[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 "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)
{

  //Default constructor

}
 

void AliITSClusterFinderV2SDD::FindRawClusters(Int_t mod){

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

}

void AliITSClusterFinderV2SDD::FindClustersSDD(TClonesArray *digits) {
  //------------------------------------------------------------
  // Actual SDD cluster finder
  //------------------------------------------------------------
  Int_t nAnodes = GetSeg()->NpzHalf();
  Int_t nzBins = nAnodes+2;
  Int_t nTimeBins = GetSeg()->Npx();
  Int_t nxBins = nTimeBins+2;
  const Int_t kMaxBin=nzBins*nxBins;

  AliBin *bins[2];
  bins[0]=new AliBin[kMaxBin];
  bins[1]=new AliBin[kMaxBin];
  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 >= nAnodes) 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 <= nAnodes){
	 bins[0][y*nzBins+z].SetQ(q);
	 bins[0][y*nzBins+z].SetMask(1);
	 bins[0][y*nzBins+z].SetIndex(i);
       } else {
	 z-=nAnodes;
	 bins[1][y*nzBins+z].SetQ(q);
	 bins[1][y*nzBins+z].SetMask(1);
	 bins[1][y*nzBins+z].SetIndex(i);
       }
     }
  }
  
  FindClustersSDD(bins, kMaxBin, nzBins, digits);

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

}

void AliITSClusterFinderV2SDD::
FindClustersSDD(AliBin* bins[2], Int_t nMaxBin, Int_t nzBins, 
		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;
  }
  Int_t ncl=0; 
  TClonesArray &cl=*clusters;
  for (Int_t s=0; s<2; s++)
    for (Int_t i=0; i<nMaxBin; i++) {
      if(NoiseSuppress(i,s,nzBins,bins[s],cal)) continue;
      if (bins[s][i].IsUsed()) continue;
      Int_t idx[32]; UInt_t msk[32]; Int_t npeaks=0;
      FindPeaks(i, nzBins, 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]/nzBins, kj=idx[k] - ki*nzBins;
	  Int_t li=idx[l]/nzBins, lj=idx[l] - li*nzBins;
	  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]), nzBins, bins[s], msk[k]);
      }
        
      for (k=0; k<npeaks; k++) {
	if (idx[k] < 0) continue; //removed peak
	AliITSRecPoint c;
	MakeCluster(idx[k], nzBins, 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++){
	    Int_t index = idx[k]+di+dj*nzBins;
	    if (index<0) continue;
	    if (index>=nMaxBin) continue;
	    AliBin *b=&bins[s][index];
	    Int_t nAnode=index%nzBins-1;
	    Int_t adcSignal=b->GetQ();
	    if(adcSignal>cal->GetThresholdAnode(nAnode)){
	      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();  //to have MPV 1 MIP = 86.4 KeV
	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) {	  
	  //	   AliBin *b=&bins[s][idx[k]];
	  //	   AliITSdigitSDD* d=(AliITSdigitSDD*)digits->UncheckedAt(b->GetIndex());
	  {
	    //Int_t lab[3];
	    //lab[0]=(d->GetTracks())[0];
	    //lab[1]=(d->GetTracks())[1];
	    //lab[2]=(d->GetTracks())[2];
	    //CheckLabels(lab);
	    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
  //------------------------------------------------------------
  rawReader->Reset();
  AliITSRawStream* inputSDD;
  if(fDetTypeRec->IsHLTmodeC()==kTRUE){
    inputSDD=new AliITSRawStreamSDDCompressed(rawReader);
  }else{
    inputSDD=new AliITSRawStreamSDD(rawReader);
  }

