Merge branch 'master' into fix/do-not-overwrite-deltas

Author: oesteban

nitransforms/io/x5.py

@@ -73,11 +73,11 @@ class X5Transform:
     For parametric models it is generally possible to obtain it analytically, so this dataset
     could not be as useful in that case.
     """
-    # additional_parameters: Optional[np.ndarray] = None
-    # AdditionalParameters is empty in the draft spec - ignore for now.
-    # Only documentation ATM is for SubType:
-    # The SubType setting enables setting the additional parameters on a dataset called
-    # "AdditionalParameters" that hangs directly from this transform node.
+    additional_parameters: Optional[np.ndarray] = None
+    """
+    An OPTIONAL field to store additional parameters, depending on the SubType of the
+    transform.
+    """
     array_length: int = 1
     """Undocumented field in the draft to enable a single transform group for 4D transforms."""
 
@@ -130,11 +130,10 @@ def to_filename(fname: str | Path, x5_list: List[X5Transform]):
                 g.create_dataset("Inverse", data=node.inverse)
             if node.jacobian is not None:
                 g.create_dataset("Jacobian", data=node.jacobian)
-            # Disabled until we need SubType and AdditionalParameters
-            # if node.additional_parameters is not None:
-            #     g.create_dataset(
-            #         "AdditionalParameters", data=node.additional_parameters
-            #     )
+            if node.additional_parameters is not None:
+                g.create_dataset(
+                    "AdditionalParameters", data=node.additional_parameters
+                )
     return fname
 
 
@@ -174,6 +173,9 @@ def _read_x5_group(node) -> X5Transform:
         inverse=np.asarray(node["Inverse"]) if "Inverse" in node else None,
         jacobian=np.asarray(node["Jacobian"]) if "Jacobian" in node else None,
         array_length=int(node.attrs.get("ArrayLength", 1)),
+        additional_parameters=np.asarray(node["AdditionalParameters"])
+        if "AdditionalParameters" in node
+        else None,
     )
 
     if "Domain" in node:

nitransforms/nonlinear.py

@@ -7,12 +7,16 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 """Nonlinear transforms."""
+
 import warnings
 from functools import partial
+from collections import namedtuple
 import numpy as np
+import nibabel as nb
 
 from nitransforms import io
 from nitransforms.io.base import _ensure_image
+from nitransforms.io.x5 import from_filename as load_x5
 from nitransforms.interp.bspline import grid_bspline_weights, _cubic_bspline
 from nitransforms.base import (
     TransformBase,
@@ -22,11 +26,17 @@
 )
 from scipy.ndimage import map_coordinates
 
+# Avoids circular imports
+try:
+    from nitransforms._version import __version__
+except ModuleNotFoundError:  # pragma: no cover
+    __version__ = "0+unknown"
+
 
 class DenseFieldTransform(TransformBase):
     """Represents dense field (voxel-wise) transforms."""
 
-    __slots__ = ("_field", "_deltas")
+    __slots__ = ("_field", "_deltas", "_is_deltas")
 
     def __init__(self, field=None, is_deltas=True, reference=None):
         """
@@ -60,14 +70,7 @@ def __init__(self, field=None, is_deltas=True, reference=None):
 
         super().__init__()
 
-        if field is not None:
-            field = _ensure_image(field)
-            self._field = np.squeeze(
-                np.asanyarray(field.dataobj) if hasattr(field, "dataobj") else field
-            )
-        else:
-            self._field = np.zeros((*reference.shape, reference.ndim), dtype="float32")
-            is_deltas = True
+        self._is_deltas = is_deltas
 
         try:
             self.reference = ImageGrid(reference if reference is not None else field)
@@ -78,24 +81,44 @@ def __init__(self, field=None, is_deltas=True, reference=None):
                 else "Reference is not a spatial image"
             )
 
+        fieldshape = (*self.reference.shape, self.reference.ndim)
+        if field is not None:
+            field = _ensure_image(field)
+            self._field = np.squeeze(
+                np.asanyarray(field.dataobj) if hasattr(field, "dataobj") else field
+            )
+            if fieldshape != self._field.shape:
+                raise TransformError(
+                    f"Shape of the field ({'x'.join(str(i) for i in self._field.shape)}) "
+                    f"doesn't match that of the reference({'x'.join(str(i) for i in fieldshape)})"
+                )
+        else:
+            self._field = np.zeros(fieldshape, dtype="float32")
+            self._is_deltas = True
+
         if self._field.shape[-1] != self.ndim:
             raise TransformError(
                 "The number of components of the field (%d) does not match "
                 "the number of dimensions (%d)" % (self._field.shape[-1], self.ndim)
             )
 
-        if is_deltas:
+        if self._is_deltas:
             self._deltas = (
                 self._field.copy()
             )  # IMPORTANT: you don't want to update deltas
             # Convert from displacements (deltas) to deformations fields
             # (just add its origin to each delta vector)
-            self._field += self.reference.ndcoords.T.reshape(self._field.shape)
+            self._field += self.reference.ndcoords.T.reshape(fieldshape)
 
     def __repr__(self):
         """Beautify the python representation."""
         return f"<{self.__class__.__name__}[{self._field.shape[-1]}D] {self._field.shape[:3]}>"
 
