[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(),
  bASide(kTRUE),
  bCSide(kTRUE),
  fHistoKrArray(72)
{
  //
  // default constructor
  //

  // TObjArray with histograms
  fHistoKrArray.SetOwner(kTRUE); // is owner of histograms
  fHistoKrArray.Clear();

  // init histograms
  Init();
}

//_____________________________________________________________________
AliTPCCalibKr::AliTPCCalibKr(const AliTPCCalibKr& pad) : 
  TObject(pad),
  
  bASide(pad.bASide),
  bCSide(pad.bCSide),
  fHistoKrArray(72)
{
  // 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 && bCSide == kTRUE) {
      TH3F *hist = CreateHisto(i);
      if(hist) fHistoKrArray.AddAt(hist,i);
	}
    
	// A - side
	if(IsCSide(i) == kFALSE && bASide == 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 cutS1("cutS1","fSize<200");    // adjust it according v seetings - cosmic tracks
    TCut cutAll = cutR0+cutR1+cutR2+cutR3+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;
  //S1
  if (cl->GetSize()>200) return kFALSE;
  if (cl->GetSize()<6)  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 nPads = 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)nPads) 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 && bCSide == kTRUE) { 
		  ((TH3F*)fHistoKrArray.At(i))->Add( ((TH3F*)entry->fHistoKrArray.At(i)) );  
		  } 

		  if(IsCSide(i) == kFALSE && bASide == 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(),
72e010d3	96	bASide(kTRUE),
72e010d3	97	bCSide(kTRUE),
72e010d3	98	fHistoKrArray(72)
	99	{
	100	//
	101	// default constructor
	102	//
afb50fd6	103
f3b61a78	104	// TObjArray with histograms
	105	fHistoKrArray.SetOwner(kTRUE); // is owner of histograms
	106	fHistoKrArray.Clear();
	107
afb50fd6	108	// init histograms
afb50fd6	109	Init();
72e010d3	110	}
	111
	112	//_____________________________________________________________________
	113	AliTPCCalibKr::AliTPCCalibKr(const AliTPCCalibKr& pad) :
	114	TObject(pad),
	115
72e010d3	116	bASide(pad.bASide),
72e010d3	117	bCSide(pad.bCSide),
72e010d3	118	fHistoKrArray(72)
	119	{
	120	// copy constructor
	121
f3b61a78	122	// TObjArray with histograms
	123	fHistoKrArray.SetOwner(kTRUE); // is owner of histograms
	124	fHistoKrArray.Clear();
	125
72e010d3	126	for (Int_t iSec = 0; iSec < 72; ++iSec)
	127	{
	128	TH3F *hOld = pad.GetHistoKr(iSec);
	129	if(hOld) {
	130	TH3F hNew = new TH3F( pad.GetHistoKr(iSec) );
	131	fHistoKrArray.AddAt(hNew,iSec);
	132	}
	133	}
	134	}
	135
	136	//_____________________________________________________________________
	137	AliTPCCalibKr::~AliTPCCalibKr()
	138	{
	139	//
	140	// destructor
	141	//
afb50fd6	142
f3b61a78	143	// for (Int_t iSec = 0; iSec < 72; ++iSec) {
	144	// if (fHistoKrArray.At(iSec)) delete fHistoKrArray.RemoveAt(iSec);
	145	// }
72e010d3	146	fHistoKrArray.Delete();
	147	}
	148
	149	//_____________________________________________________________________
	150	AliTPCCalibKr& AliTPCCalibKr::operator = (const AliTPCCalibKr &source)
	151	{
	152	// assignment operator
	153
	154	if (&source == this) return *this;
	155	new (this) AliTPCCalibKr(source);
	156
