cluster::EndPointAlg Class Reference

Algorithm to find 2D end points. More...

#include "EndPointAlg.h"

Public Member Functions
	EndPointAlg (fhicl::ParameterSet const &pset)
virtual	~EndPointAlg ()
void	reconfigure (fhicl::ParameterSet const &pset)
size_t	EndPoint (const art::PtrVector< recob::Cluster > &clusIn, std::vector< recob::EndPoint2D > &vtxcol, std::vector< art::PtrVector< recob::Hit > > &vtxHitsOut, art::Event const &evt, std::string const &label)

Private Member Functions
double	Gaussian (int x, int y, double sigma)
double	GaussianDerivativeX (int x, int y)
double	GaussianDerivativeY (int x, int y)
void	VSSaveBMPFile (const char *fileName, unsigned char *pix, int dx, int dy)

Private Attributes
int	fTimeBins
int	fMaxCorners
double	fGsigma
int	fWindow
double	fThreshold
int	fSaveVertexMap

Detailed Description

Algorithm to find 2D end points.

Definition at line 28 of file EndPointAlg.h.

Constructor & Destructor Documentation

cluster::EndPointAlg::EndPointAlg ( fhicl::ParameterSet const &  pset )

explicit

The algorithm is based on: C. Harris and M. Stephens (1988). "A combined corner and edge detector". Proceedings of the 4th Alvey Vision Conference. pp. 147-151. B. Morgan (2010). "Interest Point Detection for Reconstruction in High Granularity Tracking Detectors". arXiv:1006.3012v1 [physics.ins-det]

Definition at line 51 of file EndPointAlg.cxx.

References reconfigure().

{
  this->reconfigure(pset);
}

cluster::EndPointAlg::~EndPointAlg ( )

virtual

Definition at line 57 of file EndPointAlg.cxx.

{
}

Member Function Documentation

size_t cluster::EndPointAlg::EndPoint	(	const art::PtrVector< recob::Cluster > &	clusIn,
		std::vector< recob::EndPoint2D > &	vtxcol,
		std::vector< art::PtrVector< recob::Hit > > &	vtxHitsOut,
		art::Event const &	evt,
		std::string const &	label
	)

Definition at line 136 of file EndPointAlg.cxx.

References art::PtrVector< T >::begin(), art::PtrVector< T >::clear(), geo::CryostatID::Cryostat, geo::GeometryCore::Cryostat(), detinfo::DetectorProperties::DriftVelocity(), detinfo::DetectorProperties::Efield(), art::PtrVector< T >::end(), fGsigma, fMaxCorners, fSaveVertexMap, fThreshold, fTimeBins, fWindow, Gaussian(), GaussianDerivativeX(), GaussianDerivativeY(), n, geo::PlaneGeo::Nwires(), geo::TPCGeo::Plane(), geo::PlaneID::Plane, art::PtrVector< T >::push_back(), detinfo::DetectorProperties::ReadOutWindowSize(), detinfo::DetectorProperties::SamplingRate(), art::PtrVector< T >::size(), detinfo::DetectorProperties::Temperature(), geo::CryostatGeo::TPC(), geo::TPCID::TPC, geo::GeometryCore::Views(), VSSaveBMPFile(), w, geo::WireID::WireID(), geo::GeometryCore::WirePitch(), x, and y.

Referenced by cluster::EndPointModule::produce().

{

  art::ServiceHandle<geo::Geometry> geom;
  const detinfo::DetectorProperties* detp = lar::providerFrom<detinfo::DetectorPropertiesService>();
     
  //Point to a collection of vertices to output.
  std::vector< art::Ptr<recob::Hit> > hit;

  art::FindManyP<recob::Hit> fmh(clusIn, evt, label);
   
  int flag   = 0;
  int windex = 0;//the wire index to make sure the end point finder does not fall off the edge of the hit map
  int tindex = 0;//the time index to make sure the end point finder does not fall off the edge of the hit map
  int n      = 0; //index of window cell. There are 49 cells in the 7X7 Gaussian and Gaussian derivative windows
  unsigned int numberwires = 0;
  const unsigned int numbertimesamples = detp->ReadOutWindowSize();
  const float TicksPerBin = numbertimesamples / fTimeBins;
  
