Fixed Shielding/Source fit issue; a few other minor things.

Fixed issue with shielding/source fit when nuclide ages for an element were selected to have the same age, it would cause all sorts of badness when some of the nuclides for an element were not candidates for aging.
Fixed a couple small issues with the testing widget when there was a shielding/source fit test defined.
Added some DRF functions to the Math/Terminal tool.

Author: wcjohns

InterSpec/ShieldingSourceDisplay.h

@@ -55,6 +55,9 @@ class DetectorDisplay;
 class PopupDivMenuItem;
 class DetectorPeakResponse;
 struct ShieldingSourceModel;
+#if( INCLUDE_ANALYSIS_TEST_SUITE )
+class SpectrumViewerTester;
+#endif
 
 namespace SandiaDecay
 {
@@ -1050,6 +1053,11 @@ class ShieldingSourceDisplay : public Wt::WContainerWidget
   };//class WCartesianChart
 
   static const int sm_xmlSerializationVersion;
+  
+#if( INCLUDE_ANALYSIS_TEST_SUITE )
+  // So the tester can call updateChi2ChartActual
+  friend class SpectrumViewerTester;
+#endif
 };//class ShieldingSourceDisplay
 
 

InterSpec/TerminalModel.h

@@ -129,7 +129,12 @@ class TerminalModel {
     double gammaMinFor( const std::string& histogram );
     double gammaMax();
     double gammaMaxFor( const std::string& histogram );
-    
+  
+  double drfFWHM( const double energy );
+  double drfIntrinsicEff( const double energy );
+  double drfGeometricEff( const std::string &distance );
+  double drfEfficiency( const double energy, const std::string &distance );
+  
 protected:  /* Command methods (complete actions on Spectrum, cannot be used with parser)
              To add a new command in the Terminal tool:
                  1. Add the corresponding CommandType enum inside the TerminalModel Header file.

main.cpp

@@ -82,7 +82,7 @@ int main( int argc, char **argv )
 #endif //#if( ANDROID )
 
   std::cout << std::showbase << std::hex << "Running with Wt version "
-            << WT_VERSION << ", from executable compiled on "
+            << WT_VERSION << std::dec << ", from executable compiled on "
             << __DATE__ << std::endl;
 
 #if( PERFORM_DEVELOPER_CHECKS )

src/FeatureMarkerWidget.cpp

@@ -65,9 +65,9 @@ FeatureMarkerWindow::FeatureMarkerWindow( InterSpec *viewer )
   //m_feature->setHeight( WLength(100,WLength::Percentage) );
 
   // This next call seems to help resize the window to show all the contents, otherwise "Sum Peak"
-  //  will hang-off the bottom of the window.
-  //  Although definitely not 100% effective...
-  centerWindow();
+  //  will hang-off the bottom of the window.  Definitely a hack.
+  doJavaScript( "setTimeout( function(){ window.dispatchEvent(new Event('resize')); }, 0 );"
+                "setTimeout( function(){ window.dispatchEvent(new Event('resize')); }, 50 );" );
 
   show();
 

src/GammaInteractionCalc.cpp

@@ -1816,8 +1816,7 @@ vector< tuple<double,double,double,Wt::WColor,double> >
 
 
   EnergyCountMap energy_count_map;
-  const vector<pair<double,double> > energie_widths
-                                          = observedPeakEnergyWidths( m_peaks );
+  const vector<pair<double,double> > energie_widths = observedPeakEnergyWidths( m_peaks );
 
   if( allow_multiple_iso_contri )
   {

src/InterSpec.cpp

@@ -4594,14 +4594,9 @@ void InterSpec::loadTestStateFromN42( std::istream &input )
     const xml_node<char> *sourcefit = InterSpecNode->first_node( "ShieldingSourceFit" );
     if( sourcefit )
     {
-      if( !m_shieldingSourceFit )
-      {
-        showShieldingSourceFitWindow();
-        if( m_shieldingSourceFitWindow )
-          m_shieldingSourceFitWindow->hide();
-      }//if( !m_shieldingSourceFit )
-      
+      showShieldingSourceFitWindow();
       m_shieldingSourceFit->deSerialize( sourcefit );
+      closeShieldingSourceFitWindow();
     }//if( sourcefit )
 
     stringstream msg;

src/ShieldingSourceDisplay.cpp

@@ -2327,6 +2327,9 @@ void SourceFitModel::setSharredAgeNuclide( const SandiaDecay::Nuclide *dependant
   if( row < 0 )
     return;
 
