THcShowerArray.cxx

/** \class THcShowerArray
    \ingroup DetSupport

\brief Fly's eye array of shower blocks

*/

#include "THcShowerArray.h"
#include "THcHodoscope.h"
#include "TClonesArray.h"
#include "THcSignalHit.h"
#include "THcGlobals.h"
#include "THcParmList.h"
#include "THcHitList.h"
#include "THcShower.h"
#include "THcRawShowerHit.h"
#include "TClass.h"
#include "math.h"
#include "THaTrack.h"
#include "THaTrackProj.h"
#include "THcCherenkov.h"         //for efficiency calculations
#include "THcHallCSpectrometer.h"
#include "Helper.h"

#include <cstring>
#include <cstdio>
#include <cstdlib>
#include <iostream>
#include <cassert>
#include <fstream>

using namespace std;

ClassImp(THcShowerArray)

//______________________________________________________________________________
THcShowerArray::THcShowerArray( const char* name,
                                const char* description,
				const Int_t layernum,
				THaDetectorBase* parent )
  : THaSubDetector(name,description,parent)
{
  fADCHits = new TClonesArray("THcSignalHit",100);
  fLayerNum = layernum;

  frAdcPedRaw       = new TClonesArray("THcSignalHit", 16);
  frAdcErrorFlag    = new TClonesArray("THcSignalHit", 16);
  frAdcPulseIntRaw  = new TClonesArray("THcSignalHit", 16);
  frAdcPulseAmpRaw  = new TClonesArray("THcSignalHit", 16);
  frAdcPulseTimeRaw = new TClonesArray("THcSignalHit", 16);

  frAdcPed       = new TClonesArray("THcSignalHit", 16);
  frAdcPulseInt  = new TClonesArray("THcSignalHit", 16);
  frAdcPulseAmp  = new TClonesArray("THcSignalHit", 16);
  frAdcPulseTime = new TClonesArray("THcSignalHit", 16);

  fClusterList = new THcShowerClusterList;         // List of hit clusters
}

//______________________________________________________________________________
THcShowerArray::~THcShowerArray()
{
  // Destructor

  Clear(); // deletes allocations in fClusterList
  for (UInt_t i=0; i<fNRows; i++) {
    delete [] fXPos[i];
    delete [] fYPos[i];
    delete [] fZPos[i];
  }
  delete [] fXPos; fXPos = 0;
  delete [] fYPos; fYPos = 0;
  delete [] fZPos; fZPos = 0;

  delete [] fPedLimit;
  delete [] fGain;
  delete [] fPedSum;
  delete [] fPedSum2;
  delete [] fPedCount;
  delete [] fSig;
  delete [] fPed;
  delete [] fThresh;

  delete fADCHits; fADCHits = NULL;

  delete frAdcPedRaw; frAdcPedRaw = NULL;
  delete frAdcErrorFlag; frAdcErrorFlag = NULL;
  delete frAdcPulseIntRaw; frAdcPulseIntRaw = NULL;
  delete frAdcPulseAmpRaw; frAdcPulseAmpRaw = NULL;
  delete frAdcPulseTimeRaw; frAdcPulseTimeRaw = NULL;

  delete frAdcPed; frAdcPed = NULL;
  delete frAdcPulseInt; frAdcPulseInt = NULL;
  delete frAdcPulseAmp; frAdcPulseAmp = NULL;
  delete frAdcPulseTime; frAdcPulseTime = NULL;

  //  delete [] fA;
  //delete [] fP;
  // delete [] fA_p;

  //delete [] fE;
  delete [] fBlock_ClusterID;

  delete fClusterList; fClusterList = 0;

  delete [] fAdcTimeWindowMin; fAdcTimeWindowMin = 0;
  delete [] fAdcTimeWindowMax; fAdcTimeWindowMax = 0;
  delete [] fPedDefault; fPedDefault = 0;
}

//_____________________________________________________________________________
THaAnalysisObject::EStatus THcShowerArray::Init( const TDatime& date )
{
  // Extra initialization for shower layer: set up DataDest map

  if( IsZombie())
    return fStatus = kInitError;

  // How to get information for parent
  //  if( GetParent() )
  //    fOrigin = GetParent()->GetOrigin();
  THcHallCSpectrometer *app=dynamic_cast<THcHallCSpectrometer*>(GetApparatus());
   if(  !app ||
      !(fglHod = dynamic_cast<THcHodoscope*>(app->GetDetector("hod"))) ) {
    static const char* const here = "ReadDatabase()";
    Warning(Here(here),"Hodoscope \"%s\" not found. ","hod");
  }

  EStatus status;
  if( (status=THaSubDetector::Init( date )) )
    return fStatus = status;

  return fStatus = kOK;

}

//_____________________________________________________________________________
Int_t THcShowerArray::ReadDatabase( const TDatime& date )
{

  char prefix[2];
  prefix[0]=tolower(GetParent()->GetPrefix()[0]);
  prefix[1]='\0';

