SetEventType(MRERawEvent::c_UnknownEvent); // discard
+    RE->SetRejectionReason(MRERawEvent::c_RejectionNotEnoughHitsInTracker);
+    RE->SetEventReconstructed(true);
     return true;
   }
 

From f7f28086e47bd09faf769df63490d16a3f3c94e9 Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Tue, 15 Jul 2025 09:59:41 -0400
Subject: [PATCH 182/192] FIX: Broken dependence of MFileEventsType of
 MRERawEvent

---
 src/global/misc/inc/MFileEventsType.h   |  4 +---
 src/global/misc/src/MFileEventsType.cxx | 18 ++++--------------
 2 files changed, 5 insertions(+), 17 deletions(-)

diff --git a/src/global/misc/inc/MFileEventsType.h b/src/global/misc/inc/MFileEventsType.h
index fa878be49..acaafdf03 100644
--- a/src/global/misc/inc/MFileEventsType.h
+++ b/src/global/misc/inc/MFileEventsType.h
@@ -23,7 +23,6 @@ using namespace std;
 // MEGAlib libs:
 #include "MGlobal.h"
 #include "MFileEvents.h"
-#include "MRERawEvent.h"
 
 // Forward declarations:
 
@@ -35,7 +34,7 @@ class MFileEventsType : public MFileEvents
 {
   // public interface:
  public:
-  MFileEventsType();
+  MFileEventsType(MString GeometryFileName="None");
   virtual ~MFileEventsType();
 
   virtual bool Open(MString FileName, unsigned int Way = MFile::c_Read, bool IsBinary = false);
@@ -54,7 +53,6 @@ class MFileEventsType : public MFileEvents
 
   // private members:
  private:
-  MGeometryRevan* m_Geometry;
   MString m_GeometryFileName;
 
   long m_EventId;
diff --git a/src/global/misc/src/MFileEventsType.cxx b/src/global/misc/src/MFileEventsType.cxx
index 2f8b39f2c..8c1f09a05 100644
--- a/src/global/misc/src/MFileEventsType.cxx
+++ b/src/global/misc/src/MFileEventsType.cxx
@@ -51,16 +51,11 @@ const long MFileEventsType::c_NoId = -1;
 ////////////////////////////////////////////////////////////////////////////////
 
 
-MFileEventsType::MFileEventsType() : MFileEvents()
+MFileEventsType::MFileEventsType(MString GeometryFileName) : MFileEvents()
 {
   // Construct an instance of MFileEventsType
-  m_Geometry = nullptr;
   m_Version = 0;
-/*
-  m_Geometry = Geometry;
-  if (Geometry == 0) {
-    merr<<"Geometry pointer is zero! Aborting!"<<fatal;
-  }*/
+  m_GeometryFileName = GeometryFileName;
   Reset();
 }
 
@@ -91,11 +86,6 @@ bool MFileEventsType::Open(MString FileName, unsigned int Way, bool IsBinary)
   if (MFileEvents::Open(FileName, Way, IsBinary) == false) {
     return false;
   }
-  /* We don’t really use Geometry I think - to be removed?
-  if (m_Geometry->IsScanned() == false) {
-    merr<<"We do not have a properly initialized geometry!"<<endl;
-    return false;
-  }*/
   
   Reset();
   return true;
@@ -105,7 +95,7 @@ bool MFileEventsType::Open(MString FileName, unsigned int Way, bool IsBinary)
 void MFileEventsType::Reset()
 {
   m_EventId = c_NoId;
-  m_EventType = MRERawEvent::c_UnknownEvent;
+  m_EventType = MPhysicalEvent::c_Unknown;
   m_EventTypeProbability = 0.;
 
   m_IsFirstEvent = true;
@@ -157,7 +147,7 @@ bool MFileEventsType::GetNextEvent()
   // Reset data fields
   unsigned int status = 0; //3 LSB for id, et, tp
   m_EventId = c_NoId;
-  m_EventType = MRERawEvent::c_UnknownEvent;
+  m_EventType = MPhysicalEvent::c_Unknown;
   m_EventTypeProbability = 0.;
 
   // Resume reading file

From d8c7064ca99410f1a1c4d4cf7c97b291cc88b68f Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Tue, 15 Jul 2025 16:06:37 -0400
Subject: [PATCH 183/192] Refactor: Moved all event types in global namespace
 in MPhysicalEvent

---
 src/addon/ResponseToXSPEC.cxx                 |   4 +-
 src/addon/SensitivityOptimizer.cxx            |  12 +-
 src/addon/SimpleComptonImaging.cxx            |   2 +-
 src/addon/TraAnalyzer.cxx                     |   2 +-
 src/addon/TraFitsConverter.cxx                |   4 +-
 src/addon/VariableSourceDetector.cxx          |   2 +-
 src/eview/src/MGUIEviewMain.cxx               |   6 +-
 src/global/misc/inc/MPhysicalEvent.h          |  27 +++--
 src/global/misc/src/MComptonEvent.cxx         |   4 +-
 src/global/misc/src/MDecayEvent.cxx           |   4 +-
 src/global/misc/src/MFileEventsTra.cxx        |  22 ++--
 src/global/misc/src/MFileEventsType.cxx       |   4 +-
 src/global/misc/src/MMultiEvent.cxx           |   4 +-
 src/global/misc/src/MMuonEvent.cxx            |   4 +-
 src/global/misc/src/MPETEvent.cxx             |   4 +-
 src/global/misc/src/MPairEvent.cxx            |   4 +-
 src/global/misc/src/MPhotoEvent.cxx           |   4 +-
 src/global/misc/src/MPhysicalEvent.cxx        | 110 +++++++++---------
 src/global/misc/src/MUnidentifiableEvent.cxx  |   4 +-
 src/mimrec/src/MBackprojection.cxx            |   4 +-
 src/mimrec/src/MBackprojectionFarField.cxx    |  12 +-
 src/mimrec/src/MBackprojectionNearField.cxx   |  20 ++--
 src/mimrec/src/MEarthHorizon.cxx              |   8 +-
 src/mimrec/src/MEventSelector.cxx             |  76 ++++++------
 src/mimrec/src/MInterfaceMimrec.cxx           |  94 +++++++--------
 src/mimrec/src/MProjection.cxx                |  10 +-
 src/mimrec/src/MResponseConeShapes.cxx        |   2 +-
 src/mimrec/src/MResponseEnergyLeakage.cxx     |   2 +-
 src/mimrec/src/MResponseGaussian.cxx          |   6 +-
 src/mimrec/src/MResponseGaussianARM.cxx       |   4 +-
 .../src/MResponseGaussianByUncertainties.cxx  |   4 +-
 src/mimrec/src/MResponsePRM.cxx               |   2 +-
 src/mimrec/src/MStandardAnalysis.cxx          |   6 +-
 src/realta/src/MGUIControlCenter.cxx          |   2 +-
 src/response/src/MResponseBase.cxx            |   2 +-
 src/response/src/MResponseBuilder.cxx         |   2 +-
 .../src/MResponseComptelDataSpace.cxx         |   2 +-
 src/response/src/MResponseEarthHorizon.cxx    |   2 +-
 src/response/src/MResponseEventQuality.cxx    |   2 +-
 .../MResponseEventQualityTMVAEventFile.cxx    |   2 +-
 .../src/MResponseFirstInteractionPosition.cxx |   2 +-
 src/response/src/MResponseImaging.cxx         |   2 +-
 src/response/src/MResponseImagingARM.cxx      |   2 +-
 .../src/MResponseImagingBinnedMode.cxx        |   2 +-
 .../src/MResponseImagingCodedMask.cxx         |   2 +-
 .../src/MResponseImagingEfficiency.cxx        |   2 +-
 .../MResponseImagingEfficiencyNearField.cxx   |   2 +-
 .../src/MResponsePolarizationBinnedMode.cxx   |   2 +-
 src/revan/inc/MRERawEvent.h                   |   7 +-
 src/revan/src/MERCSR.cxx                      |  12 +-
 src/revan/src/MERCSRChiSquare.cxx             |  10 +-
 src/revan/src/MERDecay.cxx                    |   2 +-
 src/revan/src/MEREventType.cxx                |  22 ++--
 src/revan/src/MEREventTypeExternal.cxx        |   2 +-
 src/revan/src/MERTrack.cxx                    |  40 +++----
 src/revan/src/MERTrackKalman2D.cxx            |   2 +-
 src/revan/src/MERTrackKalman3D.cxx            |   2 +-
 src/revan/src/MERTrackRank.cxx                |   2 +-
 src/revan/src/MRERawEvent.cxx                 |  30 ++---
 src/revan/src/MRawEventAnalyzer.cxx           |  16 +--
 60 files changed, 332 insertions(+), 322 deletions(-)

diff --git a/src/addon/ResponseToXSPEC.cxx b/src/addon/ResponseToXSPEC.cxx
index b6a0405b9..dc8fe139f 100644
--- a/src/addon/ResponseToXSPEC.cxx
+++ b/src/addon/ResponseToXSPEC.cxx
@@ -1535,7 +1535,7 @@ vector<float> ResponseToXSPEC::SpectrumFromTra(MResponseMatrixO2 Rsp, vector<flo
 	MPhysicalEvent* Event;
 
 	while ((Event = EventFile.GetNextEvent()) != 0){
-		if (Event->GetType() == MPhysicalEvent::c_Compton || Event->GetType() == MPhysicalEvent::c_Photo){
+		if (Event->GetType() == c_ComptonEvent || Event->GetType() == c_PhotoEvent){
 			if (MimrecEventSelector.IsQualifiedEvent(Event) == true){
 				double E = Event->GetEnergy();
 
@@ -1614,7 +1614,7 @@ vector<float> ResponseToXSPEC::BkgSpecFromTra(MResponseMatrixO2 Rsp, vector<floa
 	MPhysicalEvent* Event;
 
 	while ((Event = EventFile.GetNextEvent()) != 0){
-		if (Event->GetType() == MPhysicalEvent::c_Compton || Event->GetType() == MPhysicalEvent::c_Photo){
+		if (Event->GetType() == c_ComptonEvent || Event->GetType() == c_PhotoEvent){
 			if (MimrecEventSelector.IsQualifiedEvent(Event) == true){
 				double E = Event->GetEnergy();
 
diff --git a/src/addon/SensitivityOptimizer.cxx b/src/addon/SensitivityOptimizer.cxx
index e24683524..2763fb18c 100644
--- a/src/addon/SensitivityOptimizer.cxx
+++ b/src/addon/SensitivityOptimizer.cxx
@@ -2466,7 +2466,7 @@ bool SensitivityOptimizer::Analyze()
         //mlog<<"Test qualified!"<<endl;
         if (OpenSelector.IsQualifiedEventFast(Event) == true) {
           //mlog<<"Qualified!"<<endl;
-          if (Event->GetType() == MPhysicalEvent::c_Compton) {
+          if (Event->GetType() == c_ComptonEvent) {
             //mlog<<"Good Compton!"<<endl;
             Compton = dynamic_cast<MComptonEvent*>(Event);
             
@@ -2566,7 +2566,7 @@ bool SensitivityOptimizer::Analyze()
             }
           } 
           // Pair:
-          else if (Event->GetType() == MPhysicalEvent::c_Pair) {
+          else if (Event->GetType() == c_PairEvent) {
             Pair = dynamic_cast<MPairEvent*>(Event);
             for (unsigned int d = 0; d < d_max; ++d) {
               //mlog<<"1"<<endl;
@@ -2602,7 +2602,7 @@ bool SensitivityOptimizer::Analyze()
             }
           }
           // Photo:
-          else if (Event->GetType() == MPhysicalEvent::c_Photo) {
+          else if (Event->GetType() == c_PhotoEvent) {
             for (unsigned int c = 0; c < c_max; ++c) {
               //cout<<"c: "<<c<<":"<<c_max<<endl;
               for (unsigned int b = 0; b < b_max; ++b) {
@@ -2646,7 +2646,7 @@ bool SensitivityOptimizer::Analyze()
     while ((Event = Source.GetNextEvent()) != 0) {
       if (++counts % 10000 == 0) mlog<<"Counts: "<<counts<<" after "<<TimerBackground.GetElapsed()<<" sec"<<endl;
       if (OpenSelector.IsQualifiedEventFast(Event) == true) {
-        if (Event->GetType() == MPhysicalEvent::c_Compton) {
+        if (Event->GetType() == c_ComptonEvent) {
 
           // Tracked Compton
           Compton = dynamic_cast<MComptonEvent*>(Event);
@@ -2729,7 +2729,7 @@ bool SensitivityOptimizer::Analyze()
           }
         }
         // Pairs:
-        else if (Event->GetType() == MPhysicalEvent::c_Pair) {
+        else if (Event->GetType() == c_PairEvent) {
 
           Pair = dynamic_cast<MPairEvent*>(Event);
           for (unsigned int d = 0; d < d_max; ++d) {
@@ -2768,7 +2768,7 @@ bool SensitivityOptimizer::Analyze()
           }
         }
         // Photos:
-        else if (Event->GetType() == MPhysicalEvent::c_Photo) {
+        else if (Event->GetType() == c_PhotoEvent) {
           for (unsigned int c = 0; c < c_max; ++c) {
             for (unsigned int b = 0; b < b_max; ++b) {
               for (unsigned int e = m_EnergyMax.size()-1; e < m_EnergyMax.size(); --e) {
diff --git a/src/addon/SimpleComptonImaging.cxx b/src/addon/SimpleComptonImaging.cxx
index f7ac13859..e42e7ee92 100644
--- a/src/addon/SimpleComptonImaging.cxx
+++ b/src/addon/SimpleComptonImaging.cxx
@@ -216,7 +216,7 @@ bool SimpleComptonImaging::Analyze()
   MPhysicalEvent* Event = 0;
   MComptonEvent* ComptonEvent = 0;
   while ((Event = EventFile->GetNextEvent()) != 0) {
-    if (Event->GetType() == MPhysicalEvent::c_Compton) {
+    if (Event->GetType() == c_ComptonEvent) {
       ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
       Ee = ComptonEvent->Ee();
diff --git a/src/addon/TraAnalyzer.cxx b/src/addon/TraAnalyzer.cxx
index c958929fb..78cb7ad30 100644
--- a/src/addon/TraAnalyzer.cxx
+++ b/src/addon/TraAnalyzer.cxx
@@ -202,7 +202,7 @@ bool TraAnalyzer::Analyze()
     // Hitting Ctrl-C raises this flag
     if (m_Interrupt == true) return false;
     
-    if (Event->GetType() == MPhysicalEvent::c_Compton) {
+    if (Event->GetType() == c_ComptonEvent) {
       ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
       Hist->Fill(ComptonEvent->Ei());
diff --git a/src/addon/TraFitsConverter.cxx b/src/addon/TraFitsConverter.cxx
index a89b9d05d..71e22b6be 100644
--- a/src/addon/TraFitsConverter.cxx
+++ b/src/addon/TraFitsConverter.cxx
@@ -716,7 +716,7 @@ bool TraFitsConverter::ToFits()
     }
     
     
-    if (Event->GetType() == MPhysicalEvent::c_Compton) {
+    if (Event->GetType() == c_ComptonEvent) {
       C = dynamic_cast<MComptonEvent*>(Event);
       ID.push_back(C->GetId());
       TYPE.push_back(2);
@@ -923,7 +923,7 @@ bool TraFitsConverter::ToFits()
       QUAL2.push_back(C->ComptonQualityFactor2());
       
       
-    } else if (Event->GetType() == MPhysicalEvent::c_Photo) {
+    } else if (Event->GetType() == c_PhotoEvent) {
       S = dynamic_cast<MPhotoEvent*>(Event);
       ID.push_back(S->GetId());
       TYPE.push_back(1);
diff --git a/src/addon/VariableSourceDetector.cxx b/src/addon/VariableSourceDetector.cxx
index dc1d58fe9..c3a322921 100644
--- a/src/addon/VariableSourceDetector.cxx
+++ b/src/addon/VariableSourceDetector.cxx
@@ -236,7 +236,7 @@ bool MVariableSourceDetectionTester::Analyze()
     // Hitting Ctrl-C raises this flag
     if (m_Interrupt == true) return false;
     
-    if (Event->GetType() == MPhysicalEvent::c_Compton) {
+    if (Event->GetType() == c_ComptonEvent) {
       ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
       Hist->Fill(ComptonEvent->Ei());
diff --git a/src/eview/src/MGUIEviewMain.cxx b/src/eview/src/MGUIEviewMain.cxx
index 689d7c200..de563ec95 100644
--- a/src/eview/src/MGUIEviewMain.cxx
+++ b/src/eview/src/MGUIEviewMain.cxx
@@ -1353,7 +1353,7 @@ bool MGUIEviewMain::SelectAndDraw(MRERawEvent* RE)
   
   // Add the compton sequence
   if (ShowLinks == true) {
-    if (RE->GetEventType() == MRERawEvent::c_ComptonEvent) {
+    if (RE->GetEventType() == c_ComptonEvent) {
       MRESE* Before = RE->GetStartPoint();
       MRESE* Next = Before->GetLinkAt(0);
       MRESE* After = 0;
@@ -1371,7 +1371,7 @@ bool MGUIEviewMain::SelectAndDraw(MRERawEvent* RE)
   // Add the origins:
   if (ShowOrigin == true) {
     cout<<"Type: "<<RE->GetEventType()<<endl;
-    if (RE->GetEventType() == MRERawEvent::c_MipEvent) {
+    if (RE->GetEventType() == c_MuonEvent) {
       MMuonEvent* Muon = (MMuonEvent*) RE->GetPhysicalEvent();
 
       MVector Direction = Muon->GetDirection();
@@ -1386,7 +1386,7 @@ bool MGUIEviewMain::SelectAndDraw(MRERawEvent* RE)
         (-5-Muon->GetCenterOfGravity().Z())*(1.0/Direction.Z());
       m_Geometry->AddLink(Start, Stop, 0.03, ColorOrigin);
       cout<<"Adding: "<<Start.X()<<"!"<<Start.Y()<<"!"<<Start.Z()<<" --  "<<Stop.X()<<"!"<<Stop.Y()<<"!"<<Stop.Z()<<endl;
-    } else if (RE->GetEventType() == MRERawEvent::c_ComptonEvent) {
+    } else if (RE->GetEventType() == c_ComptonEvent) {
       cout<<"Compton origin missing"<<endl;
     }
   }
diff --git a/src/global/misc/inc/MPhysicalEvent.h b/src/global/misc/inc/MPhysicalEvent.h
index c94afc1bb..bdedb8786 100644
--- a/src/global/misc/inc/MPhysicalEvent.h
+++ b/src/global/misc/inc/MPhysicalEvent.h
@@ -39,6 +39,23 @@ using namespace std;
 
 ////////////////////////////////////////////////////////////////////////////////
 
+//! Definition of all events type in a single place
+// The namespace wrapper allow for easy import in other classes
+namespace n_EventTypeWrapper {
+  enum c_EventTypeEnum {
+    c_UnknownEvent = -1,
+    c_ComptonEvent = 0,
+    c_PairEvent = 1,
+    c_MuonEvent,
+    c_ShowerEvent,
+    c_PhotoEvent,
+    c_DecayEvent,
+    c_PETEvent,
+    c_MultiEvent,
+    c_UnidentifiableEvent = 100
+  };
+};
+using namespace n_EventTypeWrapper;
 
 class MPhysicalEvent : public MRotationInterface
 {
@@ -144,16 +161,6 @@ class MPhysicalEvent : public MRotationInterface
   //! Convert content to a descriptive string of the event
   virtual MString ToString() const;
 
-  static const int c_Unknown;
-  static const int c_Compton;
-  static const int c_Pair;
-  static const int c_Muon;
-  static const int c_Shower;
-  static const int c_Photo;
-  static const int c_Decay;
-  static const int c_PET;
-  static const int c_Multi;
-  static const int c_Unidentifiable;
 
 
   // protected methods:
diff --git a/src/global/misc/src/MComptonEvent.cxx b/src/global/misc/src/MComptonEvent.cxx
index eb144e76d..8419e348b 100644
--- a/src/global/misc/src/MComptonEvent.cxx
+++ b/src/global/misc/src/MComptonEvent.cxx
@@ -56,7 +56,7 @@ MComptonEvent::MComptonEvent() : MPhysicalEvent(), m_CoincidenceWindow(0)
 {
   // standard constructor
 
