FeatureVertexFinder_module.cc

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//
// FeatureVertexFinder class
//
// jasaadi@fnal.gov
//
// This algorithm is designed to reconstruct the vertices using the
// 2D cluster information and CornerFinderAlg to find 2-d and 3-d verticies
//
// 06/05/14
// This is a major rewrite of the original code and will be factored to take
// advantage of improvements in LArSoft. The code now goes something like this:
//
// 1)Take up EndPoint2d's from Cluster Crawler and keep ones that make sense in 3d
// (this algorithm wants ClusterCrawler to have been run, but should totally work
//  even if it hasn't)
//
// 2)Take up all EndPoint2d's from the image finding CornerFinder algorithm
// (this algortithm wants CornerFinder to have been run, but should totally work
//  even if it hasn't)
//
// 3)Take up an additional clustering algorithm (dBcluster by default but can work
//   with any clustering algorithm) and use slopes and endpoints to find intersections
//
// 4)Now merge together any duplicates and sort them by their weight (which needs its units still
//   decided somehow)
//
// 5)Return a list of verticies based on what mode you run this algorithm in
//      a) Primary mode: This mode will return only a single 3d vertex and an appropriate
//                       number of EndPoint2d's corresponding to the most likely neutrino vertex
//      b) All mode: This mode returns all 3d/2d verticies that this algorithm has found but
//                   sorts the list by the most likely candidate
//
//
//
// This is Preliminary Work and needs modifications
//
// ////////////////////////////////////////////////////////////////////////

// Basic C++ Includes
#include <cmath>
#include <iomanip>
#include <iostream>
#include <string>

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

// LArSoft Includes
#include "larcore/Geometry/Geometry.h"
#include "larcorealg/Geometry/CryostatGeo.h"
#include "larcorealg/Geometry/TPCGeo.h"
#include "lardata/DetectorInfoServices/DetectorClocksService.h"
#include "lardata/DetectorInfoServices/DetectorPropertiesService.h"
#include "lardataobj/RecoBase/Cluster.h"
#include "lardataobj/RecoBase/EndPoint2D.h"
#include "lardataobj/RecoBase/Hit.h"
#include "lardataobj/RecoBase/Shower.h"
#include "lardataobj/RecoBase/Track.h"
#include "lardataobj/RecoBase/Vertex.h"

// ROOT Includes
#include "TF1.h"
#include "TGraph.h"

namespace vertex {

  class FeatureVertexFinder : public art::EDProducer {
  public:
    explicit FeatureVertexFinder(fhicl::ParameterSet const& pset);

  private:
    void produce(art::Event& evt) override;

    // This function will take in and EndPoint2d from either cluster crawler
    // or corner finder and only save points that make a 3d-candidate
    void Get3dVertexCandidates(detinfo::DetectorPropertiesData const& detProp,
                               std::vector<art::Ptr<recob::EndPoint2D>> const& EndPoints,
                               bool PlaneDet);

    // This function will take in 2d Clusters (by default dBCluster)
    // and return 2d vertex candidates for sorting later
    void Find2dClusterVertexCandidates(detinfo::DetectorPropertiesData const& detProp,
                                       art::PtrVector<recob::Cluster> RawClusters,
                                       art::FindManyP<recob::Hit> fmhit);

    // This function takes in 2d Vertex candidates (found by
    // Find2dClusterVertexCandidates), does some basic merging and
    // then finds 3d-candidates for use later
    void Find3dVtxFrom2dClusterVtxCand(detinfo::DetectorPropertiesData const& detProp,
                                       std::vector<double> const& Wire_2dvtx,
                                       std::vector<double> const& Time_2dvtx,
                                       std::vector<double> const& Plane_2dvtx);

    // This function merges and sorts all the 3d vertex candidates, it
    // merges them if they are within 2.0 cm in X, Y, and Z
    // simultaneously and then sorts the list by vertex strength and Z
    // location (lowest Z is first on the list
    void MergeAndSort3dVtxCandidate(std::vector<double> const& merge_vtxX,
                                    std::vector<double> const& merge_vtxY,
                                    std::vector<double> const& merge_vtxZ,
                                    std::vector<double> const& merge_vtxStgth);

    std::string fClusterModuleLabel;
    std::string fHitModuleLabel;
    std::string fCornerFinderModuleLabel;
    std::string fCCrawlerEndPoint2dModuleLabel;
    Double_t fRunningMode;

    bool GT2PlaneDetector = false;

    // Unsorted Raw list of 3d-Vertex candidates filled

    std::vector<double> candidate_x = {0.};
    std::vector<double> candidate_y = {0.};
    std::vector<double> candidate_z = {0.};
    std::vector<double> candidate_strength = {0.};

    // Merged and sorted list of 3d-Vertex candidates filled

    std::vector<double> MergeSort3dVtx_xpos = {0.};
    std::vector<double> MergeSort3dVtx_ypos = {0.};
    std::vector<double> MergeSort3dVtx_zpos = {0.};
    std::vector<double> MergeSort3dVtx_strength = {0.};

    // 2d Cluster based Variables

    std::vector<std::vector<int>> Cls;                //<---- Index to clusters in each view
    std::vector<double> dtdwstart = {0.};             //<----Slope (delta Time Tick vs delta Wire)
    std::vector<double> dtdwstartError = {0.};        //<---Error on the slope
    std::vector<double> Clu_Plane = {0.};             //<---Plane of the current cluster
    std::vector<double> Clu_StartPos_Wire = {0.};     //<---Starting wire number of cluster
    std::vector<double> Clu_StartPos_TimeTick = {0.}; //<---Starting TDC value of the cluster

    std::vector<double> Clu_EndPos_Wire = {0.};     //<---Ending wire number of cluster
    std::vector<double> Clu_EndPos_TimeTick = {0.}; //<---Ending TDC value of the cluster

    std::vector<double> Clu_Slope = {0.};       //<---Calculated Slope of the cluster (TDC/Wire)
    std::vector<double> Clu_Yintercept = {0.};  //<---Clusters Y Intercept using start positions
    std::vector<double> Clu_Yintercept2 = {0.}; //<---Clusters Y Intercept using end positions
    std::vector<double> Clu_Length = {0.};      //<---Calculated Length of the cluster

