From: Stefan Strohauer <sstrohauer@jspc31.x-matter.uni-frankfurt.de>
Date: Tue, 20 Aug 2013 14:01:36 +0000 (+0200)
Subject: Inital commit of ROOT analysis code
X-Git-Url: https://jspc29.x-matter.uni-frankfurt.de/git/?a=commitdiff_plain;h=41f9b403f065d3238d69b315d63c102824d906b4;p=radhard.git

Inital commit of ROOT analysis code
---

diff --git a/PlotGraph/CSVRow.C b/PlotGraph/CSVRow.C
new file mode 100644
index 0000000..9bf3cc1
--- /dev/null
+++ b/PlotGraph/CSVRow.C
@@ -0,0 +1,34 @@
+#include "CSVRow.h"
+
+#include <iostream>
+#include <sstream>
+#include <vector>
+#include <string>
+
+
+std::string const& CSVRow::operator[](std::size_t index) const {
+  return m_data[index];
+}
+
+std::size_t CSVRow::size() const {
+  return m_data.size();
+}
+
+void CSVRow::readNextRow(std::istream& str) {
+  std::string         line;
+  std::getline(str,line);
+  
+  std::stringstream   lineStream(line);
+  std::string         cell;
+  
+  m_data.clear();
+  while(std::getline(lineStream,cell,'\t')) {
+    m_data.push_back(cell);
+  }
+}
+
+std::istream& operator>>(std::istream& str,CSVRow& data) {
+  data.readNextRow(str);
+  return str;
+}  
+
diff --git a/PlotGraph/CSVRow.h b/PlotGraph/CSVRow.h
new file mode 100644
index 0000000..c11e33c
--- /dev/null
+++ b/PlotGraph/CSVRow.h
@@ -0,0 +1,22 @@
+#ifndef CSVROW_H
+#define CSVROW_H
+
+
+#include <vector>
+#include <string>
+
+class CSVRow {
+public:
+  std::string const& operator[](std::size_t index) const;
+  std::size_t size() const;
+  void readNextRow(std::istream& str);
+ 
+  friend std::istream& operator>>(std::istream& str,CSVRow& data);
+
+private:
+  std::vector<std::string>    m_data;
+};
+
+//std::istream& operator>>(std::istream& str,CSVRow& data);
+
+#endif
diff --git a/PlotGraph/PlotGraph.C b/PlotGraph/PlotGraph.C
new file mode 100644
index 0000000..3cc39d1
--- /dev/null
+++ b/PlotGraph/PlotGraph.C
@@ -0,0 +1,468 @@
+#include <iostream>
+#include <fstream>
+#include <vector>
+#include <string>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <sys/time.h>
+#include <stdlib.h>
+
+#include "CSVRow.h"
+//#ifdef __CINT__
+#include "CSVRow.C"	// bad C-style... but root wants it this way... no correct separation of declaration and implementation possible.
+//#endif
+
+#include "TFile.h"
+#include "TTree.h"
+#include "TNtuple.h"
+#include "TBranch.h"
+#include "TString.h"
+#include "TCanvas.h"
+#include "TH1F.h"
+#include "TLegend.h"
+#include "TF1.h"
+
+#define COLRUNNO 0
+#define COLTEMP 2
+#define COLTEMPSENS 3
+#define COLCHIP 5
+#define COLSOURCE 6
+#define COLMATRIX 7
+#define COLRADDOSE 8
+#define COLDONE 10
+
+#define NUMPIXELS 25
+#define RIGHT_BOUNDARY 400
+
+#define VETO_THRESHOLD 20
+
+#define LABORBUCH "RelevantRuns.csv"
+#define DATAPATH "/local/sstrohauer/data/data_8.8.2013_19:21/"
+#define DRAW_SINGLE_HISTOGRAMS true
+#define DRAW_SUMMED_HISTOGRAMS true
+#define DRAW_VETO_HISTOGRAMS true
+#define DRAW_FITS true
+#define PRINT_HEADER false
+
+void PlotGraph(Float_t selTemp, Int_t selChip, std::string selSource, Int_t selMatrix6480, Int_t selSubmatrix, Float_t selRadDose)
+{
+  Int_t		runNo;		// run number
+  Float_t	temperature;	// desired temperature
+  Float_t	tempSens;	// actual temperature
+  Int_t		chip;		// chip number (eg. 1-6)
+  std::string	source;
+  Int_t		matrix6480;	// which matrix?
+  Float_t	radDose;
+  Bool_t	runFinished;	// measurement already done?
+  std::string	matrixAB;
+  Int_t		submatrix;
+  Int_t		numSubmatrices;
+  
+  timeval start, end;
+  int diff;
+  gettimeofday(&start, 0);
+  
+  std::ifstream	file(LABORBUCH);
+  CSVRow	row;
+  file >> row;	// read first row (header) of the laboratory book
+  
+  
+  std::vector<TH1F*>	histNtuple;
+  std::vector<TH1F*>	histNtupleSum;
+  std::vector<TH1F*>	histNtupleVeto;
+  Int_t			nHistNtuple = 0;
+  std::vector<std::string>	runDetails;
+  std::vector<Float_t>	fitMaxPosX;
+  std::vector<Float_t>	fitMaxPosXSum;
+  std::vector<Float_t>	fitMaxPosXVeto;
+  
+  TLegend* leg = new TLegend(0.5,0.5,0.89,0.89);//(0.6,0.7,0.89,0.89);
+//   leg->SetHeader();//"Legend Title");
+  leg->SetFillStyle(0);
+  
+//   cout << "runNo\tTemp\tChip\tSource\tMatrix\tRadDose\tSubmtrx\n";
+  while (file >> row) {
+    
+    try {
+      if (row[COLRUNNO] == "") 
+	continue;	// no relevant data in this row
+      runNo = atoi(row[COLRUNNO].c_str());	// run number (conversion works like runNo = stoi(std::string ("300");)
+      temperature = atof(row[COLTEMP].c_str());	// temperature
+      tempSens = atof(row[COLTEMPSENS].c_str());	// temperature
+      chip = atoi(row[COLCHIP].c_str());
+      source = row[COLSOURCE];
+      matrix6480 = atoi(row[COLMATRIX].c_str());	// which matrix?      
+      radDose = atof(row[COLRADDOSE].c_str());
+      runFinished = row[COLDONE] == "y";	// measurement already done?
+      
+      if (!runFinished) 
+	continue;
+      
+      if (selMatrix6480 == 64)
+	numSubmatrices = 6;	// could change for different Mimosa chips
+      else if (selMatrix6480 == 80)
+	numSubmatrices = 6;
+      else if (selMatrix6480 == -1)
+	numSubmatrices = 6;
+      else
+	cout << "Unknown matrix: " << selMatrix6480 << endl;
+      
+      for (submatrix=0; submatrix < numSubmatrices; submatrix++){
+	if (   (temperature == selTemp || selTemp == -1)
+	  && (chip == selChip || selChip == -1)
+	  && (source == selSource || selSource == "-1")
+	  && (matrix6480 == selMatrix6480 || selMatrix6480 == -1)
+	  && (radDose == selRadDose || selRadDose == -1)
+	  && (submatrix == selSubmatrix || selSubmatrix == -1))
+	{
+// 	  cout << "runNo " << runNo << "\tTemperature " << temperature << "\tChip " << chip << "\tSource " << source << "\tMatrix " << matrix6480 << "\tRad.dose " << radDose << "\tSubmatrix " << submatrix << endl;
+	  if (PRINT_HEADER)
+	    cout << runNo << "\t" << temperature << "\t" << chip << "\t" << source << "\t" << matrix6480 << "\t" << radDose << "\t" << submatrix << endl;
+	  
+	  runDetails.push_back(Form("%i\t%.1f\t%.1f\t%i\t%s\t%i\t%.2E\t%i", runNo, temperature, tempSens, chip, source.c_str(), matrix6480, radDose, submatrix));
+	  
+	  
+	  // open the file
+	  TString path = TString(DATAPATH) + Form("%i/%i_0_%i.root", runNo, runNo, submatrix);
+	  TFile* f = TFile::Open(path);
+	  if (f->IsZombie()) {
+	    // if we cannot open the file, print an error messageForm("hist%i",nHistNtuple) and return immediatly
+	    printf("Error: cannot open %s\n", path.Data());
+	    return;
+	  }
+	  
+	  // get a pointer to the tree
+	  TNtuple* hitNtuple = (TNtuple*) f->Get("hit");
+	  TNtuple* hitsNtuple = (TNtuple*) f->Get("hits");
+	  
+	  // one array element and one branch for each pixel
+	  Float_t pixel[NUMPIXELS];
+	  TBranch* pixelBranch[NUMPIXELS];
+	  for (Int_t cnt=0; cnt<NUMPIXELS; cnt++) {
+	    hitNtuple->SetBranchAddress(Form("p%i",cnt+1), &pixel[cnt], &pixelBranch[cnt]);
+	  }
+	  Float_t frame;
+	  TBranch* frameBranch;
+	  hitNtuple->SetBranchAddress("frame", &frame, &frameBranch);
+	  
+	  Float_t frameCounts;
+	  TBranch* frameCountsBranch;
+	  hitsNtuple->SetBranchAddress("counts", &frameCounts, &frameCountsBranch);
+	  
+	  // create histogram
+	  histNtuple.push_back(new TH1F(Form("hist%i",nHistNtuple), "Histogram title", 200, 0, RIGHT_BOUNDARY));
+	  histNtupleSum.push_back(new TH1F(Form("histSum%i",nHistNtuple), "Histogram title", 200, 0, RIGHT_BOUNDARY));
+	  histNtupleVeto.push_back(new TH1F(Form("histVeto%i",nHistNtuple), "Histogram title", 200, 0, RIGHT_BOUNDARY));
+	  
+	  // loop over all hits to fill histogram
+	  Int_t nentries = hitNtuple->GetEntries();
+// 	  Double_t meanNotSeedSum=0;
+// 	  Int_t nhits=0;
+	  
+	  for (Int_t cnt=0; cnt<nentries; cnt++) {
+	    hitNtuple->GetEntry(cnt);
+	    
+	    // take only frames with a maximum of one hit
+// 	    hitsNtuple->GetEntry((Int_t) frame);
+// 	    if (frameCounts > 1)
+// 	      continue;
+	    
+	    
+	    // histogram with the single pixel
+	    histNtuple[nHistNtuple]->Fill(pixel[12]);
+	    
+	    // histogram with the summed pixels
+	    Double_t pixelSum = 0;
+	    for (Int_t i=0; i<NUMPIXELS; i++){
+	      pixelSum += pixel[i];
+	    }
+	    histNtupleSum[nHistNtuple]->Fill(pixelSum);
+	    
+	    // histogram with the single pixel and with "veto trigger"
+	    // for the "histNtupleVeto" take only hits where only the seed pixel contains charge
+	    Double_t notSeedSum = 0;
+	    for (Int_t i=0; i<12; i++)
+	      notSeedSum += pixel[i];
+	    for (Int_t i=13; i<NUMPIXELS; i++)
+	      notSeedSum += pixel[i];
+	    if (abs(notSeedSum) > VETO_THRESHOLD)
+	      continue;
+// 	    meanNotSeedSum+=notSeedSum;
+// 	    nhits++;
+	    histNtupleVeto[nHistNtuple]->Fill(pixel[12]);	// histogram with the single pixel
+	    
+	  }
+// 	  cout<<"Mittelwert"<<meanNotSeedSum/nhits<<endl;
+	  
+	  
+	  histNtuple[nHistNtuple]->SetLineColor(nHistNtuple+1);
+	  histNtuple[nHistNtuple]->SetStats(kFALSE);
+	  histNtupleSum[nHistNtuple]->SetLineColor(nHistNtuple+1);
+	  histNtupleSum[nHistNtuple]->SetStats(kFALSE);
+	  histNtupleSum[nHistNtuple]->SetLineStyle(2);	// make summed graphs dashed
+	  histNtupleVeto[nHistNtuple]->SetLineColor(nHistNtuple+1);
+	  histNtupleVeto[nHistNtuple]->SetStats(kFALSE);
+	  histNtupleVeto[nHistNtuple]->SetLineStyle(3);	// make summed graphs dotted
+// 	  TString legendEntry = Form("#splitline{Run %i: T_{set}=%.1f, T_{sens}=%.1f, Chip=%i, }{Source=%s, Matrix=%i, Submatrix=%i, RadDose=%.2E}", runNo, temperature, tempSens, chip, TString(source).Data(), matrix6480, submatrix, radDose);
+	  TString legendEntry = TString(Form("Run %i: ",runNo)) + (selTemp==-1 ? Form(" T_{set}=%.1f",temperature):"") + Form(" T_{sens}=%.1f",tempSens) + (selChip==-1 ? Form(" Chip=%i",chip):"") + (selSource=="-1" ? Form(" Source=%s",source.c_str()):"") + (selMatrix6480==-1 ? Form(" Matrix=%i",matrix6480):"") + (selSubmatrix==-1 ? Form(" Submatrix=%i",submatrix):"") + (selRadDose==-1 ? Form(" RadDose=%.2E",radDose):"");
+// 	  TString legendEntry = TString(Form("test") + (selTemp==-1 ? Form(", T_{set}=%.1f",temperature):"");// + Form(", T_{sens}=%.1f",tempSens) + (selChip==-1 ? Form(", Chip=%i",chip):"") + (selSource=="-1" ? Form(", Source=%s",source):"") + (selMatrix6480==-1 ? Form(", Matrix=%i",matrix6480):"") + (selSubmatrix==-1 ? Form(", Submatrix=%i",submatrix):"") + (selRadDose==-1 ? Form(", RadDose=%.2E",radDose):"");
+	  leg->AddEntry(histNtuple[nHistNtuple], legendEntry);
