NuShowerEff_module.cc

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////////////////////////////////////////////////////////////////////////
// Class:       NuShowerEff
// Plugin Type: analyzer (art v2_11_03)
// File:        NuShowerEff_module.cc
//
// Generated at Tue Sep 18 14:20:57 2018 by Wanwei Wu using cetskelgen
// from cetlib version v3_03_01.
////////////////////////////////////////////////////////////////////////

// Framework includes
#include "art/Framework/Core/EDAnalyzer.h"
#include "art/Framework/Core/ModuleMacros.h"
#include "art/Framework/Principal/Event.h"
#include "art/Framework/Principal/Handle.h"
#include "fhiclcpp/ParameterSet.h"
#include "messagefacility/MessageLogger/MessageLogger.h"

#include "canvas/Persistency/Common/FindManyP.h"
#include "art/Framework/Services/Registry/ServiceHandle.h"
#include "art_root_io/TFileService.h"

// LArsoft includes
#include "lardataobj/RecoBase/Hit.h"
#include "lardataobj/RecoBase/Cluster.h"
#include "lardataobj/RecoBase/Shower.h"
#include "lardataobj/RecoBase/PFParticle.h"
#include "lardataobj/AnalysisBase/BackTrackerMatchingData.h"

#include "nusimdata/SimulationBase/MCParticle.h"
#include "nusimdata/SimulationBase/MCTruth.h"
#include "larsim/MCCheater/ParticleInventoryService.h"
#include "larcore/Geometry/Geometry.h"
#include "larcore/CoreUtils/ServiceUtil.h"

// ROOT includes
#include "TTree.h"
#include "TH1.h"
#include "TEfficiency.h"
#include "TGraphAsymmErrors.h"

// user's defined constant
#define MAX_SHOWERS 1000

using namespace std;

class NuShowerEff;


class NuShowerEff : public art::EDAnalyzer {
public:
  explicit NuShowerEff(fhicl::ParameterSet const & p);
  // The compiler-generated destructor is fine for non-base
  // classes without bare pointers or other resource use.

  // Plugins should not be copied or assigned.
  NuShowerEff(NuShowerEff const &) = delete;
  NuShowerEff(NuShowerEff &&) = delete;
  NuShowerEff & operator = (NuShowerEff const &) = delete;
  NuShowerEff & operator = (NuShowerEff &&) = delete;

private:

  // Required functions.
  void analyze(art::Event const & e) override;

  // user's defined functions
  void beginJob() override;
  void endJob() override;
  void beginRun(art::Run const& run) override;
  void doEfficiencies();
  bool insideFV(double vertex[4]);
  void reset();

  // Declare member data here.

  // read from fchicl: Input Tag
  std::string fMCTruthModuleLabel;
  std::string fHitModuleLabel;
  std::string fShowerModuleLabel;
  std::string fTruthMatchDataModuleLabel;

  // read from fchicl: user's defined parameters
  int    fNeutrinoPDGcode;
  int    fLeptonPDGcode;
  bool   fSaveMCTree;
  bool   fHitShowerThroughPFParticle; // an option for getting hits associated with shower
  double fMinPurity; // for reference
  double fMinCompleteness; // for reference
  float  fFidVolCutX;// Fiducail Volume cut [cm]
  float  fFidVolCutY;
  float  fFidVolCutZ;

  // Fiducial Volume parameters
  float fFidVolXmin;
  float fFidVolXmax;
  float fFidVolYmin;
  float fFidVolYmax;
  float fFidVolZmin;
  float fFidVolZmax;

  // Event
  int Event;
  int Run;
  int SubRun;

  // MC Truth: Generator
  int MC_incoming_PDG;
  int MC_lepton_PDG;
  int MC_isCC;
  int MC_channel;
  int MC_target;
  double MC_Q2;
  double MC_W;
  double MC_vertex[4];
  double MC_incoming_P[4];
  double MC_lepton_startMomentum[4];
  double MC_lepton_endMomentum[40];
  double MC_lepton_startXYZT[4];
  double MC_lepton_endXYZT[4];
  double MC_lepton_theta;
  int    MC_leptonID;
  int    MC_LeptonTrack;

  double MC_incoming_E; // incoming neutrino energy
  double MC_lepton_startEnergy;

