EVB2 cleanup per review comments

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;

UserTools/LAPPDTimeAlignment/LAPPDTimeAlignment.cpp

@@ -305,6 +305,7 @@ double LAPPDTimeAlignment::Tfit(std::vector<double> *wf)
           }
         }
         firstcross = false;
+        delete edge;
       }
     }
     else
@@ -364,6 +365,7 @@ double LAPPDTimeAlignment::Tfit(std::vector<double> *wf)
         */
 
         firstcross = false;
+        delete edge;
       }
     }
   }

UserTools/LAPPDTreeMaker/LAPPDTreeMaker.cpp

@@ -171,7 +171,6 @@ bool LAPPDTreeMaker::Initialise(std::string configfile, DataModel &data)
   fGroupedTrigger->Branch("gTrigType", &groupedTriggerType, "gTrigType/I");
   fGroupedTrigger->Branch("gTrigNum", &TriggerGroupNumInThisEvent, "gTrigNum/I");
 
-  TriggerWordMap = new std::map<uint64_t, std::vector<uint32_t>>;
   m_data->Stores["ANNIEEvent"]->Header->Get("AnnieGeometry", _geom);
   EventNumber = 0;
 
@@ -369,7 +368,10 @@ bool LAPPDTreeMaker::Finalise()
   fTimeStamp->Write();
   fTrigger->Write();
   fGroupedTrigger->Write();
+
   file->Close();
+  delete file;
+
   return true;
 }
 
@@ -1090,4 +1092,4 @@ void LAPPDTreeMaker::LoadLAPPDMapInfo()
   {
     cout << "LAPPDTreeMaker::LoadLAPPDMapInfo, no LAPPDDataMap found" << endl;
   }
-}
+}