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 get_behavior_session(self,
behavior_session_id: int) -> BehaviorSession:
"""Returns a BehaviorSession object that contains methods to
analyze a single behavior session.
:param behavior_session_id: id that corresponds to a behavior session
:type behavior_session_id: int
:rtype: BehaviorSession
"""
return BehaviorSession(BehaviorLimsApi(behavior_session_id))
def test_behavior_session_list_data_attributes_and_methods():
# Test that data related methods/attributes/properties for
# BehaviorSession are returned properly.
# This test will need to be updated if:
# 1. Data being returned by class has changed
# 2. Inheritance of class has changed
expected = {
'behavior_session_id', 'get_performance_metrics', 'get_reward_rate',
'get_rolling_performance_df', 'licks', 'metadata', 'raw_running_speed',
'rewards', 'running_speed', 'stimulus_presentations',
'stimulus_templates', 'stimulus_timestamps', 'task_parameters',
'trials'
}
behavior_session = BehaviorSession(api=MagicMock())
obt = behavior_session.list_data_attributes_and_methods()
assert any(expected ^ set(obt)) is False
def test_behavior_session_list_data_attributes_and_methods(monkeypatch):
"""Test that data related methods/attributes/properties for
BehaviorSession are returned properly."""
def dummy_init(self):
pass
with monkeypatch.context() as ctx:
ctx.setattr(BehaviorSession, '__init__', dummy_init)
bs = BehaviorSession()
obt = bs.list_data_attributes_and_methods()
expected = {
'behavior_session_id', 'get_performance_metrics', 'get_reward_rate',
'get_rolling_performance_df', 'licks', 'metadata', 'raw_running_speed',
'rewards', 'running_speed', 'stimulus_presentations',
'stimulus_templates', 'stimulus_timestamps', 'task_parameters',
'trials'
}
assert any(expected ^ set(obt)) is False
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.from_json(session_data)
behavior_session_id = session_data['behavior_session_id']
lims_session = BehaviorSession.from_lims(behavior_session_id)
logging.info("Comparing a BehaviorSession created from JSON "
"with a BehaviorSession created from LIMS")
assert sessions_are_equal(json_session, lims_session, reraise=True)
nwbfile = lims_session.to_nwb()
with NWBHDF5IO(nwb_filepath_inprogress, 'w') as nwb_file_writer:
nwb_file_writer.write(nwbfile)
logging.info("Comparing a BehaviorSession created from JSON "
"with a BehaviorSession created from NWB")
nwb_session = BehaviorSession.from_nwb_path(nwb_filepath_inprogress)
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:
if os.path.isfile(nwb_filepath_inprogress):
os.rename(nwb_filepath_inprogress, nwb_filepath_error)
raise e
def get_behavior_session(self,
behavior_session_id: int) -> BehaviorSession:
"""get a BehaviorSession by specifying behavior_session_id
Parameters
----------
behavior_session_id: int
the id of the behavior_session
Returns
-------
BehaviorSession
Notes
-----
entries in the _behavior_session_table represent
(1) ophys_sessions which have a many-to-one mapping between nwb files
and behavior sessions. (file_id is NaN)
AND
(2) behavior only sessions, which have a one-to-one mapping with
nwb files. (file_id is not Nan)
In the case of (1) this method returns an object which is just behavior
data which is shared by all experiments in 1 session. This is extracted
from the nwb file for the first-listed ophys_experiment.
"""
row = self._behavior_session_table.query(
f"behavior_session_id=={behavior_session_id}")
if row.shape[0] != 1:
raise RuntimeError("The behavior_session_table should have "
"1 and only 1 entry for a given "
"behavior_session_id. For "
f"{behavior_session_id} "
f" there are {row.shape[0]} entries.")
row = row.squeeze()
has_file_id = not pd.isna(row[self.cache.file_id_column])
if not has_file_id:
oeid = row.ophys_experiment_id[0]
row = self._ophys_experiment_table.query(f"index=={oeid}")
file_id = str(int(row[self.cache.file_id_column]))
data_path = self._get_data_path(file_id=file_id)
return BehaviorSession.from_nwb_path(str(data_path))
def test_eye_tracking(dilation_frames, z_threshold, monkeypatch):
"""A very long test just to test that eye tracking arguments are sent to
EyeTrackingTable factory method from BehaviorOphysExperiment.from_lims"""
expected = EyeTrackingTable(eye_tracking=pd.DataFrame([1, 2, 3]))
EyeTrackingTable_mock = create_autospec(EyeTrackingTable)
EyeTrackingTable_mock.from_data_file.return_value = expected
etf = create_autospec(EyeTrackingFile, instance=True)
sf = create_autospec(SyncFile, instance=True)
with monkeypatch.context() as ctx:
ctx.setattr(
'allensdk.brain_observatory.behavior.'
