ParticleLoaderModule.cc

/**************************************************************************
 * basf2 (Belle II Analysis Software Framework)                           *
 * Author: The Belle II Collaboration                                     *
 *                                                                        *
 * See git log for contributors and copyright holders.                    *
 * This file is licensed under LGPL-3.0, see LICENSE.md.                  *
 **************************************************************************/
 
// Own header.
#include <analysis/modules/ParticleLoader/ParticleLoaderModule.h>
 
// framework aux
#include <framework/logging/Logger.h>
#include <framework/core/ModuleParam.templateDetails.h>
 
// utilities
#include <analysis/dataobjects/ParticleList.h>
#include <analysis/DecayDescriptor/ParticleListName.h>
#include <analysis/utility/PCmsLabTransform.h>
#include <analysis/utility/ValueIndexPairSorting.h>
 
#include <utility>
 
using namespace std;
using namespace Belle2;
 
//-----------------------------------------------------------------
//                 Register module
//-----------------------------------------------------------------
 
REG_MODULE(ParticleLoader);
 
//-----------------------------------------------------------------
//                 Implementation
//-----------------------------------------------------------------
 
ParticleLoaderModule::ParticleLoaderModule() : Module()
 
{
  setDescription("Loads MDST dataobjects as Particle objects to the StoreArray<Particle> and collects them in specified ParticleList.");
  setPropertyFlags(c_ParallelProcessingCertified);
 
  // Add parameters
  addParam("decayStrings", m_decayStrings,
           "List of decay strings (see :ref:`DecayString` for syntax) that specify all output ParticleLists to be created by the module.",
           {});
 
  addParam("useMCParticles", m_useMCParticles,
           "Use MCParticles instead of reconstructed MDST dataobjects (tracks, ECL, KLM, clusters, V0s, ...)", false);
 
  addParam("useROEs", m_useROEs,
           "Use ROE instead of reconstructed MDST dataobjects (tracks, ECL, KLM, clusters, V0s, ...)", false);
 
  addParam("roeMaskName", m_roeMaskName,
           "ROE mask name to load", std::string(RestOfEvent::c_defaultMaskName));
 
  addParam("sourceParticleListName", m_sourceParticleListName,
           "Particle list name from which we need to get ROEs", std::string(""));
 
  addParam("useMissing", m_useMissing,
           "If true, the Particle List will be filled with missing momentum from the ROE and signal particle.", false);
 
  addParam("writeOut", m_writeOut,
           "If true, the output ParticleList will be saved by RootOutput. If false, it will be ignored when writing the file.", false);
 
  addParam("skipInitial", m_skipInitial,
           "If true, initial MCParticles will be skipped (default). If false, initial MCParticles will be included.", true);
 
  addParam("skipNonPrimary", m_skipNonPrimary,
           "If true, the secondary MC particle will be skipped, default is false",
           false);
 
  addParam("addDaughters", m_addDaughters,
           "If true, the particles from the bottom part of the selected particle's decay chain will also be created in the datastore and mother-daughter relations are recursively set",
           false);
 
  addParam("skipNonPrimaryDaughters", m_skipNonPrimaryDaughters,
           "If true, the secondary MC daughters will be skipped, default is false",
           false);
 
  addParam("trackHypothesis", m_trackHypothesis,
           "Track hypothesis to use when loading the particle. By default, use the particle's own hypothesis.",
           0);
 
  addParam("enforceFitHypothesis", m_enforceFitHypothesis,
           "If true, a Particle is only created if a track fit with the particle hypothesis passed to the ParticleLoader is available.",
           m_enforceFitHypothesis);
 
  addParam("useDummy", m_useDummy,
           "Use Dummy instead of reconstructed MDST dataobjects (tracks, ECL, KLM, clusters, V0s, ...)", false);
 
  addParam("dummyMDSTIndex", m_dummyMDSTIndex,
           "mdst index to use for dummy particle", 0);
 
  addParam("dummyCovMatrix", m_dummyCovMatrix,
           "Diagonal value of covariance matrix to use for dummy particle", 10000.);
 
  addParam("dummyTreatAsInvisible", m_dummyTreatAsInvisible,
           "Should treeFitter treat the particle as invisible?", true);
 
  addParam("loadChargedCluster", m_loadChargedCluster,
           "Load neutral Particles from the clusters being matched with the track of the sourceParticleList",
           false);
  addParam("useOnlyMostEnergeticECLCluster", m_useOnlyMostEnergeticECLCluster,
           "If true, the most energetic ECLCluster among ones matching with the Track is used. "
           "If false, all matched ECLCluster are used. "
           "This option is checked only when loadChargedCluster=True.",
           true);
}
 
 
void ParticleLoaderModule::initialize()
{
  B2INFO("ParticleLoader's Summary of Actions:");
 
  if ((int)m_useMCParticles + (int)m_useROEs + (int)m_useDummy + (int)m_loadChargedCluster > 1)
    B2FATAL("The options on how to load the Particle are not valid. The incompatible combination of options is selected. "
            << "useMCParticles: " << m_useMCParticles << ", useROEs: " << m_useROEs << ", useDummy: " << m_useDummy
            << ", loadChargedCluster: " << m_loadChargedCluster);
 
  m_particles.registerInDataStore();
  // regsiter temporary StoreArray of Particles needed for matchedMC variable
  StoreArray<Particle>("tempParticles").registerInDataStore(DataStore::c_DontWriteOut);
  m_particleExtraInfoMap.registerInDataStore();
  //register relations if these things exists
  if (m_mcparticles.isOptional()) {
    m_particles.registerRelationTo(m_mcparticles);
    StoreArray<Particle>("tempParticles").registerRelationTo(m_mcparticles);
  }
  if (m_pidlikelihoods.isOptional()) {
    m_particles.registerRelationTo(m_pidlikelihoods);
  }
  if (m_trackfitresults.isOptional()) {
    m_particles.registerRelationTo(m_trackfitresults);
  }
 
  if (m_useMCParticles) {
    m_mcparticles.isRequired();
  }
 
  if (m_useROEs) {
    m_roes.isRequired();
    m_roes.registerRelationTo(m_particles);
 
