[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 fills the array of TH3F histograms (TPC_max_padraw,TPC_max_pad,TPC_ADC_cluster),
// its data memebers.   
// 
// As the input it requires the tree with reconstructed Kr clusters (AliTPCclusterKr objects). 
// The AliTPCCalibKr objects containing an array of TH3F histograms are stored (by default) in the 
// ouptut (outHistFile.root) file.
//
// 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. Create outHistFile.root histogram file:
//
// -- Load libXrdClient.so if data on Xrd cluster e.g. (GSI)
// gSystem->Load("/usr/local/grid/XRootd/GSI/lib64/libXrdClient.so");
//
// -- Load toolkit
// gSystem->AddIncludePath("-I$ALICE_ROOT/TPC/macros");
// gROOT->LoadMacro("$ALICE_ROOT/TPC/macros/AliXRDPROOFtoolkit.cxx+");
// AliXRDPROOFtoolkit tool;
//
// -- Make chain of files
// TChain * chain = tool.MakeChain("KrClusters.txt","Kr","",1000,0);
//
// -- Run AliTPCCalibKr task (Only TPC C side)
// AliTPCCalibKr *task = new AliTPCCalibKr;
// task->SetInputChain(chain);
// task->SetASide(kFALSE);
//
// task->Process();
// 
// 2. Analyse output histograms:
//
// TFile f("outHistFile.root");
// AliTPCCalibKr.Analyse();
//
// 3. See calibration parameters e.g.:
//
// TFile f("calibKr.root");
// spectrMean->GetCalROC(70)->GetValue(40,40);
// fitMean->GetCalROC(70)->GetValue(40,40);
//
// 4. 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(),
  
  bOutputHisto(kTRUE),
  bASide(kTRUE),
  bCSide(kTRUE),
  fClusters(0),
  fClustKr(0),
  fTree(0),
  fHistoKrArray(72)
{
  //
  // default constructor
  //
}

//_____________________________________________________________________
AliTPCCalibKr::AliTPCCalibKr(const AliTPCCalibKr& pad) : 
  TObject(pad),
  
  bOutputHisto(pad.bOutputHisto),
  bASide(pad.bASide),
  bCSide(pad.bCSide),
  fClusters(pad.fClusters),
  fClustKr(pad.fClustKr),
  fTree(pad.fTree),
  fHistoKrArray(72)
{
  // copy constructor
 
  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
  //
  if(fClustKr)  delete fClustKr; fClustKr = 0;
  if(fClusters) delete fClusters; fClusters = 0;
  if(fTree)     delete fTree; fTree = 0;
  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 input tree and output histograms 
  //

  // set input tree
  if(!fTree) { 
   Printf("ERROR: Could not read chain from input");
  }
  else {
   fTree->SetBranchStatus("*",1); 
  }

  // set branch address
  fClusters = new TClonesArray("AliTPCclusterKr");

  if(!fTree->GetBranch("fClusters")) {
    Printf("ERROR: Could not get fClusters branch from input");
  } else {
   fTree->GetBranch("fClusters")->SetAddress(&fClusters);
  }
  
  // create output TObjArray
  fHistoKrArray.Clear();

  // 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::ReadEntry(Int_t evt)
{
  // 
  // read entry from the tree
  //
  Long64_t centry = fTree->LoadTree(evt);
  if(centry < 0) return kFALSE;

  if(!fTree->GetBranch("fClusters")) 
  {
    Printf("ERROR: Could not get fClusters branch from input");
	return kFALSE;
  } else {
   fTree->GetBranch("fClusters")->SetAddress(&fClusters);
  }

  fTree->GetEntry(evt);

return kTRUE;
}
 
//_____________________________________________________________________
Bool_t AliTPCCalibKr::Process()
{
  //
  // process events 
  // call event by event
  //

  // init tree
  Init();

  // get events
  if(!fTree) return kFALSE;
  Int_t nEvents = fTree->GetEntries();

  // fill histograms 
  for(Int_t i=0; i<nEvents; ++i)
  {
    if(ReadEntry(i) == kFALSE) return kFALSE;

    if(!(i%10000)) cout << "evt: " << i << endl; 

