Update to latest NWB2 version

jonc125 commented 4 years ago

Some things changed even between #4 and the final 2.0 release. And there have been further changes since.

Some notes of potential changes from recent reading follow. These should probably be tackled in separate PRs.

Share timestamps array between TimeSeries?
Store trial times first in /intervals/trials and only once all timeseries have been added populate /intervals/epochs from this
ROI storage has changed again: https://nwb-schema.readthedocs.io/en/latest/format_release_notes.html#improved-storage-of-rois
There's an Image type now (and sub-types) which might be better for storing the reference z-stack?
See also https://nwb-schema.readthedocs.io/en/latest/format_release_notes.html
New numpy breaks my signature generation (which also needs improving for DynamicTable style data and complex data types) - see #8.

We may be best creating an extension for at least some of the Silver Lab imaging data, rather than trying to fit it into the core standard. See also https://github.com/NeurodataWithoutBorders/nwb-schema/issues/156.

ageorgou commented 4 years ago

Also, the bits_per_pixel attribute is now deprecated - see #5.

ageorgou commented 4 years ago

Most should have been tackled in #13 but leaving open to revisit in case we could make further improvements.

SilverLabUCL / PySilverLabNWB