Resampling data changes its orientation

[Kseniiakv]

Hi!

Have a question regarding the behaviour of resample_to_output and resample_from_to functions.
After resampling of the data, the orientation changes to default RAS, even if it had other orientation previously:

vol = nib.load(path)
print("Orientation before: ", nib.orientations.aff2axcodes(vol.affine))
target_vox_dim = (1, 1, 1)
resampled = nib.processing.resample_to_output(vol, target_vox_dim, order=3, mode='nearest')
print("Orientation after: ", nib.orientations.aff2axcodes(resampled.affine))

Orientation before:  ('L', 'A', 'S')
Orientation after:  ('R', 'A', 'S')

Expected behaviour: orientation of the resampled data shouldn't change

Is this expected behaviour?
Now if I want LAS orientation, I need to reorient data additionally after resampling.

[effigies]

Yes, this is expected. Resampling requires choosing a number of parameters, and the functions are intended to be fairly simple. If you want full control over the field of view, specify a shape and an affine, and use nibabel.affines.rescale_affine to preserve the rotations and shears.

vol = nib.load(path)
target_zooms = (1, 1, 1)
target_shape = vol.shape  # Or you can set anything you like
target_aff = nib.affines.rescale_affine(vol.affine, vol.shape, target_zooms, target_shape)
resampled = nib.procesing.resample_from_to(vol, (target_shape, target_aff))

Note (see #1366) that if you go from an even number of voxels to odd (or vice versa) in any dimension, you might get an affine slightly different from what you want. The resampling will be valid, however.