default setting for n sigma cut changed from TRUE to FALSE

[u/mrichter/AliRoot.git] / ANALYSIS / AliAnalysisTaskESDfilter.cxx

/**************************************************************************
 * Copyright(c) 1998-1999, ALICE Experiment at CERN, All rights reserved. *
 *                                                                        *
 * Author: The ALICE Off-line Project.                                    *
 * Contributors are mentioned in the code where appropriate.              *
 *                                                                        *
 * Permission to use, copy, modify and distribute this software and its   *
 * documentation strictly for non-commercial purposes is hereby granted   *
 * without fee, provided that the above copyright notice appears in all   *
 * copies and that both the copyright notice and this permission notice   *
 * appear in the supporting documentation. The authors make no claims     *
 * about the suitability of this software for any purpose. It is          *
 * provided "as is" without express or implied warranty.                  *
 **************************************************************************/

/* $Id: AliAnalysisTaskESDfilter.cxx 24535 2008-03-16 22:43:30Z fca $ */
 
#include <TChain.h>
#include <TTree.h>
#include <TList.h>
#include <TArrayI.h>
#include <TRandom.h>
#include <TParticle.h>

#include "AliAnalysisTaskESDfilter.h"
#include "AliAnalysisManager.h"
#include "AliESDEvent.h"
#include "AliStack.h"
#include "AliAODEvent.h"
#include "AliMCEvent.h"
#include "AliMCEventHandler.h"
#include "AliESDInputHandler.h"
#include "AliAODHandler.h"
#include "AliAODMCParticle.h"
#include "AliAnalysisFilter.h"
#include "AliESDMuonTrack.h"
#include "AliESDVertex.h"
#include "AliESDv0.h"
#include "AliESDkink.h"
#include "AliESDcascade.h"
#include "AliESDPmdTrack.h"
#include "AliESDCaloCluster.h"
#include "AliESDCaloCells.h"
#include "AliMultiplicity.h"
#include "AliLog.h"

ClassImp(AliAnalysisTaskESDfilter)

////////////////////////////////////////////////////////////////////////

AliAnalysisTaskESDfilter::AliAnalysisTaskESDfilter():
    AliAnalysisTaskSE(),
    fTrackFilter(0x0),
    fKinkFilter(0x0),
    fV0Filter(0x0),
    fHighPthreshold(0),
    fPtshape(0x0)
{
  // Default constructor
}

AliAnalysisTaskESDfilter::AliAnalysisTaskESDfilter(const char* name):
    AliAnalysisTaskSE(name),
    fTrackFilter(0x0),
    fKinkFilter(0x0),
    fV0Filter(0x0),
    fHighPthreshold(0),
    fPtshape(0x0)
{
  // Constructor
}

void AliAnalysisTaskESDfilter::UserCreateOutputObjects()
{
// Create the output container
    OutputTree()->GetUserInfo()->Add(fTrackFilter);
}

void AliAnalysisTaskESDfilter::Init()
{
    // Initialization
    if (fDebug > 1) AliInfo("Init() \n");
    // Call configuration file
}


void AliAnalysisTaskESDfilter::UserExec(Option_t */*option*/)
{
// Execute analysis for current event
//
					    
  Long64_t ientry = Entry();
  if (fDebug > 0) printf("Filter: Analysing event # %5d\n", (Int_t) ientry);
  if (fHighPthreshold == 0) AliInfo("detector PID signals are stored in each track");
  if (!fPtshape) AliInfo("detector PID signals are not stored below the pt threshold");

  ConvertESDtoAOD();
}

void AliAnalysisTaskESDfilter::ConvertESDtoAOD() {
    // ESD Filter analysis task executed for each event

    AliESDEvent* esd = dynamic_cast<AliESDEvent*>(InputEvent());
    AliESD* old = esd->GetAliESDOld();

    // Fetch Stack for debuggging if available 
    AliStack *pStack = 0;
    AliMCEventHandler *mcH = 0;
    if(MCEvent()){
      pStack = MCEvent()->Stack();
      mcH = (AliMCEventHandler*) ((AliAnalysisManager::GetAnalysisManager())->GetMCtruthEventHandler()); 
    }
    // set arrays and pointers
    Float_t posF[3];
    Double_t pos[3];
    Double_t p[3];
    Double_t p_pos[3];
    Double_t p_neg[3];
    Double_t p_pos_atv0[3];
    Double_t p_neg_atv0[3];
    Double_t covVtx[6];
    Double_t covTr[21];
    Double_t pid[10];

    for (Int_t i = 0; i < 6; i++)  covVtx[i] = 0.;
    for (Int_t i = 0; i < 21; i++) covTr [i] = 0.;

    
    // loop over events and fill them
    
    // Multiplicity information needed by the header (to be revised!)
    Int_t nTracks    = esd->GetNumberOfTracks();
    //    if (fDebug > 0) printf("-------------------Bo: Number of ESD tracks %d \n",nTracks);

    Int_t nPosTracks = 0;
//    for (Int_t iTrack = 0; iTrack < nTracks; ++iTrack) 
//	if (esd->GetTrack(iTrack)->GetSign()> 0) nPosTracks++;
    
