JetFlavourClustering.cc

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// -*- C++ -*-
//
// Package:    JetFlavourClustering
// Class:      JetFlavourClustering
//
//
// Original Author:  Dinko Ferencek
//         Created:  Wed Nov  6 00:49:55 CET 2013
//
//


// system include files
#include <memory>

// user include files
#include "FWCore/Framework/interface/Frameworkfwd.h"
#include "FWCore/Framework/interface/EDProducer.h"

#include "FWCore/Framework/interface/Event.h"
#include "FWCore/Framework/interface/MakerMacros.h"

#include "FWCore/ParameterSet/interface/ParameterSet.h"

#include "DataFormats/JetReco/interface/Jet.h"
#include "DataFormats/JetReco/interface/JetCollection.h"
#include "SimDataFormats/JetMatching/interface/JetFlavourInfo.h"
#include "SimDataFormats/JetMatching/interface/JetFlavourInfoMatching.h"
#include "DataFormats/HepMCCandidate/interface/GenParticle.h"
#include "DataFormats/HepMCCandidate/interface/GenParticleFwd.h"
#include "DataFormats/Math/interface/deltaR.h"
#include "PhysicsTools/JetMCUtils/interface/CandMCTag.h"

#include "fastjet/JetDefinition.hh"
#include "fastjet/ClusterSequence.hh"
#include "fastjet/Selector.hh"
#include "fastjet/PseudoJet.hh"

//
// constants, enums and typedefs
//
typedef boost::shared_ptr<fastjet::ClusterSequence>  ClusterSequencePtr;
typedef boost::shared_ptr<fastjet::JetDefinition>    JetDefPtr;

//
// class declaration
//
class GhostInfo : public fastjet::PseudoJet::UserInfoBase{
  public:
    GhostInfo(const bool & isHadron,
              const bool & isbHadron,
              const bool & isParton,
              const bool & isLepton,
              const reco::GenParticleRef & particleRef) :
      m_particleRef(particleRef)
    {
      m_type = 0;
      if( isHadron )  m_type |= ( 1 << 0 );
      if( isbHadron ) m_type |= ( 1 << 1 );
      if( isParton )  m_type |= ( 1 << 2 );
      if( isLepton )  m_type |= ( 1 << 3 );
    }

    const bool isHadron()  const { return ( m_type & (1 << 0) ); }
    const bool isbHadron() const { return ( m_type & (1 << 1) ); }
    const bool isParton()  const { return ( m_type & (1 << 2) ); }
    const bool isLepton()  const { return ( m_type & (1 << 3) ); }
    const reco::GenParticleRef & particleRef() const { return m_particleRef; }

  protected:
    const reco::GenParticleRef m_particleRef;
    int m_type;
};

class JetFlavourClustering : public edm::EDProducer {
   public:
      explicit JetFlavourClustering(const edm::ParameterSet&);
      ~JetFlavourClustering();

      static void fillDescriptions(edm::ConfigurationDescriptions& descriptions);

   private:
      virtual void beginJob() ;
      virtual void produce(edm::Event&, const edm::EventSetup&);
      virtual void endJob() ;

      virtual void beginRun(edm::Run&, edm::EventSetup const&);
      virtual void endRun(edm::Run&, edm::EventSetup const&);
      virtual void beginLuminosityBlock(edm::LuminosityBlock&, edm::EventSetup const&);
      virtual void endLuminosityBlock(edm::LuminosityBlock&, edm::EventSetup const&);

      void insertGhosts(const edm::Handle<reco::GenParticleRefVector>& particles,
                        const double ghostRescaling,
                        const bool isHadron, const bool isbHadron, const bool isParton, const bool isLepton,
                        std::vector<fastjet::PseudoJet>& constituents);

