Merge pull request #331 from favreau/master

Boost filesystem cleanup
BlueBrain · Nov 24, 2023 · 67d3074 · 67d3074
2 parents faa26d2 + e22e7fd
commit 67d3074
Show file tree

Hide file tree

Showing 21 changed files with 108 additions and 51 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -37,9 +37,8 @@ set(PACKAGE_REV_STRING "${PACKAGE_VERSION_MAJOR}.${PACKAGE_VERSION_MINOR}.${PACK
 
 list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/CMake)
 set(${NAME}_MODULES_DIR ${PROJECT_SOURCE_DIR})
-set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD 17)
 
-find_package(Boost REQUIRED COMPONENTS program_options filesystem)
 find_package(glm REQUIRED)
 find_package(FreeImage REQUIRED)
 find_package(ospray)

diff --git a/bioexplorer/backend/CMakeLists.txt b/bioexplorer/backend/CMakeLists.txt
@@ -253,8 +253,8 @@ include_directories(
 
 set(${NAME}_LINK_LIBRARIES
     PUBLIC ${${NAME}_PUBLIC_MODULE_LIBRARIES}
-    PRIVATE CoreParameters CoreCommon CoreEngine CoreIO mpfr
-    ${${NAME}_PRIVATE_MODULE_LIBRARIES} ${FreeImage_LIBRARIES} ${PQXX_LIBRARIES} ${OpenMP_CXX_LIBRARIES} ${Boost_FILESYSTEM_LIBRARY}
+    PRIVATE CoreParameters CoreCommon CoreEngine CoreIO mpfr stdc++fs
+    ${${NAME}_PRIVATE_MODULE_LIBRARIES} ${FreeImage_LIBRARIES} ${PQXX_LIBRARIES} ${OpenMP_CXX_LIBRARIES}
 )
 
 if(${CGAL_FOUND})

diff --git a/bioexplorer/backend/plugins/Sonata/plugin/neuroscience/common/MorphologyLoader.cpp b/bioexplorer/backend/plugins/Sonata/plugin/neuroscience/common/MorphologyLoader.cpp
@@ -35,7 +35,7 @@
 
 #include <brion/uri.h>
 
-#include <boost/filesystem.hpp>
+#include <filesystem>
 
 using namespace core;
 

diff --git a/bioexplorer/backend/plugins/Sonata/plugin/neuroscience/neuron/AbstractCircuitLoader.cpp b/bioexplorer/backend/plugins/Sonata/plugin/neuroscience/neuron/AbstractCircuitLoader.cpp
@@ -34,6 +34,7 @@
 
 #include <platform/core/common/Timer.h>
 #include <platform/core/common/scene/ClipPlane.h>
+#include <platform/core/common/utils/Utils.h>
 #include <platform/core/engineapi/Material.h>
 #include <platform/core/engineapi/Model.h>
 #include <platform/core/engineapi/Scene.h>
@@ -145,8 +146,8 @@ brain::GIDSet AbstractCircuitLoader::_getGids(const PropertyMap &properties, con
     // Pair synapse usecase
     if (!preSynapticNeuron.empty() && !postSynapticNeuron.empty())
     {
-        gids.insert(boost::lexical_cast<Gid>(preSynapticNeuron));
-        gids.insert(boost::lexical_cast<Gid>(postSynapticNeuron));
+        gids.insert(lexical_cast<Gid>(preSynapticNeuron));
+        gids.insert(lexical_cast<Gid>(postSynapticNeuron));
         return gids;
     }
 
@@ -825,8 +826,8 @@ float AbstractCircuitLoader::_importMorphologies(const PropertyMap &properties,
             const auto gid = localGids[morphologyId];
             if (prePostSynapticUsecase)
             {
-                synapsesInfo.preGid = boost::lexical_cast<Gid>(preSynapticNeuron);
-                synapsesInfo.postGid = boost::lexical_cast<Gid>(postSynapticNeuron);
+                synapsesInfo.preGid = lexical_cast<Gid>(preSynapticNeuron);
+                synapsesInfo.postGid = lexical_cast<Gid>(postSynapticNeuron);
             }
             if (loadAfferentSynapses)
                 synapsesInfo.afferentSynapses =

diff --git a/bioexplorer/backend/science/atlas/AtlasLoader.cpp b/bioexplorer/backend/science/atlas/AtlasLoader.cpp
@@ -29,7 +29,7 @@
 
 #include <platform/core/common/Properties.h>
 
-#include <boost/filesystem.hpp>
+#include <filesystem>
 
 using namespace core;
 