    // get TClonesArray entries
    fClustKr = 0;
    Int_t entries = fClusters->GetEntries();
    for(Int_t j=0; j < entries; ++j)
	{
	  fClustKr = (AliTPCclusterKr*)fClusters->At(j);

      if(fClustKr) Update(fClustKr);
	  else return kFALSE;
	}
  }

  // write output 
  return Terminate();
}

//_____________________________________________________________________
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,63,0,63,100,0,100,150,100,3000);
	} else {
	   h = new TH3F(name,name,96,0,96,100,0,100,150,100,3000);
	}
    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 (cl->GetADCcluster()/ cl->GetSize() >200)        return kFALSE;
  // R1
  if (cl->GetADCcluster()/ cl->GetSize() <7)          return kFALSE;
  //R2
  if (cl->GetMax().GetAdc()/ cl->GetADCcluster() >0.4)  return kFALSE;
  //R3
  if (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);
}

//_____________________________________________________________________
Bool_t AliTPCCalibKr::Terminate() 
{
  //
  // store AliTPCCalibKr in the output file 
  //
  if(bOutputHisto) {
    TFile *outFile = new TFile("outHistFile.root","RECREATE"); 
   
    if(outFile) 
	{
	  outFile->cd();

	  for(int i=0; i<72; ++i) {
	     if( IsCSide(i) == kTRUE && bCSide == kTRUE)
	       printf("C side chamber: %d, 3D histo entries: %10.f \n",i,((TH3F*)fHistoKrArray.At(i))->GetEntries());

	     if( IsCSide(i) == kFALSE && bASide == kTRUE)
	       printf("A side chamber: %d, 3D histo entries: %10.f \n",i,((TH3F*)fHistoKrArray.At(i))->GetEntries());
	  }
	  this->Write();
	  outFile->Close();