  // cout << "Parent name: " << GetParent()->GetPrefix() << endl;
  fNRows=fNColumns=0;
  fXFront=fYFront=fZFront=0.;
  fXStep=fYStep=fZSize=0.;
  fUsingFADC=0;
  fPedSampLow=0;
  fPedSampHigh=9;
  fDataSampLow=23;
  fDataSampHigh=49;
  fStatCerMin=1.;
  fStatSlop=3.;
  fStatMaxChi2=10.;
  DBRequest list[]={
    {"cal_arr_nrows", &fNRows, kInt},
    {"cal_arr_ncolumns", &fNColumns, kInt},
    {"cal_arr_front_x", &fXFront, kDouble},
    {"cal_arr_front_y", &fYFront, kDouble},
    {"cal_arr_front_z", &fZFront, kDouble},
    {"cal_arr_xstep", &fXStep, kDouble},
    {"cal_arr_ystep", &fYStep, kDouble},
    {"cal_arr_zsize", &fZSize, kDouble},
    {"cal_using_fadc", &fUsingFADC, kInt, 0, 1},
    {"cal_arr_ADCMode", &fADCMode, kInt, 0, 1},
    {"cal_arr_adc_tdc_offset", &fAdcTdcOffset, kDouble, 0, 1},
    {"cal_arr_AdcThreshold", &fAdcThreshold, kDouble, 0, 1},
    {"cal_ped_sample_low", &fPedSampLow, kInt, 0, 1},
    {"cal_ped_sample_high", &fPedSampHigh, kInt, 0, 1},
    {"cal_data_sample_low", &fDataSampLow, kInt, 0, 1},
    {"cal_data_sample_high", &fDataSampHigh, kInt, 0, 1},
    {"cal_debug_adc", &fDebugAdc, kInt, 0, 1},
    {"stat_cermin", &fStatCerMin, kDouble, 0, 1},
    {"stat_slop_array", &fStatSlop, kDouble, 0, 1},
    {"stat_maxchisq", &fStatMaxChi2, kDouble, 0, 1},
    {0}
  };

  fDebugAdc = 0;  // Set ADC debug parameter to false unless set in parameter file
  fADCMode=kADCDynamicPedestal;
  fAdcTdcOffset=0.0;
  fAdcThreshold=0.;

  gHcParms->LoadParmValues((DBRequest*)&list, prefix);
  fNelem = fNRows*fNColumns;

  fXPos = new Double_t* [fNRows];
  fYPos = new Double_t* [fNRows];
  fZPos = new Double_t* [fNRows];
  for (UInt_t i=0; i<fNRows; i++) {
    fXPos[i] = new Double_t [fNColumns];
    fYPos[i] = new Double_t [fNColumns];
    fZPos[i] = new Double_t [fNColumns];
  }

  //Looking to the front, the numbering goes from left to right, and from top
  //to bottom.

  for (UInt_t j=0; j<fNColumns; j++)
    for (UInt_t i=0; i<fNRows; i++) {
      fXPos[i][j] = fXFront - (fNRows-1)*fXStep/2 + fXStep*i;
      fYPos[i][j] = fYFront + (fNColumns-1)*fYStep/2 - fYStep*j;
      fZPos[i][j] = fZFront ;
  }

  fOrigin.SetXYZ(fXFront, fYFront, fZFront);

  // Debug output.

  fParent = GetParent();

  if (static_cast<THcShower*>(fParent)->fdbg_init_cal) {
    cout << "---------------------------------------------------------------\n";
    cout << "Debug output from THcShowerArray::ReadDatabase for "
    	 << GetParent()->GetPrefix() << ":" << endl;

    cout << "  Layer #" << fLayerNum << ", number of elements " << dec << fNelem
	 << endl;
    cout << "  Columns " << fNColumns << ", Rows " << fNRows << endl;

    cout << "Front X, Y Z: " << fXFront << ", " << fYFront << ", " << fZFront
	 << " cm" << endl;

    cout << "  Block to block X and Y distances: " << fXStep << ", " << fYStep
	 << " cm" << endl;

    cout << "  Block size along Z: " << fZSize << " cm" << endl;

    cout << "Block X coordinates:" << endl;
    for (UInt_t i=0; i<fNRows; i++) {
      for (UInt_t j=0; j<fNColumns; j++) {
	cout << fXPos[i][j] << " ";
      }
      cout << endl;
    }
    cout << endl;

    cout << "Block Y coordinates:" << endl;
    for (UInt_t i=0; i<fNRows; i++) {
      for (UInt_t j=0; j<fNColumns; j++) {
    	cout << fYPos[i][j] << " ";
      }
      cout << endl;
    }
    cout << endl;

    cout << "Block Z coordinates:" << endl;
    for (UInt_t i=0; i<fNRows; i++) {
      for (UInt_t j=0; j<fNColumns; j++) {
    	cout << fZPos[i][j] << " ";
      }
      cout << endl;
    }
    cout << endl;

    cout << "  Origin of Array:" << endl;
    cout << "    Xorig = " << GetOrigin().X() << endl;
    cout << "    Yorig = " << GetOrigin().Y() << endl;
    cout << "    Zorig = " << GetOrigin().Z() << endl;
    cout << endl;

    cout << "  Using FADC " << fUsingFADC << endl;
    if (fUsingFADC) {
      cout << "  FADC pedestal sample low = " << fPedSampLow << ",  high = "
	   << fPedSampHigh << endl;
      cout << "  FADC data sample low = " << fDataSampLow << ",  high = "
	   << fDataSampHigh << endl;
    }

  }

  // Here read the 2-D arrays of pedestals, gains, etc.

