def test_from_stimulus_file(self):
stimulus_file = StimulusFile.from_lims(
behavior_session_id=self.behavior_session_id, db=self.dbconn)
timestamps = StimulusTimestamps.from_stimulus_file(
stimulus_file=stimulus_file)
rewards = Rewards.from_stimulus_file(stimulus_file=stimulus_file,
stimulus_timestamps=timestamps)
assert rewards == self.expected
def setup_class(cls):
dir = Path(__file__).parent.resolve()
test_data_dir = dir / 'test_data'
stimulus_file = StimulusFile(filepath=test_data_dir /
'behavior_stimulus_file.pkl')
ts = StimulusTimestamps.from_stimulus_file(stimulus_file=stimulus_file)
cls.licks = Licks.from_stimulus_file(stimulus_file=stimulus_file,
stimulus_timestamps=ts)
def setup_method(self, method):
self.nwbfile = pynwb.NWBFile(session_description='asession',
identifier='1234',
session_start_time=datetime.now())
# Need to write stimulus timestamps first
bsf = StimulusFile(filepath=self.test_data_dir /
'behavior_stimulus_file.pkl')
ts = StimulusTimestamps.from_stimulus_file(stimulus_file=bsf)
ts.to_nwb(nwbfile=self.nwbfile)
def test_stimulus_timestamps_from_json(
monkeypatch, dict_repr, has_pkl, has_sync
):
mock_stimulus_file = create_autospec(StimulusFile)
mock_sync_file = create_autospec(SyncFile)
mock_get_behavior_stimulus_timestamps = create_autospec(
get_behavior_stimulus_timestamps
)
mock_get_ophys_stimulus_timestamps = create_autospec(
get_ophys_stimulus_timestamps
)
with monkeypatch.context() as m:
m.setattr(
"allensdk.brain_observatory.behavior.data_objects"
".timestamps.stimulus_timestamps.stimulus_timestamps.StimulusFile",
mock_stimulus_file
)
m.setattr(
"allensdk.brain_observatory.behavior.data_objects"
".timestamps.stimulus_timestamps.stimulus_timestamps.SyncFile",
mock_sync_file
)
m.setattr(
"allensdk.brain_observatory.behavior.data_objects"
".timestamps.stimulus_timestamps.stimulus_timestamps"
".get_behavior_stimulus_timestamps",
mock_get_behavior_stimulus_timestamps
)
m.setattr(
"allensdk.brain_observatory.behavior.data_objects"
".timestamps.stimulus_timestamps.stimulus_timestamps"
".get_ophys_stimulus_timestamps",
mock_get_ophys_stimulus_timestamps
)
mock_stimulus_file_instance = mock_stimulus_file.from_json(dict_repr)
ts_from_stim = StimulusTimestamps.from_stimulus_file(
stimulus_file=mock_stimulus_file_instance)
if has_pkl and has_sync:
mock_sync_file_instance = mock_sync_file.from_json(dict_repr)
ts_from_sync = StimulusTimestamps.from_sync_file(
sync_file=mock_sync_file_instance)
if has_pkl and has_sync:
mock_get_ophys_stimulus_timestamps.assert_called_once_with(
sync_path=mock_sync_file_instance.filepath
)
assert ts_from_sync._sync_file == mock_sync_file_instance
else:
assert ts_from_stim._stimulus_file == mock_stimulus_file_instance
mock_get_behavior_stimulus_timestamps.assert_called_once_with(
stimulus_pkl=mock_stimulus_file_instance.data
)
def test_from_stimulus_file(self):
stimulus_file = StimulusFile.from_lims(
behavior_session_id=self.behavior_session_id, db=self.dbconn)
stimulus_timestamps = StimulusTimestamps.from_stimulus_file(
stimulus_file=stimulus_file)
stimuli = Stimuli.from_stimulus_file(
stimulus_file=stimulus_file,
stimulus_timestamps=stimulus_timestamps,
limit_to_images=['im065'])
assert stimuli.presentations == self.expected_presentations
assert stimuli.templates == self.expected_templates
def test_stimulus_timestamps_from_json2():
dir = Path(__file__).parent.parent.resolve()
test_data_dir = dir / 'test_data'
sf_path = test_data_dir / 'stimulus_file.pkl'
sf = StimulusFile.from_json(
