Added individual source contributions to peaks for logging/tempalting…

… act fit results.

Was previously logging raw source counts, at source, but not the sources contribution to peaks.
Also added logging a few other quantities, such as total attenuation, air attenuation.
For volumetric sources added some quantities to to indicate attenuations/efficiencies.

InterSpec/GammaInteractionCalc.h

@@ -330,7 +330,7 @@ struct DistributedSrcCalc
 
   GeometryType m_geometry;
 
-  size_t m_sourceIndex;
+  size_t m_materialIndex;
   double m_detectorRadius;
   double m_observationDist;
 
@@ -371,7 +371,7 @@ struct DistributedSrcCalc
    */
   std::vector<std::tuple<std::array<double,3>,double,ShellType> > m_dimensionsTransLenAndType;
 
-  /** The activity per volume of the shielding.
+  /** The photons (i.e., sum of activities times br) per volume of the shielding.
    Is not used during integration; used to multiple integral by to get number of expected peak counts.
    */
   double m_srcVolumetricActivity;
@@ -414,10 +414,11 @@ struct PeakResultPlotInfo
 };//struct PeakResultPlotInfo
 
 
-/** A struct to capture the details of each source that contributed to a peak peak.
+  /**
+   A struct to capture the details of each source that contributed to a peak peak.
    
    This is primarily to later turn to JSON, and allow customizing log files, through inja templating.
-*/
+   */
 struct PeakDetailSrc
 {
   const SandiaDecay::Nuclide *nuclide = nullptr;
@@ -426,7 +427,7 @@ struct PeakDetailSrc
   double energy = 0.0;
   /** The number of this energy gamma, per second, for each Bq of parent nuclide. */
   double br = 0.0;
-  double cps = 0.0;
+  double cpsAtSource = 0.0;
   double age = 0.0;
 
   /** For point sources, the activity of the point source.
@@ -445,8 +446,7 @@ struct PeakDetailSrc
 
   bool isSelfAttenSource = false;//Not used - can be removed
 
-  double counts = 0.0;
-  //double countsUncert = 0.0;
+  double countsAtSource = 0.0;
   double ageUncert = 0.0;//Not used - can be removed
   //bool ageIsFit = false;
   //bool canFitAge = false;
@@ -459,6 +459,9 @@ struct PeakDetailSrc
   double massFraction = 0.0;//Not used - can be removed
   double massFractionUncert = 0.0;//Not used - can be removed
   bool isFittingMassFraction = false;//Not used - can be removed
+
+  /** The expected number of counts contributed by this source, to the peak. */
+  double modelContribToPeak = 0.0;
 };//struct PeakDetailSrc
 
 
@@ -480,19 +483,52 @@ struct PeakDetail
 
   std::string assignedNuclide;
 
+  /** Further information about the sources that contribute to this peak.
+   Please note that the `PeakDetailSrc` are not entirely filled out at creation, so do not rely on the member variables
+   being accurate until the end of the calculations.
+   */
   std::vector<PeakDetailSrc> m_sources;
 
   /** The fractional attenuation by this material (e.g., no attenuation is 1.0. Not valid for volumetric sources.
    The index of this vector is the same index as shielding in the model
    */
   std::vector<double> m_attenuations;
 
+  /** The total attenuation factor (i.e., fraction no-interactions; 1.0 is no attenuation, 0.0 is total attentuation), that
+   all the shieldings cause.
+   Only valid for point sources.
+   */
+  double m_totalShieldAttenFactor;
+  /** The attenuation, due to air, between the last shielding and the detector.
+   For volumetric sources, this is only approximate
+   */
+  double m_airAttenFactor;
+
+  /** The total attenuation of the source from all shielding and air.  For volumetric sources, this will only be approximate.
+   */
+  double m_totalAttenFactor;
+
   // TODO: for self-attenuating sources, could repeat the computation, put with only the source shell, then shell+1-other, then shell+different-1-other, and so on, to get the effect of each shell.
 
   struct VolumeSrc
   {
     bool trace; // Trace or intrinsic
+
+    /** The integral of the efficiency to make it to the detector, over the source area.
+     i.e., the shielding area times average efficiency to make it to the detector face.
+     Does not include detector intrinsic efficiency.
+     */
     double integral;
+
+    /** The volume of the shielding. */
+    double volume;
+
+    /** `integral / volume` */
+    double averageEfficiencyPerSourceGamma;
+
+    /** The gammas per second, per unit-volume, for this source energy.
+     This value times `VolumeSrc::integral` gives the expected number of gammas, at this energy, to strike the detector face.
+     */
     double srcVolumetricActivity;
 
     bool inSituExponential;        //Not used - can be removed
@@ -512,7 +548,10 @@ struct PeakDetail
   numSigmaOff( 0.0 ), observedOverExpected( 0.0 ),
   //modelInto4Pi( 0.0f ), modelInto4PiCps( 0.0f ),
   detSolidAngle( 0.0 ), detIntrinsicEff( 0.0 ), detEff( 0.0 ),
-  backgroundCounts( 0.0f ), backgroundCountsUncert( 0.0f )
+  backgroundCounts( 0.0f ), backgroundCountsUncert( 0.0f ),
+  assignedNuclide{}, m_sources{}, m_attenuations{},
+  m_totalShieldAttenFactor( 1.0 ), m_airAttenFactor( 1.0 ),
+  m_totalAttenFactor( 1.0 )
   {
   }
 };//struct PeakDetail

