From 5e02871713b79b696128ec3d969c6ed9ab9d315f Mon Sep 17 00:00:00 2001
From: David Nathan Brown <dave_brown@lbl.gov>
Date: Thu, 6 Aug 2026 08:47:55 -0700
Subject: [PATCH] Add script to select and regrow cosmic reflections

---
 JobConfig/recoMC/RefRegrow.fcl | 137 +++++++++++++++++++++++++++++++++
 1 file changed, 137 insertions(+)
 create mode 100644 JobConfig/recoMC/RefRegrow.fcl

diff --git a/JobConfig/recoMC/RefRegrow.fcl b/JobConfig/recoMC/RefRegrow.fcl
new file mode 100644
index 00000000..82a33337
--- /dev/null
+++ b/JobConfig/recoMC/RefRegrow.fcl
@@ -0,0 +1,137 @@
+#
+# Script to select and regrow reflecting cosmic ray particles starting with standard recoMC output
+# original author: D. Brown, 6/25/26
+#
+#include "Production/JobConfig/recoMC/prolog.fcl"
+outputs.CentralHelixOutput.fileName : nil
+outputs.LoopHelixOutput.fileName : nil
+services : @local::Services.Reco
+process_name: RefRegrow
+source : { module_type : RootInput }
+
+physics.filters : {
+  eidsel : {
+    module_type : EventIDFilter
+    idsToMatch: [ "*:*:*" ]
+  }
+
+  Reflecte : {
+    @table::TrkReco.filters.SelectT0Reflections
+    UpstreamKalSeedCollection : "KKUe"
+    DownstreamKalSeedCollection : "KKDe"
+  }
+
+  RegrowReflecte : {
+    @table::TrkReco.filters.SelectReflections
+    UpstreamKalSeedCollection : "RegrowKKe"
+    DownstreamKalSeedCollection : "RegrowKKe"
+  }
+
+  Reflectmu : {
+    @table::TrkReco.filters.SelectT0Reflections
+    UpstreamKalSeedCollection : "KKUmu"
+    DownstreamKalSeedCollection : "KKDmu"
+  }
+
+  RegrowReflectmu : {
+    @table::TrkReco.filters.SelectReflections
+    UpstreamKalSeedCollection : "RegrowKKmu"
+    DownstreamKalSeedCollection : "RegrowKKmu"
+  }
+
+  RegrowKKe : {
+    @table::Mu2eKinKal.RegrowLH
+    KalSeedMCAssns : "SelectReco"
+    CopyKalSeedMCs : true
+    KalSeedPtrCollection : Reflecte
+    ComboHitCollection : RegrowSH
+    MustRegrow : "All"
+ }
+
+  RegrowKKmu : {
+    @table::Mu2eKinKal.RegrowLH
+    KalSeedMCAssns : "SelectReco"
+    CopyKalSeedMCs : true
+    KalSeedPtrCollection : Reflectmu
+    ComboHitCollection : RegrowSH
+    MustRegrow : "All"
+  }
+}
+
+physics.producers : {
+  RegrowSH : {
+    @table::TrkHitReco.makeSH
+    StrawDigiCollectionTag  : "SelectReco"
+    StrawDigiADCWaveformCollectionTag : "SelectReco"
+  }
+
+# MC recompression not yet debugged: TODO
+  RefCompressRecoMCse : {
+    @table::Reconstruction.producers.compressRecoMCs
+    strawDigiMCIndexMapTag: "SelectReco:StrawDigiMap"
+    crvDigiMCIndexMapTag: "SelectReco:CrvDigiMap"
+    simParticleTags: [ "compressRecoMCs" ]
+    crvDigiMCTag: "compressRecoMCs"
+    extraStepPointMCTags: [ "compressRecoMCs:virtualdetector" ]
+    mcTrajectoryTag: "compressRecoMCs"
+    primaryParticleTag: "compressRecoMCs"
+    strawDigiMCTag: "compressRecoMCs"
+    surfaceStepTags: [ "compressRecoMCs" ]
+    caloClusterMCTag: "compressRecoMCs"
+    crvCoincClusterMCTags :  [ "compressRecoMCs:CrvCoincidenceClusterMatchMC" ]
+  }
+
+  RefCompressRecoMCsmu : {
+    @table::Reconstruction.producers.compressRecoMCs
+    strawDigiMCIndexMapTag: "SelectReco:StrawDigiMap"
+    crvDigiMCIndexMapTag: "SelectReco:CrvDigiMap"
+    simParticleTags: [ "compressRecoMCs" ]
+    crvDigiMCTag: "compressRecoMCs"
+    extraStepPointMCTags: [ "compressRecoMCs:virtualdetector" ]
+    mcTrajectoryTag: "compressRecoMCs"
+    primaryParticleTag: "compressRecoMCs"
+    strawDigiMCTag: "compressRecoMCs"
+    surfaceStepTags: [ "compressRecoMCs" ]
+    caloClusterMCTag: "compressRecoMCs"
+    crvCoincClusterMCTags :  [ "compressRecoMCs:CrvCoincidenceClusterMatchMC" ]
+  }
+}
+
+physics.RePath : [ eidsel, Reflecte, RegrowSH, RegrowKKe, RegrowReflecte ]
+physics.RmuPath : [ eidsel, Reflectmu, RegrowSH, RegrowKKmu, RegrowReflectmu ]
+
+physics.trigger_paths : [ RePath, RmuPath ]
+
+outputs.RefOutpute : {
+  @table::Reconstruction.Output
+  SelectEvents : [RePath]
+  outputCommands: [ @sequence::Reconstruction.Output.outputCommands,
+  "drop mu2e::*_KK*_*_*",
+  "drop mu2e::KalSeeds_K*_*_*",
+  "drop mu2e::Kal*_SelectReco_*_*",
+  "drop mu2e::PrimaryParticle_*_*_*",
+  "keep mu2e::*_compressRecoMCs_*_*",
+  "keep mu2e::*_RegrowKK*_*_*" ]
+}
+
+outputs.RefOutputmu : {
+  @table::Reconstruction.Output
+  fileName : "/data/HD6/users/brownd/mcs.brownd.RefRegrowmu.art"
+  SelectEvents : [RmuPath]
+  outputCommands: [ @sequence::Reconstruction.Output.outputCommands,
+  "drop mu2e::*_KK*_*_*",
+  "drop mu2e::KalSeeds_K*_*_*",
+  "drop mu2e::Kal*_SelectReco_*_*",
+  "drop mu2e::PrimaryParticle_*_*_*",
+  "keep mu2e::*_compressRecoMCs_*_*",
+  "keep mu2e::*_RegrowKK*_*_*" ]
+}
+
+physics.RefEndPath : [ RefOutpute, RefOutputmu ]
+
+physics.end_paths : [ RefEndPath ]
+
+# Uncomment and update as needed
+#services.DbService.purpose: Sim_best
+#services.DbService.version: v1_4
+#services.DbService.verbose: 2