ENH: Outsource apply() from transform objects

nitransforms/base.py

@@ -15,7 +15,6 @@
 from nibabel import funcs as _nbfuncs
 from nibabel.nifti1 import intent_codes as INTENT_CODES
 from nibabel.cifti2 import Cifti2Image
-from scipy import ndimage as ndi
 
 EQUALITY_TOL = 1e-5
 
@@ -178,7 +177,10 @@ def __ne__(self, other):
 class TransformBase:
     """Abstract image class to represent transforms."""
 
-    __slots__ = ("_reference", "_ndim",)
+    __slots__ = (
+        "_reference",
+        "_ndim",
+    )
 
     def __init__(self, reference=None):
         """Instantiate a transform."""
@@ -222,101 +224,6 @@ def ndim(self):
         """Access the dimensions of the reference space."""
         raise TypeError("TransformBase has no dimensions")
 
-    def apply(
-        self,
-        spatialimage,
-        reference=None,
-        order=3,
-        mode="constant",
-        cval=0.0,
-        prefilter=True,
-        output_dtype=None,
-    ):
-        """
-        Apply a transformation to an image, resampling on the reference spatial object.
-
-        Parameters
-        ----------
-        spatialimage : `spatialimage`
-            The image object containing the data to be resampled in reference
-            space
-        reference : spatial object, optional
-            The image, surface, or combination thereof containing the coordinates
-            of samples that will be sampled.
-        order : int, optional
-            The order of the spline interpolation, default is 3.
-            The order has to be in the range 0-5.
-        mode : {'constant', 'reflect', 'nearest', 'mirror', 'wrap'}, optional
-            Determines how the input image is extended when the resamplings overflows
-            a border. Default is 'constant'.
-        cval : float, optional
-            Constant value for ``mode='constant'``. Default is 0.0.
-        prefilter: bool, optional
-            Determines if the image's data array is prefiltered with
-            a spline filter before interpolation. The default is ``True``,
-            which will create a temporary *float64* array of filtered values
-            if *order > 1*. If setting this to ``False``, the output will be
-            slightly blurred if *order > 1*, unless the input is prefiltered,
-            i.e. it is the result of calling the spline filter on the original
-            input.
-        output_dtype: dtype specifier, optional
-            The dtype of the returned array or image, if specified.
-            If ``None``, the default behavior is to use the effective dtype of
-            the input image. If slope and/or intercept are defined, the effective
-            dtype is float64, otherwise it is equivalent to the input image's
-            ``get_data_dtype()`` (on-disk type).
-            If ``reference`` is defined, then the return value is an image, with
-            a data array of the effective dtype but with the on-disk dtype set to
-            the input image's on-disk dtype.
-
-        Returns
-        -------
-        resampled : `spatialimage` or ndarray
-            The data imaged after resampling to reference space.
-
-        """
-        if reference is not None and isinstance(reference, (str, Path)):
-            reference = _nbload(str(reference))
-
-        _ref = (
-            self.reference if reference is None else SpatialReference.factory(reference)
-        )
-
-        if _ref is None:
-            raise TransformError("Cannot apply transform without reference")
-
-        if isinstance(spatialimage, (str, Path)):
-            spatialimage = _nbload(str(spatialimage))
-
-        data = np.asanyarray(spatialimage.dataobj)
-        targets = ImageGrid(spatialimage).index(  # data should be an image
-            _as_homogeneous(self.map(_ref.ndcoords.T), dim=_ref.ndim)
-        )
-
-        resampled = ndi.map_coordinates(
-            data,
-            targets.T,
-            output=output_dtype,
-            order=order,
-            mode=mode,
-            cval=cval,
-            prefilter=prefilter,
-        )
-
-        if isinstance(_ref, ImageGrid):  # If reference is grid, reshape
-            hdr = None
-            if _ref.header is not None:
-                hdr = _ref.header.copy()
-                hdr.set_data_dtype(output_dtype or spatialimage.get_data_dtype())
-            moved = spatialimage.__class__(
-                resampled.reshape(_ref.shape),
-                _ref.affine,
-                hdr,
-            )
-            return moved
-
-        return resampled
-
     def map(self, x, inverse=False):
         r"""
         Apply :math:`y = f(x)`.
@@ -382,4 +289,8 @@ def _as_homogeneous(xyz, dtype="float32", dim=3):
 
 def _apply_affine(x, affine, dim):
     """Get the image array's indexes corresponding to coordinates."""
-    return affine.dot(_as_homogeneous(x, dim=dim).T)[:dim, ...].T
+    return np.tensordot(
+        affine,
+        _as_homogeneous(x, dim=dim).T,
+        axes=1,
+    )[:dim, ...]

nitransforms/cli.py

@@ -5,6 +5,7 @@
 
 from .linear import load as linload
 from .nonlinear import load as nlinload
+from .resampling import apply
 
 
 def cli_apply(pargs):
@@ -38,7 +39,8 @@ def cli_apply(pargs):
     # ensure a reference is set
     xfm.reference = pargs.ref or pargs.moving
 
-    moved = xfm.apply(
+    moved = apply(
+        xfm,
         pargs.moving,
         order=pargs.order,
         mode=pargs.mode,

nitransforms/linear.py

@@ -10,16 +10,12 @@
 import warnings
 import numpy as np
 from pathlib import Path
-from scipy import ndimage as ndi
 
