TrackerTrackHitFilter.cc

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#include "FWCore/Framework/interface/stream/EDProducer.h"
#include "FWCore/Framework/interface/Event.h"
#include "FWCore/Framework/interface/EventSetup.h"
#include "FWCore/Framework/interface/ESHandle.h"

#include "FWCore/MessageLogger/interface/MessageLogger.h"
#include "FWCore/ParameterSet/interface/ParameterSet.h"
#include "FWCore/Utilities/interface/InputTag.h"

#include "DataFormats/Common/interface/View.h"
#include "DataFormats/TrackReco/interface/TrackFwd.h"
#include "DataFormats/TrackReco/interface/Track.h"
#include "DataFormats/TrackCandidate/interface/TrackCandidateCollection.h"
#include "DataFormats/TrackingRecHit/interface/InvalidTrackingRecHit.h"

#include "Geometry/Records/interface/TrackerDigiGeometryRecord.h"
#include "Geometry/TrackerGeometryBuilder/interface/TrackerGeometry.h"
#include "MagneticField/Engine/interface/MagneticField.h"
#include "MagneticField/Records/interface/IdealMagneticFieldRecord.h"
#include "TrackingTools/TrajectoryState/interface/TrajectoryStateTransform.h"
#include "TrackingTools/TrajectoryState/interface/TrajectoryStateOnSurface.h"

#include "DataFormats/TrackerCommon/interface/TrackerTopology.h"
#include "Geometry/Records/interface/TrackerTopologyRcd.h"

//for S/N cut
#include "DataFormats/TrackerRecHit2D/interface/ProjectedSiStripRecHit2D.h"
#include "DataFormats/TrackerRecHit2D/interface/SiStripMatchedRecHit2D.h"
#include "DataFormats/TrackerRecHit2D/interface/SiStripRecHit2D.h"
#include "DataFormats/TrackerRecHit2D/interface/SiStripRecHit1D.h"
#include "DataFormats/TrackerRecHit2D/interface/SiPixelRecHit.h"
#include "AnalysisDataFormats/SiStripClusterInfo/interface/SiStripClusterInfo.h"
//for angle cut
#include "TrackingTools/PatternTools/interface/Trajectory.h"
#include "TrackingTools/PatternTools/interface/TrajectoryMeasurement.h"
#include "TrackingTools/TrajectoryState/interface/TrajectoryStateOnSurface.h"
#include "TrackingTools/TrackFitters/interface/TrajectoryStateCombiner.h"
#include "TrackingTools/PatternTools/interface/TrajTrackAssociation.h"
#include "TMath.h"

#include "TrackingTools/Records/interface/TransientRecHitRecord.h"
#include "TrackingTools/TransientTrackingRecHit/interface/TransientTrackingRecHit.h"
#include "TrackingTools/TransientTrackingRecHit/interface/TransientTrackingRecHitBuilder.h"

#include "DataFormats/Provenance/interface/RunLumiEventNumber.h"

#include <boost/regex.hpp>
#include <map>
//#include <math>

namespace reco {

 namespace modules {
  class TrackerTrackHitFilter : public edm::stream::EDProducer<> {
  public:
    TrackerTrackHitFilter(const edm::ParameterSet &iConfig) ;
    virtual void produce(edm::Event &iEvent, const edm::EventSetup &iSetup) override;
    int checkHit(const edm::EventSetup &iSetup,const  DetId &detid,  const TrackingRecHit * hit);
    void produceFromTrajectory( const edm::EventSetup &iSetup, const Trajectory *itt, std::vector<TrackingRecHit *>&hits);
    void produceFromTrack( const edm::EventSetup &iSetup, const Track *itt, std::vector<TrackingRecHit *>&hits);
  private:
    class Rule {
    public:
      // parse a rule from a string
      Rule(const std::string &str) ;
      // check this DetId, update the verdict if the rule has anything to say about it
      void apply(DetId detid, const TrackerTopology *tTopo, bool & verdict) const {
    // check detector
    if (detid.subdetId() == subdet_) {
      // check layer
      if ( (layer_ == 0) || (layer_ == layer(detid, tTopo)) ) {
        // override verdict
        verdict = keep_;
        //  std::cout<<"Verdict is "<<verdict<<" for subdet "<<subdet_<<", layer "<<layer_<<"! "<<std::endl;
      }
      // else std::cout<<"No, sorry, wrong layer.Retry..."<<std::endl;
    }
    //  else{ std::cout<<"No, sorry, wrong subdet.Retry..."<<std::endl;}
      }
    private:
      int  subdet_;

      int  layer_;
      bool keep_;
      int layer(DetId detid, const TrackerTopology *tTopo) const ;

    };

    edm::InputTag src_;

    edm::RunNumber_t iRun;
    edm::EventNumber_t iEvt;

    size_t minimumHits_;

    bool replaceWithInactiveHits_;
    bool stripFrontInvalidHits_;
    bool stripBackInvalidHits_;
    bool stripAllInvalidHits_;

    bool rejectBadStoNHits_;
    std::string CMNSubtractionMode_;
    std::vector<bool>   subdetStoN_;//(6); //,std::bool(false));
    std::vector<double> subdetStoNlowcut_;//(6,-1.0);
    std::vector<double> subdetStoNhighcut_;//(6,-1.0);
    bool checkStoN( const edm::EventSetup &iSetup,const DetId &id, const TrackingRecHit* therechit);
    void parseStoN(const std::string &str);

    std::vector<uint32_t> detsToIgnore_;
    std::vector<Rule> rules_;

    bool useTrajectories_;
    bool rejectLowAngleHits_;
    double TrackAngleCut_;
    bool checkHitAngle(const TrajectoryMeasurement &meas);
    bool checkPXLQuality_;
    double pxlTPLProbXY_;
    double pxlTPLProbXYQ_;
    std::vector<int32_t> pxlTPLqBin_;

    bool checkPXLCorrClustCharge(const TrajectoryMeasurement &meas);
    double PXLcorrClusChargeCut_;

    edm::ESHandle<TrackerGeometry> theGeometry;
    edm::ESHandle<MagneticField>   theMagField;

    edm::ESHandle<TransientTrackingRecHitBuilder> theBuilder;

    edm::EDGetTokenT<reco::TrackCollection> tokenTracks;
    edm::EDGetTokenT<TrajTrackAssociationCollection> tokenTrajTrack;

    bool tagOverlaps_;
    int nOverlaps;
    int layerFromId (const DetId& id, const TrackerTopology *tTopo) const;
    int sideFromId (const DetId& id, const TrackerTopology *tTopo) const;
    // bool checkOverlapHit();

