From 74c64ccacf4be87db7479ce18ed3701bd49e1c78 Mon Sep 17 00:00:00 2001
From: "Benjamin A. Beasley" <code@musicinmybrain.net>
Date: Tue, 7 Feb 2023 17:49:20 -0500
Subject: [PATCH] Account for nibabel 5.0.0 removal of .py3k shim - use
numpy.compat.py3k
Rebased from:
https://salsa.debian.org/med-team/nipy/-/blob/12a4fbea8c99c1e5dc07ee81bc3da1a450617050/debian/patches/nibabel5.0.0.patch
---
.../statistics/formula/tests/test_formula.py | 2 +-
nipy/core/image/image_spaces.py | 4 ++--
nipy/core/image/tests/test_image_spaces.py | 4 ++--
nipy/io/tests/test_image_io.py | 2 +-
nipy/labs/spatial_models/parcel_io.py | 4 ++--
.../spatial_models/tests/test_discrete_domain.py | 2 +-
nipy/labs/spatial_models/tests/test_mroi.py | 4 ++--
nipy/labs/spatial_models/tests/test_parcel_io.py | 12 ++++++------
nipy/utils/compat3.py | 2 +-
nipy/utils/tests/test_compat3.py | 2 +-
tools/run_log_examples.py | 2 +-
11 files changed, 20 insertions(+), 20 deletions(-)
diff --git a/nipy/algorithms/statistics/formula/tests/test_formula.py b/nipy/algorithms/statistics/formula/tests/test_formula.py
index b7e88d6e8b..1323a8812e 100644
--- a/nipy/algorithms/statistics/formula/tests/test_formula.py
+++ b/nipy/algorithms/statistics/formula/tests/test_formula.py
@@ -18,7 +18,7 @@
from ..formulae import terms, Term
from nipy.utils import VisibleDeprecationWarning
-from nibabel.py3k import asbytes
+from numpy.compat.py3k import asbytes
from nibabel.testing import assert_dt_equal
from nose.tools import (assert_true, assert_equal, assert_false,
diff --git a/nipy/core/image/image_spaces.py b/nipy/core/image/image_spaces.py
index c349e381fd..72c5a096fe 100644
--- a/nipy/core/image/image_spaces.py
+++ b/nipy/core/image/image_spaces.py
@@ -60,7 +60,7 @@
It also works with nibabel images, which can only have xyz_affines:
>>> import nibabel as nib
->>> nimg = nib.Nifti1Image(data, affine)
+>>> nimg = nib.Nifti1Image(data.astype('float'), affine)
>>> xyz_affine(nimg)
array([[ 2., 0., 0., 0.],
[ 0., 3., 0., 0.],
@@ -195,7 +195,7 @@ def is_xyz_affable(img, name2xyz=None):
Nibabel images always have xyz affines
>>> import nibabel as nib
- >>> nimg = nib.Nifti1Image(arr, np.diag([2,3,4,1]))
+ >>> nimg = nib.Nifti1Image(arr.astype('float'), np.diag([2,3,4,1]))
>>> is_xyz_affable(nimg)
True
"""
diff --git a/nipy/core/image/tests/test_image_spaces.py b/nipy/core/image/tests/test_image_spaces.py
index f48317d1f6..41bf724f64 100644
--- a/nipy/core/image/tests/test_image_spaces.py
+++ b/nipy/core/image/tests/test_image_spaces.py
@@ -34,7 +34,7 @@ def test_image_xyz_affine():
img4_r = img4.reordered_axes([3,2,0,1])
assert_false(is_xyz_affable(img4_r))
assert_raises(AxesError, xyz_affine, img4_r)
- nimg = nib.Nifti1Image(arr, aff)
+ nimg = nib.Nifti1Image(arr.astype('float'), aff)
assert_true(is_xyz_affable(nimg))
assert_array_equal(xyz_affine(nimg), aff)
# Any dimensions not spatial, AxesError
@@ -77,7 +77,7 @@ def test_image_as_xyz_image():
assert_array_equal(img.get_fdata(), img_t0_r.get_fdata())
assert_equal(img.coordmap, img_t0_r.coordmap)
# Test against nibabel image
- nimg = nib.Nifti1Image(arr, np.diag([2,3,4,1]))
+ nimg = nib.Nifti1Image(arr.astype('float'), np.diag([2,3,4,1]))
nimg_r = as_xyz_image(nimg)
assert_true(nimg is nimg_r)
# It's sometimes impossible to make an xyz affable image
diff --git a/nipy/io/tests/test_image_io.py b/nipy/io/tests/test_image_io.py
index 695f9313b5..37aaaca31e 100644
--- a/nipy/io/tests/test_image_io.py
+++ b/nipy/io/tests/test_image_io.py
@@ -45,7 +45,7 @@ def test_badfile():
