Merge branch 'master' of github.com:sandialabs/InterSpec

wcjohns · wcjohns · commit 073798a5ed78 · 2025-09-25T22:29:26.000-07:00
diff --git a/InterSpec/DetectorPeakResponse.h b/InterSpec/DetectorPeakResponse.h
@@ -283,8 +283,27 @@ class DetectorPeakResponse
                                const float detectorDiameter,
                                const float energyUnits,
                                const EffGeometryType geometry_type );
-  
-  
+
+  struct EnergyEffPoint
+  {
+    float energy, efficiency;
+
+    /** Currently unused efficiency uncertainty. */
+    std::optional<float> efficiencyUncert;
+  };//struct EnergyEffPoint
+
+  /** Sets the detector efficiencies by pairs of energy (in keV) and efficiencies.
+
+   @param efficiencies The eneryg/efficiency information - must have at least two entries, and its range defines `m_lowerEnergy` and `m_upperEnergy`.
+   @param detectorDiameter The detector diameter - set to zero or negative if geometry type is not EffGeometryType::FarField; must be positive if far field
+   @param geometry_type The efficiency type these points are for.
+
+   Throws exception on error.
+   */
+  void setEfficiencyPoints( const std::vector<EnergyEffPoint> &efficiencies,
+                           const float detectorDiameter,
+                           const EffGeometryType geometry_type );
+
   //setIntrinsicEfficiencyFormula(): sets m_efficiencyForm, m_efficiencyFormula,
   //  and m_efficiencyFcn to correspond to the fucntional form passed in.
   //  Formula should be in the a general functional form, where energy is
diff --git a/InterSpec/RelActCalc.h b/InterSpec/RelActCalc.h
@@ -316,10 +316,16 @@ struct PhysicalModelShieldInput
   */
   bool fit_areal_density = true;
       
-  /** The lower AD for the shielding.  Must be in range [0,500] g/cm2, if fitting AD. */
+  /** The lower AD for the shielding.  Must be in range [0,500] g/cm2, if fitting AD.
+
+   In units of `PhysicalUnits` - i.e., you need to divide by `PhysicalUnits::g_per_cm2` to printout to g/cm2 human values.
+   */
   double lower_fit_areal_density = 0.0;
       
-  /** The upper AD for the shielding.  Must be greater than to lower AD, if fitting, and must be in range [0,500] g/cm2. */
+  /** The upper AD for the shielding.  Must be greater than to lower AD, if fitting, and must be in range [0,500] g/cm2.
+
+   In units of `PhysicalUnits` - i.e., you need to divide by `PhysicalUnits::g_per_cm2` to printout to g/cm2 human values.
+   */
   double upper_fit_areal_density = 0.0;
     
   /** Checks specified constraints are obeyed - throwing an exception if not. */
diff --git a/InterSpec/RelActCalcAuto_imp.hpp b/InterSpec/RelActCalcAuto_imp.hpp
@@ -110,7 +110,7 @@ struct PeakDefImp
 
   /** Gives lower and upper energies that contain `1.0 - missing_frac` of the peak,
 
-   For skewed distributions, particularly Crystal Bal, the energy range given by the desired
+   For skewed distributions, particularly Crystal Ball, the energy range given by the desired
    peak coverage can get huge, so you can also specify the max number of FWHM to use, which will
    truncate the range in these cases of very large skew.
 
diff --git a/InterSpec/SpecMeas.h b/InterSpec/SpecMeas.h
@@ -132,9 +132,11 @@ class SpecMeas : public SpecUtils::SpecFile
                                const std::set<int> &det_nums ) const;
   /** Adds reading back in peak information (only from InterSpec exported SPE files though). */
   virtual bool load_from_iaea( std::istream &istr );
-  
+
+  virtual void load_cnf_using_reader( CAMInputOutput::CAMIO &reader );
+
   virtual std::shared_ptr< ::rapidxml::xml_document<char> > create_2012_N42_xml() const;
-  
+
   /** Same as #SpecFile::set_energy_calibration, but marks this SpecMeas as modified. */
   virtual void set_energy_calibration( const std::shared_ptr<const SpecUtils::EnergyCalibration> &cal,
                                       const std::shared_ptr<const SpecUtils::Measurement> &measurement );
diff --git a/InterSpec_resources/SpecMeasManager.css b/InterSpec_resources/SpecMeasManager.css
@@ -135,6 +135,11 @@ button.LinkBtn.NonSpecQrCodeBtn.Wt-btn.with-label
   max-width: 85vw;
 }
 