    // 2d Cluster based verticies

    std::vector<double> TwoDvtx_wire = {0.};
    std::vector<double> TwoDvtx_time = {0.};
    std::vector<double> TwoDvtx_plane = {0.};
  };

} //<---End namespace vertex

namespace vertex {

  FeatureVertexFinder::FeatureVertexFinder(fhicl::ParameterSet const& pset) : EDProducer{pset}
  {
    fCornerFinderModuleLabel = pset.get<std::string>("CornerFinderModuleLabel");
    fClusterModuleLabel = pset.get<std::string>("ClusterModuleLabel");
    fHitModuleLabel = pset.get<std::string>("HitModuleLabel");
    fCCrawlerEndPoint2dModuleLabel = pset.get<std::string>("CCrawlerEndPoint2dModuleLabel");
    fRunningMode = pset.get<double>("RunningMode");

    produces<std::vector<recob::Vertex>>();
    produces<std::vector<recob::EndPoint2D>>();
    produces<art::Assns<recob::EndPoint2D, recob::Hit>>();

    // === Don't think I'll actually have any of these associations ===
    // ===         should consider removing in the future
    produces<art::Assns<recob::Vertex, recob::Hit>>();
    produces<art::Assns<recob::Vertex, recob::Shower>>();
    produces<art::Assns<recob::Vertex, recob::Track>>();

    art::ServiceHandle<geo::Geometry const> geom;
    Cls.resize(geom->Nplanes(), std::vector<int>());
  }

  // -----------------------------------------------------------------------------
  // Produce
  void FeatureVertexFinder::produce(art::Event& evt)
  {
    art::ServiceHandle<geo::Geometry const> geom;
    auto const detProp =
      art::ServiceHandle<detinfo::DetectorPropertiesService const>()->DataFor(evt);

    // Figuring out if I have a 2 or 3 plane detector

    GT2PlaneDetector = false;

    for (auto const& tpc : geom->Iterate<geo::TPCGeo>()) {
      if (tpc.Nplanes() > 2) {
        GT2PlaneDetector = true;
        std::cout << "yeah" << std::endl;
        break;
      }
    }

    // These are the things I want to put on the event

    auto vcol = std::make_unique<std::vector<recob::Vertex>>();      // 3D vertex
    auto epcol = std::make_unique<std::vector<recob::EndPoint2D>>(); // 2D vertex
    auto assnep = std::make_unique<art::Assns<recob::EndPoint2D, recob::Hit>>();
    auto assnsh = std::make_unique<art::Assns<recob::Vertex, recob::Shower>>();
    auto assntr = std::make_unique<art::Assns<recob::Vertex, recob::Track>>();
    auto assnh = std::make_unique<art::Assns<recob::Vertex, recob::Hit>>();

    // ClusterCrawler

    // Getting the EndPoint2d's for cluster crawler

    try {
      art::Handle<std::vector<recob::EndPoint2D>> ccrawlerFinderHandle;
      evt.getByLabel(fCCrawlerEndPoint2dModuleLabel, ccrawlerFinderHandle);
      std::vector<art::Ptr<recob::EndPoint2D>> ccrawlerEndPoints;
      art::fill_ptr_vector(ccrawlerEndPoints, ccrawlerFinderHandle);

      // Passing in the EndPoint2d's from Cluster Crawler
      Get3dVertexCandidates(detProp, ccrawlerEndPoints, GT2PlaneDetector);
    }
    catch (...) {
      mf::LogWarning("FeatureVertexFinder") << "Failed to get EndPoint2d's from Cluster Crawler";
    }

    // CornerFinder EndPoint2d's

    // Getting the EndPoint2d's for Corner Finder
    try {
      art::Handle<std::vector<recob::EndPoint2D>> CornerFinderHandle;
      evt.getByLabel(fCornerFinderModuleLabel, CornerFinderHandle);
      std::vector<art::Ptr<recob::EndPoint2D>> cornerEndPoints;
      art::fill_ptr_vector(cornerEndPoints, CornerFinderHandle);

      // Passing in the EndPoint2d's from Corner Finder
      Get3dVertexCandidates(detProp, cornerEndPoints, GT2PlaneDetector);
    }
    catch (...) {
      mf::LogWarning("FeatureVertexFinder") << "Failed to get EndPoint2d's from Corner Finder";
    }

    // Making Cluster Slope EndPoint2d's

    // Retrieving the Cluster Module for the event
    try {
      art::Handle<std::vector<recob::Cluster>> clusterListHandle;
      evt.getByLabel(fClusterModuleLabel, clusterListHandle);

      // Finding hits associated with the clusters
      art::FindManyP<recob::Hit> fmh(clusterListHandle, evt, fClusterModuleLabel);

      // Filling the Cluster Vector
      art::PtrVector<recob::Cluster> clusters;
      for (unsigned int ii = 0; ii < clusterListHandle->size(); ++ii) {
        art::Ptr<recob::Cluster> clusterHolder(clusterListHandle, ii);
        clusters.push_back(clusterHolder);
      }

      // Passing in the clusters to find 2d Vertices
      Find2dClusterVertexCandidates(detProp, clusters, fmh);

      // Finding 3d Candidates from 2d cluster vertex candidates
      Find3dVtxFrom2dClusterVtxCand(detProp, TwoDvtx_wire, TwoDvtx_time, TwoDvtx_plane);
    }
    catch (...) {
      mf::LogWarning("FeatureVertexFinder") << "Failed to get Cluster from default cluster module";
    }

    // Merging and sorting 3d vertex candidates
    MergeAndSort3dVtxCandidate(candidate_x, candidate_y, candidate_z, candidate_strength);

