THcAerogel.cxx

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#include "THcAerogel.h"
#include "THcHodoscope.h"
#include "TClonesArray.h"
#include "THcSignalHit.h"
#include "THaEvData.h"
#include "THaDetMap.h"
#include "THcDetectorMap.h"
#include "THcGlobals.h"
#include "THaCutList.h"
#include "THcParmList.h"
#include "THcHitList.h"
#include "THaApparatus.h"
#include "VarDef.h"
#include "VarType.h"
#include "THaTrack.h"
#include "TClonesArray.h"
#include "TMath.h"
#include "THaTrackProj.h"
#include "THcRawAdcHit.h"
#include "THcHallCSpectrometer.h"

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

using namespace std;

//_____________________________________________________________________________
THcAerogel::THcAerogel( const char* name, const char* description,
                        THaApparatus* apparatus ) :
  THaNonTrackingDetector(name,description,apparatus), fPresentP(0),
  fAdcPosTimeWindowMin(0), fAdcPosTimeWindowMax(0), fAdcNegTimeWindowMin(0),
  fAdcNegTimeWindowMax(0),fPedNegDefault(0),fPedPosDefault(0),
  fRegionValue(0), fPosGain(0), fNegGain(0),
  frPosAdcPedRaw(0), frPosAdcPulseIntRaw(0), frPosAdcPulseAmpRaw(0),
  frPosAdcPulseTimeRaw(0), frPosAdcPed(0), frPosAdcPulseInt(0),
  frPosAdcPulseAmp(0), frPosAdcPulseTime(0), frNegAdcPedRaw(0),
  frNegAdcPulseIntRaw(0), frNegAdcPulseAmpRaw(0), frNegAdcPulseTimeRaw(0),
  frNegAdcPed(0), frNegAdcPulseInt(0), frNegAdcPulseAmp(0),
  frNegAdcPulseTime(0), fPosAdcErrorFlag(0),
  fNegAdcErrorFlag(0), fPosPedSum(0), fPosPedSum2(0), fPosPedLimit(0),
  fPosPedCount(0), fNegPedSum(0), fNegPedSum2(0), fNegPedLimit(0), fNegPedCount(0),
  fA_Pos(0), fA_Neg(0), fA_Pos_p(0), fA_Neg_p(0), fT_Pos(0), fT_Neg(0),
  fPosPed(0), fPosSig(0), fPosThresh(0), fNegPed(0), fNegSig(0),
  fNegThresh(0), fPosPedMean(0), fNegPedMean(0),
  fPosTDCHits(0), fNegTDCHits(0), fPosADCHits(0), fNegADCHits(0)
{
}

//_____________________________________________________________________________
THcAerogel::THcAerogel( ) :
  THaNonTrackingDetector(),
  fAdcPosTimeWindowMin(0), fAdcPosTimeWindowMax(0), fAdcNegTimeWindowMin(0),
  fAdcNegTimeWindowMax(0), 
  fPedNegDefault(0),fPedPosDefault(0),fRegionValue(0), fPosGain(0), fNegGain(0),
  frPosAdcPedRaw(0), frPosAdcPulseIntRaw(0), frPosAdcPulseAmpRaw(0),
  frPosAdcPulseTimeRaw(0), frPosAdcPed(0), frPosAdcPulseInt(0),
  frPosAdcPulseAmp(0), frPosAdcPulseTime(0), frNegAdcPedRaw(0),
  frNegAdcPulseIntRaw(0), frNegAdcPulseAmpRaw(0), frNegAdcPulseTimeRaw(0),
  frNegAdcPed(0), frNegAdcPulseInt(0), frNegAdcPulseAmp(0),
  frNegAdcPulseTime(0), fPosAdcErrorFlag(0),
  fNegAdcErrorFlag(0), fPosPedSum(0), fPosPedSum2(0), fPosPedLimit(0),
  fPosPedCount(0), fNegPedSum(0), fNegPedSum2(0), fNegPedLimit(0), fNegPedCount(0),
  fA_Pos(0), fA_Neg(0), fA_Pos_p(0), fA_Neg_p(0), fT_Pos(0), fT_Neg(0),
  fPosPed(0), fPosSig(0), fPosThresh(0), fNegPed(0), fNegSig(0),
  fNegThresh(0), fPosPedMean(0), fNegPedMean(0),
  fPosTDCHits(0), fNegTDCHits(0), fPosADCHits(0), fNegADCHits(0)
{
}

//_____________________________________________________________________________
THcAerogel::~THcAerogel()
{
  // Destructor
  DeleteArrays();
}

//_____________________________________________________________________________
void THcAerogel::DeleteArrays()
{
  // Delete all dynamically allocated memory

  delete frPosAdcPedRaw;       frPosAdcPedRaw       = NULL;
  delete frPosAdcPulseIntRaw;  frPosAdcPulseIntRaw  = NULL;
  delete frPosAdcPulseAmpRaw;  frPosAdcPulseAmpRaw  = NULL;
  delete frPosAdcPulseTimeRaw; frPosAdcPulseTimeRaw = NULL;
  delete frPosAdcPed;          frPosAdcPed          = NULL;
  delete frPosAdcPulseInt;     frPosAdcPulseInt     = NULL;
  delete frPosAdcPulseAmp;     frPosAdcPulseAmp     = NULL;
  delete frPosAdcPulseTime;    frPosAdcPulseTime    = NULL;
  delete frNegAdcPedRaw;       frNegAdcPedRaw       = NULL;
  delete frNegAdcPulseIntRaw;  frNegAdcPulseIntRaw  = NULL;
  delete frNegAdcPulseAmpRaw;  frNegAdcPulseAmpRaw  = NULL;
  delete frNegAdcPulseTimeRaw; frNegAdcPulseTimeRaw = NULL;
  delete frNegAdcPed;          frNegAdcPed          = NULL;
  delete frNegAdcPulseInt;     frNegAdcPulseInt     = NULL;
  delete frNegAdcPulseAmp;     frNegAdcPulseAmp     = NULL;
  delete frNegAdcPulseTime;    frNegAdcPulseTime    = NULL;
  delete fPosAdcErrorFlag;     fPosAdcErrorFlag     = NULL;
  delete fNegAdcErrorFlag;     fNegAdcErrorFlag     = NULL;

  delete [] fRegionValue;         fRegionValue = 0;
  delete [] fAdcPosTimeWindowMin; fAdcPosTimeWindowMin = 0;
  delete [] fAdcPosTimeWindowMax; fAdcPosTimeWindowMax = 0;
  delete [] fAdcNegTimeWindowMin; fAdcNegTimeWindowMin = 0;
  delete [] fAdcNegTimeWindowMax; fAdcNegTimeWindowMax = 0;
  delete [] fPedNegDefault; fPedNegDefault = 0;
  delete [] fPedPosDefault; fPedPosDefault = 0;

  // 6 GeV variables
  delete fPosTDCHits; fPosTDCHits = NULL;
  delete fNegTDCHits; fNegTDCHits = NULL;
  delete fPosADCHits; fPosADCHits = NULL;
  delete fNegADCHits; fNegADCHits = NULL;

  delete [] fPosGain; fPosGain = NULL;
  delete [] fNegGain; fNegGain = NULL;

  delete [] fA_Pos;       fA_Pos       = NULL;
  delete [] fA_Neg;       fA_Neg       = NULL;
  delete [] fA_Pos_p;     fA_Pos_p     = NULL;
  delete [] fA_Neg_p;     fA_Neg_p     = NULL;
  delete [] fT_Pos;       fT_Pos       = NULL;
  delete [] fT_Neg;       fT_Neg       = NULL;

  if (fSixGevData)
    DeletePedestalArrays();
}

//_____________________________________________________________________________
void THcAerogel::DeletePedestalArrays()
{
  // Delete all dynamically allocated memory for pedestal processing

  delete [] fPosPedLimit; fPosPedLimit = NULL;
  delete [] fNegPedLimit; fNegPedLimit = NULL;
  delete [] fPosPedMean;  fPosPedMean  = NULL;
  delete [] fNegPedMean;  fNegPedMean  = NULL;
  delete [] fPosPedSum;   fPosPedSum   = NULL;
  delete [] fPosPedSum2;  fPosPedSum2  = NULL;
  delete [] fPosPedCount; fPosPedCount = NULL;
  delete [] fNegPedSum;   fNegPedSum   = NULL;
  delete [] fNegPedSum2;  fNegPedSum2  = NULL;
  delete [] fNegPedCount; fNegPedCount = NULL;
  delete [] fPosPed;      fPosPed      = NULL;
  delete [] fPosSig;      fPosSig      = NULL;
  delete [] fPosThresh;   fPosThresh   = NULL;
  delete [] fNegPed;      fNegPed      = NULL;
  delete [] fNegSig;      fNegSig      = NULL;
  delete [] fNegThresh;   fNegThresh   = NULL;
}