    TrackCandidate makeCandidate(const reco::Track &tk, std::vector<TrackingRecHit *>::iterator hitsBegin, std::vector<TrackingRecHit *>::iterator hitsEnd) ;
    //const TransientTrackingRecHitBuilder *RHBuilder;
  }; // class



TrackerTrackHitFilter::Rule::Rule(const std::string &str) {
    static const boost::regex rule("(keep|drop)\\s+([A-Z]+)(\\s+(\\d+))?");
    boost::cmatch match;
    std::string match_1;
    std::string match_2;
    std::string match_3;
    // match and check it works
    if (!regex_match(str.c_str(), match, rule)) {
        throw cms::Exception("Configuration") << "Rule '" << str << "' not understood.\n";
    }
    else{
      edm::LogInfo("TrackerTrackHitFilter") << "*** Rule Command given to TrackerTrackHitFilter:\t"<<str;

    }
    // Set up fields:
    //  rule type
    keep_  = (strncmp(match[1].first,"keep",4 )== 0);

    //  subdet
    subdet_ = -1;
    if      (strncmp(match[2].first, "PXB", 3) == 0) subdet_ = PixelSubdetector::PixelBarrel;
    else if (strncmp(match[2].first, "PXE", 3) == 0) subdet_ = PixelSubdetector::PixelEndcap;
    else if (strncmp(match[2].first, "TIB", 3) == 0) subdet_ = StripSubdetector::TIB;
    else if (strncmp(match[2].first, "TID", 3) == 0) subdet_ = StripSubdetector::TID;
    else if (strncmp(match[2].first, "TOB", 3) == 0) subdet_ = StripSubdetector::TOB;
    else if (strncmp(match[2].first, "TEC", 3) == 0) subdet_ = StripSubdetector::TEC;
    if (subdet_ == -1) {
        throw cms::Exception("Configuration") << "Detector '" << match[2].first << "' not understood. Should be PXB, PXE, TIB, TID, TOB, TEC.\n";
    }
    //   layer (if present)
    if (match[4].first != match[4].second) {
        layer_ = atoi(match[4].first);
    } else {
        layer_ = 0;
    }
}//end Rule::Rule

 int TrackerTrackHitFilter::Rule::layer(DetId detid, const TrackerTopology *tTopo) const {
    return tTopo->layer(detid);
}

void TrackerTrackHitFilter::parseStoN(const std::string &str) {
  // match a set of capital case chars (preceded by an arbitrary number of leading blanks),
  //followed b an arbitrary number of blanks, one or more digits (not necessary, they cannot also be,
  // another set of blank spaces and, again another *eventual* digit
  // static boost::regex rule("\\s+([A-Z]+)(\\s+(\\d+)(\\.)?(\\d+))?(\\s+(\\d+)(\\.)?(\\d+))?");
 static const boost::regex rule("([A-Z]+)"
                                "\\s*(\\d+\\.*\\d*)?"
                                "\\s*(\\d+\\.*\\d*)?");


  boost::cmatch match;
  std::string match_1;
  std::string match_2;
  std::string match_3;
  // match and check it works
  if (!regex_match(str.c_str(), match, rule)) {
    throw cms::Exception("Configuration") << "Rule for S to N cut '" << str << "' not understood.\n";
  }
  else{
    std::string match_0=match[0].second;
    match_1=match[1].second;
    match_2=match[2].second;
    match_3=match[3].second;

  }

  int cnt=0;
  float subdet_ind[6];
  for(cnt=0;cnt<6;cnt++ ){
    subdet_ind[cnt]=-1.0;
  }


  bool doALL=false;
  std::string match_1a(match[1].first,match[1].second);
 if (strncmp(match[1].first, "ALL", 3) == 0) doALL=true;
  if (doALL || strncmp(match[1].first, "PXB", 3) == 0)  subdet_ind[0] = +1.0;
  if (doALL || strncmp(match[1].first, "PXE", 3) == 0)  subdet_ind[1] = +1.0;
  if (doALL || strncmp(match[1].first, "TIB", 3) == 0)  subdet_ind[2] = +1.0;
  if (doALL || strncmp(match[1].first, "TID", 3) == 0)  subdet_ind[3] = +1.0;
  if (doALL || strncmp(match[1].first, "TOB", 3) == 0)  subdet_ind[4] = +1.0;
  if (doALL || strncmp(match[1].first, "TEC", 3) == 0)  subdet_ind[5] = +1.0;

  for(cnt=0;cnt<6;cnt++ ){//loop on subdets
    if(subdet_ind[cnt]>0.0){
      subdetStoN_[cnt]=true;
      if (match[2].first != match[2].second) {
    subdetStoNlowcut_[cnt] = atof(match[2].first);
      }
      if (match[3].first != match[3].second ) {
    subdetStoNhighcut_[cnt] = atof(match[3].first);
      }
      edm::LogInfo("TrackerTrackHitFilter") <<"Setting thresholds*&^ for subdet #"<<cnt+1<<" = "<<subdetStoNlowcut_[cnt]<<" - "<<subdetStoNhighcut_[cnt];
    }
  }

  bool correct_regex=false;
  for(cnt=0;cnt<6;cnt++ ){//check that the regex was correct
    if(subdetStoN_[cnt])correct_regex=true;
  }

  if (!correct_regex) {
    throw cms::Exception("Configuration") << "Detector '" << match_1a << "' not understood in parseStoN. Should be PXB, PXE, TIB, TID, TOB, TEC.\n";
    }