    StoreArray<RestOfEvent> nestedRoes("NestedRestOfEvents");
    if (nestedRoes.isOptional())
      nestedRoes.registerRelationTo(m_particles);
  }
 
  if (m_decayStrings.empty()) {
    B2WARNING("Obsolete usage of the ParticleLoader module (load all MDST objects as all possible Particle object types). Specify the particle type via decayStrings module parameter instead.");
  } else {
    for (auto decayString : m_decayStrings) {
 
      // obtain the output particle lists from the decay string
      const bool valid = m_decaydescriptor.init(decayString);
      if (!valid)
        B2ERROR("ParticleLoaderModule::initialize Invalid input DecayString: " << decayString);
 
      // Mother particle
      const DecayDescriptorParticle* mother = m_decaydescriptor.getMother();
      int nProducts = m_decaydescriptor.getNDaughters();
 
      int pdgCode  = mother->getPDGCode();
      // The default list name is "all"
      string listName = mother->getName() + ":all";
 
      // Full name for ROE, dummy, MCParticle, chargedCluster particles, and (anti-)neutrons
      if (m_useROEs or m_useDummy or m_useMCParticles or m_loadChargedCluster or abs(pdgCode) == abs(Const::neutron.getPDGCode()))
        listName = mother->getFullName();
      // Kinks get the label "kink"
      else if (nProducts == 1)
        listName = mother->getName() + ":kink";
      // V0s get the label "V0"
      else if (nProducts > 1)
        listName = mother->getName() + ":V0";
 
      string antiListName = ParticleListName::antiParticleListName(listName);
      bool isSelfConjugatedParticle = (listName == antiListName);
 
      StoreObjPtr<ParticleList> particleList(listName);
      // if the particle list doesn't exist, we have to register it
      if (!particleList.isOptional()) {
        DataStore::EStoreFlags flags = m_writeOut ? DataStore::c_WriteOut : DataStore::c_DontWriteOut;
        particleList.registerInDataStore(flags);
        // Neutrons are not self-conjugated, but we cannot distinguish particle from anti-particle
        if (!isSelfConjugatedParticle and (abs(pdgCode) != abs(Const::neutron.getPDGCode()) or m_useMCParticles)) {
          StoreObjPtr<ParticleList> antiParticleList(antiListName);
          antiParticleList.registerInDataStore(flags);
        }
      } else if (m_useMCParticles) {
        B2WARNING("ParticleList " << listName << " already exists and will not be created again. " <<
                  "Please note that the given options (addDaughters, skipNonPrimaryDaughters, skipNonPrimary, skipInitial) do not apply to "
                  << listName);
      } else if (m_loadChargedCluster) {
        B2WARNING("ParticleList " << listName << " already exists and will not be created again. " <<
                  "Please note that the given option, useOnlyMostEnergeticECLCluster, does not apply to "
                  << listName);
      }
 
      if (not isValidPDGCode(pdgCode) and (m_useMCParticles == false and m_useROEs == false and m_useDummy == false))
        B2ERROR("Invalid particle type requested to be loaded. Set a valid decayString module parameter.");
 
      // if we're not loading MCParticles and we are loading K0S, Lambdas, or photons --> ee then this decaystring is a V0
      bool mdstSourceIsV0 = false;
      if (!m_useMCParticles &&
          (abs(pdgCode) == abs(Const::Kshort.getPDGCode()) || abs(pdgCode) == abs(Const::Lambda.getPDGCode())
           || (abs(pdgCode) == abs(Const::photon.getPDGCode()) && m_addDaughters == true)))
        mdstSourceIsV0 = true;
 
      // if we're not loading MCParticles, and we are loading kaon/pion/muon/charged sigmas with one daughter,
      // then this decaystring is a kink
      bool mdstSourceIsKink = false;
      if (!m_useMCParticles && nProducts == 1 &&
          (abs(pdgCode) == abs(Const::kaon.getPDGCode()) || abs(pdgCode) == abs(Const::pion.getPDGCode())
           || abs(pdgCode) == abs(Const::muon.getPDGCode()) || abs(pdgCode) == abs(3222) || abs(pdgCode) == abs(3112)))
        mdstSourceIsKink = true;
 
      if (mdstSourceIsV0) {
        if (nProducts == 2) {
          m_properties = m_decaydescriptor.getProperty() | mother->getProperty(); // only used for V0s
          if (m_decaydescriptor.getDaughter(0)->getMother()->getPDGCode() * m_decaydescriptor.getDaughter(1)->getMother()->getPDGCode() > 0)
            B2ERROR("MDST source of the particle list is V0, the two daughters should have opposite charge");
        } else {
          B2ERROR("ParticleLoaderModule::initialize Invalid input DecayString " << decayString
                  << ". MDST source of the particle list is V0, DecayString should contain exactly two daughters, as well as the mother particle.");
        }
      } else {
        if (!mdstSourceIsKink && nProducts > 0) {
          if (m_useROEs or m_useDummy) {
            B2INFO("ParticleLoaderModule: Replacing the source particle list name by " <<
                   m_decaydescriptor.getDaughter(0)->getMother()->getFullName()
                   << " all other daughters will be ignored.");
            m_sourceParticleListName = m_decaydescriptor.getDaughter(0)->getMother()->getFullName();
          } else {
            B2ERROR("ParticleLoaderModule::initialize Invalid input DecayString " << decayString
                    << ". DecayString should not contain any daughters, only the mother particle.");
          }
        }
      }
 
      if (m_loadChargedCluster and m_sourceParticleListName == "")
        B2ERROR("The sourceParticleListName is not given. The charged ParticleList is required for the chargedCluster loading.");
 
