/**************************************************************************
 * 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: Constantin Loizides, Salvatore Aiola
//         Adapted from analysis class from Deepa Thomas
//
//_________________________________________________________________________

// --- Root ---
#include <TClonesArray.h>
#include <TGeoManager.h>
#include <TObjArray.h>
#include <TString.h>
#include <TTree.h>
#include <TArrayI.h>

// --- AliRoot ---
#include "AliAODCaloCluster.h"
#include "AliAODEvent.h"
#include "AliAnalysisManager.h"
#include "AliCDBEntry.h"
#include "AliCDBManager.h"
#include "AliCaloCalibPedestal.h"
#include "AliEMCALAfterBurnerUF.h"
#include "AliEMCALCalibData.h"
#include "AliEMCALClusterizerNxN.h"
#include "AliEMCALClusterizerv1.h"
#include "AliEMCALClusterizerv2.h"
#include "AliEMCALClusterizerFixedWindow.h"
#include "AliEMCALDigit.h"
#include "AliEMCALGeometry.h"
#include "AliEMCALRecParam.h"
#include "AliEMCALRecPoint.h"
#include "AliEMCALRecoUtils.h"
#include "AliESDEvent.h"
#include "AliInputEventHandler.h"
#include "AliLog.h"

#include "AliAnalysisTaskEMCALClusterizeFast.h"

ClassImp(AliAnalysisTaskEMCALClusterizeFast)

//________________________________________________________________________
AliAnalysisTaskEMCALClusterizeFast::AliAnalysisTaskEMCALClusterizeFast() : 
  AliAnalysisTaskSE(), 
  fRun(-1),
  fDigitsArr(0),       
  fClusterArr(0),       
  fRecParam(new AliEMCALRecParam),
  fClusterizer(0),
  fUnfolder(0),
  fJustUnfold(kFALSE),
  fGeomName(),
  fGeomMatrixSet(kFALSE), 
  fLoadGeomMatrices(kFALSE),
  fOCDBpath(),
  fCalibData(0),
  fPedestalData(0),
  fOutputAODBranch(0),
  fOutputAODBrName(),
  fRecoUtils(0),
  fLoadCalib(kFALSE),
  fLoadPed(kFALSE),
  fAttachClusters(kTRUE),
  fSubBackground(kFALSE),
  fNPhi(4),
  fNEta(4),
  fShiftPhi(2),
  fShiftEta(2),
  fTRUShift(0),
  fInputCellType(kFEEData),
  fTrackName(),
  fCaloCellsName(),  
  fCaloClustersName("newCaloClusters"),
  fDoUpdateCells(kFALSE),
  fDoClusterize(kTRUE),
  fClusterBadChannelCheck(kFALSE),
  fRejectExoticClusters(kFALSE),
  fRejectExoticCells(kFALSE),
  fFiducial(kFALSE),
  fDoNonLinearity(kFALSE),
  fRecalDistToBadChannels(kFALSE),
  fSetCellMCLabelFromCluster(0),
  fCaloCells(0),
  fCaloClusters(0),
  fEsd(0),
  fAod(0),
  fGeom(0)
{ 
  // Constructor

  for(Int_t i = 0; i < 12; ++i) 
    fGeomMatrix[i] = 0;
}

//________________________________________________________________________
AliAnalysisTaskEMCALClusterizeFast::AliAnalysisTaskEMCALClusterizeFast(const char *name) : 
  AliAnalysisTaskSE(name), 
  fRun(-1),
  fDigitsArr(0),       
  fClusterArr(0),       
  fRecParam(new AliEMCALRecParam),
  fClusterizer(0),
  fUnfolder(0),
  fJustUnfold(kFALSE),
  fGeomName(),
  fGeomMatrixSet(kFALSE), 
  fLoadGeomMatrices(kFALSE),
  fOCDBpath(),
  fCalibData(0),
  fPedestalData(0),
  fOutputAODBranch(0),
  fOutputAODBrName(),
  fRecoUtils(0),
  fLoadCalib(kFALSE),
  fLoadPed(kFALSE),
  fAttachClusters(kTRUE),
  fSubBackground(kFALSE),
  fNPhi(4),
  fNEta(4),
  fShiftPhi(2),
  fShiftEta(2),
  fTRUShift(0),
  fInputCellType(kFEEData),
  fTrackName(),
  fCaloCellsName(),  
  fCaloClustersName("newCaloClusters"),
  fDoUpdateCells(kFALSE),
  fDoClusterize(kTRUE),
  fClusterBadChannelCheck(kFALSE),
  fRejectExoticClusters(kFALSE),
  fRejectExoticCells(kFALSE),
  fFiducial(kFALSE),
  fDoNonLinearity(kFALSE),
  fRecalDistToBadChannels(kFALSE),
  fSetCellMCLabelFromCluster(0),
  fCaloCells(0),
  fCaloClusters(0),
  fEsd(0),
  fAod(0),
  fGeom(0)
{ 
  // Constructor

  fBranchNames     = "ESD:AliESDHeader.,AliESDRun.,EMCALCells.,EMCALTrigger. AOD:header,emcalCells";
  for(Int_t i = 0; i < 12; ++i) 
    fGeomMatrix[i] = 0;
}

