[u/mrichter/AliRoot.git] / RICH / AliRICHReconstructor.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.                  *
 **************************************************************************/

#include "AliRICHReconstructor.h" //class header
#include "AliRICH.h"              //Reconstruct() 
#include "AliRICHCluster.h"       //CluQA() 
#include "AliRICHParam.h"         //FillEsd() 
#include <AliESD.h>               //FillEsd()
#include <AliRunLoader.h>         //Reconstruct() for simulated digits
#include <AliRawReader.h>         //Reconstruct() for raw digits
#include <AliRun.h>               //Reconstruct()
#include <TH1F.h>                 //CluQA() 
#include <TH2F.h>                 //CluQA() 
#include <TCanvas.h>              //CluQA() 
#include <TNtupleD.h>             //CheckPR()
ClassImp(AliRICHReconstructor)

//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
void AliRICHReconstructor::CluQA(AliRunLoader *pAL)
{
// Quality assesment plots for clusters. 
// This methode takes list of digits and form list of clusters again in order to 
// calculate cluster shape and cluster particle mixture    
  AliLoader *pRL=pAL->GetDetectorLoader("RICH");  AliRICH *pRich=(AliRICH*)pAL->GetAliRun()->GetDetector("RICH");//get pointers for RICH and RICH loader
  Int_t iNevt=pAL->GetNumberOfEvents();  if(iNevt==0)             {AliInfoClass("No events");return;}   
                                         if(pRL->LoadDigits())    {AliInfoClass("No digits file");return;}
                                            pAL->LoadHeader();
                                            pAL->LoadKinematics(); 
//                                            AliStack *pStack=pAL->Stack();
  TH1::AddDirectory(kFALSE);
  
        
  TH1F*    pQ=new TH1F("RiAllQ"  ,"Charge All"           ,4000 ,0  ,4000);// Q hists
  TH1F* pCerQ=new TH1F("RiCerQ"  ,"Charge Ckov"          ,4000 ,0  ,4000);
  TH1F* pMipQ=new TH1F("RiMipQ"  ,"Charge MIP"           ,4000 ,0  ,4000);
  
  TH1F*    pS=new TH1F("RichCluSize"    ,"Cluster size;size"         ,100  ,0  ,100 );// size hists
  TH1F* pCerS=new TH1F("RichCluCerSize" ,"Ckov size;size"            ,100  ,0  ,100 );
  TH1F* pMipS=new TH1F("RichCluMipSize" ,"MIP size;size"             ,100  ,0  ,100 );
  
  TH2F*    pM=new TH2F("RichCluMap"     ,"Cluster map;x [cm];y [cm]" ,1000 ,0  ,AliRICHDigit::SizePcX(),1000,0,AliRICHDigit::SizePcY()); // maps
  TH2F* pMipM=new TH2F("RichCluMipMap"  ,"MIP map;x [cm];y [cm]"     ,1000 ,0  ,AliRICHDigit::SizePcX(),1000,0,AliRICHDigit::SizePcY());
  TH2F* pCerM=new TH2F("RichCluCerMap"  ,"Ckov map;x [cm];y [cm]"    ,1000 ,0  ,AliRICHDigit::SizePcX(),1000,0,AliRICHDigit::SizePcY());
 
  
  
  for(Int_t iEvt=0;iEvt<iNevt;iEvt++){
    pAL->GetEvent(iEvt);               
    pRL->TreeD()->GetEntry(0); 
    TClonesArray *pCluLst=new TClonesArray("AliRICHCluster");//tmp list of clusters for this event
    
    for(Int_t iCh=0;iCh<7;iCh++) Dig2Clu(pRich->DigLst(iCh),pCluLst,kFALSE);//cluster finder for all chamber if any digits present
    
    for(Int_t iClu=0;iClu<pCluLst->GetEntriesFast();iClu++){
      AliRICHCluster *pClu = (AliRICHCluster*)pCluLst->At(iClu);
      Int_t cfm=0; for(Int_t iDig=0;iDig<pClu->Size();iDig++)  cfm+=pClu->Dig(iDig)->Ch(); //collect ckov-fee-mip structure of current cluster ?????
      Int_t iNckov=cfm/1000000;      Int_t iNfee =cfm%1000000/1000;      Int_t iNmip =cfm%1000000%1000; 

