HitEff.cc

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// Package:          CalibTracker/SiStripHitEfficiency
// Class:            HitEff
// Original Author:  Keith Ulmer--University of Colorado
//                   keith.ulmer@colorado.edu
//

// system include files
#include <memory>
#include <string>
#include <iostream>

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

#include "FWCore/ParameterSet/interface/ParameterSet.h"
#include "CalibTracker/SiStripHitEfficiency/interface/HitEff.h"
#include "DataFormats/SiStripDetId/interface/StripSubdetector.h"
#include "DataFormats/Common/interface/Handle.h"
#include "FWCore/Framework/interface/ESHandle.h"
#include "FWCore/Framework/interface/EventSetup.h"
#include "DataFormats/GeometryVector/interface/GlobalPoint.h"
#include "DataFormats/GeometryVector/interface/GlobalVector.h"
#include "DataFormats/GeometryVector/interface/LocalVector.h"
#include "DataFormats/GeometrySurface/interface/TrapezoidalPlaneBounds.h"
#include "Geometry/TrackerGeometryBuilder/interface/TrackerGeometry.h"
#include "Geometry/Records/interface/TrackerDigiGeometryRecord.h"
#include "Geometry/CommonDetUnit/interface/GeomDetType.h"
#include "Geometry/CommonDetUnit/interface/GeomDet.h"
#include "DataFormats/TrackReco/interface/Track.h"
#include "DataFormats/TrackReco/interface/TrackFwd.h"
#include "DataFormats/TrackReco/interface/TrackExtra.h"
#include "MagneticField/Records/interface/IdealMagneticFieldRecord.h"
#include "TrackingTools/Records/interface/TransientRecHitRecord.h" 
#include "DataFormats/TrackingRecHit/interface/TrackingRecHit.h"
#include "CalibTracker/SiStripHitEfficiency/interface/TrajectoryAtInvalidHit.h"
#include "DataFormats/TrackerCommon/interface/TrackerTopology.h"
#include "Geometry/Records/interface/TrackerTopologyRcd.h"
#include "RecoLocalTracker/ClusterParameterEstimator/interface/StripClusterParameterEstimator.h"
#include "TrackingTools/GeomPropagators/interface/AnalyticalPropagator.h"
#include "DataFormats/TrackReco/interface/DeDxData.h"
//#include "DataFormats/DetId/interface/DetIdCollection.h"
#include "TrackingTools/DetLayers/interface/DetLayer.h"
#include "RecoTracker/MeasurementDet/interface/MeasurementTracker.h"
#include "RecoTracker/MeasurementDet/interface/MeasurementTrackerEvent.h"

#include "RecoTracker/Record/interface/CkfComponentsRecord.h"
#include "AnalysisDataFormats/SiStripClusterInfo/interface/SiStripClusterInfo.h"
#include "CalibTracker/Records/interface/SiStripDetCablingRcd.h"
#include "CalibFormats/SiStripObjects/interface/SiStripDetCabling.h"
#include "CalibTracker/Records/interface/SiStripQualityRcd.h"
#include "CalibFormats/SiStripObjects/interface/SiStripQuality.h"
#include "DataFormats/SiStripDetId/interface/SiStripSubStructure.h"
#include "Geometry/CommonDetUnit/interface/GluedGeomDet.h"
#include "DataFormats/Common/interface/DetSetVector.h"
#include "DataFormats/Common/interface/DetSetVectorNew.h"
#include "DataFormats/SiStripCluster/interface/SiStripCluster.h" 

#include "DataFormats/MuonReco/interface/Muon.h"
#include "DataFormats/MuonReco/interface/MuonFwd.h"


#include "TMath.h"
#include "TH1F.h"

//
// constructors and destructor
//

using namespace std;
HitEff::HitEff(const edm::ParameterSet& conf) : 
  scalerToken_( consumes< LumiScalersCollection >(conf.getParameter<edm::InputTag>("lumiScalers")) ),
  commonModeToken_( mayConsume< edm::DetSetVector<SiStripRawDigi> >(conf.getParameter<edm::InputTag>("commonMode")) ),
  combinatorialTracks_token_( consumes< reco::TrackCollection >(conf.getParameter<edm::InputTag>("combinatorialTracks")) ),
  trajectories_token_( consumes< std::vector<Trajectory> >(conf.getParameter<edm::InputTag>("trajectories")) ),
  clusters_token_( consumes< edmNew::DetSetVector<SiStripCluster> >(conf.getParameter<edm::InputTag>("siStripClusters")) ),
  digis_token_( consumes< DetIdCollection >(conf.getParameter<edm::InputTag>("siStripDigis")) ),
  trackerEvent_token_( consumes< MeasurementTrackerEvent>(conf.getParameter<edm::InputTag>("trackerEvent")) ),
  conf_(conf)
{
  layers =conf_.getParameter<int>("Layer");
  DEBUG = conf_.getParameter<bool>("Debug");
  addLumi_ = conf_.getUntrackedParameter<bool>("addLumi", false);
  addCommonMode_ = conf_.getUntrackedParameter<bool>("addCommonMode", false);
}

