From 3187c76d32e00969c798fa08bfa94338e7bb8bb2 Mon Sep 17 00:00:00 2001
From: Ivan Raikov <ivan.g.raikov@gmail.com>
Date: Wed, 21 Aug 2024 18:41:47 -0500
Subject: [PATCH] support for configurable coordinates namespace

---
 src/miv_simulator/env.py     |  2 ++
 src/miv_simulator/network.py | 12 ++++++------
 src/scripts/run_network.py   |  7 +++++++
 3 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/src/miv_simulator/env.py b/src/miv_simulator/env.py
index 3a69165..d6ae557 100644
--- a/src/miv_simulator/env.py
+++ b/src/miv_simulator/env.py
@@ -94,6 +94,7 @@ def __init__(
         spike_input_path: None = None,
         spike_input_namespace: None = None,
         spike_input_attr: None = None,
+        coordinates_namespace: str = "Coordinates",
         cleanup: bool = True,
         cache_queries: bool = False,
         profile_memory: bool = False,
@@ -288,6 +289,7 @@ def __init__(
             if "Origin" in self.geometry["Parametric Surface"]:
                 self.parse_origin_coords()
 
+        self.coordinates_ns = coordinates_namespace
         self.celltypes = self.model_config["Cell Types"]
         self.cell_attribute_info = {}
         self.phenotype_dict = {}
diff --git a/src/miv_simulator/network.py b/src/miv_simulator/network.py
index 82a5a49..c499ae5 100644
--- a/src/miv_simulator/network.py
+++ b/src/miv_simulator/network.py
@@ -1022,7 +1022,7 @@ def make_cells(env: Env) -> None:
             del trees
 
         elif (pop_name in env.cell_attribute_info) and (
-            "Coordinates" in env.cell_attribute_info[pop_name]
+            env.coordinates_ns in env.cell_attribute_info[pop_name]
         ):
             if rank == 0:
                 logger.info(
@@ -1033,7 +1033,7 @@ def make_cells(env: Env) -> None:
                 cell_attr_dict = scatter_read_cell_attributes(
                     data_file_path,
                     pop_name,
-                    namespaces=["Coordinates"],
+                    namespaces=[env.coordinates_ns],
                     comm=env.comm,
                     io_size=env.io_size,
                     return_type="tuple",
@@ -1042,7 +1042,7 @@ def make_cells(env: Env) -> None:
                 cell_attr_dict = scatter_read_cell_attributes(
                     data_file_path,
                     pop_name,
-                    namespaces=["Coordinates"],
+                    namespaces=[env.coordinates_ns],
                     node_allocation=env.node_allocation,
                     comm=env.comm,
                     io_size=env.io_size,
@@ -1053,7 +1053,7 @@ def make_cells(env: Env) -> None:
                     f"*** Done reading coordinates for population {pop_name}"
                 )
 
-            coords_iter, coords_attr_info = cell_attr_dict["Coordinates"]
+            coords_iter, coords_attr_info = cell_attr_dict[env.coordinates_ns]
 
             x_index = coords_attr_info.get("X Coordinate", None)
             y_index = coords_attr_info.get("Y Coordinate", None)
@@ -1221,7 +1221,7 @@ def make_cell_selection(env):
                 num_cells += 1
 
         elif (pop_name in env.cell_attribute_info) and (
-            "Coordinates" in env.cell_attribute_info[pop_name]
+            env.coordinates_ns in env.cell_attribute_info[pop_name]
         ):
             if rank == 0:
                 logger.info(
@@ -1232,7 +1232,7 @@ def make_cell_selection(env):
                 data_file_path,
                 pop_name,
                 selection=gid_range,
-                namespace="Coordinates",
+                namespace=env.coordinates_ns,
                 comm=env.comm,
                 return_type="tuple",
             )
diff --git a/src/scripts/run_network.py b/src/scripts/run_network.py
index 8ac2d93..e75e98a 100644
--- a/src/scripts/run_network.py
+++ b/src/scripts/run_network.py
@@ -200,6 +200,12 @@ def mpi_excepthook(type, value, traceback):
     type=str,
     help="attribute name for input spikes when cell selection is specified",
 )
+@click.option(
+    "--coordinates-namespace",
+    required=False,
+    type=str,
+    help="namespace for coordinates when cells without morphologies are instantiated",
+)
 @click.option("--dt", type=float, default=0.025, help="")
 @click.option(
     "--ldbal",
@@ -268,6 +274,7 @@ def main(
     spike_input_path,
     spike_input_namespace,
     spike_input_attr,
+    coordinates_namespace,
     dt,
     ldbal,
     lptbal,