def test_FSLCommand2():
# Check default output type and environ
cmd = fsl.FSLCommand(command="junk")
assert cmd._output_type == fsl.Info.output_type()
assert cmd.inputs.environ["FSLOUTPUTTYPE"] == cmd._output_type
assert cmd._output_type in fsl.Info.ftypes
cmd = fsl.FSLCommand
cmdinst = fsl.FSLCommand(command="junk")
for out_type in fsl.Info.ftypes:
cmd.set_default_output_type(out_type)
assert cmd._output_type == out_type
if out_type != fsl.Info.output_type():
# Setting class outputtype should not effect existing instances
assert cmdinst.inputs.output_type != out_type
def test_FSLCommand2():
# Check default output type and environ
cmd = fsl.FSLCommand(command='junk')
yield assert_equal, cmd._output_type, fsl.Info.output_type()
yield assert_equal, cmd.inputs.environ['FSLOUTPUTTYPE'], cmd._output_type
yield assert_true, cmd._output_type in fsl.Info.ftypes
cmd = fsl.FSLCommand
cmdinst = fsl.FSLCommand(command='junk')
for out_type in fsl.Info.ftypes:
cmd.set_default_output_type(out_type)
yield assert_equal, cmd._output_type, out_type
if out_type != fsl.Info.output_type():
# Setting class outputtype should not effect existing instances
yield assert_not_equal, cmdinst.inputs.output_type, out_type
def test_gen_fname(args, desired_name):
# Test _gen_fname method of FSLCommand
cmd = fsl.FSLCommand(command="junk", output_type="NIFTI_GZ")
pth = os.getcwd()
fname = cmd._gen_fname("foo.nii.gz", **args)
if "dir" in desired_name.keys():
desired = os.path.join(desired_name["dir"], desired_name["file"])
else:
desired = os.path.join(pth, desired_name["file"])
assert fname == desired
def test_gen_fname():
# Test _gen_fname method of FSLCommand
cmd = fsl.FSLCommand(command='junk', output_type='NIFTI_GZ')
pth = os.getcwd()
# just the filename
fname = cmd._gen_fname('foo.nii.gz', suffix='_fsl')
desired = os.path.join(pth, 'foo_fsl.nii.gz')
yield assert_equal, fname, desired
# filename with suffix
fname = cmd._gen_fname('foo.nii.gz', suffix='_brain')
desired = os.path.join(pth, 'foo_brain.nii.gz')
yield assert_equal, fname, desired
# filename with suffix and working directory
fname = cmd._gen_fname('foo.nii.gz', suffix='_brain', cwd='/data')
desired = os.path.join('/data', 'foo_brain.nii.gz')
yield assert_equal, fname, desired
# filename with suffix and no file extension change
fname = cmd._gen_fname('foo.nii.gz', suffix='_brain.mat', change_ext=False)
desired = os.path.join(pth, 'foo_brain.mat')
yield assert_equal, fname, desired
def test_FSLCommand():
# Most methods in FSLCommand are tested in the subclasses. Only
# testing the one item that is not.
cmd = fsl.FSLCommand(command="ls")
res = cmd.run()
assert type(res) == InterfaceResult
def test_FSLCommand():
# Most methods in FSLCommand are tested in the subclasses. Only
# testing the one item that is not.
cmd = fsl.FSLCommand(command='ls')
res = cmd.run()
yield assert_equal, type(res), InterfaceResult