Source code for nireports.tools.ndimage

# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
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# Copyright 2023 The NiPreps Developers <nipreps@gmail.com>
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#     http://www.apache.org/licenses/LICENSE-2.0
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# STATEMENT OF CHANGES: This file was ported carrying over full git history from niworkflows,
# another NiPreps project licensed under the Apache-2.0 terms, and has been changed since.
# The original file this work derives from is found at:
# https://github.com/nipreps/niworkflows/blob/fa273d004c362d9562616253180e95694f07be3b/
# niworkflows/utils/images.py
"""Tooling to manipulate n-dimensional images."""

import nibabel as nb
import numpy as np



[docs]
def rotation2canonical(img):
    """Calculate the rotation w.r.t. cardinal axes of input image."""
    img = nb.as_closest_canonical(img)
    newaff = np.diag(img.header.get_zooms()[:3])
    r = newaff @ np.linalg.pinv(img.affine[:3, :3])
    if np.allclose(r, np.eye(3)):
        return None
    return r




[docs]
def rotate_affine(img, rot=None):
    """Rewrite the affine of a spatial image."""
    if rot is None:
        return img

    img = nb.as_closest_canonical(img)
    affine = np.eye(4)
    affine[:3] = rot @ img.affine[:3]
    return img.__class__(img.dataobj, affine, img.header)



def _get_values_inside_a_mask(main_file, mask_file):
    main_nii = nb.load(main_file)
    main_data = main_nii.get_fdata()
    nan_mask = np.logical_not(np.isnan(main_data))
    mask = nb.load(mask_file).get_fdata() > 0

    data = main_data[np.logical_and(nan_mask, mask)]
    return data