TrackFinderMCTruthRecoTracksModule.cc

/**************************************************************************
 * BASF2 (Belle Analysis Framework 2)                                     *
 * Copyright(C) 2010 - Belle II Collaboration                             *
 *                                                                        *
 * Author: The Belle II Collaboration                                     *
 * Contributors: Martin Heck, Oksana Brovchenko, Moritz Nadler,           *
 *               Thomas Hauth, Oliver Frost                               *
 *                                                                        *
 * This software is provided "as is" without any warranty.                *
 **************************************************************************/
 
#include <tracking/modules/trackFinderMCTruth/TrackFinderMCTruthRecoTracksModule.h>
 
#include <framework/datastore/StoreArray.h>
#include <framework/datastore/RelationArray.h>
#include <framework/datastore/StoreObjPtr.h>
#include <framework/dataobjects/EventMetaData.h>
#include <framework/gearbox/Const.h>
#include <mdst/dataobjects/MCParticle.h>
#include <cdc/dataobjects/CDCHit.h>
#include <cdc/dataobjects/CDCSimHit.h>
#include <cdc/geometry/CDCGeometryPar.h>
#include <pxd/dataobjects/PXDTrueHit.h>
#include <pxd/dataobjects/PXDCluster.h>
#include <svd/dataobjects/SVDTrueHit.h>
#include <svd/dataobjects/SVDCluster.h>
#include <top/dataobjects/TOPBarHit.h>
#include <tracking/dataobjects/RecoTrack.h>
#include <simulation/monopoles/MonopoleConstants.h>
 
#include <framework/geometry/BFieldManager.h>
#include <framework/dataobjects/Helix.h>
 
#include <TRandom.h>
 
#include <vector>
#include <string>
#include <sstream>
#include <cmath>
 
 
using namespace Belle2;
 
//-----------------------------------------------------------------
//                 Register the Module
//-----------------------------------------------------------------
REG_MODULE(TrackFinderMCTruthRecoTracks)
 
//-----------------------------------------------------------------
//                 Implementation
//-----------------------------------------------------------------
 
TrackFinderMCTruthRecoTracksModule::TrackFinderMCTruthRecoTracksModule() : Module()
{
  //Set module properties
  setDescription("Uses the MC information to create genfit::TrackCandidates for primary MCParticles and Relations between them. "
                 "Fills the created genfit::TrackCandidates with all information (start values, hit indices) needed for the fitting.");
  setPropertyFlags(c_ParallelProcessingCertified);
 
  // choose which hits to use, all hits assigned to the track candidate will be used in the fit
  addParam("UsePXDHits",
           m_usePXDHits,
           "Set true if PXDHits or PXDClusters should be used",
           true);
  addParam("UseSVDHits",
           m_useSVDHits,
           "Set true if SVDHits or SVDClusters should be used",
           true);
  addParam("UseCDCHits",
           m_useCDCHits,
           "Set true if CDCHits should be used",
           true);
  addParam("UseOnlyAxialCDCHits",
           m_useOnlyAxialCDCHits,
           "Set true if only the axial CDCHits should be used",
           false);
  addParam("UseNLoops",
           m_useNLoops,
           "Set the number of loops whose hits will be marked as priortiy hits. All other hits "
           "will be marked as auxiliary and therfore not considered for efficiency computations "
           "By default, all hits will be priority hits.",
           INFINITY);
  addParam("UseOnlyBeforeTOP",
           m_useOnlyBeforeTOP,
           "Mark hits as auxiliary after the track left the CDC and touched the TOP detector "
           "(only implemented for CDCHits).",
           false);
  addParam("UseReassignedHits",
           m_useReassignedHits,
           "Include hits reassigned from discarded seconardy daughters in the tracks.",
           false);
  addParam("UseSecondCDCHits",
           m_useSecondCDCHits,
           "Also includes the CDC 2nd hit information in the MC tracks.",
           false);
  addParam("MinPXDHits",
           m_minPXDHits,
           "Minimum number of PXD hits needed to allow the created of a track candidate",
           0);
  addParam("MinSVDHits",
           m_minSVDHits,
           "Minimum number of SVD hits needed to allow the created of a track candidate",
           0);
  addParam("MinCDCAxialHits",
           m_minCDCAxialHits,
           "Minimum number of CDC hits form an axial wire needed to allow the created of a track candidate",
           0);
  addParam("MinCDCStereoHits",
           m_minCDCStereoHits,
           "Minimum number of CDC hits form a stereo wire needed to allow the created of a track candidate",
           0);
  addParam("AllowFirstCDCSuperLayerOnly",
           m_allowFirstCDCSuperLayerOnly,
           "Allow tracks to pass the stereo hit requirement if they touched only the first (axial) CDC layer",
           false);
 
  addParam("MinimalNDF",
           m_minimalNdf,
           "Minimum number of total hits needed to allow the creation of a track candidate. "
           "It is called NDF (number of degrees of freedom) because it counts the dimensionality. "
           "2D hits are counted as 2",
           5);
 
  //choose for which particles a track candidate should be created
  //this is just an attempt to find out what is the most suitable way to select particles, if you have other/better ideas, communicate it to the tracking group...
  addParam("WhichParticles",
           m_whichParticles,
           "List of keywords to mark what properties particles must have to get a track candidate. "
           "If several properties are given all of them must be true: "
           "\"primary\" particle must come from the generator, "
           "\"PXD\", \"SVD\", \"CDC\", \"TOP\", \"ARICH\", \"ECL\" or \"KLM\" particle must have hits in the subdetector with that name. "
           "\"is:X\" where X is a PDG code: particle must have this code. "
           "\"from:X\" any of the particles's ancestors must have this (X) code",
           std::vector<std::string>(1, "primary"));
 
  addParam("EnergyCut",
           m_energyCut,
           "Track candidates are only created for MCParticles with energy larger than this cut ",
           double(0.0));
 
  addParam("Neutrals",
           m_neutrals,
           "Set true if track candidates should be created also for neutral particles",
           bool(false));
 
  addParam("MergeDecayInFlight",
           m_mergeDecayInFlight,
           "Merge decay in flights that produce a single charged particle to the mother particle",
           bool(false));
 
  addParam("SetTimeSeed",
           m_setTimeSeed,
           "Set true to forward the production time as time seed of the particles to the RecoTrack",
           true);
 
