VirtualJetProducer.cc

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//
// VirtualJetProducer
// ------------------
//
//            04/21/2009 Philipp Schieferdecker <philipp.schieferdecker@cern.ch>

#include "FWCore/ParameterSet/interface/ConfigurationDescriptions.h"
#include "FWCore/ParameterSet/interface/ParameterSetDescription.h"
#include "RecoJets/JetProducers/plugins/VirtualJetProducer.h"
#include "RecoJets/JetProducers/interface/BackgroundEstimator.h"
#include "RecoJets/JetProducers/interface/VirtualJetProducerHelper.h"

#include "DataFormats/Common/interface/RefProd.h"
#include "DataFormats/Common/interface/Ref.h"
#include "DataFormats/Common/interface/RefVector.h"

#include "FWCore/Framework/interface/Event.h"
#include "FWCore/Framework/interface/EventSetup.h"
#include "FWCore/Framework/interface/ESHandle.h"
#include "FWCore/Utilities/interface/Exception.h"
#include "FWCore/MessageLogger/interface/MessageLogger.h"
#include "FWCore/Framework/interface/MakerMacros.h"
#include "FWCore/Utilities/interface/isFinite.h"
#include "FWCore/Framework/interface/ConsumesCollector.h"

#include "DataFormats/Common/interface/View.h"
#include "DataFormats/Common/interface/Handle.h"
#include "DataFormats/VertexReco/interface/Vertex.h"
#include "DataFormats/VertexReco/interface/VertexFwd.h"
#include "DataFormats/JetReco/interface/CaloJetCollection.h"
#include "DataFormats/JetReco/interface/GenJetCollection.h"
#include "DataFormats/JetReco/interface/PFJetCollection.h"
#include "DataFormats/JetReco/interface/BasicJetCollection.h"
#include "DataFormats/JetReco/interface/TrackJetCollection.h"
#include "DataFormats/JetReco/interface/PFClusterJetCollection.h"
#include "DataFormats/Candidate/interface/CandidateFwd.h"
#include "DataFormats/Candidate/interface/LeafCandidate.h"
#include "DataFormats/Math/interface/deltaR.h"
#include "DataFormats/ParticleFlowCandidate/interface/PFCandidate.h"

#include "fastjet/SISConePlugin.hh"
#include "fastjet/CMSIterativeConePlugin.hh"
#include "fastjet/ATLASConePlugin.hh"
#include "fastjet/CDFMidPointPlugin.hh"

#include <iostream>
#include <memory>
#include <algorithm>
#include <limits>
#include <cmath>
#include <vdt/vdtMath.h>

using namespace std;
using namespace edm;


namespace reco {
  namespace helper {
    struct GreaterByPtPseudoJet {
      bool operator()( const fastjet::PseudoJet & t1, const fastjet::PseudoJet & t2 ) const {
        return t1.perp2() > t2.perp2();
      }
    };

  }
}                                                                                        

//______________________________________________________________________________
const char *const VirtualJetProducer::JetType::names[] = {
  "BasicJet","GenJet","CaloJet","PFJet","TrackJet","PFClusterJet"
};


//______________________________________________________________________________
VirtualJetProducer::JetType::Type
VirtualJetProducer::JetType::byName(const string &name)
{
  const char *const *pos = std::find(names, names + LastJetType, name);
  if (pos == names + LastJetType) {
    std::string errorMessage="Requested jetType not supported: "+name+"\n";
    throw cms::Exception("Configuration",errorMessage);
  }
  return (Type)(pos-names);
}


void VirtualJetProducer::makeProduces( std::string alias, std::string tag )
{


  if ( writeCompound_ ) {
    produces<reco::BasicJetCollection>();
  }

  if ( writeJetsWithConst_ ) {
    produces<reco::PFCandidateCollection>(tag).setBranchAlias(alias);
    produces<reco::PFJetCollection>();
  } else {
    if (makeCaloJet(jetTypeE)) {
      produces<reco::CaloJetCollection>(tag).setBranchAlias(alias);
    }
    else if (makePFJet(jetTypeE)) {
      produces<reco::PFJetCollection>(tag).setBranchAlias(alias);
    }
    else if (makeGenJet(jetTypeE)) {
      produces<reco::GenJetCollection>(tag).setBranchAlias(alias);
    }
    else if (makeTrackJet(jetTypeE)) {
      produces<reco::TrackJetCollection>(tag).setBranchAlias(alias);
    }
    else if (makePFClusterJet(jetTypeE)) {
      produces<reco::PFClusterJetCollection>(tag).setBranchAlias(alias);
    }
    else if (makeBasicJet(jetTypeE)) {
      produces<reco::BasicJetCollection>(tag).setBranchAlias(alias);
    }
  }
}

// construction / destruction

//______________________________________________________________________________
VirtualJetProducer::VirtualJetProducer(const edm::ParameterSet& iConfig) {

