[u/mrichter/AliRoot.git] / ITS / AliITSClusterFinderV2SDD.cxx

/**************************************************************************
 * Copyright(c) 1998-2003, 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.                  *
 **************************************************************************/

/* $Id$*/

////////////////////////////////////////////////////////////////////////////
//            Implementation of the ITS clusterer V2 class                //
//                                                                        //
//          Origin: Iouri Belikov, CERN, Jouri.Belikov@cern.ch            //
//                                                                        //
///////////////////////////////////////////////////////////////////////////


#include <TClonesArray.h>
#include <TBits.h>
#include "AliITSClusterFinderV2SDD.h"
#include "AliITSRecPoint.h"
#include "AliITSDetTypeRec.h"
#include "AliRawReader.h"
#include "AliITSRawStreamSDD.h"
#include "AliITSRawStreamSDDCompressed.h"
#include "AliITSCalibrationSDD.h"
#include "AliITSresponseSDD.h"
#include "AliITSDetTypeRec.h"
#include "AliITSReconstructor.h"
#include "AliITSsegmentationSDD.h"
#include "AliITSdigitSDD.h"
#include "AliITSgeomTGeo.h"

ClassImp(AliITSClusterFinderV2SDD)

AliITSClusterFinderV2SDD::AliITSClusterFinderV2SDD(AliITSDetTypeRec* dettyp):AliITSClusterFinder(dettyp),
  fNAnodes(0),
  fNTimeBins(0),
  fNZbins(0),
  fNXbins(0)
{
  //Default constructor

  fNAnodes = GetSeg()->NpzHalf();
  fNZbins = fNAnodes+2;
  fNTimeBins = GetSeg()->Npx();
  fNXbins = fNTimeBins+2;
  AliDebug(2,Form("Cells in SDD cluster finder: Andoes=%d  TimeBins=%d",fNAnodes,fNTimeBins));
  const Int_t kMaxBin=fNZbins*fNXbins;
  for(Int_t iHyb=0;iHyb<kHybridsPerDDL;iHyb++){
   fDDLBins[iHyb]=new AliBin[kMaxBin];
  }
}
 

//______________________________________________________________________
AliITSClusterFinderV2SDD::~AliITSClusterFinderV2SDD()
{
  //Destructor
  for(Int_t iHyb=0;iHyb<kHybridsPerDDL;iHyb++){ 
    delete [] fDDLBins[iHyb];
  }
}

//______________________________________________________________________
void AliITSClusterFinderV2SDD::FindRawClusters(Int_t mod){

  //Find clusters V2
  SetModule(mod);
  FindClustersSDD(fDigits);

}

//______________________________________________________________________
void AliITSClusterFinderV2SDD::FindClustersSDD(TClonesArray *digits) {
  //------------------------------------------------------------
  // Actual SDD cluster finder
  //------------------------------------------------------------

  const Int_t kMaxBin=fNZbins*fNXbins;
  AliBin *bins[2];
  bins[0]=new AliBin[kMaxBin];
  bins[1]=new AliBin[kMaxBin];
  TBits *anodeFired[2];
  anodeFired[0]=new TBits(fNAnodes);
  anodeFired[1]=new TBits(fNAnodes);
  anodeFired[0]->ResetAllBits();
  anodeFired[1]->ResetAllBits();
  AliITSCalibrationSDD* cal = (AliITSCalibrationSDD*)GetResp(fModule);
  if(cal==0){
    AliError(Form("Calibration object not present for SDD module %d\n",fModule));
    return;
  }

  AliITSdigitSDD *d=0;
  Int_t i, ndigits=digits->GetEntriesFast();
  for (i=0; i<ndigits; i++) {
     d=(AliITSdigitSDD*)digits->UncheckedAt(i);
     Int_t ian=d->GetCoord1();
     Int_t itb=d->GetCoord2();
     Int_t iSide=0;
     if (ian >= fNAnodes) iSide=1;    
     Float_t gain=cal->GetChannelGain(ian)/fDetTypeRec->GetAverageGainSDD();
     Float_t charge=d->GetSignal(); // returns expanded signal 
                                    // (10 bit, low threshold already added)
     Float_t baseline = cal->GetBaseline(ian);
     if(charge>baseline) charge-=baseline;
     else charge=0;

     if(gain>0.){ // Bad channels have gain=0.
       charge/=gain;
       if(charge<cal->GetThresholdAnode(ian)) continue;
       Int_t q=(Int_t)(charge+0.5);
       Int_t y=itb+1;   
       Int_t z=ian+1;   
       if (z <= fNAnodes){
	 bins[0][y*fNZbins+z].SetQ(q);
	 bins[0][y*fNZbins+z].SetMask(1);
	 bins[0][y*fNZbins+z].SetIndex(i);
	 anodeFired[0]->SetBitNumber(ian);
       } else {
	 z-=fNAnodes;
	 bins[1][y*fNZbins+z].SetQ(q);
	 bins[1][y*fNZbins+z].SetMask(1);
	 bins[1][y*fNZbins+z].SetIndex(i);
	 anodeFired[1]->SetBitNumber(ian-fNAnodes);
       }
     }
  }
  
  FindClustersSDD(bins, anodeFired, digits);

  delete[] bins[0];
  delete[] bins[1];
  delete anodeFired[0];
  delete anodeFired[1];

