Updated model fields to the latest BEP32 state (#278)

* bring up to speed with latest BEP

* Apply suggestion from @asmacdo

Co-authored-by: Austin Macdonald <[email protected]>

* roll back ch and zfill for string channel name

---------

Co-authored-by: Austin Macdonald <[email protected]>

Author: CodyCBakerPhD

src/nwb2bids/bids_models/_channels.py

@@ -40,21 +40,26 @@ def _infer_scalar_field(
 
 
 class Channel(BaseMetadataModel):
-    channel_name: str
-    reference: str
+    name: str
+    electrode_name: str
     type: str = "N/A"
-    unit: str = "V"
+    units: str = "V"
     sampling_frequency: float | None = None
+    low_cutoff: float | None = None
+    high_cutoff: float | None = None
+    reference: str | None = None
+    notch: str | None = None
     channel_label: str | None = None
     stream_id: str | None = None
     description: str | None = None
+    software_filter_types: str | None = None
     status: typing.Literal["good", "bad"] | None = None
     status_description: str | None = None
     gain: float | None = None
     time_offset: float | None = None
-    time_reference_channels: str | None = None
+    time_reference_channel: str | None = None
     ground: str | None = None
-    # recording_mode: str | None = None  # TODO: icephys only
+    recording_mode: str | None = None
 
 
 class ChannelTable(BaseMetadataContainerModel):
@@ -129,18 +134,14 @@ def from_nwbfiles(cls, nwbfiles: list[pydantic.InstanceOf[pynwb.NWBFile]]) -> ty
 
             channels = [
                 Channel(
-                    channel_name=(
-                        f"ch{channel_name.values[0]}"
+                    name=(
+                        f"{channel_name.values[0]}"
                         if (channel_name := electrode.get("channel_name", None)) is not None
-                        else f"ch{electrode.index[0]}"
-                    ),
-                    reference=(
-                        f"contact{contact_ids.values[0]}"  # TODO: do a deep dive into edge cases of this reference
-                        if (contact_ids := electrode.get("contact_ids", None)) is not None
-                        else f"e{electrode.index[0]}"
+                        else f"ch{str(electrode.index[0]).zfill(3)}"
                     ),
+                    electrode_name=f"e{str(electrode.index[0]).zfill(3)}",
                     type="N/A",  # TODO: in dedicated follow-up, could classify LFP based on container
-                    unit="V",
+                    units="V",
                     sampling_frequency=sampling_frequency,
                     # channel_label: str | None = None # TODO: only support with additional metadata
                     stream_id=stream_id,
@@ -150,7 +151,7 @@ def from_nwbfiles(cls, nwbfiles: list[pydantic.InstanceOf[pynwb.NWBFile]]) -> ty
                     gain=gain,
                     # Special extraction from SpikeInterface field
                     time_offset=shift[0] if (shift := electrode.get("inter_sample_shift", None)) is not None else None,
-                    # time_reference_channels: str | None = None # TODO: only support with additional metadata
+                    # time_reference_channel: str | None = None # TODO: only support with additional metadata
                     # ground: str | None = None # TODO: only support with additional metadata
                 )
                 for electrode in nwbfile.electrodes
@@ -161,7 +162,6 @@ def from_nwbfiles(cls, nwbfiles: list[pydantic.InstanceOf[pynwb.NWBFile]]) -> ty
                 for neurodata_object in nwbfile.acquisition.values()
                 if isinstance(neurodata_object, pynwb.icephys.PatchClampSeries)
             ]
-            # TODO: handle intracellular_recordings case
             electrode_name_to_series = collections.defaultdict(list)
             for series in icephys_series:
                 electrode_name_to_series[series.electrode.name].append(series)
@@ -197,19 +197,18 @@ def from_nwbfiles(cls, nwbfiles: list[pydantic.InstanceOf[pynwb.NWBFile]]) -> ty
 
             channels = [
                 Channel(
-                    channel_name=electrode.name,
-                    reference="n/a",  # TODO: think about if/how this could be any other value
+                    name=electrode.name,
+                    electrode_name=electrode.name,
                     type=electrode_name_to_type.get(electrode.name, "n/a"),
-                    unit="V",
+                    units="V",
                     sampling_frequency=electrode_name_to_sampling_frequency.get(electrode.name, None),
                     # channel_label: str | None = None # TODO: only support with additional metadata
                     stream_id=electrode_name_to_stream_ids.get(electrode.name, None),
                     # description: str | None = None  # TODO: only support with additional metadata
                     # status: typing.Literal["good", "bad"] | None = None # TODO: only support with additional metadata
                     # status_description: str | None = None # TODO: only support with additional metadata
                     gain=electrode_name_to_gain.get(electrode.name, None),
-                    # time_offset=
-                    # time_reference_channels: str | None = None # TODO: only support with additional metadata
+                    # time_reference_channel: str | None = None # TODO: only support with additional metadata
                     # ground: str | None = None # TODO: only support with additional metadata
                     recording_mode=type_to_recording_mode[electrode_name_to_type.get(electrode.name, "n/a")],
                     # TODO: add extra columns