	  return kTRUE;
	}
	else 
	  return kFALSE;
  }

return kFALSE;
}
 
//_____________________________________________________________________
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 = 5;
  UInt_t padRadius = 10;
  // 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 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.", chamber, rowLow, rowUp, padLow, padUp);
          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;
}
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	//
	51	// The AliTPCCalibKr fills the array of TH3F histograms (TPC_max_padraw,TPC_max_pad,TPC_ADC_cluster),
	52	// its data memebers.
	53	//
	54	// As the input it requires the tree with reconstructed Kr clusters (AliTPCclusterKr objects).
	55	// The AliTPCCalibKr objects containing an array of TH3F histograms are stored (by default) in the
	56	// ouptut (outHistFile.root) file.
	57	//
	58	// The ouput TH3F histograms are later used to determine the calibration parameters of TPC chambers.
	59	// These calculations are done by using AliTPCCalibKr::Analyse() function. The ouput calibration
	60	// parameters (details in AliTPCCalibKr::Analyse()) are stored in the calibKr.root file for each TPC pad.
	61	// In addition the debugCalibKr.root file with debug information is created.
	62	//
	63	// Usage example:
	64	//
65	// 1. Create outHistFile.root histogram file:
66	//
67	// -- Load libXrdClient.so if data on Xrd cluster e.g. (GSI)
68	// gSystem->Load("/usr/local/grid/XRootd/GSI/lib64/libXrdClient.so");
69	//
70	// -- Load toolkit
71	// gSystem->AddIncludePath("-I$ALICE_ROOT/TPC/macros");
72	// gROOT->LoadMacro("$ALICE_ROOT/TPC/macros/AliXRDPROOFtoolkit.cxx+");
73	// AliXRDPROOFtoolkit tool;
74	//
75	// -- Make chain of files
76	// TChain * chain = tool.MakeChain("KrClusters.txt","Kr","",1000,0);
77	//
78	// -- Run AliTPCCalibKr task (Only TPC C side)
79	// AliTPCCalibKr *task = new AliTPCCalibKr;
80	// task->SetInputChain(chain);
81	// task->SetASide(kFALSE);
82	//
83	// task->Process();
84	//
85	// 2. Analyse output histograms:
86	//
87	// TFile f("outHistFile.root");
88	// AliTPCCalibKr.Analyse();
89	//
90	// 3. See calibration parameters e.g.:
91	//
92	// TFile f("calibKr.root");
93	// spectrMean->GetCalROC(70)->GetValue(40,40);
94	// fitMean->GetCalROC(70)->GetValue(40,40);
95	//
96	// 4. See debug information e.g.:
97	//
98	// TFile f("debugCalibKr.root");
99	// .ls;
100	//
101	// -- Print calibKr TTree content
102	// calibKr->Print();
103	//
104	// -- Draw calibKr TTree variables
105	// calibKr.Draw("fitMean");
106	//
107	//
108	// Author: Jacek Otwinowski (J.Otwinowski@gsi.de) and Stafan Geartner (S.Gaertner@gsi.de)
109	//-----------------------------------------------------------------------------
110
111	ClassImp(AliTPCCalibKr)
112
113	AliTPCCalibKr::AliTPCCalibKr() :
114	TObject(),
115
116	bOutputHisto(kTRUE),
117	bASide(kTRUE),
118	bCSide(kTRUE),
119	fClusters(0),
120	fClustKr(0),
121	fTree(0),
122	fHistoKrArray(72)
123	{
124	//
125	// default constructor
126	//
127	}
128
129	//_____________________________________________________________________
130	AliTPCCalibKr::AliTPCCalibKr(const AliTPCCalibKr& pad) :
131	TObject(pad),
132
133	bOutputHisto(pad.bOutputHisto),
134	bASide(pad.bASide),
135	bCSide(pad.bCSide),
136	fClusters(pad.fClusters),
137	fClustKr(pad.fClustKr),
138	fTree(pad.fTree),
139	fHistoKrArray(72)
140	{
141	// copy constructor
142
143	for (Int_t iSec = 0; iSec < 72; ++iSec)
144	{
145	TH3F *hOld = pad.GetHistoKr(iSec);
146	if(hOld) {
147	TH3F hNew = new TH3F( pad.GetHistoKr(iSec) );
148	fHistoKrArray.AddAt(hNew,iSec);
