enh: one more test of the itk transforms io

Author: oesteban

nitransforms/io/itk.py

@@ -86,6 +86,16 @@ def from_binary(cls, byte_stream, index=0):
         mdict = _read_mat(byte_stream)
         return cls.from_matlab_dict(mdict, index=index)
 
+    @classmethod
+    def from_filename(cls, filename):
+        """Read the struct from a file given its path."""
+        if str(filename).endswith('.mat'):
+            with open(str(filename), 'rb') as fileobj:
+                return cls.from_binary(fileobj)
+
+        with open(str(filename)) as fileobj:
+            return cls.from_string(fileobj.read())
+
     @classmethod
     def from_fileobj(cls, fileobj, check=True):
         """Read the struct from a file object."""
@@ -184,7 +194,7 @@ def from_binary(cls, byte_stream):
     def from_filename(cls, filename):
         """Read the struct from a file given its path."""
         if str(filename).endswith('.mat'):
-            with open(str(filename), 'b') as f:
+            with open(str(filename), 'rb') as f:
                 return cls.from_binary(f)
 
         with open(str(filename)) as f:

nitransforms/tests/test_io.py

@@ -140,14 +140,19 @@ def test_Linear_common(tmpdir, data_path, sw, image_orientation,
 def test_ITKLinearTransform(tmpdir, data_path):
     tmpdir.chdir()
 
-    matlabfile = str(data_path / 'ds-005_sub-01_from-T1_to-OASIS_affine.mat')
-    mat = loadmat(matlabfile)
-    with open(matlabfile, 'rb') as f:
+    matlabfile = data_path / 'ds-005_sub-01_from-T1_to-OASIS_affine.mat'
+    mat = loadmat(str(matlabfile))
+    with open(str(matlabfile), 'rb') as f:
         itkxfm = itk.ITKLinearTransform.from_fileobj(f)
     assert np.allclose(itkxfm['parameters'][:3, :3].flatten(),
                        mat['AffineTransform_float_3_3'][:-3].flatten())
     assert np.allclose(itkxfm['offset'], mat['fixed'].reshape((3, )))
 
+    itkxfm = itk.ITKLinearTransform.from_filename(matlabfile)
+    assert np.allclose(itkxfm['parameters'][:3, :3].flatten(),
+                       mat['AffineTransform_float_3_3'][:-3].flatten())
+    assert np.allclose(itkxfm['offset'], mat['fixed'].reshape((3, )))
+
     # Test to_filename(textfiles)
     itkxfm.to_filename('textfile.tfm')
     with open('textfile.tfm', 'r') as f:
@@ -174,6 +179,16 @@ def test_ITKLinearTransformArray(tmpdir, data_path):
         f.seek(0)
         itklist = itk.ITKLinearTransformArray.from_fileobj(f)
 
+    itklistb = itk.ITKLinearTransformArray.from_filename(
+        data_path / 'itktflist.tfm')
+    assert itklist['nxforms'] == itklistb['nxforms']
+    assert all([np.allclose(x1['parameters'], x2['parameters'])
+                for x1, x2 in zip(itklist.xforms, itklistb.xforms)])
+
+    tmpdir.join('empty.mat').write('')
+    with pytest.raises(TransformFileError):
+        itklistb.from_filename('empty.mat')
+
     assert itklist['nxforms'] == 9
     assert text == itklist.to_string()
     with pytest.raises(ValueError):