    // Update the header

    AliAODHeader* header = AODEvent()->GetHeader();
    header->SetRunNumber(esd->GetRunNumber());
    if (old) {
	header->SetBunchCrossNumber(0);
	header->SetOrbitNumber(0);
	header->SetPeriodNumber(0);
	header->SetEventType(0);
	header->SetMuonMagFieldScale(-999.); // FIXME
	header->SetCentrality(-999.);        // FIXME
    } else {
	header->SetBunchCrossNumber(esd->GetBunchCrossNumber());
	header->SetOrbitNumber(esd->GetOrbitNumber());
	header->SetPeriodNumber(esd->GetPeriodNumber());
	header->SetEventType(esd->GetEventType());
	header->SetMuonMagFieldScale(-999.); // FIXME
	header->SetCentrality(-999.);        // FIXME
    }
    
    header->SetTriggerMask(esd->GetTriggerMask()); 
    header->SetTriggerCluster(esd->GetTriggerCluster());
    header->SetMagneticField(esd->GetMagneticField());
    header->SetZDCN1Energy(esd->GetZDCN1Energy());
    header->SetZDCP1Energy(esd->GetZDCP1Energy());
    header->SetZDCN2Energy(esd->GetZDCN2Energy());
    header->SetZDCP2Energy(esd->GetZDCP2Energy());
    header->SetZDCEMEnergy(esd->GetZDCEMEnergy(0),esd->GetZDCEMEnergy(1));
    Float_t diamxy[2]={esd->GetDiamondX(),esd->GetDiamondY()};
    Float_t diamcov[3]; esd->GetDiamondCovXY(diamcov);
    header->SetDiamond(diamxy,diamcov);
//
//    
    Int_t nV0s      = esd->GetNumberOfV0s();
    Int_t nCascades = esd->GetNumberOfCascades();
    Int_t nKinks    = esd->GetNumberOfKinks();
    Int_t nVertices = nV0s + 2*nCascades /*could lead to two vertices, one V0 and the Xi */+ nKinks + 1 /* = prim. vtx*/;    
    Int_t nJets     = 0;
    Int_t nCaloClus = esd->GetNumberOfCaloClusters();
    Int_t nFmdClus  = 0;
    Int_t nPmdClus  = esd->GetNumberOfPmdTracks();
    
    if (fDebug > 0) 
	printf("   NV0=%d  NCASCADES=%d  NKINKS=%d\n", nV0s, nCascades, nKinks);

    AODEvent()->ResetStd(nTracks, nVertices, nV0s+nCascades, nJets, nCaloClus, nFmdClus, nPmdClus);

    AliAODTrack *aodTrack = 0x0;
    AliAODPid   *detpid   = 0x0;
    Double_t timezero = 0; //TO BE FIXED
    AliAODv0    *aodV0    = 0x0;

    // RefArray to store the mapping between esd track number and newly created AOD-Track
    TRefArray   *aodRefs = NULL;
    if (nTracks > 0) aodRefs = new TRefArray(nTracks);

    // Array to take into account the tracks already added to the AOD
    Bool_t * usedTrack = NULL;
    if (nTracks>0) {
	usedTrack = new Bool_t[nTracks];
	for (Int_t iTrack=0; iTrack<nTracks; ++iTrack) usedTrack[iTrack]=kFALSE;
    }
    // Array to take into account the V0s already added to the AOD
    Bool_t * usedV0 = NULL;
    if (nV0s>0) {
	usedV0 = new Bool_t[nV0s];
	for (Int_t iV0=0; iV0<nV0s; ++iV0) usedV0[iV0]=kFALSE;
    }
    // Array to take into account the kinks already added to the AOD
    Bool_t * usedKink = NULL;
    if (nKinks>0) {
	usedKink = new Bool_t[nKinks];
	for (Int_t iKink=0; iKink<nKinks; ++iKink) usedKink[iKink]=kFALSE;
    }
    
    // Access to the AOD container of vertices
    TClonesArray &vertices = *(AODEvent()->GetVertices());
    Int_t jVertices=0;
    
    // Access to the AOD container of tracks
    TClonesArray &tracks = *(AODEvent()->GetTracks());
    Int_t jTracks=0; 
    
    // Access to the AOD container of V0s
    TClonesArray &V0s = *(AODEvent()->GetV0s());
    Int_t jV0s=0;
    
    // Add primary vertex. The primary tracks will be defined
    // after the loops on the composite objects (V0, cascades, kinks)
    const AliESDVertex *vtx = esd->GetPrimaryVertex();
    
    vtx->GetXYZ(pos); // position
    vtx->GetCovMatrix(covVtx); //covariance matrix
    
    AliAODVertex * primary = new(vertices[jVertices++])
	AliAODVertex(pos, covVtx, vtx->GetChi2toNDF(), NULL, -1, AliAODVertex::kPrimary);
    primary->SetName(vtx->GetName());
    primary->SetTitle(vtx->GetTitle());

    if (fDebug > 0) primary->Print();

    // Create vertices starting from the most complex objects
    Double_t chi2 = 0.;
    
    // Cascades
    for (Int_t nCascade = 0; nCascade < nCascades; ++nCascade) {
	AliESDcascade *cascade = esd->GetCascade(nCascade);
	
	cascade->GetXYZ(pos[0], pos[1], pos[2]);

	if (!old) {
	    chi2 = cascade->GetChi2Xi(); // = chi2/NDF since NDF = 2*2-3
	    cascade->GetPosCovXi(covVtx);
	} else {
	    chi2 = -999.;
	    for (Int_t i = 0; i < 6; i++)  covVtx[i] = 0.;
	}
	// Add the cascade vertex
	AliAODVertex * vcascade = new(vertices[jVertices++]) AliAODVertex(pos,
									  covVtx,
									  chi2,
									  primary,
									  nCascade,
									  AliAODVertex::kCascade);
	
	primary->AddDaughter(vcascade);
	
	// Add the V0 from the cascade. The ESD class have to be optimized...
	// Now we have to search for the corresponding Vo in the list of V0s
	// using the indeces of the positive and negative tracks
	
	Int_t posFromV0 = cascade->GetPindex();
	Int_t negFromV0 = cascade->GetNindex();
	
