Merge pull request #302 from favreau/master

Added synapse types to neurons
BlueBrain · Sep 13, 2023 · 16c5da6 · 16c5da6
2 parents 26bf8ed + 14b5045
commit 16c5da6
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Showing 22 changed files with 150 additions and 248 deletions.
diff --git a/bioexplorer/backend/science/api/Params.cpp b/bioexplorer/backend/science/api/Params.cpp
@@ -939,7 +939,7 @@ bool from_json(NeuronsDetails &param, const std::string &payload)
         FROM_JSON(param, js, loadAxon);
         FROM_JSON(param, js, loadBasalDendrites);
         FROM_JSON(param, js, loadApicalDendrites);
-        FROM_JSON(param, js, loadSynapses);
+        FROM_JSON(param, js, synapsesType);
         FROM_JSON(param, js, generateInternals);
         FROM_JSON(param, js, generateExternals);
         FROM_JSON(param, js, showMembrane);

diff --git a/bioexplorer/backend/science/common/SDFGeometries.cpp b/bioexplorer/backend/science/common/SDFGeometries.cpp
@@ -63,11 +63,9 @@ Vector4fs SDFGeometries::_getProcessedSectionPoints(const MorphologyRepresentati
                                                     const Vector4fs& points)
 {
     Vector4fs localPoints;
-    if (representation == MorphologyRepresentation::bezier && points.size() > DEFAULT_BEZIER_STEP * 2)
-    {
-        for (double t = 0.0; t <= 1.0; t += 1.0 / static_cast<double>(points.size() * DEFAULT_BEZIER_STEP))
+    if (representation == MorphologyRepresentation::bezier)
+        for (double t = 0.0; t <= 1.0; t += 1.0 / static_cast<double>(points.size()))
             localPoints.push_back(getBezierPoint(points, t));
-    }
     else
         localPoints = points;
     return localPoints;

diff --git a/bioexplorer/backend/science/common/ThreadSafeContainer.cpp b/bioexplorer/backend/science/common/ThreadSafeContainer.cpp
@@ -36,7 +36,7 @@ namespace common
 {
 using namespace core;
 
-const float equalityEpsilon = 0.001f;
+const float equalityEpsilon = 1e-6f;
 
 ThreadSafeContainer::ThreadSafeContainer(Model& model, const double alignToGrid, const Vector3d& position,
                                          const Quaterniond& rotation, const Vector3d& scale)
@@ -93,7 +93,7 @@ uint64_t ThreadSafeContainer::addCone(const Vector3f& sourcePosition, const floa
         _bounds.merge(scaledDstPosition - scaledDstRadius);
         return _addSDFGeometry(materialId, geom, neighbours);
     }
-    if (abs(sourceRadius - targetRadius) < equalityEpsilon)
+    if (fabs(sourceRadius - targetRadius) < equalityEpsilon)
     {
         const auto scaledSrcRadius = sourceRadius * scale.x;
         const auto scaledDstRadius = targetRadius * scale.x;

diff --git a/bioexplorer/backend/science/common/Types.h b/bioexplorer/backend/science/common/Types.h
@@ -330,8 +330,18 @@ using NeuronsPtr = std::shared_ptr<Neurons>;
 class Synapses;
 using SynapsesPtr = std::shared_ptr<Synapses>;
 
+enum class MorphologySynapseType
+{
+    none = 0,
+    afferent = 1,
+    efferent = 2,
+    debug = 4,
+    all = 8
+};
+
 typedef struct
 {
+    MorphologySynapseType type;
     uint64_t postSynapticNeuronId;
     uint64_t postSynapticSectionId;
     uint64_t postSynapticSegmentId;
@@ -1394,6 +1404,7 @@ typedef struct
     /** Amplitude applied to the radius */
     double amplitude{1.0};
 } VasculatureRadiusReportDetails;
+
 typedef struct
 {
     /** Name of the assembly containing the astrocytes */
@@ -1461,8 +1472,8 @@ typedef struct
     bool loadBasalDendrites{true};
     /** Load apical dendrites if set to true */
     bool loadApicalDendrites{true};
-    /** Load synapses if set to true */
-    bool loadSynapses{false};
+    /** Type of synapses to load */
+    morphology::MorphologySynapseType synapsesType{morphology::MorphologySynapseType::none};
     /** Generate internal components (nucleus and mitochondria) */
     bool generateInternals{false};
     /** Generate external components (myelin steath) */

diff --git a/bioexplorer/backend/science/common/Utils.cpp b/bioexplorer/backend/science/common/Utils.cpp
@@ -537,6 +537,11 @@ size_t getMaterialIdFromOrientation(const Vector3d& orientation)
     return ((rgb.x & 0x0ff) << 16) | ((rgb.y & 0x0ff) << 8) | (rgb.z & 0x0ff);
 }
 
