added FileNotFound Error message. Added option to specify data directory....

added FileNotFound Error message. Added option to specify data directory. Added checks if datafiles exists in ICRU reader class


Former-commit-id: 95321051

.gitlab-ci.yml

@@ -7,17 +7,17 @@ unit_tests:
   stage: unit_tests
   script:
     - git submodule update --init --recursive
-    - cd code/build/release
-    - cmake -G Ninja -DCMAKE_BUILD_TYPE=Debug ../../
+    - cd code/build/debug
+    - cmake -G Ninja -DCMAKE_BUILD_TYPE=Debug -DBUILD_TESTS=ON ../../
     - ninja
     - OMP_NUM_THREADS=1 ./unit_tests -r junit > unit_tests_report.xml
     - gcovr -e ../../ext/ -e ../../tests/ -r ../../
   artifacts:
     when: always
     paths:
-      - code/build/release/unit_tests_report.xml
+      - code/build/debug/unit_tests_report.xml
     reports:
-      junit: code/build/release/unit_tests_report.xml
+      junit: code/build/debug/unit_tests_report.xml
   timeout: 4h
   rules:
     - if: $CI_PIPELINE_SOURCE == "merge_request_event" || $CI_COMMIT_BRANCH == "master" || $CI_COMMIT_BRANCH == "develop"

.gitmodules

@@ -10,3 +10,6 @@
 [submodule "code/ext/parmetis"]
 	path = code/ext/parmetis
 	url = https://github.com/slydex/parmetis.git
+[submodule "code/ext/neuralEntropy"]
+	path = code/ext/neuralEntropy
+	url = https://github.com/ScSteffen/neuralEntropy.git

Dockerfile

+FROM ubuntu:20.04
+
+ENV LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib" \
+    PYTHONPATH=/usr/local/gmsh/lib:$PYTHONPATH \
+    PATH=/opt/conda/bin:/usr/local/gmsh/bin:$PATH 
+
+RUN apt-get update \
+    && DEBIAN_FRONTEND=noninteractive apt-get install -qq \
+       gcc \
+       g++ \
+       libopenmpi-dev \
+       openmpi-bin \
+       libblas-dev \
+       liblapack-dev \
+       git \
+       make \
+       ninja-build \
+       cmake \
+       wget \
+       ssh \
+       libssl-dev \
+       libxt-dev \
+       libgl1-mesa-dev \
+       libglu1 \
+       libxrender1 \
+       libxcursor-dev \
+       libxft-dev \
+       libxinerama-dev\
+       python3\
+       python3-pip\
+       vim
+ 
+RUN    pip3 install tensorflow==2.2.2\
+       pygmsh==6.1.1 Pillow pydicom gcovr \
+       matplotlib\
+       scipy
+
+RUN cd /usr/local \
+    && wget -nc --quiet  http://gmsh.info/bin/Linux/gmsh-4.7.0-Linux64-sdk.tgz \
+    && tar xzf gmsh-4.7.0-Linux64-sdk.tgz \
+    && mv gmsh-4.7.0-Linux64-sdk gmsh \
+    && rm gmsh-4.7.0-Linux64-sdk.tgz 
+
+RUN wget -nc --no-check-certificate --quiet https://www.vtk.org/files/release/8.2/VTK-8.2.0.tar.gz \
+    && tar xzf VTK-8.2.0.tar.gz \
+    && mkdir VTK-8.2.0/build \
+    && cd VTK-8.2.0/build \
+    && cmake -G Ninja -DCMAKE_BUILD_TYPE=Release -DBUILD_DOCUMENTATION=OFF -DBUILD_TESTING=OFF  ../ \
+    && ninja \
+    && ninja install > /dev/null \
+    && cd - \
+    && rm -rf VTK-*
+
+RUN apt-get clean \
+    && apt-get autoremove --purge \
+    && rm -rf /var/lib/apt/lists/* 
+    
+
+
+        
+    
+WORKDIR /home

README.md

@@ -20,6 +20,11 @@ TBD
  - VTK
  - git
  - ninja or make
+ - gmsh
+
+### Python dependencies
+- pygmsh version 6.1.1 'pip install pygmsh==6.1.1' (note that newer versions are not yet supported)
+
 
