def add_task_parameters(nwbfile, task_parameters):
OphysBehaviorTaskParameters = load_LabMetaData_extension(OphysBehaviorTaskParametersSchema, 'AIBS_ophys_behavior')
task_parameters_clean = OphysBehaviorTaskParametersSchema().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)
def add_metadata(nwbfile, metadata):
OphysBehaviorMetaData = load_LabMetaData_extension(OphysBehaviorMetaDataSchema, 'AIBS_ophys_behavior')
metadata_clean = OphysBehaviorMetaDataSchema().dump(metadata)
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
nwb_metadata = OphysBehaviorMetaData(name='metadata', **new_metadata_dict)
nwbfile.add_lab_meta_data(nwb_metadata)
import uuid
from pandas.util.testing import assert_frame_equal
import os
import math
import numpy as np
import xarray as xr
import pandas as pd
from allensdk.core.lazy_property import LazyProperty
from allensdk.brain_observatory.nwb.nwb_api import NwbApi
from allensdk.brain_observatory.behavior.trials_processing import TRIAL_COLUMN_DESCRIPTION_DICT
from allensdk.brain_observatory.behavior.schemas import OphysBehaviorMetaDataSchema, OphysBehaviorTaskParametersSchema
from allensdk.brain_observatory.nwb.metadata import load_LabMetaData_extension
from allensdk.brain_observatory.behavior.behavior_ophys_api import BehaviorOphysApiBase
load_LabMetaData_extension(OphysBehaviorMetaDataSchema, 'AIBS_ophys_behavior')
load_LabMetaData_extension(OphysBehaviorTaskParametersSchema,
'AIBS_ophys_behavior')
class BehaviorOphysNwbApi(NwbApi, BehaviorOphysApiBase):
def __init__(self, *args, **kwargs):
self.filter_invalid_rois = kwargs.pop("filter_invalid_rois", False)
super(BehaviorOphysNwbApi, self).__init__(*args, **kwargs)
def save(self, session_object):
nwbfile = NWBFile(
session_description=str(session_object.metadata['session_type']),
identifier=str(session_object.ophys_experiment_id),
session_start_time=session_object.metadata['experiment_datetime'],