def test_overlay():
filelist, outdir, cwd = create_files_in_directory()
overlay = fsl.Overlay()
# make sure command gets called
yield assert_equal, overlay.cmd, 'overlay'
# test raising error with mandatory args absent
yield assert_raises, ValueError, overlay.run
# .inputs based parameters setting
overlay.inputs.stat_image = filelist[0]
overlay.inputs.stat_thresh = (2.5, 10)
overlay.inputs.background_image = filelist[1]
overlay.inputs.auto_thresh_bg = True
overlay.inputs.show_negative_stats = True
overlay.inputs.out_file = 'foo_overlay.nii'
yield assert_equal, overlay.cmdline, \
'overlay 1 0 %s -a %s 2.50 10.00 %s -2.50 -10.00 foo_overlay.nii' % (
filelist[1], filelist[0], filelist[0])
# .run based parameter setting
overlay2 = fsl.Overlay(stat_image=filelist[0],
stat_thresh=(2.5, 10),
background_image=filelist[1],
auto_thresh_bg=True,
out_file='foo2_overlay.nii')
yield assert_equal, overlay2.cmdline, 'overlay 1 0 %s -a %s 2.50 10.00 foo2_overlay.nii' % (
filelist[1], filelist[0])
clean_directory(outdir, cwd)
def test_overlay(create_files_in_directory):
filelist, outdir, _ = create_files_in_directory
overlay = fsl.Overlay()
# make sure command gets called
assert overlay.cmd == 'overlay'
# test raising error with mandatory args absent
with pytest.raises(ValueError):
overlay.run()
# .inputs based parameters setting
overlay.inputs.stat_image = filelist[0]
overlay.inputs.stat_thresh = (2.5, 10)
overlay.inputs.background_image = filelist[1]
overlay.inputs.auto_thresh_bg = True
overlay.inputs.show_negative_stats = True
overlay.inputs.out_file = 'foo_overlay.nii'
assert overlay.cmdline == \
'overlay 1 0 %s -a %s 2.50 10.00 %s -2.50 -10.00 foo_overlay.nii' % (
filelist[1], filelist[0], filelist[0])
# .run based parameter setting
overlay2 = fsl.Overlay(stat_image=filelist[0],
stat_thresh=(2.5, 10),
background_image=filelist[1],
auto_thresh_bg=True,
out_file='foo2_overlay.nii')
assert overlay2.cmdline == 'overlay 1 0 %s -a %s 2.50 10.00 foo2_overlay.nii' % (
filelist[1], filelist[0])