TrackListMerger.cc

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//
// Package:         RecoTracker/FinalTrackSelectors
// Class:           TrackListMerger
// 
// Description:     Hit Dumper
//
// Original Author: Steve Wagner, stevew@pizero.colorado.edu
// Created:         Sat Jan 14 22:00:00 UTC 2006
//
//

#include "FWCore/Framework/interface/stream/EDProducer.h"
#include "FWCore/Framework/interface/Event.h"
#include "DataFormats/Common/interface/Handle.h"
#include "FWCore/Framework/interface/EventSetup.h"

#include "DataFormats/TrackReco/interface/TrackFwd.h"
#include "DataFormats/TrackReco/interface/Track.h"
#include "DataFormats/TrackReco/interface/TrackBase.h"
#include "DataFormats/TrackingRecHit/interface/TrackingRecHit.h"
#include "DataFormats/TrackReco/interface/TrackExtra.h"
#include "TrackingTools/PatternTools/interface/Trajectory.h"
#include "TrackingTools/PatternTools/interface/TrajTrackAssociation.h"
#include "DataFormats/TrajectorySeed/interface/TrajectorySeedCollection.h"
#include "FWCore/Utilities/interface/InputTag.h"
#include "FWCore/ParameterSet/interface/ParameterSet.h"
#include "DataFormats/Common/interface/ValueMap.h"

#include "trackAlgoPriorityOrder.h"

class dso_hidden TrackListMerger : public edm::stream::EDProducer<>
  {
  public:

    explicit TrackListMerger(const edm::ParameterSet& conf);

    virtual ~TrackListMerger();

    virtual void produce(edm::Event& e, const edm::EventSetup& c) override;

  private:
    std::auto_ptr<reco::TrackCollection> outputTrks;
    std::auto_ptr<reco::TrackExtraCollection> outputTrkExtras;
    std::auto_ptr< TrackingRecHitCollection>  outputTrkHits;
    std::auto_ptr< std::vector<Trajectory> > outputTrajs;
    std::auto_ptr< TrajTrackAssociationCollection >  outputTTAss;
    std::auto_ptr< TrajectorySeedCollection > outputSeeds;

    reco::TrackRefProd refTrks;
    reco::TrackExtraRefProd refTrkExtras;
    TrackingRecHitRefProd refTrkHits;
    edm::RefProd< std::vector<Trajectory> > refTrajs;
    edm::RefProd< TrajectorySeedCollection > refTrajSeeds;
    
    bool copyExtras_;
    bool makeReKeyedSeeds_;

    struct TkEDGetTokenss  {
        edm::InputTag tag;
        edm::EDGetTokenT<reco::TrackCollection> tk;
        edm::EDGetTokenT<std::vector<Trajectory> >        traj;
        edm::EDGetTokenT<TrajTrackAssociationCollection > tass;
        edm::EDGetTokenT<edm::ValueMap<int>   > tsel;
        edm::EDGetTokenT<edm::ValueMap<float> > tmva;
        TkEDGetTokenss() {}
        TkEDGetTokenss(const edm::InputTag &tag_, edm::EDGetTokenT<reco::TrackCollection> && tk_, 
                 edm::EDGetTokenT<std::vector<Trajectory> > && traj_, edm::EDGetTokenT<TrajTrackAssociationCollection > && tass_,
                 edm::EDGetTokenT<edm::ValueMap<int> > &&tsel_, edm::EDGetTokenT<edm::ValueMap<float> > && tmva_) :
            tag(tag_), tk(tk_), traj(traj_), tass(tass_), tsel(tsel_), tmva(tmva_) {}
    };
    TkEDGetTokenss edTokens(const edm::InputTag &tag, const edm::InputTag &seltag, const edm::InputTag &mvatag) {
        return TkEDGetTokenss(tag, consumes<reco::TrackCollection>(tag), 
                                consumes<std::vector<Trajectory> >(tag), consumes<TrajTrackAssociationCollection >(tag),
                                consumes<edm::ValueMap<int> >(seltag), consumes<edm::ValueMap<float> >(mvatag));
    }
    TkEDGetTokenss edTokens(const edm::InputTag &tag, const edm::InputTag &mvatag) {
        return TkEDGetTokenss(tag, consumes<reco::TrackCollection>(tag), 
                                consumes<std::vector<Trajectory> >(tag), consumes<TrajTrackAssociationCollection >(tag),
                                edm::EDGetTokenT<edm::ValueMap<int> >(), consumes<edm::ValueMap<float> >(mvatag));
    }
    std::vector<TkEDGetTokenss>      trackProducers_;

    double maxNormalizedChisq_;
    double minPT_;
    unsigned int minFound_;
    float epsilon_;
    float shareFrac_;
    float foundHitBonus_;
    float lostHitPenalty_;
    std::vector<double> indivShareFrac_;

    std::vector< std::vector< int> > listsToMerge_;
    std::vector<bool> promoteQuality_;
    std::vector<int> hasSelector_;
    bool copyMVA_;

    bool allowFirstHitShare_;
    reco::TrackBase::TrackQuality qualityToSet_;
    bool use_sharesInput_;
    bool trkQualMod_;


