def add_eye_tracking_rig_geometry_data_to_nwbfile(
nwbfile: NWBFile, eye_tracking_rig_geometry: dict) -> NWBFile:
""" Rig geometry dict should consist of the following fields:
monitor_position_mm: [x, y, z]
monitor_rotation_deg: [x, y, z]
camera_position_mm: [x, y, z]
camera_rotation_deg: [x, y, z]
led_position: [x, y, z]
equipment: A string describing rig
"""
eye_tracking_rig_mod = pynwb.ProcessingModule(
name='eye_tracking_rig_metadata',
description='Eye tracking rig metadata module')
ophys_eye_tracking_rig_metadata = load_pynwb_extension(
OphysEyeTrackingRigMetadataSchema, 'ndx-aibs-behavior-ophys')
rig_metadata = ophys_eye_tracking_rig_metadata(
name="eye_tracking_rig_metadata",
equipment=eye_tracking_rig_geometry['equipment'],
monitor_position=eye_tracking_rig_geometry['monitor_position_mm'],
monitor_position__unit_of_measurement="mm",
camera_position=eye_tracking_rig_geometry['camera_position_mm'],
camera_position__unit_of_measurement="mm",
led_position=eye_tracking_rig_geometry['led_position'],
led_position__unit_of_measurement="mm",
monitor_rotation=eye_tracking_rig_geometry['monitor_rotation_deg'],
monitor_rotation__unit_of_measurement="deg",
camera_rotation=eye_tracking_rig_geometry['camera_rotation_deg'],
camera_rotation__unit_of_measurement="deg")
eye_tracking_rig_mod.add_data_interface(rig_metadata)
nwbfile.add_processing_module(eye_tracking_rig_mod)
return nwbfile
def add_metadata(nwbfile, metadata: dict):
# Rename incoming metadata fields to conform with pynwb Subject fields
metadata = metadata.copy()
metadata["subject_id"] = metadata.pop("LabTracks_ID")
metadata["genotype"] = metadata.pop("full_genotype")
metadata_clean = CompleteOphysBehaviorMetadataSchema().dump(metadata)
# Subject related metadata should be saved to our BehaviorSubject
# (augmented pyNWB 'Subject') NWB class
subject_fields = {"age", "driver_line", "genotype",
"subject_id", "reporter_line", "sex"}
subject_metadata = {k: v for k, v in metadata_clean.items()
if k in subject_fields}
for subject_key in subject_metadata.keys():
metadata_clean.pop(subject_key, None)
BehaviorSubject = load_pynwb_extension(SubjectMetadataSchema,
'ndx-aibs-behavior-ophys')
nwb_subject = BehaviorSubject(
description="A visual behavior subject with a LabTracks ID",
age=subject_metadata["age"],
driver_line=subject_metadata["driver_line"],
genotype=subject_metadata["genotype"],
subject_id=str(subject_metadata["subject_id"]),
reporter_line=subject_metadata["reporter_line"],
sex=subject_metadata["sex"],
species='Mus musculus')
nwbfile.subject = nwb_subject
# Remove metadata that will go into pyNWB base classes
for key in OphysBehaviorMetadataSchema.neurodata_skip:
metadata_clean.pop(key, None)
# Remaining metadata can go into our custom extension
new_metadata_dict = {}
for key, val in metadata_clean.items():
if isinstance(val, list):
new_metadata_dict[key] = np.array(val)
elif isinstance(val, (datetime.datetime, uuid.UUID)):
new_metadata_dict[key] = str(val)
else:
new_metadata_dict[key] = val
OphysBehaviorMetadata = load_pynwb_extension(OphysBehaviorMetadataSchema,
'ndx-aibs-behavior-ophys')
nwb_metadata = OphysBehaviorMetadata(name='metadata', **new_metadata_dict)
nwbfile.add_lab_meta_data(nwb_metadata)
def add_task_parameters(nwbfile, task_parameters):
OphysBehaviorTaskParameters = load_pynwb_extension(
BehaviorTaskParametersSchema, 'ndx-aibs-behavior-ophys')
task_parameters_clean = BehaviorTaskParametersSchema().dump(
task_parameters)
new_task_parameters_dict = {}
for key, val in task_parameters_clean.items():
if isinstance(val, list):
new_task_parameters_dict[key] = np.array(val)
else:
new_task_parameters_dict[key] = val
nwb_task_parameters = OphysBehaviorTaskParameters(
name='task_parameters', **new_task_parameters_dict)
nwbfile.add_lab_meta_data(nwb_task_parameters)
BehaviorTaskParametersSchema, OphysEyeTrackingRigMetadataSchema)
from allensdk.brain_observatory.behavior.trials_processing import (
TRIAL_COLUMN_DESCRIPTION_DICT)
from allensdk.brain_observatory.nwb import TimeSeries
from allensdk.brain_observatory.nwb.eye_tracking.ndx_ellipse_eye_tracking import ( # noqa: E501
EllipseEyeTracking, EllipseSeries)
from allensdk.brain_observatory.behavior.write_nwb.extensions \
.event_detection.ndx_ophys_events import OphysEventDetection
from allensdk.brain_observatory.nwb.metadata import load_pynwb_extension
from allensdk.brain_observatory.behavior.session_apis.data_io import (
BehaviorNwbApi)
from allensdk.brain_observatory.nwb.nwb_utils import set_omitted_stop_time
from allensdk.brain_observatory.behavior.eye_tracking_processing import (
determine_outliers, determine_likely_blinks)
load_pynwb_extension(BehaviorTaskParametersSchema, 'ndx-aibs-behavior-ophys')
class BehaviorOphysNwbApi(BehaviorNwbApi, BehaviorOphysBase):
"""A data fetching class that serves as an API for fetching 'raw'
data from an NWB file that is both necessary and sufficient for filling
a 'BehaviorOphysSession'.
