def test_sanitize():
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.sanitize()
assert_equal(len(list(m.iter())), 1)
assert_equal(
err.getvalue().strip(),
'Warning: section 1 is the only child of section: 0\nIt will be merged '
'with the parent section')
# Checking that sanitize() 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.sanitize()
assert_equal(
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_neurite_wrong_root_point():
'''Test that for 3 points soma, the neurites are attached to first soma point'''
# Not 3-points soma --> OK
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
n = Morphology(os.path.join(_path, 'soma_cylinders.swc'))
assert_equal('', err.getvalue().strip())
assert_equal(len(n.root_sections), 1)
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
n = Morphology(os.path.join(_path, 'neurite_wrong_root_point.swc'))
assert_string_equal(
'''Warning: with a 3 points soma, neurites must be connected to the first soma point:
{}/neurite_wrong_root_point.swc:4:warning
{}/neurite_wrong_root_point.swc:6:warning'''.format(_path, _path),
err.getvalue())
assert_equal(len(n.root_sections), 2)
assert_array_equal(n.root_sections[0].points, [[0, 0, 0], [0, 0, 1]])
with ignored_warning(Warning.wrong_root_point):
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
n = Morphology(
os.path.join(_path, 'neurite_wrong_root_point.swc'))
assert_equal('', err.getvalue().strip())
def test_mitochondria():
morpho = Morphology()
morpho.soma.points = [[0, 0, 0], [1, 1, 1]]
morpho.soma.diameters = [1, 1]
neuronal_section_ids = [0, 0]
relative_pathlengths = np.array([0.5, 0.6], dtype=np.float32)
diameters = [10, 20]
mito_id = morpho.mitochondria.append_root_section(
MitochondriaPointLevel(neuronal_section_ids, relative_pathlengths,
diameters))
mito_id.append_section(
MitochondriaPointLevel([0, 0, 0, 0], [0.6, 0.7, 0.8, 0.9],
[20, 30, 40, 50]))
with setup_tempdir('test_mitochondria') as tmp_folder:
morpho.write(os.path.join(tmp_folder, "test.h5"))
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
morpho.write(os.path.join(tmp_folder, "test.swc"))
assert_string_equal(
err.getvalue(),
"Warning: this cell has mitochondria, they cannot be saved in "
" ASC or SWC format. Please use H5 if you want to save them."
)
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
morpho.write(os.path.join(tmp_folder, "test.asc"))
assert_string_equal(
err.getvalue(),
"Warning: this cell has mitochondria, they cannot be saved in "
" ASC or SWC format. Please use H5 if you want to save them."
)
mito = ImmutMorphology(os.path.join(tmp_folder,
'test.h5')).mitochondria
assert_array_equal(mito.root_sections[0].diameters, diameters)
assert_array_equal(mito.root_sections[0].neurite_section_ids,
neuronal_section_ids)
assert_array_equal(mito.root_sections[0].relative_path_lengths,
relative_pathlengths)
assert_equal(len(mito.root_sections), 1)
mito = Morphology(os.path.join(tmp_folder, 'test.h5')).mitochondria
assert_equal(len(mito.root_sections), 1)
assert_equal(mito.root_sections[0].neurite_section_ids,
neuronal_section_ids)
assert_array_equal(mito.section(0).diameters, diameters)
assert_array_equal(
mito.section(0).neurite_section_ids, neuronal_section_ids)
def test_write_no_soma():
morpho = Morphology()
dendrite = morpho.append_root_section(
PointLevel([[0, 0, 0],
[0, 5, 0]],
[2, 2]),
SectionType.basal_dendrite)
dendrite = morpho.append_root_section(
PointLevel([[0, 1, 0],
[0, 7, 0]],
[2, 2]),
SectionType.basal_dendrite)
with setup_tempdir('test_write_no_soma') as tmp_folder:
for ext in ['asc', 'h5', 'swc']:
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
outfile = os.path.join(tmp_folder, 'tmp.' + ext)
morpho.write(outfile)
assert_equal(err.getvalue().strip(),
'Warning: writing file without a soma')
read = Morphology(outfile)
assert_equal(len(read.soma.points), 0)
assert_equal(len(read.root_sections), 2)
assert_array_equal(read.root_sections[0].points, [[0, 0, 0], [0, 5, 0]])
assert_array_equal(read.root_sections[1].points, [[0, 1, 0], [0, 7, 0]])
def test_nested_single_child():
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
n = Morphology(os.path.join(_path, 'nested_single_children.asc'))
assert_array_equal(
n.root_sections[0].points,
[[0., 0., 0.], [0., 0., 1.], [0., 0., 2.], [0., 0., 3.], [0., 0., 4.]])
