Merge branch 'main' into add_annotation_to_vebose_on_sorting

catalystneuro · Jan 16, 2025 · f3dd4ed · f3dd4ed
2 parents b7d97c9 + 32f6834
commit f3dd4ed
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -17,9 +17,11 @@ Small fixes should be here.
 * Temporary set a ceiling for hdmf to avoid a chunking bug  [PR #1175](https://github.com/catalystneuro/neuroconv/pull/1175)
 
 ## Features
+* Add description to inter-sample-shift for `SpikeGLXRecordingInterface` [PR #1177](https://github.com/catalystneuro/neuroconv/pull/1177)
 
 ## Improvements
 * `get_json_schema_from_method_signature` now throws a more informative error when an untyped parameter is passed [#1157](https://github.com/catalystneuro/neuroconv/pull/1157)
+* Improve the naming of ElectrodeGroups in the `SpikeGLXRecordingInterface` when multi probes are present [PR #1177](https://github.com/catalystneuro/neuroconv/pull/1177)
 * Detect mismatch errors between group and group names when writing ElectrodeGroups [PR #1165](https://github.com/catalystneuro/neuroconv/pull/1165)
 * Fix metadata bug in `IntanRecordingInterface` where extra devices were added incorrectly if the recording contained multiple electrode groups or names [#1166](https://github.com/catalystneuro/neuroconv/pull/1166)
 * Source validation is no longer performed when initializing interfaces or converters [PR #1168](https://github.com/catalystneuro/neuroconv/pull/1168)

diff --git a/src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglx_utils.py b/src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglx_utils.py
@@ -18,9 +18,9 @@ def add_recording_extractor_properties(recording_extractor) -> None:
     if probe.get_shank_count() > 1:
         shank_ids = probe.shank_ids
         recording_extractor.set_property(key="shank_ids", values=shank_ids)
-        group_name = [f"{probe_name}{shank_id}" for shank_id in shank_ids]
+        group_name = [f"Neuropixels{probe_name}Shank{shank_id}" for shank_id in shank_ids]
     else:
-        group_name = [f"{probe_name}"] * len(channel_ids)
+        group_name = [f"Neuropixels{probe_name}"] * len(channel_ids)
 
     recording_extractor.set_property(key="group_name", ids=channel_ids, values=group_name)
 

diff --git a/src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxdatainterface.py b/src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxdatainterface.py
@@ -27,14 +27,6 @@ class SpikeGLXRecordingInterface(BaseRecordingExtractorInterface):
     associated_suffixes = (".imec{probe_index}", ".ap", ".lf", ".meta", ".bin")
     info = "Interface for SpikeGLX recording data."
 
-    # TODO: Add probe_index to probeinterface and propagate it from there
-    # Note to developer.
-    # In a conversion with Jennifer Colonell she refers to the number after imec as the probe index
-    # Quoting here:
-    # imec0 is the probe in the lowest slot and port number, imec1 in the next highest, and so on.
-    # If you have probes in {slot 2, port 3}, {slot 3, port1} and {slot3, port2},
-    # the probe indices in the SGLX output will be 0, 1, and 2, respectively.
-
     ExtractorName = "SpikeGLXRecordingExtractor"
 
     @classmethod
@@ -135,7 +127,7 @@ def get_metadata(self) -> dict:
 
         # Should follow pattern 'Imec0', 'Imec1', etc.
         probe_name = self._signals_info_dict["device"].capitalize()
-        device["name"] = f"Neuropixel{probe_name}"
+        device["name"] = f"Neuropixels{probe_name}"
 
