X-Git-Url: http://git.uio.no/git/?a=blobdiff_plain;f=PMD%2FAliPMDClustering.cxx;h=f9c766413b22785318f5bec30124e1b1ca879b96;hb=f1ce4cc35f8eed566aa80c7c7d42f47ebf8d62fc;hp=d3b6d644e2b0a4e79fe1d9d7b5bd218275a0878f;hpb=2264f225cf720ef970faef1c098979b8f6140f5e;p=u%2Fmrichter%2FAliRoot.git

diff --git a/PMD/AliPMDClustering.cxx b/PMD/AliPMDClustering.cxx
index d3b6d644e2b..f9c766413b2 100644
--- a/PMD/AliPMDClustering.cxx
+++ b/PMD/AliPMDClustering.cxx
@@ -1,3 +1,18 @@
+/***************************************************************************
+ * 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.                  *
+ **************************************************************************/
+
 //-----------------------------------------------------//
 //                                                     //
 //  Source File : PMDClustering.cxx, Version 00        //
@@ -8,276 +23,414 @@
 //                                                     //
 //-----------------------------------------------------//
 
-/* 
-   --------------------------------------------------------------------
-   Code developed by S. C. Phatak, Institute of Physics, 
+/* --------------------------------------------------------------------
+   Code developed by S. C. Phatak, Institute of Physics,
    Bhubaneswar 751 005 ( phatak@iopb.res.in ) Given the energy deposited
    ( or ADC value ) in each cell of supermodule ( pmd or cpv ), the code
-   builds up superclusters and breaks them into clusters. The input is 
-   in array d[ndimx][ndimy] and cluster information is in array
-   clusters[5][5000]. integer clno gives total number of clusters in the 
+   builds up superclusters and breaks them into clusters. The input is
+   in array fEdepCell[kNDIMX][kNDIMY] and cluster information is in array
+   fClusters[5][5000]. integer fClno gives total number of clusters in the
    supermodule.
 
-   d, clno  and clusters are the only global ( public ) variables. Others 
-   are local ( private ) to the code. 
-
+   fEdepCell, fClno  and fClusters are the only global ( public ) variables.
+   Others are local ( private ) to the code.
    At the moment, the data is read for whole detector ( all supermodules
    and pmd as well as cpv. This will have to be modify later )
-
    LAST UPDATE  :  October 23, 2002
------------------------------------------------------------------------
-*/
-
-
+-----------------------------------------------------------------------*/
 
+#include "Riostream.h"
 #include <TNtuple.h>
 #include <TObjArray.h>
+#include <stdio.h>
+
 #include "AliPMDcluster.h"
 #include "AliPMDClustering.h"
-#include <stdio.h>
+#include "AliLog.h"
 
 ClassImp(AliPMDClustering)
 
-const double AliPMDClustering::pi=3.141593;
-const double AliPMDClustering::sqrth=0.8660254;  // sqrth = sqrt(3.)/2.
-
+const Double_t AliPMDClustering::fgkSqroot3by2=0.8660254;  // sqrt(3.)/2.
 
-AliPMDClustering::AliPMDClustering()
+AliPMDClustering::AliPMDClustering():
+  fCutoff(0.0)
 {
-  fMessage = 0;
-  for(int i = 0; i < ndimx; i++)
+  for(int i = 0; i < kNDIMX; i++)
     {
-      for(int j = 0; j < ndimy; j++)
+      for(int j = 0; j < kNDIMY; j++)
 	{
-	  coord[0][i][j] = i+j/2.;
-	  coord[1][i][j] = sqrth*j;
+	  fCoord[0][i][j] = i+j/2.;
+	  fCoord[1][i][j] = fgkSqroot3by2*j;
+	  fEdepCell[i][j] = 0;
 	}
     }
 }
+// ------------------------------------------------------------------------ //
 AliPMDClustering::~AliPMDClustering()
 {
 
 }
-
-void AliPMDClustering::DoClust(int idet, int isup, double d1[72][72], TObjArray *pmdcont)
+// ------------------------------------------------------------------------ //
+void AliPMDClustering::DoClust(Int_t idet, Int_t ismn, Double_t celladc[48][96], TObjArray *pmdcont)
 {
-
+  // main function to call other necessary functions to do clustering
+  //
   AliPMDcluster *pmdcl = 0;
-
-  int i, i1, i2, j, nmx1, incr;
+  /*
+    int id and jd defined to read the input data.
+    It is assumed that for data we have 0 <= id <= 48
+    and 0 <= jd <=96
+  */
+  int i, i1, i2, j, nmx1, incr, id, jd;
   double  cutoff, ave;
-  Float_t clusdata[5];
-
-  const float twobysqrt3 = 1.1547; // 2./sqrt(3.)
+  Float_t clusdata[7];
 
-  //  if (fMessage == 1)
-    {
-      cout << " supermodule no. " << idet << " " << isup << endl;
-    }
+  const float ktwobysqrt3 = 1.1547; // 2./sqrt(3.)
 
