Merge pull request #316 from favreau/master

Added surface and contour representation to neurons

CMakeLists.txt

@@ -48,6 +48,7 @@ find_package(CUDA)
 find_package(assimp)
 find_package(LibJpegTurbo)
 find_package(Rockets)
+find_package(CGAL)
 
 set(BIOEXPLORER_SOURCE_DIRS ${PROJECT_SOURCE_DIR} ${CMAKE_BINARY_DIR}/generated)
 
@@ -89,13 +90,23 @@ if(OptiX7_FOUND AND CUDA_FOUND)
     if(PLATFORM_OPTIX7_ENABLED)
         set(OPTIX7_FOUND 1)
         message(STATUS "[Core] OptiX 7 module enabled")
+    else()
+        message(STATUS "[Core] Optix 7 module disabled")
     endif()
+else()
+    message(STATUS "[Core] Optix 7 not found")
 endif()
 
-set(CGAL_FOUND 0)
-if(${${NAME}_USE_CGAL})
-    set(CGAL_DATA_DIR ".")
-    find_package(CGAL REQUIRED)
+if(CGAL_FOUND)
+    if(${${NAME}_USE_CGAL})
+        message(STATUS "[Core] CGAL module enabled")
+        set(CGAL_DATA_DIR ".")
+        find_package(CGAL REQUIRED)
+    else()
+        message(STATUS "[Core] CGAL module disabled")
+    endif()
+else()
+    message(STATUS "[Core] CGAL module not found")
 endif()
 
 set(ASSIMP_FOUND 0)

bioexplorer/backend/science/common/Types.h

@@ -438,7 +438,9 @@ enum class MorphologyRepresentation
     section = 1,
     segment = 2,
     orientation = 3,
-    bezier = 4
+    bezier = 4,
+    contour = 5,
+    surface = 6
 };
 
 enum class MorphologyRealismLevel

bioexplorer/backend/science/meshing/SurfaceMesher.cpp

@@ -74,13 +74,13 @@ SurfaceMesher::SurfaceMesher(const uint32_t uuid)
 {
 }
 
-ModelDescriptorPtr SurfaceMesher::generateSurface(core::Scene& scene, const std::string& pdbId, const Vector4ds& atoms,
+ModelDescriptorPtr SurfaceMesher::generateSurface(core::Scene& scene, const std::string& name, const Vector4ds& points,
                                                   const double shrinkfactor)
 {
 #ifdef USE_CGAL
     ModelDescriptorPtr modelDescriptor{nullptr};
     MeshLoader meshLoader(scene);
-    const std::string filename = GeneralSettings::getInstance()->getMeshFolder() + pdbId + ".off";
+    const std::string filename = GeneralSettings::getInstance()->getMeshFolder() + name + ".off";
     try
     {
         PLUGIN_INFO(3, "Trying to load surface from cache " << filename);
@@ -94,10 +94,10 @@ ModelDescriptorPtr SurfaceMesher::generateSurface(core::Scene& scene, const std:
     }
 
     std::list<Weighted_point> l;
-    for (const auto& atom : atoms)
-        l.push_front(Weighted_point(Point_3(atom.x, atom.y, atom.z), atom.w));
+    for (const auto& point : points)
+        l.push_front(Weighted_point(Point_3(point.x, point.y, point.z), point.w));
 
-    PLUGIN_INFO(3, "Constructing skin surface from " << l.size() << " atoms");
+    PLUGIN_INFO(3, "Constructing skin surface from " << l.size() << " point");
 
     Polyhedron polyhedron;
     Skin_surface_3 skinSurface(l.begin(), l.end(), shrinkfactor);
@@ -115,17 +115,17 @@ ModelDescriptorPtr SurfaceMesher::generateSurface(core::Scene& scene, const std:
 #endif
 }
 