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

void HitEff::beginJob(){

  edm::Service<TFileService> fs;

  traj = fs->make<TTree>("traj","tree of trajectory positions");
  traj->Branch("TrajGlbX",&TrajGlbX,"TrajGlbX/F");
  traj->Branch("TrajGlbY",&TrajGlbY,"TrajGlbY/F");
  traj->Branch("TrajGlbZ",&TrajGlbZ,"TrajGlbZ/F");
  traj->Branch("TrajLocX",&TrajLocX,"TrajLocX/F");
  traj->Branch("TrajLocY",&TrajLocY,"TrajLocY/F");
  traj->Branch("TrajLocErrX",&TrajLocErrX,"TrajLocErrX/F");
  traj->Branch("TrajLocErrY",&TrajLocErrY,"TrajLocErrY/F");
  traj->Branch("TrajLocAngleX",&TrajLocAngleX,"TrajLocAngleX/F");
  traj->Branch("TrajLocAngleY",&TrajLocAngleY,"TrajLocAngleY/F");
  traj->Branch("ClusterLocX",&ClusterLocX,"ClusterLocX/F");
  traj->Branch("ClusterLocY",&ClusterLocY,"ClusterLocY/F");
  traj->Branch("ClusterLocErrX",&ClusterLocErrX,"ClusterLocErrX/F");
  traj->Branch("ClusterLocErrY",&ClusterLocErrY,"ClusterLocErrY/F");
  traj->Branch("ClusterStoN",&ClusterStoN,"ClusterStoN/F");
  traj->Branch("ResX",&ResX,"ResX/F");
  traj->Branch("ResXSig",&ResXSig,"ResXSig/F");
  traj->Branch("ModIsBad",&ModIsBad,"ModIsBad/i");
  traj->Branch("SiStripQualBad",&SiStripQualBad,"SiStripQualBad/i");
  traj->Branch("withinAcceptance",&withinAcceptance,"withinAcceptance/O");
  traj->Branch("nHits",&nHits,"nHits/I");
  traj->Branch("nLostHits",&nLostHits,"nLostHits/I");
  traj->Branch("chi2",&chi2,"chi2/F");
  traj->Branch("p",&p,"p/F");
  traj->Branch("pT",&pT,"pT/F");
  traj->Branch("trajHitValid", &trajHitValid, "trajHitValid/i");
  traj->Branch("Id",&Id,"Id/i");
  traj->Branch("run",&run,"run/i");
  traj->Branch("event",&event,"event/i");
  traj->Branch("layer",&whatlayer,"layer/i");
  traj->Branch("timeDT",&timeDT,"timeDT/F");
  traj->Branch("timeDTErr",&timeDTErr,"timeDTErr/F");
  traj->Branch("timeDTDOF",&timeDTDOF,"timeDTDOF/I");
  traj->Branch("timeECAL",&timeECAL,"timeECAL/F");
  traj->Branch("dedx",&dedx,"dedx/F");
  traj->Branch("dedxNOM",&dedxNOM,"dedxNOM/I"); 
  traj->Branch("tquality",&tquality,"tquality/I");
  traj->Branch("istep",&istep,"istep/I");
  traj->Branch("bunchx",&bunchx,"bunchx/I");
  if(addLumi_) {
    traj->Branch("instLumi",&instLumi,"instLumi/F");
    traj->Branch("PU",&PU,"PU/F");
  }
  if(addCommonMode_) traj->Branch("commonMode",&commonMode,"commonMode/F");

  events = 0;
  EventTrackCKF = 0;
  
}


void HitEff::analyze(const edm::Event& e, const edm::EventSetup& es){
  //Retrieve tracker topology from geometry
  edm::ESHandle<TrackerTopology> tTopoHandle;
  es.get<TrackerTopologyRcd>().get(tTopoHandle);
  const TrackerTopology* const tTopo = tTopoHandle.product();

  //  bool DEBUG = false;

  if (DEBUG)  cout << "beginning analyze from HitEff" << endl;

  using namespace edm;
  using namespace reco;
  // Step A: Get Inputs 

  int run_nr = e.id().run();
  int ev_nr = e.id().event();
  int bunch_nr = e.bunchCrossing();

  // Luminosity informations
  edm::Handle<LumiScalersCollection> lumiScalers;
  instLumi=0; PU=0;
  if(addLumi_) {
    e.getByToken(scalerToken_, lumiScalers); 
    if (lumiScalers->begin() != lumiScalers->end()) {
      instLumi = lumiScalers->begin()->instantLumi();
      PU = lumiScalers->begin()->pileup();
    }
  }
  
  // CM
  edm::Handle<edm::DetSetVector<SiStripRawDigi> > commonModeDigis;
  if(addCommonMode_) e.getByToken(commonModeToken_, commonModeDigis);

  //CombinatoriaTrack
  edm::Handle<reco::TrackCollection> trackCollectionCKF;
  //edm::InputTag TkTagCKF = conf_.getParameter<edm::InputTag>("combinatorialTracks");
  e.getByToken(combinatorialTracks_token_,trackCollectionCKF);
  
  edm::Handle<std::vector<Trajectory> > TrajectoryCollectionCKF;
  //edm::InputTag TkTrajCKF = conf_.getParameter<edm::InputTag>("trajectories");
  e.getByToken(trajectories_token_,TrajectoryCollectionCKF);
  
  // Clusters
  // get the SiStripClusters from the event
  edm::Handle< edmNew::DetSetVector<SiStripCluster> > theClusters;
  //e.getByLabel("siStripClusters", theClusters);
  e.getByToken(clusters_token_, theClusters);

  //get tracker geometry
  edm::ESHandle<TrackerGeometry> tracker;
  es.get<TrackerDigiGeometryRecord>().get(tracker);
  const TrackerGeometry * tkgeom=&(* tracker);

  //get Cluster Parameter Estimator
  //std::string cpe = conf_.getParameter<std::string>("StripCPE");
  edm::ESHandle<StripClusterParameterEstimator> parameterestimator;
  es.get<TkStripCPERecord>().get("StripCPEfromTrackAngle", parameterestimator); 
  const StripClusterParameterEstimator &stripcpe(*parameterestimator);

