Merge pull request #297 from favreau/master

Updated documentation and namespaces cleanup

bioexplorer/backend/module/ispc/renderer/DensityRenderer.cpp

@@ -31,6 +31,8 @@
 // ispc exports
 #include "DensityRenderer_ispc.h"
 
+using namespace core;
+
 namespace bioexplorer
 {
 namespace rendering

bioexplorer/backend/module/ispc/renderer/DensityRenderer.h

@@ -33,8 +33,6 @@ namespace bioexplorer
 {
 namespace rendering
 {
-using namespace ospray;
-using namespace core;
 
 /**
  * @brief The DensityRenderer class allows visualization of atom density in the
@@ -68,7 +66,7 @@ class DensityRenderer : public ospray::Renderer
     void** _lightPtr;
     ospray::Data* _lightData;
 
-    AdvancedMaterial* _bgMaterial;
+    core::AdvancedMaterial* _bgMaterial;
 
     double _timestamp{0.f};
     double _exposure{1.f};

bioexplorer/backend/module/ispc/renderer/FieldsRenderer.cpp

@@ -31,6 +31,8 @@
 // ispc exports
 #include "FieldsRenderer_ispc.h"
 
+using namespace core;
+
 namespace bioexplorer
 {
 namespace rendering

bioexplorer/backend/module/ispc/renderer/FieldsRenderer.h

@@ -33,9 +33,6 @@ namespace bioexplorer
 {
 namespace rendering
 {
-using namespace ospray;
-using namespace core;
-
 /**
  * @brief The FieldsRenderer class allows visualization of magnetic
  * fields created by atoms in the 3D scene. An Octree acceleration structure has
@@ -71,7 +68,7 @@ class FieldsRenderer : public ospray::Renderer
     void** _lightPtr;
     ospray::Data* _lightData;
 
-    AdvancedMaterial* _bgMaterial;
+    core::AdvancedMaterial* _bgMaterial;
 
     bool _useHardwareRandomizer{false};
     ospray::uint32 _randomNumber{0};

bioexplorer/backend/module/ispc/renderer/PathTracingRenderer.cpp

@@ -31,6 +31,7 @@
 #include "PathTracingRenderer_ispc.h"
 
 using namespace ospray;
+using namespace core;
 
 namespace bioexplorer
 {

bioexplorer/backend/module/ispc/renderer/PathTracingRenderer.h

@@ -30,13 +30,11 @@ namespace bioexplorer
 {
 namespace rendering
 {
-using namespace core;
-
 /**
  * @brief The PathTracingRenderer class is a renderer that processes the
  * rendering of the 3D scene using the path tracing algorythm
  */
-class PathTracingRenderer : public SimulationRenderer
+class PathTracingRenderer : public core::SimulationRenderer
 {
 public:
     PathTracingRenderer();
@@ -55,7 +53,7 @@ class PathTracingRenderer : public SimulationRenderer
     void** _lightPtr;
     ospray::Data* _lightData;
 
-    AdvancedMaterial* _bgMaterial;
+    core::AdvancedMaterial* _bgMaterial;
 
     double _exposure{1.f};
     double _aoStrength{1.f};

bioexplorer/backend/module/ispc/renderer/VoxelRenderer.cpp

@@ -28,6 +28,8 @@
 // ispc exports
 #include "VoxelRenderer_ispc.h"
 
+using namespace core;
+
 namespace bioexplorer
 {
 namespace rendering

bioexplorer/backend/module/ispc/renderer/VoxelRenderer.h

@@ -30,14 +30,11 @@ namespace bioexplorer
 {
 namespace rendering
 {
-using namespace ospray;
-using namespace core;
-
 /**
  * @brief The VoxelRenderer class can perform fast transparency
  * and mapping of simulation data on the geometry
  */
-class VoxelRenderer : public SimulationRenderer
+class VoxelRenderer : public core::SimulationRenderer
 {
 public:
     VoxelRenderer();

bioexplorer/backend/module/ispc/renderer/artistic/GolgiStyleRenderer.cpp

@@ -26,6 +26,8 @@
 // ispc exports
 #include "GolgiStyleRenderer_ispc.h"
 