      // add PList to corresponding collection of Lists
      if (isSelfConjugatedParticle or (abs(pdgCode) == Const::neutron.getPDGCode() and not m_useMCParticles))
        B2INFO(" o) creating ParticleList with name: " << listName);
      else
        B2INFO(" o) creating (anti-)ParticleList with name: " << listName << " (" << antiListName << ")");
      if (m_useROEs) {
        B2INFO("   -> MDST source: RestOfEvents");
        m_ROE2Plists.emplace_back(pdgCode, listName, antiListName, isSelfConjugatedParticle);
      } else if (m_useDummy) {
        B2INFO("   -> MDST source: No MDST source");
        m_Dummies2Plists.emplace_back(pdgCode, listName, antiListName, isSelfConjugatedParticle);
      } else if (m_useMCParticles) {
        B2INFO("   -> MDST source: MCParticles");
        m_MCParticles2Plists.emplace_back(pdgCode, listName, antiListName, isSelfConjugatedParticle);
      } else if (m_loadChargedCluster) {
        if (abs(pdgCode) == abs(Const::photon.getPDGCode()) || abs(pdgCode) == abs(Const::Klong.getPDGCode())
            || abs(pdgCode) == abs(Const::neutron.getPDGCode())) {
          m_ChargedCluster2Plists.emplace_back(pdgCode, listName, antiListName, isSelfConjugatedParticle);
          B2INFO("   -> MDST source: ECLClusters and KLMClusters being matched with Tracks");
        } else {
          B2ERROR("The Particle type must be gamma, K_L0, or (anti-)n0 for the loadChargedCluster option.");
        }
      } else {
        bool chargedFSP = Const::chargedStableSet.contains(Const::ParticleType(abs(pdgCode)));
        if (chargedFSP) {
          if (!mdstSourceIsKink) {
            B2INFO("   -> MDST source: Tracks");
            m_Tracks2Plists.emplace_back(pdgCode, listName, antiListName, isSelfConjugatedParticle);
          } else {
            B2INFO("   -> MDST source: Kinks");
            m_Kink2Plists.emplace_back(pdgCode, listName, antiListName, isSelfConjugatedParticle);
          }
        }
 
        if (abs(pdgCode) == abs(Const::photon.getPDGCode())) {
          if (m_addDaughters == false) {
            m_ECLKLMClusters2Plists.emplace_back(pdgCode, listName, antiListName, isSelfConjugatedParticle);
            B2INFO("   -> MDST source: ECLClusters and KLMClusters");
          } else {
            B2INFO("   -> MDST source: V0");
            m_V02Plists.emplace_back(pdgCode, listName, antiListName, isSelfConjugatedParticle);
          }
        }
 
        if (abs(pdgCode) == abs(Const::Kshort.getPDGCode())) {
          B2INFO("   -> MDST source: V0");
          m_V02Plists.emplace_back(pdgCode, listName, antiListName, isSelfConjugatedParticle);
        }
 
        if (abs(pdgCode) == abs(Const::Klong.getPDGCode()) || abs(pdgCode) == abs(Const::neutron.getPDGCode())) {
          B2INFO("   -> MDST source: exclusively KLMClusters or exclusively ECLClusters (matching between those not used)");
          m_ECLKLMClusters2Plists.emplace_back(pdgCode, listName, antiListName, isSelfConjugatedParticle);
        }
 
        if (abs(pdgCode) == abs(Const::Lambda.getPDGCode())) {
          B2INFO("   -> MDST source: V0");
          m_V02Plists.emplace_back(pdgCode, listName, antiListName, isSelfConjugatedParticle);
        }
      }
    }
  }
 
 
  m_chargeZeroTrackCounts = std::vector<int>(m_Tracks2Plists.size(), 0);
  m_sameChargeDaughtersV0Counts = std::vector<int>(m_V02Plists.size(), 0);
}
 
void ParticleLoaderModule::event()
{
  if (not m_particleExtraInfoMap) {
    m_particleExtraInfoMap.create();
  }
 
  if (m_useROEs)
    roeToParticles();
  else if (m_useDummy)
    dummyToParticles();
  else if (m_useMCParticles)
    mcParticlesToParticles();
  else if (m_loadChargedCluster)
    chargedClustersToParticles();
  else {
    tracksToParticles();
    eclAndKLMClustersToParticles();
    v0sToParticles();
    kinksToParticles();
 
  }
}
 
void ParticleLoaderModule::terminate()
{
  // report track errors integrated
  for (size_t i = 0; i < m_Tracks2Plists.size(); i++)
    if (m_chargeZeroTrackCounts[i] > 0) {
      auto track2Plist = m_Tracks2Plists[i];
      B2WARNING("There were " << m_chargeZeroTrackCounts[i]
                << " tracks skipped because of zero charge for "
                << get<c_PListName>(track2Plist));
    }
  // report V0 errors integrated
  for (size_t i = 0; i < m_V02Plists.size(); i++)
    if (m_sameChargeDaughtersV0Counts[i] > 0) {
      auto v02Plist = m_V02Plists[i];
      B2WARNING("There were " << m_sameChargeDaughtersV0Counts[i]
                << " v0s skipped because of same charge daughters for "
                << get<c_PListName>(v02Plist));
    }
}
 
 
void ParticleLoaderModule::dummyToParticles()
{
  if (m_Dummies2Plists.empty()) // nothing to do
    return;
  if (m_Dummies2Plists.size() != 1)
    B2ERROR("ParticleLoaderModule::dummyToParticles Multiple particle lists are not supported!");
  auto dummy2Plist = m_Dummies2Plists[0];
  string dummyListName = get<c_PListName>(dummy2Plist);
  string antiDummyListName = get<c_AntiPListName>(dummy2Plist);
  int pdgCode = get<c_PListPDGCode>(dummy2Plist);
  bool isSelfConjugatedParticle = get<c_IsPListSelfConjugated>(dummy2Plist);
 
  StoreObjPtr<ParticleList> plist(dummyListName);
  plist.create();
  plist->initialize(pdgCode, dummyListName);
 
  if (!isSelfConjugatedParticle) {
    StoreObjPtr<ParticleList> antiPlist(antiDummyListName);
    antiPlist.create();
    antiPlist->initialize(-1 * pdgCode, antiDummyListName);
    antiPlist->bindAntiParticleList(*(plist));
  }
 
  TMatrixFSym covariance(7);
  for (int row = 0; row < 7; ++row) { //diag
    covariance(row, row) = m_dummyCovMatrix;
  }
 
  Particle* newPart = nullptr;
  Particle* newAntiPart = nullptr;
 
  auto isFlavored = (isSelfConjugatedParticle) ? Particle::EFlavorType::c_Unflavored : Particle::EFlavorType::c_Flavored;
 
