Fixed bug in parent assignment and implemented Birk's law in the Step Manager

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

/**************************************************************************
 * Copyright(c) 1998-1999, 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.                  *
 **************************************************************************/

/* $Id$ */

#include <Riostream.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>

#include <TSystem.h>
#include <TROOT.h>
#include <TStopwatch.h>
#include <TCanvas.h>
#include <TF1.h>
#include <TRandom.h>
#include <TH1.h>
#include <TFile.h>
#include <TVector.h>
#include <TArrayI.h>
#include <TArrayF.h>

#include "AliRun.h"
#include "AliITS.h"
#include "AliITShit.h"
#include "AliITSdigitSDD.h"
#include "AliITSdigitSPD.h"
#include "AliITSmodule.h"
#include "AliITSpList.h"
#include "AliITSMapA1.h"
#include "AliITSMapA2.h"
#include "AliITSetfSDD.h"
#include "AliITSRawData.h"
#include "AliITSHuffman.h"
#include "AliITSgeom.h"
#include "AliITSsegmentation.h"
#include "AliITSresponse.h"
#include "AliITSsegmentationSDD.h"
#include "AliITSresponseSDD.h"
#include "AliITSsimulationSDD.h"

ClassImp(AliITSsimulationSDD)
////////////////////////////////////////////////////////////////////////
// Version: 0
// Written by Piergiorgio Cerello
// November 23 1999
//
// AliITSsimulationSDD is the simulation of SDDs.
  //
//Begin_Html
/*
 <img src="picts/ITS/AliITShit_Class_Diagram.gif">
 </pre>
 <br clear=left>
 <font size=+2 color=red>
 <p>This show the relasionships between the ITS hit class and the rest of Aliroot.
 </font>
 <pre>
 */
 //End_Html

 //______________________________________________________________________
  Int_t power(Int_t b, Int_t e) {
  // compute b to the e power, where both b and e are Int_ts.
  Int_t power = 1,i;

  for(i=0; i<e; i++) power *= b;
  return power;
}
//______________________________________________________________________
void FastFourierTransform(AliITSetfSDD *alisddetf,Double_t *real,
                          Double_t *imag,Int_t direction) {
  // Do a Fast Fourier Transform

  Int_t samples = alisddetf->GetSamples();
  Int_t l = (Int_t) ((log((Float_t) samples)/log(2.))+0.5);
  Int_t m1 = samples;
  Int_t m  = samples/2;
  Int_t m2 = samples/m1;
  Int_t i,j,k;
  for(i=1; i<=l; i++) {
    for(j=0; j<samples; j += m1) {
      Int_t p = 0;
      for(k=j; k<= j+m-1; k++) {
	Double_t wsr = alisddetf->GetWeightReal(p);
	Double_t wsi = alisddetf->GetWeightImag(p);
	if(direction == -1) wsi = -wsi;
	Double_t xr = *(real+k+m);
	Double_t xi = *(imag+k+m);
	*(real+k+m) = wsr*(*(real+k)-xr) - wsi*(*(imag+k)-xi);
	*(imag+k+m) = wsr*(*(imag+k)-xi) + wsi*(*(real+k)-xr);
	*(real+k) += xr;
	*(imag+k) += xi;
	p += m2;
      } // end for k
    } // end for j
    m1 = m;
    m /= 2;
    m2 += m2;
  } // end for i
  
  for(j=0; j<samples; j++) {
    Int_t j1 = j;
    Int_t p = 0;
    Int_t i1;
    for(i1=1; i1<=l; i1++) {
      Int_t j2 = j1;
      j1 /= 2;
      p = p + p + j2 - j1 - j1;
    } // end for i1
    if(p >= j) {
      Double_t xr = *(real+j);
      Double_t xi = *(imag+j);
      *(real+j) = *(real+p);
      *(imag+j) = *(imag+p);
      *(real+p) = xr;
      *(imag+p) = xi;
    } // end if p>=j
  } // end for j
  if(direction == -1) {
    for(i=0; i<samples; i++) {
      *(real+i) /= samples;
      *(imag+i) /= samples;
    } // end for i
  } // end if direction == -1
  return;
}
//______________________________________________________________________
AliITSsimulationSDD::AliITSsimulationSDD() {
  // Default constructor

  fResponse      = 0;
  fSegmentation  = 0;
  fHis           = 0;
  //    fpList         = 0;
  fHitMap2       = 0;
  fHitSigMap2    = 0;
  fHitNoiMap2    = 0;
  fElectronics   = 0;
  fStream        = 0;
  fInZR          = 0;
  fInZI          = 0;
  fOutZR         = 0;
  fOutZI         = 0;
  fNofMaps       = 0;
  fMaxNofSamples = 0;
  fITS           = 0;
  fTreeB         = 0;
  fAnodeFire     = 0;
  SetScaleFourier();
  SetPerpendTracksFlag();
  SetCrosstalkFlag();
  SetDoFFT();
  SetCheckNoise();
}
//______________________________________________________________________
AliITSsimulationSDD::AliITSsimulationSDD(AliITSsimulationSDD &source) :
  AliITSsimulation(source){
  // Copy constructor to satify Coding roules only.

  if(this==&source) return;
  Error("AliITSsimulationSSD","Not allowed to make a copy of "
	"AliITSsimulationSDD Using default creater instead");
  AliITSsimulationSDD();
}
//______________________________________________________________________
AliITSsimulationSDD& AliITSsimulationSDD::operator=(AliITSsimulationSDD &src){
  // Assignment operator to satify Coding roules only.

  if(this==&src) return *this;
  Error("AliITSsimulationSSD","Not allowed to make a = with "
	"AliITSsimulationSDD Using default creater instead");
  return *this ;
}
//______________________________________________________________________
AliITSsimulationSDD::AliITSsimulationSDD(AliITSsegmentation *seg,
                                         AliITSresponse *resp){
  // Standard Constructor

  fResponse      = 0;
  fSegmentation  = 0;
  fHis           = 0;
  //    fpList         = 0;
  fHitMap2       = 0;
  fHitSigMap2    = 0;
  fHitNoiMap2    = 0;
  fElectronics   = 0;
  fStream        = 0;
  fInZR          = 0;
  fInZI          = 0;
  fOutZR         = 0;
  fOutZI         = 0;
  fNofMaps       = 0;
  fMaxNofSamples = 0;
  fITS           = 0;
  fTreeB         = 0;
  SetDebug(kFALSE);

  Init((AliITSsegmentationSDD*)seg,(AliITSresponseSDD*)resp);
}
//______________________________________________________________________
void AliITSsimulationSDD::Init(AliITSsegmentationSDD *seg,
                               AliITSresponseSDD *resp){
  // Standard Constructor

  fResponse     = resp;
  fSegmentation = seg;
  SetScaleFourier();
  SetPerpendTracksFlag();
  SetCrosstalkFlag();
  SetDoFFT();
  SetCheckNoise();

  fpList = new AliITSpList( fSegmentation->Npz(),
			    fScaleSize*fSegmentation->Npx() );
  fHitSigMap2 = new AliITSMapA2(fSegmentation,fScaleSize,1);
  fHitNoiMap2 = new AliITSMapA2(fSegmentation,fScaleSize,1);
  fHitMap2 = fHitSigMap2;

  fNofMaps = fSegmentation->Npz();
  fMaxNofSamples = fSegmentation->Npx();
  fAnodeFire = new Bool_t [fNofMaps];
    
  Float_t sddLength = fSegmentation->Dx();
  Float_t sddWidth  = fSegmentation->Dz();

