[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),
  fADCValuesLG(0),
  fADCValuesHG(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),
  fADCValuesLG(0),
  fADCValuesHG(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),
  fADCValuesLG(0),
  fADCValuesHG(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;
  delete [] fADCValuesLG;
  delete [] fADCValuesHG;
}
//--------------------------------------------------------------------------------------
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);
      
      fitter->SetNBunches(0);
      Int_t sigStart  ;
      Int_t sigLength ;
      while (fRawStream->NextBunch()) { //Take first in time banch
	const UShort_t *sig = fRawStream->GetSignals();
	sigStart  = fRawStream->GetStartTimeBin();
	sigLength = fRawStream->GetBunchLength();
	fitter->Eval(sig,sigStart,sigLength);
	if      (caloFlag == AliCaloRawStreamV3::kLowGain) {
	  delete [] fADCValuesLG;
	  fADCValuesLG = new Int_t[sigLength];
	  for (Int_t i=0; i<sigLength; i++)
	    fADCValuesLG[sigLength-i-1] = sig[i];
	}
	else if (caloFlag == AliCaloRawStreamV3::kHighGain) {
	  delete [] fADCValuesHG;
	  fADCValuesHG = new Int_t[sigLength];
	  for (Int_t i=0; i<sigLength; i++)
	    fADCValuesHG[sigLength-i-1] = sig[i];
	}
      } // End of NextBunch()

      
      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,!caloFlag) ;
//       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);
	dynamic_cast<AliPHOSDigit*>(tmpLG.At(ilgDigit))->SetALTROSamplesHG(sigLength,fADCValuesLG);
	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);
	dynamic_cast<AliPHOSDigit*>(digits->At(iDigit))->SetALTROSamplesHG(sigLength,fADCValuesLG);
	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),
379c5c09	59	fRawReader(0),
54ac223e	60	fRawStream(0),
	61	fADCValuesLG(0),
	62	fADCValuesHG(0)
7e88424f	63	{
7e88424f	64	// Default constructor
70d93620	65
c0394bfb	66	fGeom=AliPHOSGeometry::GetInstance() ;
	67	if(!fGeom) fGeom = AliPHOSGeometry::GetInstance("IHEP");
	68
	69	fEmcCrystals=fGeom->GetNCristalsInModule()*fGeom->GetNModules() ;
39569d36	70	fPulseGenerator = new AliPHOSPulseGenerator();
c0394bfb	71	GetCalibrationParameters() ;
8be3a30a	72
c0394bfb	73	}
379c5c09	74	//--------------------------------------------------------------------------------------
	75	AliPHOSRawDigiProducer::AliPHOSRawDigiProducer(AliRawReader *rawReader,
	76	AliAltroMapping **mapping):
	77	TObject(),
	78	fEmcMinE(0.),
	79	fCpvMinE(0.),
	80	fSampleQualityCut(1.),
6f47f50d	81	fSampleToSec(0.),
379c5c09	82	fEmcCrystals(0),
	83	fGeom(0),
	84	fPulseGenerator(0),
	85	fRawReader(rawReader),
54ac223e	86	fRawStream(0),
	87	fADCValuesLG(0),
	88	fADCValuesHG(0)
379c5c09	89	{
	90	// Default constructor
	91
	92	fGeom=AliPHOSGeometry::GetInstance() ;
	93	if(!fGeom) fGeom = AliPHOSGeometry::GetInstance("IHEP");
	94
	95	fEmcCrystals=fGeom->GetNCristalsInModule()*fGeom->GetNModules() ;
	96	fPulseGenerator = new AliPHOSPulseGenerator();