                                             pQ   ->Fill(pClu->Q()) ; pS   ->Fill(pClu->Size()) ; pM    ->Fill(pClu->X(),pClu->Y()); //all clusters                                      
      if(iNckov!=0 && iNfee==0 && iNmip==0) {pCerQ->Fill(pClu->Q()) ; pCerS->Fill(pClu->Size()) ; pCerM ->Fill(pClu->X(),pClu->Y());}//ckov only cluster
      if(iNckov==0 && iNfee==0 && iNmip!=0) {pMipQ->Fill(pClu->Q()) ; pMipS->Fill(pClu->Size()) ; pMipM ->Fill(pClu->X(),pClu->Y());}//mip only cluster
                                       
    }//clusters loop   
    pCluLst->Clear();delete pCluLst;
  }//events loop
  
  pRL->UnloadDigits(); pAL->UnloadKinematics(); pAL->UnloadHeader();
  TCanvas *pC=new TCanvas("RichCluQA",Form("QA for cluster from %i events",iNevt),1000,900); pC->Divide(3,3);
  pC->cd(1);    pM->Draw();          pC->cd(2);    pQ->Draw();       pC->cd(3);    pS->Draw();        
  pC->cd(4); pMipM->Draw();          pC->cd(5); pMipQ->Draw();       pC->cd(6); pMipS->Draw();        
  pC->cd(7); pCerM->Draw();          pC->cd(8); pCerQ->Draw();       pC->cd(9); pCerS->Draw();        
}//CluQA()
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
void AliRICHReconstructor::Dig2Clu(TClonesArray *pDigLst,TClonesArray *pCluLst,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: pDigLst     - list of digits provided not empty
//            pCluLst     - list of clusters, provided empty     
//            isTryUnfold - flag to choose between CoG and Mathieson fitting  
//  Returns: none    
  TMatrixF digMap(AliRICHDigit::kPadAllX,AliRICHDigit::kPadAllY);  digMap=(Float_t)-1;     //digit map for single chamber reseted to -1
  for(Int_t iDig=0;iDig<pDigLst->GetEntriesFast();iDig++){                                 //digits loop to fill digits map
    AliRICHDigit *pDig= (AliRICHDigit*)pDigLst->At(iDig);                                  //get current digit
    digMap( pDig->PadX(), pDig->PadY() )=iDig;                                             //fill the map, (padx,pady) cell takes digit index
  }                                                                                        //digits loop to fill digits map 
  
  AliRICHCluster clu;                                                                      //tmp cluster to be used as current
  
  for(Int_t iDig=0;iDig<pDigLst->GetEntriesFast();iDig++){                                 //digits loop to form clusters list
    AliRICHDigit *pDig=(AliRICHDigit*)pDigLst->At(iDig);                                   //take current digit
    if(!(pDig=UseDig(pDig->PadX(),pDig->PadY(),pDigLst,&digMap))) continue;                //this digit is already taken in FormClu(), go after next digit
    FormClu(&clu,pDig,pDigLst,&digMap);                                                    //form cluster starting from this digit by recursion
    clu.Solve(pCluLst,isTryUnfold);                                                        //solve this cluster and add all unfolded clusters to provided list  
    clu.Reset();                                                                           //empty current cluster
  }                                                                                        //digits loop to form clusters list
}//Dig2Clu()
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
void  AliRICHReconstructor::FormClu(AliRICHCluster *pClu,AliRICHDigit *pDig,TClonesArray *pDigLst,TMatrixF *pDigMap)
{
// Forms the initial cluster as a sum 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 x[4],y[4];
  
  
  Int_t iPadCnt=0;  Int_t iPadX=pDig->PadX(); Int_t iPadY=pDig->PadY();
  if(iPadX != AliRICHDigit::kPad1)     {x[iPadCnt]=iPadX-1; y[iPadCnt]=iPadY;   iPadCnt++;}       //left
  if(iPadX != AliRICHDigit::kPadPcX)   {x[iPadCnt]=iPadX+1; y[iPadCnt]=iPadY;   iPadCnt++;}       //right
  if(iPadY != AliRICHDigit::kPad1)     {x[iPadCnt]=iPadX;   y[iPadCnt]=iPadY-1; iPadCnt++;}       //down
  if(iPadY != AliRICHDigit::kPadPcY)   {x[iPadCnt]=iPadX;   y[iPadCnt]=iPadY+1; iPadCnt++;}       //up
  