    // Putting Vertices on the event
    // ------------------------------------------------------------
    // Now that I have a list of 3d vertex candidates I will return
    // 3d/2d vertices based on which option the user has chosen
    // fRunningMode == 0 (this returns a full list of all 3d/2d vertex
    // candidates) fRunningMode == 1 (this returns only one vertex
    // which is established as the most likely primary)

    // Returning all vertex candidates
    if (fRunningMode == 0) {

      // Looping over Primary Verticies
      for (size_t pri = 0; pri < MergeSort3dVtx_xpos.size(); pri++) {

        // Push each primary vertex onto the event

        double tempxyz[3] = {
          MergeSort3dVtx_xpos[pri], MergeSort3dVtx_ypos[pri], MergeSort3dVtx_zpos[pri]};

        // Skipping a vertex that is zero

        if (tempxyz[0] == 0 && tempxyz[1] == 0 && tempxyz[2] == 0) { continue; }
        recob::Vertex the3Dvertex(tempxyz, vcol->size());
        vcol->push_back(the3Dvertex);

        // ---------------------------------------------------------------------
        // --- Now go make the 2DEndPoints that correspond to each 3d vertex ---
        // ---------------------------------------------------------------------

        for (auto const& planeID : geom->Iterate<geo::PlaneID>()) {
          geo::Point_t const temp2dXYZ{
            MergeSort3dVtx_xpos[pri], MergeSort3dVtx_ypos[pri], MergeSort3dVtx_zpos[pri]};
          double temp2dStrength = MergeSort3dVtx_strength[pri];

          // Skipping a vertex that is zero

          if (temp2dXYZ.X() == 0 && temp2dXYZ.Y() == 0 && temp2dXYZ.Z() == 0) { continue; }

          // Converting the 3d vertex into 2d time ticks, wire, and
          // channel

          double EndPoint2d_TimeTick = detProp.ConvertXToTicks(temp2dXYZ.X(), planeID);
          int EndPoint2d_Wire = 0;
          int EndPoint2d_Channel = 0;
          // Putting in protection in case NearestWire Fails
          try {
            EndPoint2d_Wire = geom->NearestWireID(temp2dXYZ, planeID).Wire;
          }
          catch (...) {
            mf::LogWarning("FeatureVertexFinder") << "2dWire failed";
            continue;
          }
          // Putting in protection in case NearestChannel Fails
          try {
            EndPoint2d_Channel = geom->NearestChannel(temp2dXYZ, planeID);
          }
          catch (...) {
            mf::LogWarning("FeatureVertexFinder") << "2dWire failed";
            continue;
          }

          // Making geo::WireID and getting the current View number
          geo::View_t View = geom->View(EndPoint2d_Channel);
          geo::WireID wireID(planeID, EndPoint2d_Wire);

          // Putting the 2d Vertex found on the event

          recob::EndPoint2D vertex(EndPoint2d_TimeTick, //<---TimeTick
                                   wireID,              //<---geo::WireID
                                   temp2dStrength,      //<---Vtx strength (JA: ?)
                                   epcol->size(),       //<---Vtx ID (JA: ?)
                                   View,                //<---Vtx View
                                   1); //<---Total Charge (JA: Need to figure this one?)
          epcol->push_back(vertex);
        } //<---End Plane loop
      }   //<---End pri loop
    }     //<---End fRunningMode == 0

    // ================================================
    // === Returning only primary vertex candidates ===
    // ================================================
    if (fRunningMode != 0) {
      int position = 0;
      int bail = 0;

      // Looping over Primary Verticies

      for (size_t pri = 0; pri < MergeSort3dVtx_xpos.size(); pri++) {

        // Push each primary vertex onto the event

        double tempxyz[3] = {
          MergeSort3dVtx_xpos[pri], MergeSort3dVtx_ypos[pri], MergeSort3dVtx_zpos[pri]};

        // Skipping a vertex that is zero

        if (bail > 0) { continue; }
        if (tempxyz[0] == 0 && tempxyz[1] == 0 && tempxyz[2] == 0) { continue; }
        position = pri;
        bail++;
        recob::Vertex the3Dvertex(tempxyz, vcol->size());
        vcol->push_back(the3Dvertex);
      }

      // ---------------------------------------------------------------------
      // --- Now go make the 2DEndPoints that correspond to each 3d vertex ---
      // ---------------------------------------------------------------------

      // Looping over cryostats

      for (auto const& planeID : geom->Iterate<geo::PlaneID>()) {
        geo::Point_t const temp2dXYZ{MergeSort3dVtx_xpos[position],
                                     MergeSort3dVtx_ypos[position],
                                     MergeSort3dVtx_zpos[position]};
        double temp2dStrength = MergeSort3dVtx_strength[position];

        // Converting the 3d vertex into 2d time ticks, wire, and
        // channel
        double EndPoint2d_TimeTick = detProp.ConvertXToTicks(temp2dXYZ.X(), planeID);
        int EndPoint2d_Wire = 0;
        int EndPoint2d_Channel = 0;
        // Putting in protection in case NearestWire Fails
        try {
          EndPoint2d_Wire = geom->NearestWireID(temp2dXYZ, planeID).Wire;
        }
        catch (...) {
          mf::LogWarning("FeatureVertexFinder") << "2dWire failed";
          continue;
        }
        // Putting in protection in case NearestChannel Fails
        try {
          EndPoint2d_Channel = geom->NearestChannel(temp2dXYZ, planeID);
        }
        catch (...) {
          mf::LogWarning("FeatureVertexFinder") << "2dWire failed";
          continue;
        }

        // Making geo::WireID and getting the current View number
        geo::View_t View = geom->View(EndPoint2d_Channel);
        geo::WireID wireID(planeID, EndPoint2d_Wire);

