def test_cifti2_vertices():
vs = ci.Cifti2Vertices()
with pytest.raises(ci.Cifti2HeaderError):
vs.to_xml()
vs.brain_structure = 'CIFTI_STRUCTURE_OTHER'
assert vs.to_xml().decode(
'utf-8') == '<Vertices BrainStructure="CIFTI_STRUCTURE_OTHER" />'
assert len(vs) == 0
vs.extend(np.array([0, 1, 2]))
assert len(vs) == 3
with pytest.raises(ValueError):
vs[1] = 'a'
with pytest.raises(ValueError):
vs.insert(1, 'a')
assert vs.to_xml().decode(
'utf-8'
) == '<Vertices BrainStructure="CIFTI_STRUCTURE_OTHER">0 1 2</Vertices>'
vs[0] = 10
assert vs[0] == 10
assert len(vs) == 3
vs = ci.Cifti2Vertices(vertices=[0, 1, 2])
assert len(vs) == 3
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 test_cifti2_vertices():
vs = ci.Cifti2Vertices()
assert_raises(ci.Cifti2HeaderError, vs.to_xml)
vs.brain_structure = 'CIFTI_STRUCTURE_OTHER'
assert_equal(vs.to_xml().decode('utf-8'),
'<Vertices BrainStructure="CIFTI_STRUCTURE_OTHER" />')
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>')
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_parcel():
pl = ci.Cifti2Parcel()
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_parcel():
pl = ci.Cifti2Parcel()
with pytest.raises(ci.Cifti2HeaderError):
pl.to_xml()
with pytest.raises(TypeError):
pl.append_cifti_vertices(None)
with pytest.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 len(pl.vertices) == 0
assert pl.to_xml().decode(
'utf-8'
) == '<Parcel Name="region"><VoxelIndicesIJK>1 2 3</VoxelIndicesIJK></Parcel>'
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 create_parcel(info):
"""Create a list of Cifti2Parcels from a list of ParcelInfo"""
allowed_brain_structures = (Structure.CORTEX_LEFT, Structure.CORTEX_RIGHT,
Structure.CEREBELLUM)
surfaces = []
volume = None
has_surfaces = info.surfaces is not None
has_ijk = info.voxel_ijk is not None
if not has_vertices and not has_ijk:
raise Exception
if has_vertices:
for surface in info.surfaces:
if info.brain_structure not in allowed_brain_structure:
raise Exception
surfaces.append(
ci.Cifti2Vertices(surface.brain_structure, surface.indices))
if has_indices:
volume = ci.Cifti2VoxelIndicesIJK(info.voxel_ijk)
return ci.Cifti2Parcel(info.name, volume, surfaces)