  // Pedestal limits per channel.
  fPedLimit = new Int_t [fNelem];

  Double_t cal_arr_cal_const[fNelem];
  Double_t cal_arr_gain_cor[fNelem];

  fAdcTimeWindowMin = new Double_t [fNelem];
  fAdcTimeWindowMax = new Double_t [fNelem];
  fPedDefault = new Int_t [fNelem];

  DBRequest list1[]={
    {"cal_arr_ped_limit", fPedLimit, kInt, static_cast<UInt_t>(fNelem),1},
    {"cal_arr_cal_const", cal_arr_cal_const, kDouble, static_cast<UInt_t>(fNelem)},
    {"cal_arr_gain_cor",  cal_arr_gain_cor,  kDouble, static_cast<UInt_t>(fNelem)},
    {"cal_arr_AdcTimeWindowMin", fAdcTimeWindowMin, kDouble, static_cast<UInt_t>(fNelem),1},
    {"cal_arr_AdcTimeWindowMax", fAdcTimeWindowMax, kDouble, static_cast<UInt_t>(fNelem),1},
    {"cal_arr_PedDefault", fPedDefault, kInt, static_cast<UInt_t>(fNelem),1},
    {0}
  };

   for(Int_t ip=0;ip<fNelem;ip++) {
    fAdcTimeWindowMin[ip] = -1000.;
    fAdcTimeWindowMax[ip] = 1000.;
    fPedDefault[ip] = 0;
   }

  gHcParms->LoadParmValues((DBRequest*)&list1, prefix);

  // Debug output.
  if (static_cast<THcShower*>(fParent)->fdbg_init_cal) {

    cout << "  fPedLimit:" << endl;
    Int_t el=0;
    for (UInt_t j=0; j<fNColumns; j++) {
      cout << "    ";
      for (UInt_t i=0; i<fNRows; i++) {
	cout << fPedLimit[el++] << " ";
      };
      cout <<  endl;
    };

    cout << "  cal_arr_cal_const:" << endl;
    el=0;
    for (UInt_t j=0; j<fNColumns; j++) {
      cout << "    ";
      for (UInt_t i=0; i<fNRows; i++) {
	cout << cal_arr_cal_const[el++] << " ";
      };
      cout <<  endl;
    };

    cout << "  cal_arr_gain_cor:" << endl;
    el=0;
    for (UInt_t j=0; j<fNColumns; j++) {
      cout << "    ";
      for (UInt_t i=0; i<fNRows; i++) {
	cout << cal_arr_gain_cor[el++] << " ";
      };
      cout <<  endl;
    };

  }    // end of debug output

  // Calibration constants (GeV / ADC channel).
  fGain = new Double_t [fNelem];
  for (Int_t i=0; i<fNelem; i++) {
    fGain[i] = cal_arr_cal_const[i] *  cal_arr_gain_cor[i];
  }

  // Debug output.
  if (static_cast<THcShower*>(fParent)->fdbg_init_cal) {

    cout << "  fGain:" << endl;
    Int_t el=0;
    for (UInt_t j=0; j<fNColumns; j++) {
      cout << "    ";
      for (UInt_t i=0; i<fNRows; i++) {
	cout << fGain[el++] << " ";
      };
      cout <<  endl;
    };

  }

  fMinPeds = static_cast<THcShower*>(fParent)->GetMinPeds();

  InitializePedestals();

  // Event by event amplitude and pedestal
  //fA = new Double_t[fNelem];
  //fP = new Double_t[fNelem];
  //fA_p = new Double_t[fNelem];

  fE                       = vector<Double_t> (fNelem, 0.0);
  fNumGoodAdcHits          = vector<Int_t>    (fNelem, 0.0);
  fGoodAdcPulseIntRaw      = vector<Double_t> (fNelem, 0.0);
  fGoodAdcPed              = vector<Double_t> (fNelem, 0.0);
  fGoodAdcMult              = vector<Double_t> (fNelem, 0.0);
  fGoodAdcPulseInt         = vector<Double_t> (fNelem, 0.0);
  fGoodAdcPulseAmp         = vector<Double_t> (fNelem, 0.0);
  fGoodAdcPulseTime        = vector<Double_t> (fNelem, 0.0);
  fGoodAdcTdcDiffTime        = vector<Double_t> (fNelem, 0.0);


  fBlock_ClusterID = new Int_t[fNelem];

  // Energy depositions per block.

  //fE = new Double_t[fNelem];

  // Numbers of tracks and hits , for efficiency calculations.
  
  fStatNumTrk = vector<Int_t> (fNelem, 0);
  fStatNumHit = vector<Int_t> (fNelem, 0);
  fTotStatNumTrk = 0;
  fTotStatNumHit = 0;

#ifdef HITPIC
  hitpic = new char*[fNRows];
  for(Int_t row=0;row<fNRows;row++) {
    hitpic[row] = new char[NPERLINE*(fNColumns+1)+2];
  }
  piccolumn=0;
#endif

  // Debug output.

  if (static_cast<THcShower*>(fParent)->fdbg_init_cal) {

    cout << "  fMinPeds = " << fMinPeds << endl;

    cout << "---------------------------------------------------------------\n";
  }

  return kOK;
}

//_____________________________________________________________________________
Int_t THcShowerArray::DefineVariables( EMode mode )
{
  // Initialize global variables

  if( mode == kDefine && fIsSetup ) return kOK;
  fIsSetup = ( mode == kDefine );