//_____________________________________________________________________________
THaAnalysisObject::EStatus THcAerogel::Init( const TDatime& date )
{

  // cout << "THcAerogel::Init for: " << GetName() << endl;

  char EngineDID[] = "xAERO";
  EngineDID[0] = toupper(GetApparatus()->GetName()[0]);
  if( gHcDetectorMap->FillMap(fDetMap, EngineDID) < 0 ) {
    static const char* const here = "Init()";
    Error( Here(here), "Error filling detectormap for %s.", EngineDID );
    return kInitError;
  }

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

  // Should probably put this in ReadDatabase as we will know the
  // maximum number of hits after setting up the detector map
  InitHitList(fDetMap, "THcAerogelHit", fDetMap->GetTotNumChan()+1,
              0, fADC_RefTimeCut);

 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");
  }

  fPresentP = 0;
  THaVar* vpresent = gHaVars->Find(Form("%s.present",GetApparatus()->GetName()));
  if(vpresent) {
    fPresentP = (Bool_t *) vpresent->GetValuePointer();
  }
  return fStatus = kOK;
}

//_____________________________________________________________________________
Int_t THcAerogel::ReadDatabase( const TDatime& date )
{
  // This function is called by THaDetectorBase::Init() once at the beginning
  // of the analysis.

  // cout << "THcAerogel::ReadDatabase for: " << GetName() << endl;

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

  CreateMissReportParms(Form("%saero",prefix));

  fNRegions = 1;   // Default if not set in parameter file

  DBRequest listextra[]={
    {"aero_num_pairs", &fNelem, kInt},
    {0}
  };

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

  Bool_t optional = true;

  cout << "Created aerogel detector " << GetApparatus()->GetName() << "."
       << GetName() << " with " << fNelem << " PMT pairs" << endl;

  DeleteArrays(); // avoid memory leak when reinitializing

  fPosGain = new Double_t[fNelem];
  fNegGain = new Double_t[fNelem];

  // 6 GeV variables
  fTdcOffset   = 0; // Offset to make reference time subtracted times positve
  fA_Pos       = new Float_t[fNelem];
  fA_Neg       = new Float_t[fNelem];
  fA_Pos_p     = new Float_t[fNelem];
  fA_Neg_p     = new Float_t[fNelem];
  fT_Pos       = new Float_t[fNelem];
  fT_Neg       = new Float_t[fNelem];

  // Normal constructor with name and description
  frPosAdcPedRaw       = new TClonesArray("THcSignalHit", fNelem*MaxNumAdcPulse);
  frPosAdcPulseIntRaw  = new TClonesArray("THcSignalHit", fNelem*MaxNumAdcPulse);
  frPosAdcPulseAmpRaw  = new TClonesArray("THcSignalHit", fNelem*MaxNumAdcPulse);
  frPosAdcPulseTimeRaw = new TClonesArray("THcSignalHit", fNelem*MaxNumAdcPulse);
  frPosAdcPed          = new TClonesArray("THcSignalHit", fNelem*MaxNumAdcPulse);
  frPosAdcPulseInt     = new TClonesArray("THcSignalHit", fNelem*MaxNumAdcPulse);
  frPosAdcPulseAmp     = new TClonesArray("THcSignalHit", fNelem*MaxNumAdcPulse);
  frPosAdcPulseTime    = new TClonesArray("THcSignalHit", fNelem*MaxNumAdcPulse);
  frNegAdcPedRaw       = new TClonesArray("THcSignalHit", fNelem*MaxNumAdcPulse);
  frNegAdcPulseIntRaw  = new TClonesArray("THcSignalHit", fNelem*MaxNumAdcPulse);
  frNegAdcPulseAmpRaw  = new TClonesArray("THcSignalHit", fNelem*MaxNumAdcPulse);
  frNegAdcPulseTimeRaw = new TClonesArray("THcSignalHit", fNelem*MaxNumAdcPulse);
  frNegAdcPed          = new TClonesArray("THcSignalHit", fNelem*MaxNumAdcPulse);
  frNegAdcPulseInt     = new TClonesArray("THcSignalHit", fNelem*MaxNumAdcPulse);
  frNegAdcPulseAmp     = new TClonesArray("THcSignalHit", fNelem*MaxNumAdcPulse);
  frNegAdcPulseTime    = new TClonesArray("THcSignalHit", fNelem*MaxNumAdcPulse);
  fPosAdcErrorFlag     = new TClonesArray("THcSignalHit", fNelem*MaxNumAdcPulse);
  fNegAdcErrorFlag     = new TClonesArray("THcSignalHit", fNelem*MaxNumAdcPulse);

  fNumPosAdcHits.assign(fNelem, 0);
  fNumGoodPosAdcHits.assign(fNelem, 0);
  fNumNegAdcHits.assign(fNelem, 0);
  fNumGoodNegAdcHits.assign(fNelem, 0);
  fNumTracksMatched.assign(fNelem, 0);
  fNumTracksFired.assign(fNelem, 0);
  fPosNpe.assign(fNelem, 0.0);
  fNegNpe.assign(fNelem, 0.0);
  fGoodPosAdcPed.assign(fNelem, 0.0);
  fGoodPosAdcMult.assign(fNelem, 0.0);
  fGoodPosAdcPulseInt.assign(fNelem, 0.0);
  fGoodPosAdcPulseIntRaw.assign(fNelem, 0.0);
  fGoodPosAdcPulseAmp.assign(fNelem, 0.0);
  fGoodPosAdcPulseTime.assign(fNelem, 0.0);
  fGoodPosAdcTdcDiffTime.assign(fNelem, 0.0);
  fGoodNegAdcPed.assign(fNelem, 0.0);
  fGoodNegAdcMult.assign(fNelem, 0.0);
  fGoodNegAdcPulseInt.assign(fNelem, 0.0);
  fGoodNegAdcPulseIntRaw.assign(fNelem, 0.0);
  fGoodNegAdcPulseAmp.assign(fNelem, 0.0);
  fGoodNegAdcPulseTime.assign(fNelem, 0.0);
  fGoodNegAdcTdcDiffTime.assign(fNelem, 0.0);

  // 6 GeV variables
  fPosTDCHits = new TClonesArray("THcSignalHit", fNelem*16);
  fNegTDCHits = new TClonesArray("THcSignalHit", fNelem*16);
  fPosADCHits = new TClonesArray("THcSignalHit", fNelem*MaxNumAdcPulse);
  fNegADCHits = new TClonesArray("THcSignalHit", fNelem*MaxNumAdcPulse);

  fPosNpeSixGev.assign(fNelem, 0.0);
  fNegNpeSixGev.assign(fNelem, 0.0);

  // Region parameters
  fRegionsValueMax = fNRegions * 8;
  fRegionValue         = new Double_t[fRegionsValueMax];

  fAdcPosTimeWindowMin = new Double_t [fNelem];
  fAdcPosTimeWindowMax = new Double_t [fNelem];
  fAdcNegTimeWindowMin = new Double_t [fNelem];
  fAdcNegTimeWindowMax = new Double_t [fNelem];
  fPedNegDefault = new Int_t [fNelem];
  fPedPosDefault = new Int_t [fNelem];

