PMAlgTrackMaker_module.cc

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// Class:       PMAlgTrackMaker
// Module Type: producer
// File:        PMAlgTrackMaker_module.cc
// Authors      D.Stefan (Dorota.Stefan@ncbj.gov.pl),         from DUNE, CERN/NCBJ, since May 2015
//              R.Sulej (Robert.Sulej@cern.ch),               from DUNE, FNAL/NCBJ, since May 2015
//              L.Whitehead (leigh.howard.whitehead@cern.ch), from DUNE, CERN,      since Jan 2017
//
// Creates 3D tracks and vertices using Projection Matching Algorithm,
// please see RecoAlg/ProjectionMatchingAlg.h for basics of the PMA algorithm and its settings.
//
// Progress:
//    May-June 2015:   track finding and validation, growing tracks by iterative merging of matching
//                     clusters, no attempts to build multi-track structures, however cosmic tracking
//                     works fine as they are sets of independent tracks
//    June-July 2015:  merging track parts within a single tpc and stitching tracks across tpc's
//    August 2015:     optimization of track-vertex structures (so 3D vertices are also produced)
//    November 2015:   use track-shower splitting at 2D level, then tag low-E EM cascades in 3D
//                     note: the splitter is not finished and not as good as we want it
//    January 2016:    output of track-vertex finding as a tree of PFParticles, refined vertexing
//                     code, put vertex at front of each track, flip whole track structures to
//                     selected, direction (beam/down/dQdx), use any pattern reco stored in
//                     PFParticles as a source of associated clusters
//    Mar-Apr 2016:    kinks finding, EM shower direction reconstructed for PFPaarticles tagged as
//                     electrons
//    July 2016:       redesign module: extract trajectory fitting-only to separate module, move
//                     tracking functionality to algorithm classes
//    ~Jan-May 2017:   track stitching on APA and CPA, cosmics tagging
//    July 2017:       validation on 2D ADC image
//

#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/Persistency/Common/PtrMaker.h"
#include "art_root_io/TFileService.h"
#include "canvas/Utilities/InputTag.h"
#include "fhiclcpp/types/Atom.h"
#include "fhiclcpp/types/Table.h"
#include "messagefacility/MessageLogger/MessageLogger.h"

// LArSoft includes
#include "larcore/Geometry/Geometry.h"
#include "larcore/Geometry/WireReadout.h"
#include "larcorealg/Geometry/TPCGeo.h"
#include "lardata/ArtDataHelper/MVAReader.h"
#include "lardata/DetectorInfoServices/DetectorClocksService.h"
#include "lardata/DetectorInfoServices/DetectorPropertiesService.h"
#include "lardata/Utilities/AssociationUtil.h"
#include "lardataobj/AnalysisBase/CosmicTag.h"
#include "lardataobj/AnalysisBase/T0.h"
#include "lardataobj/RecoBase/Cluster.h"
#include "lardataobj/RecoBase/Hit.h"
#include "lardataobj/RecoBase/PFParticle.h"
#include "lardataobj/RecoBase/SpacePoint.h"
#include "lardataobj/RecoBase/Track.h"
#include "lardataobj/RecoBase/TrackHitMeta.h"
#include "lardataobj/RecoBase/Vertex.h"
#include "larreco/RecoAlg/PMAlgStitching.h"
#include "larreco/RecoAlg/PMAlgTracking.h"
#include "larreco/RecoAlg/PMAlgVertexing.h"
#include "larreco/RecoAlg/ProjectionMatchingAlg.h"

#include <memory>

#include "TH1F.h"

namespace trkf {

  class PMAlgTrackMaker : public art::EDProducer {
  public:
    struct Config {
      using Name = fhicl::Name;
      using Comment = fhicl::Comment;

      fhicl::Table<pma::ProjectionMatchingAlg::Config> ProjectionMatchingAlg{
        Name("ProjectionMatchingAlg")};

      fhicl::Table<pma::PMAlgTracker::Config> PMAlgTracking{Name("PMAlgTracking")};

      fhicl::Table<pma::PMAlgVertexing::Config> PMAlgVertexing{Name("PMAlgVertexing")};

      fhicl::Table<pma::PMAlgCosmicTagger::Config> PMAlgCosmicTagging{Name("PMAlgCosmicTagging")};

      fhicl::Table<pma::PMAlgStitching::Config> PMAlgStitching{Name("PMAlgStitching")};

      fhicl::Atom<bool> SaveOnlyBranchingVtx{
        Name("SaveOnlyBranchingVtx"),
        Comment("use true to save only vertices interconnecting many tracks, otherwise vertex is "
                "added to the front of each track")};

