8000 ENH: Add a utility to calculate obliquity of affines by oesteban · Pull Request #815 · nipy/nibabel · GitHub
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ENH: Add a utility to calculate obliquity of affines #815

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Merged
merged 6 commits into from
Oct 15, 2019
Merged

ENH: Add a utility to calculate obliquity of affines #815

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3cfff0d
ENH: Add an utility to calculate obliquity of affines
oesteban Sep 20, 2019
c92d560
enh(tests): add not-oblique test, move tests to ``test_affines.py``
oesteban Sep 20, 2019
da8da56
enh: return radians unless degrees=True
oesteban Sep 22, 2019
253a256
enh: address @matthew-brett's comments
oesteban Sep 23, 2019
04584b6
doc: add link to AFNI's documentation about *obliquity* [skip ci]
oesteban Sep 24, 2019
891d85c
fix: incorrect operation ordering caught by @matthew-brett
oesteban Sep 27, 2019
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enh(tests): add not-oblique test, move tests to test_affines.py 
Addressing one of @matthew-brett's comments.
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@oesteban
oesteban committed Sep 20, 2019
commit c92d5609f37ac2ec18f94606b8bb3075759e27ea
8 changes: 0 additions & 8 deletions nibabel/affines.py
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Expand Up @@ -306,14 +306,6 @@ def obliquity(affine):
This implementation is inspired by `AFNI's implementation
<https://github.com/afni/afni/blob/b6a9f7a21c1f3231ff09efbd861f8975ad48e525/src/thd_coords.c#L660-L698>`_

>>> affine = np.array([
... [2.74999725e+00, -2.74999817e-03, 2.74999954e-03, -7.69847980e+01],
... [2.98603540e-03, 2.73886840e+00, -2.47165887e-01, -8.36692043e+01],
... [-2.49170222e-03, 2.47168626e-01, 2.73886865e+00, -8.34056848e+01],
... [ 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 1.00000000e+00]])
>>> abs(5.15699 - obliquity(affine)) < 0.0001
True

"""
vs = voxel_sizes(affine)
fig_merit = (affine[:-1, :-1] / vs[np.newaxis, ...]).max(axis=1).min()
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12 changes: 11 additions & 1 deletion nibabel/tests/test_affines.py
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Expand Up @@ -7,7 +7,7 @@

from ..eulerangles import euler2mat
from ..affines import (AffineError, apply_affine, append_diag, to_matvec,
from_matvec, dot_reduce, voxel_sizes)
from_matvec, dot_reduce, voxel_sizes, obliquity)


from nose.tools import assert_equal, assert_raises
Expand Down Expand Up @@ -178,3 +178,13 @@ def test_voxel_sizes():
rot_affine[:3, :3] = rotation
full_aff = rot_affine.dot(aff)
assert_almost_equal(voxel_sizes(full_aff), vox_sizes)


def test_obliquity():
"""Check the calculation of inclination of an affine axes."""
aligned = np.diag([2.0, 2.0, 2.3, 1.0])
aligned[:-1, -1] = [-10, -10, -7]
R = from_matvec(euler2mat(x=0.09, y=0.001, z=0.001), [0.0, 0.0, 0.0])
oblique = R.dot(aligned)
assert_almost_equal(obliquity(aligned), 0.0)
assert_almost_equal(obliquity(oblique), 5.1569948883)
0