def test_mitochondria():
morpho = Morphology()
morpho.soma.points = [[0, 0, 0], [1, 1, 1]]
morpho.soma.diameters = [1, 1]
morpho.append_root_section(
PointLevel([[2, 2, 2], [3, 3, 3]], [4, 4], [5, 5]), SectionType.axon)
mito = morpho.mitochondria
first_mito_id = mito.append_root_section(
MitochondriaPointLevel([0, 0], [0.5, 0.6], [10, 20]))
first_child = first_mito_id.append_section(
MitochondriaPointLevel([3, 4, 4, 5], [0.6, 0.7, 0.8, 0.9],
[20, 30, 40, 50]))
second_mito_id = mito.append_root_section(
MitochondriaPointLevel([0, 1, 1, 2], [0.6, 0.7, 0.8, 0.9],
[5, 6, 7, 8]))
assert_equal(mito.is_root(first_mito_id), True)
assert_equal(mito.children(first_mito_id), [first_child])
assert_equal(mito.parent(first_child), first_mito_id)
assert_equal(mito.root_sections, [first_mito_id, second_mito_id])
assert_array_equal(first_child.diameters, [20, 30, 40, 50])
assert_array_equal(first_child.neurite_section_ids, [3, 4, 4, 5])
assert_array_equal(
np.array(first_child.relative_path_lengths, dtype=np.float32),
np.array([0.6, 0.7, 0.8, 0.9], dtype=np.float32))
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)