	157	return *this;
	158	}
	159
	160	//_____________________________________________________________________
	161	void AliTPCCalibKr::Init()
	162	{
	163	//
f3b61a78	164	// init output histograms
72e010d3	165	//
72e010d3	166
	167	// add histograms to the TObjArray
	168	for(Int_t i=0; i<72; ++i) {
	169
	170	// C - side
f3b61a78	171	if(IsCSide(i) == kTRUE && bCSide == kTRUE) {
72e010d3	172	TH3F *hist = CreateHisto(i);
	173	if(hist) fHistoKrArray.AddAt(hist,i);
	174	}
	175
	176	// A - side
	177	if(IsCSide(i) == kFALSE && bASide == kTRUE) {
	178	TH3F *hist = CreateHisto(i);
	179	if(hist) fHistoKrArray.AddAt(hist,i);
	180	}
72e010d3	181	}
72e010d3	182	}
72e010d3	183
72e010d3	184	//_____________________________________________________________________
afb50fd6	185	Bool_t AliTPCCalibKr::Process(AliTPCclusterKr *cluster)
72e010d3	186	{
	187	//
	188	// process events
	189	// call event by event
	190	//
	191
afb50fd6	192	if(cluster) Update(cluster);
afb50fd6	193	else return kFALSE;
f3b61a78	194
f3b61a78	195	return kTRUE;
72e010d3	196	}
	197
	198	//_____________________________________________________________________
	199	TH3F* AliTPCCalibKr::CreateHisto(Int_t chamber)
	200	{
	201	//
	202	// create new histogram
	203	//
	204	char name[256];
	205	TH3F *h;
	206
	207	sprintf(name,"ADCcluster_ch%d",chamber);
	208
	209	if( IsIROC(chamber) == kTRUE )
	210	{
f3b61a78	211	h = new TH3F(name,name,63,0,63,108,0,108,200,100,2500);
72e010d3	212	} else {
f3b61a78	213	h = new TH3F(name,name,96,0,96,140,0,140,200,100,1700);
72e010d3	214	}
	215	h->SetXTitle("padrow");
	216	h->SetYTitle("pad");
	217	h->SetZTitle("fADC");
	218
	219	return h;
	220	}
	221
	222	//_____________________________________________________________________
	223	Bool_t AliTPCCalibKr::IsIROC(Int_t chamber)
	224	{
	225	// check if IROCs
	226	// returns kTRUE if IROCs and kFALSE if OROCs
	227
	228	if(chamber>=0 && chamber<36) return kTRUE;
	229
	230	return kFALSE;
	231	}
	232
	233	//_____________________________________________________________________
	234	Bool_t AliTPCCalibKr::IsCSide(Int_t chamber)
	235	{
	236	// check if C side
	237	// returns kTRUE if C side and kFALSE if A side
	238
	239	if((chamber>=18 && chamber<36) \|\| (chamber>=54 && chamber<72)) return kTRUE;
	240
	241	return kFALSE;
	242	}
	243
	244	//_____________________________________________________________________
	245	Bool_t AliTPCCalibKr::Update(AliTPCclusterKr *cl)
	246	{
	247	//
	248	// fill existing histograms
	249	//
72e010d3	250
045a55c4	251	if (!Accept(cl)) return kFALSE;
	252	TH3F h = (TH3F)fHistoKrArray.At(cl->GetSec());
	253	if(!h) return kFALSE;
	254
	255	h->Fill(cl->GetMax().GetRow(),cl->GetMax().GetPad(),cl->GetADCcluster());
	256
	257	return kTRUE;
	258	}
	259
afb50fd6	260	//_____________________________________________________________________
045a55c4	261	Bool_t AliTPCCalibKr::Accept(AliTPCclusterKr *cl){
	262	//
	263	// cuts
	264	//
	265	/*
	266	TCut cutR0("cutR0","fADCcluster/fSize<200"); // adjust it according v seetings -
	267	TCut cutR1("cutR1","fADCcluster/fSize>7"); // cosmic tracks and noise removal
