[WIP] Recompress files where dcm2niix failed #803
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #803 +/- ##
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- Coverage 82.48% 82.12% -0.36%
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Files 42 42
Lines 4323 4348 +25
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+ Hits 3566 3571 +5
- Misses 757 777 +20 ☔ View full report in Codecov by Sentry. |
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| "trying to salvage by recompressing ourselves. " | ||
| "This might take a while ") | ||
| if not recompress_failed(uncompressed): | ||
| raise RuntimeError("Error compressing nifti") |
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why to delay this crash here? this way you are hiding from user information on individual file and corresponding error -- why not just to just call recompress here and let error (if any happens) to bubble up?
I would also just loop here and have recompress to operate on a single file.
FWIW, I think it would be worth adding a test scenario to test this code path. I would have just mock patched the nipype_convert so that I would decompress some output file(s) and thus triggering this code path.
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Thanks, I'll look into it!
As threatened in #802 an alternative approach.
I decided to leverage the fact that heudiconv blindly moves all converted output files to
nii.gz, even if they are justniiby renaming the successfully re-compressed image to.nii. This feels ugly, but results in the shortest/least-invasive PR.