[u/mrichter/AliRoot.git] / PHOS / AliPHOSReconstructor.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.                  *
 **************************************************************************/

/* $Id$ */

//_________________________________________________________________________
//*--
//*-- Yves Schutz (SUBATECH) 
// Reconstruction class. Redesigned from the old AliReconstructionner class and 
// derived from STEER/AliReconstructor. 
// 
// --- ROOT system ---

// --- Standard library ---

// --- AliRoot header files ---
#include "AliLog.h"
#include "AliESDEvent.h"
#include "AliESDCaloCluster.h"
#include "AliPHOSReconstructor.h"
#include "AliPHOSClusterizerv1.h"
#include "AliPHOSTrackSegmentMakerv1.h"
#include "AliPHOSPIDv1.h"
#include "AliPHOSTracker.h"
#include "AliRawReader.h"
#include "AliPHOSTrigger.h"
#include "AliPHOSGeometry.h"
#include "AliPHOSRecoParam.h"
#include "AliPHOSRecoParamEmc.h"
#include "AliPHOSRecoParamCpv.h"
#include "AliPHOSDigit.h"
#include "AliPHOSTrackSegment.h"
#include "AliPHOSEmcRecPoint.h"
#include "AliPHOSRecParticle.h"
#include "AliPHOSRawDecoder.h"
#include "AliPHOSRawDecoderv1.h"
#include "AliPHOSRawDigiProducer.h"
#include "AliPHOSPulseGenerator.h"

ClassImp(AliPHOSReconstructor)

Bool_t AliPHOSReconstructor::fgDebug = kFALSE ; 
AliPHOSRecoParam* AliPHOSReconstructor::fgkRecoParamEmc =0;  // EMC rec. parameters
AliPHOSRecoParam* AliPHOSReconstructor::fgkRecoParamCpv =0;  // CPV rec. parameters

//____________________________________________________________________________
AliPHOSReconstructor::AliPHOSReconstructor() :
  fGeom(NULL)
{
  // ctor

  if (!fgkRecoParamEmc) {
    AliWarning("The Reconstruction parameters for EMC nonitialized - Used default one");
    fgkRecoParamEmc = AliPHOSRecoParamEmc::GetEmcDefaultParameters();
  }

  if (!fgkRecoParamCpv) {
    AliWarning("The Reconstruction parameters for CPV nonitialized - Used default one");
    fgkRecoParamCpv = AliPHOSRecoParamCpv::GetCpvDefaultParameters();
  }

  fGeom = AliPHOSGeometry::GetInstance("IHEP","");
}

//____________________________________________________________________________
  AliPHOSReconstructor::~AliPHOSReconstructor()
{
  // dtor
  delete fGeom;
} 

//____________________________________________________________________________
void AliPHOSReconstructor::Reconstruct(TTree* digitsTree, TTree* clustersTree) const
{
  // 'single-event' local reco method called by AliReconstruction; 
  // Only the clusterization is performed,; the rest of the reconstruction is done in FillESD because the track
  // segment maker needs access to the AliESDEvent object to retrieve the tracks reconstructed by 
  // the global tracking.

  AliPHOSClusterizerv1 clu(fGeom);
  clu.SetInput(digitsTree);
  clu.SetOutput(clustersTree);
  if ( Debug() ) 
    clu.Digits2Clusters("deb all") ; 
  else 
    clu.Digits2Clusters("") ;
}

//____________________________________________________________________________
void AliPHOSReconstructor::FillESD(TTree* digitsTree, TTree* clustersTree, 
				   AliESDEvent* esd) const
{
  // This method produces PHOS rec-particles,
  // then it creates AliESDtracks out of them and
  // write tracks to the ESD

  AliPHOSTrackSegmentMaker *tsm = new AliPHOSTrackSegmentMakerv1(fGeom);
  AliPHOSPID               *pid = new AliPHOSPIDv1              (fGeom);

  // do current event; the loop over events is done by AliReconstruction::Run()
  tsm->SetESD(esd) ; 
  tsm->SetInput(clustersTree);
  if ( Debug() ) 
    tsm->Clusters2TrackSegments("deb all") ;
  else 
    tsm->Clusters2TrackSegments("") ;
  
  pid->SetInput(clustersTree, tsm->GetTrackSegments()) ; 
  pid->SetESD(esd) ; 
  if ( Debug() ) 
    pid->TrackSegments2RecParticles("deb all") ;
  else 
    pid->TrackSegments2RecParticles("") ;


  // This function creates AliESDtracks from AliPHOSRecParticles
  //         and
  // writes them to the ESD

  TClonesArray *recParticles  = pid->GetRecParticles();
  Int_t nOfRecParticles = recParticles->GetEntries();
  
  esd->SetNumberOfPHOSClusters(nOfRecParticles) ; 
  esd->SetFirstPHOSCluster(esd->GetNumberOfCaloClusters()) ;

