Reading Allen Cell Types files

[nicain]

Problem/Use Case

Implement backwards-compatible read capability for Allen Cell Types Database files:

from allensdk.core.cell_types_cache import CellTypesCache
ctc = CellTypesCache(manifest_file='boc/manifest.json')
cell_specimen_id = 464212183
data_set = ctc.get_ephys_data(cell_specimen_id)

legacy_map = pynwb.legacy.get_type_map()
io2 = pynwb.NWBHDF5IO(data_set.file_name, extensions=legacy_map, mode='r')
nwb_data = io2.read()

Checklist

• Have you ensured the feature or change was not already reported ?
• Have you included a brief and descriptive title?
• Have you included a clear description of the problem you are trying to solve?
• Have you included a minimal code snippet that reproduces the issue you are encountering?

[nicain]

@ajtritt Ill take a first-pass at this, and let you know where I get stuck

[nicain]

It looks like the biggest stumbling block to reading these files is the use of "Custom" neurodata_type in the files, in unexpected places. For example, in /stimulus/templates, the "gain" dataset in the CurrentClampStimulusSeries has this Custom neurodata_type, triggering the construction of a builder.

[oruebel]

@nicain can this issue be closed?

[nicain]

Unfortunately not :)