# nibabel prior 2.1.0 was throwing a ImageFileError for the not-recognized
# file type. >=2.1.0 give a FileNotFoundError.
try:
- from nibabel.py3k import FileNotFoundError
+ from numpy.compat.py3k import FileNotFoundError
except ImportError:
FileNotFoundError = IOError
assert_raises((ImageFileError, FileNotFoundError), load_image, filename)
diff --git a/nipy/labs/spatial_models/parcel_io.py b/nipy/labs/spatial_models/parcel_io.py
index d50f50d2c8..4eed7931f0 100644
--- a/nipy/labs/spatial_models/parcel_io.py
+++ b/nipy/labs/spatial_models/parcel_io.py
@@ -53,7 +53,7 @@ def mask_parcellation(mask_images, nb_parcel, threshold=0, output_image=None):
else:
# mask_images should be a list
mask_data = intersect_masks(mask_images, threshold=0) > 0
- mask = Nifti1Image(mask_data.astype('u8'),
+ mask = Nifti1Image(mask_data.astype('u1'),
get_affine(load(mask_images[0])))
domain = grid_domain_from_image(mask)
@@ -99,7 +99,7 @@ def parcel_input(mask_images, learning_images, ths=.5, fdim=None):
else:
# mask_images should be a list
grp_mask = intersect_masks(mask_images, threshold=ths) > 0
- mask = Nifti1Image(grp_mask.astype('u8'),
+ mask = Nifti1Image(grp_mask.astype('u1'),
get_affine(load(mask_images[0])))
# build the domain
diff --git a/nipy/labs/spatial_models/tests/test_discrete_domain.py b/nipy/labs/spatial_models/tests/test_discrete_domain.py
index c2c6ece2af..d3b269dc9f 100644
--- a/nipy/labs/spatial_models/tests/test_discrete_domain.py
+++ b/nipy/labs/spatial_models/tests/test_discrete_domain.py
@@ -142,7 +142,7 @@ def test_image_feature():
mask = np.random.randn(*shape[:3]) > .5
noise = np.random.randn(*shape[:3])
affine = np.eye(4)
- mim = Nifti1Image(mask.astype('u8'), affine)
+ mim = Nifti1Image(mask.astype('u1'), affine)
nim = Nifti1Image(noise, affine)
ddom = grid_domain_from_image(mim)
ddom.make_feature_from_image(nim, 'noise')
diff --git a/nipy/labs/spatial_models/tests/test_mroi.py b/nipy/labs/spatial_models/tests/test_mroi.py
index 26b02da914..4c5cc35c12 100644
--- a/nipy/labs/spatial_models/tests/test_mroi.py
+++ b/nipy/labs/spatial_models/tests/test_mroi.py
@@ -205,8 +205,8 @@ def test_example():
# Test example runs correctly
eg_img = pjoin(dirname(__file__), 'some_blobs.nii')
nim = load(eg_img)
- mask_image = Nifti1Image((nim.get_fdata() ** 2 > 0).astype('u8'),
- get_affine(nim))
+ arr = nim.get_fdata() ** 2 > 0
+ mask_image = Nifti1Image(arr.astype('u1'), get_affine(nim))
domain = grid_domain_from_image(mask_image)
data = nim.get_fdata()
values = data[data != 0]
diff --git a/nipy/labs/spatial_models/tests/test_parcel_io.py b/nipy/labs/spatial_models/tests/test_parcel_io.py
index c158841f32..4d880c599e 100644
--- a/nipy/labs/spatial_models/tests/test_parcel_io.py
+++ b/nipy/labs/spatial_models/tests/test_parcel_io.py
@@ -17,7 +17,7 @@ def test_mask_parcel():
"""
n_parcels = 20