  Int_t dummy        = 0;
  Float_t anodePitch = fSegmentation->Dpz(dummy);
  Double_t timeStep  = (Double_t)fSegmentation->Dpx(dummy);
  Float_t driftSpeed = fResponse->DriftSpeed();

  if(anodePitch*(fNofMaps/2) > sddWidth) {
    Warning("AliITSsimulationSDD",
	    "Too many anodes %d or too big pitch %f \n",
	    fNofMaps/2,anodePitch);
  } // end if

  if(timeStep*fMaxNofSamples < sddLength/driftSpeed) {
    Error("AliITSsimulationSDD",
	  "Time Interval > Allowed Time Interval: exit\n");
    return;
  } // end if

  fElectronics = new AliITSetfSDD(timeStep/fScaleSize,
				  fResponse->Electronics());

  char opt1[20], opt2[20];
  fResponse->ParamOptions(opt1,opt2);
  fParam = opt2;
  char *same = strstr(opt1,"same");
  if (same) {
    fNoise.Set(0);
    fBaseline.Set(0);
  } else {
    fNoise.Set(fNofMaps);
    fBaseline.Set(fNofMaps);
  } // end if

  const char *kopt=fResponse->ZeroSuppOption();
  if (strstr(fParam.Data(),"file") ) {
    fD.Set(fNofMaps);
    fT1.Set(fNofMaps);
    if (strstr(kopt,"2D")) {
      fT2.Set(fNofMaps);
      fTol.Set(0);
      Init2D();       // desactivate if param change module by module
    } else if(strstr(kopt,"1D"))  {
      fT2.Set(2);
      fTol.Set(2);
      Init1D();      // desactivate if param change module by module
    } // end if strstr
  } else {
    fD.Set(2);
    fTol.Set(2);
    fT1.Set(2);
    fT2.Set(2);
    SetCompressParam();
  } // end if else strstr

  Bool_t write = fResponse->OutputOption();
  if(write && strstr(kopt,"2D")) MakeTreeB();

  // call here if baseline does not change by module
  // ReadBaseline();

  fITS       = (AliITS*)gAlice->GetModule("ITS");
  Int_t size = fNofMaps*fMaxNofSamples;
  fStream    = new AliITSInStream(size);

  fInZR  = new Double_t [fScaleSize*fMaxNofSamples];
  fInZI  = new Double_t [fScaleSize*fMaxNofSamples];
  fOutZR = new Double_t [fScaleSize*fMaxNofSamples];
  fOutZI = new Double_t [fScaleSize*fMaxNofSamples];  

}
//______________________________________________________________________
AliITSsimulationSDD::~AliITSsimulationSDD() { 
  // destructor

  //    delete fpList;
  delete fHitSigMap2;
  delete fHitNoiMap2;
  delete fStream;
  delete fElectronics;

  fITS = 0;

  if (fHis) {
    fHis->Delete(); 
    delete fHis;     
  } // end if fHis
  if(fTreeB) delete fTreeB;           
  if(fInZR)  delete [] fInZR;
  if(fInZI)  delete [] fInZI;        
  if(fOutZR) delete [] fOutZR;
  if(fOutZI) delete [] fOutZI;
  if(fAnodeFire) delete [] fAnodeFire;
}
//______________________________________________________________________
void AliITSsimulationSDD::InitSimulationModule( Int_t module, Int_t event ) {
  // create maps to build the lists of tracks for each summable digit
  fModule = module;
  fEvent  = event;
  ClearMaps();
  memset(fAnodeFire,0,sizeof(Bool_t)*fNofMaps);    
}
//______________________________________________________________________
void AliITSsimulationSDD::ClearMaps() {
  // clear maps
  fpList->ClearMap();
  fHitSigMap2->ClearMap();
  fHitNoiMap2->ClearMap();
}
//______________________________________________________________________
void AliITSsimulationSDD::SDigitiseModule( AliITSmodule *mod, Int_t md, Int_t ev){
  // digitize module using the "slow" detector simulator creating
  // summable digits.

  TObjArray *fHits = mod->GetHits();
  Int_t nhits      = fHits->GetEntriesFast();
  if( !nhits ) return;

  InitSimulationModule( md, ev );
  HitsToAnalogDigits( mod );
  ChargeToSignal( kFALSE ); // - Process signal without add noise
  fHitMap2 = fHitNoiMap2;   // - Swap to noise map
  ChargeToSignal( kTRUE );  // - Process only noise
  fHitMap2 = fHitSigMap2;   // - Return to signal map
  WriteSDigits();
  ClearMaps();
}
//______________________________________________________________________
Bool_t AliITSsimulationSDD::AddSDigitsToModule( TClonesArray *pItemArray, Int_t mask ) {
  // Add Summable digits to module maps.
  Int_t    nItems = pItemArray->GetEntries();
  Double_t maxadc = fResponse->MaxAdc();
  Bool_t sig = kFALSE;
    
  // cout << "Adding "<< nItems <<" SDigits to module " << fModule << endl;
  for( Int_t i=0; i<nItems; i++ ) {
    AliITSpListItem * pItem = (AliITSpListItem *)(pItemArray->At( i ));
    if( pItem->GetModule() != fModule ) {
      Error( "AliITSsimulationSDD",
	     "Error reading, SDigits module %d != current module %d: exit\n",
	     pItem->GetModule(), fModule );
      return sig;
    } // end if

    if(pItem->GetSignal()>0.0 ) sig = kTRUE;
        
    fpList->AddItemTo( mask, pItem ); // Add SignalAfterElect + noise
    AliITSpListItem * pItem2 = fpList->GetpListItem( pItem->GetIndex() );
    Double_t sigAE = pItem2->GetSignalAfterElect();
    if( sigAE >= maxadc ) sigAE = maxadc-1; // avoid overflow signal
    Int_t ia;
    Int_t it;
    fpList->GetMapIndex( pItem->GetIndex(), ia, it );
    fHitMap2->SetHit( ia, it, sigAE );
    fAnodeFire[ia] = kTRUE;
  }
  return sig;
}
//______________________________________________________________________
void AliITSsimulationSDD::FinishSDigitiseModule() {
  // digitize module using the "slow" detector simulator from
  // the sum of summable digits.
  FinishDigits() ;
  ClearMaps();
}
//______________________________________________________________________
void AliITSsimulationSDD::DigitiseModule(AliITSmodule *mod,Int_t md,Int_t ev){
  // create maps to build the lists of tracks for each digit

  TObjArray *fHits = mod->GetHits();
  Int_t nhits      = fHits->GetEntriesFast();

  InitSimulationModule( md, ev );

  if( !nhits && fCheckNoise ) {
    ChargeToSignal( kTRUE );  // process noise
    GetNoise();
    ClearMaps();
    return;
  } else 
    if( !nhits ) return;
        
  HitsToAnalogDigits( mod );
  ChargeToSignal( kTRUE );  // process signal + noise

  for( Int_t i=0; i<fNofMaps; i++ ) {
    for( Int_t j=0; j<fMaxNofSamples; j++ ) {
      Int_t jdx = j*fScaleSize;
      Int_t index = fpList->GetHitIndex( i, j );
      AliITSpListItem pItemTmp2( fModule, index, 0. );
      // put the fScaleSize analog digits in only one
      for( Int_t ik=0; ik<fScaleSize; ik++ ) {
	AliITSpListItem *pItemTmp = fpList->GetpListItem( i, jdx+ik );
	if( pItemTmp == 0 ) continue;
	pItemTmp2.Add( pItemTmp );
      }
      fpList->DeleteHit( i, j );
      fpList->AddItemTo( 0, &pItemTmp2 );
    }
  }

  FinishDigits();
  ClearMaps();
}
//______________________________________________________________________
void AliITSsimulationSDD::FinishDigits() {
  // introduce the electronics effects and do zero-suppression if required

  ApplyDeadChannels();
  if( fCrosstalkFlag ) ApplyCrosstalk();

  const char *kopt = fResponse->ZeroSuppOption();
  ZeroSuppression( kopt );
}
//______________________________________________________________________
void AliITSsimulationSDD::HitsToAnalogDigits( AliITSmodule *mod ) {
  // create maps to build the lists of tracks for each digit

  TObjArray *fHits    = mod->GetHits();
  Int_t      nhits    = fHits->GetEntriesFast();
  //    Int_t      arg[6]   = {0,0,0,0,0,0};
  Int_t    dummy      = 0;
  Int_t    nofAnodes  = fNofMaps/2;
  Float_t  sddLength  = fSegmentation->Dx();
  Float_t  sddWidth   = fSegmentation->Dz();
  Float_t  anodePitch = fSegmentation->Dpz(dummy);
  Float_t  timeStep   = fSegmentation->Dpx(dummy);
  Float_t  driftSpeed = fResponse->DriftSpeed();
  Float_t  maxadc     = fResponse->MaxAdc();    
  Float_t  topValue   = fResponse->DynamicRange();
  Float_t  cHloss     = fResponse->ChargeLoss();
  Float_t  norm       = maxadc/topValue;
  Float_t  dfCoeff, s1; fResponse->DiffCoeff(dfCoeff,s1); // Signal 2d Shape
  Double_t eVpairs    = 3.6;  // electron pair energy eV.
  Float_t  nsigma     = fResponse->NSigmaIntegration(); //
  Int_t    nlookups   = fResponse->GausNLookUp();       //
  Float_t  jitter     = ((AliITSresponseSDD*)fResponse)->JitterError(); // 

