ClusterAna_module.cc

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////////////////////////////////////////////////////////////////////////
//
// ClusterAna class
//
// Bruce Baller
//
////////////////////////////////////////////////////////////////////////

#include <TProfile.h>
#include <array>
#include <fstream>
#include <iomanip>
#include <string>

//Framework includes
#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 "art_root_io/TFileService.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/PlaneGeo.h"
#include "lardata/DetectorInfoServices/DetectorClocksService.h"
#include "lardataobj/RecoBase/Cluster.h"
#include "lardataobj/RecoBase/Hit.h"
#include "lardataobj/RecoBase/Vertex.h"
#include "larsim/MCCheater/BackTrackerService.h"
#include "larsim/MCCheater/ParticleInventoryService.h"
#include "nug4/ParticleNavigation/ParticleList.h"
#include "nusimdata/SimulationBase/MCTruth.h"

#include "art/Framework/Core/EDAnalyzer.h"

/// Cluster finding and building
namespace cluster {

  class ClusterAna : public art::EDAnalyzer {
  public:
    explicit ClusterAna(fhicl::ParameterSet const& pset);

  private:
    void analyze(const art::Event& evt) override;
    void beginJob() override;
    void endJob() override;

    TH1F* fNClusters;
    TH1F* fNHitInCluster;
    // Cosmic Rays
    TH1F* fCREP2;
    TH1F* fCRE;
    TH1F* fCRP;
    // Neutrino interactions
    TH1F* fNuKE_elec;
    TH1F* fNuKE_muon;
    TH1F* fNuKE_pion;
    TH1F* fNuKE_kaon;
    TH1F* fNuKE_prot;
    //  TH1F* fNuEP2;
    TH1F* fNuEP2_elec;
    TH1F* fNuEP2_muon;
    TH1F* fNuEP2_pion;
    TH1F* fNuEP2_kaon;
    TH1F* fNuEP2_prot;
    TH1F* fNuE_elec;
    TH1F* fNuE_muon;
    TH1F* fNuE_pion;
    TH1F* fNuE_kaon;
    TH1F* fNuE_prot;
    TH1F* fNuP_elec;
    TH1F* fNuP_muon;
    TH1F* fNuP_pion;
    TH1F* fNuP_kaon;
    TH1F* fNuP_prot;

    TH1F* fNuVtx_dx;
    TH1F* fNuVtx_dy;
    TH1F* fNuVtx_dz;

    TProfile* fNuEP2_KE_elec;
    TProfile* fNuEP2_KE_muon;
    TProfile* fNuEP2_KE_pion;
    TProfile* fNuEP2_KE_kaon;
    TProfile* fNuEP2_KE_prot;

    std::string fHitsModuleLabel;
    std::string fClusterModuleLabel;
    std::string fVertexModuleLabel;
    std::vector<float> fElecKERange;
    std::vector<float> fMuonKERange;
    std::vector<float> fPionKERange;
    std::vector<float> fKaonKERange;
    std::vector<float> fProtKERange;
    short fTrackWeightOption;
    bool fMergeDaughters;
    //  float fMergeAngleCut;
    bool fSkipCosmics;
    short fPrintLevel;
    short moduleID;

    std::ofstream outFile;

  }; // class ClusterAna

}

namespace cluster {

  //--------------------------------------------------------------------
  ClusterAna::ClusterAna(fhicl::ParameterSet const& pset)
    : EDAnalyzer(pset)
    , fHitsModuleLabel(pset.get<std::string>("HitsModuleLabel"))
    , fClusterModuleLabel(pset.get<std::string>("ClusterModuleLabel"))
    , fVertexModuleLabel(pset.get<std::string>("VertexModuleLabel"))
    , fElecKERange(pset.get<std::vector<float>>("ElecKERange"))
    , fMuonKERange(pset.get<std::vector<float>>("MuonKERange"))
    , fPionKERange(pset.get<std::vector<float>>("PionKERange"))
    , fKaonKERange(pset.get<std::vector<float>>("KaonKERange"))
    , fProtKERange(pset.get<std::vector<float>>("ProtKERange"))
    , fTrackWeightOption(pset.get<short>("TrackWeightOption"))
    , fMergeDaughters(pset.get<bool>("MergeDaughters"))
    , fSkipCosmics(pset.get<bool>("SkipCosmics"))
    , fPrintLevel(pset.get<short>("PrintLevel"))
  {

