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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.
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12 files changed

+780
-236
lines changed

12 files changed

+780
-236
lines changed

‎InterSpec/BatchActivity.h

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Original file line numberDiff line numberDiff line change
@@ -31,6 +31,8 @@
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#include <string>
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#include <vector>
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#include <boost/optional.hpp>
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#include "InterSpec/BatchPeak.h"
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// Forward declarations
@@ -62,6 +64,8 @@ namespace BatchActivity
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{
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bool use_bq = false;
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std::shared_ptr<DetectorPeakResponse> drf_override;
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boost::optional<double> distance_override;
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bool hard_background_sub;
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};//struct BatchActivityFitOptions
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@@ -77,13 +81,20 @@ namespace BatchActivity
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CouldntInitializeStaticResources,
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NoExemplar,
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CouldntOpenExemplar,
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ErrorPickingSpectrumFromExemplar,
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CouldntOpenInputFile,
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CouldntOpenBackgroundFile,
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NoInputSrcShieldModel,
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ForegroundSampleNumberUnderSpecified,
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BackgroundSampleNumberUnderSpecified,
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InvalidLiveTimeForHardBackSub,
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SpecifiedDistanceWithFixedGeomDet,
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ErrorWithHardBackgroundSubtract,
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ErrorApplyingExemplarEneCalToFore,
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ForegroundPeakFitFailed,
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BackgroundPeakFitFailed,
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NoExistingBackgroundPeaks,
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NoFitForegroundPeaks,
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NoDetEffFnct,
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InvalidDistance,

‎InterSpec/BatchPeak.h

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

‎InterSpec/GammaInteractionCalc.h

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@@ -572,6 +572,11 @@ struct SourceDetails
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const SandiaDecay::Nuclide *nuclide = nullptr;
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double activity = 0.0;
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double activityUncertainty = 0.0;
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/** If the activity is fit for.
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Note: if source type is `ShieldingSourceFitCalc::ModelSourceType::Intrinsic`, then this value will be false,
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even if a shielding dimension is being fit for.
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*/
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bool activityIsFit = false;
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double nuclideMass = 0.0;
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double age = 0.0;

‎InterSpec/ShieldingSourceFitCalc.h

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

‎InterSpec_resources/static_text/ShieldSourceFitLog/act_fit.tmplt.html

Lines changed: 25 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -148,7 +148,7 @@ <h1 class="title">
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<td> {% if existsIn(foreground,"SerialNumber") %} {{ foreground.SerialNumber }} {% else %} -- {% endif %} </td>
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{% if foreground.HasGps %}
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<th>lat/lon:</th>
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<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>
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<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>
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{% endif %}
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</tr>
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{% if foreground.HasInstrumentRid %}
@@ -449,8 +449,30 @@ <h1 class="title">
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</script>
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{% if existsIn(Shieldings,"Shields") %}
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##for shield in Shieldings.Shields
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{% if shield.FitAnyMassFraction %}
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<div class="mass_frac_{{ shield.Name }}" style="margin-top: 15px">
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Mass fractions for {{ shield.Name }}:
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<table class="InfoTable">
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<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>
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<tbody>
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##for shieldSrc in shield.SelfAttenSources
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<tr>
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<td>{{ shieldSrc.Nuclide }}</td>
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<td>{{ printFixed(shieldSrc.MassFraction,6) }}</td>
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<td>{{ shieldSrc.IsFittingMassFraction }}</td>
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<td>{% if existsIn(shieldSrc,"MassFractionUncert") %} {{ printFixed(shieldSrc.MassFractionUncert,6) }} {% endif %}</td>
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<td>{% if existsIn(shieldSrc,"Activity") %} {{ shieldSrc.Activity }} {{ shieldSrc.ActivityPostFix }} {% endif %}</td>
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<td>{% if existsIn(shieldSrc,"ActivityUncert") %} {{ shieldSrc.ActivityUncert }} {{ shieldSrc.ActivityPostFix }} {% endif %}</td>
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</tr>
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##endfor
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</tbody>
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</table>
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</div>
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{% endif %}
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##endfor
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{% endif %}
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@@ -476,7 +498,6 @@ <h1 class="title">
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##endfor
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{% endif %}
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## for src in Sources
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{{ 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 }}
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## endfor

‎InterSpec_resources/static_text/ShieldSourceFitLog/std_summary.tmplt.csv

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Original file line numberDiff line numberDiff line change
@@ -9,9 +9,14 @@ Setup
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{% if exists("ExemplarSampleNumbers") %}Exemplar samples: {{ ExemplarSampleNumbers }}{% endif %}
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Filename, Nuclide, Activity, ActivityUncertainty, ActivityUncertainty (%), NuclideAge, NuclideAgeUncertainty
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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
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## for file in Files
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## for src in file.Sources
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{{ 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 %}
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{{ file.Filename }}, {{ src.Nuclide }}, {{ src.Activity }}, {% if src.ActivityIsFit %}{{ src.ActivityUncert }}{% endif %}, {% if src.ActivityIsFit %}{{ src.ActivityUncertPercent }}%{% endif
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%}, {{ src.Activity_uCi }}, {% if src.ActivityIsFit %}{{ src.ActivityUncert_uCi }}{% endif
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%}, {{ src.Activity_pCi }}, {% if src.ActivityIsFit %}{{ src.ActivityUncert_pCi }}{% endif
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%}, {{ src.Activity_bq }}, {% if src.ActivityIsFit %}{{ src.ActivityUncert_bq }}{% endif
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%}, {{ src.Activity_MBq }}, {% if src.ActivityIsFit %}{{ src.ActivityUncert_MBq }}{% endif
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%}, {{ src.Age }}, {% if src.AgeIsFit %}{{ src.AgeUncert }}{% endif %}
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## endfor
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## endfor

‎InterSpec_resources/static_text/ShieldSourceFitLog/std_summary.tmplt.html

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@@ -247,6 +247,31 @@ <h1 class="title">
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</table>
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</div> <!-- <div id="sources" style="margin-top: 25px"> -->
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{% if existsIn(file.Shieldings, "Shields") %}
251+
##for shield in file.Shieldings.Shields
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{% if shield.FitAnyMassFraction %}
253+
<div class="mass_frac_{{ shield.Name }}" style="margin-top: 15px">
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Mass fractions for {{ shield.Name }}:
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<table class="InfoTable">
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<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>
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<tbody>
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##for shieldSrc in shield.SelfAttenSources
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<tr>
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<td>{{ shieldSrc.Nuclide }}</td>
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<td>{{ printFixed(shieldSrc.MassFraction,6) }}</td>
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<td>{{ shieldSrc.IsFittingMassFraction }}</td>
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<td>{% if existsIn(shieldSrc,"MassFractionUncert") %} {{ printFixed(shieldSrc.MassFractionUncert,6) }} {% endif %}</td>
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<td>{% if existsIn(shieldSrc,"Activity") %} {{ shieldSrc.Activity }} {{ shieldSrc.ActivityPostFix }} {% endif %}</td>
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<td>{% if existsIn(shieldSrc,"ActivityUncert") %} {{ shieldSrc.ActivityUncert }} {{ shieldSrc.ActivityPostFix }} {% endif %}</td>
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</tr>
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##endfor
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</tbody>
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</table>
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</div>
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{% endif %}
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##endfor
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{% endif %}
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<div style="margin-top: 20px">
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<ul style="list-style-type: none; padding: 0; margin: 0;">
252277
<li>There were {{ file.NumDof }} parameters fit for</li>

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