def test_slicer(create_files_in_directory_plus_output_type):
filelist, outdir, _ = create_files_in_directory_plus_output_type
slicer = fsl.Slicer()
# make sure command gets called
assert slicer.cmd == "slicer"
# test raising error with mandatory args absent
with pytest.raises(ValueError):
slicer.run()
# .inputs based parameters setting
slicer.inputs.in_file = filelist[0]
slicer.inputs.image_edges = filelist[1]
slicer.inputs.intensity_range = (10.0, 20.0)
slicer.inputs.all_axial = True
slicer.inputs.image_width = 750
slicer.inputs.out_file = "foo_bar.png"
assert slicer.cmdline == "slicer %s %s -L -i 10.000 20.000 -A 750 foo_bar.png" % (
filelist[0],
filelist[1],
)
# .run based parameter setting
slicer2 = fsl.Slicer(
in_file=filelist[0],
middle_slices=True,
label_slices=False,
out_file="foo_bar2.png",
)
assert slicer2.cmdline == "slicer %s -a foo_bar2.png" % (filelist[0])
def test_slicer():
filelist, outdir, cwd = create_files_in_directory()
slicer = fsl.Slicer()
# make sure command gets called
yield assert_equal, slicer.cmd, 'slicer'
# test raising error with mandatory args absent
yield assert_raises, ValueError, slicer.run
# .inputs based parameters setting
slicer.inputs.in_file = filelist[0]
slicer.inputs.image_edges = filelist[1]
slicer.inputs.intensity_range = (10., 20.)
slicer.inputs.all_axial = True
slicer.inputs.image_width = 750
slicer.inputs.out_file = 'foo_bar.png'
yield assert_equal, slicer.cmdline, \
'slicer %s %s -L -i 10.000 20.000 -A 750 foo_bar.png' % (
filelist[0], filelist[1])
# .run based parameter setting
slicer2 = fsl.Slicer(in_file=filelist[0],
middle_slices=True,
label_slices=False,
out_file='foo_bar2.png')
yield assert_equal, slicer2.cmdline, 'slicer %s -a foo_bar2.png' % (
filelist[0])
clean_directory(outdir, cwd)