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schnitzer-lab / EXTRACT-public

EXTRACT is a tractable and robust automated cell extraction tool for calcium imaging, which extracts the activities of cells as time series from both one-photon and two-photon calcium imaging movies.
MIT License
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empty array interpreted as 'auto' option for downsample_time_by and downsample_space_by #15

Closed cechava closed 3 years ago

cechava commented 3 years ago

fixes #14

In saving configuration parameters to an HDF5 file (such as NWB file), each parameter must take a data type. downsample_time_by and downsample_space_by can take on string (e.g. 'auto') or numeric values. In order to save these parameters to file and later reuse them, it would be ideal if the same operations that were triggered by the 'auto' string input, would also be triggered by an empty array.

This PR implements this

fatihdinc commented 3 years ago

Thanks for the suggestion and the changes, I have now merged the commit. Let me also note that I will stabilize this repo at the end of this month and will only perform bug fixes for better version control in scientific papers using EXTRACT. Any further changes towards v2 will be performed in the extract-wip repository, which is here: https://github.com/schnitzer-lab/extract-wip.

cechava commented 3 years ago

@fatihdinc Thanks for letting me know. There's one more tutorial I am finalizing showing how to write results from the EXTRACT pipeline to an NWB file, along with a helper function. Will make a PR here in the next couple of days.