      void matchReclusteredJets(const edm::Handle<edm::View<reco::Jet> >& jets,
                                const std::vector<fastjet::PseudoJet>& matchedJets,
                                std::vector<int>& matchedIndices);
      void matchGroomedJets(const edm::Handle<edm::View<reco::Jet> >& jets,
                            const edm::Handle<edm::View<reco::Jet> >& matchedJets,
                            std::vector<int>& matchedIndices);
      void matchSubjets(const std::vector<int>& groomedIndices,
                        const edm::Handle<edm::View<reco::Jet> >& groomedJets,
                        const edm::Handle<edm::View<reco::Jet> >& subjets,
                        std::vector<std::vector<int> >& matchedIndices);

      void setFlavours(const reco::GenParticleRefVector& clusteredbHadrons,
                       const reco::GenParticleRefVector& clusteredcHadrons,
                       const reco::GenParticleRefVector& clusteredPartons,
                       int&  hadronFlavour,
                       int&  partonFlavour);

      void assignToSubjets(const reco::GenParticleRefVector& clusteredParticles,
                           const edm::Handle<edm::View<reco::Jet> >& subjets,
                           const std::vector<int>& subjetIndices,
                           std::vector<reco::GenParticleRefVector>& assignedParticles);

      // ----------member data ---------------------------
      const edm::EDGetTokenT<edm::View<reco::Jet> >      jetsToken_;        // Input jet collection
      const edm::EDGetTokenT<edm::View<reco::Jet> >      groomedJetsToken_; // Input groomed jet collection
      const edm::EDGetTokenT<edm::View<reco::Jet> >      subjetsToken_;     // Input subjet collection
      const edm::EDGetTokenT<reco::GenParticleRefVector> bHadronsToken_;    // Input b hadron collection
      const edm::EDGetTokenT<reco::GenParticleRefVector> cHadronsToken_;    // Input c hadron collection
      const edm::EDGetTokenT<reco::GenParticleRefVector> partonsToken_;     // Input parton collection
      const edm::EDGetTokenT<reco::GenParticleRefVector> leptonsToken_;     // Input lepton collection

      const std::string   jetAlgorithm_;
      const double        rParam_;
      const double        jetPtMin_;
      const double        ghostRescaling_;
      const bool          hadronFlavourHasPriority_;
      const bool          useSubjets_;
      const bool          useLeptons_;

      ClusterSequencePtr  fjClusterSeq_;
      JetDefPtr           fjJetDefinition_;
};

//
// static data member definitions
//

//
// constructors and destructor
//
JetFlavourClustering::JetFlavourClustering(const edm::ParameterSet& iConfig) :

   jetsToken_(consumes<edm::View<reco::Jet> >( iConfig.getParameter<edm::InputTag>("jets")) ),
   groomedJetsToken_(mayConsume<edm::View<reco::Jet> >( iConfig.exists("groomedJets") ? iConfig.getParameter<edm::InputTag>("groomedJets") : edm::InputTag() )),
   subjetsToken_(mayConsume<edm::View<reco::Jet> >( iConfig.exists("subjets") ? iConfig.getParameter<edm::InputTag>("subjets") : edm::InputTag() )),
   bHadronsToken_(consumes<reco::GenParticleRefVector>( iConfig.getParameter<edm::InputTag>("bHadrons") )),
   cHadronsToken_(consumes<reco::GenParticleRefVector>( iConfig.getParameter<edm::InputTag>("cHadrons") )),
   partonsToken_(consumes<reco::GenParticleRefVector>( iConfig.getParameter<edm::InputTag>("partons") )),
   leptonsToken_(mayConsume<reco::GenParticleRefVector>( iConfig.exists("leptons") ? iConfig.getParameter<edm::InputTag>("leptons") : edm::InputTag() )),
   jetAlgorithm_(iConfig.getParameter<std::string>("jetAlgorithm")),
   rParam_(iConfig.getParameter<double>("rParam")),
   jetPtMin_(0.), // hardcoded to 0. since we simply want to recluster all input jets which already had some PtMin applied
   ghostRescaling_(iConfig.exists("ghostRescaling") ? iConfig.getParameter<double>("ghostRescaling") : 1e-18),
   hadronFlavourHasPriority_(iConfig.getParameter<bool>("hadronFlavourHasPriority")),
   useSubjets_(iConfig.exists("groomedJets") && iConfig.exists("subjets")),
   useLeptons_(iConfig.exists("leptons"))