+// 	  leg->AddEntry((TObject*)0, "", "");  
+	  
+// 	  histNtuple[nHistNtuple]->SetLineColor(nHistNtuple);
+// 	  histNtuple[nHistNtuple]->Draw();
+	  
+	  cout << "Hits per Frame: " << nentries/frame << endl;
+	  
+	  nHistNtuple++;	// increase 
+	}
+      }
+      
+      
+    }
+    catch(...){
+      cout << "Error while reading laboratory book (run number " << runNo << ")!\n";
+    }
+  }
+
+
+  // determine maximum y-value
+  Float_t maxY = 0;
+  for (std::vector<TH1F*>::iterator it = histNtuple.begin(); it != histNtuple.end(); ++it){
+    Int_t thismax = (*it)->GetMaximum();
+    if (thismax > maxY){
+      maxY = thismax;
+//       maxHistNum = std::distance(histNtuple.begin(), it);
+    }
+  }
+  for (std::vector<TH1F*>::iterator it = histNtupleSum.begin(); it != histNtupleSum.end(); ++it){
+    Int_t thismax = (*it)->GetMaximum();
+    if (thismax > maxY){
+      maxY = thismax;
+//       maxHistNum = std::distance(histNtuple.begin(), it);
+    }
+  }
+  for (std::vector<TH1F*>::iterator it = histNtupleVeto.begin(); it != histNtupleVeto.end(); ++it){
+    Int_t thismax = (*it)->GetMaximum();
+    if (thismax > maxY){
+      maxY = thismax;
+//       maxHistNum = std::distance(histNtuple.begin(), it);
+    }
+  }
+  
+  
+  TCanvas* c1 = new TCanvas();
+  c1->SetTitle("Testtitel");
+  TF1* fitFunc = new TF1("fitFunc","gaus",0,RIGHT_BOUNDARY);
+  // plot every single pixel histogram in one canvas
+  if (DRAW_SINGLE_HISTOGRAMS){
+    for (std::vector<TH1F*>::iterator it = histNtuple.begin(); it != histNtuple.end(); ++it){
+      Int_t cnt = std::distance(histNtuple.begin(), it) ;
+      //     (*it)->SetLineColor(cnt);
+      (*it)->SetMaximum(1.05*maxY);
+      (*it)->Draw((cnt==0)?"":"same");
+      
+      (*it)->GetXaxis()->SetRange((*it)->GetXaxis()->FindBin(20),(*it)->GetXaxis()->FindBin(RIGHT_BOUNDARY));	// look only for maxima with x greater than 20
+      Int_t xValMax = (*it)->GetBinCenter((*it)->GetMaximumBin());
+      (*it)->Fit(fitFunc, "N,Q,W", "", xValMax-10, xValMax+10);
+      (*it)->GetXaxis()->UnZoom();
+      if (DRAW_FITS)
+	fitFunc->DrawCopy("same");
+//       cout << "Maximum bin: " << (*it)->GetBinCenter((*it)->GetMaximumBin()) << endl;
+//       cout << "Maximum of gaussian fit: " << fitFunc->GetParameter(1) << "\n\n";
+      fitMaxPosX.push_back(fitFunc->GetParameter(1));
+//       runDetails[cnt] = runDetails[cnt] + Form("%.2f", fitMaxPosX);
+    }
+  }
+  // plot all summed histograms into the same histogram
+  if (DRAW_SUMMED_HISTOGRAMS){
+    for (std::vector<TH1F*>::iterator it = histNtupleSum.begin(); it != histNtupleSum.end(); ++it){
+      Int_t cnt = std::distance(histNtupleSum.begin(), it) ;
+      (*it)->SetMaximum(1.05*maxY);
+      if (!DRAW_SINGLE_HISTOGRAMS)
+	(*it)->Draw((cnt==0)?"":"same");
+      else 
+	(*it)->Draw("same");
+      
+//       (*it)->GetXaxis()->SetRange((*it)->GetXaxis()->FindBin(fitMaxPosX[cnt] + 25),(*it)->GetXaxis()->FindBin(RIGHT_BOUNDARY));	// look only for maxima with x greater than 25 more right than the peak of the seed pixel
+      (*it)->GetXaxis()->SetRange((*it)->GetXaxis()->FindBin(fitMaxPosX[cnt]),(*it)->GetXaxis()->FindBin(RIGHT_BOUNDARY));	// look only for maxima with x greater than 20
+      Int_t xValMax = (*it)->GetBinCenter((*it)->GetMaximumBin());
+      (*it)->Fit(fitFunc, "N,Q,W", "", xValMax-15, xValMax+15);
+      (*it)->GetXaxis()->UnZoom();
+      if (DRAW_FITS)
+	fitFunc->DrawCopy("same");
+//       cout << "Maximum bin: " << (*it)->GetBinCenter((*it)->GetMaximumBin()) << endl;
+//       cout << "Maximum of gaussian fit: " << fitFunc->GetParameter(1) << "\n\n";
+      fitMaxPosXSum.push_back(fitFunc->GetParameter(1));
+    }
+  }
+  // plot single pixel histograms with veto trigger in the same histogram
+  if (DRAW_VETO_HISTOGRAMS){
+    for (std::vector<TH1F*>::iterator it = histNtupleVeto.begin(); it != histNtupleVeto.end(); ++it){
+      Int_t cnt = std::distance(histNtupleVeto.begin(), it) ;
+      (*it)->SetMaximum(1.05*maxY);
+      if (!DRAW_SINGLE_HISTOGRAMS && !DRAW_SUMMED_HISTOGRAMS)
+	(*it)->Draw((cnt==0)?"":"same");
+      else 
+	(*it)->Draw("same");
+      
+//       (*it)->GetXaxis()->SetRange((*it)->GetXaxis()->FindBin(fitMaxPosX[cnt] + 25),(*it)->GetXaxis()->FindBin(RIGHT_BOUNDARY));	// look only for maxima with x greater than 25 more right than the peak of the seed pixel
+      (*it)->GetXaxis()->SetRange((*it)->GetXaxis()->FindBin(fitMaxPosX[cnt]),(*it)->GetXaxis()->FindBin(RIGHT_BOUNDARY));	// look only for maxima with x greater than 20
+      Int_t xValMax = (*it)->GetBinCenter((*it)->GetMaximumBin());
+      (*it)->Fit(fitFunc, "N,Q,W", "", xValMax-15, xValMax+15);
+      (*it)->GetXaxis()->UnZoom();
+      if (DRAW_FITS)
+	fitFunc->DrawCopy("same");
+//       cout << "Maximum bin: " << (*it)->GetBinCenter((*it)->GetMaximumBin()) << endl;
+//       cout << "Maximum of gaussian fit: " << fitFunc->GetParameter(1) << "\n\n";
+      fitMaxPosXVeto.push_back(fitFunc->GetParameter(1));
+    }
+  }
+  
+  
+  
+  // add legend
+  TString legendEntry = TString("Same Parameters: ") + (selTemp!=-1 ? Form(" T_{set}=%.1f",selTemp):"") + (selChip!=-1 ? Form(" Chip=%i",selChip):"") + (selSource!="-1" ? Form(" Source=%s",selSource.c_str()):"") + (selMatrix6480!=-1 ? Form(" Matrix=%i",selMatrix6480):"") + (selSubmatrix!=-1 ? Form(" Submatrix=%i",selSubmatrix):"") + (selRadDose!=-1 ? Form(" RadDose=%.2E",selRadDose):"");
+  leg->AddEntry((TObject*) 0, legendEntry, "");
+  leg->SetTextSize(0.02);
+  leg->Draw();
+  
+  // print all information
+  TString runDetailsHeader = TString("runNo\tT\tTSens\tChip\tSource\tMatrix\tRadDose\tSubmtrx") + (DRAW_SINGLE_HISTOGRAMS ? "\tColPeak":"") + (DRAW_SUMMED_HISTOGRAMS ? "\tSumColPeak":"") + (DRAW_VETO_HISTOGRAMS ? "\tCalibPeak":"") + "\n";
+  if (PRINT_HEADER)
+    cout << endl << runDetailsHeader;
+  for (UInt_t i=0; i<runDetails.size(); ++i){
+//     cout << runDetails[i] << Form("\t%.2f", fitMaxPosX[i]) << Form("\t%.2f", fitMaxPosXSum[i]) << endl;
+    cout << runDetails[i] << (DRAW_SINGLE_HISTOGRAMS ? Form("\t%.2f", fitMaxPosX[i]):"") << (DRAW_SUMMED_HISTOGRAMS ? Form("\t%.2f", fitMaxPosXSum[i]):"") << (DRAW_VETO_HISTOGRAMS ? Form("\t%.2f", fitMaxPosXVeto[i]):"") << endl;
+  }
+  
+  
+  gettimeofday(&end, 0);
+  diff = (int) (end.tv_sec-start.tv_sec);
+  if (PRINT_HEADER)
+    printf("\nElasped Time: %02i:%02i:%02i\n",(int)((diff%86400)/3600),(int)((diff%3600)/60),(int)(diff%60) );
+  
+}
+
+
+
+
+//   Int_t runNo = 29012;
+//   Int_t submatrix = 0;
+//   
+//   
+//   
+//   
+//   // Variables used to store the data
+//   Int_t     totalSize = 0;        // Sum of data size (in bytes) of all events
+//   Int_t     eventSize = 0;        // Size of the current event
+//   TBranch  *eventSizeBranch = 0;  // Pointer to the event.fEventsize branch
+//   
+//   // open the file
+//   TString path = TString(OUTPUTDATAPATH) + Form("%i/%i_0_%i.root", runNo, runNo, submatrix);
+//   TFile *f = TFile::Open(path);
+//   
+//   if (f == 0) {
+//     // if we cannot open the file, print an error message and return immediatly
+//     printf("Error: cannot open %s\n", path);
+//     return;
+//   }
+//   
+//   // get a pointer to the tree
+//   TNtuple* hitNtuple = (TNtuple*) f->Get("hit");
+//   
+//   hitNtuple->Draw("p13");
+// //   hitNtuple->Draw("p10","","same");
+//   
+//   delete f;
+//   
+//   Int_t runNo = 29016;
+//   Int_t submatrix = 0;
+//   TString path = TString(OUTPUTDATAPATH) + Form("%i/%i_0_%i.root", runNo, runNo, submatrix);
+//   TFile *f = TFile::Open(path);
+//   if (f == 0) {
+//     // if we cannot open the file, print an error message and return immediatly
+//     printf("Error: cannot open %s\n", path);
+//     return;
+//   }
+//   hitNtuple = (TNtuple*) f->Get("hit");
+//   hitNtuple->Draw("p13","","same");
+  
+//  TH1F *hist = new TH1F("hHitNtuple", "p13!! ist das :)");	// dynamic allocation (delete at the end)
+//   Long64_t nentries = hitNtuple->GetEntries();
+//   for (Long64_t i; i=0; i<nentries) {
+//     hist->Fill()
+//   }  
+//   delete hist;
+
+
+
+
+
+
+
+
+// {
+//    TFile f1("essai1.root");
+//    TH1F *h1=f1.Get("2");
+//    TFile f2("essai2.root");
+//    TH1F *h2=f2.Get("2");
+//    TFile f3("essai3.root");
+//    TH1F *h3=f3.Get("2");
+//    
+//    h2->SetLineColor(kRed);
+//    h3->SetLineColor(kGreen);
+//    
+//    h1->Draw("l");
+//    h2->Draw("same");
+//    h3->Draw("same");
+// }
+
+
+
+
+
+
+
+
+//  Int_t runNo = 29012;
+//   Int_t submatrix = 0;
+//   
+//   
+//   
+//   
+//   // Variables used to store the data
+//   Int_t     totalSize = 0;        // Sum of data size (in bytes) of all events
+//   Int_t     eventSize = 0;        // Size of the current event
+//   TBranch  *eventSizeBranch = 0;  // Pointer to the event.fEventsize branch
+//   
+//   // open the file
+//   TString path = TString(OUTPUTDATAPATH) + Form("%i/%i_0_%i.root", runNo, runNo, submatrix);
+//   TFile *f = TFile::Open(path);
+//   
+//   if (f == 0) {
+//     // if we cannot open the file, print an error message and return immediatly
+//     printf("Error: cannot open %s\n", path);
+//     return;
+//   }
+//   
+//   // get a pointer to the tree
+//   TNtuple* hitNtuple = (TNtuple*) f->Get("hit");
+//   
+//   hitNtuple->Draw("p13");
+// //   hitNtuple->Draw("p10","","same");
+//   
+//   delete f;
+//   
+//   Int_t runNo = 29016;
+//   Int_t submatrix = 0;
+//   TString path = TString(OUTPUTDATAPATH) + Form("%i/%i_0_%i.root", runNo, runNo, submatrix);
+//   TFile *f = TFile::Open(path);
+//   if (f == 0) {
+//     // if we cannot open the file, print an error message and return immediatly
+//     printf("Error: cannot open %s\n", path);
+//     return;
+//   }
+//   hitNtuple = (TNtuple*) f->Get("hit");
+//   hitNtuple->Draw("p13","","same");
+  
diff --git a/PlotGraph/RelevantRuns.csv b/PlotGraph/RelevantRuns.csv
new file mode 100644
index 0000000..0a85b9a
--- /dev/null
+++ b/PlotGraph/RelevantRuns.csv
@@ -0,0 +1,114 @@
+Runnr.	Date	Temperature	T-sensor	Events	Chip	Source	64/80	Radiation dose	Vbo	Done?	Allowed T-range	Comment
+29012	5/17/2013	20	21.5	50000	1	Fe55	64	0.00E+00	3.20	y	19 … 21	All the yellow marked measurements were made with a baseline in the range between 500 and 3500 for -20°C and were not modified for the other highlighted measurements.
