def fix_non_zero_segments(neuron, zero_length=_ZERO_LENGTH):
'''Return a neuron with zero length segments removed
Sections composed of a single zero length segment are deleted, where zero is parametrized
by zero_length
Args:
neuron (str|pathlib.Path|morphio.Morphology|morphio.mut.Morphology): input neuron
zero_length (float): smallest length of a segment
Returns:
a fixed morphio.mut.Morphology
'''
neuron = Morphology(neuron)
to_be_deleted = list()
for section in neuron.iter():
points = section.points
distances = np.linalg.norm(np.diff(points, axis=0), axis=1)
distances[distances < zero_length] = 0
indices = np.append(0, np.nonzero(distances)[0] + 1)
if len(indices) != len(points):
section.points = section.points[indices]
section.diameters = section.diameters[indices]
if len(indices) < 2:
to_be_deleted.append(section)
for section in to_be_deleted:
neuron.delete_section(section)
return neuron
def fix_non_zero_segments(neuron):
'''Return a neuron with zero length segments removed
Sections composed of a single zero length segment are deleted
Args:
neuron (str|pathlib.Path|morphio.Morphology|morphio.mut.Morphology): input neuron
Returns:
a fixed morphio.mut.Morphology
'''
neuron = Morphology(neuron)
to_be_deleted = list()
for section in neuron.iter():
points = section.points
distances = np.linalg.norm(np.diff(points, axis=0), axis=1)
indices = np.append(0, np.nonzero(distances)[0] + 1)
if len(indices) != len(points):
section.points = section.points[indices]
section.diameters = section.diameters[indices]
if len(indices) < 2:
to_be_deleted.append(section)
for section in to_be_deleted:
neuron.delete_section(section)
return neuron
def test_remove_rootsection_in_loop():
morpho = Morphology(DATA_DIR / 'single_point_root.asc')
assert len(morpho.root_sections) == 1
for root in morpho.root_sections:
if len(root.points) == 1:
morpho.delete_section(root, False)
assert len(morpho.root_sections) == 2
def test_remove_rootsection():
morpho = Morphology(DATA_DIR / 'single_point_root.asc')
assert len(morpho.root_sections) == 1
to_remove = []
for root in morpho.root_sections:
if len(root.points) == 1:
to_remove.append(root)
for root in to_remove:
morpho.delete_section(root, False)
assert len(morpho.root_sections) == 2
def test_equality():
set_ignored_warning([Warning.wrong_duplicate, Warning.only_child], True)
filename = joinp(DATA, 'simple2.asc')
neuron_ref = Morphology(filename)
ok_(not diff(neuron_ref, neuron_ref))
ok_(not diff(neuron_ref, filename))
ok_(not diff(neuron_ref, neuron_ref.as_immutable()))
def mundane_section(neuron):
'''Not a root section, not a leaf section'''
return neuron.root_sections[0].children[0]
a = Morphology(joinp(DATA, 'simple2.asc'))
mundane_section(a).type = SectionType.apical_dendrite
result = diff(neuron_ref, a)
ok_(result)
assert_equal(result.info, 'Section(id=1, points=[(0 5 0),..., (-6 5 0)]) and Section(id=1, points=[(0 5 0),..., (-6 5 0)]) have different section types')
a = Morphology(joinp(DATA, 'simple2.asc'))
mundane_section(a).points = [[0,0,0], [0,0,0], [0,0,1]]
result = diff(neuron_ref, a)
ok_(result)
assert_equal(result.info,
'\n'.join(['Attributes Section.points of:',
'Section(id=1, points=[(0 5 0),..., (-6 5 0)])',
'Section(id=1, points=[(0 0 0),..., (0 0 1)])',
'have the same shape but different values']))
a = Morphology(joinp(DATA, 'simple2.asc'))
mundane_section(a).diameters = [0,0,0]
result = diff(neuron_ref, a)
ok_(result)
assert_equal(result.info,
'\n'.join(['Attributes Section.diameters of:',
'Section(id=1, points=[(0 5 0),..., (-6 5 0)])',
'Section(id=1, points=[(0 5 0),..., (-6 5 0)])',
'have the same shape but different values']))
a = Morphology(joinp(DATA, 'simple2.asc'))