{
   // register your products
   produces<reco::JetFlavourInfoMatchingCollection>();
   if( useSubjets_ )
     produces<reco::JetFlavourInfoMatchingCollection>("SubJets");

   // set jet algorithm
   if (jetAlgorithm_=="Kt")
     fjJetDefinition_= JetDefPtr( new fastjet::JetDefinition(fastjet::kt_algorithm, rParam_) );
   else if (jetAlgorithm_=="CambridgeAachen")
     fjJetDefinition_= JetDefPtr( new fastjet::JetDefinition(fastjet::cambridge_algorithm, rParam_) );
   else if (jetAlgorithm_=="AntiKt")
     fjJetDefinition_= JetDefPtr( new fastjet::JetDefinition(fastjet::antikt_algorithm, rParam_) );
   else
     throw cms::Exception("InvalidJetAlgorithm") << "Jet clustering algorithm is invalid: " << jetAlgorithm_ << ", use CambridgeAachen | Kt | AntiKt" << std::endl;
}


JetFlavourClustering::~JetFlavourClustering()
{

   // do anything here that needs to be done at desctruction time
   // (e.g. close files, deallocate resources etc.)

}


//
// member functions
//

// ------------ method called to produce the data  ------------
void
JetFlavourClustering::produce(edm::Event& iEvent, const edm::EventSetup& iSetup)
{
   edm::Handle<edm::View<reco::Jet> > jets;
   iEvent.getByToken(jetsToken_, jets);

   edm::Handle<edm::View<reco::Jet> > groomedJets;
   edm::Handle<edm::View<reco::Jet> > subjets;
   if( useSubjets_ )
   {
     iEvent.getByToken(groomedJetsToken_, groomedJets);
     iEvent.getByToken(subjetsToken_, subjets);
   }

   edm::Handle<reco::GenParticleRefVector> bHadrons;
   iEvent.getByToken(bHadronsToken_, bHadrons);

   edm::Handle<reco::GenParticleRefVector> cHadrons;
   iEvent.getByToken(cHadronsToken_, cHadrons);

   edm::Handle<reco::GenParticleRefVector> partons;
   iEvent.getByToken(partonsToken_, partons);

   edm::Handle<reco::GenParticleRefVector> leptons;
   if( useLeptons_ )
     iEvent.getByToken(leptonsToken_, leptons);

   std::auto_ptr<reco::JetFlavourInfoMatchingCollection> jetFlavourInfos( new reco::JetFlavourInfoMatchingCollection(reco::JetRefBaseProd(jets)) );
   std::auto_ptr<reco::JetFlavourInfoMatchingCollection> subjetFlavourInfos;
   if( useSubjets_ )
     subjetFlavourInfos = std::auto_ptr<reco::JetFlavourInfoMatchingCollection>( new reco::JetFlavourInfoMatchingCollection(reco::JetRefBaseProd(subjets)) );

   // vector of constituents for reclustering jets and "ghosts"
   std::vector<fastjet::PseudoJet> fjInputs;
   // loop over all input jets and collect all their constituents
   for(edm::View<reco::Jet>::const_iterator it = jets->begin(); it != jets->end(); ++it)
   {
     std::vector<edm::Ptr<reco::Candidate> > constituents = it->getJetConstituents();
     std::vector<edm::Ptr<reco::Candidate> >::const_iterator m;
     for( m = constituents.begin(); m != constituents.end(); ++m )
     {
       reco::CandidatePtr constit = *m;
       if(constit->pt() == 0)
       {
         edm::LogWarning("NullTransverseMomentum") << "dropping input candidate with pt=0";
         continue;
       }
       fjInputs.push_back(fastjet::PseudoJet(constit->px(),constit->py(),constit->pz(),constit->energy()));
     }
   }
   // insert "ghost" b hadrons in the vector of constituents
   insertGhosts(bHadrons, ghostRescaling_, true, true, false, false, fjInputs);
   // insert "ghost" c hadrons in the vector of constituents
   insertGhosts(cHadrons, ghostRescaling_, true, false, false, false, fjInputs);
   // insert "ghost" partons in the vector of constituents
   insertGhosts(partons, ghostRescaling_, false, false, true, false, fjInputs);
   // if used, insert "ghost" leptons in the vector of constituents
   if( useLeptons_ )
     insertGhosts(leptons, ghostRescaling_, false, false, false, true, fjInputs);

