[MAINT] Rewrite write_tmp_imgs function and use it with pytest's `t…

…mp_path` (#4094)

* Rewrite write_tmp_imgs as function

* Update tests to use tmp_path

* Add unit tests

* Rename function

* Add whatsnew

* Rename function

* Update whatsnew

doc/changes/latest.rst

@@ -29,3 +29,4 @@ Changes
 -------
 
 - :bdg-success:`API` Expose scipy CubicSpline ``extrapolate`` parameter in :func:`~signal.clean` to control the interpolation of censored volumes in both ends of the BOLD signal data (:gh:`4028` by `Jordi Huguet`_).
+- :bdg-dark:`Code` Private utility context manager ``write_tmp_imgs`` is refactored into function ``write_imgs_to_path`` (:gh:`4094` by `Yasmin Mzayek`_).

nilearn/_utils/testing.py

@@ -1,6 +1,5 @@
 """Utilities for testing nilearn."""
 # Author: Alexandre Abraham, Philippe Gervais
-import contextlib
 import functools
 import gc
 import os
@@ -113,12 +112,10 @@ def serialize_niimg(img, gzipped=True):
             return f.read()
 
 
-@contextlib.contextmanager
-def write_tmp_imgs(*imgs, **kwargs):
-    """Context manager for writing Nifti images.
+def write_imgs_to_path(*imgs, file_path=None, **kwargs):
+    """Write Nifti images on disk.
 
-    Write nifti images in a temporary location, and remove them at the end of
-    the block.
+    Write nifti images in a specified location.
 
     Parameters
     ----------
@@ -144,6 +141,9 @@ def write_tmp_imgs(*imgs, **kwargs):
         list of string is returned.
 
     """
+    if file_path is None:
+        file_path = Path.cwd()
+
     valid_keys = {"create_files", "use_wildcards"}
     input_keys = set(kwargs.keys())
     invalid_keys = input_keys - valid_keys
@@ -160,49 +160,25 @@ def write_tmp_imgs(*imgs, **kwargs):
 
     if create_files:
         filenames = []
-        try:
-            with warnings.catch_warnings():
-                warnings.simplefilter("ignore", RuntimeWarning)
-                for img in imgs:
-                    fd, filename = tempfile.mkstemp(
-                        prefix=prefix, suffix=suffix, dir=None
-                    )
-                    os.close(fd)
-                    filenames.append(filename)
-                    img.to_filename(filename)
-                    del img
-
-                if use_wildcards:
-                    yield f"{prefix}*{suffix}"
-                else:
-                    if len(imgs) == 1:
-                        yield filenames[0]
-                    else:
-                        yield filenames
-        finally:
-            failures = []
-            # Ensure all created files are removed
-            for filename in filenames:
-                try:
-                    os.remove(filename)
-                except FileNotFoundError:
-                    # ok, file already removed
-                    pass
-                except OSError as e:
-                    # problem eg permission, or open file descriptor
-                    failures.append(e)
-            if failures:
-                failed_lines = "\n".join(str(e) for e in failures)
-                raise OSError(
-                    "The following files could not be removed:\n"
-                    f"{failed_lines}"
-                )
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore", RuntimeWarning)
+            for i, img in enumerate(imgs):
+                filename = file_path / (prefix + str(i) + suffix)
+                filenames.append(str(filename))
+                img.to_filename(filename)
+                del img
+
+            if use_wildcards:
+                return str(file_path / f"{prefix}*{suffix}")
+            else:
+                if len(filenames) == 1:
+                    return filenames[0]
+                return filenames
 
     else:  # No-op
         if len(imgs) == 1:
-            yield imgs[0]
-        else:
-            yield imgs
+            return imgs[0]
+        return imgs
 
 
 def are_tests_running():

nilearn/_utils/tests/test_niimg.py

@@ -95,7 +95,9 @@ def test_img_data_dtype(rng, affine_eye, tmp_path):
     assert not all(dtype_matches)
 
