Structure python directory as a python package

examples/analysis_example.py

@@ -4,9 +4,10 @@
 from argparse import ArgumentParser
 
 import ROOT
-import rootUtils as ut
-from experimental import analysis_toolkit
-from backports import tdirectory634
+
+import fairship.utils.root as ut
+from fairship.experimental import analysis_toolkit
+from fairship.backports import tdirectory634
 
 
 def main():

geometry/config_tester.py

@@ -1,10 +1,11 @@
 #!/usr/bin/env python
 import os
 import json
-from ShipGeoConfig import ConfigRegistry
 import logging
 import argparse
 
+from fairship.ShipGeoConfig import ConfigRegistry
+
 logging.info("")
 logger = logging.getLogger()
 logger.setLevel(logging.INFO)

geometry/geometry_config.py

@@ -1,8 +1,9 @@
 import os
 
-import shipunit as u
 import yaml
-from ShipGeoConfig import AttrDict, ConfigRegistry
+
+import fairship.core.shipunit as u
+from fairship.ShipGeoConfig import AttrDict, ConfigRegistry
 
 # the following params should be passed through 'ConfigRegistry.loadpy' method
 # nuTargetPassive = 1  #0 = with active layers, 1 = only passive

macro/ShipAna.py

@@ -3,16 +3,18 @@
 import sys
 import ROOT
 import ctypes
-import rootUtils as ut
-import shipunit as u
-from ShipGeoConfig import ConfigRegistry, load_from_root_file
-import shipRoot_conf
-from backports import tdirectory634
 from argparse import ArgumentParser
-import decorators
+
+import fairship.utils.root as ut
+import fairship.core.shipunit as u
+from fairship.ShipGeoConfig import ConfigRegistry
+from fairship.utils.rootpy_pickler import Unpickler
+from fairship.utils.root_decorators import apply_decorators
+import fairship.shipRoot_conf as shipRoot_conf
+from fairship.backports import tdirectory634
 
 shipRoot_conf.configure()
-decorators.apply_decorators()
+apply_decorators()
 PDG = ROOT.TDatabasePDG.Instance()
 
 chi2CutOff  = 4.
@@ -47,7 +49,7 @@
 dy = ShipGeo.Yheight/u.m
 
 # -----Create geometry----------------------------------------------
-import shipDet_conf
+import fairship.shipDet_conf as shipDet_conf
 run = ROOT.FairRunSim()
 run.SetName("TGeant4")  # Transport engine
 run.SetSink(ROOT.FairRootFileSink(ROOT.TMemFile('output', 'recreate')))  # Dummy output file
@@ -56,7 +58,7 @@
 # -----Create geometry----------------------------------------------
 modules = shipDet_conf.configure(run,ShipGeo)
 
-import geomGeant4
+import fairship.geomGeant4 as geomGeant4
 if hasattr(ShipGeo.Bfield,"fieldMap"):
   fieldMaker = geomGeant4.addVMCFields(ShipGeo, '', True, withVirtualMC = False)
 else:
@@ -77,7 +79,7 @@
  i+=1
 
 # prepare veto decisions
-import shipVeto
+import fairship.shipVeto as shipVeto
 veto = shipVeto.Task(sTree)
 vetoDets={}
 log={}
@@ -120,7 +122,7 @@
 ut.bookHist(h,'nrtracks','nr of tracks in signal selected',10,-0.5,9.5)
 ut.bookHist(h,'nrSBT','nr of hits in SBT',100,-0.5,99.5)
 
