THcHodoscope.cxx

/** \class THcHodoscope
    \ingroup Detectors

Class for a generic hodoscope consisting of multiple
planes with multiple paddles with phototubes on both ends.
This differs from Hall A scintillator class in that it is the whole
hodoscope array, not just one plane.

*/

#include "THcSignalHit.h"
#include "THcShower.h"
#include "THcCherenkov.h"
#include "THcHallCSpectrometer.h"

#include "THcHitList.h"
#include "THcRawShowerHit.h"
#include "TClass.h"
#include "math.h"
#include "THaSubDetector.h"

#include "THcHodoscope.h"
#include "THaEvData.h"
#include "THaDetMap.h"
#include "THcDetectorMap.h"
#include "THaGlobals.h"
#include "THaCutList.h"
#include "THcGlobals.h"
#include "THcParmList.h"
#include "VarDef.h"
#include "VarType.h"
#include "THaTrack.h"
#include "TClonesArray.h"
#include "TMath.h"

#include "THaTrackProj.h"
#include <vector>

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

using namespace std;
using std::vector;

//_____________________________________________________________________________
THcHodoscope::THcHodoscope( const char* name, const char* description,
				  THaApparatus* apparatus ) :
  THaNonTrackingDetector(name,description,apparatus)
{
  // Constructor

  //fTrackProj = new TClonesArray( "THaTrackProj", 5 );
  // Construct the planes
  fNPlanes = 0;			// No planes until we make them
  fStartTime=-1e5;
  fGoodStartTime=kFALSE;
}

//_____________________________________________________________________________
THcHodoscope::THcHodoscope( ) :
  THaNonTrackingDetector()
{
  // Constructor
}

//_____________________________________________________________________________
void THcHodoscope::Setup(const char* name, const char* description)
{

  //  static const char* const here = "Setup()";
  //  static const char* const message =
  //    "Must construct %s detector with valid name! Object construction failed.";

  cout << "In THcHodoscope::Setup()" << endl;
  // Base class constructor failed?
  if( IsZombie()) return;

  fDebug   = 1;  // Keep this at one while we're working on the code

  char prefix[2];

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

  TString temp(prefix[0]);
  fSHMS=kFALSE;
  if (temp == "p" ) fSHMS=kTRUE;
  cout << " fSHMS = " << fSHMS << endl;
  string planenamelist;
  DBRequest listextra[]={
    {"hodo_num_planes", &fNPlanes, kInt},
    {"hodo_plane_names",&planenamelist, kString},
    {0}
  };
  //fNPlanes = 4; 		// Default if not defined
  gHcParms->LoadParmValues((DBRequest*)&listextra,prefix);

  cout << "Plane Name List : " << planenamelist << endl;

  vector<string> plane_names = vsplit(planenamelist);
  // Plane names
  if(plane_names.size() != (UInt_t) fNPlanes) {
    cout << "ERROR: Number of planes " << fNPlanes << " doesn't agree with number of plane names " << plane_names.size() << endl;
    // Should quit.  Is there an official way to quit?
  }
  fPlaneNames = new char* [fNPlanes];
  for(Int_t i=0;i<fNPlanes;i++) {
    fPlaneNames[i] = new char[plane_names[i].length()+1];
    strcpy(fPlaneNames[i], plane_names[i].c_str());
  }

  // Probably shouldn't assume that description is defined
  char* desc = new char[strlen(description)+100];
  fPlanes = new THcScintillatorPlane* [fNPlanes];
  for(Int_t i=0;i < fNPlanes;i++) {
    strcpy(desc, description);
    strcat(desc, " Plane ");
    strcat(desc, fPlaneNames[i]);
    fPlanes[i] = new THcScintillatorPlane(fPlaneNames[i], desc, i+1, this); // Number planes starting from zero!!
    cout << "Created Scintillator Plane " << fPlaneNames[i] << ", " << desc << endl;
  }

  // --------------- To get energy from THcShower ----------------------
  const char* shower_detector_name = "cal";
  //  THaApparatus* app;
  THcHallCSpectrometer *app = dynamic_cast<THcHallCSpectrometer*>(GetApparatus());
  THaDetector* det = app->GetDetector( shower_detector_name );

  if( dynamic_cast<THcShower*>(det) ) {
    fShower = dynamic_cast<THcShower*>(det);
  }
  else if( !dynamic_cast<THcShower*>(det) ) {
    cout << "Warining: calorimeter analysis module "
	 << shower_detector_name << " not loaded for spectrometer "
	 << prefix << endl;

    fShower = NULL;
  }

  // --------------- To get energy from THcShower ----------------------

  // --------------- To get NPEs from THcCherenkov -------------------
  const char* chern_detector_name = "cer";
  THaDetector* detc = app->GetDetector( chern_detector_name );

  if( dynamic_cast<THcCherenkov*>(detc) ) {
    fChern = dynamic_cast<THcCherenkov*>(detc);
  }
  else if( !dynamic_cast<THcCherenkov*>(detc) ) {
    cout << "Warining: Cherenkov detector analysis module "
	 << chern_detector_name << " not loaded for spectrometer "
	 << prefix << endl;

    fChern = NULL;
  }

  // --------------- To get NPEs from THcCherenkov -------------------

  fScinShould = 0;
  fScinDid = 0;
  gHcParms->Define(Form("%shodo_did",prefix),"Total hodo tracks",fScinDid);
  gHcParms->Define(Form("%shodo_should",prefix),"Total hodo triggers",fScinShould);

  // Save the nominal particle mass
  fPartMass = app->GetParticleMass();
  fBetaNominal = app->GetBetaAtPcentral();

  delete [] desc;
}

//_____________________________________________________________________________
THaAnalysisObject::EStatus THcHodoscope::Init( const TDatime& date )
{
  cout << "In THcHodoscope::Init()" << endl;
  Setup(GetName(), GetTitle());

  char EngineDID[] = "xSCIN";
  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;
  }

  // Should probably put this in ReadDatabase as we will know the
  // maximum number of hits after setting up the detector map
  // But it needs to happen before the sub detectors are initialized
  // so that they can get the pointer to the hitlist.