 ### Obtain submodules
 Note that an **active internet connection is required for the first build** in order to download the latest versions of the required submodules!
@@ -98,7 +103,7 @@ Append `HINTS VTK_INSTALL_DIR` to the `find_package( VTK ... )` line in the CMak
 find_package( VTK REQUIRED COMPONENTS vtkIOGeometry vtkFiltersCore HINTS ~/VTK-install )
 ```
 
-Compile it
+Compile it (make sure you use GCC as compiler: module load compiler/gnu/10.2) 
 ```bash
 module load devel/cmake/3.16
 module load compiler/gnu/9.2
@@ -164,6 +169,8 @@ Please stick to the following coding style for easier code readability:
  - class variables start with an underscore and lowercase letters e.g. `_foo`
  - functions start with a capital letter e.g. `GetSettings()`
  - any variable/function names have capital letters at each individual word e.g. `GetAllCellsAdjacentTo(Cell i)`
+ - Abstract base classes for inheritance structures end with the suffix "Base" e.g. QuadratureBase, whith child classes 
+   QGaussLegendre or QProduct
 
 Please also use the provided `code/.clang-format` style format to format your code before pushing your latest commits.
 Some editors offer to automatically apply the style format upon saving a file (e.g. `Qtcreator`).

code/CMakeLists.txt

 cmake_minimum_required( VERSION 3.12.4 )
 project( KiT-RT VERSION 0.1.0 LANGUAGES CXX )
 
+### OPTIONS #####################################
+option( BUILD_TESTS "builds all available unit tests" OFF )
+option( BUILD_GUI "additionally builds a user interface" OFF )
+#################################################
 
 ### COMPILER ####################################
 set( CMAKE_CXX_STANDARD 17 )
@@ -24,7 +28,7 @@ include_directories( ${LAPACK_INCLUDE_DIR} )
 
 find_package( BLAS )
 
-find_package( VTK REQUIRED COMPONENTS vtkIOGeometry vtkFiltersCore )
+find_package( VTK COMPONENTS vtkIOGeometry vtkFiltersCore REQUIRED )
 
 find_package( Python3 COMPONENTS Interpreter Development NumPy REQUIRED )
 include_directories( ${Python3_INCLUDE_DIRS} ${Python3_NumPy_INCLUDE_DIRS} )
@@ -70,6 +74,13 @@ add_compile_definitions( GIT_HASH="${GIT_HASH}" )
 
 ### BUILD KIT-RT ################################
 file( GLOB_RECURSE SRCS RELATIVE ${CMAKE_SOURCE_DIR} "src/*.cpp" "include/*.h" )
+set( EXCLUDE_DIR "/gui/" )
+foreach( TMP_PATH ${SRCS} )
+    string( FIND ${TMP_PATH} ${EXCLUDE_DIR} EXCLUDE_DIR_FOUND )
+    if( NOT ${EXCLUDE_DIR_FOUND} EQUAL -1 )
+        list( REMOVE_ITEM SRCS ${TMP_PATH} )
+    endif()
+endforeach( TMP_PATH )
 include_directories( ${CMAKE_SOURCE_DIR}/include )
 add_executable( ${CMAKE_PROJECT_NAME} ${SRCS} ${EXT_SRCS} )
 target_link_libraries( ${CMAKE_PROJECT_NAME} ${CORE_LIBRARIES} )
@@ -81,26 +92,49 @@ target_compile_options( ${CMAKE_PROJECT_NAME} PUBLIC "$<$<CONFIG:RELEASE>:${KITR
 