'behavior_ophys_experiment.db_connection_creator',
create_autospec(db_connection_creator, instance=True))
ctx.setattr(SyncFile, 'from_lims', lambda db, ophys_experiment_id: sf)
ctx.setattr(
StimulusTimestamps, 'from_sync_file',
lambda sync_file: create_autospec(StimulusTimestamps,
instance=True))
ctx.setattr(
BehaviorSessionId, 'from_lims',
lambda db, ophys_experiment_id: create_autospec(BehaviorSessionId,
instance=True))
ctx.setattr(ImagingPlaneGroup, 'from_lims',
lambda lims_db, ophys_experiment_id: None)
ctx.setattr(
BehaviorOphysMetadata, 'from_lims',
lambda lims_db, ophys_experiment_id, is_multiplane:
create_autospec(BehaviorOphysMetadata, instance=True))
ctx.setattr(
'allensdk.brain_observatory.behavior.'
'behavior_ophys_experiment.calculate_monitor_delay',
create_autospec(calculate_monitor_delay))
ctx.setattr(
DateOfAcquisitionOphys, 'from_lims',
lambda lims_db, ophys_experiment_id: create_autospec(
DateOfAcquisitionOphys, instance=True))
ctx.setattr(
BehaviorSession, 'from_lims',
lambda lims_db, behavior_session_id, stimulus_timestamps,
monitor_delay, date_of_acquisition: BehaviorSession(
behavior_session_id=None,
stimulus_timestamps=None,
running_acquisition=None,
raw_running_speed=None,
running_speed=None,
licks=None,
rewards=None,
stimuli=None,
task_parameters=None,
trials=None,
metadata=None,
date_of_acquisition=None,
))
ctx.setattr(
OphysTimestamps, 'from_sync_file',
lambda sync_file: create_autospec(OphysTimestamps, instance=True))
ctx.setattr(
Projections, 'from_lims', lambda lims_db, ophys_experiment_id:
create_autospec(Projections, instance=True))
ctx.setattr(
CellSpecimens, 'from_lims', lambda lims_db, ophys_experiment_id,
ophys_timestamps, segmentation_mask_image_spacing, events_params,
exclude_invalid_rois: create_autospec(BehaviorSession,
instance=True))
ctx.setattr(
RigidMotionTransformFile, 'from_lims',
lambda db, ophys_experiment_id: create_autospec(
RigidMotionTransformFile, instance=True))
ctx.setattr(EyeTrackingFile, 'from_lims',
lambda db, ophys_experiment_id: etf)
ctx.setattr(
EyeTrackingTable, 'from_data_file', lambda data_file, sync_file,
z_threshold, dilation_frames: EyeTrackingTable_mock.from_data_file(
data_file=data_file,
sync_file=sync_file,
z_threshold=z_threshold,
dilation_frames=dilation_frames))
ctx.setattr(
EyeTrackingRigGeometry, 'from_lims',
lambda lims_db, ophys_experiment_id: create_autospec(
EyeTrackingRigGeometry, instance=True))
boe = BehaviorOphysExperiment.from_lims(
ophys_experiment_id=1,
eye_tracking_z_threshold=z_threshold,
eye_tracking_dilation_frames=dilation_frames)
obtained = boe.eye_tracking
assert obtained.equals(expected.value)
EyeTrackingTable_mock.from_data_file.assert_called_with(
data_file=etf,
sync_file=sf,
z_threshold=z_threshold,
dilation_frames=dilation_frames)
def __init__(self,
api=None,
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):
"""
Parameters
----------
api : object, optional
The backend api used by the session object to get behavior ophys
data, by default None.
eye_tracking_z_threshold : float, optional
The z-threshold when determining which frames likely contain
outliers for eye or pupil areas. Influences which frames
are considered 'likely blinks'. By default 3.0
eye_tracking_dilation_frames : int, optional
Determines the number of adjacent frames that will be marked
as 'likely_blink' when performing blink detection for
`eye_tracking` data, by default 2
events_filter_scale : float, optional
Stdev of halfnorm distribution used to convolve ophys events with
a 1d causal half-gaussian filter to smooth it for visualization,
by default 2.0
events_filter_n_time_steps : int, optional
Number of time steps to use for convolution of ophys events
"""
BehaviorSession.__init__(self, api=api)
ParamsMixin.__init__(self, ignore={'api'})
# eye_tracking processing params
self._eye_tracking_z_threshold = eye_tracking_z_threshold
self._eye_tracking_dilation_frames = eye_tracking_dilation_frames
# events processing params
self._events_filter_scale = events_filter_scale
self._events_filter_n_time_steps = events_filter_n_time_steps
# LazyProperty constructor provided by LazyPropertyMixin
LazyProperty = self.LazyProperty
# Initialize attributes to be lazily evaluated
self._ophys_session_id = LazyProperty(self.api.get_ophys_session_id)
self._ophys_experiment_id = LazyProperty(
self.api.get_ophys_experiment_id)
self._max_projection = LazyProperty(self.api.get_max_projection,
wrappers=[ImageApi.deserialize])
self._average_projection = LazyProperty(
self.api.get_average_projection, wrappers=[ImageApi.deserialize])
self._ophys_timestamps = LazyProperty(self.api.get_ophys_timestamps,
settable=True)
