BadChannelAna.cxx

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// --- ROOT system ---
#include <TFile.h>
#include <TH1F.h>
#include <TH2F.h>
#include <TF1.h>
#include <TSpectrum.h>
#include <TROOT.h>
#include <TLine.h>
#include <TCanvas.h>
#include <TStyle.h>
#include <TLegend.h>
#include <TString.h>
#include <TSystem.h>
#include <TList.h>
#include <TLatex.h>
#include <TError.h>

#include <Riostream.h>
#include <stdio.h>
#include <fstream>
#include <iostream>
#include <alloca.h>
#include <string>
#include <cstring>

// --- ANALYSIS system ---
#include <AliCalorimeterUtils.h>
#include <AliEMCALGeometry.h>
#include <BadChannelAna.h>
#include <AliAODEvent.h>

using std::vector;
using std::cout;
using std::endl;
using std::ofstream;
using std::flush;
using std::ios;

ClassImp(BadChannelAna);

//________________________________________________________________________
BadChannelAna::BadChannelAna():
TObject(),
  fCurrentRunNumber(-1),
  fPeriod(),
  fTrainNo(),
  fTrigger(),
  fNoOfCells(),
  fCellStartDCal(12288),
  fStartCell(0),
  fEndLowerBound(1),
  fAnalysisOutput(),
  fAnalysisInput(),
  fRunList(),
  fWorkdir(),
  fQADirect(),
  fMergedFileName(),
  fAnalysisVector(),
  fTrial(),
  fExternalFileName(""),
  fExternalBadMapName(""),
  fTestRoutine(),
  fPrint(0),
  fNMaxCols(48),
  fNMaxRows(24),
  fNMaxColsAbs(),
  fNMaxRowsAbs(),
  fFlag(),
  fCriterionCounter(),
  fWarmCell(),
  fCaloUtils(),
  fRootFile(),
  fCellAmplitude(),
  fCellTime(),
  fProcessedEvents(),
  fhCellFlag(),
  fhCellWarm()
{
  fCurrentRunNumber = 254381;
  fPeriod           = "LHC16h";
  fTrainNo          = "muon_caloLego";
  fTrigger          = "AnyINT";
  fWorkdir          = ".";
  fRunListFileName  = "runList.txt";
  fTrial            = 0;

  Init();
}

//________________________________________________________________________
BadChannelAna::BadChannelAna(TString period, TString train, TString trigger, Int_t runNumber,Int_t trial, TString workDir, TString listName):
  TObject(),
  fCurrentRunNumber(-1),
  fPeriod(),
  fTrainNo(),
  fTrigger(),
  fNoOfCells(),
  fCellStartDCal(12288),
  fStartCell(0),
  fEndLowerBound(1),
  fAnalysisOutput(),
  fAnalysisInput(),
  fRunList(),
  fRunListFileName(),
  fWorkdir(),
  fQADirect(),
  fMergedFileName(),
  fAnalysisVector(),
  fTrial(),
  fExternalFileName(""),
  fExternalBadMapName(""),
  fTestRoutine(),
  fPrint(0),
  fNMaxCols(48),
  fNMaxRows(24),
  fNMaxColsAbs(),
  fNMaxRowsAbs(),
  fFlag(),
  fCriterionCounter(),
  fWarmCell(),
  fCaloUtils(),
  fRootFile(),
  fCellAmplitude(),
  fCellTime(),
  fProcessedEvents(),
  fhCellFlag(),
  fhCellWarm()
{
  fCurrentRunNumber = runNumber;
  fPeriod           = period;
  fTrainNo          = train;   //only for folder structure
  fTrigger          = trigger; //important to select trigger in output file == different wagons in lego train
  fWorkdir          = workDir;
  fRunListFileName  = listName;
  fTrial            = trial;

  Init();
}

//________________________________________________________________________
void BadChannelAna::Init()
{
  gROOT->ProcessLine("gErrorIgnoreLevel = kWarning;"); //Does not work -
  //......................................................
  //..Default values - can be set by functions
  fTestRoutine=0;

  //..Settings for the input/output structure (hard coded)
  // TO BE CHANGED
  fAnalysisInput  =Form("AnalysisInput/%s",fPeriod.Data());
  fAnalysisOutput =Form("AnalysisOutput/%s/%s/Version%i",fPeriod.Data(),fTrainNo.Data(),fTrial);

  //..Make output directory if it doesn't exist
  //..first the period folder
  gSystem->mkdir(Form("%s/AnalysisOutput/%s",fWorkdir.Data(),fPeriod.Data()));
  //..then the Train folder
  gSystem->mkdir(Form("%s/AnalysisOutput/%s/%s",fWorkdir.Data(),fPeriod.Data(),fTrainNo.Data()));
  //..then the version folder
  gSystem->mkdir(Form("%s/%s",fWorkdir.Data(),fAnalysisOutput.Data()));

  fMergedFileName= Form("%s/%s/%s/MergedRuns_%s.root",fWorkdir.Data(),fAnalysisInput.Data(),fTrainNo.Data(),fTrigger.Data());
  fRunList       = Form("%s/%s/%s/%s",fWorkdir.Data(), fAnalysisInput.Data(), fTrainNo.Data(), fRunListFileName.Data());
  fQADirect      = Form("CaloQA_%s",fTrigger.Data());

  TString fileName = Form("%s/%s/%s_%s_Histograms_V%i.root",fWorkdir.Data(),fAnalysisOutput.Data(),fPeriod.Data(),fTrigger.Data() ,fTrial);
  fRootFile = new TFile(fileName,"recreate");
  //.. make sure the vector is empty
  fAnalysisVector.clear();

  //......................................................
  //..Initialize EMCal/DCal geometry
  fCaloUtils = new AliCalorimeterUtils();
  //..Create a dummy event for the CaloUtils
  AliAODEvent* aod = new AliAODEvent();
  fCaloUtils->SetRunNumber(fCurrentRunNumber);
  fCaloUtils->AccessGeometry(aod);

  fNoOfCells    =fCaloUtils->GetEMCALGeometry()->GetNCells(); //..Very important number, never change after that point!
  Int_t nModules=fCaloUtils->GetEMCALGeometry()->GetNumberOfSuperModules();
  //..These are the first cell IDs of each SM and a cell ID of a nonExsting SM20 to mark the end (17664)
  Int_t array_StartCellSM_Value[21]   ={0,1152,2304,3456,4608,5760,6912,8064,9216,10368,11520,11904,12288,13056,13824,14592,15360,16128,16896,17280,17664};
  memcpy (fStartCellSM, array_StartCellSM_Value, sizeof (fStartCellSM));

  //..This is how the calorimeter looks like in the current period (defined by example run ID fCurrentRunNumber)
  cout<<"Called geometry for run number: "<<fCurrentRunNumber<<endl;
  cout<<"Number of supermod: "<<nModules<<endl;
  cout<<"Number of cells: "<<fNoOfCells<<endl;
  cout<<"Cell ID of first DCal cell: "<<fCellStartDCal<<endl;
  //cout<<"Number of supermod utils: "<<fCaloUtils->GetNumberOfSuperModulesUsed()<<endl; //..will always be 22 unless set by hand

  //......................................................
  //..Initialize flag array to store how the cell is categorized
  //..In the histogram: bin 1= cellID 0, bin 2= cellID 1 etc
  //..In the array: fFlag[cellID]= some information
  fFlag     = new Int_t[fNoOfCells];
  fWarmCell = new Bool_t[fNoOfCells];
  fFlag[fNoOfCells] = {0};      //..flagged as good by default
  fWarmCell[fNoOfCells] = {0};  //..flagged as not warm by default
  fCriterionCounter=2; //This value will be written in fflag and updates after each PeriodAnalysis
  //......................................................
  //..setings for the 2D histogram
  //fNMaxCols    = 48;  //eta direction
  //fNMaxRows    = 24;  //phi direction
  fNMaxColsAbs = 2*fNMaxCols;
  fNMaxRowsAbs = Int_t (nModules/2)*fNMaxRows; //multiply by number of supermodules

  //......................................................
  //..Create TLists to organize the outputfile
  fOutputListBad       = new TList();
  fOutputListGood      = new TList();
  fOutputListBadRatio  = new TList();
  fOutputListGoodRatio = new TList();

  fOutputListBad      ->SetName("BadCell_Amplitudes");
  fOutputListGood     ->SetName("GoodCell_Amplitudes");
  fOutputListBadRatio ->SetName("BadCell_AmplitudeRatios");
  fOutputListGoodRatio->SetName("GoodCell_AmplitudeRatios");

  //fOutputListGood    ->SetOwner();//ELI instead of delete in destructor??
  //fOutputListBadRatio    ->SetOwner();
  //fOutputListGoodRatio    ->SetOwner();

  //......................................................
  //..Create Histograms to store the flag in a root file
  fhCellFlag = new TH1F("fhCellFlag","fhCellFlag",fNoOfCells+10,0,fNoOfCells+10); //..cellID+1 = histogram bin
  fhCellWarm = new TH1F("fhCellWarm","fhCellWarm",fNoOfCells+10,0,fNoOfCells+10); //..cellID+1 = histogram bin
}

//________________________________________________________________________
void BadChannelAna::Run(Bool_t mergeOnly)
{
  //  cout<<"fired trigger class"<<AliAODEvent::GetFiredTriggerClasses()<<endl;

  if(fExternalFileName=="")
  {
    //..If no extrenal file is provided merge different runs together
    cout<<". . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ."<<endl;
    cout<<". . .Start process by converting files. . . . . . . . . . . ."<<endl;
    cout<<endl;
    fMergedFileName = MergeRuns();
    if(fMergedFileName.IsNull())
    {
      Printf("File not produced, exit");
      return;
    }
    cout<<endl;
  }
  else
  {
    //..If extrenal file is provided load it
    cout<<". . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ."<<endl;
    cout<<". . .Start process by loading external file. . . . . . . . . . ."<<endl;
    fMergedFileName= Form("%s/%s/%s/%s",fWorkdir.Data(),fAnalysisInput.Data(),fTrainNo.Data(),fExternalFileName.Data());
  }
  //..if ==1 only produce filtered and merged files and do not perform a BC analysis
  if(mergeOnly==0)
  {
    cout<<". . .Load inputfile with name: "<<fMergedFileName<<" . . . . . . . ."<<endl;
    //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
    //..  Read all the needed input for the Bad/Dead Channel analysis
    //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
    TFile *mergedFileInput = new TFile(fMergedFileName);
    if(!mergedFileInput->IsOpen())
    {
      Printf("Error! Input file not found, abort");
      return;
    }
    fCellAmplitude   = (TH2F*) mergedFileInput->Get("hCellAmplitude");
    fCellTime        = (TH2F*) mergedFileInput->Get("hCellTime");
    fProcessedEvents = (TH1F*) mergedFileInput->Get("hNEvents");

    //..if you have no external bad map provided that you want
    //..to test then determine the bad maps here
    if(fExternalBadMapName=="")
    {
      cout<<". . .Continue process by . . . . . . . . . . . ."<<endl;
      //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
      //.. DEAD CELLS
      //.. Flag dead cells with fFlag=1
      //.. this excludes cells from analysis (will not appear in results)
      //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
      cout<<"o o o Flag dead cells o o o"<<endl;
      FlagAsDead();
      if(fPrint==1)cout<<endl;
      if(fPrint==1)cout<<endl;

      //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
      //.. BAD CELLS
      //.. Flag dead cells with fFlag=2 and bigger
      //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
      cout<<"o o o Flag bad cells o o o"<<endl;
      BCAnalysis();

