CalGausHFDUNE35t_module.cc

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#ifndef CALGAUSHFDUNE35T_H
#define CALGAUSHFDUNE35T_H

////////////////////////////////////////////////////////////////////////
//
// CalGausHFDUNE35t class
//
// jti3@fnal.gov
//
// 06-21-13 Branched from CalWire_module and added GausHitFinder_module code
//
// brebel@fnal.gov
//
// 11-3-09 Pulled all FFT code out and put into Utilitiess/LArFFT
//
////////////////////////////////////////////////////////////////////////

#include <string>
#include <vector>
#include <algorithm> // std::accumulate
#include <utility> // std::move

#include "art/Framework/Core/ModuleMacros.h" 
#include "art/Framework/Core/EDProducer.h"
#include "art/Framework/Principal/Event.h" 
#include "art/Framework/Principal/Handle.h" 
#include "canvas/Persistency/Common/Ptr.h" 
#include "art/Framework/Services/Registry/ServiceHandle.h" 
#include "fhiclcpp/ParameterSet.h" 
#include "messagefacility/MessageLogger/MessageLogger.h" 
#include "cetlib_except/exception.h"

#include "dunecore/Utilities/SignalShapingServiceDUNE.h"
#include "larcoreobj/SimpleTypesAndConstants/RawTypes.h" // raw::ChannelID_t
#include "larcore/Geometry/Geometry.h"
#include "larevt/Filters/ChannelFilter.h"
#include "lardataobj/RawData/RawDigit.h"
#include "lardataobj/RawData/raw.h"
#include "lardataobj/RecoBase/Hit.h"
#include "lardata/ArtDataHelper/HitCreator.h"
#include "lardata/Utilities/LArFFT.h"

// ROOT Includes 
#include "TH1D.h"
#include "TDecompSVD.h"
#include "TMath.h"
#include "TComplex.h"
#include "TFile.h"
#include "TH2D.h"
#include "TF1.h"
#include "TTree.h"
// #include "TCanvas.h"
// #include "TStyle.h"


/* unused function
namespace{
  // Fill histogram from vector (set underflow/overflow bins to zero).

  void vector_to_hist(const std::vector<double>& v, TH1D* h)
  {
    if (!h) throw cet::exception("vector_to_hist") << "no histogram specified\n";
    int nvec = v.size();
    int nbins = h->GetNbinsX();
    int nfill = std::min(nvec, nbins);
    h->SetBinContent(0, 0.);
    int zerobin = h->GetXaxis()->FindBin(0.);
    for(int i=1; i<=nfill; ++i) {
      if(i >= zerobin)
        h->SetBinContent(i, v[i - zerobin]);
      else
        h->SetBinContent(i, v[i - zerobin + nvec]);
    }
    for(int i=nfill+1; i<=nbins+1; ++i)
      h->SetBinContent(i, 0.);
  }

}
*/

///creation of calibrated signals on wires
namespace calgaushf {

  class CalGausHFDUNE35t : public art::EDProducer {

  public:
    
    // create calibrated signals on wires. this class runs 
    // an fft to remove the electronics shaping.     
    explicit CalGausHFDUNE35t(fhicl::ParameterSet const& pset); 
    virtual ~CalGausHFDUNE35t();
    
    void produce(art::Event& evt); 
    void beginJob(); 
    void endJob();                 
    void reconfigure(fhicl::ParameterSet const& p);
 
  private:
    int          fDeconvKernSize;    //< Length of truncated deconvolution kernel
    //int          fDataSize;          ///< size of raw data on one wire // unused
    int          fPostsample;        ///< number of postsample bins
    std::string  fDigitModuleLabel;  ///< module that made digits
                                                       ///< constants
    std::string  fSpillName;  ///< nominal spill is an empty string
                              ///< it is set by the DigitModuleLabel
                              ///< ex.:  "daq:preSpill" for prespill data
    std::string     fCalDataModuleLabel;
    double          fMinSigInd;     ///<Induction signal height threshold 
    double          fMinSigCol;     ///<Collection signal height threshold 
    double          fIndWidth;      ///<Initial width for induction fit
    double          fColWidth;      ///<Initial width for collection fit
    double          fIndMinWidth;   ///<Minimum induction hit width
    double          fColMinWidth;   ///<Minimum collection hit width
    int             fMaxMultiHit;   ///<maximum hits for multi fit 
    int             fAreaMethod;    ///<Type of area calculation  
    std::vector<double> fAreaNorms; ///<factors for converting area to same units as peak height 
    double          fChi2NDF;       ///< maximum Chisquared / NDF allowed for a hit to be saved
    