}

//______________________________________________________________________
void AliITSClusterFinderV2SDD::
FindClustersSDD(AliBin* bins[2], TBits* anodeFired[2],  
		TClonesArray *digits, TClonesArray *clusters, Int_t jitter) {
  //------------------------------------------------------------
  // Actual SDD cluster finder
  //------------------------------------------------------------

  static AliITSRecoParam *repa = NULL;
  if(!repa){
    repa = (AliITSRecoParam*) AliITSReconstructor::GetRecoParam();
    if(!repa){
      repa = AliITSRecoParam::GetHighFluxParam();
      AliWarning("Using default AliITSRecoParam class");
    }
  }
  const TGeoHMatrix *mT2L=AliITSgeomTGeo::GetTracking2LocalMatrix(fModule);
  AliITSCalibrationSDD* cal = (AliITSCalibrationSDD*)GetResp(fModule);
  if(cal==0){
    AliError(Form("Calibration object not present for SDD module %d\n",fModule));
    return;
  }
  const Int_t kMaxBin=fNZbins*fNXbins;
  Int_t ncl=0; 
  TClonesArray &cl=*clusters;
  for (Int_t s=0; s<2; s++){
    for(Int_t iAnode=0; iAnode<GetSeg()->NpzHalf(); iAnode++){
      if(anodeFired[s]->TestBitNumber(iAnode)==kFALSE) continue;
      for(Int_t iTimeBin=0; iTimeBin<GetSeg()->Npx(); iTimeBin++){
	Int_t index=(iTimeBin+1)*fNZbins+(iAnode+1);
	if (bins[s][index].IsUsed()) continue;
	if(NoiseSuppress(index,s,bins[s],cal)) continue;
	Int_t idx[32]; UInt_t msk[32]; Int_t npeaks=0;
	FindPeaks(index, fNZbins, bins[s], idx, msk, npeaks);

	if (npeaks>30) continue;
	if (npeaks==0) continue;

	Int_t k,l;
	for (k=0; k<npeaks-1; k++){//mark adjacent peaks
	  if (idx[k] < 0) continue; //this peak is already removed
	  for (l=k+1; l<npeaks; l++) {
	    if (idx[l] < 0) continue; //this peak is already removed
	    Int_t ki=idx[k]/fNZbins, kj=idx[k] - ki*fNZbins;
	    Int_t li=idx[l]/fNZbins, lj=idx[l] - li*fNZbins;
	    Int_t di=TMath::Abs(ki - li);
	    Int_t dj=TMath::Abs(kj - lj);
	    if (di>1 || dj>1) continue;
	    if (bins[s][idx[k]].GetQ() > bins[s][idx[l]].GetQ()) {
	      msk[l]=msk[k];
	      idx[l]*=-1;
	    } else {
	      msk[k]=msk[l];
	      idx[k]*=-1;
	      break;
	    } 
	  }
	}

	for (k=0; k<npeaks; k++) {
	  if(repa->GetUseUnfoldingInClusterFinderSDD()==kFALSE) msk[k]=msk[0];
	  MarkPeak(TMath::Abs(idx[k]), fNZbins, bins[s], msk[k]);
	}
        
	for (k=0; k<npeaks; k++) {
	  if (idx[k] < 0) continue; //removed peak
	  AliITSRecPoint c;
	  MakeCluster(idx[k], fNZbins, bins[s], msk[k], c);
	  //mi change
	  Int_t milab[10];
	  for (Int_t ilab=0;ilab<10;ilab++){
	    milab[ilab]=-2;
	  }
	  Int_t maxi=0,mini=0,maxj=0,minj=0;
	  
	  for (Int_t di=-5; di<=5;di++){
	    for (Int_t dj=-10;dj<=10;dj++){
	      index = idx[k]+di+dj*fNZbins;
	      if (index<0) continue;
	      if (index>=kMaxBin) continue;
	      AliBin *b=&bins[s][index];
	      Int_t jAnode=index%fNZbins-1;
	      Int_t adcSignal=b->GetQ();
	      if(adcSignal>cal->GetThresholdAnode(jAnode)){
		if (di>maxi) maxi=di;
		if (di<mini) mini=di;
		if (dj>maxj) maxj=dj;
		if (dj<minj) minj=dj;
	      }
	      //
	      if(digits) {
		if (TMath::Abs(di)<2&&TMath::Abs(dj)<2){
		  AliITSdigitSDD* d=(AliITSdigitSDD*)digits->UncheckedAt(b->GetIndex());
		  for (Int_t itrack=0;itrack<10;itrack++){
		    Int_t track = (d->GetTracks())[itrack];
		    if (track>=0) {
		      AddLabel(milab, track); 
		    }
		  }
		}
	      }
	    }
	  }
	  Int_t clSizAnode=maxi-mini+1;
	  Int_t clSizTb=maxj-minj+1;
	  if(repa->GetUseSDDClusterSizeSelection()){
	    if(clSizTb==1) continue; // cut common mode noise spikes
	    if(clSizAnode>3)  continue; // cut common mode noise spikes
	    if(clSizTb>10)  continue; // cut clusters on noisy anodes
	  }
	  
	  AliITSresponseSDD* rsdd = fDetTypeRec->GetResponseSDD();
	  Float_t y=c.GetY(),z=c.GetZ(), q=c.GetQ();
	  y/=q; z/=q;
	  Float_t zAnode=z-0.5;  // to have anode in range 0.-255. and centered on the mid of the pitch
	  Float_t timebin=y-0.5;  // to have time bin in range 0.-255. amd centered on the mid of the bin
	  if(s==1) zAnode += GetSeg()->NpzHalf();  // right side has anodes from 256. to 511.
	  Float_t zdet = GetSeg()->GetLocalZFromAnode(zAnode);
	  Float_t driftTimeUncorr = GetSeg()->GetDriftTimeFromTb(timebin)+jitter*rsdd->GetCarlosRXClockPeriod();
	  Float_t driftTime=driftTimeUncorr-rsdd->GetTimeZero(fModule);
	  Float_t driftSpeed = cal->GetDriftSpeedAtAnode(zAnode) + rsdd->GetDeltaVDrift(fModule);
	  Float_t driftPathMicron = driftTime*driftSpeed;
	  const Double_t kMicronTocm = 1.0e-4; 
	  Float_t xdet=(driftPathMicron-GetSeg()->Dx())*kMicronTocm; // xdet is negative
	  if (s==0) xdet=-xdet; // left side has positive local x
	  
	  if(repa->GetUseSDDCorrectionMaps()){
	    Float_t corrx=0, corrz=0;
	    cal->GetCorrections(zdet,xdet,corrz,corrx,GetSeg());
	    zdet+=corrz;
	    xdet+=corrx;
	  }
	  