  // Register counters for efficiency calculations in gHcParms so that the
  // variables can be used in end of run reports.

  gHcParms->Define(Form("%sstat_trksum_array", fParent->GetPrefix()),
		   "Number of tracks in calo. array", fTotStatNumTrk);
  gHcParms->Define(Form("%sstat_hitsum_array", fParent->GetPrefix()),
		   "Number of hits in calo. array", fTotStatNumHit);

  // Register variables in global list
  if (fDebugAdc) {
    RVarDef vars[] = {
      {"adcPedRaw",       "List of raw ADC pedestals",         "frAdcPedRaw.THcSignalHit.GetData()"},
      {"adcPulseIntRaw",  "List of raw ADC pulse integrals.",  "frAdcPulseIntRaw.THcSignalHit.GetData()"},
      {"adcPulseAmpRaw",  "List of raw ADC pulse amplitudes.", "frAdcPulseAmpRaw.THcSignalHit.GetData()"},
      {"adcPulseTimeRaw", "List of raw ADC pulse times.",      "frAdcPulseTimeRaw.THcSignalHit.GetData()"},

      {"adcPed",          "List of ADC pedestals",             "frAdcPed.THcSignalHit.GetData()"},
      {"adcPulseInt",     "List of ADC pulse integrals.",      "frAdcPulseInt.THcSignalHit.GetData()"},
      {"adcPulseAmp",     "List of ADC pulse amplitudes.",     "frAdcPulseAmp.THcSignalHit.GetData()"},
      {"adcPulseTime",    "List of ADC pulse times.",          "frAdcPulseTime.THcSignalHit.GetData()"},
      { 0 }
    };
    DefineVarsFromList( vars, mode);
  } //end debug statement

  RVarDef vars[] = {
    //{"adchits", "List of ADC hits", "fADCHits.THcSignalHit.GetPaddleNumber()"}, // appears an empty histogram in the root file

    {"adcErrorFlag",       "Error Flag When FPGA Fails",      "frAdcErrorFlag.THcSignalHit.GetData()"},

    {"adcCounter",      "List of ADC counter numbers.",      "frAdcPulseIntRaw.THcSignalHit.GetPaddleNumber()"},  //raw occupancy
    {"numGoodAdcHits", "Number of Good ADC Hits per PMT", "fNumGoodAdcHits" },                                   //good occupancy

    {"totNumAdcHits", "Total Number of ADC Hits", "fTotNumAdcHits" },                                            // raw multiplicity
    {"totNumGoodAdcHits", "Total Number of Good ADC Hits", "fTotNumGoodAdcHits" },                               // good multiplicity


    {"goodAdcPulseIntRaw", "Good Raw ADC Pulse Integrals", "fGoodAdcPulseIntRaw"},    //this is defined as pulseIntRaw, NOT ADC Amplitude in FillADC_DynamicPedestal() method
    {"goodAdcPed", "Good ADC Pedestals", "fGoodAdcPed"},
    {"goodAdcMult", "Good ADC Multiplicity", "fGoodAdcMult"},
    {"goodAdcPulseInt", "Good ADC Pulse Integrals", "fGoodAdcPulseInt"},     //this is defined as pulseInt, which is the pedestal subtracted pulse integrals, and is defined if threshold is passed
    {"goodAdcPulseAmp", "Good ADC Pulse Amplitudes", "fGoodAdcPulseAmp"},
    {"goodAdcPulseTime", "Good ADC Pulse Times", "fGoodAdcPulseTime"},     //this is defined as pulseInt, which is the pedestal subtracted pulse integrals, and is defined if threshold is passed
    {"goodAdcTdcDiffTime", "Good Hodo Starttime - ADC Pulse Times", "fGoodAdcTdcDiffTime"},     


    {"e", "Energy Depositions per block", "fE"},       //defined as fE = fA_p*fGain = pulseInt * Gain
    {"earray", "Energy Deposition in Shower Array", "fEarray"},   //defined as a Double_t and represents a sum of the total deposited energy in the shower counter

    {"nclust", "Number of clusters", "fNclust" },       //what is the difference between nclust defined here and that in THcShower.cxx ?
    {"block_clusterID", "Cluster ID number", "fBlock_ClusterID"}, // im NOT very clear about this. it is histogrammed at wither -1 or 0.
    {"ntracks", "Number of shower tracks", "fNtracks" }, //number of cluster-to-track associations
    { 0 }
  };

  return DefineVarsFromList(vars, mode );
}

//_____________________________________________________________________________
void THcShowerArray::Clear( Option_t* )
{
  // Clears the hit lists
  fADCHits->Clear();

  fTotNumAdcHits = 0;
  fTotNumGoodAdcHits = 0;
  fNclust = 0;
  fClustSize = 0;
  fNtracks = 0;
  fMatchClX = -1000.;
  fMatchClY = -1000.;
  fMatchClMaxEnergyBlock = -1000.;

  for (THcShowerClusterListIt i=fClusterList->begin(); i!=fClusterList->end();
       ++i) {
    Podd::DeleteContainer(**i);
    delete *i;
  }
  fClusterList->clear();

  frAdcPedRaw->Clear();
  frAdcErrorFlag->Clear();
  frAdcPulseIntRaw->Clear();
  frAdcPulseAmpRaw->Clear();
  frAdcPulseTimeRaw->Clear();

