def test_nodemaker_tools_nilearn_coords_RSN(atlas):
"""
Test nodemaker_tools_nilearn_coords_RSN functionality
"""
# Set example inputs
template = pkg_resources.resource_filename(
"pynets", f"templates/standard/MNI152_T1_brain_2mm.nii.gz")
subnet = "Default"
parc = False
parcels_4d_img = None
start_time = time.time()
[coords, _, _, labels] = nodemaker.fetch_nilearn_atlas_coords(atlas)
print("%s%s%s" % (
"fetch_nilearn_atlas_coords --> finished: ",
str(np.round(time.time() - start_time, 1)),
"s",
))
start_time = time.time()
[net_coords, _, net_labels,
subnet] = nodemaker.get_node_membership(subnet, template, coords, labels,
parc, parcels_4d_img)
print("%s%s%s" % (
"get_node_membership --> finished: ",
str(np.round(time.time() - start_time, 1)),
"s",
))
assert coords is not None
assert labels is not None
assert net_coords is not None
assert net_labels is not None
assert subnet is not None
def test_nodemaker_tools_nilearn_coords_RSN(atlas):
"""
Test nodemaker_tools_nilearn_coords_RSN functionality
"""
# Set example inputs
base_dir = str(Path(__file__).parent / "examples")
func_file = f"{base_dir}/BIDS/sub-0025427/ses-1/func/sub-0025427_ses-1_task-rest_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz"
network = 'Default'
parc = False
parcel_list = None
start_time = time.time()
[coords, _, _, labels] = nodemaker.fetch_nilearn_atlas_coords(atlas)
print("%s%s%s" % ('fetch_nilearn_atlas_coords --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
start_time = time.time()
[net_coords, _, 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'))
assert coords is not None
assert labels is not None
assert net_coords is not None
assert net_labels is not None
assert network is not None
def test_nodemaker_tools_nilearn_coords_RSN(atlas):
"""
Test nodemaker_tools_nilearn_coords_RSN functionality
"""
# Set example inputs
import pkg_resources
template = pkg_resources.resource_filename(
"pynets", f"templates/MNI152_T1_brain_2mm.nii.gz")
network = 'Default'
parc = False
parcel_list = None
start_time = time.time()
[coords, _, _, labels] = nodemaker.fetch_nilearn_atlas_coords(atlas)
print("%s%s%s" % ('fetch_nilearn_atlas_coords --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
start_time = time.time()
[net_coords, _, net_labels,
network] = nodemaker.get_node_membership(network, template, coords,
labels, parc, parcel_list)
print("%s%s%s" % ('get_node_membership --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
assert coords is not None
assert labels is not None
assert net_coords is not None
assert net_labels is not None
assert network is not None
def test_nodemaker_tools_nilearn_coords_RSN(atlas):
"""
Test nodemaker_tools_nilearn_coords_RSN functionality
"""
# Set example inputs
base_dir = str(Path(__file__).parent/"examples")
dir_path = base_dir + '/002/fmri'
func_file = dir_path + '/002.nii.gz'
network = 'Default'
parc = False
parcel_list = None
start_time = time.time()
[coords, _, _, labels] = nodemaker.fetch_nilearn_atlas_coords(atlas)
print("%s%s%s" % ('fetch_nilearn_atlas_coords --> finished: ', str(np.round(time.time() - start_time, 1)), 's'))
start_time = time.time()
[net_coords, _, 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'))
assert coords is not None
assert labels is not None
assert net_coords is not None
assert net_labels is not None
assert network is not None
def test_nodemaker_tools_masking_parlistfile_RSN():
"""
Test nodemaker_tools_masking_parlistfile_RSN functionality
"""
# 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():
"""
Test nodemaker_tools_parlistfile_RSN functionality
"""
import pkg_resources
# Set example inputs
base_dir = str(Path(__file__).parent / "examples")
template = pkg_resources.resource_filename(
"pynets", f"templates/MNI152_T1_brain_2mm.nii.gz")
dir_path = f"{base_dir}/BIDS/sub-25659/ses-1/func"
parlistfile = f"{base_dir}/miscellaneous/whole_brain_cluster_labels_PCA200.nii.gz"
network = 'Default'
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, template, 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_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_labels,
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 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_coords_RSN(atlas):
"""
Test nodemaker_tools_masking_coords_RSN functionality
"""
# Set example inputs
template = pkg_resources.resource_filename(
"pynets", f"templates/standard/MNI152_T1_brain_2mm.nii.gz")
dir_path = str(tempfile.TemporaryDirectory().name)
os.makedirs(dir_path, exist_ok=True)
roi = tempfile.NamedTemporaryFile(mode="w+", suffix=".nii.gz").name
data_gen.generate_mni_space_img()[1].to_filename(roi)
subnet = "Default"
parc = False
parcels_4d_img = None
error = 2
start_time = time.time()
[coords, _, _, labels] = nodemaker.fetch_nilearn_atlas_coords(atlas)
print("%s%s%s" % (
"fetch_nilearn_atlas_coords (Masking subnet version) --> "
"finished: ",
str(np.round(time.time() - start_time, 1)),
"s",
))
start_time = time.time()
[net_coords, _, net_labels,
subnet] = nodemaker.get_node_membership(subnet, template, coords, labels,
parc, parcels_4d_img)
print("%s%s%s" % (
"get_node_membership (Masking subnet version) --> "
"finished: ",
str(np.round(time.time() - start_time, 1)),
"s",
))
start_time = time.time()
[net_coords_masked,