        // Putting the 2d Vertex found on the event

        recob::EndPoint2D vertex(EndPoint2d_TimeTick, //<---TimeTick
                                 wireID,              //<---geo::WireID
                                 temp2dStrength,      //<---Vtx strength (JA: ?)
                                 epcol->size(),       //<---Vtx ID (JA: ?)
                                 View,                //<---Vtx View
                                 1); //<---Total Charge (JA: Need to figure this one?)
        epcol->push_back(vertex);
      } //<---End Plane loop
    }   //<---End fRunningMode == 1

    mf::LogVerbatim("Summary") << std::setfill('-') << std::setw(175) << "-" << std::setfill(' ');
    mf::LogVerbatim("Summary") << "FeatureVertexFinder Summary:";
    for (size_t i = 0; i < epcol->size(); ++i)
      mf::LogVerbatim("Summary") << epcol->at(i);
    for (size_t i = 0; i < vcol->size(); ++i)
      mf::LogVerbatim("Summary") << vcol->at(i);

    evt.put(std::move(epcol));
    evt.put(std::move(vcol));
    evt.put(std::move(assnep));
    evt.put(std::move(assntr));
    evt.put(std::move(assnsh));
    evt.put(std::move(assnh));

    // Clearing vectors at the end of the event

    vcol.reset();
    epcol.reset();
    candidate_x.clear();
    candidate_y.clear();
    candidate_z.clear();
    candidate_strength.clear();
    MergeSort3dVtx_xpos.clear();
    MergeSort3dVtx_ypos.clear();
    MergeSort3dVtx_zpos.clear();
    MergeSort3dVtx_strength.clear();
    dtdwstart.clear();
    dtdwstartError.clear();
    Clu_Plane.clear();
    Clu_StartPos_Wire.clear();
    Clu_StartPos_TimeTick.clear();
    Clu_EndPos_Wire.clear();
    Clu_EndPos_TimeTick.clear();
    Clu_Slope.clear();
    Clu_Yintercept.clear();
    Clu_Yintercept2.clear();
    Clu_Length.clear();
    TwoDvtx_wire.clear();
    TwoDvtx_time.clear();
    TwoDvtx_plane.clear();

  } //<--End FeatureVertexFinder::produce

  // -----------------------------------------------------------------------------
  // Get 3d Vertex Candidates
  // -----------------------------------------------------------------------------
  void vertex::FeatureVertexFinder::Get3dVertexCandidates(
    detinfo::DetectorPropertiesData const& detProp,
    std::vector<art::Ptr<recob::EndPoint2D>> const& EndPoints,
    bool PlaneDet)
  {
    art::ServiceHandle<geo::Geometry const> geom;

    double y = 0., z = 0.;
    double yy = 0., zz = 0.;
    double yy2 = 0., zz2 = 0.;
    double yy3 = 0., zz3 = 0.;

    auto const numEndPoints = size(EndPoints);

    for (auto const& tpcid : geom->Iterate<geo::TPCID>()) {
      for (size_t iendpt1 = 0; iendpt1 < numEndPoints; ++iendpt1) {
        for (size_t iendpt2 = iendpt1 + 1; iendpt2 < numEndPoints; ++iendpt2) {

          auto const& endpt1 = *EndPoints[iendpt1];
          auto const& endpt2 = *EndPoints[iendpt2];

          geo::PlaneID const endpt1_planeid{tpcid, endpt1.WireID().Plane};
          geo::PlaneID const endpt2_planeid{tpcid, endpt2.WireID().Plane};

          // Check to make sure we are comparing features from different planes
          if (endpt1_planeid.Plane == endpt2_planeid.Plane) continue;

          // Get the appropriate time offset for the two planes we are considering
          float tempXFeature1 = detProp.ConvertTicksToX(endpt1.DriftTime(), endpt1_planeid);
          float tempXFeature2 = detProp.ConvertTicksToX(endpt2.DriftTime(), endpt2_planeid);

          // Skip features that are not within 0.5 cm in projected X
          if (std::abs(tempXFeature1 - tempXFeature2) >= 0.5) continue;

          // Checking to see if these features have intersecting channels
          geo::WireID const endpt1_wireid{endpt1_planeid, endpt1.WireID().Wire};
          geo::WireID const endpt2_wireid{endpt2_planeid, endpt2.WireID().Wire};

          if (!geom->ChannelsIntersect(geom->PlaneWireToChannel(endpt1_wireid),
                                       geom->PlaneWireToChannel(endpt2_wireid),
                                       yy,
                                       zz))
            continue;

          // Use this fill if we are in a detector with fewer than 3 plane (e.g. ArgoNeuT)

          if (!PlaneDet) {
            candidate_x.push_back(tempXFeature1);
            candidate_y.push_back(yy);
            candidate_z.push_back(zz);
            candidate_strength.push_back(endpt1.Strength() + endpt2.Strength());
            continue;
          } //<---End fill for 2 plane detector

          // Now need to check for a match across more than 2 planes

          // Looping over the rest of the list

          for (size_t iendpt3 = iendpt2 + 1; iendpt3 < numEndPoints; ++iendpt3) {
            auto const& endpt3 = *EndPoints[iendpt3];

            geo::PlaneID const endpt3_planeid{tpcid, endpt3.WireID().Plane};

            // Check to make sure we are comparing features from different planes
            // N.B. We do not need to check between endpt1 and endpt2 as that has been done above.

            if (endpt3_planeid.Plane == endpt2_planeid.Plane ||
                endpt3_planeid.Plane == endpt1_planeid.Plane)
              continue;

            // Check to see that the third feature is within 1.0 cm projected in X
            geo::WireID const endpt3_wireid{endpt3_planeid, endpt3.WireID().Wire};
            float const tempXFeature3 = detProp.ConvertTicksToX(endpt3.DriftTime(), endpt3_wireid);

            if (std::abs(tempXFeature3 - tempXFeature2) >= 1.0 ||
                std::abs(tempXFeature3 - tempXFeature1) >= 1.0) {
              continue;
            }