      
	AliESDv0 * v0 = 0x0;
	Int_t indV0 = -1;
	
	for (Int_t iV0=0; iV0<nV0s; ++iV0) {
	    
	    v0 = esd->GetV0(iV0);
	    Int_t posV0 = v0->GetPindex();
	    Int_t negV0 = v0->GetNindex();
	    
	    if (posV0==posFromV0 && negV0==negFromV0) {
		indV0 = iV0;
		break;
	    }
	}
	
	AliAODVertex * vV0FromCascade = 0x0;
	
	if (indV0>-1 && !usedV0[indV0] ) {
	    
	    // the V0 exists in the array of V0s and is not used
	    
	    usedV0[indV0] = kTRUE;
	    
	    v0->GetXYZ(pos[0], pos[1], pos[2]);
	    if (!old) {
		chi2 = v0->GetChi2V0();  // = chi2/NDF since NDF = 2*2-3			     
		v0->GetPosCov(covVtx);
	    } else {
		chi2 = -999.;
		for (Int_t i = 0; i < 6; i++)  covVtx[i] = 0.;
	    }

	    vV0FromCascade = new(vertices[jVertices++]) AliAODVertex(pos,
								     covVtx,
								     chi2,
								     vcascade,
								     indV0,
								     AliAODVertex::kV0);
	} else {
	    
	    // the V0 doesn't exist in the array of V0s or was used
//	    cerr << "Error: event " << esd->GetEventNumberInFile() << " cascade " << nCascade
//		 << " The V0 " << indV0 
//		 << " doesn't exist in the array of V0s or was used!" << endl;
	    
	    cascade->GetXYZ(pos[0], pos[1], pos[2]);
	    
	    if (!old) {
		chi2 = v0->GetChi2V0();
		cascade->GetPosCov(covVtx);
	    } else {
		chi2 = -999.;
		for (Int_t i = 0; i < 6; i++)  covVtx[i] = 0.;
	    }

	    vV0FromCascade = new(vertices[jVertices++]) AliAODVertex(pos,
								     covVtx,
								     chi2, // = chi2/NDF since NDF = 2*2-3 (AM)
								     vcascade,
								     indV0,
								     AliAODVertex::kV0);
	    vcascade->AddDaughter(vV0FromCascade);
	}
	
	// Add the positive tracks from the V0
	
	if (posFromV0>-1 && !usedTrack[posFromV0]) {
	    
	    usedTrack[posFromV0] = kTRUE;
	    
	    AliESDtrack *esdTrack = esd->GetTrack(posFromV0);
	    esdTrack->GetPxPyPz(p_pos);
	    esdTrack->GetXYZ(pos);
	    esdTrack->GetCovarianceXYZPxPyPz(covTr);
	    esdTrack->GetESDpid(pid);
	    UInt_t selectInfo = 0;
	    if (fTrackFilter) {
		selectInfo = fTrackFilter->IsSelected(esdTrack);
	    }
	    
	    if(mcH)mcH->SelectParticle(esdTrack->GetLabel());
	    vV0FromCascade->AddDaughter(aodTrack =
					new(tracks[jTracks++]) AliAODTrack(esdTrack->GetID(),
									   esdTrack->GetLabel(), 
									   p_pos, 
									   kTRUE,
									   pos,
									   kFALSE,
									   covTr, 
									   (Short_t)esdTrack->GetSign(),
									   esdTrack->GetITSClusterMap(), 
									   pid,
									   vV0FromCascade,
									   kTRUE,  // check if this is right
									   vtx->UsesTrack(esdTrack->GetID()),
									   AliAODTrack::kSecondary,
									   selectInfo)
					);
	    aodRefs->AddAt(aodTrack, posFromV0);
	    
       if (esdTrack->GetSign() > 0) nPosTracks++;
	    aodTrack->ConvertAliPIDtoAODPID();
	    aodTrack->SetFlags(esdTrack->GetStatus());
            SetAODPID(esdTrack,aodTrack,detpid,timezero);
	}
	else {
//	    cerr << "Error: event " << esd->GetEventNumberInFile() << " cascade " << nCascade
//		 << " track " << posFromV0 << " has already been used!" << endl;
	}
	
	// Add the negative tracks from the V0
	
	if (negFromV0>-1 && !usedTrack[negFromV0]) {
	    
	    usedTrack[negFromV0] = kTRUE;
	    
	    AliESDtrack *esdTrack = esd->GetTrack(negFromV0);
	    esdTrack->GetPxPyPz(p_neg);
	    esdTrack->GetXYZ(pos);
	    esdTrack->GetCovarianceXYZPxPyPz(covTr);
	    esdTrack->GetESDpid(pid);
	    UInt_t selectInfo = 0;
	    if (fTrackFilter) selectInfo = fTrackFilter->IsSelected(esdTrack);	    
	    if(mcH)mcH->SelectParticle(esdTrack->GetLabel());
	    vV0FromCascade->AddDaughter(aodTrack =
					new(tracks[jTracks++]) AliAODTrack(esdTrack->GetID(),
									   esdTrack->GetLabel(),
									   p_neg,
									   kTRUE,
									   pos,
									   kFALSE,
									   covTr, 
									   (Short_t)esdTrack->GetSign(),
									   esdTrack->GetITSClusterMap(), 
									   pid,
									   vV0FromCascade,
									   kTRUE,  // check if this is right
									   vtx->UsesTrack(esdTrack->GetID()),
									   AliAODTrack::kSecondary,
									   selectInfo)
					);
	    aodRefs->AddAt(aodTrack, negFromV0);

       if (esdTrack->GetSign() > 0) nPosTracks++;
	    aodTrack->ConvertAliPIDtoAODPID();
	    aodTrack->SetFlags(esdTrack->GetStatus());	    
            SetAODPID(esdTrack,aodTrack,detpid,timezero);
	}
	else {
//	    cerr << "Error: event " << esd->GetEventNumberInFile() << " cascade " << nCascade
//		 << " track " << negFromV0 << " has already been used!" << endl;
	}
	