def test_write_merge_only_child_asc_h5():
'''The root section has only one child
When writing, children should *not* be merged with their parent section.
Note: See `test_write_merge_only_child_swc` for the SWC case.
'''
morpho = Morphology()
morpho.soma.points = [[0, 0, 0]]
morpho.soma.diameters = [2]
root = morpho.append_root_section(
PointLevel([[0, 0, 0],
[0, 5, 0]],
[2, 2]),
SectionType.basal_dendrite)
child = root.append_section(PointLevel([[0, 5, 0], [0, 6, 0]], [2, 3]))
with setup_tempdir('test_write_merge_only_child') as tmp_folder:
for extension in ['asc', 'h5']:
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
filename = Path(tmp_folder, 'test.{}'.format(extension))
morpho.write(filename)
read = Morphology(filename)
root = read.root_sections[0]
assert_array_equal(root.points,
[[0, 0, 0],
[0, 5, 0]])
assert len(root.children) == 1
def test_empty_neurite():
m = Morphology()
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
root = m.append_root_section(PointLevel(), SectionType.axon)
assert_equal(err.getvalue().strip(),
'Warning: appending empty section with id: 0')
assert_equal(len(m.root_sections), 1)
assert_equal(m.root_sections[0].type, SectionType.axon)
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
root.append_section(PointLevel(), SectionType.axon)
assert_equal(err.getvalue().strip(),
'Warning: appending empty section with id: 1')
def test_single_point_root_section():
m = Morphology()
points = []
diameters = []
# Too hide the warning: appending empty section
with captured_output():
with ostream_redirect(stdout=True, stderr=True):
m.append_root_section(PointLevel(points, diameters),
SectionType(2))
with setup_tempdir('test_single_point_root_section',
no_cleanup=True) as tmp_folder:
assert_raises(
SectionBuilderError, m.write,
os.path.join(tmp_folder, "h5/empty_vasculature.h5"))
m = Morphology()
points = [[1., 1., 1.]]
diameters = [2.]
m.append_root_section(PointLevel(points, diameters), SectionType(2))
with setup_tempdir('test_single_point_root_section',
no_cleanup=True) as tmp_folder:
assert_raises(SectionBuilderError, m.write,
os.path.join(tmp_folder, "h5/empty_vasculature.h5"))
def test_duplicate_different_diameter():
'''Test that starting a child section with a different diamete
work as expected'''
morpho = Morphology()
morpho.soma.points = [[0, 0, 0], [1, 1, 1]]
morpho.soma.diameters = [1, 1]
section = morpho.append_root_section(
PointLevel([[2, 2, 2], [3, 3, 3]], [4, 4]),
SectionType.axon,
)
section.append_section(PointLevel([[3, 3, 3], [4, 4, 4]], [10, 12]))
section.append_section(PointLevel([[3, 3, 3], [5, 5, 5]], [11, 12]))
with setup_tempdir('test_write_duplicate_different_diameter',
no_cleanup=True) as tmp_folder:
for ext in ['asc', 'h5', 'swc']:
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
outfile = os.path.join(tmp_folder, 'tmp.' + ext)
morpho.write(outfile)
read = Morphology(outfile)
assert_equal(len(read.root_sections[0].children), 2)
child1, child2 = read.root_sections[0].children
assert_array_equal(child1.points, [[3, 3, 3], [4, 4, 4]])
assert_array_equal(child2.points, [[3, 3, 3], [5, 5, 5]])
assert_array_equal(child1.diameters, [10, 12])
assert_array_equal(child2.diameters, [11, 12])
def test_write_empty_file():
'''Check that empty morphology are not written to disk'''
with captured_output() as (_, _):
with ostream_redirect(stdout=True, stderr=True):
with setup_tempdir('test_write_empty_file', no_cleanup=True) as tmp_folder:
for ext in ['asc', 'swc', 'h5']:
outname = os.path.join(tmp_folder, 'empty.' + ext)
Morphology().write(outname)
ok_(not os.path.exists(outname))
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_disconnected_neurite():
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
n = Morphology(os.path.join(_path, 'disconnected_neurite.swc'))
assert_equal(
_path + '''/disconnected_neurite.swc:10:warning
Warning: found a disconnected neurite.
