[u/mrichter/AliRoot.git] / HMPID / AliHMPIDReconstructor.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.                  *
 **************************************************************************/
//.
// HMPID base class to reconstruct an event
//.
//.
//.
#include "AliHMPIDReconstructor.h" //class header
#include "AliHMPID.h"              //Reconstruct() 
#include "AliHMPIDCluster.h"       //Dig2Clu()
#include "AliHMPIDParam.h"         //FillEsd() 
#include <AliCDBEntry.h>           //ctor
#include <AliCDBManager.h>         //ctor
#include <AliESD.h>                //FillEsd()
#include <AliRawReader.h>          //Reconstruct() for raw digits
ClassImp(AliHMPIDReconstructor)

//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
AliHMPIDReconstructor::AliHMPIDReconstructor():AliReconstructor(),fUserCut(0),fDaqSig(0),fDig(0),fClu(0)
{
//
//ctor
//

  fClu=new TObjArray(AliHMPIDDigit::kMaxCh+1); fClu->SetOwner(kTRUE);
  fDig=new TObjArray(AliHMPIDDigit::kMaxCh+1); fDig->SetOwner(kTRUE);

  for(int i=AliHMPIDDigit::kMinCh;i<=AliHMPIDDigit::kMaxCh;i++){ 
    fDig->AddAt(new TClonesArray("AliHMPIDDigit"),i);
    TClonesArray *pClus = new TClonesArray("AliHMPIDCluster");
    pClus->SetUniqueID(i);
    fClu->AddAt(pClus,i);
  }
  
  AliCDBEntry *pUserCutEnt =AliCDBManager::Instance()->Get("HMPID/Calib/UserCut");    //contains TObjArray of 14 TObject with n. of sigmas to cut charge 
  if(!pUserCutEnt) return;                                                            //No request from User to apply a more severe cut on pad charge  
  
  fUserCut = pUserCutEnt->GetObject()->GetUniqueID();

  Printf(" usercut %i ",fUserCut);
  
  AliCDBEntry *pDaqCutEnt =AliCDBManager::Instance()->Get("HMPID/Calib/DaqSigCut");     //contains TObjArray of 14 TObject with n. of sigmas to cut charge 
  if(!pDaqCutEnt) AliFatal("No pedestal sigmas cut!");
  TObjArray *pDaqCut = (TObjArray*)pDaqCutEnt->GetObject();


  for(Int_t ddl=0;ddl<14;ddl++){
    if(fUserCut<=(Int_t)pDaqCut->At(ddl)->GetUniqueID()) continue;
    AliCDBEntry *pDaqSigEnt =AliCDBManager::Instance()->Get("HMPID/Calib/DaqSig");  //contains TObjArray of TObjArray 14 TMatrixF sigmas values for pads 
    if(!pDaqSigEnt) AliFatal("No pedestals from DAQ!");
    TObjArray *pDaqSig = (TObjArray*)pDaqSigEnt->GetObject();
    SigConv(pDaqSig);
    break;
  }
}//AliHMPIDReconstructor
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
void AliHMPIDReconstructor::SigConv(TObjArray *pDaqSig)
{
// Conversion from the pedestal objects in to 7 TMatrixF(padX,padY)
//Arguments: pDaqSig pointer to the pedestal objects from OCDB
//   Returs: none
//
  fDaqSig = new TObjArray(AliHMPIDDigit::kMaxCh+1);fDaqSig->SetOwner(kTRUE);
  
  for(Int_t iCh=AliHMPIDDigit::kMinCh;iCh<=AliHMPIDDigit::kMaxCh;iCh++) fDaqSig->AddAt(new TMatrixF(1,10,0,47),iCh);
 
  AliHMPIDDigit dig;
   
  for(Int_t ddl=0;ddl<=13;ddl++){
    for(Int_t row=1;row<=24;row++)
      for(Int_t dil=1;dil<=10;dil++)
        for(Int_t adr=0;adr<=47;adr++){
          TObjArray *pDdl = (TObjArray*)pDaqSig->At(ddl);
          TObjArray *pRow = (TObjArray*)pDdl->At(row-1);
          TMatrixF *pM = (TMatrixF*)pRow;
          Float_t sigma = (*pM)(dil,adr);
          dig.Raw(ddl,row,dil,adr);
          TMatrixF* pMConv = (TMatrixF*)(fDaqSig->At(dig.Ch()));
          (*pMConv)(dig.PadChX(),dig.PadChY()) = sigma;
        }
  }
}//SigConv()
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
void AliHMPIDReconstructor::Dig2Clu(TObjArray *pDigAll,TObjArray *pCluAll,Bool_t isTryUnfold)
{
// Finds all clusters for a given digits list provided not empty. Currently digits list is a list of all digits for a single chamber.
// Puts all found clusters in separate lists, one per clusters. 
// Arguments: pDigAll     - list of digits for all chambers 
//            pCluAll     - list of clusters for all chambers
//            isTryUnfold - flag to choose between CoG and Mathieson fitting  
//  Returns: none    
  TMatrixF padMap(AliHMPIDDigit::kMinPx,AliHMPIDDigit::kMaxPcx,AliHMPIDDigit::kMinPy,AliHMPIDDigit::kMaxPcy);  //pads map for single chamber 0..159 x 0..143 
  
