def _dendrogram(neuron_, show_diameters=True):
'''Main dendrogram function
'''
from copy import deepcopy
import sys
sys.setrecursionlimit(3000)
# neuron is copied because otherwise the tree modifications that follow
# will be applied to our original object
neuron = deepcopy(neuron_)
# total number of lines equal to the total number of segments
# plus the number of horizontal lines (2) per bifurcation
n_lines = sum(
n_segments(neu) + n_bifurcations(neu) * 2 for neu in neuron.neurites)
soma_tree = _create_root_soma_tree(neuron)
n_lines += 2
# add all the neurites to the soma treen
for neurite in neuron.neurites:
soma_tree.children[0].add_child(neurite)
n_lines += 2
# initialize the lines matrix that is required for the PolyCollection
# and the colors one
lines = np.zeros((n_lines, 4, 2))
colors = np.zeros(n_lines)
# n is used as a list in order to be static
n = [0]
_generate_dendro(soma_tree,
lines,
colors,
n, [0., 0.], (40., 0.), (0., 0.),
show_diameters=show_diameters)
assert n[0] == n_lines - 1
return lines, colors
def _dendrogram(neuron_, show_diameters=True):
'''Main dendrogram function
'''
from copy import deepcopy
import sys
sys.setrecursionlimit(3000)
# neuron is copied because otherwise the tree modifications that follow
# will be applied to our original object
neuron = deepcopy(neuron_)
# total number of lines equal to the total number of segments
# plus the number of horizontal lines (2) per bifurcation
n_lines = sum(n_segments(neu) + n_bifurcations(neu) * 2 for neu in neuron.neurites)
soma_tree = _create_root_soma_tree(neuron)
n_lines += 2
# add all the neurites to the soma treen
for neurite in neuron.neurites:
soma_tree.children[0].add_child(neurite)
n_lines += 2
# initialize the lines matrix that is required for the PolyCollection
# and the colors one
lines = np.zeros((n_lines, 4, 2))
colors = np.zeros(n_lines)
# n is used as a list in order to be static
n = [0]
_generate_dendro(soma_tree, lines, colors, n, [0., 0.],
(40., 0.), (0., 0.), show_diameters=show_diameters)
assert n[0] == n_lines - 1
return lines, colors
def test_n_bifurcations():
nt.ok_(n_bifurcations(tree0) == 10)