149	}
150	}
151	}
152
153	//_____________________________________________________________________
154	AliTPCCalibKr::~AliTPCCalibKr()
155	{
156	//
157	// destructor
158	//
159	if(fClustKr) delete fClustKr; fClustKr = 0;
160	if(fClusters) delete fClusters; fClusters = 0;
161	if(fTree) delete fTree; fTree = 0;
162	fHistoKrArray.Delete();
163	}
164
165	//_____________________________________________________________________
166	AliTPCCalibKr& AliTPCCalibKr::operator = (const AliTPCCalibKr &source)
167	{
168	// assignment operator
169
170	if (&source == this) return *this;
171	new (this) AliTPCCalibKr(source);
172
173	return *this;
174	}
175
176	//_____________________________________________________________________
177	void AliTPCCalibKr::Init()
178	{
179	//
180	// init input tree and output histograms
181	//
182
183	// set input tree
184	if(!fTree) {
185	Printf("ERROR: Could not read chain from input");
186	}
187	else {
188	fTree->SetBranchStatus("*",1);
189	}
190
191	// set branch address
192	fClusters = new TClonesArray("AliTPCclusterKr");
193
194	if(!fTree->GetBranch("fClusters")) {
195	Printf("ERROR: Could not get fClusters branch from input");
196	} else {
197	fTree->GetBranch("fClusters")->SetAddress(&fClusters);
198	}
199
200	// create output TObjArray
201	fHistoKrArray.Clear();
202
203	// add histograms to the TObjArray
204	for(Int_t i=0; i<72; ++i) {
205
206	// C - side
207	if( IsCSide(i) == kTRUE && bCSide == kTRUE) {
208	TH3F *hist = CreateHisto(i);
209	if(hist) fHistoKrArray.AddAt(hist,i);
210	}
211
212	// A - side
213	if(IsCSide(i) == kFALSE && bASide == kTRUE) {
214	TH3F *hist = CreateHisto(i);
215	if(hist) fHistoKrArray.AddAt(hist,i);
216	}
217
218	}
219	}
220
221	//_____________________________________________________________________
222	Bool_t AliTPCCalibKr::ReadEntry(Int_t evt)
223	{
224	//
225	// read entry from the tree
226	//
227	Long64_t centry = fTree->LoadTree(evt);
228	if(centry < 0) return kFALSE;
229
230	if(!fTree->GetBranch("fClusters"))
231	{
232	Printf("ERROR: Could not get fClusters branch from input");
233	return kFALSE;
234	} else {
235	fTree->GetBranch("fClusters")->SetAddress(&fClusters);
236	}
237
238	fTree->GetEntry(evt);
239
240	return kTRUE;
241	}
242
243	//_____________________________________________________________________
244	Bool_t AliTPCCalibKr::Process()
245	{
246	//
247	// process events
248	// call event by event
249	//
250
251	// init tree
252	Init();
253
254	// get events
255	if(!fTree) return kFALSE;
256	Int_t nEvents = fTree->GetEntries();
257
258	// fill histograms
259	for(Int_t i=0; i<nEvents; ++i)
260	{
261	if(ReadEntry(i) == kFALSE) return kFALSE;
262
263	if(!(i%10000)) cout << "evt: " << i << endl;
264
265	// get TClonesArray entries
266	fClustKr = 0;
267	Int_t entries = fClusters->GetEntries();
268	for(Int_t j=0; j < entries; ++j)
269	{
270	fClustKr = (AliTPCclusterKr*)fClusters->At(j);
271
272	if(fClustKr) Update(fClustKr);
273	else return kFALSE;
274	}
275	}
276
277	// write output
278	return Terminate();
279	}
280
281	//_____________________________________________________________________
282	TH3F* AliTPCCalibKr::CreateHisto(Int_t chamber)
283	{
284	//
285	// create new histogram
286	//
287	char name[256];
288	TH3F *h;
289
290	sprintf(name,"ADCcluster_ch%d",chamber);
291
292	if( IsIROC(chamber) == kTRUE )
293	{
294	h = new TH3F(name,name,63,0,63,100,0,100,150,100,3000);
295	} else {
296	h = new TH3F(name,name,96,0,96,100,0,100,150,100,3000);
297	}
298	h->SetXTitle("padrow");
299	h->SetYTitle("pad");
300	h->SetZTitle("fADC");
301
302	return h;
303	}
304