            // Make sure our third feature has an intersecting channel with our other two channels.
            if (!geom->ChannelsIntersect(geom->PlaneWireToChannel(endpt3_wireid),
                                         geom->PlaneWireToChannel(endpt1_wireid),
                                         yy3,
                                         zz3) ||
                !geom->ChannelsIntersect(geom->PlaneWireToChannel(endpt3_wireid),
                                         geom->PlaneWireToChannel(endpt2_wireid),
                                         yy2,
                                         zz2)) {
              continue;
            }
            candidate_x.push_back(
              detProp.ConvertTicksToX(endpt1.DriftTime(), endpt1_wireid.asPlaneID()));

            // Finding intersection points
            geom->IntersectionPoint(endpt1_wireid, endpt2_wireid, y, z);

            candidate_y.push_back(y);
            candidate_z.push_back(z);
            candidate_strength.push_back(endpt1.Strength() + endpt2.Strength() + endpt3.Strength());

            // Note: If I've made it here I have a matched triplet...since I don't want to use any
            // of these features again I am going to iterate each of the counters so we move to the
            // next one.
            if (iendpt1 < numEndPoints) { ++iendpt1; }
            if (iendpt2 < numEndPoints) { ++iendpt2; }
            if (iendpt3 < numEndPoints) { ++iendpt3; }
          } //<---End iendpt3
        }   //<---End iendpt2 loop
      }     //<---End iendpt1 loop
    }       //<---End TPC loop
  }         //<---End Get3dVertexCandidates

  // -----------------------------------------------------------------------------
  // Get 2d Vertex Candidates from clusters
  // -----------------------------------------------------------------------------
  void vertex::FeatureVertexFinder::Find2dClusterVertexCandidates(
    detinfo::DetectorPropertiesData const& detProp,
    art::PtrVector<recob::Cluster> RawClusters,
    art::FindManyP<recob::Hit> fmhit)
  {
    art::ServiceHandle<geo::Geometry const> geom;

    int nClustersFound = 0;

    // Initialize Cls
    for (auto& c : Cls)
      c.clear();

    for (size_t iclu = 0; iclu < RawClusters.size(); ++iclu) {
      // Gathering the hits associated with the current cluster
      std::vector<art::Ptr<recob::Hit>> hit = fmhit.at(iclu);

      // I only want to consider this cluster if it has a sufficient number
      // of hits
      if (hit.size() < 15) { continue; }

      // Determine which view the current cluster is in

      const geo::View_t view = RawClusters.at(iclu)->View();
      if (view >= Cls.size()) {
        std::cerr << __PRETTY_FUNCTION__ << "\033[93m Logic error in my code ... view " << view
                  << " not supported ! \033[00m" << std::endl;
        throw std::exception();
      }

      Cls.at(RawClusters.at(iclu)->View()).push_back(iclu);

      // Filling wires and times into a TGraph for the cluster

      std::vector<double> wires;
      std::vector<double> times;

      // Counting the number of hits in the current cluster (n)
      int n = 0;

      // Looping over the hits in the cluster

      for (size_t i = 0; i < hit.size(); ++i) {
        wires.push_back(hit[i]->WireID().Wire);
        times.push_back(hit[i]->PeakTime());
        ++n;
      }

      // If there are 2 or more hits in the cluster fill a TGraph and
      // fit a from a polynomial or order 1

      if (n >= 15) {

        // Push the hits into a TGraph

        TGraph* the2Dtrack = new TGraph(n, &wires[0], &times[0]);
        // === Try to fit the TGraph with a 1st order polynomial ===
        try {
          the2Dtrack->Fit("pol1", "Q");
          TF1* pol1 = (TF1*)the2Dtrack->GetFunction("pol1");
          double par[2];
          double parerror[2];
          pol1->GetParameters(par);
          parerror[1] = pol1->GetParError(1);
          double FitChi2 = pol1->GetChisquare();
          double FitNDF = pol1->GetNDF();

          double fitGoodness = FitChi2 / FitNDF;

          // Skipping the fitted slope if the Chi2/NDF < 5
          if (fitGoodness > 10) {
            dtdwstart.push_back(std::tan(RawClusters[iclu]->StartAngle()));
            continue;
          }

          // Take change in time tick vs change in wire (dT/dW) from the fit

          dtdwstart.push_back(par[1]);
          dtdwstartError.push_back(parerror[1]);
        } //<---End try to fit with a polynomial order 1

        // If the fitter fails just take dT/dW from the cluster
        catch (...) {
          mf::LogWarning("FeatureVertexFinder")
            << "Fitter failed, using the clusters default dTdW()";
          delete the2Dtrack;
          dtdwstart.push_back(std::tan(RawClusters[iclu]->StartAngle()));
          continue;
        }

        delete the2Dtrack;
      } //<---End if the cluster has 2 or more hits

      // If the cluster has fewer than 2 hits just take the dT/dW from
      // the cluster

      else {
        dtdwstart.push_back(std::tan(RawClusters[iclu]->StartAngle()));
      }
    } //<---End loop over clusters iclu

    // Now that I have slopes for all the clusters move on to finding
    // intersection points

    // Looping over cryostats

    for (auto const& tpc : geom->Iterate<geo::TPCGeo>()) {
      for (unsigned int i = 0; i < tpc.Nplanes(); ++i) {

        // If there is at least one cluster found

        if (Cls[i].size() >= 1) {

          // Loop over each cluster

          for (unsigned int j = 0; j < Cls[i].size(); ++j) {
            // === Current Clusters Plane ===
            Clu_Plane.push_back(RawClusters.at(Cls.at(i).at(j))->View());
            // === Current Clusters StartPos ===
            Clu_StartPos_Wire.push_back(RawClusters.at(Cls.at(i).at(j))->StartWire());
            Clu_StartPos_TimeTick.push_back(RawClusters.at(Cls.at(i).at(j))->StartTick());
            // === Current Clusters EndPos ===
            Clu_EndPos_Wire.push_back(RawClusters.at(Cls.at(i).at(j))->EndWire());
            Clu_EndPos_TimeTick.push_back(RawClusters.at(Cls.at(i).at(j))->EndTick());
            // Current Clusters Slope (In Wire and Time Tick)
            Clu_Slope.push_back(dtdwstart[Cls[i][j]]);
            Clu_Length.push_back(std::sqrt(pow((RawClusters.at(Cls.at(i).at(j))->StartWire() -
                                                RawClusters.at(Cls.at(i).at(j))->EndWire()) *
                                                 13.5,
                                               2) +
                                           pow(RawClusters.at(Cls.at(i).at(j))->StartTick() -
                                                 RawClusters.at(Cls.at(i).at(j))->EndTick(),
                                               2)));

