From 00eabbe19edb016c55d505a8883d751a66921910 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 11 May 2018 16:26:09 +0100
Subject: [PATCH] TEST: Test for fileOrImage. Fixed parse_data test - depends
on FSL
---
tests/test_parse_data.py | 4 +++-
tests/test_wrapperutils.py | 23 +++++++++++++++++++++++
2 files changed, 26 insertions(+), 1 deletion(-)
diff --git a/tests/test_parse_data.py b/tests/test_parse_data.py
index 77a8dce24..ac2d0e36b 100644
--- a/tests/test_parse_data.py
+++ b/tests/test_parse_data.py
@@ -15,6 +15,7 @@ from fsl.data.atlases import Atlas
from pytest import raises
from .test_image import make_image
import os
+import pytest
datadir = op.join(op.dirname(__file__), 'testdata')
@@ -115,6 +116,7 @@ def test_image_out():
assert args.image_out == 'test.surf.gii' + extension
+@pytest.mark.fsltest
def test_atlas():
atlas_parser = argparse.ArgumentParser('reads an atlas')
atlas_parser.add_argument('atlas', type=parse_data.Atlas)
@@ -123,4 +125,4 @@ def test_atlas():
assert isinstance(args.atlas, Atlas)
with raises(SystemExit):
- atlas_parser.parse_args(['fake'])
\ No newline at end of file
+ atlas_parser.parse_args(['fake'])
diff --git a/tests/test_wrapperutils.py b/tests/test_wrapperutils.py
index 3e35d91e2..b5c393e78 100644
--- a/tests/test_wrapperutils.py
+++ b/tests/test_wrapperutils.py
@@ -21,6 +21,7 @@ import nibabel as nib
import fsl.utils.tempdir as tempdir
import fsl.utils.run as run
import fsl.utils.fslsub as fslsub
+import fsl.data.image as fslimage
import fsl.wrappers.wrapperutils as wutils
@@ -284,6 +285,28 @@ def test_fileOrImage():
assert np.all(nib.load('output.nii').get_data() == expected)
os.remove('output.nii')
+ # fslimage, file, load
+ result = func(fslimage.Image(img1), img2='img2.nii',
+ output=wutils.LOAD)['output']
+ assert isinstance(result, fslimage.Image)
+ assert np.all(result[:].squeeze() == expected)
+
+ # fslimage, fslimage, load
+ result = func(fslimage.Image(img1), img2=fslimage.Image(img2),
+ output=wutils.LOAD)['output']
+ assert isinstance(result, fslimage.Image)
+ assert np.all(result[:].squeeze() == expected)
+
+ # fslimage, nib.image, load
+ result = func(fslimage.Image(img1), img2=img2,
+ output=wutils.LOAD)['output']
+ assert isinstance(result, fslimage.Image)
+ assert np.all(result[:].squeeze() == expected)
+
+ # nib.image, nib.image, load
+ result = func(img1, img2=img2, output=wutils.LOAD)['output']
+ assert isinstance(result, nib.nifti1.Nifti1Image)
+ assert np.all(result.get_data()[:] == expected)
def test_chained_fileOrImageAndArray():
--
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