  for (Int_t i=0;i<iPadCnt;i++)
    if((pDig=UseDig(x[i],y[i],pDigLst,pDigMap))) FormClu(pClu,pDig,pDigLst,pDigMap);   //check if this neighbour hit and mark it as taken  
}//FormClu()
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
void AliRICHReconstructor::Reconstruct(AliRunLoader *pAL)const
{
//Invoked  by AliReconstruction to convert digits to clusters i.e. reconstruct simulated data
//Arguments: pAL - ALICE run loader pointer
//  Returns: none    
  AliDebug(1,"Start.");
  AliLoader *pRL=pAL->GetDetectorLoader("RICH");
  AliRICH *pRich=(AliRICH*)pAL->GetAliRun()->GetDetector("RICH");//get pointers for RICH and RICH loader
  pRL->LoadDigits();   
  pRL->LoadRecPoints("recreate");
  
  for(Int_t iEvtN=0;iEvtN<pAL->GetNumberOfEvents();iEvtN++){//events loop
    pAL->GetEvent(iEvtN); AliDebug(1,Form("Processing event %i...",iEvtN)); //switch current directory to next event    
    pRL->TreeD()->GetEntry(0);  pRL->MakeTree("R");  pRich->MakeBranch("R");  //load digits to memory  and create branches for clusters              
    
    for(Int_t iCh=0;iCh<7;iCh++) Dig2Clu(pRich->DigLst(iCh),pRich->CluLst(iCh));//cluster finder 
      
    pRL->TreeR()->Fill();            //fill tree for current event
    pRL->WriteRecPoints("OVERWRITE");//write out clusters for current event
    pRich->DigReset(); pRich->CluReset();
  }//events loop  

  pRL->UnloadDigits(); 
  pRL->UnloadRecPoints();  
    
  AliDebug(1,"Stop.");      
}//Reconstruct(for simulated digits)
//__________________________________________________________________________________________________
void AliRICHReconstructor::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("RICH");  AliRICH *pRich=(AliRICH*)pAL->GetAliRun()->GetDetector("RICH");//get pointers for RICH and RICH loader
  
