def test_convert_recenter():
with setup_tempdir('test-convert_recenter') as tmp_dir:
simple = os.path.join(DATA, 'simple.swc')
outname = os.path.join(tmp_dir, 'test.swc')
convert(simple, outname, recenter=True)
ok_(not diff(simple, outname)) #simple.swc is already centered
mut = morphio.Morphology(simple).as_mutable()
mut.soma.points = [[1, 1, 1], ]
inname = os.path.join(tmp_dir, 'moved.swc')
mut.write(inname)
convert(inname, outname, recenter=True)
simple = morphio.Morphology(simple)
centered_morph = morphio.Morphology(outname)
ok_(np.all((simple.points - centered_morph.points) == 1))
def test_convert_recenter(tmpdir):
simple = DATA / 'simple.swc'
outname = Path(tmpdir, 'test.swc')
convert(simple, outname, recenter=True)
assert not diff(simple, outname) #simple.swc is already centered
mut = morphio.Morphology(simple).as_mutable()
mut.soma.points = [
[1, 1, 1],
]
inname = Path(tmpdir, 'moved.swc')
mut.write(inname)
convert(inname, outname, recenter=True)
simple = morphio.Morphology(simple)
centered_morph = morphio.Morphology(outname)
assert np.all((simple.points - centered_morph.points) == 1)
def test_convert_sanitize(tmpdir):
# needs to have a complex contour soma
simple = DATA / 'single_child.asc'
outname = Path(tmpdir, 'single_child.swc')
with pytest.raises(MorphToolException,
match='Use `sanitize` option for converting'):
convert(simple, outname, single_point_soma=True)
convert(simple, outname, single_point_soma=True, sanitize=True)
m = morphio.Morphology(outname)
assert len(m.sections) == 1
def test_convert_swc_contour_to_sphere(tmpdir):
# needs to have a complex contour soma
simple = DATA / 'tkb061126a4_ch0_cc2_h_zk_60x_1.asc'
outname = Path(tmpdir, 'test.swc')
convert(simple, outname, single_point_soma=True)
m = morphio.Morphology(outname)
assert 1 == len(m.soma.points)
assert 1 == len(m.soma.diameters)
#value dumped from NEURON: h.area(0.5, sec=icell.soma[0])
np.testing.assert_approx_equal(m.soma.surface, 476.0504050847511)
def test_neuron_building_consistency__swc():
path = f'{DATA_PATH}/valid/C010398B-P2.CNG.swc'
neuron1 = load_neuron(path)
neuron2 = load_neuron_from_morphio(path)
_assert_neurons_equal(neuron1, neuron2)
neuron2 = load_neuron_from_morphio(morphio.Morphology(path))
_assert_neurons_equal(neuron1, neuron2)
def test_convert_swc_contour_to_sphere():
with setup_tempdir('test_convert_swc_contour_to_sphere') as tmp_dir:
# needs to have a complex contour soma
simple = os.path.join(DATA, 'tkb061126a4_ch0_cc2_h_zk_60x_1.asc')
outname = os.path.join(tmp_dir, 'test.swc')
convert(simple, outname, single_point_soma=True)
m = morphio.Morphology(outname)
assert_equal(1, len(m.soma.points))
assert_equal(1, len(m.soma.diameters))
#value dumped from NEURON: h.area(0.5, sec=icell.soma[0])
np.testing.assert_approx_equal(m.soma.surface, 476.0504050847511)
def test_convert_sanitize():
with setup_tempdir('test_convert_sanitize') as tmp_dir:
# needs to have a complex contour soma
simple = os.path.join(DATA, 'single_child.asc')
outname = os.path.join(tmp_dir, 'single_child.swc')
with assert_raises(MorphToolException) as obj:
convert(simple, outname, single_point_soma=True)
assert_equal('Use `sanitize` option for converting', str(obj.exception))
convert(simple, outname, single_point_soma=True, sanitize=True)
m = morphio.Morphology(outname)
assert_equal(len(m.sections), 1)
def sanitize(input_neuron, output_path):
'''Sanitize one morphology.
