def test_root_node_split():
'''Test that a bifurcation at the root point produces
two root sections
'''
with tmp_swc_file('''1 1 0 0 0 1 -1
2 3 1 0 0 1 1
3 3 1 1 0 1 2
4 3 1 0 1 1 2
''') as tmp_file:
n = Morphology(tmp_file.name)
assert_equal(len(n.root_sections), 2)
assert_array_equal(n.root_sections[0].points, [[1, 0, 0], [1, 1, 0]])
assert_array_equal(n.root_sections[1].points, [[1, 0, 0], [1, 0, 1]])
# Normal bifurcation
with tmp_swc_file('''1 1 0 0 0 1 -1
2 3 1 0 0 1 1
3 3 2 1 0 1 2
4 3 1 1 0 1 3
5 3 1 0 1 1 3
''') as tmp_file:
n = Morphology(tmp_file.name)
assert_equal(len(n.root_sections), 1)
root = n.root_sections[0]
assert_array_equal(root.points, [[1, 0, 0], [2, 1, 0]])
assert_equal(len(root.children), 2)
assert_array_equal(root.children[0].points, [[2, 1, 0], [1, 1, 0]])
assert_array_equal(root.children[1].points, [[2, 1, 0], [1, 0, 1]])
def test_weird_indent():
with tmp_swc_file("""
# this is the same as simple.swc
# but with a questionable styling
1 1 0 0 0 1. -1
2 3 0 0 0 1. 1
3 3 0 5 0 1. 2
4 3 -5 5 0 0. 3
5 3 6 5 0 0. 3
6 2 0 0 0 1. 1
7 2 0 -4 0 1. 6
8 2 6 -4 0 0. 7
9 2 -5 -4 0 0. 7 # 3 0 0
""") as tmp_file:
n = Morphology(tmp_file.name)
simple = Morphology(os.path.join(_path, 'simple.swc'))
assert_array_equal(simple.points, n.points)
def test_read_split_soma():
with tmp_swc_file('''# A simple neuron consisting of a two-branch soma
# with a single branch neurite on each branch.
#
# initial soma point
1 1 1 0 1 4.0 -1
# first neurite
2 3 0 0 2 0.5 1
3 3 0 0 3 0.5 2
4 3 0 0 4 0.5 3
5 3 0 0 5 0.5 4
# soma branch, off initial point
6 1 2 0 0 4.0 1
7 1 3 0 0 4.0 6
# second neurite, off soma branch
8 3 0 0 6 0.5 1
9 3 0 0 7 0.5 8
10 3 0 0 8 0.5 9
11 3 0 0 9 0.5 10
''') as tmp_file:
n = Morphology(tmp_file.name)
assert_array_equal(n.soma.points, [[1, 0, 1], [2, 0, 0], [3, 0, 0]])
nt.assert_equal(len(n.root_sections), 2)
assert_array_equal(n.root_sections[0].points,
[[0, 0, 2], [0, 0, 3], [0, 0, 4], [0, 0, 5]])
assert_array_equal(n.root_sections[1].points,
[[0, 0, 6], [0, 0, 7], [0, 0, 8], [0, 0, 9]])
nt.eq_(len(list(n.iter())), 2)
def test_unsupported_section_type():
with tmp_swc_file('''1 1 0 4 0 3.0 -1
2 3 0 0 2 0.5 1
3 -1 0 0 3 0.5 2 # <-- -1 is unsupported section type
''') as tmp_file:
with pytest.raises(RawDataError, match='.swc:3:error') as obj:
Morphology(tmp_file.name)
assert obj.match('Unsupported section type: -1')
with tmp_swc_file('''1 1 0 4 0 3.0 -1
2 3 0 0 2 0.5 1
3 11 0 0 3 0.5 2 # <-- 11 is unsupported section type
''') as tmp_file:
with pytest.raises(RawDataError, match='.swc:3:error') as obj:
Morphology(tmp_file.name)
assert obj.match('Unsupported section type: 11')
def test_no_soma():
swc_content = '''1 2 0 0 0 3.0 -1
2 2 0 0 0 3.0 1
3 2 0 0 0 3.0 2'''
with captured_output() as (_, err):
with ostream_redirect(
stdout=True,
stderr=True), tmp_swc_file(swc_content) as tmp_file:
n = Morphology(tmp_file.name)
assert ('{}:0:warning\nWarning: no soma found in file'.format(
tmp_file.name) == strip_color_codes(err.getvalue().strip()))
def test_unsupported_section_type():
with tmp_swc_file('''1 1 0 4 0 3.0 -1
2 3 0 0 2 0.5 1
3 5 0 0 3 0.5 2 # <-- 5 is unsupported section type
''') as tmp_file:
with assert_raises(RawDataError) as obj:
Morphology(tmp_file.name)
assert_substring('.swc:3:error', strip_color_codes(str(obj.exception)))
assert_substring('Unsupported section type: 5',
strip_color_codes(str(obj.exception)))
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_read_weird_ids():
'''The ordering of IDs is not required'''
with tmp_swc_file('''10000 3 0 0 5 0.5 100 # neurite 4th point
3 3 0 0 3 0.5 47 # neurite 2nd point
10 1 0 0 0 3.0 -1 # soma
47 3 0 0 2 0.5 10 # neurite 1st point
100 3 0 0 4 0.5 3 # neurite 3rd point
''') as tmp_file:
neuron = Morphology(tmp_file.name)
assert_array_equal(neuron.soma.points, [[0, 0, 0]])
assert_array_equal(
neuron.root_sections[0].points,
[[0., 0., 2.], [0., 0., 3.], [0., 0., 4.], [0., 0., 5.]])