net_labels_masked] = nodemaker.coords_masker(roi, net_coords, net_labels,
error)
print("%s%s%s" % (
"coords_masker (Masking subnet version) --> finished: ",
str(np.round(time.time() - start_time, 1)),
"s",
))
assert coords is not None
assert net_coords is not None
assert net_coords_masked is not None
assert net_labels is not None
assert net_labels_masked is not None
assert subnet is not None
def test_nodemaker_tools_parlistfile_RSN():
"""
Test nodemaker_tools_parlistfile_RSN functionality
"""
# Set example inputs
base_dir = str(Path(__file__).parent / "examples")
func_file = f"{base_dir}/BIDS/sub-0025427/ses-1/func/sub-0025427_ses-1_task-rest_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz"
dir_path = f"{base_dir}/BIDS/sub-0025427/ses-1/func"
parlistfile = f"{base_dir}/miscellaneous/whole_brain_cluster_labels_PCA200.nii.gz"
network = 'Default'
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_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_labels,
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 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_coords_RSN(atlas):
"""
Test nodemaker_tools_masking_coords_RSN functionality
"""
import pkg_resources
# Set example inputs
base_dir = str(Path(__file__).parent / "examples")
template = pkg_resources.resource_filename(
"pynets", f"templates/MNI152_T1_brain_2mm.nii.gz")
roi = f"{base_dir}/miscellaneous/pDMN_3_bin.nii.gz"
network = 'Default'
parc = False
parcel_list = None
error = 2
start_time = time.time()
[coords, _, _, labels] = nodemaker.fetch_nilearn_atlas_coords(atlas)
print("%s%s%s" %
('fetch_nilearn_atlas_coords (Masking RSN version) --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
start_time = time.time()
[net_coords, _, net_labels,
network] = nodemaker.get_node_membership(network, template, coords,
labels, parc, parcel_list)
print("%s%s%s" %
('get_node_membership (Masking RSN version) --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
start_time = time.time()
[net_coords_masked,
net_labels_masked] = nodemaker.coords_masker(roi, net_coords, net_labels,
error)
print("%s%s%s" % ('coords_masker (Masking RSN version) --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
assert coords is not None
assert net_coords is not None
assert net_coords_masked is not None
assert net_labels is not None
assert net_labels_masked is not None
assert network is not None
def test_nodemaker_tools_parlistfile_RSN():
"""
Test nodemaker_tools_parlistfile_RSN functionality
"""
# Set example inputs
template = pkg_resources.resource_filename(
"pynets", f"templates/standard/MNI152_T1_brain_2mm.nii.gz")
dir_path = str(tempfile.TemporaryDirectory().name)
parlistfile = pkg_resources.resource_filename(
"pynets", "templates/atlases/whole_brain_cluster_labels_PCA200.nii.gz")
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)}"
subnet = "Default"
parc = True
start_time = time.time()
coords = nodemaker.get_names_and_coords_of_parcels(parlistfile)[0]
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()
parcels_4d_img = nodemaker.three_to_four_parcellation(parlistfile)
[net_coords, net_parcels_4d_img, net_labels, subnet] = \
nodemaker.get_node_membership(subnet, template, coords, labels,
parc, parcels_4d_img
)
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_parcels_4d_img)
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, subnet, net_labels,
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_parcels_4d_img 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 subnet is not None
def test_nodemaker_tools_masking_parlistfile_RSN():
"""
Test nodemaker_tools_masking_parlistfile_RSN functionality
"""
# Set example inputs
template = pkg_resources.resource_filename(
"pynets", f"templates/standard/MNI152_T1_brain_2mm.nii.gz")
tmp = tempfile.TemporaryDirectory()
dir_path = str(tmp.name)
os.makedirs(dir_path, exist_ok=True)
parlistfile = pkg_resources.resource_filename(
"pynets", "templates/atlases/whole_brain_cluster_labels_PCA200.nii.gz")
shutil.copy2(parlistfile, f"{dir_path}/{os.path.basename(parlistfile)}")
parlistfile = f"{dir_path}/{os.path.basename(parlistfile)}"
roi = tempfile.NamedTemporaryFile(mode="w+", suffix=".nii.gz").name
data_gen.generate_mni_space_img()[1].to_filename(roi)
subnet = "Default"
ID = "002"
perc_overlap = 0.75
parc = True
start_time = time.time()
coords = nodemaker.get_names_and_coords_of_parcels(parlistfile)[0]
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()
parcels_4d_img = nodemaker.three_to_four_parcellation(parlistfile)
[net_coords, net_parcels_4d_img, net_labels, subnet] = \
nodemaker.get_node_membership(
subnet, template, coords, labels, parc, parcels_4d_img
)
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_parcels_4d_img_masked,
] = nodemaker.parcel_masker(
roi,
net_coords,
net_parcels_4d_img,
net_labels,
dir_path,
ID,
perc_overlap,
vox_size="2mm",
)
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_parcels_4d_img_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, subnet,
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_parcels_4d_img is not None
assert net_coords_masked is not None
assert net_labels_masked is not None
assert net_parcels_4d_img_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 subnet is not None
tmp.cleanup()
