def test_ravel_normalization_csf_masks(self):
from intensity_normalization.normalize.ravel import ravel_normalize
normalized = ravel_normalize(self.data_dir,
self.mask_dir,
'T1',
write_to_disk=False,
csf_masks=True)
def main(args=None):
args = arg_parser().parse_args(args)
if args.verbosity == 1:
level = logging.getLevelName('INFO')
elif args.verbosity >= 2:
level = logging.getLevelName('DEBUG')
else:
level = logging.getLevelName('WARNING')
logging.basicConfig(
format='%(asctime)s - %(name)s - %(levelname)s - %(message)s',
level=level)
logger = logging.getLogger(__name__)
try:
img_fns = io.glob_nii(args.img_dir)
mask_fns = io.glob_nii(args.mask_dir)
if len(img_fns) != len(mask_fns) or len(img_fns) == 0:
raise NormalizationError(
'Image directory ({}) and mask directory ({}) must contain the same '
'(positive) number of images!'.format(args.img_dir,
args.mask_dir))
logger.info('Normalizing the images according to RAVEL')
Z, _ = ravel.ravel_normalize(
args.img_dir,
args.mask_dir,
args.contrast,
do_whitestripe=args.no_whitestripe,
b=args.num_unwanted_factors,
membership_thresh=args.control_membership_threshold,
do_registration=args.no_registration,
segmentation_smoothness=args.segmentation_smoothness,
use_fcm=not args.use_atropos,
sparse_svd=args.sparse_svd,
csf_masks=args.csf_masks)
V = ravel.image_matrix(img_fns, args.contrast, masks=mask_fns)
V_norm = ravel.ravel_correction(V, Z)
normalized = ravel.image_matrix_to_images(V_norm, img_fns)
# save the normalized images to disk
output_dir = os.getcwd(
) if args.output_dir is None else args.output_dir
out_fns = []
for fn in img_fns:
_, base, ext = io.split_filename(fn)
out_fns.append(os.path.join(output_dir, base + '_ravel' + ext))
if not os.path.exists(output_dir):
os.mkdir(output_dir)
for norm, out_fn in zip(normalized, out_fns):
norm.to_filename(out_fn)
if args.plot_hist:
with warnings.catch_warnings():
warnings.filterwarnings('ignore', category=FutureWarning)
from intensity_normalization.plot.hist import all_hists
import matplotlib.pyplot as plt
ax = all_hists(output_dir, args.mask_dir)
ax.set_title('RAVEL')
plt.savefig(os.path.join(output_dir, 'hist.png'))
return 0
except Exception as e:
logger.exception(e)
return 1
def run_intensity_ravel(outfolder):
from intensity_normalization.normalize import ravel
from intensity_normalization.utilities import io, csf
try:
images = []
brainMasks = []
csfMasks = []
_, _, filenames = next(walk(outfolder))
for f in filenames:
filename = f.split(sep)[-1].split(".")[0]
images.append(io.open_nii(join(outfolder, f.split(sep)[-1])))
brainMasks.append(
io.open_nii(
join(outfolder, 'robex_masks', filename + "_mask.nii.gz")))
if not exists(join(outfolder, "Robex")):
makedirs(join(outfolder, "Robex"))
if not exists(join(outfolder, "csf_masks")):
makedirs(join(outfolder, "csf_masks"))
print("creating csf masks...")
for image, brainMask, f in zip(images, brainMasks, filenames):
filename = f.split(sep)[-1].split(".")[0]
csfMask = csf.csf_mask(image,
brainMask,
contrast='T1',
csf_thresh=0.9,
return_prob=False,
mrf=0.25,
use_fcm=False)
output = nib.Nifti1Image(csfMask, None)
io.save_nii(
output,
join(outfolder, 'csf_masks', filename + "_csfmask.nii.gz"))
shutil.move(join(outfolder,
f.split(sep)[-1]), join(outfolder, "Robex"))
print('running intensity ravel...')
ravel.ravel_normalize(join(outfolder, 'Robex'),
join(outfolder, 'csf_masks'),
'T1',
output_dir=outfolder,
write_to_disk=True,
do_whitestripe=True,
b=1,
membership_thresh=0.99,
segmentation_smoothness=0.25,
do_registration=False,
use_fcm=True,
sparse_svd=False,
csf_masks=True)
for i in filenames:
rename(
join(outfolder,
i.split(sep)[-1]),
join(outfolder,
i.split(sep)[-1].split(".")[0] + "_RAVEL.nii.gz"))
except:
e = sys.exc_info()
print("Error: ", str(e[0]))
print("Error: ", str(e[1]))
print("Error: executing ravel method")
sys.exit(2)