    //double    WireNumber[100000];
    //double    TotalSignal[100000];
    double      StartIime;
    double      StartTimeError;
    double      EndTime;
    double      EndTimeError;
    int NumOfHits;
    double      RMS;
    double      MeanPosition;
    double      MeanPosError;
    double      Amp;
    double      AmpError;
    double      Charge;
    double      ChargeError;
    double      FitGoodnes;
    int         FitNDF;
    int collectioncount;
    int inductioncount;

    
  protected: 
    //double      expfitf(double *x,double *par);
    
  }; // class CalGausHFDUNE35t

  DEFINE_ART_MODULE(CalGausHFDUNE35t)
  

  //-------------------------------------------------
  CalGausHFDUNE35t::CalGausHFDUNE35t(fhicl::ParameterSet const& pset) : EDProducer{pset}
  {
    fSpillName="";
    this->reconfigure(pset);

    // let HitCollectionCreator declare that we are going to produce
    // hits and associations with wires and raw digits
    recob::HitCollectionCreator::declare_products
      (producesCollector(), fSpillName, false /* doWireAssns */, true /* doRawDigitAssns */);
    
  }
  
  //-------------------------------------------------
  CalGausHFDUNE35t::~CalGausHFDUNE35t()
  {
  }

  //////////////////////////////////////////////////////
  void CalGausHFDUNE35t::reconfigure(fhicl::ParameterSet const& p)
  {
    fDigitModuleLabel = p.get< std::string >("DigitModuleLabel", "daq");
    fPostsample       = p.get< int >        ("PostsampleBins");
    fDeconvKernSize   = p.get< int >        ("DeconvKernSize");
    
    fSpillName="";
    
    size_t pos = fDigitModuleLabel.find(":");
    if( pos!=std::string::npos ) {
      fSpillName = fDigitModuleLabel.substr( pos+1 );
      fDigitModuleLabel = fDigitModuleLabel.substr( 0, pos );
    }
  
    // Implementation of optional member function here.
    //fCalDataModuleLabel = p.get< std::string  >("CalDataModuleLabel");
    fMinSigInd          = p.get< double       >("MinSigInd");
    fMinSigCol          = p.get< double       >("MinSigCol"); 
    fIndWidth           = p.get< double       >("IndWidth");  
    fColWidth           = p.get< double       >("ColWidth");
    fIndMinWidth        = p.get< double       >("IndMinWidth");
    fColMinWidth        = p.get< double       >("ColMinWidth");                 
    fMaxMultiHit        = p.get< int          >("MaxMultiHit");
    fAreaMethod         = p.get< int          >("AreaMethod");
    fAreaNorms          = p.get< std::vector< double > >("AreaNorms");
    fChi2NDF          = p.get< double       >("Chi2NDF");
  
  
  }

  //-------------------------------------------------
  void CalGausHFDUNE35t::beginJob()
  { 
    collectioncount = 0;
    inductioncount = 0;
 
  }

  //////////////////////////////////////////////////////
  void CalGausHFDUNE35t::endJob()
  {  
  }
  
//   //////////////////////////////////////////////////////
//   double CalGausHFDUNE35t::expfitf(double *x,double *par)
//   {
//     double arg1 = 0;
//     double arg2 = 0;
//     if (par[3] != 0) arg1 = (x-par[2])/par[3];
//     if (par[4] != 0) arg2 = (x-par[2])/par[4];

//     double fitval = par[0]*TMath::Exp(-0.5*arg*arg); par[0]+par[1]*exp(-arg1)/(1+exp(-arg2));
//     return fitval;
//   }