//________________________________________________________________________
AliAnalysisTaskEMCALClusterizeFast::~AliAnalysisTaskEMCALClusterizeFast()
{
  // Destructor.

  delete fClusterizer;
  delete fUnfolder;   
  delete fRecoUtils;
  delete fRecParam;
}

//________________________________________________________________________
void AliAnalysisTaskEMCALClusterizeFast::UserCreateOutputObjects()
{
  // Create output objects.

  if (!fOutputAODBrName.IsNull()) {
    fOutputAODBranch = new TClonesArray("AliAODCaloCluster", 0);
    fOutputAODBranch->SetName(fOutputAODBrName);
    AddAODBranch("TClonesArray", &fOutputAODBranch);
    AliInfo(Form("Created Branch: %s",fOutputAODBrName.Data()));
  }
}

//________________________________________________________________________
void AliAnalysisTaskEMCALClusterizeFast::UserExec(Option_t *) 
{
  // Main loop, called for each event

  // if no operation is requested, return
  if (!fDoClusterize && !fDoUpdateCells)
    return;

  // remove the contents of output list set in the previous event 
  if (fOutputAODBranch)
    fOutputAODBranch->Clear("C");

  fEsd = dynamic_cast<AliESDEvent*>(InputEvent());
  fAod = dynamic_cast<AliAODEvent*>(InputEvent());

  if (!fEsd&&!fAod) {
    Error("UserExec","Event not available");
    return;
  }

  LoadBranches();

  UInt_t offtrigger = 0;
  if (fEsd) {
    UInt_t mask1 = fEsd->GetESDRun()->GetDetectorsInDAQ();
    UInt_t mask2 = fEsd->GetESDRun()->GetDetectorsInReco();
    Bool_t desc1 = (mask1 >> 18) & 0x1;
    Bool_t desc2 = (mask2 >> 18) & 0x1;
    if (desc1==0 || desc2==0) { //AliDAQ::OfflineModuleName(180=="EMCAL"
      AliError(Form("EMCAL not in DAQ/RECO: %u (%u)/%u (%u)", 
		    mask1, fEsd->GetESDRun()->GetDetectorsInReco(),
		    mask2, fEsd->GetESDRun()->GetDetectorsInDAQ()));
      return;
    }
    AliAnalysisManager *am = AliAnalysisManager::GetAnalysisManager();
    offtrigger = ((AliInputEventHandler*)(am->GetInputEventHandler()))->IsEventSelected();
  } else {
    offtrigger =  ((AliVAODHeader*)fAod->GetHeader())->GetOfflineTrigger();
  }

  if (!MCEvent()) {
    if (offtrigger & AliVEvent::kFastOnly) {
      AliError(Form("EMCAL not in fast only partition"));
      return;
    }
  }
  
  Init();

  if (fJustUnfold) {
    AliWarning("Unfolding not implemented");
    return;
  }

  FillDigitsArray();

  if (fDoClusterize)
    Clusterize();

  if (fDoUpdateCells)
    UpdateCells();

  if (!fDoClusterize || (!fAttachClusters && !fOutputAODBranch) || !fCaloClusters)
    return;

  UpdateClusters();
  CalibrateClusters();

  if (fOutputAODBranch && fCaloClusters != fOutputAODBranch)
    CopyClusters(fCaloClusters, fOutputAODBranch);

}

//________________________________________________________________________
void AliAnalysisTaskEMCALClusterizeFast::CopyClusters(TClonesArray *orig, TClonesArray *dest)
{
  const Int_t Ncls = orig->GetEntries();

  for(Int_t i=0; i < Ncls; ++i) {
    AliVCluster *oc = static_cast<AliVCluster*>(orig->At(i));

    if (!oc)
      continue;

    if (!oc->IsEMCAL())
      continue;
    
    AliVCluster *dc = static_cast<AliVCluster*>(dest->New(i));
    dc->SetType(AliVCluster::kEMCALClusterv1);
    dc->SetE(oc->E());
    Float_t pos[3] = {0};
    oc->GetPosition(pos);
    dc->SetPosition(pos);
    dc->SetNCells(oc->GetNCells());
    dc->SetCellsAbsId(oc->GetCellsAbsId());
    dc->SetCellsAmplitudeFraction(oc->GetCellsAmplitudeFraction());
    dc->SetID(oc->GetID());
    dc->SetDispersion(oc->GetDispersion());
    dc->SetEmcCpvDistance(-1);
    dc->SetChi2(-1);
    dc->SetTOF(oc->GetTOF());     //time-of-flight
    dc->SetNExMax(oc->GetNExMax()); //number of local maxima
    dc->SetM02(oc->GetM02());
    dc->SetM20(oc->GetM20());
    dc->SetDistanceToBadChannel(oc->GetDistanceToBadChannel()); 
    dc->SetMCEnergyFraction(oc->GetMCEnergyFraction());

