ENH: add interface for AFNI 3dTsmooth #2948

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Merged

effigies merged 5 commits into nipy:master from gpiantoni:3dTsmooth

Sep 6, 2019

Merged

ENH: add interface for AFNI 3dTsmooth #2948

effigies merged 5 commits into nipy:master from gpiantoni:3dTsmooth

Sep 6, 2019

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@gpiantoni gpiantoni commented Jun 26, 2019

Summary

add interface for AFNI 3dTsmooth

List of changes proposed in this PR (pull-request)

add interface for AFNI 3dTsmooth
includes almost all of the options under 3dTsmooth including:
- Three Point Filtering Options
- General Linear Filtering Options
- Adaptive Mean Filtering option

Acknowledgment

[x ] (Mandatory) I acknowledge that this contribution will be available under the Apache 2 license.

effigies

effigies reviewed

Jun 26, 2019

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nipype/interfaces/afni/preprocess.py Outdated

>>> smooth.inputs.in_file = 'functional.nii'

>>> smooth.inputs.adaptive = 5

>>> smooth.cmdline

'3dTsmooth -prefix functional_smooth -adaptive 5 functional.nii'

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Suggested change

'3dTsmooth -prefix functional_smooth -adaptive 5 functional.nii'

'3dTsmooth -adaptive 5 -prefix functional_smooth functional.nii'

@effigies effigies added this to the 1.2.1 milestone

Jun 26, 2019

effigies

effigies reviewed

Jul 26, 2019

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Hi @gpiantoni, do you have a few minutes to finish this up?

nipype/interfaces/afni/preprocess.py Outdated

desc='output file from 3dTSmooth',

argstr='-prefix %s',

name_source='in_file',

genfile=True)

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nipype/interfaces/afni/preprocess.py Outdated

name_template='%s_smooth',

desc='output file from 3dTSmooth',

argstr='-prefix %s',

name_source='in_file',

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Suggested change

name_source='in_file',

name_source='in_file')

@effigies effigies modified the milestones: 1.2.1, 1.2.2

Aug 16, 2019

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effigies commented Sep 5, 2019

Hi @gpiantoni, we're planning to have the next release in a little under 3 weeks, if you want to have a shot at finishing this up.

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gpiantoni commented Sep 5, 2019

I rebased from upstream/master and force-pushed my branch. However, one test fails (because of the change from genfile=True to genfile=None).

I tried to run make check-before-commit locally. This command modifies more than 40 files with very trivial changes. See output of git diff:
nipype

I don't think I'm supposed to commit these changes but I don't know what else to do. Sorry, I don't know how to proceed from here.

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effigies commented Sep 5, 2019

Hi @gpiantoni, I re-ran make specs on the master branch, so if you rebase again, then make specs should only update your test.

@oesteban oesteban modified the milestones: 1.2.2, 1.3.0, 1.2.3

Sep 5, 2019

gpiantoni added 4 commits

September 6, 2019 10:04

@gpiantoni


 added simple version of 3dTsmooth

11d3422

@gpiantoni


 add all options for 3dTsmooth

f341089

@gpiantoni


 added autotest for TSmooth

0a05ce9

@gpiantoni


 remove genfile from out_file of TSmooth and fix order of arguments in...

8d76fd2

... command line of 3dTsmooth

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codecov bot commented Sep 6, 2019

Codecov Report

Merging #2948 into master will decrease coverage by 0.51%.
The diff coverage is 100%.

Impacted file tree graph

@@ Coverage Diff @@
## master #2948 +/- ##
==========================================
- Coverage 67.5% 66.99% -0.52% 
==========================================
 Files 344 343 -1 
 Lines 44028 44027 -1 
 Branches 5551 5548 -3 
==========================================
- Hits 29723 29496 -227 
- Misses 13556 13780 +224 
- Partials 749 751 +2

Flag	Coverage Δ
#smoketests	`50.43% <ø> (ø)`	⬆️
#unittests	`64.18% <100%> (-0.8%)`	⬇️