	  Double_t loc[3]={xdet,0.,zdet},trk[3]={0.,0.,0.};
	  mT2L->MasterToLocal(loc,trk);
	  y=trk[1];
	  z=trk[2]; 
	  
	  q/=rsdd->GetADC2keV();
	  q+=(driftTime*rsdd->GetChargevsTime()); // correction for zero supp.
	  if(cal-> IsAMAt20MHz()) q*=2.; // account for 1/2 sampling freq.
	  if(q<repa->GetMinClusterChargeSDD()) continue; // remove noise clusters
	  
	  Float_t hit[5] = {y, z, 0.0030*0.0030, 0.0020*0.0020, q};
	  Int_t  info[3] = {clSizTb, clSizAnode, fNlayer[fModule]};
	  if (digits) CheckLabels2(milab);
	  milab[3]=fNdet[fModule];
	  AliITSRecPoint cc(milab,hit,info);
	  cc.SetType(npeaks);
	  cc.SetDriftTime(driftTimeUncorr);
	  if(clusters) new (cl[ncl]) AliITSRecPoint(cc); 
	  else {
	    fDetTypeRec->AddRecPoint(cc);
	  }
	  ncl++;
	}
      }
    }
  }
 
} 
//______________________________________________________________________
void AliITSClusterFinderV2SDD::RawdataToClusters(AliRawReader* rawReader,TClonesArray** clusters){
    //------------------------------------------------------------
  // This function creates ITS clusters from raw data
  //------------------------------------------------------------

  AliITSRawStream* inputSDD=AliITSRawStreamSDD::CreateRawStreamSDD(rawReader);
  AliDebug(1,Form("%s is used",inputSDD->ClassName()));

  AliITSDDLModuleMapSDD *ddlmap=(AliITSDDLModuleMapSDD*)fDetTypeRec->GetDDLModuleMapSDD();
  inputSDD->SetDDLModuleMap(ddlmap);
  for(Int_t iddl=0; iddl<AliITSDDLModuleMapSDD::GetNDDLs(); iddl++){
    for(Int_t icar=0; icar<AliITSDDLModuleMapSDD::GetNModPerDDL();icar++){
      Int_t iMod=ddlmap->GetModuleNumber(iddl,icar);
      if(iMod==-1) continue;
      AliITSCalibrationSDD* cal = (AliITSCalibrationSDD*)GetResp(iMod);
      if(cal==0){
	AliError(Form("Calibration object not present for SDD module %d\n",iMod));
	continue;
      }
      Bool_t isZeroSupp=cal->GetZeroSupp();
      if(isZeroSupp){ 
	for(Int_t iSid=0; iSid<2; iSid++) inputSDD->SetZeroSuppLowThreshold(iMod-240,iSid,cal->GetZSLowThreshold(iSid));
      }else{
	for(Int_t iSid=0; iSid<2; iSid++) inputSDD->SetZeroSuppLowThreshold(iMod-240,iSid,0);
      }
    }
  }
  FindClustersSDD(inputSDD,clusters);
  delete inputSDD;
}

void AliITSClusterFinderV2SDD::FindClustersSDD(AliITSRawStream* input, 
					TClonesArray** clusters) 
{
  //------------------------------------------------------------
  // Actual SDD cluster finder for raw data
  //------------------------------------------------------------
  Int_t nClustersSDD = 0;
  AliBin *bins[2];
  TBits* anodeFired[2];
  TBits* ddlAnodeFired[kHybridsPerDDL];
  for(Int_t iHyb=0;iHyb<kHybridsPerDDL;iHyb++){
    ddlAnodeFired[iHyb]=new TBits(fNAnodes);
    ddlAnodeFired[iHyb]->ResetAllBits();
  }
  Int_t vectModId[kModulesPerDDL];
  for(Int_t iMod=0; iMod<kModulesPerDDL; iMod++) vectModId[iMod]=-1;

  // read raw data input stream
  while (input->Next()) {
    Int_t iModule = input->GetModuleID();
    if(iModule<0){
      AliWarning(Form("Invalid SDD module number %d\n", iModule));
      continue;
    }
    Int_t iCarlos =input->GetCarlosId();
    Int_t iSide = input->GetChannel();
    Int_t iHybrid=iCarlos*2+iSide;

    if (input->IsCompletedModule()) {
      // store the module number
      vectModId[iCarlos]=iModule;
    }
    else if (input->IsCompletedDDL()) {
      // when all data from a DDL was read, search for clusters
      Int_t jitter=input->GetJitter();
      for(Int_t iMod=0; iMod<kModulesPerDDL; iMod++){
	if(vectModId[iMod]>=0){
	  fModule = vectModId[iMod];
	  clusters[fModule] = new TClonesArray("AliITSRecPoint");
	  bins[0]=fDDLBins[iMod*2];   // first hybrid of the module
	  bins[1]=fDDLBins[iMod*2+1]; // second hybrid of the module
	  anodeFired[0]=ddlAnodeFired[iMod*2];
	  anodeFired[1]=ddlAnodeFired[iMod*2+1];
	  FindClustersSDD(bins, anodeFired, NULL, clusters[fModule],jitter);
	  Int_t nClusters = clusters[fModule]->GetEntriesFast();
	  nClustersSDD += nClusters;
	  vectModId[iMod]=-1;
	}
	for (Int_t s=0; s<2; s++){
	  Int_t indexHyb=iMod*2+s;
	  for(Int_t iAnode=0; iAnode<GetSeg()->NpzHalf(); iAnode++){
	    if(ddlAnodeFired[indexHyb]->TestBitNumber(iAnode)==kFALSE) continue;
	    for(Int_t iTimeBin=0; iTimeBin<GetSeg()->Npx(); iTimeBin++){
	      Int_t index=(iTimeBin+1)*fNZbins+(iAnode+1);
	      fDDLBins[indexHyb][index].Reset();
	    }
	  }
	}
	ddlAnodeFired[iMod*2]->ResetAllBits();
	ddlAnodeFired[iMod*2+1]->ResetAllBits();
      }
    }else{
    // fill the current digit into the bins array
      if(iHybrid<0 || iHybrid>=kHybridsPerDDL){ 
	AliWarning(Form("Invalid SDD hybrid number %d on module %d\n", iHybrid,iModule));
	continue;
      }
      AliITSCalibrationSDD* cal = (AliITSCalibrationSDD*)GetResp(iModule);    
      if(cal==0){
	AliError(Form("Calibration object not present for SDD module %d\n",iModule));
	continue;
      }
      Float_t charge=input->GetSignal();
      Int_t chan=input->GetCoord1()+fNAnodes*iSide;
      Float_t gain=cal->GetChannelGain(chan)/fDetTypeRec->GetAverageGainSDD();;
      Float_t baseline = cal->GetBaseline(chan);
      if(charge>baseline) charge-=baseline;
      else charge=0;
      if(gain>0.){ // Bad channels have gain=0
	charge/=gain;
	if(charge>=cal->GetThresholdAnode(chan)) {
	  Int_t q=(Int_t)(charge+0.5);
	  Int_t iz = input->GetCoord1();
	  Int_t itb = input->GetCoord2();
	  Int_t index = (itb+1) * fNZbins + (iz+1);
	  if((itb < fNTimeBins) && (iz < fNAnodes)) {
	    fDDLBins[iHybrid][index].SetQ(q);
	    fDDLBins[iHybrid][index].SetMask(1);
	    fDDLBins[iHybrid][index].SetIndex(index);
	    ddlAnodeFired[iHybrid]->SetBitNumber(iz);
	  }else{
	    AliWarning(Form("Invalid SDD cell: Anode=%d   TimeBin=%d",iz,itb));	  
	  }
	}
      }
    }
  }
  for(Int_t iHyb=0;iHyb<kHybridsPerDDL;iHyb++){ 
   delete ddlAnodeFired[iHyb];
  }
  Info("FindClustersSDD", "found clusters in ITS SDD: %d", nClustersSDD); 
}