  double MatrixAAsum = 0.;
  double MatrixBBsum = 0.;
  double MatrixCCsum = 0.;
  std::vector<double> Cornerness2;
  //gaussian window definitions. The cell weights are calculated here to help the algorithm's speed
  double  w[49] = {0.};
  double wx[49] = {0.};
  double wy[49] = {0.};
  int ctr = 0;
  for(int i = -3; i < 4; ++i){
    for(int j = 3; j > -4; --j){
      w[ctr] = Gaussian(i, j, fGsigma);
      wx[ctr] = GaussianDerivativeX(i,j);
      wy[ctr] = GaussianDerivativeY(i,j);
      ++ctr;
    }
  }
  
  unsigned int wire    = 0;
  unsigned int wire2   = 0;
  for(auto view : geom->Views()){
    art::PtrVector<recob::Hit> vHits;
    art::PtrVector<recob::Cluster>::const_iterator clusterIter = clusIn.begin();
    hit.clear();
    size_t cinctr = 0;
    while(clusterIter!= clusIn.end() ) {
      if((*clusterIter)->View() == view){
        hit = fmh.at(cinctr);
      }//end if cluster is in the correct view
      clusterIter++;  
      ++cinctr;
    } 
        
    if(hit.size() == 0) continue;
        
    geo::WireID wid = hit[0]->WireID();
    numberwires = geom->Cryostat(wid.Cryostat).TPC(wid.TPC).Plane(wid.Plane).Nwires();
    mf::LogInfo("EndPointAlg") << " --- endpoints check " 
                               << numberwires << " " 
                               << numbertimesamples << " " 
                               << fTimeBins;
    
    std::vector < std::vector < double > > MatrixAsum(numberwires);
    std::vector < std::vector < double > > MatrixBsum(numberwires);
    std::vector < std::vector < double > > hit_map(numberwires); //the map of hits 
    
    //the index of the hit that corresponds to the potential corner
    std::vector < std::vector < int > > hit_loc(numberwires);
    
    std::vector < std::vector < double > >  Cornerness(numberwires); //the "weight" of a corner
    
    for(unsigned int wi = 0; wi < numberwires; ++wi){  
      hit_map[wi].resize(fTimeBins,0);
      hit_loc[wi].resize(fTimeBins,-1);
      Cornerness[wi].resize(fTimeBins,0);
      MatrixAsum[wi].resize(fTimeBins,0);
      MatrixBsum[wi].resize(fTimeBins,0);
    }      
    for(unsigned int i = 0; i < hit.size(); ++i){
      wire = hit[i]->WireID().Wire;
      //pixelization using a Gaussian
    //  for(int j = 0; j <= (int)(hit[i]->EndTime()-hit[i]->StartTime()+.5); ++j)    
    //    hit_map[wire][(int)((hit[i]->StartTime()+j)*(fTimeBins/numbertimesamples)+.5)] += Gaussian((int)(j-((hit[i]->EndTime()-hit[i]->StartTime())/2.)+.5),0,hit[i]->EndTime()-hit[i]->StartTime());      
      const float center = hit[i]->PeakTime(), sigma = hit[i]->RMS();
      const int iFirstBin = int((center - 3*sigma) / TicksPerBin),
        iLastBin = int((center + 3*sigma) / TicksPerBin);
      for (int iBin = iFirstBin; iBin <= iLastBin; ++iBin) {
        const float bin_center = iBin * TicksPerBin;
        hit_map[wire][iBin] += Gaussian(bin_center, center, sigma);
      }
    }
    
    // Gaussian derivative convolution  
    for(unsigned int wire = 1; wire < numberwires-1; ++wire){
      
      for(int timebin = 1; timebin < fTimeBins-1; ++timebin){
        MatrixAsum[wire][timebin] = 0.;
        MatrixBsum[wire][timebin] = 0.;
        n = 0;
        for(int i = -3; i <= 3; ++i) {
          windex = wire+i;
          if(windex < 0 ) windex = 0;
          // this is ok, because the line before makes sure it's not negative
          else if ((unsigned int)windex >= numberwires) windex = numberwires-1; 
          
          for(int j = -3; j <= 3; ++j){
            tindex = timebin+j;
            if(tindex < 0) tindex=0;
            else if(tindex >= fTimeBins) tindex = fTimeBins-1;
            
            MatrixAsum[wire][timebin] += wx[n]*hit_map[windex][tindex];  
            MatrixBsum[wire][timebin] += wy[n]*hit_map[windex][tindex]; 
            ++n;
          } // end loop over j
        } // end loop over i
      } // end loop over time bins
    }// end loop over wires