src/nwb2bids/bids_models/_electrodes.py

@@ -15,13 +15,19 @@
 class Electrode(BaseMetadataModel):
     name: str
     probe_name: str
-    hemisphere: str = "N/A"
     x: float = numpy.nan
     y: float = numpy.nan
     z: float = numpy.nan
+    hemisphere: str = "N/A"
     impedance: float = numpy.nan  # in kOhms
     shank_id: str = "N/A"
+    size: float | None = None  # in square micrometers
+    electrode_shape: str | None = None
+    material: str | None = None
     location: str | None = None
+    pipette_solution: str | None = None
+    internal_pipette_diameter: float | None = None  # in micrometers
+    external_pipette_diameter: float | None = None  # in micrometers
 
     def __eq__(self, other: typing_extensions.Self) -> bool:
         if not isinstance(other, Electrode):
@@ -122,15 +128,13 @@ def from_nwbfiles(cls, nwbfiles: list[pydantic.InstanceOf[pynwb.NWBFile]]) -> ty
                     x=getattr(electrode, "x", numpy.nan),
                     y=getattr(electrode, "y", numpy.nan),
                     z=getattr(electrode, "z", numpy.nan),
-                    # impedance=  # Impedance must be in kOhms for BEP32 but NWB specifies Ohms
-                    # shank_id=
                     # TODO: pretty much only through additional metadata
+                    # impedance=
                     # size=
                     # electrode_shape=
                     # material=
-                    # location=
+                    location=getattr(electrode, "location", None),
                     # TODO: some icephys specific ones (would NOT use the ecephys electrode table anyway...)
-                    # Probably better off in a designated model
                     # pipette_solution=
                     # internal_pipette_diameter=
                     # external_pipette_diameter=

src/nwb2bids/bids_models/_probes.py

@@ -15,7 +15,27 @@
 class Probe(BaseMetadataModel):
     probe_name: str
     type: str = "n/a"
+    AP: float | None = None
+    ML: float | None = None
+    DV: float | None = None
+    AP_angle: float | None = None
+    ML_angle: float | None = None
     manufacturer: str | None = None
+    model: str | None = None
+    device_serial_number: str | None = None
+    electrode_count: int | None = None
+    width: float | None = None  # in millimeters
+    height: float | None = None  # in millimeters
+    depth: float | None = None
+    rotation_angle: float | None = None
+    coordinate_reference_point: str | None = None
+    anatomical_reference_point: str | None = None
+    hemisphere: typing.Literal["L", "R"] | None = None
+    associated_brain_region: str | None = None
+    associated_brain_region_id: str | None = None
+    associated_brain_region_quality_type: str | None = None
+    reference_atlas: str | None = None
+    material: str | None = None
 
 
 class ProbeTable(BaseMetadataContainerModel):
@@ -89,7 +109,7 @@ def from_nwbfiles(cls, nwbfiles: list[pydantic.InstanceOf[pynwb.NWBFile]]) -> ty
         probes = [
             Probe(
                 probe_name=device.name,
-                type="n/a",  # TODO
+                type="n/a",  # TODO via additional metadata
                 manufacturer=device.manufacturer,
                 description=device.description,
                 # TODO: handle more extra custom columns

src/nwb2bids/testing/_mocks/_tutorials.py

@@ -109,16 +109,19 @@ def _generate_icephys_file(*, nwbfile_path: pathlib.Path, subject_id: str = "001
         name="patch01",
         description="This is an example icephys electrode used for demonstration purposes.",
         device=probe1,
+        location="VISp2/3",
     )
     electrode2 = nwbfile.create_icephys_electrode(
         name="patch02",
         description="This is an example icephys electrode used for demonstration purposes.",
         device=probe2,
+        location="VISp2/3",
     )
     electrode3 = nwbfile.create_icephys_electrode(
         name="sharp01",
         description="This is an example icephys electrode used for demonstration purposes.",
         device=probe3,
+        location="PL5",
     )
 