    moduleLabel_        = iConfig.getParameter<string>  ("@module_label");
        src_                    = iConfig.getParameter<edm::InputTag>("src");
        srcPVs_                 = iConfig.getParameter<edm::InputTag>("srcPVs");
    jetType_            = iConfig.getParameter<string>  ("jetType");
    jetAlgorithm_       = iConfig.getParameter<string>  ("jetAlgorithm");
    rParam_             = iConfig.getParameter<double>  ("rParam");
    inputEtMin_         = iConfig.getParameter<double>  ("inputEtMin");
    inputEMin_          = iConfig.getParameter<double>  ("inputEMin");
    jetPtMin_           = iConfig.getParameter<double>  ("jetPtMin");
    doPVCorrection_     = iConfig.getParameter<bool>    ("doPVCorrection");
    doAreaFastjet_      = iConfig.getParameter<bool>    ("doAreaFastjet");
    doRhoFastjet_       = iConfig.getParameter<bool>    ("doRhoFastjet");
    jetCollInstanceName_    = iConfig.getParameter<string>  ("jetCollInstanceName");
    doPUOffsetCorr_     = iConfig.getParameter<bool>    ("doPUOffsetCorr");
    puSubtractorName_   = iConfig.getParameter<string>  ("subtractorName");
    useExplicitGhosts_  = iConfig.getParameter<bool>    ("useExplicitGhosts");  // use explicit ghosts in the fastjet clustering sequence?
    doAreaDiskApprox_   = iConfig.getParameter<bool>    ("doAreaDiskApprox");
    voronoiRfact_       = iConfig.getParameter<double>  ("voronoiRfact");   // Voronoi-based area calculation allows for an empirical scale factor
    rhoEtaMax_      = iConfig.getParameter<double>  ("Rho_EtaMax");         // do fasjet area / rho calcluation? => accept corresponding parameters
    ghostEtaMax_        = iConfig.getParameter<double>  ("Ghost_EtaMax");
    activeAreaRepeats_  = iConfig.getParameter<int>     ("Active_Area_Repeats");
    ghostArea_      = iConfig.getParameter<double>  ("GhostArea");
    restrictInputs_     = iConfig.getParameter<bool>    ("restrictInputs");     // restrict inputs to first "maxInputs" towers?
    maxInputs_          = iConfig.getParameter<unsigned int>("maxInputs");
    writeCompound_      = iConfig.getParameter<bool>    ("writeCompound");  // Check to see if we are writing compound jets for substructure and jet grooming
        writeJetsWithConst_     = iConfig.getParameter<bool>("writeJetsWithConst"); //write subtracted jet constituents
    doFastJetNonUniform_    = iConfig.getParameter<bool>    ("doFastJetNonUniform");
    puCenters_      = iConfig.getParameter<vector<double> >("puCenters");
    puWidth_        = iConfig.getParameter<double>  ("puWidth");
    nExclude_       = iConfig.getParameter<unsigned int>("nExclude");
    useDeterministicSeed_   = iConfig.getParameter<bool>    ("useDeterministicSeed");
    minSeed_        = iConfig.getParameter<unsigned int>("minSeed");
    verbosity_      = iConfig.getParameter<int> ("verbosity");

    anomalousTowerDef_ = unique_ptr<AnomalousTower>(new AnomalousTower(iConfig));

    input_vertex_token_ = consumes<reco::VertexCollection>(srcPVs_);
    input_candidateview_token_ = consumes<reco::CandidateView>(src_);
    input_candidatefwdptr_token_ = consumes<vector<edm::FwdPtr<reco::PFCandidate> > >(iConfig.getParameter<edm::InputTag>("src"));
    input_packedcandidatefwdptr_token_ = consumes<vector<edm::FwdPtr<pat::PackedCandidate> > >(iConfig.getParameter<edm::InputTag>("src"));
    input_gencandidatefwdptr_token_ = consumes<vector<edm::FwdPtr<reco::GenParticle> > >(iConfig.getParameter<edm::InputTag>("src"));
    input_packedgencandidatefwdptr_token_ = consumes<vector<edm::FwdPtr<pat::PackedGenParticle> > >(iConfig.getParameter<edm::InputTag>("src"));
    
    //
    // additional parameters to think about:
    // - overlap threshold (set to 0.75 for the time being)
    // - p parameter for generalized kT (set to -2 for the time being)
    // - fastjet PU subtraction parameters (not yet considered)
    //
    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 if (jetAlgorithm_=="GeneralizedKt") 
        fjJetDefinition_= JetDefPtr( new fastjet::JetDefinition(fastjet::genkt_algorithm,rParam_,-2) );

    else if (jetAlgorithm_=="SISCone") {

        fjPlugin_ = PluginPtr( new fastjet::SISConePlugin(rParam_,0.75,0,0.0,false,fastjet::SISConePlugin::SM_pttilde) );
        fjJetDefinition_= JetDefPtr( new fastjet::JetDefinition(&*fjPlugin_) );

    } else if (jetAlgorithm_=="IterativeCone") {

        fjPlugin_ = PluginPtr(new fastjet::CMSIterativeConePlugin(rParam_,1.0));
        fjJetDefinition_= JetDefPtr(new fastjet::JetDefinition(&*fjPlugin_));

    } else if (jetAlgorithm_=="CDFMidPoint") {

        fjPlugin_ = PluginPtr(new fastjet::CDFMidPointPlugin(rParam_,0.75));
        fjJetDefinition_= JetDefPtr(new fastjet::JetDefinition(&*fjPlugin_));

    } else if (jetAlgorithm_=="ATLASCone") {

        fjPlugin_ = PluginPtr(new fastjet::ATLASConePlugin(rParam_));
        fjJetDefinition_= JetDefPtr(new fastjet::JetDefinition(&*fjPlugin_));

    } else {
        throw cms::Exception("Invalid jetAlgorithm") <<"Jet algorithm for VirtualJetProducer is invalid, Abort!\n";
    }

    jetTypeE=JetType::byName(jetType_);

    if ( doPUOffsetCorr_  ) {
        if(puSubtractorName_.empty()){
            LogWarning("VirtualJetProducer") << "Pile Up correction on; however, pile up type is not specified. Using default... \n";
            subtractor_ =  boost::shared_ptr<PileUpSubtractor>(new PileUpSubtractor(iConfig, consumesCollector()));
        } else subtractor_ =  boost::shared_ptr<PileUpSubtractor>(
                PileUpSubtractorFactory::get()->create( puSubtractorName_, iConfig, consumesCollector()));
    }

    // do approximate disk-based area calculation => warn if conflicting request
    if (doAreaDiskApprox_ && doAreaFastjet_)
        throw cms::Exception("Conflicting area calculations") << "Both the calculation of jet area via fastjet and via an analytical disk approximation have been requested. Please decide on one.\n";

    if ( doAreaFastjet_ || doRhoFastjet_ ) {

        if (voronoiRfact_ <= 0) {
            fjActiveArea_     = ActiveAreaSpecPtr(new fastjet::GhostedAreaSpec(ghostEtaMax_,activeAreaRepeats_,ghostArea_));
            

            if ( !useExplicitGhosts_ ) {
                fjAreaDefinition_ = AreaDefinitionPtr( new fastjet::AreaDefinition(fastjet::active_area, *fjActiveArea_ ) );
            } else {
                fjAreaDefinition_ = AreaDefinitionPtr( new fastjet::AreaDefinition(fastjet::active_area_explicit_ghosts, *fjActiveArea_ ) );
            }
        }
        fjSelector_ =  SelectorPtr( new fastjet::Selector( fastjet::SelectorAbsRapMax(rhoEtaMax_) ) );
    } 

    if( ( doFastJetNonUniform_ ) && ( puCenters_.empty() ) ) 
        throw cms::Exception("doFastJetNonUniform") << "Parameter puCenters for doFastJetNonUniform is not defined." << std::endl;
  
