[u/mrichter/AliRoot.git] / TPC / AliTPCCalibKr.cxx

/**************************************************************************
 * Copyright(c) 1998-1999, ALICE Experiment at CERN, All rights reserved. *
 *                                                                        *
 * Author: The ALICE Off-line Project.                                    *
 * Contributors are mentioned in the code where appropriate.              *
 *                                                                        *
 * Permission to use, copy, modify and distribute this software and its   *
 * documentation strictly for non-commercial purposes is hereby granted   *
 * without fee, provided that the above copyright notice appears in all   *
 * copies and that both the copyright notice and this permission notice   *
 * appear in the supporting documentation. The authors make no claims     *
 * about the suitability of this software for any purpose. It is          *
 * provided "as is" without express or implied warranty.                  *
 **************************************************************************/


//Root includes
#include <TH1F.h>
#include <TH1D.h>
#include <TH2F.h>
#include <TH3F.h>
#include <TString.h>
#include <TMath.h>
#include <TF1.h>
#include <TRandom.h>
#include <TDirectory.h>
#include <TFile.h>
#include <TAxis.h>
//AliRoot includes
#include "AliRawReader.h"
#include "AliRawReaderRoot.h"
#include "AliRawReaderDate.h"
#include "AliTPCRawStream.h"
#include "AliTPCCalROC.h"
#include "AliTPCCalPad.h"
#include "AliTPCROC.h"
#include "AliMathBase.h"
#include "TTreeStream.h"
#include "AliTPCRawStreamFast.h"

//date
#include "event.h"

//header file
#include "AliTPCCalibKr.h"

//----------------------------------------------------------------------------
// The AliTPCCalibKr class description (TPC Kr calibration).
//
//
// The AliTPCCalibKr keeps the array of TH3F histograms (TPC_max_padraw,TPC_max_pad,TPC_ADC_cluster),
// its data memebers and is filled by AliTPCCalibKrTask under conditions (Accept()).   
// 
// The ouput TH3F histograms are later used to determine the calibration parameters of TPC chambers.
// These calculations are done by using AliTPCCalibKr::Analyse() function. The ouput calibration 
// parameters (details in AliTPCCalibKr::Analyse()) are stored in the calibKr.root file for each TPC pad.
// In addition the debugCalibKr.root file with debug information is created.
//

/*
 
// Usage example:
//

// 1. Analyse output histograms:
TFile f("outHistFile.root");
AliTPCCalibKr *obj = (AliTPCCalibKr*) cOutput.FindObject("AliTPCCalibKr")
obj->Analyse();

// 2. See calibration parameters e.g.:
TFile f("calibKr.root");
spectrMean->GetCalROC(70)->GetValue(40,40);
fitMean->GetCalROC(70)->GetValue(40,40);

// 3. See debug information e.g.:
TFile f("debugCalibKr.root");
.ls;

// -- Print calibKr TTree content 
calibKr->Print();

// -- Draw calibKr TTree variables
calibKr.Draw("fitMean");

*/


//
// Author: Jacek Otwinowski (J.Otwinowski@gsi.de) and Stafan Geartner (S.Gaertner@gsi.de)
//-----------------------------------------------------------------------------

ClassImp(AliTPCCalibKr)

AliTPCCalibKr::AliTPCCalibKr() : 
  TObject(),
  fASide(kTRUE),
  fCSide(kTRUE),
  fHistoKrArray(72),
  fADCOverClustSizeMin(0.0),
  fADCOverClustSizeMax(1.0e9),
  fMaxADCOverClustADCMin(0.0),
  fMaxADCOverClustADCMax(1.0e9),
  fTimeMin(0.0),
  fTimeMax(1.0e9),
  fClustSizeMin(0.0),
  fClustSizeMax(1.0e9)
{
  //
  // default constructor
  //

  // TObjArray with histograms
  fHistoKrArray.SetOwner(kTRUE); // is owner of histograms
  fHistoKrArray.Clear();
 
  // init cuts
  SetADCOverClustSizeRange(7,200);
  SetMaxADCOverClustADCRange(0.01,0.4);
  SetTimeRange(200,600);
  SetClustSizeRange(6,200);
 
  // init histograms
  Init();
}

//_____________________________________________________________________
AliTPCCalibKr::AliTPCCalibKr(const AliTPCCalibKr& pad) : 
  TObject(pad),
  
  fASide(pad.fASide),
  fCSide(pad.fCSide),
  fHistoKrArray(72),
  fADCOverClustSizeMin(pad.fADCOverClustSizeMin),
  fADCOverClustSizeMax(pad.fADCOverClustSizeMax),
  fMaxADCOverClustADCMin(pad.fMaxADCOverClustADCMin),
  fMaxADCOverClustADCMax(pad.fMaxADCOverClustADCMax),
  fTimeMin(pad.fTimeMin),
  fTimeMax(pad.fTimeMax),
  fClustSizeMin(pad.fClustSizeMin),
  fClustSizeMax(pad.fClustSizeMax)
{
  // copy constructor
 
  // TObjArray with histograms
  fHistoKrArray.SetOwner(kTRUE); // is owner of histograms
  fHistoKrArray.Clear();

  for (Int_t iSec = 0; iSec < 72; ++iSec) 
  {
    TH3F *hOld = pad.GetHistoKr(iSec);
	if(hOld) {
      TH3F *hNew = new TH3F( *pad.GetHistoKr(iSec) ); 
      fHistoKrArray.AddAt(hNew,iSec);
	}
  }
}

//_____________________________________________________________________
AliTPCCalibKr::~AliTPCCalibKr() 
{
  //
  // destructor
  //

  // for (Int_t iSec = 0; iSec < 72; ++iSec) {
  //     if (fHistoKrArray.At(iSec)) delete fHistoKrArray.RemoveAt(iSec);
  // }
  fHistoKrArray.Delete();
}

//_____________________________________________________________________
AliTPCCalibKr& AliTPCCalibKr::operator = (const  AliTPCCalibKr &source)
{
  // assignment operator

  if (&source == this) return *this;
  new (this) AliTPCCalibKr(source);

  return *this;
}

//_____________________________________________________________________
void AliTPCCalibKr::Init()
{
  // 
  // init output histograms 
  //

