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| # 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 <code@oscaresteban.es> | |
| # | |
| # 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() |
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