305	//_____________________________________________________________________
306	Bool_t AliTPCCalibKr::IsIROC(Int_t chamber)
307	{
308	// check if IROCs
309	// returns kTRUE if IROCs and kFALSE if OROCs
310
311	if(chamber>=0 && chamber<36) return kTRUE;
312
313	return kFALSE;
314	}
315
316	//_____________________________________________________________________
317	Bool_t AliTPCCalibKr::IsCSide(Int_t chamber)
318	{
319	// check if C side
320	// returns kTRUE if C side and kFALSE if A side
321
322	if((chamber>=18 && chamber<36) \|\| (chamber>=54 && chamber<72)) return kTRUE;
323
324	return kFALSE;
325	}
326
327	//_____________________________________________________________________
328	Bool_t AliTPCCalibKr::Update(AliTPCclusterKr *cl)
329	{
330	//
331	// fill existing histograms
332	//
72e010d3	333
045a55c4	334	if (!Accept(cl)) return kFALSE;
	335	TH3F h = (TH3F)fHistoKrArray.At(cl->GetSec());
	336	if(!h) return kFALSE;
	337
	338	h->Fill(cl->GetMax().GetRow(),cl->GetMax().GetPad(),cl->GetADCcluster());
	339
	340	return kTRUE;
	341	}
	342
	343	Bool_t AliTPCCalibKr::Accept(AliTPCclusterKr *cl){
	344	//
	345	// cuts
	346	//
	347	/*
	348	TCut cutR0("cutR0","fADCcluster/fSize<200"); // adjust it according v seetings -
	349	TCut cutR1("cutR1","fADCcluster/fSize>7"); // cosmic tracks and noise removal
	350	TCut cutR2("cutR2","fMax.fAdc/fADCcluster<0.4"); // digital noise removal
	351	TCut cutR3("cutR3","fMax.fAdc/fADCcluster>0.01"); // noise removal
	352	TCut cutS1("cutS1","fSize<200"); // adjust it according v seetings - cosmic tracks
	353	TCut cutAll = cutR0+cutR1+cutR2+cutR3+cutS1;
	354	*/
	355	//R0
	356	if (cl->GetADCcluster()/ cl->GetSize() >200) return kFALSE;
	357	// R1
	358	if (cl->GetADCcluster()/ cl->GetSize() <7) return kFALSE;
	359	//R2
	360	if (cl->GetMax().GetAdc()/ cl->GetADCcluster() >0.4) return kFALSE;
	361	//R3
	362	if (cl->GetMax().GetAdc()/ cl->GetADCcluster() <0.01) return kFALSE;
	363	//S1
	364	if (cl->GetSize()>200) return kFALSE;
	365	if (cl->GetSize()<6) return kFALSE;
	366	return kTRUE;
72e010d3	367
72e010d3	368	}
72e010d3	369
045a55c4	370
045a55c4	371
72e010d3	372	//_____________________________________________________________________
	373	TH3F* AliTPCCalibKr::GetHistoKr(Int_t chamber) const
	374	{
	375	// get histograms from fHistoKrArray
	376	return (TH3F*) fHistoKrArray.At(chamber);
	377	}
	378
	379	//_____________________________________________________________________
	380	Bool_t AliTPCCalibKr::Terminate()
	381	{
	382	//
	383	// store AliTPCCalibKr in the output file
	384	//
	385	if(bOutputHisto) {
	386	TFile *outFile = new TFile("outHistFile.root","RECREATE");
	387
	388	if(outFile)
	389	{
	390	outFile->cd();
	391
	392	for(int i=0; i<72; ++i) {
	393	if( IsCSide(i) == kTRUE && bCSide == kTRUE)
	394	printf("C side chamber: %d, 3D histo entries: %10.f \n",i,((TH3F*)fHistoKrArray.At(i))->GetEntries());
	395
	396	if( IsCSide(i) == kFALSE && bASide == kTRUE)
	397	printf("A side chamber: %d, 3D histo entries: %10.f \n",i,((TH3F*)fHistoKrArray.At(i))->GetEntries());
	398	}
	399	this->Write();
	400	outFile->Close();
	401
	402	return kTRUE;
	403	}
	404	else
	405	return kFALSE;
	406	}
	407
	408	return kFALSE;
	409	}
	410
	411	//_____________________________________________________________________
	412	void AliTPCCalibKr::Analyse()
	413	{
	414	//
	415	// analyse the histograms and extract krypton calibration parameters
	416	//
	417
	418	// AliTPCCalPads that will contain the calibration parameters
	419	AliTPCCalPad* spectrMeanCalPad = new AliTPCCalPad("spectrMean", "spectrMean");
	420	AliTPCCalPad* spectrRMSCalPad = new AliTPCCalPad("spectrRMS", "spectrRMS");
