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reformatting checks
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@CodyCBakerPhD
CodyCBakerPhD committed Sep 27, 2024
1 parent 20e2a27 commit 0b1c67c
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Showing 2 changed files with 26 additions and 32 deletions.
2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -75,7 +75,7 @@ exclude = [
line-length = 120

[tool.ruff.lint]
select = ["F", "E", "I"]
select = ["F", "E", "I", "UP031", "UP032"]
ignore = [
"PTH123",
"D203",
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56 changes: 25 additions & 31 deletions src/ibl_to_nwb/testing/_consistency_checks.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,82 +59,76 @@ def _check_lick_data(*, eid: str, one: ONE, nwbfile: NWBFile):
assert_array_equal(x=data_from_ONE, y=data_from_NWB)


def _check_RoiMotionEnergyInterface(*, eid: str, one: ONE, nwbfile: NWBFile, revision: str = None):
def _check_roi_motion_energy_data(*, eid: str, one: ONE, nwbfile: NWBFile):

camera_views = ["body", "left", "right"]

for view in camera_views:
# data
data_from_NWB = (
nwbfile.processing["behavior"].data_interfaces["%sCameraMotionEnergy" % view.capitalize()].data[:]
)
data_from_ONE = one.load_dataset(eid, "%sCamera.ROIMotionEnergy" % view, collection="alf")
data_from_NWB = nwbfile.processing["behavior"].data_interfaces[f"{view.capitalize()}CameraMotionEnergy"].data[:]
data_from_ONE = one.load_dataset(eid, f"{view}Camera.ROIMotionEnergy", collection="alf")
assert_array_equal(x=data_from_ONE, y=data_from_NWB)

# timestamps
data_from_NWB = (
nwbfile.processing["behavior"].data_interfaces["%sCameraMotionEnergy" % view.capitalize()].timestamps[:]
nwbfile.processing["behavior"].data_interfaces[f"{view.capitalize()}CameraMotionEnergy"].timestamps[:]
)
data_from_ONE = one.load_dataset(eid, "_ibl_%sCamera.times" % view, collection="alf")
data_from_ONE = one.load_dataset(eid, f"_ibl_{view}Camera.times", collection="alf")
assert_array_equal(x=data_from_ONE, y=data_from_NWB)


def _check_IblPoseEstimationInterface(*, eid: str, one: ONE, nwbfile: NWBFile, revision: str = None):
def _check_pose_estimation_data(*, eid: str, one: ONE, nwbfile: NWBFile, revision: str = None):

camera_views = ["body", "left", "right"]

for view in camera_views:
nodes = nwbfile.processing["behavior"].data_interfaces["PoseEstimation%sCamera" % view.capitalize()].nodes[:]
nodes = nwbfile.processing["behavior"].data_interfaces[f"PoseEstimation{view.capitalize()}Camera"].nodes[:]

for node in nodes:
# x
data_from_NWB = (
nwbfile.processing["behavior"]
.data_interfaces["PoseEstimation%sCamera" % view.capitalize()]
.data_interfaces[f"PoseEstimation{view.capitalize()}Camera"]
.pose_estimation_series[node]
.data[:][:, 0]
)
data_from_ONE = one.load_dataset(eid, "_ibl_%sCamera.dlc.pqt" % view, collection="alf")[
"%s_x" % node
].values
data_from_ONE = one.load_dataset(eid, f"_ibl_{view}Camera.dlc.pqt", collection="alf")[f"{node}_x"].values
assert_array_equal(x=data_from_ONE, y=data_from_NWB)

# y
data_from_NWB = (
nwbfile.processing["behavior"]
.data_interfaces["PoseEstimation%sCamera" % view.capitalize()]
.data_interfaces[f"PoseEstimation{view.capitalize()}Camera"]
.pose_estimation_series[node]
.data[:][:, 1]
)
data_from_ONE = one.load_dataset(eid, "_ibl_%sCamera.dlc.pqt" % view, collection="alf")[
"%s_y" % node
].values
data_from_ONE = one.load_dataset(eid, f"_ibl_{view}Camera.dlc.pqt", collection="alf")[f"{node}_y"].values
assert_array_equal(x=data_from_ONE, y=data_from_NWB)

