[ENH] - extra bval parsing for number of shells

[edickie]

In response to issue #64 and discussion during the hack here is a little addition to the vectors utility that can determine and report on the number of the shells (as well as masks for each shell).

Currently, it is outside of DiffusionTable because I'm unsure if we want all the methods integrated..

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Best reviewed: commit by commit

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Optimal code review plan (4 warnings)

     adding first version of bval parser

added one smoke test for bvals

...ep/utils/tests/test_vectors.py 56% changes removed in changed bval parsing...

now with a fiew passing tets

...ep/utils/tests/test_vectors.py 55% changes removed in changed bval parsing...

Merge pull request #1 from nipreps/master

dmriprep/utils/vectors.py 46% changes removed in changed bval parsing...

dmriprep/utils/images.py 41% changes removed in Merge pull request #...

docs/requirements.txt 80% changes removed in Merge pull request #...

setup.cfg 50% changes removed in Merge pull request #...

dmriprep/workflows/base.py 47% changes removed in Merge pull request #...

dmriprep/workflows/dwi/base.py 57% changes removed in Merge pull request #...

dmriprep/cli/run.py 45% changes removed in Merge pull request #...

Merge pull request #2 from nipreps/master

dmriprep/interfaces/images.py 50% changes removed in Merge pull request #...

     Merge pull request #3 from edickie/master

     changed bval parsing class to function as per suggestion

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[pep8speaks]

Hello @edickie, 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 dmriprep.

Comment last updated at 2020-04-07 22:57:59 UTC

[oesteban]

i'd reduce boilerplate and just use a function for this, but that's just an opinion :)

[oesteban]

I would probably go with a single function that accepts a DiffusionGradientTable object for this.

The function would return only a list of nonzero shell centers and the number of shells would be just the len() of that (which can be easily calculated by the user).

WDYT?

[oesteban]

Do you think you can give this a little bump for tomorrow's meeting?

[codecov]

Codecov Report

Merging #73 into master will decrease coverage by 0.01%.
The diff coverage is 21.42%.

@@            Coverage Diff             @@
##           master      #73      +/-   ##
==========================================
- Coverage   51.06%   51.05%   -0.02%     
==========================================
  Files          21       21              
  Lines        1218     1232      +14     
  Branches      161      164       +3     
==========================================
+ Hits          622      629       +7     
- Misses        581      590       +9     
+ Partials       15       13       -2     

Impacted Files	Coverage Δ
dmriprep/utils/vectors.py	87.07% <21.42%> (-3.17%)	⬇️

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[oesteban]

I believe this from #29 is highly related to this PR.

EDIT: I'll go through this PR tomorrow. Thanks for updating Erin!