	// add it to the V0 array as well
	Double_t d0[2] = { -999., -99.};
	// counting is probably wrong
	new(V0s[jV0s++]) AliAODv0(vV0FromCascade, -999., -99., p_pos, p_neg, d0); // to be refined

	// Add the bachelor track from the cascade
	
	Int_t bachelor = cascade->GetBindex();
	
	if(bachelor>-1 && !usedTrack[bachelor]) {
	    
	    usedTrack[bachelor] = kTRUE;
	    
	    AliESDtrack *esdTrack = esd->GetTrack(bachelor);
	    esdTrack->GetPxPyPz(p);
	    esdTrack->GetXYZ(pos);
	    esdTrack->GetCovarianceXYZPxPyPz(covTr);
	    esdTrack->GetESDpid(pid);
	    UInt_t selectInfo = 0;
	    if (fTrackFilter) selectInfo = fTrackFilter->IsSelected(esdTrack);

	    if(mcH)mcH->SelectParticle(esdTrack->GetLabel());
	    vcascade->AddDaughter(aodTrack =
				  new(tracks[jTracks++]) AliAODTrack(esdTrack->GetID(),
								     esdTrack->GetLabel(),
								     p,
								     kTRUE,
								     pos,
								     kFALSE,
								     covTr, 
								     (Short_t)esdTrack->GetSign(),
								     esdTrack->GetITSClusterMap(), 
								     pid,
								     vcascade,
								     kTRUE,  // check if this is right
								     vtx->UsesTrack(esdTrack->GetID()),
								     AliAODTrack::kSecondary,
								     selectInfo)
				  );
	    aodRefs->AddAt(aodTrack, bachelor);
       if (esdTrack->GetSign() > 0) nPosTracks++;
	    aodTrack->ConvertAliPIDtoAODPID();
	    aodTrack->SetFlags(esdTrack->GetStatus());
            SetAODPID(esdTrack,aodTrack,detpid,timezero);
	}
	else {
//	    cerr << "Error: event " << esd->GetEventNumberInFile() << " cascade " << nCascade
//		 << " track " << bachelor << " has already been used!" << endl;
	}
	
	// Add the primary track of the cascade (if any)
	
    } // end of the loop on cascades

    //
    // V0s
    //
    
    for (Int_t nV0 = 0; nV0 < nV0s; ++nV0) {
	
	if (usedV0[nV0]) continue; // skip if already added to the AOD
	
	AliESDv0 *v0 = esd->GetV0(nV0);
	Int_t posFromV0 = v0->GetPindex();
	Int_t negFromV0 = v0->GetNindex();
	if (posFromV0 < 0 || negFromV0 < 0) continue;

	// V0 selection 
	//
	AliESDVertex *esdVtx = new AliESDVertex(*(esd->GetPrimaryVertex()));
	AliESDtrack *esdV0Pos = esd->GetTrack(posFromV0);
	AliESDtrack *esdV0Neg = esd->GetTrack(negFromV0);
	TList v0objects;
	v0objects.AddAt(v0,                      0);
	v0objects.AddAt(esdV0Pos,                1);
	v0objects.AddAt(esdV0Neg,                2);
	v0objects.AddAt(esdVtx,                  3);
	UInt_t selectV0 = 0;
	if (fV0Filter) {
	  selectV0 = fV0Filter->IsSelected(&v0objects);
	  // this is a little awkward but otherwise the 
	  // list wants to access the pointer (delete it) 
	  // again when going out of scope
	  delete v0objects.RemoveAt(3); // esdVtx created via copy construct
	  esdVtx = 0;
	  if (!selectV0) 
	    continue;
	}
	else{
	  delete v0objects.RemoveAt(3); // esdVtx created via copy construct
	  esdVtx = 0;
	}
    
	v0->GetXYZ(pos[0], pos[1], pos[2]);

	if (!old) {
	    chi2 = v0->GetChi2V0(); // = chi2/NDF since NDF = 2*2-3
	    v0->GetPosCov(covVtx);
	} else {
	    chi2 = -999.;
	    for (Int_t i = 0; i < 6; i++)  covVtx[i] = 0.;
	}


	AliAODVertex * vV0 = 
	  new(vertices[jVertices++]) AliAODVertex(pos,
						  covVtx,
						  chi2,
						  primary,
						  nV0,
						  AliAODVertex::kV0);
	primary->AddDaughter(vV0);
	

	Float_t  dcaPosToPrimVertexXYZ[2]   = { 999., 999.}; // ..[0] = in XY plane and ..[1] = in Z
	Float_t  dcaNegToPrimVertexXYZ[2]   = { 999., 999.}; // ..[0] = in XY plane and ..[1] = in Z
	Double_t dcaDaughterToPrimVertex[2] = { 999., 999.}; // ..[0] = Pos and ..[1] = Neg
	
	Double_t  dcaV0Daughters      = v0->GetDcaV0Daughters();
	Double_t  dcaV0ToPrimVertex   = v0->GetD(esd->GetPrimaryVertex()->GetX(),esd->GetPrimaryVertex()->GetY(),esd->GetPrimaryVertex()->GetZ());
	v0->GetPPxPyPz(p_pos_atv0[0],p_pos_atv0[1],p_pos_atv0[2]); 
	v0->GetNPxPyPz(p_neg_atv0[0],p_neg_atv0[1],p_neg_atv0[2]); 