  // recob::Shower
  int n_recoShowers;
  double sh_direction_X[MAX_SHOWERS];
  double sh_direction_Y[MAX_SHOWERS];
  double sh_direction_Z[MAX_SHOWERS];
  double sh_start_X[MAX_SHOWERS];
  double sh_start_Y[MAX_SHOWERS];
  double sh_start_Z[MAX_SHOWERS];
  double sh_length[MAX_SHOWERS];
  double sh_ehit_Q[MAX_SHOWERS];
  int    sh_TrackId[MAX_SHOWERS];
  int    sh_hasPrimary_e[MAX_SHOWERS];
  double sh_allhit_Q[MAX_SHOWERS];
  double sh_purity[MAX_SHOWERS];
  double sh_completeness[MAX_SHOWERS];
  double esh_1_purity; // largest shower in a CC event that contains electron contributions
  double esh_1_completeness;
  double esh_each_purity[MAX_SHOWERS]; // each shower in a CC event that contains electron contributions
  double esh_each_completeness[MAX_SHOWERS];
  double esh_purity; // average over all electron showers in a CC event
  double esh_completeness;
  int count_primary_e_in_Event;// number of showers containing electron contribution in a CC event

  // TTree
  TTree *fEventTree;

  TH1D *h_Ev_den; // incoming neutrino energy from MC. den: denominator
  TH1D *h_Ev_num; // recon. num: numerator

  TH1D *h_Ee_den; // primary electron energy from MC
  TH1D *h_Ee_num;

  TEfficiency* h_Eff_Ev = 0;
  TEfficiency* h_Eff_Ee = 0;


};

// =====================================================================================
NuShowerEff::NuShowerEff(fhicl::ParameterSet const & p)
  :
  EDAnalyzer(p), // ,
 // More initializers here.
  //fMCTruthModuleLabel (p.get< std::string >("MCTruthModuleLabel", "generator")),
  fMCTruthModuleLabel (p.get< std::string >("MCTruthModuleLabel")),// get parameter from fcl file
  fHitModuleLabel     (p.get< std::string >("HitModuleLabel")),
  fShowerModuleLabel  (p.get< std::string >("ShowerModuleLabel")),
  fTruthMatchDataModuleLabel (p.get< std::string >("TruthMatchDataModuleLabel")),
  fNeutrinoPDGcode    (p.get<int>("NeutrinoPDGcode")),
  fLeptonPDGcode      (p.get<int>("LeptonPDGcode")),
  fSaveMCTree         (p.get<bool>("SaveMCTree")),
  fHitShowerThroughPFParticle (p.get<bool>("HitShowerThroughPFParticle")),
  fMinPurity          (p.get<double>("MinPurity")),
  fMinCompleteness    (p.get<double>("MinCompleteness")),
  fFidVolCutX         (p.get<float>("FidVolCutX")),
  fFidVolCutY         (p.get<float>("FidVolCutY")),
  fFidVolCutZ         (p.get<float>("FidVolCutZ"))
{
  //cout << "\n===== Please refer the fchicl for the values of preset parameters ====\n" << endl;
}

//============================================================================
void NuShowerEff::beginJob(){
  //cout << "\n===== function: beginJob() ====\n" << endl;

  // Get geometry: Fiducial Volume
  auto const* geo = lar::providerFrom<geo::Geometry>();
  double minx = 1e9; // [cm]
  double maxx = -1e9;
  double miny = 1e9;
  double maxy = -1e9;
  double minz = 1e9;
  double maxz = -1e9;
  //cout << "\nGeometry:\n\tgeo->NTPC(): " << geo->NTPC() << endl;
  for (size_t i = 0; i<geo->NTPC(); ++i){
    double local[3] = {0.,0.,0.};
    double world[3] = {0.,0.,0.};
    const geo::TPCGeo &tpc = geo->TPC(i);
    tpc.LocalToWorld(local,world);
    //cout << "\tlocal: " << local[0] << " ; " << local[1] << " ; " << local[2] << endl;
    //cout << "\tworld: " << world[0] << " ; " << world[1] << " ; " << world[2] << endl;
    //cout << "\tgeo->DetHalfWidth(" << i << "): " << geo->DetHalfWidth(i) << endl;
    //cout << "\tgeo->DetHalfHeight(" << i << "): " << geo->DetHalfHeight(i) << endl;
    //cout << "\tgeo->DetLength(" << i << "): " << geo->DetLength(i) << endl;

    if (minx > world[0] - geo->DetHalfWidth(i))  minx = world[0]-geo->DetHalfWidth(i);
    if (maxx < world[0] + geo->DetHalfWidth(i))  maxx = world[0]+geo->DetHalfWidth(i);
    if (miny > world[1] - geo->DetHalfHeight(i)) miny = world[1]-geo->DetHalfHeight(i);
    if (maxy < world[1] + geo->DetHalfHeight(i)) maxy = world[1]+geo->DetHalfHeight(i);
    if (minz > world[2] - geo->DetLength(i)/2.)  minz = world[2]-geo->DetLength(i)/2.;
    if (maxz < world[2] + geo->DetLength(i)/2.)  maxz = world[2]+geo->DetLength(i)/2.;
  }

  fFidVolXmin = minx + fFidVolCutX;
  fFidVolXmax = maxx - fFidVolCutX;
  fFidVolYmin = miny + fFidVolCutY;
  fFidVolYmax = maxy - fFidVolCutY;
  fFidVolZmin = minz + fFidVolCutZ;
  fFidVolZmax = maxz - fFidVolCutZ;