  //////////////////////////////////////////////////////
  void CalGausHFDUNE35t::produce(art::Event& evt)
  {      



    // get the geometry
    art::ServiceHandle<geo::Geometry> geom;


    // Get signal shaping service.
    art::ServiceHandle<util::SignalShapingServiceDUNE> sss;


    //Gaussian hit finder initializations etc.
    TH1::AddDirectory(kFALSE);
    
    
    // ---------------------------
    // --- Seed Fit Functions  --- (This function used to "seed" the mean peak position)
    // ---------------------------
    TF1 *hit    = new TF1("hit","gaus",0,3200); // FIXME use DetectorProperties
    
    // ###############################################
    // ### Making a ptr vector to put on the event ###
    // ###############################################
    // this contains the hit collection
    // and its associations to raw digits (not to wires)
    recob::HitCollectionCreator hcol(
      evt, fSpillName, false /* doWireAssns */, true /* doRawDigitAssns */
      );
    
    // ##########################################
    // ### Reading in the Wire List object(s) ###
    // ##########################################
    //auto wireVecHandle = evt.getHandle< std::vector<recob::Wire> >(fCalDataModuleLabel);
    //art::ServiceHandle<geo::Geometry> geom;
    
    // #########################################################
    // ### List of useful variables used throughout the code ###
    // #########################################################  
    double threshold              = 0.;               // minimum signal size for id'ing a hit
    double fitWidth               = 0.;               //hit fit width initial value
    double minWidth               = 0.;               //minimum hit width
    //channel              = 0;                // channel number
    geo::SigType_t sigType;                           // Signal Type (Collection or Induction)
    geo::View_t view;                                // view
    std::vector<int> startTimes;                    // stores time of 1st local minimum
    std::vector<int> maxTimes;                      // stores time of local maximum    
    std::vector<int> endTimes;                      // stores time of 2nd local minimum
    int time             = 0;                         // current time bin
    int minTimeHolder    = 0;                         // current start time
    
    std::string eqn        = "gaus(0)";      // string for equation for gaus fit
    //std::string seed        = "gaus(0)";      // string for equation seed gaus fit
    
    
    bool maxFound        = false;            // Flag for whether a peak > threshold has been found
    std::stringstream numConv;
          

    // Read in the digit List object(s).
    art::InputTag itag1(fDigitModuleLabel, fSpillName);
    art::Handle< std::vector<raw::RawDigit> > digitVecHandle;
    if(fSpillName.size()>0) digitVecHandle = evt.getHandle< std::vector<raw::RawDigit> >(itag1);
    else digitVecHandle = evt.getHandle< std::vector<raw::RawDigit> >(fDigitModuleLabel);

    if (!digitVecHandle->size())  return;
    mf::LogInfo("CalGausHFDUNE35t") << "CalGausHFDUNE35t:: digitVecHandle size is " << digitVecHandle->size();

    // Use the handle to get a particular (0th) element of collection.
    art::Ptr<raw::RawDigit> digitVec0(digitVecHandle, 0);
    
    if (digitVec0->Compression() != raw::kZeroSuppression) {
      throw art::Exception(art::errors::UnimplementedFeature)
        << "CalGausHFDUNE only supports zero-suppressed raw digit input!";
    } // if


    uint32_t     channel(0); // channel number
    unsigned int bin(0);     // time bin loop variable
    
    filter::ChannelFilter *chanFilt = new filter::ChannelFilter();  

    std::vector<float> holder;                // holds signal data
    std::vector<float> rawadc_conv;           // holds signal data before time domain deconvolution
    std::vector<short> rawadc;  // vector holding uncompressed adc values

    // loop over all wires    
    for(size_t rdIter = 0; rdIter < digitVecHandle->size(); ++rdIter){ // ++ move
      holder.clear();
      
      // get the reference to the current raw::RawDigit
      art::Ptr<raw::RawDigit> digitVec(digitVecHandle, rdIter);
      channel = digitVec->Channel();