  AliDebug(2,Form("%d rec. particles, option %s",nOfRecParticles,GetOption()));

  //#########Calculate trigger and set trigger info###########
 
  AliPHOSTrigger tr ;
  //   tr.SetPatchSize(1);//create 4x4 patches
  tr.Trigger();
  
  Float_t maxAmp2x2  = tr.Get2x2MaxAmplitude();
  Float_t maxAmpnxn  = tr.GetnxnMaxAmplitude();
  Float_t ampOutOfPatch2x2  = tr.Get2x2AmpOutOfPatch() ;
  Float_t ampOutOfPatchnxn  = tr.GetnxnAmpOutOfPatch() ;

  Int_t iSM2x2      = tr.Get2x2SuperModule();
  Int_t iSMnxn      = tr.GetnxnSuperModule();
  Int_t iCrystalPhi2x2 = tr.Get2x2CrystalPhi();
  Int_t iCrystalPhinxn = tr.GetnxnCrystalPhi();
  Int_t iCrystalEta2x2 = tr.Get2x2CrystalEta();
  Int_t iCrystalEtanxn = tr.GetnxnCrystalEta();

  AliDebug(2, Form("Trigger 2x2 max amp %f, out amp %f, SM %d, iphi %d ieta %d",  maxAmp2x2, ampOutOfPatch2x2, iSM2x2,iCrystalPhi2x2, iCrystalEta2x2));
  AliDebug(2, Form("Trigger 4x4 max amp %f , out amp %f, SM %d, iphi %d, ieta %d",  maxAmpnxn, ampOutOfPatchnxn, iSMnxn,iCrystalPhinxn, iCrystalEtanxn));

  Int_t iRelId2x2 []= {iSM2x2+1,0,iCrystalPhi2x2,iCrystalEta2x2};// PHOS modules in order to calculate AbsId need to be 1-5 not 0-4 as returns trigger.
  Int_t iAbsId2x2 =-1;
  Int_t iRelIdnxn []= {iSMnxn+1,0,iCrystalPhinxn,iCrystalEtanxn};// PHOS modules in order to calculate AbsId need to be 1-5 not 0-4 as returns trigger.
  Int_t iAbsIdnxn =-1;
  TVector3    pos2x2(-1,-1,-1);
  TVector3    posnxn(-1,-1,-1);
  fGeom->RelToAbsNumbering(iRelId2x2, iAbsId2x2);
  fGeom->RelToAbsNumbering(iRelIdnxn, iAbsIdnxn);
  fGeom->RelPosInAlice(iAbsId2x2, pos2x2);
  fGeom->RelPosInAlice(iAbsIdnxn, posnxn);

  TArrayF triggerPosition(6);
  triggerPosition[0] = pos2x2(0) ;   
  triggerPosition[1] = pos2x2(1) ;   
  triggerPosition[2] = pos2x2(2) ;  
  triggerPosition[3] = posnxn(0) ;   
  triggerPosition[4] = posnxn(1) ;   
  triggerPosition[5] = posnxn(2) ;  

  TArrayF triggerAmplitudes(4);
  triggerAmplitudes[0] = maxAmp2x2 ;   
  triggerAmplitudes[1] = ampOutOfPatch2x2 ;    
  triggerAmplitudes[2] = maxAmpnxn ;   
  triggerAmplitudes[3] = ampOutOfPatchnxn ;   

  //esd->SetPHOSTriggerCells(triggerPosition);
  esd->AddPHOSTriggerPosition(triggerPosition);
  esd->AddPHOSTriggerAmplitudes(triggerAmplitudes);
  
  //######################################
  
  // Read digits array
  TBranch *branch = digitsTree->GetBranch("PHOS");
  if (!branch) { 
    AliError("can't get the branch with the PHOS digits !");
    return;
  }
  TClonesArray *fDigitsArr    = new TClonesArray("AliPHOSDigit",100);
  branch->SetAddress(&fDigitsArr);
  branch->GetEntry(0);

  // Get the clusters array
  TBranch *emcbranch = clustersTree->GetBranch("PHOSEmcRP");
  if (!emcbranch) { 
    AliError("can't get the branch with the PHOS EMC clusters !");
    return;
  }

  TObjArray *fEmcRecPoints = new TObjArray(100) ;
  emcbranch->SetAddress(&fEmcRecPoints);
  emcbranch->GetEntry(0);