      //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
      //..In the end summarize results
      //..in a .pdf and a .txt file
      //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
      if(fPrint==1)cout<<"o o o Write .txt for each period analyis with bad cells  o o o"<<endl;
      SummarizeResultsByFlag();
    }
    //..if you have an external bad map provided load the flags and histograms
    else
    {
      LoadExternalBadMap();
    }
  }


  if(fPrint==1)cout<<"o o o Create summary documents for the entire analysis o o o"<<endl;
  SummarizeResults();
  fRootFile->WriteObject(fFlag,"FlagArray");
  fRootFile->Close();
  cout<<endl;

  //..make a reccomendation about the used energy range to be investigated
  //..and the binning
  TH1D *hRefDistr = BuildMeanFromGood();
  Double_t totalevents = fProcessedEvents->Integral();
  //..Find bin where reference has value "totalevents" (means 1 hit/event), and the corresponding x-value
  Int_t binHeightOne            = hRefDistr->FindLastBinAbove(1.0/totalevents);
  Double_t binCentreHeightOne   = hRefDistr->GetBinCenter(binHeightOne);
  cout<<". . .Recomendation:"<<endl;
  cout<<". . .With the current statistic on average a cell has 1 hit at "<<binCentreHeightOne<<" GeV"<<endl;
  cout<<". . .so it makes no sense to select energy ranges >"<<binCentreHeightOne<<"GeV as cells will be"<<endl;
  cout<<". . .marked bad just due to the lack of statistic"<<endl;
  cout<<". . .your selected lower bond is "<<fEndLowerBound<<" GeV"<<endl;
    if(binCentreHeightOne>=fEndLowerBound)  cout<<". . .This means you are OK!"<<endl;
    if(binCentreHeightOne< fEndLowerBound)    cout<<". . .#!#!#!#! CAREFUL THIS COULD CAUSE TROUBLE AND THROW OUT MORE CELLS THAN NECESSARY #!#!#!#! "<<endl;
  cout<<". . .End of process . . . . . . . . . . . . . . . . . . . . ."<<endl;
  cout<<". . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ."<<endl;
}
//________________________________________________________________________
TString BadChannelAna::MergeRuns()
{
  cout<<"o o o Start conversion process o o o"<<endl;
  cout<<"o o o period: " << fPeriod << ", pass: " << fTrainNo << ",  trigger: "<<fTrigger<< endl;

  //..Create histograms needed for adding all the files together
  TH1F *hNEventsProcessedPerRun= new TH1F("hNEvents","Number of processed events in analyzed runs",1,0,1);
  TH2F *hCellAmplitude;
  TH2F *hCellTime;

  //..Open the text file with the run list numbers and run index
  cout<<"o o o Open .txt file with run indices. Name = " << fRunList << endl;
  FILE *pFile = fopen(fRunList.Data(), "r");
  if(!pFile)
  {
    cout<<"couldn't open file!"<<endl;
    return "";
  }
  Int_t nEntr;
  Int_t nEntrTot=0;
  Int_t q;
  Int_t ncols;
  Int_t nlines = 0 ;
  Int_t runId[500] ;
  while (1)
  {
    ncols = fscanf(pFile,"  %d ",&q);
    if (ncols< 0) break;
    runId[nlines]=q;
    nlines++;
  }
  fclose(pFile);


  //..Open the different .root files with help of the run numbers from the text file
  const Int_t nRun = nlines ;
  TString base;
  TString infile;
  TString singleRunFileName;

  cout<<"o o o Start merging process of " << nRun <<" files"<< endl;
  Int_t usedFiles=0;
  //..loop over the amount of run numbers found in the previous text file.
  for(Int_t i = 0 ; i < nRun ; i++)
  {
    base  = Form("%s/%s/%s/%d", fWorkdir.Data(), fAnalysisInput.Data(), fTrainNo.Data(), runId[i]);
    //..This is a run2 case
    infile = Form("%s.root",base.Data()) ;

    cout<<"    o Open .root file with name: "<<infile<<endl;
    TFile *f = TFile::Open(infile);

    //..Do some basic checks
    if(!f)
    {
      cout<<"Couldn't open/find .root file: "<<infile<<endl;
      continue;
    }
    TDirectoryFile *dir = (TDirectoryFile *)f->Get(fQADirect);
    if(!dir)
    {
      cout<<"Couln't open directory file in .root file: "<<infile<<", directory: "<<fQADirect<<endl;
      continue;
    }
    TList *outputList = (TList*)dir->Get(fQADirect);
    if(!outputList)
    {
      cout << "Couln't get TList from directory file: "<<fQADirect<<endl;
      continue;
    }
        usedFiles++;
    TH2F *hAmpId;
    TH2F *hTimeId;
    TH1F *hNEvents;

    hAmpId =(TH2F*)outputList->FindObject("EMCAL_hAmpId");
    if(!hAmpId)
    {
      Printf("hAmpId not found");
      outputList->ls();
      continue;
    }
    else
    {
      hAmpId->SetName("hCellAmplitude");
      hAmpId->SetTitle("Cell Amplitude");
    }

    hTimeId =(TH2F*)outputList->FindObject("EMCAL_hTimeId");
    if(!hTimeId)
    {
      Printf("hTimeId not found");
      outputList->ls();
      continue;
    }
    else
    {
      hTimeId->SetName("hCellTime");
      hTimeId->SetTitle("Cell Time");
    }

    if(i==0)
    {
      //..copy the properties of the mother histogram for adding them all up
      hCellAmplitude=(TH2F*)hAmpId->Clone("DummyName1");
      hCellAmplitude->Reset();
      hCellAmplitude->SetDirectory(0); //otherwise histogram will dissapear when file is closed
      //..copy the properties of the mother histogram for adding them all up
      hCellTime=(TH2F*)hTimeId->Clone("DummyName2");
      hCellTime->Reset();
      hCellTime->SetDirectory(0); //otherwise histogram will dissapear when file is closed
    }

    hNEvents =(TH1F *)outputList->FindObject("hNEvents");
    if(!hNEvents)
    {
      Printf("hNEvents not found");
      outputList->ls();
      continue;
    }
    nEntr =  (Int_t)hNEvents->GetEntries();

    //..does that mean do not merge small files?
    if (nEntr<100)
    {
      cout <<"    o File to small to be merged. Only N entries " << nEntr << endl;
      continue ;
    }
    cout <<"    o File with N entries " << nEntr<<" will be merged"<< endl;
    nEntrTot+=nEntr;
    hCellAmplitude->Add(hAmpId);
    hCellTime->Add(hTimeId);
    hNEventsProcessedPerRun->Add(hNEvents);

    //..Create copies of the original root files just with the bad channel QA
    //..So that a run by run bad channel analysis can be performed more easily
    singleRunFileName= Form("%s/%s/%s/%d_%sFiltered.root",fWorkdir.Data(),fAnalysisInput.Data(),fTrainNo.Data(),runId[i],fTrigger.Data());
    TFile *singleRunFile = TFile::Open(singleRunFileName,"recreate");
    //..do not yet normalize by number of events
    //..due to binning issues in later histograms
    //..but rather do it at the very end of the analysis
    hAmpId ->Write();
    hTimeId->Write();
    hNEvents->Write();
    singleRunFile->Close();

    outputList->Delete();
    dir->Delete();
    f->Close();
    delete f;
  }
  //..avoid creating empty files
  if(usedFiles>0)
  {
    //.. Save the merged histograms
    cout<<"o o o Save the merged histogramms to .root file with name: "<<fMergedFileName<<endl;
    cout<<"o o o "<<nEntrTot<<" events were merged"<<endl;
    TFile *BCF = TFile::Open(fMergedFileName,"recreate");
    //hNEventsProcessedPerRun->SetName("hNEvents");
    //hNEventsProcessedPerRun->SetTitle("Number of processed events");
    hNEventsProcessedPerRun->Write();
    hCellAmplitude->SetName("hCellAmplitude");
    hCellAmplitude->SetTitle("Cell Amplitude");
    hCellAmplitude->Write();
    hCellTime->SetName("hCellTime");
    hCellTime->SetTitle("Cell Time");
    hCellTime->Write();
    BCF->Close();
    cout<<"o o o End conversion process o o o"<<endl;
    return fMergedFileName;
  }
  else
  {
    return "";
  }
}
//_________________________________________________________________________
void BadChannelAna::LoadExternalBadMap()
{
  if(fExternalBadMapName=="")cout<<"Error - no external Bad Map provided"<<endl;

  //..access the standart root output of a bad channel analysis to
  //..get the necessary histogram
  TString extRootFileName = Form("./AnalysisOutput/%s/%s/%s",fPeriod.Data(),fTrainNo.Data(),fExternalBadMapName.Data());
  TFile* outputRoot       = TFile::Open(extRootFileName.Data());

  TH1F* hFlags             =(TH1F*)outputRoot->Get("fhCellFlag");

  //..set info from external source
  //..Direction of cell ID
  for (Int_t cell = fStartCell; cell < fNoOfCells; cell++)
  {
    Double_t extFlag = hFlags->GetBinContent(cell+1);
    //..Cell flagged as dead.
    //..Flag only if it hasn't been flagged before
    fFlag[cell] =extFlag;
  }
}
//_________________________________________________________________________
void BadChannelAna::BCAnalysis()
{
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //.. BAD CELLS
  //.. Flag bad cells with fFlag= 2,3,4,5.. etc
  //.. this excludes cells from subsequent analysis
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  TArrayD periodArray;
  for(Int_t i=0;i<(Int_t)fAnalysisVector.size();i++)
  {
    periodArray=fAnalysisVector.at(i);
    PeriodAnalysis(periodArray.At(0),periodArray.At(1),periodArray.At(2),periodArray.At(3));
    fCriterionCounter++;
    if(fPrint==1)cout<<endl;
    if(fPrint==1)cout<<endl;
  }
  cout<<"o o o End of bad channel analysis o o o"<<endl;
}
//
// Mask an entire SM before doing the BC analysis
// This is useful when you get info from QA that there are problems with one SM
// and you want to clean up your bad channels beforehand
//
//________________________________________________________________________
void BadChannelAna::AddMaskSM(Int_t iSM)
{
  cout<<"o o o Manually mask SM "<<iSM<<" o o o"<<endl;
  //..Loop over cell ID
  for (Int_t cell = fStartCell; cell < fNoOfCells; cell++)
  {
    //..check to which SM the cell belongs
    if(cell>=fStartCellSM[iSM] && cell<fStartCellSM[iSM+1])
    {
      fFlag[cell] =1;
    }
  }
}
//________________________________________________________________________
void BadChannelAna::AddPeriodAnalysis(Int_t criteria, Double_t nsigma, Double_t emin, Double_t emax)
{
  TArrayD periodArray;
  periodArray.Set(4);
  periodArray.AddAt((Double_t)criteria,0);
  periodArray.AddAt(nsigma,1);
  periodArray.AddAt(emin,2);
  periodArray.AddAt(emax,3);
  fAnalysisVector.push_back(periodArray);
}
//____________________________________________________________________
void BadChannelAna::PeriodAnalysis(Int_t criterion, Double_t nsigma, Double_t emin, Double_t emax)
{
  //.. criterion should be between 1-4
  if(fPrint==1)cout<<"o o o o o o o o o o o o o o o o o o o o o o o o o"<<endl;
  if(fPrint==1)cout<<"o o o PeriodAnalysis for flag "<<criterion<<" o o o"<<endl;
  if(fPrint==1 && criterion < 3)cout<<"o o o Done in the energy range E "<<emin<<" - "<<emax<<endl;
  if(fPrint==1 && criterion == 3)cout<<"o o o Done in the time range t "<<emin<<" - "<<emax<<endl;

