add removed line in previous commit

[u/mrichter/AliRoot.git] / PWGGA / EMCALTasks / AliAnalysisTaskEMCALClusterize.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.                  *
 **************************************************************************/

//_________________________________________________________________________
// This analysis provides a new list of clusters to be used in other analysis
//
// Author: Gustavo Conesa Balbastre,
//         Adapted from analysis class from Deepa Thomas
//
//
//_________________________________________________________________________

// --- Root ---
#include "TString.h"
#include "TRefArray.h"
#include "TClonesArray.h"
#include "TTree.h"
#include "TGeoManager.h"
#include "TROOT.h"
#include "TInterpreter.h"
#include "TFile.h"

// --- AliRoot Analysis Steering
#include "AliAnalysisTask.h"
#include "AliAnalysisManager.h"
#include "AliESDEvent.h"
#include "AliGeomManager.h"
#include "AliVCaloCells.h"
#include "AliAODCaloCluster.h"
#include "AliCDBManager.h"
#include "AliCDBStorage.h"
#include "AliCDBEntry.h"
#include "AliLog.h"
#include "AliVEventHandler.h"
#include "AliAODInputHandler.h"
#include "AliOADBContainer.h"

// --- EMCAL
#include "AliEMCALAfterBurnerUF.h"
#include "AliEMCALGeometry.h"
#include "AliEMCALClusterizerNxN.h"
#include "AliEMCALClusterizerv1.h"
#include "AliEMCALClusterizerv2.h"
#include "AliEMCALRecPoint.h"
#include "AliEMCALDigit.h"
#include "AliCaloCalibPedestal.h"
#include "AliEMCALCalibData.h"

#include "AliAnalysisTaskEMCALClusterize.h"

ClassImp(AliAnalysisTaskEMCALClusterize)

//______________________________________________________________________________
AliAnalysisTaskEMCALClusterize::AliAnalysisTaskEMCALClusterize(const char *name) 
: AliAnalysisTaskSE(name)
, fEvent(0)
, fGeom(0),               fGeomName("") 
, fGeomMatrixSet(kFALSE), fLoadGeomMatrices(kFALSE)
, fCalibData(0),          fPedestalData(0)
, fOCDBpath(""),          fAccessOCDB(kFALSE)
, fDigitsArr(0),          fClusterArr(0),             fCaloClusterArr(0)
, fRecParam(0),           fClusterizer(0)
, fUnfolder(0),           fJustUnfold(kFALSE) 
, fOutputAODBranch(0),    fOutputAODBranchName("")
, fFillAODFile(kTRUE),    fFillAODHeader(0)
, fFillAODCaloCells(0),   fRun(-1)
, fRecoUtils(0),          fConfigName("")
, fCellLabels(),          fCellSecondLabels(),        fCellTime()
, fCellMatchdEta(),       fCellMatchdPhi()
, fMaxEvent(0),           fDoTrackMatching(kFALSE)
, fSelectCell(kFALSE),    fSelectCellMinE(0),         fSelectCellMinFrac(0)
, fRemoveLEDEvents(kTRUE), fRemoveExoticEvents(kFALSE)
, fImportGeometryFromFile(kFALSE), fImportGeometryFilePath("") 
, fOADBSet(kFALSE),       fAccessOADB(kTRUE),         fOADBFilePath("")           
{
  //ctor
  for(Int_t i = 0; i < 12;    i++)  fGeomMatrix[i] =  0;
  for(Int_t j = 0; j < 24*48*11; j++)  
  {
    fCellLabels[j]       = -1;
    fCellSecondLabels[j] = -1;
    fCellTime[j]         =  0.;    
    fCellMatchdEta[j]    = -999;
    fCellMatchdPhi[j]    = -999;
  }  
  
  
}

//______________________________________________________________
AliAnalysisTaskEMCALClusterize::AliAnalysisTaskEMCALClusterize() 
: AliAnalysisTaskSE("DefaultAnalysis_AliAnalysisTaskEMCALClusterize")
, fEvent(0)
, fGeom(0),                 fGeomName("") 
, fGeomMatrixSet(kFALSE),   fLoadGeomMatrices(kFALSE)
, fCalibData(0),            fPedestalData(0)
, fOCDBpath(""),            fAccessOCDB(kFALSE)
, fDigitsArr(0),            fClusterArr(0),             fCaloClusterArr(0)
, fRecParam(0),             fClusterizer(0)
, fUnfolder(0),             fJustUnfold(kFALSE) 
, fOutputAODBranch(0),      fOutputAODBranchName("")
, fFillAODFile(kTRUE),      fFillAODHeader(0)
, fFillAODCaloCells(0),     fRun(-1)
, fRecoUtils(0),            fConfigName("")
, fCellLabels(),            fCellSecondLabels(),        fCellTime()
, fCellMatchdEta(),         fCellMatchdPhi()
, fMaxEvent(0),             fDoTrackMatching(kFALSE)
, fSelectCell(kFALSE),      fSelectCellMinE(0),         fSelectCellMinFrac(0)
, fRemoveLEDEvents(kTRUE), fRemoveExoticEvents(kFALSE)
, fImportGeometryFromFile(kFALSE), fImportGeometryFilePath("")
, fOADBSet(kFALSE),         fAccessOADB(kTRUE),        fOADBFilePath("")           

{
  // Constructor
  for(Int_t i = 0; i < 12;    i++)  fGeomMatrix[i] =  0;
  for(Int_t j = 0; j < 24*48*11; j++)  
  {
    fCellLabels[j]       = -1;
    fCellSecondLabels[j] = -1;
    fCellTime[j]         =  0.; 
    fCellMatchdEta[j]    = -999;
    fCellMatchdPhi[j]    = -999;
  }

}


//_______________________________________________________________
AliAnalysisTaskEMCALClusterize::~AliAnalysisTaskEMCALClusterize()
{
  //dtor 
  
  if (fDigitsArr){
    fDigitsArr->Clear("C");
    delete fDigitsArr; 
  }
  
  if (fClusterArr){
    fClusterArr->Delete();
    delete fClusterArr;
  }
  
  if (fCaloClusterArr){
    fCaloClusterArr->Delete();
    delete fCaloClusterArr; 
  }
  
  if(fClusterizer) delete fClusterizer;
  if(fUnfolder)    delete fUnfolder;   
  if(fRecoUtils)   delete fRecoUtils;
  
}

//_______________________________________________
void AliAnalysisTaskEMCALClusterize::AccessOADB()
{
  // Set the AODB calibration, bad channels etc. parameters at least once
  // alignment matrices from OADB done in SetGeometryMatrices
  
  //Set it only once
  if(fOADBSet) return ; 
  
  Int_t   runnumber = InputEvent()->GetRunNumber() ;
  TString pass      = GetPass();
  
  printf("AliAnalysisTaskEMCALClusterize::SetOADBParameters() - Get AODB parameters from EMCAL in %s for run %d, and <%s> \n",fOADBFilePath.Data(),runnumber,pass.Data());
  
  Int_t nSM = fGeom->GetNumberOfSuperModules();
  
  // Bad map
  if(fRecoUtils->IsBadChannelsRemovalSwitchedOn())
  {
    AliOADBContainer *contBC=new AliOADBContainer("");
    contBC->InitFromFile(Form("%s/EMCALBadChannels.root",fOADBFilePath.Data()),"AliEMCALBadChannels"); 
    
