def test_write_perimeter():
morpho = Morphology()
morpho.soma.points = [[0, 0, 0]]
morpho.soma.diameters = [2]
dendrite = morpho.append_root_section(
PointLevel([[0, 0, 0], [0, 5, 0]], [2, 2], [5, 6]),
SectionType.basal_dendrite)
dendrite.append_section(PointLevel([[0, 5, 0], [-5, 5, 0]], [2, 3],
[6, 7]))
dendrite.append_section(PointLevel([[0, 5, 0], [6, 5, 0]], [2, 3], [6, 8]))
with setup_tempdir('test_write_perimeter') as tmp_folder:
h5_out = os.path.join(tmp_folder, "test_write.h5")
morpho.write(h5_out)
assert_array_equal(
ImmutMorphology(h5_out).perimeters, [5., 6., 6., 7., 6., 8.])
# Cannot right a morph with perimeter data to ASC and SWC
for ext in ['swc', 'asc']:
out_path = os.path.join(tmp_folder, "test_write_perimeter." + ext)
assert_raises(WriterError, morpho.write, out_path)
def test_self_graft():
'''Grafting a neuron with its own neuron'''
filename = os.path.join(_path, 'neuron.asc')
new_axon = graft.find_axon(ImmutMorphology(filename))
neuron = Morphology(filename)
graft.graft_axon(neuron, new_axon)
expected = Morphology(filename)
ok_(not diff(expected, neuron))
def test_write_basic():
morpho = Morphology()
morpho.soma.points = [[0, 0, 0]]
morpho.soma.diameters = [2]
dendrite = morpho.append_root_section(PointLevel([[0, 0, 0], [0, 5, 0]], [2, 2]),
SectionType.basal_dendrite)
dendrite.append_section(PointLevel([[0, 5, 0], [-5, 5, 0]], [2, 3]))
dendrite.append_section(PointLevel([[0, 5, 0], [6, 5, 0]], [2, 3]))
axon = morpho.append_root_section(
PointLevel([[0, 0, 0],
[0, -4, 0]],
[2, 2]),
SectionType.axon)
axon.append_section(PointLevel([[0, -4, 0],
[6, -4, 0]],
[2, 4]))
axon = axon.append_section(PointLevel([[0, -4, 0],
[-5, -4, 0]],
[2, 4]))
with setup_tempdir('test_write_basic') as tmp_folder:
morpho.write(Path(tmp_folder, "test_write.asc"))
morpho.write(Path(tmp_folder, "test_write.swc"))
h5_out = Path(tmp_folder, "test_write.h5")
morpho.write(h5_out)
expected = [[0., 0., 0.], [0., 5., 0.], [0., 5., 0.], [-5., 5., 0.],
[0., 5., 0.], [6., 5., 0.], [0., 0., 0.], [0., -4., 0.],
[0., -4., 0.], [6., -4., 0.], [0., -4., 0.], [-5., -4., 0.]]
assert_array_equal(ImmutMorphology(Path(tmp_folder, "test_write.asc")).points, expected)
assert_array_equal(ImmutMorphology(Path(tmp_folder, "test_write.swc")).points, expected)
h5_morph = ImmutMorphology(Path(tmp_folder, "test_write.h5"))
assert_array_equal(h5_morph.points, expected)
assert h5_morph.version == ('h5', 1, 2)
import h5py
with h5py.File(h5_out, 'r') as h5_file:
assert '/perimeters' not in h5_file.keys()
def test_self_graft():
'''Grafting a neuron with its own neuron'''
filename = DATA / 'neuron.asc'
new_axon = graft.find_axon(ImmutMorphology(filename))
neuron = Morphology(filename)
graft.graft_axon(neuron, new_axon)
expected = Morphology(filename)
assert not diff(expected, neuron)
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_load_neuron_from_other_neurons():
filename = SWC_PATH / 'simple.swc'
expected_points = [[0., 0., 0., 1.], [0., 5., 0., 1.], [0., 5., 0., 1.],
[-5., 5., 0., 0.], [0., 5., 0., 1.], [6., 5., 0., 0.],
[0., 0., 0., 1.], [0., -4., 0., 1.], [0., -4., 0., 1.],
[6., -4., 0., 0.], [0., -4., 0., 1.],
[-5., -4., 0., 0.]]
