Swap row and columns in Calibrate()

[u/mrichter/AliRoot.git] / PHOS / AliPHOSClusterizerv1.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.                  *
 **************************************************************************/

/* $Id$ */

/* History of cvs commits:
 *
 * $Log$
 * Revision 1.82  2005/09/02 15:43:13  kharlov
 * Add comments in GetCalibrationParameters and Calibrate
 *
 * Revision 1.81  2005/09/02 14:32:07  kharlov
 * Calibration of raw data
 *
 * Revision 1.80  2005/08/24 15:31:36  kharlov
 * Setting raw digits flag
 *
 * Revision 1.79  2005/07/25 15:53:53  kharlov
 * Read raw data
 *
 * Revision 1.78  2005/05/28 14:19:04  schutz
 * Compilation warnings fixed by T.P.
 *
 */

//*-- Author: Yves Schutz (SUBATECH)  & Dmitri Peressounko (SUBATECH & Kurchatov Institute)
//////////////////////////////////////////////////////////////////////////////
//  Clusterization class. Performs clusterization (collects neighbouring active cells) and 
//  unfolds the clusters having several local maxima.  
//  Results are stored in TreeR#, branches PHOSEmcRP (EMC recPoints),
//  PHOSCpvRP (CPV RecPoints) and AliPHOSClusterizer (Clusterizer with all 
//  parameters including input digits branch title, thresholds etc.)
//  This TTask is normally called from Reconstructioner, but can as well be used in 
//  standalone mode.
// Use Case:
//  root [0] AliPHOSClusterizerv1 * cl = new AliPHOSClusterizerv1("galice.root", "recpointsname", "digitsname")  
//  Warning in <TDatabasePDG::TDatabasePDG>: object already instantiated
//               // reads gAlice from header file "galice.root", uses digits stored in the branch names "digitsname" (default = "Default")
//               // and saves recpoints in branch named "recpointsname" (default = "digitsname")                       
//  root [1] cl->ExecuteTask()  
//               //finds RecPoints in all events stored in galice.root
//  root [2] cl->SetDigitsBranch("digits2") 
//               //sets another title for Digitis (input) branch
//  root [3] cl->SetRecPointsBranch("recp2")  
//               //sets another title four output branches
//  root [4] cl->SetEmcLocalMaxCut(0.03)  
//               //set clusterization parameters
//  root [5] cl->ExecuteTask("deb all time")  
//               //once more finds RecPoints options are 
//               // deb - print number of found rec points
//               // deb all - print number of found RecPoints and some their characteristics 
//               // time - print benchmarking results

// --- ROOT system ---

#include "TMath.h" 
#include "TMinuit.h"
#include "TTree.h" 
#include "TBenchmark.h"

// --- Standard library ---

// --- AliRoot header files ---
#include "AliLog.h"
#include "AliPHOSGetter.h"
#include "AliPHOSGeometry.h" 
#include "AliPHOSClusterizerv1.h"
#include "AliPHOSEmcRecPoint.h"
#include "AliPHOSCpvRecPoint.h"
#include "AliPHOSDigit.h"
#include "AliPHOSDigitizer.h"
#include "AliPHOSCalibrationDB.h"

ClassImp(AliPHOSClusterizerv1)
  
//____________________________________________________________________________
  AliPHOSClusterizerv1::AliPHOSClusterizerv1() : AliPHOSClusterizer()
{
  // default ctor (to be used mainly by Streamer)
  
  InitParameters() ; 
  fDefaultInit = kTRUE ; 
}

//____________________________________________________________________________
AliPHOSClusterizerv1::AliPHOSClusterizerv1(const TString alirunFileName, const TString eventFolderName)
:AliPHOSClusterizer(alirunFileName, eventFolderName)
{
  // ctor with the indication of the file where header Tree and digits Tree are stored
  
  InitParameters() ;
  Init() ;
  fDefaultInit = kFALSE ; 
}

//____________________________________________________________________________
  AliPHOSClusterizerv1::~AliPHOSClusterizerv1()
{
  // dtor

}
//____________________________________________________________________________
const TString AliPHOSClusterizerv1::BranchName() const 
{  
  return GetName();
}
 
//____________________________________________________________________________
Float_t  AliPHOSClusterizerv1::Calibrate(Int_t amp, Int_t absId)
{  
  // Convert digitized amplitude into energy.
  // Calibration parameters are taken from calibration data base for raw data,
  // or from digitizer parameters for simulated data.

  if(fCalibData){
    Int_t relId[4];
    AliPHOSGetter *gime = AliPHOSGetter::Instance();
    gime->PHOSGeometry()->AbsToRelNumbering(absId,relId) ;
    Int_t   module = relId[0];
    Int_t   row    = relId[2];
    Int_t   column = relId[3];
    if(absId <= fEmcCrystals) { //calibrate as EMC 
      fADCchanelEmc   = fCalibData->GetADCchannelEmc (module,column,row);
      fADCpedestalEmc = fCalibData->GetADCpedestalEmc(module,column,row);
      return fADCpedestalEmc + amp*fADCchanelEmc ;        
    }
    else //calibrate as CPV, not implemented yet
      return 0;
  }
  else{ //simulation
    if(absId <= fEmcCrystals) //calibrate as EMC 
      return fADCpedestalEmc + amp*fADCchanelEmc ;        
    else //calibrate as CPV
      return fADCpedestalCpv+ amp*fADCchanelCpv ;       
  }
}

//____________________________________________________________________________
void AliPHOSClusterizerv1::Exec(Option_t *option)
{
  // Steering method to perform clusterization for events
  // in the range from fFirstEvent to fLastEvent.
  // This range is optionally set by SetEventRange().
  // if fLastEvent=-1 (by default), then process events until the end.