shape = (10, 10, 10)
- mask_image = Nifti1Image(np.ones(shape), np.eye(4))
+ mask_image = Nifti1Image(np.ones(shape).astype('u1'), np.eye(4))
wim = mask_parcellation(mask_image, n_parcels)
assert_equal(np.unique(wim.get_fdata()), np.arange(n_parcels))
@@ -33,8 +33,8 @@ def test_mask_parcel_multi_subj():
with InTemporaryDirectory():
for subject in range(n_subjects):
path = 'mask%s.nii' % subject
- save(Nifti1Image((rng.rand(*shape) > .1).astype('u8'),
- np.eye(4)), path)
+ arr = rng.rand(*shape) > .1
+ save(Nifti1Image(arr.astype('u1'), np.eye(4)), path)
mask_images.append(path)
wim = mask_parcellation(mask_images, n_parcels)
@@ -47,7 +47,7 @@ def test_parcel_intra_from_3d_image():
# Generate an image
shape = (10, 10, 10)
n_parcel, nn, mu = 10, 6, 1.
- mask_image = Nifti1Image(np.ones(shape), np.eye(4))
+ mask_image = Nifti1Image(np.ones(shape).astype('u1'), np.eye(4))
with InTemporaryDirectory() as dir_context:
surrogate_3d_dataset(mask=mask_image, out_image_file='image.nii')
@@ -67,7 +67,7 @@ def test_parcel_intra_from_3d_images_list():
shape = (10, 10, 10)
n_parcel, nn, mu = 10, 6, 1.
method = 'ward'
- mask_image = Nifti1Image(np.ones(shape), np.eye(4))
+ mask_image = Nifti1Image(np.ones(shape).astype('u1'), np.eye(4))
with InTemporaryDirectory() as dir_context:
data_image = ['image_%d.nii' % i for i in range(5)]
@@ -88,7 +88,7 @@ def test_parcel_intra_from_4d_image():
shape = (10, 10, 10)
n_parcel, nn, mu = 10, 6, 1.
method = 'ward'
- mask_image = Nifti1Image(np.ones(shape), np.eye(4))
+ mask_image = Nifti1Image(np.ones(shape).astype('u1'), np.eye(4))
with InTemporaryDirectory() as dir_context:
surrogate_3d_dataset(n_subj=10, mask=mask_image,
out_image_file='image.nii')
diff --git a/nipy/utils/compat3.py b/nipy/utils/compat3.py
index d5a1c175d9..b9bb01e9f3 100644
--- a/nipy/utils/compat3.py
+++ b/nipy/utils/compat3.py
@@ -1,6 +1,6 @@
""" Routines for Python 3 compatibility
-These are in addition to the nibabel.py3k routines.
+These are in addition to the numpy.compat.py3k routines.
"""
from __future__ import absolute_import
diff --git a/nipy/utils/tests/test_compat3.py b/nipy/utils/tests/test_compat3.py
index 59175ee3e7..4b25b581cd 100644
--- a/nipy/utils/tests/test_compat3.py
+++ b/nipy/utils/tests/test_compat3.py
@@ -3,7 +3,7 @@
from __future__ import with_statement
from __future__ import absolute_import
-from nibabel.py3k import asstr, asbytes
+from numpy.compat.py3k import asstr, asbytes
from ..compat3 import to_str, open4csv
diff --git a/tools/run_log_examples.py b/tools/run_log_examples.py
index d3fd0fab86..e98c47cedc 100755
--- a/tools/run_log_examples.py
+++ b/tools/run_log_examples.py
@@ -25,7 +25,7 @@
from subprocess import Popen, PIPE
import re
-from nibabel.py3k import asstr
+from numpy.compat.py3k import asstr
from argparse import ArgumentParser, RawDescriptionHelpFormatter