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 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)