      fhicl::Atom<bool> SavePmaNodes{
        Name("SavePmaNodes"),
        Comment("save track nodes (only for algorithm development purposes)")};

      fhicl::Atom<art::InputTag> HitModuleLabel{
        Name("HitModuleLabel"),
        Comment("tag of unclustered hits, which were used to validate tracks")};

      fhicl::Atom<art::InputTag> WireModuleLabel{Name("WireModuleLabel"),
                                                 Comment("tag of recob::Wire producer.")};

      fhicl::Atom<art::InputTag> ClusterModuleLabel{
        Name("ClusterModuleLabel"),
        Comment("tag of cluster collection, these clusters are used for track building")};

      fhicl::Atom<art::InputTag> EmClusterModuleLabel{
        Name("EmClusterModuleLabel"),
        Comment("EM-like clusters, will be excluded from tracking if provided")};
    };
    using Parameters = art::EDProducer::Table<Config>;

    explicit PMAlgTrackMaker(Parameters const& config);

    PMAlgTrackMaker(PMAlgTrackMaker const&) = delete;
    PMAlgTrackMaker(PMAlgTrackMaker&&) = delete;
    PMAlgTrackMaker& operator=(PMAlgTrackMaker const&) = delete;
    PMAlgTrackMaker& operator=(PMAlgTrackMaker&&) = delete;

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

    // will try to get EM- and track-like values from various lenght MVA vectors
    template <size_t N>
    bool init(const art::Event& evt, pma::PMAlgTracker& pmalgTracker) const;

    // calculate EM/track value for hits in track, in its best 2D projection
    // (tracks are built starting from track-like cluster, some electrons
    // still may look track-like)
    template <size_t N>
    int getPdgFromCnnOnHits(const art::Event& evt, const pma::Track3D& trk) const;

    // convert to a vector of LArSoft's cosmic tags
    std::vector<anab::CosmicTagID_t> getCosmicTag(const pma::Track3D::ETag pmaTag) const;

    // ******************** fcl parameters **********************
    art::InputTag fHitModuleLabel;  // tag for hits collection (used for trk validation)
    art::InputTag fWireModuleLabel; // tag for recob::Wire collection (used for trk validation)
    art::InputTag fCluModuleLabel;  // tag for input cluster collection
    art::InputTag fEmModuleLabel;   // tag for em-like cluster collection

    pma::ProjectionMatchingAlg::Config fPmaConfig;
    pma::PMAlgTracker::Config fPmaTrackerConfig;
    pma::PMAlgCosmicTagger::Config fPmaTaggingConfig;
    pma::PMAlgVertexing::Config fPmaVtxConfig;
    pma::PMAlgStitching::Config fPmaStitchConfig;

    bool fSaveOnlyBranchingVtx; // for debugging, save only vertices which connect many tracks
    bool fSavePmaNodes;         // for debugging, save only track nodes

    // ********** instance names (collections, assns) ************
    static const std::string kKinksName; // kinks on tracks
    static const std::string kNodesName; // pma nodes

    // *********************** geometry **************************
    geo::GeometryCore const* fGeom;

    // histograms created only for the calibration of the ADC-based track validation mode
    std::vector<TH1F*> fAdcInPassingPoints, fAdcInRejectedPoints;
  };
  // -------------------------------------------------------------
  const std::string PMAlgTrackMaker::kKinksName = "kink";
  const std::string PMAlgTrackMaker::kNodesName = "node";
  // -------------------------------------------------------------

  PMAlgTrackMaker::PMAlgTrackMaker(PMAlgTrackMaker::Parameters const& config)
    : EDProducer{config}
    , fHitModuleLabel(config().HitModuleLabel())
    , fWireModuleLabel(config().WireModuleLabel())
    , fCluModuleLabel(config().ClusterModuleLabel())
    , fEmModuleLabel(config().EmClusterModuleLabel())
    , fPmaConfig(config().ProjectionMatchingAlg())
    , fPmaTrackerConfig(config().PMAlgTracking())
    , fPmaTaggingConfig(config().PMAlgCosmicTagging())
    , fPmaVtxConfig(config().PMAlgVertexing())
    , fPmaStitchConfig(config().PMAlgStitching())
    , fSaveOnlyBranchingVtx(config().SaveOnlyBranchingVtx())
    , fSavePmaNodes(config().SavePmaNodes())
    , fGeom(art::ServiceHandle<geo::Geometry const>().get())
  {
    produces<std::vector<recob::Track>>();
    produces<std::vector<recob::SpacePoint>>();
    produces<std::vector<recob::Vertex>>();           // no instance name for interaction vertices
    produces<std::vector<recob::Vertex>>(kKinksName); // collection of kinks on tracks
    produces<std::vector<recob::Vertex>>(kNodesName); // collection of pma nodes
    produces<std::vector<anab::T0>>();
    produces<std::vector<anab::CosmicTag>>(); // Cosmic ray tags