  //Fill CaloClusters 
  const Float_t kBigShort = std::numeric_limits<short int>::max() - 1;
  const Float_t nsec100   = 1e9*100.; // units of 0.01 ns
  const Float_t gev500    = 500.;     // units of GeV/500

  for (Int_t recpart = 0 ; recpart < nOfRecParticles ; recpart++) {
    AliPHOSRecParticle * rp = dynamic_cast<AliPHOSRecParticle*>(recParticles->At(recpart));
    if (Debug()) 
      rp->Print();
    // Get track segment and EMC rec.point associated with this rec.particle
    AliPHOSTrackSegment *ts    = static_cast<AliPHOSTrackSegment *>(tsm->GetTrackSegments()->At(rp->GetPHOSTSIndex()));

    AliPHOSEmcRecPoint  *emcRP = static_cast<AliPHOSEmcRecPoint *>(fEmcRecPoints->At(ts->GetEmcIndex()));
    AliESDCaloCluster   *ec    = new AliESDCaloCluster() ; 
    
    Float_t xyz[3];
    for (Int_t ixyz=0; ixyz<3; ixyz++) 
      xyz[ixyz] = rp->GetPos()[ixyz];
    
    AliDebug(2,Form("Global position xyz=(%f,%f,%f)",xyz[0],xyz[1],xyz[2]));
   
    //Create digits lists
    Int_t  digitMult  = emcRP->GetDigitsMultiplicity();
    Int_t *digitsList = emcRP->GetDigitsList();
    Float_t *rpElist   = emcRP->GetEnergiesList() ;
    Short_t *amplList  = new Short_t[digitMult];
    Short_t *timeList  = new Short_t[digitMult];
    Short_t *digiList  = new Short_t[digitMult];


    // Convert Float_t* and Int_t* to Short_t* to save memory
    for (Int_t iDigit=0; iDigit<digitMult; iDigit++) {

      AliPHOSDigit *digit = static_cast<AliPHOSDigit *>(fDigitsArr->At(digitsList[iDigit]));
      amplList[iDigit] =
	(Short_t)(TMath::Min(rpElist[iDigit]*gev500,kBigShort)); // Energy in units of GeV/500
// We should add here not full energy of digit, but unfolded one, stored in RecPoint
//       amplList[iDigit] =
//	(Short_t)(TMath::Min(digit->GetEnergy()*gev500,kBigShort)); // Energy in units of GeV/500
     timeList[iDigit] =
	(Short_t)(TMath::Max(-kBigShort,TMath::Min(digit->GetTime()*nsec100,kBigShort))); // time in units of 0.01 ns
      digiList[iDigit] = (Short_t)(digit->GetId());
    }
    

    //Primaries
    Int_t  primMult  = 0;
    Int_t *primList =  emcRP->GetPrimaries(primMult);
        
    // fills the ESDCaloCluster
 
    ec->SetClusterType(AliESDCaloCluster::kPHOSCluster);
    ec->SetPosition(xyz);                 //rec.point position in MARS
    ec->SetE(rp->Energy());         //total particle energy
    ec->SetClusterDisp(emcRP->GetDispersion()); //cluster dispersion
    ec->SetPid(rp->GetPID()) ;                  //array of particle identification
    ec->SetM02(emcRP->GetM2x()) ;               //second moment M2x
    ec->SetM20(emcRP->GetM2z()) ;               //second moment M2z
    ec->SetNExMax(emcRP->GetNExMax());          //number of local maxima
    ec->SetEmcCpvDistance(ts->GetCpvDistance("r"));                  //Only radius, what about separate x,z????
    ec->SetClusterChi2(-1);                     //not yet implemented
    ec->SetM11(-1) ;                            //not yet implemented
 
    //Digits Lists
    TArrayS arrayAmpList(digitMult,amplList);
    TArrayS arrayTimeList(digitMult,timeList);
    TArrayS arrayIndexList(digitMult,digiList);
    ec->AddDigitAmplitude(arrayAmpList);
    ec->AddDigitTime(arrayTimeList);
    ec->AddDigitIndex(arrayIndexList);

    //Distance to the nearest bad crystal
    ec->SetDistanceToBadChannel(emcRP->GetDistanceToBadCrystal()); 
  
    //Array of MC indeces
    TArrayI arrayPrim(primMult,primList);
    ec->AddLabels(arrayPrim);

    //Array of tracks uncomment when available in future
    //TArrayS arrayTrackMatched(1);// Only one track, temporal solution.
    //arrayTrackMatched[0]= (Short_t)(matchedTrack[iClust]);
    //ec->AddTracksMatched(arrayTrackMatched);
    
    // add the track to the esd object
    esd->AddCaloCluster(ec);
    delete ec;   
    delete [] amplList;
    delete [] timeList;
    delete [] digiList;    
  }
  fDigitsArr   ->Delete();
  delete fDigitsArr;
  fEmcRecPoints->Delete();
  delete fEmcRecPoints;
  delete tsm;
  delete pid;
}