  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //.. ANALYSIS OF CELLS WITH ENTRIES
  //.. Build average distributions and fit them
  //.. Three tests for bad cells:
  //.. 1) Average energy per hit
  //.. 2) Average hit per event
  //.. 3) Average max of cell time distribution
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  TH1F* histogram;
  if(fPrint==1)cout<<"o o o Analyze average cell distributions o o o"<<endl;
  //..For case 1 or 2
  if(criterion < 3)   histogram = BuildHitAndEnergyMean(criterion, emin, emax);
  if(criterion == 3)  histogram = BuildTimeMean(criterion, emin, emax); //.. in case of crit 3 emin is tmin and emax is tmax

  if(criterion==1)
  {
//    if(emin>=1.8)FlagAsBad(criterion, histogram, nsigma, -1);//..do not apply a lower boundary
    if(emin>=fEndLowerBound)FlagAsBad(criterion, histogram, nsigma, -1);//..do not apply a lower boundary
    else         FlagAsBad(criterion, histogram, nsigma, 200);//400
  }
  if(criterion==2)
  {
//    if(emin>=1.8)FlagAsBad(criterion, histogram, nsigma, -1);//..do not narrow the integration window
    if(emin>=fEndLowerBound)FlagAsBad(criterion, histogram, nsigma, -1);//..do not narrow the integration window
    else         FlagAsBad(criterion, histogram, nsigma, 601);
  }
  if(criterion==3) FlagAsBad(criterion, histogram, nsigma, 602);
}

//_________________________________________________________________________
TH1F* BadChannelAna::BuildHitAndEnergyMean(Int_t crit, Double_t emin, Double_t emax)
{
  if(fPrint==1)cout<<"    o Calculate average cell hit per event and average cell energy per hit "<<endl;
  TH1F *histogram;
  if(crit==1)histogram = new TH1F(Form("hCellEtoN_E%.2f-%.2f",emin,emax),Form("Energy per hit, %.2f < E < %.2f GeV",emin,emax), fNoOfCells,0,fNoOfCells);
  if(crit==2)histogram = new TH1F(Form("hCellNtoEvt_E%.2f-%.2f",emin,emax),Form("Number of hits in cell, %.2f < E < %.2f GeV",emin,emax), fNoOfCells,0,fNoOfCells);
  histogram->SetXTitle("Abs. Cell Id");
  if(crit==1)histogram->SetYTitle("Energy per hit");
  if(crit==2)histogram->SetYTitle("Number of hits in cell");
  histogram->GetXaxis()->SetNdivisions(510);

  //..count Events in Energy Range
  TH1F* pojection  = (TH1F*)fCellAmplitude->ProjectionX("Intermediate");
  fnEventsInRange  = pojection->Integral(pojection->GetBinContent(emin),pojection->GetBinContent(emax));

  //..here the average hit per event and the average energy per hit is caluclated for each cell.
  for (Int_t cell = fStartCell; cell < fNoOfCells; cell++)
  {
    Double_t Esum = 0;
    Double_t Nsum = 0;

    for (Int_t j = 1; j <= fCellAmplitude->GetNbinsX(); j++)
    {
      //To Do: I think one should also take the different bin width into account
      Double_t E = fCellAmplitude->GetXaxis()->GetBinCenter(j);
      Double_t N = fCellAmplitude->GetBinContent(j, cell+1);
      //..investigate only cells that were not flagged as dead ore bad
      if (E < emin || E > emax || fFlag[cell]!=0) continue;
      Esum += E*N;
      Nsum += N;
    }
    //..Set the values only for cells that are not yet marked as bad
    if(fFlag[cell]==0)
    {
      if(crit==2)             histogram->SetBinContent(cell+1, Nsum);  //..number of hits (per event -> not anymore)
      if(Nsum > 0. && crit==1)histogram->SetBinContent(cell+1, Esum/(Nsum)); //..average energy per hit
    }
  }
  return histogram;
}
//_________________________________________________________________________
TH1F* BadChannelAna::BuildTimeMean(Int_t crit, Double_t tmin, Double_t tmax)
{
  if(fPrint==1)cout<<"    o Calculate maximum of cell time distribution "<<endl;
  TString name;
  TH1F *histogram;
  histogram = new TH1F(Form("timeMax_t%.2f-%.2f",tmin,tmax),Form("Maximum of time distr., %.2f < t < %.2f GeV",tmin,tmax), fNoOfCells,0,fNoOfCells);
  histogram->SetXTitle("Abs. Cell Id");
  histogram->SetYTitle("time max");
  histogram->GetXaxis()->SetNdivisions(510);

  //..Time information
  for (Int_t cell = fStartCell; cell < fNoOfCells; cell++)
  {
    Double_t timeMax = -100;
    //..search for the maximum bin between tmin and tmax
    name=Form("Cell %d",cell);
    //sprintf(name, "Cell %d",channelVector.at(i)) ;
    TH1 *hCell = fCellTime->ProjectionX(name,cell+1,cell+1);
    hCell->GetXaxis()->SetRangeUser(tmin,tmax);

    timeMax = hCell->GetXaxis()->GetBinCenter(hCell->GetMaximumBin());
    if(cell>55 &&cell<65)cout<<"Integral: "<<hCell->Integral()<<endl;
    if(hCell->Integral()<=0)timeMax=-40;
    //..Set the values only for cells that are not yet marked as bad
    if(fFlag[cell]==0)
    {
      histogram->SetBinContent(cell+1, timeMax);  //..number of hits per event
    }
    else
    {
      histogram->SetBinContent(cell+1, -50);  //..number of hits per event
    }

  }
  return histogram;
}

//_________________________________________________________________________
void BadChannelAna::FlagAsDead()
{
  Int_t sumOfExcl=0;
  Int_t manualMaskCounter=0;
  //..sort the elements in manual mask list
  std::sort (fManualMask.begin(), fManualMask.end());

  //..Direction of cell ID
  for (Int_t cell = fStartCell; cell < fNoOfCells; cell++)
  {
    Double_t nSum = 0;
    //..Direction of amplitude (Checks energies from 0-nBins GeV)
    for (Int_t amp = 1; amp <= fCellAmplitude->GetNbinsX(); amp++)
    {
      //..cellID+1 = histogram bin
      Double_t N = fCellAmplitude->GetBinContent(amp,cell+1);
      nSum += N;
    }
    //..If the amplitude in one cell is basically 0
    //..mark the cell as excluded
    if(nSum == 0 && fFlag[cell]==0)
    {
      //..Cell flagged as dead.
      //..Flag only if it hasn't been flagged before
      fFlag[cell] =1;
      sumOfExcl++;
    }
    //..add here the manual masking
    if(manualMaskCounter<(Int_t)fManualMask.size() && fManualMask.at(manualMaskCounter)==cell)
    {
      fFlag[cell] = 2;
      manualMaskCounter++;
    }
  }
  if(fPrint==1)cout<<"    o Number of dead cells: "<<sumOfExcl<<endl;
  if(fPrint==1)cout<<"     ("<<sumOfExcl<<")"<<endl;
}

//_________________________________________________________________________
void BadChannelAna::FlagAsBad(Int_t crit, TH1F* inhisto, Double_t nsigma, Double_t dnbins)
{  
    gStyle->SetOptStat(0); //..Do not plot stat boxes
  gStyle->SetOptFit(0);  //
  if(fPrint==1 && crit==1)cout<<"    o Fit average energy per hit distribution"<<endl;
  if(fPrint==1 && crit==2)cout<<"    o Fit average hit per event distribution"<<endl;
  if(fPrint==1 && crit==3)cout<<"    o Fit average hit maximum distribution"<<endl;

  Int_t cellColumn=0,cellRow=0;
  Int_t cellColumnAbs=0,cellRowAbs=0;
  Int_t trash;

  TString histoName=inhisto->GetName();
  Double_t goodmax = 0. ;
  Double_t goodmin = 0. ;
  //..set a user range so that the min and max is only found in a certain range
  inhisto->GetXaxis()->SetRangeUser(fStartCell,fNoOfCells);//..
  Double_t dminVal = inhisto->GetMinimum(0);
  Double_t dmaxVal = inhisto->GetMaximum();
  Double_t inputBins=dnbins;
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //. . .determine settings for the histograms (range and binning)
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //cout<<"max value: "<<dmaxVal<<", min value: "<<dminVal<<endl;
  //
  if(crit==2 && inputBins==-1)  dnbins=dmaxVal-dminVal;
  if(crit==1 && inputBins==-1)  dnbins=200; //100 or lower, if you have problems with low statistic

    //..For histograms with lower statistic (typically higher energy ranges)
  //..find a proper binning automatically (mostly done to avoid steplike structures, 0 entries in bins etc)
  if(inputBins!=-1)
  {
    //..calculate and print the "median"
    Int_t numBins = inhisto->GetXaxis()->GetNbins();

    numBins-=fStartCell;
    Double_t *x = new Double_t[numBins];
    Double_t* y = new Double_t[numBins];
    for (int i = 0; i < numBins; i++)
    {
      x[i] = inhisto->GetBinContent(i+fStartCell);
      y[i] = 1; //each value with weight 1
      if(x[i]==0)y[i] = 0;
    }
    Double_t medianOfHisto = TMath::Median(numBins,x,y);

    //..if dmaxVal is too far away from medianOfHisto the histogram
    //..range will be too large -> reduce the range
    //cout<<"max value: "<<dmaxVal<<", min: "<<dminVal<<" median of histogram: "<<medianOfHisto<<endl;
    if(medianOfHisto*10<dmaxVal)
    {
      //cout<<"- - - median too far away from max range"<<endl;
      dmaxVal=medianOfHisto+0.2*(dmaxVal-medianOfHisto);  //..reduce the distance between max and mean drastically to cut out the outliers
    }

    if(crit==2)
    {
      dnbins=dmaxVal-dminVal;
      if(dnbins>100)
      {
        if(dnbins>2000)dnbins=0.01*(dmaxVal-dminVal); //..maximum 5000 bins. changed to 3000 .. lets see..
        if(dnbins>2000)dnbins=0.001*(dmaxVal-dminVal);//..maximum 5000 bins.
        if(dnbins<100) dnbins=0.02*(dmaxVal-dminVal); //..minimum 100 bins.
      }
    }
    if(crit==1)
    {
      dnbins=(dmaxVal-dminVal)*500;  //300 if you have problems with low statistic
    }
  }
  //cout<<"number of bins: "<<dnbins<<endl;

  if(crit==3)
  {
    //..obtain the binwidth for
    Int_t binWidth = fCellTime->GetXaxis()->GetBinWidth(1);
    dnbins = fCellTime->GetXaxis()->GetNbins();
    dminVal= fCellTime->GetXaxis()->GetBinCenter(1)-(binWidth*1.0)/2.0;
    dmaxVal= fCellTime->GetXaxis()->GetBinCenter(dnbins)+(binWidth*1.0)/2.0;
    cout<<"set the new histo with following settings- bins: "<<dnbins<<", min val = "<<dminVal<<", max val:"<<dmaxVal<<endl;
  }
  //..build histos
  TH1F *distrib = new TH1F(Form("%sDistr",(const char*)histoName), "", dnbins, dminVal, dmaxVal);
  distrib->SetXTitle(inhisto->GetYaxis()->GetTitle());
  distrib->SetYTitle("Entries");
  TH1F *distrib_wTRDStruc = new TH1F(Form("%sDistr_wTRD",(const char*)histoName), "", dnbins, dminVal, dmaxVal);
  TH1F *distrib_woTRDStruc= new TH1F(Form("%sDistr_woTRD",(const char*)histoName), "", dnbins, dminVal, dmaxVal);

