/**************************************************************************
 * 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 <AliRawReader.h>         //Reconstruct(...)
#include <AliRun.h>               //ConvertDigits uses gAlice
#include <AliESD.h>               //RichAna()
#include <AliStack.h>             //RichAna()
#include <TFile.h>                //RichAna()
#include <TFile.h>                //RichAna()
#include <TParticle.h>            //RichAna()
#include <TH1F.h>                 //CluQA() 
#include <TH2F.h>                 //CluQA() 
#include <TCanvas.h>              //CluQA() 
#include <TNtupleD.h>             //CheckPR()
#include <TPolyMarker.h>          //Test()
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("RichCluQdc"     ,"All QDC;q [QDC]"           ,4000 ,0  ,4000);// QDC hists
  TH1F* pCerQ=new TH1F("RichCluCerQdc"  ,"Ckov QDC;q [QDC]"          ,4000 ,0  ,4000);
  TH1F* pMipQ=new TH1F("RichCluMipQdc"  ,"MIP QDC;q [QDC]"           ,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  ,AliRICHParam::PcSizeX(),1000,0,AliRICHParam::PcSizeY()); // maps
  TH2F* pMipM=new TH2F("RichCluMipMap"  ,"MIP map;x [cm];y [cm]"     ,1000 ,0  ,AliRICHParam::PcSizeX(),1000,0,AliRICHParam::PcSizeY());
  TH2F* pCerM=new TH2F("RichCluCerMap"  ,"Ckov map;x [cm];y [cm]"    ,1000 ,0  ,AliRICHParam::PcSizeX(),1000,0,AliRICHParam::PcSizeY());
 
  
  TClonesArray *pCluLst=new TClonesArray("AliRICHCluster");//tmp list of clusters
  
  for(Int_t iEvtN=0; iEvtN<iNevt; iEvtN++){
    pAL->GetEvent(iEvtN);               
    pRL->TreeD()->GetEntry(0); 
    for(Int_t iChN=1;iChN<=AliRICHParam::kNch;iChN++){//chambers loop
      if(pRich->Digs(iChN)->GetEntriesFast()>0) Dig2Clu(pRich->Digs(iChN),pCluLst,kFALSE);//cluster finder for the current chamber if any digits present
    }//chambers loop
    
    for(Int_t iCluN=0 ; iCluN < pCluLst->GetEntriesFast() ; iCluN++){
      AliRICHCluster *pClu = (AliRICHCluster*)pCluLst->At(iCluN);
      Int_t cfm=0; for(Int_t iDig=0;iDig<pClu->Size();iDig++)  cfm+=pClu->Dig(iDig)->Cfm(); //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   
  }//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::CheckPR()
{
//Pattern recognition with stack particles
  TFile *pFile = new TFile("$(HOME)/RPR.root","RECREATE","RICH Pattern Recognition");
  TNtupleD *hn = new TNtupleD("hn","ntuple","Pmod:Charge:TrackTheta:TrackPhi:TrackX:TrackY:MinX:MinY:ChargeMIP:ThetaCerenkov:NPhotons:MipIndex:Chamber:Particle");
//  printf("\n\n");
//  printf("Pattern Recognition done for event %5i",0);
  AliRICH *pRich=((AliRICH*)gAlice->GetDetector("RICH"));
  AliMagF * magf = gAlice->Field();
  AliTracker::SetFieldMap(magf,kTRUE);
  for(Int_t iEvtN=0;iEvtN<pRich->GetLoader()->GetRunLoader()->GetNumberOfEvents();iEvtN++) {
    pRich->GetLoader()->GetRunLoader()->GetEvent(iEvtN);
    AliRICHTracker *tr = new AliRICHTracker();
    tr->RecWithStack(hn);
    AliInfoClass(Form("Pattern Recognition done for event %i \b",iEvtN));
//    printf("\b\b\b\b\b%5i",iEvtN+1);
  }
  printf("\n\n");
  pFile->Write();pFile->Close();
}
//__________________________________________________________________________________________________
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.
//If pStack not 0 then also finds Ckov-Fee-Mip composition for formed clusters.  
//Puts all found clusters in the given clusters list. 
//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(1,AliRICHParam::NpadsX(),1,AliRICHParam::NpadsY());  digMap=(Float_t)-1; //digit map for one chamber reseted to -1
  for(Int_t iDigN=0 ; iDigN < pDigLst->GetEntriesFast() ; iDigN++){                        //digits loop to fill digits map
    AliRICHDigit *pDig= (AliRICHDigit*)pDigLst->At(iDigN);                                   //get current digit
    digMap( pDig->PadX(), pDig->PadY() )=iDigN;                                              //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 iDigN=0;iDigN<pDigLst->GetEntriesFast();iDigN++){                              //digits loop to form clusters list
    AliRICHDigit *pDig=(AliRICHDigit*)pDigLst->At(iDigN);                                  //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 iNnei=AliRICHParam::PadNeighbours(pDig->PadX(),pDig->PadY(),x,y);//returns in x,y all possible neighbours of the given padx,pady
  for (Int_t i=0;i<iNnei;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 iChN=1;iChN<=7;iChN++){//chambers loop
      if(pRich->Digs(iChN)->GetEntriesFast()>0) Dig2Clu(pRich->Digs(iChN),pRich->Clus(iChN));//cluster finder for the current chamber if any digits present
    }//chambers loop
    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
  TClonesArray *pDigList=new TClonesArray("AliRICHDigit"); Int_t iDigCnt=0; //tmp list of digits for single chamber only
  