  //std::cout<<"Reached end of parseStoN"<<std::endl;
}//end parseStoN


TrackerTrackHitFilter::TrackerTrackHitFilter(const edm::ParameterSet &iConfig) :
    src_(iConfig.getParameter<edm::InputTag>("src")),
    minimumHits_(iConfig.getParameter<uint32_t>("minimumHits")),
    replaceWithInactiveHits_(iConfig.getParameter<bool>("replaceWithInactiveHits")),
    stripFrontInvalidHits_(iConfig.getParameter<bool>("stripFrontInvalidHits")),
    stripBackInvalidHits_( iConfig.getParameter<bool>("stripBackInvalidHits") ),
    stripAllInvalidHits_(  iConfig.getParameter<bool>("stripAllInvalidHits")  ),
    rejectBadStoNHits_(  iConfig.getParameter<bool>("rejectBadStoNHits")  ),
    CMNSubtractionMode_(  iConfig.getParameter<std::string>("CMNSubtractionMode")  ),
    detsToIgnore_( iConfig.getParameter<std::vector<uint32_t> >("detsToIgnore") ),
    useTrajectories_( iConfig.getParameter<bool>("useTrajectories") ),
    rejectLowAngleHits_( iConfig.getParameter<bool>("rejectLowAngleHits") ),
    TrackAngleCut_( iConfig.getParameter<double>("TrackAngleCut") ),
    checkPXLQuality_(iConfig.getParameter<bool>("usePixelQualityFlag") ),
    pxlTPLProbXY_(iConfig.getParameter<double>("PxlTemplateProbXYCut")),
    pxlTPLProbXYQ_(iConfig.getParameter<double>("PxlTemplateProbXYChargeCut")),
    pxlTPLqBin_(iConfig.getParameter<std::vector<int32_t> >("PxlTemplateqBinCut")),
    PXLcorrClusChargeCut_(iConfig.getParameter<double>("PxlCorrClusterChargeCut")),
    tagOverlaps_( iConfig.getParameter<bool>("tagOverlaps") )
{

    if(useTrajectories_) tokenTrajTrack = consumes<TrajTrackAssociationCollection>(src_);
    else tokenTracks = consumes<reco::TrackCollection>(src_);

    // sanity check
    if (stripAllInvalidHits_ && replaceWithInactiveHits_) {
        throw cms::Exception("Configuration") << "Inconsistent Configuration: you can't set both 'stripAllInvalidHits' and 'replaceWithInactiveHits' to true\n";
    }
    if(rejectLowAngleHits_ && !useTrajectories_){
      throw cms::Exception("Configuration") << "Wrong configuration of TrackerTrackHitFilter. You cannot apply the cut on the track angle without using Trajectories!\n";
    }
    if (!useTrajectories_ && PXLcorrClusChargeCut_>0){
      throw cms::Exception("Configuration") << "Wrong configuration of TrackerTrackHitFilter. You cannot apply the cut on the corrected pixel cluster charge without using Trajectories!\n";
    }

    if(pxlTPLqBin_.size()>2){
      edm::LogInfo("TrackerTrackHitFIlter")<<"Warning from TrackerTrackHitFilter: vector with qBin cuts has size > 2. Additional items will be ignored.";
    }



    // read and parse commands
    std::vector<std::string> str_rules = iConfig.getParameter<std::vector<std::string> >("commands");
    rules_.reserve(str_rules.size());
    for (std::vector<std::string>::const_iterator it = str_rules.begin(), ed = str_rules.end(); it != ed; ++it) {
        rules_.push_back(Rule(*it));
    }

    if(rejectBadStoNHits_){//commands for S/N cut

      subdetStoN_.reserve(6);
      subdetStoNlowcut_.reserve(6);
      subdetStoNhighcut_.reserve(6);
      int cnt=0;
      for(cnt=0;cnt<6;cnt++ ){
    subdetStoN_[cnt]=false;
    subdetStoNlowcut_[cnt]=-1.0;
    subdetStoNhighcut_[cnt]=-1.0;
      }

      std::vector<std::string> str_StoNrules = iConfig.getParameter<std::vector<std::string> >("StoNcommands");
       for (std::vector<std::string>::const_iterator str_StoN = str_StoNrules.begin(); str_StoN != str_StoNrules.end();  ++str_StoN) {
     parseStoN(*str_StoN);
       }
       edm::LogInfo("TrackerTrackHitFilter")<<"Finished parsing S/N. Applying following cuts to subdets:";
      for(cnt=0;cnt<6;cnt++ ){
        edm::LogVerbatim("TrackerTrackHitFilter")<<"Subdet #"<<cnt+1<<" -> "<<subdetStoNlowcut_[cnt]<<" , "<<subdetStoNhighcut_[cnt];
      }
    }//end if rejectBadStoNHits_


    if(rejectLowAngleHits_ )    edm::LogInfo("TrackerTrackHitFilter")<<"\nApplying cut on angle track = "<<TrackAngleCut_;


    // sort detids to ignore
    std::sort(detsToIgnore_.begin(), detsToIgnore_.end());

    // issue the produce<>
    produces<TrackCandidateCollection>();
}

void
TrackerTrackHitFilter::produce(edm::Event &iEvent, const edm::EventSetup &iSetup)
{
  //Dump Run and Event
  iRun=iEvent.id().run();
  iEvt=iEvent.id().event();

