def test_nodemaker_tools_masking_parlistfile_WB():
"""
Test nodemaker_tools_masking_parlistfile_WB functionality
"""
# Set example inputs
base_dir = str(Path(__file__).parent / "examples")
dir_path = f"{base_dir}/BIDS/sub-0025427/ses-1/func"
parlistfile = f"{base_dir}/miscellaneous/whole_brain_cluster_labels_PCA200.nii.gz"
atlas = 'whole_brain_cluster_labels_PCA200'
roi = f"{base_dir}/miscellaneous/pDMN_3_bin.nii.gz"
ID = '002'
parc = True
perc_overlap = 0.10
start_time = time.time()
[WB_coords, _, _] = nodemaker.get_names_and_coords_of_parcels(parlistfile)
print("%s%s%s" % (
'get_names_and_coords_of_parcels (Masking whole-brain version) --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
WB_labels = np.arange(len(WB_coords) +
1)[np.arange(len(WB_coords) + 1) != 0].tolist()
start_time = time.time()
WB_parcel_list = nodemaker.gen_img_list(parlistfile)
[_, _, WB_parcel_list_masked
] = nodemaker.parcel_masker(roi, WB_coords, WB_parcel_list, WB_labels,
dir_path, ID, perc_overlap)
print("%s%s%s" %
('parcel_masker (Masking whole-brain version) --> finished: ',
np.round(time.time() - start_time, 1), 's'))
start_time = time.time()
[WB_parcels_map_nifti,
parcel_list_exp] = nodemaker.create_parcel_atlas(WB_parcel_list_masked)
print("%s%s%s" %
('create_parcel_atlas (Masking whole-brain version) --> finished: ',
np.round(time.time() - start_time, 1), 's'))
start_time = time.time()
[WB_net_parcels_map_nifti_unmasked, WB_coords_unmasked, _, _, _,
dir_path] = nodemaker.node_gen(WB_coords, WB_parcel_list, WB_labels,
dir_path, ID, parc, atlas, parlistfile)
print("%s%s%s" % ('node_gen (Masking whole-brain version) --> finished: ',
np.round(time.time() - start_time, 1), 's'))
start_time = time.time()
[
WB_net_parcels_map_nifti_masked, WB_coords_masked, WB_labels_masked, _,
_, _
] = nodemaker.node_gen_masking(roi, WB_coords, WB_parcel_list, WB_labels,
dir_path, ID, parc, atlas, parlistfile)
print("%s%s%s" %
('node_gen_masking (Masking whole-brain version) --> finished: ',
np.round(time.time() - start_time, 1), 's'))
assert WB_coords is not None
assert WB_labels is not None
assert WB_parcel_list is not None
assert WB_coords_masked is not None
assert WB_labels_masked is not None
assert WB_parcel_list_masked is not None
assert WB_parcels_map_nifti is not None
assert parcel_list_exp is not None
assert WB_net_parcels_map_nifti_unmasked is not None
assert WB_coords_unmasked is not None
assert WB_net_parcels_map_nifti_masked is not None
assert WB_coords_masked is not None
def test_nodemaker_tools_masking_parlistfile_WB():
"""
Test nodemaker_tools_masking_parlistfile_WB functionality
"""
# Set example inputs
parlistfile = pkg_resources.resource_filename(
"pynets", "templates/atlases/whole_brain_cluster_labels_PCA200.nii.gz")
dir_path = str(tempfile.TemporaryDirectory().name)
os.makedirs(dir_path, exist_ok=True)
shutil.copy2(parlistfile, f"{dir_path}/{os.path.basename(parlistfile)}")
parlistfile = f"{dir_path}/{os.path.basename(parlistfile)}"
atlas = "whole_brain_cluster_labels_PCA200"
roi = tempfile.NamedTemporaryFile(mode="w+", suffix=".nii.gz").name
data_gen.generate_mni_space_img()[1].to_filename(roi)
ID = "002"
parc = True
perc_overlap = 0.10
start_time = time.time()
[WB_coords, _, _,
_] = nodemaker.get_names_and_coords_of_parcels(parlistfile)
print("%s%s%s" % (
"get_names_and_coords_of_parcels (Masking whole-brain "
"version) --> finished: ",
str(np.round(time.time() - start_time, 1)),
"s",
))
WB_labels = np.arange(len(WB_coords) +
1)[np.arange(len(WB_coords) + 1) != 0].tolist()
start_time = time.time()
WB_parcel_list = nodemaker.three_to_four_parcellation(parlistfile)
start_time = time.time()
[
WB_net_parcels_map_nifti_unmasked,
WB_coords_unmasked,
_,
_,
_,
dir_path,
] = nodemaker.node_gen(WB_coords, WB_parcel_list, WB_labels, dir_path, ID,
parc, atlas, parlistfile)
print("%s%s%s" % (
"node_gen (Masking whole-brain version) --> finished: ",
np.round(time.time() - start_time, 1),
"s",
))
start_time = time.time()
WB_parcel_list = nodemaker.three_to_four_parcellation(parlistfile)
[WB_parcels_map_nifti,
parcel_list_exp] = nodemaker.create_parcel_atlas(WB_parcel_list)
print("%s%s%s" % (
"create_parcel_atlas (Masking whole-brain version) --> finished: ",
np.round(time.time() - start_time, 1),
"s",
))
start_time = time.time()
WB_parcel_list = nodemaker.three_to_four_parcellation(parlistfile)
[
WB_net_parcels_map_nifti_masked,
WB_coords_masked,
WB_labels_masked,
_,
_,
_,
] = nodemaker.node_gen_masking(
roi,
WB_coords,
WB_parcel_list,
WB_labels,
dir_path,
ID,
parc,
atlas,
parlistfile,
vox_size="2mm",
)
WB_parcel_list = nodemaker.three_to_four_parcellation(parlistfile)
WB_parcel_list_masked = nodemaker.parcel_masker(
roi,
WB_coords,
WB_parcel_list,
WB_labels,
dir_path,
ID,
perc_overlap,
vox_size="2mm",
)[2]
print("%s%s%s" % (
"parcel_masker (Masking whole-brain version) --> "
"finished: ",
np.round(time.time() - start_time, 1),
"s",
))
print("%s%s%s" % (
"node_gen_masking (Masking whole-brain version) --> "
"finished: ",
np.round(time.time() - start_time, 1),
"s",
))
assert WB_coords is not None
assert WB_labels is not None
assert WB_parcel_list is not None
assert WB_coords_masked is not None
assert WB_labels_masked is not None
assert WB_parcel_list_masked is not None
assert WB_parcels_map_nifti is not None
assert parcel_list_exp is not None
assert WB_net_parcels_map_nifti_unmasked is not None
assert WB_coords_unmasked is not None
assert WB_net_parcels_map_nifti_masked is not None
assert WB_coords_masked is not None