Merge pull request #372 from favreau/master

Added connectome population name to add_astrocytes API

bioexplorer/backend/science/api/Params.cpp

@@ -944,6 +944,7 @@ bool from_json(AstrocytesDetails &param, const std::string &payload)
         FROM_JSON(param, js, assemblyName);
         FROM_JSON(param, js, populationName);
         FROM_JSON(param, js, vasculaturePopulationName);
+        FROM_JSON(param, js, connectomePopulationName);
         FROM_JSON(param, js, loadSomas);
         FROM_JSON(param, js, loadDendrites);
         FROM_JSON(param, js, generateInternals);

bioexplorer/backend/science/common/Types.h

@@ -1469,9 +1469,10 @@ typedef struct
     std::string assemblyName;
     /** Name of the population of astrocytes */
     std::string populationName;
-    /** Name of the vasculature population. If not empty, endfeet are
-     * automatically loaded */
+    /** Name of the vasculature population. If not empty, endfeet are automatically loaded */
     std::string vasculaturePopulationName;
+    /** Name of the connectome population. If not empty, endfeet are automatically loaded */
+    std::string connectomePopulationName;
     /** Load somas if set to true */
     bool loadSomas{true};
     /** Load dendrites if set to true */

bioexplorer/backend/science/io/db/DBConnector.cpp

@@ -48,7 +48,6 @@ namespace db
 {
 const std::string DB_SCHEMA_OUT_OF_CORE = "outofcore";
 const std::string DB_SCHEMA_METABOLISM = "metabolism";
-const std::string DB_SCHEMA_CONNECTOME = "connectome";
 
 DBConnector* DBConnector::_instance = nullptr;
 std::mutex DBConnector::_mutex;
@@ -568,7 +567,7 @@ SectionMap DBConnector::getAstrocyteSections(const std::string& populationName,
     return sections;
 }
 
-EndFootMap DBConnector::getAstrocyteEndFeet(const std::string& vasculaturePopulationName,
+EndFootMap DBConnector::getAstrocyteEndFeet(const std::string& vasculaturePopulationName, const std::string& connectomePopulationName,
                                             const uint64_t astrocyteId) const
 {
     CHECK_DB_INITIALIZATION
@@ -584,7 +583,7 @@ EndFootMap DBConnector::getAstrocyteEndFeet(const std::string& vasculaturePopula
             "c.endfoot_compartment_length, c.endfoot_compartment_diameter "
             "* "
             "0.5 FROM " +
-            DB_SCHEMA_CONNECTOME + ".glio_vascular as c, " + vasculaturePopulationName +
+            connectomePopulationName + ".glio_vascular as c, " + vasculaturePopulationName +
             ".node as n WHERE c.vasculature_node_guid=n.guid AND "
             "c.astrocyte_guid=" +
             std::to_string(astrocyteId);

bioexplorer/backend/science/io/db/DBConnector.h

@@ -220,10 +220,11 @@ class DBConnector
      * @brief Get the end-feet as nodes for a given astrocyte
      *
      * @param vasculaturePopulationName Name of the vasculature population
+     * @param connectomePopulationName Name of the connectome population
      * @param astrocyteId Identifier of the astrocyte
      * @return EndFootNodesMap A map of end-feet
      */
-    morphology::EndFootMap getAstrocyteEndFeet(const std::string& vasculaturePopulationName,
+    morphology::EndFootMap getAstrocyteEndFeet(const std::string& vasculaturePopulationName, const std::string& connectomePopulationName,
                                                const uint64_t astrocyteId) const;
 
     /**

bioexplorer/backend/science/morphologies/Astrocytes.cpp

@@ -170,7 +170,7 @@ void Astrocytes::_buildModel(const LoaderProgress& callback, const doubles& radi
             // End feet
             EndFootMap endFeet;
             if (loadEndFeet)
-                endFeet = connector.getAstrocyteEndFeet(_details.vasculaturePopulationName, somaId);
+                endFeet = connector.getAstrocyteEndFeet(_details.vasculaturePopulationName, _details.connectomePopulationName, somaId);
 
             // Soma radius
             uint64_t count = 1;
@@ -421,6 +421,8 @@ void Astrocytes::_addEndFoot(ThreadSafeContainer& container, const Vector3d& som
                 connector.getVasculatureNodes(_details.vasculaturePopulationName,
                                               "section_guid=" + std::to_string(endFoot.second.vasculatureSectionId));
 