  // read with View, so we can read also a TrackRefVector
  edm::Handle<std::vector<reco::Track> > tracks;
  edm::Handle<TrajTrackAssociationCollection> assoMap;

  if(useTrajectories_)iEvent.getByToken(tokenTrajTrack,  assoMap);
  else iEvent.getByToken(tokenTracks, tracks);

  // read from EventSetup
  iSetup.get<TrackerDigiGeometryRecord>().get(theGeometry);
  iSetup.get<IdealMagneticFieldRecord>().get(theMagField);
  //iSetup.get<TransientRecHitRecord>().get("WithTrackAngle",theBuilder);
  // RHBuilder=   theBuilder.product();


  // prepare output collection
  size_t  candcollsize;
  if(useTrajectories_)candcollsize= assoMap->size();
  else candcollsize=tracks->size();
  std::auto_ptr<TrackCandidateCollection> output(new TrackCandidateCollection());

  output->reserve(candcollsize);

  // working area and tools
  std::vector<TrackingRecHit *> hits;

  if(useTrajectories_){
    for (TrajTrackAssociationCollection::const_iterator itass = assoMap->begin();  itass != assoMap->end(); ++itass){

      const edm::Ref<std::vector<Trajectory> >traj = itass->key;//trajectory in the collection
      const reco::TrackRef tkref = itass->val;//associated track track in the collection
      //std::cout<<"The hit collection has size "<<hits.size()<<" (should be 0) while the track contains initially "<< tkref->recHitsEnd() - tkref->recHitsBegin()<<std::endl;

      const Track *trk = &(*tkref);
      const Trajectory * myTrajectory= &(*traj);
      produceFromTrajectory(iSetup,myTrajectory,hits);

      std::vector<TrackingRecHit *>::iterator begin = hits.begin(), end = hits.end();

      // strip invalid hits at the beginning
      if (stripFrontInvalidHits_) {
    while ( (begin != end) && ( (*begin)->isValid() == false ) ) ++begin;
      }
      // strip invalid hits at the end
      if (stripBackInvalidHits_ && (begin != end)) {
    --end;
    while ( (begin != end) && ( (*end)->isValid() == false ) ) --end;
    ++end;
      }

         // if we still have some hits build the track candidate
      if(replaceWithInactiveHits_){
    int nvalidhits=0;
    for( std::vector<TrackingRecHit *>::iterator ithit=begin;ithit!=end;++ithit){
      if( (*ithit)->isValid())nvalidhits++;
    }
    if(nvalidhits >= int(minimumHits_)){
      output->push_back( makeCandidate ( *trk, begin, end ) );
    }
      }
      else{//all invalid hits have been already kicked out
    if ((end - begin) >= int(minimumHits_)) {
      output->push_back( makeCandidate ( *trk, begin, end ) );
    }
      }


      // if we still have some hits build the track candidate
      //if ((end - begin) >= int(minimumHits_)) {
      //    output->push_back( makeCandidate ( *trk, begin, end ) );
      //}


      // now delete the hits not used by the candidate
      for (begin = hits.begin(), end = hits.end(); begin != end; ++begin) {
    if (*begin) delete *begin;
      }
      hits.clear();
    } // loop on trajectories


  }
  else{ //use plain tracks

    // loop on tracks
    for (std::vector<reco::Track>::const_iterator ittrk = tracks->begin(), edtrk = tracks->end(); ittrk != edtrk; ++ittrk) {

      //    std::cout<<"The hit collection has size "<<hits.size()<<" (should be 0) while the track contains initially "<< ittrk->recHitsEnd() - ittrk->recHitsBegin()<<std::endl;

      const Track *trk = &(*ittrk);

      produceFromTrack(iSetup,trk,hits);
      //-----------------------
      /*
      std::cout<<"Hit collection in output has size "<<hits.size()<<". Dumping hit positions..."<<std::endl;
        for (std::vector<TrackingRecHit *>::iterator ith = hits.begin(), edh = hits.end(); ith != edh; ++ith) {
      const TrackingRecHit *myhit = *(ith);
        TransientTrackingRecHit::RecHitPointer ttrh;
        float radius=0.0;
        float xx=-999.0,yy=-999.0,zz=-999.0;
        unsigned int myid=0;
        if(myhit->isValid()){
          ttrh = RHBuilder->build(myhit);
          xx=ttrh->globalPosition().x();
          yy=ttrh->globalPosition().y();
          zz=ttrh->globalPosition().z();
          radius = sqrt( pow(xx,2)+pow(yy,2) );
          myid=myhit->geographicalId().rawId();
        }
        std::cout<<"-$-$ OUTPUT Hit position: ( "<<xx<<" , " <<yy<<" , " <<zz<<" ) , RADIUS = "  <<radius<<"  on DetID= "<< myid<<std::endl;
    }//end loop on hits
      */
      //-----------------------


      std::vector<TrackingRecHit *>::iterator begin = hits.begin(), end = hits.end();
      // std::cout << "Back in the main producer (TRK), the final hit collection has size " << hits.size() << std::endl;
      // strip invalid hits at the beginning
      if (stripFrontInvalidHits_) {
    while ( (begin != end) && ( (*begin)->isValid() == false ) ) ++begin;
      }
      // strip invalid hits at the end
      if (stripBackInvalidHits_ && (begin != end)) {
    --end;
    while ( (begin != end) && ( (*end)->isValid() == false ) ) --end;
    ++end;
      }

      // if we still have some hits build the track candidate
      if(replaceWithInactiveHits_){
    int nvalidhits=0;
    for( std::vector<TrackingRecHit *>::iterator ithit=begin;ithit!=end;++ithit){
      if( (*ithit)->isValid())nvalidhits++;
    }
    if(nvalidhits >= int(minimumHits_)){
      output->push_back( makeCandidate ( *ittrk, begin, end ) );
    }

