From eade067efa821ab8a1b26f63e10e94259fb5c0ac Mon Sep 17 00:00:00 2001
From: Giuseppe Cerati <cerati@fnal.gov>
Date: Thu, 10 Apr 2025 21:25:50 -0500
Subject: [PATCH 1/6] add first NuGraph2 info to CAF

---
 sbncode/CAFMaker/CAFMakerParams.h   | 18 +++++++
 sbncode/CAFMaker/CAFMaker_module.cc | 39 +++++++++++++++
 sbncode/CAFMaker/FillReco.cxx       | 73 +++++++++++++++++++++++++++++
 sbncode/CAFMaker/FillReco.h         | 14 ++++++
 4 files changed, 144 insertions(+)

diff --git a/sbncode/CAFMaker/CAFMakerParams.h b/sbncode/CAFMaker/CAFMakerParams.h
index d05eb8b9b..636fcda57 100644
--- a/sbncode/CAFMaker/CAFMakerParams.h
+++ b/sbncode/CAFMaker/CAFMakerParams.h
@@ -340,6 +340,24 @@ namespace caf
       "" //Empty by default, configured in icaruscode cafmaker_defs
     };
 
+    Atom<art::InputTag> NuGraphSliceHitLabel {
+      Name("NuGraphSliceHitLabel"),
+      Comment("Label of NuGraph slice hit map."),
+	art::InputTag("nuslhits")
+    };
+
+    Atom<art::InputTag> NuGraphFilterLabel {
+      Name("NuGraphFilterLabel"),
+      Comment("Label of NuGraph filter."),
+	art::InputTag("NuGraph","filter")
+    };
+
+    Atom<art::InputTag> NuGraphSemanticLabel {
+      Name("NuGraphSemanticLabel"),
+      Comment("Label of NuGraph semantic."),
+	art::InputTag("NuGraph","semantic")
+    };
+
     Atom<string> OpFlashLabel {
       Name("OpFlashLabel"),
       Comment("Label of PMT flash."),
diff --git a/sbncode/CAFMaker/CAFMaker_module.cc b/sbncode/CAFMaker/CAFMaker_module.cc
index 2728b395f..38a6e416c 100644
--- a/sbncode/CAFMaker/CAFMaker_module.cc
+++ b/sbncode/CAFMaker/CAFMaker_module.cc
@@ -95,6 +95,7 @@
 #include "lardataobj/RecoBase/Vertex.h"
 #include "lardataobj/RecoBase/Shower.h"
 #include "lardataobj/RecoBase/MCSFitResult.h"
+#include "lardataobj/RecoBase/Cluster.h"
 
 #include "nusimdata/SimulationBase/MCFlux.h"
 #include "nusimdata/SimulationBase/MCTruth.h"
@@ -1696,6 +1697,17 @@ void CAFMaker::produce(art::Event& evt) noexcept {
     }
   }
 
+  // nu graph
+  std::vector< art::Handle<std::vector<unsigned int>> > ng2_slice_hit_map_handle(pandora_tag_suffixes.size());
+  std::vector< art::Handle<std::vector<anab::FeatureVector<1>>> > ng2_filter_handle(pandora_tag_suffixes.size());
+  std::vector< art::Handle<std::vector<anab::FeatureVector<5>>> > ng2_semantic_handle(pandora_tag_suffixes.size());
+  for (unsigned i_tag = 0; i_tag < pandora_tag_suffixes.size(); i_tag++) {
+    const std::string &pandora_tag_suffix = pandora_tag_suffixes[i_tag];
+    GetByLabelIfExists(evt, fParams.NuGraphSliceHitLabel().encode() + pandora_tag_suffix, ng2_slice_hit_map_handle[i_tag]);
+    GetByLabelIfExists(evt, fParams.NuGraphFilterLabel().label() + pandora_tag_suffix + ":" + fParams.NuGraphFilterLabel().instance(), ng2_filter_handle[i_tag]);
+    GetByLabelIfExists(evt, fParams.NuGraphSemanticLabel().label() + pandora_tag_suffix + ":" + fParams.NuGraphSemanticLabel().instance(), ng2_semantic_handle[i_tag]);
+  }
+
   // The Standard Record
   // Branch entry definition -- contains list of slices, CRT information, and truth information
   StandardRecord rec;
@@ -1752,6 +1764,12 @@ void CAFMaker::produce(art::Event& evt) noexcept {
       }
     }
 
+    std::vector<art::Ptr<anab::FeatureVector<1>>> ng2_filter_vec;
+    std::vector<art::Ptr<anab::FeatureVector<5>>> ng2_semantic_vec;
+    art::fill_ptr_vector(ng2_filter_vec,ng2_filter_handle[producer]);
+    art::fill_ptr_vector(ng2_semantic_vec,ng2_semantic_handle[producer]);
+    FillSliceNuGraph(slcHits,*ng2_slice_hit_map_handle[producer],ng2_filter_vec,ng2_semantic_vec,recslc);
+
     art::FindManyP<sbn::OpT0Finder> fmOpT0 =
       FindManyPStrict<sbn::OpT0Finder>(sliceList, evt, fParams.OpT0Label() + slice_tag_suff);
     std::vector<art::Ptr<sbn::OpT0Finder>> slcOpT0;
@@ -1798,6 +1816,25 @@ void CAFMaker::produce(art::Event& evt) noexcept {
     art::FindManyP<recob::PFParticle> fmSpacePointPFPs =
       FindManyPStrict<recob::PFParticle>(slcSpacePoints, evt, fParams.PFParticleLabel() + slice_tag_suff);
 
