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datajoint / element-array-ephys

DataJoint Element for Neuropixels analysis with Kilosort
https://datajoint.com/docs
MIT License
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matnwb cannot read output NWB file #81

Open CBroz1 opened 2 years ago

CBroz1 commented 2 years ago

A user reported difficulty reading an nwb file produced by the export function.

Screenshot 2022-06-27 at 18 04 43

@bendichter - Should files exported here be readable with matnwb ?

bendichter commented 2 years ago

@CBroz1 yes it should be. Would you be able to send me this file? @lawrence-mbf, do you have any idea what might be going on here?

CBroz1 commented 2 years ago

@CBroz1 yes it should be. Would you be able to send me this file?

Of course. I'll send over slack. Thanks for looking into it!

lawrence-mbf commented 2 years ago

@CBroz1 This unfortunately is a really old issue where MatNWB doesn't support anonymous type definitions: https://github.com/NeurodataWithoutBorders/matnwb/issues/43

Thankfully, I think this is localised in the waveform_mean VectorData object as we haven't seen the same elsewhere. A workaround could just be to make a waveform_mean_unit vectordata object if you really need it in MatNWB.

CBroz1 commented 2 years ago

Thanks @lawrence-mbf for your insights!

@kabilar - I'm thinking we should make that edit so resulting files are more accessible. What do you think?

kabilar commented 2 years ago

Thanks all. Yes, let's make the update. I couldn't find documentation on waveform_mean_unit so not sure how we would make this update.

lawrence-mbf commented 2 years ago

@kabilar @CBroz1 It would really just be repeating that unit value as a vector column with the same number of rows. It is an ugly duplication of code and may one day throw warnings when validating but it will guarantee MatNWB support for now.