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_gmm_normalization(self):
from intensity_normalization.normalize import gmm
normalized = gmm.gmm_normalize(self.img,
self.brain_mask,
norm_value=self.norm_val)
self.assertAlmostEqual(
normalized.get_data()[self.wm_mask.get_data()].mean(),
self.norm_val,
delta=20)
def run_intensity_gmm(infile, outfolder):
from intensity_normalization.normalize import gmm
from intensity_normalization.utilities import io
try:
if not exists(join(outfolder, "Robex")):
makedirs(join(outfolder, "Robex"))
filename = infile.split(sep)[-1].split(".")[0]
i = io.open_nii(join(outfolder, infile))
b_mask = io.open_nii(
join(outfolder, "robex_masks", filename + "_mask.nii.gz"))
normalized = gmm.gmm_normalize(i, b_mask)
io.save_nii(normalized, join(outfolder, filename + "_gmm.nii.gz"))
shutil.move(join(outfolder, infile), join(outfolder, "Robex"))
except:
e = sys.exc_info()
print("Error: ", str(e[0]))
print("Error: ", str(e[1]))
print("Error: executing gmm method")
sys.exit(2)
def gmm_normalisation(self):
agent = nib.load(self.registration_path)
new_agent = gmm.gmm_normalize(agent)
nib.save(new_agent, self.normalisation_path)