  // add histograms to the TObjArray
  for(Int_t i=0; i<72; ++i) {
    
	// C - side
	if(IsCSide(i) == kTRUE && fCSide == kTRUE) {
      TH3F *hist = CreateHisto(i);
      if(hist) fHistoKrArray.AddAt(hist,i);
	}
    
	// A - side
	if(IsCSide(i) == kFALSE && fASide == kTRUE) {
      TH3F *hist = CreateHisto(i);
      if(hist) fHistoKrArray.AddAt(hist,i);
	}
  }
}
 
//_____________________________________________________________________
Bool_t AliTPCCalibKr::Process(AliTPCclusterKr *cluster)
{
  //
  // process events 
  // call event by event
  //

  if(cluster) Update(cluster);
  else return kFALSE;
 
 return kTRUE;
}

//_____________________________________________________________________
TH3F* AliTPCCalibKr::CreateHisto(Int_t chamber)
{
    //
    // create new histogram
	//
    char name[256];
	TH3F *h;

    sprintf(name,"ADCcluster_ch%d",chamber);

    if( IsIROC(chamber) == kTRUE ) 
	{
	   h = new TH3F(name,name,63,0,63,108,0,108,200,100,2500);
	} else {
	   h = new TH3F(name,name,96,0,96,140,0,140,200,100,1700);
	}
    h->SetXTitle("padrow");
    h->SetYTitle("pad");
    h->SetZTitle("fADC");

return h;
}

//_____________________________________________________________________
Bool_t AliTPCCalibKr::IsIROC(Int_t chamber)
{
// check if IROCs
// returns kTRUE if IROCs and kFALSE if OROCs 

  if(chamber>=0 && chamber<36) return kTRUE;

return kFALSE;
}

//_____________________________________________________________________
Bool_t AliTPCCalibKr::IsCSide(Int_t chamber)
{
// check if C side
// returns kTRUE if C side and kFALSE if A side

  if((chamber>=18 && chamber<36) || (chamber>=54 && chamber<72)) return kTRUE;

return kFALSE;
}
 
//_____________________________________________________________________
Bool_t AliTPCCalibKr::Update(AliTPCclusterKr  *cl)
{
  //
  // fill existing histograms
  //

  if (!Accept(cl)) return kFALSE;
  TH3F *h = (TH3F*)fHistoKrArray.At(cl->GetSec());
  if(!h) return kFALSE;
  
  h->Fill(cl->GetMax().GetRow(),cl->GetMax().GetPad(),cl->GetADCcluster());
  
  return kTRUE;
}

//_____________________________________________________________________
Bool_t AliTPCCalibKr::Accept(AliTPCclusterKr  *cl){
  //
  // cuts
  //
  /*
    TCut cutR0("cutR0","fADCcluster/fSize<200");        // adjust it according v seetings - 
    TCut cutR1("cutR1","fADCcluster/fSize>7");          // cosmic tracks and noise removal
    TCut cutR2("cutR2","fMax.fAdc/fADCcluster<0.4");    // digital noise removal
    TCut cutR3("cutR3","fMax.fAdc/fADCcluster>0.01");   // noise removal
    TCut cutR4("cutR4","fMax.fTime>200");   // noise removal
    TCut cutR5("cutR5","fMax.fTime<600");   // noise removal
    TCut cutS1("cutS1","fSize<200");    // adjust it according v seetings - cosmic tracks
    TCut cutAll = cutR0+cutR1+cutR2+cutR3+cutR4+cutR5+cutS1;
  */
  /*
  //R0
  if ((float)cl->GetADCcluster()/ cl->GetSize() >200)        return kFALSE;
  // R1
  if ((float)cl->GetADCcluster()/ cl->GetSize() <7)          return kFALSE;
  //R2
  if ((float)cl->GetMax().GetAdc()/ cl->GetADCcluster() >0.4)  return kFALSE;
  //R3
  if ((float)cl->GetMax().GetAdc()/ cl->GetADCcluster() <0.01) return kFALSE;
  //R4
  if (cl->GetMax().GetTime() < 200) return kFALSE;
  //R5
  if (cl->GetMax().GetTime() > 600) return kFALSE;
  //S1
  if (cl->GetSize()>200) return kFALSE;
  if (cl->GetSize()<6)  return kFALSE;

  SetADCOverClustSizeRange(7,200);
  SetMaxADCOverClustADCRange(0.01,0.4);
  SetTimeRange(200,600);
  SetClustSizeRange(6,200);
  */

  //R0
  if ((float)cl->GetADCcluster()/ cl->GetSize() >fADCOverClustSizeMax)        return kFALSE;
  // R1
  if ((float)cl->GetADCcluster()/ cl->GetSize() <fADCOverClustSizeMin)          return kFALSE;
  //R2
  if ((float)cl->GetMax().GetAdc()/ cl->GetADCcluster() >fMaxADCOverClustADCMax)  return kFALSE;
  //R3
  if ((float)cl->GetMax().GetAdc()/ cl->GetADCcluster() <fMaxADCOverClustADCMin) return kFALSE;
  //R4
  if (cl->GetMax().GetTime() > fTimeMax) return kFALSE;
  //R5
  if (cl->GetMax().GetTime() < fTimeMin) return kFALSE;
  //S1
  if (cl->GetSize()>fClustSizeMax) return kFALSE;
  if (cl->GetSize()<fClustSizeMin)  return kFALSE;

  return kTRUE;

}

//_____________________________________________________________________
TH3F* AliTPCCalibKr::GetHistoKr(Int_t chamber) const
{
  // get histograms from fHistoKrArray
  return (TH3F*) fHistoKrArray.At(chamber);
}
 
//_____________________________________________________________________
void AliTPCCalibKr::Analyse() 
{
  //
  // analyse the histograms and extract krypton calibration parameters
  //

