def calculate_and_plot_end_to_end_distance(path):
'''Calculate and plot the end-to-end distance vs the number of segments for
an increasingly larger part of a given path.
Note that the plots are not very meaningful for bifurcating trees.'''
end_to_end_distance = [morphmath.point_dist(segment[1], path.value)
for segment in tree.val_iter(tree.isegment(path))]
make_end_to_end_distance_plot(np.arange(len(end_to_end_distance)) + 1, end_to_end_distance,
path.type)
def i_section_radial_dist(tree, pos=None, use_start_point=False):
'''Return an iterator of radial distances of tree sections to a given point
The radial distance is the euclidian distance between the either the
end-point or rhe start point of the section and the point in question.
Parameters:
tree: tree object
pos: origin to which distances are measured. It must have at least 3\
components. The first 3 components are (x, y, z).\
(default tree origin)
use_start_point: If true, calculate distance from section start point,\
else from end-point (default, False)
'''
pos = tree.value if pos is None else pos
sec_idx = 0 if use_start_point else -1
return tr.imap_val(lambda s: mm.point_dist(s[sec_idx], pos), tr.isection(tree))
def i_section_radial_dist(tree, pos=None, use_start_point=False):
'''Return an iterator of radial distances of tree sections to a given point
The radial distance is the euclidian distance between the either the
end-point or rhe start point of the section and the point in question.
Parameters:
tree: tree object
pos: origin to which distances are measured. It must have at least 3\
components. The first 3 components are (x, y, z).\
(default tree origin)
use_start_point: If true, calculate distance from section start point,\
else from end-point (default, False)
'''
pos = tree.value if pos is None else pos
sec_idx = 0 if use_start_point else -1
return tr.imap_val(lambda s: mm.point_dist(s[sec_idx], pos),
tr.isection(tree))
def _dist(section):
'''Hacky closure'''
return mm.point_dist(pos, section[sec_idx])
def test_point_dist():
p1 = Point(3.0, 4.0, 5.0, 3.0, 1)
p2 = Point(4.0, 5.0, 6.0, 3.0, 1)
dist = point_dist(p1,p2)
nt.ok_(dist==sqrt(3))
def test_segment_radial_dist():
seg = ((11,11,11), (33, 33, 33))
nt.assert_almost_equal(segment_radial_dist(seg, (0,0,0)),
point_dist((0,0,0), (22,22,22)))
def path_end_to_end_distance(path):
'''Calculate and return end-to-end-distance of a given path.'''
trunk = path.value
return max(morphmath.point_dist(l, trunk) for l in tree.val_iter(tree.ileaf(path)))