-  m_EventType = c_Compton;
+  m_EventType = c_ComptonEvent;
 
   Reset();
 }
@@ -665,7 +665,7 @@ bool MComptonEvent::Assimilate(MPhysicalEvent* Event)
 {
   // Simply Call: MComptonEvent::Assimilate(const MComptonEventData *ComptonEventData)
   
-  if (Event->GetType() == MPhysicalEvent::c_Compton) {
+  if (Event->GetType() == c_ComptonEvent) {
     return Assimilate(dynamic_cast<MComptonEvent*>(Event));
   } else {
     return false; 
diff --git a/src/global/misc/src/MDecayEvent.cxx b/src/global/misc/src/MDecayEvent.cxx
index d73172753..ca755bcb5 100644
--- a/src/global/misc/src/MDecayEvent.cxx
+++ b/src/global/misc/src/MDecayEvent.cxx
@@ -52,7 +52,7 @@ MDecayEvent::MDecayEvent()
 {
   // standard constructor
 
-  m_EventType = c_Decay;
+  m_EventType = c_DecayEvent;
 
   Reset();
 }
@@ -125,7 +125,7 @@ bool MDecayEvent::Assimilate(MPhysicalEvent* Event)
 {
   // Simply Call: MDecayEvent::Assimilate(const MDecayEventData *DecayEventData)
 
-  if (Event->GetType() == MPhysicalEvent::c_Decay) {
+  if (Event->GetType() == c_DecayEvent) {
     return Assimilate((MDecayEvent *) Event);
   } else {
     return false; 
diff --git a/src/global/misc/src/MFileEventsTra.cxx b/src/global/misc/src/MFileEventsTra.cxx
index d01a1d76a..2741a5b34 100644
--- a/src/global/misc/src/MFileEventsTra.cxx
+++ b/src/global/misc/src/MFileEventsTra.cxx
@@ -68,7 +68,7 @@ MFileEventsTra::MFileEventsTra() : MFileEvents()
 {
   // Construct an instance of MFileEventsTra
 
-  m_EventType = MPhysicalEvent::c_Unknown;
+  m_EventType = c_UnknownEvent;
 
   m_FileType = "tra";
 
@@ -350,7 +350,7 @@ MPhysicalEvent* MFileEventsTra::ReadNextEvent()
     }
   }
 
-  m_EventType = MPhysicalEvent::c_Unknown;
+  m_EventType = c_UnknownEvent;
 
   // Read until we reach a CO or PA or <to be continued>
   MString Line;
@@ -361,54 +361,54 @@ MPhysicalEvent* MFileEventsTra::ReadNextEvent()
     if (Line[0] == 'E' && Line[1] == 'T') {
       if (Line.Length() < 5) {
         cout<<"Error reading event type"<<endl;
-        m_EventType = MPhysicalEvent::c_Unknown;
+        m_EventType = c_UnknownEvent;
         break;
       }
       if (Line[3] == 'C' && Line[4] == 'O') {
         MComptonEvent* P = new MComptonEvent();
         P->Stream(*this, m_Version, true, m_Fast, m_ParseDelayed);
-        m_EventType = MPhysicalEvent::c_Compton;
+        m_EventType = c_ComptonEvent;
         Phys = (MPhysicalEvent*) P;
         break;
       } else  if (Line[3] == 'P' && Line[4] == 'A') {
         MPairEvent* P = new MPairEvent();
         P->Stream(*this, m_Version, true, m_Fast, m_ParseDelayed);
-        m_EventType = MPhysicalEvent::c_Pair;
+        m_EventType = c_PairEvent;
         Phys = (MPhysicalEvent*) P;
         break;
       } else  if (Line[3] == 'P' && Line[4] == 'H') {
         MPhotoEvent* P = new MPhotoEvent();
         P->Stream(*this, m_Version, true, m_Fast, m_ParseDelayed);
-        m_EventType = MPhysicalEvent::c_Photo;
+        m_EventType = c_PhotoEvent;
         Phys = (MPhysicalEvent*) P;
         break;
       } else  if (Line[3] == 'M' && Line[4] == 'U') {
         MMuonEvent* P = new MMuonEvent();
         P->Stream(*this, m_Version, true, m_Fast, m_ParseDelayed);
-        m_EventType = MPhysicalEvent::c_Muon;
+        m_EventType = c_MuonEvent;
         Phys = (MPhysicalEvent*) P;
         break;
       } else  if (Line[3] == 'P' && Line[4] == 'T') {
         MPETEvent* P = new MPETEvent();
         P->Stream(*this, m_Version, true, m_Fast, m_ParseDelayed);
-        m_EventType = MPhysicalEvent::c_Muon;
+        m_EventType = c_MuonEvent;
         Phys = (MPhysicalEvent*) P;
         break;
       } else  if (Line[3] == 'M' && Line[4] == 'T') {
         MMultiEvent* P = new MMultiEvent();
         P->Stream(*this, m_Version, true, m_Fast, m_ParseDelayed);
-        m_EventType = MPhysicalEvent::c_Muon;
+        m_EventType = c_MuonEvent;
         Phys = (MPhysicalEvent*) P;
         break;
       } else  if (Line[3] == 'U' && Line[4] == 'N') {
         MUnidentifiableEvent* P = new MUnidentifiableEvent();
         P->Stream(*this, m_Version, true, m_Fast, m_ParseDelayed);
-        m_EventType = MPhysicalEvent::c_Unidentifiable;
+        m_EventType = c_UnidentifiableEvent;
         Phys = (MPhysicalEvent*) P;
         break;
       } else {
         cout<<"Unknown event"<<endl;
-        m_EventType = MPhysicalEvent::c_Unknown;
+        m_EventType = c_UnknownEvent;
         break;
       }
     } else if (Line[0] == 'N' && Line[1] == 'F') {
diff --git a/src/global/misc/src/MFileEventsType.cxx b/src/global/misc/src/MFileEventsType.cxx
index 8c1f09a05..abaf193b4 100644
--- a/src/global/misc/src/MFileEventsType.cxx
+++ b/src/global/misc/src/MFileEventsType.cxx
@@ -95,7 +95,7 @@ bool MFileEventsType::Open(MString FileName, unsigned int Way, bool IsBinary)
 void MFileEventsType::Reset()
 {
   m_EventId = c_NoId;
-  m_EventType = MPhysicalEvent::c_Unknown;
+  m_EventType = c_UnknownEvent;
   m_EventTypeProbability = 0.;
 
   m_IsFirstEvent = true;
@@ -147,7 +147,7 @@ bool MFileEventsType::GetNextEvent()
   // Reset data fields
   unsigned int status = 0; //3 LSB for id, et, tp
   m_EventId = c_NoId;
-  m_EventType = MPhysicalEvent::c_Unknown;
+  m_EventType = c_UnknownEvent;
   m_EventTypeProbability = 0.;
 
   // Resume reading file
diff --git a/src/global/misc/src/MMultiEvent.cxx b/src/global/misc/src/MMultiEvent.cxx
index 6b204ade3..f81a96861 100644
--- a/src/global/misc/src/MMultiEvent.cxx
+++ b/src/global/misc/src/MMultiEvent.cxx
@@ -58,7 +58,7 @@ ClassImp(MMultiEvent)
 //! Default constructor
 MMultiEvent::MMultiEvent()
 {
-  m_EventType = c_Multi;
+  m_EventType = c_MultiEvent;
 
   Reset();
 }
@@ -114,7 +114,7 @@ bool MMultiEvent::Assimilate(MPhysicalEvent* Event)
 {
   // Simply Call: MMultiEvent::Assimilate(const MMultiEventData *MultiEventData)
 
-  if (Event->GetType() == MPhysicalEvent::c_Multi) {
+  if (Event->GetType() == c_MultiEvent) {
     return Assimilate(dynamic_cast<MMultiEvent*>(Event));
   } else {
     merr<<"Trying to assimilate a non-Multi event!"<<endl; 
diff --git a/src/global/misc/src/MMuonEvent.cxx b/src/global/misc/src/MMuonEvent.cxx
index 5819a093c..167a994ee 100644
--- a/src/global/misc/src/MMuonEvent.cxx
+++ b/src/global/misc/src/MMuonEvent.cxx
@@ -52,7 +52,7 @@ MMuonEvent::MMuonEvent()
 {
   // standard constructor
 
-  m_EventType = c_Muon;
+  m_EventType = c_MuonEvent;
 
   Reset();
 }
@@ -126,7 +126,7 @@ bool MMuonEvent::Assimilate(MPhysicalEvent* Event)
 {
   // Simply Call: MMuonEvent::Assimilate(const MMuonEventData *MuonEventData)
 
-  if (Event->GetType() == MPhysicalEvent::c_Muon) {
+  if (Event->GetType() == c_MuonEvent) {
     return Assimilate((MMuonEvent *) Event);
   } else {
     merr<<"Trying to assimilate a non muon event!"<<endl; 
diff --git a/src/global/misc/src/MPETEvent.cxx b/src/global/misc/src/MPETEvent.cxx
index ca5ecc876..5f0c748ed 100644
--- a/src/global/misc/src/MPETEvent.cxx
+++ b/src/global/misc/src/MPETEvent.cxx
@@ -52,7 +52,7 @@ ClassImp(MPETEvent)
 //! Default constructor
 MPETEvent::MPETEvent()
 {
-  m_EventType = c_PET;
+  m_EventType = c_PETEvent;
 
   Reset();
 }
@@ -146,7 +146,7 @@ bool MPETEvent::Assimilate(MPhysicalEvent* Event)
 {
   // Simply Call: MPETEvent::Assimilate(const MPETEventData *PETEventData)
 
-  if (Event->GetType() == MPhysicalEvent::c_PET) {
+  if (Event->GetType() == c_PETEvent) {
     return Assimilate(dynamic_cast<MPETEvent*>(Event));
   } else {
     merr<<"Trying to assimilate a non-PET event!"<<endl; 
diff --git a/src/global/misc/src/MPairEvent.cxx b/src/global/misc/src/MPairEvent.cxx
index 3a3b750fa..e46a94e99 100644
--- a/src/global/misc/src/MPairEvent.cxx
+++ b/src/global/misc/src/MPairEvent.cxx
@@ -58,7 +58,7 @@ MPairEvent::MPairEvent()
 {
   // standard constructor
 
-  m_EventType = c_Pair;
+  m_EventType = c_PairEvent;
 
   Reset();
 }
@@ -163,7 +163,7 @@ bool MPairEvent::Assimilate(MPairEvent* PairEventData)
 
 bool MPairEvent::Assimilate(MPhysicalEvent* Event)
 {
-  if (Event->GetType() == MPhysicalEvent::c_Pair) {
+  if (Event->GetType() == c_PairEvent) {
     return Assimilate(dynamic_cast<MPairEvent*>(Event));
   } else {
     return false;
diff --git a/src/global/misc/src/MPhotoEvent.cxx b/src/global/misc/src/MPhotoEvent.cxx
index de0565f2d..dfe13deda 100644
--- a/src/global/misc/src/MPhotoEvent.cxx
+++ b/src/global/misc/src/MPhotoEvent.cxx
@@ -53,7 +53,7 @@ MPhotoEvent::MPhotoEvent()
 {
   // standard constructor
 
-  m_EventType = c_Photo;
+  m_EventType = c_PhotoEvent;
 
   Reset();
 }
@@ -125,7 +125,7 @@ bool MPhotoEvent::Assimilate(MPhysicalEvent* Event)
 {
   // Simply Call: MPhotoEvent::Assimilate(const MPhotoEventData *PhotoEventData)
 
-  if (Event->GetType() == MPhysicalEvent::c_Photo) {
+  if (Event->GetType() == c_PhotoEvent) {
     return Assimilate(dynamic_cast<MPhotoEvent*>(Event));
   } else {
     merr<<"Trying to assimilate a non photo event!"<<endl; 
diff --git a/src/global/misc/src/MPhysicalEvent.cxx b/src/global/misc/src/MPhysicalEvent.cxx
index a43c7d65d..cfed43e7d 100644
--- a/src/global/misc/src/MPhysicalEvent.cxx
+++ b/src/global/misc/src/MPhysicalEvent.cxx
@@ -49,18 +49,18 @@ ClassImp(MPhysicalEvent)
 
 ////////////////////////////////////////////////////////////////////////////////
 
-
-const int MPhysicalEvent::c_Unknown        = -1;
-const int MPhysicalEvent::c_Compton        =  0;
-const int MPhysicalEvent::c_Pair           =  1;
-const int MPhysicalEvent::c_Muon           =  2;
-const int MPhysicalEvent::c_Shower         =  3;
-const int MPhysicalEvent::c_Photo          =  4;
-const int MPhysicalEvent::c_Decay          =  5;
-const int MPhysicalEvent::c_PET            =  6;
-const int MPhysicalEvent::c_Multi          =  7;
-const int MPhysicalEvent::c_Unidentifiable =  100;
-
+/*
+const int c_UnknownEventEvent        = -1;
+const int c_ComptonEventEvent        =  0;
+const int c_PairEventEvent           =  1;
+const int c_MuonEventEvent           =  2;
+const int c_ShowerEvent         =  3;
+const int c_PhotoEventEvent          =  4;
+const int c_DecayEventEvent          =  5;
+const int c_PETEventEvent            =  6;
+const int c_MultiEventEvent          =  7;
+const int MPhysicalEvent::c_UnidentifiableEvent =  100;
+*/
 
 ////////////////////////////////////////////////////////////////////////////////
 
@@ -69,7 +69,7 @@ MPhysicalEvent::MPhysicalEvent() : MRotationInterface(), m_Time(0)
 {
   // default constructor
 
-  m_EventType = c_Unknown;
+  m_EventType = c_UnknownEvent;
 
   Reset();
 }
@@ -92,23 +92,23 @@ MString MPhysicalEvent::GetTypeString() const
   // Return the event type:
   
   MString String;
-  if (m_EventType == c_Compton) {
+  if (m_EventType == c_ComptonEvent) {
     String = "Compton";
-  } else if  (m_EventType == c_Pair) {
+  } else if  (m_EventType == c_PairEvent) {
     String = "Pair";
-  } else if  (m_EventType == c_Muon) {
+  } else if  (m_EventType == c_MuonEvent) {
     String = "Muon";
-  } else if  (m_EventType == c_Shower) {
+  } else if  (m_EventType == c_ShowerEvent) {
     String = "Shower";
-  } else if  (m_EventType == c_Photo) {
+  } else if  (m_EventType == c_PhotoEvent) {
     String = "Photo";
-  } else if  (m_EventType == c_Decay) {
+  } else if  (m_EventType == c_DecayEvent) {
     String = "Decay";
-  } else if  (m_EventType == c_PET) {
+  } else if  (m_EventType == c_PETEvent) {
     String = "PET";
-  } else if  (m_EventType == c_Multi) {
+  } else if  (m_EventType == c_MultiEvent) {
     String = "Multi";
-  } else if  (m_EventType == c_Unidentifiable) {
+  } else if  (m_EventType == c_UnidentifiableEvent) {
     String = "Unidentifiable";
   } else {
     String = "Unknown"; 
@@ -266,21 +266,21 @@ const MPhysicalEventHit& MPhysicalEvent::GetHit(unsigned int i) const
 MString MPhysicalEvent::GetTypeStringCode(int evtype)
 {
   switch (evtype) {
-    case c_Compton:
+    case c_ComptonEvent:
       return MString("CO");
-    case c_Pair:
+    case c_PairEvent:
       return MString("PA");
-    case c_Photo:
+    case c_PhotoEvent:
       return MString("PH");
-    case c_Muon:
+    case c_MuonEvent:
       return MString("MU");
-    case c_Decay:
+    case c_DecayEvent:
       return MString("DY");
-    case c_PET:
+    case c_PETEvent:
       return MString("PT");
-    case c_Multi:
+    case c_MultiEvent:
       return MString("MT");
-    case c_Unidentifiable:
+    case c_UnidentifiableEvent:
       return MString("UN");
     default:
       massert(false);
@@ -294,28 +294,28 @@ MString MPhysicalEvent::ToTraString() const
 
   ostringstream S;
 /*  switch (m_EventType) {
-  case c_Compton:
+  case c_ComptonEvent:
     S<<"ET CO"<<endl;
     break;
-  case c_Pair:
+  case c_PairEvent:
     S<<"ET PA"<<endl;
     break;
-  case c_Photo:
+  case c_PhotoEvent:
     S<<"ET PH"<<endl;
     break;
-  case c_Muon:
+  case c_MuonEvent:
     S<<"ET MU"<<endl;
     break;
-  case c_Decay:
+  case c_DecayEvent:
     S<<"ET DY"<<endl;
     break;
-  case c_PET:
+  case c_PETEvent:
     S<<"ET PT"<<endl;
     break;
-  case c_Multi:
+  case c_MultiEvent:
     S<<"ET MT"<<endl;
     break;
-  case c_Unidentifiable:
+  case c_UnidentifiableEvent:
     S<<"ET UN"<<endl;
     break;
   default:
@@ -417,17 +417,17 @@ bool MPhysicalEvent::ParseDelayed(bool Fast)
 ////////////////////////////////////////////////////////////////////////////////
 int MPhysicalEvent::ParseET(const char* type)
 {
-  if (type[0] == 'C' && type[1] == 'O') return c_Compton;
-  else if (type[0] == 'P' && type[1] == 'A') return c_Pair;
-  else if (type[0] == 'P' && type[1] == 'H') return c_Photo;
-  else if (type[0] == 'M' && type[1] == 'U') return c_Muon;
-  else if (type[0] == 'D' && type[1] == 'Y') return c_Decay;
-  else if (type[0] == 'P' && type[1] == 'T') return c_PET;
-  else if (type[0] == 'M' && type[1] == 'T') return c_Multi;
-  else if (type[0] == 'U' && type[1] == 'N') return c_Unidentifiable;
+  if (type[0] == 'C' && type[1] == 'O') return c_ComptonEvent;
+  else if (type[0] == 'P' && type[1] == 'A') return c_PairEvent;
+  else if (type[0] == 'P' && type[1] == 'H') return c_PhotoEvent;
+  else if (type[0] == 'M' && type[1] == 'U') return c_MuonEvent;
+  else if (type[0] == 'D' && type[1] == 'Y') return c_DecayEvent;
+  else if (type[0] == 'P' && type[1] == 'T') return c_PETEvent;
+  else if (type[0] == 'M' && type[1] == 'T') return c_MultiEvent;
+  else if (type[0] == 'U' && type[1] == 'N') return c_UnidentifiableEvent;
   else {
     mout<<"int MPhysicalEvent::ParseET: Unkown event type..."<<endl;
-    return c_Unknown;
+    return c_UnknownEvent;
   }
 }
 