    TObjArray *arrayBC=(TObjArray*)contBC->GetObject(runnumber);
    
    if(arrayBC)
    {
      TObjArray * arrayBCpass = 0x0; 
      if(pass!="")arrayBCpass = (TObjArray*)arrayBC->FindObject(pass);
      // There are no passes for simulation, in order to get the bad map put pass1
      else        arrayBCpass = (TObjArray*)arrayBC->FindObject("pass1");
      
      if(arrayBCpass)
      {
        fRecoUtils->SwitchOnDistToBadChannelRecalculation();
        printf("AliAnalysisTaskEMCALClusterize::SetOADBParameters() - Remove EMCAL bad cells \n");
        
        for (Int_t i=0; i<nSM; ++i) 
        {
          TH2I *hbm = fRecoUtils->GetEMCALChannelStatusMap(i);
          
          if (hbm)
            delete hbm;
          
          hbm=(TH2I*)arrayBCpass->FindObject(Form("EMCALBadChannelMap_Mod%d",i));
          
          if (!hbm) 
          {
            AliError(Form("Can not get EMCALBadChannelMap_Mod%d",i));
            continue;
          }
          
          hbm->SetDirectory(0);
          fRecoUtils->SetEMCALChannelStatusMap(i,hbm);
          
        } // loop
      } else printf("AliAnalysisTaskEMCALClusterize::SetOADBParameters() - Do NOT remove EMCAL bad channels 1\n"); // pass array
    } else printf("AliAnalysisTaskEMCALClusterize::SetOADBParameters() - Do NOT remove EMCAL bad channels 2\n"); // run array
  }  // Remove bad
  
  // Energy Recalibration
  if(fRecoUtils->IsRecalibrationOn())
  {
    AliOADBContainer *contRF=new AliOADBContainer("");
    
    contRF->InitFromFile(Form("%s/EMCALRecalib.root",fOADBFilePath.Data()),"AliEMCALRecalib");
    
    TObjArray *recal=(TObjArray*)contRF->GetObject(runnumber); 
    
    if(recal)
    {
      TObjArray *recalpass=(TObjArray*)recal->FindObject(pass);
      
      if(recalpass)
      {
        TObjArray *recalib=(TObjArray*)recalpass->FindObject("Recalib");
        
        if(recalib)
        {
          printf("AliAnalysisTaskEMCALClusterize::SetOADBParameters() - Recalibrate EMCAL \n");
          for (Int_t i=0; i<nSM; ++i) 
          {
            TH2F *h = fRecoUtils->GetEMCALChannelRecalibrationFactors(i);
            
            if (h)
              delete h;
            
            h = (TH2F*)recalib->FindObject(Form("EMCALRecalFactors_SM%d",i));
            
            if (!h) 
            {
              AliError(Form("Could not load EMCALRecalFactors_SM%d",i));
              continue;
            }
            
            h->SetDirectory(0);
            
            fRecoUtils->SetEMCALChannelRecalibrationFactors(i,h);
          } // SM loop
        }else printf("AliAnalysisTaskEMCALClusterize::SetOADBParameters() - Do NOT recalibrate EMCAL 1\n"); // array ok
      }else printf("AliAnalysisTaskEMCALClusterize::SetOADBParameters() - Do NOT recalibrate EMCAL 2\n"); // array pass ok
    }else printf("AliAnalysisTaskEMCALClusterize::SetOADBParameters() - Do NOT recalibrate EMCAL 3\n");  // run number array ok
    
    // once set, apply run dependent corrections if requested
    fRecoUtils->SetRunDependentCorrections(runnumber);
    
  } // Recalibration on
  
  
  // Time Recalibration
  if(fRecoUtils->IsTimeRecalibrationOn())
  {
    AliOADBContainer *contTRF=new AliOADBContainer("");
    
    contTRF->InitFromFile(Form("%s/EMCALTimeCalib.root",fOADBFilePath.Data()),"AliEMCALTimeCalib");
    
    TObjArray *trecal=(TObjArray*)contTRF->GetObject(runnumber); 
    
    if(trecal)
    {
      TObjArray *trecalpass=(TObjArray*)trecal->FindObject(pass);
      
      if(trecalpass)
      {
        printf("AliCalorimeterUtils::SetOADBParameters() - Time Recalibrate EMCAL \n");
        for (Int_t ibc = 0; ibc < 4; ++ibc) 
        {
          TH1F *h = fRecoUtils->GetEMCALChannelTimeRecalibrationFactors(ibc);
          
          if (h)
            delete h;
          
          h = (TH1F*)trecalpass->FindObject(Form("hAllTimeAvBC%d",ibc));
          
          if (!h) 
          {
            AliError(Form("Could not load hAllTimeAvBC%d",ibc));
            continue;
          }
          
          h->SetDirectory(0);
          
          fRecoUtils->SetEMCALChannelTimeRecalibrationFactors(ibc,h);
        } // bunch crossing loop
      }else printf("AliCalorimeterUtils::SetOADBParameters() - Do NOT recalibrate time EMCAL 1\n"); // array pass ok
    }else printf("AliCalorimeterUtils::SetOADBParameters() - Do NOT recalibrate time EMCAL 2\n");  // run number array ok
    
  } // Time recalibration on    
  
  // Parameters already set once, so do not it again
  fOADBSet = kTRUE;
  
}  

//_________________________________________________
Bool_t AliAnalysisTaskEMCALClusterize::AccessOCDB()
{
  //Access to OCDB stuff
  
  fEvent = InputEvent();
  if (!fEvent)
  {
    Warning("AccessOCDB","Event not available!!!");
    return kFALSE;
  }
  
  if (fEvent->GetRunNumber()==fRun)
    return kTRUE;
  fRun = fEvent->GetRunNumber();
  
  if(DebugLevel() > 1 )
    printf("AliAnalysisTaksEMCALClusterize::AccessODCD() - Begin");
    
  AliCDBManager *cdb = AliCDBManager::Instance();
  
  
  if (fOCDBpath.Length()){
    cdb->SetDefaultStorage(fOCDBpath.Data());
    printf("AliAnalysisTaksEMCALClusterize::AccessOCDB() - Default storage %s",fOCDBpath.Data());
  }
  
  cdb->SetRun(fEvent->GetRunNumber());
  
  //
  // EMCAL from RAW OCDB
  if (fOCDBpath.Contains("alien:"))
  {
    cdb->SetSpecificStorage("EMCAL/Calib/Data","alien://Folder=/alice/data/2010/OCDB");
    cdb->SetSpecificStorage("EMCAL/Calib/Pedestals","alien://Folder=/alice/data/2010/OCDB");
  }
  
  TString path = cdb->GetDefaultStorage()->GetBaseFolder();
  
  // init parameters:
  
  //Get calibration parameters	
  if(!fCalibData)
  {
    AliCDBEntry *entry = (AliCDBEntry*) 
    AliCDBManager::Instance()->Get("EMCAL/Calib/Data");
    
    if (entry) fCalibData =  (AliEMCALCalibData*) entry->GetObject();
  }
  
  if(!fCalibData)
    AliFatal("Calibration parameters not found in CDB!");
  
  //Get calibration parameters	
  if(!fPedestalData)
  {
    AliCDBEntry *entry = (AliCDBEntry*) 
    AliCDBManager::Instance()->Get("EMCAL/Calib/Pedestals");
    
    if (entry) fPedestalData =  (AliCaloCalibPedestal*) entry->GetObject();
  }
  
  if(!fPedestalData)
    AliFatal("Dead map not found in CDB!");
  
  return kTRUE;
}

//_____________________________________________________
void AliAnalysisTaskEMCALClusterize::CheckAndGetEvent()
{
  // Get the input event, it can depend in embedded events what you want to get
  // Also check if the quality of the event is good if not reject it
  
  fEvent = 0x0;
  
  AliAODInputHandler* aodIH = dynamic_cast<AliAODInputHandler*>((AliAnalysisManager::GetAnalysisManager())->GetInputEventHandler());
  Int_t eventN = Entry();
  if(aodIH) eventN = aodIH->GetReadEntry(); 
  
  if (eventN > fMaxEvent) 
    return ;
  
  //printf("Clusterizer --- Event %d-- \n",eventN);