        // make the "produces" statements
        makeProduces( moduleLabel_, jetCollInstanceName_ );
    produces<vector<double> >("rhos");
    produces<vector<double> >("sigmas");
    produces<double>("rho");
    produces<double>("sigma");

  
}

//______________________________________________________________________________
VirtualJetProducer::~VirtualJetProducer()
{
} 


// implementation of member functions

//______________________________________________________________________________
void VirtualJetProducer::produce(edm::Event& iEvent,const edm::EventSetup& iSetup)
{

  // If requested, set the fastjet random seed to a deterministic function
  // of the run/lumi/event. 
  // NOTE!!! The fastjet random number sequence is a global singleton.
  // Thus, we have to create an object and get access to the global singleton
  // in order to change it. 
  if ( useDeterministicSeed_ ) {
    fastjet::GhostedAreaSpec gas;
    std::vector<int> seeds(2);
    unsigned int runNum_uint = static_cast <unsigned int> (iEvent.id().run());
    unsigned int evNum_uint = static_cast <unsigned int> (iEvent.id().event()); 
    seeds[0] = std::max(runNum_uint,minSeed_ + 3) + 3 * evNum_uint;
    seeds[1] = std::max(runNum_uint,minSeed_ + 5) + 5 * evNum_uint;
    gas.set_random_status(seeds);
  }

  LogDebug("VirtualJetProducer") << "Entered produce\n";
  //determine signal vertex2
  vertex_=reco::Jet::Point(0,0,0);
  if ( (makeCaloJet(jetTypeE) || makePFJet(jetTypeE)) &&doPVCorrection_) {
    LogDebug("VirtualJetProducer") << "Adding PV info\n";
    edm::Handle<reco::VertexCollection> pvCollection;
    iEvent.getByToken(input_vertex_token_ , pvCollection);
    if (!pvCollection->empty()) vertex_=pvCollection->begin()->position();
  }

  // For Pileup subtraction using offset correction:
  // set up geometry map
  if ( doPUOffsetCorr_ ) {
     subtractor_->setupGeometryMap(iEvent, iSetup);
  }

  // clear data
  LogDebug("VirtualJetProducer") << "Clear data\n";
  fjInputs_.clear();
  fjJets_.clear();
  inputs_.clear();  
  
  // get inputs and convert them to the fastjet format (fastjet::PeudoJet)
  edm::Handle<reco::CandidateView> inputsHandle;
  
  edm::Handle< std::vector<edm::FwdPtr<reco::PFCandidate> > > pfinputsHandleAsFwdPtr; 
  edm::Handle< std::vector<edm::FwdPtr<pat::PackedCandidate> > > packedinputsHandleAsFwdPtr; 
  edm::Handle< std::vector<edm::FwdPtr<reco::GenParticle> > > geninputsHandleAsFwdPtr; 
  edm::Handle< std::vector<edm::FwdPtr<pat::PackedGenParticle> > > packedgeninputsHandleAsFwdPtr; 
  
  bool isView = iEvent.getByToken(input_candidateview_token_, inputsHandle);
  if ( isView ) {
    if ( inputsHandle->empty()) {
      output( iEvent, iSetup );
      return;
    }
    for (size_t i = 0; i < inputsHandle->size(); ++i) {
      inputs_.push_back(inputsHandle->ptrAt(i));
    }
  } else {
    bool isPF = iEvent.getByToken(input_candidatefwdptr_token_, pfinputsHandleAsFwdPtr);
    bool isPFFwdPtr = iEvent.getByToken(input_packedcandidatefwdptr_token_, packedinputsHandleAsFwdPtr);
    bool isGen = iEvent.getByToken(input_gencandidatefwdptr_token_, geninputsHandleAsFwdPtr);
    bool isGenFwdPtr = iEvent.getByToken(input_packedgencandidatefwdptr_token_, packedgeninputsHandleAsFwdPtr);
    
    if ( isPF ) {
      if ( pfinputsHandleAsFwdPtr->empty()) {
    output( iEvent, iSetup );
    return;
      }
      for (size_t i = 0; i < pfinputsHandleAsFwdPtr->size(); ++i) {
    if ( (*pfinputsHandleAsFwdPtr)[i].ptr().isAvailable() ) {
      inputs_.push_back( (*pfinputsHandleAsFwdPtr)[i].ptr() );
    }
    else if ( (*pfinputsHandleAsFwdPtr)[i].backPtr().isAvailable() ) {
      inputs_.push_back( (*pfinputsHandleAsFwdPtr)[i].backPtr() );
    }
      }
    } else if ( isPFFwdPtr ) {
      if ( packedinputsHandleAsFwdPtr->empty()) {
    output( iEvent, iSetup );
    return;
      }
      for (size_t i = 0; i < packedinputsHandleAsFwdPtr->size(); ++i) {
    if ( (*packedinputsHandleAsFwdPtr)[i].ptr().isAvailable() ) {
      inputs_.push_back( (*packedinputsHandleAsFwdPtr)[i].ptr() );
    }
    else if ( (*packedinputsHandleAsFwdPtr)[i].backPtr().isAvailable() ) {
      inputs_.push_back( (*packedinputsHandleAsFwdPtr)[i].backPtr() );
    }
      }
    } else if ( isGen ) {
      if ( geninputsHandleAsFwdPtr->empty()) {
    output( iEvent, iSetup );
    return;
      }
      for (size_t i = 0; i < geninputsHandleAsFwdPtr->size(); ++i) {
    if ( (*geninputsHandleAsFwdPtr)[i].ptr().isAvailable() ) {
      inputs_.push_back( (*geninputsHandleAsFwdPtr)[i].ptr() );
    }
    else if ( (*geninputsHandleAsFwdPtr)[i].backPtr().isAvailable() ) {
      inputs_.push_back( (*geninputsHandleAsFwdPtr)[i].backPtr() );
    }
      }
    } else if ( isGenFwdPtr ) {
      if ( geninputsHandleAsFwdPtr->empty()) {
    output( iEvent, iSetup );
    return;
      }
      for (size_t i = 0; i < packedgeninputsHandleAsFwdPtr->size(); ++i) {
    if ( (*packedgeninputsHandleAsFwdPtr)[i].ptr().isAvailable() ) {
      inputs_.push_back( (*packedgeninputsHandleAsFwdPtr)[i].ptr() );
    }
    else if ( (*packedgeninputsHandleAsFwdPtr)[i].backPtr().isAvailable() ) {
      inputs_.push_back( (*packedgeninputsHandleAsFwdPtr)[i].backPtr() );
    }
      }
    }
    else {
    throw cms::Exception("Invalid Jet Inputs") <<"Did not specify appropriate inputs for VirtualJetProducer, Abort!\n";    
    }
  }
  LogDebug("VirtualJetProducer") << "Got inputs\n";
  