  };



#include <memory>
#include <string>
#include <iostream>
#include <cmath>
#include <vector>

#include "DataFormats/TrackerRecHit2D/interface/SiStripMatchedRecHit2DCollection.h"
#include "DataFormats/TrackerRecHit2D/interface/SiStripRecHit2DCollection.h"
#include "DataFormats/TrackerRecHit2D/interface/SiStripRecHit1DCollection.h"
#include "DataFormats/TrajectorySeed/interface/TrajectorySeedCollection.h"
#include "DataFormats/TrackCandidate/interface/TrackCandidateCollection.h"
#include "DataFormats/Common/interface/ValueMap.h"
#include "FWCore/Framework/interface/ESHandle.h"

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

#include "Geometry/CommonDetUnit/interface/GeomDetUnit.h"
#include "Geometry/CommonDetUnit/interface/GeomDet.h"
#include "Geometry/TrackerGeometryBuilder/interface/TrackerGeometry.h"
#include "Geometry/Records/interface/TrackerDigiGeometryRecord.h"

//#include "DataFormats/TrackReco/src/classes.h"

#include "DataFormats/TrackerRecHit2D/interface/ClusterRemovalRefSetter.h"

#ifdef STAT_TSB
#include <x86intrin.h>
#endif

namespace {
#ifdef STAT_TSB
inline volatile unsigned long long rdtsc() {
 return __rdtsc();
}

  struct StatCount {
    float maxDP=0.;
    float maxDE=0.;
    unsigned long long st;
    long long totBegin=0;
    long long totPre=0;
    long long totEnd=0;
    unsigned long long timeNo;  // no-overlap
    unsigned long long timeOv;  // overlap
    void begin(int tt) {
      totBegin+=tt;
    }
    void start() { st=rdtsc(); }
    void noOverlap() { timeNo += (rdtsc()-st);}
    void overlap() { timeOv += (rdtsc()-st);}
    void pre(int tt) { totPre+=tt;}
    void end(int tt) { totEnd+=tt;}
    void de(float d) { if (d>maxDE) maxDE=d;}
    void dp(float d) { if (d>maxDP) maxDP=d;}


    void print() const {
      std::cout << "TrackListMerger stat\nBegin/Pre/End/maxDPhi/maxDEta/Overlap/NoOverlap "
                <<  totBegin <<'/'<< totPre <<'/'<< totEnd <<'/'<< maxDP <<'/'<< maxDE
        <<'/'<< timeOv/1000 <<'/'<< timeNo/1000
        << std::endl;
    }
    StatCount() {}
    ~StatCount() { print();}
  };
  StatCount statCount;

#else
  struct StatCount {
    void begin(int){}
    void pre(int){}
    void end(int){}
    void start(){}
    void noOverlap(){}
    void overlap(){}
    void de(float){}
    void dp(float){}


  };
  [[cms::thread_safe]] StatCount statCount;
#endif


}



namespace {
  edm::ProductID clusterProductB( const TrackingRecHit *hit){
    return reinterpret_cast<const BaseTrackerRecHit *>(hit)->firstClusterRef().id();
  }
}


TrackListMerger::TrackListMerger(edm::ParameterSet const& conf) {
  copyExtras_ = conf.getUntrackedParameter<bool>("copyExtras", true);
  
  std::vector<edm::InputTag> trackProducerTags(conf.getParameter<std::vector<edm::InputTag> >("TrackProducers"));
  //which of these do I need to turn into vectors?
  maxNormalizedChisq_ =  conf.getParameter<double>("MaxNormalizedChisq");
  minPT_ =  conf.getParameter<double>("MinPT");
  minFound_ = (unsigned int)conf.getParameter<int>("MinFound");
  epsilon_ =  conf.getParameter<double>("Epsilon");
  shareFrac_ =  conf.getParameter<double>("ShareFrac");
  allowFirstHitShare_ = conf.getParameter<bool>("allowFirstHitShare");
  foundHitBonus_ = conf.getParameter<double>("FoundHitBonus");
  lostHitPenalty_ = conf.getParameter<double>("LostHitPenalty");
  indivShareFrac_=conf.getParameter<std::vector<double> >("indivShareFrac");
  std::string qualityStr = conf.getParameter<std::string>("newQuality");
  
