Fix default electrical series naming for SpikeGLXConverter (#957)

Co-authored-by: CodyCBakerPhD <[email protected]>

CHANGELOG.md

@@ -1,7 +1,9 @@
 # Upcoming
 
-### Improvements
+### Bug fixes
+* Fixed the default naming of multiple electrical series in the `SpikeGLXConverterPipe`. [PR #957](https://github.com/catalystneuro/neuroconv/pull/957)
 
+### Improvements
 * The `OpenEphysBinaryRecordingInterface` now uses `lxml` for extracting the session start time from the settings.xml file and does not depend on `pyopenephys` anymore. [PR #971](https://github.com/catalystneuro/neuroconv/pull/971)
 * Swap the majority of package setup and build steps to `pyproject.toml` instead of `setup.py`. [PR #955](https://github.com/catalystneuro/neuroconv/pull/955)
 * The `DeeplabcutInterface` now skips inferring timestamps from movie when timestamps are specified, running faster. [PR #967](https://github.com/catalystneuro/neuroconv/pull/967)

src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglx_utils.py

@@ -12,12 +12,15 @@ def add_recording_extractor_properties(recording_extractor) -> None:
     probe = recording_extractor.get_probe()
     channel_ids = recording_extractor.get_channel_ids()
 
+    # Should follow pattern 'Imec0', 'Imec1', etc.
+    probe_name = recording_extractor.stream_id[:5].capitalize()
+
     if probe.get_shank_count() > 1:
-        group_name = [contact_id.split("e")[0] for contact_id in probe.contact_ids]
         shank_electrode_number = [int(contact_id.split("e")[1]) for contact_id in probe.contact_ids]
+        group_name = [f"{probe_name}{contact_id.split('e')[0]}" for contact_id in probe.contact_ids]
     else:
         shank_electrode_number = recording_extractor.ids_to_indices(channel_ids)
-        group_name = ["s0"] * len(channel_ids)
+        group_name = [f"{probe_name}Shank0"] * len(channel_ids)
 
     recording_extractor.set_property(key="shank_electrode_number", ids=channel_ids, values=shank_electrode_number)
     recording_extractor.set_property(key="group_name", ids=channel_ids, values=group_name)
@@ -113,9 +116,9 @@ def get_device_metadata(meta) -> dict:
     if "imDatBsc_pn" in meta:
         metadata_dict.update(connected_base_station_part_number=meta["imDatBsc_pn"])
 
-    description_string = "no description"
+    description_string = "A Neuropixel probe of unknown subtype."
     if metadata_dict:
         description_string = json.dumps(metadata_dict)
-    device_metadata = dict(name="Neuropixel-Imec", description=description_string, manufacturer="Imec")
+    device_metadata = dict(name="NeuropixelImec", description=description_string, manufacturer="Imec")
 
     return device_metadata

src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxconverter.py

@@ -67,14 +67,16 @@ def __init__(
                 file_path = (
                     folder_path / f"{folder_path.stem}_{probe_name}" / f"{folder_path.stem}_t0.{probe_name}.ap.bin"
                 )
-                interface = SpikeGLXRecordingInterface(file_path=file_path)
-            if "lf" in stream:
+                es_key = f"ElectricalSeriesAP{probe_name.capitalize()}"
+                interface = SpikeGLXRecordingInterface(file_path=file_path, es_key=es_key)
+            elif "lf" in stream:
                 probe_name = stream[:5]
                 file_path = (
                     folder_path / f"{folder_path.stem}_{probe_name}" / f"{folder_path.stem}_t0.{probe_name}.lf.bin"
                 )
-                interface = SpikeGLXRecordingInterface(file_path=file_path)
-            if "nidq" in stream:
+                es_key = f"ElectricalSeriesLF{probe_name.capitalize()}"
+                interface = SpikeGLXRecordingInterface(file_path=file_path, es_key=es_key)
+            elif "nidq" in stream:
                 file_path = folder_path / f"{folder_path.stem}_t0.nidq.bin"
                 interface = SpikeGLXNIDQInterface(file_path=file_path)
             data_interfaces.update({str(stream): interface})  # Without str() casting, is a numpy string

src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxdatainterface.py

@@ -76,12 +76,16 @@ def get_metadata(self) -> dict:
         # Device metadata
         device = get_device_metadata(self.meta)
 
