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AllenInstitute / bmtk

Brain Modeling Toolkit
https://alleninstitute.github.io/bmtk/
BSD 3-Clause "New" or "Revised" License
266 stars 86 forks source link

adding compression for spikes/rates outputs #302

Closed shixnya closed 1 year ago

shixnya commented 1 year ago

Compression capability is added for spike/rate h5 files.

The option can be given in the 'output' or 'report' section of the config files for bionet, pointnet, and filternet. String values such as 'gzip', 'lzf', or 'none', or integer 0-9 (level for gzip) are accepted.

The default is 'gzip', and this option will be ignored if h5 file will not be saved. Simple tests in test_sonata_adaptor.py are implemented, but tests for for the individual components (bionet, pointnet, and filternet) are not implemented. Let's discuss if more comprehensive tests are desired.

shixnya commented 1 year ago

I've implemented it as an option for SpikesMod as the config options are directly passed to it. Kael, if you want another implementation, please let me know.

shixnya commented 1 year ago

Thanks, Kael. I merged it.