PrintDQ toolchain (#315)

* PrintDQ toolchain

Toolchain to print run quality statistics

* Delete configfiles/PrintDQ/CreateProcessedList.sh

redundant script - there is another one that does the same thing

* Update README.md

update README

configfiles/PrintDQ/ClusterClassifiersConfig

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+verbosity 0

configfiles/PrintDQ/ClusterFinderConfig

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+# ClusterFinder Config File
+
+verbosity 0
+HitStore Hits #Either MCHits or Hits (accessed in ANNIEEvent store)
+OutputFile BeamRun_ClusterFinder_DefaultOutput #Output root prefix name for the current run
+ClusterFindingWindow 40 # in ns, size of the window used to "clusterize"
+AcqTimeWindow 70000 # in ns, size of the acquisition window
+ClusterIntegrationWindow 40 # 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/PrintDQ/EventSelectorConfig

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+# 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 1000	#Maximum energy in MeV
+MRDRecoCut 0
+RecoPMTVolCut 0
+RecoFVCut 0
+NHitCut 0
+NHitmin 4	#Minimum number of hit digits
+PMTMRDCoincCut 0
+PMTMRDOffset 755
+PromptTrigOnly 0
+TriggerWord -1
+SaveStatusToStore 1
+NoVeto 0
+Veto 0
+ThroughGoing 0
+IsMC 0		#MC or Data?

configfiles/PrintDQ/FindMrdTracksConfig

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+# FindMrdTracks Config File
+# all variables retrieved with m_variables.Get() must be defined here!
+
+verbosity 0
+IsData 1
+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/PrintDQ/FitRWMWaveformConfig

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+verbosityFitRWMWaveform 0
+printToRootFile 0
+
+

configfiles/PrintDQ/LoadANNIEEventConfig

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+verbose 1
+FileForListOfInputs ./configfiles/PrintDQ/my_inputs.txt
+EventOffset 0
+GlobalEvNr 1

configfiles/PrintDQ/PrintDQConfig

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+verbosity 0

configfiles/PrintDQ/README.md

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+# PrintDQ
+
+***********************
+# Description
+***********************
+
+The `PrintDQ` toolchain runs the clustering tools (MRD + PMT) over the ProcessedData files created by the event building toolchain to output run quality statistics. For more information, check out the README for the tool: https://github.com/ANNIEsoft/ToolAnalysis/tree/Application/UserTools/PrintDQ. This tool can be used for assessing the quality of Processed runs to help identify issues with the detector.
+
+************************
+# Usage
+************************
+
+- Populate the `my_inputs.txt` file with all part files from a Processed runs. Running the script `sh create_my_inputs.sh <run_number>` will automatically populate the input file with all Processed Data part files for that run.
+- Run the toolchain via: `./Analyse ./configfiles/PrintDQ/ToolChain`
+- Run statistics will be outputted via `std::out` once the toolchain completes.
+
+
+************************
+# Additional information
+************************
+
+- The current version of the `PrintDQ` tool is intended to be run over 1 run at a time. As the clustering tools may take some time to compile, the processing time of this toolchain may take several minutes (for a ~100 part file run) to ~1 hour (~thousands of part files) depending on how many part files exist.

configfiles/PrintDQ/TimeClusteringConfig

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+#TimeClustering config file
+
+verbosity 0
+MinDigitsForTrack 3
+MaxMrdSubEventDuration 30
+MinSubeventTimeSep 30
+MakeMrdDigitTimePlot 0
+LaunchTApplication 0
+IsData 1
+#OutputROOTFile TimeClustering_MRDTest28_cluster40ns
+OutputROOTFile STEC_TimeClusteringOut
+MapChankey_WCSimID ./configfiles/SimpleTankEnergyCalibrator/MRD_Chankey_WCSimID.dat
+

configfiles/PrintDQ/ToolChainConfig

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+#ToolChain dynamic setup file
+
+##### Runtime Parameters #####
+verbose 1 ## Verbosity level of ToolChain
+error_level 0 # 0= do not exit, 1= exit on unhandled errors only, 2= exit on unhandled errors and handled errors
+attempt_recover 1 ## 1= will attempt to finalise if an execute fails
+
+###### Logging #####
+log_mode Interactive # Interactive=cout , Remote= remote logging system "serservice_name Remote_Logging" , Local = local file log;
+log_local_path ./log
+log_service LogStore
+
+
+###### Service discovery ##### Ignore these settings for local analysis
+service_publish_sec -1
+service_kick_sec -1
+
+##### Tools To Add #####
+Tools_File configfiles/PrintDQ/ToolsConfig  ## list of tools to run and their config files
+
+##### Run Type #####
+Inline -1 ## number of Execute steps in program, -1 infinite loop that is ended by user 
+Interactive 0 ## set to 1 if you want to run the code interactively
+

configfiles/PrintDQ/ToolsConfig

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+myLoadANNIEEvent LoadANNIEEvent ./configfiles/PrintDQ/LoadANNIEEventConfig
+myLoadGeometry LoadGeometry ./configfiles/LoadGeometry/LoadGeometryConfig
+myTimeClustering TimeClustering configfiles/PrintDQ/TimeClusteringConfig
+myFindMrdTracks FindMrdTracks configfiles/PrintDQ/FindMrdTracksConfig
+myClusterFinder ClusterFinder ./configfiles/PrintDQ/ClusterFinderConfig
+myClusterClassifiers ClusterClassifiers ./configfiles/PrintDQ/ClusterClassifiersConfig
+myEventSelector EventSelector ./configfiles/PrintDQ/EventSelectorConfig
+myFitRWMWaveform FitRWMWaveform ./configfiles/PrintDQ/FitRWMWaveformConfig
+
+myPrintDQ PrintDQ ./configfiles/PrintDQ/PrintDQConfig

configfiles/PrintDQ/create_my_inputs.sh

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+#!/bin/bash
+
+if [[ -z "$1" ]]; then
+    echo ""
+    echo "##############################"
+    echo "Error: No run number provided."
+    echo "Usage: $0 <run_number>"
+    echo ""
+    exit 1
+fi
+
+run=$1
+
+output_file="my_inputs.txt"
+processed_dir="/pnfs/annie/persistent/processed/processed_EBV2/R${run}/"
+
+find "$processed_dir" -type f -name "Processed*" | sort -t'/' -k2V > "$output_file"
+
+echo "done"