Update Cellpose for reproducibility#1593
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bgruening merged 5 commits intobgruening:masterfrom Mar 15, 2025
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Tests have passed, looking good. Just some file sizes are too large (I guess they have been before too). |
bgruening
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Mar 15, 2025
tools/cellpose/cp_segmentation.py
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| # Make sure, that MKL_NUM_THREADS is set to 1, to ensure reproducibility: | ||
| # https://forum.image.sc/t/reproducibility-how-we-spent-years-building-containers-and-then-mkl-decided-to-screw-our-results/109599 | ||
| assert str(os.environ['MKL_NUM_THREADS']) == '1' |
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instead of asserting, could we also set this variable here again?
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The question is, at what point MKL is loaded. My guess is that this happens when NumPy is loaded. I have made some adjustments based on your suggestion accordingly in 66fb725.
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Thanks a lot! |
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This PR (hopefully) solves the reproducibility issues with Cellpose.
Main changes:
MKL_NUM_THREADSis set to 1 (see this for details, much thanks to @bgruening for helping to figure this out)Can't test the tool locally due to weird planemo error (probably unrelated to the tool itself).