-  for (i = 0; i < ndimx; i++)
+  for (id = 0; id < kNDIMXr; id++)
     {
-      for (j = 0; j < ndimy; j++)
+      for (jd = 0; jd < kNDIMYr; jd++)
 	{
-	  d[i][j] = d1[i][j];
+	  j=jd;
+	  i=id+(kNDIMYr/2-1)-(jd/2);
+	  fEdepCell[i][j] = celladc[id][jd];
 	}
     }
-  order(idet); // order the data
-  cutoff=400.; // cutoff used to discard cells having ener. dep. 
-  ave=0.; 
+  Order(); // order the data
+  cutoff = fCutoff; // cutoff used to discard cells having ener. dep.
+  ave=0.;
   nmx1=-1;
 
-  for(j=0;j<nmx; j++)
+  for(j=0;j<kNMX; j++)
     {
-      i1 = iord[0][j];
-      i2 = iord[1][j];
-      if (d[i1][i2] > 0.) {ave=ave+d[i1][i2];}
-      if (d[i1][i2] >= cutoff ) nmx1 = nmx1 + 1;
+      i1 = fIord[0][j];
+      i2 = fIord[1][j];
+      if (fEdepCell[i1][i2] > 0.) {ave = ave + fEdepCell[i1][i2];}
+      if (fEdepCell[i1][i2] > cutoff ) nmx1 = nmx1 + 1;
     }
   // nmx1 --- number of cells having ener dep >= cutoff
-  if (fMessage == 1)
-    {
-      cout << " nmx1 " << nmx1 << endl;
-    }
-  ave=ave/nmx1;
-  if (fMessage == 1)
-    {
-      cout <<"nmx " << nmx << " nmx1 " << nmx1<< " ave "<<ave<<
-	" cutoff " << cutoff << endl;
-    }
 
-  incr = crclust(ave, cutoff, nmx1, idet);
+  AliDebug(1,Form("Number of cells having energy >= %f are %d",cutoff,nmx1));
 
-  refclust(incr, i, idet);
-  if (fMessage == 1)
-    {
-      if(idet == 0)cout <<" supermodule ( pmd ) = "<< isup <<" done "
-			<<endl;
-      if(idet == 1)cout <<" supermodule ( cpv ) = "<< isup <<" done "
-			<<endl;
-      cout << "clno " << clno << endl;
-    }
+  //  if (nmx1 == 0 | nmx1 == -1) return;
 
+  if (nmx1 == 0) nmx1 = 1;
+  ave=ave/nmx1;
 
-  for(i1=0; i1<clno; i1++)
-    {
-      float clu_xc    = (float) clusters[0][i1];
-      float clu_yc    = (float) clusters[1][i1];
-      float clu_adc   = (float) clusters[2][i1];
-      float clu_cells = (float) clusters[3][i1];
-      float clu_rad   = (float) clusters[4][i1];
-      
-      float clu_y0 = twobysqrt3*clu_yc;
-      float clu_x0 = clu_xc - clu_y0/2.;
+  AliDebug(1,Form("Number of cells in a SuperM = %d and Average = %f",
+		  kNMX,ave));
+	   
+  incr = CrClust(ave, cutoff, nmx1);
+  RefClust(incr);
 
