Reduce required synapse configuration for h5type creation

GazzolaLab · Oct 27, 2023 · 1a1bb08 · 1a1bb08
1 parent 9815199
commit 1a1bb08
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Showing 2 changed files with 9 additions and 5 deletions.
diff --git a/src/miv_simulator/interface/h5_types.py b/src/miv_simulator/interface/h5_types.py
@@ -3,15 +3,18 @@
 from miv_simulator import config
 from mpi4py import MPI
 from miv_simulator.utils import io as io_utils, from_yaml
-from typing import Dict
+from typing import Dict, List
 
 
 class H5Types(Component):
     class Config(BaseModel):
         model_config = ConfigDict(extra="forbid")
 
         cell_distributions: config.CellDistributions = Field("???")
-        synapses: config.Synapses = Field("???")
+        projections: Dict[
+            config.PostSynapticPopulationName,
+            List[config.PreSynapticPopulationName],
+        ] = Field("???")
 
     def config_from_file(self, filename: str) -> Dict:
         return from_yaml(filename)
@@ -25,6 +28,9 @@ def __call__(self) -> None:
             io_utils.create_neural_h5(
                 self.output_filepath,
                 self.config.cell_distributions,
-                self.config.synapses,
+                synapses={
+                    post: {pre: True for pre in v}
+                    for post, v in self.config.projections.items()
+                },
             )
         MPI.COMM_WORLD.barrier()
diff --git a/src/miv_simulator/interface/network_architecture.py b/src/miv_simulator/interface/network_architecture.py
@@ -31,7 +31,6 @@ class Config(BaseModel):
 
         filepath: str = Field("???")
         cell_distributions: config.CellDistributions = Field("???")
-        synapses: config.Synapses = Field("???")
         layer_extents: config.LayerExtents = Field("???")
         rotation: config.Rotation = (0.0, 0.0, 0.0)
         cell_constraints: config.CellConstraints = {}
@@ -123,7 +122,6 @@ def generate_connections(self, version=None, uses=None):
             [
                 {
                     "filepath": self.config.filepath,
-                    "synapses": self.config.synapses,
                     "coordinates_namespace": self.config.coordinate_namespace,
                 }
             ]