  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;
  Int_t nAnodes = GetSeg()->NpzHalf();
  Int_t nzBins = nAnodes+2;
  Int_t nTimeBins = GetSeg()->Npx();
  Int_t nxBins = nTimeBins+2;
  const Int_t kMaxBin=nzBins*nxBins;
  AliBin *bins[2];
  AliBin *ddlbins[kHybridsPerDDL]; // 12 modules (=24 hybrids) of 1 DDL read "in parallel"
  for(Int_t iHyb=0;iHyb<kHybridsPerDDL;iHyb++) ddlbins[iHyb]=new AliBin[kMaxBin];
  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]=ddlbins[iMod*2];   // first hybrid of the module
	  bins[1]=ddlbins[iMod*2+1]; // second hybrid of the module
	  FindClustersSDD(bins, kMaxBin, nzBins, NULL, clusters[fModule],jitter);
	  Int_t nClusters = clusters[fModule]->GetEntriesFast();
	  nClustersSDD += nClusters;
	  vectModId[iMod]=-1;
	}
	for(Int_t iBin=0;iBin<kMaxBin; iBin++){
	  ddlbins[iMod*2][iBin].Reset();
	  ddlbins[iMod*2+1][iBin].Reset();
	}
      }
    }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()+nAnodes*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) * nzBins + (iz+1);
	  if(index<kMaxBin){
	    ddlbins[iHybrid][index].SetQ(q);
	    ddlbins[iHybrid][index].SetMask(1);
	    ddlbins[iHybrid][index].SetIndex(index);
	  }else{
	    AliWarning(Form("Invalid SDD cell: Anode=%d   TimeBin=%d",iz,itb));	  
	  }
	}
      }
    }
  }
  for(Int_t iHyb=0;iHyb<kHybridsPerDDL;iHyb++) delete [] ddlbins[iHyb];
  Info("FindClustersSDD", "found clusters in ITS SDD: %d", nClustersSDD);
}

