FFTHitFinder_module.cc

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#ifndef FFTHITFINDER_H
#define FFTHITFINDER_H
//
// FFTHitFinder class
//
// pagebri3@msu.edu
//
//  This algorithm is designed to find hits on wires after deconvolution
//  with an average shape used as the input response.

// C/C++ standard library
#include <string>
#include <vector>
#include <utility> // std::move
#include <algorithm> // std::accumulate

// Framework includes
#include "art/Framework/Core/ModuleMacros.h" 
#include "art/Framework/Principal/Event.h" 
#include "art/Framework/Core/EDProducer.h" 
#include "canvas/Persistency/Common/FindOneP.h"
#include "art/Framework/Services/Registry/ServiceHandle.h"

// LArSoft Includes
#include "larcoreobj/SimpleTypesAndConstants/geo_types.h"
#include "larcoreobj/SimpleTypesAndConstants/RawTypes.h" // raw::ChannelID_t
#include "larcore/Geometry/Geometry.h"
#include "larcorealg/Geometry/CryostatGeo.h"
#include "larcorealg/Geometry/TPCGeo.h"
#include "larcorealg/Geometry/PlaneGeo.h"
#include "lardataobj/RawData/RawDigit.h"
#include "lardataobj/RecoBase/Wire.h"
#include "lardataobj/RecoBase/Hit.h"
#include "lardata/ArtDataHelper/HitCreator.h"

// ROOT Includes 
#include "TH1D.h"
#include "TDecompSVD.h"
#include "TMath.h"
#include "TF1.h"

namespace hit{

  class FFTHitFinder : public art::EDProducer {
    
  public:
    
    explicit FFTHitFinder(fhicl::ParameterSet const& pset); 
    virtual ~FFTHitFinder();
         
    void produce(art::Event& evt); 
    void beginJob(); 
    void endJob(); 
    void reconfigure(fhicl::ParameterSet const& p);                

  private:
        
    std::string     fCalDataModuleLabel;
    double          fMinSigInd;     
    double          fMinSigCol;     
    double          fIndWidth;      
    double          fColWidth;      
    double          fIndMinWidth;   
    double          fColMinWidth;   
    int             fMaxMultiHit;   
    int             fAreaMethod;    
    std::vector<double> fAreaNorms; 
  protected: 
    
  
  }; // class FFTHitFinder  
  
  //-------------------------------------------------
  FFTHitFinder::FFTHitFinder(fhicl::ParameterSet const& pset)
  {
    this->reconfigure(pset);
    
    // let HitCollectionCreator declare that we are going to produce
    // hits and associations with wires and raw digits
    // (with no particular product label)
    recob::HitCollectionCreator::declare_products(*this);
  }


  //-------------------------------------------------
  FFTHitFinder::~FFTHitFinder()
  {
  }
  
  //-------------------------------------------------
  void FFTHitFinder::reconfigure(fhicl::ParameterSet const& p)
  {
    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");
  }  

  //-------------------------------------------------
  void FFTHitFinder::beginJob()
  { 
  }

  //-------------------------------------------------
  void FFTHitFinder::endJob()
  {
  }

  //  This algorithm uses the fact that deconvolved signals are very smooth 
  //  and looks for hits as areas between local minima that have signal above 
  //  threshold.
  //-------------------------------------------------
  void FFTHitFinder::produce(art::Event& evt)
  { 
    
    // this object contains the hit collection
    // and its associations to wires and raw digits:
    recob::HitCollectionCreator hcol(*this, evt);
  
    // Read in the wire List object(s).
    art::Handle< std::vector<recob::Wire> > wireVecHandle;
    evt.getByLabel(fCalDataModuleLabel,wireVecHandle);
    art::ServiceHandle<geo::Geometry> geom;
   
    // also get the raw digits associated with wires
    art::FindOneP<raw::RawDigit> WireToRawDigits
      (wireVecHandle, evt, fCalDataModuleLabel);
    
