[u/mrichter/AliRoot.git] / PHOS / AliPHOSRawDigiProducer.cxx

/**************************************************************************
 * Copyright(c) 2007, 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.                  *
 **************************************************************************/

/* $Id$ */

//This class produces PHOS digits of one event
//using AliPHOSRawFitter. 
//
//   For example:
//   TClonesArray *digits = new TClonesArray("AliPHOSDigit",100);
//   AliRawReader* rawReader = new AliRawReaderDate("2006run2211.raw");
//   AliPHOSRawDecoder dc(rawReader);
//   while (rawReader->NextEvent()) {
//     AliPHOSRawDigiProducer producer;
//     producer.MakeDigits(digits,&dc);
//   }

// Author: Boris Polichtchouk

// --- ROOT system ---
#include "TClonesArray.h"

// --- AliRoot header files ---
#include "AliPHOSRawDigiProducer.h"
#include "AliPHOSRawFitterv0.h"
#include "AliPHOSGeometry.h"
#include "AliPHOSDigit.h"
#include "AliPHOSCalibData.h"
#include "AliPHOSPulseGenerator.h"
#include "AliCaloRawStreamV3.h"
#include "AliLog.h"

ClassImp(AliPHOSRawDigiProducer)

AliPHOSCalibData * AliPHOSRawDigiProducer::fgCalibData  = 0 ; 

//--------------------------------------------------------------------------------------
AliPHOSRawDigiProducer::AliPHOSRawDigiProducer():
  TObject(),
  fEmcMinE(0.),
  fCpvMinE(0.),
  fSampleQualityCut(1.),
  fEmcCrystals(0),
  fGeom(0),
  fPulseGenerator(0),
  fRawReader(0),
  fRawStream(0)
{
  // Default constructor

  fGeom=AliPHOSGeometry::GetInstance() ;
  if(!fGeom) fGeom = AliPHOSGeometry::GetInstance("IHEP");

  fEmcCrystals=fGeom->GetNCristalsInModule()*fGeom->GetNModules() ;
  fPulseGenerator = new AliPHOSPulseGenerator();
  GetCalibrationParameters() ; 

}
//--------------------------------------------------------------------------------------
AliPHOSRawDigiProducer::AliPHOSRawDigiProducer(AliRawReader *rawReader,
					       AliAltroMapping **mapping):
  TObject(),
  fEmcMinE(0.),
  fCpvMinE(0.),
  fSampleQualityCut(1.),
  fEmcCrystals(0),
  fGeom(0),
  fPulseGenerator(0),
  fRawReader(rawReader),
  fRawStream(0)
{
  // Default constructor

  fGeom=AliPHOSGeometry::GetInstance() ;
  if(!fGeom) fGeom = AliPHOSGeometry::GetInstance("IHEP");

  fEmcCrystals=fGeom->GetNCristalsInModule()*fGeom->GetNModules() ;
  fPulseGenerator = new AliPHOSPulseGenerator();
  GetCalibrationParameters() ; 

  fRawStream = new AliCaloRawStreamV3(rawReader,"PHOS",mapping);

}
//--------------------------------------------------------------------------------------
AliPHOSRawDigiProducer::AliPHOSRawDigiProducer(const AliPHOSRawDigiProducer &dp):
  TObject(),
  fEmcMinE(0.),
  fCpvMinE(0.),
  fSampleQualityCut(1.),
  fEmcCrystals(0),
  fGeom(0),
  fPulseGenerator(0),
  fRawReader(0),
  fRawStream(0)
{                                                          
  // Copy constructor

  fEmcMinE = dp.fEmcMinE ;
  fCpvMinE = dp.fCpvMinE ;
  fSampleQualityCut = dp.fSampleQualityCut;
  fEmcCrystals = dp.fEmcCrystals ;
  fPulseGenerator = new AliPHOSPulseGenerator();
  fGeom = dp.fGeom ;
}
//--------------------------------------------------------------------------------------
AliPHOSRawDigiProducer& AliPHOSRawDigiProducer::operator= (const AliPHOSRawDigiProducer &dp)
{
  // Assign operator

  if(&dp == this) return *this;

