def write_behavior_nwb(session_data, nwb_filepath):
nwb_filepath_inprogress = nwb_filepath+'.inprogress'
nwb_filepath_error = nwb_filepath+'.error'
# Clean out files from previous runs:
for filename in [nwb_filepath_inprogress,
nwb_filepath_error,
nwb_filepath]:
if os.path.exists(filename):
os.remove(filename)
try:
json_session = BehaviorSession(api=BehaviorJsonApi(session_data))
lims_api = BehaviorLimsApi(
behavior_session_id=session_data['behavior_session_id'])
lims_session = BehaviorSession(api=lims_api)
logging.info("Comparing a BehaviorSession created from JSON "
"with a BehaviorSession created from LIMS")
assert sessions_are_equal(json_session, lims_session, reraise=True)
BehaviorNwbApi(nwb_filepath_inprogress).save(json_session)
logging.info("Comparing a BehaviorSession created from JSON "
"with a BehaviorSession created from NWB")
nwb_api = BehaviorNwbApi(nwb_filepath_inprogress)
nwb_session = BehaviorSession(api=nwb_api)
assert sessions_are_equal(json_session, nwb_session, reraise=True)
os.rename(nwb_filepath_inprogress, nwb_filepath)
return {'output_path': nwb_filepath}
except Exception as e:
os.rename(nwb_filepath_inprogress, nwb_filepath_error)
raise e
def test_add_stimulus_presentations(nwbfile, stimulus_presentations_behavior,
stimulus_timestamps, roundtrip,
roundtripper,
stimulus_templates: StimulusTemplate):
nwb.add_stimulus_timestamps(nwbfile, stimulus_timestamps)
nwb.add_stimulus_presentations(nwbfile, stimulus_presentations_behavior)
nwb.add_stimulus_template(nwbfile=nwbfile,
stimulus_template=stimulus_templates)
# Add index for this template to NWB in-memory object:
nwb_template = nwbfile.stimulus_template[stimulus_templates.image_set_name]
compare = (stimulus_presentations_behavior['image_set'] ==
nwb_template.name)
curr_stimulus_index = stimulus_presentations_behavior[compare]
nwb.add_stimulus_index(nwbfile, curr_stimulus_index, nwb_template)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorNwbApi)
else:
obt = BehaviorNwbApi.from_nwbfile(nwbfile)
expected = stimulus_presentations_behavior.copy()
expected['is_change'] = [False, True, True, True, True]
obtained = obt.get_stimulus_presentations()
pd.testing.assert_frame_equal(expected[sorted(expected.columns)],
obtained[sorted(obtained.columns)],
check_dtype=False)
def test_add_task_parameters_stim_nan(nwbfile, roundtrip,
roundtripper,
task_parameters_nan_stimulus_duration):
"""
Same as test_add_task_parameters, but stimulus_duration_sec is NaN
"""
task_params = task_parameters_nan_stimulus_duration
nwb.add_task_parameters(nwbfile, task_params)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorNwbApi)
else:
obt = BehaviorNwbApi.from_nwbfile(nwbfile)
task_parameters_obt = obt.get_task_parameters()
assert len(task_parameters_obt) == len(task_params)
for key, val in task_params.items():
if key in ('omitted_flash_fraction',
'stimulus_duration_sec'):
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_licks(nwbfile, roundtrip, roundtripper, licks):
nwb.add_licks(nwbfile, licks)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorNwbApi)
else:
obt = BehaviorNwbApi.from_nwbfile(nwbfile)
pd.testing.assert_frame_equal(licks, obt.get_licks(), check_dtype=False)
def test_add_stimulus_timestamps(nwbfile, stimulus_timestamps,
roundtrip, roundtripper):
nwb.add_stimulus_timestamps(nwbfile, stimulus_timestamps)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorNwbApi)
else:
obt = BehaviorNwbApi.from_nwbfile(nwbfile)
np.testing.assert_array_almost_equal(stimulus_timestamps,
obt.get_stimulus_timestamps())
def test_add_stimulus_templates(nwbfile, behavior_stimuli_data_fixture,
roundtrip, roundtripper):
stimulus_templates = get_stimulus_templates(behavior_stimuli_data_fixture,
grating_images_dict={})
nwb.add_stimulus_template(nwbfile, stimulus_templates)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorNwbApi)
else:
obt = BehaviorNwbApi.from_nwbfile(nwbfile)
stimulus_templates_obt = obt.get_stimulus_templates()
assert stimulus_templates_obt == stimulus_templates
def test_add_running_acquisition_to_nwbfile(nwbfile, roundtrip, roundtripper,
running_acquisition_df_fixture):
nwbfile = nwb.add_running_acquisition_to_nwbfile(
nwbfile, running_acquisition_df_fixture)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorNwbApi)
else:
obt = BehaviorNwbApi.from_nwbfile(nwbfile)
obt_running_acq_df = obt.get_running_acquisition_df()
pd.testing.assert_frame_equal(running_acquisition_df_fixture,
obt_running_acq_df,
check_like=True)
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, BehaviorNwbApi)
else:
obt = BehaviorNwbApi.from_nwbfile(nwbfile)
obt_running_speed = obt.get_running_speed()
assert np.allclose(running_speed.timestamps,
obt_running_speed['timestamps'])
assert np.allclose(running_speed.values, obt_running_speed['speed'])
def test_add_behavior_only_metadata(roundtrip, roundtripper,
behavior_only_metadata_fixture):
metadata = behavior_only_metadata_fixture
nwbfile = pynwb.NWBFile(session_description='asession',
identifier='afile',
session_start_time=metadata['date_of_acquisition'])
nwb.add_metadata(nwbfile, metadata, behavior_only=True)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorNwbApi)
else:
obt = BehaviorNwbApi.from_nwbfile(nwbfile)
metadata_obt = obt.get_metadata()
assert len(metadata_obt) == len(metadata)
for key, val in metadata.items():
assert val == metadata_obt[key]
def test_add_task_parameters(nwbfile, roundtrip,
roundtripper, task_parameters):
nwb.add_task_parameters(nwbfile, task_parameters)
if roundtrip:
obt = roundtripper(nwbfile, BehaviorNwbApi)
else:
obt = BehaviorNwbApi.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 from_nwb_path(cls, nwb_path: str,
**api_kwargs: Any) -> "BehaviorSession":
return cls(api=BehaviorNwbApi.from_path(path=nwb_path, **api_kwargs))