Fixed some coding violations and warnings. Added some FIXME's

[u/mrichter/AliRoot.git] / ITS / AliITS.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.                  *
 **************************************************************************/

/* $Id$ */


///////////////////////////////////////////////////////////////////////////////
//                                                                           //
//      An overview of the basic philosophy of the ITS code development      //
// and analysis is show in the figure below.                                 //
//Begin_Html                                                                 //
/*                                               
<img src="picts/ITS/ITS_Analysis_schema.gif">
</pre>
<br clear=left>
<font size=+2 color=red>
<p>Roberto Barbera is in charge of the ITS Offline code (1999).
<a href="mailto:roberto.barbera@ct.infn.it">Roberto Barbera</a>.
</font>
<pre>
*/
//End_Html
//
//  AliITS. Inner Traking System base class.
//  This class contains the base procedures for the Inner Tracking System
//
//Begin_Html
/*
<img src="picts/ITS/AliITS_Class_Diagram.gif">
</pre>
<br clear=left>
<font size=+2 color=red>
<p>This show the class diagram of the different elements that are part of
the AliITS class.
</font>
<pre>
*/
//End_Html
//
// Version: 0
// Written by Rene Brun, Federico Carminati, and Roberto Barbera
//
// Version: 1
// Modified and documented by Bjorn S. Nilsen
// July 11 1999
//
// Version: 2
// Modified and documented by A. Bologna
// October 18 1999
//
// AliITS is the general base class for the ITS. Also see AliDetector for
// futher information.
//
///////////////////////////////////////////////////////////////////////////////

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

#include <TBranch.h>
#include <TClonesArray.h>
#include <TFile.h>
#include <TMath.h>
#include <TObjectTable.h>
#include <TROOT.h>
#include <TRandom.h>
#include <TString.h>
#include <TTree.h>
#include <TVector.h>
#include <TVirtualMC.h>

#include "AliConfig.h"
#include "AliHeader.h"
#include "AliITS.h"
#include "AliITSClusterFinderSDD.h"
#include "AliITSClusterFinderSPD.h"
#include "AliITSClusterFinderSSD.h"
#include "AliITSClusterFinderV2SDD.h"
#include "AliITSClusterFinderV2SPD.h"
#include "AliITSClusterFinderV2SSD.h"
#include "AliITSDetType.h"
#include "AliITSLoader.h"
#include "AliITSRawClusterSPD.h"
#include "AliITSRawClusterSDD.h"
#include "AliITSRawClusterSSD.h"
#include "AliITSRecPoint.h"
#include "AliITSclusterV2.h"
#include "AliITSdigitSPD.h"
#include "AliITSdigitSDD.h"
#include "AliITSdigitSSD.h"
#include "AliITSgeom.h"
#include "AliITShit.h"
#include "AliITSmodule.h"
#include "AliITSpList.h"
#include "AliITSresponseSDD.h"
#include "AliITSresponseSPD.h"
#include "AliITSresponseSSD.h"
#include "AliITSsegmentationSDD.h"
#include "AliITSsegmentationSPD.h"
#include "AliITSsegmentationSSD.h"
#include "AliITSsimulationSDD.h"
#include "AliITSsimulationSPD.h"
#include "AliITSsimulationSSD.h"
#include "AliMC.h"
#include "AliITSDigitizer.h"
#include "AliITSDDLRawData.h"
#include "AliRun.h"
#include "AliRawReader.h"

ClassImp(AliITS)

//______________________________________________________________________
AliITS::AliITS() : AliDetector(),
    fITSgeom(0),
    fEuclidOut(0),
    fITSmodules(0),
    fOpt("All"),
    fIdN(0),
    fIdSens(0),
    fIdName(0),
    fNDetTypes(kNTYPES),
    fDetTypes(0),
    fSDigits(0),
    fNSDigits(0),
    fDtype(0),
    fNdtype(0),
    fCtype(0),
    fNctype(0),
    fRecPoints(0),
    fNRecPoints(0),
    fClustersV2(0),
    fNClustersV2(0),		   
    fSelectedVertexer(0){
    // Default initializer for ITS
    //      The default constructor of the AliITS class. In addition to
    // creating the AliITS class it zeros the variables fIshunt (a member
    // of AliDetector class), fEuclidOut, and fIdN, and zeros the pointers
    // fITSpoints, fIdSens, and fIdName. The AliDetector default constructor
    // is also called.
    // Inputs:
    //      none.
    // Outputs:
    //      none.
    // Return:
    //      Blank ITS class.

    fIshunt     = 0;   // not zeroed in AliDetector.

    // AliITS variables.
//    SetDetectors(); // default to fOpt="All". This variable not written out.
    SetMarkerColor(kRed);
    SelectVertexer(" ");
}
//______________________________________________________________________
AliITS::AliITS(const char *name, const char *title):AliDetector(name,title),
    fITSgeom(0),
    fEuclidOut(0),
    fITSmodules(0),
    fOpt("All"),
    fIdN(0),
    fIdSens(0),
    fIdName(0),
    fNDetTypes(kNTYPES),
    fDetTypes(0),
    fSDigits(0),
    fNSDigits(0),
    fDtype(0),
    fNdtype(0),
    fCtype(0),
    fNctype(0),
    fRecPoints(0),
    fNRecPoints(0),
    fClustersV2(0),
    fNClustersV2(0),						    
    fSelectedVertexer(0){
    //     The standard Constructor for the ITS class. In addition to 
    // creating the AliITS class, it allocates memory for the TClonesArrays 
    // fHits, fSDigits, fDigits, fITSpoints, and the TObjArray of fCtype 
    // (clusters). It also zeros the variables
    // fIshunt (a member of AliDetector class), fEuclidOut, and fIdN, and zeros
    // the pointers fIdSens and fIdName. To help in displaying hits via the
    // ROOT macro display.C AliITS also sets the marker color to red. The
    // variables passes with this constructor, const char *name and *title,
    // are used by the constructor of AliDetector class. See AliDetector
    // class for a description of these parameters and its constructor
    // functions.
    // Inputs:
    //      const char *name      Detector name. Should always be "ITS"
    //      const char *title     Detector title.
    // Outputs:
    //      none.
    // Return:
    //      An ITS class.

    fIshunt     = 0;  // not zeroed in AliDetector
    fHits       = new TClonesArray("AliITShit", 1560);//not done in AliDetector
    // Not done in AliDetector.
    if(gAlice->GetMCApp()) gAlice->GetMCApp()->AddHitList(fHits);

    fEuclidOut  = 0;
    fITSgeom    = 0;
    fITSmodules = 0;
    SetDetectors(); // default to fOpt="All". This variable not written out.

    fIdN        = 0;
    fIdName     = 0;
    fIdSens     = 0;

    fNDetTypes  = kNTYPES;
    fDetTypes   = new TObjArray(fNDetTypes);

    fSDigits    = new TClonesArray("AliITSpListItem",1000);
    fNSDigits   = 0;

    fNdtype     = new Int_t[fNDetTypes];
    fDtype      = new TObjArray(fNDetTypes);

    fCtype      = new TObjArray(fNDetTypes);
    fNctype     = new Int_t[fNDetTypes];

    fRecPoints  = new TClonesArray("AliITSRecPoint",1000);
    fNRecPoints = 0;
    fClustersV2 = new TClonesArray("AliITSclusterV2",3000);
    fNClustersV2=0;

    Int_t i;
    for(i=0;i<fNDetTypes;i++) {
        fDetTypes->AddAt(new AliITSDetType(),i); 
        fNdtype[i] = 0;
        fNctype[i] = 0;
    } // end for i

    SetMarkerColor(kRed);
    SelectVertexer(" ");
}
//______________________________________________________________________
AliITS::~AliITS(){
    // Default destructor for ITS.
    //     The default destructor of the AliITS class. In addition to deleting
    // the AliITS class it deletes the memory pointed to by the fHits, fDigits,
    // fSDigits, fCtype, fITSmodules, fITSgeom, fRecPoints, fIdSens, fIdName, 
    // fITSpoints, fDetType and it's contents.
    // Inputs:
    //      none.
    // Outputs:
    //      none.
    // Return:
    //      none.

