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@rly
rly committed Jun 30, 2024
1 parent 6df9d51 commit a2ec469
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14 changes: 7 additions & 7 deletions src/pynwb/ndx_extracellular_channels/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,8 +17,8 @@


def from_probeinterface(
probe_or_probegroup: Union[probeinterface.Probe, probeinterface.ProbeGroup],
name: Union[str, list] = None,
probe_or_probegroup: Union[probeinterface.Probe, probeinterface.ProbeGroup],
name: Union[str, list] = None,
) -> List[ndx_extracellular_channels.Probe]:
"""
Construct ndx-extracellular-channels Probe objects from a probeinterface.Probe or probeinterface.ProbeGroup.
Expand All @@ -43,8 +43,9 @@ def from_probeinterface(
"To use the probeinterface conversion functions, install probeinterface: pip install probeinterface"
)

assert isinstance(probe_or_probegroup, (probeinterface.Probe, probeinterface.ProbeGroup)), \
f"The input must be a Probe or ProbeGroup, not {type(probe_or_probegroup)}."
assert isinstance(
probe_or_probegroup, (probeinterface.Probe, probeinterface.ProbeGroup)
), f"The input must be a Probe or ProbeGroup, not {type(probe_or_probegroup)}."
if isinstance(probe_or_probegroup, probeinterface.Probe):
probes = [probe_or_probegroup]
else:
Expand Down Expand Up @@ -155,8 +156,7 @@ def to_probeinterface(ndx_probe: ndx_extracellular_channels.Probe) -> probeinter


def _single_probe_to_ndx_probe(
probe: probeinterface.Probe,
name: Union[str, None] = None
probe: probeinterface.Probe, name: Union[str, None] = None
) -> ndx_extracellular_channels.Probe:
contacts_arr = probe.to_numpy()

Expand Down Expand Up @@ -219,4 +219,4 @@ def _single_probe_to_ndx_probe(
identifier=probe.serial_number,
)

return probe
return probe
8 changes: 4 additions & 4 deletions src/pynwb/tests/test_classes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -474,8 +474,8 @@ def test_constructor_add_row(self):
name="Neuropixels1ChannelsTable", # test custom name
description="Test channels table",
reference_mode="Referenced to channel 2.",
position_reference = "(AP, ML, DV) = (0, 0, 0) corresponds to bregma at the cortical surface.",
position_confirmation_method = "Histology",
position_reference="(AP, ML, DV) = (0, 0, 0) corresponds to bregma at the cortical surface.",
position_confirmation_method="Histology",
probe=probe,
probe_insertion=pi,
target_tables={
Expand Down Expand Up @@ -555,8 +555,8 @@ def addContainer(self):
name="Neuropixels1ChannelsTable", # test custom name
description="Test channels table",
reference_mode="Referenced to channel 2.",
position_reference = "(AP, ML, DV) = (0, 0, 0) corresponds to bregma at the cortical surface.",
position_confirmation_method = "Histology",
position_reference="(AP, ML, DV) = (0, 0, 0) corresponds to bregma at the cortical surface.",
position_confirmation_method="Histology",
probe=probe,
probe_insertion=pi,
target_tables={
Expand Down
4 changes: 2 additions & 2 deletions src/pynwb/tests/test_example_usage_all.py
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Original file line number Diff line number Diff line change
Expand Up @@ -85,8 +85,8 @@
name="Neuropixels1ChannelsTable", # test custom name
description="Test channels table",
reference_mode="Referenced to channel 2.",
position_reference = "(AP, ML, DV) = (0, 0, 0) corresponds to bregma at the cortical surface.",
position_confirmation_method = "Histology",
position_reference="(AP, ML, DV) = (0, 0, 0) corresponds to bregma at the cortical surface.",
position_confirmation_method="Histology",
probe=probe,
probe_insertion=pi,
target_tables={
Expand Down
41 changes: 30 additions & 11 deletions src/pynwb/tests/test_example_usage_probeinterface.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
import pynwb
import uuid


def test_from_probeinterface():

# following the probeinterface tutorial, create a few probes
Expand All @@ -27,7 +28,7 @@ def test_from_probeinterface():
)
probe0.set_contacts(positions=positions, shapes="circle", shape_params={"radius": 5})

polygon = [(-20., -30.), (20., -110.), (60., -30.), (60., 190.), (-20., 190.)]
polygon = [(-20.0, -30.0), (20.0, -110.0), (60.0, -30.0), (60.0, 190.0), (-20.0, 190.0)]
probe0.set_planar_contour(polygon)