  for(Int_t iCh=AliHMPIDDigit::kMinCh;iCh<=AliHMPIDDigit::kMaxCh;iCh++){                  //chambers loop 
    TClonesArray *pDigCur=(TClonesArray*)pDigAll->At(iCh);                                //get list of digits for current chamber
    if(pDigCur->GetEntriesFast()==0) continue;                                            //no digits for current chamber
  
    padMap=(Float_t)-1;                                                                   //reset map to -1 (means no digit for this pad)  
    TClonesArray *pCluCur=(TClonesArray*)pCluAll->At(iCh);                                //get list of clusters for current chamber
    
    for(Int_t iDig=0;iDig<pDigCur->GetEntriesFast();iDig++){                              //digits loop to fill pads map
      AliHMPIDDigit *pDig= (AliHMPIDDigit*)pDigCur->At(iDig);                             //get current digit
      padMap( pDig->PadChX(), pDig->PadChY() )=iDig;                                      //fill the map, (padx,pady) cell takes digit index
    }//digits loop to fill digits map 
    
    AliHMPIDCluster clu;                                                                  //tmp cluster to be used as current
    for(Int_t iDig=0;iDig<pDigCur->GetEntriesFast();iDig++){                              //digits loop for current chamber
      AliHMPIDDigit *pDig=(AliHMPIDDigit*)pDigCur->At(iDig);                              //take current digit
      if(!(pDig=UseDig(pDig->PadChX(),pDig->PadChY(),pDigCur,&padMap))) continue;         //this digit is already taken in FormClu(), go after next digit
      FormClu(&clu,pDig,pDigCur,&padMap);                                                 //form cluster starting from this digit by recursion
      
      clu.Solve(pCluCur,isTryUnfold);                                                     //solve this cluster and add all unfolded clusters to provided list  
      clu.Reset();                                                                        //empty current cluster
    }//digits loop for current chamber
  }//chambers loop
}//Dig2Clu()
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
void  AliHMPIDReconstructor::FormClu(AliHMPIDCluster *pClu,AliHMPIDDigit *pDig,TClonesArray *pDigLst,TMatrixF *pDigMap)
{
// Forms the initial cluster as a combination of all adjascent digits. Starts from the given digit then calls itself recursevly  for all neighbours.
// Arguments: pClu - pointer to cluster being formed
//   Returns: none   
  pClu->DigAdd(pDig);//take this digit in cluster

  Int_t cnt=0,cx[4],cy[4];
  
  if(pDig->PadPcX() != AliHMPIDDigit::kMinPx){cx[cnt]=pDig->PadChX()-1; cy[cnt]=pDig->PadChY()  ;cnt++;}       //left
  if(pDig->PadPcX() != AliHMPIDDigit::kMaxPx){cx[cnt]=pDig->PadChX()+1; cy[cnt]=pDig->PadChY()  ;cnt++;}       //right
  if(pDig->PadPcY() != AliHMPIDDigit::kMinPy){cx[cnt]=pDig->PadChX()  ; cy[cnt]=pDig->PadChY()-1;cnt++;}       //down
  if(pDig->PadPcY() != AliHMPIDDigit::kMaxPy){cx[cnt]=pDig->PadChX()  ; cy[cnt]=pDig->PadChY()+1;cnt++;}       //up
  
  for (Int_t i=0;i<cnt;i++){//neighbours loop
    if((pDig=UseDig(cx[i],cy[i],pDigLst,pDigMap))) FormClu(pClu,pDig,pDigLst,pDigMap);   //check if this neighbour pad fired and mark it as taken  
  }//neighbours loop  
}//FormClu()
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
void AliHMPIDReconstructor::Reconstruct(TTree *pDigTree,TTree *pCluTree)const
{
//Invoked  by AliReconstruction to convert digits to clusters i.e. reconstruct simulated data
//Arguments: pDigTree - pointer to Digit tree
//           pCluTree - poitner to Cluster tree
//  Returns: none    
  AliDebug(1,"Start.");
  for(Int_t iCh=AliHMPIDDigit::kMinCh;iCh<=AliHMPIDDigit::kMaxCh;iCh++) {
    pCluTree->Branch(Form("HMPID%d",iCh),&((*fClu)[iCh]),4000,0);
    pDigTree->SetBranchAddress(Form("HMPID%d",iCh),&((*fDig)[iCh]));
  }   
  pDigTree->GetEntry(0);
  Dig2Clu(fDig,fClu);              //cluster finder 
  pCluTree->Fill();                //fill tree for current event
  
  for(Int_t iCh=AliHMPIDDigit::kMinCh;iCh<=AliHMPIDDigit::kMaxCh;iCh++){
    fDig->At(iCh)->Clear();
    fClu->At(iCh)->Clear();
  }
  