  if (qualityStr != "") {
    qualityToSet_ = reco::TrackBase::qualityByName(conf.getParameter<std::string>("newQuality"));
  }
  else
    qualityToSet_ = reco::TrackBase::undefQuality;
  
  use_sharesInput_ = true;
  if ( epsilon_ > 0.0 )use_sharesInput_ = false;
  
  edm::VParameterSet setsToMerge=conf.getParameter<edm::VParameterSet>("setsToMerge");
  
  for ( unsigned int i=0; i<setsToMerge.size(); i++) {
    listsToMerge_.push_back(setsToMerge[i].getParameter<std::vector< int> >("tLists"));
    promoteQuality_.push_back(setsToMerge[i].getParameter<bool>("pQual"));
  }
  hasSelector_ = conf.getParameter<std::vector<int> > ("hasSelector");
  copyMVA_     = conf.getParameter<bool>("copyMVA"); 

  std::vector<edm::InputTag> selectors(conf.getParameter<std::vector<edm::InputTag> >("selectedTrackQuals"));
  std::vector<edm::InputTag> mvaStores;
  if(conf.exists("mvaValueTags")){
    mvaStores = conf.getParameter<std::vector<edm::InputTag> >("mvaValueTags");
  }else{
    for (int i = 0; i < (int)selectors.size(); i++){
      edm::InputTag ntag(selectors[i].label(),"MVAVals");
      mvaStores.push_back(ntag);
    }
  }
  unsigned int numTrkColl = trackProducerTags.size();
  if (numTrkColl != hasSelector_.size() || numTrkColl != selectors.size()) {
    throw cms::Exception("Inconsistent size") << "need same number of track collections and selectors";
  }
  if (numTrkColl != hasSelector_.size() || numTrkColl != mvaStores.size()) {
    throw cms::Exception("Inconsistent size") << "need same number of track collections and MVA stores";
  }
  for (unsigned int i = indivShareFrac_.size(); i < numTrkColl; i++) {
    //      edm::LogWarning("TrackListMerger") << "No indivShareFrac for " << trackProducersTags <<". Using default value of 1";
    indivShareFrac_.push_back(1.0);
  }
  
  trkQualMod_=conf.getParameter<bool>("writeOnlyTrkQuals");
  if ( trkQualMod_) {
    bool ok=true;
    for ( unsigned int i=1; i<numTrkColl; i++) {
      if (!(trackProducerTags[i]==trackProducerTags[0])) ok=false;
    }
    if ( !ok) {
      throw cms::Exception("Bad input") << "to use writeOnlyTrkQuals=True all input InputTags must be the same";
    }
    produces<edm::ValueMap<int> >();
  }
  else{
    produces<reco::TrackCollection>();
    
    makeReKeyedSeeds_ = conf.getUntrackedParameter<bool>("makeReKeyedSeeds",false);
    if (makeReKeyedSeeds_){
      copyExtras_=true;
      produces<TrajectorySeedCollection>();
    }
    
    if (copyExtras_) {
      produces<reco::TrackExtraCollection>();
      produces<TrackingRecHitCollection>();
    }
    produces< std::vector<Trajectory> >();
    produces< TrajTrackAssociationCollection >();
  }
  produces<edm::ValueMap<float> >("MVAVals");
  
  // Do all the consumes
  trackProducers_.resize(numTrkColl);
  for (unsigned int i = 0; i < numTrkColl; ++i) {
    trackProducers_[i] = hasSelector_[i]>0 ? edTokens(trackProducerTags[i], selectors[i], mvaStores[i]) : edTokens(trackProducerTags[i], mvaStores[i]);
  }
}


// Virtual destructor needed.
TrackListMerger::~TrackListMerger() { }

  // Functions that gets called by framework every event
  void TrackListMerger::produce(edm::Event& e, const edm::EventSetup& es)
  {
    // extract tracker geometry
    //
    //edm::ESHandle<TrackerGeometry> theG;
    //es.get<TrackerDigiGeometryRecord>().get(theG);

    //    using namespace reco;