  AliRICHDigit dig; //tmp digit, raw digit will be converted to it
  
  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
      TClonesArray *pDigLst=new TClonesArray("AliRICHDigit"); Int_t iDigCnt=0; //tmp list of digits for single chamber
      pRR->Select("RICH",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.ReadRaw(ddl,w32);  
        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.PadX(),dig.PadY(),dig.Q()));
        new((*pDigLst)[iDigCnt++]) AliRICHDigit(dig); //add this digit to the tmp list
      }//raw records loop
      if(iDigCnt) Dig2Clu(pDigLst,pRich->CluLst(iCh));//cluster finder for the current chamber if any digits present
      pRR->Reset();        
      pDigLst->Delete();  iDigCnt=0;//clean up list of digits for the current chamber
    }//chambers loop
    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 AliRICHReconstructor::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->GetRICHsignal()<=0){//RICH 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->SetRICHpid(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)/(AliRICHParam::Instance()->MeanIdxRad()*pmod);
      if(cosThetaTh<1) //calculate the height of theortical theta ckov on the gaus of experimental one
        h[iPart] =TMath::Gaus(TMath::ACos(cosThetaTh),pTrk->GetRICHsignal(),TMath::Sqrt(pTrk->GetRICHchi2()),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->GetRICHsignal()-4*TMath::Sqrt(pTrk->GetRICHchi2()),pTrk->GetRICHsignal(),TMath::Sqrt(pTrk->GetRICHchi2()),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->SetRICHpid(pid);
  }//ESD tracks loop
  //last line is to check if the nearest thetacerenkov to the teorethical one is within 5 sigma, otherwise no response (equal prob to every particle
}//FillESD
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Commit	Line	Data
121a60bd	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	**************************************************************************/
	15
0422a446	16	#include "AliRICHReconstructor.h" //class header
e30ca504	17	#include "AliRICH.h" //Reconstruct()
	18	#include "AliRICHCluster.h" //CluQA()
	19	#include "AliRICHParam.h" //FillEsd()
	20	#include <AliESD.h> //FillEsd()
	21	#include <AliRunLoader.h> //Reconstruct() for simulated digits
	22	#include <AliRawReader.h> //Reconstruct() for raw digits
	23	#include <AliRun.h> //Reconstruct()
db910db9	24	#include <TH1F.h> //CluQA()
	25	#include <TH2F.h> //CluQA()
	26	#include <TCanvas.h> //CluQA()
	27	#include <TNtupleD.h> //CheckPR()
121a60bd	28	ClassImp(AliRICHReconstructor)
121a60bd	29
2714766e	30	//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
db910db9	31	void AliRICHReconstructor::CluQA(AliRunLoader *pAL)
	32	{
	33	// Quality assesment plots for clusters.
	34	// This methode takes list of digits and form list of clusters again in order to
	35	// calculate cluster shape and cluster particle mixture
	36	AliLoader pRL=pAL->GetDetectorLoader("RICH"); AliRICH pRich=(AliRICH*)pAL->GetAliRun()->GetDetector("RICH");//get pointers for RICH and RICH loader
	37	Int_t iNevt=pAL->GetNumberOfEvents(); if(iNevt==0) {AliInfoClass("No events");return;}
	38	if(pRL->LoadDigits()) {AliInfoClass("No digits file");return;}
	39	pAL->LoadHeader();
	40	pAL->LoadKinematics();
	41	// AliStack *pStack=pAL->Stack();
	42	TH1::AddDirectory(kFALSE);
	43
db910db9	44
e30ca504	45	TH1F* pQ=new TH1F("RiAllQ" ,"Charge All" ,4000 ,0 ,4000);// Q hists
	46	TH1F* pCerQ=new TH1F("RiCerQ" ,"Charge Ckov" ,4000 ,0 ,4000);
	47	TH1F* pMipQ=new TH1F("RiMipQ" ,"Charge MIP" ,4000 ,0 ,4000);
db910db9	48
f936e4b2	49	TH1F* pS=new TH1F("RichCluSize" ,"Cluster size;size" ,100 ,0 ,100 );// size hists
	50	TH1F* pCerS=new TH1F("RichCluCerSize" ,"Ckov size;size" ,100 ,0 ,100 );