     # Icephys series

tests/integration/test_convert_nwb_dataset.py

@@ -152,7 +152,7 @@ def test_ecephys_tutorial_convert_nwb_dataset(
     )
     electrodes_tsv_lines = electrodes_tsv_file_path.read_text().splitlines()
     expected_electrodes_tsv_lines = [
-        "name\tprobe_name\themisphere\tx\ty\tz\timpedance\tshank_id\tlocation",
+        "name\tprobe_name\tx\ty\tz\themisphere\timpedance\tshank_id\tlocation",
         "e000\tExampleProbe\tN/A\tN/A\tN/A\tN/A\t150.0\tExampleShank\thippocampus",
         "e001\tExampleProbe\tN/A\tN/A\tN/A\tN/A\t150.0\tExampleShank\thippocampus",
         "e002\tExampleProbe\tN/A\tN/A\tN/A\tN/A\t150.0\tExampleShank\thippocampus",
@@ -167,15 +167,15 @@ def test_ecephys_tutorial_convert_nwb_dataset(
     channels_tsv_file_path = temporary_bids_directory / "sub-001" / "ses-A" / "ecephys" / "sub-001_ses-A_channels.tsv"
     channels_tsv_lines = channels_tsv_file_path.read_text().splitlines()
     expected_channels_tsv_lines = [
-        "channel_name\treference\ttype\tunit\tsampling_frequency\tstream_id\tgain",
-        "ch0\te0\tN/A\tV\t30000.0\tExampleElectricalSeries\t3.02734375e-06",
-        "ch1\te1\tN/A\tV\t30000.0\tExampleElectricalSeries\t3.02734375e-06",
-        "ch2\te2\tN/A\tV\t30000.0\tExampleElectricalSeries\t3.02734375e-06",
-        "ch3\te3\tN/A\tV\t30000.0\tExampleElectricalSeries\t3.02734375e-06",
-        "ch4\te4\tN/A\tV\t30000.0\tExampleElectricalSeries\t3.02734375e-06",
-        "ch5\te5\tN/A\tV\t30000.0\tExampleElectricalSeries\t3.02734375e-06",
-        "ch6\te6\tN/A\tV\t30000.0\tExampleElectricalSeries\t3.02734375e-06",
-        "ch7\te7\tN/A\tV\t30000.0\tExampleElectricalSeries\t3.02734375e-06",
+        "name\telectrode_name\ttype\tunits\tsampling_frequency\tstream_id\tgain",
+        "ch000\te000\tN/A\tV\t30000.0\tExampleElectricalSeries\t3.02734375e-06",
+        "ch001\te001\tN/A\tV\t30000.0\tExampleElectricalSeries\t3.02734375e-06",
+        "ch002\te002\tN/A\tV\t30000.0\tExampleElectricalSeries\t3.02734375e-06",
+        "ch003\te003\tN/A\tV\t30000.0\tExampleElectricalSeries\t3.02734375e-06",
+        "ch004\te004\tN/A\tV\t30000.0\tExampleElectricalSeries\t3.02734375e-06",
+        "ch005\te005\tN/A\tV\t30000.0\tExampleElectricalSeries\t3.02734375e-06",
+        "ch006\te006\tN/A\tV\t30000.0\tExampleElectricalSeries\t3.02734375e-06",
+        "ch007\te007\tN/A\tV\t30000.0\tExampleElectricalSeries\t3.02734375e-06",
     ]
     assert channels_tsv_lines == expected_channels_tsv_lines
 
@@ -237,7 +237,7 @@ def test_ecephys_minimal_convert_nwb_dataset(
     )
     electrodes_tsv_lines = electrodes_tsv_file_path.read_text().splitlines()
     expected_electrodes_tsv_lines = [
-        "name\tprobe_name\themisphere\tx\ty\tz\timpedance\tshank_id\tlocation",
+        "name\tprobe_name\tx\ty\tz\themisphere\timpedance\tshank_id\tlocation",
         "e000\tExampleProbe\tN/A\tN/A\tN/A\tN/A\tN/A\tExampleShank\tunknown",
         "e001\tExampleProbe\tN/A\tN/A\tN/A\tN/A\tN/A\tExampleShank\tunknown",
         "e002\tExampleProbe\tN/A\tN/A\tN/A\tN/A\tN/A\tExampleShank\tunknown",
@@ -252,15 +252,15 @@ def test_ecephys_minimal_convert_nwb_dataset(
     channels_tsv_file_path = temporary_bids_directory / "sub-001" / "ses-A" / "ecephys" / "sub-001_ses-A_channels.tsv"
     channels_tsv_lines = channels_tsv_file_path.read_text().splitlines()
     expected_channels_tsv_lines = [
-        "channel_name\treference\ttype\tunit",
-        "ch0\te0\tN/A\tV",
-        "ch1\te1\tN/A\tV",
-        "ch2\te2\tN/A\tV",
-        "ch3\te3\tN/A\tV",
-        "ch4\te4\tN/A\tV",
-        "ch5\te5\tN/A\tV",
-        "ch6\te6\tN/A\tV",
-        "ch7\te7\tN/A\tV",
+        "name\telectrode_name\ttype\tunits",
+        "ch000\te000\tN/A\tV",
+        "ch001\te001\tN/A\tV",
+        "ch002\te002\tN/A\tV",
+        "ch003\te003\tN/A\tV",
+        "ch004\te004\tN/A\tV",
+        "ch005\te005\tN/A\tV",
+        "ch006\te006\tN/A\tV",
+        "ch007\te007\tN/A\tV",
     ]
     assert channels_tsv_lines == expected_channels_tsv_lines
 

tests/unit/test_remote_dataset_converter.py

@@ -77,10 +77,10 @@ def test_remote_dataset_converter_metadata_extraction(temporary_bids_directory:
     assert session_metadata.channel_table is not None
     assert len(session_metadata.channel_table.channels) == 65
     assert session_metadata.channel_table.channels[0] == nwb2bids.bids_models.Channel(
-        channel_name="ch0",
-        reference="e0",
+        name="ch000",
+        electrode_name="e000",
         type="N/A",
-        unit="V",
+        units="V",
         sampling_frequency=1250.0,
         stream_id="LFP",
         gain=1.9499999999999999e-07,