From 73995f722102a88c13961cd62a73053d334b2ca4 Mon Sep 17 00:00:00 2001
From: Andrew Edmonds <aedmonds@york.cuny.edu>
Date: Mon, 27 Jul 2026 09:25:55 -0500
Subject: [PATCH 01/16] Initial bits of the subrun stuff

---
 fcl/prolog.fcl                 |  6 ++++++
 src/EventNtupleMaker_module.cc | 17 +++++++++++++++++
 2 files changed, 23 insertions(+)

diff --git a/fcl/prolog.fcl b/fcl/prolog.fcl
index 4b8b68d8..bc37ae20 100644
--- a/fcl/prolog.fcl
+++ b/fcl/prolog.fcl
@@ -389,6 +389,12 @@ EventNtupleMaker : {
   mcsteps : {
     surfaceStepsTag : "compressRecoMCs"
   }
+
+#  subruns : {
+#    genEventCount : { fill : true inputTag : "genCounter" totalsHistogram : true }
+#    procEventCount : { fill : true inputTag : "" totalsHistogram : true }
+#    cosmicLivetime : { fill : true inputTag : "" totalsHistogram : true }
+#  }
 }
 # instance for processing trigger (digitization) output from simulation
 EventNtupleMakerTTMC : {
diff --git a/src/EventNtupleMaker_module.cc b/src/EventNtupleMaker_module.cc
index 94991962..8845255a 100644
--- a/src/EventNtupleMaker_module.cc
+++ b/src/EventNtupleMaker_module.cc
@@ -10,6 +10,7 @@
 #include "Offline/MCDataProducts/inc/CaloClusterMC.hh"
 #include "Offline/MCDataProducts/inc/CaloHitMC.hh"
 #include "Offline/MCDataProducts/inc/ProtonBunchTimeMC.hh"
+#include "Offline/MCDataProducts/inc/GenEventCount.hh"
 #include "Offline/RecoDataProducts/inc/KalSeed.hh"
 #include "Offline/RecoDataProducts/inc/KalSeedAssns.hh"
 #include "Offline/RecoDataProducts/inc/CaloCluster.hh"
@@ -311,6 +312,7 @@ namespace mu2e {
       TTree* _ntuple;
       TH1I* _hVersion;
       TH1I* _hProcEvents;
+      TTree* _subrunInfo;
       // general event info branch
       EventInfo _einfo;
       EventInfoMC _einfomc;
@@ -440,6 +442,9 @@ namespace mu2e {
       // for trigger branch:
       bool firstEvent = true;
 
+      // For subrun ntuple
+      long _genEventCount;
+
       // ── Gating helpers ─────────────────────────────────────────────────────
       // Event-level MC gate (simParticles, mcTrajectories, primaryParticle).
       // Also gates tracker MC and CRV MC.
@@ -710,10 +715,22 @@ namespace mu2e {
         _ntuple->Branch(("mcsteps_"+inst+".").c_str(),&_stepPointMCInfos[icoll],_buffsize,_splitlevel);
       }
     }
+
+    // Subrun tree
+    _subrunInfo = tfs->make<TTree>("subruns","Mu2e SubRun Ntuple");
+    //    _subrunInfo->Branch("run"
+    //    _subrunInfo->Branch("subrun"
+    _subrunInfo->Branch("genEventCount", &_genEventCount, _buffsize, _splitlevel);
   }
 
   void EventNtupleMaker::beginSubRun(const art::SubRun & subrun ) {
     _infoStructHelper.updateSubRun();
+
+    art::Handle<GenEventCount> genEventCountHandle;
+    subrun.getByLabel<GenEventCount>("genCounter", genEventCountHandle);
+    _genEventCount = genEventCountHandle->count();
+    std::cout << "AE: count = " << _genEventCount << std::endl;
+    _subrunInfo->Fill();
   }
 
   void EventNtupleMaker::resolveCrvPlanes() {

From 544be2f5cd3767dbfbdbbbcc2a00cfb718f61930 Mon Sep 17 00:00:00 2001
From: Andrew Edmonds <aedmonds@york.cuny.edu>
Date: Mon, 27 Jul 2026 11:07:25 -0500
Subject: [PATCH 02/16] Add SubRun info

---
 inc/SubRunInfo.hh              | 16 ++++++++++++++++
 src/EventNtupleMaker_module.cc | 16 ++++++++++------
 src/classes.h                  |  1 +
 src/classes_def.xml            |  1 +
 4 files changed, 28 insertions(+), 6 deletions(-)
 create mode 100644 inc/SubRunInfo.hh

diff --git a/inc/SubRunInfo.hh b/inc/SubRunInfo.hh
new file mode 100644
index 00000000..8e4a9b70
--- /dev/null
+++ b/inc/SubRunInfo.hh
@@ -0,0 +1,16 @@
+//
+// SubRunInfo: subrun information
+// Andy Edmonds (2026)
+//
+#ifndef SubRunInfo_HH
+#define SubRunInfo_HH
+#include <string>
+namespace mu2e
+{
+  struct SubRunInfo {
+    int run = 0; // run number
+    int subrun = 0; // subrun number
+    void reset() {*this = SubRunInfo(); }
+  };
+}
+#endif
diff --git a/src/EventNtupleMaker_module.cc b/src/EventNtupleMaker_module.cc
index 8845255a..6204f7ca 100644
--- a/src/EventNtupleMaker_module.cc
+++ b/src/EventNtupleMaker_module.cc
@@ -86,6 +86,7 @@
 #include "EventNtuple/inc/MCStepSummaryInfo.hh"
 #include "EventNtuple/inc/CaloDigiMCInfo.hh"
 #include "Offline/MCDataProducts/inc/CaloShowerSim.hh"
+#include "EventNtuple/inc/SubRunInfo.hh"
 
 // C++ includes.
 #include <iostream>
@@ -312,7 +313,7 @@ namespace mu2e {
       TTree* _ntuple;
       TH1I* _hVersion;
       TH1I* _hProcEvents;
-      TTree* _subrunInfo;
+      TTree* _subrunNtuple;
       // general event info branch
       EventInfo _einfo;
       EventInfoMC _einfomc;
@@ -443,6 +444,7 @@ namespace mu2e {
       bool firstEvent = true;
 
       // For subrun ntuple
+      mu2e::SubRunInfo _srinfo;
       long _genEventCount;
 
       // ── Gating helpers ─────────────────────────────────────────────────────
@@ -717,20 +719,22 @@ namespace mu2e {
     }
 
     // Subrun tree
-    _subrunInfo = tfs->make<TTree>("subruns","Mu2e SubRun Ntuple");
-    //    _subrunInfo->Branch("run"
-    //    _subrunInfo->Branch("subrun"
-    _subrunInfo->Branch("genEventCount", &_genEventCount, _buffsize, _splitlevel);
+    _subrunNtuple = tfs->make<TTree>("subrunNtuple","Mu2e SubRun Ntuple");
+    _subrunNtuple->Branch("srinfo", &_srinfo, _buffsize, _splitlevel);
+    _subrunNtuple->Branch("genEventCount", &_genEventCount, _buffsize, _splitlevel);
   }
 
   void EventNtupleMaker::beginSubRun(const art::SubRun & subrun ) {
     _infoStructHelper.updateSubRun();
 
+    _srinfo.run = subrun.run();
+    _srinfo.subrun = subrun.subRun();
+
     art::Handle<GenEventCount> genEventCountHandle;
     subrun.getByLabel<GenEventCount>("genCounter", genEventCountHandle);
     _genEventCount = genEventCountHandle->count();
     std::cout << "AE: count = " << _genEventCount << std::endl;
-    _subrunInfo->Fill();
+    _subrunNtuple->Fill();
   }
 
   void EventNtupleMaker::resolveCrvPlanes() {
diff --git a/src/classes.h b/src/classes.h
index 95f93a4f..356b6341 100644
--- a/src/classes.h
+++ b/src/classes.h
@@ -37,3 +37,4 @@
 #include "EventNtuple/inc/MVAResultInfo.hh"
 #include "EventNtuple/inc/SurfaceStepInfo.hh"
 #include "EventNtuple/inc/TrigInfo.hh"
+#include "EventNtuple/inc/SubRunInfo.hh"
diff --git a/src/classes_def.xml b/src/classes_def.xml
index c086ee96..b4177d73 100644
--- a/src/classes_def.xml
+++ b/src/classes_def.xml
@@ -78,4 +78,5 @@
   <class name="std::vector<std::vector<mu2e::SurfaceStepInfo> >" />
   <class name="mu2e::TrigInfo" />
   <class name="std::vector<mu2e::TrigInfo>" />
+  <class name="mu2e::SubRunInfo" />
 </lcgdict>

From 08e28bf007ed13d0a56c65d72bca11859a3c7a87 Mon Sep 17 00:00:00 2001
From: Andrew Edmonds <aedmonds@york.cuny.edu>
Date: Mon, 27 Jul 2026 11:18:07 -0500
Subject: [PATCH 03/16] First version of fcl configuration

---
 fcl/prolog.fcl                 |  8 ++++++--
 src/EventNtupleMaker_module.cc | 34 +++++++++++++++++++++++++++++-----
 2 files changed, 35 insertions(+), 7 deletions(-)

diff --git a/fcl/prolog.fcl b/fcl/prolog.fcl
index bc37ae20..b6cb54c9 100644
--- a/fcl/prolog.fcl
+++ b/fcl/prolog.fcl
@@ -390,8 +390,12 @@ EventNtupleMaker : {
     surfaceStepsTag : "compressRecoMCs"
   }
 
-#  subruns : {
-#    genEventCount : { fill : true inputTag : "genCounter" totalsHistogram : true }
+  subruns : {
+    makeNtuple : true
+    genEventCount : { inputTag : "genCounter" fillNtuple : true }
+  }
+#    makeTotalsHists : true
+
 #    procEventCount : { fill : true inputTag : "" totalsHistogram : true }
 #    cosmicLivetime : { fill : true inputTag : "" totalsHistogram : true }
 #  }
diff --git a/src/EventNtupleMaker_module.cc b/src/EventNtupleMaker_module.cc
index 6204f7ca..3fc52d66 100644
--- a/src/EventNtupleMaker_module.cc
+++ b/src/EventNtupleMaker_module.cc
@@ -265,6 +265,25 @@ namespace mu2e {
         fhicl::Table<MCConfig> mc{Name("mc"), Comment("CRV MC filling options")};
       };
 