  // Convert candidates to fastjet::PseudoJets.
  // Also correct to Primary Vertex. Will modify fjInputs_
  // and use inputs_
  fjInputs_.reserve(inputs_.size());
  inputTowers();
  LogDebug("VirtualJetProducer") << "Inputted towers\n";

  // For Pileup subtraction using offset correction:
  // Subtract pedestal. 
  if ( doPUOffsetCorr_ ) {
     subtractor_->setDefinition(fjJetDefinition_);
     subtractor_->reset(inputs_,fjInputs_,fjJets_);
     subtractor_->calculatePedestal(fjInputs_); 
     subtractor_->subtractPedestal(fjInputs_);    
     LogDebug("VirtualJetProducer") << "Subtracted pedestal\n";
  }
  // Run algorithm. Will modify fjJets_ and allocate fjClusterSeq_. 
  // This will use fjInputs_
  runAlgorithm( iEvent, iSetup );

  // if ( doPUOffsetCorr_ ) {
  //    subtractor_->setAlgorithm(fjClusterSeq_);
  // }

  LogDebug("VirtualJetProducer") << "Ran algorithm\n";
  // For Pileup subtraction using offset correction:
  // Now we find jets and need to recalculate their energy,
  // mark towers participated in jet,
  // remove occupied towers from the list and recalculate mean and sigma
  // put the initial towers collection to the jet,   
  // and subtract from initial towers in jet recalculated mean and sigma of towers 
  if ( doPUOffsetCorr_ ) {
    LogDebug("VirtualJetProducer") << "Do PUOffsetCorr\n";
    vector<fastjet::PseudoJet> orphanInput;
    subtractor_->calculateOrphanInput(orphanInput);
    subtractor_->calculatePedestal(orphanInput);
    subtractor_->offsetCorrectJets();
  }
  // Write the output jets.
  // This will (by default) call the member function template
  // "writeJets", but can be overridden. 
  // this will use inputs_
  output( iEvent, iSetup );
  LogDebug("VirtualJetProducer") << "Wrote jets\n";
  
  // Clear the work vectors so that memory is free for other modules.
  // Use the trick of swapping with an empty vector so that the memory
  // is actually given back rather than silently kept.
  decltype(fjInputs_)().swap(fjInputs_);
  decltype(fjJets_)().swap(fjJets_);
  decltype(inputs_)().swap(inputs_);  

  return;
}

//______________________________________________________________________________
  
void VirtualJetProducer::inputTowers( )
{
  auto inBegin = inputs_.begin(),
    inEnd = inputs_.end(), i = inBegin;
  for (; i != inEnd; ++i ) {
    auto const & input = **i;
    // std::cout << "CaloTowerVI jets " << input->pt() << " " << input->et() << ' '<< input->energy() << ' ' << (isAnomalousTower(input) ? " bad" : " ok") << std::endl; 
    if (edm::isNotFinite(input.pt()))           continue;
    if (input.et()    <inputEtMin_)  continue;
    if (input.energy()<inputEMin_)   continue;
    if (isAnomalousTower(*i))      continue;
    // Change by SRR : this is no longer an error nor warning, this can happen with PU mitigation algos.
    // Also switch to something more numerically safe. (VI: 10^-42GeV????)
    if (input.pt() < 100 * std::numeric_limits<double>::epsilon() ) { 
      continue;
    }
    if (makeCaloJet(jetTypeE)&&doPVCorrection_) {
      const CaloTower & tower = dynamic_cast<const CaloTower &>(input);
      auto const &  ct = tower.p4(vertex_);  // very expensive as computed in eta/phi
      fjInputs_.emplace_back(ct.px(),ct.py(),ct.pz(),ct.energy());
      //std::cout << "tower:" << *tower << '\n';
    }
    else {
      /*
      if(makePFJet(jetTypeE)) {
    reco::PFCandidate& pfc = (reco::PFCandidate&)input;
    std::cout << "PF cand:" << pfc << '\n';
      }
      */
      fjInputs_.emplace_back(input.px(),input.py(),input.pz(),
                         input.energy());
    }
    fjInputs_.back().set_user_index(i - inBegin);
  }

  if ( restrictInputs_ && fjInputs_.size() > maxInputs_ ) {
    reco::helper::GreaterByPtPseudoJet   pTComparator;
    std::sort(fjInputs_.begin(), fjInputs_.end(), pTComparator);
    fjInputs_.resize(maxInputs_);
    edm::LogWarning("JetRecoTooManyEntries") << "Too many inputs in the event, limiting to first " << maxInputs_ << ". Output is suspect.";
  }
}

//______________________________________________________________________________
bool VirtualJetProducer::isAnomalousTower(reco::CandidatePtr input)
{
  if (!makeCaloJet(jetTypeE)) 
      return false;
  else
      return (*anomalousTowerDef_)(*input);
}

//------------------------------------------------------------------------------
// This is pure virtual. 
//______________________________________________________________________________
// void VirtualJetProducer::runAlgorithm( edm::Event & iEvent, edm::EventSetup const& iSetup,
//                                        std::vector<edm::Ptr<reco::Candidate> > const & inputs_);

//______________________________________________________________________________
void VirtualJetProducer::copyConstituents(const vector<fastjet::PseudoJet>& fjConstituents,
                                          reco::Jet* jet)
{
  for (unsigned int i=0;i<fjConstituents.size();++i) { 
    int index = fjConstituents[i].user_index();
    if ( index >= 0 && static_cast<unsigned int>(index) < inputs_.size() )
      jet->addDaughter(inputs_[index]);
  }
}