  //cout << "\nFiducial Volume (length unit: cm):\n"
       //<< "\t" << fFidVolXmin<<"\t< x <\t"<<fFidVolXmax<<"\n"
       //<< "\t" << fFidVolYmin<<"\t< y <\t"<<fFidVolYmax<<"\n"
       //<< "\t" << fFidVolZmin<<"\t< z <\t"<<fFidVolZmax<<"\n";

  art::ServiceHandle<art::TFileService const> tfs;

  double E_bins[21] = {0,0.5,1.0,1.5,2.0,2.5,3.0,3.5,4,4.5,5.0,5.5,6.0,7.0,8.0,10.0,12.0,14.0,17.0,20.0,25.0};
//  double theta_bins[44]= { 0.,1.,2.,3.,4.,5.,6.,7.,8.,9.,10.,11.,12.,13.,14.,15.,16.,17.,18.,19.,20.,22.,24.,26.,28.,30.,32.,34.,36.,38.,40.,42.,44.,46.,48.,50.,55.,60.,65.,70.,75.,80.,85.,90.};
  //  double Pbins[18] ={0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0,1.2,1.4,1.6,1.8,2.0,2.5,3.0};

  h_Ev_den = tfs->make<TH1D>("h_Ev_den", "Neutrino Energy; Neutrino Energy (GeV); Shower Reconstruction Efficiency", 20, E_bins);
  h_Ev_den->Sumw2();
  h_Ev_num = tfs->make<TH1D>("h_Ev_num","Neutrino Energy; Neutrino Energy (GeV); Shower Reconstruction Efficiency",20,E_bins);
  h_Ev_num->Sumw2();

  h_Ee_den = tfs->make<TH1D>("h_Ee_den","Electron Energy; Electron Energy (GeV); Shower Reconstruction Efficiency",20,E_bins);
  h_Ee_den->Sumw2();
  h_Ee_num = tfs->make<TH1D>("h_Ee_num","Electron Energy; Electron Energy (GeV); Shower Reconstruction Efficiency",20,E_bins);
  h_Ee_num->Sumw2();

  if (fSaveMCTree) {
    fEventTree = new TTree("Event", "Event Tree from Sim & Reco");
    fEventTree->Branch("eventNo", &Event); // only select event in FV
    fEventTree->Branch("runNo", &Run);
    fEventTree->Branch("subRunNo", &SubRun);

    fEventTree->Branch("MC_incoming_E", &MC_incoming_E);
    fEventTree->Branch("MC_lepton_startEnergy", &MC_lepton_startEnergy);

    fEventTree->Branch("n_showers", &n_recoShowers);
    fEventTree->Branch("sh_hasPrimary_e", &sh_hasPrimary_e, "sh_hasPrimary_e[n_showers]/I");
    //fEventTree->Branch("sh_purity", &sh_purity, "sh_purity[n_showers]/D");
    //fEventTree->Branch("sh_completeness", &sh_completeness, "sh_completeness[n_showers]/D");
    fEventTree->Branch("count_primary_e_in_Event", &count_primary_e_in_Event);
    fEventTree->Branch("esh_1_purity", &esh_1_purity);
    fEventTree->Branch("esh_1_completeness", &esh_1_completeness);
    fEventTree->Branch("esh_each_purity", &esh_each_purity, "esh_each_purity[count_primary_e_in_Event]/D");
    fEventTree->Branch("esh_each_completeness", &esh_each_completeness, "esh_each_completeness[count_primary_e_in_Event]/D");
    fEventTree->Branch("esh_purity", &esh_purity);
    fEventTree->Branch("esh_completeness", &esh_completeness);
  }

}

//============================================================================
void NuShowerEff::endJob(){
  //cout << "\n===== function: endJob() =====\n" << endl;
  doEfficiencies();
}

//============================================================================
void NuShowerEff::beginRun(art::Run const & run){
  //cout << "\n===== function: beginRun() =====\n" << endl;
  mf::LogInfo("ShowerEff") << "==== begin run ... ====" << endl;
}