  // Piergiorgio's part (apart for few variables which I made float
  // when i thought that can be done
  // Fill detector maps with GEANT hits
  // loop over hits in the module

  const Float_t kconv = 1.0e+6;  // GeV->KeV
  Int_t    itrack      = 0;
  Int_t    hitDetector; // detector number (lay,lad,hitDetector)
  Int_t    iWing;       // which detector wing/side.
  Int_t    detector;    // 2*(detector-1)+iWing
  Int_t    ii,kk,ka,kt; // loop indexs
  Int_t    ia,it,index; // sub-pixel integration indexies
  Int_t    iAnode;      // anode number.
  Int_t    timeSample;  // time buckett.
  Int_t    anodeWindow; // anode direction charge integration width
  Int_t    timeWindow;  // time direction charge integration width
  Int_t    jamin,jamax; // anode charge integration window
  Int_t    jtmin,jtmax; // time charge integration window
  Int_t    ndiv;        // Anode window division factor.
  Int_t    nsplit;      // the number of splits in anode and time windows==1.
  Int_t    nOfSplits;   // number of times track length is split into
  Float_t  nOfSplitsF;  // Floating point version of nOfSplits.
  Float_t  kkF;         // Floating point version of loop index kk.
  Float_t  pathInSDD; // Track length in SDD.
  Float_t  drPath; // average position of track in detector. in microns
  Float_t  drTime; // Drift time
  Float_t  nmul;   // drift time window multiplication factor.
  Float_t  avDrft;  // x position of path length segment in cm.
  Float_t  avAnode; // Anode for path length segment in Anode number (float)
  Float_t  xAnode;  // Floating point anode number.
  Float_t  driftPath; // avDrft in microns.
  Float_t  width;     // width of signal at anodes.
  Double_t  depEnergy; // Energy deposited in this GEANT step.
  Double_t  xL[3],dxL[3]; // local hit coordinates and diff.
  Double_t sigA; // sigma of signal at anode.
  Double_t sigT; // sigma in time/drift direction for track segment
  Double_t aStep,aConst; // sub-pixel size and offset anode
  Double_t tStep,tConst; // sub-pixel size and offset time
  Double_t amplitude; // signal amplitude for track segment in nanoAmpere
  Double_t chargeloss; // charge loss for track segment.
  Double_t anodeAmplitude; // signal amplitude in anode direction
  Double_t aExpo;          // exponent of Gaussian anode direction
  Double_t timeAmplitude;  // signal amplitude in time direction
  Double_t tExpo;          // exponent of Gaussian time direction
  //  Double_t tof;            // Time of flight in ns of this step.    

  for(ii=0; ii<nhits; ii++) {
    if(!mod->LineSegmentL(ii,xL[0],dxL[0],xL[1],dxL[1],xL[2],dxL[2],
			  depEnergy,itrack)) continue;
    xL[0] += 0.0001*gRandom->Gaus( 0, jitter ); //
    depEnergy  *= kconv;
    hitDetector = mod->GetDet();
    //tof         = 1.E+09*(mod->GetHit(ii)->GetTOF()); // tof in ns.
    //if(tof>sddLength/driftSpeed) continue; // hit happed too late.

    // scale path to simulate a perpendicular track
    // continue if the particle did not lose energy
    // passing through detector
    if (!depEnergy) {
      if(GetDebug()){ 
	Warning("HitsToAnalogDigits", 
		"fTrack = %d hit=%d module=%d This particle has"
		" passed without losing energy!",
		itrack,ii,mod->GetIndex());
      }
      continue;
    } // end if !depEnergy

    pathInSDD = TMath::Sqrt(dxL[0]*dxL[0]+dxL[1]*dxL[1]+dxL[2]*dxL[2]);

    if (fFlag && pathInSDD) { depEnergy *= (0.03/pathInSDD); }
    drPath = 10000.*(dxL[0]+2.*xL[0])*0.5;
    if(drPath < 0) drPath = -drPath;
    drPath = sddLength-drPath;
    if(drPath < 0) {
      if(GetDebug()){ // this should be fixed at geometry level
	Warning("HitsToAnalogDigits",
		"negative drift path drPath=%e sddLength=%e dxL[0]=%e "
		"xL[0]=%e",
		drPath,sddLength,dxL[0],xL[0]);
      }
      continue;
    } // end if drPath < 0

    // Compute number of segments to brake step path into
    drTime = drPath/driftSpeed;  //   Drift Time
    sigA   = TMath::Sqrt(2.*dfCoeff*drTime+s1*s1);// Sigma along the anodes
    // calcuate the number of time the path length should be split into.
    nOfSplits = (Int_t) (1. + 10000.*pathInSDD/sigA);
    if(fFlag) nOfSplits = 1;

    // loop over path segments, init. some variables.
    depEnergy /= nOfSplits;
    nOfSplitsF = (Float_t) nOfSplits;
    for(kk=0;kk<nOfSplits;kk++) { // loop over path segments
      kkF       = (Float_t) kk + 0.5;
      avDrft    = xL[0]+dxL[0]*kkF/nOfSplitsF;
      avAnode   = xL[2]+dxL[2]*kkF/nOfSplitsF;
      driftPath = 10000.*avDrft;

      iWing = 2;  // Assume wing is 2
      if(driftPath < 0) { // if wing is not 2 it is 1.
	iWing     = 1;
	driftPath = -driftPath;
      } // end if driftPath < 0
      driftPath = sddLength-driftPath;
      detector  = 2*(hitDetector-1) + iWing;
      if(driftPath < 0) {
	if(GetDebug()){ // this should be fixed at geometry level
	  Warning("HitsToAnalogDigits","negative drift path "
		  "driftPath=%e sddLength=%e avDrft=%e dxL[0]=%e "
		  "xL[0]=%e",driftPath,sddLength,avDrft,dxL[0],xL[0]);
	}
	continue;
      } // end if driftPath < 0

      //   Drift Time
      drTime     = driftPath/driftSpeed; // drift time for segment.
      timeSample = (Int_t) (fScaleSize*drTime/timeStep + 1);
      // compute time Sample including tof information. The tof only 
      // effects the time of the signal is recoreded and not the
      // the defusion.
      // timeSample = (Int_t) (fScaleSize*(drTime+tof)/timeStep + 1);
      if(timeSample > fScaleSize*fMaxNofSamples) {
	Warning("HitsToAnalogDigits","Wrong Time Sample: %e",
		timeSample);
	continue;
      } // end if timeSample > fScaleSize*fMaxNoofSamples

      //   Anode
      xAnode = 10000.*(avAnode)/anodePitch + nofAnodes/2;  // +1?
      if(xAnode*anodePitch > sddWidth || xAnode*anodePitch < 0.) 
	Warning("HitsToAnalogDigits",
		"Exceedubg sddWidth=%e Z = %e",
		sddWidth,xAnode*anodePitch);
      iAnode = (Int_t) (1.+xAnode); // xAnode?
      if(iAnode < 1 || iAnode > nofAnodes) {
	Warning("HitToAnalogDigits","Wrong iAnode: 1<%d>%d",
		iAnode,nofAnodes);
	continue;
      } // end if iAnode < 1 || iAnode > nofAnodes

      // store straight away the particle position in the array
      // of particles and take idhit=ii only when part is entering (this
      // requires FillModules() in the macro for analysis) :
    