	// Add the positive tracks from the V0
	

	esdV0Pos->GetPxPyPz(p_pos);
	esdV0Pos->GetXYZ(pos);
	esdV0Pos->GetCovarianceXYZPxPyPz(covTr);
	esdV0Pos->GetESDpid(pid);
	esdV0Pos->GetImpactParameters(dcaPosToPrimVertexXYZ[0],dcaPosToPrimVertexXYZ[1]);
	if (!usedTrack[posFromV0]) {
	    usedTrack[posFromV0] = kTRUE;
	    UInt_t selectInfo = 0;
	    if (fTrackFilter) selectInfo = fTrackFilter->IsSelected(esdV0Pos);
	    if(mcH)mcH->SelectParticle(esdV0Pos->GetLabel());
	    aodTrack = new(tracks[jTracks++]) AliAODTrack(esdV0Pos->GetID(),
							  esdV0Pos->GetLabel(), 
							  p_pos, 
							  kTRUE,
							  pos,
							  kFALSE,
							  covTr, 
							  (Short_t)esdV0Pos->GetSign(),
							  esdV0Pos->GetITSClusterMap(), 
							  pid,
							  vV0,
							  kTRUE,  // check if this is right
							  vtx->UsesTrack(esdV0Pos->GetID()),
							  AliAODTrack::kSecondary,
							  selectInfo);
	    aodRefs->AddAt(aodTrack,posFromV0);
	    //	    if (fDebug > 0) printf("-------------------Bo: pos track from original pt %.3f \n",aodTrack->Pt());
	    if (esdV0Pos->GetSign() > 0) nPosTracks++;
	    aodTrack->ConvertAliPIDtoAODPID();
	    aodTrack->SetFlags(esdV0Pos->GetStatus());
            SetAODPID(esdV0Pos,aodTrack,detpid,timezero);
	}
	else {
	    aodTrack = dynamic_cast<AliAODTrack*>(aodRefs->At(posFromV0));
	    //	    if (fDebug > 0) printf("-------------------Bo pos track from refArray pt %.3f \n",aodTrack->Pt());
	}
	vV0->AddDaughter(aodTrack);
    
	// Add the negative tracks from the V0
	
	esdV0Neg->GetPxPyPz(p_neg);
	esdV0Neg->GetXYZ(pos);
	esdV0Neg->GetCovarianceXYZPxPyPz(covTr);
	esdV0Neg->GetESDpid(pid);
	esdV0Neg->GetImpactParameters(dcaNegToPrimVertexXYZ[0],dcaNegToPrimVertexXYZ[1]);
	
	if (!usedTrack[negFromV0]) {
	    usedTrack[negFromV0] = kTRUE;
	    UInt_t selectInfo = 0;
	    if (fTrackFilter) selectInfo = fTrackFilter->IsSelected(esdV0Neg);
	    if(mcH)mcH->SelectParticle(esdV0Neg->GetLabel());
	    aodTrack = new(tracks[jTracks++]) AliAODTrack(esdV0Neg->GetID(),
							  esdV0Neg->GetLabel(),
							  p_neg,
							  kTRUE,
							  pos,
							  kFALSE,
							  covTr, 
							  (Short_t)esdV0Neg->GetSign(),
							  esdV0Neg->GetITSClusterMap(), 
							  pid,
							  vV0,
							  kTRUE,  // check if this is right
							  vtx->UsesTrack(esdV0Neg->GetID()),
							  AliAODTrack::kSecondary,
							  selectInfo);
	    
	    aodRefs->AddAt(aodTrack,negFromV0);
	    //	    if (fDebug > 0) printf("-------------------Bo: neg track from original pt %.3f \n",aodTrack->Pt());
	    if (esdV0Neg->GetSign() > 0) nPosTracks++;
	    aodTrack->ConvertAliPIDtoAODPID();
	    aodTrack->SetFlags(esdV0Neg->GetStatus());
            SetAODPID(esdV0Neg,aodTrack,detpid,timezero);
	}
	else {
	    aodTrack = dynamic_cast<AliAODTrack*>(aodRefs->At(negFromV0));
	    //	    if (fDebug > 0) printf("-------------------Bo neg track from refArray pt %.3f \n",aodTrack->Pt());
	}
	vV0->AddDaughter(aodTrack);
 	dcaDaughterToPrimVertex[0] = 
	    TMath::Sqrt(dcaPosToPrimVertexXYZ[0]*dcaPosToPrimVertexXYZ[0]
			+dcaPosToPrimVertexXYZ[1]*dcaPosToPrimVertexXYZ[1]);
	dcaDaughterToPrimVertex[1] = 
	    TMath::Sqrt(dcaNegToPrimVertexXYZ[0]*dcaNegToPrimVertexXYZ[0]
			+dcaNegToPrimVertexXYZ[1]*dcaNegToPrimVertexXYZ[1]);
	// add it to the V0 array as well
	aodV0 = new(V0s[jV0s++]) 
	    AliAODv0(vV0, dcaV0Daughters, dcaV0ToPrimVertex, p_pos_atv0, p_neg_atv0, dcaDaughterToPrimVertex); // to be refined
	// set the aod v0 on-the-fly status
	aodV0->SetOnFlyStatus(v0->GetOnFlyStatus());
    } 
    V0s.Expand(jV0s);	 
    // end of the loop on V0s
    
    // Kinks: it is a big mess the access to the information in the kinks
    // The loop is on the tracks in order to find the mother and daugther of each kink
    
    
    for (Int_t iTrack=0; iTrack<nTracks; ++iTrack) {
	
	AliESDtrack * esdTrack = esd->GetTrack(iTrack);
	
	Int_t ikink = esdTrack->GetKinkIndex(0);
	
	if (ikink && nKinks) {
	    // Negative kink index: mother, positive: daughter
	    
	    // Search for the second track of the kink
	    
	    for (Int_t jTrack = iTrack+1; jTrack<nTracks; ++jTrack) {
		
		AliESDtrack * esdTrack1 = esd->GetTrack(jTrack);
		