 
-def test_load_niimg(img1):
-    with testing.write_tmp_imgs(img1, create_files=True) as filename:
-        filename = Path(filename)
-        load_niimg(filename)
+def test_load_niimg(img1, tmp_path):
+    filename = testing.write_imgs_to_path(
+        img1, file_path=tmp_path, create_files=True
+    )
+    filename = Path(filename)
+    load_niimg(filename)

nilearn/_utils/tests/test_niimg_conversions.py

@@ -101,7 +101,7 @@ def test_check_same_fov(affine_eye):
         )
 
 
-def test_check_niimg_3d(affine_eye, img_3d_zeros_eye):
+def test_check_niimg_3d(affine_eye, img_3d_zeros_eye, tmp_path):
     # check error for non-forced but necessary resampling
     with pytest.raises(TypeError, match="nibabel format"):
         _utils.check_niimg(0)
@@ -124,8 +124,10 @@ def test_check_niimg_3d(affine_eye, img_3d_zeros_eye):
     data[20, 20, 20] = 1
     data_img = Nifti1Image(data, affine_eye)
 
-    with testing.write_tmp_imgs(data_img, create_files=True) as filename:
-        _utils.check_niimg_3d(filename)
+    filename = testing.write_imgs_to_path(
+        data_img, file_path=tmp_path, create_files=True
+    )
+    _utils.check_niimg_3d(filename)
 
     # check data dtype equal with dtype='auto'
     img_check = _utils.check_niimg_3d(img_3d_zeros_eye, dtype="auto")
@@ -242,12 +244,12 @@ def test_check_niimg(img_3d_zeros_eye, img_4d_zeros_eye):
     )
 
 
-def test_check_niimg_pathlike(img_3d_zeros_eye):
-    with testing.write_tmp_imgs(
-        img_3d_zeros_eye, create_files=True
-    ) as filename:
-        filename = Path(filename)
-        _utils.check_niimg_3d(filename)
+def test_check_niimg_pathlike(img_3d_zeros_eye, tmp_path):
+    filename = testing.write_imgs_to_path(
+        img_3d_zeros_eye, file_path=tmp_path, create_files=True
+    )
+    filename = Path(filename)
+    _utils.check_niimg_3d(filename)
 
 
 def test_check_niimg_wildcards_errors():
@@ -278,58 +280,55 @@ def test_check_niimg_wildcards_errors():
 @pytest.mark.parametrize(
     "wildcards", [True, False]
 )  # (With globbing behavior or not)
-def test_check_niimg_wildcards(affine_eye, shape, wildcards):
+def test_check_niimg_wildcards(affine_eye, shape, wildcards, tmp_path):
     # First create some testing data
     img = Nifti1Image(np.zeros(shape), affine_eye)
 
-    with testing.write_tmp_imgs(img, create_files=True) as filename:
-        assert_array_equal(
-            get_data(_utils.check_niimg(filename, wildcards=wildcards)),
-            get_data(img),
-        )
-
+    filename = testing.write_imgs_to_path(
+        img, file_path=tmp_path, create_files=True
+    )
+    assert_array_equal(
+        get_data(_utils.check_niimg(filename, wildcards=wildcards)),
+        get_data(img),
+    )
 
-def test_check_niimg_wildcards_one_file_name(img_3d_zeros_eye):
-    tmp_dir = tempfile.tempdir + os.sep
 
+def test_check_niimg_wildcards_one_file_name(img_3d_zeros_eye, tmp_path):
     file_not_found_msg = "File not found: '%s'"
 