      // skip bad channels
      if(!chanFilt->BadChannel(channel)) {


        // unpack the zero-suppressed raw data without adding all zeros back
        //raw::Uncompress(digitVec->fADC, rawadc, digitVec->Compression());

        const int numberofblocks = digitVec->ADC(1);

        int zerosuppressedindex = numberofblocks*2 + 2;

        //loop over all nonzero blocks
        for(int i=0; i<numberofblocks; i++){

          const int lengthofblock = digitVec->ADC(2+numberofblocks+i);
          rawadc.resize(lengthofblock);
          holder.resize(lengthofblock);
          rawadc_conv.resize(lengthofblock);


          for (int j=0;j<lengthofblock;j++)
            {
              rawadc[j] = digitVec->ADC(zerosuppressedindex);
              zerosuppressedindex++;
            }
                  
          
          // loop over all adc values and subtract the pedestal
          for(bin = 0; bin < rawadc.size(); ++bin) 
            rawadc_conv[bin]=(rawadc[bin]-digitVec->GetPedestal());


          sigType = geom->SignalType(channel);
          view = geom->View(channel);

          if(sigType == geo::kCollection){

            //Leave collection plane signals as is
            for(bin = 0; bin < rawadc_conv.size(); ++bin)
              holder[bin] = rawadc_conv[bin];
          }
          else if(sigType == geo::kInduction){

            //Integrate over signal in induction planes
            for(bin = 0;  bin < rawadc_conv.size(); ++bin) 
              holder[bin] = (bin>0) ? rawadc_conv[bin] + holder[bin-1] : rawadc_conv[bin];
          }


          
          //Beginning of Gaussian hit finder loop over signal blocks


          //##############################
          //### Looping over the wires ###
          //############################## 
          
          //for(size_t wireIter = 0; wireIter < wirecol->size(); wireIter++){
          
          //art::Ptr<recob::Wire> wire(wirecol, wireIter);
          
          //std::vector<recob::Wire>::iterator wire;
          //for(wire=wirecol->begin(); wire != wirecol->end(); wire++){
          // --- Setting Channel Number and Wire Number as well as signal type ---
          //channel = wire->RawDigit()->Channel();
          
          
          // -----------------------------------------------------------
          // -- Clearing variables at the start of looping over wires --
          // -----------------------------------------------------------
          startTimes.clear();
          maxTimes.clear();
          endTimes.clear();
          //std::vector<float> signal(wire->Signal());
          std::vector<float> signal(holder);
          std::vector<float>::iterator timeIter;            // iterator for time bins
          time          = 0;
          minTimeHolder = 0;
          maxFound      = false;
          // -- Setting the appropriate signal widths and thresholds --
          // --    for either the collection or induction plane      --
          if(sigType == geo::kInduction){
            threshold     = fMinSigInd;
            fitWidth      = fIndWidth;
            minWidth      = fIndMinWidth;
          }//<-- End if Induction Plane
          else if(sigType == geo::kCollection){
            threshold = fMinSigCol;
            fitWidth  = fColWidth;
            minWidth  = fColMinWidth;
          }//<-- End if Collection Plane
          
          
          // ##################################
          // ### Looping over Signal Vector ###
          // ##################################
          for(timeIter = signal.begin();timeIter+2<signal.end();timeIter++){
            // ##########################################################
            // ###                LOOK FOR A MINIMUM                  ###
            // ### Testing if the point timeIter+1 is at a minimum by ###
            // ###  checking if timeIter and timeIter+1 and if it is  ###
            // ###         then we add this to the endTimes           ###
            // ##########################################################
            if(*timeIter > *(timeIter+1) && *(timeIter+1) < *(timeIter+2)){
              //--- Note: We only keep the a minimum if we've already ---
              //---          found a point above threshold            ---
              if(maxFound){
                endTimes.push_back(time+1);
                maxFound = false;
                //keep these in case new hit starts right away
                minTimeHolder = time+2; 
              }
              else minTimeHolder = time+1; 
              