  frAdcPed->Clear();
  frAdcPulseInt->Clear();
  frAdcPulseAmp->Clear();
  frAdcPulseTime->Clear();

  for (UInt_t ielem = 0; ielem < fGoodAdcPed.size(); ielem++) {
    fGoodAdcPulseIntRaw.at(ielem)      = 0.0;
    fGoodAdcPed.at(ielem)              = 0.0;
    fGoodAdcMult.at(ielem)              = 0.0;
    fGoodAdcPulseInt.at(ielem)         = 0.0;
    fGoodAdcPulseAmp.at(ielem)         = 0.0;
    fGoodAdcPulseTime.at(ielem)        = kBig;
    fGoodAdcTdcDiffTime.at(ielem)        = kBig;
    fNumGoodAdcHits.at(ielem)          = 0.0;
    fE.at(ielem)                       = 0.0;
  }

}

//_____________________________________________________________________________
Int_t THcShowerArray::Decode( const THaEvData& evdata )
{
  // Doesn't actually get called.  Use Fill method instead

  return 0;
}

//_____________________________________________________________________________
Int_t THcShowerArray::CoarseProcess( TClonesArray& tracks )
{

  // Fill set of unclustered shower array hits.
  // Reuse hit class pertained to the HMS/SOS type calorimeters.
  // Save energy deposition in the module as hit mean energy, do not use
  // positive and negative side energies.

  THcShowerHitSet HitSet;         //set of hits

  UInt_t k=0;
  for(UInt_t j=0; j < fNColumns; j++) {
    for (UInt_t i=0; i<fNRows; i++) {

      if (fGoodAdcPulseInt.at(k) > 0) {    //hit

	THcShowerHit* hit =
	  new THcShowerHit(i, j, fXPos[i][j], fYPos[i][j], fZPos[i][j], fE[k], 0., 0.);

	HitSet.insert(hit);
      }

      k++;
    }
  }
  //Debug output, print out hits before clustering.

  if (static_cast<THcShower*>(fParent)->fdbg_clusters_cal) {
    cout << "---------------------------------------------------------------\n";
    cout << "Debug output from THcShowerArray::CoarseProcess for " << GetName()
	 << endl;

    cout << "  List of unclustered hits. Total hits:     " << fTotNumAdcHits << endl;
    THcShowerHitIt it = HitSet.begin();    //<set> version
    for (Int_t i=0; i!=fTotNumGoodAdcHits; i++) {
      cout << "  hit " << i << ": ";
      (*(it++))->show();
    }
  }

  ////Sanity check. (Vardan)

  // if ((int)HitSet.size() != fTotNumGoodAdcHits) {
  //	cout << "***" << endl;
  //	cout << "*** THcShowerArray::CoarseProcess: HitSet.size = " << HitSet.size()
  //	     << " != fTotNumGoodAdcHits = " << fTotNumGoodAdcHits << endl;
  //	cout << "***" << endl;
  //    }

  // Cluster hits and fill list of clusters.

  static_cast<THcShower*>(fParent)->ClusterHits(HitSet, fClusterList);
  assert( HitSet.empty() );  // else bug in ClusterHits()

  fNclust = (*fClusterList).size();         //number of clusters

  // Set cluster ID for each block
  Int_t ncl=0;
  Int_t block;
    for (THcShowerClusterListIt ppcl = (*fClusterList).begin();
	 ppcl != (*fClusterList).end(); ++ppcl) {
      for (THcShowerClusterIt pph=(**ppcl).begin(); pph!=(**ppcl).end();
	   ++pph) {
       block = ((**pph).hitColumn())*fNRows + (**pph).hitRow()+1;
       fBlock_ClusterID[block-1] = ncl;
      }
      ncl++;
    }

  //Debug output, print out clustered hits.

  if (static_cast<THcShower*>(fParent)->fdbg_clusters_cal) {

    cout << "  Clustered hits. Number of clusters: " << fNclust << endl;

    UInt_t i = 0;
    for (THcShowerClusterListIt ppcl = (*fClusterList).begin();
	 ppcl != (*fClusterList).end(); ++ppcl) {

      cout << "  Cluster #" << i++
	   <<":  E=" << clE(*ppcl)
	   << "  Epr=" << clEpr(*ppcl)
	   << "  X=" << clX(*ppcl)
	   << "  Y=" << clY(*ppcl)
	   << "  Z=" << clZ(*ppcl)
	   << "  size=" << (**ppcl).size()
	   << endl;

      Int_t j=0;
      for (THcShowerClusterIt pph=(**ppcl).begin(); pph!=(**ppcl).end();
	   ++pph) {
	cout << "  hit " << j++ << ": ";
	(**pph).show();
      }

    }

    cout << "---------------------------------------------------------------\n";
  }

  return 0;
}

//-----------------------------------------------------------------------------

Int_t THcShowerArray::MatchCluster(THaTrack* Track,
				   Double_t& XTrFront, Double_t& YTrFront)
{
  // Match an Array cluster to a given track. Return the cluster number,
  // and track coordinates at the front of Array.

  XTrFront = kBig;
  YTrFront = kBig;
  Double_t pathl = kBig;

  // Track interception with face of Array. The coordinates are
  // in the Array's local system.

  fOrigin = GetOrigin();

  static_cast<THcShower*>(fParent)->CalcTrackIntercept(Track, pathl, XTrFront, YTrFront);

  // Transform coordiantes to the spectrometer's coordinate system.

