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Updated model fields to the latest BEP32 state #278

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Merged
CodyCBakerPhD merged 6 commits into from
Jan 23, 2026
Merged

Updated model fields to the latest BEP32 state #278

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c81f45c
bring up to speed with latest BEP
CodyCBakerPhD Jan 21, 2026
e7f822d
Merge branch 'main' into update-bep
CodyCBakerPhD Jan 21, 2026
e6f1dc1
Merge branch 'main' into update-bep
CodyCBakerPhD Jan 21, 2026
cfd2ab1
Apply suggestion from @asmacdo
CodyCBakerPhD Jan 22, 2026
b5fa5a1
roll back ch and zfill for string channel name
CodyCBakerPhD Jan 22, 2026
8cd551c
Merge branch 'main' into update-bep
CodyCBakerPhD Jan 23, 2026
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35 changes: 17 additions & 18 deletions src/nwb2bids/bids_models/_channels.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
ground: str | None = None
# recording_mode: str | None = None # TODO: icephys only
recording_mode: str | None = None
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@asmacdo asmacdo Jan 22, 2026

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IIUC this is only meaninful in icephys, should we keep some comment?

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@CodyCBakerPhD CodyCBakerPhD Jan 22, 2026

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There are many fields which are subtly used in only one or the other; these are expressed or inferred below in the initializer from NWB contents but not validated outside that

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@CodyCBakerPhD CodyCBakerPhD Jan 22, 2026

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(So I'd rather not leave comments and do something more formal in a follow-up if that is something you feel strongly about checking)



class ChannelTable(BaseMetadataContainerModel):
Expand Down Expand Up @@ -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"ch{channel_name.values[0].zfill(3)}"
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@asmacdo asmacdo Jan 22, 2026

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Probably pedantic, but if there were a non-numeric channel name, should we still do this? ie "A1" -> "ch0A1"? Should we validate that its only digits? And is 3 digits enough to be future proof?

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@CodyCBakerPhD CodyCBakerPhD Jan 22, 2026 •
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Fair enough in the first case of the ternary

The second case however, is guaranteed to be an integer, and zfill 3 simply matches the convention of the BEP examples (beyond that number of digits can happen in modern multi-probe Neuropixels, but I think at that point it looks fine, e.g., ch1024)

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,
Expand All @@ -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)
Expand Down Expand Up @@ -197,18 +197,17 @@ 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
# 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")],
Expand Down
14 changes: 9 additions & 5 deletions src/nwb2bids/bids_models/_electrodes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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):
Expand Down Expand Up @@ -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=
Expand Down
22 changes: 21 additions & 1 deletion src/nwb2bids/bids_models/_probes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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):
Expand Down Expand Up @@ -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
Expand Down
3 changes: 3 additions & 0 deletions src/nwb2bids/testing/_mocks/_tutorials.py
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Expand Up @@ -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
Expand Down
40 changes: 20 additions & 20 deletions tests/integration/test_convert_nwb_dataset.py
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Expand Up @@ -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",
Expand All @@ -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

Expand Down Expand Up @@ -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",
Expand All @@ -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

Expand Down
6 changes: 3 additions & 3 deletions tests/unit/test_remote_dataset_converter.py
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Expand Up @@ -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,
Expand Down
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