//______________________________________________________________________________
vector<reco::CandidatePtr>
VirtualJetProducer::getConstituents(const vector<fastjet::PseudoJet>&fjConstituents)
{
  vector<reco::CandidatePtr> result; result.reserve(fjConstituents.size()/2);
  for (unsigned int i=0;i<fjConstituents.size();i++) {
    auto index = fjConstituents[i].user_index();
    if ( index >= 0 && static_cast<unsigned int>(index) < inputs_.size() ) {
      result.emplace_back(inputs_[index]);
    }
  }
  return result;
}


//_____________________________________________________________________________

void VirtualJetProducer::output(edm::Event & iEvent, edm::EventSetup const& iSetup)
{
  // Write jets and constitutents. Will use fjJets_, inputs_
  // and fjClusterSeq_

  if ( writeCompound_ ) {
    // Write jets and subjets
    switch( jetTypeE ) {
    case JetType::CaloJet :
      writeCompoundJets<reco::CaloJet>( iEvent, iSetup );
      break;
    case JetType::PFJet :
      writeCompoundJets<reco::PFJet>( iEvent, iSetup );
      break;
    case JetType::GenJet :
      writeCompoundJets<reco::GenJet>( iEvent, iSetup );
      break;
    case JetType::BasicJet :
      writeCompoundJets<reco::BasicJet>( iEvent, iSetup );
      break;
    default:
      throw cms::Exception("InvalidInput") << "invalid jet type in CompoundJetProducer\n";
      break;
    };
  } else if ( writeJetsWithConst_ ) {
    // Write jets and new constituents.
    writeJetsWithConstituents<reco::PFJet>( iEvent, iSetup );
  } else {
    switch( jetTypeE ) {
    case JetType::CaloJet :
      writeJets<reco::CaloJet>( iEvent, iSetup);
      break;
    case JetType::PFJet :
      writeJets<reco::PFJet>( iEvent, iSetup);
      break;
    case JetType::GenJet :
      writeJets<reco::GenJet>( iEvent, iSetup);
      break;
    case JetType::TrackJet :
      writeJets<reco::TrackJet>( iEvent, iSetup);
      break;
    case JetType::PFClusterJet :
      writeJets<reco::PFClusterJet>( iEvent, iSetup);
      break;
    case JetType::BasicJet :
      writeJets<reco::BasicJet>( iEvent, iSetup);
      break;
    default:
           throw cms::Exception("InvalidInput") << "invalid jet type in VirtualJetProducer\n";
      break;
    };
  }
  
}

namespace {
template< typename T >
struct Area { static float get(T const &) {return 0;}};

template<>
struct Area<reco::CaloJet>{ static float get(reco::CaloJet const & jet) {
   return jet.getSpecific().mTowersArea;
}
};
}

template< typename T >
void VirtualJetProducer::writeJets( edm::Event & iEvent, edm::EventSetup const& iSetup )
{
  // std::cout << "writeJets " << typeid(T).name() 
  //          << (doRhoFastjet_ ? " doRhoFastjet " : "")
  //          << (doAreaFastjet_ ? " doAreaFastjet " : "")
  //          << (doAreaDiskApprox_ ? " doAreaDiskApprox " : "")
  //          << std::endl;

  if (doRhoFastjet_) {
    // declare jet collection without the two jets, 
    // for unbiased background estimation.
    std::vector<fastjet::PseudoJet> fjexcluded_jets;
    fjexcluded_jets=fjJets_;
    
    if(fjexcluded_jets.size()>2) fjexcluded_jets.resize(nExclude_);
    
    if(doFastJetNonUniform_){
      auto rhos = std::make_unique<std::vector<double>>();
      auto sigmas = std::make_unique<std::vector<double>>();
      int nEta = puCenters_.size();
      rhos->reserve(nEta);
      sigmas->reserve(nEta);
      fastjet::ClusterSequenceAreaBase const* clusterSequenceWithArea =
        dynamic_cast<fastjet::ClusterSequenceAreaBase const *> ( fjClusterSeq_.get() );

      if (clusterSequenceWithArea ==nullptr ){
    if (!fjJets_.empty()) {
      throw cms::Exception("LogicError")<<"fjClusterSeq is not initialized while inputs are present\n ";
    }
      } else {
    for(int ie = 0; ie < nEta; ++ie){
      double eta = puCenters_[ie];
      double etamin=eta-puWidth_;
      double etamax=eta+puWidth_;
      fastjet::RangeDefinition range_rho(etamin,etamax);
      fastjet::BackgroundEstimator bkgestim(*clusterSequenceWithArea,range_rho);
      bkgestim.set_excluded_jets(fjexcluded_jets);
      rhos->push_back(bkgestim.rho());
      sigmas->push_back(bkgestim.sigma());
    }
      }
      iEvent.put(std::move(rhos),"rhos");
      iEvent.put(std::move(sigmas),"sigmas");
    }else{
      auto rho = std::make_unique<double>(0.0);
      auto sigma = std::make_unique<double>(0.0);
      double mean_area = 0;
      
      fastjet::ClusterSequenceAreaBase const* clusterSequenceWithArea =
        dynamic_cast<fastjet::ClusterSequenceAreaBase const *> ( fjClusterSeq_.get() );
      if (clusterSequenceWithArea ==nullptr ){
    if (!fjJets_.empty()) {
      throw cms::Exception("LogicError")<<"fjClusterSeq is not initialized while inputs are present\n ";
    }
      } else {
    clusterSequenceWithArea->get_median_rho_and_sigma(*fjSelector_,false,*rho,*sigma,mean_area);
    if((*rho < 0)|| (edm::isNotFinite(*rho))) {
      edm::LogError("BadRho") << "rho value is " << *rho << " area:" << mean_area << " and n_empty_jets: " << clusterSequenceWithArea->n_empty_jets(*fjSelector_) << " with range " << fjSelector_->description()
                  <<". Setting rho to rezo.";
      *rho = 0;
    }
      }
      iEvent.put(std::move(rho),"rho");
      iEvent.put(std::move(sigma),"sigma");
    }
  } // doRhoFastjet_
  