  // AliTPCCalPads that will contain the calibration parameters
  AliTPCCalPad* spectrMeanCalPad = new AliTPCCalPad("spectrMean", "spectrMean");
  AliTPCCalPad* spectrRMSCalPad = new AliTPCCalPad("spectrRMS", "spectrRMS");
  AliTPCCalPad* fitMeanCalPad = new AliTPCCalPad("fitMean", "fitMean");
  AliTPCCalPad* fitRMSCalPad = new AliTPCCalPad("fitRMS", "fitRMS");
  AliTPCCalPad* fitNormChi2CalPad = new AliTPCCalPad("fitNormChi2", "fitNormChi2");
  AliTPCCalPad* entriesCalPad = new AliTPCCalPad("entries", "entries");

  // file stream for debugging purposes
  TTreeSRedirector* debugStream = new TTreeSRedirector("debugCalibKr.root");

  // if entries in spectrum less than minEntries, then the fit won't be performed
  Int_t minEntries = 1; //300;

  Double_t windowFrac = 0.12;
  // the 3d histogram will be projected on the pads given by the following window size
  // set the numbers to 0 if you want to do a pad-by-pad calibration
  UInt_t rowRadius = 2;
  UInt_t padRadius = 4;
  
  // the step size by which pad and row are incremented is given by the following numbers
  // set them to 1 if you want the finest granularity
  UInt_t rowStep = 1;    // formerly: 2*rowRadius
  UInt_t padStep = 1;    // formerly: 2*padRadius

  for (Int_t chamber = 0; chamber < 72; chamber++) {
    //if (chamber != 71) continue;
    AliTPCCalROC roc(chamber);  // I need this only for GetNrows() and GetNPads()
    
    // Usually I would traverse each pad, take the spectrum for its neighbourhood and
    // obtain the calibration parameters. This takes very long, so instead I assign the same
    // calibration values to the whole neighbourhood and then go on to the next neighbourhood.
    UInt_t nRows = roc.GetNrows();
    for (UInt_t iRow = 0; iRow < nRows; iRow += rowStep) {
      UInt_t nPads = roc.GetNPads(iRow);
      //if (iRow >= 10) break;
      for (UInt_t iPad = 0; iPad < nPads; iPad += padStep) {
        //if (iPad >= 20) break;
        TH3F* h = GetHistoKr(chamber);
        if (!h) continue;
        
        // the 3d histogram will be projected on the pads given by the following bounds
        // for rows and pads
        Int_t rowLow = iRow - rowRadius;
        UInt_t rowUp = iRow + rowRadius;
        Int_t padLow = iPad - padRadius;
        UInt_t padUp = iPad + padRadius;
        // if window goes out of chamber
        if (rowLow < 0) rowLow = 0;
        if (rowUp >= nRows) rowUp = nRows - 1;
        if (padLow < 0) padLow = 0;
        if (padUp >= nPads) padUp = nPads - 1;

        // project the histogram
        //TH1D* projH = h->ProjectionZ("projH", rowLow, rowUp, padLow, padUp); // SLOW
        TH1D* projH = ProjectHisto(h, "projH", rowLow, rowUp, padLow, padUp);
    
        // get the number of entries in the spectrum
        Double_t entries = projH->GetEntries();
        if (entries < minEntries) { delete projH; continue; }
        
        // get the two calibration parameters mean of spectrum and RMS of spectrum
        Double_t histMean = projH->GetMean();
        Double_t histRMS = (histMean != 0) ? projH->GetRMS() / histMean : 0.;
    
        // find maximum in spectrum to define a range (given by windowFrac) for which a Gauss is fitted
        Double_t maxEntries = projH->GetBinCenter(projH->GetMaximumBin());
		Int_t minBin = projH->FindBin((1.-windowFrac) * maxEntries);
		Int_t maxBin = projH->FindBin((1.+windowFrac) * maxEntries);
        Double_t integCharge =  projH->Integral(minBin,maxBin); 

        Int_t fitResult = projH->Fit("gaus", "Q0", "", (1.-windowFrac) * maxEntries, (1.+windowFrac) * maxEntries);

        if (fitResult != 0) {
          Error("Analyse", "Error while fitting spectrum for chamber %i, rows %i - %i, pads %i - %i, integrated charge %f.", chamber, rowLow, rowUp, padLow, padUp, integCharge);
          //printf("[ch%i r%i, p%i] entries = %f, maxEntries = %f,  %f\n", chamber, iRow, iPad, entries, maxEntries);
    
          delete projH;
          continue;
        }
    
        // get the two calibration parameters mean of gauss fit and sigma of gauss fit
        TF1* gausFit = projH->GetFunction("gaus");
        Double_t fitMean = gausFit->GetParameter(1);
        Double_t fitRMS = gausFit->GetParameter(2);
        Int_t numberFitPoints = gausFit->GetNumberFitPoints();
        if (numberFitPoints == 0) continue;
        Double_t fitNormChi2 = gausFit->GetChisquare() / numberFitPoints;
        delete gausFit;
        delete projH;
        if (fitMean <= 0) continue;
        //printf("[ch%i r%i, p%i] entries = %f, maxEntries = %f, fitMean = %f, fitRMS = %f\n", chamber, iRow, iPad, entries, maxEntries, fitMean, fitRMS);
    
        // write the calibration parameters for each pad that the 3d histogram was projected onto
        // (with considering the step size) to the CalPads
        // rowStep (padStep) odd: round down s/2 and fill this # of rows (pads) in both directions
        // rowStep (padStep) even: fill s/2 rows (pads) in ascending direction, s/2-1 in descending direction
        for (Int_t r = iRow - (rowStep/2 - (rowStep+1)%2); r <= (Int_t)(iRow + rowStep/2); r++) {
          if (r < 0 || r >= (Int_t)nRows) continue;
          UInt_t nPadsR = roc.GetNPads(r);
          for (Int_t p = iPad - (padStep/2 - (padStep+1)%2); p <= (Int_t)(iPad + padStep/2); p++) {
            if (p < 0 || p >= (Int_t)nPadsR) continue;
            spectrMeanCalPad->GetCalROC(chamber)->SetValue(r, p, histMean);
            spectrRMSCalPad->GetCalROC(chamber)->SetValue(r, p, histRMS);
            fitMeanCalPad->GetCalROC(chamber)->SetValue(r, p, fitMean);
            fitRMSCalPad->GetCalROC(chamber)->SetValue(r, p, fitRMS);
            fitNormChi2CalPad->GetCalROC(chamber)->SetValue(r, p, fitNormChi2);
            entriesCalPad->GetCalROC(chamber)->SetValue(r, p, entries);

