Fix bug where when exporting only a sub-set of samples from a file, t…

…he peaks in the N42 file would be assigned the wrong sample numbers.

The sample numbers of the exported measurement would be changed from original, but the sample numbers of the peaks would not be changed.

InterSpec/SpecMeas.h

@@ -188,6 +188,8 @@ class SpecMeas : public SpecUtils::SpecFile
    */
   void cleanup_orphaned_info();
 
+  virtual void change_sample_numbers( const std::vector<std::pair<int,int>> &from_to_sample_nums );
+
   std::shared_ptr< std::deque< std::shared_ptr<const PeakDef> > >
                                  peaks( const std::set<int> &samplenums );
   /** CAUTION: the returned deque may be modified elsewhere in the app, if for

src/ExportSpecFile.cpp

@@ -2911,7 +2911,7 @@ std::shared_ptr<const SpecMeas> ExportSpecFileTool::generateFileToSave()
   if( !meas_to_remove.empty() )
   {
     vector<shared_ptr<const SpecUtils::Measurement>> to_remove( begin(meas_to_remove), end(meas_to_remove) );
-    answer->remove_measurements( to_remove );
+    answer->remove_measurements( to_remove ); //This calls `cleanup_after_load(...)`
   }
 
   if( !meas_to_add.empty() )
@@ -2923,7 +2923,7 @@ std::shared_ptr<const SpecMeas> ExportSpecFileTool::generateFileToSave()
   if( !meas_to_remove.empty() || !meas_to_add.empty() )
   {
     answer->set_uuid( "" );
-    answer->cleanup_after_load();
+    answer->cleanup_after_load( SpecUtils::SpecFile::DontChangeOrReorderSamples );
 
     // `detectors` and `samples` are maybe no longer valid, since we may have summed them together
     //  - we will fix this up, although it probably makes more sense to just filter out unwanted
@@ -2951,6 +2951,17 @@ std::shared_ptr<const SpecMeas> ExportSpecFileTool::generateFileToSave()
     }
     for( const int sample : samples_to_remove )
       samples.erase( sample );
+
+    // Now lets map sample numbers to 1 through N
+    int new_sample_number = 0;
+    vector<pair<int,int>> old_to_new_samplenum;
+    for( const int old_sample_number : answer->sample_numbers() )
+    {
+      ++new_sample_number;
+      old_to_new_samplenum.emplace_back( old_sample_number, new_sample_number );
+    }//for( loop over sample numbers )
+
+    answer->change_sample_numbers( old_to_new_samplenum );
   }//if( !meas_to_remove.empty() || !meas_to_add.empty() )
 
 

src/SpecMeas.cpp

@@ -2269,6 +2269,59 @@ void SpecMeas::cleanup_orphaned_info()
 }//void cleanup_orphaned_info()
 
 
+void SpecMeas::change_sample_numbers( const vector<pair<int,int>> &from_to_sample_nums )
+{
+  SpecFile::change_sample_numbers( from_to_sample_nums );
+
+  // I *think*, m_peaks, m_autoSearchPeaks, and m_dbUserStateIndexes are the only
+  //  SpecMeas specific things that use the sample numbers
+
+  auto update_peak_map = [&from_to_sample_nums]( SampleNumsToPeakMap &peaks ){
+    SampleNumsToPeakMap new_peak_map;
+
+    for( const SampleNumsToPeakMap::value_type &t : peaks )
+    {
+      set<int> new_samples;
+      for( const int orig_sample : t.first )
+      {
+        const auto pos = std::find_if( begin(from_to_sample_nums), end(from_to_sample_nums),
+                    [orig_sample]( const pair<int,int> &val ){ return val.first == orig_sample;} );
+        new_samples.insert( (pos == end(from_to_sample_nums)) ? orig_sample : pos->second );
+      }//for( loop over original sample numbers )
+
+      new_peak_map[new_samples] = t.second;
+    }//for( const SampleNumsToPeakMap::value_type &t : peaks )
+
+    peaks = new_peak_map;
+  };//update_peak_map
+
+  if( m_peaks )
+    update_peak_map( *m_peaks );
+
+  update_peak_map( m_autoSearchPeaks );
+
+
+  // Need to update m_dbUserStateIndexes
+  map<set<int>,long long int> newDbUserStateIndexes;
+  for( const auto &samplenums_dbindex : m_dbUserStateIndexes )
+  {
+    set<int> new_sample_nums;
+    for( const int sample : samplenums_dbindex.first )
+    {
+      // Put original sample number in `new_sample_nums`, unless it is one of the sample numbers
+      //  to change, in which case put in the new sample number
+      const auto pos = std::find_if( begin(from_to_sample_nums), end(from_to_sample_nums),
+                      [sample](const pair<int,int> &lhs) -> bool { return lhs.first == sample; } );
+
+      new_sample_nums.insert( (pos == end(from_to_sample_nums)) ? sample : pos->second );
+    }//for( const int sample : samplenums_dbindex.first )
+
+    newDbUserStateIndexes[new_sample_nums] = samplenums_dbindex.second;
+  }//for( const auto &samplenums_dbindex : m_dbUserStateIndexes )
+
+  m_dbUserStateIndexes = newDbUserStateIndexes;
+}//void change_sample_numbers( const std::vector<std::pair<int,int>> &from_to_sample_nums );
+
 
 Wt::Signal<> &SpecMeas::aboutToBeDeleted()
 {