+    art::FindManyP<recob::Cluster> fmPFPClusters =
+      FindManyPStrict<recob::Cluster>(fmPFPart, evt, fParams.PFParticleLabel() + slice_tag_suff);
+
+    std::vector<std::vector<art::Ptr<recob::Hit>>> fmPFPartHits;
+    // make Ptr's to clusters for cluster -> other object associations
+    if (fmPFPClusters.isValid()) {
+      for (size_t ipf=0; ipf<fmPFPart.size();++ipf) {
+	std::vector<art::Ptr<recob::Hit>> pfphits;
+	std::vector<art::Ptr<recob::Cluster>> pfclusters = fmPFPClusters.at(ipf);
+	art::FindManyP<recob::Hit> fmCluHits = FindManyPStrict<recob::Hit>(pfclusters, evt, fParams.PFParticleLabel() + slice_tag_suff);
+	for (size_t icl=0; icl<fmCluHits.size();icl++) {
+	  for (auto hit : fmCluHits.at(icl)) {
+	    pfphits.push_back(hit);
+	  }
+	}
+	fmPFPartHits.push_back(pfphits);
+      }
+    }
+
     art::FindManyP<recob::Shower> fmShower =
       FindManyPStrict<recob::Shower>(fmPFPart, evt, fParams.RecoShowerLabel() + slice_tag_suff);
 
@@ -2105,6 +2142,8 @@ void CAFMaker::produce(art::Event& evt) noexcept {
         FillCNNScores(thisParticle, cnnScores, pfp);
       }
 
+      FillPPFNuGraph(*ng2_slice_hit_map_handle[producer], ng2_filter_vec, ng2_semantic_vec, fmPFPartHits.at(iPart), pfp);
+
       if (!thisTrack.empty())  { // it has a track!
         assert(thisTrack.size() == 1);
 
diff --git a/sbncode/CAFMaker/FillReco.cxx b/sbncode/CAFMaker/FillReco.cxx
index f47265c1e..67b8b8f22 100644
--- a/sbncode/CAFMaker/FillReco.cxx
+++ b/sbncode/CAFMaker/FillReco.cxx
@@ -544,6 +544,26 @@ namespace caf
     }
   }
 
+
+  void FillSliceNuGraph(const std::vector<art::Ptr<recob::Hit>> &inputHits,
+			const std::vector<unsigned int> &sliceHitsMap,
+			const std::vector<art::Ptr<anab::FeatureVector<1>>> &ngFilterResult,
+			const std::vector<art::Ptr<anab::FeatureVector<5>>> &ngSemanticResult,
+			caf::SRSlice &slice)
+  {
+
+    //need to double check that the slice processed by NuGraph is the same under consideration
+    std::cout << "sizes=" << inputHits.size() << " " << sliceHitsMap.size() << " " << ngFilterResult.size() << " " << ngSemanticResult.size() << std::endl;
+    unsigned int nHits = inputHits.size();
+    if (nHits==0 || nHits!=sliceHitsMap.size() || inputHits[0].key()!=sliceHitsMap[0]) return;//not the same slice!
+
+    unsigned int npass = 0;
+    for ( unsigned int i = 0; i < nHits; i++ ) {
+      if (ngFilterResult.at(i)->at(0)>0.5) npass++;
+    }
+    slice.ng_filt_pass_frac = float(npass)/nHits;
+  }
+
   //......................................................................
 
   void FillTrackCRTHit(const std::vector<art::Ptr<anab::T0>> &t0match,
@@ -950,6 +970,59 @@ namespace caf
     srpfp.cnnscore.nclusters = cnnscore->nClusters;
   }
 
