TrackingTruthAccumulator.cc

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#include "SimGeneral/TrackingAnalysis/plugins/TrackingTruthAccumulator.h"

#include "SimGeneral/MixingModule/interface/DigiAccumulatorMixModFactory.h"
#include "FWCore/MessageLogger/interface/MessageLogger.h"
#include "FWCore/Framework/interface/ConsumesCollector.h"
#include "FWCore/Framework/interface/Event.h"
#include "FWCore/Framework/interface/EventSetup.h"
#include "FWCore/ParameterSet/interface/ParameterSet.h"
#include "SimGeneral/MixingModule/interface/PileUpEventPrincipal.h"
#include "FWCore/Framework/interface/stream/EDProducer.h"
#include "SimGeneral/TrackingAnalysis/interface/EncodedTruthId.h"
#include "SimDataFormats/GeneratorProducts/interface/HepMCProduct.h"
#include "SimDataFormats/TrackingAnalysis/interface/TrackingParticle.h"
#include "SimDataFormats/TrackingAnalysis/interface/TrackingVertex.h"
#include "SimDataFormats/TrackingHit/interface/PSimHit.h"
#include "FWCore/MessageLogger/interface/MessageLogger.h"

#include "DataFormats/SiPixelDetId/interface/PixelSubdetector.h"
#include "DataFormats/SiStripDetId/interface/StripSubdetector.h"
#include "DataFormats/HepMCCandidate/interface/GenParticle.h"
#include "DataFormats/TrackerCommon/interface/TrackerTopology.h"
#include "Geometry/Records/interface/TrackerTopologyRcd.h"
#include "FWCore/Framework/interface/ESHandle.h"
#include "FWCore/Utilities/interface/isFinite.h"

//Turn on integrity checking
//#define DO_DEBUG_TESTING


//---------------------------------------------------------------------------------
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//------                                                                     ------
//------  Declarations for utility classes and functions in the unnamed      ------
//------  namespace. The definitions are right at the bottom of the file.    ------
//------                                                                     ------
//---------------------------------------------------------------------------------
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namespace
{
    struct DecayChainTrack
    {
        int simTrackIndex;
        struct DecayChainVertex* pParentVertex;
        // Some things have multiple decay vertices. Not sure how that works but it seems to be mostly electrons and some photons.
        std::vector<struct DecayChainVertex*> daughterVertices;
        DecayChainTrack* pMergedBremSource;
        DecayChainTrack() : simTrackIndex(-1), pParentVertex(nullptr), pMergedBremSource(nullptr) {}
        DecayChainTrack( int newSimTrackIndex ) : simTrackIndex(newSimTrackIndex), pParentVertex(nullptr), pMergedBremSource() {}
    };

    struct DecayChainVertex
    {
        int simVertexIndex;
        DecayChainTrack* pParentTrack;
        std::vector<DecayChainTrack*> daughterTracks;
        DecayChainVertex* pMergedBremSource;
        DecayChainVertex() : simVertexIndex(-1), pParentTrack(nullptr), pMergedBremSource(nullptr) {}
        DecayChainVertex( int newIndex ) : simVertexIndex(newIndex), pParentTrack(nullptr), pMergedBremSource(nullptr) {}
    };

    struct DecayChain
    {
    public:
        DecayChain( const std::vector<SimTrack>& trackCollection, const std::vector<SimVertex>& vertexCollection );
        const size_t decayTracksSize;
        const size_t decayVerticesSize;

#if defined(DO_DEBUG_TESTING)

        void integrityCheck();
#endif
        const SimTrack& getSimTrack( const ::DecayChainTrack* pDecayTrack ) const { return simTrackCollection_.at( pDecayTrack->simTrackIndex ); }
        const SimVertex& getSimVertex( const ::DecayChainVertex* pDecayVertex ) const { return simVertexCollection_.at( pDecayVertex->simVertexIndex ); }
    private:
        void findBrem( const std::vector<SimTrack>& trackCollection, const std::vector<SimVertex>& vertexCollection );
        std::unique_ptr< ::DecayChainTrack[]> decayTracks_;
        std::unique_ptr< ::DecayChainVertex[]> decayVertices_;

        std::vector< ::DecayChainVertex*> rootVertices_;

        // Keep a record of the constructor parameters
        const std::vector<SimTrack>& simTrackCollection_;
        const std::vector<SimVertex>& simVertexCollection_;
    public:
        const std::unique_ptr< ::DecayChainTrack[]>& decayTracks; 
        const std::unique_ptr< ::DecayChainVertex[]>& decayVertices; 
        const std::vector< ::DecayChainVertex*>& rootVertices; 
    };

    class TrackingParticleFactory
    {
    public:
        TrackingParticleFactory( const ::DecayChain& decayChain, const edm::Handle< std::vector<reco::GenParticle> >& hGenParticles,
                const edm::Handle< edm::HepMCProduct >& hepMCproduct, const edm::Handle< std::vector<int> >& hHepMCGenParticleIndices,
                const std::vector<const PSimHit*>& simHits, double volumeRadius, double volumeZ, double vertexDistanceCut, bool allowDifferentProcessTypes );
        TrackingParticle createTrackingParticle( const DecayChainTrack* pTrack, const TrackerTopology *tTopo ) const;
        TrackingVertex createTrackingVertex( const DecayChainVertex* pVertex) const;
        bool vectorIsInsideVolume( const math::XYZTLorentzVectorD& vector ) const;
    private:
        const ::DecayChain& decayChain_;
        const edm::Handle< std::vector<reco::GenParticle> >& hGenParticles_;
        const edm::Handle< edm::HepMCProduct >& hepMCproduct_;
        std::vector<int> genParticleIndices_;
        const std::vector<const PSimHit*>& simHits_;
        const double volumeRadius_;
        const double volumeZ_;
        const double vertexDistanceCut2_; // distance based on which HepMC::GenVertexs are added to SimVertexs
        std::multimap<unsigned int, size_t> trackIdToHitIndex_; 
        bool allowDifferentProcessTypeForDifferentDetectors_; 
    };

    class OutputCollectionWrapper
    {
    public:
        OutputCollectionWrapper( const DecayChain& decayChain, TrackingTruthAccumulator::OutputCollections& outputCollections );
        TrackingParticle* addTrackingParticle( const ::DecayChainTrack* pDecayTrack, const TrackingParticle& trackingParticle );
        TrackingVertex* addTrackingVertex( const ::DecayChainVertex* pDecayVertex, const TrackingVertex& trackingVertex );
        TrackingParticle* getTrackingParticle( const ::DecayChainTrack* pDecayTrack );
        void setProxy( const ::DecayChainTrack* pOriginalTrack, const ::DecayChainTrack* pProxyTrack );
        void setProxy( const ::DecayChainVertex* pOriginalVertex, const ::DecayChainVertex* pProxyVertex );
        TrackingVertex* getTrackingVertex( const ::DecayChainVertex* pDecayVertex );
        TrackingParticleRef getRef( const ::DecayChainTrack* pDecayTrack );
        TrackingVertexRef getRef( const ::DecayChainVertex* pDecayVertex );
    private:
        void associateToExistingObjects( const ::DecayChainVertex* pChainVertex );
        void associateToExistingObjects( const ::DecayChainTrack* pChainTrack );
        TrackingTruthAccumulator::OutputCollections& output_;
        std::vector<int> trackingParticleIndices_;
        std::vector<int> trackingVertexIndices_;
    };