@@ -449,42 +449,42 @@ int MPhysicalEvent::ParseLine(const char* Line, bool Fast)
       Ret = 1;
     }
 /*    if (Line[3] == 'C' && Line[4] == 'O') {
-      if (m_EventType != c_Compton) {
+      if (m_EventType != c_ComptonEvent) {
         cout<<"int MPhysicalEvent::ParseLine: Event is no Compton event as suggested but a "<<GetTypeString()<<"!"<<endl;
         Ret = 1;
       }
     } else if (Line[3] == 'P' && Line[4] == 'A') {
-      if (m_EventType != c_Pair) {
+      if (m_EventType != c_PairEvent) {
         cout<<"int MPhysicalEvent::ParseLine: Event is no Pair event as suggested but a "<<GetTypeString()<<"!"<<endl;
         Ret = 1;
       }
     } else if (Line[3] == 'P' && Line[4] == 'H') {
-      if (m_EventType != c_Photo) {
+      if (m_EventType != c_PhotoEvent) {
         cout<<"int MPhysicalEvent::ParseLine: Event is no Photo event as suggested but a "<<GetTypeString()<<"!"<<endl;
         Ret = 1;
       }
     } else if (Line[3] == 'M' && Line[4] == 'U') {
-      if (m_EventType != c_Muon) {
+      if (m_EventType != c_MuonEvent) {
         cout<<"int MPhysicalEvent::ParseLine: Event is no Muon event as suggested but a "<<GetTypeString()<<"!"<<endl;
         Ret = 1;
       }
     } else if (Line[3] == 'D' && Line[4] == 'Y') {
-      if (m_EventType != c_Decay) {
+      if (m_EventType != c_DecayEvent) {
         cout<<"int MPhysicalEvent::ParseLine: Event is no Decay event as suggested but a "<<GetTypeString()<<"!"<<endl;
         Ret = 1;
       }
     } else if (Line[3] == 'P' && Line[4] == 'T') {
-      if (m_EventType != c_PET) {
+      if (m_EventType != c_PETEvent) {
         cout<<"int MPhysicalEvent::ParseLine: Event is no PET event as suggested but a "<<GetTypeString()<<"!"<<endl;
         Ret = 1;
       }
     } else if (Line[3] == 'M' && Line[4] == 'T') {
-      if (m_EventType != c_Multi) {
+      if (m_EventType != c_MultiEvent) {
         cout<<"int MPhysicalEvent::ParseLine: Event is no Multi event as suggested but a "<<GetTypeString()<<"!"<<endl;
         Ret = 1;
       }
     } else if (Line[3] == 'U' && Line[4] == 'N') {
-      if (m_EventType != c_Unidentifiable) {
+      if (m_EventType != c_UnidentifiableEvent) {
         cout<<"int MPhysicalEvent::ParseLine: Event is no Unidentifiable event as suggested but a "<<GetTypeString()<<"!"<<endl;
         Ret = 1;
       }
diff --git a/src/global/misc/src/MUnidentifiableEvent.cxx b/src/global/misc/src/MUnidentifiableEvent.cxx
index 827d27364..f8a4c7a4c 100644
--- a/src/global/misc/src/MUnidentifiableEvent.cxx
+++ b/src/global/misc/src/MUnidentifiableEvent.cxx
@@ -52,7 +52,7 @@ MUnidentifiableEvent::MUnidentifiableEvent()
 {
   // standard constructor
 
-  m_EventType = c_Unidentifiable;
+  m_EventType = c_UnidentifiableEvent;
 
   Reset();
 }
@@ -113,7 +113,7 @@ bool MUnidentifiableEvent::Assimilate(MPhysicalEvent* Event)
 {
   // Simply Call: MUnidentifiableEvent::Assimilate(const MUnidentifiableEventData *UnidentifiableEventData)
 
-  if (Event->GetType() == MPhysicalEvent::c_Unidentifiable) {
+  if (Event->GetType() == c_UnidentifiableEvent) {
     return Assimilate((MUnidentifiableEvent *) Event);
   } else {
     return false; 
diff --git a/src/mimrec/src/MBackprojection.cxx b/src/mimrec/src/MBackprojection.cxx
index 4e5873e2e..2e8248722 100644
--- a/src/mimrec/src/MBackprojection.cxx
+++ b/src/mimrec/src/MBackprojection.cxx
@@ -137,8 +137,8 @@ bool MBackprojection::Assimilate(MPhysicalEvent* Event)
   if (MProjection::Assimilate(Event) == false) return false;
 
   // Let the response get the event data:
-  if (Event->GetType() == MPhysicalEvent::c_Compton || 
-      Event->GetType() == MPhysicalEvent::c_Pair) {
+  if (Event->GetType() == c_ComptonEvent || 
+      Event->GetType() == c_PairEvent) {
     if (m_Response->AnalyzeEvent(Event) == false) return false;
   }
 
diff --git a/src/mimrec/src/MBackprojectionFarField.cxx b/src/mimrec/src/MBackprojectionFarField.cxx
index 892d1f831..d453a12ae 100644
--- a/src/mimrec/src/MBackprojectionFarField.cxx
+++ b/src/mimrec/src/MBackprojectionFarField.cxx
@@ -279,9 +279,9 @@ bool MBackprojectionFarField::Assimilate(MPhysicalEvent *Event)
 
   if (MBackprojection::Assimilate(Event) == false) return false;
   
-  if (Event->GetType() == MPhysicalEvent::c_Compton || 
-      Event->GetType() == MPhysicalEvent::c_Pair || 
-      Event->GetType() == MPhysicalEvent::c_Photo) {
+  if (Event->GetType() == c_ComptonEvent || 
+      Event->GetType() == c_PairEvent || 
+      Event->GetType() == c_PhotoEvent) {
     return true;
   } else {
     return false;
@@ -302,11 +302,11 @@ bool MBackprojectionFarField::Backproject(MPhysicalEvent* Event, double* Image,
 
   if (Assimilate(Event) == false) return false;
 
-  if (Event->GetType() == MPhysicalEvent::c_Compton) {
+  if (Event->GetType() == c_ComptonEvent) {
     return BackprojectionCompton(Image, Bins, NUsedBins, Maximum);
-  } else if (Event->GetType() == MPhysicalEvent::c_Pair) {
+  } else if (Event->GetType() == c_PairEvent) {
     return BackprojectionPair(Image, Bins, NUsedBins, Maximum);
-  } else if (Event->GetType() == MPhysicalEvent::c_Photo) {
+  } else if (Event->GetType() == c_PhotoEvent) {
     return BackprojectionPhoto(Image, Bins, NUsedBins, Maximum);
   } else {
     cout<<"Error: Unknown event type for imaging: "<<Event->GetType()<<". Skipping event."<<endl;
diff --git a/src/mimrec/src/MBackprojectionNearField.cxx b/src/mimrec/src/MBackprojectionNearField.cxx
index 636ad5dd8..81de797d5 100644
--- a/src/mimrec/src/MBackprojectionNearField.cxx
+++ b/src/mimrec/src/MBackprojectionNearField.cxx
@@ -78,11 +78,11 @@ bool MBackprojectionNearField::Assimilate(MPhysicalEvent* Event)
   }
 
   // Those are the event types we handle:
-  if (Event->GetType() == MPhysicalEvent::c_Compton ||
-    Event->GetType() == MPhysicalEvent::c_Pair ||
-    Event->GetType() == MPhysicalEvent::c_Photo ||
-    Event->GetType() == MPhysicalEvent::c_PET ||
-    Event->GetType() == MPhysicalEvent::c_Multi) {
+  if (Event->GetType() == c_ComptonEvent ||
+    Event->GetType() == c_PairEvent ||
+    Event->GetType() == c_PhotoEvent ||
+    Event->GetType() == c_PETEvent ||
+    Event->GetType() == c_MultiEvent) {
     return true;
   }
 
@@ -101,13 +101,13 @@ bool MBackprojectionNearField::Backproject(MPhysicalEvent* Event, double* Image,
 
   if (MBackprojectionNearField::Assimilate(Event) == false) return false;
 
-  if (Event->GetType() == MPhysicalEvent::c_Compton) {
+  if (Event->GetType() == c_ComptonEvent) {
     return BackprojectionCompton(Image, Bins, NUsedBins, Maximum);
-  } else if (Event->GetType() == MPhysicalEvent::c_Pair) {
+  } else if (Event->GetType() == c_PairEvent) {
     return BackprojectionPair(Image, Bins, NUsedBins, Maximum);
-  } else if (Event->GetType() == MPhysicalEvent::c_PET) {
+  } else if (Event->GetType() == c_PETEvent) {
     return BackprojectionPET(Image, Bins, NUsedBins, Maximum);
-  } else if (Event->GetType() == MPhysicalEvent::c_Multi) {
+  } else if (Event->GetType() == c_MultiEvent) {
     return BackprojectionMulti(Image, Bins, NUsedBins, Maximum);
   } else  {
     cout<<"Near-field backprojection does not work for this event type: "<<Event->GetTypeString()<<endl;
@@ -579,7 +579,7 @@ bool MBackprojectionNearField::BackprojectionMulti(double* SparseImage, int* Spa
   bool First = true;
   for (unsigned int i = 0; i < Multi->GetNumberOfEvents(); ++i) {
     // It is not working for photo...
-    if (Multi->GetEvent(i)->GetType() == MPhysicalEvent::c_Photo) continue;
+    if (Multi->GetEvent(i)->GetType() == c_PhotoEvent) continue;
     
     Assimilate(Multi->GetEvent(i));
     NUsedBins = 0;
diff --git a/src/mimrec/src/MEarthHorizon.cxx b/src/mimrec/src/MEarthHorizon.cxx
index 9b9eb2a6f..e64d3a7dc 100644
--- a/src/mimrec/src/MEarthHorizon.cxx
+++ b/src/mimrec/src/MEarthHorizon.cxx
@@ -265,7 +265,7 @@ bool MEarthHorizon::IsEventFromEarth(MPhysicalEvent* Event, bool DumpOutput) con
 //! Return true if the event originates from Earth via intersection test
 bool MEarthHorizon::IsEventFromEarthByIntersectionTest(MPhysicalEvent* Event, bool DumpOutput) const
 {
-  if (Event->GetType() == MPhysicalEvent::c_Compton) {
+  if (Event->GetType() == c_ComptonEvent) {
     MComptonEvent* C = dynamic_cast<MComptonEvent*>(Event);
 
     double Phi = C->Phi();
@@ -287,7 +287,7 @@ bool MEarthHorizon::IsEventFromEarthByIntersectionTest(MPhysicalEvent* Event, bo
       }
       return true;
     }
-  } else if (Event->GetType() == MPhysicalEvent::c_Pair) {
+  } else if (Event->GetType() == c_PairEvent) {
     MPairEvent* P = dynamic_cast<MPairEvent*>(Event); 
     double AxisDist = m_PositionEarth.Angle(P->GetOrigin());
     
@@ -311,7 +311,7 @@ bool MEarthHorizon::IsEventFromEarthByProbabilityTest(MPhysicalEvent* Event, boo
 {
   massert(Event != 0);
 
-  if (Event->GetType() == MPhysicalEvent::c_Compton) {
+  if (Event->GetType() == c_ComptonEvent) {
     MComptonEvent* C = dynamic_cast<MComptonEvent*>(Event);
 
     // Take care of scatter angles larger than 90 deg:
@@ -472,7 +472,7 @@ bool MEarthHorizon::IsEventFromEarthByProbabilityTest(MPhysicalEvent* Event, boo
         }
       }
     } 
-  } else if (Event->GetType() == MPhysicalEvent::c_Pair) {
+  } else if (Event->GetType() == c_PairEvent) {
     MPairEvent* P = dynamic_cast<MPairEvent*>(Event); 
     double AxisDist = m_PositionEarth.Angle(P->GetOrigin());
     
diff --git a/src/mimrec/src/MEventSelector.cxx b/src/mimrec/src/MEventSelector.cxx
index 5e6709cb9..81ea866d4 100644
--- a/src/mimrec/src/MEventSelector.cxx
+++ b/src/mimrec/src/MEventSelector.cxx
@@ -538,9 +538,9 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
 
 //   double Radius = 1.27;
 //   MVector Pos;
-//   if (Event->GetType() == MPhysicalEvent::c_Compton ||
-//       Event->GetType() == MPhysicalEvent::c_Pair) {
-//     if (Event->GetType() == MPhysicalEvent::c_Compton) {
+//   if (Event->GetType() == c_ComptonEvent ||
+//       Event->GetType() == c_PairEvent) {
+//     if (Event->GetType() == c_ComptonEvent) {
 //       Pos = ((MComptonEvent *) Event)->C1();
 //     } else {
 //       Pos = ((MPairEvent *) Event)->GetPairCreationIA();
@@ -575,7 +575,7 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
 //   // Second hit has to be in bottom calorimeters:
 //   MVector BottomCenter(0, 0, 6.3);
 //   MVector BottomDim(9, 8, 6); //4);
-//   if (Event->GetType() == MPhysicalEvent::c_Compton) {
+//   if (Event->GetType() == c_ComptonEvent) {
 //     MVector Pos = ((MComptonEvent *) Event)->C2();
 //     Pos -= BottomCenter;
 //     if (fabs(Pos[0]) - BottomDim[0] > 0 || fabs(Pos[1]) - BottomDim[1] > 0 || fabs(Pos[2]) - BottomDim[2] > 0) {
@@ -607,7 +607,7 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
   // Only start in certain detectors - needs an active geometry
   if (m_Geometry != 0) {
     if (m_ExcludedFirstIADetectors.size() > 0) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton || Event->GetType() == MPhysicalEvent::c_Pair || Event->GetType() == MPhysicalEvent::c_Photo) {
+      if (Event->GetType() == c_ComptonEvent || Event->GetType() == c_PairEvent || Event->GetType() == c_PhotoEvent) {
         MDVolumeSequence V = m_Geometry->GetVolumeSequence(Event->GetPosition(), true, false);
         if (V.GetDetector() == 0) {
           cout<<"ID "<<Event->GetId()<<": You have a hit without detector! --> You probably selected the wrong geometry: "<<Event->GetPosition()<<endl;
@@ -626,7 +626,7 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
       }
     }
     if (m_ExcludedSecondIADetectors.size() > 0) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         MComptonEvent* C = (MComptonEvent *) Event;
         MDVolumeSequence V = m_Geometry->GetVolumeSequence(C->C2(), true, false);
         if (V.GetDetector() == 0) {
@@ -721,9 +721,9 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
     Return = false;
   }
   if (m_UseBeam == true) {
-    if (Event->GetType() == MPhysicalEvent::c_Photo ||
-        Event->GetType() == MPhysicalEvent::c_Compton ||
-        Event->GetType() == MPhysicalEvent::c_Pair) {
+    if (Event->GetType() == c_PhotoEvent ||
+        Event->GetType() == c_ComptonEvent ||
+        Event->GetType() == c_PairEvent) {
       MVector Position = Event->GetPosition();
       // The same equations appear in MResponseMultipleComptonLens
       double Radius = (Position - m_BeamFocalSpot).Cross(m_BeamStart - m_BeamFocalSpot).Mag()/(m_BeamStart - m_BeamFocalSpot).Mag();
@@ -740,9 +740,9 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
     }
   }
   if (m_UseBox == true) {
-    if (Event->GetType() == MPhysicalEvent::c_Photo ||
-        Event->GetType() == MPhysicalEvent::c_Compton || 
-        Event->GetType() == MPhysicalEvent::c_Pair) {
+    if (Event->GetType() == c_PhotoEvent ||
+        Event->GetType() == c_ComptonEvent || 
+        Event->GetType() == c_PairEvent) {
       MVector Position = Event->GetPosition();
 
       if (m_BoxFirstIAMin.AtLeastOneSmaller(Position) == true || m_BoxFirstIAMax.AtLeastOneLarger(Position) == true) {
@@ -754,7 +754,7 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
         Return = false;
       }
       
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         Position = dynamic_cast<MComptonEvent*>(Event)->C2();
         if (m_BoxSecondIAMin.AtLeastOneSmaller(Position) == true || m_BoxSecondIAMax.AtLeastOneLarger(Position) == true) {
           if (DumpOutput == true) {
@@ -810,7 +810,7 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
   // ATTENTION: PUT ALL CHANGES HERE INTO BOTH (FAST & DETAILED) VERSION OF THIS FUNCTION
 
   // Compton events:
-  if (Event->GetType() == MPhysicalEvent::c_Compton) {
+  if (Event->GetType() == c_ComptonEvent) {
     MComptonEvent *C = (MComptonEvent *) Event;
 
     // Deselect bottom calorimeters in MPE prototype
@@ -995,7 +995,7 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
 
   // ATTENTION: PUT ALL CHANGES HERE INTO BOTH (FAST & DETAILED) VERSION OF THIS FUNCTION
 
-  } else if (Event->GetType() == MPhysicalEvent::c_Pair) {
+  } else if (Event->GetType() == c_PairEvent) {
     MPairEvent* Pair = (MPairEvent*) Event;
 
     if (m_UsePairs == false) {
@@ -1058,7 +1058,7 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
 
   // ATTENTION: PUT ALL CHANGES HERE INTO BOTH (FAST & DETAILED) VERSION OF THIS FUNCTION
 
-  } else if (Event->GetType() == MPhysicalEvent::c_Photo) {
+  } else if (Event->GetType() == c_PhotoEvent) {
     //MPhotoEvent* Photo = (MPhotoEvent*) Event;
 
     if (m_UsePhotos == false) {
@@ -1068,19 +1068,19 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
       m_NRejectedUsePhotos++;
       Return = false;
     }
-  } else if (Event->GetType() == MPhysicalEvent::c_Muon) {
+  } else if (Event->GetType() == c_MuonEvent) {
     if (DumpOutput == true) {
       cout<<"ID "<<Event->GetId()<<": Unwanted muon event!"<<endl;
     }
     m_NRejectedUseMuons++;
     Return = false;
-  } else if (Event->GetType() == MPhysicalEvent::c_Decay) {
+  } else if (Event->GetType() == c_DecayEvent) {
     if (DumpOutput == true) {
       cout<<"ID "<<Event->GetId()<<": Unwanted decay event!"<<endl;
     }
     m_NRejectedUseDecays++;
     Return = false;
-  } else if (Event->GetType() == MPhysicalEvent::c_Unidentifiable) {
+  } else if (Event->GetType() == c_UnidentifiableEvent) {
     if (m_UseUnidentifiables == false) {
       if (DumpOutput == true) {
         cout<<"ID "<<Event->GetId()<<": Unwanted unidentifiable event!"<<endl;
@@ -1088,7 +1088,7 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
       m_NRejectedUseUnidentifiables++;
       Return = false;
     }
-  } else if (Event->GetType() == MPhysicalEvent::c_PET) {
+  } else if (Event->GetType() == c_PETEvent) {
     if (m_UsePETs == false) {
       if (DumpOutput == true) {
         cout<<"ID "<<Event->GetId()<<": Unwanted PET event!"<<endl;
@@ -1096,7 +1096,7 @@ bool MEventSelector::IsQualifiedEvent(MPhysicalEvent* Event, bool DumpOutput)
       m_NRejectedUsePETs++;
       Return = false;
     }
-  } else if (Event->GetType() == MPhysicalEvent::c_Multi) {
+  } else if (Event->GetType() == c_MultiEvent) {
     if (m_UseMulties == false) {
       if (DumpOutput == true) {
         cout<<"ID "<<Event->GetId()<<": Unwanted multi event!"<<endl;
@@ -1151,7 +1151,7 @@ bool MEventSelector::IsQualifiedEventFast(MPhysicalEvent* Event)
 
 
   // Compton events:
-  if (Event->GetType() == MPhysicalEvent::c_Compton) {
+  if (Event->GetType() == c_ComptonEvent) {
     MComptonEvent *C = (MComptonEvent *) Event;
 
 
@@ -1239,7 +1239,7 @@ bool MEventSelector::IsQualifiedEventFast(MPhysicalEvent* Event)
 
   // ATTENTION: PUT ALL CHANGES HERE INTO BOTH (FAST & DETAILED) VERSION OF THIS FUNCTION
 
-  } else if (Event->GetType() == MPhysicalEvent::c_Pair) {
+  } else if (Event->GetType() == c_PairEvent) {
     MPairEvent* Pair = (MPairEvent*) Event;
 
     if (m_UsePairs == false) {
@@ -1271,25 +1271,25 @@ bool MEventSelector::IsQualifiedEventFast(MPhysicalEvent* Event)
 