  //..build two dimensional histogram with values row vs. column
  TH2F *plot2D = new TH2F(Form("%s_HitRowColumn",(const char*)histoName),Form("%s_HitRowColumn",(const char*)histoName),fNMaxColsAbs+1,-0.5,fNMaxColsAbs+0.5, fNMaxRowsAbs+1,-0.5,fNMaxRowsAbs+0.5);
  plot2D->GetXaxis()->SetTitle("cell column (#eta direction)");
  plot2D->GetYaxis()->SetTitle("cell row (#phi direction)");

  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //. . .build the distribution of average values
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  for (Int_t cell = fStartCell; cell < fNoOfCells; cell++)
  {
    //..Do that only for cell ids also accepted by the code
    if(!fCaloUtils->GetEMCALGeometry()->CheckAbsCellId(cell))continue;

    //..Fill histograms only for cells that are not yet flagged as bad
    if(fFlag[cell]==0)
    {
      //..fill the distribution of avarge cell values
      distrib->Fill(inhisto->GetBinContent(cell+1));
      //if(cell<fCellStartDCal)distrib_wTRDStruc->Fill(inhisto->GetBinContent(cell+1));
      //else                   distrib_woTRDStruc ->Fill(inhisto->GetBinContent(cell+1));
      //..Get Row and Collumn for cell ID
      fCaloUtils->GetModuleNumberCellIndexesAbsCaloMap(cell,0,cellColumn,cellRow,trash,cellColumnAbs,cellRowAbs);
      if(cellColumnAbs> fNMaxColsAbs || cellRowAbs>fNMaxRowsAbs)
      {
        cout<<"Problem! wrong calculated number of max col and max rows"<<endl;
        cout<<"current col: "<<cellColumnAbs<<", max col"<<fNMaxColsAbs<<endl;
        cout<<"current row: "<<cellRowAbs<<", max row"<<fNMaxRowsAbs<<endl;
      }
      plot2D->SetBinContent(cellColumnAbs,cellRowAbs,inhisto->GetBinContent(cell+1));
      //..check TRD support structure
      if(IsCoveredByTRD(cellRowAbs,cellColumnAbs)==1)
      {
        distrib_wTRDStruc->Fill(inhisto->GetBinContent(cell+1));
      }
      else
      {
        distrib_woTRDStruc ->Fill(inhisto->GetBinContent(cell+1));
      }
    }
  }

  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //. . .draw histogram + distribution
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  TCanvas *c1 = new TCanvas(histoName,histoName,900,900);
  c1->ToggleEventStatus();
  TPad*    upperPad      = new TPad("upperPad", "upperPad",.005, .5, .995, .995);
  TPad*    lowerPadLeft  = new TPad("lowerPadL", "lowerPadL",.005, .005, .5, .5);
  TPad*    lowerPadRight = new TPad("lowerPadR", "lowerPadR",.5, .005, .995, .5);
  upperPad->Draw();
  lowerPadLeft->Draw();
  lowerPadRight->Draw();

  upperPad->cd();
  upperPad->SetLeftMargin(0.05);
  upperPad->SetRightMargin(0.05);
  if(crit<3)upperPad->SetLogy();
  inhisto->SetTitleOffset(0.6,"Y");
  inhisto->GetXaxis()->SetRangeUser(0,fNoOfCells+1);
  inhisto->GetYaxis()->SetTitleOffset(0.7);
  inhisto->SetLineColor(kBlue+1);
  inhisto->Draw();

  lowerPadRight->cd();
  lowerPadRight->SetLeftMargin(0.09);
  lowerPadRight->SetRightMargin(0.12);
  plot2D->GetYaxis()->SetTitleOffset(1.3);
  plot2D->Draw("colz");

  lowerPadLeft->cd();
  lowerPadLeft->SetLeftMargin(0.09);
  lowerPadLeft->SetRightMargin(0.07);
  lowerPadLeft->SetLogy();
  distrib->SetLineColor(kBlue+1);
  distrib->GetYaxis()->SetTitleOffset(1.3);
  distrib->Draw();
  distrib_wTRDStruc->SetLineColor(kGreen+1);
  distrib_wTRDStruc->DrawCopy("same");
  distrib_woTRDStruc->SetLineColor(kMagenta+1);
  distrib_woTRDStruc->DrawCopy("same");

  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //. . .fit histogram
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

  //..to exclude first 2 bins from max finding
  distrib->GetXaxis()->SetRangeUser(distrib->GetBinCenter(2),distrib->GetBinCenter(dnbins));
  Double_t maxDistr  = distrib->GetMaximum();
  Int_t    maxBin    = distrib->GetMaximumBin();
  Double_t maxCenter = distrib->GetBinCenter(maxBin);

  //..good range is around the max value as long as the
  //..bin content is larger than 2 entries
  for(Int_t i = maxBin ; i<=dnbins ; i++)
  {
    if(distrib->GetBinContent(i)<2) break ;
    goodmax = distrib->GetBinCenter(i);
  }
  for(Int_t i = maxBin ; i>2 ; i--)
  {
    if(distrib->GetBinContent(i)<2) break ;
    goodmin = distrib->GetBinLowEdge(i);
  }
  //if(maxBin<2)goodmin = distrib->GetBinLowEdge(2);

  //..Define min/max range of the fit function
  Double_t   minFitRange=goodmin;
    Double_t   maxFitRange=goodmax;
  //if(crit==2)minFitRange=distrib->GetBinLowEdge(2);//..exclude first 2 bins
  //if(crit==2)maxFitRange=dmaxVal;
    if(crit==3)minFitRange=-20;
  if(crit==3)maxFitRange=20;

  //cout<<"max bin:    "<<maxBin<<", max value: "<<maxDistr<<endl;
  //cout<<"start mean: "<<maxCenter<<", mean range: 0-"<<dmaxVal<<endl;
  //cout<<"fit range:  "<<minFitRange<<" - "<<maxFitRange<<endl;
  TF1 *fit2 = new TF1("fit2", "gaus",minFitRange,maxFitRange);
  //..start the fit with a mean of the highest value
  fit2->SetParLimits(0,0,maxDistr); //..do not allow negative ampl values
  fit2->SetParameter(1,maxCenter);  //..set the start value for the mean
  fit2->SetParLimits(1,0,dmaxVal);  //..do not allow negative mean values

  //..ELI - TO DO: eventually fit with TRD and without TRD seperatley
  distrib->Fit(fit2, "0LQEM", "", minFitRange, maxFitRange);
  Double_t sig, mean;// chi2ndf;
  mean    = fit2->GetParameter(1);
  sig     = fit2->GetParameter(2);

  //..for case 1 and 2 lower than 0 is an unphysical value
  if(crit<3 && mean <0.) mean=0.;

  goodmin = mean - nsigma*sig ;
  goodmax = mean + nsigma*sig ;
  //..for case 1 and 2 lower than 0 is an unphysical value
  if(crit<3 && goodmin <0.) goodmin=0.;
  //..this (below) is a special case for energy ranges where cell do not have many
  //..entries typically. One should not apply a lower bound in this case.
  if(inputBins==-1)         goodmin=-1;
  if(fPrint==1)cout<<"    o Result of fit: "<<endl;
  if(fPrint==1)cout<<"    o  "<<endl;
  if(fPrint==1)cout<<"    o Mean: "<<mean <<" sigma: "<<sig<<endl;
  if(fPrint==1)cout<<"    o good range : "<<goodmin <<" - "<<goodmax<<endl;

  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //. . .Add info to histogram
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  TLine *lline = new TLine(goodmin, 0, goodmin, distrib->GetMaximum());
  lline->SetLineColor(kGreen+2);
  lline->SetLineStyle(7);
  lline->Draw();

  TLine *rline = new TLine(goodmax, 0, goodmax, distrib->GetMaximum());
  rline->SetLineColor(kGreen+2);
  rline->SetLineStyle(7);
  rline->Draw();

  TLegend *leg = new TLegend(0.60,0.70,0.9,0.85);
  leg->AddEntry(lline,"Good region boundary","l");
  leg->AddEntry(distrib_wTRDStruc,"Covered by TRD","l");
  leg->AddEntry(distrib_woTRDStruc,"wo TRD structure","l");
  leg->SetBorderSize(0);
  leg->Draw("same");

  fit2->SetLineColor(kOrange-3);
  fit2->SetLineStyle(1);//7
  fit2->Draw("same");

  TLatex* text = 0x0;
  if(crit==1) text = new TLatex(0.12,0.85,Form("Good range: %.2f-%.2f",goodmin,goodmax));
  if(crit==2) text = new TLatex(0.12,0.85,Form("Good range: %.2f-%.2f",goodmin,goodmax));
  if(crit==3) text = new TLatex(0.12,0.85,Form("Good range: %.2f-%.2f",goodmin,goodmax));
  text->SetTextSize(0.06);
  text->SetNDC();
  text->SetTextColor(1);
  text->Draw();

  upperPad->cd();
  TLine *uline = new TLine(0, goodmax,fNoOfCells,goodmax);
  uline->SetLineColor(kGreen+2);
  uline->SetLineStyle(7);
  uline->Draw();
  TLine *lowline = new TLine(0, goodmin,fNoOfCells,goodmin);
  lowline->SetLineColor(kGreen+2);
  lowline->SetLineStyle(7);
  lowline->Draw();
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //. . .Save histogram
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  c1->Update();
  TString name   =Form("%s/%s/criteria-_%d.gif",fWorkdir.Data(), fAnalysisOutput.Data(), crit);
  if(crit==1)name=Form("%s/%s/AverageEperHit_%s.gif",fWorkdir.Data(), fAnalysisOutput.Data(), (const char*)histoName);
  if(crit==2)name=Form("%s/%s/AverageHitperEvent_%s.gif",fWorkdir.Data(), fAnalysisOutput.Data(), (const char*)histoName);
  if(crit==3)name=Form("%s/%s/AverageTimeMax_%s.gif",fWorkdir.Data(), fAnalysisOutput.Data(), (const char*)histoName);
  c1->SaveAs(name);

  fRootFile->WriteObject(c1,c1->GetName());
  fRootFile->WriteObject(plot2D,plot2D->GetName());
  fRootFile->WriteObject(distrib,distrib->GetName());
  fRootFile->WriteObject(inhisto,inhisto->GetName());
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //. . . Mark the bad cells in the fFlag array
  //. . .(fCriterionCounter= bad because cell average value lower than min allowed)
  //. . .(fCriterionCounter= bad because cell average value higher than max allowed)
  //. . .(0 by default - good cell)
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  if(fPrint==1)cout<<"    o Flag bad cells that are outside the good range "<<endl;
  for(Int_t cell = fStartCell; cell < fNoOfCells; cell++)
  {
    //..cell=0 and bin=1, cell=1 and bin=2
    //.. <= throws out zeros, might not be a dead cell but still have zero entries in a given energy range
    if(inhisto->GetBinContent(cell+1) <= goodmin && fFlag[cell]==0)
    {
      //cout<<"smaller than min value: "<<inhisto->GetBinContent(cell+1)<<endl;
      fFlag[cell]=fCriterionCounter;
    }
    if(inhisto->GetBinContent(cell+1) > goodmax && fFlag[cell]==0)
    {
      //cout<<"bigger than max value: "<<inhisto->GetBinContent(cell+1)<<endl;
      fFlag[cell]=fCriterionCounter;
    }
  }
  if(fPrint==1)cout<<"    o o o o o o o o o o o o o o o o o o o o o o o"<<endl;
}

//________________________________________________________________________
void BadChannelAna::SummarizeResultsByFlag()
{
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //.. RESULTS
  //.. 1) Print the bad cells
  //..    and write the results to a file
  //..    for each added period analysis
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  TArrayD periodArray;
  Double_t emin,emax,sig;
  Int_t criterion;
  TString output;
  Int_t nb1=0;