    produces<art::Assns<recob::Track,
                        recob::Hit>>(); // ****** REMEMBER to remove when FindMany improved ******
    produces<art::Assns<recob::Track, recob::Hit, recob::TrackHitMeta>>();

    produces<art::Assns<recob::Track, recob::SpacePoint>>();
    produces<art::Assns<recob::SpacePoint, recob::Hit>>();
    produces<
      art::Assns<recob::Vertex,
                 recob::Track>>(); // no instance name for assns of tracks to interaction vertices
    produces<art::Assns<recob::Track, recob::Vertex>>(kKinksName); // assns of kinks to tracks
    produces<art::Assns<recob::Track, anab::T0>>();
    produces<art::Assns<recob::Track, anab::CosmicTag>>(); // Cosmic ray tags associated to tracks

    produces<std::vector<recob::PFParticle>>();
    produces<art::Assns<recob::PFParticle, recob::Cluster>>();
    produces<art::Assns<recob::PFParticle, recob::Vertex>>();
    produces<art::Assns<recob::PFParticle, recob::Track>>();

    if (fPmaTrackerConfig.Validation() == "calib") // create histograms only in the calibration mode
    {
      art::ServiceHandle<art::TFileService const> tfs;
      auto const& wireReadoutGeom = art::ServiceHandle<geo::WireReadout>()->Get();
      for (size_t p = 0; p < wireReadoutGeom.MaxPlanes(); ++p) {
        std::ostringstream ss1;
        ss1 << "adc_plane_" << p;
        fAdcInPassingPoints.push_back(tfs->make<TH1F>(
          (ss1.str() + "_passing").c_str(), "max adc around the point on track", 100., 0., 5.));
        fAdcInRejectedPoints.push_back(tfs->make<TH1F>(
          (ss1.str() + "_rejected").c_str(), "max adc around spurious point ", 100., 0., 5.));
      }
    }
  }
  // ------------------------------------------------------

  template <size_t N>
  int PMAlgTrackMaker::getPdgFromCnnOnHits(const art::Event& evt, const pma::Track3D& trk) const
  {
    int pdg = 0;
    if (fPmaTrackerConfig.TrackLikeThreshold() > 0) {
      auto hitResults = anab::MVAReader<recob::Hit, N>::create(evt, fCluModuleLabel);
      if (hitResults) {
        int trkLikeIdx = hitResults->getIndex("track");
        int emLikeIdx = hitResults->getIndex("em");
        if ((trkLikeIdx < 0) || (emLikeIdx < 0)) {
          throw cet::exception("PMAlgTrackMaker")
            << "No em/track labeled columns in MVA data products." << std::endl;
        }

        size_t nh[3] = {0, 0, 0};
        for (size_t hidx = 0; hidx < trk.size(); ++hidx) {
          ++nh[trk[hidx]->View2D()];
        }

        size_t best_view = 2;                                          // collection
        if ((nh[0] >= nh[1]) && (nh[0] > 1.25 * nh[2])) best_view = 0; // ind1
        if ((nh[1] >= nh[0]) && (nh[1] > 1.25 * nh[2])) best_view = 1; // ind2

        std::vector<art::Ptr<recob::Hit>> trkHitPtrList;
        trkHitPtrList.reserve(nh[best_view]);
        for (size_t hidx = 0; hidx < trk.size(); ++hidx) {
          if (trk[hidx]->View2D() == best_view) {
            trkHitPtrList.emplace_back(trk[hidx]->Hit2DPtr());
          }
        }
        auto vout = hitResults->getOutput(trkHitPtrList);
        double trk_like = -1, trk_or_em = vout[trkLikeIdx] + vout[emLikeIdx];
        if (trk_or_em > 0) {
          trk_like = vout[trkLikeIdx] / trk_or_em;
          if (trk_like < fPmaTrackerConfig.TrackLikeThreshold()) pdg = 11; // tag if EM-like
          // (don't set pdg for track-like, for the moment don't like the idea of using "13")
        }
        //std::cout << "trk:" << best_view << ":" << trk.size() << ":" << trkHitPtrList.size() << " p=" << trk_like << std::endl;
      }
    }
    return pdg;
  }