 
 ### BUILD UNIT TESTS ############################
-include( CTest )
-set( CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/ext/Catch2/contrib ${CMAKE_MODULE_PATH} )
-include( Catch )
-set( CATCH_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/Catch2/single_include/catch2 )
-add_compile_definitions( BUILD_TESTING )
-add_compile_definitions( TESTS_PATH="${CMAKE_SOURCE_DIR}/tests/" )
-add_library( Catch INTERFACE )
-target_include_directories( Catch INTERFACE ${CATCH_INCLUDE_DIR} )
-file( GLOB_RECURSE TEST_SRCS RELATIVE ${CMAKE_SOURCE_DIR} "tests/*.cpp" )
-list( REMOVE_ITEM SRCS "src/main.cpp" )
-add_executable( unit_tests ${TEST_SRCS} ${SRCS} ${EXT_SRCS} )
-target_link_libraries( unit_tests Catch ${CORE_LIBRARIES} )
-target_compile_options( unit_tests PUBLIC "$<$<CONFIG:DEBUG>:${KITRT_DEBUG_OPTIONS}>" )
-if( CMAKE_COMPILER_IS_GNUCXX )
-    set( CODE_COVERAGE_OPTIONS --coverage -g -O0 -w )
-    target_compile_options( unit_tests PUBLIC "$<$<CONFIG:DEBUG>:${CODE_COVERAGE_OPTIONS}>" )
-    target_link_libraries( unit_tests Catch gcov )
+if( BUILD_TESTS )
+    include( CTest )
+    set( CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/ext/Catch2/contrib ${CMAKE_MODULE_PATH} )
+    include( Catch )
+    set( CATCH_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/Catch2/single_include/catch2 )
+    add_library( Catch INTERFACE )
+    target_include_directories( Catch INTERFACE ${CATCH_INCLUDE_DIR} )
+    file( GLOB_RECURSE TEST_SRCS RELATIVE ${CMAKE_SOURCE_DIR} "tests/*.cpp" )
+    list( REMOVE_ITEM SRCS "src/main.cpp" )
+    add_executable( unit_tests ${TEST_SRCS} ${SRCS} ${EXT_SRCS} )
+    target_compile_definitions( unit_tests PUBLIC BUILD_TESTING )
+    target_compile_definitions( unit_tests PUBLIC TESTS_PATH="${CMAKE_SOURCE_DIR}/tests/" )
+    target_link_libraries( unit_tests Catch ${CORE_LIBRARIES} )
+    target_compile_options( unit_tests PUBLIC "$<$<CONFIG:DEBUG>:${KITRT_DEBUG_OPTIONS}>" )
+    if( CMAKE_COMPILER_IS_GNUCXX )
+        set( CODE_COVERAGE_OPTIONS --coverage -g -O0 -w )
+        target_compile_options( unit_tests PUBLIC "$<$<CONFIG:DEBUG>:${CODE_COVERAGE_OPTIONS}>" )
+        target_link_libraries( unit_tests Catch gcov )
+    endif()
+    target_compile_options( unit_tests PUBLIC "$<$<CONFIG:RELWITHDEBINFO>:${KITRT_RELWITHDEBINFO_OPTIONS}>" )
+    target_compile_options( unit_tests PUBLIC "$<$<CONFIG:RELEASE>:${KITRT_RELEASE_OPTIONS}>" )
+    catch_discover_tests( unit_tests )
+endif()
+#################################################
+
+
+### BUILD GUI ###################################
+if( BUILD_GUI )
+    find_package( Qt5 COMPONENTS Core Widgets Gui OpenGL REQUIRED )
+    find_package( VTK COMPONENTS vtkGUISupportQt vtkInteractionStyle vtkInteractionWidgets vtkRenderingAnnotation vtkRenderingCore vtkRenderingFreeType vtkRenderingOpenGL2 REQUIRED )
+    include_directories( ${CMAKE_SOURCE_DIR}/include/gui )
+    file( GLOB_RECURSE GUI_SRCS RELATIVE ${CMAKE_SOURCE_DIR} "src/gui/*" )
+    file( GLOB_RECURSE GUI_INCL RELATIVE ${CMAKE_SOURCE_DIR} "include/gui/*" )
+    add_executable( ${CMAKE_PROJECT_NAME}_gui ${SRCS} ${EXT_SRCS} ${GUI_SRCS} ${GUI_INCL})
+    target_compile_definitions( ${CMAKE_PROJECT_NAME}_gui PUBLIC BUILD_GUI )
+    set_target_properties( ${CMAKE_PROJECT_NAME}_gui PROPERTIES AUTOMOC ON )
+    set_target_properties( ${CMAKE_PROJECT_NAME}_gui PROPERTIES AUTOUIC ON )
+    set_target_properties( ${CMAKE_PROJECT_NAME}_gui PROPERTIES AUTORCC ON )
+    set( GUI_LIBRARIES Qt5::Core Qt5::Widgets Qt5::Gui Qt5::OpenGL ${VTK_LIBRARIES} )
+    target_link_libraries( ${CMAKE_PROJECT_NAME}_gui ${CORE_LIBRARIES} ${GUI_LIBRARIES} )
+    set_target_properties( ${CMAKE_PROJECT_NAME}_gui PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_SOURCE_DIR}/bin" )
+    target_compile_options( ${CMAKE_PROJECT_NAME}_gui PUBLIC "$<$<CONFIG:DEBUG>:${KITRT_DEBUG_OPTIONS}>" )
+    target_compile_options( ${CMAKE_PROJECT_NAME}_gui PUBLIC "$<$<CONFIG:RELWITHDEBINFO>:${KITRT_RELWITHDEBINFO_OPTIONS}>" )
+    target_compile_options( ${CMAKE_PROJECT_NAME}_gui PUBLIC "$<$<CONFIG:RELEASE>:${KITRT_RELEASE_OPTIONS}>" )
 endif()
-target_compile_options( unit_tests PUBLIC "$<$<CONFIG:RELWITHDEBINFO>:${KITRT_RELWITHDEBINFO_OPTIONS}>" )
-target_compile_options( unit_tests PUBLIC "$<$<CONFIG:RELEASE>:${KITRT_RELEASE_OPTIONS}>" )
-catch_discover_tests( unit_tests )
-enable_testing()
 #################################################

