]> git.uio.no Git - u/mrichter/AliRoot.git/blobdiff - PHOS/AliPHOSReconstructor.cxx
Charged jets (pPb): Improved trackcut analysis
[u/mrichter/AliRoot.git] / PHOS / AliPHOSReconstructor.cxx
index 24824c599b34e70887955c2d094791a4966fe96a..3dc6b251233cc0b969eeb6ec194d214076d4ce49 100644 (file)
 /* $Id$ */
 
 //_________________________________________________________________________
-//*--
-//*-- Yves Schutz (SUBATECH) 
+//--
+//-- Yves Schutz (SUBATECH) 
 // Reconstruction class. Redesigned from the old AliReconstructionner class and 
 // derived from STEER/AliReconstructor. 
 // 
 // --- ROOT system ---
+#include "TGeoManager.h"
+#include "TGeoMatrix.h"
 
 // --- Standard library ---
 
 // --- AliRoot header files ---
-#include "AliESD.h"
+#include "AliLog.h"
+#include "AliAltroMapping.h"
+#include "AliESDEvent.h"
+#include "AliESDCaloCluster.h"
+#include "AliESDCaloCells.h"
 #include "AliPHOSReconstructor.h"
 #include "AliPHOSClusterizerv1.h"
 #include "AliPHOSTrackSegmentMakerv1.h"
 #include "AliPHOSPIDv1.h"
-#include "AliPHOSGetter.h"
 #include "AliPHOSTracker.h"
 #include "AliRawReader.h"
+#include "AliPHOSCalibData.h"
+#include "AliCDBEntry.h"
+#include "AliCDBManager.h"
+#include "AliPHOSTrigger.h"
+#include "AliPHOSGeometry.h"
+#include "AliPHOSDigit.h"
+#include "AliPHOSTrackSegment.h"
+#include "AliPHOSEmcRecPoint.h"
+#include "AliPHOSRecParticle.h"
+#include "AliPHOSRawFitterv0.h"
+#include "AliPHOSRawFitterv1.h"
+#include "AliPHOSRawFitterv2.h"
+#include "AliPHOSRawFitterv3.h"
+#include "AliPHOSRawFitterv4.h"
+#include "AliPHOSRawDigiProducer.h"
+#include "AliPHOSPulseGenerator.h"
+#include "AliPHOSTriggerRawDigit.h"
+#include "AliPHOSTriggerRawDigiProducer.h"
+#include "AliPHOSTriggerParameters.h"
 
 ClassImp(AliPHOSReconstructor)
 
 Bool_t AliPHOSReconstructor::fgDebug = kFALSE ; 
+TClonesArray*     AliPHOSReconstructor::fgDigitsArray = 0;   // Array of PHOS digits
+TObjArray*        AliPHOSReconstructor::fgEMCRecPoints = 0;   // Array of EMC rec.points
+AliPHOSCalibData * AliPHOSReconstructor::fgCalibData  = 0 ;
+TClonesArray*     AliPHOSReconstructor::fgTriggerDigits = 0;   // Array of PHOS trigger digits
 
 //____________________________________________________________________________
-  AliPHOSReconstructor::AliPHOSReconstructor() 
+AliPHOSReconstructor::AliPHOSReconstructor() :
+  fGeom(NULL),fClusterizer(NULL),fTSM(NULL),fPID(NULL),fTmpDigLG(NULL)
 {
   // ctor
-
-} 
+  fGeom          = AliPHOSGeometry::GetInstance("IHEP","");
+  fClusterizer   = new AliPHOSClusterizerv1      (fGeom);
+  fTSM           = new AliPHOSTrackSegmentMakerv1(fGeom);
+  fPID           = new AliPHOSPIDv1              (fGeom);
+  fTmpDigLG      = new TClonesArray("AliPHOSDigit",100);
+  fgDigitsArray  = new TClonesArray("AliPHOSDigit",100);
+  fgEMCRecPoints = new TObjArray(100) ;
+  if (!fgCalibData)
+    fgCalibData = new AliPHOSCalibData(-1); //use AliCDBManager's run number
+  
+  fgTriggerDigits  = new TClonesArray("AliPHOSTriggerRawDigit",100);
+  
+  AliInfo(Form("PHOS bad channel map contains %d bad channel(s).\n",
+               fgCalibData->GetNumOfEmcBadChannels()));
+}
 