# confidence
data_from_NWB = (
nwbfile.processing["behavior"]
.data_interfaces["PoseEstimation%sCamera" % view.capitalize()]
.data_interfaces[f"PoseEstimation{view.capitalize()}Camera"]
.pose_estimation_series[node]
.confidence[:]
)
data_from_ONE = one.load_dataset(eid, "_ibl_%sCamera.dlc.pqt" % view, collection="alf")[
"%s_likelihood" % node
data_from_ONE = one.load_dataset(eid, f"_ibl_{view}Camera.dlc.pqt", collection="alf")[
f"{node}_likelihood"
].values
assert_array_equal(x=data_from_ONE, y=data_from_NWB)

# timestamps
data_from_NWB = (
nwbfile.processing["behavior"]
.data_interfaces["PoseEstimation%sCamera" % view.capitalize()]
.data_interfaces[f"PoseEstimation{view.capitalize()}Camera"]
.pose_estimation_series[node]
.timestamps[:]
)
data_from_ONE = one.load_dataset(eid, "_ibl_%sCamera.times" % view, collection="alf")
data_from_ONE = one.load_dataset(eid, f"_ibl_{view}Camera.times", collection="alf")
assert_array_equal(x=data_from_ONE, y=data_from_NWB)


def _check_BrainwideMapTrialsInterface(*, eid: str, one: ONE, nwbfile: NWBFile, revision: str = None):
def _check_trials_data(*, eid: str, one: ONE, nwbfile: NWBFile):

data_from_NWB = nwbfile.trials[:]
data_from_ONE = one.load_dataset(eid, "_ibl_trials.table", collection="alf")
Expand Down Expand Up @@ -165,18 +159,18 @@ def _check_BrainwideMapTrialsInterface(*, eid: str, one: ONE, nwbfile: NWBFile,
assert_frame_equal(left=data_from_NWB, right=data_from_ONE)


def _check_PupilTrackingInterface(*, eid: str, one: ONE, nwbfile: NWBFile, revision: str = None):
def _check_PupilTrackingInterface(*, eid: str, one: ONE, nwbfile: NWBFile):

camera_views = ["left", "right"]
for view in camera_views:
# raw
data_from_NWB = (
nwbfile.processing["behavior"]
.data_interfaces["%sPupilTracking" % view.capitalize()]
.time_series["%sRawPupilDiameter" % view.capitalize()]
.data_interfaces[f"{view.capitalize()}PupilTracking"]
.time_series[f"{view.capitalize()}RawPupilDiameter"]
.data[:]
)
data_from_ONE = one.load_dataset(eid, "_ibl_%sCamera.features.pqt" % view, collection="alf")[
data_from_ONE = one.load_dataset(eid, f"_ibl_{view}Camera.features.pqt", collection="alf")[
"pupilDiameter_raw"
].values

Expand All @@ -185,18 +179,18 @@ def _check_PupilTrackingInterface(*, eid: str, one: ONE, nwbfile: NWBFile, revis
# smooth
data_from_NWB = (
nwbfile.processing["behavior"]
.data_interfaces["%sPupilTracking" % view.capitalize()]
.time_series["%sSmoothedPupilDiameter" % view.capitalize()]
.data_interfaces[f"{view.capitalize()}PupilTracking"]
.time_series[f"{view.capitalize()}SmoothedPupilDiameter"]
.data[:]
)
data_from_ONE = one.load_dataset(eid, "_ibl_%sCamera.features.pqt" % view, collection="alf")[
data_from_ONE = one.load_dataset(eid, f"_ibl_{view}Camera.features.pqt", collection="alf")[
"pupilDiameter_smooth"
].values

assert_array_equal(x=data_from_ONE, y=data_from_NWB)


def _check_IblSortingInterface(*, eid: str, one: ONE, nwbfile: NWBFile, revision: str = None):
def _check_spike_sorting_data(*, eid: str, one: ONE, nwbfile: NWBFile, revision: str = None):

units_table = nwbfile.units[:]
probe_names = units_table["probe_name"].unique()
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