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())
mim_none = ci.Cifti2MatrixIndicesMap(None, 'CIFTI_INDEX_TYPE_LABELS')
mim_0 = ci.Cifti2MatrixIndicesMap(0, 'CIFTI_INDEX_TYPE_LABELS')
mim_1 = ci.Cifti2MatrixIndicesMap(1, 'CIFTI_INDEX_TYPE_LABELS')
mim_01 = ci.Cifti2MatrixIndicesMap([0, 1], 'CIFTI_INDEX_TYPE_LABELS')
assert_raises(ci.Cifti2HeaderError, m.insert, 0, mim_none)
assert_equal(m.mapped_indices, [])
h = ci.Cifti2Header(matrix=m)
assert_equal(m.mapped_indices, [])
m.insert(0, mim_0)
assert_equal(h.mapped_indices, [0])
assert_equal(h.number_of_mapped_indices, 1)
assert_raises(ci.Cifti2HeaderError, m.insert, 0, mim_0)
assert_raises(ci.Cifti2HeaderError, m.insert, 0, mim_01)
m[0] = mim_1
assert_equal(list(m.mapped_indices), [1])
m.insert(0, mim_0)
assert_equal(list(sorted(m.mapped_indices)), [0, 1])
assert_equal(h.number_of_mapped_indices, 2)
assert_equal(h.get_index_map(0), mim_0)
assert_equal(h.get_index_map(1), mim_1)
assert_raises(ci.Cifti2HeaderError, h.get_index_map, 2)
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_matrixindicesmap():
mim = ci.Cifti2MatrixIndicesMap(0, 'CIFTI_INDEX_TYPE_LABELS')
volume = ci.Cifti2Volume()
volume2 = ci.Cifti2Volume()
parcel = ci.Cifti2Parcel()
assert_is_none(mim.volume)
mim.append(volume)
mim.append(parcel)
assert_equal(mim.volume, volume)
assert_raises(ci.Cifti2HeaderError, mim.insert, 0, volume)
assert_raises(ci.Cifti2HeaderError, mim.__setitem__, 1, volume)
mim[0] = volume2
assert_equal(mim.volume, volume2)
del mim.volume
assert_is_none(mim.volume)
assert_raises(ValueError, delattr, mim, 'volume')
mim.volume = volume
assert_equal(mim.volume, volume)
mim.volume = volume2
assert_equal(mim.volume, volume2)
assert_raises(ValueError, setattr, mim, 'volume', parcel)
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_matrixindicesmap():
mim = ci.Cifti2MatrixIndicesMap(0, 'CIFTI_INDEX_TYPE_LABELS')
volume = ci.Cifti2Volume()
volume2 = ci.Cifti2Volume()
parcel = ci.Cifti2Parcel()
assert mim.volume is None
mim.append(volume)
mim.append(parcel)
assert mim.volume == volume
with pytest.raises(ci.Cifti2HeaderError):
mim.insert(0, volume)
with pytest.raises(ci.Cifti2HeaderError):
mim[1] = volume
mim[0] = volume2
assert mim.volume == volume2
del mim.volume
assert mim.volume is None
with pytest.raises(ValueError):
del mim.volume
mim.volume = volume
assert mim.volume == volume
mim.volume = volume2
assert mim.volume == volume2
with pytest.raises(ValueError):
mim.volume = parcel
def test_matrix():
m = ci.Cifti2Matrix()
with pytest.raises(ValueError):
m.metadata = ci.Cifti2Parcel()
with pytest.raises(TypeError):
m[0] = ci.Cifti2Parcel()
with pytest.raises(TypeError):
m.insert(0, ci.Cifti2Parcel())
mim_none = ci.Cifti2MatrixIndicesMap(None, 'CIFTI_INDEX_TYPE_LABELS')
mim_0 = ci.Cifti2MatrixIndicesMap(0, 'CIFTI_INDEX_TYPE_LABELS')
mim_1 = ci.Cifti2MatrixIndicesMap(1, 'CIFTI_INDEX_TYPE_LABELS')
mim_01 = ci.Cifti2MatrixIndicesMap([0, 1], 'CIFTI_INDEX_TYPE_LABELS')
with pytest.raises(ci.Cifti2HeaderError):
m.insert(0, mim_none)
assert m.mapped_indices == []
h = ci.Cifti2Header(matrix=m)
assert m.mapped_indices == []
m.insert(0, mim_0)
assert h.mapped_indices == [0]
assert h.number_of_mapped_indices == 1
with pytest.raises(ci.Cifti2HeaderError):
m.insert(0, mim_0)
with pytest.raises(ci.Cifti2HeaderError):
m.insert(0, mim_01)
m[0] = mim_1
assert list(m.mapped_indices) == [1]
m.insert(0, mim_0)
assert list(sorted(m.mapped_indices)) == [0, 1]
assert h.number_of_mapped_indices == 2
assert h.get_index_map(0) == mim_0
assert h.get_index_map(1) == mim_1
with pytest.raises(ci.Cifti2HeaderError):
h.get_index_map(2)
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)