"""
def __init__(self, *args, **kwargs):
self.filter_invalid_rois = kwargs.pop("filter_invalid_rois", False)
super().__init__(*args, **kwargs)
def save(self, session_object):
# Cannot type session_object due to a circular dependency
# TODO fix circular dependency and add type
def add_metadata(nwbfile, metadata: dict, behavior_only: bool):
# Rename or reformat incoming metadata fields to conform with pynwb fields
tmp_metadata = metadata.copy()
tmp_metadata["subject_id"] = tmp_metadata.pop("mouse_id")
tmp_metadata["genotype"] = tmp_metadata.pop("full_genotype")
if not behavior_only:
imaging_plane_group = metadata["imaging_plane_group"]
if imaging_plane_group is None:
tmp_metadata["imaging_plane_group"] = -1
else:
tmp_metadata["imaging_plane_group"] = imaging_plane_group
metadata_clean = CompleteOphysBehaviorMetadataSchema().dump(tmp_metadata)
# Subject related metadata should be saved to our BehaviorSubject
# (augmented pyNWB 'Subject') NWB class
subject_fields = {
"age_in_days", "driver_line", "genotype", "subject_id",
"reporter_line", "sex"
}
subject_metadata = {
k: v
for k, v in metadata_clean.items() if k in subject_fields
}
for subject_key in subject_metadata.keys():
metadata_clean.pop(subject_key, None)
BehaviorSubject = load_pynwb_extension(SubjectMetadataSchema,
'ndx-aibs-behavior-ophys')
def _get_age(age_in_days: Optional[int]) -> Optional[str]:
"""Convert numeric age_in_days to ISO 8601"""
if age_in_days is None:
return 'null'
return f'P{age_in_days}D'
nwb_subject = BehaviorSubject(
description="A visual behavior subject with a LabTracks ID",
age=_get_age(age_in_days=subject_metadata['age_in_days']),
driver_line=subject_metadata["driver_line"],
genotype=subject_metadata["genotype"],
subject_id=str(subject_metadata["subject_id"]),
reporter_line=subject_metadata["reporter_line"],
sex=subject_metadata["sex"],
species='Mus musculus')
nwbfile.subject = nwb_subject
# Remove metadata that will go into pyNWB base classes
for key in OphysBehaviorMetadataSchema.neurodata_skip:
metadata_clean.pop(key, None)
# Remaining metadata can go into our custom extension
new_metadata_dict = {}
for key, val in metadata_clean.items():
if isinstance(val, list):
new_metadata_dict[key] = np.array(val)
elif isinstance(val, (datetime.datetime, uuid.UUID)):
new_metadata_dict[key] = str(val)
else:
new_metadata_dict[key] = val
if behavior_only:
BehaviorMetadata = load_pynwb_extension(BehaviorMetadataSchema,
'ndx-aibs-behavior-ophys')
nwb_metadata = BehaviorMetadata(name='metadata', **new_metadata_dict)
else:
OphysBehaviorMetadata = load_pynwb_extension(
OphysBehaviorMetadataSchema, 'ndx-aibs-behavior-ophys')
nwb_metadata = OphysBehaviorMetadata(name='metadata',
**new_metadata_dict)
nwbfile.add_lab_meta_data(nwb_metadata)