+29013	5/17/2013	20	21.5	50000	1	Fe55	80	0.00E+00	3.12	y		
+29014	5/17/2013	-20	-15.5	50000	1	Fe55	64	0.00E+00	3.19	y	-12 … -19	
+29015	5/17/2013	-20	-16.0	50000	1	Fe55	80	0.00E+00	3.12	y		
+29016	5/18/2013	-70	-58.0	50000	1	Fe55	64	0.00E+00	3.18	y	-30 … -60	
+29017	5/18/2013	-70	-58.0	50000	1	Fe55	80	0.00E+00	3.10	y		
+												
+29018	5/16/2013	20	20.0	50000	1	none	64	0.00E+00	3.20	y		
+29019	5/16/2013	20	20.5	50000	1	none	80	0.00E+00	3.12	y		
+29020	5/16/2013	-20	-16.5	50000	1	none	64	0.00E+00	3.19	y		
+29021	5/16/2013	-20	-17.0	50000	1	none	80	0.00E+00	3.12	y		
+29022	5/16/2013	-70	-57.5	50000	1	none	64	0.00E+00	3.18	y		
+29023	5/16/2013	-70	-59.5	50000	1	none	80	0.00E+00	3.10	y		
+												
+29024	5/21/2013	20	21.5	50000	1	Sr90	64	0.00E+00	3.20	y		
+29025	5/21/2013	20	21.5	50000	1	Sr90	80	0.00E+00	3.12	y		
+29026	5/21/2013	-20	-14.0	50000	1	Sr90	64	0.00E+00	3.19	y		
+29027	5/21/2013	-20	-14.5	50000	1	Sr90	80	0.00E+00	3.12	y		
+29028	5/21/2013	-70	-53.5	50000	1	Sr90	64	0.00E+00	3.18	y		
+29029	5/21/2013	-70	-54.5	50000	1	Sr90	80	0.00E+00	3.10	y		
+												
+29030	5/27/2013	20	21.0	50000	1	Fe55,dimmed	64	0.00E+00	3.20	y		same as run 29012, but dimmed
+29031	5/27/2013	20	21.0	50000	1	Fe55,dimmed	80	0.00E+00	3.12	y		same as run 29013, but dimmed
+29032	5/28/2013	-20	-16.5	50000	1	Fe55,dimmed	64	0.00E+00	3.19	y		same as run 29014, but dimmed
+29033	5/28/2013	-20	-16.5	50000	1	Fe55,dimmed	80	0.00E+00	3.12	y		same as run 29015, but dimmed
+												
+												
+29034	5/29/2013	20	21.5	50000	2	Fe55,dimmed	64	1.50E+05	3.15	y	19 … 21	
+29035	5/29/2013	20	21.0	50000	2	Fe55,dimmed	80	1.50E+05	3.15	y		
+29036	5/29/2013	-20	-16.0	50000	2	Fe55,dimmed	64	1.50E+05	3.15	y	-12 … -19	
+29037	5/30/2013	-20	-16.0	50000	2	Fe55,dimmed	80	1.50E+05	3.15	y		
+29038	5/30/2013	-70	-57.0	50000	2	Fe55,dimmed	64	1.50E+05	3.15	y	-30 … -60	
+29039	5/30/2013	-70	-56.5	50000	2	Fe55,dimmed	80	1.50E+05	3.15	y		
+												
+29040	5/28/2013	20	21.0	50000	2	none	64	1.50E+05	3.08	y		
+29041	5/28/2013	20	21.0	50000	2	none	80	1.50E+05	3.08	y		
+29042	5/28/2013	-20	-13.5	50000	2	none	64	1.50E+05	3.08	y		
+29043	5/28/2013	-20	-14.5	50000	2	none	80	1.50E+05	3.08	y		
+29044	5/29/2013	-70	-52.5	50000	2	none	64	1.50E+05	3.08	y		
+29045	5/29/2013	-70	-53.5	50000	2	none	80	1.50E+05	3.08	y		
+												
+29046	5/31/2013	20	21.6	50000	2	Sr90	64	1.50E+05	3.15	y		
+29047	5/31/2013	20	21.0	50000	2	Sr90	80	1.50E+05	3.15	y		
+29048	5/31/2013	-20	-15.5	50000	2	Sr90	64	1.50E+05	3.15	y		
+29049	6/2/2013	-20	-16.0	50000	2	Sr90	80	1.50E+05	3.15	y		
+29050	6/2/2013	-70	-54.5	50000	2	Sr90	64	1.50E+05	3.15	y		
+29051	6/2/2013	-70	-54.5	50000	2	Sr90	80	1.50E+05	3.15	y		
+												
+												
+29052	6/7/2013	20	21.0	50000	4	Fe55,dimmed	64	1.00E+12	1.52	y	19 … 21	
+29053	6/7/2013	20	21.0	50000	4	Fe55,dimmed	80	1.00E+12	1.52	y		
+29054	6/7/2013	-20	-15.5	50000	4	Fe55,dimmed	64	1.00E+12	1.52	y	-12 … -19	
+29055	6/7/2013	-20	-16.5	50000	4	Fe55,dimmed	80	1.00E+12	1.52	y		
+29056	6/7/2013	-70	-58.0	50000	4	Fe55,dimmed	64	1.00E+12	1.52	y	-30 … -60	
+29057	6/7/2013	-70	-58.0	50000	4	Fe55,dimmed	80	1.00E+12	1.52	y		
+												
+29058	6/6/2013	20	21.5	50000	4	none	64	1.00E+12	1.52	y		
+29059	6/6/2013	20	21.0	50000	4	none	80	1.00E+12	1.52	y		
+29060	6/6/2013	-20	-15.5	50000	4	none	64	1.00E+12	1.52	y		
+29061	6/6/2013	-20	-15.5	50000	4	none	80	1.00E+12	1.52	y		
+29062	6/6/2013	-70	-54.5	50000	4	none	64	1.00E+12	1.52	y		
+29063	6/6/2013	-70	-56.0	50000	4	none	80	1.00E+12	1.52	y		
+												
+29064	6/10/2013	20	22.0	50000	4	Sr90	64	1.00E+12	1.52	y		
+29065	6/10/2013	20	21.5	50000	4	Sr90	80	1.00E+12	1.52	y		
+29066	6/10/2013	-20	-13.5	50000	4	Sr90	64	1.00E+12	1.52	y		
+29067	6/10/2013	-20	-14.0	50000	4	Sr90	80	1.00E+12	1.52	y		
+29068	6/10/2013	-70	-53.0	50000	4	Sr90	64	1.00E+12	1.52	y		
+29069	6/10/2013	-70	-54.0	50000	4	Sr90	80	1.00E+12	1.52	y		
+												
+												
+29070	6/14/2013	20	21.5	50000	5	Fe55,dimmed	64	3.00E+12	1.57	y	19 … 21	
+29071	6/14/2013	20	21.0	50000	5	Fe55,dimmed	80	3.00E+12	1.55	y		
+29072	6/14/2013	-20	-16.0	50000	5	Fe55,dimmed	64	3.00E+12	1.57	y	-12 … -19	
+29073	6/14/2013	-20	-16.5	50000	5	Fe55,dimmed	80	3.00E+12	1.55	y		
+29074	6/14/2013	-70	-58.5	50000	5	Fe55,dimmed	64	3.00E+12	1.57	y	-30 … -60	
+29075	6/14/2013	-70	-58.5	50000	5	Fe55,dimmed	80	3.00E+12	1.55	y		
+												
+29076	6/13/2013	20	20.5	50000	5	none	64	3.00E+12	1.57	y		
+29077	6/13/2013	20	20.5	50000	5	none	80	3.00E+12	1.55	y		
+29078	6/13/2013	-20	-16.5	50000	5	none	64	3.00E+12	1.57	y		
+29079	6/13/2013	-20	-17.0	50000	5	none	80	3.00E+12	1.55	y		
+29080	6/13/2013	-70	-57.0	50000	5	none	64	3.00E+12	1.57	y		
+29081	6/13/2013	-70	-59.5	50000	5	none	80	3.00E+12	1.55	y		
+												
+29082	6/17/2013	20	21.5	50000	5	Sr90	64	3.00E+12	1.57	y		
+29083	6/17/2013	20	21.0	50000	5	Sr90	80	3.00E+12	1.55	y		
+29084	6/17/2013	-20	-14.0	50000	5	Sr90	64	3.00E+12	1.57	y		
+29085	6/17/2013	-20	-15.0	50000	5	Sr90	80	3.00E+12	1.55	y		
+29086	6/17/2013	-70	-54.0	50000	5	Sr90	64	3.00E+12	1.57	y		
+29087	6/17/2013	-70	-54.5	50000	5	Sr90	80	3.00E+12	1.55	y		
+												
+												
+29088	6/20/2013	20	21.0	50000	6	Fe55,dimmed	64	1.00E+13	1.54	y	19 … 21	
+29089	6/20/2013	20	21.0	50000	6	Fe55,dimmed	80	1.00E+13	1.53	y		
+29090	6/20/2013	-20	-16.5	50000	6	Fe55,dimmed	64	1.00E+13	1.54	y	-12 … -19	
+29091	6/20/2013	-20	-16.5	50000	6	Fe55,dimmed	80	1.00E+13	1.53	y		
+29092	6/20/2013	-70	-58.5	50000	6	Fe55,dimmed	64	1.00E+13	1.54	y	-30 … -60	
+29093	6/20/2013	-70	-59.5	50000	6	Fe55,dimmed	80	1.00E+13	1.53	y		
+												
+29094	6/18/2013	20	20.5	50000	6	none	64	1.00E+13	1.54	y		
+29095	6/18/2013	20	20.5	50000	6	none	80	1.00E+13	1.53	y		
+29096	6/18/2013	-20	-15.5	50000	6	none	64	1.00E+13	1.54	y		
+29097	6/18/2013	-20	-15.5	50000	6	none	80	1.00E+13	1.53	y		
+29098	6/19/2013	-70	-60.0	50000	6	none	64	1.00E+13	1.54	y		
+29099	6/19/2013	-70	-60.0	50000	6	none	80	1.00E+13	1.53	y		
+												
+29100	6/24/2013	20	21.0	50000	6	Sr90	64	1.00E+13	1.54	y		
+29101	6/24/2013	20	21.0	50000	6	Sr90	80	1.00E+13	1.53	y		
+29102	6/24/2013	-20	-15.0	50000	6	Sr90	64	1.00E+13	1.54	y		
+29103	6/24/2013	-20	-16.0	50000	6	Sr90	80	1.00E+13	1.53	y		
+29104	6/24/2013	-70	-54.5	50000	6	Sr90	64	1.00E+13	1.54	y		
+29105	6/24/2013	-70	-55.5	50000	6	Sr90	80	1.00E+13	1.53	y		
diff --git a/ProcessMeasurements/CSVRow.C b/ProcessMeasurements/CSVRow.C
new file mode 100644
index 0000000..9bf3cc1
--- /dev/null
+++ b/ProcessMeasurements/CSVRow.C
@@ -0,0 +1,34 @@
+#include "CSVRow.h"
+
+#include <iostream>
+#include <sstream>
+#include <vector>
+#include <string>
+
+
+std::string const& CSVRow::operator[](std::size_t index) const {
+  return m_data[index];
+}
+
+std::size_t CSVRow::size() const {
+  return m_data.size();
+}
+
+void CSVRow::readNextRow(std::istream& str) {
+  std::string         line;
+  std::getline(str,line);
+  
+  std::stringstream   lineStream(line);
+  std::string         cell;
+  
+  m_data.clear();
+  while(std::getline(lineStream,cell,'\t')) {
+    m_data.push_back(cell);
+  }
+}
+
+std::istream& operator>>(std::istream& str,CSVRow& data) {
+  data.readNextRow(str);
+  return str;
+}  
+
diff --git a/ProcessMeasurements/CSVRow.h b/ProcessMeasurements/CSVRow.h
new file mode 100644
index 0000000..71c7183
--- /dev/null
+++ b/ProcessMeasurements/CSVRow.h
@@ -0,0 +1,19 @@
+#ifndef CSVROW_H
+#define CSVROW_H
+
+
+#include <vector>
+#include <string>
+
+class CSVRow {
+public:
+  std::string const& operator[](std::size_t index) const;
+  std::size_t size() const;
+  void readNextRow(std::istream& str);
+private:
+  std::vector<std::string>    m_data;
+};
+
+std::istream& operator>>(std::istream& str,CSVRow& data);
+
+#endif
\ No newline at end of file
diff --git a/ProcessMeasurements/LaborbuchMi29.csv b/ProcessMeasurements/LaborbuchMi29.csv
new file mode 100644
index 0000000..72da025
--- /dev/null
+++ b/ProcessMeasurements/LaborbuchMi29.csv
@@ -0,0 +1,120 @@
+Runnr.	Date	Temperature	T-sensor	Events	Chip	Source	64/80	Radiation dose	Vbo	Done?	Allowed T-range	Comment
+29008	4/23/2013	-20	-15.0	5000	1	Fe55	64	0.00E+00		y		
+29009	4/23/2013	-20	-15.0	5000	1	none	64	0.00E+00		y		
+29010	4/23/2013	-20	-15.0	5000	1	Fe55	80	0.00E+00		y		
+29011	4/23/2013	-20	-15.0	5000	1	none	80	0.00E+00				
+												
+												
+29012	5/17/2013	20	21.5	50000	1	Fe55	64	0.00E+00	3.20	y	19 … 21	All the yellow marked measurements were made with a baseline in the range between 500 and 3500 for -20°C and were not modified for the other highlighted measurements.
