enh: add parametric test of from/to_ras

Author: oesteban

nitransforms/io/afni.py

@@ -27,7 +27,7 @@ def to_string(self, banner=True):
         return string % self
 
     @classmethod
-    def from_ras(cls, ras, moving, reference):
+    def from_ras(cls, ras, moving=None, reference=None):
         """Create an ITK affine from a nitransform's RAS+ matrix."""
         ras = ras.copy()
         pre = LPS.copy()
@@ -77,7 +77,7 @@ class AFNILinearTransformArray(BaseLinearTransformList):
 
     _inner_type = AFNILinearTransform
 
-    def to_ras(self, moving, reference):
+    def to_ras(self, moving=None, reference=None):
         """Return a nitransforms' internal RAS matrix."""
         return np.stack([xfm.to_ras(moving=moving, reference=reference)
                          for xfm in self.xforms])
@@ -90,7 +90,7 @@ def to_string(self):
         return '\n'.join(strings)
 
     @classmethod
-    def from_ras(cls, ras, moving, reference):
+    def from_ras(cls, ras, moving=None, reference=None):
         """Create an ITK affine from a nitransform's RAS+ matrix."""
         _self = cls()
         _self.xforms = [cls._inner_type.from_ras(

nitransforms/io/base.py

@@ -64,7 +64,7 @@ def to_filename(self, filename):
         with open(str(filename), 'w') as f:
             f.write(self.to_string())
 
-    def to_ras(self):
+    def to_ras(self, moving=None, reference=None):
         """Return a nitransforms internal RAS+ matrix."""
         raise NotImplementedError
 
@@ -126,7 +126,7 @@ def to_filename(self, filename):
         with open(str(filename), 'w') as f:
             f.write(self.to_string())
 
-    def to_ras(self, moving, reference):
+    def to_ras(self, moving=None, reference=None):
         """Return a nitransforms' internal RAS matrix."""
         raise NotImplementedError
 
@@ -147,7 +147,7 @@ def from_fileobj(cls, fileobj, check=True):
         return cls.from_string(fileobj.read())
 
     @classmethod
-    def from_ras(cls, ras, moving, reference):
+    def from_ras(cls, ras, moving=None, reference=None):
         """Create an ITK affine from a nitransform's RAS+ matrix."""
         raise NotImplementedError
 

nitransforms/io/fsl.py

@@ -19,7 +19,7 @@ def to_string(self):
         return self.__str__()
 
     @classmethod
-    def from_ras(cls, ras, moving, reference):
+    def from_ras(cls, ras, moving=None, reference=None):
         """Create an ITK affine from a nitransform's RAS+ matrix."""
         # Adjust for reference image offset and orientation
         refswp, refspc = _fsl_aff_adapt(reference)
@@ -64,7 +64,7 @@ def to_filename(self, filename):
             with open('%s.%03d' % (filename, i), 'w') as f:
                 f.write(xfm.to_string())
 
-    def to_ras(self, moving, reference):
+    def to_ras(self, moving=None, reference=None):
         """Return a nitransforms' internal RAS matrix."""
         return np.stack([xfm.to_ras(moving=moving, reference=reference)
                          for xfm in self.xforms])
@@ -79,7 +79,7 @@ def from_fileobj(cls, fileobj, check=True):
         return cls.from_string(fileobj.read())
 
     @classmethod
-    def from_ras(cls, ras, moving, reference):
+    def from_ras(cls, ras, moving=None, reference=None):
         """Create an ITK affine from a nitransform's RAS+ matrix."""
         _self = cls()
         _self.xforms = [cls._inner_type.from_ras(

nitransforms/io/itk.py

@@ -60,7 +60,7 @@ def to_filename(self, filename):
         with open(str(filename), 'w') as f:
             f.write(self.to_string())
 
-    def to_ras(self):
+    def to_ras(self, moving=None, reference=None):
         """Return a nitransforms internal RAS+ matrix."""
         sa = self.structarr
         matrix = sa['parameters']
@@ -108,7 +108,7 @@ def from_matlab_dict(cls, mdict, index=0):
         return tf
 
