AssignBunchTimingMC tool to add the BNB spill structure to MC cluster…

… times (#304)

* Add files via upload

New tool to assign BNB spill structure to MC cluster times

* Update Factory.cpp

* Update Unity.h

* Update AssignBunchTimingMC.cpp

silly missed bug

UserTools/AssignBunchTimingMC/AssignBunchTimingMC.cpp

@@ -0,0 +1,245 @@
+#include "AssignBunchTimingMC.h"
+
+AssignBunchTimingMC::AssignBunchTimingMC():Tool(){}
+
+//------------------------------------------------------------------------------
+
+bool AssignBunchTimingMC::Initialise(std::string configfile, DataModel &data){
+
+    // Get configuration variables and set default values if necessary
+
+    if ( !configfile.empty() ) m_variables.Initialise(configfile);
+    m_data = &data;
+
+    bool got_verbosity = m_variables.Get("verbosity", verbosity);
+    bool got_width     = m_variables.Get("bunchwidth", fbunchwidth);
+    bool got_interval  = m_variables.Get("bunchinterval", fbunchinterval);
+    bool got_count     = m_variables.Get("bunchcount", fbunchcount);
+    bool got_sample    = m_variables.Get("sampletype", fsample);
+    bool got_trigger   = m_variables.Get("prompttriggertime", ftriggertime);
+
+    if (!got_verbosity) {
+        verbosity = 0;
+        logmessage = "Warning (AssignBunchTimingMC): \"verbosity\" not set in the config, defaulting to 0";
+        Log(logmessage, v_warning, verbosity);
+    }
+
+
+    // default bunch parameters from MicroBooNE paper: https://doi.org/10.1103/PhysRevD.108.052010
+
+    if (!got_width) {
+        fbunchwidth = 1.308;  // ns
+        logmessage = ("Warning (AssignBunchTimingMC): \"bunchwidth\" not "
+            "set in the config file. Using default: 1.308ns");
+        Log(logmessage, v_warning, verbosity);
+    }
+
+    if (!got_interval) {
+        fbunchinterval = 18.936;  // ns
+        logmessage = ("Warning (AssignBunchTimingMC): \"bunchinterval\" not "
+            "set in the config file. Using default: 18.936ns");
+        Log(logmessage, v_warning, verbosity);
+    }
+
+    if (!got_count) {
+        fbunchwidth = 81;
+        logmessage = ("Warning (AssignBunchTimingMC): \"bunchcount\" not "
+            "set in the config file. Using default: 81");
+        Log(logmessage, v_warning, verbosity);
+    }
+
+    if (!got_sample) {
+        fsample = 0;    // assume they are using the Tank samples
+        logmessage = ("Warning (AssignBunchTimingMC): \"sampletype\" not "
+            "set in the config file. Using default: 0 (GENIE tank samples)");
+        Log(logmessage, v_warning, verbosity);
+    }
+
+    if (!got_trigger) {
+        ftriggertime = 0;    // assume they are using the old WCSim prompt trigger time (t = 0, first particle arrival)
+        logmessage = ("Warning (AssignBunchTimingMC): \"prompttriggertime\" not "
+            "set in the config file. Using default: 0 (WCSim prompt trigger time = 0)");
+        Log(logmessage, v_warning, verbosity);
+    }
+
+
+    if (verbosity >= v_message) {
+        std::cout<<"------------------------------------"<<"\n";
+        std::cout<<"AssignBunchTimingMC: Config settings"<<"\n";
+        std::cout<<"------------------------------------"<<"\n";
+        std::cout<<"bunch width       = "<<fbunchwidth<<" ns"<<"\n";
+        std::cout<<"bunch interval    = "<<fbunchinterval<<" ns"<<"\n";
+        std::cout<<"number of bunches = "<<fbunchcount<<"\n";
+        std::cout<<"sample type       = "<<(fsample == 0 ? "(0) Tank" : "(1) World")<<"\n";
+        std::cout<<"trigger time      = "<<(ftriggertime == 0 ? "(0) prompt trigger starts when first particle arrives (default WCSim)" 
+                                                   : "(1) prompt trigger starts at beam dump (modified WCSim)")<<"\n";
+    }
+
+    fbunchTimes = new std::map<double, double>;   // set up pointer; Store will handle deletion in Finalize
+
+    return true;
+}
+
+//------------------------------------------------------------------------------
+
+
+bool AssignBunchTimingMC::Execute()
+{
+
+    if (verbosity >= v_debug) {
+        std::cout << "AssignBunchTimingMC: Executing tool..." << std::endl;
+    }
+
+    if (!LoadStores())      // Load info from store
+        return false;
+    if (verbosity >= v_debug) {
+        std::cout << "AssignBunchTimingMC: Store info loading successful" << std::endl;
+    }
+
+    fbunchTimes->clear();   // clear map
+
+    BNBtiming();            // grab BNB structure
+    if (verbosity >= v_debug) {
+        std::cout << "AssignBunchTimingMC: BNB timing successful" << std::endl;
+    }
+
+    for (std::pair<double, std::vector<MCHit>>&& apair : *fClusterMapMC) {
+        double totalHitTime = 0;
+        int hitCount = 0;
+        int totalHits = apair.second.size();
