Add webknossos_annotation.py #11
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Co-authored-by: Kabilar Gunalan <[email protected]>
Co-authored-by: Kabilar Gunalan <[email protected]>
Co-authored-by: Kabilar Gunalan <[email protected]>
Co-authored-by: Kabilar Gunalan <[email protected]>
| max_load: int = 16384, | ||
| nii: bool = False, | ||
| has_channel: int = 1, | ||
| ): |
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Can you document what each input/option does?
scripts/webknossos_annotation.py
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| low_res_offsets.append([t,b,l,r]) | ||
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| # load jp2 image to get voxel size info | ||
| j2k = glymur.Jp2k(jp2_dir) |
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It might be better to reference the zarr file that was annotated. It should have the voxel size info as well.
scripts/webknossos_annotation.py
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| dic_EB = {0:0, 1:1, 9:2, 2:3, 4:4, 10:5, 11:6, 8:7, 3:8} | ||
| dic_JS = {0:0, 4:2, 5:3, 9:4, 6:5, 2:6, 7:7, 3:8} | ||
| dic_JW = {0:0, 1:1, 2:2, 3:3, 4:4, 6:5, 7:6, 8:7, 9:8} |
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Can you add a comment to describe what these dictionaries contain?
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Also, should this be an input option somehow?
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| nblevel = 9 | ||
| # Write each level |
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we should probably get the number of levels from the data, not hardcode it.
scripts/webknossos_annotation.py
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| for level in range(nblevel): | ||
| omz_res = omz_data[level] | ||
| size = omz_res.shape[-2:] | ||
| shape = [1, 20] + [i for i in size] |
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Same comment - do we need to harcode this?
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| # Write OME-Zarr multiscale metadata | ||
| print('Write metadata') |
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Do the annotation have the exact same shape as the annotated zarr file? I feel like we should just copy that info from the input zarr.
scripts/webknossos_annotation.py
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| def generate_mask(mask): | ||
| final_mask = np.zeros_like(mask).astype(np.uint8) |
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What is this doing? Is it a good thing to process the data in a "conversion" script?
kabilar
changed the title
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Hi @jingjingwu1225, while the details of this script are fresh on our minds, perhaps this is a good time to add unit and/or integration tests alongside the script? Integrating these tests within a GitHub Actions workflow would be straightforward and I can help with this process. Thanks for considering.
cc @balbasty
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Hi @kabilar, thanks for the comment. I'll modify the script first based on comments of Yael and then we can start integrating tests, you help is appreciated! |
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@kabilar @jingjingwu1225 We're about to merge the refactored package in main. It would be great to integrate the script and tests into this refactored package. @calvinchai can provide guidance. |
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