//______________________________________________________________________
Bool_t AliITSClusterFinderV2SDD::NoiseSuppress(Int_t k, Int_t sid,Int_t nzBins, 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%nzBins)-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-nzBins].GetQ();
  if(eE>tL) nLow++;
  if(eE>tH) nHigh++;
  Int_t wW=bins[k+nzBins].GetQ();
  if(wW>tL) nLow++;
  if(wW>tH) nHigh++;
  if(nLow<3 || 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>
04366a57	28	#include "AliITSClusterFinderV2SDD.h"
00a7cc50	29	#include "AliITSRecPoint.h"
7d62fb64	30	#include "AliITSDetTypeRec.h"
04366a57	31	#include "AliRawReader.h"
0599a018	32	#include "AliITSRawStreamSDD.h"
2f8ed7ab	33	#include "AliITSRawStreamSDDCompressed.h"
5bfe44ce	34	#include "AliITSCalibrationSDD.h"
253e68a0	35	#include "AliITSresponseSDD.h"
5bfe44ce	36	#include "AliITSDetTypeRec.h"
debf7b78	37	#include "AliITSReconstructor.h"
5bfe44ce	38	#include "AliITSsegmentationSDD.h"
04366a57	39	#include "AliITSdigitSDD.h"
b4704be3	40	#include "AliITSgeomTGeo.h"
debf7b78	41
04366a57	42	ClassImp(AliITSClusterFinderV2SDD)
04366a57	43
5d2c2f86	44	AliITSClusterFinderV2SDD::AliITSClusterFinderV2SDD(AliITSDetTypeRec* dettyp):AliITSClusterFinder(dettyp)
a66a0eb6	45	{
04366a57	46
	47	//Default constructor
	48
04366a57	49	}
	50
	51
	52	void AliITSClusterFinderV2SDD::FindRawClusters(Int_t mod){
	53
	54	//Find clusters V2
	55	SetModule(mod);
	56	FindClustersSDD(fDigits);
	57
	58	}
	59
	60	void AliITSClusterFinderV2SDD::FindClustersSDD(TClonesArray *digits) {
	61	//------------------------------------------------------------
	62	// Actual SDD cluster finder
	63	//------------------------------------------------------------
4952f440	64	Int_t nAnodes = GetSeg()->NpzHalf();
	65	Int_t nzBins = nAnodes+2;
	66	Int_t nTimeBins = GetSeg()->Npx();
	67	Int_t nxBins = nTimeBins+2;
f6b6d58e	68	const Int_t kMaxBin=nzBins*nxBins;
04366a57	69
04366a57	70	AliBin *bins[2];
4952f440	71	bins[0]=new AliBin[kMaxBin];
4952f440	72	bins[1]=new AliBin[kMaxBin];
404c1c29	73	AliITSCalibrationSDD* cal = (AliITSCalibrationSDD*)GetResp(fModule);
9c7f5947	74	if(cal==0){
	75	AliError(Form("Calibration object not present for SDD module %d\n",fModule));
	76	return;
	77	}
83ec5e27	78
04366a57	79	AliITSdigitSDD *d=0;
	80	Int_t i, ndigits=digits->GetEntriesFast();
	81	for (i=0; i<ndigits; i++) {
	82	d=(AliITSdigitSDD*)digits->UncheckedAt(i);
20f3f947	83	Int_t ian=d->GetCoord1();
	84	Int_t itb=d->GetCoord2();
	85	Int_t iSide=0;
	86	if (ian >= nAnodes) iSide=1;
75065a60	87	Float_t gain=cal->GetChannelGain(ian)/fDetTypeRec->GetAverageGainSDD();
83ec5e27	88	Float_t charge=d->GetSignal(); // returns expanded signal
83ec5e27	89	// (10 bit, low threshold already added)
20f3f947	90	Float_t baseline = cal->GetBaseline(ian);
	91	if(charge>baseline) charge-=baseline;
	92	else charge=0;
5683bd96	93
9c7f5947	94	if(gain>0.){ // Bad channels have gain=0.
9c7f5947	95	charge/=gain;
20f3f947	96	if(charge<cal->GetThresholdAnode(ian)) continue;
9c7f5947	97	Int_t q=(Int_t)(charge+0.5);
20f3f947	98	Int_t y=itb+1;
20f3f947	99	Int_t z=ian+1;
9c7f5947	100	if (z <= nAnodes){
	101	bins[0][y*nzBins+z].SetQ(q);
	102	bins[0][y*nzBins+z].SetMask(1);
	103	bins[0][y*nzBins+z].SetIndex(i);
	104	} else {
	105	z-=nAnodes;
	106	bins[1][y*nzBins+z].SetQ(q);
	107	bins[1][y*nzBins+z].SetMask(1);
	108	bins[1][y*nzBins+z].SetIndex(i);
