enh: add test comparing bsplines and displacements fields

Author: oesteban

nitransforms/nonlinear.py

@@ -31,10 +31,21 @@ class DisplacementsFieldTransform(TransformBase):
     __slots__ = ["_field"]
 
     def __init__(self, field, reference=None):
-        """Create a dense deformation field transform."""
+        """
+        Create a dense deformation field transform.
+
+        Example
+        -------
+        >>> DisplacementsFieldTransform(test_dir / "someones_displacement_field.nii.gz")
+        <(57, 67, 56) field of 3D displacements>
+
+        """
         super().__init__()
 
-        self._field = np.asanyarray(field.dataobj) if hasattr(field, "dataobj") else field
+        field = _ensure_image(field)
+        self._field = np.squeeze(
+            np.asanyarray(field.dataobj) if hasattr(field, "dataobj") else field
+        )
         self.reference = reference or field.__class__(
             np.zeros(self._field.shape[:-1]), field.affine, field.header
         )
@@ -46,6 +57,10 @@ def __init__(self, field, reference=None):
                 "the number of dimensions (%d)" % (self._field.shape[-1], ndim)
             )
 
+    def __repr__(self):
+        """Beautify the python representation."""
+        return f"<{self._field.shape[:3]} field of {self._field.shape[-1]}D displacements>"
+
     def map(self, x, inverse=False):
         r"""
         Apply the transformation to a list of physical coordinate points.
@@ -71,15 +86,12 @@ def map(self, x, inverse=False):
 
         Examples
         --------
-        >>> field = np.zeros((10, 10, 10, 3))
-        >>> field[..., 0] = 4.0
-        >>> fieldimg = nb.Nifti1Image(field, np.diag([2., 2., 2., 1.]))
-        >>> xfm = DisplacementsFieldTransform(fieldimg)
-        >>> xfm([4.0, 4.0, 4.0]).tolist()
-        [[8.0, 4.0, 4.0]]
+        >>> xfm = DisplacementsFieldTransform(test_dir / "someones_displacement_field.nii.gz")
+        >>> xfm.map([-6.5, -36., -19.5]).tolist()
+        [[-6.5, -36.475167989730835, -19.5]]
 
-        >>> xfm([[4.0, 4.0, 4.0], [8, 2, 10]]).tolist()
-        [[8.0, 4.0, 4.0], [12.0, 2.0, 10.0]]
+        >>> xfm.map([[-6.5, -36., -19.5], [-1., -41.5, -11.25]]).tolist()
+        [[-6.5, -36.475167989730835, -19.5], [-1.0, -42.038356602191925, -11.25]]
 
         """
         if inverse is True:
@@ -112,26 +124,31 @@ class BSplineFieldTransform(TransformBase):
 
     __slots__ = ['_coeffs', '_knots', '_weights', '_order', '_moving']
 
-    def __init__(self, reference, coefficients, order=3):
+    def __init__(self, coefficients, reference=None, order=3):
         """Create a smooth deformation field using B-Spline basis."""
         super(BSplineFieldTransform, self).__init__()
         self._order = order
-        self.reference = reference
 
         coefficients = _ensure_image(coefficients)
-        if coefficients.shape[-1] != self.ndim:
-            raise ValueError(
-                'Number of components of the coefficients does '
-                'not match the number of dimensions')
 
         self._coeffs = np.asanyarray(coefficients.dataobj)
         self._knots = ImageGrid(four_to_three(coefficients)[0])
         self._weights = None
+        if reference is not None:
+            self.reference = reference
+
+            if coefficients.shape[-1] != self.ndim:
+                raise ValueError(
+                    'Number of components of the coefficients does '
+                    'not match the number of dimensions')
 
-    def to_field(self, reference=None):
+    def to_field(self, reference=None, dtype="float32"):
         """Generate a displacements deformation field from this B-Spline field."""
         reference = _ensure_image(reference)
         _ref = self.reference if reference is None else SpatialReference.factory(reference)
+        if _ref is None:
+            raise ValueError("A reference must be defined")
+
         ndim = self._coeffs.shape[-1]
 