  template <size_t N>
  bool PMAlgTrackMaker::init(const art::Event& evt, pma::PMAlgTracker& pmalgTracker) const
  {
    auto cluResults = anab::MVAReader<recob::Cluster, N>::create(evt, fCluModuleLabel);
    if (!cluResults) { return false; }

    int trkLikeIdx = cluResults->getIndex("track");
    int emLikeIdx = cluResults->getIndex("em");
    if ((trkLikeIdx < 0) || (emLikeIdx < 0)) { return false; }

    const art::FindManyP<recob::Hit> hitsFromClusters(
      cluResults->dataHandle(), evt, cluResults->dataTag());
    const auto& cnnOuts = cluResults->outputs();
    std::vector<float> trackLike(cnnOuts.size());
    for (size_t i = 0; i < cnnOuts.size(); ++i) {
      double trkOrEm = cnnOuts[i][trkLikeIdx] + cnnOuts[i][emLikeIdx];
      if (trkOrEm > 0) { trackLike[i] = cnnOuts[i][trkLikeIdx] / trkOrEm; }
      else {
        trackLike[i] = 0;
      }
    }
    pmalgTracker.init(hitsFromClusters, trackLike);
    return true;
  }

  std::vector<anab::CosmicTagID_t> PMAlgTrackMaker::getCosmicTag(
    const pma::Track3D::ETag pmaTag) const
  {
    std::vector<anab::CosmicTagID_t> anabTags;

    if (pmaTag & pma::Track3D::kOutsideDrift_Partial) {
      anabTags.push_back(anab::CosmicTagID_t::kOutsideDrift_Partial);
    }
    if (pmaTag & pma::Track3D::kOutsideDrift_Complete) {
      anabTags.push_back(anab::CosmicTagID_t::kOutsideDrift_Complete);
    }
    if (pmaTag & pma::Track3D::kBeamIncompatible) {
      anabTags.push_back(anab::CosmicTagID_t::kFlash_BeamIncompatible);
    }
    if (pmaTag & pma::Track3D::kGeometry_XX) {
      anabTags.push_back(anab::CosmicTagID_t::kGeometry_XX);
    }
    if (pmaTag & pma::Track3D::kGeometry_YY) {
      anabTags.push_back(anab::CosmicTagID_t::kGeometry_YY);
    }
    if (pmaTag & pma::Track3D::kGeometry_ZZ) {
      anabTags.push_back(anab::CosmicTagID_t::kGeometry_ZZ);
    }
    if (pmaTag & pma::Track3D::kGeometry_YZ) {
      anabTags.push_back(anab::CosmicTagID_t::kGeometry_YZ);
    }
    if (pmaTag & pma::Track3D::kGeometry_Y) {
      anabTags.push_back(anab::CosmicTagID_t::kGeometry_Y);
    }

    if (anabTags.empty()) { anabTags.push_back(anab::CosmicTagID_t::kUnknown); }

    return anabTags;
  }

  void PMAlgTrackMaker::produce(art::Event& evt)
  {
    // ---------------- Create data products --------------------------
    auto tracks = std::make_unique<std::vector<recob::Track>>();
    auto allsp = std::make_unique<std::vector<recob::SpacePoint>>();
    auto vtxs = std::make_unique<std::vector<recob::Vertex>>(); // interaction vertices
    auto kinks = std::make_unique<
      std::vector<recob::Vertex>>(); // kinks on tracks (no new particles start in kinks)
    auto nodes = std::make_unique<std::vector<recob::Vertex>>(); // pma nodes
    auto t0s = std::make_unique<std::vector<anab::T0>>();
    auto cosmicTags = std::make_unique<std::vector<anab::CosmicTag>>();

    auto trk2hit_oldway = std::make_unique<
      art::Assns<recob::Track,
                 recob::Hit>>(); // ****** REMEMBER to remove when FindMany improved ******
    auto trk2hit = std::make_unique<art::Assns<recob::Track, recob::Hit, recob::TrackHitMeta>>();

    auto trk2sp = std::make_unique<art::Assns<recob::Track, recob::SpacePoint>>();
    auto trk2t0 = std::make_unique<art::Assns<recob::Track, anab::T0>>();
    auto trk2ct = std::make_unique<art::Assns<recob::Track, anab::CosmicTag>>();

