EVB2 cleanup per review comments (#378)

* update EBMRD per #334
* update EBLAPPD per #336
* update EBSaver per #337 (except no-op functions)
* update ANNIEEventTreeMaker per #339
* update LAPPDTreeMaker per #340
* update EBLoadRaw per #338
deferring proposed improvements to regex matching and path configs.
* remove RingCounting models, load from pnfs path
Removing the RingCounting v1.0.0 model here, but not pruning it from the
git repo to avoid rewriting history.
The config is updated to point to the model directory that already
exists on pnfs rather than a user directory.
* increment class version for Channel and LAPPDPulse
* remove no-op tool LAPPDBSCharging
* fix memory leak in LAPPDTimeAlignment
Note: it may be more efficient to allocate this once rather than within
the loop, but this is a minimal fix.
* remove LAPPD offset script, updated in #356
* Update Channel.h
only archive channelType if it exists in this version
* Update LAPPDPulse.h
Only archive pulseFollowTime and pulseFollowCharge if they exist in this version of the class

---------

Author: mastbaum

DataModel/Channel.h

@@ -101,10 +101,12 @@ class Channel : public SerialisableObject{
 			ar & hv_card;
 			ar & hv_channel;
 			ar & status;
-			ar & channelType;
+			if(version > 0) ar & channelType;
 		}
 	}
 
 };
 
+BOOST_CLASS_VERSION(Channel, 1)
+
 #endif

DataModel/LAPPDPulse.h

@@ -68,12 +68,16 @@ class LAPPDPulse : public Hit{
 			ar & halfHeightTime;
 			ar & halfEndTime;
 			ar & baseline;
-			ar & pulseFollowTime;
-			ar & pulseFollowCharge;
+			if(version>0){
+				ar & pulseFollowTime;
+				ar & pulseFollowCharge;
+			}
 		}
 	}
 };
 
+BOOST_CLASS_VERSION(LAPPDPulse, 1)
+
 /*  Derived classes, if there's a reason to have them. So far...not really
 
 class TDCHit : public Hit {

UserTools/ANNIEEventTreeMaker/ANNIEEventTreeMaker.cpp

@@ -670,6 +670,18 @@ bool ANNIEEventTreeMaker::Execute()
 
 bool ANNIEEventTreeMaker::Finalise()
 {
+  if (MCTruth_fill) {
+    delete fTrueNeutCapVtxX;
+    delete fTrueNeutCapVtxY;
+    delete fTrueNeutCapVtxZ;
+    delete fTrueNeutCapNucleus;
+    delete fTrueNeutCapTime;
+    delete fTrueNeutCapGammas;
+    delete fTrueNeutCapE;
+    delete fTrueNeutCapGammaE;
+    delete fTruePrimaryPdgs;
+  }
+
   Log("ANNIEEventTreeMaker Tool: Got " + std::to_string(processedEvents) + " events", 0, ANNIEEventTreeMakerVerbosity);
   fOutput_tfile->cd();
   fANNIETree->Write();

UserTools/EBLAPPD/EBLAPPD.cpp

@@ -276,7 +276,7 @@ bool EBLAPPD::LoadLAPPDData()
 
 bool EBLAPPD::Matching(int targetTrigger, int matchToTrack)
 {
-  cout << "\033[1;34m******* EBLAPPD : Matching *******\033[0m" << endl;
+  Log("\033[1;34m******* EBLAPPD : Matching *******\033[0m", v_message, verbosityEBLAPPD);
   Log("EBLAPPD: Matching LAPPD data with target trigger " + std::to_string(targetTrigger) + " in track " + std::to_string(matchToTrack), v_message, verbosityEBLAPPD);
 
   std::map<int, std::vector<std::map<uint64_t, uint32_t>>> GroupedTriggersInTotal; // each map is a group of triggers, with the key is the target trigger word
@@ -308,7 +308,7 @@ bool EBLAPPD::Matching(int targetTrigger, int matchToTrack)
     int matchedTrack = 0;
     int matchedIndex = 0;
 
-    for (std::pair<int, std::vector<std::map<uint64_t, uint32_t>>> pair : GroupedTriggersInTotal)
+    for (const std::pair<int, std::vector<std::map<uint64_t, uint32_t>>>& pair : GroupedTriggersInTotal)
     {
       int TrackTriggerWord = pair.first;
       if (matchedNumberInTrack.find(TrackTriggerWord) == matchedNumberInTrack.end())
@@ -318,13 +318,13 @@ bool EBLAPPD::Matching(int targetTrigger, int matchToTrack)
         // Log("EBLAPPD: Skipping TrackTriggerWord " + std::to_string(TrackTriggerWord), v_debug, verbosityEBLAPPD);
         continue;
       }
-      vector<std::map<uint64_t, uint32_t>> GroupedTriggers = pair.second;
+      const vector<std::map<uint64_t, uint32_t>>& GroupedTriggers = pair.second;
 
