diff --git a/config/LecroyScope_v12.config b/config/LecroyScope_v12.config
index f850064..a08deaf 100644
--- a/config/LecroyScope_v12.config
+++ b/config/LecroyScope_v12.config
@@ -9,5 +9,5 @@ z_DUT -15, -12, -9, -6, -3, 0, 3, 6, 9, 12
 3 +. 0.05 0.15 0. 0. LP2+G40  0.
 4 +. 0.05 0.15 0. 0. LP2+G40  0.
 5 +. 0.05 0.15 0. 0. LP2+G40  0.
-6 +. 0.05 0.15 0. 0. LP2+G40  0.
-7 +. 0.05 0.15 0. 0. LP2+G40  0.
\ No newline at end of file
+6 +  0.05 0.15 0. 0. Re+G40  0.
+7 +. 0.05 0.15 0. 0. LP2+G40  0.
diff --git a/include/DatAnalyzer.hh b/include/DatAnalyzer.hh
index 7350563..ac79bb9 100644
--- a/include/DatAnalyzer.hh
+++ b/include/DatAnalyzer.hh
@@ -9,6 +9,7 @@
 // SYS includes
 #include <sys/types.h>
 #include <sys/stat.h>
+#include <typeinfo>
 
 // ROOT INCLUDES
 #include "TFile.h"
@@ -70,6 +71,7 @@ class DatAnalyzer {
         virtual void Analyze();
 
         float GetPulseIntegral(float *a, float *t, unsigned int i_st, unsigned int i_stop); //returns charge in pC asssuming 50 Ohm termination
+        int GetMinIndex(float* array);
         unsigned int GetIdxClosest(float value, float* v, unsigned int i_st, int direction=+1);
         unsigned int GetIdxFirstCross(float value, float* v, unsigned int i_st, int direction=+1);
         void AnalyticalPolinomialSolver(unsigned int Np, float* in_x, float* in_y, unsigned int deg, float* &out_coeff, float* err = 0);
diff --git a/setup_cmslpc_python3.sh b/setup_cmslpc_python3.sh
new file mode 100755
index 0000000..d63c6d6
--- /dev/null
+++ b/setup_cmslpc_python3.sh
@@ -0,0 +1,15 @@
+#!/bin/bash
+echo Setting up CMS TimingDAQ.
+
+source /cvmfs/sft.cern.ch/lcg/releases/LCG_103/Python/3.9.12/x86_64-ubuntu2004-gcc9-opt/Python-env.sh
+source /cvmfs/sft.cern.ch/lcg/releases/LCG_103/ROOT/6.28.00/x86_64-ubuntu2004-gcc9-opt/ROOT-env.sh
+source /cvmfs/sft.cern.ch/lcg/releases/LCG_103/scipy/1.8.0/x86_64-ubuntu2004-gcc9-opt/scipy-env.sh
+
+
+# source /cvmfs/sft.cern.ch/lcg/releases/LCG_88/gcc/4.9.3/x86_64-slc6/setup.sh
+# source /cvmfs/sft.cern.ch/lcg/releases/LCG_96python3/Python/3.6.5/x86_64-slc6-gcc8-opt/Python-env.sh
+# source /cvmfs/sft.cern.ch/lcg/releases/LCG_88/ROOT/6.08.06/x86_64-slc6-gcc49-opt/bin/thisroot.sh
+
+# source /cvmfs/sft.cern.ch/lcg/releases/LCG_96python3/Python/3.6.5/x86_64-slc6-gcc8-opt/Python-env.sh
+# source /cvmfs/sft.cern.ch/lcg/releases/LCG_88/ROOT/6.08.06/x86_64-slc6-gcc49-opt/ROOT-env.sh
+# source /cvmfs/sft.cern.ch/lcg/releases/LCG_88/scipy/0.18.1/x86_64-slc6-gcc49-opt/scipy-env.sh
diff --git a/src/DatAnalyzer.cc b/src/DatAnalyzer.cc
index dc15d9f..d9bc2c9 100644
--- a/src/DatAnalyzer.cc
+++ b/src/DatAnalyzer.cc
@@ -263,11 +263,16 @@ void DatAnalyzer::Analyze(){
       /*******************************
       // -------------- Do  linear fit
       ********************************/
-      if( config->channels[i].algorithm.Contains("Re") ) {
-        unsigned int i_min = GetIdxFirstCross(config->channels[i].re_bounds[0]*amp, channel[i], idx_min, -1);
-        unsigned int i_max = GetIdxFirstCross(config->channels[i].re_bounds[1]*amp, channel[i], i_min, +1);
+      if(config->channels[i].algorithm.Contains("Re") ) {
+        // cout<<sizeof(time[GetTimeIndex(i)])/sizeof(time[GetTimeIndex(i)][0])<<endl;
+        // unsigned int i_min = GetMinIndex(channel[i]); // GetIdxFirstCross(config->channels[i].re_bounds[0]*amp, channel[i], idx_min, -1); config->channels[i].re_bounds[0]*amp
+        unsigned int i_min = GetIdxFirstCross(config->channels[i].re_bounds[0]*amp, channel[i], idx_min, -1); // GetIdxClosest(min(channel[i]), channel[i], idx_min, -1);
+        unsigned int i_max = GetIdxFirstCross(config->channels[i].re_bounds[1]*amp, channel[i], i_min  , +1);
         float t_min = time[GetTimeIndex(i)][i_min];
         float t_max = time[GetTimeIndex(i)][i_max];
+        // cout<<i_min<<"  -----------  "<<i_max<<endl;
+        // cout<<t_min<<"  -----------  "<<t_max<<endl;
+        // cout<<"==========================================="<<endl;
 