-from nibabel.loadsave import load as _nbload
 from nibabel.affines import from_matvec
-from nibabel.arrayproxy import get_obj_dtype
 
 from nitransforms.base import (
     ImageGrid,
     TransformBase,
-    SpatialReference,
     _as_homogeneous,
     EQUALITY_TOL,
 )
@@ -113,6 +109,10 @@ def __invert__(self):
         """
         return self.__class__(self._inverse)
 
+    def __len__(self):
+        """Enable using len()."""
+        return 1 if self._matrix.ndim == 2 else len(self._matrix)
+
     def __matmul__(self, b):
         """
         Compose two Affines.
@@ -330,10 +330,6 @@ def __getitem__(self, i):
         """Enable indexed access to the series of matrices."""
         return Affine(self.matrix[i, ...], reference=self._reference)
 
-    def __len__(self):
-        """Enable using len()."""
-        return len(self._matrix)
-
     def map(self, x, inverse=False):
         r"""
         Apply :math:`y = f(x)`.
@@ -402,119 +398,6 @@ def to_filename(self, filename, fmt="X5", moving=None):
             ).to_filename(filename)
         return filename
 
-    def apply(
-        self,
-        spatialimage,
-        reference=None,
-        order=3,
-        mode="constant",
-        cval=0.0,
-        prefilter=True,
-        output_dtype=None,
-    ):
-        """
-        Apply a transformation to an image, resampling on the reference spatial object.
-
-        Parameters
-        ----------
-        spatialimage : `spatialimage`
-            The image object containing the data to be resampled in reference
-            space
-        reference : spatial object, optional
-            The image, surface, or combination thereof containing the coordinates
-            of samples that will be sampled.
-        order : int, optional
-            The order of the spline interpolation, default is 3.
-            The order has to be in the range 0-5.
-        mode : {"constant", "reflect", "nearest", "mirror", "wrap"}, optional
-            Determines how the input image is extended when the resamplings overflows
-            a border. Default is "constant".
-        cval : float, optional
-            Constant value for ``mode="constant"``. Default is 0.0.
-        prefilter: bool, optional
-            Determines if the image's data array is prefiltered with
-            a spline filter before interpolation. The default is ``True``,
-            which will create a temporary *float64* array of filtered values
-            if *order > 1*. If setting this to ``False``, the output will be
-            slightly blurred if *order > 1*, unless the input is prefiltered,
-            i.e. it is the result of calling the spline filter on the original
-            input.
-
-        Returns
-        -------
-        resampled : `spatialimage` or ndarray
-            The data imaged after resampling to reference space.
-
-        """
-
-        if reference is not None and isinstance(reference, (str, Path)):
-            reference = _nbload(str(reference))
-
-        _ref = (
-            self.reference if reference is None else SpatialReference.factory(reference)
-        )
-
-        if isinstance(spatialimage, (str, Path)):
-            spatialimage = _nbload(str(spatialimage))
-
-        # Avoid opening the data array just yet
-        input_dtype = get_obj_dtype(spatialimage.dataobj)
-        output_dtype = output_dtype or input_dtype
-
-        # Prepare physical coordinates of input (grid, points)
-        xcoords = _ref.ndcoords.astype("f4").T
-
-        # Invert target's (moving) affine once
-        ras2vox = ~Affine(spatialimage.affine)
-
-        if spatialimage.ndim == 4 and (len(self) != spatialimage.shape[-1]):
-            raise ValueError(
-                "Attempting to apply %d transforms on a file with "
-                "%d timepoints" % (len(self), spatialimage.shape[-1])
-            )
-
-        # Order F ensures individual volumes are contiguous in memory
-        # Also matches NIfTI, making final save more efficient
-        resampled = np.zeros(
-            (xcoords.shape[0], len(self)), dtype=output_dtype, order="F"
-        )
-
-        dataobj = (
-            np.asanyarray(spatialimage.dataobj, dtype=input_dtype)
-            if spatialimage.ndim in (2, 3)
-            else None
-        )
-
-        for t, xfm_t in enumerate(self):
-            # Map the input coordinates on to timepoint t of the target (moving)
-            ycoords = xfm_t.map(xcoords)[..., : _ref.ndim]
-
-            # Calculate corresponding voxel coordinates
-            yvoxels = ras2vox.map(ycoords)[..., : _ref.ndim]
-
-            # Interpolate
-            resampled[..., t] = ndi.map_coordinates(
-                (
-                    dataobj
-                    if dataobj is not None
-                    else spatialimage.dataobj[..., t].astype(input_dtype, copy=False)
-                ),
-                yvoxels.T,
-                output=output_dtype,
-                order=order,
-                mode=mode,
-                cval=cval,
-                prefilter=prefilter,
-            )
-
-        if isinstance(_ref, ImageGrid):  # If reference is grid, reshape
-            newdata = resampled.reshape(_ref.shape + (len(self),))
-            moved = spatialimage.__class__(newdata, _ref.affine, spatialimage.header)
-            moved.header.set_data_dtype(output_dtype)
-            return moved
-
-        return resampled
-
 
 def load(filename, fmt=None, reference=None, moving=None):
     """