   // define jet clustering sequence
   fjClusterSeq_ = ClusterSequencePtr( new fastjet::ClusterSequence( fjInputs, *fjJetDefinition_ ) );
   // recluster jet constituents and inserted "ghosts"
   std::vector<fastjet::PseudoJet> inclusiveJets = fastjet::sorted_by_pt( fjClusterSeq_->inclusive_jets(jetPtMin_) );

   if( inclusiveJets.size() < jets->size() )
     edm::LogError("TooFewReclusteredJets") << "There are fewer reclustered (" << inclusiveJets.size() << ") than original jets (" << jets->size() << "). Please check that the jet algorithm and jet size match those used for the original jet collection.";

   // match reclustered and original jets
   std::vector<int> reclusteredIndices;
   matchReclusteredJets(jets,inclusiveJets,reclusteredIndices);

   // match groomed and original jets
   std::vector<int> groomedIndices;
   if( useSubjets_ )
   {
     if( groomedJets->size() > jets->size() )
       edm::LogError("TooManyGroomedJets") << "There are more groomed (" << groomedJets->size() << ") than original jets (" << jets->size() << "). Please check that the two jet collections belong to each other.";

     matchGroomedJets(jets,groomedJets,groomedIndices);
   }

   // match subjets and original jets
   std::vector<std::vector<int> > subjetIndices;
   if( useSubjets_ )
   {
     matchSubjets(groomedIndices,groomedJets,subjets,subjetIndices);
   }

   // determine jet flavour
   for(size_t i=0; i<jets->size(); ++i)
   {
     // since the "ghosts" are extremely soft, the configuration and ordering of the reclustered and original jets should in principle stay the same
     if( ( fabs( inclusiveJets.at(reclusteredIndices.at(i)).pt() - jets->at(i).pt() ) / jets->at(i).pt() ) > 1e-3 ) // 0.1% difference in Pt should be sufficient to detect possible misconfigurations
     {
       if( jets->at(i).pt() < 10. )  // special handling for low-Pt jets (Pt<10 GeV)
         edm::LogWarning("JetPtMismatchAtLowPt") << "The reclustered and original jet " << i << " have different Pt's (" << inclusiveJets.at(reclusteredIndices.at(i)).pt() << " vs " << jets->at(i).pt() << " GeV, respectively).\n"
                                                 << "Please check that the jet algorithm and jet size match those used for the original jet collection and also make sure the original jets are uncorrected. In addition, make sure you are not using CaloJets which are presently not supported.\n"
                                                 << "Since the mismatch is at low Pt, it is ignored and only a warning is issued.\n"
                                                 << "\nIn extremely rare instances the mismatch could be caused by a difference in the machine precision in which case make sure the original jet collection is produced and reclustering is performed in the same job.";
       else
         edm::LogError("JetPtMismatch") << "The reclustered and original jet " << i << " have different Pt's (" << inclusiveJets.at(reclusteredIndices.at(i)).pt() << " vs " << jets->at(i).pt() << " GeV, respectively).\n"
                                        << "Please check that the jet algorithm and jet size match those used for the original jet collection and also make sure the original jets are uncorrected. In addition, make sure you are not using CaloJets which are presently not supported.\n"
                                        << "\nIn extremely rare instances the mismatch could be caused by a difference in the machine precision in which case make sure the original jet collection is produced and reclustering is performed in the same job.";
     }

     reco::GenParticleRefVector clusteredbHadrons;
     reco::GenParticleRefVector clusteredcHadrons;
     reco::GenParticleRefVector clusteredPartons;
     reco::GenParticleRefVector clusteredLeptons;

