neurom.features.section

Section functions and functional tools.

Functions

branch_order(section)

Branching order of a tree section.

downstream_pathlength(section[, iterator_type])

Compute the total downstream length starting from a section.

locate_segment_position(section, fraction)

Segment ID / offset corresponding to a given fraction of section length.

number_of_segments(section)

Returns the number of segments within a section.

section_area(section)

Surface area of a section.

section_end_distance(section)

End to end distance of a section.

section_length(section)

Length of a section.

section_mean_radius(section)

Compute the mean radius of a section weighted by segment lengths.

section_meander_angles(section)

Inter-segment opening angles in a section.

section_path_length(section[, stop_node])

Path length from section to root.

section_points(section)

Returns the points in the section.

section_radial_distance(section, origin)

Return the radial distances of a tree section to a given origin point.

section_tortuosity(section)

Tortuosity of a section.

section_volume(section)

Volume of a section.

segment_areas(section)

Returns the list of segment areas within the section.

segment_lengths(section[, prepend_zero])

Returns the list of segment lengths within the section.

segment_mean_radii(section)

Returns the list of segment mean radii within the section.

segment_midpoint_radial_distances(section[, ...])

Returns the list of segment midpoint radial distances to the origin.

segment_midpoints(section)

Returns the list of segment midpoints within the section.

segment_taper_rates(section)

Returns the list of segment taper rates within the section.

segment_volumes(section)

Returns the list of segment volumes within the section.

strahler_order(section)

Branching order of a tree section.

taper_rate(section)

Taper rate from fit along a section.

neurom.features.section.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.

neurom.features.section.downstream_pathlength(section, iterator_type=<function Section.ipreorder>)

Compute the total downstream length starting from a section.

neurom.features.section.locate_segment_position(section, fraction)

Segment ID / offset corresponding to a given fraction of section length.

neurom.features.section.number_of_segments(section)

Returns the number of segments within a section.

neurom.features.section.section_area(section)

Surface area of a section.

neurom.features.section.section_end_distance(section)

End to end distance of a section.

The end to end distance of a section is defined as the euclidian distnce between its end points.

If the section contains less than 2 points, the value 0 is returned.

neurom.features.section.section_length(section)

Length of a section.

neurom.features.section.section_mean_radius(section)

Compute the mean radius of a section weighted by segment lengths.

neurom.features.section.section_meander_angles(section)

Inter-segment opening angles in a section.

neurom.features.section.section_path_length(section, stop_node=None)

Path length from section to root.

Parameters:
  • section – Section object.

  • stop_node – Node to stop the upstream traversal. If None, it stops when no parent is found.

neurom.features.section.section_points(section)

Returns the points in the section.

neurom.features.section.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).

neurom.features.section.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.

neurom.features.section.section_volume(section)

Volume of a section.

neurom.features.section.segment_areas(section)

Returns the list of segment areas within the section.

neurom.features.section.segment_lengths(section, prepend_zero=False)

Returns the list of segment lengths within the section.

neurom.features.section.segment_mean_radii(section)

Returns the list of segment mean radii within the section.

neurom.features.section.segment_midpoint_radial_distances(section, origin=None)

Returns the list of segment midpoint radial distances to the origin.

neurom.features.section.segment_midpoints(section)

Returns the list of segment midpoints within the section.

neurom.features.section.segment_taper_rates(section)

Returns the list of segment taper rates within the section.

neurom.features.section.segment_volumes(section)

Returns the list of segment volumes within the section.

neurom.features.section.strahler_order(section)

Branching order of a tree section.

The strahler order is the inverse of the branch order, since this is computed from the tips of the tree towards the root.

This implementation is a translation of the three steps described in Wikipedia (https://en.wikipedia.org/wiki/Strahler_number):

  • If the node is a leaf (has no children), its Strahler number is one.

  • If the node has one child with Strahler number i, and all other children have Strahler numbers less than i, then the Strahler number of the node is i again.

  • If the node has two or more children with Strahler number i, and no children with greater number, then the Strahler number of the node is i + 1.

No efforts have been invested in making it computationnaly efficient, but it computes acceptably fast on tested morphologies (i.e., no waiting time).

neurom.features.section.taper_rate(section)

Taper rate from fit along a section.