      }
      else{//all invalid hits have been already kicked out
    if ((end - begin) >= int(minimumHits_)) {
      output->push_back( makeCandidate ( *ittrk, begin, end ) );
    }
      }

      // now delete the hits not used by the candidate
      for (begin = hits.begin(), end = hits.end(); begin != end; ++begin) {
    if (*begin) delete *begin;
      }
      hits.clear();
    } // loop on tracks
  }//end else useTracks

  // std::cout<<"OUTPUT SIZE: "<<output->size()<<std::endl;

  iEvent.put(output);
}

TrackCandidate
TrackerTrackHitFilter::makeCandidate(const reco::Track &tk, std::vector<TrackingRecHit *>::iterator hitsBegin, std::vector<TrackingRecHit *>::iterator hitsEnd) {


    PropagationDirection   pdir = tk.seedDirection();
    PTrajectoryStateOnDet state;
    if ( pdir == anyDirection ) throw cms::Exception("UnimplementedFeature") << "Cannot work with tracks that have 'anyDirecton' \n";

    //  double innerP=sqrt( pow(tk.innerMomentum().X(),2)+pow(tk.innerMomentum().Y(),2)+pow(tk.innerMomentum().Z(),2) );
    //  if ( (pdir == alongMomentum) == ( innerP >= tk.outerP() ) ) {

    if ( (pdir == alongMomentum) == (  (tk.outerPosition()-tk.innerPosition()).Dot(tk.momentum()) >= 0    ) ) {
        // use inner state
        TrajectoryStateOnSurface originalTsosIn(trajectoryStateTransform::innerStateOnSurface(tk, *theGeometry, &*theMagField));
        state = trajectoryStateTransform::persistentState( originalTsosIn, DetId(tk.innerDetId()) );
    } else {
        // use outer state
        TrajectoryStateOnSurface originalTsosOut(trajectoryStateTransform::outerStateOnSurface(tk, *theGeometry, &*theMagField));
        state = trajectoryStateTransform::persistentState( originalTsosOut, DetId(tk.outerDetId()) );
    }
    TrajectorySeed seed(state, TrackCandidate::RecHitContainer(), pdir);
    TrackCandidate::RecHitContainer ownHits;
    ownHits.reserve(hitsEnd - hitsBegin);
    for ( ; hitsBegin != hitsEnd; ++hitsBegin) {
      //if(! (*hitsBegin)->isValid() ) std::cout<<"Putting in the trackcandidate an INVALID HIT !"<<std::endl;
      ownHits.push_back( *hitsBegin );
    }

    TrackCandidate cand(ownHits, seed, state, tk.seedRef());

    return cand;
}

void TrackerTrackHitFilter::produceFromTrack(const edm::EventSetup &iSetup, const Track *itt , std::vector<TrackingRecHit *>&hits){

    // loop on tracks
        hits.clear(); // extra safety

        for (trackingRecHit_iterator ith = itt->recHitsBegin(), edh = itt->recHitsEnd(); ith != edh; ++ith) {
      const TrackingRecHit * hit = (*ith); // ith is an iterator on edm::Ref to rechit

        DetId detid = hit->geographicalId();

        //check that the hit is a real hit and not a constraint
        if(hit->isValid() && hit==0 && detid.rawId()==0) continue;

        int verdict=checkHit(iSetup,detid,hit);
        if (verdict == 0) {
          // just copy the hit
          hits.push_back(hit->clone());
        }
        else if(verdict<-2){//hit rejected because did not pass the selections
                            // still, if replaceWithInactiveHits is true we have to put a new hit
          if (replaceWithInactiveHits_) {
        hits.push_back(new InvalidTrackingRecHit(*(hit->det()), TrackingRecHit::inactive));
          }
        }
        else if(verdict==-2) hits.push_back(hit->clone());//hit not in the tracker
        else if(verdict==-1){ //hit not valid
          if (!stripAllInvalidHits_) {
        hits.push_back(hit->clone());
          }
        }
    } // loop on hits

}//end TrackerTrackHitFilter::produceFromTrack


void TrackerTrackHitFilter::produceFromTrajectory(const edm::EventSetup &iSetup, const Trajectory *itt, std::vector<TrackingRecHit *>&hits){
  hits.clear(); // extra safety
  nOverlaps=0;

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


  std::vector<TrajectoryMeasurement> tmColl =itt->measurements();

  //---OverlapBegin needed eventually for overlaps, but I must create them here in any case
  const TrajectoryMeasurement* previousTM(0);
  DetId previousId(0);
  //int previousLayer(-1);

  int constrhits=0;

  for(std::vector<TrajectoryMeasurement>::const_iterator itTrajMeas = tmColl.begin(); itTrajMeas!=tmColl.end(); itTrajMeas++){
     TransientTrackingRecHit::ConstRecHitPointer hitpointer = itTrajMeas->recHit();

     //check that the hit is a real hit and not a constraint
     if(hitpointer->isValid() && hitpointer->hit()==0){constrhits++; continue;}

    const TrackingRecHit *hit=((*hitpointer).hit());
    DetId detid = hit->geographicalId();
    int verdict=checkHit(iSetup,detid,hit);

    if (verdict == 0) {
      if( rejectLowAngleHits_ && !checkHitAngle(*itTrajMeas) ){//check angle of track on module if requested
    verdict=-6;//override previous verdicts
      }
    }

    /*
    //this has been included in checkHitAngle(*itTrajMeas)
    if (verdict == 0) {
    if( PXLcorrClusChargeCut_>0.0  && !checkPXLCorrClustCharge(*itTrajMeas) ){//check angle of track on module if requested
    verdict=-7;//override previous verdicts
    }
    }
    */


    if(verdict==0){// Hit TAKEN !!!!

