From 8dc8d8213228b31ccb2cdb9c9610f54800bd0535 Mon Sep 17 00:00:00 2001
From: Lindsey Gray <lindsey.gray@gmail.com>
Date: Wed, 23 Jul 2014 20:28:46 +0200
Subject: [PATCH 1/3] hack to remove linking in the same layer

---
 RecoParticleFlow/PFClusterProducer/src/Arbor.cc | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/RecoParticleFlow/PFClusterProducer/src/Arbor.cc b/RecoParticleFlow/PFClusterProducer/src/Arbor.cc
index c1fef9c44aa89..3405ec5e40032 100644
--- a/RecoParticleFlow/PFClusterProducer/src/Arbor.cc
+++ b/RecoParticleFlow/PFClusterProducer/src/Arbor.cc
@@ -286,7 +286,7 @@ void BuildInitLink()
 	  const auto& PosB = cleanedHits[found[j0].data];
 	  PosDiffAB = PosA - PosB;
 	  
-	  if( PosDiffAB.Mag2() < InitLinkThreshold2 ) // || ( PosDiffAB.Mag() < 1.6*InitLinkThreshold && PosDiffAB.Dot(PosB) < 0.9*PosDiffAB.Mag()*PosB.Mag() )  )	//Distance threshold to be optimized - should also depends on Geometry
+	  if( std::abs(PosDiffAB.Z()) > 1e-3 && PosDiffAB.Mag2() < InitLinkThreshold2 ) // || ( PosDiffAB.Mag() < 1.6*InitLinkThreshold && PosDiffAB.Dot(PosB) < 0.9*PosDiffAB.Mag()*PosB.Mag() )  )	//Distance threshold to be optimized - should also depends on Geometry
 	    {
 	      std::pair<int, int> a_Link;
 	      if( PosA.Mag2() > PosB.Mag2() )
@@ -461,7 +461,8 @@ void LinkIteration()	//Energy corrections, semi-local correction
       PosB = cleanedHits[found[j1].data];
       DiffPosAB = PosB - PosA; 
       
-      if( DiffPosAB.Mag2() < IterLinkThreshold2 && 
+      if( std::abs(DiffPosAB.Z()) > 1e-3 &&
+	  DiffPosAB.Mag2() < IterLinkThreshold2 && 
 	  DiffPosAB.Mag2() > InitLinkThreshold2 && 
 	  DiffPosAB.Angle(RefDir[i1]) < 0.8 ) {
 	

From 941fb6d443d8bf5924ac9752a0689db6b8411cb1 Mon Sep 17 00:00:00 2001
From: Lindsey Gray <lindsey.gray@gmail.com>
Date: Mon, 4 Aug 2014 12:01:38 +0100
Subject: [PATCH 2/3] use hash map when finding HGC neighbours instead of tree
 based map

---
 .../interface/PFRecHitCaloNavigator.h         | 185 +++++++++-------
 .../interface/PFRecHitNavigatorBase.h         |  24 +-
 .../plugins/PFRecHitProducer.cc               |  21 +-
 .../plugins/PFRecHitProducer.h                |   1 +
 .../python/particleFlowRecHitHGCEE_cfi.py     |   1 +
 .../python/particleFlowRecHitHGCHEB_cfi.py    |   1 +
 .../python/particleFlowRecHitHGCHEF_cfi.py    |   1 +
 .../PFClusterProducer/test/hgcal_rechits.fwc  | 208 +++++++++++++++---
 .../PFClusterProducer/test/run_display.sh     |   2 +-
 9 files changed, 328 insertions(+), 116 deletions(-)

diff --git a/RecoParticleFlow/PFClusterProducer/interface/PFRecHitCaloNavigator.h b/RecoParticleFlow/PFClusterProducer/interface/PFRecHitCaloNavigator.h
index 5c7d18ad6d6a4..35d73971e3649 100644
--- a/RecoParticleFlow/PFClusterProducer/interface/PFRecHitCaloNavigator.h
+++ b/RecoParticleFlow/PFClusterProducer/interface/PFRecHitCaloNavigator.h
@@ -41,84 +41,113 @@ class PFRecHitCaloNavigator : public PFRecHitNavigatorBase {
 
