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

Author: wcjohns

CMakeLists.txt

@@ -532,6 +532,7 @@ set(sources
     src/MakeDrfFit.cpp
     src/FluxTool.cpp
     src/NativeFloatSpinBox.cpp
+    src/SwitchCheckbox.cpp
     src/EnergyCalTool.cpp
     src/EnergyCal.cpp
     src/EnergyCalGraphical.cpp
@@ -616,6 +617,7 @@ set(headers
     InterSpec/MakeDrfFit.h
     InterSpec/FluxTool.h
     InterSpec/NativeFloatSpinBox.h
+    InterSpec/SwitchCheckbox.h
     InterSpec/EnergyCalTool.h
     InterSpec/EnergyCal.h
     InterSpec/EnergyCalGraphical.h

InterSpec/D3SpectrumDisplayDiv.h

@@ -95,7 +95,7 @@ class D3SpectrumDisplayDiv : public Wt::WContainerWidget
   void setPeakModel( PeakModel *model );
 
   void setData( std::shared_ptr<SpecUtils::Measurement> data_hist, const bool keep_curent_xrange );
-  void setSecondData( std::shared_ptr<SpecUtils::Measurement> hist, const bool ownAxis );
+  void setSecondData( std::shared_ptr<SpecUtils::Measurement> hist );
   void setBackground( std::shared_ptr<SpecUtils::Measurement> background );
 
   void scheduleUpdateForeground();

InterSpec/D3TimeChart.h

@@ -142,6 +142,12 @@ class D3TimeChart : public Wt::WContainerWidget
   bool verticalLinesShowing() const;
   bool horizontalLinesShowing() const;
 
+  void setDontRebin( const bool dontRebin );
+  bool dontRebin() const;
+  
+  void setNeutronsHidden( const bool hide );
+  bool neutronsHidden() const;
+  
   void setXAxisRangeSamples( const int min_sample_num, const int max_sample_num );
 
   /** Returns the current user-entered gamma energy range that should be summed to create this gross count chart. */
@@ -241,7 +247,8 @@ class D3TimeChart : public Wt::WContainerWidget
   bool m_compactXAxis;
   bool m_showVerticalLines;
   bool m_showHorizontalLines;
-  
+  bool m_dontRebin;
+  bool m_hideNeutrons;
 
   std::shared_ptr<const SpecUtils::SpecFile> m_spec;
 

InterSpec/DetectorEdit.h

@@ -220,6 +220,16 @@ class DetectorEdit : public Wt::WContainerWidget
   //   on deplandcies)
   static std::shared_ptr<DetectorPeakResponse> initARelEffDetector( const SpecUtils::DetectorType type, InterSpec *interspec );
 
+  
+  /** Checks if file at passed in path is a TSV/CSV file that contains
+   coefficients for the exp( c0 + c1*logx + c2*logx^2 + ...) equation.
+   If so, returns detector.  If not, returns nullptr.
+   
+   ToDo: Currently reads in most of the information exported in the CSV from MakeDrf tool, but maybe not all.
+   */
+  static std::shared_ptr<DetectorPeakResponse> parseRelEffCsvFile( const std::string filePath );
+  
+  
   //Callbacks for when detector is changed or modified
   void gadrasDetectorSelectCallback();
   void relEffDetectorSelectCallback();
@@ -259,20 +269,13 @@ class DetectorEdit : public Wt::WContainerWidget
   //a row is selected, so update det and charts
   void dbTableSelectionChanged();
 
+  
 protected:
   void setAcceptButtonEnabled( const bool enable );
 
-  /** Checks if file at passed in path is a TSV/CSV file that contains
-      coeffeicents for the exp( c0 + c1*logx + c2*logx^2 + ...) equation.
-      If so, returns detector.  If not, returns nullptr.
-   
-   ToDo: Currently reads in most of the information exported in the CSV from
-     MakeDrf tool, except the uncertainities - should add this in.  Also, need
-     to cleanup the GUI during loading of this one CSV that has all the info
-     (def not correct, should hide detector diameter and option to upload
-      Detector.dat).
-   */
-  static std::shared_ptr<DetectorPeakResponse> checkIfFileIsRelEff( const std::string tsvfilepath );
+  /** Called when user changes value in m_uploadedDetName; sets m_detector name. */
+  void handleUserChangedUploadedDrfName();
+  
 
 protected:
   WContainerWidget *m_footer;
@@ -315,6 +318,8 @@ class DetectorEdit : public Wt::WContainerWidget
   Wt::WTabWidget *m_tabs;
 