  fEmcMinE = dp.fEmcMinE ;
  fCpvMinE = dp.fCpvMinE ;
  fSampleQualityCut = dp.fSampleQualityCut ;
  fEmcCrystals = dp.fEmcCrystals ;
  fGeom = dp.fGeom ;
  if(fPulseGenerator) delete fPulseGenerator ;
  fPulseGenerator = new AliPHOSPulseGenerator();
  return  *this;
} 
//--------------------------------------------------------------------------------------
AliPHOSRawDigiProducer::~AliPHOSRawDigiProducer()
{
  // Destructor
  if(fPulseGenerator) delete fPulseGenerator ;
  fPulseGenerator=0 ;
  delete fRawStream;
}
//--------------------------------------------------------------------------------------
void AliPHOSRawDigiProducer::MakeDigits(TClonesArray *digits, AliPHOSRawFitterv0* fitter) 
{
  //Makes the job.
  //TClonesArray *digits and raw data fitter should be provided by calling function.

  digits->Clear();
 
  Int_t iDigit=0 ;
  Int_t relId[4], absId=-1, caloFlag=-1;
  
  const Double_t baseLine=1. ; //Minimal energy of digit in ADC ch. 
  
  //Temporary array for LowGain digits
  TClonesArray tmpLG("AliPHOSDigit",10000) ;
  Int_t ilgDigit=0 ;

  //Let fitter subtract pedestals in case of ZS
  fitter->SetCalibData(fgCalibData) ;
  
  while (fRawStream->NextDDL()) {
    while (fRawStream->NextChannel()) {
      relId[0] = fRawStream->GetModule() + 1; // counts from 1 to 5
      relId[1] = 0;
      relId[2] = fRawStream->GetCellX()  + 1; // counts from 1 to 64
      relId[3] = fRawStream->GetCellZ()  + 1; // counts from 1 to 56
      caloFlag = fRawStream->GetCaloFlag();   // 0=LG, 1=HG, 2=TRU
      
      if(caloFlag!=0 && caloFlag!=1) continue; //TRU data!
      
      if(fitter->GetAmpOffset()==0 && fitter->GetAmpThreshold()==0) {
	short value = fRawStream->GetAltroCFG1();
	bool ZeroSuppressionEnabled = (value >> 15) & 0x1;
	if(ZeroSuppressionEnabled) {
	  short offset = (value >> 10) & 0xf;
	  short threshold = value & 0x3ff;
	  fitter->SubtractPedestals(kFALSE);
	  fitter->SetAmpOffset(offset);
	  fitter->SetAmpThreshold(threshold);
	}
      }
      
      fGeom->RelToAbsNumbering(relId, absId);
      
      Int_t nBunches = 0;
      while (fRawStream->NextBunch()) {
	nBunches++;
	if (nBunches > 1) continue;
	const UShort_t *sig = fRawStream->GetSignals();
	Int_t sigStart  = fRawStream->GetStartTimeBin();
	Int_t sigLength = fRawStream->GetBunchLength();
	fitter->SetChannelGeo(relId[0],relId[2],relId[3],caloFlag);
	fitter->Eval(sig,sigStart,sigLength);
      } // End of NextBunch()

      fitter->SetNBunches(nBunches);
      
      Double_t energy = fitter->GetEnergy() ; 
      Double_t time   = fitter->GetTime() ;
      if(energy<=baseLine) //in ADC channels
	continue ;

      //remove digits with bad shape. Fitter should calculate quality so that 
      //in default case quality [0,1], while larger values of quality mean somehow 
      //corrupted samples, 999 means obviously corrupted sample.
      //It is difficult to fit samples with overflow (even setting cut on overflow values)
      //because too few points are left to fit. So we do not evaluate samples with overflow

      if(fitter->GetSignalQuality() > fSampleQualityCut && !(fitter->IsOverflow()))
	continue ;
      
