def denoise_masks(options):
"""
Denoise input masks to reduce noise.
Using anisotropic Diffusion (Perona and Malik)
"""
for mod in options['modalities']:
current_image = mod + '.nii.gz' if mod == 'T1'\
else 'r' + mod + '.nii.gz'
tmp_scan = nib.load(os.path.join(options['tmp_folder'], current_image))
tmp_scan.get_data()[:] = ans_dif(tmp_scan.get_data(),
niter=options['denoise_iter'])
tmp_scan.to_filename(
os.path.join(options['tmp_folder'], 'd' + current_image))
if options['debug']:
print "> DEBUG: Denoising ", current_image
def denoise_masks(options):
"""
Denoise input masks to reduce noise.
Using anisotropic Diffusion (Perona and Malik)
"""
# if options['register_modalities_kind'] != 'FlairtoT1' and options['register_modalities_kind'] != 'T1toFlair':
# print("registration must be either FlairtoT1 or T1toFlair and not", options['register_modalities_kind'])
# print("> ERROR:", "quiting program.")
# sys.stdout.flush()
# time.sleep(1)
# os.kill(os.getpid(), signal.SIGTERM)
for mod in options['modalities']:
# current_image = mod + '.nii.gz' if mod == 'T1'\
# else 'r' + mod + '.nii.gz'
if options['reg_space'] == 'T1toFlair':
current_image = mod + '.nii.gz' if mod == 'FLAIR' \
else 'r' + mod + '.nii.gz'
if options['reg_space'] == 'FlairtoT1':
current_image = mod + '.nii.gz' if mod == 'T1' \
else 'r' + mod + '.nii.gz'
if options['reg_space'] != 'FlairtoT1' and options[
'reg_space'] != 'T1toFlair':
current_image = 'r' + mod + '.nii.gz'
tmp_scan = nib.load(os.path.join(options['tmp_folder'], current_image))
tmp_scan.get_data()[:] = ans_dif(tmp_scan.get_data(),
niter=options['denoise_iter'])
tmp_scan.to_filename(
os.path.join(options['tmp_folder'], 'd' + current_image))
if options['debug']:
print("> DEBUG: Denoising ", current_image)