/**************************************************************************
 * 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.                  *
 **************************************************************************/

#include "AliITSClusterFinderSPD.h"
#include "AliITS.h"
#include "AliITSgeom.h"
#include "AliITSdigit.h"
#include "AliITSRawCluster.h"
#include "AliITSRecPoint.h"
#include "AliITSsegmentation.h"
#include "AliITSresponse.h"
#include "AliRun.h"

//#define DEBUG

ClassImp(AliITSClusterFinderSPD)

//----------------------------------------------------------
AliITSClusterFinderSPD::AliITSClusterFinderSPD(AliITSsegmentation *seg,
					       TClonesArray *digits,
					       TClonesArray *recp){
    // constructor

    fSegmentation = seg;
    fDigits       = digits;
    fClusters     = recp;
    fNclusters    = fClusters->GetEntriesFast();
    SetDx();
    SetDz();
}
//______________________________________________________________________
AliITSClusterFinderSPD::AliITSClusterFinderSPD(){
    // constructor

    fSegmentation = 0;
    fDigits       = 0;
    fClusters     = 0;
    fNclusters    = 0;
    SetDx();
    SetDz();
}
//_____________________________________________________________________
AliITSClusterFinderSPD::AliITSClusterFinderSPD(const AliITSClusterFinderSPD 
					       &source){
    //     Copy Constructor 

    if(&source == this) return;
    this->fClusters  = source.fClusters ;
    this->fNclusters = source.fNclusters ;
    this->fDz        = source.fDz ;
    this->fDx        = source.fDx ;
    return;
}
//______________________________________________________________________
AliITSClusterFinderSPD& AliITSClusterFinderSPD::operator=(
                                       const AliITSClusterFinderSPD &source) {
    //    Assignment operator

    if(&source == this) return *this;
    this->fClusters  = source.fClusters ;
    this->fNclusters = source.fNclusters ;
    this->fDz        = source.fDz ;
    this->fDx        = source.fDx ;
    return *this;
}
//______________________________________________________________________
void AliITSClusterFinderSPD::FindRawClusters(Int_t module){   
    // input of Cluster Finder
    Int_t   digitcount  = 0;
    Int_t   numberd     = 100000;
    Int_t   *digx       = new Int_t[numberd];
    Int_t   *digz       = new Int_t[numberd];
    Int_t   *digtr1     = new Int_t[numberd];
    Int_t   *digtr2     = new Int_t[numberd];
    Int_t   *digtr3     = new Int_t[numberd];
    Int_t   *digtr4     = new Int_t[numberd];
    //  output of Cluster Finder    
    Int_t   numberc     = 10000;
    Float_t *xcenterl   = new Float_t[numberc];
    Float_t *zcenterl   = new Float_t[numberc];
    Float_t *errxcenter = new Float_t[numberc];
    Float_t *errzcenter = new Float_t[numberc];
    Int_t   *tr1clus    = new Int_t[numberc];
    Int_t   *tr2clus    = new Int_t[numberc];
    Int_t   *tr3clus    = new Int_t[numberc];
    Int_t   nclus;

    digitcount=0;
    Int_t ndigits = fDigits->GetEntriesFast();  
    if (!ndigits) return;