+      // Configuration for specific subrun quantities
+      struct SubRunBranchConfig {
+        using Name=fhicl::Name;
+        using Comment=fhicl::Comment;
+
+        fhicl::Atom<art::InputTag> inputTag{Name("inputTag"), Comment("InputTag for subrun quantity")};
+        fhicl::Atom<bool> fillNtuple{Name("fillNtuple"), Comment("True/false to add this quantity to the ntuple")};
+      };
+
+      // Overal configuration for subrun ntuple and histograms
+      struct SubRunConfig {
+        using Name=fhicl::Name;
+        using Comment=fhicl::Comment;
+
+        fhicl::Atom<bool> makeNtuple{Name("makeNtuple"), Comment("True/false of whether to make the subrun ntuple")};
+        fhicl::Table<SubRunBranchConfig> genEventCount{Name("genEventCount"), Comment("Number of generated events (MC)")};
+      };
+
+
       struct Config {
         using Name=fhicl::Name;
         using Comment=fhicl::Comment;
@@ -295,6 +314,7 @@ namespace mu2e {
         fhicl::Table<HelixConfig>       helices     {Name("helices"),     Comment("Helix seed branches config")};
         fhicl::Table<TimeClusterConfig> timeclusters{Name("timeclusters"),Comment("Time cluster branch config")};
         fhicl::Table<MCStepsConfig>     mcsteps     {Name("mcsteps"),     Comment("MC step collection branches config")};
+        fhicl::Table<SubRunConfig>      subruns     {Name("subruns"),     Comment("SubRun ntuple/histogram config")};
       };
       typedef art::EDAnalyzer::Table<Config> Parameters;
 
@@ -719,9 +739,11 @@ namespace mu2e {
     }
 
     // Subrun tree
-    _subrunNtuple = tfs->make<TTree>("subrunNtuple","Mu2e SubRun Ntuple");
-    _subrunNtuple->Branch("srinfo", &_srinfo, _buffsize, _splitlevel);
-    _subrunNtuple->Branch("genEventCount", &_genEventCount, _buffsize, _splitlevel);
+    if (_conf.subruns().makeNtuple()) {
+      _subrunNtuple = tfs->make<TTree>("subrunNtuple","Mu2e SubRun Ntuple");
+      _subrunNtuple->Branch("srinfo", &_srinfo, _buffsize, _splitlevel);
+      _subrunNtuple->Branch("genEventCount", &_genEventCount, _buffsize, _splitlevel);
+    }
   }
 
   void EventNtupleMaker::beginSubRun(const art::SubRun & subrun ) {
@@ -733,8 +755,10 @@ namespace mu2e {
     art::Handle<GenEventCount> genEventCountHandle;
     subrun.getByLabel<GenEventCount>("genCounter", genEventCountHandle);
     _genEventCount = genEventCountHandle->count();
-    std::cout << "AE: count = " << _genEventCount << std::endl;
-    _subrunNtuple->Fill();
+
+    if (_conf.subruns().makeNtuple()) {
+      _subrunNtuple->Fill();
+    }
   }
 
   void EventNtupleMaker::resolveCrvPlanes() {

From c6ab3e78f0b5066fb454a4ca300330c11b2878ac Mon Sep 17 00:00:00 2001
From: Andrew Edmonds <aedmonds@york.cuny.edu>
Date: Mon, 27 Jul 2026 11:27:03 -0500
Subject: [PATCH 04/16] Make sure genEventCount branch respects switch

---
 src/EventNtupleMaker_module.cc | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/EventNtupleMaker_module.cc b/src/EventNtupleMaker_module.cc
index 3fc52d66..180376bd 100644
--- a/src/EventNtupleMaker_module.cc
+++ b/src/EventNtupleMaker_module.cc
@@ -742,7 +742,11 @@ namespace mu2e {
     if (_conf.subruns().makeNtuple()) {
       _subrunNtuple = tfs->make<TTree>("subrunNtuple","Mu2e SubRun Ntuple");
       _subrunNtuple->Branch("srinfo", &_srinfo, _buffsize, _splitlevel);
-      _subrunNtuple->Branch("genEventCount", &_genEventCount, _buffsize, _splitlevel);
+
+      if (_conf.subruns().genEventCount().fillNtuple()) {
+        _subrunNtuple->Branch("genEventCount", &_genEventCount, _buffsize, _splitlevel);
+      }
+      // check whether to make a totals histogram as well
     }
   }
 

From b2bc6a8653ac0377c87f56fe80cd7cde483517bd Mon Sep 17 00:00:00 2001
From: Andrew Edmonds <aedmonds@york.cuny.edu>
Date: Mon, 27 Jul 2026 11:39:34 -0500
Subject: [PATCH 05/16] Add totals histogram for GenEventCount

---
 fcl/prolog.fcl                 |  4 ++--
 src/EventNtupleMaker_module.cc | 12 +++++++++++-
 2 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/fcl/prolog.fcl b/fcl/prolog.fcl
index b6cb54c9..41de5974 100644
--- a/fcl/prolog.fcl
+++ b/fcl/prolog.fcl
@@ -392,9 +392,9 @@ EventNtupleMaker : {
 
   subruns : {
     makeNtuple : true
-    genEventCount : { inputTag : "genCounter" fillNtuple : true }
+    makeTotalsHistograms : true
+    genEventCount : { inputTag : "genCounter" fillNtuple : true fillTotalsHistogram : true}
   }
-#    makeTotalsHists : true
 
 #    procEventCount : { fill : true inputTag : "" totalsHistogram : true }
 #    cosmicLivetime : { fill : true inputTag : "" totalsHistogram : true }
diff --git a/src/EventNtupleMaker_module.cc b/src/EventNtupleMaker_module.cc
index 180376bd..62c65bd6 100644
--- a/src/EventNtupleMaker_module.cc
+++ b/src/EventNtupleMaker_module.cc
@@ -272,6 +272,7 @@ namespace mu2e {
 
         fhicl::Atom<art::InputTag> inputTag{Name("inputTag"), Comment("InputTag for subrun quantity")};
         fhicl::Atom<bool> fillNtuple{Name("fillNtuple"), Comment("True/false to add this quantity to the ntuple")};
+        fhicl::Atom<bool> fillTotalsHistogram{Name("fillTotalsHistogram"), Comment("True/false to make a totals histogram for this quantity")};
       };
 
       // Overal configuration for subrun ntuple and histograms
@@ -280,6 +281,7 @@ namespace mu2e {
         using Comment=fhicl::Comment;
 
         fhicl::Atom<bool> makeNtuple{Name("makeNtuple"), Comment("True/false of whether to make the subrun ntuple")};
+        fhicl::Atom<bool> makeTotalsHistograms{Name("makeTotalsHistograms"), Comment("True/false of whether to make the totals histograms")};
         fhicl::Table<SubRunBranchConfig> genEventCount{Name("genEventCount"), Comment("Number of generated events (MC)")};
       };
 
@@ -334,6 +336,7 @@ namespace mu2e {
       TH1I* _hVersion;
       TH1I* _hProcEvents;
       TTree* _subrunNtuple;
+      TH1I* _hGenEventCount;
       // general event info branch
       EventInfo _einfo;
       EventInfoMC _einfomc;
@@ -746,7 +749,11 @@ namespace mu2e {
       if (_conf.subruns().genEventCount().fillNtuple()) {
         _subrunNtuple->Branch("genEventCount", &_genEventCount, _buffsize, _splitlevel);
       }
-      // check whether to make a totals histogram as well
+    }
+    if (_conf.subruns().makeTotalsHistograms()) {
+      if (_conf.subruns().genEventCount().fillTotalsHistogram()) {
+        _hGenEventCount = tfs->make<TH1I>("n_gen_events", "total number of generated events", 1,0,1);
+      }
     }
   }
 
@@ -759,6 +766,9 @@ namespace mu2e {
     art::Handle<GenEventCount> genEventCountHandle;
     subrun.getByLabel<GenEventCount>("genCounter", genEventCountHandle);
     _genEventCount = genEventCountHandle->count();
+    if (_conf.subruns().genEventCount().fillTotalsHistogram()) {
+      _hGenEventCount->Fill(0.0, genEventCountHandle->count());
+    }
 
     if (_conf.subruns().makeNtuple()) {
       _subrunNtuple->Fill();

From a11ce8476110a6677c71ad36477f55b79da513ba Mon Sep 17 00:00:00 2001
From: Andrew Edmonds <aedmonds@york.cuny.edu>
Date: Mon, 27 Jul 2026 11:52:45 -0500
Subject: [PATCH 06/16] Add an include flag for the subrun quantities

---
 fcl/prolog.fcl                 |  2 +-
 src/EventNtupleMaker_module.cc | 18 +++++++++++-------
 2 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/fcl/prolog.fcl b/fcl/prolog.fcl
index 41de5974..5b6c3d04 100644
--- a/fcl/prolog.fcl
+++ b/fcl/prolog.fcl
@@ -393,7 +393,7 @@ EventNtupleMaker : {
   subruns : {
     makeNtuple : true
     makeTotalsHistograms : true
-    genEventCount : { inputTag : "genCounter" fillNtuple : true fillTotalsHistogram : true}
+    genEventCount : { include : false inputTag : "genCounter" fillNtuple : true fillTotalsHistogram : true}
   }
 
 #    procEventCount : { fill : true inputTag : "" totalsHistogram : true }
diff --git a/src/EventNtupleMaker_module.cc b/src/EventNtupleMaker_module.cc
index 62c65bd6..97e9e7d5 100644
--- a/src/EventNtupleMaker_module.cc
+++ b/src/EventNtupleMaker_module.cc
@@ -270,6 +270,7 @@ namespace mu2e {
         using Name=fhicl::Name;
         using Comment=fhicl::Comment;
 
