Move spine_morphologies_dir to edge population

mgeplf · mgeplf · commit c995b87b8e0a · 2024-10-17T11:08:40.000+02:00
* per BlueBrain/sonata-extension#62
diff --git a/include/bbp/sonata/config.h b/include/bbp/sonata/config.h
@@ -92,11 +92,6 @@ struct SONATA_API NodePopulationProperties: public CommonPopulationProperties {
      * mandatory.
      */
     nonstd::optional<std::string> microdomainsFile{nonstd::nullopt};
-
-    /**
-     * Path to the directory containing the dendritic spine morphologies.
-     */
-    nonstd::optional<std::string> spineMorphologiesDir{nonstd::nullopt};
 };
 
 /**
@@ -112,6 +107,11 @@ struct SONATA_API EdgePopulationProperties: public CommonPopulationProperties {
      * Path to spatial_segment_index
      */
     nonstd::optional<std::string> endfeetMeshesFile{nonstd::nullopt};
+
+    /**
+     * Path to the directory containing the dendritic spine morphologies.
+     */
+    nonstd::optional<std::string> spineMorphologiesDir{nonstd::nullopt};
 };
 
 /**
diff --git a/python/bindings.cpp b/python/bindings.cpp
@@ -570,10 +570,7 @@ PYBIND11_MODULE(_libsonata, m) {
                       DOC_NODE_POPULATION_PROPERTIES(vasculatureMesh))
         .def_readonly("microdomains_file",
                       &NodePopulationProperties::microdomainsFile,
-                      DOC_NODE_POPULATION_PROPERTIES(microdomainsFile))
-        .def_readonly("spine_morphologies_dir",
-                      &NodePopulationProperties::spineMorphologiesDir,
-                      DOC_NODE_POPULATION_PROPERTIES(spineMorphologiesDir));
+                      DOC_NODE_POPULATION_PROPERTIES(microdomainsFile));
 
     py::class_<EdgePopulationProperties, CommonPopulationProperties>(
         m, "EdgePopulationProperties", "Stores edge population-specific network information")
@@ -582,7 +579,10 @@ PYBIND11_MODULE(_libsonata, m) {
                       DOC_EDGE_POPULATION_PROPERTIES(spatialSynapseIndexDir))
         .def_readonly("endfeet_meshes_file",
                       &EdgePopulationProperties::endfeetMeshesFile,
-                      DOC_EDGE_POPULATION_PROPERTIES(endfeetMeshesFile));
+                      DOC_EDGE_POPULATION_PROPERTIES(endfeetMeshesFile))
+        .def_readonly("spine_morphologies_dir",
+                      &EdgePopulationProperties::spineMorphologiesDir,
+                      DOC_EDGE_POPULATION_PROPERTIES(spineMorphologiesDir));
 
     py::enum_<CircuitConfig::ConfigStatus>(m, "CircuitConfigStatus")
         .value("invalid", CircuitConfig::ConfigStatus::invalid)
diff --git a/python/generated/docstrings.h b/python/generated/docstrings.h
@@ -181,6 +181,8 @@ static const char *__doc_bbp_sonata_EdgePopulationProperties_endfeetMeshesFile =
 
 static const char *__doc_bbp_sonata_EdgePopulationProperties_spatialSynapseIndexDir = R"doc(Path to spatial_synapse_index)doc";
 
+static const char *__doc_bbp_sonata_EdgePopulationProperties_spineMorphologiesDir = R"doc(Path to the directory containing the dendritic spine morphologies.)doc";
+
 static const char *__doc_bbp_sonata_EdgePopulation_EdgePopulation = R"doc()doc";
 
 static const char *__doc_bbp_sonata_EdgePopulation_EdgePopulation_2 = R"doc()doc";
@@ -302,8 +304,6 @@ populations where it is mandatory.)doc";
 
 static const char *__doc_bbp_sonata_NodePopulationProperties_spatialSegmentIndexDir = R"doc(Path to spatial_segment_index)doc";
 
