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_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_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)