    //MC
    UInt_t nlabels = oc->GetNLabels();
    Int_t *labels = oc->GetLabels();

    if (nlabels == 0 || !labels)
      continue;

    AliESDCaloCluster *esdClus = dynamic_cast<AliESDCaloCluster*>(dc);
    if (esdClus) {
      TArrayI parents(nlabels, labels);
      esdClus->AddLabels(parents); 
    }
    else {
      AliAODCaloCluster *aodClus = dynamic_cast<AliAODCaloCluster*>(dc);
      if (aodClus) 
	aodClus->SetLabel(labels, nlabels); 
    }
  }
}

//________________________________________________________________________
void AliAnalysisTaskEMCALClusterizeFast::Clusterize()
{
  // Clusterize

  if (fSubBackground) {
    fClusterizer->SetInputCalibrated(kTRUE);   
    fClusterizer->SetCalibrationParameters(0);
  }

  fClusterizer->Digits2Clusters("");
 
  if (fSubBackground) {
    if (fCalibData) {
      fClusterizer->SetInputCalibrated(kFALSE);   
      fClusterizer->SetCalibrationParameters(fCalibData);
    }
  }
}

//________________________________________________________________________
void AliAnalysisTaskEMCALClusterizeFast::FillDigitsArray()
{
  // Fill digits array

  fDigitsArr->Clear("C");
  switch (fInputCellType) {

  case kFEEData :
  case kFEEDataMCOnly :
  case kFEEDataExcludeMC :
    {
      // In case of MC productions done before aliroot tag v5-02-Rev09
      // assing the cluster label to all the cells belonging to this cluster
      // very rough
      // Copied and simplified from AliEMCALTenderSupply
      Int_t cellLabels[12672]={-1};
      if (fSetCellMCLabelFromCluster) {
        Int_t nClusters = InputEvent()->GetNumberOfCaloClusters();
        for (Int_t i = 0; i < nClusters; i++) {
          AliVCluster *clus =  InputEvent()->GetCaloCluster(i);
      
          if (!clus) continue;
          if (!clus->IsEMCAL()) continue ;
      
          Int_t      label = clus->GetLabel();
          UShort_t * index = clus->GetCellsAbsId() ;
      
          for (Int_t icell=0; icell < clus->GetNCells(); icell++) cellLabels[index[icell]] = label;
        } // cluster loop
      }

      Double_t avgE        = 0; // for background subtraction
      const Int_t ncells   = fCaloCells->GetNumberOfCells();
      for (Int_t icell = 0, idigit = 0; icell < ncells; ++icell) {
	Double_t cellAmplitude=0, cellTime=0, cellEFrac = 0;
	Short_t  cellNumber=0;
	Int_t cellMCLabel=-1;
	if (fCaloCells->GetCell(icell, cellNumber, cellAmplitude, cellTime, cellMCLabel, cellEFrac) != kTRUE)
	  break;

        if (fSetCellMCLabelFromCluster) cellMCLabel = cellLabels[cellNumber];

	if (cellMCLabel > 0 && cellEFrac < 1e-6) 
	  cellEFrac = 1;

	if (cellAmplitude < 1e-6 || cellNumber < 0)
	  continue;	

	if (fInputCellType == kFEEDataMCOnly) {
	  if (cellMCLabel <= 0)
	    continue;
	  else {
	    cellAmplitude *= cellEFrac;
	    cellEFrac = 1;
	  }
	}
	else if (fInputCellType == kFEEDataExcludeMC) {
	  if (cellMCLabel > 0) 
	    continue;
	  else {
	    cellAmplitude *= 1 - cellEFrac;
	    cellEFrac = 0;
	  }
	}

	if(!AcceptCell(cellNumber)) continue;