  InitHitList(fDetMap, "THcRawHodoHit", fDetMap->GetTotNumChan()+1);

  EStatus status;
  // This triggers call of ReadDatabase and DefineVariables
  if( (status = THaNonTrackingDetector::Init( date )) )
    return fStatus=status;

  for(Int_t ip=0;ip<fNPlanes;ip++) {
    if((status = fPlanes[ip]->Init( date ))) {
      return fStatus=status;
    }
  }

  // Replace with what we need for Hall C
  //  const DataDest tmp[NDEST] = {
  //    { &fRTNhit, &fRANhit, fRT, fRT_c, fRA, fRA_p, fRA_c, fROff, fRPed, fRGain },
  //    { &fLTNhit, &fLANhit, fLT, fLT_c, fLA, fLA_p, fLA_c, fLOff, fLPed, fLGain }
  //  };
  //  memcpy( fDataDest, tmp, NDEST*sizeof(DataDest) );

  fNScinHits     = new Int_t [fNPlanes];
  fGoodPlaneTime = new Bool_t [fNPlanes];
  fNPlaneTime    = new Int_t [fNPlanes];
  fSumPlaneTime  = new Double_t [fNPlanes];

  //  Double_t  fHitCnt4 = 0., fHitCnt3 = 0.;

  // Int_t m = 0;
  // fScinHit = new Double_t*[fNPlanes];
  // for ( m = 0; m < fNPlanes; m++ ){
  //   fScinHit[m] = new Double_t[fNPaddle[0]];
  // }

  for (int ip=0; ip<fNPlanes; ++ip) {
    fScinHitPaddle.push_back(std::vector<Int_t>(fNPaddle[ip], 0));
  }

  return fStatus = kOK;
}
//_____________________________________________________________________________
Int_t THcHodoscope::ReadDatabase( const TDatime& date )
{

  // Read this detector's parameters from the database file 'fi'.
  // This function is called by THaDetectorBase::Init() once at the
  // beginning of the analysis.
  // 'date' contains the date/time of the run being analyzed.

  //  static const char* const here = "ReadDatabase()";
  char prefix[2];
  char parname[100];

  // Read data from database
  // Pull values from the THcParmList instead of reading a database
  // file like Hall A does.

  // Will need to determine which spectrometer in order to construct
  // the parameter names (e.g. hscin_1x_nr vs. sscin_1x_nr)

  prefix[0]=tolower(GetApparatus()->GetName()[0]);
  //
  prefix[1]='\0';
  strcpy(parname,prefix);
  strcat(parname,"scin_");
  //  Int_t plen=strlen(parname);
  cout << " readdatabse hodo fnplanes = " << fNPlanes << endl;

  fBetaNoTrk = 0.;
  fBetaNoTrkChiSq = 0.;

  fNPaddle = new UInt_t [fNPlanes];
  fFPTime = new Double_t [fNPlanes];
  fPlaneCenter = new Double_t[fNPlanes];
  fPlaneSpacing = new Double_t[fNPlanes];

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

  for(Int_t i=0;i<fNPlanes;i++) {

    DBRequest list[]={
      {Form("scin_%s_nr",fPlaneNames[i]), &fNPaddle[i], kInt},
      {0}
    };
    gHcParms->LoadParmValues((DBRequest*)&list,prefix);
  }

  // GN added
  // reading variables from *hodo.param
  fMaxScinPerPlane=fNPaddle[0];
  for (Int_t i=1;i<fNPlanes;i++) {
    fMaxScinPerPlane=(fMaxScinPerPlane > fNPaddle[i])? fMaxScinPerPlane : fNPaddle[i];
  }
// need this for "padded arrays" i.e. 4x16 lists of parameters (GN)
  fMaxHodoScin=fMaxScinPerPlane*fNPlanes;
  if (fDebug>=1)  cout <<"fMaxScinPerPlane = "<<fMaxScinPerPlane<<" fMaxHodoScin = "<<fMaxHodoScin<<endl;

   fHodoVelLight=new Double_t [fMaxHodoScin];
 fHodoPosSigma=new Double_t [fMaxHodoScin];
  fHodoNegSigma=new Double_t [fMaxHodoScin];
  fHodoPosMinPh=new Double_t [fMaxHodoScin];
  fHodoNegMinPh=new Double_t [fMaxHodoScin];
  fHodoPosPhcCoeff=new Double_t [fMaxHodoScin];
  fHodoNegPhcCoeff=new Double_t [fMaxHodoScin];
  fHodoPosTimeOffset=new Double_t [fMaxHodoScin];
  fHodoNegTimeOffset=new Double_t [fMaxHodoScin];
  fHodoPosPedLimit=new Int_t [fMaxHodoScin];
  fHodoNegPedLimit=new Int_t [fMaxHodoScin];
  fHodoPosInvAdcOffset=new Double_t [fMaxHodoScin];
  fHodoNegInvAdcOffset=new Double_t [fMaxHodoScin];
  fHodoPosInvAdcLinear=new Double_t [fMaxHodoScin];
  fHodoNegInvAdcLinear=new Double_t [fMaxHodoScin];
  fHodoPosInvAdcAdc=new Double_t [fMaxHodoScin];
  fHodoNegInvAdcAdc=new Double_t [fMaxHodoScin];

  fNHodoscopes = 2;
  fxLoScin = new Int_t [fNHodoscopes];
  fxHiScin = new Int_t [fNHodoscopes];
  fyLoScin = new Int_t [fNHodoscopes];
  fyHiScin = new Int_t [fNHodoscopes];
  fHodoSlop = new Double_t [fNPlanes];
   fTdcOffset = new Int_t [fNPlanes];
  for(Int_t ip=0;ip<fNPlanes;ip++) { // Set a large default window
   fTdcOffset[ip] = 0 ;
  }

