/data/doxygen/doxygen-1.7.3/gen/CMSSW_4_2_8/src/RecoJets/JetAlgorithms/src/SubJetAlgorithm.cc

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#include "RecoJets/JetAlgorithms/interface/SubJetAlgorithm.h"
#include "FWCore/MessageLogger/interface/MessageLogger.h"
#include "FWCore/Utilities/interface/Exception.h"
#include "fastjet/ClusterSequenceArea.hh"

using namespace std;
using namespace edm;

void SubJetAlgorithm::set_zcut(double z){
    zcut_ = z;
}

void SubJetAlgorithm::set_rcut_factor(double r){
    rcut_factor_ = r;
}


//  Run the algorithm
//  ------------------
void SubJetAlgorithm::run( const vector<fastjet::PseudoJet> & cell_particles, 
                           vector<CompoundPseudoJet> & hardjetsOutput ) {

  //for actual jet clustering, either the pruned or the original version is used.
  //For the pruned version, a new jet definition using the PrunedRecombPlugin is required:
  fastjet::FastPrunePlugin PRplugin(*fjJetDefinition_,
                                    *fjJetDefinition_,
                                    zcut_,
                                    rcut_factor_);
  fastjet::JetDefinition pjetdef(&PRplugin);



  // cluster the jets with the jet definition jetDef:
  // run algorithm
  boost::shared_ptr<fastjet::ClusterSequence> fjClusterSeq;
  if ( !doAreaFastjet_ ) {
    fjClusterSeq = 
      boost::shared_ptr<fastjet::ClusterSequence>( new fastjet::ClusterSequence( cell_particles, 
                                                                                 pjetdef ) );
  } else if (voronoiRfact_ <= 0) {
    fjClusterSeq = 
      boost::shared_ptr<fastjet::ClusterSequence>( new fastjet::ClusterSequenceActiveArea( cell_particles, 
                                                                                           pjetdef , 
                                                                                           *fjActiveArea_ ) );
  } else {
    fjClusterSeq = 
      boost::shared_ptr<fastjet::ClusterSequence>( new fastjet::ClusterSequenceVoronoiArea( cell_particles, 
                                                                                            pjetdef , 
                                                                                            fastjet::VoronoiAreaSpec(voronoiRfact_) ) );
  }

  vector<fastjet::PseudoJet> inclusiveJets = fjClusterSeq->inclusive_jets(ptMin_);

  // These will store the indices of each subjet that 
  // are present in each jet
  vector<vector<int> > indices(inclusiveJets.size());
  // Loop over inclusive jets, attempt to find substructure
  vector<fastjet::PseudoJet>::iterator jetIt = inclusiveJets.begin();
  for ( ; jetIt != inclusiveJets.end(); ++jetIt ) {
    //decompose into requested number of subjets:
    vector<fastjet::PseudoJet> subjets = fjClusterSeq->exclusive_subjets(*jetIt, nSubjets_);
    //create the subjets objects to put into the "output" objects
    vector<CompoundPseudoSubJet>  subjetsOutput;
    std::vector<fastjet::PseudoJet>::const_iterator itSubJetBegin = subjets.begin(),
      itSubJet = itSubJetBegin, itSubJetEnd = subjets.end();
    for (; itSubJet != itSubJetEnd; ++itSubJet ){
      // Get the transient subjet constituents from fastjet
      vector<fastjet::PseudoJet> subjetFastjetConstituents = fjClusterSeq->constituents( *itSubJet );
      // Get the indices of the constituents:
      vector<int> constituents;
      vector<fastjet::PseudoJet>::const_iterator fastSubIt = subjetFastjetConstituents.begin(),
        transConstBegin = subjetFastjetConstituents.begin(),
        transConstEnd = subjetFastjetConstituents.end();
      for ( ; fastSubIt != transConstEnd; ++fastSubIt ) {
        if (fastSubIt->user_index() >= 0) {
          constituents.push_back( fastSubIt->user_index() );
        }
      }

      double subJetArea = (doAreaFastjet_) ?
        dynamic_cast<fastjet::ClusterSequenceActiveArea&>(*fjClusterSeq).area(*itSubJet) : 0.0;


      // Make a CompoundPseudoSubJet object to hold this subjet and the indices of its constituents
      subjetsOutput.push_back( CompoundPseudoSubJet( *itSubJet, subJetArea, constituents ) );

    }


    double fatJetArea = (doAreaFastjet_) ?
      dynamic_cast<fastjet::ClusterSequenceActiveArea&>(*fjClusterSeq).area(*jetIt) : 0.0;

    // Make a CompoundPseudoJet object to hold this hard jet, and the subjets that make it up
    hardjetsOutput.push_back( CompoundPseudoJet( *jetIt,fatJetArea,subjetsOutput));
  }
}