         # Add groups metadata
         metadata["Ecephys"]["Device"] = [device]
@@ -155,6 +147,13 @@ def get_metadata(self) -> dict:
             dict(name="group_name", description="Name of the ElectrodeGroup this electrode is a part of."),
             dict(name="contact_shapes", description="The shape of the electrode"),
             dict(name="contact_ids", description="The id of the contact on the electrode"),
+            dict(
+                name="inter_sample_shift",
+                description=(
+                    "Array of relative phase shifts for each channel, with values ranging from 0 to 1, "
+                    "representing the fractional delay within the sampling period due to sequential ADC."
+                ),
+            ),
         ]
 
         if self.recording_extractor.get_probe().get_shank_count() > 1:

diff --git a/tests/test_on_data/ecephys/spikeglx_multi_probe_metadata.json b/tests/test_on_data/ecephys/spikeglx_multi_probe_metadata.json
@@ -5,28 +5,28 @@
   "Ecephys": {
     "Device": [
       {
-        "name": "NeuropixelImec0",
+        "name": "NeuropixelsImec0",
         "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",
+        "name": "NeuropixelsImec1",
         "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": "Imec0",
-        "description": "A group representing probe/shank 'Imec0'.",
+        "name": "NeuropixelsImec0",
+        "description": "A group representing probe/shank 'NeuropixelsImec0'.",
         "location": "unknown",
-        "device": "NeuropixelImec0"
+        "device": "NeuropixelsImec0"
       },
       {
-        "name": "Imec1",
-        "description": "A group representing probe/shank 'Imec1'.",
+        "name": "NeuropixelsImec1",
+        "description": "A group representing probe/shank 'NeuropixelsImec1'.",
         "location": "unknown",
-        "device": "NeuropixelImec1"
+        "device": "NeuropixelsImec1"
       }
     ],
     "ElectricalSeriesAPImec0": {
@@ -45,6 +45,10 @@
       {
         "name": "contact_ids",
         "description": "The id of the contact on the electrode"
+      },
+      {
+        "name": "inter_sample_shift",
+        "description": "Array of relative phase shifts for each channel, with values ranging from 0 to 1, representing the fractional delay within the sampling period due to sequential ADC."
       }
     ],
     "ElectricalSeriesAPImec1": {

diff --git a/tests/test_on_data/ecephys/spikeglx_single_probe_metadata.json b/tests/test_on_data/ecephys/spikeglx_single_probe_metadata.json
@@ -5,17 +5,17 @@
   "Ecephys": {
     "Device": [
       {
-        "name": "NeuropixelImec0",
+        "name": "NeuropixelsImec0",
         "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": "Imec0",
-        "description": "A group representing probe/shank 'Imec0'.",
+        "name": "NeuropixelsImec0",
+        "description": "A group representing probe/shank 'NeuropixelsImec0'.",
         "location": "unknown",
-        "device": "NeuropixelImec0"
+        "device": "NeuropixelsImec0"
       }
 
     ],
@@ -35,6 +35,10 @@
       {
         "name": "contact_ids",
         "description": "The id of the contact on the electrode"
+      },
+      {
+        "name": "inter_sample_shift",
+        "description": "Array of relative phase shifts for each channel, with values ranging from 0 to 1, representing the fractional delay within the sampling period due to sequential ADC."
       }
     ],
     "ElectricalSeriesLF": {

diff --git a/tests/test_on_data/ecephys/test_recording_interfaces.py b/tests/test_on_data/ecephys/test_recording_interfaces.py
@@ -670,7 +670,7 @@ class TestSpikeGLXRecordingInterface(RecordingExtractorInterfaceTestMixin):
     def check_extracted_metadata(self, metadata: dict):
         assert metadata["NWBFile"]["session_start_time"] == datetime(2020, 11, 3, 10, 35, 10)
         assert metadata["Ecephys"]["Device"][-1] == dict(
-            name="NeuropixelImec0",
+            name="NeuropixelsImec0",
             description="{"
             '"probe_type": "0", '
             '"probe_type_description": "NP1.0", '
@@ -698,7 +698,7 @@ class TestSpikeGLXRecordingInterfaceLongNHP(RecordingExtractorInterfaceTestMixin
     def check_extracted_metadata(self, metadata: dict):
         assert metadata["NWBFile"]["session_start_time"] == datetime(2024, 1, 3, 11, 51, 51)
         assert metadata["Ecephys"]["Device"][-1] == dict(
-            name="NeuropixelImec0",
+            name="NeuropixelsImec0",
             description="{"
             '"probe_type": "1030", '
             '"probe_type_description": "NP1.0 NHP", '

