Icreased testing coverage. Cleaned up code

Author: demianw

nibabel/cifti2/__init__.py

@@ -23,4 +23,4 @@
                      Cifti2MatrixIndicesMap, Cifti2NamedMap, Cifti2Parcel,
                      Cifti2Surface, Cifti2TransformationMatrixVoxelIndicesIJKtoXYZ,
                      Cifti2Vertices, Cifti2Volume, CIFTI_BrainStructures, CIFTI2HeaderError,
-                     Cifti2DenseDataSeries, CIFTI_MODEL_TYPES, load, save)
+                     CIFTI_MODEL_TYPES, load, save)

nibabel/cifti2/cifti2.py

@@ -404,7 +404,7 @@ def __setitem__(self, index, value):
                 value = [int(v) for v in value]
                 if len(value) != 3:
                     raise ValueError('rows are triples of ints')
-                self._indices[index[0]] = value
+                self._indices[index] = value
             except ValueError:
                 raise ValueError('value must be a triple of ints')
         elif len(index) == 2:
@@ -521,8 +521,8 @@ def voxel_indices_ijk(self):
     def voxel_indices_ijk(self, value):
         self._voxel_indices_ijk = _value_if_klass(value, Cifti2VoxelIndicesIJK)
 
-    def add_cifti_vertices(self, vertices):
-        """ Adds a vertices to the Cifti2Parcel
+    def append_cifti_vertices(self, vertices):
+        """ Appends a Cifti2Vertices element to the Cifti2Parcel
 
         Parameters
         ----------
@@ -532,8 +532,8 @@ def add_cifti_vertices(self, vertices):
             raise TypeError("Not a valid Cifti2Vertices instance")
         self.vertices.append(vertices)
 
-    def remove_cifti2_vertices(self, ith):
-        """ Removes the ith vertices element from the Cifti2Parcel """
+    def pop_cifti2_vertices(self, ith):
+        """ Pops the ith vertices element from the Cifti2Parcel """
         self.vertices.pop(ith)
 
     def _to_xml_element(self):
@@ -871,10 +871,10 @@ def metadata(self, meta):
         -------
         None
         """
-        self._meta = _value_if_klass(meta, Cifti2MetaData, False)
+        self._meta = _value_if_klass(meta, Cifti2MetaData, True)
 
     def __setitem__(self, key, value):
-        if not isinstance(mim, Cifti2MatrixIndicesMap):
+        if not isinstance(value, Cifti2MatrixIndicesMap):
             raise TypeError("Not a valid Cifti2MatrixIndicesMap instance")
         self._mims[key] = value
 
@@ -1055,35 +1055,35 @@ def to_file_map(self, file_map=None):
         img.to_file_map(file_map or self.file_map)
 
 
-class Cifti2DenseDataSeriesHeader(Cifti2Header):
-    @classmethod
-    def may_contain_header(klass, binaryblock):
-        from .parse_cifti2_fast import _Cifti2DenseDataSeriesNiftiHeader
-        return _Cifti2DenseDataSeriesNiftiHeader.may_contain_header(binaryblock)
-
-
-class Cifti2DenseDataSeries(Cifti2Image):
-    """Class to handle Dense Data Series
+# class Cifti2DenseDataSeriesHeader(Cifti2Header):
+#    @classmethod
+#    def may_contain_header(klass, binaryblock):
+#        from .parse_cifti2_fast import _Cifti2DenseDataSeriesNiftiHeader
+#        return _Cifti2DenseDataSeriesNiftiHeader.may_contain_header(binaryblock)
 