    //calculate the cornerness of each pixel while making sure not to fall off the hit map.
    for(unsigned int wire = 1; wire < numberwires-1; ++wire){
      
      for(int timebin = 1; timebin < fTimeBins-1; ++timebin){    
        MatrixAAsum = 0.;
        MatrixBBsum = 0.;
        MatrixCCsum = 0.;
        //Gaussian smoothing convolution
        n = 0;
        for(int i = -3; i <= 3; ++i){
          windex = wire+i;
          if(windex<0) windex = 0;
          // this is ok, because the line before makes sure it's not negative
          else if((unsigned int)windex >= numberwires) windex = numberwires-1; 
          
          for(int j = -3; j <= 3; ++j){
            tindex = timebin+j;
            if(tindex < 0) tindex = 0;
            else if(tindex >= fTimeBins) tindex = fTimeBins-1;
            
            MatrixAAsum += w[n]*pow(MatrixAsum[windex][tindex],2);  
            MatrixBBsum += w[n]*pow(MatrixBsum[windex][tindex],2);                   
            MatrixCCsum += w[n]*MatrixAsum[windex][tindex]*MatrixBsum[windex][tindex]; 
            ++n;
          }// end loop over j
        }// end loop over i
        
        if((MatrixAAsum + MatrixBBsum) > 0)             
          Cornerness[wire][timebin] = (MatrixAAsum*MatrixBBsum-pow(MatrixCCsum,2))/(MatrixAAsum+MatrixBBsum);
        else
          Cornerness[wire][timebin] = 0;
        
        if(Cornerness[wire][timebin] > 0){        
          for(unsigned int i = 0;i < hit.size(); ++i){
            wire2 = hit[i]->WireID().Wire;       
            //make sure the end point candidate coincides with an actual hit.
            if(wire == wire2 
               && std::abs(hit[i]->TimeDistanceAsRMS(timebin*(numbertimesamples/fTimeBins))) < 1.){
              //this index keeps track of the hit number
              hit_loc[wire][timebin] = i;
              Cornerness2.push_back(Cornerness[wire][timebin]);
              break;
            }           
          }// end loop over hits             
        }// end if cornerness > 0           
      } // end loop over time bins     
    }  // end wire loop 
    
    std::sort(Cornerness2.rbegin(), Cornerness2.rend());
    
    for(int vertexnum = 0; vertexnum < fMaxCorners; ++vertexnum){
      flag = 0;
      for(unsigned int wire = 0; wire < numberwires && flag == 0; ++wire){
        for(int timebin = 0; timebin < fTimeBins && flag == 0; ++timebin){    
          if(Cornerness2.size() > (unsigned int)vertexnum)
            if(Cornerness[wire][timebin] == Cornerness2[vertexnum] 
               && Cornerness[wire][timebin] > 0. 
               && hit_loc[wire][timebin] > -1){
              ++flag;
              
              //thresholding
              if(Cornerness2.size())
                if(Cornerness[wire][timebin] < (fThreshold*Cornerness2[0]))
                  vertexnum = fMaxCorners;
              vHits.push_back(hit[hit_loc[wire][timebin]]);
              
              // get the total charge from the associated hits
              double totalQ = 0.;
              for(size_t vh = 0; vh < vHits.size(); ++vh) totalQ += vHits[vh]->Integral();
              
              recob::EndPoint2D endpoint(hit[hit_loc[wire][timebin]]->PeakTime(),
                                         hit[hit_loc[wire][timebin]]->WireID(),
                                         Cornerness[wire][timebin],
                                         vtxcol.size(),
                                         view,
                                         totalQ);
              vtxcol.push_back(endpoint);
              vtxHitsOut.push_back(vHits);
              vHits.clear();
              
              // non-maximal suppression on a square window. The wire coordinate units are 
              // converted to time ticks so that the window is truly square. 
              // Note that there are 1/0.0743=13.46 time samples per 4.0 mm (wire pitch in ArgoNeuT), 
              // assuming a 1.5 mm/us drift velocity for a 500 V/cm E-field 
              
              double drifttick  = detp->DriftVelocity(detp->Efield(),detp->Temperature());
              drifttick *= detp->SamplingRate()*1.e-3;
              double wirepitch  = geom->WirePitch();
              double corrfactor = drifttick/wirepitch;
              