         TF1* flinear = new TF1("flinear"+name, "[0]*x+[1]", t_min, t_max);
         flinear->SetLineColor(2);
@@ -278,14 +283,61 @@ void DatAnalyzer::Analyze(){
         pulse->Fit("flinear"+name, opt);
         Re_slope = flinear->GetParameter(0);
         Re_b     = flinear->GetParameter(1);
-
+        // cout<<"==========================================="<<endl;
+        // cout<<config->channels[i].algorithm<<endl;
         for ( auto f : config->constant_fraction ) {
-          var[Form("linear_RE_%d", (int)(100*f))][i] = (f*amp-Re_b)/Re_slope;
+          var[Form("linear_RE_%d", (int)(100*f))][i] = (f*amp-Re_b)/Re_slope + myTimeOffset;
         }
+        // cout<<var[Form("linear_RE_%d", (int)(100*0.2))][i]<<endl;
+        // cout<<"==========================================="<<endl;
 
         for ( auto thr : config->constant_threshold ) {
-          var[Form("linear_RE__%dmV", (int)(fabs(thr)))][i] = (thr-Re_b)/Re_slope;
+            var[Form("linear_RE__%dmV", (int)(fabs(thr)))][i] = (thr-Re_b)/Re_slope + myTimeOffset;
+        }
+        cout<<"==========================================="<<endl;
+
+        // if (i_evt > 0 && i_evt < 10) { // Plotting the clock and the fitted line.
+        TCanvas * c = new TCanvas(Form("fit_results%d", i_evt), Form("fit_results%d", i_evt));
+        // pulse->Draw(Form("channels[%d]:time", i), Form("event==%d", i_evt));
+        const int bins = NUM_SAMPLES; // round(sizeof(channel[i])/sizeof(int));
+        if (var[Form("linear_RE_%d", (int)(100*0.2))][i] == 0) {
+            cout<<"Clock time stamp is 0: "<<0.2*amp<<"     "<<Re_b<<endl;
+        }
+        // cout<<t_min<<"     "<<t_max<<"     "<<bins<<endl;
+
+        float line[bins] = {};
+        float t = t_min;
+        float time_array[bins] = {};
+        // float clock_waveform[bins] = {};
+        for (int b = 0; b < bins; b++) {
+            t += b*(t_max - t_min)/bins;
+            time_array[b] = t;
+            line[b] = Re_slope * t + Re_b;
+            // clock_waveform[b] = channel[i][b]
+            // cout<<t<<"         "<<line[b]<<endl;
         }
+        // [GetTimeIndex(i)]
+        // for (int k =0; k<bins; k++) {
+        //     cout<<k<<")     "<<typeid(time[k]).name()<<"     "<<typeid(channel[k]).name()<<endl;
+        // }
+        TGraph * clock_plot = new TGraph(bins, time[GetTimeIndex(i)], channel[i]);
+        TGraph * line_plot  = new TGraph(bins, time_array, line);
+        cout<<"The size of the time:    "<<sizeof(time[GetTimeIndex(i)])/sizeof(time[GetTimeIndex(i)][0])<<endl;
+        cout<<"The size of the channel: "<<sizeof(channel[i])/sizeof(channel[i][0])<<endl;
+        line_plot->SetLineColor(2);
+        line_plot->SetLineWidth(2);
+        clock_plot->SetLineColor(4);
+        clock_plot->SetLineWidth(2);
+
+        clock_plot->Draw("");
+        line_plot->Draw("same");
+
+        c->SaveAs(Form("/home/daq/ETROC2_Test_Stand/module_test_sw/analysis/FIT_PLOTS_TEST/fit_results%d.png", i_evt));
+        delete clock_plot;
+        delete line_plot;
+        delete c;
+
+        // }
 
