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teamtomo / membrain-seg

membrane segmentation in 3D for cryo-ET
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Add UNet #1

Closed kevinyamauchi closed 1 year ago

kevinyamauchi commented 1 year ago

This PR adds a unet for semantic segmentation as a pytorch lightning model. We can add a dataset and some example code as a follow-up PR.

kevinyamauchi commented 1 year ago

@alisterburt and @lorenzlamm, I removed python 3.11 as it was causing issues with torch/monai. I think this is fine, as 3.11 is pretty bleeding edge at this point. What do you think?

Otherwise, I think this is ready for review!

kevinyamauchi commented 1 year ago

Thanks for the review @alisterburt ! The line breaks you flagged are required by our pre-commit. I would suggest that we leave them as is and the re-vist the pre-commit separately if you prefer a different style. I added the docstring you suggested.

qs around monai:

is it stable/likely to change (should we consider vendoring?)

In my experience, it is stable. I would recommend that we keep the dependency and vendor only if necessary.

is it a clean dep to bring in?

yeah, as specified, it will only bring in numpy and torch (which we will depend on anyway here)

https://github.com/Project-MONAI/MONAI/blob/9fd6d4ced3efb344cf3b24c51d899d8fafc882d5/setup.cfg#L44-L46

alisterburt commented 1 year ago

excellent! Not sure what you mean by line breaks exactly (I only added a link after the existing doc) but it's a minor thing, let's merge!