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 /**
  * \file GEMSegmentAlgorithm.cc
  *  based on CSCSegAlgoST.cc
  * 
  *  \authors: Piet Verwilligen, Jason Lee
  */
 
 #include "GEMSegmentAlgorithm.h"
 #include "MuonSegFit.h"
 
 #include "FWCore/ParameterSet/interface/ParameterSet.h"
 #include "FWCore/MessageLogger/interface/MessageLogger.h"
 #include "DataFormats/GeometryVector/interface/GlobalPoint.h"
 #include "DataFormats/Math/interface/deltaPhi.h"
 #include "CommonTools/Statistics/interface/ChiSquaredProbability.h"
 
 #include <algorithm>
 #include <cmath>
 #include <iostream>
 #include <string>
 
 /* Constructor
  *
  */
 GEMSegmentAlgorithm::GEMSegmentAlgorithm(const edm::ParameterSet& ps)
     : GEMSegmentAlgorithmBase(ps), myName("GEMSegmentAlgorithm") {
   minHitsPerSegment = ps.getParameter<unsigned int>("minHitsPerSegment");
   preClustering = ps.getParameter<bool>("preClustering");
   dXclusBoxMax = ps.getParameter<double>("dXclusBoxMax");
   dYclusBoxMax = ps.getParameter<double>("dYclusBoxMax");
   preClustering_useChaining = ps.getParameter<bool>("preClusteringUseChaining");
   dPhiChainBoxMax = ps.getParameter<double>("dPhiChainBoxMax");
   dEtaChainBoxMax = ps.getParameter<double>("dEtaChainBoxMax");
   maxRecHitsInCluster = ps.getParameter<int>("maxRecHitsInCluster");
   clusterOnlySameBXRecHits = ps.getParameter<bool>("clusterOnlySameBXRecHits");
 
   // maybe to be used in the future ???
   // Pruning                = ps.getParameter<bool>("Pruning");
   // BrutePruning           = ps.getParameter<bool>("BrutePruning");
   // maxRecHitsInCluster is the maximal number of hits in a precluster that is being processed
   // This cut is intended to remove messy events. Currently nothing is returned if there are
   // more that maxRecHitsInCluster hits. It could be useful to return an estimate of the
   // cluster position, which is available.
   // maxRecHitsInCluster    = ps.getParameter<int>("maxRecHitsInCluster");
   // onlyBestSegment        = ps.getParameter<bool>("onlyBestSegment");
 
   // CSC uses pruning to remove clearly bad hits, using as much info from the rechits as possible: charge, position, timing, ...
   // In fits with bad chi^2 they look for the worst hit (hit with abnormally large residual)
   // if worst hit was found, refit without worst hit and select if considerably better than original fit.
 }
 
 /* Destructor
  *
  */
 GEMSegmentAlgorithm::~GEMSegmentAlgorithm() {}
 
 std::vector<GEMSegment> GEMSegmentAlgorithm::run(const GEMEnsemble& ensemble, const EnsembleHitContainer& rechits) {
   // pre-cluster rechits and loop over all sub clusters separately
   std::vector<GEMSegment> segments_temp;
   std::vector<GEMSegment> segments;
   ProtoSegments rechits_clusters;  // this is a collection of groups of rechits
 
   if (preClustering) {
     // run a pre-clusterer on the given rechits to split obviously separated segment seeds:
     if (preClustering_useChaining) {
       // it uses X,Y,Z information; there are no configurable parameters used;
       // the X, Y, Z "cuts" are just (much) wider than reasonable high pt segments
       edm::LogVerbatim("GEMSegmentAlgorithm") << "[GEMSegmentAlgorithm::run] preClustering :: use Chaining";
       rechits_clusters = this->chainHits(ensemble, rechits);
     } else {
       // it uses X,Y information + configurable parameters
       edm::LogVerbatim("GEMSegmentAlgorithm") << "[GEMSegmentAlgorithm::run] Clustering";
       rechits_clusters = this->clusterHits(ensemble, rechits);
     }
     // loop over the found clusters:
     edm::LogVerbatim("GEMSegmentAlgorithm") << "[GEMSegmentAlgorithm::run] Loop over clusters and build segments";
     for (auto sub_rechits = rechits_clusters.begin(); sub_rechits != rechits_clusters.end(); ++sub_rechits) {
       // clear the buffer for the subset of segments:
       segments_temp.clear();
       // build the subset of segments:
       this->buildSegments(ensemble, (*sub_rechits), segments_temp);
       // add the found subset of segments to the collection of all segments in this chamber:
       segments.insert(segments.end(), segments_temp.begin(), segments_temp.end());
     }
 
     return segments;
   } else {
     this->buildSegments(ensemble, rechits, segments);
     return segments;
   }
 }
 