Catch2 @ 0e9bae1c

-Subproject commit ff349a50bfc6214b4081f4ca63c7de35e2162f60
+Subproject commit 0e9bae1cdb5d7bcd967bcab10539805cc3bccb32

blaze @ 69e2fe55

-Subproject commit 0380370f0626de2ad0ec7ea815803e22bbf6b42e
+Subproject commit 69e2fe554e72d90efc39ceec72d8cbddf88802a8

neuralEntropy @ 54f38c0a

+Subproject commit 54f38c0a6154004efa2f8cad4737d127f6dcde59

spdlog @ 83b91499

-Subproject commit cbe9448650176797739dbab13961ef4c07f4290f
+Subproject commit 83b9149930f392d7797b54fe97a66ab3f2120671

code/include/common/config.h

 /*!
  * @file config.h
- * @brief Class to handle all options and their pre and postprocessing.
+ * @brief: Class to handle all options and their pre and postprocessing.
+ *         DO NOT CREATE SETTERS FOR THIS CLASS! ALL OPTIONS ARE CONSTANT (after SetPostprocessing).
+ *
  * @author S. Schotthöfer
  *
- * Disclaimer: This class structure was copied and modifed with open source permission from SU2 v7.0.3 https://su2code.github.io/
+ * Disclaimer: This class structure was copied and (heavily) modifed with open source permission from SU2 v7.0.3 https://su2code.github.io/
  */
 
 #ifndef CONFIG_H
@@ -48,7 +50,17 @@ class Config
     unsigned _nQuadPoints;
 
     // Mesh
-    unsigned _nCells;
+    unsigned _nCells;    /*!< @brief: Number of cells in the mesh */
+    unsigned short _dim; /*!< @brief: spatial dimensionality of the mesh/test case */
+
+    // Boundary Conditions
+    /*!< @brief List of all Pairs (marker, BOUNDARY_TYPE), e.g. (farfield,DIRICHLET).
+         Each Boundary Conditions must have an entry in enum BOUNDARY_TYPE*/
+    std::vector<std::pair<std::string, BOUNDARY_TYPE>> _boundaries;
+    unsigned short _nMarkerDirichlet;          /*!< @brief Number of Dirichlet BC markers. Enum entry: DIRICHLET */
+    unsigned short _nMarkerNeumann;            /*!< @brief Number of Neumann BC markers. Enum entry: Neumann */
+    std::vector<std::string> _MarkerDirichlet; /*!< @brief Dirichlet BC markers. */
+    std::vector<std::string> _MarkerNeumann;   /*!< @brief Neumann BC markers. */
 
     // Solver
     double _CFL;                     /*!< @brief CFL Number for Solver*/
@@ -59,38 +71,40 @@ class Config
     unsigned short _maxMomentDegree; /*!< @brief Maximal Order of Moments for PN and MN Solver */
     unsigned short _reconsOrder;     /*!< @brief Spatial Order of Accuracy for Solver */
 
-    // Linesource
-    double _sigmaS; /*!< @brief Scattering coeffient for Linesource test case */
-
     /*!< @brief If true, very low entries (10^-10 or smaller) of the flux matrices will be set to zero,
      * to improve floating point accuracy */
     bool _cleanFluxMat;
     bool _allGaussPts; /*!< @brief If true, the SN Solver uses all Gauss pts in the quadrature */
+    bool _csd;         /*!< @brief If true, continuous slowing down approximation will be used */
 
-    bool _csd;                 /*!< @brief If true, continuous slowing down approximation will be used */
-    std::string _hydrogenFile; /*!< @brief Name of hydrogen cross section file */
-    std::string _oxygenFile;   /*!< @brief Name of oxygen cross section file */
+    // --- Problems ---
 
-    // Boundary Conditions
-    /*!< @brief List of all Pairs (marker, BOUNDARY_TYPE), e.g. (farfield,DIRICHLET).
-         Each Boundary Conditions must have an entry in enum BOUNDARY_TYPE*/
-    std::vector<std::pair<std::string, BOUNDARY_TYPE>> _boundaries;
-    unsigned short _nMarkerDirichlet;          /*!< @brief Number of Dirichlet BC markers. Enum entry: DIRICHLET */
-    unsigned short _nMarkerNeumann;            /*!< @brief Number of Neumann BC markers. Enum entry: Neumann */
-    std::vector<std::string> _MarkerDirichlet; /*!< @brief Dirichlet BC markers. */
-    std::vector<std::string> _MarkerNeumann;   /*!< @brief Neumann BC markers. */
+    // Linesource
+    double _sigmaS; /*!< @brief Scattering coeffient for Linesource test case */
+
+    // Database ICRU
+    std::string _dataDir; /*!< @brief material directory */
+    // ElectronRT
+    std::string _hydrogenFile;      /*!< @brief Name of hydrogen cross section file path*/
+    std::string _oxygenFile;        /*!< @brief Name of oxygen cross section file path */
+    std::string _stoppingPowerFile; /*!< @brief Name of stopping power file path */
 