- fixes non zero segments
- raises if the morphology has no soma
- raises if the morphology has negative diameters
Args:
input_neuron (str|pathlib.Path|morphio.Morphology|morphio.mut.Morphology): input neuron
output_path (str|pathlib.Path): output name
'''
neuron = morphio.Morphology(input_neuron)
if neuron.soma.type == SomaType.SOMA_UNDEFINED: # pylint: disable=no-member
raise CorruptedMorphology('{} has no soma'.format(input_neuron))
if np.any(neuron.diameters < 0):
raise CorruptedMorphology('{} negative diameters'.format(input_neuron))
fix_non_zero_segments(neuron).write(str(output_path))
def unravel(filename, window_half_length=DEFAULT_WINDOW_HALF_LENGTH):
'''Return an unravelled neuron
Segment are unravelled iteratively
Each segment direction is replaced by the averaged direction in a sliding window
around this segment. And the original segment length is preserved.
The start position of the new segment is the end of the latest unravelled segment
Args:
filename (str): the neuron to unravel
window_half_length (int): the number of segments that defines half of the sliding window
Returns:
a tuple (morphio.mut.Morphology, dict) where first item is the unravelled
morphology and the second one is the mapping of each point coordinate
before and after unravelling
'''
morph = morphio.Morphology(filename)
new_morph = morphio.mut.Morphology(morph) # pylint: disable=no-member
coord_before = np.empty([0, 3])
coord_after = np.empty([0, 3])
for sec, new_section in zip(morph.iter(), new_morph.iter()):
_unravel_section(sec, new_section, window_half_length)
coord_before = np.append(coord_before, sec.points, axis=0)
coord_after = np.append(coord_after, new_section.points, axis=0)
mapping = pd.DataFrame({
'x0': coord_before[:, 0],
'y0': coord_before[:, 1],
'z0': coord_before[:, 2],
'x1': coord_after[:, 0],
'y1': coord_after[:, 1],
'z1': coord_after[:, 2],
})
L.info('Unravel successful for file: %s', filename)
return new_morph, mapping
def unravel(filename,
window_half_length=None,
legacy_behavior=False,
use_path_length=True):
'''Return an unravelled neuron
Segment are unravelled iteratively
Each segment direction is replaced by the averaged direction in a sliding window
around this segment, preserving the original segment length.
The start position of the new segment is the end of the latest unravelled segment
Based initially on:
DOI: 10.7551/mitpress/9780262013277.001.0001
Section: 9.2 Repair of Neuronal Dendrites
Args:
filename (str): the neuron to unravel
window_half_length (int): path length that defines half of the sliding window
legacy_behavior (bool): if yes, when the soma has more than one point, the first point of
the soma is appended to the start of each neurite.
use_path_length (bool): if False, the argument window_half_length will be recasted to an int
and correspond to number of points on each side of the window.
Returns:
a tuple (morphio.mut.Morphology, dict) where first item is the unravelled
morphology and the second one is the mapping of each point coordinate
before and after unravelling
'''
morph = morphio.Morphology(filename, options=morphio.Option.nrn_order)
new_morph = morphio.mut.Morphology(morph, options=morphio.Option.nrn_order) # noqa, pylint: disable=no-member
if window_half_length is None:
window_half_length = DEFAULT_WINDOW_HALF_LENGTH_PATH \
if use_path_length else DEFAULT_WINDOW_HALF_LENGTH
coord_before = np.empty([0, 3])
coord_after = np.empty([0, 3])
for sec, new_section in zip(morph.iter(), new_morph.iter()):
if use_path_length:
_unravel_section_path_length(new_section, window_half_length,
morph.soma, legacy_behavior)
else:
_unravel_section(new_section, int(window_half_length), morph.soma,
legacy_behavior)
coord_before = np.append(coord_before, sec.points, axis=0)
coord_after = np.append(coord_after, new_section.points, axis=0)
if legacy_behavior and len(morph.soma.points) > 1: # pylint: disable=no-member
coord_before = np.vstack((morph.soma.points[0], coord_before)) # noqa, pylint: disable=no-member
mapping = pd.DataFrame({
'x0': coord_before[:, 0],
'y0': coord_before[:, 1],
'z0': coord_before[:, 2],
'x1': coord_after[:, 0],
'y1': coord_after[:, 1],
'z1': coord_after[:, 2],
})
L.debug('Unravel successful for file: %s', filename)
return new_morph, mapping
def _get(self, name, options=None):
filepath = os.path.join(self.base_dir, name + self.file_ext)
if options is None:
return morphio.Morphology(filepath)
else:
return morphio.Morphology(filepath, options)