  DBRequest list[]={
    {"aero_num_regions",      &fNRegions,         kInt},
    {"aero_red_chi2_min",     &fRedChi2Min,       kDouble},
    {"aero_red_chi2_max",     &fRedChi2Max,       kDouble},
    {"aero_beta_min",         &fBetaMin,          kDouble},
    {"aero_beta_max",         &fBetaMax,          kDouble},
    {"aero_enorm_min",        &fENormMin,         kDouble},
    {"aero_enorm_max",        &fENormMax,         kDouble},
    {"aero_dp_min",           &fDpMin,            kDouble},
    {"aero_dp_max",           &fDpMax,            kDouble},
    {"aero_diff_box_zpos",    &fDiffBoxZPos,      kDouble},
    {"aero_npe_thresh",       &fNpeThresh,        kDouble},
    {"aero_adcPosTimeWindowMin", fAdcPosTimeWindowMin, kDouble, static_cast<UInt_t>(fNelem), 1},
    {"aero_adcPosTimeWindowMax", fAdcPosTimeWindowMax, kDouble, static_cast<UInt_t>(fNelem), 1},
    {"aero_adcNegTimeWindowMin", fAdcNegTimeWindowMin, kDouble, static_cast<UInt_t>(fNelem), 1},
    {"aero_adcNegTimeWindowMax", fAdcNegTimeWindowMax, kDouble, static_cast<UInt_t>(fNelem), 1},
    {"aero_PedNegDefault", fPedNegDefault, kInt, static_cast<UInt_t>(fNelem), 1},
    {"aero_PedPosDefault", fPedPosDefault, kInt, static_cast<UInt_t>(fNelem), 1},
    {"aero_adc_tdc_offset",   &fAdcTdcOffset,     kDouble, 0, 1},
    {"aero_debug_adc",        &fDebugAdc,         kInt,    0, 1},
    {"aero_six_gev_data",     &fSixGevData,       kInt,    0, 1},
    {"aero_pos_gain",         fPosGain,           kDouble, (UInt_t) fNelem},
    {"aero_neg_gain",         fNegGain,           kDouble, (UInt_t) fNelem},
    {"aero_tdc_offset",       &fTdcOffset,        kInt,    0,               optional},
    {"aero_region",           &fRegionValue[0],   kDouble, (UInt_t) fRegionsValueMax},
    {"aero_adcrefcut",        &fADC_RefTimeCut,   kInt,    0, 1},
    {0}
  };

  for(Int_t ip=0;ip<fNelem;ip++) {
   fAdcPosTimeWindowMin[ip] = -1000.;
   fAdcNegTimeWindowMin[ip] = -1000.;
   fAdcPosTimeWindowMax[ip] = 1000.;
   fAdcNegTimeWindowMax[ip] = 1000.;
   fPedNegDefault[ip] = 0.;
   fPedPosDefault[ip] = 0.;
  }

  fSixGevData = 0; // Set 6 GeV data parameter to false unless set in parameter file
  fDebugAdc   = 0; // Set ADC debug parameter to false unless set in parameter file
  fAdcTdcOffset = 0.0;
  fADC_RefTimeCut = 0;

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

  if (fSixGevData) {
    // Create arrays to hold pedestal results
    InitializePedestals();

    DBRequest list2[]={
      {"aero_pos_ped_limit",    fPosPedLimit,       kInt,    (UInt_t) fNelem, optional},
      {"aero_neg_ped_limit",    fNegPedLimit,       kInt,    (UInt_t) fNelem, optional},
      {"aero_pos_ped_mean",     fPosPedMean,        kDouble, (UInt_t) fNelem, optional},
      {"aero_neg_ped_mean",     fNegPedMean,        kDouble, (UInt_t) fNelem, optional},
      {"aero_min_peds",         &fMinPeds,          kInt,    0,               optional},
      {0}
    };
    gHcParms->LoadParmValues((DBRequest*)&list2, prefix);

    cout << "6 GeV Data Analysis Flag Set To TRUE" << endl;
  }

  fIsInit = true;

  // cout << "Track Matching Parameters for: " << GetApparatus()->GetName()
  //      << "." << GetName() << endl;
  // for (Int_t iregion = 0; iregion < fNRegions; iregion++) {
  //   cout << "Region = " << iregion + 1 << endl;
  //   for (Int_t ivalue = 0; ivalue < 8; ivalue++)
  //     cout << fRegionValue[GetIndex(iregion, ivalue)] << "  ";
  //   cout << endl;
  // }

  return kOK;
}

//_____________________________________________________________________________
Int_t THcAerogel::DefineVariables( EMode mode )
{
  // Initialize global variables for histogramming and tree

  // cout << "THcAerogel::DefineVariables called for: " << GetName() << endl;

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

  // Register variables in global list

  // Do we need to put the number of pos/neg TDC/ADC hits into the variables?
  // No.  They show up in tree as Ndata.H.aero.postdchits for example

  if (fDebugAdc) {
    RVarDef vars[] = {
      {"posGain", "Positive PMT gains", "fPosGain"},
      {"negGain", "Negative PMT gains", "fNegGain"},

      {"numPosAdcHits",        "Number of Positive ADC Hits Per PMT",      "fNumPosAdcHits"},        // Aerogel occupancy
      {"totNumPosAdcHits",     "Total Number of Positive ADC Hits",        "fTotNumPosAdcHits"},     // Aerogel multiplicity
      {"numNegAdcHits",        "Number of Negative ADC Hits Per PMT",      "fNumNegAdcHits"},        // Aerogel occupancy
      {"totNumNegAdcHits",     "Total Number of Negative ADC Hits",        "fTotNumNegAdcHits"},     // Aerogel multiplicity
      {"totnumAdcHits",       "Total Number of ADC Hits Per PMT",          "fTotNumAdcHits"},        // Aerogel multiplicity

      {"posAdcPedRaw",       "Positive Raw ADC pedestals",        "frPosAdcPedRaw.THcSignalHit.GetData()"},
      {"posAdcPulseIntRaw",  "Positive Raw ADC pulse integrals",  "frPosAdcPulseIntRaw.THcSignalHit.GetData()"},
      {"posAdcPulseAmpRaw",  "Positive Raw ADC pulse amplitudes", "frPosAdcPulseAmpRaw.THcSignalHit.GetData()"},
      {"posAdcPulseTimeRaw", "Positive Raw ADC pulse times",      "frPosAdcPulseTimeRaw.THcSignalHit.GetData()"},
      {"posAdcPed",          "Positive ADC pedestals",            "frPosAdcPed.THcSignalHit.GetData()"},
      {"posAdcPulseInt",     "Positive ADC pulse integrals",      "frPosAdcPulseInt.THcSignalHit.GetData()"},
      {"posAdcPulseAmp",     "Positive ADC pulse amplitudes",     "frPosAdcPulseAmp.THcSignalHit.GetData()"},
      {"posAdcPulseTime",    "Positive ADC pulse times",          "frPosAdcPulseTime.THcSignalHit.GetData()"},