 //____________________________________________________________________________
-  AliPHOSReconstructor::~AliPHOSReconstructor()
+AliPHOSReconstructor::~AliPHOSReconstructor()
 {
   // dtor
-
+  delete fGeom;
+  delete fClusterizer;
+  delete fTSM;
+  delete fPID;
+  delete fTmpDigLG;
+  delete fgDigitsArray;
+  delete fgEMCRecPoints;
+  delete fgTriggerDigits;
 } 
 
 //____________________________________________________________________________
-void AliPHOSReconstructor::Reconstruct(AliRunLoader* runLoader) const 
+void AliPHOSReconstructor::Reconstruct(TTree* digitsTree, TTree* clustersTree) const
 {
-  // method called by AliReconstruction; 
+  // '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 AliESD object to retrieve the tracks reconstructed by 
+  // segment maker needs access to the AliESDEvent object to retrieve the tracks reconstructed by 
   // the global tracking.
-  TString headerFile(runLoader->GetFileName()) ; 
-  TString branchName(runLoader->GetEventFolder()->GetName()) ;  
-  
-  AliPHOSClusterizerv1 clu(headerFile, branchName);
-  clu.SetEventRange(0, -1) ; // do all the events
+
+  fClusterizer->InitParameters();
+  fClusterizer->SetInput(digitsTree);
+  fClusterizer->SetOutput(clustersTree);
   if ( Debug() ) 
-    clu.ExecuteTask("deb all") ; 
+    fClusterizer->Digits2Clusters("deb all") ; 
   else 
-    clu.ExecuteTask("") ;  
-
+    fClusterizer->Digits2Clusters("") ;
 }
 
 //____________________________________________________________________________
-void AliPHOSReconstructor::Reconstruct(AliRunLoader* runLoader, AliRawReader* rawreader) const 
+void AliPHOSReconstructor::FillESD(TTree* digitsTree, TTree* clustersTree, 
+                                  AliESDEvent* esd) const
 {
-  // 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 AliESD object to retrieve the tracks reconstructed by 
-  // the global tracking.
-  // Here we reconstruct from Raw Data
-  
-  rawreader->Reset() ; 
-  TString headerFile(runLoader->GetFileName()) ; 
-  TString branchName(runLoader->GetEventFolder()->GetName()) ;  
+  // This method produces PHOS rec-particles,
+  // then it creates AliESDtracks out of them and
+  // write tracks to the ESD
+
+
+  // do current event; the loop over events is done by AliReconstruction::Run()
+  fTSM->SetESD(esd) ; 
+  fTSM->SetInput(clustersTree);
+  if ( Debug() ) 
+    fTSM->Clusters2TrackSegments("deb all") ;
+  else 
+    fTSM->Clusters2TrackSegments("") ;
   
-  AliPHOSClusterizerv1 clu(headerFile, branchName);
-  clu.SetEventRange(0, -1) ; // do all the events
-  clu.SetRawReader(rawreader);
+  fPID->SetInput(clustersTree, fTSM->GetTrackSegments()) ; 
+  fPID->SetESD(esd) ; 
   if ( Debug() ) 
-    clu.ExecuteTask("deb all") ; 
+    fPID->TrackSegments2RecParticles("deb all") ;
   else 
-    clu.ExecuteTask("") ;
+    fPID->TrackSegments2RecParticles("") ;
 
-}
+  TClonesArray *recParticles  = fPID->GetRecParticles();
+  Int_t nOfRecParticles = recParticles->GetEntriesFast();
+  
+  AliDebug(2,Form("%d rec. particles, option %s",nOfRecParticles,GetOption()));
+  
+  // Read digits array
 
-//____________________________________________________________________________
-void AliPHOSReconstructor::FillESD(AliRunLoader* runLoader, AliESD* esd) const
-{
-  // This function creates AliESDtracks from AliPHOSRecParticles
-  //         and
-  // writes them to the ESD
+  TBranch *branch = digitsTree->GetBranch("PHOS");
+  if (!branch) { 
+    AliError("can't get the branch with the PHOS digits !");
+    return;
+  }
+  branch->SetAddress(&fgDigitsArray);
+  branch->GetEntry(0);
 