    if (fPrintLevel == -1) {
      // encode the clustermodule label into an integer
      moduleID = 0;
      size_t found = fClusterModuleLabel.find("traj");
      if (found != std::string::npos) moduleID = 1;
      found = fClusterModuleLabel.find("line");
      if (found != std::string::npos) moduleID = 2;
      found = fClusterModuleLabel.find("fuzz");
      if (found != std::string::npos) moduleID = 3;
      found = fClusterModuleLabel.find("pand");
      if (found != std::string::npos) moduleID = 4;
      std::cout << "fClusterModuleLabel " << fClusterModuleLabel << " ID " << moduleID << "\n";

      std::string fileName = fClusterModuleLabel + ".tru";
      outFile.open(fileName);
    }
  }

  //------------------------------------------------------------------
  void
  ClusterAna::beginJob()
  {

    // get access to the TFile service
    art::ServiceHandle<art::TFileService const> tfs;

    fNClusters = tfs->make<TH1F>("fNoClustersInEvent", "Number of Clusters", 40, 0, 400);
    fNHitInCluster = tfs->make<TH1F>("fNHitInCluster", "NHitInCluster", 100, 0, 100);

    if (!fSkipCosmics) {
      // Cosmic ray histos
      fCREP2 = tfs->make<TH1F>("CREP2", "CREP2", 50, 0, 1);
      fCRE = tfs->make<TH1F>("CRE", "CR Efficiency", 50, 0, 1);
      fCRP = tfs->make<TH1F>("CRP", "CR Purity", 50, 0, 1);
    }
    // Neutrino Int histos
    fNuKE_elec = tfs->make<TH1F>("NuKE_elec", "NuKE electron", 100, 0, 4000);
    fNuKE_muon = tfs->make<TH1F>("NuKE_muon", "NuKE muon", 100, 0, 4000);
    fNuKE_pion = tfs->make<TH1F>("NuKE_pion", "NuKE pion", 100, 0, 4000);
    fNuKE_kaon = tfs->make<TH1F>("NuKE_kaon", "NuKE kaon", 100, 0, 4000);
    fNuKE_prot = tfs->make<TH1F>("NuKE_prot", "NuKE proton", 100, 0, 4000);

    fNuEP2_elec = tfs->make<TH1F>("NuEP2_elec", "NuEP2 electron", 50, 0, 1);
    fNuEP2_muon = tfs->make<TH1F>("NuEP2_muon", "NuEP2 muon", 50, 0, 1);
    fNuEP2_pion = tfs->make<TH1F>("NuEP2_pion", "NuEP2 pion", 50, 0, 1);
    fNuEP2_kaon = tfs->make<TH1F>("NuEP2_kaon", "NuEP2 kaon", 50, 0, 1);
    fNuEP2_prot = tfs->make<TH1F>("NuEP2_prot", "NuEP2 proton", 50, 0, 1);

    fNuE_elec = tfs->make<TH1F>("NuE_elec", "Nu Efficiency electron", 50, 0, 1);
    fNuE_muon = tfs->make<TH1F>("NuE_muon", "Nu Efficiency muon", 50, 0, 1);
    fNuE_pion = tfs->make<TH1F>("NuE_pion", "Nu Efficiency pion", 50, 0, 1);
    fNuE_kaon = tfs->make<TH1F>("NuE_kaon", "Nu Efficiency kaon", 50, 0, 1);
    fNuE_prot = tfs->make<TH1F>("NuE_prot", "Nu Efficiency proton", 50, 0, 1);

    fNuP_elec = tfs->make<TH1F>("NuP_elec", "Nu Purity electron", 50, 0, 1);
    fNuP_muon = tfs->make<TH1F>("NuP_muon", "Nu Purity muon", 50, 0, 1);
    fNuP_pion = tfs->make<TH1F>("NuP_pion", "Nu Purity pion", 50, 0, 1);
    fNuP_kaon = tfs->make<TH1F>("NuP_kaon", "Nu Purity kaon", 50, 0, 1);
    fNuP_prot = tfs->make<TH1F>("NuP_prot", "Nu Purity proton", 50, 0, 1);