  if(strstr(option,"tim"))
    gBenchmark->Start("PHOSClusterizer"); 
  
  if(strstr(option,"print")) {
    Print() ; 
    return ;
  }

  AliPHOSGetter * gime = AliPHOSGetter::Instance() ; 
  if (fRawReader == 0)
    gime->SetRawDigits(kFALSE);
  else
    gime->SetRawDigits(kTRUE);
  GetCalibrationParameters() ;
  
  if (fLastEvent == -1) 
    fLastEvent = gime->MaxEvent() - 1 ;
  else 
    fLastEvent = TMath::Min(fFirstEvent, gime->MaxEvent()); // one event at the time 
  Int_t nEvents   = fLastEvent - fFirstEvent + 1;

  Int_t ievent ;
  for (ievent = fFirstEvent; ievent <= fLastEvent; ievent++) {
    if (fRawReader == 0)
      gime->Event(ievent    ,"D"); // Read digits from simulated data
    else
      gime->Event(fRawReader,"W"); // Read digits from raw data
    
    fNumberOfEmcClusters  = fNumberOfCpvClusters  = 0 ;
    
    MakeClusters() ;

    if(fToUnfold)             
      MakeUnfolding() ;

    WriteRecPoints();

    if(strstr(option,"deb"))  
      PrintRecPoints(option) ;

    //increment the total number of recpoints per run 
    fRecPointsInRun += gime->EmcRecPoints()->GetEntriesFast() ;  
    fRecPointsInRun += gime->CpvRecPoints()->GetEntriesFast() ;  
    }
  
  if(fWrite) //do not unload in "on flight" mode
    Unload();
  
  if(strstr(option,"tim")){
    gBenchmark->Stop("PHOSClusterizer");
    AliInfo(Form("took %f seconds for Clusterizing %f seconds per event \n",
	 gBenchmark->GetCpuTime("PHOSClusterizer"), 
	 gBenchmark->GetCpuTime("PHOSClusterizer")/nEvents )) ; 
  } 
}

//____________________________________________________________________________
Bool_t AliPHOSClusterizerv1::FindFit(AliPHOSEmcRecPoint * emcRP, AliPHOSDigit ** maxAt, Float_t * maxAtEnergy,
				    Int_t nPar, Float_t * fitparameters) const
{ 
  // Calls TMinuit to fit the energy distribution of a cluster with several maxima 
  // The initial values for fitting procedure are set equal to the positions of local maxima.
  // Cluster will be fitted as a superposition of nPar/3 electromagnetic showers

  
  AliPHOSGetter * gime = AliPHOSGetter::Instance();
  TClonesArray * digits = gime->Digits(); 
  

  gMinuit->mncler();                     // Reset Minuit's list of paramters
  gMinuit->SetPrintLevel(-1) ;           // No Printout
  gMinuit->SetFCN(AliPHOSClusterizerv1::UnfoldingChiSquare) ;  
                                         // To set the address of the minimization function 

  TList * toMinuit = new TList();
  toMinuit->AddAt(emcRP,0) ;
  toMinuit->AddAt(digits,1) ;
  
  gMinuit->SetObjectFit(toMinuit) ;         // To tranfer pointer to UnfoldingChiSquare

  // filling initial values for fit parameters
  AliPHOSDigit * digit ;

  Int_t ierflg  = 0; 
  Int_t index   = 0 ;
  Int_t nDigits = (Int_t) nPar / 3 ;

  Int_t iDigit ;

  const AliPHOSGeometry * geom = gime->PHOSGeometry() ; 

  for(iDigit = 0; iDigit < nDigits; iDigit++){
    digit = maxAt[iDigit]; 

    Int_t relid[4] ;
    Float_t x = 0.;
    Float_t z = 0.;
    geom->AbsToRelNumbering(digit->GetId(), relid) ;
    geom->RelPosInModule(relid, x, z) ;

    Float_t energy = maxAtEnergy[iDigit] ;

    gMinuit->mnparm(index, "x",  x, 0.1, 0, 0, ierflg) ;
    index++ ;   
    if(ierflg != 0){ 
      Warning("FindFit", "PHOS Unfolding unable to set initial value for fit procedure : x = %f\n", x ) ;
      return kFALSE;
    }
    gMinuit->mnparm(index, "z",  z, 0.1, 0, 0, ierflg) ;
    index++ ;   
    if(ierflg != 0){
       Warning("FindFit", "PHOS Unfolding unable to set initial value for fit procedure : z =%f\n", z ) ;
      return kFALSE;
    }
    gMinuit->mnparm(index, "Energy",  energy , 0.05*energy, 0., 4.*energy, ierflg) ;
    index++ ;   
    if(ierflg != 0){
      Warning("FindFit", "PHOS Unfolding unable to set initial value for fit procedure : energy = %f\n", energy ) ;      
      return kFALSE;
    }
  }

  Double_t p0 = 0.1 ; // "Tolerance" Evaluation stops when EDM = 0.0001*p0 ; The number of function call slightly
                      //  depends on it. 
  Double_t p1 = 1.0 ;
  Double_t p2 = 0.0 ;

  gMinuit->mnexcm("SET STR", &p2, 0, ierflg) ;   // force TMinuit to reduce function calls  
  gMinuit->mnexcm("SET GRA", &p1, 1, ierflg) ;   // force TMinuit to use my gradient  
  gMinuit->SetMaxIterations(5);
  gMinuit->mnexcm("SET NOW", &p2 , 0, ierflg) ;  // No Warnings

  gMinuit->mnexcm("MIGRAD", &p0, 0, ierflg) ;    // minimize 

  if(ierflg == 4){  // Minimum not found   
    Warning("FindFit", "PHOS Unfolding fit not converged, cluster abandoned\n" );      
    return kFALSE ;
  }            
  for(index = 0; index < nPar; index++){
    Double_t err ;
    Double_t val ;
    gMinuit->GetParameter(index, val, err) ;    // Returns value and error of parameter index
    fitparameters[index] = val ;
   }

  delete toMinuit ;
  return kTRUE;