    // get Inputs
    // if 1 input list doesn't exist, make an empty list, issue a warning, and continue
    // this allows TrackListMerger to be used as a cleaner only if handed just one list
    // if both input lists don't exist, will issue 2 warnings and generate an empty output collection
    //
    static const reco::TrackCollection s_empty;

    std::vector<const reco::TrackCollection *> trackColls;
    std::vector<edm::Handle<reco::TrackCollection> > trackHandles(trackProducers_.size());
    for ( unsigned int i=0; i<trackProducers_.size(); i++) {
      trackColls.push_back(0);
      //edm::Handle<reco::TrackCollection> trackColl;
      e.getByToken(trackProducers_[i].tk, trackHandles[i]);
      if (trackHandles[i].isValid()) {
    trackColls[i]= trackHandles[i].product();
      } else {
    edm::LogWarning("TrackListMerger") << "TrackCollection " << trackProducers_[i].tag <<" not found";
    trackColls[i]=&s_empty;
      }
    }

    unsigned int collsSize =trackColls.size();
    unsigned int rSize=0;
    unsigned int trackCollSizes[collsSize];
    unsigned int trackCollFirsts[collsSize];
    for (unsigned int i=0; i!=collsSize; i++) {
      trackCollSizes[i]=trackColls[i]->size();
      trackCollFirsts[i]=rSize;
      rSize+=trackCollSizes[i];
    }

    statCount.begin(rSize);

    //
    //  quality cuts first
    //
    int i=-1;

    int selected[rSize];
    int indexG[rSize];
    bool trkUpdated[rSize];
    int trackCollNum[rSize];
    int trackQuals[rSize];
    float trackMVAs[rSize];
    reco::TrackBase::TrackAlgorithm oriAlgo[rSize];
    std::vector<reco::TrackBase::AlgoMask> algoMask(rSize);
    for (unsigned int j=0; j<rSize;j++) {
      indexG[j]=-1; selected[j]=1; trkUpdated[j]=false; trackCollNum[j]=0; trackQuals[j]=0;trackMVAs[j] = -998.0;oriAlgo[j]=reco::TrackBase::undefAlgorithm;
    }

    int ngood=0;
    for (unsigned int j=0; j!= collsSize; j++) {
      const reco::TrackCollection *tC1=trackColls[j];

      edm::Handle<edm::ValueMap<int> > trackSelColl;
      edm::Handle<edm::ValueMap<float> > trackMVAStore;
      if ( copyMVA_ )
    e.getByToken(trackProducers_[j].tmva, trackMVAStore);
      if ( hasSelector_[j]>0 ){
    e.getByToken(trackProducers_[j].tsel, trackSelColl);
      }

      if ( 0<tC1->size() ){
    unsigned int iC=0;
    for (reco::TrackCollection::const_iterator track=tC1->begin(); track!=tC1->end(); track++){
      i++;
      trackCollNum[i]=j;
      trackQuals[i]=track->qualityMask();
          oriAlgo[i]=track->originalAlgo();
          algoMask[i]=track->algoMask();
 
      reco::TrackRef trkRef=reco::TrackRef(trackHandles[j],iC);
      if ( copyMVA_ )
        if( (*trackMVAStore).contains(trkRef.id()) ) trackMVAs[i] = (*trackMVAStore)[trkRef];
      if ( hasSelector_[j]>0 ) {
        int qual=(*trackSelColl)[trkRef];
        if ( qual < 0 ) {
          selected[i]=0;
          iC++;
          continue;
        }else{
          trackQuals[i]=qual;
        }
      }
      iC++;
      selected[i]=trackQuals[i]+10;//10 is magic number used throughout...
      if ((short unsigned)track->ndof() < 1){
        selected[i]=0;
        continue;
      }
      if (track->normalizedChi2() > maxNormalizedChisq_){
        selected[i]=0;
        continue;
      }
      if (track->found() < minFound_){
        selected[i]=0;
        continue;
      }
      if (track->pt() < minPT_){
        selected[i]=0;
        continue;
      }
      // good!
      indexG[i] = ngood++;
      //if ( beVerb) std::cout << "inverb " << track->pt() << " " << selected[i] << std::endl;
    }//end loop over tracks
      }//end more than 0 track
    } // loop over trackcolls


    statCount.pre(ngood);