      {"negAdcPedRaw",       "Negative Raw ADC pedestals",        "frNegAdcPedRaw.THcSignalHit.GetData()"},
      {"negAdcPulseIntRaw",  "Negative Raw ADC pulse integrals",  "frNegAdcPulseIntRaw.THcSignalHit.GetData()"},
      {"negAdcPulseAmpRaw",  "Negative Raw ADC pulse amplitudes", "frNegAdcPulseAmpRaw.THcSignalHit.GetData()"},
      {"negAdcPulseTimeRaw", "Negative Raw ADC pulse times",      "frNegAdcPulseTimeRaw.THcSignalHit.GetData()"},
      {"negAdcPed",          "Negative ADC pedestals",            "frNegAdcPed.THcSignalHit.GetData()"},
      {"negAdcPulseInt",     "Negative ADC pulse integrals",      "frNegAdcPulseInt.THcSignalHit.GetData()"},
      {"negAdcPulseAmp",     "Negative ADC pulse amplitudes",     "frNegAdcPulseAmp.THcSignalHit.GetData()"},
      {"negAdcPulseTime",    "Negative ADC pulse times",          "frNegAdcPulseTime.THcSignalHit.GetData()"},
      { 0 }
    };
    DefineVarsFromList( vars, mode);
  } //end debug statement

  if (fSixGevData) {
    RVarDef vars[] = {
      {"apos",            "Positive Raw ADC Amplitudes",            "fA_Pos"},
      {"aneg",            "Negative Raw ADC Amplitudes",            "fA_Neg"},
      {"apos_p",          "Positive Ped-subtracted ADC Amplitudes", "fA_Pos_p"},
      {"aneg_p",          "Negative Ped-subtracted ADC Amplitudes", "fA_Neg_p"},
      {"tpos",            "Positive Raw TDC",                       "fT_Pos"},
      {"tneg",            "Negative Raw TDC",                       "fT_Neg"},
      {"ntdc_pos_hits",   "Number of Positive Tube Hits",           "fNTDCPosHits"},
      {"ntdc_neg_hits",   "Number of Negative Tube Hits",           "fNTDCNegHits"},
      {"posadchits",      "Positive ADC hits",                      "fPosADCHits.THcSignalHit.GetPaddleNumber()"},
      {"negadchits",      "Negative ADC hits",                      "fNegADCHits.THcSignalHit.GetPaddleNumber()"},
      {"postdchits",      "Positive TDC hits",                      "fPosTDCHits.THcSignalHit.GetPaddleNumber()"},
      {"negtdchits",      "Negative TDC hits",                      "fNegTDCHits.THcSignalHit.GetPaddleNumber()"},
      {"nGoodHits",       "Total number of good hits",              "fNGoodHits"},
      {"posNpeSixGev",    "Number of Positive PEs",                 "fPosNpeSixGev"},
      {"negNpeSixGev",    "Number of Negative PEs",                 "fNegNpeSixGev"},
      {"posNpeSumSixGev", "Total Number of Positive PEs",           "fPosNpeSumSixGev"},
      {"negNpeSumSixGev", "Total Number of Negative PEs",           "fNegNpeSumSixGev"},
      {"npeSumSixGev",    "Total Number of PEs",                    "fNpeSumSixGev"},
      { 0 }
    };
    DefineVarsFromList( vars, mode);
  } //end fSixGevData statement

  RVarDef vars[] = {
    {"posAdcCounter",   "Positive ADC counter numbers",   "frPosAdcPulseIntRaw.THcSignalHit.GetPaddleNumber()"},
    {"negAdcCounter",   "Negative ADC counter numbers",   "frNegAdcPulseIntRaw.THcSignalHit.GetPaddleNumber()"},
    {"posAdcErrorFlag", "Error Flag for When FPGA Fails", "fPosAdcErrorFlag.THcSignalHit.GetData()"},
    {"negAdcErrorFlag", "Error Flag for When FPGA Fails", "fNegAdcErrorFlag.THcSignalHit.GetData()"},

    {"numGoodPosAdcHits",    "Number of Good Positive ADC Hits Per PMT", "fNumGoodPosAdcHits"},    // Aerogel occupancy
    {"numGoodNegAdcHits",    "Number of Good Negative ADC Hits Per PMT", "fNumGoodNegAdcHits"},    // Aerogel occupancy
    {"totNumGoodPosAdcHits", "Total Number of Good Positive ADC Hits",   "fTotNumGoodPosAdcHits"}, // Aerogel multiplicity
    {"totNumGoodNegAdcHits", "Total Number of Good Negative ADC Hits",   "fTotNumGoodNegAdcHits"}, // Aerogel multiplicity

    {"totnumGoodAdcHits",   "TotalNumber of Good ADC Hits Per PMT",      "fTotNumGoodAdcHits"},    // Aerogel multiplicity
    {"numTracksMatched",    "Number of Tracks Matched Per Region",       "fNumTracksMatched"},
    {"numTracksFired",      "Number of Tracks that Fired Per Region",    "fNumTracksFired"},
    {"totNumTracksMatched", "Total Number of Tracks Matched Per Region", "fTotNumTracksMatched"},
    {"totNumTracksFired",   "Total Number of Tracks that Fired",         "fTotNumTracksFired"},

    {"xAtAero",       "Track X at Aero diffusion box",    "fXAtAero"},
    {"yAtAero",       "Track Y at Aero diffusion box",    "fYAtAero"},

    {"posNpe",    "Number of Positive PEs",       "fPosNpe"},
    {"negNpe",    "Number of Negative PEs",       "fNegNpe"},
    {"posNpeSum", "Total Number of Positive PEs", "fPosNpeSum"},
    {"negNpeSum", "Total Number of Negative PEs", "fNegNpeSum"},
    {"npeSum",    "Total Number of PEs",          "fNpeSum"},

    {"goodPosAdcPed",         "Good Negative ADC pedestals",           "fGoodPosAdcPed"},
    {"goodPosAdcMult",         "Good Positive ADC mult",           "fGoodPosAdcMult"},
    {"goodPosAdcPulseInt",    "Good Negative ADC pulse integrals",     "fGoodPosAdcPulseInt"},
    {"goodPosAdcPulseIntRaw", "Good Negative ADC raw pulse integrals", "fGoodPosAdcPulseIntRaw"},
    {"goodPosAdcPulseAmp",    "Good Negative ADC pulse amplitudes",    "fGoodPosAdcPulseAmp"},
    {"goodPosAdcPulseTime",   "Good Negative ADC pulse times",         "fGoodPosAdcPulseTime"},
    {"goodPosAdcTdcDiffTime",   "Good Positive hodo Start - ADC pulse times",         "fGoodPosAdcTdcDiffTime"},

    {"goodNegAdcPed",         "Good Negative ADC pedestals",           "fGoodNegAdcPed"},
    {"goodNegAdcMult",         "Good Negative ADC Mult",           "fGoodNegAdcMult"},
    {"goodNegAdcPulseInt",    "Good Negative ADC pulse integrals",     "fGoodNegAdcPulseInt"},
    {"goodNegAdcPulseIntRaw", "Good Negative ADC raw pulse integrals", "fGoodNegAdcPulseIntRaw"},
    {"goodNegAdcPulseAmp",    "Good Negative ADC pulse amplitudes",    "fGoodNegAdcPulseAmp"},
    {"goodNegAdcPulseTime",   "Good Negative ADC pulse times",         "fGoodNegAdcPulseTime"},
    {"goodNegAdcTdcDiffTime",   "Good Negative hodo Start - ADC pulse times",         "fGoodNegAdcTdcDiffTime"},
    { 0 }
  };

  return DefineVarsFromList(vars, mode);
}
//_____________________________________________________________________________
inline
void THcAerogel::Clear(Option_t* opt)
{
  // Clear the hit lists
  fNhits                = 0;
  fTotNumAdcHits        = 0;
  fTotNumGoodAdcHits    = 0;
  fTotNumPosAdcHits     = 0;
  fTotNumNegAdcHits     = 0;
  fTotNumGoodPosAdcHits = 0;
  fTotNumGoodNegAdcHits = 0;
  fTotNumTracksMatched  = 0;
  fTotNumTracksFired    = 0;

  fXAtAero   = 0.0;
  fYAtAero   = 0.0;

  fNpeSum    = 0.0;
  fPosNpeSum = 0.0;
  fNegNpeSum = 0.0;

  frPosAdcPedRaw->Clear();
  frPosAdcPulseIntRaw->Clear();
  frPosAdcPulseAmpRaw->Clear();
  frPosAdcPulseTimeRaw->Clear();
  frPosAdcPed->Clear();
  frPosAdcPulseInt->Clear();
  frPosAdcPulseAmp->Clear();
  frPosAdcPulseTime->Clear();