//============================================================================
void NuShowerEff::analyze(art::Event const & e)
{
  // Implementation of required member function here.
  //cout << "\n===== function: analyze() =====\n" << endl;

  reset(); // for some variables

  Event = e.id().event();
  Run = e.run();
  SubRun = e.subRun();
  //cout << "Event information:" << endl;
  //cout << "\tEvent: " << Event << endl;
  //cout << "\tRun: " << Run << endl;
  //cout << "\tSubRun: " << SubRun << endl;


  // -------- find Geant4 TrackId that corresponds to e+/e- from neutrino interaction ----------
  // MCTruth: Generator
  art::Handle<std::vector<simb::MCTruth>> MCtruthHandle;
  e.getByLabel(fMCTruthModuleLabel, MCtruthHandle);
  std::vector<art::Ptr<simb::MCTruth>> MCtruthlist;
  art::fill_ptr_vector(MCtruthlist, MCtruthHandle);
  art::Ptr<simb::MCTruth> MCtruth;
  // MC (neutrino) interaction
  int MCinteractions = MCtruthlist.size();
  //cout << "\nMCinteractions: " << MCinteractions << endl;
  for (int i=0; i<MCinteractions; i++){
    MCtruth = MCtruthlist[i];
    if ( MCtruth->NeutrinoSet() ) {  // NeutrinoSet(): whether the neutrino information has been set
      simb::MCNeutrino nu = MCtruth->GetNeutrino();// GetNeutrino(): reference to neutrino info
      if( nu.CCNC()==0 ) MC_isCC = 1;
      else if (nu.CCNC()==1) MC_isCC = 0;
      simb::MCParticle neutrino = nu.Nu(); // Nu(): the incoming neutrino
      MC_target = nu.Target(); // Target(): nuclear target, as PDG code
      MC_incoming_PDG = std::abs(nu.Nu().PdgCode());// here not use std::abs()
      MC_Q2 = nu.QSqr();// QSqr(): momentum transfer Q^2, in GeV^2
      MC_channel = nu.InteractionType();// 1001: CCQE
      MC_W = nu.W(); // W(): hadronic invariant mass
      const TLorentzVector& nu_momentum = nu.Nu().Momentum(0);
      nu_momentum.GetXYZT(MC_incoming_P);
      const TLorentzVector& vertex =neutrino.Position(0);
      vertex.GetXYZT(MC_vertex);
      simb::MCParticle lepton = nu.Lepton();// Lepton(): the outgoing lepton
      MC_lepton_PDG = lepton.PdgCode();

      MC_incoming_E = MC_incoming_P[3];

      //cout << "\tMCinteraction: " << i              << "\n\t"
      //     << "neutrino PDG: "  << MC_incoming_PDG  << "\n\t"
      //     << "MC_lepton_PDG: " << MC_lepton_PDG    << "\n\t"
      //     << "MC_channel: "    << MC_channel       << "\n\t"
      //     << "incoming E: "    << MC_incoming_P[3] << "\n\t"
      //     << "MC_vertex: " << MC_vertex[0] << " , " << MC_vertex[1] << " , " <<MC_vertex[2] << " , " <<MC_vertex[3] << endl;
    }
    // MCTruth Generator Particles
    int nParticles =  MCtruthlist[0]->NParticles();
    //cout << "\n\tNparticles: " << MCtruth->NParticles() <<endl;
    for (int i=0; i<nParticles; i++){
      simb::MCParticle pi = MCtruthlist[0]->GetParticle(i);
      //cout << "\tparticle: " << i << "\n\t\t"
           //<< "Pdgcode: " << pi.PdgCode() << "; Mother: " << pi.Mother() << "; TrackId: " << pi.TrackId() << endl;
    // Mother(): mother = -1 means that this particle has no mother
    // TrackId(): same as the index in the MCParticleList
    }
  }

  // Geant4: MCParticle -> lepton (e)
  // Note: generator level MCPartilceList is different from Geant4 level MCParticleList.  MCParticleList(Geant4) contains all particles in MCParticleList(generator) but their the indexes (TrackIds) are different.
  simb::MCParticle *MClepton = NULL; //Geant4 level
  art::ServiceHandle<cheat::ParticleInventoryService const> pi_serv;
  const sim::ParticleList& plist = pi_serv->ParticleList();
  simb::MCParticle *particle=0;

  for (sim::ParticleList::const_iterator ipar = plist.begin(); ipar!=plist.end();++ipar){
    particle = ipar->second; // first is index(TrackId), second is value (point address)