            // Given a slope and a point find the y-intercept
            //                   c = y-mx

            Clu_Yintercept.push_back(
              RawClusters.at(Cls.at(i).at(j))->StartTick() -
              (dtdwstart[Cls[i][j]] * RawClusters.at(Cls.at(i).at(j))->StartWire()));

            // Also calculating the y-intercept but using the end
            // time of the cluster correct for the possibility that
            // the clustering didn't get start and end points right

            Clu_Yintercept2.push_back(
              RawClusters.at(Cls.at(i).at(j))->EndTick() -
              (dtdwstart[Cls[i][j]] * RawClusters.at(Cls.at(i).at(j))->EndWire()));

            // Iterating on the total number of clusters found

            nClustersFound++;
          } //<---End loop over all clusters

        } //<---End check if we have at least one cluster

        // If no clusters were found then put in dummy vertex values
        else {
          TwoDvtx_wire.push_back(-1);
          TwoDvtx_time.push_back(-1);
          TwoDvtx_plane.push_back(-1);
        }

      } //<---End loop over planes (i)
    }   //<---End loop over tpc's

    // Now loop over all the clusters found and establish a
    // preliminary set of 2d-verticies based on the slope/intercept of
    // those clusters

    for (unsigned int n = nClustersFound; n > 0; n--) {

      // Looping over the clusters starting from the first cluster and
      // checking against the nCluster

      for (unsigned int m = 0; m < n; m++) {

        // Checking to make sure clusters are in the same view

        if (Clu_Plane[n] == Clu_Plane[m]) {
          // --- Skip the vertex if the lines slope don't intercept ---
          if (Clu_Slope[m] - Clu_Slope[n] == 0) { break; }

          // === X intersection = (yInt2 - yInt1) / (slope1 - slope2) ===
          float intersection_X =
            (Clu_Yintercept[n] - Clu_Yintercept[m]) / (Clu_Slope[m] - Clu_Slope[n]);

          // === Y intersection = (slope1 * XInt) + yInt1 ===
          float intersection_Y = (Clu_Slope[m] * intersection_X) + Clu_Yintercept[m];

          // === X intersection = (yInt2 - yInt1) / (slope1 - slope2) ===
          float intersection_X2 =
            (Clu_Yintercept2[n] - Clu_Yintercept2[m]) / (Clu_Slope[m] - Clu_Slope[n]);

          // === Y intersection = (slope1 * XInt) + yInt1 ===
          float intersection_Y2 = (Clu_Slope[m] * intersection_X2) + Clu_Yintercept2[m];

          // Skipping crap intersection points
          geo::PlaneID const planeid(0, 0, Clu_Plane[m]);
          if (intersection_X2 < 1) { intersection_X2 = -999; }
          if (intersection_X2 > geom->Nwires(planeid)) { intersection_X2 = -999; }
          if (intersection_Y2 < 0) { intersection_Y2 = -999; }
          if (intersection_Y2 > detProp.NumberTimeSamples()) { intersection_Y2 = -999; }
          if (intersection_X < 1) { intersection_X = -999; }
          if (intersection_X > geom->Nwires(planeid)) { intersection_X = -999; }
          if (intersection_Y < 0) { intersection_Y = -999; }
          if (intersection_Y > detProp.NumberTimeSamples()) { intersection_Y = -999; }

          // Putting in a protection for the findManyHit function

          try {
            // Gathering the hits associated with the current cluster
            std::vector<art::Ptr<recob::Hit>> hitClu1 = fmhit.at(m);
            std::vector<art::Ptr<recob::Hit>> hitClu2 = fmhit.at(n);

            // If the intersection point is 80 or more wires away from
            // either cluster and one of the clusters has fewer than 8 hits the
            // intersection is likely a crap one and we won't save this point
            if ((abs(Clu_EndPos_Wire[m] - intersection_X2) > 80 && hitClu1.size() < 8) ||
                (abs(Clu_EndPos_Wire[n] - intersection_X2) > 80 && hitClu2.size() < 8)) {
              intersection_X2 = -999;
              intersection_Y2 = -999;
            }

            if ((abs(Clu_StartPos_Wire[m] - intersection_X) > 80 && hitClu1.size() < 8) ||
                (abs(Clu_StartPos_Wire[n] - intersection_X) > 80 && hitClu2.size() < 8)) {
              intersection_X = -999;
              intersection_Y = -999;
            }

            // If the intersection point is 50 or more wires away from
            // either cluster and the one of the clusters has fewer than 3 hits
            // the intersection is likely a crap one and we won't save this
            // point
            if ((abs(Clu_EndPos_Wire[m] - intersection_X2) > 50 && hitClu1.size() < 4) ||
                (abs(Clu_EndPos_Wire[n] - intersection_X2) > 50 && hitClu2.size() < 4)) {
              intersection_X2 = -999;
              intersection_Y2 = -999;
            }

            if ((abs(Clu_StartPos_Wire[m] - intersection_X) > 50 && hitClu1.size() < 4) ||
                (abs(Clu_StartPos_Wire[n] - intersection_X) > 50 && hitClu2.size() < 4)) {
              intersection_X = -999;
              intersection_Y = -999;
            }
          }
          catch (...) {
            mf::LogWarning("FeatureVertexFinder") << "FindManyHit Function faild";
            intersection_X = -999;
            intersection_Y = -999;
            intersection_X2 = -999;
            intersection_Y2 = -999;
            continue;
          }

          // Push back a candidate 2dClusterVertex if it is inside the
          // detector

          if (intersection_X2 > 1 && intersection_Y2 > 0 &&
              (intersection_X2 < geom->Nwires(planeid)) &&
              (intersection_Y2 < detProp.NumberTimeSamples())) {

