Update read_openephys and add OneBox tests (#4456)

Author: alejoe91

src/spikeinterface/extractors/neoextractors/openephys.py

@@ -315,54 +315,36 @@ def __init__(
 
             # find settings file
             if "#" in stream_name:
-                record_node, oe_stream = stream_name.split("#")
+                record_node, oe_stream_name = stream_name.split("#")
             else:
                 record_node = ""
-                oe_stream = stream_name
-            exp_ids = sorted(list(self.neo_reader.folder_structure[record_node]["experiments"].keys()))
+                oe_stream_name = stream_name
+            node_structure = self.neo_reader.folder_structure[record_node]
+            exp_ids = sorted(list(node_structure["experiments"].keys()))
             if block_index is None:
                 exp_id = exp_ids[0]
             else:
                 exp_id = exp_ids[block_index]
-            rec_ids = sorted(
-                list(self.neo_reader.folder_structure[record_node]["experiments"][exp_id]["recordings"].keys())
-            )
+            rec_ids = sorted(list(node_structure["experiments"][exp_id]["recordings"].keys()))
 
             # do not load probe for NIDQ stream or if load_sync_channel is True
             if "NI-DAQmx" not in stream_name and not load_sync_channel:
-                settings_file = self.neo_reader.folder_structure[record_node]["experiments"][exp_id]["settings_file"]
+                settings_file = node_structure["experiments"][exp_id]["settings_file"]
 
                 if Path(settings_file).is_file():
                     probe = probeinterface.read_openephys(
-                        settings_file=settings_file, stream_name=stream_name, raise_error=False
+                        settings_file=settings_file, stream_name=oe_stream_name, raise_error=False
                     )
                 else:
                     probe = None
 
                 if probe is not None:
-                    # Ensure device channel index corresponds to channel_ids
-                    probe_channel_names = probe.contact_annotations.get("channel_name", None)
-                    if probe_channel_names is not None and not np.array_equal(probe_channel_names, self.channel_ids):
-                        if set(probe_channel_names) == set(self.channel_ids):
-                            device_channel_indices = []
-                            probe_channel_names = list(probe_channel_names)
-                            device_channel_indices = np.zeros(len(self.channel_ids), dtype=int)
-                            for i, ch in enumerate(self.channel_ids):
-                                index_in_probe = probe_channel_names.index(ch)
-                                device_channel_indices[index_in_probe] = i
-                            probe.set_device_channel_indices(device_channel_indices)
-                        else:
-                            warnings.warn(
-                                "Channel names in the probe do not match the channel ids from Neo. "
-                                "Cannot set device channel indices, but this might lead to incorrect probe geometries"
-                            )
-
                     if probe.shank_ids is not None:
                         self.set_probe(probe, in_place=True, group_mode="by_shank")
                     else:
                         self.set_probe(probe, in_place=True)
                     # get inter-sample shifts based on the probe information and mux channels
-                    sample_shifts = get_neuropixels_sample_shifts_from_probe(probe, stream_name=self.stream_name)
+                    sample_shifts = get_neuropixels_sample_shifts_from_probe(probe)
                     if sample_shifts is not None:
                         self.set_property("inter_sample_shift", sample_shifts)
 
@@ -371,7 +353,7 @@ def __init__(
             stream_folders = []
             for segment_index, rec_id in enumerate(rec_ids):
                 stream_folder = (
-                    recording_folder / f"experiment{exp_id}" / f"recording{rec_id}" / "continuous" / oe_stream
+                    recording_folder / f"experiment{exp_id}" / f"recording{rec_id}" / "continuous" / oe_stream_name
                 )
                 stream_folders.append(stream_folder)
                 if load_sync_timestamps:

src/spikeinterface/extractors/neoextractors/spikeglx.py

@@ -94,7 +94,7 @@ def __init__(
                 self.set_probe(probe, in_place=True)
 
             # get inter-sample shifts based on the probe information and mux channels
-            sample_shifts = get_neuropixels_sample_shifts_from_probe(probe, stream_name=self.stream_name)
+            sample_shifts = get_neuropixels_sample_shifts_from_probe(probe)
             if sample_shifts is not None:
                 self.set_property("inter_sample_shift", sample_shifts)
         else:

src/spikeinterface/extractors/neuropixels_utils.py

@@ -4,17 +4,14 @@
 from probeinterface import Probe
 
 
-def get_neuropixels_sample_shifts_from_probe(probe: Probe, stream_name: str = "ap") -> np.ndarray:
+def get_neuropixels_sample_shifts_from_probe(probe: Probe) -> np.ndarray:
     """
     Get the inter-sample shifts for Neuropixels probes based on the probe information.
 
     Parameters
     ----------
     probe : Probe
         The probe object containing channel and ADC information.
-    stream_name : str, default: "ap"
-        The name of the stream for which to calculate the sample shifts.
-        This is used for Neuropixels 1.0 technology to correctly set the number of cycles.
 
     Returns
     -------

src/spikeinterface/extractors/tests/test_neoextractors.py

@@ -6,6 +6,7 @@
 import importlib.util
 
 import pytest
+import numpy as np
 
 from spikeinterface import get_global_dataset_folder
 from spikeinterface.extractors.extractor_classes import (
@@ -121,9 +122,6 @@ class OpenEphysBinaryRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
         ("openephysbinary/v0.5.x_two_nodes", {"stream_id": "0"}),
         ("openephysbinary/v0.5.x_two_nodes", {"stream_id": "1"}),
         ("openephysbinary/v0.6.x_neuropixels_multiexp_multistream", {"stream_id": "0", "block_index": 0}),
-        # TODO: block_indices 1/2 of v0.6.x_neuropixels_multiexp_multistream have a mismatch in the channel names between
-        # the settings files (starting with CH0) and structure.oebin (starting at CH1).
-        # Currently, the extractor will skip remapping to match order in oebin and settings file, raising a warning
         ("openephysbinary/v0.6.x_neuropixels_multiexp_multistream", {"stream_id": "1", "block_index": 1}),
         (
             "openephysbinary/v0.6.x_neuropixels_multiexp_multistream",
@@ -134,8 +132,30 @@ class OpenEphysBinaryRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
             "openephysbinary/v0.6.x_neuropixels_multiexp_multistream",
             {"stream_id": "2", "block_index": 2, "load_sync_timestamps": True},
         ),
+        (
+            "openephysbinary/v0.6.x_onebox_neuropixels",
+            {"stream_name": "Record Node 101#OneBox-100.ProbeA-AP", "block_index": 0},
+        ),
+        (
+            "openephysbinary/v0.6.x_onebox_neuropixels_nontrivial_wiring",
+            {"stream_name": "Record Node 101#OneBox-111.ProbeA", "block_index": 0},
+        ),
     ]
 
+    def test_non_trivial_wiring(self):
+        """
+        Test that we can load the probe information and sample shifts for a one box neuropixels recording with
+        non trivial wiring.
+        """
+        folder_path = local_folder / "openephysbinary/v0.6.x_onebox_neuropixels_nontrivial_wiring"
+        stream_name = "Record Node 101#OneBox-111.ProbeA"
+        block_index = 0
+
+        recording = self.ExtractorClass(folder_path, stream_name=stream_name, block_index=block_index)
+        # check that channel_ids and settings_channel_key contact annotations are correctly loaded
+        probe = recording.get_probe()
+        np.testing.assert_array_equal(recording.channel_ids, probe.contact_annotations["settings_channel_key"])
+
 
 class OpenEphysBinaryEventTest(EventCommonTestSuite, unittest.TestCase):
     ExtractorClass = OpenEphysBinaryEventExtractor