	51	TH1F* pMipS=new TH1F("RichCluMipSize" ,"MIP size;size" ,100 ,0 ,100 );
	52
e30ca504	53	TH2F* pM=new TH2F("RichCluMap" ,"Cluster map;x [cm];y [cm]" ,1000 ,0 ,AliRICHDigit::SizePcX(),1000,0,AliRICHDigit::SizePcY()); // maps
	54	TH2F* pMipM=new TH2F("RichCluMipMap" ,"MIP map;x [cm];y [cm]" ,1000 ,0 ,AliRICHDigit::SizePcX(),1000,0,AliRICHDigit::SizePcY());
	55	TH2F* pCerM=new TH2F("RichCluCerMap" ,"Ckov map;x [cm];y [cm]" ,1000 ,0 ,AliRICHDigit::SizePcX(),1000,0,AliRICHDigit::SizePcY());
db910db9	56
db910db9	57
db910db9	58
e30ca504	59	for(Int_t iEvt=0;iEvt<iNevt;iEvt++){
e30ca504	60	pAL->GetEvent(iEvt);
db910db9	61	pRL->TreeD()->GetEntry(0);
e30ca504	62	TClonesArray *pCluLst=new TClonesArray("AliRICHCluster");//tmp list of clusters for this event
	63
	64	for(Int_t iCh=0;iCh<7;iCh++) Dig2Clu(pRich->DigLst(iCh),pCluLst,kFALSE);//cluster finder for all chamber if any digits present
db910db9	65
e30ca504	66	for(Int_t iClu=0;iClu<pCluLst->GetEntriesFast();iClu++){
	67	AliRICHCluster pClu = (AliRICHCluster)pCluLst->At(iClu);
	68	Int_t cfm=0; for(Int_t iDig=0;iDig<pClu->Size();iDig++) cfm+=pClu->Dig(iDig)->Ch(); //collect ckov-fee-mip structure of current cluster ?????
f936e4b2	69	Int_t iNckov=cfm/1000000; Int_t iNfee =cfm%1000000/1000; Int_t iNmip =cfm%1000000%1000;
f936e4b2	70
db910db9	71	pQ ->Fill(pClu->Q()) ; pS ->Fill(pClu->Size()) ; pM ->Fill(pClu->X(),pClu->Y()); //all clusters
db910db9	72	if(iNckov!=0 && iNfee==0 && iNmip==0) {pCerQ->Fill(pClu->Q()) ; pCerS->Fill(pClu->Size()) ; pCerM ->Fill(pClu->X(),pClu->Y());}//ckov only cluster
db910db9	73	if(iNckov==0 && iNfee==0 && iNmip!=0) {pMipQ->Fill(pClu->Q()) ; pMipS->Fill(pClu->Size()) ; pMipM ->Fill(pClu->X(),pClu->Y());}//mip only cluster
	74
	75	}//clusters loop
e30ca504	76	pCluLst->Clear();delete pCluLst;
db910db9	77	}//events loop
	78
	79	pRL->UnloadDigits(); pAL->UnloadKinematics(); pAL->UnloadHeader();
	80	TCanvas *pC=new TCanvas("RichCluQA",Form("QA for cluster from %i events",iNevt),1000,900); pC->Divide(3,3);
f936e4b2	81	pC->cd(1); pM->Draw(); pC->cd(2); pQ->Draw(); pC->cd(3); pS->Draw();
	82	pC->cd(4); pMipM->Draw(); pC->cd(5); pMipQ->Draw(); pC->cd(6); pMipS->Draw();
	83	pC->cd(7); pCerM->Draw(); pC->cd(8); pCerQ->Draw(); pC->cd(9); pCerS->Draw();
db910db9	84	}//CluQA()
2714766e	85	//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
db910db9	86	void AliRICHReconstructor::Dig2Clu(TClonesArray pDigLst,TClonesArray pCluLst,Bool_t isTryUnfold)
db910db9	87	{
e30ca504	88	// Finds all clusters for a given digits list provided not empty. Currently digits list is a list of all digits for a single chamber.
	89	// Puts all found clusters in separate lists, one per clusters.
	90	// Arguments: pDigLst - list of digits provided not empty
	91	// pCluLst - list of clusters, provided empty
	92	// isTryUnfold - flag to choose between CoG and Mathieson fitting
db910db9	93	// Returns: none
e30ca504	94	TMatrixF digMap(AliRICHDigit::kPadAllX,AliRICHDigit::kPadAllY); digMap=(Float_t)-1; //digit map for single chamber reseted to -1
	95	for(Int_t iDig=0;iDig<pDigLst->GetEntriesFast();iDig++){ //digits loop to fill digits map
	96	AliRICHDigit pDig= (AliRICHDigit)pDigLst->At(iDig); //get current digit
	97	digMap( pDig->PadX(), pDig->PadY() )=iDig; //fill the map, (padx,pady) cell takes digit index
db910db9	98	} //digits loop to fill digits map
	99
	100	AliRICHCluster clu; //tmp cluster to be used as current
	101
e30ca504	102	for(Int_t iDig=0;iDig<pDigLst->GetEntriesFast();iDig++){ //digits loop to form clusters list
e30ca504	103	AliRICHDigit pDig=(AliRICHDigit)pDigLst->At(iDig); //take current digit
db910db9	104	if(!(pDig=UseDig(pDig->PadX(),pDig->PadY(),pDigLst,&digMap))) continue; //this digit is already taken in FormClu(), go after next digit