//______________________________________________________________________
Bool_t AliITSClusterFinderV2SDD::NoiseSuppress(Int_t k, Int_t sid, AliBin* bins, AliITSCalibrationSDD* cal) const {
  // applies zero suppression using the measured noise of each anode
  // threshold values from ALICE-INT-1999-28 V10
  // returns kTRUE if the digit should eb noise suppressed, kFALSE if it should be kept
  Float_t xfactL=2.2; 
  Float_t xfactH=4.0;
  //

  Int_t iAn=(k%fNZbins)-1;
  if(iAn<0 || iAn>255) return kTRUE;
  if(sid==1) iAn+=256;
  Int_t nLow=0, nHigh=0;
  Float_t noise=cal->GetNoiseAfterElectronics(iAn);
  Float_t noisem1=noise;
  if(iAn>1) noisem1=cal->GetNoiseAfterElectronics(iAn-1);
  Float_t noisep1=noise;
  if(iAn<511) noisep1=cal->GetNoiseAfterElectronics(iAn+1);
  Float_t tL=noise*xfactL;
  Float_t tH=noise*xfactH;
  Float_t tLp1=noisep1*xfactL;
  Float_t tHp1=noisep1*xfactH;
  Float_t tLm1=noisem1*xfactL;
  Float_t tHm1=noisem1*xfactH;
  Int_t cC=bins[k].GetQ();
  if(cC<=tL){
    bins[k].SetQ(0);
    bins[k].SetMask(0xFFFFFFFE);
    return kTRUE;;
  }
  nLow++; // cC is greater than tL
  if(cC>tH) nHigh++;
  Int_t sS=bins[k-1].GetQ();
  if(sS>tLm1) nLow++;
  if(sS>tHm1) nHigh++;
  Int_t nN=bins[k+1].GetQ();
  if(nN>tLp1) nLow++;
  if(nN>tHp1) nHigh++;
  Int_t eE=bins[k-fNZbins].GetQ();
  if(eE>tL) nLow++;
  if(eE>tH) nHigh++;
  Int_t wW=bins[k+fNZbins].GetQ();
  if(wW>tL) nLow++;
  if(wW>tH) nHigh++;
  if(nLow<2 || nHigh<1) return kTRUE;
  else return kFALSE;
}
Commit	Line	Data
04366a57	1	/**************************************************************************
	2	* Copyright(c) 1998-2003, 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	**************************************************************************/
d76cb3ad	15
	16	/* $Id$*/
	17
04366a57	18	////////////////////////////////////////////////////////////////////////////
	19	// Implementation of the ITS clusterer V2 class //
	20	// //
	21	// Origin: Iouri Belikov, CERN, Jouri.Belikov@cern.ch //
	22	// //
	23	///////////////////////////////////////////////////////////////////////////
	24
	25
04366a57	26
ae485645	27	#include <TClonesArray.h>
add58ef6	28	#include <TBits.h>
04366a57	29	#include "AliITSClusterFinderV2SDD.h"
00a7cc50	30	#include "AliITSRecPoint.h"
7d62fb64	31	#include "AliITSDetTypeRec.h"
04366a57	32	#include "AliRawReader.h"
0599a018	33	#include "AliITSRawStreamSDD.h"
2f8ed7ab	34	#include "AliITSRawStreamSDDCompressed.h"
5bfe44ce	35	#include "AliITSCalibrationSDD.h"
253e68a0	36	#include "AliITSresponseSDD.h"
5bfe44ce	37	#include "AliITSDetTypeRec.h"
debf7b78	38	#include "AliITSReconstructor.h"
5bfe44ce	39	#include "AliITSsegmentationSDD.h"
04366a57	40	#include "AliITSdigitSDD.h"
b4704be3	41	#include "AliITSgeomTGeo.h"
debf7b78	42
04366a57	43	ClassImp(AliITSClusterFinderV2SDD)
04366a57	44
add58ef6	45	AliITSClusterFinderV2SDD::AliITSClusterFinderV2SDD(AliITSDetTypeRec* dettyp):AliITSClusterFinder(dettyp),
	46	fNAnodes(0),
	47	fNTimeBins(0),
	48	fNZbins(0),
	49	fNXbins(0)
a66a0eb6	50	{
04366a57	51	//Default constructor
04366a57	52
add58ef6	53	fNAnodes = GetSeg()->NpzHalf();
	54	fNZbins = fNAnodes+2;
	55	fNTimeBins = GetSeg()->Npx();
	56	fNXbins = fNTimeBins+2;
	57	AliDebug(2,Form("Cells in SDD cluster finder: Andoes=%d TimeBins=%d",fNAnodes,fNTimeBins));
	58	const Int_t kMaxBin=fNZbins*fNXbins;
	59	for(Int_t iHyb=0;iHyb<kHybridsPerDDL;iHyb++){
	60	fDDLBins[iHyb]=new AliBin[kMaxBin];
	61	}
04366a57	62	}
	63
	64
add58ef6	65	//______________________________________________________________________
	66	AliITSClusterFinderV2SDD::~AliITSClusterFinderV2SDD()
	67	{
	68	//Destructor
	69	for(Int_t iHyb=0;iHyb<kHybridsPerDDL;iHyb++){
	70	delete [] fDDLBins[iHyb];
	71	}
	72	}
	73
	74	//______________________________________________________________________
04366a57	75	void AliITSClusterFinderV2SDD::FindRawClusters(Int_t mod){
	76
	77	//Find clusters V2
	78	SetModule(mod);
	79	FindClustersSDD(fDigits);
	80
	81	}
	82
add58ef6	83	//______________________________________________________________________