    TrackingParticle* addTrackAndParentVertex( ::DecayChainTrack* pDecayTrack, const TrackingParticle& trackingParticle, ::OutputCollectionWrapper* pOutput );

    void addTrack( ::DecayChainTrack* pDecayChainTrack, const TrackingParticleSelector* pSelector, ::OutputCollectionWrapper* pUnmergedOutput, ::OutputCollectionWrapper* pMergedOutput, const ::TrackingParticleFactory& objectFactory, bool addAncestors, const TrackerTopology *tTopo);

} // end of the unnamed namespace




//---------------------------------------------------------------------------------
//---------------------------------------------------------------------------------
//---------------------------------------------------------------------------------
//------                                                                     ------
//------  Definitions for the TrackingTruthAccumulator methods               ------
//------  are below.                                                         ------
//------                                                                     ------
//---------------------------------------------------------------------------------
//---------------------------------------------------------------------------------
//---------------------------------------------------------------------------------

TrackingTruthAccumulator::TrackingTruthAccumulator( const edm::ParameterSet & config, edm::stream::EDProducerBase& mixMod, edm::ConsumesCollector& iC) :
        messageCategory_("TrackingTruthAccumulator"),
        volumeRadius_( config.getParameter<double>("volumeRadius") ),
        volumeZ_( config.getParameter<double>("volumeZ") ),
        vertexDistanceCut_( config.getParameter<double>("vertexDistanceCut") ),
        ignoreTracksOutsideVolume_( config.getParameter<bool>("ignoreTracksOutsideVolume") ),
        maximumPreviousBunchCrossing_( config.getParameter<unsigned int>("maximumPreviousBunchCrossing") ),
        maximumSubsequentBunchCrossing_( config.getParameter<unsigned int>("maximumSubsequentBunchCrossing") ),
        createUnmergedCollection_( config.getParameter<bool>("createUnmergedCollection") ),
        createMergedCollection_(config.getParameter<bool>("createMergedBremsstrahlung") ),
        createInitialVertexCollection_(config.getParameter<bool>("createInitialVertexCollection") ),
        addAncestors_( config.getParameter<bool>("alwaysAddAncestors") ),
        removeDeadModules_( config.getParameter<bool>("removeDeadModules") ),
        simTrackLabel_( config.getParameter<edm::InputTag>("simTrackCollection") ),
        simVertexLabel_( config.getParameter<edm::InputTag>("simVertexCollection") ),
        collectionTags_( ),
        genParticleLabel_( config.getParameter<edm::InputTag>("genParticleCollection") ),
        hepMCproductLabel_( config.getParameter<edm::InputTag>("HepMCProductLabel") ),
        allowDifferentProcessTypeForDifferentDetectors_( config.getParameter<bool>("allowDifferentSimHitProcesses") )
{
    //
    // Make sure at least one of the merged and unmerged collections have been set
    // to be created.
    //
    if( !createUnmergedCollection_ && !createMergedCollection_ )
        edm::LogError(messageCategory_) << "Both \"createUnmergedCollection\" and \"createMergedBremsstrahlung\" have been"
            << "set to false, which means no collections will be created";

    // Initialize selection for building TrackingParticles
    //
    if( config.exists( "select" ) )
    {
        edm::ParameterSet param=config.getParameter<edm::ParameterSet>("select");
        selector_=TrackingParticleSelector( param.getParameter<double>( "ptMinTP" ),
                param.getParameter<double>( "ptMaxTP" ),
                param.getParameter<double>( "minRapidityTP" ),
                param.getParameter<double>( "maxRapidityTP" ),
                param.getParameter<double>( "tipTP" ),
                param.getParameter<double>( "lipTP" ),
                param.getParameter<int>( "minHitTP" ),
                param.getParameter<bool>( "signalOnlyTP" ),
                param.getParameter<bool>( "intimeOnlyTP" ),
                param.getParameter<bool>( "chargedOnlyTP" ),
                param.getParameter<bool>( "stableOnlyTP" ),
                param.getParameter<std::vector<int> >("pdgIdTP") );
        selectorFlag_=true;

        // Also set these two variables, which are used to drop out early if the SimTrack doesn't conform.
        // The selector_ requires a full TrackingParticle object, but these two variables can veto things early.
        chargedOnly_=param.getParameter<bool>( "chargedOnlyTP" );
        signalOnly_=param.getParameter<bool>( "signalOnlyTP" );
    }
    else
    {
        selectorFlag_=false;
        chargedOnly_=false;
        signalOnly_=false;
    }

    //
    // Need to state what collections are going to be added to the event. This
    // depends on which of the merged and unmerged collections have been configured
    // to be created.
    //
    if( createUnmergedCollection_ )
    {
        mixMod.produces<TrackingVertexCollection>();
        mixMod.produces<TrackingParticleCollection>();
    }

    if( createMergedCollection_ )
    {
        mixMod.produces<TrackingParticleCollection>("MergedTrackTruth");
        mixMod.produces<TrackingVertexCollection>("MergedTrackTruth");
    }

    if( createInitialVertexCollection_ )
    {
        mixMod.produces<TrackingVertexCollection>("InitialVertices");
    }

    iC.consumes<std::vector<SimTrack> >(simTrackLabel_);
    iC.consumes<std::vector<SimVertex> >(simVertexLabel_);
    iC.consumes<std::vector<reco::GenParticle> >(genParticleLabel_);
    iC.consumes<std::vector<int> >(genParticleLabel_);
    iC.consumes<std::vector<int> >(hepMCproductLabel_);

    // Fill the collection tags
        const edm::ParameterSet& simHitCollectionConfig=config.getParameterSet("simHitCollections");
    std::vector<std::string> parameterNames=simHitCollectionConfig.getParameterNames();

    for( const auto& parameterName : parameterNames )
    {
           std::vector<edm::InputTag> tags=simHitCollectionConfig.getParameter<std::vector<edm::InputTag> >(parameterName);
           collectionTags_.insert(collectionTags_.end(), tags.begin(), tags.end());
        }

    for( const auto& collectionTag : collectionTags_ ) {
      iC.consumes<std::vector<PSimHit> >(collectionTag);
        }

}

void TrackingTruthAccumulator::initializeEvent( edm::Event const& event, edm::EventSetup const& setup )
{
    if( createUnmergedCollection_ )
    {
        unmergedOutput_.pTrackingParticles.reset( new TrackingParticleCollection );
        unmergedOutput_.pTrackingVertices.reset( new TrackingVertexCollection );
        unmergedOutput_.refTrackingParticles=const_cast<edm::Event&>( event ).getRefBeforePut<TrackingParticleCollection>();
        unmergedOutput_.refTrackingVertexes=const_cast<edm::Event&>( event ).getRefBeforePut<TrackingVertexCollection>();
    }

    if( createMergedCollection_ )
    {
        mergedOutput_.pTrackingParticles.reset( new TrackingParticleCollection );
        mergedOutput_.pTrackingVertices.reset( new TrackingVertexCollection );
        mergedOutput_.refTrackingParticles=const_cast<edm::Event&>( event ).getRefBeforePut<TrackingParticleCollection>("MergedTrackTruth");
        mergedOutput_.refTrackingVertexes=const_cast<edm::Event&>( event ).getRefBeforePut<TrackingVertexCollection>("MergedTrackTruth");
    }

    if( createInitialVertexCollection_ )
    {
        pInitialVertices_.reset( new TrackingVertexCollection );
    }
}


void TrackingTruthAccumulator::accumulate( edm::Event const& event, edm::EventSetup const& setup )
{
    // Call the templated version that does the same for both signal and pileup events
    
    edm::Handle< edm::HepMCProduct > hepmc;
    event.getByLabel(hepMCproductLabel_, hepmc);
    
    accumulateEvent( event, setup, hepmc );
}

void TrackingTruthAccumulator::accumulate( PileUpEventPrincipal const& event, edm::EventSetup const& setup, edm::StreamID const& )
{
    // If this bunch crossing is outside the user configured limit, don't do anything.
    if( event.bunchCrossing()>=-static_cast<int>(maximumPreviousBunchCrossing_) && event.bunchCrossing()<=static_cast<int>(maximumSubsequentBunchCrossing_) )
    {
        //edm::LogInfo(messageCategory_) << "Analysing pileup event for bunch crossing " << event.bunchCrossing();
        