+            if (vasculatureNodes.empty())
+                continue;
             uint64_t startIndex = 0;
             uint64_t endIndex = 1;
             const auto halfLength = endFoot.second.length / 2.0;

bioexplorer/pythonsdk/bioexplorer/bio_explorer.py

@@ -112,6 +112,8 @@ class BioExplorer:
     morphology_representation = MorphologyRepresentation
     morphology_color_scheme = MorphologyColorScheme
     morphology_realism_level = MorphologyRealismLevel
+
+    population_color_scheme = PopulationColorScheme
 
     synapse_representation = SynapseRepresentation
 
@@ -2814,6 +2816,7 @@ def add_astrocytes(
         assembly_name,
         population_name,
         vasculature_population_name="",
+        connectome_population_name="",
         realism_level=MorphologyRealismLevel.NONE,
         load_somas=True,
         load_dendrites=True,
@@ -2838,6 +2841,8 @@ def add_astrocytes(
         :population_name: Name of the population of astrocytes
         :vasculature_population_name: Name of the vasculature population. Automatically load
                                       end-feet if not empty
+        :connectome_population_name: Name of the connectome population. Automatically load
+                                      end-feet if not empty
         :load_somas: Load somas if set to true
         :load_dendrites: Load dendrites if set to true
         :generate_internals: Generate internals (Nucleus and mitochondria)
@@ -2859,11 +2864,15 @@ def add_astrocytes(
         assert isinstance(scale, Vector3)
         assert isinstance(animation_params, CellAnimationParams)
         assert isinstance(displacement_params, AstrocyteDisplacementParams)
+        if vasculature_population_name != '':
+            if connectome_population_name == '':
+                raise RuntimeError("A connectome population must be specified together with the vasculature population")
 
         params = dict()
         params["assemblyName"] = assembly_name
         params["populationName"] = population_name
         params["vasculaturePopulationName"] = vasculature_population_name
+        params["connectomePopulationName"] = connectome_population_name
         params["loadSomas"] = load_somas
         params["loadDendrites"] = load_dendrites
         params["generateInternals"] = generate_internals

bioexplorer/pythonsdk/notebooks/astrocytes/BioExplorer_astrocytes.ipynb

@@ -66,6 +66,7 @@
                 "    assembly_name=assembly_name,\n",
                 "    population_name='Astrocytes',\n",
                 "    vasculature_population_name='vasculature',\n",
+                "    connectome_population_name='connectome',\n",
                 "    load_micro_domains=False,\n",
                 "    load_dendrites=True,\n",
                 "    morphology_color_scheme=be.morphology_color_scheme.SECTION_TYPE,\n",

bioexplorer/pythonsdk/notebooks/astrocytes/animation/BioExplorer_animated_astrocytes.ipynb

@@ -132,7 +132,8 @@
                 "        assembly_name=assembly_name,\n",
                 "        population_name='astrocytes',\n",
                 "        vasculature_population_name='vasculature',\n",
-                "        population_color_scheme=be.POPULATION_COLOR_SCHEME_ID,\n",
+                "        connectome_population_name='connectome',\n",
+                "        population_color_scheme=be.population_color_scheme.ID,\n",
                 "        radius_multiplier=1.0,\n",
                 "        morphology_color_scheme=be.morphology_color_scheme.SECTION_TYPE,\n",
                 "        realism_level=be.morphology_realism_level.ALL,\n",
@@ -144,7 +145,7 @@
         },
         {
             "cell_type": "code",
-            "execution_count": null,
+            "execution_count": 13,
             "id": "7cd24ef9",
             "metadata": {},
             "outputs": [],
@@ -205,9 +206,9 @@
             "name": "python",
             "nbconvert_exporter": "python",
             "pygments_lexer": "ipython3",
-            "version": "3.8.10"
+            "version": "3.10.12"
         }
     },
     "nbformat": 4,
     "nbformat_minor": 5
-}
+}

bioexplorer/pythonsdk/notebooks/neuromodulation/BioExplorer_neuromodulation_movie.ipynb

@@ -69,6 +69,7 @@
                 "neuron_population_name = 'o1'\n",
                 "vasculature_population_name = 'vasculature'\n",
                 "astrocytes_population_name = 'astrocytes'\n",
+                "connectome_population_name='connectome'\n",
                 "\n",
                 "if load_neuron:\n",
                 "    neuron_sql_filter = 'guid=%d' % neuron_guid\n",
@@ -79,7 +80,7 @@
                 "        assembly_name=neuron_assembly_name,\n",
                 "        morphology_color_scheme=be.morphology_color_scheme.SECTION_TYPE,\n",
                 "        population_name=neuron_population_name,\n",
-                "        realism_level=realism_level, generate_buttons=True,\n",
+                "        realism_level=realism_level,\n",
                 "        synapses_type=be.neuron_synapse_type.AFFERENT, show_membrane=not load_mesh_neuron,\n",
                 "        generate_internals=True, generate_externals=False,\n",
                 "        sql_node_filter=neuron_sql_filter, scale=scale,\n",
@@ -106,6 +107,7 @@
                 "        assembly_name=astrocytes_assembly_name,\n",
                 "        population_name=astrocytes_population_name,\n",
                 "        vasculature_population_name=vasculature_population_name,\n",
+                "        connectome_population_name=connectome_population_name,\n",
                 "        radius_multiplier=0.5,\n",
                 "        realism_level=realism_level, generate_internals=True,\n",
                 "        load_somas=True, load_dendrites=True,\n",
@@ -752,9 +754,9 @@
             "name": "python",
             "nbconvert_exporter": "python",
             "pygments_lexer": "ipython3",
-            "version": "3.8.10"
+            "version": "3.10.12"
         }
     },
     "nbformat": 4,
     "nbformat_minor": 5
-}
+}