04366a57	84	void AliITSClusterFinderV2SDD::FindClustersSDD(TClonesArray *digits) {
	85	//------------------------------------------------------------
	86	// Actual SDD cluster finder
	87	//------------------------------------------------------------
04366a57	88
add58ef6	89	const Int_t kMaxBin=fNZbins*fNXbins;
04366a57	90	AliBin *bins[2];
4952f440	91	bins[0]=new AliBin[kMaxBin];
4952f440	92	bins[1]=new AliBin[kMaxBin];
add58ef6	93	TBits *anodeFired[2];
	94	anodeFired[0]=new TBits(fNAnodes);
	95	anodeFired[1]=new TBits(fNAnodes);
	96	anodeFired[0]->ResetAllBits();
	97	anodeFired[1]->ResetAllBits();
404c1c29	98	AliITSCalibrationSDD* cal = (AliITSCalibrationSDD*)GetResp(fModule);
9c7f5947	99	if(cal==0){
	100	AliError(Form("Calibration object not present for SDD module %d\n",fModule));
	101	return;
	102	}
83ec5e27	103
04366a57	104	AliITSdigitSDD *d=0;
	105	Int_t i, ndigits=digits->GetEntriesFast();
	106	for (i=0; i<ndigits; i++) {
	107	d=(AliITSdigitSDD*)digits->UncheckedAt(i);
20f3f947	108	Int_t ian=d->GetCoord1();
	109	Int_t itb=d->GetCoord2();
	110	Int_t iSide=0;
add58ef6	111	if (ian >= fNAnodes) iSide=1;
75065a60	112	Float_t gain=cal->GetChannelGain(ian)/fDetTypeRec->GetAverageGainSDD();
83ec5e27	113	Float_t charge=d->GetSignal(); // returns expanded signal
83ec5e27	114	// (10 bit, low threshold already added)
20f3f947	115	Float_t baseline = cal->GetBaseline(ian);
	116	if(charge>baseline) charge-=baseline;
	117	else charge=0;
5683bd96	118
9c7f5947	119	if(gain>0.){ // Bad channels have gain=0.
9c7f5947	120	charge/=gain;
20f3f947	121	if(charge<cal->GetThresholdAnode(ian)) continue;
9c7f5947	122	Int_t q=(Int_t)(charge+0.5);
20f3f947	123	Int_t y=itb+1;
20f3f947	124	Int_t z=ian+1;
add58ef6	125	if (z <= fNAnodes){
	126	bins[0][y*fNZbins+z].SetQ(q);
	127	bins[0][y*fNZbins+z].SetMask(1);
	128	bins[0][y*fNZbins+z].SetIndex(i);
	129	anodeFired[0]->SetBitNumber(ian);
9c7f5947	130	} else {
add58ef6	131	z-=fNAnodes;
	132	bins[1][y*fNZbins+z].SetQ(q);
	133	bins[1][y*fNZbins+z].SetMask(1);
	134	bins[1][y*fNZbins+z].SetIndex(i);
	135	anodeFired[1]->SetBitNumber(ian-fNAnodes);
9c7f5947	136	}
04366a57	137	}
	138	}
	139
add58ef6	140	FindClustersSDD(bins, anodeFired, digits);
04366a57	141
	142	delete[] bins[0];
	143	delete[] bins[1];
add58ef6	144	delete anodeFired[0];
add58ef6	145	delete anodeFired[1];
04366a57	146
	147	}
	148
add58ef6	149	//______________________________________________________________________
04366a57	150	void AliITSClusterFinderV2SDD::
add58ef6	151	FindClustersSDD(AliBin* bins[2], TBits* anodeFired[2],
de075dae	152	TClonesArray digits, TClonesArray clusters, Int_t jitter) {
04366a57	153	//------------------------------------------------------------
	154	// Actual SDD cluster finder
	155	//------------------------------------------------------------
b4704be3	156
debf7b78	157	static AliITSRecoParam *repa = NULL;
	158	if(!repa){
	159	repa = (AliITSRecoParam*) AliITSReconstructor::GetRecoParam();
	160	if(!repa){
ed446fa3	161	repa = AliITSRecoParam::GetHighFluxParam();
debf7b78	162	AliWarning("Using default AliITSRecoParam class");
	163	}
	164	}
b4704be3	165	const TGeoHMatrix *mT2L=AliITSgeomTGeo::GetTracking2LocalMatrix(fModule);
404c1c29	166	AliITSCalibrationSDD* cal = (AliITSCalibrationSDD*)GetResp(fModule);
9c7f5947	167	if(cal==0){
	168	AliError(Form("Calibration object not present for SDD module %d\n",fModule));
	169	return;
	170	}
add58ef6	171	const Int_t kMaxBin=fNZbins*fNXbins;
04366a57	172	Int_t ncl=0;
04366a57	173	TClonesArray &cl=*clusters;
add58ef6	174	for (Int_t s=0; s<2; s++){
	175	for(Int_t iAnode=0; iAnode<GetSeg()->NpzHalf(); iAnode++){
	176	if(anodeFired[s]->TestBitNumber(iAnode)==kFALSE) continue;
	177	for(Int_t iTimeBin=0; iTimeBin<GetSeg()->Npx(); iTimeBin++){
	178	Int_t index=(iTimeBin+1)*fNZbins+(iAnode+1);
	179	if (bins[s][index].IsUsed()) continue;
	180	if(NoiseSuppress(index,s,bins[s],cal)) continue;
	181	Int_t idx[32]; UInt_t msk[32]; Int_t npeaks=0;
	182	FindPeaks(index, fNZbins, bins[s], idx, msk, npeaks);