        //simply create empty handle as we do not have a HepMCProduct in PU anyway
        edm::Handle< edm::HepMCProduct > hepmc;
        accumulateEvent( event, setup, hepmc );
    }
    else edm::LogInfo(messageCategory_) << "Skipping pileup event for bunch crossing " << event.bunchCrossing();
}

void TrackingTruthAccumulator::finalizeEvent( edm::Event& event, edm::EventSetup const& setup )
{

    if( createUnmergedCollection_ )
    {
        edm::LogInfo("TrackingTruthAccumulator") << "Adding " << unmergedOutput_.pTrackingParticles->size() << " TrackingParticles and " << unmergedOutput_.pTrackingVertices->size()
                << " TrackingVertexs to the event.";

        event.put(std::move(unmergedOutput_.pTrackingParticles));
        event.put(std::move(unmergedOutput_.pTrackingVertices));
    }

    if( createMergedCollection_ )
    {
        edm::LogInfo("TrackingTruthAccumulator") << "Adding " << mergedOutput_.pTrackingParticles->size() << " merged TrackingParticles and " << mergedOutput_.pTrackingVertices->size()
                << " merged TrackingVertexs to the event.";

        event.put(std::move(mergedOutput_.pTrackingParticles), "MergedTrackTruth" );
        event.put(std::move(mergedOutput_.pTrackingVertices), "MergedTrackTruth" );
    }

    if( createInitialVertexCollection_ )
    {
        edm::LogInfo("TrackingTruthAccumulator") << "Adding " << pInitialVertices_->size() << " initial TrackingVertexs to the event.";

        event.put(std::move(pInitialVertices_), "InitialVertices" );
    }
}

template<class T> void TrackingTruthAccumulator::accumulateEvent( const T& event, const edm::EventSetup& setup, const edm::Handle< edm::HepMCProduct >& hepMCproduct)
{
    //
    // Get the collections
    //
    edm::Handle<std::vector<SimTrack> > hSimTracks;
    edm::Handle<std::vector<SimVertex> > hSimVertices;
    edm::Handle< std::vector<reco::GenParticle> > hGenParticles;
    edm::Handle< std::vector<int> > hGenParticleIndices;

    event.getByLabel( simTrackLabel_, hSimTracks );
    event.getByLabel( simVertexLabel_, hSimVertices );

    try
    {
        event.getByLabel( genParticleLabel_, hGenParticles );
        event.getByLabel( genParticleLabel_, hGenParticleIndices );
    }
    catch( cms::Exception& exception )
    {
        //
        // The Monte Carlo is not always available, e.g. for pileup events. The information
        // is only used if it's available, but for some reason the PileUpEventPrincipal
        // wrapper throws an exception here rather than waiting to see if the handle is
        // used (as is the case for edm::Event). So I just want to catch this exception
        // and use the normal handle checking later on.
        //
    }

    //Retrieve tracker topology from geometry
    edm::ESHandle<TrackerTopology> tTopoHandle;
    setup.get<TrackerTopologyRcd>().get(tTopoHandle);
    const TrackerTopology* const tTopo = tTopoHandle.product();


    // Run through the collections and work out the decay chain of each track/vertex. The
    // information in SimTrack and SimVertex only allows traversing upwards, but this will
    // allow traversal in both directions. This is required for things like grouping electrons
    // that bremsstrahlung as one TrackingParticle if "mergedBremsstrahlung" is set in the
    // config file.
    DecayChain decayChain( *hSimTracks, *hSimVertices );

    // I only want to create these collections if they're actually required
    std::unique_ptr< ::OutputCollectionWrapper> pUnmergedCollectionWrapper;
    std::unique_ptr< ::OutputCollectionWrapper> pMergedCollectionWrapper;
    if( createUnmergedCollection_ ) pUnmergedCollectionWrapper.reset( new ::OutputCollectionWrapper( decayChain, unmergedOutput_ ) );
    if( createMergedCollection_ ) pMergedCollectionWrapper.reset( new ::OutputCollectionWrapper( decayChain, mergedOutput_ ) );

    std::vector<const PSimHit*> simHitPointers;
    fillSimHits( simHitPointers, event, setup );
    TrackingParticleFactory objectFactory( decayChain, hGenParticles, hepMCproduct, hGenParticleIndices, simHitPointers, volumeRadius_, volumeZ_, vertexDistanceCut_, allowDifferentProcessTypeForDifferentDetectors_ );

#if defined(DO_DEBUG_TESTING)
    // While I'm testing, perform some checks.
    // TODO - drop this call once I'm happy it works in all situations.
    decayChain.integrityCheck();
#endif

    TrackingParticleSelector* pSelector=nullptr;
    if( selectorFlag_ ) pSelector=&selector_;

    // Run over all of the SimTracks, but because I'm interested in the decay hierarchy
    // do it through the DecayChainTrack objects. These are looped over in sequence here
    // but they have the hierarchy information for the functions called to traverse the
    // decay chain.

    for( size_t index=0; index<decayChain.decayTracksSize; ++index )
    {
        ::DecayChainTrack* pDecayTrack=&decayChain.decayTracks[index];
        const SimTrack& simTrack=hSimTracks->at(pDecayTrack->simTrackIndex);


        // Perform some quick checks to see if we can drop out early. Note that these are
        // a subset of the cuts in the selector_ so the created TrackingParticle could still
        // fail. The selector_ requires the full TrackingParticle to be made however, which
        // can be computationally expensive.
        if( chargedOnly_ && simTrack.charge()==0 ) continue;
        if( signalOnly_ && (simTrack.eventId().bunchCrossing()!=0 || simTrack.eventId().event()!=0) ) continue;

        // Also perform a check to see if the production vertex is inside the tracker volume (if required).
        if( ignoreTracksOutsideVolume_ )
        {
            const SimVertex& simVertex=hSimVertices->at( pDecayTrack->pParentVertex->simVertexIndex );
            if( !objectFactory.vectorIsInsideVolume( simVertex.position() ) ) continue;
        }


        // This function creates the TrackinParticle and adds it to the collection if it
        // passes the selection criteria specified in the configuration. If the config
        // specifies adding ancestors, the function is called recursively to do that.
        ::addTrack( pDecayTrack, pSelector, pUnmergedCollectionWrapper.get(), pMergedCollectionWrapper.get(), objectFactory, addAncestors_, tTopo );
    }