//       energy = CalibrateE(energy,relId,lowGainFlag) ;
//       time   = CalibrateT(time,relId,lowGainFlag) ;
      
      if(energy <= 0.) 
	continue;
      
      if (caloFlag == AliCaloRawStreamV3::kLowGain) {
	new(tmpLG[ilgDigit]) AliPHOSDigit(-1,absId,(Float_t)energy,(Float_t)time);
	ilgDigit++ ; 
      }
      else if (caloFlag == AliCaloRawStreamV3::kHighGain) {
	if(fitter->IsOverflow()) //Keep this digit to replace it by Low Gain later.
	  //If there is no LogGain it wil be removed by cut on Min E
	  new((*digits)[iDigit]) AliPHOSDigit(-1,absId,-1.f,(Float_t)time);
	else
	  new((*digits)[iDigit]) AliPHOSDigit(-1,absId,(Float_t)energy,(Float_t)time);
	iDigit++;
      }
    } // End of NextChannel()

    //Now scan created LG and HG digits and keep only those which appeared in both lists 
    //replace energy of HighGain digits only if there is overflow
    //negative energy (overflow)
    digits->Sort() ;
    tmpLG.Sort() ;
    Int_t iLG = 0;
    Int_t nLG1 = tmpLG.GetEntriesFast()-1 ;
    
    for(Int_t iDig=0 ; iDig < digits->GetEntriesFast() ; iDig++) { 
      AliPHOSDigit * digHG = dynamic_cast<AliPHOSDigit*>(digits->At(iDig)) ;
      if (!digHG) continue;
      AliPHOSDigit * digLG = dynamic_cast<AliPHOSDigit*>(tmpLG.At(iLG)) ;
      while(digLG && iLG<nLG1 && digHG->GetId()> digLG->GetId()){
	iLG++ ;
	digLG = dynamic_cast<AliPHOSDigit*>(tmpLG.At(iLG)) ;
      }
      absId=digHG->GetId() ;
      fGeom->AbsToRelNumbering(absId,relId) ;
 
      if(digLG && digHG->GetId() == digLG->GetId()){ //we found pair
	if(digHG->GetEnergy()<0.){ //This is overflow in HG
	  digHG->SetTime(digLG->GetTime()) ;
	  digHG->SetEnergy(digLG->GetEnergy()) ;
	}
      }
      else{ //no pair - remove
	if(digHG->GetEnergy()<0.) //no pair, in saturation
	  digits->RemoveAt(iDig) ;                                                          
      }
    }
  } // End of NextDDL()

  CleanDigits(digits) ;
  
}
//____________________________________________________________________________
Double_t AliPHOSRawDigiProducer::CalibrateE(Double_t amp, Int_t* relId, Bool_t isLowGain)
{
  // Convert EMC LG amplitude to HG (multipli by ~16)
  // Calibration parameters are taken from calibration data base 
  if(fgCalibData){ 
    Int_t   module = relId[0];  
    Int_t   column = relId[3];
    Int_t   row    = relId[2];
    if(relId[1]==0) { // this is EMC 
      if(isLowGain){
        amp*= fgCalibData->GetHighLowRatioEmc(module,column,row);
      }
      return amp ;         
    }         
  }          
  return 0;        
}
//____________________________________________________________________________
Double_t AliPHOSRawDigiProducer::CalibrateT(Double_t time, Int_t * relId, Bool_t /* isLowGain */)
{
  //Calibrate time
  time*=fPulseGenerator->GetRawFormatTimeTrigger() ;
  if(fgCalibData){
    Int_t   module = relId[0];
    Int_t   column = relId[3];
    Int_t   row    = relId[2];
    if(relId[1]==0) { // this is EMC
      time += fgCalibData->GetTimeShiftEmc(module,column,row);                   
      return time ;             
    }
  }
 
  return -999.;
}
//____________________________________________________________________________
void AliPHOSRawDigiProducer::CleanDigits(TClonesArray * digits)
{
  // remove digits with amplitudes below threshold.
  // remove digits in bad channels
  // sort digits with icreasing AbsId
  