	183
	184	if (npeaks>30) continue;
	185	if (npeaks==0) continue;
	186
	187	Int_t k,l;
	188	for (k=0; k<npeaks-1; k++){//mark adjacent peaks
	189	if (idx[k] < 0) continue; //this peak is already removed
	190	for (l=k+1; l<npeaks; l++) {
	191	if (idx[l] < 0) continue; //this peak is already removed
	192	Int_t ki=idx[k]/fNZbins, kj=idx[k] - ki*fNZbins;
	193	Int_t li=idx[l]/fNZbins, lj=idx[l] - li*fNZbins;
	194	Int_t di=TMath::Abs(ki - li);
	195	Int_t dj=TMath::Abs(kj - lj);
	196	if (di>1 \|\| dj>1) continue;
	197	if (bins[s][idx[k]].GetQ() > bins[s][idx[l]].GetQ()) {
	198	msk[l]=msk[k];
	199	idx[l]*=-1;
	200	} else {
	201	msk[k]=msk[l];
	202	idx[k]*=-1;
	203	break;
	204	}
	205	}
	206	}
04366a57	207
add58ef6	208	for (k=0; k<npeaks; k++) {
	209	if(repa->GetUseUnfoldingInClusterFinderSDD()==kFALSE) msk[k]=msk[0];
	210	MarkPeak(TMath::Abs(idx[k]), fNZbins, bins[s], msk[k]);
f6b6d58e	211	}
add58ef6	212
	213	for (k=0; k<npeaks; k++) {
	214	if (idx[k] < 0) continue; //removed peak
	215	AliITSRecPoint c;
	216	MakeCluster(idx[k], fNZbins, bins[s], msk[k], c);
	217	//mi change
	218	Int_t milab[10];
	219	for (Int_t ilab=0;ilab<10;ilab++){
	220	milab[ilab]=-2;
	221	}
	222	Int_t maxi=0,mini=0,maxj=0,minj=0;
	223
	224	for (Int_t di=-5; di<=5;di++){
	225	for (Int_t dj=-10;dj<=10;dj++){
85bdbebe	226	index = idx[k]+di+dj*fNZbins;
add58ef6	227	if (index<0) continue;
	228	if (index>=kMaxBin) continue;
	229	AliBin *b=&bins[s][index];
85bdbebe	230	Int_t jAnode=index%fNZbins-1;
add58ef6	231	Int_t adcSignal=b->GetQ();
85bdbebe	232	if(adcSignal>cal->GetThresholdAnode(jAnode)){
add58ef6	233	if (di>maxi) maxi=di;
	234	if (di<mini) mini=di;
	235	if (dj>maxj) maxj=dj;
	236	if (dj<minj) minj=dj;
	237	}
	238	//
	239	if(digits) {
	240	if (TMath::Abs(di)<2&&TMath::Abs(dj)<2){
	241	AliITSdigitSDD* d=(AliITSdigitSDD*)digits->UncheckedAt(b->GetIndex());
	242	for (Int_t itrack=0;itrack<10;itrack++){
	243	Int_t track = (d->GetTracks())[itrack];
	244	if (track>=0) {
	245	AddLabel(milab, track);
	246	}
f6b6d58e	247	}
	248	}
	249	}
	250	}
	251	}
add58ef6	252	Int_t clSizAnode=maxi-mini+1;
	253	Int_t clSizTb=maxj-minj+1;
	254	if(repa->GetUseSDDClusterSizeSelection()){
	255	if(clSizTb==1) continue; // cut common mode noise spikes
	256	if(clSizAnode>3) continue; // cut common mode noise spikes
	257	if(clSizTb>10) continue; // cut clusters on noisy anodes
f6b6d58e	258	}
add58ef6	259
	260	AliITSresponseSDD* rsdd = fDetTypeRec->GetResponseSDD();
	261	Float_t y=c.GetY(),z=c.GetZ(), q=c.GetQ();
	262	y/=q; z/=q;
	263	Float_t zAnode=z-0.5; // to have anode in range 0.-255. and centered on the mid of the pitch
	264	Float_t timebin=y-0.5; // to have time bin in range 0.-255. amd centered on the mid of the bin
	265	if(s==1) zAnode += GetSeg()->NpzHalf(); // right side has anodes from 256. to 511.
	266	Float_t zdet = GetSeg()->GetLocalZFromAnode(zAnode);
	267	Float_t driftTimeUncorr = GetSeg()->GetDriftTimeFromTb(timebin)+jitter*rsdd->GetCarlosRXClockPeriod();
	268	Float_t driftTime=driftTimeUncorr-rsdd->GetTimeZero(fModule);
	269	Float_t driftSpeed = cal->GetDriftSpeedAtAnode(zAnode) + rsdd->GetDeltaVDrift(fModule);
	270	Float_t driftPathMicron = driftTime*driftSpeed;
	271	const Double_t kMicronTocm = 1.0e-4;
	272	Float_t xdet=(driftPathMicron-GetSeg()->Dx())*kMicronTocm; // xdet is negative
	273	if (s==0) xdet=-xdet; // left side has positive local x
	274
	275	if(repa->GetUseSDDCorrectionMaps()){
	276	Float_t corrx=0, corrz=0;
	277	cal->GetCorrections(zdet,xdet,corrz,corrx,GetSeg());
	278	zdet+=corrz;
	279	xdet+=corrx;
	280	}
	281
	282	Double_t loc[3]={xdet,0.,zdet},trk[3]={0.,0.,0.};
	283	mT2L->MasterToLocal(loc,trk);
	284	y=trk[1];
	285	z=trk[2];
	286
	287	q/=rsdd->GetADC2keV();
	288	q+=(driftTime*rsdd->GetChargevsTime()); // correction for zero supp.
	289	if(cal-> IsAMAt20MHz()) q*=2.; // account for 1/2 sampling freq.
	290	if(q<repa->GetMinClusterChargeSDD()) continue; // remove noise clusters
	291
	292	Float_t hit[5] = {y, z, 0.00300.0030, 0.00200.0020, q};
