Deal with nibabel deprecation of get_header and get_data
#3879
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Except for examples which end in a filename, to avoid confusion.
Since we now depend on version 1.5.0, instead of 1.4.1. https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/5.7/requirements-freeze.txt#L15
It's all explained in the helps string.
There's no hdr_1, hdr_2, etc.
Since these are nibabel image objects and numpy arrays: img -> nii img_denoised -> nii_denoised img_diff -> nii_diff denoised -> data_denoised diff_4d -> data_diff According to the naming convention on the wiki: https://github.com/spinalcordtoolbox/spinalcordtoolbox/wiki/Programming%3A-Naming-conventions-(variables,-files)
Also this brings the numpy array computations together, separate from the "Save files" step.
mguaypaq
added
refactoring
joshuacwnewton
approved these changes
Sep 8, 2022
Co-authored-by: Joshua Newton <joshuacwnewton@gmail.com>
joshuacwnewton
approved these changes
Sep 13, 2022
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Description
nibabelhas deprecated theget_header()andget_data()methods, in favour of theheaderproperty and theget_fdata()method, respectively. Thesct_dmri_denoise_patch2self.pyscript is one of the three callers of these methods in SCT, so it needs to be updated. And since it's such a small script, I decided to do a general cleanup while I was at it.This is probably easier to review commit-by-commit, since each one is a single change.
I think the only controversial change is that I added the second output file to the
display_viewer_syntaxcall at the end (which was possibly showing an incorrect filename anyway if-owasn't used).Linked issues
Part of #3854.