InterSpec_resources/static_text/ShieldSourceFitLog/act_fit.tmplt.html

@@ -389,7 +389,6 @@ <h2 style="color: orange;">Warnings</h2>
 
 {% if exists("Sources") %}
 <div id="PeakContributions" style="margin-top: 25px">
-<span style="color: red; font-weight: bold;">(Gamma contribution counts currently not correct!)</span>
 <ul style="list-style-type: none; padding: 0; margin: 0;">
 ## for src in Sources
   <li style="margin-top: 10px;"> Peak contributions from {{ src.Nuclide }}:
@@ -398,12 +397,19 @@ <h2 style="color: orange;">Warnings</h2>
       <thead>
         <tr>
           <th>Energy (keV)</th>
-          <th>Signal Counts</th>
+          <th>Observed Counts</th>
           <th>&Delta;Counts</th>
-          <th>Model Sum</th>
+          <th>Pred. Model Sum</th>
+          <th>Det. Intrinsic Eff.</th>
+          <th>Det. Solid Angle.</th>
+          <th>Det. Eff.</th>
+          <th>Shield Atten. Factor</th>
+          <th>Air Atten. Factor</th>
+          <th>Total Atten. Factor</th>
           <th>Nuclide</th>
           <th>&gamma; Energy</th>
-          <th>&gamma; Counts</th>
+          <th>Pred. &gamma;</th>
+          <th>&gamma; into 4pi</th>
         </tr>
       </thead>
 
@@ -414,7 +420,12 @@ <h2 style="color: orange;">Warnings</h2>
           <td>{{ printCompact(peak.SignalCounts,5) }}</td>
           <td>{{ printCompact(peak.SignalCountsUncert,5) }}</td>
           <td>{{ printCompact(peak.PredictedCounts,5) }}</td>
-
+          <td>{{ printCompact(peak.DetectorIntrinsicEff,5) }}</td>
+          <td>{{ printCompact(peak.DetectorSolidAngleFraction,5) }}</td>
+          <td>{{ printCompact(peak.DetectorEff,5) }}</td>
+          <td>{{ printCompact(peak.AttenuationByShieldingFactor,5) }}</td>
+          <td>{{ printCompact(peak.AttenuationByAirFactor,5) }}</td>
+          <td>{{ printCompact(peak.AttenuationTotalFactor,5) }}</td>
     {% if existsIn(peak,"ThisNucsGammasForPeak") %}
 ## for src in peak.ThisNucsGammasForPeak
         {% if loop.is_first %}
@@ -424,16 +435,24 @@ <h2 style="color: orange;">Warnings</h2>
           <td></td>
           <td></td>
           <td></td>
+          <td></td>
+          <td></td>
+          <td></td>
+          <td></td>
+          <td></td>
+          <td></td>
         {% endif %}
           <td>{{ src.Nuclide }}</td>
           <td>{{ printFixed(src.Energy_keV,3) }}</td>
-          <td>{{ printCompact(src.CountsContributedToPeak,6) }}</td>
+          <td>{{ printCompact(src.PredictedCounts,6) }}</td>
+          <td>{{ printCompact(src.SourcePhotons,6) }}</td>
         </tr>
 ##endfor
     {% else %}
           <td></td>
           <td></td>
           <td></td>
+          <td></td>
         </tr>
     {% endif %}    
 ##endfor