+  void FillPPFNuGraph(const std::vector<unsigned int> &sliceHitsMap,
+		      const std::vector<art::Ptr<anab::FeatureVector<1>>> &ngFilterResult,
+		      const std::vector<art::Ptr<anab::FeatureVector<5>>> &ngSemanticResult,
+		      const std::vector<art::Ptr<recob::Hit>> &pfpHits,
+		      caf::SRPFP& srpfp,
+		      bool allowEmpty)
+  {
+
+    auto arg_max = [](std::vector<float> const& vec) {
+      return std::distance(vec.begin(), std::max_element(vec.begin(), vec.end()));
+    };
+
+    // the nugraph elements are ordered the same as the sliceHitsMap
+    std::vector<size_t> mappedhits;
+    for (auto& hit : pfpHits) {
+      auto it = std::find(sliceHitsMap.begin(), sliceHitsMap.end(), hit.key());
+      if (it != sliceHitsMap.end()) {
+	size_t index = std::distance(sliceHitsMap.begin(), it);
+	mappedhits.push_back(index);
+      }
+    }
+
+    if (mappedhits.size()>0) {
+      std::vector<float> ng2sempfpcounts(5,0);
+      size_t ng2bkgpfpcount = 0;
+      for (size_t pos : mappedhits) {
+	auto scores = ngSemanticResult.at(pos);
+	std::vector<float> ng2semscores;
+	for (size_t i=0;i<scores->size();i++) ng2semscores.push_back(scores->at(i));
+	size_t sem_label = arg_max(ng2semscores);
+	ng2sempfpcounts[sem_label]++;
+	auto bkgscore = ngFilterResult.at(pos);
+	if (bkgscore->at(0)<0.5) ng2bkgpfpcount++;
+      }
+      srpfp.ng_sem_cat = arg_max(ng2sempfpcounts);
+      srpfp.ng_mip_frac = float(ng2sempfpcounts[0])/pfpHits.size();
+      srpfp.ng_hip_frac = float(ng2sempfpcounts[1])/pfpHits.size();
+      srpfp.ng_shr_frac = float(ng2sempfpcounts[2])/pfpHits.size();
+      srpfp.ng_mhl_frac = float(ng2sempfpcounts[3])/pfpHits.size();
+      srpfp.ng_dif_frac = float(ng2sempfpcounts[4])/pfpHits.size();
+      srpfp.ng_bkg_frac = float(ng2bkgpfpcount)/pfpHits.size();
+    } else {
+      srpfp.ng_sem_cat = -1;
+      srpfp.ng_mip_frac = -1.;
+      srpfp.ng_hip_frac = -1.;
+      srpfp.ng_shr_frac = -1.;
+      srpfp.ng_mhl_frac = -1.;
+      srpfp.ng_dif_frac = -1.;
+      srpfp.ng_bkg_frac = -1.;
+    }
+
+  }
+
   void FillHitVars(const recob::Hit& hit,
                    unsigned producer,
                    const recob::SpacePoint& spacepoint,
diff --git a/sbncode/CAFMaker/FillReco.h b/sbncode/CAFMaker/FillReco.h
index c6df1ab39..5482077f1 100644
--- a/sbncode/CAFMaker/FillReco.h
+++ b/sbncode/CAFMaker/FillReco.h
@@ -20,6 +20,7 @@
 #include "lardataobj/RecoBase/OpFlash.h"
 #include "lardataobj/RecoBase/OpHit.h"
 #include "lardataobj/AnalysisBase/Calorimetry.h"
+#include "lardataobj/AnalysisBase/MVAOutput.h"
 #include "lardataobj/AnalysisBase/ParticleID.h"
 #include "lardataobj/AnalysisBase/T0.h"
 #include "lardataobj/RecoBase/PFParticleMetadata.h"
@@ -104,6 +105,12 @@ namespace caf
                            const std::vector<art::Ptr<recob::SpacePoint>> &inputPoints,
                            caf::SRSlice &slice);
 
+  void FillSliceNuGraph(const std::vector<art::Ptr<recob::Hit>> &inputHits,
+			const std::vector<unsigned int> &sliceHitsMap,
+			const std::vector<art::Ptr<anab::FeatureVector<1>>> &ngFilterResult,
+			const std::vector<art::Ptr<anab::FeatureVector<5>>> &ngSemanticResult,
+			caf::SRSlice &slice);
+
   bool SelectSlice(const caf::SRSlice &slice, bool cut_clear_cosmic);
 
   void FillTrackVars(const recob::Track& track,
@@ -130,6 +137,13 @@ namespace caf
                      caf::SRPFP& srpfp,
                      bool allowEmpty = false);
 
+  void FillPPFNuGraph(const std::vector<unsigned int> &sliceHitsMap,
+		      const std::vector<art::Ptr<anab::FeatureVector<1>>> &ngFilterResult,
+		      const std::vector<art::Ptr<anab::FeatureVector<5>>> &ngSemanticResult,
+		      const std::vector<art::Ptr<recob::Hit>> &pfpHits,
+		      caf::SRPFP& srpfp,
+		      bool allowEmpty= false);
+
   void FillTrackCRTHit(const std::vector<art::Ptr<anab::T0>> &t0match,
                        const std::vector<art::Ptr<sbn::crt::CRTHit>> &hitmatch,
                        bool use_ts0,

From 33f56fbff4b31a34bb4787731269543ee85c99b0 Mon Sep 17 00:00:00 2001
From: Giuseppe Cerati <cerati@fnal.gov>
Date: Thu, 10 Apr 2025 22:35:15 -0500
Subject: [PATCH 2/6] ensure CAF works if NuGraph2 products are not found