    AliITSdigitSPD *dig;
    Int_t ndig,i;
    for(ndig=0; ndig<ndigits; ndig++) {
	dig= (AliITSdigitSPD*)fDigits->UncheckedAt(ndig);
	digx[digitcount] = dig->fCoord2+1;  //starts at 1
	digz[digitcount] = dig->fCoord1+1;  //starts at 1
	digtr1[digitcount] = dig->fTracks[0];
	digtr2[digitcount] = -3;
	digtr3[digitcount] = -3;
	i=1;
	while(digtr1[digitcount]==dig->fTracks[i] && i<dig->GetNTracks()) i++;
	if(i<dig->GetNTracks()){
	    digtr2[digitcount] = dig->fTracks[i];
	    while(digtr1[digitcount]==dig->fTracks[i] && 
		  i<dig->GetNTracks()) i++;
	    if(i<dig->GetNTracks()) digtr3[digitcount] = dig->fTracks[i];
	} // end if
	digtr4[digitcount] = dig->fSignal;
	digitcount++;
    } // end for ndig
    ClusterFinder(digitcount,digx,digz,digtr1,digtr2,digtr3,digtr4,
		  nclus,xcenterl,zcenterl,errxcenter,errzcenter,
		  tr1clus, tr2clus, tr3clus,module);
    DigitToPoint(nclus,xcenterl,zcenterl,errxcenter,errzcenter,
		 tr1clus, tr2clus, tr3clus);
    delete[] digx;
    delete[] digz;
    delete[] digtr1;
    delete[] digtr2;
    delete[] digtr3;
    delete[] digtr4;
    delete[] xcenterl;
    delete[] zcenterl;
    delete[] errxcenter;
    delete[] errzcenter;
    delete[] tr1clus;
    delete[] tr2clus;
    delete[] tr3clus;
}
//----------------------------------------------------------------------
void AliITSClusterFinderSPD::ClusterFinder(Int_t ndigits,Int_t digx[],
					   Int_t digz[],Int_t digtr1[],
					   Int_t digtr2[],Int_t digtr3[],
					   Int_t digtr4[],Int_t &nclus,
					   Float_t xcenter[],Float_t zcenter[],
					   Float_t errxcenter[],
					   Float_t errzcenter[],
					   Int_t tr1clus[],Int_t tr2clus[],
					   Int_t tr3clus[],Int_t module){
    // Search for clusters of fired pixels (digits). Two digits are linked
    // inside a cluster if they are countiguous both in row or column
    // direction.  Diagonal digits are not linked.
    // xcenter, ycenter, zcenter are the coordinates of the center
    // of each found cluster, calculated from the averaging the corresponding
    // coordinate of the center of the linked digits. The coordinates are
    // given in the local reference sistem. 
    // errxcenter, errycenter, errzcenter are the errors associated to
    // the corresponding average.
    Int_t   if1, min, max, nd;
    Int_t   x1, z1, t1, t2, t3, t4;
    Int_t   ndx, ndz, ndxmin=0, ndxmax=0, ndzmin=0, ndzmax=0;
    Float_t dx, dz; 
    Int_t   i,k,ipos=0;
    Float_t xdum, zdum;      
    Int_t   kmax, sigmax;
    Float_t deltax, deltaz;
    Float_t ndig;
    Int_t   numberd = 10000;
    Int_t   *ifpad  = new Int_t[numberd];
    Int_t   *xpad   = new Int_t[numberd];
    Int_t   *zpad   = new Int_t[numberd];
    Int_t   *tr1pad = new Int_t[numberd];
    Int_t   *tr2pad = new Int_t[numberd];
    Int_t   *tr3pad = new Int_t[numberd];
    Int_t   *tr4pad = new Int_t[numberd];
    Int_t   *iclus  = new Int_t[numberd];

    nclus=1;
    for (i=0; i < ndigits ; i++){
	ifpad[i] = -1;
	iclus[i] = 0;
    } // end for i

    ifpad[0]=0;
    for (i=0; i < ndigits-1 ; i++) {
	if ( ifpad[i] == -1 ) { 
	    nclus++;
	    ipos++;
	    ifpad[i]=nclus-1;
	} // end if ipad[i]
	for (Int_t j=i+1 ; j < ndigits ; j++)  {  
	    if (ifpad[j]== -1 ) {
		dx = TMath::Abs(digx[i]-digx[j]);
		dz = TMath::Abs(digz[i]-digz[j]);
		// if ( ( dx+dz )==1 )  //clusters are not diagonal
		if(( dx+dz )==1 || (dx==1 && dz==1)){
		    //diagonal clusters allowed
   		    ipos++;
		    ifpad[j] = ifpad[i];

   		    x1         = digx[j];
   		    z1         = digz[j];
   		    digx[j]    = digx[ipos];
   		    digz[j]    = digz[ipos];
   		    digx[ipos] = x1;
   		    digz[ipos] = z1;