  virtual ~PFRecHitCaloNavigator() { if(!ownsTopo) { topology_.release(); } }
 
-  void associateNeighbours(reco::PFRecHit& hit,std::auto_ptr<reco::PFRecHitCollection>& hits,edm::RefProd<reco::PFRecHitCollection>& refProd) {
-    constexpr unsigned short halfDim = 1; // range in each dimension
-    constexpr unsigned short dimSize = 3;
-    constexpr CaloDirection directions[6] = { NORTH, SOUTH, EAST, WEST, UP, DOWN }; // max available directions
-    
-    DET detid( hit.detId() );
-    if( detid.null() ) return;
-    // this is a ripoff of getWindow() from CaloSubDetTopology
-    NeighbourInfo cellsInWindow;
-    DET tmpId(detid);
-    NeighbourInfo fringe;
-    fringe.emplace_back(tmpId,std::make_tuple(0,0,0));
-    
-    std::vector<std::pair<CellInfo,Coordinate> > visited_cells;
-    visited_cells.resize(std::pow(dimSize,DIM));
-    
-    while (fringe.size() > 0) {
-      NeighbourInfo::value_type cur = fringe.back();
-      fringe.pop_back();
-      // check all 2*DIM neighbours (in case of 2D only check NSEW)
-      for (unsigned dirnum = 0; dirnum < 2*DIM; ++dirnum) {
-	Coordinate neighbour = getNeighbourIndex(cur.second,directions[dirnum]);
-	//If outside the window range
-	if ( std::get<0>(neighbour) < -halfDim ||
-	     std::get<0>(neighbour) > halfDim ||
-	     std::get<1>(neighbour) < -halfDim ||
-	     std::get<1>(neighbour) > halfDim ||
-	     std::get<2>(neighbour) < -halfDim ||
-	     std::get<2>(neighbour) > halfDim )
-	  continue;
-	
-	//Found integer index in the matrix
-	unsigned int_index = ( std::get<0>(neighbour) + halfDim +
-			       dimSize * (std::get<1>(neighbour) + halfDim ) +
-			       (DIM==3)*dimSize*dimSize * ( std::get<2>(neighbour) + halfDim ) );	
-	assert(int_index < visited_cells.size());
-	
-	// check whether we have seen this neighbour already
-	if (visited_cells[int_index].first.visited)
-	  // we have seen this one already
-	  continue;
-	
-	// a new cell, get the DetId of the neighbour, mark it
-	// as visited and add it to the fringe
-	visited_cells[int_index].first.visited = true;
-	std::vector<DetId> neighbourCells = getNeighbours(cur.first,directions[dirnum]);
-	
-	if ( neighbourCells.size() == 1 ) {
-	  visited_cells[int_index].first.cell = neighbourCells[0];
-	  visited_cells[int_index].second = neighbour;
-	} else if ( neighbourCells.size() == 0 ) {
-	  visited_cells[int_index].first.cell = DetId(0);
-	  visited_cells[int_index].second = neighbour;
-	} else {
-	  throw cms::Exception("getWindowError") << "Not supported subdetector for getWindow method";
-	}
-	
-	if (!visited_cells[int_index].first.cell.null())
-	  fringe.emplace_back(visited_cells[int_index].first.cell,neighbour);
-	
-      } // loop over all possible directions
-    } // while some cells are left on the fringe
-    
-    for (unsigned int i=0; i<visited_cells.size(); i++) {
-      if (!visited_cells[i].first.cell.null()) {
-	const DetId& id = visited_cells[i].first.cell;
-	const Coordinate& coord = visited_cells[i].second;
-	if( std::get<0>(coord) != 0 ||
-	    std::get<1>(coord) != 0 ||
-	    std::get<2>(coord) != 0 ) {
-	  associateNeighbour( id,hit,hits,refProd,
-			      std::get<0>(coord),
-			      std::get<1>(coord),
-			      std::get<2>(coord) );
-	}
-      }
-    } 
-  }
+ void associateNeighbours(reco::PFRecHit& hit, 
+			  std::auto_ptr<reco::PFRecHitCollection>& hits,
+			  const DetIdToHitIdx& hitmap,
+			  edm::RefProd<reco::PFRecHitCollection>& refProd) override {
+   auto visited_cells = std::move( getWindow( hit ) );
+   for (unsigned int i=0; i<visited_cells.size(); i++) {
+     if (!visited_cells[i].first.cell.null()) {
+       const DetId& id = visited_cells[i].first.cell;
+       const Coordinate& coord = visited_cells[i].second;
+       if( std::get<0>(coord) != 0 ||
+	   std::get<1>(coord) != 0 ||
+	   std::get<2>(coord) != 0 ) {
+	 associateNeighbour( id,hit,hits,hitmap,refProd,
+			     std::get<0>(coord),
+			     std::get<1>(coord),
+			     std::get<2>(coord) );
+       }
+     }
+   } 
+ }
+
+ void associateNeighbours(reco::PFRecHit& hit,
+			  std::auto_ptr<reco::PFRecHitCollection>& hits,
+			  edm::RefProd<reco::PFRecHitCollection>& refProd) {
+   auto visited_cells = std::move( getWindow( hit ) );
+   for (unsigned int i=0; i<visited_cells.size(); i++) {
+     if (!visited_cells[i].first.cell.null()) {
+       const DetId& id = visited_cells[i].first.cell;
+       const Coordinate& coord = visited_cells[i].second;
+       if( std::get<0>(coord) != 0 ||
+	   std::get<1>(coord) != 0 ||
+	   std::get<2>(coord) != 0 ) {
+	 associateNeighbour( id,hit,hits,refProd,
+			     std::get<0>(coord),
+			     std::get<1>(coord),
+			     std::get<2>(coord) );
+       }
+     }
+   }
+ }
+ 
+
+ std::vector<std::pair<CellInfo,Coordinate> > getWindow(reco::PFRecHit& hit) {
+   constexpr unsigned short halfDim = 1; // range in each dimension
+   constexpr unsigned short dimSize = 3;
+   constexpr CaloDirection directions[6] = { NORTH, SOUTH, EAST, WEST, UP, DOWN }; // max available directions
+   
+   DET detid( hit.detId() );
+   if( detid.null() ) return std::vector<std::pair<CellInfo,Coordinate> >();
+   // this is a ripoff of getWindow() from CaloSubDetTopology
+   NeighbourInfo cellsInWindow;
+   DET tmpId(detid);
+   NeighbourInfo fringe;
+   fringe.emplace_back(tmpId,std::make_tuple(0,0,0));
+   
+   std::vector<std::pair<CellInfo,Coordinate> > visited_cells;
+   visited_cells.resize(std::pow(dimSize,DIM));
+   
+   while (fringe.size() > 0) {
+     NeighbourInfo::value_type cur = fringe.back();
+     fringe.pop_back();
+     // check all 2*DIM neighbours (in case of 2D only check NSEW)
+     for (unsigned dirnum = 0; dirnum < 2*DIM; ++dirnum) {
+       Coordinate neighbour = getNeighbourIndex(cur.second,directions[dirnum]);
+       //If outside the window range
+       if ( std::get<0>(neighbour) < -halfDim ||
+	    std::get<0>(neighbour) > halfDim ||
+	    std::get<1>(neighbour) < -halfDim ||
+	    std::get<1>(neighbour) > halfDim ||
+	    std::get<2>(neighbour) < -halfDim ||
+	    std::get<2>(neighbour) > halfDim )
+	 continue;
+       
+       //Found integer index in the matrix
+       unsigned int_index = ( std::get<0>(neighbour) + halfDim +
+			      dimSize * (std::get<1>(neighbour) + halfDim ) +
+			      (DIM==3)*dimSize*dimSize * ( std::get<2>(neighbour) + halfDim ) );	
+       assert(int_index < visited_cells.size());
+       
+       // check whether we have seen this neighbour already
+       if (visited_cells[int_index].first.visited)
+	 // we have seen this one already
+	 continue;
+       
+       // a new cell, get the DetId of the neighbour, mark it
+       // as visited and add it to the fringe
+       visited_cells[int_index].first.visited = true;
+       std::vector<DetId> neighbourCells = getNeighbours(cur.first,directions[dirnum]);
+       
+       if ( neighbourCells.size() == 1 ) {
+	 visited_cells[int_index].first.cell = neighbourCells[0];
+	 visited_cells[int_index].second = neighbour;
+       } else if ( neighbourCells.size() == 0 ) {
+	 visited_cells[int_index].first.cell = DetId(0);
+	 visited_cells[int_index].second = neighbour;
+       } else {
+	 throw cms::Exception("getWindowError") << "Not supported subdetector for getWindow method";
+       }
+       
+       if (!visited_cells[int_index].first.cell.null())
+	 fringe.emplace_back(visited_cells[int_index].first.cell,neighbour);
+       
+     } // loop over all possible directions
+   } // while some cells are left on the fringe
+   
+   return visited_cells;
+ }
 