-import TrackExtrapolateTool
+from fairship.utils.track_extrapolate import extrapolateToPlane
 
 def VertexError(t1,t2,PosDir,CovMat,scalFac):
 # with improved Vx x,y resolution
@@ -246,7 +248,7 @@ def checkFiducialVolume(sTree,tkey,dy):
    inside = True
    if not fiducialCut: return True
    fT = sTree.FitTracks[tkey]
-   rc,pos,mom = TrackExtrapolateTool.extrapolateToPlane(fT,ShipGeo.Bfield.z)
+   rc,pos,mom = extrapolateToPlane(fT,ShipGeo.Bfield.z)
    if not rc: return False
    if not dist2InnerWall(pos.X(),pos.Y(),pos.Z())>0: return False
    return inside
@@ -637,7 +639,7 @@ def myEventLoop(n):
 # check extrapolation to TimeDet if exists
   if hasattr(ShipGeo,"TimeDet"):
    for fT in sTree.FitTracks:
-     rc,pos,mom = TrackExtrapolateTool.extrapolateToPlane(fT,ShipGeo.TimeDet.z)
+     rc,pos,mom = extrapolateToPlane(fT,ShipGeo.TimeDet.z)
      if rc:
       for aPoint in sTree.TimeDetPoint:
        h['extrapTimeDetX'].Fill(pos.X()-aPoint.GetX())

macro/ShipReco.py

@@ -17,11 +17,12 @@ def mem_monitor():
     print("memory: virtual = %5.2F MB  physical = %5.2F MB"%(vmsize/1.0E3,pmsize/1.0E3))
 
 import ROOT,os,sys
-import global_variables
-import rootUtils as ut
-import shipunit as u
-import shipRoot_conf
-from backports import tdirectory634
+
+import fairship.core.global_variables as global_variables
+import fairship.utils.root as ut
+import fairship.core.shipunit as u
+import fairship.shipRoot_conf as shipRoot_conf
+from fairship.backports import tdirectory634
 
 shipRoot_conf.configure()
 
@@ -78,7 +79,9 @@ def mem_monitor():
 fgeo = ROOT.TFile.Open(options.geoFile)
 geoMat =  ROOT.genfit.TGeoMaterialInterface()  # if only called in ShipDigiReco -> crash, reason unknown
 
-from ShipGeoConfig import ConfigRegistry, load_from_root_file
+from fairship.ShipGeoConfig import ConfigRegistry, load_from_root_file
+from fairship.utils.rootpy_pickler import Unpickler
+
 #load Shipgeo dictionary
 ShipGeo = load_from_root_file(fgeo, 'ShipGeo')
 
@@ -91,7 +94,7 @@ def mem_monitor():
  ut.bookHist(h, 'nmeas', 'nr measurments', 100, 0., 50.)
  ut.bookHist(h,'chi2','Chi2/DOF',100,0.,20.)
 
-import shipDet_conf
+import fairship.shipDet_conf as shipDet_conf
 run = ROOT.FairRunSim()
 run.SetName("TGeant4")  # Transport engine
 run.SetSink(ROOT.FairRootFileSink(ROOT.TMemFile('output', 'recreate')))  # Dummy output file
@@ -101,7 +104,7 @@ def mem_monitor():
 modules = shipDet_conf.configure(run,ShipGeo)
 # run.Init()
 fgeo["FAIRGeom"]
-import geomGeant4
+import fairship.geomGeant4 as geomGeant4
 
 if hasattr(ShipGeo.Bfield,"fieldMap"):
   fieldMaker = geomGeant4.addVMCFields(ShipGeo, '', True,withVirtualMC = False)
@@ -121,7 +124,7 @@ def mem_monitor():
 global_variables.iEvent = 0
 
 # import reco tasks
-import shipDigiReco
+import fairship.shipDigiReco as shipDigiReco
 
 SHiP = shipDigiReco.ShipDigiReco(outFile,fgeo)
 options.nEvents   = min(SHiP.sTree.GetEntries(),options.nEvents)

macro/checkZpositions.py

@@ -1,5 +1,9 @@
-import ROOT,sys
-from ShipGeoConfig import load_from_root_file
+import ROOT
+import sys
+
+from fairship.ShipGeoConfig import load_from_root_file
+from fairship.utils.rootpy_pickler import Unpickler
+
 badBoys={}
 f1,f2 = sys.argv[1], sys.argv[2]
 fgeoOld=ROOT.TFile(f1)

macro/create_field_perturbation.py

@@ -1,13 +1,13 @@
 import ROOT as r
-import shipunit as u
-import geomGeant4
-from ShipGeoConfig import ConfigRegistry
-import shipDet_conf
-import saveBasicParameters
 import os
-import ShieldUtils
 from argparse import ArgumentParser
 