---
 sbncode/CAFMaker/CAFMakerParams.h   |  6 +++---
 sbncode/CAFMaker/CAFMaker_module.cc | 16 ++++++++++++----
 sbncode/CAFMaker/FillReco.cxx       |  2 +-
 3 files changed, 16 insertions(+), 8 deletions(-)

diff --git a/sbncode/CAFMaker/CAFMakerParams.h b/sbncode/CAFMaker/CAFMakerParams.h
index 636fcda57..cf4cd7292 100644
--- a/sbncode/CAFMaker/CAFMakerParams.h
+++ b/sbncode/CAFMaker/CAFMakerParams.h
@@ -343,19 +343,19 @@ namespace caf
     Atom<art::InputTag> NuGraphSliceHitLabel {
       Name("NuGraphSliceHitLabel"),
       Comment("Label of NuGraph slice hit map."),
-	art::InputTag("nuslhits")
+      "" //Empty by default, please set to e.g. art::InputTag("nuslhits")
     };
 
     Atom<art::InputTag> NuGraphFilterLabel {
       Name("NuGraphFilterLabel"),
       Comment("Label of NuGraph filter."),
-	art::InputTag("NuGraph","filter")
+      "" //Empty by default, please set to e.g. art::InputTag("NuGraph","filter")
     };
 
     Atom<art::InputTag> NuGraphSemanticLabel {
       Name("NuGraphSemanticLabel"),
       Comment("Label of NuGraph semantic."),
-	art::InputTag("NuGraph","semantic")
+      "" //Empty by default, please set to e.g. art::InputTag("NuGraph","semantic")
     };
 
     Atom<string> OpFlashLabel {
diff --git a/sbncode/CAFMaker/CAFMaker_module.cc b/sbncode/CAFMaker/CAFMaker_module.cc
index 38a6e416c..0e8b88482 100644
--- a/sbncode/CAFMaker/CAFMaker_module.cc
+++ b/sbncode/CAFMaker/CAFMaker_module.cc
@@ -1766,9 +1766,15 @@ void CAFMaker::produce(art::Event& evt) noexcept {
 
     std::vector<art::Ptr<anab::FeatureVector<1>>> ng2_filter_vec;
     std::vector<art::Ptr<anab::FeatureVector<5>>> ng2_semantic_vec;
-    art::fill_ptr_vector(ng2_filter_vec,ng2_filter_handle[producer]);
-    art::fill_ptr_vector(ng2_semantic_vec,ng2_semantic_handle[producer]);
-    FillSliceNuGraph(slcHits,*ng2_slice_hit_map_handle[producer],ng2_filter_vec,ng2_semantic_vec,recslc);
+    if (ng2_filter_handle[producer].isValid()) {
+      art::fill_ptr_vector(ng2_filter_vec,ng2_filter_handle[producer]);
+    }
+    if (ng2_semantic_handle[producer].isValid()) {
+      art::fill_ptr_vector(ng2_semantic_vec,ng2_semantic_handle[producer]);
+    }
+    if (ng2_slice_hit_map_handle[producer].isValid()) {
+      FillSliceNuGraph(slcHits,*ng2_slice_hit_map_handle[producer],ng2_filter_vec,ng2_semantic_vec,recslc);
+    }
 
     art::FindManyP<sbn::OpT0Finder> fmOpT0 =
       FindManyPStrict<sbn::OpT0Finder>(sliceList, evt, fParams.OpT0Label() + slice_tag_suff);
@@ -2142,7 +2148,9 @@ void CAFMaker::produce(art::Event& evt) noexcept {
         FillCNNScores(thisParticle, cnnScores, pfp);
       }
 
-      FillPPFNuGraph(*ng2_slice_hit_map_handle[producer], ng2_filter_vec, ng2_semantic_vec, fmPFPartHits.at(iPart), pfp);
+      if (ng2_slice_hit_map_handle[producer].isValid()) {
+	FillPPFNuGraph(*ng2_slice_hit_map_handle[producer], ng2_filter_vec, ng2_semantic_vec, fmPFPartHits.at(iPart), pfp);
+      }
 
       if (!thisTrack.empty())  { // it has a track!
         assert(thisTrack.size() == 1);
diff --git a/sbncode/CAFMaker/FillReco.cxx b/sbncode/CAFMaker/FillReco.cxx
index 67b8b8f22..1224a10da 100644
--- a/sbncode/CAFMaker/FillReco.cxx
+++ b/sbncode/CAFMaker/FillReco.cxx
@@ -553,7 +553,7 @@ namespace caf
   {
 
     //need to double check that the slice processed by NuGraph is the same under consideration
-    std::cout << "sizes=" << inputHits.size() << " " << sliceHitsMap.size() << " " << ngFilterResult.size() << " " << ngSemanticResult.size() << std::endl;
+    //std::cout << "sizes=" << inputHits.size() << " " << sliceHitsMap.size() << " " << ngFilterResult.size() << " " << ngSemanticResult.size() << std::endl;
     unsigned int nHits = inputHits.size();
     if (nHits==0 || nHits!=sliceHitsMap.size() || inputHits[0].key()!=sliceHitsMap[0]) return;//not the same slice!
 