            (*debugStream) << "calibKr" <<
              "sector=" << chamber <<          // chamber number
              "row=" << r <<                   // row number
              "pad=" << p <<                   // pad number
              "histMean=" << histMean <<       // mean of the spectrum
              "histRMS=" << histRMS <<         // RMS of the spectrum divided by the mean
              "fitMean=" << fitMean <<         // Gauss fitted mean of the 41.6 keV Kr peak
              "fitRMS=" << fitRMS <<           // Gauss fitted sigma of the 41.6 keV Kr peak
              "fitNormChi2" << fitNormChi2 <<  // normalized chi square of the Gauss fit
              "entries=" << entries <<         // number of entries for the spectrum
              "\n";
          }
        }
      }
    }
  }

  TFile f("calibKr.root", "recreate");
  spectrMeanCalPad->Write();
  spectrRMSCalPad->Write();
  fitMeanCalPad->Write();
  fitRMSCalPad->Write();
  fitNormChi2CalPad->Write();
  entriesCalPad->Write();
  f.Close();
  delete spectrMeanCalPad;
  delete spectrRMSCalPad;
  delete fitMeanCalPad;
  delete fitRMSCalPad;
  delete fitNormChi2CalPad;
  delete entriesCalPad;
  delete debugStream;
}

//_____________________________________________________________________
TH1D* AliTPCCalibKr::ProjectHisto(TH3F* histo3D, const char* name, Int_t xMin, Int_t xMax, Int_t yMin, Int_t yMax)
{
  // project the z-axis of a 3d histo to a specific range of the x- and y-axes,
  // replaces TH3F::ProjectZ() to gain more speed

  TAxis* xAxis = histo3D->GetXaxis();
  TAxis* yAxis = histo3D->GetYaxis();
  TAxis* zAxis = histo3D->GetZaxis();
  Double_t zMinVal = zAxis->GetXmin();
  Double_t zMaxVal = zAxis->GetXmax();
  
  Int_t nBinsZ = zAxis->GetNbins();
  TH1D* projH = new TH1D(name, name, nBinsZ, zMinVal, zMaxVal);

  Int_t nx = xAxis->GetNbins()+2;
  Int_t ny = yAxis->GetNbins()+2;
  Int_t bin = 0;
  Double_t entries = 0.;
  for (Int_t x = xMin; x <= xMax; x++) {
    for (Int_t y = yMin; y <= yMax; y++) {
      for (Int_t z = 0; z <= nBinsZ+1; z++) {
        bin = x + nx * (y + ny * z);
        Double_t val = histo3D->GetBinContent(bin);
        projH->Fill(zAxis->GetBinCenter(z), val);
        entries += val;
      }
    }
  }
  projH->SetEntries((Long64_t)entries);
  return projH;
}

//_____________________________________________________________________
Long64_t AliTPCCalibKr::Merge(TCollection* list) {
// merge function 
//
cout << "Merge " << endl;

if (!list)
return 0;

if (list->IsEmpty())
return 1;

TIterator* iter = list->MakeIterator();
TObject* obj = 0;

    iter->Reset();
    Int_t count=0;
	while((obj = iter->Next()) != 0)
	{
	  AliTPCCalibKr* entry = dynamic_cast<AliTPCCalibKr*>(obj);
	  if (entry == 0) continue; 

		for(int i=0; i<72; ++i) { 
		  if(IsCSide(i) == kTRUE && fCSide == kTRUE) { 
		  ((TH3F*)fHistoKrArray.At(i))->Add( ((TH3F*)entry->fHistoKrArray.At(i)) );  
		  } 

		  if(IsCSide(i) == kFALSE && fASide == kTRUE) { 
		    ((TH3F*)fHistoKrArray.At(i))->Add( ((TH3F*)entry->fHistoKrArray.At(i)) );  
		  } 
		} 