	105	FormClu(&clu,pDig,pDigLst,&digMap); //form cluster starting from this digit by recursion
	106	clu.Solve(pCluLst,isTryUnfold); //solve this cluster and add all unfolded clusters to provided list
	107	clu.Reset(); //empty current cluster
	108	} //digits loop to form clusters list
	109	}//Dig2Clu()
e30ca504	110	//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
db910db9	111	void AliRICHReconstructor::FormClu(AliRICHCluster pClu,AliRICHDigit pDig,TClonesArray pDigLst,TMatrixF pDigMap)
db910db9	112	{
e30ca504	113	// Forms the initial cluster as a sum of all adjascent digits. Starts from the given digit
	114	// then calls itself recursevly for all neighbours.
	115	// Arguments: pClu - pointer to cluster being formed
db910db9	116	// Returns: none
	117	pClu->DigAdd(pDig);//take this digit in cluster
	118
	119	Int_t x[4],y[4];
	120
e30ca504	121
	122	Int_t iPadCnt=0; Int_t iPadX=pDig->PadX(); Int_t iPadY=pDig->PadY();
	123	if(iPadX != AliRICHDigit::kPad1) {x[iPadCnt]=iPadX-1; y[iPadCnt]=iPadY; iPadCnt++;} //left
	124	if(iPadX != AliRICHDigit::kPadPcX) {x[iPadCnt]=iPadX+1; y[iPadCnt]=iPadY; iPadCnt++;} //right
	125	if(iPadY != AliRICHDigit::kPad1) {x[iPadCnt]=iPadX; y[iPadCnt]=iPadY-1; iPadCnt++;} //down
	126	if(iPadY != AliRICHDigit::kPadPcY) {x[iPadCnt]=iPadX; y[iPadCnt]=iPadY+1; iPadCnt++;} //up
	127
	128	for (Int_t i=0;i<iPadCnt;i++)
db910db9	129	if((pDig=UseDig(x[i],y[i],pDigLst,pDigMap))) FormClu(pClu,pDig,pDigLst,pDigMap); //check if this neighbour hit and mark it as taken
db910db9	130	}//FormClu()
e30ca504	131	//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
db910db9	132	void AliRICHReconstructor::Reconstruct(AliRunLoader *pAL)const
	133	{
	134	//Invoked by AliReconstruction to convert digits to clusters i.e. reconstruct simulated data
	135	//Arguments: pAL - ALICE run loader pointer
	136	// Returns: none
	137	AliDebug(1,"Start.");
194e649f	138	AliLoader *pRL=pAL->GetDetectorLoader("RICH");
194e649f	139	AliRICH pRich=(AliRICH)pAL->GetAliRun()->GetDetector("RICH");//get pointers for RICH and RICH loader
db910db9	140	pRL->LoadDigits();
194e649f	141	pRL->LoadRecPoints("recreate");
db910db9	142
db910db9	143	for(Int_t iEvtN=0;iEvtN<pAL->GetNumberOfEvents();iEvtN++){//events loop
4b10d461	144	pAL->GetEvent(iEvtN); AliDebug(1,Form("Processing event %i...",iEvtN)); //switch current directory to next event
db910db9	145	pRL->TreeD()->GetEntry(0); pRL->MakeTree("R"); pRich->MakeBranch("R"); //load digits to memory and create branches for clusters
e30ca504	146
	147	for(Int_t iCh=0;iCh<7;iCh++) Dig2Clu(pRich->DigLst(iCh),pRich->CluLst(iCh));//cluster finder
	148
db910db9	149	pRL->TreeR()->Fill(); //fill tree for current event
	150	pRL->WriteRecPoints("OVERWRITE");//write out clusters for current event
	151	pRich->DigReset(); pRich->CluReset();
	152	}//events loop
	153
	154	pRL->UnloadDigits();
	155	pRL->UnloadRecPoints();
	156
	157	AliDebug(1,"Stop.");
	158	}//Reconstruct(for simulated digits)
	159	//__________________________________________________________________________________________________
0422a446	160	void AliRICHReconstructor::Reconstruct(AliRunLoader pAL,AliRawReader pRR)const
0422a446	161	{
122efc54	162	//Invoked by AliReconstruction to convert raw digits from DDL files to clusters
	163	//Arguments: pAL - ALICE run loader pointer
	164	// pRR - ALICE raw reader pointer
	165	// Returns: none
	166	AliLoader pRL=pAL->GetDetectorLoader("RICH"); AliRICH pRich=(AliRICH*)pAL->GetAliRun()->GetDetector("RICH");//get pointers for RICH and RICH loader
0422a446	167
0422a446	168	AliRICHDigit dig; //tmp digit, raw digit will be converted to it
0422a446	169
	170	Int_t iEvtN=0;
	171	while(pRR->NextEvent()){//events loop
	172	pAL->GetEvent(iEvtN++);