From 0b5ad313d5a7cb64f0d6fded578cdceac887b05c Mon Sep 17 00:00:00 2001
From: Giuseppe Cerati <cerati@fnal.gov>
Date: Tue, 6 May 2025 12:02:17 -0500
Subject: [PATCH 3/6] address BH comments

---
 sbncode/CAFMaker/CAFMaker_module.cc |  1 +
 sbncode/CAFMaker/FillReco.cxx       | 31 ++++++++++++++---------------
 2 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/sbncode/CAFMaker/CAFMaker_module.cc b/sbncode/CAFMaker/CAFMaker_module.cc
index 0e8b88482..74f08272a 100644
--- a/sbncode/CAFMaker/CAFMaker_module.cc
+++ b/sbncode/CAFMaker/CAFMaker_module.cc
@@ -96,6 +96,7 @@
 #include "lardataobj/RecoBase/Shower.h"
 #include "lardataobj/RecoBase/MCSFitResult.h"
 #include "lardataobj/RecoBase/Cluster.h"
+#include "lardataobj/AnalysisBase/MVAOutput.h"
 
 #include "nusimdata/SimulationBase/MCFlux.h"
 #include "nusimdata/SimulationBase/MCTruth.h"
diff --git a/sbncode/CAFMaker/FillReco.cxx b/sbncode/CAFMaker/FillReco.cxx
index 1224a10da..7dab1547d 100644
--- a/sbncode/CAFMaker/FillReco.cxx
+++ b/sbncode/CAFMaker/FillReco.cxx
@@ -978,10 +978,6 @@ namespace caf
 		      bool allowEmpty)
   {
 
-    auto arg_max = [](std::vector<float> const& vec) {
-      return std::distance(vec.begin(), std::max_element(vec.begin(), vec.end()));
-    };
-
     // the nugraph elements are ordered the same as the sliceHitsMap
     std::vector<size_t> mappedhits;
     for (auto& hit : pfpHits) {
@@ -996,20 +992,23 @@ namespace caf
       std::vector<float> ng2sempfpcounts(5,0);
       size_t ng2bkgpfpcount = 0;
       for (size_t pos : mappedhits) {
-	auto scores = ngSemanticResult.at(pos);
-	std::vector<float> ng2semscores;
-	for (size_t i=0;i<scores->size();i++) ng2semscores.push_back(scores->at(i));
-	size_t sem_label = arg_max(ng2semscores);
-	ng2sempfpcounts[sem_label]++;
 	auto bkgscore = ngFilterResult.at(pos);
-	if (bkgscore->at(0)<0.5) ng2bkgpfpcount++;
+	if (bkgscore->at(0)<0.5) {
+	  ng2bkgpfpcount++;
+	} else {
+	  auto scores = ngSemanticResult.at(pos);
+	  std::vector<float> ng2semscores;
+	  for (size_t i=0;i<scores->size();i++) ng2semscores.push_back(scores->at(i));
+	  size_t sem_label = std::distance(ng2semscores.begin(), std::max_element(ng2semscores.begin(), ng2semscores.end()));//arg_max(ng2semscores);
+	  ng2sempfpcounts[sem_label]++;
+	}
       }
-      srpfp.ng_sem_cat = arg_max(ng2sempfpcounts);
-      srpfp.ng_mip_frac = float(ng2sempfpcounts[0])/pfpHits.size();
-      srpfp.ng_hip_frac = float(ng2sempfpcounts[1])/pfpHits.size();
-      srpfp.ng_shr_frac = float(ng2sempfpcounts[2])/pfpHits.size();
-      srpfp.ng_mhl_frac = float(ng2sempfpcounts[3])/pfpHits.size();
-      srpfp.ng_dif_frac = float(ng2sempfpcounts[4])/pfpHits.size();
+      srpfp.ng_sem_cat = std::distance(ng2sempfpcounts.begin(), std::max_element(ng2sempfpcounts.begin(), ng2sempfpcounts.end()));//arg_max(ng2sempfpcounts);
+      srpfp.ng_mip_frac = (pfpHits.size()>ng2bkgpfpcount ? float(ng2sempfpcounts[0])/(pfpHits.size()-ng2bkgpfpcount) : -1.);
+      srpfp.ng_hip_frac = (pfpHits.size()>ng2bkgpfpcount ? float(ng2sempfpcounts[1])/(pfpHits.size()-ng2bkgpfpcount) : -1.);
+      srpfp.ng_shr_frac = (pfpHits.size()>ng2bkgpfpcount ? float(ng2sempfpcounts[2])/(pfpHits.size()-ng2bkgpfpcount) : -1.);
+      srpfp.ng_mhl_frac = (pfpHits.size()>ng2bkgpfpcount ? float(ng2sempfpcounts[3])/(pfpHits.size()-ng2bkgpfpcount) : -1.);
+      srpfp.ng_dif_frac = (pfpHits.size()>ng2bkgpfpcount ? float(ng2sempfpcounts[4])/(pfpHits.size()-ng2bkgpfpcount) : -1.);
       srpfp.ng_bkg_frac = float(ng2bkgpfpcount)/pfpHits.size();
     } else {
       srpfp.ng_sem_cat = -1;

From b36ce76b7d5f5d255902eb2d1a924b8167c00b52 Mon Sep 17 00:00:00 2001
From: Giuseppe Cerati <cerati@fnal.gov>
Date: Wed, 7 May 2025 13:27:30 -0500
Subject: [PATCH 4/6] fix typo