  //remove digits in bad map and below threshold
  Bool_t isBadMap = 0 ;
  if(fgCalibData->GetNumOfEmcBadChannels()){
    isBadMap=1 ;
  }
  
  for(Int_t i=0; i<digits->GetEntriesFast(); i++){
    AliPHOSDigit * digit = static_cast<AliPHOSDigit*>(digits->At(i)) ;
    if(!digit)
      continue  ;
    if ( (IsInEMC(digit) && digit->GetEnergy() < fEmcMinE) ||
	 (IsInCPV(digit) && digit->GetEnergy() < fCpvMinE) ){
      digits->RemoveAt(i) ;
      continue ;
    }
    if(isBadMap){ //check bad map now
      Int_t relid[4] ;
      fGeom->AbsToRelNumbering(digit->GetId(), relid) ; 
      if(fgCalibData->IsBadChannelEmc(relid[0],relid[3],relid[2])){
	digits->RemoveAt(i) ;
      }
    }
  }

  //Compress, sort and set indexes
  digits->Compress() ;
//  digits->Sort(); already sorted earlier
  for (Int_t i = 0 ; i < digits->GetEntriesFast() ; i++) { 
    AliPHOSDigit *digit = static_cast<AliPHOSDigit*>( digits->At(i) ) ; 
    digit->SetIndexInList(i) ;     
  }
}
//____________________________________________________________________________
Bool_t AliPHOSRawDigiProducer::IsInEMC(AliPHOSDigit * digit) const
{
  // Tells if (true) or not (false) the digit is in a PHOS-EMC module
  return digit->GetId() <= fEmcCrystals ;

}

//____________________________________________________________________________
Bool_t AliPHOSRawDigiProducer::IsInCPV(AliPHOSDigit * digit) const
{
  // Tells if (true) or not (false) the digit is in a PHOS-CPV module
  return digit->GetId() > fEmcCrystals ;
}
//____________________________________________________________________________
void AliPHOSRawDigiProducer::GetCalibrationParameters() 
{
  // Set calibration parameters:
  // if calibration database exists, they are read from database,
  // otherwise, reconstruction stops in the constructor of AliPHOSCalibData
  //
  // It is a user responsilibity to open CDB before reconstruction, for example: 
  // AliCDBStorage* storage = AliCDBManager::Instance()->GetStorage("local://CalibDB");