     // get jet constituents (sorted by Pt)
     std::vector<fastjet::PseudoJet> constituents = fastjet::sorted_by_pt( inclusiveJets.at(reclusteredIndices.at(i)).constituents() );

     // loop over jet constituents and try to find "ghosts"
     for(std::vector<fastjet::PseudoJet>::const_iterator it = constituents.begin(); it != constituents.end(); ++it)
     {
       if( !it->has_user_info() ) continue; // skip if not a "ghost"

       // "ghost" hadron
       if( it->user_info<GhostInfo>().isHadron() )
       {
         // "ghost" b hadron
         if( it->user_info<GhostInfo>().isbHadron() )
           clusteredbHadrons.push_back(it->user_info<GhostInfo>().particleRef());
         // "ghost" c hadron
         else
           clusteredcHadrons.push_back(it->user_info<GhostInfo>().particleRef());
       }
       // "ghost" parton
       else if( it->user_info<GhostInfo>().isParton() )
         clusteredPartons.push_back(it->user_info<GhostInfo>().particleRef());
       // "ghost" lepton
       else if( it->user_info<GhostInfo>().isLepton() )
         clusteredLeptons.push_back(it->user_info<GhostInfo>().particleRef());
     }

     int hadronFlavour = 0; // default hadron flavour set to 0 (= undefined)
     int partonFlavour = 0; // default parton flavour set to 0 (= undefined)

     // set hadron- and parton-based flavours
     setFlavours(clusteredbHadrons, clusteredcHadrons, clusteredPartons, hadronFlavour, partonFlavour);

     // set the JetFlavourInfo for this jet
     (*jetFlavourInfos)[jets->refAt(i)] = reco::JetFlavourInfo(clusteredbHadrons, clusteredcHadrons, clusteredPartons, clusteredLeptons, hadronFlavour, partonFlavour);

     // if subjets are used, determine their flavour
     if( useSubjets_ )
     {
       if( subjetIndices.at(i).size()==0 ) continue; // continue if the original jet does not have subjets assigned

       // define vectors of GenParticleRefVectors for hadrons and partons assigned to different subjets
       std::vector<reco::GenParticleRefVector> assignedbHadrons(subjetIndices.at(i).size(),reco::GenParticleRefVector());
       std::vector<reco::GenParticleRefVector> assignedcHadrons(subjetIndices.at(i).size(),reco::GenParticleRefVector());
       std::vector<reco::GenParticleRefVector> assignedPartons(subjetIndices.at(i).size(),reco::GenParticleRefVector());
       std::vector<reco::GenParticleRefVector> assignedLeptons(subjetIndices.at(i).size(),reco::GenParticleRefVector());

       // loop over clustered b hadrons and assign them to different subjets based on smallest dR
       assignToSubjets(clusteredbHadrons, subjets, subjetIndices.at(i), assignedbHadrons);
       // loop over clustered c hadrons and assign them to different subjets based on smallest dR
       assignToSubjets(clusteredcHadrons, subjets, subjetIndices.at(i), assignedcHadrons);
       // loop over clustered partons and assign them to different subjets based on smallest dR
       assignToSubjets(clusteredPartons, subjets, subjetIndices.at(i), assignedPartons);
       // if used, loop over clustered leptons and assign them to different subjets based on smallest dR
       if( useLeptons_ )
         assignToSubjets(clusteredLeptons, subjets, subjetIndices.at(i), assignedLeptons);

       // loop over subjets and determine their flavour
       for(size_t sj=0; sj<subjetIndices.at(i).size(); ++sj)
       {
         int subjetHadronFlavour = 0; // default hadron flavour set to 0 (= undefined)
         int subjetPartonFlavour = 0; // default parton flavour set to 0 (= undefined)