---
 sbncode/CAFMaker/CAFMaker_module.cc | 2 +-
 sbncode/CAFMaker/FillReco.cxx       | 2 +-
 sbncode/CAFMaker/FillReco.h         | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/sbncode/CAFMaker/CAFMaker_module.cc b/sbncode/CAFMaker/CAFMaker_module.cc
index 74f08272a..948181bf2 100644
--- a/sbncode/CAFMaker/CAFMaker_module.cc
+++ b/sbncode/CAFMaker/CAFMaker_module.cc
@@ -2150,7 +2150,7 @@ void CAFMaker::produce(art::Event& evt) noexcept {
       }
 
       if (ng2_slice_hit_map_handle[producer].isValid()) {
-	FillPPFNuGraph(*ng2_slice_hit_map_handle[producer], ng2_filter_vec, ng2_semantic_vec, fmPFPartHits.at(iPart), pfp);
+	FillPFPNuGraph(*ng2_slice_hit_map_handle[producer], ng2_filter_vec, ng2_semantic_vec, fmPFPartHits.at(iPart), pfp);
       }
 
       if (!thisTrack.empty())  { // it has a track!
diff --git a/sbncode/CAFMaker/FillReco.cxx b/sbncode/CAFMaker/FillReco.cxx
index 0979d93fe..33b435fd9 100644
--- a/sbncode/CAFMaker/FillReco.cxx
+++ b/sbncode/CAFMaker/FillReco.cxx
@@ -970,7 +970,7 @@ namespace caf
     srpfp.cnnscore.nclusters = cnnscore->nClusters;
   }
 
-  void FillPPFNuGraph(const std::vector<unsigned int> &sliceHitsMap,
+  void FillPFPNuGraph(const std::vector<unsigned int> &sliceHitsMap,
 		      const std::vector<art::Ptr<anab::FeatureVector<1>>> &ngFilterResult,
 		      const std::vector<art::Ptr<anab::FeatureVector<5>>> &ngSemanticResult,
 		      const std::vector<art::Ptr<recob::Hit>> &pfpHits,
diff --git a/sbncode/CAFMaker/FillReco.h b/sbncode/CAFMaker/FillReco.h
index 5482077f1..45cf2ea2b 100644
--- a/sbncode/CAFMaker/FillReco.h
+++ b/sbncode/CAFMaker/FillReco.h
@@ -137,7 +137,7 @@ namespace caf
                      caf::SRPFP& srpfp,
                      bool allowEmpty = false);
 
-  void FillPPFNuGraph(const std::vector<unsigned int> &sliceHitsMap,
+  void FillPFPNuGraph(const std::vector<unsigned int> &sliceHitsMap,
 		      const std::vector<art::Ptr<anab::FeatureVector<1>>> &ngFilterResult,
 		      const std::vector<art::Ptr<anab::FeatureVector<5>>> &ngSemanticResult,
 		      const std::vector<art::Ptr<recob::Hit>> &pfpHits,

From 0157111590797da7ce620909cebab78653bce80b Mon Sep 17 00:00:00 2001
From: Giuseppe Cerati <cerati@fnal.gov>
Date: Wed, 7 May 2025 19:00:19 -0500
Subject: [PATCH 5/6] address GP's comments

---
 sbncode/CAFMaker/FillReco.cxx | 38 +++++++++++++++++------------------
 sbncode/CAFMaker/FillReco.h   | 20 ++++++++++++++++++
 2 files changed, 39 insertions(+), 19 deletions(-)

diff --git a/sbncode/CAFMaker/FillReco.cxx b/sbncode/CAFMaker/FillReco.cxx
index 33b435fd9..0106aaf61 100644
--- a/sbncode/CAFMaker/FillReco.cxx
+++ b/sbncode/CAFMaker/FillReco.cxx
@@ -12,6 +12,7 @@
 
 namespace caf
 {
+  const float ng_filter_cut = 0.5;
 
   //......................................................................
   bool SelectSlice(const caf::SRSlice &slice, bool cut_clear_cosmic) {
@@ -544,7 +545,6 @@ namespace caf
     }
   }
 
-
   void FillSliceNuGraph(const std::vector<art::Ptr<recob::Hit>> &inputHits,
 			const std::vector<unsigned int> &sliceHitsMap,
 			const std::vector<art::Ptr<anab::FeatureVector<1>>> &ngFilterResult,
@@ -559,7 +559,7 @@ namespace caf
 
