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[ENH] Add emc helper functions - vectors #76

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@dPys dPys commented Feb 11, 2020

*All of these support the signal prediction routines.
*Each function will need a unit test.

@dPys dPys changed the title [ENH] Miscellaneous emc helper functions vectors [ENH] Miscellaneous emc helper functions -- vectors Feb 11, 2020
@dPys dPys changed the title [ENH] Miscellaneous emc helper functions -- vectors [ENH] Add emc helper functions - vectors Feb 11, 2020
@dPys dPys requested a review from oesteban February 12, 2020 02:48
arokem added a commit to arokem/dmriprep that referenced this pull request Feb 25, 2020
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Unit tests for _nonoverlapping_qspace_samples would be great to have and it is a very low hanging fruit - we want this function to be super-robust.

dmriprep/utils/vectors.py Outdated Show resolved Hide resolved
Comment on lines 404 to 432
def _rasb_to_bvec_list(in_rasb):
"""
Create a list of b-vectors from a rasb gradient table.

Parameters
----------
in_rasb : str or os.pathlike
File path to a RAS-B gradient table.
"""
import numpy as np

ras_b_mat = np.genfromtxt(in_rasb, delimiter="\t")
bvec = [vec for vec in ras_b_mat[:, 0:3] if not np.isclose(all(vec), 0)]
return list(bvec)


def _rasb_to_bval_floats(in_rasb):
"""
Create a list of b-values from a rasb gradient table.

Parameters
----------
in_rasb : str or os.pathlike
File path to a RAS-B gradient table.
"""
import numpy as np

ras_b_mat = np.genfromtxt(in_rasb, delimiter="\t")
return [float(bval) for bval in ras_b_mat[:, 3] if bval > 0]
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Can you point me at the location where these are needed? I believe our Gradients class has already this covered.

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(and not covered in Gradients class)

@oesteban oesteban added this to the 0.4.0 milestone Mar 23, 2020
dmriprep/utils/vectors.py Outdated Show resolved Hide resolved
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pep8speaks commented Mar 24, 2020

Hello @dPys, 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 2020-03-24 20:09:36 UTC

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codecov bot commented Mar 24, 2020

Codecov Report

Merging #76 into master will decrease coverage by 0.59%.
The diff coverage is 100%.

Impacted file tree graph

@@            Coverage Diff            @@
##           master      #76     +/-   ##
=========================================
- Coverage   52.37%   51.77%   -0.6%     
=========================================
  Files          16       21      +5     
  Lines         907     1240    +333     
  Branches      114      164     +50     
=========================================
+ Hits          475      642    +167     
- Misses        431      586    +155     
- Partials        1       12     +11
Impacted Files Coverage Δ
dmriprep/utils/vectors.py 90.1% <100%> (-9.9%) ⬇️
dmriprep/config/__init__.py 56.72% <0%> (-43.28%) ⬇️
dmriprep/cli/run.py 4.1% <0%> (-26.3%) ⬇️
dmriprep/workflows/base.py 24.67% <0%> (-4.91%) ⬇️
dmriprep/interfaces/vectors.py 100% <0%> (ø) ⬆️
dmriprep/__init__.py 100% <0%> (ø) ⬆️
dmriprep/utils/images.py 13.33% <0%> (ø)
dmriprep/cli/parser.py 56.57% <0%> (ø)
dmriprep/utils/misc.py 50% <0%> (ø)
... and 4 more

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dmriprep/utils/vectors.py Outdated Show resolved Hide resolved
Co-Authored-By: Ariel Rokem <arokem@gmail.com>
@dPys dPys force-pushed the miscellaneous_emc_helper_functions_vectors branch from 49e0a0a to 7e1b11e Compare March 24, 2020 18:12
@dPys dPys mentioned this pull request Mar 25, 2020
@oesteban oesteban modified the milestones: 0.4.0, 0.5.0 Dec 10, 2020
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4 participants