              for(int wireout=(int)wire-(int)((fWindow*(numbertimesamples/fTimeBins)*corrfactor)+.5);
                  wireout <= (int)wire+(int)((fWindow*(numbertimesamples/fTimeBins)*corrfactor)+.5); ++wireout){
                for(int timebinout=timebin-fWindow;timebinout <= timebin+fWindow; timebinout++){
                  if(std::sqrt(pow(wire-wireout,2)+pow(timebin-timebinout,2))<fWindow)//circular window 
                    Cornerness[wireout][timebinout]=0;    
                }
              }
            }
        }     
      }
    }
    Cornerness2.clear();
    hit.clear();
    if(clusterIter != clusIn.end()) clusterIter++;
    
    if((int)wid.Plane == fSaveVertexMap){ 
      unsigned char *outPix = new unsigned char [fTimeBins*numberwires];
      //finds the maximum cell in the map for image scaling
      int cell    = 0;
      int pix     = 0;
      int maxCell = 0;
      //int xmaxx, ymaxx;
      for (int y = 0; y < fTimeBins; ++y){
        for (unsigned int x = 0; x < numberwires; ++x){
          cell = (int)(hit_map[x][y]*1000);
          if (cell > maxCell){
            maxCell = cell;
            //  xmaxx=x;
            //  ymaxx=y;
          }
        }
      }
      for (int y = 0; y < fTimeBins; ++y){
        for (unsigned int x = 0; x<numberwires; ++x){ 
          //scales the pixel weights based on the maximum cell value     
          if(maxCell>0)
            pix = (int)((1500000*hit_map[x][y])/maxCell);
          outPix[y*numberwires + x] = pix;
        }
      }
      
      // add 3x3 pixel squares to with the harris vertex finders to the .bmp file
      
      for(unsigned int ii = 0; ii < vtxcol.size(); ++ii){
        if(vtxcol[ii].View() == (unsigned int)view){
          pix = (int)(255);
          outPix[(int)(vtxcol[ii].DriftTime()*(fTimeBins/numbertimesamples))*numberwires + vtxcol[ii].WireID().Wire] = pix;
          outPix[(int)(vtxcol[ii].DriftTime()*(fTimeBins/numbertimesamples))*numberwires + vtxcol[ii].WireID().Wire-1] = pix;
          outPix[(int)(vtxcol[ii].DriftTime()*(fTimeBins/numbertimesamples))*numberwires + vtxcol[ii].WireID().Wire+1] = pix;
          outPix[(int)((vtxcol[ii].DriftTime()*(fTimeBins/numbertimesamples))-1)*numberwires + vtxcol[ii].WireID().Wire] = pix;
          outPix[(int)((vtxcol[ii].DriftTime()*(fTimeBins/numbertimesamples))+1)*numberwires + vtxcol[ii].WireID().Wire] = pix;
          outPix[(int)((vtxcol[ii].DriftTime()*(fTimeBins/numbertimesamples))-1)*numberwires + vtxcol[ii].WireID().Wire-1] = pix;
          outPix[(int)((vtxcol[ii].DriftTime()*(fTimeBins/numbertimesamples))-1)*numberwires + vtxcol[ii].WireID().Wire-2] = pix;
          outPix[(int)((vtxcol[ii].DriftTime()*(fTimeBins/numbertimesamples))+1)*numberwires + vtxcol[ii].WireID().Wire+1] = pix;
          outPix[(int)((vtxcol[ii].DriftTime()*(fTimeBins/numbertimesamples))+1)*numberwires + vtxcol[ii].WireID().Wire+2] = pix;
        }
      }
      
      VSSaveBMPFile(Form("harrisvertexmap_%d_%d.bmp",(*clusIn.begin())->ID(),wid.Plane), outPix, numberwires, fTimeBins);
      delete [] outPix;
    }   
  } // end loop over views
  
  return vtxcol.size();   
}

double cluster::EndPointAlg::Gaussian ( int  x, int  y, double  sigma  )

private

Definition at line 73 of file EndPointAlg.cxx.

References fhicl::detail::atom::value().

Referenced by EndPoint().

{
  double Norm=1./std::sqrt(2*TMath::Pi()*pow(sigma,2));
  double value=Norm*exp(-(pow(x,2)+pow(y,2))/(2*pow(sigma,2)));
  return value;
}

double cluster::EndPointAlg::GaussianDerivativeX ( int  x, int  y  )

private

Definition at line 81 of file EndPointAlg.cxx.

References fGsigma, fhicl::detail::atom::value(), and x.

Referenced by EndPoint().