+.simple-dialog.EccDrfDialog .body.NonSpecDialogBody
+{
+  padding-bottom: 8px;
+}
+
 .simple-dialog.EccDrfDialog .HowToUseGrp
 {
   display: flex;
@@ -146,12 +151,15 @@ button.LinkBtn.NonSpecQrCodeBtn.Wt-btn.with-label
 {
   margin-left: 40px;
   margin-top: 10px;
+
 }
 
 .simple-dialog.EccDrfDialog table.FarFieldOptTbl td
 {
   vertical-align: middle;
-  padding-left: 5px
+  padding-left: 5px;
+  padding-bottom: 2px;
+  padding-top: 2px;
 }
 
 .simple-dialog.EccDrfDialog .EccDrfTypeBtn
diff --git a/InterSpec_resources/app_text/RefSpectraWidget.xml b/InterSpec_resources/app_text/RefSpectraWidget.xml
@@ -2,8 +2,10 @@
 <messages>
   <!-- rs- is short for Reference Spectra -->
   <message id="rs-dialog-title">Reference Spectra</message>
-  <message id="rs-show-foreground">Show Foreground</message>
-  <message id="rs-show-background">Background</message>
+  <message id="rs-show-foreground">Compare Foreground</message>
+  <message id="rs-show-foreground-portrait">Compare</message>
+  <message id="rs-show-background">Show Background</message>
+  <message id="rs-show-background-portrait">Background</message>
   <message id="rs-tt-add-dir-btn">Add directory to open reference spectra from.</message>
   <message id="rs-tt-delete-dir-btn">Removes the currently selected directory from the list of places to show reference spectra from.</message>
   <message id="rs-no-dir-selected-desktop">
diff --git a/InterSpec_resources/app_text/SpecMeasManager.xml b/InterSpec_resources/app_text/SpecMeasManager.xml
@@ -133,7 +133,7 @@
   <message id="smm-ecc-fix-geom-act-m2">Fixed Geometry - activity per m2</message>
   <message id="smm-ecc-fix-geom-act-gram">Fixed Geometry - activity per gram</message>
   <message id="smm-ecc-det-diam">Detector diam.</message>
-  <message id="smm-ecc-dist">Distance.</message>
+  <message id="smm-ecc-dist">Distance</message>
   <message id="smm-ecc-use-drf">Use DRF</message>
   <message id="smm-ecc-error">Error creating DRF from ECC: {1}</message>
 
diff --git a/external_libs/SpecUtils b/external_libs/SpecUtils
@@ -1 +1 @@
-Subproject commit 2dd250c6bf6d3960d99ced29ca97683b734005b5
+Subproject commit 0074e1ac79b0739db077b42d637a51db2e0ffa85
diff --git a/src/DetectorPeakResponse.cpp b/src/DetectorPeakResponse.cpp
@@ -898,6 +898,46 @@ void DetectorPeakResponse::fromEnergyEfficiencyCsv( std::istream &input,
 }//void fromEnergyEfficiencyCsv(...)
 
 
+void DetectorPeakResponse::setEfficiencyPoints( const std::vector<DetectorPeakResponse::EnergyEffPoint> &efficiencies,
+                         const float detectorDiameter,
+                         const EffGeometryType geometry_type )
+{
+  if( (geometry_type == EffGeometryType::FarField)
+     && ((detectorDiameter <= 0.0) || IsInf(detectorDiameter) || IsNan(detectorDiameter)) )
+    throw runtime_error( "Detector diameter must be greater than 0.0" );
+
+  if( efficiencies.size() < 2 )
+    throw runtime_error( "DetectorPeakResponse::setEfficiencyPoints(): need at least two efficiency points." );
+
+  m_energyEfficiencies.clear();
+  for( const EnergyEffPoint &p : efficiencies )
+  {
+    if( p.energy < 0.0 || p.efficiency < 0.0 )
+      throw runtime_error( "Energy and efficiency musst be >= 0" );
+
+    EnergyEfficiencyPair eep;
+    eep.energy = p.energy;
+    eep.efficiency = p.efficiency;
+
+    m_energyEfficiencies.push_back( std::move(eep) );
+  }//for( const EnergyEffPoint &p : efficiencies )
+
+  std::sort( begin(m_energyEfficiencies), end(m_energyEfficiencies) );
+
+  m_detectorDiameter = detectorDiameter;
+  m_efficiencyEnergyUnits = static_cast<float>(PhysicalUnits::keV);
+
+  m_flags = 0;
+
+  m_lowerEnergy = m_energyEfficiencies.front().energy;
+  m_upperEnergy = m_energyEfficiencies.back().energy;
+
+  m_lastUsedUtc = m_createdUtc = std::time(nullptr);
+  m_geomType = geometry_type;
+
+  computeHash();
+}//void setEfficiencyPoints(...)
+
 