bioexplorer/pythonsdk/notebooks/neuromodulation/BioExplorer_neuronmodulation_components.ipynb

@@ -151,7 +151,7 @@
                 "vasculature_model = be.add_vasculature(\n",
                 "    assembly_name=vasculature_assembly_name,\n",
                 "    population_name=vasculature_population_name,\n",
-                "    representation=be.VASCULATURE_REPRESENTATION_SECTION,\n",
+                "    representation=be.vascular_representation.SECTION,\n",
                 "    realism_level=be.morphology_realism_level.ALL,\n",
                 "    sql_filter='sqrt(pow(x - %f, 2) + pow(y - %f, 2) + pow(z - %f, 2)) < 200' % (target[0], target[1], target[2])\n",
                 ")"
@@ -165,11 +165,14 @@
             "outputs": [],
             "source": [
                 "astrocytes_assembly_name = 'Astrocytes'\n",
+                "astrocytes_population_name = 'astrocytes'\n",
+                "connectome_population_name = 'connectome'\n",
                 "be.remove_assembly(astrocytes_assembly_name)\n",
                 "astrocytes_assembly = be.add_assembly(astrocytes_assembly_name)\n",
                 "astrocytes_model = be.add_astrocytes(\n",
                 "    assembly_name=astrocytes_assembly_name,\n",
-                "    population_name=vasculature_population_name,\n",
+                "    population_name=astrocytes_population_name,\n",
+                "    connectome_population_name=connectome_population_name,\n",
                 "    realism_level=be.morphology_realism_level.ALL,\n",
                 "    generate_internals=True,\n",
                 "    load_somas=True, load_dendrites=True,\n",
@@ -213,12 +216,12 @@
                 "    for material_id in material_ids:\n",
                 "        mid = material_id % palette_size\n",
                 "        colors.append(palette[mid])\n",
-                "        if mid == be.NEURON_MATERIAL_SYNAPSE:\n",
+                "        if mid in [be.neuron_material.AFFERENT_SYNAPSE, be.neuron_material.EFFERENT_SYNAPSE]:\n",
                 "            opacities.append(opacity)\n",
                 "            shading_modes.append(shading_mode)\n",
                 "            glossinesses.append(glossiness)\n",
                 "            specular_exponents.append(5.0)\n",
-                "        elif mid in [be.NEURON_MATERIAL_VARICOSITY]:\n",
+                "        elif mid in [be.neuron_material.VARICOSITY]:\n",
                 "            opacities.append(opacity)\n",
                 "            shading_modes.append(shading_mode)\n",
                 "            glossinesses.append(glossiness)\n",
@@ -343,9 +346,9 @@
             "name": "python",
             "nbconvert_exporter": "python",
             "pygments_lexer": "ipython3",
-            "version": "3.8.10"
+            "version": "3.10.12"
         }
     },
     "nbformat": 4,
     "nbformat_minor": 5
-}
+}

bioexplorer/pythonsdk/notebooks/neuromodulation/BioExplorer_neuronmodulation_covers.ipynb

