enh: update tests

Author: oesteban

nitransforms/tests/test_io_itk.py

@@ -0,0 +1,41 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""Test io module for ITK transforms."""
+
+import pytest
+
+import numpy as np
+import nibabel as nb
+
+from nitransforms.base import TransformError
+from nitransforms.io.base import TransformFileError
+from nitransforms.io.itk import ITKDisplacementsField
+from nitransforms.nonlinear import (
+    DenseFieldTransform,
+)
+
+
+@pytest.mark.parametrize("size", [(20, 20, 20), (20, 20, 20, 3)])
+def test_itk_disp_load(size):
+    """Checks field sizes."""
+    with pytest.raises(TransformFileError):
+        ITKDisplacementsField.from_image(
+            nb.Nifti1Image(np.zeros(size), np.eye(4), None)
+        )
+
+
+@pytest.mark.parametrize("size", [(20, 20, 20), (20, 20, 20, 2, 3), (20, 20, 20, 1, 4)])
+def test_displacements_bad_sizes(size):
+    """Checks field sizes."""
+    with pytest.raises(TransformError):
+        DenseFieldTransform(nb.Nifti1Image(np.zeros(size), np.eye(4), None))
+
+
+def test_itk_disp_load_intent():
+    """Checks whether the NIfTI intent is fixed."""
+    with pytest.warns(UserWarning):
+        field = ITKDisplacementsField.from_image(
+            nb.Nifti1Image(np.zeros((20, 20, 20, 1, 3)), np.eye(4), None)
+        )
+
+    assert field.header.get_intent()[0] == "vector"

nitransforms/tests/test_nonlinear.py

@@ -9,39 +9,10 @@
 import nibabel as nb
 from nitransforms.resampling import apply
 from nitransforms.base import TransformError
-from nitransforms.io.base import TransformFileError
 from nitransforms.nonlinear import (
     BSplineFieldTransform,
     DenseFieldTransform,
 )
-from nitransforms import io
-from ..io.itk import ITKDisplacementsField
-
-
-@pytest.mark.parametrize("size", [(20, 20, 20), (20, 20, 20, 3)])
-def test_itk_disp_load(size):
-    """Checks field sizes."""
-    with pytest.raises(TransformFileError):
-        ITKDisplacementsField.from_image(
-            nb.Nifti1Image(np.zeros(size), np.eye(4), None)
-        )
-
-
-@pytest.mark.parametrize("size", [(20, 20, 20), (20, 20, 20, 2, 3), (20, 20, 20, 1, 4)])
-def test_displacements_bad_sizes(size):
-    """Checks field sizes."""
-    with pytest.raises(TransformError):
-        DenseFieldTransform(nb.Nifti1Image(np.zeros(size), np.eye(4), None))
-
-
-def test_itk_disp_load_intent():
-    """Checks whether the NIfTI intent is fixed."""
-    with pytest.warns(UserWarning):
-        field = ITKDisplacementsField.from_image(
-            nb.Nifti1Image(np.zeros((20, 20, 20, 1, 3)), np.eye(4), None)
-        )
-
-    assert field.header.get_intent()[0] == "vector"
 
 
 def test_displacements_init():
@@ -96,76 +67,39 @@ def test_bsplines_references(testdata_path):
     )
 
 
+@pytest.mark.xfail(
+    reason="Disable while #266 is developed.",
+    strict=False,
+)
 def test_bspline(tmp_path, testdata_path):
+    """
+    Cross-check B-Splines and deformation field.
+
+    This test is disabled and will be split into two separate tests.
+    The current implementation will be moved into test_resampling.py,
+    since that's what it actually tests.
+
+    In GH-266, this test will be re-implemented by testing the equivalence
+    of the B-Spline and deformation field transforms by calling the
+    transform's `map()` method on points.
+
+    """
+    assert True
+
+
+def test_map_bspline_vs_displacement(tmp_path, testdata_path):
     """Cross-check B-Splines and deformation field."""
     os.chdir(str(tmp_path))
 
     img_name = testdata_path / "someones_anatomy.nii.gz"
     disp_name = testdata_path / "someones_displacement_field.nii.gz"
     bs_name = testdata_path / "someones_bspline_coefficients.nii.gz"
 
-    bsplxfm = BSplineFieldTransform(bs_name, reference=img_name)
+    bsplxfm = BSplineFieldTransform(bs_name, reference=img_name).to_field()
     dispxfm = DenseFieldTransform(disp_name)
 
-    out_disp = apply(dispxfm, img_name)
-    out_bspl = apply(bsplxfm, img_name)
-
-    out_disp.to_filename("resampled_field.nii.gz")
-    out_bspl.to_filename("resampled_bsplines.nii.gz")
-
-    assert (
-        np.sqrt(
-            (out_disp.get_fdata(dtype="float32") - out_bspl.get_fdata(dtype="float32"))
-            ** 2
-        ).mean()
-        < 0.2
-    )
-
-
-@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 = 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"
-    io.x5.to_filename(fname, [node])
-
-    xfm2 = 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 = 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"
-    io.x5.to_filename(fname, [node])
-
-    xfm2 = 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)
+    # Interpolating the field should be reasonably similar
+    np.testing.assert_allclose(dispxfm._field, bsplxfm._field, atol=1e-1, rtol=1e-4)
 
 
 @pytest.mark.parametrize("is_deltas", [True, False])

nitransforms/tests/test_x5.py

@@ -1,8 +1,10 @@
 import numpy as np
+import nibabel as nb
 import pytest
 from h5py import File as H5File
 
-from ..io.x5 import X5Transform, X5Domain, to_filename, from_filename
+from nitransforms.nonlinear import DenseFieldTransform, BSplineFieldTransform
+from nitransforms.io.x5 import X5Transform, X5Domain, to_filename, from_filename
 
 
 def test_x5_transform_defaults():
@@ -75,3 +77,49 @@ def test_from_filename_invalid(tmp_path):
 
     with pytest.raises(TypeError):
         from_filename(fname)
+
+
+@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 = 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"
+    to_filename(fname, [node])
+
+    xfm2 = 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 = 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"
+    to_filename(fname, [node])
+
+    xfm2 = 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)