	421	AliTPCCalPad* fitMeanCalPad = new AliTPCCalPad("fitMean", "fitMean");
	422	AliTPCCalPad* fitRMSCalPad = new AliTPCCalPad("fitRMS", "fitRMS");
	423	AliTPCCalPad* fitNormChi2CalPad = new AliTPCCalPad("fitNormChi2", "fitNormChi2");
	424	AliTPCCalPad* entriesCalPad = new AliTPCCalPad("entries", "entries");
	425
	426	// file stream for debugging purposes
	427	TTreeSRedirector* debugStream = new TTreeSRedirector("debugCalibKr.root");
	428
	429	// if entries in spectrum less than minEntries, then the fit won't be performed
	430	Int_t minEntries = 1; //300;
	431
	432	Double_t windowFrac = 0.12;
	433	// the 3d histogram will be projected on the pads given by the following window size
	434	// set the numbers to 0 if you want to do a pad-by-pad calibration
	435	UInt_t rowRadius = 5;
436	UInt_t padRadius = 10;
437	// the step size by which pad and row are incremented is given by the following numbers
438	// set them to 1 if you want the finest granularity
439	UInt_t rowStep = 1; // formerly: 2*rowRadius
440	UInt_t padStep = 1; // formerly: 2*padRadius
441
442	for (Int_t chamber = 0; chamber < 72; chamber++) {
443	//if (chamber != 71) continue;
444	AliTPCCalROC roc(chamber); // I need this only for GetNrows() and GetNPads()
445
446	// Usually I would traverse each pad, take the spectrum for its neighbourhood and
447	// obtain the calibration parameters. This takes very long, so instead I assign the same
448	// calibration values to the whole neighbourhood and then go on to the next neighbourhood.
449	UInt_t nRows = roc.GetNrows();
450	for (UInt_t iRow = 0; iRow < nRows; iRow += rowStep) {
451	UInt_t nPads = roc.GetNPads(iRow);
452	//if (iRow >= 10) break;
453	for (UInt_t iPad = 0; iPad < nPads; iPad += padStep) {
454	//if (iPad >= 20) break;
455	TH3F* h = GetHistoKr(chamber);
456	if (!h) continue;
457
458	// the 3d histogram will be projected on the pads given by the following bounds
459	// for rows and pads
460	Int_t rowLow = iRow - rowRadius;
461	UInt_t rowUp = iRow + rowRadius;
462	Int_t padLow = iPad - padRadius;
463	UInt_t padUp = iPad + padRadius;
464	// if window goes out of chamber
465	if (rowLow < 0) rowLow = 0;
466	if (rowUp >= nRows) rowUp = nRows - 1;
467	if (padLow < 0) padLow = 0;
468	if (padUp >= nPads) padUp = nPads - 1;
469
470	// project the histogram
471	//TH1D* projH = h->ProjectionZ("projH", rowLow, rowUp, padLow, padUp); // SLOW
472	TH1D* projH = ProjectHisto(h, "projH", rowLow, rowUp, padLow, padUp);
473
474	// get the number of entries in the spectrum
475	Double_t entries = projH->GetEntries();
476	if (entries < minEntries) { delete projH; continue; }
477
478	// get the two calibration parameters mean of spectrum and RMS of spectrum
479	Double_t histMean = projH->GetMean();
480	Double_t histRMS = (histMean != 0) ? projH->GetRMS() / histMean : 0.;
481
482	// find maximum in spectrum to define a range (given by windowFrac) for which a Gauss is fitted
483	Double_t maxEntries = projH->GetBinCenter(projH->GetMaximumBin());
484	Int_t fitResult = projH->Fit("gaus", "Q0", "", (1.-windowFrac) * maxEntries, (1.+windowFrac) * maxEntries);
485	if (fitResult != 0) {
486	Error("Analyse", "Error while fitting spectrum for chamber %i, rows %i - %i, pads %i - %i.", chamber, rowLow, rowUp, padLow, padUp);
487	delete projH;
488	continue;
489	}
490
491	// get the two calibration parameters mean of gauss fit and sigma of gauss fit
492	TF1* gausFit = projH->GetFunction("gaus");
493	Double_t fitMean = gausFit->GetParameter(1);
494	Double_t fitRMS = gausFit->GetParameter(2);
495	Int_t numberFitPoints = gausFit->GetNumberFitPoints();