@@ -76,7 +76,7 @@ ModelDescriptorPtr AtlasLoader::importFromStorage(const std::string& storage, co
     props.merge(properties);
 
     details::AtlasDetails details;
-    const auto baseName = boost::filesystem::basename(storage);
+    const auto baseName = std::filesystem::path(storage).filename();
     details.assemblyName = baseName;
     details.cellSqlFilter = props.getProperty<std::string>(LOADER_PROPERTY_ATLAS_CELL_SQL_FILTER.name);
     details.regionSqlFilter = props.getProperty<std::string>(LOADER_PROPERTY_ATLAS_REGION_SQL_FILTER.name);

diff --git a/bioexplorer/backend/science/connectomics/whitematter/WhiteMatterLoader.cpp b/bioexplorer/backend/science/connectomics/whitematter/WhiteMatterLoader.cpp
@@ -29,7 +29,7 @@
 
 #include <platform/core/common/Properties.h>
 
-#include <boost/filesystem.hpp>
+#include <filesystem>
 
 using namespace core;
 
@@ -76,7 +76,7 @@ ModelDescriptorPtr WhiteMatterLoader::importFromStorage(const std::string& stora
     props.merge(properties);
 
     details::WhiteMatterDetails details;
-    const auto baseName = boost::filesystem::basename(storage);
+    const auto baseName = std::filesystem::path(storage).filename();
     details.assemblyName = baseName;
     details.populationName = baseName;
     details.sqlFilter = props.getProperty<std::string>(LOADER_PROPERTY_DATABASE_SQL_FILTER.name);

diff --git a/bioexplorer/backend/science/morphologies/AstrocytesLoader.cpp b/bioexplorer/backend/science/morphologies/AstrocytesLoader.cpp
@@ -29,7 +29,7 @@
 
 #include <platform/core/common/Properties.h>
 
-#include <boost/filesystem.hpp>
+#include <filesystem>
 
 using namespace core;
 
@@ -76,7 +76,7 @@ ModelDescriptorPtr AstrocytesLoader::importFromStorage(const std::string& storag
     props.merge(properties);
 
     details::AstrocytesDetails details;
-    const auto baseName = boost::filesystem::basename(storage);
+    const auto baseName = std::filesystem::path(storage).filename();
     details.assemblyName = baseName;
     details.populationName = baseName;
     details.vasculaturePopulationName =

diff --git a/bioexplorer/backend/science/morphologies/NeuronsLoader.cpp b/bioexplorer/backend/science/morphologies/NeuronsLoader.cpp
@@ -29,7 +29,7 @@
 
 #include <platform/core/common/Properties.h>
 
-#include <boost/filesystem.hpp>
+#include <filesystem>
 
 using namespace core;
 
@@ -76,7 +76,7 @@ ModelDescriptorPtr NeuronsLoader::importFromStorage(const std::string& storage,
     props.merge(properties);
 
     details::NeuronsDetails details;
-    const auto baseName = boost::filesystem::basename(storage);
+    const auto baseName = std::filesystem::path(storage).filename();
     details.assemblyName = baseName;
     details.populationName = baseName;
     details.sqlNodeFilter = props.getProperty<std::string>(LOADER_PROPERTY_DATABASE_SQL_FILTER.name);

diff --git a/bioexplorer/backend/science/vasculature/VasculatureLoader.cpp b/bioexplorer/backend/science/vasculature/VasculatureLoader.cpp
@@ -29,7 +29,7 @@
 
 #include <platform/core/common/Properties.h>
 
-#include <boost/filesystem.hpp>
+#include <filesystem>
 
 using namespace core;
 
@@ -76,7 +76,7 @@ ModelDescriptorPtr VasculatureLoader::importFromStorage(const std::string& stora
     props.merge(properties);
 
     details::VasculatureDetails details;
-    const auto baseName = boost::filesystem::basename(storage);
+    const auto baseName = std::filesystem::path(storage).filename();
     details.assemblyName = baseName;
     details.populationName = baseName;
     details.sqlFilter = props.getProperty<std::string>(LOADER_PROPERTY_DATABASE_SQL_FILTER.name);

diff --git a/bioexplorer/backend/tests/CMakeLists.txt b/bioexplorer/backend/tests/CMakeLists.txt
@@ -33,7 +33,7 @@ foreach(FILE ${TESTS_SRC})
 
     target_link_libraries(${NAME}
         PRIVATE
-        Core CoreParameters CoreCommon CoreEngine CoreIO OSPRayEngine CorePluginRockets
+        Core CoreParameters CoreCommon CoreEngine CoreIO OSPRayEngine CorePluginRockets stdc++fs
         ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}
         ${LIBRARY_NAME}
     )