  // produce output jet collection
  
  using namespace reco;

  // allocate fjJets_.size() Ts in vector  
  auto jets = std::make_unique<std::vector<T>>(fjJets_.size());
  
  // Distance between jet centers and overlap area -- for disk-based area calculation
  using RIJ = std::pair<double,double>; 
  std::vector<RIJ>   rijStorage(fjJets_.size()*(fjJets_.size()/2));
  RIJ * rij[fjJets_.size()];
  unsigned int k=0;
  for (unsigned int ijet=0;ijet<fjJets_.size();++ijet) {
     rij[ijet] = &rijStorage[k]; k+=ijet;
  }

  float etaJ[fjJets_.size()],  phiJ[fjJets_.size()];

  auto orParam_ = 1./rParam_;
  // fill jets 
  for (unsigned int ijet=0;ijet<fjJets_.size();++ijet) {
    auto & jet = (*jets)[ijet];
    // get the fastjet jet
    const fastjet::PseudoJet& fjJet = fjJets_[ijet];
    // get the constituents from fastjet
    std::vector<fastjet::PseudoJet> const & fjConstituents = fastjet::sorted_by_pt(fjJet.constituents());
    // convert them to CandidatePtr vector
    std::vector<CandidatePtr> const & constituents = getConstituents(fjConstituents);

    // write the specifics to the jet (simultaneously sets 4-vector, vertex).
    // These are overridden functions that will call the appropriate
    // specific allocator.
    writeSpecific(jet,
                  Particle::LorentzVector(fjJet.px(),
                                          fjJet.py(),
                                          fjJet.pz(),
                                          fjJet.E()),
                  vertex_,
                  constituents, iSetup);
    phiJ[ijet] = jet.phi();
    etaJ[ijet] = jet.eta();
  }

   // calcuate the jet area
  for (unsigned int ijet=0;ijet<fjJets_.size();++ijet) {
    // calcuate the jet area
    double jetArea=0.0;
    // get the fastjet jet
    const auto & fjJet = fjJets_[ijet];
    if ( doAreaFastjet_ && fjJet.has_area() ) {
      jetArea = fjJet.area();
    }
    else if ( doAreaDiskApprox_ ) {
      // Here it is assumed that fjJets_ is in decreasing order of pT, 
      // which should happen in FastjetJetProducer::runAlgorithm() 
      jetArea   = M_PI;
        RIJ *  distance  = rij[ijet];
        for (unsigned jJet = 0; jJet < ijet; ++jJet) {
          distance[jJet].first      = std::sqrt(reco::deltaR2(etaJ[ijet],phiJ[ijet], etaJ[jJet],phiJ[jJet]))*orParam_;
          distance[jJet].second = reco::helper::VirtualJetProducerHelper::intersection(distance[jJet].first);
          jetArea            -=distance[jJet].second;
          for (unsigned kJet = 0; kJet < jJet; ++kJet) {
            jetArea          += reco::helper::VirtualJetProducerHelper::intersection(distance[jJet].first, distance[kJet].first, rij[jJet][kJet].first, 
                                                                                     distance[jJet].second, distance[kJet].second, rij[jJet][kJet].second);
          } // end loop over harder jets
        } // end loop over harder jets
      jetArea  *= (rParam_*rParam_);
    } 
    auto & jet = (*jets)[ijet]; 
    jet.setJetArea (jetArea);
    
    if(doPUOffsetCorr_){
      jet.setPileup(subtractor_->getPileUpEnergy(ijet));
    }else{
      jet.setPileup (0.0);
    }
        
   // std::cout << "area " << ijet << " " << jetArea << " " << Area<T>::get(jet) << std::endl;
   // std::cout << "JetVI " << ijet << ' '<< jet.pt() << " " << jet.et() << ' '<< jet.energy() << ' '<< jet.mass() << std::endl;

  }
  // put the jets in the collection
  iEvent.put(std::move(jets),jetCollInstanceName_);
}

template< class T>
void VirtualJetProducer::writeCompoundJets(  edm::Event & iEvent, edm::EventSetup const& iSetup)
{
  if ( verbosity_ >= 1 ) { 
    std::cout << "<VirtualJetProducer::writeCompoundJets (moduleLabel = " << moduleLabel_ << ")>:" << std::endl;
  }

  // get a list of output jets
  auto jetCollection = std::make_unique<reco::BasicJetCollection>();
  // get a list of output subjets
  auto subjetCollection = std::make_unique<std::vector<T>>();

  // This will store the handle for the subjets after we write them
  edm::OrphanHandle< std::vector<T> > subjetHandleAfterPut;
  // this is the mapping of subjet to hard jet
  std::vector< std::vector<int> > indices;
  // this is the list of hardjet 4-momenta
  std::vector<math::XYZTLorentzVector> p4_hardJets;
  // this is the hardjet areas
  std::vector<double> area_hardJets;

  // Loop over the hard jets
  std::vector<fastjet::PseudoJet>::const_iterator it = fjJets_.begin(),
    iEnd = fjJets_.end(),
    iBegin = fjJets_.begin();
  indices.resize( fjJets_.size() );
  for ( ; it != iEnd; ++it ) {
    fastjet::PseudoJet const & localJet = *it;
    unsigned int jetIndex = it - iBegin;
    // Get the 4-vector for the hard jet
    p4_hardJets.push_back( math::XYZTLorentzVector(localJet.px(), localJet.py(), localJet.pz(), localJet.e() ));
    double localJetArea = 0.0;
    if ( doAreaFastjet_ && localJet.has_area() ) {
      localJetArea = localJet.area();
    }
    area_hardJets.push_back( localJetArea );