  if (!fgCalibData){
    fgCalibData = new AliPHOSCalibData(-1); //use AliCDBManager's run number
  }
  if (fgCalibData->GetCalibDataEmc() == 0)
    AliFatal("Calibration parameters for PHOS EMC not found. Stop reconstruction.\n");
  if (fgCalibData->GetCalibDataCpv() == 0)
    AliFatal("Calibration parameters for PHOS CPV not found. Stop reconstruction.\n");
}
Commit	Line	Data
7bc140a5	1	/**************************************************************************
	2	* Copyright(c) 2007, 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
	16	/* $Id$ */
	17
	18	//This class produces PHOS digits of one event
379c5c09	19	//using AliPHOSRawFitter.
7bc140a5	20	//
	21	// For example:
	22	// TClonesArray *digits = new TClonesArray("AliPHOSDigit",100);
	23	// AliRawReader* rawReader = new AliRawReaderDate("2006run2211.raw");
	24	// AliPHOSRawDecoder dc(rawReader);
	25	// while (rawReader->NextEvent()) {
	26	// AliPHOSRawDigiProducer producer;
	27	// producer.MakeDigits(digits,&dc);
	28	// }
	29
	30	// Author: Boris Polichtchouk
	31
	32	// --- ROOT system ---
88fb5e50	33	#include "TClonesArray.h"
88fb5e50	34
7bc140a5	35	// --- AliRoot header files ---
88fb5e50	36	#include "AliPHOSRawDigiProducer.h"
379c5c09	37	#include "AliPHOSRawFitterv0.h"
88fb5e50	38	#include "AliPHOSGeometry.h"
88fb5e50	39	#include "AliPHOSDigit.h"
c0394bfb	40	#include "AliPHOSCalibData.h"
39569d36	41	#include "AliPHOSPulseGenerator.h"
379c5c09	42	#include "AliCaloRawStreamV3.h"
c0394bfb	43	#include "AliLog.h"
88fb5e50	44
	45	ClassImp(AliPHOSRawDigiProducer)
	46
c0394bfb	47	AliPHOSCalibData * AliPHOSRawDigiProducer::fgCalibData = 0 ;
	48
	49	//--------------------------------------------------------------------------------------
7e88424f	50	AliPHOSRawDigiProducer::AliPHOSRawDigiProducer():
	51	TObject(),
	52	fEmcMinE(0.),
	53	fCpvMinE(0.),
	54	fSampleQualityCut(1.),
	55	fEmcCrystals(0),
	56	fGeom(0),
379c5c09	57	fPulseGenerator(0),
	58	fRawReader(0),
	59	fRawStream(0)
7e88424f	60	{
7e88424f	61	// Default constructor
70d93620	62
c0394bfb	63	fGeom=AliPHOSGeometry::GetInstance() ;
	64	if(!fGeom) fGeom = AliPHOSGeometry::GetInstance("IHEP");
	65
	66	fEmcCrystals=fGeom->GetNCristalsInModule()*fGeom->GetNModules() ;
39569d36	67	fPulseGenerator = new AliPHOSPulseGenerator();
c0394bfb	68	GetCalibrationParameters() ;
8be3a30a	69
c0394bfb	70	}
379c5c09	71	//--------------------------------------------------------------------------------------
	72	AliPHOSRawDigiProducer::AliPHOSRawDigiProducer(AliRawReader *rawReader,
	73	AliAltroMapping **mapping):
	74	TObject(),
	75	fEmcMinE(0.),
	76	fCpvMinE(0.),
	77	fSampleQualityCut(1.),
	78	fEmcCrystals(0),
	79	fGeom(0),
	80	fPulseGenerator(0),
	81	fRawReader(rawReader),
	82	fRawStream(0)
	83	{
	84	// Default constructor
	85
	86	fGeom=AliPHOSGeometry::GetInstance() ;
	87	if(!fGeom) fGeom = AliPHOSGeometry::GetInstance("IHEP");
	88
	89	fEmcCrystals=fGeom->GetNCristalsInModule()*fGeom->GetNModules() ;
	90	fPulseGenerator = new AliPHOSPulseGenerator();
	91	GetCalibrationParameters() ;
	92
	93	fRawStream = new AliCaloRawStreamV3(rawReader,"PHOS",mapping);
	94
	95	}
	96	//--------------------------------------------------------------------------------------
7e88424f	97	AliPHOSRawDigiProducer::AliPHOSRawDigiProducer(const AliPHOSRawDigiProducer &dp):
	98	TObject(),
	99	fEmcMinE(0.),
	100	fCpvMinE(0.),
	101	fSampleQualityCut(1.),
	102	fEmcCrystals(0),
	103	fGeom(0),
379c5c09	104	fPulseGenerator(0),
	105	fRawReader(0),
	106	fRawStream(0)