-static const char *__doc_bbp_sonata_NodePopulationProperties_spineMorphologiesDir = R"doc(Path to the directory containing the dendritic spine morphologies.)doc";
-
 static const char *__doc_bbp_sonata_NodePopulationProperties_vasculatureFile =
 R"doc(Path to the .h5 file containing the vasculature morphology. Only for
 vasculature node populations where it is mandatory.)doc";
@@ -833,8 +833,6 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputBase_Module_ornstein_u
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputBase_Module_pulse = R"doc()doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_InputBase_Module_sinusoidal = R"doc()doc";
-
 static const char *__doc_bbp_sonata_SimulationConfig_InputBase_Module_relative_linear = R"doc()doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputBase_Module_relative_ornstein_uhlenbeck = R"doc()doc";
@@ -845,6 +843,8 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputBase_Module_seclamp =
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputBase_Module_shot_noise = R"doc()doc";
 
+static const char *__doc_bbp_sonata_SimulationConfig_InputBase_Module_sinusoidal = R"doc()doc";
+
 static const char *__doc_bbp_sonata_SimulationConfig_InputBase_Module_subthreshold = R"doc()doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputBase_Module_synapse_replay = R"doc()doc";
@@ -913,16 +913,6 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputPulse_representsPhysic
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputPulse_width = R"doc(The length of time each pulse lasts (ms))doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_InputSinusoidal = R"doc()doc";
-
-static const char *__doc_bbp_sonata_SimulationConfig_InputSinusoidal_ampStart = R"doc(The amount of current initially injected (nA))doc";
-
-static const char *__doc_bbp_sonata_SimulationConfig_InputSinusoidal_frequency = R"doc(The frequency of the waveform (Hz))doc";
-
-static const char *__doc_bbp_sonata_SimulationConfig_InputSinusoidal_dt = R"doc(Timestep of generated signal in ms. Default is 0.025 ms)doc";
-
-static const char *__doc_bbp_sonata_SimulationConfig_InputSinusoidal_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
-
 static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeLinear = R"doc()doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeLinear_percentEnd = R"doc(The percentage of a cell's threshold current to inject at the end)doc";
@@ -1014,6 +1004,16 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputShotNoise_reversal = R
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputShotNoise_riseTime = R"doc(The rise time of the bi-exponential shots (ms))doc";
 
+static const char *__doc_bbp_sonata_SimulationConfig_InputSinusoidal = R"doc()doc";
+
+static const char *__doc_bbp_sonata_SimulationConfig_InputSinusoidal_ampStart = R"doc(The peak amplitude of the sinusoid. Given in nA.)doc";
+
+static const char *__doc_bbp_sonata_SimulationConfig_InputSinusoidal_dt = R"doc(Timestep of generated signal in ms. Default is 0.025 ms)doc";
+
+static const char *__doc_bbp_sonata_SimulationConfig_InputSinusoidal_frequency = R"doc(The frequency of the sinusoidal waveform. Given in Hz.)doc";
+
+static const char *__doc_bbp_sonata_SimulationConfig_InputSinusoidal_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
+
 static const char *__doc_bbp_sonata_SimulationConfig_InputSubthreshold = R"doc()doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputSubthreshold_percentLess = R"doc(A percentage adjusted from 100 of a cell's threshold current)doc";
@@ -1334,14 +1334,16 @@ static const char *__doc_bbp_sonata_SpikeReader_Population_getRawArrays = R"doc(
 
 static const char *__doc_bbp_sonata_SpikeReader_Population_getSorting = R"doc(Return the way data are sorted ('none', 'by_id', 'by_time'))doc";
 
-static const char *__doc_bbp_sonata_SpikeReader_Population_getTimes = R"doc(Return (tstart, tstop) of the population)doc";
-
 static const char *__doc_bbp_sonata_SpikeReader_Population_getTimeUnits = R"doc(Return the unit of time)doc";
 
+static const char *__doc_bbp_sonata_SpikeReader_Population_getTimes = R"doc(Return (tstart, tstop) of the population)doc";
+
 static const char *__doc_bbp_sonata_SpikeReader_Population_sorting = R"doc()doc";
 
 static const char *__doc_bbp_sonata_SpikeReader_Population_spike_times = R"doc()doc";
 