	  count++;
	}

return count;
}
Commit	Line	Data
72e010d3	1	/**************************************************************************
	2	* Copyright(c) 1998-1999, ALICE Experiment at CERN, All rights reserved. *
	3	* *
	4	* Author: The ALICE Off-line Project. *
	5	* Contributors are mentioned in the code where appropriate. *
	6	* *
	7	* Permission to use, copy, modify and distribute this software and its *
	8	* documentation strictly for non-commercial purposes is hereby granted *
	9	* without fee, provided that the above copyright notice appears in all *
	10	* copies and that both the copyright notice and this permission notice *
	11	* appear in the supporting documentation. The authors make no claims *
	12	* about the suitability of this software for any purpose. It is *
	13	* provided "as is" without express or implied warranty. *
	14	**************************************************************************/
	15
	16
	17	//Root includes
	18	#include <TH1F.h>
	19	#include <TH1D.h>
	20	#include <TH2F.h>
	21	#include <TH3F.h>
	22	#include <TString.h>
	23	#include <TMath.h>
	24	#include <TF1.h>
	25	#include <TRandom.h>
	26	#include <TDirectory.h>
	27	#include <TFile.h>
	28	#include <TAxis.h>
	29	//AliRoot includes
	30	#include "AliRawReader.h"
	31	#include "AliRawReaderRoot.h"
	32	#include "AliRawReaderDate.h"
	33	#include "AliTPCRawStream.h"
	34	#include "AliTPCCalROC.h"
	35	#include "AliTPCCalPad.h"
	36	#include "AliTPCROC.h"
	37	#include "AliMathBase.h"
	38	#include "TTreeStream.h"
	39	#include "AliTPCRawStreamFast.h"
	40
	41	//date
	42	#include "event.h"
	43
	44	//header file
	45	#include "AliTPCCalibKr.h"
	46
	47	//----------------------------------------------------------------------------
	48	// The AliTPCCalibKr class description (TPC Kr calibration).
	49	//
	50	//
afb50fd6	51	// The AliTPCCalibKr keeps the array of TH3F histograms (TPC_max_padraw,TPC_max_pad,TPC_ADC_cluster),
afb50fd6	52	// its data memebers and is filled by AliTPCCalibKrTask under conditions (Accept()).
72e010d3	53	//
72e010d3	54	// The ouput TH3F histograms are later used to determine the calibration parameters of TPC chambers.
	55	// These calculations are done by using AliTPCCalibKr::Analyse() function. The ouput calibration
	56	// parameters (details in AliTPCCalibKr::Analyse()) are stored in the calibKr.root file for each TPC pad.
	57	// In addition the debugCalibKr.root file with debug information is created.
	58	//
afb50fd6	59
	60	/*
	61
72e010d3	62	// Usage example:
72e010d3	63	//
afb50fd6	64
	65	// 1. Analyse output histograms:
	66	TFile f("outHistFile.root");
	67	AliTPCCalibKr obj = (AliTPCCalibKr) cOutput.FindObject("AliTPCCalibKr")
	68	obj->Analyse();
	69
	70	// 2. See calibration parameters e.g.:
	71	TFile f("calibKr.root");
	72	spectrMean->GetCalROC(70)->GetValue(40,40);
	73	fitMean->GetCalROC(70)->GetValue(40,40);
	74
	75	// 3. See debug information e.g.:
	76	TFile f("debugCalibKr.root");
	77	.ls;
	78
72e010d3	79	// -- Print calibKr TTree content
afb50fd6	80	calibKr->Print();
afb50fd6	81
72e010d3	82	// -- Draw calibKr TTree variables
afb50fd6	83	calibKr.Draw("fitMean");
	84
	85	*/
	86
	87
72e010d3	88	//
	89	// Author: Jacek Otwinowski (J.Otwinowski@gsi.de) and Stafan Geartner (S.Gaertner@gsi.de)
	90	//-----------------------------------------------------------------------------
	91
	92	ClassImp(AliTPCCalibKr)
	93
	94	AliTPCCalibKr::AliTPCCalibKr() :
	95	TObject(),
ff0df25d	96	fASide(kTRUE),
ff0df25d	97	fCSide(kTRUE),
aa967a06	98	fHistoKrArray(72),
	99	fADCOverClustSizeMin(0.0),
	100	fADCOverClustSizeMax(1.0e9),
	101	fMaxADCOverClustADCMin(0.0),
	102	fMaxADCOverClustADCMax(1.0e9),
	103	fTimeMin(0.0),
	104	fTimeMax(1.0e9),
	105	fClustSizeMin(0.0),
	106	fClustSizeMax(1.0e9)
72e010d3	107	{
	108	//
	109	// default constructor
	110	//
afb50fd6	111
f3b61a78	112	// TObjArray with histograms
	113	fHistoKrArray.SetOwner(kTRUE); // is owner of histograms
	114	fHistoKrArray.Clear();
aa967a06	115
	116	// init cuts
	117	SetADCOverClustSizeRange(7,200);
	118	SetMaxADCOverClustADCRange(0.01,0.4);
	119	SetTimeRange(200,600);
	120	SetClustSizeRange(6,200);
	121
afb50fd6	122	// init histograms
afb50fd6	123	Init();
72e010d3	124	}
	125
	126	//_____________________________________________________________________
	127	AliTPCCalibKr::AliTPCCalibKr(const AliTPCCalibKr& pad) :
	128	TObject(pad),
	129
ff0df25d	130	fASide(pad.fASide),
ff0df25d	131	fCSide(pad.fCSide),
aa967a06	132	fHistoKrArray(72),
	133	fADCOverClustSizeMin(pad.fADCOverClustSizeMin),
	134	fADCOverClustSizeMax(pad.fADCOverClustSizeMax),
	135	fMaxADCOverClustADCMin(pad.fMaxADCOverClustADCMin),
	136	fMaxADCOverClustADCMax(pad.fMaxADCOverClustADCMax),
	137	fTimeMin(pad.fTimeMin),
	138	fTimeMax(pad.fTimeMax),
	139	fClustSizeMin(pad.fClustSizeMin),
	140	fClustSizeMax(pad.fClustSizeMax)
72e010d3	141	{
	142	// copy constructor
	143
f3b61a78	144	// TObjArray with histograms
	145	fHistoKrArray.SetOwner(kTRUE); // is owner of histograms
	146	fHistoKrArray.Clear();
	147
72e010d3	148	for (Int_t iSec = 0; iSec < 72; ++iSec)
	149	{
	150	TH3F *hOld = pad.GetHistoKr(iSec);
	151	if(hOld) {