-    Dense Data Series
-    -----------------
 
-    Intent_code: 3002, NIFTI_INTENT_CONNECTIVITY_DENSE_SERIES
-    Intent_name: ConnDenseSeries
-    File extension: .dtseries.nii
-    AppliesToMatrixDimension 0: series
-    AppliesToMatrixDimension 1: brain models
-
-    This file type represents data points in a series for every vertex and voxel
-    in the mapping.  A row is a complete data series,for a single vertex or
-    voxel in the mapping that applies along the second dimension. A data series
-    is often a timeseries, but it can also represent other data types such as a
-    series of sampling depths along the surface normal from the white to pial
-    surface.  It retains the 't' in dtseries from CIFTI-1 naming conventions.
-    """
-    header_class = Cifti2DenseDataSeriesHeader
-    valid_exts = ('.dtseries.nii',)
-    files_types = (('image', '.dtseries.nii'),)
+# class Cifti2DenseDataSeries(Cifti2Image):
+#    """Class to handle Dense Data Series
+#
+#    Dense Data Series
+#    -----------------
+#
+#    Intent_code: 3002, NIFTI_INTENT_CONNECTIVITY_DENSE_SERIES
+#    Intent_name: ConnDenseSeries
+#    File extension: .dtseries.nii
+#    AppliesToMatrixDimension 0: series
+#    AppliesToMatrixDimension 1: brain models
+#
+#    This file type represents data points in a series for every vertex and voxel
+#    in the mapping.  A row is a complete data series,for a single vertex or
+#    voxel in the mapping that applies along the second dimension. A data series
+#    is often a timeseries, but it can also represent other data types such as a
+#    series of sampling depths along the surface normal from the white to pial
+#    surface.  It retains the 't' in dtseries from CIFTI-1 naming conventions.
+#    """
+#    header_class = Cifti2DenseDataSeriesHeader
+#    valid_exts = ('.dtseries.nii',)
+#    files_types = (('image', '.dtseries.nii'),)
 
 
 def load(filename):

nibabel/cifti2/parse_cifti2_fast.py

@@ -327,7 +327,7 @@ def StartElementHandler(self, name, attrs):
                 raise CIFTI2HeaderError(
                     'BrainStructure for this Vertices element is not valid'
                 )
-            parcel.add_cifti_vertices(vertices)
+            parcel.append_cifti_vertices(vertices)
             self.fsm_state.append('Vertices')
             self.struct_state.append(vertices)
             self.write_to = 'Vertices'
@@ -576,10 +576,10 @@ def pending_data(self):
         return self._char_blocks is not None
 
 
-class _Cifti2DenseDataSeriesNiftiHeader(_Cifti2AsNiftiHeader):
-
-    @classmethod
-    def _valid_intent_code(klass, intent_code):
-        """ Return True if `intent_code` matches our class `klass`
-        """
-        return intent_code == 3002
+# class _Cifti2DenseDataSeriesNiftiHeader(_Cifti2AsNiftiHeader):
+#
+#    @classmethod
+#    def _valid_intent_code(klass, intent_code):
+#        """ Return True if `intent_code` matches our class `klass`
+#        """
+#        return intent_code == 3002

nibabel/cifti2/tests/test_cifti2.py

@@ -22,7 +22,10 @@ def compare_xml_leaf(str1, str2):
     if len(x1) > 0 or len(x2) > 0:
         raise ValueError
 
-    return (x1.tag == x2.tag) and (x1.attrib and x2.attrib)
+    test = (x1.tag == x2.tag) and (x1.attrib == x2.attrib) and (x1.text == x2.text)
+    print((x1.tag, x1.attrib, x1.text))
+    print((x2.tag, x2.attrib, x2.text))
+    return test
 
 def test_cifti2_metadata():
     md = ci.Cifti2MetaData()
@@ -120,11 +123,7 @@ def test_cifti2_label():
 def test_cifti2_parcel():
     pl = ci.Cifti2Parcel()
     assert_raises(ci.CIFTI2HeaderError, pl.to_xml)
-    assert_raises(TypeError, pl.add_cifti_vertices, None)
-
-def test_cifti2_voxelindicesijk():
-    vi = ci.Cifti2VoxelIndicesIJK()
-    assert_raises(ci.CIFTI2HeaderError, vi.to_xml)
+    assert_raises(TypeError, pl.append_cifti_vertices, None)
 
 def test_cifti2_vertices():
     vs = ci.Cifti2Vertices()
@@ -143,10 +142,18 @@ def test_cifti2_vertices():
         '<Vertices BrainStructure="CIFTI_STRUCTURE_OTHER">0 1 2</Vertices>'
     )
 
+    vs[0] = 10
+    assert_equal(vs[0], 10)
+    assert_equal(len(vs), 3)
+
 def test_cifti2_transformationmatrixvoxelindicesijktoxyz():
     tr = ci.Cifti2TransformationMatrixVoxelIndicesIJKtoXYZ()
     assert_raises(ci.CIFTI2HeaderError, tr.to_xml)
 