	97	GetCalibrationParameters() ;
	98
	99	fRawStream = new AliCaloRawStreamV3(rawReader,"PHOS",mapping);
	100
	101	}
	102	//--------------------------------------------------------------------------------------
7e88424f	103	AliPHOSRawDigiProducer::AliPHOSRawDigiProducer(const AliPHOSRawDigiProducer &dp):
	104	TObject(),
	105	fEmcMinE(0.),
	106	fCpvMinE(0.),
	107	fSampleQualityCut(1.),
6f47f50d	108	fSampleToSec(0.),
7e88424f	109	fEmcCrystals(0),
7e88424f	110	fGeom(0),
379c5c09	111	fPulseGenerator(0),
379c5c09	112	fRawReader(0),
54ac223e	113	fRawStream(0),
	114	fADCValuesLG(0),
	115	fADCValuesHG(0)
	116
7e88424f	117	{
7e88424f	118	// Copy constructor
c0394bfb	119
	120	fEmcMinE = dp.fEmcMinE ;
	121	fCpvMinE = dp.fCpvMinE ;
f78c9781	122	fSampleQualityCut = dp.fSampleQualityCut;
6f47f50d	123	fSampleToSec = dp.fSampleToSec ;
c0394bfb	124	fEmcCrystals = dp.fEmcCrystals ;
39569d36	125	fPulseGenerator = new AliPHOSPulseGenerator();
c0394bfb	126	fGeom = dp.fGeom ;
	127	}
	128	//--------------------------------------------------------------------------------------
7e88424f	129	AliPHOSRawDigiProducer& AliPHOSRawDigiProducer::operator= (const AliPHOSRawDigiProducer &dp)
	130	{
	131	// Assign operator
	132
c0394bfb	133	if(&dp == this) return *this;
	134
	135	fEmcMinE = dp.fEmcMinE ;
	136	fCpvMinE = dp.fCpvMinE ;
70d93620	137	fSampleQualityCut = dp.fSampleQualityCut ;
6f47f50d	138	fSampleToSec = dp.fSampleToSec ;
c0394bfb	139	fEmcCrystals = dp.fEmcCrystals ;
c0394bfb	140	fGeom = dp.fGeom ;
39569d36	141	if(fPulseGenerator) delete fPulseGenerator ;
39569d36	142	fPulseGenerator = new AliPHOSPulseGenerator();
c0394bfb	143	return *this;
c0394bfb	144	}
379c5c09	145	//--------------------------------------------------------------------------------------
7e88424f	146	AliPHOSRawDigiProducer::~AliPHOSRawDigiProducer()
7e88424f	147	{
379c5c09	148	// Destructor
7e88424f	149	if(fPulseGenerator) delete fPulseGenerator ;
7e88424f	150	fPulseGenerator=0 ;
379c5c09	151	delete fRawStream;
54ac223e	152	delete [] fADCValuesLG;
54ac223e	153	delete [] fADCValuesHG;
39569d36	154	}
7bc140a5	155	//--------------------------------------------------------------------------------------
379c5c09	156	void AliPHOSRawDigiProducer::MakeDigits(TClonesArray digits, AliPHOSRawFitterv0 fitter)
88fb5e50	157	{
7bc140a5	158	//Makes the job.
379c5c09	159	//TClonesArray *digits and raw data fitter should be provided by calling function.
7bc140a5	160
88fb5e50	161	digits->Clear();
88fb5e50	162
379c5c09	163	Int_t iDigit=0 ;
379c5c09	164	Int_t relId[4], absId=-1, caloFlag=-1;
fdd91c5a	165
c0394bfb	166	const Double_t baseLine=1. ; //Minimal energy of digit in ADC ch.
6f47f50d	167
	168	//Calculate conversion coeff. from Sample time step to seconds
	169	//If OCDB contains negative or zero value - use one from RCU trailer
	170	//Negative value in OCDB is used only for simulation of raw digits
	171	if(fgCalibData->GetSampleTimeStep()>0.)