    if (fHits) {
      fHits->Delete();
      delete fHits;
      fHits=0;
    }
    if (fSDigits) {
      fSDigits->Delete();
      delete fSDigits;
      fSDigits=0;
    }
    if (fDigits) {
      fDigits->Delete();
      delete fDigits;
      fDigits=0;
    }
    if (fRecPoints) {
      fRecPoints->Delete();
      delete fRecPoints;
      fRecPoints=0;
    }
    if(fClustersV2){
      fClustersV2->Delete();
      delete fClustersV2;
      fClustersV2=0;
    }
    delete[] fIdName;  // Array of TStrings
    delete[] fIdSens;
    if(fITSmodules) {
        this->ClearModules();
        delete fITSmodules;
	fITSmodules = 0;
    }// end if fITSmodules!=0

    if(fDtype) {
        fDtype->Delete();
        delete fDtype;
    } // end if fDtype
    delete [] fNdtype;
    if (fCtype) {
        fCtype->Delete();
        delete fCtype;
	fCtype = 0;
    } // end if fCtype
    delete [] fNctype;

    if (fDetTypes) {
        fDetTypes->Delete();
        delete fDetTypes;
	fDetTypes = 0;
    } // end if fDetTypes


    if (fITSgeom) delete fITSgeom;
}
//______________________________________________________________________
AliITS::AliITS(const AliITS &source) : AliDetector(source){
    // Copy constructor. This is a function which is not allowed to be
    // done to the ITS. It exits with an error.
    // Inputs:
    //      AliITS &source  An AliITS class.
    // Outputs:
    //      none.
    // Return:
    //      none.

    if(this==&source) return;
    Error("Copy constructor",
          "You are not allowed to make a copy of the AliITS");
    exit(1);
}
//______________________________________________________________________
AliITS& AliITS::operator=(AliITS &source){
    // Assignment operator. This is a function which is not allowed to be
    // done to the ITS. It exits with an error.
    // Inputs:
    //      AliITS &source  An AliITS class.
    // Outputs:
    //      none.
    // Return:
    //      none.

    if(this==&source) return *this;
    Error("operator=","You are not allowed to make a copy of the AliITS");
    exit(1);
    return *this; //fake return
}
//______________________________________________________________________
AliDigitizer* AliITS::CreateDigitizer(AliRunDigitizer* manager)const{
    // Creates the AliITSDigitizer in a standard way for use via AliModule.
    // This function can not be included in the .h file because of problems
    // with the order of inclusion (recursive).
    // Inputs:
    //    AliRunDigitizer *manager  The Manger class for Digitization
    // Output:
    //    none.
    // Return:
    //    A new AliITSRunDigitizer (cast as a AliDigitizer).

     return new AliITSDigitizer(manager);
}
//______________________________________________________________________
void AliITS::Init(){
    // Initializer ITS after it has been built
    //     This routine initializes the AliITS class. It is intended to be
    // called from the Init function in AliITSv?. Besides displaying a banner
    // indicating that it has been called it initializes the array fIdSens
    // and sets the default segmentation, response, digit and raw cluster
    // classes therefore it should be called after a call to CreateGeometry.
    // Inputs:
    //      none.
    // Outputs:
    //      none.
    // Return:
    //      none.
    Int_t i;

    SetDefaults();
    // Array of TStrings
    if(gMC) for(i=0;i<fIdN;i++) fIdSens[i] = gMC->VolId(fIdName[i]);
}
//______________________________________________________________________
void AliITS::SetDefaults(){
    // sets the default segmentation, response, digit and raw cluster classes.
    // Inputs:
    //      none.
    // Outputs:
    //      none.
    // Return:
    //      none.
    AliITSsegmentation *seg;
    AliITSresponse    *resp;
    AliITSDetType *iDetType;

    if(fDebug) Info("SetDefauls","%s: SetDefaults",ClassName());

    //SPD
    iDetType = DetType(kSPD);
    if(iDetType){
        if (!iDetType->GetSegmentationModel()) {
            seg = new AliITSsegmentationSPD(fITSgeom);
            SetSegmentationModel(kSPD,seg); 
        } // end if
        if (!iDetType->GetResponseModel()) {
            SetResponseModel(kSPD,new AliITSresponseSPD()); 
        } // end if
        // set digit and raw cluster classes to be used

        const char *kData0=(iDetType->GetResponseModel())->DataType();
        if (strstr(kData0,"real")) {
            iDetType->ClassNames("AliITSdigit","AliITSRawClusterSPD");
        } else iDetType->ClassNames("AliITSdigitSPD","AliITSRawClusterSPD");
    } // end if iDetType

    // SDD
    iDetType = DetType(kSDD); 
    if(iDetType){
        if (!iDetType->GetResponseModel()) {
            SetResponseModel(kSDD,new AliITSresponseSDD("simulated")); 
        } // end if
        resp = iDetType->GetResponseModel();
        if (!iDetType->GetSegmentationModel()) {
            seg = new AliITSsegmentationSDD(fITSgeom,resp);
            SetSegmentationModel(kSDD,seg); 
        } // end if
        const char *kData1 = (iDetType->GetResponseModel())->DataType();
        const char *kopt = iDetType->GetResponseModel()->ZeroSuppOption();
        if((!strstr(kopt,"2D"))&&(!strstr(kopt,"1D")) || 
                                   strstr(kData1,"real") ){
            iDetType->ClassNames("AliITSdigit","AliITSRawClusterSDD");
        } else iDetType->ClassNames("AliITSdigitSDD","AliITSRawClusterSDD");
    } // end if iDetType

    // SSD
    iDetType = DetType(kSSD); 
    if(iDetType){
        if (!iDetType->GetSegmentationModel()) {
            seg = new AliITSsegmentationSSD(fITSgeom);
            SetSegmentationModel(kSSD,seg); 
        } // end if
        if (!iDetType->GetResponseModel()) {
            SetResponseModel(kSSD,new AliITSresponseSSD("simulated"));
        } // end if
        const char *kData2 = (iDetType->GetResponseModel())->DataType();
        if (strstr(kData2,"real")) {
            iDetType->ClassNames("AliITSdigit","AliITSRawClusterSSD");
        } else iDetType->ClassNames("AliITSdigitSSD","AliITSRawClusterSSD");
    } // end if iDetType

    if (kNTYPES>3) {
        Warning("SetDefaults",
                "Only the three basic detector types are initialized!");
    }  // end if
}
//______________________________________________________________________
void AliITS::SetDefaultSimulation(){
    // sets the default simulation.
    // Inputs:
    //      none.
    // Outputs:
    //      none.
    // Return:
    //      none.
    AliITSDetType *iDetType;
    AliITSsimulation *sim;
    AliITSsegmentation *seg;
    AliITSresponse *res;

    iDetType = DetType(kSPD);
    if(iDetType){
        sim = iDetType->GetSimulationModel();
        if (!sim) {
            seg = (AliITSsegmentation*)iDetType->GetSegmentationModel();
            res = (AliITSresponse*)iDetType->GetResponseModel();
            sim = new AliITSsimulationSPD(seg,res);
            SetSimulationModel(kSPD,sim);
        }else{ // simulation exists, make sure it is set up properly.
            if(sim->GetResponseModel()==0) sim->SetResponseModel(
                (AliITSresponse*)iDetType->GetResponseModel());
            if(sim->GetSegmentationModel()==0) sim->SetSegmentationModel(
                (AliITSsegmentation*)iDetType->GetSegmentationModel());
            sim->Init();
        } // end if
    }// end if iDetType
    iDetType  = DetType(kSDD);
    if(iDetType){
        sim = iDetType->GetSimulationModel();
        if (!sim) {
            seg = (AliITSsegmentation*)iDetType->GetSegmentationModel();
            res =  (AliITSresponse*)iDetType->GetResponseModel();
            sim = new AliITSsimulationSDD(seg,res);
            SetSimulationModel(kSDD,sim);
        }else{ // simulation exists, make sure it is set up properly.
            if(sim->GetResponseModel()==0) sim->SetResponseModel(
                (AliITSresponse*)iDetType->GetResponseModel());
            if(sim->GetSegmentationModel()==0) sim->SetSegmentationModel(
                (AliITSsegmentation*)iDetType->GetSegmentationModel());
            sim->Init();
        } //end if
    }// end if iDetType
    iDetType = DetType(kSSD);
    if(iDetType){
        sim = iDetType->GetSimulationModel();
        if (!sim) {
            seg =(AliITSsegmentation*)iDetType->GetSegmentationModel();
            res =  (AliITSresponse*)iDetType->GetResponseModel();
            sim = new AliITSsimulationSSD(seg,res);
            SetSimulationModel(kSSD,sim);
        }else{ // simulation exists, make sure it is set up properly.
            if(sim->GetResponseModel()==0) sim->SetResponseModel(
                (AliITSresponse*)iDetType->GetResponseModel());
            if(sim->GetSegmentationModel()==0) sim->SetSegmentationModel(
                (AliITSsegmentation*)iDetType->GetSegmentationModel());
            sim->Init();
        } // end if
    } // end if iDetType
}
//______________________________________________________________________
void AliITS::SetDefaultClusterFinders(){
    // Sets the default cluster finders. Used in finding RecPoints.
    // Inputs:
    //      none.
    // Outputs:
    //      none.
    // Return:
    //      none.
    AliITSDetType *iDetType;
    AliITSsegmentation *seg;
    AliITSClusterFinder *clf;
    AliITSresponse *res;