  //smearing of MCMomentum
  addParam("Smearing",
           m_smearing,
           "Smearing of MCMomentum/MCVertex prior to storing it in genfit::TrackCandidate (in %). "
           "A negative value will switch off smearing. This is also the default.",
           -1.0);
 
  addParam("SmearingCov",
           m_smearingCov,
           "Covariance matrix used to smear the true pos and mom before passed to track candidate. "
           "This matrix will also passed to Genfit as the initial covarance matrix. "
           "If any diagonal value is negative this feature will not be used. "
           "OFF DIAGONAL ELEMENTS DO NOT HAVE AN EFFECT AT THE MOMENT",
           std::vector<double>(36, -1.0));
 
  addParam("SplitAfterDeltaT",
           m_splitAfterDeltaT,
           "Minimal time delay between two sim hits (in ns) after which MC reco track will be "
           "split into seperate tracks. If < 0, don't do splitting."
           "This feature was designed to be used in MC cosmics reconstruction to get two MCRecoTracks"
           "when track pass through empty SVD region, so that number of MCRecoTracks can be compared with"
           "number of non merged reco tracks. ",
           -1.0);
 
  // names of output containers
  addParam("RecoTracksStoreArrayName",
           m_recoTracksStoreArrayName,
           "Name of store array holding the RecoTracks (output)",
           std::string(""));
 
  addParam("TrueHitMustExist",
           m_enforceTrueHit,
           "If set true only cluster hits that have a relation to a TrueHit will be included in the track candidate",
           false);
 
  addParam("discardAuxiliaryHits",
           m_discardAuxiliaryHits,
           "If set true hits marked as auxiliary (e.g. hits in higher loops) will not be included in the track candidate.",
           m_discardAuxiliaryHits);
 
 
 
}
 
void TrackFinderMCTruthRecoTracksModule::initialize()
{
  StoreArray<MCParticle> mcparticles;
  if (mcparticles.isOptional()) {
    m_mcParticlesPresent = true;
 
    //output store arrays have to be registered in initialize()
    StoreArray<RecoTrack> recoTracks(m_recoTracksStoreArrayName);
    recoTracks.registerInDataStore(DataStore::c_ErrorIfAlreadyRegistered);
 
    recoTracks.registerRelationTo(mcparticles);
 
    RecoTrack::registerRequiredRelations(recoTracks);
 
    // build a bit mask with all properties a MCParticle should have to lead to the creation of a track candidate
    m_particleProperties = 0;
    int aPdgCode = 0;
    const int nProperties = m_whichParticles.size();
    for (int i = 0; i not_eq nProperties; ++i) {
      if (m_whichParticles[i] == "primary") {
        m_particleProperties += 1;
      } else if (m_whichParticles[i] == "PXD") {
        m_particleProperties += 2;
      } else if (m_whichParticles[i] == "SVD") {
        m_particleProperties += 4;
      } else if (m_whichParticles[i] == "CDC") {
        m_particleProperties += 8;
      } else if (m_whichParticles[i] == "TOP") {
        m_particleProperties += 16;
      } else if (m_whichParticles[i] == "ARICH") {
        m_particleProperties += 32;
      } else if (m_whichParticles[i] == "ECL") {
        m_particleProperties += 64;
      } else if (m_whichParticles[i] == "KLM") {
        m_particleProperties += 128;
      } else if (m_whichParticles[i].substr(0, 3) == "is:") {
        std::string pdgCodeString = m_whichParticles[i].substr(3);
        std::stringstream(pdgCodeString) >> aPdgCode;
        B2DEBUG(20, "PDG code added to m_particlePdgCodes " << aPdgCode << " *******");
        m_particlePdgCodes.push_back(aPdgCode);
      } else if (m_whichParticles[i].substr(0, 5) == "from:") {
        std::string pdgCodeString = m_whichParticles[i].substr(5);
        std::stringstream(pdgCodeString) >> aPdgCode;
        B2DEBUG(20, "PDG code added to m_fromPdgCodes " << aPdgCode << " *******");
        m_fromPdgCodes.push_back(aPdgCode);
      } else {
        B2FATAL("Invalid values were given to the MCTrackFinder parameter WhichParticles");
      }
    }
 
 
 
    //transfom the smearingCov vector into a TMatrixD
    //first check if it can be transformed into a 6x6 matrix
    if (m_smearingCov.size() != 36) {
      B2FATAL("SmearingCov does not have exactly 36 elements. So 6x6 covariance matrix can be formed from it");
    }
    m_initialCov.ResizeTo(6, 6);
    m_initialCov = TMatrixDSym(6, &m_smearingCov[0]);
    for (int i = 0; i != 6; ++i) {
      if (m_initialCov(i, i) < 0.0) {
        m_initialCov(0, 0) = -1.0; // if first element of matrix is negative this using this matrix will be switched off
      }
    }
 
    if (m_smearing > 0.0 && m_initialCov(0, 0) > 0.0) {
      B2FATAL("Both relative smearing (Smearing) and using a smearing cov (SmearingCov) is activated but only one of both can be used");
    }
  }
}
 
void TrackFinderMCTruthRecoTracksModule::beginRun()
{
  m_notEnoughtHitsCounter = 0;
  m_noTrueHitCounter = 0;
  m_nRecoTracks = 0;
}
 
 
void TrackFinderMCTruthRecoTracksModule::event()
{
  // Skip in the case there are no MC particles present.
  if (not m_mcParticlesPresent) {
    B2DEBUG(20, "Skipping MC Track Finder as there are no MC Particles registered in the DataStore.");
    return;
  }
 
