Changed Cifti2Vertices such that it behaves like a sequence. Added corresponding tests

Author: demianw

nibabel/cifti2/cifti2.py

@@ -439,35 +439,60 @@ def _to_xml_element(self):
         return vox_ind
 
 
-class Cifti2Vertices(xml.XmlSerializable):
+class Cifti2Vertices(xml.XmlSerializable, collections.MutableSequence):
     """Cifti2 vertices - association of brain structure and a list of vertices
 
     "Contains a BrainStructure type and a list of vertex indices within a
     Parcel."
 
     Attribute descriptions are from the CIFTI-2 spec dated 2014-03-01.
+    The class behaves like a list of Vertex indices
+    (which are independent for each surface, and zero-based)
 
     Attributes
     ----------
     brain_structure : str
         A string from the BrainStructure list to identify what surface this
         vertex list is from (usually left cortex, right cortex, or cerebellum).
-    vertices : ndarray shape (N,)
-        Vertex indices (which are independent for each surface, and zero-based)
     """
     def __init__(self, brain_structure=None, vertices=None):
-        self.vertices = vertices
+        self._vertices = []
+        if vertices is not None:
+            self.extend(vertices)
+
         self.brain_structure = brain_structure
 
+    def __len__(self):
+        return len(self._vertices)
+
+    def __delitem__(self, index):
+        del self._vertices[index]
+
+    def __getitem__(self, index):
+        return self._vertices[index]
+
+    def __setitem__(self, index, value):
+        try:
+            value = int(value)
+            self._vertices[index] = value
+        except ValueError:
+            raise ValueError('value must be an int')
+
+    def insert(self, index, value):
+        try:
+            value = int(value)
+            self._vertices.insert(index, value)
+        except ValueError:
+            raise ValueError('value must be an int')
+
     def _to_xml_element(self):
         if self.brain_structure is None:
             raise CIFTI2HeaderError('Vertices element require a BrainStructure')
 
         vertices = xml.Element('Vertices')
         vertices.attrib['BrainStructure'] = str(self.brain_structure)
 
-        if self.vertices is not None:
-            vertices.text = ' '.join(self.vertices.astype(str))
+        vertices.text = ' '.join([str(i) for i in self])
         return vertices
 
 

nibabel/cifti2/parse_cifti2_fast.py

@@ -538,7 +538,7 @@ def flush_chardata(self):
             # conversion to numpy array
             c = BytesIO(data.strip().encode('utf-8'))
             vertices = self.struct_state[-1]
-            vertices.vertices = np.genfromtxt(c, dtype=np.int)
+            vertices.extend(np.genfromtxt(c, dtype=np.int))
             c.close()
 
         elif self.write_to == 'VoxelIndices':

nibabel/cifti2/tests/test_cifti2.py

@@ -134,7 +134,10 @@ def test_cifti2_vertices():
         vs.to_xml().decode('utf-8'),
         '<Vertices BrainStructure="CIFTI_STRUCTURE_OTHER" />'
     )
-    vs.vertices = np.array([0, 1, 2])
+    assert_equal(len(vs), 0)
+    vs.extend(np.array([0, 1, 2]))
+    assert_equal(len(vs), 3)
+
     assert_equal(
         vs.to_xml().decode('utf-8'),
         '<Vertices BrainStructure="CIFTI_STRUCTURE_OTHER">0 1 2</Vertices>'
@@ -159,7 +162,6 @@ def test_cifti2_vertexindices():
         '<VertexIndices>0 1 2</VertexIndices>'
     )
 
-
 def test_cifti2_cifti2voxelindicesijk():
     vi = ci.Cifti2VoxelIndicesIJK()
     assert_equal(len(vi), 0)