		Int_t jkink = esdTrack1->GetKinkIndex(0);
		
		if ( TMath::Abs(ikink)==TMath::Abs(jkink) ) {
		    
		    // The two tracks are from the same kink
		    
		    if (usedKink[TMath::Abs(ikink)-1]) continue; // skip used kinks
		    
		    Int_t imother = -1;
		    Int_t idaughter = -1;
		    
		    if (ikink<0 && jkink>0) {
			
			imother = iTrack;
			idaughter = jTrack;
		    }
		    else if (ikink>0 && jkink<0) {
			
			imother = jTrack;
			idaughter = iTrack;
		    }
		    else {
//			cerr << "Error: Wrong combination of kink indexes: "
//			     << ikink << " " << jkink << endl;
			continue;
		    }
		    
		    // Add the mother track if it passed primary track selection cuts
		    
		    AliAODTrack * mother = NULL;
		    
		    UInt_t selectInfo = 0;
		    if (fTrackFilter) {
			selectInfo = fTrackFilter->IsSelected(esd->GetTrack(imother));
			if (!selectInfo) continue;
		    }
		    
		    if (!usedTrack[imother]) {
			
			usedTrack[imother] = kTRUE;
			
			AliESDtrack *esdTrackM = esd->GetTrack(imother);
			esdTrackM->GetPxPyPz(p);
			esdTrackM->GetXYZ(pos);
			esdTrackM->GetCovarianceXYZPxPyPz(covTr);
			esdTrackM->GetESDpid(pid);
			if(mcH)mcH->SelectParticle(esdTrackM->GetLabel());
			mother = 
			    new(tracks[jTracks++]) AliAODTrack(esdTrackM->GetID(),
							       esdTrackM->GetLabel(),
							       p,
							       kTRUE,
							       pos,
							       kFALSE,
							       covTr, 
							       (Short_t)esdTrackM->GetSign(),
							       esdTrackM->GetITSClusterMap(), 
							       pid,
							       primary,
							       kTRUE, // check if this is right
							       vtx->UsesTrack(esdTrack->GetID()),
							       AliAODTrack::kPrimary,
							       selectInfo);
			aodRefs->AddAt(mother, imother);
			
			if (esdTrackM->GetSign() > 0) nPosTracks++;
			mother->SetFlags(esdTrackM->GetStatus());
			mother->ConvertAliPIDtoAODPID();
			primary->AddDaughter(mother);
			mother->ConvertAliPIDtoAODPID();
                        SetAODPID(esdTrackM,mother,detpid,timezero);
		    }
		    else {
//			cerr << "Error: event " << esd->GetEventNumberInFile() << " kink " << TMath::Abs(ikink)-1
//			     << " track " << imother << " has already been used!" << endl;
		  }
		    
		    // Add the kink vertex
		    AliESDkink * kink = esd->GetKink(TMath::Abs(ikink)-1);
		    
		    AliAODVertex * vkink = 
			new(vertices[jVertices++]) AliAODVertex(kink->GetPosition(),
								NULL,
								0.,
								mother,
								esdTrack->GetID(),  // This is the track ID of the mother's track!
								AliAODVertex::kKink);
		    // Add the daughter track
		  
		    AliAODTrack * daughter = NULL;
		    
		    if (!usedTrack[idaughter]) {
			
			usedTrack[idaughter] = kTRUE;
			
			AliESDtrack *esdTrackD = esd->GetTrack(idaughter);
			esdTrackD->GetPxPyPz(p);
			esdTrackD->GetXYZ(pos);
			esdTrackD->GetCovarianceXYZPxPyPz(covTr);
			esdTrackD->GetESDpid(pid);
			selectInfo = 0;
			if (fTrackFilter) selectInfo = fTrackFilter->IsSelected(esdTrackD);
			if(mcH)mcH->SelectParticle(esdTrackD->GetLabel());
			daughter = 
			    new(tracks[jTracks++]) AliAODTrack(esdTrackD->GetID(),
							       esdTrackD->GetLabel(),
							       p,
							       kTRUE,
							       pos,
							       kFALSE,
							       covTr, 
							       (Short_t)esdTrackD->GetSign(),
							       esdTrackD->GetITSClusterMap(), 
							       pid,
							       vkink,
							       kTRUE, // check if this is right
							       vtx->UsesTrack(esdTrack->GetID()),
							       AliAODTrack::kSecondary,
							       selectInfo);
			
			aodRefs->AddAt(daughter, idaughter);
			
			if (esdTrackD->GetSign() > 0) nPosTracks++;
			daughter->SetFlags(esdTrackD->GetStatus());
			daughter->ConvertAliPIDtoAODPID();
			vkink->AddDaughter(daughter);
			daughter->ConvertAliPIDtoAODPID();
                       SetAODPID(esdTrackD,daughter,detpid,timezero);
		    }
		    else {
//			cerr << "Error: event " << esd->GetEventNumberInFile() << " kink " << TMath::Abs(ikink)-1
//			     << " track " << idaughter << " has already been used!" << endl;
		    }
		}
	    }
	}      
    }
    
  
    // Tracks (primary and orphan)

    if (fDebug > 0) printf("NUMBER OF ESD TRACKS %5d\n", nTracks);
    
    for (Int_t nTrack = 0; nTrack < nTracks; ++nTrack) {
	
	
	if (usedTrack[nTrack]) continue;

	AliESDtrack *esdTrack = esd->GetTrack(nTrack);
	UInt_t selectInfo = 0;
	//
	// Track selection
	if (fTrackFilter) {
	    selectInfo = fTrackFilter->IsSelected(esdTrack);
	    if (!selectInfo && !vtx->UsesTrack(esdTrack->GetID())) continue;
	}
	
