minor changes + include spikes report in write_reports()

Author: ilkilic

bluecellulab/circuit_simulation.py

@@ -812,6 +812,7 @@ def write_reports(self):
                     )
                 compartment_sets = self.circuit_access.config.get_compartment_sets()
                 write_compartment_report(
+                    report_name=report_name,
                     output_path=output_path,
                     cells=self.cells,
                     report_cfg=report_cfg,
@@ -827,13 +828,16 @@ def write_reports(self):
                         "for node-based section recording (must be 'center' or 'all')."
                     )
                 write_compartment_report(
+                    report_name=report_name,
                     output_path=output_path,
                     cells=self.cells,
                     report_cfg=report_cfg,
                     source_sets=node_sets,
                     source_type="node_set"
                 )
 
+        self.write_spike_report()
+
     def write_spike_report(self):
         """Collect and write in-memory recorded spike times to a SONATA HDF5
         file, grouped by population as required by the SONATA specification."""

bluecellulab/simulation/report.py

@@ -18,6 +18,7 @@
 import h5py
 from typing import List
 import numpy as np
+import os
 
 from bluecellulab.tools import resolve_segments, resolve_source_nodes
 from bluecellulab.cell.cell_dict import CellDict
@@ -58,14 +59,20 @@ def configure_all_reports(cells, simulation_config):
             source_type = "compartment_set"
             source_sets = simulation_config.get_compartment_sets()
             source_name = report_cfg.get("compartments")
+            if not source_name:
+                logger.warning(f"Report '{report_name}' does not specify a node set in 'compartments' for {source_type}.")
+                continue
         else:
             source_type = "node_set"
             source_sets = simulation_config.get_node_sets()
             source_name = report_cfg.get("cells")
+            if not source_name:
+                logger.warning(f"Report '{report_name}' does not specify a node set in 'cells' for {source_type}.")
+                continue
 
         source = source_sets.get(source_name)
         if not source:
-            logger.warning(f"{source_type.title()} '{source_name}' not found for report '{report_name}'")
+            logger.warning(f"{source_type.title()} '{source_name}' not found for report '{report_name}', skipping recording.")
             continue
 
         population = source["population"]
@@ -79,6 +86,7 @@ def configure_all_reports(cells, simulation_config):
 
 
 def write_compartment_report(
+    report_name: str,
     output_path: str,
     cells: CellDict,
     report_cfg: dict,
@@ -112,7 +120,8 @@ def write_compartment_report(
     source_name = report_cfg.get("cells") if source_type == "node_set" else report_cfg.get("compartments")
     source = source_sets.get(source_name)
     if not source:
-        raise ValueError(f"{source_type} '{source_name}' not found.")
+        logger.warning(f"{source_type.title()} '{source_name}' not found for report '{report_name}', skipping write.")
+        return
 
     population = source["population"]
 
@@ -201,6 +210,7 @@ def write_sonata_spikes(f_name: str, spikes_dict: dict[int, np.ndarray], populat
     node_ids_sorted = np.array(all_node_ids, dtype=np.uint64)[sorted_indices]
     timestamps_sorted = np.array(all_timestamps, dtype=np.float64)[sorted_indices]
 
+    os.makedirs(os.path.dirname(f_name), exist_ok=True)
     with h5py.File(f_name, 'a') as f:  # 'a' to allow multiple writes
         spikes_group = f.require_group("spikes")
         if population in spikes_group:

examples/2-sonata-network/sonata-network.ipynb

@@ -943,16 +943,14 @@
     "\n",
     "After running the simulation, results can be saved in SONATA format.\n",
     "\n",
-    "Calling `sim.write_spike_report()` will store all spike events in a structured `.h5` file, grouped by population.\n",
+    "To write the reports defined in the simulation config (e.g. soma report) and the spike report, use `sim.write_reports()`. \n",
     "\n",
-    "To write the reports defined in the simulation config (e.g. soma report), use `sim.write_reports()`. \n",
-    "\n",
-    "Both reports are saved in the directory specified by the output_dir field in the output section of the simulation configuration file."
+    "Reports are saved in the directory specified by the output_dir field in the output section of the simulation configuration file."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -964,7 +962,6 @@
     }
    ],
    "source": [
-    "sim.write_spike_report()\n",
     "sim.write_reports()"
    ]
   }