}

//____________________________________________________________________________
void AliPHOSClusterizerv1::GetCalibrationParameters() 
{
  // Set calibration parameters:
  // For raw data they are read from the calibration database,
  // for simulated data they are taken from digitizer.
  //
  // It is a user responsilibity to open CDB and set
  // AliPHOSCalibData object by the following operators:
  // 
  // AliCDBLocal *loc = new AliCDBLocal("deCalibDB");
  // AliPHOSCalibData* clb = (AliPHOSCalibData*)AliCDBStorage::Instance()
  //    ->Get(path_to_calibdata,run_number);
  // AliPHOSGetter* gime = AliPHOSGetter::Instance("galice.root");
  // gime->SetCalibData(clb);

  AliPHOSGetter * gime = AliPHOSGetter::Instance();
  if(gime->IsRawDigits()){
    fCalibData = gime->CalibData();    
  }
  else{
    if ( !gime->Digitizer() ) 
      gime->LoadDigitizer();
    AliPHOSDigitizer * dig = gime->Digitizer(); 
    fADCchanelEmc   = dig->GetEMCchannel() ;
    fADCpedestalEmc = dig->GetEMCpedestal();
    
    fADCchanelCpv   = dig->GetCPVchannel() ;
    fADCpedestalCpv = dig->GetCPVpedestal() ; 
  }  
}

//____________________________________________________________________________
void AliPHOSClusterizerv1::Init()
{
  // Make all memory allocations which can not be done in default constructor.
  // Attach the Clusterizer task to the list of PHOS tasks
 
  AliPHOSGetter* gime = AliPHOSGetter::Instance() ;
  if(!gime)
    gime = AliPHOSGetter::Instance(GetTitle(), fEventFolderName.Data());

  AliPHOSGeometry * geom = gime->PHOSGeometry();

  fEmcCrystals = geom->GetNModules() *  geom->GetNCristalsInModule() ;

  if(!gMinuit) 
    gMinuit = new TMinuit(100);

  if ( !gime->Clusterizer() ) {
    gime->PostClusterizer(this);
  }
}

//____________________________________________________________________________
void AliPHOSClusterizerv1::InitParameters()
{

  fNumberOfCpvClusters     = 0 ; 
  fNumberOfEmcClusters     = 0 ; 
  
  fCpvClusteringThreshold  = 0.0;
  fEmcClusteringThreshold  = 0.2;   
  
  fEmcLocMaxCut            = 0.03 ;
  fCpvLocMaxCut            = 0.03 ;

  fEmcMinE                 = 0.01 ;
  fCpvMinE                 = 0.0  ;

  fW0                      = 4.5 ;
  fW0CPV                   = 4.0 ;

  fEmcTimeGate             = 1.e-8 ; 
  
  fToUnfold                = kTRUE ;
    
  fRecPointsInRun          = 0 ;

  fWrite                   = kTRUE ;

  fCalibData               = 0 ;

  SetEventRange(0,-1) ;
}

//____________________________________________________________________________
Int_t AliPHOSClusterizerv1::AreNeighbours(AliPHOSDigit * d1, AliPHOSDigit * d2)const
{
  // Gives the neighbourness of two digits = 0 are not neighbour but continue searching 
  //                                       = 1 are neighbour
  //                                       = 2 are not neighbour but do not continue searching
  // neighbours are defined as digits having at least a common vertex 
  // The order of d1 and d2 is important: first (d1) should be a digit already in a cluster 
  //                                      which is compared to a digit (d2)  not yet in a cluster  

  AliPHOSGeometry * geom = AliPHOSGetter::Instance()->PHOSGeometry() ;

  Int_t rv = 0 ; 

  Int_t relid1[4] ; 
  geom->AbsToRelNumbering(d1->GetId(), relid1) ; 

  Int_t relid2[4] ; 
  geom->AbsToRelNumbering(d2->GetId(), relid2) ; 
 
  if ( (relid1[0] == relid2[0]) && (relid1[1]==relid2[1]) ) { // inside the same PHOS module 
    Int_t rowdiff = TMath::Abs( relid1[2] - relid2[2] ) ;  
    Int_t coldiff = TMath::Abs( relid1[3] - relid2[3] ) ;  
    
    if (( coldiff <= 1 )  && ( rowdiff <= 1 )){
      if((relid1[1] != 0) || (TMath::Abs(d1->GetTime() - d2->GetTime() ) < fEmcTimeGate))
      rv = 1 ; 
    }
    else {
      if((relid2[2] > relid1[2]) && (relid2[3] > relid1[3]+1)) 
        rv = 2; //  Difference in row numbers is too large to look further 
    }

  } 
  else {
    
    if( (relid1[0] < relid2[0]) || (relid1[1] != relid2[1]) )  
      rv=2 ;

  }

  return rv ; 
}
//____________________________________________________________________________
void AliPHOSClusterizerv1::CleanDigits(TClonesArray * digits){
  for(Int_t i=0; i<digits->GetEntriesFast(); i++){
    AliPHOSDigit * digit = static_cast<AliPHOSDigit*>(digits->At(i)) ;
    Float_t cut = IsInEmc(digit) ? fEmcMinE : fCpvMinE ;
    if(Calibrate(digit->GetAmp(),digit->GetId()) < cut)
      digits->RemoveAt(i) ;
  }
  digits->Compress() ;
  for (Int_t i = 0 ; i < digits->GetEntriesFast() ; i++) { 
    AliPHOSDigit *digit = static_cast<AliPHOSDigit*>( digits->At(i) ) ; 
    digit->SetIndexInList(i) ;     
  }