  ROOT::Math::PxPyPzEVector zero4Vector = {0., 0., 0., 0.};
 
  newPart = m_particles.appendNew(zero4Vector, pdgCode, isFlavored, Particle::EParticleSourceObject::c_NoMDSTSource,
                                  m_dummyMDSTIndex);
  if (m_dummyCovMatrix > 0.) newPart->setMomentumVertexErrorMatrix(covariance);
  if (m_dummyTreatAsInvisible) newPart->writeExtraInfo("treeFitterTreatMeAsInvisible", 1);
  plist->addParticle(newPart);
 
  if (!isSelfConjugatedParticle) {
    newAntiPart = m_particles.appendNew(zero4Vector, -pdgCode, isFlavored, Particle::EParticleSourceObject::c_NoMDSTSource,
                                        m_dummyMDSTIndex);
    if (m_dummyCovMatrix > 0.) newAntiPart->setMomentumVertexErrorMatrix(covariance);
    if (m_dummyTreatAsInvisible) newAntiPart->writeExtraInfo("treeFitterTreatMeAsInvisible", 1);
    plist->addParticle(newAntiPart);
  }
 
}
 
 
void ParticleLoaderModule::roeToParticles()
{
  if (m_ROE2Plists.empty()) // nothing to do
    return;
  // Multiple particle lists are not supported
  auto roe2Plist = m_ROE2Plists[0];
  string listName = get<c_PListName>(roe2Plist);
  string antiListName = get<c_AntiPListName>(roe2Plist);
  int pdgCode = get<c_PListPDGCode>(roe2Plist);
  bool isSelfConjugatedParticle = get<c_IsPListSelfConjugated>(roe2Plist);
 
  StoreObjPtr<ParticleList> plist(listName);
  // since a particle list in the ParticleLoader always contains all possible objects
  // we check whether it already exists in this path and can skip any further steps if it does
  if (plist.isValid())
    return;
  plist.create();
  plist->initialize(pdgCode, listName);
 
  if (!isSelfConjugatedParticle) {
    StoreObjPtr<ParticleList> antiPlist(antiListName);
    antiPlist.create();
    antiPlist->initialize(-1 * pdgCode, antiListName);
    antiPlist->bindAntiParticleList(*(plist));
  }
  if (m_sourceParticleListName != "") {
    // Take related ROEs from a particle list
    StoreObjPtr<ParticleList> pList(m_sourceParticleListName);
    if (!pList.isValid())
      B2FATAL("ParticleList " << m_sourceParticleListName << " could not be found or is not valid!");
 
    for (unsigned int i = 0; i < pList->getListSize(); i++) {
      RestOfEvent* roe = pList->getParticle(i)->getRelatedTo<RestOfEvent>("ALL");
      if (!roe) {
        B2ERROR("ParticleList " << m_sourceParticleListName << " has no associated ROEs!");
      } else {
 
        if (isSelfConjugatedParticle)
          addROEToParticleList(roe, i, pdgCode, isSelfConjugatedParticle);
        else if (i < pList->getListSize(false))
          addROEToParticleList(roe, i, pdgCode, isSelfConjugatedParticle);
        else
          addROEToParticleList(roe, i, -1 * pdgCode, isSelfConjugatedParticle);
      }
    }
 
  } else {
    // Take all ROE if no particle list provided
    for (int i = 0; i < m_roes.getEntries(); i++) {
      addROEToParticleList(m_roes[i], i);
    }
  }
}
 
void ParticleLoaderModule::addROEToParticleList(RestOfEvent* roe, int mdstIndex, int pdgCode, bool isSelfConjugatedParticle)
{
 
  Particle* newPart = nullptr;
  if (!m_useMissing) {
    // Convert ROE to particle
    newPart = roe->convertToParticle(m_roeMaskName, pdgCode, isSelfConjugatedParticle);
  } else {
    // Create a particle from missing momentum
    auto* signalSideParticle = roe->getRelatedFrom<Particle>();
    PCmsLabTransform T;
    ROOT::Math::PxPyPzEVector boost4Vector = T.getBeamFourMomentum();
 
    ROOT::Math::PxPyPzEVector signal4Vector = signalSideParticle->get4Vector();
    ROOT::Math::PxPyPzEVector roe4Vector = roe->get4Vector(m_roeMaskName);
    ROOT::Math::PxPyPzEVector missing4Vector = boost4Vector - signal4Vector - roe4Vector;
    auto isFlavored = (isSelfConjugatedParticle) ? Particle::EFlavorType::c_Unflavored : Particle::EFlavorType::c_Flavored;
    newPart = m_particles.appendNew(missing4Vector, pdgCode, isFlavored, Particle::EParticleSourceObject::c_Undefined, mdstIndex);
  }
 
  roe->addRelationTo(newPart);
 
  for (auto roe2Plist : m_ROE2Plists) {
    string listName = get<c_PListName>(roe2Plist);
    StoreObjPtr<ParticleList> plist(listName);
    plist->addParticle(newPart);
  }
}
 
 
void ParticleLoaderModule::v0sToParticles()
{
  if (m_V02Plists.empty()) // nothing to do
    return;
 
  // check if the order of the daughters in the decay string (decided by the user) is the same as the v0 daughters' order (fixed)
  bool matchingDaughtersOrder = true;
  if (m_decaydescriptor.getDaughter(0)->getMother()->getPDGCode() < 0
      && m_decaydescriptor.getDaughter(1)->getMother()->getPDGCode() > 0)
    matchingDaughtersOrder = false;
 
  // loop over all ParticleLists
  for (size_t ilist = 0; ilist < m_V02Plists.size(); ilist++) {
    auto v02Plist = m_V02Plists[ilist];
    string listName = get<c_PListName>(v02Plist);
    string antiListName = get<c_AntiPListName>(v02Plist);
    int pdgCode = get<c_PListPDGCode>(v02Plist);
    bool isSelfConjugatedParticle = get<c_IsPListSelfConjugated>(v02Plist);
 
    StoreObjPtr<ParticleList> plist(listName);
    // since a particle list in the ParticleLoader always contains all possible objects
    // we check whether it already exists in this path and can skip any further steps if it does
    if (plist.isValid())
      continue;
    plist.create();
    plist->initialize(pdgCode, listName);
 
    if (!isSelfConjugatedParticle) {
      StoreObjPtr<ParticleList> antiPlist(antiListName);
      antiPlist.create();
      antiPlist->initialize(-1 * pdgCode, antiListName);
 
      antiPlist->bindAntiParticleList(*(plist));
    }
 
    plist->setEditable(true); // :V0 list is originally reserved. we have to set it as editable.
 