  StoreObjPtr<EventMetaData> eventMetaDataPtr("EventMetaData", DataStore::c_Event);
  const int eventCounter = eventMetaDataPtr->getEvent();
  B2DEBUG(20, "*******   MCTrackFinderModule processing event number: " << eventCounter << " *******");
 
  //all the input containers. First: MCParticles
  StoreArray<MCParticle> mcParticles;
  const int nMcParticles = mcParticles.getEntries();
  B2DEBUG(20, "MCTrackFinder: total Number of MCParticles: " << nMcParticles);
 
  //PXD trueHits
  StoreArray<PXDTrueHit> pxdTrueHits;
  const int nPXDHits = pxdTrueHits.getEntries();
  B2DEBUG(20, "MCTrackFinder: Number of PXDTrueHits: " << nPXDHits);
 
  RelationArray mcPartToPXDTrueHits(mcParticles, pxdTrueHits);
  const int nMcPartToPXDHits = mcPartToPXDTrueHits.getEntries();
  B2DEBUG(20, "MCTrackFinder: Number of relations between MCParticles and PXDHits: " << nMcPartToPXDHits);
 
  //PXD clusters
  StoreArray<PXDCluster> pxdClusters;
  const int nPXDClusters = pxdClusters.getEntries();
  B2DEBUG(20, "MCTrackFinder: Number of PXDClusters: " << nPXDClusters);
 
  RelationArray pxdClusterToMCParticle(pxdClusters, mcParticles);
  const int nPxdClusterToMCPart = pxdClusterToMCParticle.getEntries();
  B2DEBUG(20, "MCTrackFinder: Number of relations between PXDCluster and MCParticles: " << nPxdClusterToMCPart);
 
  //SVD truehits
  StoreArray<SVDTrueHit> svdTrueHits;
  const int nSVDHits = svdTrueHits.getEntries();
  B2DEBUG(20, "MCTrackFinder: Number of SVDDHits: " << nSVDHits);
 
  RelationArray mcPartToSVDTrueHits(mcParticles, svdTrueHits);
  const int nMcPartToSVDHits = mcPartToSVDTrueHits.getEntries();
  B2DEBUG(20, "MCTrackFinder: Number of relations between MCParticles and SVDHits: " << nMcPartToSVDHits);
 
  //SVD clusters
  StoreArray<SVDCluster> svdClusters;
  const int nSVDClusters = svdClusters.getEntries();
  B2DEBUG(20, "MCTrackFinder: Number of SVDClusters: " << nSVDClusters);
 
  RelationArray svdClusterToMCParticle(svdClusters, mcParticles);
  const int nSvdClusterToMCPart = svdClusterToMCParticle.getEntries();
  B2DEBUG(20, "MCTrackFinder: Number of relations between SVDCluster and MCParticles: " << nSvdClusterToMCPart);
 
  //CDC
  StoreArray<CDCHit> cdcHits;
  const int nCDCHits = cdcHits.getEntries();
  B2DEBUG(20, "MCTrackFinder: Number of CDCHits: " << nCDCHits);
 
  RelationArray mcPartToCDCHits(mcParticles, cdcHits);
  const int nMcPartToCDCHits = mcPartToCDCHits.getEntries();
  B2DEBUG(20, "MCTrackFinder: Number of relations between MCParticles and CDCHits: " << nMcPartToCDCHits);
 
  StoreArray<CDCSimHit> cdcSimHits("");
  const int nCDCSimHits = cdcSimHits.getEntries();
  B2DEBUG(20, "MCTrackFinder: Number of CDCSimHits: " << nCDCSimHits);
 
  RelationArray cdcSimHitToHitRel(cdcSimHits, cdcHits);
  const int nCdcSimHitToHitRel = cdcSimHitToHitRel.getEntries();
  B2DEBUG(20, "MCTrackFinder: Number of relations between CDCSimHit and CDCHits: " << nCdcSimHitToHitRel);
 
  // prepare rejection of CDC/PXD/SVD hits from higher order loops
  const double Bz = BFieldManager::getField(0, 0, 0).Z() / Unit::T;
 
  //register StoreArray which will be filled by this module
  StoreArray<RecoTrack> recoTracks(m_recoTracksStoreArrayName);
 
  // loop over MCParticles. And check several user selected properties. Make a track candidate only if MCParticle has properties wanted by user options.
  std::set<int> alreadyConsumedMCParticles;
  for (int iPart = 0; iPart < nMcParticles; ++iPart) {
    if (alreadyConsumedMCParticles.count(iPart)) continue;
    alreadyConsumedMCParticles.insert(iPart);
 
    MCParticle* aMcParticlePtr = mcParticles[iPart];
    // Ignore particles that didn't propagate significantly, they cannot make tracks.
    if ((aMcParticlePtr->getDecayVertex() - aMcParticlePtr->getProductionVertex()).Mag() < 1 * Unit::cm) {
      B2DEBUG(20, "Particle that did not propagate significantly cannot make track.");
      continue;
    }
 