     # Testing with a glob matching exactly one filename
     # Using a glob matching one file containing a 3d image returns a 4d image
     # with 1 as last dimension.
-    with testing.write_tmp_imgs(
-        img_3d_zeros_eye, create_files=True, use_wildcards=True
-    ) as globs:
-        glob_input = tmp_dir + globs
-        assert_array_equal(
-            get_data(_utils.check_niimg(glob_input))[..., 0],
-            get_data(img_3d_zeros_eye),
-        )
+    globs = testing.write_imgs_to_path(
+        img_3d_zeros_eye,
+        file_path=tmp_path,
+        create_files=True,
+        use_wildcards=True,
+    )
+    assert_array_equal(
+        get_data(_utils.check_niimg(globs))[..., 0],
+        get_data(img_3d_zeros_eye),
+    )
     # Disabled globbing behavior should raise an ValueError exception
-    with testing.write_tmp_imgs(
-        img_3d_zeros_eye, create_files=True, use_wildcards=True
-    ) as globs:
-        glob_input = tmp_dir + globs
-        with pytest.raises(
-            ValueError, match=file_not_found_msg % re.escape(glob_input)
-        ):
-            _utils.check_niimg(glob_input, wildcards=False)
+    with pytest.raises(
+        ValueError, match=file_not_found_msg % re.escape(globs)
+    ):
+        _utils.check_niimg(globs, wildcards=False)
 
     # Testing with a glob matching multiple filenames
     img_4d = _utils.check_niimg_4d((img_3d_zeros_eye, img_3d_zeros_eye))
-    with testing.write_tmp_imgs(
+    globs = testing.write_imgs_to_path(
         img_3d_zeros_eye,
         img_3d_zeros_eye,
+        file_path=tmp_path,
         create_files=True,
         use_wildcards=True,
-    ) as globs:
-        assert_array_equal(
-            get_data(_utils.check_niimg(glob_input)), get_data(img_4d)
-        )
+    )
+    assert_array_equal(get_data(_utils.check_niimg(globs)), get_data(img_4d))
 
 
 def test_check_niimg_wildcards_no_expand_wildcards(
-    img_3d_zeros_eye, img_4d_zeros_eye
+    img_3d_zeros_eye, img_4d_zeros_eye, tmp_path
 ):
     nofile_path = "/tmp/nofile"
 
@@ -350,20 +349,20 @@ def test_check_niimg_wildcards_no_expand_wildcards(
         _utils.check_niimg(nofile_path, wildcards=False)
 
     # Testing with an exact filename matching (3d case)
-    with testing.write_tmp_imgs(
-        img_3d_zeros_eye, create_files=True
-    ) as filename:
-        assert_array_equal(
-            get_data(_utils.check_niimg(filename)), get_data(img_3d_zeros_eye)
-        )
+    filename = testing.write_imgs_to_path(
+        img_3d_zeros_eye, file_path=tmp_path, create_files=True
+    )
+    assert_array_equal(
+        get_data(_utils.check_niimg(filename)), get_data(img_3d_zeros_eye)
+    )
 
     # Testing with an exact filename matching (4d case)
-    with testing.write_tmp_imgs(
-        img_4d_zeros_eye, create_files=True
-    ) as filename:
-        assert_array_equal(
-            get_data(_utils.check_niimg(filename)), get_data(img_4d_zeros_eye)
-        )
+    filename = testing.write_imgs_to_path(
+        img_4d_zeros_eye, file_path=tmp_path, create_files=True
+    )
+    assert_array_equal(
+        get_data(_utils.check_niimg(filename)), get_data(img_4d_zeros_eye)
+    )
 
     # Reverting to default behavior
     ni.EXPAND_PATH_WILDCARDS = True

nilearn/_utils/tests/test_testing.py

@@ -8,6 +8,7 @@
     assert_memory_less_than,
     check_deprecation,
     with_memory_profiler,
+    write_imgs_to_path,
 )
 