	172	fSampleToSec=fgCalibData->GetSampleTimeStep() ;
	173	else
	174	fSampleToSec=fRawStream->GetTSample() ;
fdd91c5a	175
c0394bfb	176	//Temporary array for LowGain digits
	177	TClonesArray tmpLG("AliPHOSDigit",10000) ;
	178	Int_t ilgDigit=0 ;
bafc1087	179
379c5c09	180	//Let fitter subtract pedestals in case of ZS
379c5c09	181	fitter->SetCalibData(fgCalibData) ;
c0394bfb	182
379c5c09	183	while (fRawStream->NextDDL()) {
379c5c09	184	while (fRawStream->NextChannel()) {
fc44a661	185	relId[0] = 5 - fRawStream->GetModule() ; // counts from 1 to 5
379c5c09	186	relId[1] = 0;
1281504a	187	relId[2] = fRawStream->GetCellX() + 1; // counts from 1 to 64
	188	relId[3] = fRawStream->GetCellZ() + 1; // counts from 1 to 56
	189	caloFlag = fRawStream->GetCaloFlag(); // 0=LG, 1=HG, 2=TRU
f4ca5622	190
	191	if(caloFlag!=0 && caloFlag!=1) continue; //TRU data!
	192
e10f780e	193	fitter->SetChannelGeo(relId[0],relId[2],relId[3],caloFlag);
fc44a661	194
c4dad9d2	195	if(fitter->GetAmpOffset()==0 && fitter->GetAmpThreshold()==0) {
	196	short value = fRawStream->GetAltroCFG1();
	197	bool ZeroSuppressionEnabled = (value >> 15) & 0x1;
	198	if(ZeroSuppressionEnabled) {
	199	short offset = (value >> 10) & 0xf;
	200	short threshold = value & 0x3ff;
	201	fitter->SubtractPedestals(kFALSE);
	202	fitter->SetAmpOffset(offset);
	203	fitter->SetAmpThreshold(threshold);
	204	}
	205	}
	206
379c5c09	207	fGeom->RelToAbsNumbering(relId, absId);
f4ca5622	208
c01c5641	209	fitter->SetNBunches(0);
54ac223e	210	Int_t sigStart ;
54ac223e	211	Int_t sigLength ;
c01c5641	212	while (fRawStream->NextBunch()) { //Take first in time banch
379c5c09	213	const UShort_t *sig = fRawStream->GetSignals();
54ac223e	214	sigStart = fRawStream->GetStartTimeBin();
54ac223e	215	sigLength = fRawStream->GetBunchLength();
92236b27	216	fitter->Eval(sig,sigStart,sigLength);
54ac223e	217	if (caloFlag == AliCaloRawStreamV3::kLowGain) {
	218	delete [] fADCValuesLG;
	219	fADCValuesLG = new Int_t[sigLength];
	220	for (Int_t i=0; i<sigLength; i++)
	221	fADCValuesLG[sigLength-i-1] = sig[i];
	222	}
	223	else if (caloFlag == AliCaloRawStreamV3::kHighGain) {
	224	delete [] fADCValuesHG;
	225	fADCValuesHG = new Int_t[sigLength];
	226	for (Int_t i=0; i<sigLength; i++)
	227	fADCValuesHG[sigLength-i-1] = sig[i];
	228	}
379c5c09	229	} // End of NextBunch()
70d93620	230
379c5c09	231
	232	Double_t energy = fitter->GetEnergy() ;
	233	Double_t time = fitter->GetTime() ;
	234	if(energy<=baseLine) //in ADC channels
	235	continue ;
88fb5e50	236
379c5c09	237	//remove digits with bad shape. Fitter should calculate quality so that
	238	//in default case quality [0,1], while larger values of quality mean somehow
	239	//corrupted samples, 999 means obviously corrupted sample.
	240	//It is difficult to fit samples with overflow (even setting cut on overflow values)
	241	//because too few points are left to fit. So we do not evaluate samples with overflow
c0394bfb	242
379c5c09	243	if(fitter->GetSignalQuality() > fSampleQualityCut && !(fitter->IsOverflow()))
	244	continue ;
	245
817744df	246	energy = CalibrateE(energy,relId,!caloFlag) ;
379c5c09	247	// time = CalibrateT(time,relId,lowGainFlag) ;
6f47f50d	248
	249	//convert time from sample bin units to s
	250	time*=fSampleToSec ;
379c5c09	251
	252	if(energy <= 0.)