+29013	5/17/2013	20	21.5	50000	1	Fe55	80	0.00E+00	3.12	y		
+29014	5/17/2013	-20	-15.5	50000	1	Fe55	64	0.00E+00	3.19	y	-12 … -19	
+29015	5/17/2013	-20	-16.0	50000	1	Fe55	80	0.00E+00	3.12	y		
+29016	5/18/2013	-70	-58.0	50000	1	Fe55	64	0.00E+00	3.18	y	-30 … -60	
+29017	5/18/2013	-70	-58.0	50000	1	Fe55	80	0.00E+00	3.10	y		
+												
+29018	5/16/2013	20	20.0	50000	1	none	64	0.00E+00	3.20	y		
+29019	5/16/2013	20	20.5	50000	1	none	80	0.00E+00	3.12	y		
+29020	5/16/2013	-20	-16.5	50000	1	none	64	0.00E+00	3.19	y		
+29021	5/16/2013	-20	-17.0	50000	1	none	80	0.00E+00	3.12	y		
+29022	5/16/2013	-70	-57.5	50000	1	none	64	0.00E+00	3.18	y		
+29023	5/16/2013	-70	-59.5	50000	1	none	80	0.00E+00	3.10	y		
+												
+29024	5/21/2013	20	21.5	50000	1	Sr-90	64	0.00E+00	3.20	y		
+29025	5/21/2013	20	21.5	50000	1	Sr-90	80	0.00E+00	3.12	y		
+29026	5/21/2013	-20	-14.0	50000	1	Sr-90	64	0.00E+00	3.19	y		
+29027	5/21/2013	-20	-14.5	50000	1	Sr-90	80	0.00E+00	3.12	y		
+29028	5/21/2013	-70	-53.5	50000	1	Sr-90	64	0.00E+00	3.18	y		
+29029	5/21/2013	-70	-54.5	50000	1	Sr-90	80	0.00E+00	3.10	y		
+												
+29030	5/27/2013	20	21.0	50000	1	Fe55, dimmed	64	0.00E+00	3.20	y		same as run 29012, but dimmed
+29031	5/27/2013	20	21.0	50000	1	Fe55, dimmed	80	0.00E+00	3.12	y		same as run 29013, but dimmed
+29032	5/28/2013	-20	-16.5	50000	1	Fe55, dimmed	64	0.00E+00	3.19	y		same as run 29014, but dimmed
+29033	5/28/2013	-20	-16.5	50000	1	Fe55, dimmed	80	0.00E+00	3.12	y		same as run 29015, but dimmed
+												
+												
+29034	5/29/2013	20	21.5	50000	2	Fe55, dimmed	64	1.50E+05	3.15	y	19 … 21	
+29035	5/29/2013	20	21.0	50000	2	Fe55, dimmed	80	1.50E+05	3.15	y		
+29036	5/29/2013	-20	-16.0	50000	2	Fe55, dimmed	64	1.50E+05	3.15	y	-12 … -19	
+29037	5/30/2013	-20	-16.0	50000	2	Fe55, dimmed	80	1.50E+05	3.15	y		
+29038	5/30/2013	-70	-57.0	50000	2	Fe55, dimmed	64	1.50E+05	3.15	y	-30 … -60	
+29039	5/30/2013	-70	-56.5	50000	2	Fe55, dimmed	80	1.50E+05	3.15	y		
+												
+29040	5/28/2013	20	21.0	50000	2	none	64	1.50E+05	3.08	y		
+29041	5/28/2013	20	21.0	50000	2	none	80	1.50E+05	3.08	y		
+29042	5/28/2013	-20	-13.5	50000	2	none	64	1.50E+05	3.08	y		
+29043	5/28/2013	-20	-14.5	50000	2	none	80	1.50E+05	3.08	y		
+29044	5/29/2013	-70	-52.5	50000	2	none	64	1.50E+05	3.08	y		
+29045	5/29/2013	-70	-53.5	50000	2	none	80	1.50E+05	3.08	y		
+												
+29046	5/31/2013	20	21.6	50000	2	Sr-90	64	1.50E+05	3.15	y		
+29047	5/31/2013	20	21.0	50000	2	Sr-90	80	1.50E+05	3.15	y		
+29048	5/31/2013	-20	-15.5	50000	2	Sr-90	64	1.50E+05	3.15	y		
+29049	6/2/2013	-20	-16.0	50000	2	Sr-90	80	1.50E+05	3.15	y		
+29050	6/2/2013	-70	-54.5	50000	2	Sr-90	64	1.50E+05	3.15	y		
+29051	6/2/2013	-70	-54.5	50000	2	Sr-90	80	1.50E+05	3.15	y		
+												
+												
+29052	6/7/2013	20	21.0	50000	4	Fe55, dimmed	64	1.00E+12	1.52	y	19 … 21	
+29053	6/7/2013	20	21.0	50000	4	Fe55, dimmed	80	1.00E+12	1.52	y		
+29054	6/7/2013	-20	-15.5	50000	4	Fe55, dimmed	64	1.00E+12	1.52	y	-12 … -19	
+29055	6/7/2013	-20	-16.5	50000	4	Fe55, dimmed	80	1.00E+12	1.52	y		
+29056	6/7/2013	-70	-58.0	50000	4	Fe55, dimmed	64	1.00E+12	1.52	y	-30 … -60	
+29057	6/7/2013	-70	-58.0	50000	4	Fe55, dimmed	80	1.00E+12	1.52	y		
+												
+29058	6/6/2013	20	21.5	50000	4	none	64	1.00E+12	1.52	y		
+29059	6/6/2013	20	21.0	50000	4	none	80	1.00E+12	1.52	y		
+29060	6/6/2013	-20	-15.5	50000	4	none	64	1.00E+12	1.52	y		
+29061	6/6/2013	-20	-15.5	50000	4	none	80	1.00E+12	1.52	y		
+29062	6/6/2013	-70	-54.5	50000	4	none	64	1.00E+12	1.52	y		
+29063	6/6/2013	-70	-56.0	50000	4	none	80	1.00E+12	1.52	y		
+												
+29064	6/10/2013	20	22.0	50000	4	Sr-90	64	1.00E+12	1.52	y		
+29065	6/10/2013	20	21.5	50000	4	Sr-90	80	1.00E+12	1.52	y		
+29066	6/10/2013	-20	-13.5	50000	4	Sr-90	64	1.00E+12	1.52	y		
+29067	6/10/2013	-20	-14.0	50000	4	Sr-90	80	1.00E+12	1.52	y		
+29068	6/10/2013	-70	-53.0	50000	4	Sr-90	64	1.00E+12	1.52	y		
+29069	6/10/2013	-70	-54.0	50000	4	Sr-90	80	1.00E+12	1.52	y		
+												
+												
+29070	6/14/2013	20	21.5	50000	5	Fe55, dimmed	64	3.00E+12	1.57	y	19 … 21	
+29071	6/14/2013	20	21.0	50000	5	Fe55, dimmed	80	3.00E+12	1.55	y		
+29072	6/14/2013	-20	-16.0	50000	5	Fe55, dimmed	64	3.00E+12	1.57	y	-12 … -19	
+29073	6/14/2013	-20	-16.5	50000	5	Fe55, dimmed	80	3.00E+12	1.55	y		
+29074	6/14/2013	-70	-58.5	50000	5	Fe55, dimmed	64	3.00E+12	1.57	y	-30 … -60	
+29075	6/14/2013	-70	-58.5	50000	5	Fe55, dimmed	80	3.00E+12	1.55	y		
+												
+29076	6/13/2013	20	20.5	50000	5	none	64	3.00E+12	1.57	y		
+29077	6/13/2013	20	20.5	50000	5	none	80	3.00E+12	1.55	y		
+29078	6/13/2013	-20	-16.5	50000	5	none	64	3.00E+12	1.57	y		
+29079	6/13/2013	-20	-17.0	50000	5	none	80	3.00E+12	1.55	y		
+29080	6/13/2013	-70	-57.0	50000	5	none	64	3.00E+12	1.57	y		
+29081	6/13/2013	-70	-59.5	50000	5	none	80	3.00E+12	1.55	y		
+												
+29082	6/17/2013	20	21.5	50000	5	Sr-90	64	3.00E+12	1.57	y		
+29083	6/17/2013	20	21.0	50000	5	Sr-90	80	3.00E+12	1.55	y		
+29084	6/17/2013	-20	-14.0	50000	5	Sr-90	64	3.00E+12	1.57	y		
+29085	6/17/2013	-20	-15.0	50000	5	Sr-90	80	3.00E+12	1.55	y		
+29086	6/17/2013	-70	-54.0	50000	5	Sr-90	64	3.00E+12	1.57	y		
+29087	6/17/2013	-70	-54.5	50000	5	Sr-90	80	3.00E+12	1.55	y		
+												
+												
+29088	6/20/2013	20	21.0	50000	6	Fe55, dimmed	64	1.00E+13	1.54	y	19 … 21	
+29089	6/20/2013	20	21.0	50000	6	Fe55, dimmed	80	1.00E+13	1.53	y		
+29090	6/20/2013	-20	-16.5	50000	6	Fe55, dimmed	64	1.00E+13	1.54	y	-12 … -19	
+29091	6/20/2013	-20	-16.5	50000	6	Fe55, dimmed	80	1.00E+13	1.53	y		
+29092	6/20/2013	-70	-58.5	50000	6	Fe55, dimmed	64	1.00E+13	1.54	y	-30 … -60	
+29093	6/20/2013	-70	-59.5	50000	6	Fe55, dimmed	80	1.00E+13	1.53	y		
+												
+29094	6/18/2013	20	20.5	50000	6	none	64	1.00E+13	1.54	y		
+29095	6/18/2013	20	20.5	50000	6	none	80	1.00E+13	1.53	y		
+29096	6/18/2013	-20	-15.5	50000	6	none	64	1.00E+13	1.54	y		
+29097	6/18/2013	-20	-15.5	50000	6	none	80	1.00E+13	1.53	y		
+29098	6/19/2013	-70	-60.0	50000	6	none	64	1.00E+13	1.54	y		
+29099	6/19/2013	-70	-60.0	50000	6	none	80	1.00E+13	1.53	y		
+												
+29100	6/24/2013	20	21.0	50000	6	Sr-90	64	1.00E+13	1.54	y		
+29101	6/24/2013	20	21.0	50000	6	Sr-90	80	1.00E+13	1.53	y		
+29102	6/24/2013	-20	-15.0	50000	6	Sr-90	64	1.00E+13	1.54	y		
+29103	6/24/2013	-20	-16.0	50000	6	Sr-90	80	1.00E+13	1.53	y		
+29104	6/24/2013	-70	-54.5	50000	6	Sr-90	64	1.00E+13	1.54	y		
+29105	6/24/2013	-70	-55.5	50000	6	Sr-90	80	1.00E+13	1.53	y		
diff --git a/ProcessMeasurements/LaborbuchMi29.xls b/ProcessMeasurements/LaborbuchMi29.xls
new file mode 100755
index 0000000..15ead53
Binary files /dev/null and b/ProcessMeasurements/LaborbuchMi29.xls differ
diff --git a/ProcessMeasurements/MAPS.C b/ProcessMeasurements/MAPS.C
new file mode 100644
index 0000000..5fc55d2
--- /dev/null
+++ b/ProcessMeasurements/MAPS.C
@@ -0,0 +1,1046 @@
+#include <stdlib.h>
+#include <TClass.h>
+#include <fstream>
+#include <iostream>
+#include "Riostream.h"
+#include <string>
+#include "TString.h"
+#include "TMath.h"
+#include <TFile.h>
+#include <TNtuple.h>
+#include <TH1F.h>
+#include <TH2F.h>
+#include "TH1.h"
+#include "TF1.h"
+#include "TROOT.h"
+#include <TApplication.h>
+#include "TCanvas.h"
+#include "TObject.h"
+#include "TStyle.h"
+#include "TEnv.h"
+#include "TGraph.h"
+#include "TGaxis.h"
+#include "TStyle.h"
+#include "TFrame.h"
+#include "TVector.h"
+#include "TVectorD.h"
+#include "Foption.h"
+#include "TRandom.h"
+#include "TSpline.h"
+#include "TPaveStats.h"
+#include "TVirtualFitter.h"
+#include "TVirtualPad.h"
+#include "TVirtualGraphPainter.h"
+#include "TBrowser.h"
+#include "TSystem.h"
+#include "TPluginManager.h"
+#include "TPad.h"
+#include <TQObject.h>
+#include <TMultiGraph.h>
+#include <iostream>
+#include <fstream>
+
+using namespace std;
+
+#include"MAPS.h"
+//####################################################################
+
+MAPS::MAPS() {
+
+};
+
+//####################################################################
+
+MAPS::MAPS( TString InDir, TString OutDir, Int_t RunNumber, Int_t Rows, Int_t Columns, TString OrderCode, Int_t SubMatrix, bool Save , Int_t Matrices, Int_t Matrix) {
+//-----------------------------------------------
+	unsigned short int vi,vj;
+	for (vi = 0; vi <= 0xFF; vi++) {
+	for (vj = 0; vj <= 0xFF; vj++) {
+	value2[vi][vj] = (vi + (vj & 0x0F) * 256);
+	value1[vi][vj] = (vj*16 + (vi & 0xF0) / 16); } }
+//-----------------------------------------------
+//Set:
+    fInDir		= InDir;
+    fOutDir		= OutDir;
+    fRunNumber	= RunNumber;
+    fRows		= Rows;
+    fColumns	= Columns;
+    fPixels		= fRows * fColumns;
+    fMatrices	= Matrices;
+	fMatrix		= Matrix;
+	fSubMatrix	= SubMatrix;
+	fBuffer		= 4*(fPixels+29);
+	fSave		= Save;
+	fOk			= false;
+	fOrderCode	= OrderCode;
+//-----------------------------------------------
+//PARAMETER:
+    TString		FILENAME;
+    Long64_t	LENGTH;
+	
+    fF0matrix	= new Int_t		[fPixels];
+    fF1matrix	= new Int_t		[fPixels];
+    fCdsmatrix	= new Float_t	[fPixels];
+	fNoise		= new Float_t	[fPixels];
+	fPedestals	= new Float_t	[fPixels];
+	
+	fNoiseOk = false;
+//-----------------------------------------------
+//Tell-me
+	cout<<"-----------------------"<<endl;
+	cout<<"Initiate MAPS() ..."<<endl;
+	cout<<"--------------"<<endl;
+	cout<<"Input  Directory      : "<<fInDir<<endl;
+	cout<<"Output Directory      : "<<fOutDir<<endl;
+	cout<<"Runnumber             : "<<fRunNumber<<endl;
+	cout<<"Pixels                : "<<fRows<<" x "<<fColumns<<endl;
+	cout<<"Matrices              : "<<fMatrices<<endl;
+	cout<<"Matrix to scan        : "<<fMatrix<<endl;