	173	pRL->MakeTree("R"); pRich->MakeBranch("R");
	174
6df508f9	175	for(Int_t iCh=0;iCh<7;iCh++){//chambers loop
e30ca504	176	TClonesArray *pDigLst=new TClonesArray("AliRICHDigit"); Int_t iDigCnt=0; //tmp list of digits for single chamber
6df508f9	177	pRR->Select("RICH",2iCh,2iCh+1);//select only DDL files for the current chamber
0422a446	178	UInt_t w32=0;
	179	while(pRR->ReadNextInt(w32)){//raw records loop (in selected DDL files)
	180	UInt_t ddl=pRR->GetDDLID(); //returns 0,1,2 ... 13
e30ca504	181	dig.ReadRaw(ddl,w32);
0ffc02cf	182	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.PadX(),dig.PadY(),dig.Q()));
e30ca504	183	new((*pDigLst)[iDigCnt++]) AliRICHDigit(dig); //add this digit to the tmp list
0422a446	184	}//raw records loop
0ffc02cf	185	if(iDigCnt) Dig2Clu(pDigLst,pRich->CluLst(iCh));//cluster finder for the current chamber if any digits present
0422a446	186	pRR->Reset();
e30ca504	187	pDigLst->Delete(); iDigCnt=0;//clean up list of digits for the current chamber
0422a446	188	}//chambers loop
	189	pRL->TreeR()->Fill(); //fill tree for current event
	190	pRL->WriteRecPoints("OVERWRITE");//write out clusters for current event
db910db9	191	pRich->CluReset();
0422a446	192	}//events loop
	193	pRL->UnloadRecPoints();
	194	}//Reconstruct raw data
2714766e	195	//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
84093f6f	196
	197	void AliRICHReconstructor::FillESD(AliRunLoader , AliESD pESD) const
	198	{
	199	// Calculates probability to be a electron-muon-pion-kaon-proton
	200	// from the given Cerenkov angle and momentum assuming no initial particle composition
	201	// (i.e. apriory probability to be the particle of the given sort is the same for all sorts)
	202
	203	AliPID ppp; //needed
	204	Double_t pid[AliPID::kSPECIES],h[AliPID::kSPECIES];
84093f6f	205
84093f6f	206	for(Int_t iTrk=0;iTrk<pESD->GetNumberOfTracks();iTrk++){//ESD tracks loop
e30ca504	207	AliESDtrack *pTrk = pESD->GetTrack(iTrk);// get next reconstructed track
e30ca504	208	if(pTrk->GetRICHsignal()<=0){//RICH does not find anything reasonable for this track, assign 0.2 for all species
84093f6f	209	for(Int_t iPart=0;iPart<AliPID::kSPECIES;iPart++) pid[iPart]=1.0/AliPID::kSPECIES;
e30ca504	210	pTrk->SetRICHpid(pid);
84093f6f	211	continue;
84093f6f	212	}
e30ca504	213	Double_t pmod = pTrk->GetP();
84093f6f	214	Double_t hTot=0;
	215	for(Int_t iPart=0;iPart<AliPID::kSPECIES;iPart++){
	216	Double_t mass = AliPID::ParticleMass(iPart);
e30ca504	217	Double_t cosThetaTh = TMath::Sqrt(massmass+pmodpmod)/(AliRICHParam::Instance()->MeanIdxRad()*pmod);
84093f6f	218	if(cosThetaTh<1) //calculate the height of theortical theta ckov on the gaus of experimental one
e30ca504	219	h[iPart] =TMath::Gaus(TMath::ACos(cosThetaTh),pTrk->GetRICHsignal(),TMath::Sqrt(pTrk->GetRICHchi2()),kTRUE);
84093f6f	220
	221	else //beta < 1/ref. idx. => no light at all
	222	h[iPart] =0 ;
	223	hTot +=h[iPart]; //total height of all theoretical heights for normalization
	224	}//species loop
	225
e30ca504	226	Double_t hMin=TMath::Gaus(pTrk->GetRICHsignal()-4*TMath::Sqrt(pTrk->GetRICHchi2()),pTrk->GetRICHsignal(),TMath::Sqrt(pTrk->GetRICHchi2()),kTRUE);//5 sigma protection
84093f6f	227
	228	for(Int_t iPart=0;iPart<AliPID::kSPECIES;iPart++)//species loop to assign probabilities
	229	if(hTot>hMin)
	230	pid[iPart]=h[iPart]/hTot;
	231	else //all theoretical values are far away from experemental one
	232	pid[iPart]=1.0/AliPID::kSPECIES;
e30ca504	233	pTrk->SetRICHpid(pid);
84093f6f	234	}//ESD tracks loop
	235	//last line is to check if the nearest thetacerenkov to the teorethical one is within 5 sigma, otherwise no response (equal prob to every particle
	236	}//FillESD
e30ca504	237	//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++