+        fhicl::Atom<bool> include{Name("include"), Comment("True/false to include this quantity or not (master switch)")};
         fhicl::Atom<art::InputTag> inputTag{Name("inputTag"), Comment("InputTag for subrun quantity")};
         fhicl::Atom<bool> fillNtuple{Name("fillNtuple"), Comment("True/false to add this quantity to the ntuple")};
         fhicl::Atom<bool> fillTotalsHistogram{Name("fillTotalsHistogram"), Comment("True/false to make a totals histogram for this quantity")};
@@ -746,12 +747,12 @@ namespace mu2e {
       _subrunNtuple = tfs->make<TTree>("subrunNtuple","Mu2e SubRun Ntuple");
       _subrunNtuple->Branch("srinfo", &_srinfo, _buffsize, _splitlevel);
 
-      if (_conf.subruns().genEventCount().fillNtuple()) {
+      if (_conf.subruns().genEventCount().include() && _conf.subruns().genEventCount().fillNtuple()) {
         _subrunNtuple->Branch("genEventCount", &_genEventCount, _buffsize, _splitlevel);
       }
     }
     if (_conf.subruns().makeTotalsHistograms()) {
-      if (_conf.subruns().genEventCount().fillTotalsHistogram()) {
+      if (_conf.subruns().genEventCount().include() && _conf.subruns().genEventCount().fillTotalsHistogram()) {
         _hGenEventCount = tfs->make<TH1I>("n_gen_events", "total number of generated events", 1,0,1);
       }
     }
@@ -763,11 +764,14 @@ namespace mu2e {
     _srinfo.run = subrun.run();
     _srinfo.subrun = subrun.subRun();
 
-    art::Handle<GenEventCount> genEventCountHandle;
-    subrun.getByLabel<GenEventCount>("genCounter", genEventCountHandle);
-    _genEventCount = genEventCountHandle->count();
-    if (_conf.subruns().genEventCount().fillTotalsHistogram()) {
-      _hGenEventCount->Fill(0.0, genEventCountHandle->count());
+    if (_conf.subruns().genEventCount().include()) {
+      art::Handle<GenEventCount> genEventCountHandle;
+      subrun.getByLabel<GenEventCount>(_conf.subruns().genEventCount().inputTag(), genEventCountHandle);
+
+      _genEventCount = genEventCountHandle->count();
+      if (_conf.subruns().genEventCount().fillTotalsHistogram()) {
+        _hGenEventCount->Fill(0.0, genEventCountHandle->count());
+      }
     }
 
     if (_conf.subruns().makeNtuple()) {

From a125da9031e75ada9ce91f556d1cebc133690a7b Mon Sep 17 00:00:00 2001
From: Andrew Edmonds <aedmonds@york.cuny.edu>
Date: Mon, 27 Jul 2026 12:04:06 -0500
Subject: [PATCH 07/16] Add number of processed events to subrun ntuple. Also
 move filling to a new endSubRun function

---
 fcl/prolog.fcl                 |  4 ++--
 src/EventNtupleMaker_module.cc | 28 +++++++++++++++++++++++++---
 2 files changed, 27 insertions(+), 5 deletions(-)

diff --git a/fcl/prolog.fcl b/fcl/prolog.fcl
index 5b6c3d04..824487a4 100644
--- a/fcl/prolog.fcl
+++ b/fcl/prolog.fcl
@@ -393,10 +393,10 @@ EventNtupleMaker : {
   subruns : {
     makeNtuple : true
     makeTotalsHistograms : true
-    genEventCount : { include : false inputTag : "genCounter" fillNtuple : true fillTotalsHistogram : true}
+    genEventCount : { include : true inputTag : "genCounter" fillNtuple : true fillTotalsHistogram : true}
+    procEventCount : { include : true inputTag : "" fillNtuple : true fillTotalsHistogram : true }
   }
 
-#    procEventCount : { fill : true inputTag : "" totalsHistogram : true }
 #    cosmicLivetime : { fill : true inputTag : "" totalsHistogram : true }
 #  }
 }
diff --git a/src/EventNtupleMaker_module.cc b/src/EventNtupleMaker_module.cc
index 97e9e7d5..ffa99943 100644
--- a/src/EventNtupleMaker_module.cc
+++ b/src/EventNtupleMaker_module.cc
@@ -284,6 +284,7 @@ namespace mu2e {
         fhicl::Atom<bool> makeNtuple{Name("makeNtuple"), Comment("True/false of whether to make the subrun ntuple")};
         fhicl::Atom<bool> makeTotalsHistograms{Name("makeTotalsHistograms"), Comment("True/false of whether to make the totals histograms")};
         fhicl::Table<SubRunBranchConfig> genEventCount{Name("genEventCount"), Comment("Number of generated events (MC)")};
+        fhicl::Table<SubRunBranchConfig> procEventCount{Name("procEventCount"), Comment("Number of processed events")};
       };
 
 
@@ -327,6 +328,7 @@ namespace mu2e {
       void beginJob() override;
       void beginSubRun(const art::SubRun & subrun ) override;
       void analyze(const art::Event& e) override;
+      void endSubRun(const art::SubRun & subrun ) override;
 
     private:
 
@@ -335,9 +337,9 @@ namespace mu2e {
       // main TTree
       TTree* _ntuple;
       TH1I* _hVersion;
-      TH1I* _hProcEvents;
       TTree* _subrunNtuple;
       TH1I* _hGenEventCount;
+      TH1I* _hProcEventCount;
       // general event info branch
       EventInfo _einfo;
       EventInfoMC _einfomc;
@@ -470,6 +472,7 @@ namespace mu2e {
       // For subrun ntuple
       mu2e::SubRunInfo _srinfo;
       long _genEventCount;
+      long _procEventCount;
 
       // ── Gating helpers ─────────────────────────────────────────────────────
       // Event-level MC gate (simParticles, mcTrajectories, primaryParticle).
@@ -598,7 +601,6 @@ namespace mu2e {
     _hVersion->GetXaxis()->SetBinLabel(1, "major"); _hVersion->SetBinContent(1, 6);
     _hVersion->GetXaxis()->SetBinLabel(2, "minor"); _hVersion->SetBinContent(2, 12);
     _hVersion->GetXaxis()->SetBinLabel(3, "patch"); _hVersion->SetBinContent(3, 1);
-    _hProcEvents = tfs->make<TH1I>("n_proc_events", "number of processed events", 1,0,1);
     // event info branch
     _ntuple->Branch("evtinfo",&_einfo,_buffsize,_splitlevel);
     if (fillEventMC()) {
@@ -750,11 +752,19 @@ namespace mu2e {
       if (_conf.subruns().genEventCount().include() && _conf.subruns().genEventCount().fillNtuple()) {
         _subrunNtuple->Branch("genEventCount", &_genEventCount, _buffsize, _splitlevel);
       }
+
+      if (_conf.subruns().procEventCount().include() && _conf.subruns().procEventCount().fillNtuple()) {
+        _subrunNtuple->Branch("procEventCount", &_procEventCount, _buffsize, _splitlevel);
+      }
+
     }
     if (_conf.subruns().makeTotalsHistograms()) {
       if (_conf.subruns().genEventCount().include() && _conf.subruns().genEventCount().fillTotalsHistogram()) {
         _hGenEventCount = tfs->make<TH1I>("n_gen_events", "total number of generated events", 1,0,1);
       }
+      if (_conf.subruns().procEventCount().include() && _conf.subruns().procEventCount().fillTotalsHistogram()) {
+        _hProcEventCount = tfs->make<TH1I>("n_proc_events", "total number of processed events", 1,0,1);
+      }
     }
   }
 
@@ -764,6 +774,10 @@ namespace mu2e {
     _srinfo.run = subrun.run();
     _srinfo.subrun = subrun.subRun();
 
+  }
+
+  void EventNtupleMaker::endSubRun(const art::SubRun & subrun ) {
+
     if (_conf.subruns().genEventCount().include()) {
       art::Handle<GenEventCount> genEventCountHandle;
       subrun.getByLabel<GenEventCount>(_conf.subruns().genEventCount().inputTag(), genEventCountHandle);
@@ -777,6 +791,14 @@ namespace mu2e {
     if (_conf.subruns().makeNtuple()) {
       _subrunNtuple->Fill();
     }
+
+    if (_conf.subruns().procEventCount().include()) {
+      if (_conf.subruns().procEventCount().fillTotalsHistogram()) {
+        _hProcEventCount->Fill(0.0, _procEventCount);
+      }
+    }
+
+    _procEventCount = 0; // reset procEventCount every subrun
   }
 
   void EventNtupleMaker::resolveCrvPlanes() {
@@ -1230,7 +1252,7 @@ namespace mu2e {
     if(fill) {
       _ntuple->Fill();
     }
-    _hProcEvents->Fill(0);
+    _procEventCount++;
   }
 
 

From 07b6689180fe395b39459fe991816acd7f4b048a Mon Sep 17 00:00:00 2001
From: Andrew Edmonds <aedmonds@york.cuny.edu>
Date: Mon, 27 Jul 2026 12:15:09 -0500
Subject: [PATCH 08/16] Add cosmic livetime to subrun ntuple

---
 fcl/prolog.fcl                 |  5 ++---
 src/EventNtupleMaker_module.cc | 23 +++++++++++++++++++++++
 2 files changed, 25 insertions(+), 3 deletions(-)

diff --git a/fcl/prolog.fcl b/fcl/prolog.fcl
index 824487a4..9663496a 100644
--- a/fcl/prolog.fcl
+++ b/fcl/prolog.fcl
@@ -390,15 +390,14 @@ EventNtupleMaker : {
     surfaceStepsTag : "compressRecoMCs"
   }
 