    if(tagOverlaps_){   
      //std::cout<<"Looking for overlaps in Run="<<iRun<<" , Event ="<<iEvt<<std::flush;

      int side(sideFromId(detid,tTopo));//side 0=barrel, 1=minus , 2=plus
      int layer(layerFromId(detid,tTopo));//layer or disk
      int subDet = detid.subdetId();
      //std::cout  << "  Check Subdet #" <<subDet << ", layer = " <<layer<<" stereo: "<< ((subDet > 2)?(SiStripDetId(detid).stereo()):2);

        if ( ( previousTM!=0 )&& (layer!=-1 )) {
          //std::cout<<"A previous TM exists! "<<std::endl;
          for (std::vector<TrajectoryMeasurement>::const_iterator itmCompare =itTrajMeas-1;itmCompare >= tmColl.begin() &&  itmCompare > itTrajMeas - 4;--itmCompare){

        DetId compareId = itmCompare->recHit()->geographicalId();
        if ( subDet != compareId.subdetId() ||
             side != sideFromId(compareId,tTopo) ||
             layer  != layerFromId(compareId,tTopo)) break;
        if (!itmCompare->recHit()->isValid()) continue;
        if(GeomDetEnumerators::isTrackerPixel(theGeometry->geomDetSubDetector(detid.subdetId())) ||
           (GeomDetEnumerators::isTrackerStrip(theGeometry->geomDetSubDetector(detid.subdetId())) &&
            SiStripDetId(detid).stereo()==SiStripDetId(compareId).stereo()))
          {//if either pixel or strip stereo module
            //  overlapHits.push_back(std::make_pair(&(*itmCompare),&(*itm)));
            //std::cout<< "Adding pair "<< ((subDet >2)?(SiStripDetId(detid).stereo()):2)
            //     << " from SubDet = "<<subDet<<" , layer = " << layer<<"  Run:"<<iRun<<"\tEv: "<<iEvt<<"\tId1: "<<compareId.rawId()<<"\tId2: "<<detid.rawId()<<std::endl;
            // if(abs(compareId.rawId()-detid.rawId())==1)std::cout<<"These two are from the same det! Id1= "<<detid.rawId()<<" has stereo type "<<SiStripDetId(detid).stereo() <<"\tId2: "<<compareId.rawId()<<" has stereo type "<<SiStripDetId(compareId).stereo()<<std::endl;
            // if(detid.rawId()<compareId.rawId()){
              // std::cout<< "+++ "<< "\t"<<iRun<<"\t"<<iEvt<<"\t"<<detid.rawId()<<"\t"<<compareId.rawId()<<std::endl;
            // }
            //else  std::cout<< "+++ "<< "\t"<<iRun<<"\t"<<iEvt<<"\t"<<compareId.rawId()<<"\t"<<detid.rawId()<<std::endl;

            nOverlaps++;
            break;
          }
          }//end second loop on TM for overlap tagging

        }//end   if ( (layer!=-1 )&&(acceptLayer[subDet]))

        previousTM = &(* itTrajMeas);
        previousId = detid;
        //previousLayer = layer;
    }//end if look for overlaps

    hits.push_back(hit->clone());   //just copy it
    }//end if HIT TAKEN
    else if(verdict<-2){//hit rejected because did not pass the selections
      // still, if replaceWithInactiveHits is true we have to put a new hit
      if (replaceWithInactiveHits_) {
    hits.push_back(new InvalidTrackingRecHit(*hit->det(), TrackingRecHit::inactive));
      }
    }
    else if(verdict==-2) hits.push_back(hit->clone());//hit not in the tracker
    else if(verdict==-1){ //hit not valid
      if (!stripAllInvalidHits_) {
    hits.push_back(hit->clone());
      }
    }
  } // loop on hits

  std::reverse(hits.begin(),hits.end());
  //  std::cout<<"Finished producefromTrajecotries. Nhits in final coll"<<hits.size() <<"   Nconstraints="<<constrhits<<std::endl;
} //end TrackerTrackHitFilter::produceFromTrajectories

int TrackerTrackHitFilter::checkHit(const edm::EventSetup &iSetup,const  DetId &detid,  const TrackingRecHit * hit){

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

  int hitresult=0;
  if (hit->isValid()) {

    if (detid.det() == DetId::Tracker) {  // check for tracker hits
       bool  verdict = true;
      // first check at structure level
      for (std::vector<Rule>::const_iterator itr = rules_.begin(), edr = rules_.end(); itr != edr; ++itr) {
    itr->apply(detid, tTopo, verdict);
      }

      // if the hit is good, check again at module level
      if ( verdict){
    if(std::binary_search(detsToIgnore_.begin(), detsToIgnore_.end(), detid.rawId())) {
      hitresult=-4;
    }
      }
      else hitresult=-3;
       //if the hit is in the desired part of the det, check other things
      if( hitresult==0 && rejectBadStoNHits_){
    if(!checkStoN(iSetup, detid, hit))hitresult=-5;
      }//end if S/N is ok
    }//end hit in tracker
    else hitresult =-2;
  }//end hit is valid
  else hitresult = -1; //invalid hit
  return hitresult;
}//end  TrackerTrackHitFilter::checkHit()



bool TrackerTrackHitFilter::checkStoN(const edm::EventSetup &iSetup, const DetId &id, const TrackingRecHit* therechit){

  bool  keepthishit=true;
  // const uint32_t& recHitDetId = id.rawId();

   //check StoN only if subdet was set by the user
  //  int subdet_cnt=0;
  int subdet_cnt=id.subdetId();