	AliEMCALDigit *digit = new((*fDigitsArr)[idigit]) AliEMCALDigit(cellMCLabel, cellMCLabel, cellNumber,
									(Float_t)cellAmplitude, (Float_t)cellTime,
									AliEMCALDigit::kHG,idigit, 0, 0, cellEFrac*cellAmplitude);

	if (!fDoClusterize||fSubBackground) {
	  Float_t energy = cellAmplitude;
	  Float_t time   = cellTime;
	  fClusterizer->Calibrate(energy,time,cellNumber);
	  digit->SetAmplitude(energy);
	  avgE += energy;
	}
	idigit++;
      }

      if (fSubBackground) {
	avgE /= fGeom->GetNumberOfSuperModules()*48*24;
	Int_t ndigis = fDigitsArr->GetEntries();
	for (Int_t i = 0; i < ndigis; ++i) {
	  AliEMCALDigit *digit = static_cast<AliEMCALDigit*>(fDigitsArr->At(i));
	  Double_t energy = digit->GetAmplitude() - avgE;
	  if (energy<=0.001) {
	    digit->SetAmplitude(0);
	  } else {
	    digit->SetAmplitude(energy);
	  }
	}
      }
    }
    break;
    
  case kPattern :    
    {
      // Fill digits from a pattern
      Int_t maxd = fGeom->GetNCells() / 4;
      for (Int_t idigit = 0; idigit < maxd; idigit++){
	if (idigit % 24 == 12) idigit += 12;
	AliEMCALDigit *digit = static_cast<AliEMCALDigit*>(fDigitsArr->New(idigit));
	digit->SetId(idigit * 4);
	digit->SetTime(600);
	digit->SetTimeR(600);
	digit->SetIndexInList(idigit);
	digit->SetType(AliEMCALDigit::kHG);
	digit->SetAmplitude(0.1);	
      }
    }
    break;

  case kL0FastORs    : 
  case kL0FastORsTC  :
  case kL1FastORs    :
    {
      // Fill digits from FastORs
      
      AliVCaloTrigger *triggers = InputEvent()->GetCaloTrigger("EMCAL");
      
      if (!triggers || !(triggers->GetEntries() > 0))
	return;
      
      Int_t idigit = 0;
      triggers->Reset();
      
      while ((triggers->Next())) {
	Float_t L0Amplitude = 0;
	triggers->GetAmplitude(L0Amplitude);
	
	if (L0Amplitude <= 0 && fInputCellType != kL1FastORs)
	  continue;

	Int_t L1Amplitude = 0;
	triggers->GetL1TimeSum(L1Amplitude);
	
	if (L1Amplitude <= 0 && fInputCellType == kL1FastORs)
	  continue;
      
	Int_t triggerTime = 0;
	Int_t ntimes = 0;
	triggers->GetNL0Times(ntimes);
	
	if (ntimes < 1 && fInputCellType == kL0FastORsTC) 
	  continue;
	
	if (ntimes > 0) {
	  Int_t trgtimes[25];
	  triggers->GetL0Times(trgtimes);
	  triggerTime = trgtimes[0];
	}

	Int_t triggerCol = 0, triggerRow = 0;
	triggers->GetPosition(triggerCol, triggerRow);
	
	Int_t find = -1;
	fGeom->GetAbsFastORIndexFromPositionInEMCAL(triggerCol, triggerRow, find);
	
	if (find < 0)
	  continue;
      
	Int_t cidx[4] = {-1};
	Bool_t ret = fGeom->GetCellIndexFromFastORIndex(find, cidx);
	
	if (!ret)
	  continue;

	Float_t triggerAmplitude = 0;
	
	if (fInputCellType == kL1FastORs) {
	  triggerAmplitude = 0.25 * L1Amplitude;  // it will add 4 cells for 1 amplitude
	}
	else {
	  triggerAmplitude = L0Amplitude;      // 10 bit truncated, so it is already divided by 4
	}
	
	for (Int_t idxpos = 0; idxpos < 4; idxpos++) {
	  Int_t triggerNumber = cidx[idxpos];
	  AliEMCALDigit *digit = static_cast<AliEMCALDigit*>(fDigitsArr->New(idigit));
	  digit->SetId(triggerNumber);
	  digit->SetTime(triggerTime);
	  digit->SetTimeR(triggerTime);
	  digit->SetIndexInList(idigit);
	  digit->SetType(AliEMCALDigit::kHG);
	  digit->SetAmplitude(triggerAmplitude);
	  idigit++;
	} 
      }
    }
    break;
  }
}

//________________________________________________________________________________________
Bool_t AliAnalysisTaskEMCALClusterizeFast::AcceptCell(Int_t cellNumber) {

  Bool_t accept = kTRUE;
  if(fRejectExoticCells) {
    //Remove exotic cells before making digits
    Bool_t exRemoval = fRecoUtils->IsRejectExoticCell();
    fRecoUtils->SwitchOnRejectExoticCell();//switch on and off
    Int_t bunchCrossNo = InputEvent()->GetBunchCrossNumber();
    Bool_t isEx = fRecoUtils->IsExoticCell(cellNumber, fCaloCells, bunchCrossNo);
    if(isEx) accept = kFALSE;
    if(!exRemoval) fRecoUtils->SwitchOffRejectExoticCell();//switch on and off
  }
  return accept;
}