+  # -- SubRun quantities ---------------------------------------------------
   subruns : {
     makeNtuple : true
     makeTotalsHistograms : true
     genEventCount : { include : true inputTag : "genCounter" fillNtuple : true fillTotalsHistogram : true}
     procEventCount : { include : true inputTag : "" fillNtuple : true fillTotalsHistogram : true }
+    cosmicLivetime : { include : true inputTag : "generate" fillNtuple : true fillTotalsHistogram : true }
   }
-
-#    cosmicLivetime : { fill : true inputTag : "" totalsHistogram : true }
-#  }
 }
 # instance for processing trigger (digitization) output from simulation
 EventNtupleMakerTTMC : {
diff --git a/src/EventNtupleMaker_module.cc b/src/EventNtupleMaker_module.cc
index ffa99943..5bacfbf5 100644
--- a/src/EventNtupleMaker_module.cc
+++ b/src/EventNtupleMaker_module.cc
@@ -11,6 +11,7 @@
 #include "Offline/MCDataProducts/inc/CaloHitMC.hh"
 #include "Offline/MCDataProducts/inc/ProtonBunchTimeMC.hh"
 #include "Offline/MCDataProducts/inc/GenEventCount.hh"
+#include "Offline/MCDataProducts/inc/CosmicLivetime.hh"
 #include "Offline/RecoDataProducts/inc/KalSeed.hh"
 #include "Offline/RecoDataProducts/inc/KalSeedAssns.hh"
 #include "Offline/RecoDataProducts/inc/CaloCluster.hh"
@@ -285,6 +286,7 @@ namespace mu2e {
         fhicl::Atom<bool> makeTotalsHistograms{Name("makeTotalsHistograms"), Comment("True/false of whether to make the totals histograms")};
         fhicl::Table<SubRunBranchConfig> genEventCount{Name("genEventCount"), Comment("Number of generated events (MC)")};
         fhicl::Table<SubRunBranchConfig> procEventCount{Name("procEventCount"), Comment("Number of processed events")};
+        fhicl::Table<SubRunBranchConfig> cosmicLivetime{Name("cosmicLivetime"), Comment("Cosmic livetime [s]")};
       };
 
 
@@ -337,9 +339,11 @@ namespace mu2e {
       // main TTree
       TTree* _ntuple;
       TH1I* _hVersion;
+      // subrun quantities
       TTree* _subrunNtuple;
       TH1I* _hGenEventCount;
       TH1I* _hProcEventCount;
+      TH1F* _hCosmicLivetime;
       // general event info branch
       EventInfo _einfo;
       EventInfoMC _einfomc;
@@ -473,6 +477,7 @@ namespace mu2e {
       mu2e::SubRunInfo _srinfo;
       long _genEventCount;
       long _procEventCount;
+      float _cosmicLivetime;
 
       // ── Gating helpers ─────────────────────────────────────────────────────
       // Event-level MC gate (simParticles, mcTrajectories, primaryParticle).
@@ -757,6 +762,10 @@ namespace mu2e {
         _subrunNtuple->Branch("procEventCount", &_procEventCount, _buffsize, _splitlevel);
       }
 
+      if (_conf.subruns().cosmicLivetime().include() && _conf.subruns().cosmicLivetime().fillNtuple()) {
+        _subrunNtuple->Branch("cosmicLivetime", &_cosmicLivetime, _buffsize, _splitlevel);
+      }
+
     }
     if (_conf.subruns().makeTotalsHistograms()) {
       if (_conf.subruns().genEventCount().include() && _conf.subruns().genEventCount().fillTotalsHistogram()) {
@@ -765,6 +774,10 @@ namespace mu2e {
       if (_conf.subruns().procEventCount().include() && _conf.subruns().procEventCount().fillTotalsHistogram()) {
         _hProcEventCount = tfs->make<TH1I>("n_proc_events", "total number of processed events", 1,0,1);
       }
+      if (_conf.subruns().cosmicLivetime().include() && _conf.subruns().cosmicLivetime().fillTotalsHistogram()) {
+        _hCosmicLivetime = tfs->make<TH1F>("cosmic_livetime", "total cosmic livetime [sec]", 1,0,1);
+      }
+
     }
   }
 
@@ -788,6 +801,16 @@ namespace mu2e {
       }
     }
 
+    if (_conf.subruns().cosmicLivetime().include()) {
+      art::Handle<CosmicLivetime> cosmicLivetimeHandle;
+      subrun.getByLabel<CosmicLivetime>(_conf.subruns().cosmicLivetime().inputTag(), cosmicLivetimeHandle);
+
+      _cosmicLivetime = cosmicLivetimeHandle->liveTime();
+      if (_conf.subruns().cosmicLivetime().fillTotalsHistogram()) {
+        _hCosmicLivetime->Fill(0.0, cosmicLivetimeHandle->liveTime());
+      }
+    }
+
     if (_conf.subruns().makeNtuple()) {
       _subrunNtuple->Fill();
     }

From 581b8ef82c919904ce4390472005223ba2f7ce03 Mon Sep 17 00:00:00 2001
From: Andrew Edmonds <aedmonds@york.cuny.edu>
Date: Mon, 27 Jul 2026 12:29:10 -0500
Subject: [PATCH 09/16] Don't try to fill histograms if they weren't originally
 made

---
 src/EventNtupleMaker_module.cc | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/EventNtupleMaker_module.cc b/src/EventNtupleMaker_module.cc
index 5bacfbf5..5f7bd378 100644
--- a/src/EventNtupleMaker_module.cc
+++ b/src/EventNtupleMaker_module.cc
@@ -796,7 +796,7 @@ namespace mu2e {
       subrun.getByLabel<GenEventCount>(_conf.subruns().genEventCount().inputTag(), genEventCountHandle);
 
       _genEventCount = genEventCountHandle->count();
-      if (_conf.subruns().genEventCount().fillTotalsHistogram()) {
+      if (_conf.subruns().makeTotalsHistograms() && _conf.subruns().genEventCount().fillTotalsHistogram()) {
         _hGenEventCount->Fill(0.0, genEventCountHandle->count());
       }
     }
@@ -806,7 +806,7 @@ namespace mu2e {
       subrun.getByLabel<CosmicLivetime>(_conf.subruns().cosmicLivetime().inputTag(), cosmicLivetimeHandle);
 
       _cosmicLivetime = cosmicLivetimeHandle->liveTime();
-      if (_conf.subruns().cosmicLivetime().fillTotalsHistogram()) {
+      if (_conf.subruns().makeTotalsHistograms() && _conf.subruns().cosmicLivetime().fillTotalsHistogram()) {
         _hCosmicLivetime->Fill(0.0, cosmicLivetimeHandle->liveTime());
       }
     }
@@ -816,7 +816,7 @@ namespace mu2e {
     }
 
     if (_conf.subruns().procEventCount().include()) {
-      if (_conf.subruns().procEventCount().fillTotalsHistogram()) {
+      if (_conf.subruns().makeTotalsHistograms() && _conf.subruns().procEventCount().fillTotalsHistogram()) {
         _hProcEventCount->Fill(0.0, _procEventCount);
       }
     }

From d66f47c225e3954beaf16926b738f49435d1b4ce Mon Sep 17 00:00:00 2001
From: Andrew Edmonds <aedmonds@york.cuny.edu>
Date: Mon, 27 Jul 2026 12:31:14 -0500
Subject: [PATCH 10/16] Add a printout of the totals histograms into
 checkEventNtuple script

---
 bin/checkEventNtuple | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/bin/checkEventNtuple b/bin/checkEventNtuple
index 5899ec45..c73e6816 100755
--- a/bin/checkEventNtuple
+++ b/bin/checkEventNtuple
@@ -38,6 +38,19 @@ def main():
                     print("For trigger definitions, please contact the Trigger group.")
                 else:
                     print("{} tree does not exist in {}...".format(treename, filename))
+
+                # Print totals histograms
+                print("\nTotals histograms:")
+                totals_histnames = ["n_gen_events", "n_proc_events", "cosmic_livetime"]
+                any_found = False
+                for totals_histname in totals_histnames:
+                    if (folder.GetListOfKeys().Contains(totals_histname)):
+                        h = f.Get(foldername+"/"+totals_histname)
+                        print(" - {} contains {:.02f} entries".format(totals_histname, h.GetBinContent(1)))
+                        any_found = True
+                if not any_found:
+                    print(" - no totals histograms (e.g. n_proc_events) found")
+
             else:
                 print("{}/ folder does not exist in {}".format(foldername, filename))
         except OSError:

From bedf0db16e7fd3d484aacf3656bf199f756043b8 Mon Sep 17 00:00:00 2001
From: Andrew Edmonds <aedmonds@york.cuny.edu>
Date: Mon, 27 Jul 2026 12:50:05 -0500
Subject: [PATCH 11/16] Update README

---
 README.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index caef2b2c..3267241a 100644
--- a/README.md
+++ b/README.md
@@ -24,6 +24,8 @@ A [list of branches is available](./doc/branches.md)
 
 The help understand what all the branches and leaves mean, we have an [```ntuplehelper```](doc/ntuplehelper.md) tool
 
+Alongside the EventNtuple itself we have a SubRunNtuple that contains subrun-level quantities. These quantites are also summed into the "totals histograms".
+
 ## How to Check the EventNtuple
 You can get some basic information about the EventNtuple file useing ```checkEventNtuple``` like so:
 