}
//____________________________________________________________________________
Bool_t AliPHOSClusterizerv1::IsInEmc(AliPHOSDigit * digit) const
{
  // Tells if (true) or not (false) the digit is in a PHOS-EMC module
 
  Bool_t rv = kFALSE ; 
  AliPHOSGeometry * geom = AliPHOSGetter::Instance()->PHOSGeometry() ;

  Int_t nEMC = geom->GetNModules()*geom->GetNPhi()*geom->GetNZ();  

  if(digit->GetId() <= nEMC )   rv = kTRUE; 

  return rv ; 
}

//____________________________________________________________________________
Bool_t AliPHOSClusterizerv1::IsInCpv(AliPHOSDigit * digit) const
{
  // Tells if (true) or not (false) the digit is in a PHOS-CPV module
 
  Bool_t rv = kFALSE ; 
  
  AliPHOSGeometry * geom = AliPHOSGetter::Instance()->PHOSGeometry() ;

  Int_t nEMC = geom->GetNModules()*geom->GetNPhi()*geom->GetNZ();

  if(digit->GetId() > nEMC )   rv = kTRUE;

  return rv ; 
}

//____________________________________________________________________________
void AliPHOSClusterizerv1::Unload() 
{
  AliPHOSGetter * gime = AliPHOSGetter::Instance() ; 
  gime->PhosLoader()->UnloadDigits() ; 
  gime->PhosLoader()->UnloadRecPoints() ; 
}

//____________________________________________________________________________
void AliPHOSClusterizerv1::WriteRecPoints()
{

  // Creates new branches with given title
  // fills and writes into TreeR.

  AliPHOSGetter * gime = AliPHOSGetter::Instance();

  TObjArray * emcRecPoints = gime->EmcRecPoints() ; 
  TObjArray * cpvRecPoints = gime->CpvRecPoints() ; 
  TClonesArray * digits = gime->Digits() ; 
 
 
  Int_t index ;
  //Evaluate position, dispersion and other RecPoint properties..
  Int_t nEmc = emcRecPoints->GetEntriesFast();
  for(index = 0; index < nEmc; index++){
    AliPHOSEmcRecPoint * rp = dynamic_cast<AliPHOSEmcRecPoint *>( emcRecPoints->At(index) );
    rp->Purify(fEmcMinE) ;
    if(rp->GetMultiplicity()>0.) //If this RP is not empty
      rp->EvalAll(fW0,digits) ;
    else{
      emcRecPoints->RemoveAt(index) ;
      delete rp ;
    }
  }
  emcRecPoints->Compress() ;
  emcRecPoints->Sort() ;
  //  emcRecPoints->Expand(emcRecPoints->GetEntriesFast()) ;
  for(index = 0; index < emcRecPoints->GetEntries(); index++){
    dynamic_cast<AliPHOSEmcRecPoint *>( emcRecPoints->At(index) )->SetIndexInList(index) ;
  }
  
  //Now the same for CPV
  for(index = 0; index < cpvRecPoints->GetEntries(); index++){
    AliPHOSCpvRecPoint * rp = dynamic_cast<AliPHOSCpvRecPoint *>( cpvRecPoints->At(index) );
    rp->EvalAll(fW0CPV,digits) ;
  }
  cpvRecPoints->Sort() ;
  
  for(index = 0; index < cpvRecPoints->GetEntries(); index++)
    dynamic_cast<AliPHOSCpvRecPoint *>( cpvRecPoints->At(index) )->SetIndexInList(index) ;
  
  cpvRecPoints->Expand(cpvRecPoints->GetEntriesFast()) ;
  
  if(fWrite){ //We write TreeR
    TTree * treeR = gime->TreeR();
    
    Int_t bufferSize = 32000 ;    
    Int_t splitlevel = 0 ;
    
    //First EMC
    TBranch * emcBranch = treeR->Branch("PHOSEmcRP","TObjArray",&emcRecPoints,bufferSize,splitlevel);
    emcBranch->SetTitle(BranchName());
    
    //Now CPV branch
    TBranch * cpvBranch = treeR->Branch("PHOSCpvRP","TObjArray",&cpvRecPoints,bufferSize,splitlevel);
    cpvBranch->SetTitle(BranchName());
    
    emcBranch        ->Fill() ;
    cpvBranch        ->Fill() ;
    
    gime->WriteRecPoints("OVERWRITE");
    gime->WriteClusterizer("OVERWRITE");
  }
}

//____________________________________________________________________________
void AliPHOSClusterizerv1::MakeClusters()
{
  // Steering method to construct the clusters stored in a list of Reconstructed Points
  // A cluster is defined as a list of neighbour digits

  
  AliPHOSGetter * gime = AliPHOSGetter::Instance();

  TObjArray * emcRecPoints = gime->EmcRecPoints() ; 
  TObjArray * cpvRecPoints = gime->CpvRecPoints() ; 

  emcRecPoints->Delete() ;
  cpvRecPoints->Delete() ;
  
  TClonesArray * digits = gime->Digits() ; 

  //Remove digits below threshold
  CleanDigits(digits) ;


  TClonesArray * digitsC =  static_cast<TClonesArray*>( digits->Clone() ) ;
  
 
  // Clusterization starts  

  TIter nextdigit(digitsC) ; 
  AliPHOSDigit * digit ; 
  Bool_t notremoved = kTRUE ;

  while ( (digit = dynamic_cast<AliPHOSDigit *>( nextdigit()) ) ) { // scan over the list of digitsC
    