  AliDebug(1,"Stop.");      
}//Reconstruct(for simulated digits)
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
void AliHMPIDReconstructor::Reconstruct(AliRunLoader *pAL,AliRawReader* pRR)const
{
//Invoked  by AliReconstruction to convert raw digits from DDL files to clusters
//Arguments: pAL - ALICE run loader pointer
//           pRR - ALICE raw reader pointer
//  Returns: none
  AliLoader *pRL=pAL->GetDetectorLoader("HMPID");  AliHMPID *pRich=(AliHMPID*)pAL->GetAliRun()->GetDetector("HMPID");//get pointers for HMPID and HMPID loader

  AliHMPIDDigit dig; //tmp digit, raw digit will be converted to it

  TObjArray digLst; Int_t iDigCnt[7]; for(Int_t i=0;i<7;i++){digLst.AddAt(new TClonesArray("AliHMPIDDigit"),i); iDigCnt[i]=0;} //tmp list of digits for allchambers

  Int_t iEvtN=0;
  while(pRR->NextEvent()){//events loop
    pAL->GetEvent(iEvtN++);
    pRL->MakeTree("R");  pRich->MakeBranch("R");

    for(Int_t iCh=0;iCh<7;iCh++){//chambers loop
      pRR->Select("HMPID",2*iCh,2*iCh+1);//select only DDL files for the current chamber
      UInt_t w32=0;
      while(pRR->ReadNextInt(w32)){//raw records loop (in selected DDL files)
        UInt_t ddl=pRR->GetDDLID(); //returns 0,1,2 ... 13
        dig.Raw(w32,ddl,pRR);
        AliDebug(1,Form("Ch=%i DDL=%i raw=0x%x digit=(%3i,%3i,%3i,%3i) Q=%5.2f",iCh,ddl,w32,dig.Ch(),dig.Pc(),dig.PadPcX(),dig.PadPcY(),dig.Q()));
        if(!IsDigSurvive(&dig)) continue;                                             //sigma cut test
        new((*((TClonesArray*)digLst.At(iCh)))[iDigCnt[iCh]++]) AliHMPIDDigit(dig); //add this digit to the tmp list
      }//raw records loop
      pRR->Reset();
    }//chambers loop

    Dig2Clu(&digLst,pRich->CluLst());//cluster finder for all chambers
    for(Int_t i=0;i<7;i++){digLst.At(i)->Delete(); iDigCnt[i]=0;}                    //clean up list of digits for all chambers

    pRL->TreeR()->Fill();            //fill tree for current event
    pRL->WriteRecPoints("OVERWRITE");//write out clusters for current event
    pRich->CluReset();
  }//events loop
  pRL->UnloadRecPoints();
}//Reconstruct raw data
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
void AliHMPIDReconstructor::ConvertDigits(AliRawReader *pRR,TTree *pDigTree)const
{
//Invoked  by AliReconstruction to convert raw digits from DDL files to digits
//Arguments: pRR - ALICE raw reader pointer
//           pDigTree - pointer to Digit tree
//  Returns: none    
  AliDebug(1,"Start.");
  AliHMPIDDigit dig; //tmp digit, raw digit will be converted to it
  for(Int_t iCh=AliHMPIDDigit::kMinCh;iCh<=AliHMPIDDigit::kMaxCh;iCh++) {
    pDigTree->Branch(Form("HMPID%d",iCh),&((*fDig)[iCh]),4000,0);
    pRR->Select("HMPID",2*iCh,2*iCh+1);//select only DDL files for the current chamber      
    Int_t iDigCnt=0;
    UInt_t w32=0;
    while(pRR->ReadNextInt(w32)){//raw records loop (in selected DDL files)
      UInt_t ddl=pRR->GetDDLID(); //returns 0,1,2 ... 13
      if (!dig.Raw(w32,ddl,pRR)) continue;
      AliDebug(1,Form("Ch=%i DDL=%i raw=0x%x digit=(%3i,%3i,%3i,%3i) Q=%5.2f",iCh,ddl,w32,dig.Ch(),dig.Pc(),dig.PadPcX(),dig.PadPcY(),dig.Q()));
      if(!IsDigSurvive(&dig)) continue;                                       //sigma cut test
      new((*((TClonesArray*)fDig->At(iCh)))[iDigCnt++]) AliHMPIDDigit(dig); //add this digit to the tmp list
    }//raw records loop
    pRR->Reset();        
  }//chambers loop
  pDigTree->Fill();
  for(Int_t iCh=AliHMPIDDigit::kMinCh;iCh<=AliHMPIDDigit::kMaxCh;iCh++)fDig->At(iCh)->Clear();
  AliDebug(1,"Stop.");
}//Reconstruct digits from raw digits
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
void AliHMPIDReconstructor::FillESD(AliRunLoader *, AliESD *pESD) const
{
// Calculates probability to be a electron-muon-pion-kaon-proton
// from the given Cerenkov angle and momentum assuming no initial particle composition
// (i.e. apriory probability to be the particle of the given sort is the same for all sorts)

