fabian_reorient.py

# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
#
# Copyright 2023 Oscar Esteban <[email protected]>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# We support and encourage derived works from this project, please read
# about our expectations at
#
#     https://www.nipreps.org/community/licensing/
#
"""CLI."""
import numpy as np
import click
import nibabel as nb


@click.group()
@click.version_option(message="Manipulate NIfTI files")
def cli():
    """Manipulating NIfTI files."""


@cli.command()
@click.option("-i", "--in_file", type=click.Path(exists=True))
@click.option("-o", "--out_file", type=click.Path(), default=None)
def reorient(in_file, out_file):
    """Reorient the input to be RAS and have (0, 0, 0) [mm] at the center of the volume."""
    in_nii = nb.load(in_file)

    # Get orientation codes of input
    in_codes = nb.aff2axcodes(in_nii.affine)
    # Transform to reorder axes so that voxels/coordinates are IJK/XYZ
    ornt_xfm = nb.orientations.axcodes2ornt(in_codes)
    # Do not flip any axes
    ornt_xfm[:, 1] = 1.0

    # Data array will now be in the correct order
    in_ijk_axes = in_nii.as_reoriented(ornt_xfm)

    if out_file is None:
        out_file = str(in_file).replace(".nii", "_reoriented.nii")

    # Let NiBabel calculate the canonical (RAS) orientation
    in_ras = nb.as_closest_canonical(in_ijk_axes)

    # Fix input's eccentricity
    ras_affine = in_ras.affine.copy()
    ras_affine[:3, 3] = -1.0 * (
        ras_affine[:3, :3] @ ((np.array(in_ras.shape) - 1) * 0.5)
    )

    outnii = nb.Nifti1Image(in_ijk_axes.dataobj, ras_affine, in_ras.header)
    outnii.header.set_sform(ras_affine, code=1)
    outnii.header.set_qform(ras_affine, code=1)
    outnii.to_filename(out_file)


if __name__ == "__main__":
    """ Install entry-point """
    cli()