def test_add_events(tmp_path, nwbfile, roundtripper, roundtrip,
cell_specimen_table, metadata_fixture, dff_traces,
ophys_timestamps):
# Need to add metadata, cell specimen table, dff traces first
nwb.add_metadata(nwbfile, metadata_fixture, behavior_only=False)
nwb.add_cell_specimen_table(nwbfile, cell_specimen_table, metadata_fixture)
nwb.add_dff_traces(nwbfile, dff_traces, ophys_timestamps)
events = pd.DataFrame({
'events': [np.array([0., 0., .69]), np.array([.3, 0.0, .2])],
'filtered_events': [
np.array([0.0, 0.0, 0.22949295]),
np.array([0.09977954, 0.08805513, 0.127039049])
],
'lambda': [0., 1.0],
'noise_std': [.25, .3],
'cell_roi_id': [123, 321]
}, index=pd.Index([42, 84], name='cell_specimen_id'))
api = BehaviorOphysNwbApi.from_nwbfile(nwbfile)
nwbfile = api.add_events(
nwbfile=nwbfile,
events=events
)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorOphysNwbApi)
else:
obt = BehaviorOphysNwbApi.from_nwbfile(nwbfile)
obtained = obt.get_events()
pd.testing.assert_frame_equal(obtained, events, check_like=True)
def test_add_eye_tracking_rig_geometry_data_to_nwbfile(nwbfile, roundtripper,
roundtrip,
rig_geometry,
expected):
api = BehaviorOphysNwbApi.from_nwbfile(nwbfile)
nwbfile = api.add_eye_tracking_rig_geometry_data_to_nwbfile(nwbfile,
rig_geometry)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorOphysNwbApi)
else:
obt = BehaviorOphysNwbApi.from_nwbfile(nwbfile)
obtained_eye_rig_geometry = obt.get_eye_tracking_rig_geometry()
assert obtained_eye_rig_geometry == expected
def test_add_partial_metadata(test_partial_metadata, roundtrip, roundtripper,
cell_specimen_table,
metadata_fixture, partial_metadata_fixture):
if test_partial_metadata:
meta = partial_metadata_fixture
else:
meta = metadata_fixture
nwbfile = pynwb.NWBFile(
session_description='asession',
identifier='afile',
session_start_time=meta['date_of_acquisition']
)
nwb.add_metadata(nwbfile, meta, behavior_only=False)
if not test_partial_metadata:
nwb.add_cell_specimen_table(nwbfile, cell_specimen_table, meta)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorOphysNwbApi)
else:
obt = BehaviorOphysNwbApi.from_nwbfile(nwbfile)
if not test_partial_metadata:
metadata_obt = obt.get_metadata()
else:
with warnings.catch_warnings(record=True) as record:
metadata_obt = obt.get_metadata()
exp_warn_msg = "Could not locate 'ophys' module in NWB"
print(record)
assert record[0].message.args[0].startswith(exp_warn_msg)
assert len(metadata_obt) == len(meta)
for key, val in meta.items():
assert val == metadata_obt[key]
def test_get_corrected_fluorescence_traces(
nwbfile, roundtrip, filter_invalid_rois, valid_roi_ids, roundtripper,
dff_traces, corrected_fluorescence_traces, cell_specimen_table,
metadata_fixture, ophys_timestamps):
nwb.add_metadata(nwbfile, metadata_fixture, behavior_only=False)
nwb.add_cell_specimen_table(nwbfile, cell_specimen_table, metadata_fixture)
nwb.add_dff_traces(nwbfile, dff_traces, ophys_timestamps)
nwb.add_corrected_fluorescence_traces(nwbfile,
corrected_fluorescence_traces)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorOphysNwbApi,
filter_invalid_rois=filter_invalid_rois)
else:
obt = BehaviorOphysNwbApi.from_nwbfile(
nwbfile, filter_invalid_rois=filter_invalid_rois)
if filter_invalid_rois:
corrected_fluorescence_traces = corrected_fluorescence_traces[
corrected_fluorescence_traces["cell_roi_id"].isin(valid_roi_ids)]
print(corrected_fluorescence_traces)
print(obt.get_corrected_fluorescence_traces())
pd.testing.assert_frame_equal(
corrected_fluorescence_traces,
obt.get_corrected_fluorescence_traces(), check_dtype=False)
def test_add_licks(nwbfile, roundtrip, roundtripper, licks):