     unsigned int npass = 0;
     for ( unsigned int i = 0; i < nHits; i++ ) {
-      if (ngFilterResult.at(i)->at(0)>0.5) npass++;
+      if (ngFilterResult.at(i)->at(0)>=ng_filter_cut) npass++;
     }
     slice.ng_filt_pass_frac = float(npass)/nHits;
   }
@@ -992,32 +992,32 @@ namespace caf
       std::vector<float> ng2sempfpcounts(5,0);
       size_t ng2bkgpfpcount = 0;
       for (size_t pos : mappedhits) {
-	auto bkgscore = ngFilterResult.at(pos);
-	if (bkgscore->at(0)<0.5) {
+	auto const& bkgscore = ngFilterResult.at(pos);
+	if (bkgscore->at(0)<ng_filter_cut) {
 	  ng2bkgpfpcount++;
 	} else {
-	  auto scores = ngSemanticResult.at(pos);
+	  auto const& scores = ngSemanticResult.at(pos);
 	  std::vector<float> ng2semscores;
 	  for (size_t i=0;i<scores->size();i++) ng2semscores.push_back(scores->at(i));
 	  size_t sem_label = std::distance(ng2semscores.begin(), std::max_element(ng2semscores.begin(), ng2semscores.end()));//arg_max(ng2semscores);
 	  ng2sempfpcounts[sem_label]++;
 	}
       }
-      srpfp.ng_sem_cat = std::distance(ng2sempfpcounts.begin(), std::max_element(ng2sempfpcounts.begin(), ng2sempfpcounts.end()));//arg_max(ng2sempfpcounts);
-      srpfp.ng_mip_frac = (pfpHits.size()>ng2bkgpfpcount ? float(ng2sempfpcounts[0])/(pfpHits.size()-ng2bkgpfpcount) : -1.);
-      srpfp.ng_hip_frac = (pfpHits.size()>ng2bkgpfpcount ? float(ng2sempfpcounts[1])/(pfpHits.size()-ng2bkgpfpcount) : -1.);
-      srpfp.ng_shr_frac = (pfpHits.size()>ng2bkgpfpcount ? float(ng2sempfpcounts[2])/(pfpHits.size()-ng2bkgpfpcount) : -1.);
-      srpfp.ng_mhl_frac = (pfpHits.size()>ng2bkgpfpcount ? float(ng2sempfpcounts[3])/(pfpHits.size()-ng2bkgpfpcount) : -1.);
-      srpfp.ng_dif_frac = (pfpHits.size()>ng2bkgpfpcount ? float(ng2sempfpcounts[4])/(pfpHits.size()-ng2bkgpfpcount) : -1.);
-      srpfp.ng_bkg_frac = float(ng2bkgpfpcount)/pfpHits.size();
+      srpfp.ngscore.sem_cat = SRNuGraphScore::NuGraphCategory(std::distance(ng2sempfpcounts.begin(), std::max_element(ng2sempfpcounts.begin(), ng2sempfpcounts.end())));//arg_max(ng2sempfpcounts);
+      srpfp.ngscore.mip_frac = (pfpHits.size()>ng2bkgpfpcount ? float(ng2sempfpcounts[0])/(pfpHits.size()-ng2bkgpfpcount) : -1.);
+      srpfp.ngscore.hip_frac = (pfpHits.size()>ng2bkgpfpcount ? float(ng2sempfpcounts[1])/(pfpHits.size()-ng2bkgpfpcount) : -1.);
+      srpfp.ngscore.shr_frac = (pfpHits.size()>ng2bkgpfpcount ? float(ng2sempfpcounts[2])/(pfpHits.size()-ng2bkgpfpcount) : -1.);
+      srpfp.ngscore.mhl_frac = (pfpHits.size()>ng2bkgpfpcount ? float(ng2sempfpcounts[3])/(pfpHits.size()-ng2bkgpfpcount) : -1.);
+      srpfp.ngscore.dif_frac = (pfpHits.size()>ng2bkgpfpcount ? float(ng2sempfpcounts[4])/(pfpHits.size()-ng2bkgpfpcount) : -1.);
+      srpfp.ngscore.bkg_frac = float(ng2bkgpfpcount)/pfpHits.size();
     } else {
-      srpfp.ng_sem_cat = -1;
-      srpfp.ng_mip_frac = -1.;
-      srpfp.ng_hip_frac = -1.;
-      srpfp.ng_shr_frac = -1.;
-      srpfp.ng_mhl_frac = -1.;
-      srpfp.ng_dif_frac = -1.;
-      srpfp.ng_bkg_frac = -1.;
+      srpfp.ngscore.sem_cat = SRNuGraphScore::NuGraphCategory::Unset;
+      srpfp.ngscore.mip_frac = -1.;
+      srpfp.ngscore.hip_frac = -1.;
+      srpfp.ngscore.shr_frac = -1.;
+      srpfp.ngscore.mhl_frac = -1.;
+      srpfp.ngscore.dif_frac = -1.;
+      srpfp.ngscore.bkg_frac = -1.;
     }
 
   }
diff --git a/sbncode/CAFMaker/FillReco.h b/sbncode/CAFMaker/FillReco.h
index 45cf2ea2b..efe582756 100644
--- a/sbncode/CAFMaker/FillReco.h
+++ b/sbncode/CAFMaker/FillReco.h
@@ -105,6 +105,16 @@ namespace caf
                            const std::vector<art::Ptr<recob::SpacePoint>> &inputPoints,
                            caf::SRSlice &slice);
 