  Int_t iEvtN=0;
  while(pRR->NextEvent()){//events loop
    pAL->GetEvent(iEvtN++);
    pRL->MakeTree("R");  pRich->MakeBranch("R");
    
    for(Int_t iChN=1;iChN<=7;iChN++){//chambers loop
      pRR->Select("RICH",2*iChN-2,2*iChN-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.Raw2Dig(ddl,w32);  
        AliDebug(1,Form("Ch=%i DDL=%i raw=0x%x digit=(%3i,%3i,%3i,%3i) Q=%5.2f",iChN,ddl,w32,dig.C(),dig.S(),dig.PadX(),dig.PadY(),dig.Qdc()));
        new((*pDigList)[iDigCnt++]) AliRICHDigit(dig); //add this digit to the tmp list
      }//raw records loop
      if(iDigCnt) Dig2Clu(pDigList,pRich->Clus(iChN));//cluster finder for the current chamber if any digits present
      pRR->Reset();        
      pDigList->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::Test(Bool_t isTryUnfold)
{
// Test the cluster finding algorithm by providing predifined set of digits
// Arguments: none
//   Returns: none  
  TClonesArray *pDigTst=new TClonesArray("AliRICHDigit");       TClonesArray *pCluTst=new TClonesArray("AliRICHCluster");     
  Int_t iDigCnt=0;
  Int_t c,padx,pady,qdc;
//ckov cluster  
  new((*pDigTst)[iDigCnt++]) AliRICHDigit(AliRICHDigit::P2A(c=1,padx= 89,pady=13),qdc= 10);
  new((*pDigTst)[iDigCnt++]) AliRICHDigit(AliRICHDigit::P2A(c=1,padx= 90,pady=13),qdc=  7);
  new((*pDigTst)[iDigCnt++]) AliRICHDigit(AliRICHDigit::P2A(c=1,padx= 90,pady=12),qdc=  6);
  new((*pDigTst)[iDigCnt++]) AliRICHDigit(AliRICHDigit::P2A(c=1,padx= 91,pady=12),qdc=  7);
//mip cluster  
  new((*pDigTst)[iDigCnt++]) AliRICHDigit(AliRICHDigit::P2A(c=1,padx= 99,pady=21),qdc=  9);
  new((*pDigTst)[iDigCnt++]) AliRICHDigit(AliRICHDigit::P2A(c=1,padx= 99,pady=22),qdc= 26);
  new((*pDigTst)[iDigCnt++]) AliRICHDigit(AliRICHDigit::P2A(c=1,padx=100,pady=21),qdc= 39);
  new((*pDigTst)[iDigCnt++]) AliRICHDigit(AliRICHDigit::P2A(c=1,padx=100,pady=22),qdc=109);
  new((*pDigTst)[iDigCnt++]) AliRICHDigit(AliRICHDigit::P2A(c=1,padx=100,pady=23),qdc=  7);
  new((*pDigTst)[iDigCnt++]) AliRICHDigit(AliRICHDigit::P2A(c=1,padx=101,pady=22),qdc= 11);
  