  XTrFront += GetOrigin().X();
  YTrFront += GetOrigin().Y();

  Bool_t inFidVol = true;            // In Fiducial Volume flag

  // Re-evaluate Fid. Volume Flag if fid. volume test is requested

  if (static_cast<THcShower*>(fParent)->fvTest) {

    TVector3 Origin = fOrigin;         //save fOrigin

    // Track coordinates at the back of the detector.

    // Origin at the back of counter.
    fOrigin.SetXYZ(GetOrigin().X(), GetOrigin().Y(), GetOrigin().Z() + fZSize);

    Double_t XTrBack = kBig;
    Double_t YTrBack = kBig;

    static_cast<THcShower*>(fParent)->CalcTrackIntercept(Track, pathl, XTrBack, YTrBack);

    XTrBack += GetOrigin().X();   // from local coord. system
    YTrBack += GetOrigin().Y();   // to the spectrometer system

    inFidVol = (XTrFront <= static_cast<THcShower*>(fParent)->fvXmax) && (XTrFront >= static_cast<THcShower*>(fParent)->fvXmin) &&
               (YTrFront <= static_cast<THcShower*>(fParent)->fvYmax) && (YTrFront >= static_cast<THcShower*>(fParent)->fvYmin) &&
               (XTrBack <= static_cast<THcShower*>(fParent)->fvXmax) && (XTrBack >= static_cast<THcShower*>(fParent)->fvXmin) &&
               (YTrBack <= static_cast<THcShower*>(fParent)->fvYmax) && (YTrBack >= static_cast<THcShower*>(fParent)->fvYmin);

    fOrigin = Origin;         //restore fOrigin
  }

  // Match a cluster to the track. Choose closest to the track cluster.

  Int_t mclust = -1;    // The match cluster #, initialize with a bogus value.
  Double_t Delta = kBig;   // Track to cluster distance

  if (inFidVol) {

    // Since hits and clusters are in reverse order (with respect to Engine),
    // search backwards to be consistent with Engine.

    for (Int_t i=fNclust-1; i>-1; i--) {

      THcShowerCluster* cluster = *(fClusterList->begin()+i);
      fClustSize = (*cluster).size();
      Double_t dx = TMath::Abs( clX(cluster) - XTrFront );
      Double_t dy = TMath::Abs( clY(cluster) - YTrFront );
      Double_t distance = TMath::Sqrt(dx*dx+dy*dy);        //cluster-track dist.
  if (static_cast<THcShower*>(fParent)->fdbg_tracks_cal) {
    cout << " match clust = " << i << " clX = " << clX(cluster)<< " clY = " << clY(cluster) << " distacne = " << distance << " test = " << (0.5*(fXStep + fYStep) + static_cast<THcShower*>(fParent)->fSlop) << endl;
  }

      //Choice of threshold on distance is not unuque. Use the simplest for now.

      if (distance <= (0.5*(fXStep + fYStep) + static_cast<THcShower*>(fParent)->fSlop)) {
	fNtracks++;
	if (distance < Delta) {
	  mclust = i;
          fMatchClX= clX(cluster);
          fMatchClY= clY(cluster);
          fMatchClMaxEnergyBlock=clMaxEnergyBlock(cluster);
	  Delta = distance;
	}
      }
    }
  }

  //Debug output.

  if (static_cast<THcShower*>(fParent)->fdbg_tracks_cal) {
    cout << "---------------------------------------------------------------\n";
    cout << "Debug output from THcShowerArray::MatchCluster for " << GetName()
	 << endl;

    cout << "  Track at DC:"
	 << "  X = " << Track->GetX()
	 << "  Y = " << Track->GetY()
	 << "  Theta = " << Track->GetTheta()
	 << "  Phi = " << Track->GetPhi()
	 << endl;
    cout << "  Track at the front of Array:"
	 << "  X = " << XTrFront
	 << "  Y = " << YTrFront
	 << "  Pathl = " << pathl
	 << endl;
    if (static_cast<THcShower*>(fParent)->fvTest)
      cout << "  Fiducial volume test: inFidVol = " << inFidVol << endl;

    cout << "  Matched cluster #" << mclust << ",  Delta = " << Delta << endl;
    cout << "---------------------------------------------------------------\n";
  }

  return mclust;
}

//_____________________________________________________________________________
Float_t THcShowerArray::GetShEnergy(THaTrack* Track) {

  // Get total energy deposited in the Array cluster matched to the given
  // spectrometer Track.

  // Track coordinates at the front of Array, initialize out of acceptance.
  Double_t Xtr = -100.;
  Double_t Ytr = -100.;

  // Associate a cluster to the track.

  Int_t mclust = MatchCluster(Track, Xtr, Ytr);

  // Coordinate corrected total energy deposition in the cluster.