+  /**
+   * @brief Fills the results from NuGraph at slice level
+   * @param inputHits (pointers to) the hits associated to the slice
+   * @param sliceHitsMap maps position of hits in collection input to NuGraph (slice only) to the one input to Pandora (all gaus hits)
+   * @param ngFilterResult NuGraph filter result, for each hit
+   * @param ngSemanticResult NuGraph semnatic result, for each hit (MIP track, HIP, shower, Michel electron, diffuse activity)
+   * @param[out] slice the destination slice object
+   *
+   * Hits with filter value (`ngFilterResult`) lower than `ng_filter_cut` are counted as background.
+   */
   void FillSliceNuGraph(const std::vector<art::Ptr<recob::Hit>> &inputHits,
 			const std::vector<unsigned int> &sliceHitsMap,
 			const std::vector<art::Ptr<anab::FeatureVector<1>>> &ngFilterResult,
@@ -137,6 +147,16 @@ namespace caf
                      caf::SRPFP& srpfp,
                      bool allowEmpty = false);
 
+  /**
+   * @brief Fills the results from NuGraph at slice level
+   * @param sliceHitsMap maps position of hits in collection input to NuGraph (slice only) to the one input to Pandora (all gaus hits)
+   * @param ngFilterResult NuGraph filter result, for each hit
+   * @param ngSemanticResult NuGraph semnatic result, for each hit (MIP track, HIP, shower, Michel electron, diffuse activity)
+   * @param pfpHits Vector of hits associated to the PFParticle
+   * @param[out] srpfp the destination PFParticle object
+   *
+   * Hits with filter value (`ngFilterResult`) lower than `ng_filter_cut` are counted as background.
+   */
   void FillPFPNuGraph(const std::vector<unsigned int> &sliceHitsMap,
 		      const std::vector<art::Ptr<anab::FeatureVector<1>>> &ngFilterResult,
 		      const std::vector<art::Ptr<anab::FeatureVector<5>>> &ngSemanticResult,

From cae5b11869ac295ad72061d4cd4de77fcd81744c Mon Sep 17 00:00:00 2001
From: Giuseppe Cerati <cerati@fnal.gov>
Date: Wed, 7 May 2025 19:22:29 -0500
Subject: [PATCH 6/6] address GP's comments

---
 sbncode/CAFMaker/FillReco.cxx | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/sbncode/CAFMaker/FillReco.cxx b/sbncode/CAFMaker/FillReco.cxx
index d01cb1d91..d81cb5890 100644
--- a/sbncode/CAFMaker/FillReco.cxx
+++ b/sbncode/CAFMaker/FillReco.cxx
@@ -1058,11 +1058,12 @@ namespace caf
 	}
       }
       srpfp.ngscore.sem_cat = SRNuGraphScore::NuGraphCategory(std::distance(ng2sempfpcounts.begin(), std::max_element(ng2sempfpcounts.begin(), ng2sempfpcounts.end())));//arg_max(ng2sempfpcounts);
-      srpfp.ngscore.mip_frac = (pfpHits.size()>ng2bkgpfpcount ? float(ng2sempfpcounts[0])/(pfpHits.size()-ng2bkgpfpcount) : -1.);
-      srpfp.ngscore.hip_frac = (pfpHits.size()>ng2bkgpfpcount ? float(ng2sempfpcounts[1])/(pfpHits.size()-ng2bkgpfpcount) : -1.);
-      srpfp.ngscore.shr_frac = (pfpHits.size()>ng2bkgpfpcount ? float(ng2sempfpcounts[2])/(pfpHits.size()-ng2bkgpfpcount) : -1.);
-      srpfp.ngscore.mhl_frac = (pfpHits.size()>ng2bkgpfpcount ? float(ng2sempfpcounts[3])/(pfpHits.size()-ng2bkgpfpcount) : -1.);
-      srpfp.ngscore.dif_frac = (pfpHits.size()>ng2bkgpfpcount ? float(ng2sempfpcounts[4])/(pfpHits.size()-ng2bkgpfpcount) : -1.);
+      size_t nonBkgHits = (pfpHits.size() > ng2bkgpfpcount ? pfpHits.size()-ng2bkgpfpcount : 0);
+      srpfp.ngscore.mip_frac = (nonBkgHits>0 ? float(ng2sempfpcounts[0])/nonBkgHits : -1.);
+      srpfp.ngscore.hip_frac = (nonBkgHits>0 ? float(ng2sempfpcounts[1])/nonBkgHits : -1.);
+      srpfp.ngscore.shr_frac = (nonBkgHits>0 ? float(ng2sempfpcounts[2])/nonBkgHits : -1.);
+      srpfp.ngscore.mhl_frac = (nonBkgHits>0 ? float(ng2sempfpcounts[3])/nonBkgHits : -1.);
+      srpfp.ngscore.dif_frac = (nonBkgHits>0 ? float(ng2sempfpcounts[4])/nonBkgHits : -1.);
       srpfp.ngscore.bkg_frac = float(ng2bkgpfpcount)/pfpHits.size();
     } else {
       srpfp.ngscore.sem_cat = SRNuGraphScore::NuGraphCategory::Unset;