 
@@ -56,3 +57,32 @@ def dummy_deprecation(start_version, end_version):
 
 def test_check_deprecation():
     check_deprecation(dummy_deprecation, "Deprecated")("0.0.1", "0.0.2")
+
+
+@pytest.mark.parametrize("create_files", [True, False])
+@pytest.mark.parametrize("use_wildcards", [True, False])
+def test_write_tmp_imgs_default(
+    monkeypatch, tmp_path, img_3d_mni, create_files, use_wildcards
+):
+    """Write imgs to default location."""
+    monkeypatch.chdir(tmp_path)
+
+    write_imgs_to_path(
+        img_3d_mni,
+        create_files=create_files,
+        use_wildcards=use_wildcards,
+    )
+
+
+@pytest.mark.parametrize("create_files", [True, False])
+@pytest.mark.parametrize("use_wildcards", [True, False])
+def test_write_tmp_imgs_set_path(
+    tmp_path, img_3d_mni, create_files, use_wildcards
+):
+    """Write imgs to a specified location."""
+    write_imgs_to_path(
+        img_3d_mni,
+        file_path=tmp_path,
+        create_files=create_files,
+        use_wildcards=use_wildcards,
+    )

nilearn/decomposition/tests/test_canica.py

@@ -5,10 +5,9 @@
 from nibabel import Nifti1Image
 from numpy.testing import assert_array_almost_equal
 
-from nilearn._utils.testing import write_tmp_imgs
+from nilearn._utils.testing import write_imgs_to_path
 from nilearn.conftest import _affine_eye, _rng
 from nilearn.decomposition.canica import CanICA
-from nilearn.decomposition.tests.test_multi_pca import _tmp_dir
 from nilearn.image import get_data, iter_img
 from nilearn.maskers import MultiNiftiMasker
 
@@ -256,44 +255,46 @@ def test_components_img(canica_data, mask_img):
     assert components_img.shape, check_shape
 
 
-def test_with_globbing_patterns_with_single_subject(mask_img):
+def test_with_globbing_patterns_with_single_subject(mask_img, tmp_path):
     # single subject
     data, *_ = _make_canica_test_data(n_subjects=1)
     n_components = 3
 
     canica = CanICA(n_components=n_components, mask=mask_img)
 
-    with write_tmp_imgs(data[0], create_files=True, use_wildcards=True) as img:
-        input_image = _tmp_dir() + img
-        canica.fit(input_image)
-        components_img = canica.components_img_
+    img = write_imgs_to_path(
+        data[0], file_path=tmp_path, create_files=True, use_wildcards=True
+    )
+    canica.fit(img)
+    components_img = canica.components_img_
 
-        assert isinstance(components_img, Nifti1Image)
+    assert isinstance(components_img, Nifti1Image)
 
-        # n_components = 3
-        check_shape = data[0].shape[:3] + (3,)
+    # n_components = 3
+    check_shape = data[0].shape[:3] + (3,)
 
-        assert components_img.shape, check_shape
+    assert components_img.shape, check_shape
 
 
-def test_with_globbing_patterns_with_multi_subjects(canica_data, mask_img):
+def test_with_globbing_patterns_with_multi_subjects(
+    canica_data, mask_img, tmp_path
+):
     # Multi subjects
     n_components = 3
     canica = CanICA(n_components=n_components, mask=mask_img)
 
-    with write_tmp_imgs(
-        *canica_data, create_files=True, use_wildcards=True
-    ) as img:
-        input_image = _tmp_dir() + img
-        canica.fit(input_image)
-        components_img = canica.components_img_
+    img = write_imgs_to_path(
+        *canica_data, file_path=tmp_path, create_files=True, use_wildcards=True
+    )
+    canica.fit(img)
+    components_img = canica.components_img_
 
-        assert isinstance(components_img, Nifti1Image)
+    assert isinstance(components_img, Nifti1Image)
 
-        # n_components = 3
-        check_shape = canica_data[0].shape[:3] + (3,)
+    # n_components = 3
+    check_shape = canica_data[0].shape[:3] + (3,)
 
-        assert components_img.shape, check_shape
+    assert components_img.shape, check_shape
 
 
 def test_canica_score(canica_data, mask_img):