    AliPHOSRecPoint * clu = 0 ; 

    TArrayI clusterdigitslist(1500) ;   
    Int_t index ;

    if (( IsInEmc (digit) && Calibrate(digit->GetAmp(),digit->GetId()) > fEmcClusteringThreshold  ) || 
        ( IsInCpv (digit) && Calibrate(digit->GetAmp(),digit->GetId()) > fCpvClusteringThreshold  ) ) {
      Int_t iDigitInCluster = 0 ; 
      
      if  ( IsInEmc(digit) ) {   
        // start a new EMC RecPoint
        if(fNumberOfEmcClusters >= emcRecPoints->GetSize()) 
          emcRecPoints->Expand(2*fNumberOfEmcClusters+1) ;
          
        emcRecPoints->AddAt(new  AliPHOSEmcRecPoint(""), fNumberOfEmcClusters) ;
        clu = dynamic_cast<AliPHOSEmcRecPoint *>( emcRecPoints->At(fNumberOfEmcClusters) ) ; 
          fNumberOfEmcClusters++ ; 
        clu->AddDigit(*digit, Calibrate(digit->GetAmp(),digit->GetId())) ; 
        clusterdigitslist[iDigitInCluster] = digit->GetIndexInList() ;        
        iDigitInCluster++ ; 
        digitsC->Remove(digit) ; 

      } else { 
        
        // start a new CPV cluster
        if(fNumberOfCpvClusters >= cpvRecPoints->GetSize()) 
          cpvRecPoints->Expand(2*fNumberOfCpvClusters+1);

        cpvRecPoints->AddAt(new AliPHOSCpvRecPoint(""), fNumberOfCpvClusters) ;

        clu =  dynamic_cast<AliPHOSCpvRecPoint *>( cpvRecPoints->At(fNumberOfCpvClusters) ) ;  
        fNumberOfCpvClusters++ ; 
        clu->AddDigit(*digit, Calibrate(digit->GetAmp(),digit->GetId()) ) ;        
        clusterdigitslist[iDigitInCluster] = digit->GetIndexInList()  ;        
        iDigitInCluster++ ; 
        digitsC->Remove(digit) ; 
        nextdigit.Reset() ;
        
        // Here we remove remaining EMC digits, which cannot make a cluster
        
        if( notremoved ) { 
          while( ( digit = dynamic_cast<AliPHOSDigit *>( nextdigit() ) ) ) {
            if( IsInEmc(digit) ) 
              digitsC->Remove(digit) ;
            else 
              break ;
          }
          notremoved = kFALSE ;
        }
        
      } // else        
      
      nextdigit.Reset() ;
      
      AliPHOSDigit * digitN ; 
      index = 0 ;
      while (index < iDigitInCluster){ // scan over digits already in cluster 
        digit =  dynamic_cast<AliPHOSDigit*>( digits->At(clusterdigitslist[index]) )  ;      
        index++ ; 
        while ( (digitN = dynamic_cast<AliPHOSDigit *>( nextdigit() ) ) ) { // scan over the reduced list of digits 
          Int_t ineb = AreNeighbours(digit, digitN);       // call (digit,digitN) in THAT oder !!!!!
          switch (ineb ) {
          case 0 :   // not a neighbour
            break ;
          case 1 :   // are neighbours 
            clu->AddDigit(*digitN, Calibrate( digitN->GetAmp(), digitN->GetId() ) ) ;
            clusterdigitslist[iDigitInCluster] = digitN->GetIndexInList() ; 
            iDigitInCluster++ ; 
            digitsC->Remove(digitN) ;
            break ;
          case 2 :   // too far from each other
            goto endofloop;   
          } // switch
          
        } // while digitN
        
      endofloop: ;
        nextdigit.Reset() ; 
        
      } // loop over cluster     

    } // energy theshold  

    
  } // while digit

  delete digitsC ;

}

//____________________________________________________________________________
void AliPHOSClusterizerv1::MakeUnfolding()
{
  // Unfolds clusters using the shape of an ElectroMagnetic shower
  // Performs unfolding of all EMC/CPV clusters

  AliPHOSGetter * gime = AliPHOSGetter::Instance();

  const AliPHOSGeometry * geom = gime->PHOSGeometry() ;

  TObjArray * emcRecPoints = gime->EmcRecPoints() ; 
  TObjArray * cpvRecPoints = gime->CpvRecPoints() ; 
  TClonesArray * digits = gime->Digits() ; 
  
  // Unfold first EMC clusters 
  if(fNumberOfEmcClusters > 0){

    Int_t nModulesToUnfold = geom->GetNModules() ; 

    Int_t numberofNotUnfolded = fNumberOfEmcClusters ; 
    Int_t index ;   
    for(index = 0 ; index < numberofNotUnfolded ; index++){
      
      AliPHOSEmcRecPoint * emcRecPoint = dynamic_cast<AliPHOSEmcRecPoint *>( emcRecPoints->At(index) ) ;
      if(emcRecPoint->GetPHOSMod()> nModulesToUnfold)
        break ;
      
      Int_t nMultipl = emcRecPoint->GetMultiplicity() ; 
      AliPHOSDigit ** maxAt = new AliPHOSDigit*[nMultipl] ;
      Float_t * maxAtEnergy = new Float_t[nMultipl] ;
      Int_t nMax = emcRecPoint->GetNumberOfLocalMax(maxAt, maxAtEnergy,fEmcLocMaxCut,digits) ;
      
      if( nMax > 1 ) {     // if cluster is very flat (no pronounced maximum) then nMax = 0       
        UnfoldCluster(emcRecPoint, nMax, maxAt, maxAtEnergy) ;
        emcRecPoints->Remove(emcRecPoint); 
        emcRecPoints->Compress() ;
        index-- ;
        fNumberOfEmcClusters -- ;
        numberofNotUnfolded-- ;
      }
      else{
        emcRecPoint->SetNExMax(1) ; //Only one local maximum
      }
      
      delete[] maxAt ; 
      delete[] maxAtEnergy ; 
    }
  } 
  // Unfolding of EMC clusters finished