   Wt::WLineEdit *m_detectorDiameter;
+  Wt::WContainerWidget *m_uploadedDetNameDiv;
+  Wt::WLineEdit *m_uploadedDetName;
   Wt::WContainerWidget *m_detectrDiameterDiv;
   Wt::WFileUpload *m_efficiencyCsvUpload;
   Wt::WContainerWidget *m_detectrDotDatDiv;

InterSpec/DetectorPeakResponse.h

@@ -332,13 +332,15 @@ class DetectorPeakResponse
    
    \param coefs The coefficients for the exp(A0 + A1*log(x) + A2*log(x)^2...)
           equation.  If coefficients are not for intrinsic efficiency (e.g.,
-          characterizationDist is not 0.0), they coeffcients will be converted
+          characterizationDist is not 0.0), they coefficients will be converted
           to intrinsic for internal use
-   \param characterizationDist Distance used when fitting coefficents.  If
+   \param uncerts The uncertainties of the coefficients; must either be empty,
+          or the same size as \p coefs.
+   \param characterizationDist Distance used when fitting coefficients.  If
           coefficients are for intrinsic efficiency, then this value will be
           0.0f.
-   \param equationEnergyUnits The energy units equation should be evalueated
-          in. If equn is in MeV, this will be 1000.  If in keV, will be 1.0.
+   \param equationEnergyUnits The energy units equation should be evaluated
+          in. If eqn is in MeV, this will be 1000.  If in keV, will be 1.0.
    \param lowerEnergy Lower energy, in keV, the equation is good for; if
           unknown pass a value of 0.0f for this parameter and upperEnergy.
    \param upperEnergy Upper energy, in keV, the equation is good for; if
@@ -347,6 +349,7 @@ class DetectorPeakResponse
    Recomputes hash value.
   */
   void fromExpOfLogPowerSeriesAbsEff( const std::vector<float> &coefs,
+                                      const std::vector<float> &uncerts,
                                       const float characterizationDist,
                                       const float detector_diameter,
                                       const float equationEnergyUnits,

InterSpec/EnergyCalMultiFile.h

@@ -116,12 +116,15 @@ class EnergyCalMultiFileModel : public  Wt::WAbstractItemModel
   void refreshData();
 
 protected:
-  typedef std::tuple< std::shared_ptr<const SpecUtils::EnergyCalibration>, \
-                      bool, \
-                      std::shared_ptr<const PeakDef>, \
-                      std::shared_ptr<SpectraFileHeader> > PeakInfo_t;
+  typedef std::tuple< bool, std::shared_ptr<const PeakDef> > UsePeakInfo_t;
+  
+  typedef std::tuple<std::shared_ptr<SpectraFileHeader>, \
+                     std::set<int>, \
+                     std::shared_ptr<const SpecUtils::EnergyCalibration>, \
+                     std::vector<UsePeakInfo_t> > SamplesPeakInfo_t;
+  
+  std::vector<std::vector<SamplesPeakInfo_t>> m_data;
 
-  std::vector< std::vector<PeakInfo_t> > m_peaks;
   EnergyCalTool *m_calibrator;
   SpectraFileModel *m_fileModel;
 

InterSpec/GadrasGamFileParser.h

@@ -28,65 +28,103 @@
 #include <iostream>
 
 /** Opens GADRAS GAM files.
- * Opens only the newer format of GAM files (that start with two 0's).
+ *
+ * Currently only opens .gam files that start with two 0's, called version 1, and GamFileVersion = 2.0 and  2.1.
+ *
+ * Does not currently parse all information, such as model geometry, largest dimension, multiplicity, etc.
  */
 class GadrasGamFile
 {
 public:
   GadrasGamFile();
 