  Float_t Etrk = 0.;
  if (mclust >= 0) {         // if there is a matched cluster

    // Get matched cluster.
    THcShowerCluster* cluster = *(fClusterList->begin()+mclust);

    // No coordinate correction for now.
    Etrk = clE(cluster);

  }   //mclust>=0

  //Debug output.

  if (static_cast<THcShower*>(fParent)->fdbg_tracks_cal) {
    cout << "---------------------------------------------------------------\n";
    cout << "Debug output from THcShowerArray::GetShEnergy for "
	 << GetName() << endl;

    cout << "  Track at Array: X = " << Xtr << "  Y = " << Ytr;
    if (mclust >= 0)
      cout << ", matched cluster #" << mclust << "." << endl;
    else
      cout << ", no matched cluster found." << endl;

    cout << "  Track's Array energy = " << Etrk << "." << endl;
    cout << "---------------------------------------------------------------\n";
  }

  return Etrk;
}

//_____________________________________________________________________________
Int_t THcShowerArray::FineProcess( TClonesArray& tracks )
{
  return 0;
}

//_____________________________________________________________________________
Int_t THcShowerArray::CoarseProcessHits()
{
    Int_t ADCMode=static_cast<THcShower*>(fParent)->GetADCMode();
    if(ADCMode == kADCDynamicPedestal) {
      FillADC_DynamicPedestal();
    } else if (ADCMode == kADCSampleIntegral) {
      FillADC_SampleIntegral();
    } else if (ADCMode == kADCSampIntDynPed) {
      FillADC_SampIntDynPed();
        } else {
      FillADC_Standard();
    }
    //
  if (static_cast<THcShower*>(fParent)->fdbg_decoded_cal) {

    cout << "---------------------------------------------------------------\n";
    cout << "Debug output from THcShowerArray::ProcessHits for "
    	 << static_cast<THcShower*>(fParent)->GetPrefix() << ":" << endl;

    cout << "  Sparsified hits for shower array, plane #" << fLayerNum
	 << ", " << GetName() << ":" << endl;

    Int_t nspar = 0;
    Int_t k=0;
    for(UInt_t j=0; j < fNColumns; j++) {
    for (UInt_t i=0; i<fNRows; i++) {
      if(fGoodAdcPulseIntRaw.at(k) > fThresh[k]) {
	cout << "  counter =  " << k
	     << "  E = " << fE[k]
	     << endl;
	nspar++;
      }
       k++;
    }
    }

    if (nspar == 0) cout << "  No hits\n";

    cout << "  Earray = " << fEarray << endl;
    cout << "---------------------------------------------------------------\n";
  }
  //
  return 1;
}
//_____________________________________________________________________________
void THcShowerArray::FillADC_SampIntDynPed()
{
  //    adc_pos = hit->GetRawAdcHitPos().GetSampleInt();
  //    adc_neg = hit->GetRawAdcHitNeg().GetSampleInt();
  //   adc_pos_pedsub = hit->GetRawAdcHitPos().GetSampleIntRaw();
  //   adc_neg_pedsub = hit->GetRawAdcHitNeg().GetSampleIntRaw();
  // Need to create
}
//_____________________________________________________________________________
void THcShowerArray::FillADC_SampleIntegral()
{
  ///			adc_pos_pedsub = hit->GetRawAdcHitPos().GetSampleIntRaw() - fPosPed[hit->fCounter -1];
  //			adc_neg_pedsub = hit->GetRawAdcHitNeg().GetSampleIntRaw() - fNegPed[hit->fCounter -1];
  //			adc_pos = hit->GetRawAdcHitPos().GetSampleIntRaw();
  //			adc_neg = hit->GetRawAdcHitNeg().GetSampleIntRaw();
  // need to create
}
//_____________________________________________________________________________
void THcShowerArray::FillADC_Standard()
{
}
//_____________________________________________________________________________
void THcShowerArray::FillADC_DynamicPedestal()
{
  Double_t StartTime = 0.0;
  if( fglHod ) StartTime = fglHod->GetStartTime();
   Double_t OffsetTime = 0.0;
   if( fglHod ) OffsetTime = fglHod->GetOffsetTime();
  for (Int_t ielem=0;ielem<frAdcPulseInt->GetEntries();ielem++) {
    
    Int_t npad           = ((THcSignalHit*) frAdcPulseInt->ConstructedAt(ielem))->GetPaddleNumber() - 1;
    Double_t pulseIntRaw = ((THcSignalHit*) frAdcPulseIntRaw->ConstructedAt(ielem))->GetData();
    Double_t pulsePed    = ((THcSignalHit*) frAdcPed->ConstructedAt(ielem))->GetData();
    Double_t pulseInt    = ((THcSignalHit*) frAdcPulseInt->ConstructedAt(ielem))->GetData();
    Double_t pulseAmp    = ((THcSignalHit*) frAdcPulseAmp->ConstructedAt(ielem))->GetData();
    Double_t pulseTime   = ((THcSignalHit*) frAdcPulseTime->ConstructedAt(ielem))->GetData();
    Double_t adctdcdiffTime = StartTime-pulseTime+OffsetTime;
    Bool_t pulseTimeCut  = (adctdcdiffTime > fAdcTimeWindowMin[npad]) &&  (adctdcdiffTime < fAdcTimeWindowMax[npad]);
	fGoodAdcMult.at(npad) += 1;
    if (pulseTimeCut) {
      
      fTotNumAdcHits++;
      fGoodAdcPulseIntRaw.at(npad) = pulseIntRaw;

      if(fGoodAdcPulseIntRaw.at(npad) >  fThresh[npad] && fGoodAdcPulseInt.at(npad)==0) {
       fTotNumGoodAdcHits++;
       fGoodAdcPulseInt.at(npad) = pulseInt;
       fE.at(npad) = fGoodAdcPulseInt.at(npad)*fGain[npad];
       fEarray += fE.at(npad);

       fGoodAdcPed.at(npad) = pulsePed;
       fGoodAdcPulseAmp.at(npad) = pulseAmp;
       fGoodAdcPulseTime.at(npad) = pulseTime;
       fGoodAdcTdcDiffTime.at(npad) = adctdcdiffTime;

       fNumGoodAdcHits.at(npad) = npad + 1;
      }
     }
   }
  //
}
//_____________________________________________________________________________
Int_t THcShowerArray::ProcessHits(TClonesArray* rawhits, Int_t nexthit)
{
  // Extract the data for this layer from hit list.