//________________________________________________________________________________________
void AliAnalysisTaskEMCALClusterizeFast::CalibrateClusters()
{
  // Go through clusters one by one and process separate correction
  // as those were defined or not

  Int_t nclusters = fCaloClusters->GetEntriesFast();
  for (Int_t icluster=0; icluster < nclusters; ++icluster) { 
    AliVCluster *clust = static_cast<AliVCluster*>(fCaloClusters->At(icluster));
    if (!clust) 
      continue;
    if (!clust->IsEMCAL()) 
      continue;

    // REMOVE CLUSTERS WITH BAD CELLS -----------------------------
    if (fClusterBadChannelCheck) {
      // careful, the the ClusterContainsBadChannel is dependent on
      // SwitchOnBadChannelsRemoval, switching it ON automatically
      // and returning to original value after processing
      Bool_t badRemoval = fRecoUtils->IsBadChannelsRemovalSwitchedOn();
      fRecoUtils->SwitchOnBadChannelsRemoval();
      
      Bool_t badResult = fRecoUtils->ClusterContainsBadChannel(fGeom, clust->GetCellsAbsId(), clust->GetNCells());

      // switch the bad channels removal back
      if (!badRemoval)
        fRecoUtils->SwitchOffBadChannelsRemoval();
      
      if (badResult) {
        delete fCaloClusters->RemoveAt(icluster);
        continue; //TODO is it really needed to remove it? Or should we flag it?
      }
    }
    
    // REMOVE EXOTIC CLUSTERS -------------------------------------
    // does process local cell recalibration energy and time without replacing
    // the global cell values, in case of no cell recalib done yet
    if (fRejectExoticClusters) {
      // careful, the IsExoticCluster is dependent on
      // SwitchOnRejectExoticCell, switching it ON automatically
      // and returning to original value after processing
      Bool_t exRemoval = fRecoUtils->IsRejectExoticCell();
      fRecoUtils->SwitchOnRejectExoticCell();

      // get bunch crossing
      Int_t bunchCrossNo = InputEvent()->GetBunchCrossNumber();

      Bool_t exResult = fRecoUtils->IsExoticCluster(clust, fCaloCells, bunchCrossNo);

      // switch the exotic channels removal back
      if (!exRemoval)
        fRecoUtils->SwitchOffRejectExoticCell();
      
      if (exResult) {
        delete fCaloClusters->RemoveAt(icluster);
        continue; //TODO is it really needed to remove it? Or should we flag it?
      }
    }
    
    // FIDUCIAL CUT -----------------------------------------------
    if (fFiducial) {
      // depends on SetNumberOfCellsFromEMCALBorder
      // SwitchOnNoFiducialBorderInEMCALEta0
      if (!fRecoUtils->CheckCellFiducialRegion(fGeom, clust, fCaloCells)){
        delete fCaloClusters->RemoveAt(icluster);
        continue; //TODO it would be nice to store the distance
      }
    }

    // NONLINEARITY -----------------------------------------------
    if (fDoNonLinearity) {
      Float_t correctedEnergy = fRecoUtils->CorrectClusterEnergyLinearity(clust);
      clust->SetE(correctedEnergy);
    }

    // DISTANCE TO BAD CHANNELS -----------------------------------
    if (fRecalDistToBadChannels)
      fRecoUtils->RecalculateClusterDistanceToBadChannel(fGeom, fCaloCells, clust);  
  }

  fCaloClusters->Compress();
}

//________________________________________________________________________________________
void AliAnalysisTaskEMCALClusterizeFast::TrackClusterMatching(AliVCluster *c, TClonesArray *tarr)
{
  Float_t g[3]={0};
  c->GetPosition(g);
  TVector3 gpos(g);

  Double_t dEtaMin  = 1e9;
  Double_t dPhiMin  = 1e9;
  Int_t    imin     = -1;
  Double_t ceta     = gpos.Eta();
  Double_t cphi     = gpos.Phi();
  const Int_t ntrks = tarr->GetEntries();
  for(Int_t t = 0; t<ntrks; ++t) {
    AliVTrack *track = static_cast<AliVTrack*>(tarr->At(t));
    if (!track)
      continue;
    const AliExternalTrackParam *outp = track->GetOuterParam();
    if (!outp)
      continue;
    Double_t trkPos[3] = {0.,0.,0.};
    if (!outp->GetXYZ(trkPos)) 
      continue;
    TVector3 vec(trkPos[0],trkPos[1],trkPos[2]);
    Double_t veta = vec.Eta();
    Double_t vphi = vec.Phi();
    if(vphi<0)
      vphi += 2*TMath::Pi();
    if (TMath::Abs(veta)>0.75 || (vphi<70*TMath::DegToRad()) || (vphi>190*TMath::DegToRad()))
      continue;
    Double_t dR = vec.DeltaR(gpos);
    if(dR > 25) 
      continue;
    Float_t tmpEta=0, tmpPhi=0;
    if (0) {
      AliExternalTrackParam trkParTemp(*outp); // retrieve the starting point every time before the extrapolation
      Bool_t ret = fRecoUtils->ExtrapolateTrackToCluster(&trkParTemp, c, fRecoUtils->GetMass(), fRecoUtils->GetStep(), tmpEta, tmpPhi); 
      if (!ret)
	continue;
    } else {
      tmpEta = ceta - veta;
      tmpPhi = cphi - vphi;
    }
    if (TMath::Abs(tmpEta)<TMath::Abs(dEtaMin) && TMath::Abs(tmpPhi)<TMath::Abs(dPhiMin)) {
      dEtaMin = tmpEta;
      dPhiMin = tmpPhi;
      imin = t;
    }
  }
  c->SetEmcCpvDistance(imin);
  c->SetTrackDistance(dPhiMin, dEtaMin);
}

