RingCounting ToolChain example (#263)

* Expanded RingCounting functionality

- Add RC data flow from boost stores, not requiring a pre-computed CNNImage file anymore
- Add "load_from_file" config parameter. Config setting: 0/1
- Add Execute() method in Tool class
- Add get_next_event() method in Tool class
- Change functionality of other methods to support both "load_from_file" settings
- The Tool expects a CNNImage formatted input (std::vector<double>) called "CNNImageCharge" within the "RecoEvent" boost store when not using the input from file
- The predictions are stored in the "RecoEvent" boost store as "RingCountingSRPrediction" and "RingCountingMRPrediction"

Ringcounting/README.md:
- Specify where the predictions are stored (RecoEvent)
- Complete list of config parameters

* RingCounting Tool:
- README.md updated to reflect recent changes more accurately. Hopefully makes things a bit clearer.

* RingCounting Tool:
- README.md updated to reflect recent changes more accurately. Hopefully makes things a bit clearer.

RingCounting ToolChain:
- Added exemplary configuration with CNNImage and previous data loading

---------

UserTools/RingCounting/README.md

@@ -6,32 +6,51 @@ For this a CNN-based machine learning approach is used.
 This Tool uses PMT data in the CNNImage format (see UserTools/CNNImage). For further details on the tool and
 the models used (including performance etc.) see the documentation found on the anniegpvm-machines at (**Todo**)
 ```
-/pnfs/annie/persistent/users/dschmid/RingCountingStore/documentation/
-```
+/pnfs/annie/persistent/reconstruction/RingCounting/RingCountingStore/documentation/
+``` 
+
 ---
 
 All models can be found at
 ```
-/pnfs/annie/persistent/users/dschmid/RingCountingStore/models/
+/pnfs/annie/persistent/reconstruction/RingCounting/RingCountingStore/models/
 ```
 
 ## Data
 
 - In the "load_from_file" mode, this tool adds single- and multi-ring (SR/MR) predictions to the RecoEvent BoostStore. When theh "load_from_file" config parameter is set to 0, the tool instead outputs the predictions to a csv file.
 - The predictions are stored in the "RingCountingSRPrediction" and "RingCountingMRPrediction" variables 
 
+The predictions are given as probabilities in the interval [0,1] as doubles, and sum to 1 for both classes.
+
+Implemented as:
+```
+reco_event_bs = self.m_data.Stores.at("RecoEvent")
+
+reco_event_bs.Set("RingCountingSRPrediction", predicted_sr)
+reco_event_bs.Set("RingCountingMRPrediction", predicted_mr)
+```
+
 ---
 ## Configuration
 
-The following configuration variables must be set for the tool to function properly (further details)
-are found at the top of the RingCounting.py file.
+The following configuration variables must be set for the tool to function properly.
+
 ---
 Exemplary configuration:
 ```
+PythonScript RingCounting
+
+InitialiseFunction Initialise
+ExecuteFunction Execute
+FinaliseFunction Finalise
+
+verbose 1
+
 load_from_file 0                                                # If set to 1, load CNNImage formatted csv files
 files_to_load configfiles/RingCounting/files_to_load.txt        # txt file containing files to load in case load_from_file == 1
 version 1_0_0                                                   # Model version
 model_path /annie/app/users/dschmid/RingCountingStore/models/   # Model path
-pmt_mask november_22                                            # PMT mask (zeroed out)
-save_to RC_output.csv                                           # if load_from_file == 1, save predictions as csv
+pmt_mask november_22                                            # Masked PMTs (name of hard-coded set of PMTs to ignore)
+save_to RC_output.csv                                           # Prediction output file, used if load_from_file == 1
 ```

configfiles/RingCounting/CNNImageConfig

@@ -0,0 +1,15 @@
+# CNNImage config file
+
+verbosity 1
+DataMode Normal			#options: Normal / Charge-Weighted / TimeEvolution
