Some small fixes from use.

Add refreshing kinetic reference lines when peaks are added/removed/refreshed.
Remove kinetic reference lines when they are disabled.
Fix a potential uncaught excetion in ExternalRid, as well as some other small improvements.
Fix using a wrong name in batch analysis warning.
Add current to-do, known issues to kinetic ref lines.
Set AD to me non-zero to start with in RelActAuto, for the self-attenuating shielding.

Author: wcjohns

InterSpec/RefLineKinetic.h

@@ -45,6 +45,21 @@ struct ExternalRidResults;
 class D3SpectrumDisplayDiv;
 class DetectorPeakResponse;
 
+/**
+TODO items:
+ - Extend the energy lines to the full-height of the window - maybe either use a dotted line, or one with some alpha, or make the solid line, but a dot at the original height
+ - For the random sum peaks, also show likely nuclides
+ - When multiple nuclides are candidates, need to allow switching between them, or indicate things in some way to either cycle through them, and/or let the user
+ - Each "catagory" of nuclides should get a different color, controllable by the color theme
+
+ Current shortcommings:
+ - Cascade sums not accounted for
+ - The filtering the number of lines for each set could def use improvement
+ - Lines not updated when there is an energy calibration change (the auto-serch peak should also be updated - and any being searched for need to be cancelled and restarted)
+ - Should be able to handle RID output results like DU, Uranium, HEU, Neutrons, "Sr-85/Kr85", Annihilation, etc
+ - Having a peak with a source associated with it should _really_ increase the weight (see HPGe Lu177 spectrum for example why).
+ - Should pick the most important line, get the profile weight for the source, and adjust the source weight a bit using this
+ */
 class RefLineKinetic : public Wt::WObject
 {
 public:
@@ -105,7 +120,11 @@ class RefLineKinetic : public Wt::WObject
 
   /** Helper method to assign color to ReferenceLineInfo, applying fallback logic. */
   void assignColorToInput( ReferenceLineInfo &input ) const;
-  
+
+  void peaksAdded();
+  void peaksRemoved();
+  void peakModified();
+
   InterSpec *m_interspec;
   D3SpectrumDisplayDiv *m_chart;
 

src/BatchPeak.cpp

@@ -812,7 +812,10 @@ BatchPeak::BatchPeakFitResult fit_peaks_in_file( const std::string &exemplar_fil
 
     if( !exemplar_is_n42 && (options.use_exemplar_energy_cal || options.use_exemplar_energy_cal_for_background) )
       throw runtime_error( "Exemplar file wasnt an N42 file, but using its energy cal was specified - not allowed." );
-    
+
+    if( exemplar_is_n42 )
+      
+
     if( exemplar_is_n42 )
       exemplar_n42 = exemplar;
   }//if( !cached_exemplar_n42 )
@@ -857,7 +860,7 @@ BatchPeak::BatchPeakFitResult fit_peaks_in_file( const std::string &exemplar_fil
   }//if( exemplar_is_n42 )
 
   BatchPeakFitResult results;
-  results.file_path = exemplar_filename;
+  results.file_path = filename;
   results.options = options;
   results.exemplar = exemplar_n42;
   results.exemplar_sample_nums = exemplar_sample_nums;
@@ -878,8 +881,11 @@ BatchPeak::BatchPeakFitResult fit_peaks_in_file( const std::string &exemplar_fil
       const bool loaded = specfile->load_file( filename, SpecUtils::ParserType::Auto, filename );
       if( !loaded || !specfile->num_measurements() )
       {
-        results.warnings.push_back( "Couldnt read in '" + filename + "' as a spectrum file -- skipping." );
-        
+        if( SpecUtils::is_file(filename) )
+          results.warnings.push_back( "Couldnt read in '" + filename + "' as a spectrum file -- skipping." );
+        else
+          results.warnings.push_back( "Could not access '" + filename + "' -- skipping." );
+
         return results;
       }//if( !loaded )
     }//if( cached_spectrum ) / else

src/ExternalRidResult.cpp

@@ -23,6 +23,8 @@
 
 #include "InterSpec_config.h"
 
+#include "SpecUtils/StringAlgo.h"
+
 #include "InterSpec/ExternalRidResult.h"
 #include "InterSpec/DecayDataBaseServer.h"
 #include "InterSpec/InterSpec.h"
@@ -85,13 +87,22 @@ void ExternalRidIsotope::init()
       if( const SandiaDecay::Element * const el = db->element(name) )
       {
         source = el;
-      }else if( const ReactionGamma * const rctn_db = ReactionGammaServer::database() )
+      }else if( ((name.find('(')!=std::string::npos) && (name.find(')')!=std::string::npos))
+               || SpecUtils::icontains(name,"ann") )
       {
-        std::vector<ReactionGamma::ReactionPhotopeak> possible_rctns;
-        rctn_db->gammas( name, possible_rctns );
-        
-        if( !possible_rctns.empty() && possible_rctns[0].reaction ) // Take the first reaction found
-          source = possible_rctns[0].reaction;
+        try
+        {
+          std::vector<ReactionGamma::ReactionPhotopeak> possible_rctns;
+          const ReactionGamma * const rctn_db = ReactionGammaServer::database();
+          if( rctn_db )
+            rctn_db->gammas( name, possible_rctns );
+
+          if( !possible_rctns.empty() && possible_rctns[0].reaction ) // Take the first reaction found
+            source = possible_rctns[0].reaction;
+        }catch( std::exception & )
+        {
+          // ReactionGammaServer::gammas throw if invalid reaction name.
+        }
       }
     }//if( !nuc )
   }//if( std::holds_alternative<std::monostate>(source) && !name.empty() )