   // ATTENTION: PUT ALL CHANGES HERE INTO BOTH (FAST & DETAILED) VERSION OF THIS FUNCTION
 
-  } else if (Event->GetType() == MPhysicalEvent::c_Photo) {
+  } else if (Event->GetType() == c_PhotoEvent) {
     //MPhotoEvent* Photo = (MPhotoEvent*) Event;
 
     if (m_UsePhotos == false) {
       return false;
     }
-  } else if (Event->GetType() == MPhysicalEvent::c_Muon) {
+  } else if (Event->GetType() == c_MuonEvent) {
     return false;
-  } else if (Event->GetType() == MPhysicalEvent::c_Decay) {
+  } else if (Event->GetType() == c_DecayEvent) {
     return false;
-  } else if (Event->GetType() == MPhysicalEvent::c_PET) {
+  } else if (Event->GetType() == c_PETEvent) {
     if (m_UsePETs == false) {
       return false;
     }
-  } else if (Event->GetType() == MPhysicalEvent::c_Multi) {
+  } else if (Event->GetType() == c_MultiEvent) {
     if (m_UseMulties == false) {
       return false;
     }
-  } else if (Event->GetType() == MPhysicalEvent::c_Unidentifiable) {
+  } else if (Event->GetType() == c_UnidentifiableEvent) {
     if (m_UseUnidentifiables == false) {
       return false;
     }
@@ -1326,9 +1326,9 @@ bool MEventSelector::IsQualifiedEventFast(MPhysicalEvent* Event)
   // ATTENTION: PUT ALL CHANGES HERE INTO BOTH (FAST & DETAILED) VERSION OF THIS FUNCTION
 
   if (m_UseBeam == true) {
-    if (Event->GetType() == MPhysicalEvent::c_Photo ||
-        Event->GetType() == MPhysicalEvent::c_Compton ||
-        Event->GetType() == MPhysicalEvent::c_Pair) {
+    if (Event->GetType() == c_PhotoEvent ||
+        Event->GetType() == c_ComptonEvent ||
+        Event->GetType() == c_PairEvent) {
       MVector Position = Event->GetPosition();
       // The same equations appear in MResponseMultipleComptonLens
       double Radius = (Position - m_BeamFocalSpot).Cross(m_BeamStart - m_BeamFocalSpot).Mag()/(m_BeamStart - m_BeamFocalSpot).Mag();
@@ -1341,16 +1341,16 @@ bool MEventSelector::IsQualifiedEventFast(MPhysicalEvent* Event)
   }
   
   if (m_UseBox == true) {
-    if (Event->GetType() == MPhysicalEvent::c_Photo ||
-        Event->GetType() == MPhysicalEvent::c_Compton || 
-        Event->GetType() == MPhysicalEvent::c_Pair) {
+    if (Event->GetType() == c_PhotoEvent ||
+        Event->GetType() == c_ComptonEvent || 
+        Event->GetType() == c_PairEvent) {
       MVector Position = Event->GetPosition();
 
       if (m_BoxFirstIAMin.AtLeastOneSmaller(Position) == true || m_BoxFirstIAMax.AtLeastOneLarger(Position) == true) {
         return false;
       }
       
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         Position = dynamic_cast<MComptonEvent*>(Event)->C2();
         if (m_BoxSecondIAMin.AtLeastOneSmaller(Position) == true || m_BoxSecondIAMax.AtLeastOneLarger(Position) == true) {
           return false;
@@ -1391,7 +1391,7 @@ bool MEventSelector::IsQualifiedEventFast(MPhysicalEvent* Event)
   // Only start in certain detectors - needs an active geometry
   if (m_Geometry != 0) {
     if (m_ExcludedFirstIADetectors.size() > 0) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton || Event->GetType() == MPhysicalEvent::c_Pair || Event->GetType() == MPhysicalEvent::c_Photo) {
+      if (Event->GetType() == c_ComptonEvent || Event->GetType() == c_PairEvent || Event->GetType() == c_PhotoEvent) {
         MDVolumeSequence V = m_Geometry->GetVolumeSequence(Event->GetPosition(), true, false);
         if (V.GetDetector() == 0) {
           cout<<"ID "<<Event->GetId()<<": You have a hit without detector! --> You probably selected the wrong geometry: "<<Event->GetPosition()<<endl;
@@ -1405,7 +1405,7 @@ bool MEventSelector::IsQualifiedEventFast(MPhysicalEvent* Event)
       }
     }
     if (m_ExcludedSecondIADetectors.size() > 0) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         MComptonEvent* C = (MComptonEvent*) Event;
         MDVolumeSequence V = m_Geometry->GetVolumeSequence(C->C2(), true, false);
         if (V.GetDetector() == 0) {
diff --git a/src/mimrec/src/MInterfaceMimrec.cxx b/src/mimrec/src/MInterfaceMimrec.cxx
index 0ac8d6508..860fa60fd 100644
--- a/src/mimrec/src/MInterfaceMimrec.cxx
+++ b/src/mimrec/src/MInterfaceMimrec.cxx
@@ -1080,7 +1080,7 @@ void MInterfaceMimrec::ThetaOriginDistribution()
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
       if (Event->GetOrigin() != g_VectorNotDefined) {
-        if (Event->GetType() == MPhysicalEvent::c_Compton) {
+        if (Event->GetType() == c_ComptonEvent) {
           Hist->Fill(dynamic_cast<MComptonEvent*>(Event)->Di().Theta()*c_Deg);
         } else {
           Hist->Fill(Event->GetOrigin().Theta()*c_Deg);
@@ -1142,7 +1142,7 @@ void MInterfaceMimrec::ARMGamma()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
         Fitter.AddARMValue(ComptonEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem())*c_Deg);
         FoundEvents = true;
@@ -1233,7 +1233,7 @@ void MInterfaceMimrec::ARMGammaClassic()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
         Value = ComptonEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem());
@@ -1245,7 +1245,7 @@ void MInterfaceMimrec::ARMGammaClassic()
         Average += ComptonEvent->Phi()*c_Deg;
         NEvents++;
         NAverages++;
-//       } else if (Event->GetType() == MPhysicalEvent::c_Pair) {
+//       } else if (Event->GetType() == c_PairEvent) {
 //         PairEvent = dynamic_cast<MPairEvent*>(Event);
 
 //         Value = PairEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem());
@@ -1621,7 +1621,7 @@ void MInterfaceMimrec::DualARM()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
         xValue = ComptonEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem());
@@ -1746,7 +1746,7 @@ void MInterfaceMimrec::ARMResponseComparison()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
         double ARM = ComptonEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem())*c_Deg;
         ARMHist->Fill(ARM, 1);
@@ -1831,7 +1831,7 @@ void MInterfaceMimrec::AngularResolutionPairs()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Pair) {
+      if (Event->GetType() == c_PairEvent) {
         PairEvent = dynamic_cast<MPairEvent*>(Event);
 
         Value = PairEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem());
@@ -1959,7 +1959,7 @@ void MInterfaceMimrec::ResolutionMeasurePET()
     
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_PET) {
+      if (Event->GetType() == c_PETEvent) {
         PETEvent = dynamic_cast<MPETEvent*>(Event);
         
         Value = PETEvent->GetResolutionMeasure(TestPosition, m_Settings->GetCoordinateSystem());
@@ -2054,7 +2054,7 @@ void MInterfaceMimrec::PhiKinVsPhiGeo()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
         // Comtpon scatter angle via geometry - take care of coordinate systems:
@@ -2132,7 +2132,7 @@ void MInterfaceMimrec::ARMGammaVsComptonScatterAngle()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
         Hist->Fill(ComptonEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem())*c_Deg,
@@ -2217,7 +2217,7 @@ void MInterfaceMimrec::ARMGammaVsDistance()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
         Hist->Fill(ComptonEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem())*c_Deg,
@@ -2402,7 +2402,7 @@ void MInterfaceMimrec::SignificanceMap()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
         // Go through each bin and record the counts
         for (int i_X=0; i_X<NBinsXAngle; i_X++) {
@@ -2864,7 +2864,7 @@ void MInterfaceMimrec::SPDElectronVsCompton()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
         Hist->Fill(ComptonEvent->GetSPDElectron(TestPosition)*c_Deg,
@@ -2997,7 +2997,7 @@ void MInterfaceMimrec::ComptonProbabilityWithARMSelection()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
         ArmValue = ComptonEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem())*c_Deg;
@@ -3064,7 +3064,7 @@ void MInterfaceMimrec::ARMGammaVsComptonProbability()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
         ARMValues.push_back(ComptonEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem())*c_Deg);
@@ -3158,7 +3158,7 @@ void MInterfaceMimrec::ARMGammaVsClusteringProbability()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
         Hist->Fill(ComptonEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem())*c_Deg,
@@ -3245,7 +3245,7 @@ void MInterfaceMimrec::SPDVsTrackQualityFactor()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
         Hist->Fill(ComptonEvent->GetSPDElectron(TestPosition)*c_Deg,
@@ -3320,7 +3320,7 @@ void MInterfaceMimrec::SPDVsTotalScatterAngleDeviation()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
         Hist->Fill(ComptonEvent->GetSPDElectron(TestPosition)*c_Deg,
@@ -3410,7 +3410,7 @@ void MInterfaceMimrec::EnergyVsComptonProbability()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
         Hist->Fill(ComptonEvent->Ei(),
@@ -3483,7 +3483,7 @@ void MInterfaceMimrec::ComptonSequenceLengthVsComptonProbability()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         Compton = dynamic_cast<MComptonEvent*>(Event);
 
         if (Compton->SequenceLength() > MaxSequenceLength) MaxSequenceLength = Compton->SequenceLength();
@@ -3573,7 +3573,7 @@ void MInterfaceMimrec::SPDElectron()
       delete Event;
       continue;
     }
-    if (Event->GetType() != MPhysicalEvent::c_Compton) {
+    if (Event->GetType() != c_ComptonEvent) {
       delete Event;
       continue;
     }
@@ -3734,7 +3734,7 @@ void MInterfaceMimrec::ARMElectron()
       delete Event;
       continue;
     }
-    if (Event->GetType() != MPhysicalEvent::c_Compton) {
+    if (Event->GetType() != c_ComptonEvent) {
       delete Event;
       continue;
     }
@@ -3934,7 +3934,7 @@ void MInterfaceMimrec::EnergySpectra()
     }
 
     if (UseTestPosition == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         if (fabs(((MComptonEvent*) Event)->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem()))*c_Deg < Disk) {
           InsideWindow++;
           Hist->Fill(Event->GetEnergy());
@@ -3943,7 +3943,7 @@ void MInterfaceMimrec::EnergySpectra()
         } else {
           OutsideWindow++;
         }
-      } else if (Event->GetType() == MPhysicalEvent::c_Pair) {
+      } else if (Event->GetType() == c_PairEvent) {
         if (fabs(((MPairEvent*) Event)->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem()))*c_Deg < Disk) {
           InsideWindow++;
           Hist->Fill(Event->GetEnergy());
@@ -4106,7 +4106,7 @@ void MInterfaceMimrec::InitialEnergyDeposit()
       continue;
     }
 
-    if (Event->GetType() == MPhysicalEvent::c_Pair) {
+    if (Event->GetType() == c_PairEvent) {
       Hist->Fill(((MPairEvent*) Event)->GetInitialEnergyDeposit());
     }
 
@@ -4185,7 +4185,7 @@ void MInterfaceMimrec::EnergyDistributionElectronPhoton()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         Compton = dynamic_cast<MComptonEvent*>(Event);
         if (UseTestPosition == true) {
           if (fabs(Compton->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem()))*c_Deg < Disk) {
@@ -4289,10 +4289,10 @@ void MInterfaceMimrec::TimeWalkArmDistribution()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
         TWHist->Fill(Event->GetTimeWalk(), fabs(ComptonEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem()))*c_Deg);
-      } else if (Event->GetType() == MPhysicalEvent::c_Pair) {
+      } else if (Event->GetType() == c_PairEvent) {
         PairEvent = dynamic_cast<MPairEvent*>(Event);
         TWHist->Fill(Event->GetTimeWalk(), fabs(PairEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem()))*c_Deg);
       }
@@ -4397,7 +4397,7 @@ void MInterfaceMimrec::ScatterAnglesDistribution()
       delete Event;
       continue;
     }
-    if (Event->GetType() != MPhysicalEvent::c_Compton) {
+    if (Event->GetType() != c_ComptonEvent) {
       delete Event;
       continue;
     }
@@ -4551,7 +4551,7 @@ void MInterfaceMimrec::ClusteringQualityFactor()
       delete Event;
       continue;
     }
-    if (Event->GetType() != MPhysicalEvent::c_Compton) {
+    if (Event->GetType() != c_ComptonEvent) {
       delete Event;
       continue;
     }
@@ -4620,7 +4620,7 @@ void MInterfaceMimrec::ComptonQualityFactor()
       delete Event;
       continue;
     }
-    if (Event->GetType() != MPhysicalEvent::c_Compton) {
+    if (Event->GetType() != c_ComptonEvent) {
       delete Event;
       continue;
     }
@@ -4689,7 +4689,7 @@ void MInterfaceMimrec::TrackQualityFactor()
       delete Event;
       continue;
     }
-    if (Event->GetType() != MPhysicalEvent::c_Compton) {
+    if (Event->GetType() != c_ComptonEvent) {
       delete Event;
       continue;
     }
@@ -4753,7 +4753,7 @@ void MInterfaceMimrec::EarthCenterDistance()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true &&
-        Event->GetType() == MPhysicalEvent::c_Compton) {
+        Event->GetType() == c_ComptonEvent) {
       Compton = (MComptonEvent*) Event;
       Hist->Fill(Compton->GetARMGamma(Position, m_Settings->GetCoordinateSystem())*c_Deg);
       NEvents++;
@@ -4825,7 +4825,7 @@ void MInterfaceMimrec::DistanceDistribution()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true &&
-        Event->GetType() == MPhysicalEvent::c_Compton) {
+        Event->GetType() == c_ComptonEvent) {
       Compton = (MComptonEvent*) Event;
       FirstHist->Fill((Compton->C2()-Compton->C1()).Mag());
       AnyHist->Fill(Compton->LeverArm());
@@ -4932,7 +4932,7 @@ void MInterfaceMimrec::SequenceLengths()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true &&
-        Event->GetType() == MPhysicalEvent::c_Compton) {
+        Event->GetType() == c_ComptonEvent) {
       Compton = (MComptonEvent*) Event;
       if (Compton->TrackLength() > MaxTrackLength) MaxTrackLength = Compton->TrackLength();
       TrackHist->Fill(Compton->TrackLength());
@@ -5176,7 +5176,7 @@ void MInterfaceMimrec::CoincidenceWindowDistribution()
   // First check on the size of the histogram:
   MComptonEvent* ComptonEvent;
   while ((Event = GetNextEvent()) != 0) {
-    if (Event->GetType() == MPhysicalEvent::c_Compton) {
+    if (Event->GetType() == c_ComptonEvent) {
       ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
       if (ComptonEvent->CoincidenceWindow().GetAsDouble() < MinTime) MinTime = ComptonEvent->CoincidenceWindow().GetAsDouble();
@@ -5266,7 +5266,7 @@ void MInterfaceMimrec::LocationOfFirstIA()
       continue;
     }
 
-    if (Event->GetType() == MPhysicalEvent::c_Compton) Compton.Assimilate(dynamic_cast<MComptonEvent*>(Event));
+    if (Event->GetType() == c_ComptonEvent) Compton.Assimilate(dynamic_cast<MComptonEvent*>(Event));
 
     //cout<<Compton.GetSecondComptonIA().X()<<"!"<<Compton.GetSecondComptonIA().Y()<<endl;
     x = (int) ((Compton.C2().X() - x1Min)/x1BinWidth);
@@ -5362,7 +5362,7 @@ void MInterfaceMimrec::Polarization()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
 
@@ -5382,7 +5382,7 @@ void MInterfaceMimrec::Polarization()
         } else {
           OutsideArmCutSource++;
         }
-      } else if (Event->GetType() == MPhysicalEvent::c_Pair) {
+      } else if (Event->GetType() == c_PairEvent) {
         PairEvent = dynamic_cast<MPairEvent*>(Event);
 
         if (fabs(PairEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem()))*c_Deg < ArmCut) {
@@ -5436,7 +5436,7 @@ void MInterfaceMimrec::Polarization()
 
     // Only accept Comptons within the selected ranges...
     if (SecondSelector.IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
         if (fabs(ComptonEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem()))*c_Deg < ArmCut) {
@@ -5455,7 +5455,7 @@ void MInterfaceMimrec::Polarization()
         } else {
           OutsideArmCutBackground++;
         }
-      } else if (Event->GetType() == MPhysicalEvent::c_Pair) {
+      } else if (Event->GetType() == c_PairEvent) {
         PairEvent = dynamic_cast<MPairEvent*>(Event);
 
         if (fabs(PairEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem()))*c_Deg < ArmCut) {
@@ -5700,7 +5700,7 @@ void MInterfaceMimrec::AzimuthalComptonScatterAngle()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
         if (fabs(ComptonEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem()))*c_Deg < Disk) {
 
@@ -5784,7 +5784,7 @@ void MInterfaceMimrec::AzimuthalElectronScatterAngle()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
         if (ComptonEvent->HasTrack() == true) {
           if (fabs(ComptonEvent->GetARMGamma(Origin, m_Settings->GetCoordinateSystem()))*c_Deg < ArmCut) {
@@ -5857,7 +5857,7 @@ void MInterfaceMimrec::OpeningAnglePair()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Pair) {
+      if (Event->GetType() == c_PairEvent) {
         PairEvent = dynamic_cast<MPairEvent*>(Event);
         Hist->Fill(PairEvent->GetOpeningAngle()*c_Deg);
       }
@@ -5917,7 +5917,7 @@ void MInterfaceMimrec::AngularResolutionVsQualityFactorPair()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Pair) {
+      if (Event->GetType() == c_PairEvent) {
         PairEvent = dynamic_cast<MPairEvent*>(Event);
 
         Value = PairEvent->GetARMGamma(TestPosition, m_Settings->GetCoordinateSystem());
@@ -5984,7 +5984,7 @@ void MInterfaceMimrec::DirectionScatteredGammaRay()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
         Hist->Fill(ComptonEvent->Dg().Phi()*c_Deg, ComptonEvent->Dg().Theta()*c_Deg);
@@ -6095,7 +6095,7 @@ void MInterfaceMimrec::InteractionDepth()
 
     // Only accept Comptons within the selected ranges...
     if (m_Selector->IsQualifiedEventFast(Event) == true) {
-      if (Event->GetType() == MPhysicalEvent::c_Compton) {
+      if (Event->GetType() == c_ComptonEvent) {
         ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
         D1->Fill(ComptonEvent->C1()[2]);
         D2->Fill(ComptonEvent->C2()[2]);
diff --git a/src/mimrec/src/MProjection.cxx b/src/mimrec/src/MProjection.cxx
index 0aca38f69..499ff9693 100644
--- a/src/mimrec/src/MProjection.cxx
+++ b/src/mimrec/src/MProjection.cxx
@@ -96,15 +96,15 @@ bool MProjection::Assimilate(MPhysicalEvent* Event)
   m_PET = nullptr;
   m_Multi = nullptr;
 
-  if (Event->GetType() == MPhysicalEvent::c_Compton) {
+  if (Event->GetType() == c_ComptonEvent) {
     m_C = dynamic_cast<MComptonEvent*>(Event);
-  } else if (Event->GetType() == MPhysicalEvent::c_Pair) {
+  } else if (Event->GetType() == c_PairEvent) {
     m_P = dynamic_cast<MPairEvent*>(Event);
-  } else if (Event->GetType() == MPhysicalEvent::c_Photo) {
+  } else if (Event->GetType() == c_PhotoEvent) {
     m_Photo = dynamic_cast<MPhotoEvent*>(Event);
-  } else if (Event->GetType() == MPhysicalEvent::c_PET) {
+  } else if (Event->GetType() == c_PETEvent) {
     m_PET = dynamic_cast<MPETEvent*>(Event);
-  } else if (Event->GetType() == MPhysicalEvent::c_Multi) {
+  } else if (Event->GetType() == c_MultiEvent) {
     m_Multi = dynamic_cast<MMultiEvent*>(Event);
   } else {
     cout<<"Unhandled event type: "<<Event->GetTypeString()<<endl;
diff --git a/src/mimrec/src/MResponseConeShapes.cxx b/src/mimrec/src/MResponseConeShapes.cxx
index 8b90f328a..b0343c7d2 100644
--- a/src/mimrec/src/MResponseConeShapes.cxx
+++ b/src/mimrec/src/MResponseConeShapes.cxx
@@ -133,7 +133,7 @@ bool MResponseConeShapes::AnalyzeEvent(MPhysicalEvent* Event)
   //if (Passes++ < 10) return false;
   //if (Passes > 80) return false;
 
-  if (Event->GetType() == MPhysicalEvent::c_Compton) {
+  if (Event->GetType() == c_ComptonEvent) {
     MComptonEvent* Compton = dynamic_cast<MComptonEvent*>(Event);
     m_Ei = Compton->Ei();
     m_Phi = Compton->Phi()*c_Deg;
diff --git a/src/mimrec/src/MResponseEnergyLeakage.cxx b/src/mimrec/src/MResponseEnergyLeakage.cxx
index 24850b199..eee168f82 100644
--- a/src/mimrec/src/MResponseEnergyLeakage.cxx
+++ b/src/mimrec/src/MResponseEnergyLeakage.cxx
@@ -265,7 +265,7 @@ bool MResponseEnergyLeakage::AnalyzeEvent(MPhysicalEvent* Event)
 
