Add more batch options.

Added option to specify a different distance when fitting act/shield. Add option to do hard background subtract. Add option to use existing background peaks. Add option to apply exemplar energy cal to background. Fixed up a few more issues. Fix some issues with templates.
sandialabs · Sep 12, 2024 · 3a188b1 · 3a188b1
1 parent 293b56d
commit 3a188b1
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Showing 12 changed files with 780 additions and 236 deletions.
diff --git a/InterSpec/BatchActivity.h b/InterSpec/BatchActivity.h
@@ -31,6 +31,8 @@
 #include <string>
 #include <vector>
 
+#include <boost/optional.hpp>
+
 #include "InterSpec/BatchPeak.h"
 
 // Forward declarations
@@ -62,6 +64,8 @@ namespace BatchActivity
   {
     bool use_bq = false;
     std::shared_ptr<DetectorPeakResponse> drf_override;
+    boost::optional<double> distance_override;
+    bool hard_background_sub;
   };//struct BatchActivityFitOptions
 
 
@@ -77,13 +81,20 @@ namespace BatchActivity
       CouldntInitializeStaticResources,
       NoExemplar,
       CouldntOpenExemplar,
+      ErrorPickingSpectrumFromExemplar,
       CouldntOpenInputFile,
       CouldntOpenBackgroundFile,
       NoInputSrcShieldModel,
       ForegroundSampleNumberUnderSpecified,
       BackgroundSampleNumberUnderSpecified,
+      InvalidLiveTimeForHardBackSub,
+      SpecifiedDistanceWithFixedGeomDet,
+      ErrorWithHardBackgroundSubtract,
+      ErrorApplyingExemplarEneCalToFore,
 
       ForegroundPeakFitFailed,
+      BackgroundPeakFitFailed,
+      NoExistingBackgroundPeaks,
       NoFitForegroundPeaks,
       NoDetEffFnct,
       InvalidDistance,

diff --git a/InterSpec/BatchPeak.h b/InterSpec/BatchPeak.h
@@ -38,6 +38,7 @@ class SpecMeas;
 namespace SpecUtils
 {
   class Measurement;
+  class EnergyCalibration;
 }//namespace SpecUtils
 
 
@@ -71,6 +72,8 @@ namespace BatchPeak
     std::string output_dir;
     std::string background_subtract_file;
     std::set<int> background_subtract_samples;
+    bool use_existing_background_peaks;
+    bool use_exemplar_energy_cal_for_background;
 
     /** The directory to allow report template to look in to include other templates.
      If specified, then the standard report directory cant be used.
@@ -106,8 +109,12 @@ namespace BatchPeak
     std::set<int> sample_numbers;
     std::deque<std::shared_ptr<const PeakDef>> fit_peaks;
 
-    /** Background spectrum that was subtracted from the foreground, to make `spectrum`, if any. */
-    std::shared_ptr<const SpecUtils::Measurement> background;
+    /** Background spectrum that was subtracted from the foreground, to make `spectrum`, if any. 
+     
+     The background subtraction can either be on a peak-by-peak basis, or a hard
+     background subtraction, see `BatchPeakFitOptions::use_exemplar_energy_cal_for_background`.
+     */
+    std::shared_ptr<SpecUtils::Measurement> background;
 
     bool success;
     std::vector<std::string> warnings;
@@ -137,6 +144,33 @@ namespace BatchPeak
                           std::set<int> foreground_sample_numbers,
                           const BatchPeakFitOptions &options );
 
+  /** Function that applies the energy calibration from the exemplar spectrum, to a spectrum from a different file.
+   
+   @param energy_cal The energy calibration to apply to `to_spectrum`, and optionally `to_specfile`
+   @param to_spectrum The spectrum, which may or may not be in `to_specfile`, to apply the energy calibration from `from_spectrum`
+   @param to_specfile The (optional) spectrum file to apply the energy calibration to; this will also take care of shifting peak energies
+   @param used_sample_nums The sample numbers used to create the `to_spectrum` from the `to_specfile` - used to keep peaks from
+          being moved twice.
+   */
+  void propagate_energy_cal( const std::shared_ptr<const SpecUtils::EnergyCalibration> &energy_cal,
+                                          std::shared_ptr<SpecUtils::Measurement> &to_spectrum,
+                                          std::shared_ptr<SpecMeas> &to_specfile,
+                                          const std::set<int> &used_sample_nums );
+
+  /** Finds the spectrum, peaks, and sample numbers to use from the exemplar file.
+   
+   @param [out] exemplar_spectrum Will be set to the spectrum to use as the exemplar spectrum (may be a sum of
+          multiple Measurements)
+   @param [out] exemplar_peaks Will be set to the peaks to use from the exemplar file.
+   @param [in|out] exemplar_sample_nums Sample numbers to use in the exemplar file.  If non-empty, these sample
+          number will be used to retrieve the spectrum to use.  Contents will be set to the used sample numbers.
+   @param [in] exemplar_n42 The spectrum file to retrieve the spectrum/peaks for
+   */
+  void get_exemplar_spectrum_and_peaks(
+                                       std::shared_ptr<const SpecUtils::Measurement> &exemplar_spectrum,
+                                       std::shared_ptr<const std::deque<std::shared_ptr<const PeakDef>>> &exemplar_peaks,
+                                       std::set<int> &exemplar_sample_nums,
+                                       const std::shared_ptr<const SpecMeas> &exemplar_n42 );
 }//namespace BatchPeak
 