nwb.add_licks(nwbfile, licks)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorOphysNwbApi)
else:
obt = BehaviorOphysNwbApi.from_nwbfile(nwbfile)
pd.testing.assert_frame_equal(licks, obt.get_licks(), check_dtype=False)
def test_add_eye_tracking_data_to_nwbfile(
tmp_path, nwbfile, eye_tracking_data,
rig_geometry, roundtripper, roundtrip):
api = BehaviorOphysNwbApi.from_nwbfile(nwbfile)
nwbfile = api.add_eye_tracking_data_to_nwb(
nwbfile=nwbfile,
eye_tracking_df=eye_tracking_data,
eye_tracking_rig_geometry=rig_geometry
)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorOphysNwbApi)
else:
obt = BehaviorOphysNwbApi.from_nwbfile(nwbfile)
obtained = obt.get_eye_tracking()
pd.testing.assert_frame_equal(obtained,
eye_tracking_data, check_like=True)
def test_segmentation_mask_image(nwbfile, roundtrip, roundtripper,
segmentation_mask_image, image_api):
nwb.add_segmentation_mask_image(nwbfile, segmentation_mask_image)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorOphysNwbApi)
else:
obt = BehaviorOphysNwbApi.from_nwbfile(nwbfile)
assert image_api.deserialize(segmentation_mask_image) == \
image_api.deserialize(obt.get_segmentation_mask_image())
def test_add_average_image(nwbfile, roundtrip, roundtripper, average_image,
image_api):
nwb.add_average_image(nwbfile, average_image)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorOphysNwbApi)
else:
obt = BehaviorOphysNwbApi.from_nwbfile(nwbfile)
assert image_api.deserialize(average_image) == \
image_api.deserialize(obt.get_average_projection())
def test_add_stimulus_timestamps(nwbfile, stimulus_timestamps,
roundtrip, roundtripper):
nwb.add_stimulus_timestamps(nwbfile, stimulus_timestamps)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorOphysNwbApi)
else:
obt = BehaviorOphysNwbApi.from_nwbfile(nwbfile)
np.testing.assert_array_almost_equal(stimulus_timestamps,
obt.get_stimulus_timestamps())
def test_add_max_projection(nwbfile, roundtrip, roundtripper,
max_projection, image_api):
nwb.add_max_projection(nwbfile, max_projection)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorOphysNwbApi)
else:
obt = BehaviorOphysNwbApi.from_nwbfile(nwbfile)
assert image_api.deserialize(max_projection) == \
image_api.deserialize(obt.get_max_projection())
def test_add_running_speed_to_nwbfile(nwbfile, running_speed, roundtrip,
roundtripper):
nwbfile = nwb.add_running_speed_to_nwbfile(nwbfile, running_speed)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorOphysNwbApi)
else:
obt = BehaviorOphysNwbApi.from_nwbfile(nwbfile)
running_speed_obt = obt.get_running_speed()
assert np.allclose(running_speed.timestamps, running_speed_obt.timestamps)
assert np.allclose(running_speed.values, running_speed_obt.values)
def test_add_stimulus_templates(nwbfile, stimulus_templates, roundtrip,
roundtripper):
for key, val in stimulus_templates.items():
nwb.add_stimulus_template(nwbfile, val, key)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorOphysNwbApi)
else:
obt = BehaviorOphysNwbApi.from_nwbfile(nwbfile)
stimulus_templates_obt = obt.get_stimulus_templates()
for key in set(stimulus_templates.keys()).union(
set(stimulus_templates_obt.keys())):
np.testing.assert_array_almost_equal(stimulus_templates[key],
stimulus_templates_obt[key])
def test_get_motion_correction(nwbfile, roundtrip, roundtripper,
motion_correction, ophys_timestamps, metadata,
cell_specimen_table, dff_traces):
nwb.add_metadata(nwbfile, metadata)
nwb.add_cell_specimen_table(nwbfile, cell_specimen_table, metadata)
nwb.add_dff_traces(nwbfile, dff_traces, ophys_timestamps)
