How to convert a Nifti image affine.

ornt_transform.py

import os
from argparse import ArgumentParser

import numpy as np
import nibabel as nib
import nibabel.orientations as ornts

def main(args):
    image = nib.load(args.input)
    
    src_ornt = ornts.io_orientation(image.affine)
    dst_ornt = ornts.axcodes2ornt(args.axcodes)
    
    # Get orientation transform
    ornt_t = ornts.ornt_transform(src_ornt, dst_ornt)
    
    # Apply orientation transform on image data
    data = ornts.apply_orientation(image.dataobj, ornt_t)
    # Apply orientation transform on image affine
    inv_ornt_t = ornts.ornt_transform(dst_ornt, src_ornt) # may be unnecessary
    affine_t = ornts.inv_ornt_aff(inv_ornt_t, image.shape)
    affine = np.matmul(image.affine, affine_t)
    
    output = nib.Nifti1Image(data, affine)
    nib.save(output, args.output)
    
if __name__ == "__main__":
    parser = ArgumentParser()
    parser.add_argument("--input", "-i", type=str, help="Input Nifti image for affine transform")
    parser.add_argument("--output", "-o", type=str, help="Path to save transformed Nifti image")
    parser.add_argument("--axcodes", "-a", type=str, help="Target orientation axis codes")
    args = parser.parse_args()
    
    main(args)