  DBRequest list[]={
    {"cosmicflag",                       &fCosmicFlag,            kInt,            0,  1},
    {"start_time_center",                &fStartTimeCenter,                      kDouble},
    {"start_time_slop",                  &fStartTimeSlop,                        kDouble},
    {"scin_tdc_to_time",                 &fScinTdcToTime,                        kDouble},
    {"scin_tdc_min",                     &fScinTdcMin,                           kDouble},
    {"scin_tdc_max",                     &fScinTdcMax,                           kDouble},
    {"tof_tolerance",                    &fTofTolerance,          kDouble,         0,  1},
    {"pathlength_central",               &fPathLengthCentral,                    kDouble},
    {"hodo_pos_sigma",                   &fHodoPosSigma[0],       kDouble,  fMaxHodoScin},
    {"hodo_neg_sigma",                   &fHodoNegSigma[0],       kDouble,  fMaxHodoScin},
    {"hodo_pos_ped_limit",               &fHodoPosPedLimit[0],    kInt,     fMaxHodoScin},
    {"hodo_neg_ped_limit",               &fHodoNegPedLimit[0],    kInt,     fMaxHodoScin},
    {"tofusinginvadc",                   &fTofUsingInvAdc,        kInt,            0,  1},
    {"xloscin",                          &fxLoScin[0],            kInt,     (UInt_t) fNHodoscopes},
    {"xhiscin",                          &fxHiScin[0],            kInt,     (UInt_t) fNHodoscopes},
    {"yloscin",                          &fyLoScin[0],            kInt,     (UInt_t) fNHodoscopes},
    {"yhiscin",                          &fyHiScin[0],            kInt,     (UInt_t) fNHodoscopes},
    {"track_eff_test_num_scin_planes",   &fTrackEffTestNScinPlanes,                 kInt},
    {"cer_npe",                          &fNCerNPE,               kDouble,         0,  1},
    {"normalized_energy_tot",            &fNormETot,              kDouble,         0,  1},
    {"hodo_slop",                        fHodoSlop,               kDouble,  (UInt_t) fNPlanes},
    {"debugprintscinraw",                &fdebugprintscinraw,               kInt,  0,1},
    {"hodo_tdc_offset",                  fTdcOffset,              kInt,     (UInt_t) fNPlanes, 1},
    {"dumptof",                          &fDumpTOF,               kInt,    0, 1},
    {"dumptof_filename",                 &fTOFDumpFile,           kString, 0, 1},
    {0}
  };

  // Defaults if not defined in parameter file

  fdebugprintscinraw=0;
  fDumpTOF = 0;
  fTOFDumpFile="";
  fTofUsingInvAdc = 1;
  fTofTolerance = 3.0;
  fNCerNPE = 2.0;
  fNormETot = 0.7;
  fCosmicFlag=0;
  // Gets added to each reference time corrected raw TDC value
  // to make sure valid range is all positive.

  gHcParms->LoadParmValues((DBRequest*)&list,prefix);
  if (fCosmicFlag==1) cout << " setup for cosmics in TOF"<< endl;
  cout << " cosmic flag = " << fCosmicFlag << endl;
  if(fDumpTOF) {
      fDumpOut.open(fTOFDumpFile.c_str());
   if(fDumpOut.is_open()) {
     //fDumpOut << "Hodoscope Time of Flight calibration data" << endl;
    } else {
      fDumpTOF = 0;
      cout << "WARNING: Unable to open TOF Dump file " << fTOFDumpFile << endl;
      cout << "Data for TOF calibration not being written." << endl;
    }
  }

  cout << " x1 lo = " << fxLoScin[0]
       << " x2 lo = " << fxLoScin[1]
       << " x1 hi = " << fxHiScin[0]
       << " x2 hi = " << fxHiScin[1]
       << endl;

  cout << " y1 lo = " << fyLoScin[0]
       << " y2 lo = " << fyLoScin[1]
       << " y1 hi = " << fyHiScin[0]
       << " y2 hi = " << fyHiScin[1]
       << endl;

  cout << "Hdososcope planes hits for trigger = " << fTrackEffTestNScinPlanes
       << " normalized energy min = " << fNormETot
       << " number of photo electrons = " << fNCerNPE
       << endl;