  // get the SiStripQuality records
  edm::ESHandle<SiStripQuality> SiStripQuality_;
//LQ commenting the try/catch that causes problem in 74X calibTree production
//  try {
//    es.get<SiStripQualityRcd>().get("forCluster",SiStripQuality_);
//  }
//  catch (...) {
    es.get<SiStripQualityRcd>().get(SiStripQuality_);
//  }
  
  edm::ESHandle<MagneticField> magFieldHandle;
  es.get<IdealMagneticFieldRecord>().get(magFieldHandle);
  const MagneticField* magField_ = magFieldHandle.product();

  // get the list of module IDs with FED-detected errors
  edm::Handle< DetIdCollection > fedErrorIds;
  //e.getByLabel("siStripDigis", fedErrorIds );
  e.getByToken(digis_token_, fedErrorIds );

  ESHandle<MeasurementTracker> measurementTrackerHandle;
  es.get<CkfComponentsRecord>().get(measurementTrackerHandle);

  edm::Handle<MeasurementTrackerEvent> measurementTrackerEvent;
  //e.getByLabel("MeasurementTrackerEvent", measurementTrackerEvent);
  e.getByToken(trackerEvent_token_,measurementTrackerEvent);

  edm::ESHandle<Chi2MeasurementEstimatorBase> est;
  es.get<TrackingComponentsRecord>().get("Chi2",est);

  edm::ESHandle<Propagator> prop;
  es.get<TrackingComponentsRecord>().get("PropagatorWithMaterial",prop);
  const Propagator* thePropagator = prop.product();

  events++;
  
  // *************** SiStripCluster Collection
  const edmNew::DetSetVector<SiStripCluster>& input = *theClusters;

  //go through clusters to write out global position of good clusters for the layer understudy for comparison
  // Loop through clusters just to print out locations
  // Commented out to avoid discussion, should really be deleted.
  /*
  for (edmNew::DetSetVector<SiStripCluster>::const_iterator DSViter = input.begin(); DSViter != input.end(); DSViter++) {
    // DSViter is a vector of SiStripClusters located on a single module
    unsigned int ClusterId = DSViter->id();
    DetId ClusterDetId(ClusterId);
    const StripGeomDetUnit * stripdet=(const StripGeomDetUnit*)tkgeom->idToDetUnit(ClusterDetId);
    
    edmNew::DetSet<SiStripCluster>::const_iterator begin=DSViter->begin();
    edmNew::DetSet<SiStripCluster>::const_iterator end  =DSViter->end();
    for(edmNew::DetSet<SiStripCluster>::const_iterator iter=begin;iter!=end;++iter) {
      //iter is a single SiStripCluster
      StripClusterParameterEstimator::LocalValues parameters=stripcpe.localParameters(*iter,*stripdet);
      
      const Surface* surface;
      surface = &(tracker->idToDet(ClusterDetId)->surface());
      LocalPoint lp = parameters.first;
      GlobalPoint gp = surface->toGlobal(lp);
      unsigned int layer = checkLayer(ClusterId, tTopo);
            if(DEBUG) cout << "Found hit in cluster collection layer = " << layer << " with id = " << ClusterId << "   local X position = " << lp.x() << " +- " << sqrt(parameters.second.xx()) << "   matched/stereo/rphi = " << ((ClusterId & 0x3)==0) << "/" << ((ClusterId & 0x3)==1) << "/" << ((ClusterId & 0x3)==2) << endl;
    }
  }
  */
  
  // Tracking 
  const   reco::TrackCollection *tracksCKF=trackCollectionCKF.product();
  if (DEBUG)  cout << "number ckf tracks found = " << tracksCKF->size() << endl;
  //if (tracksCKF->size() == 1 ){
  if (tracksCKF->size() > 0 && tracksCKF->size()<100) {
    if (DEBUG)    cout << "starting checking good event with < 100 tracks" << endl;

    EventTrackCKF++;  

    /*

    //get dEdx info if available
    Handle<ValueMap<DeDxData> >          dEdxUncalibHandle;
    if (e.getByLabel("dedxMedianCTF", dEdxUncalibHandle)) {
      const ValueMap<DeDxData> dEdxTrackUncalib = *dEdxUncalibHandle.product();
      
      reco::TrackRef itTrack  = reco::TrackRef( trackCollectionCKF, 0 );
      dedx = dEdxTrackUncalib[itTrack].dEdx();
      dedxNOM  = dEdxTrackUncalib[itTrack].numberOfMeasurements();
    } else {
      dedx = -999.0; dedxNOM = -999;
    }

    */

    //get muon and ecal timing info if available
    Handle<MuonCollection> muH;
    if(e.getByLabel("muonsWitht0Correction",muH)){
      const MuonCollection & muonsT0  =  *muH.product();
      if(muonsT0.size()!=0) {
    MuonTime mt0 = muonsT0[0].time();
    timeDT = mt0.timeAtIpInOut; 
    timeDTErr = mt0.timeAtIpInOutErr;
    timeDTDOF = mt0.nDof;
    
    bool hasCaloEnergyInfo = muonsT0[0].isEnergyValid();
    if (hasCaloEnergyInfo) timeECAL = muonsT0[0].calEnergy().ecal_time;
      }
    } else {
      timeDT = -999.0; timeDTErr = -999.0; timeDTDOF = -999; timeECAL = -999.0;
    }

    // actually should do a loop over all the tracks in the event here

    for (vector<Trajectory>::const_iterator itraj = TrajectoryCollectionCKF.product()->begin();
     itraj != TrajectoryCollectionCKF.product()->end();
     itraj++) {