+def test_cifti2_surface():
+    s = ci.Cifti2Surface()
+    assert_raises(ci.CIFTI2HeaderError, s.to_xml)
+
 def test_cifti2_volume():
     vo = ci.Cifti2Volume()
     assert_raises(ci.CIFTI2HeaderError, vo.to_xml)
@@ -161,8 +168,16 @@ def test_cifti2_vertexindices():
         vi.to_xml().decode('utf-8'),
         '<VertexIndices>0 1 2</VertexIndices>'
     )
+    assert_raises(ValueError, vi.__setitem__, 0, 'a')
+    vi[0] = 10
+    assert_equal(vi[0], 10)
+    assert_equal(len(vi), 3)
+    
+
+def test_cifti2_voxelindicesijk():
+    vi = ci.Cifti2VoxelIndicesIJK()
+    assert_raises(ci.CIFTI2HeaderError, vi.to_xml)
 
-def test_cifti2_cifti2voxelindicesijk():
     vi = ci.Cifti2VoxelIndicesIJK()
     assert_equal(len(vi), 0)
     assert_raises(ci.CIFTI2HeaderError, vi.to_xml)
@@ -177,7 +192,11 @@ def test_cifti2_cifti2voxelindicesijk():
     assert_equal(len(vi), 2)
 
     assert_equal(vi[1], [3, 4, 5])
+    vi[1] = [3, 4, 6]
+    assert_equal(vi[1], [3, 4, 6])
+    assert_raises(ValueError, vi.__setitem__, 1, [2, 3])
     assert_equal(vi[1, 1], 4)
+    assert_raises(ValueError, vi.__setitem__, [1, 1], 'a')
     assert_equal(vi[0, 1:], [1, 2])
     vi[0, 1] = 10
     assert_equal(vi[0, 1], 10)
@@ -190,10 +209,9 @@ def test_cifti2_cifti2voxelindicesijk():
     assert_raises(ValueError, vi.__getitem__, (0, 0, 0))
     assert_raises(ValueError, vi.__setitem__, (0, 0, 0), 0)
 
-
     assert_equal(
         vi.to_xml().decode('utf-8'),
-        '<VoxelIndicesIJK>0 1 2\n3 4 5</VoxelIndicesIJK>'
+        '<VoxelIndicesIJK>0 1 2\n3 4 6</VoxelIndicesIJK>'
     )
 
 def test_matrixindicesmap():
@@ -225,6 +243,13 @@ def test_matrixindicesmap():
 
     assert_raises(ValueError, setattr, mim, 'volume', parcel)
 
+def test_matrix():
+    m = ci.Cifti2Matrix()
+    assert_raises(TypeError, m, setattr, 'metadata', ci.Cifti2Parcel())
+    assert_raises(TypeError, m.__setitem__, 0, ci.Cifti2Parcel())
+    assert_raises(TypeError, m.insert, 0, ci.Cifti2Parcel())
+
+
 def test_underscoring():
     # Pairs taken from inflection tests
     # https://github.com/jpvanhal/inflection/blob/663982e/test_inflection.py#L113-L125

nibabel/imageclasses.py

@@ -9,7 +9,7 @@
 ''' Define supported image classes and names '''
 
 from .analyze import AnalyzeImage
-from .cifti2 import Cifti2Image, Cifti2DenseDataSeries
+from .cifti2 import Cifti2Image
 from .freesurfer import MGHImage
 from .gifti import GiftiImage
 from .minc1 import Minc1Image
@@ -28,7 +28,7 @@
 
 # Ordered by the load/save priority.
 all_image_classes = [Nifti1Pair, Nifti1Image, Nifti2Pair,
-                     Cifti2DenseDataSeries, Cifti2Image, Nifti2Image,  # Cifti2 before Nifti2
+                     Cifti2Image, Nifti2Image,  # Cifti2 before Nifti2
                      Spm2AnalyzeImage, Spm99AnalyzeImage, AnalyzeImage,
                      Minc1Image, Minc2Image, MGHImage,
                      PARRECImage, GiftiImage]