	//
	esdTrack->GetPxPyPz(p);
	esdTrack->GetXYZ(pos);
	esdTrack->GetCovarianceXYZPxPyPz(covTr);
	esdTrack->GetESDpid(pid);
	if(mcH)mcH->SelectParticle(esdTrack->GetLabel());
	primary->AddDaughter(aodTrack =
			     new(tracks[jTracks++]) AliAODTrack(esdTrack->GetID(),
								esdTrack->GetLabel(),
								p,
								kTRUE,
								pos,
								kFALSE,
								covTr, 
								(Short_t)esdTrack->GetSign(),
								esdTrack->GetITSClusterMap(), 
								pid,
								primary,
								kTRUE, // check if this is right
								vtx->UsesTrack(esdTrack->GetID()),
								AliAODTrack::kPrimary, 
								selectInfo)
			     );
	aodRefs->AddAt(aodTrack, nTrack);
	
	if (esdTrack->GetSign() > 0) nPosTracks++;
	aodTrack->SetFlags(esdTrack->GetStatus());
	aodTrack->ConvertAliPIDtoAODPID();
	SetAODPID(esdTrack,aodTrack,detpid,timezero);
    } // end of loop on tracks
    
    // Update number of AOD tracks in header at the end of track loop (M.G.)
    header->SetRefMultiplicity(jTracks);
    header->SetRefMultiplicityPos(nPosTracks);
    header->SetRefMultiplicityNeg(jTracks - nPosTracks);
    if (fDebug > 0) 
      printf("   NAODTRACKS=%d  NPOS=%d  NNEG=%d\n", jTracks, nPosTracks, jTracks - nPosTracks);
    // Do not shrink the array of tracks - other filters may add to it (M.G)
//    tracks.Expand(jTracks); // remove 'empty slots' due to unwritten tracks
  
    // Access to the AOD container of PMD clusters
    TClonesArray &pmdClusters = *(AODEvent()->GetPmdClusters());
    Int_t jPmdClusters=0;
  
    for (Int_t iPmd = 0; iPmd < nPmdClus; ++iPmd) {
      // file pmd clusters, to be revised!
      AliESDPmdTrack *pmdTrack = esd->GetPmdTrack(iPmd);
      Int_t nLabel = 0;
      Int_t *label = 0x0;
      Double_t posPmd[3] = { pmdTrack->GetClusterX(), pmdTrack->GetClusterY(), pmdTrack->GetClusterZ()};
      Double_t pidPmd[9] = { 0., 0., 0., 0., 0., 0., 0., 0., 0. }; // to be revised!
      // type not set!
      // assoc cluster not set
      new(pmdClusters[jPmdClusters++]) AliAODPmdCluster(iPmd, nLabel, label, pmdTrack->GetClusterADC(), posPmd, pidPmd);
    }

    // Access to the AOD container of clusters
    TClonesArray &caloClusters = *(AODEvent()->GetCaloClusters());
    Int_t jClusters=0;
 
    for (Int_t iClust=0; iClust<nCaloClus; ++iClust) {

      AliESDCaloCluster * cluster = esd->GetCaloCluster(iClust);

      Int_t id        = cluster->GetID();
      Int_t nLabel    = cluster->GetNLabels();
      TArrayI* labels = cluster->GetLabels();
      Int_t *label = 0;
      if (labels){
	label = (cluster->GetLabels())->GetArray();
	for(int i = 0;i < labels->GetSize();++i){
	  if(mcH)mcH->SelectParticle(label[i]);
	}
      }     

      Float_t energy = cluster->E();
      cluster->GetPosition(posF);
      Char_t ttype = AliAODCluster::kUndef; 

      if (cluster->GetClusterType() == AliESDCaloCluster::kPHOSCluster) {
	ttype=AliAODCluster::kPHOSNeutral;
      } 
      else if (cluster->GetClusterType() == AliESDCaloCluster::kEMCALClusterv1) {
	ttype = AliAODCluster::kEMCALClusterv1;
      }

      
      AliAODCaloCluster *caloCluster = new(caloClusters[jClusters++]) AliAODCaloCluster(id,
											nLabel,
											label,
											energy,
											posF,
											NULL,
											ttype);
      
      caloCluster->SetCaloCluster(cluster->GetDistanceToBadChannel(),
				  cluster->GetClusterDisp(),
				  cluster->GetM20(), cluster->GetM02(),
				  cluster->GetEmcCpvDistance(),  
				  cluster->GetNExMax(),cluster->GetTOF()) ;

      caloCluster->SetPIDFromESD(cluster->GetPid());
      caloCluster->SetNCells(cluster->GetNCells());
      caloCluster->SetCellsAbsId(cluster->GetCellsAbsId());
      caloCluster->SetCellsAmplitudeFraction(cluster->GetCellsAmplitudeFraction());

      TArrayI* matchedT = 	cluster->GetTracksMatched();
      if (matchedT && cluster->GetTrackMatched() >= 0) {	
	for (Int_t im = 0; im < matchedT->GetSize(); im++) {
	    Int_t iESDtrack = matchedT->At(im);;
	    if (aodRefs->At(iESDtrack) != 0) {
		caloCluster->AddTrackMatched((AliAODTrack*)aodRefs->At(iESDtrack));
	    }
	}
      }
      
    } 
    caloClusters.Expand(jClusters); // resize TObjArray to 'remove' slots for pseudo clusters	 
    // end of loop on calo clusters

    // fill EMCAL cell info
    if (esd->GetEMCALCells()) { // protection against missing ESD information
      AliESDCaloCells &esdEMcells = *(esd->GetEMCALCells());
      Int_t nEMcell = esdEMcells.GetNumberOfCells() ;
      