  //Check if input event are embedded events
  //If so, take output event
  if (aodIH && aodIH->GetMergeEvents()) 
  {
    fEvent  = AODEvent();
    
    if(!aodIH->GetMergeEMCALCells()) 
      AliFatal("Events merged but not EMCAL cells, check analysis settings!");
    
    if(DebugLevel() > 1)
    {
      printf("AliAnalysisTaksEMCALClusterize::UserExec() - Use embedded events\n");
      
      printf("\t InputEvent  N Clusters %d, N Cells %d\n",InputEvent()->GetNumberOfCaloClusters(),
             InputEvent()->GetEMCALCells()->GetNumberOfCells());
      
      printf("\t MergedEvent  N Clusters %d, N Cells %d\n",aodIH->GetEventToMerge()->GetNumberOfCaloClusters(),
             aodIH->GetEventToMerge()->GetEMCALCells()->GetNumberOfCells());
      
      for (Int_t icl=0; icl < aodIH->GetEventToMerge()->GetNumberOfCaloClusters(); icl++) 
      {
        AliAODCaloCluster *sigCluster = aodIH->GetEventToMerge()->GetCaloCluster(icl);
        if(sigCluster->IsEMCAL()) printf("\t \t Signal cluster: i %d, E  %f\n",icl,sigCluster->E());
      }
      
      printf("\t OutputEvent N Clusters %d, N Cells %d\n", AODEvent()->GetNumberOfCaloClusters(),
             AODEvent()->GetEMCALCells()->GetNumberOfCells());
    }
  }
  else 
  {
    fEvent =  InputEvent();
    if(fFillAODCaloCells) FillAODCaloCells();   
    if(fFillAODHeader)    FillAODHeader();
  }
  
  if (!fEvent) 
  {
    Error("UserExec","Event not available");
    return ;
  }
  
  //-------------------------------------------------------------------------------------
  // Reject events if LED was firing, use only for LHC11a data 
  // Reject event if triggered by exotic cell and remove exotic cells if not triggered
  //-------------------------------------------------------------------------------------
  
  if( IsLEDEvent( InputEvent()->GetRunNumber() ) ) { fEvent = 0x0 ; return ; }
  
  if( IsExoticEvent() )                            { fEvent = 0x0 ; return ; }
  
  //Magic line to write events to AOD filem put after event rejection
  AliAnalysisManager::GetAnalysisManager()->GetOutputEventHandler()->SetFillAOD(fFillAODFile);
  
}

//____________________________________________________
void AliAnalysisTaskEMCALClusterize::ClusterizeCells()
{ 
  // Recluster calocells, transform them into digits, 
  // feed the clusterizer with them and get new list of clusters
  
  //In case of MC, first loop on the clusters and fill MC label to array  
  Int_t nClusters     = fEvent->GetNumberOfCaloClusters();
  Int_t nClustersOrg  = 0;

  AliAODInputHandler* aodIH = dynamic_cast<AliAODInputHandler*>((AliAnalysisManager::GetAnalysisManager())->GetInputEventHandler());
  if(aodIH && aodIH->GetEventToMerge())  //Embedding
    nClusters = aodIH->GetEventToMerge()->GetNumberOfCaloClusters(); //Get clusters directly from embedded signal
  
  for (Int_t i = 0; i < nClusters; i++)
  {
    AliVCluster *clus = 0;
    if(aodIH && aodIH->GetEventToMerge()) //Embedding
      clus = aodIH->GetEventToMerge()->GetCaloCluster(i); //Get clusters directly from embedded signal
    else      
      clus = fEvent->GetCaloCluster(i);
    
    if(!clus) return;
    
    if(clus->IsEMCAL())
    {   
      Int_t label = clus->GetLabel();
      Int_t label2 = -1 ;
      //printf("Org cluster E %f, Time  %e, Id = ", clus->E(), clus->GetTOF() );
      if (clus->GetNLabels()>=2) label2 = clus->GetLabelAt(1) ;
      UShort_t * index    = clus->GetCellsAbsId() ;
      for(Int_t icell=0; icell < clus->GetNCells(); icell++ )
      {
        fCellLabels[index[icell]]       = label;
        fCellSecondLabels[index[icell]] = label2;
        fCellTime[index[icell]]         = clus->GetTOF();    
        fCellMatchdEta[index[icell]]    = clus->GetTrackDz();
        fCellMatchdPhi[index[icell]]    = clus->GetTrackDx();
        //printf(" %d,", index[icell] );
      }
      nClustersOrg++;
    }
     // printf("\n");
  } 
  
  // Transform CaloCells into Digits

  Int_t    idigit =  0;
  Int_t    id     = -1;
  Float_t  amp    = -1; 
  Double_t time   = -1; 
  
  AliVCaloCells *cells   = fEvent->GetEMCALCells();
  
  TFile* file = new TFile("tmpTree.root","recreate"); // Trick to avoid annoying messages FIXME
  TTree *digitsTree = new TTree("digitstree","digitstree");
  digitsTree->Branch("EMCAL","TClonesArray", &fDigitsArr, 32000);

  Int_t bc = InputEvent()->GetBunchCrossNumber();
  for (Int_t icell = 0; icell < cells->GetNumberOfCells(); icell++)
  {
    
    // Get cell values, recalibrate and not include bad channels found in analysis, nor cells with too low energy, nor exotic cell
    id = cells->GetCellNumber(icell);
    Bool_t accept = fRecoUtils->AcceptCalibrateCell(id,bc,amp,time,cells);
    
    // Do not include cells with too low energy, nor exotic cell
    if(amp < fRecParam->GetMinECut() ) accept = kFALSE;
    
    // In case of AOD analysis cell time is 0, approximate replacing by time of the cluster the digit belongs.
    if (time*1e9 < 1.) 
    { 
      time = fCellTime[id];
      //printf("cell %d time org %f - ",id, time*1.e9);
      fRecoUtils->RecalibrateCellTime(id,bc,time);
      //printf("recal %f\n",time*1.e9);
    }
    
    if(  accept && fRecoUtils->IsExoticCell(id,cells,bc))
    {
      accept = kFALSE;
    }

    if( !accept )
    {
      fCellLabels[id]      =-1; //reset the entry in the array for next event
      fCellSecondLabels[id]=-1; //reset the entry in the array for next event
      fCellTime[id]        = 0.; 
      fCellMatchdEta[id]   =-999;
      fCellMatchdPhi[id]   =-999;
      if( DebugLevel() > 2 )
        printf("AliAnalysisTaksEMCALClusterize::ClusterizeCells() - Remove channel absId %d, index %d of %d, amp %f, time %f\n",
                                    id,icell, cells->GetNumberOfCells(), amp, time*1.e9);
      continue;
    }
            
    //Create the digit, put a fake primary deposited energy to trick the clusterizer when checking the most likely primary
    new((*fDigitsArr)[idigit]) AliEMCALDigit( fCellLabels[id], fCellLabels[id],id, amp, time,AliEMCALDigit::kHG,idigit, 0, 0, 1); 
 
    fCellLabels[id]      =-1; //reset the entry in the array for next event
    
    idigit++;
  }
  
  //Fill the tree with digits
  digitsTree->Fill();
  
  //-------------------------------------------------------------------------------------
  //Do the clusterization
  //-------------------------------------------------------------------------------------        
  TTree *clustersTree = new TTree("clustertree","clustertree");
  
  fClusterizer->SetInput(digitsTree);
  fClusterizer->SetOutput(clustersTree);
  fClusterizer->Digits2Clusters("");
  
  //-------------------------------------------------------------------------------------
  //Transform the recpoints into AliVClusters
  //-------------------------------------------------------------------------------------
  
  clustersTree->SetBranchStatus("*",0); //disable all branches
  clustersTree->SetBranchStatus("EMCALECARP",1); //Enable only the branch we need
  
  TBranch *branch = clustersTree->GetBranch("EMCALECARP");
  branch->SetAddress(&fClusterArr);

  branch->GetEntry(0);

