[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.),
  fSampleToSec(0.),
  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.),
  fSampleToSec(0.),
  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.),
  fSampleToSec(0.),
  fEmcCrystals(0),
  fGeom(0),
  fPulseGenerator(0),
  fRawReader(0),
  fRawStream(0)
{                                                          
  // Copy constructor

  fEmcMinE = dp.fEmcMinE ;
  fCpvMinE = dp.fCpvMinE ;
  fSampleQualityCut = dp.fSampleQualityCut;
  fSampleToSec = dp.fSampleToSec ;
  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 ;
  fSampleToSec = dp.fSampleToSec ;
  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. 

  //Calculate conversion coeff. from Sample time step to seconds
  //If OCDB contains negative or zero value - use one from RCU trailer
  //Negative value in OCDB is used only for simulation of raw digits
  if(fgCalibData->GetSampleTimeStep()>0.)
    fSampleToSec=fgCalibData->GetSampleTimeStep() ;
  else
    fSampleToSec=fRawStream->GetTSample() ;
  
  //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] = 5 - fRawStream->GetModule() ; // 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!
      
      fitter->SetChannelGeo(relId[0],relId[2],relId[3],caloFlag);

      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->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) ;

      //convert time from sample bin units to s
      time*=fSampleToSec ;
      
      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.),
6f47f50d	55	fSampleToSec(0.),
7e88424f	56	fEmcCrystals(0),
7e88424f	57	fGeom(0),
379c5c09	58	fPulseGenerator(0),
	59	fRawReader(0),
	60	fRawStream(0)
7e88424f	61	{
7e88424f	62	// Default constructor
70d93620	63
c0394bfb	64	fGeom=AliPHOSGeometry::GetInstance() ;
	65	if(!fGeom) fGeom = AliPHOSGeometry::GetInstance("IHEP");
	66
	67	fEmcCrystals=fGeom->GetNCristalsInModule()*fGeom->GetNModules() ;
39569d36	68	fPulseGenerator = new AliPHOSPulseGenerator();
c0394bfb	69	GetCalibrationParameters() ;
8be3a30a	70
c0394bfb	71	}
379c5c09	72	//--------------------------------------------------------------------------------------
	73	AliPHOSRawDigiProducer::AliPHOSRawDigiProducer(AliRawReader *rawReader,
	74	AliAltroMapping **mapping):
	75	TObject(),
	76	fEmcMinE(0.),
	77	fCpvMinE(0.),
	78	fSampleQualityCut(1.),
6f47f50d	79	fSampleToSec(0.),
379c5c09	80	fEmcCrystals(0),
	81	fGeom(0),
	82	fPulseGenerator(0),
	83	fRawReader(rawReader),
	84	fRawStream(0)
	85	{
	86	// Default constructor
	87
	88	fGeom=AliPHOSGeometry::GetInstance() ;
	89	if(!fGeom) fGeom = AliPHOSGeometry::GetInstance("IHEP");
	90
	91	fEmcCrystals=fGeom->GetNCristalsInModule()*fGeom->GetNModules() ;
	92	fPulseGenerator = new AliPHOSPulseGenerator();
	93	GetCalibrationParameters() ;
	94
	95	fRawStream = new AliCaloRawStreamV3(rawReader,"PHOS",mapping);
	96
	97	}
	98	//--------------------------------------------------------------------------------------
7e88424f	99	AliPHOSRawDigiProducer::AliPHOSRawDigiProducer(const AliPHOSRawDigiProducer &dp):
	100	TObject(),
	101	fEmcMinE(0.),
	102	fCpvMinE(0.),
	103	fSampleQualityCut(1.),
6f47f50d	104	fSampleToSec(0.),
7e88424f	105	fEmcCrystals(0),
7e88424f	106	fGeom(0),
379c5c09	107	fPulseGenerator(0),
	108	fRawReader(0),
	109	fRawStream(0)
7e88424f	110	{
7e88424f	111	// Copy constructor
c0394bfb	112
	113	fEmcMinE = dp.fEmcMinE ;
	114	fCpvMinE = dp.fCpvMinE ;
f78c9781	115	fSampleQualityCut = dp.fSampleQualityCut;
6f47f50d	116	fSampleToSec = dp.fSampleToSec ;
c0394bfb	117	fEmcCrystals = dp.fEmcCrystals ;
