Some code that exposed a bug

mschacter_example.py

"""
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

from pynwb import NWBFile, get_manager, NWBHDF5IO
from pynwb.ecephys import ElectricalSeries, SpikeEventSeries

nf = NWBFile('some recording', 'a session',
             'bla bla bla',
             datetime.now(),
             experimenter='Jane Randn',
             lab='The Lab',
             institution='University of Bug Reports',
             experiment_description='no description',
             session_id='12345')

protocol_epoch = nf.create_epoch(source='', name='the epoch', start=0.0, stop=5200.,
                                         tags=('bug', 'report'),
                                         description="")

electrode_array = nf.create_device(name='16 electrode array', source='')

electrode_group = nf.create_electrode_group('my group',
                                            source='a brain',
                                            description='',
                                            location='somewhere',
                                            device=electrode_array)

electrode_indices = np.arange(1)

for e in electrode_indices:
    nf.add_electrode(e,
                     x=0.0, y=0.0, z=0.0,
                     imp=0.0,
                     location='somewhere',
                     filtering='none',
                     description='',
                     group=electrode_group)

etable = nf.create_electrode_table_region(list(electrode_indices), 'All electrodes in array')

spike_series = SpikeEventSeries('a_unit', 'unit desc',
                                np.random.randn(5, 18),
                                np.arange(5),
                                etable,
                                resolution=1e-12,
                                conversion=1e6,
                                comments='no comments',
                                description=''
                               )
nf.add_acquisition(spike_series, [protocol_epoch])

path =  'tmp_somefile.nwb'

io = NWBHDF5IO(path, manager=get_manager(), mode='w')
io.write(nf)
io.close()

# now read it back in
reader = NWBHDF5IO(path, mode='r')
nf_in = reader.read()
spikes_in = nf_in.get_acquisition('a_unit')
reader.close()