    // load reconstructed V0s as Kshorts (pi-pi+ combination), Lambdas (p+pi- combinations), and converted photons (e-e+ combinations)
    for (int i = 0; i < m_v0s.getEntries(); i++) {
      const V0* v0 = m_v0s[i];
      Const::ParticleType v0Type = v0->getV0Hypothesis();
 
      if (abs(pdgCode) != abs(v0Type.getPDGCode()))
        continue;
 
      // check if the charge of the 2 V0's daughters is opposite
      if (v0->getTrackFitResults().first->getChargeSign() == v0->getTrackFitResults().second->getChargeSign()) {
        B2DEBUG(19, "V0 with same charge daughters skipped!");
        m_sameChargeDaughtersV0Counts[ilist]++;
        continue;
      }
 
      Const::ChargedStable pTypeP(Const::pion);
      Const::ChargedStable pTypeM(Const::pion);
      Particle::EFlavorType v0FlavorType = Particle::c_Unflavored;
 
      if (v0Type.getPDGCode() == Const::Kshort.getPDGCode()) { // K0s -> pi+ pi-
        pTypeP = Const::pion;
        pTypeM = Const::pion;
      } else if (v0Type.getPDGCode() == Const::Lambda.getPDGCode()) { // Lambda -> p+ pi-
        pTypeP = Const::proton;
        pTypeM = Const::pion;
        v0FlavorType = Particle::c_Flavored; // K0s are not flavoured, lambdas are
      } else if (v0Type.getPDGCode() == Const::antiLambda.getPDGCode()) { // anti-Lambda -> pi+ anti-p-
        pTypeP = Const::pion;
        pTypeM = Const::proton;
        v0FlavorType = Particle::c_Flavored;
      } else if (v0Type.getPDGCode() == Const::photon.getPDGCode()) { // gamma -> e+ e-
        pTypeP = Const::electron;
        pTypeM = Const::electron;
      } else {
        B2WARNING("Unknown V0 hypothesis!");
      }
 
      // check if, given the initial user's decay descriptor, the current v0 is a particle or an anti-particle.
      // in the V0 the order of the daughters is fixed, first the positive and then the negative; to be coherent with the decay descriptor, when creating
      // one particle list and one anti-particle, the v0 daughters' order has to be switched only in one case
      bool correctOrder = matchingDaughtersOrder;
      if (abs(v0Type.getPDGCode()) == abs(m_decaydescriptor.getMother()->getPDGCode())
          && v0Type.getPDGCode() != m_decaydescriptor.getMother()->getPDGCode())
        correctOrder = !correctOrder;
 
      std::pair<Track*, Track*> v0Tracks = v0->getTracks();
      std::pair<TrackFitResult*, TrackFitResult*> v0TrackFitResults = v0->getTrackFitResults();
 
      Particle daugP((v0Tracks.first)->getArrayIndex(), v0TrackFitResults.first, pTypeP);
      Particle daugM((v0Tracks.second)->getArrayIndex(), v0TrackFitResults.second, pTypeM);
 
      const PIDLikelihood* pidP = (v0Tracks.first)->getRelated<PIDLikelihood>();
      const PIDLikelihood* pidM = (v0Tracks.second)->getRelated<PIDLikelihood>();
 
      const auto& mcParticlePWithWeight = (v0Tracks.first)->getRelatedToWithWeight<MCParticle>();
      const auto& mcParticleMWithWeight = (v0Tracks.second)->getRelatedToWithWeight<MCParticle>();
 
      // add V0 daughters to the Particle StoreArray
      Particle* newDaugP;
      Particle* newDaugM;
 
      if (correctOrder) {
        newDaugP = m_particles.appendNew(daugP);
        newDaugM = m_particles.appendNew(daugM);
      } else {
        newDaugM = m_particles.appendNew(daugM);
        newDaugP = m_particles.appendNew(daugP);
      }
 
      // if there are PIDLikelihoods and MCParticles then also add relations to the particles
      if (pidP)
        newDaugP->addRelationTo(pidP);
      if (mcParticlePWithWeight.first)
        newDaugP->addRelationTo(mcParticlePWithWeight.first, mcParticlePWithWeight.second);
      newDaugP->addRelationTo(v0TrackFitResults.first);
 
      if (pidM)
        newDaugM->addRelationTo(pidM);
      if (mcParticleMWithWeight.first)
        newDaugM->addRelationTo(mcParticleMWithWeight.first, mcParticleMWithWeight.second);
      newDaugM->addRelationTo(v0TrackFitResults.second);
 
      // sum the 4-momenta of the daughters and construct a particle object
      ROOT::Math::PxPyPzEVector v0Momentum = newDaugP->get4Vector() + newDaugM->get4Vector();
      Particle v0P(v0Momentum, v0Type.getPDGCode(), v0FlavorType,
                   Particle::EParticleSourceObject::c_V0, v0->getArrayIndex());
      v0P.setProperty(m_properties);
 
      // add the daughters of the V0 (in the correct order) and don't update
      // the type to c_Composite (i.e. maintain c_V0)
      if (correctOrder) {
        v0P.appendDaughter(newDaugP, false);
        v0P.appendDaughter(newDaugM, false);
      } else {
        v0P.appendDaughter(newDaugM, false);
        v0P.appendDaughter(newDaugP, false);
      }
 
      // append the particle to the Particle StoreArray and add the new particle to the ParticleList
      Particle* newPart = m_particles.appendNew(v0P);
      plist->addParticle(newPart);
    }
 
    plist->setEditable(false); // set the :V0 list as not editable.
  }
}
 
void ParticleLoaderModule::kinksToParticles()
{
 
  if (m_Kink2Plists.empty()) // nothing to do
    return;
 
  // loop over all ParticleLists
  for (size_t ilist = 0; ilist < m_Kink2Plists.size(); ilist++) {
    auto kink2Plist = m_Kink2Plists[ilist];
    string listName = get<c_PListName>(kink2Plist);
    string antiListName = get<c_AntiPListName>(kink2Plist);
    int pdgCode = get<c_PListPDGCode>(kink2Plist);
    bool isSelfConjugatedParticle = get<c_IsPListSelfConjugated>(kink2Plist);
 
    StoreObjPtr<ParticleList> plist(listName);
    // since a particle list in the ParticleLoader always contains all possible objects
    // we check whether it already exists in this path and can skip any further steps if it does
    if (plist.isValid())
      continue;
    plist.create();
    plist->initialize(pdgCode, listName);
 
    if (!isSelfConjugatedParticle) {
      StoreObjPtr<ParticleList> antiPlist(antiListName);
      antiPlist.create();
      antiPlist->initialize(-1 * pdgCode, antiListName);
 
      antiPlist->bindAntiParticleList(*(plist));
    }
 
    plist->setEditable(true); // :kink list is originally reserved. we have to set it as editable.
 