39569d36	118	fPulseGenerator = new AliPHOSPulseGenerator();
c0394bfb	119	fGeom = dp.fGeom ;
	120	}
	121	//--------------------------------------------------------------------------------------
7e88424f	122	AliPHOSRawDigiProducer& AliPHOSRawDigiProducer::operator= (const AliPHOSRawDigiProducer &dp)
	123	{
	124	// Assign operator
	125
c0394bfb	126	if(&dp == this) return *this;
	127
	128	fEmcMinE = dp.fEmcMinE ;
	129	fCpvMinE = dp.fCpvMinE ;
70d93620	130	fSampleQualityCut = dp.fSampleQualityCut ;
6f47f50d	131	fSampleToSec = dp.fSampleToSec ;
c0394bfb	132	fEmcCrystals = dp.fEmcCrystals ;
c0394bfb	133	fGeom = dp.fGeom ;
39569d36	134	if(fPulseGenerator) delete fPulseGenerator ;
39569d36	135	fPulseGenerator = new AliPHOSPulseGenerator();
c0394bfb	136	return *this;
c0394bfb	137	}
379c5c09	138	//--------------------------------------------------------------------------------------
7e88424f	139	AliPHOSRawDigiProducer::~AliPHOSRawDigiProducer()
7e88424f	140	{
379c5c09	141	// Destructor
7e88424f	142	if(fPulseGenerator) delete fPulseGenerator ;
7e88424f	143	fPulseGenerator=0 ;
379c5c09	144	delete fRawStream;
39569d36	145	}
7bc140a5	146	//--------------------------------------------------------------------------------------
379c5c09	147	void AliPHOSRawDigiProducer::MakeDigits(TClonesArray digits, AliPHOSRawFitterv0 fitter)
88fb5e50	148	{
7bc140a5	149	//Makes the job.
379c5c09	150	//TClonesArray *digits and raw data fitter should be provided by calling function.
7bc140a5	151
88fb5e50	152	digits->Clear();
88fb5e50	153
379c5c09	154	Int_t iDigit=0 ;
379c5c09	155	Int_t relId[4], absId=-1, caloFlag=-1;
fdd91c5a	156
c0394bfb	157	const Double_t baseLine=1. ; //Minimal energy of digit in ADC ch.
6f47f50d	158
	159	//Calculate conversion coeff. from Sample time step to seconds
	160	//If OCDB contains negative or zero value - use one from RCU trailer
	161	//Negative value in OCDB is used only for simulation of raw digits
	162	if(fgCalibData->GetSampleTimeStep()>0.)
	163	fSampleToSec=fgCalibData->GetSampleTimeStep() ;
	164	else
	165	fSampleToSec=fRawStream->GetTSample() ;
fdd91c5a	166
c0394bfb	167	//Temporary array for LowGain digits
	168	TClonesArray tmpLG("AliPHOSDigit",10000) ;
	169	Int_t ilgDigit=0 ;
bafc1087	170
379c5c09	171	//Let fitter subtract pedestals in case of ZS
379c5c09	172	fitter->SetCalibData(fgCalibData) ;
c0394bfb	173
379c5c09	174	while (fRawStream->NextDDL()) {
379c5c09	175	while (fRawStream->NextChannel()) {
fc44a661	176	relId[0] = 5 - fRawStream->GetModule() ; // counts from 1 to 5
379c5c09	177	relId[1] = 0;
1281504a	178	relId[2] = fRawStream->GetCellX() + 1; // counts from 1 to 64
	179	relId[3] = fRawStream->GetCellZ() + 1; // counts from 1 to 56
	180	caloFlag = fRawStream->GetCaloFlag(); // 0=LG, 1=HG, 2=TRU
f4ca5622	181
	182	if(caloFlag!=0 && caloFlag!=1) continue; //TRU data!
	183
e10f780e	184	fitter->SetChannelGeo(relId[0],relId[2],relId[3],caloFlag);
fc44a661	185
c4dad9d2	186	if(fitter->GetAmpOffset()==0 && fitter->GetAmpThreshold()==0) {
	187	short value = fRawStream->GetAltroCFG1();
	188	bool ZeroSuppressionEnabled = (value >> 15) & 0x1;
	189	if(ZeroSuppressionEnabled) {
	190	short offset = (value >> 10) & 0xf;
	191	short threshold = value & 0x3ff;
	192	fitter->SubtractPedestals(kFALSE);
	193	fitter->SetAmpOffset(offset);
	194	fitter->SetAmpThreshold(threshold);
	195	}
	196	}
	197
379c5c09	198	fGeom->RelToAbsNumbering(relId, absId);
f4ca5622	199
379c5c09	200	Int_t nBunches = 0;
	201	while (fRawStream->NextBunch()) {
	202	nBunches++;
	203	if (nBunches > 1) continue;
	204	const UShort_t *sig = fRawStream->GetSignals();