+import fairship.shipunit as u
+import fairship.shipDet_conf as shipDet_conf
+from fairship.utils.shield import find_shield_center
+from fairship.geomGeant4 import addVMCFields
+from fairship.ShipGeoConfig import ConfigRegistry
+
 
 globalDesigns = {'dy': 10., 'dv': 6, 'ds': 9, 'nud': 3, 'caloDesign': 3, 'strawDesign': 10}
 
@@ -42,9 +42,9 @@ def create_csv_field_map(options):
     run.SetGenerator(primGen)
     run.SetStoreTraj(r.kFALSE)
     run.Init()
-    fieldMaker = geomGeant4.addVMCFields(ship_geo, '', True)
+    fieldMaker = addVMCFields(ship_geo, '', True)
 
-    field_center, shield_half_length = ShieldUtils.find_shield_center(ship_geo)
+    field_center, shield_half_length = find_shield_center(ship_geo)
     print("SHIELD ONLY: CENTER: {}, HALFLENGTH: {}, half_X: {}, half_Y: {}".format(field_center,
                                                                                    shield_half_length,
                                                                                    ship_geo.muShield.half_X_max,

macro/dumpEvent.py

@@ -1,8 +1,10 @@
 # example for dumping an MC event
 import ROOT,os,sys
-import rootUtils as ut
-import shipunit as u
-import ShipGeoConfig
+
+import fairship.utils.root as ut
+import fairship.core.shipunit as u
+import fairship.ShipGeoConfig as ShipGeoConfig
+
 ship_geo = ShipGeoConfig.Config().loadpy("$FAIRSHIP/geometry/geometry_config.py")
 PDG = ROOT.TDatabasePDG.Instance()
 

macro/evd_addParticleFollower.py

@@ -1,6 +1,7 @@
 import ROOT,evd_fillEnergy
 gEve=ROOT.gEve
 import eveGlobal
+
 def execute():
  if not gEve.GetViewers().FindChild('Bar Embedded Viewer side'):
   slot = ROOT.TEveWindow.CreateWindowInTab(gEve.GetBrowser().GetTabRight())

macro/evd_fillEnergy.py

@@ -1,7 +1,7 @@
 import ROOT
-import shipunit as u
-import  eveGlobal
+import eveGlobal
 
+import fairship.core.shipunit as u
 
 def collect_hits(lsOfGlobals, checked_muons):
   MUON = 13

macro/eventDisplay.py

@@ -1,22 +1,23 @@
-#!/usr/bin/env python -i
+#!/us/bin/env python -i
 import ROOT
 import os
 import tkinter
 import atexit
+from argparse import ArgumentParser
+from array import array
 
 ROOT.gROOT.ProcessLine('#include "FairEventHeader.h"')
 # only helps if class version in FairEventHeader.h is increased
 
-from argparse import ArgumentParser
-from ShipGeoConfig import ConfigRegistry, load_from_root_file
-from array import array
-import shipunit as u
-import shipRoot_conf
-import shipDet_conf
-import decorators
+from fairship.ShipGeoConfig import ConfigRegistry
+from fairship.utils.rootpy_pickler import Unpickler
+from fairship.utils.root_decorators import apply_decorators
+import fairship.core.shipunit as u
+import fairship.shipRoot_conf as shipRoot_conf
+import fairship.shipDet_conf as shipDet_conf
 
 shipRoot_conf.configure()
-decorators.apply_decorators()
+apply_decorators()
 
 
 def evExit():
@@ -499,7 +500,7 @@ def DrawFittedTracks(self, option=""):
             pid = fstate.getPDG()
             zs = self.z_start
             for i in range(self.niter):
-                rc, newpos, newmom = TrackExtrapolateTool.extrapolateToPlane(fT, zs)
+                rc, newpos, newmom = extrapolateToPlane(fT, zs)
                 if rc:
                     DTrack.SetNextPoint(newpos.X(), newpos.Y(), newpos.Z())
                 else:
@@ -1180,7 +1181,11 @@ def debugStraw(n):
 
