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@pytest.mark.parametrize("atlas", ['coords_dosenbach_2010', 'coords_power_2011'])
def test_nodemaker_tools_masking_coords_RSN(atlas):
"""
Test nodemaker_tools_masking_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'
roi = base_dir + '/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, func_file, 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
@pytest.mark.parametrize("atlas", ['coords_dosenbach_2010', 'coords_power_2011'])
def test_nodemaker_tools_nilearn_coords_WB(atlas):
"""
Test nodemaker_tools_nilearn_coords_WB functionality
"""
start_time = time.time()
[WB_coords, _, _, WB_labels] = nodemaker.fetch_nilearn_atlas_coords(atlas)
print("%s%s%s" % ('fetch_nilearn_atlas_coords (Whole-brain version) --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
assert WB_coords is not None
assert WB_labels is not None
@pytest.mark.parametrize("atlas", ['coords_dosenbach_2010', 'coords_power_2011'])
def test_nodemaker_tools_masking_coords_WB(atlas):
"""
Test nodemaker_tools_masking_coords_WB functionality
"""
# Set example inputs
base_dir = str(Path(__file__).parent/"examples")
roi = base_dir + '/pDMN_3_bin.nii.gz'
error = 2
start_time = time.time()
[WB_coords, _, _, WB_labels] = nodemaker.fetch_nilearn_atlas_coords(atlas)
print("%s%s%s" % ('fetch_nilearn_atlas_coords (Masking whole-brain coords version) --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
start_time = time.time()
[WB_coords_masked, WB_labels_masked] = nodemaker.coords_masker(roi, WB_coords, WB_labels, error)
print("%s%s%s" % ('coords_masker (Masking whole-brain coords version) --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
assert WB_coords is not None
assert WB_coords is not None
assert WB_coords_masked is not None
assert WB_labels is not None
assert WB_labels_masked is not None
@pytest.mark.parametrize("atlas", ['coords_dosenbach_2010', 'coords_power_2011'])
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
[labels, networks_list, uatlas] = nodemaker.nilearn_atlas_helper(atlas, parc)
if uatlas:
if not isinstance(uatlas, str):
nib.save(uatlas, "%s%s%s" % ('/tmp/', atlas, '.nii.gz'))
uatlas = "%s%s%s" % ('/tmp/', atlas, '.nii.gz')
[coords, _, par_max] = nodemaker.get_names_and_coords_of_parcels(uatlas)
if parc is True:
parcel_list = nodemaker.gen_img_list(uatlas)
else:
parcel_list = None
else:
raise ValueError("%s%s%s" % ('\nERROR: Atlas file for ', atlas, ' not found!'))
elif uatlas is None and parc is False and atlas in nilearn_coords_atlases:
print('Fetching coords and labels from nilearn coordinate-based atlas library...')
# Fetch nilearn atlas coords
[coords, _, networks_list, labels] = nodemaker.fetch_nilearn_atlas_coords(atlas)
parcel_list = None
par_max = None
elif uatlas is None and parc is False and atlas in nilearn_prob_atlases:
from nilearn.plotting import find_probabilistic_atlas_cut_coords
print('Fetching coords and labels from nilearn probabilistic atlas library...')
# Fetch nilearn atlas coords
[labels, networks_list, uatlas] = nodemaker.nilearn_atlas_helper(atlas, parc)
coords = find_probabilistic_atlas_cut_coords(maps_img=uatlas)
if uatlas:
if not isinstance(uatlas, str):
nib.save(uatlas, "%s%s%s" % ('/tmp/', atlas, '.nii.gz'))
uatlas = "%s%s%s" % ('/tmp/', atlas, '.nii.gz')
if parc is True:
parcel_list = nodemaker.gen_img_list(uatlas)
else:
parcel_list = None
[labels, networks_list, uatlas] = nodemaker.nilearn_atlas_helper(atlas, parc)
if uatlas:
if not isinstance(uatlas, str):
nib.save(uatlas, "%s%s%s" % ('/tmp/', atlas, '.nii.gz'))
uatlas = "%s%s%s" % ('/tmp/', atlas, '.nii.gz')
[coords, _, par_max] = nodemaker.get_names_and_coords_of_parcels(uatlas)
if parc is True:
parcel_list = nodemaker.gen_img_list(uatlas)
else:
parcel_list = None
else:
raise ValueError("%s%s%s" % ('\nERROR: Atlas file for ', atlas, ' not found!'))
elif uatlas is None and parc is False and atlas in nilearn_coords_atlases:
print('Fetching coords and labels from nilearn coordinate-based atlas library...')
# Fetch nilearn atlas coords
[coords, _, networks_list, labels] = nodemaker.fetch_nilearn_atlas_coords(atlas)
parcel_list = None
par_max = None
elif uatlas is None and parc is False and atlas in nilearn_prob_atlases:
from nilearn.plotting import find_probabilistic_atlas_cut_coords
print('Fetching coords and labels from nilearn probabilistic atlas library...')
# Fetch nilearn atlas coords
[labels, networks_list, uatlas] = nodemaker.nilearn_atlas_helper(atlas, parc)
coords = find_probabilistic_atlas_cut_coords(maps_img=uatlas)
if uatlas:
if not isinstance(uatlas, str):
nib.save(uatlas, "%s%s%s" % ('/tmp/', atlas, '.nii.gz'))
uatlas = "%s%s%s" % ('/tmp/', atlas, '.nii.gz')
if parc is True:
parcel_list = nodemaker.gen_img_list(uatlas)
else:
parcel_list = None