  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //..Save the results in a tWiki format for the webpage (https://twiki.cern.ch/twiki/bin/view/ALICE/EMCalQABadChannels2)
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  TString aliceTwikiTable = Form("%s/%s/%s_TwikiTable_V%i.txt",fWorkdir.Data(), fAnalysisOutput.Data(), fTrigger.Data() ,fTrial); ;
  ofstream file2(aliceTwikiTable, ios::out | ios::trunc);
  if(file2)
  {
    file2<<"|*Criterium* | *E_min !GeV* | *E_max !GeV* | *sigma* | *Excluded Cells* |"<<endl;
  }
  file2.close();

  for(Int_t i=0;i<(Int_t)fAnalysisVector.size();i++)
  {
    periodArray=fAnalysisVector.at(i);
    criterion  =periodArray.At(0);
    emin       =periodArray.At(2);
    emax       =periodArray.At(3);
    sig        =periodArray.At(1);

    //..Print the results on the screen and
    //..write the results in a file
    output.Form("%s/%s/Criterion%d_Emin-%.2f_Emax-%.2f.txt",fWorkdir.Data(), fAnalysisOutput.Data(), criterion,emin,emax);
    ofstream file(output, ios::out | ios::trunc);
    if(!file)
    {
      cout<<"#### Major Error. Check the textfile!"<<endl;
    }
    file<<"fFlag="<<i+2<<"means Criterion : "<<criterion<<", emin = "<<emin<<" GeV"<<", emax = "<<emax<<" GeV"<<endl;
    if(fPrint==1)cout<<"    o Criterion : "<<criterion<<", emin = "<<emin<<" GeV"<<", emax = "<<emax<<" GeV"<<" (Method "<<i<<")"<<endl;

    nb1=0;
    for(Int_t cellID=fStartCell ;cellID<fNoOfCells;cellID++)
    {
      if(fFlag[cellID]==(i+2))
      {
        nb1++;
        file<<cellID<<", ";
      }
    }
    file<<"Total number of bad cells with fFlag=="<<i+2<<endl;
    file<<"("<<nb1<<")"<<endl;
    file.close();
    if(fPrint==1)cout<<"    o Total number of bad cells ("<<nb1<<")"<<endl;
    if(fPrint==1)cout<<endl;
    //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
    //..Save the results in a tWiki format for the webpage (https://twiki.cern.ch/twiki/bin/view/ALICE/EMCalQABadChannels2)
    //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
    ofstream file2(aliceTwikiTable, ios::out | ios::app);
    if(file2)
    {
      file2<<"|     "<<criterion<<"      |    "<<emin<<"      |    "<<emax<<"      |    "<<sig<<"   |       "<<nb1<<"        |"<<endl;
    }
    file2.close();
  }
}
//________________________________________________________________________
void BadChannelAna::SummarizeResults()
{
  Int_t cellID, nDeadDCalCells = 0, nDeadEMCalCells = 0, nDCalCells = 0, nEMCalCells = 0;
  Double_t perDeadEMCal,perDeadDCal,perBadEMCal,perBadDCal,perWarmEMCal,perWarmDCal;
  TString aliceTwikiTable, cellSummaryFile, deadPdfName, badPdfName, ratioOfBad,goodCells,goodCellsRatio,cellProp;
  TString OADBFile_bad, OADBFile_dead, OADBFile_warm;
  TH2F* cellAmp_masked = (TH2F*)fCellAmplitude->Clone("hcellAmp_masked");
  TH2F* cellTime_masked= (TH2F*)fCellTime->Clone("fCellTime");

  deadPdfName     = Form("%s/%s/%s_Dead_Ampl_V%i.pdf",fWorkdir.Data(), fAnalysisOutput.Data(), fTrigger.Data() ,fTrial);
  badPdfName      = Form("%s/%s/%s_Bad_Ampl_V%i.pdf",fWorkdir.Data(), fAnalysisOutput.Data(), fTrigger.Data() ,fTrial);
  ratioOfBad      = Form("%s/%s/%s_Bad_Ampl_Ratio_V%i.pdf",fWorkdir.Data(), fAnalysisOutput.Data(), fTrigger.Data() ,fTrial);
  goodCells       = Form("%s/%s/%s_Good_Ampl_V%i.pdf",fWorkdir.Data(), fAnalysisOutput.Data(), fTrigger.Data() ,fTrial);
  goodCellsRatio  = Form("%s/%s/%s_Good_Ampl_Ratio_V%i.pdf",fWorkdir.Data(), fAnalysisOutput.Data(), fTrigger.Data() ,fTrial);
  cellSummaryFile = Form("%s/%s/%s_%s_Bad_Ampl_V%i.txt",fWorkdir.Data(), fAnalysisOutput.Data(),fPeriod.Data(), fTrigger.Data() ,fTrial); ;
  OADBFile_bad    = Form("%s/%s/%s_%s_OADBFile_Bad_V%i.txt",fWorkdir.Data(), fAnalysisOutput.Data(),fPeriod.Data(), fTrigger.Data() ,fTrial); ;
  OADBFile_dead   = Form("%s/%s/%s_%s_OADBFile_Dead_V%i.txt",fWorkdir.Data(), fAnalysisOutput.Data(),fPeriod.Data(), fTrigger.Data() ,fTrial); ;
  OADBFile_warm   = Form("%s/%s/%s_%s_OADBFile_Warm_V%i.txt",fWorkdir.Data(), fAnalysisOutput.Data(),fPeriod.Data(), fTrigger.Data() ,fTrial); ;
  aliceTwikiTable = Form("%s/%s/%s_TwikiTable_V%i.txt",fWorkdir.Data(), fAnalysisOutput.Data(), fTrigger.Data() ,fTrial); ;
  cellProp        = Form("%s/%s/%s_CellProp_V%i.pdf",fWorkdir.Data(), fAnalysisOutput.Data(), fTrigger.Data() ,fTrial);

  cout<<"    o Final results o "<<endl;
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //..Create a masked version of the Amp vs. ID and Time vs. ID histograms
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  for (Int_t cell = fStartCell; cell < fNoOfCells; cell++)
  {
    //..Direction of amplitude (Checks energies from 0-nBins GeV)
    for (Int_t amp = 1; amp <= fCellAmplitude->GetNbinsX(); amp++)
    {
      if(fFlag[cell]!=0)
      {
        //..cellID+1 = histogram bin
        cellAmp_masked->SetBinContent(amp,cell+1,0);
      }
    }
    //..Direction of time (Checks times from -275-975 GeV)
    for (Int_t time = 1; time <= fCellTime->GetNbinsX(); time++)
    {
      if(fFlag[cell]!=0)
      {
        //..cellID+1 = histogram bin
        cellTime_masked->SetBinContent(time,cell+1,0);
      }
    }
  }
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //..Plot some summary canvases
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  TCanvas *c1 = new TCanvas("CellProp","I summary of cell properties",1000,1000);
  c1->ToggleEventStatus();
  c1->Divide(2,2);
  c1->cd(1)->SetLogz();
  //lowerPadRight->SetLeftMargin(0.09);
  //lowerPadRight->SetRightMargin(0.06);
  fCellAmplitude->SetXTitle("Cell Energy [GeV]");
  fCellAmplitude->SetYTitle("Abs. Cell Id");
  fCellAmplitude->GetYaxis()->SetTitleOffset(1.6);
  fCellAmplitude->Draw("colz");
  c1->cd(2)->SetLogz();
  fCellTime->SetXTitle("Cell Time [ns]");
  fCellTime->SetYTitle("Abs. Cell Id");
  fCellTime->GetYaxis()->SetTitleOffset(1.6);
  fCellTime->Draw("colz");
  c1->cd(3)->SetLogz();
  //lowerPadRight->SetLeftMargin(0.09);
  //lowerPadRight->SetRightMargin(0.06);
  cellAmp_masked->SetTitle("Masked Cell Amplitude");
  cellAmp_masked->SetXTitle("Cell Energy [GeV]");
  cellAmp_masked->SetYTitle("Abs. Cell Id");
  cellAmp_masked->GetYaxis()->SetTitleOffset(1.6);
  cellAmp_masked->Draw("colz");
  c1->cd(4)->SetLogz();
  cellTime_masked->SetTitle("Masked Cell Time");
  cellTime_masked->SetXTitle("Cell Time [ns]");
  cellTime_masked->SetYTitle("Abs. Cell Id");
  cellTime_masked->GetYaxis()->SetTitleOffset(1.6);
  cellTime_masked->Draw("colz");
  c1->Update();

  TCanvas *c1_ratio = new TCanvas("CellPropRatio","II summary of cell properties ratio",1000,500);
  c1_ratio->ToggleEventStatus();
  c1_ratio->Divide(2);
  c1_ratio->cd(1)->SetLogz();
  cellAmp_masked->SetTitle("Masked Cell Amplitude");
  cellAmp_masked->GetZaxis()->SetRangeUser(0.0001,10e7);
  cellAmp_masked->Draw("colz");
  c1_ratio->cd(2)->SetLogz();

  TH1D *hRefDistr  = BuildMeanFromGood();
  TH2F* ratio2DAmp =(TH2F*)cellAmp_masked->Clone("ratio2DAmp");
  TH2F* Sum2DIdeal =(TH2F*)cellAmp_masked->Clone("Sum2DIdeal");
  Sum2DIdeal->Reset();
    //..Create an ideal 2D energy distribution for division.
  //..Helps to identify whether there are some cells that still
  //..need to be masked by hand
  for(Int_t eBin=0;eBin<Sum2DIdeal->GetNbinsX();eBin++)
  {
    Double_t binVal=hRefDistr->GetBinContent(eBin+1);
    for(Int_t icell=0;icell<Sum2DIdeal->GetNbinsY();icell++)
    {
      Sum2DIdeal->SetBinContent(eBin+1,icell+1,binVal);
    }
  }
  ratio2DAmp->SetTitle("Ratio of cell Amplitude to mean cell ampl.");
  ratio2DAmp->Divide(Sum2DIdeal);
  ratio2DAmp->GetZaxis()->UnZoom();
  ratio2DAmp->Draw("colz");

  TLatex* textSM = new TLatex(0.1,0.1,"*test*");
  textSM->SetTextSize(0.06);
  textSM->SetTextColor(1);
  textSM->SetNDC();

  TCanvas *c1_proj = new TCanvas("CellPropPProj","III summary of cell properties",1000,500);
  c1_proj->ToggleEventStatus();
  c1_proj->Divide(2);
  c1_proj->cd(1)->SetLogy();
  TH1* projEnergyMask = cellAmp_masked->ProjectionX(Form("%sMask_Proj",cellAmp_masked->GetName()),fStartCell,fNoOfCells);
  projEnergyMask->SetXTitle("Cell Energy [GeV]");
  projEnergyMask->GetYaxis()->SetTitleOffset(1.6);
  projEnergyMask->SetLineColor(kGreen+1);
  projEnergyMask->DrawCopy(" hist");
  TH1* projEnergy = fCellAmplitude->ProjectionX(Form("%s_Proj",fCellAmplitude->GetName()),fStartCell,fNoOfCells);
  projEnergy->DrawCopy("same hist");
  TLegend *leg = new TLegend(0.50,0.75,0.7,0.87);
  leg->AddEntry(projEnergy,"all cells","l");
  leg->AddEntry(projEnergyMask,"good cells","l");
  leg->SetTextSize(0.05);
  leg->SetBorderSize(0);
  leg->SetFillColorAlpha(10, 0);
  leg->Draw("same");
  TLegend *legBig = (TLegend*)leg->Clone("legBig");
  legBig->SetTextSize(0.08);
  legBig->SetX1NDC(0.2);

  c1_proj->cd(2)->SetLogy();
  TH1* projTimeMask = cellTime_masked->ProjectionX(Form("%s_Proj",cellTime_masked->GetName()),fStartCell,fNoOfCells);
  projTimeMask->SetXTitle("Cell Time [ns]");
  projTimeMask->GetYaxis()->SetTitleOffset(1.6);
  projTimeMask->GetYaxis()->SetRangeUser(1,projTimeMask->GetMaximum()*20);
  projTimeMask->SetLineColor(kGreen+1);
  projTimeMask->DrawCopy("hist");
  TH1* projTime = fCellTime->ProjectionX(Form("%s_Proj",fCellTime->GetName()),fStartCell,fNoOfCells);
  projTime->DrawCopy("same hist");
  leg->Draw("same");
  c1_proj->Update();