            TwoDvtx_wire.push_back(intersection_X2);
            TwoDvtx_time.push_back(intersection_Y2);
            TwoDvtx_plane.push_back(Clu_Plane[m]);
          } //<---End saving a "good 2d vertex" candidate

          // Push back a candidate 2dClusterVertex if it is inside the
          // detector

          if (intersection_X > 1 && intersection_Y > 0 &&
              (intersection_X < geom->Nwires(planeid)) &&
              (intersection_Y < detProp.NumberTimeSamples())) {
            TwoDvtx_wire.push_back(intersection_X);
            TwoDvtx_time.push_back(intersection_Y);
            TwoDvtx_plane.push_back(Clu_Plane[m]);
          } //<---End saving a "good 2d vertex" candidate

        } //<---End check that they are in differnt planes
      }   //<---End m loop
    }     //<---End n loop

  } //<---End 2dClusterVertexCandidates

  // -----------------------------------------------------------------------------
  // Get 3d Vertex Candidates from clusters 2d Vertex candidates
  // -----------------------------------------------------------------------------
  void vertex::FeatureVertexFinder::Find3dVtxFrom2dClusterVtxCand(
    detinfo::DetectorPropertiesData const& detProp,
    std::vector<double> const& Wire_2dvtx,
    std::vector<double> const& Time_2dvtx,
    std::vector<double> const& Plane_2dvtx)
  {

    std::vector<double> vtx_wire_merged;
    std::vector<double> vtx_time_merged;
    std::vector<double> vtx_plane_merged;

    double y_coord = 0, z_coord = 0;

    bool merged = false;

    art::ServiceHandle<geo::Geometry const> geom;

    // MERGING THE LONG LIST OF 2D CANDIDATES

    // Looping over 2d-verticies (loop1)

    for (size_t vtxloop1 = 0; vtxloop1 < Wire_2dvtx.size(); vtxloop1++) {
      if (Wire_2dvtx[vtxloop1] < 0) { continue; }

      merged = false;

      // Looping over 2d-verticies (loop2)

      for (size_t vtxloop2 = vtxloop1 + 1; vtxloop2 < Wire_2dvtx.size(); vtxloop2++) {
        if (Wire_2dvtx[vtxloop2] < 0) { continue; }

        // Make sure the 2d-Verticies are in the same plane

        if (Plane_2dvtx[vtxloop1] == Plane_2dvtx[vtxloop2]) {

          // Considering merging 2d vertices if they
          //    are within 3 wires of each other

          if (fabs(Wire_2dvtx[vtxloop1] - Wire_2dvtx[vtxloop2]) < 4) {

            // Merge the verticies if they are within 10 time ticks

            if (fabs(Time_2dvtx[vtxloop1] - Time_2dvtx[vtxloop2]) < 10) {
              vtx_wire_merged.push_back(((Wire_2dvtx[vtxloop2] + Wire_2dvtx[vtxloop1]) / 2));
              vtx_time_merged.push_back(((Time_2dvtx[vtxloop2] + Time_2dvtx[vtxloop1]) / 2));
              vtx_plane_merged.push_back(Plane_2dvtx[vtxloop1]);

              merged = true;
              if (vtxloop2 < Wire_2dvtx.size()) { vtxloop2++; }
              if (vtxloop1 < Wire_2dvtx.size()) { vtxloop1++; }
            } //<---End the check within 10 time ticks for merging
          }   //<---Looking at vertices that are within 3 wires of each other
        }     //<---Only looking at vertices that are in the same plane
      }       //<---End vtxloop2
      if (!merged) {
        vtx_wire_merged.push_back(Wire_2dvtx[vtxloop1]);
        vtx_time_merged.push_back(Time_2dvtx[vtxloop1]);
        vtx_plane_merged.push_back(Plane_2dvtx[vtxloop1]);
      } //<---end saving unmerged verticies
    }   //<---End vtxloop1

    // Variables for channel numbers

    uint32_t vtx1_channel = 0;
    uint32_t vtx2_channel = 0;

    // Having now found a very long list of potential 2-d end points
    // we need to check if any of them match between planes and only
    // keep those that have matches

    for (auto const& tpcid : geom->Iterate<geo::TPCID>()) {
      for (unsigned int vtx = vtx_wire_merged.size(); vtx > 0; --vtx) {
        for (unsigned int vtx1 = 0; vtx1 < vtx; ++vtx1) {

          // Make sure we are comparing verticies from different planes
          if (vtx_plane_merged[vtx1] == vtx_plane_merged[vtx]) continue;

          // To figure out if these two verticies are from a common
          // point we need to check if the channels intersect and if
          // they are close in time ticks as well...to do this we have
          // to do some converting to use geom->PlaneWireToChannel(...)
          geo::PlaneID const vtx1_planeid(tpcid, vtx_plane_merged[vtx1]);
          geo::WireID const vtx1_wireid(vtx1_planeid, vtx_wire_merged[vtx1]);
          try {
            vtx1_channel = geom->PlaneWireToChannel(vtx1_wireid);
          }
          catch (...) {
            mf::LogWarning("FeatureVertexFinder") << "PlaneWireToChannel Failed";
            continue;
          }

          geo::PlaneID const vtx2_planeid(tpcid, vtx_plane_merged[vtx]);
          geo::WireID const vtx2_wireid(vtx2_planeid, vtx_wire_merged[vtx]);
          try {
            vtx2_channel = geom->PlaneWireToChannel(vtx2_wireid);
          }
          catch (...) {
            mf::LogWarning("FeatureVertexFinder") << "PlaneWireToChannel Failed";
            continue;
          }

          // Check to see if the channels intersect and save the y and z coordinate
          if (!geom->ChannelsIntersect(vtx1_channel, vtx2_channel, y_coord, z_coord)) {
            mf::LogWarning("FeatureVertexFinder") << "match failed for some reason";
            continue;
          }

