Updated changes from main

.github/pull_request_template.md

@@ -0,0 +1,12 @@
+## Describe your changes
+
+## Checklist before submitting your PR
+- [ ] This PR implements a single change (one new/modified Tool, or a set of changes to implement one new/modified feature)
+- [ ] This PR alters the minimum number of files to affect this change
+- [ ] If this PR includes a new Tool, a README and minimal demonstration ToolChain is provided
+- [ ] If a new Tool/ToolChain requires model or configuration files, their paths are not hard-coded, and means of generating those files is described in the readme, with examples provided on /pnfs/annie/persistent
+- [ ] For every `new` usage, there is a reason the data must be on the heap
+- [ ] For every `new` there is a `delete`, unless I explicitly know why (e.g. ROOT or a BoostStore takes ownership)
+
+## Additional Material
+Attach any validation or demonstration files here. You may also link to relavant docdb articles.

.github/workflows/tempbuild.yml

@@ -100,6 +100,7 @@ jobs:
             echo `pwd`
             ls -l
             cd /TA
+            git config --global --add safe.directory /TA
             ls -l
             ln -s /ToolAnalysis/ToolDAQ $PWD/ToolDAQ
             ls -l ./ToolDAQ

.gitignore

@@ -34,4 +34,5 @@ DataModel/DataModel_Linkdef.hh
 # These are imported as part of ToolPack
 UserTools/ImportedTools
 UserTools/InactiveTools
+UserTools/MyFactory
 

DataModel/ADCPulse.cpp

@@ -7,9 +7,11 @@
 ADCPulse::ADCPulse(int TubeId, double start_time, double peak_time,
   double baseline, double sigma_baseline, unsigned long area,
   unsigned short raw_amplitude, double calibrated_amplitude,
-  double charge) : Hit(TubeId, start_time, charge),
+  double charge, const std::vector<double>& trace_x, const std::vector<double>& trace_y) : 
+  Hit(TubeId, start_time, charge),
   start_time_(start_time), peak_time_(peak_time),
   baseline_(baseline), sigma_baseline_(sigma_baseline), raw_area_(area),
-  raw_amplitude_(raw_amplitude), calibrated_amplitude_(calibrated_amplitude)
+  raw_amplitude_(raw_amplitude), calibrated_amplitude_(calibrated_amplitude),
+  trace_x_(trace_x), trace_y_(trace_y)
 {
 }

DataModel/ADCPulse.h

@@ -9,6 +9,7 @@
 // ToolAnalysis includes
 #include "ChannelKey.h"
 #include "Hit.h"
+#include <vector>
 
 class ADCPulse : public Hit {
 
@@ -22,8 +23,9 @@ class ADCPulse : public Hit {
     // int TubeId member
     ADCPulse(int TubeId, double start_time, double peak_time,
       double baseline, double sigma_baseline, unsigned long raw_area,
-      unsigned short raw_amplitude, double calibrated_amplitude,
-      double charge);
+      unsigned short raw_amplitude, double calibrated_amplitude, double charge, 
+      const std::vector<double>& trace_x = std::vector<double>(),
+      const std::vector<double>& trace_y = std::vector<double>());
 
     // @brief Returns the start time (ns) of the pulse relative to the
     // start of its minibuffer
@@ -59,6 +61,10 @@ class ADCPulse : public Hit {
     // (baseline-subtracted) pulse
     inline double amplitude() const { return calibrated_amplitude_; }
 
+    // @brief Returns the x [ns] and y [ADC] points of the "found" pulse (baseline-subtracted and relative to pulse start point)
+    inline const std::vector<double>& GetTraceXPoints() const { return trace_x_; }
+    inline const std::vector<double>& GetTraceYPoints() const { return trace_y_; }
+
     template <class Archive> void serialize(Archive& ar,
       const unsigned int version)
     {
@@ -71,6 +77,10 @@ class ADCPulse : public Hit {
       ar & raw_area_;
       ar & raw_amplitude_;
       ar & calibrated_amplitude_;
+      if (version > 0) {
+        ar & trace_x_;
+        ar & trace_y_;
+      }
     }
 
   protected:
@@ -83,4 +93,11 @@ class ADCPulse : public Hit {
 
     unsigned short raw_amplitude_; // ADC
     double calibrated_amplitude_; // V
+
+    std::vector<double> trace_x_ = {};  // x points of the pulse (start at 0, relative to pulse start) [ns]
+    std::vector<double> trace_y_ = {};  // y points of the pulse (baseline-subtracted) [ADC]
 };
+
+// (From Andrew Sutton) Need to increment the class version since we added time as a new variable
+// the version number ensures backward compatibility when serializing 
+BOOST_CLASS_VERSION(ADCPulse, 1)