	268	TCut cutR2("cutR2","fMax.fAdc/fADCcluster<0.4"); // digital noise removal
	269	TCut cutR3("cutR3","fMax.fAdc/fADCcluster>0.01"); // noise removal
	270	TCut cutS1("cutS1","fSize<200"); // adjust it according v seetings - cosmic tracks
	271	TCut cutAll = cutR0+cutR1+cutR2+cutR3+cutS1;
	272	*/
	273	//R0
f3b61a78	274	if ((float)cl->GetADCcluster()/ cl->GetSize() >200) return kFALSE;
045a55c4	275	// R1
f3b61a78	276	if ((float)cl->GetADCcluster()/ cl->GetSize() <7) return kFALSE;
045a55c4	277	//R2
f3b61a78	278	if ((float)cl->GetMax().GetAdc()/ cl->GetADCcluster() >0.4) return kFALSE;
045a55c4	279	//R3
f3b61a78	280	if ((float)cl->GetMax().GetAdc()/ cl->GetADCcluster() <0.01) return kFALSE;
045a55c4	281	//S1
	282	if (cl->GetSize()>200) return kFALSE;
	283	if (cl->GetSize()<6) return kFALSE;
	284	return kTRUE;
72e010d3	285
72e010d3	286	}
	287
	288	//_____________________________________________________________________
	289	TH3F* AliTPCCalibKr::GetHistoKr(Int_t chamber) const
	290	{
	291	// get histograms from fHistoKrArray
	292	return (TH3F*) fHistoKrArray.At(chamber);
	293	}
72e010d3	294
	295	//_____________________________________________________________________
	296	void AliTPCCalibKr::Analyse()
	297	{
	298	//
	299	// analyse the histograms and extract krypton calibration parameters
	300	//
	301
	302	// AliTPCCalPads that will contain the calibration parameters
	303	AliTPCCalPad* spectrMeanCalPad = new AliTPCCalPad("spectrMean", "spectrMean");
	304	AliTPCCalPad* spectrRMSCalPad = new AliTPCCalPad("spectrRMS", "spectrRMS");
	305	AliTPCCalPad* fitMeanCalPad = new AliTPCCalPad("fitMean", "fitMean");
	306	AliTPCCalPad* fitRMSCalPad = new AliTPCCalPad("fitRMS", "fitRMS");
	307	AliTPCCalPad* fitNormChi2CalPad = new AliTPCCalPad("fitNormChi2", "fitNormChi2");
	308	AliTPCCalPad* entriesCalPad = new AliTPCCalPad("entries", "entries");
	309
	310	// file stream for debugging purposes
	311	TTreeSRedirector* debugStream = new TTreeSRedirector("debugCalibKr.root");
	312
	313	// if entries in spectrum less than minEntries, then the fit won't be performed
	314	Int_t minEntries = 1; //300;
	315
	316	Double_t windowFrac = 0.12;
	317	// the 3d histogram will be projected on the pads given by the following window size
	318	// set the numbers to 0 if you want to do a pad-by-pad calibration
f3b61a78	319	UInt_t rowRadius = 2;
	320	UInt_t padRadius = 4;
	321
72e010d3	322	// the step size by which pad and row are incremented is given by the following numbers
	323	// set them to 1 if you want the finest granularity
	324	UInt_t rowStep = 1; // formerly: 2*rowRadius
	325	UInt_t padStep = 1; // formerly: 2*padRadius
	326
	327	for (Int_t chamber = 0; chamber < 72; chamber++) {
	328	//if (chamber != 71) continue;
	329	AliTPCCalROC roc(chamber); // I need this only for GetNrows() and GetNPads()
	330
	331	// Usually I would traverse each pad, take the spectrum for its neighbourhood and
	332	// obtain the calibration parameters. This takes very long, so instead I assign the same
	333	// calibration values to the whole neighbourhood and then go on to the next neighbourhood.