       for (int j = 0; j < GroupedTriggers.size(); j++)
       {
-        map<uint64_t, uint32_t> groupedTrigger = GroupedTriggers.at(j);
+        const map<uint64_t, uint32_t>& groupedTrigger = GroupedTriggers.at(j);
         // itearte over all the grouped triggers, if the value is target trigger, then calculate the time difference
-        for (std::pair<uint64_t, uint32_t> p : groupedTrigger)
+        for (const std::pair<uint64_t, uint32_t>& p : groupedTrigger)
         {
           if (matchToAllTriggers || p.second == targetTrigger)
           {
@@ -379,4 +379,4 @@ bool EBLAPPD::Matching(int targetTrigger, int matchToTrack)
   }
 
   return true;
-}
+}

UserTools/EBLoadRaw/EBLoadRaw.cpp

@@ -336,6 +336,10 @@ std::vector<std::string> EBLoadRaw::OrganizeRunParts(std::string FileList)
       OrganizedFiles.push_back(SortingVector.at(j).second);
     }
   }
+  else
+  {
+    std::cerr << "EBLoadRaw::OrganizeRunParts: Failed to open file list " << FileList << std::endl;
+  }
   // print the OrganizedFiles
   for (int i = 0; i < (int)OrganizedFiles.size(); i++)
   {

UserTools/EBMRD/EBMRD.cpp

@@ -45,17 +45,17 @@ bool EBMRD::Execute()
   Log("EBMRD: Current buffer size is " + std::to_string(MRDEventsBuffer.size()), v_message, verbosityEBMRD);
   // loop the MRDEvents, save every event to MRDEventsBuffer if it's not already in the buffer
   int newLoadedEvents = 0;
-  for (std::pair<uint64_t, std::vector<std::pair<unsigned long, int>>> p : MRDEvents)
+  for (const std::pair<uint64_t, std::vector<std::pair<unsigned long, int>>>& p : MRDEvents)
   {
-    uint64_t MTCtime = p.first;
-    std::vector<std::pair<unsigned long, int>> WaveMap = p.second;
+    const uint64_t MTCtime = p.first;
+    const std::vector<std::pair<unsigned long, int>>& WaveMap = p.second;
     // if find the MTCtime in the PairedMRDTimeStamps, then skip
     if (PairedMRDTimeStamps.size() > 0)
     {
       bool skip = false;
-      for (std::pair<int, std::vector<uint64_t>> pair : PairedMRDTimeStamps)
+      for (const std::pair<int, std::vector<uint64_t>>& pair : PairedMRDTimeStamps)
       {
-        for (uint64_t t : pair.second)
+        for (const uint64_t t : pair.second)
         {
           if (t == MTCtime)
           {
@@ -135,7 +135,7 @@ bool EBMRD::Finalise()
 
 bool EBMRD::Matching(int targetTrigger, int matchToTrack)
 {
-  cout << "\033[1;34m******* EBMRD : Matching *******\033[0m" << endl;
+  Log("\033[1;34m******* EBMRD : Matching *******\033[0m", v_message, verbosityEBMRD);
   std::map<int, std::vector<std::map<uint64_t, uint32_t>>> GroupedTriggersInTotal; // each map is a group of triggers, with the key is the target trigger word
   m_data->CStore.Get("GroupedTriggersInTotal", GroupedTriggersInTotal);
 
@@ -148,20 +148,20 @@ bool EBMRD::Matching(int targetTrigger, int matchToTrack)
   // in each group of trigger, find the target trigger word and it's time
   // fine the minimum time difference, if smaller than matchTolerance_ns, then save the time to PairedCTCTimeStamps and PairedMRDTimeStamps
   int loopNum = 0;
-  for (std::pair<uint64_t, std::vector<std::pair<unsigned long, int>>> mrdpair : MRDEventsBuffer)
+  for (const std::pair<uint64_t, std::vector<std::pair<unsigned long, int>>>& mrdpair : MRDEventsBuffer)
   {
     if (verbosityEBMRD > 11)
       cout << "******************EBMRD: new MRD event: " << loopNum << endl;
-    uint64_t MTCtime = mrdpair.first;
-    std::vector<std::pair<unsigned long, int>> WaveMap = mrdpair.second;
+    const uint64_t MTCtime = mrdpair.first;
+    const std::vector<std::pair<unsigned long, int>>& WaveMap = mrdpair.second;
     // set minDT to 5 min
     uint64_t minDT = 5 * 60 * 1e9;
     uint64_t minDTTrigger = 0;
     uint64_t dt = 0;
     uint32_t matchedTrigWord = 0;
     int matchedTrack = 0;
     int matchedIndex = 0;
-    for (std::pair<int, std::vector<std::map<uint64_t, uint32_t>>> pair : GroupedTriggersInTotal)
+    for (const std::pair<int, std::vector<std::map<uint64_t, uint32_t>>>& pair : GroupedTriggersInTotal)
     {
       int TrackTriggerWord = pair.first;
       if (TrackTriggerWord != matchToTrack && !matchToAllTriggers)
@@ -172,13 +172,13 @@ bool EBMRD::Matching(int targetTrigger, int matchToTrack)
       if (matchedNumberInTrack.find(TrackTriggerWord) == matchedNumberInTrack.end())
         matchedNumberInTrack.emplace(TrackTriggerWord, 0);
 
