def diameter_power_relation(bif_point, method='first'):
"""Calculate the diameter power relation at a bifurcation point.
The diameter power relation is defined in https://www.ncbi.nlm.nih.gov/pubmed/18568015
This quantity gives an indication of how far the branching is from
the Rall ratio
diameter_power_relation==1 means perfect Rall ratio
"""
_raise_if_not_bifurcation(bif_point)
if method not in {'first', 'mean'}:
raise ValueError(
'Please provide a valid method for sibling ratio, found %s' %
method)
if method == 'first':
d_child = bif_point.points[-1, COLS.R]
d_child1 = bif_point.children[0].points[0, COLS.R]
d_child2 = bif_point.children[1].points[0, COLS.R]
if method == 'mean':
d_child = sectionfunc.section_mean_radius(bif_point)
d_child1 = sectionfunc.section_mean_radius(bif_point.children[0])
d_child2 = sectionfunc.section_mean_radius(bif_point.children[1])
return (d_child / d_child1)**(1.5) + (d_child / d_child2)**(1.5)
def test_mean_radius():
s = load_neuron(StringIO(u"""
((CellBody)
(0 0 0 1))
((Dendrite)
(0 0 0 0)
(3 0 4 200)
(6 4 4 400))"""),
reader='asc').neurites[0]
nt.assert_equal(_sf.section_mean_radius(s), 100.)
def test_mean_radius():
n = load_neuron(StringIO(u"""
((CellBody)
(0 0 0 1))
((Dendrite)
(0 0 0 0)
(3 0 4 200)
(6 4 4 400))"""),
reader='asc')
assert (_sf.section_mean_radius(n.neurites[0]) == 100.)
def sibling_ratio(bif_point, method='first'):
"""Calculate the sibling ratio of a bifurcation point.
The sibling ratio is the ratio between the diameters of the
smallest and the largest child. It is a real number between
0 and 1. Method argument allows one to consider mean diameters
along the child section instead of diameter of the first point.
"""
_raise_if_not_bifurcation(bif_point)
if method not in {'first', 'mean'}:
raise ValueError(
'Please provide a valid method for sibling ratio, found %s' %
method)
if method == 'first':
n = bif_point.children[0].points[0, COLS.R]
m = bif_point.children[1].points[0, COLS.R]
if method == 'mean':
n = sectionfunc.section_mean_radius(bif_point.children[0])
m = sectionfunc.section_mean_radius(bif_point.children[1])
return min(n, m) / max(n, m)