  frNegAdcPedRaw->Clear();
  frNegAdcPulseIntRaw->Clear();
  frNegAdcPulseAmpRaw->Clear();
  frNegAdcPulseTimeRaw->Clear();
  frNegAdcPed->Clear();
  frNegAdcPulseInt->Clear();
  frNegAdcPulseAmp->Clear();
  frNegAdcPulseTime->Clear();

  fPosAdcErrorFlag->Clear();
  fNegAdcErrorFlag->Clear();

  for (UInt_t ielem = 0; ielem < fNumPosAdcHits.size(); ielem++)
    fNumPosAdcHits.at(ielem) = 0;
  for (UInt_t ielem = 0; ielem < fNumNegAdcHits.size(); ielem++)
    fNumNegAdcHits.at(ielem) = 0;
  for (UInt_t ielem = 0; ielem < fNumGoodPosAdcHits.size(); ielem++)
    fNumGoodPosAdcHits.at(ielem) = 0;
  for (UInt_t ielem = 0; ielem < fNumGoodNegAdcHits.size(); ielem++)
    fNumGoodNegAdcHits.at(ielem) = 0;
  for (UInt_t ielem = 0; ielem < fNumTracksMatched.size(); ielem++)
    fNumTracksMatched.at(ielem) = 0;
  for (UInt_t ielem = 0; ielem < fNumTracksFired.size(); ielem++)
    fNumTracksFired.at(ielem) = 0;

  for (UInt_t ielem = 0; ielem < fGoodPosAdcPed.size(); ielem++) {
    fGoodPosAdcPed.at(ielem)         = 0.0;
    fGoodPosAdcMult.at(ielem)         = 0.0;
    fGoodPosAdcPulseInt.at(ielem)    = 0.0;
    fGoodPosAdcPulseIntRaw.at(ielem) = 0.0;
    fGoodPosAdcPulseAmp.at(ielem)    = 0.0;
    fGoodPosAdcPulseTime.at(ielem)   = kBig;
    fGoodPosAdcTdcDiffTime.at(ielem)   = kBig;
    fPosNpe.at(ielem)                = 0.0;
  }
  for (UInt_t ielem = 0; ielem < fGoodNegAdcPed.size(); ielem++) {
    fGoodNegAdcPed.at(ielem)         = 0.0;
    fGoodNegAdcMult.at(ielem)         = 0.0;
    fGoodNegAdcPulseInt.at(ielem)    = 0.0;
    fGoodNegAdcPulseIntRaw.at(ielem) = 0.0;
    fGoodNegAdcPulseAmp.at(ielem)    = 0.0;
    fGoodNegAdcPulseTime.at(ielem)   = kBig;
    fGoodNegAdcTdcDiffTime.at(ielem)   = kBig;
    fNegNpe.at(ielem)                = 0.0;
  }

  // 6 GeV variables
  fNGoodHits       = 0;
  fNADCPosHits     = 0;
  fNADCNegHits     = 0;
  fNTDCPosHits     = 0;
  fNTDCNegHits     = 0;
  fNpeSumSixGev    = 0.0;
  fPosNpeSumSixGev = 0.0;
  fNegNpeSumSixGev = 0.0;
  fPosTDCHits->Clear();
  fNegTDCHits->Clear();
  fPosADCHits->Clear();
  fNegADCHits->Clear();

  for (UInt_t ielem = 0; ielem < fPosNpeSixGev.size(); ielem++)
    fPosNpeSixGev.at(ielem) = 0.0;
  for (UInt_t ielem = 0; ielem < fNegNpeSixGev.size(); ielem++)
    fNegNpeSixGev.at(ielem) = 0.0;

  for(Int_t itube = 0;itube < fNelem;itube++) {
    fA_Pos[itube]   = 0;
    fA_Neg[itube]   = 0;
    fA_Pos_p[itube] = 0;
    fA_Neg_p[itube] = 0;
    fT_Pos[itube]   = 0;
    fT_Neg[itube]   = 0;
  }

}

//_____________________________________________________________________________
Int_t THcAerogel::Decode( const THaEvData& evdata )
{
  // Get the Hall C style hitlist (fRawHitList) for this event
  Bool_t present = kTRUE;       // Suppress reference time warnings
  if(fPresentP) {               // if this spectrometer not part of trigger
    present = *fPresentP;
  }
  fNhits = DecodeToHitList(evdata, !present);

  if (fSixGevData) {
    if(gHaCuts->Result("Pedestal_event")) {
      AccumulatePedestals(fRawHitList);
      fAnalyzePedestals = 1;    // Analyze pedestals first normal events
      return(0);
    }
    if(fAnalyzePedestals) {
      CalculatePedestals();
      Print("");
      fAnalyzePedestals = 0;    // Don't analyze pedestals next event
    }
  }

  Int_t  ihit         = 0;
  UInt_t nrPosAdcHits = 0;
  UInt_t nrNegAdcHits = 0;

  while(ihit < fNhits) {
    THcAerogelHit* hit          = (THcAerogelHit*) fRawHitList->At(ihit);
    Int_t          npmt         = hit->fCounter;
    THcRawAdcHit&  rawPosAdcHit = hit->GetRawAdcHitPos();
    THcRawAdcHit&  rawNegAdcHit = hit->GetRawAdcHitNeg();

    for (UInt_t thit=0; thit<rawPosAdcHit.GetNPulses(); ++thit) {

      ((THcSignalHit*) frPosAdcPedRaw->ConstructedAt(nrPosAdcHits))->Set(npmt, rawPosAdcHit.GetPedRaw());
      ((THcSignalHit*) frPosAdcPed->ConstructedAt(nrPosAdcHits))->Set(npmt, rawPosAdcHit.GetPed());

      ((THcSignalHit*) frPosAdcPulseIntRaw->ConstructedAt(nrPosAdcHits))->Set(npmt, rawPosAdcHit.GetPulseIntRaw(thit));
      ((THcSignalHit*) frPosAdcPulseInt->ConstructedAt(nrPosAdcHits))->Set(npmt, rawPosAdcHit.GetPulseInt(thit));

      ((THcSignalHit*) frPosAdcPulseAmpRaw->ConstructedAt(nrPosAdcHits))->Set(npmt, rawPosAdcHit.GetPulseAmpRaw(thit));
      ((THcSignalHit*) frPosAdcPulseAmp->ConstructedAt(nrPosAdcHits))->Set(npmt, rawPosAdcHit.GetPulseAmp(thit));

      ((THcSignalHit*) frPosAdcPulseTimeRaw->ConstructedAt(nrPosAdcHits))->Set(npmt, rawPosAdcHit.GetPulseTimeRaw(thit));
      ((THcSignalHit*) frPosAdcPulseTime->ConstructedAt(nrPosAdcHits))->Set(npmt, rawPosAdcHit.GetPulseTime(thit)+fAdcTdcOffset);

      if (rawPosAdcHit.GetPulseAmpRaw(thit) > 0)  ((THcSignalHit*) fPosAdcErrorFlag->ConstructedAt(nrPosAdcHits))->Set(npmt, 0);
      if (rawPosAdcHit.GetPulseAmpRaw(thit) <= 0) ((THcSignalHit*) fPosAdcErrorFlag->ConstructedAt(nrPosAdcHits))->Set(npmt, 1);
 
     if (rawPosAdcHit.GetPulseAmpRaw(thit) <= 0) {
        Double_t PeakPedRatio= rawPosAdcHit.GetF250_PeakPedestalRatio();
        Int_t NPedSamples= rawPosAdcHit.GetF250_NPedestalSamples();
        Double_t AdcToC =  rawPosAdcHit.GetAdcTopC();
        Double_t AdcToV =  rawPosAdcHit.GetAdcTomV();
        if (fPedPosDefault[npmt-1] !=0) {
          Double_t tPulseInt = AdcToC*(rawPosAdcHit.GetPulseIntRaw(thit) - fPedPosDefault[npmt-1]*PeakPedRatio);
          ((THcSignalHit*) frPosAdcPulseInt->ConstructedAt(nrPosAdcHits))->Set(npmt, tPulseInt);
          ((THcSignalHit*) frPosAdcPedRaw->ConstructedAt(nrPosAdcHits))->Set(npmt, fPedPosDefault[npmt-1]);
          ((THcSignalHit*) frPosAdcPed->ConstructedAt(nrPosAdcHits))->Set(npmt, float(fPedPosDefault[npmt-1])/float(NPedSamples)*AdcToV);
          
