def test_ibifurcation_point_upstream():
leaves = [l for l in ileaf(REF_TREE2)]
ref_paths = [[11, 0], [11, 0], [11, 0], [11, 0], [1211, 12, 0],
[1211, 12, 0], [12, 0]]
for l, ref in zip(leaves, ref_paths):
nt.assert_equal(
[s for s in val_iter(ibifurcation_point(l, iupstream))], ref)
def test_ibifurcation_point_upstream():
leaves = [l for l in ileaf(REF_TREE2)]
ref_paths = [
[11, 0], [11, 0], [11, 0], [11, 0],
[1211, 12, 0], [1211, 12, 0], [12, 0]
]
for l, ref in zip(leaves, ref_paths):
nt.assert_equal([s for s in val_iter(ibifurcation_point(l, iupstream))], ref)
def i_remote_bifurcation_angle(tree):
'''Return the opening angle between the last segments of two out-going
sections of a bifurcation point
'''
def _remangle(t):
'''Helper to calculate the remote angle'''
end_points = tuple(p for p in tr.i_branch_end_points(t))
return mm.angle_3points(t.value, end_points[0].value, end_points[1].value)
return imap(_remangle, tr.ibifurcation_point(tree))
def i_remote_bifurcation_angle(tree):
'''Return the opening angle between the last segments of two out-going
sections of a bifurcation point
'''
def _remangle(t):
'''Helper to calculate the remote angle'''
end_points = tuple(p for p in tr.i_branch_end_points(t))
return mm.angle_3points(t.value, end_points[0].value,
end_points[1].value)
return imap(_remangle, tr.ibifurcation_point(tree))
def partition(tree):
'''Measures the distribution of sections
to the children subtrees at each bifurcation point.
Partition is defined as the max/min number of sections
between the children subtrees of a bifurcation point.
Returns:
List of partition for each bifurcation point.
'''
def partition_at_point(bif_point):
'''Partition at each bif point.'''
n = n_sections(bif_point.children[0])
m = n_sections(bif_point.children[1])
return max(n, m) / min(n, m)
return [partition_at_point(i)
for i in tr.ibifurcation_point(tree)]
def test_valiter_bifurcation_point():
nt.ok_(list(val_iter(ibifurcation_point(REF_TREE2))) ==
[0, 11, 12, 1211])
def test_ibifurcation_point_postorder():
nt.assert_equal([n.value for n in ibifurcation_point(REF_TREE2, ipostorder)],
[11, 1211, 12, 0])
def test_ibifurcation_point():
nt.assert_equal([n.value for n in ibifurcation_point(REF_TREE2)],
[0, 11, 12, 1211])
def n_bifurcations(tree):
"""
Return number of bifurcations in tree
"""
return sum(1 for _ in tr.ibifurcation_point(tree))
def i_local_bifurcation_angle(tree):
'''Return the opening angle between two out-going segments
in a bifurcation point
'''
return imap(local_bifurcation_angle,
tr.ibifurcation_point(tree))
def test_valiter_bifurcation_point():
nt.ok_(list(val_iter(ibifurcation_point(REF_TREE2))) == [0, 11, 12, 1211])
def test_ibifurcation_point_postorder():
nt.assert_equal(
[n.value for n in ibifurcation_point(REF_TREE2, ipostorder)],
[11, 1211, 12, 0])
def test_ibifurcation_point():
nt.assert_equal([n.value for n in ibifurcation_point(REF_TREE2)],
[0, 11, 12, 1211])
def n_bifurcations(tree):
"""
Return number of bifurcations in tree
"""
return sum(1 for _ in tr.ibifurcation_point(tree))
def i_local_bifurcation_angle(tree):
'''Return the opening angle between two out-going segments
in a bifurcation point
'''
return imap(local_bifurcation_angle, tr.ibifurcation_point(tree))