     // Scattering Kernel
     KERNEL_NAME _kernelName; /*!< @brief Scattering Kernel Name*/
 
+    // Spherical Basis
+    SPHERICAL_BASIS_NAME _sphericalBasisName; /*!< @brief: Name of the basis on the unit sphere */
+
     // Optimizer
     OPTIMIZER_NAME _entropyOptimizerName; /*!< @brief Choice of optimizer */
     double _optimizerEpsilon;             /*!< @brief termination criterion epsilon for Newton Optmizer */
-    unsigned short _newtonIter;           /*!< @brief Maximal Number of newton iterations */
+    unsigned long _newtonIter;            /*!< @brief Maximal Number of newton iterations */
     double _newtonStepSize;               /*!< @brief Stepsize factor for newton optimizer */
-    unsigned short _newtonLineSearchIter; /*!< @brief Maximal Number of line search iterations for newton optimizer */
+    unsigned long _newtonLineSearchIter;  /*!< @brief Maximal Number of line search iterations for newton optimizer */
     bool _newtonFastMode;                 /*!< @brief If true, we skip the NewtonOptimizer for quadratic entropy and assign alpha = u */
 
+    // NeuralModel
+    unsigned short _neuralModel; /*!< @brief:  Version number of the employed neural model */
     // Output Options
     unsigned short _nVolumeOutput;            /*!< @brief Number of volume outputs */
     std::vector<VOLUME_OUTPUT> _volumeOutput; /*!< @brief Output groups for volume output*/
@@ -104,6 +118,13 @@ class Config
     std::vector<SCALAR_OUTPUT> _historyOutput; /*!< @brief Output groups for screen output*/
     unsigned short _historyOutputFrequency;    /*!< @brief Frequency of screen output*/
 
+    // Data Generator Settings
+    /*!< @brief Check, if data generator mode is active. If yes, no solver is called, but instead the data generator is executed */
+    bool _dataGeneratorMode;
+    unsigned long _tainingSetSize;         /*!< @brief Size of training data set for data generator */
+    unsigned long _maxValFirstMoment;      /*!< @brief Size of training data set for data generator */
+    double _boundaryDistanceRealizableSet; /*! @brief Distance of the sampled moments to the boundary of the realizable set */
+
     // --- Parsing Functionality and Initializing of Options ---
     /*!
      * @brief Set default values for all options not yet set.
@@ -223,13 +244,18 @@ class Config
      */
     // File structure
     std::string inline GetCTFile() const { return std::filesystem::path( _ctFile ).lexically_normal(); }
-    std::string inline GetHydrogenFile() const { return std::filesystem::path( _hydrogenFile ).lexically_normal(); }
+
     std::string inline GetLogDir() const { return std::filesystem::path( _logDir ).lexically_normal(); }
     std::string inline GetLogFile() const { return std::filesystem::path( _logFileName ).lexically_normal(); }
     std::string inline GetMeshFile() const { return std::filesystem::path( _meshFile ).lexically_normal(); }
     std::string inline GetOutputDir() const { return std::filesystem::path( _outputDir ).lexically_normal(); }
     std::string inline GetOutputFile() const { return std::filesystem::path( _outputFile ).lexically_normal(); }
+
+    // Problem Files
+    std::string inline GetHydrogenFile() const { return std::filesystem::path( _hydrogenFile ).lexically_normal(); }
     std::string inline GetOxygenFile() const { return std::filesystem::path( _oxygenFile ).lexically_normal(); }
+    std::string inline GetStoppingPowerFile() const { return std::filesystem::path( _stoppingPowerFile ).lexically_normal(); }
+    std::string inline GetDataDir() const { return std::filesystem::path( _dataDir ).lexically_normal(); }
 
     // Quadrature Structure
     unsigned GetNQuadPoints() { return _nQuadPoints; }
@@ -238,6 +264,7 @@ class Config
 
     // Mesh Structure
     unsigned GetNCells() { return _nCells; }
+    unsigned short GetDim() { return _dim; }
 
     // Solver Structure
     double inline GetCFL() const { return _CFL; }
@@ -256,18 +283,23 @@ class Config
 
