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FIX: apply() fails with 4D singleton images #278

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Merged
merged 2 commits into from
Aug 14, 2025
Merged

FIX: apply() fails with 4D singleton images #278

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be5ddd6
test: reproduce 4d singleton issue
oesteban Aug 14, 2025
01cb7cd
fix: squeeze last dimension of moving image in ``apply()``
oesteban Aug 14, 2025
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3 changes: 3 additions & 0 deletions nitransforms/resampling.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@
from nibabel.loadsave import load as _nbload
from nibabel.arrayproxy import get_obj_dtype
from nibabel.spatialimages import SpatialImage
from nibabel.funcs import squeeze_image
from scipy import ndimage as ndi

from nitransforms.base import (
Expand Down Expand Up @@ -233,6 +234,8 @@ def apply(
if isinstance(spatialimage, (str, Path)):
spatialimage = _nbload(str(spatialimage))

spatialimage = squeeze_image(spatialimage)

# Avoid opening the data array just yet
input_dtype = cap_dtype(get_obj_dtype(spatialimage.dataobj), dtype_width)

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9 changes: 9 additions & 0 deletions nitransforms/tests/test_resampling.py
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Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,15 @@
}


def test_apply_singleton_time_dimension():
"""Resampling fails when the input image has a trailing singleton dimension (gh-270)."""

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)


@pytest.mark.parametrize(
"image_orientation",
[
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