diff --git a/bioexplorer/pythonsdk/notebooks/widgets/BioExplorer_widgets.ipynb b/bioexplorer/pythonsdk/notebooks/widgets/BioExplorer_widgets.ipynb
@@ -17,11 +17,56 @@
    "source": [
     "from bioexplorer import BioExplorer, Widgets\n",
     "\n",
-    "url = 'localhost:5000'\n",
+    "url = 'r5i2n23:5000'\n",
     "be = BioExplorer(url)\n",
     "w = Widgets(be)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'accumulation': True,\n",
+       " 'background_color': [1.0, 1.0, 1.0],\n",
+       " 'current': 'advanced',\n",
+       " 'head_light': True,\n",
+       " 'max_accum_frames': 357,\n",
+       " 'samples_per_pixel': 1,\n",
+       " 'subsampling': 4,\n",
+       " 'types': ['advanced',\n",
+       "  'albedo',\n",
+       "  'ambient_occlusion',\n",
+       "  'basic',\n",
+       "  'bio_explorer_density',\n",
+       "  'bio_explorer_golgi_style',\n",
+       "  'bio_explorer_path_tracing',\n",
+       "  'bio_explorer_voxel',\n",
+       "  'cell_growth',\n",
+       "  'depth',\n",
+       "  'metabolism',\n",
+       "  'point_fields',\n",
+       "  'proximity_detection',\n",
+       "  'radiance',\n",
+       "  'raycast_Ng',\n",
+       "  'raycast_Ns',\n",
+       "  'scivis',\n",
+       "  'shadow',\n",
+       "  'vector_fields']}"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "be.core_api().get_renderer()"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -31,6 +76,15 @@
     "w.display_clipping_planes([-50, 50])"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "be.core_api().inspect([0.5,0.5])"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -48,31 +102,16 @@
    },
    "outputs": [],
    "source": [
-    "w.display_focal_distance(with_preview=False)"
+    "w.display_focal_distance(with_preview=True)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {
     "scrolled": false
    },
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "69fcc02ea4a74618a602999313058ed2",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "VBox(children=(HBox(children=(Select(description='Models:', options=('Demo scene', 'vasculature', 'astrocytes'…"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "w.display_palette_for_models()"
    ]

diff --git a/extensions/medicalimaging/dicom/CMakeLists.txt b/extensions/medicalimaging/dicom/CMakeLists.txt
@@ -103,7 +103,6 @@ add_library(
 
 target_link_libraries(
   ${LIBRARY_NAME}
-  ${Boost_PROGRAM_OPTIONS_LIBRARY} ${Boost_FILESYSTEM_LIBRARY}
   ${${NAME}_LINK_LIBRARIES})
 
 # ================================================================================

diff --git a/extensions/medicalimaging/dicom/plugin/io/DICOMLoader.cpp b/extensions/medicalimaging/dicom/plugin/io/DICOMLoader.cpp
@@ -34,7 +34,7 @@
 #include <dcmtk/dcmdata/dctk.h>
 #include <dcmtk/dcmimgle/dcmimage.h>
 
-#include <boost/filesystem.hpp>
+#include <filesystem>
 
 namespace medicalimagingexplorer
 {
@@ -210,8 +210,8 @@ DICOMImageDescriptors DICOMLoader::_parseDICOMImagesData(const std::string& file
                         str.replace(str.find("\\"), 1, "/");
 
                     // Full image filename
-                    boost::filesystem::path path = fileName;
-                    boost::filesystem::path folder = path.parent_path();
+                    const std::filesystem::path path = fileName;
+                    const std::filesystem::path folder = path.parent_path();
                     const std::string imageFileName = std::string(folder.string()) + "/" + str;
 
                     // Load image from file
@@ -413,7 +413,7 @@ ModelDescriptorPtr DICOMLoader::importFromStorage(const std::string& storage, co
                                                   const PropertyMap& /*properties*/) const
 {
     PLUGIN_INFO("Importing DICOM dataset from " << storage);
-    const auto extension = boost::filesystem::extension(storage);
+    const auto extension = std::filesystem::path(storage).extension().string();
     if (extension == "." + SUPPORTED_EXTENSION_DCM)
         return _readFile(storage);
     return _readDirectory(storage, callback);
@@ -436,7 +436,7 @@ std::vector<std::string> DICOMLoader::getSupportedStorage() const
 