	253	continue;
	254
	255	if (caloFlag == AliCaloRawStreamV3::kLowGain) {
	256	new(tmpLG[ilgDigit]) AliPHOSDigit(-1,absId,(Float_t)energy,(Float_t)time);
54ac223e	257	dynamic_cast<AliPHOSDigit*>(tmpLG.At(ilgDigit))->SetALTROSamplesHG(sigLength,fADCValuesLG);
379c5c09	258	ilgDigit++ ;
	259	}
	260	else if (caloFlag == AliCaloRawStreamV3::kHighGain) {
	261	if(fitter->IsOverflow()) //Keep this digit to replace it by Low Gain later.
	262	//If there is no LogGain it wil be removed by cut on Min E
	263	new((*digits)[iDigit]) AliPHOSDigit(-1,absId,-1.f,(Float_t)time);
	264	else
	265	new((*digits)[iDigit]) AliPHOSDigit(-1,absId,(Float_t)energy,(Float_t)time);
54ac223e	266	dynamic_cast<AliPHOSDigit*>(digits->At(iDigit))->SetALTROSamplesHG(sigLength,fADCValuesLG);
379c5c09	267	iDigit++;
	268	}
	269	} // End of NextChannel()
c0394bfb	270
379c5c09	271	//Now scan created LG and HG digits and keep only those which appeared in both lists
	272	//replace energy of HighGain digits only if there is overflow
	273	//negative energy (overflow)
	274	digits->Sort() ;
	275	tmpLG.Sort() ;
	276	Int_t iLG = 0;
	277	Int_t nLG1 = tmpLG.GetEntriesFast()-1 ;
	278
	279	for(Int_t iDig=0 ; iDig < digits->GetEntriesFast() ; iDig++) {
	280	AliPHOSDigit * digHG = dynamic_cast<AliPHOSDigit*>(digits->At(iDig)) ;
	281	if (!digHG) continue;
	282	AliPHOSDigit * digLG = dynamic_cast<AliPHOSDigit*>(tmpLG.At(iLG)) ;
	283	while(digLG && iLG<nLG1 && digHG->GetId()> digLG->GetId()){
	284	iLG++ ;
	285	digLG = dynamic_cast<AliPHOSDigit*>(tmpLG.At(iLG)) ;
	286	}
	287	absId=digHG->GetId() ;
	288	fGeom->AbsToRelNumbering(absId,relId) ;
a7c985dc	289
379c5c09	290	if(digLG && digHG->GetId() == digLG->GetId()){ //we found pair
	291	if(digHG->GetEnergy()<0.){ //This is overflow in HG
	292	digHG->SetTime(digLG->GetTime()) ;
	293	digHG->SetEnergy(digLG->GetEnergy()) ;
	294	}
379c5c09	295	}
379c5c09	296	else{ //no pair - remove
fdd91c5a	297	if(digHG->GetEnergy()<0.) //no pair, in saturation
fdd91c5a	298	digits->RemoveAt(iDig) ;
88fb5e50	299	}
88fb5e50	300	}
379c5c09	301	} // End of NextDDL()
c0394bfb	302
c0394bfb	303	CleanDigits(digits) ;
379c5c09	304
c0394bfb	305	}
	306	//____________________________________________________________________________
	307	Double_t AliPHOSRawDigiProducer::CalibrateE(Double_t amp, Int_t* relId, Bool_t isLowGain)
	308	{
634d2178	309	// Convert EMC LG amplitude to HG (multipli by ~16)
634d2178	310	// Calibration parameters are taken from calibration data base
c0394bfb	311	if(fgCalibData){
	312	Int_t module = relId[0];
	313	Int_t column = relId[3];
	314	Int_t row = relId[2];
	315	if(relId[1]==0) { // this is EMC
	316	if(isLowGain){
	317	amp*= fgCalibData->GetHighLowRatioEmc(module,column,row);
88fb5e50	318	}
c0394bfb	319	return amp ;
	320	}
	321	}
	322	return 0;
	323	}
	324	//____________________________________________________________________________
	325	Double_t AliPHOSRawDigiProducer::CalibrateT(Double_t time, Int_t * relId, Bool_t /* isLowGain */)
	326	{
	327	//Calibrate time
39569d36	328	time*=fPulseGenerator->GetRawFormatTimeTrigger() ;
c0394bfb	329	if(fgCalibData){
	330	Int_t module = relId[0];
	331	Int_t column = relId[3];
	332	Int_t row = relId[2];
	333	if(relId[1]==0) { // this is EMC
	334	time += fgCalibData->GetTimeShiftEmc(module,column,row);
	335	return time ;
	336	}
	337	}
	338
	339	return -999.;
	340	}
	341	//____________________________________________________________________________
	342	void AliPHOSRawDigiProducer::CleanDigits(TClonesArray * digits)
	343	{
	344	// remove digits with amplitudes below threshold.