  protected:
   std::unique_ptr<const TOPO> topology_;
diff --git a/RecoParticleFlow/PFClusterProducer/interface/PFRecHitNavigatorBase.h b/RecoParticleFlow/PFClusterProducer/interface/PFRecHitNavigatorBase.h
index ddebf1960f1af..c4d7ddb59ea3a 100644
--- a/RecoParticleFlow/PFClusterProducer/interface/PFRecHitNavigatorBase.h
+++ b/RecoParticleFlow/PFClusterProducer/interface/PFRecHitNavigatorBase.h
@@ -21,9 +21,12 @@
 #include "Geometry/CaloGeometry/interface/TruncatedPyramid.h"
 #include "Geometry/Records/interface/CaloGeometryRecord.h"
 
+#include <unordered_map>
 
 class PFRecHitNavigatorBase {
  public:
+  typedef std::unordered_map<unsigned,unsigned> DetIdToHitIdx;
+
   PFRecHitNavigatorBase() {}
   PFRecHitNavigatorBase(const edm::ParameterSet& iConfig) {}
 
@@ -31,10 +34,14 @@ class PFRecHitNavigatorBase {
 
   virtual void beginEvent(const edm::EventSetup&)=0;
   virtual void associateNeighbours(reco::PFRecHit&,std::auto_ptr<reco::PFRecHitCollection>&,edm::RefProd<reco::PFRecHitCollection>&)=0;
+  virtual void associateNeighbours(reco::PFRecHit&,
+				   std::auto_ptr<reco::PFRecHitCollection>&,
+				   const DetIdToHitIdx&,
+				   edm::RefProd<reco::PFRecHitCollection>&) {};
 
 
  protected:
-
+  // assumes sorted
   void associateNeighbour(const DetId& id, reco::PFRecHit& hit,std::auto_ptr<reco::PFRecHitCollection>& hits,edm::RefProd<reco::PFRecHitCollection>& refProd,short eta, short phi,short depth) {
     const reco::PFRecHit temp(id,PFLayer::NONE,0.0,math::XYZPoint(0,0,0),math::XYZVector(0,0,0),std::vector<math::XYZPoint>());
     auto found_hit = std::lower_bound(hits->begin(),hits->end(),
@@ -47,7 +54,20 @@ class PFRecHitNavigatorBase {
       hit.addNeighbour(eta,phi,depth,reco::PFRecHitRef(refProd,std::distance(hits->begin(),found_hit)));
     }    
   }
-
+  // map to indices is provided
+  void associateNeighbour(const DetId& id, 
+			  reco::PFRecHit& hit,
+			  std::auto_ptr<reco::PFRecHitCollection>& hits,
+			  const DetIdToHitIdx& hitmap,
+			  edm::RefProd<reco::PFRecHitCollection>& refProd,
+			  short eta, short phi,short depth) {
+    auto found_hit = hitmap.find(id.rawId());
+    if( found_hit != hitmap.end() ) {
+      auto begin = hits->begin();
+      auto hit_pos = begin + found_hit->second;
+      hit.addNeighbour(eta,phi,depth,reco::PFRecHitRef(refProd,std::distance(begin,hit_pos)));
+    }    
+  }
 
 };
 
diff --git a/RecoParticleFlow/PFClusterProducer/plugins/PFRecHitProducer.cc b/RecoParticleFlow/PFClusterProducer/plugins/PFRecHitProducer.cc
index 5da9d34e27dbf..ab1fd3a1410c3 100644
--- a/RecoParticleFlow/PFClusterProducer/plugins/PFRecHitProducer.cc
+++ b/RecoParticleFlow/PFClusterProducer/plugins/PFRecHitProducer.cc
@@ -7,7 +7,8 @@ namespace {
   }
 }
 
- PFRecHitProducer:: PFRecHitProducer(const edm::ParameterSet& iConfig)
+PFRecHitProducer:: PFRecHitProducer(const edm::ParameterSet& iConfig):
+  _useHitMap(iConfig.getUntrackedParameter<bool>("useHitMap",false))
 {
 
   produces<reco::PFRecHitCollection>();
@@ -52,14 +53,26 @@ void
      creators_.at(i)->importRecHits(out,cleaned,iEvent,iSetup);
    }
 
-   std::sort(out->begin(),out->end(),sortByDetId);
+   if(!_useHitMap) std::sort(out->begin(),out->end(),sortByDetId);
+
+   reco::PFRecHitCollection& outprod = *out;
+   PFRecHitNavigatorBase::DetIdToHitIdx hitmap(outprod.size());
+   if( _useHitMap ) {
+     for( unsigned i = 0 ; i < outprod.size(); ++i ) {
+       hitmap[outprod[i].detId()] = i;
+     }
+   }
 