 bool DICOMLoader::isSupported(const std::string& storage, const std::string& extension) const
 {
-    const auto basename = boost::filesystem::basename(storage);
+    const auto basename = std::filesystem::path(storage).filename();
     const std::set<std::string> basenames = {SUPPORTED_BASENAME_DICOMDIR};
     const std::set<std::string> extensions = {SUPPORTED_EXTENSION_DCM};
     return (basenames.find(basename) != basenames.end() || extensions.find(extension) != extensions.end());

diff --git a/platform/apps/viewer/ui/CMakeLists.txt b/platform/apps/viewer/ui/CMakeLists.txt
@@ -26,7 +26,6 @@ set(${NAME}_SOURCES BaseWindow.cpp)
 set(${NAME}_PUBLIC_HEADERS BaseWindow.h)
 set(${NAME}_LINK_LIBRARIES
     PUBLIC Core CoreParameters 
-      ${Boost_FILESYSTEM_LIBRARY} ${Boost_SYSTEM_LIBRARY}
     PRIVATE glut ${OPENGL_gl_LIBRARY} ${glew_LIBRARIES}
 )
 

diff --git a/platform/core/common/utils/Utils.cpp b/platform/core/common/utils/Utils.cpp
@@ -26,6 +26,7 @@
 #include <platform/core/common/utils/FileSystem.h>
 
 #include <algorithm>
+#include <charconv>
 #include <cmath>
 #include <set>
 #include <sstream>
@@ -134,4 +135,12 @@ Vector3fs getRainbowColormap(const uint32_t colormapSize)
     return colormap;
 }
 
+template <typename To, typename From>
+To lexical_cast(const From& from)
+{
+    To to;
+    std::from_chars(from.data(), from.data() + from.size(), to);
+    return to;
+}
+
 } // namespace core
diff --git a/platform/core/common/utils/Utils.h b/platform/core/common/utils/Utils.h
@@ -68,4 +68,15 @@ Vector4f getBezierPoint(const Vector4fs& controlPoints, const float t);
  */
 Vector3fs getRainbowColormap(const uint32_t colormapSize);
 
+/**
+ * @brief Function template taking two template parameters (To and From) representing the source and target types
+ *
+ * @tparam To Source type
+ * @tparam From Destination type
+ * @param from Input data
+ * @return To Output data
+ */
+template <typename To, typename From>
+To lexical_cast(const From& from);
+
 } // namespace core
diff --git a/platform/core/engineapi/CMakeLists.txt b/platform/core/engineapi/CMakeLists.txt
@@ -65,7 +65,7 @@ target_link_libraries(
     ${LIBRARY_NAME}
     ${${NAME}_LINK_LIBRARIES}
     PUBLIC Async++
-    PRIVATE CoreParameters ${GLM_LIBRARIES} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${FREEIMAGE_LIBRARIES}
+    PRIVATE CoreParameters ${GLM_LIBRARIES} ${FREEIMAGE_LIBRARIES}
 )
 
 # ==============================================================================

diff --git a/platform/core/manipulators/CMakeLists.txt b/platform/core/manipulators/CMakeLists.txt
@@ -43,7 +43,7 @@ set(${NAME}_PUBLIC_HEADERS
 include_directories(${BIOEXPLORER_SOURCE_DIRS})
 
 set(${NAME}_LINK_LIBRARIES
-    PRIVATE ${GLM_LIBRARIES} ${Boost_PROGRAM_OPTIONS_LIBRARY}
+    PRIVATE ${GLM_LIBRARIES} 
 )
 
 add_library(

diff --git a/platform/core/tasks/CMakeLists.txt b/platform/core/tasks/CMakeLists.txt
@@ -44,7 +44,7 @@ set(${NAME}_PUBLIC_HEADERS
 include_directories(${BIOEXPLORER_SOURCE_DIRS})
 
 set(${NAME}_LINK_LIBRARIES
-    PRIVATE ${GLM_LIBRARIES} ${Boost_PROGRAM_OPTIONS_LIBRARY}
+    PRIVATE ${GLM_LIBRARIES}
 )
 
 add_library(

diff --git a/platform/engines/ospray/CMakeLists.txt b/platform/engines/ospray/CMakeLists.txt
@@ -162,7 +162,7 @@ target_link_libraries(
     ${LIBRARY_NAME}
     ${${NAME}_LINK_LIBRARIES}
     PUBLIC Async++
-    PRIVATE CoreParameters ${GLM_LIBRARIES} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${FREEIMAGE_LIBRARIES}
+    PRIVATE CoreParameters ${GLM_LIBRARIES} ${FREEIMAGE_LIBRARIES}
 )
 
 # ==============================================================================