	205	Int_t sigStart = fRawStream->GetStartTimeBin();
	206	Int_t sigLength = fRawStream->GetBunchLength();
92236b27	207	fitter->Eval(sig,sigStart,sigLength);
379c5c09	208	} // End of NextBunch()
70d93620	209
379c5c09	210	fitter->SetNBunches(nBunches);
379c5c09	211
	212	Double_t energy = fitter->GetEnergy() ;
	213	Double_t time = fitter->GetTime() ;
	214	if(energy<=baseLine) //in ADC channels
	215	continue ;
88fb5e50	216
379c5c09	217	//remove digits with bad shape. Fitter should calculate quality so that
	218	//in default case quality [0,1], while larger values of quality mean somehow
	219	//corrupted samples, 999 means obviously corrupted sample.
	220	//It is difficult to fit samples with overflow (even setting cut on overflow values)
	221	//because too few points are left to fit. So we do not evaluate samples with overflow
c0394bfb	222
379c5c09	223	if(fitter->GetSignalQuality() > fSampleQualityCut && !(fitter->IsOverflow()))
	224	continue ;
	225
	226	// energy = CalibrateE(energy,relId,lowGainFlag) ;
	227	// time = CalibrateT(time,relId,lowGainFlag) ;
6f47f50d	228
	229	//convert time from sample bin units to s
	230	time*=fSampleToSec ;
379c5c09	231
	232	if(energy <= 0.)
	233	continue;
	234
	235	if (caloFlag == AliCaloRawStreamV3::kLowGain) {
	236	new(tmpLG[ilgDigit]) AliPHOSDigit(-1,absId,(Float_t)energy,(Float_t)time);
	237	ilgDigit++ ;
	238	}
	239	else if (caloFlag == AliCaloRawStreamV3::kHighGain) {
	240	if(fitter->IsOverflow()) //Keep this digit to replace it by Low Gain later.
	241	//If there is no LogGain it wil be removed by cut on Min E
	242	new((*digits)[iDigit]) AliPHOSDigit(-1,absId,-1.f,(Float_t)time);
	243	else
	244	new((*digits)[iDigit]) AliPHOSDigit(-1,absId,(Float_t)energy,(Float_t)time);
	245	iDigit++;
	246	}
	247	} // End of NextChannel()
c0394bfb	248
379c5c09	249	//Now scan created LG and HG digits and keep only those which appeared in both lists
	250	//replace energy of HighGain digits only if there is overflow
	251	//negative energy (overflow)
	252	digits->Sort() ;
	253	tmpLG.Sort() ;
	254	Int_t iLG = 0;
	255	Int_t nLG1 = tmpLG.GetEntriesFast()-1 ;
	256
	257	for(Int_t iDig=0 ; iDig < digits->GetEntriesFast() ; iDig++) {
	258	AliPHOSDigit * digHG = dynamic_cast<AliPHOSDigit*>(digits->At(iDig)) ;
	259	if (!digHG) continue;
	260	AliPHOSDigit * digLG = dynamic_cast<AliPHOSDigit*>(tmpLG.At(iLG)) ;
	261	while(digLG && iLG<nLG1 && digHG->GetId()> digLG->GetId()){
	262	iLG++ ;
	263	digLG = dynamic_cast<AliPHOSDigit*>(tmpLG.At(iLG)) ;
	264	}
	265	absId=digHG->GetId() ;
	266	fGeom->AbsToRelNumbering(absId,relId) ;
a7c985dc	267
379c5c09	268	if(digLG && digHG->GetId() == digLG->GetId()){ //we found pair
	269	if(digHG->GetEnergy()<0.){ //This is overflow in HG
	270	digHG->SetTime(digLG->GetTime()) ;
	271	digHG->SetEnergy(digLG->GetEnergy()) ;
	272	}
379c5c09	273	}
379c5c09	274	else{ //no pair - remove
fdd91c5a	275	if(digHG->GetEnergy()<0.) //no pair, in saturation
fdd91c5a	276	digits->RemoveAt(iDig) ;
88fb5e50	277	}
88fb5e50	278	}
379c5c09	279	} // End of NextDDL()
c0394bfb	280
c0394bfb	281	CleanDigits(digits) ;
379c5c09	282
c0394bfb	283	}
	284	//____________________________________________________________________________
	285	Double_t AliPHOSRawDigiProducer::CalibrateE(Double_t amp, Int_t* relId, Bool_t isLowGain)
	286	{
634d2178	287	// Convert EMC LG amplitude to HG (multipli by ~16)
634d2178	288	// Calibration parameters are taken from calibration data base
c0394bfb	289	if(fgCalibData){
	290	Int_t module = relId[0];
	291	Int_t column = relId[3];
	292	Int_t row = relId[2];
	293	if(relId[1]==0) { // this is EMC
	294	if(isLowGain){