Neurites are not supposed to have parentId: -1
(although this is normal if this neuron has no soma)''',
strip_color_codes(err.getvalue().strip()))
def test_no_duplicate():
with captured_output():
with ostream_redirect(stdout=True, stderr=True):
m = Morphology(SIMPLE, options=Option.no_duplicates)
neurite1 = [[[0., 0., 0.], [0, 5, 0]], [[-5, 5, 0]], [[6, 5, 0]]]
neurite2 = [[[0, 0, 0], [0, -4, 0]], [[6, -4, 0]], [[-5, -4, 0]]]
assert_array_equal([section.points.tolist() for section in m.iter()],
neurite1 + neurite2)
# Combining options NO_DUPLICATES and NRN_ORDER
with captured_output():
with ostream_redirect(stdout=True, stderr=True):
m = Morphology(SIMPLE,
options=Option.no_duplicates | Option.nrn_order)
assert_array_equal([section.points.tolist() for section in m.iter()],
neurite2 + neurite1)
def test_no_duplicate():
with captured_output():
with ostream_redirect(stdout=True, stderr=True):
m = Morphology(SIMPLE, options=Option.no_duplicates)
neurite1 = np.array([[0., 0., 0.], [0, 5, 0], [-5, 5, 0], [6, 5, 0]])
neurite2 = np.array([[0, 0, 0], [0, -4, 0], [6, -4, 0], [-5, -4, 0]])
assert_array_equal(np.vstack([section.points for section in m.iter()]),
np.vstack([neurite1, neurite2]))
# Combining options NO_DUPLICATES and NRN_ORDER
with captured_output():
with ostream_redirect(stdout=True, stderr=True):
m = Morphology(SIMPLE,
options=Option.no_duplicates | Option.nrn_order)
assert_array_equal(np.vstack([section.points for section in m.iter()]),
np.vstack([neurite2, neurite1]))
def test_no_soma():
swc_content = '''1 2 0 0 0 3.0 -1
2 2 0 0 0 3.0 1
3 2 0 0 0 3.0 2'''
with captured_output() as (_, err):
with ostream_redirect(
stdout=True,
stderr=True), tmp_swc_file(swc_content) as tmp_file:
n = Morphology(tmp_file.name)
assert ('{}:0:warning\nWarning: no soma found in file'.format(
tmp_file.name) == strip_color_codes(err.getvalue().strip()))
def test_neurite_followed_by_soma():
# Capturing the output to keep the unit test suite stdout clean
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
_test_swc_exception(
'''# An orphan neurite with a soma child
1 3 0 0 1 0.5 -1
2 3 0 0 2 0.5 1
3 3 0 0 3 0.5 2
4 3 0 0 4 0.5 3
5 3 0 0 5 0.5 4
6 1 0 0 0 3.0 5 # <-- soma child''', SomaError,
'Found a soma point with a neurite as parent', ':7:error')
def test_zero_diameter():
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True),\
tmp_swc_file('''1 1 1 0 0 3.0 -1
2 1 2 0 0 3.0 1
3 1 3 0 0 3.0 2
4 3 4 0 0 0.0 1
5 3 5 0 0 3.0 4
''') as tmp_file:
Morphology(tmp_file.name)
assert_string_equal(
f'{tmp_file.name}:4:warning\nWarning: zero diameter in file\n',
err.getvalue())
def test_write_merge_only_child():
'''The root section has only one child
The child should be merged with its parent section
Special care must be given for the potential duplicate point
o
/
/ son 1
root child /
o--------o----------o<
\
\ son 2
\
o
'''
morpho = Morphology()
morpho.soma.points = [[0, 0, 0]]
morpho.soma.diameters = [2]