    // create the subjet list
    std::vector<fastjet::PseudoJet> constituents;
    if ( it->has_pieces() ) {
      constituents = it->pieces();
    } else if ( it->has_constituents() ) {
      constituents = it->constituents();
    }

    std::vector<fastjet::PseudoJet>::const_iterator itSubJetBegin = constituents.begin(),
      itSubJet = itSubJetBegin, itSubJetEnd = constituents.end();
    for (; itSubJet != itSubJetEnd; ++itSubJet ){

      fastjet::PseudoJet const & subjet = *itSubJet;      
      if ( verbosity_ >= 1 ) {
    std::cout << "subjet #" << (itSubJet - itSubJetBegin) << ": Pt = " << subjet.pt() << ", eta = " << subjet.eta() << ", phi = " << subjet.phi() << ", mass = " << subjet.m() 
          << " (#constituents = " << subjet.constituents().size() << ")" << std::endl;
    std::vector<fastjet::PseudoJet> subjet_constituents = subjet.constituents();
    int idx_constituent = 0;
    for ( std::vector<fastjet::PseudoJet>::const_iterator constituent = subjet_constituents.begin();
          constituent != subjet_constituents.end(); ++constituent ) {
      if ( constituent->pt() < 1.e-3 ) continue; // CV: skip ghosts
      std::cout << "  constituent #" << idx_constituent << ": Pt = " << constituent->pt() << ", eta = " << constituent->eta() << ", phi = " << constituent->phi() << "," 
            << " mass = " << constituent->m() << std::endl;
      ++idx_constituent;
    }
      }

      if ( verbosity_ >= 1 ) {
    std::cout << "subjet #" << (itSubJet - itSubJetBegin) << ": Pt = " << subjet.pt() << ", eta = " << subjet.eta() << ", phi = " << subjet.phi() << ", mass = " << subjet.m() 
          << " (#constituents = " << subjet.constituents().size() << ")" << std::endl;
    std::vector<fastjet::PseudoJet> subjet_constituents = subjet.constituents();
    int idx_constituent = 0;
    for ( std::vector<fastjet::PseudoJet>::const_iterator constituent = subjet_constituents.begin();
          constituent != subjet_constituents.end(); ++constituent ) {
      if ( constituent->pt() < 1.e-3 ) continue; // CV: skip ghosts
      std::cout << " constituent #" << idx_constituent << ": Pt = " << constituent->pt() << ", eta = " << constituent->eta() << ", phi = " << constituent->phi() << "," 
            << " mass = " << constituent->m() << std::endl;
      ++idx_constituent;
    }
      }

      math::XYZTLorentzVector p4Subjet(subjet.px(), subjet.py(), subjet.pz(), subjet.e() );
      reco::Particle::Point point(0,0,0);

      // This will hold ptr's to the subjets
      std::vector<reco::CandidatePtr> subjetConstituents;

      // Get the transient subjet constituents from fastjet
      std::vector<fastjet::PseudoJet> subjetFastjetConstituents = subjet.constituents();
      std::vector<reco::CandidatePtr> constituents =
    getConstituents(subjetFastjetConstituents );    

      indices[jetIndex].push_back( subjetCollection->size() );

      // Add the concrete subjet type to the subjet list to write to event record
      T jet;
      reco::writeSpecific( jet, p4Subjet, point, constituents, iSetup);
      double subjetArea = 0.0;
      if ( doAreaFastjet_ && itSubJet->has_area() ){
    subjetArea = itSubJet->area();
      }
      jet.setJetArea( subjetArea );
      subjetCollection->push_back( jet );
    }
  }

  // put subjets into event record
  subjetHandleAfterPut = iEvent.put(std::move(subjetCollection), jetCollInstanceName_);
  
  // Now create the hard jets with ptr's to the subjets as constituents
  std::vector<math::XYZTLorentzVector>::const_iterator ip4 = p4_hardJets.begin(),
    ip4Begin = p4_hardJets.begin(),
    ip4End = p4_hardJets.end();

  for ( ; ip4 != ip4End; ++ip4 ) {
    int p4_index = ip4 - ip4Begin;
    std::vector<int> & ind = indices[p4_index];
    std::vector<reco::CandidatePtr> i_hardJetConstituents;
    // Add the subjets to the hard jet
    for( std::vector<int>::const_iterator isub = ind.begin();
     isub != ind.end(); ++isub ) {
      reco::CandidatePtr candPtr( subjetHandleAfterPut, *isub, false );
      i_hardJetConstituents.push_back( candPtr );
    }   
    reco::Particle::Point point(0,0,0);
    reco::BasicJet toput( *ip4, point, i_hardJetConstituents);
    toput.setJetArea( area_hardJets[ip4 - ip4Begin] );
    jetCollection->push_back( toput );
  }

  // put hard jets into event record
  // Store the Orphan handle for adding HTT information
  edm::OrphanHandle<reco::BasicJetCollection>  oh = iEvent.put(std::move(jetCollection));

  if (fromHTTTopJetProducer_){
    addHTTTopJetTagInfoCollection( iEvent, iSetup, oh);
  }

}

template< class T>
void VirtualJetProducer::writeJetsWithConstituents(  edm::Event & iEvent, edm::EventSetup const& iSetup)
{
  if ( verbosity_ >= 1 ) {
    std::cout << "<VirtualJetProducer::writeJetsWithConstituents (moduleLabel = " << moduleLabel_ << ")>:" << std::endl;
  }

  // get a list of output jets  MV: make this compatible with template
  auto jetCollection = std::make_unique<reco::PFJetCollection>();
  
  // this is the mapping of jet to constituents
  std::vector< std::vector<int> > indices;
  // this is the list of jet 4-momenta
  std::vector<math::XYZTLorentzVector> p4_Jets;
  // this is the jet areas
  std::vector<double> area_Jets;

  // get a list of output constituents
  auto constituentCollection = std::make_unique<reco::PFCandidateCollection>();
  
  // This will store the handle for the constituents after we write them
  edm::OrphanHandle<reco::PFCandidateCollection> constituentHandleAfterPut;
    
  // Loop over the jets and extract constituents
  std::vector<fastjet::PseudoJet> constituentsSub;
  std::vector<fastjet::PseudoJet>::const_iterator it = fjJets_.begin(),
    iEnd = fjJets_.end(),
    iBegin = fjJets_.begin();
  indices.resize( fjJets_.size() );

  for ( ; it != iEnd; ++it ) {
    fastjet::PseudoJet const & localJet = *it;
    unsigned int jetIndex = it - iBegin;
    // Get the 4-vector for the hard jet
    p4_Jets.push_back( math::XYZTLorentzVector(localJet.px(), localJet.py(), localJet.pz(), localJet.e() ));
    double localJetArea = 0.0;
    if ( doAreaFastjet_ && localJet.has_area() ) {
      localJetArea = localJet.area();
    }
    area_Jets.push_back( localJetArea );

