# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
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'''Section functions and functional tools'''
from neurom import morphmath as mm
from neurom._compat import range
[docs]def section_path_length(section):
'''Path length from section to root'''
return sum(s.length for s in section.iupstream())
[docs]def section_volume(section):
'''Volume of a section'''
return section.volume
[docs]def section_area(section):
'''Surface area of a section'''
return section.area
[docs]def section_tortuosity(section):
'''Tortuosity of a section
The tortuosity is defined as the ratio of the path length of a section
and the euclidian distnce between its end points.
The path length is the sum of distances between consecutive points.
If the section contains less than 2 points, the value 1 is returned.
'''
pts = section.points
return 1 if len(pts) < 2 else mm.section_length(pts) / mm.point_dist(pts[-1], pts[0])
[docs]def branch_order(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.
'''
return sum(1 for _ in section.iupstream()) - 1
[docs]def section_radial_distance(section, origin):
'''Return the radial distances of a tree section to a given origin point
The radial distance is the euclidian distance between the
end-point point of the section and the origin point in question.
Parameters:
section: neurite section object
origin: point to which distances are measured. It must have at least 3\
components. The first 3 components are (x, y, z).
'''
return mm.point_dist(section.points[-1], origin)
[docs]def section_meander_angles(section):
'''Inter-segment opening angles in a section'''
p = section.points
return [mm.angle_3points(p[i - 1], p[i - 2], p[i])
for i in range(2, len(p))]