    MakeTreeC();

    // SPD
    iDetType=DetType(kSPD);
    if(iDetType){
        if (!iDetType->GetReconstructionModel()) {
            seg =(AliITSsegmentation*)iDetType->GetSegmentationModel();
            TClonesArray  *dig0 = DigitsAddress(0);
            TClonesArray *recp0 = ClustersAddress(0);
            clf = new AliITSClusterFinderSPD(seg,dig0,recp0);
            SetReconstructionModel(kSPD,clf);
        } // end if
    } // end if iDetType

    // SDD
    iDetType=DetType(kSDD);
    if(iDetType){
        if (!iDetType->GetReconstructionModel()) {
            seg = (AliITSsegmentation*)iDetType->GetSegmentationModel();
            res = (AliITSresponse*)iDetType->GetResponseModel();
            TClonesArray  *dig1 = DigitsAddress(1);
            TClonesArray *recp1 = ClustersAddress(1);
            clf = new AliITSClusterFinderSDD(seg,res,dig1,recp1);
            SetReconstructionModel(kSDD,clf);
        } // end if
    } // end if iDetType

    // SSD
    iDetType=DetType(kSSD);
    if(iDetType){
        if (!iDetType->GetReconstructionModel()) {
            seg = (AliITSsegmentation*)iDetType->GetSegmentationModel();
            TClonesArray *dig2 = DigitsAddress(2);
            clf = new AliITSClusterFinderSSD(seg,dig2);
            SetReconstructionModel(kSSD,clf);
        } // end if
    } // end if iDetType
}


//______________________________________________________________________
void AliITS::SetDefaultClusterFindersV2(){
    // Sets the default cluster finders. Used in finding RecPoints.
    // Inputs:
    //      none.
    // Outputs:
    //      none.
    // Return:
    //      none.
    AliITSDetType *iDetType;
    AliITSsegmentation *seg;
    AliITSClusterFinder *clf;

    MakeTreeC();

    // SPD
    iDetType=DetType(kSPD);
    if(iDetType){
        if (!iDetType->GetReconstructionModel()) {
            seg =(AliITSsegmentation*)iDetType->GetSegmentationModel();
            clf = new AliITSClusterFinderV2SPD();
	    clf->SetSegmentation(seg);
	    clf->SetDigits(DigitsAddress(0));
            SetReconstructionModel(kSPD,clf);
        } // end if
    } // end if iDetType

    // SDD
    iDetType=DetType(kSDD);
    if(iDetType){
        if (!iDetType->GetReconstructionModel()) {
            seg = (AliITSsegmentation*)iDetType->GetSegmentationModel();
            clf = new AliITSClusterFinderV2SDD();
	    clf->SetSegmentation(seg);
	    clf->SetDigits(DigitsAddress(1));
            SetReconstructionModel(kSDD,clf);
        } // end if
    } // end if iDetType

    // SSD
    iDetType=DetType(kSSD);
    if(iDetType){
        if (!iDetType->GetReconstructionModel()) {
            seg = (AliITSsegmentation*)iDetType->GetSegmentationModel();
            clf = new AliITSClusterFinderV2SSD();
	    clf->SetSegmentation(seg);
	    clf->SetDigits(DigitsAddress(2));
            SetReconstructionModel(kSSD,clf);
        } // end if
    } // end if iDetType
}


//______________________________________________________________________
void AliITS::MakeBranch(Option_t* option){
    // Creates Tree branches for the ITS.
    // Inputs:
    //      Option_t *option    String of Tree types S,D, and/or R.
    //      const char *file    String of the file name where these branches
    //                          are to be stored. If blank then these branches
    //                          are written to the same tree as the Hits were
    //                          read from.
    // Outputs:
    //      none.
    // Return:
    //      none.
    Bool_t cH = (strstr(option,"H")!=0);
    Bool_t cS = (strstr(option,"S")!=0);
    Bool_t cD = (strstr(option,"D")!=0);
    Bool_t cR = (strstr(option,"R")!=0);
    Bool_t cRF = (strstr(option,"RF")!=0);
    Bool_t v2 = (strstr(option,"v2")!=0);
    

    if(cRF)cR = kFALSE;
    if(cH && (fHits == 0x0)) fHits  = new TClonesArray("AliITShit", 1560);
    
    AliDetector::MakeBranch(option);

    if(cS) MakeBranchS(0);
    if(cD) MakeBranchD(0);
    if(cR) MakeBranchR(0);
    if(cRF) MakeBranchRF(0);
    if(v2) MakeBranchR(0,"v2");
}
//______________________________________________________________________
void AliITS::SetTreeAddress(){
    // Set branch address for the Trees.
    // Inputs:
    //      none.
    // Outputs:
    //      none.
    // Return:
    //      none.
    TTree *treeS = fLoader->TreeS();
    TTree *treeD = fLoader->TreeD();
    TTree *treeR = fLoader->TreeR();
    if (fLoader->TreeH() && (fHits == 0x0)) 
        fHits = new TClonesArray("AliITShit", 1560);

    AliDetector::SetTreeAddress();

    SetTreeAddressS(treeS);
    SetTreeAddressD(treeD);
    SetTreeAddressR(treeR);
}
//______________________________________________________________________
void AliITS::AddHit(Int_t track, Int_t *vol, Float_t *hits){
    // Add an ITS hit
    //     The function to add information to the AliITShit class. See the
    // AliITShit class for a full description. This function allocates the
    // necessary new space for the hit information and passes the variable
    // track, and the pointers *vol and *hits to the AliITShit constructor
    // function.
    // Inputs:
    //      Int_t   track   Track number which produced this hit.
    //      Int_t   *vol    Array of Integer Hit information. See AliITShit.h
    //      Float_t *hits   Array of Floating Hit information.  see AliITShit.h
    // Outputs:
    //      none.
    // Return:
    //      none.

