SONATA update: expect synapse_replay files as h5

bluecellulab/circuit/simulation_access.py

@@ -18,6 +18,7 @@
 from pathlib import Path
 from typing import Optional, Protocol
 
+import h5py
 import pandas as pd
 
 from bluecellulab.circuit.config import SimulationConfig, SonataSimulationConfig
@@ -172,12 +173,14 @@ def get_spikes(self) -> dict[CellId, np.ndarray]:
 
 def get_synapse_replay_spikes(f_name: str) -> dict:
     """Read the .dat file containing the spike replays."""
-    data = np.genfromtxt(f_name, skip_header=1)
-    spikes = pd.DataFrame(data=data, columns=["t", "node_id"]).astype({"node_id": int})
-    # subtract 1 from all node_ids to make them 0-based
-    # source: https://sonata-extension.readthedocs.io/
-    # en/latest/blueconfig-projection-example.html#dat-spike-files
-    spikes["node_id"] -= 1
+    with h5py.File(f_name, 'r') as f:
+        # Access the timestamps and node_ids datasets
+        timestamps = f['/spikes/All/timestamps'][:]
+        node_ids = f['/spikes/All/node_ids'][:]
+
+        spikes = pd.DataFrame(data={'t': timestamps, 'node_id': node_ids})
+        spikes = spikes.astype({"node_id": int})
+
     if (spikes["t"] < 0).any():
         logger.warning("Found negative spike times... Clipping them to 0")
         spikes["t"].clip(lower=0., inplace=True)

pyproject.toml

@@ -36,6 +36,7 @@ dependencies = [
     "pydantic>=2.5.2,<3.0.0",
     "typing-extensions>=4.8.0",
     "networkx>=3.1",
+    "h5py>=3.11.0",
 ]
 requires-python = ">=3.8"
 

tests/examples/sonata_unit_test_sims/synapse_replay/simulation_config.json

@@ -25,7 +25,7 @@
       "delay": 0.0,
       "duration": 300.0,
       "module": "synapse_replay",
-      "spike_file": "tests/examples/sonata_unit_test_sims/synapse_replay/synapse_replay.dat"
+      "spike_file": "tests/examples/sonata_unit_test_sims/synapse_replay/synapse_replay.h5"
       }
   },
   "connection_overrides": [

tests/test_circuit/test_simulation_access.py

@@ -85,7 +85,7 @@ def test_get_spikes(self):
 def test_get_synapse_replay_spikes():
     """.Test get_synapse_replay_spikes."""
     res = get_synapse_replay_spikes(
-        parent_dir / "data" / "synapse_replay_file" / "spikes.dat"
+        parent_dir / "data" / "synapse_replay_file" / "spikes.h5"
     )
     assert set(res.keys()) == {5382}
     assert res[5382].tolist() == [1500.0, 2000.0, 2500.0]

tox.ini

@@ -15,7 +15,6 @@ deps =
     pytest-timeout>=2.1.0
     pytest-xdist>=3.3.1  # multiprocessing
     pytest-forked>=1.6.0  # isolation
-    libsonata<=0.1.25  # 0.1.26 supports h5 synapse_replay only, some of our tests atm use .dat
 download = true
 allowlist_externals =
     make