    //create a refprod here
    edm::RefProd<reco::PFRecHitCollection> refProd = 
      iEvent.getRefBeforePut<reco::PFRecHitCollection>();
 
-   for( unsigned int i=0;i<out->size();++i) {
-     navigator_->associateNeighbours(out->at(i),out,refProd);
+   for( unsigned int i=0;i<outprod.size();++i) {
+     if( _useHitMap ) {
+       navigator_->associateNeighbours(outprod[i],out,hitmap,refProd);
+     } else {
+       navigator_->associateNeighbours(outprod[i],out,refProd);
+     }
    }
 
    iEvent.put(out,"");
diff --git a/RecoParticleFlow/PFClusterProducer/plugins/PFRecHitProducer.h b/RecoParticleFlow/PFClusterProducer/plugins/PFRecHitProducer.h
index 28983036cae60..a3db544c01c25 100644
--- a/RecoParticleFlow/PFClusterProducer/plugins/PFRecHitProducer.h
+++ b/RecoParticleFlow/PFClusterProducer/plugins/PFRecHitProducer.h
@@ -26,6 +26,7 @@ class PFRecHitProducer : public edm::EDProducer {
       static void fillDescriptions(edm::ConfigurationDescriptions& descriptions);
 
    private:
+      const bool _useHitMap;
       virtual void produce(edm::Event&, const edm::EventSetup&) override;
       std::vector<std::unique_ptr<PFRecHitCreatorBase> > creators_;
       std::unique_ptr<PFRecHitNavigatorBase> navigator_;
diff --git a/RecoParticleFlow/PFClusterProducer/python/particleFlowRecHitHGCEE_cfi.py b/RecoParticleFlow/PFClusterProducer/python/particleFlowRecHitHGCEE_cfi.py
index 2cc4652982e89..049c21f86f523 100644
--- a/RecoParticleFlow/PFClusterProducer/python/particleFlowRecHitHGCEE_cfi.py
+++ b/RecoParticleFlow/PFClusterProducer/python/particleFlowRecHitHGCEE_cfi.py
@@ -1,6 +1,7 @@
 import FWCore.ParameterSet.Config as cms
 
 particleFlowRecHitHGCEE = cms.EDProducer("PFRecHitProducer",
+    useHitMap = cms.untracked.bool(True),
     navigator = cms.PSet(
         name = cms.string("PFRecHitHGCEENavigator"),
         topologySource = cms.string("HGCalEESensitive"),
diff --git a/RecoParticleFlow/PFClusterProducer/python/particleFlowRecHitHGCHEB_cfi.py b/RecoParticleFlow/PFClusterProducer/python/particleFlowRecHitHGCHEB_cfi.py
index c7f63b3ca916f..e7cb507b278a6 100644
--- a/RecoParticleFlow/PFClusterProducer/python/particleFlowRecHitHGCHEB_cfi.py
+++ b/RecoParticleFlow/PFClusterProducer/python/particleFlowRecHitHGCHEB_cfi.py
@@ -1,6 +1,7 @@
 import FWCore.ParameterSet.Config as cms
 
 particleFlowRecHitHGCHEB = cms.EDProducer("PFRecHitProducer",
+    useHitMap = cms.untracked.bool(True),
     navigator = cms.PSet(
         name = cms.string("PFRecHitHGCHENavigator"),
         topologySource = cms.string("HGCalHEScintillatorSensitive"),
diff --git a/RecoParticleFlow/PFClusterProducer/python/particleFlowRecHitHGCHEF_cfi.py b/RecoParticleFlow/PFClusterProducer/python/particleFlowRecHitHGCHEF_cfi.py
index 5615b9ca7da57..e8d01dd94ee9c 100644
--- a/RecoParticleFlow/PFClusterProducer/python/particleFlowRecHitHGCHEF_cfi.py
+++ b/RecoParticleFlow/PFClusterProducer/python/particleFlowRecHitHGCHEF_cfi.py
@@ -1,6 +1,7 @@
 import FWCore.ParameterSet.Config as cms
 