    auto sp2hit = std::make_unique<art::Assns<recob::SpacePoint, recob::Hit>>();
    auto vtx2trk = std::make_unique<
      art::Assns<recob::Vertex,
                 recob::Track>>(); // one or more tracks (particles) start in the vertex
    auto trk2kink =
      std::make_unique<art::Assns<recob::Track, recob::Vertex>>(); // one or more kinks on the track

    auto pfps = std::make_unique<std::vector<recob::PFParticle>>();

    auto pfp2clu = std::make_unique<art::Assns<recob::PFParticle, recob::Cluster>>();
    auto pfp2vtx = std::make_unique<art::Assns<recob::PFParticle, recob::Vertex>>();
    auto pfp2trk = std::make_unique<art::Assns<recob::PFParticle, recob::Track>>();

    // --------------------- Wires & Hits -----------------------------
    auto wireHandle = evt.getValidHandle<std::vector<recob::Wire>>(fWireModuleLabel);
    auto allHitListHandle = evt.getValidHandle<std::vector<recob::Hit>>(fHitModuleLabel);
    std::vector<art::Ptr<recob::Hit>> allhitlist;
    art::fill_ptr_vector(allhitlist, allHitListHandle);

    // -------------- PMA Tracker for this event ----------------------
    auto pmalgTracker = pma::PMAlgTracker(allhitlist,
                                          *wireHandle,
                                          fPmaConfig,
                                          fPmaTrackerConfig,
                                          fPmaVtxConfig,
                                          fPmaStitchConfig,
                                          fPmaTaggingConfig,
                                          fAdcInPassingPoints,
                                          fAdcInRejectedPoints);

    size_t mvaLength = 0;
    if (fEmModuleLabel != "") // ----------- Exclude EM parts ---------
    {
      auto cluListHandle = evt.getValidHandle<std::vector<recob::Cluster>>(fCluModuleLabel);
      auto splitCluHandle = evt.getValidHandle<std::vector<recob::Cluster>>(fEmModuleLabel);

      art::FindManyP<recob::Hit> hitsFromClusters(cluListHandle, evt, fCluModuleLabel);
      art::FindManyP<recob::Hit> hitsFromEmParts(splitCluHandle, evt, fEmModuleLabel);
      pmalgTracker.init(hitsFromClusters, hitsFromEmParts);
    }
    else if (fPmaTrackerConfig.TrackLikeThreshold() > 0) // --- CNN EM/trk separation ----
    {
      // try to dig out 4- or 3-output MVA data product
      if (init<4>(evt, pmalgTracker)) { mvaLength = 4; } // e.g.: EM / track / Michel / none
      else if (init<3>(evt, pmalgTracker)) {
        mvaLength = 3;
      } // e.g.: EM / track / none
      else if (init<2>(evt, pmalgTracker)) {
        mvaLength = 2;
      } // just EM / track (LArIAT starts with this style)
      else {
        throw cet::exception("PMAlgTrackMaker") << "No EM/track MVA data products." << std::endl;
      }
    }
    else // ------------------------ Use ALL clusters -----------------
    {
      auto cluListHandle = evt.getValidHandle<std::vector<recob::Cluster>>(fCluModuleLabel);
      art::FindManyP<recob::Hit> hitsFromClusters(cluListHandle, evt, fCluModuleLabel);
      pmalgTracker.init(hitsFromClusters);
    }

    // ------------------ Do the job here: ----------------------------
    auto const clockData = art::ServiceHandle<detinfo::DetectorClocksService const>()->DataFor(evt);
    auto const detProp =
      art::ServiceHandle<detinfo::DetectorPropertiesService const>()->DataFor(evt, clockData);
    int retCode = pmalgTracker.build(clockData, detProp);
    // ----------------------------------------------------------------
    switch (retCode) {
    case -2: mf::LogError("Summary") << "problem"; break;
    case -1: mf::LogWarning("Summary") << "no input"; break;
    case 0: mf::LogVerbatim("Summary") << "no tracks done"; break;
    default:
      if (retCode < 0)
        mf::LogVerbatim("Summary") << "unknown result";
      else if (retCode == 1)
        mf::LogVerbatim("Summary") << retCode << " track ready";
      else
        mf::LogVerbatim("Summary") << retCode << " tracks ready";
      break;
    }