      // for each track, fill some variables such as number of hits and momentum
      nHits = itraj->foundHits();
      nLostHits = itraj->lostHits();
      chi2 = (itraj->chiSquared()/itraj->ndof());
      pT = sqrt( ( itraj->lastMeasurement().updatedState().globalMomentum().x() *
           itraj->lastMeasurement().updatedState().globalMomentum().x()) +
         ( itraj->lastMeasurement().updatedState().globalMomentum().y() *
           itraj->lastMeasurement().updatedState().globalMomentum().y()) );
      p = itraj->lastMeasurement().updatedState().globalMomentum().mag();
      
      //Put in code to check track quality
      
      
      std::vector<TrajectoryMeasurement> TMeas=itraj->measurements();
      vector<TrajectoryMeasurement>::iterator itm;
      double xloc = 0.;
      double yloc = 0.;
      double xErr = 0.;
      double yErr = 0.;
      double angleX = -999.;
      double angleY = -999.;
      double xglob,yglob,zglob;
      
      for (itm=TMeas.begin();itm!=TMeas.end();itm++){
    auto theInHit = (*itm).recHit();
    
    if(DEBUG) cout << "theInHit is valid = " << theInHit->isValid() << endl;
    
    unsigned int iidd = theInHit->geographicalId().rawId();
    
    unsigned int TKlayers = checkLayer(iidd, tTopo);
    if (DEBUG)  cout << "TKlayer from trajectory: " << TKlayers << "  from module = " << iidd <<  "   matched/stereo/rphi = " << ((iidd & 0x3)==0) << "/" << ((iidd & 0x3)==1) << "/" << ((iidd & 0x3)==2) << endl;

    // If Trajectory measurement from TOB 6 or TEC 9, skip it because it's always valid they are filled later
    if ( TKlayers == 10 || TKlayers == 22 ) {
      if (DEBUG) cout << "skipping original TM for TOB 6 or TEC 9" << endl;
      continue;
    }

    // Make vector of TrajectoryAtInvalidHits to hold the trajectories
    std::vector<TrajectoryAtInvalidHit> TMs;
    
    // Make AnalyticalPropagator to use in TAVH constructor
    AnalyticalPropagator propagator(magField_,anyDirection); 
    
    // for double sided layers check both sensors--if no hit was found on either sensor surface,
    // the trajectory measurements only have one invalid hit entry on the matched surface
    // so get the TrajectoryAtInvalidHit for both surfaces and include them in the study
    if (isDoubleSided(iidd, tTopo) &&  ((iidd & 0x3)==0) ) {
      // do hit eff check twice--once for each sensor
      //add a TM for each surface
      TMs.push_back(TrajectoryAtInvalidHit(*itm, tTopo, tkgeom, propagator, 1));
      TMs.push_back(TrajectoryAtInvalidHit(*itm, tTopo, tkgeom, propagator, 2));
    } else if ( isDoubleSided(iidd, tTopo) && (!check2DPartner(iidd, TMeas)) ) {
      // if only one hit was found the trajectory measurement is on that sensor surface, and the other surface from
      // the matched layer should be added to the study as well
      TMs.push_back(TrajectoryAtInvalidHit(*itm, tTopo, tkgeom, propagator, 1));
      TMs.push_back(TrajectoryAtInvalidHit(*itm, tTopo, tkgeom, propagator, 2));
      if (DEBUG) cout << " found a hit with a missing partner" << endl;
    } else {
      //only add one TM for the single surface and the other will be added in the next iteration
      TMs.push_back(TrajectoryAtInvalidHit(*itm, tTopo, tkgeom, propagator));
    }

    //Now check for tracks at TOB6 and TEC9

    // to make sure we only propagate on the last TOB5 hit check the next entry isn't also in TOB5
    // to avoid bias, make sure the TOB5 hit is valid (an invalid hit on TOB5 could only exist with a valid hit on TOB6)

    bool isValid = theInHit->isValid();
    bool isLast = (itm==(TMeas.end()-1));
    bool isLastTOB5 = true;
    if (!isLast) {
      if ( checkLayer((++itm)->recHit()->geographicalId().rawId(), tTopo) == 9 ) isLastTOB5 = false;
      else isLastTOB5 = true;
      --itm;
    }
    
    if ( TKlayers==9 && isValid && isLastTOB5 ) {
      //      if ( TKlayers==9 && itm==TMeas.rbegin()) {
    //    if ( TKlayers==9 && (itm==TMeas.back()) ) {     // to check for only the last entry in the trajectory for propagation
      std::vector< BarrelDetLayer const*> barrelTOBLayers = measurementTrackerHandle->geometricSearchTracker()->tobLayers() ;
      const DetLayer* tob6 = barrelTOBLayers[barrelTOBLayers.size()-1];
      const MeasurementEstimator* estimator = est.product();
      const LayerMeasurements* theLayerMeasurements = new LayerMeasurements(*measurementTrackerHandle, *measurementTrackerEvent);
      const TrajectoryStateOnSurface tsosTOB5 = itm->updatedState();
      vector<TrajectoryMeasurement> tmp = theLayerMeasurements->measurements(*tob6, tsosTOB5, *thePropagator, *estimator);
      
      if ( !tmp.empty()) {
        if (DEBUG) cout << "size of TM from propagation = " << tmp.size() << endl;