  RecPoints2Clusters(fDigitsArr, fClusterArr, fCaloClusterArr);
  
  if(!fCaloClusterArr)
  { 
    printf("AliAnalysisTaksEMCALClusterize::UserExec() - No array with CaloClusters, input RecPoints entries %d\n",fClusterArr->GetEntriesFast());
    return;    
  }
  
  if( DebugLevel() > 0 )
  {
    printf("AliAnalysisTaksEMCALClusterize::ClusterizeCells() - N clusters: before recluster %d, after recluster %d\n",nClustersOrg, fCaloClusterArr->GetEntriesFast());

    if(fCaloClusterArr->GetEntriesFast() != fClusterArr->GetEntriesFast()){
      printf("\t Some RecRoints not transformed into CaloClusters (clusterizer %d, unfold %d): Input entries %d - Output entries %d - %d (not fast)\n",
             fRecParam->GetClusterizerFlag(),fRecParam->GetUnfold(),
             fClusterArr->GetEntriesFast(), fCaloClusterArr->GetEntriesFast(), fCaloClusterArr->GetEntries());
    }
  }
  
  //Reset the array with second labels for this event
  memset(fCellSecondLabels, -1, sizeof(fCellSecondLabels));
  
  //---CLEAN UP-----
  fClusterizer->Clear();
  fDigitsArr  ->Clear("C");
  fClusterArr ->Delete(); // Do not Clear(), it leaks, why?
  
  clustersTree->Delete("all");  
  digitsTree  ->Delete("all");  
  
  // Trick to avoid annoying messages FIXME
  file->Close();
  delete file;
}

//_____________________________________________________
void AliAnalysisTaskEMCALClusterize::ClusterUnfolding()
{
  // Take the event clusters and unfold them
  
  AliVCaloCells *cells   = fEvent->GetEMCALCells();
  Double_t cellAmplitude = 0;
  Double_t cellTime      = 0;
  Short_t  cellNumber    = 0;
  Int_t    nClustersOrg  = 0;
  
  // Fill the array with the EMCAL clusters, copy them
  for (Int_t i = 0; i < fEvent->GetNumberOfCaloClusters(); i++)
  {
    AliVCluster *clus = fEvent->GetCaloCluster(i);
    if(clus->IsEMCAL()){        
      
      //recalibrate/remove bad channels/etc if requested
      if(fRecoUtils->ClusterContainsBadChannel(fGeom,clus->GetCellsAbsId(), clus->GetNCells())){
        continue;
      } 
      
      if(fRecoUtils->IsRecalibrationOn()){
        
        //Calibrate cluster
        fRecoUtils->RecalibrateClusterEnergy(fGeom, clus, cells);
        
        //CalibrateCells
        for (Int_t icell = 0; icell < cells->GetNumberOfCells(); icell++)
        {
          if (cells->GetCell(icell, cellNumber, cellAmplitude, cellTime) != kTRUE)
            break;
          
          Int_t imod = -1, iphi =-1, ieta=-1,iTower = -1, iIphi = -1, iIeta = -1; 
          fGeom->GetCellIndex(cellNumber,imod,iTower,iIphi,iIeta); 
          fGeom->GetCellPhiEtaIndexInSModule(imod,iTower,iIphi, iIeta,iphi,ieta);	
          
          //Do not include bad channels found in analysis?
          if( fRecoUtils->IsBadChannelsRemovalSwitchedOn() && 
             fRecoUtils->GetEMCALChannelStatus(imod, ieta, iphi)){
            fCellLabels[cellNumber]      =-1; //reset the entry in the array for next event
            fCellSecondLabels[cellNumber]=-1; //reset the entry in the array for next event
            fCellTime[cellNumber]        = 0.;   
            fCellMatchdEta[cellNumber]   =-999;
            fCellMatchdPhi[cellNumber]   =-999;
            continue;
          }
          
          cells->SetCell(icell, cellNumber, cellAmplitude*fRecoUtils->GetEMCALChannelRecalibrationFactor(imod,ieta,iphi),cellTime);
          
        }// cells loop            
      }// recalibrate
      
      //Cast to ESD or AOD, needed to create the cluster array
      AliESDCaloCluster * esdCluster = dynamic_cast<AliESDCaloCluster*> (clus);
      AliAODCaloCluster * aodCluster = dynamic_cast<AliAODCaloCluster*> (clus);
      if     (esdCluster){
        fCaloClusterArr->Add( new AliESDCaloCluster(*esdCluster) );   
      }//ESD
      else if(aodCluster){
        fCaloClusterArr->Add( new AliAODCaloCluster(*aodCluster) );   
      }//AOD
      else 
        Warning("UserExec()"," - Wrong CaloCluster type?");
      nClustersOrg++;
    }
  }
  
  //Do the unfolding
  fUnfolder->UnfoldClusters(fCaloClusterArr, cells);
  
  //CLEAN-UP
  fUnfolder->Clear();
  
}

//_____________________________________________________
void AliAnalysisTaskEMCALClusterize::FillAODCaloCells() 
{
  // Put calo cells in standard branch  
  AliVCaloCells &eventEMcells = *(fEvent->GetEMCALCells());
  Int_t nEMcell = eventEMcells.GetNumberOfCells() ;
  
  AliAODCaloCells &aodEMcells = *(AODEvent()->GetEMCALCells());
  aodEMcells.CreateContainer(nEMcell);
  aodEMcells.SetType(AliVCaloCells::kEMCALCell);
  Double_t calibFactor = 1.;   
  for (Int_t iCell = 0; iCell < nEMcell; iCell++) { 
    Int_t imod = -1, iphi =-1, ieta=-1,iTower = -1, iIphi = -1, iIeta = -1; 
    fGeom->GetCellIndex(eventEMcells.GetCellNumber(iCell),imod,iTower,iIphi,iIeta); 
    fGeom->GetCellPhiEtaIndexInSModule(imod,iTower,iIphi, iIeta,iphi,ieta);	
    
    if(fRecoUtils->IsRecalibrationOn()){ 
      calibFactor = fRecoUtils->GetEMCALChannelRecalibrationFactor(imod,ieta,iphi);
    }
    
    if(!fRecoUtils->GetEMCALChannelStatus(imod, ieta, iphi)){ //Channel is not declared as bad
      aodEMcells.SetCell(iCell,eventEMcells.GetCellNumber(iCell),eventEMcells.GetAmplitude(iCell)*calibFactor);
    }
    else {
      aodEMcells.SetCell(iCell,eventEMcells.GetCellNumber(iCell),0);
    }
  }
  aodEMcells.Sort();
  
}

//__________________________________________________
void AliAnalysisTaskEMCALClusterize::FillAODHeader() 
{
  //Put event header information in standard AOD branch
  
  AliESDEvent* esdevent = dynamic_cast<AliESDEvent*> (fEvent);
  AliAODEvent* aodevent = dynamic_cast<AliAODEvent*> (fEvent);
  
  Double_t pos[3]   ;
  Double_t covVtx[6];
  for (Int_t i = 0; i < 6; i++)  covVtx[i] = 0.;
  
  AliAODHeader* header = AODEvent()->GetHeader();
  header->SetRunNumber(fEvent->GetRunNumber());
  
  if(esdevent){
    TTree* tree = fInputHandler->GetTree();
    if (tree) {
      TFile* file = tree->GetCurrentFile();
      if (file) header->SetESDFileName(file->GetName());
    }
  }
  else if (aodevent) header->SetESDFileName(aodevent->GetHeader()->GetESDFileName());
  
  header->SetBunchCrossNumber(fEvent->GetBunchCrossNumber());
  header->SetOrbitNumber(fEvent->GetOrbitNumber());
  header->SetPeriodNumber(fEvent->GetPeriodNumber());
  header->SetEventType(fEvent->GetEventType());
  
