def test_remove_unifurcations():
m = Morphology()
section = m.append_root_section(
PointLevel([[1, 0, 0], [2, 0, 0]], [2, 2], [20, 20]), SectionType.axon)
section.append_section(PointLevel([[2, 0, 0], [3, 0, 0]], [2, 2],
[20, 20]))
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
m.remove_unifurcations()
assert len(list(m.iter())) == 1
assert (
err.getvalue().strip() ==
'Warning: section 1 is the only child of section: 0\nIt will be merged '
'with the parent section')
# Checking that remove_unifurcations() issues a warning on missing duplicate
m = Morphology()
section = m.append_root_section(
PointLevel([[1, 0, 0], [2, 0, 0]], [2, 2], [20, 20]), SectionType.axon)
section.append_section(PointLevel([[2, 0, 0], [3, 0, 0]], [2, 2],
[20, 20]))
with captured_output() as (_, err):
with ostream_redirect():
section.append_section(
PointLevel([[2, 1, 0], [2, 0, 0]], [2, 2], [20, 20]))
with captured_output() as (_, err):
with ostream_redirect():
m.remove_unifurcations()
assert (
err.getvalue().strip() ==
'Warning: while appending section: 2 to parent: 0\nThe section first point should be parent section last point: \n : X Y Z Diameter\nparent last point :[2.000000, 0.000000, 0.000000, 2.000000]\nchild first point :[2.000000, 1.000000, 0.000000, 2.000000]'
)
def test_nested_single_child():
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
n = Morphology(DATA_DIR / 'nested_single_children.asc')
n.remove_unifurcations()
assert_array_equal(
n.root_sections[0].points,
[[0., 0., 0.], [0., 0., 1.], [0., 0., 2.], [0., 0., 3.], [0., 0., 4.]])
assert_array_equal(n.root_sections[0].diameters,
np.array([8, 7, 6, 5, 4], dtype=np.float32))
def test_empty_sibling():
'''The empty sibling will be removed and the single child will be merged
with its parent'''
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
with tmp_asc_file('''((Dendrite)
(3 -4 0 10)
(3 -6 0 9)
(3 -8 0 8)
(3 -10 0 7)
(
(3 -10 0 6)
(0 -10 0 5)
(-3 -10 0 4)
| ; <-- empty sibling but still works !
)
)
''') as tmp_file:
n = Morphology(tmp_file.name)
n.remove_unifurcations()
assert_substring('is the only child of section: 0',
err.getvalue().strip())
assert_substring('It will be merged with the parent section',
err.getvalue().strip())
assert len(n.root_sections) == 1
assert_array_equal(
n.root_sections[0].points,
np.array([[3, -4, 0], [3, -6, 0], [3, -8, 0], [3, -10, 0], [0, -10, 0],
[-3, -10, 0]],
dtype=np.float32))
assert_array_equal(n.root_sections[0].diameters,
np.array([10, 9, 8, 7, 5, 4], dtype=np.float32))
assert len(n.annotations) == 1
annotation = n.annotations[0]
assert annotation.type == morphio.AnnotationType.single_child
assert annotation.line_number == -1
assert_array_equal(annotation.points,
[[3, -10, 0], [0, -10, 0], [-3, -10, 0]])
assert_array_equal(annotation.diameters, [6, 5, 4])
def test_annotation():
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
with tmp_asc_file("""((Dendrite)
(3 -4 0 2)
(3 -6 0 2)
(3 -8 0 2)
(3 -10 0 2)
(
(3 -10 0 2)
(0 -10 0 2)
(-3 -10 0 2)
| ; <-- empty sibling but still works !
)
)
""") as tmp_file:
cell = Morphology(tmp_file.name)
cell.remove_unifurcations()
for n in (cell, cell.as_immutable(), cell.as_immutable().as_mutable()):
assert len(n.annotations) == 1
annotation = n.annotations[0]
assert annotation.type == morphio.AnnotationType.single_child
def sanitize(input_neuron, output_path):
'''Sanitize one morphology.
- ensures it can be loaded with MorphIO
- raises if the morphology has no soma or of invalid format
- removes unifurcations
- set negative diameters to zero
- raises if the morphology has a neurite whose type changes along the way
- removes segments with near zero lengths (shorter than 1e-4)
Args:
input_neuron (str|pathlib.Path|morphio.Morphology|morphio.mut.Morphology): input neuron
output_path (str|pathlib.Path): output name
'''
neuron = Morphology(input_neuron)
if neuron.soma.type == SomaType.SOMA_UNDEFINED: # pylint: disable=no-member
raise CorruptedMorphology(
'{} has an invalid or no soma'.format(input_neuron))
neuron.remove_unifurcations()
for section in neuron.iter():
section.diameters = np.clip(section.diameters, 0, None)
for root in neuron.root_sections: # pylint: disable=not-an-iterable
for section in root.iter():
if section.type != root.type:
raise CorruptedMorphology(
f'{input_neuron} has a neurite whose type changes along '
'the way\n'
f'Child section (id: {section.id}) has a different type '
f'({section.type}) than its parent (id: '
f'{section.parent.id}) (type: {section.parent.type})')
fix_non_zero_segments(neuron).write(str(output_path))
def convert(input_file,
outputfile,
recenter=False,
nrn_order=False,
single_point_soma=False,
sanitize=False):
'''Run the appropriate converter
Args:
input_file(str): path to input file
outputfile(str): path to output file
recenter(bool): whether to recenter the morphology based on the
center of gravity of the soma
nrn_order(bool): whether to traverse the neuron in the NEURON fashion
single_point_soma(bool): For SWC only
sanitize(bool): whether to sanitize the morphology
'''
kwargs = {}
if nrn_order:
kwargs['options'] = Option.nrn_order
neuron = Morphology(input_file, **kwargs)
if sanitize:
neuron.remove_unifurcations()
output_ext = Path(outputfile).suffix
if single_point_soma and output_ext.lower() != '.swc':
raise Exception('Single point soma is only applicable for swc output')
if output_ext.lower() not in (
'.swc',
'.asc',
'.h5',
):
raise Exception('Output file format should be one swc, asc or h5')
output_ext = output_ext[1:] # Remove the dot
try:
converter = {
'swc': from_swc,
'asc': from_h5_or_asc,
'h5': from_h5_or_asc,
}[neuron.version[0]]
except KeyError as e:
raise Exception('No converter for morphology type: {}'.format(
neuron.version)) from e
L.info('Original soma type: %s', neuron.soma_type)
new = converter(neuron, output_ext)
if single_point_soma:
soma_to_single_point(new.soma)
if recenter:
transform.translate(new, -1 * new.soma.center)
try:
new.write(outputfile)
except WriterError as e:
raise MorphToolException('Use `sanitize` option for converting') from e
try:
# pylint: disable=import-outside-toplevel
from morph_tool.neuron_surface import get_NEURON_surface
L.info(
'Soma surface as computed by NEURON:\n'
'before conversion: %s\n'
'after conversion: %s', get_NEURON_surface(input_file),
get_NEURON_surface(outputfile))
except: # noqa pylint: disable=bare-except
L.info(
'Final NEURON soma surface check was skipped probably because BluePyOpt'
' or NEURON is not installed')