diff --git a/tests/test_on_data/ecephys/test_spikeglx_converter.py b/tests/test_on_data/ecephys/test_spikeglx_converter.py
@@ -41,11 +41,11 @@ def assertNWBFileStructure(self, nwbfile_path: FilePath, expected_session_start_
 
             assert len(nwbfile.acquisition) == 3
 
-            assert "NeuropixelImec0" in nwbfile.devices
+            assert "NeuropixelsImec0" in nwbfile.devices
             assert "NIDQBoard" in nwbfile.devices
             assert len(nwbfile.devices) == 2
 
-            assert "Imec0" in nwbfile.electrode_groups
+            assert "NeuropixelsImec0" in nwbfile.electrode_groups
             assert len(nwbfile.electrode_groups) == 1
 
     def test_single_probe_spikeglx_converter(self):
@@ -132,12 +132,12 @@ def assertNWBFileStructure(self, nwbfile_path: FilePath, expected_session_start_
         assert "ElectricalSeriesLFImec11" in nwbfile.acquisition
         assert len(nwbfile.acquisition) == 16
 
-        assert "NeuropixelImec0" in nwbfile.devices
-        assert "NeuropixelImec1" in nwbfile.devices
+        assert "NeuropixelsImec0" in nwbfile.devices
+        assert "NeuropixelsImec1" in nwbfile.devices
         assert len(nwbfile.devices) == 2
 
-        assert "Imec0" in nwbfile.electrode_groups
-        assert "Imec1" in nwbfile.electrode_groups
+        assert "NeuropixelsImec0" in nwbfile.electrode_groups
+        assert "NeuropixelsImec1" in nwbfile.electrode_groups
         assert len(nwbfile.electrode_groups) == 2
 
     def test_multi_probe_spikeglx_converter(self):
@@ -160,8 +160,16 @@ def test_multi_probe_spikeglx_converter(self):
 
         device_metadata = test_ecephys_metadata.pop("Device")
         expected_device_metadata = expected_ecephys_metadata.pop("Device")
-
         assert device_metadata == expected_device_metadata
+
+        assert test_ecephys_metadata["ElectrodeGroup"] == expected_ecephys_metadata["ElectrodeGroup"]
+        assert test_ecephys_metadata["Electrodes"] == expected_ecephys_metadata["Electrodes"]
+        assert test_ecephys_metadata["ElectricalSeriesAPImec0"] == expected_ecephys_metadata["ElectricalSeriesAPImec0"]
+        assert test_ecephys_metadata["ElectricalSeriesAPImec1"] == expected_ecephys_metadata["ElectricalSeriesAPImec1"]
+        assert test_ecephys_metadata["ElectricalSeriesLFImec0"] == expected_ecephys_metadata["ElectricalSeriesLFImec0"]
+        assert test_ecephys_metadata["ElectricalSeriesLFImec1"] == expected_ecephys_metadata["ElectricalSeriesLFImec1"]
+
+        # Test all the dictionary
         assert test_ecephys_metadata == expected_ecephys_metadata
 
         nwbfile_path = self.tmpdir / "test_multi_probe_spikeglx_converter.nwb"

diff --git a/tests/test_on_data/ecephys/test_spikeglx_metadata.py b/tests/test_on_data/ecephys/test_spikeglx_metadata.py
@@ -32,7 +32,8 @@ def test_spikelgx_recording_property_addition():
     probe_name = "Imec0"
 
     expected_shank_ids = probe.shank_ids
-    expected_group_name = [f"{probe_name}{shank_id}" for shank_id in expected_shank_ids]
+    expected_group_name = [f"Neuropixels{probe_name}Shank{shank_id}" for shank_id in expected_shank_ids]
+
     expected_contact_shapes = ["square"] * n_channels
     expected_contact_ids = probe.contact_ids