From e4d6b20751022dd2c9516642b060f76a0a0cedbd Mon Sep 17 00:00:00 2001
From: William Johnson <wcjohns@sandia.gov>
Date: Thu, 10 Oct 2024 09:15:30 -0700
Subject: [PATCH] Some slight improvements to reporting for batch analysis.

Now if background or exemplar cant be opened, analysis will just be stopped, rather than spitting errors for each input files.
The report templates now check for presence of foreground/background file, to help avoid templating errors.
The JSON for peaks could be invalid, causing templating errors (I guess browsers were tolerant enough to not complain).
---
 .../ShieldSourceFitLog/act_fit.tmplt.html          | 11 ++++++++---
 .../ShieldSourceFitLog/std_fit_log.tmplt.txt       |  2 +-
 src/BatchActivity.cpp                              |  3 ++-
 src/GammaInteractionCalc.cpp                       |  2 +-
 src/PeakDef.cpp                                    | 14 +++++++-------
 5 files changed, 19 insertions(+), 13 deletions(-)

diff --git a/InterSpec_resources/static_text/ShieldSourceFitLog/act_fit.tmplt.html b/InterSpec_resources/static_text/ShieldSourceFitLog/act_fit.tmplt.html
index bed9cc96..1448eece 100644
--- a/InterSpec_resources/static_text/ShieldSourceFitLog/act_fit.tmplt.html
+++ b/InterSpec_resources/static_text/ShieldSourceFitLog/act_fit.tmplt.html
@@ -98,6 +98,7 @@ <h2 style="color: orange;">Warnings</h2>
 
     <div id="GeneralInfo">
     <ul style="list-style-type: none; padding: 0; margin: 0;">
+{% if exists("foreground") %}
     <li>
         {% if exists("background") %} Foreground: {% endif %}
         <table class="InfoTable">
@@ -179,7 +180,9 @@ <h2 style="color: orange;">Warnings</h2>
             {% endif %}
         </table>
     </li>
-    {% if exists("background") %} 
+  {% endif %} <!-- if exists("foreground") -->
+
+  {% if exists("background") %} 
     <li>
         Background:
         <table class="InfoTable">
@@ -278,7 +281,6 @@ <h2 style="color: orange;">Warnings</h2>
         Branching ratios are being corrected for nuclide decay during measurement.
     </li>    
     {% endif %} <!-- if ActShieldFitSetup.FitOptions.DecayDuringMeasurement -->
-    {% endif %} <!-- if HasFitResults -->
 
     {% if exists("background") %}
       <li>
@@ -288,7 +290,8 @@ <h2 style="color: orange;">Warnings</h2>
       Background peaks are not being subtracted.
       {% endif %}
       </li>
-    {% endif %}
+    {% endif %} <!--if exists("background") -->
+    {% endif %} <!-- if HasFitResults -->
 
     </ul>
     </div> <!-- <div id="GeneralInfo"> -->
@@ -450,6 +453,7 @@ <h2 style="color: orange;">Warnings</h2>
 
   </div>  <!-- <div id="results" style="margin-top: 15px"> -->
 
+{% if exists("foreground") %}
   <script>
     let spec_chart_specchart = new SpectrumChartD3( 'specchart',  {
     'title': '', 'xlabel' : 'Energy (keV)', 'ylabel': 'Counts'
@@ -469,6 +473,7 @@ <h2 style="color: orange;">Warnings</h2>
       spec_chart_specchart.setData( spectrum_json );
       spec_chart_specchart.setLogY( true );
   </script>
+{% endif %} <!-- if exists("foreground") --> 
 
 {% if exists("Shieldings") %}
 {% if existsIn(Shieldings,"Shields") %}
diff --git a/InterSpec_resources/static_text/ShieldSourceFitLog/std_fit_log.tmplt.txt b/InterSpec_resources/static_text/ShieldSourceFitLog/std_fit_log.tmplt.txt
index 6fa88df6..b6e72e48 100644
--- a/InterSpec_resources/static_text/ShieldSourceFitLog/std_fit_log.tmplt.txt
+++ b/InterSpec_resources/static_text/ShieldSourceFitLog/std_fit_log.tmplt.txt
@@ -1,4 +1,4 @@
-Foreground LiveTime: {% if foreground.LiveTime_s %}{{ foreground.LiveTime_s }} seconds{% endif %} {% if foreground.LiveTime %}({{ foreground.LiveTime }}){% endif %}
+{% if exists("foreground") %}Foreground LiveTime: {% if foreground.LiveTime_s %}{{ foreground.LiveTime_s }} seconds{% endif %} {% if foreground.LiveTime %}({{ foreground.LiveTime }}){% endif %}{% else %}No foreground spectrum{% endif %}
 {% if HasFitResults %}{% if FixedGeometryDetector %}Results given as {{ ActShieldFitSetup.FixedGeometryType }}.{% else %}Distance to source center from detector: {{ ActShieldFitSetup.Distance }}{% endif %}{% endif %}
 {% if exists("Detector") %}{% if Detector %}Detector: {{ Detector.Name }} radius {{ printFixed(Detector.Radius_cm,1) }}{% endif %}{% endif %}
 {% if HasFitResults %}
diff --git a/src/BatchActivity.cpp b/src/BatchActivity.cpp
index 430e5715..4af43b1b 100644
--- a/src/BatchActivity.cpp
+++ b/src/BatchActivity.cpp
@@ -316,7 +316,8 @@ void fit_activities_in_files( const std::string &exemplar_filename,
                  = fit_activities_in_file( exemplar_filename, exemplar_sample_nums,
                                      cached_exemplar_n42, filename, options );
     