-  Int_t eventNumber = runLoader->GetEventNumber() ;
+  // Get the clusters array
 
-  AliPHOSGetter::Instance()->Event(eventNumber, "P") ; 
-  TClonesArray *recParticles = AliPHOSGetter::Instance()->RecParticles();
-  Int_t nOfRecParticles = recParticles->GetEntries();
-  esd->SetNumberOfPHOSParticles(nOfRecParticles) ; 
-  esd->SetFirstPHOSParticle(esd->GetNumberOfTracks()) ; 
+  TBranch *emcbranch = clustersTree->GetBranch("PHOSEmcRP");
+  if (!emcbranch) { 
+    AliError("can't get the branch with the PHOS EMC clusters !");
+    return;
+  }
+
+  emcbranch->SetAddress(&fgEMCRecPoints);
+  emcbranch->GetEntry(0);
+  
+  
+  // Trigger
+  
+  TBranch *tbranch = digitsTree->GetBranch("TPHOS");
+  if (tbranch) { 
+    
+    tbranch->SetAddress(&fgTriggerDigits);
+    tbranch->GetEntry(0);
+    
+    AliESDCaloTrigger* trgESD = esd->GetCaloTrigger("PHOS");
+    
+    if (trgESD) {
+      trgESD->Allocate(fgTriggerDigits->GetEntriesFast());
+      
+      for (Int_t i = 0; i < fgTriggerDigits->GetEntriesFast(); i++) {
+       AliPHOSTriggerRawDigit* tdig = (AliPHOSTriggerRawDigit*)fgTriggerDigits->At(i);
+       
+       Int_t mod,modX,modZ;
+       tdig->GetModXZ(mod,modX,modZ);
+       
+       const Int_t relId[4] = {5-mod,0,modX+1,modZ+1};
+       Int_t absId;
+       
+       fGeom->RelToAbsNumbering(relId,absId);
+       trgESD->Add(mod,absId,tdig->GetAmp(),0.,(Int_t*)NULL,0,0,0);
+      }
+    }  
+  }
+  
+//   //#########Calculate trigger and set trigger info###########
+
+//   AliPHOSTrigger tr ;
+//   //   tr.SetPatchSize(1);//create 4x4 patches
+//   tr.SetSimulation(kFALSE);
+//   tr.Trigger(fgDigitsArray);
+  
+//   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));
+
+//   // Attention! PHOS modules in order to calculate AbsId need to be 1-5 not 0-4 as returns trigger.
+//   Int_t iRelId2x2 []= {iSM2x2+1,0,iCrystalPhi2x2,iCrystalEta2x2};
+//   Int_t iAbsId2x2 =-1;
+//   Int_t iRelIdnxn []= {iSMnxn+1,0,iCrystalPhinxn,iCrystalEtanxn};
+//   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);
+  
+
+  //########################################
+  //############# Fill CaloCells ###########
+  //########################################
+
+  Int_t nDigits = fgDigitsArray->GetEntries();
+  Int_t idignew = 0 ;
+  AliDebug(1,Form("%d digits",nDigits));
+
+  const Int_t knEMC = fGeom->GetNModules()*fGeom->GetNPhi()*fGeom->GetNZ();
+  AliESDCaloCells &phsCells = *(esd->GetPHOSCells());
+  phsCells.CreateContainer(nDigits);
+  phsCells.SetType(AliESDCaloCells::kPHOSCell);
+
+  // Add to CaloCells only EMC digits with non-zero energy 
+  for (Int_t idig = 0 ; idig < nDigits ; idig++) {
+    const AliPHOSDigit * dig = (const AliPHOSDigit*)fgDigitsArray->At(idig);
+    if(dig->GetId() <= knEMC && 
+       Calibrate(dig->GetEnergy(),dig->GetId()) > GetRecoParam()->GetEMCMinE() ){
+      Int_t primary = dig->GetPrimary(1) ;
+      phsCells.SetCell(idignew,dig->GetId(), Calibrate(dig->GetEnergy(),dig->GetId()),
+                                             CalibrateT(dig->GetTime(),dig->GetId(),dig->IsLG()),
+                                             primary,0.,!dig->IsLG()) ;
+                                            
+      idignew++;
+    }
+  }
+  phsCells.SetNumberOfCells(idignew);
+  phsCells.Sort();
+
+  //########################################
+  //############## Fill CaloClusters #######
+  //########################################
 