 void DetectorPeakResponse::setIntrinsicEfficiencyFormula( const string &fcnstr,
                                                           const float diameter,
diff --git a/src/PeakFitLM.cpp b/src/PeakFitLM.cpp
@@ -1509,11 +1509,20 @@ vector<shared_ptr<const PeakDef>> fit_peaks_in_roi_LM( const vector<shared_ptr<c
     options.min_trust_region_radius = 1e-32;
     // Lower bound for the relative decrease before a step is accepted.
     options.min_relative_decrease = 1e-3; //pseudo optimized based on success rate of fitting peaks - but unknown effect on accuracy of fits.
-    options.max_num_iterations = 50000;
+
+    // It looks like it usually takes well below 100 calls to solve most problems, but a tail up to ~500, and then rare
+    //  (pathelogical?) cases that can take >50k
+    //  However, for these pathological cases, if we just try again starting from where it left off, it will solve
+    //  it super quick - I guess because there will be more "momentum" to find the minimum, or something, not totally
+    //  sure.
+    //  We could probably reduce this number of iterations to ~100 - but the effects or impact of this hasnt been
+    //  evaluated.
+    //  Also, have not checked dependence on number of peaks at all
+    options.max_num_iterations = (coFitPeaks.size() > 2) ? 1000 : 500;
 #ifndef NDEBUG
-    options.max_solver_time_in_seconds = 300.0;
+    options.max_solver_time_in_seconds = (coFitPeaks.size() > 2) ? 180.0 : 120;
 #else
-    options.max_solver_time_in_seconds = 30.0;
+    options.max_solver_time_in_seconds = (coFitPeaks.size() > 2) ? 30.0 : 150.0;
 #endif
 
 #if( PRINT_VERBOSE_PEAK_FIT_LM_INFO )
@@ -1546,18 +1555,48 @@ vector<shared_ptr<const PeakDef>> fit_peaks_in_roi_LM( const vector<shared_ptr<c
     std::cout << summary.FullReport() << "\n";
     cout << "Took " << cost_functor->m_ncalls.load() << " calls to solve." << endl;
 #endif
-    
+
     switch( summary.termination_type )
     {
       case ceres::CONVERGENCE:
       case ceres::USER_SUCCESS:
         break;
         
       case ceres::NO_CONVERGENCE:
+      {
 #if( PRINT_VERBOSE_PEAK_FIT_LM_INFO )
         cerr << "The L-M ceres::Solver solving failed - NO_CONVERGENCE:\n" << summary.FullReport() << endl;
 #endif
+        // We will give it another go - for most cases it seems the solution will now be succesffuly found really
+        //  quickly.  The guess is this is from momentum, or whatever, but not really sure.
+        //cerr << "Initial L-M ceres::Solver failed with " << cost_functor->m_ncalls.load() << " calls and "
+        //  << summary.num_successful_steps << " steps - will try again" << endl;
+
+        options.max_num_iterations = 5000;
+        // TODO: see if we should loosed any of the following up.
+        //options.function_tolerance = 1e-6;
+        //options.parameter_tolerance = 1e-9;
+        //options.initial_trust_region_radius = 35*(cost_functor->number_parameters() - prob_setup.m_constant_parameters.size());
+        cost_functor->m_ncalls = 0;
+
+        summary = ceres::Solver::Summary();
+
+        ceres::Solve(options, &problem, &summary);
+
+        if( (summary.termination_type == ceres::CONVERGENCE)
+            || (summary.termination_type == ceres::USER_SUCCESS) )
+        {
+          //cerr << "Retry of L-M ceres::Solver worked with "
+          //<< cost_functor->m_ncalls.load() << " fcn additional calls in "
+          //<< summary.num_successful_steps << " succesfull steps"
+          //<< endl;
+          break;
+        }
+
+        cerr << "Retry of L-M ceres::Solver Failed with " << cost_functor->m_ncalls.load() << " additional calls" << endl;
+
         throw runtime_error( "The L-M ceres::Solver solving failed - NO_CONVERGENCE." );
+      }
 