src/RefLineKinetic.cpp

@@ -158,7 +158,14 @@ RefLineKinetic::RefLineKinetic( D3SpectrumDisplayDiv *chart, InterSpec *interspe
 
   m_interspec->externalRidResultsRecieved().connect( boost::bind( &RefLineKinetic::autoRidResultsRecieved, this, boost::placeholders::_1 ) );
   m_interspec->colorThemeChanged().connect( boost::bind( &RefLineKinetic::colorThemeChanged, this, boost::placeholders::_1 ) );
-  
+  PeakModel * const pmodel = m_interspec->peakModel();
+  if( pmodel )
+  {
+    pmodel->rowsInserted().connect( boost::bind( &RefLineKinetic::peaksAdded, this ) );
+    pmodel->rowsRemoved().connect( boost::bind( &RefLineKinetic::peaksRemoved, this ) );
+    pmodel->dataChanged().connect( boost::bind( &RefLineKinetic::peakModified, this ) );
+  }
+
   // TODO: We also need to update lines after an energy calbration is done
   // TODO: We also need to make sure hint peaks are adjusted for energy changes
 
@@ -244,16 +251,55 @@ void RefLineKinetic::assignColorToInput( ReferenceLineInfo &lines ) const
 }//void RefLineKinetic::assignColorToInput(...)
 
 
+void RefLineKinetic::peaksAdded()
+{
+  if( !m_active )
+    return;
+
+  m_renderFlags |= KineticRefLineRenderFlags::UpdateLines;
+  m_chart->scheduleRenderKineticRefLine();
+  m_current_ref_lines.reset();
+}
+
+
+void RefLineKinetic::peaksRemoved()
+{
+  if( !m_active )
+    return;
+
+  m_renderFlags |= KineticRefLineRenderFlags::UpdateLines;
+  m_chart->scheduleRenderKineticRefLine();
+  m_current_ref_lines.reset();
+}
+
+
+void RefLineKinetic::peakModified()
+{
+  if( !m_active )
+    return;
+
+  m_renderFlags |= KineticRefLineRenderFlags::UpdateLines;
+  m_chart->scheduleRenderKineticRefLine();
+  m_current_ref_lines.reset();
+}
+
+
 void RefLineKinetic::setActive( bool active )
 {
   if( m_active == active )
     return;
 
   m_active = active;
-  
-  m_renderFlags |= KineticRefLineRenderFlags::UpdateLines;
-  m_chart->scheduleRenderKineticRefLine();
+
   m_current_ref_lines.reset();
+  if( m_active )
+  {
+    m_renderFlags |= KineticRefLineRenderFlags::UpdateLines;
+    m_chart->scheduleRenderKineticRefLine();
+  }else
+  {
+    m_chart->setKineticRefernceLines( vector<pair<double,ReferenceLineInfo>>{}, "" );
+  }
 }//void RefLineKinetic::setActive( bool active )
 
 
@@ -270,6 +316,9 @@ shared_ptr<vector<pair<double,ReferenceLineInfo>>> RefLineKinetic::current_lines
 
 void RefLineKinetic::autoSearchPeaksSet( const SpecUtils::SpectrumType spectrum )
 {
+  if( !m_active )
+    return;
+  
   m_renderFlags |= KineticRefLineRenderFlags::UpdateLines;
   m_chart->scheduleRenderKineticRefLine();
   m_current_ref_lines.reset();
@@ -1154,15 +1203,21 @@ void RefLineKinetic::startUpdateLines()
         }else if( reaction_db )
         {
           // Try to get reaction from ReactionGamma database
-          vector<ReactionGamma::ReactionPhotopeak> possible_rctns;
-          reaction_db->gammas( result.nuclide_, possible_rctns );
-          
-          if( !possible_rctns.empty() )
+          try
           {
-            canonical_name = possible_rctns[0].reaction->name();
-            found_source = true;
+            vector<ReactionGamma::ReactionPhotopeak> possible_rctns;
+            reaction_db->gammas( result.nuclide_, possible_rctns );
+
+            if( !possible_rctns.empty() )
+            {
+              canonical_name = possible_rctns[0].reaction->name();
+              found_source = true;
+            }
+          }catch( std::exception & )
+          {
+            //we get here for example if nuclide did have paranthesis
           }
-        }
+        }//
       }//if( result.nuclide_ is nuclide ) / else
 
       if( !found_source )

src/RelActCalcAuto.cpp

@@ -2746,7 +2746,13 @@ struct RelActAutoCostFcn /* : ROOT::Minuit2::FCNBase() */
 
               assert( manual_solution.m_rel_eff_eqn_coefficients.size() > manual_index );
               parameters[this_rel_eff_start + 1] = manual_solution.m_rel_eff_eqn_coefficients.at(manual_index); //Areal density; both manual and auto RelEff use g/cm2
-              
+
+              if( rel_eff_curve.phys_model_self_atten->fit_areal_density )
+              {
+                if( parameters[this_rel_eff_start + 1]  < 1.0E-4 )
+                  parameters[this_rel_eff_start + 1] = std::min( std::max( 1.0, rel_eff_curve.phys_model_self_atten->lower_fit_areal_density), rel_eff_curve.phys_model_self_atten->upper_fit_areal_density );
+              }//if( rel_eff_curve.phys_model_self_atten->fit_areal_density )
+
               manual_index += 1;
             }//if( options.phys_model_self_atten )