	109	}
04366a57	110	}
	111	}
	112
4952f440	113	FindClustersSDD(bins, kMaxBin, nzBins, digits);
04366a57	114
	115	delete[] bins[0];
	116	delete[] bins[1];
	117
	118	}
	119
	120	void AliITSClusterFinderV2SDD::
	121	FindClustersSDD(AliBin* bins[2], Int_t nMaxBin, Int_t nzBins,
de075dae	122	TClonesArray digits, TClonesArray clusters, Int_t jitter) {
04366a57	123	//------------------------------------------------------------
	124	// Actual SDD cluster finder
	125	//------------------------------------------------------------
b4704be3	126
debf7b78	127	static AliITSRecoParam *repa = NULL;
	128	if(!repa){
	129	repa = (AliITSRecoParam*) AliITSReconstructor::GetRecoParam();
	130	if(!repa){
ed446fa3	131	repa = AliITSRecoParam::GetHighFluxParam();
debf7b78	132	AliWarning("Using default AliITSRecoParam class");
	133	}
	134	}
b4704be3	135	const TGeoHMatrix *mT2L=AliITSgeomTGeo::GetTracking2LocalMatrix(fModule);
404c1c29	136	AliITSCalibrationSDD* cal = (AliITSCalibrationSDD*)GetResp(fModule);
9c7f5947	137	if(cal==0){
	138	AliError(Form("Calibration object not present for SDD module %d\n",fModule));
	139	return;
	140	}
04366a57	141	Int_t ncl=0;
	142	TClonesArray &cl=*clusters;
	143	for (Int_t s=0; s<2; s++)
	144	for (Int_t i=0; i<nMaxBin; i++) {
2b025386	145	if(NoiseSuppress(i,s,nzBins,bins[s],cal)) continue;
04366a57	146	if (bins[s][i].IsUsed()) continue;
	147	Int_t idx[32]; UInt_t msk[32]; Int_t npeaks=0;
	148	FindPeaks(i, nzBins, bins[s], idx, msk, npeaks);
	149
	150	if (npeaks>30) continue;
	151	if (npeaks==0) continue;
	152
	153	Int_t k,l;
	154	for (k=0; k<npeaks-1; k++){//mark adjacent peaks
	155	if (idx[k] < 0) continue; //this peak is already removed
	156	for (l=k+1; l<npeaks; l++) {
f6b6d58e	157	if (idx[l] < 0) continue; //this peak is already removed
	158	Int_t ki=idx[k]/nzBins, kj=idx[k] - ki*nzBins;
	159	Int_t li=idx[l]/nzBins, lj=idx[l] - li*nzBins;
	160	Int_t di=TMath::Abs(ki - li);
	161	Int_t dj=TMath::Abs(kj - lj);
	162	if (di>1 \|\| dj>1) continue;
	163	if (bins[s][idx[k]].GetQ() > bins[s][idx[l]].GetQ()) {
	164	msk[l]=msk[k];
	165	idx[l]*=-1;
	166	} else {
	167	msk[k]=msk[l];
	168	idx[k]*=-1;
	169	break;
	170	}
04366a57	171	}
	172	}
	173
	174	for (k=0; k<npeaks; k++) {
debf7b78	175	if(repa->GetUseUnfoldingInClusterFinderSDD()==kFALSE) msk[k]=msk[0];
04366a57	176	MarkPeak(TMath::Abs(idx[k]), nzBins, bins[s], msk[k]);
	177	}
	178
	179	for (k=0; k<npeaks; k++) {
f6b6d58e	180	if (idx[k] < 0) continue; //removed peak
	181	AliITSRecPoint c;
	182	MakeCluster(idx[k], nzBins, bins[s], msk[k], c);
	183	//mi change
	184	Int_t milab[10];
	185	for (Int_t ilab=0;ilab<10;ilab++){
	186	milab[ilab]=-2;
	187	}
	188	Int_t maxi=0,mini=0,maxj=0,minj=0;
2b025386	189
b779c7dc	190	for (Int_t di=-5; di<=5;di++){
b779c7dc	191	for (Int_t dj=-10;dj<=10;dj++){
f6b6d58e	192	Int_t index = idx[k]+di+dj*nzBins;
	193	if (index<0) continue;
	194	if (index>=nMaxBin) continue;
	195	AliBin *b=&bins[s][index];
	196	Int_t nAnode=index%nzBins-1;
	197	Int_t adcSignal=b->GetQ();
	198	if(adcSignal>cal->GetThresholdAnode(nAnode)){
	199	if (di>maxi) maxi=di;
	200	if (di<mini) mini=di;
	201	if (dj>maxj) maxj=dj;
	202	if (dj<minj) minj=dj;
	203	}
	204	//
	205	if(digits) {
	206	if (TMath::Abs(di)<2&&TMath::Abs(dj)<2){
	207	AliITSdigitSDD* d=(AliITSdigitSDD*)digits->UncheckedAt(b->GetIndex());
	208	for (Int_t itrack=0;itrack<10;itrack++){
