Sketch out implementation of batch activity/shielding fitting.

Start implementation of being able to use fit-peaks and shielding/src model from an exemplar, to refit these quantities for different, but similar, files, from the command line.
Right now more of a proof of concept stage - I'm sure a ton of edge cases arent handled, the output is just partially dumped to stdout (no formatting, no reporting, etc), and a ton of things arent complete, or implemented, or correct.

InterSpec/BatchActivity.h

@@ -42,7 +42,10 @@ namespace SpecUtils
   class Measurement;
 }//namespace SpecUtils
 
-
+namespace ShieldingSourceFitCalc
+{
+  struct ModelFitResults;
+}
 
 /** The functions necessary to batch-fit activity and shielding.  */
 namespace BatchActivity
@@ -68,8 +71,61 @@ namespace BatchActivity
 
   struct BatchActivityFitResult
   {
+    enum class ResultCode
+    {
+      CouldntInitializeStaticResources,
+      NoExemplar,
+      CouldntOpenExemplar,
+      CouldntOpenInputFile,
+      CouldntOpenBackgroundFile,
+      NoInputSrcShieldModel,
+      ForegroundSampleNumberUnderSpecified,
+      BackgroundSampleNumberUnderSpecified,
+
+      ForegroundPeakFitFailed,
+      NoFitForegroundPeaks,
+      NoDetEffFnct,
+      InvalidDistance,
+      InvalidGeometry,
+      InvalidFitOptions,
+      ExemplarUsedBackSubButNoBackground,
+      NoShieldingsNode,
+      ErrorParsingShielding,
+      MissingNuclidesNode,
+      InvalidNuclideNode,
+      NoSourceNuclides,
+
+      FitNotSuccessful,
+      DidNotFitAllSources,
+
+      UnknownStatus,
+      Success
+    };//enum class ResultCode
+
+    ResultCode m_result_code;
+    std::string m_error_msg;
+    std::vector<std::string> m_warnings;
+
+    std::string m_filename;
+    std::shared_ptr<const SpecMeas> m_foreground_file;
+    std::set<int> m_foreground_sample_numbers;  ///!< right now limited to single sample - may change in future
+    std::shared_ptr<const SpecUtils::Measurement> m_foreground;
+
+    std::shared_ptr<const SpecMeas> m_exemplar_file;
+    std::set<int> m_exemplar_sample_numbers;    ///!< right now limited to single sample - may change in future
+    std::shared_ptr<const SpecUtils::Measurement> m_exemplar;
+
+    std::shared_ptr<const SpecMeas> m_background_file;  ///!< May be same as foreground or exemplar
+    std::set<int> m_background_sample_numbers;  ///!< right now limited to single sample - may change in future
+    std::shared_ptr<const SpecUtils::Measurement> m_background;
+
+    BatchActivityFitOptions m_options;
+
     // Blah blah blah
-    std::shared_ptr<const BatchPeak::BatchPeakFitResult> peak_fit_results;
+    std::shared_ptr<const BatchPeak::BatchPeakFitResult> m_peak_fit_results;
+    std::shared_ptr<const BatchPeak::BatchPeakFitResult> m_background_peak_fit_results;
+
+    std::shared_ptr<ShieldingSourceFitCalc::ModelFitResults> m_fit_results;
   };//struct BatchActivityFitResult
 
 

InterSpec/BatchPeak.h

@@ -68,6 +68,7 @@ namespace BatchPeak
     bool show_nonfit_peaks;
     std::string output_dir;
     std::string background_subtract_file;
+    std::set<int> background_subtract_samples;
   };//struct BatchPeakFitOptions
 
 
@@ -109,13 +110,18 @@ namespace BatchPeak
    @param cached_exemplar_n42 If non-null, then `exemplar_filename` will be ignored, and this file will be used; to avoid re-parsing
           of the exemplar file over-and-over again.
    @param filename The name of the spectrum file to fit peaks to.
+   @param cached_spectrum If you have already parsed/opened the `filename` spectrum file, you can provide it here to
+          avoid overhead of re-parsing it.
+   @param foreground_sample_numbers The sample numbers to fit the peaks to.  If left empty, will try to automatically determine.
    @param options The options to use for fitting peaks; note, not all options are used, as some of them are only applicable to
           #fit_peaks_in_files
    */
   BatchPeakFitResult fit_peaks_in_file( const std::string &exemplar_filename,
                           std::set<int> exemplar_sample_nums,
                           std::shared_ptr<const SpecMeas> cached_exemplar_n42,
                           const std::string &filename,
+                          std::shared_ptr<SpecMeas> cached_spectrum,
+                          std::set<int> foreground_sample_numbers,
                           const BatchPeakFitOptions &options );
 
 }//namespace BatchPeak