InterSpec_resources/static_text/ShieldSourceFitLog/std_fit_log.tmplt.txt

@@ -22,7 +22,7 @@ Sources:
   For {{ src.Nuclide }} at age {{ src.Age }}{% if src.AgeIsFit %} +- {{ src.AgeUncert }} {% endif %} with activity {{ src.Activity }}{% if src.ActivityIsFit %} +- {{ src.ActivityUncert }} {% endif %}{% if src.IsTraceSource %}(src.TraceDisplayActivity{% if src.ActivityIsFit %} +- {{ src.TraceDisplayActivityUncert }} {% endif %}){% endif %}:
 ## for peak in src.PeaksThisNucContributesTo
 ## for gamma in peak.ThisNucsGammasForPeak
-    Peak attributed to {{ peak.DecayParticleEnergy }} keV received {{ gamma.CpsContributedToPeak }} from {{ gamma.Energy }} keV line{% if existsIn(gamma,"DecayCorrection") %} (decay correction {{ gamma.DecayCorrection }}){% endif %}, which has I={{ gamma.BranchingRatio }}
+    Peak attributed to {{ peak.DecayParticleEnergy }} keV received {{ gamma.PredictedCounts }} from {{ gamma.Energy }} keV line{% if existsIn(gamma,"DecayCorrection") %} (decay correction {{ gamma.DecayCorrection }}){% endif %}, which has I={{ gamma.BranchingRatio }}
 ##endfor
 ##endfor
 ##endfor

src/BatchInfoLog.cpp

@@ -688,6 +688,10 @@ void add_basic_src_details( const GammaInteractionCalc::SourceDetails &src,
     peak_json["CpsUncert"] = peak.cpsUncert;
     peak_json["ShieldAttenuations"] = peak.m_attenuations;
 
+    peak_json["AttenuationByShieldingFactor"] = peak.m_totalShieldAttenFactor;
+    peak_json["AttenuationByAirFactor"] = peak.m_airAttenFactor;
+    peak_json["AttenuationTotalFactor"] = peak.m_totalAttenFactor;
+
     if( peak.backgroundCounts > 0.0 )
     {
       peak_json["BackgroundCounts"] = peak.backgroundCounts;
@@ -736,11 +740,14 @@ void add_basic_src_details( const GammaInteractionCalc::SourceDetails &src,
     gamma_json["BranchingRatio"] = ps.br;
     gamma_json["BranchingRatioStr"] = SpecUtils::printCompact( ps.br, 5 );
 
-    gamma_json["CpsContributedToPeak"] = ps.cps;
-    gamma_json["CpsContributedToPeakStr"] = SpecUtils::printCompact( ps.cps, 5 );
+    gamma_json["PredictedCounts"] = ps.modelContribToPeak;
+    gamma_json["PredictedCountsStr"] = SpecUtils::printCompact(ps.modelContribToPeak, 4);
+
+    gamma_json["SourcePhotonsCps"] = ps.cpsAtSource;
+    gamma_json["SourcePhotonsCpsStr"] = SpecUtils::printCompact( ps.cpsAtSource, 5 );
 
-    gamma_json["CountsContributedToPeak"] = ps.counts;
-    gamma_json["CountsContributedToPeakStr"] = SpecUtils::printCompact( ps.counts, 5 );
+    gamma_json["SourcePhotons"] = ps.countsAtSource;
+    gamma_json["SourcePhotonsStr"] = SpecUtils::printCompact( ps.countsAtSource, 5 );
 
     gamma_json["HasDecayCorrection"] = (ps.decayCorrection > 0.0);
     if( ps.decayCorrection > 0.0 )
@@ -1127,15 +1134,18 @@ void add_basic_src_details( const GammaInteractionCalc::SourceDetails &src,
           src_json["Energy"] = string(buffer);
           src_json["Energy_keV"] = pksrc.energy;
 
-          src_json["Cps"] = pksrc.cps;
-          src_json["CpsStr"] = SpecUtils::printCompact(pksrc.cps, 4);
+          src_json["SourcePhotonsCps"] = pksrc.cpsAtSource;
+          src_json["SourcePhotonsCpsStr"] = SpecUtils::printCompact(pksrc.cpsAtSource, 4);
 
           src_json["BranchingRatio"] = pksrc.br;
           src_json["BranchingRatioStr"] = SpecUtils::printCompact( pksrc.br, 5 );
 
-          snprintf( buffer, sizeof(buffer), "%.2f", pksrc.counts );
-          src_json["Counts"] = pksrc.counts;
-          src_json["CountsStr"] = string(buffer);
+          snprintf( buffer, sizeof(buffer), "%.2f", pksrc.countsAtSource );
+          src_json["SourcePhotons"] = pksrc.countsAtSource;
+          src_json["SourcePhotonsStr"] = string(buffer);
+
+          src_json["PredictedCounts"] = pksrc.modelContribToPeak;
+          src_json["PredictedCountsStr"] = SpecUtils::printCompact(pksrc.modelContribToPeak, 4);
         }//for( const GammaInteractionCalc::PeakDetailSrc &pksrc : peak.m_sources )
 
         // We could loop over the volumetric sources, and add info, but...
@@ -1144,6 +1154,8 @@ void add_basic_src_details( const GammaInteractionCalc::SourceDetails &src,
         {
           bool trace;
           double integral;
+          double volume;
+          double averageEfficiencyPerSourceGamma;
           double srcVolumetricActivity;
           bool inSituExponential;
           double inSituRelaxationLength;