#!/usr/bin/env python3
"""
Use ``img_pad`` from UNRAVEL to add 15 percent of padding to an image.nii.gz and save it.
Usage:
------
img_pad -i reg_inputs/autofl_50um.nii.gz [-ort RAS] [-r reg_inputs/autofl_50um.nii.gz] [-o reg_inputs/autofl_50um_pad.nii.gz] [-zero] [-v]
"""
import nibabel as nib
import numpy as np
from rich.traceback import install
from unravel.image_io.nii_info import nii_axis_codes
from unravel.image_io.reorient_nii import reorient_nii
from unravel.core.help_formatter import RichArgumentParser, SuppressMetavar, SM
from unravel.core.config import Configuration
from unravel.core.img_tools import pad
from unravel.core.utils import log_command, verbose_start_msg, verbose_end_msg
[docs]
def parse_args():
parser = RichArgumentParser(formatter_class=SuppressMetavar, add_help=False, docstring=__doc__)
reqs = parser.add_argument_group('Required arguments')
reqs.add_argument('-i', '--input', help='path/img.nii.gz', required=True, action=SM)
opts = parser.add_argument_group('Optional arguments')
opts.add_argument('-ort', '--ort_code', help='3 letter orientation code of fixed image if not set in fixed_img (e.g., RAS)', action=SM)
opts.add_argument('-r', '--ref_nii', help='Reference image for setting the orientation code', action=SM)
opts.add_argument('-o', '--output', help='path/img.nii.gz. Default: None (saves as path/img_pad.nii.gz) ', default=None, action=SM)
opts.add_argument('-zero', '--zero_origin', help='Set the origin to zero in the affine matrix. Default: False', action='store_true', default=False)
general = parser.add_argument_group('General arguments')
general.add_argument('-v', '--verbose', help='Increase verbosity. Default: False', action='store_true', default=False)
return parser.parse_args()
[docs]
@log_command
def main():
install()
args = parse_args()
Configuration.verbose = args.verbose
verbose_start_msg()
nii = nib.load(args.input)
data_type = nii.header.get_data_dtype()
img = np.asanyarray(nii.dataobj, dtype=data_type).squeeze()
# Pad the image
img = pad(img, pad_width=0.15)
# Save the padded image
fixed_img_padded_nii = nib.Nifti1Image(img, nii.affine, nii.header)
fixed_img_padded_nii.set_data_dtype(data_type)
# Set the orientation of the image (use if not already set correctly in the header; check with ``io_reorient_nii``)
if args.ort_code:
fixed_img_padded_nii = reorient_nii(fixed_img_padded_nii, args.ort_code, zero_origin=args.zero_origin, apply=False, form_code=1)
elif args.ref_nii:
ref_nii = nib.load(args.ref_nii)
ort_code = nii_axis_codes(ref_nii)
fixed_img_padded_nii = reorient_nii(fixed_img_padded_nii, ort_code, zero_origin=args.zero_origin, apply=False, form_code=1)
else:
fixed_img_padded_nii = reorient_nii(fixed_img_padded_nii, nii_axis_codes(nii), zero_origin=args.zero_origin, apply=False, form_code=1)
if args.output is None:
padded_img_path = args.input.replace('.nii.gz', '_pad.nii.gz')
else:
padded_img_path = args.output
nib.save(fixed_img_padded_nii, padded_img_path)
verbose_end_msg()
if __name__ == '__main__':
main()