       case ceres::FAILURE:
 #if( PRINT_VERBOSE_PEAK_FIT_LM_INFO )
diff --git a/src/PeakSearchGuiUtils.cpp b/src/PeakSearchGuiUtils.cpp
@@ -2821,12 +2821,13 @@ void search_for_peaks_worker( std::weak_ptr<const SpecUtils::Measurement> weak_d
     server->post( sessionID, callback );
     return;
   }
-  
+
+  auto results = make_shared<vector<shared_ptr<const PeakDef>>>();
+
   try
   {
-    *resultpeaks = ExperimentalAutomatedPeakSearch::search_for_peaks( data, drf, existingPeaks, singleThread, isHPGe );
-    
-    *resultpeaks = assign_srcs_from_ref_lines( data, *resultpeaks, displayed, setColor, false, true );
+    *results = ExperimentalAutomatedPeakSearch::search_for_peaks( data, drf, existingPeaks, singleThread, isHPGe );
+    *results = assign_srcs_from_ref_lines( data, *results, displayed, setColor, false, true );
   }catch( std::exception &e )
   {
     string msg = "InterSpec::search_for_peaks_worker(): caught exception: '";
@@ -2841,7 +2842,11 @@ void search_for_peaks_worker( std::weak_ptr<const SpecUtils::Measurement> weak_d
   }//try / catch
   
   
-  server->post( sessionID, callback );
+  server->post( sessionID, [callback,results,resultpeaks](){
+    if( resultpeaks )
+      *resultpeaks = *results;
+    callback();
+  } );
 }//void search_for_peaks_worker(...)
 
   
diff --git a/src/RefSpectraModel.cpp b/src/RefSpectraModel.cpp
@@ -268,7 +268,10 @@ void RefSpectraModel::populateNode( Node *node ) const
 {
   try 
   {
-    vector<tuple<std::string,std::string,bool>> dir_entries;
+    const SandiaDecay::SandiaDecayDataBase * const db = DecayDataBaseServer::database();
+    assert( db );
+
+    vector<tuple<std::string,std::string,bool,const SandiaDecay::Nuclide *>> dir_entries;
     for( const auto &entry : fs::directory_iterator(node->fullPath) )
     {
       const fs::path entryPath = entry.path();
@@ -285,11 +288,15 @@ void RefSpectraModel::populateNode( Node *node ) const
         continue;
       }
 
-      dir_entries.emplace_back( entryName, entryPathStr, isDir );
+      const std::string::size_type underscore_pos = entryName.find( '_' );
+      const SandiaDecay::Nuclide * const nuc = ((underscore_pos != string::npos) && !isDir)
+                                                  ? db->nuclide(entryName.substr(0,underscore_pos))
+                                                  : nullptr;
+
+      dir_entries.emplace_back( entryName, entryPathStr, isDir, nuc );
     }//for( const auto &entry : fs::directory_iterator(node->fullPath) )
 
-    const SandiaDecay::SandiaDecayDataBase * const db = DecayDataBaseServer::database();
-    assert( db );
+
 
     std::sort( begin(dir_entries), end(dir_entries), [db]( const auto &lhs, const auto &rhs ) -> bool {
       const string &lhs_name = std::get<0>(lhs);
@@ -306,16 +313,16 @@ void RefSpectraModel::populateNode( Node *node ) const
       if( lhs_is_dir && rhs_is_dir )
         return lhs_name < rhs_name;
 
+      const bool lhs_is_back = SpecUtils::istarts_with(lhs_name, "background");
+      const bool rhs_is_back = SpecUtils::istarts_with(rhs_name, "background");
+      if( lhs_is_back || rhs_is_back )
+        return lhs_is_back > rhs_is_back;
 
       //If the name is like "U238_Sh_raw_...", try to extract the nuclide
       //  We could use a bit more sophisticated of a regex to extract Nuclide name, but for now we'll just try
       //  whatever comes before the first underscore.
-
-      const std::string::size_type lhs_pos = lhs_name.find( '_' );
-      const std::string::size_type rhs_pos = rhs_name.find( '_' );
-
-      const SandiaDecay::Nuclide * const lhs_nuc = (lhs_pos != string::npos) ? db->nuclide(lhs_name.substr(0,lhs_pos)) : nullptr;
-      const SandiaDecay::Nuclide * const rhs_nuc = (rhs_pos != string::npos) ? db->nuclide(rhs_name.substr(0,rhs_pos)) : nullptr;
+      const SandiaDecay::Nuclide * const lhs_nuc = std::get<3>(lhs);
+      const SandiaDecay::Nuclide * const rhs_nuc = std::get<3>(rhs);
 
       if( !lhs_nuc && !rhs_nuc )
         return lhs_name < rhs_name;
@@ -337,7 +344,7 @@ void RefSpectraModel::populateNode( Node *node ) const
     } );
 