    auto & truth = pi_serv->ParticleToMCTruth_P(particle);// beam neutrino only
    if ( truth->Origin()==simb::kBeamNeutrino && std::abs(particle->PdgCode()) == fLeptonPDGcode &&  particle->Mother()==0){ // primary lepton; Mother() = 0 means e^{-} for v+n=e^{-}+p
      const TLorentzVector& lepton_momentum =particle->Momentum(0);
      const TLorentzVector& lepton_position =particle->Position(0);
      const TLorentzVector& lepton_positionEnd   = particle->EndPosition();
      const TLorentzVector& lepton_momentumEnd   = particle->EndMomentum();
      lepton_momentum.GetXYZT(MC_lepton_startMomentum);
      lepton_position.GetXYZT(MC_lepton_startXYZT);
      lepton_positionEnd.GetXYZT(MC_lepton_endXYZT);
      lepton_momentumEnd.GetXYZT(MC_lepton_endMomentum);
      MC_leptonID = particle->TrackId();

      MC_lepton_startEnergy = MC_lepton_startMomentum[3];
      //cout << "\nGeant Track ID for electron/positron: " << endl;
      //cout << "\tMClepton PDG: " << particle->PdgCode() <<  " ; MC_leptonID: " << MC_leptonID << endl;
      MClepton = particle;
      //cout << "\tMClepton PDG:" << MClepton->PdgCode() <<endl;
      //cout << "\tipar->first (TrackId): " << ipar->first << endl;
    }
  }

  // check if the interaction is inside the Fiducial Volume
  bool isFiducial = false;
  isFiducial = insideFV( MC_vertex);
  if (isFiducial) {
    //cout <<"\nInfo: Interaction is inside the Fiducial Volume.\n" << endl;
  }
  else {
    //cout << "\n********Interaction is NOT inside the Fiducial Volume. RETURN**********" << endl;
    return;
  }

  if (MC_isCC && (fNeutrinoPDGcode == std::abs(MC_incoming_PDG))) {
    if (MClepton){
      h_Ev_den->Fill(MC_incoming_P[3]);
      h_Ee_den->Fill(MC_lepton_startMomentum[3]);
    }
  }

  //if (MC_isCC && (fNeutrinoPDGcode == std::abs(MC_incoming_PDG)) && MC_incoming_E < 0.5) {
    // cout << "\n------output CC event info for neutrino energy less than 0.5 GeV ------\n" << endl;
   // cout << "\tEvent   : " << Event  << "\n"
   //   << "\tRun     : " << Run    << "\n"
   //   << "\tSubRun  : " << SubRun << "\n"
    //  << "\tMC_incoming_E: " << MC_incoming_E << endl;
 // }

  // recob::Hit
  // ---- build a map for total hit charges corresponding to MC_leptonID (Geant4) ----

  art::Handle<std::vector<recob::Hit>> hitHandle;
  std::vector<art::Ptr<recob::Hit>> all_hits;
  if(e.getByLabel(fHitModuleLabel,hitHandle)){
    art::fill_ptr_vector(all_hits, hitHandle);
  }
  //cout << "\nTotal hits:" << endl;
  //cout << "\tall_hits.size(): " << all_hits.size() << endl;

  double ehit_total =0.0;

  art::FindManyP<simb::MCParticle,anab::BackTrackerHitMatchingData> fmhitmc(hitHandle, e, fTruthMatchDataModuleLabel);// need #include "lardataobj/AnalysisBase/BackTrackerMatchingData.h"

  std::map<int,double> all_hits_trk_Q;//Q for charge: Integral()
  for (size_t i=0; i <  all_hits.size(); ++i) {
    art::Ptr<recob::Hit> hit = all_hits[i];
    auto particles = fmhitmc.at(hit.key());// particles here is a pointer. A hit may come from multiple particles.
    auto hitmatch = fmhitmc.data(hit.key());// metadata
    double maxenergy = -1e9;
    int hit_TrackId = 0;
    for (size_t j = 0; j < particles.size(); ++j){
      if (!particles[j]) continue;
      if (!pi_serv->TrackIdToMotherParticle_P(particles[j]->TrackId())) continue;
      size_t trkid = (pi_serv->TrackIdToMotherParticle_P(particles[j]->TrackId()))->TrackId();

      if ( (hitmatch[j]->energy) > maxenergy ){
        maxenergy = hitmatch[j]->energy;
        hit_TrackId = trkid;
      }
   }
   if (hit_TrackId == MC_leptonID) ehit_total += hit->Integral();
   all_hits_trk_Q[hit_TrackId] += hit->Integral(); // Integral(): the integral under the calibrated signal waveform of the hit, in tick x ADC units
  }
  //cout << "....ehit_total: " << ehit_total << endl;
  //cout << "\tall_hits_trk_Q.size(): " << all_hits_trk_Q.size() << endl;