  //Centrality
  if(fEvent->GetCentrality()){
    header->SetCentrality(new AliCentrality(*(fEvent->GetCentrality())));
  }
  else{
    header->SetCentrality(0);
  }
  
  //Trigger  
  header->SetOfflineTrigger(fInputHandler->IsEventSelected()); // propagate the decision of the physics selection
  if      (esdevent) header->SetFiredTriggerClasses(esdevent->GetFiredTriggerClasses());
  else if (aodevent) header->SetFiredTriggerClasses(aodevent->GetFiredTriggerClasses());
  header->SetTriggerMask(fEvent->GetTriggerMask()); 
  header->SetTriggerCluster(fEvent->GetTriggerCluster());
  if(esdevent){
    header->SetL0TriggerInputs(esdevent->GetHeader()->GetL0TriggerInputs());    
    header->SetL1TriggerInputs(esdevent->GetHeader()->GetL1TriggerInputs());    
    header->SetL2TriggerInputs(esdevent->GetHeader()->GetL2TriggerInputs());    
  }
  else if (aodevent){
    header->SetL0TriggerInputs(aodevent->GetHeader()->GetL0TriggerInputs());    
    header->SetL1TriggerInputs(aodevent->GetHeader()->GetL1TriggerInputs());    
    header->SetL2TriggerInputs(aodevent->GetHeader()->GetL2TriggerInputs());    
  }
  
  header->SetMagneticField(fEvent->GetMagneticField());
  //header->SetMuonMagFieldScale(esdevent->GetCurrentDip()/6000.); 
  
  header->SetZDCN1Energy(fEvent->GetZDCN1Energy());
  header->SetZDCP1Energy(fEvent->GetZDCP1Energy());
  header->SetZDCN2Energy(fEvent->GetZDCN2Energy());
  header->SetZDCP2Energy(fEvent->GetZDCP2Energy());
  header->SetZDCEMEnergy(fEvent->GetZDCEMEnergy(0),fEvent->GetZDCEMEnergy(1));
  
  Float_t diamxy[2]={fEvent->GetDiamondX(),fEvent->GetDiamondY()};
  Float_t diamcov[3];
  fEvent->GetDiamondCovXY(diamcov);
  header->SetDiamond(diamxy,diamcov);
  if      (esdevent) header->SetDiamondZ(esdevent->GetDiamondZ(),esdevent->GetSigma2DiamondZ());
  else if (aodevent) header->SetDiamondZ(aodevent->GetDiamondZ(),aodevent->GetSigma2DiamondZ());
  
  //
  //
  Int_t nVertices = 1 ;/* = prim. vtx*/;
  Int_t nCaloClus = fEvent->GetNumberOfCaloClusters();
  
  AODEvent()->ResetStd(0, nVertices, 0, 0, 0, nCaloClus, 0, 0);
  
  // Access to the AOD container of vertices
  TClonesArray &vertices = *(AODEvent()->GetVertices());
  Int_t jVertices=0;
  
  // Add primary vertex. The primary tracks will be defined
  // after the loops on the composite objects (V0, cascades, kinks)
  fEvent->GetPrimaryVertex()->GetXYZ(pos);
  Float_t chi = 0;
  if      (esdevent){
    esdevent->GetPrimaryVertex()->GetCovMatrix(covVtx);
    chi = esdevent->GetPrimaryVertex()->GetChi2toNDF();
  }
  else if (aodevent){
    aodevent->GetPrimaryVertex()->GetCovMatrix(covVtx);
    chi = aodevent->GetPrimaryVertex()->GetChi2perNDF();//Different from ESD?
  }
  
  AliAODVertex * primary = new(vertices[jVertices++])
  AliAODVertex(pos, covVtx, chi, NULL, -1, AliAODVertex::kPrimary);
  primary->SetName(fEvent->GetPrimaryVertex()->GetName());
  primary->SetTitle(fEvent->GetPrimaryVertex()->GetTitle());
  
}

//_______________________________________________
TString AliAnalysisTaskEMCALClusterize::GetPass()
{
  // Get passx from filename.
  
  if (!AliAnalysisManager::GetAnalysisManager()->GetTree()) 
  {
    AliError("AliAnalysisTaskEMCALClusterize::GetPass() - Pointer to tree = 0, returning null\n");
    return TString("");
  }
  
  if (!AliAnalysisManager::GetAnalysisManager()->GetTree()->GetCurrentFile()) 
  {
    AliError("AliAnalysisTaskEMCALClusterize::GetPass() - Null pointer input file, returning null\n");
    return TString("");
  }
  
  TString pass(AliAnalysisManager::GetAnalysisManager()->GetTree()->GetCurrentFile()->GetName());
  if      (pass.Contains("ass1")) return TString("pass1");
  else if (pass.Contains("ass2")) return TString("pass2");
  else if (pass.Contains("ass3")) return TString("pass3");
  
  // No condition fullfilled, give a default value
  printf("AliAnalysisTaskEMCALClusterize::GetPass() - Pass number string not found \n");
  return TString("");            
  
}

//_________________________________________
void AliAnalysisTaskEMCALClusterize::Init()
{
  //Init analysis with configuration macro if available
  
  fOADBSet           = kFALSE;
  if(fOADBFilePath == "") fOADBFilePath = "$ALICE_ROOT/OADB/EMCAL" ;          
  
  fDigitsArr         = new TClonesArray("AliEMCALDigit",12000);
  fClusterArr        = new TObjArray(10000);
  fCaloClusterArr    = new TObjArray(10000);
  fBranchNames       = "ESD:AliESDHeader.,EMCALCells.";
  
  if(!fRecParam)     fRecParam  = new AliEMCALRecParam;
  if(!fRecoUtils)    fRecoUtils = new AliEMCALRecoUtils();  
  
  if(fMaxEvent          <= 0) fMaxEvent          = 1000000000;
  if(fSelectCellMinE    <= 0) fSelectCellMinE    = 0.005;     
  if(fSelectCellMinFrac <= 0) fSelectCellMinFrac = 0.001;
  
  if (fOCDBpath            == "") fOCDBpath            = "raw://" ;
  if (fOutputAODBranchName == "") fOutputAODBranchName = "newEMCALClusters" ;
  
  if(gROOT->LoadMacro(fConfigName) >=0)
  {
    printf("AliAnalysisTaksEMCALClusterize::Init() - Configure analysis with %s\n",fConfigName.Data());
    AliAnalysisTaskEMCALClusterize *clus = (AliAnalysisTaskEMCALClusterize*)gInterpreter->ProcessLine("ConfigEMCALClusterize()");
    fGeomName         = clus->fGeomName; 
    fLoadGeomMatrices = clus->fLoadGeomMatrices;
    fOCDBpath         = clus->fOCDBpath;   
    fAccessOCDB       = clus->fAccessOCDB;
    fRecParam         = clus->fRecParam;
    fJustUnfold       = clus->fJustUnfold;
    fFillAODFile      = clus->fFillAODFile;
    fRecoUtils        = clus->fRecoUtils; 
    fConfigName       = clus->fConfigName;
    fMaxEvent         = clus->fMaxEvent;
    fDoTrackMatching  = clus->fDoTrackMatching;
    fOutputAODBranchName = clus->fOutputAODBranchName;
    for(Int_t i = 0; i < 12; i++) fGeomMatrix[i] = clus->fGeomMatrix[i] ;
  }
  
  // Init geometry, I do not like much to do it like this ...
  if(fImportGeometryFromFile && !gGeoManager) 
  {
    if (fImportGeometryFilePath == "") fImportGeometryFilePath = "$ALICE_ROOT/PWGGA/EMCALTasks/macros/geometry.root" ; // "$ALICE_ROOT/EVE/alice-data/default_geo.root"
    printf("AliAnalysisTaskEMCALClusterize::Init() - Import %s\n",fImportGeometryFilePath.Data());
    TGeoManager::Import(fImportGeometryFilePath) ; 
  }

