a fix for internal variable name and more tests

Author: satra

nibabel/__init__.py

@@ -51,6 +51,7 @@
 from .nifti2 import Nifti2Header, Nifti2Image, Nifti2Pair
 from .minc1 import Minc1Image
 from .minc2 import Minc2Image
+from .cifti2 import Cifti2Header, Cifti2Image
 # Deprecated backwards compatiblity for MINC1
 from .deprecated import ModuleProxy as _ModuleProxy
 minc = _ModuleProxy('nibabel.minc')

nibabel/cifti2/cifti2.py

@@ -603,8 +603,12 @@ class Cifti2Parcel(xml.XmlSerializable):
     """
     def __init__(self, name=None, voxel_indices_ijk=None, vertices=None):
         self.name = name
-        self.voxel_indices_ijk = voxel_indices_ijk
+        self._voxel_indices_ijk = voxel_indices_ijk
         self.vertices = vertices if vertices is not None else []
+        for val in self.vertices:
+            if not isinstance(val, Cifti2Vertices):
+                raise ValueError(('Cifti2Parcel vertices must be instances of '
+                                  'Cifti2Vertices'))
 
     @property
     def voxel_indices_ijk(self):

nibabel/cifti2/tests/test_cifti2.py

@@ -7,7 +7,7 @@
 
 from nibabel import cifti2 as ci
 from nibabel.nifti2 import Nifti2Header
-from nibabel.cifti2.cifti2 import _float_01
+from nibabel.cifti2.cifti2 import _float_01, _value_if_klass, Cifti2HeaderError
 
 from nose.tools import assert_true, assert_equal, assert_raises, assert_is_none
 
@@ -26,6 +26,12 @@ def compare_xml_leaf(str1, str2):
     return test
 
 
+def test_value_if_klass():
+    assert_equal(_value_if_klass(None, list), None)
+    assert_equal(_value_if_klass([1], list), [1])
+    assert_raises(ValueError, _value_if_klass, 1, list)
+
+
 def test_cifti2_metadata():
     md = ci.Cifti2MetaData(metadata={'a': 'aval'})
     assert_equal(len(md), 1)
@@ -83,6 +89,7 @@ def test_cifti2_labeltable():
     lt = ci.Cifti2LabelTable()
     assert_equal(len(lt), 0)
     assert_raises(ci.Cifti2HeaderError, lt.to_xml)
+    assert_raises(ci.Cifti2HeaderError, lt._to_xml_element)
 
     label = ci.Cifti2Label(label='Test', key=0)
     lt[0] = label
@@ -146,6 +153,17 @@ def test_cifti2_parcel():
     assert_raises(ci.Cifti2HeaderError, pl.to_xml)
     assert_raises(TypeError, pl.append_cifti_vertices, None)
 
+    assert_raises(ValueError, ci.Cifti2Parcel, **{'vertices': [1, 2, 3]})
+    pl = ci.Cifti2Parcel(name='region',
+                         voxel_indices_ijk=ci.Cifti2VoxelIndicesIJK([[1, 2, 3]]),
+                         vertices=[ci.Cifti2Vertices([0, 1, 2])])
+    pl.pop_cifti2_vertices(0)
+    assert_equal(len(pl.vertices), 0)
+    assert_equal(
+        pl.to_xml().decode('utf-8'),
+        '<Parcel Name="region"><VoxelIndicesIJK>1 2 3</VoxelIndicesIJK></Parcel>'
+    )
+
 
 def test_cifti2_vertices():
     vs = ci.Cifti2Vertices()
@@ -158,7 +176,8 @@ def test_cifti2_vertices():
     assert_equal(len(vs), 0)
     vs.extend(np.array([0, 1, 2]))
     assert_equal(len(vs), 3)
-
+    assert_raises(ValueError, vs.__setitem__, 1, 'a')
+    assert_raises(ValueError, vs.insert, 1, 'a')
     assert_equal(
         vs.to_xml().decode('utf-8'),
         '<Vertices BrainStructure="CIFTI_STRUCTURE_OTHER">0 1 2</Vertices>'
@@ -167,6 +186,8 @@ def test_cifti2_vertices():
     vs[0] = 10
     assert_equal(vs[0], 10)
     assert_equal(len(vs), 3)
+    vs = ci.Cifti2Vertices(vertices=[0, 1, 2])
+    assert_equal(len(vs), 3)
 
 
 def test_cifti2_transformationmatrixvoxelindicesijktoxyz():
@@ -220,6 +241,8 @@ def test_cifti2_voxelindicesijk():
     assert_equal(vi[1], [3, 4, 5])
     vi[1] = [3, 4, 6]
     assert_equal(vi[1], [3, 4, 6])
+    assert_raises(ValueError, vi.__setitem__, 'a', [1, 2, 3])
+    assert_raises(TypeError, vi.__setitem__, [1, 2], [1, 2, 3])
     assert_raises(ValueError, vi.__setitem__, 1, [2, 3])
     assert_equal(vi[1, 1], 4)
     assert_raises(ValueError, vi.__setitem__, [1, 1], 'a')
@@ -239,6 +262,9 @@ def test_cifti2_voxelindicesijk():
         vi.to_xml().decode('utf-8'),
         '<VoxelIndicesIJK>0 1 2\n3 4 6</VoxelIndicesIJK>'
     )
+    assert_raises(TypeError, ci.Cifti2VoxelIndicesIJK, [0, 1])
+    vi = ci.Cifti2VoxelIndicesIJK([[1, 2, 3]])
+    assert_equal(len(vi), 1)
 
 
 def test_matrixindicesmap():

setup.py

@@ -108,7 +108,6 @@ def main(**extra_args):
                            pjoin('externals', 'tests', 'data', '*'),
                            pjoin('nicom', 'tests', 'data', '*'),
                            pjoin('gifti', 'tests', 'data', '*'),
-                           pjoin('cifti2', 'tests', 'data', '*'),
                            pjoin('streamlines', 'tests', 'data', '*'),
                           ]},
           scripts      = [pjoin('bin', 'parrec2nii'),