+double rnd0()
+{
+    return static_cast<double>(rand() % 1000) / 1000.0;
+}
+
 double rnd1()
 {
     return static_cast<double>(rand() % 1000 - 500) / 1000.0;

diff --git a/bioexplorer/backend/science/common/Utils.h b/bioexplorer/backend/science/common/Utils.h
@@ -212,6 +212,13 @@ double worleyNoise(const core::Vector3d& p, const double cellCount);
 
 size_t getMaterialIdFromOrientation(const core::Vector3d& orientation);
 
+/**
+ * @brief Return a random double between 0 and 1
+ *
+ * @return double A random double between 0 and 1
+ */
+double rnd0();
+
 /**
  * @brief Return a random double between -0.5 and 0.5
  *

diff --git a/bioexplorer/backend/science/io/db/DBConnector.cpp b/bioexplorer/backend/science/io/db/DBConnector.cpp
@@ -743,8 +743,8 @@ SectionMap DBConnector::getNeuronSections(const std::string& populationName, con
     return sections;
 }
 
-SectionSynapseMap DBConnector::getNeuronSynapses(const std::string& populationName, const uint64_t neuronId,
-                                                 const std::string& sqlCondition) const
+SectionSynapseMap DBConnector::getNeuronAfferentSynapses(const std::string& populationName, const uint64_t neuronId,
+                                                         const std::string& sqlCondition) const
 {
     CHECK_DB_INITIALIZATION
     SectionSynapseMap sectionSynapseMap;
@@ -776,6 +776,7 @@ SectionSynapseMap DBConnector::getNeuronSynapses(const std::string& populationNa
             const auto preSynapticSectionId = c[0].as<uint64_t>();
             const auto preSynapticSegmentId = c[1].as<uint64_t>();
             Synapse synapse;
+            synapse.type = MorphologySynapseType::afferent;
             synapse.preSynapticSegmentDistance = c[2].as<double>();
             synapse.postSynapticNeuronId = c[3].as<uint64_t>();
             synapse.postSynapticSectionId = c[4].as<uint64_t>();

diff --git a/bioexplorer/backend/science/io/db/DBConnector.h b/bioexplorer/backend/science/io/db/DBConnector.h
@@ -258,16 +258,16 @@ class DBConnector
                                              const std::string& sqlCondition = "") const;
 
     /**
-     * @brief Get the synapses attached to a given neuron
+     * @brief Get the afferent synapses attached to a given neuron
      *
      * @param populationName Name of the population
      * @param neuronId Identifier of the neuron
      * @param sqlCondition String containing an WHERE condition for the SQL
      * statement
      * @return SectionSynapseMap A map of synapses
      */
-    morphology::SectionSynapseMap getNeuronSynapses(const std::string& populationName, const uint64_t neuronId,
-                                                    const std::string& sqlCondition = "") const;
+    morphology::SectionSynapseMap getNeuronAfferentSynapses(const std::string& populationName, const uint64_t neuronId,
+                                                            const std::string& sqlCondition = "") const;
 
     /**
      * @brief Get a selection of spikes from a neuron spike report

diff --git a/bioexplorer/backend/science/morphologies/Morphologies.h b/bioexplorer/backend/science/morphologies/Morphologies.h
@@ -37,7 +37,8 @@ const size_t MATERIAL_OFFSET_SOMA = 1;
 const size_t MATERIAL_OFFSET_AXON = 2;
 const size_t MATERIAL_OFFSET_DENDRITE = 3;
 const size_t MATERIAL_OFFSET_APICAL_DENDRITE = 4;
-const size_t MATERIAL_OFFSET_SYNAPSE = 5;
+const size_t MATERIAL_OFFSET_AFFERENT_SYNAPSE = 5;
+const size_t MATERIAL_OFFSET_EFFERENT_SYNAPSE = 6;
 const size_t MATERIAL_OFFSET_MITOCHONDRION = 7;
 const size_t MATERIAL_OFFSET_NUCLEUS = 8;
 const size_t MATERIAL_OFFSET_MYELIN_SHEATH = 9;