-      vector<std::map<uint64_t, uint32_t>> groupedTriggers = pair.second;
+      const vector<std::map<uint64_t, uint32_t>>& groupedTriggers = pair.second;
 
       for (int i = 0; i < groupedTriggers.size(); i++)
       {
-        map<uint64_t, uint32_t> groupedTrigger = groupedTriggers.at(i);
+        const map<uint64_t, uint32_t>& groupedTrigger = groupedTriggers.at(i);
         // itearte over all the grouped triggers, if the value is target trigger, then calculate the time difference
-        for (std::pair<uint64_t, uint32_t> p : groupedTrigger)
+        for (const std::pair<uint64_t, uint32_t>& p : groupedTrigger)
         {
           if (matchToAllTriggers || p.second == targetTrigger)
           {
@@ -234,4 +234,4 @@ bool EBMRD::Matching(int targetTrigger, int matchToTrack)
   }
 
   return true;
-}
+}

UserTools/EBSaver/EBSaver.cpp

@@ -64,20 +64,10 @@ bool EBSaver::Initialise(std::string configfile, DataModel &data)
   m_data->CStore.Get("AmBeTriggerMain", AmBeTriggerMain);
   m_data->CStore.Get("PPSMain", PPSMain);
 
-  InProgressHits = new std::map<uint64_t, std::map<unsigned long, std::vector<Hit>> *>;
-  InProgressChkey = new std::map<uint64_t, std::vector<unsigned long>>;
-  InProgressRecoADCHits = new std::map<uint64_t, std::map<unsigned long, std::vector<std::vector<ADCPulse>>>>;
-  InProgressRecoADCHitsAux = new std::map<uint64_t, std::map<unsigned long, std::vector<std::vector<ADCPulse>>>>;
-  InProgressHitsAux = new std::map<uint64_t, std::map<unsigned long, std::vector<Hit>> *>;
-  FinishedRawAcqSize = new std::map<uint64_t, std::map<unsigned long, std::vector<int>>>;
-
-  RWMRawWaveforms = new std::map<uint64_t, std::vector<uint16_t>>;
-  BRFRawWaveforms = new std::map<uint64_t, std::vector<uint16_t>>;
-
   if (saveBeamInfo)
   {
     Log("EBSaver: saveBeamInfo is true, loading Beam Info", v_message, verbosityEBSaver);
-    LoadBeamInfo();
+    return LoadBeamInfo();
   }
 
   return true;
@@ -1304,16 +1294,25 @@ void EBSaver::BuildEmptyLAPPDData()
   ANNIEEvent->Set("LAPPDTS_PPSMissing", LAPPDTS_PPSMissing);
 }
 
-void EBSaver::LoadBeamInfo()
+bool EBSaver::LoadBeamInfo()
 {
   TFile *file = new TFile(beamInfoFileName.c_str(), "READ");
+
+  if (file->IsZombie()) {
+    delete file;
+    Log("EBSaver: Failed to load beam info from file with name: " + beamInfoFileName, v_error, verbosityEBSaver);
+    return false;
+  }
+
   TTree *tree;
   file->GetObject("BeamTree", tree);
 
   if (!tree)
   {
-    cout << "EBSaver: Failed to load beam info from file with name: " << beamInfoFileName << endl;
-    return;
+    file->Close();
+    delete file;
+    Log("EBSaver: Failed to load beam info from file with name: " + beamInfoFileName, v_error, verbosityEBSaver);
+    return false;
   }
 
   // copy from IFBeamDBInterfaceV2.cpp
@@ -1401,7 +1400,9 @@ void EBSaver::LoadBeamInfo()
 
   Log("EBSaver: Finished loading beam info from " + beamInfoFileName, v_message, verbosityEBSaver);
 
-  return;
+  file->Close();
+  delete file;
+  return true;
 }
 
 bool EBSaver::SaveBeamInfo(uint64_t TriggerTime)

UserTools/EBSaver/EBSaver.h

@@ -59,7 +59,7 @@ class EBSaver : public Tool
     void BuildEmptyMRDData();
     void BuildEmptyLAPPDData();
 
-    void LoadBeamInfo();
+    bool LoadBeamInfo();
 
 private:
     int saveRunNumber;

UserTools/Factory/Factory.cpp

@@ -186,7 +186,6 @@ if (tool=="ProcessedLAPPDFilter") ret=new ProcessedLAPPDFilter;
 if (tool=="BeamQuality") ret=new BeamQuality;
 if (tool=="FitRWMWaveform") ret=new FitRWMWaveform;
 if (tool=="LAPPDLoadTXT") ret=new LAPPDLoadTXT;
-if (tool=="LAPPDBSCharging") ret=new LAPPDBSCharging;
 if (tool=="MuonFitter") ret=new MuonFitter;
 if (tool=="BackTracker") ret=new BackTracker;
 if (tool=="PrintDQ") ret=new PrintDQ;