TEST: Test for fileOrImage. Fixed parse_data test - depends on FSL

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'])

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():