  // Unfold now CPV clusters
  if(fNumberOfCpvClusters > 0){
    
    Int_t nModulesToUnfold = geom->GetNModules() ;

    Int_t numberofCpvNotUnfolded = fNumberOfCpvClusters ;     
    Int_t index ;   
    for(index = 0 ; index < numberofCpvNotUnfolded ; index++){
      
      AliPHOSRecPoint * recPoint = dynamic_cast<AliPHOSRecPoint *>( cpvRecPoints->At(index) ) ;

      if(recPoint->GetPHOSMod()> nModulesToUnfold)
        break ;
      
      AliPHOSEmcRecPoint * emcRecPoint = dynamic_cast<AliPHOSEmcRecPoint*>(recPoint) ; 
      
      Int_t nMultipl = emcRecPoint->GetMultiplicity() ; 
      AliPHOSDigit ** maxAt = new AliPHOSDigit*[nMultipl] ;
      Float_t * maxAtEnergy = new Float_t[nMultipl] ;
      Int_t nMax = emcRecPoint->GetNumberOfLocalMax(maxAt, maxAtEnergy,fCpvLocMaxCut,digits) ;
      
      if( nMax > 1 ) {     // if cluster is very flat (no pronounced maximum) then nMax = 0       
        UnfoldCluster(emcRecPoint, nMax, maxAt, maxAtEnergy) ;
        cpvRecPoints->Remove(emcRecPoint); 
        cpvRecPoints->Compress() ;
        index-- ;
        numberofCpvNotUnfolded-- ;
        fNumberOfCpvClusters-- ;
      }
      
      delete[] maxAt ; 
      delete[] maxAtEnergy ; 
    } 
  }
  //Unfolding of Cpv clusters finished
  
}

//____________________________________________________________________________
Double_t  AliPHOSClusterizerv1::ShowerShape(Double_t r)
{ 
  // Shape of the shower (see PHOS TDR)
  // If you change this function, change also the gradient evaluation in ChiSquare()

  Double_t r4    = r*r*r*r ;
  Double_t r295  = TMath::Power(r, 2.95) ;
  Double_t shape = TMath::Exp( -r4 * (1. / (2.32 + 0.26 * r4) + 0.0316 / (1 + 0.0652 * r295) ) ) ;
  return shape ;
}

//____________________________________________________________________________
void  AliPHOSClusterizerv1::UnfoldCluster(AliPHOSEmcRecPoint * iniEmc, 
                                          Int_t nMax, 
                                          AliPHOSDigit ** maxAt, 
                                          Float_t * maxAtEnergy)
{ 
  // Performs the unfolding of a cluster with nMax overlapping showers 

  AliPHOSGetter * gime = AliPHOSGetter::Instance();

  const AliPHOSGeometry * geom = gime->PHOSGeometry() ;

  const TClonesArray * digits = gime->Digits() ; 
  TObjArray * emcRecPoints = gime->EmcRecPoints() ; 
  TObjArray * cpvRecPoints = gime->CpvRecPoints() ; 

  Int_t nPar = 3 * nMax ;
  Float_t * fitparameters = new Float_t[nPar] ;

  Bool_t rv = FindFit(iniEmc, maxAt, maxAtEnergy, nPar, fitparameters) ;
  if( !rv ) {
    // Fit failed, return and remove cluster
    iniEmc->SetNExMax(-1) ;
    delete[] fitparameters ; 
    return ;
  }

  // create ufolded rec points and fill them with new energy lists
  // First calculate energy deposited in each sell in accordance with fit (without fluctuations): efit[]
  // and later correct this number in acordance with actual energy deposition

  Int_t nDigits = iniEmc->GetMultiplicity() ;  
  Float_t * efit = new Float_t[nDigits] ;
  Float_t xDigit=0.,zDigit=0.,distance=0. ;
  Float_t xpar=0.,zpar=0.,epar=0.  ;
  Int_t relid[4] ;
  AliPHOSDigit * digit = 0 ;
  Int_t * emcDigits = iniEmc->GetDigitsList() ;

  Int_t iparam ;
  Int_t iDigit ;
  for(iDigit = 0 ; iDigit < nDigits ; iDigit ++){
    digit = dynamic_cast<AliPHOSDigit*>( digits->At(emcDigits[iDigit] ) ) ;   
    geom->AbsToRelNumbering(digit->GetId(), relid) ;
    geom->RelPosInModule(relid, xDigit, zDigit) ;
    efit[iDigit] = 0;

    iparam = 0 ;    
    while(iparam < nPar ){
      xpar = fitparameters[iparam] ;
      zpar = fitparameters[iparam+1] ;
      epar = fitparameters[iparam+2] ;
      iparam += 3 ;
      distance = (xDigit - xpar) * (xDigit - xpar) + (zDigit - zpar) * (zDigit - zpar)  ;
      distance =  TMath::Sqrt(distance) ;
      efit[iDigit] += epar * ShowerShape(distance) ;
    }
  }
  

  // Now create new RecPoints and fill energy lists with efit corrected to fluctuations
  // so that energy deposited in each cell is distributed betwin new clusters proportionally
  // to its contribution to efit

  Float_t * emcEnergies = iniEmc->GetEnergiesList() ;
  Float_t ratio ;

  iparam = 0 ;
  while(iparam < nPar ){
    xpar = fitparameters[iparam] ;
    zpar = fitparameters[iparam+1] ;
    epar = fitparameters[iparam+2] ;
    iparam += 3 ;    
    