    //cache the id and rechits of valid hits
    typedef std::pair<unsigned int, const TrackingRecHit*> IHit;
    std::vector<std::vector<IHit>> rh1(ngood);  // "not an array" of vectors!
    //const TrackingRecHit*  fh1[ngood];  // first hit...
    uint8_t algo[ngood];
    float score[ngood];


    for ( unsigned int j=0; j<rSize; j++) {
      if (selected[j]==0) continue;
      int i = indexG[j];
      assert(i>=0);
      unsigned int collNum=trackCollNum[j];
      unsigned int trackNum=j-trackCollFirsts[collNum];
      const reco::Track *track=&((trackColls[collNum])->at(trackNum));

      algo[i]=track->algo();
      int validHits=track->numberOfValidHits();
      int validPixelHits=track->hitPattern().numberOfValidPixelHits();
      int lostHits=track->numberOfLostHits();
      score[i] = foundHitBonus_*validPixelHits+foundHitBonus_*validHits - lostHitPenalty_*lostHits - track->chi2();


      rh1[i].reserve(validHits) ;
      auto compById = [](IHit const &  h1, IHit const & h2) {return h1.first < h2.first;};
      for (trackingRecHit_iterator it = track->recHitsBegin();  it != track->recHitsEnd(); ++it) {
    const TrackingRecHit* hit = (*it);
    unsigned int id = hit->rawId() ;
    if(hit->geographicalId().subdetId()>2)  id &= (~3); // mask mono/stereo in strips...
    if likely(hit->isValid()) { rh1[i].emplace_back(id,hit); std::push_heap(rh1[i].begin(),rh1[i].end(),compById); }
      }
      std::sort_heap(rh1[i].begin(),rh1[i].end(),compById);
    }

    //DL here
    if likely(ngood>1 && collsSize>1)
    for ( unsigned int ltm=0; ltm<listsToMerge_.size(); ltm++) {
      int saveSelected[rSize];
      bool notActive[collsSize];
      for (unsigned int cn=0;cn!=collsSize;++cn)
    notActive[cn]= find(listsToMerge_[ltm].begin(),listsToMerge_[ltm].end(),cn)==listsToMerge_[ltm].end();

      for ( unsigned int i=0; i<rSize; i++) saveSelected[i]=selected[i];

      //DL protect against 0 tracks?
      for ( unsigned int i=0; i<rSize-1; i++) {
    if (selected[i]==0) continue;
    unsigned int collNum=trackCollNum[i];

    //check that this track is in one of the lists for this iteration
    if (notActive[collNum]) continue;

    int k1 = indexG[i];
    unsigned int nh1=rh1[k1].size();
    int qualityMaskT1 = trackQuals[i];

    int nhit1 = nh1; // validHits[k1];
    float score1 = score[k1];

    // start at next collection
    for ( unsigned int j=i+1; j<rSize; j++) {
      if (selected[j]==0) continue;
      unsigned int collNum2=trackCollNum[j];
      if ( (collNum == collNum2) && indivShareFrac_[collNum] > 0.99) continue;
      //check that this track is in one of the lists for this iteration
      if (notActive[collNum2]) continue;

      int k2 = indexG[j];

      int newQualityMask = -9; //avoid resetting quality mask if not desired 10+ -9 =1
      if (promoteQuality_[ltm]) {
        int maskT1= saveSelected[i]>1? saveSelected[i]-10 : qualityMaskT1;
        int maskT2= saveSelected[j]>1? saveSelected[j]-10 : trackQuals[j];
        newQualityMask =(maskT1 | maskT2); // take OR of trackQuality
      }
      unsigned int nh2=rh1[k2].size();
      int nhit2 = nh2;


      auto share = use_sharesInput_ ?
        [](const TrackingRecHit*  it,const TrackingRecHit*  jt, float)->bool { return it->sharesInput(jt,TrackingRecHit::some); } :
      [](const TrackingRecHit*  it,const TrackingRecHit*  jt, float eps)->bool {
        float delta = std::abs ( it->localPosition().x()-jt->localPosition().x() );
        return (it->geographicalId()==jt->geographicalId())&&(delta<eps);
      };

      statCount.start();

      //loop over rechits
      int noverlap=0;
      int firstoverlap=0;
      // check first hit  (should use REAL first hit?)
      if unlikely(allowFirstHitShare_ && rh1[k1][0].first==rh1[k2][0].first ) {
          const TrackingRecHit*  it = rh1[k1][0].second;
          const TrackingRecHit*  jt = rh1[k2][0].second;
          if (share(it,jt,epsilon_)) firstoverlap=1;
        }


      // exploit sorting
      unsigned int jh=0;
      unsigned int ih=0;
      while (ih!=nh1 && jh!=nh2) {
        // break if not enough to go...
        // if ( nprecut-noverlap+firstoverlap > int(nh1-ih)) break;
        // if ( nprecut-noverlap+firstoverlap > int(nh2-jh)) break;
        auto const id1 = rh1[k1][ih].first;
        auto const id2 = rh1[k2][jh].first;
        if (id1<id2) ++ih;
        else if (id2<id1) ++jh;
        else {
          // in case of split-hit do full conbinatorics
          auto li=ih; while( (++li)!=nh1 && id1 == rh1[k1][li].first);
          auto lj=jh; while( (++lj)!=nh2 && id2 == rh1[k2][lj].first);
          for (auto ii=ih; ii!=li; ++ii)
        for (auto jj=jh; jj!=lj; ++jj) {
          const TrackingRecHit*  it = rh1[k1][ii].second;
          const TrackingRecHit*  jt = rh1[k2][jj].second;
          if (share(it,jt,epsilon_))  noverlap++;
        }
          jh=lj; ih=li;
        } // equal ids