    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
    raw::ChannelID_t channel = raw::InvalidChannelID; // channel number
    bool maxFound          = false;          // Flag for whether a peak > threshold has been found
    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
    std::string eqn        = "gaus(0)";      // string for equation to fit
    geo::SigType_t sigType = geo::kInduction;// type of plane we are looking at
    std::stringstream numConv;


    //loop over wires
    for(unsigned int wireIter = 0; wireIter < wireVecHandle->size(); wireIter++) {

      art::Ptr<recob::Wire> wire(wireVecHandle, wireIter);
      startTimes.clear();
      maxTimes.clear();
      endTimes.clear();
      std::vector<float> signal(wire->Signal());
      std::vector<float>::iterator timeIter;   // iterator for time bins
      time          = 0;
      minTimeHolder = 0;
      maxFound      = false;
      channel       = wire->Channel();
      sigType       = geom->SignalType(channel);

      //Set the appropriate signal widths and thresholds
      if(sigType == geo::kInduction){
        threshold     = fMinSigInd;
        fitWidth      = fIndWidth;
        minWidth      = fIndMinWidth;
      }
      else if(sigType == geo::kCollection){
        threshold = fMinSigCol;
        fitWidth  = fColWidth;
        minWidth  = fColMinWidth;
      }
      // loop over signal
      for(timeIter = signal.begin(); timeIter+2 < signal.end(); timeIter++){    
        //test if timeIter+1 is a local minimum
        if(*timeIter > *(timeIter+1) && *(timeIter+1) < *(timeIter+2)){
          //only add points if already found a local max 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; 
        }
        //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 no inflection found before end, but peak found add end point
      while(maxTimes.size()>endTimes.size()) 
        endTimes.push_back(signal.size()-1); 
      if(startTimes.size() == 0) continue;
      
      //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), position(0), width(0);  //fit parameters
      double amplitudeErr(0), positionErr(0), widthErr(0);  //fit errors
      double goodnessOfFit(0), chargeErr(0);  //Chi2/NDF and error on charge
      double minPeakHeight(0);  //lowest peak height in multi-hit fit
     
      //stores gaussian paramters first index is the hit number
      //the second refers to height, position, and width respectively
      std::vector<double>  hitSig;

      //add found hits to hit vector      
      while(hitIndex < (signed)startTimes.size()) {
        
        startT = endT = 0;
        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]];

          ++numHits;
        }

        //finds the first point > 1/2 the smallest peak
        startT = startTimes[hitIndex];

        while(signal[(int)startT] < minPeakHeight/2.0) ++startT;

        //finds the first point from the end > 1/2 the smallest peak
        endT = endTimes[hitIndex+numHits-1];

        while(signal[(int)endT] <minPeakHeight/2.0) --endT;
        size = (int)(endT-startT);
        TH1D hitSignal("hitSignal","",size,startT,endT);
        for(int i = (int)startT; i < (int)endT; ++i)
          hitSignal.Fill(i,signal[i]);

        //build the TFormula
        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 gSum("gSum",eqn.c_str(),0,size);

        if(numHits > 1) {
          TArrayD data(numHits*numHits);
          TVectorD amps(numHits); 
          for(int i = 0; i < numHits; ++i) {
            amps[i] = signal[maxTimes[hitIndex+i]];
            for(int j = 0; j < numHits;j++) 
              data[i+numHits*j] = TMath::Gaus(maxTimes[hitIndex+j],
                                              maxTimes[hitIndex+i],
                                              fitWidth);
          }//end loop over hits
          