probe1 = probeinterface.generate_dummy_probe(elec_shapes="circle")
Expand Down Expand Up @@ -81,8 +82,14 @@ def test_from_probeinterface():
with pynwb.NWBHDF5IO("test_probeinterface.nwb", "r", load_namespaces=True) as io:
nwbfile = io.read()
assert set(nwbfile.devices.keys()) == {
"probe0", "probe1", "probe2", "probe3", "a1x32-edge-5mm-20-177_H32", "Dummy Neuropixels 1.0",
"Dummy Neuropixels 2.0", "Dummy Neuropixels 3.0"
"probe0",
"probe1",
"probe2",
"probe3",
"a1x32-edge-5mm-20-177_H32",
"Dummy Neuropixels 1.0",
"Dummy Neuropixels 2.0",
"Dummy Neuropixels 3.0",
}
for device in nwbfile.devices.values():
assert isinstance(device, (ndx_extracellular_channels.ProbeModel, ndx_extracellular_channels.Probe))
Expand All @@ -103,37 +110,49 @@ def test_from_probeinterface():
assert np.all(nwbfile.devices["probe0"].probe_model.planar_contour_in_um == polygon)
assert np.allclose(nwbfile.devices["probe0"].probe_model.contacts_table.relative_position_in_mm, positions)
assert np.all(nwbfile.devices["probe0"].probe_model.contacts_table["shape"].data[:] == "circle")
assert np.all(nwbfile.devices["probe0"].probe_model.contacts_table["radius_in_um"].data[:] == 5.)
assert np.all(nwbfile.devices["probe0"].probe_model.contacts_table["radius_in_um"].data[:] == 5.0)

assert nwbfile.devices["probe1"].name == "probe1"
assert nwbfile.devices["probe1"].identifier == "1000"
assert nwbfile.devices["probe1"].probe_model.name == "Dummy Neuropixels 1.0"
assert nwbfile.devices["probe1"].probe_model.manufacturer == "IMEC"
assert nwbfile.devices["probe1"].probe_model.ndim == 2
assert np.allclose(nwbfile.devices["probe1"].probe_model.planar_contour_in_um, probe1.probe_planar_contour)
assert np.allclose(nwbfile.devices["probe1"].probe_model.contacts_table.relative_position_in_mm, probe1.contact_positions)
assert np.allclose(
nwbfile.devices["probe1"].probe_model.contacts_table.relative_position_in_mm, probe1.contact_positions
)
assert np.all(nwbfile.devices["probe1"].probe_model.contacts_table["shape"].data[:] == "circle")
assert np.all(nwbfile.devices["probe1"].probe_model.contacts_table["radius_in_um"].data[:] == probe1.to_numpy()["radius"])
assert np.all(
nwbfile.devices["probe1"].probe_model.contacts_table["radius_in_um"].data[:] == probe1.to_numpy()["radius"]
)

assert nwbfile.devices["probe2"].name == "probe2"
assert nwbfile.devices["probe2"].identifier == "1001"
assert nwbfile.devices["probe2"].probe_model.name == "Dummy Neuropixels 2.0"
assert nwbfile.devices["probe2"].probe_model.manufacturer == "IMEC"
assert nwbfile.devices["probe2"].probe_model.ndim == 2
assert np.allclose(nwbfile.devices["probe2"].probe_model.planar_contour_in_um, probe2.probe_planar_contour)
assert np.allclose(nwbfile.devices["probe2"].probe_model.contacts_table.relative_position_in_mm, probe2.contact_positions)
assert np.allclose(
nwbfile.devices["probe2"].probe_model.contacts_table.relative_position_in_mm, probe2.contact_positions
)
assert np.all(nwbfile.devices["probe2"].probe_model.contacts_table["shape"].data[:] == "square")
assert np.all(nwbfile.devices["probe2"].probe_model.contacts_table["width_in_um"].data[:] == probe2.to_numpy()["width"])
assert np.all(
nwbfile.devices["probe2"].probe_model.contacts_table["width_in_um"].data[:] == probe2.to_numpy()["width"]
)

assert nwbfile.devices["probe3"].name == "probe3"
assert nwbfile.devices["probe3"].identifier == "1002"
assert nwbfile.devices["probe3"].probe_model.name == "Dummy Neuropixels 3.0"
assert nwbfile.devices["probe3"].probe_model.manufacturer == "IMEC"
assert nwbfile.devices["probe3"].probe_model.ndim == 2
assert np.allclose(nwbfile.devices["probe3"].probe_model.planar_contour_in_um, probe3.probe_planar_contour)
assert np.allclose(nwbfile.devices["probe3"].probe_model.contacts_table.relative_position_in_mm, probe3.contact_positions)
assert np.allclose(
nwbfile.devices["probe3"].probe_model.contacts_table.relative_position_in_mm, probe3.contact_positions
)
assert np.all(nwbfile.devices["probe3"].probe_model.contacts_table["shape"].data[:] == "circle")
assert np.all(nwbfile.devices["probe3"].probe_model.contacts_table["radius_in_um"].data[:] == probe3.to_numpy()["radius"])
assert np.all(
nwbfile.devices["probe3"].probe_model.contacts_table["radius_in_um"].data[:] == probe3.to_numpy()["radius"]
)