   		    t1 = digtr1[j];
   		    t2 = digtr2[j];
   		    t3 = digtr3[j];
   		    t4 = digtr4[j];
   		    digtr1[j] = digtr1[ipos];
   		    digtr2[j] = digtr2[ipos];
   		    digtr3[j] = digtr3[ipos];
   		    digtr4[j] = digtr4[ipos];
   		    digtr1[ipos] = t1;
   		    digtr2[ipos] = t2;
   		    digtr3[ipos] = t3;
   		    digtr4[ipos] = t4;

   		    if1 = ifpad[j];
   		    ifpad[j] = ifpad[ipos];
   		    ifpad[ipos] = if1;
		} // end dx+dx...
	    }// end if ifpad[j]== -1 
	} // end for j
    }//end loop on digits
    if ( ifpad[ndigits-1] == -1 ) {
	nclus++;
	ifpad[ndigits-1]=nclus-1;
    } // end if ifpad[ndigits-1] == -1

    for (i=0 ; i < ndigits ; i++) iclus[ifpad[i]]++;

    min=0;
    max=0;
    // loop on found clusters 
    for (i=0 ; i < nclus ; i++){
	min = max;
	max += iclus[i];
	deltax = fSegmentation->Dpx(0);
	if (iclus[i]!=1){
	    //cluster with more than one digit
	    nd=iclus[i];
	    ndig=(Float_t) nd;
	    Int_t count=0;
	    for (k=min;k<min+nd;k++){
		xpad[count] = digx[k];	   
		zpad[count] = digz[k];

		tr1pad[count] = digtr1[k];	   
		tr2pad[count] = digtr2[k];	   
		tr3pad[count] = digtr3[k];	   
		tr4pad[count] = digtr4[k];	   

		count++; 
	    } // end for k
	    ndxmin = xpad[TMath::LocMin(nd,xpad)];
	    ndxmax = xpad[TMath::LocMax(nd,xpad)];
	    ndzmin = zpad[TMath::LocMin(nd,zpad)];
	    ndzmax = zpad[TMath::LocMax(nd,zpad)];
	    ndx = ndxmax - ndxmin+1;
	    ndz = ndzmax - ndzmin+1;

	    // calculate x and z coordinates of the center of the cluster
	    fSegmentation->GetPadCxz(digx[min],digz[min]-1,xdum, zdum);

	    if (ndx == 1) {
		xcenter[i] = xdum;
	    }else{ 
		xcenter[i] = 0.;
		for (k=0;k<nd;k++) {
		    fSegmentation->GetPadCxz(xpad[k],zpad[k]-1,xdum,zdum);
	            xcenter[i] += (xdum / nd);
		} // end for k               
	    } // end if ndx

	    if (ndz == 1) {
		zcenter[i] = zdum;
	    } else {
		zcenter[i] = 0.;
		for (k=0;k<nd;k++) {	      
		    fSegmentation->GetPadCxz(xpad[k],zpad[k]-1,xdum,zdum);
		    zcenter[i] += (zdum / nd);
		} // end for k
	    } // end if ndz

