def test_nodemaker_tools_parlistfile_RSN():
##Set example inputs##
base_dir = str(Path(__file__).parent / "examples")
#base_dir = '/Users/PSYC-dap3463/Applications/PyNets/tests/examples'
dir_path = base_dir + '/997'
func_file = dir_path + '/sub-997_ses-01_task-REST_run-01_bold_space-MNI152NLin2009cAsym_preproc_masked.nii.gz'
parlistfile = base_dir + '/whole_brain_cluster_labels_PCA200.nii.gz'
network = 'Default'
parc = True
atlas_select = 'whole_brain_cluster_labels_PCA200'
[coords, atlas_select, par_max,
parcel_list] = nodemaker.get_names_and_coords_of_parcels(parlistfile)
label_names = np.arange(len(coords) +
1)[np.arange(len(coords) + 1) != 0].tolist()
[net_coords, net_parcel_list, net_label_names,
network] = nodemaker.get_node_membership(network, func_file, coords,
label_names, parc, parcel_list)
[net_parcels_map_nifti,
parcel_list_exp] = nodemaker.create_parcel_atlas(net_parcel_list)
out_path = nodemaker.gen_network_parcels(parlistfile, network,
net_label_names, dir_path)
assert coords is not None
assert net_coords is not None
assert net_label_names is not None
assert net_parcel_list is not None
assert out_path is not None
assert net_parcels_map_nifti is not None
assert parcel_list_exp is not None
assert network is not None
def test_nodemaker_tools_masking_parlistfile_RSN():
# Set example inputs
base_dir = str(Path(__file__).parent / "examples")
#base_dir = '/Users/rxh180012/PyNets-development/tests/examples'
dir_path = base_dir + '/997'
func_file = dir_path + '/sub-997_ses-01_task-REST_run-01_bold_space-MNI152NLin2009cAsym_preproc_masked.nii.gz'
parlistfile = base_dir + '/whole_brain_cluster_labels_PCA200.nii.gz'
mask = dir_path + '/pDMN_3_bin.nii.gz'
network = 'Default'
ID = '997'
perc_overlap = 0.10
parc = True
start_time = time.time()
[coords, _, _] = nodemaker.get_names_and_coords_of_parcels(parlistfile)
print("%s%s%s" % ('get_names_and_coords_of_parcels --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
label_names = np.arange(len(coords) +
1)[np.arange(len(coords) + 1) != 0].tolist()
start_time = time.time()
parcel_list = nodemaker.gen_img_list(parlistfile)
[net_coords, net_parcel_list, net_label_names,
network] = nodemaker.get_node_membership(network, func_file, coords,
label_names, parc, parcel_list)
print("%s%s%s" % ('get_node_membership --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
start_time = time.time()
[net_coords_masked, net_label_names_masked, net_parcel_list_masked
] = nodemaker.parcel_masker(mask, net_coords, net_parcel_list,
net_label_names, dir_path, ID, perc_overlap)
print("%s%s%s" % ('parcel_masker --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
start_time = time.time()
[net_parcels_map_nifti,
parcel_list_exp] = nodemaker.create_parcel_atlas(net_parcel_list_masked)
print("%s%s%s" % ('create_parcel_atlas --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
start_time = time.time()
out_path = nodemaker.gen_network_parcels(parlistfile, network,
net_label_names_masked, dir_path)
print("%s%s%s" % ('gen_network_parcels --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
assert coords is not None
assert net_coords is not None
assert net_label_names is not None
assert net_parcel_list is not None
assert net_coords_masked is not None
assert net_label_names_masked is not None
assert net_parcel_list_masked is not None
assert out_path is not None
assert net_parcels_map_nifti is not None
assert parcel_list_exp is not None
assert network is not None
def test_nodemaker_tools_masking_parlistfile_RSN():
# Set example inputs
base_dir = str(Path(__file__).parent / "examples")
dir_path = base_dir + '/002/fmri'
func_file = dir_path + '/002.nii.gz'
parlistfile = base_dir + '/whole_brain_cluster_labels_PCA200.nii.gz'
roi = base_dir + '/pDMN_3_bin.nii.gz'
network = 'Default'
ID = '002'
perc_overlap = 0.10
parc = True
start_time = time.time()
[coords, _, _] = nodemaker.get_names_and_coords_of_parcels(parlistfile)
print("%s%s%s" % ('get_names_and_coords_of_parcels --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
labels = np.arange(len(coords) +
1)[np.arange(len(coords) + 1) != 0].tolist()
start_time = time.time()
parcel_list = nodemaker.gen_img_list(parlistfile)
[net_coords, net_parcel_list, net_labels,
network] = nodemaker.get_node_membership(network, func_file, coords,
labels, parc, parcel_list)
print("%s%s%s" % ('get_node_membership --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
start_time = time.time()
[net_coords_masked, net_labels_masked, net_parcel_list_masked
] = nodemaker.parcel_masker(roi, net_coords, net_parcel_list, net_labels,
dir_path, ID, perc_overlap)
print("%s%s%s" % ('parcel_masker --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
start_time = time.time()
[net_parcels_map_nifti,
parcel_list_exp] = nodemaker.create_parcel_atlas(net_parcel_list_masked)
print("%s%s%s" % ('create_parcel_atlas --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
start_time = time.time()
out_path = nodemaker.gen_network_parcels(parlistfile, network,
net_labels_masked, dir_path)
print("%s%s%s" % ('gen_network_parcels --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
assert coords is not None
assert net_coords is not None
assert net_labels is not None
assert net_parcel_list is not None
assert net_coords_masked is not None
assert net_labels_masked is not None
assert net_parcel_list_masked is not None
assert out_path is not None
assert net_parcels_map_nifti is not None
assert parcel_list_exp is not None
assert network is not None
def test_nodemaker_tools_parlistfile_RSN():
# Set example inputs
base_dir = str(Path(__file__).parent / "examples")
#base_dir = '/Users/PSYC-dap3463/Applications/PyNets/tests/examples'
dir_path = base_dir + '/997'
func_file = dir_path + '/sub-997_ses-01_task-REST_run-01_bold_space-MNI152NLin2009cAsym_preproc_masked.nii.gz'
parlistfile = base_dir + '/whole_brain_cluster_labels_PCA200.nii.gz'
network = 'Default'
parc = True
start_time = time.time()
[coords, _, _,
parcel_list] = nodemaker.get_names_and_coords_of_parcels(parlistfile)
print("%s%s%s" % ('get_names_and_coords_of_parcels --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
label_names = np.arange(len(coords) +
1)[np.arange(len(coords) + 1) != 0].tolist()
start_time = time.time()
[net_coords, net_parcel_list, net_label_names,
network] = nodemaker.get_node_membership(network, func_file, coords,
label_names, parc, parcel_list)
print("%s%s%s" % ('get_node_membership --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
start_time = time.time()
[net_parcels_map_nifti,
parcel_list_exp] = nodemaker.create_parcel_atlas(net_parcel_list)
print("%s%s%s" % ('create_parcel_atlas --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
start_time = time.time()
out_path = nodemaker.gen_network_parcels(parlistfile, network,
net_label_names, dir_path)
print("%s%s%s" % ('gen_network_parcels --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
assert coords is not None
assert net_coords is not None
assert net_label_names is not None
assert net_parcel_list is not None
assert out_path is not None
assert net_parcels_map_nifti is not None
assert parcel_list_exp is not None
assert network is not None