         delete flinear;
       }
@@ -1288,15 +1340,14 @@ unsigned int DatAnalyzer::GetIdxClosest(float value, float* v, unsigned int i_st
 
 unsigned int DatAnalyzer::GetIdxFirstCross(float value, float* v, unsigned int i_st, int direction) {
   unsigned int idx_end = direction>0 ? NUM_SAMPLES-1 : 0;
+  bool rising = value > v[i_st]? true : false; // Check if the given max value is greater than the given waveform amplitude at a given start time (i_st).
 
-  bool rising = value > v[i_st]? true : false;
-
+  // if it is: the value of the waveform needs to rise and otherwise it doesn't need so the function will return the i_st.
   unsigned int i = i_st;
-
-  while( i != idx_end ) {
-    if(rising && v[i] > value) break;
-    else if( !rising && v[i] < value) break;
-    i += direction;
+  while( (i != idx_end)) { // loop over the time bins
+    if(rising && v[i] > value) break; // check if the rising variable is true and if the waveform value is going higher than the given amplitude value. And stops the loop.
+    else if( !rising && v[i] < value) break; // check if the rising variable is false and if the waveform value is still lower than the given amplitude value. And stops the loop.
+    i += direction; // Otherwise it moves to the next time bin.
   }
 
   return i;
@@ -1437,6 +1488,21 @@ int DatAnalyzer::TimeOverThreshold(Interpolator *voltage, double tThresh, double
 
 };
 
+int DatAnalyzer::GetMinIndex(float* array) {
+    float min = 10000;
+    int index = 10000;
+    for (int i = 0; i < (sizeof(array) / sizeof(array[0])); i++) {
+        if (array[i] < min) {
+            min = array[i];
+            cout<<i<<", ";
+            index = i;
+        }
+    }
+    cout<<endl;
+    cout<<min<<endl;
+    return index;
+};
+
 float DatAnalyzer::FrequencySpectrum(double freq, double tMin, double tMax, int ich, int t_index){
 
 	const int range = 0; // extension of samples to be used beyond [tMin, tMax]
@@ -1460,21 +1526,21 @@ float DatAnalyzer::FrequencySpectrum(double freq, double tMin, double tMax, int
 
 float DatAnalyzer::FrequencySpectrum(double freq, double tMin, double tMax, unsigned int n_samples, float* my_channel, float* my_time)
 {
-  const int range = 0; // extension of samples to be used beyond [tMin, tMax]
-	double deltaT = (my_time[n_samples - 1] - my_time[0])/(double)(n_samples - 1); // sampling time interval
-	double fCut = 0.5/deltaT; // cut frequency = 0.5 * sampling frequency from WST
-	int n_min = floor(tMin/deltaT) - range; // first sample to use
-	int n_max = ceil(tMax/deltaT) + range; // last sample to use
-	n_min = std::max(n_min,0); // check low limit
-	n_max = std::min(n_max, (int)(n_samples - 1)); // check high limit
+  const int range = 0;
+	double deltaT = (my_time[n_samples - 1] - my_time[0])/(double)(n_samples - 1);
+	double fCut = 0.5/deltaT;
+	int n_min = floor(tMin/deltaT) - range;
+	int n_max = ceil(tMax/deltaT) + range;
+	n_min = std::max(n_min,0);
+	n_max = std::min(n_max, (int)(n_samples - 1));
 	int n_0 = (n_min + n_max)/2;
 
-	TComplex s(0.,0.); // Fourier transform at freq
-	TComplex I(0.,1.); // i
+	TComplex s(0.,0.);
+	TComplex I(0.,1.);
 
 	for(int n = n_min; n <= n_max; n++)
 	{
-    s += deltaT*(double)my_channel[n]*TComplex::Exp(-I*(2.*TMath::Pi()*freq*(n-n_0)*deltaT));//maybe don't need n_0 here, I think it will just add a phase to the fourier transform
+    s += deltaT*(double)my_channel[n]*TComplex::Exp(-I*(2.*TMath::Pi()*freq*(n-n_0)*deltaT));
 	}
   return s.Rho();
 };