  AliPID ppp; //needed
  Double_t pid[AliPID::kSPECIES],h[AliPID::kSPECIES];
   
  for(Int_t iTrk=0;iTrk<pESD->GetNumberOfTracks();iTrk++){//ESD tracks loop
    AliESDtrack *pTrk = pESD->GetTrack(iTrk);// get next reconstructed track
    if(pTrk->GetHMPIDsignal()<=0){//HMPID does not find anything reasonable for this track, assign 0.2 for all species
      for(Int_t iPart=0;iPart<AliPID::kSPECIES;iPart++) pid[iPart]=1.0/AliPID::kSPECIES;
      pTrk->SetHMPIDpid(pid);
      continue;
    } 
    Double_t pmod = pTrk->GetP();
    Double_t hTot=0;
    for(Int_t iPart=0;iPart<AliPID::kSPECIES;iPart++){
      Double_t mass = AliPID::ParticleMass(iPart);
      Double_t cosThetaTh = TMath::Sqrt(mass*mass+pmod*pmod)/(AliHMPIDParam::Instance()->MeanIdxRad()*pmod);
      if(cosThetaTh<1) //calculate the height of theoretical theta ckov on the gaus of experimental one
        h[iPart] =TMath::Gaus(TMath::ACos(cosThetaTh),pTrk->GetHMPIDsignal(),TMath::Sqrt(pTrk->GetHMPIDchi2()),kTRUE);      
      else             //beta < 1/ref. idx. => no light at all  
        h[iPart] =0 ;       
      hTot    +=h[iPart]; //total height of all theoretical heights for normalization
    }//species loop
     
    Double_t hMin=TMath::Gaus(pTrk->GetHMPIDsignal()-4*TMath::Sqrt(pTrk->GetHMPIDchi2()),pTrk->GetHMPIDsignal(),TMath::Sqrt(pTrk->GetHMPIDchi2()),kTRUE);//5 sigma protection
    