  //  for(subdet_cnt=0;subdet_cnt<6; ++subdet_cnt){

  //  if( subdetStoN_[subdet_cnt-1]&& (id.subdetId()==subdet_cnt)  ){//check that hit is in a det belonging to a subdet where we decided to apply a S/N cut


    if(GeomDetEnumerators::isTrackerStrip(theGeometry->geomDetSubDetector(id.subdetId()))) {
      if( subdetStoN_[subdet_cnt-1]){//check that hit is in a det belonging to a subdet where we decided to apply a S/N cut
    const std::type_info &type = typeid(*therechit);
    const SiStripCluster* cluster;
    if (type == typeid(SiStripRecHit2D)) {
      const SiStripRecHit2D* hit = dynamic_cast<const SiStripRecHit2D*>(therechit);
      if (hit!=0)    cluster = &*(hit->cluster());
      else{
        edm::LogError("TrackerTrackHitFilter")<< "TrackerTrackHitFilter::checkStoN : Unknown valid tracker hit in subdet " << id.subdetId()<< "(detID="<<id.rawId()<<")\n ";
        keepthishit = false;
      }
    }
    else if (type == typeid(SiStripRecHit1D)) {
      const SiStripRecHit1D* hit = dynamic_cast<const SiStripRecHit1D*>(therechit);
      if (hit!=0)    cluster = &*(hit->cluster());
      else{
        edm::LogError("TrackerTrackHitFilter")<< "TrackerTrackHitFilter::checkStoN : Unknown valid tracker hit in subdet " << id.subdetId()<< "(detID="<<id.rawId()<<")\n ";
        keepthishit = false;
      }
    }
    //the following two cases should not happen anymore since CMSSW > 2_0_X because of hit splitting in stereo modules
    //const SiStripMatchedRecHit2D* matchedhit = dynamic_cast<const SiStripMatchedRecHit2D*>(therechit);
    //const ProjectedSiStripRecHit2D* unmatchedhit = dynamic_cast<const ProjectedSiStripRecHit2D*>(therechit);
    else{
      throw cms::Exception("Unknown RecHit Type") << "RecHit of type " << type.name() <<
        " not supported. (use c++filt to demangle the name)";
    }

    if(keepthishit){
      SiStripClusterInfo clusterInfo = SiStripClusterInfo( *cluster, iSetup, id.rawId());
      if ( (subdetStoNlowcut_[subdet_cnt-1]>0) && (clusterInfo.signalOverNoise() < subdetStoNlowcut_[subdet_cnt-1])  ) keepthishit = false;
      if ( (subdetStoNhighcut_[subdet_cnt-1]>0) && (clusterInfo.signalOverNoise() > subdetStoNhighcut_[subdet_cnt-1])  ) keepthishit = false;
      //if(!keepthishit)std::cout<<"Hit rejected because of bad S/N: "<<clusterInfo.signalOverNoise()<<std::endl;
    }

      }//end if  subdetStoN_[subdet_cnt]&&...

    }//end if subdet_cnt >2
    else if (GeomDetEnumerators::isTrackerPixel(theGeometry->geomDetSubDetector(id.subdetId()))){//pixel 
      //pixels have naturally a very low noise (because of their low capacitance). So the S/N cut is
      //irrelevant in this case. Leave it dummy
      keepthishit = true;

      /**************
       * Cut on cluster charge corr by angle embedded in the checkHitAngle() function
       *
       *************/

      if(checkPXLQuality_){
      const SiPixelRecHit* pixelhit = dynamic_cast<const SiPixelRecHit*>(therechit);
      if(pixelhit!=0){
    //std::cout << "ClusterCharge=" <<std::flush<<pixelhit->cluster()->charge() << std::flush;
        float xyprob=pixelhit->clusterProbability(0);//x-y combined log_e probability of the pixel cluster
                                                   //singl x- and y-prob not stored sicne CMSSW 3_9_0
    float xychargeprob   =pixelhit->clusterProbability(1);//xy-prob * charge prob
    //  float chargeprob   =pixelhit->clusterProbability(2);//charge prob
    bool haspassed_tplreco= pixelhit->hasFilledProb(); //the cluster was associted to a template
    int qbin      =pixelhit->qBin(); //R==meas_charge/pred_charge:  Qbin=0 ->R>1.5 , =1->1<R<1.5 ,=2->0.85<R<1 ,
                                     // Qbin=3->0.95*Qminpred<R<0.85 ,=4->, =5->meas_charge<0.95*Qminpred

    //  if(haspassed_tplreco)   std::cout<<"  CLUSTPROB=\t"<<xprob<<"\t"<<yprob<<"\t"<<combprob<<"\t"<<qbin<<std::endl;
    //  else std::cout<<"CLUSTPROBNOTDEF=\t"<<xprob<<"\t"<<yprob<<"\t"<<combprob<<"\t"<<qbin<<std::endl;

    keepthishit = false;
    //  std::cout<<"yyyyy "<<qbin<<" "<<xprob<<"  "<<yprob<<std::endl;
    if( haspassed_tplreco && xyprob>pxlTPLProbXY_ && xychargeprob>pxlTPLProbXYQ_ && qbin>pxlTPLqBin_[0] && qbin<=pxlTPLqBin_[1] )keepthishit = true;

      }
      else {edm::LogInfo("TrackerTrackHitFilter")<<"HIT IN PIXEL ("<<subdet_cnt <<") but PixelRecHit is EMPTY!!!";}
      }//end if check pixel quality flag
    }
    //    else  throw cms::Exception("TrackerTrackHitFilter") <<"Loop over subdetector out of range when applying the S/N cut: "<<subdet_cnt;