  //--------- Loop over all showers: find the associated hits for each shower ------------
  const simb::MCParticle *MClepton_reco = NULL;

  double temp_sh_ehit_Q = 0.0;
  double temp_sh_allHit_Q = 0.0;
  int temp_sh_TrackId = -999;
  count_primary_e_in_Event = 0;

  art::Handle<std::vector<recob::Shower>> showerHandle;
  std::vector<art::Ptr<recob::Shower>> showerlist;
  if(e.getByLabel(fShowerModuleLabel,showerHandle)){
    art::fill_ptr_vector(showerlist, showerHandle);
  }
  n_recoShowers= showerlist.size();
  //cout << "\nRecon Showers: " << endl;
  //cout << "\tn_recoShowers: " << n_recoShowers << endl;
  art::FindManyP<recob::Hit> sh_hitsAll(showerHandle, e, fShowerModuleLabel);

  //std::vector<std::map<int,double>> showers_hits_trk_Q;
  std::map<int,double> showers_trk_Q;
  for (int i=0; i<n_recoShowers;i++){ // loop over showers
    //const simb::MCParticle *particle;
    sh_hasPrimary_e[i] = 0;

    std::map<int,double> sh_hits_trk_Q;//Q for charge: Integral()
    sh_hits_trk_Q.clear();

    art::Ptr<recob::Shower> shower = showerlist[i];
    sh_direction_X[i] = shower->Direction().X(); // Direction(): direction cosines at start of the shower
    sh_direction_Y[i] = shower->Direction().Y();
    sh_direction_Z[i] = shower->Direction().Z();
    sh_start_X[i] = shower->ShowerStart().X();
    sh_start_Y[i] = shower->ShowerStart().Y();
    sh_start_Z[i] = shower->ShowerStart().Z();
    sh_length[i] = shower->Length(); // shower length in [cm]
    //cout << "\tInfo of shower " << i << "\n\t\t"
    //<< "direction (cosines): " << sh_direction_X[i] << ", " << sh_direction_Y[i] << ", " << sh_start_Z[i] << "\n\t\t"
    //<< "start position: " << sh_start_X[i] << ", " << sh_start_Y[i] << ", " << sh_start_Z[i] << "\n\t\t"
    //<< "shower length: " << sh_length[i] << endl;


    std::vector<art::Ptr<recob::Hit>> sh_hits;// associated hits for ith shower
    //In mcc8, if we get hits associated with the shower through shower->hits association directly for pandora, the hit list is incomplete. The recommended way of getting hits is through association with pfparticle:
    //shower->pfparticle->clusters->hits
    //----------getting hits through PFParticle (an option here)-------------------
    if (fHitShowerThroughPFParticle) {
      //cout << "\n==== Getting Hits associated with shower THROUGH PFParticle ====\n" << endl;
      //cout << "\nHits in a shower through PFParticle:\n" << endl;

      // PFParticle
      art::Handle<std::vector<recob::PFParticle> > pfpHandle;
      std::vector<art::Ptr<recob::PFParticle> > pfps;
      if (e.getByLabel(fShowerModuleLabel, pfpHandle)) art::fill_ptr_vector(pfps, pfpHandle);
      // Clusters
      art::Handle<std::vector<recob::Cluster> > clusterHandle;
      std::vector<art::Ptr<recob::Cluster> > clusters;
      if (e.getByLabel(fShowerModuleLabel, clusterHandle)) art::fill_ptr_vector(clusters, clusterHandle);
      art::FindManyP<recob::PFParticle> fmps(showerHandle, e, fShowerModuleLabel);// PFParticle in Shower
      art::FindManyP<recob::Cluster> fmcp(pfpHandle, e, fShowerModuleLabel); // Cluster vs. PFParticle
      art::FindManyP<recob::Hit> fmhc(clusterHandle, e, fShowerModuleLabel); // Hit in Shower
      if (fmps.isValid()){
        std::vector<art::Ptr<recob::PFParticle>> pfs = fmps.at(i);
        for (size_t ipf = 0; ipf<pfs.size(); ++ipf){
          if (fmcp.isValid()){
            std::vector<art::Ptr<recob::Cluster>> clus = fmcp.at(pfs[ipf].key());
            for (size_t iclu = 0; iclu<clus.size(); ++iclu){
              if (fmhc.isValid()){
                std::vector<art::Ptr<recob::Hit>> hits = fmhc.at(clus[iclu].key());
                for (size_t ihit = 0; ihit<hits.size(); ++ihit){
                  sh_hits.push_back(hits[ihit]);
                }
              }
            }
          }
        }
      }

