def test_segment_path_length():
leaves = [l for l in tr.ileaf(NEURON_TREE)]
for l in leaves:
nt.ok_(mtr.path_length(l) == 9)
leaves = [l for l in tr.ileaf(SIMPLE_TREE)]
for l in leaves:
nt.ok_(mtr.path_length(l) == 8)
def branch_order(tree_section):
'''Branching order of a tree section
The branching order is defined as the depth of the tree section.
Note:
The first level has branch order 1.
'''
node = tree_section[-1]
bo = sum(1 for _ in tr.iforking_point(node, tr.iupstream))
return bo - 1 if tr.is_forking_point(node) else bo
def generate(self):
'''Generate dendrogram
'''
offsets = (0., 0.)
n_previous = 0
# set recursion limit with respect to
# the max number of nodes on the trees
old_depth = sys.getrecursionlimit()
max_depth = old_depth if old_depth > self._max_rec_depth else self._max_rec_depth
# TODO: This should be fixed so we don't set sys.setrecursionlimit at all
sys.setrecursionlimit(max_depth)
if isinstance(self._obj, Neurite):
max_diameter = _max_diameter(self._obj.root_node)
dummy_section = Tree()
dummy_section.add_child(self._obj.root_node)
self._generate_dendro(dummy_section, (max_diameter, 0.), offsets)
self._groups.append((0., self._n))
self._dims.append(self._max_dims)
else:
for neurite in self._obj.neurites:
neurite = neurite.root_node
max_diameter = _max_diameter(neurite)
dummy_section = Tree()
dummy_section.add_child(neurite)
self._generate_dendro(dummy_section, (max_diameter, 0.),
offsets)
# store in trees the indices for the slice which corresponds
# to the current neurite
self._groups.append((n_previous, self._n))
# store the max dims per neurite for view positioning
self._dims.append(self._max_dims)
# reset the max dimensions for the next tree in line
self._max_dims = [0., 0.]
# keep track of the next tree start index in list
n_previous = self._n
# set it back to its initial value
sys.setrecursionlimit(old_depth)
def compare_trees(tree1, tree2):
'''
Comparison between all the nodes and their respective radii between two trees.
Ids are do not have to be identical between the trees, and swapping is allowed
Returns:
False if the trees are not identical. True otherwise.
'''
leaves1 = list(tr.ileaf(tree1))
leaves2 = list(tr.ileaf(tree2))
if len(leaves1) != len(leaves2):
return False
else:
nleaves = len(leaves1)
for leaf1, leaf2 in product(leaves1, leaves2):
is_equal = True
for node1, node2 in izip(val_iter(tr.iupstream(leaf1)),
val_iter(tr.iupstream(leaf2))):
if any(node1[0:5] != node2[0:5]):
is_equal = False
continue
if is_equal:
nleaves -= 1
return nleaves == 0
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 = float(n_sections(bif_point.children[0]))
m = float(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 generate(self):
'''Generate dendrogram
'''
offsets = (0., 0.)
n_previous = 0
# set recursion limit with respect to
# the max number of nodes on the trees
old_depth = sys.getrecursionlimit()
max_depth = old_depth if old_depth > self._max_rec_depth else self._max_rec_depth
# TODO: This should be fixed so we don't set sys.setrecursionlimit at all
sys.setrecursionlimit(max_depth)
if isinstance(self._obj, Neurite):
max_diameter = _max_diameter(self._obj.root_node)
dummy_section = Tree()
dummy_section.add_child(self._obj.root_node)
self._generate_dendro(dummy_section, (max_diameter, 0.), offsets)
self._groups.append((0, self._n))
self._dims.append(self._max_dims)
else:
for neurite in self._obj.neurites:
neurite = neurite.root_node
max_diameter = _max_diameter(neurite)
dummy_section = Tree()
dummy_section.add_child(neurite)
self._generate_dendro(dummy_section, (max_diameter, 0.), offsets)
# store in trees the indices for the slice which corresponds
# to the current neurite
self._groups.append((n_previous, self._n))
# store the max dims per neurite for view positioning
self._dims.append(self._max_dims)
# reset the max dimensions for the next tree in line
self._max_dims = [0., 0.]
# keep track of the next tree start index in list
n_previous = self._n
# set it back to its initial value
sys.setrecursionlimit(old_depth)
def _skip_0_length(p, c):
'''Return the first child c with non-zero distance to parent p'''
while np.all(p.value[:COLS.R] == c.value[:COLS.R])\
and not tr.is_leaf(c) and not tr.is_forking_point(c):
c = c.children[0]
return c
def n_terminations(tree):
"""
Return number of terminations in tree
"""
return sum(1 for _ in tr.ileaf(tree))
def n_bifurcations(tree):
"""
Return number of bifurcations in tree
"""
return sum(1 for _ in tr.ibifurcation_point(tree))