          // If the channels intersect establish if they are close in "X"
          float tempXCluster1 = detProp.ConvertTicksToX(vtx_time_merged[vtx1], vtx1_planeid);
          float tempXCluster2 = detProp.ConvertTicksToX(vtx_time_merged[vtx], vtx2_planeid);

          // Now check if the matched channels are within 0.5 cm when
          // projected in X and that we have less than 100 of these
          // candidates...because more than that seems silly

          if (std::abs(tempXCluster1 - tempXCluster2) < 0.5 && candidate_x.size() < 101) {
            candidate_x.push_back(detProp.ConvertTicksToX(vtx_time_merged[vtx1], vtx1_planeid));
            candidate_y.push_back(y_coord);
            candidate_z.push_back(z_coord);
            candidate_strength.push_back(
              10); //<--For cluster verticies I give it a strength of "10"
                   // arbitrarily for now

          } //<---End Checking if the vertices agree "well enough" in time tick
        }   //<---end vtx1 for loop
      }     //<---End vtx for loop
    }       //<---End loop over TPC's

  } //<---End Find3dVtxFrom2dClusterVtxCand

  // -----------------------------------------------------------------------------
  // Get 3d Vertex Candidates from clusters 2d Vertex candidates
  // -----------------------------------------------------------------------------
  void vertex::FeatureVertexFinder::MergeAndSort3dVtxCandidate(
    std::vector<double> const& merge_vtxX,
    std::vector<double> const& merge_vtxY,
    std::vector<double> const& merge_vtxZ,
    std::vector<double> const& merge_vtxStgth)
  {

    std::vector<double> x_3dVertex_dupRemoved = {0.};
    std::vector<double> y_3dVertex_dupRemoved = {0.};
    std::vector<double> z_3dVertex_dupRemoved = {0.};
    std::vector<double> strength_dupRemoved = {0.};

    // Looping over the 3d candidates found thus far

    for (size_t dup = 0; dup < merge_vtxX.size(); dup++) {
      // Temperary storing the current vertex
      float tempX_dup = merge_vtxX[dup];
      float tempY_dup = merge_vtxY[dup];
      float tempZ_dup = merge_vtxZ[dup];
      float tempStgth = merge_vtxStgth[dup];

      // Setting a boolian to see if this is a duplicate

      bool duplicate_found = false;

      // Looping over the rest of the list for duplicate check

      for (size_t check = dup + 1; check < merge_vtxX.size(); check++) {

        // I am going to call a duplicate vertex one that matches in x, y,
        // and z within 0.1 cm for all 3 coordinates simultaneously

        if (std::abs(merge_vtxX[check] - tempX_dup) < 0.1 &&
            std::abs(merge_vtxY[check] - tempY_dup) < 0.1 &&
            std::abs(merge_vtxZ[check] - tempZ_dup) < 0.1) {
          duplicate_found = true;
        } //<---End checking to see if this is a duplicate vertex

      } //<---End check for loop

      // If we didn't find a duplicate then lets save this 3d vertex
      // as a real candidate for consideration

      if (!duplicate_found && tempX_dup > 0) {
        x_3dVertex_dupRemoved.push_back(tempX_dup);
        y_3dVertex_dupRemoved.push_back(tempY_dup);
        z_3dVertex_dupRemoved.push_back(tempZ_dup);
        strength_dupRemoved.push_back(tempStgth);
      } //<---End storing only non-duplicates

    } //<---End dup for loop

    // Sorting the verticies I have found such that the first in the
    // list is the vertex with the highest vertex strength and the
    // lowest z location

    int flag = 1;
    double tempX, tempY, tempZ, tempS;

    // Looping over all duplicate removed candidates

    for (size_t npri = 0; (npri < x_3dVertex_dupRemoved.size()) && flag; npri++) {
      flag = 0;
      for (size_t mpri = 0; mpri < x_3dVertex_dupRemoved.size() - 1; mpri++) {
        // Swap the order of the two elements
        if (strength_dupRemoved[mpri + 1] > strength_dupRemoved[mpri] ||
            (strength_dupRemoved[mpri + 1] == strength_dupRemoved[mpri] &&
             z_3dVertex_dupRemoved[mpri] > z_3dVertex_dupRemoved[mpri + 1])) {
          tempX = x_3dVertex_dupRemoved[mpri];
          x_3dVertex_dupRemoved[mpri] = x_3dVertex_dupRemoved[mpri + 1];
          x_3dVertex_dupRemoved[mpri + 1] = tempX;

          tempY = y_3dVertex_dupRemoved[mpri];
          y_3dVertex_dupRemoved[mpri] = y_3dVertex_dupRemoved[mpri + 1];
          y_3dVertex_dupRemoved[mpri + 1] = tempY;

          tempZ = z_3dVertex_dupRemoved[mpri];
          z_3dVertex_dupRemoved[mpri] = z_3dVertex_dupRemoved[mpri + 1];
          z_3dVertex_dupRemoved[mpri + 1] = tempZ;

          tempS = strength_dupRemoved[mpri];
          strength_dupRemoved[mpri] = strength_dupRemoved[mpri + 1];
          strength_dupRemoved[mpri + 1] = tempS;

          flag = 1;

        } //<---Inside swap loop
      }   //<---End mpri
    }     //<---End npri loop

    // Pushing into a vector of merged and sorted verticies

    for (size_t count = 0; count < x_3dVertex_dupRemoved.size(); count++) {
      MergeSort3dVtx_xpos.push_back(x_3dVertex_dupRemoved[count]);
      MergeSort3dVtx_ypos.push_back(y_3dVertex_dupRemoved[count]);
      MergeSort3dVtx_zpos.push_back(z_3dVertex_dupRemoved[count]);
      MergeSort3dVtx_strength.push_back(strength_dupRemoved[count]);
    }

  } // End MergeAndSort3dVtxCandidate

  DEFINE_ART_MODULE(FeatureVertexFinder)

  // -----------------------------------------------------------------------------

} //<---End namespace vertex