[ENH] Mrtrix3 enhancements #3426

GalKepler · 2021-12-22T15:56:29Z

Summary

Made some changes and additions to Mrtrix3's interfaces in the nipype platform.

Fixes #3400 and #3402 .

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

Added json and gradient table-related kwargs to mrconvert interface.
Added mrcatinterface.
Added mrtransform interface.

Acknowledgment

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

… tensor2metric

…orts. WIP

…issing required file paths.

codecov · 2021-12-22T21:02:03Z

Codecov Report

Merging #3426 (8375356) into master (1342d62) will increase coverage by 0.01%.
The diff coverage is 73.68%.

@@            Coverage Diff             @@
##           master    #3426      +/-   ##
==========================================
+ Coverage   65.22%   65.23%   +0.01%     
==========================================
  Files         308      308              
  Lines       40536    40625      +89     
  Branches     5355     5361       +6     
==========================================
+ Hits        26439    26503      +64     
- Misses      13022    13046      +24     
- Partials     1075     1076       +1

Flag	Coverage Δ
unittests	`64.96% <73.68%> (+0.01%)`	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
nipype/interfaces/mrtrix/convert.py	`16.58% <ø> (ø)`
nipype/interfaces/mrtrix/preprocess.py	`64.10% <ø> (ø)`
nipype/interfaces/mrtrix3/preprocess.py	`82.83% <ø> (ø)`
nipype/interfaces/mrtrix3/base.py	`59.01% <60.00%> (-0.64%)`	⬇️
nipype/interfaces/mrtrix3/utils.py	`80.06% <73.25%> (-2.95%)`	⬇️
nipype/interfaces/mrtrix3/__init__.py	`100.00% <100.00%> (ø)`

Continue to review full report at Codecov.

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…x formatting changes.

ZviBaratz · 2021-12-23T08:37:27Z

Hi 😃

@GalBenZvi and I are trying to get this PR to pass the build (the tests pass locally), but it seems like we're missing something.

There are two issues we're currently facing:

Contribution checks' tests raising:

 M nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py
 M nipype/interfaces/mrtrix3/tests/test_auto_ConstrainedSphericalDeconvolution.py
 M nipype/interfaces/mrtrix3/tests/test_auto_DWIBiasCorrect.py
 M nipype/interfaces/mrtrix3/tests/test_auto_DWIDenoise.py
 M nipype/interfaces/mrtrix3/tests/test_auto_DWIExtract.py
 M nipype/interfaces/mrtrix3/tests/test_auto_DWIPreproc.py
 M nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py
 M nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py
 M nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py
 M nipype/interfaces/mrtrix3/tests/test_auto_MRCat.py
 M nipype/interfaces/mrtrix3/tests/test_auto_MRConvert.py
 M nipype/interfaces/mrtrix3/tests/test_auto_MRDeGibbs.py
 M nipype/interfaces/mrtrix3/tests/test_auto_MRMath.py
 M nipype/interfaces/mrtrix3/tests/test_auto_MRResize.py
 M nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py
 M nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py
 M nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py
++ git status -s
+ test -z ' M nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py
 M nipype/interfaces/mrtrix3/tests/test_auto_ConstrainedSphericalDeconvolution.py
 M nipype/interfaces/mrtrix3/tests/test_auto_DWIBiasCorrect.py
 M nipype/interfaces/mrtrix3/tests/test_auto_DWIDenoise.py
 M nipype/interfaces/mrtrix3/tests/test_auto_DWIExtract.py
 M nipype/interfaces/mrtrix3/tests/test_auto_DWIPreproc.py
 M nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py
 M nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py
 M nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py
 M nipype/interfaces/mrtrix3/tests/test_auto_MRCat.py
 M nipype/interfaces/mrtrix3/tests/test_auto_MRConvert.py
 M nipype/interfaces/mrtrix3/tests/test_auto_MRDeGibbs.py
 M nipype/interfaces/mrtrix3/tests/test_auto_MRMath.py
 M nipype/interfaces/mrtrix3/tests/test_auto_MRResize.py
 M nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py
 M nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py
 M nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py'
Error: Process completed with exit code 1.