}  

//_______________________________________________________
void AliAnalysisTaskEMCALClusterize::InitClusterization()
{
  //Select clusterization/unfolding algorithm and set all the needed parameters
  
  if (fJustUnfold){
    // init the unfolding afterburner 
    delete fUnfolder;
    fUnfolder =  new AliEMCALAfterBurnerUF(fRecParam->GetW0(),fRecParam->GetLocMaxCut(),fRecParam->GetMinECut());
    return;
  }
  
  //First init the clusterizer
  delete fClusterizer;
  if     (fRecParam->GetClusterizerFlag() == AliEMCALRecParam::kClusterizerv1)
    fClusterizer = new AliEMCALClusterizerv1 (fGeom, fCalibData, fPedestalData);
  else if(fRecParam->GetClusterizerFlag() == AliEMCALRecParam::kClusterizerv2) 
    fClusterizer = new AliEMCALClusterizerv2(fGeom, fCalibData, fPedestalData);
  else if(fRecParam->GetClusterizerFlag() == AliEMCALRecParam::kClusterizerNxN){ 
    fClusterizer = new AliEMCALClusterizerNxN(fGeom, fCalibData, fPedestalData);
    fClusterizer->SetNRowDiff(fRecParam->GetNRowDiff());
    fClusterizer->SetNColDiff(fRecParam->GetNColDiff());
  } else {
    AliFatal(Form("Clusterizer < %d > not available", fRecParam->GetClusterizerFlag()));
  }
  
  //Now set the parameters
  fClusterizer->SetECAClusteringThreshold( fRecParam->GetClusteringThreshold() );
  fClusterizer->SetECALogWeight          ( fRecParam->GetW0()                  );
  fClusterizer->SetMinECut               ( fRecParam->GetMinECut()             );    
  fClusterizer->SetUnfolding             ( fRecParam->GetUnfold()              );
  fClusterizer->SetECALocalMaxCut        ( fRecParam->GetLocMaxCut()           );
  fClusterizer->SetTimeCut               ( fRecParam->GetTimeCut()             );
  fClusterizer->SetTimeMin               ( fRecParam->GetTimeMin()             );
  fClusterizer->SetTimeMax               ( fRecParam->GetTimeMax()             );
  fClusterizer->SetInputCalibrated       ( kTRUE                               );
  fClusterizer->SetJustClusters          ( kTRUE                               );  
  //In case of unfolding after clusterization is requested, set the corresponding parameters
  if(fRecParam->GetUnfold()){
    Int_t i=0;
    for (i = 0; i < 8; i++) {
      fClusterizer->SetSSPars(i, fRecParam->GetSSPars(i));
    }//end of loop over parameters
    for (i = 0; i < 3; i++) {
      fClusterizer->SetPar5  (i, fRecParam->GetPar5(i));
      fClusterizer->SetPar6  (i, fRecParam->GetPar6(i));
    }//end of loop over parameters
    
    fClusterizer->InitClusterUnfolding();
    
  }// to unfold
}

//_________________________________________________
void AliAnalysisTaskEMCALClusterize::InitGeometry()
{
  // Init geometry and set the geometry matrix, for the first event, skip the rest
  // Also set once the run dependent calibrations
  
  if(fGeomMatrixSet) return;
  
  Int_t runnumber = InputEvent()->GetRunNumber() ;
  if (!fGeom)
  {
    if(fGeomName=="")
    {
      if     (runnumber < 140000) fGeomName = "EMCAL_FIRSTYEARV1";
      else if(runnumber < 171000) fGeomName = "EMCAL_COMPLETEV1";
      else                        fGeomName = "EMCAL_COMPLETE12SMV1";  
      printf("AliAnalysisTaskEMCALClusterize::InitGeometry() - Set EMCAL geometry name to <%s> for run %d\n",fGeomName.Data(),runnumber);
    }
    
		fGeom = AliEMCALGeometry::GetInstance(fGeomName);
    
		if(fDebug > 0)
    {
			printf("AliAnalysisTaskEMCALClusterize::InitGeometry(run=%d)",runnumber);
			if (!gGeoManager) printf(" - Careful!, gGeoManager not loaded, load misalign matrices");
			printf("\n");
		}
	} // geometry pointer did not exist before
  
  if(fLoadGeomMatrices)
  {
    printf("AliAnalysisTaskEMCALClusterize::InitGeometry() - Load user defined EMCAL geometry matrices\n");
    
    // OADB if available
    AliOADBContainer emcGeoMat("AliEMCALgeo");
    emcGeoMat.InitFromFile(Form("%s/EMCALlocal2master.root",fOADBFilePath.Data()),"AliEMCALgeo");
    TObjArray *matEMCAL=(TObjArray*)emcGeoMat.GetObject(runnumber,"EmcalMatrices");
    
    
    for(Int_t mod=0; mod < (fGeom->GetEMCGeometry())->GetNumberOfSuperModules(); mod++)
    {
      
      if (!fGeomMatrix[mod]) // Get it from OADB
      {
        if(fDebug > 1 ) 
          printf("AliAnalysisTaskEMCALClusterize::InitGeometry() - EMCAL matrices SM %d, %p\n",
                 mod,((TGeoHMatrix*) matEMCAL->At(mod)));
        //((TGeoHMatrix*) matEMCAL->At(mod))->Print();
        
        fGeomMatrix[mod] = (TGeoHMatrix*) matEMCAL->At(mod) ;
      }        
      
      if(fGeomMatrix[mod])
      {
        if(DebugLevel() > 1) 
          fGeomMatrix[mod]->Print();
        
        fGeom->SetMisalMatrix(fGeomMatrix[mod],mod) ;  
      }
      
      fGeomMatrixSet=kTRUE;
      
    }//SM loop
  }//Load matrices
  else if(!gGeoManager)
  {
    printf("AliAnalysisTaksEMCALClusterize::InitGeometry() - Get geo matrices from data");
    //Still not implemented in AOD, just a workaround to be able to work at least with ESDs	
    if(!strcmp(fEvent->GetName(),"AliAODEvent")) 
    {
      if(DebugLevel() > 1) 
        Warning("UserExec","Use ideal geometry, values geometry matrix not kept in AODs.");
    }//AOD
    else 
    {	
      if(DebugLevel() > 1) 
        printf("AliAnalysisTaksEMCALClusterize::InitGeometry() - AliAnalysisTaskEMCALClusterize Load Misaligned matrices.");
      
      AliESDEvent* esd = dynamic_cast<AliESDEvent*>(fEvent) ;
      
      if(!esd)
      {
        Error("InitGeometry"," - This event does not contain ESDs?");
        AliAnalysisManager::GetAnalysisManager()->GetOutputEventHandler()->SetFillAOD(kFALSE);
        return;
      }
      
      for(Int_t mod=0; mod < (fGeom->GetEMCGeometry())->GetNumberOfSuperModules(); mod++)
      {
        if(DebugLevel() > 1) 
          esd->GetEMCALMatrix(mod)->Print();
        
        if(esd->GetEMCALMatrix(mod)) fGeom->SetMisalMatrix(esd->GetEMCALMatrix(mod),mod) ;
        
      } 
      
      fGeomMatrixSet=kTRUE;
      
    }//ESD
  }//Load matrices from Data 
  
  
}

//____________________________________________________
Bool_t AliAnalysisTaskEMCALClusterize::IsExoticEvent()
{
  
  // Check if event is exotic, get an exotic cell and compare with triggered patch
  // If there is a match remove event ... to be completed, filled with something provisional
  
  if(!fRemoveExoticEvents) return kFALSE;
  
  // Loop on cells
  AliVCaloCells * cells = fEvent->GetEMCALCells();
  Float_t totCellE = 0;
  Int_t bc = InputEvent()->GetBunchCrossNumber();
  for(Int_t icell = 0; icell < cells->GetNumberOfCells(); icell++){
    