	209	Int_t track = (d->GetTracks())[itrack];
	210	if (track>=0) {
	211	AddLabel(milab, track);
	212	}
	213	}
	214	}
	215	}
	216	}
	217	}
b779c7dc	218	Int_t clSizAnode=maxi-mini+1;
	219	Int_t clSizTb=maxj-minj+1;
	220	if(repa->GetUseSDDClusterSizeSelection()){
	221	if(clSizTb==1) continue; // cut common mode noise spikes
	222	if(clSizAnode>3) continue; // cut common mode noise spikes
	223	if(clSizTb>10) continue; // cut clusters on noisy anodes
	224	}
f6b6d58e	225
253e68a0	226	AliITSresponseSDD* rsdd = fDetTypeRec->GetResponseSDD();
253e68a0	227	Float_t y=c.GetY(),z=c.GetZ(), q=c.GetQ();
f6b6d58e	228	y/=q; z/=q;
	229	Float_t zAnode=z-0.5; // to have anode in range 0.-255. and centered on the mid of the pitch
	230	Float_t timebin=y-0.5; // to have time bin in range 0.-255. amd centered on the mid of the bin
	231	if(s==1) zAnode += GetSeg()->NpzHalf(); // right side has anodes from 256. to 511.
	232	Float_t zdet = GetSeg()->GetLocalZFromAnode(zAnode);
de075dae	233	Float_t driftTimeUncorr = GetSeg()->GetDriftTimeFromTb(timebin)+jitter*rsdd->GetCarlosRXClockPeriod();
3176641e	234	Float_t driftTime=driftTimeUncorr-rsdd->GetTimeZero(fModule);
69b82143	235	Float_t driftSpeed = cal->GetDriftSpeedAtAnode(zAnode) + rsdd->GetDeltaVDrift(fModule);
69b82143	236	Float_t driftPathMicron = driftTime*driftSpeed;
f6b6d58e	237	const Double_t kMicronTocm = 1.0e-4;
	238	Float_t xdet=(driftPathMicron-GetSeg()->Dx())*kMicronTocm; // xdet is negative
	239	if (s==0) xdet=-xdet; // left side has positive local x
c9a38d3d	240
ba0a07bf	241	if(repa->GetUseSDDCorrectionMaps()){
	242	Float_t corrx=0, corrz=0;
	243	cal->GetCorrections(zdet,xdet,corrz,corrx,GetSeg());
	244	zdet+=corrz;
	245	xdet+=corrx;
	246	}
f6b6d58e	247
	248	Double_t loc[3]={xdet,0.,zdet},trk[3]={0.,0.,0.};
	249	mT2L->MasterToLocal(loc,trk);
	250	y=trk[1];
	251	z=trk[2];
	252
253e68a0	253	q/=rsdd->GetADC2keV(); //to have MPV 1 MIP = 86.4 KeV
aebba721	254	if(cal-> IsAMAt20MHz()) q*=2.; // account for 1/2 sampling freq.
b779c7dc	255	if(q<repa->GetMinClusterChargeSDD()) continue; // remove noise clusters
b779c7dc	256
f6b6d58e	257	Float_t hit[5] = {y, z, 0.00300.0030, 0.00200.0020, q};
b779c7dc	258	Int_t info[3] = {clSizTb, clSizAnode, fNlayer[fModule]};
f6b6d58e	259	if (digits) {
	260	// AliBin *b=&bins[s][idx[k]];
	261	// AliITSdigitSDD* d=(AliITSdigitSDD*)digits->UncheckedAt(b->GetIndex());
	262	{
	263	//Int_t lab[3];
	264	//lab[0]=(d->GetTracks())[0];
	265	//lab[1]=(d->GetTracks())[1];
	266	//lab[2]=(d->GetTracks())[2];
	267	//CheckLabels(lab);
	268	CheckLabels2(milab);
	269	}
	270	}
	271	milab[3]=fNdet[fModule];
f6b6d58e	272	AliITSRecPoint cc(milab,hit,info);
f6b6d58e	273	cc.SetType(npeaks);
b2558977	274	cc.SetDriftTime(driftTimeUncorr);
f6b6d58e	275	if(clusters) new (cl[ncl]) AliITSRecPoint(cc);
	276	else {
	277	fDetTypeRec->AddRecPoint(cc);
	278	}
	279	ncl++;
04366a57	280	}
04366a57	281	}
24c98369	282
04366a57	283	}
f6b6d58e	284	//______________________________________________________________________
04366a57	285	void AliITSClusterFinderV2SDD::RawdataToClusters(AliRawReader* rawReader,TClonesArray** clusters){
	286	//------------------------------------------------------------
	287	// This function creates ITS clusters from raw data
	288	//------------------------------------------------------------
	289	rawReader->Reset();
2f8ed7ab	290	AliITSRawStream* inputSDD;