//________________________________________________________________________________________
void AliAnalysisTaskEMCALClusterizeFast::RecPoints2Clusters(TClonesArray *clus)
{
  // Cluster energy, global position, cells and their amplitude fractions are restored.
  
  // tracks array for track/cluster matching
  TClonesArray *tarr = 0;
  if (!fTrackName.IsNull()) {
    tarr = dynamic_cast<TClonesArray*>(InputEvent()->FindListObject(fTrackName));
    if (!tarr) {
      AliError(Form("Cannot get tracks named %s", fTrackName.Data()));
    }
  }
  
  const Int_t Ncls = fClusterArr->GetEntries();
  AliDebug(1, Form("total no of clusters %d", Ncls)); 
  for(Int_t i=0, nout=clus->GetEntries(); i < Ncls; ++i) {
    AliEMCALRecPoint *recpoint = static_cast<AliEMCALRecPoint*>(fClusterArr->At(i));
    Int_t ncells_true = 0;
    const Int_t ncells = recpoint->GetMultiplicity();
    UShort_t   absIds[ncells];  
    Double32_t ratios[ncells];
    Int_t *dlist = recpoint->GetDigitsList();
    Float_t *elist = recpoint->GetEnergiesList();
    Double_t mcEnergy = 0;
    for (Int_t c = 0; c < ncells; ++c) {
      AliEMCALDigit *digit = static_cast<AliEMCALDigit*>(fDigitsArr->At(dlist[c]));
      absIds[ncells_true] = digit->GetId();
      ratios[ncells_true] = elist[c]/recpoint->GetEnergy();
      if (digit->GetIparent(1) > 0)
	mcEnergy += digit->GetDEParent(1)/recpoint->GetEnergy();
      ++ncells_true;
    }
    
    if (ncells_true < 1) {
      AliWarning("Skipping cluster with no cells");
      continue;
    }
    
    // calculate new cluster position
    TVector3 gpos;
    recpoint->GetGlobalPosition(gpos);
    Float_t g[3];
    gpos.GetXYZ(g);
    
    AliDebug(1, Form("energy %f", recpoint->GetEnergy()));
    
    AliVCluster *c = static_cast<AliVCluster*>(clus->New(nout++));
    c->SetType(AliVCluster::kEMCALClusterv1);
    c->SetE(recpoint->GetEnergy());
    c->SetPosition(g);
    c->SetNCells(ncells_true);
    c->SetCellsAbsId(absIds);
    c->SetCellsAmplitudeFraction(ratios);
    c->SetID(recpoint->GetUniqueID());
    c->SetDispersion(recpoint->GetDispersion());
    c->SetEmcCpvDistance(-1);
    c->SetChi2(-1);
    c->SetTOF(recpoint->GetTime()) ;     //time-of-flight
    c->SetNExMax(recpoint->GetNExMax()); //number of local maxima
    Float_t elipAxis[2];
    recpoint->GetElipsAxis(elipAxis);
    c->SetM02(elipAxis[0]*elipAxis[0]);
    c->SetM20(elipAxis[1]*elipAxis[1]);
    c->SetMCEnergyFraction(mcEnergy);