         // set hadron- and parton-based flavours
         setFlavours(assignedbHadrons.at(sj), assignedcHadrons.at(sj), assignedPartons.at(sj), subjetHadronFlavour, subjetPartonFlavour);

         // set the JetFlavourInfo for this subjet
         (*subjetFlavourInfos)[subjets->refAt(subjetIndices.at(i).at(sj))] = reco::JetFlavourInfo(assignedbHadrons.at(sj), assignedcHadrons.at(sj), assignedPartons.at(sj), assignedLeptons.at(sj), subjetHadronFlavour, subjetPartonFlavour);
       }
     }
   }

   // put jet flavour infos in the event
   iEvent.put( jetFlavourInfos );
   // put subjet flavour infos in the event
   if( useSubjets_ )
     iEvent.put( subjetFlavourInfos, "SubJets" );
}

// ------------ method that inserts "ghost" particles in the vector of jet constituents ------------
void
JetFlavourClustering::insertGhosts(const edm::Handle<reco::GenParticleRefVector>& particles,
                                   const double ghostRescaling,
                                   const bool isHadron, const bool isbHadron, const bool isParton, const bool isLepton,
                                   std::vector<fastjet::PseudoJet>& constituents)
{
   // insert "ghost" particles in the vector of jet constituents
   for(reco::GenParticleRefVector::const_iterator it = particles->begin(); it != particles->end(); ++it)
   {
     fastjet::PseudoJet p((*it)->px(),(*it)->py(),(*it)->pz(),(*it)->energy());
     p*=ghostRescaling; // rescale particle momentum
     p.set_user_info(new GhostInfo(isHadron, isbHadron, isParton, isLepton, *it));
     constituents.push_back(p);
   }
}

// ------------ method that matches reclustered and original jets based on minimum dR ------------
void
JetFlavourClustering::matchReclusteredJets(const edm::Handle<edm::View<reco::Jet> >& jets,
                                           const std::vector<fastjet::PseudoJet>& reclusteredJets,
                                           std::vector<int>& matchedIndices)
{
   std::vector<bool> matchedLocks(reclusteredJets.size(),false);

   for(size_t j=0; j<jets->size(); ++j)
   {
     double matchedDR2 = 1e9;
     int matchedIdx = -1;

     for(size_t rj=0; rj<reclusteredJets.size(); ++rj)
     {
       if( matchedLocks.at(rj) ) continue; // skip jets that have already been matched

       double tempDR2 = reco::deltaR2( jets->at(j).rapidity(), jets->at(j).phi(), reclusteredJets.at(rj).rapidity(), reclusteredJets.at(rj).phi_std() );
       if( tempDR2 < matchedDR2 )
       {
         matchedDR2 = tempDR2;
         matchedIdx = rj;
       }
     }

     if( matchedIdx>=0 )
     {
       if ( matchedDR2 > rParam_*rParam_ )
       {
         edm::LogError("JetMatchingFailed") << "Matched reclustered jet " << matchedIdx << " and original jet " << j <<" are separated by dR=" << sqrt(matchedDR2) << " which is greater than the jet size R=" << rParam_ << ".\n"
                                            << "This is not expected so please check that the jet algorithm and jet size match those used for the original jet collection.";
       }
       else
         matchedLocks.at(matchedIdx) = true;
     }
     else
       edm::LogError("JetMatchingFailed") << "Matching reclustered to original jets failed. Please check that the jet algorithm and jet size match those used for the original jet collection.";

     matchedIndices.push_back(matchedIdx);
   }
}

// ------------ method that matches groomed and original jets based on minimum dR ------------
void
JetFlavourClustering::matchGroomedJets(const edm::Handle<edm::View<reco::Jet> >& jets,
                                       const edm::Handle<edm::View<reco::Jet> >& groomedJets,
                                       std::vector<int>& matchedIndices)
{
   std::vector<bool> jetLocks(jets->size(),false);
   std::vector<int>  jetIndices;

   for(size_t gj=0; gj<groomedJets->size(); ++gj)
   {
     double matchedDR2 = 1e9;
     int matchedIdx = -1;