    //set the property mask for this particle and compare it to the one generated from user input
    int mcParticleProperties = 0;
    if (aMcParticlePtr->hasStatus(MCParticle::c_PrimaryParticle)) {
      mcParticleProperties += 1;
    }
    if (aMcParticlePtr->hasSeenInDetector(Const::PXD)) {
      mcParticleProperties += 2;
    }
    if (aMcParticlePtr->hasSeenInDetector(Const::SVD)) {
      mcParticleProperties += 4;
    }
    if (aMcParticlePtr->hasSeenInDetector(Const::CDC)) {
      mcParticleProperties += 8;
    }
    if (aMcParticlePtr->hasSeenInDetector(Const::TOP)) {
      mcParticleProperties += 16;
    }
    if (aMcParticlePtr->hasSeenInDetector(Const::ARICH)) {
      mcParticleProperties += 32;
    }
    if (aMcParticlePtr->hasSeenInDetector(Const::ECL)) {
      mcParticleProperties += 64;
    }
    if (aMcParticlePtr->hasSeenInDetector(Const::KLM)) {
      mcParticleProperties += 128;
    }
    // check all "seen in" properties that the mcparticle should have in one line.
    if ((mcParticleProperties bitand m_particleProperties) != m_particleProperties) {
      B2DEBUG(20, "PDG: " << aMcParticlePtr->getPDG() <<  " | property mask of particle " <<  mcParticleProperties <<
              " demanded property mask " << m_particleProperties);
      continue; //goto next mcParticle, do not make track candidate
    }
    //make links only for interesting MCParticles: energy cut
    if (aMcParticlePtr->getEnergy() < m_energyCut) {
      B2DEBUG(20, "particle energy too low.  MC particle will be skipped");
      continue; //goto next mcParticle, do not make track candidate
    }
 
    //check if particle has the pdg code the user wants to have. If user did not set any pdg code every code is fine for track candidate creation
 
    const int nPdgCodes = m_particlePdgCodes.size();
    if (nPdgCodes not_eq 0) {
      const int currentPdgCode = aMcParticlePtr->getPDG();
      int nFalsePdgCodes = 0;
      for (int i = 0; i not_eq nPdgCodes; ++i) {
        if (m_particlePdgCodes[i] not_eq currentPdgCode) {
          ++nFalsePdgCodes;
        }
      }
      if (nFalsePdgCodes == nPdgCodes) {
        B2DEBUG(20, "particle does not have one of the user provided pdg codes and will therefore be skipped");
        continue; //goto next mcParticle, do not make track candidate
      }
    }
 
 
    //check if particle has an ancestor selected by the user. If user did not set any pdg code every code is fine for track candidate creation
    const int nFromPdgCodes = m_fromPdgCodes.size();
    if (nFromPdgCodes not_eq 0) {
      MCParticle* currentMother = aMcParticlePtr->getMother();
      int nFalsePdgCodes = 0;
      int nAncestor = 0;
      while (currentMother not_eq NULL) {
        int currentMotherPdgCode = currentMother->getPDG();
        for (int i = 0; i not_eq nFromPdgCodes; ++i) {
          if (m_fromPdgCodes[i] not_eq currentMotherPdgCode) {
            ++nFalsePdgCodes;
          }
        }
 
        currentMother = currentMother->getMother();
        ++nAncestor;
      }
      if (nFalsePdgCodes == (nAncestor * nFromPdgCodes)) {
        B2DEBUG(20, "particle does not have and ancestor with one of the user provided pdg codes and will therefore be skipped");
        continue; //goto next mcParticle, do not make track candidate
      }
    }
 
    // Ignore baryons, except for deuteron.  The purpose is mainly to
    // avoid an error message when getCharge() is called below.
    if (abs(aMcParticlePtr->getPDG()) > 1000000000
        && abs(aMcParticlePtr->getPDG()) != 1000010020) {
      B2DEBUG(20, "Skipped Baryon.");
      continue; //goto next mcParticle, do not make track candidate
 
    }
 
    // ignore neutrals (unless requested) (and unless monopoles)
    if (!m_neutrals && (aMcParticlePtr->getCharge() == 0 && abs(aMcParticlePtr->getPDG()) != Monopoles::c_monopolePDGCode)) {
      B2DEBUG(20, "particle does not have the right charge. MC particle will be skipped");
      continue; //goto next mcParticle, do not make track candidate
    }
 
 
    B2DEBUG(20, "Build a track for the MCParticle with index: " << iPart << " (PDG: " << aMcParticlePtr->getPDG() << ")");
 
    std::vector<const MCParticle*> trackMCParticles;
    trackMCParticles.push_back(aMcParticlePtr);
 
    if (m_mergeDecayInFlight and aMcParticlePtr->getCharge() != 0) {
      std::vector<MCParticle*> daughters = aMcParticlePtr->getDaughters();
      std::vector<MCParticle*> decayInFlightParticles;
      for (MCParticle* daughter : daughters) {
        if (daughter->getSecondaryPhysicsProcess() > 200 and daughter->getCharge() != 0) {
          decayInFlightParticles.push_back(daughter);
        }
      }
      if (decayInFlightParticles.size() == 1) {
        trackMCParticles.push_back(decayInFlightParticles.front());
        alreadyConsumedMCParticles.insert(trackMCParticles.back()->getArrayIndex());
      }
    }
 
    //assign indices of the Hits from all detectors.
    // entry 0: global event of each hit
    // entry 1: indices in the respective hit arrays (PXD, SVD, CDC, ...)
    // entry 2: the category of the hit: either a high priority and should be found or not so important
    // entry 3: identifier for the detector type
    typedef std::tuple<double, int, RecoHitInformation::OriginTrackFinder, Const::EDetector> TimeHitIDDetector;
    std::vector<TimeHitIDDetector> hitsWithTimeAndDetectorInformation;
 
    int ndf = 0; // count the ndf of one track candidate
 
    // create a list containing the indices to the PXDHits that belong to one track
    if (m_usePXDHits) {
      int hitCounter = 0;
      for (const MCParticle* trackMCParticle : trackMCParticles) {
        const RelationVector<PXDCluster>& relatedClusters = trackMCParticle->getRelationsFrom<PXDCluster>();
 
        for (size_t i = 0; i < relatedClusters.size(); ++i) {
          bool isReassigned = relatedClusters.weight(i) < 0;
          if (!m_useReassignedHits && isReassigned) continue;  // skip hits from secondary particles
 