 // ********************************************************************;
 GEMSegmentAlgorithm::ProtoSegments GEMSegmentAlgorithm::clusterHits(const GEMEnsemble& ensemble,
                                                                     const EnsembleHitContainer& rechits) {
   // think how to implement BX requirement here
 
   ProtoSegments rechits_clusters;  // this is a collection of groups of rechits
 
   float dXclus_box = 0.0;
   float dYclus_box = 0.0;
 
   ProtoSegments seeds;
   seeds.reserve(rechits.size());
 
   std::vector<float> running_meanX;
   running_meanX.reserve(rechits.size());
   std::vector<float> running_meanY;
   running_meanY.reserve(rechits.size());
 
   std::vector<float> seed_minX;
   seed_minX.reserve(rechits.size());
   std::vector<float> seed_maxX;
   seed_maxX.reserve(rechits.size());
   std::vector<float> seed_minY;
   seed_minY.reserve(rechits.size());
   std::vector<float> seed_maxY;
   seed_maxY.reserve(rechits.size());
 
   // split rechits into subvectors and return vector of vectors:
   // Loop over rechits
   // Create one seed per hit
   for (unsigned int i = 0; i < rechits.size(); ++i) {
     seeds.push_back(EnsembleHitContainer(1, rechits[i]));
 
     GEMDetId rhID = rechits[i]->gemId();
     const GEMEtaPartition* rhEP = (ensemble.second.find(rhID.rawId()))->second;
     if (!rhEP)
       throw cms::Exception("GEMEtaPartition not found")
           << "Corresponding GEMEtaPartition to GEMDetId: " << rhID << " not found in the GEMEnsemble";
     const GEMSuperChamber* rhCH = ensemble.first;
     LocalPoint rhLP_inEtaPartFrame = rechits[i]->localPosition();
     GlobalPoint rhGP_inCMSFrame = rhEP->toGlobal(rhLP_inEtaPartFrame);
     LocalPoint rhLP_inChamberFrame = rhCH->toLocal(rhGP_inCMSFrame);
 
     running_meanX.push_back(rhLP_inChamberFrame.x());
     running_meanY.push_back(rhLP_inChamberFrame.y());
 
     // set min/max X and Y for box containing the hits in the precluster:
     seed_minX.push_back(rhLP_inChamberFrame.x());
     seed_maxX.push_back(rhLP_inChamberFrame.x());
     seed_minY.push_back(rhLP_inChamberFrame.y());
     seed_maxY.push_back(rhLP_inChamberFrame.y());
   }
 
   // merge clusters that are too close
   // measure distance between final "running mean"
   for (size_t NNN = 0; NNN < seeds.size(); ++NNN) {
     for (size_t MMM = NNN + 1; MMM < seeds.size(); ++MMM) {
       if (running_meanX[MMM] == running_max || running_meanX[NNN] == running_max) {
         LogDebug("GEMSegmentAlgorithm") << "[GEMSegmentAlgorithm::clusterHits]: ALARM! Skipping used seeds, this "
                                            "should not happen - inform developers!";
         continue;  //skip seeds that have been used
       }
 
       // calculate cut criteria for simple running mean distance cut:
       //dXclus = fabs(running_meanX[NNN] - running_meanX[MMM]);
       //dYclus = fabs(running_meanY[NNN] - running_meanY[MMM]);
       // calculate minmal distance between precluster boxes containing the hits:
       if (running_meanX[NNN] > running_meanX[MMM])
         dXclus_box = seed_minX[NNN] - seed_maxX[MMM];
       else
         dXclus_box = seed_minX[MMM] - seed_maxX[NNN];
       if (running_meanY[NNN] > running_meanY[MMM])
         dYclus_box = seed_minY[NNN] - seed_maxY[MMM];
       else
         dYclus_box = seed_minY[MMM] - seed_maxY[NNN];
 
       if (dXclus_box < dXclusBoxMax && dYclus_box < dYclusBoxMax) {
         // merge clusters!
         // merge by adding seed NNN to seed MMM and erasing seed NNN
 