    Float_t  ecell = 0 ;
    Double_t tcell = 0 ;
    
    Int_t absID   = cells->GetCellNumber(icell);
    Bool_t accept = fRecoUtils->AcceptCalibrateCell(absID,bc,ecell,tcell,cells);
    if(accept && !fRecoUtils->IsExoticCell(absID,cells,bc)) totCellE += ecell;
  }
  
  //  TString triggerclasses = "";
  //  if(esdevent) triggerclasses = esdevent             ->GetFiredTriggerClasses();
  //  else         triggerclasses = ((AliAODEvent*)event)->GetFiredTriggerClasses();
  //    //  
  //    printf("AliAnalysisTaskEMCALClusterize - reject event %d with cluster  - reject event with ncells in SM3 %d and SM4 %d\n",(Int_t)Entry(),ncellsSM3, ncellsSM4);
  //    AliAnalysisManager::GetAnalysisManager()->GetOutputEventHandler()->SetFillAOD(kFALSE);
  //    return;
  //  
  
  //printf("TotE cell %f\n",totCellE);
  if(totCellE < 1) return kTRUE;
  
  return kFALSE;
  
} 

//________________________________________________________________
Bool_t AliAnalysisTaskEMCALClusterize::IsLEDEvent(const Int_t run)
{
  //Check if event is LED
  
  if(!fRemoveLEDEvents) return kFALSE;
  
  //check events of LHC11a period
  if(run < 140000  || run > 146860) return kFALSE ;
  
  // Count number of cells with energy larger than 0.1 in SM3, cut on this number
  Int_t ncellsSM3 = 0;
  Int_t ncellsSM4 = 0;
  AliVCaloCells * cells = fEvent->GetEMCALCells();
  for(Int_t icell = 0; icell < cells->GetNumberOfCells(); icell++)
  {
    if(cells->GetAmplitude(icell) > 0.1 && cells->GetCellNumber(icell)/(24*48)==3) ncellsSM3++;
    if(cells->GetAmplitude(icell) > 0.1 && cells->GetCellNumber(icell)/(24*48)==4) ncellsSM4++;      
  }
  
  TString triggerclasses = "";
  
  AliESDEvent *esdevent = dynamic_cast<AliESDEvent*>(fEvent);
  if(esdevent) triggerclasses = esdevent              ->GetFiredTriggerClasses();
  else         triggerclasses = ((AliAODEvent*)fEvent)->GetFiredTriggerClasses();
  
  Int_t ncellcut = 21;
  if(triggerclasses.Contains("EMC")) ncellcut = 35;
  
  if( ncellsSM3 >= ncellcut || ncellsSM4 >= 100 )
  {
    printf("AliAnalysisTaksEMCALClusterize::IsLEDEvent() - reject event %d with ncells in SM3 %d and SM4 %d\n",(Int_t)Entry(),ncellsSM3, ncellsSM4);
    AliAnalysisManager::GetAnalysisManager()->GetOutputEventHandler()->SetFillAOD(kFALSE);
    return kTRUE;
  }
  
  return kFALSE;
  
} 

//______________________________________________________________________________
void AliAnalysisTaskEMCALClusterize::RecPoints2Clusters(TClonesArray *digitsArr, 
                                                        TObjArray *recPoints, 
                                                        TObjArray *clusArray)
{
  // Restore clusters from recPoints
  // Cluster energy, global position, cells and their amplitude fractions are restored
  Int_t j = 0;
  for(Int_t i = 0; i < recPoints->GetEntriesFast(); i++)
  {
    AliEMCALRecPoint *recPoint = (AliEMCALRecPoint*) recPoints->At(i);
    
    const Int_t ncells = recPoint->GetMultiplicity();
    Int_t ncellsTrue = 0;
    
    if(recPoint->GetEnergy() < fRecParam->GetClusteringThreshold()) continue;
    
    // cells and their amplitude fractions
    UShort_t   absIds[ncells];  
    Double32_t ratios[ncells];
    
    //For later check embedding
    AliAODInputHandler* aodIH = dynamic_cast<AliAODInputHandler*>((AliAnalysisManager::GetAnalysisManager())->GetInputEventHandler());
    
    Float_t clusterE = 0; 
    for (Int_t c = 0; c < ncells; c++) 
    {
      AliEMCALDigit *digit = (AliEMCALDigit*) digitsArr->At(recPoint->GetDigitsList()[c]);
      
      absIds[ncellsTrue] = digit->GetId();
      ratios[ncellsTrue] = recPoint->GetEnergiesList()[c]/digit->GetAmplitude();
      
      // In case of unfolding, remove digits with unfolded energy too low      
      if(fSelectCell){
        if     (recPoint->GetEnergiesList()[c] < fSelectCellMinE || ratios[ncellsTrue] < fSelectCellMinFrac)  
        {
          if(DebugLevel() > 1)  
          {
            printf("AliAnalysisTaksEMCALClusterize::RecPoints2Clusters() - Too small energy in cell of cluster: cluster cell %f, digit %f\n",
                   recPoint->GetEnergiesList()[c],digit->GetAmplitude());
          }
          
          continue;
          
        } // if cuts
      }// Select cells
      
      //Recalculate cluster energy and number of cluster cells in case any of the cells was rejected
      ncellsTrue++;
      clusterE  +=recPoint->GetEnergiesList()[c];
      
      // In case of embedding, fill ratio with amount of signal, 
      if (aodIH && aodIH->GetMergeEvents()) 
      {
        //AliVCaloCells* inEMCALCells = InputEvent()->GetEMCALCells();
        AliVCaloCells* meEMCALCells = aodIH->GetEventToMerge()->GetEMCALCells();
        AliVCaloCells* ouEMCALCells = AODEvent()->GetEMCALCells();
        
        Float_t sigAmplitude = meEMCALCells->GetCellAmplitude(absIds[ncellsTrue]);
        //Float_t bkgAmplitude = inEMCALCells->GetCellAmplitude(absIds[ncellsTrue]);
        Float_t sumAmplitude = ouEMCALCells->GetCellAmplitude(absIds[ncellsTrue]);
        //printf("\t AbsID %d, amplitude : bkg %f, sigAmplitude %f, summed %f - %f\n",absIds[ncellsTrue], bkgAmplitude, sigAmplitude, sumAmplitude, digit->GetAmplitude());
        
        if(sumAmplitude > 0) ratios[ncellsTrue] = sigAmplitude/sumAmplitude;
        //printf("\t \t ratio %f\n",ratios[ncellsTrue]);
        
      }//Embedding
      
    }// cluster cell loop
    
    if (ncellsTrue < 1) 
    {
      if (DebugLevel() > 1) 
        printf("AliAnalysisTaskEMCALClusterize::RecPoints2Clusters() - Skipping cluster with no cells avobe threshold E = %f, ncells %d\n",
               recPoint->GetEnergy(), ncells);
      continue;
    }
    
    //if(ncellsTrue != ncells) printf("Old E %f, ncells %d; New E %f, ncells %d\n",recPoint->GetEnergy(),ncells,clusterE,ncellsTrue);
    
    if(clusterE <  fRecParam->GetClusteringThreshold()) 
    {
      if (DebugLevel()>1)
        printf("AliAnalysisTaskEMCALClusterize::RecPoints2Clusters() - Remove cluster with energy below seed threshold %f\n",clusterE);
      continue;
    }
    
    TVector3 gpos;
    Float_t g[3];
    
    // calculate new cluster position
    recPoint->EvalGlobalPosition(fRecParam->GetW0(), digitsArr);
    recPoint->GetGlobalPosition(gpos);
    gpos.GetXYZ(g);
    