    //  }//end loop on subdets


  return  keepthishit;
}//end CheckStoN



bool TrackerTrackHitFilter::checkHitAngle(const TrajectoryMeasurement &meas){

  bool angle_ok=false;
  bool corrcharge_ok=true;
  TrajectoryStateOnSurface tsos = meas.updatedState();
  /*
  edm::LogDebug("TrackerTrackHitFilter")<<"TSOS parameters: ";
  edm::LogDebug("TrackerTrackHitFilter") <<"Global momentum: "<<tsos.globalMomentum().x()<<"  "<<tsos.globalMomentum().y()<<"  "<<tsos.globalMomentum().z();
  edm::LogDebug("TrackerTrackHitFilter") <<"Local momentum: "<<tsos.localMomentum().x()<<"  "<<tsos.localMomentum().y()<<"  "<<tsos.localMomentum().z();
  edm::LogDebug("TrackerTrackHitFilter") <<"Track charge: "  <<tsos.charge();
  edm::LogDebug("TrackerTrackHitFilter")<<"Local position: "  <<tsos.localPosition().x()<<"  "<<tsos.localPosition().y()<<"  "<<tsos.localPosition().z();
  */
  if(tsos.isValid()){
    //check the angle of this tsos
    float mom_x=tsos.localDirection().x();
    float mom_y=tsos.localDirection().y();
    float mom_z=tsos.localDirection().z();
    //we took LOCAL momentum, i.e. respect to surface. Thus the plane is z=0
    float angle=TMath::ASin(TMath::Abs(mom_z) / sqrt(pow(mom_x,2)+pow(mom_y,2)+pow(mom_z,2) )  );
    if(!rejectLowAngleHits_ || angle>=TrackAngleCut_) angle_ok=true;// keep this hit
    // else  std::cout<<"Hit rejected because angle is "<< angle<<" ( <"<<TrackAngleCut_<<" )"<<std::endl;

    if(angle_ok &&  PXLcorrClusChargeCut_>0.0){
      //
      //get the hit from the TM and check that it is in the pixel
      TransientTrackingRecHit::ConstRecHitPointer hitpointer = meas.recHit();
      if(hitpointer->isValid()){
      const TrackingRecHit *hit=(*hitpointer).hit();
      if(GeomDetEnumerators::isTrackerPixel(theGeometry->geomDetSubDetector(hit->geographicalId().subdetId()))) {//do it only for pixel hits
    corrcharge_ok=false;
    float clust_alpha= atan2( mom_z, mom_x );
    float clust_beta=  atan2( mom_z, mom_y );

    //Now get the cluster charge

    const SiPixelRecHit* pixelhit = dynamic_cast<const SiPixelRecHit*>(hit);
    float clust_charge=pixelhit->cluster()->charge();
    float corr_clust_charge=clust_charge *  sqrt( 1.0 / ( 1.0/pow( tan(clust_alpha), 2 ) +
                                  1.0/pow( tan(clust_beta ), 2 ) +
                                  1.0 )
                              );
    //std::cout<<"xxxxx "<<clust_charge<<" "<<corr_clust_charge<<"  " <<pixelhit->qBin()<<"  "<<pixelhit->clusterProbability(1)<<"  "<<pixelhit->clusterProbability(2)<< std::endl;
    if(corr_clust_charge>PXLcorrClusChargeCut_){
      corrcharge_ok=true;
    }
      }       //end if hit is in pixel
      }//end if hit is valid

    }//check corr cluster charge for pixel hits

  }//end if TSOS is valid
  else{
    edm::LogWarning("TrackerTrackHitFilter") <<"TSOS not valid ! Impossible to calculate track angle.";
  }

  return angle_ok&&corrcharge_ok;
}//end TrackerTrackHitFilter::checkHitAngle


bool TrackerTrackHitFilter::checkPXLCorrClustCharge(const TrajectoryMeasurement &meas){
  /*
    Code taken from DPGAnalysis/SiPixelTools/plugins/PixelNtuplizer_RealData.cc
  */

  bool corrcharge_ok=false;
  //get the hit from the TM and check that it is in the pixel
  TransientTrackingRecHit::ConstRecHitPointer hitpointer = meas.recHit();
  if(!hitpointer->isValid()) return corrcharge_ok;
  const TrackingRecHit *hit=(*hitpointer).hit();
  if(GeomDetEnumerators::isTrackerStrip(theGeometry->geomDetSubDetector(hit->geographicalId().subdetId()))) {//SiStrip hit, skip
     return corrcharge_ok;
  }

  TrajectoryStateOnSurface tsos = meas.updatedState();
  if(tsos.isValid()){
    float mom_x=tsos.localDirection().x();
    float mom_y=tsos.localDirection().y();
    float mom_z=tsos.localDirection().z();
    float clust_alpha= atan2( mom_z, mom_x );
    float clust_beta=  atan2( mom_z, mom_y );

    //Now get the cluster charge

      const SiPixelRecHit* pixelhit = dynamic_cast<const SiPixelRecHit*>(hit);
      float clust_charge=pixelhit->cluster()->charge();
      float corr_clust_charge=clust_charge *  sqrt( 1.0 / ( 1.0/pow( tan(clust_alpha), 2 ) +
                              1.0/pow( tan(clust_beta ), 2 ) +
                              1.0 )
                          );
      if(corr_clust_charge>PXLcorrClusChargeCut_)corrcharge_ok=true;

  }//end if TSOS is valid
  return corrcharge_ok;

}//end TrackerTrackHitFilter::checkPXLCorrClustCharge



int TrackerTrackHitFilter::layerFromId (const DetId& id, const TrackerTopology *tTopo) const
{
  return tTopo->layer(id);
}

int TrackerTrackHitFilter::sideFromId (const DetId& id, const TrackerTopology *tTopo) const
{
  return tTopo->side(id);
}

}} //namespaces


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

using reco::modules::TrackerTrackHitFilter;
DEFINE_FWK_MODULE(TrackerTrackHitFilter);