    TClonesArray &lhits = *fHits;
    new(lhits[fNhits++]) AliITShit(fIshunt,track,vol,hits);
}
//______________________________________________________________________
void AliITS::InitModules(Int_t size,Int_t &nmodules){
    // Initialize the modules array.
    // Inputs:
    //      Int_t size  Size of array of the number of modules to be
    //                  created. If size <=0 then the number of modules
    //                  is gotten from AliITSgeom class kept in fITSgeom.
    // Outputs:
    //      Int_t &nmodules The number of modules existing.
    // Return:
    //      none.

    if(fITSmodules){ 
        fITSmodules->Delete();
        delete fITSmodules;
    } // end fir fITSmoudles

    Int_t nl,indexMAX,index;

    if(size<=0){ // default to using data stored in AliITSgeom
        if(fITSgeom==0) {
            Error("InitModules","fITSgeom not defined");
            return;
        } // end if fITSgeom==0
        nl = fITSgeom->GetNlayers();
        indexMAX = fITSgeom->GetIndexMax();
        nmodules = indexMAX;
        fITSmodules = new TObjArray(indexMAX);
        for(index=0;index<indexMAX;index++){
            fITSmodules->AddAt( new AliITSmodule(index),index);
        } // end for index
    }else{
        fITSmodules = new TObjArray(size);
        for(index=0;index<size;index++) {
            fITSmodules->AddAt( new AliITSmodule(index),index);
        } // end for index

        nmodules = size;
    } // end i size<=0
}
//______________________________________________________________________
void AliITS::FillModules(Int_t evnt,Int_t bgrev,Int_t nmodules,
                         Option_t *option, const char *filename){
    // fill the modules with the sorted by module hits; add hits from
    // background if option=Add.
    // Inputs:
    //      Int_t evnt       Event to be processed.
    //      Int_t bgrev      Background Hit tree number.
    //      Int_t nmodules   Not used.
    //      Option_t *option String indicating if merging hits or not. To
    //                       merge hits set equal to "Add". Otherwise no
    //                       background hits are considered.
    //      Test_t *filename File name containing the background hits..
    // Outputs:
    //      none.
    // Return:
    //      none.
    static TTree *trH1;                 //Tree with background hits
    static Bool_t first=kTRUE;
    static TFile *file;
    const char *addBgr = strstr(option,"Add");

    evnt = nmodules; // Dummy use of variables to remove warnings
    if (addBgr ) {
        if(first) {
            file=new TFile(filename);
        } // end if first
        first=kFALSE;
        file->cd();
        file->ls();
        // Get Hits Tree header from file
        if(trH1) delete trH1;
        trH1=0;

        char treeName[20];
        sprintf(treeName,"TreeH%d",bgrev);
        trH1 = (TTree*)gDirectory->Get(treeName);
        if (!trH1) {
            Error("FillModules","cannot find Hits Tree for event:%d",bgrev);
        } // end if !trH1
        // Set branch addresses
    } // end if addBgr

    FillModules(fLoader->TreeH(),0); // fill from this file's tree.
    
    if (addBgr ) {
        FillModules(trH1,10000000); // Default mask 10M.
        TTree *fAli=fLoader->GetRunLoader()->TreeK();
        TFile *fileAli=0;
        if (fAli) fileAli =fAli->GetCurrentFile();
        fileAli->cd();
    } // end if add
}
//______________________________________________________________________
void AliITS::FillModules(TTree *treeH, Int_t mask) {
    // fill the modules with the sorted by module hits; 
    // can be called many times to do a merging
    // Inputs:
    //      TTree *treeH  The tree containing the hits to be copied into
    //                    the modules.
    //      Int_t mask    The track number mask to indecate which file
    //                    this hits came from.
    // Outputs:
    //      none.
    // Return:
    //      none.

    if (treeH == 0x0)
     {
       Error("FillModules","Tree is NULL");
     }
    Int_t lay,lad,det,index;
    AliITShit *itsHit=0;
    AliITSmodule *mod=0;
    char branchname[20];
    sprintf(branchname,"%s",GetName());
    TBranch *branch = treeH->GetBranch(branchname);
    if (!branch) {
        Error("FillModules","%s branch in TreeH not found",branchname);
        return;
    } // end if !branch
    branch->SetAddress(&fHits);
    Int_t nTracks =(Int_t) treeH->GetEntries();
    Int_t iPrimTrack,h;
    for(iPrimTrack=0; iPrimTrack<nTracks; iPrimTrack++){
        ResetHits();
        Int_t nBytes = treeH->GetEvent(iPrimTrack);
        if (nBytes <= 0) continue;
        Int_t nHits = fHits->GetEntriesFast();
        for(h=0; h<nHits; h++){
            itsHit = (AliITShit *)fHits->UncheckedAt(h);
            itsHit->GetDetectorID(lay,lad,det);
            if (fITSgeom) {
                index = fITSgeom->GetModuleIndex(lay,lad,det);
            } else {
                index=det-1; // This should not be used.
            } // end if [You must have fITSgeom for this to work!]
            mod = GetModule(index);
            itsHit->SetTrack(itsHit->GetTrack()+mask); // Set track mask.
            mod->AddHit(itsHit,iPrimTrack,h);
        } // end loop over hits 
    } // end loop over tracks
}
//______________________________________________________________________
void AliITS::MakeBranchS(const char *fl){
    // Creates Tree Branch for the ITS summable digits.
    // Inputs:
    //      cont char *fl  File name where SDigits branch is to be written
    //                     to. If blank it write the SDigits to the same
    //                     file in which the Hits were found.
    // Outputs:
    //      none.
    // Return:
    //      none.
    Int_t buffersize = 4000;
    char branchname[30];

    // only one branch for SDigits.
    sprintf(branchname,"%s",GetName());
    

    if(fLoader->TreeS()){
        if(fSDigits==0x0) fSDigits = new TClonesArray("AliITSpListItem",1000);
        MakeBranchInTree(fLoader->TreeS(),branchname,&fSDigits,buffersize,fl);
    } // end if
}
//______________________________________________________________________
void AliITS::SetTreeAddressS(TTree *treeS){
    // Set branch address for the ITS summable digits Trees.
    // Inputs:
    //      TTree *treeS   Tree containing the SDigits.
    // Outputs:
    //      none.
    // Return:
    //      none.
    char branchname[30];

    if(!treeS) return;
    if (fSDigits == 0x0)  fSDigits = new TClonesArray("AliITSpListItem",1000);
    TBranch *branch;
    sprintf(branchname,"%s",GetName());
    branch = treeS->GetBranch(branchname);
    if (branch) branch->SetAddress(&fSDigits);
}
//______________________________________________________________________
void AliITS::MakeBranchInTreeD(TTree *treeD,const char *file){
    // Creates Tree branches for the ITS.
    // Inputs:
    //      TTree     *treeD Pointer to the Digits Tree.
    //      cont char *file  File name where Digits branch is to be written
    //                       to. If blank it write the SDigits to the same
    //                       file in which the Hits were found.
    // Outputs:
    //      none.
    // Return:
    //      none.
    // one branch for digits per type of detector
    const Char_t *det[3] = {"SPD","SDD","SSD"};
    TString digclass;
    Int_t i;
    Int_t buffersize = 4000;
    Char_t branchname[30];

    if (fDtype == 0x0) fDtype = new TObjArray(fNDetTypes);
    for (i=0; i<kNTYPES ;i++) {
        digclass = DetType(i)->GetDigitClassName();
        // digits
        if(!(fDtype->At(i))){
            fDtype->AddAt(new TClonesArray(digclass.Data(),1000),i);
        }else{
            ResetDigits(i);
        } // end if
        if (kNTYPES==3) sprintf(branchname,"%sDigits%s",GetName(),det[i]);
        else  sprintf(branchname,"%sDigits%d",GetName(),i+1);      
        if (fDtype && treeD) {
            MakeBranchInTree(treeD,branchname,&((*fDtype)[i]),buffersize,file);
        } // end if
    } // end for i
         /*
    for (i=0; i<kNTYPES ;i++) {
        if (kNTYPES==3) sprintf(branchname,"%sDigits%s",GetName(),det[i]);
        else  sprintf(branchname,"%sDigits%d",GetName(),i+1);      
        if (fDtype && treeD) {
            MakeBranchInTree(treeD,branchname,&((*fDtype)[i]),buffersize,file);
        } // end if
    } // end for i
         */
}
//______________________________________________________________________
void AliITS::SetTreeAddressD(TTree *treeD){
    // Set branch address for the Trees.
    // Inputs:
    //      TTree *treeD   Tree containing the Digits.
    // Outputs:
    //      none.
    // Return:
    //      none.
    const char *det[3] = {"SPD","SDD","SSD"};
    TBranch *branch;
    TString digclass;
    Int_t i;
    char branchname[30];

    if(!treeD) return;
    if (fDtype == 0x0) fDtype = new TObjArray(fNDetTypes);
    for (i=0; i<kNTYPES; i++) {
        digclass = DetType(i)->GetDigitClassName();
        // digits
        if(!(fDtype->At(i))) {
            fDtype->AddAt(new TClonesArray(digclass.Data(),1000),i);
        }else{
            ResetDigits(i);
        } // end if
        if (kNTYPES==3) sprintf(branchname,"%sDigits%s",GetName(),det[i]);
        else  sprintf(branchname,"%sDigits%d",GetName(),i+1);
        if (fDtype) {
            branch = treeD->GetBranch(branchname);
            if (branch) branch->SetAddress(&((*fDtype)[i]));
        } // end if fDtype
    } // end for i
}
//______________________________________________________________________
void AliITS::Hits2SDigits(){
    // Standard Hits to summable Digits function.
    // Inputs:
    //      none.
    // Outputs:
    //      none.