+
+        CalculateClusterAndBunchTimes(apair.second, totalHitTime, hitCount, totalHits);
+
+        // store the cluster time in a map (e.g., keyed by cluster identifier)
+        fbunchTimes->emplace(apair.first, bunchTime);
+    }
+
+    if (verbosity >= v_debug) {
+        std::cout << "AssignBunchTimingMC: Assigned bunch time successfully. Writing to Store..." << std::endl;
+    }
+
+    // send to store
+    m_data->Stores.at("ANNIEEvent")->Set("bunchTimes", fbunchTimes);
+
+    return true;
+
+}
+
+
+//------------------------------------------------------------------------------
+
+bool AssignBunchTimingMC::Finalise()
+{
+  return true;
+}
+
+//------------------------------------------------------------------------------
+
+
+
+
+bool AssignBunchTimingMC::LoadStores()
+{
+    // grab necessary information from Stores
+
+    bool get_MCClusters = m_data->CStore.Get("ClusterMapMC", fClusterMapMC);
+    if (!get_MCClusters) {
+        Log("AssignBunchTimingMC: no ClusterMapMC in the CStore! Are you sure you ran the ClusterFinder tool?", v_error, verbosity);
+        return false;
+    }
+
+    bool get_AnnieEvent = m_data->Stores.count("ANNIEEvent");
+    if (!get_AnnieEvent) {
+        Log("AssignBunchTimingMC: no ANNIEEvent store!", v_error, verbosity);
+        return false;
+    }
+
+    bool get_MCHits = m_data->Stores.at("ANNIEEvent")->Get("MCHits", fMCHitsMap);
+    if (!get_MCHits) {
+        Log("AssignBunchTimingMC: no MCHits in the ANNIEEvent!", v_error, verbosity);
+        return false;
+    }
+
+    bool get_neutrino_vtxt = m_data->Stores["GenieInfo"]->Get("NuIntxVtx_T",TrueNuIntxVtx_T);   // grab neutrino interaction time
+    if (!get_neutrino_vtxt) {
+        Log("AssignBunchTimingMC: no GENIE neutrino interaction time info in the ANNIEEvent! Are you sure you ran the LoadGENIEEvent tool?", v_error, verbosity);
+        return false;
+    }
+
+    return true;
+}
+
+
+//------------------------------------------------------------------------------
+
+
+void AssignBunchTimingMC::BNBtiming()
+{
+    // Determined from GENIE samples (as of Oct 2024)
+    const double tank_time = 67.0;    // Tank neutrino arrival time: 67ns
+    const double world_time = 33.0;   // WORLD neutrino arrival time: 33ns
+
+    if (ftriggertime == 0) {
+        new_nu_time = (fsample == 0) ? (TrueNuIntxVtx_T - tank_time) : (TrueNuIntxVtx_T - world_time);
+    } else if (ftriggertime == 1) {
+        new_nu_time = (fsample == 0) ? -tank_time : -world_time;
+    }
+
+    // seed random number generator with the current time
+    unsigned seed = std::chrono::system_clock::now().time_since_epoch().count();
+    generator.seed(seed);
+    if (verbosity >= v_debug) {
+        std::cout << "AssignBunchTimingMC: Random seed selected: " << seed << std::endl;
+    }
+
+
+    // per event, assign BNB structure (random bunch number + jitter based on intrinsic bunch width + new_nu_time)
+    bunchNumber = rand() % fbunchcount;
+    std::normal_distribution<double> distribution(0, fbunchwidth); 
+    jitter = distribution(generator);
+
+    if (verbosity >= v_message) {
+        std::string logmessage = "AssignBunchTimingMC: bunchNumber = " + std::to_string(bunchNumber) + " | t0 = " + std::to_string(new_nu_time);
+        Log(logmessage, v_debug, verbosity);
+    }
+
+}
+
+
+//------------------------------------------------------------------------------
+
+
+void AssignBunchTimingMC::CalculateClusterAndBunchTimes(std::vector<MCHit> const &mchits, double &totalHitTime, int &hitCount, int &totalHits)
+{
+
+    // loop over the hits to get their times
+    for (auto mchit : mchits) { 
+        double hitTime = mchit.GetTime();
+        totalHitTime += hitTime;
+        hitCount++;
+        if (verbosity >= v_debug) {
+            std::string logmessage = "AssignBunchTimingMC: (" + std::to_string(hitCount) + "/" + std::to_string(totalHits) + ") MCHit time = " + std::to_string(hitTime);
+            Log(logmessage, v_debug, verbosity);
+        }
+    }
+
+    // find nominal cluster time (average hit time)
+    double clusterTime = (hitCount > 0) ? totalHitTime / hitCount : -9999;
+    if (verbosity >= v_debug) {
+        std::string logmessage = "AssignBunchTimingMC: ClusterTime = " + std::to_string(clusterTime);
+        Log(logmessage, v_debug, verbosity);
+    }
+
+    // calculate BunchTime
+    bunchTime = fbunchinterval * bunchNumber + clusterTime + jitter + new_nu_time ;
+    if (verbosity >= v_debug) {
+        std::string logmessage = "AssignBunchTimingMC: bunchTime = " + std::to_string(bunchTime);
+        Log(logmessage, v_debug, verbosity);
+    }
+
+}
+
+
+//------------------------------------------------------------------------------
+
+// done

