From c1e5a34786871424182ee11dbb8e2f33195a80b9 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 3 May 2024 17:17:20 +0100
Subject: [PATCH] TEST: Failing regression test for fileOrImage file suffix
issue
---
fsl/tests/test_wrappers/test_wrapperutils.py | 52 +++++++++++++++++++-
1 file changed, 50 insertions(+), 2 deletions(-)
diff --git a/fsl/tests/test_wrappers/test_wrapperutils.py b/fsl/tests/test_wrappers/test_wrapperutils.py
index d806cc9f7..b9a86a296 100644
--- a/fsl/tests/test_wrappers/test_wrapperutils.py
+++ b/fsl/tests/test_wrappers/test_wrapperutils.py
@@ -27,8 +27,8 @@ import fsl.data.image as fslimage
import fsl.wrappers.wrapperutils as wutils
-from .. import mockFSLDIR, cleardir, checkdir, testdir, touch
-from ..test_run import mock_fsl_sub
+from fsl.tests import mockFSLDIR, cleardir, checkdir, testdir, touch
+from fsl.tests.test_run import mock_fsl_sub
def test_applyArgStyle_default():
@@ -407,6 +407,54 @@ def test_fileOrImage():
assert np.all(np.asanyarray(result.dataobj)[:] == expected)
+
+# fsl/fslpy!452
+def test_fileOrImage_FSLOUTPUTTYPE():
+
+ @wutils.fileOrImage('img', 'output')
+ def func(img, output):
+ img = np.asanyarray(nib.load(img).dataobj)
+
+ # Save without specifying file suffix,
+ # so the Image object uses $FSLOUTPUTTYPE
+ fslimage.Image(img * 5, xform=np.eye(4)).save(fslimage.removeExt(output))
+
+ fsloutputtypes = [fslimage.FileType.NIFTI,
+ fslimage.FileType.NIFTI2,
+ fslimage.FileType.NIFTI_GZ,
+ fslimage.FileType.NIFTI2_GZ]
+
+ for fsloutputtype in fsloutputtypes:
+ with tempdir.tempdir(), \
+ mock.patch.dict(os.environ, FSLOUTPUTTYPE=fsloutputtype.name):
+
+ img = fslimage.Image(
+ np.array([[[1, 2], [ 3, 4]]], dtype=np.int32), xform=np.eye(4))
+ expected = np.array([[[5, 10], [15, 20]]], dtype=np.int32)
+
+ imgfname = op.join(os.getcwd(), f'image{fslimage.defaultExt()}')
+
+ img.save(imgfname)
+
+ result1 = func(imgfname, wutils.LOAD)
+ result2 = func(img, wutils.LOAD)
+
+ r1data = np.asanyarray(result1['output'].dataobj)
+ r2data = result2['output'].data
+
+ # first call will return a nibabel image,
+ # second a fsl Image
+ assert np.all(r1data == expected)
+ assert np.all(r2data == expected)
+
+ for inarg in (img, imgfname):
+ with tempdir.tempdir():
+ func(inarg, 'output')
+ assert op.exists(f'output{fslimage.defaultExt()}')
+ out = fslimage.Image('output')
+ assert np.all(out.data == expected.data)
+
+
def test_fileOrThing_sequence():
@wutils.fileOrArray('arrs', 'out')
--
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