nwb.add_motion_correction(nwbfile, motion_correction)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorOphysNwbApi)
else:
obt = BehaviorOphysNwbApi.from_nwbfile(nwbfile)
pd.testing.assert_frame_equal(motion_correction,
obt.get_motion_correction(),
check_dtype=False)
def test_add_running_data_df_to_nwbfile(nwbfile, running_data_df, roundtrip,
roundtripper):
unit_dict = {
'v_sig': 'V',
'v_in': 'V',
'speed': 'cm/s',
'timestamps': 's',
'dx': 'cm'
}
nwbfile = nwb.add_running_data_df_to_nwbfile(nwbfile, running_data_df,
unit_dict)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorOphysNwbApi)
else:
obt = BehaviorOphysNwbApi.from_nwbfile(nwbfile)
pd.testing.assert_frame_equal(running_data_df, obt.get_running_data_df())
def test_add_task_parameters(nwbfile, roundtrip,
roundtripper, task_parameters):
nwb.add_task_parameters(nwbfile, task_parameters)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorOphysNwbApi)
else:
obt = BehaviorOphysNwbApi.from_nwbfile(nwbfile)
task_parameters_obt = obt.get_task_parameters()
assert len(task_parameters_obt) == len(task_parameters)
for key, val in task_parameters.items():
if key == 'omitted_flash_fraction':
if math.isnan(val):
assert math.isnan(task_parameters_obt[key])
if math.isnan(task_parameters_obt[key]):
assert math.isnan(val)
else:
assert val == task_parameters_obt[key]
def test_add_stimulus_presentations(nwbfile, stimulus_presentations_behavior,
stimulus_timestamps, roundtrip,
roundtripper, stimulus_templates):
nwb.add_stimulus_timestamps(nwbfile, stimulus_timestamps)
nwb.add_stimulus_presentations(nwbfile, stimulus_presentations_behavior)
for key, val in stimulus_templates.items():
nwb.add_stimulus_template(nwbfile, val, key)
# Add index for this template to NWB in-memory object:
nwb_template = nwbfile.stimulus_template[key]
curr_stimulus_index = stimulus_presentations_behavior[
stimulus_presentations_behavior['image_set'] == nwb_template.name]
nwb.add_stimulus_index(nwbfile, curr_stimulus_index, nwb_template)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorOphysNwbApi)
else:
obt = BehaviorOphysNwbApi.from_nwbfile(nwbfile)
pd.testing.assert_frame_equal(stimulus_presentations_behavior,
obt.get_stimulus_presentations(),
check_dtype=False)
def test_get_dff_traces(nwbfile, roundtrip, filter_invalid_rois, valid_roi_ids,
roundtripper, dff_traces, cell_specimen_table,
metadata, ophys_timestamps):
nwb.add_metadata(nwbfile, metadata)
nwb.add_cell_specimen_table(nwbfile, cell_specimen_table, metadata)
nwb.add_dff_traces(nwbfile, dff_traces, ophys_timestamps)
if roundtrip:
obt = roundtripper(nwbfile,
BehaviorOphysNwbApi,
filter_invalid_rois=filter_invalid_rois)
else:
obt = BehaviorOphysNwbApi.from_nwbfile(
nwbfile, filter_invalid_rois=filter_invalid_rois)
if filter_invalid_rois:
dff_traces = dff_traces[dff_traces["cell_roi_id"].isin(valid_roi_ids)]
pd.testing.assert_frame_equal(dff_traces,
obt.get_dff_traces(),
check_dtype=False)
def test_get_cell_specimen_table(nwbfile, roundtrip, filter_invalid_rois,
valid_roi_ids, roundtripper,
cell_specimen_table, metadata_fixture,
ophys_timestamps):
nwb.add_metadata(nwbfile, metadata_fixture, behavior_only=False)
nwb.add_cell_specimen_table(nwbfile, cell_specimen_table, metadata_fixture)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorOphysNwbApi,
filter_invalid_rois=filter_invalid_rois)
else:
obt = BehaviorOphysNwbApi.from_nwbfile(
nwbfile, filter_invalid_rois=filter_invalid_rois)
if filter_invalid_rois:
cell_specimen_table = \
cell_specimen_table[
cell_specimen_table["cell_roi_id"].isin(
valid_roi_ids)]
pd.testing.assert_frame_equal(
cell_specimen_table,
obt.get_cell_specimen_table(),
check_dtype=False)