@@ -31,7 +33,7 @@ You can get some basic information about the EventNtuple file useing ```checkEve
 checkEventNtuple file1.root file2.root
 ```
 
-This will print the version number (for versions after v6.3.0) and the trigger branches in the file (for versions after v6.8.0)
+This will print the version number (for versions after v6.3.0) and the trigger branches in the file (for versions after v6.8.0). It will also print the number of entries in the "totals histograms" if any exist (for versions after v6.13.0)
 
 
 ## How to Analyze an EventNtuple

From ae86e0cd517705ccf5a977f90c0f8a96d24eb9ae Mon Sep 17 00:00:00 2001
From: Andrew Edmonds <aedmonds@york.cuny.edu>
Date: Mon, 27 Jul 2026 15:13:03 -0500
Subject: [PATCH 12/16] Update fcls with new parameters

---
 fcl/from_dig-OnSpill.fcl       | 4 ++++
 fcl/from_dig-calo.fcl          | 2 ++
 fcl/from_dig-mockdata.fcl      | 4 +++-
 fcl/from_mcs-DeCalib.fcl       | 1 +
 fcl/from_mcs-ceSimReco.fcl     | 1 -
 fcl/from_mcs-mockdata.fcl      | 4 +++-
 fcl/from_mcs-mockdata_noMC.fcl | 1 -
 fcl/from_mcs-primary.fcl       | 2 +-
 fcl/prolog.fcl                 | 4 +---
 9 files changed, 15 insertions(+), 8 deletions(-)

diff --git a/fcl/from_dig-OnSpill.fcl b/fcl/from_dig-OnSpill.fcl
index f8b54a19..f2b513a4 100644
--- a/fcl/from_dig-OnSpill.fcl
+++ b/fcl/from_dig-OnSpill.fcl
@@ -56,3 +56,7 @@ physics.analyzers.EventNtupleTTMCMpr.trk.mc.kalSeedMCAssns : "TTMprDeKSFMC"
 end_paths : [ EndPath ]
 physics.trigger_paths : [ "TrigPath" ]
 services.TFileService.fileName: "nts.owner.trkana-triggerMC.version.sequencer.root"
+physics.analyzers.EventNtupleTTMCApr.subruns.cosmicLivetime.include : false
+physics.analyzers.EventNtupleTTMCTpr.subruns.cosmicLivetime.include : false
+physics.analyzers.EventNtupleTTMCCpr.subruns.cosmicLivetime.include : false
+physics.analyzers.EventNtupleTTMCMpr.subruns.cosmicLivetime.include : false
diff --git a/fcl/from_dig-calo.fcl b/fcl/from_dig-calo.fcl
index d3318d7d..b1dcd364 100644
--- a/fcl/from_dig-calo.fcl
+++ b/fcl/from_dig-calo.fcl
@@ -54,3 +54,5 @@ physics.analyzers.EventNtuple.calo.mc.fillDigiSim : true
 physics.analyzers.EventNtuple.calo.mc.fillDigis : true
 
 services.TFileService.fileName: "nts.owner.description.version.sequencer.root"
+
+physics.analyzers.EventNtuple.subruns.cosmicLivetime.include : false
diff --git a/fcl/from_dig-mockdata.fcl b/fcl/from_dig-mockdata.fcl
index af375ddd..a34489b1 100644
--- a/fcl/from_dig-mockdata.fcl
+++ b/fcl/from_dig-mockdata.fcl
@@ -36,7 +36,7 @@ physics.EventNtuplePath : [
   @sequence::Reconstruction.OnSpillPath,
   @sequence::EventNtuple.Path
 ]
-physics.EventNtupleEndPath : [ @sequence::EventNtuple.EndPathNoMC ]
+physics.EventNtupleEndPath : [ @sequence::EventNtuple.EndPath ]
 physics.analyzers.EventNtuple.SelectEvents : [ "EventNtuplePath" ]
 
 physics.trigger_paths : [ EventNtuplePath ]
@@ -54,3 +54,5 @@ services.TFileService.fileName: "nts.owner.description.version.sequencer.root"
 #include "Production/JobConfig/reco/drop_trigger.fcl"
 
 #include "Production/Validation/database.fcl"
+
+physics.analyzers.EventNtuple.subruns.cosmicLivetime.include : false
diff --git a/fcl/from_mcs-DeCalib.fcl b/fcl/from_mcs-DeCalib.fcl
index b2c528e8..4c1476df 100644
--- a/fcl/from_mcs-DeCalib.fcl
+++ b/fcl/from_mcs-DeCalib.fcl
@@ -24,3 +24,4 @@ physics.end_paths : [ EndPath ]
 physics.producers.TrkQualDe.KalSeedPtrCollection : "MergeKKDeCalib"
 services.TimeTracker.printSummary: true
 services.TFileService.fileName: "nts.owner.EventNtupleDeCalib.version.sequence.root"
+physics.analyzers.EventNtuple.subruns.cosmicLivetime.include : false
diff --git a/fcl/from_mcs-ceSimReco.fcl b/fcl/from_mcs-ceSimReco.fcl
index c32c7550..67ae1310 100644
--- a/fcl/from_mcs-ceSimReco.fcl
+++ b/fcl/from_mcs-ceSimReco.fcl
@@ -4,4 +4,3 @@ physics.analyzers.EventNtuple.trk.fits : [ @local::De ]
 physics.analyzers.EventNtuple.trk.fits[0].branchname : "trk"
 physics.analyzers.EventNtuple.FillTriggerInfo : false
 physics.EventNtuplePath : [ MergeKKDe, PBIWeight, TrkQualDe, TrkPIDDe ]
-physics.EventNtupleEndPath : [ EventNtuple, genCountLogger ]
diff --git a/fcl/from_mcs-mockdata.fcl b/fcl/from_mcs-mockdata.fcl
index 04f965fb..60b32434 100644
--- a/fcl/from_mcs-mockdata.fcl
+++ b/fcl/from_mcs-mockdata.fcl
@@ -16,7 +16,7 @@ physics :
 }
 
 physics.EventNtuplePath : [ @sequence::EventNtuple.Path ]
-physics.EventNtupleEndPath : [ @sequence::EventNtuple.EndPathNoMC ]
+physics.EventNtupleEndPath : [ @sequence::EventNtuple.EndPath ]
 
 physics.trigger_paths : [ EventNtuplePath ]
 physics.end_paths : [ EventNtupleEndPath ]
@@ -24,3 +24,5 @@ physics.end_paths : [ EventNtupleEndPath ]
 #include "Production/JobConfig/common/epilog.fcl"
 services.TFileService.fileName: "nts.owner.description.version.sequencer.root"
 
+physics.analyzers.EventNtuple.subruns.genEventCount.include : false
+physics.analyzers.EventNtuple.subruns.cosmicLivetime.include : false
diff --git a/fcl/from_mcs-mockdata_noMC.fcl b/fcl/from_mcs-mockdata_noMC.fcl
index 72698c77..e4b08dd0 100644
--- a/fcl/from_mcs-mockdata_noMC.fcl
+++ b/fcl/from_mcs-mockdata_noMC.fcl
@@ -4,4 +4,3 @@ physics.analyzers.EventNtuple.mc.fill : false
 physics.analyzers.EventNtuple.calo.mc.fill : false
 
 physics.EventNtuplePath : [ @sequence::EventNtuple.PathNoMC ]
-physics.EventNtupleEndPath : [ @sequence::EventNtuple.EndPathNoMC ]
diff --git a/fcl/from_mcs-primary.fcl b/fcl/from_mcs-primary.fcl
index e9650a82..21e5605e 100644
--- a/fcl/from_mcs-primary.fcl
+++ b/fcl/from_mcs-primary.fcl
@@ -1,3 +1,3 @@
 #include "EventNtuple/fcl/from_mcs-mockdata.fcl"
 
-physics.EventNtupleEndPath : [ @sequence::EventNtuple.EndPath ] # adds back genCountLogger
+physics.analyzers.EventNtuple.subruns.genEventCount.include : true
diff --git a/fcl/prolog.fcl b/fcl/prolog.fcl
index 9663496a..f809b366 100644
--- a/fcl/prolog.fcl
+++ b/fcl/prolog.fcl
@@ -434,7 +434,6 @@ EventNtuple : {
 
   analyzers : {
     EventNtuple : { @table::EventNtupleMaker  }
-    genCountLogger : @local::genCountLogger
   }
 
   #  TrigSequence : [ PBIWeight, @sequence::TrkQualProducersPath, @sequence::TrkPIDProducersPath]
@@ -443,8 +442,7 @@ EventNtuple : {
   PathOff : [ @sequence::MergeKKOffSpillPath ]
   PathSeparate : [ @sequence::MergeKKSeparatePath, PBIWeight, @sequence::TrkQualProducersPath]
   PathNoMC : [ @sequence::MergeKKProducersPath, TrkQualAll, TrkPIDAll ]
-  EndPath : [ EventNtuple, genCountLogger ]
-  EndPathNoMC : [ EventNtuple ]
+  EndPath : [ EventNtuple ]
 
 }
 

From bdbabf98a9952367438964d9769b1c07f257bc8c Mon Sep 17 00:00:00 2001
From: Andrew Edmonds <aedmonds@york.cuny.edu>
Date: Thu, 30 Jul 2026 08:32:20 -0500
Subject: [PATCH 13/16] Add genEventCount and cosmicLivetime counting to
 extracted datasets

---
 fcl/from_mcs-extracted.fcl | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/fcl/from_mcs-extracted.fcl b/fcl/from_mcs-extracted.fcl
index 330f0efd..b1f020bc 100644
--- a/fcl/from_mcs-extracted.fcl
+++ b/fcl/from_mcs-extracted.fcl
@@ -4,5 +4,7 @@ physics.EventNtuplePath : [ @sequence::EventNtuple.PathExt ] # path for extracte
 physics.analyzers.EventNtuple.trk.fits : [ @local::Ext ]
 physics.analyzers.EventNtuple.FitType : KinematicLine
 physics.analyzers.EventNtuple.trk.fillTrkQual : false
+physics.analyzers.EventNtuple.subruns.genEventCount.include : true
+physics.analyzers.EventNtuple.subruns.cosmicLivetime.include : true
 
 services.GeometryService.inputFile: "Production/JobConfig/cosmic/geom_cosmic_extracted.txt"

From 5e844f252159cd355cf9f8577780101133d5e520 Mon Sep 17 00:00:00 2001
From: Andrew Edmonds <aedmonds@york.cuny.edu>
Date: Thu, 30 Jul 2026 08:33:41 -0500
Subject: [PATCH 14/16] Add copilots work for implementing subrun accessing
 into rooutil

---
 rooutil/README.md                   |  41 +++++--
 rooutil/examples/SubRunCounting.C   |  21 ++++
 rooutil/inc/BranchUtils.hh          |  13 +++
 rooutil/inc/Event.hh                |  10 +-
 rooutil/inc/RooUtil.hh              | 168 ++++++++++++++++++++++++----
 rooutil/inc/SubRun.hh               |  27 +++++
 validation/test_rooutil_examples.sh |   2 +-
 7 files changed, 242 insertions(+), 40 deletions(-)
 create mode 100644 rooutil/examples/SubRunCounting.C
 create mode 100644 rooutil/inc/BranchUtils.hh
 create mode 100644 rooutil/inc/SubRun.hh

diff --git a/rooutil/README.md b/rooutil/README.md
index 54af35a7..7e2649ad 100644
--- a/rooutil/README.md
+++ b/rooutil/README.md
@@ -3,17 +3,18 @@
 ## Table of Contents
 1. [Introduction](#Introduction)
 2. [```RooUtil``` Class](#RooUtil-Class)
-3. [The ```Event``` Class](#The-Event-Class)
-4. [User-Friendly Classes](#User-Friendly-Classes)
-5. [Accessing User-Friendly Classes](#Accessing-User-Friendly-Classes)
-6. [Cut Functions](#Cut-Functions)
-7. [Common Cut Functions](#Common-Cut-Functions)
-8. [Combining Cut Function](#Combining-Cut-Functions)
-9. [Creating Ntuples From EventNtuple](#Creating-Ntuples-From-EventNtuple)
-10. [```roodask```](#roodask)
-11. [Speed Optimizations](#Speed-Optimizations)
-12. [Debugging](#Debugging)
-13. [For Developers](#For-Developers)
+3. [SubRun Data and Totals](#SubRun-Data-and-Totals)
+4. [The ```Event``` Class](#The-Event-Class)
+5. [User-Friendly Classes](#User-Friendly-Classes)
+6. [Accessing User-Friendly Classes](#Accessing-User-Friendly-Classes)
+7. [Cut Functions](#Cut-Functions)
+8. [Common Cut Functions](#Common-Cut-Functions)
+9. [Combining Cut Function](#Combining-Cut-Functions)
+10. [Creating Ntuples From EventNtuple](#Creating-Ntuples-From-EventNtuple)
+11. [```roodask```](#roodask)
+12. [Speed Optimizations](#Speed-Optimizations)
+13. [Debugging](#Debugging)
+14. [For Developers](#For-Developers)
 
 ## Introduction
 
@@ -29,6 +30,24 @@ The constructor takes two arguments:
 * ```filename``` can be the name of a single ROOT file (ending in ```.root```) or a list of ROOT files
 * (optional) ```treename``` the name of the tree
 