   // Only the Compton angle is of interest:
 
-  if (Event->GetType() == MPhysicalEvent::c_Compton) {
+  if (Event->GetType() == c_ComptonEvent) {
     if (((MComptonEvent*) Event)->HasTrack() == false) return false;
     m_Compton = (MComptonEvent*) Event;
     
diff --git a/src/mimrec/src/MResponseGaussian.cxx b/src/mimrec/src/MResponseGaussian.cxx
index 8c8b7c89c..6119d1e85 100644
--- a/src/mimrec/src/MResponseGaussian.cxx
+++ b/src/mimrec/src/MResponseGaussian.cxx
@@ -261,13 +261,13 @@ bool MResponseGaussian::AnalyzeEvent(MPhysicalEvent* Event)
   // Extract all necessary information out of the event:
 
   // Only the Compton angle is of interest:
-  if (Event->GetType() == MPhysicalEvent::c_Compton) {
+  if (Event->GetType() == c_ComptonEvent) {
     m_Phi = dynamic_cast<MComptonEvent*>(Event)->Phi();
     m_HasTrack = dynamic_cast<MComptonEvent*>(Event)->HasTrack();
     return true;
-  } else if (Event->GetType() == MPhysicalEvent::c_Pair) {
+  } else if (Event->GetType() == c_PairEvent) {
     return true;
-  } else if (Event->GetType() == MPhysicalEvent::c_PET) {
+  } else if (Event->GetType() == c_PETEvent) {
     return true;
   }
 
diff --git a/src/mimrec/src/MResponseGaussianARM.cxx b/src/mimrec/src/MResponseGaussianARM.cxx
index cd47c597f..d487c2078 100644
--- a/src/mimrec/src/MResponseGaussianARM.cxx
+++ b/src/mimrec/src/MResponseGaussianARM.cxx
@@ -270,11 +270,11 @@ bool MResponseGaussian::AnalyzeEvent(MPhysicalEvent* Event)
   // Extract all necessary information out of the event:
 
   // Only the Compton angle is of interest:
-  if (Event->GetType() == MPhysicalEvent::c_Compton) {
+  if (Event->GetType() == c_ComptonEvent) {
     m_Phi = dynamic_cast<MComptonEvent*>(Event)->Phi();
     m_HasTrack = dynamic_cast<MComptonEvent*>(Event)->HasTrack();
     return true;
-  } else if (Event->GetType() == MPhysicalEvent::c_Pair) {
+  } else if (Event->GetType() == c_PairEvent) {
     return true;
   }
 
diff --git a/src/mimrec/src/MResponseGaussianByUncertainties.cxx b/src/mimrec/src/MResponseGaussianByUncertainties.cxx
index d9ae00fc6..d81423291 100644
--- a/src/mimrec/src/MResponseGaussianByUncertainties.cxx
+++ b/src/mimrec/src/MResponseGaussianByUncertainties.cxx
@@ -84,7 +84,7 @@ bool MResponseGaussianByUncertainties::AnalyzeEvent(MPhysicalEvent* Event)
   // Extract all necessary information out of the event:
 
   // Only the Compton angle is of interest:
-  if (Event->GetType() == MPhysicalEvent::c_Compton) {
+  if (Event->GetType() == c_ComptonEvent) {
     m_Phi = dynamic_cast<MComptonEvent*>(Event)->Phi();
     m_HasTrack = dynamic_cast<MComptonEvent*>(Event)->HasTrack();
     
@@ -99,7 +99,7 @@ bool MResponseGaussianByUncertainties::AnalyzeEvent(MPhysicalEvent* Event)
     SetGaussians(dPhi, 30, 2, 1);
      
     return true;
-  } else if (Event->GetType() == MPhysicalEvent::c_Pair) {
+  } else if (Event->GetType() == c_PairEvent) {
     return true;
   }
 
diff --git a/src/mimrec/src/MResponsePRM.cxx b/src/mimrec/src/MResponsePRM.cxx
index df0d1bb85..af98a6c27 100644
--- a/src/mimrec/src/MResponsePRM.cxx
+++ b/src/mimrec/src/MResponsePRM.cxx
@@ -159,7 +159,7 @@ bool MResponsePRM::AnalyzeEvent(MPhysicalEvent* Event)
 {
   // Extract all necessary information out of the event:
 
-  if (Event->GetType() == MPhysicalEvent::c_Compton) {
+  if (Event->GetType() == c_ComptonEvent) {
     MComptonEvent* Compton = dynamic_cast<MComptonEvent*>(Event);
     m_Ei = Compton->Ei();
     m_Ee = Compton->Ee();
diff --git a/src/mimrec/src/MStandardAnalysis.cxx b/src/mimrec/src/MStandardAnalysis.cxx
index eac5ef8f9..60cf04655 100644
--- a/src/mimrec/src/MStandardAnalysis.cxx
+++ b/src/mimrec/src/MStandardAnalysis.cxx
@@ -221,7 +221,7 @@ bool MStandardAnalysis::Analyze()
     // Only accept Comptons within the selected ranges...
     if (m_Selector.IsQualifiedEvent(Event) == true) {
       if (Event->GetEnergy() >= EnergyMean - SigmaWindow*EnergySigma && Event->GetEnergy() <= EnergyMean + SigmaWindow*EnergySigma) {
-        if (Event->GetType() == MPhysicalEvent::c_Compton) {
+        if (Event->GetType() == c_ComptonEvent) {
           ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
           double ARMValue = ComptonEvent->GetARMGamma(m_Position)*c_Deg;
@@ -290,7 +290,7 @@ bool MStandardAnalysis::Analyze()
     // Only accept Comptons within the selected ranges...
     if (m_Selector.IsQualifiedEvent(Event) == true) {
       if (Event->GetEnergy() >= EnergyMean - SigmaWindow*EnergySigma && Event->GetEnergy() <= EnergyMean + SigmaWindow*EnergySigma) {
-        if (Event->GetType() == MPhysicalEvent::c_Compton) {
+        if (Event->GetType() == c_ComptonEvent) {
           ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
 
           ARMHistR2->Fill(ComptonEvent->GetARMGamma(m_Position)*c_Deg);
@@ -356,7 +356,7 @@ bool MStandardAnalysis::Analyze()
       ++CountsSelected;
       if (Event->GetEnergy() >= EnergyMean - SigmaWindow*EnergySigma && Event->GetEnergy() <= EnergyMean + SigmaWindow*EnergySigma) {
         ++CountsSelectedPhotoPeak;
-        if (Event->GetType() == MPhysicalEvent::c_Compton) {
+        if (Event->GetType() == c_ComptonEvent) {
           ++CountsSelectedComptonPhotoPeak;
           ComptonEvent = dynamic_cast<MComptonEvent*>(Event);
           double ARMValue = ComptonEvent->GetARMGamma(m_Position)*c_Deg;
diff --git a/src/realta/src/MGUIControlCenter.cxx b/src/realta/src/MGUIControlCenter.cxx
index d34f74388..66c8634d3 100644
--- a/src/realta/src/MGUIControlCenter.cxx
+++ b/src/realta/src/MGUIControlCenter.cxx
@@ -685,7 +685,7 @@ void MGUIControlCenter::StartControlLoop()
         
         if (Event->GetPhysicalEvent() != 0) { 
           m_FullSpectrum->Add(Event->GetPhysicalEvent()->GetEnergy(), 1);
-          if (Event->GetPhysicalEvent()->GetEventType() == MPhysicalEvent::c_Compton) {
+          if (Event->GetPhysicalEvent()->GetEventType() == c_ComptonEvent) {
             m_ARM->Add(((MComptonEvent *) (Event->GetPhysicalEvent()))->
                        GetARMGamma(MVector(m_GUIDataImaging->GetARMGammaX(),
                                             m_GUIDataImaging->GetARMGammaY(),
diff --git a/src/response/src/MResponseBase.cxx b/src/response/src/MResponseBase.cxx
index 7bc88c2bb..3f694658f 100644
--- a/src/response/src/MResponseBase.cxx
+++ b/src/response/src/MResponseBase.cxx
@@ -256,7 +256,7 @@ bool MResponseBase::InitializeNextMatchingEvent()
       if (m_ReEvents.size() > 0) m_ReEvent = m_ReEvents[0];
 
       // Decide future:
-      if (m_ReEvent != 0 && m_ReEvent->GetEventType() != MRERawEvent::c_PairEvent) {
+      if (m_ReEvent != 0 && m_ReEvent->GetEventType() != c_PairEvent) {
         if (m_ReEvent->GetEventID() < m_RevanEventID) {
           m_RevanLevel++; 
         }
diff --git a/src/response/src/MResponseBuilder.cxx b/src/response/src/MResponseBuilder.cxx
index dd54ba2bf..bd21b52aa 100644
--- a/src/response/src/MResponseBuilder.cxx
+++ b/src/response/src/MResponseBuilder.cxx
@@ -473,7 +473,7 @@ bool MResponseBuilder::InitializeNextMatchingEvent()
       
       
       // Decide future:
-      if (m_ReEvent != nullptr && m_ReEvent->GetEventType() != MRERawEvent::c_PairEvent) {
+      if (m_ReEvent != nullptr && m_ReEvent->GetEventType() != c_PairEvent) {
         if (m_ReEvent->GetEventID() < m_RevanEventID) {
           m_RevanLevel++; 
         }
diff --git a/src/response/src/MResponseComptelDataSpace.cxx b/src/response/src/MResponseComptelDataSpace.cxx
index 645253ebc..7b6c88bd2 100644
--- a/src/response/src/MResponseComptelDataSpace.cxx
+++ b/src/response/src/MResponseComptelDataSpace.cxx
@@ -262,7 +262,7 @@ bool MResponseComptelDataSpace::Analyze()
   }
   
   // ... which needs to be a Compton event
-  if (Event->GetType() != MPhysicalEvent::c_Compton) {
+  if (Event->GetType() != c_ComptonEvent) {
     return true;
   }
   
diff --git a/src/response/src/MResponseEarthHorizon.cxx b/src/response/src/MResponseEarthHorizon.cxx
index 35e221f4e..4d9839595 100644
--- a/src/response/src/MResponseEarthHorizon.cxx
+++ b/src/response/src/MResponseEarthHorizon.cxx
@@ -138,7 +138,7 @@ bool MResponseEarthHorizon::CreateResponse()
       Event = REList->GetOptimumEvents()[0]->GetPhysicalEvent();
       if (Event != 0) {
         if (m_MimrecEventSelector.IsQualifiedEvent(Event) == true) {
-          if (Event->GetType() == MPhysicalEvent::c_Compton) {
+          if (Event->GetType() == c_ComptonEvent) {
             Compton = (MComptonEvent*) Event;
             //Compton->Calculate();
             if (Compton->IsKinematicsOK() == false) continue;
diff --git a/src/response/src/MResponseEventQuality.cxx b/src/response/src/MResponseEventQuality.cxx
index 048bd3f10..7847bbca4 100644
--- a/src/response/src/MResponseEventQuality.cxx
+++ b/src/response/src/MResponseEventQuality.cxx
@@ -136,7 +136,7 @@ bool MResponseEventQuality::Analyze()
   }
   
   // ... which needs to be a Compton event
-  if (Event->GetType() != MPhysicalEvent::c_Compton) {
+  if (Event->GetType() != c_ComptonEvent) {
     return true;
   }
   
diff --git a/src/response/src/MResponseEventQualityTMVAEventFile.cxx b/src/response/src/MResponseEventQualityTMVAEventFile.cxx
index 0c23cb3f2..518ca2bad 100644
--- a/src/response/src/MResponseEventQualityTMVAEventFile.cxx
+++ b/src/response/src/MResponseEventQualityTMVAEventFile.cxx
@@ -257,7 +257,7 @@ bool MResponseEventQualityTMVAEventFile::Analyze()
   }
   
   // ... which needs to be a Compton event
-  if (Event->GetType() != MPhysicalEvent::c_Compton) {
+  if (Event->GetType() != c_ComptonEvent) {
     return true;
   }
   
diff --git a/src/response/src/MResponseFirstInteractionPosition.cxx b/src/response/src/MResponseFirstInteractionPosition.cxx
index f027b73be..9cd2c7c4e 100644
--- a/src/response/src/MResponseFirstInteractionPosition.cxx
+++ b/src/response/src/MResponseFirstInteractionPosition.cxx
@@ -142,7 +142,7 @@ bool MResponseFirstInteractionPosition::CreateResponse()
       Event = REList->GetOptimumEvents()[0]->GetPhysicalEvent();
       if (Event != nullptr) {
         if (m_MimrecEventSelector.IsQualifiedEvent(Event) == true) {
-          if (Event->GetType() == MPhysicalEvent::c_Compton) {
+          if (Event->GetType() == c_ComptonEvent) {
             Compton = (MComptonEvent*) Event;
 
             if (Compton->IsKinematicsOK() == false) continue;
diff --git a/src/response/src/MResponseImaging.cxx b/src/response/src/MResponseImaging.cxx
index bea669d27..3b355f06a 100644
--- a/src/response/src/MResponseImaging.cxx
+++ b/src/response/src/MResponseImaging.cxx
@@ -214,7 +214,7 @@ bool MResponseImaging::CreateResponse()
       Event = REList->GetOptimumEvents()[0]->GetPhysicalEvent();
       if (Event != 0) {
         if (m_MimrecEventSelector.IsQualifiedEvent(Event) == true) {
-          if (Event->GetType() == MPhysicalEvent::c_Compton) {
+          if (Event->GetType() == c_ComptonEvent) {
             Compton = (MComptonEvent*) Event;
 
             if (Compton->IsKinematicsOK() == false) continue;
diff --git a/src/response/src/MResponseImagingARM.cxx b/src/response/src/MResponseImagingARM.cxx
index 95bb150bf..d8c2da1fc 100644
--- a/src/response/src/MResponseImagingARM.cxx
+++ b/src/response/src/MResponseImagingARM.cxx
@@ -200,7 +200,7 @@ bool MResponseImagingARM::Analyze()
     if (Event != 0) {
       ++m_NOptimumEvents;
       if (m_MimrecEventSelector.IsQualifiedEvent(Event) == true) {
-        if (Event->GetType() == MPhysicalEvent::c_Compton) {
+        if (Event->GetType() == c_ComptonEvent) {
           MComptonEvent* Compton = (MComptonEvent*) Event;
           
           if (Compton->IsKinematicsOK() == false) return true;
diff --git a/src/response/src/MResponseImagingBinnedMode.cxx b/src/response/src/MResponseImagingBinnedMode.cxx
index eb7d9b544..99ec799ef 100644
--- a/src/response/src/MResponseImagingBinnedMode.cxx
+++ b/src/response/src/MResponseImagingBinnedMode.cxx
@@ -410,7 +410,7 @@ bool MResponseImagingBinnedMode::Analyze()
   }
   
   // ... which needs to be a Compton event
-  if (Event->GetType() != MPhysicalEvent::c_Compton) {
+  if (Event->GetType() != c_ComptonEvent) {
     return true;
   }
   
diff --git a/src/response/src/MResponseImagingCodedMask.cxx b/src/response/src/MResponseImagingCodedMask.cxx
index ff455d207..27658e968 100644
--- a/src/response/src/MResponseImagingCodedMask.cxx
+++ b/src/response/src/MResponseImagingCodedMask.cxx
@@ -117,7 +117,7 @@ bool MResponseImagingCodedMask::CreateResponse()
       Event = REList->GetOptimumEvents()[0]->GetPhysicalEvent();
       if (Event != 0) {
         if (m_MimrecEventSelector.IsQualifiedEvent(Event) == true) {
-          if (Event->GetType() == MPhysicalEvent::c_Photo) {
+          if (Event->GetType() == c_PhotoEvent) {
             Photo = (MPhotoEvent*) Event;
 
             // First compute the y-Axis vector:
diff --git a/src/response/src/MResponseImagingEfficiency.cxx b/src/response/src/MResponseImagingEfficiency.cxx
index c2508ee5f..59e886871 100644
--- a/src/response/src/MResponseImagingEfficiency.cxx
+++ b/src/response/src/MResponseImagingEfficiency.cxx
@@ -132,7 +132,7 @@ bool MResponseImagingEfficiency::Analyze()
     MPhysicalEvent* Event = REList->GetOptimumEvents()[0]->GetPhysicalEvent();
     if (Event != 0) {
       if (m_MimrecEventSelector.IsQualifiedEvent(Event) == true) {
-        if (Event->GetType() == MPhysicalEvent::c_Compton) {
+        if (Event->GetType() == c_ComptonEvent) {
           MComptonEvent* Compton = (MComptonEvent*) Event;
           
           if (Compton->IsKinematicsOK() == false) return true;
diff --git a/src/response/src/MResponseImagingEfficiencyNearField.cxx b/src/response/src/MResponseImagingEfficiencyNearField.cxx
index 187d6df1d..d30bf76c6 100644
--- a/src/response/src/MResponseImagingEfficiencyNearField.cxx
+++ b/src/response/src/MResponseImagingEfficiencyNearField.cxx
@@ -397,7 +397,7 @@ bool MResponseImagingEfficiencyNearField::Analyze()
     MPhysicalEvent* Event = REList->GetOptimumEvents()[0]->GetPhysicalEvent();
     if (Event != 0) {
       if (m_MimrecEventSelector.IsQualifiedEvent(Event) == true) {
-        if (Event->GetType() == MPhysicalEvent::c_Compton) {
+        if (Event->GetType() == c_ComptonEvent) {
           MComptonEvent* Compton = (MComptonEvent*) Event;
 
           if (Compton->IsKinematicsOK() == false) return true;
diff --git a/src/response/src/MResponsePolarizationBinnedMode.cxx b/src/response/src/MResponsePolarizationBinnedMode.cxx
index bbe7f90f0..5bd5d52e8 100644
--- a/src/response/src/MResponsePolarizationBinnedMode.cxx
+++ b/src/response/src/MResponsePolarizationBinnedMode.cxx
@@ -402,7 +402,7 @@ bool MResponsePolarizationBinnedMode::Analyze()
   }
   
   // ... which needs to be a Compton event
-  if (Event->GetType() != MPhysicalEvent::c_Compton) {
+  if (Event->GetType() != c_ComptonEvent) {
     return true;
   }
   
diff --git a/src/revan/inc/MRERawEvent.h b/src/revan/inc/MRERawEvent.h
index a0de2fee6..65f4e8ce7 100644
--- a/src/revan/inc/MRERawEvent.h
+++ b/src/revan/inc/MRERawEvent.h
@@ -251,12 +251,15 @@ class MRERawEvent : public MRESE, public MRotationInterface
   // The event types:
    