//____________________________________________________________________________
AliTracker* AliPHOSReconstructor::CreateTracker() const
{
  // creates the PHOS tracker
  return new AliPHOSTracker();
}

//____________________________________________________________________________
void  AliPHOSReconstructor::ConvertDigits(AliRawReader* rawReader, TTree* digitsTree) const
{
  // Converts raw data to
  // PHOS digits
  // Works on a single-event basis

  rawReader->Reset() ; 

  AliPHOSRawDecoder * dc ;

  if(strcmp(fgkRecoParamEmc->DecoderVersion(),"v1")==0) 
    dc=new AliPHOSRawDecoderv1(rawReader);
  else
    dc=new AliPHOSRawDecoder(rawReader);

  TString option = GetOption();
  if (option.Contains("OldRCUFormat"))
    dc->SetOldRCUFormat(kTRUE);
  else
    dc->SetOldRCUFormat(kFALSE);
  
  dc->SubtractPedestals(fgkRecoParamEmc->SubtractPedestals());
  
  TClonesArray *digits = new TClonesArray("AliPHOSDigit",1);
  digits->SetName("DIGITS");
  Int_t bufsize = 32000;
  digitsTree->Branch("PHOS", &digits, bufsize);

  AliPHOSRawDigiProducer pr;
  pr.MakeDigits(digits,dc);

  delete dc ;

  //ADC counts -> GeV
  if(strcmp(fgkRecoParamEmc->DecoderVersion(),"v1")==0){ //"Energy" calculated as fit
    for(Int_t i=0; i<digits->GetEntries(); i++) {
      AliPHOSDigit* digit = (AliPHOSDigit*)digits->At(i);
      digit->SetEnergy(digit->GetEnergy()*0.005); //We assume here 5 MeV/ADC channel
      digit->SetTime(digit->GetTime()*1.e-7) ;    //Here we assume sample step==100 ns TO BE FIXED!!!!!!!!!!!!!
    }
  }
  else{ //Digits energy calculated as maximal energy
    for(Int_t i=0; i<digits->GetEntries(); i++) {
      AliPHOSDigit* digit = (AliPHOSDigit*)digits->At(i);
      digit->SetEnergy(digit->GetEnergy()/AliPHOSPulseGenerator::GeV2ADC());
    }
  }
  
  // Clean up digits below the noise threshold
  // Assuming the digit noise to be 4 MeV, we suppress digits within
  // 3-sigma of the noise.
  // This parameter should be passed via AliPHOSRecoParamEmc later

  const Double_t emcDigitThreshold = 0.012;
  for(Int_t i=0; i<digits->GetEntries(); i++) {
    AliPHOSDigit* digit = (AliPHOSDigit*)digits->At(i);
    if(digit->GetEnergy() < emcDigitThreshold)
      digits->RemoveAt(i) ;
  }
  digits->Compress() ;  

  //!!!!for debug!!!
  Int_t modMax=-111;
  Int_t colMax=-111;
  Int_t rowMax=-111;
  Float_t eMax=-333;
  //!!!for debug!!!

  Int_t relId[4];
  for(Int_t iDigit=0; iDigit<digits->GetEntries(); iDigit++) {
    AliPHOSDigit* digit = (AliPHOSDigit*)digits->At(iDigit);
    if(digit->GetEnergy()>eMax) {
      fGeom->AbsToRelNumbering(digit->GetId(),relId);
      eMax=digit->GetEnergy();
      modMax=relId[0];
      rowMax=relId[2];
      colMax=relId[3];
    }
  }

  AliDebug(1,Form("Digit with max. energy:  modMax %d colMax %d rowMax %d  eMax %f\n\n",
		  modMax,colMax,rowMax,eMax));