	293	Int_t info[3] = {clSizTb, clSizAnode, fNlayer[fModule]};
	294	if (digits) CheckLabels2(milab);
	295	milab[3]=fNdet[fModule];
	296	AliITSRecPoint cc(milab,hit,info);
	297	cc.SetType(npeaks);
	298	cc.SetDriftTime(driftTimeUncorr);
	299	if(clusters) new (cl[ncl]) AliITSRecPoint(cc);
	300	else {
	301	fDetTypeRec->AddRecPoint(cc);
	302	}
	303	ncl++;
f6b6d58e	304	}
04366a57	305	}
04366a57	306	}
add58ef6	307	}
85bdbebe	308
85bdbebe	309	}
f6b6d58e	310	//______________________________________________________________________
04366a57	311	void AliITSClusterFinderV2SDD::RawdataToClusters(AliRawReader* rawReader,TClonesArray** clusters){
	312	//------------------------------------------------------------
	313	// This function creates ITS clusters from raw data
	314	//------------------------------------------------------------
d9ed1779	315
	316	AliITSRawStream* inputSDD=AliITSRawStreamSDD::CreateRawStreamSDD(rawReader);
	317	AliDebug(1,Form("%s is used",inputSDD->ClassName()));
2f8ed7ab	318
979b5a5f	319	AliITSDDLModuleMapSDD ddlmap=(AliITSDDLModuleMapSDD)fDetTypeRec->GetDDLModuleMapSDD();
2f8ed7ab	320	inputSDD->SetDDLModuleMap(ddlmap);
83ec5e27	321	for(Int_t iddl=0; iddl<AliITSDDLModuleMapSDD::GetNDDLs(); iddl++){
	322	for(Int_t icar=0; icar<AliITSDDLModuleMapSDD::GetNModPerDDL();icar++){
	323	Int_t iMod=ddlmap->GetModuleNumber(iddl,icar);
	324	if(iMod==-1) continue;
	325	AliITSCalibrationSDD* cal = (AliITSCalibrationSDD*)GetResp(iMod);
	326	if(cal==0){
	327	AliError(Form("Calibration object not present for SDD module %d\n",iMod));
	328	continue;
	329	}
253e68a0	330	Bool_t isZeroSupp=cal->GetZeroSupp();
253e68a0	331	if(isZeroSupp){
2f8ed7ab	332	for(Int_t iSid=0; iSid<2; iSid++) inputSDD->SetZeroSuppLowThreshold(iMod-240,iSid,cal->GetZSLowThreshold(iSid));
83ec5e27	333	}else{
2f8ed7ab	334	for(Int_t iSid=0; iSid<2; iSid++) inputSDD->SetZeroSuppLowThreshold(iMod-240,iSid,0);
83ec5e27	335	}
	336	}
	337	}
2f8ed7ab	338	FindClustersSDD(inputSDD,clusters);
2f8ed7ab	339	delete inputSDD;
04366a57	340	}
	341
	342	void AliITSClusterFinderV2SDD::FindClustersSDD(AliITSRawStream* input,
	343	TClonesArray** clusters)
	344	{
	345	//------------------------------------------------------------
	346	// Actual SDD cluster finder for raw data
	347	//------------------------------------------------------------
	348	Int_t nClustersSDD = 0;
ae485645	349	AliBin *bins[2];
add58ef6	350	TBits* anodeFired[2];
	351	TBits* ddlAnodeFired[kHybridsPerDDL];
	352	for(Int_t iHyb=0;iHyb<kHybridsPerDDL;iHyb++){
	353	ddlAnodeFired[iHyb]=new TBits(fNAnodes);
	354	ddlAnodeFired[iHyb]->ResetAllBits();
	355	}
de075dae	356	Int_t vectModId[kModulesPerDDL];
	357	for(Int_t iMod=0; iMod<kModulesPerDDL; iMod++) vectModId[iMod]=-1;
	358
04366a57	359	// read raw data input stream
14dceddf	360	while (input->Next()) {
e4da2288	361	Int_t iModule = input->GetModuleID();
93a93288	362	if(iModule<0){
	363	AliWarning(Form("Invalid SDD module number %d\n", iModule));
	364	continue;
	365	}
6297cc01	366	Int_t iCarlos =input->GetCarlosId();
6297cc01	367	Int_t iSide = input->GetChannel();
14dceddf	368	Int_t iHybrid=iCarlos*2+iSide;
de075dae	369
14dceddf	370	if (input->IsCompletedModule()) {
de075dae	371	// store the module number
	372	vectModId[iCarlos]=iModule;
	373	}
	374	else if (input->IsCompletedDDL()) {
	375	// when all data from a DDL was read, search for clusters
	376	Int_t jitter=input->GetJitter();
	377	for(Int_t iMod=0; iMod<kModulesPerDDL; iMod++){
	378	if(vectModId[iMod]>=0){
	379	fModule = vectModId[iMod];
	380	clusters[fModule] = new TClonesArray("AliITSRecPoint");
add58ef6	381	bins[0]=fDDLBins[iMod*2]; // first hybrid of the module
	382	bins[1]=fDDLBins[iMod*2+1]; // second hybrid of the module
	383	anodeFired[0]=ddlAnodeFired[iMod*2];
	384	anodeFired[1]=ddlAnodeFired[iMod*2+1];
	385	FindClustersSDD(bins, anodeFired, NULL, clusters[fModule],jitter);
de075dae	386	Int_t nClusters = clusters[fModule]->GetEntriesFast();
	387	nClustersSDD += nClusters;
	388	vectModId[iMod]=-1;
	389	}
add58ef6	390	for (Int_t s=0; s<2; s++){
