neurom.features.section¶

Section functions and functional tools.

Functions

`branch_order`(section)	Branching order of a tree section.
`downstream_pathlength`(section)	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)	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_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)¶: 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)¶: Path length from section to root.

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_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.