def run(self, args, extra_args):
dwi_name = os.path.splitext(os.path.realpath(args.dwi))[0]
dwi_name = dwi_name.replace('.nii', '')
if args.output_name:
output_name = os.path.realpath(args.output_name)
else:
output_name = dwi_name + '_mask.nii.gz'
if args.cl_device_ind:
if isinstance(args.cl_device_ind, int):
mot.configuration.set_cl_environments(
[self.available_devices[args.cl_device_ind]])
else:
mot.configuration.set_cl_environments([
self.available_devices[ind] for ind in args.cl_device_ind
])
mot.configuration.set_load_balancer(EvenDistribution())
mdt.create_median_otsu_brain_mask(os.path.realpath(args.dwi),
os.path.realpath(args.protocol),
output_name,
median_radius=args.median_radius,
numpass=args.numpass,
dilate=args.dilate,
mask_threshold=args.mask_threshold)
logger = logging.getLogger(__name__)
logger.info('Saved the mask to: {}'.format(output_name))
def run(self):
create_median_otsu_brain_mask(*self._args, **self._kwargs)
self.finished.emit()