 #endif //BatchPeak_h
diff --git a/InterSpec/GammaInteractionCalc.h b/InterSpec/GammaInteractionCalc.h
@@ -572,6 +572,11 @@ struct SourceDetails
   const SandiaDecay::Nuclide *nuclide = nullptr;
   double activity = 0.0;
   double activityUncertainty = 0.0;
+  /** If the activity is fit for.
+   
+   Note: if source type is `ShieldingSourceFitCalc::ModelSourceType::Intrinsic`, then this value will be false,
+   even if a shielding dimension is being fit for.
+   */
   bool activityIsFit = false;
   double nuclideMass = 0.0;
   double age = 0.0;

diff --git a/InterSpec/ShieldingSourceFitCalc.h b/InterSpec/ShieldingSourceFitCalc.h
@@ -97,6 +97,11 @@ namespace ShieldingSourceFitCalc
 
     //activity: in units of PhysicalUnits
     double activity;
+    /** If the activity is fit for.
+     
+     Note: if source type is `ShieldingSourceFitCalc::ModelSourceType::Intrinsic`, then this value will be false,
+     even if a shielding dimension is being fit for.
+     */
     bool fitActivity;
 
     //age: in units of PhysicalUnits::second

diff --git a/InterSpec_resources/static_text/ShieldSourceFitLog/act_fit.tmplt.html b/InterSpec_resources/static_text/ShieldSourceFitLog/act_fit.tmplt.html
@@ -148,7 +148,7 @@ <h1 class="title">
                 <td> {% if existsIn(foreground,"SerialNumber") %} {{ foreground.SerialNumber }} {% else %} -- {% endif %} </td>
                 {% if foreground.HasGps %}
                 <th>lat/lon:</th>
-                <td colspan="2"> <a target="_blank" rel="noopener noreferrer" href="https://maps.google.com/?q={{ printFixed(foreground.Latitude,7) }},{{ printFixed(foreground.Longitude,7) }}">{{ printFixed(foreground.Latitude,7) }}{{ printFixed(foreground.Longitude,7) }}</a> </td>
+                <td colspan="2"> <a target="_blank" rel="noopener noreferrer" href="https://maps.google.com/?q={{ printFixed(foreground.Latitude,7) }},{{ printFixed(foreground.Longitude,7) }}">{{ printFixed(foreground.Latitude,7) }},{{ printFixed(foreground.Longitude,7) }}</a> </td>
                 {% endif %}
             </tr>
             {% if foreground.HasInstrumentRid %}
@@ -449,8 +449,30 @@ <h1 class="title">
   </script>
 
 
-
-
+{% if existsIn(Shieldings,"Shields") %}
+##for shield in Shieldings.Shields
+{% if shield.FitAnyMassFraction %}
+<div class="mass_frac_{{ shield.Name }}" style="margin-top: 15px">
+Mass fractions for {{ shield.Name }}:
+<table class="InfoTable">
+  <thead><tr><th>Nuclide</th><th>Mass Fraction</th><th>Fit Mass Frac?</th><th>Mass Fraction Uncert</th><th>Activity</th><th>ActivityUncert</th></tr></thead>
+  <tbody>
+##for shieldSrc in shield.SelfAttenSources
+    <tr>
+      <td>{{ shieldSrc.Nuclide }}</td>
+      <td>{{ printFixed(shieldSrc.MassFraction,6) }}</td>
+      <td>{{ shieldSrc.IsFittingMassFraction }}</td>
+      <td>{% if existsIn(shieldSrc,"MassFractionUncert") %}  {{ printFixed(shieldSrc.MassFractionUncert,6) }} {% endif %}</td>
+      <td>{% if existsIn(shieldSrc,"Activity") %}  {{ shieldSrc.Activity }} {{ shieldSrc.ActivityPostFix }} {% endif %}</td>
+      <td>{% if existsIn(shieldSrc,"ActivityUncert") %}  {{ shieldSrc.ActivityUncert }} {{ shieldSrc.ActivityPostFix }} {% endif %}</td>
+    </tr>
+##endfor
+  </tbody>
+</table>
+</div>
+{% endif %}
+##endfor
+{% endif %}
 
 
 