+	cout<<"Sub-Matrix to scan    : "<<fSubMatrix<<endl;
+	cout<<"Ordering according to : "<<fOrderCode<<endl;
+	cout<<"Save/Overwrite data   : "<<fSave<<endl;
+	if(fMatrix>=fMatrices) {cout<<"ERROR: Matrix can only possible if between 0 and "<<fMatrices-1<<"!"<<endl;}
+	cout<<"-----------------------"<<endl;
+//-----------------------------------------------
+//Count Files
+	fFile		= -1;
+	ifstream inn;
+	
+	do
+	{
+		fFile++;
+		FILENAME=fInDir+Form("%i/RUN_%i_%i.rz",fRunNumber,fRunNumber,fFile);
+		inn.open(FILENAME, ios::binary);
+		inn.close();
+	}while(inn.good());
+//-----------------------------------------------
+//Check and open Data Files
+	fEvents = new Int_t		[fFile];
+	fInn	= new ifstream	[fFile];
+	fEventsSum	= 0;
+		
+	for(Int_t j=0;j<fFile;j++)
+	{
+		FILENAME=fInDir+Form("%i/RUN_%i_%i.rz",fRunNumber,fRunNumber,j);
+		fInn[j].open(FILENAME, ios::binary);
+		fInn[j].seekg(0, ios::beg);
+		fInn[j].seekg(0, ios::end);
+		LENGTH = fInn[j].tellg();
+		fEvents[j]	= (Int_t)(LENGTH/fBuffer/fMatrices);
+		fEventsSum	+= fEvents[j];
+		fInn[j].seekg(0, ios::beg);
+		
+		Float_t TMP = (Float_t)(LENGTH)*10./fBuffer/fMatrices;
+		if(((Int_t)(TMP))%10!=0){cout<<"Irregularities have occurred! Check specifications: Matrices .. Matrix! Errors may occur..."<<endl;}
+		
+// 		cout<<Form("RUN_%i_%i.rz",fRunNumber,j)<<" found!\t"<<(Float_t)(LENGTH/1048576.)<<" MBytes"<<"\t"<<LENGTH<<" Bytes"<< "\t--> "<<fEvents[j]<<" Frames"<<endl;
+
+		fOk	= true;
+	}
+	cout<<"-----------------------"<<endl;
+//-----------------------------------------------
+//Open Output File:
+	if(fSave && fOk)
+	{
+		FILENAME = fOutDir+Form("%i/%i_%i_%i.root",fRunNumber,fRunNumber,fMatrix,fSubMatrix);
+		cout<<"File '"<<FILENAME<<"' recreated!"<<endl;
+		fOutputFile  	= new TFile(FILENAME,"RECREATE");
+// 		fHitNtup		= new TNtuple("hit",		"hit",			"frame:pixel:p1:p2:p3:p4:p5:p6:p7:p8:p9:p10:p11:p12:p13:p14:p15:p16:p17:p18:p19:p20:p21:p22:p23:p24:p25:xpos:ypos");
+		fHitNtup		= new TNtuple("hit",		"hit",			"frame:pixel:p1:p2:p3:p4:p5:p6:p7:p8:p9:p10:p11:p12:p13:p14:p15:p16:p17:p18:p19:p20:p21:p22:p23:p24:p25");
+		fHitsNtup		= new TNtuple("hits",		"hits",			"frame:counts");
+		fNoiseNtup		= new TNtuple("noise",		"noise",		"pixel:noise:pedestal");
+// 		fMeanNoiseNtup	= new TNtuple("meannoise",	"meannoise",	"frame:noise:pedestal");
+		cout<<"-----------------------"<<endl;
+	}
+	
+	if(!fOk){cout<<"No files found!"<<endl;}
+	
+//-----------------------------------------------
+	plotHint	= false;
+	hint1		= new TH2F("Hitmulit", "Hit multiplicity", 			fColumns, 0, fColumns, fRows, 0, fRows);
+	hint2		= new TH2F("Pixmulit", "Pix multiplicity", 			fColumns, 0, fColumns, fRows, 0, fRows);
+//-----------------------------------------------
+}
+
+//####################################################################
+
+MAPS::~MAPS(void) {
+	
+	if(plotHint)
+	{
+		TCanvas* cm3;
+		cm3 = new TCanvas("cc23","Matrix",50,100,1200,800);
+		cm3->Divide(2,1);
+		gStyle->SetOptFit(1011);
+		gStyle->SetPalette(1);
+		gStyle->SetCanvasColor(0);
+		gStyle->SetFrameFillColor(10);
+		gStyle->SetOptStat(0);
+		
+		cm3->cd(1);
+		hint1->Draw("colz");
+		hint1->GetXaxis()->SetRangeUser(0, fColumnsSub);
+		hint1->GetYaxis()->SetRangeUser(0, fRowsSub);
+		hint1->GetXaxis()->SetTitle("column");
+		hint1->GetYaxis()->SetTitle("row");
+		hint1->GetZaxis()->SetTitle("Signal [ADC]");
+		
+		cm3->cd(2);
+		hint2->Draw("col2z");
+		hint2->GetXaxis()->SetRangeUser(0, fColumnsSub);
+		hint2->GetYaxis()->SetRangeUser(0, fRowsSub);
+		hint2->GetXaxis()->SetTitle("column");
+		hint2->GetYaxis()->SetTitle("row");
+		hint2->GetZaxis()->SetTitle("Signal [ADC]");
+		
+		cm3->DrawClone();
+		cm3->Close();
+		cm3->Update();
+	}
+	if(fSave && fOk) 
+	{
+		fOutputFile->cd();
+		
+		fHitNtup->Write("",TObject::kOverwrite);
+		fHitsNtup->Write("",TObject::kOverwrite);
+		fNoiseNtup->Write("",TObject::kOverwrite);
+// 		fMeanNoiseNtup->Write("",TObject::kOverwrite);
+        fOutputFile->Save();
+		fOutputFile->Close();
+		
+		cout<<"-----------------------"<<endl;
+		cout<<"Ntuples written!"<<endl;
+		cout<<"File '"<<fOutDir+Form("%i/%i_%i_%i.root",fRunNumber,fRunNumber,fMatrix,fSubMatrix)<<"' saved!"<<endl;
+		//fOutputFile->Close();
+// 		cout<<"...finished!"<<endl;
+		cout<<"-----------------------"<<endl;
+		
+// 		TString FILENAME = fOutDir+Form("%i/%i_%i_%i.root",fRunNumber,fRunNumber,fMatrix,fSubMatrix);
+// 		TFile::Open(FILENAME);
+// 		gROOT->ProcessLine("new TBrowser;");
+		
+// 		delete[] fOutputFile;
+// 		delete[] fHitNtup;
+// 		delete[] fNoiseNtup;
+// 		delete[] fMeanNoiseNtup;
+	}
+	
+	for(Int_t i=0;i<fFile;i++)
+	{
+		fInn[i].close();
+	}
+			
+	delete[] fEvents;
+	delete[] fF0matrix;
+	delete[] fF1matrix;
+	delete[] fCdsmatrix;
+	delete[] fNoise;
+	delete[] fPedestals;
+	
+};
+
+//####################################################################
+
+bool MAPS::getFrame(Int_t FrameNumber) {
+
+	fFrameNumber = FrameNumber;
+	
+	if(fFrameNumber<fEventsSum)
+	{
+		Int_t EVENTSUM = 0;
+		Int_t FFILE=0;
+		
+		for(Int_t i=0; i<fFile;i++)
+		{
+			EVENTSUM+=fEvents[i];
+			
+			if(fFrameNumber<EVENTSUM) {FFILE=i; EVENTSUM-=fEvents[i]; break;}
+		}
+		
+		Int_t POSFILE		= fBuffer*fMatrices*fFrameNumber + fBuffer*fMatrix - fBuffer*fMatrices*EVENTSUM;
+		Int_t HDRLENGTH		= 4*28;
+		Int_t BYTELENGTH	= 4*fPixels;
+
+		char* HDRDATA;		//delete[] HDRDATA;
+		char* RAWDATA;		//delete[] RAWDATA;
+		HDRDATA	= new char[HDRLENGTH];
+		RAWDATA	= new char[BYTELENGTH];
+			
+		fInn[FFILE].seekg(POSFILE, ios::beg);
+		fInn[FFILE].read(HDRDATA,HDRLENGTH);
+		fInn[FFILE].read(RAWDATA,BYTELENGTH);
+
+		Int_t COUNT=0;
+		for(Int_t i=0;i<BYTELENGTH;i+=4)
+		{
+			fF0matrix[COUNT]	= value1	[(UChar_t)RAWDATA[i+1]]	[(UChar_t)RAWDATA[i+2]];
+			fF1matrix[COUNT]	= value2	[(UChar_t)RAWDATA[i]]	[(UChar_t)RAWDATA[i+1]];
+			
+			fCdsmatrix[COUNT]	= fF0matrix[COUNT]- fF1matrix[COUNT];
+			COUNT++;
+		}
+		
+		if			(fOrderCode == "")		{ fPixelsSub=fPixels;	fRowsSub=fRows, fColumnsSub=fColumns; }
+		else if		(fOrderCode == "Mi26")	{ reorderMi26();	}
+		else if		(fOrderCode == "Mi29a")	{ reorderMi29a();	}
+		else if		(fOrderCode == "Mi29b")	{ reorderMi29b();	}
+		
+		delete[] HDRDATA;
+		delete[] RAWDATA;
+		
+		fFrameOk = true;
+		return true;
+	}
+	else
+	{
+		cout<<"Event number: "<<fFrameNumber<<" is too big! Max: "<<fEventsSum<<endl;
+		fFrameOk = false;
+		return false;
+	}
+};
+
+//####################################################################
+
+void MAPS::filterCommonMode() {
+  
+  Float_t CommonModeInRow = 0;
+  // Int_t Count = 0;
+  bool warning = false;
+  
+  Float_t* Arr = new Float_t[fColumns];
+  
+  for(int row=0; row<fRows; row++ )
+  {
+    CommonModeInRow = 0;
+    // Count = 0;
+    
+    for(int column=0; column<fColumns; column++ )
+    {
+      // CommonModeInRow += fCdsmatrix[ row*fColumns+column ];
+      Arr[column] = fCdsmatrix[ row*fColumns+column ];
+    }
+    
+    // CommonModeInRow = CommonModeInRow/fColumns;
+    CommonModeInRow = TMath::Median(fColumns, Arr);
+    // cout<<CommonModeInRow<<endl;
+    // CommonModeInRow = 0;
+    if(TMath::Abs(CommonModeInRow)>100)
+    {
+      warning = true;
+    }
+    
+    for(int column=0; column<fColumns; column++ )
+    {
+      // cout<<CommonModeInRow<<"\t"<<fCdsmatrix[ row*fColumns+column ]<<"\t";
+      fCdsmatrix[ row*fColumns+column ] = fCdsmatrix[ row*fColumns+column ] - CommonModeInRow;
+      // cout<<fCdsmatrix[ row*fColumns+column ]<<endl;
+    }
+  }
+  
+  if(warning) { cout<<"\rFrame: "<<fFrameNumber<<" --> Common Mode suspiciously high! "<<endl; }
+}
+
+//####################################################################
+
+bool MAPS::getNoise(Int_t Frames, Int_t Offset, bool Mode) {
+//Noise + Pedestals
+// 	if(fNoiseOk){cout<<"Noise has been already set!"<<endl;}
+	if(fNoiseOk){cout<<"Noise already calculated!"<<endl; return true;}
+	if(!Mode)
+	{
+		cout<<"Run getNoise() ..."<<endl;
+//Check amount of Frames
+		if(Frames<50)
+		{
+			cout<<"Too few Frames! Change Frames from "<<Frames<<" to ";
+			Frames = 50;
+			cout<<Frames<<" !"<<endl;
+		}
+//Check availabilty of Frames
+		if(Frames+Offset>fEventsSum)
+		{
+			cout<<"Change Offset from "<<Offset<<" to ";
+			Offset	= fEventsSum-Frames;
+			cout<<Offset<<" !"<<endl;
+		}
+// Get fPixelsSub and allocate array
+		getFrame(0);
+		
+		Int_t *ARR = new Int_t[Frames*fPixelsSub];
+		Float_t PEDESTAL;
+		Float_t NOISE;
+
+		for(Int_t i=Offset; i<Frames+Offset;i++)
+		{
+			getFrame(i);
+			
+			for(Int_t j=0; j<fPixelsSub;j++)
+			{
+				ARR[(i-Offset)*fPixelsSub+j] = fCdsmatrix[j];
+			}
+		}
+		
+		for(Int_t i=0; i<fPixelsSub;i++)
+		{
+			PEDESTAL	= 0;
+			NOISE		= 0;
+
+			for(Int_t j=0; j<Frames;j++)
+			{
+				PEDESTAL+=ARR[j*fPixelsSub+i];
+			}
+
+			PEDESTAL = PEDESTAL/Frames;
+			
+			for(Int_t j=0; j<Frames;j++)
+			{
+				NOISE+=TMath::Power(ARR[j*fPixelsSub+i]-PEDESTAL,2);
+			}
+
+			NOISE = TMath::Sqrt(NOISE/(Frames-1));
+			
+			fNoise[i]		= NOISE;
+			fPedestals[i]	= PEDESTAL;
+			
+			if(fSave)	{ fNoiseNtup->Fill(i, NOISE, PEDESTAL); }
+		}
+		
+		cout<<"-----------------------"<<endl;
+				
+		delete[] ARR;
+		fNoiseOk = true;
+		return true;
+	}
+	else
+	{
+		fNoiseOk = false;
+		return false;
+	}
+};
+
+//####################################################################
+
+bool MAPS::loadNoise( TString InDir, Int_t RunNumber, Int_t SubMatrix, Int_t Matrix) {
+	
+	TString FILENAME = InDir+Form("%i/%i_%i_%i.root",RunNumber,RunNumber,Matrix,SubMatrix);