    // ---------- Translate output to data products: ------------------
    auto const& result = pmalgTracker.result();
    if (!result.empty()) // ok, there is something to save
    {
      size_t spStart = 0, spEnd = 0;
      double sp_pos[3], sp_err[6];
      for (size_t i = 0; i < 3; ++i)
        sp_pos[i] = 0.0;
      for (size_t i = 0; i < 6; ++i)
        sp_err[i] = 1.0;

      auto const make_pfpptr = art::PtrMaker<recob::PFParticle>(evt);
      auto const make_trkptr = art::PtrMaker<recob::Track>(evt); // PtrMaker Step #1
      auto const make_vtxptr = art::PtrMaker<recob::Vertex>(evt);
      auto const make_kinkptr = art::PtrMaker<recob::Vertex>(evt, kKinksName);
      auto const make_t0ptr = art::PtrMaker<anab::T0>(evt);
      auto const make_ctptr = art::PtrMaker<anab::CosmicTag>(evt);

      tracks->reserve(result.size());
      art::ServiceHandle<geo::Geometry> geometry;
      auto const& wireReadoutGeom = art::ServiceHandle<geo::WireReadout>()->Get();
      for (size_t trkIndex = 0; trkIndex < result.size(); ++trkIndex) {
        pma::Track3D* trk = result[trkIndex].Track();

        trk->SelectHits(); // just in case, set all to enabled
        unsigned int itpc = trk->FrontTPC(), icryo = trk->FrontCryo();
        pma::dedx_map dedx_tmp;
        geo::TPCGeo const& tpcgeo = geometry->TPC({icryo, itpc});
        auto const& tpcid = tpcgeo.ID();
        auto has_plane = [&wireReadoutGeom, &tpcid](auto const view) {
          return wireReadoutGeom.HasPlane(geo::PlaneID(tpcid, view));
        };
        if (has_plane(geo::kU)) {
          trk->CompleteMissingWires(detProp, geo::kU);
          trk->GetRawdEdxSequence(dedx_tmp, geo::kU, 1);
        }
        if (has_plane(geo::kV)) {
          trk->CompleteMissingWires(detProp, geo::kV);
          trk->GetRawdEdxSequence(dedx_tmp, geo::kV, 1);
        }
        if (has_plane(geo::kX)) {
          trk->CompleteMissingWires(detProp, geo::kX);
          trk->GetRawdEdxSequence(dedx_tmp, geo::kX, 1);
        }
        if (has_plane(geo::kY)) {
          trk->CompleteMissingWires(detProp, geo::kY);
          trk->GetRawdEdxSequence(dedx_tmp, geo::kY, 1);
        }
        if (has_plane(geo::kZ)) {
          trk->CompleteMissingWires(detProp, geo::kZ);
          trk->GetRawdEdxSequence(dedx_tmp, geo::kZ, 1);
        }

        //gc: make sure no tracks are created with less than 2 points
        if (trk->size() < 2) continue;

        int pdg = 0;
        if (mvaLength == 4)
          pdg = getPdgFromCnnOnHits<4>(evt, *(result[trkIndex].Track()));
        else if (mvaLength == 3)
          pdg = getPdgFromCnnOnHits<3>(evt, *(result[trkIndex].Track()));
        else if (mvaLength == 2)
          pdg = getPdgFromCnnOnHits<2>(evt, *(result[trkIndex].Track()));
        //else mf::LogInfo("PMAlgTrackMaker") << "Not using PID from CNN.";

        tracks->push_back(pma::convertFrom(*trk, trkIndex, pdg));

        auto const trkPtr = make_trkptr(tracks->size() - 1); // PtrMaker Step #2

        if (trk->HasT0()) {
          // TriggBits=3 means from 3d reco (0,1,2 mean something else)
          t0s->push_back(anab::T0(trk->GetT0(), 0, 3, tracks->back().ID()));

          auto const t0Ptr = make_t0ptr(t0s->size() - 1); // PtrMaker Step #3
          trk2t0->addSingle(trkPtr, t0Ptr);
        }

        // Check if this is a cosmic ray and create an association if it is.
        if (trk->HasTagFlag(pma::Track3D::kCosmic)) {
          // Get the track end points
          std::vector<float> trkEnd0;
          std::vector<float> trkEnd1;
          // Get the drift direction, but don't care about the sign
          // Also need to subtract 1 due to the definition.
          auto const [axis, _] = tpcgeo.DriftAxisWithSign();

          for (int i = 0; i < 3; ++i) {
            // Get the drift direction and apply the opposite of the drift shift in order to
            // give the CosmicTag the drift coordinate assuming T0 = T_beam as it requests.
            double shift = 0.0;
            if (i == to_int(axis)) { shift = trk->Nodes()[0]->GetDriftShift(); }
            trkEnd0.push_back(trk->Nodes()[0]->Point3D()[i] - shift);
            trkEnd1.push_back(trk->Nodes()[trk->Nodes().size() - 1]->Point3D()[i] - shift);
          }
          // Make the tag object. For now, let's say this is very likely a cosmic (3rd argument = 1).
          // Set the type of cosmic to the value saved in pma::Track.
          auto tags = getCosmicTag(trk->GetTag());
          for (const auto t : tags) {
            cosmicTags->emplace_back(trkEnd0, trkEnd1, 1, t);
            auto const cosmicPtr = make_ctptr(cosmicTags->size() - 1);
            trk2ct->addSingle(trkPtr, cosmicPtr);
          }
        }