    // True - Reco vertex difference
    fNuVtx_dx = tfs->make<TH1F>("Vtx dx", "Vtx dx", 80, -10, 10);
    fNuVtx_dy = tfs->make<TH1F>("Vtx dy", "Vtx dy", 80, -10, 10);
    fNuVtx_dz = tfs->make<TH1F>("Vtx dz", "Vtx dz", 80, -10, 10);

    fNuEP2_KE_elec = tfs->make<TProfile>("NuEP2_KE_elec", "NuEP2 electron vs KE", 200, 0, 2000);
    fNuEP2_KE_muon = tfs->make<TProfile>("NuEP2_KE_muon", "NuEP2 muon vs KE", 200, 0, 2000);
    fNuEP2_KE_pion = tfs->make<TProfile>("NuEP2_KE_pion", "NuEP2 pion vs KE", 200, 0, 2000);
    fNuEP2_KE_kaon = tfs->make<TProfile>("NuEP2_KE_kaon", "NuEP2 kaon vs KE", 200, 0, 2000);
    fNuEP2_KE_prot = tfs->make<TProfile>("NuEP2_KE_prot", "NuEP2 proton vs KE", 200, 0, 2000);
  }

  void
  ClusterAna::endJob()
  {
    if (fPrintLevel == -1) outFile.close();
  }

  void
  ClusterAna::analyze(const art::Event& evt)
  {
    // code stolen from TrackAna_module.cc
    art::ServiceHandle<geo::Geometry const> geom;
    if (geom->Nplanes() > 3) {
      mf::LogError("ClusterAna") << "Too many planes for this code...";
      return;
    }

    // get all hits in the event
    art::Handle<std::vector<recob::Hit>> hitListHandle;
    evt.getByLabel(fHitsModuleLabel, hitListHandle);
    std::vector<art::Ptr<recob::Hit>> allhits;
    art::fill_ptr_vector(allhits, hitListHandle);
    if (allhits.size() == 0) return;

    // get clusters and cluster-hit associations
    art::Handle<std::vector<recob::Cluster>> clusterListHandle;
    evt.getByLabel(fClusterModuleLabel, clusterListHandle);
    art::FindManyP<recob::Hit> fmh(clusterListHandle, evt, fClusterModuleLabel);
    if (clusterListHandle->size() == 0) {
      std::cout << "No clusters in event. Hits size " << allhits.size() << "\n";
      // don't return or the statistics will be off
    }

    // get 3D vertices
    art::Handle<std::vector<recob::Vertex>> vertexListHandle;
    double xyz[3] = {0, 0, 0};
    art::PtrVector<recob::Vertex> recoVtxList;
    if (vertexListHandle.isValid()) {
      evt.getByLabel(fVertexModuleLabel, vertexListHandle);
      for (unsigned int ii = 0; ii < vertexListHandle->size(); ++ii) {
        art::Ptr<recob::Vertex> vertex(vertexListHandle, ii);
        recoVtxList.push_back(vertex);
        vertex->XYZ(xyz);
      } // ii
    }   // vertexListHandle

    // list of all true particles
    art::ServiceHandle<cheat::BackTrackerService const> bt_serv;
    art::ServiceHandle<cheat::ParticleInventoryService const> pi_serv;
    sim::ParticleList const& plist = pi_serv->ParticleList();
    // list of all true particles that will be considered
    std::vector<const simb::MCParticle*> plist2;
    // true (reconstructed) hits for each particle in plist2
    std::vector<std::vector<art::Ptr<recob::Hit>>> hlist2;
    // index of cluster matched to each particle in plist2 in each plane
    std::vector<std::vector<short>> truToCl;
    // number of true hits in each plane and cluster
    std::vector<std::vector<unsigned short>> nTruHitInCl;
    //number of reconstructed hits in all clusters
    std::vector<unsigned short> nRecHitInCl;