  //THcShower* fParent;
  //fParent = (THcShower*) GetParent();

  // Initialize variables.

  fADCHits->Clear();

  frAdcPedRaw->Clear();
  frAdcErrorFlag->Clear();
  frAdcPulseIntRaw->Clear();
  frAdcPulseAmpRaw->Clear();
  frAdcPulseTimeRaw->Clear();

  frAdcPed->Clear();
  frAdcPulseInt->Clear();
  frAdcPulseAmp->Clear();
  frAdcPulseTime->Clear();

  for(Int_t i=0;i<fNelem;i++) {
    //fA[i] = 0;
    //fA_p[i] = 0;
    //fE[i] = 0;

    fBlock_ClusterID[i] = -1;
  }

  fEarray = 0;
 
  // Process raw hits. Get ADC hits for the plane, assign variables for each
  // channel.

  Int_t nrawhits = rawhits->GetLast()+1;

  Int_t ihit = nexthit;

  UInt_t nrAdcHits = 0;

  while(ihit < nrawhits) {
    THcRawShowerHit* hit = (THcRawShowerHit *) rawhits->At(ihit);

    if(hit->fPlane != fLayerNum) {
      break;
    }

    Int_t padnum = hit->fCounter;
    THcRawAdcHit& rawAdcHit = hit->GetRawAdcHitPos();
    //
    for (UInt_t thit=0; thit<rawAdcHit.GetNPulses(); ++thit) {
      ((THcSignalHit*) frAdcPedRaw->ConstructedAt(nrAdcHits))->Set(padnum, rawAdcHit.GetPedRaw());
        fThresh[padnum-1]=rawAdcHit.GetPedRaw()*rawAdcHit.GetF250_PeakPedestalRatio()+fAdcThreshold;
     ((THcSignalHit*) frAdcPed->ConstructedAt(nrAdcHits))->Set(padnum, rawAdcHit.GetPed());

      ((THcSignalHit*) frAdcPulseIntRaw->ConstructedAt(nrAdcHits))->Set(padnum, rawAdcHit.GetPulseIntRaw(thit));
      ((THcSignalHit*) frAdcPulseInt->ConstructedAt(nrAdcHits))->Set(padnum, rawAdcHit.GetPulseInt(thit));

      ((THcSignalHit*) frAdcPulseAmpRaw->ConstructedAt(nrAdcHits))->Set(padnum, rawAdcHit.GetPulseAmpRaw(thit));
      ((THcSignalHit*) frAdcPulseAmp->ConstructedAt(nrAdcHits))->Set(padnum, rawAdcHit.GetPulseAmp(thit));

      ((THcSignalHit*) frAdcPulseTimeRaw->ConstructedAt(nrAdcHits))->Set(padnum, rawAdcHit.GetPulseTimeRaw(thit));
      ((THcSignalHit*) frAdcPulseTime->ConstructedAt(nrAdcHits))->Set(padnum, rawAdcHit.GetPulseTime(thit)+fAdcTdcOffset);

      if (rawAdcHit.GetPulseAmp(thit)>0&&rawAdcHit.GetPulseIntRaw(thit)>0) {
	((THcSignalHit*) frAdcErrorFlag->ConstructedAt(nrAdcHits))->Set(padnum,0);
      } else {
	((THcSignalHit*) frAdcErrorFlag->ConstructedAt(nrAdcHits))->Set(padnum,1);
      }

      if (rawAdcHit.GetPulseAmpRaw(thit) <= 0) {
	Double_t PeakPedRatio= rawAdcHit.GetF250_PeakPedestalRatio();
	Int_t NPedSamples= rawAdcHit.GetF250_NPedestalSamples();
	Double_t AdcToC =  rawAdcHit.GetAdcTopC();
	Double_t AdcToV =  rawAdcHit.GetAdcTomV();
	if (fPedDefault[padnum-1] !=0) {
	  Double_t tPulseInt = AdcToC*(rawAdcHit.GetPulseIntRaw(thit) - fPedDefault[padnum-1]*PeakPedRatio);
	  ((THcSignalHit*) frAdcPulseInt->ConstructedAt(nrAdcHits))->Set(padnum, tPulseInt);
          ((THcSignalHit*) frAdcPedRaw->ConstructedAt(nrAdcHits))->Set(padnum, fPedDefault[padnum-1]);
          ((THcSignalHit*) frAdcPed->ConstructedAt(nrAdcHits))->Set(padnum, float(fPedDefault[padnum-1])/float(NPedSamples)*AdcToV);
	  
	}
	((THcSignalHit*) frAdcPulseAmp->ConstructedAt(nrAdcHits))->Set(padnum, 0.);