-      clusdata[0] = clu_cells;
-      clusdata[1] = clu_x0;
-      clusdata[2] = clu_y0;
-      clusdata[3] = clu_adc;
-      clusdata[4] = clu_rad;
-      
-      pmdcl = new AliPMDcluster(clusdata);
+  AliDebug(1,Form("Detector Plane = %d  Serial Module No = %d Number of clusters = %d",idet, ismn, fClno));
+  
+  for(i1=0; i1<=fClno; i1++)
+    {
+      Float_t cluXC    = (Float_t) fClusters[0][i1];
+      Float_t cluYC    = (Float_t) fClusters[1][i1];
+      Float_t cluADC   = (Float_t) fClusters[2][i1];
+      Float_t cluCELLS = (Float_t) fClusters[3][i1];
+      Float_t cluRAD   = (Float_t) fClusters[4][i1];
+      Float_t cluY0    = ktwobysqrt3*cluYC;
+      Float_t cluX0    = cluXC - cluY0/2.;
+      // 
+      // Cluster X centroid is back transformed
+      //
+      clusdata[0]      = cluX0 - (48-1) + cluY0/2.;
+      clusdata[1]      = cluY0;
+      clusdata[2]      = cluADC;
+      clusdata[3]      = cluCELLS;
+      clusdata[4]      = cluRAD;
+
+      pmdcl = new AliPMDcluster(idet, ismn, clusdata);
       pmdcont->Add(pmdcl);
     }
-
-  delete pmdcl;
-
 }
-
-void AliPMDClustering::order(int /*idet*/)
+// ------------------------------------------------------------------------ //
+void AliPMDClustering::Order()
 {
-  // using simple sort
-  double dd[nmx], adum;// matrix d converted into 
+  // Sorting algorithm
+  // sorts the ADC values from higher to lower
+  //
+  double dd[kNMX];
+  // matrix fEdepCell converted into
   // one dimensional array dd. adum a place holder for double
-  int i, j, i1, i2, iord1[nmx], itst, idum; // information of 
+  int i, j, i1, i2, iord1[kNMX];
+  // information of
   // ordering is stored in iord1, original array not ordered
   //
   // define arrays dd and iord1
-  for(i1=0; i1 < ndimx; i1++){
-    for(i2=0; i2 < ndimy; i2++){
-      i=i1+i2*ndimx;
-      iord1[i]=i; dd[i]=d[i1][i2];
+  for(i1=0; i1 < kNDIMX; i1++)
+    {
+      for(i2=0; i2 < kNDIMY; i2++)
+	{
+	  i        = i1 + i2*kNDIMX;
+	  iord1[i] = i;
+	  dd[i]    = fEdepCell[i1][i2];
+	}
     }
+  // sort and store sorting information in iord1
+//   for(j=1; j < kNMX; j++)
+//     {
+//       itst = 0;
+//       adum = dd[j];
+//       idum = iord1[j];
+//       for(i1=0; i1 < j ; i1++)
+// 	{
+// 	  if(adum > dd[i1] && itst == 0)
+// 	    {
+// 	      itst = 1;
+// 	      for(i2=j-1; i2 >= i1 ; i2=i2--)
+// 		{
+// 		  dd[i2+1]    = dd[i2];
+// 		  iord1[i2+1] = iord1[i2];
+// 		}
+// 	      dd[i1]    = adum;
+// 	      iord1[i1] = idum;
+// 	    }
+// 	}
+//     }
+
+  TMath::Sort(kNMX,dd,iord1); //PH Using much better algorithm...
+  // store the sorted information in fIord for later use
+  for(i=0; i<kNMX; i++)
+    {
+      j  = iord1[i];
+      i2 = j/kNDIMX;
+      i1 = j-i2*kNDIMX;
+      fIord[0][i]=i1;
+      fIord[1][i]=i2;
+    }
+}
+// ------------------------------------------------------------------------ //
+int AliPMDClustering::CrClust(double ave, double cutoff, int nmx1)
+{
+  // Does crude clustering
+  // Finds out only the big patch by just searching the
+  // connected cells
+  //
+  int i,j,k,id1,id2,icl, numcell, clust[2][5000];
+  int jd1,jd2, icell, cellcount;
+  static int neibx[6]={1,0,-1,-1,0,1}, neiby[6]={0,1,1,0,-1,-1};
+  // neibx and neiby define ( incremental ) (i,j) for the neighbours of a
+  // cell. There are six neighbours.
+  // cellcount --- total number of cells having nonzero ener dep
+  // numcell --- number of cells in a given supercluster
+  // ofstream ofl0("cells_loc",ios::out);
+  // initialize fInfocl[2][kNDIMX][kNDIMY]
+
+  AliDebug(1,Form("kNMX = %d nmx1 = %d kNDIMX = %d kNDIMY = %d ave = %f cutoff = %f",kNMX,nmx1,kNDIMX,kNDIMY,ave,cutoff));
+  
+  for (j=0; j < kNDIMX; j++){
+    for(k=0; k < kNDIMY; k++){
+      fInfocl[0][j][k] = 0;
+      fInfocl[1][j][k] = 0;
+    }
+  }
+  for(i=0; i < kNMX; i++){
+    fInfcl[0][i] = -1;
+    id1=fIord[0][i];
+    id2=fIord[1][i];
+    if(fEdepCell[id1][id2] <= cutoff){fInfocl[0][id1][id2]=-1;}
   }
-  // sort and store sorting information in iord1 
-  for(j=1; j < nmx; j++){
-    itst=0; adum=dd[j]; idum=iord1[j];
-    for(i1=0; i1 < j ; i1++){
-      if(adum > dd[i1] && itst == 0){
-	itst=1;
-	for(i2=j-1; i2 >= i1 ; i2=i2--){
-	  dd[i2+1]=dd[i2]; 
-	  iord1[i2+1]=iord1[i2];
+  // ---------------------------------------------------------------
+  // crude clustering begins. Start with cell having largest adc
+  // count and loop over the cells in descending order of adc count
+  // ---------------------------------------------------------------
+  icl=-1;
+  cellcount=-1;
+  for(icell=0; icell <= nmx1; icell++){
+    id1=fIord[0][icell];
+    id2=fIord[1][icell];
+    if(fInfocl[0][id1][id2] == 0 ){
+      // ---------------------------------------------------------------
+      // icl -- cluster #, numcell -- # of cells in it, clust -- stores
+      // coordinates of the cells in a cluster, fInfocl[0][i1][i2] is 1 for
+      // primary and 2 for secondary cells,
+      // fInfocl[1][i1][i2] stores cluster #
+      // ---------------------------------------------------------------
+      icl=icl+1;
+      numcell=0;
+      cellcount = cellcount + 1;
+      fInfocl[0][id1][id2]=1;
+      fInfocl[1][id1][id2]=icl;
+      fInfcl[0][cellcount]=icl;
+      fInfcl[1][cellcount]=id1;
+      fInfcl[2][cellcount]=id2;
+
+      clust[0][numcell]=id1;
+      clust[1][numcell]=id2;
+      for(i=1; i<5000; i++)clust[0][i]=0;
+      // ---------------------------------------------------------------
+      // check for adc count in neib. cells. If ne 0 put it in this clust
+      // ---------------------------------------------------------------
+      for(i=0; i<6; i++){
+	jd1=id1+neibx[i];
+	jd2=id2+neiby[i];
+	if( (jd1 >= 0 && jd1 < kNDIMX) && (jd2 >= 0 && jd2 < kNDIMY) &&
+	    fInfocl[0][jd1][jd2] == 0){
+	  numcell=numcell+1;
+	  fInfocl[0][jd1][jd2]=2;
+	  fInfocl[1][jd1][jd2]=icl;
+	  clust[0][numcell]=jd1;