  Printf("Initial digits (1 ckov cluster and 1 mip cluster):"); pDigTst->Print();
  Dig2Clu(pDigTst,pCluTst,isTryUnfold);   
  Printf("Resulting clusters (expecting to have 2):"); pCluTst->Print(); 
  delete pDigTst; delete pCluTst;
}//Test()
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
void AliRICHReconstructor::Test(TClonesArray *pDigLst,Bool_t isTryUnfold)
{
// Test the cluster finding algorithm for given list of digits. Note that list of digits will not be deleted.
// Arguments: pDigLst- list of digits
//   Returns: none  
  TClonesArray *pCluLst=new TClonesArray("AliRICHCluster");     
  Dig2Clu(pDigLst,pCluLst,isTryUnfold);   
  
  Int_t iNdig=pDigLst->GetEntriesFast();
  Int_t iNclu=pCluLst->GetEntriesFast();
  
  TH2F *pH2=new TH2F("RDH2",Form("Tst dig->clu Digs: %i Clus: %i;cm;cm",iNdig,iNclu),AliRICHParam::NpadsX(),0,AliRICHParam::PcSizeX(),AliRICHParam::NpadsY(),0,AliRICHParam::PcSizeY());
  pH2->SetStats(kFALSE);
  for(Int_t iDig=0;iDig < iNdig;iDig++) {//digits loop
    AliRICHDigit *pDig = (AliRICHDigit*)pDigLst->At(iDig);
    TVector2 x2=AliRICHParam::Pad2Loc(pDig->Pad());
    pH2->Fill(x2.X(),x2.Y(),pDig->Qdc());
  }//digits loop
  
  TPolyMarker *pCluMarker=new TPolyMarker(iNclu); pCluMarker->SetMarkerStyle(5); pCluMarker->SetMarkerColor(kBlue);
  for(Int_t iClu=0;iClu < iNclu;iClu++) {//clusters loop
    AliRICHCluster *pClu = (AliRICHCluster*)pCluLst->At(iClu);
    pCluMarker->SetNextPoint(pClu->X(),pClu->Y());
  }//digits loop
  
  pH2->Draw("col");
  pCluMarker->Draw();  
  AliRICHParam::DrawSectors();
  delete pCluLst;
}//Test()
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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];
  Double_t refIndex=AliRICHParam::Instance()->IdxC6F14(AliRICHParam::EckovMean());
   
  for(Int_t iTrk=0;iTrk<pESD->GetNumberOfTracks();iTrk++){//ESD tracks loop
    AliESDtrack *pTrack = pESD->GetTrack(iTrk);// get next reconstructed track
    if(pTrack->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;
      pTrack->SetRICHpid(pid);
      continue;
    } 
    Double_t pmod = pTrack->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)/(refIndex*pmod);
      if(cosThetaTh<1) //calculate the height of theortical theta ckov on the gaus of experimental one
        h[iPart] =TMath::Gaus(TMath::ACos(cosThetaTh),pTrack->GetRICHsignal(),TMath::Sqrt(pTrack->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(pTrack->GetRICHsignal()-4*TMath::Sqrt(pTrack->GetRICHchi2()),pTrack->GetRICHsignal(),TMath::Sqrt(pTrack->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; 
    pTrack->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