Avoid eager C-order copies in NibabelReader (Fixes: #8107)

Nibabel exposes NIfTI voxel buffers in their native Fortran layout, but
MONAI was forcing np.asanyarray(img.dataobj, order="C") in
NibabelReader._get_array_data(). For compressed .nii.gz inputs that adds
a full dense memory reorder on top of the file read/decompression step,
which is the hot path reported in issue #8107.

Drop the forced C-order conversion and keep nibabel's native array layout
instead. Downstream MONAI conversion paths already handle contiguity when
they actually need it, so the reader does not need to pay that cost
eagerly at load time.

Add a regression test that loads a small NIfTI image through
NibabelReader and asserts the returned data is still correct while
preserving the native F-contiguous layout. This guards against
reintroducing the eager copy in the reader path.

Signed-off-by: Soumya Snigdha Kundu <[email protected]>

Author: aymuos15

monai/data/image_reader.py

@@ -1217,7 +1217,7 @@ def _get_array_data(self, img, filename):
             data_offset = img.dataobj.offset
             data_dtype = img.dataobj.dtype
             return image[data_offset:].view(data_dtype).reshape(data_shape, order="F")
-        return np.asanyarray(img.dataobj, order="C")
+        return np.asanyarray(img.dataobj)
 
 
 class NumpyReader(ImageReader):

tests/data/test_init_reader.py

@@ -11,8 +11,12 @@
 
 from __future__ import annotations
 
+import os
+import tempfile
 import unittest
 
+import numpy as np
+
 from monai.data import ITKReader, NibabelReader, NrrdReader, NumpyReader, PILReader, PydicomReader
 from monai.transforms import LoadImage, LoadImaged
 from tests.test_utils import SkipIfNoModule
@@ -76,6 +80,23 @@ def test_readers_to_gpu(self):
             inst = NibabelReader(to_gpu=to_gpu)
             self.assertIsInstance(inst, NibabelReader)
 
+    @SkipIfNoModule("nibabel")
+    def test_nibabel_reader_avoids_eager_c_order_copy(self):
+        import nibabel as nib
+
+        test_image = np.arange(2 * 3 * 4, dtype=np.int16).reshape(2, 3, 4)
+        with tempfile.TemporaryDirectory() as tempdir:
+            filename = os.path.join(tempdir, "test_image.nii.gz")
+            nib.save(nib.Nifti1Image(test_image, np.eye(4)), filename)
+
+            reader = NibabelReader(mmap=False)
+            img = reader.read(filename)
+            data, _ = reader.get_data(img)
+
+            np.testing.assert_array_equal(data, test_image)
+            self.assertTrue(data.flags.f_contiguous)
+            self.assertFalse(data.flags.c_contiguous)
+
 
 if __name__ == "__main__":
     unittest.main()