+static const char *__doc_bbp_sonata_SpikeReader_Population_time_units = R"doc()doc";
+
 static const char *__doc_bbp_sonata_SpikeReader_Population_tstart = R"doc()doc";
 
 static const char *__doc_bbp_sonata_SpikeReader_Population_tstop = R"doc()doc";
diff --git a/python/tests/test_config.py b/python/tests/test_config.py
@@ -68,6 +68,10 @@ def test_get_population_properties(self):
 
         self.assertEqual(edge_prop.types_path, '')
         self.assertTrue(edge_prop.elements_path.endswith('tests/data/edges1.h5'))
+        self.assertTrue(edge_prop.spine_morphologies_dir.endswith('spine_morphologies_dir_edges-AC'))
+
+        edge_prop = self.config.edge_population_properties('edges-AB')
+        self.assertTrue(edge_prop.spine_morphologies_dir.endswith('spine_morphologies_dir_component'))
 
     def test_partial(self):
         contents = { "metadata": { "status": "NOT A TYPE" }, }
diff --git a/src/config.cpp b/src/config.cpp
@@ -830,9 +830,6 @@ class CircuitConfig::Parser
             if (!component.microdomainsFile) {
                 component.microdomainsFile = defaultComponents.microdomainsFile;
             }
-            if (!component.spineMorphologiesDir) {
-                component.spineMorphologiesDir = defaultComponents.spineMorphologiesDir;
-            }
         }
     }
 
@@ -846,6 +843,9 @@ class CircuitConfig::Parser
             if (!component.endfeetMeshesFile) {
                 component.endfeetMeshesFile = defaultComponents.endfeetMeshesFile;
             }
+            if (!component.spineMorphologiesDir) {
+                component.spineMorphologiesDir = defaultComponents.spineMorphologiesDir;
+            }
         }
     }
 
@@ -926,8 +926,6 @@ class CircuitConfig::Parser
             popProperties.vasculatureFile = getOptionalJSONPath(popData, "vasculature_file");
             popProperties.vasculatureMesh = getOptionalJSONPath(popData, "vasculature_mesh");
             popProperties.microdomainsFile = getOptionalJSONPath(popData, "microdomains_file");
-            popProperties.spineMorphologiesDir = getOptionalJSONPath(popData,
-                                                                     "spine_morphologies_dir");
             });
     }
 
@@ -939,6 +937,8 @@ class CircuitConfig::Parser
             [&](EdgePopulationProperties& popProperties, const nlohmann::json& popData) {
             popProperties.spatialSynapseIndexDir = getJSONPath(popData, "spatial_synapse_index_dir");
             popProperties.endfeetMeshesFile = getOptionalJSONPath(popData, "endfeet_meshes_file");
+            popProperties.spineMorphologiesDir = getOptionalJSONPath(popData,
+                                                                     "spine_morphologies_dir");
             });
     }
 
diff --git a/tests/data/config/circuit_config.json b/tests/data/config/circuit_config.json
@@ -9,7 +9,8 @@
     "morphologies_dir": "$COMPONENT_DIR/morphologies",
     "biophysical_neuron_models_dir": "$COMPONENT_DIR/biophysical_neuron_models",
     "vasculature_file": "$COMPONENT_DIR/some_file",
-    "vasculature_mesh": "$COMPONENT_DIR/some_file"
+    "vasculature_mesh": "$COMPONENT_DIR/some_file",
+    "spine_morphologies_dir": "$COMPONENT_DIR/spine_morphologies_dir_component"
   },
   "node_sets_file": "$BASE_DIR/node_sets.json",
   "networks": {
@@ -33,7 +34,8 @@
         "populations": {
             "edges-AB": {},
             "edges-AC": {
-                "spatial_synapse_index_dir": "$COMPONENT_DIR/spatial_synapse_index_dir"
+                "spatial_synapse_index_dir": "$COMPONENT_DIR/spatial_synapse_index_dir",
+                "spine_morphologies_dir": "$COMPONENT_DIR/spine_morphologies_dir_edges-AC"
             }
         }
       }