    // calculate average EP2 for every event to facilitate code development
    // Beam Neutrinos - muons and not-muons

    float aveNuEP2mu = 0.;
    float numNuEP2mu = 0.;
    float aveNuEP2nm = 0.;
    float numNuEP2nm = 0.;
    // Cosmic Rays
    float aveCREP2 = 0.;
    float numCREP2 = 0.;

    // track ID of the neutrino (or single particle)
    int neutTrackID = -1;
    std::vector<int> tidlist;
    float neutEnergy = -1.;
    int neutIntType = -1;
    int neutCCNC = -1;
    bool isNeutrino = false;
    bool isSingleParticle = false;

    auto const clockData = art::ServiceHandle<detinfo::DetectorClocksService const>()->DataFor(evt);

    for (sim::ParticleList::const_iterator ipart = plist.begin(); ipart != plist.end(); ++ipart) {
      const simb::MCParticle* part = (*ipart).second;
      assert(part != 0);
      int pdg = abs(part->PdgCode());
      int trackID = part->TrackId();
      art::Ptr<simb::MCTruth> theTruth = pi_serv->TrackIdToMCTruth_P(trackID);
      if (fSkipCosmics && theTruth->Origin() == simb::kCosmicRay) continue;
      if (theTruth->Origin() == simb::kBeamNeutrino) isNeutrino = true;
      if (theTruth->Origin() == simb::kSingleParticle) isSingleParticle = true;
      float KE = 1000 * (part->E() - part->Mass());

      // Get the neutrino track ID. Assume that there is only one neutrino
      // interaction and it is first in the list of BeamNeutrino particles
      if ((isNeutrino || isSingleParticle) && neutTrackID < 0) {
        neutTrackID = trackID;
        if (isNeutrino) {
          simb::MCNeutrino theNeutrino = theTruth->GetNeutrino();
          neutEnergy = 1000. * theNeutrino.Nu().E();
          neutIntType = theNeutrino.InteractionType();
          neutCCNC = theNeutrino.CCNC();
        }

        for (unsigned short iv = 0; iv < recoVtxList.size(); ++iv) {
          recoVtxList[iv]->XYZ(xyz);
          fNuVtx_dx->Fill(part->Vx() - xyz[0]);
          fNuVtx_dy->Fill(part->Vy() - xyz[1]);
          fNuVtx_dz->Fill(part->Vz() - xyz[2]);
        } // iv
      }   // theTruth->Origin() == simb::kBeamNeutrino && neutTrackID <

      if (fPrintLevel > 3)
        mf::LogVerbatim("ClusterAna") << "Origin " << theTruth->Origin() << " trackID " << trackID
                                      << " PDG " << part->PdgCode() << " KE " << (int)KE << " MeV "
                                      << " neutTrackID " << neutTrackID << " Mother "
                                      << part->Mother() << " Proc " << part->Process();

      bool isCharged = (pdg == 11) || (pdg == 13) || (pdg == 211) || (pdg == 321) || (pdg == 2212);

      if (!isCharged) continue;

      // KE (MeV) cuts
      if (pdg == 11) {
        if (fElecKERange[0] < 0) continue;
        // only allow primary electrons
        if (part->Process() != "primary") continue;
        if (KE < fElecKERange[0] || KE > fElecKERange[1]) continue;
      }
      if (pdg == 13) {
        if (fMuonKERange[0] < 0) continue;
        if (KE < fMuonKERange[0] || KE > fMuonKERange[1]) continue;
      }
      if (pdg == 211) {
        if (fPionKERange[0] < 0) continue;
        if (KE < fPionKERange[0] || KE > fPionKERange[1]) continue;
      }
      if (pdg == 321) {
        if (fKaonKERange[0] < 0) continue;
        if (KE < fKaonKERange[0] || KE > fKaonKERange[1]) continue;
      }
      if (pdg == 2212) {
        if (fProtKERange[0] < 0) continue;
        if (KE < fProtKERange[0] || KE > fProtKERange[1]) continue;
      }
      // ignore secondaries from neutron interactions
      if (part->Process() == "NeutronInelastic") continue;
      plist2.push_back(part);
      tidlist.push_back(trackID);
      // initialize the true->(cluster,plane) association
      std::vector<short> temp{-1, -1, -1};
      truToCl.push_back(temp);
      // initialize the true hit count
      std::vector<unsigned short> temp2(3);
      nTruHitInCl.push_back(temp2);

      if (fPrintLevel > 2)
        mf::LogVerbatim("ClusterAna")
          << "plist2[" << plist2.size() - 1 << "]"
          << " Origin " << theTruth->Origin() << " trackID " << trackID << " PDG "
          << part->PdgCode() << " KE " << (int)KE << " Mother " << part->Mother() + neutTrackID - 1
          << " Proc " << part->Process();
    }

    if (plist2.size() == 0) return;