+        # Should follow pattern 'Imec0', 'Imec1', etc.
+        probe_name = self.stream_id[:5].capitalize()
+        device["name"] = f"Neuropixel{probe_name}"
+
         # Add groups metadata
         metadata["Ecephys"]["Device"] = [device]
         electrode_groups = [
             dict(
                 name=group_name,
-                description=f"a group representing shank {group_name}",
+                description=f"A group representing probe/shank '{group_name}'.",
                 location="unknown",
                 device=device["name"],
             )

src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxnidqinterface.py

@@ -3,7 +3,7 @@
 
 import numpy as np
 
-from .spikeglx_utils import get_device_metadata, get_session_start_time
+from .spikeglx_utils import get_session_start_time
 from ..baserecordingextractorinterface import BaseRecordingExtractorInterface
 from ....tools.signal_processing import get_rising_frames_from_ttl
 from ....utils import FilePathType, get_schema_from_method_signature
@@ -72,7 +72,11 @@ def get_metadata(self) -> dict:
             metadata["NWBFile"]["session_start_time"] = session_start_time
 
         # Device metadata
-        device = get_device_metadata(self.meta)
+        device = dict(
+            name="NIDQBoard",
+            description="A NIDQ board used in conjunction with SpikeGLX.",
+            manufacturer="National Instruments",
+        )
 
         # Add groups metadata
         metadata["Ecephys"]["Device"] = [device]

tests/test_ecephys/test_mock_nidq_interface.py

@@ -49,13 +49,17 @@ def test_mock_metadata():
     expected_ecephys_metadata = {
         "Ecephys": {
             "Device": [
-                {"description": "no description", "manufacturer": "Imec", "name": "Neuropixel-Imec"},
+                {
+                    "name": "NIDQBoard",
+                    "description": "A NIDQ board used in conjunction with SpikeGLX.",
+                    "manufacturer": "National Instruments",
+                },
             ],
             "ElectrodeGroup": [
                 {
                     "name": "NIDQChannelGroup",
                     "description": "A group representing the NIDQ channels.",
-                    "device": "Neuropixel-Imec",
+                    "device": "NIDQBoard",
                     "location": "unknown",
                 },
             ],
@@ -68,7 +72,7 @@ def test_mock_metadata():
             },
         }
     }
-    print(metadata["Ecephys"])
+
     assert metadata["Ecephys"] == expected_ecephys_metadata["Ecephys"]
 
     expected_start_time = datetime(2020, 11, 3, 10, 35, 10)
@@ -88,7 +92,13 @@ def test_mock_run_conversion(tmpdir: pathlib.Path):
     with NWBHDF5IO(path=nwbfile_path, mode="r") as io:
         nwbfile = io.read()
 
-        assert "Neuropixel-Imec" in nwbfile.devices
+        assert "NIDQBoard" in nwbfile.devices
+        assert len(nwbfile.devices) == 1
+
         assert "NIDQChannelGroup" in nwbfile.electrode_groups
+        assert len(nwbfile.electrode_groups) == 1
+
         assert list(nwbfile.electrodes.id[:]) == [0, 1, 2, 3, 4, 5, 6, 7]
+
         assert "ElectricalSeriesNIDQ" in nwbfile.acquisition
+        assert len(nwbfile.acquisition) == 1