     if( groomedJets->at(gj).pt()>0. ) // skips pathological cases of groomed jets with Pt=0
     {
       for(size_t j=0; j<jets->size(); ++j)
       {
         if( jetLocks.at(j) ) continue; // skip jets that have already been matched

         double tempDR2 = reco::deltaR2( jets->at(j).rapidity(), jets->at(j).phi(), groomedJets->at(gj).rapidity(), groomedJets->at(gj).phi() );
         if( tempDR2 < matchedDR2 )
         {
           matchedDR2 = tempDR2;
           matchedIdx = j;
         }
       }
     }

     if( matchedIdx>=0 )
     {
       if ( matchedDR2 > rParam_*rParam_ )
       {
         edm::LogWarning("MatchedJetsFarApart") << "Matched groomed jet " << gj << " and original jet " << matchedIdx <<" are separated by dR=" << sqrt(matchedDR2) << " which is greater than the jet size R=" << rParam_ << ".\n"
                                                << "This is not expected so the matching of these two jets has been discarded. Please check that the two jet collections belong to each other.";
         matchedIdx = -1;
       }
       else
         jetLocks.at(matchedIdx) = true;
     }
     jetIndices.push_back(matchedIdx);
   }

   for(size_t j=0; j<jets->size(); ++j)
   {
     std::vector<int>::iterator matchedIndex = std::find( jetIndices.begin(), jetIndices.end(), j );

     matchedIndices.push_back( matchedIndex != jetIndices.end() ? std::distance(jetIndices.begin(),matchedIndex) : -1 );
   }
}

// ------------ method that matches subjets and original jets ------------
void
JetFlavourClustering::matchSubjets(const std::vector<int>& groomedIndices,
                                   const edm::Handle<edm::View<reco::Jet> >& groomedJets,
                                   const edm::Handle<edm::View<reco::Jet> >& subjets,
                                   std::vector<std::vector<int> >& matchedIndices)
{
   for(size_t g=0; g<groomedIndices.size(); ++g)
   {
     std::vector<int> subjetIndices;

     if( groomedIndices.at(g)>=0 )
     {
       for(size_t s=0; s<groomedJets->at(groomedIndices.at(g)).numberOfDaughters(); ++s)
       {
         const edm::Ptr<reco::Candidate> & subjet = groomedJets->at(groomedIndices.at(g)).daughterPtr(s);

         for(size_t sj=0; sj<subjets->size(); ++sj)
         {
           if( subjet == edm::Ptr<reco::Candidate>(subjets->ptrAt(sj)) )
           {
             subjetIndices.push_back(sj);
             break;
           }
         }
       }

       if( subjetIndices.size() == 0 )
         edm::LogError("SubjetMatchingFailed") << "Matching subjets to original jets failed. Please check that the groomed jet and subjet collections belong to each other.";

       matchedIndices.push_back(subjetIndices);
     }
     else
       matchedIndices.push_back(subjetIndices);
   }
}

// ------------ method that sets hadron- and parton-based flavours ------------
void
JetFlavourClustering::setFlavours(const reco::GenParticleRefVector& clusteredbHadrons,
                                  const reco::GenParticleRefVector& clusteredcHadrons,
                                  const reco::GenParticleRefVector& clusteredPartons,
                                  int&  hadronFlavour,
                                  int&  partonFlavour)
{
   reco::GenParticleRef hardestParton;
   reco::GenParticleRef hardestLightParton;
   reco::GenParticleRef flavourParton;

   // loop over clustered partons (already sorted by Pt)
   for(reco::GenParticleRefVector::const_iterator it = clusteredPartons.begin(); it != clusteredPartons.end(); ++it)
   {
     // hardest parton
     if( hardestParton.isNull() )
       hardestParton = (*it);
     // hardest light-flavour parton
     if( hardestLightParton.isNull() )
     {
       if( CandMCTagUtils::isLightParton( *(*it) ) )
         hardestLightParton = (*it);
     }
     // c flavour
     if( flavourParton.isNull() && ( abs( (*it)->pdgId() ) == 4 ) )
       flavourParton = (*it);
     // b flavour gets priority
     if( abs( (*it)->pdgId() ) == 5 )
     {
       if( flavourParton.isNull() )
         flavourParton = (*it);
       else if( abs( flavourParton->pdgId() ) != 5 )
         flavourParton = (*it);
     }
   }

