def test_fslmaths(create_files_in_directory_plus_output_type):
filelist, outdir, _ = create_files_in_directory_plus_output_type
math = fsl.ImageMaths()
# make sure command gets called
assert math.cmd == "fslmaths"
# test raising error with mandatory args absent
with pytest.raises(ValueError):
math.run()
# .inputs based parameters setting
math.inputs.in_file = filelist[0]
math.inputs.op_string = "-add 2.5 -mul input_volume2"
math.inputs.out_file = "foo_math.nii"
assert (
math.cmdline
== "fslmaths %s -add 2.5 -mul input_volume2 foo_math.nii" % filelist[0]
)
# .run based parameter setting
math2 = fsl.ImageMaths(
in_file=filelist[0], op_string="-add 2.5", out_file="foo2_math.nii"
)
assert math2.cmdline == "fslmaths %s -add 2.5 foo2_math.nii" % filelist[0]
def test_fslmaths():
filelist, outdir, cwd = create_files_in_directory()
math = fsl.ImageMaths()
# make sure command gets called
yield assert_equal, math.cmd, 'fslmaths'
# test raising error with mandatory args absent
yield assert_raises, ValueError, math.run
# .inputs based parameters setting
math.inputs.in_file = filelist[0]
math.inputs.op_string = '-add 2.5 -mul input_volume2'
math.inputs.out_file = 'foo_math.nii'
yield assert_equal, math.cmdline, \
'fslmaths %s -add 2.5 -mul input_volume2 foo_math.nii' % filelist[0]
# .run based parameter setting
math2 = fsl.ImageMaths(in_file=filelist[0],
op_string='-add 2.5',
out_file='foo2_math.nii')
yield assert_equal, math2.cmdline, 'fslmaths %s -add 2.5 foo2_math.nii' % filelist[
0]
# test arguments for opt_map
# Fslmath class doesn't have opt_map{}
clean_directory(outdir, cwd)
def test_fslmaths(create_files_in_directory):
filelist, outdir, _ = create_files_in_directory
math = fsl.ImageMaths()
# make sure command gets called
assert math.cmd == 'fslmaths'
# test raising error with mandatory args absent
with pytest.raises(ValueError):
math.run()
# .inputs based parameters setting
math.inputs.in_file = filelist[0]
math.inputs.op_string = '-add 2.5 -mul input_volume2'
math.inputs.out_file = 'foo_math.nii'
assert math.cmdline == \
'fslmaths %s -add 2.5 -mul input_volume2 foo_math.nii' % filelist[0]
# .run based parameter setting
math2 = fsl.ImageMaths(in_file=filelist[0],
op_string='-add 2.5',
out_file='foo2_math.nii')
assert math2.cmdline == 'fslmaths %s -add 2.5 foo2_math.nii' % filelist[0]
def test_imagemaths():
input_map = dict(
args=dict(argstr='%s', ),
environ=dict(),
in_file=dict(
argstr='%s',
mandatory=True,
),
in_file2=dict(argstr='%s', ),
op_string=dict(argstr='%s', ),
out_data_type=dict(argstr='-odt %s', ),
out_file=dict(argstr='%s', ),
output_type=dict(),
suffix=dict(),
)
instance = fsl.ImageMaths()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(instance.inputs.traits()[key],
metakey), value