  digitsTree->Fill();
  digits->Delete();
  delete digits;
}
Commit	Line	Data
	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	/* $Id$ */
	17
	18	//_________________________________________________________________________
	19	//*--
	20	//*-- Yves Schutz (SUBATECH)
	21	// Reconstruction class. Redesigned from the old AliReconstructionner class and
	22	// derived from STEER/AliReconstructor.
	23	//
	24	// --- ROOT system ---
	25
	26	// --- Standard library ---
	27
	28	// --- AliRoot header files ---
	29	#include "AliLog.h"
	30	#include "AliESDEvent.h"
	31	#include "AliESDCaloCluster.h"
	32	#include "AliPHOSReconstructor.h"
	33	#include "AliPHOSClusterizerv1.h"
	34	#include "AliPHOSTrackSegmentMakerv1.h"
	35	#include "AliPHOSPIDv1.h"
	36	#include "AliPHOSTracker.h"
	37	#include "AliRawReader.h"
	38	#include "AliPHOSTrigger.h"
	39	#include "AliPHOSGeometry.h"
	40	#include "AliPHOSRecoParam.h"
	41	#include "AliPHOSRecoParamEmc.h"
	42	#include "AliPHOSRecoParamCpv.h"
	43	#include "AliPHOSDigit.h"
	44	#include "AliPHOSTrackSegment.h"
	45	#include "AliPHOSEmcRecPoint.h"
	46	#include "AliPHOSRecParticle.h"
	47	#include "AliPHOSRawDecoder.h"
	48	#include "AliPHOSRawDecoderv1.h"
	49	#include "AliPHOSRawDigiProducer.h"
	50	#include "AliPHOSPulseGenerator.h"
	51
	52	ClassImp(AliPHOSReconstructor)
	53
	54	Bool_t AliPHOSReconstructor::fgDebug = kFALSE ;
	55	AliPHOSRecoParam* AliPHOSReconstructor::fgkRecoParamEmc =0; // EMC rec. parameters
	56	AliPHOSRecoParam* AliPHOSReconstructor::fgkRecoParamCpv =0; // CPV rec. parameters
	57
	58	//____________________________________________________________________________
	59	AliPHOSReconstructor::AliPHOSReconstructor() :
	60	fGeom(NULL)
	61	{
	62	// ctor
	63
	64	if (!fgkRecoParamEmc) {
	65	AliWarning("The Reconstruction parameters for EMC nonitialized - Used default one");
	66	fgkRecoParamEmc = AliPHOSRecoParamEmc::GetEmcDefaultParameters();
	67	}
	68
	69	if (!fgkRecoParamCpv) {
	70	AliWarning("The Reconstruction parameters for CPV nonitialized - Used default one");
	71	fgkRecoParamCpv = AliPHOSRecoParamCpv::GetCpvDefaultParameters();
	72	}
	73
	74	fGeom = AliPHOSGeometry::GetInstance("IHEP","");
	75	}
	76
	77	//____________________________________________________________________________
	78	AliPHOSReconstructor::~AliPHOSReconstructor()
	79	{
	80	// dtor
	81	delete fGeom;
	82	}
	83
	84	//____________________________________________________________________________
	85	void AliPHOSReconstructor::Reconstruct(TTree* digitsTree, TTree* clustersTree) const
	86	{
	87	// 'single-event' local reco method called by AliReconstruction;
	88	// Only the clusterization is performed,; the rest of the reconstruction is done in FillESD because the track
	89	// segment maker needs access to the AliESDEvent object to retrieve the tracks reconstructed by
	90	// the global tracking.
	91
	92	AliPHOSClusterizerv1 clu(fGeom);
	93	clu.SetInput(digitsTree);
	94	clu.SetOutput(clustersTree);
	95	if ( Debug() )
	96	clu.Digits2Clusters("deb all") ;
	97	else
	98	clu.Digits2Clusters("") ;
	99	}
	100
	101	//____________________________________________________________________________
	102	void AliPHOSReconstructor::FillESD(TTree* digitsTree, TTree* clustersTree,
	103	AliESDEvent* esd) const
	104	{
	105	// This method produces PHOS rec-particles,
	106	// then it creates AliESDtracks out of them and
	107	// write tracks to the ESD
	108
	109	AliPHOSTrackSegmentMaker *tsm = new AliPHOSTrackSegmentMakerv1(fGeom);
	110	AliPHOSPID *pid = new AliPHOSPIDv1 (fGeom);
	111
	112	// do current event; the loop over events is done by AliReconstruction::Run()
	113	tsm->SetESD(esd) ;
