def run_intensity_fcm(infile, outfolder):
from intensity_normalization.normalize import fcm
from intensity_normalization.utilities import io
try:
if not exists(join(outfolder, "Robex")):
makedirs(join(outfolder, "Robex"))
if not exists(join(outfolder, "wm_masks")):
makedirs(join(outfolder, "wm_masks"))
filename = infile.split(sep)[-1].split(".")[0]
i = io.open_nii(infile)
b_mask = io.open_nii(
join(outfolder, "robex_masks", filename + "_mask.nii.gz"))
wm_mask = fcm.find_tissue_mask(i, b_mask)
normalized = fcm.fcm_normalize(i, wm_mask)
io.save_nii(wm_mask,
join(outfolder, "wm_masks", filename + "_wmmask.nii.gz"))
io.save_nii(normalized, join(outfolder, filename + "_fcm.nii.gz"))
shutil.move(join(infile), join(outfolder, "Robex"))
except:
e = sys.exc_info()
print("Error: ", str(e[0]))
print("Error: ", str(e[1]))
print("Error: executing fcm method")
sys.exit(2)
def test_fcm_normalization(self):
normalized = fcm.fcm_normalize(self.img,
self.wm_mask,
norm_value=self.norm_val)
self.assertAlmostEqual(
normalized.get_data()[self.wm_mask.get_data()].mean(),
self.norm_val,
places=3)
def process(image_fn, brain_mask_fn, wm_mask_fn, output_dir, args, logger):
img = io.open_nii(image_fn)
dirname, base, _ = io.split_filename(image_fn)
if output_dir is not None:
dirname = output_dir
if not os.path.exists(dirname):
logger.info('Making output directory: {}'.format(dirname))
os.mkdir(dirname)
if brain_mask_fn is not None:
mask = io.open_nii(brain_mask_fn)
wm_mask = fcm.find_wm_mask(img, mask)
outfile = os.path.join(dirname, base + '_wmmask.nii.gz')
io.save_nii(wm_mask, outfile, is_nii=True)
if wm_mask_fn is not None:
wm_mask = io.open_nii(wm_mask_fn)
normalized = fcm.fcm_normalize(img, wm_mask, args.norm_value)
outfile = os.path.join(dirname, base + '_fcm.nii.gz')
logger.info('Normalized image saved: {}'.format(outfile))
io.save_nii(normalized, outfile, is_nii=True)