     //  Optimizer
     double inline GetNewtonOptimizerEpsilon() const { return _optimizerEpsilon; }
-    unsigned inline GetNewtonIter() const { return _newtonIter; }
+    unsigned long inline GetNewtonIter() const { return _newtonIter; }
     double inline GetNewtonStepSize() const { return _newtonStepSize; }
-    unsigned inline GetNewtonMaxLineSearches() const { return _newtonLineSearchIter; }
+    unsigned long inline GetNewtonMaxLineSearches() const { return _newtonLineSearchIter; }
     bool inline GetNewtonFastMode() const { return _newtonFastMode; }
     OPTIMIZER_NAME inline GetOptimizerName() const { return _entropyOptimizerName; }
 
+    // Neural Closure
+    unsigned short inline GetNeuralModel() { return _neuralModel; }
+
     // Boundary Conditions
     BOUNDARY_TYPE GetBoundaryType( std::string nameMarker ) const; /*! @brief Get Boundary Type of given marker */
 
     // Scattering Kernel
     KERNEL_NAME inline GetKernelName() const { return _kernelName; }
 
+    // Basis name
+    SPHERICAL_BASIS_NAME inline GetSphericalBasisName() const { return _sphericalBasisName; }
     // Output Structure
     std::vector<VOLUME_OUTPUT> inline GetVolumeOutput() { return _volumeOutput; }
     unsigned short inline GetNVolumeOutput() { return _nVolumeOutput; }
@@ -280,10 +312,17 @@ class Config
     std::vector<SCALAR_OUTPUT> inline GetHistoryOutput() { return _historyOutput; }
     unsigned short inline GetNHistoryOutput() { return _nHistoryOutput; }
     unsigned short inline GetHistoryOutputFrequency() { return _historyOutputFrequency; }
-    // ---- Setters for option structure
 
+    // Data generator
+    bool inline GetDataGeneratorMode() { return _dataGeneratorMode; }
+    unsigned long inline GetTrainingDataSetSize() { return _tainingSetSize; }
+    unsigned long inline GetMaxValFirstMoment() { return _maxValFirstMoment; }
+    double GetBoundaryDistanceRealizableSet() { return _boundaryDistanceRealizableSet; }
+
+    // ---- Setters for option structure
+    // This section is dangerous
     // Quadrature Structure
-    void SetNQuadPoints( unsigned nq ) { _nQuadPoints = nq; }
+    void SetNQuadPoints( unsigned nq ) { _nQuadPoints = nq; }           /*! @brief Never change the nq! This is only for the test framework. */
     void SetQuadName( QUAD_NAME quadName ) { _quadName = quadName; }    /*! @brief Never change the quadName! This is only for the test framework. */
     void SetQuadOrder( unsigned quadOrder ) { _quadOrder = quadOrder; } /*! @brief Never change the quadOrder! This is only for the test framework. */
     void SetSNAllGaussPts( bool useall ) { _allGaussPts = useall; }     /*! @brief Never change the this! This is only for the test framework. */

code/include/common/globalconstants.h

-/*!
+/*!
  * \file GlobalConstants.h
  * \brief All global defined (physical) constants, enums etc
  * \author <blank>
@@ -55,7 +55,16 @@ enum BOUNDARY_TYPE { DIRICHLET, NEUMANN, NONE, INVALID };
 /*! @brief Enum for all currently available quadratures in rtsn.
  *         Option enums are written in capital letters with underscores as spaces (e.g option "time integration" has option enum "TIME_INTEGRATION")
  */
-enum QUAD_NAME { QUAD_MonteCarlo, QUAD_GaussLegendreTensorized, QUAD_GaussLegendre1D, QUAD_LevelSymmetric, QUAD_Lebedev, QUAD_LDFESA, QUAD_Product };
+enum QUAD_NAME {
+    QUAD_MonteCarlo,
+    QUAD_GaussLegendreTensorized,
+    QUAD_GaussLegendre1D,
+    QUAD_LevelSymmetric,
+    QUAD_Lebedev,
+    QUAD_LDFESA,
+    QUAD_Product,
+    QUAD_GaussChebyshev1D
+};
 
 /*! @brief Conversion Map String to enum
  */
@@ -77,7 +86,8 @@ enum PROBLEM_NAME {
     PROBLEM_LineSource_Pseudo_1D_Physics,
     PROBLEM_AirCavity,
     PROBLEM_MuscleBoneLung,
-    PROBLEM_Phantom2D
+    PROBLEM_Phantom2D,
+    PROBLEM_IsotropicSource_2D
 };
 
 inline std::map<std::string, PROBLEM_NAME> Problem_Map{ { "LINESOURCE", PROBLEM_LineSource },
@@ -87,6 +97,7 @@ inline std::map<std::string, PROBLEM_NAME> Problem_Map{ { "LINESOURCE", PROBLEM_
                                                         { "AIRCAVITY", PROBLEM_AirCavity },
                                                         { "MUSCLEBONELUNG", PROBLEM_MuscleBoneLung },
                                                         { "PHANTOM2D", PROBLEM_Phantom2D },
+                                                        { "ISOTROPICPOINTSOURCE2D", PROBLEM_IsotropicSource_2D },
                                                         { "LINESOURCE_PSEUDO_1D", PROBLEM_LineSource_Pseudo_1D },
                                                         { "LINESOURCE_PSEUDO_1D_PHYSICS", PROBLEM_LineSource_Pseudo_1D_Physics } };
 
