From a8faab52ca5e59069ac871f63a8604d2ac26c433 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 b7e88d6e..1323a881 100644

--- a/nipy/algorithms/statistics/formula/tests/test_formula.py

+++ b/nipy/algorithms/statistics/formula/tests/test_formula.py

@@ -18,7 +18,7 @@ from .. import formulae as F

 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 c349e381..72c5a096 100644

--- a/nipy/core/image/image_spaces.py

+++ b/nipy/core/image/image_spaces.py

@@ -60,7 +60,7 @@ array([[ 2.,  0.,  0.,  0.],

 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 262b27f7..528bdf7f 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_data(), img_t0_r.get_data())

     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 5c5d940f..b15fea54 100644

--- a/nipy/io/tests/test_image_io.py

+++ b/nipy/io/tests/test_image_io.py

@@ -44,7 +44,7 @@ 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 89030f8d..934d9faa 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 c2c6ece2..d3b269dc 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 7f8c5420..0ceb7ad8 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_data() ** 2 > 0).astype('u8'),

-                             get_affine(nim))

+    arr = nim.get_data() ** 2 > 0

+    mask_image = Nifti1Image(arr.astype('u1'), get_affine(nim))

     domain = grid_domain_from_image(mask_image)

     data = nim.get_data()

     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 62d03318..87e8f26b 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_data()), 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 d5a1c175..b9bb01e9 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 59175ee3..4b25b581 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 d3fd0fab..e98c47ce 100755

--- a/tools/run_log_examples.py

+++ b/tools/run_log_examples.py

@@ -25,7 +25,7 @@ from os.path import (abspath, expanduser, join as pjoin, sep as psep, isfile,

 from subprocess import Popen, PIPE

 import re

-from nibabel.py3k import asstr

+from numpy.compat.py3k import asstr

 from argparse import ArgumentParser, RawDescriptionHelpFormatter

-- 

2.39.1