+	TFile *f = new TFile(FILENAME,"READ");
+	
+	if(f->IsZombie()) 
+	{
+		cerr<<"ERROR: loadNoise() failed!"<<endl;
+		cerr<<FILENAME<<" not found!"<<endl;
+		cerr<<"-----------------------"<<endl;
+		return false;
+		exit(-1);
+	}
+	else
+	{
+		cout<<"Noise/Pedestals loaded from:"<< FILENAME << "!"<<endl;
+		
+		TNtuple *noiseNtup	= (TNtuple*) f->Get("noise");
+		Int_t entries		= noiseNtup->GetEntries();
+		Float_t *noiseData;
+		
+		for(Int_t i=0; i<entries; i++)
+		{
+			noiseNtup->GetEntry(i);
+			noiseData = noiseNtup->GetArgs();
+			
+			fNoise[i]		= noiseData[1];
+			fPedestals[i]	= noiseData[2];
+		}
+		cout<<"-----------------------"<<endl;
+		fNoiseOk = true;
+		return true;
+	}
+};
+
+//####################################################################
+
+Float_t MAPS::GetMeanNoise() {
+	Float_t noiseMean=0;
+  for(Int_t pix=0;pix<fPixelsSub;pix++)
+  {
+	noiseMean+=fNoise[pix];
+
+  }
+  noiseMean=noiseMean/fPixelsSub;
+  return noiseMean;
+  };
+  
+//####################################################################
+
+bool MAPS::setNoise(Float_t Noise) {
+	
+	for(Int_t i=0; i<fPixelsSub; i++)
+	{
+		fNoise[i]		= Noise;
+	}
+	
+	fNoiseOk = true;
+	return true;
+};
+
+//####################################################################
+
+bool MAPS::setPedestals(Float_t Pedestals) {
+	
+	for(Int_t i=0; i<fPixelsSub; i++)
+	{
+		fPedestals[i]	= Pedestals;
+	}
+	
+// 	fNoiseOk = true;
+	return true;
+};
+
+//####################################################################
+
+void MAPS::plotFrame() {
+	
+	if(!fFrameOk) {cout<<"No frame loaded!"<<endl;}
+	else {
+
+	TCanvas* cm1;
+	cm1 = new TCanvas("cc2","Matrix",50,100,1200,800);
+	cm1->Divide(2,3);
+	gStyle->SetOptFit(1011);
+	gStyle->SetPalette(1);
+	gStyle->SetCanvasColor(0);
+	gStyle->SetFrameFillColor(10);
+	gStyle->SetOptStat(0);
+	
+	TH2F *h1  = new TH2F("CDS matrix", "CDS matrix", 			fColumnsSub, 0, fColumnsSub, fRowsSub, 0, fRowsSub);
+	TH2F *h2  = new TH2F("Frame 0 matrix", "Frame 0 matrix", 	fColumnsSub, 0, fColumnsSub, fRowsSub, 0, fRowsSub);
+	TH2F *h3  = new TH2F("Frame 1 matrix", "Frame 1 matrix", 	fColumnsSub, 0, fColumnsSub, fRowsSub, 0, fRowsSub);
+	TH1F *h4  = new TH1F("Frame 0 histo", "Frame 0 histo", 		4096, 0, 4096);
+	TH1F *h5  = new TH1F("Frame 1 histo", "Frame 1 histo", 		4096, 0, 4096);
+	
+	Int_t column;
+	Int_t row;
+	Float_t F0,F1,CDS;
+	
+	for(Int_t i=0; i<fPixelsSub;i++)
+	{
+		row		= i/fColumnsSub;
+		column	= i%fColumnsSub;
+		
+		CDS	= fCdsmatrix[i];
+		F0	= fF0matrix[i];
+		F1	= fF1matrix[i];
+
+		h1->Fill(column,row,CDS);
+		h2->Fill(column,row,F0);
+		h3->Fill(column,row,F1);
+		h4->Fill(F0);
+		h5->Fill(F1);
+		
+	}
+
+	cm1->cd(1);
+	h1->Draw("colz");
+	h1->GetXaxis()->SetTitle("column");
+	h1->GetYaxis()->SetTitle("row");
+	h1->GetZaxis()->SetTitle("Signal [ADC]");
+
+	cm1->cd(2);
+	h1->Draw("surf2z");
+	h1->GetXaxis()->SetTitle("column");
+	h1->GetYaxis()->SetTitle("row");
+	h1->GetZaxis()->SetTitle("Signal [ADC]");
+	
+	cm1->cd(3);
+	h2->Draw("surf2z");
+	h2->GetXaxis()->SetTitle("column");
+	h2->GetYaxis()->SetTitle("row");
+	h2->GetZaxis()->SetTitle("Signal [ADC]");
+	
+	cm1->cd(4);
+	h3->Draw("surf2z");
+	h3->GetXaxis()->SetTitle("column");
+	h3->GetYaxis()->SetTitle("row");
+	h3->GetZaxis()->SetTitle("Signal [ADC]");
+	
+	cm1->cd(5);
+	h4->Draw();
+	h4->GetXaxis()->SetTitle("Signal [ADC]");
+	h4->GetYaxis()->SetTitle("Counts");
+	
+	cm1->cd(6);
+	h5->Draw();
+	h5->GetXaxis()->SetTitle("Signal [ADC]");
+	h5->GetYaxis()->SetTitle("Counts");
+
+	cm1->DrawClone();
+	cm1->Close();
+	cm1->Update();
+	cout<<"\rPIXELMATRIX plotted!                           "<<endl;
+	cout<<"-------------------"<<endl;
+	}
+}
+
+//####################################################################
+
+void MAPS::plotNoise() {
+
+	if(!fNoiseOk) {cout<<"Noise/Pedestals not calculated/set!"<<endl;}
+	else {
+
+	getFrame(0);
+	TCanvas* cm2;
+	cm2 = new TCanvas("cc3","Noise",50,100,1200,800);
+ 	cm2->Divide(2,2);
+	gStyle->SetOptFit(1011);
+	gStyle->SetPalette(1);
+	gStyle->SetCanvasColor(0);
+	gStyle->SetFrameFillColor(10);
+	gStyle->SetOptStat(1);
+	
+	TH1F *h1  = new TH1F("noisee", 			"noise",			10000, 0, 100);
+	TH1F *h2  = new TH1F("pedestal", 		"pedestal",			10000, -20, 20);
+	TH2F *h3  = new TH2F("noise matrix", 	"noise matrix", 	fColumnsSub, 0, fColumnsSub, fRowsSub, 0, fRowsSub);
+	TH2F *h4  = new TH2F("pedestal matrix",	"pedestal matrix", 	fColumnsSub, 0, fColumnsSub, fRowsSub, 0, fRowsSub);
+	
+	Int_t column;
+	Int_t row;
+	Float_t NOISE,PEDESTAL;
+	
+	for(Int_t i=0; i<fPixelsSub;i++)
+	{
+		
+		column	= i%fColumnsSub;
+		row		= i/fColumnsSub;
+		NOISE		= fNoise[i];
+		PEDESTAL	= fPedestals[i];
+
+		h1->Fill(NOISE);
+		h2->Fill(PEDESTAL);
+		h3->Fill(column,row,NOISE);
+		h4->Fill(column,row,PEDESTAL);
+	}
+	
+	cm2->cd(1);
+	h3->Draw("colz");
+	h3->GetXaxis()->SetTitle("column");
+	h3->GetYaxis()->SetTitle("row");
+	h3->GetZaxis()->SetTitle("Noise [ADC]");
+	
+	cm2->cd(2);
+	h4->Draw("colz");
+	h4->GetXaxis()->SetTitle("column");
+	h4->GetYaxis()->SetTitle("row");
+	h4->GetZaxis()->SetTitle("Pedstals [ADC]");
+	
+	cm2->cd(3);
+	h1->Draw();
+	h1->GetXaxis()->SetTitle("Noise [ADC]");
+	h1->GetYaxis()->SetTitle("Counts");
+	
+	cm2->cd(4);
+	h2->Draw();
+	h2->GetXaxis()->SetTitle("Pedestal [ADC]");
+	h2->GetYaxis()->SetTitle("Counts");
+
+	cm2->Update();
+	cout<<"NOISE plotted!"<<endl;
+	cout<<"-------------------"<<endl;
+	}
+}
+
+//####################################################################
+
+void MAPS::hitana() {
+
+	if(!fFrameOk) 		{cout<<"No frame loaded!"<<endl;}
+	else if(!fNoiseOk)	{cout<<"Noise/Pedestals not set!"<<endl;}
+	else {
+
+//Local variables
+	TArrayI HITS;
+	Int_t HITNR = 0;
+	Int_t *Hitlist;
+	Int_t A;
+	Int_t B;
+	Int_t DUMMY=0;
+	Float_t CLUSTER[25];
+// 	Float_t CLUSTER9[9];
+// 	Int_t POSC9;
+	Int_t CHANCE;
+// 	Float_t XCOM;
+// 	Float_t YCOM;
+// 	Int_t XV;
+// 	Int_t YV;
+// 	Float_t MALL;
+// 	Float_t REST;
+	
+	for(Int_t i=0; i<fPixelsSub; i++)
+	{
+		if( (float)(fCdsmatrix[i]-fPedestals[i]) >= 0		&&		(float)(fCdsmatrix[i]-fPedestals[i]) > (5.*fNoise[i])		 )
+		{
+			HITNR++;
+			HITS.Set(HITNR);
+			HITS.AddAt(i,(HITNR-1));
+			
+			if(plotHint)	{hint2->Fill(i%fColumnsSub, (int)(i/fColumnsSub));}
+		}
+	}
+
+//Rewrite HITS to fHitlist array
+	Hitlist= new Int_t[HITNR];
+	
+	for(Int_t i=0;i<HITNR;i++) 
+	{
+		Hitlist[i]=HITS.At(i); 
+	}
+
+//Begin: loop over all potential seed pixels:
+//Determine 'hit-vicinity':
+	Int_t HIT_count=0;
+	
+	for(Int_t hit=0; hit<HITNR;hit++)
+	{
+		A = (Hitlist[hit])/fColumnsSub;			// A: row of seed
+		B = (Hitlist[hit])%fColumnsSub;			// B: column of seed
+	
+	
+		
+	
+	// Consider boundaries => Remove hits where the seed pixel is within 2 pixels beside the edge
+	if (Hitlist[hit]/fColumnsSub < 2 || Hitlist[hit]/fColumnsSub > fRowsSub-3 || Hitlist[hit]%fColumnsSub < 2 || Hitlist[hit]%fColumnsSub > fRowsSub-3)
+	  continue;
+	
+	
+	
+	
+	
+	
+	
+	
+	
+	
+	
+	
+	
+	
+	
+	
+	
+	
+	
+	
+	
+	
+	
+//Provide 5x5 clusters with CDS - content:
+		for(Int_t row=0;row<5;row++)
+		{
+			for(Int_t column=0;column<5;column++)
+			{
+				if			( (row==0) && (A<2) )					{CLUSTER[(row*5)+column]=DUMMY; }
+				else if 	( (row==1) && (A<1) )					{CLUSTER[(row*5)+column]=DUMMY; }
+				else if 	( (row==3) && (A>= (fRowsSub-1)) )		{CLUSTER[(row*5)+column]=DUMMY; }
+				else if 	( (row==4) && (A>= (fRowsSub-2)) )		{CLUSTER[(row*5)+column]=DUMMY; }
+				else
+				{
+					if		( (column==0) && (B<2) )				{CLUSTER[(row*5)+column]=DUMMY; }
+					else if	( (column==1) && (B==0) )				{CLUSTER[(row*5)+column]=DUMMY; }
+					else if	( (column==3) && (B==fColumnsSub-1))	{CLUSTER[(row*5)+column]=DUMMY; }
+					else if	( (column==4) && (B>fColumnsSub-3))		{CLUSTER[(row*5)+column]=DUMMY; }
+// 					else											{CLUSTER[(row*5)+column] = fCdsmatrix[Hitlist[hit]+(row-2)*fColumnsSub+(column-2)];}
+					else											{CLUSTER[(row*5)+column] = 1.*fCdsmatrix[Hitlist[hit]+(row-2)*fColumnsSub+(column-2)] - fPedestals[Hitlist[hit]+(row-2)*fColumnsSub+(column-2)] ;}
+				}
+			}
+		}
+		
+		
+		
+		
+		
+		
+		
+		
+		
+		
+		
+		
+		
+		
+		
+		
+		
+		
+		
+		
+		
+		// Check wether the summed charge of the whole cluster is > 3*noise
+		Double_t clusterSum=0;
+		for(Int_t i=0;i<25;i++)
+		{
+		  clusterSum+=CLUSTER[i];// Charge of whole cluster
+		  
+		}
+		if(clusterSum<3.*GetMeanNoise()){continue;} //Cut on whole cluster 3 times Mean(noise)
+		
+		
+		
+		
+		
+		
+		
+		
+		
+		
+//Check seeds (whether highest entry in cluster):
+// 		POSC9=0;
+		for(Int_t i=6;i<19;i++)
+		{
+// 			CLUSTER9[POSC9]=CLUSTER[i];
+// 			POSC9++;
+			if      	( (i!=12) && (CLUSTER[i] > CLUSTER[12]) )				{CHANCE=0; break;}
+			else if 	( (i!=12) && (CLUSTER[i] == CLUSTER[12]) && i>12 )		{CHANCE=0; break;} 	//NOTE: potential error source
+			else																{CHANCE=100;  if(i%5==3) {i+=2;}; }
+		}
+
+//Begin: loop evaluate true seeds:
+		if(CHANCE==100)
+		{
+
+//Sort hit-clusters:
+// 			sort(CLUSTER9,9);
+			
+//Hit: centre of mass + hit details
+// 			XCOM=0;
+// 			YCOM=0;
+// 			XV=0;
+// 			YV=-3;
+// 			MALL=0;
+// // 			REST=0;
+// 			for(Int_t i=0; i<25;i++)
+// 			{				
+// 				XV=((i%5)-2);
+// 				if(i%5==0){YV++;}
+// 				
+// 				XCOM += CLUSTER[i]*XV;
+// 				YCOM += CLUSTER[i]*YV;
+// 				MALL += CLUSTER[i];
+// 				
+// 			}
+// 			
+// 			if(MALL!=0)
+// 			{
+// 				XCOM = XCOM/MALL;
+// 				YCOM = YCOM/MALL;
+// 			}
+// 			else
+// 			{
+// 				XCOM = 0;