     // cout << "\tsh_hits.size(): " << sh_hits.size() << endl;

     // for (size_t k=0;k<sh_hits.size();k++){
     //   art::Ptr<recob::Hit> hit = sh_hits[k];
     //   cout << k << "\thit.key(): " << hit.key() << endl;
     //   cout << k << "\thit->Integral(): " << hit->Integral() << endl;
     // }
    } else {

      // ----- using shower->hit association for getting hits associated with shower-----
      sh_hits = sh_hitsAll.at(i);// associated hits for ith shower (using association of hits and shower)
      //cout << "\t\tsh_hits.size(): " << sh_hits.size() << endl;
    } // we only choose one method for hits associated with shower here.


    for (size_t k=0; k <  sh_hits.size(); ++k) {
      art::Ptr<recob::Hit> hit = sh_hits[k];
      auto particles = fmhitmc.at(hit.key());
      auto hitmatch = fmhitmc.data(hit.key());
      double maxenergy = -1e9;
      int hit_TrackId = 0;
      for (size_t j = 0; j < particles.size(); ++j){
        if (!particles[j]) continue;
        if (!pi_serv->TrackIdToMotherParticle_P(particles[j]->TrackId())) continue;
        size_t trkid = (pi_serv->TrackIdToMotherParticle_P(particles[j]->TrackId()))->TrackId();

        if ( (hitmatch[j]->energy) > maxenergy ){
          maxenergy = hitmatch[j]->energy;
          hit_TrackId = trkid;
        }
      }
      if (hit_TrackId == MC_leptonID) {
        sh_ehit_Q[i] += hit->Integral();
      }
      sh_allhit_Q[i] += hit->Integral();
      sh_hits_trk_Q[hit_TrackId] += hit->Integral();// Q from the same hit_TrackId
    }
    //cout << "\tsh_hits_trk_Q.size(): " << sh_hits_trk_Q.size() << endl;
    //showers_hits_trk_Q.push_back(sh_hits_trk_Q);

    // get TrackId for a shower
    double maxshowerQ = -1.0e9;
    //sh_TrackId[i] = 0;
    for(std::map<int,double>::iterator k = sh_hits_trk_Q.begin(); k != sh_hits_trk_Q.end(); k++) {
      //cout << k->first << "\t;\t" << k->second << endl;
      if (k->second > maxshowerQ) {
        maxshowerQ = k->second;
       sh_TrackId[i] = k->first;//assign a sh_TrackId with TrackId from hit(particle) that contributing largest to the shower.
      }
    }

    //---------------------------------------------------------------------------------
    //cout << "\nRecon Shower: " << i << endl;
    //cout << "\t*****shower primary TrackId: " << sh_TrackId[i] << endl;

    if (sh_TrackId[i] == MC_leptonID && sh_ehit_Q[i] >0) {
      temp_sh_TrackId = sh_TrackId[i];
      sh_hasPrimary_e[i] = 1;
      count_primary_e_in_Event += 1;
      MClepton_reco = pi_serv->TrackIdToParticle_P(sh_TrackId[i]);

      if (sh_allhit_Q[i] >0 && sh_ehit_Q[i] <= sh_allhit_Q[i]){
        sh_purity[i] = sh_ehit_Q[i]/sh_allhit_Q[i];
        //cout << "\t*****shower purity: " << sh_purity[i] << endl;
      } else {
        sh_purity[i] = 0;
      }
      if(ehit_total >0 && sh_ehit_Q[i] <= sh_allhit_Q[i]){
        sh_completeness[i] = sh_ehit_Q[i] / ehit_total;
        //cout << "\t*****shower completeness: " << sh_completeness[i] << endl;
      } else {
        sh_completeness[i] = 0;
      }
      temp_sh_ehit_Q += sh_ehit_Q[i];
      temp_sh_allHit_Q += sh_allhit_Q[i];
    }

    showers_trk_Q[sh_TrackId[i]] += maxshowerQ;
    //cout << "\tsh_TrackId: " << sh_TrackId[i] <<" ; maxshowerQ: " << maxshowerQ << endl;