  TCanvas *c1_projSM = new TCanvas("CellPropPProjSM","III summary of cell Energy per SM",1200,900);
  c1_projSM->Divide(5,4,0.001,0.001);
  TH1* projEnergyMaskSM[20];
  TH1* projEnergySM[20];
  for(Int_t iSM=0;iSM<20;iSM++)
  {
    c1_projSM->cd(iSM+1)->SetLogy();
    gPad->SetTopMargin(0.03);
    gPad->SetBottomMargin(0.11);
    projEnergyMaskSM[iSM] = cellAmp_masked->ProjectionX(Form("%sMask_ProjSM%i",cellAmp_masked->GetName(),iSM),fStartCellSM[iSM]+1,fStartCellSM[iSM+1]); //histogram bin 1 has cell ID0
    projEnergyMaskSM[iSM]->SetTitle("");
    projEnergyMaskSM[iSM]->SetXTitle(Form("Cell Energy [GeV], SM%i",iSM));
    projEnergyMaskSM[iSM]->GetYaxis()->SetTitleOffset(1.6);
    projEnergyMaskSM[iSM]->GetYaxis()->SetLabelSize(0.06);
    projEnergyMaskSM[iSM]->GetXaxis()->SetLabelSize(0.06);
    projEnergyMaskSM[iSM]->GetXaxis()->SetRangeUser(0,20);
    projEnergyMaskSM[iSM]->GetXaxis()->SetTitleSize(0.06);
    projEnergyMaskSM[iSM]->SetLineColor(kGreen+1);
    projEnergyMaskSM[iSM]->DrawCopy(" hist");

    projEnergySM[iSM] = fCellAmplitude->ProjectionX(Form("%s_ProjSM%i",fCellAmplitude->GetName(),iSM),fStartCellSM[iSM],fStartCellSM[iSM+1]-1);
    projEnergySM[iSM]->DrawCopy("same hist");
    if(iSM==0)legBig->Draw("same");
    //textSM->Draw();
    textSM->SetTitle(Form("Includes cell IDs %d-%d",fStartCellSM[iSM],fStartCellSM[iSM+1]-1));
    textSM->DrawLatex(0.2,0.9,Form("Includes cell IDs %d-%d",fStartCellSM[iSM],fStartCellSM[iSM+1]-1));
  }

  TCanvas *c1_projRSM = new TCanvas("CellPropPProjRSM","III summary of cell Energy Ratio per SM",1200,900);
  c1_projRSM->Divide(5,4,0.001,0.001);
  for(Int_t iSM=0;iSM<20;iSM++)
  {
    c1_projRSM->cd(iSM+1)->SetLogy();
    gPad->SetTopMargin(0.03);
    gPad->SetBottomMargin(0.11);
    //projEnergyMaskSM[iSM]->GetXaxis()->SetRangeUser(0,10);
    projEnergyMaskSM[iSM]->SetLineColor(kGray+1);
    projEnergyMaskSM[iSM]->Divide(hRefDistr);
    projEnergyMaskSM[iSM]->DrawCopy("hist");
  }

  TCanvas *c1_projTimeSM = new TCanvas("CellPropPProjTimeSM","III summary of cell Time per SM",1200,900);
  c1_projTimeSM->Divide(5,4,0.001,0.001);
  TH1* projTimeMaskSM[20];
  TH1* projTimeSM[20];
  for(Int_t iSM=0;iSM<20;iSM++)
  {
    c1_projTimeSM->cd(iSM+1)->SetLogy();
    gPad->SetTopMargin(0.03);
    gPad->SetBottomMargin(0.11);
    projTimeMaskSM[iSM] = cellTime_masked->ProjectionX(Form("%sMask_ProjSMTime%i",cellAmp_masked->GetName(),iSM),fStartCellSM[iSM]+1,fStartCellSM[iSM+1]);
    projTimeMaskSM[iSM]->SetTitle("");
    projTimeMaskSM[iSM]->SetXTitle(Form("Cell Time [ns], SM%i",iSM));
    projTimeMaskSM[iSM]->GetYaxis()->SetTitleOffset(1.6);
    projTimeMaskSM[iSM]->GetYaxis()->SetLabelSize(0.06);
    projTimeMaskSM[iSM]->GetXaxis()->SetLabelSize(0.06);
    //projTimeMaskSM[iSM]->GetXaxis()->SetRangeUser(0,20);
    projTimeMaskSM[iSM]->GetXaxis()->SetTitleSize(0.06);
    projTimeMaskSM[iSM]->SetLineColor(kGreen+1);
    projTimeMaskSM[iSM]->DrawCopy(" hist");

    if(iSM==0)legBig->Draw("same");
    projTimeSM[iSM] = fCellTime->ProjectionX(Form("%s_ProjSMTime%i",fCellAmplitude->GetName(),iSM),fStartCellSM[iSM],fStartCellSM[iSM+1]-1);
    projTimeSM[iSM]->DrawCopy("same hist");
  }

  //..save to a PDF
  c1           ->Print(Form("%s(",cellProp.Data()));
  c1_ratio     ->Print(Form("%s",cellProp.Data()));
  c1_proj      ->Print(Form("%s",cellProp.Data()));
  c1_projSM    ->Print(Form("%s",cellProp.Data()));
  c1_projRSM   ->Print(Form("%s",cellProp.Data()));
  c1_projTimeSM->Print(Form("%s)",cellProp.Data()));

  //..Scale the histogtams by the number of events
  //..so that they are more comparable for a run-by-run
  //..analysis
  Double_t totalevents = fProcessedEvents->Integral();
  fCellAmplitude ->Scale(1.0/totalevents);
  cellAmp_masked ->Scale(1.0/totalevents);
  fCellTime      ->Scale(1.0/totalevents);

  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //..Write the final results of dead and bad cells in a file and on screen
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  ofstream file(cellSummaryFile, ios::out | ios::trunc);
  ofstream fileBad(OADBFile_bad, ios::out | ios::trunc);
  ofstream fileDead(OADBFile_dead, ios::out | ios::trunc);
  ofstream fileWarm(OADBFile_warm, ios::out | ios::trunc);
  if(file)
  {
    file<<"Dead cells : "<<endl;
    cout<<"    o Dead cells : "<<endl;
    for(cellID=fStartCell; cellID<fNoOfCells; cellID++)
    {
      if(cellID==0)
      {
        file<<"In EMCal: "<<endl;
      }
      if(cellID==fCellStartDCal)
      {
        file<<"\n"<<endl;
        file<<"In DCal: "<<endl;
      }
      if(fFlag[cellID]==1)
      {
        file<<cellID<<", ";
        if(cellID<fCellStartDCal)nDeadEMCalCells++;
        else                     nDeadDCalCells++;
      }
      if(fFlag[cellID]==1)fileDead<<cellID<<endl;
      if(fFlag[cellID]>1)fileBad<<cellID<<endl;
    }
    file<<"\n"<<endl;
    perDeadEMCal=100*nDeadEMCalCells/(1.0*fCellStartDCal);
    perDeadDCal=100*nDeadDCalCells/(1.0*fNoOfCells-fCellStartDCal);
    file<<"EMCal ("<<nDeadEMCalCells<<" ="<<perDeadEMCal<<"%), DCal ("<<nDeadDCalCells<<" ="<<perDeadDCal<<"%)"<<endl;
    cout<<"    o EMCal ("<<nDeadEMCalCells<<" ="<<perDeadEMCal<<"%), DCal ("<<nDeadDCalCells<<" ="<<perDeadDCal<<"%)"<<endl;

    file<<"Bad cells: "<<endl;
    cout<<"    o Bad cells: "<<endl;
    for(cellID=fStartCell;cellID<fNoOfCells;cellID++)
    {
      if(cellID==0)
      {
        file<<"In EMCal: "<<endl;
      }
      if(cellID==fCellStartDCal)
      {
        file<<"\n"<<endl;
        file<<"In DCal: "<<endl;
      }
      if(fFlag[cellID]>1)
      {
        file<<cellID<<", ";
        if(cellID<fCellStartDCal)nEMCalCells++;
        else                     nDCalCells++;
      }
    }
    file<<"\n"<<endl;
    perBadEMCal=100*nEMCalCells/(1.0*fCellStartDCal);
    perBadDCal =100*nDCalCells/(1.0*fNoOfCells-fCellStartDCal);
    file<<"EMCal ("<<nEMCalCells<<" ="<<perBadEMCal<<"%), DCal ("<<nDCalCells<<" ="<<perBadDCal<<"%)"<<endl;
    cout<<"    o EMCal ("<<nEMCalCells<<" ="<<perBadEMCal<<"%), DCal ("<<nDCalCells<<" ="<<perBadDCal<<"%)"<<endl;
  }
  file.close();
  cout<<"    o Total: "<<endl;
  cout<<"    o Bad+Dead cells: "<<nDeadEMCalCells+nEMCalCells+nDeadDCalCells+nDCalCells<<", this is "<<(nDeadEMCalCells+nEMCalCells+nDeadDCalCells+nDCalCells)*100/(1.0*fNoOfCells)<<"% of the whole detector"<<endl;

  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //..Determine the number of warm cells and save the flagged cells to .pdf files
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  if(fPrint==1)cout<<"    o Save the bad channel spectra to a .pdf file"<<endl;
  SaveBadCellsToPDF(1,badPdfName) ;
  SaveBadCellsToPDF(10,ratioOfBad) ; //..Special case
  if(fTestRoutine==1)SaveBadCellsToPDF(2,goodCells) ;   //..Special case all good cells to check, should all have a flag naming them *Candidate*
  if(fTestRoutine==1)SaveBadCellsToPDF(20,goodCellsRatio) ;   //..Special case all good cells to check, should all have a flag naming them *Candidate*

  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //..Fill the histograms with the flag information
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  for (Int_t cell = fStartCell; cell < fNoOfCells; cell++)
  {
    fhCellFlag->SetBinContent(cell+1,fFlag[cell]);
    fhCellWarm->SetBinContent(cell+1,fWarmCell[cell]);
    if(fWarmCell[cell]==1)fileWarm<<cell<<endl;
  }
  TCanvas *c2 = new TCanvas("CellFlag","summary of cell flags",1200,800);
  c2->ToggleEventStatus();
  c2->Divide(1,2);
  c2->cd(1);
  fhCellFlag->SetTitle("cell flag");
  fhCellFlag->SetXTitle("Abs. Cell Id");
  fhCellFlag->SetYTitle("flag by which cell was excluded");
  fhCellFlag->DrawCopy("hist");
  c2->cd(2);
  fhCellWarm->SetTitle("Warm cells");
  fhCellWarm->SetXTitle("Abs. Cell Id");
  fhCellWarm->SetYTitle("warm=1");
  fhCellWarm->DrawCopy("hist");
  c2->Update();