@@ -476,7 +498,6 @@ <h1 class="title">
 ##endfor
 {% endif %}
 
-
 ## for src in Sources
 {{ src.Nuclide }} fit activity {{ src.Activity }}{% if src.ActivityIsFit %} with uncertainty {{ src.ActivityUncert }} ({{ src.ActivityUncertPercent }}) {% endif %} at {% if src.AgeIsFit %}assumed {% else %}fit {% endif %} age {{ src.Age }}
 ## endfor

diff --git a/InterSpec_resources/static_text/ShieldSourceFitLog/std_summary.tmplt.csv b/InterSpec_resources/static_text/ShieldSourceFitLog/std_summary.tmplt.csv
@@ -9,9 +9,14 @@ Setup
     {% if exists("ExemplarSampleNumbers") %}Exemplar samples: {{ ExemplarSampleNumbers }}{% endif %}
 
 
-Filename, Nuclide, Activity, ActivityUncertainty, ActivityUncertainty (%), NuclideAge, NuclideAgeUncertainty
+Filename, Nuclide, Activity, ActivityUncertainty, ActivityUncertainty (%), Activity (uCi), ActivityUncertainty (uCi), Activity (pCi), ActivityUncertainty (pCi), Activity (bq), ActivityUncertainty (bq), Activity (mega-bq), ActivityUncertainty (mega-bq), NuclideAge, NuclideAgeUncertainty
 ## for file in Files
 ## for src in file.Sources
-{{ file.Filename }},{{ src.Nuclide }}, {{ src.Activity }}, {% if src.ActivityIsFit %}{{ src.ActivityUncert }}{% endif %}, {% if src.ActivityIsFit %}{{ src.ActivityUncertPercent }}%{% endif %}, {{ src.Age }}, {% if src.AgeIsFit %}{{ src.AgeUncert }}{% endif %}
+{{ file.Filename }}, {{ src.Nuclide }}, {{ src.Activity }}, {% if src.ActivityIsFit %}{{ src.ActivityUncert }}{% endif %}, {% if src.ActivityIsFit %}{{ src.ActivityUncertPercent }}%{% endif 
+%}, {{ src.Activity_uCi }}, {% if src.ActivityIsFit %}{{ src.ActivityUncert_uCi }}{% endif 
+%}, {{ src.Activity_pCi }}, {% if src.ActivityIsFit %}{{ src.ActivityUncert_pCi }}{% endif 
+%}, {{ src.Activity_bq }}, {% if src.ActivityIsFit %}{{ src.ActivityUncert_bq }}{% endif 
+%}, {{ src.Activity_MBq }}, {% if src.ActivityIsFit %}{{ src.ActivityUncert_MBq }}{% endif 
+%}, {{ src.Age }}, {% if src.AgeIsFit %}{{ src.AgeUncert }}{% endif %}
 ## endfor
 ## endfor
diff --git a/InterSpec_resources/static_text/ShieldSourceFitLog/std_summary.tmplt.html b/InterSpec_resources/static_text/ShieldSourceFitLog/std_summary.tmplt.html
@@ -247,6 +247,31 @@ <h1 class="title">
   </table>   
 </div> <!-- <div id="sources" style="margin-top: 25px"> -->
 
+{% if existsIn(file.Shieldings, "Shields") %}
+##for shield in file.Shieldings.Shields
+{% if shield.FitAnyMassFraction %}
+<div class="mass_frac_{{ shield.Name }}" style="margin-top: 15px">
+Mass fractions for {{ shield.Name }}:
+  <table class="InfoTable">
+    <thead><tr><th>Nuclide</th><th>Mass Fraction</th><th>Fit Mass Frac?</th><th>Mass Fraction Uncert</th><th>Activity</th><th>ActivityUncert</th></tr></thead>
+    <tbody>
+##for shieldSrc in shield.SelfAttenSources
+      <tr>
+        <td>{{ shieldSrc.Nuclide }}</td>
+        <td>{{ printFixed(shieldSrc.MassFraction,6) }}</td>
+        <td>{{ shieldSrc.IsFittingMassFraction }}</td>
+        <td>{% if existsIn(shieldSrc,"MassFractionUncert") %}  {{ printFixed(shieldSrc.MassFractionUncert,6) }} {% endif %}</td>
+        <td>{% if existsIn(shieldSrc,"Activity") %}  {{ shieldSrc.Activity }} {{ shieldSrc.ActivityPostFix }} {% endif %}</td>
+        <td>{% if existsIn(shieldSrc,"ActivityUncert") %}  {{ shieldSrc.ActivityUncert }} {{ shieldSrc.ActivityPostFix }} {% endif %}</td>
+      </tr>
+##endfor
+    </tbody>
+  </table>
+  </div>
+{% endif %}
+##endfor
+{% endif %}
+
 <div style="margin-top: 20px">
 <ul style="list-style-type: none; padding: 0; margin: 0;">
   <li>There were {{ file.NumDof }} parameters fit for</li>