    // get the hits (in all planes) that are matched to the true tracks
    hlist2 = bt_serv->TrackIdsToHits_Ps(clockData, tidlist, allhits);
    if (hlist2.size() != plist2.size()) {
      mf::LogError("ClusterAna") << "MC particle list size " << plist2.size()
                                 << " != size of MC particle true hits lists " << hlist2.size();
      return;
    }
    tidlist.clear();

    // vector of (mother, daughter) pairs
    std::vector<std::pair<unsigned short, unsigned short>> moda;
    // Deal with mother-daughter tracks
    if (fMergeDaughters && neutTrackID >= 0) {
      // Assume that daughters appear later in the list. Step backwards
      // to accumulate all generations of daughters
      unsigned short ii, dpl, jj, jpl, kpl;
      for (ii = 0; ii < plist2.size(); ++ii) {
        dpl = plist2.size() - 1 - ii;
        // no mother
        if (plist2[dpl]->Mother() == 0) continue;
        // electron
        if (abs(plist2[dpl]->PdgCode()) == 11) continue;
        // the actual mother trackID is offset from the neutrino trackID
        int motherID = neutTrackID + plist2[dpl]->Mother() - 1;
        // ensure that we are only looking at BeamNeutrino or single particle daughters
        if (motherID != neutTrackID) continue;
        // count the number of daughters
        int ndtr = 0;
        for (kpl = 0; kpl < plist2.size(); ++kpl) {
          if (plist2[kpl]->Mother() == motherID) ++ndtr;
        }
        // require only one daughter
        if (ndtr > 1) continue;
        // find the mother in the list
        int mpl = -1;
        for (jj = 0; jj < plist2.size(); ++jj) {
          jpl = plist2.size() - 1 - jj;
          if (plist2[jpl]->TrackId() == motherID) {
            mpl = jpl;
            break;
          }
        } // jpl
        // mother not found for some reason
        if (mpl < 0) {
          mf::LogVerbatim("ClusterAna")
            << " mother of daughter " << dpl << " not found. mpl = " << mpl;
          continue;
        }
        // ensure that PDG code for mother and daughter are the same
        if (plist2[dpl]->PdgCode() != plist2[mpl]->PdgCode()) continue;
        moda.push_back(std::make_pair(mpl, dpl));
      } //  dpl
    }   // MergeDaughters

    // Now match reconstructed clusters to true particles.
    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);
    }

    fNClusters->Fill(clusterListHandle->size());
    nRecHitInCl.resize(clusters.size());

    // get the plane from the view. Perhaps there is a method that does
    // this somewhere...
    std::map<geo::View_t, unsigned int> ViewToPlane;
    for (unsigned int plane = 0; plane < geom->Nplanes(); ++plane) {
      geo::View_t view = geom->Plane(plane).View();
      ViewToPlane[view] = plane;
    }
    for (size_t icl = 0; icl < clusters.size(); ++icl) {
      unsigned int plane = ViewToPlane[clusters[icl]->View()];
      std::vector<art::Ptr<recob::Hit>> cluhits = fmh.at(icl);
      fNHitInCluster->Fill(cluhits.size());
      nRecHitInCl[icl] = cluhits.size();
      // count the number of hits matched to each true particle in plist2
      std::vector<unsigned short> nHitInPl2(plist2.size());
      for (size_t iht = 0; iht < cluhits.size(); ++iht) {