      AliAODCaloCells &aodEMcells = *(AODEvent()->GetEMCALCells());
      aodEMcells.CreateContainer(nEMcell);
      aodEMcells.SetType(AliAODCaloCells::kEMCAL);
      for (Int_t iCell = 0; iCell < nEMcell; iCell++) {      
	aodEMcells.SetCell(iCell,esdEMcells.GetCellNumber(iCell),esdEMcells.GetAmplitude(iCell));
      }
      aodEMcells.Sort();
    }

    // fill PHOS cell info
    if (esd->GetPHOSCells()) { // protection against missing ESD information
      AliESDCaloCells &esdPHcells = *(esd->GetPHOSCells());
      Int_t nPHcell = esdPHcells.GetNumberOfCells() ;
      
      AliAODCaloCells &aodPHcells = *(AODEvent()->GetPHOSCells());
      aodPHcells.CreateContainer(nPHcell);
      aodPHcells.SetType(AliAODCaloCells::kPHOS);
      for (Int_t iCell = 0; iCell < nPHcell; iCell++) {      
	aodPHcells.SetCell(iCell,esdPHcells.GetCellNumber(iCell),esdPHcells.GetAmplitude(iCell));
      }
      aodPHcells.Sort();
    }

    // tracklets    
    AliAODTracklets &SPDTracklets = *(AODEvent()->GetTracklets());
    const AliMultiplicity *mult = esd->GetMultiplicity();
    if (mult) {
      if (mult->GetNumberOfTracklets()>0) {
	SPDTracklets.CreateContainer(mult->GetNumberOfTracklets());

	for (Int_t n=0; n<mult->GetNumberOfTracklets(); n++) {
	  if(mcH){
	    mcH->SelectParticle(mult->GetLabel(n, 0));
	    mcH->SelectParticle(mult->GetLabel(n, 1));
	  }
	  SPDTracklets.SetTracklet(n, mult->GetTheta(n), mult->GetPhi(n), mult->GetDeltaPhi(n), mult->GetLabel(n, 0),mult->GetLabel(n, 1));
	}
      }
    } else {
      //Printf("ERROR: AliMultiplicity could not be retrieved from ESD");
    }

    delete [] usedTrack;
    delete [] usedV0;
    delete [] usedKink;
    delete    aodRefs;

    return;
}


void AliAnalysisTaskESDfilter::SetAODPID(AliESDtrack *esdtrack, AliAODTrack *aodtrack, AliAODPid *detpid, Double_t timezero)
{
  //
  // Setter for the raw PID detector signals
  //

  if(esdtrack->Pt()>fHighPthreshold) {
    detpid = new AliAODPid();
    SetDetectorRawSignals(detpid,esdtrack,timezero);
    aodtrack->SetDetPID(detpid);
  } else {
    if(fPtshape){
      if(esdtrack->Pt()> fPtshape->GetXmin()){
	Double_t y = fPtshape->Eval(esdtrack->Pt())/fPtshape->Eval(fHighPthreshold);
	if(gRandom->Rndm(0)<1./y){
	  detpid = new AliAODPid();
	  SetDetectorRawSignals(detpid,esdtrack,timezero);
	  aodtrack->SetDetPID(detpid);
	}//end rndm
      }//end if p < pmin
    }//end if p function
  }// end else
}

void AliAnalysisTaskESDfilter::SetDetectorRawSignals(AliAODPid *aodpid, AliESDtrack *track, Double_t timezero)
{
//
//assignment of the detector signals (AliXXXesdPID inspired)
//
 if(!track){
 AliInfo("no ESD track found. .....exiting");
 return;
 }

 aodpid->SetITSsignal(track->GetITSsignal());
 aodpid->SetTPCsignal(track->GetTPCsignal());
 //n TRD planes = 6

 Int_t nslices = track->GetNumberOfTRDslices()*6;
 Double_t *trdslices = new Double_t[nslices];
 for(Int_t iSl =0; iSl < track->GetNumberOfTRDslices(); iSl++) {
     for(Int_t iPl =0; iPl<6; iPl++) trdslices[iPl*track->GetNumberOfTRDslices()+iSl] = track->GetTRDslice(iPl,iSl);
    }


 aodpid->SetTRDsignal(track->GetNumberOfTRDslices()*6,trdslices);
 Double_t times[AliAODPid::kSPECIES]; track->GetIntegratedTimes(times);
 aodpid->SetIntegratedTimes(times);

 aodpid->SetTOFsignal(track->GetTOFsignal()-timezero); // to be fixed
 aodpid->SetHMPIDsignal(track->GetHMPIDsignal());

}

void AliAnalysisTaskESDfilter::Terminate(Option_t */*option*/)
{
// Terminate analysis
//
    if (fDebug > 1) printf("AnalysisESDfilter: Terminate() \n");
}

void  AliAnalysisTaskESDfilter::PrintMCInfo(AliStack *pStack,Int_t label){
  if(!pStack)return;
  label = TMath::Abs(label);
  TParticle *part = pStack->Particle(label);
  Printf("########################");
  Printf("%s:%d %d UniqueID %d PDG %d P %3.3f",(char*)__FILE__,__LINE__,label,part->GetUniqueID(),part->GetPdgCode(),part->P());
  part->Print();
  TParticle* mother = part;
  Int_t imo = part->GetFirstMother();
  Int_t nprim = pStack->GetNprimary();
  //  while((imo >= nprim) && (mother->GetUniqueID() == 4)) {
  while((imo >= nprim)) {
    mother =  pStack->Particle(imo);
    Printf("Mother %s:%d Label %d UniqueID %d PDG %d P %3.3f",(char*)__FILE__,__LINE__,imo,mother->GetUniqueID(),mother->GetPdgCode(),mother->P());
    mother->Print();
    imo =  mother->GetFirstMother();
  }
  Printf("########################");
}