def from_json(cls,
session_data: dict,
monitor_delay: Optional[float] = None) \
-> "BehaviorSession":
"""
Parameters
----------
session_data
Dict of input data necessary to construct a session
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
Returns
-------
`BehaviorSession` instance
"""
behavior_session_id = BehaviorSessionId.from_json(
dict_repr=session_data)
stimulus_file = StimulusFile.from_json(dict_repr=session_data)
stimulus_timestamps = StimulusTimestamps.from_json(
dict_repr=session_data)
running_acquisition = RunningAcquisition.from_json(
dict_repr=session_data)
raw_running_speed = RunningSpeed.from_json(dict_repr=session_data,
filtered=False)
running_speed = RunningSpeed.from_json(dict_repr=session_data)
metadata = BehaviorMetadata.from_json(dict_repr=session_data)
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
)
date_of_acquisition = DateOfAcquisition.from_json(
dict_repr=session_data)\
.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=metadata,
licks=licks,
rewards=rewards,
stimuli=stimuli,
task_parameters=task_parameters,
trials=trials,
date_of_acquisition=date_of_acquisition)
def test_running_acquisition_from_json(monkeypatch, dict_repr,
returned_running_acq_df,
expected_running_acq_df):
mock_stimulus_file = create_autospec(StimulusFile)
mock_stimulus_timestamps = create_autospec(StimulusTimestamps)
mock_get_running_df = create_autospec(get_running_df)
mock_get_running_df.return_value = returned_running_acq_df
with monkeypatch.context() as m:
m.setattr(
"allensdk.brain_observatory.behavior.data_objects"
".running_speed.running_acquisition.StimulusFile",
mock_stimulus_file)
m.setattr(
"allensdk.brain_observatory.behavior.data_objects"
".running_speed.running_acquisition.StimulusTimestamps",
mock_stimulus_timestamps)
m.setattr(
"allensdk.brain_observatory.behavior.data_objects"
".running_speed.running_acquisition.get_running_df",
mock_get_running_df)
obt = RunningAcquisition.from_json(dict_repr)
mock_stimulus_file.from_json.assert_called_once_with(dict_repr)
mock_stimulus_file_instance = mock_stimulus_file.from_json(dict_repr)
assert obt._stimulus_file == mock_stimulus_file_instance
mock_stimulus_timestamps.from_json.assert_called_once_with(dict_repr)
mock_stimulus_timestamps_instance = mock_stimulus_timestamps.from_json(
dict_repr)
assert obt._stimulus_timestamps == mock_stimulus_timestamps_instance
mock_get_running_df.assert_called_once_with(
data=mock_stimulus_file_instance.data,
time=mock_stimulus_timestamps_instance.value,
)
pd.testing.assert_frame_equal(obt.value, expected_running_acq_df)