            }//<---End Checking if this is a minimum
            
            
            // ######################################################## 
            // ### Testing if the point timeIter+1 is a maximum and ###
            // ###  if it and is above threshold then we add it to  ###
            // ###                  the startTime                   ###
            // ########################################################
            //if not a minimum, test if we are at a local maximum 
            //if so, and the max value is above threshold, add it and proceed.
            else if(*timeIter < *(timeIter+1) && *(timeIter+1) > *(timeIter+2) && *(timeIter+1) > threshold){ 
              maxFound = true;
              maxTimes.push_back(time+1);
              startTimes.push_back(minTimeHolder);          
            }
            
            time++;
            
          }//end loop over signal vec 
          
          // ###########################################################    
          // ### If there was no minimum found before the end, but a ### 
          // ###  maximum was found then add an end point to the end ###
          // ###########################################################
          while( maxTimes.size() > endTimes.size() ){ 
            endTimes.push_back(signal.size()-1);
            
          }//<---End maxTimes.size > endTimes.size
          
          // ####################################################
          // ### If no startTime hit was found skip this wire ###
          // ####################################################
          if( startTimes.size() == 0 ){
            continue;
          }  
          
          /////////////////////////////////////////////////////////////////////////////
          /////////////////////////////////////////////////////////////////////////////
          
          // ##########################################################
          // ### PERFORM THE FITTING, ADDING HITS TO THE HIT VECTOR ###
          // ##########################################################
          
          //All code below does the fitting, adding of hits
          //to the hit vector and when all wires are complete 
          //saving them 
          
          double totSig(0);                                             //stores the total hit signal
          double startT(0);                                             //stores the start time
          double endT(0);                                               //stores the end time
          int numHits(0);                                               //number of consecutive hits being fitted
          int size(0);                                                  //size of data vector for fit
          int hitIndex(0);                                              //index of current hit in sequence
          double amplitude(0);                                          //fit parameters
          double minPeakHeight(0);                                      //lowest peak height in multi-hit fit
          
          
          StartIime = 0;                                                        // stores the start time of the hit
          StartTimeError = 0;                                           // stores the error assoc. with the start time of the hit
          EndTime = 0;                                                  // stores the end time of the hit
          EndTimeError = 0;                                             // stores the error assoc. with the end time of the hit
          RMS = 0;                                                      // stores the RMS of the gaussian shape of the hit
          MeanPosition = 0;                                             // stores the peak time position of the hit
          MeanPosError = 0;                                             // stores the error assoc. with thte peak time of the hit
          Charge = 0;                                                   // stores the total charge assoc. with the hit
          ChargeError = 0;                                                      // stores the error on the charge
          Amp = 0;                                                      // stores the amplitude of the hit
          AmpError = 0;                                                 // stores the error assoc. with the amplitude
          NumOfHits = 0;                                                // stores the multiplicity of the hit
          FitGoodnes = 0;                                                       // stores the Chi2/NDF of the hit
          FitNDF = -1;                                                          // stores the NDF of the hit
          
          
          
          //stores gaussian paramters first index is the hit number
          //the second refers to height, position, and width respectively
          std::vector<double>  hitSig;  
          
          // ########################################
          // ### Looping over the hitIndex Vector ###
          // ########################################
          while( hitIndex < (signed)startTimes.size() ) {
            // --- Zeroing Start Times and End Times ---
            startT = 0;
            endT   = 0;
            // Note: numHits is hardcoded to one here (Need to fix!)
            numHits=1;
            
            minPeakHeight = signal[maxTimes[hitIndex]];
            
            // consider adding pulse to group of consecutive hits if:
            // 1 less than max consecutive hits
            // 2 we are not at the last point in the signal vector
            // 3 the height of the dip between the two is greater than threshold/2
            // 4 and there is no gap between them
            while(numHits < fMaxMultiHit && numHits+hitIndex < (signed)endTimes.size() && 
                  signal[endTimes[hitIndex+numHits-1]] >threshold/2.0 &&  
                  startTimes[hitIndex+numHits] - endTimes[hitIndex+numHits-1] < 2){
              if(signal[maxTimes[hitIndex+numHits]] < minPeakHeight){ 
                minPeakHeight=signal[maxTimes[hitIndex+numHits]];
                
              }//<---Only move the mean peakHeight in this hit
              
              numHits++;//<---Interate the multihit function
              
            }//<---End multihit while loop
            
            
            
