#!/usr/bin/env python3
"""
Use ``img_resample`` (``resample``) from UNRAVEL to resample an image.nii.gz and save it.
Usage with reference image:
---------------------------
img_resample -i image.nii.gz -ref reference_image.nii.gz [-zo 0] [-o image_resampled.nii.gz] [-v]
Usage for isotropic resampling:
-------------------------------
img_resample -i image.nii.gz -tr 50 [-zo 0] [-o image_resampled.nii.gz] [-v]
Usage for anisotropic resampling:
---------------------------------
img_resample -i image.nii.gz -tr 200 10 10 -o image_200x10x10.nii.gz [-zo 0] [-v]
"""
import nibabel as nib
from rich.traceback import install
import numpy as np
from unravel.core.help_formatter import RichArgumentParser, SuppressMetavar, SM
from unravel.core.config import Configuration
from unravel.core.img_tools import resample_nii
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/input_image.nii.gz', required=True, action=SM)
reqs.add_argument('-ref', '--reference', help='Reference image (.nii.gz) for resampling', required=False, action=SM)
reqs.add_argument('-tr', '--target_res', help='Target resolution in microns for resampling (can be isotropic or anisotropic)', default=None, type=float, nargs='*', action=SM)
reqs.add_argument('-td', '--target_dims', help='Target dimensions for resampling (can be isotropic or anisotropic)', default=None, type=int, nargs='*', action=SM)
opts = parser.add_argument_group('Optional arguments')
opts.add_argument('-zo', '--zoom_order', help='SciPy zoom order. Default: 0 (nearest-neighbor). Use 1 for linear interpolation.', default=0, type=int, action=SM)
opts.add_argument('-o', '--output', help='path/output_image.nii.gz. Default: None (saves as path/input_image_resampled.nii.gz)', default=None, action=SM)
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()
# TODO: Add support for other image formats (e.g., tifs to tifs). Add args for scaling by a factor for each dimension.
[docs]
@log_command
def main():
install()
args = parse_args()
Configuration.verbose = args.verbose
verbose_start_msg()
nii = nib.load(args.input)
if args.reference is not None:
ref_nii = nib.load(args.reference)
target_res = ref_nii.header.get_zooms()[:3]
target_dims = ref_nii.shape
resampled_nii = resample_nii(nii, target_res=target_res, target_dims=target_dims, zoom_order=args.zoom_order)
elif args.target_res is not None:
target_res = [res / 1000 for res in args.target_res] # Convert target resolution from microns to mm
if len(target_res) == 1:
target_res = target_res * 3 # Use isotropic resolution if only one value is provided
resampled_nii = resample_nii(nii, target_res=target_res, target_dims=args.target_dims, zoom_order=args.zoom_order)
elif args.target_dims is not None:
resampled_nii = resample_nii(nii, target_res=None, target_dims=args.target_dims, zoom_order=args.zoom_order)
else:
raise ValueError("Either target resolution, target dimensions, or a reference image must be specified.")
data_type = nii.header.get_data_dtype()
resampled_nii.set_data_dtype(data_type)
if args.output is None:
resampled_img_path = args.input.replace('.nii.gz', '_resampled.nii.gz')
else:
resampled_img_path = args.output
nib.save(resampled_nii, resampled_img_path)
verbose_end_msg()
if __name__ == '__main__':
main()