neuror.zero_diameter_fixer¶

Fix zero diameters.

Note

This module is a re-implementation of: https://bbpgitlab.epfl.ch/nse/morphologyrepair/MUK/-/blob/main/apps/Fix_Zero_Diameter.cpp with sections recursion instead of point recursion

Module Attributes

The class used to store a point as a section and point ID in this section.

Functions

`_connect_average`	Apply a ramp diameter between the two points.
`_connect_average_legacy`	Apply a ramp diameter between the two points.
`_fix_downstream`	Ensure that diameters are decreasing in downstream direction.
`_fix_in_between`	Fix diameters between two points with valid diameters by applying a ramp.
`_fix_upstream`	Reset the diameter to upstream_good_diameter if the current value and all child values are below threshold.
`_get_point_diameter`
`_next_point_upstream`	Yield upstream points until reaching the root.
`_set_point_diameter`	Set a given diameter.
`fix_neurite`	Apply all fixes to a neurite.
`fix_zero_diameters`	Fix zero diameters.

Classes

The class used to store a point as a section and point ID in this section.

class neuror.zero_diameter_fixer.Point(section, point_id)¶

The class used to store a point as a section and point ID in this section.

neuror.zero_diameter_fixer._fix_downstream(section)[source]¶

Ensure that diameters are decreasing in downstream direction.

If the current diameter is below the threshold, change its value to the biggest value among the 1-degree children downstream diameters.

This is recursive only until a diameter above threshold is found so this fixes zero diameters that are located at the beginning of the neurite.

Fixes this: Soma--0--0--0--1--1--1

But not this: Soma--1--1--1--0--0--0--1--1

Note

neuror.zero_diameter_fixer._fix_in_between(section, stack, legacy)[source]¶

Fix diameters between two points with valid diameters by applying a ramp.

Note

Parameters:

point – the current points
stack – the stack of upstream points
legacy – whether to use legacy algorithm that didn’t account for path lengths

neuror.zero_diameter_fixer._fix_upstream(section, upstream_good_diameter)[source]¶

Reset the diameter to upstream_good_diameter if the current value and all child values are below threshold.

Note

Parameters:

section – the current section
upstream_good_diameter – the diameter value coming from upstream that will be used if the current diameter is not suitable

Returns:

The current diameter if above threshold, else the smallest child value above threshold else (if no child value is above threshold) returns 0.

Return type:

(float)

neuror.zero_diameter_fixer.fix_neurite(root_section, legacy=False)[source]¶: Apply all fixes to a neurite.

neuror.zero_diameter_fixer.fix_zero_diameters(neuron, legacy=False)[source]¶: Fix zero diameters.