    //MC
    AliESDCaloCluster *esdClus = dynamic_cast<AliESDCaloCluster*>(c);
    if (esdClus) {
      Int_t  parentMult = 0;
      Int_t *parentList = recpoint->GetParents(parentMult);
      if (parentMult > 0) {
	TArrayI parents(parentMult, parentList);
	esdClus->AddLabels(parents); 
      }
    }
    else {
      AliAODCaloCluster *aodClus = dynamic_cast<AliAODCaloCluster*>(c);
      if (aodClus) {
	Int_t  parentMult = 0;
	Int_t *parentList = recpoint->GetParents(parentMult);
	aodClus->SetLabel(parentList, parentMult); 
      }
    }

    if (tarr)
      TrackClusterMatching(c, tarr);
  }
}

//________________________________________________________________________
void AliAnalysisTaskEMCALClusterizeFast::UpdateCells()
{
  // Update cells in case re-calibration was done.
  if (!fCalibData&&!fSubBackground)
    return;

  const Int_t   ncells = fCaloCells->GetNumberOfCells();
  const Int_t   ndigis = fDigitsArr->GetEntries();
  if (ncells!=ndigis) {
    fCaloCells->DeleteContainer();
    fCaloCells->CreateContainer(ndigis);
  }
  for (Int_t idigit = 0; idigit < ndigis; ++idigit) {
    AliEMCALDigit *digit = static_cast<AliEMCALDigit*>(fDigitsArr->At(idigit));
    Double_t cellAmplitude = digit->GetCalibAmp();
    Short_t cellNumber     = digit->GetId();
    Double_t cellTime      = digit->GetTime();
    fCaloCells->SetCell(idigit, cellNumber, cellAmplitude, cellTime);
  }
}

//________________________________________________________________________
void AliAnalysisTaskEMCALClusterizeFast::UpdateClusters()
{
  // Update cells in case re-calibration was done.
  
  const Int_t nents = fCaloClusters->GetEntries();
  for (Int_t i=0;i<nents;++i) {
    AliVCluster *c = static_cast<AliVCluster*>(fCaloClusters->At(i));
    if (!c)
      continue;
    if (c->IsEMCAL())
      delete fCaloClusters->RemoveAt(i);
  }

  fCaloClusters->Compress();
  
  RecPoints2Clusters(fCaloClusters);
}

//________________________________________________________________________________________
void AliAnalysisTaskEMCALClusterizeFast::Init()
{
  // Select clusterization/unfolding algorithm and set all the needed parameters.

  if (InputEvent()->GetRunNumber()==fRun)
    return;
  fRun = InputEvent()->GetRunNumber();

  if (fJustUnfold){
    // init the unfolding afterburner 
    delete fUnfolder;
    fUnfolder = new AliEMCALAfterBurnerUF(fRecParam->GetW0(),fRecParam->GetLocMaxCut(),fRecParam->GetMinECut());
    return;
  }

  if (fGeomName.Length()>0) 
    fGeom = AliEMCALGeometry::GetInstance(fGeomName);
  else
    fGeom = AliEMCALGeometry::GetInstance();
  if (!fGeom) {
    AliFatal("Geometry not available!!!");
    return;
  }

  if (!fGeomMatrixSet) {
    if (fLoadGeomMatrices) {
      for(Int_t mod=0; mod < fGeom->GetNumberOfSuperModules(); ++mod) {
        if (fGeomMatrix[mod]){
          if (DebugLevel() > 2) 
            fGeomMatrix[mod]->Print();
          fGeom->SetMisalMatrix(fGeomMatrix[mod],mod);  
        }
      }
    } else { // get matrix from file (work around bug in aliroot)
      for(Int_t mod=0; mod < fGeom->GetEMCGeometry()->GetNumberOfSuperModules(); ++mod) {
        const TGeoHMatrix *gm = 0;
        if (fEsd) {
          gm = fEsd->GetEMCALMatrix(mod);
        } else {
          AliAODHeader *aodheader = dynamic_cast<AliAODHeader*>(fAod->GetHeader());
          if(!aodheader) AliFatal("Not a standard AOD");
          if (aodheader) {
            gm = aodheader->GetEMCALMatrix(mod);
          }
        }
        if (gm) {
          if (DebugLevel() > 2) 
            gm->Print();
          fGeom->SetMisalMatrix(gm,mod);
        }
      }
    }
    fGeomMatrixSet=kTRUE;
  }
  
  // setup digit array if needed
  if (!fDigitsArr) {
    fDigitsArr = new TClonesArray("AliEMCALDigit", 1000);
    fDigitsArr->SetOwner(1);
  }