UserTools/AssignBunchTimingMC/AssignBunchTimingMC.h

@@ -0,0 +1,67 @@
+#ifndef AssignBunchTimingMC_H
+#define AssignBunchTimingMC_H
+
+#include <string>
+#include <iostream>
+#include <random>
+
+#include "Tool.h"
+#include "Hit.h"
+
+
+/**
+ * \class AssignBunchTimingMC
+ *
+ * A tool to assign BNB bunch structure to GENIE events
+*
+* $Author: S.Doran $
+* $Date: 2024/10/09 $
+* Contact: [email protected]
+*/
+class AssignBunchTimingMC: public Tool {
+
+    public:
+
+        AssignBunchTimingMC(); ///< Simple constructor
+        bool Initialise(std::string configfile,DataModel &data); ///< Initialise Function for setting up Tool resources. @param configfile The path and name of the dynamic configuration file to read in. @param data A reference to the transient data class used to pass information between Tools.
+        bool Execute(); ///< Execute function used to perform Tool purpose.
+        bool Finalise(); ///< Finalise function used to clean up resources.
+
+        bool LoadStores(); ///< Loads all relevant information from the store, away from the Execute function
+        void BNBtiming(); ///< Calculates the appropriate BNB timing to apply to the clusters
+        void CalculateClusterAndBunchTimes(std::vector<MCHit> const &mchits, double &totalHitTime, int &hitCount, int &totalHits); ///< Loops through the MCHits, finds the cluster times (avg hit time), and calculates the new bunch timing
+
+    private:
+
+        std::map<unsigned long, std::vector<MCHit>> *fMCHitsMap    = nullptr;  ///< All of the MCHits keyed by channel number
+        std::map<double, std::vector<MCHit>>        *fClusterMapMC = nullptr;  ///< All MC clusters
+        double TrueNuIntxVtx_T;                                                ///< true neutrino interaction time in ns, from GenieInfo store
+
+        std::map<double, double> *fbunchTimes                      = nullptr;  ///< Bunch-realistic timing from the cluster times; 
+                                                                               ///  map linking updated bunch time to normal cluster time
+
+        std::default_random_engine generator;                                  ///< Random number generator for bunch number
+
+        double fbunchwidth;       ///< BNB intrinsic bunch width in ns
+        double fbunchinterval;    ///< BNB bunch spacing in ns
+        int fbunchcount;          ///< number of BNB bunches per spill
+        int fsample;              ///< GENIE Tank or WORLD samples
+        int ftriggertime;         ///< whether the samples used the default WCSim prompt trigger = 0 (when particles enter the volume), or the adjusted prompt trigger based on the start of the beam dump
+
+        double new_nu_time;       ///< offset needed to make the cluster times beam realistic
+        int bunchNumber;          ///< randomly assigned bunch number
+        double jitter;            ///< random jitter based on the intrinsic bunch width
+        double bunchTime;         ///< individual bunch time assigned for a specific cluster
+
+        /// \brief verbosity levels: if 'verbosity' < this level, the message type will be logged.
+        int verbosity;
+        int v_error=0;            // STOP THE SHOW
+        int v_warning=1;          // this and below the show will go on
+        int v_message=2;
+        int v_debug=3;
+        std::string logmessage;
+
+};
+
+
+#endif