        // take the last of the TMs, which is always an invalid hit
        // if no detId is available, ie detId==0, then no compatible layer was crossed
        // otherwise, use that TM for the efficiency measurement
        TrajectoryMeasurement tob6TM(tmp.back());
        auto tob6Hit = tob6TM.recHit();
        
        if (tob6Hit->geographicalId().rawId()!=0) {
          if (DEBUG) cout << "tob6 hit actually being added to TM vector" << endl;
          TMs.push_back(TrajectoryAtInvalidHit(tob6TM, tTopo, tkgeom, propagator));
        }
      }
    }

    bool isLastTEC8 = true;
    if (!isLast) {
      if ( checkLayer((++itm)->recHit()->geographicalId().rawId(), tTopo) == 21 ) isLastTEC8 = false;
      else isLastTEC8 = true;
      --itm;
    }
    
    if ( TKlayers==21 && isValid && isLastTEC8 ) {
      
      std::vector< const ForwardDetLayer*> posTecLayers = measurementTrackerHandle->geometricSearchTracker()->posTecLayers() ;
      const DetLayer* tec9pos = posTecLayers[posTecLayers.size()-1];
      std::vector< const ForwardDetLayer*> negTecLayers = measurementTrackerHandle->geometricSearchTracker()->negTecLayers() ;
      const DetLayer* tec9neg = negTecLayers[negTecLayers.size()-1];
      
      const MeasurementEstimator* estimator = est.product();
      const LayerMeasurements* theLayerMeasurements = new LayerMeasurements(*measurementTrackerHandle, *measurementTrackerEvent);
      const TrajectoryStateOnSurface tsosTEC9 = itm->updatedState();
      
      // check if track on positive or negative z
      if (DEBUG)  if (!(iidd ==  StripSubdetector::TEC)) cout << "there is a problem with TEC 9 extrapolation" << endl;
      
      //cout << " tec9 id = " << iidd << " and side = " << tTopo->tecSide(iidd) << endl;
      vector<TrajectoryMeasurement> tmp;
      if ( tTopo->tecSide(iidd) == 1 ) {
        tmp = theLayerMeasurements->measurements(*tec9neg, tsosTEC9, *thePropagator, *estimator);
        //cout << "on negative side" << endl;
      }
      if ( tTopo->tecSide(iidd) == 2 ) {
        tmp = theLayerMeasurements->measurements(*tec9pos, tsosTEC9, *thePropagator, *estimator);
        //cout << "on positive side" << endl;
      }

      if ( !tmp.empty()) {
        // take the last of the TMs, which is always an invalid hit
        // if no detId is available, ie detId==0, then no compatible layer was crossed
        // otherwise, use that TM for the efficiency measurement
        TrajectoryMeasurement tec9TM(tmp.back());
        auto tec9Hit = tec9TM.recHit();
        
        unsigned int tec9id = tec9Hit->geographicalId().rawId();
        if (DEBUG) cout << "tec9id = " << tec9id << " is Double sided = " <<  isDoubleSided(tec9id, tTopo) << "  and 0x3 = " << (tec9id & 0x3) << endl;
        
        if (tec9Hit->geographicalId().rawId()!=0) {
          if (DEBUG) cout << "tec9 hit actually being added to TM vector" << endl;
          // in tec the hit can be single or doubled sided. whenever the invalid hit at the end of vector of TMs is
          // double sided it is always on the matched surface, so we need to split it into the true sensor surfaces
          if (isDoubleSided(tec9id, tTopo)) {
        TMs.push_back(TrajectoryAtInvalidHit(tec9TM, tTopo, tkgeom, propagator, 1));
        TMs.push_back(TrajectoryAtInvalidHit(tec9TM, tTopo, tkgeom, propagator, 2));
          } else 
        TMs.push_back(TrajectoryAtInvalidHit(tec9TM, tTopo, tkgeom, propagator));
        }
      } //else cout << "tec9 tmp empty" << endl;
    }
    
    
    // Modules Constraints

    for(std::vector<TrajectoryAtInvalidHit>::const_iterator TM=TMs.begin();TM!=TMs.end();++TM) {
      
      // --> Get trajectory from combinatedState 
      iidd = TM->monodet_id();
      if (DEBUG) cout << "setting iidd = " << iidd << " before checking efficiency and ";
      
      xloc = TM->localX();
      yloc = TM->localY();
      
      xErr =  TM->localErrorX();
      yErr =  TM->localErrorY();
      
      angleX = atan( TM->localDxDz() );
      angleY = atan( TM->localDyDz() );
      
      xglob = TM->globalX();
      yglob = TM->globalY();
      zglob = TM->globalZ();
      withinAcceptance = TM->withinAcceptance();
      
      trajHitValid = TM->validHit();
      int TrajStrip = -1;

      // reget layer from iidd here, to account for TOB 6 and TEC 9 TKlayers being off
      TKlayers = checkLayer(iidd, tTopo);

      if ( (layers == TKlayers) || (layers == 0) ) {   // Look at the layer not used to reconstruct the track
        whatlayer = TKlayers;
        if (DEBUG)    cout << "Looking at layer under study" << endl;
        TrajGlbX = 0.0; TrajGlbY = 0.0; TrajGlbZ = 0.0; ModIsBad = 2; Id = 0; SiStripQualBad = 0; 
        run = 0; event = 0; TrajLocX = 0.0; TrajLocY = 0.0; TrajLocErrX = 0.0; TrajLocErrY = 0.0; 
        TrajLocAngleX = -999.0; TrajLocAngleY = -999.0; ResX = 0.0; ResXSig = 0.0;
        ClusterLocX = 0.0; ClusterLocY = 0.0; ClusterLocErrX = 0.0; ClusterLocErrY = 0.0; ClusterStoN = 0.0;
        bunchx = 0; commonMode = -100;
        