Original file line number	Diff line number	Diff line change
`@@ -830,9 +830,6 @@ class CircuitConfig::Parser`
`830`	`830`	`if (!component.microdomainsFile) {`
`831`	`831`	`component.microdomainsFile = defaultComponents.microdomainsFile;`
`832`	`832`	`}`
`833`		`- if (!component.spineMorphologiesDir) {`
`834`		`- component.spineMorphologiesDir = defaultComponents.spineMorphologiesDir;`
`835`		`- }`
`836`	`833`	`}`
`837`	`834`	`}`
`838`	`835`
`@@ -846,6 +843,9 @@ class CircuitConfig::Parser`
`846`	`843`	`if (!component.endfeetMeshesFile) {`
`847`	`844`	`component.endfeetMeshesFile = defaultComponents.endfeetMeshesFile;`
`848`	`845`	`}`
	`846`	`+ if (!component.spineMorphologiesDir) {`
	`847`	`+ component.spineMorphologiesDir = defaultComponents.spineMorphologiesDir;`
	`848`	`+ }`
`849`	`849`	`}`
`850`	`850`	`}`
`851`	`851`
`@@ -926,8 +926,6 @@ class CircuitConfig::Parser`
`926`	`926`	`popProperties.vasculatureFile = getOptionalJSONPath(popData, "vasculature_file");`
`927`	`927`	`popProperties.vasculatureMesh = getOptionalJSONPath(popData, "vasculature_mesh");`
`928`	`928`	`popProperties.microdomainsFile = getOptionalJSONPath(popData, "microdomains_file");`
`929`		`- popProperties.spineMorphologiesDir = getOptionalJSONPath(popData,`
`930`		`- "spine_morphologies_dir");`
`931`	`929`	`});`
`932`	`930`	`}`
`933`	`931`
`@@ -939,6 +937,8 @@ class CircuitConfig::Parser`
`939`	`937`	`[&](EdgePopulationProperties& popProperties, const nlohmann::json& popData) {`
`940`	`938`	`popProperties.spatialSynapseIndexDir = getJSONPath(popData, "spatial_synapse_index_dir");`
`941`	`939`	`popProperties.endfeetMeshesFile = getOptionalJSONPath(popData, "endfeet_meshes_file");`
	`940`	`+ popProperties.spineMorphologiesDir = getOptionalJSONPath(popData,`
	`941`	`+ "spine_morphologies_dir");`
`942`	`942`	`});`
`943`	`943`	`}`
`944`	`944`
Original file line number	Diff line number	Diff line change
`@@ -9,7 +9,8 @@`
`9`	`9`	`"morphologies_dir": "$COMPONENT_DIR/morphologies",`
`10`	`10`	`"biophysical_neuron_models_dir": "$COMPONENT_DIR/biophysical_neuron_models",`
`11`	`11`	`"vasculature_file": "$COMPONENT_DIR/some_file",`
`12`		`- "vasculature_mesh": "$COMPONENT_DIR/some_file"`
	`12`	`+ "vasculature_mesh": "$COMPONENT_DIR/some_file",`
	`13`	`+ "spine_morphologies_dir": "$COMPONENT_DIR/spine_morphologies_dir_component"`
`13`	`14`	`},`
`14`	`15`	`"node_sets_file": "$BASE_DIR/node_sets.json",`
`15`	`16`	`"networks": {`
`@@ -33,7 +34,8 @@`
`33`	`34`	`"populations": {`
`34`	`35`	`"edges-AB": {},`
`35`	`36`	`"edges-AC": {`
`36`		`- "spatial_synapse_index_dir": "$COMPONENT_DIR/spatial_synapse_index_dir"`
	`37`	`+ "spatial_synapse_index_dir": "$COMPONENT_DIR/spatial_synapse_index_dir",`
	`38`	`+ "spine_morphologies_dir": "$COMPONENT_DIR/spine_morphologies_dir_edges-AC"`
`37`	`39`	`}`
`38`	`40`	`}`
`39`	`41`	`}`