        }
        ((THcSignalHit*) frPosAdcPulseAmp->ConstructedAt(nrPosAdcHits))->Set(npmt, 0.); 
      }

      ++nrPosAdcHits;
      fTotNumAdcHits++;
      fTotNumPosAdcHits++;
      fNumPosAdcHits.at(npmt-1) = npmt;
    }

    for (UInt_t thit=0; thit<rawNegAdcHit.GetNPulses(); ++thit) {
      ((THcSignalHit*) frNegAdcPedRaw->ConstructedAt(nrNegAdcHits))->Set(npmt, rawNegAdcHit.GetPedRaw());
      ((THcSignalHit*) frNegAdcPed->ConstructedAt(nrNegAdcHits))->Set(npmt, rawNegAdcHit.GetPed());

      ((THcSignalHit*) frNegAdcPulseIntRaw->ConstructedAt(nrNegAdcHits))->Set(npmt, rawNegAdcHit.GetPulseIntRaw(thit));
      ((THcSignalHit*) frNegAdcPulseInt->ConstructedAt(nrNegAdcHits))->Set(npmt, rawNegAdcHit.GetPulseInt(thit));

      ((THcSignalHit*) frNegAdcPulseAmpRaw->ConstructedAt(nrNegAdcHits))->Set(npmt, rawNegAdcHit.GetPulseAmpRaw(thit));
      ((THcSignalHit*) frNegAdcPulseAmp->ConstructedAt(nrNegAdcHits))->Set(npmt, rawNegAdcHit.GetPulseAmp(thit));

      ((THcSignalHit*) frNegAdcPulseTimeRaw->ConstructedAt(nrNegAdcHits))->Set(npmt, rawNegAdcHit.GetPulseTimeRaw(thit));
      ((THcSignalHit*) frNegAdcPulseTime->ConstructedAt(nrNegAdcHits))->Set(npmt, rawNegAdcHit.GetPulseTime(thit));

      if (rawNegAdcHit.GetPulseAmpRaw(thit) > 0)  ((THcSignalHit*) fNegAdcErrorFlag->ConstructedAt(nrNegAdcHits))->Set(npmt, 0);
      if (rawNegAdcHit.GetPulseAmpRaw(thit) <= 0) ((THcSignalHit*) fNegAdcErrorFlag->ConstructedAt(nrNegAdcHits))->Set(npmt, 1);

     if (rawNegAdcHit.GetPulseAmpRaw(thit) <= 0) {
        Double_t PeakPedRatio= rawNegAdcHit.GetF250_PeakPedestalRatio();
        Int_t NPedSamples= rawNegAdcHit.GetF250_NPedestalSamples();
        Double_t AdcToC =  rawNegAdcHit.GetAdcTopC();
        Double_t AdcToV =  rawNegAdcHit.GetAdcTomV();
        if (fPedNegDefault[npmt-1] !=0) {
          Double_t tPulseInt = AdcToC*(rawNegAdcHit.GetPulseIntRaw(thit) - fPedNegDefault[npmt-1]*PeakPedRatio);
          ((THcSignalHit*) frNegAdcPulseInt->ConstructedAt(nrNegAdcHits))->Set(npmt, tPulseInt);
          ((THcSignalHit*) frNegAdcPedRaw->ConstructedAt(nrNegAdcHits))->Set(npmt, fPedNegDefault[npmt-1]);
          ((THcSignalHit*) frNegAdcPed->ConstructedAt(nrNegAdcHits))->Set(npmt, float(fPedNegDefault[npmt-1])/float(NPedSamples)*AdcToV);
          
        }
        ((THcSignalHit*) frNegAdcPulseAmp->ConstructedAt(nrNegAdcHits))->Set(npmt, 0.); 
      }

      ++nrNegAdcHits;
      fTotNumAdcHits++;
      fTotNumNegAdcHits++;
      fNumNegAdcHits.at(npmt-1) = npmt;
    }
    ihit++;
  }
  return ihit;
}

//_____________________________________________________________________________
Int_t THcAerogel::ApplyCorrections( void )
{
  return(0);
}

//_____________________________________________________________________________
Int_t THcAerogel::CoarseProcess( TClonesArray&  ) //tracks
{
  Double_t StartTime = 0.0;
  if( fglHod ) StartTime = fglHod->GetStartTime();
   Double_t OffsetTime = 0.0;
   if( fglHod ) OffsetTime = fglHod->GetOffsetTime();
  //cout << " starttime = " << StartTime << endl;
    // Loop over the elements in the TClonesArray
    for(Int_t ielem = 0; ielem < frPosAdcPulseInt->GetEntries(); ielem++) {

      Int_t    npmt         = ((THcSignalHit*) frPosAdcPulseInt->ConstructedAt(ielem))->GetPaddleNumber() - 1;
      Double_t pulsePed     = ((THcSignalHit*) frPosAdcPed->ConstructedAt(ielem))->GetData();
      Double_t pulseInt     = ((THcSignalHit*) frPosAdcPulseInt->ConstructedAt(ielem))->GetData();
      Double_t pulseIntRaw  = ((THcSignalHit*) frPosAdcPulseIntRaw->ConstructedAt(ielem))->GetData();
      Double_t pulseAmp     = ((THcSignalHit*) frPosAdcPulseAmp->ConstructedAt(ielem))->GetData();
      Double_t pulseTime    = ((THcSignalHit*) frPosAdcPulseTime->ConstructedAt(ielem))->GetData();
      Double_t adctdcdiffTime = StartTime-pulseTime+OffsetTime;
      Bool_t   pulseTimeCut = adctdcdiffTime > fAdcPosTimeWindowMin[npmt] && adctdcdiffTime < fAdcPosTimeWindowMax[npmt];

      // By default, the last hit within the timing cut will be considered "good"
        fGoodPosAdcMult.at(npmt) += 1;
     if (pulseTimeCut) {
        fGoodPosAdcPed.at(npmt)         = pulsePed;
        //      cout << " out = " << npmt << " " <<   frPosAdcPulseInt->GetEntries() << " " <<fGoodPosAdcMult.at(npmt); 
        fGoodPosAdcPulseInt.at(npmt)    = pulseInt;
        fGoodPosAdcPulseIntRaw.at(npmt) = pulseIntRaw;
        fGoodPosAdcPulseAmp.at(npmt)    = pulseAmp;
        fGoodPosAdcPulseTime.at(npmt)   = pulseTime;
        fGoodPosAdcTdcDiffTime.at(npmt)   = adctdcdiffTime;

        fPosNpe.at(npmt) = fPosGain[npmt]*fGoodPosAdcPulseInt.at(npmt);
        fPosNpeSum += fPosNpe.at(npmt);

        fTotNumGoodAdcHits++;
        fTotNumGoodPosAdcHits++;
        fNumGoodPosAdcHits.at(npmt) = npmt + 1;
      }
    }

    // Loop over the elements in the TClonesArray
    for(Int_t ielem = 0; ielem < frNegAdcPulseInt->GetEntries(); ielem++) {