    fLoader->LoadHits("read");
    fLoader->LoadSDigits("recreate");
    AliRunLoader* rl = fLoader->GetRunLoader(); 

    for (Int_t iEvent = 0; iEvent < rl->GetNumberOfEvents(); iEvent++) {
        // Do the Hits to Digits operation. Use Standard input values.
        // Event number from file, no background hit merging , use size from
        // AliITSgeom class, option="All", input from this file only.
        rl->GetEvent(iEvent);
        if (!fLoader->TreeS()) fLoader->MakeTree("S");
        MakeBranch("S");
        SetTreeAddress();
        HitsToPreDigits(iEvent,0,-1," ",fOpt," ");
    } // end for iEvent
    
    fLoader->UnloadHits();
    fLoader->UnloadSDigits();
}
//______________________________________________________________________
void AliITS::SDigitsToDigits(Option_t *opt){
    // Standard Summable digits to Digits function.
    // Inputs:
    //      none.
    // Outputs:
    //      none.
    char name[20] = {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0};

    if(!GetITSgeom()) return; // need transformations to do digitization.
    AliITSgeom *geom = GetITSgeom();

    const char *all = strstr(opt,"All");
    const char *det[3] = {strstr(opt,"SPD"),strstr(opt,"SDD"),
                          strstr(opt,"SSD")};
    if( !det[0] && !det[1] && !det[2] ) all = "All";
    else all = 0;
    static Bool_t setDef = kTRUE;
    if(setDef) SetDefaultSimulation();
    setDef = kFALSE;

    AliITSsimulation *sim      = 0;
    AliITSDetType    *iDetType = 0;
    TTree            *trees    = fLoader->TreeS();
    if( !(trees && this->GetSDigits()) ){
        Error("SDigits2Digits","Error: No trees or SDigits. Returning.");
        return;
    } // end if
    sprintf( name, "%s", this->GetName() );
    TBranch *brchSDigits = trees->GetBranch( name );
    
    Int_t id,module;
    for(module=0;module<geom->GetIndexMax();module++){
        id       = geom->GetModuleType(module);
        if (!all && !det[id]) continue;
        iDetType = DetType(id);
        sim      = (AliITSsimulation*)iDetType->GetSimulationModel();
        if (!sim) {
            Error("SDigit2Digits","The simulation class was not "
                  "instanciated for module %d type %s!",module,
                  geom->GetModuleTypeName(module));
            exit(1);
        } // end if !sim
        sim->InitSimulationModule(module,gAlice->GetEvNumber());
        //
        // add summable digits to module
        this->GetSDigits()->Clear();
        brchSDigits->GetEvent(module);
        sim->AddSDigitsToModule(GetSDigits(),0);
        //
        // Digitise current module sum(SDigits)->Digits
        sim->FinishSDigitiseModule();

        // fills all branches - wasted disk space
        fLoader->TreeD()->Fill();
        this->ResetDigits();
    } // end for module

    fLoader->TreeD()->GetEntries();

    fLoader->TreeD()->AutoSave();
    // reset tree
    fLoader->TreeD()->Reset();
    
}
//______________________________________________________________________
void AliITS::Hits2Digits(){
    // Standard Hits to Digits function.
    // Inputs:
    //      none.
    // Outputs:
    //      none.

    fLoader->LoadHits("read");
    fLoader->LoadDigits("recreate");
    AliRunLoader* rl = fLoader->GetRunLoader(); 

    for (Int_t iEvent = 0; iEvent < rl->GetNumberOfEvents(); iEvent++) {
        // Do the Hits to Digits operation. Use Standard input values.
        // Event number from file, no background hit merging , use size from
        // AliITSgeom class, option="All", input from this file only.
        rl->GetEvent(iEvent);
        if (!fLoader->TreeD()) fLoader->MakeTree("D");
        MakeBranch("D");
        SetTreeAddress();   
        HitsToDigits(iEvent,0,-1," ",fOpt," ");
    } // end for iEvent

    fLoader->UnloadHits();
    fLoader->UnloadDigits();
}
//______________________________________________________________________
void AliITS::HitsToPreDigits(Int_t evNumber,Int_t bgrev,Int_t size,
                             Option_t *option,Option_t *opt,
                             const char *filename){
    //   Keep galice.root for signal and name differently the file for 
    // background when add! otherwise the track info for signal will be lost !
    // the condition below will disappear when the geom class will be
    // initialized for all versions - for the moment it is only for v5 !
    // 7 is the SDD beam test version.
    // Inputs:
    //      Int_t evnt       Event to be processed.
    //      Int_t bgrev      Background Hit tree number.
    //      Int_t nmodules   Not used.
    //      Option_t *option String indicating if merging hits or not. To
    //                       merge hits set equal to "Add". Otherwise no
    //                       background hits are considered.
    //      Test_t *filename File name containing the background hits..
    // Outputs:
    //      none.
    // Return:
    //      none.

    if(!GetITSgeom()) return; // need transformations to do digitization.
    AliITSgeom *geom = GetITSgeom();

    const char *all = strstr(opt,"All");
    const char *det[3] = {strstr(opt,"SPD"),strstr(opt,"SDD"),
                          strstr(opt,"SSD")};
    static Bool_t setDef=kTRUE;
    if (setDef) SetDefaultSimulation();
    setDef=kFALSE;

    Int_t nmodules;
    InitModules(size,nmodules);
    FillModules(evNumber,bgrev,nmodules,option,filename);

    AliITSsimulation *sim      = 0;
    AliITSDetType    *iDetType = 0;
    AliITSmodule     *mod      = 0;
    Int_t id,module;
    for(module=0;module<geom->GetIndexMax();module++){
        id       = geom->GetModuleType(module);
        if (!all && !det[id]) continue;
        iDetType = DetType(id);
        sim      = (AliITSsimulation*)iDetType->GetSimulationModel();
        if (!sim) {
            Error("HitsToSDigits","The simulation class was not "
                  "instanciated for module %d type %s!",module,
                  geom->GetModuleTypeName(module));
            exit(1);
        } // end if !sim
        mod      = (AliITSmodule *)fITSmodules->At(module);
        sim->SDigitiseModule(mod,module,evNumber);
        // fills all branches - wasted disk space
        fLoader->TreeS()->Fill(); 
        ResetSDigits();
    } // end for module

    ClearModules();

    fLoader->TreeS()->GetEntries();
    fLoader->TreeS()->AutoSave();
    fLoader->WriteSDigits("OVERWRITE");
    // reset tree
    fLoader->TreeS()->Reset();
}
//______________________________________________________________________
void AliITS::HitsToDigits(Int_t evNumber,Int_t bgrev,Int_t size,
                          Option_t *option,Option_t *opt,
                          const char *filename){
    //   Keep galice.root for signal and name differently the file for 
    // background when add! otherwise the track info for signal will be lost !
    // the condition below will disappear when the geom class will be
    // initialized for all versions - for the moment it is only for v5 !
    // 7 is the SDD beam test version.
    // Inputs:
    //      Int_t evnt       Event to be processed.
    //      Int_t bgrev      Background Hit tree number.
    //      Int_t nmodules   Not used.
    //      Option_t *option String indicating if merging hits or not. To
    //                       merge hits set equal to "Add". Otherwise no
    //                       background hits are considered.
    //      Test_t *filename File name containing the background hits..
    // Outputs:
    //      none.
    // Return:
    //      none.