{
  double Norm=1./(std::sqrt(2*TMath::Pi())*pow(fGsigma,3));
  double value=Norm*(-x)*exp(-(pow(x,2)+pow(y,2))/(2*pow(fGsigma,2)));
  return value;
}

double cluster::EndPointAlg::GaussianDerivativeY ( int  x, int  y  )

private

Definition at line 89 of file EndPointAlg.cxx.

References fGsigma, fhicl::detail::atom::value(), and y.

Referenced by EndPoint().

{
  double Norm=1./(std::sqrt(2*TMath::Pi())*pow(fGsigma,3));
  double value=Norm*(-y)*exp(-(pow(x,2)+pow(y,2))/(2*pow(fGsigma,2)));
  return value;
}

void cluster::EndPointAlg::reconfigure

(

fhicl::ParameterSet const &

pset

)

Definition at line 62 of file EndPointAlg.cxx.

References fGsigma, fMaxCorners, fSaveVertexMap, fThreshold, fTimeBins, fWindow, and fhicl::ParameterSet::get().

Referenced by EndPointAlg(), and cluster::EndPointModule::reconfigure().

{
  fTimeBins      = p.get< int    >("TimeBins");
  fMaxCorners    = p.get< int    >("MaxCorners");
  fGsigma        = p.get< double >("Gsigma");
  fWindow        = p.get< int    >("Window");
  fThreshold     = p.get< double >("Threshold");
  fSaveVertexMap = p.get< int    >("SaveVertexMap");
}

void cluster::EndPointAlg::VSSaveBMPFile ( const char *  fileName, unsigned char *  pix, int  dx, int  dy  )

private

Definition at line 99 of file EndPointAlg.cxx.

Referenced by EndPoint().

{
  std::ofstream bmpFile(fileName, std::ios::binary);
  bmpFile.write("B", 1);
  bmpFile.write("M", 1);
  int bitsOffset = 54 +256*4; 
  int size = bitsOffset + dx*dy; //header plus 256 entry LUT plus pixels
  bmpFile.write((const char *)&size, 4);
  int reserved = 0;
  bmpFile.write((const char *)&reserved, 4);
  bmpFile.write((const char *)&bitsOffset, 4);
  int bmiSize = 40;
  bmpFile.write((const char *)&bmiSize, 4);
  bmpFile.write((const char *)&dx, 4);
  bmpFile.write((const char *)&dy, 4);
  short planes = 1;
  bmpFile.write((const char *)&planes, 2);
  short bitCount = 8;
  bmpFile.write((const char *)&bitCount, 2);
  int i, temp = 0;
  for (i=0; i<6; i++)
    bmpFile.write((const char *)&temp, 4);  // zero out optional color info
  // write a linear LUT
  char lutEntry[4]; // blue,green,red
  lutEntry[3] = 0;  // reserved part
  for (i=0; i<256; i++)
    {
      lutEntry[0] =i;
      lutEntry[1] =i+1;
      lutEntry[2] = i+2;
      bmpFile.write(lutEntry, sizeof lutEntry);
    }
  // write the actual pixels
  bmpFile.write((const char *)pix, dx*dy);
}

Member Data Documentation

double cluster::EndPointAlg::fGsigma

private

Definition at line 53 of file EndPointAlg.h.

Referenced by EndPoint(), GaussianDerivativeX(), GaussianDerivativeY(), and reconfigure().

int cluster::EndPointAlg::fMaxCorners

private

Definition at line 52 of file EndPointAlg.h.

Referenced by EndPoint(), and reconfigure().

int cluster::EndPointAlg::fSaveVertexMap

private

Definition at line 56 of file EndPointAlg.h.

Referenced by EndPoint(), and reconfigure().

double cluster::EndPointAlg::fThreshold

private

Definition at line 55 of file EndPointAlg.h.

Referenced by EndPoint(), and reconfigure().

int cluster::EndPointAlg::fTimeBins

private

Definition at line 51 of file EndPointAlg.h.

Referenced by EndPoint(), and reconfigure().

int cluster::EndPointAlg::fWindow

private

Definition at line 54 of file EndPointAlg.h.

Referenced by EndPoint(), and reconfigure().

---

The documentation for this class was generated from the following files:

• /cvmfs/larsoft.opensciencegrid.org/products/larreco/v07_10_02/source/larreco/RecoAlg/EndPointAlg.h
• /cvmfs/larsoft.opensciencegrid.org/products/larreco/v07_10_02/source/larreco/RecoAlg/EndPointAlg.cxx