	391	Int_t indexHyb=iMod*2+s;
	392	for(Int_t iAnode=0; iAnode<GetSeg()->NpzHalf(); iAnode++){
	393	if(ddlAnodeFired[indexHyb]->TestBitNumber(iAnode)==kFALSE) continue;
	394	for(Int_t iTimeBin=0; iTimeBin<GetSeg()->Npx(); iTimeBin++){
	395	Int_t index=(iTimeBin+1)*fNZbins+(iAnode+1);
	396	fDDLBins[indexHyb][index].Reset();
	397	}
	398	}
de075dae	399	}
add58ef6	400	ddlAnodeFired[iMod*2]->ResetAllBits();
add58ef6	401	ddlAnodeFired[iMod*2+1]->ResetAllBits();
44c5b268	402	}
5dfa68c5	403	}else{
04366a57	404	// fill the current digit into the bins array
44c5b268	405	if(iHybrid<0 \|\| iHybrid>=kHybridsPerDDL){
	406	AliWarning(Form("Invalid SDD hybrid number %d on module %d\n", iHybrid,iModule));
	407	continue;
	408	}
e4da2288	409	AliITSCalibrationSDD* cal = (AliITSCalibrationSDD*)GetResp(iModule);
9c7f5947	410	if(cal==0){
	411	AliError(Form("Calibration object not present for SDD module %d\n",iModule));
	412	continue;
	413	}
5683bd96	414	Float_t charge=input->GetSignal();
add58ef6	415	Int_t chan=input->GetCoord1()+fNAnodes*iSide;
75065a60	416	Float_t gain=cal->GetChannelGain(chan)/fDetTypeRec->GetAverageGainSDD();;
20f3f947	417	Float_t baseline = cal->GetBaseline(chan);
	418	if(charge>baseline) charge-=baseline;
	419	else charge=0;
9c7f5947	420	if(gain>0.){ // Bad channels have gain=0
	421	charge/=gain;
	422	if(charge>=cal->GetThresholdAnode(chan)) {
	423	Int_t q=(Int_t)(charge+0.5);
	424	Int_t iz = input->GetCoord1();
	425	Int_t itb = input->GetCoord2();
add58ef6	426	Int_t index = (itb+1) * fNZbins + (iz+1);
	427	if((itb < fNTimeBins) && (iz < fNAnodes)) {
	428	fDDLBins[iHybrid][index].SetQ(q);
	429	fDDLBins[iHybrid][index].SetMask(1);
	430	fDDLBins[iHybrid][index].SetIndex(index);
	431	ddlAnodeFired[iHybrid]->SetBitNumber(iz);
9c7f5947	432	}else{
	433	AliWarning(Form("Invalid SDD cell: Anode=%d TimeBin=%d",iz,itb));
	434	}
93a93288	435	}
5dfa68c5	436	}
04366a57	437	}
04366a57	438	}
add58ef6	439	for(Int_t iHyb=0;iHyb<kHybridsPerDDL;iHyb++){
	440	delete ddlAnodeFired[iHyb];
	441	}
	442	Info("FindClustersSDD", "found clusters in ITS SDD: %d", nClustersSDD);
04366a57	443	}
04366a57	444
e3ee4984	445	//______________________________________________________________________
add58ef6	446	Bool_t AliITSClusterFinderV2SDD::NoiseSuppress(Int_t k, Int_t sid, AliBin* bins, AliITSCalibrationSDD* cal) const {
e3ee4984	447	// applies zero suppression using the measured noise of each anode
e3ee4984	448	// threshold values from ALICE-INT-1999-28 V10
2b025386	449	// returns kTRUE if the digit should eb noise suppressed, kFALSE if it should be kept
83ec5e27	450	Float_t xfactL=2.2;
83ec5e27	451	Float_t xfactH=4.0;
e3ee4984	452	//
e3ee4984	453
add58ef6	454	Int_t iAn=(k%fNZbins)-1;
2b025386	455	if(iAn<0 \|\| iAn>255) return kTRUE;
e3ee4984	456	if(sid==1) iAn+=256;
	457	Int_t nLow=0, nHigh=0;
	458	Float_t noise=cal->GetNoiseAfterElectronics(iAn);
	459	Float_t noisem1=noise;
	460	if(iAn>1) noisem1=cal->GetNoiseAfterElectronics(iAn-1);
	461	Float_t noisep1=noise;
	462	if(iAn<511) noisep1=cal->GetNoiseAfterElectronics(iAn+1);
83ec5e27	463	Float_t tL=noise*xfactL;
	464	Float_t tH=noise*xfactH;
	465	Float_t tLp1=noisep1*xfactL;
	466	Float_t tHp1=noisep1*xfactH;
	467	Float_t tLm1=noisem1*xfactL;
	468	Float_t tHm1=noisem1*xfactH;
2b025386	469	Int_t cC=bins[k].GetQ();
e3ee4984	470	if(cC<=tL){
	471	bins[k].SetQ(0);
	472	bins[k].SetMask(0xFFFFFFFE);
2b025386	473	return kTRUE;;
e3ee4984	474	}
	475	nLow++; // cC is greater than tL
	476	if(cC>tH) nHigh++;
	477	Int_t sS=bins[k-1].GetQ();
	478	if(sS>tLm1) nLow++;
	479	if(sS>tHm1) nHigh++;
	480	Int_t nN=bins[k+1].GetQ();
	481	if(nN>tLp1) nLow++;
	482	if(nN>tHp1) nHigh++;
add58ef6	483	Int_t eE=bins[k-fNZbins].GetQ();
e3ee4984	484	if(eE>tL) nLow++;
e3ee4984	485	if(eE>tH) nHigh++;
add58ef6	486	Int_t wW=bins[k+fNZbins].GetQ();
e3ee4984	487	if(wW>tL) nLow++;
e3ee4984	488	if(wW>tH) nHigh++;
ad98389f	489	if(nLow<2 \|\| nHigh<1) return kTRUE;
2b025386	490	else return kFALSE;
e3ee4984	491	}
e3ee4984	492
04366a57	493
d97eb3fe	494