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FIX: Respect singleton 4th-D #279

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Merged
merged 4 commits into from
Aug 15, 2025
Merged

FIX: Respect singleton 4th-D #279

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faef239
fix: respect singleton 4d
oesteban Aug 14, 2025
bfa39e1
tst: ensure singleton 4th dim is respected
oesteban Aug 15, 2025
ebae5c7
tst: improve test with more specific inputs
oesteban Aug 15, 2025
0857139
Merge branch 'master' into fix/finalize-270
oesteban Aug 15, 2025
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4 changes: 3 additions & 1 deletion nitransforms/resampling.py
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Original file line number Diff line number Diff line change
Expand Up @@ -234,6 +234,7 @@ def apply(
if isinstance(spatialimage, (str, Path)):
spatialimage = _nbload(str(spatialimage))

singleton_4d = spatialimage.ndim == 4 and spatialimage.shape[-1] == 1
spatialimage = squeeze_image(spatialimage)

# Avoid opening the data array just yet
Expand Down Expand Up @@ -370,7 +371,8 @@ def apply(
with suppress(ValueError):
resampled = np.squeeze(resampled, axis=3)

moved = spatialimage.__class__(resampled, _ref.affine, hdr)
moved = spatialimage.__class__(
resampled[..., None] if singleton_4d else resampled, _ref.affine, hdr)
return moved

output_dtype = output_dtype or input_dtype
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9 changes: 7 additions & 2 deletions nitransforms/tests/test_resampling.py
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Expand Up @@ -56,8 +56,13 @@ def test_apply_singleton_time_dimension():

data = np.reshape(np.arange(27, dtype=np.uint8), (3, 3, 3, 1))
nii = nb.Nifti1Image(data, np.eye(4))
xfm = nitl.Affine(np.eye(4), reference=nii)
apply(xfm, nii)
ref = nb.Nifti1Image(np.zeros((4, 4, 4)), np.eye(4))
xfm = nitl.Affine(np.eye(4), reference=ref)
movednii = apply(xfm, nii)
assert movednii.shape == ref.shape + (1, )

movednii = apply(xfm, nii, reference=ref)
assert movednii.shape == ref.shape + (1, )


@pytest.mark.parametrize(
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