    // If configured to create a collection of initial vertices, add them from this bunch
    // crossing. No selection is applied on this collection, but it also has no links to
    // the TrackingParticle decay products.
    // There are a lot of "initial vertices", I'm not entirely sure what they all are
    // (nuclear interactions in the detector maybe?), but the one for the main event is
    // the one with vertexId==0.
    if( createInitialVertexCollection_ )
    {
        // Pretty sure the one with vertexId==0 is always the first one, but doesn't hurt to check
        for( const auto& pRootVertex : decayChain.rootVertices )
        {
            const SimVertex& vertex=hSimVertices->at(decayChain.rootVertices[0]->simVertexIndex);
            if( vertex.vertexId()!=0 ) continue;

            pInitialVertices_->push_back( objectFactory.createTrackingVertex(pRootVertex) );
            break;
        }
    }
}

template<class T> void TrackingTruthAccumulator::fillSimHits( std::vector<const PSimHit*>& returnValue, const T& event, const edm::EventSetup& setup )
{
    // loop over the collections
    for( const auto& collectionTag : collectionTags_ )
    {
        edm::Handle< std::vector<PSimHit> > hSimHits;
        event.getByLabel( collectionTag, hSimHits );

        // TODO - implement removing the dead modules
        for( const auto& simHit : *hSimHits )
        {
            returnValue.push_back( &simHit );
        }

    } // end of loop over InputTags

        // sort the SimHits according to their time of flight,
        // necessary for looping over them "in order" in
        // TrackingParticleFactory::createTrackingParticle()
        std::sort(returnValue.begin(), returnValue.end(), [](const PSimHit *a, const PSimHit *b) {
            const auto atof = edm::isFinite(a->timeOfFlight()) ? a->timeOfFlight() : std::numeric_limits<decltype(a->timeOfFlight())>::max();
            const auto btof = edm::isFinite(b->timeOfFlight()) ? b->timeOfFlight() : std::numeric_limits<decltype(b->timeOfFlight())>::max();
            return atof < btof;
          });
}


//---------------------------------------------------------------------------------
//---------------------------------------------------------------------------------
//---------------------------------------------------------------------------------
//------                                                                     ------
//------  End of the definitions for the TrackingTruthAccumulator methods.   ------
//------  Definitions for the functions and classes declared in the unnamed  ------
//------  namespace are below. Documentation for those is above, where       ------
//------  they're declared.                                                  ------
//------                                                                     ------
//---------------------------------------------------------------------------------
//---------------------------------------------------------------------------------
//---------------------------------------------------------------------------------


namespace // Unnamed namespace for things only used in this file
{
    //---------------------------------------------------------------------------------
    //---------------------------------------------------------------------------------
    //----   TrackingParticleFactory methods   ----------------------------------------
    //---------------------------------------------------------------------------------
    //---------------------------------------------------------------------------------

    ::TrackingParticleFactory::TrackingParticleFactory( const ::DecayChain& decayChain, const edm::Handle< std::vector<reco::GenParticle> >& hGenParticles,
            const edm::Handle< edm::HepMCProduct >& hepMCproduct, const edm::Handle< std::vector<int> >& hHepMCGenParticleIndices, const std::vector<const PSimHit*>& simHits,
            double volumeRadius, double volumeZ, double vertexDistanceCut, bool allowDifferentProcessTypes )
        : decayChain_(decayChain), hGenParticles_(hGenParticles), hepMCproduct_(hepMCproduct), simHits_(simHits), volumeRadius_(volumeRadius),
          volumeZ_(volumeZ), vertexDistanceCut2_(vertexDistanceCut*vertexDistanceCut), allowDifferentProcessTypeForDifferentDetectors_(allowDifferentProcessTypes)
    {
        // Need to create a multimap to get from a SimTrackId to all of the hits in it. The SimTrackId
        // is an unsigned int.
        for( size_t index=0; index<simHits_.size(); ++index )
        {
            trackIdToHitIndex_.insert( std::make_pair( simHits_[index]->trackId(), index ) );
        }

        if( hHepMCGenParticleIndices.isValid() ) // Monte Carlo might not be available for the pileup events
        {
            genParticleIndices_.resize( hHepMCGenParticleIndices->size()+1 );

            // What I need is the reverse mapping of this vector. The sizes are already equivalent because I set
            // the size in the initialiser list.
            for( size_t recoGenParticleIndex=0; recoGenParticleIndex<hHepMCGenParticleIndices->size(); ++recoGenParticleIndex )
            {
                size_t hepMCGenParticleIndex=(*hHepMCGenParticleIndices)[recoGenParticleIndex];

                // They should be the same size, give or take a fencepost error, so this should never happen - but just in case
                if( genParticleIndices_.size()<=hepMCGenParticleIndex ) genParticleIndices_.resize(hepMCGenParticleIndex+1);

                genParticleIndices_[ hepMCGenParticleIndex ]=recoGenParticleIndex;
            }
        }
    }

    TrackingParticle TrackingParticleFactory::createTrackingParticle( const ::DecayChainTrack* pChainTrack, const TrackerTopology *tTopo ) const
    {
        typedef math::XYZTLorentzVectorD LorentzVector;
        typedef math::XYZPoint Vector;

        const SimTrack& simTrack=decayChain_.getSimTrack( pChainTrack );
        const SimVertex& parentSimVertex=decayChain_.getSimVertex( pChainTrack->pParentVertex );

        LorentzVector position( 0, 0, 0, 0 );
        if( !simTrack.noVertex() ) position=parentSimVertex.position();

        int pdgId=simTrack.type();

        TrackingParticle returnValue;
        // N.B. The sim track is added a few lines below, the parent and decay vertices are added in
        // another function later on.

        //
        // If there is some valid Monte Carlo for this track, take some information from that.
        // Only do so if it is from the signal event however. Not sure why but that's what the
        // old code did.
        //
        if( simTrack.eventId().event()==0 && simTrack.eventId().bunchCrossing()==0 ) // if this is a track in the signal event
        {
            int hepMCGenParticleIndex=simTrack.genpartIndex();
            if( hepMCGenParticleIndex>=0 && hepMCGenParticleIndex<static_cast<int>(genParticleIndices_.size()) && hGenParticles_.isValid() )
            {
                int recoGenParticleIndex=genParticleIndices_[hepMCGenParticleIndex];
                reco::GenParticleRef generatorParticleRef( hGenParticles_, recoGenParticleIndex );
                pdgId=generatorParticleRef->pdgId();
                returnValue.addGenParticle( generatorParticleRef );
            }
        }

        returnValue.addG4Track( simTrack );

        // I need to run over the sim hits and count up the different types of hits. To be honest
        // I don't fully understand this next section of code, I copied it from the old TrackingTruthProducer
        // to provide the same results. The different types of hits that I need to count are:
        size_t matchedHits=0; // As far as I can tell, this is the number of tracker layers with hits on them, i.e. taking account of overlaps.
        size_t numberOfHits=0; // The total number of hits not taking account of overlaps.
        size_t numberOfTrackerHits=0; // The number of tracker hits not taking account of overlaps.

        bool init=true;
        int processType=0;
        int particleType=0;
        int oldLayer = 0;
        int newLayer = 0;
        DetId oldDetector;
        DetId newDetector;

        // Loop over the SimHits associated to this SimTrack
        // in the order defined by time of flight, which is
        // probably the best quantity available for going
        // through the hits "in order" (ok, most important is
        // to get the first hit right because processType and
        // particleType are taken from it)
        for( auto iHitIndex=trackIdToHitIndex_.lower_bound( simTrack.trackId() ), end=trackIdToHitIndex_.upper_bound( simTrack.trackId() );
                iHitIndex!=end;
                ++iHitIndex )
        {
            const auto& pSimHit=simHits_[ iHitIndex->second ];

                        // Skip hits with particle type different from SimTrack pdgId
                        if(pSimHit->particleType() != pdgId)
                          continue;

