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.')
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.")
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()
template, facemask = initial_checks(args.template, args.facemask)
infile = args.infile
outfile = output_checks(infile, args.outfile, args.force)
# temporary files
_, tmpmat = tempfile.mkstemp()
tmpmat = tmpmat + '.mat'
_, tmpfile = tempfile.mkstemp()
tmpfile = tmpfile + '.nii.gz'
if args.verbose:
print("Temporary files:\n %s\n %s" % (tmpmat, tmpfile))
_, tmpfile2 = tempfile.mkstemp()
_, tmpmat2 = tempfile.mkstemp()
print('Defacing...\n %s' % args.infile)
# register template to infile
flirt = fsl.FLIRT()
flirt.inputs.cost_func = args.cost
flirt.inputs.in_file = template
flirt.inputs.out_matrix_file = tmpmat
flirt.inputs.out_file = tmpfile2
flirt.inputs.reference = infile
flirt.run()
# warp facemask to infile
flirt = fsl.FLIRT()
flirt.inputs.in_file = facemask
flirt.inputs.in_matrix_file = tmpmat
flirt.inputs.apply_xfm = True
flirt.inputs.reference = infile
flirt.inputs.out_file = tmpfile
flirt.inputs.out_matrix_file = tmpmat2
flirt.run()
# multiply mask by infile and save
infile_img = load(infile)
tmpfile_img = load(tmpfile)
try:
outdata = infile_img.get_data().squeeze() * tmpfile_img.get_data()
except ValueError:
tmpdata = np.stack([tmpfile_img.get_data()] *
infile_img.get_data().shape[-1],
axis=-1)
outdata = infile_img.get_data() * tmpdata
outfile_img = Nifti1Image(outdata, infile_img.get_affine(),
infile_img.get_header())
outfile_img.to_filename(outfile)
print("Defaced image saved as:\n %s" % outfile)
# 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() * tmpfile_img.get_data()
applyfile_img = Nifti1Image(outdata, applyfile_img.get_affine(),
applyfile_img.get_header())
outfile = output_checks(applyfile)
applyfile_img.to_filename(outfile)
print(' %s' % applyfile)
if args.nocleanup:
pass
else:
os.remove(tmpfile)
os.remove(tmpfile2)
os.remove(tmpmat)
print('Finished.')