            // ###########################################################      
            // ### Finding the first point from the beginning (startT) ###
            // ###     which is greater then 1/2 the smallest peak     ###
            // ###########################################################
            startT=startTimes[hitIndex];
            while(signal[(int)startT] < minPeakHeight/2.0)  {startT++;}
            
            // #########################################################        
            // ### Finding the first point from the end (endT) which ###
            // ###      is greater then 1/2 the smallest peak        ###
            // #########################################################
            endT=endTimes[hitIndex+numHits-1];
            while(signal[(int)endT] <minPeakHeight/2.0) {endT--;}
            
            
            // ###############################################################
            // ### Putting the current considered hit into a 1-D Histogram ###
            // ###############################################################
            //--- Size of hit = endT - startT ---
            size = (int)(endT-startT);
            
            // ###########################################################################
            // ###    Bug Fix: For ADC counts occuring at the end of the ticks range   ###
            // ### the hitfinder incorrectly assigns the size of the hit as a negative ###
            // ###      number...so we fix this to be 0 so that this hit is skipped    ###
            // ###########################################################################
            if(size < 0){size = 0;}
            
            
            // --- TH1D HitSignal ---
            TH1D hitSignal("hitSignal","",size,startT,endT);
            
            for(int i = (int)startT; i < (int)endT; i++){
              // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
              // ~~~ Filling the pulse signals into TH1D histograms ~~~
              // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
              hitSignal.Fill(i,signal[i]);
              
              //std::cout<<"i = "<<i<<" , signal[i] = "<<signal[i]<<std::endl;
            }//<---End for looping over startT and endT
            
            
            // ##################################################################################################
            // ### Trying to utilize the old approach of builing my TF1 and then implementing this new method ###
            // ##################################################################################################
            
            // ########################################################
            // ### Building TFormula for seedHit and basic Gaussian ###
            // ########################################################
            eqn = "gaus(0)";
            for(int i = 3; i < numHits*3; i+=3){
              eqn.append("+gaus(");
              numConv.str("");
              numConv << i;
              eqn.append(numConv.str());
              eqn.append(")");
            }
            
            
            
            // --- TF1 function for GausHit  ---
            TF1 Gaus("Gaus",eqn.c_str(),0,size);
            
            // ##############################################################################
            // ### For multi-pulse hits we loop over all the hits and fit N Gaus function ###
            // ##############################################################################
            if(numHits > 1) {
              // --- Loop over numHits ---
              for(int i = 0; i < numHits; ++i){
                
                // ###################################################################
                // ### Set the parameters of the Gaus hit based on the seedHit fit ###
                // ###################################################################
                //amplitude = 0.5*(threshold+signal[maxTimes[hitIndex+i]]);
                
                amplitude = signal[maxTimes[hitIndex+i]];
                Gaus.SetParameter(3*i,amplitude);
                Gaus.SetParameter(1+3*i, maxTimes[hitIndex+i]);
                Gaus.SetParameter(2+3*i, fitWidth);
                Gaus.SetParLimits(3*i, 0.0, 3.0*amplitude);
                Gaus.SetParLimits(1+3*i, startT , endT);
                Gaus.SetParLimits(2+3*i, 0.0, 10.0*fitWidth);
              }//end loop over hits
            }//end if numHits > 1
            
            // ######################################################################
            // ### For single pulse hits we perform a fit using a single Gaussian ###
            // ######################################################################
            else{
              
              Gaus.SetParameters(signal[maxTimes[hitIndex]],maxTimes[hitIndex],fitWidth);
              Gaus.SetParLimits(0,0.0,1.5*signal[maxTimes[hitIndex]]);
              Gaus.SetParLimits(1, startT , endT);
              Gaus.SetParLimits(2,0.0,10.0*fitWidth);
            }
            
            // ####################################################
            // ### PERFORMING THE TOTAL GAUSSIAN FIT OF THE HIT ###
            // ####################################################
            hitSignal.Sumw2();


            hitSignal.Fit(&Gaus,"QNRW","", startT, endT);
            //hitSignal.Fit(&Gaus,"QR0LLi","", startT, endT);