    for(Int_t iPart=0;iPart<AliPID::kSPECIES;iPart++)//species loop to assign probabilities
      if(hTot>hMin)  
        pid[iPart]=h[iPart]/hTot;
      else                               //all theoretical values are far away from experemental one
        pid[iPart]=1.0/AliPID::kSPECIES; 
    pTrk->SetHMPIDpid(pid);
  }//ESD tracks loop
}//FillESD()
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Commit	Line	Data
d3da6dc4	1	/**************************************************************************
	2	* Copyright(c) 1998-1999, ALICE Experiment at CERN, All rights reserved. *
	3	* *
	4	* Author: The ALICE Off-line Project. *
	5	* Contributors are mentioned in the code where appropriate. *
	6	* *
	7	* Permission to use, copy, modify and distribute this software and its *
	8	* documentation strictly for non-commercial purposes is hereby granted *
	9	* without fee, provided that the above copyright notice appears in all *
	10	* copies and that both the copyright notice and this permission notice *
	11	* appear in the supporting documentation. The authors make no claims *
	12	* about the suitability of this software for any purpose. It is *
	13	* provided "as is" without express or implied warranty. *
	14	**************************************************************************/
423554a3	15	//.
	16	// HMPID base class to reconstruct an event
	17	//.
	18	//.
	19	//.
d3da6dc4	20	#include "AliHMPIDReconstructor.h" //class header
d3da6dc4	21	#include "AliHMPID.h" //Reconstruct()
a1d55ff3	22	#include "AliHMPIDCluster.h" //Dig2Clu()
d3da6dc4	23	#include "AliHMPIDParam.h" //FillEsd()
a0e5c1b9	24	#include <AliCDBEntry.h> //ctor
	25	#include <AliCDBManager.h> //ctor
	26	#include <AliESD.h> //FillEsd()
	27	#include <AliRawReader.h> //Reconstruct() for raw digits
d3da6dc4	28	ClassImp(AliHMPIDReconstructor)
d3da6dc4	29
94b1fbfa	30	//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
a0e5c1b9	31	AliHMPIDReconstructor::AliHMPIDReconstructor():AliReconstructor(),fUserCut(0),fDaqSig(0),fDig(0),fClu(0)
94b1fbfa	32	{
	33	//
	34	//ctor
	35	//
a0e5c1b9	36
	37	fClu=new TObjArray(AliHMPIDDigit::kMaxCh+1); fClu->SetOwner(kTRUE);
	38	fDig=new TObjArray(AliHMPIDDigit::kMaxCh+1); fDig->SetOwner(kTRUE);
	39
94b1fbfa	40	for(int i=AliHMPIDDigit::kMinCh;i<=AliHMPIDDigit::kMaxCh;i++){
94b1fbfa	41	fDig->AddAt(new TClonesArray("AliHMPIDDigit"),i);
611e810d	42	TClonesArray *pClus = new TClonesArray("AliHMPIDCluster");
	43	pClus->SetUniqueID(i);
	44	fClu->AddAt(pClus,i);
94b1fbfa	45	}
a0e5c1b9	46
a0e5c1b9	47	AliCDBEntry *pUserCutEnt =AliCDBManager::Instance()->Get("HMPID/Calib/UserCut"); //contains TObjArray of 14 TObject with n. of sigmas to cut charge
	48	if(!pUserCutEnt) return; //No request from User to apply a more severe cut on pad charge
	49
	50	fUserCut = pUserCutEnt->GetObject()->GetUniqueID();
	51
	52	Printf(" usercut %i ",fUserCut);
	53
	54	AliCDBEntry *pDaqCutEnt =AliCDBManager::Instance()->Get("HMPID/Calib/DaqSigCut"); //contains TObjArray of 14 TObject with n. of sigmas to cut charge
	55	if(!pDaqCutEnt) AliFatal("No pedestal sigmas cut!");
	56	TObjArray pDaqCut = (TObjArray)pDaqCutEnt->GetObject();
	57
	58
	59	for(Int_t ddl=0;ddl<14;ddl++){
	60	if(fUserCut<=(Int_t)pDaqCut->At(ddl)->GetUniqueID()) continue;
	61	AliCDBEntry *pDaqSigEnt =AliCDBManager::Instance()->Get("HMPID/Calib/DaqSig"); //contains TObjArray of TObjArray 14 TMatrixF sigmas values for pads
	62	if(!pDaqSigEnt) AliFatal("No pedestals from DAQ!");
	63	TObjArray pDaqSig = (TObjArray)pDaqSigEnt->GetObject();
	64	SigConv(pDaqSig);
	65	break;
	66	}
94b1fbfa	67	}//AliHMPIDReconstructor
d3da6dc4	68	//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
a0e5c1b9	69	void AliHMPIDReconstructor::SigConv(TObjArray *pDaqSig)
	70	{
	71	// Conversion from the pedestal objects in to 7 TMatrixF(padX,padY)
