support isodatetime dtype

[oruebel]

@nclack @ln-vidrio this is a heads-up. When you sync up with the spec next time. The following pending PR https://github.com/NeurodataWithoutBorders/pynwb/pull/641 adds "isodatetime" as a dtype to the schema language. In HDF5 this simply maps to H5_TEXT (same as UTF-8 string). The main difference is that on the API side this implies that this should be a ISO 8601 date string. From a basic read/write perspective I think not much changes for MatNWB (since these are just string datasets), however, eventually this means you probably want a way to:

• represent these strings as Matlab datetime objects
• use Matlab datetime objects as inputs for isodatetime dtypes
• possibly additional validation on read/write

[bendichter]

Under the new schema (currently merged in pynwb/dev but unmerged in matnwb/master) there is an error constructing an NWBFile object in matnwb and an error reading an nwbfile constructed using pynwb. Both errors have to do with the new format of file_created_date (and likely this will present in session_start_time as well).

construction error

nwb = nwbfile( 'source', 'acquired on rig2', ...
    'session_description', 'a test NWB File', ...
    'identifier', 'mouse004_day4', ...
    'session_start_time', datestr(date, 'yyyy-mm-ddTHH:MM:SS'), ...
    'file_create_date', datestr(now, 'yyyy-mm-ddTHH:MM:SS'));

gives the following error:

Error using types.util.checkDtype (line 106)
Property `file_create_date` must be a .

Error in types.core.NWBFile/validate_file_create_date (line 302)
        val = types.util.checkDtype('file_create_date', '', val);

Error in types.core.NWBFile/set.file_create_date (line 188)
        obj.file_create_date = obj.validate_file_create_date(val);

Error in types.core.NWBFile (line 138)
        obj.file_create_date = p.Results.file_create_date;

Error in nwbfile (line 15)
            obj = obj@types.core.NWBFile(varargin{:});

read error

file generated in python with:

from pynwb import NWBHDF5IO, NWBFile
from datetime import datetime

nwbfile = NWBFile('source', 'session_description', 'identifier', datetime.now().astimezone())

with NWBHDF5IO('test_file.nwb', 'w') as io:
    io.write(nwbfile)

attempt to read in matlab gets the following error:

>> generateCore('schema/core/nwb.namespace.yaml')
>> nwbRead('/Users/bendichter/dev/pynwb/test_file.nwb')
Error using types.util.checkDtype (line 106)
Property `file_create_date` must be a .

Error in types.core.NWBFile/validate_file_create_date (line 302)
        val = types.util.checkDtype('file_create_date', '', val);

Error in types.core.NWBFile/set.file_create_date (line 188)
        obj.file_create_date = obj.validate_file_create_date(val);

Error in types.core.NWBFile (line 138)
        obj.file_create_date = p.Results.file_create_date;

Error in nwbfile (line 15)
            obj = obj@types.core.NWBFile(varargin{:});

Error in io.parseGroup (line 68)
        parsed = nwbfile(kwargs{:});

Error in nwbRead (line 20)
    nwb = io.parseGroup(filename, info);

[bendichter]

@ln-vidrio could you take a look at this?

[bendichter]

thanks for taking a stab at this, @ln-vidrio! Let me know if I can help

[lawrence-mbf]

f4afdf2023d413b3f245e53cf5fe3a304d3b7238 How does the python compatibility look?

[bendichter]

Both tests work now! Thanks!!

[oruebel]

Note https://github.com/NeurodataWithoutBorders/pynwb/pull/641 has been merged now.