+SaveMode Static 		#options: Static / Geometric / PMT-wise
+DimensionX 16			#choose something suitable (32/64/...)
+DimensionY 10			#choose something suitable (32/64/...)
+OutputFile cnnimage_electron_la_sE_1_94
+MCStaticMapping configfiles/CNNImage/mc_cnnimage_mapping.csv
+DataStaticMapping configfiles/CNNImage/data_cnnimage_mapping.csv
+DimensionLAPPD 5                #Size of the LAPPD pannal 
+IncludeTopBottom 1
+DetectorConf ANNIEp2v7		#specify the detector version used in simulation
+useLAPPDs 0
+WriteToFile 0

configfiles/RingCounting/Chankey_WCSimID_v7.txt

@@ -0,0 +1,132 @@
+332    1
+333    2
+334    3
+335    4
+336    5
+337    6
+338    7
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+459    128
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+461    130
+462    131
+463    132

configfiles/RingCounting/ClusterClassifiersConfig

@@ -0,0 +1,3 @@
+#ClusterClassifiers Config file
+verbosity 0
+IsData 0

configfiles/RingCounting/ClusterFinderConfig

@@ -0,0 +1,12 @@
+# ClusterFinder Config File
+
+verbosity 0
+HitStore MCHits #Either MCHits or Hits (accessed in ANNIEEvent store)
+OutputFile BCAMC_CLUSTERFINDER_ibd_SE_0_0-99 #Output root prefix name for the current run
+ClusterFindingWindow 100 # in ns, size of the window used to "clusterize"
+AcqTimeWindow 70000 # in ns, size of the acquisition window
+ClusterIntegrationWindow 100 # in ns, all hits with +/- 1/2 of this window are considered in the cluster
+MinHitsPerCluster 5 # group of hits are considered clusters above this amount of hits
+end_of_window_time_cut 0.95 # from o to 1, length of the window you want to loop over with respect to acq. window (1 for full window, 0.95 for 95% from the start)
+Plots2D 0 #Draw 2D charge-vs-time plots?
+ChankeyToPMTIDMap ./configfiles/EventDisplay/Data-RecoEvent/Chankey_WCSimID.dat

configfiles/RingCounting/DeadPMTIDs_p2v7.txt

@@ -0,0 +1,11 @@
+2
+6
+11
+14
+15
+18
+21
+85
+100
+113
+114

configfiles/RingCounting/DigitBuilderConfig

@@ -0,0 +1,11 @@
+# DigitBuilder config file
+
+verbosity 0
+ParametricModel 1
+#Reading in MC files
+IsMC 1
+# There are three configurations: "PMT_only", "LAPPD_only", "All"
+PhotoDetectorConfiguration PMT_only
+#File must be in /pnfs/ space when loading on Fermilab cluster
+LAPPDIDFile ./configfiles/VertexReco/PhaseIIRecoTruth/LAPPDIDs.txt
+DigitChargeThr 0

configfiles/RingCounting/EnergyExtractorConfig

@@ -0,0 +1,11 @@
+OutputFile cnnimage_energy_output_test
+Verbosity 0
+SaveNeutrino 1
+SaveElectron 1
+SaveGamma 0
+SaveMuon 1
+SavePion 1
+SaveKaon 1
+SaveNeutron 1
+SaveVisible 1
+

configfiles/RingCounting/EventSelectorConfig

@@ -0,0 +1,26 @@
+# EventSelector config file
+
+verbosity 0
+MCPMTVolCut 0
+MCFVCut 0
+MCMRDCut 0
+MCPiKCut 0
+MCIsMuonCut 0
+MCIsElectronCut 0
+MCIsSingleRingCut 0
+MCIsMultiRingCut 0
+MCProjectedMRDHit 0
+MCEnergyCut 0
+Emin 0		#Minimum energy in MeV
+Emax 500	#Maximum energy in MeV
+MRDRecoCut 0
+RecoPMTVolCut 0
+RecoFVCut 0
+NHitCut 0
+NHitmin 4	#Minimum number of hit digits
+PMTMRDCoincCut 0
+PMTMRDOffset 0
+PromptTrigOnly 0
+TriggerWord -1
+SaveStatusToStore 1
+IsMC 1		#MC or Data?

configfiles/RingCounting/FindMrdTracksConfig

@@ -0,0 +1,12 @@
+# FindMrdTracks Config File
+# all variables retrieved with m_variables.Get() must be defined here!
+
+verbosity 0
+IsData 0
+OutputDirectory .
+OutputFile STEC_MRDTracks_cluster40ns
+DrawTruthTracks 0 # whether to add MC Truth track info for drawing in MrdPaddlePlot Tool
+                  ## note you need to run that tool to actually view the tracks!
+WriteTracksToFile 0	# should the track information be written to a ROOT-file?
+SelectTriggerType 0	#should the loaded data be filtered by trigger type?
+TriggerType Beam	#options: Cosmic, Beam, No Loopback

configfiles/RingCounting/LoadANNIEEventConfig

@@ -0,0 +1,3 @@
+verbose 0
+FileForListOfInputs ./configfiles/BeamClusterAnalysisMC/my_inputs.txt
+EventOffset 0

configfiles/RingCounting/LoadGenieEventConfig

@@ -0,0 +1,12 @@
+verbosity 0