+	  clust[1][numcell]=jd2;
+	  cellcount=cellcount+1;
+	  fInfcl[0][cellcount]=icl;
+	  fInfcl[1][cellcount]=jd1;
+	  fInfcl[2][cellcount]=jd2;
+	}
+      }
+      // ---------------------------------------------------------------
+      // check adc count for neighbour's neighbours recursively and
+      // if nonzero, add these to the cluster.
+      // ---------------------------------------------------------------
+      for(i=1;i < 5000;i++){
+	if(clust[0][i] != 0){
+	  id1=clust[0][i];
+	  id2=clust[1][i];
+	  for(j=0; j<6 ; j++){
+	    jd1=id1+neibx[j];
+	    jd2=id2+neiby[j];
+	    if( (jd1 >= 0 && jd1 < kNDIMX) && (jd2 >= 0 && jd2 < kNDIMY) &&
+		fInfocl[0][jd1][jd2] == 0 ){
+	      fInfocl[0][jd1][jd2] = 2;
+	      fInfocl[1][jd1][jd2] = icl;
+	      numcell              = numcell + 1;
+	      clust[0][numcell]    = jd1;
+	      clust[1][numcell]    = jd2;
+	      cellcount            = cellcount+1;
+	      fInfcl[0][cellcount] = icl;
+	      fInfcl[1][cellcount] = jd1;
+	      fInfcl[2][cellcount] = jd2;
+	    }
+	  }
 	}
-	dd[i1]=adum; iord1[i1]=idum;
       }
     }
   }
-  // store the sorted information in iord for later use
-  for(i=0; i<nmx; i++){
-    j=iord1[i]; i2=j/ndimx; 
-    i1=j-i2*ndimx; 
-    iord[0][i]=i1; 
-    iord[1][i]=i2;
-  }
+  //  for(icell=0; icell<=cellcount; icell++){
+  //    ofl0 << fInfcl[0][icell] << " " << fInfcl[1][icell] << " " <<
+  //      fInfcl[2][icell] << endl;
+  //  }
+  return cellcount;
 }
-
-void AliPMDClustering::refclust(int incr, int /*supmod*/, int /*idet*/)
+// ------------------------------------------------------------------------ //
+void AliPMDClustering::RefClust(int incr)
 {
-  int i, j, k, i1, i2, id, icl, ncl[4500], iord[4500], itest; 
+  // Does the refining of clusters
+  // Takes the big patch and does gaussian fitting and
+  // finds out the more refined clusters
+  //
+  int i, j, k, i1, i2, id, icl, ncl[4500], iord[4500], itest;
   int ihld;
   int ig, nsupcl, lev1[20], lev2[20];
   double x[4500], y[4500], z[4500], x1, y1, z1, x2, y2, z2, dist;
   double xc[4500], yc[4500], zc[4500], cells[4500], sum, rc[4500], rr;
-  // clno counts the final clusters
+  // fClno counts the final clusters
   // nsupcl =  # of superclusters; ncl[i]= # of cells in supercluster i
   // x, y and z store (x,y) coordinates of and energy deposited in a cell
   // xc, yc store (x,y) coordinates of the cluster center
   // zc stores the energy deposited in a cluster
   // rc is cluster radius
   // finally the cluster information is put in 2-dimensional array clusters
-  //  ofstream ofl1("checking.5",ios::app);
-  clno=-1;
-  nsupcl=-1;
+  // ofstream ofl1("checking.5",ios::app);
+  fClno  = -1;
+  nsupcl = -1;
   for(i=0; i<4500; i++){ncl[i]=-1;}
   for(i=0; i<incr; i++){
-    if(infcl[0][i] != nsupcl){ nsupcl=nsupcl+1; }
+    if(fInfcl[0][i] != nsupcl){ nsupcl=nsupcl+1; }
+    if (nsupcl > 4500) {
+      AliWarning("RefClust: Too many superclusters!");
+      nsupcl = 4500;
+      break;
+    }
     ncl[nsupcl]=ncl[nsupcl]+1;
   }
-  if (fMessage == 1)
-    {
-      cout << " # of cells " <<incr+1 << " # of superclusters " << nsupcl+1
-	   << endl;
-    }
+
+  AliDebug(1,Form("Number of cells = %d Number of Superclusters = %d",
+		  incr+1,nsupcl+1));
+
   id=-1;
   icl=-1;
   for(i=0; i<nsupcl; i++){
-    if(ncl[i] == 0){ 
-      id=id+1; 
+    if(ncl[i] == 0){
+      id=id+1;
       icl=icl+1;
       // one  cell super-clusters --> single cluster
       // cluster center at the centyer of the cell
       // cluster radius = half cell dimension
-      clno=clno+1; 
-      i1=infcl[1][id]; 
-      i2=infcl[2][id];
-      clusters[0][clno]=coord[0][i1][i2]; 
-      clusters[1][clno]=coord[1][i1][i2];
-      clusters[2][clno]=d[i1][i2]; 
-      clusters[3][clno]=1.; 
-      clusters[4][clno]=0.5;
-      //ofl1 << icl << " " << coord[0][i1][i2] << " " << coord[1][i1][i2] << 
-      //" " << d[i1][i2] << " " << clusters[3][clno] <<endl; 
+      if (fClno >= 5000) {
+	AliWarning("RefClust: Too many clusters! more than 5000");
+	return;
+      }
+      fClno = fClno + 1;
+      i1 = fInfcl[1][id];
+      i2 = fInfcl[2][id];
+      fClusters[0][fClno] = fCoord[0][i1][i2];
+      fClusters[1][fClno] = fCoord[1][i1][i2];
+      fClusters[2][fClno] = fEdepCell[i1][i2];
+      fClusters[3][fClno] = 1.;
+      fClusters[4][fClno] = 0.5;
+      //ofl1 << icl << " " << fCoord[0][i1][i2] << " " << fCoord[1][i1][i2] <<
+      //" " << fEdepCell[i1][i2] << " " << fClusters[3][fClno] <<endl;
     }else if(ncl[i] == 1){
       // two cell super-cluster --> single cluster
       // cluster center is at ener. dep.-weighted mean of two cells
       // cluster radius == half cell dimension
-      id=id+1; 
-      icl=icl+1;
-      clno=clno+1; 
-      i1=infcl[1][id]; 
-      i2=infcl[2][id]; 
-      x1=coord[0][i1][i2];
-      y1=coord[1][i1][i2]; 
-      z1=d[i1][i2];
-      id=id+1; 
-      i1=infcl[1][id]; 
-      i2=infcl[2][id];
-      x2=coord[0][i1][i2]; 
-      y2=coord[1][i1][i2]; 
-      z2=d[i1][i2];
-      clusters[0][clno]=(x1*z1+x2*z2)/(z1+z2); 
-      clusters[1][clno]=(y1*z1+y2*z2)/(z1+z2);
-      clusters[2][clno]=z1+z2; 
-      clusters[3][clno]=2.; 
-      clusters[4][clno]=0.5;
-      //ofl1 << icl << " " << clusters[0][clno] << " " << clusters[1][clno]
-      //   << " " << clusters[2][clno] << " " <<clusters[3][clno] <<endl; 
-    }else{
-      id=id+1; 
-      iord[0]=0;
-      // super-cluster of more than two cells - broken up into smaller 
-      // clusters gaussian centers computed. (peaks separated by > 1 cell) 
+      id   = id + 1;
+      icl  = icl+1;
+      if (fClno >= 5000) {
+	AliWarning("RefClust: Too many clusters! more than 5000");
+	return;
+      }
+      fClno = fClno+1;
+      i1   = fInfcl[1][id];
+      i2   = fInfcl[2][id];
+      x1   = fCoord[0][i1][i2];
+      y1   = fCoord[1][i1][i2];
+      z1   = fEdepCell[i1][i2];
+      id   = id+1;