          // currently only priority Hits for PXD
          auto mcFinder = RecoHitInformation::OriginTrackFinder::c_MCTrackFinderPriorityHit;
 
          // Reassigned hits are auxiliary
          if (isReassigned) {
            mcFinder = RecoHitInformation::OriginTrackFinder::c_MCTrackFinderAuxiliaryHit;
          }
 
          // Mark higher order hits as auxiliary, if m_useNLoops has been set
          if (std::isfinite(m_useNLoops) and not isWithinNLoops<PXDCluster, PXDTrueHit>(Bz, relatedClusters.object(i), m_useNLoops)) {
            mcFinder = RecoHitInformation::OriginTrackFinder::c_MCTrackFinderAuxiliaryHit;
          }
 
          // if flag is set discard all auxiliary hits:
          if (m_discardAuxiliaryHits and mcFinder == RecoHitInformation::OriginTrackFinder::c_MCTrackFinderAuxiliaryHit) continue;
 
          const PXDCluster* pxdCluster = relatedClusters.object(i);
          const RelationVector<PXDTrueHit>& relatedTrueHits = pxdCluster->getRelationsTo<PXDTrueHit>();
 
          if (relatedTrueHits.size() == 0 and m_enforceTrueHit) {
            // there is not trueHit! throw away hit because there is no time information for sorting
            ++m_noTrueHitCounter;
            continue;
          }
 
          float time = NAN;
          for (const PXDTrueHit& pxdTrueHit : relatedTrueHits) {
            // Make sure only a true hit is taken that really comes from the current mcParticle.
            // This must be carefully checked because several trueHits from different real tracks can be melted into one cluster
            const RelationVector<MCParticle>& relatedMCParticles = pxdTrueHit.getRelationsFrom<MCParticle>();
            if (std::find_if(relatedMCParticles.begin(),
                             relatedMCParticles.end(),
            [trackMCParticle](const MCParticle & mcParticle) {
            return &mcParticle == trackMCParticle;
          }) != relatedMCParticles.end()) {
              time = pxdTrueHit.getGlobalTime();
              break;
            }
          }
          if (not std::isnan(time)) {
            hitsWithTimeAndDetectorInformation.emplace_back(time, pxdCluster->getArrayIndex(), mcFinder, Const::PXD);
            ++hitCounter;
            ndf += 2;
          }
        }
 
        B2DEBUG(20, "     add " << hitCounter << " PXDClusters. " << relatedClusters.size() - hitCounter <<
                " PXDClusters were not added because they do not have a corresponding PXDTrueHit");
      } // next trackMCParticle
 
      if (hitCounter < m_minPXDHits) {
        ++m_notEnoughtHitsCounter;
        continue; //goto next mcParticle, do not make track candidate
      }
    } // end if m_usePXDHits
 
    // create a list containing the indices to the SVDHits that belong to one track
    if (m_useSVDHits) {
      int hitCounter = 0;
      for (const MCParticle* trackMCParticle : trackMCParticles) {
        const RelationVector<SVDCluster>& relatedClusters = trackMCParticle->getRelationsFrom<SVDCluster>();
 
        for (size_t i = 0; i < relatedClusters.size(); ++i) {
          bool isReassigned = relatedClusters.weight(i) < 0;
          if (!m_useReassignedHits && isReassigned) continue;  // skip hits from secondary particles
 
          auto mcFinder = RecoHitInformation::OriginTrackFinder::c_MCTrackFinderPriorityHit;
 
          // Reassigned hits are auxiliary
          if (isReassigned) {
            mcFinder = RecoHitInformation::OriginTrackFinder::c_MCTrackFinderAuxiliaryHit;
          }
 
          // Mark higher order hits as auxiliary, if m_useNLoops has been set
          if (std::isfinite(m_useNLoops) and not isWithinNLoops<SVDCluster, SVDTrueHit>(Bz, relatedClusters.object(i), m_useNLoops)) {
            mcFinder = RecoHitInformation::OriginTrackFinder::c_MCTrackFinderAuxiliaryHit;
          }
 
          // if flag is set discard all auxiliary hits:
          if (m_discardAuxiliaryHits and mcFinder == RecoHitInformation::OriginTrackFinder::c_MCTrackFinderAuxiliaryHit) continue;
 
          const SVDCluster* svdCluster = relatedClusters.object(i);
          const RelationVector<SVDTrueHit>& relatedTrueHits = svdCluster->getRelationsTo<SVDTrueHit>();
 
          if (relatedTrueHits.size() == 0 and m_enforceTrueHit) {
            // there is not trueHit! throw away hit because there is no time information for sorting
            ++m_noTrueHitCounter;
            continue;
          }
 
          float time = NAN;
          for (const SVDTrueHit& svdTrueHit : relatedTrueHits) {
            // Make sure only a true hit is taken that really comes from the current mcParticle.
            // This must be carefully checked because several trueHits from different real tracks can be melted into one cluster
            const RelationVector<MCParticle>& relatedMCParticles = svdTrueHit.getRelationsFrom<MCParticle>();
            if (std::find_if(relatedMCParticles.begin(),
                             relatedMCParticles.end(),
            [trackMCParticle](const MCParticle & mcParticle) {
            return &mcParticle == trackMCParticle;
          }) != relatedMCParticles.end()) {
              time = svdTrueHit.getGlobalTime();
              break;
            }
          }
          if (not std::isnan(time)) {
            hitsWithTimeAndDetectorInformation.emplace_back(time, svdCluster->getArrayIndex(), mcFinder, Const::SVD);
            ++hitCounter;
            ndf += 1;
          }
        }
 