   // TODO: Need to be moved in own class and be identical to what is in MPhysicalEvent
+  // Done
+  //using namespace MPhysicalEvent::n_EventTypeWrapper;
+  /*
   static const int c_UnknownEvent;
   static const int c_ComptonEvent;
   static const int c_PairEvent;
-  static const int c_MipEvent;
+  static const int c_MuonEvent;
   static const int c_ShowerEvent;
-  static const int c_PhotoEvent;
+  static const int c_PhotoEvent;*/
 
   static const int c_RejectionNone                               =  0;
   static const int c_RejectionTooManyHitsCSR                     =  1;
diff --git a/src/revan/src/MERCSR.cxx b/src/revan/src/MERCSR.cxx
index 910ebc4cd..f739db613 100644
--- a/src/revan/src/MERCSR.cxx
+++ b/src/revan/src/MERCSR.cxx
@@ -122,7 +122,7 @@ bool MERCSR::Analyze(MRawEventIncarnations* List)
 
     for (int e = 0; e < e_max; ++e) {
       RE = m_List->GetRawEventAt(e);
-      if (RE->GetEventType() == MRERawEvent::c_ComptonEvent) {// Iterate only over Compton events
+      if (RE->GetEventType() == c_ComptonEvent) {// Iterate only over Compton events
         MRawEventIncarnations* NewList = CreateOnlyPermutations(RE);
         if (NewList != 0) {
           m_List->DeleteRawEvent(RE);
@@ -140,7 +140,7 @@ bool MERCSR::Analyze(MRawEventIncarnations* List)
     //int e_max = m_List->GetNRawEvents();
     for (int e = 0; e < e_max; ++e) {
       RE = m_List->GetRawEventAt(e);
-      if (RE->GetEventType() == MRERawEvent::c_ComptonEvent) {// Iterate only over Compton events
+      if (RE->GetEventType() == c_ComptonEvent) {// Iterate only over Compton events
         FindComptonSequence(RE);
       }
     }
@@ -150,14 +150,14 @@ bool MERCSR::Analyze(MRawEventIncarnations* List)
     double BestQualityFactor = c_CSRFailed;
     for (int e = m_List->GetNRawEvents()-1; e >= 0; e--) {
       RE = m_List->GetRawEventAt(e);
-      if (RE->GetEventType() == MRERawEvent::c_ComptonEvent) {
+      if (RE->GetEventType() == c_ComptonEvent) {
         if (RE->IsGoodEvent() == true) {
           if (RE->GetComptonQualityFactor() < BestQualityFactor) {
             BestQualityFactor = RE->GetComptonQualityFactor();
             m_List->SetOptimumEvent(RE);
             m_List->SetBestTryEvent(RE);
           }
-        } else if (RE->GetEventType() == MRERawEvent::c_PhotoEvent) {//A.L. This doesn’t happen anymore - need to reimplement somewhere else
+        } else if (RE->GetEventType() == c_PhotoEvent) {//A.L. This doesn’t happen anymore - need to reimplement somewhere else
           m_List->SetOptimumEvent(RE);
           m_List->SetBestTryEvent(RE);
         }
@@ -259,7 +259,7 @@ void MERCSR::FindComptonSequence(MRERawEvent* RE)
     //RE->SetRejectionReason(MRERawEvent::c_RejectionSingleSiteEvent); // We could use that after event type identification?
     if (RE->GetRESEAt(0)->GetType() == MRESE::c_Hit || 
         RE->GetRESEAt(0)->GetType() == MRESE::c_Cluster) {
-      RE->SetEventType(MRERawEvent::c_PhotoEvent);
+      RE->SetEventType(c_PhotoEvent);
       RE->SetGoodEvent(true);
       RE->SetEventReconstructed(true);
     } else {
@@ -375,7 +375,7 @@ void MERCSR::FindComptonSequence(MRERawEvent* RE)
   mout<<"CSR - Sequence: Good event with TS: "<<BestQualityFactor<<endl;
     
   RE->SetComptonQualityFactors(BestQualityFactor, SecondBestQualityFactor);
-  //RE->SetEventType(MRERawEvent::c_ComptonEvent);
+  //RE->SetEventType(c_ComptonEvent);
   RE->SetGoodEvent(true);      
   RE->SetEventReconstructed(true);
 }
diff --git a/src/revan/src/MERCSRChiSquare.cxx b/src/revan/src/MERCSRChiSquare.cxx
index 942c158b5..74e7c2b8f 100644
--- a/src/revan/src/MERCSRChiSquare.cxx
+++ b/src/revan/src/MERCSRChiSquare.cxx
@@ -145,7 +145,7 @@ void MERCSRChiSquare::FindComptonSequenceDualHitEvent(MRERawEvent* RE)
   
   if (RE->GetNRESEs() != 2) {
     merr<<"FindComptonSequenceDualHitEvent called with "<<RE->GetNRESEs()<<" hits instead of exactly 2!"<<endl;
-    RE->SetEventType(MRERawEvent::c_UnknownEvent);
+    RE->SetEventType(c_UnknownEvent);
     RE->SetEventReconstructed(true);
     return;
   }
@@ -481,7 +481,7 @@ void MERCSRChiSquare::FindComptonSequenceDualHitEvent(MRERawEvent* RE)
   if (IsGood == true) {
     if (EstimatedFirst < 0) {
       merr<<"ERROR: We missed some condition during handling of two-site events... Bug!"<<endl;
-      RE->SetEventType(MRERawEvent::c_UnknownEvent);
+      RE->SetEventType(c_UnknownEvent);
       RE->SetEventReconstructed(true);
       return;
     }
@@ -511,7 +511,7 @@ void MERCSRChiSquare::FindComptonSequenceDualHitEvent(MRERawEvent* RE)
       
       if (IsGood == true) {
         mdebug<<"CSR-CS - Dual hit: Good Compton event"<<endl;
-        RE->SetEventType(MRERawEvent::c_ComptonEvent);
+        RE->SetEventType(c_ComptonEvent);
         if (m_TypeTestStatistics == c_TSSimple) {
           if (QualityFactor1 < 0) {
             RE->SetComptonQualityFactors(0, 1);
@@ -570,7 +570,7 @@ void MERCSRChiSquare::FindComptonSequence(MRERawEvent* RE)
     mdebug<<"CSR-CS - Sequence: Only single hit event!"<<endl;
     //RE->SetRejectionReason(MRERawEvent::c_RejectionSingleSiteEvent);
     if (RE->GetRESEAt(0)->GetType() == MRESE::c_Hit || RE->GetRESEAt(0)->GetType() == MRESE::c_Cluster) {
-      RE->SetEventType(MRERawEvent::c_PhotoEvent);
+      RE->SetEventType(c_PhotoEvent);
       RE->SetGoodEvent(true);
       RE->SetEventReconstructed(true);
     } else {
@@ -678,7 +678,7 @@ void MERCSRChiSquare::FindComptonSequence(MRERawEvent* RE)
   mdebug<<"CSR-CS - Sequence: Good event with TS: "<<BestQualityFactor<<endl;
   
   RE->SetComptonQualityFactors(BestQualityFactor, SecondBestQualityFactor);
-  //RE->SetEventType(MRERawEvent::c_ComptonEvent);
+  //RE->SetEventType(c_ComptonEvent);
   RE->SetGoodEvent(true);
   RE->SetEventReconstructed(true);
 }
diff --git a/src/revan/src/MERDecay.cxx b/src/revan/src/MERDecay.cxx
index 72b527e9e..c6a165198 100644
--- a/src/revan/src/MERDecay.cxx
+++ b/src/revan/src/MERDecay.cxx
@@ -136,7 +136,7 @@ bool MERDecay::Analyze(MRawEventIncarnations* List)
     RE = m_List->GetRawEventAt(e);
     massert(RE != 0);
 
-    if (RE->GetEventType() == MRERawEvent::c_ComptonEvent) {
+    if (RE->GetEventType() == c_ComptonEvent) {
 
       // Check all combinations - execpt the total event: 
       if (m_Mode == c_AllButOneCombination) {
diff --git a/src/revan/src/MEREventType.cxx b/src/revan/src/MEREventType.cxx
index cc22ebf15..1b31c8aa8 100644
--- a/src/revan/src/MEREventType.cxx
+++ b/src/revan/src/MEREventType.cxx
@@ -186,7 +186,7 @@ bool MEREventType::Analyze(MRawEventIncarnations* REList)
     for (int e = 0; e < m_List->GetNRawEvents(); e++) {
       RE = m_List->GetRawEventAt(e);
       CheckForPhoto(RE);
-      Identified = RE->GetEventType() == MRERawEvent::c_PhotoEvent;
+      Identified = RE->GetEventType() == c_PhotoEvent;
     }
   }
   m_TimePhoto += Timer.ElapsedTime();
@@ -229,7 +229,7 @@ bool MEREventType::Analyze(MRawEventIncarnations* REList)
     for (int e = 0; e < e_max; e++) {
       RE = m_List->GetRawEventAt(e);
       CheckForPair(RE);
-      Identified = RE->GetEventType() == MRERawEvent::c_PairEvent;
+      Identified = RE->GetEventType() == c_PairEvent;
       /*
       if () {
         m_List->DeleteRawEvent(RE);
@@ -276,13 +276,13 @@ bool MEREventType::Analyze(MRawEventIncarnations* REList)
       CheckForMips(RE);
       //Identified = RE->IsGoodEvent();
       // If we have found a MIP then we are done!
-      if (RE->GetEventType() == MRERawEvent::c_MipEvent) {
+      if (RE->GetEventType() == c_MuonEvent) {
         mdebug<<"Tracking: Successful identification: MIP (probably muon)"<<endl;
         Identified = true;
         //m_List->SetOptimumEvent(RE);
         //m_List->SetBestTryEvent(RE);
       }
-      if (RE->GetEventType() == MRERawEvent::c_ShowerEvent) {
+      if (RE->GetEventType() == c_ShowerEvent) {
         mdebug<<"Tracking: Successful identification: Shower"<<endl;
         Identified = true;
         //m_List->SetOptimumEvent(RE);
@@ -302,7 +302,7 @@ bool MEREventType::Analyze(MRawEventIncarnations* REList)
     for (int e = 0; e < m_List->GetNRawEvents(); e++) {
       RE = m_List->GetRawEventAt(e);
       CheckForCompton(RE);
-      Identified = RE->GetEventType() == MRERawEvent::c_ComptonEvent;
+      Identified = RE->GetEventType() == c_ComptonEvent;
     }
   }
 
@@ -311,7 +311,7 @@ bool MEREventType::Analyze(MRawEventIncarnations* REList)
     // Set all to unknown
     for (int e = 0; e < m_List->GetNRawEvents(); e++) {
       RE = m_List->GetRawEventAt(e);
-      RE->SetEventType(MRERawEvent::c_UnknownEvent);
+      RE->SetEventType(c_UnknownEvent);
     }
   }
 
@@ -480,7 +480,7 @@ void MEREventType::CheckForPhoto(MRERawEvent* RE)
   if (RE->GetNRESEs() == 1) {
     if (RE->GetRESEAt(0)->GetType() == MRESE::c_Hit || 
       RE->GetRESEAt(0)->GetType() == MRESE::c_Cluster) {
-      RE->SetEventType(MRERawEvent::c_PhotoEvent);
+      RE->SetEventType(c_PhotoEvent);
       //RE->SetGoodEvent(true);
     }
   }
@@ -493,7 +493,7 @@ void MEREventType::CheckForPhoto(MRERawEvent* RE)
 void MEREventType::CheckForCompton(MRERawEvent* RE)
 {
   // If we get there, this is a Compton event by default
-  RE->SetEventType(MRERawEvent::c_ComptonEvent);
+  RE->SetEventType(c_ComptonEvent);
   //RE->SetGoodEvent(true);
 }
 
@@ -631,7 +631,7 @@ void MEREventType::CheckForPair(MRERawEvent* RE)
       RE->SetVertex(0);
       List->AddRawEvent(New);
       mdebug<<"Search vertex: Found vertex: "<<Vertex->GetID()<<endl;*/
-      RE->SetEventType(MRERawEvent::c_PairEvent);
+      RE->SetEventType(c_PairEvent);
       //RE->SetGoodEvent(true);
       break; // Only take first right now
     }
@@ -784,13 +784,13 @@ void MEREventType::CheckForMips(MRERawEvent* RE)
 
     // d. This is a good event...
     RE->SetPhysicalEvent(Muon);*/
-    RE->SetEventType(MRERawEvent::c_MipEvent);
+    RE->SetEventType(c_MuonEvent);
     //RE->SetGoodEvent(true);
   }
   // b. A shower
   else if (TrackArray.size() > 1) {
     mdebug<<"==> Found a shower!"<<endl;
-    RE->SetEventType(MRERawEvent::c_ShowerEvent);
+    RE->SetEventType(c_ShowerEvent);
     //RE->SetGoodEvent(true);
 /*
     // b. Integrate all tracks into this raw event:
diff --git a/src/revan/src/MEREventTypeExternal.cxx b/src/revan/src/MEREventTypeExternal.cxx
index d26ef01d4..42a64a756 100644
--- a/src/revan/src/MEREventTypeExternal.cxx
+++ b/src/revan/src/MEREventTypeExternal.cxx
@@ -86,7 +86,7 @@ bool MEREventTypeExternal::Analyze(MRawEventIncarnations* List)
       RE->SetEventTypeProbability( m_FileEventsType->GetEventTypeProbability() );
     } else {
       merr << "MEREventTypeExternal: No event type found for event ID " << RE->GetEventId() << endl;
-      RE->SetEventType( MRERawEvent::c_UnknownEvent );
+      RE->SetEventType( c_UnknownEvent );
       RE->SetEventTypeProbability( 0. );
     }
   }
diff --git a/src/revan/src/MERTrack.cxx b/src/revan/src/MERTrack.cxx
index 90ad47cb4..8af8d3881 100644
--- a/src/revan/src/MERTrack.cxx
+++ b/src/revan/src/MERTrack.cxx
@@ -250,7 +250,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
 
   if (StartTracking == false) {
     mdebug<<"Not enough hits in tracker!"<<endl;
-    RE->SetEventType(MRERawEvent::c_UnknownEvent); // discard
+    RE->SetEventType(c_UnknownEvent); // discard
     RE->SetRejectionReason(MRERawEvent::c_RejectionNotEnoughHitsInTracker);
     RE->SetEventReconstructed(true);
     return true;
@@ -258,13 +258,13 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
 
   // Step B: Pairs
   Timer.Start();
-  if (HasOneREOfType(MRERawEvent::c_PairEvent)) {
+  if (HasOneREOfType(c_PairEvent)) {
     mdebug<<"* Search for pairs: Vertex"<<endl;
     bool HasVertices = false;
     int e_max = m_List->GetNRawEvents();
     for (int e = 0; e < e_max; e++) {
       RE = m_List->GetRawEventAt(e);
-      if (RE->GetEventType() == MRERawEvent::c_PairEvent) {// Iterate only over pair events
+      if (RE->GetEventType() == c_PairEvent) {// Iterate only over pair events
         List = CheckForPair(RE);//Check for vertices
         if (List) { // if vertices
           mdebug<<"List: "<<List->GetNRawEvents()<<endl;
@@ -298,7 +298,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
           m_List->SetOptimumEvent(RE);
           m_List->SetBestTryEvent(RE);
         } else { // if no vertices
-          RE->SetEventType(MRERawEvent::c_UnknownEvent); // discard
+          RE->SetEventType(c_UnknownEvent); // discard
         }
         RE->SetEventReconstructed(true);
       }
@@ -310,26 +310,26 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
   // Step C: Mips
 
   Timer.Start();
-  if (HasOneREOfType(MRERawEvent::c_MipEvent) || HasOneREOfType(MRERawEvent::c_ShowerEvent)) {
+  if (HasOneREOfType(c_MuonEvent) || HasOneREOfType(c_ShowerEvent)) {
   //if (m_SearchMIPs == true) {
     mdebug<<"* Search for MIPs"<<endl;
     for (int e = 0; e < m_List->GetNRawEvents(); e++) {
       RE = m_List->GetRawEventAt(e);
-      if (RE->GetEventType() == MRERawEvent::c_MipEvent || RE->GetEventType() == MRERawEvent::c_ShowerEvent) {// Iterate only over MIP/shower events
+      if (RE->GetEventType() == c_MuonEvent || RE->GetEventType() == c_ShowerEvent) {// Iterate only over MIP/shower events
         CheckForMips(RE);
         // If we have found a MIP then we are done!
-        if (RE->GetEventType() == MRERawEvent::c_MipEvent) {
+        if (RE->GetEventType() == c_MuonEvent) {
           mdebug<<"Tracking: Successful identification: MIP (probably muon)"<<endl;
           //Identified = true;
           m_List->SetOptimumEvent(RE);
           m_List->SetBestTryEvent(RE);
-        } else if (RE->GetEventType() == MRERawEvent::c_ShowerEvent) {
+        } else if (RE->GetEventType() == c_ShowerEvent) {
           mdebug<<"Tracking: Successful identification: Shower"<<endl;
           //Identified = true;
           m_List->SetOptimumEvent(RE);
           m_List->SetBestTryEvent(RE);
         } else {
-          RE->SetEventType(MRERawEvent::c_UnknownEvent); // discard
+          RE->SetEventType(c_UnknownEvent); // discard
         }
         RE->SetEventReconstructed(true);
       }
@@ -343,7 +343,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
 
   // Step C: Compton tracks:
   // IsEventReconstructed stays false until CSR is performed
-  if (HasOneREOfType(MRERawEvent::c_ComptonEvent)) {
+  if (HasOneREOfType(c_ComptonEvent)) {
     mdebug<<"* Search for Comptons"<<endl;
 
     // Step C.1: Generate the links
@@ -354,10 +354,10 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
     int e_max = m_List->GetNRawEvents();
     for (int e = 0; e < e_max; e++) {
       RE = m_List->GetRawEventAt(e);
-      if (RE->GetEventType() == MRERawEvent::c_ComptonEvent) {
-        //RE->SetEventType(MRERawEvent::c_UnknownEvent);
+      if (RE->GetEventType() == c_ComptonEvent) {
+        //RE->SetEventType(c_UnknownEvent);
         List = TrackComptons(RE);
-        //RE->SetEventType(MRERawEvent::c_ComptonEvent);
+        //RE->SetEventType(c_ComptonEvent);
         if (List != 0) {
           m_List->DeleteRawEvent(RE);
           e--;
@@ -380,7 +380,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
       for (int e = 0; e < m_List->GetNRawEvents(); e++) {
         int CurrentN = 0;
         RE = m_List->GetRawEventAt(e);
-        if (RE->GetEventType() == MRERawEvent::c_ComptonEvent) {
+        if (RE->GetEventType() == c_ComptonEvent) {
           for (int r = 0; r < RE->GetNRESEs(); r++) {
             RESE = RE->GetRESEAt(r);
             if (IsInTracker(RESE) == true) CurrentN++;
@@ -392,7 +392,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
       for (int e = 0; e < m_List->GetNRawEvents(); e++) {
         int CurrentN = 0;
         RE = m_List->GetRawEventAt(e);
-        if (RE->GetEventType() == MRERawEvent::c_ComptonEvent) {
+        if (RE->GetEventType() == c_ComptonEvent) {
           for (int r = 0; r < RE->GetNRESEs(); r++) {
             RESE = RE->GetRESEAt(r);
             if (IsInTracker(RESE) == true) CurrentN++;
@@ -418,7 +418,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
 
     for (int e = 0; e < m_List->GetNRawEvents(); e++) {
       RE = m_List->GetRawEventAt(e);
-      if (RE->GetEventType() == MRERawEvent::c_ComptonEvent) {
+      if (RE->GetEventType() == c_ComptonEvent) {
         for (int r = 0; r < RE->GetNRESEs(); r++) {
           RESE = RE->GetRESEAt(r);
           IDRESE = RESE->GetID();
@@ -443,7 +443,7 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
 
     for (int e = 0; e < m_List->GetNRawEvents(); e++) {
       RE = m_List->GetRawEventAt(e);
-      if (RE->GetEventType() == MRERawEvent::c_ComptonEvent) EvaluateTracks(RE);
+      if (RE->GetEventType() == c_ComptonEvent) EvaluateTracks(RE);
     }
     SortByTrackQualityFactor(m_List);
 
@@ -1180,13 +1180,13 @@ void MERTrack::CheckForMips(MRERawEvent* RE)
 
     // d. This is a good event...
     RE->SetPhysicalEvent(Muon);
-    //RE->SetEventType(MRERawEvent::c_MipEvent);
+    //RE->SetEventType(c_MuonEvent);
     RE->SetGoodEvent(true);
   }
   // b. A shower
   else if (TrackArray.size() > 1) {
     mdebug<<"==> Found a shower!"<<endl;
-    RE->SetEventType(MRERawEvent::c_ShowerEvent);
+    RE->SetEventType(c_ShowerEvent);
 
     // b. Integrate all tracks into this raw event:
     for (unsigned int i = 0; i < TrackArray.size(); ++i) {
@@ -1688,7 +1688,7 @@ bool MERTrack::EvaluatePairs(MRERawEvent* RE)
     RE->SetGoodEvent(false);
   } else {
     mdebug<<"Pair found..."<<endl;
-    RE->SetEventType(MRERawEvent::c_PairEvent);
+    RE->SetEventType(c_PairEvent);
     RE->SetGoodEvent(true);
   }
 
diff --git a/src/revan/src/MERTrackKalman2D.cxx b/src/revan/src/MERTrackKalman2D.cxx
index b3098ddce..9ef4d7678 100644
--- a/src/revan/src/MERTrackKalman2D.cxx
+++ b/src/revan/src/MERTrackKalman2D.cxx
@@ -702,7 +702,7 @@ void MERTrackKalman2D::TrackPairs(MRERawEvent* RE)
     //RE->SetTrackQualityFactor((ChiT1y+ChiT2y)/100);
     RE->SetPairQualityFactor((ChiT1y+ChiT2y));
     RE->SetGoodEvent(true);
-    //RE->SetEventType(MRERawEvent::c_PairEvent);
+    //RE->SetEventType(c_PairEvent);
     RE->SetEventReconstructed(true);
 