+// 				YCOM = 0;
+// 			}
+//Fill hit ntupel:
+			HIT_tmp[ 0] = fFrameNumber;
+			HIT_tmp[ 1] = Hitlist[hit];
+			HIT_tmp[ 2] = CLUSTER[0];
+			HIT_tmp[ 3] = CLUSTER[1];
+			HIT_tmp[ 4] = CLUSTER[2];
+			HIT_tmp[ 5] = CLUSTER[3];
+			HIT_tmp[ 6] = CLUSTER[4];
+			HIT_tmp[ 7] = CLUSTER[5];
+			HIT_tmp[ 8] = CLUSTER[6];
+			HIT_tmp[ 9] = CLUSTER[7];
+			HIT_tmp[10] = CLUSTER[8];
+			HIT_tmp[11] = CLUSTER[9];
+			HIT_tmp[12] = CLUSTER[10];
+			HIT_tmp[13] = CLUSTER[11];
+			HIT_tmp[14] = CLUSTER[12];
+			HIT_tmp[15] = CLUSTER[13];
+			HIT_tmp[16] = CLUSTER[14];
+			HIT_tmp[17] = CLUSTER[15];
+			HIT_tmp[18] = CLUSTER[16];
+			HIT_tmp[19] = CLUSTER[17];
+			HIT_tmp[20] = CLUSTER[18];
+			HIT_tmp[21] = CLUSTER[19];
+			HIT_tmp[22] = CLUSTER[20];
+			HIT_tmp[23] = CLUSTER[21];
+			HIT_tmp[24] = CLUSTER[22];
+			HIT_tmp[25] = CLUSTER[23];
+			HIT_tmp[26] = CLUSTER[24];
+// 			HIT_tmp[27] = XCOM;
+// 			HIT_tmp[28] = YCOM;
+			
+			if(fSave)	{ fHitNtup->Fill(HIT_tmp); }
+			if(plotHint)	{hint1->Fill(Hitlist[hit]%fColumnsSub, (int)(Hitlist[hit]/fColumnsSub));}
+			HIT_count++;
+		}
+	}	
+//End: loop evaluate true seeds:
+//End: loop over all potential seed pixels:
+
+	HITS_tmp[0] = fFrameNumber;
+	HITS_tmp[1] = HIT_count;
+	if(fSave)	{ fHitsNtup	->Fill(HITS_tmp); }
+	delete[] Hitlist;
+}}
+
+//####################################################################
+
+void MAPS::sort(Float_t *array,Int_t size) {
+	Int_t i = size-1;
+	Int_t LASTAKTION;
+	while(i>0)
+	{
+		LASTAKTION = 0;
+
+		for(Int_t j=0;j<i;++j)
+		{
+			if(array[j]>array[j+1])
+			{
+				swap(&array[j],&array[j+1]);
+				LASTAKTION = j;
+			}
+		}
+		i = LASTAKTION;
+	}
+}
+
+//####################################################################
+
+void MAPS::swap(Float_t *a,Float_t *b) {
+	Float_t tmp = *a;
+	*a = *b;
+	*b = tmp;
+}
+
+//####################################################################
+
+void MAPS::reorderMi26() {
+
+	Int_t matrixF0_tmp[576*1152];
+	Int_t matrixF1_tmp[576*1152];
+	Int_t matrixCD_tmp[576*1152];
+	
+	Int_t row		= 0;
+	Int_t column	= 0;
+	Int_t block 	= 0;
+	Int_t pos;
+	
+	for(Int_t i=0; i<fPixels; i++)
+	{
+		matrixF0_tmp[i] = fF0matrix[i];
+		matrixF1_tmp[i] = fF1matrix[i];
+		matrixCD_tmp[i] = fCdsmatrix[i];
+	}
+	
+	for(Int_t i=0; i<fPixels; i++)
+	{
+		pos = row*1152 + column + block*8;
+		
+		fF0matrix[pos]		= matrixF0_tmp[i];
+		fF1matrix[pos]		= matrixF1_tmp[i];
+		fCdsmatrix[pos]		= matrixCD_tmp[i];
+		
+		row++;
+		if(row==576)	{ row=0;	block++; }
+		if(block==144)	{ block=0;	column++; }
+	}
+	
+	fPixelsSub	= fPixels;
+	fColumnsSub	= fColumns;
+	fRowsSub	= fRows;
+}
+
+//####################################################################
+
+void MAPS::reorderMi29a() {
+	
+	if( fSubMatrix>5 )
+	{
+		cerr<<"ERROR: "<<fSubMatrix<<". Sub-Matrix not found! Choose: 0 to 5 !"<<endl;
+		cerr<<"-----------------------"<<endl;
+		fRowsSub	= 0;
+		fColumnsSub	= 0;
+		fPixelsSub	= 0;
+	}
+	else
+	{
+		Int_t ROWSSUB[6]	= {48,48,32,32,32,32};
+		Int_t OFFSET		= 0;
+		
+		for(Int_t i=0;i<fSubMatrix;i++)
+		{
+			OFFSET+=ROWSSUB[i];
+		}
+		OFFSET = OFFSET*48;
+		
+		fRowsSub	= ROWSSUB[fSubMatrix];
+		fColumnsSub	= 48;
+		fPixelsSub	= fRowsSub*fColumnsSub;
+		
+		Int_t CDSMATRIX	[fPixelsSub];
+		Int_t F0MATRIX	[fPixelsSub];
+		Int_t F1MATRIX	[fPixelsSub];
+		
+		for(Int_t i=0;i<fPixelsSub;i++)
+		{
+			CDSMATRIX	[i] = fCdsmatrix[OFFSET+i];
+			F0MATRIX	[i] = fF0matrix	[OFFSET+i];
+			F1MATRIX	[i] = fF1matrix	[OFFSET+i];
+		}
+		
+		for(Int_t i=0;i<fPixelsSub;i++)
+		{
+			fCdsmatrix	[i] = CDSMATRIX	[i];
+			fF0matrix	[i] = F0MATRIX	[i];
+			fF1matrix	[i] = F1MATRIX	[i];
+		}
+	}
+}
+
+//####################################################################
+
+void MAPS::reorderMi29b() {
+	
+	if( fSubMatrix>5 )
+	{
+		cerr<<"ERROR: "<<fSubMatrix<<". Sub-Matrix not found! Choose: 0 to 5 !"<<endl;
+		cerr<<"-----------------------"<<endl;
+		fRowsSub	= 0;
+		fColumnsSub	= 0;
+		fPixelsSub	= 0;
+	}
+	else
+	{
+		Int_t ROWSSUB[6]	= {64,64,32,32,32,32};
+		Int_t OFFSET		= 0;
+		
+		for(Int_t i=0;i<fSubMatrix;i++)
+		{
+			OFFSET+=ROWSSUB[i];
+		}
+		OFFSET = OFFSET*51;
+		
+		fRowsSub	= ROWSSUB[fSubMatrix];
+		fColumnsSub	= 51;
+		fPixelsSub	= fRowsSub*fColumnsSub;
+		
+		Int_t CDSMATRIX	[fPixelsSub];
+		Int_t F0MATRIX	[fPixelsSub];
+		Int_t F1MATRIX	[fPixelsSub];
+		
+		for(Int_t i=0;i<fPixelsSub;i++)
+		{
+			CDSMATRIX	[i] = fCdsmatrix[OFFSET+i];
+			F0MATRIX	[i] = fF0matrix	[OFFSET+i];
+			F1MATRIX	[i] = fF1matrix	[OFFSET+i];
+		}
+		
+		for(Int_t i=0;i<fPixelsSub;i++)
+		{
+			fCdsmatrix	[i] = CDSMATRIX	[i];
+			fF0matrix	[i] = F0MATRIX	[i];
+			fF1matrix	[i] = F1MATRIX	[i];
+		}
+	}
+}
+
+//####################################################################
+//####################################################################
\ No newline at end of file
diff --git a/ProcessMeasurements/MAPS.h b/ProcessMeasurements/MAPS.h
new file mode 100644
index 0000000..944a074
--- /dev/null
+++ b/ProcessMeasurements/MAPS.h
@@ -0,0 +1,106 @@
+#ifndef MAPS_H
+#define MAPS_H
+
+#include <TFile.h>
+#include <TNtuple.h>
+#include <TH2F.h>
+
+class MAPS {
+
+private:
+		
+	TString fInDir;
+	TString fOutDir;
+	TString fOrderCode;
+	Int_t fRunNumber;
+	Int_t fPixels;
+	Int_t fPixelsSub;
+	Int_t fRows;
+	Int_t fRowsSub;
+	Int_t fColumns;
+	Int_t fColumnsSub;
+	Int_t fMatrices;
+	Int_t fMatrix;
+	Int_t fSubMatrix;
+	Int_t fBuffer;
+	Int_t fEventsSum;
+	Int_t fFile;
+	bool fOk;
+	bool fSave;
+	ifstream*	fInn;	
+	
+	Int_t *fEvents;
+	Int_t *fF0matrix;
+	Int_t *fF1matrix;
+	Float_t *fCdsmatrix;
+	Float_t *fNoise;
+	Float_t *fPedestals;
+	
+	TFile *fOutputFile;
+	TNtuple *fHitNtup;
+	TNtuple *fHitsNtup;
+	TNtuple *fNoiseNtup;
+// 	TNtuple *fMeanNoiseNtup;
+	
+	TH2F *hint1,*hint2;
+	bool plotHint;
+	
+	Int_t fFrameNumber;
+	bool fFrameOk;
+	bool fNoiseOk;
+	
+	unsigned short int value1[0x100][0x100];
+	unsigned short int value2[0x100][0x100];
+	
+	Float_t HIT_tmp[29];
+	Float_t HITS_tmp[2];
+	
+	void sort(Float_t *array,Int_t size);
+	void swap(Float_t *a,Float_t *b);
+	void reorderMi26();
+	void reorderMi29a();
+	void reorderMi29b();
+	
+public:
+	
+	MAPS(); 
+	MAPS( TString InDir, TString OutDir, Int_t RunNumber, Int_t Rows, Int_t Columns, TString OrderCode="", Int_t SubMatrix=0, bool Save=1, Int_t Matrices=1, Int_t Matrix=0);
+	~MAPS(void);
+	bool getFrame(Int_t FrameNumber);
+	bool getNoise(Int_t Frames, Int_t Offset=0, bool Mode=0);
+	bool setNoise(Float_t Noise);
+	bool loadNoise(TString InDir, Int_t RunNumber, Int_t SubMatrix, Int_t Matrix=0);
+	bool setPedestals(Float_t Pedestals);
+	void hitana();
+	void filterCommonMode();
+	void plotFrame(void);
+	void plotNoise(void);
+	Float_t	GetMeanNoise();
+	
+	Int_t			GetNumberRun()					{ return fRunNumber;					}
+	Int_t			GetNumberEvents()				{ return fEventsSum;					}
+	Int_t			GetNumberPixels()				{ return fPixels;						}
+	Int_t			GetNumberRows()					{ return fRows;							}
+	Int_t			GetNumberColumn()				{ return fColumns;						}
+	Float_t*		GetCDSFrame()				{ return fCdsmatrix;					}
+	Int_t*			GetF0Frame()					{ return fF0matrix;						}
+	Int_t*			GetF1Frame()					{ return fF1matrix;						}
+	Float_t*		GetNoise()						{ return fNoise;						}
+// 		
+// 	Int_t			GetEventNumber()				{ return EventNumber;					}
+// 	Int_t			GetBoardNumber()				{ return BoardNumber;					}
+// 	Int_t			GetNumberOfTriggers()			{ return ListOfTriggers->size();		}
+// 	vector<Int_t>*	GetTriggers()					{ return ListOfTriggers;				}
+// 	Int_t			GetTriggerAt(Int_t index)		{ return ListOfTriggers->at(index);		}
+// 	Int_t			GetNumberOfFrames()				{ return ListOfFrames->size();			}
+// 	Int_t			GetFrameAt(Int_t index)			{ return ListOfFrames->at(index);		}
+// 	Int_t			GetNumberOfPixels()				{ return ListOfPixels->size();			}
+// 	vector<Int_t>*	GetPixels()						{ return ListOfPixels;					}
+// 	Int_t			GetPixelAt(Int_t index)			{ return ListOfPixels->at(index);		}
+// 	vector<Int_t>*	GetPixelEntries()				{ return ListOfPixelEntries;			}
+// 	Int_t			GetPixelEntryAt(Int_t index)	{ return ListOfPixelEntries->at(index);	}
+
+};
+
+
+#endif
\ No newline at end of file
diff --git a/ProcessMeasurements/ProcessMeasurements.C b/ProcessMeasurements/ProcessMeasurements.C
new file mode 100644
index 0000000..4fdb718
--- /dev/null
+++ b/ProcessMeasurements/ProcessMeasurements.C
@@ -0,0 +1,214 @@
+#include <iostream>
+#include <fstream>
+#include <vector>
+#include <string>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <sys/time.h>
+#include <sstream>
+
+
+#include "TRandom1.h"
+#include "CSVRow.h"
+#include "analyzeRun.h"
+
+#define COLRUNNO 0
+#define COLTEMP 2
+#define COLTEMPSENS 3
+#define COLCHIP 5
+#define COLSOURCE 6
+#define COLMATRIX 7
+#define COLDONE 10
+
+#define LABORBUCH "LaborbuchMi29.csv"
+#define INPUTDATAPATH "/jspc12_F/Mi29/"
+#define OUTPUTDATAPATH_MAINFOLDER "/local/sstrohauer/data/"
+
+using std::cout;
+using std::endl;
+
+struct noiseRun {Int_t runNo; Float_t temperature; Int_t chip; Int_t matrix6480;};
+
+void ProcessMeasurements(Bool_t overwrite = false, Bool_t useSeperateNoiseRun = true, Int_t processRunNo = -1, std::string matrixAB = "Mi29a", Int_t seperateNoiseRunNo = -1) { 
+  
+  Bool_t	runIsNoise;	// is current run a noise run or with source?
+  Int_t		runNo;		// run number
+  Float_t	temperature;	// desired temperature
+  Float_t	tempSens;	// actual temperature
+  Int_t		chip;		// chip number (eg. 1-6)
+  Int_t		matrix6480;	// which matrix?
+  Bool_t	runFinished;	// measurement already done?
