def test_multiple_soma():
with assert_raises(SomaError) as obj:
Morphology(os.path.join(_path, 'multiple_soma.swc'))
assert_substring(
''.join([
'Multiple somata found: \n\n',
os.path.join(_path, 'multiple_soma.swc:2:error\n\n\n'),
os.path.join(_path, 'multiple_soma.swc:11:error')
]), strip_color_codes(str(obj.exception)))
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_single_children():
'''Single children are merged with their parent'''
with tmp_asc_file('''
((Dendrite)
(3 -4 0 2)
(3 -6 0 2)
(3 -8 0 2)
(3 -10 0 2)
(
(3 -10 0 2) ; merged with parent section
(0 -10 0 2) ; merged with parent section
(-3 -10 0 2) ; merged with parent section
(
(-5 -5 5 5)
|
(-6 -6 6 6)
)
)
)
''') as tmp_file:
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
n = Morphology(tmp_file.name)
assert_substring('is the only child of section: 0 starting at:',
err.getvalue().strip())
assert_substring('It will be merged with the parent section',
err.getvalue().strip())
nt.assert_equal(len(n.soma.points), 0)
nt.assert_equal(len(n.soma.points), 0)
assert_equal(len(n.root_sections), 1)
assert_array_equal(n.root_sections[0].points,
np.array([[3, -4, 0],
[3, -6, 0],
[3, -8, 0],
[3, -10, 0],
[0, -10, 0],
[-3, -10, 0]],
dtype=np.float32))
assert_equal(len(n.root_sections[0].children), 2)
assert_array_equal(n.root_sections[0].children[0].points,
np.array([[-3, -10, 0],
[-5, -5, 5]]))
assert_array_equal(n.root_sections[0].children[1].points,
np.array([[-3, -10, 0],
[-6, -6, 6]]))
def test_non_C_nparray():
m = Morphology(os.path.join(_path, "simple.swc"))
section = m.root_sections[0]
points = np.array([[1, 2, 3], [4, 5, 6]])
section.points = points
assert_array_equal(section.points, points)
with assert_raises(MorphioError) as obj:
section.points = points.T
assert_substring("Wrong array shape. Expected: (X, 3), got: (3, 2)",
str(obj.exception))
non_standard_stride = np.asfortranarray(points)
section.points = non_standard_stride
assert_array_equal(section.points, points)
def test_point_level():
a = PointLevel([[1, 2, 3]], [2], [])
assert_equal(a.points, [[1, 2, 3]])
assert_equal(a.diameters, [2])
with assert_raises(SectionBuilderError) as obj:
a = PointLevel([[1, 2, 3], [1, 2, 3]], [2], [])
assert_substring(
"Point vector have size: 2 while Diameter vector has size: 1",
str(obj.exception))
with assert_raises(SectionBuilderError) as obj:
a = PointLevel([[1, 2, 3], [1, 2, 3]], [2, 3], [4])
assert_substring(
"Point vector have size: 2 while Perimeter vector has size: 1",
str(obj.exception))
def test_empty_sibling():
'''The empty sibling will be removed and the single child will be merged
with its parent'''
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
with tmp_asc_file('''((Dendrite)
(3 -4 0 10)
(3 -6 0 9)
(3 -8 0 8)
(3 -10 0 7)
(
(3 -10 0 6)
(0 -10 0 5)
(-3 -10 0 4)
| ; <-- empty sibling but still works !
)
)
''') as tmp_file:
n = Morphology(tmp_file.name)
n.remove_unifurcations()
assert_substring('is the only child of section: 0',
err.getvalue().strip())
assert_substring('It will be merged with the parent section',
err.getvalue().strip())
assert len(n.root_sections) == 1
assert_array_equal(
n.root_sections[0].points,
np.array([[3, -4, 0], [3, -6, 0], [3, -8, 0], [3, -10, 0], [0, -10, 0],
[-3, -10, 0]],
dtype=np.float32))
assert_array_equal(n.root_sections[0].diameters,
np.array([10, 9, 8, 7, 5, 4], dtype=np.float32))
assert len(n.annotations) == 1
annotation = n.annotations[0]
assert annotation.type == morphio.AnnotationType.single_child
assert annotation.line_number == -1
assert_array_equal(annotation.points,
[[3, -10, 0], [0, -10, 0], [-3, -10, 0]])
assert_array_equal(annotation.diameters, [6, 5, 4])
def test_empty_sibling():
'''The empty sibling will be removed and the single child will be merged
with its parent'''
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
with tmp_asc_file('''((Dendrite)
(3 -4 0 2)
(3 -6 0 2)
(3 -8 0 2)
(3 -10 0 2)
(
(3 -10 0 2)
(0 -10 0 2)
(-3 -10 0 2)
| ; <-- empty sibling but still works !
)
)
''') as tmp_file:
n = Morphology(tmp_file.name)
assert_substring('is the only child of section: 0 starting at:',
err.getvalue().strip())
assert_substring('It will be merged with the parent section',
err.getvalue().strip())
assert_equal(len(n.root_sections), 1)
assert_array_equal(n.root_sections[0].points,
np.array([[3, -4, 0],
[3, -6, 0],
[3, -8, 0],
[3, -10, 0],
[0, -10, 0],
[-3, -10, 0]],
dtype=np.float32))
assert_equal(len(n.annotations), 1)
annotation = n.annotations[0]
assert_equal(annotation.type, morphio.AnnotationType.single_child)
assert_equal(annotation.line_number, 6)
assert_array_equal(annotation.points, [[3, -10, 0], [0, -10, 0], [-3, -10, 0]])
assert_array_equal(annotation.diameters, [2, 2, 2])