# for device in nwbfile.devices.values():
# print("-------------------")
Expand All @@ -148,4 +167,4 @@ def test_from_probeinterface():
# pi_probe = ndx_extracellular_channels.to_probeinterface(device)
# print(pi_probe)

# TODO add more tests for other probeinterface IO functions
# TODO add more tests for other probeinterface IO functions
52 changes: 32 additions & 20 deletions src/spec/create_extension_spec.py
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Original file line number Diff line number Diff line change
Expand Up @@ -78,13 +78,15 @@ def main():
# NOTE: cannot end this name with "_index" because it conflicts with ragged arrays
name="device_channel",
neurodata_type_inc="VectorData",
doc=("Index of the channel connected to the contact on the device. "
"Probes can have a complex contact indexing system due to the probe layout. "
"When they are plugged into a recording device like an Open Ephys with an Intan headstage, "
"the channel order can be mixed again. So the physical contact channel index "
"is rarely the channel index on the device. See the probeinterface tutorial on automatic "
"wiring for an example: "
"https://probeinterface.readthedocs.io/en/main/examples/ex_11_automatic_wiring.html#sphx-glr-examples-ex-11-automatic-wiring-py"),
doc=(
"Index of the channel connected to the contact on the device. "
"Probes can have a complex contact indexing system due to the probe layout. "
"When they are plugged into a recording device like an Open Ephys with an Intan headstage, "
"the channel order can be mixed again. So the physical contact channel index "
"is rarely the channel index on the device. See the probeinterface tutorial on automatic "
"wiring for an example: "
"https://probeinterface.readthedocs.io/en/main/examples/ex_11_automatic_wiring.html#sphx-glr-examples-ex-11-automatic-wiring-py"
),
dtype="int",
quantity="?",
),
Expand Down Expand Up @@ -162,8 +164,10 @@ def main():
probe_model = NWBGroupSpec(
neurodata_type_def="ProbeModel",
neurodata_type_inc="Device",
doc=("Neural probe object, compatible with the ProbeInterface specification. The name of the object should "
'be the model name of the probe, e.g., "Neuropixels 1.0".'),
doc=(
"Neural probe object, compatible with the ProbeInterface specification. The name of the object should "
'be the model name of the probe, e.g., "Neuropixels 1.0".'
),
groups=[
NWBGroupSpec(
name="contacts_table",
Expand All @@ -184,11 +188,13 @@ def main():
),
NWBAttributeSpec(
name="planar_contour_in_um", # TODO should this just be "contour"?
doc=("The coordinates of the nodes of the polygon that describe the shape (contour) of the probe, "
"in micrometers. The first and last points are connected to close the polygon. "
"e.g., [(-20., -30.), (20., -110.), (60., -30.), (60., 190.), (-20., 190.)]."
"See 'probe_planar_contour' in "
"https://probeinterface.readthedocs.io/en/main/format_spec.html for more details."),
doc=(
"The coordinates of the nodes of the polygon that describe the shape (contour) of the probe, "
"in micrometers. The first and last points are connected to close the polygon. "
"e.g., [(-20., -30.), (20., -110.), (60., -30.), (60., 190.), (-20., 190.)]."
"See 'probe_planar_contour' in "
"https://probeinterface.readthedocs.io/en/main/format_spec.html for more details."
),
dtype="float",
dims=[["num_points", "x, y"], ["num_points", "x, y, z"]],
shape=[[None, 2], [None, 3]],
Expand Down Expand Up @@ -422,22 +428,28 @@ def main():
attributes=[
NWBAttributeSpec(
name="position_reference",
doc=("Location of the origin (0, 0, 0) for `{X}_position_{Y}_in_mm` coordinates, e.g., "
'"(AP, ML, DV) = (0, 0, 0) corresponds to bregma at the cortical surface".'),
doc=(
"Location of the origin (0, 0, 0) for `{X}_position_{Y}_in_mm` coordinates, e.g., "
'"(AP, ML, DV) = (0, 0, 0) corresponds to bregma at the cortical surface".'
),
dtype="text",
required=False,
),
NWBAttributeSpec(
name="reference_mode",
doc=('The reference mode used for the recording; e.g., "external wire in CSF", '
'common reference", "skull screw over frontal cortex".'),
doc=(
'The reference mode used for the recording; e.g., "external wire in CSF", '
'common reference", "skull screw over frontal cortex".'
),
dtype="text",
required=False,
),
NWBAttributeSpec(
name="position_confirmation_method",
doc=("Description of the method used to confirm the position of the contacts or brain area, "
'e.g., "histology", "MRI".'),
doc=(
"Description of the method used to confirm the position of the contacts or brain area, "
'e.g., "histology", "MRI".'
),
dtype="text",
required=False,
),
Expand Down

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