@@ -48,7 +48,6 @@
                 "from tqdm.notebook import tqdm\n",
                 "\n",
                 "db_host = os.getenv('DB_HOST')\n",
-                "db_host = '10.80.7.21'\n",
                 "db_name = os.getenv('DB_NAME')\n",
                 "db_user = os.getenv('DB_USER')\n",
                 "db_password = os.getenv('DB_PASSWORD')\n",
@@ -165,12 +164,15 @@
             "outputs": [],
             "source": [
                 "astrocytes_assembly_name = 'Astrocytes'\n",
+                "astrocytes_population_name = 'astrocytes'\n",
+                "connectome_population_name = 'connectome'\n",
                 "be.remove_assembly(astrocytes_assembly_name)\n",
                 "astrocytes_assembly = be.add_assembly(astrocytes_assembly_name)\n",
                 "astrocytes_model = be.add_astrocytes(\n",
                 "    assembly_name=astrocytes_assembly_name,\n",
-                "    population_name=vasculature_population_name,\n",
+                "    population_name=astrocytes_population_name,\n",
                 "    vasculature_population_name=vasculature_population_name,\n",
+                "    connectome_population_name=connectome_population_name,\n",
                 "    radius_multiplier=0.5,\n",
                 "    realism_level=be.morphology_realism_level.ALL,\n",
                 "    generate_internals=True, load_somas=True, load_dendrites=True,\n",
@@ -191,7 +193,7 @@
                 "acetylcholin_path = os.path.join(pdb_folder, 'neuromodulation', 'acetylcholin.pdb')\n",
                 "\n",
                 "def add_acetylcholin(radius, nb_molecules, radius_multiplier, frame=0):\n",
-                "    protein_representation = be.REPRESENTATION_ATOMS\n",
+                "    protein_representation = be.protein_representation.ATOMS\n",
                 "\n",
                 "    acetylcholin_assembly_name = 'Acetylcholin'\n",
                 "    acetylcholin_name = 'Acetylcholin'\n",
@@ -210,7 +212,7 @@
                 "    )\n",
                 "    volume = Volume(\n",
                 "        name=acetylcholin_assembly_name,\n",
-                "        shape=be.ASSEMBLY_SHAPE_FILLED_SPHERE,\n",
+                "        shape=be.assembly_shape.FILLED_SPHERE,\n",
                 "        shape_params=Vector3(radius, 0.0, 0.0),\n",
                 "        protein=acetylcholin)\n",
                 "    be.add_volume(\n",
@@ -258,7 +260,7 @@
                 "\n",
                 "    for material_id in material_ids:\n",
                 "        mid = material_id % palette_size\n",
-                "        if mid == be.NEURON_MATERIAL_SYNAPSE:\n",
+                "        if mid == [be.neuron_material.AFFERENT_SYNAPSE, be.neuron_material.EFFERENT_SYNAPSE]:\n",
                 "            colors.append(palette[0])\n",
                 "            opacities.append(1.0)\n",
                 "            shading_modes.append(shading_mode)\n",
@@ -560,9 +562,9 @@
             "name": "python",
             "nbconvert_exporter": "python",
             "pygments_lexer": "ipython3",
-            "version": "3.8.10"
+            "version": "3.10.12"
         }
     },
     "nbformat": 4,
     "nbformat_minor": 5
-}
+}

bioexplorer/pythonsdk/notebooks/neuromodulation/BioExplorer_neuronmodulation_full_movie.ipynb

@@ -235,12 +235,15 @@
             "outputs": [],
             "source": [
                 "astrocytes_assembly_name = 'Astrocytes'\n",
+                "astrocytes_population_name = 'astrocytes'\n",
+                "connectome_population_name = 'connectome'\n",
                 "be.remove_assembly(astrocytes_assembly_name)\n",
                 "astrocytes_assembly = be.add_assembly(astrocytes_assembly_name)\n",
                 "astrocytes_model = be.add_astrocytes(\n",
                 "    assembly_name=astrocytes_assembly_name,\n",
-                "    population_name=vasculature_population_name,\n",
+                "    population_name=astrocytes_population_name,\n",
                 "    vasculature_population_name=vasculature_population_name,\n",
+                "    connectome_population_name=connectome_population_name,\n",
                 "    radius_multiplier=0.5,\n",
                 "    realism_level=be.morphology_realism_level.ALL,\n",
                 "    generate_internals=True, load_somas=True, load_dendrites=True,\n",
@@ -323,13 +326,13 @@
                 "\n",
                 "    for material_id in material_ids:\n",
                 "        mid = material_id % palette_size\n",
-                "        if mid == be.NEURON_MATERIAL_SYNAPSE:\n",
+                "        if mid in [be.neuron_material.AFFERENT_SYNAPSE, be.neuron_material.EFFERENT_SYNAPSE]:\n",
                 "            colors.append(palette[1])\n",
                 "            opacities.append(1.0)\n",
                 "            shading_modes.append(shading_mode)\n",
                 "            glossinesses.append(glossiness)\n",
                 "            specular_exponents.append(5.0)\n",
-                "        elif mid in [be.NEURON_MATERIAL_VARICOSITY]:\n",
+                "        elif mid in [be.neuron_material.VARICOSITY]:\n",
                 "            colors.append(palette[min(2, palette_size-1)])\n",
                 "            opacities.append(1.0)\n",
                 "            shading_modes.append(shading_mode)\n",
@@ -630,9 +633,9 @@
             "name": "python",
             "nbconvert_exporter": "python",
             "pygments_lexer": "ipython3",
-            "version": "3.8.10"
+            "version": "3.10.12"
         }
     },
     "nbformat": 4,
     "nbformat_minor": 5
-}
+}