    AliPHOSEmcRecPoint * emcRP = 0 ;  

    if(iniEmc->IsEmc()){ //create new entries in fEmcRecPoints...
      
      if(fNumberOfEmcClusters >= emcRecPoints->GetSize())
        emcRecPoints->Expand(2*fNumberOfEmcClusters) ;
      
      (*emcRecPoints)[fNumberOfEmcClusters] = new AliPHOSEmcRecPoint("") ;
      emcRP = dynamic_cast<AliPHOSEmcRecPoint *>( emcRecPoints->At(fNumberOfEmcClusters) ) ;
      fNumberOfEmcClusters++ ;
      emcRP->SetNExMax((Int_t)nPar/3) ;
    }
    else{//create new entries in fCpvRecPoints
      if(fNumberOfCpvClusters >= cpvRecPoints->GetSize())
        cpvRecPoints->Expand(2*fNumberOfCpvClusters) ;
      
      (*cpvRecPoints)[fNumberOfCpvClusters] = new AliPHOSCpvRecPoint("") ;
      emcRP = dynamic_cast<AliPHOSEmcRecPoint *>( cpvRecPoints->At(fNumberOfCpvClusters) ) ;
      fNumberOfCpvClusters++ ;
    }
    
    Float_t eDigit ;
    for(iDigit = 0 ; iDigit < nDigits ; iDigit ++){
      digit = dynamic_cast<AliPHOSDigit*>( digits->At( emcDigits[iDigit] ) ) ; 
      geom->AbsToRelNumbering(digit->GetId(), relid) ;
      geom->RelPosInModule(relid, xDigit, zDigit) ;
      distance = (xDigit - xpar) * (xDigit - xpar) + (zDigit - zpar) * (zDigit - zpar)  ;
      distance =  TMath::Sqrt(distance) ;
      ratio = epar * ShowerShape(distance) / efit[iDigit] ; 
      eDigit = emcEnergies[iDigit] * ratio ;
      emcRP->AddDigit( *digit, eDigit ) ;
    }        
  }
 
  delete[] fitparameters ; 
  delete[] efit ; 
  
}

//_____________________________________________________________________________
void AliPHOSClusterizerv1::UnfoldingChiSquare(Int_t & nPar, Double_t * Grad, Double_t & fret, Double_t * x, Int_t iflag)
{
  // Calculates the Chi square for the cluster unfolding minimization
  // Number of parameters, Gradient, Chi squared, parameters, what to do

  TList * toMinuit = dynamic_cast<TList*>( gMinuit->GetObjectFit() ) ;

  AliPHOSEmcRecPoint * emcRP = dynamic_cast<AliPHOSEmcRecPoint*>( toMinuit->At(0) )  ;
  TClonesArray * digits = dynamic_cast<TClonesArray*>( toMinuit->At(1) )  ;


  
  //  AliPHOSEmcRecPoint * emcRP = dynamic_cast<AliPHOSEmcRecPoint *>( gMinuit->GetObjectFit() ) ; // EmcRecPoint to fit

  Int_t * emcDigits     = emcRP->GetDigitsList() ;

  Int_t nOdigits = emcRP->GetDigitsMultiplicity() ; 

  Float_t * emcEnergies = emcRP->GetEnergiesList() ;
  
  const AliPHOSGeometry * geom = AliPHOSGetter::Instance()->PHOSGeometry() ; 
  fret = 0. ;     
  Int_t iparam ;

  if(iflag == 2)
    for(iparam = 0 ; iparam < nPar ; iparam++)    
      Grad[iparam] = 0 ; // Will evaluate gradient
  
  Double_t efit ;    

  AliPHOSDigit * digit ;
  Int_t iDigit ;

  for( iDigit = 0 ; iDigit < nOdigits ; iDigit++) {

    digit = dynamic_cast<AliPHOSDigit*>( digits->At( emcDigits[iDigit] ) ); 

    Int_t relid[4] ;
    Float_t xDigit ;
    Float_t zDigit ;

    geom->AbsToRelNumbering(digit->GetId(), relid) ;

    geom->RelPosInModule(relid, xDigit, zDigit) ;

     if(iflag == 2){  // calculate gradient
       Int_t iParam = 0 ;
       efit = 0 ;
       while(iParam < nPar ){
         Double_t distance = (xDigit - x[iParam]) * (xDigit - x[iParam]) ;
         iParam++ ; 
         distance += (zDigit - x[iParam]) * (zDigit - x[iParam]) ; 
         distance = TMath::Sqrt( distance ) ; 
         iParam++ ;          
         efit += x[iParam] * ShowerShape(distance) ;
         iParam++ ;
       }
       Double_t sum = 2. * (efit - emcEnergies[iDigit]) / emcEnergies[iDigit] ; // Here we assume, that sigma = sqrt(E) 
       iParam = 0 ;
       while(iParam < nPar ){
         Double_t xpar = x[iParam] ;
         Double_t zpar = x[iParam+1] ;
         Double_t epar = x[iParam+2] ;
         Double_t dr = TMath::Sqrt( (xDigit - xpar) * (xDigit - xpar) + (zDigit - zpar) * (zDigit - zpar) );
         Double_t shape = sum * ShowerShape(dr) ;
         Double_t r4 = dr*dr*dr*dr ;
         Double_t r295 = TMath::Power(dr,2.95) ;
         Double_t deriv =-4. * dr*dr * ( 2.32 / ( (2.32 + 0.26 * r4) * (2.32 + 0.26 * r4) ) +
                                         0.0316 * (1. + 0.0171 * r295) / ( ( 1. + 0.0652 * r295) * (1. + 0.0652 * r295) ) ) ;
         