root = morpho.append_root_section(
PointLevel([[0, 0, 0],
[0, 5, 0]],
[2, 2]),
SectionType.basal_dendrite)
child = root.append_section(PointLevel([[0, 5, 0], [0, 6, 0]], [2, 3]))
son1 = child.append_section(PointLevel([[0, 6, 0], [0, 7, 0]], [2, 3]))
son2 = child.append_section(PointLevel([[0, 6, 0], [4, 5, 6]], [3, 3]))
with setup_tempdir('test_write_merge_only_child') as tmp_folder:
for extension in ['swc', 'asc', 'h5']:
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
filename = os.path.join(tmp_folder, 'test.{}'.format(extension))
morpho.write(filename)
assert_equal(err.getvalue().strip(),
'Warning: section 1 is the only child of section: 0\nIt will be merged with the parent section')
read = Morphology(filename)
root = read.root_sections[0]
assert_array_equal(root.points,
[[0, 0, 0],
[0, 5, 0],
[0, 6, 0]])
assert_equal(len(root.children), 2)
assert_array_equal(root.children[0].points,
[[0, 6, 0], [0, 7, 0]])
assert_array_equal(root.children[1].points,
[[0, 6, 0], [4, 5, 6]])
def test_single_children():
'''Single children are merged with their parent'''
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) ; merged with parent section
(0 -10 0 2) ; merged with parent section
(-3 -10 0 2) ; merged with parent section
(
(-5 -5 5 5)
|
(-6 -6 6 6)
)
)
)
''') as tmp_file:
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
n = Morphology(tmp_file.name)
assert_substring('is the only child of section: 0 starting at:',
err.getvalue().strip())
assert_substring('It will be merged with the parent section',
err.getvalue().strip())
nt.assert_equal(len(n.soma.points), 0)
nt.assert_equal(len(n.soma.points), 0)
assert_equal(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_equal(len(n.root_sections[0].children), 2)
assert_array_equal(n.root_sections[0].children[0].points,
np.array([[-3, -10, 0],
[-5, -5, 5]]))
assert_array_equal(n.root_sections[0].children[1].points,
np.array([[-3, -10, 0],
[-6, -6, 6]]))
def test_append_no_duplicate():
m = Morphology()
section = m.append_root_section(
PointLevel([[1, 2, 3], [4, 5, 6]], [2, 2], [20, 20]), SectionType.axon)
assert_equal(section.id, 0)
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
section.append_section(
PointLevel([[400, 5, 6], [7, 8, 9]], [2, 3], [20, 30]))
assert_equal(
err.getvalue().strip(),
'Warning: while appending section: 1 to parent: 0\n'
'The section first point should be parent section last point: \n'
' : X Y Z Diameter\n'
'parent last point :[4.000000, 5.000000, 6.000000, 2.000000]\n'
'child first point :[400.000000, 5.000000, 6.000000, 2.000000]'
)
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:
n = Morphology(tmp_file.name)
assert_equal(len(n.annotations), 1)
annotation = n.annotations[0]
assert_equal(annotation.type, morphio.AnnotationType.single_child)
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_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 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:
n = Morphology(tmp_file.name)
assert_substring('is the only child of section: 0 starting at:',
err.getvalue().strip())
assert_substring('It will be merged with the parent section',
err.getvalue().strip())
assert_equal(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_equal(len(n.annotations), 1)
annotation = n.annotations[0]
assert_equal(annotation.type, morphio.AnnotationType.single_child)
assert_equal(annotation.line_number, 6)
assert_array_equal(annotation.points, [[3, -10, 0], [0, -10, 0], [-3, -10, 0]])
assert_array_equal(annotation.diameters, [2, 2, 2])
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 test_single_children():
with captured_output() as (_, _):
with ostream_redirect(stdout=True, stderr=True):
neuron = Morphology(H5V1_PATH / 'two_child_unmerged.h5')
assert len(list(neuron.iter())) == 8
def test_single_children():
with captured_output() as (_, _):
with ostream_redirect(stdout=True, stderr=True):
neuron = Morphology(
os.path.join(H5V1_PATH, 'two_child_unmerged.h5'))
assert_equal(len(list(neuron.iter())), 3)
def test_soma_type():
'''The ordering of IDs is not required'''
# 1 point soma
with tmp_swc_file('''1 1 0 0 0 3.0 -1''') as tmp_file:
assert_equal(
Morphology(tmp_file.name).soma_type, SomaType.SOMA_SINGLE_POINT)
# 2 point soma
with tmp_swc_file('''1 1 0 0 0 3.0 -1
2 1 0 0 0 3.0 1''') as tmp_file:
assert_equal(
Morphology(tmp_file.name).soma_type, SomaType.SOMA_UNDEFINED)
# > 3 points soma
with tmp_swc_file('''1 1 0 0 0 3.0 -1
2 1 0 0 0 3.0 1
3 1 0 0 0 3.0 2
4 1 0 0 0 3.0 3
5 1 0 0 0 3.0 4''') as tmp_file:
assert_equal(
Morphology(tmp_file.name).soma_type, SomaType.SOMA_CYLINDERS)
# 3 points soma can be of type SOMA_CYLINDERS or SOMA_NEUROMORPHO_THREE_POINT_CYLINDERS
# depending on the point layout
# SOMA_NEUROMORPHO_THREE_POINT_CYLINDERS are characterized by
# one soma point with 2 children
with tmp_swc_file('''1 1 0 0 0 3.0 -1
2 1 0 -3 0 3.0 1
3 1 0 3 0 3.0 1 # PID is 1''') as tmp_file:
assert_equal(
Morphology(tmp_file.name).soma_type,
SomaType.SOMA_NEUROMORPHO_THREE_POINT_CYLINDERS)
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
with tmp_swc_file('''1 1 0 0 0 3.0 -1
2 1 1 -3 0 3.0 1
3 1 0 0 0 3.0 1 # PID is 1''') as tmp_file:
assert_equal(
Morphology(tmp_file.name).soma_type,
SomaType.SOMA_NEUROMORPHO_THREE_POINT_CYLINDERS)
assert_string_equal(
'''{}:0:warning
Warning: the soma does not conform the three point soma spec
The only valid neuro-morpho soma is:
1 1 x y z r -1
2 1 x (y-r) z r 1
3 1 x (y+r) z r 1
Got:
1 1 0 0 0 3 -1
2 1 1.000000 (exp. 0.000000) -3.000000 0.000000 3.000000 1
3 1 0.000000 0.000000 (exp. 3.000000) 0.000000 3.000000 1'''
.format(tmp_file.name),
err.getvalue(),
)
# If this configuration is not respected -> SOMA_CYLINDERS
with tmp_swc_file('''1 1 0 0 0 3.0 -1
2 1 0 0 0 3.0 1
3 1 0 0 0 3.0 2 # PID is 2''') as tmp_file:
assert_equal(
Morphology(tmp_file.name).soma_type, SomaType.SOMA_CYLINDERS)