        // look for this hit in all of the truth hit lists
        short hitInPl2 = -1;
        for (unsigned short ipl = 0; ipl < plist2.size(); ++ipl) {
          unsigned short imat = 0;
          for (imat = 0; imat < hlist2[ipl].size(); ++imat) {
            if (cluhits[iht] == hlist2[ipl][imat]) break;
          } // imat
          if (imat < hlist2[ipl].size()) {
            hitInPl2 = ipl;
            break;
          }
        } // ipl
        if (hitInPl2 < 0) continue;
        // Assign the hit count to the mother if this is a daughter.
        // Mother-daughter pairs are entered in the moda vector in reverse
        // order, so assign daughter hits to the highest generation mother.
        for (unsigned short imd = 0; imd < moda.size(); ++imd) {
          if (moda[imd].second == hitInPl2) hitInPl2 = moda[imd].first;
        }
        // count
        ++nHitInPl2[hitInPl2];
      } // iht
      // Associate the cluster with the truth particle that has the highest
      // number of cluster hits
      unsigned short nhit = 0;
      short imtru = -1;
      for (unsigned int ipl = 0; ipl < nHitInPl2.size(); ++ipl) {
        if (nHitInPl2[ipl] > nhit) {
          nhit = nHitInPl2[ipl];
          imtru = ipl;
        }
      } // ipl
      // make the cluster->(true,plane) association and save the
      // number of true hits in the cluster
      if (imtru != -1) {
        // clobber a previously made association?
        if (nhit > nTruHitInCl[imtru][plane]) {
          truToCl[imtru][plane] = icl;
          nTruHitInCl[imtru][plane] = nhit;
        }
      } // imtru != 1
    }   // icl

    // ready to calculate Efficiency, Purity in each plane and EP2
    for (unsigned short ipl = 0; ipl < plist2.size(); ++ipl) {
      // ignore daughters
      bool skipit = false;
      for (unsigned short ii = 0; ii < moda.size(); ++ii) {
        if (moda[ii].second == ipl) {
          skipit = true;
          break;
        }
      } // ii
      if (skipit) continue;
      // ignore true particles with few true hits. Outside the detector
      // or not reconstructable?
      if (hlist2[ipl].size() < 3) continue;

      int trackID = plist2[ipl]->TrackId();
      art::Ptr<simb::MCTruth> theTruth = pi_serv->TrackIdToMCTruth_P(trackID);
      bool isCosmic = (theTruth->Origin() == simb::kCosmicRay);
      float KE = 1000 * (plist2[ipl]->E() - plist2[ipl]->Mass());
      int PDG = abs(plist2[ipl]->PdgCode());

      std::vector<short> nTru(geom->Nplanes());
      std::vector<short> nRec(geom->Nplanes());
      std::vector<short> nTruRec(geom->Nplanes());
      std::vector<float> eff(geom->Nplanes());
      std::vector<float> pur(geom->Nplanes());
      std::vector<float> ep(geom->Nplanes());
      for (unsigned int plane = 0; plane < geom->Nplanes(); ++plane) {
        // count the number of true hits in this plane for the true particle.
        // First count the mother hits
        for (unsigned short ii = 0; ii < hlist2[ipl].size(); ++ii) {
          if (ViewToPlane[hlist2[ipl][ii]->View()] == plane) ++nTru[plane];
        } // ii

        // next look for daughters and count those hits in all generations
        unsigned short mom = ipl;
        std::vector<std::pair<unsigned short, unsigned short>>::reverse_iterator rit =
          moda.rbegin();
        while (rit != moda.rend()) {
          if ((*rit).first == mom) {
            unsigned short dau = (*rit).second;
            for (unsigned short jj = 0; jj < hlist2[dau].size(); ++jj) {
              if (ViewToPlane[hlist2[dau][jj]->View()] == plane) ++nTru[plane];
            } // jj
            // It is likely that one hit appears in the mother list
            // as well as the daughter list, so subtract one from the count
            mom = (*rit).second;
          } // (*rit).first == mom
          ++rit;
        } // rit