        //gc: save associated hits in the same order as trajectory points
        for (size_t h = 0, cnt = 0; h < trk->size(); h++) {
          pma::Hit3D* h3d = (*trk)[h];
          if (!h3d->IsEnabled()) continue;

          recob::TrackHitMeta metadata(cnt++, h3d->Dx());
          trk2hit->addSingle(trkPtr, h3d->Hit2DPtr(), metadata);
          trk2hit_oldway->addSingle(
            trkPtr, h3d->Hit2DPtr()); // ****** REMEMBER to remove when FindMany improved ******
        }

        art::PtrVector<recob::Hit> sp_hits;
        spStart = allsp->size();
        //rs: so make also associations to space points in the order of trajectory points
        for (size_t h = 0; h < trk->size(); ++h) {
          pma::Hit3D* h3d = (*trk)[h];
          if (!h3d->IsEnabled()) continue;

          double hx = h3d->Point3D().X();
          double hy = h3d->Point3D().Y();
          double hz = h3d->Point3D().Z();

          if ((h == 0) || (std::fabs(sp_pos[0] - hx) > 1.0e-5) ||
              (std::fabs(sp_pos[1] - hy) > 1.0e-5) || (std::fabs(sp_pos[2] - hz) > 1.0e-5)) {
            if (sp_hits.size()) // hits assigned to the previous sp
            {
              util::CreateAssn(evt, *allsp, sp_hits, *sp2hit);
              sp_hits.clear();
            }
            sp_pos[0] = hx;
            sp_pos[1] = hy;
            sp_pos[2] = hz;
            allsp->push_back(recob::SpacePoint(sp_pos, sp_err, 1.0));
          }
          sp_hits.push_back(h3d->Hit2DPtr());
        }

        if (sp_hits.size()) // hits assigned to the last sp
        {
          util::CreateAssn(evt, *allsp, sp_hits, *sp2hit);
        }
        spEnd = allsp->size();

        if (spEnd > spStart) util::CreateAssn(evt, *tracks, *allsp, *trk2sp, spStart, spEnd);
      }

      auto vsel = pmalgTracker.getVertices(
        fSaveOnlyBranchingVtx);            // vtx pos's with vector of connected track idxs
      auto ksel = pmalgTracker.getKinks(); // pairs of kink position - associated track idx
      std::map<size_t, art::Ptr<recob::Vertex>> frontVtxs; // front vertex ptr for each track index

      if (fPmaTrackerConfig.RunVertexing()) // save vertices and vtx-trk assns
      {
        double xyz[3];
        for (auto const& v : vsel) {
          xyz[0] = v.first.X();
          xyz[1] = v.first.Y();
          xyz[2] = v.first.Z();
          mf::LogVerbatim("Summary") << "  vtx:" << xyz[0] << ":" << xyz[1] << ":" << xyz[2]
                                     << "  (" << v.second.size() << " tracks)";

          size_t vidx = vtxs->size();
          vtxs->push_back(recob::Vertex(xyz, vidx));

          auto const vptr = make_vtxptr(vidx);
          if (!v.second.empty()) {
            for (const auto& vEntry : v.second) {
              size_t tidx = vEntry.first;
              bool isFront = vEntry.second;

              if (isFront) frontVtxs[tidx] = vptr; // keep ptr of the front vtx

              auto const tptr = make_trkptr(tidx);
              vtx2trk->addSingle(vptr, tptr);
            }
          }
          else
            mf::LogWarning("PMAlgTrackMaker") << "No tracks found at this vertex.";
        }
        mf::LogVerbatim("Summary") << vtxs->size() << " vertices ready";

        for (auto const& k : ksel) {
          xyz[0] = k.first.X();
          xyz[1] = k.first.Y();
          xyz[2] = k.first.Z();
          mf::LogVerbatim("Summary") << "  kink:" << xyz[0] << ":" << xyz[1] << ":" << xyz[2];