  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //..Plot the 2D distribution of cells by flag
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  PlotFlaggedCells2D(0);    //..all good cells
  PlotFlaggedCells2D(1);    //..all dead cells
  PlotFlaggedCells2D(2,fCriterionCounter);  //..all bad cells
  PlotFlaggedCells2D(0,0);  //..Special case - Warm cells

  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //..Add different histograms/canvases to the output root file
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  TString name1,name2,name3,name4,name5,name6;
  name1   = Form("%s/%s/CellPropertiesRatio.gif", fWorkdir.Data(),fAnalysisOutput.Data());
  c1_ratio->SaveAs(name1);
  name2   = Form("%s/%s/CellProperties.gif", fWorkdir.Data(),fAnalysisOutput.Data());
  c1->SaveAs(name2);
  name3   = Form("%s/%s/CellPropertiesProj.gif", fWorkdir.Data(),fAnalysisOutput.Data());
  c1_proj->SaveAs(name3);
  name4   = Form("%s/%s/CellEnergySM.gif", fWorkdir.Data(),fAnalysisOutput.Data());
  c1_projSM->SaveAs(name4);
  name5   = Form("%s/%s/CellEnergySMratio.gif", fWorkdir.Data(),fAnalysisOutput.Data());
  c1_projRSM->SaveAs(name5);
  name6   = Form("%s/%s/CellTime.gif", fWorkdir.Data(),fAnalysisOutput.Data());
  c1_projTimeSM->SaveAs(name6);

  fRootFile->WriteObject(c1,c1->GetName());
  fRootFile->WriteObject(c1_ratio,c1_ratio->GetName());
  fRootFile->WriteObject(c1_proj,c1_proj->GetName());
  fRootFile->WriteObject(c1_projSM,c1_projSM->GetName());
  fRootFile->WriteObject(c1_projRSM,c1_projRSM->GetName());
  fRootFile->WriteObject(c1_projTimeSM,c1_projTimeSM->GetName());
  fRootFile->WriteObject(c2,c2->GetName());
  fRootFile->WriteObject(fCellAmplitude,fCellAmplitude->GetName());
  fRootFile->WriteObject(cellAmp_masked,cellAmp_masked->GetName());
  fRootFile->WriteObject(ratio2DAmp,ratio2DAmp->GetName());
  fRootFile->WriteObject(fCellTime,fCellTime->GetName());
  fRootFile->WriteObject(fProcessedEvents,fProcessedEvents->GetName());
  fRootFile->WriteObject(fhCellFlag,fhCellFlag->GetName());
  fRootFile->WriteObject(fhCellWarm,fhCellWarm->GetName());
  fRootFile->WriteObject(projEnergyMask,projEnergyMask->GetName());
  fRootFile->WriteObject(projEnergy,projEnergy->GetName());
  //..Save all amplitudes to the root file
  SaveHistoToFile();

  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //..Save also the identified warm channels into a text file.
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  Int_t nWEMCalCells =0;
  Int_t nWDCalCells  =0;
  file.open(cellSummaryFile, ios::out | ios::app);
  if(file)
  {
    file<<"Warm cells : "<<endl;
    if(fPrint==1)cout<<"    o Warm cells : "<<endl;
    for(cellID=fStartCell; cellID<fNoOfCells; cellID++)
    {
      if(cellID==0)
      {
        file<<"In EMCal: "<<endl;
      }
      if(cellID==fCellStartDCal)
      {
        file<<"\n"<<endl;
        file<<"In DCal: "<<endl;
      }
      if(fWarmCell[cellID]==1)
      {
        file<<cellID<<", ";
        if(cellID<fCellStartDCal)nWEMCalCells++;
        else                     nWDCalCells++;
      }
    }
    file<<"\n"<<endl;
    perWarmEMCal= 100*nWEMCalCells/(1.0*fCellStartDCal);
    perWarmDCal = 100*nWDCalCells/(1.0*fNoOfCells-fCellStartDCal);
    file<<"EMCal ("<<nWEMCalCells<<" ="<<perWarmEMCal<<"%), DCal ("<<nWDCalCells<<" ="<<perWarmDCal<<"%)"<<endl;
    if(fPrint==1)cout<<"    o EMCal ("<<nWEMCalCells<<" ="<<perWarmEMCal<<"%), DCal ("<<nWDCalCells<<" ="<<perWarmDCal<<"%)"<<endl;
  }
  file.close();
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //..Save the results in a tWiki format for the webpage (https://twiki.cern.ch/twiki/bin/view/ALICE/EMCalQABadChannels2)
  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  ofstream file2(aliceTwikiTable, ios::out | ios::app);
  if(file2)
  {
    file2<<"1=energy/hit, 2= hit/event"<<endl;
    file2<<"\n"<<endl;
    file2<<"| *Detector* |    *No of cells*    |  *percentage*  |"<<endl;
    file2<<"| Dead EMCal |    "<<nDeadEMCalCells<<"    |  "<<perDeadEMCal<<"%  |"<<endl;
    file2<<"| Bad EMCal |    "<<nEMCalCells<<"    |  "<<perBadEMCal<<"%  |"<<endl;
    file2<<"|  - Warm EMCal |    "<<nWEMCalCells<<"    |  "<<perWarmEMCal<<"%  |"<<endl;
    file2<<"| Dead DCal |    "<<nDeadDCalCells<<"    |  "<<perDeadDCal<<"%  |"<<endl;
    file2<<"| Bad DCal |    "<<nDCalCells<<"    |  "<<perBadDCal<<"%  |"<<endl;
    file2<<"|  - Warm DCal |    "<<nWDCalCells<<"    |  "<<perWarmDCal<<"%  |"<<endl;
    file2<<"| Summ D+B |    "<<nDeadEMCalCells+nEMCalCells+nDeadDCalCells+nDCalCells<<"    |  "<<(nDeadEMCalCells+nEMCalCells+nDeadDCalCells+nDCalCells)*100/(1.0*fNoOfCells)<<"%  |"<<endl;
    file2<<"\n"<<endl;
  }
  file2.close();

}

//________________________________________________________________________
void BadChannelAna::SaveBadCellsToPDF(Int_t version, TString pdfName)
{
  gROOT->SetStyle("Plain");
  gStyle->SetOptStat(0);
  gStyle->SetFillColor(kWhite);
  gStyle->SetTitleFillColor(kWhite);
  gStyle->SetPalette(1);

  char title[100];
  char name[100];

  TH1D *hRefDistr = BuildMeanFromGood();
  fRootFile->WriteObject(hRefDistr,hRefDistr->GetName());
  Int_t firstCanvas=0;
  Bool_t candidate;
  TLatex* text = new TLatex(0.2,0.8,"*Candidate*");
  text->SetTextSize(0.07);
  text->SetTextColor(kOrange-3);
  text->SetNDC();

  TLatex* text2 = new TLatex(0.2,0.8,"*Not a Candidate*");
  text2->SetTextSize(0.08);
  text2->SetTextColor(8);
  text2->SetNDC();

  TLatex* textA = new TLatex(0.65,0.62,"*test*");
  textA->SetTextSize(0.04);
  textA->SetTextColor(1);
  textA->SetNDC();

  //..collect cells in an internal vector.
  //..when the vector is of size=9 or at the end of being filled
  //..plot the channels into a canvas
  std::vector<Int_t> channelVector;
  channelVector.clear();
  cout<<"    o Start printing into .pdf for version: "<<version<<endl;
  for(Int_t cell=fStartCell;cell<fNoOfCells;cell++)
  {
    if(fFlag[cell]==1 && version==0)channelVector.push_back(cell);
    if(fFlag[cell]>1  && version==1)channelVector.push_back(cell);
    if(fFlag[cell]==0 && version==2)channelVector.push_back(cell);
    if(fFlag[cell]>1  && version==10)channelVector.push_back(cell);
    if(fFlag[cell]==0 && version==20)channelVector.push_back(cell);

    if(cell%2000==0)cout<<"...cell No."<<cell<<endl;
    //..when 9 bad cells are collected or we are at the end of the list, fill the canvas
    if(channelVector.size()==9 || cell == fNoOfCells-1)
    {
      cout<<"."<<flush;

      TString internal_pdfName=pdfName;
      TCanvas *c1 = new TCanvas("badcells","badcells",1000,750);
      if(channelVector.size() > 6)        c1->Divide(3,3);
      else if (channelVector.size() > 3)  c1->Divide(3,2);
      else                                c1->Divide(3,1);

      TLegend *leg = new TLegend(0.7, 0.7, 0.9, 0.9);
      for(Int_t i=0; i< (Int_t)channelVector.size() ; i++)
      {
        sprintf(name, "Cell %d",channelVector.at(i)) ;
        TH1 *hCell = fCellAmplitude->ProjectionX(name,channelVector.at(i)+1,channelVector.at(i)+1);
        sprintf(title,"Cell No: %d    Entries: %d",channelVector.at(i), (Int_t)hCell->GetEntries()) ;

        c1->cd(i%9 + 1);
        c1->cd(i%9 + 1)->SetLogy();
        if(i==0)
        {
          leg->AddEntry(hRefDistr,"mean of good","l");
          leg->AddEntry(hCell,"current","l");
        }
        //..Check the distribution whether it looks like a *Candidate* for a miscalibrated warm cell
        candidate = CheckDistribution(hCell,hRefDistr);
                if(candidate==1)fWarmCell[channelVector.at(i)]=candidate;
        if(version>2)//..These are ratio plots of energy distr. of cell and mean of all good cells
        {
          hCell->Divide(hRefDistr);
        }
        //.. save histograms to file
        if(version==1) fOutputListBad->Add(hCell);
        if(version==10)fOutputListBadRatio->Add(hCell);
        if(version==2) fOutputListGood->Add(hCell);
        if(version==20)fOutputListGoodRatio->Add(hCell);

        hCell->SetLineColor(kBlue+1);
        hCell->GetXaxis()->SetTitle("E (GeV)");
        hCell->GetYaxis()->SetTitle("N Entries");
        hCell->GetXaxis()->SetRangeUser(0.,10.);
        hCell->SetLineWidth(1) ;
        hCell->SetTitle(title);
        hRefDistr->SetLineColor(kGray+2);
        hRefDistr->SetLineWidth(1);

        hCell->Draw("hist");

        if(version==1 || version==2)hRefDistr->Draw("same") ;