tests/test_on_data/test_format_converters/spikeglx_multi_probe_metadata.json

@@ -0,0 +1,63 @@
+{
+  "NWBFile": {
+    "session_description": ""
+  },
+  "Ecephys": {
+    "Device": [
+      {
+        "name": "NeuropixelImec0",
+        "description": "{\"probe_type\": \"0\", \"probe_type_description\": \"NP1.0\", \"flex_part_number\": \"NP2_FLEX_0\", \"connected_base_station_part_number\": \"NP2_QBSC_00\"}",
+        "manufacturer": "Imec"
+      },
+      {
+        "name": "NeuropixelImec1",
+        "description": "{\"probe_type\": \"0\", \"probe_type_description\": \"NP1.0\", \"flex_part_number\": \"NP2_FLEX_0\", \"connected_base_station_part_number\": \"NP2_QBSC_00\"}",
+        "manufacturer": "Imec"
+      }
+    ],
+    "ElectrodeGroup": [
+      {
+        "name": "Imec0Shank0",
+        "description": "A group representing probe/shank 'Imec0Shank0'.",
+        "location": "unknown",
+        "device": "NeuropixelImec0"
+      },
+      {
+        "name": "Imec1Shank0",
+        "description": "A group representing probe/shank 'Imec1Shank0'.",
+        "location": "unknown",
+        "device": "NeuropixelImec1"
+      }
+    ],
+    "ElectricalSeriesAPImec0": {
+      "name": "ElectricalSeriesAPImec0",
+      "description": "Acquisition traces for the ElectricalSeriesAPImec0."
+    },
+    "Electrodes": [
+      {
+        "name": "shank_electrode_number",
+        "description": "0-indexed channel within a shank."
+      },
+      {
+        "name": "group_name",
+        "description": "Name of the ElectrodeGroup this electrode is a part of."
+      },
+      {
+        "name": "contact_shapes",
+        "description": "The shape of the electrode"
+      }
+    ],
+    "ElectricalSeriesAPImec1": {
+      "name": "ElectricalSeriesAPImec1",
+      "description": "Acquisition traces for the ElectricalSeriesAPImec1."
+    },
+    "ElectricalSeriesLFImec0": {
+      "name": "ElectricalSeriesLFImec0",
+      "description": "Acquisition traces for the ElectricalSeriesLFImec0."
+    },
+    "ElectricalSeriesLFImec1": {
+      "name": "ElectricalSeriesLFImec1",
+      "description": "Acquisition traces for the ElectricalSeriesLFImec1."
+    }
+  }
+}

tests/test_on_data/test_format_converters/spikeglx_single_probe_metadata.json

@@ -0,0 +1,59 @@
+{
+  "NWBFile": {
+    "session_description": ""
+  },
+  "Ecephys": {
+    "Device": [
+      {
+        "name": "NeuropixelImec0",
+        "description": "{\"probe_type\": \"0\", \"probe_type_description\": \"NP1.0\", \"flex_part_number\": \"NP2_FLEX_0\", \"connected_base_station_part_number\": \"NP2_QBSC_00\"}",
+        "manufacturer": "Imec"
+      },
+      {
+        "name": "NIDQBoard",
+        "description": "A NIDQ board used in conjunction with SpikeGLX.",
+        "manufacturer": "National Instruments"
+      }
+    ],
+    "ElectrodeGroup": [
+      {
+        "name": "Imec0Shank0",
+        "description": "A group representing probe/shank 'Imec0Shank0'.",
+        "location": "unknown",
+        "device": "NeuropixelImec0"
+      },
+      {
+        "name": "NIDQChannelGroup",
+        "description": "A group representing the NIDQ channels.",
+        "location": "unknown",
+        "device": "NIDQBoard"
+      }
+    ],
+    "ElectricalSeriesAPImec0": {
+      "name": "ElectricalSeriesAPImec0",
+      "description": "Acquisition traces for the ElectricalSeriesAPImec0."
+    },
+    "Electrodes": [
+      {
+        "name": "shank_electrode_number",
+        "description": "0-indexed channel within a shank."
+      },
+      {
+        "name": "group_name",
+        "description": "Name of the ElectrodeGroup this electrode is a part of."
+      },
+      {
+        "name": "contact_shapes",
+        "description": "The shape of the electrode"
+      }
+    ],
+    "ElectricalSeriesNIDQ": {
+      "name": "ElectricalSeriesNIDQ",
+      "description": "Raw acquisition traces from the NIDQ (.nidq.bin) channels."
+    },
+    "ElectricalSeriesLFImec0": {
+      "name": "ElectricalSeriesLFImec0",
+      "description": "Acquisition traces for the ElectricalSeriesLFImec0."
+    }
+  }
+}