Merge pull request #274 from nipy/enh/extract-test-from-266

ENH: Add unit test on dense fields (extracted from #266)

Author: oesteban

nitransforms/tests/test_nonlinear.py

@@ -13,6 +13,9 @@
     BSplineFieldTransform,
     DenseFieldTransform,
 )
+from nitransforms.tests.utils import get_points
+
+rng = np.random.default_rng()
 
 
 def test_displacements_init():
@@ -74,24 +77,81 @@ 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.
+@pytest.mark.parametrize("image_orientation", ["RAS", "LAS", "LPS", "oblique"])
+@pytest.mark.parametrize("ongrid", [True, False])
+def test_densefield_map(get_testdata, image_orientation, ongrid):
+    """Create a constant displacement field and compare mappings."""
+
+    nii = get_testdata[image_orientation]
+
+    # Get sampling indices
+    coords_xyz, points_ijk, grid_xyz, shape, ref_affine, reference, subsample = (
+        get_points(nii, ongrid, rng=rng)
+    )
+
+    coords_map = grid_xyz.reshape(*shape, 3)
+    deltas = np.stack(
+        (
+            np.zeros(np.prod(shape), dtype="float32").reshape(shape),
+            np.linspace(-80, 80, num=np.prod(shape), dtype="float32").reshape(shape),
+            np.linspace(-50, 50, num=np.prod(shape), dtype="float32").reshape(shape),
+        ),
+        axis=-1,
+    )
+
+    if ongrid:
+        atol = 1e-3 if image_orientation == "oblique" or not ongrid else 1e-7
+        # Build an identity transform (deltas)
+        id_xfm_deltas = DenseFieldTransform(reference=reference)
+        np.testing.assert_array_equal(coords_map, id_xfm_deltas._field)
+        np.testing.assert_allclose(coords_xyz, id_xfm_deltas.map(coords_xyz))
+
+        # Build an identity transform (deformation)
+        id_xfm_field = DenseFieldTransform(
+            coords_map, is_deltas=False, reference=reference
+        )
+        np.testing.assert_array_equal(coords_map, id_xfm_field._field)
+        np.testing.assert_allclose(coords_xyz, id_xfm_field.map(coords_xyz), atol=atol)
 
-    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.
+        # Collapse to zero transform (deltas)
+        zero_xfm_deltas = DenseFieldTransform(-coords_map, reference=reference)
+        np.testing.assert_array_equal(
+            np.zeros_like(zero_xfm_deltas._field), zero_xfm_deltas._field
+        )
+        np.testing.assert_allclose(
+            np.zeros_like(coords_xyz), zero_xfm_deltas.map(coords_xyz), atol=atol
+        )
 
-    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.
+        # Collapse to zero transform (deformation)
+        zero_xfm_field = DenseFieldTransform(
+            np.zeros_like(deltas), is_deltas=False, reference=reference
+        )
+        np.testing.assert_array_equal(
+            np.zeros_like(zero_xfm_field._field), zero_xfm_field._field
+        )
+        np.testing.assert_allclose(
+            np.zeros_like(coords_xyz), zero_xfm_field.map(coords_xyz), atol=atol
+        )
+
+    # Now let's apply a transform
+    xfm = DenseFieldTransform(deltas, reference=reference)
+    np.testing.assert_array_equal(deltas, xfm._deltas)
+    np.testing.assert_array_equal(coords_map + deltas, xfm._field)
 
-    """
-    assert True
+    mapped = xfm.map(coords_xyz)
+    nit_deltas = mapped - coords_xyz
+
+    if ongrid:
+        mapped_image = mapped.reshape(*shape, 3)
+        np.testing.assert_allclose(deltas + coords_map, mapped_image)
+        np.testing.assert_allclose(deltas, nit_deltas.reshape(*shape, 3), atol=1e-4)
+        np.testing.assert_allclose(xfm._field, mapped_image)
+    else:
+        ongrid_xyz = xfm.map(grid_xyz[subsample])
+        assert (
+            (np.linalg.norm(ongrid_xyz - mapped, axis=1) > 2).sum()
+            / ongrid_xyz.shape[0]
+        ) < 0.5
 
 
 def test_map_bspline_vs_displacement(tmp_path, testdata_path):

nitransforms/tests/utils.py

@@ -2,8 +2,10 @@
 
 from pathlib import Path
 import numpy as np
+import nibabel as nb
 
-from .. import linear as nbl
+from nitransforms import linear as nbl
+from nitransforms.base import ImageGrid
 
 
 def assert_affines_by_filename(affine1, affine2):
@@ -26,3 +28,26 @@ def assert_affines_by_filename(affine1, affine2):
         xfm1 = np.loadtxt(str(affine1))
         xfm2 = np.loadtxt(str(affine2))
         assert np.allclose(xfm1, xfm2, atol=1e-04)
+
+
+def get_points(reference_nii, ongrid, npoints=5000, rng=None):
+    """Get points in RAS space."""
+    if rng is None:
+        rng = np.random.default_rng()
+
+    # Get sampling indices
+    shape = reference_nii.shape[:3]
+    ref_affine = reference_nii.affine.copy()
+    reference = ImageGrid(nb.Nifti1Image(np.zeros(shape), ref_affine, None))
+    grid_ijk = reference.ndindex
+    grid_xyz = reference.ras(grid_ijk)
+
+    subsample = rng.choice(grid_ijk.shape[0], npoints)
+    points_ijk = grid_ijk.copy() if ongrid else grid_ijk[subsample]
+    coords_xyz = (
+        grid_xyz
+        if ongrid
+        else reference.ras(points_ijk) + rng.normal(size=points_ijk.shape)
+    )
+
+    return coords_xyz, points_ijk, grid_xyz, shape, ref_affine, reference, subsample