      } //loop over ih & jh

      bool dupfound = (collNum != collNum2) ? (noverlap-firstoverlap) > (std::min(nhit1,nhit2)-firstoverlap)*shareFrac_ :
        (noverlap-firstoverlap) > (std::min(nhit1,nhit2)-firstoverlap)*indivShareFrac_[collNum];

          auto seti = [&](unsigned int ii, unsigned int jj) {
             selected[jj]=0;
             selected[ii]=10+newQualityMask; // add 10 to avoid the case where mask = 1
             trkUpdated[ii]=true;
             if (trackAlgoPriorityOrder[oriAlgo[jj]] < trackAlgoPriorityOrder[oriAlgo[ii]]) oriAlgo[ii] = oriAlgo[jj];
             algoMask[ii] |= algoMask[jj];
             algoMask[jj] = algoMask[ii];  // in case we keep discarded
         };

      if ( dupfound ) {
        float score2 = score[k2];
        constexpr float almostSame = 0.01f; // difference rather than ratio due to possible negative values for score
        if ( score1 - score2 > almostSame ) {
          seti(i,j);
        } else if ( score2 - score1 > almostSame ) {
          seti(j,i);
        }else{
          // If tracks from both iterations are virtually identical, choose the one with the best quality or with lower algo
          if ((trackQuals[j] & (1<<reco::TrackBase::loose|1<<reco::TrackBase::tight|1<<reco::TrackBase::highPurity) ) ==
          (trackQuals[i] & (1<<reco::TrackBase::loose|1<<reco::TrackBase::tight|1<<reco::TrackBase::highPurity) )) {
        //same quality, pick earlier algo
        if (trackAlgoPriorityOrder[algo[k1]] <= trackAlgoPriorityOrder[algo[k2]]) {
                  seti(i,j);    
        } else {
                  seti(j,i);    
        }
          } else if ((trackQuals[j] & (1<<reco::TrackBase::loose|1<<reco::TrackBase::tight|1<<reco::TrackBase::highPurity) ) <
             (trackQuals[i] & (1<<reco::TrackBase::loose|1<<reco::TrackBase::tight|1<<reco::TrackBase::highPurity) )) {
                seti(i,j);
          }else{
                seti(j,i);
          }
        }//end fi < fj
        statCount.overlap();
        /*
        if (at0[k1]&&at0[k2]) {
          statCount.dp(dphi);
          if (dz<1.f) statCount.de(deta);
        }
        */
      }//end got a duplicate
      else {
        statCount.noOverlap();
      }
      //stop if the ith track is now unselected
      if (selected[i]==0) break;
    }//end track2 loop
      }//end track loop
    } //end loop over track list sets



    std::auto_ptr<edm::ValueMap<float> > vmMVA = std::auto_ptr<edm::ValueMap<float> >(new edm::ValueMap<float>);
    edm::ValueMap<float>::Filler fillerMVA(*vmMVA);



    // special case - if just doing the trkquals
    if (trkQualMod_) {
      unsigned int tSize=trackColls[0]->size();
      std::auto_ptr<edm::ValueMap<int> > vm = std::auto_ptr<edm::ValueMap<int> >(new edm::ValueMap<int>);
      edm::ValueMap<int>::Filler filler(*vm);

      std::vector<int> finalQuals(tSize,-1); //default is unselected
      for ( unsigned int i=0; i<rSize; i++) {
    unsigned int tNum=i%tSize;

    if (selected[i]>1 ) {
      finalQuals[tNum]=selected[i]-10;
      if (trkUpdated[i])
        finalQuals[tNum]=(finalQuals[tNum] | (1<<qualityToSet_));
    }
    if ( selected[i]==1 )
      finalQuals[tNum]=trackQuals[i];
      }

      filler.insert(trackHandles[0], finalQuals.begin(),finalQuals.end());
      filler.fill();

      e.put(vm);

      std::vector<float> mvaVec(tSize,-99);

      for(unsigned int i = 0; i < rSize; i++){
    unsigned int tNum = i % tSize;
    mvaVec[tNum] = trackMVAs[tNum];
      }

      fillerMVA.insert(trackHandles[0],mvaVec.begin(),mvaVec.end());
      fillerMVA.fill();
      if ( copyMVA_) 
    e.put(vmMVA,"MVAVals");
      return;
    }