        if (nTru[plane] == 0) continue;
        // Ignore short truth clusters
        if (nTru[plane] < 3) continue;
        short icl = truToCl[ipl][plane];
        if (icl < 0) { nRec[plane] = 0; }
        else {
          nRec[plane] = nRecHitInCl[icl];
        }
        nTruRec[plane] = nTruHitInCl[ipl][plane];
        eff[plane] = 0;
        pur[plane] = 0;
        if (nTru[plane] > 0) eff[plane] = (float)nTruRec[plane] / (float)nTru[plane];
        if (nRec[plane] > 0) pur[plane] = (float)nTruRec[plane] / (float)nRec[plane];
        // do this to prevent histogram under/over flow
        if (eff[plane] == 0) { eff[plane] = 0.001; }
        if (pur[plane] == 0) { pur[plane] = 0.001; }
        if (eff[plane] >= 1) { eff[plane] = 0.999; }
        if (pur[plane] >= 1) { pur[plane] = 0.999; }
        ep[plane] = eff[plane] * pur[plane];
        if (fPrintLevel == -1)
          outFile << moduleID << " " << evt.id().event() << " " << trackID << " " << PDG << " "
                  << (int)KE << " " << plane << " " << nTru[plane] << " " << std::setprecision(3)
                  << eff[plane] << " " << pur[plane] << "\n";
      } // plane
      // sort the ep values in ascending order
      std::vector<float> temp;
      temp = ep;
      std::sort(temp.begin(), temp.end());
      // EP2 is the second highest value
      unsigned short ii = temp.size() - 2;
      float ep2 = temp[ii];
      // find the plane that defined EP2
      short ep2Plane = 0;
      short ep2Cluster = 0;
      for (unsigned short jj = 0; jj < temp.size(); ++jj) {
        if (ep[jj] == ep2) {
          ep2Plane = jj;
          ep2Cluster = truToCl[ipl][ep2Plane];
          break;
        }
      } // jj
      // find the US and DS ends of the cluster for printing
      std::array<double, 2> clBeg, clEnd;
      if (ep2Cluster >= 0) {
        clBeg[0] = clusters[ep2Cluster]->StartWire();
        clBeg[1] = clusters[ep2Cluster]->StartTick();
        clEnd[0] = clusters[ep2Cluster]->EndWire();
        clEnd[1] = clusters[ep2Cluster]->EndTick();
      }
      else {
        clBeg.fill(0.);
        clEnd.fill(0.);
      }
      // fill histograms
      if (isCosmic) {
        fCREP2->Fill(ep2);
        fCRE->Fill(eff[ep2Plane]);
        fCRP->Fill(pur[ep2Plane]);
        aveCREP2 += ep2;
        numCREP2 += 1.;
        if (fPrintLevel > 1)
          mf::LogVerbatim("ClusterAna")
            << ">>>CREP2 " << std::fixed << std::setprecision(2) << ep2 << " E " << eff[ep2Plane]
            << std::setprecision(2) << " P " << pur[ep2Plane] << " P:W:T " << ep2Plane << ":"
            << (int)clBeg[0] << ":" << (int)clBeg[1] << "-" << ep2Plane << ":" << (int)clEnd[0]
            << ":" << (int)clEnd[1] << " PDG " << PDG << " KE " << (int)KE << " MeV";
      } // isCosmic
      else {
        float wght = 1.;
        if (fTrackWeightOption == 1) wght = KE;
        // accumulate statistics for muons and not-muons
        if (PDG == 13) {
          aveNuEP2mu += ep2 * wght;
          numNuEP2mu += wght;
        }
        else {
          aveNuEP2nm += ep2 * wght;
          numNuEP2nm += wght;
        }
        if (PDG == 11) {
          fNuKE_elec->Fill(KE, wght);
          fNuE_elec->Fill(eff[ep2Plane], wght);
          fNuP_elec->Fill(pur[ep2Plane], wght);
          fNuEP2_elec->Fill(ep2, wght);
          fNuEP2_KE_elec->Fill(KE, ep2, wght);
        }
        else if (PDG == 13) {
          fNuKE_muon->Fill(KE, wght);
          fNuE_muon->Fill(eff[ep2Plane], wght);
          fNuP_muon->Fill(pur[ep2Plane], wght);
          fNuEP2_muon->Fill(ep2, wght);
          fNuEP2_KE_muon->Fill(KE, ep2, wght);
        }
        else if (PDG == 211) {
          fNuKE_pion->Fill(KE, wght);
          fNuE_pion->Fill(eff[ep2Plane], wght);
          fNuP_pion->Fill(pur[ep2Plane], wght);
          fNuEP2_pion->Fill(ep2, wght);
          fNuEP2_KE_pion->Fill(KE, ep2, wght);
        }
        else if (PDG == 321) {
          fNuKE_kaon->Fill(KE, wght);
          fNuE_kaon->Fill(eff[ep2Plane], wght);
          fNuP_kaon->Fill(pur[ep2Plane], wght);
          fNuEP2_kaon->Fill(ep2, wght);
          fNuEP2_KE_kaon->Fill(KE, ep2, wght);
        }
        else if (PDG == 2212) {
          fNuKE_prot->Fill(KE, wght);
          fNuE_prot->Fill(eff[ep2Plane], wght);
          fNuP_prot->Fill(pur[ep2Plane], wght);
          fNuEP2_prot->Fill(ep2, wght);
          fNuEP2_KE_prot->Fill(KE, ep2, wght);
        }
        if (fPrintLevel > 1)
          mf::LogVerbatim("ClusterAna")
            << ">>>NuEP2 " << std::fixed << std::setprecision(2) << ep2 << " E " << eff[ep2Plane]
            << std::setprecision(2) << " P " << pur[ep2Plane] << " P:W:T " << ep2Plane << ":"
            << (int)clBeg[0] << ":" << (int)clBeg[1] << "-" << ep2Plane << ":" << (int)clEnd[0]
            << ":" << (int)clEnd[1] << " PDG " << PDG << " KE " << (int)KE << " MeV ";
        if (fPrintLevel > 2) {
          // print out the begin/end true hits
          mf::LogVerbatim mfp("ClusterAna");
          mfp << " Truth P:W:T ";
          for (unsigned int plane = 0; plane < geom->Nplanes(); ++plane) {
            unsigned short loW = 9999;
            unsigned short loT = 0;
            unsigned short hiW = 0;
            unsigned short hiT = 0;
            for (unsigned short ii = 0; ii < hlist2[ipl].size(); ++ii) {
              if (ViewToPlane[hlist2[ipl][ii]->View()] == plane) {
                art::Ptr<recob::Hit> theHit = hlist2[ipl][ii];
                if (theHit->WireID().Wire < loW) {
                  loW = theHit->WireID().Wire;
                  loT = theHit->PeakTime();
                }
                if (theHit->WireID().Wire > hiW) {
                  hiW = theHit->WireID().Wire;
                  hiT = theHit->PeakTime();
                }
              } // correct view
            }   // ii
            mfp << plane << ":" << loW << ":" << loT << "-" << plane << ":" << hiW << ":" << hiT
                << " ";
          } // plane
        }   // fPrintLevel > 2
      }     // !isCosmic
    }       // ipl