 particleFlowRecHitHGCHEF = cms.EDProducer("PFRecHitProducer",
+    useHitMap = cms.untracked.bool(True),
     navigator = cms.PSet(
         name = cms.string("PFRecHitHGCHENavigator"),
         topologySource = cms.string("HGCalHESiliconSensitive"),
diff --git a/RecoParticleFlow/PFClusterProducer/test/hgcal_rechits.fwc b/RecoParticleFlow/PFClusterProducer/test/hgcal_rechits.fwc
index 1b918813d32cf..6fb000b21c9a1 100644
--- a/RecoParticleFlow/PFClusterProducer/test/hgcal_rechits.fwc
+++ b/RecoParticleFlow/PFClusterProducer/test/hgcal_rechits.fwc
@@ -96,10 +96,10 @@
  <config name="EventItems" version="1">
   <config name="Jets" version="6">
    <config name="type" version="0">
-     <string>std::vector&lt;reco::CaloJet&gt;</string>
+     <string>std::vector&lt;reco::PFJet&gt;</string>
    </config>
    <config name="moduleLabel" version="0">
-     <string>iterativeCone5CaloJets</string>
+     <string>ak5PFJets</string>
    </config>
    <config name="productInstanceLabel" version="0">
      <string></string>
@@ -362,10 +362,10 @@
   </config>
   <config name="MET" version="6">
    <config name="type" version="0">
-     <string>std::vector&lt;reco::MET&gt;</string>
+     <string>std::vector&lt;reco::PFMET&gt;</string>
    </config>
    <config name="moduleLabel" version="0">
-     <string>tcMet</string>
+     <string>pfMet</string>
    </config>
    <config name="productInstanceLabel" version="0">
      <string></string>
@@ -652,7 +652,7 @@
      <string>1009</string>
    </config>
    <config name="isVisible" version="0">
-     <string>t</string>
+     <string>f</string>
    </config>
    <config name="layer" version="0">
      <string>31</string>
@@ -686,7 +686,7 @@
      <string>1011</string>
    </config>
    <config name="isVisible" version="0">
-     <string>t</string>
+     <string>f</string>
    </config>
    <config name="layer" version="0">
      <string>32</string>
@@ -720,7 +720,7 @@
      <string>1014</string>
    </config>
    <config name="isVisible" version="0">
-     <string>t</string>
+     <string>f</string>
    </config>
    <config name="layer" version="0">
      <string>33</string>
@@ -734,6 +734,116 @@
    <config name="PBConfig" version="1">
    </config>
   </config>
+  <config name="genParticles" version="6">
+   <config name="type" version="0">
+     <string>std::vector&lt;reco::GenParticle&gt;</string>
+   </config>
+   <config name="moduleLabel" version="0">
+     <string>genParticles</string>
+   </config>
+   <config name="productInstanceLabel" version="0">
+     <string></string>
+   </config>
+   <config name="processName" version="0">
+     <string></string>
+   </config>
+   <config name="filterExpression" version="0">
+     <string></string>
+   </config>
+   <config name="color" version="0">
+     <string>1019</string>
+   </config>
+   <config name="isVisible" version="0">
+     <string>t</string>
+   </config>
+   <config name="layer" version="0">
+     <string>34</string>
+   </config>
+   <config name="purpose" version="0">
+     <string>GenParticles</string>
+   </config>
+   <config name="transparency" version="0">
+     <string>0</string>
+   </config>
+   <config name="PBConfig" version="1">
+    <config name="Var" version="1">
+     <config name="MarkerStyle" version="0">
+       <string>0</string>
+     </config>
+     <config name="MarkerSize" version="0">
+       <string>2</string>
+     </config>
+    </config>
+   </config>
+  </config>
+  <config name="g4SimHits" version="6">
+   <config name="type" version="0">
+     <string>std::vector&lt;SimTrack&gt;</string>
+   </config>
+   <config name="moduleLabel" version="0">
+     <string>g4SimHits</string>
+   </config>
+   <config name="productInstanceLabel" version="0">
+     <string></string>
+   </config>
+   <config name="processName" version="0">
+     <string></string>
+   </config>
+   <config name="filterExpression" version="0">
+     <string></string>
+   </config>
+   <config name="color" version="0">
+     <string>1029</string>
+   </config>
+   <config name="isVisible" version="0">
+     <string>t</string>
+   </config>
+   <config name="layer" version="0">
+     <string>35</string>
+   </config>
+   <config name="purpose" version="0">
+     <string>SimTracks</string>
+   </config>
+   <config name="transparency" version="0">
+     <string>0</string>
+   </config>
+   <config name="PBConfig" version="1">
+   </config>
+  </config>
+  <config name="particleFlow" version="6">
+   <config name="type" version="0">
+     <string>std::vector&lt;reco::PFCandidate&gt;</string>
+   </config>
+   <config name="moduleLabel" version="0">
+     <string>particleFlow</string>
+   </config>
+   <config name="productInstanceLabel" version="0">
+     <string></string>
+   </config>
+   <config name="processName" version="0">
+     <string></string>
+   </config>
+   <config name="filterExpression" version="0">
+     <string></string>
+   </config>
+   <config name="color" version="0">
+     <string>1000</string>
+   </config>
+   <config name="isVisible" version="0">
+     <string>t</string>
+   </config>
+   <config name="layer" version="0">
+     <string>36</string>
+   </config>
+   <config name="purpose" version="0">
+     <string>PF Candidates</string>
+   </config>
+   <config name="transparency" version="0">
+     <string>0</string>
+   </config>
+   <config name="PBConfig" version="1">
+   </config>
+  </config>
  </config>
  <config name="EventNavigator" version="1">
   <config name="EventFilters" version="1">
@@ -787,7 +897,7 @@
      <string>54</string>
    </config>
    <config name="y" version="0">
-     <string>31</string>
+     <string>44</string>
    </config>
    <config name="width" version="0">
      <string>1263</string>
@@ -901,22 +1011,22 @@
       <string>1</string>
     </config>
     <config name="cameraMatrix0Plain3D" version="0">
-      <string>-0.660885</string>
+      <string>-0.401173</string>
     </config>
