Added more granular PeakDef XML versioning, and some other small cleanup.

Renamed some PeakDef  member variables to avoid ambitious terminology.
Made PeakDef XML versioning to be Major.Minor format, to better handle backwards compatible upgrades.

Author: wcjohns

InterSpec/PeakDef.h

@@ -384,17 +384,10 @@ class PeakDef
     Mean,
     Sigma,
     GaussAmplitude,
-    LandauAmplitude,   //multiplies peak ampliture (so is between 0.0 and ~0.2)
+    LandauAmplitude,   //multiplies peak amplitude (so is between 0.0 and ~0.2)
     LandauMode,
     LandauSigma,
-//    OffsetPolynomial0,
-//    OffsetPolynomial1,
-//    OffsetPolynomial2,
-//    OffsetPolynomial3,
-//    OffsetPolynomial4,
-//    RangeStartEnergy,
-//    RangeEndEnergy,
-    Chi2DOF,  //for peaks that share a ROI/Continuum, this values is for entire ROI/Continuum
+    Chi2DOF,           //for peaks that share a ROI/Continuum, this values is for entire ROI/Continuum
     NumCoefficientTypes
   };//enum CoefficientType
 
@@ -485,28 +478,22 @@ class PeakDef
   inline void setAmplitudeUncert( const double a );
 
 
-  inline bool useForCalibration() const;
-  inline void useForCalibration( const bool use );
+  inline bool useForEnergyCalibration() const;
+  inline void useForEnergyCalibration( const bool use );
 
   inline bool useForShieldingSourceFit() const;
   inline void useForShieldingSourceFit( const bool use );
-
-  /** Returns if should use for DRF fit.  If has not been explicitly set, will
-   return true if their is a nuclide and transition defined, and the source
-   gamma type is SourceGammaType::NormalGamma.
-   \sa MakeDrf
-   */
-  inline bool useForDrfFit() const;
 
-  /** Sets if the peak should be used or not for DRF fit.
-   \sa MakeDrf
+  /** Returns if should use for DRF intrinsic efficiency fit.  Note that this does not check that the nuclide and transition has actually
+   been defined.
    */
-  inline void useForDrfFit( const bool use );
+  inline bool useForDrfIntrinsicEffFit() const;
+  inline void setUseForDrfIntrinsicEffFit( const bool use );
+  inline bool useForDrfFwhmFit() const;
+  inline void setUseForDrfFwhmFit( const bool use );
+  inline bool useForDrfDepthOfInteractionFit() const;
+  inline void setUseForDrfDepthOfInteractionFit( const bool use );
 
-  /** Resets if the peak should be used for DRF fit.
-   \sa MakeDrf
-   */
-  inline void resetUseForDrfFit();
 
   inline double chi2dof() const;
   inline bool chi2Defined() const;
@@ -824,7 +811,13 @@ class PeakDef
 
   std::shared_ptr<PeakContinuum> m_continuum;
 
-  static const int sm_xmlSerializationVersion;
+  /** For versioning the XML we will use a major.minor notation.
+   Changes made to the XML that are backward compatible (e.g., will read into older version of InterSpec just fine - so this is like if you
+   just add a field), increment the minor version.  Breaking changes (e.x., a change to the name of a XML tag) increment the major version
+   and will cause older versions of InterSpec to not read in the peak.
+   */
+  static const int sm_xmlSerializationMajorVersion;
+  static const int sm_xmlSerializationMinorVersion;
 
   //A maximum of one of the following will be valid: m_parentNuclide,
   //  m_xrayElement, or m_reaction
@@ -843,23 +836,18 @@ class PeakDef
   const ReactionGamma::Reaction *m_reaction;
   float m_reactionEnergy;
 
-  bool m_useForCalibration;
+  bool m_useForEnergyCal;
   bool m_useForShieldingSourceFit;
+
 
-  /** Variable to tell if this peak should be used in the detector response
-   model fit; currently the MakeDRF widget only sets this when saving a N42
-   fit.
-   Can only take on the values {-1,0,1}.
-    -1 means it has not been set and so some simple heuristics will be used to
-       determine if it should be set
-     0 means do not use
-     1 means do use
-   
-   ///ToDo: Implement logic similar to #PeakModel::kUseForShieldingSourceFit
-            for this variable, and maybe make it a bool.  Also have MakeDrf
-            widget update it as the user changes it in the widget.
-   */
-  int m_useForDetectorResponseFit;
+  /** Fif this peak should be used in the detector response function model fit for intrinsic efficiency */
+  bool m_useForDrfIntrinsicEffFit;
+  bool m_useForDrfFwhmFit;
+  bool m_useForDrfDepthOfInteractionFit;
+  
+  static const bool sm_defaultUseForDrfIntrinsicEffFit;
+  static const bool sm_defaultUseForDrfFwhmFit;
+  static const bool sm_defaultUseForDrfDepthOfInteractionFit;
 