def test_read_single_neurite():
'''Test reading a simple neuron consisting of a point soma
and a single branch neurite.'''
with tmp_swc_file('''1 1 0 4 0 3.0 -1
2 3 0 0 2 0.5 1
3 3 0 0 3 0.5 2
4 3 0 0 4 0.5 3
5 3 0 0 5 0.5 4''') as tmp_file:
n = Morphology(tmp_file.name)
assert_array_equal(n.soma.points, [[0, 4, 0]])
assert_array_equal(n.soma.diameters, [6.0])
assert len(n.root_sections) == 1
assert n.root_sections[0].id == 0
assert len(n.root_sections) == 1
assert_array_equal(n.root_sections[0].points,
np.array([[0, 0, 2], [0, 0, 3], [0, 0, 4], [0, 0, 5]]))
assert_array_equal(n.section_offsets, [0, 4])
def test_skip_comments():
'''Test skipping comments'''
with tmp_swc_file(('#a comment\n'
'# a comment\n'
' # a comment\n'
' # a comment\n'
'1 1 0 4 0 3.0 -1\n'
'\t#a tab comment\n'
'\t#\ta tab comment\n'
'\t\t#\t\ta a tab comment\n'
'2 3 0 0 2 0.5 1\n'
'3 3 0 0 3 0.5 2\n'
'4 3 0 0 4 0.5 3\n'
'5 3 0 0 5 0.5 4\n')) as tmp_file:
n = Morphology(tmp_file.name)
assert_array_equal(n.soma.points, [[0, 4, 0]])
assert_array_equal(n.soma.diameters, [6.0])
nt.eq_(len(n.root_sections), 1)
assert_array_equal(n.root_sections[0].points,
np.array([[0, 0, 2], [0, 0, 3], [0, 0, 4], [0, 0, 5]]))
def test_simple_reversed():
with tmp_swc_file('''# This is the same as 'simple.swc',
# except w/ leaf nodes before their parents
1 1 0 0 0 1. -1
2 3 -5 5 0 0. 7
3 3 6 5 0 0. 7
4 2 6 -4 0 0. 9
5 2 -5 -4 0 0. 9
6 3 0 0 0 1. 1
7 3 0 5 0 1. 6
8 2 0 0 0 1. 1
9 2 0 -4 0 1. 8 ''') as tmp_file:
n = Morphology(tmp_file.name)
assert_array_equal(n.soma.points, [[0, 0, 0]])
nt.assert_equal(len(n.root_sections), 2)
assert_array_equal(n.root_sections[0].points, [[0, 0, 0], [0, 5, 0]])
assert_array_equal(n.root_sections[1].points, [[0, 0, 0], [0, -4, 0]])
assert_array_equal(n.root_sections[1].children[0].points,
[[0, -4, 0], [6, -4, 0]])
assert_array_equal(n.root_sections[1].children[1].points,
[[0, -4, 0], [-5, -4, 0]])
def test_read_duplicate():
'''Test reading a simple neuron consisting of a point soma
and a single branch neurite.'''
with tmp_swc_file('''# A simple neuron with a duplicate point
# at the bifurcation
#
# soma point
1 1 1 0 1 4.0 -1
# root section
2 3 0 0 2 0.5 1
3 3 0 0 3 0.5 2
# first child: real duplicate
4 3 0 0 3 0.5 3
5 3 0 0 7 0.5 4
# second child: duplicate with different diameter
6 3 0 0 3 2.3 3
7 3 0 0 8 3.5 6
# third child: no duplicate
8 3 1 0 0 2.3 3
9 3 1 1 0 3.5 8''') as tmp_file:
n = Morphology(tmp_file.name)
nt.eq_(len(n.root_sections), 1)
nt.eq_(len(n.root_sections[0].children), 3)
child1, child2, child3 = n.root_sections[0].children
assert_array_equal(n.root_sections[0].points,
np.array([[0, 0, 2], [0, 0, 3]]))
assert_array_equal(child1.points, np.array([[0, 0, 3], [0, 0, 7]]))
assert_array_equal(child2.points, np.array([[0, 0, 3], [0, 0, 8]]))
assert_array_equal(child3.points,
np.array([[0, 0, 3], [1, 0, 0], [1, 1, 0]]))
assert_array_equal(child1.diameters, np.array([1, 1]))
assert_array_equal(child2.diameters, np.array([4.6, 7], dtype=np.float32))
assert_array_equal(child3.diameters, np.array([1, 4.6, 7],
dtype=np.float32))
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)