     <config name="cameraMatrix1Plain3D" version="0">
-      <string>-0.653181</string>
+      <string>-0.563483</string>
     </config>
     <config name="cameraMatrix2Plain3D" version="0">
-      <string>0.369579</string>
+      <string>0.722185</string>
     </config>
     <config name="cameraMatrix3Plain3D" version="0">
       <string>0</string>
     </config>
     <config name="cameraMatrix4Plain3D" version="0">
-      <string>0.702949</string>
+      <string>0.814632</string>
     </config>
     <config name="cameraMatrix5Plain3D" version="0">
-      <string>-0.71124</string>
+      <string>-0.579978</string>
     </config>
     <config name="cameraMatrix6Plain3D" version="0">
       <string>0</string>
@@ -925,25 +1035,25 @@
       <string>0</string>
     </config>
     <config name="cameraMatrix8Plain3D" version="0">
-      <string>0.262858</string>
+      <string>0.41885</string>
     </config>
     <config name="cameraMatrix9Plain3D" version="0">
-      <string>0.259795</string>
+      <string>0.588315</string>
     </config>
     <config name="cameraMatrix10Plain3D" version="0">
-      <string>0.9292</string>
+      <string>0.691701</string>
     </config>
     <config name="cameraMatrix11Plain3D" version="0">
       <string>0</string>
     </config>
     <config name="cameraMatrix12Plain3D" version="0">
-      <string>-2205.43</string>
+      <string>-1458.17</string>
     </config>
     <config name="cameraMatrix13Plain3D" version="0">
-      <string>-2147.69</string>
+      <string>-2016.83</string>
     </config>
     <config name="cameraMatrix14Plain3D" version="0">
-      <string>1314.98</string>
+      <string>2612.92</string>
     </config>
     <config name="cameraMatrix15Plain3D" version="0">
       <string>1</string>
@@ -985,19 +1095,19 @@
       <string>0</string>
     </config>
     <config name="cameraMatrixBase12Plain3D" version="0">
-      <string>-0.180542</string>
+      <string>-52.4547</string>
     </config>
     <config name="cameraMatrixBase13Plain3D" version="0">
-      <string>0.521286</string>
+      <string>-37.8377</string>
     </config>
     <config name="cameraMatrixBase14Plain3D" version="0">
-      <string>24.0227</string>
+      <string>317.74</string>
     </config>
     <config name="cameraMatrixBase15Plain3D" version="0">
       <string>1</string>
     </config>
     <config name="Plain3D FOV" version="0">
-      <string>28.329</string>
+      <string>3.09973</string>
     </config>
    </config>
    <config name="Rho Phi" version="7">
@@ -1399,7 +1509,7 @@
     <string>0</string>
   </config>
   <config name="reco::CaloJet" version="1">
-    <string>Pt</string>
+    <string>pT</string>
     <string>pt</string>
     <string>1</string>
     <string>eta</string>
@@ -1417,12 +1527,6 @@
     <string>emf</string>
     <string>emEnergyFraction()</string>
     <string>3</string>
-    <string>size_eta</string>
-    <string>sqrt(etaetaMoment)</string>
-    <string>3</string>
-    <string>size_phi</string>
-    <string>sqrt(phiphiMoment)</string>
-    <string>3</string>
   </config>
   <config name="reco::GenParticle" version="1">
     <string>pT</string>
@@ -1482,7 +1586,7 @@
     <string>3</string>
   </config>
   <config name="reco::MET" version="1">
-    <string>MET</string>
+    <string>et</string>
     <string>et</string>
     <string>1</string>
     <string>phi</string>
@@ -1533,6 +1637,46 @@
     <string>charge</string>
     <string>0</string>
   </config>
+  <config name="reco::PFJet" version="1">
+    <string>Pt</string>
+    <string>pt</string>
+    <string>1</string>
+    <string>eta</string>
+    <string>eta</string>
+    <string>3</string>
+    <string>phi</string>
+    <string>phi</string>
+    <string>3</string>
+    <string>ECAL</string>
+    <string>p4().E() * emEnergyFraction()</string>
+    <string>1</string>
+    <string>HCAL</string>
+    <string>p4().E() * energyFractionHadronic()</string>
+    <string>1</string>
+    <string>emf</string>
+    <string>emEnergyFraction()</string>
+    <string>3</string>
+    <string>size_eta</string>
+    <string>sqrt(etaetaMoment)</string>
+    <string>3</string>
+    <string>size_phi</string>
+    <string>sqrt(phiphiMoment)</string>
+    <string>3</string>
+  </config>
+  <config name="reco::PFMET" version="1">
+    <string>MET</string>
+    <string>et</string>
+    <string>1</string>
+    <string>phi</string>
+    <string>phi</string>
+    <string>3</string>
+    <string>sumEt</string>
+    <string>sumEt</string>
+    <string>1</string>
+    <string>mEtSig</string>
+    <string>mEtSig</string>
+    <string>3</string>
+  </config>
   <config name="reco::Photon" version="1">
     <string>pT</string>
     <string>pt</string>
@@ -1634,6 +1778,8 @@
     <string>reco::Jet</string>
     <string>reco::MET</string>
     <string>reco::Muon</string>
+    <string>reco::PFJet</string>
+    <string>reco::PFMET</string>
     <string>reco::Photon</string>
     <string>reco::Track</string>
     <string>reco::Vertex</string>
diff --git a/RecoParticleFlow/PFClusterProducer/test/run_display.sh b/RecoParticleFlow/PFClusterProducer/test/run_display.sh
index 72b3beb6f68d4..f36f11d10a0e0 100755
--- a/RecoParticleFlow/PFClusterProducer/test/run_display.sh
+++ b/RecoParticleFlow/PFClusterProducer/test/run_display.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-cmsShow -c ${CMSSW_BASE}/src/RecoParticleFlow/PFClusterProducer/test/hgcal_rechits.fwc -g /afs/cern.ch/user/l/lgray/work/public/xHGCAL/cmsRecoGeom1-HGCAL.root --sim-geom-file /afs/cern.ch/user/l/lgray/work/public/xHGCAL/cmsSimGeom-14-HGCAL.root /afs/cern.ch/user/l/lgray/work/public/CMSSW_6_2_X_SLHC_2014-07-17-0200/src/matrix_tests/simple_jet_gun/step3.root
+cmsShow -c ${CMSSW_BASE}/src/RecoParticleFlow/PFClusterProducer/test/hgcal_rechits.fwc -g /home/lgray/xHGCAL/cmsRecoGeom1-HGCAL.root --sim-geom-file /home/lgray/xHGCAL/cmsSimGeom-14-HGCAL.root /home/lgray/CMSSW_6_2_0_SLHC16/src/matrix_tests/simple_jet_gun/step3.root
 