	334	UInt_t nRows = roc.GetNrows();
	335	for (UInt_t iRow = 0; iRow < nRows; iRow += rowStep) {
	336	UInt_t nPads = roc.GetNPads(iRow);
	337	//if (iRow >= 10) break;
	338	for (UInt_t iPad = 0; iPad < nPads; iPad += padStep) {
	339	//if (iPad >= 20) break;
	340	TH3F* h = GetHistoKr(chamber);
	341	if (!h) continue;
	342
	343	// the 3d histogram will be projected on the pads given by the following bounds
	344	// for rows and pads
	345	Int_t rowLow = iRow - rowRadius;
	346	UInt_t rowUp = iRow + rowRadius;
	347	Int_t padLow = iPad - padRadius;
	348	UInt_t padUp = iPad + padRadius;
	349	// if window goes out of chamber
	350	if (rowLow < 0) rowLow = 0;
	351	if (rowUp >= nRows) rowUp = nRows - 1;
	352	if (padLow < 0) padLow = 0;
	353	if (padUp >= nPads) padUp = nPads - 1;
	354
	355	// project the histogram
	356	//TH1D* projH = h->ProjectionZ("projH", rowLow, rowUp, padLow, padUp); // SLOW
	357	TH1D* projH = ProjectHisto(h, "projH", rowLow, rowUp, padLow, padUp);
	358
	359	// get the number of entries in the spectrum
	360	Double_t entries = projH->GetEntries();
	361	if (entries < minEntries) { delete projH; continue; }
	362
	363	// get the two calibration parameters mean of spectrum and RMS of spectrum
	364	Double_t histMean = projH->GetMean();
	365	Double_t histRMS = (histMean != 0) ? projH->GetRMS() / histMean : 0.;
	366
	367	// find maximum in spectrum to define a range (given by windowFrac) for which a Gauss is fitted
	368	Double_t maxEntries = projH->GetBinCenter(projH->GetMaximumBin());
f3b61a78	369	Int_t minBin = projH->FindBin((1.-windowFrac) * maxEntries);
	370	Int_t maxBin = projH->FindBin((1.+windowFrac) * maxEntries);
	371	Double_t integCharge = projH->Integral(minBin,maxBin);
	372
72e010d3	373	Int_t fitResult = projH->Fit("gaus", "Q0", "", (1.-windowFrac) * maxEntries, (1.+windowFrac) * maxEntries);
f3b61a78	374
72e010d3	375	if (fitResult != 0) {
f3b61a78	376	Error("Analyse", "Error while fitting spectrum for chamber %i, rows %i - %i, pads %i - %i, integrated charge %f.", chamber, rowLow, rowUp, padLow, padUp, integCharge);
	377	//printf("[ch%i r%i, p%i] entries = %f, maxEntries = %f, %f\n", chamber, iRow, iPad, entries, maxEntries);
	378
72e010d3	379	delete projH;
	380	continue;
	381	}
	382
	383	// get the two calibration parameters mean of gauss fit and sigma of gauss fit
	384	TF1* gausFit = projH->GetFunction("gaus");
	385	Double_t fitMean = gausFit->GetParameter(1);
	386	Double_t fitRMS = gausFit->GetParameter(2);
	387	Int_t numberFitPoints = gausFit->GetNumberFitPoints();
	388	if (numberFitPoints == 0) continue;
	389	Double_t fitNormChi2 = gausFit->GetChisquare() / numberFitPoints;
	390	delete gausFit;
	391	delete projH;
	392	if (fitMean <= 0) continue;
afb50fd6	393	//printf("[ch%i r%i, p%i] entries = %f, maxEntries = %f, fitMean = %f, fitRMS = %f\n", chamber, iRow, iPad, entries, maxEntries, fitMean, fitRMS);
72e010d3	394
	395	// write the calibration parameters for each pad that the 3d histogram was projected onto
	396	// (with considering the step size) to the CalPads
	397	// rowStep (padStep) odd: round down s/2 and fill this # of rows (pads) in both directions
	398	// rowStep (padStep) even: fill s/2 rows (pads) in ascending direction, s/2-1 in descending direction
	399	for (Int_t r = iRow - (rowStep/2 - (rowStep+1)%2); r <= (Int_t)(iRow + rowStep/2); r++) {
	400	if (r < 0 \|\| r >= (Int_t)nRows) continue;
	401	UInt_t nPads = roc.GetNPads(r);
	402	for (Int_t p = iPad - (padStep/2 - (padStep+1)%2); p <= (Int_t)(iPad + padStep/2); p++) {
	403	if (p < 0 \|\| p >= (Int_t)nPads) continue;