+      i1   = fInfcl[1][id];
+      i2   = fInfcl[2][id];
+      x2   = fCoord[0][i1][i2];
+      y2   = fCoord[1][i1][i2];
+      z2   = fEdepCell[i1][i2];
+      fClusters[0][fClno] = (x1*z1+x2*z2)/(z1+z2);
+      fClusters[1][fClno] = (y1*z1+y2*z2)/(z1+z2);
+      fClusters[2][fClno] = z1+z2;
+      fClusters[3][fClno] = 2.;
+      fClusters[4][fClno] = 0.5;
+      //ofl1 << icl << " " << fClusters[0][fClno] << " " << fClusters[1][fClno]
+      //   << " " << fClusters[2][fClno] << " " <<fClusters[3][fClno] <<endl;
+    }
+    else{
+      id      = id + 1;
+      iord[0] = 0;
+      // super-cluster of more than two cells - broken up into smaller
+      // clusters gaussian centers computed. (peaks separated by > 1 cell)
       // Begin from cell having largest energy deposited This is first
       // cluster center
-      i1=infcl[1][id]; 
-      i2=infcl[2][id];
-      x[0]=coord[0][i1][i2]; 
-      y[0]=coord[1][i1][i2]; 
-      z[0]=d[i1][i2];
-      iord[0]=0;
+      i1      = fInfcl[1][id];
+      i2      = fInfcl[2][id];
+      x[0]    = fCoord[0][i1][i2];
+      y[0]    = fCoord[1][i1][i2];
+      z[0]    = fEdepCell[i1][i2];
+      iord[0] = 0;
       for(j=1;j<=ncl[i];j++){
-	id=id+1;
-	i1=infcl[1][id]; 
-	i2=infcl[2][id];
-	iord[j]=j;
-	x[j]=coord[0][i1][i2]; 
-	y[j]=coord[1][i1][i2]; 
-	z[j]=d[i1][i2];
+
+	id      = id + 1;
+	i1      = fInfcl[1][id];
+	i2      = fInfcl[2][id];
+	iord[j] = j;
+	x[j]    = fCoord[0][i1][i2];
+	y[j]    = fCoord[1][i1][i2];
+	z[j]    = fEdepCell[i1][i2];
       }
-      // arranging cells within supercluster in decreasing order 
+      // arranging cells within supercluster in decreasing order
       for(j=1;j<=ncl[i];j++){
-	itest=0; ihld=iord[j];
+	itest=0;
+	ihld=iord[j];
 	for(i1=0;i1<j;i1++){
 	  if(itest == 0 && z[iord[i1]] < z[ihld]){
 	    itest=1;
@@ -288,60 +441,61 @@ void AliPMDClustering::refclust(int incr, int /*supmod*/, int /*idet*/)
 	  }
 	}
       }
-      // compute the number of Gaussians and their centers ( first 
-      // guess ) 
+
+      // compute the number of Gaussians and their centers ( first
+      // guess )
       // centers must be separated by cells having smaller ener. dep.
       // neighbouring centers should be either strong or well-separated
       ig=0;
-      xc[ig]=x[iord[0]]; 
-      yc[ig]=y[iord[0]]; 
+      xc[ig]=x[iord[0]];
+      yc[ig]=y[iord[0]];
       zc[ig]=z[iord[0]];
       for(j=1;j<=ncl[i];j++){
-	itest=-1; 
-	x1=x[iord[j]]; 
+	itest=-1;
+	x1=x[iord[j]];
 	y1=y[iord[j]];
 	for(k=0;k<=ig;k++){
-	  x2=xc[k]; y2=yc[k]; 
-	  rr=Dist(x1,y1,x2,y2);
+	  x2=xc[k]; y2=yc[k];
+	  rr=Distance(x1,y1,x2,y2);
 	  if( rr >= 1.1 && rr < 1.8 && z[iord[j]] > zc[k]/4.)
 	    itest=itest+1;
 	  if( rr >= 1.8 && rr < 2.1 && z[iord[j]] > zc[k]/10.)
 	    itest=itest+1;
 	  if( rr >= 2.1)itest=itest+1;
-	} 
+	}
 	if(itest == ig){
-	  ig=ig+1; 
-	  xc[ig]=x1; 
-	  yc[ig]=y1; 
+	  ig=ig+1;
+	  xc[ig]=x1;
+	  yc[ig]=y1;
 	  zc[ig]=z[iord[j]];
 	}
       }
       // for(j=0; j<=ig; j++){
       //ofl1 << icl+j+1 << " " << xc[j] << " " <<yc[j] <<" "<<zc[j]<<endl;
       //}
-      // gaussfit to adjust cluster parameters to minimize
-      gaussfit(ncl[i], ig, x[0], y[0] ,z[0], xc[0], yc[0], zc[0], rc[0]);
+      // GaussFit to adjust cluster parameters to minimize
+      GaussFit(ncl[i], ig, x[0], y[0] ,z[0], xc[0], yc[0], zc[0], rc[0]);
       icl=icl+ig+1;
       // compute the number of cells belonging to each cluster.
-      // cell is shared between several clusters ( if they are equidistant 
+      // cell is shared between several clusters ( if they are equidistant
       // from it ) in the ratio of cluster energy deposition
       for(j=0; j<=ig; j++){
 	cells[j]=0.;
       }
       if(ig > 0){
 	for(j=0; j<=ncl[i]; j++){
-	  lev1[0]=0; 
+	  lev1[0]=0;
 	  lev2[0]=0;
 	  for(k=0; k<=ig; k++){
-	    dist=Dist(x[j], y[j], xc[k], yc[k]);
+	    dist=Distance(x[j], y[j], xc[k], yc[k]);
 	    if(dist < sqrt(3.) ){
-	      lev1[0]++; 
-	      i1=lev1[0]; 
+	      lev1[0]++;
+	      i1=lev1[0];
 	      lev1[i1]=k;
 	    }else{
 	      if(dist < 2.1){
-		lev2[0]++; 
-		i1=lev2[0]; 
+		lev2[0]++;
+		i1=lev2[0];
 		lev2[i1]=k;
 	      }
 	    }
@@ -372,109 +526,112 @@ void AliPMDClustering::refclust(int incr, int /*supmod*/, int /*idet*/)
 	}
       }
       for(j=0; j<=ig; j++){
-	clno=clno+1; 
-	clusters[0][clno]=xc[j]; 
-	clusters[1][clno]=yc[j]; 
-	clusters[2][clno]=zc[j];
-	clusters[4][clno]=rc[j];
+	if (fClno >= 5000) {
+	  AliWarning("RefClust: Too many clusters! more than 5000");
+	  return;
+	}
+	fClno               = fClno + 1;
+	fClusters[0][fClno] = xc[j];
+	fClusters[1][fClno] = yc[j];
+	fClusters[2][fClno] = zc[j];
+	fClusters[4][fClno] = rc[j];
 	if(ig == 0){
-	  clusters[3][clno]=ncl[i];
+	  fClusters[3][fClno] = ncl[i];
 	}else{
-	  clusters[3][clno]=cells[j];
+	  fClusters[3][fClno] = cells[j];
 	}
       }
     }
   }
-
 }
-
-
-void AliPMDClustering::gaussfit(int ncell, int nclust, double &x, double &y ,double &z, double &xc, double &yc, double &zc, double &rc)
+// ------------------------------------------------------------------------ //
+void AliPMDClustering::GaussFit(Int_t ncell, Int_t nclust, Double_t &x, Double_t &y ,Double_t &z, Double_t &xc, Double_t &yc, Double_t &zc, Double_t &rc)
 {
-  int i, j, i1, i2, jmax, novar, idd, jj;
-  double xx[4500], yy[4500], zz[4500], xxc[4500], yyc[4500]; 
+  // Does gaussian fitting
+  //
+  int i, j, i1, i2, novar, idd, jj;
+  double xx[4500], yy[4500], zz[4500], xxc[4500], yyc[4500];
   double a[4500], b[4500], c[4500], d[4500], ha[4500], hb[4500];
   double hc[4500], hd[4500], zzc[4500], rrc[4500];
   int neib[4500][50];
   double sum, dx, dy, str, str1, aint, sum1, rr, dum;
   double x1, x2, y1, y2;
-  str=0.; 
-  str1=0.; 
-  rr=0.3; 
-  novar=0;
-
+  str   = 0.;
+  str1  = 0.;
+  rr    = 0.3;
+  novar = 0;
   j = 0;  // Just put not to see the compiler warning, BKN
 