  // then setup clusterizer
  if (fClusterizer) {
    // avoid to delete digits array
    fClusterizer->SetDigitsArr(0);
    delete fClusterizer;
  }
  if (fRecParam->GetClusterizerFlag() == AliEMCALRecParam::kClusterizerv1)
    fClusterizer = new AliEMCALClusterizerv1(fGeom);
  else if (fRecParam->GetClusterizerFlag() == AliEMCALRecParam::kClusterizerNxN) {
    AliEMCALClusterizerNxN *clusterizer = new AliEMCALClusterizerNxN(fGeom);
    clusterizer->SetNRowDiff(fRecParam->GetNRowDiff()); //MV: already done in AliEMCALClusterizer::InitParameters
    clusterizer->SetNColDiff(fRecParam->GetNColDiff()); //MV: already done in AliEMCALClusterizer::InitParameters
    fClusterizer = clusterizer;
  } 
  else if (fRecParam->GetClusterizerFlag() == AliEMCALRecParam::kClusterizerv2) 
    fClusterizer = new AliEMCALClusterizerv2(fGeom);
  else if (fRecParam->GetClusterizerFlag() == AliEMCALRecParam::kClusterizerFW) {
    AliEMCALClusterizerFixedWindow *clusterizer = new AliEMCALClusterizerFixedWindow(fGeom);
    clusterizer->SetNphi(fNPhi);
    clusterizer->SetNeta(fNEta);
    clusterizer->SetShiftPhi(fShiftPhi);
    clusterizer->SetShiftEta(fShiftEta);
    clusterizer->SetTRUshift(fTRUShift);
    fClusterizer = clusterizer;
  }
  else {
    AliFatal(Form("Clusterizer < %d > not available", fRecParam->GetClusterizerFlag()));
  }
  fClusterizer->InitParameters(fRecParam);

  if ((!fCalibData&&fLoadCalib) || (!fPedestalData&&fLoadPed)) {
    AliCDBManager *cdb = AliCDBManager::Instance();
    if (!cdb->IsDefaultStorageSet() && !fOCDBpath.IsNull())
      cdb->SetDefaultStorage(fOCDBpath);
    if (fRun!=cdb->GetRun())
      cdb->SetRun(fRun);
  }
  if (!fCalibData&&fLoadCalib&&fRun>0) {
    AliCDBEntry *entry = static_cast<AliCDBEntry*>(AliCDBManager::Instance()->Get("EMCAL/Calib/Data"));
    if (entry) 
      fCalibData =  static_cast<AliEMCALCalibData*>(entry->GetObject());
    if (!fCalibData)
      AliFatal("Calibration parameters not found in CDB!");
  }
  if (!fPedestalData&&fLoadPed&&fRun>0) {
    AliCDBEntry *entry = static_cast<AliCDBEntry*>(AliCDBManager::Instance()->Get("EMCAL/Calib/Pedestals"));
    if (entry) 
      fPedestalData =  static_cast<AliCaloCalibPedestal*>(entry->GetObject());
  }
  if (fCalibData) {
    fClusterizer->SetInputCalibrated(kFALSE);   
    fClusterizer->SetCalibrationParameters(fCalibData);
  } else {
    fClusterizer->SetInputCalibrated(kTRUE);   
  }
  fClusterizer->SetCaloCalibPedestal(fPedestalData);
  fClusterizer->SetJustClusters(kTRUE);
  fClusterizer->SetDigitsArr(fDigitsArr);
  fClusterizer->SetOutput(0);
  fClusterArr = const_cast<TObjArray *>(fClusterizer->GetRecPoints());

  // Get the emcal cells
  if ((fInputCellType == kFEEData ||  fInputCellType == kFEEDataMCOnly || fInputCellType == kFEEDataExcludeMC) && !fCaloCells) {
    if (fCaloCellsName.IsNull()) {
      fCaloCells = InputEvent()->GetEMCALCells();
    }
    else {
      fCaloCells =  dynamic_cast<AliVCaloCells*>(InputEvent()->FindListObject(fCaloCellsName));
      if (!fCaloCells) 
	AliError(Form("%s: Could not retrieve cells %s!", GetName(), fCaloCellsName.Data()));
    }
    if (!fCaloCells)
      AliFatal("Could not get EMCal cells!");
  }

  // Set output clusters collection
  if (!fAttachClusters) {
    fCaloClusters = fOutputAODBranch;
    return;
  }

  if (!fCaloClusters) {
    if (fCaloClustersName.IsNull()) { //overwrite mode
      if (fEsd)
	fCaloClusters = static_cast<TClonesArray*>(InputEvent()->FindListObject("CaloClusters"));
      else if (fAod)
	fCaloClusters = static_cast<TClonesArray*>(InputEvent()->FindListObject("caloClusters"));
    }
    else {
      fCaloClusters = static_cast<TClonesArray*>(InputEvent()->FindListObject(fCaloClustersName));

      if (!fCaloClusters) {
	if (fEsd)
	  fCaloClusters = new TClonesArray("AliESDCaloCluster");
	else if (fAod)
	  fCaloClusters = new TClonesArray("AliAODCaloCluster");
	
	fCaloClusters->SetName(fCaloClustersName);
	InputEvent()->AddObject(fCaloClusters);
      }
    }

    if (!fCaloClusters)
      AliFatal("Could not get cluster collection!");

    TClass *cl = fCaloClusters->GetClass();
    if (!cl->GetBaseClass("AliVCluster")) {
      AliFatal(Form("%s: Collection %s does not contain AliVCluster objects!", GetName(), fCaloClusters->GetName())); 
      fCaloClusters = 0;
      return;
    }
  }
}