def get_apical_point(neurite, morph, tuft_percent=27):
'''Attempt to find the apical point in 'tufted' neurons
Consider a neuron:
| / | Tuft = 20%
|--/ |
| /
|--/
|
----.-----
All endpoints in the top 'tuft_percent' are found, then their common
branch segment, furthest from the soma, is identified.
Args:
morph: neurom.fst._core.Neuron
tuft_percent: percentage of the 'height' of the apical dendrite that
would enclose the tuft, only leaves in this volume are considered as
endpoints. Note that this a spherical shell centered at the soma
Returns:
Section whose *end* is where the apical branching begins, or None if there
is a problem
'''
apical = neurite
max_distance2 = -float('inf')
for leaf in apical.root_node.ileaf():
point = leaf.points[-1, COLS.XYZ]
max_distance2 = max(max_distance2, point_dist2(point,
morph.soma.center))
min_distance2 = max_distance2 * (1 - tuft_percent / 100.)**2
common_parents = set(nm.iter_sections(apical))
#Iterator to the sections in a neurite, neuron or neuron population.
all_parents = set([])
for leaf in apical.root_node.ileaf():
point = leaf.points[-1, COLS.XYZ]
if min_distance2 <= point_dist2(point, morph.soma.center):
parents = leaf.iupstream()
set_parents = set(parents)
common_parents &= set_parents
all_parents |= set_parents
apical_point_section = None
for parent_section in nm.iter_sections(apical):
if parent_section in common_parents:
common_parents.remove(parent_section)
if not common_parents:
#print parent_section
if parent_section in all_parents:
#return parent_section
apical_point_section = parent_section
else:
apical_point_section = None
#return None
return apical_point_section
def _count_crossings(neurite, radius):
"""Used to count_crossings of segments in neurite with radius."""
r2 = radius**2
count = 0
for start, end in iter_segments(neurite):
start_dist2, end_dist2 = (morphmath.point_dist2(center, start),
morphmath.point_dist2(center, end))
count += int(start_dist2 <= r2 <= end_dist2
or end_dist2 <= r2 <= start_dist2)
return count
def _seg_rd(sec, pos):
'''list of radial distances of all segments of a section'''
# TODO: remove this disable when pylint is fixed
# pylint: disable=assignment-from-no-return
mid_pts = np.divide(
np.add(sec.points[:-1], sec.points[1:])[:, :3], 2.0)
return np.sqrt([morphmath.point_dist2(p, pos) for p in mid_pts])
def _seg_rd(sec, pos):
'''list of radial distances of all segments of a section'''
mid_pts = np.divide(np.add(sec.points[:-1], sec.points[1:])[:, :3], 2.0)
return np.sqrt([morphmath.point_dist2(p, pos) for p in mid_pts])
def test_point_dist2():
p1 = Point(3.0, 4.0, 5.0, 3.0)
p2 = Point(4.0, 5.0, 6.0, 3.0)
dist = mm.point_dist2(p1, p2)
assert dist == 3
def test_point_dist2():
p1 = Point(3.0, 4.0, 5.0, 3.0, 1)
p2 = Point(4.0, 5.0, 6.0, 3.0, 1)
dist = mm.point_dist2(p1, p2)
nt.eq_(dist, 3)
def _seg_rd(sec, pos):
"""list of radial distances of all segments of a section"""
mid_pts = np.divide(np.add(sec.points[:-1], sec.points[1:])[:, :3], 2.0)
return np.sqrt([morphmath.point_dist2(p, pos) for p in mid_pts])
def _seg_rd(sec, pos):
'''list of radial distances of all segments of a section'''
# TODO: remove this disable when pylint is fixed
# pylint: disable=assignment-from-no-return
mid_pts = np.divide(np.add(sec.points[:-1], sec.points[1:])[:, :3], 2.0)
return np.sqrt([morphmath.point_dist2(p, pos) for p in mid_pts])