-    if( fit_results.m_result_code == BatchActivityFitResult::ResultCode::CouldntOpenExemplar )
+    if( (fit_results.m_result_code == BatchActivityFitResult::ResultCode::CouldntOpenExemplar)
+       || (fit_results.m_result_code == BatchActivityFitResult::ResultCode::CouldntOpenBackgroundFile) )
       throw runtime_error( fit_results.m_error_msg );
     
     if( !cached_exemplar_n42 )
diff --git a/src/GammaInteractionCalc.cpp b/src/GammaInteractionCalc.cpp
index a19be7cc..7a4baf3d 100644
--- a/src/GammaInteractionCalc.cpp
+++ b/src/GammaInteractionCalc.cpp
@@ -2693,7 +2693,7 @@ std::pair<std::shared_ptr<ShieldingSourceChi2Fcn>, ROOT::Minuit2::MnUserParamete
   }//for(...)
   
   if( peaks.empty() )
-    throw runtime_error( "There are not peaks selected for the fit" );
+    throw runtime_error( "There are no peaks selected for the fit" );
   
   double liveTime = foreground ? foreground->live_time() : 1.0f;
   double realTime = foreground ? foreground->real_time() : 0.0f;
diff --git a/src/PeakDef.cpp b/src/PeakDef.cpp
index 03ff46dd..1d64da07 100644
--- a/src/PeakDef.cpp
+++ b/src/PeakDef.cpp
@@ -2729,14 +2729,14 @@ std::string PeakDef::gaus_peaks_to_json(const std::vector<std::shared_ptr<const
         //  And somewhat surprisingly, rounding causes visual artifacts of the continuum when
         //  the 'continuumEnergies' and 'continuumCounts' arrays are used, which are only accurate
         //  to float levels.  So we will increase accuracy of the 'answer' stream here, which appears
-        //  to be enough to avoid these artifcats, but also commented out is how we could compute
+        //  to be enough to avoid these artifacts, but also commented out is how we could compute
         //  to double precision to match what happens in the JS.
         const auto oldprecision = answer.precision();  //probably 6 always
         answer << std::setprecision(std::numeric_limits<float>::digits10 + 1);
         
         answer << "," << q << "continuumEnergies" << q << ":[";
         for (size_t i = firstbin; i <= lastbin; ++i)
-          answer << (i ? "," : "") << foreground->gamma_channel_lower(i);
+          answer << ((i!=firstbin) ? "," : "") << foreground->gamma_channel_lower(i);
         answer << "]," << q << "continuumCounts" << q << ":[";
         
         /*
@@ -2759,14 +2759,14 @@ std::string PeakDef::gaus_peaks_to_json(const std::vector<std::shared_ptr<const
               energy = SpecUtils::fullrangefraction_energy( i, coefs, nchannel, dev_pairs );
             else
               energy = SpecUtils::polynomial_energy( i, coefs, dev_pairs );
-            answer << (i ? "," : "") << energy;
+            answer << ((i!=firstbin) ? "," : "") << energy;
           }
           answer << "]," << q << "continuumCounts" << q << ":[";
         }else
         {
           answer << "," << q << "continuumEnergies" << q << ":[";
           for (size_t i = firstbin; i <= lastbin; ++i)
-            answer << (i ? "," : "") << foreground->gamma_channel_lower(i);
+            answer << ((i!=firstbin) ? "," : "") << foreground->gamma_channel_lower(i);
           answer << "]," << q << "continuumCounts" << q << ":[";
         }
          */
@@ -2778,7 +2778,7 @@ std::string PeakDef::gaus_peaks_to_json(const std::vector<std::shared_ptr<const
           const float lower_x = foreground->gamma_channel_lower( i );
           const float upper_x = foreground->gamma_channel_upper( i );
           const float cont_counts = continuum->offset_integral( lower_x, upper_x, foreground );
-          answer << (i ? "," : "") << cont_counts;
+          answer << ((i!=firstbin) ? "," : "") << cont_counts;
         }
         answer << "]";
         
@@ -2809,10 +2809,10 @@ std::string PeakDef::gaus_peaks_to_json(const std::vector<std::shared_ptr<const
 
         answer << "," << q << "continuumEnergies" << q << ":[";
         for (size_t i = firstbin; i <= lastbin; ++i)
-          answer << (i ? "," : "") << hist->gamma_channel_lower(i);
+          answer << ((i!=firstbin) ? "," : "") << hist->gamma_channel_lower(i);
         answer << "]," << q << "continuumCounts" << q << ":[";
         for (size_t i = firstbin; i <= lastbin; ++i)
-          answer << (i ? "," : "") << hist->gamma_channel_content(i);
+          answer << ((i!=firstbin) ? "," : "") << hist->gamma_channel_content(i);
         answer << "]";
         
         answer << std::setprecision(9);