        // RPhi RecHit Efficiency 
        
        if (input.size() > 0 ) {  
          if (DEBUG) cout << "Checking clusters with size = " << input.size() << endl;
          int nClusters = 0;
          std::vector< std::vector<float> > VCluster_info; //fill with X residual, X residual pull, local X, sig(X), local Y, sig(Y), StoN
          for (edmNew::DetSetVector<SiStripCluster>::const_iterator DSViter = input.begin(); DSViter != input.end(); DSViter++) {
        // DSViter is a vector of SiStripClusters located on a single module
        //if (DEBUG)      cout << "the ID from the DSViter = " << DSViter->id() << endl; 
        unsigned int ClusterId = DSViter->id();
        if (ClusterId == iidd) {
          if (DEBUG) cout << "found  (ClusterId == iidd) with ClusterId = " << ClusterId << " and iidd = " << iidd << endl;
          DetId ClusterDetId(ClusterId);
          const StripGeomDetUnit * stripdet=(const StripGeomDetUnit*)tkgeom->idToDetUnit(ClusterDetId);
          const StripTopology& Topo  = stripdet->specificTopology();
          
                  float hbedge   = 0.0;
                  float htedge   = 0.0;
                  float hapoth   = 0.0;
                  float uylfac   = 0.0;
                  float uxlden   = 0.0;
                  if(TKlayers>=11) {
                     const BoundPlane plane = stripdet->surface();
                     const TrapezoidalPlaneBounds* trapezoidalBounds( dynamic_cast<const TrapezoidalPlaneBounds*>(&(plane.bounds())));
             std::array<const float, 4> const & parameterTrap = (*trapezoidalBounds).parameters(); // el bueno aqui
                     hbedge         = parameterTrap[0];
                     htedge         = parameterTrap[1];
                     hapoth         = parameterTrap[3];
                     uylfac   = (htedge-hbedge)/(htedge+hbedge)/hapoth;
                     uxlden   = 1 + yloc*uylfac;
                  }
          
          // Need to know position of trajectory in strip number for selecting the right APV later
          if( TrajStrip==-1 ) {
            int nstrips = Topo.nstrips();
            float pitch = stripdet->surface().bounds().width() / nstrips;
            TrajStrip = xloc/pitch + nstrips/2.0;
            // Need additionnal corrections for endcap
            if(TKlayers>=11) {
              float TrajLocXMid = xloc / (1 + (htedge-hbedge)*yloc/(htedge+hbedge)/hapoth) ; // radialy extrapolated x loc position at middle
              TrajStrip = TrajLocXMid/pitch + nstrips/2.0;
            }
            //cout<<" Layer "<<TKlayers<<" TrajStrip: "<<nstrips<<" "<<pitch<<" "<<TrajStrip<<endl;
          }


          for(edmNew::DetSet<SiStripCluster>::const_iterator iter=DSViter->begin();iter!=DSViter->end();++iter) {
            //iter is a single SiStripCluster
            StripClusterParameterEstimator::LocalValues parameters=stripcpe.localParameters(*iter,*stripdet);
            float res = (parameters.first.x() - xloc);
            float sigma = checkConsistency(parameters , xloc, xErr);
            // The consistency is probably more accurately measured with the Chi2MeasurementEstimator. To use it
            // you need a TransientTrackingRecHit instead of the cluster
            //theEstimator=       new Chi2MeasurementEstimator(30);
            //const Chi2MeasurementEstimator *theEstimator(100);
            //theEstimator->estimate(TM->tsos(), TransientTrackingRecHit);

                    if(TKlayers>=11) {
                       res = parameters.first.x() - xloc/uxlden ; // radialy extrapolated x loc position at middle           
                       sigma = abs(res) / sqrt(parameters.second.xx() + xErr*xErr/uxlden/uxlden + yErr*yErr*xloc*xloc*uylfac*uylfac/uxlden/uxlden/uxlden/uxlden);
                    }
            
            SiStripClusterInfo clusterInfo = SiStripClusterInfo(*iter, es, ClusterId);  
            // signal to noise from SiStripClusterInfo not working in 225. I'll fix this after the interface
            // redesign in 300 -ku
            //float cluster_info[7] = {res, sigma, parameters.first.x(), sqrt(parameters.second.xx()), parameters.first.y(), sqrt(parameters.second.yy()), signal_to_noise};
            std::vector< float > cluster_info;
            cluster_info.push_back(res); 
            cluster_info.push_back(sigma);
            cluster_info.push_back(parameters.first.x()); 
            cluster_info.push_back(sqrt(parameters.second.xx()));
            cluster_info.push_back(parameters.first.y());
            cluster_info.push_back(sqrt(parameters.second.yy()));
            cluster_info.push_back( clusterInfo.signalOverNoise() );
            //cluster_info.push_back( clusterInfo.getSignalOverNoise() );
            VCluster_info.push_back(cluster_info);
            nClusters++;
            if (DEBUG) cout << "Have ID match. residual = " << VCluster_info.back()[0] << "  res sigma = " << VCluster_info.back()[1] << endl;
            if (DEBUG) cout << "trajectory measurement compatability estimate = " << (*itm).estimate() << endl;
            if (DEBUG) cout << "hit position = " << parameters.first.x() << "  hit error = " << sqrt(parameters.second.xx()) << "  trajectory position = " << xloc << "  traj error = " << xErr << endl;
          }
        }
          }
          float FinalResSig = 1000.0;
          float FinalCluster[7]= {1000.0, 1000.0, 0.0, 0.0, 0.0, 0.0, 0.0};
          if (nClusters > 0) {
        if (DEBUG) cout << "found clusters > 0" << endl;
        if (nClusters > 1) {
          //get the smallest one
          vector< vector<float> >::iterator ires;
          for (ires=VCluster_info.begin(); ires!=VCluster_info.end(); ires++){
            if ( abs((*ires)[1]) < abs(FinalResSig)) {
              FinalResSig = (*ires)[1];
              for (unsigned int i = 0; i<ires->size(); i++) {
            if (DEBUG) cout << "filling final cluster. i = " << i << " before fill FinalCluster[i]=" << FinalCluster[i] << " and (*ires)[i] =" << (*ires)[i] << endl;
            FinalCluster[i] = (*ires)[i];
            if (DEBUG) cout << "filling final cluster. i = " << i << " after fill FinalCluster[i]=" << FinalCluster[i] << " and (*ires)[i] =" << (*ires)[i] << endl;
              }
            }
            if (DEBUG) cout << "iresidual = " << (*ires)[0] << "  isigma = " << (*ires)[1] << "  and FinalRes = " << FinalCluster[0] << endl;
          }
        }
        else {
          FinalResSig = VCluster_info.at(0)[1];
          for (unsigned int i = 0; i<VCluster_info.at(0).size(); i++) {
            FinalCluster[i] = VCluster_info.at(0)[i];
          }
        }
        nClusters=0;
        VCluster_info.clear();
          }
          
