Allow Codec for compression for use with LINDI #1162
Closed
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Motivation
While hdf5 does not allow numcodecs.Codec for compression, lindi does. Right now hdmf does type checking for the compression parameter and raises an exception if the type is not in (str, bool, int). This PR simply allows the Codec type to be passed through so that it can be used with lindi.
How to test the behavior?
Here's an example that applies a custom compressor to filtered ephys data
https://github.com/NeurodataWithoutBorders/lindi/blob/lindi-tar/examples/DANDI/preprocess_ephys.py
You need to install the lindi-tar branch of lindi and
pip install qfc
. See https://github.com/magland/qfc@oruebel @rly
Checklist
CHANGELOG.md
with your changes?