MatNWB compatibility

[ehennestad]

I just wanted to check in on this statement from the README:

Matlab: The Matlab extension is under development.

Similar statements appear in the documentation:

The ndx-hed extension is not currently supported in MATLAB, although support is planned in the future.

and

The ndx-hed extension for MATLAB is under development and not available.

There was a recent update in MatNWB allowing quick installation of registered extensions. With the most recent release (v2.9.0) of MatNWB (on MATLAB's search path) the following command will install and generate type classes for the ndx-hed extension for use in MATLAB:

nwbInstallExtension("ndx-hed")

I tested it and it works fine.

I have also tried to run the Quickstart example from the README in MatNWB and that seems to work as well:

nwb = NwbFile( ...
    'session_description', "Example session with HED annotations", ...
    'identifier', "example_session_001", ...
    'session_start_time', datetime('now','TimeZone','local'));

hedMeta = types.ndx_hed.HedLabMetaData( ...
    'hed_schema_version', '8.4.0');

nwb.general.set('hed', hedMeta);

% Build the trials TimeIntervals
trials = types.core.TimeIntervals(...
    'description', 'Trials with HED annotations', ...
    'colnames', {'start_time',  'stop_time'});

hedCol = types.ndx_hed.HedTags(...
    'description', 'HED annotations for trials (ndx-hed)', ...
    'data', []);
trials.addColumn('HED', hedCol)

trials.addRow( ...
    'start_time', 0.0, ...
    'stop_time',  1.0, ...
    'HED', "Experimental-trial, (Sensory-event, Visual-presentation)");

% Attach and save
nwb.intervals_trials = trials;

outPath = "example_session_001_with_ndx_hed.nwb";
nwbExport(nwb, outPath);

If you are aware of problems/issues related to using the extension in MatNWB, please let us now by following up here, or raising an issue on the MatNWB repo

[VisLab]

@ehennestad We did not do an explicit implementation in MATLAB and thought we would need to write additional code. The ndx-hed relies on the hedtools python library. I'm not sure how it is able to work unless it is calling the underlying python library from MATLAB? The hedtools and ndx-hed extension require at least HED python 3.10.

Could you give us some guidance on this?

[ehennestad]

I did not realise it relies on the hedtools python library, but looking at examples 5-7 I understand what you mean.

It is possible to call these python libraries directly from MATLAB, but with some extra setup requirements. I can follow up with some details on this!

[VisLab]

We have Matlab wrappers for all of the validators and many other functions in: https://github.com/hed-standard/hed-matlab. These wrappers give two options --- one with the hedtools installed in Matlab and the other by accessing web-services. We would like to support the MATLAB for ndx-hed, but are unsure what is needed. Details and guidance would be appreciated.

[ehennestad]

From what I can see, MATLAB users should be able to use ndx-hed already, using nwbInstallExtension("ndx-hed") in MATLAB and by installing the hed-matlab wrapper.

At a minimum, these two installation instructions could be mentioned. A benefit for MATLAB users would also be MATLAB versions of the examples, although that might require some work.