	152	TH3F hNew = new TH3F( pad.GetHistoKr(iSec) );
	153	fHistoKrArray.AddAt(hNew,iSec);
	154	}
	155	}
	156	}
	157
	158	//_____________________________________________________________________
	159	AliTPCCalibKr::~AliTPCCalibKr()
	160	{
	161	//
	162	// destructor
	163	//
afb50fd6	164
f3b61a78	165	// for (Int_t iSec = 0; iSec < 72; ++iSec) {
	166	// if (fHistoKrArray.At(iSec)) delete fHistoKrArray.RemoveAt(iSec);
	167	// }
72e010d3	168	fHistoKrArray.Delete();
	169	}
	170
	171	//_____________________________________________________________________
	172	AliTPCCalibKr& AliTPCCalibKr::operator = (const AliTPCCalibKr &source)
	173	{
	174	// assignment operator
	175
	176	if (&source == this) return *this;
	177	new (this) AliTPCCalibKr(source);
	178
	179	return *this;
	180	}
	181
	182	//_____________________________________________________________________
	183	void AliTPCCalibKr::Init()
	184	{
	185	//
f3b61a78	186	// init output histograms
72e010d3	187	//
72e010d3	188
	189	// add histograms to the TObjArray
	190	for(Int_t i=0; i<72; ++i) {
	191
	192	// C - side
ff0df25d	193	if(IsCSide(i) == kTRUE && fCSide == kTRUE) {
72e010d3	194	TH3F *hist = CreateHisto(i);
	195	if(hist) fHistoKrArray.AddAt(hist,i);
	196	}
	197
	198	// A - side
ff0df25d	199	if(IsCSide(i) == kFALSE && fASide == kTRUE) {
72e010d3	200	TH3F *hist = CreateHisto(i);
	201	if(hist) fHistoKrArray.AddAt(hist,i);
	202	}
72e010d3	203	}
72e010d3	204	}
72e010d3	205
72e010d3	206	//_____________________________________________________________________
afb50fd6	207	Bool_t AliTPCCalibKr::Process(AliTPCclusterKr *cluster)
72e010d3	208	{
	209	//
	210	// process events
	211	// call event by event
	212	//
	213
afb50fd6	214	if(cluster) Update(cluster);
afb50fd6	215	else return kFALSE;
f3b61a78	216
f3b61a78	217	return kTRUE;
72e010d3	218	}
	219
	220	//_____________________________________________________________________
	221	TH3F* AliTPCCalibKr::CreateHisto(Int_t chamber)
	222	{
	223	//
	224	// create new histogram
	225	//
	226	char name[256];
	227	TH3F *h;
	228
	229	sprintf(name,"ADCcluster_ch%d",chamber);
	230
	231	if( IsIROC(chamber) == kTRUE )
	232	{
f3b61a78	233	h = new TH3F(name,name,63,0,63,108,0,108,200,100,2500);
72e010d3	234	} else {
f3b61a78	235	h = new TH3F(name,name,96,0,96,140,0,140,200,100,1700);
72e010d3	236	}
	237	h->SetXTitle("padrow");
	238	h->SetYTitle("pad");
	239	h->SetZTitle("fADC");
	240
	241	return h;
	242	}
	243
	244	//_____________________________________________________________________
	245	Bool_t AliTPCCalibKr::IsIROC(Int_t chamber)
	246	{
	247	// check if IROCs
	248	// returns kTRUE if IROCs and kFALSE if OROCs
	249
	250	if(chamber>=0 && chamber<36) return kTRUE;
	251
	252	return kFALSE;
	253	}
	254
	255	//_____________________________________________________________________
	256	Bool_t AliTPCCalibKr::IsCSide(Int_t chamber)
	257	{
	258	// check if C side
	259	// returns kTRUE if C side and kFALSE if A side
	260
	261	if((chamber>=18 && chamber<36) \|\| (chamber>=54 && chamber<72)) return kTRUE;
	262
	263	return kFALSE;
	264	}
	265
	266	//_____________________________________________________________________
	267	Bool_t AliTPCCalibKr::Update(AliTPCclusterKr *cl)
	268	{
	269	//
	270	// fill existing histograms
	271	//
72e010d3	272
045a55c4	273	if (!Accept(cl)) return kFALSE;
	274	TH3F h = (TH3F)fHistoKrArray.At(cl->GetSec());
	275	if(!h) return kFALSE;
	276
	277	h->Fill(cl->GetMax().GetRow(),cl->GetMax().GetPad(),cl->GetADCcluster());
	278
	279	return kTRUE;
	280	}
	281
afb50fd6	282	//_____________________________________________________________________
045a55c4	283	Bool_t AliTPCCalibKr::Accept(AliTPCclusterKr *cl){
	284	//
	285	// cuts
	286	//
	287	/*
	288	TCut cutR0("cutR0","fADCcluster/fSize<200"); // adjust it according v seetings -
	289	TCut cutR1("cutR1","fADCcluster/fSize>7"); // cosmic tracks and noise removal
	290	TCut cutR2("cutR2","fMax.fAdc/fADCcluster<0.4"); // digital noise removal
	291	TCut cutR3("cutR3","fMax.fAdc/fADCcluster>0.01"); // noise removal
aa967a06	292	TCut cutR4("cutR4","fMax.fTime>200"); // noise removal
aa967a06	293	TCut cutR5("cutR5","fMax.fTime<600"); // noise removal
045a55c4	294	TCut cutS1("cutS1","fSize<200"); // adjust it according v seetings - cosmic tracks
aa967a06	295	TCut cutAll = cutR0+cutR1+cutR2+cutR3+cutR4+cutR5+cutS1;
045a55c4	296	*/
aa967a06	297	/*
045a55c4	298	//R0
f3b61a78	299	if ((float)cl->GetADCcluster()/ cl->GetSize() >200) return kFALSE;
045a55c4	300	// R1
f3b61a78	301	if ((float)cl->GetADCcluster()/ cl->GetSize() <7) return kFALSE;
045a55c4	302	//R2
f3b61a78	303	if ((float)cl->GetMax().GetAdc()/ cl->GetADCcluster() >0.4) return kFALSE;
045a55c4	304	//R3
f3b61a78	305	if ((float)cl->GetMax().GetAdc()/ cl->GetADCcluster() <0.01) return kFALSE;
aa967a06	306	//R4
	307	if (cl->GetMax().GetTime() < 200) return kFALSE;
	308	//R5
	309	if (cl->GetMax().GetTime() > 600) return kFALSE;
045a55c4	310	//S1
	311	if (cl->GetSize()>200) return kFALSE;
	312	if (cl->GetSize()<6) return kFALSE;
aa967a06	313
	314	SetADCOverClustSizeRange(7,200);
	315	SetMaxADCOverClustADCRange(0.01,0.4);
	316	SetTimeRange(200,600);
