How to use the pynwb.NWBFile function in pynwb

def test_no_tags(self):
        nwbfile = NWBFile("a file with header data", "NB123A", datetime(1970, 1, 1, tzinfo=tz.tzutc()))
        df = self.get_dataframe()
        for i, row in df.iterrows():
            nwbfile.add_epoch(start_time=row['start_time'], stop_time=row['stop_time'])

def test_create_electrode_group_invalid_index(self):
        """
        Test the case where the user creates an electrode table region with
        indexes that are out of range of the amount of electrodes added.
        """
        nwbfile = NWBFile('a', 'b', datetime.now(tzlocal()))
        device = nwbfile.create_device('a')
        elecgrp = nwbfile.create_electrode_group('a', 'b', device=device, location='a')
        for i in range(4):
            nwbfile.add_electrode(np.nan, np.nan, np.nan, np.nan, 'a', 'a', elecgrp, id=i)
        with self.assertRaises(IndexError):
            nwbfile.create_electrode_table_region(list(range(6)), 'test')

def setUpContainer(self):
        container = NWBFile('a test NWB File', 'TEST123',
                            self.start_time,
                            timestamps_reference_time=self.ref_time,
                            file_create_date=self.create_date,
                            experimenter='test experimenter',
                            stimulus_notes='test stimulus notes',
                            experiment_description='test experiment description',
                            data_collection='test data collection notes',
                            institution='nomad',
                            lab='nolab',
                            notes='nonotes',
                            pharmacology='nopharmacology',
                            protocol='noprotocol',
                            related_publications='nopubs',
                            session_id='007',
                            slices='noslices',
                            source_script='nosources',

def setUp(self):
        self.nwbfile = NWBFile("a file with header data", "NB123A", datetime(2017, 5, 1, 12, 0, 0, tzinfo=tzlocal()))

def test_container(self):
        """ Test properties of the SweepTable read from file """
        description = 'a file to test writing and reading a %s' % self.container_type
        identifier = 'TEST_%s' % self.container_type
        nwbfile = NWBFile(description, identifier, self.start_time, file_create_date=self.create_date)
        self.addContainer(nwbfile)

        sweep_table = self.getContainer(nwbfile)
        self.assertEqual(len(sweep_table['series'].data), 1)
        self.assertEqual(sweep_table.id[0], 0)
        self.assertEqual(sweep_table['sweep_number'].data[0], 4711)

ns_builder = NWBNamespaceBuilder('Extension for use in my Lab', self.prefix, version='0.1.0')
        test_meta_ext = NWBGroupSpec(
            neurodata_type_def='MyTestMetaData',
            neurodata_type_inc='LabMetaData',
            doc='my test meta data',
            attributes=[
                NWBAttributeSpec(name='test_attr', dtype='float', doc='test_dtype')])
        ns_builder.add_spec(self.ext_source, test_meta_ext)
        ns_builder.export(self.ns_path, outdir=self.tempdir)
        ns_abs_path = os.path.join(self.tempdir, self.ns_path)

        load_namespaces(ns_abs_path)

        MyTestMetaData = get_class('MyTestMetaData', self.prefix)

        nwbfile = NWBFile("a file with header data", "NB123A", datetime(2017, 5, 1, 12, 0, 0, tzinfo=tzlocal()))

        nwbfile.add_lab_meta_data(MyTestMetaData(name='test_name', test_attr=5.))

def get_container_location(container):
        location = list()
        curr = container
        top_container = curr
        while curr.parent:
            location.append(HDF5ContainerRenderer.relative_location(curr.parent, curr))
            top_container = curr.parent
            curr = curr.parent

        if not isinstance(top_container, NWBFile):
            raise Exception('highest container not a file: %s (%s) --> ... --> %s (%s)' % (container, type(container), top_container, type(top_container)))

        container_source = top_container.container_source
        container_path = '/%s' % posixpath.join(*reversed(location))
        #container_path = posixpath.join(*reversed(location))
        return (container_source, container_path)

def main():
    nwb_path = 'ophys_example.nwb'
    # create your NWBFile object
    nwbfile = NWBFile('the PyNWB tutorial', 'my first synthetic recording', 'EXAMPLE_ID', datetime.now(),
                      experimenter='Dr. Bilbo Baggins',
                      lab='Bag End Laboratory',
                      institution='University of Middle Earth at the Shire',
                      experiment_description='I went on an adventure with thirteen dwarves to reclaim vast treasures.',
                      session_id='LONELYMTN')

    # create acquisition metadata
    optical_channel = OpticalChannel('test_optical_channel', 'optical channel source',
                                     'optical channel description', '3.14')
    imaging_plane = nwbfile.create_imaging_plane('test_imaging_plane',
                                                 'ophys integration tests',
                                                 optical_channel,
                                                 'imaging plane description',
                                                 'imaging_device_1',
                                                 '6.28', '2.718', 'GFP', 'somewhere in the brain',
                                                 (1, 2, 1, 2, 3), 4.0, 'manifold unit', 'A frame to refer to')

"""

####################
# The NWB file
# ------------
#
#

from datetime import datetime
from pynwb import NWBFile

start_time = datetime(2017, 4, 3, 11, 0, 0)
create_date = datetime(2017, 4, 15, 12, 0, 0)

nwbfile = NWBFile('PyNWB tutorial', 'demonstrate NWBFile basics', 'NWB123', start_time,
                  file_create_date=create_date)

####################
# .. _basic_timeseries:
#
# Time series data
# ----------------
#
# PyNWB stores time series data using the :py:class:`~pynwb.base.TimeSeries` class and its subclasses.
# The main components of a :py:class:`~pynwb.base.TimeSeries` are the *data* and the *timestamps*.
# You will also need to supply a *source* and *description* of the data and the unit for *data*.

from pynwb import TimeSeries

data = list(range(100, 200, 10))
timestamps = list(range(10))

# Create data representing the ImageSegmentation results
iS = ImageSegmentation('test source', ps, name='test_iS')

#####################
# Now create our ROI dF/F data
rrs = RoiResponseSeries('test_ts', 'a hypothetical source', list(), 'unit', ['name1'], iS, timestamps=list())
dof = DfOverF('test_dof', rrs)

#####################
# Create the NWBFile object

NA = 'THIS FIELD INTENTIONALLY LEFT BLANK'

import datetime as dt
from pynwb import NWBFile
nwb = NWBFile(
    source = NA,
    session_description = NA,
    identifier = NA,
    session_start_time = dt.datetime.now(),
)

#####################
# create a processing module to put it all in
ophys_module = nwb.create_processing_module(
    name="ophys",
    description="calcium responses",
    source="Allen Brain Observatory: Visual Behavior",
)

#####################
# only add the top level container?