         // calculate running mean for the merged seed:
         if (seeds[NNN].size() + seeds[MMM].size() != 0) {
           running_meanX[MMM] = (running_meanX[NNN] * seeds[NNN].size() + running_meanX[MMM] * seeds[MMM].size()) /
                                (seeds[NNN].size() + seeds[MMM].size());
           running_meanY[MMM] = (running_meanY[NNN] * seeds[NNN].size() + running_meanY[MMM] * seeds[MMM].size()) /
                                (seeds[NNN].size() + seeds[MMM].size());
         }
 
         // update min/max X and Y for box containing the hits in the merged cluster:
         if (seed_minX[NNN] < seed_minX[MMM])
           seed_minX[MMM] = seed_minX[NNN];
         if (seed_maxX[NNN] > seed_maxX[MMM])
           seed_maxX[MMM] = seed_maxX[NNN];
         if (seed_minY[NNN] < seed_minY[MMM])
           seed_minY[MMM] = seed_minY[NNN];
         if (seed_maxY[NNN] > seed_maxY[MMM])
           seed_maxY[MMM] = seed_maxY[NNN];
 
         // add seed NNN to MMM (lower to larger number)
         seeds[MMM].insert(seeds[MMM].end(), seeds[NNN].begin(), seeds[NNN].end());
 
         // mark seed NNN as used (at the moment just set running mean to 999999.)
         running_meanX[NNN] = running_max;
         running_meanY[NNN] = running_max;
         // we have merged a seed (NNN) to the highter seed (MMM) - need to contimue to
         // next seed (NNN+1)
         break;
       }
     }
   }
 
   // hand over the final seeds to the output
   // would be more elegant if we could do the above step with
   // erasing the merged ones, rather than the
   for (size_t NNN = 0; NNN < seeds.size(); ++NNN) {
     if (running_meanX[NNN] == running_max)
       continue;  //skip seeds that have been marked as used up in merging
     rechits_clusters.push_back(seeds[NNN]);
   }
 
   return rechits_clusters;
 }
 
 GEMSegmentAlgorithm::ProtoSegments GEMSegmentAlgorithm::chainHits(const GEMEnsemble& ensemble,
                                                                   const EnsembleHitContainer& rechits) {
   ProtoSegments rechits_chains;
   ProtoSegments seeds;
   seeds.reserve(rechits.size());
   std::vector<bool> usedCluster(rechits.size(), false);
 
   // split rechits into subvectors and return vector of vectors:
   // Loop over rechits
   // Create one seed per hit
   for (unsigned int i = 0; i < rechits.size(); ++i)
     seeds.push_back(EnsembleHitContainer(1, rechits[i]));
 
   // merge chains that are too close ("touch" each other)
   for (size_t NNN = 0; NNN < seeds.size(); ++NNN) {
     for (size_t MMM = NNN + 1; MMM < seeds.size(); ++MMM) {
       if (usedCluster[MMM] || usedCluster[NNN]) {
         continue;
       }
       // all is in the way we define "good";
       // try not to "cluster" the hits but to "chain" them;
       // it does the clustering but also does a better job
       // for inclined tracks (not clustering them together;
       // crossed tracks would be still clustered together)
       // 22.12.09: In fact it is not much more different
       // than the "clustering", we just introduce another
       // variable in the game - Z. And it makes sense
       // to re-introduce Y (or actually wire group mumber)
       // in a similar way as for the strip number - see
       // the code below.
       bool goodToMerge = isGoodToMerge(ensemble, seeds[NNN], seeds[MMM]);
       if (goodToMerge) {
         // merge chains!
         // merge by adding seed NNN to seed MMM and erasing seed NNN
 
         // add seed NNN to MMM (lower to larger number)
         seeds[MMM].insert(seeds[MMM].end(), seeds[NNN].begin(), seeds[NNN].end());
 
         // mark seed NNN as used
         usedCluster[NNN] = true;
         // we have merged a seed (NNN) to the highter seed (MMM) - need to contimue to
         // next seed (NNN+1)
         break;
       }
     }
   }
 