    // load reconstructed Kinks according to requested mother hypothesis
    for (int i = 0; i < m_kinks.getEntries(); i++) {
      const Kink* kink = m_kinks[i];
 
      Const::ChargedStable motherType(abs(pdgCode));
      const Track* motherTrack = kink->getMotherTrack();
      const TrackFitResult* motherTrackFit = kink->getMotherTrackFitResultStart();
 
      int motherCharge = motherTrackFit->getChargeSign();
      if (motherCharge == 0) {
        B2DEBUG(19, "Kink track with charge = 0 skipped!");
        continue;
      }
 
      const auto& motherMCParticleWithWeight = motherTrack->getRelatedToWithWeight<MCParticle>();
      const PIDLikelihood* motherPID = motherTrack->getRelated<PIDLikelihood>();
 
      // a particle object creation from kink mother with the correct option
      Particle kinkP(kink, motherType, kink->getTrackFitResultIndexMotherStart());
 
      // append the particle to the Particle StoreArray
      Particle* newPart = m_particles.appendNew(kinkP);
 
      if (motherPID)
        newPart->addRelationTo(motherPID);
      if (motherMCParticleWithWeight.first)
        newPart->addRelationTo(motherMCParticleWithWeight.first, motherMCParticleWithWeight.second);
      newPart->writeExtraInfo("kinkDaughterPDGCode", m_decaydescriptor.getDaughter(0)->getMother()->getPDGCode());
 
      // add the new particle to the ParticleList
      plist->addParticle(newPart);
    }
 
    plist->setEditable(false); // set the :kink list as not editable.
  }
}
 
void ParticleLoaderModule::tracksToParticles()
{
  if (m_Tracks2Plists.empty()) // nothing to do
    return;
 
  // loop over all requested particle lists
  for (size_t ilist = 0; ilist < m_Tracks2Plists.size(); ilist++) {
    auto track2Plist = m_Tracks2Plists[ilist];
    string listName = get<c_PListName>(track2Plist);
    string antiListName = get<c_AntiPListName>(track2Plist);
    int pdgCode = get<c_PListPDGCode>(track2Plist);
    bool isSelfConjugatedParticle = get<c_IsPListSelfConjugated>(track2Plist);
 
    StoreObjPtr<ParticleList> plist(listName);
    // since a particle list in the ParticleLoader always contains all possible objects
    // we check whether it already exists in this path and can skip any further steps if it does
    if (plist.isValid())
      continue;
    plist.create();
    plist->initialize(pdgCode, listName);
 
    // if cc exists then also create and bind that list
    if (!isSelfConjugatedParticle) {
      StoreObjPtr<ParticleList> antiPlist(antiListName);
      antiPlist.create();
      antiPlist->initialize(-1 * pdgCode, antiListName);
 
      antiPlist->bindAntiParticleList(*(plist));
    }
 
    plist->setEditable(true); // :all list is originally reserved. we have to set it as editable.
 
    // the inner loop over all tracks from which Particles
    // are created, and get sorted in the particle lists
    for (int i = 0; i < m_tracks.getEntries(); i++) {
      const Track* track = m_tracks[i];
      const PIDLikelihood* pid = track->getRelated<PIDLikelihood>();
      const auto& mcParticleWithWeight = track->getRelatedToWithWeight<MCParticle>();
 
      // if a special track hypothesis is requested, use it
      if (m_trackHypothesis != 0) pdgCode = m_trackHypothesis;
      Const::ChargedStable type(abs(pdgCode));
 
      // load the TrackFitResult for the requested particle or if not available use
      // the one with the closest mass
      const TrackFitResult* trackFit = track->getTrackFitResultWithClosestMass(type);
 
      if (!trackFit) { // should never happen with the "closest mass" getter - leave as a sanity check
        B2WARNING("Track returned null TrackFitResult pointer for ChargedStable::getPDGCode()  = " << type.getPDGCode());
        continue;
      }
 
      if (m_enforceFitHypothesis && (trackFit->getParticleType().getPDGCode() != type.getPDGCode())) {
        // the required hypothesis does not exist for this track, skip it
        continue;
      }
 
      // charge zero tracks can appear, filter them and
      // count number of tracks filtered out
      int charge = trackFit->getChargeSign();
      if (charge == 0) {
        B2DEBUG(19, "Track with charge = 0 skipped!");
        m_chargeZeroTrackCounts[ilist]++;
        continue;
      }
 
      // create particle and add it to the Particle list.
      Particle particle(track->getArrayIndex(), trackFit, type);
 
      if (particle.getParticleSource() == Particle::c_Track) { // should always hold but...
 
        Particle* newPart = m_particles.appendNew(particle);
        if (pid)
          newPart->addRelationTo(pid);
        if (mcParticleWithWeight.first)
          newPart->addRelationTo(mcParticleWithWeight.first, mcParticleWithWeight.second);
        newPart->addRelationTo(trackFit);
 
        plist->addParticle(newPart);
 
      } // sanity check correct particle type
    } // loop over tracks
 
    plist->setEditable(false); // set the :all list as not editable.
  } // particle lists
}
 
void ParticleLoaderModule::eclAndKLMClustersToParticles()
{
  if (m_ECLKLMClusters2Plists.empty()) // nothing to do
    return;
 
  // loop over all ParticleLists
  for (auto eclKLMCluster2Plist : m_ECLKLMClusters2Plists) {
    string listName = get<c_PListName>(eclKLMCluster2Plist);
    int pdgCode = get<c_PListPDGCode>(eclKLMCluster2Plist);
    Const::ParticleType thisType(pdgCode);
 
    StoreObjPtr<ParticleList> plist(listName);
    // since a particle list in the ParticleLoader always contains all possible objects
    // we check whether it already exists in this path and can skip any further steps if it does
    if (plist.isValid())
      continue;
    plist.create();
    plist->initialize(pdgCode, listName);
 
    plist->setEditable(true); // :all list is originally reserved. we have to set it as editable.
 