    // create a new cluster
    (*clusArray)[j] = new AliAODCaloCluster() ;
    AliAODCaloCluster *clus = dynamic_cast<AliAODCaloCluster *>( clusArray->At(j) ) ;
    j++;
    clus->SetType(AliVCluster::kEMCALClusterv1);
    clus->SetE(clusterE);
    clus->SetPosition(g);
    clus->SetNCells(ncellsTrue);
    clus->SetCellsAbsId(absIds);
    clus->SetCellsAmplitudeFraction(ratios);
    clus->SetChi2(-1); //not yet implemented
    clus->SetTOF(recPoint->GetTime()) ; //time-of-flight
    clus->SetNExMax(recPoint->GetNExMax()); //number of local maxima
    clus->SetDistanceToBadChannel(recPoint->GetDistanceToBadTower()); 

    if(ncells == ncellsTrue)
    {
      Float_t elipAxis[2];
      recPoint->GetElipsAxis(elipAxis);
      clus->SetM02(elipAxis[0]*elipAxis[0]) ;
      clus->SetM20(elipAxis[1]*elipAxis[1]) ;
      clus->SetDispersion(recPoint->GetDispersion());
    }
    else if(fSelectCell)
    {
      // In case some cells rejected, in unfolding case, recalculate
      // shower shape parameters and position
      //if(DebugLevel() > 1) 
        printf("AliAnalysisTaskEMCALClusterize::RecPoints2Clusters() - Cells removed from cluster (ncells %d, ncellsTrue %d), recalculate Shower Shape\n",ncells,ncellsTrue);
      AliVCaloCells* cells = 0x0; 
      if (aodIH && aodIH->GetMergeEvents()) cells = AODEvent()  ->GetEMCALCells();
      else                                  cells = InputEvent()->GetEMCALCells();
      fRecoUtils->RecalculateClusterShowerShapeParameters(fGeom,cells,clus);
      fRecoUtils->RecalculateClusterPID(clus);
      fRecoUtils->RecalculateClusterPosition(fGeom,cells,clus); 
      
    }
    
    //MC
    Int_t  parentMult = 0;
    Int_t *parentList = recPoint->GetParents(parentMult);
    clus->SetLabel(parentList, parentMult); 
    
    //Write the second major contributor to each MC cluster.
    Int_t iNewLabel ;
    for ( Int_t iLoopCell = 0 ; iLoopCell < clus->GetNCells() ; iLoopCell++ )
    {
      
      Int_t idCell = clus->GetCellAbsId(iLoopCell) ;
      if(idCell>=0){
        iNewLabel = 1 ; //iNewLabel makes sure we  don't write twice the same label.
        for ( UInt_t iLoopLabels = 0 ; iLoopLabels < clus->GetNLabels() ; iLoopLabels++ )
        {
          if ( fCellSecondLabels[idCell] == -1 )  iNewLabel = 0;  // -1 is never a good second label.
          if ( fCellSecondLabels[idCell] == clus->GetLabelAt(iLoopLabels) )  iNewLabel = 0;
        }
        if (iNewLabel == 1) 
        {
          Int_t * newLabelArray = new Int_t[clus->GetNLabels()+1] ;
          for ( UInt_t iLoopNewLabels = 0 ; iLoopNewLabels < clus->GetNLabels() ; iLoopNewLabels++ )
          {
            newLabelArray[iLoopNewLabels] = clus->GetLabelAt(iLoopNewLabels) ;
          }
          
          newLabelArray[clus->GetNLabels()] = fCellSecondLabels[idCell] ;
          clus->SetLabel(newLabelArray,clus->GetNLabels()+1) ;
          delete [] newLabelArray;
        }
      }//positive cell number
    }
    
  } // recPoints loop
  
}


//____________________________________________________________
void AliAnalysisTaskEMCALClusterize::UserCreateOutputObjects()
{
  // Init geometry, create list of output clusters
  
  if(fOutputAODBranchName.Length()!=0)
  {
    fOutputAODBranch = new TClonesArray("AliAODCaloCluster", 0);
    fOutputAODBranch->SetName(fOutputAODBranchName);
    //fOutputAODBranch->SetOwner(kFALSE);
    AddAODBranch("TClonesArray", &fOutputAODBranch);
  }
  else
  {
    AliFatal("fOutputAODBranchName not set\n");
  }
  
  //PostData(0,fOutputAODBranch);
  
}

//_______________________________________________________
void AliAnalysisTaskEMCALClusterize::UserExec(Option_t *) 
{
  // Main loop
  // Called for each event
  
  //Remove the contents of output list set in the previous event 
  fOutputAODBranch->Clear("C");
  
  LoadBranches();
  
  //Get the event, do some checks and settings
  CheckAndGetEvent() ;
  
  if (!fEvent) 
  {
    if(DebugLevel() > 0 ) printf("AliAnalysisTaksEMCALClusterize::UserExec() - Skip Event %d", (Int_t) Entry());
    return ;
  }
  
  //Init pointers, geometry, clusterizer, ocdb, aodb
  
  InitGeometry(); // only once, must be done before OADB, geo OADB accessed here
  
  if(fAccessOCDB) AccessOCDB();
  if(fAccessOADB) AccessOADB(); // only once

  InitClusterization();
  
  // Make clusters
  if (fJustUnfold) ClusterUnfolding();
  else             ClusterizeCells() ;
    
  //Recalculate track-matching for the new clusters
  if(fDoTrackMatching) 
  {
    fRecoUtils->FindMatches(fEvent,fCaloClusterArr,fGeom);
  }
  //Put the new clusters in the AOD list
  
  Int_t kNumberOfCaloClusters   = fCaloClusterArr->GetEntriesFast();
  for(Int_t i = 0; i < kNumberOfCaloClusters; i++){
    AliAODCaloCluster *newCluster = (AliAODCaloCluster *) fCaloClusterArr->At(i);
    
    newCluster->SetID(i);

    //Add matched track
    if(fDoTrackMatching)
    {
      Int_t trackIndex = fRecoUtils->GetMatchedTrackIndex(i);
      if(trackIndex >= 0)
      {
        newCluster->AddTrackMatched(fEvent->GetTrack(trackIndex));
        if(DebugLevel() > 1) 
          printf("AliAnalysisTaksEMCALClusterize::UserExec() - Matched Track index %d to new cluster %d \n",trackIndex,i);
      }
      
      Float_t dR = 999., dZ = 999.;
      fRecoUtils->GetMatchedResiduals(newCluster->GetID(),dR,dZ);
      newCluster->SetTrackDistance(dR,dZ);
      
    }
    else 
    {// Assign previously assigned matched track in reco, very very rough
      Int_t absId0 = newCluster->GetCellsAbsId()[0]; // Assign match of first cell in cluster
      newCluster->SetTrackDistance(fCellMatchdPhi[absId0],fCellMatchdEta[absId0]);
    }

    //printf("New cluster E %f, Time  %e, Id = ", newCluster->E(), newCluster->GetTOF() );
    //for(Int_t icell=0; icell < newCluster->GetNCells(); icell++ ) printf(" %d,", newCluster->GetCellsAbsId() [icell] );
    //printf("\n");

    // Calculate distance to bad channel for new cluster. Make sure you give the list of bad channels.
    fRecoUtils->RecalculateClusterDistanceToBadChannel(fGeom, fEvent->GetEMCALCells(), newCluster);
    
    new((*fOutputAODBranch)[i])  AliAODCaloCluster(*newCluster);
        
    if(DebugLevel() > 1 )    
      printf("AliAnalysisTaksEMCALClusterize::UserExec() - New cluster %d of %d, energy %f\n",newCluster->GetID(), kNumberOfCaloClusters, newCluster->E());
    
  } // cluster loop
  
  fOutputAODBranch->Expand(kNumberOfCaloClusters); // resize TObjArray to 'remove' slots
  
  // Clean up
  fCaloClusterArr->Delete(); // Do not Clear(), it leaks, why?
  
}