	317	SetClustSizeRange(6,200);
	318	*/
	319
	320	//R0
	321	if ((float)cl->GetADCcluster()/ cl->GetSize() >fADCOverClustSizeMax) return kFALSE;
	322	// R1
	323	if ((float)cl->GetADCcluster()/ cl->GetSize() <fADCOverClustSizeMin) return kFALSE;
	324	//R2
	325	if ((float)cl->GetMax().GetAdc()/ cl->GetADCcluster() >fMaxADCOverClustADCMax) return kFALSE;
	326	//R3
	327	if ((float)cl->GetMax().GetAdc()/ cl->GetADCcluster() <fMaxADCOverClustADCMin) return kFALSE;
	328	//R4
	329	if (cl->GetMax().GetTime() > fTimeMax) return kFALSE;
	330	//R5
	331	if (cl->GetMax().GetTime() < fTimeMin) return kFALSE;
	332	//S1
	333	if (cl->GetSize()>fClustSizeMax) return kFALSE;
	334	if (cl->GetSize()<fClustSizeMin) return kFALSE;
	335
045a55c4	336	return kTRUE;
72e010d3	337
72e010d3	338	}
	339
	340	//_____________________________________________________________________
	341	TH3F* AliTPCCalibKr::GetHistoKr(Int_t chamber) const
	342	{
	343	// get histograms from fHistoKrArray
	344	return (TH3F*) fHistoKrArray.At(chamber);
	345	}
72e010d3	346
	347	//_____________________________________________________________________
	348	void AliTPCCalibKr::Analyse()
	349	{
	350	//
	351	// analyse the histograms and extract krypton calibration parameters
	352	//
	353
	354	// AliTPCCalPads that will contain the calibration parameters
	355	AliTPCCalPad* spectrMeanCalPad = new AliTPCCalPad("spectrMean", "spectrMean");
	356	AliTPCCalPad* spectrRMSCalPad = new AliTPCCalPad("spectrRMS", "spectrRMS");
	357	AliTPCCalPad* fitMeanCalPad = new AliTPCCalPad("fitMean", "fitMean");
	358	AliTPCCalPad* fitRMSCalPad = new AliTPCCalPad("fitRMS", "fitRMS");
	359	AliTPCCalPad* fitNormChi2CalPad = new AliTPCCalPad("fitNormChi2", "fitNormChi2");
	360	AliTPCCalPad* entriesCalPad = new AliTPCCalPad("entries", "entries");
	361
	362	// file stream for debugging purposes
	363	TTreeSRedirector* debugStream = new TTreeSRedirector("debugCalibKr.root");
	364
	365	// if entries in spectrum less than minEntries, then the fit won't be performed
	366	Int_t minEntries = 1; //300;
	367
	368	Double_t windowFrac = 0.12;
	369	// the 3d histogram will be projected on the pads given by the following window size
	370	// set the numbers to 0 if you want to do a pad-by-pad calibration
f3b61a78	371	UInt_t rowRadius = 2;
	372	UInt_t padRadius = 4;
	373
72e010d3	374	// the step size by which pad and row are incremented is given by the following numbers
	375	// set them to 1 if you want the finest granularity
	376	UInt_t rowStep = 1; // formerly: 2*rowRadius
	377	UInt_t padStep = 1; // formerly: 2*padRadius
	378
	379	for (Int_t chamber = 0; chamber < 72; chamber++) {
	380	//if (chamber != 71) continue;
	381	AliTPCCalROC roc(chamber); // I need this only for GetNrows() and GetNPads()
	382
	383	// Usually I would traverse each pad, take the spectrum for its neighbourhood and
	384	// obtain the calibration parameters. This takes very long, so instead I assign the same
	385	// calibration values to the whole neighbourhood and then go on to the next neighbourhood.
	386	UInt_t nRows = roc.GetNrows();
	387	for (UInt_t iRow = 0; iRow < nRows; iRow += rowStep) {
	388	UInt_t nPads = roc.GetNPads(iRow);
	389	//if (iRow >= 10) break;
	390	for (UInt_t iPad = 0; iPad < nPads; iPad += padStep) {
	391	//if (iPad >= 20) break;
	392	TH3F* h = GetHistoKr(chamber);
	393	if (!h) continue;
	394
	395	// the 3d histogram will be projected on the pads given by the following bounds
	396	// for rows and pads
	397	Int_t rowLow = iRow - rowRadius;
	398	UInt_t rowUp = iRow + rowRadius;
	399	Int_t padLow = iPad - padRadius;
	400	UInt_t padUp = iPad + padRadius;
	401	// if window goes out of chamber
	402	if (rowLow < 0) rowLow = 0;
	403	if (rowUp >= nRows) rowUp = nRows - 1;
	404	if (padLow < 0) padLow = 0;
	405	if (padUp >= nPads) padUp = nPads - 1;
	406
	407	// project the histogram
	408	//TH1D* projH = h->ProjectionZ("projH", rowLow, rowUp, padLow, padUp); // SLOW
	409	TH1D* projH = ProjectHisto(h, "projH", rowLow, rowUp, padLow, padUp);
	410
	411	// get the number of entries in the spectrum
	412	Double_t entries = projH->GetEntries();
	413	if (entries < minEntries) { delete projH; continue; }
	414
	415	// get the two calibration parameters mean of spectrum and RMS of spectrum
	416	Double_t histMean = projH->GetMean();
	417	Double_t histRMS = (histMean != 0) ? projH->GetRMS() / histMean : 0.;
	418
	419	// find maximum in spectrum to define a range (given by windowFrac) for which a Gauss is fitted
	420	Double_t maxEntries = projH->GetBinCenter(projH->GetMaximumBin());
f3b61a78	421	Int_t minBin = projH->FindBin((1.-windowFrac) * maxEntries);
	422	Int_t maxBin = projH->FindBin((1.+windowFrac) * maxEntries);
	423	Double_t integCharge = projH->Integral(minBin,maxBin);
	424
72e010d3	425	Int_t fitResult = projH->Fit("gaus", "Q0", "", (1.-windowFrac) * maxEntries, (1.+windowFrac) * maxEntries);
f3b61a78	426
72e010d3	427	if (fitResult != 0) {
f3b61a78	428	Error("Analyse", "Error while fitting spectrum for chamber %i, rows %i - %i, pads %i - %i, integrated charge %f.", chamber, rowLow, rowUp, padLow, padUp, integCharge);