	404	spectrMeanCalPad->GetCalROC(chamber)->SetValue(r, p, histMean);
	405	spectrRMSCalPad->GetCalROC(chamber)->SetValue(r, p, histRMS);
	406	fitMeanCalPad->GetCalROC(chamber)->SetValue(r, p, fitMean);
	407	fitRMSCalPad->GetCalROC(chamber)->SetValue(r, p, fitRMS);
	408	fitNormChi2CalPad->GetCalROC(chamber)->SetValue(r, p, fitNormChi2);
	409	entriesCalPad->GetCalROC(chamber)->SetValue(r, p, entries);
	410
	411	(*debugStream) << "calibKr" <<
	412	"sector=" << chamber << // chamber number
	413	"row=" << r << // row number
	414	"pad=" << p << // pad number
	415	"histMean=" << histMean << // mean of the spectrum
	416	"histRMS=" << histRMS << // RMS of the spectrum divided by the mean
	417	"fitMean=" << fitMean << // Gauss fitted mean of the 41.6 keV Kr peak
	418	"fitRMS=" << fitRMS << // Gauss fitted sigma of the 41.6 keV Kr peak
	419	"fitNormChi2" << fitNormChi2 << // normalized chi square of the Gauss fit
	420	"entries=" << entries << // number of entries for the spectrum
	421	"\n";
	422	}
	423	}
	424	}
	425	}
	426	}
	427
	428	TFile f("calibKr.root", "recreate");
	429	spectrMeanCalPad->Write();
	430	spectrRMSCalPad->Write();
	431	fitMeanCalPad->Write();
	432	fitRMSCalPad->Write();
	433	fitNormChi2CalPad->Write();
	434	entriesCalPad->Write();
	435	f.Close();
	436	delete spectrMeanCalPad;
	437	delete spectrRMSCalPad;
	438	delete fitMeanCalPad;
	439	delete fitRMSCalPad;
	440	delete fitNormChi2CalPad;
	441	delete entriesCalPad;
	442	delete debugStream;
	443	}
	444
	445	//_____________________________________________________________________
	446	TH1D* AliTPCCalibKr::ProjectHisto(TH3F* histo3D, const char* name, Int_t xMin, Int_t xMax, Int_t yMin, Int_t yMax)
	447	{
	448	// project the z-axis of a 3d histo to a specific range of the x- and y-axes,
	449	// replaces TH3F::ProjectZ() to gain more speed
	450
	451	TAxis* xAxis = histo3D->GetXaxis();
	452	TAxis* yAxis = histo3D->GetYaxis();
	453	TAxis* zAxis = histo3D->GetZaxis();
	454	Double_t zMinVal = zAxis->GetXmin();
	455	Double_t zMaxVal = zAxis->GetXmax();
	456
	457	Int_t nBinsZ = zAxis->GetNbins();
458	TH1D* projH = new TH1D(name, name, nBinsZ, zMinVal, zMaxVal);
459
460	Int_t nx = xAxis->GetNbins()+2;
461	Int_t ny = yAxis->GetNbins()+2;
462	Int_t bin = 0;
463	Double_t entries = 0.;
464	for (Int_t x = xMin; x <= xMax; x++) {
465	for (Int_t y = yMin; y <= yMax; y++) {
466	for (Int_t z = 0; z <= nBinsZ+1; z++) {
467	bin = x + nx * (y + ny * z);
468	Double_t val = histo3D->GetBinContent(bin);
469	projH->Fill(zAxis->GetBinCenter(z), val);
470	entries += val;
471	}
472	}
473	}
474	projH->SetEntries((Long64_t)entries);
475	return projH;
476	}
afb50fd6	477
	478	//_____________________________________________________________________
	479	Long64_t AliTPCCalibKr::Merge(TCollection* list) {
	480	// merge function
	481	//
	482	cout << "Merge " << endl;
	483
	484	if (!list)
	485	return 0;
	486
	487	if (list->IsEmpty())
	488	return 1;
	489
	490	TIterator* iter = list->MakeIterator();
	491	TObject* obj = 0;
	492
	493	iter->Reset();
	494	Int_t count=0;
	495	while((obj = iter->Next()) != 0)
	496	{
	497	AliTPCCalibKr* entry = dynamic_cast<AliTPCCalibKr*>(obj);
	498	if (entry == 0) continue;
	499
	500	for(int i=0; i<72; ++i) {
	501	if(IsCSide(i) == kTRUE && bCSide == kTRUE) {
	502	((TH3F)fHistoKrArray.At(i))->Add( ((TH3F)entry->fHistoKrArray.At(i)) );
	503	}
	504
	505	if(IsCSide(i) == kFALSE && bASide == kTRUE) {
	506	((TH3F)fHistoKrArray.At(i))->Add( ((TH3F)entry->fHistoKrArray.At(i)) );
	507	}
	508	}
	509
	510	count++;
	511	}
	512
	513	return count;
	514	}