+## SubRun Data and Totals
+
+RooUtil loads the optional ```EventNtuple/subrunNtuple``` independently of the event tree. Each entry is represented by a ```SubRun``` object with the ```srinfo``` run/subrun identifier and any configured ```genEventCount```, ```procEventCount```, and ```cosmicLivetime``` quantities.
+
+```
+RooUtil util(filename);
+for (int i_subrun = 0; i_subrun < util.GetNSubRuns(); ++i_subrun) {
+  const auto& subrun = util.GetSubRun(i_subrun);
+  std::cout << subrun.srinfo->run << ":" << subrun.srinfo->subrun << std::endl;
+}
+```
+
+Use ```FindSubRun(run, subrun)``` to retrieve the SubRun corresponding to an event. It returns ```nullptr``` when the requested run/subrun is unavailable. ```GetSubRunIndices(cut)``` returns the indices of entries passing a function with signature ```bool cut(const SubRun&)```. ```CreateOutputSubRunNtuple()``` and ```FillOutputSubRunNtuple()``` create a reduced SubRun tree.
+
+The one-bin totals histograms are summed across every input file. ```GetTotal(name)``` returns ```std::optional<double>```, so a missing or incomplete total is distinct from a valid zero. The available names are ```n_gen_events```, ```n_proc_events```, and ```cosmic_livetime```. ```GetGeneratedEvents()```, ```GetProcessedEvents()```, and ```GetCosmicLivetime()``` are convenience accessors; ```GetRate(count)``` returns ```count / cosmic_livetime``` when a nonzero livetime is available. ```GetNProcEvents()``` remains available for compatibility and returns ```-1``` when the processed-event total is unavailable.
+
+Example: [SubRunCounting.C](./examples/SubRunCounting.C).
+
 ## The Event Class
 All branches and leaves can be accessed through the ```Event``` class like so:
 
diff --git a/rooutil/examples/SubRunCounting.C b/rooutil/examples/SubRunCounting.C
new file mode 100644
index 00000000..fdfdeae0
--- /dev/null
+++ b/rooutil/examples/SubRunCounting.C
@@ -0,0 +1,21 @@
+#include "EventNtuple/rooutil/inc/RooUtil.hh"
+
+#include <iostream>
+
+using namespace rooutil;
+
+void SubRunCounting(std::string filename) {
+  RooUtil util(filename);
+
+  std::cout << filename << " contains " << util.GetNSubRuns() << " subruns" << std::endl;
+  for (int i_subrun = 0; i_subrun < util.GetNSubRuns(); ++i_subrun) {
+    const auto& subrun = util.GetSubRun(i_subrun);
+    std::cout << "run " << subrun.srinfo->run << ", subrun " << subrun.srinfo->subrun;
+    if (subrun.has_proc_event_count) std::cout << ": " << subrun.procEventCount << " processed events";
+    std::cout << std::endl;
+  }
+
+  if (const auto processed_events = util.GetProcessedEvents()) {
+    std::cout << "Total processed events: " << *processed_events << std::endl;
+  }
+}
diff --git a/rooutil/inc/BranchUtils.hh b/rooutil/inc/BranchUtils.hh
new file mode 100644
index 00000000..3a382231
--- /dev/null
+++ b/rooutil/inc/BranchUtils.hh
@@ -0,0 +1,13 @@
+#ifndef BranchUtils_hh_
+#define BranchUtils_hh_
+
+#include "TChain.h"
+
+namespace rooutil {
+  inline bool CheckForBranch(TChain* ntuple, const char* branch_name, void* address = nullptr) {
+    if (ntuple->GetBranch(branch_name) == nullptr || ntuple->GetBranchStatus(branch_name) == 0) return false;
+    if (address != nullptr) ntuple->SetBranchAddress(branch_name, address);
+    return true;
+  }
+} // namespace rooutil
+#endif
diff --git a/rooutil/inc/Event.hh b/rooutil/inc/Event.hh
index e8789f3e..a7205bd6 100644
--- a/rooutil/inc/Event.hh
+++ b/rooutil/inc/Event.hh
@@ -47,8 +47,7 @@
 #include "EventNtuple/rooutil/inc/CaloCluster.hh"
 #include "EventNtuple/rooutil/inc/Trigger.hh"
 #include "EventNtuple/rooutil/inc/CaloHit.hh"
-
-#include "TChain.h"
+#include "EventNtuple/rooutil/inc/BranchUtils.hh"
 
 namespace rooutil {
   struct Event {
@@ -100,13 +99,6 @@ namespace rooutil {
       CheckForBranch(ntuple, "mcsteps_virtualdetector", &this->mcsteps_virtualdetector);
     }
 
-    // Check if a branch exists in the TChain, and optionally set its address
-    bool CheckForBranch(TChain* ntuple, const char* branch_name, void* address = nullptr) {
-      if(ntuple->GetBranch(branch_name) == nullptr || ntuple->GetBranchStatus(branch_name) == 0) return false;
-      if(address != nullptr) ntuple->SetBranchAddress(branch_name, address);
-      return true;
-    }
-
     // Add trigger branches and store the path name information
     void AddTriggerInfo(TChain* ntuple) {
       trigger.SetTrigInfo(&triginfo); // pointer to the underlying trigger data read in event-by-event
diff --git a/rooutil/inc/RooUtil.hh b/rooutil/inc/RooUtil.hh
index 0ba2cdd4..993ab791 100644
--- a/rooutil/inc/RooUtil.hh
+++ b/rooutil/inc/RooUtil.hh
@@ -2,25 +2,30 @@
 #define RooUtil_hh_
 
 #include <fstream>
+#include <map>
+#include <optional>
+#include <set>
+#include <stdexcept>
 
 #include "TFile.h"
 #include "TTree.h"
 #include "TH1I.h"
 
 #include "EventNtuple/rooutil/inc/Event.hh"
+#include "EventNtuple/rooutil/inc/SubRun.hh"
 
 namespace rooutil {
   class RooUtil {
   public:
-    RooUtil(std::string filename, bool debug = false, std::string treename = "EventNtuple/ntuple") : debug(debug), n_proc_events(0) {
+    RooUtil(std::string filename, bool debug = false, std::string treename = "EventNtuple/ntuple") : debug(debug) {
       ntuple = new TChain(treename.c_str());
+      subrun_ntuple = new TChain("EventNtuple/subrunNtuple");
 
       // Check if the given filename contains .root at the end
       std::string root_suffix = ".root";
-      if (filename.compare(filename.size() - root_suffix.size(), root_suffix.size(), root_suffix) == 0) {
-        ntuple->Add(filename.c_str());
+      if (filename.size() >= root_suffix.size() && filename.compare(filename.size() - root_suffix.size(), root_suffix.size(), root_suffix) == 0) {
+        AddFile(filename);
         SetVersionNumber(filename);
-        SetNProcessedEvents(filename);
       }
       else { //  assume its a file list
         std::ifstream filelist(filename);
@@ -29,13 +34,13 @@ namespace rooutil {
           std::string line;
           bool first_line = true;
           while (std::getline(filelist, line)) {
-            ntuple->Add(line.c_str());
+            if (line.empty()) continue;
+            AddFile(line);
 
             if (first_line) {
               SetVersionNumber(line);
               first_line = false;
             }
-            SetNProcessedEvents(line);
           }
           filelist.close();
         } else {
@@ -44,6 +49,7 @@ namespace rooutil {
       }
 
       event = new Event(ntuple);
+      subrun = new SubRun(subrun_ntuple);
     }
 
     void Debug(bool dbg) { debug = dbg; }
@@ -68,21 +74,63 @@ namespace rooutil {
       delete file;
     }
 