    if(!GetITSgeom()) return; // need transformations to do digitization.
    AliITSgeom *geom = GetITSgeom();

    const char *all = strstr(opt,"All");
    const char *det[3] = {strstr(opt,"SPD"),strstr(opt,"SDD"),
                          strstr(opt,"SSD")};
    static Bool_t setDef=kTRUE;
    if (setDef) SetDefaultSimulation();
    setDef=kFALSE;

    Int_t nmodules;
    InitModules(size,nmodules);
    FillModules(evNumber,bgrev,nmodules,option,filename);

    AliITSsimulation *sim      = 0;
    AliITSDetType    *iDetType = 0;
    AliITSmodule     *mod      = 0;
    Int_t id,module;
    for(module=0;module<geom->GetIndexMax();module++){
        id       = geom->GetModuleType(module);
        if (!all && !det[id]) continue;
        iDetType = DetType(id);
        sim      = (AliITSsimulation*)iDetType->GetSimulationModel();
        if (!sim) {
            Error("HitsToDigits","The simulation class was not "
                  "instanciated for module %d type %s!",module,
                  geom->GetModuleTypeName(module));
            exit(1);
        } // end if !sim
        mod      = (AliITSmodule *)fITSmodules->At(module);
        sim->DigitiseModule(mod,module,evNumber);
        // fills all branches - wasted disk space
        fLoader->TreeD()->Fill(); 
        ResetDigits();
    } // end for module

    ClearModules();

    fLoader->TreeD()->GetEntries();
    fLoader->TreeD()->AutoSave();
    // reset tree
    fLoader->TreeD()->Reset();
}
//______________________________________________________________________
void AliITS::ResetDigits(){
    // Reset number of digits and the digits array for the ITS detector.
    // Inputs:
    //      none.
    // Outputs:
    //      none.

    if (!fDtype) return;

    Int_t i;
    for (i=0;i<kNTYPES;i++ ) {
        ResetDigits(i);
    } // end for i
}
//______________________________________________________________________
void AliITS::ResetDigits(Int_t i){
    // Reset number of digits and the digits array for this branch.
    // Inputs:
    //      none.
    // Outputs:
    //      none.

    if (fDtype->At(i)) ((TClonesArray*)fDtype->At(i))->Clear();
    if (fNdtype)       fNdtype[i]=0;
}
//______________________________________________________________________
void AliITS::AddSumDigit(AliITSpListItem &sdig){
    // Adds the a module full of summable digits to the summable digits tree.
    // Inputs:
    //      AliITSpListItem &sdig   SDigit to be added to SDigits tree.
    // Outputs:
    //      none.
    // Return:
    //      none.

    TClonesArray &lsdig = *fSDigits;
    new(lsdig[fNSDigits++]) AliITSpListItem(sdig);
}
//______________________________________________________________________
void AliITS::AddRealDigit(Int_t id, Int_t *digits){
    //   Add a real digit - as coming from data.
    // Inputs:
    //      Int_t id        Detector type number.
    //      Int_t *digits   Integer array containing the digits info. See 
    //                      AliITSdigit.h
    // Outputs:
    //      none.
    // Return:
    //      none.

    TClonesArray &ldigits = *((TClonesArray*)fDtype->At(id));
    new(ldigits[fNdtype[id]++]) AliITSdigit(digits);
}
//______________________________________________________________________
void AliITS::AddSimDigit(Int_t id, AliITSdigit *d){
    //    Add a simulated digit.
    // Inputs:
    //      Int_t id        Detector type number.
    //      AliITSdigit *d  Digit to be added to the Digits Tree. See 
    //                      AliITSdigit.h
    // Outputs:
    //      none.
    // Return:
    //      none.

    TClonesArray &ldigits = *((TClonesArray*)fDtype->At(id));

    switch(id){
    case 0:
        new(ldigits[fNdtype[id]++]) AliITSdigitSPD(*((AliITSdigitSPD*)d));
        break;
    case 1:
        new(ldigits[fNdtype[id]++]) AliITSdigitSDD(*((AliITSdigitSDD*)d));
        break;
    case 2:
        new(ldigits[fNdtype[id]++]) AliITSdigitSSD(*((AliITSdigitSSD*)d));
        break;
    } // end switch id
}
//______________________________________________________________________
void AliITS::AddSimDigit(Int_t id,Float_t phys,Int_t *digits,Int_t *tracks,
                         Int_t *hits,Float_t *charges){
  //   Add a simulated digit to the list.
  // Inputs:
  //      Int_t id        Detector type number.
  //      Float_t phys    Physics indicator. See AliITSdigits.h
  //      Int_t *digits   Integer array containing the digits info. See 
  //                      AliITSdigit.h
  //      Int_t *tracks   Integer array [AliITSdigitS?D::GetNTracks()] 
  //                      containing the track numbers that contributed to
  //                      this digit.
  //      Int_t *hits     Integer array [AliITSdigitS?D::GetNTracks()]
  //                      containing the hit numbers, from AliITSmodule, that
  //                      contributed to this digit.
  //      Float_t *charge Floating point array of the signals contributed
  //                      to this digit by each track.
  // Outputs:
  //      none.
  // Return:
  //      none.

  TClonesArray &ldigits = *((TClonesArray*)fDtype->At(id));
  AliITSresponseSDD *resp = 0;
  switch(id){
  case 0:
      new(ldigits[fNdtype[id]++]) AliITSdigitSPD(digits,tracks,hits);
      break;
  case 1:
      resp = (AliITSresponseSDD*)DetType(1)->GetResponseModel();
      new(ldigits[fNdtype[id]++]) AliITSdigitSDD(phys,digits,tracks,
                                                 hits,charges,resp);
      break;
  case 2:
      new(ldigits[fNdtype[id]++]) AliITSdigitSSD(digits,tracks,hits);
      break;
  } // end switch id
}
//______________________________________________________________________
void AliITS::Digits2Raw(){
    // convert digits of the current event to raw data

  fLoader->LoadDigits();
  TTree* digits = fLoader->TreeD();
  if (!digits) {
      Error("Digits2Raw", "no digits tree");
      return;
  }
  SetTreeAddressD(digits);

  AliITSDDLRawData rawWriter;
  //Verbose level
  // 0: Silent
  // 1: cout messages
  // 2: txt files with digits 
  //BE CAREFUL, verbose level 2 MUST be used only for debugging and
  //it is highly suggested to use this mode only for debugging digits files
  //reasonably small, because otherwise the size of the txt files can reach
  //quickly several MB wasting time and disk space.
  rawWriter.SetVerbose(0);
    
  //SILICON PIXEL DETECTOR
  Info("Digits2Raw", "Formatting raw data for SPD");
  rawWriter.RawDataSPD(digits->GetBranch("ITSDigitsSPD"));
    
  //SILICON DRIFT DETECTOR
  Info("Digits2Raw", "Formatting raw data for SDD");
  rawWriter.RawDataSDD(digits->GetBranch("ITSDigitsSDD"));
    
  //SILICON STRIP DETECTOR
  Info("Digits2Raw", "Formatting raw data for SSD");
  rawWriter.RawDataSSD(digits->GetBranch("ITSDigitsSSD"));

  fLoader->UnloadDigits();
}

//______________________________________________________________________
void AliITS::MakeTreeC(Option_t *option){
  //   Create a separate tree to store the clusters.
  // Inputs:
  //      Option_t *option  string which must contain "C" otherwise
  //                        no Cluster Tree is created.
  // Outputs:
  //      none.
  // Return:
  //      none.