      // Sigma along the anodes for track segment.
      sigA       = TMath::Sqrt(2.*dfCoeff*drTime+s1*s1);
      sigT       = sigA/driftSpeed;
      // Peak amplitude in nanoAmpere
      amplitude  = fScaleSize*160.*depEnergy/
	(timeStep*eVpairs*2.*acos(-1.)*sigT*sigA);
      amplitude *= timeStep/25.; // WARNING!!!!! Amplitude scaling to 
      // account for clock variations 
      // (reference value: 40 MHz)
      chargeloss = 1.-cHloss*driftPath/1000;
      amplitude *= chargeloss;
      width  = 2.*nsigma/(nlookups-1);
      // Spread the charge 
      // Pixel index
      ndiv = 2;
      nmul = 3.; 
      if(drTime > 1200.) { 
	ndiv = 4;
	nmul = 1.5;
      } // end if drTime > 1200.
      // Sub-pixel index
      nsplit = 4; // hard-wired //nsplit=4;nsplit = (nsplit+1)/2*2;
      // Sub-pixel size see computation of aExpo and tExpo.
      aStep  = anodePitch/(nsplit*fScaleSize*sigA);
      aConst = xAnode*anodePitch/sigA;
      tStep  = timeStep/(nsplit*fScaleSize*sigT);
      tConst = drTime/sigT;
      // Define SDD window corresponding to the hit
      anodeWindow = (Int_t)(fScaleSize*nsigma*sigA/anodePitch+1);
      timeWindow  = (Int_t) (fScaleSize*nsigma*sigT/timeStep+1.);
      jamin = (iAnode - anodeWindow/ndiv - 1)*fScaleSize*nsplit +1;
      jamax = (iAnode + anodeWindow/ndiv)*fScaleSize*nsplit;
      if(jamin <= 0) jamin = 1;
      if(jamax > fScaleSize*nofAnodes*nsplit) 
	jamax = fScaleSize*nofAnodes*nsplit;
      // jtmin and jtmax are Hard-wired
      jtmin = (Int_t)(timeSample-timeWindow*nmul-1)*nsplit+1;
      jtmax = (Int_t)(timeSample+timeWindow*nmul)*nsplit;
      if(jtmin <= 0) jtmin = 1;
      if(jtmax > fScaleSize*fMaxNofSamples*nsplit) 
	jtmax = fScaleSize*fMaxNofSamples*nsplit;
      // Spread the charge in the anode-time window
      for(ka=jamin; ka <=jamax; ka++) {
	ia = (ka-1)/(fScaleSize*nsplit) + 1;
	if(ia <= 0) {
	  Warning("HitsToAnalogDigits","ia < 1: ");
	  continue;
	} // end if
	if(ia > nofAnodes) ia = nofAnodes;
	aExpo     = (aStep*(ka-0.5)-aConst);
	if(TMath::Abs(aExpo) > nsigma)  anodeAmplitude = 0.;
	else {
	  dummy          = (Int_t) ((aExpo+nsigma)/width);
	  anodeAmplitude = amplitude*fResponse->GausLookUp(dummy);
	} // end if TMath::Abs(aEspo) > nsigma
	// index starts from 0
	index = ((detector+1)%2)*nofAnodes+ia-1;
	if(anodeAmplitude) for(kt=jtmin; kt<=jtmax; kt++) {
	  it = (kt-1)/nsplit+1;  // it starts from 1
	  if(it<=0){
	    Warning("HitsToAnalogDigits","it < 1:");
	    continue;
	  } // end if 
	  if(it>fScaleSize*fMaxNofSamples)
	    it = fScaleSize*fMaxNofSamples;
	  tExpo    = (tStep*(kt-0.5)-tConst);
	  if(TMath::Abs(tExpo) > nsigma) timeAmplitude = 0.;
	  else {
	    dummy         = (Int_t) ((tExpo+nsigma)/width);
	    timeAmplitude = anodeAmplitude*
	      fResponse->GausLookUp(dummy);
	  } // end if TMath::Abs(tExpo) > nsigma
	  // build the list of Sdigits for this module        
	  //                    arg[0]         = index;
	  //                    arg[1]         = it;
	  //                    arg[2]         = itrack; // track number
	  //                    arg[3]         = ii-1; // hit number.
	  timeAmplitude *= norm;
	  timeAmplitude *= 10;
	  //                    ListOfFiredCells(arg,timeAmplitude,alst,padr);
	  Double_t charge = timeAmplitude;
	  charge += fHitMap2->GetSignal(index,it-1);
	  fHitMap2->SetHit(index, it-1, charge);
	  fpList->AddSignal(index,it-1,itrack,ii-1,
			    mod->GetIndex(),timeAmplitude);
	  fAnodeFire[index] = kTRUE;                 
	} // end if anodeAmplitude and loop over time in window
      } // loop over anodes in window
    } // end loop over "sub-hits"
  } // end loop over hits
}

/*
//______________________________________________________________________
void AliITSsimulationSDD::ListOfFiredCells(Int_t *arg,Double_t timeAmplitude,
					   TObjArray *alist,TClonesArray *padr){
  // Returns the list of "fired" cells.

  Int_t index     = arg[0];
  Int_t ik        = arg[1];
  Int_t idtrack   = arg[2];
  Int_t idhit     = arg[3];
  Int_t counter   = arg[4];
  Int_t countadr  = arg[5];
  Double_t charge = timeAmplitude;
  charge += fHitMap2->GetSignal(index,ik-1);
  fHitMap2->SetHit(index, ik-1, charge);

  Int_t digits[3];
  Int_t it = (Int_t)((ik-1)/fScaleSize);
  digits[0] = index;
  digits[1] = it;
  digits[2] = (Int_t)timeAmplitude;
  Float_t phys;
  if (idtrack >= 0) phys = (Float_t)timeAmplitude;
  else phys = 0;

  Double_t cellcharge = 0.;
  AliITSTransientDigit* pdigit;
  // build the list of fired cells and update the info
  if (!fHitMap1->TestHit(index, it)) {
    new((*padr)[countadr++]) TVector(3);
    TVector &trinfo=*((TVector*) (*padr)[countadr-1]);
    trinfo(0) = (Float_t)idtrack;
    trinfo(1) = (Float_t)idhit;
    trinfo(2) = (Float_t)timeAmplitude;

    alist->AddAtAndExpand(new AliITSTransientDigit(phys,digits),counter);
    fHitMap1->SetHit(index, it, counter);
    counter++;
    pdigit=(AliITSTransientDigit*)alist->At(alist->GetLast());
    // list of tracks
    TObjArray *trlist=(TObjArray*)pdigit->TrackList();
    trlist->Add(&trinfo);
  } else {
    pdigit = (AliITSTransientDigit*) fHitMap1->GetHit(index, it);
    for(Int_t kk=0;kk<fScaleSize;kk++) {
      cellcharge += fHitMap2->GetSignal(index,fScaleSize*it+kk);
    }  // end for kk
    // update charge
    (*pdigit).fSignal = (Int_t)cellcharge;
    (*pdigit).fPhysics += phys;                        
    // update list of tracks
    TObjArray* trlist = (TObjArray*)pdigit->TrackList();
    Int_t lastentry = trlist->GetLast();
    TVector *ptrkp = (TVector*)trlist->At(lastentry);
    TVector &trinfo = *ptrkp;
    Int_t lasttrack = Int_t(trinfo(0));
    Float_t lastcharge=(trinfo(2));
    if (lasttrack==idtrack ) {
      lastcharge += (Float_t)timeAmplitude;
      trlist->RemoveAt(lastentry);
      trinfo(0) = lasttrack;
      trinfo(1) = idhit;
      trinfo(2) = lastcharge;
      trlist->AddAt(&trinfo,lastentry);
    } else {                  
      new((*padr)[countadr++]) TVector(3);
      TVector &trinfo=*((TVector*) (*padr)[countadr-1]);
      trinfo(0) = (Float_t)idtrack;
      trinfo(1) = (Float_t)idhit;
      trinfo(2) = (Float_t)timeAmplitude;
      trlist->Add(&trinfo);
    } // end if lasttrack==idtrack

#ifdef print
    // check the track list - debugging
    Int_t trk[20], htrk[20];
    Float_t chtrk[20];  
    Int_t nptracks = trlist->GetEntriesFast();
    if (nptracks > 2) {
      Int_t tr;
      for (tr=0;tr<nptracks;tr++) {
	TVector *pptrkp = (TVector*)trlist->At(tr);
	TVector &pptrk  = *pptrkp;
	trk[tr]   = Int_t(pptrk(0));
	htrk[tr]  = Int_t(pptrk(1));
	chtrk[tr] = (pptrk(2));
	cout << "nptracks "<<nptracks << endl;
      } // end for tr
    } // end if nptracks
#endif
  } //  end if pdigit