      Int_t    npmt         = ((THcSignalHit*) frNegAdcPulseInt->ConstructedAt(ielem))->GetPaddleNumber() - 1;
      Double_t pulsePed     = ((THcSignalHit*) frNegAdcPed->ConstructedAt(ielem))->GetData();
      Double_t pulseInt     = ((THcSignalHit*) frNegAdcPulseInt->ConstructedAt(ielem))->GetData();
      Double_t pulseIntRaw  = ((THcSignalHit*) frNegAdcPulseIntRaw->ConstructedAt(ielem))->GetData();
      Double_t pulseAmp     = ((THcSignalHit*) frNegAdcPulseAmp->ConstructedAt(ielem))->GetData();
      Double_t pulseTime    = ((THcSignalHit*) frNegAdcPulseTime->ConstructedAt(ielem))->GetData();
      Double_t adctdcdiffTime = StartTime-pulseTime+OffsetTime;
      Bool_t   pulseTimeCut = adctdcdiffTime > fAdcNegTimeWindowMin[npmt] && adctdcdiffTime < fAdcNegTimeWindowMax[npmt];
        fGoodNegAdcMult.at(npmt) += 1;
 
      // By default, the last hit within the timing cut will be considered "good"
      if (pulseTimeCut) {
        fGoodNegAdcPed.at(npmt)         = pulsePed;
        fGoodNegAdcPulseIntRaw.at(npmt) = pulseIntRaw;
        fGoodNegAdcPulseAmp.at(npmt)    = pulseAmp;
        fGoodNegAdcPulseInt.at(npmt)    = pulseInt;
        fGoodNegAdcPulseTime.at(npmt)   = pulseTime;
        fGoodNegAdcTdcDiffTime.at(npmt)   = adctdcdiffTime;

        fNegNpe.at(npmt) = fNegGain[npmt]*fGoodNegAdcPulseInt.at(npmt);
        fNegNpeSum += fNegNpe.at(npmt);

        fTotNumGoodAdcHits++;
        fTotNumGoodNegAdcHits++;
        fNumGoodNegAdcHits.at(npmt) = npmt + 1;
      }
    }

       fNpeSum = fNegNpeSum + fPosNpeSum;

    for(Int_t ihit=0; ihit < fNhits; ihit++) {

      Int_t nPosTDCHits = 0;
      Int_t nNegTDCHits = 0;
      Int_t nPosADCHits = 0;
      Int_t nNegADCHits = 0;

      // 6 GeV calculations
      Int_t adc_pos;
      Int_t adc_neg;
      Int_t tdc_pos = -1;
      Int_t tdc_neg = -1;
      if (fSixGevData) {
        THcAerogelHit* hit = (THcAerogelHit*) fRawHitList->At(ihit);
        Int_t npmt = hit->fCounter - 1;

        // Sum positive and negative hits to fill tot_good_hits
        if(fPosNpe.at(npmt) > 0.3) {fNADCPosHits++; fNGoodHits++;}
        if(fNegNpe.at(npmt) > 0.3) {fNADCNegHits++; fNGoodHits++;}

        // ADC positive hit
        if((adc_pos = hit->GetRawAdcHitPos().GetPulseInt()) > 0) {
          THcSignalHit *sighit = (THcSignalHit*) fPosADCHits->ConstructedAt(nPosADCHits++);
          sighit->Set(hit->fCounter, adc_pos);
        }
        // ADC negative hit
        if((adc_neg = hit->GetRawAdcHitNeg().GetPulseInt()) > 0) {
          THcSignalHit *sighit = (THcSignalHit*) fNegADCHits->ConstructedAt(nNegADCHits++);
          sighit->Set(hit->fCounter, adc_neg);
        }
        // TDC positive hit
        if(hit->GetRawTdcHitPos().GetNHits() >  0) {
          THcSignalHit *sighit = (THcSignalHit*) fPosTDCHits->ConstructedAt(nPosTDCHits++);
          tdc_pos = hit->GetRawTdcHitPos().GetTime()+fTdcOffset;
          sighit->Set(hit->fCounter, tdc_pos);
        }
        // TDC negative hit
        if(hit->GetRawTdcHitNeg().GetNHits() >  0) {
          THcSignalHit *sighit = (THcSignalHit*) fNegTDCHits->ConstructedAt(nNegTDCHits++);
          tdc_neg = hit->GetRawTdcHitNeg().GetTime()+fTdcOffset;
          sighit->Set(hit->fCounter, tdc_neg);
        }
        // For each TDC, identify the first hit that is positive.
        tdc_pos = -1;
        tdc_neg = -1;
        for(UInt_t thit=0; thit<hit->GetRawTdcHitPos().GetNHits(); thit++) {
          Int_t tdc = hit->GetRawTdcHitPos().GetTime(thit);
          if(tdc >=0 ) {
            tdc_pos = tdc;
            break;
          }
        }
        for(UInt_t thit=0; thit<hit->GetRawTdcHitNeg().GetNHits(); thit++) {
          Int_t tdc = hit->GetRawTdcHitNeg().GetTime(thit);
          if(tdc >= 0) {
            tdc_neg = tdc;
            break;
          }
        }

        fA_Pos[npmt] = adc_pos;
        fA_Neg[npmt] = adc_neg;
        fA_Pos_p[npmt] = fA_Pos[npmt] - fPosPedMean[npmt];
        fA_Neg_p[npmt] = fA_Neg[npmt] - fNegPedMean[npmt];
        fT_Pos[npmt] = tdc_pos;
        fT_Neg[npmt] = tdc_neg;

        if(fA_Pos[npmt] < 8000) fPosNpeSixGev[npmt] = fPosGain[npmt]*fA_Pos_p[npmt];
        else fPosNpeSixGev[npmt] = 100.0;

        if(fA_Neg[npmt] < 8000) fNegNpeSixGev[npmt] = fNegGain[npmt]*fA_Neg_p[npmt];
        else fNegNpeSixGev[npmt] = 100.0;

        fPosNpeSumSixGev += fPosNpeSixGev[npmt];
        fNegNpeSumSixGev += fNegNpeSixGev[npmt];

        // Sum positive and negative hits to fill tot_good_hits
        if(fPosNpeSixGev[npmt] > 0.3) {fNADCPosHits++; fNGoodHits++;}
        if(fNegNpeSixGev[npmt] > 0.3) {fNADCNegHits++; fNGoodHits++;}

        if(fT_Pos[npmt] > 0 && fT_Pos[npmt] < 8000) fNTDCPosHits++;
        if(fT_Neg[npmt] > 0 && fT_Neg[npmt] < 8000) fNTDCNegHits++;
      }

      if (fPosNpeSumSixGev > 0.5 || fNegNpeSumSixGev > 0.5)
        fNpeSumSixGev = fPosNpeSumSixGev + fNegNpeSumSixGev;
      else fNpeSumSixGev = 0.0;
      // If total hits are 0, then give a noticable ridiculous NPE
      if (fNhits < 1) fNpeSumSixGev = 0.0;

    }
    return 0;
}

//_____________________________________________________________________________
Int_t THcAerogel::FineProcess( TClonesArray& tracks )
{

  Int_t nTracks = tracks.GetLast() + 1;

  for (Int_t itrack = 0; itrack < nTracks; itrack++) {

    THaTrack* track = dynamic_cast<THaTrack*> (tracks[itrack]);
    if (track->GetIndex() != 0) continue;  // Select the best track

    Double_t trackChi2    = track->GetChi2();
    Int_t    trackNDoF    = track->GetNDoF();
    Double_t trackRedChi2 = trackChi2/trackNDoF;
    Double_t trackBeta    = track->GetBeta();
    Double_t trackEnergy  = track->GetEnergy();
    Double_t trackMom     = track->GetP();
    Double_t trackENorm   = trackEnergy/trackMom;
    Double_t trackDp      = track->GetDp();
    Double_t trackXfp     = track->GetX();
    Double_t trackYfp     = track->GetY();
    Double_t trackTheta   = track->GetTheta();
    Double_t trackPhi     = track->GetPhi();