@@ -130,10 +141,10 @@ enum OPTIMIZER_NAME { NEWTON, ML };
 inline std::map<std::string, OPTIMIZER_NAME> Optimizer_Map{ { "NEWTON", NEWTON }, { "ML", ML } };
 
 // Volume output
-enum VOLUME_OUTPUT { ANALYTIC, MINIMAL, MOMENTS, DUAL_MOMENTS, DOSE };
+enum VOLUME_OUTPUT { ANALYTIC, MINIMAL, MOMENTS, DUAL_MOMENTS, MEDICAL };
 
 inline std::map<std::string, VOLUME_OUTPUT> VolOutput_Map{
-    { "ANALYTIC", ANALYTIC }, { "MINIMAL", MINIMAL }, { "MOMENTS", MOMENTS }, { "DUAL_MOMENTS", DUAL_MOMENTS }, { "DOSE", DOSE } };
+    { "ANALYTIC", ANALYTIC }, { "MINIMAL", MINIMAL }, { "MOMENTS", MOMENTS }, { "DUAL_MOMENTS", DUAL_MOMENTS }, { "MEDICAL", MEDICAL } };
 
 // Scalar output
 enum SCALAR_OUTPUT { ITER, MASS, RMS_FLUX, VTK_OUTPUT, CSV_OUTPUT };
@@ -141,4 +152,10 @@ enum SCALAR_OUTPUT { ITER, MASS, RMS_FLUX, VTK_OUTPUT, CSV_OUTPUT };
 inline std::map<std::string, SCALAR_OUTPUT> ScalarOutput_Map{
     { "ITER", ITER }, { "MASS", MASS }, { "RMS_FLUX", RMS_FLUX }, { "VTK_OUTPUT", VTK_OUTPUT }, { "CSV_OUTPUT", CSV_OUTPUT } };
 
+// Spherical Basis Name
+enum SPHERICAL_BASIS_NAME { SPHERICAL_HARMONICS, SPHERICAL_MONOMIALS };
+
+inline std::map<std::string, SPHERICAL_BASIS_NAME> SphericalBasis_Map{ { "SPHERICAL_HARMONICS", SPHERICAL_HARMONICS },
+                                                                       { "SPHERICAL_MONOMIALS", SPHERICAL_MONOMIALS } };
+
 #endif    // GLOBAL_CONSTANTS_H

code/include/common/optionstructure.h

@@ -22,7 +22,7 @@ class OptionBase
     std::vector<std::string> _value; /*! @brief: String name of the option */
 
   public:
-    OptionBase(){};
+    OptionBase() {}
     virtual ~OptionBase() = 0;
 
     virtual std::string SetValue( std::vector<std::string> value ); /*! @brief: Set string name of the option */
@@ -45,7 +45,7 @@ class OptionDouble : public OptionBase
   public:
     OptionDouble( std::string option_field_name, double& option_field, double default_value );
 
-    ~OptionDouble() override{};
+    ~OptionDouble() override {}
 
     std::string SetValue( std::vector<std::string> option_value ) override;
 
@@ -61,7 +61,7 @@ class OptionString : public OptionBase
   public:
     OptionString( std::string option_field_name, std::string& option_field, std::string default_value );
 
-    ~OptionString() override{};
+    ~OptionString() override {}
 
     std::string SetValue( std::vector<std::string> option_value ) override;
 
@@ -77,7 +77,7 @@ class OptionInt : public OptionBase
   public:
     OptionInt( std::string option_field_name, int& option_field, int default_value );
 
-    ~OptionInt() override{};
+    ~OptionInt() override {}
 
     std::string SetValue( std::vector<std::string> option_value ) override;
 
@@ -93,7 +93,7 @@ class OptionULong : public OptionBase
   public:
     OptionULong( std::string option_field_name, unsigned long& option_field, unsigned long default_value );
 
-    ~OptionULong() override{};
+    ~OptionULong() override {}
 
     std::string SetValue( std::vector<std::string> option_value ) override;
 
@@ -109,7 +109,7 @@ class OptionUShort : public OptionBase
   public:
     OptionUShort( std::string option_field_name, unsigned short& option_field, unsigned short default_value );
 