-    void SetNProcessedEvents(std::string filename) {
-      TFile* file = new TFile(filename.c_str(), "READ");
-      TH1I* hProcEvents = (TH1I*) file->Get("EventNtuple/n_proc_events");
-      if (!hProcEvents) {
-        std::cout << "Warning: this EventNtuple file does not contain the n_proc_events histogram. It is either v06_09_02 or older. This is just a warning..." << std::endl;
+    void AddFile(const std::string& filename) {
+      ntuple->Add(filename.c_str());
+      TFile file(filename.c_str(), "READ");
+      if (!file.IsZombie() && file.Get("EventNtuple/subrunNtuple") != nullptr) {
+        subrun_ntuple->Add(filename.c_str());
       }
-      else {
-        n_proc_events += hProcEvents->GetBinContent(1);
+      SetTotals(filename);
+    }
+
+    void SetTotals(const std::string& filename) {
+      TFile* file = new TFile(filename.c_str(), "READ");
+      for (const auto& total_name : TotalNames()) {
+        TH1* histogram = dynamic_cast<TH1*>(file->Get(("EventNtuple/" + total_name).c_str()));
+        if (histogram == nullptr) {
+          incomplete_totals.insert(total_name);
+          continue;
+        }
+        totals[total_name] += histogram->GetBinContent(1);
       }
       file->Close();
       delete file;
     }
 
     int GetNEvents() { return ntuple->GetEntries(); }
-    int GetNProcEvents() { return n_proc_events; }
+    int GetNProcEvents() {
+      const auto total = GetTotal("n_proc_events");
+      return total ? static_cast<int>(*total) : -1;
+    }
+
+    std::optional<double> GetTotal(const std::string& total_name) const {
+      if (incomplete_totals.count(total_name) != 0) return std::nullopt;
+      const auto total = totals.find(total_name);
+      if (total == totals.end()) return std::nullopt;
+      return total->second;
+    }
+
+    bool HasTotal(const std::string& total_name) const {
+      return GetTotal(total_name).has_value();
+    }
+
+    std::vector<std::string> GetAvailableTotals() const {
+      std::vector<std::string> available_totals;
+      for (const auto& total_name : TotalNames()) {
+        if (HasTotal(total_name)) available_totals.push_back(total_name);
+      }
+      return available_totals;
+    }
+
+    std::optional<double> GetGeneratedEvents() const { return GetTotal("n_gen_events"); }
+    std::optional<double> GetProcessedEvents() const { return GetTotal("n_proc_events"); }
+    std::optional<double> GetCosmicLivetime() const { return GetTotal("cosmic_livetime"); }
+
+    std::optional<double> GetRate(double count) const {
+      const auto livetime = GetCosmicLivetime();
+      if (!livetime || *livetime == 0.0) return std::nullopt;
+      return count / *livetime;
+    }
 
     Event& GetEvent(int i_event) {
       if (debug) { std::cout << "RooUtil::GetEvent(): Getting event " << i_event << std::endl; }
@@ -95,6 +143,33 @@ namespace rooutil {
       return *event;
     }
 
+    int GetNSubRuns() { return subrun_ntuple->GetEntries(); }
+
+    SubRun& GetSubRun(int i_subrun) {
+      if (i_subrun < 0 || i_subrun >= GetNSubRuns()) {
+        throw std::out_of_range("RooUtil::GetSubRun(): SubRun index is out of range");
+      }
+      subrun_ntuple->GetEntry(i_subrun);
+      return *subrun;
+    }
+
+    SubRun* FindSubRun(int run, int subrun_number) {
+      BuildSubRunIndex();
+      const auto entry = subrun_indices.find(std::make_pair(run, subrun_number));
+      if (entry == subrun_indices.end()) return nullptr;
+      return &GetSubRun(entry->second);
+    }
+
+    using SubRunCut = bool (*)(const SubRun&);
+
+    std::vector<int> GetSubRunIndices(SubRunCut cut) {
+      std::vector<int> selected_subruns;
+      for (int i_subrun = 0; i_subrun < GetNSubRuns(); ++i_subrun) {
+        if (cut(GetSubRun(i_subrun))) selected_subruns.push_back(i_subrun);
+      }
+      return selected_subruns;
+    }
+
     void TurnOffBranch(const std::string& branchname) {
       ntuple->SetBranchStatus(branchname.c_str(), 0);
     }
@@ -117,9 +192,22 @@ namespace rooutil {
     void TurnOnAllBranches() {
       TurnOnBranch("*");
     }
+    void TurnOffSubRunBranch(const std::string& branchname) {
+      subrun_ntuple->SetBranchStatus(branchname.c_str(), 0);
+    }
+    void TurnOnSubRunBranch(const std::string& branchname) {
+      subrun_ntuple->SetBranchStatus(branchname.c_str(), 1);
+    }
+    void TurnOffAllSubRunBranches() {
+      TurnOffSubRunBranch("*");
+    }
+    void TurnOnAllSubRunBranches() {
+      TurnOnSubRunBranch("*");
+    }
 
     void CreateOutputEventNtuple(TFile* outfile) {
-      auto dir = outfile->mkdir("EventNtuple");
+      auto dir = outfile->GetDirectory("EventNtuple");
+      if (dir == nullptr) dir = outfile->mkdir("EventNtuple");
       dir->cd();
       output_ntuple = new TTree("ntuple", "reduced ntuple");
 
@@ -172,22 +260,64 @@ namespace rooutil {
       if (event->mcsteps_virtualdetector) { output_ntuple->Branch("mcsteps_virtualdetector", event->mcsteps_virtualdetector); }
 
       // Write out histograms from input to output
-      hVersion->Write();
+      if (hVersion != nullptr) hVersion->Write();
     }
 
     void FillOutputEventNtuple() {
       output_ntuple->Fill();
     }
 
+    void CreateOutputSubRunNtuple(TFile* outfile) {
+      auto dir = outfile->GetDirectory("EventNtuple");
+      if (dir == nullptr) dir = outfile->mkdir("EventNtuple");
+      dir->cd();
+      output_subrun_ntuple = new TTree("subrunNtuple", "reduced subrun ntuple");
+
+      if (subrun->has_srinfo) { output_subrun_ntuple->Branch("srinfo", subrun->srinfo); }
+      if (subrun->has_gen_event_count) { output_subrun_ntuple->Branch("genEventCount", &subrun->genEventCount); }
+      if (subrun->has_proc_event_count) { output_subrun_ntuple->Branch("procEventCount", &subrun->procEventCount); }
+      if (subrun->has_cosmic_livetime) { output_subrun_ntuple->Branch("cosmicLivetime", &subrun->cosmicLivetime); }
+    }
+
+    void FillOutputSubRunNtuple() {
+      output_subrun_ntuple->Fill();
+    }
+
   private:
+    static const std::vector<std::string>& TotalNames() {
+      static const std::vector<std::string> total_names{
+        "n_gen_events", "n_proc_events", "cosmic_livetime"
+      };
+      return total_names;
+    }
+
+    void BuildSubRunIndex() {
+      if (subrun_index_built) return;
+      if (!subrun->has_srinfo) {
+        subrun_index_built = true;
+        return;
+      }
+      for (int i_subrun = 0; i_subrun < GetNSubRuns(); ++i_subrun) {
+        const auto& current_subrun = GetSubRun(i_subrun);
+        subrun_indices[std::make_pair(current_subrun.srinfo->run, current_subrun.srinfo->subrun)] = i_subrun;
+      }
+      subrun_index_built = true;
+    }
+
     TChain* ntuple;
     Event* event; // holds all the variables for SetBranchAddress
+    TChain* subrun_ntuple;
+    SubRun* subrun;
     bool debug;
 
-    TH1I* hVersion;
-    int n_proc_events;
+    TH1I* hVersion = nullptr;
+    std::map<std::string, double> totals;
+    std::set<std::string> incomplete_totals;
+    std::map<std::pair<int, int>, int> subrun_indices;
+    bool subrun_index_built = false;
 
-    TTree* output_ntuple; // for output
+    TTree* output_ntuple = nullptr; // for output
+    TTree* output_subrun_ntuple = nullptr;
   };
 } // namespace rooutil
 #endif
diff --git a/rooutil/inc/SubRun.hh b/rooutil/inc/SubRun.hh
new file mode 100644
index 00000000..dfe087b7
--- /dev/null
+++ b/rooutil/inc/SubRun.hh
@@ -0,0 +1,27 @@
+#ifndef SubRun_hh_
+#define SubRun_hh_
+
+#include "EventNtuple/inc/SubRunInfo.hh"
+#include "EventNtuple/rooutil/inc/BranchUtils.hh"
+
+namespace rooutil {
+  struct SubRun {
+    explicit SubRun(TChain* ntuple) {
+      has_srinfo = CheckForBranch(ntuple, "srinfo", &srinfo);
+      has_gen_event_count = CheckForBranch(ntuple, "genEventCount", &genEventCount);
+      has_proc_event_count = CheckForBranch(ntuple, "procEventCount", &procEventCount);
+      has_cosmic_livetime = CheckForBranch(ntuple, "cosmicLivetime", &cosmicLivetime);
+    }
+
+    mu2e::SubRunInfo* srinfo = nullptr;
+    long genEventCount = 0;
+    long procEventCount = 0;
+    float cosmicLivetime = 0.0;
+
+    bool has_srinfo = false;
+    bool has_gen_event_count = false;
+    bool has_proc_event_count = false;
+    bool has_cosmic_livetime = false;
+  };
+} // namespace rooutil
+#endif
diff --git a/validation/test_rooutil_examples.sh b/validation/test_rooutil_examples.sh
index 4fabbb25..d7f5e497 100644
--- a/validation/test_rooutil_examples.sh
+++ b/validation/test_rooutil_examples.sh
@@ -5,7 +5,7 @@ scripts=( "PrintEvents.C" "CreateNtuple.C" "CreateTrackNtuple.C" "PlotCRVPEs.C"
           "PlotMCParentPosZ.C" "PlotMCParticleMom.C" "PlotMuonPosZ.C" "PlotStoppingTargetFoilSegment.C" "PlotTrackNHits_RecoVsTrue.C"
           "PlotTrkCaloHitEnergy.C" "PrintEventsNoMC.C" "TrackCounting.C" "PlotTrackHitTimes.C" "PlotTrackHitTimesMC.C" "PlotStrawMaterials.C"
           "PlotGenCosmicMom.C" "PlotCRVTotalPEs.C" "PlotEntranceMomentum_UpstreamDownstream.C" "PlotVDSteps.C" "PlotCaloClusterEnergy_RecoVsTrue.C"
-          "PlotCaloClusterAndHits.C" "PlotCaloCluster_SimParticles.C"
+          "PlotCaloClusterAndHits.C" "PlotCaloCluster_SimParticles.C" "SubRunCounting.C"
          )
 
 for script in "${scripts[@]}"