    Bool_t trackRedChi2Cut = trackRedChi2 > fRedChi2Min && trackRedChi2 < fRedChi2Max;
    Bool_t trackBetaCut    = trackBeta    > fBetaMin    && trackBeta    < fBetaMax;
    Bool_t trackENormCut   = trackENorm   > fENormMin   && trackENorm   < fENormMax;
    Bool_t trackDpCut      = trackDp      > fDpMin      && trackDp      < fDpMax;
        fXAtAero = trackXfp + trackTheta * fDiffBoxZPos;
        fYAtAero = trackYfp + trackPhi   * fDiffBoxZPos;

    if (trackRedChi2Cut && trackBetaCut && trackENormCut && trackDpCut) {

        // Project the track to the Aerogel diffuser box plane

        // cout << "Aerogel Detector: " << GetName() << endl;
        // cout << "nTracks = " << nTracks << "\t" << "trackChi2 = " << trackChi2
        //         << "\t" << "trackNDof = " << trackNDoF << "\t" << "trackRedChi2 = " << trackRedChi2 << endl;
        // cout << "trackBeta = " << trackBeta << "\t" << "trackEnergy = " << trackEnergy << "\t"
        //         << "trackMom = " << trackMom << "\t" << "trackENorm = " << trackENorm << endl;
        // cout << "trackXfp = " << trackXfp << "\t" << "trackYfp = " << trackYfp << "\t"
        //         << "trackTheta = " << trackTheta << "\t" << "trackPhi = " << trackPhi << endl;
        // cout << "fDiffBoxZPos = " << fDiffBoxZPos << "\t" << "fXAtAero = " << fXAtAero << "\t" << "fYAtAero = " << fYAtAero << endl;
        // cout << "=:=:=:=:=:=:=:=:=:=:=:=:=:=:=:=:=:=:=:=:=:=:=:=:=:=:=:=:=:=:=:=:=:=:=:=:=:=:=:" << endl;


        for (Int_t iregion = 0; iregion < fNRegions; iregion++) {

            if ((TMath::Abs(fRegionValue[GetIndex(iregion, 0)] - fXAtAero)   < fRegionValue[GetIndex(iregion, 4)]) &&
                (TMath::Abs(fRegionValue[GetIndex(iregion, 1)] - fYAtAero)   < fRegionValue[GetIndex(iregion, 5)]) &&
                (TMath::Abs(fRegionValue[GetIndex(iregion, 2)] - trackTheta) < fRegionValue[GetIndex(iregion, 6)]) &&
                (TMath::Abs(fRegionValue[GetIndex(iregion, 3)] - trackPhi)   < fRegionValue[GetIndex(iregion, 7)])) {

                fTotNumTracksMatched++;
                fNumTracksMatched.at(iregion) = iregion + 1;

                if (fNpeSum > fNpeThresh) {
                    fTotNumTracksFired++;
                    fNumTracksFired.at(iregion) = iregion + 1;
                }  // NPE threshold cut
            }  // Regional cuts
        }  // Loop over regions
    }  // Tracking cuts
  }  // Track loop

  return 0;
}

//_____________________________________________________________________________
// Method for initializing pedestals in the 6 GeV era
void THcAerogel::InitializePedestals()
{
  fNPedestalEvents = 0;
  fMinPeds         = 0;                    // Do not calculate pedestals by default

  DeletePedestalArrays();
  fPosPedLimit = new Int_t [fNelem];
  fNegPedLimit = new Int_t [fNelem];
  fPosPedMean  = new Double_t[fNelem];
  fNegPedMean  = new Double_t[fNelem];
  fPosPedSum   = new Int_t [fNelem];
  fPosPedSum2  = new Int_t [fNelem];
  fPosPedCount = new Int_t [fNelem];
  fNegPedSum   = new Int_t [fNelem];
  fNegPedSum2  = new Int_t [fNelem];
  fNegPedCount = new Int_t [fNelem];
  fPosPed      = new Double_t [fNelem];
  fPosThresh   = new Double_t [fNelem];
  fNegPed      = new Double_t [fNelem];
  fNegThresh   = new Double_t [fNelem];

  for(Int_t i = 0;i < fNelem; i++) {
    fPosPedSum[i]   = 0;
    fPosPedSum2[i]  = 0;
    fPosPedLimit[i] = 1000;   // In engine, this are set in parameter file
    fPosPedCount[i] = 0;
    fNegPedSum[i]   = 0;
    fNegPedSum2[i]  = 0;
    fNegPedLimit[i] = 1000;   // In engine, this are set in parameter file
    fNegPedCount[i] = 0;
    fPosPedMean[i]  = 0;       // Default pedestal values
    fNegPedMean[i]  = 0;       // Default pedestal values
  }

}

//_____________________________________________________________________________
// Method for accumulating pedestals in the 6 GeV era
void THcAerogel::AccumulatePedestals(TClonesArray* rawhits)
{
  // Extract data from the hit list, accumulating into arrays for
  // calculating pedestals

  Int_t nrawhits = rawhits->GetLast()+1;
  Int_t ihit     = 0;

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

    Int_t element = hit->fCounter - 1;
    Int_t adcpos  = hit->GetRawAdcHitPos().GetPulseInt();
    Int_t adcneg  = hit->GetRawAdcHitNeg().GetPulseInt();
    if(adcpos <= fPosPedLimit[element]) {
      fPosPedSum[element]  += adcpos;
      fPosPedSum2[element] += adcpos*adcpos;
      fPosPedCount[element]++;
      if(fPosPedCount[element] == fMinPeds/5)
        fPosPedLimit[element] = 100 + fPosPedSum[element]/fPosPedCount[element];
    }
    if(adcneg <= fNegPedLimit[element]) {
      fNegPedSum[element] += adcneg;
      fNegPedSum2[element] += adcneg*adcneg;
      fNegPedCount[element]++;
      if(fNegPedCount[element] == fMinPeds/5)
        fNegPedLimit[element] = 100 + fNegPedSum[element]/fNegPedCount[element];
    }
    ihit++;
  }
  fNPedestalEvents++;
  return;
}

//_____________________________________________________________________________
// Method for calculating pedestals in the 6 GeV era
void THcAerogel::CalculatePedestals()
{
  // Use the accumulated pedestal data to calculate pedestals
  // Later add check to see if pedestals have drifted ("Danger Will Robinson!")
  //  cout << "Plane: " << fPlaneNum << endl;
  for(Int_t i=0; i<fNelem;i++) {

    // Positive tubes
    fPosPed[i]    = ((Double_t) fPosPedSum[i]) / TMath::Max(1, fPosPedCount[i]);
    fPosThresh[i] = fPosPed[i] + 15;
    // Negative tubes
    fNegPed[i]    = ((Double_t) fNegPedSum[i]) / TMath::Max(1, fNegPedCount[i]);
    fNegThresh[i] = fNegPed[i] + 15;
    //    cout << i+1 << " " << fPosPed[i] << " " << fNegPed[i] << endl;

    // Just a copy for now, but allow the possibility that fXXXPedMean is set
    // in a parameter file and only overwritten if there is a sufficient number of
    // pedestal events.  (So that pedestals are sensible even if the pedestal events were
    // not acquired.)
    if(fMinPeds > 0) {
      if(fPosPedCount[i] > fMinPeds)
        fPosPedMean[i] = fPosPed[i];
      if(fNegPedCount[i] > fMinPeds)
        fNegPedMean[i] = fNegPed[i];
    }
  }
}

//_____________________________________________________________________________
Int_t THcAerogel::GetIndex(Int_t nRegion, Int_t nValue)
{
  return fNRegions * nValue + nRegion;
}

//_____________________________________________________________________________
void THcAerogel::Print(const Option_t* opt) const
{
  THaNonTrackingDetector::Print(opt);

  // Print out the pedestals
  if (fSixGevData) {
    cout << endl;
    cout << "Aerogel Pedestals" << endl;
    cout << "No.   Neg    Pos" << endl;
    for(Int_t i=0; i<fNelem; i++)
      cout << " " << i << "\t" << fNegPedMean[i] << "\t" << fPosPedMean[i] << endl;
    cout << endl;
    cout << " fMinPeds = " << fMinPeds << endl;
    cout << endl;
  }
}
//_____________________________________________________________________________
Int_t THcAerogel::End(THaRunBase* run)
{
  MissReport(Form("%s.%s", GetApparatus()->GetName(), GetName()));
  return 0;
}
ClassImp(THcAerogel)