    float ave1 = -1.;
    if (numNuEP2mu > 0.) ave1 = aveNuEP2mu / numNuEP2mu;

    float ave2 = -1.;
    if (numNuEP2nm > 0.) ave2 = aveNuEP2nm / numNuEP2nm;

    float ave3 = -1.;
    if (numCREP2 > 0.) ave3 = aveCREP2 / numCREP2;

    if (fPrintLevel > 0) {
      std::string nuType = "Other";
      if (neutCCNC == simb::kCC) {
        if (neutIntType == 1001) nuType = "CCQE";
        if (neutIntType == 1091) nuType = "DIS";
        if (neutIntType == 1097) nuType = "COH";
        if (neutIntType > 1002 && neutIntType < 1091) nuType = "RES";
      }
      else if (neutCCNC == simb::kNC) {
        nuType = "NC";
      }
      else {
        nuType = "Unknown";
      }
      mf::LogVerbatim("ClusterAna")
        << "EvtEP2 " << evt.id().event() << " NuType " << nuType << " Enu " << std::fixed
        << std::setprecision(0) << neutEnergy << std::right << std::fixed << std::setprecision(2)
        << " NuMuons " << ave1 << " NuPiKp " << ave2 << " CosmicRays " << ave3 << " CCNC "
        << neutCCNC << " IntType " << neutIntType;
    }
  } // analyze

} // end namespace

DEFINE_ART_MODULE(cluster::ClusterAna)