+  if( PeakDef::ageFitNotAllowed( dependantNuc ) )
+    definingNuc = nullptr;
+  
   if( definingNuc )
   {
     const int definingRow = nuclideIndex( definingNuc );
@@ -2347,7 +2350,7 @@ void SourceFitModel::setSharredAgeNuclide( const SandiaDecay::Nuclide *dependant
                          " defining nuclides must have same atomic number" );
 
   iso.ageDefiningNuc = definingNuc;
-  dataChanged().emit( createIndex(row,kAge,(void *)0),
+  dataChanged().emit( createIndex(row,kFitAge,(void *)0),
                       createIndex(row,kAgeUncertainty,(void *)0) );
 }//void makeAgeFitable( const SandiaDecay::Nuclide *nuc, bool fit )
 
@@ -2404,13 +2407,13 @@ void SourceFitModel::setUseSameAgeForIsotopes( bool useSame )
   if( !m_sameAgeForIsotopes )
   {
     for( size_t i = 0; i < m_nuclides.size(); ++i )
-      setSharredAgeNuclide( m_nuclides[i].nuclide, NULL );
+      setSharredAgeNuclide( m_nuclides[i].nuclide, nullptr );
     return;
   }//if( !m_sameAgeForIsotopes )
 
   //construct map from element number to isotopes being fit for
   //if there is more than one isotope, choose the youngest age to assign to
-  //all of the isotopes.  Do the assignemnet and update the chart
+  //all of the isotopes.  Do the assignment and update the chart
   typedef map< int, vector<const SandiaDecay::Nuclide *> > ElToNucMap_t;
   ElToNucMap_t elToNucMap;
 
@@ -2424,29 +2427,46 @@ void SourceFitModel::setUseSameAgeForIsotopes( bool useSame )
   {
     const vector<const SandiaDecay::Nuclide *> &nucs = vt.second;
     if( nucs.size() < 2 )
+    {
+      if( !nucs.empty() )
+        setSharredAgeNuclide( nucs[0], nullptr );
       continue;
+    }
 
     bool fitAgeWanted = false;
-    size_t minIndex = 0;
+    size_t minIndex = 0, numSharingAge = 0;
     double minAge = std::numeric_limits<double>::infinity();
     for( size_t i = 0; i < nucs.size(); ++i )
     {
       const SandiaDecay::Nuclide *nuc = nucs[i];
+      if( PeakDef::ageFitNotAllowed( nuc ) )
+      {
+        setSharredAgeNuclide( nuc, nullptr ); // jic, I guess, but not really needed, probably
+        continue;
+      }
+        
       const int ind = nuclideIndex( nuc );
       const double thisage = age( ind );
       if( thisage < minAge )
       {
         minIndex = i;
         minAge = thisage;
       }//if( age < minAge )
+      
+      numSharingAge += 1;
       fitAgeWanted = (fitAgeWanted || fitAge(ind));
     }//for( const SandiaDecay::Nuclide *nuc : nucs )
 
     for( size_t i = 0; i < nucs.size(); ++i )
     {
       const SandiaDecay::Nuclide *nuc = nucs[i];
-      
-      if( i == minIndex )
+      if( PeakDef::ageFitNotAllowed( nuc ) )
+        continue;
+        
+      if( numSharingAge < 2 )
+      {
+        setSharredAgeNuclide( nuc, nullptr );
+      }else if( i == minIndex )
       {
         WModelIndex ind = index( nuc, SourceFitModel::kAge );
         setData( ind, fitAgeWanted );
@@ -2486,6 +2506,7 @@ void SourceFitModel::insertPeak( const PeakShrdPtr peak )
   newIso.fitActivity = true;
   newIso.nuclide = peak->parentNuclide();
   newIso.age = PeakDef::defaultDecayTime( newIso.nuclide );
+  newIso.ageDefiningNuc = nullptr;
   newIso.fitAge = false;
   newIso.ageIsFittable = !PeakDef::ageFitNotAllowed( newIso.nuclide );
 
