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_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,
ophys_experiment_id: int,
eye_tracking_z_threshold: float = 3.0,
eye_tracking_dilation_frames: int = 2,
events_filter_scale: float = 2.0,
events_filter_n_time_steps: int = 20,
exclude_invalid_rois=True,
skip_eye_tracking=False) -> \
"BehaviorOphysExperiment":
"""
Parameters
----------
ophys_experiment_id
eye_tracking_z_threshold
See `BehaviorOphysExperiment.from_nwb`
eye_tracking_dilation_frames
See `BehaviorOphysExperiment.from_nwb`
events_filter_scale
See `BehaviorOphysExperiment.from_nwb`
events_filter_n_time_steps
See `BehaviorOphysExperiment.from_nwb`
exclude_invalid_rois
Whether to exclude invalid rois
skip_eye_tracking
Used to skip returning eye tracking data
"""
def _is_multi_plane_session():
imaging_plane_group_meta = ImagingPlaneGroup.from_lims(
ophys_experiment_id=ophys_experiment_id, lims_db=lims_db)
return cls._is_multi_plane_session(
imaging_plane_group_meta=imaging_plane_group_meta)
def _get_motion_correction():
rigid_motion_transform_file = RigidMotionTransformFile.from_lims(
ophys_experiment_id=ophys_experiment_id, db=lims_db)
return MotionCorrection.from_data_file(
rigid_motion_transform_file=rigid_motion_transform_file)
def _get_eye_tracking_table(sync_file: SyncFile):
eye_tracking_file = EyeTrackingFile.from_lims(
db=lims_db, ophys_experiment_id=ophys_experiment_id)
eye_tracking_table = EyeTrackingTable.from_data_file(
data_file=eye_tracking_file,
sync_file=sync_file,
z_threshold=eye_tracking_z_threshold,
dilation_frames=eye_tracking_dilation_frames)
return eye_tracking_table
lims_db = db_connection_creator(
fallback_credentials=LIMS_DB_CREDENTIAL_MAP)
sync_file = SyncFile.from_lims(db=lims_db,
ophys_experiment_id=ophys_experiment_id)
stimulus_timestamps = StimulusTimestamps.from_sync_file(
sync_file=sync_file)
behavior_session_id = BehaviorSessionId.from_lims(
db=lims_db, ophys_experiment_id=ophys_experiment_id)
is_multiplane_session = _is_multi_plane_session()
meta = BehaviorOphysMetadata.from_lims(
ophys_experiment_id=ophys_experiment_id,
lims_db=lims_db,
is_multiplane=is_multiplane_session)
monitor_delay = calculate_monitor_delay(
sync_file=sync_file, equipment=meta.behavior_metadata.equipment)
date_of_acquisition = DateOfAcquisitionOphys.from_lims(
ophys_experiment_id=ophys_experiment_id, lims_db=lims_db)
behavior_session = BehaviorSession.from_lims(
lims_db=lims_db,
behavior_session_id=behavior_session_id.value,
stimulus_timestamps=stimulus_timestamps,
monitor_delay=monitor_delay,
date_of_acquisition=date_of_acquisition)
if is_multiplane_session:
ophys_timestamps = OphysTimestampsMultiplane.from_sync_file(
sync_file=sync_file,
group_count=meta.ophys_metadata.imaging_plane_group_count,
plane_group=meta.ophys_metadata.imaging_plane_group)
else:
ophys_timestamps = OphysTimestamps.from_sync_file(
sync_file=sync_file)
projections = Projections.from_lims(
ophys_experiment_id=ophys_experiment_id, lims_db=lims_db)
cell_specimens = CellSpecimens.from_lims(
ophys_experiment_id=ophys_experiment_id,
lims_db=lims_db,
ophys_timestamps=ophys_timestamps,
segmentation_mask_image_spacing=projections.max_projection.spacing,
events_params=EventsParams(
filter_scale=events_filter_scale,
filter_n_time_steps=events_filter_n_time_steps),
exclude_invalid_rois=exclude_invalid_rois)
motion_correction = _get_motion_correction()
if skip_eye_tracking:
eye_tracking_table = None
eye_tracking_rig_geometry = None
else:
eye_tracking_table = _get_eye_tracking_table(sync_file=sync_file)
eye_tracking_rig_geometry = EyeTrackingRigGeometry.from_lims(
ophys_experiment_id=ophys_experiment_id, lims_db=lims_db)
return BehaviorOphysExperiment(
behavior_session=behavior_session,
cell_specimens=cell_specimens,
ophys_timestamps=ophys_timestamps,
metadata=meta,
projections=projections,
motion_correction=motion_correction,
eye_tracking_table=eye_tracking_table,
eye_tracking_rig_geometry=eye_tracking_rig_geometry,
date_of_acquisition=date_of_acquisition)