   } else{
diff --git a/src/revan/src/MERTrackKalman3D.cxx b/src/revan/src/MERTrackKalman3D.cxx
index 1259f7ea2..da9e65c19 100644
--- a/src/revan/src/MERTrackKalman3D.cxx
+++ b/src/revan/src/MERTrackKalman3D.cxx
@@ -1208,7 +1208,7 @@ void MERTrackKalman3D::TrackPairs(MRERawEvent* RE)
   //RE->SetTrackQualityFactor(ChiT1+ChiT2);
   RE->SetPairQualityFactor(ChiT1+ChiT2);
   RE->SetGoodEvent(true);
-  //RE->SetEventType(MRERawEvent::c_PairEvent);
+  //RE->SetEventType(c_PairEvent);
   RE->SetEventReconstructed(true);
 
 }
diff --git a/src/revan/src/MERTrackRank.cxx b/src/revan/src/MERTrackRank.cxx
index b8c5d6e6f..4272079e3 100644
--- a/src/revan/src/MERTrackRank.cxx
+++ b/src/revan/src/MERTrackRank.cxx
@@ -92,7 +92,7 @@ bool MERTrackRank::EvaluateTracks(MRERawEvent* RE)
     if (RE->GetVertex() != 0) {
       mimp<<"Hacked sanity check..."<<endl; 
       RE->SetPairQualityFactor(1-QF);
-      RE->SetEventType(MRERawEvent::c_PairEvent);
+      RE->SetEventType(c_PairEvent);
       RE->SetGoodEvent(true);
     } else {
       RE->SetTrackQualityFactor(QF);
diff --git a/src/revan/src/MRERawEvent.cxx b/src/revan/src/MRERawEvent.cxx
index 5010d22ae..8fc350878 100644
--- a/src/revan/src/MRERawEvent.cxx
+++ b/src/revan/src/MRERawEvent.cxx
@@ -81,14 +81,14 @@ ClassImp(MRERawEvent)
 
 ////////////////////////////////////////////////////////////////////////////////
 
-
-const int MRERawEvent::c_UnknownEvent = MPhysicalEvent::c_Unknown;
-const int MRERawEvent::c_ComptonEvent = MPhysicalEvent::c_Compton;
-const int MRERawEvent::c_PairEvent    = MPhysicalEvent::c_Pair;
-const int MRERawEvent::c_MipEvent     = MPhysicalEvent::c_Muon;
-const int MRERawEvent::c_ShowerEvent  = MPhysicalEvent::c_Shower;
-const int MRERawEvent::c_PhotoEvent   = MPhysicalEvent::c_Photo;
-
+/*
+const int c_UnknownEvent = c_UnknownEvent;
+const int c_ComptonEvent = c_ComptonEvent;
+const int c_PairEvent    = c_PairEvent;
+const int c_MuonEvent     = c_MuonEvent;
+const int c_ShowerEvent  = c_ShowerEvent;
+const int c_PhotoEvent   = c_PhotoEvent;
+*/
 const double MRERawEvent::c_NoQualityFactor = numeric_limits<double>::max()/3;
 const double MRERawEvent::c_NoScore = numeric_limits<double>::max()/3; // remove later
 
@@ -165,19 +165,19 @@ MRERawEvent::MRERawEvent(MRERawEvent* RE) : MRESE((MRESE *) RE)
 
 
   if (RE->GetPhysicalEvent() != 0) {
-    if (m_EventType == MRERawEvent::c_ComptonEvent) {
+    if (m_EventType == c_ComptonEvent) {
       m_Event = new MComptonEvent();
       m_Event->Assimilate(RE->GetPhysicalEvent());
-    } else if (m_EventType == MRERawEvent::c_PairEvent) {
+    } else if (m_EventType == c_PairEvent) {
       m_Event = new MPairEvent();
       m_Event->Assimilate(RE->GetPhysicalEvent());
-    } else if (m_EventType == MRERawEvent::c_MipEvent) {
+    } else if (m_EventType == c_MuonEvent) {
       m_Event = new MMuonEvent();
       m_Event->Assimilate(RE->GetPhysicalEvent());
-    } else if (m_EventType == MRERawEvent::c_PhotoEvent) {
+    } else if (m_EventType == c_PhotoEvent) {
       m_Event = new MPhotoEvent();
       m_Event->Assimilate(RE->GetPhysicalEvent());
-    } else if (m_EventType == MRERawEvent::c_UnknownEvent) {
+    } else if (m_EventType == c_UnknownEvent) {
       m_Event = new MUnidentifiableEvent();
       m_Event->Assimilate(RE->GetPhysicalEvent());
     } else {
@@ -693,7 +693,7 @@ MString MRERawEvent::GetEventTypeAsString()
     return "Compton";
   } else if (m_EventType == c_PairEvent) {
     return "Pair";
-  } else if (m_EventType == c_MipEvent) {
+  } else if (m_EventType == c_MuonEvent) {
     return "MIP";
   } else if (m_EventType == c_ShowerEvent) {
     return "Shower";
@@ -1190,7 +1190,7 @@ MPhysicalEvent* MRERawEvent::GetPhysicalEvent()
       Photo->SetPosition(GetRESEAt(0)->GetPosition());
 
       m_Event = (MPhysicalEvent*) Photo;
-      // } else if (m_EventType == c_MipEvent) {
+      // } else if (m_EventType == c_MuonEvent) {
       //mout<<"Do not store muons"<<endl;
       //} else if (m_EventType == c_ShowerEvent) {
       //mout<<"Do not store showers"<<endl;
diff --git a/src/revan/src/MRawEventAnalyzer.cxx b/src/revan/src/MRawEventAnalyzer.cxx
index fc4319edd..ffff8e1ee 100644
--- a/src/revan/src/MRawEventAnalyzer.cxx
+++ b/src/revan/src/MRawEventAnalyzer.cxx
@@ -735,7 +735,7 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
       MRawEventIncarnations* REI = m_RawEvents->Get(i);
       for (int e = 0; e < REI->GetNRawEvents(); e++) {
         MRERawEvent* RE = REI->GetRawEventAt(e);
-        if (RE->GetEventType() == MRERawEvent::c_PhotoEvent) {
+        if (RE->GetEventType() == c_PhotoEvent) {
           RE->SetEventReconstructed(true);
         }
       }
@@ -852,10 +852,10 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
     }
     mdebug<<Event->ToString()<<endl;
     m_NGoodEvents++;
-    if (Event->GetType() == MPhysicalEvent::c_Photo) {
+    if (Event->GetType() == c_PhotoEvent) {
       mdebug<<"ER - Good photo event..."<<endl;
       m_NPhotoEvents++;
-    } else if (Event->GetType() == MPhysicalEvent::c_Compton) {
+    } else if (Event->GetType() == c_ComptonEvent) {
       if (Event->IsDecay() == true) {
         mdebug<<"ER - Compton event - probably decay..."<<endl;
         m_NDecayEvents++;
@@ -863,19 +863,19 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
         mdebug<<"ER - Good Compton event..."<<endl;
       }
       m_NComptonEvents++;
-    } else if (Event->GetType() == MPhysicalEvent::c_Pair) {
+    } else if (Event->GetType() == c_PairEvent) {
       mdebug<<"ER - Good pair event..."<<endl;
       m_NPairEvents++;
-    } else if (Event->GetType() == MPhysicalEvent::c_Muon) {
+    } else if (Event->GetType() == c_MuonEvent) {
       mdebug<<"ER - Good muon event..."<<endl;
       m_NMuonEvents++;
-    } else if (Event->GetType() == MPhysicalEvent::c_PET) {
+    } else if (Event->GetType() == c_PETEvent) {
       mdebug<<"ER - Good PET event..."<<endl;
       m_NPETEvents++;
-    } else if (Event->GetType() == MPhysicalEvent::c_Multi) {
+    } else if (Event->GetType() == c_MultiEvent) {
       mdebug<<"ER - Good multi event..."<<endl;
       m_NMultiEvents++;
-    } else if (Event->GetType() == MPhysicalEvent::c_Unidentifiable) {
+    } else if (Event->GetType() == c_UnidentifiableEvent) {
       mdebug<<"ER - Undefinable event..."<<endl;
       m_NUnidentifiableEvents++;
     } else {

From 453f5368febcc17fcb133aa2b4d3e5552dc198a3 Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Tue, 15 Jul 2025 17:09:08 -0400
Subject: [PATCH 184/192] Fix: Search Photos stay selected on revan re-launch

---
 src/revan/src/MSettingsEventReconstruction.cxx | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/revan/src/MSettingsEventReconstruction.cxx b/src/revan/src/MSettingsEventReconstruction.cxx
index fc98323cb..ca7d33005 100644
--- a/src/revan/src/MSettingsEventReconstruction.cxx
+++ b/src/revan/src/MSettingsEventReconstruction.cxx
@@ -78,6 +78,7 @@ MSettingsEventReconstruction::MSettingsEventReconstruction() : MSettingsInterfac
 
   // Event type identification
   m_DoTracking = true;
+  m_SearchPhoto = true;
   m_SearchPairs = true;
   m_SearchMIPs = true;
   m_SearchComptons = true;
@@ -190,6 +191,7 @@ bool MSettingsEventReconstruction::WriteXml(MXmlNode* Node)
 
   new MXmlNode(Node, "DoTracking", m_DoTracking);
   new MXmlNode(Node, "SearchPairs", m_SearchPairs);
+  new MXmlNode(Node, "SearchPhoto", m_SearchPhoto);
   new MXmlNode(Node, "SearchMIPs", m_SearchMIPs);
   new MXmlNode(Node, "SearchComptons", m_SearchComptons);
   new MXmlNode(Node, "EventTypeFileName", m_EventTypeFileName);
@@ -337,6 +339,9 @@ bool MSettingsEventReconstruction::ReadXml(MXmlNode* Node)
   if ((aNode = Node->GetNode("DoTracking")) != 0) {
     m_DoTracking = aNode->GetValueAsBoolean();
   }
+  if ((aNode = Node->GetNode("SearchPhoto")) != 0) {
+    m_SearchPhoto = aNode->GetValueAsBoolean();
+  }
   if ((aNode = Node->GetNode("SearchPairs")) != 0) {
     m_SearchPairs = aNode->GetValueAsBoolean();
   }

From b234142157e52544036fefd38f2bfa99a8e83f47 Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Tue, 15 Jul 2025 18:01:26 -0400
Subject: [PATCH 185/192] Fix: Single site events classified unknown by
 tracking algorithm and various small bugs

---
 src/revan/src/MEREventType.cxx      |  2 --
 src/revan/src/MERTrack.cxx          | 14 +++++---
 src/revan/src/MGUIERAlgorithm.cxx   | 54 ++++++++++++++++++-----------
 src/revan/src/MRawEventAnalyzer.cxx |  3 ++
 4 files changed, 46 insertions(+), 27 deletions(-)

diff --git a/src/revan/src/MEREventType.cxx b/src/revan/src/MEREventType.cxx
index 1b31c8aa8..3c2125fbf 100644
--- a/src/revan/src/MEREventType.cxx
+++ b/src/revan/src/MEREventType.cxx
@@ -481,7 +481,6 @@ void MEREventType::CheckForPhoto(MRERawEvent* RE)
     if (RE->GetRESEAt(0)->GetType() == MRESE::c_Hit || 
       RE->GetRESEAt(0)->GetType() == MRESE::c_Cluster) {
       RE->SetEventType(c_PhotoEvent);
-      //RE->SetGoodEvent(true);
     }
   }
 }
@@ -494,7 +493,6 @@ void MEREventType::CheckForCompton(MRERawEvent* RE)
 {
   // If we get there, this is a Compton event by default
   RE->SetEventType(c_ComptonEvent);
-  //RE->SetGoodEvent(true);
 }
 
 
diff --git a/src/revan/src/MERTrack.cxx b/src/revan/src/MERTrack.cxx
index 8af8d3881..8b018117e 100644
--- a/src/revan/src/MERTrack.cxx
+++ b/src/revan/src/MERTrack.cxx
@@ -249,11 +249,15 @@ bool MERTrack::Analyze(MRawEventIncarnations* REList)
   }
 
   if (StartTracking == false) {
-    mdebug<<"Not enough hits in tracker!"<<endl;
-    RE->SetEventType(c_UnknownEvent); // discard
-    RE->SetRejectionReason(MRERawEvent::c_RejectionNotEnoughHitsInTracker);
-    RE->SetEventReconstructed(true);
-    return true;
+    for (int e = 0; e < m_List->GetNRawEvents(); e++) {
+      RE = m_List->GetRawEventAt(e);
+      if (RE->GetEventType() == c_PairEvent) {// Iterate only over pair events
+        mdebug<<"Not enough hits in tracker!"<<endl;
+        RE->SetEventType(c_UnknownEvent); // discard
+        RE->SetRejectionReason(MRERawEvent::c_RejectionNotEnoughHitsInTracker);
+        RE->SetEventReconstructed(true);
+      }
+    }
   }
 
   // Step B: Pairs
diff --git a/src/revan/src/MGUIERAlgorithm.cxx b/src/revan/src/MGUIERAlgorithm.cxx
index d32b810d9..0b29ac169 100644
--- a/src/revan/src/MGUIERAlgorithm.cxx
+++ b/src/revan/src/MGUIERAlgorithm.cxx
@@ -143,26 +143,32 @@ void MGUIERAlgorithm::Create()
   m_TrackingList->Add("Kalman Filter 2D (work in progress)"); // 8
   m_TrackingList->Add("Kalman Filter 3D (work in progress)"); // 9
   m_TrackingList->Add("First two layers (to be implemented)"); // 10
-  m_TrackingList->SetSelected(m_Data->GetTrackingAlgorithm());
-//  if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoNone) {
-//    m_TrackingList->SetSelected(0);
-//  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoModifiedPearson) {
-//    m_TrackingList->SetSelected(1);
-//  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoPearson) {
-//    m_TrackingList->SetSelected(2);
-//  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoRank) {
-//    m_TrackingList->SetSelected(3);
-//  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoChiSquare) {
-//    m_TrackingList->SetSelected(4);
-//  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoGas) {
-//    m_TrackingList->SetSelected(5);
-//  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoDirectional) {
-//    m_TrackingList->SetSelected(6);
-//  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoBayesian) {
-//    m_TrackingList->SetSelected(7);
-//  } else {
-//    m_TrackingList->SetSelected(0);
-//  }
+  if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoNone) {
+    m_TrackingList->SetSelected(0);
+  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoModifiedPearson) {
+    m_TrackingList->SetSelected(1);
+  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoPearson) {
+    m_TrackingList->SetSelected(2);
+  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoRank) {
+    m_TrackingList->SetSelected(3);
+  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoChiSquare) {
+    m_TrackingList->SetSelected(4);
+  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoGas) {
+    m_TrackingList->SetSelected(5);
+  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoDirectional) {
+    m_TrackingList->SetSelected(6);
+  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoBayesian) {
+    m_TrackingList->SetSelected(7);
+  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoKalman2D) {
+    m_TrackingList->SetSelected(8);
+  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoKalman3D) {
+    m_TrackingList->SetSelected(9);
+  } else if (m_Data->GetTrackingAlgorithm() == MRawEventAnalyzer::c_TrackingAlgoFirstLayer) {
+    merr << "First two layers tracking is not implemented yet! No tracking algorithm selected." << endl;
+    m_TrackingList->SetSelected(0);
+  } else {
+    m_TrackingList->SetSelected(0);
+  }
   m_TrackingList->Create();
   AddFrame(m_TrackingList, m_ListLayout);
 /*
@@ -252,6 +258,14 @@ bool MGUIERAlgorithm::OnApply()
     m_Data->SetTrackingAlgorithm(MRawEventAnalyzer::c_TrackingAlgoDirectional);
   } else if (m_TrackingList->GetSelected() == 7) {
     m_Data->SetTrackingAlgorithm(MRawEventAnalyzer::c_TrackingAlgoBayesian);
+  } else if (m_TrackingList->GetSelected() == 8) {
+    m_Data->SetTrackingAlgorithm(MRawEventAnalyzer::c_TrackingAlgoKalman2D);
+  } else if (m_TrackingList->GetSelected() == 9) {
+    m_Data->SetTrackingAlgorithm(MRawEventAnalyzer::c_TrackingAlgoKalman3D);
+  } else if (m_TrackingList->GetSelected() == 10) {
+    merr << "First two layers tracking is not implemented yet! No tracking algorithm selected." << endl;
+    m_Data->SetTrackingAlgorithm(MRawEventAnalyzer::c_TrackingAlgoNone);
+    //m_Data->SetTrackingAlgorithm(MRawEventAnalyzer::c_TrackingAlgoFirstLayer);
   }
   // Pair
   //m_Data->SetPairAlgorithm(m_PairList->GetSelected());
diff --git a/src/revan/src/MRawEventAnalyzer.cxx b/src/revan/src/MRawEventAnalyzer.cxx
index ffff8e1ee..1a278f55e 100644
--- a/src/revan/src/MRawEventAnalyzer.cxx
+++ b/src/revan/src/MRawEventAnalyzer.cxx
@@ -727,6 +727,8 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
 
   }
 
+  //mout << "AL evtid=" << m_RawEvents->Get(0)->GetRawEventAt(0)->GetEventId() << " evtype=" << m_RawEvents->Get(0)->GetRawEventAt(0)->GetEventTypeAsString() << endl;
+
 
   // Section P: Photo events
 
@@ -766,6 +768,7 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
     mdebug<<"I am not doing Tracking!"<<endl;
   }
   
+  //mout << "AL evtid=" << m_RawEvents->Get(0)->GetRawEventAt(0)->GetEventId() << " evtype=" << m_RawEvents->Get(0)->GetRawEventAt(0)->GetEventTypeAsString() << endl;
   
   
   // Section E: Compton sequence reconstruction       

From c27a5ee338c6ff594958a17dc04c6d6e6c97bc3b Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Wed, 16 Jul 2025 13:01:03 -0400
Subject: [PATCH 186/192] Fix: Reproduce behavior of Compton and Photo events
 when no CSR algorithm is selected

---
 src/revan/src/MRawEventAnalyzer.cxx | 158 ++++++++++++++++++----------
 1 file changed, 105 insertions(+), 53 deletions(-)

diff --git a/src/revan/src/MRawEventAnalyzer.cxx b/src/revan/src/MRawEventAnalyzer.cxx
index 1a278f55e..5e638fb73 100644
--- a/src/revan/src/MRawEventAnalyzer.cxx
+++ b/src/revan/src/MRawEventAnalyzer.cxx
@@ -738,7 +738,10 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
       for (int e = 0; e < REI->GetNRawEvents(); e++) {
         MRERawEvent* RE = REI->GetRawEventAt(e);
         if (RE->GetEventType() == c_PhotoEvent) {
+          // Use a MERConstruction class dedicated to Photo events?
+          RE->SetGoodEvent(true);
           RE->SetEventReconstructed(true);
+          REI->SetBestTryEvent(RE);
         }
       }
     }
@@ -747,25 +750,40 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
 
   // Section D: Tracking:
   