  // update counter and countadr for next call.
  arg[4] = counter;
  arg[5] = countadr;
}
*/

//____________________________________________
void AliITSsimulationSDD::AddDigit( Int_t i, Int_t j, Int_t signal ) {
  // Adds a Digit.
  Int_t size = AliITSdigitSPD::GetNTracks();
  Int_t digits[3];
  Int_t * tracks = new Int_t[size];
  Int_t * hits = new Int_t[size];
  Float_t phys;
  Float_t * charges = new Float_t[size];

  digits[0] = i;
  digits[1] = j;
  digits[2] = signal;

  AliITSpListItem *pItem = fpList->GetpListItem( i, j );
  if( pItem == 0 ) {
    phys = 0.0;
    for( Int_t l=0; l<size; l++ ) {
      tracks[l]  = 0;
      hits[l]    = 0;
      charges[l] = 0.0;
    }
  } else {
    Int_t idtrack =  pItem->GetTrack( 0 );
    if( idtrack >= 0 ) phys = pItem->GetSignal();  
    else phys = 0.0;

    for( Int_t l=0; l<size; l++ ) if(l<pItem->GetMaxKept()) {
      tracks[l]  = pItem->GetTrack( l );
      hits[l]    = pItem->GetHit( l );
      charges[l] = pItem->GetSignal( l );
    }else{
      tracks[l]  = -3;
      hits[l]    = -1;
      charges[l] = 0.0;
    }// end for if
  }

  fITS->AddSimDigit( 1, phys, digits, tracks, hits, charges ); 
  delete [] tracks;
  delete [] hits;
  delete [] charges;
}

//______________________________________________________________________
void AliITSsimulationSDD::ChargeToSignal(Bool_t bAddNoise) {
  // add baseline, noise, electronics and ADC saturation effects

  char opt1[20], opt2[20];
  fResponse->ParamOptions(opt1,opt2);
  char *read = strstr(opt1,"file");
  Float_t baseline, noise; 

  if (read) {
    static Bool_t readfile=kTRUE;
    //read baseline and noise from file
    if (readfile) ReadBaseline();
    readfile=kFALSE;
  } else fResponse->GetNoiseParam(noise,baseline);

  Float_t contrib=0;
  Int_t i,k,kk;
  Float_t maxadc = fResponse->MaxAdc();    
  if(!fDoFFT) {
    for (i=0;i<fNofMaps;i++) {
      if( !fAnodeFire[i] ) continue;
      if (read && i<fNofMaps) GetAnodeBaseline(i,baseline,noise);
      for(k=0; k<fScaleSize*fMaxNofSamples; k++) {
	fInZR[k]  = fHitMap2->GetSignal(i,k);
	if( bAddNoise ) {
	  contrib   = (baseline + noise*gRandom->Gaus());
	  fInZR[k] += contrib;
	}
      } // end for k
      for(k=0; k<fMaxNofSamples; k++) {
	Double_t newcont = 0.;
	Double_t maxcont = 0.;
	for(kk=0;kk<fScaleSize;kk++) {
	  newcont = fInZR[fScaleSize*k+kk];
	  if(newcont > maxcont) maxcont = newcont;
	} // end for kk
	newcont = maxcont;
	if (newcont >= maxadc) newcont = maxadc -1;
	if(newcont >= baseline){
	  Warning("","newcont=%d>=baseline=%d",newcont,baseline);
	} // end if
	// back to analog: ?
	fHitMap2->SetHit(i,k,newcont);
      }  // end for k
    } // end for i loop over anodes
    return;
  } // end if DoFFT

  for (i=0;i<fNofMaps;i++) {
    if( !fAnodeFire[i] ) continue;
    if  (read && i<fNofMaps) GetAnodeBaseline(i,baseline,noise);
    for(k=0; k<fScaleSize*fMaxNofSamples; k++) {
      fInZR[k]  = fHitMap2->GetSignal(i,k);
      if( bAddNoise ) {
	contrib   = (baseline + noise*gRandom->Gaus());
	fInZR[k] += contrib;
      }
      fInZI[k]  = 0.;
    } // end for k
    FastFourierTransform(fElectronics,&fInZR[0],&fInZI[0],1);
    for(k=0; k<fScaleSize*fMaxNofSamples; k++) {
      Double_t rw = fElectronics->GetTraFunReal(k);
      Double_t iw = fElectronics->GetTraFunImag(k);
      fOutZR[k]   = fInZR[k]*rw - fInZI[k]*iw;
      fOutZI[k]   = fInZR[k]*iw + fInZI[k]*rw;
    } // end for k
    FastFourierTransform(fElectronics,&fOutZR[0],&fOutZI[0],-1);
    for(k=0; k<fMaxNofSamples; k++) {
      Double_t newcont1 = 0.;
      Double_t maxcont1 = 0.;
      for(kk=0;kk<fScaleSize;kk++) {
	newcont1 = fOutZR[fScaleSize*k+kk];
	if(newcont1 > maxcont1) maxcont1 = newcont1;
      } // end for kk
      newcont1 = maxcont1;
      if (newcont1 >= maxadc) newcont1 = maxadc -1;
      fHitMap2->SetHit(i,k,newcont1);
    } // end for k
  } // end for i loop over anodes
  return;
}
//____________________________________________________________________
void AliITSsimulationSDD::ApplyDeadChannels() {    
  // Set dead channel signal to zero
  AliITSresponseSDD * response = (AliITSresponseSDD *)fResponse;
    
  // nothing to do
  if( response->GetDeadModules() == 0 && 
      response->GetDeadChips() == 0 && 
      response->GetDeadChannels() == 0 )
    return;  
    
  static AliITS *iTS = (AliITS*)gAlice->GetModule( "ITS" );

  Int_t fMaxNofSamples = fSegmentation->Npx();    
  AliITSgeom *geom = iTS->GetITSgeom();
  Int_t firstSDDMod = geom->GetStartDet( 1 );
  // loop over wings
  for( Int_t j=0; j<2; j++ ) {
    Int_t mod = (fModule-firstSDDMod)*2 + j;
    for( Int_t u=0; u<response->Chips(); u++ )
      for( Int_t v=0; v<response->Channels(); v++ ) {
	Float_t Gain = response->Gain( mod, u, v );
	for( Int_t k=0; k<fMaxNofSamples; k++ ) {
	  Int_t i = j*response->Chips()*response->Channels() +
	    u*response->Channels() + 
	    v;
	  Double_t signal =  Gain * fHitMap2->GetSignal( i, k );
	  fHitMap2->SetHit( i, k, signal );  ///
	}
      }
  }    
}
//______________________________________________________________________
void AliITSsimulationSDD::ApplyCrosstalk() {
  // function add the crosstalk effect to signal
  // temporal function, should be checked...!!!
    