	72	//Arguments: pDaqSig pointer to the pedestal objects from OCDB
	73	// Returs: none
	74	//
	75	fDaqSig = new TObjArray(AliHMPIDDigit::kMaxCh+1);fDaqSig->SetOwner(kTRUE);
	76
	77	for(Int_t iCh=AliHMPIDDigit::kMinCh;iCh<=AliHMPIDDigit::kMaxCh;iCh++) fDaqSig->AddAt(new TMatrixF(1,10,0,47),iCh);
	78
	79	AliHMPIDDigit dig;
	80
	81	for(Int_t ddl=0;ddl<=13;ddl++){
	82	for(Int_t row=1;row<=24;row++)
	83	for(Int_t dil=1;dil<=10;dil++)
	84	for(Int_t adr=0;adr<=47;adr++){
	85	TObjArray pDdl = (TObjArray)pDaqSig->At(ddl);
	86	TObjArray pRow = (TObjArray)pDdl->At(row-1);
	87	TMatrixF pM = (TMatrixF)pRow;
	88	Float_t sigma = (*pM)(dil,adr);
	89	dig.Raw(ddl,row,dil,adr);
	90	TMatrixF* pMConv = (TMatrixF*)(fDaqSig->At(dig.Ch()));
	91	(*pMConv)(dig.PadChX(),dig.PadChY()) = sigma;
	92	}
	93	}
	94	}//SigConv()
	95	//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
3c6274c1	96	void AliHMPIDReconstructor::Dig2Clu(TObjArray pDigAll,TObjArray pCluAll,Bool_t isTryUnfold)
d3da6dc4	97	{
	98	// Finds all clusters for a given digits list provided not empty. Currently digits list is a list of all digits for a single chamber.
	99	// Puts all found clusters in separate lists, one per clusters.
3c6274c1	100	// Arguments: pDigAll - list of digits for all chambers
3c6274c1	101	// pCluAll - list of clusters for all chambers
d3da6dc4	102	// isTryUnfold - flag to choose between CoG and Mathieson fitting
d3da6dc4	103	// Returns: none
a1d55ff3	104	TMatrixF padMap(AliHMPIDDigit::kMinPx,AliHMPIDDigit::kMaxPcx,AliHMPIDDigit::kMinPy,AliHMPIDDigit::kMaxPcy); //pads map for single chamber 0..159 x 0..143
3c6274c1	105
a1d55ff3	106	for(Int_t iCh=AliHMPIDDigit::kMinCh;iCh<=AliHMPIDDigit::kMaxCh;iCh++){ //chambers loop
3c6274c1	107	TClonesArray pDigCur=(TClonesArray)pDigAll->At(iCh); //get list of digits for current chamber
3c6274c1	108	if(pDigCur->GetEntriesFast()==0) continue; //no digits for current chamber
d3da6dc4	109
3c6274c1	110	padMap=(Float_t)-1; //reset map to -1 (means no digit for this pad)
	111	TClonesArray pCluCur=(TClonesArray)pCluAll->At(iCh); //get list of clusters for current chamber
	112
	113	for(Int_t iDig=0;iDig<pDigCur->GetEntriesFast();iDig++){ //digits loop to fill pads map
	114	AliHMPIDDigit pDig= (AliHMPIDDigit)pDigCur->At(iDig); //get current digit
	115	padMap( pDig->PadChX(), pDig->PadChY() )=iDig; //fill the map, (padx,pady) cell takes digit index
	116	}//digits loop to fill digits map
	117
	118	AliHMPIDCluster clu; //tmp cluster to be used as current
3c6274c1	119	for(Int_t iDig=0;iDig<pDigCur->GetEntriesFast();iDig++){ //digits loop for current chamber
	120	AliHMPIDDigit pDig=(AliHMPIDDigit)pDigCur->At(iDig); //take current digit
	121	if(!(pDig=UseDig(pDig->PadChX(),pDig->PadChY(),pDigCur,&padMap))) continue; //this digit is already taken in FormClu(), go after next digit
	122	FormClu(&clu,pDig,pDigCur,&padMap); //form cluster starting from this digit by recursion
	123
	124	clu.Solve(pCluCur,isTryUnfold); //solve this cluster and add all unfolded clusters to provided list
	125	clu.Reset(); //empty current cluster
	126	}//digits loop for current chamber
	127	}//chambers loop
d3da6dc4	128	}//Dig2Clu()
	129	//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
	130	void AliHMPIDReconstructor::FormClu(AliHMPIDCluster pClu,AliHMPIDDigit pDig,TClonesArray pDigLst,TMatrixF pDigMap)
	131	{
a1d55ff3	132	// Forms the initial cluster as a combination of all adjascent digits. Starts from the given digit then calls itself recursevly for all neighbours.
d3da6dc4	133	// Arguments: pClu - pointer to cluster being formed
a1d55ff3	134	// Returns: none
d3da6dc4	135	pClu->DigAdd(pDig);//take this digit in cluster
d3da6dc4	136
3c6274c1	137	Int_t cnt=0,cx[4],cy[4];
d3da6dc4	138
a1d55ff3	139	if(pDig->PadPcX() != AliHMPIDDigit::kMinPx){cx[cnt]=pDig->PadChX()-1; cy[cnt]=pDig->PadChY() ;cnt++;} //left
