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 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_file_from_lims(stimulus_file_fixture, behavior_session_id):
stim_pkl_path, stim_pkl_data = stimulus_file_fixture
mock_db_conn = create_autospec(PostgresQueryMixin, instance=True)
# Basic test case
mock_db_conn.fetchone.return_value = str(stim_pkl_path)
stimulus_file = StimulusFile.from_lims(mock_db_conn, behavior_session_id)
assert stimulus_file.data == stim_pkl_data
# Now test caching by deleting stimulus_file and also asserting db
# `fetchone` called only once
stim_pkl_path.unlink()
stimfile_cached = StimulusFile.from_lims(mock_db_conn, behavior_session_id)
assert stimfile_cached.data == stim_pkl_data
query = STIMULUS_FILE_QUERY_TEMPLATE.format(
behavior_session_id=behavior_session_id)
mock_db_conn.fetchone.assert_called_once_with(query, strict=True)
def from_lims(
cls,
db: PostgresQueryMixin,
behavior_session_id: int,
ophys_experiment_id: Optional[int] = None) -> "StimulusTimestamps":
stimulus_file = StimulusFile.from_lims(db, behavior_session_id)
if ophys_experiment_id:
sync_file = SyncFile.from_lims(
db=db, ophys_experiment_id=ophys_experiment_id)
return cls.from_sync_file(sync_file=sync_file)
else:
return cls.from_stimulus_file(stimulus_file=stimulus_file)
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 _get_stimulus_data():
lims_db = db_connection_creator(
fallback_credentials=LIMS_DB_CREDENTIAL_MAP)
stimulus_file = StimulusFile.from_lims(
db=lims_db, behavior_session_id=behavior_experiment_id)
return stimulus_file.data
def test_from_stimulus_file(self):
stimulus_file = StimulusFile.from_lims(
behavior_session_id=self.behavior_session_id, db=self.dbconn)
tp = TaskParameters.from_stimulus_file(stimulus_file=stimulus_file)
assert tp == self.expected
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)