 
 # ----Load the default libraries------
-from basiclibs import *
+from fairship.utils.basiclibs import load_basic_libs
+load_basic_libs()
+
+# -----   Reconstruction run   -------------------------------------------
+fRun = ROOT.FairRunAna()
 if options.geoFile:
     fRun.SetGeomFile(options.geoFile)
 
@@ -1291,7 +1296,7 @@ def debugStraw(n):
     fM = ROOT.genfit.FieldManager.getInstance()
     fM.init(bfield)
 
-import TrackExtrapolateTool
+from fairship.utils.track_extrapolate import extrapolateToPlane
 
 br = gEve.GetBrowser()
 br.HideBottomTab()  # make more space for graphics

macro/flux_map.py

@@ -2,10 +2,11 @@
 import argparse
 import numpy as np
 import ROOT as r
-import shipunit as u
-import rootUtils as ut
 import logger as log
 
+import fairship.core.shipunit as u
+import fairship.utils.root as ut
+
 
 def main():
     parser = argparse.ArgumentParser(description='Script to create flux maps.')

macro/inspectGeant4Geo.py

@@ -1,7 +1,10 @@
 import sys
 import ROOT
-from ShipGeoConfig import load_from_root_file
-import shipRoot_conf
+
+from fairship.ShipGeoConfig import load_from_root_file
+from fairship.utils.rootpy_pickler import Unpickler
+import fairship.shipRoot_conf as shipRoot_conf
+
 shipRoot_conf.configure()
 
 fname = 'geofile_full.10.0.Pythia8-TGeant4.root'
@@ -10,7 +13,7 @@
 
 fgeo = ROOT.TFile(fname)
 sGeo = fgeo.Get("FAIRGeom")
-import shipDet_conf
+import fairship.shipDet_conf as shipDet_conf
 run = ROOT.FairRunSim()
 ShipGeo = load_from_root_file(fgeo, 'ShipGeo')
 modules = shipDet_conf.configure(run, ShipGeo)
@@ -19,6 +22,6 @@
 run.SetSink(ROOT.FairRootFileSink(ROOT.TMemFile('output', 'recreate')))
 run.Init()
 run.Run(0)
-import geomGeant4
+import fairship.geomGeant4 as geomGeant4
 geomGeant4.printVMCFields()
 geomGeant4.printWeightsandFields()

macro/makeCascade.py

@@ -1,6 +1,7 @@
 import ROOT,time,os,sys,random,copy,argparse
 from array import array
-import rootUtils as ut
+
+import fairship.utils.root as ut
 
 ROOT.gROOT.LoadMacro("$VMCWORKDIR/gconfig/basiclibs.C")
 ROOT.basiclibs()

macro/makeDecay.py

@@ -1,7 +1,9 @@
 #Use Pythia8 to decay the signals (Charm/Beauty) as produced by makeCascade.
 #Output is an ntuple with muon/neutrinos
 import ROOT,time,os,sys,random,getopt
-import rootUtils as ut
+
+import fairship.utils.root as ut
+
 ROOT.gROOT.LoadMacro("$VMCWORKDIR/gconfig/basiclibs.C")
 ROOT.basiclibs()
 

macro/makeGenieEvents.py

@@ -36,9 +36,9 @@
 from collections.abc import Mapping, Sequence
 from pathlib import Path
 
+import fairship.shipRoot_conf as shipRoot_conf
 import ROOT  # type: ignore
-import shipRoot_conf
-from genie_interface import (
+from fairship.utils.genie_interface import (
     add_hists,
     generate_genie_events,
     get_1D_flux_name,
@@ -65,6 +65,7 @@
 NUPDGLIST = [16, -16, 14, -14, 12, -12]
 
 # ------------------------------ Helpers ---------------------------------------
+shipRoot_conf.configure()
 
 
 def extract_nu_over_nubar(