@@ -2506,13 +2527,13 @@ void SourceFitModel::insertPeak( const PeakShrdPtr peak )
   if( m_previousResults.size() > 100 )
     m_previousResults.clear();
 
-  if( m_sameAgeForIsotopes )
+  if( m_sameAgeForIsotopes && newIso.ageIsFittable )
   {
     vector<size_t> thisElementIndexs;
     for( size_t i = 0; i < m_nuclides.size(); ++i )
     {
       const IsoFitStruct &iso = m_nuclides[i];
-      if( iso.nuclide->atomicNumber == newIso.nuclide->atomicNumber )
+      if( iso.ageIsFittable && (iso.nuclide->atomicNumber == newIso.nuclide->atomicNumber) )
       {
         thisElementIndexs.push_back( i );
         if( !iso.ageDefiningNuc )
@@ -2531,7 +2552,7 @@ void SourceFitModel::insertPeak( const PeakShrdPtr peak )
 //      else
 //        newIso.ageDefiningNuc = previso.nuclide;
     }//if( !newIso.ageDefiningNuc && !thisElementIndexs.empty() )
-  }//if( m_sameAgeForIsotopes )
+  }//if( m_sameAgeForIsotopes && newIso.ageIsFittable )
 
 
 
@@ -2547,6 +2568,7 @@ void SourceFitModel::insertPeak( const PeakShrdPtr peak )
         progeny.insert( trans->parent );
     }
   }//for( loop over peaks)
+  
   newIso.numProgenyPeaksSelected = progeny.size();
 
   std::vector<IsoFitStruct>::iterator pos;
@@ -2756,7 +2778,7 @@ void SourceFitModel::peakModelDataChangedCallback( Wt::WModelIndex topLeft,
   for( const IsoFitStruct &ifs : m_nuclides )
     postisotopes.push_back( ifs.nuclide );
 
-  if( m_sameAgeForIsotopes && (preisotopes.size()!=postisotopes.size()) )
+  if( m_sameAgeForIsotopes && (preisotopes.size() != postisotopes.size()) )
   {
     vector<const SandiaDecay::Nuclide *> removednucs, addednucs;
     for( const SandiaDecay::Nuclide *nuc : preisotopes )
@@ -2779,7 +2801,7 @@ void SourceFitModel::peakModelDataChangedCallback( Wt::WModelIndex topLeft,
 
       for( IsoFitStruct &ifs : m_nuclides )
       {
-        if( ifs.nuclide->atomicNumber == nuc->atomicNumber )
+        if( ifs.ageIsFittable && (ifs.nuclide->atomicNumber == nuc->atomicNumber) )
         {
           if( ifs.age < minage )
           {
@@ -2794,20 +2816,25 @@ void SourceFitModel::peakModelDataChangedCallback( Wt::WModelIndex topLeft,
       {
         for( IsoFitStruct &ifs : m_nuclides )
         {
-          if( ifs.nuclide->atomicNumber == nuc->atomicNumber )
+          if( ifs.ageIsFittable && (ifs.nuclide->atomicNumber == nuc->atomicNumber) )
             setSharredAgeNuclide( ifs.nuclide, defining );
         }//for( IsoFitStruct &ifs : m_nuclides )
       }//if( removedADefining )
     }//for( const SandiaDecay::Nuclide *nuc : removednucs )
 
     for( const SandiaDecay::Nuclide *nuc : addednucs )
     {
+      if( PeakDef::ageFitNotAllowed( nuc ) )
+        continue;
+      
       const SandiaDecay::Nuclide *defining = NULL;
       double minage = std::numeric_limits<double>::infinity();
 