   for (Int_t recpart = 0 ; recpart < nOfRecParticles ; recpart++) {
-    AliPHOSRecParticle * rp = dynamic_cast<AliPHOSRecParticle*>(recParticles->At(recpart));
+    AliPHOSRecParticle  *rp    = static_cast<AliPHOSRecParticle*>(recParticles->At(recpart));
     if (Debug()) 
       rp->Print();
-    AliESDtrack * et = new AliESDtrack() ; 
-    // fills the ESDtrack
-    Double_t xyz[3];
+    // Get track segment and EMC rec.point associated with this rec.particle
+    AliPHOSTrackSegment *ts    = static_cast<AliPHOSTrackSegment *>(fTSM->GetTrackSegments()
+                                                                   ->At(rp->GetPHOSTSIndex()));
+
+    AliPHOSEmcRecPoint  *emcRP = static_cast<AliPHOSEmcRecPoint *>(fgEMCRecPoints->At(ts->GetEmcIndex()));
+    AliESDCaloCluster   *ec    = new AliESDCaloCluster() ; 
+    
+    Float_t xyz[3];
     for (Int_t ixyz=0; ixyz<3; ixyz++) 
       xyz[ixyz] = rp->GetPos()[ixyz];
-    et->SetPHOSposition(xyz) ; 
-    et->SetPHOSsignal  (rp->Energy()) ; 
-    et->SetPHOSpid     (rp->GetPID()) ;
-    et->SetLabel       (rp->GetPrimaryIndex());
-    // add the track to the esd object
-    esd->AddTrack(et);
-    delete et;
+    
+    AliDebug(2,Form("Global position xyz=(%f,%f,%f)",xyz[0],xyz[1],xyz[2]));
+   
+    // Create cell lists
+
+    Int_t     cellMult   = emcRP->GetDigitsMultiplicity();
+    Int_t    *digitsList = emcRP->GetDigitsList();
+    Float_t  *rpElist    = emcRP->GetEnergiesList() ;
+    UShort_t *absIdList  = new UShort_t[cellMult];
+    Double_t *fracList   = new Double_t[cellMult];
+
+    for (Int_t iCell=0; iCell<cellMult; iCell++) {
+      AliPHOSDigit *digit = static_cast<AliPHOSDigit *>(fgDigitsArray->At(digitsList[iCell]));
+      absIdList[iCell] = (UShort_t)(digit->GetId());
+      if (digit->GetEnergy() > 0)
+       fracList[iCell] = rpElist[iCell]/(Calibrate(digit->GetEnergy(),digit->GetId()));
+      else
+       fracList[iCell] = 0;
+    }
+
+    //Primaries
+    Int_t  primMult  = 0;
+    Int_t *primList =  emcRP->GetPrimaries(primMult);
+
+    Float_t energy=0.;
+    if (GetRecoParam()->EMCEcore2ESD())
+      energy = emcRP->GetCoreEnergy();
+    else
+      energy = rp->Energy();
+    //Apply nonlinearity correction
+    if(GetRecoParam()->GetEMCEnergyCorrectionOn())
+      energy=CorrectNonlinearity(energy) ;
+
+    // fills the ESDCaloCluster
+    ec->SetType(AliVCluster::kPHOSNeutral);
+    ec->SetPosition(xyz);                       //rec.point position in MARS
+    ec->SetE(energy);                           //total or core particle energy
+    ec->SetDispersion(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->SetTrackDistance(ts->GetCpvDistance("x"),ts->GetCpvDistance("z")); 
+    ec->SetChi2(-1);                     //not yet implemented
+    ec->SetTOF(emcRP->GetTime());               //Time of flight - already calibrated in EMCRecPoint
+
+    //Cells contributing to clusters
+    ec->SetNCells(cellMult);
+    ec->SetCellsAbsId(absIdList);
+    ec->SetCellsAmplitudeFraction(fracList);
+
+    //Distance to the nearest bad crystal
+    ec->SetDistanceToBadChannel(emcRP->GetDistanceToBadCrystal()); 
+  
+    //Array of MC indeces
+    TArrayI arrayPrim(primMult,primList);
+    ec->AddLabels(arrayPrim);
+    
+    //Matched ESD track
+    TArrayI arrayTrackMatched(1);
+    arrayTrackMatched[0]= ts->GetTrackIndex();
+    ec->AddTracksMatched(arrayTrackMatched);
+    
+    Int_t index = esd->AddCaloCluster(ec);
+
+    //Set pointer to this cluster in ESD track
+    Int_t nt=esd->GetNumberOfTracks();
+    for (Int_t itr=0; itr<nt; itr++) {
+      AliESDtrack *esdTrack=esd->GetTrack(itr);
+      if(!esdTrack->IsPHOS())