-
-  for(i=0; i<=ncell; i++){
-    xx[i]=*(&x+i); 
-    yy[i]=*(&y+i); 
-    zz[i]=*(&z+i);
-    str=str+zz[i];
-  }
-  for(i=0; i<=nclust; i++){
-    xxc[i]=*(&xc+i); 
-    yyc[i]=*(&yc+i); 
-    zzc[i]=*(&zc+i); 
-    str1=str1+zzc[i]; 
-    rrc[i]=0.5;
-
-  }
-  for(i=0; i<=nclust; i++){
-    zzc[i]=str/str1*zzc[i];
-    ha[i]=xxc[i]; 
-    hb[i]=yyc[i]; 
-    hc[i]=zzc[i]; 
-    hd[i]=rrc[i];
-    x1=xxc[i]; 
-    y1=yyc[i];
-  }
+  for(i=0; i<=ncell; i++)
+    {
+      xx[i] = *(&x+i);
+      yy[i] = *(&y+i);
+      zz[i] = *(&z+i);
+      str   = str + zz[i];
+    }
+  for(i=0; i<=nclust; i++)
+    {
+      xxc[i] = *(&xc+i);
+      yyc[i] = *(&yc+i);
+      zzc[i] = *(&zc+i);
+      str1   = str1 + zzc[i];
+      rrc[i] = 0.5;
+    }
+  for(i=0; i<=nclust; i++)
+    {
+      zzc[i] = str/str1*zzc[i];
+      ha[i]  = xxc[i];
+      hb[i]  = yyc[i];
+      hc[i]  = zzc[i];
+      hd[i]  = rrc[i];
+      x1     = xxc[i];
+      y1     = yyc[i];
+    }
   for(i=0; i<=ncell; i++){
-    idd=0; 
-    x1=xx[i]; 
+    idd=0;
+    x1=xx[i];
     y1=yy[i];
     for(j=0; j<=nclust; j++){
-      x2=xxc[j]; 
+      x2=xxc[j];
       y2=yyc[j];
-      if(Dist(x1,y1,x2,y2) <= 3.){ idd=idd+1; neib[i][idd]=j; }
+      if(Distance(x1,y1,x2,y2) <= 3.){ idd=idd+1; neib[i][idd]=j; }
     }
-
     neib[i][0]=idd;
   }
   sum=0.;
   for(i1=0; i1<=ncell; i1++){
-    aint=0.; 
+    aint=0.;
     idd=neib[i1][0];
     for(i2=1; i2<=idd; i2++){
       jj=neib[i1][i2];
-      dx=xx[i1]-xxc[jj]; 
-      dy=yy[i1]-yyc[jj]; 
+      dx=xx[i1]-xxc[jj];
+      dy=yy[i1]-yyc[jj];
       dum=rrc[j]*rrc[jj]+rr*rr;
       aint=aint+exp(-(dx*dx+dy*dy)/dum)*zzc[idd]*rr*rr/dum;
     }
     sum=sum+(aint-zz[i1])*(aint-zz[i1])/str;
   }
-  jmax=nclust*1000; 
-  if(nclust > 20)jmax=20000;
-  for(j=0; j<jmax; j++){
+//   jmax=nclust*1000;
+//   if(nclust > 20)jmax=20000;
+//   for(j=0; j<jmax; j++){
     str1=0.;
     for(i=0; i<=nclust; i++){
-      a[i]=xxc[i]+0.6*(ranmar()-0.5); 
-      b[i]=yyc[i]+0.6*(ranmar()-0.5);
-      c[i]=zzc[i]*(1.+(ranmar()-0.5)*0.2); 
+      a[i]=xxc[i]+0.6*(Ranmar()-0.5);
+      b[i]=yyc[i]+0.6*(Ranmar()-0.5);
+      c[i]=zzc[i]*(1.+(Ranmar()-0.5)*0.2);
       str1=str1+zzc[i];
-      d[i]=rrc[i]*(1.+(ranmar()-0.5)*0.1);
+      d[i]=rrc[i]*(1.+(Ranmar()-0.5)*0.1);
       if(d[i] < 0.25)d[i]=0.25;
     }
     for(i=0; i<=nclust; i++){ c[i]=c[i]*str/str1; }
     sum1=0.;
     for(i1=0; i1<=ncell; i1++){
-      aint=0.; 
+      aint=0.;
       idd=neib[i1][0];
       for(i2=1; i2<=idd; i2++){
 	jj=neib[i1][i2];
-	dx=xx[i1]-a[jj]; 
-	dy=yy[i1]-b[jj]; 
+	dx=xx[i1]-a[jj];
+	dy=yy[i1]-b[jj];
 	dum=d[jj]*d[jj]+rr*rr;
 	aint=aint+exp(-(dx*dx+dy*dy)/dum)*c[i2]*rr*rr/dum;
       }
@@ -483,140 +640,31 @@ void AliPMDClustering::gaussfit(int ncell, int nclust, double &x, double &y ,dou
 