  } // end: for loop over showers

  // ---------------------------------------------------------------
  if (MClepton_reco && MClepton) {
    if ((temp_sh_TrackId == MC_leptonID) && MC_isCC && (fNeutrinoPDGcode == std::abs(MC_incoming_PDG))) {
      if ((temp_sh_allHit_Q >= temp_sh_ehit_Q) && (temp_sh_ehit_Q > 0.0)) {
        esh_purity = temp_sh_ehit_Q/temp_sh_allHit_Q;
        esh_completeness = temp_sh_ehit_Q/ehit_total;

        if (esh_purity > fMinPurity &&
          esh_completeness > fMinCompleteness) {
          //cout << "\nInfo: fill h_Ev_num ........\n" << endl;
          h_Ev_num->Fill(MC_incoming_P[3]);
          h_Ee_num->Fill(MC_lepton_startMomentum[3]);
        }
      }
    }
  }
  // --------------------------------------------------------------

  if ( (MClepton_reco && MClepton) && MC_isCC && (fNeutrinoPDGcode == std::abs(MC_incoming_PDG))){
    //cout << "\n count_primary_e_in_Event: " << count_primary_e_in_Event << endl;
    for (int j=0; j<count_primary_e_in_Event; j++){
      esh_each_purity[j] = 0.0;
    }

    double temp_esh_1_allhit = -1.0e9;
    int temp_shower_index = -999;
    int temp_esh_index = 0;
    for (int i=0; i<n_recoShowers; i++) {
      if (sh_TrackId[i] == MC_leptonID) {

        // for each electron shower
        if (sh_ehit_Q[i] >0){
          esh_each_purity[temp_esh_index] = sh_purity[i];
          esh_each_completeness[temp_esh_index] = sh_completeness[i];
          temp_esh_index += 1;
        }

        // find largest shower
        if ((sh_allhit_Q[i] > temp_esh_1_allhit) && (sh_ehit_Q[i] > 0.0) ) {
          temp_esh_1_allhit = sh_allhit_Q[i];
          temp_shower_index = i;
        }
      }
    }
    //if (temp_esh_index != count_primary_e_in_Event){
    //  cout << "wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww" << endl;
    //}
    // largest shower with electron contribution
    esh_1_purity = sh_purity[temp_shower_index];
    esh_1_completeness = sh_completeness[temp_shower_index];
  }

  if (count_primary_e_in_Event>0 && MC_isCC && fSaveMCTree) { fEventTree->Fill();}// so far, only save CC event
}

// ====================================================================================
void NuShowerEff::doEfficiencies(){
  //cout << "\n==== function: doEfficiencies() ====" << endl;

  art::ServiceHandle<art::TFileService const> tfs;

  if(TEfficiency::CheckConsistency(*h_Ev_num,*h_Ev_den)){
    h_Eff_Ev = tfs->make<TEfficiency>(*h_Ev_num,*h_Ev_den);
    TGraphAsymmErrors *grEff_Ev = h_Eff_Ev->CreateGraph();
    grEff_Ev->Write("grEff_Ev");
    h_Eff_Ev->Write("h_Eff_Ev");
  }

  if(TEfficiency::CheckConsistency(*h_Ee_num,*h_Ee_den)){
    h_Eff_Ee = tfs->make<TEfficiency>(*h_Ee_num,*h_Ee_den);
    TGraphAsymmErrors *grEff_Ee = h_Eff_Ee->CreateGraph();
    grEff_Ee->Write("grEff_Ee");
    h_Eff_Ee->Write("h_Eff_Ee");
  }

}

// ====================================================================================
bool NuShowerEff::insideFV( double vertex[4] ){
  //cout << "\n==== function: insideFV() ====" << endl;
  double x = vertex[0];
  double y = vertex[1];
  double z = vertex[2];

  if (x>fFidVolXmin && x<fFidVolXmax&&
      y>fFidVolYmin && y<fFidVolYmax&&
      z>fFidVolZmin && z<fFidVolZmax)
    {return true;}
  else
    {return false;}
}

// ====================================================================================
void NuShowerEff::reset(){
  //cout << "\n===== function: reset() =====\n" << endl;

  MC_incoming_PDG = -999;
  MC_lepton_PDG =-999;
  MC_isCC =-999;
  MC_channel =-999;
  MC_target =-999;
  MC_Q2 =-999.0;
  MC_W =-999.0;
  MC_lepton_theta = -999.0;
  MC_leptonID = -999;
  MC_LeptonTrack = -999;

  for(int i=0; i<MAX_SHOWERS; i++){
    sh_direction_X[i] = -999.0;
    sh_direction_Y[i] = -999.0;
    sh_direction_Z[i] = -999.0;
    sh_start_X[i] = -999.0;
    sh_start_Y[i] = -999.0;
    sh_start_Z[i] = -999.0;
    sh_length[i] = -999.0;
    sh_hasPrimary_e[i] = -999;
    sh_ehit_Q[i] = 0.0;
    sh_allhit_Q[i] = 0.0;
    sh_purity[i] = 0.0;
    sh_completeness[i] = 0.0;
  }

}
DEFINE_ART_MODULE(NuShowerEff)