  if (fTofUsingInvAdc) {
    DBRequest list2[]={
    {"hodo_vel_light",                   &fHodoVelLight[0],       kDouble,  fMaxHodoScin},
      {"hodo_pos_invadc_offset",&fHodoPosInvAdcOffset[0],kDouble,fMaxHodoScin},
      {"hodo_neg_invadc_offset",&fHodoNegInvAdcOffset[0],kDouble,fMaxHodoScin},
      {"hodo_pos_invadc_linear",&fHodoPosInvAdcLinear[0],kDouble,fMaxHodoScin},
      {"hodo_neg_invadc_linear",&fHodoNegInvAdcLinear[0],kDouble,fMaxHodoScin},
      {"hodo_pos_invadc_adc",&fHodoPosInvAdcAdc[0],kDouble,fMaxHodoScin},
      {"hodo_neg_invadc_adc",&fHodoNegInvAdcAdc[0],kDouble,fMaxHodoScin},
      {0}
    };
    gHcParms->LoadParmValues((DBRequest*)&list2,prefix);
  };
  if (!fTofUsingInvAdc) {
    DBRequest list3[]={
    {"hodo_vel_light",                   &fHodoVelLight[0],       kDouble,  fMaxHodoScin},
    {"hodo_pos_minph",                   &fHodoPosMinPh[0],       kDouble,  fMaxHodoScin},
    {"hodo_neg_minph",                   &fHodoNegMinPh[0],       kDouble,  fMaxHodoScin},
    {"hodo_pos_phc_coeff",               &fHodoPosPhcCoeff[0],    kDouble,  fMaxHodoScin},
    {"hodo_neg_phc_coeff",               &fHodoNegPhcCoeff[0],    kDouble,  fMaxHodoScin},
    {"hodo_pos_time_offset",             &fHodoPosTimeOffset[0],  kDouble,  fMaxHodoScin},
    {"hodo_neg_time_offset",             &fHodoNegTimeOffset[0],  kDouble,  fMaxHodoScin},
      {0}
    };
    gHcParms->LoadParmValues((DBRequest*)&list3,prefix);
  };
  if (fDebug >=1) {
    cout <<"******* Testing Hodoscope Parameter Reading ***\n";
    cout<<"StarTimeCenter = "<<fStartTimeCenter<<endl;
    cout<<"StartTimeSlop = "<<fStartTimeSlop<<endl;
    cout <<"ScintTdcToTime = "<<fScinTdcToTime<<endl;
    cout <<"TdcMin = "<<fScinTdcMin<<" TdcMax = "<<fScinTdcMax<<endl;
    cout <<"TofTolerance = "<<fTofTolerance<<endl;
    cout <<"*** VelLight ***\n";
    for (Int_t i1=0;i1<fNPlanes;i1++) {
      cout<<"Plane "<<i1<<endl;
      for (UInt_t i2=0;i2<fMaxScinPerPlane;i2++) {
	cout<<fHodoVelLight[GetScinIndex(i1,i2)]<<" ";
      }
      cout <<endl;
    }
    cout <<endl<<endl;
    // check fHodoPosPhcCoeff
    /*
    cout <<"fHodoPosPhcCoeff = ";
    for (int i1=0;i1<fMaxHodoScin;i1++) {
      cout<<this->GetHodoPosPhcCoeff(i1)<<" ";
    }
    cout<<endl;
    */
  }
  //
  if ((fTofTolerance > 0.5) && (fTofTolerance < 10000.)) {
    cout << "USING "<<fTofTolerance<<" NSEC WINDOW FOR FP NO_TRACK CALCULATIONS.\n";
  }
  else {
    fTofTolerance= 3.0;
    cout << "*** USING DEFAULT 3 NSEC WINDOW FOR FP NO_TRACK CALCULATIONS!! ***\n";
  }
  fIsInit = true;
  return kOK;
}

//_____________________________________________________________________________
Int_t THcHodoscope::DefineVariables( EMode mode )
{
  // Initialize global variables and lookup table for decoder
  cout << "THcHodoscope::DefineVariables called " << GetName() << endl;
  if( mode == kDefine && fIsSetup ) return kOK;
  fIsSetup = ( mode == kDefine );

  // Register variables in global list

  RVarDef vars[] = {
    // Move these into THcHallCSpectrometer using track fTracks
    {"beta",       "Beta including track info",                "fBeta"},
    {"betanotrack",       "Beta from scintillator hits",                "fBetaNoTrk"},
    {"betachisqnotrack",  "Chi square of beta from scintillator hits",  "fBetaNoTrkChiSq"},
    {"fpHitsTime",        "Time at focal plane from all hits",            "fFPTimeAll"},
    {"starttime",         "Hodoscope Start Time",                         "fStartTime"},
    {"goodstarttime",     "Hodoscope Good Start Time (logical flag)",                    "fGoodStartTime"},
    {"goodscinhit",       "Hit in fid area",                              "fGoodScinHits"},
    //    {"goodscinhitx",    "Hit in fid x range",                     "fGoodScinHitsX"},
    {"scinshould",        "Total scin Hits in fid area",                  "fScinShould"},
    {"scindid",           "Total scin Hits in fid area with a track",     "fScinDid"},
    { 0 }
  };
  return DefineVarsFromList( vars, mode );
  //  return kOK;
}

//_____________________________________________________________________________
THcHodoscope::~THcHodoscope()
{
  // Destructor. Remove variables from global list.

  delete [] fFPTime;
  delete [] fPlaneCenter;
  delete [] fPlaneSpacing;

  if( fIsSetup )
    RemoveVariables();
  if( fIsInit )
    DeleteArrays();
  if (fTrackProj) {
    fTrackProj->Clear();
    delete fTrackProj; fTrackProj = 0;
  }
}

