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_sanitize():
with TemporaryDirectory('test-sanitize') as tmp_folder:
output_path = Path(tmp_folder, 'sanitized.asc')
sanitize(Path(PATH, 'simple-with-duplicates.asc'), output_path)
neuron = Morphology(output_path)
assert_equal(len(neuron.root_sections), 1)
assert_array_equal(
neuron.section(0).points,
[[0., 0., 0.], [1., 1., 0.], [2., 0., 0.], [3., 0., 0.]])
for input_morph, expected_exception in [
('no-soma.asc',
'{} has an invalid or no soma'.format(Path(PATH, 'no-soma.asc'))),
('neurite-with-multiple-types.swc',
('{} has a neurite whose type changes along the way\n'
'Child section (id: 5) has a different type (SectionType.basal_dendrite) '
'than its parent (id: 3) (type: SectionType.axon)').format(
Path(PATH, 'neurite-with-multiple-types.swc')))
]:
with assert_raises(CorruptedMorphology) as cm:
sanitize(PATH / input_morph, Path(tmp_folder, 'output.asc'))
assert_equal(str(cm.exception), expected_exception)
out_path = Path(tmp_folder, 'output.asc')
sanitize(PATH / 'negative-diameters.asc', out_path)
assert_equal(next(Morphology(out_path).iter()).diameters, [2, 2, 0, 2])
def test_more_iter():
'''This used to fail at commit f74ce1f56de805ebeb27584051bbbb3a65cd1213'''
m = Morphology(os.path.join(_path, 'simple.asc'))
sections = list(m.iter())
assert_array_equal([s1.id for s1 in sections], [0, 1, 2, 3, 4, 5])
sections = list(m.iter(IterType.breadth_first))
assert_array_equal([s.id for s in sections], [0, 3, 1, 2, 4, 5])
sections = list(m.section(2).iter(IterType.upstream))
assert_array_equal([s.id for s in sections], [2, 0])
def test_build_read_only():
m = Morphology()
m.soma.points = [[-1, -2, -3]]
m.soma.diameters = [-4]
section = m.append_root_section(
PointLevel([[1, 2, 3], [4, 5, 6]], [2, 2], [20, 20]), SectionType.axon)
section.append_section(PointLevel([[4, 5, 6], [7, 8, 9]], [2, 3],
[20, 30]))
section.append_section(
PointLevel([[4, 5, 6], [10, 11, 12]], [2, 2], [20, 20]))
immutable_morphology = ImmutableMorphology(m)
sections = list(immutable_morphology.iter())
assert_equal(len(sections), 3)
assert_array_equal(immutable_morphology.soma.points, [[-1, -2, -3]])
assert_array_equal(immutable_morphology.soma.diameters, [-4])
assert_array_equal(
immutable_morphology.section(0).points, [[1, 2, 3], [4, 5, 6]])
assert_array_equal(immutable_morphology.section(0).diameters, [2, 2])
assert_array_equal(immutable_morphology.section(0).perimeters, [20, 20])
assert_equal(len(immutable_morphology.section(0).children), 2)
child = immutable_morphology.section(0).children[0]
assert_array_equal(child.points, [[4, 5, 6], [7, 8, 9]])
assert_array_equal(child.diameters, [2, 3])
assert_array_equal(child.perimeters, [20, 30])
same_child = immutable_morphology.section(1)
assert_array_equal(same_child.points, [[4, 5, 6], [7, 8, 9]])
assert_array_equal(same_child.diameters, [2, 3])
assert_array_equal(same_child.perimeters, [20, 30])
def test_sanitize():
with TemporaryDirectory('test-sanitize') as tmp_folder:
output_path = Path(tmp_folder, 'sanitized.asc')
sanitize(Path(PATH, 'simple-with-duplicates.asc'), output_path)
neuron = Morphology(output_path)
assert_equal(len(neuron.root_sections), 1)
assert_array_equal(
neuron.section(0).points,
[[0., 0., 0.], [1., 1., 0.], [2., 0., 0.], [3., 0., 0.]])
assert_raises(CorruptedMorphology, sanitize, Path(PATH, 'no-soma.asc'),
Path(tmp_folder, 'no-soma.asc'))
assert_raises(CorruptedMorphology, sanitize,
Path(PATH, 'negative-diameters.asc'),
Path(tmp_folder, 'negative-diameter.asc'))