        B2DEBUG(20, "     add " << hitCounter << " SVDClusters. " << relatedClusters.size() - hitCounter <<
                " SVDClusters were not added because they do not have a corresponding SVDTrueHit");
      }
 
      if (hitCounter < m_minSVDHits) {
        ++m_notEnoughtHitsCounter;
        continue; //goto next mcParticle, do not make track candidate
      }
    } // end if m_useSVDHits
 
 
    auto didParticleExitCDC = [](const CDCHit * hit) {
      const CDCSimHit* simHit = hit->getRelated<CDCSimHit>();
      if (not simHit) return false;
 
      const MCParticle* mcParticle = simHit->getRelated<MCParticle>();
      if (not mcParticle) return false;
      if (not mcParticle->hasSeenInDetector(Const::TOP)) return false;
 
      RelationVector<TOPBarHit> topHits = mcParticle->getRelationsWith<TOPBarHit>();
      if (topHits.size() == 0) return false;
 
      // Get hit with the smallest time.
      auto lessTime = [](const TOPBarHit & lhs, const TOPBarHit & rhs) {
        return lhs.getTime() < rhs.getTime();
      };
      auto itFirstTopHit = std::min_element(topHits.begin(), topHits.end(), lessTime);
 
      return simHit->getGlobalTime() > itFirstTopHit->getTime();
    };
 
    if (m_useCDCHits) {
      // create a list containing the indices to the CDCHits that belong to one track
      int nAxialHits = 0;
      int nStereoHits = 0;
      std::array<int, 9> nHitsBySuperLayerId{};
 
      for (const MCParticle* trackMCParticle : trackMCParticles) {
        const RelationVector<CDCHit>& relatedHits = trackMCParticle->getRelationsTo<CDCHit>();
 
        for (size_t i = 0; i < relatedHits.size(); ++i) {
          bool isReassigned = relatedHits.weight(i) < 0;
          if (!m_useReassignedHits && isReassigned) continue;  // skip hits from secondary particles
 
          const CDCHit* cdcHit = relatedHits.object(i);
 
          // continue if this is a 2nd CDC hit information and we do not want to use it
          if (!m_useSecondCDCHits && cdcHit->is2ndHit()) {
            continue;
          }
 
          auto mcFinder = RecoHitInformation::OriginTrackFinder::c_MCTrackFinderPriorityHit;
 
          // Reassigned hits are auxiliary
          if (isReassigned) {
            mcFinder = RecoHitInformation::OriginTrackFinder::c_MCTrackFinderAuxiliaryHit;
          }
 
          // Mark higher order hits as auxiliary, if m_useNLoops has been set
          if (std::isfinite(m_useNLoops) and not isWithinNLoops<CDCHit, CDCSimHit>(Bz, cdcHit, m_useNLoops)) {
            mcFinder = RecoHitInformation::OriginTrackFinder::c_MCTrackFinderAuxiliaryHit;
          }
 
          // check if the particle left hits in TOP and add mark hits after that as auxiliary.
          if (m_useOnlyBeforeTOP and didParticleExitCDC(cdcHit)) {
            mcFinder = RecoHitInformation::OriginTrackFinder::c_MCTrackFinderAuxiliaryHit;
          }
 
          // if flag is set discard all auxiliary hits:
          if (m_discardAuxiliaryHits and mcFinder == RecoHitInformation::OriginTrackFinder::c_MCTrackFinderAuxiliaryHit) continue;
 
          int superLayerId = cdcHit->getISuperLayer();
 
          const CDCSimHit* aCDCSimHitPtr = cdcHit->getRelatedFrom<CDCSimHit>();
          if (not aCDCSimHitPtr) {
            B2DEBUG(20, "     Skipping CDCHit without related CDCSimHit.");
            continue;
          }
          double time = aCDCSimHitPtr->getFlightTime();
 
          // Here it is hardcoded what superlayer has axial wires and what has stereo wires.
          // Maybe it would be better if the WireId would know this
          if (superLayerId % 2 == 0) {
            hitsWithTimeAndDetectorInformation.emplace_back(time, cdcHit->getArrayIndex(), mcFinder, Const::CDC);
            ndf += 1;
            ++nAxialHits;
            ++nHitsBySuperLayerId[superLayerId];
          } else {
            if (not m_useOnlyAxialCDCHits) {
              hitsWithTimeAndDetectorInformation.emplace_back(time, cdcHit->getArrayIndex(), mcFinder, Const::CDC);
              ndf += 1;
              ++nStereoHits;
              ++nHitsBySuperLayerId[superLayerId];
            }
          }
        }
      } // next trackMCParticle
      B2DEBUG(20, "    added " << nAxialHits << " axial and " << nStereoHits << " stereo CDCHits");
      if (nAxialHits < m_minCDCAxialHits) {
        // Not enough axial hits. Next MCParticle.
        ++m_notEnoughtHitsCounter;
        continue;
      }
 
      if (not m_useOnlyAxialCDCHits and (nStereoHits < m_minCDCStereoHits)) {
        if (m_allowFirstCDCSuperLayerOnly and
            nHitsBySuperLayerId[0] == nAxialHits and
            (nAxialHits + nStereoHits >= m_minCDCAxialHits + m_minCDCStereoHits)) {
          // Special rule for low momentum tracks that only touch the first axial superlayer
          // If there still enough hits combined from the axial and stereo hit limit -> keep the track.
        } else {
          // Not enough stereo hits. Next MCParticle.
          ++m_notEnoughtHitsCounter;
          continue;
        }
      }
    } // end if m_useCDCHits
 
    if (m_initialCov(0, 0) > 0.0) { //using a user set initial cov and corresponding smearing of inital state adds information
      ndf += 5;
    }
    if (ndf < m_minimalNdf) {
      ++m_notEnoughtHitsCounter;
      continue; //goto next mcParticle, do not make track candidate
    }
 
    std::sort(hitsWithTimeAndDetectorInformation.begin(), hitsWithTimeAndDetectorInformation.end(),
    [](const TimeHitIDDetector & rhs, const TimeHitIDDetector & lhs) {
      return std::get<0>(rhs) < std::get<0>(lhs);
    });
 