	140	if(pDig->PadPcX() != AliHMPIDDigit::kMaxPx){cx[cnt]=pDig->PadChX()+1; cy[cnt]=pDig->PadChY() ;cnt++;} //right
	141	if(pDig->PadPcY() != AliHMPIDDigit::kMinPy){cx[cnt]=pDig->PadChX() ; cy[cnt]=pDig->PadChY()-1;cnt++;} //down
	142	if(pDig->PadPcY() != AliHMPIDDigit::kMaxPy){cx[cnt]=pDig->PadChX() ; cy[cnt]=pDig->PadChY()+1;cnt++;} //up
d3da6dc4	143
a1d55ff3	144	for (Int_t i=0;i<cnt;i++){//neighbours loop
3c6274c1	145	if((pDig=UseDig(cx[i],cy[i],pDigLst,pDigMap))) FormClu(pClu,pDig,pDigLst,pDigMap); //check if this neighbour pad fired and mark it as taken
a1d55ff3	146	}//neighbours loop
d3da6dc4	147	}//FormClu()
d3da6dc4	148	//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
94b1fbfa	149	void AliHMPIDReconstructor::Reconstruct(TTree pDigTree,TTree pCluTree)const
d3da6dc4	150	{
d3da6dc4	151	//Invoked by AliReconstruction to convert digits to clusters i.e. reconstruct simulated data
94b1fbfa	152	//Arguments: pDigTree - pointer to Digit tree
94b1fbfa	153	// pCluTree - poitner to Cluster tree
d3da6dc4	154	// Returns: none
d3da6dc4	155	AliDebug(1,"Start.");
94b1fbfa	156	for(Int_t iCh=AliHMPIDDigit::kMinCh;iCh<=AliHMPIDDigit::kMaxCh;iCh++) {
	157	pCluTree->Branch(Form("HMPID%d",iCh),&((*fClu)[iCh]),4000,0);
	158	pDigTree->SetBranchAddress(Form("HMPID%d",iCh),&((*fDig)[iCh]));
	159	}
	160	pDigTree->GetEntry(0);
	161	Dig2Clu(fDig,fClu); //cluster finder
	162	pCluTree->Fill(); //fill tree for current event
	163
	164	for(Int_t iCh=AliHMPIDDigit::kMinCh;iCh<=AliHMPIDDigit::kMaxCh;iCh++){
	165	fDig->At(iCh)->Clear();
	166	fClu->At(iCh)->Clear();
	167	}
d3da6dc4	168
d3da6dc4	169	AliDebug(1,"Stop.");
d3da6dc4	170	}//Reconstruct(for simulated digits)
a1d55ff3	171	//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
d3da6dc4	172	void AliHMPIDReconstructor::Reconstruct(AliRunLoader pAL,AliRawReader pRR)const
	173	{
	174	//Invoked by AliReconstruction to convert raw digits from DDL files to clusters
	175	//Arguments: pAL - ALICE run loader pointer
94b1fbfa	176	// pRR - ALICE raw reader pointer
94b1fbfa	177	// Returns: none
d3da6dc4	178	AliLoader pRL=pAL->GetDetectorLoader("HMPID"); AliHMPID pRich=(AliHMPID*)pAL->GetAliRun()->GetDetector("HMPID");//get pointers for HMPID and HMPID loader
94b1fbfa	179
d3da6dc4	180	AliHMPIDDigit dig; //tmp digit, raw digit will be converted to it
94b1fbfa	181
	182	TObjArray digLst; Int_t iDigCnt[7]; for(Int_t i=0;i<7;i++){digLst.AddAt(new TClonesArray("AliHMPIDDigit"),i); iDigCnt[i]=0;} //tmp list of digits for allchambers
	183
d3da6dc4	184	Int_t iEvtN=0;
	185	while(pRR->NextEvent()){//events loop
	186	pAL->GetEvent(iEvtN++);
	187	pRL->MakeTree("R"); pRich->MakeBranch("R");
94b1fbfa	188
d3da6dc4	189	for(Int_t iCh=0;iCh<7;iCh++){//chambers loop
94b1fbfa	190	pRR->Select("HMPID",2iCh,2iCh+1);//select only DDL files for the current chamber
d3da6dc4	191	UInt_t w32=0;
	192	while(pRR->ReadNextInt(w32)){//raw records loop (in selected DDL files)
	193	UInt_t ddl=pRR->GetDDLID(); //returns 0,1,2 ... 13
49dfd67a	194	dig.Raw(w32,ddl,pRR);
da08475b	195	AliDebug(1,Form("Ch=%i DDL=%i raw=0x%x digit=(%3i,%3i,%3i,%3i) Q=%5.2f",iCh,ddl,w32,dig.Ch(),dig.Pc(),dig.PadPcX(),dig.PadPcY(),dig.Q()));
a0e5c1b9	196	if(!IsDigSurvive(&dig)) continue; //sigma cut test
3c6274c1	197	new((((TClonesArray)digLst.At(iCh)))[iDigCnt[iCh]++]) AliHMPIDDigit(dig); //add this digit to the tmp list
d3da6dc4	198	}//raw records loop
94b1fbfa	199	pRR->Reset();
d3da6dc4	200	}//chambers loop
94b1fbfa	201
3c6274c1	202	Dig2Clu(&digLst,pRich->CluLst());//cluster finder for all chambers
3c6274c1	203	for(Int_t i=0;i<7;i++){digLst.At(i)->Delete(); iDigCnt[i]=0;} //clean up list of digits for all chambers
94b1fbfa	204
d3da6dc4	205	pRL->TreeR()->Fill(); //fill tree for current event
	206	pRL->WriteRecPoints("OVERWRITE");//write out clusters for current event
	207	pRich->CluReset();