	    // error on points in x and z directions

	    if (ndx == 1) {
		errxcenter[i] = deltax / TMath::Sqrt(12.);
	    } else {
		errxcenter[i] = 0.;	 		
		for (k=0;k<nd;k++){ 
		    fSegmentation->GetPadCxz(xpad[k],zpad[k]-1,xdum,zdum);
		    errxcenter[i] += ((xdum-xcenter[i])*(xdum-xcenter[i]))/
			             (nd*(nd-1)); 
		} // end for k
		errxcenter[i] = TMath::Sqrt(errxcenter[i]);
	    } // end if ndx	
	    if (ndz == 1) {
		deltaz = fSegmentation->Dpz(digz[min]);	              
	        errzcenter[i] = deltaz / TMath::Sqrt(12.);
	    } else {
	        errzcenter[i] = 0.;
	        for (k=0;k<nd;k++){ 
		    fSegmentation->GetPadCxz(xpad[k],zpad[k]-1,xdum,zdum);
		    errzcenter[i] += ((zdum-zcenter[i])*(zdum-zcenter[i]))/
			             (nd*(nd-1));
	        } // end for k
	        errzcenter[i] = TMath::Sqrt(errzcenter[i]);
	    } // end if ndz
	    // take three track numbers for the cluster
	    // choose the track numbers of the digit with higher signal 
	    kmax = 0;
	    sigmax = 0;
	    for (k=0;k<nd;k++){
		if(tr4pad[k] > sigmax){
		    sigmax = tr4pad[k];
		    kmax   = k;
		} // end if tr4pad[k]
	    } // end for k
	    if(sigmax != 0) {
		tr1clus[i]= tr1pad[kmax];
		tr2clus[i]= tr2pad[kmax];
		tr3clus[i]= tr3pad[kmax];
	    } else {
		tr1clus[i]= -2;
		tr2clus[i]= -2;
		tr3clus[i]= -2;
	    } // end if sigmax
	} else {
	    // cluster with single digit
	    ndig= 1.;
	    ndx = 1;
	    ndz = 1;
	    fSegmentation->GetPadCxz(digx[min],digz[min]-1,xdum,zdum);
	    xcenter[i] = xdum;
	    zcenter[i] = zdum;
	    tr1clus[i]=digtr1[min];
	    tr2clus[i]=digtr2[min];
	    tr3clus[i]=digtr3[min];
	    deltaz = fSegmentation->Dpz(digz[min]);
	    errxcenter[i] = deltax / TMath::Sqrt(12.);
  	    errzcenter[i] = deltaz / TMath::Sqrt(12.);
	} // end if iclus[i]

	// store the cluster information to the AliITSRawCLusterSPD object
	static AliITS *iTS=(AliITS*)gAlice->GetModule("ITS");

	//put the cluster center in local reference frame of the detector
	// and in microns
	xcenter[i] = xcenter[i] - fSegmentation->Dx()/2.; 
	zcenter[i] = zcenter[i] - fSegmentation->Dz()/2.;

	AliITSRawClusterSPD *clust = new AliITSRawClusterSPD(zcenter[i], //f
							     xcenter[i], //f
							     ndig, //f
							     ndz,ndx, //ii
							     ndxmin,ndxmax,//ii
							     (Float_t) ndzmin,
							     (Float_t) ndzmax,
							     0,module); //ii
	iTS->AddCluster(0,clust);
	delete clust;
    }//end loop on clusters   
    delete[] ifpad;
    delete[] xpad ;
    delete[] zpad ;
    delete[] iclus;
    delete[] tr1pad;
    delete[] tr2pad;
    delete[] tr3pad;
    delete[] tr4pad;
}
//______________________________________________________----------------
void AliITSClusterFinderSPD::DigitToPoint(Int_t nclus,
					  Float_t *xcenter,Float_t *zcenter,
					  Float_t *errxcenter,
					  Float_t *errzcenter, 
					  Int_t *tr1clus, Int_t *tr2clus,
					  Int_t *tr3clus){
    // A point is associated to each cluster of SPD digits. The points
    // and their associated errors are stored in the file galiceSP.root.
    Float_t l[3],xg,zg;
    const Float_t kconv = 1.0e-4; // micron -> cm

    // get rec points
    static AliITS *iTS=(AliITS*)gAlice->GetModule("ITS");
    for (Int_t i=0; i<nclus; i++){
        l[0] = kconv*xcenter[i];
        l[1] = kconv*fSegmentation->Dy()/2.;
        l[2] = kconv*zcenter[i];

        xg = l[0]; 
        zg = l[2]; 

	Float_t sigma2x = (kconv*errxcenter[i]) * (kconv*errxcenter[i]);
	Float_t sigma2z = (kconv*errzcenter[i]) * (kconv*errzcenter[i]);
        AliITSRecPoint rnew;
        rnew.SetX(xg);
        rnew.SetZ(zg);
        rnew.SetQ(1.);
        rnew.SetdEdX(0.);
        rnew.SetSigmaX2(sigma2x);
        rnew.SetSigmaZ2(sigma2z);
        rnew.fTracks[0]=tr1clus[i];
        rnew.fTracks[1]=tr2clus[i];
        rnew.fTracks[2]=tr3clus[i];
        iTS->AddRecPoint(rnew); 
    } // end for i
}