def test_run_roi_stats_via_CLI():
" ensures the CLI works. "
sys.argv = shlex.split('graynet -s {} -i {} -r median gmean -o {} -a {}'
''.format(sub_list, example_dir, out_dir, atlas))
run_cli()
def test_CLI_weight():
" ensures the CLI works. "
sys.argv = shlex.split('graynet -s {} -i {} -w manhattan -o {} -a {}'
''.format(sub_list, example_dir, out_dir, atlas))
run_cli()
def test_CLI_only_weight_or_stats():
" ensures the CLI works. "
with raises(SystemExit):
sys.argv = shlex.split(
'graynet -s {} -i {} -w cosine -r median gmean -o {} -a {}'
''.format(sub_list, example_dir, out_dir, atlas))
run_cli()
def test_multi_edge_CLI():
sys.argv = shlex.split(
'graynet -s {} -i {} '
' -f freesurfer_thickness freesurfer_curv'
' --do_multi_edge --multi_edge_range 0.0 5.0 -0.3 +0.3 '
' -w manhattan -o {} -a {}'
''.format(sub_list, example_dir, out_dir, atlas))
run_cli()
def test_empty_subject_list():
# API
with raises(ValueError):
ew = graynet.extract([], fs_dir)
# in CLI, only non-Freesurfer lead to an error
for feat in cfg.features_volumetric: # invalid list
with raises(ValueError):
sys.argv = shlex.split('graynet -i {} -f {}'.format(fs_dir, feat))
run_cli()
def test_multi_edge_summary_stat_CLI():
ss_list = ' '.join(
['prod', 'median', 'max', 'min', 'gmean', 'hmean', 'std'])
sys.argv = shlex.split(
'graynet -s {} -i {} '
' -f freesurfer_thickness freesurfer_curv'
' --do_multi_edge --multi_edge_range 0.0 5.0 -0.3 +0.3 '
' -w manhattan cosine --summary_stat {} '
'-o {} -a {}'
''.format(sub_list, example_dir, ss_list, out_dir, atlas))
run_cli()