def _run_interface(self, runtime):
out = extractnetstats(self.inputs.ID, self.inputs.network,
self.inputs.thr, self.inputs.conn_model,
self.inputs.est_path, self.inputs.roi,
self.inputs.prune, self.inputs.node_size,
self.inputs.norm, self.inputs.binary)
setattr(self, '_outpath', out)
return runtime
def test_extractnetstats(binary, prune, norm):
"""
Test extractnetstats functionality
"""
base_dir = str(Path(__file__).parent / "examples")
ID = '002'
network = 'Default'
thr = 0.95
conn_model = 'cov'
est_path = f"{base_dir}/miscellaneous/sub-0021001_rsn-Default_nodetype-parc_model-sps_template-MNI152_T1_thrtype-DENS_thr-0.19.npy"
prune = 1
norm = 1
binary = False
roi = None
start_time = time.time()
out_path = netstats.extractnetstats(ID, network, thr, conn_model, est_path,
roi, prune, norm, binary)
print("%s%s%s" % (
'thresh_and_fit (Functional, proportional thresholding) --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
assert out_path is not None
# Cover exceptions. This can definiely be improved. It increases coverage, but not as throughly
# as I hoped.
from tempfile import NamedTemporaryFile
f_temp = NamedTemporaryFile(mode='w+', suffix='.npy')
nan_array = np.empty((5, 5))
nan_array[:] = np.nan
np.save(f_temp.name, nan_array)
est_path = f_temp.name
try:
out_path = netstats.extractnetstats(ID, network, thr, conn_model,
est_path, roi, prune, norm, binary)
except PermissionError:
pass
def test_extractnetstats():
base_dir = str(Path(__file__).parent/"examples")
ID = '002'
network = 'Default'
thr = 0.95
conn_model = 'cov'
est_path = base_dir + '/002/fmri/002_Default_est_cov_0.95prop_TESTmm_3nb_2fwhm_0.1Hz.npy'
prune = 1
node_size = 'parc'
norm = 1
binary = False
roi = None
start_time = time.time()
out_path = netstats.extractnetstats(ID, network, thr, conn_model, est_path, roi, prune, node_size, norm, binary)
print("%s%s%s" % ('thresh_and_fit (Functional, proportional thresholding) --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
assert out_path is not None
def test_extractnetstats(binary, prune, norm):
"""
Test extractnetstats functionality
"""
base_dir = str(Path(__file__).parent / "examples")
ID = '002'
network = 'Default'
thr = 0.95
conn_model = 'cov'
est_path = base_dir + '/002/fmri/DesikanKlein2012/graphs/0021001_Default_est_sps_0.19densparc_mm.npy'
prune = 1
norm = 1
binary = False
roi = None
start_time = time.time()
out_path = netstats.extractnetstats(ID, network, thr, conn_model, est_path,
roi, prune, norm, binary)
print("%s%s%s" % (
'thresh_and_fit (Functional, proportional thresholding) --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
assert out_path is not None