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Add support to pass shape and affine to Resample #640

Merged
merged 5 commits into from
Aug 31, 2021
Merged

Add support to pass shape and affine to Resample #640

merged 5 commits into from
Aug 31, 2021

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fepegar
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@fepegar fepegar commented Aug 30, 2021 •
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Fixes #638.

Checklist

  • I have read the CONTRIBUTING docs and have a developer setup (especially important are pre-commitand pytest)
  • Non-breaking change (would not break existing functionality)
  • Breaking change (would cause existing functionality to change)
  • Tests added or modified to cover the changes
  • Integration tests passed locally by running pytest
  • In-line docstrings updated
  • Documentation updated, tested running make html inside the docs/ folder
  • This pull request is ready to be reviewed
  • If the PR is ready and there are multiple commits, I have squashed them and force-pushed

@fepegar
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fepegar commented Aug 30, 2021 •
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TODO: update docstring.

@romainVala Can you try your snippet in #638 and see if this is better?

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codecov bot commented Aug 30, 2021 •
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Codecov Report

Merging #640 (1097139) into master (e4342b2) will increase coverage by 0.00%.
The diff coverage is 100.00%.

Impacted file tree graph

@@           Coverage Diff           @@
##           master     #640   +/-   ##
=======================================
  Coverage   96.85%   96.86%           
=======================================
  Files         126      126           
  Lines        6517     6564   +47     
=======================================
+ Hits         6312     6358   +46     
- Misses        205      206    +1
Impacted Files Coverage Δ
tests/data/test_io.py 100.00% <100.00%> (ø)
tests/transforms/preprocessing/test_resample.py 100.00% <100.00%> (ø)
torchio/data/io.py 96.91% <100.00%> (+0.48%) ⬆️
...ansforms/augmentation/spatial/random_anisotropy.py 93.33% <100.00%> (+0.31%) ⬆️
...rchio/transforms/preprocessing/spatial/resample.py 90.27% <100.00%> (-0.50%) ⬇️
torchio/typing.py 100.00% <100.00%> (ø)

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@romainVala
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just get a quick look !
amazing quite a lot of changes and the result seems to be ok for me !
the pickel is ok, and the history looks as expected

great job, i'll look more to better understand, but difficult to review

romainVala
romainVala reviewed Aug 30, 2021
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looks good

torchio/transforms/preprocessing/spatial/resample.py Outdated Show resolved Hide resolved
torchio/transforms/preprocessing/spatial/resample.py Outdated Show resolved Hide resolved
@fepegar fepegar marked this pull request as ready for review August 30, 2021 22:12
@fepegar fepegar marked this pull request as draft August 30, 2021 22:59
@fepegar fepegar marked this pull request as ready for review August 31, 2021 09:41
@fepegar fepegar merged commit e85db2b into master Aug 31, 2021
@fepegar fepegar deleted the 638-support-shape-affine-resample branch August 31, 2021 11:43
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fepegar commented Aug 31, 2021

Thanks for reporting and reviewing, @romainVala!

@fepegar fepegar restored the 638-support-shape-affine-resample branch July 4, 2022 22:01
@fepegar fepegar deleted the 638-support-shape-affine-resample branch July 4, 2022 22:02
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Successfully merging this pull request may close these issues.

Resample transform should not need Image attribut
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@fepegar @romainVala