for section in a.iter():
section.perimeters = [1] * len(section.points)
result = diff(neuron_ref, a)
ok_(result)
assert_equal(result.info,
'\n'.join(['Attributes Section.perimeters of:',
'Section(id=0, points=[(0 0 0),..., (0 5 0)])',
'Section(id=0, points=[(0 0 0),..., (0 5 0)])',
'have different shapes: (0,) vs (2,)']))
a = Morphology(joinp(DATA, 'simple2.asc'))
mundane_section(a).append_section(PointLevel([[-6, 5, 0], [4, 5, 6]], [2, 3]))
result = diff(neuron_ref, a)
ok_(result)
assert_equal(result.info, 'Section(id=1, points=[(0 5 0),..., (-6 5 0)]) and Section(id=1, points=[(0 5 0),..., (-6 5 0)]) have different a different number of children')
a = Morphology(joinp(DATA, 'simple2.asc'))
a.delete_section(a.root_sections[0])
result = diff(neuron_ref, a)
ok_(result)
assert_equal(result.info, 'Both morphologies have different a different number of root sections')
result = diff(joinp(DATA, 'single_child.asc'), joinp(DATA, 'not_single_child.asc'))
ok_(not result)
set_ignored_warning([Warning.wrong_duplicate, Warning.only_child], False)
def test_equality():
set_ignored_warning([Warning.wrong_duplicate, Warning.only_child], True)
filename = DATA / 'simple2.asc'
neuron_ref = Morphology(filename)
assert not diff(neuron_ref, neuron_ref)
assert not diff(neuron_ref, filename)
assert not diff(neuron_ref, neuron_ref.as_immutable())
def mundane_section(neuron):
'''Not a root section, not a leaf section'''
return neuron.root_sections[0].children[0]
a = Morphology(DATA / 'simple2.asc')
mundane_section(a).type = SectionType.apical_dendrite
result = diff(neuron_ref, a)
assert result
assert result.info == 'Section(id=1, points=[(0 5 0),..., (-6 5 0)]) and Section(id=1, points=[(0 5 0),..., (-6 5 0)]) have different section types'
a = Morphology(DATA / 'simple2.asc')
mundane_section(a).points = [[0,0,0], [0,0,0], [0,0,1]]
result = diff(neuron_ref, a)
assert result
assert (result.info ==
'\n'.join(['Attributes Section.points of:',
'Section(id=1, points=[(0 5 0),..., (-6 5 0)])',
'Section(id=1, points=[(0 0 0),..., (0 0 1)])',
'have the same shape but different values',
'Vector points differs at index 0: [0. 5. 0.] != [0. 0. 0.]']))
a = Morphology(DATA / 'simple2.asc')
mundane_section(a).diameters = [0,0,0]
result = diff(neuron_ref, a)
assert result
assert (result.info ==
'\n'.join(['Attributes Section.diameters of:',
'Section(id=1, points=[(0 5 0),..., (-6 5 0)])',
'Section(id=1, points=[(0 5 0),..., (-6 5 0)])',
'have the same shape but different values',
'Vector diameters differs at index 0: 3.0 != 0.0']))
a = Morphology(DATA / 'simple2.asc')
for section in a.iter():
section.perimeters = [1] * len(section.points)
result = diff(neuron_ref, a)
assert result
assert (result.info ==
'\n'.join(['Attributes Section.perimeters of:',
'Section(id=0, points=[(0 0 0),..., (0 5 0)])',
'Section(id=0, points=[(0 0 0),..., (0 5 0)])',
'have different shapes: (0,) vs (2,)']))
a = Morphology(DATA / 'simple2.asc')
mundane_section(a).append_section(PointLevel([[-6, 5, 0], [4, 5, 6]], [2, 3]))
result = diff(neuron_ref, a)
assert result
assert result.info == 'Section(id=1, points=[(0 5 0),..., (-6 5 0)]) and Section(id=1, points=[(0 5 0),..., (-6 5 0)]) have a different number of children'
a = Morphology(DATA / 'simple2.asc')
a.delete_section(a.root_sections[0])
result = diff(neuron_ref, a)
assert result
assert result.info == 'Both morphologies have a different number of root sections'
result = diff(DATA / 'single_child.asc', DATA / 'not_single_child.asc')
if parse_version(get_distribution("morphio").version) < parse_version("3"):
assert not result
else:
assert result
set_ignored_warning([Warning.wrong_duplicate, Warning.only_child], False)
