nicain

from pynwb import NWBNamespaceBuilder, NWBGroupSpec, NWBAttributeSpec
import numpy as np
from pynwb import get_class, load_namespaces
from datetime import datetime
from pynwb import NWBFile
from form.backends.hdf5 import HDF5IO
from pynwb import get_build_manager


ns_path = "mylab.namespace.yaml"

nicain

from pynwb import NWBNamespaceBuilder, NWBGroupSpec, NWBDatasetSpec
import numpy as np
from pynwb import get_class, load_namespaces
from datetime import datetime
from pynwb import NWBFile
from form.backends.hdf5 import HDF5IO
from pynwb import get_build_manager


ns_path = "alleninstitute.namespace.yaml"

nicain

import numpy as np
import xarray

from allensdk.core.brain_observatory_cache import BrainObservatoryCache
from allensdk.brain_observatory import stimulus_info as si

TIME = 'time'
SEC = 'second'
MS = 'millisecond'
IDX = 'index'

nicain

from datetime import datetime
from pynwb import NWBFile
from form.backends.hdf5 import HDF5IO
from pynwb import get_build_manager
from pynwb.base import TimeSeries
import numpy as np

f = NWBFile('tmp.nwb', 'my first synthetic recording', 'EXAMPLE_ID', identifier='hi',
            experimenter='Dr. Bilbo Baggins',
            lab='Bag End Labatory',

nicain

import numpy as np
import h5py
import xarray as xr
import os
import types
import json

# https://github.com/pydata/xarray/issues/1599
# https://github.com/nicain/xarray/tree/feature/1599-to_dict_numpy
# https://codereview.stackexchange.com/questions/120802/recursively-save-python-dictionaries-to-hdf5-files-using-h5py

nicain

import allensdk
from allensdk.core.brain_observatory_cache import BrainObservatoryCache
import os
from distutils.version import StrictVersion
assert allensdk.__version__ == StrictVersion('0.14.2')
from allensdk.brain_observatory.brain_observatory_exceptions import EpochSeparationException        
import matplotlib.pyplot as plt

# Settings:
oeid = 556363813

nicain

import pandas as pd
import collections
import numpy as np
import matplotlib.pyplot as plt

from allensdk.core.brain_observatory_nwb_data_set import BrainObservatoryNwbDataSet

df = pd.read_csv('/allen/aibs/technology/nicholasc/brain_observatory_cell_df.csv', sep=' ').drop('Unnamed: 0', axis=1)
# print df.columns

nicain

import numpy as np
import h5py
import os

def pass_function(*args): return

def visit(group, group_callback=pass_function, 
                 dataset_callback=pass_function, 
                 softlink_callback=pass_function, 
                 broken_link_callback=pass_function, path='/'):

nicain

import warnings

from allensdk.core.brain_observatory_cache import BrainObservatoryCache
import allensdk.brain_observatory.stimulus_info as si
import pynwb

ophys_experiment_id = 570014520
boc = BrainObservatoryCache(manifest_file=brain_observatory_cache_manifest_file)
exp = boc.get_ophys_experiment_data(ophys_experiment_id)
legacy_map = pynwb.legacy.get_type_map()

nicain

class EphysBrainObservatoryAdapter(object):
    
    def __init__(self, nwb_file_name, analysis_dir, probe_unit_dict=cortex_probe_dict):

        
        

        self.convert_inner_unit_to_unit = {}
        self.convert_unit_to_inner_unit = {}
        self.probe_unit_id_dict = {}