def test_nodemaker_tools_masking_parlistfile_WB():
# Set example inputs
base_dir = str(Path(__file__).parent/"examples")
#base_dir = '/Users/rxh180012/PyNets-development/tests/examples'
dir_path = base_dir + '/997'
parlistfile = base_dir + '/whole_brain_cluster_labels_PCA200.nii.gz'
atlas_select = 'whole_brain_cluster_labels_PCA200'
roi = dir_path + '/pDMN_3_bin.nii.gz'
mask = None
ID = '997'
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_label_names = 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_label_names, dir_path,
ID, mask, perc_overlap)
print("%s%s%s" % ('parcel_masker (Masking whole-brain version) --> finished: ',
str(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: ',
str(np.round(time.time() - start_time, 1)), 's'))
start_time = time.time()
[WB_net_parcels_map_nifti_unmasked, WB_coords_unmasked, _,
WB_atlas_select, WB_uatlas_select] = nodemaker.node_gen(WB_coords, WB_parcel_list, WB_label_names, dir_path,
ID, parc, atlas_select, parlistfile)
print("%s%s%s" % ('node_gen (Masking whole-brain version) --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
start_time = time.time()
[WB_net_parcels_map_nifti_masked, WB_coords_masked, WB_label_names_masked,
WB_atlas_select, WB_uatlas_select] = nodemaker.node_gen_masking(roi, WB_coords, WB_parcel_list, WB_label_names,
dir_path, ID, parc, atlas_select, parlistfile,
mask)
print("%s%s%s" % ('node_gen_masking (Masking whole-brain version) --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
assert WB_coords is not None
assert WB_label_names is not None
assert WB_parcel_list is not None
assert WB_coords_masked is not None
assert WB_label_names_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():
##Set example inputs##
base_dir = str(Path(__file__).parent / "examples")
dir_path = base_dir + '/997'
parlistfile = base_dir + '/whole_brain_cluster_labels_PCA200.nii.gz'
mask = dir_path + '/pDMN_3_bin.nii.gz'
ID = '997'
atlas_select = 'whole_brain_cluster_labels_PCA200'
parc = True
[WB_coords, atlas_select, par_max,
WB_parcel_list] = nodemaker.get_names_and_coords_of_parcels(parlistfile)
WB_label_names = np.arange(len(WB_coords) +
1)[np.arange(len(WB_coords) + 1) != 0].tolist()
[WB_coords_masked, WB_label_names_masked, WB_parcel_list_masked
] = nodemaker.parcel_masker(mask, WB_coords, WB_parcel_list,
WB_label_names, dir_path, ID)
[WB_parcels_map_nifti,
parcel_list_exp] = nodemaker.create_parcel_atlas(WB_parcel_list_masked)
[
WB_net_parcels_map_nifti_unmasked, WB_coords_unmasked,
WB_label_names_unmasked
] = nodemaker.node_gen(WB_coords, WB_parcel_list, WB_label_names, dir_path,
ID, parc)
[WB_net_parcels_map_nifti_masked, WB_coords_masked, WB_label_names_masked
] = nodemaker.node_gen_masking(mask, WB_coords, WB_parcel_list,
WB_label_names, dir_path, ID, parc)
assert WB_coords is not None
assert WB_label_names is not None
assert WB_parcel_list is not None
assert WB_coords_masked is not None
assert WB_label_names_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