-ModelDescriptorPtr SurfaceMesher::generateUnionOfBalls(core::Scene& scene, const std::string& pdbId,
-                                                       const Vector4ds& atoms)
+ModelDescriptorPtr SurfaceMesher::generateUnionOfBalls(core::Scene& scene, const std::string& name,
+                                                       const Vector4ds& points)
 {
 #ifdef USE_CGAL
     std::list<Weighted_point> l;
-    for (const auto& atom : atoms)
-        l.push_front(Weighted_point(Point_3(atom.x, atom.y, atom.z), atom.w));
+    for (const auto& point : points)
+        l.push_front(Weighted_point(Point_3(point.x, point.y, point.z), point.w));
 
     ModelDescriptorPtr modelDescriptor{nullptr};
     MeshLoader meshLoader(scene);
-    const std::string filename = GeneralSettings::getInstance()->getMeshFolder() + pdbId + ".off";
+    const std::string filename = GeneralSettings::getInstance()->getMeshFolder() + name + ".off";
     try
     {
         PLUGIN_INFO(3, "Trying to load union of balls from cache " << filename);
@@ -138,7 +138,7 @@ ModelDescriptorPtr SurfaceMesher::generateUnionOfBalls(core::Scene& scene, const
         PLUGIN_INFO(3, "Failed to load union of balls from cache (" << e.what() << "), constructing it...");
     }
 
-    PLUGIN_INFO(3, "Constructing union of balls from " << l.size() << " atoms");
+    PLUGIN_INFO(3, "Constructing union of balls from " << l.size() << " points");
 
     Polyhedron polyhedron;
     Union_of_balls_3 union_of_balls(l.begin(), l.end());

bioexplorer/backend/science/meshing/SurfaceMesher.h

@@ -36,18 +36,18 @@ class SurfaceMesher
 
     /** Generates a triangle based mesh model
      *
-     * @param atoms atoms used to generate the mesh
+     * @param points points used to generate the mesh
      * @param triangles Generated triangles
      */
-    core::ModelDescriptorPtr generateSurface(core::Scene& scene, const std::string& pdbId, const Vector4ds& atoms,
+    core::ModelDescriptorPtr generateSurface(core::Scene& scene, const std::string& name, const Vector4ds& points,
                                              const double shrinkfactor = 0.5);
 
     /** Generates a triangle based mesh model
      *
-     * @param atoms atoms used to generate the mesh
+     * @param points points used to generate the mesh
      * @param triangles Generated triangles
      */
-    core::ModelDescriptorPtr generateUnionOfBalls(core::Scene& scene, const std::string& pdbId, const Vector4ds& atoms);
+    core::ModelDescriptorPtr generateUnionOfBalls(core::Scene& scene, const std::string& name, const Vector4ds& points);
 
 private:
     uint32_t _uuid;

bioexplorer/backend/science/morphologies/Neurons.cpp

@@ -37,6 +37,11 @@
 #include <platform/core/engineapi/Model.h>
 #include <platform/core/engineapi/Scene.h>
 
+#ifdef USE_CGAL
+#include <science/meshing/PointCloudMesher.h>
+#include <science/meshing/SurfaceMesher.h>
+#endif
+
 #include <omp.h>
 
 using namespace core;
@@ -47,6 +52,10 @@ using namespace details;
 using namespace common;
 using namespace io;
 using namespace db;
+#ifdef USE_CGAL
+using namespace meshing;
+#endif
+
 namespace morphology
 {
 const uint64_t NB_MYELIN_FREE_SEGMENTS = 4;
@@ -133,6 +142,56 @@ void Neurons::_logRealismParams()
     PLUGIN_INFO(1, "----------------------------------------------------");
 }
 
