demonstration of pynwb issue #146

make_bad_nwb_file.py

## create minimal set of objects for defining a dF/F object

from pynwb.ophys import TwoPhotonSeries, RoiResponseSeries, DfOverF, Fluorescence, PlaneSegmentation, \
    ImageSegmentation, OpticalChannel, ImagingPlane, ROI
from pynwb.image import ImageSeries

w, h = 5, 5
img_mask = [[0 for x in range(w)] for y in range(h)]
w, h = 5, 2
pix_mask = [[0 for x in range(w)] for y in range(h)]
pix_mask_weight = [0 for x in range(w)]
iSS = ImageSeries(
    name='test_iS', source='a hypothetical source', data=list(), unit='unit', external_file=['external_file'],
    starting_frame=[1, 2, 3], format='tiff', timestamps=list())

roi1 = ROI('roi1', 'test source', 'roi description1', pix_mask, pix_mask_weight, img_mask, iSS)
roi2 = ROI('roi2', 'test source', 'roi description2', pix_mask, pix_mask_weight, img_mask, iSS)
roi_list = (roi1, roi2)

oc = OpticalChannel('test_optical_channel', 'test_source', 'description', 'emission_lambda')
ip = ImagingPlane(
    'test_imaging_plane', 'test_source', oc, 'description', 'device', 'excitation_lambda',
    'imaging_rate', 'indicator', 'location', (1, 2, 1, 2, 3), 4.0, 'unit', 'reference_frame')

ps = PlaneSegmentation('name', 'test source', 'description', roi_list, ip, iSS)

iS = ImageSegmentation('test source', ps, name='test_iS')

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?
ophys_module.add_container(dof)


# now write the file
from pynwb import NWBHDF5IO as HDF5IO
io = HDF5IO('ophys_badfile.nwb',mode='w')
io.write(nwb)
io.close()

# and try to read it back out
reader = HDF5IO('ophys_badfile.nwb',mode='r')

read_data = reader.read()