7e88424f	107	{
7e88424f	108	// Copy constructor
c0394bfb	109
	110	fEmcMinE = dp.fEmcMinE ;
	111	fCpvMinE = dp.fCpvMinE ;
f78c9781	112	fSampleQualityCut = dp.fSampleQualityCut;
c0394bfb	113	fEmcCrystals = dp.fEmcCrystals ;
39569d36	114	fPulseGenerator = new AliPHOSPulseGenerator();
c0394bfb	115	fGeom = dp.fGeom ;
	116	}
	117	//--------------------------------------------------------------------------------------
7e88424f	118	AliPHOSRawDigiProducer& AliPHOSRawDigiProducer::operator= (const AliPHOSRawDigiProducer &dp)
	119	{
	120	// Assign operator
	121
c0394bfb	122	if(&dp == this) return *this;
	123
	124	fEmcMinE = dp.fEmcMinE ;
	125	fCpvMinE = dp.fCpvMinE ;
70d93620	126	fSampleQualityCut = dp.fSampleQualityCut ;
c0394bfb	127	fEmcCrystals = dp.fEmcCrystals ;
c0394bfb	128	fGeom = dp.fGeom ;
39569d36	129	if(fPulseGenerator) delete fPulseGenerator ;
39569d36	130	fPulseGenerator = new AliPHOSPulseGenerator();
c0394bfb	131	return *this;
c0394bfb	132	}
379c5c09	133	//--------------------------------------------------------------------------------------
7e88424f	134	AliPHOSRawDigiProducer::~AliPHOSRawDigiProducer()
7e88424f	135	{
379c5c09	136	// Destructor
7e88424f	137	if(fPulseGenerator) delete fPulseGenerator ;
7e88424f	138	fPulseGenerator=0 ;
379c5c09	139	delete fRawStream;
39569d36	140	}
7bc140a5	141	//--------------------------------------------------------------------------------------
379c5c09	142	void AliPHOSRawDigiProducer::MakeDigits(TClonesArray digits, AliPHOSRawFitterv0 fitter)
88fb5e50	143	{
7bc140a5	144	//Makes the job.
379c5c09	145	//TClonesArray *digits and raw data fitter should be provided by calling function.
7bc140a5	146
88fb5e50	147	digits->Clear();
88fb5e50	148
379c5c09	149	Int_t iDigit=0 ;
379c5c09	150	Int_t relId[4], absId=-1, caloFlag=-1;
fdd91c5a	151
c0394bfb	152	const Double_t baseLine=1. ; //Minimal energy of digit in ADC ch.
fdd91c5a	153
c0394bfb	154	//Temporary array for LowGain digits
	155	TClonesArray tmpLG("AliPHOSDigit",10000) ;
	156	Int_t ilgDigit=0 ;
bafc1087	157
379c5c09	158	//Let fitter subtract pedestals in case of ZS
379c5c09	159	fitter->SetCalibData(fgCalibData) ;
c0394bfb	160
379c5c09	161	while (fRawStream->NextDDL()) {
379c5c09	162	while (fRawStream->NextChannel()) {
1281504a	163	relId[0] = fRawStream->GetModule() + 1; // counts from 1 to 5
379c5c09	164	relId[1] = 0;
1281504a	165	relId[2] = fRawStream->GetCellX() + 1; // counts from 1 to 64
	166	relId[3] = fRawStream->GetCellZ() + 1; // counts from 1 to 56
	167	caloFlag = fRawStream->GetCaloFlag(); // 0=LG, 1=HG, 2=TRU
f4ca5622	168
	169	if(caloFlag!=0 && caloFlag!=1) continue; //TRU data!
	170
c4dad9d2	171	if(fitter->GetAmpOffset()==0 && fitter->GetAmpThreshold()==0) {
	172	short value = fRawStream->GetAltroCFG1();
	173	bool ZeroSuppressionEnabled = (value >> 15) & 0x1;
	174	if(ZeroSuppressionEnabled) {
	175	short offset = (value >> 10) & 0xf;
	176	short threshold = value & 0x3ff;
	177	fitter->SubtractPedestals(kFALSE);
	178	fitter->SetAmpOffset(offset);
	179	fitter->SetAmpThreshold(threshold);
	180	}
	181	}
	182
379c5c09	183	fGeom->RelToAbsNumbering(relId, absId);
f4ca5622	184
379c5c09	185	Int_t nBunches = 0;
	186	while (fRawStream->NextBunch()) {
	187	nBunches++;
	188	if (nBunches > 1) continue;
	189	const UShort_t *sig = fRawStream->GetSignals();
	190	Int_t sigStart = fRawStream->GetStartTimeBin();
	191	Int_t sigLength = fRawStream->GetBunchLength();
92236b27	192	fitter->SetChannelGeo(relId[0],relId[2],relId[3],caloFlag);
