def test_conperm_workflow_cli_smoke(testdata_ibma, tmp_path_factory):
tmpdir = tmp_path_factory.mktemp("test_conperm_workflow_cli_smoke")
dset = testdata_ibma
files = dset.get_images(imtype="beta")
mask_image = op.join(get_test_data_path(), "test_pain_dataset",
"mask.nii.gz")
prefix = "test"
cli._main([
"conperm",
"--output_dir",
str(tmpdir),
"--mask",
mask_image,
"--prefix",
prefix,
"--n_iters",
"5",
] + files)
assert op.isfile(op.join(tmpdir, "{}_logp.nii.gz".format(prefix)))
def test_ale_workflow_cli_smoke(tmp_path_factory):
"""Run smoke test for Sleuth ALE workflow."""
tmpdir = tmp_path_factory.mktemp("test_ale_workflow_cli_smoke")
sleuth_file = op.join(get_test_data_path(), "test_sleuth_file.txt")
prefix = "test"
cli._main(
[
"ale",
"--output_dir",
str(tmpdir),
"--prefix",
prefix,
"--n_iters",
"10",
"--n_cores",
"1",
sleuth_file,
]
)
assert op.isfile(op.join(tmpdir, f"{prefix}_input_coordinates.txt"))
def test_scale_workflow_cli_smoke(tmp_path_factory):
tmpdir = tmp_path_factory.mktemp("test_scale_workflow_cli_smoke")
sleuth_file = op.join(get_test_data_path(), "test_sleuth_file.txt")
prefix = "test"
baseline = op.join(get_test_data_path(), "test_baseline.txt")
cli._main([
"scale",
"--baseline",
baseline,
"--output_dir",
str(tmpdir),
"--prefix",
prefix,
"--n_iters",
"5",
"--n_cores",
"1",
sleuth_file,
])
assert op.isfile(op.join(tmpdir,
"{}_input_coordinates.txt".format(prefix)))
def test_conperm_workflow_cli_smoke(testdata_ibma, tmp_path_factory):
"""Run smoke test of the contrast permutation workflow as a CLI."""
tmpdir = tmp_path_factory.mktemp("test_conperm_workflow_cli_smoke")
dset = testdata_ibma
files = dset.get_images(imtype="beta")
mask_image = op.join(get_test_data_path(), "test_pain_dataset", "mask.nii.gz")
prefix = "test"
cli._main(
[
"conperm",
"--output_dir",
str(tmpdir),
"--mask",
mask_image,
"--prefix",
prefix,
"--n_iters",
"5",
]
+ files
)
assert op.isfile(op.join(tmpdir, f"{prefix}_logp.nii.gz"))
def test_ale_workflow_cli_smoke_2(tmp_path_factory):
"""
Smoke test for Sleuth ALE workflow with subtraction analysis
"""
tmpdir = tmp_path_factory.mktemp("test_ale_workflow_cli_smoke_2")
sleuth_file = op.join(get_test_data_path(), "test_sleuth_file.txt")
prefix = "test"
cli._main([
"ale",
"--output_dir",
str(tmpdir),
"--prefix",
prefix,
"--n_iters",
"10",
"--n_cores",
"1",
"--file2",
sleuth_file,
sleuth_file,
])
assert op.isfile(
op.join(tmpdir, "{}_group2_input_coordinates.txt".format(prefix)))
def test_scale_workflow_cli_smoke(tmp_path_factory):
"""Run smoke test of the SCALE workflow as a CLI."""
tmpdir = tmp_path_factory.mktemp("test_scale_workflow_cli_smoke")
sleuth_file = op.join(get_test_data_path(), "test_sleuth_file.txt")
prefix = "test"
baseline = op.join(get_test_data_path(), "test_baseline.txt")
cli._main(
[
"scale",
"--baseline",
baseline,
"--output_dir",
str(tmpdir),
"--prefix",
prefix,
"--n_iters",
"5",
"--n_cores",
"1",
sleuth_file,
]
)
assert op.isfile(op.join(tmpdir, f"{prefix}_input_coordinates.txt"))