	291	if(fDetTypeRec->IsHLTmodeC()==kTRUE){
	292	inputSDD=new AliITSRawStreamSDDCompressed(rawReader);
	293	}else{
	294	inputSDD=new AliITSRawStreamSDD(rawReader);
	295	}
	296
979b5a5f	297	AliITSDDLModuleMapSDD ddlmap=(AliITSDDLModuleMapSDD)fDetTypeRec->GetDDLModuleMapSDD();
2f8ed7ab	298	inputSDD->SetDDLModuleMap(ddlmap);
83ec5e27	299	for(Int_t iddl=0; iddl<AliITSDDLModuleMapSDD::GetNDDLs(); iddl++){
	300	for(Int_t icar=0; icar<AliITSDDLModuleMapSDD::GetNModPerDDL();icar++){
	301	Int_t iMod=ddlmap->GetModuleNumber(iddl,icar);
	302	if(iMod==-1) continue;
	303	AliITSCalibrationSDD* cal = (AliITSCalibrationSDD*)GetResp(iMod);
	304	if(cal==0){
	305	AliError(Form("Calibration object not present for SDD module %d\n",iMod));
	306	continue;
	307	}
253e68a0	308	Bool_t isZeroSupp=cal->GetZeroSupp();
253e68a0	309	if(isZeroSupp){
2f8ed7ab	310	for(Int_t iSid=0; iSid<2; iSid++) inputSDD->SetZeroSuppLowThreshold(iMod-240,iSid,cal->GetZSLowThreshold(iSid));
83ec5e27	311	}else{
2f8ed7ab	312	for(Int_t iSid=0; iSid<2; iSid++) inputSDD->SetZeroSuppLowThreshold(iMod-240,iSid,0);
83ec5e27	313	}
	314	}
	315	}
2f8ed7ab	316	FindClustersSDD(inputSDD,clusters);
2f8ed7ab	317	delete inputSDD;
04366a57	318	}
	319
	320	void AliITSClusterFinderV2SDD::FindClustersSDD(AliITSRawStream* input,
	321	TClonesArray** clusters)
	322	{
	323	//------------------------------------------------------------
	324	// Actual SDD cluster finder for raw data
	325	//------------------------------------------------------------
	326	Int_t nClustersSDD = 0;
4952f440	327	Int_t nAnodes = GetSeg()->NpzHalf();
	328	Int_t nzBins = nAnodes+2;
	329	Int_t nTimeBins = GetSeg()->Npx();
	330	Int_t nxBins = nTimeBins+2;
f6b6d58e	331	const Int_t kMaxBin=nzBins*nxBins;
ae485645	332	AliBin *bins[2];
93a93288	333	AliBin *ddlbins[kHybridsPerDDL]; // 12 modules (=24 hybrids) of 1 DDL read "in parallel"
93a93288	334	for(Int_t iHyb=0;iHyb<kHybridsPerDDL;iHyb++) ddlbins[iHyb]=new AliBin[kMaxBin];
de075dae	335	Int_t vectModId[kModulesPerDDL];
	336	for(Int_t iMod=0; iMod<kModulesPerDDL; iMod++) vectModId[iMod]=-1;
	337
04366a57	338	// read raw data input stream
14dceddf	339	while (input->Next()) {
e4da2288	340	Int_t iModule = input->GetModuleID();
93a93288	341	if(iModule<0){
	342	AliWarning(Form("Invalid SDD module number %d\n", iModule));
	343	continue;
	344	}
6297cc01	345	Int_t iCarlos =input->GetCarlosId();
6297cc01	346	Int_t iSide = input->GetChannel();
14dceddf	347	Int_t iHybrid=iCarlos*2+iSide;
de075dae	348
14dceddf	349	if (input->IsCompletedModule()) {
de075dae	350	// store the module number
	351	vectModId[iCarlos]=iModule;
	352	}
	353	else if (input->IsCompletedDDL()) {
	354	// when all data from a DDL was read, search for clusters
	355	Int_t jitter=input->GetJitter();
	356	for(Int_t iMod=0; iMod<kModulesPerDDL; iMod++){
	357	if(vectModId[iMod]>=0){
	358	fModule = vectModId[iMod];
	359	clusters[fModule] = new TClonesArray("AliITSRecPoint");
	360	bins[0]=ddlbins[iMod*2]; // first hybrid of the module
	361	bins[1]=ddlbins[iMod*2+1]; // second hybrid of the module
	362	FindClustersSDD(bins, kMaxBin, nzBins, NULL, clusters[fModule],jitter);
	363	Int_t nClusters = clusters[fModule]->GetEntriesFast();
	364	nClustersSDD += nClusters;
	365	vectModId[iMod]=-1;
	366	}
	367	for(Int_t iBin=0;iBin<kMaxBin; iBin++){
	368	ddlbins[iMod*2][iBin].Reset();
	369	ddlbins[iMod*2+1][iBin].Reset();
	370	}
44c5b268	371	}
