tst: ramping up coverage

nitransforms/base.py

@@ -173,9 +173,11 @@ class TransformBase(object):
 
     __slots__ = ['_reference']
 
-    def __init__(self):
+    def __init__(self, reference=None):
         """Instantiate a transform."""
         self._reference = None
+        if reference:
+            self.reference = reference
 
     def __call__(self, x, inverse=False):
         """Apply y = f(x)."""

nitransforms/linear.py

@@ -55,19 +55,16 @@ def __init__(self, matrix=None, reference=None):
                [0, 0, 0, 1]])
 
         """
-        super().__init__()
-        if matrix is None:
-            matrix = np.eye(4)
-
-        self._matrix = np.array(matrix)
-        if self._matrix.ndim != 2:
-            raise TypeError('Affine should be 2D.')
-
-        if self._matrix.shape[0] != self._matrix.shape[1]:
-            raise TypeError('Matrix is not square.')
+        super().__init__(reference=reference)
+        self._matrix = np.eye(4)
 
-        if reference:
-            self.reference = reference
+        if matrix is not None:
+            matrix = np.array(matrix)
+            if matrix.ndim != 2:
+                raise TypeError('Affine should be 2D.')
+            elif matrix.shape[0] != matrix.shape[1]:
+                raise TypeError('Matrix is not square.')
+            self._matrix = matrix
 
     def __eq__(self, other):
         """
@@ -162,7 +159,7 @@ def to_filename(self, filename, fmt='X5', moving=None):
             # xform info
             lt = io.LinearTransform()
             lt['sigma'] = 1.
-            lt['m_L'] = [self.matrix]
+            lt['m_L'] = self.matrix
             # Just for reference, nitransforms does not write VOX2VOX
             lt['src'] = io.VolumeGeometry.from_image(moving)
             lt['dst'] = io.VolumeGeometry.from_image(self.reference)
@@ -299,7 +296,7 @@ def map(self, x, inverse=False):
 
     def to_filename(self, filename, fmt='X5', moving=None):
         """Store the transform in BIDS-Transforms HDF5 file format (.x5)."""
-        if fmt.lower() in ['itk', 'ants', 'elastix']:
+        if fmt.lower() in ('itk', 'ants', 'elastix'):
             itkobj = io.itk.ITKLinearTransformArray.from_ras(self.matrix)
             itkobj.to_filename(filename)
             return filename
@@ -323,18 +320,19 @@ def to_filename(self, filename, fmt='X5', moving=None):
             fslobj.to_filename(filename)
             return filename
 
-        if fmt.lower() == 'fs':
+        if fmt.lower() in ('fs', 'lta'):
             # xform info
-            lt = io.LinearTransform()
-            lt['sigma'] = 1.
-            lt['m_L'] = self.matrix
-            # Just for reference, nitransforms does not write VOX2VOX
-            lt['src'] = io.VolumeGeometry.from_image(moving)
-            lt['dst'] = io.VolumeGeometry.from_image(self.reference)
             # to make LTA file format
             lta = io.LinearTransformArray()
             lta['type'] = 1  # RAS2RAS
-            lta['xforms'].append(lt)
+            for m in self.matrix:
+                lt = io.LinearTransform()
+                lt['sigma'] = 1.
+                lt['m_L'] = m
+                # Just for reference, nitransforms does not write VOX2VOX
+                lt['src'] = io.VolumeGeometry.from_image(moving)
+                lt['dst'] = io.VolumeGeometry.from_image(self.reference)
+                lta['xforms'].append(lt)
 
             with open(filename, 'w') as f:
                 f.write(lta.to_string())

nitransforms/tests/test_linear.py

@@ -46,15 +46,30 @@ def test_linear_typeerrors(data_path):
         ntl.Affine.from_filename(data_path / 'itktflist.tfm', fmt='itk')
 
 
-def test_loadsave(tmp_path, data_path):
+def test_loadsave_itk(tmp_path, data_path):
     """Test idempotency."""
+    ref_file = data_path / 'someones_anatomy.nii.gz'
     xfm = ntl.load(data_path / 'itktflist2.tfm', fmt='itk')
+    xfm.reference = ref_file
     xfm.to_filename(tmp_path / 'writtenout.tfm', fmt='itk')
 
     assert (data_path / 'itktflist2.tfm').read_text() \
         == (tmp_path / 'writtenout.tfm').read_text()
 
 
+@pytest.mark.xfail(reason="Not fully implemented")
+@pytest.mark.parametrize('fmt', ['itk', 'fsl', 'afni', 'lta'])
+def test_loadsave(tmp_path, data_path, fmt):
+    """Test idempotency."""
+    ref_file = data_path / 'someones_anatomy.nii.gz'
+    xfm = ntl.load(data_path / 'itktflist2.tfm', fmt='itk')
+    xfm.reference = ref_file
+
+    fname = tmp_path / '.'.join(('wrttenout', fmt))
+    xfm.to_filename(fname, fmt=fmt)
+    xfm == ntl.load(fname, fmt=fmt, reference=ref_file)
+
+
 @pytest.mark.xfail(reason="Not fully implemented")
 @pytest.mark.parametrize('image_orientation', ['RAS', 'LAS', 'LPS', 'oblique'])
 @pytest.mark.parametrize('sw_tool', ['itk', 'fsl', 'afni', 'fs'])