	295	amp*= fgCalibData->GetHighLowRatioEmc(module,column,row);
88fb5e50	296	}
c0394bfb	297	return amp ;
	298	}
	299	}
	300	return 0;
	301	}
	302	//____________________________________________________________________________
	303	Double_t AliPHOSRawDigiProducer::CalibrateT(Double_t time, Int_t * relId, Bool_t /* isLowGain */)
	304	{
	305	//Calibrate time
39569d36	306	time*=fPulseGenerator->GetRawFormatTimeTrigger() ;
c0394bfb	307	if(fgCalibData){
	308	Int_t module = relId[0];
	309	Int_t column = relId[3];
	310	Int_t row = relId[2];
	311	if(relId[1]==0) { // this is EMC
	312	time += fgCalibData->GetTimeShiftEmc(module,column,row);
	313	return time ;
	314	}
	315	}
	316
	317	return -999.;
	318	}
	319	//____________________________________________________________________________
	320	void AliPHOSRawDigiProducer::CleanDigits(TClonesArray * digits)
	321	{
	322	// remove digits with amplitudes below threshold.
	323	// remove digits in bad channels
	324	// sort digits with icreasing AbsId
	325
	326	//remove digits in bad map and below threshold
	327	Bool_t isBadMap = 0 ;
	328	if(fgCalibData->GetNumOfEmcBadChannels()){
	329	isBadMap=1 ;
	330	}
	331
	332	for(Int_t i=0; i<digits->GetEntriesFast(); i++){
	333	AliPHOSDigit * digit = static_cast<AliPHOSDigit*>(digits->At(i)) ;
	334	if(!digit)
	335	continue ;
	336	if ( (IsInEMC(digit) && digit->GetEnergy() < fEmcMinE) \|\|
	337	(IsInCPV(digit) && digit->GetEnergy() < fCpvMinE) ){
	338	digits->RemoveAt(i) ;
	339	continue ;
	340	}
	341	if(isBadMap){ //check bad map now
	342	Int_t relid[4] ;
	343	fGeom->AbsToRelNumbering(digit->GetId(), relid) ;
a65517aa	344	if(fgCalibData->IsBadChannelEmc(relid[0],relid[3],relid[2])){
c0394bfb	345	digits->RemoveAt(i) ;
88fb5e50	346	}
88fb5e50	347	}
88fb5e50	348	}
88fb5e50	349
c0394bfb	350	//Compress, sort and set indexes
	351	digits->Compress() ;
	352	// digits->Sort(); already sorted earlier
	353	for (Int_t i = 0 ; i < digits->GetEntriesFast() ; i++) {
	354	AliPHOSDigit digit = static_cast<AliPHOSDigit>( digits->At(i) ) ;
	355	digit->SetIndexInList(i) ;
	356	}
	357	}
	358	//____________________________________________________________________________
	359	Bool_t AliPHOSRawDigiProducer::IsInEMC(AliPHOSDigit * digit) const
	360	{
	361	// Tells if (true) or not (false) the digit is in a PHOS-EMC module
	362	return digit->GetId() <= fEmcCrystals ;
	363
	364	}
	365
	366	//____________________________________________________________________________
	367	Bool_t AliPHOSRawDigiProducer::IsInCPV(AliPHOSDigit * digit) const
	368	{
	369	// Tells if (true) or not (false) the digit is in a PHOS-CPV module
	370	return digit->GetId() > fEmcCrystals ;
	371	}
	372	//____________________________________________________________________________
	373	void AliPHOSRawDigiProducer::GetCalibrationParameters()
	374	{
	375	// Set calibration parameters:
	376	// if calibration database exists, they are read from database,
	377	// otherwise, reconstruction stops in the constructor of AliPHOSCalibData
	378	//
	379	// It is a user responsilibity to open CDB before reconstruction, for example:
	380	// AliCDBStorage* storage = AliCDBManager::Instance()->GetStorage("local://CalibDB");
	381
	382	if (!fgCalibData){
	383	fgCalibData = new AliPHOSCalibData(-1); //use AliCDBManager's run number
	384	}
	385	if (fgCalibData->GetCalibDataEmc() == 0)
	386	AliFatal("Calibration parameters for PHOS EMC not found. Stop reconstruction.\n");
	387	if (fgCalibData->GetCalibDataCpv() == 0)
	388	AliFatal("Calibration parameters for PHOS CPV not found. Stop reconstruction.\n");
88fb5e50	389	}