          //This section uses a linear approximation in order to get an
          //initial value of the individual hit amplitudes 
          try{
            TMatrixD h(numHits,numHits);
            h.Use(numHits,numHits,data.GetArray());
            TDecompSVD a(h);
            a.Solve(amps);
          }
          catch(...){
            mf::LogInfo("FFTHitFinder")<<"TDcompSVD failed";
            hitIndex += numHits;
            continue;
          }
      
          for(int i = 0; i < numHits; ++i) {
            //if the approximation makes a peak vanish
            //set initial height as average of threshold and
            //raw peak height
            if(amps[i] > 0 ) amplitude = amps[i];
            else amplitude = 0.5*(threshold+signal[maxTimes[hitIndex+i]]);
            gSum.SetParameter(3*i,amplitude);
            gSum.SetParameter(1+3*i, maxTimes[hitIndex+i]);
            gSum.SetParameter(2+3*i, fitWidth);
            gSum.SetParLimits(3*i, 0.0, 3.0*amplitude);
            gSum.SetParLimits(1+3*i, startT , endT);
            gSum.SetParLimits(2+3*i, 0.0, 10.0*fitWidth);
          }//end loop over hits
        }//end if numHits > 1
        else {
          gSum.SetParameters(signal[maxTimes[hitIndex]],maxTimes[hitIndex],fitWidth);
          gSum.SetParLimits(0,0.0,1.5*signal[maxTimes[hitIndex]]);
          gSum.SetParLimits(1, startT , endT);
          gSum.SetParLimits(2,0.0,10.0*fitWidth);
        }

        hitSignal.Fit(&gSum,"QNRW","", startT, endT);
        for(int hitNumber = 0; hitNumber < numHits; ++hitNumber) {
          totSig = 0;
          if(gSum.GetParameter(3*hitNumber)   > threshold/2.0 && 
             gSum.GetParameter(3*hitNumber+2) > minWidth) { 
            amplitude     = gSum.GetParameter(3*hitNumber);
            position      = gSum.GetParameter(3*hitNumber+1);
            width         = gSum.GetParameter(3*hitNumber+2);
            amplitudeErr  = gSum.GetParError(3*hitNumber);
            positionErr   = gSum.GetParError(3*hitNumber+1);
            widthErr      = gSum.GetParError(3*hitNumber+2);
            goodnessOfFit = gSum.GetChisquare()/(double)gSum.GetNDF();
       int DoF = gSum.GetNDF();

            //estimate error from area of Gaussian
            chargeErr = std::sqrt(TMath::Pi())*(amplitudeErr*width+widthErr*amplitude);   

            hitSig.resize(size);

            for(int sigPos = 0; sigPos < size; ++sigPos){
              hitSig[sigPos] = amplitude*TMath::Gaus(sigPos+startT,position, width);
              totSig += hitSig[(int)sigPos];              
            }                       

            if(fAreaMethod) 
              totSig = std::sqrt(2*TMath::Pi())*amplitude*width/fAreaNorms[(size_t)sigType];              

            // get the WireID for this hit
            std::vector<geo::WireID> wids = geom->ChannelToWire(channel);
            // for now, just take the first option returned from ChannelToWire
            geo::WireID wid = wids[0];

            // make the hit
            recob::HitCreator hit(
              *wire,          // wire
              wid,            // wireID
              (int) startT,   // start_tick
              (int) endT,     // end_tick
              width,          // rms
              position,       // peak_time
              positionErr,    // sigma_peak_time
              amplitude,      // peak_amplitude
              amplitudeErr,   // sigma_peak_amplitude
              totSig,         // hit_integral
              chargeErr,      // hit_sigma_integral
              std::accumulate // summedADC
                (signal.begin() + (int) startT, signal.begin() + (int) endT, 0.),
              1,              // multiplicity
              -1,             // local_index
              goodnessOfFit,  // goodness_of_fit
              DoF             // dof
              );
            
            // get the object associated with the original hit
            art::Ptr<raw::RawDigit> rawdigits = WireToRawDigits.at(wireIter);
            
            hcol.emplace_back(hit.move(), wire, rawdigits);
          }//end if over threshold
        }//end loop over hits
        hitIndex += numHits;    
      } // end while on hitIndex<(signed)startTimes.size()

    } // while on Wires
    
    // put the hit collection and associations into the event
    hcol.put_into(evt);

  } // End of produce()  
  

  
  DEFINE_ART_MODULE(FFTHitFinder)

} // end of hit namespace


#endif // FFTHITFINDER_H