94b1fbfa	208	}//events loop
94b1fbfa	209	pRL->UnloadRecPoints();
d3da6dc4	210	}//Reconstruct raw data
d3da6dc4	211	//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
94b1fbfa	212	void AliHMPIDReconstructor::ConvertDigits(AliRawReader pRR,TTree pDigTree)const
	213	{
	214	//Invoked by AliReconstruction to convert raw digits from DDL files to digits
	215	//Arguments: pRR - ALICE raw reader pointer
	216	// pDigTree - pointer to Digit tree
	217	// Returns: none
	218	AliDebug(1,"Start.");
	219	AliHMPIDDigit dig; //tmp digit, raw digit will be converted to it
	220	for(Int_t iCh=AliHMPIDDigit::kMinCh;iCh<=AliHMPIDDigit::kMaxCh;iCh++) {
	221	pDigTree->Branch(Form("HMPID%d",iCh),&((*fDig)[iCh]),4000,0);
	222	pRR->Select("HMPID",2iCh,2iCh+1);//select only DDL files for the current chamber
	223	Int_t iDigCnt=0;
	224	UInt_t w32=0;
49dfd67a	225	while(pRR->ReadNextInt(w32)){//raw records loop (in selected DDL files)
94b1fbfa	226	UInt_t ddl=pRR->GetDDLID(); //returns 0,1,2 ... 13
49dfd67a	227	if (!dig.Raw(w32,ddl,pRR)) continue;
94b1fbfa	228	AliDebug(1,Form("Ch=%i DDL=%i raw=0x%x digit=(%3i,%3i,%3i,%3i) Q=%5.2f",iCh,ddl,w32,dig.Ch(),dig.Pc(),dig.PadPcX(),dig.PadPcY(),dig.Q()));
a0e5c1b9	229	if(!IsDigSurvive(&dig)) continue; //sigma cut test
94b1fbfa	230	new((((TClonesArray)fDig->At(iCh)))[iDigCnt++]) AliHMPIDDigit(dig); //add this digit to the tmp list
	231	}//raw records loop
	232	pRR->Reset();
	233	}//chambers loop
	234	pDigTree->Fill();
	235	for(Int_t iCh=AliHMPIDDigit::kMinCh;iCh<=AliHMPIDDigit::kMaxCh;iCh++)fDig->At(iCh)->Clear();
	236	AliDebug(1,"Stop.");
	237	}//Reconstruct digits from raw digits
	238	//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
d3da6dc4	239	void AliHMPIDReconstructor::FillESD(AliRunLoader , AliESD pESD) const
	240	{
	241	// Calculates probability to be a electron-muon-pion-kaon-proton
	242	// from the given Cerenkov angle and momentum assuming no initial particle composition
	243	// (i.e. apriory probability to be the particle of the given sort is the same for all sorts)
	244
	245	AliPID ppp; //needed
	246	Double_t pid[AliPID::kSPECIES],h[AliPID::kSPECIES];
	247
	248	for(Int_t iTrk=0;iTrk<pESD->GetNumberOfTracks();iTrk++){//ESD tracks loop
	249	AliESDtrack *pTrk = pESD->GetTrack(iTrk);// get next reconstructed track
	250	if(pTrk->GetHMPIDsignal()<=0){//HMPID does not find anything reasonable for this track, assign 0.2 for all species
	251	for(Int_t iPart=0;iPart<AliPID::kSPECIES;iPart++) pid[iPart]=1.0/AliPID::kSPECIES;
	252	pTrk->SetHMPIDpid(pid);
	253	continue;
	254	}
	255	Double_t pmod = pTrk->GetP();
	256	Double_t hTot=0;
	257	for(Int_t iPart=0;iPart<AliPID::kSPECIES;iPart++){
	258	Double_t mass = AliPID::ParticleMass(iPart);
	259	Double_t cosThetaTh = TMath::Sqrt(massmass+pmodpmod)/(AliHMPIDParam::Instance()->MeanIdxRad()*pmod);
a1d55ff3	260	if(cosThetaTh<1) //calculate the height of theoretical theta ckov on the gaus of experimental one
a1d55ff3	261	h[iPart] =TMath::Gaus(TMath::ACos(cosThetaTh),pTrk->GetHMPIDsignal(),TMath::Sqrt(pTrk->GetHMPIDchi2()),kTRUE);
d3da6dc4	262	else //beta < 1/ref. idx. => no light at all
	263	h[iPart] =0 ;
	264	hTot +=h[iPart]; //total height of all theoretical heights for normalization
	265	}//species loop
	266
	267	Double_t hMin=TMath::Gaus(pTrk->GetHMPIDsignal()-4*TMath::Sqrt(pTrk->GetHMPIDchi2()),pTrk->GetHMPIDsignal(),TMath::Sqrt(pTrk->GetHMPIDchi2()),kTRUE);//5 sigma protection
	268
	269	for(Int_t iPart=0;iPart<AliPID::kSPECIES;iPart++)//species loop to assign probabilities
	270	if(hTot>hMin)
	271	pid[iPart]=h[iPart]/hTot;
	272	else //all theoretical values are far away from experemental one
	273	pid[iPart]=1.0/AliPID::kSPECIES;
	274	pTrk->SetHMPIDpid(pid);
	275	}//ESD tracks loop
a1d55ff3	276	}//FillESD()
d3da6dc4	277	//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++