  AliITSLoader *pITSLoader = (AliITSLoader*)fLoader;    
    
  if (pITSLoader == 0x0) {
      Error("MakeTreeC","fLoader == 0x0 option=%s",option);
      return;
  }
  if (pITSLoader->TreeC() == 0x0) pITSLoader->MakeTree("C");
  MakeBranchC();
}
//----------------------------------------------------------------------
void AliITS::MakeBranchC(){
    //Makes barnches in treeC
    AliITSLoader *pITSLoader = (AliITSLoader*)fLoader;    
    if (pITSLoader == 0x0) {
        Error("MakeTreeC","fLoader == 0x0");
        return;
    }
    TTree * lTC = pITSLoader->TreeC();
    if (lTC == 0x0){
        Error("MakeTreeC","Can not get TreeC from Loader");
        return;
    }

    Int_t buffersize = 4000;
    char branchname[30];
    const char *det[3] = {"SPD","SDD","SSD"};
    char digclass[40];
    char clclass[40];
    
    // one branch for Clusters per type of detector
    Int_t i;   
    for (i=0; i<kNTYPES ;i++) {
        AliITSDetType *iDetType=DetType(i); 
        iDetType->GetClassNames(digclass,clclass);
        // clusters
        if (fCtype == 0x0) fCtype  = new TObjArray(fNDetTypes);
        if(!ClustersAddress(i)){
            fCtype->AddAt(new TClonesArray(clclass,1000),i);
        }
        if (kNTYPES==3) sprintf(branchname,"%sClusters%s",GetName(),det[i]);
        else  sprintf(branchname,"%sClusters%d",GetName(),i+1);
        if (fCtype  && lTC) {
            if (lTC->GetBranch(branchname)){
                Warning("MakeBranchC","Branch %s alread exists in TreeC",
                        branchname);
            }else{
                Info("MakeBranchC","Creating branch %s in TreeC",branchname);
                lTC->Branch(branchname,&((*fCtype)[i]), buffersize);
            }
        } // end if fCtype && lTC
    } // end for i
}
//______________________________________________________________________
void AliITS::GetTreeC(Int_t event){
    //    Get the clusters tree for this event and set the branch address.
    // Inputs:
    //      Int_t event    Event number for the cluster tree.
    // Outputs:
    //      none.
    // Return:
    //      none.
    char branchname[30];
    const char *det[3] = {"SPD","SDD","SSD"};

    AliITSLoader *pITSLoader = (AliITSLoader*)fLoader;
    TTree * lTC = pITSLoader->TreeC();

    ResetClusters();
    if (lTC) {
        pITSLoader->CleanRawClusters();
    } // end if TreeC()

    TBranch *branch;

    if (lTC) {
        Int_t i;
        char digclass[40];
        char clclass[40];
        for (i=0; i<kNTYPES; i++) {
            AliITSDetType *iDetType=DetType(i); 
            iDetType->GetClassNames(digclass,clclass);
            // clusters
            if (fCtype == 0x0) fCtype  = new TObjArray(fNDetTypes);
            if(!fCtype->At(i)) fCtype->AddAt(new TClonesArray(clclass,1000),i);
            if(kNTYPES==3) sprintf(branchname,"%sClusters%s",GetName(),det[i]);
            else  sprintf(branchname,"%sClusters%d",GetName(),i+1);
            if (fCtype) {
                branch = lTC->GetBranch(branchname);
                if (branch) branch->SetAddress(&((*fCtype)[i]));
            } // end if fCtype
        } // end for i
    } else {
        Error("GetTreeC","cannot find Clusters Tree for event:%d",event);
    } // end if lTC
}
//______________________________________________________________________
void AliITS::AddCluster(Int_t id, AliITSRawCluster *c){
    //   Add a cluster to the list.
    // Inputs:
    //      Int_t id             Detector type number.
    //      AliITSRawCluster *c  Cluster class to be added to the tree of
    //                           clusters.
    // Outputs:
    //      none.
    // Return:
    //      none.

    TClonesArray &lc = *((TClonesArray*)fCtype->At(id));

    switch(id){
    case 0:
        new(lc[fNctype[id]++]) AliITSRawClusterSPD(*((AliITSRawClusterSPD*)c));
        break;
    case 1:
        new(lc[fNctype[id]++]) AliITSRawClusterSDD(*((AliITSRawClusterSDD*)c));
        break;
    case 2:
        new(lc[fNctype[id]++]) AliITSRawClusterSSD(*((AliITSRawClusterSSD*)c));
        break;
    } // end switch id
}
//______________________________________________________________________
void AliITS::ResetClusters(Int_t i){
    //    Reset number of clusters and the clusters array for this branch.
    // Inputs:
    //      Int_t i        Detector type number.
    // Outputs:
    //      none.
    // Return:
    //      none.

    if (fCtype->At(i))    ((TClonesArray*)fCtype->At(i))->Clear();
    if (fNctype)  fNctype[i]=0;
}
//______________________________________________________________________
void AliITS::MakeBranchR(const char *file, Option_t *opt){
    // Creates Tree branches for the ITS Reconstructed points.
    // Inputs:
    //      cont char *file  File name where RecPoints branch is to be written
    //                       to. If blank it write the SDigits to the same
    //                       file in which the Hits were found.
    // Outputs:
    //      none.
    // Return:
    //      none.
    Int_t buffsz = 4000;
    char branchname[30];

    // only one branch for rec points for all detector types
    Bool_t oFast= (strstr(opt,"Fast")!=0);
    Bool_t v2 = (strstr(opt,"v2")!=0);
    

    if(oFast){
        sprintf(branchname,"%sRecPointsF",GetName());
    } else if(v2){
        sprintf(branchname,"Clusters");
    } else {
        sprintf(branchname,"%sRecPoints",GetName());
    }

    if(v2){
      
      if(!fClustersV2)fClustersV2 = new TClonesArray("AliITSclusterV2",3000);
      if(fLoader->TreeR()){
	if(fClustersV2==0x0) fClustersV2 = new TClonesArray("AliITSclusterV2",3000);
	MakeBranchInTree(fLoader->TreeR(),branchname,&fClustersV2,buffsz,file);

      }
    }else{
      if(!fRecPoints)fRecPoints = new TClonesArray("AliITSRecPoint",1000);
      if (fLoader->TreeR()) {
        if(fRecPoints==0x0) fRecPoints = new TClonesArray("AliITSRecPoint",
                                                          1000);
        MakeBranchInTree(fLoader->TreeR(),branchname,&fRecPoints,buffsz,file);
      } // end if
    }
}
//______________________________________________________________________
void AliITS::SetTreeAddressR(TTree *treeR){
    // Set branch address for the Reconstructed points Trees.
    // Inputs:
    //      TTree *treeR   Tree containing the RecPoints.
    // Outputs:
    //      none.
    // Return:
    //      none.
    char branchname[30];

    if(!treeR) return;
    if(fRecPoints==0x0) fRecPoints = new TClonesArray("AliITSRecPoint",1000);
    TBranch *branch1;
    sprintf(branchname,"Clusters");
    branch1 = treeR->GetBranch(branchname);
    if(branch1){
      if(fClustersV2==0x0) fClustersV2 = new TClonesArray("AliITSclusterV2",3000);
      branch1->SetAddress(&fClustersV2);
    }
    else{
      TBranch *branch;
      sprintf(branchname,"%sRecPoints",GetName());
      branch = treeR->GetBranch(branchname);
      if (branch) {
        branch->SetAddress(&fRecPoints);
      }else {
        sprintf(branchname,"%sRecPointsF",GetName());
        branch = treeR->GetBranch(branchname);
        if (branch) {
	  branch->SetAddress(&fRecPoints);
        }
      }
    }
}
//______________________________________________________________________
void AliITS::AddRecPoint(const AliITSRecPoint &r){
    // Add a reconstructed space point to the list
    // Inputs:
    //      const AliITSRecPoint &r RecPoint class to be added to the tree
    //                              of reconstructed points TreeR.
    // Outputs:
    //      none.
    // Return:
    //      none.

    TClonesArray &lrecp = *fRecPoints;
    new(lrecp[fNRecPoints++]) AliITSRecPoint(r);
}
//______________________________________________________________________
void AliITS::AddClusterV2(const AliITSclusterV2 &r){
    // Add a reconstructed space point to the list
    // Inputs:
    //      const AliITSClusterV2 &r class to be added to the tree
    //                              of reconstructed points TreeR.
    // Outputs:
    //      none.
    // Return:
    //      none.

