def process(image, brain_mask, args, logger):
img = io.open_nii(image)
mask = io.open_nii(brain_mask)
dirname, base, ext = io.split_filename(image)
if args.output_dir is not None:
dirname = args.output_dir
if not os.path.exists(dirname):
logger.info('Making output directory: {}'.format(dirname))
os.mkdir(dirname)
if args.find_background_mask:
bg_mask = background_mask(img)
bgfile = os.path.join(dirname, base + '_bgmask' + ext)
io.save_nii(bg_mask, bgfile, is_nii=True)
if args.wm_peak is not None:
logger.info('Loading WM peak: ', args.wm_peak)
peak = float(np.load(args.wm_peak))
else:
peak = gmm_class_mask(img, brain_mask=mask, contrast=args.contrast)
if args.save_wm_peak:
np.save(os.path.join(dirname, base + '_wmpeak.npy'), peak)
normalized = gmm.gmm_normalize(img, mask, args.norm_value, args.contrast,
args.background_mask, peak)
outfile = os.path.join(dirname, base + '_gmm' + ext)
logger.info('Normalized image saved: {}'.format(outfile))
io.save_nii(normalized, outfile, is_nii=True)
def test_bg_mask(self):
bkgd = mask.background_mask(self.img, seed=0)
self.assertEqual(sum(bkgd.get_data().shape),
sum(self.img.get_data().shape))