+        continue ;
+      if(esdTrack->GetPHOScluster()==-recpart){ //we store negative cluster number
+        esdTrack->SetPHOScluster(index) ;
+//no garatie that only one track matched this cluster
+//      break ;
+      }
+    }
+    delete ec;   
+    delete [] fracList;
+    delete [] absIdList;
+  }
+  fgDigitsArray ->Clear("C");
+  fgEMCRecPoints->Clear("C");
+  recParticles  ->Clear();
+
+  //Store PHOS misalignment matrixes
+  FillMisalMatrixes(esd) ;
+
+}
+
+//____________________________________________________________________________
+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() ; 
+
+  AliPHOSRawFitterv0 * fitter ;
+
+  const TObjArray* maps = AliPHOSRecoParam::GetMappings();
+  if(!maps) AliFatal("Cannot retrieve ALTRO mappings!!");
+
+  AliAltroMapping *mapping[20];
+  for(Int_t i = 0; i < 20; i++) {
+    mapping[i] = (AliAltroMapping*)maps->At(i);
+  }
+
+  if      (strcmp(GetRecoParam()->EMCFitterVersion(),"v0")==0) 
+    fitter=new AliPHOSRawFitterv0();
+  else if (strcmp(GetRecoParam()->EMCFitterVersion(),"v1")==0) 
+    fitter=new AliPHOSRawFitterv1();
+  else if (strcmp(GetRecoParam()->EMCFitterVersion(),"v2")==0) 
+    fitter=new AliPHOSRawFitterv2();
+  else if (strcmp(GetRecoParam()->EMCFitterVersion(),"v3")==0) 
+    fitter=new AliPHOSRawFitterv3();
+  else
+    fitter=new AliPHOSRawFitterv4();
+
+  fitter->SubtractPedestals(GetRecoParam()->EMCSubtractPedestals());
+  fitter->SetAmpOffset     (GetRecoParam()->GetGlobalAltroOffset());
+  fitter->SetAmpThreshold  (GetRecoParam()->GetGlobalAltroThreshold());
+
+  TClonesArray *digits = new TClonesArray("AliPHOSDigit",1);
+  digits->SetName("DIGITS");
+  Int_t bufsize = 32000;
+  digitsTree->Branch("PHOS", &digits, bufsize);
+
+  AliPHOSRawDigiProducer rdp(rawReader,mapping);
+
+  rdp.SetEmcMinAmp(GetRecoParam()->GetEMCRawDigitThreshold()); // in ADC
+  rdp.SetCpvMinAmp(GetRecoParam()->GetCPVMinE());
+  rdp.SetSampleQualityCut(GetRecoParam()->GetEMCSampleQualityCut());
+  rdp.MakeDigits(digits,fTmpDigLG,fitter);
+
+  delete fitter ;
+
+  TClonesArray *tdigits = new TClonesArray("AliPHOSTriggerRawDigit",1);
+  tdigits->SetName("TDIGITS");
+  digitsTree->Branch("TPHOS", &tdigits, bufsize);  
+
+  rawReader->Reset();
+  AliPHOSTriggerRawDigiProducer tdp(rawReader);
+  
+  AliPHOSTriggerParameters* parameters = (AliPHOSTriggerParameters*)AliPHOSRecoParam::GetTriggerParameters();
+  
+  tdp.SetTriggerParameters(parameters);
+  tdp.ProcessEvent(tdigits);
+  
+  if (AliLog::GetGlobalDebugLevel() == 1) {
+    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;
+  
+  tdigits->Delete();
+  delete tdigits;
+}
+//==================================================================================
+Float_t AliPHOSReconstructor::Calibrate(Float_t amp, Int_t absId)const{
+  // Calibrate EMC digit, i.e. multiply its Amp by a factor read from CDB
+
+  const AliPHOSGeometry *geom = AliPHOSGeometry::GetInstance() ;
+
+  //Determine rel.position of the cell absolute ID
+  Int_t relId[4];
+  geom->AbsToRelNumbering(absId,relId);
+  Int_t module=relId[0];
+  Int_t row   =relId[2];
+  Int_t column=relId[3];
+  if(relId[1]){ //CPV
+    Float_t calibration = fgCalibData->GetADCchannelCpv(module,column,row);
+    return amp*calibration ;
+  }
+  else{ //EMC
+    Float_t calibration = fgCalibData->GetADCchannelEmc(module,column,row);
+    return amp*calibration ;
   }
 }
+//==================================================================================
+Float_t AliPHOSReconstructor::CalibrateT(Float_t time, Int_t absId,Bool_t isLG)const{
+  // Calibrate EMC digit, i.e. multiply its Amp by a factor read from CDB
 