self._dff_traces = LazyProperty(self.api.get_dff_traces, settable=True)
self._events = LazyProperty(self.api.get_events, settable=True)
self._cell_specimen_table = LazyProperty(
self.api.get_cell_specimen_table, settable=True)
self._corrected_fluorescence_traces = LazyProperty(
self.api.get_corrected_fluorescence_traces, settable=True)
self._motion_correction = LazyProperty(self.api.get_motion_correction,
settable=True)
self._segmentation_mask_image = LazyProperty(
self.get_segmentation_mask_image)
self._eye_tracking = LazyProperty(
self.api.get_eye_tracking,
settable=True,
z_threshold=self._eye_tracking_z_threshold,
dilation_frames=self._eye_tracking_dilation_frames)
self._eye_tracking_rig_geometry = LazyProperty(
self.api.get_eye_tracking_rig_geometry)
def from_json(cls,
session_data: dict,
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
----------
session_data
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_json(
dict_repr=session_data)
return cls._is_multi_plane_session(
imaging_plane_group_meta=imaging_plane_group_meta)
def _get_motion_correction():
rigid_motion_transform_file = RigidMotionTransformFile.from_json(
dict_repr=session_data)
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_json(
dict_repr=session_data)
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
sync_file = SyncFile.from_json(dict_repr=session_data)
is_multiplane_session = _is_multi_plane_session()
meta = BehaviorOphysMetadata.from_json(
dict_repr=session_data, is_multiplane=is_multiplane_session)
monitor_delay = calculate_monitor_delay(
sync_file=sync_file, equipment=meta.behavior_metadata.equipment)
behavior_session = BehaviorSession.from_json(
session_data=session_data, monitor_delay=monitor_delay)
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_json(dict_repr=session_data)
cell_specimens = CellSpecimens.from_json(
dict_repr=session_data,
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_json(
dict_repr=session_data)
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=behavior_session._date_of_acquisition)
def from_nwb(cls,
nwbfile: NWBFile,
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) -> "BehaviorOphysExperiment":
"""
Parameters
----------
nwbfile
eye_tracking_z_threshold : float, optional
The z-threshold when determining which frames likely contain
outliers for eye or pupil areas. Influences which frames
are considered 'likely blinks'. By default 3.0
eye_tracking_dilation_frames : int, optional
Determines the number of adjacent frames that will be marked
as 'likely_blink' when performing blink detection for
`eye_tracking` data, by default 2
events_filter_scale : float, optional
Stdev of halfnorm distribution used to convolve ophys events with
a 1d causal half-gaussian filter to smooth it for visualization,
by default 2.0
events_filter_n_time_steps : int, optional
Number of time steps to use for convolution of ophys events
exclude_invalid_rois
Whether to exclude invalid rois
"""
def _is_multi_plane_session():
imaging_plane_group_meta = ImagingPlaneGroup.from_nwb(
nwbfile=nwbfile)
return cls._is_multi_plane_session(
imaging_plane_group_meta=imaging_plane_group_meta)
behavior_session = BehaviorSession.from_nwb(nwbfile=nwbfile)
projections = Projections.from_nwb(nwbfile=nwbfile)
cell_specimens = CellSpecimens.from_nwb(
nwbfile=nwbfile,
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)
eye_tracking_rig_geometry = EyeTrackingRigGeometry.from_nwb(
nwbfile=nwbfile)
eye_tracking_table = EyeTrackingTable.from_nwb(
nwbfile=nwbfile,
z_threshold=eye_tracking_z_threshold,
dilation_frames=eye_tracking_dilation_frames)
motion_correction = MotionCorrection.from_nwb(nwbfile=nwbfile)
is_multiplane_session = _is_multi_plane_session()
metadata = BehaviorOphysMetadata.from_nwb(
nwbfile=nwbfile, is_multiplane=is_multiplane_session)
if is_multiplane_session:
ophys_timestamps = OphysTimestampsMultiplane.from_nwb(
nwbfile=nwbfile)
else:
ophys_timestamps = OphysTimestamps.from_nwb(nwbfile=nwbfile)
date_of_acquisition = DateOfAcquisitionOphys.from_nwb(nwbfile=nwbfile)
return BehaviorOphysExperiment(
behavior_session=behavior_session,
cell_specimens=cell_specimens,
eye_tracking_rig_geometry=eye_tracking_rig_geometry,
eye_tracking_table=eye_tracking_table,
motion_correction=motion_correction,
metadata=metadata,
ophys_timestamps=ophys_timestamps,
projections=projections,
date_of_acquisition=date_of_acquisition)
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)
def test_cache_clear_no_warning(self, caplog):
caplog.clear()
bs = BehaviorSession(api=DummyApiCache())
bs.cache_clear()
assert len(caplog.record_tuples) == 0
def setup_class(cls):
cls.behavior_session = BehaviorSession(api=DummyApi())
