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@CKalicki I think to keep the structure of the repo consistent we should have a losses/cryoLLGI.py rather than cryo/loss.py. Similarly, have the current cryo/alignment.py merge with utils/geometry.py where relevant (or have a new file if certain alignment functions should be in a different category).
Last thing – note ruff and build tests are failing, they need to pass for PR to merge!
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