496	if (numberFitPoints == 0) continue;
497	Double_t fitNormChi2 = gausFit->GetChisquare() / numberFitPoints;
498	delete gausFit;
499	delete projH;
500	if (fitMean <= 0) continue;
501	printf("[ch%i r%i, p%i] entries = %f, maxEntries = %f, fitMean = %f, fitRMS = %f\n", chamber, iRow, iPad, entries, maxEntries, fitMean, fitRMS);
502
503	// write the calibration parameters for each pad that the 3d histogram was projected onto
504	// (with considering the step size) to the CalPads
505	// rowStep (padStep) odd: round down s/2 and fill this # of rows (pads) in both directions
506	// rowStep (padStep) even: fill s/2 rows (pads) in ascending direction, s/2-1 in descending direction
507	for (Int_t r = iRow - (rowStep/2 - (rowStep+1)%2); r <= (Int_t)(iRow + rowStep/2); r++) {
508	if (r < 0 \|\| r >= (Int_t)nRows) continue;
509	UInt_t nPads = roc.GetNPads(r);
510	for (Int_t p = iPad - (padStep/2 - (padStep+1)%2); p <= (Int_t)(iPad + padStep/2); p++) {
511	if (p < 0 \|\| p >= (Int_t)nPads) continue;
512	spectrMeanCalPad->GetCalROC(chamber)->SetValue(r, p, histMean);
513	spectrRMSCalPad->GetCalROC(chamber)->SetValue(r, p, histRMS);
514	fitMeanCalPad->GetCalROC(chamber)->SetValue(r, p, fitMean);
515	fitRMSCalPad->GetCalROC(chamber)->SetValue(r, p, fitRMS);
516	fitNormChi2CalPad->GetCalROC(chamber)->SetValue(r, p, fitNormChi2);
517	entriesCalPad->GetCalROC(chamber)->SetValue(r, p, entries);
518
519	(*debugStream) << "calibKr" <<
520	"sector=" << chamber << // chamber number
521	"row=" << r << // row number
522	"pad=" << p << // pad number
523	"histMean=" << histMean << // mean of the spectrum
524	"histRMS=" << histRMS << // RMS of the spectrum divided by the mean
525	"fitMean=" << fitMean << // Gauss fitted mean of the 41.6 keV Kr peak
526	"fitRMS=" << fitRMS << // Gauss fitted sigma of the 41.6 keV Kr peak
527	"fitNormChi2" << fitNormChi2 << // normalized chi square of the Gauss fit
528	"entries=" << entries << // number of entries for the spectrum
529	"\n";
530	}
531	}
532	}
533	}
534	}
535
536	TFile f("calibKr.root", "recreate");
537	spectrMeanCalPad->Write();
538	spectrRMSCalPad->Write();
539	fitMeanCalPad->Write();
540	fitRMSCalPad->Write();
541	fitNormChi2CalPad->Write();
542	entriesCalPad->Write();
543	f.Close();
544	delete spectrMeanCalPad;
545	delete spectrRMSCalPad;
546	delete fitMeanCalPad;
547	delete fitRMSCalPad;
548	delete fitNormChi2CalPad;
549	delete entriesCalPad;
550	delete debugStream;
551	}
552
553	//_____________________________________________________________________
554	TH1D* AliTPCCalibKr::ProjectHisto(TH3F* histo3D, const char* name, Int_t xMin, Int_t xMax, Int_t yMin, Int_t yMax)
555	{
556	// project the z-axis of a 3d histo to a specific range of the x- and y-axes,
557	// replaces TH3F::ProjectZ() to gain more speed
558
559	TAxis* xAxis = histo3D->GetXaxis();
560	TAxis* yAxis = histo3D->GetYaxis();
561	TAxis* zAxis = histo3D->GetZaxis();
562	Double_t zMinVal = zAxis->GetXmin();
563	Double_t zMaxVal = zAxis->GetXmax();
564
565	Int_t nBinsZ = zAxis->GetNbins();
566	TH1D* projH = new TH1D(name, name, nBinsZ, zMinVal, zMaxVal);
567
568	Int_t nx = xAxis->GetNbins()+2;
569	Int_t ny = yAxis->GetNbins()+2;
570	Int_t bin = 0;
571	Double_t entries = 0.;
572	for (Int_t x = xMin; x <= xMax; x++) {
573	for (Int_t y = yMin; y <= yMax; y++) {
574	for (Int_t z = 0; z <= nBinsZ+1; z++) {
575	bin = x + nx * (y + ny * z);
576	Double_t val = histo3D->GetBinContent(bin);
577	projH->Fill(zAxis->GetBinCenter(z), val);
578	entries += val;
579	}
580	}
581	}
582	projH->SetEntries((Long64_t)entries);
583	return projH;
584	}