          if (DEBUG) cout << "Final residual in X = " << FinalCluster[0] << "+-" << (FinalCluster[0]/FinalResSig) << endl;
          if (DEBUG) cout << "Checking location of trajectory: abs(yloc) = " << abs(yloc) << "  abs(xloc) = " << abs(xloc) << endl;
          if (DEBUG) cout << "Checking location of cluster hit: yloc = " << FinalCluster[4] << "+-" << FinalCluster[5] << "  xloc = " << FinalCluster[2] << "+-" << FinalCluster[3] << endl;
          if (DEBUG) cout << "Final cluster signal to noise = " << FinalCluster[6] << endl;
          
          float exclusionWidth = 0.4;
          float TOBexclusion = 0.0;
          float TECexRing5 = -0.89;
          float TECexRing6 = -0.56;
          float TECexRing7 = 0.60;
          //Added by Chris Edelmaier to do TEC bonding exclusion
          int subdetector = ((iidd>>25) & 0x7);            
          int ringnumber = ((iidd>>5) & 0x7);
          
          //New TOB and TEC bonding region exclusion zone
          if((TKlayers >= 5 && TKlayers < 11)||((subdetector == 6)&&( (ringnumber >= 5)&&(ringnumber <=7) ))) {
        //There are only 2 cases that we need to exclude for
        float highzone = 0.0;
        float lowzone = 0.0;
        float higherr = yloc + 5.0*yErr;
        float lowerr = yloc - 5.0*yErr;
        if(TKlayers >= 5 && TKlayers < 11) {
          //TOB zone
          highzone = TOBexclusion + exclusionWidth;
          lowzone = TOBexclusion - exclusionWidth;
        } else if (ringnumber == 5) {
          //TEC ring 5
          highzone = TECexRing5 + exclusionWidth;
          lowzone = TECexRing5 - exclusionWidth;
        } else if (ringnumber == 6) {
          //TEC ring 6
          highzone = TECexRing6 + exclusionWidth;
          lowzone = TECexRing6 - exclusionWidth;
        } else if (ringnumber == 7) {
          //TEC ring 7
          highzone = TECexRing7 + exclusionWidth;
          lowzone = TECexRing7 - exclusionWidth;
        }
        //Now that we have our exclusion region, we just have to properly identify it
        if((highzone <= higherr)&&(highzone >= lowerr)) withinAcceptance = false;
        if((lowzone >= lowerr)&&(lowzone <= higherr)) withinAcceptance = false;
        if((higherr <= highzone)&&(higherr >= lowzone)) withinAcceptance = false;
        if((lowerr >= lowzone)&&(lowerr <= highzone)) withinAcceptance = false;
          }
          
          // fill ntuple varibles
          //get global position from module id number iidd
          TrajGlbX = xglob;
          TrajGlbY = yglob;
          TrajGlbZ = zglob;   
          Id = iidd;
          run = run_nr;
          event = ev_nr;
          bunchx = bunch_nr;
          //if ( SiStripQuality_->IsModuleBad(iidd) ) {
          if ( SiStripQuality_->getBadApvs(iidd)!=0 ) {
        SiStripQualBad = 1; 
        if(DEBUG) cout << "strip is bad from SiStripQuality" << endl;
          } else {
        SiStripQualBad = 0; 
        if(DEBUG) cout << "strip is good from SiStripQuality" << endl;
          }

          //check for FED-detected errors and include those in SiStripQualBad
          for (unsigned int ii=0;ii< fedErrorIds->size();ii++) {
        if (iidd == (*fedErrorIds)[ii].rawId() )
          SiStripQualBad = 1;
          }
          
          TrajLocX = xloc;
          TrajLocY = yloc;
          TrajLocErrX = xErr;
          TrajLocErrY = yErr;
          TrajLocAngleX = angleX;
          TrajLocAngleY = angleY;
          ResX = FinalCluster[0];
          ResXSig = FinalResSig;
          if (FinalResSig != FinalCluster[1]) if (DEBUG) cout << "Problem with best cluster selection because FinalResSig = " << FinalResSig << " and FinalCluster[1] = " << FinalCluster[1] << endl;
          ClusterLocX = FinalCluster[2];
          ClusterLocY = FinalCluster[4];
          ClusterLocErrX = FinalCluster[3];
          ClusterLocErrY = FinalCluster[5];
          ClusterStoN = FinalCluster[6];
          