            // Initial condition for consistent simhit selection
            if( init )
            {
                processType=pSimHit->processType();
                particleType=pSimHit->particleType();
                newDetector=DetId( pSimHit->detUnitId() );
                init=false;
            }

            oldDetector=newDetector;
            newDetector=DetId( pSimHit->detUnitId() );

            // Fast sim seems to have different processType between tracker and muons, so if this flag
            // has been set allow the processType to change if the detector changes.
            if( allowDifferentProcessTypeForDifferentDetectors_ && newDetector.det()!=oldDetector.det() ) processType=pSimHit->processType();

            // Check for delta and interaction products discards
            if( processType==pSimHit->processType() && particleType==pSimHit->particleType() )
            {
                ++numberOfHits;
                oldLayer=newLayer;
                                newLayer=0;
                if( newDetector.det() == DetId::Tracker ) {
                                  ++numberOfTrackerHits;

                                  newLayer=tTopo->layer( newDetector );

                                  // Count hits using layers for glued detectors
                                  if( (oldLayer!=newLayer || (oldLayer==newLayer && oldDetector.subdetId()!=newDetector.subdetId())) ) ++matchedHits;
                                }
            }
        } // end of loop over the sim hits for this sim track

        returnValue.setNumberOfTrackerLayers( matchedHits );
        returnValue.setNumberOfHits( numberOfHits );
        returnValue.setNumberOfTrackerHits( numberOfTrackerHits );

        return returnValue;
    }

    TrackingVertex TrackingParticleFactory::createTrackingVertex( const ::DecayChainVertex* pChainVertex) const
    {
                
        typedef math::XYZTLorentzVectorD LorentzVector;
        typedef math::XYZPoint Vector;
        typedef edm::Ref<edm::HepMCProduct, HepMC::GenVertex >   GenVertexRef;
        
        const SimVertex& simVertex=decayChain_.getSimVertex( pChainVertex );

        bool isInVolume=this->vectorIsInsideVolume( simVertex.position() );

        TrackingVertex returnValue( simVertex.position(), isInVolume, simVertex.eventId() );
        
        // add the SimVertex to the TrackingVertex
        returnValue.addG4Vertex(simVertex);
                
        // also add refs to nearby HepMC::GenVertexs; the way this is done (i.e. based on the position) is transcribed over from the old TrackingTruthProducer
        if( simVertex.eventId().event()==0 && simVertex.eventId().bunchCrossing()==0 && hepMCproduct_.isValid()) // if this is a track in the signal event
        {
            const HepMC::GenEvent* genEvent = hepMCproduct_->GetEvent();
            
            if (genEvent != nullptr)
            {
                Vector tvPosition(returnValue.position().x(), returnValue.position().y(), returnValue.position().z());
                
                for (HepMC::GenEvent::vertex_const_iterator iGenVertex = genEvent->vertices_begin(); iGenVertex != genEvent->vertices_end(); ++iGenVertex)
                {
                    HepMC::ThreeVector rawPosition = (*iGenVertex)->position();
                    
                    Vector genPosition(rawPosition.x()*0.1, rawPosition.y()*0.1, rawPosition.z()*0.1);
                    
                    auto distance2 = (tvPosition - genPosition).mag2();
                    
                    if (distance2 < vertexDistanceCut2_)
                        returnValue.addGenVertex( GenVertexRef(hepMCproduct_, (*iGenVertex)->barcode()) );
                }
            }
        }
                
        return returnValue;
    }

    bool ::TrackingParticleFactory::vectorIsInsideVolume( const math::XYZTLorentzVectorD& vector ) const
    {
        return ( vector.Pt()<volumeRadius_ && std::abs( vector.z() )<volumeZ_ );
    }

    //---------------------------------------------------------------------------------
    //---------------------------------------------------------------------------------
    //----   DecayChain methods   -----------------------------------------------------
    //---------------------------------------------------------------------------------
    //---------------------------------------------------------------------------------

    ::DecayChain::DecayChain( const std::vector<SimTrack>& trackCollection, const std::vector<SimVertex>& vertexCollection )
        : decayTracksSize( trackCollection.size() ),
          decayVerticesSize( vertexCollection.size() ),
          decayTracks_( new DecayChainTrack[decayTracksSize] ),
          decayVertices_( new DecayChainVertex[decayVerticesSize] ),
          simTrackCollection_( trackCollection ),
          simVertexCollection_( vertexCollection ),
          decayTracks( decayTracks_ ), // These const references map onto the actual members for public const access
          decayVertices( decayVertices_ ),
          rootVertices( rootVertices_ )
    {
        // I need some maps to be able to get object pointers from the track/vertex ID
        std::map<int,::DecayChainTrack*> trackIdToDecayTrack;
        std::map<int,::DecayChainVertex*> vertexIdToDecayVertex;

        // First create a DecayChainTrack for every SimTrack and make a note of the
        // trackIds in the map. Also add a pointer to the daughter list of the parent
        // DecayChainVertex, which might include creating the vertex object if it
        // doesn't already exist.
        size_t decayVertexIndex=0; // The index of the next free slot in the DecayChainVertex array.
        for( size_t index=0; index<trackCollection.size(); ++index )
        {
            ::DecayChainTrack* pDecayTrack=&decayTracks_[index]; // Get a pointer for ease of use

            // This is the array index of the SimTrack that this DecayChainTrack corresponds to. At
            // the moment this is a 1 to 1 relationship with the DecayChainTrack index, but they won't
            // necessarily be accessed through the array later so it's still required to store it.
            pDecayTrack->simTrackIndex=index;

            trackIdToDecayTrack[ trackCollection[index].trackId() ]=pDecayTrack;

            int parentVertexIndex=trackCollection[index].vertIndex();
            if( parentVertexIndex>=0 )
            {
                // Get the DecayChainVertex corresponding to this SimVertex, or initialise it if it hasn't been done already.
                ::DecayChainVertex*& pParentVertex=vertexIdToDecayVertex[parentVertexIndex];
                if( pParentVertex==nullptr )
                {
                    // Note that I'm using a reference, so changing pParentVertex will change the entry in the map too.
                    pParentVertex=&decayVertices_[decayVertexIndex];
                    ++decayVertexIndex;
                    pParentVertex->simVertexIndex=parentVertexIndex;
                }
                pParentVertex->daughterTracks.push_back(pDecayTrack);
                pDecayTrack->pParentVertex=pParentVertex;
            }
            else throw std::runtime_error( "TrackingTruthAccumulator: Found a track with an invalid parent vertex index." );
        }

        // This assert was originally in to check the internal consistency of the decay chain. Fast sim
        // pileup seems to have a load of vertices with no tracks pointing to them though, so fast sim fails
        // this assert if pileup is added. I don't think the problem is vital however, so if the assert is
        // taken out these extra vertices are ignored.
        //assert( vertexIdToDecayVertex.size()==vertexCollection.size() && vertexCollection.size()==decayVertexIndex );

        // I still need to set DecayChainTrack::daughterVertices and DecayChainVertex::pParentTrack.
        // The information to do this comes from SimVertex::parentIndex. I couldn't do this before
        // because I need all of the DecayChainTracks initialised.
        for( auto& decayVertexMapPair : vertexIdToDecayVertex )
        {
            ::DecayChainVertex* pDecayVertex=decayVertexMapPair.second;
            int parentTrackIndex=vertexCollection[pDecayVertex->simVertexIndex].parentIndex();
            if( parentTrackIndex!=-1 )
            {
                std::map<int,::DecayChainTrack*>::iterator iParentTrackMapPair=trackIdToDecayTrack.find(parentTrackIndex);
                if( iParentTrackMapPair==trackIdToDecayTrack.end() )
                {
                    std::stringstream errorStream;
                    errorStream << "TrackingTruthAccumulator: Something has gone wrong with the indexing. Parent track index is " << parentTrackIndex << ".";
                    throw std::runtime_error( errorStream.str() );
                }