    // Now create vectors of vectors, which will either contain hits the full vector WithTimeanddetectorInformation
    // or slices of it, when cutting SplitAfterDeltaT is positive, each slice corresponding to a (sub-) reco track
    // created by the MC particle.
    std::vector< std::vector<TimeHitIDDetector> > hitsWithTimeAndDetectorInformationVectors;
 
    if (m_splitAfterDeltaT < 0.0) { // no splitting, vector will only contain a single hitInformation vector
      hitsWithTimeAndDetectorInformationVectors.push_back(hitsWithTimeAndDetectorInformation);
    } else { // split on delta t
 
      std::vector<TimeHitIDDetector>::size_type splitFromIdx = 0; // whenever splitting subtrack, start slice from this index
      for (std::vector<TimeHitIDDetector>::size_type i = 1; i != hitsWithTimeAndDetectorInformation.size(); i++) {
 
        double delta_t = (std::get<0>(hitsWithTimeAndDetectorInformation[i])
                          - std::get<0>(hitsWithTimeAndDetectorInformation[i - 1]));
 
        if (delta_t > m_splitAfterDeltaT) {
          // push slice of `hitsWithTimeAndDetectorInformation' between splitFromidx  and previous index
          hitsWithTimeAndDetectorInformationVectors
          .emplace_back(hitsWithTimeAndDetectorInformation.begin() + splitFromIdx,
                        hitsWithTimeAndDetectorInformation.begin() + i);
          splitFromIdx = i;
        }
      }
      // add subtrack after last splitting to list of tracks
      hitsWithTimeAndDetectorInformationVectors
      .emplace_back(hitsWithTimeAndDetectorInformation.begin() + splitFromIdx,
                    hitsWithTimeAndDetectorInformation.end());
    }
 
    //Now create TrackCandidate
    int counter = recoTracks.getEntries();
    B2DEBUG(20, "We came pass all filter of the MCPartile and hit properties. TrackCandidate " << counter <<
            " will be created from the MCParticle with index: " << iPart << " (PDG: " << aMcParticlePtr->getPDG() << ")");
 
 
 
    //set track parameters from MCParticle information
    TVector3 positionTrue = aMcParticlePtr->getProductionVertex();
    TVector3 momentumTrue = aMcParticlePtr->getMomentum();
    double timeTrue = aMcParticlePtr->getProductionTime();
 
    // if no kind of smearing is activated the initial values (seeds) for track fit will be the simulated truth
    TVector3 momentum = momentumTrue;
    TVector3 position = positionTrue;
    double time = timeTrue;
    TVectorD stateSeed(6); //this will
    TMatrixDSym covSeed(6);
    covSeed.Zero(); // just to be save
    covSeed(0, 0) = 1; covSeed(1, 1) = 1; covSeed(2, 2) = 2 * 2;
    covSeed(3, 3) = 0.1 * 0.1; covSeed(4, 4) = 0.1 * 0.1; covSeed(5, 5) = 0.2 * 0.2;
    //it may have positive effect on the fit not to start with exactly precise true values (or it may be just interesting to study this)
    //one can smear the starting momentum values with a gaussian
    //this calculation is always performed, but with the default value of m_smearing = 0 it has no effect on momentum and position (true values are taken)
 
    if (m_smearing > 0.0) {
      double smearing = m_smearing / 100.0;  //the module parameter m_smearing goes from 0 to 100, smearing should go from 0 to 1
 
      double smearedX = gRandom->Gaus(positionTrue.x(), smearing * positionTrue.x());
      double smearedY = gRandom->Gaus(positionTrue.y(), smearing * positionTrue.y());
      double smearedZ = gRandom->Gaus(positionTrue.z(), smearing * positionTrue.z());
      position.SetXYZ(smearedX, smearedY, smearedZ);
      double smearedPX = gRandom->Gaus(momentumTrue.x(), smearing * momentumTrue.x());
      double smearedPY = gRandom->Gaus(momentumTrue.y(), smearing * momentumTrue.y());
      double smearedPZ = gRandom->Gaus(momentumTrue.z(), smearing * momentumTrue.z());
      momentum.SetXYZ(smearedPX, smearedPY, smearedPZ);
    }
 
    //Errors for the position/momentum values can also be passed to genfit::TrackCandidate
    //Default values in Genfit are (1.,1.,1.,), they seem to be not good!!
    //The best way to set the 'correct' errors has to be investigated....
    if (m_initialCov(0, 0) > 0.0) { // alternative seamring with according to a covariance matrix
      double smearedX = gRandom->Gaus(positionTrue.x(), sqrt(m_initialCov(0, 0)));
      double smearedY = gRandom->Gaus(positionTrue.y(), sqrt(m_initialCov(1, 1)));
      double smearedZ = gRandom->Gaus(positionTrue.z(), sqrt(m_initialCov(2, 2)));
      position.SetXYZ(smearedX, smearedY, smearedZ);
      double smearedPX = gRandom->Gaus(momentumTrue.x(), sqrt(m_initialCov(3, 3)));
      double smearedPY = gRandom->Gaus(momentumTrue.y(), sqrt(m_initialCov(4, 4)));
      double smearedPZ = gRandom->Gaus(momentumTrue.z(), sqrt(m_initialCov(5, 5)));
      momentum.SetXYZ(smearedPX, smearedPY, smearedPZ);
      covSeed = m_initialCov;
    }
 
    // Finally create RecoTracks for MC particle.
    // Either only one or multiple tracks, if SplitAfterDeltaT is positive
    for (const auto& hitInformationVector : hitsWithTimeAndDetectorInformationVectors) {
 
      // TODO: In former times, the track candidate also stored the PDG code!!!
      short int charge = static_cast<short int>(aMcParticlePtr->getCharge());
 
