#!/usr/bin/env python3
"""
Use ``vstats_mirror`` from UNRAVEL to load a `*`.nii.gz, flip a copy [and shift content], average original and copy together, and save as .nii.gz.
Note:
- Use -ax 2 and -s 0 for the CCFv3 2020 atlas.
- Use -ax 0 and -s 2 for the 25 um Gubra atlas.
Usage:
------
vstats_mirror [-p '<asterisk>.nii.gz'] [-ax 2] [-s 0] [-v]
"""
import os
import numpy as np
import nibabel as nib
from pathlib import Path
from rich.traceback import install
from unravel.core.help_formatter import RichArgumentParser, SuppressMetavar, SM
from unravel.core.config import Configuration
from unravel.core.utils import log_command, verbose_start_msg, verbose_end_msg, print_func_name_args_times
[docs]
def parse_args():
parser = RichArgumentParser(formatter_class=SuppressMetavar, add_help=False, docstring=__doc__)
opts = parser.add_argument_group('Optional arguments')
opts.add_argument('-p', '--pattern', help='Pattern to match files. Default: *.nii.gz', default='*.nii.gz', action=SM)
opts.add_argument('-ax', '--axis', help='Axis to flip the image along. Default: 2', default=2, type=int, action=SM)
opts.add_argument('-s', '--shift', help='Number of voxels to shift content after flipping. Default: 0', default=0, type=int, action=SM)
general = parser.add_argument_group('General arguments')
general.add_argument('-v', '--verbose', help='Increase verbosity. Default: False', default=False, action='store_true')
return parser.parse_args()
[docs]
@print_func_name_args_times()
def mirror(img, axis=2, shift=0):
"""Mirror an image along the specified axis and shift the content by the specified number of voxels.
Args:
img (np.ndarray): Image data to mirror
axis (int): Axis to flip the image along. Default: 0
shift (int): Number of voxels to shift content after flipping. Default: 2 (useful when the atlas is not centered)"""
# Flip the image data along the specified axis
flipped_img = np.flip(img, axis=axis)
if shift == 0:
return flipped_img
else:
# Shift the image data by padding with zeros on the left and cropping on the right
# This adds 2 voxels of zeros on the left side (beginning) and removes 2 voxels from the right side (end)
if axis == 0:
mirrored_img = np.pad(flipped_img, ((shift, 0), (0, 0), (0, 0)), mode='constant', constant_values=0)[:-shift, :, :]
return mirrored_img
else:
print('[red1]Logic for shifting content in axeses other than 0 has not been added. Please request this if needed.')
return
[docs]
@log_command
def main():
install()
args = parse_args()
Configuration.verbose = args.verbose
verbose_start_msg()
files = Path().cwd().glob(args.pattern)
for file in files:
basename = Path(file).name
mirrored_filename = f"mirror_{basename}"
if not os.path.exists(mirrored_filename):
nii = nib.load(file)
img = np.asanyarray(nii.dataobj, dtype=nii.header.get_data_dtype()).squeeze()
mirrored_img = mirror(img, axis=args.axis, shift=args.shift)
mirrored_nii = nib.Nifti1Image(mirrored_img, nii.affine, nii.header)
nib.save(mirrored_nii, mirrored_filename)
verbose_end_msg()
if __name__ == '__main__':
main()