   // set hadron-based flavour
   if( clusteredbHadrons.size()>0 )
     hadronFlavour = 5;
   else if( clusteredcHadrons.size()>0 && clusteredbHadrons.size()==0 )
     hadronFlavour = 4;
   // set parton-based flavour
   if( flavourParton.isNull() )
   {
     if( hardestParton.isNonnull() ) partonFlavour = hardestParton->pdgId();
   }
   else
     partonFlavour = flavourParton->pdgId();

   // if enabled, check for conflicts between hadron- and parton-based flavours and give priority to the hadron-based flavour
   if( hadronFlavourHasPriority_ )
   {
     if( hadronFlavour==0 && (abs(partonFlavour)==4 || abs(partonFlavour)==5) )
       partonFlavour = ( hardestLightParton.isNonnull() ? hardestLightParton->pdgId() : 0 );
     else if( hadronFlavour!=0 && abs(partonFlavour)!=hadronFlavour )
       partonFlavour = hadronFlavour;
   }
}

// ------------ method that assigns clustered particles to subjets ------------
void
JetFlavourClustering::assignToSubjets(const reco::GenParticleRefVector& clusteredParticles,
                                      const edm::Handle<edm::View<reco::Jet> >& subjets,
                                      const std::vector<int>& subjetIndices,
                                      std::vector<reco::GenParticleRefVector>& assignedParticles)
{
   // loop over clustered particles and assign them to different subjets based on smallest dR
   for(reco::GenParticleRefVector::const_iterator it = clusteredParticles.begin(); it != clusteredParticles.end(); ++it)
   {
     std::vector<double> dR2toSubjets;

     for(size_t sj=0; sj<subjetIndices.size(); ++sj)
       dR2toSubjets.push_back( reco::deltaR2( (*it)->rapidity(), (*it)->phi(), subjets->at(subjetIndices.at(sj)).rapidity(), subjets->at(subjetIndices.at(sj)).phi() ) );

     // find the closest subjet
     int closestSubjetIdx = std::distance( dR2toSubjets.begin(), std::min_element(dR2toSubjets.begin(), dR2toSubjets.end()) );

     assignedParticles.at(closestSubjetIdx).push_back( *it );
   }
}

// ------------ method called once each job just before starting event loop  ------------
void
JetFlavourClustering::beginJob()
{
}

// ------------ method called once each job just after ending the event loop  ------------
void
JetFlavourClustering::endJob() {
}

// ------------ method called when starting to processes a run  ------------
void
JetFlavourClustering::beginRun(edm::Run&, edm::EventSetup const&)
{
}

// ------------ method called when ending the processing of a run  ------------
void
JetFlavourClustering::endRun(edm::Run&, edm::EventSetup const&)
{
}

// ------------ method called when starting to processes a luminosity block  ------------
void
JetFlavourClustering::beginLuminosityBlock(edm::LuminosityBlock&, edm::EventSetup const&)
{
}

// ------------ method called when ending the processing of a luminosity block  ------------
void
JetFlavourClustering::endLuminosityBlock(edm::LuminosityBlock&, edm::EventSetup const&)
{
}

// ------------ method fills 'descriptions' with the allowed parameters for the module  ------------
void
JetFlavourClustering::fillDescriptions(edm::ConfigurationDescriptions& descriptions) {
  //The following says we do not know what parameters are allowed so do no validation
  // Please change this to state exactly what you do use, even if it is no parameters
  edm::ParameterSetDescription desc;
  desc.setUnknown();
  descriptions.addDefault(desc);
}

//define this as a plug-in
DEFINE_FWK_MODULE(JetFlavourClustering);