    //
    //  output selected tracks - if any
    //

    std::vector<reco::TrackRef> trackRefs(rSize);
    std::vector<edm::RefToBase<TrajectorySeed>> seedsRefs(rSize);

    unsigned int nToWrite=0;
    for ( unsigned int i=0; i<rSize; i++)
      if (selected[i]!=0) nToWrite++;

    std::vector<float> mvaVec;

    outputTrks = std::auto_ptr<reco::TrackCollection>(new reco::TrackCollection);
    outputTrks->reserve(nToWrite);
    refTrks = e.getRefBeforePut<reco::TrackCollection>();

    if (copyExtras_) {
      outputTrkExtras = std::auto_ptr<reco::TrackExtraCollection>(new reco::TrackExtraCollection);
      outputTrkExtras->reserve(nToWrite);
      refTrkExtras    = e.getRefBeforePut<reco::TrackExtraCollection>();
      outputTrkHits   = std::auto_ptr<TrackingRecHitCollection>(new TrackingRecHitCollection);
      outputTrkHits->reserve(nToWrite*25);
      refTrkHits      = e.getRefBeforePut<TrackingRecHitCollection>();
      if (makeReKeyedSeeds_){
    outputSeeds = std::auto_ptr<TrajectorySeedCollection>(new TrajectorySeedCollection);
    outputSeeds->reserve(nToWrite);
    refTrajSeeds = e.getRefBeforePut<TrajectorySeedCollection>();
      }
    }


    outputTrajs = std::auto_ptr< std::vector<Trajectory> >(new std::vector<Trajectory>());
    outputTrajs->reserve(rSize);

    for ( unsigned int i=0; i<rSize; i++) {
      if (selected[i]==0) {
    trackRefs[i]=reco::TrackRef();
    continue;
      }

      unsigned int collNum=trackCollNum[i];
      unsigned int trackNum=i-trackCollFirsts[collNum];
      const reco::Track *track=&((trackColls[collNum])->at(trackNum));
      outputTrks->push_back( reco::Track( *track ) );
      mvaVec.push_back(trackMVAs[i]);
      if (selected[i]>1 ) {
    outputTrks->back().setQualityMask(selected[i]-10);
    if (trkUpdated[i]) 
      outputTrks->back().setQuality(qualityToSet_);
      }
      //might duplicate things, but doesnt hurt
      if ( selected[i]==1 ) 
    outputTrks->back().setQualityMask(trackQuals[i]);
      outputTrks->back().setOriginalAlgorithm(oriAlgo[i]);
      outputTrks->back().setAlgoMask(algoMask[i]);

      // if ( beVerb ) std::cout << "selected " << outputTrks->back().pt() << " " << outputTrks->back().qualityMask() << " " << selected[i] << std::endl;

      //fill the TrackCollection
      if (copyExtras_) {
    edm::RefToBase<TrajectorySeed> origSeedRef = track->seedRef();
    //creating a seed with rekeyed clusters if required
    if (makeReKeyedSeeds_){
      bool doRekeyOnThisSeed=false;

      edm::InputTag clusterRemovalInfos("");
      //grab on of the hits of the seed
      if (origSeedRef->nHits()!=0){
        TrajectorySeed::const_iterator firstHit=origSeedRef->recHits().first;
        const TrackingRecHit *hit = &*firstHit;
        if (firstHit->isValid()){
          edm::ProductID  pID=clusterProductB(hit);
          // the cluster collection either produced a removalInfo or mot
          //get the clusterremoval info from the provenance: will rekey if this is found
          edm::Handle<reco::ClusterRemovalInfo> CRIh;
          edm::Provenance prov=e.getProvenance(pID);
          clusterRemovalInfos=edm::InputTag(prov.moduleLabel(),
                        prov.productInstanceName(),
                        prov.processName());
          doRekeyOnThisSeed=e.getByLabel(clusterRemovalInfos,CRIh);
        }//valid hit
      }//nhit!=0