                ::DecayChainTrack* pParentTrackHierarchy=iParentTrackMapPair->second;

                pParentTrackHierarchy->daughterVertices.push_back( pDecayVertex );
                pDecayVertex->pParentTrack=pParentTrackHierarchy;
            }
            else rootVertices_.push_back(pDecayVertex); // Has no parent so is at the top of the decay chain.
        } // end of loop over the vertexIdToDecayVertex map

        findBrem( trackCollection, vertexCollection );

    } // end of ::DecayChain constructor

#if defined(DO_DEBUG_TESTING)
    // Function documentation is with the declaration above. This function is only used for testing.
    void ::DecayChain::integrityCheck()
    {
        //
        // Start off checking the tracks
        //
        for( size_t index=0; index<decayTracksSize; ++index )
        {
            const auto& decayTrack=decayTracks[index];
            //
            // Tracks should always have a production vertex
            //
            if( decayTrack.pParentVertex==NULL ) throw std::runtime_error( "TrackingTruthAccumulator.cc integrityCheck(): Found DecayChainTrack with no parent vertex." );

            //
            // Make sure the parent has this as a child. Also make sure it's only listed once.
            //
            size_t numberOfTimesListed=0;
            for( const auto pSiblingTrack : decayTrack.pParentVertex->daughterTracks )
            {
                if( pSiblingTrack==&decayTrack ) ++numberOfTimesListed;
            }
            if( numberOfTimesListed!=1 ) throw std::runtime_error( "TrackingTruthAccumulator.cc integrityCheck(): Found DecayChainTrack whose parent does not have it listed once and only once as a child." );

            //
            // Make sure all of the children have this listed as a parent.
            //
            for( const auto pDaughterVertex : decayTrack.daughterVertices )
            {
                if( pDaughterVertex->pParentTrack!=&decayTrack ) throw std::runtime_error( "TrackingTruthAccumulator.cc integrityCheck(): Found DecayChainTrack whose child does not have it listed as the parent." );
            }

            //
            // Follow the chain up to the root vertex, and make sure that is listed in rootVertices
            //
            const DecayChainVertex* pAncestorVertex=decayTrack.pParentVertex;
            while( pAncestorVertex->pParentTrack!=NULL )
            {
                if( pAncestorVertex->pParentTrack->pParentVertex==NULL ) throw std::runtime_error( "TrackingTruthAccumulator.cc integrityCheck(): Found DecayChainTrack with no parent vertex higher in the decay chain." );
                pAncestorVertex=pAncestorVertex->pParentTrack->pParentVertex;
            }
            if( std::find( rootVertices.begin(), rootVertices.end(), pAncestorVertex )==rootVertices.end() )
            {
                throw std::runtime_error( "TrackingTruthAccumulator.cc integrityCheck(): Found DecayChainTrack whose root vertex is not recorded anywhere." );
            }
        } // end of loop over decayTracks

        //
        // Now check the vertices
        //
        for( size_t index=0; index<decayVerticesSize; ++index )
        {
            const auto& decayVertex=decayVertices[index];

            //
            // Make sure this, or a vertex higher in the chain, is in the list of root vertices.
            //
            const DecayChainVertex* pAncestorVertex=&decayVertex;
            while( pAncestorVertex->pParentTrack!=NULL )
            {
                if( pAncestorVertex->pParentTrack->pParentVertex==NULL ) throw std::runtime_error( "TrackingTruthAccumulator.cc integrityCheck(): Found DecayChainTrack with no parent vertex higher in the vertex decay chain." );
                pAncestorVertex=pAncestorVertex->pParentTrack->pParentVertex;
            }
            if( std::find( rootVertices.begin(), rootVertices.end(), pAncestorVertex )==rootVertices.end() )
            {
                throw std::runtime_error( "TrackingTruthAccumulator.cc integrityCheck(): Found DecayChainTrack whose root vertex is not recorded anywhere." );
            }

            //
            // Make sure the parent has this listed in its daughters once and only once.
            //
            if( decayVertex.pParentTrack!=NULL )
            {
                size_t numberOfTimesListed=0;
                for( const auto pSibling : decayVertex.pParentTrack->daughterVertices )
                {
                    if( pSibling==&decayVertex ) ++numberOfTimesListed;
                }
                if( numberOfTimesListed!=1 ) throw std::runtime_error( "TrackingTruthAccumulator.cc integrityCheck(): Found DecayChainVertex whose parent does not have it listed once and only once as a child." );
            }

            //
            // Make sure all of the children have this listed as the parent
            //
            for( const auto pDaughter : decayVertex.daughterTracks )
            {
                if( pDaughter->pParentVertex!=&decayVertex ) throw std::runtime_error( "TrackingTruthAccumulator.cc integrityCheck(): Found DecayChainVertex whose child does not have it listed as the parent." );
            }
        } // end of loop over decay vertices

        std::cout << "TrackingTruthAccumulator.cc integrityCheck() completed successfully" << std::endl;
    } // end of ::DecayChain::integrityCheck()
#endif

    void ::DecayChain::findBrem( const std::vector<SimTrack>& trackCollection, const std::vector<SimVertex>& vertexCollection )
    {
        for( size_t index=0; index<decayVerticesSize; ++index )
        {
            auto& vertex=decayVertices_[index];

            // Make sure parent is an electron
            if( vertex.pParentTrack==nullptr ) continue;
            int parentTrackPDG=trackCollection[vertex.pParentTrack->simTrackIndex].type();
            if( std::abs( parentTrackPDG )!=11 ) continue;

            size_t numberOfElectrons=0;
            size_t numberOfNonElectronsOrPhotons=0;
            for( auto& pDaughterTrack : vertex.daughterTracks )
            {
                const auto& simTrack=trackCollection[pDaughterTrack->simTrackIndex];
                if( simTrack.type()==11 || simTrack.type()==-11 ) ++numberOfElectrons;
                else if( simTrack.type()!=22 ) ++numberOfNonElectronsOrPhotons;
            }
            if( numberOfElectrons==1 && numberOfNonElectronsOrPhotons==0 )
            {
                // This is a valid brem, run through and tell all daughters to use the parent
                // as the brem
                for( auto& pDaughterTrack : vertex.daughterTracks ) pDaughterTrack->pMergedBremSource=vertex.pParentTrack;
                vertex.pMergedBremSource=vertex.pParentTrack->pParentVertex;
            }
        }
    } // end of ::DecayChain::findBrem()


    //---------------------------------------------------------------------------------
    //---------------------------------------------------------------------------------
    //----   OutputCollectionWrapper methods   ----------------------------------------
    //---------------------------------------------------------------------------------
    //---------------------------------------------------------------------------------

    ::OutputCollectionWrapper::OutputCollectionWrapper( const ::DecayChain& decayChain, TrackingTruthAccumulator::OutputCollections& outputCollections )
        : output_(outputCollections),
          trackingParticleIndices_(decayChain.decayTracksSize,-1),
          trackingVertexIndices_(decayChain.decayVerticesSize,-1)
    {
        // No operation besides the initialiser list
    }

