ajtritt

#fix of https://gist.github.com/nicain/be598d5b7be5f2ffe1fd7e8d27c87ec3
# 
from pynwb.spec import NWBNamespaceBuilder, NWBGroupSpec, NWBAttributeSpec
import numpy as np
from pynwb import get_class, load_namespaces

mylab = 'alleninstitute'
ns_path = "%s.namespace.yaml" % mylab
ext_source = "%s.extensions.yaml" % mylab

ajtritt

import os
import h5py
import numpy as np

# Create compound data type
# a table with columns channel ID, xyz-coordinates, and impedence
coord_dt = np.dtype([('x', np.float), ('y', np.float), ('z', np.float)])
ch_dt = np.dtype([("id", np.int), ("coord", coord_dt), ("imp", np.float)])

# Make a fake channel table

ajtritt

import numpy as np
from pynwb import get_class, load_namespaces
from datetime import datetime
from pynwb import NWBFile
import pandas as pd
from form.backends.hdf5 import HDF5IO
from pynwb import get_build_manager

ns_path = "alleninstitute.namespace.yaml"
ext_source = "alleninstitute.extensions.yaml"

ajtritt

import numpy as np
from pynwb import get_class, load_namespaces
from datetime import datetime
from pynwb import NWBFile
import pandas as pd
from form.backends.hdf5 import HDF5IO
from pynwb import get_build_manager

ns_path = "alleninstitute.namespace.yaml"
ext_source = "alleninstitute.extensions.yaml"

ajtritt

from datetime import datetime
from timeit import timeit

iso_setup = '''
from datetime import datetime
iso_start = "2017-08-30T16:01:18Z"
iso_end = "2017-08-30T16:01:20Z"
fmt = "%Y-%m-%dT%H:%M:%SZ"
'''

ajtritt

import pynwb

foo_ext_path = 'foo.namespace.yaml' # custom extension
foo_nwb_path = 'foo.nwb'            # file using custom extension
bar_ext_path = 'bar.namespace.yaml' # another custom extension
bar_nwb_path = 'bar.nwb'            # file using this other custom extension
baz_nwb_path = 'baz.nwb'            # file with no extensions

############ READ #############

ajtritt

import filterframework
import pynwb
import multiprocessing  # this is a core Python package

def my_analysis_func(...):
    # user writes this
    ...

nwb_file = pynwb.NWBFile(...)
query_string = 'a toy query string'

ajtritt

    
def get_builder_ns(self, builder):
    return 'core'

def get_builder_dt(self, builder):
    attrs = builder.attributes
    ndt = attrs.get('neurodata_type')
    if ndt == 'Module':
        return 'ProcessingModule'
    elif ndt == 'TimeSeries':

ajtritt

""" import the pynwb packages"""
from pynwb import NWBFile, TimeSeries, get_manager
from pynwb.form.backends.hdf5 import HDF5IO
from pynwb.icephys import CurrentClampSeries
from pynwb.icephys import VoltageClampSeries
import datetime
import numpy as np
import os

experimentID = 'BJ5523'#folderPath.split('/')[-1]

ajtritt

"""
This code was breaking at write. See https://github.com/NeurodataWithoutBorders/pynwb/issues/317

mschachter hacked PyNWB and then had problems reading.  See https://github.com/NeurodataWithoutBorders/pynwb/issues/318

This commit should fix both of these issues: https://github.com/NeurodataWithoutBorders/pynwb/commit/72fafa686748de25571d0abd6aa43cd3ab889bb9
"""
import json
from datetime import datetime
import numpy as np