+using namespace core;
+
 namespace bioexplorer
 {
 namespace rendering

bioexplorer/backend/module/ispc/renderer/artistic/GolgiStyleRenderer.h

@@ -33,10 +33,7 @@ namespace bioexplorer
 {
 namespace rendering
 {
-using namespace ospray;
-using namespace core;
-
-class GolgiStyleRenderer : public Renderer
+class GolgiStyleRenderer : public ospray::Renderer
 {
 public:
     GolgiStyleRenderer();
@@ -49,7 +46,7 @@ class GolgiStyleRenderer : public Renderer
     void commit() final;
 
 private:
-    AdvancedMaterial* _bgMaterial{nullptr};
+    core::AdvancedMaterial* _bgMaterial{nullptr};
     float _exponent{5.f};
     bool _inverse{false};
 };

bioexplorer/backend/plugins/MediaMaker/plugin/MediaMakerPlugin.h

@@ -56,7 +56,7 @@ class MediaMakerPlugin : public core::ExtensionPlugin
     ExportFramesToDisk _exportFramesToDiskPayload;
     bool _exportFramesToDiskDirty{false};
     uint16_t _frameNumber{0};
-    Vector2ui _frameBufferSize;
+    core::Vector2ui _frameBufferSize;
     int16_t _accumulationFrameNumber{0};
     std::string _baseName;
 

bioexplorer/backend/plugins/Metabolism/module/ispc/render/MetabolismRenderer.cpp

@@ -33,6 +33,8 @@
 // ispc exports
 #include "MetabolismRenderer_ispc.h"
 
+using namespace ospray;
+
 namespace metabolism
 {
 namespace rendering

bioexplorer/backend/plugins/Metabolism/module/ispc/render/MetabolismRenderer.h

@@ -28,8 +28,6 @@ namespace metabolism
 {
 namespace rendering
 {
-using namespace ospray;
-
 /**
  * @brief The MetabolismRenderer class allows visualization of atom Metabolism
  * in the 3D scene
@@ -62,7 +60,7 @@ class MetabolismRenderer : public ospray::Renderer
     void** _lightPtr;
     ospray::Data* _lightData;
 
-    Material* _bgMaterial;
+    ospray::Material* _bgMaterial;
 
     float _exposure{1.f};
 

bioexplorer/backend/plugins/Metabolism/plugin/MetabolismPlugin.cpp

@@ -34,12 +34,13 @@
 
 #include <fstream>
 
+using namespace core;
+
 namespace bioexplorer
 {
+using namespace details;
 namespace metabolism
 {
-using namespace bioexplorer;
-using namespace details;
 
 const std::string PLUGIN_VERSION = "0.1.0";
 const std::string PLUGIN_API_PREFIX = "mb-";

bioexplorer/backend/plugins/Metabolism/plugin/MetabolismPlugin.h

@@ -31,8 +31,6 @@ namespace bioexplorer
 {
 namespace metabolism
 {
-using namespace details;
-
 /**
  * @brief This class implements the MetabolismPlugin plugin
  */
@@ -47,7 +45,7 @@ class MetabolismPlugin : public core::ExtensionPlugin
     void _parseCommandLineArguments(int argc, char **argv);
 
     // Metabolism
-    Response _attachHandler(const AttachHandlerDetails &payload);
+    bioexplorer::details::Response _attachHandler(const AttachHandlerDetails &payload);
 
     // Command line arguments
     CommandLineArguments _commandLineArguments;

bioexplorer/backend/plugins/Metabolism/plugin/api/Params.cpp

@@ -23,10 +23,9 @@
 #include "Params.h"
 #include <common/json.hpp>
 
-namespace bioexplorer
-{
-namespace metabolism
-{
+using namespace bioexplorer;
+using namespace metabolism;
+
 #ifndef PLATFORM_DEBUG_JSON_ENABLED
 #define FROM_JSON(PARAM, JSON, NAME) PARAM.NAME = JSON[#NAME].get<decltype(PARAM.NAME)>()
 #else
@@ -61,5 +60,3 @@ bool from_json(AttachHandlerDetails &param, const std::string &payload)
     }
     return true;
 }
-} // namespace metabolism
-} // namespace bioexplorer

bioexplorer/backend/plugins/Metabolism/plugin/api/Params.h

@@ -27,10 +27,4 @@
 #include <bioexplorer/backend/science/api/Params.h>
 #include <plugin/common/Types.h>
 