          // CM of APV crossed by traj
          if(addCommonMode_)
          if(commonModeDigis.isValid() && TrajStrip>=0 && TrajStrip<=768) {
            edm::DetSetVector<SiStripRawDigi>::const_iterator digiframe = commonModeDigis->find(iidd);
            if(digiframe != commonModeDigis->end())
              if( (unsigned) TrajStrip/128 < digiframe->data.size())
                commonMode = digiframe->data.at(TrajStrip/128).adc();
          }

          if (DEBUG)          cout << "before check good" << endl;
          
          if ( FinalResSig < 999.0) {  //could make requirement on track/hit consistency, but for
        //now take anything with a hit on the module
        if (DEBUG) cout << "hit being counted as good " << FinalCluster[0] << " FinalRecHit " << 
          iidd << "   TKlayers  "  <<  TKlayers  << " xloc " <<  xloc << " yloc  " << yloc << " module " << iidd << 
          "   matched/stereo/rphi = " << ((iidd & 0x3)==0) << "/" << ((iidd & 0x3)==1) << "/" << ((iidd & 0x3)==2) << endl;
        ModIsBad = 0;
        traj->Fill();
          }
          else {
        if (DEBUG)  cout << "hit being counted as bad   ######### Invalid RPhi FinalResX " << FinalCluster[0] << " FinalRecHit " << 
          iidd << "   TKlayers  "  <<  TKlayers  << " xloc " <<  xloc << " yloc  " << yloc << " module " << iidd << 
          "   matched/stereo/rphi = " << ((iidd & 0x3)==0) << "/" << ((iidd & 0x3)==1) << "/" << ((iidd & 0x3)==2) << endl;
        ModIsBad = 1;
        traj->Fill();
        
        if (DEBUG) cout << " RPhi Error " << sqrt(xErr*xErr + yErr*yErr) << " ErrorX " << xErr << " yErr " <<  yErr <<  endl;
          } if (DEBUG) cout << "after good location check" << endl;
        } if (DEBUG) cout << "after list of clusters" << endl;
      } if (DEBUG) cout << "After layers=TKLayers if" << endl;
    } if (DEBUG) cout << "After looping over TrajAtValidHit list" << endl;
      } if (DEBUG) cout << "end TMeasurement loop" << endl;
    } if (DEBUG) cout << "end of trajectories loop" << endl;
  }
}

void HitEff::endJob(){
  traj->GetDirectory()->cd();
  traj->Write();  
  
  if (DEBUG) cout << " Events Analysed             " <<  events          << endl;
  if (DEBUG) cout << " Number Of Tracked events    " <<  EventTrackCKF   << endl;
}

double HitEff::checkConsistency(const StripClusterParameterEstimator::LocalValues& parameters, double xx, double xerr) {
  double error = sqrt(parameters.second.xx() + xerr*xerr);
  double separation = abs(parameters.first.x() - xx);
  double consistency = separation/error;
  return consistency;
}

bool HitEff::isDoubleSided(unsigned int iidd, const TrackerTopology* tTopo) const {
  StripSubdetector strip=StripSubdetector(iidd);
  unsigned int subid=strip.subdetId();
  unsigned int layer = 0;
  if (subid ==  StripSubdetector::TIB) { 
    
    layer = tTopo->tibLayer(iidd);
    if (layer == 1 || layer == 2) return true;
    else return false;
  }
  else if (subid ==  StripSubdetector::TOB) { 
    
    layer = tTopo->tobLayer(iidd) + 4 ; 
    if (layer == 5 || layer == 6) return true;
    else return false;
  }
  else if (subid ==  StripSubdetector::TID) { 
    
    layer = tTopo->tidRing(iidd) + 10;
    if (layer == 11 || layer == 12) return true;
    else return false;
  }
  else if (subid ==  StripSubdetector::TEC) { 
    
    layer = tTopo->tecRing(iidd) + 13 ; 
    if (layer == 14 || layer == 15 || layer == 18) return true;
    else return false;
  }
  else
    return false;
}

bool HitEff::check2DPartner(unsigned int iidd, const std::vector<TrajectoryMeasurement>& traj) {
  unsigned int partner_iidd = 0;
  bool found2DPartner = false;
  // first get the id of the other detector
  if ((iidd & 0x3)==1) partner_iidd = iidd+1;
  if ((iidd & 0x3)==2) partner_iidd = iidd-1;
  // next look in the trajectory measurements for a measurement from that detector
  // loop through trajectory measurements to find the partner_iidd
  for (std::vector<TrajectoryMeasurement>::const_iterator iTM=traj.begin(); iTM!=traj.end(); ++iTM) {
    if (iTM->recHit()->geographicalId().rawId()==partner_iidd) {
      found2DPartner = true;
    }
  }
  return found2DPartner;
}

unsigned int HitEff::checkLayer( unsigned int iidd, const TrackerTopology* tTopo) {
  StripSubdetector strip=StripSubdetector(iidd);
  unsigned int subid=strip.subdetId();
  if (subid ==  StripSubdetector::TIB) { 
    
    return tTopo->tibLayer(iidd);
  }
  if (subid ==  StripSubdetector::TOB) { 
    
    return tTopo->tobLayer(iidd) + 4 ; 
  }
  if (subid ==  StripSubdetector::TID) { 
    
    return tTopo->tidWheel(iidd) + 10;
  }
  if (subid ==  StripSubdetector::TEC) { 
    
    return tTopo->tecWheel(iidd) + 13 ; 
  }
  return 0;
}

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