    // create the constituent list
    std::vector<fastjet::PseudoJet> constituents,ghosts;
    if ( it->has_pieces() )
      constituents = it->pieces();
    else if ( it->has_constituents() )
      fastjet::SelectorIsPureGhost().sift(it->constituents(), ghosts, constituents); //filter out ghosts

    //loop over constituents of jet (can be subjets or normal constituents)
    indices[jetIndex].reserve(constituents.size());
    constituentsSub.reserve(constituentsSub.size()+constituents.size());
    for (fastjet::PseudoJet const& constit : constituents) {
      indices[jetIndex].push_back( constituentsSub.size() );
      constituentsSub.push_back(constit);
    }
  }

  //Loop over constituents and store in the event
  static const reco::PFCandidate dummySinceTranslateIsNotStatic;
  for (fastjet::PseudoJet const& constit : constituentsSub) {
    auto orig = inputs_[constit.user_index()];
    auto id = dummySinceTranslateIsNotStatic.translatePdgIdToType(orig->pdgId());
    reco::PFCandidate pCand( reco::PFCandidate(orig->charge(), orig->p4(), id) );
    math::XYZTLorentzVector pVec;
    pVec.SetPxPyPzE(constit.px(),constit.py(),constit.pz(),constit.e());
    pCand.setP4(pVec);
    pCand.setSourceCandidatePtr( orig->sourceCandidatePtr(0) );
    constituentCollection->push_back(pCand);
  }
  // put constituents into event record
  constituentHandleAfterPut = iEvent.put(std::move(constituentCollection), jetCollInstanceName_ );

  // Now create the jets with ptr's to the constituents
  std::vector<math::XYZTLorentzVector>::const_iterator ip4 = p4_Jets.begin(),
    ip4Begin = p4_Jets.begin(),
    ip4End = p4_Jets.end();

  for ( ; ip4 != ip4End; ++ip4 ) {
    int p4_index = ip4 - ip4Begin;
    std::vector<int> & ind = indices[p4_index];
    std::vector<reco::CandidatePtr> i_jetConstituents;
    // Add the constituents to the jet
    for( std::vector<int>::const_iterator iconst = ind.begin(); iconst != ind.end(); ++iconst ) {
      reco::CandidatePtr candPtr( constituentHandleAfterPut, *iconst, false );
      i_jetConstituents.push_back( candPtr );
    }
    if(!i_jetConstituents.empty()) { //only keep jets which have constituents after subtraction
      reco::Particle::Point point(0,0,0);
      reco::PFJet jet;
      reco::writeSpecific(jet,*ip4,point,i_jetConstituents,iSetup);
      jet.setJetArea( area_Jets[ip4 - ip4Begin] );
      jetCollection->emplace_back( jet );
    }
  }

  // put jets into event record
  iEvent.put(std::move(jetCollection));
}

// ------------ method fills 'descriptions' with the allowed parameters for the module  ------------
void VirtualJetProducer::fillDescriptions(edm::ConfigurationDescriptions& descriptions) {

    edm::ParameterSetDescription desc;
        fillDescriptionsFromVirtualJetProducer(desc);
    desc.add<string>("jetCollInstanceName", ""  );

        // addDefault must be used here instead of add unless
        // all the classes that inherit from this class redefine
        // the fillDescriptions function. Otherwise, the autogenerated
        // cfi filenames are the same and conflict.
    descriptions.addDefault(desc);
}

void VirtualJetProducer::fillDescriptionsFromVirtualJetProducer(edm::ParameterSetDescription& desc)
{
    desc.add<edm::InputTag>("src",      edm::InputTag("particleFlow") );
    desc.add<edm::InputTag>("srcPVs",   edm::InputTag("") );
    desc.add<string>("jetType",     "PFJet" );
    desc.add<string>("jetAlgorithm",    "AntiKt" );
    desc.add<double>("rParam",      0.4 );
    desc.add<double>("inputEtMin",      0.0 );
    desc.add<double>("inputEMin",       0.0 );
    desc.add<double>("jetPtMin",        5. );
    desc.add<bool>  ("doPVCorrection",  false );
    desc.add<bool>  ("doAreaFastjet",   false );
    desc.add<bool>  ("doRhoFastjet",    false );
    desc.add<bool>  ("doPUOffsetCorr",  false   );
    desc.add<double>("puPtMin",             10.);
        desc.add<double>("nSigmaPU",            1.0 );
        desc.add<double>("radiusPU",            0.5 );
    desc.add<string>("subtractorName",  ""  );
    desc.add<bool>  ("useExplicitGhosts",   false   );
    desc.add<bool>  ("doAreaDiskApprox",    false   );
    desc.add<double>("voronoiRfact",    -0.9    );
    desc.add<double>("Rho_EtaMax",      4.4     );
    desc.add<double>("Ghost_EtaMax",    5.  );
    desc.add<int>   ("Active_Area_Repeats", 1   );
    desc.add<double>("GhostArea",       0.01    );
    desc.add<bool>  ("restrictInputs",  false   );
    desc.add<unsigned int>  ("maxInputs",   1   );
    desc.add<bool>  ("writeCompound",   false   );
        desc.add<bool>  ("writeJetsWithConst",  false   );
    desc.add<bool>  ("doFastJetNonUniform", false   );
    desc.add<bool>  ("useDeterministicSeed",false   );
    desc.add<unsigned int>  ("minSeed",     14327   );
    desc.add<int>   ("verbosity",       0   );
    desc.add<double>("puWidth",     0.  );
    desc.add<unsigned int>("nExclude",  0   );
    desc.add<unsigned int>("maxBadEcalCells",   9999999 );
    desc.add<unsigned int>("maxBadHcalCells",   9999999 );
    desc.add<unsigned int>("maxProblematicEcalCells",   9999999 );
    desc.add<unsigned int>("maxProblematicHcalCells",   9999999 );
    desc.add<unsigned int>("maxRecoveredEcalCells", 9999999 );
    desc.add<unsigned int>("maxRecoveredHcalCells", 9999999 );
    vector<double>  puCentersDefault;
    desc.add<vector<double>>("puCenters",   puCentersDefault);
}