Impacted Files	Coverage Δ
nipype/interfaces/afni/__init__.py	`100% <ø> (ø)`	⬆️
nipype/interfaces/afni/preprocess.py	`82.34% <100%> (+0.32%)`	⬆️
nipype/interfaces/nilearn.py	`40% <0%> (-56.67%)`	⬇️
nipype/testing/fixtures.py	`77.33% <0%> (-21.34%)`	⬇️
nipype/interfaces/freesurfer/base.py	`61.01% <0%> (-19.5%)`	⬇️
nipype/workflows/smri/freesurfer/autorecon2.py	`65.9% <0%> (-9.2%)`	⬇️
nipype/workflows/smri/freesurfer/ba_maps.py	`91.66% <0%> (-8.34%)`	⬇️
nipype/workflows/smri/freesurfer/recon.py	`66.66% <0%> (-7.81%)`	⬇️
nipype/workflows/smri/freesurfer/autorecon3.py	`68.4% <0%> (-6.95%)`	⬇️
nipype/workflows/smri/freesurfer/autorecon1.py	`41.66% <0%> (-5.1%)`	⬇️
... and 11 more

Continue to review full report at Codecov.

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Δ = absolute <relative> (impact), ø = not affected, ? = missing data
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codecov bot commented Sep 6, 2019 •

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Codecov Report

Merging #2948 into master will decrease coverage by 0.51%.
The diff coverage is 100%.

Impacted file tree graph

@@ Coverage Diff @@
## master #2948 +/- ##
==========================================
- Coverage 67.5% 66.99% -0.52% 
==========================================
 Files 344 343 -1 
 Lines 44028 44026 -2 
 Branches 5551 5548 -3 
==========================================
- Hits 29723 29495 -228 
- Misses 13556 13780 +224 
- Partials 749 751 +2

Flag	Coverage Δ
#smoketests	`50.43% <ø> (ø)`	⬆️
#unittests	`64.18% <100%> (-0.8%)`	⬇️

Impacted Files	Coverage Δ
nipype/interfaces/afni/__init__.py	`100% <ø> (ø)`	⬆️
nipype/interfaces/afni/preprocess.py	`82.34% <100%> (+0.32%)`	⬆️
nipype/interfaces/nilearn.py	`40% <0%> (-56.67%)`	⬇️
nipype/testing/fixtures.py	`77.33% <0%> (-21.34%)`	⬇️
nipype/interfaces/freesurfer/base.py	`61.01% <0%> (-19.5%)`	⬇️
nipype/workflows/smri/freesurfer/autorecon2.py	`65.9% <0%> (-9.2%)`	⬇️
nipype/workflows/smri/freesurfer/ba_maps.py	`91.66% <0%> (-8.34%)`	⬇️
nipype/workflows/smri/freesurfer/recon.py	`66.66% <0%> (-7.81%)`	⬇️
nipype/workflows/smri/freesurfer/autorecon3.py	`68.4% <0%> (-6.95%)`	⬇️
nipype/workflows/smri/freesurfer/autorecon1.py	`41.66% <0%> (-5.1%)`	⬇️
... and 11 more

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 64c7b24...018cc43. Read the comment docs.

effigies

effigies reviewed

Sep 6, 2019

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nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py Show resolved Hide resolved

@gpiantoni


 added auto test for 3dTsmooth (without removing other files)

56e5715

effigies

effigies approved these changes

Sep 6, 2019

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LGTM. Will merge when tests pass.

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effigies commented Sep 6, 2019

Thanks for your patience, @gpiantoni. In it goes.

@effigies effigies merged commit 09d55ec into nipy:master

Sep 6, 2019

@oesteban oesteban mentioned this pull request

Sep 7, 2019

REL: 1.2.2 #3015

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ENH: add interface for AFNI 3dTsmooth #2948

ENH: add interface for AFNI 3dTsmooth #2948

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@gpiantoni gpiantoni commented Jun 26, 2019

Summary

List of changes proposed in this PR (pull-request)

Acknowledgment

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effigies commented Sep 5, 2019

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effigies commented Sep 6, 2019

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