          size_t kidx = kinks->size();
          size_t tidx = k.second; // track idx on which this kink was found

          kinks->push_back(
            recob::Vertex(xyz, tidx)); // save index of track (will have color of trk in evd)

          auto const tptr = make_trkptr(tidx);
          auto const kptr = make_kinkptr(kidx);
          trk2kink->addSingle(tptr, kptr);
        }
        mf::LogVerbatim("Summary") << ksel.size() << " kinks ready";
      }

      if (fSavePmaNodes) {
        double xyz[3];
        for (size_t t = 0; t < result.size(); ++t) {
          auto const& trk = *(result[t].Track());
          for (auto const* node : trk.Nodes()) {
            xyz[0] = node->Point3D().X();
            xyz[1] = node->Point3D().Y();
            xyz[2] = node->Point3D().Z();
            nodes->push_back(recob::Vertex(xyz, t));
          }
        }
      }

      for (size_t t = 0; t < result.size(); ++t) {
        size_t parentIdx = recob::PFParticle::kPFParticlePrimary;
        if (result[t].Parent() >= 0) parentIdx = (size_t)result[t].Parent();

        std::vector<size_t> daughterIdxs;
        for (size_t idx : result[t].Daughters()) {
          daughterIdxs.push_back(idx);
        }

        size_t pfpidx = pfps->size();
        pfps->emplace_back((*tracks)[t].ParticleId(), pfpidx, parentIdx, daughterIdxs);

        auto const pfpptr = make_pfpptr(pfpidx);
        auto const tptr = make_trkptr(t);
        pfp2trk->addSingle(pfpptr, tptr);

        // add assns to FRONT vertex of each particle
        if (fPmaTrackerConfig.RunVertexing()) {
          art::Ptr<recob::Vertex> vptr = frontVtxs[t];
          if (!vptr.isNull())
            pfp2vtx->addSingle(pfpptr, vptr);
          else
            mf::LogWarning("PMAlgTrackMaker") << "Front vertex for PFParticle is missing.";
        }
      }
      mf::LogVerbatim("Summary") << pfps->size()
                                 << " PFParticles created for reconstructed tracks.";
      mf::LogVerbatim("Summary") << "Adding " << result.parents().size() << " primary PFParticles.";
      for (size_t t = 0; t < result.parents().size(); ++t) {
        std::vector<size_t> daughterIdxs;
        for (size_t idx : result.parents()[t].Daughters()) {
          daughterIdxs.push_back(idx);
        }

        size_t pfpidx = pfps->size();
        size_t parentIdx = recob::PFParticle::kPFParticlePrimary;
        pfps->emplace_back(0, pfpidx, parentIdx, daughterIdxs);

        // add assns to END vertex of primary
        if (fPmaTrackerConfig.RunVertexing() && !daughterIdxs.empty()) {
          auto const pfpptr = make_pfpptr(pfpidx);
          art::Ptr<recob::Vertex> vptr =
            frontVtxs[daughterIdxs.front()]; // same vertex for all daughters
          if (!vptr.isNull())
            pfp2vtx->addSingle(pfpptr, vptr);
          else
            mf::LogWarning("PMAlgTrackMaker") << "Front vertex for PFParticle is missing.";
        }
      }
      mf::LogVerbatim("Summary") << pfps->size() << " PFParticles created in total.";
    }

    // for (const auto & ct : *cosmicTags) { std::cout << "Cosmic tag: " << ct << std::endl; }

    evt.put(std::move(tracks));
    evt.put(std::move(allsp));
    evt.put(std::move(vtxs));
    evt.put(std::move(kinks), kKinksName);
    evt.put(std::move(nodes), kNodesName);
    evt.put(std::move(t0s));
    evt.put(std::move(cosmicTags));

    evt.put(std::move(trk2hit_oldway)); // ****** REMEMBER to remove when FindMany improved ******
    evt.put(std::move(trk2hit));
    evt.put(std::move(trk2sp));
    evt.put(std::move(trk2t0));
    evt.put(std::move(trk2ct));

    evt.put(std::move(sp2hit));
    evt.put(std::move(vtx2trk));
    evt.put(std::move(trk2kink), kKinksName);

    evt.put(std::move(pfps));
    evt.put(std::move(pfp2clu));
    evt.put(std::move(pfp2vtx));
    evt.put(std::move(pfp2trk));
  }
  // ------------------------------------------------------
  // ------------------------------------------------------
  // ------------------------------------------------------

  DEFINE_ART_MODULE(PMAlgTrackMaker)

} // namespace trkf