      if (doRekeyOnThisSeed && !(clusterRemovalInfos==edm::InputTag(""))) {
        ClusterRemovalRefSetter refSetter(e,clusterRemovalInfos);
        TrajectorySeed::recHitContainer  newRecHitContainer;
        newRecHitContainer.reserve(origSeedRef->nHits());
        TrajectorySeed::const_iterator iH=origSeedRef->recHits().first;
        TrajectorySeed::const_iterator iH_end=origSeedRef->recHits().second;
        for (;iH!=iH_end;++iH){
          newRecHitContainer.push_back(*iH);
          refSetter.reKey(&newRecHitContainer.back());
        }
        outputSeeds->push_back( TrajectorySeed( origSeedRef->startingState(),
                            newRecHitContainer,
                            origSeedRef->direction()));
      }
      //doRekeyOnThisSeed=true
      else{
        //just copy the one we had before
        outputSeeds->push_back( TrajectorySeed(*origSeedRef));
      }
      edm::Ref<TrajectorySeedCollection> pureRef(refTrajSeeds, outputSeeds->size()-1);
      origSeedRef=edm::RefToBase<TrajectorySeed>( pureRef);
    }//creating a new seed and rekeying it rechit clusters.

    // Fill TrackExtra collection
    outputTrkExtras->push_back( reco::TrackExtra(
                             track->outerPosition(), track->outerMomentum(), track->outerOk(),
                             track->innerPosition(), track->innerMomentum(), track->innerOk(),
                             track->outerStateCovariance(), track->outerDetId(),
                             track->innerStateCovariance(), track->innerDetId(),
                             track->seedDirection(), origSeedRef ) );
    seedsRefs[i]=origSeedRef;
    outputTrks->back().setExtra( reco::TrackExtraRef( refTrkExtras, outputTrkExtras->size() - 1) );
    reco::TrackExtra & tx = outputTrkExtras->back();
    tx.setResiduals(track->residuals());

    // fill TrackingRecHits
    unsigned nh1=track->recHitsSize();
        tx.setHits(refTrkHits,outputTrkHits->size(),nh1);
        for (auto hh = track->recHitsBegin(), eh=track->recHitsEnd(); hh!=eh; ++hh ) {
          outputTrkHits->push_back( (*hh)->clone() );
        }
      }
      trackRefs[i] = reco::TrackRef(refTrks, outputTrks->size() - 1);


    }//end faux loop over tracks

    //Fill the trajectories, etc. for 1st collection
    refTrajs    = e.getRefBeforePut< std::vector<Trajectory> >();

    outputTTAss = std::auto_ptr< TrajTrackAssociationCollection >(new TrajTrackAssociationCollection());

    for (unsigned int ti=0; ti<trackColls.size(); ti++) {
      edm::Handle< std::vector<Trajectory> >  hTraj1;
      edm::Handle< TrajTrackAssociationCollection >  hTTAss1;
      e.getByToken(trackProducers_[ti].traj, hTraj1);
      e.getByToken(trackProducers_[ti].tass, hTTAss1);

      if (hTraj1.failedToGet() || hTTAss1.failedToGet()) continue;

      for (size_t i = 0, n = hTraj1->size(); i < n; ++i) {
    edm::Ref< std::vector<Trajectory> > trajRef(hTraj1, i);
    TrajTrackAssociationCollection::const_iterator match = hTTAss1->find(trajRef);
    if (match != hTTAss1->end()) {
      const edm::Ref<reco::TrackCollection> &trkRef = match->val;
      short oldKey = trackCollFirsts[ti]+static_cast<short>(trkRef.key());
      if (trackRefs[oldKey].isNonnull()) {
        outputTrajs->push_back( *trajRef );
        //if making extras and the seeds at the same time, change the seed ref on the trajectory
        if (copyExtras_ && makeReKeyedSeeds_)
          outputTrajs->back().setSeedRef( seedsRefs[oldKey] );
        outputTTAss->insert ( edm::Ref< std::vector<Trajectory> >(refTrajs, outputTrajs->size() - 1),
                  trackRefs[oldKey] );
      }
    }
      }
    }

    statCount.end(outputTrks->size());

    edm::ProductID nPID = refTrks.id();
    edm::TestHandle<reco::TrackCollection> outHandle(outputTrks.get(),nPID);
    fillerMVA.insert(outHandle,mvaVec.begin(),mvaVec.end());
    fillerMVA.fill();

    e.put(outputTrks);
    if ( copyMVA_ )
      e.put(vmMVA,"MVAVals");
    if (copyExtras_) {
      e.put(outputTrkExtras);
      e.put(outputTrkHits);
      if (makeReKeyedSeeds_)
    e.put(outputSeeds);
    }
    e.put(outputTrajs);
    e.put(outputTTAss);
    return;

  }//end produce


#include "FWCore/PluginManager/interface/ModuleDef.h"
#include "FWCore/Framework/interface/MakerMacros.h"

DEFINE_FWK_MODULE(TrackListMerger);