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FIX: Update all SpatialImage.get_data -> get_fdata #426

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Merged
merged 4 commits into from
Nov 25, 2019
Merged

FIX: Update all SpatialImage.get_data -> get_fdata #426

merged 4 commits into from
Nov 25, 2019

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oesteban
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For compatibility with nibabel:

find ./niworkflows -name "*.py" -exec sed -i 's+\.get_data(+.get_fdata(+g' {} \;

@oesteban oesteban requested a review from effigies November 25, 2019 00:10
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pull-assistant bot commented Nov 25, 2019 •
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Score: 0.69

Best reviewed: commit by commit

Optimal code review plan (1 warning)

FIX: Update all SpatialImage.get_data -> get_fdata

...iworkflows/interfaces/cifti.py 50% changes removed in fix: get_data of int...

...workflows/interfaces/images.py 75% changes removed in Apply suggestions fr...

...flows/interfaces/freesurfer.py 57% changes removed in Apply suggestions fr...

...iworkflows/interfaces/masks.py 67% changes removed in Apply suggestions fr...

...orkflows/interfaces/nilearn.py 67% changes removed in Apply suggestions fr...

...iworkflows/interfaces/utils.py 83% changes removed in Apply suggestions fr...

niworkflows/interfaces/mni.py 75% changes removed in Apply suggestions fr...

     fix: get_data of integer types

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oesteban
oesteban commented Nov 25, 2019
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codecov bot commented Nov 25, 2019 •
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Codecov Report

Merging #426 into master will decrease coverage by 4.64%.
The diff coverage is 19.23%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #426      +/-   ##
==========================================
- Coverage   59.09%   54.44%   -4.65%     
==========================================
  Files          56       42      -14     
  Lines        5366     4746     -620     
  Branches      630      630              
==========================================
- Hits         3171     2584     -587     
+ Misses       2151     2046     -105     
- Partials       44      116      +72
Flag Coverage Δ
#masks ?
#reportlettests ?
#unittests ?
Impacted Files Coverage Δ
niworkflows/anat/ants.py 12.5% <0%> (-0.08%) ⬇️
niworkflows/interfaces/nilearn.py 52.32% <0%> (ø) ⬆️
niworkflows/interfaces/freesurfer.py 43.44% <0%> (-0.82%) ⬇️
niworkflows/viz/plots.py 46.31% <0%> (ø) ⬆️
niworkflows/interfaces/masks.py 62.87% <0%> (-2.4%) ⬇️
niworkflows/interfaces/itk.py 28.39% <0%> (-10.5%) ⬇️
niworkflows/interfaces/registration.py 51.72% <0%> (-10.35%) ⬇️
niworkflows/interfaces/cifti.py 33.62% <0%> (+0.58%) ⬆️
niworkflows/interfaces/utils.py 38.09% <0%> (-10%) ⬇️
niworkflows/interfaces/images.py 45.91% <12.5%> (-6.19%) ⬇️
... and 31 more

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Δ = absolute <relative> (impact), ø = not affected, ? = missing data
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effigies
effigies reviewed Nov 25, 2019
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Please merge master.

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pep8speaks commented Nov 25, 2019 •
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Hello @oesteban, Thank you for updating!

Cheers! There are no style issues detected in this Pull Request. 🍻 To test for issues locally, pip install flake8 and then run flake8 niworkflows.

Comment last updated at 2019-11-25 18:03:59 UTC

oesteban and others added 3 commits November 25, 2019 09:40
@oesteban
FIX: Update all SpatialImage.get_data -> get_fdata
0fdf451 
For compatibility with nibabel:
```
find ./niworkflows -name "*.py" -exec sed -i 's+\.get_data(+.get_fdata(+g' {} \;
```
@oesteban
fix: get_data of integer types
86c4449
@oesteban @effigies
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b757e35 
Co-Authored-By: Chris Markiewicz <[email protected]>
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Thanks very much @effigies, I badly needed this update about how to access image's data and handle dtypes. 👍

effigies
effigies reviewed Nov 25, 2019
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No need to create a new image again. Just save the squeezed image.

effigies
effigies reviewed Nov 25, 2019
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2f37f7b 
Co-Authored-By: Chris Markiewicz <[email protected]>
@oesteban oesteban merged commit dda0b5f into nipreps:master Nov 25, 2019
@oesteban oesteban deleted the fix/nb-get_data branch November 25, 2019 18:57
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@oesteban @effigies @pep8speaks