	429	//printf("[ch%i r%i, p%i] entries = %f, maxEntries = %f, %f\n", chamber, iRow, iPad, entries, maxEntries);
	430
72e010d3	431	delete projH;
	432	continue;
	433	}
	434
	435	// get the two calibration parameters mean of gauss fit and sigma of gauss fit
	436	TF1* gausFit = projH->GetFunction("gaus");
	437	Double_t fitMean = gausFit->GetParameter(1);
	438	Double_t fitRMS = gausFit->GetParameter(2);
	439	Int_t numberFitPoints = gausFit->GetNumberFitPoints();
	440	if (numberFitPoints == 0) continue;
	441	Double_t fitNormChi2 = gausFit->GetChisquare() / numberFitPoints;
	442	delete gausFit;
	443	delete projH;
	444	if (fitMean <= 0) continue;
afb50fd6	445	//printf("[ch%i r%i, p%i] entries = %f, maxEntries = %f, fitMean = %f, fitRMS = %f\n", chamber, iRow, iPad, entries, maxEntries, fitMean, fitRMS);
72e010d3	446
	447	// write the calibration parameters for each pad that the 3d histogram was projected onto
	448	// (with considering the step size) to the CalPads
	449	// rowStep (padStep) odd: round down s/2 and fill this # of rows (pads) in both directions
	450	// rowStep (padStep) even: fill s/2 rows (pads) in ascending direction, s/2-1 in descending direction
	451	for (Int_t r = iRow - (rowStep/2 - (rowStep+1)%2); r <= (Int_t)(iRow + rowStep/2); r++) {
	452	if (r < 0 \|\| r >= (Int_t)nRows) continue;
23354e27	453	UInt_t nPadsR = roc.GetNPads(r);
72e010d3	454	for (Int_t p = iPad - (padStep/2 - (padStep+1)%2); p <= (Int_t)(iPad + padStep/2); p++) {
23354e27	455	if (p < 0 \|\| p >= (Int_t)nPadsR) continue;
72e010d3	456	spectrMeanCalPad->GetCalROC(chamber)->SetValue(r, p, histMean);
	457	spectrRMSCalPad->GetCalROC(chamber)->SetValue(r, p, histRMS);
	458	fitMeanCalPad->GetCalROC(chamber)->SetValue(r, p, fitMean);
	459	fitRMSCalPad->GetCalROC(chamber)->SetValue(r, p, fitRMS);
	460	fitNormChi2CalPad->GetCalROC(chamber)->SetValue(r, p, fitNormChi2);
	461	entriesCalPad->GetCalROC(chamber)->SetValue(r, p, entries);
	462
	463	(*debugStream) << "calibKr" <<
	464	"sector=" << chamber << // chamber number
	465	"row=" << r << // row number
	466	"pad=" << p << // pad number
	467	"histMean=" << histMean << // mean of the spectrum
	468	"histRMS=" << histRMS << // RMS of the spectrum divided by the mean
	469	"fitMean=" << fitMean << // Gauss fitted mean of the 41.6 keV Kr peak
	470	"fitRMS=" << fitRMS << // Gauss fitted sigma of the 41.6 keV Kr peak
	471	"fitNormChi2" << fitNormChi2 << // normalized chi square of the Gauss fit
	472	"entries=" << entries << // number of entries for the spectrum
	473	"\n";
	474	}
	475	}
	476	}
	477	}
	478	}
	479
	480	TFile f("calibKr.root", "recreate");
	481	spectrMeanCalPad->Write();
	482	spectrRMSCalPad->Write();
	483	fitMeanCalPad->Write();
	484	fitRMSCalPad->Write();
	485	fitNormChi2CalPad->Write();
	486	entriesCalPad->Write();
	487	f.Close();
	488	delete spectrMeanCalPad;
	489	delete spectrRMSCalPad;
	490	delete fitMeanCalPad;
	491	delete fitRMSCalPad;
	492	delete fitNormChi2CalPad;
	493	delete entriesCalPad;
	494	delete debugStream;
	495	}
	496
	497	//_____________________________________________________________________
	498	TH1D* AliTPCCalibKr::ProjectHisto(TH3F* histo3D, const char* name, Int_t xMin, Int_t xMax, Int_t yMin, Int_t yMax)
	499	{
	500	// project the z-axis of a 3d histo to a specific range of the x- and y-axes,
	501	// replaces TH3F::ProjectZ() to gain more speed
	502
	503	TAxis* xAxis = histo3D->GetXaxis();
	504	TAxis* yAxis = histo3D->GetYaxis();
	505	TAxis* zAxis = histo3D->GetZaxis();
	506	Double_t zMinVal = zAxis->GetXmin();
	507	Double_t zMaxVal = zAxis->GetXmax();
	508
	509	Int_t nBinsZ = zAxis->GetNbins();
	510	TH1D* projH = new TH1D(name, name, nBinsZ, zMinVal, zMaxVal);
	511
	512	Int_t nx = xAxis->GetNbins()+2;
	513	Int_t ny = yAxis->GetNbins()+2;
	514	Int_t bin = 0;
	515	Double_t entries = 0.;
	516	for (Int_t x = xMin; x <= xMax; x++) {
	517	for (Int_t y = yMin; y <= yMax; y++) {
	518	for (Int_t z = 0; z <= nBinsZ+1; z++) {
	519	bin = x + nx * (y + ny * z);
520	Double_t val = histo3D->GetBinContent(bin);
521	projH->Fill(zAxis->GetBinCenter(z), val);
522	entries += val;
523	}
524	}
525	}
526	projH->SetEntries((Long64_t)entries);
527	return projH;
528	}
afb50fd6	529
	530	//_____________________________________________________________________
	531	Long64_t AliTPCCalibKr::Merge(TCollection* list) {
	532	// merge function
	533	//
	534	cout << "Merge " << endl;
	535
	536	if (!list)
	537	return 0;
	538
	539	if (list->IsEmpty())
	540	return 1;
	541
	542	TIterator* iter = list->MakeIterator();
	543	TObject* obj = 0;
	544
	545	iter->Reset();
	546	Int_t count=0;
	547	while((obj = iter->Next()) != 0)
	548	{
	549	AliTPCCalibKr* entry = dynamic_cast<AliTPCCalibKr*>(obj);
	550	if (entry == 0) continue;
	551
	552	for(int i=0; i<72; ++i) {
ff0df25d	553	if(IsCSide(i) == kTRUE && fCSide == kTRUE) {
afb50fd6	554	((TH3F)fHistoKrArray.At(i))->Add( ((TH3F)entry->fHistoKrArray.At(i)) );
	555	}
	556
ff0df25d	557	if(IsCSide(i) == kFALSE && fASide == kTRUE) {
afb50fd6	558	((TH3F)fHistoKrArray.At(i))->Add( ((TH3F)entry->fHistoKrArray.At(i)) );
	559	}
	560	}
	561
	562	count++;
	563	}
	564
	565	return count;
	566	}