+    @property
+    def is_deltas(self):
+        """Check whether this is a displacements (``True``) or a deformation (``False``) field."""
+        return self._is_deltas
+
     @property
     def ndim(self):
         """Get the dimensions of the transform."""
@@ -224,22 +247,60 @@ def __eq__(self, other):
         True
 
         """
-        _eq = np.array_equal(self._field, other._field)
+        _eq = np.allclose(self._field, other._field)
         if _eq and self._reference != other._reference:
             warnings.warn("Fields are equal, but references do not match.")
         return _eq
 
+    def to_x5(self, metadata=None):
+        """Return an :class:`~nitransforms.io.x5.X5Transform` representation."""
+        metadata = {"WrittenBy": f"NiTransforms {__version__}"} | (metadata or {})
+
+        domain = None
+        if (reference := self.reference) is not None:
+            domain = io.x5.X5Domain(
+                grid=True,
+                size=getattr(reference, "shape", (0, 0, 0)),
+                mapping=reference.affine,
+                coordinates="cartesian",
+            )
+
+        kinds = tuple("space" for _ in range(self.ndim)) + ("vector",)
+
+        return io.x5.X5Transform(
+            type="nonlinear",
+            subtype="densefield",
+            representation="displacements" if self.is_deltas else "deformations",
+            metadata=metadata,
+            transform=self._deltas if self.is_deltas else self._field,
+            dimension_kinds=kinds,
+            domain=domain,
+        )
+
     @classmethod
     def from_filename(cls, filename, fmt="X5"):
         _factory = {
             "afni": io.afni.AFNIDisplacementsField,
             "itk": io.itk.ITKDisplacementsField,
             "fsl": io.fsl.FSLDisplacementsField,
+            "X5": None,
         }
-        if fmt not in _factory:
+        fmt = fmt.upper()
+        if fmt not in {k.upper() for k in _factory}:
             raise NotImplementedError(f"Unsupported format <{fmt}>")
 
-        return cls(_factory[fmt].from_filename(filename))
+        if fmt == "X5":
+            x5_xfm = load_x5(filename)[0]
+            Domain = namedtuple("Domain", "affine shape")
+            reference = Domain(x5_xfm.domain.mapping, x5_xfm.domain.size)
+            field = nb.Nifti1Image(x5_xfm.transform, reference.affine)
+            return cls(
+                field,
+                is_deltas=x5_xfm.representation == "displacements",
+                reference=reference,
+            )
+
+        return cls(_factory[fmt.lower()].from_filename(filename))
 
 
 load = DenseFieldTransform.from_filename
@@ -274,6 +335,24 @@ def ndim(self):
         """Get the dimensions of the transform."""
         return self._coeffs.ndim - 1
 
+    @classmethod
+    def from_filename(cls, filename, fmt="X5"):
+        _factory = {
+            "X5": None,
+        }
+        fmt = fmt.upper()
+        if fmt not in {k.upper() for k in _factory}:
+            raise NotImplementedError(f"Unsupported format <{fmt}>")
+
+        x5_xfm = load_x5(filename)[0]
+        Domain = namedtuple("Domain", "affine shape")
+        reference = Domain(x5_xfm.domain.mapping, x5_xfm.domain.size)
+
+        coefficients = nb.Nifti1Image(x5_xfm.transform, x5_xfm.additional_parameters)
+        return cls(coefficients, reference=reference)
+
+        # return cls(_factory[fmt.lower()].from_filename(filename))
+
     def to_field(self, reference=None, dtype="float32"):
         """Generate a displacements deformation field from this B-Spline field."""
         _ref = (
@@ -295,6 +374,32 @@ def to_field(self, reference=None, dtype="float32"):
             field.astype(dtype).reshape(*_ref.shape, -1), reference=_ref
         )
 
+    def to_x5(self, metadata=None):
+        """Return an :class:`~nitransforms.io.x5.X5Transform` representation."""
+        metadata = {"WrittenBy": f"NiTransforms {__version__}"} | (metadata or {})
+
+        domain = None
+        if (reference := self.reference) is not None:
+            domain = io.x5.X5Domain(
+                grid=True,
+                size=getattr(reference, "shape", (0, 0, 0)),
+                mapping=reference.affine,
+                coordinates="cartesian",
+            )
+
+        kinds = tuple("space" for _ in range(self.ndim)) + ("vector",)
+
+        return io.x5.X5Transform(
+            type="nonlinear",
+            subtype="bspline",
+            representation="coefficients",
+            metadata=metadata,
+            transform=self._coeffs,
+            dimension_kinds=kinds,
+            domain=domain,
+            additional_parameters=self._knots.affine,
+        )
+
     def map(self, x, inverse=False):
         r"""
         Apply the transformation to a list of physical coordinate points.

nitransforms/tests/test_nonlinear.py

@@ -14,6 +14,7 @@
     BSplineFieldTransform,
     DenseFieldTransform,
 )
+from nitransforms import io
 from ..io.itk import ITKDisplacementsField
 
 
@@ -119,3 +120,49 @@ def test_bspline(tmp_path, testdata_path):
         ).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)