 
-    for( const tuple<std::string,std::string,bool> &entry : dir_entries )
+    for( const tuple<std::string,std::string,bool,const SandiaDecay::Nuclide *> &entry : dir_entries )
     {
       std::string entryName = std::get<0>(entry);
       const std::string entryPathStr = std::get<1>(entry);
diff --git a/src/RefSpectraWidget.cpp b/src/RefSpectraWidget.cpp
@@ -464,22 +464,22 @@ void RefSpectraWidget::setupUI()
   HelpSystem::attachToolTipOn( m_deleteDirButton, WString::tr("rs-tt-delete-dir-btn"), showToolTips );
 #endif // !IOS && !ANDROID && !BUILD_FOR_WEB_DEPLOYMENT
 
-
-  m_showCurrentForeground = new Wt::WCheckBox( WString::tr("rs-show-foreground"), stackOptions );
+  m_showCurrentForeground = new Wt::WCheckBox( WString::tr(portrait ? "rs-show-foreground-portrait" : "rs-show-foreground"), stackOptions );
   m_showCurrentForeground->addStyleClass( "CbNoLineBreak" );
   m_showCurrentForeground->changed().connect( this, &RefSpectraWidget::updatePreview );
   
 
-  m_refBackground = new Wt::WCheckBox( WString::tr("rs-show-background"), stackOptions );
+  m_refBackground = new Wt::WCheckBox( WString::tr(portrait ? "rs-show-background-portrait" : "rs-show-background"), stackOptions );
   m_refBackground->addStyleClass( "CbNoLineBreak" );
   m_refBackground->changed().connect( this, &RefSpectraWidget::updatePreview );
   m_refBackground->setHiddenKeepsGeometry( true );
   m_refBackground->setHidden( true );
   
   if( portrait )
   {
-    mainLayout->setRowStretch( 0, 1 );
-    mainLayout->setRowStretch( 1, 1 );
+    //mainLayout->setRowStretch( 0, 1 );
+    //mainLayout->setRowStretch( 1, 1 );
+    mainLayout->setRowResizable( 0, true, WLength(50,WLength::Percentage) ); //This is just to make the tree-view and chart-area split the heiht 50/50
   }else
   {
     mainLayout->setRowStretch( 0, 1 );
diff --git a/src/ReferenceLineInfo.cpp b/src/ReferenceLineInfo.cpp
@@ -3581,8 +3581,8 @@ std::shared_ptr<ReferenceLineInfo> ReferenceLineInfo::generateRefLineInfo( RefLi
       const float &first_energy = get<2>( casc );
       const float &second_energy = get<3>( casc );
       const float &coinc_frac = get<4>( casc );
-      const double &second_br = get<5>( casc );
-      
+      //const double &second_br = get<5>( casc );
+
       const float energy = first_energy + second_energy;
       
       ReferenceLineInfo::RefLine line;
diff --git a/src/RelActCalcAuto.cpp b/src/RelActCalcAuto.cpp
diff --git a/src/SpecFileQueryDbCache.cpp b/src/SpecFileQueryDbCache.cpp
diff --git a/src/SpecMeas.cpp b/src/SpecMeas.cpp
diff --git a/target/ios/InterSpec/CMakeLists.txt b/target/ios/InterSpec/CMakeLists.txt

Original file line number	Diff line number	Diff line change
`@@ -135,6 +135,11 @@ button.LinkBtn.NonSpecQrCodeBtn.Wt-btn.with-label`
`135`	`135`	`max-width: 85vw;`
`136`	`136`	`}`
`137`	`137`
	`138`	`+.simple-dialog.EccDrfDialog .body.NonSpecDialogBody`
	`139`	`+{`
	`140`	`+ padding-bottom: 8px;`
	`141`	`+}`
	`142`	`+`
`138`	`143`	`.simple-dialog.EccDrfDialog .HowToUseGrp`
`139`	`144`	`{`
`140`	`145`	`display: flex;`
`@@ -146,12 +151,15 @@ button.LinkBtn.NonSpecQrCodeBtn.Wt-btn.with-label`
`146`	`151`	`{`
`147`	`152`	`margin-left: 40px;`
`148`	`153`	`margin-top: 10px;`
	`154`	`+`
`149`	`155`	`}`
`150`	`156`
`151`	`157`	`.simple-dialog.EccDrfDialog table.FarFieldOptTbl td`
`152`	`158`	`{`
`153`	`159`	`vertical-align: middle;`
`154`		`- padding-left: 5px`
	`160`	`+ padding-left: 5px;`
	`161`	`+ padding-bottom: 2px;`
	`162`	`+ padding-top: 2px;`
`155`	`163`	`}`
`156`	`164`
`157`	`165`	`.simple-dialog.EccDrfDialog .EccDrfTypeBtn`