-AliTracker* AliPHOSReconstructor::CreateTracker(AliRunLoader* runLoader) const
+  const AliPHOSGeometry *geom = AliPHOSGeometry::GetInstance() ;
+
+  //Determine rel.position of the cell absolute ID
+  Int_t relId[4];
+  geom->AbsToRelNumbering(absId,relId);
+  Int_t module=relId[0];
+  Int_t row   =relId[2];
+  Int_t column=relId[3];
+  if(relId[1]){ //CPV
+    return 0. ;
+  }
+  else{ //EMC
+    if(isLG)
+      time += fgCalibData->GetLGTimeShiftEmc(module,column,row);
+    else
+      time += fgCalibData->GetTimeShiftEmc(module,column,row);
+    return time ;
+  }
+}
+//==================================================================================
+void AliPHOSReconstructor::FillMisalMatrixes(AliESDEvent* esd)const{
+  //Store PHOS matrixes in ESD Header
+
+  //Check, if matrixes was already stored
+  for(Int_t mod=0 ;mod<5; mod++){
+    if(esd->GetPHOSMatrix(mod)!=0)
+      return ;
+  }
+
+  //Create and store matrixes
+  if(!gGeoManager){
+    AliError("Can not store misal. matrixes: no gGeoManager! \n") ;
+    return ;
+  }
+  //Note, that owner of copied marixes will be header
+  char path[255] ;
+  TGeoHMatrix * m ;
+  for(Int_t mod=0; mod<5; mod++){
+    snprintf(path,255,"/ALIC_1/PHOS_%d",mod+1) ; //In Geometry modules numbered 1,2,.,5
+    if (gGeoManager->cd(path)){
+      m = gGeoManager->GetCurrentMatrix() ;
+      esd->SetPHOSMatrix(new TGeoHMatrix(*m),mod) ;
+    }
+    else{
+      esd->SetPHOSMatrix(NULL,mod) ;
+    }
+  }
+
+}
+//==================================================================================
+Float_t AliPHOSReconstructor::CorrectNonlinearity(Float_t en){
+
+  //For backward compatibility, if no RecoParameters found
+  if(!GetRecoParam()){
+    return 0.0241+1.0504*en+0.000249*en*en ;
+  }
+
+  if(strcmp(GetRecoParam()->GetNonlinearityCorrectionVersion(),"NoCorrection")==0){
+    return en ;
+  }
+  if(strcmp(GetRecoParam()->GetNonlinearityCorrectionVersion(),"Gustavo2005")==0){
+    const Float_t *par=GetRecoParam()->GetNonlinearityParams() ;
+    return par[0]+par[1]*en + par[2]*en*en ;
+  }
+  if(strcmp(GetRecoParam()->GetNonlinearityCorrectionVersion(),"Henrik2010")==0){
+     const Float_t *par=GetRecoParam()->GetNonlinearityParams() ;
+     return en*(par[0]+par[1]*TMath::Exp(-en*par[2]))*(1.+par[3]*TMath::Exp(-en*par[4]))*(1.+par[6]/(en*en+par[5])) ;
+  }
+  //For backward compatibility
+  if(strcmp(GetRecoParam()->GetNonlinearityCorrectionVersion(),"")==0){
+    return 0.0241+1.0504*en+0.000249*en*en ;
+  }
+  return en ;
+}
+
+void AliPHOSReconstructor::readTRUParameters(AliPHOSTriggerParameters* parameters) const
 {
-// creates the PHOS tracker
-  if (!runLoader) return NULL; 
-  return new AliPHOSTracker(runLoader);
+  //Read trigger parameters.
+