     @classmethod
-    def from_ras(cls, ras, index=0):
+    def from_ras(cls, ras, index=0, moving=None, reference=None):
         """Create an ITK affine from a nitransform's RAS+ matrix."""
         tf = cls()
         sa = tf.structarr
@@ -163,7 +163,7 @@ def to_filename(self, filename):
         with open(str(filename), 'w') as f:
             f.write(self.to_string())
 
-    def to_ras(self):
+    def to_ras(self, moving=None, reference=None):
         """Return a nitransforms' internal RAS matrix."""
         return np.stack([xfm.to_ras() for xfm in self.xforms])
 
@@ -199,10 +199,10 @@ def from_fileobj(cls, fileobj, check=True):
         return cls.from_string(fileobj.read())
 
     @classmethod
-    def from_ras(cls, ras):
+    def from_ras(cls, ras, moving=None, reference=None):
         """Create an ITK affine from a nitransform's RAS+ matrix."""
         _self = cls()
-        _self.xforms = [cls._inner_type.from_ras(ras[i, ...], i)
+        _self.xforms = [cls._inner_type.from_ras(ras[i, ...], index=i)
                         for i in range(ras.shape[0])]
         return _self
 

nitransforms/io/lta.py

@@ -159,7 +159,7 @@ def set_type(self, new_type):
             )
         )
 
-    def to_ras(self):
+    def to_ras(self, moving=None, reference=None):
         """Return a nitransforms internal RAS+ matrix."""
         self.set_type(1)
         return self.structarr['m_L']

nitransforms/tests/test_io.py

@@ -94,20 +94,26 @@ def test_LT_conversions(data_path):
     assert np.allclose(r2r_m, v2v_m, atol=1e-05)
 
 
-@pytest.mark.xfail(raises=FileNotFoundError)
+@pytest.mark.xfail(raises=(FileNotFoundError, NotImplementedError))
 @pytest.mark.parametrize('image_orientation', [
     'RAS', 'LAS', 'LPS', 'oblique',
 ])
 @pytest.mark.parametrize('sw', ['afni', 'fsl', 'fs', 'itk'])
-def test_Linear_common(tmpdir, data_path, sw, image_orientation):
+def test_Linear_common(tmpdir, data_path, sw, image_orientation,
+                       get_testdata):
     tmpdir.chdir()
 
+    moving = get_testdata[image_orientation]
+    reference = get_testdata[image_orientation]
+
     ext = ''
     if sw == 'afni':
         factory = afni.AFNILinearTransform
     elif sw == 'fsl':
         factory = fsl.FSLLinearTransform
     elif sw == 'itk':
+        reference = None
+        moving = None
         ext = '.tfm'
         factory = itk.ITKLinearTransform
     elif sw == 'fs':
@@ -125,9 +131,10 @@ def test_Linear_common(tmpdir, data_path, sw, image_orientation):
     xfm.to_filename(fname)
     assert filecmp.cmp(fname, str((data_path / fname).resolve()))
 
-    # Generate test transform
-    # T = from_matvec(euler2mat(x=0.9, y=0.001, z=0.001), [4.0, 2.0, -1.0])
     # Test from_ras
+    RAS = from_matvec(euler2mat(x=0.9, y=0.001, z=0.001), [4.0, 2.0, -1.0])
+    xfm = factory.from_ras(RAS, reference=reference, moving=moving)
+    assert np.allclose(xfm.to_ras(reference=reference, moving=moving), RAS)
 
 
 def test_ITKLinearTransform(tmpdir, data_path):
@@ -156,6 +163,7 @@ def test_ITKLinearTransform(tmpdir, data_path):
     rasmat = from_matvec(euler2mat(x=0.9, y=0.001, z=0.001), [4.0, 2.0, -1.0])
     itkxfm = itk.ITKLinearTransform.from_ras(rasmat)
     assert np.allclose(itkxfm['parameters'], ITK_MAT * rasmat)
+    assert np.allclose(itkxfm.to_ras(), rasmat)
 
 
 def test_ITKLinearTransformArray(tmpdir, data_path):