ENH: Rename resample() with apply()

Closes #7

Author: oesteban

nitransforms/base.py

@@ -131,8 +131,8 @@ def ndim(self):
         """Access the dimensions of the reference space."""
         return self.reference.ndim
 
-    def resample(self, moving, order=3, mode='constant', cval=0.0, prefilter=True,
-                 output_dtype=None):
+    def apply(self, moving, order=3, mode='constant', cval=0.0, prefilter=True,
+              output_dtype=None):
         """
         Resample the moving image in reference space.
 

nitransforms/nonlinear.py

@@ -145,26 +145,3 @@ def map(self, x, inverse=False, index=0):
 #     def _map_voxel(self, index, moving=None):
 #         """Apply ijk' = f_ijk((i, j, k)), equivalent to the above with indexes."""
 #         return tuple(self._moving[index + self.__s])
-
-#     def resample(self, moving, order=3, mode='constant', cval=0.0, prefilter=True,
-#                  output_dtype=None):
-#         """
-#         Resample the ``moving`` image applying the deformation field.
-
-#         Examples
-#         --------
-#         >>> ref = nb.load(os.path.join(datadir, 'someones_anatomy.nii.gz'))
-#         >>> coeffs = np.zeros((6, 6, 6, 3))
-#         >>> coeffs[2, 2, 2, ...] = [10.0, -20.0, 0]
-#         >>> aff = ref.affine
-#         >>> aff[:3, :3] = aff[:3, :3].dot(np.eye(3) * np.array(
-#         ...     ref.header.get_zooms()[:3]) / 6.0
-#         ... )
-#         >>> coeffsimg = nb.Nifti1Image(coeffs, ref.affine, ref.header)
-#         >>> xfm = BSplineFieldTransform(ref, coeffsimg)  # doctest: +SKIP
-#         >>> new = xfm.resample(ref)  # doctest: +SKIP
-
-#         """
-#         self._cache_moving()
-#         return super(BSplineFieldTransform, self).resample(
-#             moving, order=order, mode=mode, cval=cval, prefilter=prefilter)

nitransforms/tests/test_base.py

@@ -62,7 +62,7 @@ def _to_hdf5(klass, x5_root):
     xfm = TransformBase()
     xfm.reference = fname
     assert xfm.ndim == 3
-    moved = xfm.resample(fname, order=0)
+    moved = xfm.apply(fname, order=0)
     assert np.all(nb.load(fname).get_fdata() == moved.get_fdata())
 
     xfm.to_filename('data.x5')

nitransforms/tests/test_linear.py

@@ -151,7 +151,7 @@ def test_apply_linear_transform(
     assert exit_code == 0
     sw_moved = nb.load('resampled.nii.gz')
 
-    nt_moved = xfm.resample(img, order=0)
+    nt_moved = xfm.apply(img, order=0)
     diff = sw_moved.get_fdata() - nt_moved.get_fdata()
     # A certain tolerance is necessary because of resampling at borders
     assert (np.abs(diff) > 1e-3).sum() / diff.size < TESTS_BORDER_TOLERANCE

nitransforms/tests/test_nonlinear.py

@@ -59,7 +59,7 @@ def test_displacements_field(tmp_path, data_path, sw_tool):
     assert exit_code == 0
     sw_moved = nb.load('resampled.nii.gz')
 
-    nt_moved = xfm.resample(img_fname, order=0)
+    nt_moved = xfm.apply(img_fname, order=0)
     nt_moved.to_filename('nt_resampled.nii.gz')
     diff = sw_moved.get_fdata() - nt_moved.get_fdata()
     # A certain tolerance is necessary because of resampling at borders