//_____________________________________________________________________________
void THcHodoscope::DeleteArrays()
{
  // Delete member arrays. Used by destructor.
  // Int_t k;
  // for( k = 0; k < fNPlanes; k++){
  //   delete [] fScinHit[k];
  // }
  // delete [] fScinHit;

  delete [] fxLoScin;             fxLoScin = NULL;
  delete [] fxHiScin;             fxHiScin = NULL;
  delete [] fHodoSlop;            fHodoSlop = NULL;

  delete [] fNPaddle;             fNPaddle = NULL;
  delete [] fHodoVelLight;        fHodoVelLight = NULL;
  delete [] fHodoPosSigma;        fHodoPosSigma = NULL;
  delete [] fHodoNegSigma;        fHodoNegSigma = NULL;
  delete [] fHodoPosMinPh;        fHodoPosMinPh = NULL;
  delete [] fHodoNegMinPh;        fHodoNegMinPh = NULL;
  delete [] fHodoPosPhcCoeff;     fHodoPosPhcCoeff = NULL;
  delete [] fHodoNegPhcCoeff;     fHodoNegPhcCoeff = NULL;
  delete [] fHodoPosTimeOffset;   fHodoPosTimeOffset = NULL;
  delete [] fHodoNegTimeOffset;   fHodoNegTimeOffset = NULL;
  delete [] fHodoPosPedLimit;     fHodoPosPedLimit = NULL;
  delete [] fHodoNegPedLimit;     fHodoNegPedLimit = NULL;
  delete [] fHodoPosInvAdcOffset; fHodoPosInvAdcOffset = NULL;
  delete [] fHodoNegInvAdcOffset; fHodoNegInvAdcOffset = NULL;
  delete [] fHodoPosInvAdcLinear; fHodoPosInvAdcLinear = NULL;
  delete [] fHodoNegInvAdcLinear; fHodoNegInvAdcLinear = NULL;
  delete [] fHodoPosInvAdcAdc;    fHodoPosInvAdcAdc = NULL;
  delete [] fGoodPlaneTime;       fGoodPlaneTime = NULL;
  delete [] fNPlaneTime;          fNPlaneTime = NULL;
  delete [] fSumPlaneTime;        fSumPlaneTime = NULL;
  delete [] fNScinHits;           fNScinHits = NULL;
  delete [] fTdcOffset;           fTdcOffset = NULL;

}

//_____________________________________________________________________________
inline
void THcHodoscope::ClearEvent()
{
  /*! \brief Clears variables
   *
   *  Called by  THcHodoscope::Decode
   *
   */

  fBeta = 0.0;
  fBetaNoTrk = 0.0;
  fBetaNoTrkChiSq = 0.0;
  fStartTime  = 0.0;
  fFPTimeAll= -1000.;
  fGoodStartTime = kFALSE;
  fGoodScinHits = 0;
  fScinShould = 0;
  fScinDid = 0;

  for(Int_t ip=0;ip<fNPlanes;ip++) {
    fPlanes[ip]->Clear();
    fFPTime[ip]=0.;
    fPlaneCenter[ip]=0.;
    fPlaneSpacing[ip]=0.;
    for(UInt_t iPaddle=0;iPaddle<fNPaddle[ip]; ++iPaddle) {
      fScinHitPaddle[ip][iPaddle]=0;
    }
  }
  fdEdX.clear();
  fNScinHit.clear();
  fNClust.clear();
  fThreeScin.clear();
  fGoodScinHitsX.clear();
}

//_____________________________________________________________________________
Int_t THcHodoscope::Decode( const THaEvData& evdata )
{
  /*! \brief Decodes raw data and processes raw data into hits for each instance of  THcScintillatorPlane
   *
   *  - Calls THcHodoscope::ClearEvent
   *  - Reads raw data using THcHitList::DecodeToHitList
   *  - If one wants to subtract pedestals (assumed to be a set of data at beginning of run)
   *    + Must define "Pedestal_event" cut in the cuts definition file
   *    + For each "Pedestal_event" calls THcScintillatorPlane::AccumulatePedestals and returns
   *    + After First event which is not a  "Pedestal_event" calls THcScintillatorPlane::CalculatePedestals
   *  - For each scintillator plane THcScintillatorPlane::ProcessHits
   *  - Calls THcHodoscope::EstimateFocalPlaneTime
   *
   *
   */
  ClearEvent();
  // Get the Hall C style hitlist (fRawHitList) for this event
  fNHits = DecodeToHitList(evdata);

  //
  // GN: print event number so we can cross-check with engine
  // if (evdata.GetEvNum()>1000)
  //   cout <<"\nhcana_event " << evdata.GetEvNum()<<endl;

  fCheckEvent = evdata.GetEvNum();
  fEventType =  evdata.GetEvType();

  if(gHaCuts->Result("Pedestal_event")) {
    Int_t nexthit = 0;
    for(Int_t ip=0;ip<fNPlanes;ip++) {

      nexthit = fPlanes[ip]->AccumulatePedestals(fRawHitList, nexthit);
    }
    fAnalyzePedestals = 1;	// Analyze pedestals first normal events
    return(0);
  }
  if(fAnalyzePedestals) {
    for(Int_t ip=0;ip<fNPlanes;ip++) {

      fPlanes[ip]->CalculatePedestals();
    }
    fAnalyzePedestals = 0;	// Don't analyze pedestals next event
  }

  // Let each plane get its hits
  Int_t nexthit = 0;

  fNfptimes=0;
  for(Int_t ip=0;ip<fNPlanes;ip++) {

    fPlaneCenter[ip] = fPlanes[ip]->GetPosCenter(0) + fPlanes[ip]->GetPosOffset();
    fPlaneSpacing[ip] = fPlanes[ip]->GetSpacing();