dict_repr={'behavior_stimulus_file': str(sf_path)})
stimulus_timestamps = StimulusTimestamps.from_stimulus_file(
stimulus_file=sf)
expected = np.array([0.016 * i for i in range(11)])
assert np.allclose(expected, stimulus_timestamps.value)
def from_lims(
cls,
db: PostgresQueryMixin,
behavior_session_id: int,
filtered: bool = True,
zscore_threshold: float = 10.0,
stimulus_timestamps: Optional[StimulusTimestamps] = None
) -> "RunningSpeed":
stimulus_file = StimulusFile.from_lims(db, behavior_session_id)
if stimulus_timestamps is None:
stimulus_timestamps = StimulusTimestamps.from_stimulus_file(
stimulus_file=stimulus_file)
running_speed = cls._get_running_speed_df(stimulus_file,
stimulus_timestamps,
filtered, zscore_threshold)
return cls(running_speed=running_speed,
stimulus_file=stimulus_file,
stimulus_timestamps=stimulus_timestamps,
filtered=filtered)
def from_lims(
cls,
db: PostgresQueryMixin,
behavior_session_id: int,
ophys_experiment_id: Optional[int] = None,
) -> "RunningAcquisition":
stimulus_file = StimulusFile.from_lims(db, behavior_session_id)
stimulus_timestamps = StimulusTimestamps.from_stimulus_file(
stimulus_file=stimulus_file)
running_acq_df = get_running_df(
data=stimulus_file.data,
time=stimulus_timestamps.value,
)
running_acq_df.drop("speed", axis=1, inplace=True)
return cls(
running_acquisition=running_acq_df,
stimulus_file=stimulus_file,
stimulus_timestamps=stimulus_timestamps,
)
def test_stimulus_timestamps_from_json3():
"""
Test that StimulusTimestamps.from_stimulus_file
just returns the sum of the intervalsms field in the
behavior stimulus pickle file, padded with a zero at the
first timestamp.
"""
dir = Path(__file__).parent.parent.resolve()
test_data_dir = dir / 'test_data'
sf_path = test_data_dir / 'stimulus_file.pkl'
sf = StimulusFile.from_json(
dict_repr={'behavior_stimulus_file': str(sf_path)})
sf._data['items']['behavior']['intervalsms'] = [0.1, 0.2, 0.3, 0.4]
stimulus_timestamps = StimulusTimestamps.from_stimulus_file(
stimulus_file=sf)
expected = np.array([0., 0.0001, 0.0003, 0.0006, 0.001])
np.testing.assert_array_almost_equal(stimulus_timestamps.value,
expected,
decimal=10)
def test_from_stimulus_file(self):
st = StimulusTimestamps.from_stimulus_file(
stimulus_file=self.stimulus_file)
licks = Licks.from_stimulus_file(stimulus_file=self.stimulus_file,
stimulus_timestamps=st)
assert licks == self.expected
def test_stimulus_timestamps_from_lims(
monkeypatch, behavior_session_id, ophys_experiment_id
):
mock_db_conn = create_autospec(PostgresQueryMixin, instance=True)
mock_stimulus_file = create_autospec(StimulusFile)
mock_sync_file = create_autospec(SyncFile)
mock_get_behavior_stimulus_timestamps = create_autospec(
get_behavior_stimulus_timestamps
)
mock_get_ophys_stimulus_timestamps = create_autospec(
get_ophys_stimulus_timestamps
)
with monkeypatch.context() as m:
m.setattr(
"allensdk.brain_observatory.behavior.data_objects"
".timestamps.stimulus_timestamps.stimulus_timestamps.StimulusFile",
mock_stimulus_file
)
m.setattr(
"allensdk.brain_observatory.behavior.data_objects"
".timestamps.stimulus_timestamps.stimulus_timestamps.SyncFile",
mock_sync_file
)
m.setattr(
"allensdk.brain_observatory.behavior.data_objects"
".timestamps.stimulus_timestamps.stimulus_timestamps"
".get_behavior_stimulus_timestamps",
mock_get_behavior_stimulus_timestamps
)
m.setattr(
"allensdk.brain_observatory.behavior.data_objects"
".timestamps.stimulus_timestamps.stimulus_timestamps"
".get_ophys_stimulus_timestamps",
mock_get_ophys_stimulus_timestamps
)
