def test_neuron_not_corrupted():
# Regression for #492: dendrogram was corrupting
# neuron used to construct it.
# This caused the section path distance calculation
# to raise a KeyError exception.
neuron = load_neuron(NEURON_PATH)
dm.Dendrogram(neuron)
assert get('section_path_distances', neuron).size > 0
def test_create_dendrogram_neuron():
neuron = load_neuron(NEURON_PATH)
dendrogram = dm.Dendrogram(neuron)
assert NeuriteType.soma == dendrogram.neurite_type
soma_len = 1.0
assert soma_len == dendrogram.height
assert soma_len == dendrogram.width
assert_array_almost_equal(
[[-.5, 0], [-.5, soma_len], [.5, soma_len], [.5, 0]],
dendrogram.coords)
assert len(neuron.neurites) == len(dendrogram.children)
def test_create_dendrogram_neuron():
neuron = load_neuron(NEURON_PATH)
dendrogram = dm.Dendrogram(neuron)
nt.assert_equal(NeuriteType.soma, dendrogram.neurite_type)
soma_len = 1.0
nt.assert_equal(soma_len, dendrogram.height)
nt.assert_equal(soma_len, dendrogram.width)
assert_array_almost_equal(
[[-.5, 0], [-.5, soma_len], [.5, soma_len], [.5, 0]],
dendrogram.coords)
nt.assert_equal(len(neuron.neurites), len(dendrogram.children))
def test_create_dendrogram_neurite():
def assert_trees(neurom_section, dendrogram):
assert len(neurom_section.children) == len(dendrogram.children)
for i, d in enumerate(dendrogram.children):
section = neurom_section.children[i]
assert section.type == d.neurite_type
neuron = load_neuron(NEURON_PATH)
neurite = neuron.neurites[0]
dendrogram = dm.Dendrogram(neurite)
assert neurite.type == dendrogram.neurite_type
assert_trees(neurite.root_node, dendrogram)
def test_create_dendrogram_neurite():
def assert_trees(neurom_section, dendrogram):
nt.assert_equal(len(neurom_section.children), len(dendrogram.children))
for i, d in enumerate(dendrogram.children):
section = neurom_section.children[i]
nt.assert_equal(section.type, d.neurite_type)
neuron = load_neuron(NEURON_PATH)
neurite = neuron.neurites[0]
dendrogram = dm.Dendrogram(neurite)
nt.assert_equal(neurite.type, dendrogram.neurite_type)
assert_trees(neurite.root_node, dendrogram)
def test_layout_dendrogram():
def assert_layout(dendrogram):
for i, child in enumerate(dendrogram.children):
# child is higher than parent in Y coordinate
assert (positions[child][1] >=
positions[dendrogram][1] + dendrogram.height)
if i < len(dendrogram.children) - 1:
next_child = dendrogram.children[i + 1]
# X space between child is enough for their widths
assert (positions[next_child][0] - positions[child][0] > .5 *
(next_child.width + child.width))
assert_layout(child)
neuron = load_neuron(NEURON_PATH)
dendrogram = dm.Dendrogram(neuron)
positions = dm.layout_dendrogram(dendrogram, np.array([0, 0]))
assert_layout(dendrogram)