+FluxVersion 1  # use 0 to load genie files based on bnb_annie_0000.root etc files
+               # use 1 to load files based on beammc_annie_0000.root etc files
+#FileDir NA     # specify "NA" for newer files: full path is saved in WCSim
+FileDir /pnfs/annie/persistent/simulations/genie3/G1810a0211a/standard/tank
+#FileDir /pnfs/annie/persistent/users/moflaher/genie/BNB_World_10k_11-03-18_gsimpleflux
+#FilePattern gntp.*.ghep.root
+FilePattern LoadWCSimTool      ## use this pattern to load corresponding genie info with the LoadWCSimTool
+                               ## N.B: FileDir must still be specified for now! (WCSim files do not record their directory)
+ManualFileMatching 0
+FileEvents 1000
+EventOffset 0

configfiles/RingCounting/LoadGeometryConfig

@@ -0,0 +1,8 @@
+verbosity 0
+LAPPDChannelCount 60
+FACCMRDGeoFile ./configfiles/LoadGeometry/FullMRDGeometry.csv
+DetectorGeoFile ./configfiles/LoadGeometry/DetectorGeometrySpecs.csv
+LAPPDGeoFile ./configfiles/LoadGeometry/LAPPDGeometry.csv
+TankPMTGeoFile ./configfiles/LoadGeometry/FullTankPMTGeometry.csv
+TankPMTGainFile ./configfiles/LoadGeometry/ChannelSPEGains2023.csv
+AuxiliaryChannelFile ./configfiles/LoadGeometry/AuxChannels.csv

configfiles/RingCounting/LoadWCSimConfig

@@ -0,0 +1,13 @@
+verbose 0
+
+InputFile /pnfs/annie/persistent/simulations/wcsim/G1810a0211a/standard/tank/pmt/wcsim_0.19.19.root
+
+WCSimVersion 3               ## should reflect the WCSim version of the files being loaded
+HistoricTriggeroffset 0      ## time offset of digits relative to the trigger
+UseDigitSmearedTime 1        ## whether to use smeared digit time (T), or true time of first photon (F)
+LappdNumStrips 60            ## num channels to construct from each LAPPD
+LappdStripLength 100         ## relative x position of each LAPPD strip, for dual-sided readout [mm]
+LappdStripSeparation 10      ## stripline separation, for calculating relative y position of each LAPPD strip [mm]
+PMTMask configfiles/BeamClusterAnalysisMC/DeadPMTIDs_p2v7.txt ## Which PMTs should be masked out? / are dead?
+ChankeyToPMTIDMap ./configfiles/BeamClusterAnalysisMC/Chankey_WCSimID_v7.txt
+SplitSubTriggers 0		# should subtriggers be loaded in separate Execute steps?

configfiles/RingCounting/LoadWCSimLAPPDConfig

@@ -0,0 +1,17 @@
+#LoadWCSimLAPPD Config File
+# all variables retrieved with m_variables.Get() must be defined here!
+verbose 0
+
+#InputFile /pnfs/annie/persistent/users/moflaher/wcsim/multipmt/tankonly/wcsim_25_04_19_ANNIEp2v6_nodigit_BNB_Water_10k_22-05-17/wcsim_lappd_0.1.9.root
+#InputFile /annie/app/users/mnieslon/WCSim_build/wcsim_ambe_port5_z0_lappd_0.root
+#InputFile /pnfs/annie/persistent/users/mnieslon/wcsim/output/tankonly/wcsim_ANNIEp2v7_beam/lappd-files/LAPPD_wcsim_beam_gst_1046_38_0.5438.root
+#InputFile /pnfs/annie/persistent/users/mnieslon/wcsim/output/tankonly/wcsim_ANNIEp2v7_beam/lappd-files/LAPPD_wcsim_beam_gst_1079_9_0.9009.root
+#InputFile /annie/app/users/mnieslon/WCSim_build/wcsim_michel_1000_lappd_0.root
+#/pnfs/annie/persistent/users/mnieslon/wcsim/output/tankonly/wcsim_ANNIEp2v7_throughgoing/wcsim_throughgoing_muon_R2614_lappd_0.0.root
+#InputFile /pnfs/annie/scratch/users/dschmid/output/mcc_mu_10/WCSim_10_1_lappd_0.root
+
+InputFile /pnfs/annie/persistent/simulations/wcsim/wcsim_ANNIEp2v7_beam/lappd-files/LAPPD_wcsim_beam_gst_1046_50_0.5450.root
+
+WCSimVersion 3               ## should reflect the WCSim version of the files being loaded
+InnerStructureRadius 1.3545  ## octagonal inner structure radius in m (from drawings 106.64")
+DrawDebugGraphs 0            ## whether to draw TPolyMarker3D's of hits

configfiles/RingCounting/MCParticlePropertiesConfig

@@ -0,0 +1,4 @@
+# MCParticleProperties configuration file
+
+verbosity 0
+hasGENIE true

configfiles/RingCounting/MCRecoEventLoaderConfig

@@ -0,0 +1,11 @@
+# MCRecoEventLoader config file
+
+verbosity 0
+GetPionKaonInfo 1
+GetNRings 1
+ParticleID -13
+DoParticleSelection 0
+xshift 0.0
+yshift 14.46469
+zshift -168.1
+IsMC 1