     if(sum1 < sum){
       for(i2=0; i2<=nclust; i2++){
-	xxc[i2]=a[i2]; 
-	yyc[i2]=b[i2]; 
-	zzc[i2]=c[i2]; 
-	rrc[i2]=d[i2]; 
+	xxc[i2]=a[i2];
+	yyc[i2]=b[i2];
+	zzc[i2]=c[i2];
+	rrc[i2]=d[i2];
 	sum=sum1;
-
       }
     }
-  }
+//   }
   for(j=0; j<=nclust; j++){
-    *(&xc+j)=xxc[j]; 
-    *(&yc+j)=yyc[j]; 
-    *(&zc+j)=zzc[j]; 
+    *(&xc+j)=xxc[j];
+    *(&yc+j)=yyc[j];
+    *(&zc+j)=zzc[j];
     *(&rc+j)=rrc[j];
   }
 }
-
-
-double AliPMDClustering::Dist(double x1, double y1, double x2, double y2)
+// ------------------------------------------------------------------------ //
+double AliPMDClustering::Distance(double x1, double y1, double x2, double y2)
 {
   return sqrt((x1-x2)*(x1-x2) + (y1-y2)*(y1-y2));
 }
-
-  
-int AliPMDClustering::crclust(double /*ave*/, double cutoff, int nmx1, int /*idet*/)
-{
-  int i,j,k,id1,id2,icl, numcell, clust[2][5000];
-  int jd1,jd2, icell, cellcount;
-  static int neibx[6]={1,0,-1,-1,0,1}, neiby[6]={0,1,1,0,-1,-1};
-  // neibx and neiby define ( incremental ) (i,j) for the neighbours of a 
-  // cell. There are six neighbours.
-  // cellcount --- total number of cells having nonzero ener dep
-  // numcell --- number of cells in a given supercluster
-  //ofstream ofl0("cells_loc",ios::out);
-  // initialize infocl[2][ndimx][ndimy] 
-  for (j=0; j < 72; j++){
-    for(k=0; k < 72; k++){
-      infocl[0][j][k] = 0; 
-      infocl[1][j][k] = 0;
-    }
-  }
-  for(i=0; i < nmx; i++){
-    infcl[0][i] = -1;
-    id1=iord[0][i]; 
-    id2=iord[1][i];
-    if(d[id1][id2] <= cutoff){infocl[0][id1][id2]=-1;}
-  }
-  // ---------------------------------------------------------------
-  // crude clustering begins. Start with cell having largest adc 
-  // count and loop over the cells in descending order of adc count
-  // ---------------------------------------------------------------
-  icl=-1;
-  cellcount=-1;
-  for(icell=0; icell <= nmx1; icell++){
-    id1=iord[0][icell]; 
-    id2=iord[1][icell]; 
-    if(infocl[0][id1][id2] == 0 ){
-      // ---------------------------------------------------------------
-      // icl -- cluster #, numcell -- # of cells in it, clust -- stores 
-      // coordinates of the cells in a cluster, infocl[0][i1][i2] is 1 for 
-      // primary and 2 for secondary cells, 
-      // infocl[1][i1][i2] stores cluster #
-      // ---------------------------------------------------------------
-      icl=icl+1; 
-      numcell=0; 
-      cellcount=cellcount+1;
-      infocl[0][id1][id2]=1; 
-      infocl[1][id1][id2]=icl;
-      infcl[0][cellcount]=icl; 
-      infcl[1][cellcount]=id1; 
-      infcl[2][cellcount]=id2;
-      clust[0][numcell]=id1;
-      clust[1][numcell]=id2;
-      for(i=1; i<5000; i++)clust[0][i]=0;
-      // ---------------------------------------------------------------
-      // check for adc count in neib. cells. If ne 0 put it in this clust
-      // ---------------------------------------------------------------
-      for(i=0; i<6; i++){
-	jd1=id1+neibx[i]; 
-	jd2=id2+neiby[i];
-	if( (jd1 >= 0 && jd1 < 72) && (jd2 >= 0 && jd2 < 72) && 
-	    infocl[0][jd1][jd2] == 0){
-	  numcell=numcell+1;
-	  infocl[0][jd1][jd2]=2; 
-	  infocl[1][jd1][jd2]=icl;
-	  clust[0][numcell]=jd1;
-	  clust[1][numcell]=jd2;
-	  cellcount=cellcount+1;
-	  infcl[0][cellcount]=icl; 
-	  infcl[1][cellcount]=jd1; 
-	  infcl[2][cellcount]=jd2;
-	}
-      }
-      // ---------------------------------------------------------------
-      // check adc count for neighbour's neighbours recursively and 
-      // if nonzero, add these to the cluster.
-      // ---------------------------------------------------------------
-      for(i=1;i < 5000;i++){
-	if(clust[0][i] != 0){
-	  id1=clust[0][i]; 
-	  id2=clust[1][i];
-	  for(j=0; j<6 ; j++){
-	    jd1=id1+neibx[j]; 
-	    jd2=id2+neiby[j];
-	    if( (jd1 >= 0 && jd1 < 72) && (jd2 >= 0 && jd2 < 72) && 
-		infocl[0][jd1][jd2] == 0 ){
-	      infocl[0][jd1][jd2]=2; 
-	      infocl[1][jd1][jd2]=icl;
-	      numcell=numcell+1; 
-	      clust[0][numcell]=jd1;
-	      clust[1][numcell]=jd2;
-	      cellcount=cellcount+1;
-	      infcl[0][cellcount]=icl; 
-	      infcl[1][cellcount]=jd1; 
-	      infcl[2][cellcount]=jd2;
-	    }
-	  }
-	}
-      }
-    }
-  }
-  //  for(icell=0; icell<=cellcount; icell++){
-  //    ofl0 << infcl[0][icell] << " " << infcl[1][icell] << " " << 
-  //      infcl[2][icell] << endl;
-  //  }
-  return cellcount;
-}
-
-double AliPMDClustering::ranmar()
+// ------------------------------------------------------------------------ //
+double AliPMDClustering::Ranmar() const
 {
-  /*                                   C==========================C*/
-  /*===================================C==========================*/
-  /*  Universal random number generator proposed by Marsaglia and Zaman
-      in report FSU-SCRI-87-50 */
+  //  Universal random number generator proposed by Marsaglia and Zaman
+  //  in report FSU-SCRI-87-50
 