   /** Line color of the peak.  Will also (currently) be used to set the fill of
       the peak, just with the alpha channel lowered.
@@ -1042,21 +1030,21 @@ void PeakDef::setAmplitudeUncert( const double a )
 }
 
 
-bool PeakDef::useForCalibration() const
+bool PeakDef::useForEnergyCalibration() const
 {
-  return ( m_useForCalibration &&
+  return ( m_useForEnergyCal &&
            ( (m_radparticleIndex>=0 && m_transition && m_parentNuclide)
             || (m_parentNuclide && (m_sourceGammaType==PeakDef::AnnihilationGamma))
             || (m_xrayElement && m_xrayEnergy>0.0)
             || (m_reaction && m_reactionEnergy>0.0)
            ) );
-}//void useForCalibration() const
+}//void useForEnergyCalibration() const
 
 
-void PeakDef::useForCalibration( const bool use )
+void PeakDef::useForEnergyCalibration( const bool use )
 {
-  m_useForCalibration = use;
-}//void useForCalibration( const bool use )
+  m_useForEnergyCal = use;
+}//void useForEnergyCalibration( const bool use )
 
 
 bool PeakDef::useForShieldingSourceFit() const
@@ -1086,27 +1074,42 @@ void PeakDef::useForShieldingSourceFit( const bool use )
 }//void useForShieldingSourceFit( const bool use )
 
 
-bool PeakDef::useForDrfFit() const
+bool PeakDef::useForDrfIntrinsicEffFit() const
 {
-  if( m_useForDetectorResponseFit == 1 )
-    return true;
-  if( m_useForDetectorResponseFit == 0 )
-    return false;
-  
-  if( m_parentNuclide && m_transition && m_sourceGammaType==SourceGammaType::NormalGamma )
-    return true;
+  //if( !m_parentNuclide || !m_transition || (m_sourceGammaType != SourceGammaType::NormalGamma) )
+  //  return false;
 
-  return false;
+  return m_useForDrfIntrinsicEffFit;
 }
 
-void PeakDef::useForDrfFit( const bool use )
+
+void PeakDef::setUseForDrfIntrinsicEffFit( const bool use )
 {
-  m_useForDetectorResponseFit = (use ? 1 : 0);
+  m_useForDrfIntrinsicEffFit = use;
 }
 
-void PeakDef::resetUseForDrfFit()
+
+bool PeakDef::useForDrfFwhmFit() const
+{
+  return m_useForDrfFwhmFit;
+}
+
+
+void PeakDef::setUseForDrfFwhmFit( const bool use )
+{
+  m_useForDrfFwhmFit = use;
+}
+
+
+bool PeakDef::useForDrfDepthOfInteractionFit() const
+{
+  return m_useForDrfDepthOfInteractionFit;
+}
+
+
+void PeakDef::setUseForDrfDepthOfInteractionFit( const bool use )
 {
-  m_useForDetectorResponseFit = -1;
+  m_useForDrfDepthOfInteractionFit = use;
 }
 
 #endif

src/D3SpectrumDisplayDiv.cpp

@@ -1092,7 +1092,6 @@ void D3SpectrumDisplayDiv::setSearchEnergies( const vector<pair<double,double>>
 
 bool D3SpectrumDisplayDiv::removeDecorativeHighlightRegion( size_t uniqueid )
 {
-  cerr << "D3SpectrumDisplayDiv::removeDecorativeHighlightRegion: uniqueid=" << uniqueid << endl;
   if( uniqueid < 3 )
     return false;
 
