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PeyracheLab / miniscoPy

A package to analyse calcium imaging data recorded with the Miniscope.
GNU General Public License v2.0
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normcorre Packet.decode_one is deprecated #22

Closed maximilianrutz closed 5 years ago

maximilianrutz commented 5 years ago

Dear All,

when running the normcorre function in the main_cnmfe_e Skript the first of four operations isn't executed (stays at 0/1 and the black beam doesnt fill up). The warning "C:\Users\Admin\miniscoPy\miniscopy\base\motion_correction.py:312: MethodDeprecationWarning: Packet.decode_one is deprecated" is raised.

Do you have a suggestion to update the method? If it was only for the warning we might ignore it, but since the operation doesn't go through we are worrying about later issues in the pipeline.

Best regards and thanks Max

gviejo commented 5 years ago

Dear Max,

I patched motion correction so that the warning is not raised anymore.

For your issue, the current version of normcorre is quite slow. We are working on an update to make it faster. If your dataset is really big, that might be the reason. You can try with the example video we provided to make sure the script goes to the end.

Best

Guillaume