      // extrapolate the position and momentum to the point of the first hit on the helix
      if (hitInformationVector.size() != 0) {
        // reset the time to the time of the first hit  (assumes time > production time)
        time = std::get<0>(hitInformationVector.at(0));
        const double deltaT = time - aMcParticlePtr->getProductionTime();
        // build the 4-vector with the smeared momentum
        TLorentzVector lorentzV;
        lorentzV.SetVectM(momentum, aMcParticlePtr->get4Vector().M());
        const double beta_xy = momentum.Perp() / lorentzV.E();
        // calculate arclength in 2D of the track
        const double arclength2D = beta_xy * Const::speedOfLight * deltaT;
 
        // get the position and momentum from the helix at the acrlength corresponding to the first hit
        Belle2::Helix helix = Belle2::Helix(position, momentum, charge, Bz);
        momentum = helix.getMomentumAtArcLength2D(arclength2D, Bz);
        position = helix.getPositionAtArcLength2D(arclength2D);
      }
 
 
      RecoTrack* newRecoTrack = recoTracks.appendNew(position, momentum, charge);
      if (m_setTimeSeed) {
        newRecoTrack->setTimeSeed(time);
      }
      ++m_nRecoTracks;
 
      //create relation between the track candidates and the mcParticle (redundant to saving the MCId)
      newRecoTrack->addRelationTo(aMcParticlePtr);
      B2DEBUG(20, " --- Create relation between genfit::TrackCand " << counter << " and MCParticle " << iPart);
 
      int hitCounter = 0;
      for (const TimeHitIDDetector& hitInformation : hitInformationVector) {
 
        const Const::EDetector& detectorInformation = std::get<3>(hitInformation);
        const int hitID = std::get<1>(hitInformation);
        const auto hitOriginMCFinderType = std::get<2>(hitInformation);
 
 
        if (detectorInformation == Const::CDC) {
          const CDCHit* cdcHit = cdcHits[hitID];
          const CDCSimHit* aCDCSimHitPtr = cdcHit->getRelatedFrom<CDCSimHit>();
 
          //now determine the correct sign to resolve the left right ambiguity in the fitter
          TVector3 simHitPos = aCDCSimHitPtr->getPosTrack();
          TVector3 simMom = aCDCSimHitPtr->getMomentum();
          TVector3 simHitPosOnWire = aCDCSimHitPtr->getPosWire();
 
          CDC::CDCGeometryPar& cdcGeometry = CDC::CDCGeometryPar::Instance();
          const unsigned short isRightHit = cdcGeometry.getNewLeftRightRaw(simHitPosOnWire, simHitPos, simMom);
 
          if (isRightHit) {
            newRecoTrack->addCDCHit(cdcHit, hitCounter, RecoHitInformation::RightLeftInformation::c_right, hitOriginMCFinderType);
          } else {
            newRecoTrack->addCDCHit(cdcHit, hitCounter, RecoHitInformation::RightLeftInformation::c_left, hitOriginMCFinderType);
          }
          B2DEBUG(20, "CDC hit " << hitID << " has reft/right sign " << isRightHit);
        } else if (detectorInformation == Const::PXD) {
          const PXDCluster* pxdCluster = pxdClusters[hitID];
          newRecoTrack->addPXDHit(pxdCluster, hitCounter, hitOriginMCFinderType);
        } else if (detectorInformation == Const::SVD) {
          const SVDCluster* svdCluster = svdClusters[hitID];
          newRecoTrack->addSVDHit(svdCluster, hitCounter, hitOriginMCFinderType);
        }
        ++hitCounter;
      } // end loop over hits
 
      B2DEBUG(20, "New RecoTrack: #PXDHits: " << newRecoTrack->getPXDHitList().size() <<
              " #SVDHits: " << newRecoTrack->getSVDHitList().size() <<
              " #CDCHits: " << newRecoTrack->getCDCHitList().size());
 
    } // end loop over vector
  }//end loop over MCParticles
}
 
 
 
template< class THit, class TSimHit>
bool TrackFinderMCTruthRecoTracksModule::isWithinNLoops(double Bz, const THit* aHit, double nLoops)
{
  // for SVD there are cases with more than one simhit attached
  const RelationVector<TSimHit>& relatedSimHits = aHit->template getRelationsWith<TSimHit>();
 
  // take the first best simhit with mcParticle attached
  const MCParticle* mcParticle = nullptr;
  const TSimHit* aSimHit = nullptr;
  for (const auto& thisSimHit : relatedSimHits) {
    mcParticle = thisSimHit.template getRelated<MCParticle>();
    aSimHit = &thisSimHit;
    if (mcParticle) break;
  }
  if (not mcParticle or not aSimHit) {
    return false;
  }
 
  // subtract the production time here in order for this classification to also work
  // for particles produced at times t' > t0
  const double tof = aSimHit->getGlobalTime() - mcParticle->getProductionTime();
  const double speed = mcParticle->get4Vector().Beta() * Const::speedOfLight;
  const float absMom3D = mcParticle->getMomentum().Mag();
 
  const double loopLength = 2 * M_PI * absMom3D / (Bz * 0.00299792458);
  const double loopTOF =  loopLength / speed;
  if (tof > loopTOF * nLoops) {
    return false;
  } else {
    return true;
  }
}
 
 
 
void TrackFinderMCTruthRecoTracksModule::endRun()
{
  if (m_notEnoughtHitsCounter != 0) {
    B2WARNING(m_notEnoughtHitsCounter << " tracks had not enough hits to have at least " << m_minimalNdf <<
              " number of degrees of freedom (NDF). No Track Candidates were created from them so they will not be passed to the track fitter");
  }
  if (m_noTrueHitCounter != 0) {
    B2WARNING(m_noTrueHitCounter <<
              " cluster hits did not have a relation to a true hit and were therefore not included in a track candidate");
  }
  B2INFO("The MCTrackFinder created a total of " << m_nRecoTracks << " track candidates");
}