92236b27	193	fitter->Eval(sig,sigStart,sigLength);
379c5c09	194	} // End of NextBunch()
70d93620	195
379c5c09	196	fitter->SetNBunches(nBunches);
379c5c09	197
	198	Double_t energy = fitter->GetEnergy() ;
	199	Double_t time = fitter->GetTime() ;
	200	if(energy<=baseLine) //in ADC channels
	201	continue ;
88fb5e50	202
379c5c09	203	//remove digits with bad shape. Fitter should calculate quality so that
	204	//in default case quality [0,1], while larger values of quality mean somehow
	205	//corrupted samples, 999 means obviously corrupted sample.
	206	//It is difficult to fit samples with overflow (even setting cut on overflow values)
	207	//because too few points are left to fit. So we do not evaluate samples with overflow
c0394bfb	208
379c5c09	209	if(fitter->GetSignalQuality() > fSampleQualityCut && !(fitter->IsOverflow()))
	210	continue ;
	211
	212	// energy = CalibrateE(energy,relId,lowGainFlag) ;
	213	// time = CalibrateT(time,relId,lowGainFlag) ;
	214
	215	if(energy <= 0.)
	216	continue;
	217
	218	if (caloFlag == AliCaloRawStreamV3::kLowGain) {
	219	new(tmpLG[ilgDigit]) AliPHOSDigit(-1,absId,(Float_t)energy,(Float_t)time);
	220	ilgDigit++ ;
	221	}
	222	else if (caloFlag == AliCaloRawStreamV3::kHighGain) {
	223	if(fitter->IsOverflow()) //Keep this digit to replace it by Low Gain later.
	224	//If there is no LogGain it wil be removed by cut on Min E
	225	new((*digits)[iDigit]) AliPHOSDigit(-1,absId,-1.f,(Float_t)time);
	226	else
	227	new((*digits)[iDigit]) AliPHOSDigit(-1,absId,(Float_t)energy,(Float_t)time);
	228	iDigit++;
	229	}
	230	} // End of NextChannel()
c0394bfb	231
379c5c09	232	//Now scan created LG and HG digits and keep only those which appeared in both lists
	233	//replace energy of HighGain digits only if there is overflow
	234	//negative energy (overflow)
	235	digits->Sort() ;
	236	tmpLG.Sort() ;
	237	Int_t iLG = 0;
	238	Int_t nLG1 = tmpLG.GetEntriesFast()-1 ;
	239
	240	for(Int_t iDig=0 ; iDig < digits->GetEntriesFast() ; iDig++) {
	241	AliPHOSDigit * digHG = dynamic_cast<AliPHOSDigit*>(digits->At(iDig)) ;
	242	if (!digHG) continue;
	243	AliPHOSDigit * digLG = dynamic_cast<AliPHOSDigit*>(tmpLG.At(iLG)) ;
	244	while(digLG && iLG<nLG1 && digHG->GetId()> digLG->GetId()){
	245	iLG++ ;
	246	digLG = dynamic_cast<AliPHOSDigit*>(tmpLG.At(iLG)) ;
	247	}
	248	absId=digHG->GetId() ;
	249	fGeom->AbsToRelNumbering(absId,relId) ;
a7c985dc	250
379c5c09	251	if(digLG && digHG->GetId() == digLG->GetId()){ //we found pair
	252	if(digHG->GetEnergy()<0.){ //This is overflow in HG
	253	digHG->SetTime(digLG->GetTime()) ;
	254	digHG->SetEnergy(digLG->GetEnergy()) ;
	255	}
379c5c09	256	}
379c5c09	257	else{ //no pair - remove
fdd91c5a	258	if(digHG->GetEnergy()<0.) //no pair, in saturation
fdd91c5a	259	digits->RemoveAt(iDig) ;
88fb5e50	260	}
88fb5e50	261	}
379c5c09	262	} // End of NextDDL()
c0394bfb	263
c0394bfb	264	CleanDigits(digits) ;
379c5c09	265
c0394bfb	266	}
	267	//____________________________________________________________________________
	268	Double_t AliPHOSRawDigiProducer::CalibrateE(Double_t amp, Int_t* relId, Bool_t isLowGain)
	269	{
634d2178	270	// Convert EMC LG amplitude to HG (multipli by ~16)
634d2178	271	// Calibration parameters are taken from calibration data base
c0394bfb	272	if(fgCalibData){
	273	Int_t module = relId[0];
	274	Int_t column = relId[3];
	275	Int_t row = relId[2];
	276	if(relId[1]==0) { // this is EMC
	277	if(isLowGain){
	278	amp*= fgCalibData->GetHighLowRatioEmc(module,column,row);
88fb5e50	279	}