   //  clock_t start;
   int ii, jj;
@@ -639,9 +687,9 @@ double AliPMDClustering::ranmar()
     if(ii > 31328 ) ii = ii - ( ii / 31328 ) * 31328;
     if(jj > 30081 ) jj = jj - ( jj / 30081 ) * 30081;
     itest=itest+1;
-    if((( ii > 0 ) &&  ( ii <= 31328 )) && (( jj > 0 ) && 
+    if((( ii > 0 ) &&  ( ii <= 31328 )) && (( jj > 0 ) &&
 					    ( jj <= 30081 ))){
-      i1=ii/177+2; i2=ii-(i1-2)*177+2; i3=jj/169+1; i4=jj-(i3-1)*169; 
+      i1=ii/177+2; i2=ii-(i1-2)*177+2; i3=jj/169+1; i4=jj-(i3-1)*169;
       i4 = jj - (i3-1)*169;
       count1=0;
       while ( count1 < 97 ){
@@ -660,25 +708,31 @@ double AliPMDClustering::ranmar()
 	u[count1] = s;
 	count1 = count1 +1;
       }
-      c = 362436./16777216.;  cd = 7654321./16777216.; 
+      c = 362436./16777216.;  cd = 7654321./16777216.;
       cm = 16777213./16777216.;
     }
     else{
-      cout << " wrong initialization " << endl;
+      AliWarning("Wrong initialization");
     }
   }
   else{
-    uni = u[i] - u[j]; if( uni < 0.) uni = uni + 1; u[i] = uni; 
+    uni = u[i] - u[j];
+    if( uni < 0.) uni = uni + 1;
+    u[i] = uni;
     i = i -1;
-    if( i < 0 ) i = 96; j = j - 1; if ( j < 0 ) j = 96; c = c - cd;
-    if( c < 0. ) c = c+cm; uni = uni-c ; if( uni < 0. )uni = uni+1.;
-    //    return uni;
+    if( i < 0 ) i = 96;
+    j = j - 1;
+    if ( j < 0 ) j = 96;
+    c = c - cd;
+    if( c < 0. ) c = c+cm;
+    uni = uni-c ;
+    if( uni < 0. )uni = uni+1.;
   }
   return uni;
-
-}   
-
-void AliPMDClustering::SetMessage(Int_t imessage)
+}
+// ------------------------------------------------------------------------ //
+void AliPMDClustering::SetEdepCut(Float_t decut)
 {
-  fMessage = imessage;
+  fCutoff = decut;
 }
+// ------------------------------------------------------------------------ //