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FIX: Import nibabel reorientation bug fix #2912

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Merged
merged 1 commit into from
Apr 9, 2019
Merged

FIX: Import nibabel reorientation bug fix #2912

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16 changes: 6 additions & 10 deletions nipype/interfaces/image.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
from ..utils.filemanip import fname_presuffix
from .base import (SimpleInterface, TraitedSpec, BaseInterfaceInputSpec,
traits, File)
from .. import LooseVersion


class RescaleInputSpec(BaseInterfaceInputSpec):
Expand Down Expand Up @@ -186,8 +187,8 @@ def _run_interface(self, runtime):
transform = ornt_transform(orig_ornt, targ_ornt)
affine_xfm = inv_ornt_aff(transform, orig_img.shape)

# Check can be eliminated when minimum nibabel version >= 2.2
if hasattr(orig_img, 'as_reoriented'):
# Check can be eliminated when minimum nibabel version >= 2.4
if LooseVersion(nb.__version__) >= LooseVersion('2.4.0'):
reoriented = orig_img.as_reoriented(transform)
else:
reoriented = _as_reoriented_backport(orig_img, transform)
Expand All @@ -212,7 +213,7 @@ def _run_interface(self, runtime):


def _as_reoriented_backport(img, ornt):
"""Backport of img.as_reoriented as of nibabel 2.2.0"""
"""Backport of img.as_reoriented as of nibabel 2.4.0"""
import numpy as np
import nibabel as nb
from nibabel.orientations import inv_ornt_aff
Expand All @@ -225,13 +226,8 @@ def _as_reoriented_backport(img, ornt):

if isinstance(reoriented, nb.Nifti1Pair):
# Also apply the transform to the dim_info fields
new_dim = list(reoriented.header.get_dim_info())
for idx, value in enumerate(new_dim):
# For each value, leave as None if it was that way,
# otherwise check where we have mapped it to
if value is None:
continue
new_dim[idx] = np.where(ornt[:, 0] == idx)[0]
new_dim = [None if orig_dim is None else int(ornt[orig_dim, 0])
for orig_dim in img.header.get_dim_info()]

reoriented.header.set_dim_info(*new_dim)

Expand Down
4 changes: 2 additions & 2 deletions nipype/interfaces/tests/test_image.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,10 @@
from ..image import _as_reoriented_backport, _orientations
from ... import LooseVersion

nibabel22 = LooseVersion(nb.__version__) >= LooseVersion('2.2.0')
nibabel24 = LooseVersion(nb.__version__) >= LooseVersion('2.4.0')


@pytest.mark.skipif(not nibabel22,
@pytest.mark.skipif(not nibabel24,
reason="Old nibabel - can't directly compare")
def test_reorientation_backport():
pixdims = ((1, 1, 1), (2, 2, 3))
Expand Down