-namespace bioexplorer
-{
-namespace metabolism
-{
-bool from_json(AttachHandlerDetails &param, const std::string &payload);
-} // namespace metabolism
-} // namespace bioexplorer
+bool from_json(bioexplorer::metabolism::AttachHandlerDetails &param, const std::string &payload);

bioexplorer/backend/plugins/Metabolism/plugin/common/Types.h

@@ -26,8 +26,6 @@
 
 #include <bioexplorer/backend/science/common/Types.h>
 
-using namespace core;
-
 namespace bioexplorer
 {
 namespace metabolism
@@ -49,6 +47,14 @@ const std::string ARG_DB_USER = "--db-user";
 const std::string ARG_DB_PASSWORD = "--db-password";
 const std::string ARG_DB_SCHEMA = "--db-schema";
 
+typedef struct
+{
+    uint32_t guid;
+    std::string code;
+    core::Vector3f color;
+} Location;
+using Locations = std::vector<Location>;
+
 typedef struct
 {
     std::string connectionString;
@@ -58,14 +64,5 @@ typedef struct
     int32_t referenceFrame;
     bool relativeConcentration{false};
 } AttachHandlerDetails;
-
-typedef struct
-{
-    uint32_t guid;
-    std::string code;
-    Vector3f color;
-} Location;
-using Locations = std::vector<Location>;
-
 } // namespace metabolism
 } // namespace bioexplorer

bioexplorer/backend/plugins/Metabolism/plugin/common/Utils.h

@@ -26,8 +26,5 @@
 
 namespace metabolism
 {
-using namespace core;
-
 void setTransferFunction(core::TransferFunction& tf);
-
 } // namespace metabolism

bioexplorer/backend/plugins/Metabolism/plugin/io/db/DBConnector.cpp

@@ -28,10 +28,14 @@
 
 #define DEFAULT_NUM_FRAMES 1000
 
+using namespace core;
+
 namespace bioexplorer
 {
 namespace metabolism
 {
+using namespace details;
+
 DBConnector::DBConnector(const CommandLineArguments& args)
 {
     _parseArguments(args);

bioexplorer/backend/plugins/Metabolism/plugin/io/handlers/MetabolismHandler.cpp

@@ -26,6 +26,8 @@
 
 #include <fstream>
 
+using namespace core;
+
 namespace bioexplorer
 {
 namespace metabolism
@@ -100,19 +102,6 @@ void* MetabolismHandler::getFrameData(const uint32_t frame)
     }
 
     _frameSize = _frameData.size();
-
-#if 0
-    std::string s;
-    for (uint64_t i = 0; i < _frameData.size(); ++i)
-    {
-        if (!s.empty())
-            s += ",";
-        s += "[" + std::to_string(_locations[i - 1].guid) + "] " +
-             std::to_string(_frameData[i]);
-    }
-    PLUGIN_INFO(s);
-#endif
-
     return _frameData.data();
 }
 

bioexplorer/backend/plugins/Metabolism/plugin/io/handlers/MetabolismHandler.h

@@ -33,8 +33,6 @@ namespace bioexplorer
 {
 namespace metabolism
 {
-using namespace core;
-
 /**
  * @brief The MetabolismHandler class handles metabolite concentrations
  */
@@ -55,7 +53,7 @@ class MetabolismHandler : public core::AbstractSimulationHandler
 
     bool isReady() const final { return true; }
 
-    AbstractSimulationHandlerPtr clone() const final;
+    core::AbstractSimulationHandlerPtr clone() const final;
 
     void setMetaboliteIds(const int32_ts& metaboliteIds) { _metaboliteIds = metaboliteIds; }
 

bioexplorer/backend/plugins/Sonata/module/ispc/render/CellGrowthRenderer.cpp

@@ -28,7 +28,7 @@
 // ispc exports
 #include "CellGrowthRenderer_ispc.h"
 
-using namespace ospray;
+using namespace core;
 
 namespace sonataexplorer
 {

bioexplorer/backend/plugins/Sonata/module/ispc/render/CellGrowthRenderer.h

@@ -26,13 +26,11 @@
 
 namespace sonataexplorer
 {
-using namespace core;
-
 /**
  * @brief The CellGrowthRenderer class can perform fast transparency
  * and mapping of simulation data on the geometry
  */
-class CellGrowthRenderer : public SimulationRenderer
+class CellGrowthRenderer : public core::SimulationRenderer
 {
 public:
     CellGrowthRenderer();

bioexplorer/backend/plugins/Sonata/module/ispc/render/ProximityDetectionRenderer.cpp

@@ -27,6 +27,8 @@
 // ispc exports
 #include "ProximityDetectionRenderer_ispc.h"
 
+using namespace core;
+
 namespace sonataexplorer
 {
 void ProximityDetectionRenderer::commit()