	114	tsm->SetInput(clustersTree);
	115	if ( Debug() )
	116	tsm->Clusters2TrackSegments("deb all") ;
	117	else
	118	tsm->Clusters2TrackSegments("") ;
	119
	120	pid->SetInput(clustersTree, tsm->GetTrackSegments()) ;
	121	pid->SetESD(esd) ;
	122	if ( Debug() )
	123	pid->TrackSegments2RecParticles("deb all") ;
	124	else
	125	pid->TrackSegments2RecParticles("") ;
	126
	127
	128	// This function creates AliESDtracks from AliPHOSRecParticles
	129	// and
	130	// writes them to the ESD
	131
	132	TClonesArray *recParticles = pid->GetRecParticles();
	133	Int_t nOfRecParticles = recParticles->GetEntries();
	134
	135	esd->SetNumberOfPHOSClusters(nOfRecParticles) ;
	136	esd->SetFirstPHOSCluster(esd->GetNumberOfCaloClusters()) ;
	137
	138	AliDebug(2,Form("%d rec. particles, option %s",nOfRecParticles,GetOption()));
	139
	140	//#########Calculate trigger and set trigger info###########
	141
	142	AliPHOSTrigger tr ;
	143	// tr.SetPatchSize(1);//create 4x4 patches
	144	tr.Trigger();
	145
	146	Float_t maxAmp2x2 = tr.Get2x2MaxAmplitude();
	147	Float_t maxAmpnxn = tr.GetnxnMaxAmplitude();
	148	Float_t ampOutOfPatch2x2 = tr.Get2x2AmpOutOfPatch() ;
	149	Float_t ampOutOfPatchnxn = tr.GetnxnAmpOutOfPatch() ;
	150
	151	Int_t iSM2x2 = tr.Get2x2SuperModule();
	152	Int_t iSMnxn = tr.GetnxnSuperModule();
	153	Int_t iCrystalPhi2x2 = tr.Get2x2CrystalPhi();
	154	Int_t iCrystalPhinxn = tr.GetnxnCrystalPhi();
	155	Int_t iCrystalEta2x2 = tr.Get2x2CrystalEta();
	156	Int_t iCrystalEtanxn = tr.GetnxnCrystalEta();
	157
	158	AliDebug(2, Form("Trigger 2x2 max amp %f, out amp %f, SM %d, iphi %d ieta %d", maxAmp2x2, ampOutOfPatch2x2, iSM2x2,iCrystalPhi2x2, iCrystalEta2x2));
	159	AliDebug(2, Form("Trigger 4x4 max amp %f , out amp %f, SM %d, iphi %d, ieta %d", maxAmpnxn, ampOutOfPatchnxn, iSMnxn,iCrystalPhinxn, iCrystalEtanxn));
	160
	161	Int_t iRelId2x2 []= {iSM2x2+1,0,iCrystalPhi2x2,iCrystalEta2x2};// PHOS modules in order to calculate AbsId need to be 1-5 not 0-4 as returns trigger.
	162	Int_t iAbsId2x2 =-1;
	163	Int_t iRelIdnxn []= {iSMnxn+1,0,iCrystalPhinxn,iCrystalEtanxn};// PHOS modules in order to calculate AbsId need to be 1-5 not 0-4 as returns trigger.
	164	Int_t iAbsIdnxn =-1;
	165	TVector3 pos2x2(-1,-1,-1);
	166	TVector3 posnxn(-1,-1,-1);
	167	fGeom->RelToAbsNumbering(iRelId2x2, iAbsId2x2);
	168	fGeom->RelToAbsNumbering(iRelIdnxn, iAbsIdnxn);
	169	fGeom->RelPosInAlice(iAbsId2x2, pos2x2);
	170	fGeom->RelPosInAlice(iAbsIdnxn, posnxn);
	171
	172	TArrayF triggerPosition(6);
	173	triggerPosition[0] = pos2x2(0) ;
	174	triggerPosition[1] = pos2x2(1) ;
	175	triggerPosition[2] = pos2x2(2) ;
	176	triggerPosition[3] = posnxn(0) ;
	177	triggerPosition[4] = posnxn(1) ;
	178	triggerPosition[5] = posnxn(2) ;
	179
	180	TArrayF triggerAmplitudes(4);
	181	triggerAmplitudes[0] = maxAmp2x2 ;
	182	triggerAmplitudes[1] = ampOutOfPatch2x2 ;
	183	triggerAmplitudes[2] = maxAmpnxn ;
	184	triggerAmplitudes[3] = ampOutOfPatchnxn ;
	185
	186	//esd->SetPHOSTriggerCells(triggerPosition);
	187	esd->AddPHOSTriggerPosition(triggerPosition);
	188	esd->AddPHOSTriggerAmplitudes(triggerAmplitudes);
	189
	190	//######################################
	191
	192	// Read digits array
	193	TBranch *branch = digitsTree->GetBranch("PHOS");
	194	if (!branch) {
	195	AliError("can't get the branch with the PHOS digits !");
	196	return;
	197	}
	198	TClonesArray *fDigitsArr = new TClonesArray("AliPHOSDigit",100);
	199	branch->SetAddress(&fDigitsArr);
	200	branch->GetEntry(0);
	201
	202	// Get the clusters array
	203	TBranch *emcbranch = clustersTree->GetBranch("PHOSEmcRP");
	204	if (!emcbranch) {
	205	AliError("can't get the branch with the PHOS EMC clusters !");