        //..Mark the histogram that could be miscalibrated and labelled as warm
        if(candidate==1 && (version==1 || version==10))
        {
          gPad->SetFrameFillColor(kYellow-10);
          text->Draw();
        }
        if(version==1)
        {
          textA->SetTitle(Form("Excluded by No. %d",fFlag[channelVector.at(i)]));
          textA->DrawLatex(0.65,0.62,Form("Excluded by No. %d",fFlag[channelVector.at(i)]));
        }
        if(candidate==0 && (version==2 || version==20))
        {
          gPad->SetFrameFillColor(kYellow-10);
          text2->Draw(); //..Draw a marker in the histogram that was falsley missed as a good candidate
          leg->Draw();
        }
        if(version<2)leg->Draw();
      }

      if(channelVector.size()<9 || cell == fNoOfCells-1)
      {
        internal_pdfName +=")";
        c1->Print(internal_pdfName.Data());
      }
      else if(firstCanvas==0)
      {
        internal_pdfName +="(";
        c1->Print(internal_pdfName.Data());
        firstCanvas=1;
      }
      else
      {
        c1->Print(internal_pdfName.Data());
      }
      delete c1;
      delete leg;
      channelVector.clear();
    }
  }
  cout<<endl;
  delete hRefDistr;
  //..Add the subdirectories to the file
  if(version==1) fRootFile->WriteObject(fOutputListBad,fOutputListBad->GetName());
  if(version==10)fRootFile->WriteObject(fOutputListBadRatio,fOutputListBadRatio->GetName());
  if(version==2) fRootFile->WriteObject(fOutputListGoodRatio,fOutputListGoodRatio->GetName());
  if(version==20)fRootFile->WriteObject(fOutputListGood,fOutputListGood->GetName());

  if(fPrint==1)cout<<endl;
}
//_________________________________________________________________________
TH1D* BadChannelAna::BuildMeanFromGood(Int_t warmIn)
{
  TH1D* hGoodAmp;
  TH1D* hgoodMean = (TH1D*)fCellAmplitude->ProjectionX("hgoodMean");
  hgoodMean->Reset();
  Int_t NrGood=0;

  for (Int_t cell = fStartCell; cell < fNoOfCells; cell++)
  {
    if(warmIn==0 && fFlag[cell]!=0 )continue;
    if(warmIn==1 && fFlag[cell]!=0 && fWarmCell[cell]==0)continue;
    if(warmIn==2 && fWarmCell[cell]==0)continue;
    NrGood++;

    hGoodAmp = (TH1D*)fCellAmplitude->ProjectionX("hGoodCells",cell+1,cell+1);
    hgoodMean->Add(hGoodAmp);
  }
  hgoodMean->Scale(1.0/NrGood);

  return hgoodMean;
}
//_________________________________________________________________________
Bool_t BadChannelAna::CheckDistribution(TH1* histogram, TH1* reference)
{
  TString Name = Form("%s_ratio",histogram->GetName());
  TH1* ratio=(TH1*)histogram->Clone(Name);
  ratio->Divide(reference);

  Double_t percentageOfLast=0.6;
  Double_t higherThanMean=5;
  Double_t highestRatio=1000;
  Double_t maxMean=10;
  Double_t minMean=0.1;
  Double_t cliffSize=2;       //height before cliff shouldn't be double as high than after cliff

  //..By default each cell is a candidate for recalibration
  Bool_t candidate=1;
  //..Find bin where reference has value 1, and the corresponding x-value
  Double_t totalevents        = fProcessedEvents->Integral();
  Int_t binHeightOne          = reference->FindLastBinAbove(1.0/totalevents);//..look at the spectrum until there is 1hit/event GeV
  Double_t binCentreHeightOne = reference->GetBinCenter(binHeightOne);
  Double_t thirdBinCentre     = reference->GetBinCenter(3);

  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //..Check the histogram
  //..Different checks to see whether the
  //..cell is really bad. Set candidate to 0.

  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //..check end of spectrum, should be larger than "percentageOfLast"% of the end of the mean histogram
  if(ratio->FindLastBinAbove(0)<ratio->FindBin(binCentreHeightOne*percentageOfLast))
  {
    candidate=0;
    //cout<<"1"<<endl;
  }

  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //..Check maximum of ratio. Cell should not have "highestRatio" times more entries than reference in any bin
  //ELI - TO DO: check that crieteria carfully - seems to work but not shure about it
  ratio->GetXaxis()->SetRangeUser(thirdBinCentre,10);//..zoom in to find the  maximum between "not first 2 bins" - 10 GeV
  if(ratio->GetMaximum()>highestRatio)//
  {
    candidate=0;
    //cout<<"2"<<endl;
  }

  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //..check whether the ratio is much larger than 1
  //..calculate the mean in the relevant energy range
  Double_t mean=0;
  Int_t nullEntries=0;
  for(Int_t i=2;i<binHeightOne;i++)
  {
    if(ratio->GetBinContent(i)!=0)mean+=ratio->GetBinContent(i);
    else nullEntries++;
  }
  mean*=1.0/(binHeightOne-1-nullEntries);//..divide by number of bins (excluding bins without entries)
  if(mean>maxMean || mean<minMean)
  {
    candidate=0;
    //cout<<"3"<<endl;
  }

  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //..check whether there are large spikes in the histogram
  //..compare bin values to mean of the ratio. If there is a bin value with
  //..content "higherThanMean" times lareger than mean it's losing it candidate status
  mean=0;
  //..Find the maximum in the mean range (0-binHeightOne)
  ratio->GetXaxis()->SetRangeUser(0,binCentreHeightOne);
  Double_t localMaxBin=ratio->GetMaximumBin();

  for(Int_t i=2;i<binHeightOne;i++)
  {
    //..Exclude 0 bins and exclude bins near the maximum
    if(ratio->GetBinContent(i)<=0)        continue;
    if(i>localMaxBin-3 && i<localMaxBin+3)continue;
    mean+=ratio->GetBinContent(i);
  }
  mean*=1.0/(binHeightOne-1);//..divide by number of bins
  ratio->GetXaxis()->SetRangeUser(thirdBinCentre,binCentreHeightOne);//..zoom in to find the  maximum between 0-BinOne
  //cout<<"mean: "<<mean<<", max: "<<ratio->GetMaximum()<<endl;
  if(ratio->GetMaximum()>mean*higherThanMean)
  {
    candidate=0;
    //cout<<"4"<<endl;
  }

  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
    //..Check for a cliff at 4GeV, happens in some cases
  Double_t beforeCliff=0;
  Double_t afterCliff=0;
  Int_t binsBefore=0;
  Int_t binsAfter=0;
  Int_t cliffBin = ratio->FindBin(4);
  for(Int_t i=cliffBin-10;i<cliffBin+11;i++)
  {
    //..Exclude 0 bins
    if(ratio->GetBinContent(i)<=0)continue;
    if(i<=cliffBin) binsBefore++;
    if(i>cliffBin)  binsAfter++;
    if(i<=cliffBin) beforeCliff+=ratio->GetBinContent(i);
    if(i>cliffBin)   afterCliff+=ratio->GetBinContent(i);
    beforeCliff*=1.0/binsBefore;
    afterCliff*=1.0/binsAfter;
  }
  if((beforeCliff-afterCliff)>cliffSize*afterCliff)
  {
    if(beforeCliff!=0 && afterCliff!=0)candidate=0;
    if(beforeCliff!=0 && afterCliff!=0)cout<<"5"<<endl;
  }

  //. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
  //..Employ peak finder
/*  if(candidate==1)
  {
    TSpectrum *spec = new TSpectrum(2,1);  //..Nr peaks, resol. 1=3sigma distance
    Int_t nfound = spec->Search(ratio,4.3,"nobackground new",0.70);
    //GetNPeaks();
    //cout<<"found N peaks: "<<nfound<<endl;
  }
*/
  return candidate;
}

//_________________________________________________________________________
Bool_t BadChannelAna::IsCoveredByTRD(Int_t row, Int_t collumn)
{
  //..TRD support structure
  //..(determined by eye, could be improved, but is already very acurate):
  //..collumn 4,5,6,7,8   33,34,35,36     58,59,60   85,86,87,88,89
  //..row     1    (21),22,23,24   45,46,47,(48)     69,70,71,(72)  (92),93,94,95   117,118,(119)  127   149,150,151   (173),174,175,(176)    198,199,200
  Bool_t coveredByTRDSupportStruc=0;

  if((collumn>3 && collumn<9) || (collumn>32 && collumn<37) || (collumn>57 && collumn<61) || (collumn>84 && collumn<90) ||
     (row==1) ||(row>20 && row<25) || (row>44 && row<49) || (row>68 && row<73) || (row>91 && row<96) ||
     (row>116 && row<120)|| row==127 || (row>148 && row<152) || (row>172 && row<177) || (row>197 && row<201)
  )
  {
    coveredByTRDSupportStruc=1;
  }
  return coveredByTRDSupportStruc;
}
//_________________________________________________________________________
void BadChannelAna::PlotFlaggedCells2D(Int_t flagBegin,Int_t flagEnd)
{
  //..build two dimensional histogram with values row vs. column
  TString histoName;
  histoName = Form("2DChannelMap_Flag%d_V%i",flagBegin,fTrial);
  if(flagBegin==0 && flagEnd==0)histoName = Form("2DChannelMap_Flag100_V%i",fTrial);

  TH2F *plot2D = new TH2F(histoName,histoName,fNMaxColsAbs+1,-0.5,fNMaxColsAbs+0.5, fNMaxRowsAbs+1,-0.5,fNMaxRowsAbs+0.5);
  plot2D->GetXaxis()->SetTitle("cell column (#eta direction)");
  plot2D->GetYaxis()->SetTitle("cell row (#phi direction)");

  Int_t cellColumn=0,cellRow=0;
  Int_t cellColumnAbs=0,cellRowAbs=0;
  Int_t trash;

  for (Int_t cell = fStartCell; cell < fNoOfCells; cell++)
  {
    //..Do that only for cell ids also accepted by the code
    if(!fCaloUtils->GetEMCALGeometry()->CheckAbsCellId(cell))continue;

    //..Get Row and Collumn for cell ID c
    fCaloUtils->GetModuleNumberCellIndexesAbsCaloMap(cell,0,cellColumn,cellRow,trash,cellColumnAbs,cellRowAbs);
    if(cellColumnAbs> fNMaxColsAbs || cellRowAbs>fNMaxRowsAbs)
    {
      cout<<"Problem! wrong calculated number of max col and max rows"<<endl;
      cout<<"current col: "<<cellColumnAbs<<", max col"<<fNMaxColsAbs<<endl;
      cout<<"current row: "<<cellRowAbs<<", max row"<<fNMaxRowsAbs<<endl;
    }
    if(flagEnd==-1  && fFlag[cell]==flagBegin)                        plot2D->SetBinContent(cellColumnAbs,cellRowAbs,1);
    if(flagEnd!=0   && flagEnd!=-1 && fFlag[cell]>=flagBegin && fFlag[cell]<=flagEnd)plot2D->SetBinContent(cellColumnAbs,cellRowAbs,1);
    if(flagBegin==0 && flagEnd==0 && fWarmCell[cell]==1)             plot2D->SetBinContent(cellColumnAbs,cellRowAbs,1); //warm cells


  }
  TCanvas *c1 = new TCanvas(histoName,histoName,500,500);
  c1->ToggleEventStatus();
  c1->cd();
  //lowerPadRight->SetLeftMargin(0.09);
  //lowerPadRight->SetRightMargin(0.06);
  plot2D->Draw("colz");

  TLatex* text = 0x0;
  if(flagBegin==0 && flagEnd==-1) text = new TLatex(0.2,0.8,"Good Cells");
  if(flagBegin==1) text = new TLatex(0.2,0.8,"Dead Cells");
  if(flagBegin>1)  text = new TLatex(0.2,0.8,"Bad Cells");
  if(flagBegin==0 && flagEnd==0) text = new TLatex(0.2,0.8,"Warm Cells");
  text->SetTextSize(0.06);
  text->SetNDC();
  text->SetTextColor(1);
  text->Draw();

  c1->Update();
  TString name =Form("%s/%s/%s_%s.gif", fWorkdir.Data(),fAnalysisOutput.Data(),fPeriod.Data() , histoName.Data());
  c1->SaveAs(name);
  fRootFile->WriteObject(plot2D,plot2D->GetName());

}
//_________________________________________________________________________
void BadChannelAna::SaveHistoToFile()
{
  char name[100];
  for(Int_t cell=fStartCell;cell<fNoOfCells;cell++)
  {
    sprintf(name, "Cell %d",cell) ;
    TH1 *hCell = fCellAmplitude->ProjectionX(name,cell+1,cell+1);
    if(fFlag[cell]==0)fOutputListGood->Add(hCell);
  }
  fRootFile->WriteObject(fOutputListGood,fOutputListGood->GetName());
}