-    ~OptionUShort() override{};
+    ~OptionUShort() override {}
 
     std::string SetValue( std::vector<std::string> option_value ) override;
 
@@ -125,7 +125,7 @@ class OptionLong : public OptionBase
   public:
     OptionLong( std::string option_field_name, long& option_field, long default_value );
 
-    ~OptionLong() override{};
+    ~OptionLong() override {}
 
     std::string SetValue( std::vector<std::string> option_value ) override;
 
@@ -141,7 +141,7 @@ class OptionBool : public OptionBase
   public:
     OptionBool( std::string option_field_name, bool& option_field, bool default_value );
 
-    ~OptionBool() override{};
+    ~OptionBool() override {}
 
     std::string SetValue( std::vector<std::string> option_value ) override;
 
@@ -157,7 +157,7 @@ class OptionStringList : public OptionBase
   public:
     OptionStringList( std::string option_field_name, unsigned short& list_size, std::vector<std::string>& option_field );
 
-    ~OptionStringList() override{};
+    ~OptionStringList() override {}
 
     std::string SetValue( std::vector<std::string> option_value ) override;
 

code/include/gui/cmap.h

+#ifndef CMAP_H
+#define CMAP_H
+
+#include "common/typedef.h"
+
+const Matrix viridis{ { 0.0, 0.267004, 0.004874, 0.329415 },
+                      { 0.00392156862745098, 0.26851, 0.009605, 0.335427 },
+                      { 0.00784313725490196, 0.269944, 0.014625, 0.341379 },
+                      { 0.011764705882352941, 0.271305, 0.019942, 0.347269 },
+                      { 0.01568627450980392, 0.272594, 0.025563, 0.353093 },
+                      { 0.0196078431372549, 0.273809, 0.031497, 0.358853 },
+                      { 0.023529411764705882, 0.274952, 0.037752, 0.364543 },
+                      { 0.027450980392156862, 0.276022, 0.044167, 0.370164 },
+                      { 0.03137254901960784, 0.277018, 0.050344, 0.375715 },
+                      { 0.03529411764705882, 0.277941, 0.056324, 0.381191 },
+                      { 0.0392156862745098, 0.278791, 0.062145, 0.386592 },
+                      { 0.043137254901960784, 0.279566, 0.067836, 0.391917 },
+                      { 0.047058823529411764, 0.280267, 0.073417, 0.397163 },
+                      { 0.050980392156862744, 0.280894, 0.078907, 0.402329 },
+                      { 0.054901960784313725, 0.281446, 0.08432, 0.407414 },
+                      { 0.058823529411764705, 0.281924, 0.089666, 0.412415 },
+                      { 0.06274509803921569, 0.282327, 0.094955, 0.417331 },
+                      { 0.06666666666666667, 0.282656, 0.100196, 0.42216 },
+                      { 0.07058823529411765, 0.28291, 0.105393, 0.426902 },
+                      { 0.07450980392156863, 0.283091, 0.110553, 0.431554 },
+                      { 0.0784313725490196, 0.283197, 0.11568, 0.436115 },
+                      { 0.08235294117647059, 0.283229, 0.120777, 0.440584 },
+                      { 0.08627450980392157, 0.283187, 0.125848, 0.44496 },
+                      { 0.09019607843137255, 0.283072, 0.130895, 0.449241 },
+                      { 0.09411764705882353, 0.282884, 0.13592, 0.453427 },
+                      { 0.09803921568627451, 0.282623, 0.140926, 0.457517 },
+                      { 0.10196078431372549, 0.28229, 0.145912, 0.46151 },
+                      { 0.10588235294117647, 0.281887, 0.150881, 0.465405 },
+                      { 0.10980392156862745, 0.281412, 0.155834, 0.469201 },
+                      { 0.11372549019607843, 0.280868, 0.160771, 0.472899 },
+                      { 0.11764705882352941, 0.280255, 0.165693, 0.476498 },
+                      { 0.12156862745098039, 0.279574, 0.170599, 0.479997 },
+                      { 0.12549019607843137, 0.278826, 0.17549, 0.483397 },
+                      { 0.12941176470588237, 0.278012, 0.180367, 0.486697 },
+                      { 0.13333333333333333, 0.277134, 0.185228, 0.489898 },
+                      { 0.13725490196078433, 0.276194, 0.190074, 0.493001 },
+                      { 0.1411764705882353, 0.275191, 0.194905, 0.496005 },
+                      { 0.1450980392156863, 0.274128, 0.199721, 0.498911 },
+                      { 0.14901960784313725, 0.273006, 0.20452, 0.501721 },