   // hand over the final seeds to the output
   // would be more elegant if we could do the above step with
   // erasing the merged ones, rather than the
   for (size_t NNN = 0; NNN < seeds.size(); ++NNN) {
     if (usedCluster[NNN])
       continue;  //skip seeds that have been marked as used up in merging
     rechits_chains.push_back(seeds[NNN]);
   }
 
   //***************************************************************
 
   return rechits_chains;
 }
 
 bool GEMSegmentAlgorithm::isGoodToMerge(const GEMEnsemble& ensemble,
                                         const EnsembleHitContainer& newChain,
                                         const EnsembleHitContainer& oldChain) {
   bool phiRequirementOK = false;  // once it is true in the loop, it is ok to merge
   bool etaRequirementOK = false;  // once it is true in the loop, it is ok to merge
   bool bxRequirementOK = false;   // once it is true in the loop, it is ok to merge
 
   for (size_t iRH_new = 0; iRH_new < newChain.size(); ++iRH_new) {
     int layer_new = (newChain[iRH_new]->gemId().station() - 1) * 2 + newChain[iRH_new]->gemId().layer();
 
     const GEMEtaPartition* rhEP = (ensemble.second.find(newChain[iRH_new]->gemId().rawId()))->second;
     GlobalPoint pos_new = rhEP->toGlobal(newChain[iRH_new]->localPosition());
 
     for (size_t iRH_old = 0; iRH_old < oldChain.size(); ++iRH_old) {
       int layer_old = (oldChain[iRH_old]->gemId().station() - 1) * 2 + oldChain[iRH_old]->gemId().layer();
       // Layers - hits on the same layer should not be allowed ==> if abs(layer_new - layer_old) > 0 is ok. if = 0 is false
       if (layer_new == layer_old)
         return false;
 
       const GEMEtaPartition* oldrhEP = (ensemble.second.find(oldChain[iRH_old]->gemId().rawId()))->second;
       GlobalPoint pos_old = oldrhEP->toGlobal(oldChain[iRH_old]->localPosition());
 
       // Eta & Phi- to be chained, two hits need also to be "close" in phi and eta
       if (phiRequirementOK == false)
         phiRequirementOK = std::abs(reco::deltaPhi(float(pos_new.phi()), float(pos_old.phi()))) < dPhiChainBoxMax;
       if (etaRequirementOK == false)
         etaRequirementOK = std::abs(pos_new.eta() - pos_old.eta()) < dEtaChainBoxMax;
       // and they should have a time difference compatible with the hypothesis
       // that the rechits originate from the same particle, but were detected in different layers
       if (bxRequirementOK == false) {
         if (!clusterOnlySameBXRecHits) {
           bxRequirementOK = true;
         } else {
           if (newChain[iRH_new]->BunchX() == oldChain[iRH_old]->BunchX())
             bxRequirementOK = true;
         }
       }
 
       if (phiRequirementOK && etaRequirementOK && bxRequirementOK)
         return true;
     }
   }
   return false;
 }
 
 void GEMSegmentAlgorithm::buildSegments(const GEMEnsemble& ensemble,
                                         const EnsembleHitContainer& rechits,
                                         std::vector<GEMSegment>& gemsegs) {
   if (rechits.size() < minHitsPerSegment)
     return;
 
   MuonSegFit::MuonRecHitContainer muonRecHits;
   proto_segment.clear();
 
   // select hits from the ensemble and sort it
   const GEMSuperChamber* suCh = ensemble.first;
   for (auto rh = rechits.begin(); rh != rechits.end(); rh++) {
     proto_segment.push_back(*rh);
 
     // for segFit - using local point in chamber frame
     const GEMEtaPartition* thePartition = (ensemble.second.find((*rh)->gemId()))->second;
     GlobalPoint gp = thePartition->toGlobal((*rh)->localPosition());
     const LocalPoint lp = suCh->toLocal(gp);
 
     GEMRecHit* newRH = (*rh)->clone();
     newRH->setPosition(lp);
     MuonSegFit::MuonRecHitPtr trkRecHit(newRH);
     muonRecHits.push_back(trkRecHit);
   }
 