DataModel/ANNIEGeometry.cpp

@@ -190,8 +190,8 @@ void ANNIEGeometry::SetGeometry(){
   //WCSim
   fCylRadius = 152.0; //cm
   fCylLength = 396.0; //cm
-  fCylFiducialRadius = 0.0;
-  fCylFiducialLength = 0.0;
+  fCylFiducialRadius = 100.0; //cm
+  fCylFiducialLength = 200.0; //cm
   fXoffset = 0.0;
   fYoffset = 0.0; 
   fZoffset = 0.0;
@@ -337,11 +337,11 @@ bool ANNIEGeometry::InsideDetector(double x, double y, double z)
 bool ANNIEGeometry::InsideFiducialVolume(double x, double y, double z)
 {
   if( fGeoType==ANNIEGeometry::kCylinder ){
-    if( z>=-0.5*fCylFiducialLength && z<=+0.5*fCylFiducialLength
-     && x*x+y*y<=fCylFiducialRadius*fCylFiducialRadius ){
+    if( y>=-0.5*fCylFiducialLength && y<=+0.5*fCylFiducialLength
+     && x*x+z*z<=fCylFiducialRadius*fCylFiducialRadius ){
       return 1;
     }
-  } else std::cout<<"WTF ANNIE Should Be A Cylinder!!!!"<<std::endl;
+  } else std::cout<<"WTH ANNIE Should Be A Cylinder!!!!"<<std::endl;
 
   return 0;
 }
@@ -377,42 +377,43 @@ double ANNIEGeometry::DistanceToEdge(double x, double y, double z)
       double dr = 0.0;
       if( fCylRadius>dr ) dr = fCylRadius;
       if( 0.5*fCylLength>dr ) dr = 0.5*fCylLength;
-      if( -sqrt(x*x+y*y)+fCylRadius<dr ) dr = -sqrt(x*x+y*y)+fCylRadius;
-      if( -z+0.5*fCylLength<dr ) dr = -z+0.5*fCylLength;
-      if( +z+0.5*fCylLength<dr ) dr = +z+0.5*fCylLength;
+      if( -sqrt(x*x+z*z)+fCylRadius<dr ) dr = -sqrt(x*x+z*z)+fCylRadius;
+      if( -y+0.5*fCylLength<dr ) dr = -y+0.5*fCylLength;
+      if( y+0.5*fCylLength<dr ) dr = y+0.5*fCylLength;
       return dr;
     }
 
     // outside detector (convention: -ve dr)
     else{
 
       // side region
-      if( z>=-0.5*fCylLength && z<=+0.5*fCylLength ){
-        return -sqrt(x*x+y*y)+fCylRadius;
+      if( y>=-0.5*fCylLength && y<=+0.5*fCylLength ){
+        return -sqrt(x*x+z*z)+fCylRadius;
       }
 
-      // top region
-      if( z<=-0.5*fCylLength
-       && x*x+y*y<fCylRadius*fCylRadius ){
-        return +z+0.5*fCylLength;
+      // below tank
+      if( y<=-0.5*fCylLength
+       && x*x+z*z<fCylRadius*fCylRadius ){
+        return y+0.5*fCylLength;
       }
-      if( z>=+0.5*fCylLength
-       && x*x+y*y<fCylRadius*fCylRadius ){
-        return -z+0.5*fCylLength;
+      // above tank
+      if( y>=+0.5*fCylLength
+       && x*x+z*z<fCylRadius*fCylRadius ){
+        return -y+0.5*fCylLength;
       }
 
       // corner regions
-      if( z>=+0.5*fCylLength
-       && x*x+y*y>=fCylRadius ){
-        double dr = sqrt(x*x+y*y)-fCylRadius;
-        double dz = -z+0.5*fCylLength;
-        return -sqrt(dr*dr+dz*dz);
+      if( y>=+0.5*fCylLength
+       && x*x+z*z>=fCylRadius ){
+        double dr = sqrt(x*x+z*z)-fCylRadius;
+        double dy = -y+0.5*fCylLength;
+        return -sqrt(dr*dr+dy*dy);
       }
-      if( z<=-0.5*fCylLength
-       && x*x+y*y>=fCylRadius ){
-        double dr = sqrt(x*x+y*y)-fCylRadius;
-        double dz = +z+0.5*fCylLength;
-        return -sqrt(dr*dr+dz*dz);
+      if( y<=-0.5*fCylLength
+       && x*x+z*z>=fCylRadius ){
+        double dr = sqrt(x*x+z*z)-fCylRadius;
+        double dy = y+0.5*fCylLength;
+        return -sqrt(dr*dr+dy*dy);
       }
     }
   }