Source code for unravel.image_io.nii_info

#!/usr/bin/env python3

"""
Use ``io_nii_info`` from UNRAVEL to load an .nii.gz image and print its data type, shape, voxel sizes, and affine matrix using nibabel.

Usage:
------
    io_nii_info -i path/img.nii.gz [-v]
"""

import nibabel as nib
import numpy as np
from rich import print
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




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', 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()




def nii_axis_codes(nii):
    """Get and return axes codes (three letter orientation like RAS) from an nibabel NIfTI image"""
    axcodes_tuple = nib.orientations.aff2axcodes(nii.affine) 
    axcodes = ''.join(axcodes_tuple) 
    return axcodes





@log_command
def main():
    install()
    args = parse_args()
    Configuration.verbose = args.verbose
    verbose_start_msg()
    
    nii = nib.load(args.input)
    
    np.set_printoptions(precision=2, suppress=True)

    # Print data type
    data_type = nii.get_data_dtype()
    print(f'\nData type:\n[default bold]{data_type}')

    # Print dimensions
    print(f'\nShape (x, y, z):\n{nii.shape}')

    # Print the voxel sizes
    voxel_sizes = nii.header.get_zooms()
    voxel_sizes = tuple(np.array(voxel_sizes) * 1000)
    print(f'\nVoxel sizes (in microns):\n{voxel_sizes}')

    # Print orientation and affine
    axcodes = nii_axis_codes(nii)
    np.set_printoptions(precision=4, suppress=True)
    print(f'\nAffine matrix ([default bold]{axcodes}[/]):\n{nii.affine}\n')

    verbose_end_msg()



if __name__ == '__main__':
    main()