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RF: Use np.flip instead of flip_axis #916

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Merged
merged 4 commits into from
May 26, 2020
Merged

RF: Use np.flip instead of flip_axis #916

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09bdafd
RF: Use np.flip instead of flip_axis
jond01 May 25, 2020
164d46c
MNT: Defer orientation_affine deprecation to v4.0
jond01 May 25, 2020
884c8f0
Update nibabel/orientations.py
jond01 May 25, 2020
e537732
Update nibabel/orientations.py
effigies May 26, 2020
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37 changes: 11 additions & 26 deletions nibabel/orientations.py
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Original file line number Diff line number Diff line change
Expand Up @@ -165,7 +165,7 @@ def apply_orientation(arr, ornt):
# apply ornt transformations
for ax, flip in enumerate(ornt[:, 1]):
if flip == -1:
t_arr = flip_axis(t_arr, axis=ax)
t_arr = np.flip(t_arr, axis=ax)
full_transpose = np.arange(t_arr.ndim)
# ornt indicates the transpose that has occurred - we reverse it
full_transpose[:n] = np.argsort(ornt[:, 0])
Expand Down Expand Up @@ -230,20 +230,21 @@ def inv_ornt_aff(ornt, shape):


@deprecate_with_version('orientation_affine deprecated. '
'Please use inv_ornt_aff instead'
'Please use inv_ornt_aff instead.',
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Oof. Good catch. I guess bumping back to 4.0 is the right thing to do, though hopefully nobody is depending on it, still.

'1.3',
'3.0')
'4.0')
def orientation_affine(ornt, shape):
return inv_ornt_aff(ornt, shape)


@deprecate_with_version('flip_axis is deprecated. '
'Please use numpy.flip instead.',
'3.2',
'5.0')
def flip_axis(arr, axis=0):
''' Flip contents of `axis` in array `arr`
""" Flip contents of `axis` in array `arr`

``flip_axis`` is the same transform as ``np.flipud``, but for any
axis. For example ``flip_axis(arr, axis=0)`` is the same transform
as ``np.flipud(arr)``, and ``flip_axis(arr, axis=1)`` is the same
transform as ``np.fliplr(arr)``
Equivalent to ``np.flip(arr, axis=0)``.

Parameters
----------
Expand All @@ -255,24 +256,8 @@ def flip_axis(arr, axis=0):
-------
farr : array
Array with axis `axis` flipped

Examples
--------
>>> a = np.arange(6).reshape((2,3))
>>> a
array([[0, 1, 2],
[3, 4, 5]])
>>> flip_axis(a, axis=0)
array([[3, 4, 5],
[0, 1, 2]])
>>> flip_axis(a, axis=1)
array([[2, 1, 0],
[5, 4, 3]])
'''
arr = np.asanyarray(arr)
arr = arr.swapaxes(0, axis)
arr = np.flipud(arr)
return arr.swapaxes(axis, 0)
"""
return np.flip(arr, axis)


def ornt2axcodes(ornt, labels=None):
Expand Down
30 changes: 8 additions & 22 deletions nibabel/tests/test_orientations.py
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Expand Up @@ -140,28 +140,6 @@ def test_apply():
assert_array_equal(a.shape, np.array(t_arr.shape)[np.array(ornt)[:, 0]])


def test_flip_axis():
a = np.arange(24).reshape((2, 3, 4))
assert_array_equal(
flip_axis(a),
np.flipud(a))
assert_array_equal(
flip_axis(a, axis=0),
np.flipud(a))
assert_array_equal(
flip_axis(a, axis=1),
np.fliplr(a))
# check accepts array-like
assert_array_equal(
flip_axis(a.tolist(), axis=0),
np.flipud(a))
# third dimension
b = a.transpose()
b = np.flipud(b)
b = b.transpose()
assert_array_equal(flip_axis(a, axis=2), b)


def test_io_orientation():
for shape in ((2, 3, 4), (20, 15, 7)):
for in_arr, out_ornt in zip(IN_ARRS, OUT_ORNTS):
Expand Down Expand Up @@ -381,3 +359,11 @@ def test_orientation_affine_deprecation():
with pytest.deprecated_call():
aff2 = orientation_affine([[0, 1], [1, -1], [2, 1]], (3, 4, 5))
assert_array_equal(aff1, aff2)


def test_flip_axis_deprecation():
a = np.arange(24).reshape((2, 3, 4))
axis = 1
with pytest.deprecated_call():
a_flipped = flip_axis(a, axis)
assert_array_equal(a_flipped, np.flip(a, axis))
4 changes: 2 additions & 2 deletions nibabel/tests/test_processing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@
conform)
from nibabel.nifti1 import Nifti1Image
from nibabel.nifti2 import Nifti2Image
from nibabel.orientations import aff2axcodes, flip_axis, inv_ornt_aff
from nibabel.orientations import aff2axcodes, inv_ornt_aff
from nibabel.affines import (AffineError, from_matvec, to_matvec, apply_affine,
voxel_sizes)
from nibabel.eulerangles import euler2mat
Expand Down Expand Up @@ -110,7 +110,7 @@ def test_resample_from_to():
ax_flip_ornt = flip_ornt.copy()
ax_flip_ornt[axis, 1] = -1
aff_flip_i = inv_ornt_aff(ax_flip_ornt, (2, 3, 4))
flipped_img = Nifti1Image(flip_axis(data, axis),
flipped_img = Nifti1Image(np.flip(data, axis),
np.dot(affine, aff_flip_i))
out = resample_from_to(flipped_img, ((2, 3, 4), affine))
assert_almost_equal(img.dataobj, out.dataobj)
Expand Down
10 changes: 5 additions & 5 deletions nibabel/tests/test_scripts.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@
import nibabel as nib
from ..tmpdirs import InTemporaryDirectory
from ..loadsave import load
from ..orientations import flip_axis, aff2axcodes, inv_ornt_aff
from ..orientations import aff2axcodes, inv_ornt_aff

import unittest
import pytest
Expand Down Expand Up @@ -273,20 +273,20 @@ def test_parrec2nii():
assert code == 1
# Default scaling is dv
pr_img = load(fname)
flipped_data = flip_axis(pr_img.get_fdata(), 1)
flipped_data = np.flip(pr_img.get_fdata(), 1)
base_cmd = ['parrec2nii', '--overwrite', fname]
check_conversion(base_cmd, flipped_data, out_froot)
check_conversion(base_cmd + ['--scaling=dv'],
flipped_data,
out_froot)
# fp
pr_img = load(fname, scaling='fp')
flipped_data = flip_axis(pr_img.get_fdata(), 1)
flipped_data = np.flip(pr_img.get_fdata(), 1)
check_conversion(base_cmd + ['--scaling=fp'],
flipped_data,
out_froot)
# no scaling
unscaled_flipped = flip_axis(pr_img.dataobj.get_unscaled(), 1)
unscaled_flipped = np.flip(pr_img.dataobj.get_unscaled(), 1)
check_conversion(base_cmd + ['--scaling=off'],
unscaled_flipped,
out_froot)
Expand Down Expand Up @@ -335,7 +335,7 @@ def test_parrec2nii_with_data():
assert np.all(np.abs(aff_off / vox_sizes) <= 0.501)
# The data is very close, unless it's the fieldmap
if par_root != 'fieldmap':
conved_data_lps = flip_axis(conved_img.dataobj, 1)
conved_data_lps = np.flip(conved_img.dataobj, 1)
assert np.allclose(conved_data_lps, philips_img.dataobj)
with InTemporaryDirectory():
# Test some options
Expand Down