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_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_single_neurite():
m = Morphology()
m.append_root_section(PointLevel([[1, 2, 3]], [2], [20]),
SectionType.axon)
assert_array_equal(m.root_sections[0].points,
[[1, 2, 3]])
assert_equal(m.root_sections[0].diameters,
[2])
assert_equal(m.root_sections[0].perimeters,
[20])
m.root_sections[0].points = [[10, 20, 30]]
assert_array_equal(m.root_sections[0].points,
[[10, 20, 30]],
'Points array should have been mutated')
m.root_sections[0].diameters = [7]
assert_equal(m.root_sections[0].diameters,
[7],
'Diameter array should have been mutated')
m.root_sections[0].perimeters = [27]
assert_equal(m.root_sections[0].perimeters,
[27],
'Perimeter array should have been mutated')
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_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_append_mutable_section():
morpho = Morphology()
second_children_first_root = SIMPLE.root_sections[0].children[1]
morpho.append_root_section(second_children_first_root)
assert_equal(len(morpho.root_sections), 1)
assert_array_equal(morpho.root_sections[0].points,
second_children_first_root.points)
def test_dendrites_mean_direction():
donor_neuron = Morphology(os.path.join(_path, 'simple3.asc'))
assert_array_equal(graft._dendrites_mean_direction(donor_neuron),
np.array([0.6666667, 4.6666665, 3.], dtype=np.float32))
no_dendrite = Morphology()
no_dendrite.append_root_section(PointLevel([[0, 0, 0], [1, 1, 1]], [1, 1]),
SectionType.axon)
with assert_raises(MorphToolException) as obj:
graft._dendrites_mean_direction(no_dendrite)
def test_mut_copy_ctor():
simple = Morphology(os.path.join(_path, "simple.swc"))
assert_equal([sec.id for sec in simple.iter()], [0, 1, 2, 3, 4, 5])
copy = Morphology(simple)
copy.append_root_section(
PointLevel([[1, 2, 3], [4, 5, 6]], [2, 2], [20, 20]), SectionType.axon)
# test that first object has not been mutated
assert_equal([sec.id for sec in simple.iter()], [0, 1, 2, 3, 4, 5])
assert_equal([sec.id for sec in copy.iter()], [0, 1, 2, 3, 4, 5, 6])
def test_lifetime_copy_single_section():
"""Copying a single section from a destroyed morphology works because it
does not use any topological information"""
section = _get_section()
# Proof that the morphology has really been destroyed
with pytest.raises(RuntimeError):
section.children
morph = Morphology()
morph.append_root_section(section)
del section
assert len(morph.root_sections) == 1
assert_array_equal(
morph.root_sections[0].points,
np.array([[0., 0., 0.], [0., 5., 0.]], dtype=np.float32))
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_child_section():
m = Morphology()
section = m.append_root_section(PointLevel([[1, 2, 3]], [2], [20]),
SectionType.axon)
ok_(section.is_root)
section.append_section(PointLevel([[1, 2, 3], [4, 5, 6]],
[2, 3],
[20, 30]))
children = m.root_sections[0].children
assert_equal(len(children),
1)
assert_array_equal(children[0].points,
[[1, 2, 3], [4, 5, 6]])
assert_array_equal(children[0].diameters,
[2, 3])
assert_array_equal(children[0].perimeters,
[20, 30])
children[0].points = [[7, 8, 9], [10, 11, 12]]
assert_array_equal(children[0].points,
[[7, 8, 9], [10, 11, 12]])
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_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_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_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_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_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_write_merge_only_child_swc():
'''Attempts to write a morphology with unifurcations with SWC should result
in an exception.
'''
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 pytest.raises(WriterError, match=r"Section 0 has a single child section\. "
r"Single child section are not allowed when writing to SWC format\. "
r"Please sanitize the morphology first\."):
morpho.write('/tmp/bla.swc') # the path does not need to exists since it will fail before
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]'
)