       for( IsoFitStruct &ifs : m_nuclides )
       {
-        if( (ifs.age<minage) && (ifs.nuclide->atomicNumber==nuc->atomicNumber) )
+        if( ifs.ageIsFittable
+           && (ifs.age < minage)
+           && (ifs.nuclide->atomicNumber == nuc->atomicNumber) )
         {
           minage = ifs.age;
           defining = ifs.nuclide;
@@ -2818,10 +2845,12 @@ void SourceFitModel::peakModelDataChangedCallback( Wt::WModelIndex topLeft,
         defining = nuc;
 
       for( IsoFitStruct &ifs : m_nuclides )
-        if( ifs.nuclide->atomicNumber == nuc->atomicNumber )
+      {
+        if( ifs.ageIsFittable && (ifs.nuclide->atomicNumber == nuc->atomicNumber) )
           setSharredAgeNuclide( ifs.nuclide, defining );
+      }
     }//for( const SandiaDecay::Nuclide *nuc : addednucs )
-  }//if( m_sameAgeForIsotopes && (preisotopes!=postisotopes) )
+  }//if( m_sameAgeForIsotopes && (preisotopes != postisotopes) )
 
 
   if( npreisotopes == m_nuclides.size() )
@@ -5254,7 +5283,7 @@ std::tuple<int,int,bool> ShieldingSourceDisplay::numTruthValuesForFitValues()
 
   if( nQuantitiesCan != nFitQuantities )
   {
-    cerr << "Dont have: nQuantitiesCan != nFitQuantities" << nQuantitiesCan << " != " << nFitQuantities << endl;
+    cerr << "Dont have: nQuantitiesCan != nFitQuantities (" << nQuantitiesCan << " != " << nFitQuantities << ")" << endl;
     isValid = false;
   }
 
@@ -8192,6 +8221,8 @@ ShieldingSourceDisplay::Chi2FcnShrdPtr ShieldingSourceDisplay::shieldingFitnessF
       if( age > 0 )
         ageStep = std::min( 0.1*age, ageStep );
 
+      // cout << "For nuclide " << nuclide->symbol << " adding age=" << age << ", with step " << ageStep << " and max age " << maxAge << endl;
+      
       inputPrams.Add( nuclide->symbol + "Age", age, ageStep, 0, maxAge  );
     }else if( hasOwnAge )
     {

src/SpectraFileModel.cpp

@@ -287,9 +287,9 @@ SpectraFileHeader::~SpectraFileHeader() noexcept(true)
         {
           saveToDatabaseFromTempFile();
           //passMessage ("memObj saveToDatabaseFromTempFile", "", WarningWidget::WarningMsgMedium);
-            WString msg = "Autosaved previously opened spectra '";
-            msg += (!!memObj ? memObj->filename() : fileSystemLocation);
-            msg += "'";
+            //WString msg = "Autosaved previously opened spectra '";
+            //msg += (!!memObj ? memObj->filename() : fileSystemLocation);
+            //msg += "'";
             //passMessage( msg, "", WarningWidget::WarningMsgInfo );
         }
         else //probably shouldnt happen

src/SpectrumViewerTester.cpp

@@ -1978,6 +1978,7 @@ SpectrumViewerTester::Score SpectrumViewerTester::testShieldSourceFit()
     note.m_text = "";
     note.m_title = "Fit Chi2 Graphic";
     note.m_originalImage = make_shared<Wt::WSvgImage>(m_picWidth, m_picHeight);
+    disp->updateChi2ChartActual();
     disp->renderChi2Chart( *note.m_originalImage );
 
     // Set all the quantities being fit for to some default values, so we wont be starting off in
@@ -1986,7 +1987,7 @@ SpectrumViewerTester::Score SpectrumViewerTester::testShieldSourceFit()
 
     shared_ptr<ShieldingSourceDisplay::ModelFitResults> result = disp->doModelFit( false );
 
-    // Uhg, sometimes users have to hit  a coupel times right now - this should be fixed
+    // Uhg, sometimes users have to hit  a couple times right now - this should be fixed
     result = disp->doModelFit( false );
 
     note.m_testImage = make_shared<Wt::WSvgImage>(m_picWidth, m_picHeight);