enh: remove code that does not pertain to this PR, hit more lines

Author: oesteban

nitransforms/base.py

@@ -443,80 +443,6 @@ def map(self, x, inverse=False):
         return x
 
 
-class TransformMapping(TransformBase):
-    """Implements a four-dimensional series of transforms."""
-
-    __slots__ = ('_transforms', )
-
-    def __init__(self, transforms=None):
-        """Initialize a chain of transforms."""
-        self._transforms = None
-        if transforms is not None:
-            self.transforms = transforms
-
-    def __getitem__(self, i):
-        """
-        Enable indexed access of transform chains.
-
-        Example
-        -------
-        >>> T1 = TransformBase()
-        >>> xfm4d = TransformMapping([T1, TransformBase(), TransformBase()])
-        >>> xfm4d[0] is T1
-        True
-
-        """
-        return self.transforms[i]
-
-    def __len__(self):
-        """Enable using len()."""
-        return len(self.transforms)
-
-    @property
-    def transforms(self):
-        """Get the internal list of transforms."""
-        return self._transforms
-
-    @transforms.setter
-    def transforms(self, value):
-        self._transforms = value
-
-    def append(self, x):
-        """
-        Concatenate one element to the chain.
-
-        Example
-        -------
-        >>> xfm4d = TransformMapping([TransformBase(), TransformBase()])
-        >>> xfm4d.append(TransformBase())
-        >>> len(xfm4d)
-        3
-
-        """
-        self.transforms.append(x)
-
-    def insert(self, i, x):
-        """
-        Insert an item at a given position.
-
-        Example
-        -------
-        >>> xfm4d = TransformMapping([TransformBase(), TransformBase()])
-        >>> xfm4d.insert(1, TransformBase())
-        >>> len(xfm4d)
-        3
-
-        """
-        self.transforms.insert(i, x)
-
-    def map(self, x, inverse=False):
-        """Apply a map of transforms, e.g., :math:`y_t = f_t(x_t)`."""
-        if not self.transforms:
-            raise TransformError('Cannot apply an empty transforms mapping.')
-
-        return [xfm(x, inverse=inverse) for xfm in self.transforms]
-
-
 def _as_homogeneous(xyz, dtype='float32', dim=3):
     """
     Convert 2D and 3D coordinates into homogeneous coordinates.

nitransforms/tests/test_linear.py

@@ -76,13 +76,17 @@ def test_loadsave(tmp_path, data_path, fmt):
     fname = tmp_path / '.'.join(('transform-mapping', fmt))
     xfm.to_filename(fname, fmt=fmt)
     xfm == ntl.load(fname, fmt=fmt, reference=ref_file)
+    xfm.to_filename(fname, fmt=fmt, moving=ref_file)
+    xfm == ntl.load(fname, fmt=fmt, reference=ref_file)
 
     ref_file = data_path / 'someones_anatomy.nii.gz'
     xfm = ntl.load(data_path / 'affine-LAS.itk.tfm', fmt='itk')
     xfm.reference = ref_file
     fname = tmp_path / '.'.join(('single-transform', fmt))
     xfm.to_filename(fname, fmt=fmt)
     xfm == ntl.load(fname, fmt=fmt, reference=ref_file)
+    xfm.to_filename(fname, fmt=fmt, moving=ref_file)
+    xfm == ntl.load(fname, fmt=fmt, reference=ref_file)
 
 
 @pytest.mark.xfail(reason="Not fully implemented")
@@ -185,7 +189,8 @@ def test_LinearTransformsMapping_apply(tmp_path, data_path):
     assert isinstance(hmc, ntl.LinearTransformsMapping)
 
     # Test-case: realing functional data on to sbref
-    nii = hmc.apply(data_path / 'func.nii.gz', order=1)
+    nii = hmc.apply(data_path / 'func.nii.gz', order=1,
+                    reference=data_path / 'sbref.nii.gz')
     assert nii.dataobj.shape[-1] == len(hmc)
 
     # Test-case: write out a fieldmap moved with head
@@ -194,3 +199,9 @@ def test_LinearTransformsMapping_apply(tmp_path, data_path):
         reference=data_path / 'func.nii.gz')
     nii = hmcinv.apply(data_path / 'fmap.nii.gz', order=1)
     assert nii.dataobj.shape[-1] == len(hmc)
+
+    # Ensure a ValueError is issued when trying to do weird stuff
+    hmc = ntl.LinearTransformsMapping(hmc.matrix[:1, ...])
+    with pytest.raises(ValueError):
+        hmc.apply(data_path / 'func.nii.gz', order=1,
+                  reference=data_path / 'sbref.nii.gz')