Cherry-pick various fixes from optimization branch

src/miv_simulator/config.py

@@ -215,19 +215,20 @@ class Synapse(BaseModel):
     layers: conlist(LayersDefOrStr)
     proportions: conlist(float)
     mechanisms: Dict[SynapseMechanismsLiteral, Mechanism]
+    contacts: int = 1
 
 
 def _origin_value_to_callable(value: Union[str, float]) -> Callable:
-    if isinstance(value, (float, int)):
+    if isinstance(value, float):
         return lambda _: value
 
     return getattr(np, value)
 
 
 class Origin(BaseModel):
-    U: Union[str, float, int]
-    V: Union[str, float, int]
-    L: Union[str, float, int]
+    U: Union[str, float]
+    V: Union[str, float]
+    L: Union[str, float]
 
     def as_spec(self):
         return {
@@ -245,7 +246,6 @@ class ParametricSurface(BaseModel):
 
 class CellType(BaseModel):
     template: str
-    mechanism: Union[str, Dict, None]
     synapses: Dict[
         Literal["density"],
         Dict[

src/miv_simulator/connections.py

@@ -611,7 +611,7 @@ def generate_uv_distance_connections(
             projection_config[source_population].layers,
             projection_config[source_population].sections,
             projection_config[source_population].proportions,
-            projection_config[source_population].get("contacts", 1),
+            projection_config[source_population].contacts,
         )
         for source_population in source_populations
     }

src/miv_simulator/geometry/geometry.py

@@ -601,7 +601,7 @@ def distance_interpolant(
 
     vol_dist = get_volume_distances(
         ip_volume,
-        origin_spec=config.Origin(**origin).as_spec(),
+        origin_spec=origin,
         nsample=n_sample,
         comm=comm,
         alpha_radius=alpha_radius,

src/miv_simulator/interface/distances.py

@@ -42,7 +42,7 @@ def __call__(self):
             cell_distributions=self.config.cell_distributions,
             layer_extents=self.config.layer_extents,
             rotation=self.config.rotation,
-            origin=self.config.origin,
+            origin=config.Origin(**self.config.origin).as_spec(),
             n_sample=self.config.n_sample,
             alpha_radius=self.config.alpha_radius,
             io_size=self.config.io_size,

src/miv_simulator/opto/run.py

@@ -91,7 +91,7 @@ def init_mechanisms(self):
             rho_dict = self.pop_rho_dict[pop_name]
             mech = getattr(h, self.mechanisms[self.model.nStates])
 
-            expProb = self.rho_params["expProb"]
+            expProb = self.rho_params.get("expProb", 1.0)
 
             for gid in gid_set:
                 if not self.pc.gid_exists(gid):

src/miv_simulator/simulator/generate_connections.py

@@ -86,9 +86,6 @@ def generate_distance_connections(
         synapses=env.connection_config,
         axon_extents=env.connection_extents,
         use_coreneuron=env.use_coreneuron,
-        dt=env.dt,
-        tstop=env.tstop,
-        celsius=env.celsius,
         output_filepath=connectivity_path,
         connectivity_namespace=connectivity_namespace,
         coordinates_namespace=coords_namespace,

src/miv_simulator/simulator/generate_network_architecture.py

@@ -7,7 +7,6 @@
 import random
 import sys
 from collections import defaultdict
-import importlib
 
 import h5py
 import numpy as np
@@ -171,7 +170,7 @@ def generate_soma_coordinates(
         layer_extents=env.geometry["Parametric Surface"]["Layer Extents"],
         rotation=env.geometry["Parametric Surface"]["Rotation"],
         cell_distributions=env.geometry["Cell Distribution"],
-        cell_constraints=env.geometry["Cell Constraints"],
+        cell_constraints=env.geometry.get("Cell Constraints", None),
         output_namespace=output_namespace,
         geometry_filepath=geometry_path,
         populations=populations,
@@ -191,7 +190,7 @@ def generate_network_architecture(
     cell_distributions: config.CellDistributions,
     layer_extents: config.LayerExtents,
     rotation: config.Rotation,
-    cell_constraints: config.CellConstraints,
+    cell_constraints: Optional[config.CellConstraints],
     output_namespace: str,
     geometry_filepath: Optional[str],
     populations: Optional[Tuple[str, ...]],
@@ -342,26 +341,6 @@ def generate_network_architecture(
                 if count <= 0:
                     continue
 
-                if layer.startswith("@"):
-                    # generate via callback
-                    module_path, _, obj_name = layer[1:].rpartition(".")
-                    if module_path == "__main__" or module_path == "":
-                        module = sys.modules["__main__"]
-                    else:
-                        module = importlib.import_module(module_path)
-                    callback = getattr(module, obj_name)
-
-                    nodes = callback(count, layer_extents[layer])
-
-                    if not len(nodes) == count:
-                        logger.error(
-                            f"Generator {layer} produced mismatch between actual count {len(nodes)} and configured count {count}"
-                        )
-
-                    xyz_coords_lst.append(nodes.reshape(-1, 3))
-
-                    continue
-
                 alpha = layer_alpha_shapes[layer]
 
                 vert = alpha.points
@@ -604,12 +583,6 @@ def generate_network_architecture(
                 for i in range(delta):
                     for layer, count in pop_layers.items():
                         if count > 0:
-                            if layer.startswith("@"):
-                                logger.warning(
-                                    f"Generator {layer} did not return the specified number of coordinates"
-                                )
-                                continue
-
                             min_extent = layer_extents[layer][0]
                             max_extent = layer_extents[layer][1]
                             coord_u = np.random.uniform(

src/miv_simulator/simulator/measure_distances.py

@@ -42,6 +42,7 @@ def measure_distances_(
     populations,
     resolution,
     nsample,
+    alpha_radius,
     io_size,
     chunk_size,
     value_chunk_size,
@@ -52,15 +53,18 @@ def measure_distances_(
     utils.config_logging(verbose)
     env = Env(comm=MPI.COMM_WORLD, config=config, config_prefix=config_prefix)
 
+    parametric_surface = env.geometry["Parametric Surface"]
     return measure_distances(
         filepath=coords_path,
         geometry_filepath=geometry_path,
         coordinate_namespace=coords_namespace,
         populations=populations,
         cell_distributions=env.geometry["Cell Distribution"],
-        layer_extents=env.geometry["Layer Extents"],
-        rotation=env.geometry["Rotation"],
-        origin=env.geometry["Origin"],
+        layer_extents=parametric_surface["Layer Extents"],
+        rotation=parametric_surface["Rotation"],
+        origin=parametric_surface["Origin"],
+        resolution=resolution,
+        alpha_radius=alpha_radius,
         n_sample=nsample,
         io_size=io_size,
         chunk_size=chunk_size,

src/scripts/measure_distances.py

@@ -36,6 +36,7 @@
 @click.option("--populations", "-i", required=True, multiple=True, type=str)
 @click.option("--resolution", type=(int, int, int), default=(30, 30, 10))
 @click.option("--nsample", type=int, default=1000)
+@click.option("--alpha-radius", type=float, default=100)
 @click.option("--io-size", type=int, default=-1)
 @click.option("--chunk-size", type=int, default=1000)
 @click.option("--value-chunk-size", type=int, default=1000)
@@ -50,6 +51,7 @@ def main(
     populations,
     resolution,
     nsample,
+    alpha_radius,
     io_size,
     chunk_size,
     value_chunk_size,
@@ -64,6 +66,7 @@ def main(
         populations,
         resolution,
         nsample,
+        alpha_radius,
         io_size,
         chunk_size,
         value_chunk_size,