 #12202_SinglePionPt35+SinglePionPt35_Extended2023HGCalMuon_GenSimFull+DigiFull_Extended2023HGCalMuon+RecoFull_Extended2023HGCalMuon+HARVESTFull_Extended2023HGCalMuon
 

From f03a5d1b972888955c8f199f497c99eae8d093d8 Mon Sep 17 00:00:00 2001
From: Lindsey Gray <lindsey.gray@gmail.com>
Date: Wed, 24 Sep 2014 12:42:23 +0200
Subject: [PATCH 3/3] tuning up clustering based on initial geometry fixes

Conflicts:
	RecoParticleFlow/PFClusterProducer/test/run_display.sh
---
 .../python/particleFlowClusterHGCEE_cfi.py    |  4 +--
 .../python/particleFlowClusterHGCHEB_cfi.py   |  4 +--
 .../python/particleFlowClusterHGCHEF_cfi.py   |  6 ++--
 .../PFClusterProducer/test/hgcal_rechits.fwc  | 34 +++++++++----------
 .../PFClusterProducer/test/run_display.sh     |  3 +-
 .../plugins/kdtrees/KDTreeLinkerTrackHGC.h    |  9 +++--
 6 files changed, 32 insertions(+), 28 deletions(-)

diff --git a/RecoParticleFlow/PFClusterProducer/python/particleFlowClusterHGCEE_cfi.py b/RecoParticleFlow/PFClusterProducer/python/particleFlowClusterHGCEE_cfi.py
index 50bb5301bed76..df7362265294c 100644
--- a/RecoParticleFlow/PFClusterProducer/python/particleFlowClusterHGCEE_cfi.py
+++ b/RecoParticleFlow/PFClusterProducer/python/particleFlowClusterHGCEE_cfi.py
@@ -26,8 +26,8 @@
 _manqiArborClusterizer_HGCEE = cms.PSet(
     algoName = cms.string("SimpleArborClusterizer"), 
     # use basic pad sizes in HGCEE
-    cellSize = cms.double(10.0),
-    layerThickness = cms.double(16.0),
+    cellSize = cms.double(16.0),
+    layerThickness = cms.double(18.0),
     distSeedForMerge = cms.double(20.0),
     killNoiseClusters = cms.bool(True),
     maxNoiseClusterSize = cms.uint32(3),
diff --git a/RecoParticleFlow/PFClusterProducer/python/particleFlowClusterHGCHEB_cfi.py b/RecoParticleFlow/PFClusterProducer/python/particleFlowClusterHGCHEB_cfi.py
index c74a8e068b2aa..68e2aabd180bf 100644
--- a/RecoParticleFlow/PFClusterProducer/python/particleFlowClusterHGCHEB_cfi.py
+++ b/RecoParticleFlow/PFClusterProducer/python/particleFlowClusterHGCHEB_cfi.py
@@ -23,8 +23,8 @@
 _manqiArborClusterizer_HGCHEB = cms.PSet(
     algoName = cms.string("SimpleArborClusterizer"), 
     # use basic pad sizes in HGCEE
-    cellSize = cms.double(30.0),
-    layerThickness = cms.double(55.0),
+    cellSize = cms.double(35.0),
+    layerThickness = cms.double(65.0),
     distSeedForMerge = cms.double(20.0),
     killNoiseClusters = cms.bool(True),
     maxNoiseClusterSize = cms.uint32(3),
diff --git a/RecoParticleFlow/PFClusterProducer/python/particleFlowClusterHGCHEF_cfi.py b/RecoParticleFlow/PFClusterProducer/python/particleFlowClusterHGCHEF_cfi.py
index 1b45cd31973e6..1fb91a182e124 100644
--- a/RecoParticleFlow/PFClusterProducer/python/particleFlowClusterHGCHEF_cfi.py
+++ b/RecoParticleFlow/PFClusterProducer/python/particleFlowClusterHGCHEF_cfi.py
@@ -23,9 +23,9 @@
 _manqiArborClusterizer_HGCHEF = cms.PSet(
     algoName = cms.string("SimpleArborClusterizer"), 
     # use basic pad sizes in HGCEE
-    cellSize = cms.double(10.0),
-    layerThickness = cms.double(45.0),
-    distSeedForMerge = cms.double(20.0),
+    cellSize = cms.double(15.0),
+    layerThickness = cms.double(55.0),
+    distSeedForMerge = cms.double(30.0),
     killNoiseClusters = cms.bool(True),
     maxNoiseClusterSize = cms.uint32(3),
     thresholdsByDetector = cms.VPSet( )
diff --git a/RecoParticleFlow/PFClusterProducer/test/hgcal_rechits.fwc b/RecoParticleFlow/PFClusterProducer/test/hgcal_rechits.fwc
index 6fb000b21c9a1..8e45338d548dc 100644
--- a/RecoParticleFlow/PFClusterProducer/test/hgcal_rechits.fwc
+++ b/RecoParticleFlow/PFClusterProducer/test/hgcal_rechits.fwc
@@ -894,10 +894,10 @@
  <config name="GUI" version="1">
   <config name="main window" version="3">
    <config name="x" version="0">
-     <string>54</string>
+     <string>106</string>
    </config>
    <config name="y" version="0">
-     <string>44</string>
+     <string>23</string>
    </config>
    <config name="width" version="0">
      <string>1263</string>
@@ -1011,22 +1011,22 @@
       <string>1</string>
     </config>
     <config name="cameraMatrix0Plain3D" version="0">
-      <string>-0.401173</string>
+      <string>0.769709</string>
     </config>
     <config name="cameraMatrix1Plain3D" version="0">
-      <string>-0.563483</string>
+      <string>0.13655</string>
     </config>
     <config name="cameraMatrix2Plain3D" version="0">
-      <string>0.722185</string>
+      <string>0.623623</string>
     </config>
     <config name="cameraMatrix3Plain3D" version="0">
       <string>0</string>
     </config>
     <config name="cameraMatrix4Plain3D" version="0">
-      <string>0.814632</string>
+      <string>-0.174677</string>
     </config>
     <config name="cameraMatrix5Plain3D" version="0">
-      <string>-0.579978</string>
+      <string>0.984626</string>
     </config>
     <config name="cameraMatrix6Plain3D" version="0">
       <string>0</string>
@@ -1035,25 +1035,25 @@
       <string>0</string>
     </config>
     <config name="cameraMatrix8Plain3D" version="0">
-      <string>0.41885</string>
+      <string>-0.614034</string>
     </config>
     <config name="cameraMatrix9Plain3D" version="0">
-      <string>0.588315</string>
+      <string>-0.108934</string>
     </config>
     <config name="cameraMatrix10Plain3D" version="0">
-      <string>0.691701</string>
+      <string>0.781726</string>
     </config>
     <config name="cameraMatrix11Plain3D" version="0">
       <string>0</string>
     </config>
     <config name="cameraMatrix12Plain3D" version="0">
-      <string>-1458.17</string>
+      <string>2877.96</string>
     </config>
     <config name="cameraMatrix13Plain3D" version="0">
-      <string>-2016.83</string>
+      <string>498.315</string>
     </config>
     <config name="cameraMatrix14Plain3D" version="0">
-      <string>2612.92</string>
+      <string>2219.76</string>
     </config>
     <config name="cameraMatrix15Plain3D" version="0">
       <string>1</string>
@@ -1095,19 +1095,19 @@
       <string>0</string>
     </config>
     <config name="cameraMatrixBase12Plain3D" version="0">
-      <string>-52.4547</string>
+      <string>0.281389</string>
     </config>
     <config name="cameraMatrixBase13Plain3D" version="0">
-      <string>-37.8377</string>
+      <string>0.577909</string>
     </config>
     <config name="cameraMatrixBase14Plain3D" version="0">
-      <string>317.74</string>
+      <string>6.85455</string>
     </config>
     <config name="cameraMatrixBase15Plain3D" version="0">
       <string>1</string>
     </config>
     <config name="Plain3D FOV" version="0">
-      <string>3.09973</string>
+      <string>5.46292</string>
     </config>
    </config>
    <config name="Rho Phi" version="7">
diff --git a/RecoParticleFlow/PFClusterProducer/test/run_display.sh b/RecoParticleFlow/PFClusterProducer/test/run_display.sh
index f36f11d10a0e0..45f194a88c37e 100755
--- a/RecoParticleFlow/PFClusterProducer/test/run_display.sh
+++ b/RecoParticleFlow/PFClusterProducer/test/run_display.sh
@@ -1,6 +1,7 @@
 #!/bin/bash
 