  Int_t fNofMaps = fSegmentation->Npz();
  Int_t fMaxNofSamples = fSegmentation->Npx();

  // create and inizialice crosstalk map
  Float_t* ctk = new Float_t[fNofMaps*fMaxNofSamples+1];
  if( ctk == NULL ) {
    Error( "ApplyCrosstalk", "no memory for temporal map: exit \n" );
    return;
  }
  memset( ctk, 0, sizeof(Float_t)*(fNofMaps*fMaxNofSamples+1) );
    
  Float_t noise, baseline;
  fResponse->GetNoiseParam( noise, baseline );
    
  for( Int_t z=0; z<fNofMaps; z++ ) {
    Bool_t on = kFALSE;
    Int_t tstart = 0;
    Int_t tstop = 0;
    Int_t nTsteps = 0;
        
    for( Int_t l=0; l<fMaxNofSamples; l++ ) {
      Float_t fadc = (Float_t)fHitMap2->GetSignal( z, l );
      if( fadc > baseline ) {
	if( on == kFALSE && l<fMaxNofSamples-4 ) {
	  Float_t fadc1 = (Float_t)fHitMap2->GetSignal( z, l+1 );
	  if( fadc1 < fadc ) continue;
	  on = kTRUE;
	  nTsteps = 0;
	  tstart = l;
	}
	nTsteps++;
      }
      else { // end fadc > baseline
	if( on == kTRUE ) {        
	  if( nTsteps > 2 ) {
	    tstop = l;
	    // make smooth derivative
	    Float_t* dev = new Float_t[fMaxNofSamples+1];
	    memset( dev, 0, sizeof(Float_t)*(fMaxNofSamples+1) );
	    if( ctk == NULL ) {
	      Error( "ApplyCrosstalk", 
		     "no memory for temporal array: exit \n" );
	      return;
	    }
	    for( Int_t i=tstart; i<tstop; i++ ) {   
	      if( i > 2 && i < fMaxNofSamples-2 )
		dev[i] = -0.2*fHitMap2->GetSignal( z,i-2 ) 
		  -0.1*fHitMap2->GetSignal( z,i-1 ) 
		  +0.1*fHitMap2->GetSignal( z,i+1 ) 
		  +0.2*fHitMap2->GetSignal( z,i+2 );
	    }
                        
	    // add crosstalk contribution to neibourg anodes  
	    for( Int_t i=tstart; i<tstop; i++ ) {
	      Int_t anode = z - 1;
	      Int_t i1 = (Int_t)((i-tstart)*.61+tstart+0.5); // 
	      Float_t ctktmp =  -dev[i1] * 0.25;
	      if( anode > 0 ) {
		ctk[anode*fMaxNofSamples+i] += ctktmp;           
	      }
	      anode = z + 1;
	      if( anode < fNofMaps ) {
		ctk[anode*fMaxNofSamples+i] += ctktmp;
	      }
	    }
	    delete [] dev;
                        
	  } // if( nTsteps > 2 )
	  on = kFALSE;
	}  // if( on == kTRUE )
      }  // else
    }
  }
    
  for( Int_t a=0; a<fNofMaps; a++ )
    for( Int_t t=0; t<fMaxNofSamples; t++ ) {     
      Float_t signal = fHitMap2->GetSignal( a, t ) + ctk[a*fMaxNofSamples+t];
      fHitMap2->SetHit( a, t, signal );
    }
    
  delete [] ctk;
}
//______________________________________________________________________
void AliITSsimulationSDD::GetAnodeBaseline(Int_t i,Float_t &baseline,
                                           Float_t &noise){
  // Returns the Baseline for a particular anode.
  baseline = fBaseline[i];
  noise    = fNoise[i];
}
//______________________________________________________________________
void AliITSsimulationSDD::CompressionParam(Int_t i,Int_t &db,Int_t &tl,
                                           Int_t &th){
  // Returns the compression alogirthm parameters
  Int_t size = fD.GetSize();
  if (size > 2 ) {
    db=fD[i]; tl=fT1[i]; th=fT2[i];
  } else {
    if (size <= 2 && i>=fNofMaps/2) {
      db=fD[1]; tl=fT1[1]; th=fT2[1];
    } else {
      db=fD[0]; tl=fT1[0]; th=fT2[0];
    } // end if size <=2 && i>=fNofMaps/2
  } // end if size >2
}
//______________________________________________________________________
void AliITSsimulationSDD::CompressionParam(Int_t i,Int_t &db,Int_t &tl){
  // returns the compression alogirthm parameters
  Int_t size = fD.GetSize();

  if (size > 2 ) {
    db=fD[i]; tl=fT1[i];
  } else {
    if (size <= 2 && i>=fNofMaps/2) {
      db=fD[1]; tl=fT1[1]; 
    } else {
      db=fD[0]; tl=fT1[0]; 
    } // end if size <=2 && i>=fNofMaps/2
    //	Warning("CompressionParam","\n Size= %d . Values i=%d ; db= %d ; tl= %d",size,i,db,tl);
  } // end if size > 2
}
//______________________________________________________________________
void AliITSsimulationSDD::SetCompressParam(){
  // Sets the compression alogirthm parameters  
  Int_t cp[8],i;

  fResponse->GiveCompressParam(cp);
  for (i=0; i<2; i++) {
    fD[i]   = cp[i];
    fT1[i]  = cp[i+2];
    fT2[i]  = cp[i+4];
    fTol[i] = cp[i+6];
  } // end for i
}
//______________________________________________________________________
void AliITSsimulationSDD::ReadBaseline(){
  // read baseline and noise from file - either a .root file and in this
  // case data should be organised in a tree with one entry for each
  // module => reading should be done accordingly
  // or a classic file and do smth. like this:
  // Read baselines and noise for SDD

  Int_t na,pos;
  Float_t bl,n;
  char input[100], base[100], param[100];
  char *filtmp;

  fResponse->Filenames(input,base,param);
  fFileName=base;
  //
  filtmp = gSystem->ExpandPathName(fFileName.Data());
  FILE *bline = fopen(filtmp,"r");
  na = 0;

  if(bline) {
    while(fscanf(bline,"%d %f %f",&pos, &bl, &n) != EOF) {
      if (pos != na+1) {
	Error("ReadBaseline","Anode number not in increasing order!",
	      filtmp);
	exit(1);
      } // end if pos != na+1
      fBaseline[na]=bl;
      fNoise[na]=n;
      na++;
    } // end while
  } else {
    Error("ReadBaseline"," THE BASELINE FILE %s DOES NOT EXIST !",filtmp);
    exit(1);
  } // end if(bline)

  fclose(bline);
  delete [] filtmp;
}
//______________________________________________________________________
Int_t AliITSsimulationSDD::Convert10to8(Int_t signal) const {
  // To the 10 to 8 bit lossive compression.
  // code from Davide C. and Albert W.

  if (signal < 128)  return signal;
  if (signal < 256)  return (128+((signal-128)>>1));
  if (signal < 512)  return (192+((signal-256)>>3));
  if (signal < 1024) return (224+((signal-512)>>4));
  return 0;
}

/*
//______________________________________________________________________
AliITSMap*   AliITSsimulationSDD::HitMap(Int_t i){
  //Return the correct map.

  return ((i==0)? fHitMap1 : fHitMap2);
}
*/

//______________________________________________________________________
void AliITSsimulationSDD::ZeroSuppression(const char *option) {
  // perform the zero suppresion

  if (strstr(option,"2D")) {
    //Init2D();              // activate if param change module by module
    Compress2D();
  } else if (strstr(option,"1D")) {
    //Init1D();              // activate if param change module by module
    Compress1D();  
  } else StoreAllDigits();
}
//______________________________________________________________________
void AliITSsimulationSDD::Init2D(){
  // read in and prepare arrays: fD, fT1, fT2
  //                         savemu[nanodes], savesigma[nanodes] 
  // read baseline and noise from file - either a .root file and in this
  // case data should be organised in a tree with one entry for each
  // module => reading should be done accordingly
  // or a classic file and do smth. like this ( code from Davide C. and
  // Albert W.) :
  // Read 2D zero-suppression parameters for SDD

  if (!strstr(fParam.Data(),"file")) return;

  Int_t na,pos,tempTh;
  Float_t mu,sigma;
  Float_t *savemu    = new Float_t [fNofMaps];
  Float_t *savesigma = new Float_t [fNofMaps];
  char input[100],basel[100],par[100];
  char *filtmp;
  Float_t tmp1,tmp2;
  fResponse->Thresholds(tmp1,tmp2);
  Int_t minval = static_cast<Int_t>(tmp1);

  fResponse->Filenames(input,basel,par);
  fFileName = par;
  //
  filtmp = gSystem->ExpandPathName(fFileName.Data());
  FILE *param = fopen(filtmp,"r");
  na = 0;

  if(param) {
    while(fscanf(param,"%d %f %f",&pos, &mu, &sigma) != EOF) {
      if (pos != na+1) {
	Error("Init2D","Anode number not in increasing order!",filtmp);
	exit(1);
      } // end if pos != na+1
      savemu[na] = mu;
      savesigma[na] = sigma;
      if ((2.*sigma) < mu) {
	fD[na] = (Int_t)floor(mu - 2.0*sigma + 0.5);
	mu = 2.0 * sigma;
      } else fD[na] = 0;
      tempTh = (Int_t)floor(mu+2.25*sigma+0.5) - minval;
      if (tempTh < 0) tempTh=0;
      fT1[na] = tempTh;
      tempTh = (Int_t)floor(mu+3.0*sigma+0.5) - minval;
      if (tempTh < 0) tempTh=0;
      fT2[na] = tempTh;
      na++;
    } // end while
  } else {
    Error("Init2D","THE FILE %s DOES NOT EXIST !",filtmp);
    exit(1);
  } // end if(param)

  fclose(param);
  delete [] filtmp;
  delete [] savemu;
  delete [] savesigma;
}
//______________________________________________________________________
void AliITSsimulationSDD::Compress2D(){
  // simple ITS cluster finder -- online zero-suppression conditions