@@ -1103,11 +1102,15 @@ bool D3SpectrumDisplayDiv::removeDecorativeHighlightRegion( size_t uniqueid )
     {
       m_highlights.erase( m_highlights.begin() + i );
       setHighlightRegionsToClient();
-      cout << "Found it" << endl;
       return true;
     }
   }
-  cout << "Didnt find it" << endl;
+  
+#if( PERFORM_DEVELOPER_CHECKS )
+  log_developer_error( __func__, ("D3SpectrumDisplayDiv::removeDecorativeHighlightRegion:"
+                                  " Didnt find uniqueid=" + std::to_string(uniqueid)).c_str() );
+#endif
+  
   return false;
 }//void removeDecorativeHighlightRegions()
 

src/EnergyCalMultiFile.cpp

@@ -1176,7 +1176,7 @@ WFlags<ItemFlag> EnergyCalMultiFileModel::flags( const WModelIndex &index ) cons
 
 boost::any EnergyCalMultiFileModel::headerData( int section, Wt::Orientation orientation,
                                                 int role ) const
-{  
+{
 //  if( role == DisplayRole )
 //  {
 //    switch( section )
@@ -1249,10 +1249,14 @@ void EnergyCalMultiFileModel::refreshData()
       if( cal && measpeaks )
       {
         for( const PeakPtr &peak : *measpeaks )
-          samplespeaks.emplace_back( peak->useForEnergyCalibration(), peak );
+        {
+          if( peak && peak->hasSourceGammaAssigned() )
+            samplespeaks.emplace_back( peak->useForEnergyCalibration(), peak );
+        }
       }
 
-      peaks.push_back( samplesinfo );
+      if( !samplespeaks.empty() )
+        peaks.push_back( samplesinfo );
     }//for( const IntSet &samplnums : peaksamplenums )
 
     newdata.push_back( peaks );

src/EnergyCalTool.cpp

@@ -2384,7 +2384,7 @@ bool EnergyCalTool::canDoEnergyFit()
 
   size_t nPeaksToUse = 0;
   for( const PeakModel::PeakShrdPtr &p : *peaks )
-    nPeaksToUse += (p && p->useForCalibration());
+    nPeaksToUse += (p && p->useForEnergyCalibration());
 
   if( nPeaksToUse < 1 )
     return false;
@@ -2517,7 +2517,7 @@ void EnergyCalTool::fitCoefficients()
         continue;
       const PeakDef &peak = *peakptr;
 
-      if( !peak.useForCalibration() )
+      if( !peak.useForEnergyCalibration() )
         continue;
 
       const double wantedEnergy = peak.gammaParticleEnergy();

src/GammaInteractionCalc.cpp

@@ -956,24 +956,24 @@ void PointSourceShieldingChi2Fcn::massFraction( double &massFrac,
                                         const std::vector<double> &errors ) const
 {
   massFrac = uncert = 0.0;
-  typedef MaterialToNucsMap::const_iterator MaterialToNucsMapIter;
+  
   if( !material || !nuc )
-    throw runtime_error( "PointSourceShieldingChi2Fcn::massFraction(): invalid "
-                         "input" );
-  MaterialToNucsMapIter matpos = m_nuclidesToFitMassFractionFor.find(material);
+    throw runtime_error( "PointSourceShieldingChi2Fcn::massFraction(): invalid input" );
 
-  if( matpos == m_nuclidesToFitMassFractionFor.end() )
+  const auto matpos = m_nuclidesToFitMassFractionFor.find(material);
+  
+  if( matpos == end(m_nuclidesToFitMassFractionFor) )
     throw runtime_error( "PointSourceShieldingChi2Fcn::massFraction(): "
                          + material->name + " is not a material with a variable"
                          " mass fraction" );
-  const std::vector<const SandiaDecay::Nuclide *> &nucs
-                        = m_nuclidesToFitMassFractionFor.find(material)->second;
-  vector<const SandiaDecay::Nuclide *>::const_iterator pos;
+  
+  const std::vector<const SandiaDecay::Nuclide *> &nucs = matpos->second;
+  
   //nucs is actually sorted by symbol name, could do better than linear search
-  pos = std::find( nucs.begin(), nucs.end(), nuc );
-  if( pos == nucs.end() )
+  const auto pos = std::find( begin(nucs), end(nucs), nuc );
+  if( pos == end(nucs) )
     throw runtime_error( "PointSourceShieldingChi2Fcn::massFraction(): "
-                         +nuc->symbol + " was not a nuc fit for mass fraction"
+                         + nuc->symbol + " was not a nuc fit for mass fraction"
                          " in " + material->name );
 
   double totalfrac = 0.0;
@@ -989,8 +989,7 @@ void PointSourceShieldingChi2Fcn::massFraction( double &massFrac,
   }//for( const SandiaDecay::Nuclide *n : nucs )
 
   size_t matmassfracstart = 0;
-  for( MaterialToNucsMapIter iter = m_nuclidesToFitMassFractionFor.begin();
-      iter != matpos; ++iter )
+  for( auto iter = begin(m_nuclidesToFitMassFractionFor); iter != matpos; ++iter )
   {
     if( iter->second.size() )
       matmassfracstart += (iter->second.size()-1);