	206	return;
	207	}
	208
	209	TObjArray *fEmcRecPoints = new TObjArray(100) ;
	210	emcbranch->SetAddress(&fEmcRecPoints);
	211	emcbranch->GetEntry(0);
	212
	213	//Fill CaloClusters
	214	const Float_t kBigShort = std::numeric_limits<short int>::max() - 1;
	215	const Float_t nsec100 = 1e9*100.; // units of 0.01 ns
	216	const Float_t gev500 = 500.; // units of GeV/500
	217
	218	for (Int_t recpart = 0 ; recpart < nOfRecParticles ; recpart++) {
	219	AliPHOSRecParticle * rp = dynamic_cast<AliPHOSRecParticle*>(recParticles->At(recpart));
	220	if (Debug())
	221	rp->Print();
	222	// Get track segment and EMC rec.point associated with this rec.particle
	223	AliPHOSTrackSegment ts = static_cast<AliPHOSTrackSegment >(tsm->GetTrackSegments()->At(rp->GetPHOSTSIndex()));
	224
	225	AliPHOSEmcRecPoint emcRP = static_cast<AliPHOSEmcRecPoint >(fEmcRecPoints->At(ts->GetEmcIndex()));
	226	AliESDCaloCluster *ec = new AliESDCaloCluster() ;
	227
	228	Float_t xyz[3];
	229	for (Int_t ixyz=0; ixyz<3; ixyz++)
	230	xyz[ixyz] = rp->GetPos()[ixyz];
	231
	232	AliDebug(2,Form("Global position xyz=(%f,%f,%f)",xyz[0],xyz[1],xyz[2]));
	233
	234	//Create digits lists
	235	Int_t digitMult = emcRP->GetDigitsMultiplicity();
	236	Int_t *digitsList = emcRP->GetDigitsList();
	237	Float_t *rpElist = emcRP->GetEnergiesList() ;
	238	Short_t *amplList = new Short_t[digitMult];
	239	Short_t *timeList = new Short_t[digitMult];
	240	Short_t *digiList = new Short_t[digitMult];
	241
	242
	243	// Convert Float_t* and Int_t* to Short_t* to save memory
	244	for (Int_t iDigit=0; iDigit<digitMult; iDigit++) {
	245
	246	AliPHOSDigit digit = static_cast<AliPHOSDigit >(fDigitsArr->At(digitsList[iDigit]));
	247	amplList[iDigit] =
	248	(Short_t)(TMath::Min(rpElist[iDigit]*gev500,kBigShort)); // Energy in units of GeV/500
	249	// We should add here not full energy of digit, but unfolded one, stored in RecPoint
	250	// amplList[iDigit] =
	251	// (Short_t)(TMath::Min(digit->GetEnergy()*gev500,kBigShort)); // Energy in units of GeV/500
	252	timeList[iDigit] =
	253	(Short_t)(TMath::Max(-kBigShort,TMath::Min(digit->GetTime()*nsec100,kBigShort))); // time in units of 0.01 ns
	254	digiList[iDigit] = (Short_t)(digit->GetId());
	255	}
	256
	257
	258
	259	//Primaries
	260	Int_t primMult = 0;
	261	Int_t *primList = emcRP->GetPrimaries(primMult);
	262
	263	// fills the ESDCaloCluster
	264
	265	ec->SetClusterType(AliESDCaloCluster::kPHOSCluster);
	266	ec->SetPosition(xyz); //rec.point position in MARS
	267	ec->SetE(rp->Energy()); //total particle energy
	268	ec->SetClusterDisp(emcRP->GetDispersion()); //cluster dispersion
	269	ec->SetPid(rp->GetPID()) ; //array of particle identification
	270	ec->SetM02(emcRP->GetM2x()) ; //second moment M2x
	271	ec->SetM20(emcRP->GetM2z()) ; //second moment M2z
	272	ec->SetNExMax(emcRP->GetNExMax()); //number of local maxima
	273	ec->SetEmcCpvDistance(ts->GetCpvDistance("r")); //Only radius, what about separate x,z????
	274	ec->SetClusterChi2(-1); //not yet implemented
	275	ec->SetM11(-1) ; //not yet implemented
	276
	277	//Digits Lists
	278	TArrayS arrayAmpList(digitMult,amplList);
	279	TArrayS arrayTimeList(digitMult,timeList);
	280	TArrayS arrayIndexList(digitMult,digiList);
	281	ec->AddDigitAmplitude(arrayAmpList);
	282	ec->AddDigitTime(arrayTimeList);
	283	ec->AddDigitIndex(arrayIndexList);
	284
	285	//Distance to the nearest bad crystal
	286	ec->SetDistanceToBadChannel(emcRP->GetDistanceToBadCrystal());
	287
	288	//Array of MC indeces
	289	TArrayI arrayPrim(primMult,primList);
	290	ec->AddLabels(arrayPrim);
	291
	292	//Array of tracks uncomment when available in future