+  std::string	source;
+  std::vector<noiseRun>	noiseRunList;	// here we store all run numbers which are a noise run
+  std::ofstream	logfile;
+  
+  timeval start, end;
+  int diff;
+  gettimeofday(&start, 0);
+  
+  // ----------------
+  // create logfile
+  time_t timestamp;
+  tm *now;
+  timestamp = time(0);
+  now = localtime(&timestamp);
+  std::stringstream timeSS;
+  timeSS << now->tm_mday << '.' << now->tm_mon+1 << '.' << now->tm_year+1900 << "_" << now->tm_hour << ':' << now->tm_min;
+  cout << timeSS.str() << endl;
+  
+  std::string logfileName = "logfile_" + timeSS.str() + ".txt";
+  logfile.open(logfileName, std::ios::trunc);
+  logfile << "This is a log file which lists all processed entries in the lab book.\n\n";
+  logfile << "runNo\tmatrix\tsubmtrx\tcomment\n";
+  logfile.close();
+  // ----------------
+  
+  
+  std::string outputDataPath = std::string(OUTPUTDATAPATH_MAINFOLDER) + "data_" + timeSS.str() + "/";
+  mkdir(outputDataPath.c_str(), 0755);	// create directory for this evaluation if not existent
+  
+  // 1. case: Process one single run, chosen by the user while calling main()
+  if (processRunNo != -1){
+    if (useSeperateNoiseRun){
+      mkdir((outputDataPath + std::to_string(seperateNoiseRunNo) +"/").c_str(), 0755);	// create directory if not existent
+      mkdir((outputDataPath + std::to_string(processRunNo) +"/").c_str(), 0755);	// create directory if not existent
+      // use seperate files for noise and run
+      analyzeRun(INPUTDATAPATH, outputDataPath.c_str(), seperateNoiseRunNo, matrixAB, true, true, -1, overwrite, logfileName);	// noise
+      analyzeRun(INPUTDATAPATH, outputDataPath.c_str(), processRunNo, matrixAB, true, false, seperateNoiseRunNo, overwrite, logfileName);	// run
+    }
+    else {
+      mkdir((outputDataPath + std::to_string(processRunNo) +"/").c_str(), 0755);	// create directory if not existent
+      mkdir((outputDataPath + std::string("noise/")).c_str(), 0755);	// create directory if not existent
+      mkdir((outputDataPath + std::string("noise/") + std::to_string(processRunNo) + "/").c_str(), 0755);	// create directory if not existent
+      // use same run for calculating noise
+      analyzeRun(INPUTDATAPATH, outputDataPath.c_str(), processRunNo, matrixAB, false, false, -1, overwrite, logfileName);	// noise & run
+    }
+    return;	// that's all if processing a single run
+  }
+  
+  // 2. case: Go through lab journal. In a first iteration analyze all noise data, in the second iteration analyze all runs
+  for (Int_t firstNoiseSecondRun = 0; firstNoiseSecondRun < 2; firstNoiseSecondRun++){
+    std::ifstream	file(LABORBUCH);
+    CSVRow	row;
+    
+    file >> row;	// read first row (header) of the laboratory book
+    
+    if (firstNoiseSecondRun == 0){
+      cout << "=====================================================================\n";
+      cout << "=====================================================================\n";
+      cout << "First: Analyzing only runs WITH NO source (for noise)...\n";
+    }
+    else{
+      cout << "=====================================================================\n";
+      cout << "=====================================================================\n";
+      cout << "Second: Analyzing only runs WITH source...\n";
+    }
+    while(file >> row) {	// for each row
+      
+      try {
+	if (row[COLRUNNO] == "")
+	  continue;	// no relevant data in this row
+	runNo = stoi(row[COLRUNNO]);	// run number (conversion works like runNo = stoi(std::string ("300");)
+	temperature = stod(row[COLTEMP]);	// temperature
+	tempSens = stod(row[COLTEMPSENS]);	// temperature
+	chip = stoi(row[COLCHIP]);
+	source = row[COLSOURCE];
+	matrix6480 = stoi(row[COLMATRIX]);	// which matrix?      
+	runFinished = row[COLDONE] == "y";	// measurement already done?
+	
+	// print info about current run to process
+	cout << "\n\n=========================\n";
+	cout << "runNo\t" << "tempSens\t" << "matrix6480\t" << "runFinished\t\n";
+	if (runFinished)
+	  cout << runNo << "\t" << tempSens << "\t\t" << matrix6480 << "\t\t" << runFinished << endl;
+	else {
+	  cout << runNo << "\t" << tempSens << "\t\t" << matrix6480 << "\t\t" << runFinished << " ======> skipped because measurement not done yet" << endl;
+	  continue;
+	}
+	
+	if (matrix6480 == 64)
+	  matrixAB = "Mi29a";
+	else if (matrix6480 == 80)
+	  matrixAB = "Mi29b";
+	else
+	  cout << "Unknown matrix! 64 and 80 are allowed values.\n";
+	
+	
+	if (source == "none" && firstNoiseSecondRun == 0 && useSeperateNoiseRun){
+	  mkdir((outputDataPath + row[COLRUNNO] +"/").c_str(), 0755);	// create directory if not existent
+	  // analyze noise in the first for loop
+	  noiseRun tmpnoiseRun = {runNo, temperature, chip, matrix6480};
+	  noiseRunList.push_back(tmpnoiseRun);	// store noiseRun in list
+	  analyzeRun(INPUTDATAPATH, outputDataPath.c_str(), runNo, matrixAB.c_str(), true, true, -1, overwrite, logfileName);
+	}
+	else if (source != "none" && firstNoiseSecondRun == 1){
+	  mkdir((outputDataPath + row[COLRUNNO] +"/").c_str(), 0755);	// create directory if not existent
+	  // analyze run in second for loop
+	  Int_t noiseRunNo;
+	  for(std::vector<noiseRun>::iterator it = noiseRunList.begin(); it != noiseRunList.end(); ++it){
+	    if ((it->temperature == temperature) && (it->chip == chip) && (it->matrix6480 == matrix6480))
+	      noiseRunNo = it->runNo;	// get correct noiseRun number for this run
+	  }
+	  if (!noiseRunNo){
+	    cout << "Corresponding noise run to run number " << runNo << " not found! ===> skipped\n";
+	    continue;
+	  }
+	  analyzeRun(INPUTDATAPATH, outputDataPath.c_str(), runNo, matrixAB, true, false, noiseRunNo, overwrite, logfileName);
+	}
+	else {
+	  cout << "==> skipped in " << firstNoiseSecondRun+1 << ". step (currently processing " << ((firstNoiseSecondRun == 0) ? "noise)":"runs)") << endl; 
+	}
+      }
+      catch(...){
+	cout << "Error while reading laboratory book (run number " << runNo << ")!\n";
+      }
+      
+    }
+    
+  }
+  
+  // copy file to output folder
+  std::ifstream  src(logfileName, std::ios::binary);
+  std::ofstream  dst(outputDataPath + logfileName,   std::ios::binary);
+  dst << src.rdbuf();
+  
+  gettimeofday(&end, 0);
+  diff = (int) (end.tv_sec-start.tv_sec);
+  printf("\nElasped Time: %02i:%02i:%02i\n",(int)((diff%86400)/3600),(int)((diff%3600)/60),(int)(diff%60) );
+  
+}
+
+
+# ifndef __CINT__
+int main(int argc, char* argv[])
+{
+  Bool_t overwrite = false;
+  Bool_t useSeperateNoiseRun = true;
+  Int_t processRunNo = -1;
+  std::string matrixAB = "Mi29a";
+  Int_t seperateNoiseRunNo = -1;
+  
+  switch(argc){
+    case 6: seperateNoiseRunNo = std::stoi(argv[5]);
+    case 5: matrixAB = argv[4];
+    case 4: processRunNo = std::stoi(argv[3]);
+    case 3: useSeperateNoiseRun = !strcmp(argv[2], "1");
+    case 2: overwrite = !strcmp(argv[1], "1");
+  }
+  
+  cout << "---------------------- Parameters --------------------------\n";
+  cout << "Usage:\nmain [BOOL overwrite?] [BOOL use seperate noise run?] [INT run number to process] [STRING matrixAB] [INT run number for seperate noise file]\n\n";
+  cout << "Values chosen:\n";
+  cout << "Overwrite: " << overwrite << (overwrite ? " (yes)\n":" (no)\n");
+  cout << "Use seperate noise run: " << useSeperateNoiseRun << (useSeperateNoiseRun ? " (yes)\n":" (no)\n");
+  cout << "Run number to process (default (-1): using the lab journal): " << processRunNo << endl;
+  cout << "Noise run number to use (default (-1): using the lab journal): " << seperateNoiseRunNo << endl;
+  cout << "Input directory: " << INPUTDATAPATH << endl;
+  cout << "Output directory: " << OUTPUTDATAPATH_MAINFOLDER << endl;
+  cout << "------------------------------------------------------------\n\n";
+  
+  
+  ProcessMeasurements(overwrite, useSeperateNoiseRun, processRunNo, matrixAB, seperateNoiseRunNo);
+  return 0;
+}
+# endif
\ No newline at end of file
diff --git a/ProcessMeasurements/analyzeRun.C b/ProcessMeasurements/analyzeRun.C
new file mode 100644
index 0000000..acfafd0
--- /dev/null
+++ b/ProcessMeasurements/analyzeRun.C
@@ -0,0 +1,157 @@
+#include "analyzeRun.h"
+
+#include <cstring>
+#include <string>
+#include <iostream>
+//#include <boost/filesystem/operations.hpp>
+#include <ctime>
+#include <iostream>
+#include <sstream>
+#include <fstream>
+
+
+
+
+
+
+
+#include <unistd.h>
+
+
+
+
+
+
+
+
+
+
+#include "TString.h"
+
+#include "MAPS.h"
+
+#define NUMEVENTSFORNOISE 1000
+
+void analyzeRun(const char *const inputDataPath, const char *const outputDataPath, Int_t runNo, std::string matrixAB, Bool_t useSeperateNoiseRun, Bool_t runIsNoise, Int_t noiseRunNo, Bool_t overwrite, std::string logfileName)
+{
+  using namespace std;
+  
+  Int_t matrixNoRows;
+  Int_t matrixNoCoulmns;
+  Int_t numSubmatrices;
+  std::ofstream	logfile;
+  Int_t b=0;
+  Int_t b_tmp=0;
+
+  if (matrixAB == "Mi29a"){
+    matrixNoRows = 272;
+    matrixNoCoulmns = 48;
+    numSubmatrices = 6;
+  }
+  else if (matrixAB == "Mi29b"){
+    matrixNoRows = 256;
+    matrixNoCoulmns = 51;
+    numSubmatrices = 6;
+  }
+  else {
+    cout << "This matrix (" << matrixAB << ") does not exist! Please choose either Mi29a or Mi29b.\n";
+    return;
+  }
+  
+  
+  for (Int_t submatrix = 0; submatrix < numSubmatrices; submatrix++){
+    logfile.open(logfileName, std::ios::out | std::ios::app);
+    
+    // file exists already?
+    TString pathString = TString(outputDataPath) + Form("%i/%i_0_%i.root", runNo, runNo, submatrix);	//std::to_string(runNo) + "/" + std::to_string(runNo) + "_" + matrixAorB + "_" + std::to_string(submatrix) + ".root";
+    TFile f(pathString);
+    if (!f.IsZombie() && !overwrite) {
+      // file exists, so skip it!
+      cout << pathString << " does already exist! ==> skipped\n\n";
+      logfile << runNo << "\t" << matrixAB << "\t" << submatrix << "\talready exists ==> skipped\n";
+      logfile.close();
+      continue;	// skip this submatrix if file already exists
+    }
+    else {
+      cout << "\n" << pathString << " ==> processing now...\n\n";
+    }
+    
+    
+    if (runIsNoise) {
+      MAPS *mapsi = new MAPS(inputDataPath,outputDataPath,runNo,matrixNoRows,matrixNoCoulmns,matrixAB.c_str(),submatrix);
+      mapsi->getNoise(NUMEVENTSFORNOISE,0,0);
+      delete mapsi;
+      logfile << runNo << "\t" << matrixAB << "\t" << submatrix << "\tprocessed as NOISE\n";
+    }
+    else {
+      std::string noiseOutputDataPath = std::string(outputDataPath);
+      if (!useSeperateNoiseRun){
+	MAPS *mapsiNoise = new MAPS(inputDataPath,std::string(outputDataPath)+"noise/",runNo,matrixNoRows,matrixNoCoulmns,matrixAB.c_str(),submatrix);
+	mapsiNoise->getNoise(NUMEVENTSFORNOISE,0,0);
+	delete mapsiNoise;
+	logfile << runNo << "\t" << matrixAB << "\t" << submatrix << "\tprocessed as NOISE\n";
+	noiseRunNo = runNo;
+	noiseOutputDataPath = std::string(outputDataPath)+"noise/";
+// 	int pipi;
+// 	cin >> pipi;
+// 	cout << "hi2";
+      }
+	
+      MAPS *mapsi = new MAPS(inputDataPath,outputDataPath,runNo,matrixNoRows,matrixNoCoulmns,matrixAB.c_str(),submatrix);
+      Int_t events = mapsi->GetNumberEvents();
+      mapsi->loadNoise(noiseOutputDataPath, noiseRunNo, submatrix);
+      for(Int_t i=0; i<events; i++) {
+	mapsi->getFrame(i);
+	mapsi->filterCommonMode();
+	mapsi->hitana();
+	
+	if(i==103)
+	  mapsi->plotFrame();
+	
+	b = (Int_t)(((i+1)*100)/(events)*10);
+	if(b!=b_tmp)
+	  printf("\r---> %4i%% %10i Frames processed!", (100*i/(events-1)), i+1 ); fflush(stdout); b_tmp=b; // In 10% steps	
+      }
+      cout<<endl;
+      
+      delete mapsi;
+      logfile << runNo << "\t" << matrixAB << "\t" << submatrix << "\tprocessed with noise\t" << noiseRunNo << endl;
+    }
+    logfile.close();
+  }
+  
+  
+}
+
+
+
+
+    
+    //   // file exists already?
+    //   string pathString = string(outputDataPath) + std::to_string(runNo) + "/" + std::to_string(runNo) + "_" + matrixAorB + "_" + std::to_string(submatrix) + ".root";
+    //   if (boost::filesystem::exists(boost::filesystem::path(pathString)) ) {
+    //     cout << "Das hier steckt in path: " << pathString;
+    //     cout << "joa ES EXISTIERT UND IST EINDEUTIG :D!\n\n\n\n";
+    //     return;
+    //   }
+    //   else{
+    //     cout << "Das hier steckt in path: " << pathString;
+    //     cout << "joa ex net... NIIICHT!!\n\n\n\n";
+    //   }
+    
+    
+    
+    //       std::time_t t = boost::filesystem::last_write_time( p ) ;
+    //       std::cout << "On " << std::ctime( &t ) << " the file " << argv[ 1 ] 
+    // 	 << " was modified the last time!\n" ;
+    //       std::cout << "Setting the modification time to now:\n" ;
+    //       std::time_t n = std::time( 0 ) ;
+    //       boost::filesystem::last_write_time( p , n ) ; 
+    //       t = boost::filesystem::last_write_time( p ) ;
+    //       std::cout << "Now the modification time is " << std::ctime( &t ) << std::endl ;
+    //       return 0 ;
+    //    } else {
+    //       std::cout << "Could not find file " << argv[ 1 ] << '\n' ;
+    //       return 2 ;
+    //    }
+    
\ No newline at end of file
diff --git a/ProcessMeasurements/analyzeRun.h b/ProcessMeasurements/analyzeRun.h
new file mode 100644
index 0000000..1a87823
--- /dev/null
+++ b/ProcessMeasurements/analyzeRun.h
@@ -0,0 +1,8 @@
+#ifndef ANALYZERUN_H
+#define ANALYZERUN_H
+
+#include <TNtuple.h>
+
+void analyzeRun(const char *const inputDataPath, const char *const outputDataPath, Int_t runNo, std::string matrixAB, Bool_t useSeperateNoiseRun, Bool_t runIsNoise, Int_t noiseRunNo, Bool_t overwrite, std::string logfileName);
+
+#endif
\ No newline at end of file