-  if (SelectionsPassed == true && m_TrackingAlgorithm > c_TrackingAlgoNone) {
-    Timer.Start();
-    
-    if (m_Tracker == nullptr) {
-      merr<<"Tracker pointer is zero. You changed the event reconstruction setup without calling PreAnalysis()!"<<show;
-      return c_AnalysisUndefinedError;
-    }
-    
-    for (unsigned int i = 0; i < m_RawEvents->Size(); ++i) {
-      MRawEventIncarnations* REI = m_RawEvents->Get(i);
-      m_Tracker->Analyze(REI);
+  if (SelectionsPassed == true) {
+    if (m_TrackingAlgorithm > c_TrackingAlgoNone) {
+      Timer.Start();
+      
+      if (m_Tracker == nullptr) {
+        merr<<"Tracker pointer is zero. You changed the event reconstruction setup without calling PreAnalysis()!"<<show;
+        return c_AnalysisUndefinedError;
+      }
+      
+      for (unsigned int i = 0; i < m_RawEvents->Size(); ++i) {
+        MRawEventIncarnations* REI = m_RawEvents->Get(i);
+        m_Tracker->Analyze(REI);
+      }
+      
+      if (m_RawEvents->IsAnyEventValid() == false) SelectionsPassed = false;    
+      
+      m_TimeTrack += Timer.ElapsedTime();
+      
+    } else {
+      mdebug<<"I am not doing Tracking!"<<endl;
+      // Set all Pair and Mip events an unknown
+      for (unsigned int i = 0; i < m_RawEvents->Size(); ++i) {
+        MRawEventIncarnations* REI = m_RawEvents->Get(i);
+        for (int e = 0; e < REI->GetNRawEvents(); e++) {
+          MRERawEvent* RE = REI->GetRawEventAt(e);
+          if (RE->GetEventType() == c_PairEvent || RE->GetEventType() == c_MuonEvent || RE->GetEventType() == c_ShowerEvent) {
+            RE->SetEventType(c_UnknownEvent);
+            RE->SetGoodEvent(true);
+            RE->SetEventReconstructed(true);
+            REI->SetBestTryEvent(RE);
+          }
+        }
+      }
     }
-    
-    if (m_RawEvents->IsAnyEventValid() == false) SelectionsPassed = false;    
-    
-    m_TimeTrack += Timer.ElapsedTime();
-    
-  } else {
-    mdebug<<"I am not doing Tracking!"<<endl;
   }
   
   //mout << "AL evtid=" << m_RawEvents->Get(0)->GetRawEventAt(0)->GetEventId() << " evtype=" << m_RawEvents->Get(0)->GetRawEventAt(0)->GetEventTypeAsString() << endl;
@@ -773,49 +791,83 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
   
   // Section E: Compton sequence reconstruction       
   
-  if (SelectionsPassed == true && m_CSRAlgorithm > c_CSRAlgoNone) {
-    
-    Timer.Start();
-    
-    if (m_CSR == nullptr) {
-      merr<<"CSR pointer is zero. You changed the event reconstruction setup without calling PreAnalysis()!"<<show;
-      return c_AnalysisUndefinedError;
-    }
-    
-    for (unsigned int i = 0; i < m_RawEvents->Size(); ++i) {
-      MRawEventIncarnations* REI = m_RawEvents->Get(i);
-      if (REI->HasOptimumEvent() == false) {
-        m_CSR->Analyze(REI);
+  if (SelectionsPassed == true) {
+    if (m_CSRAlgorithm > c_CSRAlgoNone) {
+      
+      Timer.Start();
+      
+      if (m_CSR == nullptr) {
+        merr<<"CSR pointer is zero. You changed the event reconstruction setup without calling PreAnalysis()!"<<show;
+        return c_AnalysisUndefinedError;
       }
-    }
-    
-    if (m_RawEvents->IsAnyEventValid() == false) SelectionsPassed = false;
+      
+      for (unsigned int i = 0; i < m_RawEvents->Size(); ++i) {
+        MRawEventIncarnations* REI = m_RawEvents->Get(i);
+        if (REI->HasOptimumEvent() == false) {
+          m_CSR->Analyze(REI);
+        }
+      }
+      
+      if (m_RawEvents->IsAnyEventValid() == false) SelectionsPassed = false;
 
-    m_TimeCSR += Timer.ElapsedTime();
-    
-  } else {
-    mdebug<<"I am not doing CSR!"<<endl;
+      m_TimeCSR += Timer.ElapsedTime();
+      
+    } else {
+      mdebug<<"I am not doing CSR!"<<endl;
+      // Set all Compton events an unknown
+      for (unsigned int i = 0; i < m_RawEvents->Size(); ++i) {
+        MRawEventIncarnations* REI = m_RawEvents->Get(i);
+        for (int e = 0; e < REI->GetNRawEvents(); e++) {
+          MRERawEvent* RE = REI->GetRawEventAt(e);
+          if (RE->GetEventType() == c_ComptonEvent || RE->GetEventType() == c_PhotoEvent) {
+            // Adrien to Andreas:
+            // Photo events here because historically they were identified in the CSR method.
+            // So no CSR algorithm meant Photo events are of type Unknown in the Tra file
+            // We may not want to keep that behavior in the future
+            RE->SetEventType(c_UnknownEvent);
+            RE->SetGoodEvent(true);
+            RE->SetEventReconstructed(true);
+            REI->SetBestTryEvent(RE);
+          }
+        }
+      }
+    }
   }
   
   
   
   // Section F: Decay algorithm
-  if (SelectionsPassed == true && m_DecayAlgorithm > c_DecayAlgoNone) {
-    
-    if (m_Decay == nullptr) {
-      merr<<"Decay pointer is zero. You changed the event reconstruction setup without calling PreAnalysis()!"<<show;
-      return c_AnalysisUndefinedError;
-    }
-    
-    for (unsigned int i = 0; i < m_RawEvents->Size(); ++i) {
-      MRawEventIncarnations* REI = m_RawEvents->Get(i);
-      m_Decay->Analyze(REI);
+  if (SelectionsPassed == true) {
+    if (m_DecayAlgorithm > c_DecayAlgoNone) {
+      
+      if (m_Decay == nullptr) {
+        merr<<"Decay pointer is zero. You changed the event reconstruction setup without calling PreAnalysis()!"<<show;
+        return c_AnalysisUndefinedError;
+      }
+      
+      for (unsigned int i = 0; i < m_RawEvents->Size(); ++i) {
+        MRawEventIncarnations* REI = m_RawEvents->Get(i);
+        m_Decay->Analyze(REI);
+      }
+      
+      if (m_RawEvents->IsAnyEventValid() == false) SelectionsPassed = false;    
+      
+    } else {
+      mdebug<<"I am not doing Decay!"<<endl;
+      // Set all Decay events an unknown
+      for (unsigned int i = 0; i < m_RawEvents->Size(); ++i) {
+        MRawEventIncarnations* REI = m_RawEvents->Get(i);
+        for (int e = 0; e < REI->GetNRawEvents(); e++) {
+          MRERawEvent* RE = REI->GetRawEventAt(e);
+          if (RE->GetEventType() == c_DecayEvent) {
+            RE->SetEventType(c_UnknownEvent);
+            RE->SetGoodEvent(true);
+            RE->SetEventReconstructed(true);
+            REI->SetBestTryEvent(RE);
+          }
+        }
+      }
     }
-    
-    if (m_RawEvents->IsAnyEventValid() == false) SelectionsPassed = false;    
-    
-  } else {
-    mdebug<<"I am not doing Decay!"<<endl;
   }
   
   

From a262fcd33beecbfa64f0577a2e08a913bc627a0b Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Thu, 11 Sep 2025 15:52:09 -0400
Subject: [PATCH 187/192] [Style] Changed indent on 2 lines

---
 src/revan/src/MERTrackKalman3D.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/revan/src/MERTrackKalman3D.cxx b/src/revan/src/MERTrackKalman3D.cxx
index da9e65c19..54a819730 100644
--- a/src/revan/src/MERTrackKalman3D.cxx
+++ b/src/revan/src/MERTrackKalman3D.cxx
@@ -1140,8 +1140,8 @@ void MERTrackKalman3D::TrackPairs(MRERawEvent* RE)
       if (Electron->ComputeMinDistance(RE->GetRESEAt(r)) < Positron->ComputeMinDistance(RE->GetRESEAt(r))) {
         Electron->AddRESE(RE->GetRESEAt(r));
       } else {
-	Positron->AddRESE(RE->GetRESEAt(r));
-	}
+        Positron->AddRESE(RE->GetRESEAt(r));
+      }
     }
   }
 

From 321a0b7013f812da98a02aceac941e287123c39e Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Thu, 25 Sep 2025 16:25:38 -0400
Subject: [PATCH 188/192] Fix: External event type works when events are
 missing in etp file

---
 src/revan/inc/MRERawEvent.h            |  1 +
 src/revan/src/MEREventTypeExternal.cxx | 16 ++++++++++++----
 src/revan/src/MRERawEvent.cxx          |  7 +++++++
 3 files changed, 20 insertions(+), 4 deletions(-)

diff --git a/src/revan/inc/MRERawEvent.h b/src/revan/inc/MRERawEvent.h
index 65f4e8ce7..0055de75e 100644
--- a/src/revan/inc/MRERawEvent.h
+++ b/src/revan/inc/MRERawEvent.h
@@ -298,6 +298,7 @@ class MRERawEvent : public MRESE, public MRotationInterface
   static const int c_RejectionEventClusteringNoOrigins           = 34;
   static const int c_RejectionEventClusteringEnergyOutOfBounds   = 35;
   static const int c_RejectionNotEnoughHitsInTracker             = 36;
+  static const int c_RejectionNoExternalEventType                = 37;
 
   
   static const double c_NoQualityFactor;
diff --git a/src/revan/src/MEREventTypeExternal.cxx b/src/revan/src/MEREventTypeExternal.cxx
index 42a64a756..bfcbafd1b 100644
--- a/src/revan/src/MEREventTypeExternal.cxx
+++ b/src/revan/src/MEREventTypeExternal.cxx
@@ -74,21 +74,29 @@ bool MEREventTypeExternal::Analyze(MRawEventIncarnations* List)
   }
 
   // Read file
-  streampos filePos = m_FileEventsType->GetFilePosition(); // Position at start of REI
   MRERawEvent* RE = nullptr;  
   for (int e = 0; e < m_List->GetNRawEvents(); e++) {
-    m_FileEventsType->Seek(filePos);// Rewind to position at start of REI
     RE = m_List->GetRawEventAt(e);
-    while(m_FileEventsType->GetNextEvent() && m_FileEventsType->GetEventId() != RE->GetEventId()) {}
+    mout << "Looking for event id=" << RE->GetEventId() << endl;
+    while(m_FileEventsType->GetNextEvent() && m_FileEventsType->GetEventId() != RE->GetEventId()) {
+      mout << " - Got event id=" <<  m_FileEventsType->GetEventId() << " at pos=" << m_FileEventsType->GetFilePosition() << endl;
+    }
     mout << "evtid=" << m_FileEventsType->GetEventId() << endl;
+    if (m_FileEventsType->GetEventId() == -1) {//If reached end of file
+       m_FileEventsType->Rewind(false);
+    }
     if (m_FileEventsType->GetEventId() == RE->GetEventId()) { // if found matching ID
       RE->SetEventType( m_FileEventsType->GetEventType() );
       RE->SetEventTypeProbability( m_FileEventsType->GetEventTypeProbability() );
     } else {
-      merr << "MEREventTypeExternal: No event type found for event ID " << RE->GetEventId() << endl;
+      mout << "MEREventTypeExternal: No event type found for event ID " << RE->GetEventId() << endl;
       RE->SetEventType( c_UnknownEvent );
       RE->SetEventTypeProbability( 0. );
+      RE->SetEventReconstructed();
+      RE->SetRejectionReason(MRERawEvent::c_RejectionNoExternalEventType);// TBC of course!!!!!
     }
+    //m_FileEventsType->Rewind(false);
+    //m_FileEventsType->Seek(filePos);// Be kind, Rewind to position at start of REI
   }
   return true;
 }
diff --git a/src/revan/src/MRERawEvent.cxx b/src/revan/src/MRERawEvent.cxx
index 8fc350878..604333270 100644
--- a/src/revan/src/MRERawEvent.cxx
+++ b/src/revan/src/MRERawEvent.cxx
@@ -1017,6 +1017,13 @@ MString MRERawEvent::GetRejectionReasonAsString(int r, bool Short)
       out<<"Not enough hits in tracker";
     }
     break;
+  case c_RejectionNoExternalEventType:
+    if (Short == true) {
+      out<<"NoExternalEventType";
+    } else {
+      out<<"No External Event Type Provided";
+    }
+    break;
   default:
     if (Short == true) {
       out<<"";

From a907f65fc8b0ffc5799789190465cd7a06786b6a Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@hotmail.fr>
Date: Tue, 30 Sep 2025 12:21:35 -0400
Subject: [PATCH 189/192] Fix: External event type works when events are
 missing in etp file

---
 src/revan/src/MEREventTypeExternal.cxx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/revan/src/MEREventTypeExternal.cxx b/src/revan/src/MEREventTypeExternal.cxx
index bfcbafd1b..0062668ee 100644
--- a/src/revan/src/MEREventTypeExternal.cxx
+++ b/src/revan/src/MEREventTypeExternal.cxx
@@ -77,11 +77,11 @@ bool MEREventTypeExternal::Analyze(MRawEventIncarnations* List)
   MRERawEvent* RE = nullptr;  
   for (int e = 0; e < m_List->GetNRawEvents(); e++) {
     RE = m_List->GetRawEventAt(e);
-    mout << "Looking for event id=" << RE->GetEventId() << endl;
+    //mout << "Looking for event id=" << RE->GetEventId() << endl;
     while(m_FileEventsType->GetNextEvent() && m_FileEventsType->GetEventId() != RE->GetEventId()) {
-      mout << " - Got event id=" <<  m_FileEventsType->GetEventId() << " at pos=" << m_FileEventsType->GetFilePosition() << endl;
+      //mout << " - Got event id=" <<  m_FileEventsType->GetEventId() << " at pos=" << m_FileEventsType->GetFilePosition() << endl;
     }
-    mout << "evtid=" << m_FileEventsType->GetEventId() << endl;
+    //mout << "evtid=" << m_FileEventsType->GetEventId() << endl;
     if (m_FileEventsType->GetEventId() == -1) {//If reached end of file
        m_FileEventsType->Rewind(false);
     }

From c30ba089a6bb3ad1fed30e5750eba4dc3f708d70 Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@hotmail.fr>
Date: Tue, 30 Sep 2025 15:46:44 -0400
Subject: [PATCH 190/192] Perf: Add quick lookup of external event type

---
 src/revan/inc/MEREventTypeExternal.h   |  2 +-
 src/revan/src/MEREventTypeExternal.cxx | 18 ++++++++----------
 2 files changed, 9 insertions(+), 11 deletions(-)

diff --git a/src/revan/inc/MEREventTypeExternal.h b/src/revan/inc/MEREventTypeExternal.h
index 7812bb452..f00f64b72 100644
--- a/src/revan/inc/MEREventTypeExternal.h
+++ b/src/revan/inc/MEREventTypeExternal.h
@@ -40,7 +40,7 @@ class MEREventTypeExternal : public MEREventType
 
   //! Global parameters used by all electron tracking algorithms
   virtual void SetParameters(MString EventTypeFileName);
-  bool Analyze(MRawEventIncarnations* List);
+  bool Analyze(MRawEventIncarnations* List, bool quick);
 
   bool PostAnalysis();
   MString ToString(bool CoreOnly = false) const;
diff --git a/src/revan/src/MEREventTypeExternal.cxx b/src/revan/src/MEREventTypeExternal.cxx
index 0062668ee..a2ef1bb8f 100644
--- a/src/revan/src/MEREventTypeExternal.cxx
+++ b/src/revan/src/MEREventTypeExternal.cxx
@@ -64,7 +64,7 @@ bool MEREventTypeExternal::PostAnalysis()
 
 ////////////////////////////////////////////////////////////////////////////////
 
-bool MEREventTypeExternal::Analyze(MRawEventIncarnations* List)
+bool MEREventTypeExternal::Analyze(MRawEventIncarnations* List, bool quick = true)
 {
   massert(m_FileEventsType);
   MERConstruction::Analyze(List);
@@ -77,13 +77,13 @@ bool MEREventTypeExternal::Analyze(MRawEventIncarnations* List)
   MRERawEvent* RE = nullptr;  
   for (int e = 0; e < m_List->GetNRawEvents(); e++) {
     RE = m_List->GetRawEventAt(e);
-    //mout << "Looking for event id=" << RE->GetEventId() << endl;
-    while(m_FileEventsType->GetNextEvent() && m_FileEventsType->GetEventId() != RE->GetEventId()) {
-      //mout << " - Got event id=" <<  m_FileEventsType->GetEventId() << " at pos=" << m_FileEventsType->GetFilePosition() << endl;
-    }
-    //mout << "evtid=" << m_FileEventsType->GetEventId() << endl;
-    if (m_FileEventsType->GetEventId() == -1) {//If reached end of file
-       m_FileEventsType->Rewind(false);
+    if (quick) {
+      m_FileEventsType->GetNextEvent(); 
+    } else {
+      while(m_FileEventsType->GetNextEvent() && m_FileEventsType->GetEventId() != RE->GetEventId()) {}
+      if (m_FileEventsType->GetEventId() == -1) {//If reached end of file
+         m_FileEventsType->Rewind(false);
+      }
     }
     if (m_FileEventsType->GetEventId() == RE->GetEventId()) { // if found matching ID
       RE->SetEventType( m_FileEventsType->GetEventType() );
@@ -95,8 +95,6 @@ bool MEREventTypeExternal::Analyze(MRawEventIncarnations* List)
       RE->SetEventReconstructed();
       RE->SetRejectionReason(MRERawEvent::c_RejectionNoExternalEventType);// TBC of course!!!!!
     }
-    //m_FileEventsType->Rewind(false);
-    //m_FileEventsType->Seek(filePos);// Be kind, Rewind to position at start of REI
   }
   return true;
 }

From 909d86a721bff1158566eb30bb6d95c87e0923b5 Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@nasa.gov>
Date: Wed, 1 Oct 2025 21:17:15 -0400
Subject: [PATCH 191/192] Style: minor changes

---
 src/revan/src/MEREventTypeExternal.cxx | 2 +-
 src/revan/src/MRERawEvent.cxx          | 2 +-
 src/revan/src/MRawEventAnalyzer.cxx    | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/revan/src/MEREventTypeExternal.cxx b/src/revan/src/MEREventTypeExternal.cxx
index a2ef1bb8f..6b77a0bfe 100644
--- a/src/revan/src/MEREventTypeExternal.cxx
+++ b/src/revan/src/MEREventTypeExternal.cxx
@@ -93,7 +93,7 @@ bool MEREventTypeExternal::Analyze(MRawEventIncarnations* List, bool quick = tru
       RE->SetEventType( c_UnknownEvent );
       RE->SetEventTypeProbability( 0. );
       RE->SetEventReconstructed();
-      RE->SetRejectionReason(MRERawEvent::c_RejectionNoExternalEventType);// TBC of course!!!!!
+      RE->SetRejectionReason(MRERawEvent::c_RejectionNoExternalEventType);
     }
   }
   return true;
diff --git a/src/revan/src/MRERawEvent.cxx b/src/revan/src/MRERawEvent.cxx
index 604333270..9cb1e9f76 100644
--- a/src/revan/src/MRERawEvent.cxx
+++ b/src/revan/src/MRERawEvent.cxx
@@ -1021,7 +1021,7 @@ MString MRERawEvent::GetRejectionReasonAsString(int r, bool Short)
     if (Short == true) {
       out<<"NoExternalEventType";
     } else {
-      out<<"No External Event Type Provided";
+      out<<"The etp file does not contain an event type for this event ID";
     }
     break;
   default:
diff --git a/src/revan/src/MRawEventAnalyzer.cxx b/src/revan/src/MRawEventAnalyzer.cxx
index 5e638fb73..ccbf21b5d 100644
--- a/src/revan/src/MRawEventAnalyzer.cxx
+++ b/src/revan/src/MRawEventAnalyzer.cxx
@@ -770,7 +770,7 @@ unsigned int MRawEventAnalyzer::AnalyzeEvent()
       
     } else {
       mdebug<<"I am not doing Tracking!"<<endl;
-      // Set all Pair and Mip events an unknown
+      // Set all Pair and Mip events as unknown
       for (unsigned int i = 0; i < m_RawEvents->Size(); ++i) {
         MRawEventIncarnations* REI = m_RawEvents->Get(i);
         for (int e = 0; e < REI->GetNRawEvents(); e++) {

From 67f0d9de6f6c1882383a7c673ddc6c3dc8092db6 Mon Sep 17 00:00:00 2001
From: Adrien Laviron <adrien.laviron@hotmail.fr>
Date: Mon, 22 Dec 2025 19:48:51 -0500
Subject: [PATCH 192/192] Minor: allow root 6.28 through 6.36

---
 config/AllowedROOTVersions.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/AllowedROOTVersions.txt b/config/AllowedROOTVersions.txt
index ad5788043..832740832 100644
--- a/config/AllowedROOTVersions.txt
+++ b/config/AllowedROOTVersions.txt
@@ -1 +1 @@
-632 636 
+628 636