assert_array_equal(
nm.load_neuron(nm.load_neuron(filename)).points, expected_points)
assert_array_equal(
nm.load_neuron(Morphology(filename)).points, expected_points)
assert_array_equal(
nm.load_neuron(ImmutMorphology(filename)).points, expected_points)
def test_contour_surface():
# # circle contour
# assert_almost_equal(ImmutMorphology(os.path.join(_path, "circle_contour.asc")).soma.surface,
# np.pi, decimal=2)
# assert_almost_equal(Morphology(os.path.join(_path, "circle_contour.asc")).soma.surface,
# np.pi, decimal=2)
# # triangular contour
# assert_almost_equal(ImmutMorphology(os.path.join(_path, "h5/v1/Neuron.h5")).soma.surface,
# 0.01, decimal=5)
# assert_almost_equal(Morphology(os.path.join(_path, "h5/v1/Neuron.h5")).soma.surface,
# 0.01, decimal=5)
# # single point ASC
# assert_almost_equal(ImmutMorphology(os.path.join(_path, "simple.asc")).soma.surface,
# 4 * np.pi, decimal=2)
# assert_almost_equal(Morphology(os.path.join(_path, "simple.asc")).soma.surface,
# 4 * np.pi, decimal=2)
# single point SWC
assert_almost_equal(ImmutMorphology(os.path.join(
_path, "simple.swc")).soma.surface,
4 * np.pi,
decimal=2)
assert_almost_equal(Morphology(os.path.join(_path,
"simple.swc")).soma.surface,
4 * np.pi,
decimal=2)
# single point H5
assert_almost_equal(ImmutMorphology(os.path.join(
_path, "h5/v1/simple.h5")).soma.surface,
4 * np.pi,
decimal=2)
assert_almost_equal(Morphology(os.path.join(
_path, "h5/v1/simple.h5")).soma.surface,
4 * np.pi,
decimal=2)
# SWC three points cylinder
assert_almost_equal(ImmutMorphology(
os.path.join(_path, "soma_three_points_cylinder.swc")).soma.surface,
4 * np.pi * 81,
decimal=2)
assert_almost_equal(Morphology(
os.path.join(_path, "soma_three_points_cylinder.swc")).soma.surface,
4 * np.pi * 81,
decimal=2)
# SWC consecutive cylinders (3 cylinders along X)
assert_almost_equal(ImmutMorphology(
os.path.join(_path, "soma_cylinders.swc")).soma.surface,
2 * np.pi * 40 * 3,
decimal=2)
assert_almost_equal(Morphology(os.path.join(
_path, "soma_cylinders.swc")).soma.surface,
2 * np.pi * 40 * 3,
decimal=2)
with pytest.raises(SomaError):
_ = Morphology(os.path.join(_path, "no_soma.swc")).soma.surface
assert_almost_equal(Morphology(
os.path.join(_path, "soma_single_frustum.swc")).soma.surface,
1201.428,
decimal=3)
# SWC multiple frustums
assert_almost_equal(ImmutMorphology(
os.path.join(_path, "soma_multiple_frustums.swc")).soma.surface,
4164.610254415956,
decimal=3)
assert_almost_equal(Morphology(
os.path.join(_path, "soma_multiple_frustums.swc")).soma.surface,
4164.610254415956,
decimal=3)
# SWC complex
assert_almost_equal(ImmutMorphology(os.path.join(
_path, "complexe.swc")).soma.surface,
13.980,
decimal=2)