    // load reconstructed neutral ECL clusters as photons or Klongs or neutrons
    for (int i = 0; i < m_eclclusters.getEntries(); i++) {
      const ECLCluster* cluster      = m_eclclusters[i];
 
      if (!isValidECLCluster(cluster, pdgCode, true))
        continue;
 
      // create particle and check it before adding to list
      Particle particle(cluster, thisType);
      if (particle.getParticleSource() != Particle::c_ECLCluster) {
        B2FATAL("Particle created from ECLCluster does not have ECLCluster type.");
        continue;
      }
      Particle* newPart = m_particles.appendNew(particle);
 
      assignMCParticleFromECLCluster(newPart, cluster);
 
      // add particle to list
      plist->addParticle(newPart);
    }
 
    // load reconstructed KLM clusters as Klongs or neutrons or photons
    for (int i = 0; i < m_klmclusters.getEntries(); i++) {
      const KLMCluster* cluster      = m_klmclusters[i];
 
      if (std::isnan(cluster->getMomentumMag())) {
        B2DEBUG(19, "Skipping KLMCluster because its momentum is NaN. "
                "This can happen if the timing calibration is missing or wrong, so that the velocity is calculated to be negative.");
        continue;
      }
 
      const MCParticle* mcParticle = cluster->getRelated<MCParticle>();
 
      // create particle and check its type before adding it to list
      Particle particle(cluster, pdgCode);
      if (particle.getParticleSource() != Particle::c_KLMCluster) {
        B2FATAL("Particle created from KLMCluster does not have KLMCluster type.");
      }
      Particle* newPart = m_particles.appendNew(particle);
 
      if (mcParticle)
        newPart->addRelationTo(mcParticle);
 
      // add particle to list
      plist->addParticle(newPart);
    }
 
    plist->setEditable(false); // set the :all list as not editable.
  } // loop over particle lists
}
 
bool ParticleLoaderModule::isValidECLCluster(const ECLCluster* cluster, const int pdgCode, bool onlyNeutral) const
{
  if (!cluster)
    return false;
 
  // ECLClusters can be reconstructed under different hypotheses, for
  // example photons or neutral hadrons, we only load particles from these
  // for now
  if (!cluster->isNeutral() and onlyNeutral)
    return false;
 
  if (not cluster->hasHypothesis(ECLCluster::EHypothesisBit::c_nPhotons)
      and not cluster->hasHypothesis(ECLCluster::EHypothesisBit::c_neutralHadron))
    return false;
 
  // don't fill photon list with clusters that don't have
  // the nPhotons hypothesis (ECL people call this N1)
  if (pdgCode == Const::photon.getPDGCode()
      and not cluster->hasHypothesis(ECLCluster::EHypothesisBit::c_nPhotons))
    return false;
 
  // don't fill a KLong nor a (anti-)neutron list with clusters that don't have the neutral
  // hadron hypothesis set (ECL people call this N2)
  if ((pdgCode == Const::Klong.getPDGCode() or abs(pdgCode) == Const::neutron.getPDGCode())
      and not cluster->hasHypothesis(ECLCluster::EHypothesisBit::c_neutralHadron))
    return false;
 
  return true;
}
 
void ParticleLoaderModule::assignMCParticleFromECLCluster(Particle* newPart, const ECLCluster* cluster) const
{
  // ECLCluster can be matched to multiple MCParticles
  // order the relations by weights and set Particle -> multiple MCParticle relation
  // preserve the weight
  const RelationVector<MCParticle> mcRelations = cluster->getRelationsTo<MCParticle>();
 
  // order relations by weights
  std::vector<std::pair<double, int>> weightsAndIndices;
  for (unsigned int iMCParticle = 0; iMCParticle < mcRelations.size(); iMCParticle++) {
    const MCParticle* relMCParticle = mcRelations[iMCParticle];
    if (relMCParticle) {
      double weight = mcRelations.weight(iMCParticle);
      weightsAndIndices.emplace_back(weight, relMCParticle->getArrayIndex());
    }
  }
 
  // sort descending by weight
  std::sort(weightsAndIndices.begin(), weightsAndIndices.end(),
            ValueIndexPairSorting::higherPair<decltype(weightsAndIndices)::value_type>);
 
  // set relations to mcparticles
  for (auto& weightsAndIndex : weightsAndIndices) {
    const MCParticle* relMCParticle = m_mcparticles[weightsAndIndex.second];
    double weight = weightsAndIndex.first;
 
    // TODO: study this further and avoid hard-coded values
    // set the relation only if the MCParticle(reconstructed Particle)'s
    // energy contribution to this cluster amounts to at least 30(20)%
    if (relMCParticle)
      if (weight / newPart->getECLClusterEnergy() > 0.20
          && weight / relMCParticle->getEnergy() > 0.30)
        newPart->addRelationTo(relMCParticle, weight);
  }
 
}
 
void ParticleLoaderModule::chargedClustersToParticles()
{
  if (m_ChargedCluster2Plists.empty()) // nothing to do
    return;
 
  // loop over all ParticleLists
  for (auto chargedCluster2Plist : m_ChargedCluster2Plists) {
 
    string listName = get<c_PListName>(chargedCluster2Plist);
    string antiListName = get<c_AntiPListName>(chargedCluster2Plist);
    int pdgCode = get<c_PListPDGCode>(chargedCluster2Plist);
    bool isSelfConjugatedParticle = get<c_IsPListSelfConjugated>(chargedCluster2Plist);
    Const::ParticleType thisType(pdgCode);
 
    StoreObjPtr<ParticleList> plist(listName);
    // since a particle list in the ParticleLoader always contains all possible objects
    // we check whether it already exists in this path and can skip any further steps if it does
    if (plist.isValid())
      continue;
    plist.create();
    plist->initialize(pdgCode, listName);
 