    TClonesArray &lrecp = *fClustersV2;
    new(lrecp[fNClustersV2++]) AliITSclusterV2(r);
}
//______________________________________________________________________
void AliITS::HitsToFastRecPoints(Int_t evNumber,Int_t bgrev,Int_t size,
                                  Option_t *opt0,Option_t *opt1,
                                 const char *flnm){
    // keep galice.root for signal and name differently the file for 
    // background when add! otherwise the track info for signal will be lost !
    // the condition below will disappear when the geom class will be
    // initialized for all versions - for the moment it is only for v5 !
    // Inputs:
    //      Int_t evnt       Event to be processed.
    //      Int_t bgrev      Background Hit tree number.
    //      Int_t size       Size used by InitModules. See InitModules.
    //      Option_t *opt0   Option passed to FillModules. See FillModules.
    //      Option_t *opt1   String indicating if merging hits or not. To
    //                       merge hits set equal to "Add". Otherwise no
    //                       background hits are considered.
    //      Test_t *flnm     File name containing the background hits..
    // Outputs:
    //      none.
    // Return:
    //      none.

    if(!GetITSgeom()) return;
    AliITSLoader *pITSloader = (AliITSLoader*)fLoader;
    AliITSgeom *geom = GetITSgeom();

    const char *all = strstr(opt1,"All");
    const char *det[3] ={strstr(opt1,"SPD"),strstr(opt1,"SDD"),
                         strstr(opt1,"SSD")};
    Int_t nmodules;
    InitModules(size,nmodules);
    FillModules(evNumber,bgrev,nmodules,opt0,flnm);

    AliITSsimulation *sim      = 0;
    AliITSDetType    *iDetType = 0;
    AliITSmodule     *mod      = 0;
    Int_t id,module;

    //m.b. : this change is nothing but a nice way to make sure
    //the CPU goes up !
    
    if(GetDebug()) cout<<"HitsToFastRecPoints: N mod = "<<
                       geom->GetIndexMax()<<endl;
    for(module=0;module<geom->GetIndexMax();module++){
        id       = geom->GetModuleType(module);
        if (!all && !det[id]) continue;
        iDetType = DetType(id);
        sim      = (AliITSsimulation*)iDetType->GetSimulationModel();
        if (!sim) {
            Error("HitsToFastPoints","The simulation class was not "
                  "instanciated for module %d type %x!",module,
                  geom->GetModuleTypeName(module));
            exit(1);
        } // end if !sim
        mod      = (AliITSmodule *)fITSmodules->At(module);
        sim->CreateFastRecPoints(mod,module,gRandom);
        cout<<module<<"\r";fflush(0);
        //gAlice->TreeR()->Fill();
        TTree *lTR = pITSloader->TreeR();
        TBranch *br=lTR->GetBranch("ITSRecPointsF");
        br->Fill();
        ResetRecPoints();
    } // end for module

    ClearModules();
    fLoader->WriteRecPoints("OVERWRITE");
}
//______________________________________________________________________
void AliITS::DigitsToRecPoints(Int_t evNumber,Int_t lastentry,Option_t *opt){
  // cluster finding and reconstruction of space points
  // the condition below will disappear when the geom class will be
  // initialized for all versions - for the moment it is only for v5 !
  // 7 is the SDD beam test version
  // Inputs:
  //      Int_t evNumber   Event number to be processed.
  //      Int_t lastentry  Offset for module when not all of the modules
  //                       are processed.
  //      Option_t *opt    String indicating which ITS sub-detectors should
  //                       be processed. If ="All" then all of the ITS
  //                       sub detectors are processed.
  // Outputs:
  //      none.
  // Return:
  //      none.

  if(!GetITSgeom()) return;
  AliITSgeom *geom = GetITSgeom();
    
  const char *all = strstr(opt,"All");
  const char *det[3] = {strstr(opt,"SPD"),strstr(opt,"SDD"),
                        strstr(opt,"SSD")};
  static Bool_t setRec=kTRUE;
  if (setRec) SetDefaultClusterFinders();
  setRec=kFALSE;

  AliITSLoader *pITSloader = (AliITSLoader*)fLoader;
  TTree *treeC=pITSloader->TreeC();
  AliITSClusterFinder *rec     = 0;
  AliITSDetType      *iDetType = 0;
  Int_t id,module,first=0;
  for(module=0;module<geom->GetIndexMax();module++){
      id       = geom->GetModuleType(module);
      if (!all && !det[id]) continue;
      if(det[id]) first = geom->GetStartDet(id);
      iDetType = DetType(id);
      rec = (AliITSClusterFinder*)iDetType->GetReconstructionModel();
      TClonesArray *itsDigits  = this->DigitsAddress(id);
      if (!rec) {
          Error("DigitsToRecPoints",
                "The reconstruction class was not instanciated! event=%d",
                evNumber);
          exit(1);
      } // end if !rec
      this->ResetDigits();
      TTree *lTD = pITSloader->TreeD();
      if (all) {
          lTD->GetEvent(lastentry+module);
      }else {
          lTD->GetEvent(lastentry+(module-first));
      }
      Int_t ndigits = itsDigits->GetEntriesFast();
      if(ndigits>0){
          rec->SetDigits(DigitsAddress(id));
          rec->SetClusters(ClustersAddress(id));
          rec->FindRawClusters(module);
      } // end if
      pITSloader->TreeR()->Fill();
      ResetRecPoints();
      ResetClustersV2();
      treeC->Fill();
      ResetClusters();
  } // end for module

  pITSloader->WriteRecPoints("OVERWRITE");
  pITSloader->WriteRawClusters("OVERWRITE");
}
//______________________________________________________________________
void AliITS::DigitsToRecPoints(AliRawReader* rawReader){
  // cluster finding and reconstruction of space points
  // the condition below will disappear when the geom class will be
  // initialized for all versions - for the moment it is only for v5 !
  // 7 is the SDD beam test version
  // Inputs:
  //      Int_t evNumber   Event number to be processed.
  //      Int_t lastentry  Offset for module when not all of the modules
  //                       are processed.
  //      Option_t *opt    String indicating which ITS sub-detectors should
  //                       be processed. If ="All" then all of the ITS
  //                       sub detectors are processed.
  // Outputs:
  //      none.
  // Return:
  //      none.
  if(!GetITSgeom()) return;
  AliITSgeom *geom = GetITSgeom();
  
    
  SetDefaultClusterFindersV2();
  
  AliITSLoader *pITSloader = (AliITSLoader*)fLoader;
  AliITSClusterFinderV2 *rec     = 0;
  AliITSDetType      *iDetType = 0;
  Int_t id=0;

  if(!pITSloader->TreeR()) pITSloader->MakeTree("R");
  TTree* cTree = pITSloader->TreeR();
  TClonesArray *array=new TClonesArray("AliITSclusterV2",1000);
  cTree->Branch("Clusters",&array);
  delete array;
 
  TClonesArray** clusters = new TClonesArray*[geom->GetIndexMax()]; 
  for (Int_t iModule = 0; iModule < geom->GetIndexMax(); iModule++) {
    clusters[iModule] = NULL;
  }
  for(id=0;id<3;id++){
    iDetType = DetType(id);
    rec = (AliITSClusterFinderV2*)iDetType->GetReconstructionModel();
    if (!rec) {
      Error("DigitsToRecPoints",
	    "The reconstruction class was not instanciated");
      exit(1);
    } 
    rec->RawdataToClusters(rawReader,clusters);    
  } 
  Int_t nClusters =0;
  for(Int_t iModule=0;iModule<geom->GetIndexMax();iModule++){
    array = clusters[iModule];
    if(!array){
      Error("DigitsToRecPoints","data for module %d missing!",iModule);
      array = new TClonesArray("AliITSclusterV2");
    }
    cTree->SetBranchAddress("Clusters",&array);
    cTree->Fill();
    nClusters+=array->GetEntriesFast();
    delete array;
  }
  pITSloader->WriteRecPoints("OVERWRITE");

  delete[] clusters;
  Info("DigitsToRecPoints", "total number of found clustersV2 in ITS: %d\n", 
       nClusters);
  
}

//______________________________________________________________________
AliLoader* AliITS::MakeLoader(const char* topfoldername){ 
    //builds ITSgetter (AliLoader type)
    //if detector wants to use castomized getter, it must overload this method

    Info("MakeLoader","Creating AliITSLoader. Top folder is %s.",
         topfoldername);
    fLoader = new AliITSLoader(GetName(),topfoldername);
    return fLoader;
}