mock_stimulus_file_instance = mock_stimulus_file.from_lims(
mock_db_conn, behavior_session_id
)
ts_from_stim = StimulusTimestamps.from_stimulus_file(
stimulus_file=mock_stimulus_file_instance)
assert ts_from_stim._stimulus_file == mock_stimulus_file_instance
if behavior_session_id is not None and ophys_experiment_id is not None:
mock_sync_file_instance = mock_sync_file.from_lims(
mock_db_conn, ophys_experiment_id
)
ts_from_sync = StimulusTimestamps.from_sync_file(
sync_file=mock_sync_file_instance)
if behavior_session_id is not None and ophys_experiment_id is not None:
mock_get_ophys_stimulus_timestamps.assert_called_once_with(
sync_path=mock_sync_file_instance.filepath
)
assert ts_from_sync._sync_file == mock_sync_file_instance
else:
mock_stimulus_file.from_lims.assert_called_with(
mock_db_conn, behavior_session_id
)
mock_get_behavior_stimulus_timestamps.assert_called_once_with(
stimulus_pkl=mock_stimulus_file_instance.data
)
def from_lims(cls, behavior_session_id: int,
lims_db: Optional[PostgresQueryMixin] = None,
stimulus_timestamps: Optional[StimulusTimestamps] = None,
monitor_delay: Optional[float] = None,
date_of_acquisition: Optional[DateOfAcquisition] = None) \
-> "BehaviorSession":
"""
Parameters
----------
behavior_session_id
Behavior session id
lims_db
Database connection. If not provided will create a new one.
stimulus_timestamps
Stimulus timestamps. If not provided, will calculate stimulus
timestamps from stimulus file.
monitor_delay
Monitor delay. If not provided, will use an estimate.
To provide this value, see for example
allensdk.brain_observatory.behavior.data_objects.stimuli.util.
calculate_monitor_delay
date_of_acquisition
Date of acquisition. If not provided, will read from
behavior_sessions table.
Returns
-------
`BehaviorSession` instance
"""
if lims_db is None:
lims_db = db_connection_creator(
fallback_credentials=LIMS_DB_CREDENTIAL_MAP)
behavior_session_id = BehaviorSessionId(behavior_session_id)
stimulus_file = StimulusFile.from_lims(
db=lims_db, behavior_session_id=behavior_session_id.value)
if stimulus_timestamps is None:
stimulus_timestamps = StimulusTimestamps.from_stimulus_file(
stimulus_file=stimulus_file)
running_acquisition = RunningAcquisition.from_lims(
lims_db, behavior_session_id.value)
raw_running_speed = RunningSpeed.from_lims(
lims_db,
behavior_session_id.value,
filtered=False,
stimulus_timestamps=stimulus_timestamps)
running_speed = RunningSpeed.from_lims(
lims_db,
behavior_session_id.value,
stimulus_timestamps=stimulus_timestamps)
behavior_metadata = BehaviorMetadata.from_lims(
behavior_session_id=behavior_session_id, lims_db=lims_db)
if monitor_delay is None:
monitor_delay = cls._get_monitor_delay()
licks, rewards, stimuli, task_parameters, trials = \
cls._read_data_from_stimulus_file(
stimulus_file=stimulus_file,
stimulus_timestamps=stimulus_timestamps,
trial_monitor_delay=monitor_delay
)
if date_of_acquisition is None:
date_of_acquisition = DateOfAcquisition.from_lims(
behavior_session_id=behavior_session_id.value, lims_db=lims_db)
date_of_acquisition = date_of_acquisition.validate(
stimulus_file=stimulus_file,
behavior_session_id=behavior_session_id.value)
return BehaviorSession(behavior_session_id=behavior_session_id,
stimulus_timestamps=stimulus_timestamps,
running_acquisition=running_acquisition,
raw_running_speed=raw_running_speed,
running_speed=running_speed,
metadata=behavior_metadata,
licks=licks,
rewards=rewards,
stimuli=stimuli,
task_parameters=task_parameters,
trials=trials,
date_of_acquisition=date_of_acquisition)