 
-  /** Parses the cooresponding stream.
+  /** Parses the corresponding stream.
    * Throws runtime_error exception when the file is not formatted properly.
    */
   void parse_data( std::istream &strm );
 
 
+  enum class GamFileVersion
+  {
+    /** The .gam files that start with two 0's.
+     The gamma lines do not include shielding information.
+     */
+    Version_1,
+    
+    /** Indicated by a "GamFileVersion = 2.0" header in the file. */
+    Version_2_0,
+    
+    /** Indicated by a "GamFileVersion = 2.1" header in the file. */
+    Version_2_1,
+    
+    /**  */
+    NumGamFileVersions
+  };//enum class GamFileVersion
 
-  /* A relevant note from the GADRAS users manual:
-   * If the width of the group exceeds 1% of the average energy of the group,
-   * the radiation within the group is assumed to be distributed uniformly 
-   * within the group.  For groups that have widths under 1% of the average 
-   * energy, any excess flux within the group relative to a linear interpolation 
-   * of surrounding groups is assumed to be emitted at a discrete energy, 
-   * corresponding to the midpoint of the group.
+  
+  /** Writes the .gam file to the provided stream.
+   *
+   * Currently only supports writing GamFileVersion::Version_2_0, and will throw exception for other versions.
+   *
+   * Throws runtime_error exception if output fails or errors encountered.
+   */
+  void write_gam( std::ostream &output, const GamFileVersion version );
+  
+  
+  /*
+   A relevant note is:
+   If the width, W, or a photon group with lower energy EL, meets any of the following conditions,
+   GADRAS transport will treat the group as a discrete line:
+   - W < 0.25 keV
+   - W < 0.4 keV and EL > 200 keV
+   - W < 1.0 keV and EL > 10 MeV
+   If any of these conditions are met, GADRAS will look at the (assumed) continuum groups above and
+   below the potential discrete group. The counts-per-keV in the potential discrete group must be
+   greater than the adjacent continuum groups. If it is, it uses the higher-energy continuum group
+   and subtracts those counts from the discrete group to get the net discrete counts, with energy
+   equal to the midpoint of the group.
+   */
+  
+  /** The gamma file version parsed.
    */
+  GamFileVersion m_version;
 
-  /** Energy, in keV of the un-collided gamma rays. 
+  /** Energy, in keV of the un-collided gamma rays.
    * Will have same number of entries as, and coorespond index-wise to
    * #m_photon_lines_flux, #m_photon_lines_an, and #m_photon_lines_ad.
    */
   std::vector<float> m_photon_lines_energy;
 
-  /** The flux into 4pi for the cooresponding m_photon_lines_energy energy.*/
+  /** The flux into 4pi for the corresponding m_photon_lines_energy energy.*/
   std::vector<float> m_photon_lines_flux;
 
-  /** The yeild-effective weighted atomic number of interveining material. */
+  /** The yield-effective weighted atomic number of intervening material. */
   std::vector<float> m_photon_lines_an;
 
-  /** The yield-effective weighted areal density of interveining material. */
+  /** The yield-effective weighted areal density of intervening material. */
   std::vector<float> m_photon_lines_ad;
 
 
-  /** Lower energy of energy group for the cooresponding (index-wise) 
+  /** Lower energy of energy group for the corresponding (index-wise)
    * #m_photon_group_flux.  Energy is in keV.
    */
   std::vector<float> m_photon_group_boundries;
 
-  /** Flux of the continuum for the given energy group. 
+  /** Flux of the continuum for the given energy group.
    * Note that the last last entry should have a flux of 0, in order to allow
    * defining the upper energy of the last group.
    */
   std::vector<float> m_photon_group_flux;
 
 
-  /** Lower energy of the neutron energy group.  Will have same number of 
+  /** Lower energy of the neutron energy group.  Will have same number of
    * entries as #m_neutron_group_flux.
    * Energy is in keV (note that .gam files use eV).
    */
   std::vector<float> m_neutron_group_boundries;
 
-  /** Flux in cooresponding energy group.
+  /** Flux in corresponding energy group.
    */
   std::vector<float> m_neutron_group_flux;
 };//class GadrasGamFile