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Fix NibabelIOWithReorient saver function #2478

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Sep 17, 2024
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Fix NibabelIOWithReorient saver function #2478

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8 changes: 6 additions & 2 deletions nnunetv2/imageio/nibabel_reader_writer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@
import warnings
from typing import Tuple, Union, List
import numpy as np
from nibabel import io_orientation
from nibabel.orientations import io_orientation, axcodes2ornt, ornt_transform

from nnunetv2.imageio.base_reader_writer import BaseReaderWriter
import nibabel
Expand Down Expand Up @@ -174,7 +174,11 @@ def write_seg(self, seg: np.ndarray, output_fname: str, properties: dict) -> Non
seg = seg.transpose((2, 1, 0)).astype(np.uint8, copy=False)

seg_nib = nibabel.Nifti1Image(seg, affine=properties['nibabel_stuff']['reoriented_affine'])
seg_nib_reoriented = seg_nib.as_reoriented(io_orientation(properties['nibabel_stuff']['original_affine']))
# Solution from https://github.com/nipy/nibabel/issues/1063#issuecomment-967124057
img_ornt = io_orientation(properties['nibabel_stuff']['original_affine'])
ras_ornt = axcodes2ornt("RAS")
from_canonical = ornt_transform(ras_ornt, img_ornt)
seg_nib_reoriented = seg_nib.as_reoriented(from_canonical)
if not np.allclose(properties['nibabel_stuff']['original_affine'], seg_nib_reoriented.affine):
print(f'WARNING: Restored affine does not match original affine. File: {output_fname}')
print(f'Original affine\n', properties['nibabel_stuff']['original_affine'])
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