    //    nexthit = fPlanes[ip]->ProcessHits(fRawHitList, nexthit);
    // GN: select only events that have reasonable TDC values to start with
    // as per the Engine h_strip_scin.f
    nexthit = fPlanes[ip]->ProcessHits(fRawHitList,nexthit);
  }
  EstimateFocalPlaneTime();

  if (fdebugprintscinraw == 1) {
    cout << " Event number = " << evdata.GetEvNum()<<endl;
  for(UInt_t ihit = 0; ihit < fNRawHits ; ihit++) {
//    THcRawHodoHit* hit = (THcRawHodoHit *) fRawHitList->At(ihit);
//    cout << ihit << " : " << hit->fPlane << ":" << hit->fCounter << " : "
//	 << hit->fADC_pos << " " << hit->fADC_neg << " "  <<  hit->fTDC_pos
//	 << " " <<  hit->fTDC_neg << endl;
  }
  cout << endl;
  }


  return fNHits;
}

//_____________________________________________________________________________
void THcHodoscope::EstimateFocalPlaneTime( void )
{
  /*! \brief Calculates the Drift Chamber start time and fBetaNoTrk (velocity determined without track info)
   *
   *  - Called by  THcHodoscope::Decode
   *  - selects good scintillator paddle hits
   *     + loops through hits in each scintillator plane and fills histogram array, "timehist", with corrected times for positive
   *        and negative ends of each paddle
   *     + Determines the peak of "timehist"
   *
   */

  Int_t timehist[200];
  for (Int_t i=0;i<200;i++) {
    timehist[i] = 0;
  }
  Int_t ihit=0;
  Int_t nscinhits=0;		// Total # hits with at least one good tdc
  for(Int_t ip=0;ip<fNPlanes;ip++) {
    Int_t nphits=fPlanes[ip]->GetNScinHits();
    nscinhits += nphits;
    TClonesArray* hodoHits = fPlanes[ip]->GetHits();
    for(Int_t i=0;i<nphits;i++) {
      THcHodoHit *hit = (THcHodoHit*)hodoHits->At(i);
      if(hit->GetHasCorrectedTimes()) {
	Double_t postime=hit->GetPosTOFCorrectedTime();
	Double_t negtime=hit->GetNegTOFCorrectedTime();
	for (Int_t k=0;k<200;k++) {
	  Double_t tmin=0.5*(k+1);
	  if ((postime> tmin) && (postime < tmin+fTofTolerance)) {
	    timehist[k]++;
	  }
	  if ((negtime> tmin) && (negtime < tmin+fTofTolerance)) {
	    timehist[k]++;
	  }
	}
      }
    }
  }

  // Find the bin with most hits
  Int_t binmax=0;
  Int_t maxhit=0;
  for(Int_t i=0;i<200;i++) {
    if(timehist[i]>maxhit) {
      binmax = i+1;
      maxhit = timehist[i];
    }
  }
  ihit = 0;
  Double_t fpTimeSum = 0.0;
  fNfptimes=0;
  Int_t  Ngood_hits_plane=0;
  Double_t Plane_fptime_sum=0.0;

  Bool_t goodplanetime[fNPlanes];
  Bool_t twogoodtimes[nscinhits];
  Int_t temp_planes=fNPlanes;
  if (fSHMS) temp_planes=3;
  for(Int_t ip=0;ip<temp_planes;ip++) {
    goodplanetime[ip] = kFALSE;
    Int_t nphits=fPlanes[ip]->GetNScinHits();
    TClonesArray* hodoHits = fPlanes[ip]->GetHits();
    Ngood_hits_plane=0;
    Plane_fptime_sum=0.0;
    for(Int_t i=0;i<nphits;i++) {
      THcHodoHit *hit = (THcHodoHit*)hodoHits->At(i);
      twogoodtimes[ihit] = kFALSE;
      if(hit->GetHasCorrectedTimes()) {
      Double_t tmin = 0.5*binmax;
      Double_t postime=hit->GetPosTOFCorrectedTime();
      Double_t negtime=hit->GetNegTOFCorrectedTime();
      if ((postime>tmin) && (postime<tmin+fTofTolerance) &&
	  (negtime>tmin) && (negtime<tmin+fTofTolerance)) {
	hit->SetTwoGoodTimes(kTRUE);
	twogoodtimes[ihit] = kTRUE;	// Both tubes fired
        Int_t index=hit->GetPaddleNumber()-1;	 //
        Double_t fptime;
        if(fCosmicFlag==1) {
	   fptime = hit->GetScinCorrectedTime()
	  + (fPlanes[ip]->GetZpos()+(index%2)*fPlanes[ip]->GetDzpos())
	  / (29.979 * fBetaNominal);
	}else{
	   fptime = hit->GetScinCorrectedTime()
	  - (fPlanes[ip]->GetZpos()+(index%2)*fPlanes[ip]->GetDzpos())
	  / (29.979 * fBetaNominal);
	}
	if(TMath::Abs(fptime-fStartTimeCenter)<=fStartTimeSlop) {
          Ngood_hits_plane++;
	  Plane_fptime_sum+=fptime;
	  fpTimeSum += fptime;
	  fNfptimes++;
	  goodplanetime[ip] = kTRUE;
	}
      } else {
	hit->SetTwoGoodTimes(kFALSE);
      }
      }
    }
    ihit++;
      fPlanes[ip]->SetFpTime(Plane_fptime_sum/float(Ngood_hits_plane));
      fPlanes[ip]->SetNGoodHits(Ngood_hits_plane);
  }

  if(fNfptimes>0) {
    fStartTime = fpTimeSum/fNfptimes;
    fGoodStartTime=kTRUE;
      fFPTimeAll = fStartTime ;
  } else {
    fStartTime = fStartTimeCenter;
    fGoodStartTime=kFALSE;
    fFPTimeAll = fStartTime ;
  }
  if((goodplanetime[0]||goodplanetime[1])
     &&(goodplanetime[2]||goodplanetime[3])) {