    TrackingParticle* ::OutputCollectionWrapper::addTrackingParticle( const ::DecayChainTrack* pDecayTrack, const TrackingParticle& trackingParticle )
    {
        if( trackingParticleIndices_[pDecayTrack->simTrackIndex]!=-1 ) throw std::runtime_error( "OutputCollectionWrapper::addTrackingParticle - trying to add a particle twice" );

        trackingParticleIndices_[pDecayTrack->simTrackIndex]=output_.pTrackingParticles->size();
        output_.pTrackingParticles->push_back( trackingParticle );

        // Clear any associations in case there were any beforehand
        output_.pTrackingParticles->back().clearDecayVertices();
        output_.pTrackingParticles->back().clearParentVertex();

        // Associate to the objects that are already in the output collections
        associateToExistingObjects( pDecayTrack );

        return &output_.pTrackingParticles->back();
    }

    TrackingVertex* ::OutputCollectionWrapper::addTrackingVertex( const ::DecayChainVertex* pDecayVertex, const TrackingVertex& trackingVertex )
    {
        if( trackingVertexIndices_[pDecayVertex->simVertexIndex]!=-1 ) throw std::runtime_error( "OutputCollectionWrapper::addTrackingVertex - trying to add a vertex twice" );

        trackingVertexIndices_[pDecayVertex->simVertexIndex]=output_.pTrackingVertices->size();
        output_.pTrackingVertices->push_back( trackingVertex );

        // Associate the new vertex to any parents or children that are already in the output collections
        associateToExistingObjects( pDecayVertex );

        return &output_.pTrackingVertices->back();
    }

    TrackingParticle* ::OutputCollectionWrapper::getTrackingParticle( const ::DecayChainTrack* pDecayTrack )
    {
        const int index=trackingParticleIndices_[pDecayTrack->simTrackIndex];
        if( index==-1 ) return nullptr;
        else return &(*output_.pTrackingParticles)[index];
    }

    TrackingVertex* ::OutputCollectionWrapper::getTrackingVertex( const ::DecayChainVertex* pDecayVertex )
    {
        const int index=trackingVertexIndices_[pDecayVertex->simVertexIndex];
        if( index==-1 ) return nullptr;
        else return &(*output_.pTrackingVertices)[index];
    }

    TrackingParticleRef OutputCollectionWrapper::getRef( const ::DecayChainTrack* pDecayTrack )
    {
        const int index=trackingParticleIndices_[pDecayTrack->simTrackIndex];
        if( index==-1 ) throw std::runtime_error( "OutputCollectionWrapper::getRefTrackingParticle - ref requested for a non existent TrackingParticle" );
        else return TrackingParticleRef( output_.refTrackingParticles, index );
    }

    TrackingVertexRef OutputCollectionWrapper::getRef( const ::DecayChainVertex* pDecayVertex )
    {
        const int index=trackingVertexIndices_[pDecayVertex->simVertexIndex];
        if( index==-1 ) throw std::runtime_error( "OutputCollectionWrapper::getRefTrackingParticle - ref requested for a non existent TrackingVertex" );
        else return TrackingVertexRef( output_.refTrackingVertexes, index );
    }

    void ::OutputCollectionWrapper::setProxy( const ::DecayChainTrack* pOriginalTrack, const ::DecayChainTrack* pProxyTrack )
    {
        int& index=trackingParticleIndices_[pOriginalTrack->simTrackIndex];
        if( index!=-1 ) throw std::runtime_error( "OutputCollectionWrapper::setProxy() was called for a TrackingParticle that has already been created" );
        // Note that index is a reference so this call changes the value in the vector too
        index=trackingParticleIndices_[pProxyTrack->simTrackIndex];
    }

    void ::OutputCollectionWrapper::setProxy( const ::DecayChainVertex* pOriginalVertex, const ::DecayChainVertex* pProxyVertex )
    {
        int& index=trackingVertexIndices_[pOriginalVertex->simVertexIndex];
        const int newIndex=trackingVertexIndices_[pProxyVertex->simVertexIndex];

        if( index!=-1 && index!=newIndex ) throw std::runtime_error( "OutputCollectionWrapper::setProxy() was called for a TrackingVertex that has already been created" );

        // Note that index is a reference so this call changes the value in the vector too
        index=newIndex;
    }

    void ::OutputCollectionWrapper::associateToExistingObjects( const ::DecayChainVertex* pChainVertex )
    {
        // First make sure the DecayChainVertex supplied has been turned into a TrackingVertex
        TrackingVertex* pTrackingVertex=getTrackingVertex( pChainVertex );
        if( pTrackingVertex==nullptr ) throw std::runtime_error( "associateToExistingObjects was passed a non existent TrackingVertex" );

        //
        // Associate to the parent track (if there is one)
        //
        ::DecayChainTrack* pParentChainTrack=pChainVertex->pParentTrack;
        if( pParentChainTrack!=nullptr ) // Make sure there is a parent track first
        {
            // There is a parent track, but it might not have been turned into a TrackingParticle yet
            TrackingParticle* pParentTrackingParticle=getTrackingParticle(pParentChainTrack);
            if( pParentTrackingParticle!=nullptr )
            {
                pParentTrackingParticle->addDecayVertex( getRef(pChainVertex) );
                pTrackingVertex->addParentTrack( getRef(pParentChainTrack) );
            }
            // Don't worry about the "else" case - the parent track might not necessarily get added
            // to the output collection at all. A check is done on daughter vertices when tracks
            // are added, so the association will be picked up then.
        }

        //
        // A parent TrackingVertex is always associated to a daughter TrackingParticle when
        // the TrackingParticle is created. Hence there is no need to check the list of
        // daughter tracks.
        //
    }

    void ::OutputCollectionWrapper::associateToExistingObjects( const ::DecayChainTrack* pChainTrack )
    {
        //
        // First make sure this DecayChainTrack has been turned into a TrackingParticle
        //
        TrackingParticle* pTrackingParticle=getTrackingParticle( pChainTrack );
        if( pTrackingParticle==nullptr ) throw std::runtime_error( "associateToExistingObjects was passed a non existent TrackingParticle" );

        // Get the parent vertex. This should always already have been turned into a TrackingVertex, and
        // there should always be a parent DecayChainVertex.
        ::DecayChainVertex* pParentChainVertex=pChainTrack->pParentVertex;
        TrackingVertex* pParentTrackingVertex=getTrackingVertex( pParentChainVertex );

        //
        // First associate to the parent vertex.
        //
        pTrackingParticle->setParentVertex( getRef(pParentChainVertex) );
        pParentTrackingVertex->addDaughterTrack( getRef(pChainTrack) );

        // If there are any daughter vertices that have already been made into a TrackingVertex
        // make sure they know about each other. If the daughter vertices haven't been made into
        // TrackingVertexs yet, I won't do anything and create the association when the vertex is
        // made.
        for( auto pDaughterChainVertex : pChainTrack->daughterVertices )
        {
            TrackingVertex* pDaughterTrackingVertex=getTrackingVertex( pDaughterChainVertex );
            if( pDaughterTrackingVertex!=nullptr )
            {
                pTrackingParticle->addDecayVertex( getRef(pDaughterChainVertex) );
                pDaughterTrackingVertex->addParentTrack( getRef(pChainTrack) );
            }
        }
    }