            
            for(int hitNumber = 0; hitNumber < numHits; ++hitNumber){
              totSig = 0;       
              
              
              // ###########################################################
              // ### Record this hit if the amplitude is > threshold/2.0 ###
              // ###             and the width is > minWidth             ###
              // ###########################################################
              if(Gaus.GetParameter(3*hitNumber) > threshold/2.0 && 
                 Gaus.GetParameter(3*hitNumber+2) > minWidth){
                StartIime                       = Gaus.GetParameter(3*hitNumber+1) - Gaus.GetParameter(3*hitNumber+2); // position - width
                
                EndTime                 = Gaus.GetParameter(3*hitNumber+1) + Gaus.GetParameter(3*hitNumber+2); // position + width
                
                MeanPosition            = Gaus.GetParameter(3*hitNumber+1);
                RMS                     = Gaus.GetParameter(3*hitNumber+2);
                
                //StartTimeError                        = TMath::Sqrt( (Gaus.GetParError(3*hitNumber+1)*Gaus.GetParError(3*hitNumber+1)) + 
                //                                             (Gaus.GetParError(3*hitNumber+2)*Gaus.GetParError(3*hitNumber+2)));
                
                //EndTimeError                  = TMath::Sqrt( (Gaus.GetParError(3*hitNumber+1)*Gaus.GetParError(3*hitNumber+1)) + 
                //                                             (Gaus.GetParError(3*hitNumber+2)*Gaus.GetParError(3*hitNumber+2)));
                
                
                //MeanPosError                  = Gaus.GetParError(3*hitNumber+1);
                
                
                
                
                hitSig.resize(size);
                for(int sigPos = 0; sigPos<size; sigPos++){ //<---Loop over the size (endT - startT)
                  
                  hitSig[sigPos] = Gaus.GetParameter(3*hitNumber)*TMath::Gaus(sigPos+startT,Gaus.GetParameter(3*hitNumber+1), Gaus.GetParameter(3*hitNumber+2));
                  totSig+=hitSig[(int)sigPos];
                  
                }//<---End Signal postion loop
                
                // --- Getting the total charge using the area method ---
                if(fAreaMethod) {
                  totSig = std::sqrt(2*TMath::Pi())*Gaus.GetParameter(3*hitNumber)*Gaus.GetParameter(3*hitNumber+2)/fAreaNorms[(size_t)sigType];
                  
                }//<---End Area Method
                Charge                          = totSig;
                // ---------------------------------------------------------------------------------
                // --- chargeErr=TMath::Sqrt(TMath::Pi())*(amplitudeErr*width+widthErr*amplitude); ---
                // -----------------------------------------------------------------------------------
                ChargeError                     = TMath::Sqrt(TMath::Pi())*(Gaus.GetParError(3*hitNumber+0)*Gaus.GetParameter(3*hitNumber+2)+
                                                                            Gaus.GetParError(3*hitNumber+2)*Gaus.GetParameter(3*hitNumber+0));   //estimate from area of Gaussian
            Amp                         = Gaus.GetParameter(3*hitNumber);
            AmpError                    = Gaus.GetParError(3*hitNumber);
            NumOfHits                   = numHits;
            
            // #######################################################
            // ### Using seeded values to get a better estimate of ###
            // ###        the errors associated with the fit       ###
            // #######################################################
            // -----------------------------------------
            // --- Determing the goodness of the fit ---
            // -----------------------------------------
            hit->SetParameters(Amp,MeanPosition, Gaus.GetParameter(3*hitNumber+2));
            hit->FixParameter(0,Amp);
            //hit->SetParLimits(0,Amp/2, Amp*2);
            //hit->FixParameter(1,MeanPosition);
            hit->SetParLimits(1,MeanPosition - 3, MeanPosition + 3);
            //hit->FixParameter(2,Gaus.GetParameter(3*hitNumber+2));//<---Should I be setting the fitWidth initally
            // #############################
            // ### Perform Hit on Signal ###
            // #############################
            