  Int_t db,tl,th; 
  Float_t tmp1,tmp2;
  fResponse->Thresholds(tmp1,tmp2); 
  Int_t minval   = static_cast<Int_t>(tmp1);
  Bool_t write   = fResponse->OutputOption();   
  Bool_t do10to8 = fResponse->Do10to8();
  Int_t nz, nl, nh, low, i, j; 

  for (i=0; i<fNofMaps; i++) {
    CompressionParam(i,db,tl,th);
    nz  = 0; 
    nl  = 0;
    nh  = 0;
    low = 0;
    for (j=0; j<fMaxNofSamples; j++) {
      Int_t signal=(Int_t)(fHitMap2->GetSignal(i,j));
      signal -= db; // if baseline eq. is done here
      if (signal <= 0) {nz++; continue;}
      if ((signal - tl) < minval) low++;
      if ((signal - th) >= minval) {
	nh++;
	Bool_t cond=kTRUE;
	FindCluster(i,j,signal,minval,cond);
	if(cond && j &&
	   ((TMath::Abs(fHitMap2->GetSignal(i,j-1))-th)>=minval)){
	  if(do10to8) signal = Convert10to8(signal);
	  AddDigit(i,j,signal);
	} // end if cond&&j&&()
      } else if ((signal - tl) >= minval) nl++;
    } // end for j loop time samples
    if (write) TreeB()->Fill(nz,nl,nh,low,i+1);
  } //end for i loop anodes

  char hname[30];
  if (write) {
    sprintf(hname,"TNtuple%d_%d",fModule,fEvent);
    TreeB()->Write(hname);
    // reset tree
    TreeB()->Reset();
  } // end if write
}
//______________________________________________________________________
void  AliITSsimulationSDD::FindCluster(Int_t i,Int_t j,Int_t signal,
                                       Int_t minval,Bool_t &cond){
  // Find clusters according to the online 2D zero-suppression algorithm
  Bool_t do10to8 = fResponse->Do10to8();
  Bool_t high    = kFALSE;

  fHitMap2->FlagHit(i,j);
  //
  //  check the online zero-suppression conditions
  //  
  const Int_t kMaxNeighbours = 4;
  Int_t nn;
  Int_t dbx,tlx,thx;  
  Int_t xList[kMaxNeighbours], yList[kMaxNeighbours];
  fSegmentation->Neighbours(i,j,&nn,xList,yList);
  Int_t in,ix,iy,qns;
  for (in=0; in<nn; in++) {
    ix=xList[in];
    iy=yList[in];
    if (fHitMap2->TestHit(ix,iy)==kUnused) {
      CompressionParam(ix,dbx,tlx,thx);
      Int_t qn = (Int_t)(fHitMap2->GetSignal(ix,iy));
      qn -= dbx; // if baseline eq. is done here
      if ((qn-tlx) < minval) {
	fHitMap2->FlagHit(ix,iy);
	continue;
      } else {
	if ((qn - thx) >= minval) high=kTRUE;
	if (cond) {
	  if(do10to8) signal = Convert10to8(signal);
	  AddDigit(i,j,signal);
	} // end if cond
	if(do10to8) qns = Convert10to8(qn);
	else qns=qn;
	if (!high) AddDigit(ix,iy,qns);
	cond=kFALSE;
	if(!high) fHitMap2->FlagHit(ix,iy);
      } // end if qn-tlx < minval
    } // end if  TestHit
  } // end for in loop over neighbours
}
//______________________________________________________________________
void AliITSsimulationSDD::Init1D(){
  // this is just a copy-paste of input taken from 2D algo
  // Torino people should give input
  // Read 1D zero-suppression parameters for SDD

  if (!strstr(fParam.Data(),"file")) return;

  Int_t na,pos,tempTh;
  Float_t mu,sigma;
  Float_t *savemu    = new Float_t [fNofMaps];
  Float_t *savesigma = new Float_t [fNofMaps];
  char input[100],basel[100],par[100];
  char *filtmp;
  Float_t tmp1,tmp2;
  fResponse->Thresholds(tmp1,tmp2);
  Int_t minval = static_cast<Int_t>(tmp1);

  fResponse->Filenames(input,basel,par);
  fFileName=par;

  //  set first the disable and tol param
  SetCompressParam();
  //
  filtmp = gSystem->ExpandPathName(fFileName.Data());
  FILE *param = fopen(filtmp,"r");
  na = 0;

  if (param) {
    fscanf(param,"%d %d %d %d ", &fT2[0], &fT2[1], &fTol[0], &fTol[1]);
    while(fscanf(param,"%d %f %f",&pos, &mu, &sigma) != EOF) {
      if (pos != na+1) {
	Error("Init1D","Anode number not in increasing order!",filtmp);
	exit(1);
      } // end if pos != na+1
      savemu[na]=mu;
      savesigma[na]=sigma;
      if ((2.*sigma) < mu) {
	fD[na] = (Int_t)floor(mu - 2.0*sigma + 0.5);
	mu = 2.0 * sigma;
      } else fD[na] = 0;
      tempTh = (Int_t)floor(mu+2.25*sigma+0.5) - minval;
      if (tempTh < 0) tempTh=0;
      fT1[na] = tempTh;
      na++;
    } // end while
  } else {
    Error("Init1D","THE FILE %s DOES NOT EXIST !",filtmp);
    exit(1);
  } // end if(param)

  fclose(param);
  delete [] filtmp;
  delete [] savemu;
  delete [] savesigma;
} 
//______________________________________________________________________
void AliITSsimulationSDD::Compress1D(){
  // 1D zero-suppression algorithm (from Gianluca A.)
  Int_t    dis,tol,thres,decr,diff;
  UChar_t *str=fStream->Stream();
  Int_t    counter=0;
  Bool_t   do10to8=fResponse->Do10to8();
  Int_t    last=0;
  Int_t    k,i,j;

  for (k=0; k<2; k++) {
    tol = Tolerance(k);
    dis = Disable(k);  
    for (i=0; i<fNofMaps/2; i++) {
      Bool_t firstSignal=kTRUE;
      Int_t idx=i+k*fNofMaps/2;
      if( !fAnodeFire[idx] ) continue;
      CompressionParam(idx,decr,thres); 

      for (j=0; j<fMaxNofSamples; j++) {
	Int_t signal=(Int_t)(fHitMap2->GetSignal(idx,j));
	signal -= decr;  // if baseline eq.
	if(do10to8) signal = Convert10to8(signal);
	if (signal <= thres) {
	  signal=0;
	  diff=128; 
	  last=0; 
	  // write diff in the buffer for HuffT
	  str[counter]=(UChar_t)diff;
	  counter++;
	  continue;
	} // end if signal <= thres
	diff=signal-last;
	if (diff > 127) diff=127;
	if (diff < -128) diff=-128;
	if (signal < dis) {
	  // tol has changed to 8 possible cases ? - one can write
	  // this if(TMath::Abs(diff)<tol) ... else ...
	  if(TMath::Abs(diff)<tol) diff=0;
	  // or keep it as it was before
	  AddDigit(idx,j,last+diff);
	} else {
	  AddDigit(idx,j,signal);
	} // end if singal < dis
	diff += 128;
	// write diff in the buffer used to compute Huffman tables
	if (firstSignal) str[counter]=(UChar_t)signal;
	else str[counter]=(UChar_t)diff;
	counter++;
	last=signal;
	firstSignal=kFALSE;
      } // end for j loop time samples
    } // end for i loop anodes  one half of detector 
  } //  end for k

    // check
  fStream->CheckCount(counter);