 #ifdef EDM_ML_DEBUG  // have lines below only compiled when in debug mode
   edm::LogVerbatim("GEMSegmentAlgorithm")
       << "[GEMSegmentAlgorithm::buildSegments] will now try to fit a GEMSegment from collection of " << rechits.size()
       << " GEM RecHits";
   for (auto rh = rechits.begin(); rh != rechits.end(); ++rh) {
     auto gemid = (*rh)->gemId();
     auto rhLP = (*rh)->localPosition();
     edm::LogVerbatim("GEMSegmentAlgorithm")
         << "[RecHit :: Loc x = " << std::showpos << std::setw(9) << rhLP.x() << " Loc y = " << std::showpos
         << std::setw(9) << rhLP.y() << " BX = " << std::showpos << (*rh)->BunchX() << " -- " << gemid.rawId() << " = "
         << gemid << " ]";
   }
 #endif
 
   // The actual fit on all hits of the vector of the selected Tracking RecHits:
   sfit_ = std::make_unique<MuonSegFit>(muonRecHits);
   bool goodfit = sfit_->fit();
   edm::LogVerbatim("GEMSegmentAlgorithm")
       << "[GEMSegmentAlgorithm::buildSegments] GEMSegment fit done :: fit is good = " << goodfit;
 
   // quit function if fit was not OK
   if (!goodfit) {
     for (auto rh : muonRecHits)
       rh.reset();
     return;
   }
   // obtain all information necessary to make the segment:
   LocalPoint protoIntercept = sfit_->intercept();
   LocalVector protoDirection = sfit_->localdir();
   AlgebraicSymMatrix protoErrors = sfit_->covarianceMatrix();
   double protoChi2 = sfit_->chi2();
 
   // Calculate the bunch crossing of the GEM Segment
   float bx = 0.0;
   for (auto rh = rechits.begin(); rh != rechits.end(); ++rh) {
     bx += (*rh)->BunchX();
   }
   if (!rechits.empty())
     bx = bx * 1.0 / (rechits.size());
 
   // Calculate the central value and uncertainty of the segment time
   // if we want to study impact of 2-3ns time resolution on GEM Segment
   // (if there will be TDCs in readout and not just BX determination)
   // then implement tof() method for rechits and use this here
   /*`
   float averageTime=0.;
   for (auto rh=rechits.begin(); rh!=rechits.end(); ++rh){
     GEMEtaPartition thePartition = ensemble.second.find((*rh)->gemId));
     GlobalPoint pos = (thePartition->toGlobal((*rh)->localPosition());
     float tof = pos.mag() * 0.01 / 0.2997925 + 25.0*(*rh)->BunchX(); 
     averageTime += pos;                                          
   }
   if(rechits.size() != 0) averageTime=averageTime/(rechits.size());
   float timeUncrt=0.;
   for (auto rh=rechits.begin(); rh!=rechits.end(); ++rh){
     GEMEtaPartition thePartition = ensemble.second.find((*rh)->gemId));
     GlobalPoint pos = (thePartition->toGlobal((*rh)->localPosition());
     float tof = pos.mag() * 0.01 / 0.2997925 + 25.0*(*rh)->BunchX();
     timeUncrt += pow(tof-averageTime,2);
   }
   if(rechits.size() != 0) timeUncrt=timeUncrt/(rechits.size());
   timeUncrt = sqrt(timeUncrt);
   */
 
   // save all information inside GEMCSCSegment
   edm::LogVerbatim("GEMSegmentAlgorithm")
       << "[GEMSegmentAlgorithm::buildSegments] will now wrap fit info in GEMSegment dataformat";
   GEMSegment tmp(proto_segment, protoIntercept, protoDirection, protoErrors, protoChi2, bx);
   // GEMSegment tmp(proto_segment, protoIntercept, protoDirection, protoErrors, protoChi2, averageTime, timeUncrt);
 
   edm::LogVerbatim("GEMSegmentAlgorithm")
       << "[GEMSegmentAlgorithm::buildSegments] GEMSegment made in " << tmp.gemDetId();
   edm::LogVerbatim("GEMSegmentAlgorithm") << "[GEMSegmentAlgorithm::buildSegments] " << tmp;
 
   for (auto rh : muonRecHits)
     rh.reset();
   gemsegs.push_back(tmp);
 }

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