	293	//TArrayS arrayTrackMatched(1);// Only one track, temporal solution.
	294	//arrayTrackMatched[0]= (Short_t)(matchedTrack[iClust]);
	295	//ec->AddTracksMatched(arrayTrackMatched);
	296
	297	// add the track to the esd object
	298	esd->AddCaloCluster(ec);
	299	delete ec;
	300	delete [] amplList;
	301	delete [] timeList;
	302	delete [] digiList;
	303	}
	304	fDigitsArr ->Delete();
	305	delete fDigitsArr;
	306	fEmcRecPoints->Delete();
	307	delete fEmcRecPoints;
	308	delete tsm;
	309	delete pid;
	310	}
	311
	312	//____________________________________________________________________________
	313	AliTracker* AliPHOSReconstructor::CreateTracker() const
	314	{
	315	// creates the PHOS tracker
	316	return new AliPHOSTracker();
	317	}
	318
	319	//____________________________________________________________________________
	320	void AliPHOSReconstructor::ConvertDigits(AliRawReader* rawReader, TTree* digitsTree) const
	321	{
	322	// Converts raw data to
	323	// PHOS digits
	324	// Works on a single-event basis
	325
	326	rawReader->Reset() ;
	327
	328	AliPHOSRawDecoder * dc ;
	329
	330	if(strcmp(fgkRecoParamEmc->DecoderVersion(),"v1")==0)
	331	dc=new AliPHOSRawDecoderv1(rawReader);
	332	else
	333	dc=new AliPHOSRawDecoder(rawReader);
	334
	335	TString option = GetOption();
	336	if (option.Contains("OldRCUFormat"))
	337	dc->SetOldRCUFormat(kTRUE);
	338	else
	339	dc->SetOldRCUFormat(kFALSE);
	340
	341	dc->SubtractPedestals(fgkRecoParamEmc->SubtractPedestals());
	342
	343	TClonesArray *digits = new TClonesArray("AliPHOSDigit",1);
	344	digits->SetName("DIGITS");
	345	Int_t bufsize = 32000;
	346	digitsTree->Branch("PHOS", &digits, bufsize);
	347
	348	AliPHOSRawDigiProducer pr;
	349	pr.MakeDigits(digits,dc);
	350
	351	delete dc ;
	352
	353	//ADC counts -> GeV
	354	if(strcmp(fgkRecoParamEmc->DecoderVersion(),"v1")==0){ //"Energy" calculated as fit
	355	for(Int_t i=0; i<digits->GetEntries(); i++) {
	356	AliPHOSDigit* digit = (AliPHOSDigit*)digits->At(i);
	357	digit->SetEnergy(digit->GetEnergy()*0.005); //We assume here 5 MeV/ADC channel
	358	digit->SetTime(digit->GetTime()*1.e-7) ; //Here we assume sample step==100 ns TO BE FIXED!!!!!!!!!!!!!
	359	}
	360	}
	361	else{ //Digits energy calculated as maximal energy
	362	for(Int_t i=0; i<digits->GetEntries(); i++) {
	363	AliPHOSDigit* digit = (AliPHOSDigit*)digits->At(i);
	364	digit->SetEnergy(digit->GetEnergy()/AliPHOSPulseGenerator::GeV2ADC());
	365	}
	366	}
	367
	368	// Clean up digits below the noise threshold
	369	// Assuming the digit noise to be 4 MeV, we suppress digits within
	370	// 3-sigma of the noise.
	371	// This parameter should be passed via AliPHOSRecoParamEmc later
	372
	373	const Double_t emcDigitThreshold = 0.012;
	374	for(Int_t i=0; i<digits->GetEntries(); i++) {
	375	AliPHOSDigit* digit = (AliPHOSDigit*)digits->At(i);
	376	if(digit->GetEnergy() < emcDigitThreshold)
	377	digits->RemoveAt(i) ;
	378	}
	379	digits->Compress() ;
	380
	381	//!!!!for debug!!!
	382	Int_t modMax=-111;
	383	Int_t colMax=-111;
	384	Int_t rowMax=-111;
	385	Float_t eMax=-333;
	386	//!!!for debug!!!
	387
	388	Int_t relId[4];
	389	for(Int_t iDigit=0; iDigit<digits->GetEntries(); iDigit++) {
	390	AliPHOSDigit* digit = (AliPHOSDigit*)digits->At(iDigit);
	391	if(digit->GetEnergy()>eMax) {
	392	fGeom->AbsToRelNumbering(digit->GetId(),relId);
	393	eMax=digit->GetEnergy();
	394	modMax=relId[0];
	395	rowMax=relId[2];
	396	colMax=relId[3];
	397	}
	398	}
	399
	400	AliDebug(1,Form("Digit with max. energy: modMax %d colMax %d rowMax %d eMax %f\n\n",
	401	modMax,colMax,rowMax,eMax));
	402
	403	digitsTree->Fill();
	404	digits->Delete();
	405	delete digits;
	406	}