fix: remove sign flip as it seems incorrect

Author: oesteban

nitransforms/io/itk.py

@@ -348,8 +348,6 @@ def from_image(cls, imgobj):
             hdr.set_intent("vector")
 
         field = np.squeeze(np.asanyarray(imgobj.dataobj)).transpose(2, 1, 0, 3)
-        field[..., (0, 1)] *= -1.0
-
         return imgobj.__class__(field, LPS @ imgobj.affine, hdr)
 
     @classmethod
@@ -360,7 +358,6 @@ def to_image(cls, imgobj):
         hdr.set_intent("vector")
 
         field = imgobj.get_fdata().transpose(2, 1, 0, 3)[..., None, :]
-        field[..., (0, 1)] *= -1.0
         return imgobj.__class__(field, LPS @ imgobj.affine, hdr)
 
 

nitransforms/tests/test_io.py

@@ -17,11 +17,13 @@
 from nibabel.affines import from_matvec
 from scipy.io import loadmat
 from nitransforms.linear import Affine
+from nitransforms import nonlinear as nitnl
 from nitransforms.io import (
     afni,
     fsl,
     lta as fs,
     itk,
+    x5
 )
 from nitransforms.io.lta import (
     VolumeGeometry as VG,
@@ -695,6 +697,17 @@ def test_itk_linear_h5(tmpdir, data_path, testdata_path):
         itk.ITKLinearTransform.from_filename("test.h5")
 
 
+
+def test_itk_disp_load_intent():
+    """Checks whether the NIfTI intent is fixed."""
+    with pytest.warns(UserWarning):
+        field = itk.ITKDisplacementsField.from_image(
+            nb.Nifti1Image(np.zeros((20, 20, 20, 1, 3)), np.eye(4), None)
+        )
+
+    assert field.header.get_intent()[0] == "vector"
+
+
 # Added tests for displacements fields orientations (ANTs/ITK)
 @pytest.mark.parametrize("image_orientation", ["RAS", "LAS", "LPS", "oblique"])
 def test_itk_displacements(tmp_path, get_testdata, image_orientation):
@@ -736,12 +749,63 @@ def test_itk_displacements(tmp_path, get_testdata, image_orientation):
     np.testing.assert_allclose(itk_nii.dataobj, nit_nii.dataobj)
     np.testing.assert_allclose(itk_nii.affine, nit_nii.affine)
 
+    # Check ITK-generated field has LPS-rotated affine
+    np.testing.assert_allclose(itk_nii.affine, LPS @ ref_affine)
+    # Test ITK-generated dataobject vs. original field
+    np.testing.assert_allclose(itk_nii.dataobj, field.transpose(2, 1, 0, 3)[..., None, :])
+
     # Test round trip
     assert itk_nit_nii.shape == field.shape
+    np.testing.assert_allclose(itk_nit_nii.dataobj, field)
+    np.testing.assert_allclose(itk_nit_nii.dataobj.transpose(2, 1, 0, 3)[..., None, :], nit_nii.dataobj)
     np.testing.assert_allclose(itk_nit_nii.affine, ref_affine)
+    np.testing.assert_allclose(LPS @ itk_nit_nii.affine, nit_nii.affine)
 
-    field[..., (0, 1)] *= -1.0  # Undo LPS flip
-    np.testing.assert_allclose(itk_nit_nii.dataobj, field)
+
+@pytest.mark.parametrize("is_deltas", [True, False])
+def test_densefield_x5_roundtrip(tmp_path, is_deltas):
+    """Ensure dense field transforms roundtrip via X5."""
+    ref = nb.Nifti1Image(np.zeros((2, 2, 2), dtype="uint8"), np.eye(4))
+    disp = nb.Nifti1Image(np.random.rand(2, 2, 2, 3).astype("float32"), np.eye(4))
+
+    xfm = nitnl.DenseFieldTransform(disp, is_deltas=is_deltas, reference=ref)
+
+    node = xfm.to_x5(metadata={"GeneratedBy": "pytest"})
+    assert node.type == "nonlinear"
+    assert node.subtype == "densefield"
+    assert node.representation == "displacements" if is_deltas else "deformations"
+    assert node.domain.size == ref.shape
+    assert node.metadata["GeneratedBy"] == "pytest"
+
+    fname = tmp_path / "test.x5"
+    x5.to_filename(fname, [node])
+
+    xfm2 = nitnl.DenseFieldTransform.from_filename(fname, fmt="X5")
+
+    assert xfm2.reference.shape == ref.shape
+    assert np.allclose(xfm2.reference.affine, ref.affine)
+    assert xfm == xfm2
+
+
+def test_bspline_to_x5(tmp_path):
+    """Check BSpline transforms export to X5."""
+    coeff = nb.Nifti1Image(np.zeros((2, 2, 2, 3), dtype="float32"), np.eye(4))
+    ref = nb.Nifti1Image(np.zeros((2, 2, 2), dtype="uint8"), np.eye(4))
+
+    xfm = nitnl.BSplineFieldTransform(coeff, reference=ref)
+    node = xfm.to_x5(metadata={"tool": "pytest"})
+    assert node.type == "nonlinear"
+    assert node.subtype == "bspline"
+    assert node.representation == "coefficients"
+    assert node.metadata["tool"] == "pytest"
+
+    fname = tmp_path / "bspline.x5"
+    x5.to_filename(fname, [node])
+
+    xfm2 = nitnl.BSplineFieldTransform.from_filename(fname, fmt="X5")
+    assert np.allclose(xfm._coeffs, xfm2._coeffs)
+    assert xfm2.reference.shape == ref.shape
+    assert np.allclose(xfm2.reference.affine, ref.affine)
 
 
 # Added tests for h5 orientation bug