def to_mapping(self, dim):
"""
Converts the parcels to a MatrixIndicesMap for storage in CIFTI format
Parameters
----------
dim : int
which dimension of the CIFTI vector/matrix is described by this dataset (zero-based)
Returns
-------
cifti2.Cifti2MatrixIndicesMap
"""
mim = cifti2.Cifti2MatrixIndicesMap([dim], 'CIFTI_INDEX_TYPE_PARCELS')
if self.affine is not None:
affine = cifti2.Cifti2TransformationMatrixVoxelIndicesIJKtoXYZ(-3, matrix=self.affine)
mim.volume = cifti2.Cifti2Volume(self.volume_shape, affine)
for name, nvertex in self.nvertices.items():
mim.append(cifti2.Cifti2Surface(name, nvertex))
for name, voxels, vertices in self.arr:
cifti_voxels = cifti2.Cifti2VoxelIndicesIJK(voxels)
element = cifti2.Cifti2Parcel(name, cifti_voxels)
for name, idx_vertices in vertices.items():
element.vertices.append(cifti2.Cifti2Vertices(name, idx_vertices))
mim.append(element)
return mim
def create_parcel_map(applies_to_matrix_dimension):
mapping = ci.Cifti2MatrixIndicesMap(applies_to_matrix_dimension,
'CIFTI_INDEX_TYPE_PARCELS')
for name, elements in parcels:
surfaces = []
volume = None
for element in elements:
if isinstance(element[0], str):
surfaces.append(ci.Cifti2Vertices(element[0], element[1]))
else:
volume = ci.Cifti2VoxelIndicesIJK(element)
mapping.append(ci.Cifti2Parcel(name, volume, surfaces))
mapping.extend([
ci.Cifti2Surface('CIFTI_STRUCTURE_CORTEX_%s' % orientation,
number_of_vertices)
for orientation in ['LEFT', 'RIGHT']
])
mapping.volume = ci.Cifti2Volume(
dimensions,
ci.Cifti2TransformationMatrixVoxelIndicesIJKtoXYZ(-3, affine))
return mapping
def test_cifti2_surface():
s = ci.Cifti2Surface()
assert_raises(ci.Cifti2HeaderError, s.to_xml)
def test_cifti2_surface():
s = ci.Cifti2Surface()
with pytest.raises(ci.Cifti2HeaderError):
s.to_xml()