         Grad[iParam] += epar * shape * deriv * (xpar - xDigit) ;  // Derivative over x    
         iParam++ ; 
         Grad[iParam] += epar * shape * deriv * (zpar - zDigit) ;  // Derivative over z         
         iParam++ ; 
         Grad[iParam] += shape ;                                  // Derivative over energy             
         iParam++ ; 
       }
     }
     efit = 0;
     iparam = 0 ;

     while(iparam < nPar ){
       Double_t xpar = x[iparam] ;
       Double_t zpar = x[iparam+1] ;
       Double_t epar = x[iparam+2] ;
       iparam += 3 ;
       Double_t distance = (xDigit - xpar) * (xDigit - xpar) + (zDigit - zpar) * (zDigit - zpar)  ;
       distance =  TMath::Sqrt(distance) ;
       efit += epar * ShowerShape(distance) ;
     }

     fret += (efit-emcEnergies[iDigit])*(efit-emcEnergies[iDigit])/emcEnergies[iDigit] ; 
     // Here we assume, that sigma = sqrt(E)
  }

}

//____________________________________________________________________________
void AliPHOSClusterizerv1::Print(const Option_t *)const
{
  // Print clusterizer parameters

  TString message ; 
  TString taskName(GetName()) ; 
  taskName.ReplaceAll(Version(), "") ;
  
  if( strcmp(GetName(), "") !=0 ) {  
    // Print parameters
    message  = "\n--------------- %s %s -----------\n" ; 
    message += "Clusterizing digits from the file: %s\n" ;
    message += "                           Branch: %s\n" ; 
    message += "                       EMC Clustering threshold = %f\n" ; 
    message += "                       EMC Local Maximum cut    = %f\n" ; 
    message += "                       EMC Logarothmic weight   = %f\n" ;
    message += "                       CPV Clustering threshold = %f\n" ;
    message += "                       CPV Local Maximum cut    = %f\n" ;
    message += "                       CPV Logarothmic weight   = %f\n" ;
    if(fToUnfold)
      message += " Unfolding on\n" ;
    else
      message += " Unfolding off\n" ;
    
    message += "------------------------------------------------------------------" ;
  }
  else 
    message = " AliPHOSClusterizerv1 not initialized " ;
  
  AliInfo(Form("%s, %s %s %s %s %s %s %s %s %s %s", message.Data(),  
       taskName.Data(), 
       GetTitle(),
       taskName.Data(), 
       GetName(), 
       fEmcClusteringThreshold, 
       fEmcLocMaxCut, 
       fW0, 
       fCpvClusteringThreshold, 
       fCpvLocMaxCut, 
       fW0CPV )) ; 
}


//____________________________________________________________________________
void AliPHOSClusterizerv1::PrintRecPoints(Option_t * option)
{
  // Prints list of RecPoints produced at the current pass of AliPHOSClusterizer

  AliPHOSGetter * gime = AliPHOSGetter::Instance();
 
  TObjArray * emcRecPoints = gime->EmcRecPoints() ; 
  TObjArray * cpvRecPoints = gime->CpvRecPoints() ; 

  AliInfo(Form("\nevent %d \n    Found %d EMC RecPoints and %d CPV RecPoints", 
	       gAlice->GetEvNumber(),
	       emcRecPoints->GetEntriesFast(),
	       cpvRecPoints->GetEntriesFast() ))  ;
 
  fRecPointsInRun +=  emcRecPoints->GetEntriesFast() ; 
  fRecPointsInRun +=  cpvRecPoints->GetEntriesFast() ; 
  
  
  if(strstr(option,"all")) {
    printf("\n EMC clusters \n") ;
    printf("Index    Ene(MeV) Multi Module     X    Y   Z    Lambdas_1  Lambda_2  # of prim  Primaries list\n") ;      
    Int_t index ;
    for (index = 0 ; index < emcRecPoints->GetEntries() ; index++) {
      AliPHOSEmcRecPoint * rp = (AliPHOSEmcRecPoint * )emcRecPoints->At(index) ; 
      TVector3  locpos;  
      rp->GetLocalPosition(locpos);
      Float_t lambda[2]; 
      rp->GetElipsAxis(lambda);
      Int_t * primaries; 
      Int_t nprimaries;
      primaries = rp->GetPrimaries(nprimaries);
      printf("\n%6d  %8.2f  %3d     %2d     %4.1f   %4.1f   %4.1f   %4f  %4f    %2d     : ", 
	      rp->GetIndexInList(), rp->GetEnergy(), rp->GetMultiplicity(), rp->GetPHOSMod(), 
	      locpos.X(), locpos.Y(), locpos.Z(), lambda[0], lambda[1], nprimaries) ; 
      
      for (Int_t iprimary=0; iprimary<nprimaries; iprimary++) {
	printf("%d ", primaries[iprimary] ) ; 
      }
      printf("\n") ;
    }

    //Now plot CPV recPoints
    printf("\n CPV clusters \n") ;
    printf("Index    Ene(MeV) Module     X     Y    Z  \n") ;      
    for (index = 0 ; index < cpvRecPoints->GetEntries() ; index++) {
      AliPHOSCpvRecPoint * rp = (AliPHOSCpvRecPoint * )cpvRecPoints->At(index) ; 
      
      TVector3  locpos;  
      rp->GetLocalPosition(locpos);
      
      printf("\n%6d  %8.2f  %2d     %4.1f    %4.1f %4.1f \n", 
	     rp->GetIndexInList(), rp->GetEnergy(), rp->GetPHOSMod(), 
	     locpos.X(), locpos.Y(), locpos.Z()) ; 
    }
  }
}