From 3ca6b6197b62f58ecaa56d74b9f5d59caab4fe0c Mon Sep 17 00:00:00 2001
From: Andrew Edmonds <aedmonds@york.cuny.edu>
Date: Thu, 30 Jul 2026 10:00:52 -0500
Subject: [PATCH 15/16] Update subrun counting example

---
 rooutil/examples/SubRunCounting.C | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/rooutil/examples/SubRunCounting.C b/rooutil/examples/SubRunCounting.C
index fdfdeae0..41b34395 100644
--- a/rooutil/examples/SubRunCounting.C
+++ b/rooutil/examples/SubRunCounting.C
@@ -11,11 +11,19 @@ void SubRunCounting(std::string filename) {
   for (int i_subrun = 0; i_subrun < util.GetNSubRuns(); ++i_subrun) {
     const auto& subrun = util.GetSubRun(i_subrun);
     std::cout << "run " << subrun.srinfo->run << ", subrun " << subrun.srinfo->subrun;
-    if (subrun.has_proc_event_count) std::cout << ": " << subrun.procEventCount << " processed events";
+    if (subrun.has_gen_event_count) { std::cout << ": " << subrun.genEventCount << " generated events"; }
+    if (subrun.has_proc_event_count) { std::cout << ", " << subrun.procEventCount << " processed events"; }
+    if (subrun.has_cosmic_livetime) { std::cout << ", " << subrun.cosmicLivetime << " s of cosmic livetime"; }
     std::cout << std::endl;
   }
 
+  if (const auto generated_events = util.GetGeneratedEvents()) {
+    std::cout << "Total generated events: " << *generated_events << std::endl;
+  }
   if (const auto processed_events = util.GetProcessedEvents()) {
     std::cout << "Total processed events: " << *processed_events << std::endl;
   }
+  if (const auto cosmic_livetime = util.GetCosmicLivetime()) {
+    std::cout << "Total cosmic livetime: " << *cosmic_livetime << " s" << std::endl;
+  }
 }

From e3c487ed51232eca671964366e0f1fa5ec10ff03 Mon Sep 17 00:00:00 2001
From: Andrew Edmonds <aedmonds@york.cuny.edu>
Date: Thu, 30 Jul 2026 10:01:27 -0500
Subject: [PATCH 16/16] Add a couple more examples showing how to cut on
 subruns, find a subrun, and normalize a plot

---
 rooutil/README.md                             |  2 +-
 ...smicTrackCrvZResidual_LivetimeNormalized.C | 52 +++++++++++++++++++
 rooutil/examples/SelectSubRuns.C              | 37 +++++++++++++
 validation/test_rooutil_examples.sh           |  2 +-
 4 files changed, 91 insertions(+), 2 deletions(-)
 create mode 100644 rooutil/examples/PlotCosmicTrackCrvZResidual_LivetimeNormalized.C
 create mode 100644 rooutil/examples/SelectSubRuns.C

diff --git a/rooutil/README.md b/rooutil/README.md
index 7e2649ad..056faa59 100644
--- a/rooutil/README.md
+++ b/rooutil/README.md
@@ -46,7 +46,7 @@ Use ```FindSubRun(run, subrun)``` to retrieve the SubRun corresponding to an eve
 
 The one-bin totals histograms are summed across every input file. ```GetTotal(name)``` returns ```std::optional<double>```, so a missing or incomplete total is distinct from a valid zero. The available names are ```n_gen_events```, ```n_proc_events```, and ```cosmic_livetime```. ```GetGeneratedEvents()```, ```GetProcessedEvents()```, and ```GetCosmicLivetime()``` are convenience accessors; ```GetRate(count)``` returns ```count / cosmic_livetime``` when a nonzero livetime is available. ```GetNProcEvents()``` remains available for compatibility and returns ```-1``` when the processed-event total is unavailable.
 
-Example: [SubRunCounting.C](./examples/SubRunCounting.C).
+Examples: [SubRunCounting.C](./examples/SubRunCounting.C), [SelectSubRuns.C](./examples/SelectSubRuns.C) for selecting SubRuns and retrieving the SubRun for an event, and [PlotCosmicTrackCrvZResidual_LivetimeNormalized.C](./examples/PlotCosmicTrackCrvZResidual_LivetimeNormalized.C) for normalizing a histogram with ```GetRate()```.
 
 ## The Event Class
 All branches and leaves can be accessed through the ```Event``` class like so:
diff --git a/rooutil/examples/PlotCosmicTrackCrvZResidual_LivetimeNormalized.C b/rooutil/examples/PlotCosmicTrackCrvZResidual_LivetimeNormalized.C
new file mode 100644
index 00000000..3238bfa7
--- /dev/null
+++ b/rooutil/examples/PlotCosmicTrackCrvZResidual_LivetimeNormalized.C
@@ -0,0 +1,52 @@
+#include "EventNtuple/rooutil/inc/RooUtil.hh"
+#include "EventNtuple/rooutil/inc/common_cuts.hh"
+
+#include "TCanvas.h"
+#include "TH1F.h"
+
+#include <iostream>
+
+using namespace rooutil;
+
+bool crv_top_surface(TrackSegment& segment) {
+  if (segment.trkseg == nullptr) return false;
+
+  const int surface_id = segment.trkseg->sid;
+  return surface_id == mu2e::SurfaceIdDetail::TCRV; // note: this is a deprecated surface id, but it is what is in the file I'm testing
+}
+
+void PlotCosmicTrackCrvZResidual_LivetimeNormalized(std::string filename) {
+  RooUtil util(filename);
+  TH1F* crv_track_z_residual = new TH1F("crv_track_z_residual", "CRV coincidence-track z residual;z_{CRV coincidence} - z_{track} [mm];tracks / s", 100, -500, 500);
+
+  for (int i_event = 0; i_event < util.GetNEvents(); ++i_event) {
+    auto& event = util.GetEvent(i_event);
+    const auto tracks = event.GetTracks();
+    auto crv_coincs = event.GetCrvCoincs();
+    for (auto track : tracks) {
+      auto crv_top_segments = track.GetSegments([](TrackSegment& segment) {
+        return crv_top_surface(segment) && has_reco_step(segment);
+      });
+      for (auto& segment : crv_top_segments) {
+        for (auto& crv_coinc : crv_coincs) {
+          if (track_crv_coincidence(segment, crv_coinc)) {
+            crv_track_z_residual->Fill(crv_coinc.reco->pos.z() - segment.trkseg->pos.z());
+          }
+        }
+      }
+    }
+  }
+
+  const auto entries = crv_track_z_residual->Integral();
+  if (entries > 0.0) {
+    if (const auto rate = util.GetRate(entries)) {
+      crv_track_z_residual->Scale(*rate / entries);
+    } else {
+      std::cout << "Cannot normalize histogram: cosmic livetime is unavailable." << std::endl;
+    }
+  }
+
+  TCanvas* canvas = new TCanvas("canvas", "CRV coincidence-track z residual");
+  crv_track_z_residual->Draw("HIST");
+  canvas->SaveAs("crv_track_z_residual_rate.pdf");
+}
diff --git a/rooutil/examples/SelectSubRuns.C b/rooutil/examples/SelectSubRuns.C
new file mode 100644
index 00000000..7195be64
--- /dev/null
+++ b/rooutil/examples/SelectSubRuns.C
@@ -0,0 +1,37 @@
+#include "EventNtuple/rooutil/inc/RooUtil.hh"
+
+#include <iostream>
+
+using namespace rooutil;
+
+bool has_more_than_100_processed_events(const SubRun& subrun) {
+  return subrun.has_proc_event_count && subrun.procEventCount > 100;
+}
+
+void SelectSubRuns(std::string filename) {
+  RooUtil util(filename);
+
+  const auto selected_subruns = util.GetSubRunIndices(has_more_than_100_processed_events);
+  std::cout << "SubRuns with more than 100 processed events:" << std::endl;
+  for (const auto i_subrun : selected_subruns) {
+    const auto& subrun = util.GetSubRun(i_subrun);
+    std::cout << subrun.srinfo->run << ":" << subrun.srinfo->subrun
+              << " has " << subrun.procEventCount << " processed events" << std::endl;
+  }
+
+  if (util.GetNEvents() == 0) return;
+
+  const auto& event = util.GetEvent(0);
+  const auto* event_subrun = util.FindSubRun(event.evtinfo->run, event.evtinfo->subrun);
+  if (event_subrun == nullptr) {
+    std::cout << "No SubRun information is available for the first event." << std::endl;
+    return;
+  }
+
+  std::cout << "First event belongs to " << event_subrun->srinfo->run << ":"
+            << event_subrun->srinfo->subrun;
+  if (event_subrun->has_cosmic_livetime) {
+    std::cout << " with " << event_subrun->cosmicLivetime << " s of cosmic livetime";
+  }
+  std::cout << std::endl;
+}
diff --git a/validation/test_rooutil_examples.sh b/validation/test_rooutil_examples.sh
index d7f5e497..6a1920bf 100644
--- a/validation/test_rooutil_examples.sh
+++ b/validation/test_rooutil_examples.sh
@@ -5,7 +5,7 @@ scripts=( "PrintEvents.C" "CreateNtuple.C" "CreateTrackNtuple.C" "PlotCRVPEs.C"
           "PlotMCParentPosZ.C" "PlotMCParticleMom.C" "PlotMuonPosZ.C" "PlotStoppingTargetFoilSegment.C" "PlotTrackNHits_RecoVsTrue.C"
           "PlotTrkCaloHitEnergy.C" "PrintEventsNoMC.C" "TrackCounting.C" "PlotTrackHitTimes.C" "PlotTrackHitTimesMC.C" "PlotStrawMaterials.C"
           "PlotGenCosmicMom.C" "PlotCRVTotalPEs.C" "PlotEntranceMomentum_UpstreamDownstream.C" "PlotVDSteps.C" "PlotCaloClusterEnergy_RecoVsTrue.C"
-          "PlotCaloClusterAndHits.C" "PlotCaloCluster_SimParticles.C" "SubRunCounting.C"
+          "PlotCaloClusterAndHits.C" "PlotCaloCluster_SimParticles.C" "SubRunCounting.C" "SelectSubRuns.C" "PlotCosmicTrackCrvZResidual_LivetimeNormalized.C"
          )
 
 for script in "${scripts[@]}"