def test_annotation():
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:
cell = Morphology(tmp_file.name)
cell.remove_unifurcations()
for n in (cell, cell.as_immutable(), cell.as_immutable().as_mutable()):
assert len(n.annotations) == 1
annotation = n.annotations[0]
assert annotation.type == morphio.AnnotationType.single_child
def get(self, node_id, transform=False):
"""Return NeuroM morphology object corresponding to `node_id`.
Args:
node_id (int/CircuitNodeId): could be a single int or a CircuitNodeId.
transform (bool): If `transform` is True, rotate and translate morphology points
according to `node_id` position in the circuit.
"""
filepath = self.get_filepath(node_id)
result = Morphology(filepath)
if transform:
T = np.eye(4)
T[:3, :3] = self._population.orientations(node_id) # rotations
T[:3,
3] = self._population.positions(node_id).values # translations
transformations.transform(result, T)
return result.as_immutable()
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)