5dfa68c5	372	}else{
04366a57	373	// fill the current digit into the bins array
44c5b268	374	if(iHybrid<0 \|\| iHybrid>=kHybridsPerDDL){
	375	AliWarning(Form("Invalid SDD hybrid number %d on module %d\n", iHybrid,iModule));
	376	continue;
	377	}
e4da2288	378	AliITSCalibrationSDD* cal = (AliITSCalibrationSDD*)GetResp(iModule);
9c7f5947	379	if(cal==0){
	380	AliError(Form("Calibration object not present for SDD module %d\n",iModule));
	381	continue;
	382	}
5683bd96	383	Float_t charge=input->GetSignal();
14dceddf	384	Int_t chan=input->GetCoord1()+nAnodes*iSide;
75065a60	385	Float_t gain=cal->GetChannelGain(chan)/fDetTypeRec->GetAverageGainSDD();;
20f3f947	386	Float_t baseline = cal->GetBaseline(chan);
	387	if(charge>baseline) charge-=baseline;
	388	else charge=0;
9c7f5947	389	if(gain>0.){ // Bad channels have gain=0
	390	charge/=gain;
	391	if(charge>=cal->GetThresholdAnode(chan)) {
	392	Int_t q=(Int_t)(charge+0.5);
	393	Int_t iz = input->GetCoord1();
	394	Int_t itb = input->GetCoord2();
	395	Int_t index = (itb+1) * nzBins + (iz+1);
	396	if(index<kMaxBin){
	397	ddlbins[iHybrid][index].SetQ(q);
	398	ddlbins[iHybrid][index].SetMask(1);
	399	ddlbins[iHybrid][index].SetIndex(index);
	400	}else{
	401	AliWarning(Form("Invalid SDD cell: Anode=%d TimeBin=%d",iz,itb));
	402	}
93a93288	403	}
5dfa68c5	404	}
04366a57	405	}
04366a57	406	}
93a93288	407	for(Int_t iHyb=0;iHyb<kHybridsPerDDL;iHyb++) delete [] ddlbins[iHyb];
04366a57	408	Info("FindClustersSDD", "found clusters in ITS SDD: %d", nClustersSDD);
04366a57	409	}
04366a57	410
e3ee4984	411	//______________________________________________________________________
2b025386	412	Bool_t AliITSClusterFinderV2SDD::NoiseSuppress(Int_t k, Int_t sid,Int_t nzBins, AliBin* bins, AliITSCalibrationSDD* cal) const {
e3ee4984	413	// applies zero suppression using the measured noise of each anode
e3ee4984	414	// threshold values from ALICE-INT-1999-28 V10
2b025386	415	// returns kTRUE if the digit should eb noise suppressed, kFALSE if it should be kept
83ec5e27	416	Float_t xfactL=2.2;
83ec5e27	417	Float_t xfactH=4.0;
e3ee4984	418	//
	419
	420	Int_t iAn=(k%nzBins)-1;
2b025386	421	if(iAn<0 \|\| iAn>255) return kTRUE;
e3ee4984	422	if(sid==1) iAn+=256;
	423	Int_t nLow=0, nHigh=0;
	424	Float_t noise=cal->GetNoiseAfterElectronics(iAn);
	425	Float_t noisem1=noise;
	426	if(iAn>1) noisem1=cal->GetNoiseAfterElectronics(iAn-1);
	427	Float_t noisep1=noise;
	428	if(iAn<511) noisep1=cal->GetNoiseAfterElectronics(iAn+1);
83ec5e27	429	Float_t tL=noise*xfactL;
	430	Float_t tH=noise*xfactH;
	431	Float_t tLp1=noisep1*xfactL;
	432	Float_t tHp1=noisep1*xfactH;
	433	Float_t tLm1=noisem1*xfactL;
	434	Float_t tHm1=noisem1*xfactH;
2b025386	435	Int_t cC=bins[k].GetQ();
e3ee4984	436	if(cC<=tL){
	437	bins[k].SetQ(0);
	438	bins[k].SetMask(0xFFFFFFFE);
2b025386	439	return kTRUE;;
e3ee4984	440	}
	441	nLow++; // cC is greater than tL
	442	if(cC>tH) nHigh++;
	443	Int_t sS=bins[k-1].GetQ();
	444	if(sS>tLm1) nLow++;
	445	if(sS>tHm1) nHigh++;
	446	Int_t nN=bins[k+1].GetQ();
	447	if(nN>tLp1) nLow++;
	448	if(nN>tHp1) nHigh++;
	449	Int_t eE=bins[k-nzBins].GetQ();
	450	if(eE>tL) nLow++;
	451	if(eE>tH) nHigh++;
	452	Int_t wW=bins[k+nzBins].GetQ();
	453	if(wW>tL) nLow++;
	454	if(wW>tH) nHigh++;
2b025386	455	if(nLow<3 \|\| nHigh<1) return kTRUE;
2b025386	456	else return kFALSE;
e3ee4984	457	}
e3ee4984	458
04366a57	459
d97eb3fe	460