    Double_t sumW = 0.;
    Double_t sumT = 0.;
    Double_t sumZ = 0.;
    Double_t sumZZ = 0.;
    Double_t sumTZ = 0.;
    Int_t ihhit = 0;

    temp_planes=fNPlanes;
  if (fSHMS) temp_planes=3;
    for(Int_t ip=0;ip<temp_planes;ip++) {
      Int_t nphits=fPlanes[ip]->GetNScinHits();
      TClonesArray* hodoHits = fPlanes[ip]->GetHits();

      for(Int_t i=0;i<nphits;i++) {
	Int_t index=((THcHodoHit*)hodoHits->At(i))->GetPaddleNumber()-1;

	if(twogoodtimes[ihhit]){

	  Double_t sigma = 0.5 * ( TMath::Sqrt( TMath::Power( fHodoPosSigma[GetScinIndex(ip,index)],2) +
						TMath::Power( fHodoNegSigma[GetScinIndex(ip,index)],2) ) );
	  Double_t scinWeight = 1 / TMath::Power(sigma,2);
	  Double_t zPosition = fPlanes[ip]->GetZpos() + (index%2)*fPlanes[ip]->GetDzpos();
 	  //	  cout << "hit = " << ihhit + 1 << "   zpos = " << zPosition << "   sigma = " << sigma << endl;

	  sumW  += scinWeight;
	  sumT  += scinWeight * ((THcHodoHit*)hodoHits->At(i))->GetScinCorrectedTime();
	  sumZ  += scinWeight * zPosition;
	  sumZZ += scinWeight * ( zPosition * zPosition );
	  sumTZ += scinWeight * zPosition * ((THcHodoHit*)hodoHits->At(i))->GetScinCorrectedTime();

	} // condition of good scin time
	ihhit ++;
      } // loop over hits of plane
    } // loop over planes

    Double_t tmp = sumW * sumZZ - sumZ * sumZ ;
    Double_t t0 = ( sumT * sumZZ - sumZ * sumTZ ) / tmp ;
    Double_t tmpDenom = sumW * sumTZ - sumZ * sumT;

    if ( TMath::Abs( tmpDenom ) > ( 1 / 10000000000.0 ) ) {

      fBetaNoTrk = tmp / tmpDenom;
      fBetaNoTrkChiSq = 0.;
      ihhit = 0;

      for (Int_t ip = 0; ip < temp_planes; ip++ ){                           // Loop over planes
	Int_t nphits=fPlanes[ip]->GetNScinHits();
	TClonesArray* hodoHits = fPlanes[ip]->GetHits();

	for(Int_t i=0;i<nphits;i++) {
	  Int_t index=((THcHodoHit*)hodoHits->At(i))->GetPaddleNumber()-1;

	  if(twogoodtimes[ihhit]) {

	    Double_t zPosition = fPlanes[ip]->GetZpos() + (index%2)*fPlanes[ip]->GetDzpos();
	    Double_t timeDif = ( ((THcHodoHit*)hodoHits->At(i))->GetScinCorrectedTime() - t0 );
	    Double_t sigma = 0.5 * ( TMath::Sqrt( TMath::Power( fHodoPosSigma[GetScinIndex(ip,index)],2) +
						  TMath::Power( fHodoNegSigma[GetScinIndex(ip,index)],2) ) );
	    fBetaNoTrkChiSq += ( ( zPosition / fBetaNoTrk - timeDif ) *
				 ( zPosition / fBetaNoTrk - timeDif ) ) / ( sigma * sigma );


	  } // condition for good scin time
	  ihhit++;
	} // loop over hits of a plane
      } // loop over planes

      Double_t pathNorm = 1.0;

      fBetaNoTrk = fBetaNoTrk * pathNorm;
      fBetaNoTrk = fBetaNoTrk / 29.979;    // velocity / c

    }  // condition for fTmpDenom
    else {
      fBetaNoTrk = 0.;
      fBetaNoTrkChiSq = -2.;
    } // else condition for fTmpDenom
  }
   fGoodEventTOFCalib=kFALSE;
  if (!fSHMS&&goodplanetime[0]&&goodplanetime[1]&&goodplanetime[2]&&goodplanetime[3]&&fPlanes[0]->GetNGoodHits()==1&&fPlanes[1]->GetNGoodHits()==1&&fPlanes[2]->GetNGoodHits()==1&&fPlanes[3]->GetNGoodHits()==1) fGoodEventTOFCalib=kTRUE;
  if (fSHMS&&goodplanetime[0]&&goodplanetime[1]&&goodplanetime[2]&&fPlanes[0]->GetNGoodHits()==1&&fPlanes[1]->GetNGoodHits()==1&&fPlanes[2]->GetNGoodHits()==1) fGoodEventTOFCalib=kTRUE;

}
//_____________________________________________________________________________
Int_t THcHodoscope::ApplyCorrections( void )
{
  return(0);
}
//_____________________________________________________________________________
Double_t THcHodoscope::TimeWalkCorrection(const Int_t& paddle,
					     const ESide side)
{
  return(0.0);
}


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

  Int_t ntracks = tracks.GetLast()+1; // Number of reconstructed tracks
  Int_t timehist[200];
  // -------------------------------------------------

  //  fDumpOut << " ntrack =  " << ntracks  << endl;
  Int_t temp_planes=fNPlanes;
  if (fSHMS) temp_planes=3;

  if (tracks.GetLast()+1 > 0 ) {

    // **MAIN LOOP: Loop over all tracks and get corrected time, tof, beta...
    Double_t* nPmtHit = new Double_t [ntracks];
    Double_t* timeAtFP = new Double_t [ntracks];
    for ( Int_t itrack = 0; itrack < ntracks; itrack++ ) { // Line 133
      nPmtHit[itrack]=0;
      timeAtFP[itrack]=0;

