Merge pull request #278 from nipy/codex/investigate-issue-#270-and-propose-tests

FIX: ``apply()`` fails with 4D singleton images

Author: oesteban

nitransforms/resampling.py

@@ -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 (
@@ -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)
 

nitransforms/tests/test_resampling.py

@@ -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",
     [