[ENH] Registration tools

[dPys]

*This new module adds a set of Dipy-based linear registration tools to dMRIprep to use for EMC. These are based on @arokem 's original API's, though have been modified to input/output NIfti1Images rather than numpy arrays, includes support for inverted transform application, and includes a new average affine utility (@oesteban -- might something like this already be available from nitransforms?).

The original API's have additionally been modified to draw the hyperparameters for 3Dtransform from several presets which are stored in coarse/precise affine/rigid templates now located in the config module.

[pull-assistant[bot]]

Best reviewed: commit by commit

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Optimal code review plan (1 warning)

     [ENH] Add affine registration tools for EMC

     [ENH] Add coarse/precise affine/rigid templates

     Add test for affine_registration and add interfaces to use for emc

     Add test for affine_registration and add interfaces to use for emc

Add test for affine_registration and add interfaces to use for emc

...ils/tests/test_registration.py 53% changes removed in sty: run black

     [ENH] Add affine registration tools for EMC

     Add test for affine_registration and add interfaces to use for emc

     sty: run black

     Update dmriprep/interfaces/registration.py

     Update dmriprep/interfaces/registration.py

     Update dmriprep/interfaces/registration.py

     Update dmriprep/interfaces/registration.py

     Update dmriprep/interfaces/registration.py

     Update dmriprep/interfaces/registration.py

     Update dmriprep/interfaces/registration.py

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[arokem]

This looks good to me. I think that the travis failure is because we need to up our nibabel requirements (to 3.0.1) to comply with niworkflows requirements.

[dPys]

Great, I will proceed to write some unit tests for it then (unless @oesteban has any additional revision requests).

[sider[bot]]

Warnings are found on analyzing the commit 756a1ef492391095ce23e457496e74fcf31a96c1.

1 warning:

• ⚠️ Goodcheck

We recommend to address them as possible, for example, update outdated dependencies, fix the tool's configuration, configure sider.yml, turn off unused tools, and so on.

If you are struggling with these errors or warnings, feel free to ask us via chat. 💬

[codecov[bot]]

Codecov Report

Merging #78 into master will decrease coverage by 1.01%. The diff coverage is 52.47%.

@@            Coverage Diff            @@
##           master     #78      +/-   ##
=========================================
- Coverage   52.71%   51.7%   -1.02%     
=========================================
  Files          16      23       +7     
  Lines         901    1319     +418     
  Branches      111     166      +55     
=========================================
+ Hits          475     682     +207     
- Misses        425     626     +201     
- Partials        1      11      +10

Impacted Files	Coverage Δ
dmriprep/utils/registration.py	35.55% <35.55%> (ø)
dmriprep/interfaces/registration.py	66.07% <66.07%> (ø)
dmriprep/config/__init__.py	56.72% <0%> (-43.28%)	:arrow_down:
dmriprep/cli/run.py	4.1% <0%> (-26.98%)	:arrow_down:
dmriprep/utils/vectors.py	94.37% <0%> (-5.63%)	:arrow_down:
dmriprep/workflows/base.py	24.67% <0%> (-4.91%)	:arrow_down:
dmriprep/interfaces/vectors.py	100% <0%> (ø)	:arrow_up:
dmriprep/__init__.py	100% <0%> (ø)	:arrow_up:
dmriprep/cli/parser.py	56.57% <0%> (ø)
dmriprep/config/testing.py	26.92% <0%> (ø)
... and 7 more

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Continue to review full report at Codecov.

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[pep8speaks]

Hello @dPys, Thank you for updating!

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

Comment last updated at 2020-09-24 05:31:28 UTC

[dPys]

All of your suggested changes committed @oesteban :-) Merge?

[oesteban]

The new tests are failing (TravisCI). I just fixed the CircleCI failure, that's not a problem of this PR.