    // create anti-particle list if necessary
    if (!isSelfConjugatedParticle) {
      StoreObjPtr<ParticleList> antiPlist(antiListName);
      antiPlist.create();
      antiPlist->initialize(-1 * pdgCode, antiListName);
 
      antiPlist->bindAntiParticleList(*(plist));
    }
 
    const StoreObjPtr<ParticleList> sourceList(m_sourceParticleListName);
    if (!sourceList.isValid())
      B2FATAL("ParticleList " << m_sourceParticleListName << " could not be found or is not valid!");
 
    for (unsigned int iPart = 0; iPart < sourceList->getListSize(); iPart++) {
 
      const Particle* sourcePart = sourceList->getParticle(iPart);
      const Track* sourceTrack = sourceList->getParticle(iPart)->getTrack();
      if (!sourceTrack)
        continue;
 
      // ECL clusters
      if (m_useOnlyMostEnergeticECLCluster) {
 
        const ECLCluster* cluster = sourcePart->getECLCluster();
        if (isValidECLCluster(cluster, pdgCode, false)) {
          Particle particle(cluster, thisType);
          if (particle.getParticleSource() != Particle::c_ECLCluster) {
            B2FATAL("Particle created from ECLCluster does not have ECLCluster type.");
          }
          Particle* newPart = m_particles.appendNew(particle);
          assignMCParticleFromECLCluster(newPart, cluster);
          plist->addParticle(newPart);
        }
      } else {
 
        // loop over all clusters matched to this track
        const RelationVector<ECLCluster> clusters =  sourceTrack->getRelationsTo<ECLCluster>();
        for (unsigned int iCluster = 0; iCluster < clusters.size(); iCluster++) {
          const ECLCluster* cluster = clusters[iCluster];
          if (!isValidECLCluster(cluster, pdgCode, false))
            continue; // go to next iCluster
 
          Particle particle(cluster, thisType);
          if (particle.getParticleSource() != Particle::c_ECLCluster) {
            B2FATAL("Particle created from ECLCluster does not have ECLCluster type.");
          }
          Particle* newPart = m_particles.appendNew(particle);
          assignMCParticleFromECLCluster(newPart, cluster);
          plist->addParticle(newPart);
        }
      }
 
      // KLM clusters
      const KLMCluster* cluster = sourcePart->getKLMCluster();
      if (!cluster) continue; // go to next iPart
 
      if (std::isnan(cluster->getMomentumMag())) {
        B2DEBUG(19, "Skipping KLMCluster because its momentum is NaN. "
                "This can happen if the timing calibration is missing or wrong, so that the velocity is calculated to be negative.");
        continue;
      }
 
      // create particle and check its type before adding it to list
      Particle particle(cluster, pdgCode);
      if (particle.getParticleSource() != Particle::c_KLMCluster) {
        B2FATAL("Particle created from KLMCluster does not have KLMCluster type.");
      }
      Particle* newPart = m_particles.appendNew(particle);
 
      const MCParticle* mcParticle = cluster->getRelated<MCParticle>();
      if (mcParticle) newPart->addRelationTo(mcParticle);
 
      plist->addParticle(newPart);
    }
 
  } // loop over particle lists
}
 
void ParticleLoaderModule::mcParticlesToParticles()
{
  if (m_MCParticles2Plists.empty()) // nothing to do
    return;
 
  // create all lists
  for (auto mcParticle2Plist : m_MCParticles2Plists) {
    string listName = get<c_PListName>(mcParticle2Plist);
    string antiListName = get<c_AntiPListName>(mcParticle2Plist);
    int pdgCode = get<c_PListPDGCode>(mcParticle2Plist);
    bool isSelfConjugatedParticle = get<c_IsPListSelfConjugated>(mcParticle2Plist);
 
    StoreObjPtr<ParticleList> plist(listName);
    if (plist.isValid())
      continue;
    plist.create();
    plist->initialize(pdgCode, listName);
 
    if (!isSelfConjugatedParticle) {
      StoreObjPtr<ParticleList> antiPlist(antiListName);
      antiPlist.create();
      antiPlist->initialize(-1 * pdgCode, antiListName);
 
      antiPlist->bindAntiParticleList(*(plist));
    }
 
    for (int i = 0; i < m_mcparticles.getEntries(); i++) {
      const MCParticle* mcParticle = m_mcparticles[i];
 
      if (abs(pdgCode) != abs(mcParticle->getPDG()))
        continue;
 
      if (m_skipNonPrimary and !mcParticle->hasStatus(MCParticle::c_PrimaryParticle))
        continue;
 
      if (m_skipInitial and mcParticle->isInitial())
        continue;
 
      Particle particle(mcParticle);
      Particle* newPart = m_particles.appendNew(particle);
      newPart->addRelationTo(mcParticle);
 
      //append the whole bottom part of the decay tree to this particle
      if (m_addDaughters) appendDaughtersRecursive(newPart);
 
      plist->addParticle(newPart);
    }
 
  }
}
 
bool ParticleLoaderModule::isValidPDGCode(const int pdgCode)
{
  bool result = false;
 
  // is particle type = charged final state particle?
  if (Const::chargedStableSet.find(abs(pdgCode)) != Const::invalidParticle)
    return true;
 
  if (abs(pdgCode) == abs(Const::photon.getPDGCode()))
    return true;
 
  if (abs(pdgCode) == abs(Const::Kshort.getPDGCode()))
    return true;
 
  if (abs(pdgCode) == abs(Const::Klong.getPDGCode()))
    return true;
 
  if (abs(pdgCode) == abs(Const::Lambda.getPDGCode()))
    return true;
 
  if (abs(pdgCode) == abs(Const::neutron.getPDGCode()))
    return true;
 
  return result;
}
 
void ParticleLoaderModule::appendDaughtersRecursive(Particle* mother)
{
  auto* mcmother = mother->getRelated<MCParticle>();
 
  if (!mcmother)
    return;
 
  vector<MCParticle*> mcdaughters = mcmother->getDaughters();
 
  for (auto& mcdaughter : mcdaughters) {
    if (!mcdaughter->hasStatus(MCParticle::c_PrimaryParticle) and m_skipNonPrimaryDaughters) continue;
    Particle particle(mcdaughter);
    Particle* daughter = m_particles.appendNew(particle);
    daughter->addRelationTo(mcdaughter);
    mother->appendDaughter(daughter, false);
 
    if (mcdaughter->getNDaughters() > 0)
      appendDaughtersRecursive(daughter);
  }
}