    TrackingParticle* addTrackAndParentVertex( ::DecayChainTrack* pDecayTrack, const TrackingParticle& trackingParticle, ::OutputCollectionWrapper* pOutput )
    {
        // See if this TrackingParticle has already been created (could be if the DecayChainTracks are
        // looped over in a funny order). If it has then there's no need to do anything.
        TrackingParticle* pTrackingParticle=pOutput->getTrackingParticle( pDecayTrack );
        if( pTrackingParticle==nullptr )
        {
            // Need to make sure the production vertex has been created first
            if( pOutput->getTrackingVertex( pDecayTrack->pParentVertex ) == nullptr )
            {
                // TrackingVertex doesn't exist in the output collection yet. However, it's already been
                // created in the addTrack() function and a temporary reference to it set in the TrackingParticle.
                // I'll use that reference to create a copy in the output collection. When the TrackingParticle
                // is added to the output collection a few lines below the temporary reference to the parent
                // vertex will be cleared, and the correct one referring to the output collection will be set.
                pOutput->addTrackingVertex( pDecayTrack->pParentVertex, *trackingParticle.parentVertex() );
            }


            pTrackingParticle=pOutput->addTrackingParticle( pDecayTrack, trackingParticle );
        }

        return pTrackingParticle;
    }

    void addTrack( ::DecayChainTrack* pDecayChainTrack, const TrackingParticleSelector* pSelector, ::OutputCollectionWrapper* pUnmergedOutput, ::OutputCollectionWrapper* pMergedOutput, const ::TrackingParticleFactory& objectFactory, bool addAncestors, const TrackerTopology *tTopo )
    {
        if( pDecayChainTrack==nullptr ) return; // This is required for when the addAncestors_ recursive call reaches the top of the chain

        // Check to see if this particle has already been processed while traversing up the parents
        // of another split in the decay chain. The check in the line above only stops when the top
        // of the chain is reached, whereas this will stop when a previously traversed split is reached.
        { // block to limit the scope of temporary variables
            bool alreadyProcessed=true;
            if( pUnmergedOutput!=nullptr )
            {
                if( pUnmergedOutput->getTrackingParticle( pDecayChainTrack )==nullptr ) alreadyProcessed=false;
            }
            if( pMergedOutput!=nullptr )
            {
                if( pMergedOutput->getTrackingParticle( pDecayChainTrack )==nullptr ) alreadyProcessed=false;
            }
            if( alreadyProcessed ) return;
        }

        // Create a TrackingParticle.
        TrackingParticle newTrackingParticle=objectFactory.createTrackingParticle( pDecayChainTrack, tTopo );

        // The selector checks the impact parameters from the vertex, so I need to have a valid reference
        // to the parent vertex in the TrackingParticle before that can be called. TrackingParticle needs
        // an edm::Ref for the parent TrackingVertex though. I still don't know if this is going to be
        // added to the collection so I can't take it from there, so I need to create a temporary one.
        // When the addTrackAndParentVertex() is called (assuming it passes selection) it will use the
        // temporary reference to create a copy of the parent vertex, put that in the output collection,
        // and then set the reference in the TrackingParticle properly.
        TrackingVertexCollection dummyCollection; // Only needed to create an edm::Ref
        dummyCollection.push_back( objectFactory.createTrackingVertex( pDecayChainTrack->pParentVertex) );
        TrackingVertexRef temporaryRef( &dummyCollection, 0 );
        newTrackingParticle.setParentVertex( temporaryRef );

        // If a selector has been supplied apply it on the new TrackingParticle and return if it fails.
        if( pSelector )
        {
            if( !(*pSelector)( newTrackingParticle ) ) return; // Return if the TrackingParticle fails selection
        }

        // Add the ancestors first (if required) so that the collection has some kind of chronological
        // order. I don't know how important that is but other code might assume chronological order.
        // If adding ancestors, no selection is applied. Note that I've already checked that all
        // DecayChainTracks have a pParentVertex.
        if( addAncestors ) addTrack( pDecayChainTrack->pParentVertex->pParentTrack, nullptr, pUnmergedOutput, pMergedOutput, objectFactory, addAncestors, tTopo );

        // If creation of the unmerged collection has been turned off in the config this pointer
        // will be null.
        if( pUnmergedOutput!=nullptr ) addTrackAndParentVertex( pDecayChainTrack, newTrackingParticle, pUnmergedOutput );

        // If creation of the merged collection has been turned off in the config this pointer
        // will be null.
        if( pMergedOutput!=nullptr )
        {
            ::DecayChainTrack* pBremParentChainTrack=pDecayChainTrack;
            while( pBremParentChainTrack->pMergedBremSource!=nullptr ) pBremParentChainTrack=pBremParentChainTrack->pMergedBremSource;

            if( pBremParentChainTrack!=pDecayChainTrack )
            {
                TrackingParticle* pBremParentTrackingParticle=addTrackAndParentVertex( pBremParentChainTrack, newTrackingParticle, pMergedOutput );
                // The original particle in the bremsstrahlung decay chain has been
                // created (or retrieved if it already existed), now copy in the
                // extra information.
                // TODO - copy extra information.

                if( std::abs( newTrackingParticle.pdgId() ) == 22 )
                {
                    // Photons are added as separate TrackingParticles, but with the production
                    // vertex changed to be the production vertex of the original electron.

                    // Set up a proxy, so that all requests for the parent TrackingVertex get
                    // redirected to the brem parent's TrackingVertex.
                    pMergedOutput->setProxy( pDecayChainTrack->pParentVertex, pBremParentChainTrack->pParentVertex );

                    // Now that pMergedOutput thinks the parent vertex is the brem parent's vertex I can
                    // call this and it will set the TrackingParticle parent vertex correctly to the brem
                    // parent vertex.
                    addTrackAndParentVertex( pDecayChainTrack, newTrackingParticle, pMergedOutput );
                }
                else if( std::abs( newTrackingParticle.pdgId() ) == 11 )
                {
                    // Electrons have their G4 tracks and SimHits copied to the parent TrackingParticle.
                    for( const auto& trackSegment : newTrackingParticle.g4Tracks() )
                    {
                        pBremParentTrackingParticle->addG4Track( trackSegment );
                    }

                    // Also copy the generator particle references
                    for( const auto& genParticleRef : newTrackingParticle.genParticles() )
                    {
                        pBremParentTrackingParticle->addGenParticle( genParticleRef );
                    }

                    pBremParentTrackingParticle->setNumberOfHits(pBremParentTrackingParticle->numberOfHits()+newTrackingParticle.numberOfHits());
                    pBremParentTrackingParticle->setNumberOfTrackerHits(pBremParentTrackingParticle->numberOfTrackerHits()+newTrackingParticle.numberOfTrackerHits());
                    pBremParentTrackingParticle->setNumberOfTrackerLayers(pBremParentTrackingParticle->numberOfTrackerLayers()+newTrackingParticle.numberOfTrackerLayers());

                    // Set a proxy in the output collection wrapper so that any attempt to get objects for
                    // this DecayChainTrack again get redirected to the brem parent.
                    pMergedOutput->setProxy( pDecayChainTrack, pBremParentChainTrack );
                }
            }
            else
            {
                // This is not the result of bremsstrahlung so add to the collection as normal.
                addTrackAndParentVertex( pDecayChainTrack, newTrackingParticle, pMergedOutput );
            }
        } // end of "if( pMergedOutput!=NULL )", i.e. end of "if bremsstrahlung merging is turned on"

    } // end of addTrack function

} // end of the unnamed namespace

// Register with the framework
DEFINE_DIGI_ACCUMULATOR (TrackingTruthAccumulator);