def test_deface_image():
if which('fsl'):
test_img = (Path(__file__).parent.parent.joinpath(
'tests', 'data',
'ds000031_sub-01_ses-006_run-001_T1w.nii.gz').as_posix())
# From https://stackoverflow.com/a/7244263
data_url = 'https://openneuro.org/crn/datasets/ds000031/files/sub-01:ses-006:anat:sub-01_ses-006_run-001_T1w.nii.gz'
urllib.request.urlretrieve(data_url, test_img)
pdu.deface_image(test_img, forcecleanup=True, force=True)
pdu.cleanup_files(test_img)
else:
pytest.skip("no fsl to run defacing.")
def test_cleanup_files():
files = []
for p in range(3):
files.append(tempfile.mkstemp()[1])
pdu.cleanup_files(files[0])
pdu.cleanup_files(*files[1:])
# should not fail if files do not exist
pdu.cleanup_files(*files)
def main():
"""Command line call argument parsing."""
parser = argparse.ArgumentParser()
parser.add_argument('infile', metavar='path', help="Path to input nifti.")
parser.add_argument("--outfile",
metavar='path',
required=False,
help="If not provided adds '_defaced' suffix.")
parser.add_argument("--force",
action='store_true',
help="Force to rewrite the output even if it exists.")
parser.add_argument(
'--applyto',
nargs='+',
required=False,
metavar='',
help="Apply the created face mask to other images. Can take multiple "
"arguments.")
parser.add_argument(
"--cost",
metavar='mutualinfo',
required=False,
default='mutualinfo',
help="FSL-FLIRT cost function. Default is 'mutualinfo'.")
parser.add_argument(
"--template",
metavar='path',
required=False,
help=("Optional template image that will be used as the registration "
"target instead of the default."))
parser.add_argument(
"--facemask",
metavar='path',
required=False,
help="Optional face mask image that will be used instead of the "
"default.")
parser.add_argument("--nocleanup",
action='store_true',
help="Do not cleanup temporary files. Off by default.")
parser.add_argument("--verbose",
action='store_true',
help="Show additional status prints. Off by default.")
parser.add_argument('--debug',
action='store_true',
dest='debug',
help='Do not catch exceptions and show exception '
'traceback (Drop into pdb debugger).')
welcome_str = 'pydeface ' + require("pydeface")[0].version
welcome_decor = '-' * len(welcome_str)
print(welcome_decor + '\n' + welcome_str + '\n' + welcome_decor)
args = parser.parse_args()
if args.debug:
setup_exceptionhook()
warped_mask_img, warped_mask, template_reg, template_reg_mat =\
pdu.deface_image(**vars(args))
# apply mask to other given images
if args.applyto is not None:
print("Defacing mask also applied to:")
for applyfile in args.applyto:
applyfile_img = load(applyfile)
outdata = applyfile_img.get_data() * warped_mask_img.get_data()
applyfile_img = Nifti1Image(outdata, applyfile_img.get_affine(),
applyfile_img.get_header())
outfile = pdu.output_checks(applyfile)
applyfile_img.to_filename(outfile)
print(' %s' % applyfile)
if not args.nocleanup:
pdu.cleanup_files(warped_mask, template_reg, template_reg_mat)
print('Finished.')