      THaTrack* theTrack = dynamic_cast<THaTrack*>( tracks.At(itrack) );
      if (!theTrack) return -1;

      for (Int_t ip = 0; ip < temp_planes; ip++ ){
	fGoodPlaneTime[ip] = kFALSE;
	fNScinHits[ip] = 0;
	fNPlaneTime[ip] = 0;
	fSumPlaneTime[ip] = 0.;
      }
      std::vector<Double_t> dedx_temp;
      fdEdX.push_back(dedx_temp); // Create array of dedx per hit
      std::vector<std::vector<GoodFlags> > goodflagstmp1;
      fGoodFlags.push_back(goodflagstmp1);

      Int_t nFPTime = 0;
      Double_t betaChiSq = -3;
      Double_t beta = 0;
      //      timeAtFP[itrack] = 0.;
      Double_t sumFPTime = 0.; // Line 138
      fNScinHit.push_back(0);

      //! Calculate all corrected hit times and histogram
      //! This uses a copy of code below. Results are save in time_pos,neg
      //! including the z-pos. correction assuming nominal value of betap
      //! Code is currently hard-wired to look for a peak in the
      //! range of 0 to 100 nsec, with a group of times that all
      //! agree withing a time_tolerance of time_tolerance nsec. The normal
      //! peak position appears to be around 35 nsec.
      //! NOTE: if want to find particles with beta different than
      //! reference particle, need to make sure this is big enough
      //! to accomodate difference in TOF for other particles
      //! Default value in case user hasnt defined something reasonable

      for (Int_t j=0; j<200; j++) { timehist[j]=0; } // Line 176

      // Loop over scintillator planes.
      // In ENGINE, its loop over good scintillator hits.

      fTOFCalc.clear();   // SAW - Can we
      fTOFPInfo.clear();  // SAW - combine these two?
      Int_t ihhit = 0;		// Hit # overall

     for(Int_t ip = 0; ip < temp_planes; ip++ ) {

	std::vector<GoodFlags> goodflagstmp2;
	fGoodFlags[itrack].push_back(goodflagstmp2);

	fNScinHits[ip] = fPlanes[ip]->GetNScinHits();
	TClonesArray* hodoHits = fPlanes[ip]->GetHits();

	Double_t zPos = fPlanes[ip]->GetZpos();
	Double_t dzPos = fPlanes[ip]->GetDzpos();

	// first loop over hits with in a single plane
	for (Int_t iphit = 0; iphit < fNScinHits[ip]; iphit++ ){
	  // iphit is hit # within a plane
	  THcHodoHit *hit = (THcHodoHit*)hodoHits->At(iphit);

	  fTOFPInfo.push_back(TOFPInfo());
	  // Can remove these as we will initialize in the constructor
	  //	  fTOFPInfo[ihhit].time_pos = -99.0;
	  //	  fTOFPInfo[ihhit].time_neg = -99.0;
	  //	  fTOFPInfo[ihhit].keep_pos = kFALSE;
	  //	  fTOFPInfo[ihhit].keep_neg = kFALSE;
	  fTOFPInfo[ihhit].scin_pos_time = 0.0;
	  fTOFPInfo[ihhit].scin_neg_time = 0.0;
	  fTOFPInfo[ihhit].hit = hit;
	  fTOFPInfo[ihhit].planeIndex = ip;
	  fTOFPInfo[ihhit].hitNumInPlane = iphit;
	  fTOFPInfo[ihhit].onTrack = kFALSE;

	  Int_t paddle = hit->GetPaddleNumber()-1;
	  Double_t zposition = zPos + (paddle%2)*dzPos;

	  Double_t xHitCoord = theTrack->GetX() + theTrack->GetTheta() *
	    ( zposition ); // Line 183

	  Double_t yHitCoord = theTrack->GetY() + theTrack->GetPhi() *
	    ( zposition ); // Line 184

	  Double_t scinTrnsCoord, scinLongCoord;
	  if ( ( ip == 0 ) || ( ip == 2 ) ){ // !x plane. Line 185
	    scinTrnsCoord = xHitCoord;
	    scinLongCoord = yHitCoord;
	  }

	  else if ( ( ip == 1 ) || ( ip == 3 ) ){ // !y plane. Line 188
	    scinTrnsCoord = yHitCoord;
	    scinLongCoord = xHitCoord;
	  }
	  else { return -1; } // Line 195
	  fTOFPInfo[ihhit].scinTrnsCoord = scinTrnsCoord;
	  fTOFPInfo[ihhit].scinLongCoord = scinLongCoord;

	  Double_t scinCenter = fPlanes[ip]->GetPosCenter(paddle) + fPlanes[ip]->GetPosOffset();

	  // Index to access the 2d arrays of paddle/scintillator properties
	  Int_t fPIndex = GetScinIndex(ip,paddle);
          
	  if ( TMath::Abs( scinCenter - scinTrnsCoord ) <
	       ( fPlanes[ip]->GetSize() * 0.5 + fPlanes[ip]->GetHodoSlop() ) ){ // Line 293

	    fTOFPInfo[ihhit].onTrack = kTRUE;
	    Double_t zcor = zposition/(29.979*fBetaNominal)*
		TMath::Sqrt(1. + theTrack->GetTheta()*theTrack->GetTheta()
			    + theTrack->GetPhi()*theTrack->GetPhi());
	    fTOFPInfo[ihhit].zcor = zcor;
	    if (fCosmicFlag) {
	    Double_t zcor = -zposition/(29.979*1.0)*
		TMath::Sqrt(1. + theTrack->GetTheta()*theTrack->GetTheta()
			    + theTrack->GetPhi()*theTrack->GetPhi());
	    fTOFPInfo[ihhit].zcor = zcor;