            
            float TempStartTime = MeanPosition - 4;
            float TempEndTime   = MeanPosition  + 4;


            hitSignal.Fit(hit,"QNRLLi","", TempStartTime, TempEndTime);

//          char outputfilename[100];
//          if(size>0){
//            if(sigType == geo::kInduction && inductioncount < 100){
//              sprintf(outputfilename,"/dune/data/users/jti3/fits/induction_calgaus_fit_%d.eps",inductioncount);
//              TCanvas *c1 = new TCanvas("c1","plot");
//              c1->SetFillColor(0);
//              gStyle->SetOptFit(1);
//              hitSignal.Draw();
//              hitSignal.Fit(hit,"QRLLi","", TempStartTime, TempEndTime);
//              //hitSignal.Draw();
//              c1->Print(outputfilename);
//              c1->Close();
//              inductioncount++;
                
//            }
//            else if(sigType == geo::kCollection && collectioncount < 100){
//              sprintf(outputfilename,"/dune/data/users/jti3/fits/collection_calgaus_fit_%d.eps",collectioncount);
//              TCanvas *c1 = new TCanvas("c1","plot");
//              c1->SetFillColor(0);
//              gStyle->SetOptFit(1);
//              hitSignal.Draw();
//              hitSignal.Fit(hit,"QRLLi","", TempStartTime, TempEndTime);
//              //hitSignal.Draw();
//              c1->Print(outputfilename);
//              c1->Close();
//              collectioncount++;
//            }
              
//            else
//              hitSignal.Fit(hit,"QNRLLi","", TempStartTime, TempEndTime);
//          }
//          else hitSignal.Fit(hit,"QNRLLi","", TempStartTime, TempEndTime);

            
            FitGoodnes                  = hit->GetChisquare() / hit->GetNDF();
            FitNDF                      = hit->GetNDF();
            
            StartTimeError                      = TMath::Sqrt( (hit->GetParError(1)*hit->GetParError(1)) + 
                                                               (hit->GetParError(2)*hit->GetParError(2)));
            
            EndTimeError                        = TMath::Sqrt( (hit->GetParError(1)*hit->GetParError(1)) + 
                                                               (hit->GetParError(2)*hit->GetParError(2)));
            
            
            MeanPosError                        = hit->GetParError(1);
            
            // ####################################################################################
            // ### Skipping hits with a chi2/NDF larger than the value defined in the .fcl file ###
            // ####################################################################################
            if(FitGoodnes > fChi2NDF){continue;}
            
            // get the WireID for this hit
            std::vector<geo::WireID> wids = geom->ChannelToWire(channel);
            ///\todo need to have a disambiguation algorithm somewhere in here
            // for now, just take the first option returned from ChannelToWire
            geo::WireID wid = wids[0];
            
            
            recob::Hit hit(
              channel,                 // channel
              (raw::TDCtick_t) startT, // start_tick
              (raw::TDCtick_t) endT,   // end_tick
              MeanPosition,            // peak_time
              MeanPosError,            // sigma_peak_time
              RMS,                     // rms,
              Amp,                     // peak_amplitude,
              AmpError,                // sigma_peak_amplitude
              std::accumulate          // summedADC
                (signal.begin() + TempStartTime, signal.begin() + TempEndTime, 0.),
              Charge,                  // hit_integral
              ChargeError,             // hit_sigma_integral
              NumOfHits,               // multiplicity
              hitNumber,               // local_index
              FitGoodnes,              // goodness_of_fit
              FitNDF,                  // dof
              view,                    // view
              sigType,                 // signal_type
              wid                      // wireID
              );
            hcol.emplace_back(std::move(hit), digitVec);
            
              }//<---End looking at hits over threshold
              
            }//<---End Looping over numHits
            
            
            hitIndex+=numHits;
          }//<---End while hitIndex < startTimes.size()
          
          

          
        } // end loop over nonzero blocks
        
        
      } // end if not a bad channel 
      
      
    } // end loop over wires
    
    // move the hit collection and the associations into the event
    hcol.put_into(evt);

    delete chanFilt;      
    
    
    return;
  }
  
} // end namespace calgaushf


#endif // CALGAUSHFDUNE35T_H