c0394bfb	280	return amp ;
	281	}
	282	}
	283	return 0;
	284	}
	285	//____________________________________________________________________________
	286	Double_t AliPHOSRawDigiProducer::CalibrateT(Double_t time, Int_t * relId, Bool_t /* isLowGain */)
	287	{
	288	//Calibrate time
39569d36	289	time*=fPulseGenerator->GetRawFormatTimeTrigger() ;
c0394bfb	290	if(fgCalibData){
	291	Int_t module = relId[0];
	292	Int_t column = relId[3];
	293	Int_t row = relId[2];
	294	if(relId[1]==0) { // this is EMC
	295	time += fgCalibData->GetTimeShiftEmc(module,column,row);
	296	return time ;
	297	}
	298	}
	299
	300	return -999.;
	301	}
	302	//____________________________________________________________________________
	303	void AliPHOSRawDigiProducer::CleanDigits(TClonesArray * digits)
	304	{
	305	// remove digits with amplitudes below threshold.
	306	// remove digits in bad channels
	307	// sort digits with icreasing AbsId
	308
	309	//remove digits in bad map and below threshold
	310	Bool_t isBadMap = 0 ;
	311	if(fgCalibData->GetNumOfEmcBadChannels()){
	312	isBadMap=1 ;
	313	}
	314
	315	for(Int_t i=0; i<digits->GetEntriesFast(); i++){
	316	AliPHOSDigit * digit = static_cast<AliPHOSDigit*>(digits->At(i)) ;
	317	if(!digit)
	318	continue ;
	319	if ( (IsInEMC(digit) && digit->GetEnergy() < fEmcMinE) \|\|
	320	(IsInCPV(digit) && digit->GetEnergy() < fCpvMinE) ){
	321	digits->RemoveAt(i) ;
	322	continue ;
	323	}
	324	if(isBadMap){ //check bad map now
	325	Int_t relid[4] ;
	326	fGeom->AbsToRelNumbering(digit->GetId(), relid) ;
a65517aa	327	if(fgCalibData->IsBadChannelEmc(relid[0],relid[3],relid[2])){
c0394bfb	328	digits->RemoveAt(i) ;
88fb5e50	329	}
88fb5e50	330	}
88fb5e50	331	}
88fb5e50	332
c0394bfb	333	//Compress, sort and set indexes
	334	digits->Compress() ;
	335	// digits->Sort(); already sorted earlier
	336	for (Int_t i = 0 ; i < digits->GetEntriesFast() ; i++) {
	337	AliPHOSDigit digit = static_cast<AliPHOSDigit>( digits->At(i) ) ;
	338	digit->SetIndexInList(i) ;
	339	}
	340	}
	341	//____________________________________________________________________________
	342	Bool_t AliPHOSRawDigiProducer::IsInEMC(AliPHOSDigit * digit) const
	343	{
	344	// Tells if (true) or not (false) the digit is in a PHOS-EMC module
	345	return digit->GetId() <= fEmcCrystals ;
	346
	347	}
	348
	349	//____________________________________________________________________________
	350	Bool_t AliPHOSRawDigiProducer::IsInCPV(AliPHOSDigit * digit) const
	351	{
	352	// Tells if (true) or not (false) the digit is in a PHOS-CPV module
	353	return digit->GetId() > fEmcCrystals ;
	354	}
	355	//____________________________________________________________________________
	356	void AliPHOSRawDigiProducer::GetCalibrationParameters()
	357	{
	358	// Set calibration parameters:
	359	// if calibration database exists, they are read from database,
	360	// otherwise, reconstruction stops in the constructor of AliPHOSCalibData
	361	//
	362	// It is a user responsilibity to open CDB before reconstruction, for example:
	363	// AliCDBStorage* storage = AliCDBManager::Instance()->GetStorage("local://CalibDB");
	364
	365	if (!fgCalibData){
	366	fgCalibData = new AliPHOSCalibData(-1); //use AliCDBManager's run number
	367	}
	368	if (fgCalibData->GetCalibDataEmc() == 0)
	369	AliFatal("Calibration parameters for PHOS EMC not found. Stop reconstruction.\n");
	370	if (fgCalibData->GetCalibDataCpv() == 0)
	371	AliFatal("Calibration parameters for PHOS CPV not found. Stop reconstruction.\n");
88fb5e50	372	}