Merge pull request #1594 from alejoe91/open-ephys-partial

OpenEphysBinary: Skip streams if folder doesn't exist

Author: zm711

neo/rawio/openephysbinaryrawio.py

@@ -12,6 +12,7 @@
 import os
 import json
 from pathlib import Path
+from warnings import warn
 
 import numpy as np
 
@@ -570,6 +571,15 @@ def explore_folder(dirname, experiment_names=None):
                         stream_name = node_name + "#" + oe_stream_name
                     else:
                         stream_name = oe_stream_name
+
+                    # skip streams if folder is on oebin, but doesn't exist
+                    if not (recording_folder / "continuous" / info["folder_name"]).is_dir():
+                        warn(
+                            f"For {recording_folder} the folder continuous/{info['folder_name']} is missing. "
+                            f"Skipping {stream_name} continuous stream."
+                        )
+                        continue
+
                     raw_filename = recording_folder / "continuous" / info["folder_name"] / "continuous.dat"
 
                     # Updates for OpenEphys v0.6:
@@ -604,6 +614,14 @@ def explore_folder(dirname, experiment_names=None):
                     else:
                         stream_name = oe_stream_name
 
+                    # skip streams if folder is on oebin, but doesn't exist
+                    if not (recording_folder / "events" / info["folder_name"]).is_dir():
+                        warn(
+                            f"For {recording_folder} the folder events/{info['folder_name']} is missing. "
+                            f"Skipping {stream_name} event stream."
+                        )
+                        continue
+
                     event_stream = info.copy()
                     for name in _possible_event_stream_names:
                         npy_filename = root / "events" / info["folder_name"] / f"{name}.npy"

neo/test/rawiotest/test_openephysbinaryrawio.py

@@ -13,6 +13,7 @@ class TestOpenEphysBinaryRawIO(BaseTestRawIO, unittest.TestCase):
         "openephysbinary/v0.5.x_two_nodes",
         "openephysbinary/v0.6.x_neuropixels_multiexp_multistream",
         "openephysbinary/v0.6.x_neuropixels_with_sync",
+        "openephysbinary/v0.6.x_neuropixels_missing_folders"
     ]
 
     def test_sync(self):
@@ -48,6 +49,14 @@ def test_no_sync(self):
             )
             rawio_no_sync.parse_header()
 
+    def test_missing_folders(self):
+        # missing folders should raise an error
+        with self.assertWarns(UserWarning):
+            rawio = OpenEphysBinaryRawIO(
+                self.get_local_path("openephysbinary/v0.6.x_neuropixels_missing_folders"), load_sync_channel=False
+            )
+            rawio.parse_header()
+
 
 if __name__ == "__main__":
     unittest.main()