-cmsShow -c ${CMSSW_BASE}/src/RecoParticleFlow/PFClusterProducer/test/hgcal_rechits.fwc -g /home/lgray/xHGCAL/cmsRecoGeom1-HGCAL.root --sim-geom-file /home/lgray/xHGCAL/cmsSimGeom-14-HGCAL.root /home/lgray/CMSSW_6_2_0_SLHC16/src/matrix_tests/simple_jet_gun/step3.root
+cmsShow -c ${CMSSW_BASE}/src/RecoParticleFlow/PFClusterProducer/test/hgcal_rechits.fwc -g ~/work/public/xHGCAL/cmsRecoGeom1-HGCAL.root --sim-geom-file ~/work/public/xHGCAL/cmsSimGeom-14-HGCAL.root ${CMSSW_BASE}/src/matrix_tests/14801_FourMuPt1_200+FourMuPt_1_200_Extended2023HGCalV4_GenSimFull+DigiFull_Extended2023HGCalV4+RecoFull_Extended2023HGCalV4+HARVESTFull_Extended2023HGCalV4/step3.root
+
 
 #12202_SinglePionPt35+SinglePionPt35_Extended2023HGCalMuon_GenSimFull+DigiFull_Extended2023HGCalMuon+RecoFull_Extended2023HGCalMuon+HARVESTFull_Extended2023HGCalMuon
 
diff --git a/RecoParticleFlow/PFProducer/plugins/kdtrees/KDTreeLinkerTrackHGC.h b/RecoParticleFlow/PFProducer/plugins/kdtrees/KDTreeLinkerTrackHGC.h
index a9d49e131db53..203d3b52c2353 100644
--- a/RecoParticleFlow/PFProducer/plugins/kdtrees/KDTreeLinkerTrackHGC.h
+++ b/RecoParticleFlow/PFProducer/plugins/kdtrees/KDTreeLinkerTrackHGC.h
@@ -99,6 +99,7 @@ KDTreeLinkerTrackHGC<the_layer,RHscaling>::insertFieldClusterElt(reco::PFBlockEl
   
   // We create a list of hgcCluster
   fieldClusterSet_.insert(hgcCluster);
+  /*
   DetId seedId( clusterref->seed() );
   unsigned seedLayer = 1000;  
   if( seedId.det() == DetId::Forward ) {
@@ -111,10 +112,12 @@ KDTreeLinkerTrackHGC<the_layer,RHscaling>::insertFieldClusterElt(reco::PFBlockEl
     throw cms::Exception("BadSeedRecHit") 
       << "HGC KDTree Linker only accepts HGC DetIds! got: " << seedId.det();
   }
+  */
   
   for(size_t rhit = 0; rhit < fraction.size(); ++rhit) {
     const reco::PFRecHitRef& rh = fraction[rhit].recHitRef();
     double fract = fraction[rhit].fraction();
+    /*
     DetId rhId( rh->detId() );
     unsigned rhLayer = 1000;
 
@@ -128,8 +131,8 @@ KDTreeLinkerTrackHGC<the_layer,RHscaling>::insertFieldClusterElt(reco::PFBlockEl
       throw cms::Exception("BadRecHit") 
 	<< "HGC KDTree Linker only accepts HGC DetIds! got: " << rhId.det();
     }
-
-    if ( (rh.isNull()) || (fract < 1E-4) ||  rhLayer != seedLayer )
+    */
+    if ( (rh.isNull()) || (fract < 1E-4) ) // ||  rhLayer != seedLayer )
       continue;
       
     const reco::PFRecHit& rechit = *rh;
@@ -233,7 +236,7 @@ void
     
     // Estimate the maximal envelope in phi/eta that will be used to find rechit candidates.
     // Same envelope for cap et barrel rechits.
-    double range = getCristalPhiEtaMaxSize() * (2.0 + 1.0 / std::min(1., trackPt / 2.)); 
+    double range = getCristalPhiEtaMaxSize() * (2.0 + 1.0 / std::min(1., 0.5*trackPt )); 
 
     // We search for all candidate recHits, ie all recHits contained in the maximal size envelope.
     std::vector<KDTreeNodeInfo> recHits;