+void Neurons::_buildContours(ThreadSafeContainer& container, const NeuronSomaMap& somas, const size_t baseMaterialId)
+{
+#ifdef USE_CGAL
+    uint64_t progress = 0;
+    PointCloud pointCloud;
+
+    for (const auto soma : somas)
+    {
+        PLUGIN_PROGRESS("Loading somas", progress, somas.size());
+        ++progress;
+
+        const Vector3d position = soma.second.position;
+        pointCloud[baseMaterialId].push_back({position.x, position.y, position.z, _details.radiusMultiplier});
+    }
+
+    PointCloudMesher pcm;
+    pcm.toConvexHull(container, pointCloud);
+#else
+    PLUGIN_THROW("The BioExplorer was not compiled with the CGAL library")
+#endif
+}
+
+void Neurons::_buildSurface(const NeuronSomaMap& somas)
+{
+#ifdef USE_CGAL
+    uint64_t progress = 0;
+    PointCloud pointCloud;
+    size_t materialId = 0;
+
+    for (const auto soma : somas)
+    {
+        PLUGIN_PROGRESS("Loading somas", progress, somas.size());
+        ++progress;
+
+        const Vector3d position = soma.second.position;
+        pointCloud[materialId].push_back({position.x, position.y, position.z, _details.radiusMultiplier});
+    }
+
+    SurfaceMesher sm(_uuid);
+    _modelDescriptor = sm.generateSurface(_scene, _details.assemblyName, pointCloud[materialId]);
+    if (_modelDescriptor)
+        _scene.addModel(_modelDescriptor);
+    else
+        PLUGIN_THROW("Failed to generate surface")
+
+#else
+    PLUGIN_THROW("The BioExplorer was not compiled with the CGAL library")
+#endif
+}
+
 void Neurons::_buildNeurons()
 {
     const auto& connector = DBConnector::getInstance();
@@ -164,13 +223,34 @@ void Neurons::_buildNeurons()
         _details.loadSomas && !_details.loadAxon && !_details.loadApicalDendrites && !_details.loadBasalDendrites;
 
     ThreadSafeContainers containers;
-    if (somasOnly || _details.morphologyRepresentation == MorphologyRepresentation::orientation)
+    if (somasOnly || _details.morphologyRepresentation == MorphologyRepresentation::orientation ||
+        _details.morphologyRepresentation == MorphologyRepresentation::contour)
     {
         ThreadSafeContainer container(*model, _alignToGrid, _position, _rotation, _scale);
-        if (_details.morphologyRepresentation == MorphologyRepresentation::orientation)
+        switch (_details.morphologyRepresentation)
+        {
+        case MorphologyRepresentation::orientation:
+        {
             _buildOrientations(container, somas, baseMaterialId);
-        else
+            break;
+        }
+        case MorphologyRepresentation::contour:
+        {
+            _buildContours(container, somas, baseMaterialId);
+            break;
+        }
+        case MorphologyRepresentation::surface:
+        {
+            _buildSurface(somas);
+            return;
+            break;
+        }
+        default:
+        {
             _buildSomasOnly(container, somas, baseMaterialId);
+            break;
+        }
+        }
         containers.push_back(container);
     }
     else

bioexplorer/backend/science/morphologies/Neurons.h

@@ -74,6 +74,11 @@ class Neurons : public Morphologies
 
     void _buildNeurons();
 
+    void _buildContours(common::ThreadSafeContainer& container, const NeuronSomaMap& somas,
+                        const size_t baseMaterialId);
+
+    void _buildSurface(const NeuronSomaMap& somas);
+
     void _buildSomasOnly(common::ThreadSafeContainer& container, const NeuronSomaMap& somas,
                          const size_t baseMaterialId);
 

bioexplorer/pythonsdk/bioexplorer/bio_explorer.py

@@ -659,6 +659,8 @@ class BioExplorer:
     MORPHOLOGY_REPRESENTATION_SEGMENT = 2
     MORPHOLOGY_REPRESENTATION_ORIENTATION = 3
     MORPHOLOGY_REPRESENTATION_BEZIER = 4
+    MORPHOLOGY_REPRESENTATION_CONTOUR = 5
+    MORPHOLOGY_REPRESENTATION_SURFACE = 6
 
     MICRO_DOMAIN_REPRESENTATION_MESH = 0
     MICRO_DOMAIN_REPRESENTATION_CONVEX_HULL = 1