Rename architecture interface to distinguish from network

GazzolaLab · Mar 25, 2024 · b51ef65 · b51ef65
1 parent 1069fe2
commit b51ef65
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Showing 3 changed files with 17 additions and 15 deletions.
diff --git a/...mulator/interface/network_architecture.py → src/miv_simulator/interface/architecture.py b/...mulator/interface/network_architecture.py → src/miv_simulator/interface/architecture.py
@@ -23,7 +23,7 @@ def _join(*args):
     return uses
 
 
-class NetworkArchitecture(Component):
+class Architecture(Component):
     """Creates the network architecture by generating the soma coordinates within specified layer geometry."""
 
     class Config(BaseModel):

diff --git a/src/miv_simulator/interface/network.py b/src/miv_simulator/interface/network.py
@@ -15,7 +15,9 @@ class Config(BaseModel):
         morphology_path: str = "./morphology"
 
     def launch(self):
-        config = Config.from_yaml(self.config.config_filepath)
+        self.source_config = config = Config.from_yaml(
+            self.config.config_filepath
+        )
 
         self.h5_types = get(
             "miv_simulator.interface.h5_types",
@@ -27,8 +29,8 @@ def launch(self):
             ],
         ).launch()
 
-        self.network = get(
-            "miv_simulator.interface.network_architecture",
+        self.architecture = get(
+            "miv_simulator.interface.architecture",
             [
                 {
                     "filepath": self.h5_types.output_filepath,
@@ -39,10 +41,10 @@ def launch(self):
             uses=self.h5_types,
         ).launch()
 
-        self.distances = self.network.measure_distances().launch()
+        self.distances = self.architecture.measure_distances().launch()
 
         self.synapse_forest = {
-            population: self.network.generate_synapse_forest(
+            population: self.architecture.generate_synapse_forest(
                 {
                     "population": population,
                     "morphology": os.path.join(
@@ -55,7 +57,7 @@ def launch(self):
         }
 
         self.synapses = {
-            population: self.network.distribute_synapses(
+            population: self.architecture.distribute_synapses(
                 {
                     "forest_filepath": self.synapse_forest[
                         population
@@ -74,7 +76,7 @@ def launch(self):
         }
 
         self.connections = {
-            population: self.network.generate_connections(
+            population: self.architecture.generate_connections(
                 {
                     "synapses": config.synapses,
                     "forest_filepath": self.synapses[
@@ -93,7 +95,7 @@ def launch(self):
         self.neural_h5 = get(
             "miv_simulator.interface.neuroh5_graph",
             uses=[
-                self.network,
+                self.architecture,
                 self.distances,
                 *self.synapse_forest.values(),
                 *self.synapses.values(),

diff --git a/src/miv_simulator/interface/neuroh5_graph.py b/src/miv_simulator/interface/neuroh5_graph.py
@@ -21,16 +21,16 @@ def graph(self) -> None:
 
     def __call__(self) -> None:
         print("Merging H5 data")
-        self.network = None
+        self.architecture = None
         self.distances = None
         self.synapses = {}
         self.synapse_forest = {}
         self.connections = {}
         populations = []
         for u in self.uses:
             name = u.module.replace("miv_simulator.interface.", "")
-            if name == "network_architecture":
-                self.network = u
+            if name == "architecture":
+                self.architecture = u
             elif name == "distances":
                 self.distances = u
             elif name == "connections":
@@ -60,9 +60,9 @@ def __call__(self) -> None:
                     )
                 self.synapses[u.config.population] = u
 
-        self.graph.import_h5types(self.network.config.filepath)
+        self.graph.import_h5types(self.architecture.config.filepath)
         self.graph.import_soma_coordinates(
-            self.network.config.filepath,
+            self.architecture.config.filepath,
             populations=list(populations) + ["STIM"],
         )
         for p in self.synapse_forest.keys():
@@ -80,7 +80,7 @@ def __call__(self) -> None:
         self.save_file(
             "graph.json",
             {
-                "network": self.network.serialize(),
+                "architecture": self.architecture.serialize(),
                 "distances": self.distances.serialize(),
                 "connections": {
                     k: v.serialize() for k, v in self.connections.items()