UserTools/AssignBunchTimingMC/README.md

@@ -0,0 +1,31 @@
+# AssignBunchTimingMC
+
+`AssignBunchTimingMC` applies the spill structure of the BNB to MC clusters. Currently, all MC events are "triggered" at the same time in WCSim; for certain analyses revolving around beam timing it may be necessary to have a beam-realistic simulation. The tool works by taking in a cluster produced by the `ClusterFinder` tool of form std::map<double, std::vector<MCHit>> from the CStore ("ClusterMapMC"), and applies a corrective timing factor to each event. The tool also leverages the true neutrino interaction vertex time from GENIE to accurately create a spill structure. For this reason, both the `LoadGenieEvent` and `ClusterFinder` tools must be ran beforehand. This tool is designed for use on Genie Tank and World WCSim samples. 
+
+## Data
+
+`AssignBunchTimingMC` produces a map of spill-adjusted cluster times and puts them into the ANNIEEvent store (all map keys are the original cluster time):
+
+**fbunchTimes**  `std::map<double, double>`
+
+
+## Configuration
+```
+# AssignBunchTimingMC Config File
+
+verbosity 0
+
+# BNB properties taken from: MicroBooNE https://doi.org/10.1103/PhysRevD.108.052010
+bunchwidth 1.308       # BNB instrinic bunch spread [ns]
+bunchinterval 18.936   # BNB bunch spacings [ns]
+bunchcount 81          # number of BNB bunches per spill
+
+sampletype 0           # Tank (0) or World (1) genie samples you are running over
+prompttriggertime 0    # WCSim prompt trigger settings: (0 = default, t0 = 0 when a particle enters the volume)
+                       #                                (1 = modified, t0 = 0 when the neutrino beam dump begins)
+```
+
+
+## Additional information
+
+The "bunchTimes" have a spill structure that starts at ~0 ns and extends to M ns (depending on the bunch spacing and number of bunches). The tool is currently configured to the most recent Genie sample production (tank: 2023, world: early 2024) for both the WCSim tank and world events (both of which have different "beam dump" starting times and prompt trigger times).

UserTools/Factory/Factory.cpp

@@ -171,5 +171,6 @@ if (tool=="ReadConfigInfo") ret=new ReadConfigInfo;
 if (tool=="MuonFitter") ret=new MuonFitter;
 if (tool=="BeamQuality") ret=new BeamQuality;
 if (tool=="BackTracker") ret=new BackTracker;
+if (tool=="AssignBunchTimingMC") ret=new AssignBunchTimingMC;
 return ret;
 }

UserTools/Unity.h

@@ -179,3 +179,4 @@
 #include "MuonFitter.h"
 #include "BeamQuality.h"
 #include "BackTracker.h"
+#include "AssignBunchTimingMC.h"