	345	// remove digits in bad channels
	346	// sort digits with icreasing AbsId
	347
	348	//remove digits in bad map and below threshold
	349	Bool_t isBadMap = 0 ;
	350	if(fgCalibData->GetNumOfEmcBadChannels()){
	351	isBadMap=1 ;
	352	}
	353
	354	for(Int_t i=0; i<digits->GetEntriesFast(); i++){
	355	AliPHOSDigit * digit = static_cast<AliPHOSDigit*>(digits->At(i)) ;
	356	if(!digit)
	357	continue ;
	358	if ( (IsInEMC(digit) && digit->GetEnergy() < fEmcMinE) \|\|
	359	(IsInCPV(digit) && digit->GetEnergy() < fCpvMinE) ){
	360	digits->RemoveAt(i) ;
	361	continue ;
	362	}
	363	if(isBadMap){ //check bad map now
	364	Int_t relid[4] ;
	365	fGeom->AbsToRelNumbering(digit->GetId(), relid) ;
a65517aa	366	if(fgCalibData->IsBadChannelEmc(relid[0],relid[3],relid[2])){
c0394bfb	367	digits->RemoveAt(i) ;
88fb5e50	368	}
88fb5e50	369	}
88fb5e50	370	}
88fb5e50	371
c0394bfb	372	//Compress, sort and set indexes
	373	digits->Compress() ;
	374	// digits->Sort(); already sorted earlier
	375	for (Int_t i = 0 ; i < digits->GetEntriesFast() ; i++) {
	376	AliPHOSDigit digit = static_cast<AliPHOSDigit>( digits->At(i) ) ;
	377	digit->SetIndexInList(i) ;
	378	}
	379	}
	380	//____________________________________________________________________________
	381	Bool_t AliPHOSRawDigiProducer::IsInEMC(AliPHOSDigit * digit) const
	382	{
	383	// Tells if (true) or not (false) the digit is in a PHOS-EMC module
	384	return digit->GetId() <= fEmcCrystals ;
	385
	386	}
	387
	388	//____________________________________________________________________________
	389	Bool_t AliPHOSRawDigiProducer::IsInCPV(AliPHOSDigit * digit) const
	390	{
	391	// Tells if (true) or not (false) the digit is in a PHOS-CPV module
	392	return digit->GetId() > fEmcCrystals ;
	393	}
	394	//____________________________________________________________________________
	395	void AliPHOSRawDigiProducer::GetCalibrationParameters()
	396	{
	397	// Set calibration parameters:
	398	// if calibration database exists, they are read from database,
	399	// otherwise, reconstruction stops in the constructor of AliPHOSCalibData
	400	//
	401	// It is a user responsilibity to open CDB before reconstruction, for example:
	402	// AliCDBStorage* storage = AliCDBManager::Instance()->GetStorage("local://CalibDB");
	403
	404	if (!fgCalibData){
	405	fgCalibData = new AliPHOSCalibData(-1); //use AliCDBManager's run number
	406	}
	407	if (fgCalibData->GetCalibDataEmc() == 0)
	408	AliFatal("Calibration parameters for PHOS EMC not found. Stop reconstruction.\n");
	409	if (fgCalibData->GetCalibDataCpv() == 0)
	410	AliFatal("Calibration parameters for PHOS CPV not found. Stop reconstruction.\n");
88fb5e50	411	}