Even though the pre-commit hook is run successfully before pushing, it seems like there are many formatting changes being applied.

@effigies @satra I tried looking into checkspecs.py but haven't managed to track down the problem. Any help resolving this would be greatly appreciated 🙏

Co-authored-by: GalBenZvi <hershkovitz1@mail.tau.ac.il> Co-authored-by: Zvi Baratz <z.baratz@gmail.com>

effigies · 2022-04-02T17:11:18Z

Hi @ZviBaratz @GalBenZvi, apologies for the very slow response. I went ahead and pared down a lot of the unrelated changes and squashed this into a single commit in #3445. Could you review that and let me know if that fully replaces what you were trying to do here?

GalKepler · 2022-04-04T19:56:23Z

Hi @effigies,
The PR looks good (I think it's most of what I tried to add some time ago but had some trouble with the checks).

I was wondering whether you'd like me to create interfaces to some other mrtrix's functions?
I saw there's another release coming and wouldn't want to delay it.

ENH: Add MRTrix3 interfaces (pared-down gh-3426)

effigies · 2022-04-04T20:36:17Z

@GalBenZvi Thanks for looking it over. I'm going to try to release tomorrow or the day after, but please feel free to submit more interfaces when you have the opportunity.

GalKepler and others added 23 commits October 30, 2021 18:50

added kwarg json_import to mrconvert interface

ec35b55

added kwarg json_export to mrconvert interface

412f7af

refractoring

b5246a8

refractoring w/ black...

5979cb8

Created an interface for mrtrix3's mrcat function

aa64ccd

forgot to run make before commit...

1b74350

refractored black formatting

a156154

Merge branch 'mrcat'

87f999c

fixed a small issue with output listing

480c1f9

Merge branch 'mrconvert'

97c3a89

just added some tensor-derived metrics for the interface of mrtrix3's…

dbed52b

… tensor2metric

a small addition for the mrconvert interface to include bvec/bval exp…

e263d36

…orts. WIP

a small addition for the mrconvert interface to include bvec/bval exp…

9311658

…orts. WIP

updated some small changes

8462a45

added interface for mrtrix3's transformconvert and mrtransform

c42ac75

added interface for mrtrix3's transformconvert and mrtransform

7a77fdd

Merge branch 'master' of https://github.com/nipy/nipype

a79c5d4

Fixed dwipreproc default value in tests.

3334c58

Fixed TransformFSLConvert import path in example docs.

a6472dc

Tried changing file names to mif files in other doctests.

1413f30

Reverted DWIPreprocInputSpec.out_grad_mrtrix default value change.

9414af8

Reverted test value change.

ed6b685

Removed TransformFSLConvert example to avoid doctest failure due to m…

054e0b1

…issing required file paths.

ZviBaratz added 3 commits December 23, 2021 09:23

Tried manually generating the missing automatic test modules.

947bef2

Re-ran formatting.

3782d28

Reinstalled dev env requirements and triggered a commit to try and fi…

fd470a5

…x formatting changes.

effigies added a commit to effigies/nipype that referenced this pull request Apr 2, 2022

ENH: Add MRTrix3 interfaces (pared-down nipygh-3426)

3f13aba

effigies added a commit to effigies/nipype that referenced this pull request Apr 2, 2022

ENH: Add MRTrix3 interfaces (pared-down nipygh-3426)

af8d36c

Co-authored-by: GalBenZvi <hershkovitz1@mail.tau.ac.il> Co-authored-by: Zvi Baratz <z.baratz@gmail.com>

effigies mentioned this pull request Apr 2, 2022

ENH: Add MRTrix3 interfaces (pared-down gh-3426) #3445

Merged

effigies added this to the 1.7.1 milestone Apr 3, 2022

Merge branch 'master' into mrtrix

8375356

effigies closed this in #3445 Apr 4, 2022

effigies added a commit that referenced this pull request Apr 4, 2022

Merge pull request #3445 from effigies/mrtrix3-squash

4ac2189

ENH: Add MRTrix3 interfaces (pared-down gh-3426)

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GalKepler commented Dec 22, 2021

Summary

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

Acknowledgment

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