  // open file and write out the stream of diff's
  static Bool_t open=kTRUE;
  static TFile *outFile;
  Bool_t write = fResponse->OutputOption();
  TDirectory *savedir = gDirectory;
 
  if (write ) {
    if(open) {
      SetFileName("stream.root");
      cout<<"filename "<<fFileName<<endl;
      outFile=new TFile(fFileName,"recreate");
      cout<<"I have opened "<<fFileName<<" file "<<endl;
    } // end if open
    open = kFALSE;
    outFile->cd();
    fStream->Write();
  }  // endif write        

  fStream->ClearStream();

  // back to galice.root file
  if(savedir) savedir->cd();
}
//______________________________________________________________________
void AliITSsimulationSDD::StoreAllDigits(){
  // if non-zero-suppressed data
  Bool_t do10to8 = fResponse->Do10to8();
  Int_t i, j, digits[3];

  for (i=0; i<fNofMaps; i++) {
    for (j=0; j<fMaxNofSamples; j++) {
      Int_t signal=(Int_t)(fHitMap2->GetSignal(i,j));
      if(do10to8) signal = Convert10to8(signal);
      digits[0] = i;
      digits[1] = j;
      digits[2] = signal;
      fITS->AddRealDigit(1,digits);
    } // end for j
  } // end for i
} 
//______________________________________________________________________
void AliITSsimulationSDD::CreateHistograms(Int_t scale){
  // Creates histograms of maps for debugging
  Int_t i;

  fHis=new TObjArray(fNofMaps);
  for (i=0;i<fNofMaps;i++) {
    TString sddName("sdd_");
    Char_t candNum[4];
    sprintf(candNum,"%d",i+1);
    sddName.Append(candNum);
    fHis->AddAt(new TH1F(sddName.Data(),"SDD maps",scale*fMaxNofSamples,
			 0.,(Float_t) scale*fMaxNofSamples), i);
  } // end for i
}
//______________________________________________________________________
void AliITSsimulationSDD::FillHistograms(){
  // fill 1D histograms from map

  if (!fHis) return;

  for( Int_t i=0; i<fNofMaps; i++) {
    TH1F *hist =(TH1F *)fHis->UncheckedAt(i);
    Int_t nsamples = hist->GetNbinsX();
    for( Int_t j=0; j<nsamples; j++) {
      Double_t signal=fHitMap2->GetSignal(i,j);
      hist->Fill((Float_t)j,signal);
    } // end for j
  } // end for i
}
//______________________________________________________________________
void AliITSsimulationSDD::ResetHistograms(){
  // Reset histograms for this detector
  Int_t i;

  for (i=0;i<fNofMaps;i++ ) {
    if (fHis->At(i))    ((TH1F*)fHis->At(i))->Reset();
  } // end for i
}
//______________________________________________________________________
TH1F *AliITSsimulationSDD::GetAnode(Int_t wing, Int_t anode) { 
  // Fills a histogram from a give anode.  

  if (!fHis) return 0;

  if(wing <=0 || wing > 2) {
    Warning("GetAnode","Wrong wing number: %d",wing);
    return NULL;
  } // end if wing <=0 || wing >2
  if(anode <=0 || anode > fNofMaps/2) {
    Warning("GetAnode","Wrong anode number: %d",anode);
    return NULL;
  } // end if ampde <=0 || andoe > fNofMaps/2

  Int_t index = (wing-1)*fNofMaps/2 + anode-1;
  return (TH1F*)(fHis->At(index));
}
//______________________________________________________________________
void AliITSsimulationSDD::WriteToFile(TFile *hfile) {
  // Writes the histograms to a file

  if (!fHis) return;

  hfile->cd();
  Int_t i;
  for(i=0; i<fNofMaps; i++)  fHis->At(i)->Write(); //fAdcs[i]->Write();
  return;
}
//______________________________________________________________________
Float_t AliITSsimulationSDD::GetNoise() {  
  // Returns the noise value
  //Bool_t do10to8=fResponse->Do10to8();
  //noise will always be in the liniar part of the signal
  Int_t decr;
  Int_t threshold = fT1[0];
  char opt1[20], opt2[20];

  fResponse->ParamOptions(opt1,opt2);
  fParam=opt2;
  char *same = strstr(opt1,"same");
  Float_t noise,baseline;
  if (same) {
    fResponse->GetNoiseParam(noise,baseline);
  } else {
    static Bool_t readfile=kTRUE;
    //read baseline and noise from file
    if (readfile) ReadBaseline();
    readfile=kFALSE;
  } // end if same

  TCanvas *c2 = (TCanvas*)gROOT->GetListOfCanvases()->FindObject("c2");
  if(c2) delete c2->GetPrimitive("noisehist");
  if(c2) delete c2->GetPrimitive("anode");
  else     c2=new TCanvas("c2");
  c2->cd();
  c2->SetFillColor(0);

  TH1F *noisehist = new TH1F("noisehist","noise",100,0.,(float)2*threshold);
  TH1F *anode = new TH1F("anode","Anode Projection",fMaxNofSamples,0.,
			 (float)fMaxNofSamples);
  Int_t i,k;
  for (i=0;i<fNofMaps;i++) {
    CompressionParam(i,decr,threshold); 
    if  (!same) GetAnodeBaseline(i,baseline,noise);
    anode->Reset();
    for (k=0;k<fMaxNofSamples;k++) {
      Float_t signal=(Float_t)fHitMap2->GetSignal(i,k);
      //if (signal <= (float)threshold) noisehist->Fill(signal-baseline);
      if (signal <= (float)(threshold+decr)) noisehist->Fill(signal);
      anode->Fill((float)k,signal);
    } // end for k
    anode->Draw();
    c2->Update();
  } // end for i
  TF1 *gnoise = new TF1("gnoise","gaus",0.,threshold);
  noisehist->Fit("gnoise","RQ");
  noisehist->Draw();
  c2->Update();
  Float_t mnoise = gnoise->GetParameter(1);
  cout << "mnoise : " << mnoise << endl;
  Float_t rnoise = gnoise->GetParameter(2);
  cout << "rnoise : " << rnoise << endl;
  delete noisehist;
  return rnoise;
}
//______________________________________________________________________
void AliITSsimulationSDD::WriteSDigits(){
  // Fills the Summable digits Tree
  static AliITS *aliITS = (AliITS*)gAlice->GetModule("ITS");

  for( Int_t i=0; i<fNofMaps; i++ ) {
    if( !fAnodeFire[i] ) continue;
    for( Int_t j=0; j<fMaxNofSamples; j++ ) {
      Double_t sig = fHitMap2->GetSignal( i, j );
      if( sig > 0.2 ) {
	Int_t jdx = j*fScaleSize;
	Int_t index = fpList->GetHitIndex( i, j );
	AliITSpListItem pItemTmp2( fModule, index, 0. );
	// put the fScaleSize analog digits in only one
	for( Int_t ik=0; ik<fScaleSize; ik++ ) {
	  AliITSpListItem *pItemTmp = fpList->GetpListItem( i, jdx+ik );
	  if( pItemTmp == 0 ) continue;
	  pItemTmp2.Add( pItemTmp );
	}
	pItemTmp2.AddSignalAfterElect( fModule, index, sig );
	pItemTmp2.AddNoise( fModule, index, fHitNoiMap2->GetSignal( i, j ) );         
	aliITS->AddSumDigit( pItemTmp2 );
      } // end if (sig > 0.2)
    }
  }
  return;
}
//______________________________________________________________________
void AliITSsimulationSDD::Print() {
  // Print SDD simulation Parameters

  cout << "**************************************************" << endl;
  cout << "   Silicon Drift Detector Simulation Parameters   " << endl;
  cout << "**************************************************" << endl;
  cout << "Flag for Perpendicular tracks: " << (Int_t) fFlag << endl;
  cout << "Flag for noise checking: " << (Int_t) fCheckNoise << endl;
  cout << "Flag to switch off electronics: " << (Int_t) fDoFFT << endl;
  cout << "Number pf Anodes used: " << fNofMaps << endl;
  cout << "Number of Time Samples: " << fMaxNofSamples << endl;
  cout << "Scale size factor: " << fScaleSize << endl;
  cout << "**************************************************" << endl;
}