         # If locations to be interpolated are on a grid, use faster tensor-bspline calculation
@@ -143,7 +160,7 @@ def to_field(self, reference=None):
         for d in range(ndim):
             field[:, d] = self._coeffs[..., d].reshape(-1) @ self._weights
 
-        return field.astype("float32")
+        return field.astype(dtype)
 
     def apply(
         self,
@@ -215,23 +232,22 @@ def map(self, x, inverse=False):
 
         Examples
         --------
-        >>> field = np.zeros((10, 10, 10, 3))
-        >>> field[..., 0] = 4.0
-        >>> fieldimg = nb.Nifti1Image(field, np.diag([2., 2., 2., 1.]))
-        >>> xfm = DisplacementsFieldTransform(fieldimg)
-        >>> xfm([4.0, 4.0, 4.0]).tolist()
-        [[8.0, 4.0, 4.0]]
-
-        >>> xfm([[4.0, 4.0, 4.0], [8, 2, 10]]).tolist()
-        [[8.0, 4.0, 4.0], [12.0, 2.0, 10.0]]
+        >>> xfm = BSplineFieldTransform(test_dir / "someones_bspline_coefficients.nii.gz")
+        >>> xfm.reference = test_dir / "someones_anatomy.nii.gz"
+        >>> xfm.map([-6.5, -36., -19.5]).tolist()
+        [[-6.5, -31.476097418406784, -19.5]]
+
+        >>> xfm.map([[-6.5, -36., -19.5], [-1., -41.5, -11.25]]).tolist()
+        [[-6.5, -31.476097418406784, -19.5], [-1.0, -3.8072675377121996, -11.25]]
+
         """
         vfunc = partial(
             _map_xyz,
             reference=self.reference,
             knots=self._knots,
             coeffs=self._coeffs,
         )
-        return [vfunc(_x) for _x in np.atleast_2d(x)]
+        return np.array([vfunc(_x).tolist() for _x in np.atleast_2d(x)])
 
 
 def _map_xyz(x, reference, knots, coeffs):

nitransforms/tests/test_nonlinear.py

@@ -9,7 +9,11 @@
 import numpy as np
 import nibabel as nb
 from ..io.base import TransformFileError
-from ..nonlinear import DisplacementsFieldTransform, load as nlload
+from ..nonlinear import (
+    BSplineFieldTransform,
+    DisplacementsFieldTransform,
+    load as nlload,
+)
 from ..io.itk import ITKDisplacementsField
 
 
@@ -33,21 +37,21 @@
 def test_itk_disp_load(size):
     """Checks field sizes."""
     with pytest.raises(TransformFileError):
-        ITKDisplacementsField.from_image(nb.Nifti1Image(np.zeros(size), None, None))
+        ITKDisplacementsField.from_image(nb.Nifti1Image(np.zeros(size), np.eye(4), None))
 
 
-@pytest.mark.parametrize("size", [(20, 20, 20), (20, 20, 20, 1, 3)])
+@pytest.mark.parametrize("size", [(20, 20, 20), (20, 20, 20, 2, 3)])
 def test_displacements_bad_sizes(size):
     """Checks field sizes."""
     with pytest.raises(ValueError):
-        DisplacementsFieldTransform(nb.Nifti1Image(np.zeros(size), None, None))
+        DisplacementsFieldTransform(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)), None, None)
+            nb.Nifti1Image(np.zeros((20, 20, 20, 1, 3)), np.eye(4), None)
         )
 
     assert field.header.get_intent()[0] == "vector"
@@ -177,3 +181,25 @@ def test_displacements_field2(tmp_path, testdata_path, sw_tool):
     )
     # A certain tolerance is necessary because of resampling at borders
     assert np.sqrt((diff ** 2).mean()) < RMSE_TOL
+
+
+def test_bspline(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)
+    dispxfm = DisplacementsFieldTransform(disp_name)
+
+    out_disp = dispxfm.apply(img_name)
+    out_bspl = bsplxfm.apply(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