+  TString path(gSystem->Getenv("ALICE_ROOT"));
+  path += "/PHOS/macros/Trigger/OCDB/";
+  
+  for (Int_t mod = 2; mod < 5; ++mod) { // module
+    for (Int_t tru = 0; tru < 4; tru++) { // tru row
+      for (Int_t branch = 0; branch < 2; branch++) { // branch
+       
+       // Open the Appropriate pedestal file
+       TString fileName = path;
+       fileName += "pedestal_m";
+       fileName = fileName += mod;
+       fileName+="_r";
+       fileName+=tru;
+       fileName+="_b";
+       fileName+=branch;
+       fileName+=".dat";
+       std::ifstream instream;
+       instream.open(fileName.Data());
+       
+       // Read pedestals from file
+       if( ! instream.is_open() )
+         Printf("E-TRUPedestals: could not open %s", fileName.Data());
+       else
+         {
+           Int_t ped[112];
+           
+           char ch_s[36];
+           char *ch_s_p = ch_s;
+           //Int_t nlines = 0;
+           
+           Int_t t_ped_0 =0;
+           Int_t t_ped_1 =0;
+           Int_t t_ped_2 =0;
+           
+           for(Int_t n=0; n<112; n++)
+             {
+               instream.getline(ch_s_p,36);
+               if (ch_s_p[23]<='9' && ch_s_p[23]>='0')
+                 {
+                   t_ped_0 = ch_s_p[23]-'0';
+                 }
+               else if (ch_s_p[23]>='A' && ch_s_p[23]<='Z')
+                 {
+                   t_ped_0 = ch_s_p[23]-'A'+10;
+                   
+                 }
+                 
+               if (ch_s_p[22]<='9' && ch_s_p[22]>='0')
+                 {
+                   t_ped_1 = ch_s_p[22]-'0';
+                 }
+               else if (ch_s_p[22]<='Z' && ch_s_p[22]>='A')
+                 {
+                   t_ped_1 = ch_s_p[22]-'A'+10;
+                 }
+               
+               if (ch_s_p[21]<='9' && ch_s_p[21]>='0')
+                 {
+                   t_ped_2 = ch_s_p[21]-'0';
+                 }
+               else if (ch_s_p[21]<='Z' && ch_s_p[21]>='A')
+                 {
+                   t_ped_2 = ch_s_p[21]-'A'+10;
+                 }
+               
+               ped[n]=t_ped_2*256+t_ped_1*16+t_ped_0;
+               
+               
+             }
+           for (Int_t xrow = 0; xrow < 8; xrow++){
+             for (Int_t zcol = 0; zcol < 14; zcol++){
+               Int_t pedestal = ped[zcol*8+xrow];
+               
+               if( pedestal < 612 && pedestal > 412 ) // resonable
+                 parameters->SetTRUPedestal(pedestal, mod, tru, branch, xrow, zcol);
+               else // unresonable
+                 continue;
+             }
+           }
+         } // Ends read of pedestals from branch from file.
+       instream.close();
+      }// end branch
+    }// end tru
+    
+  }// end for mod
 }
 
+
+
+