neurom.check.neuron_checks

NeuroM neuron checking functions.

Contains functions for checking validity of neuron neurites and somata. Tests assumes neurites and/or soma have been succesfully built where applicable, i.e. soma- and neurite-related structural tests pass.

Functions

has_all_monotonic_neurites	Check that a neuron has only neurites that are monotonic
has_all_nonzero_neurite_radii	Check presence of neurite points with radius not above threshold
has_all_nonzero_section_lengths	Check presence of neuron sections with length not above threshold
has_all_nonzero_segment_lengths	Check presence of neuron segments with length not above threshold
has_apical_dendrite	Check if a neuron has apical dendrites
has_axon	Check if a neuron has an axon
has_basal_dendrite	Check if a neuron has basal dendrites
has_no_dangling_branch	Check if the neuron has dangling neurites
has_no_fat_ends	Check if leaf points are too large
has_no_flat_neurites	Check that a neuron has no flat neurites
has_no_jumps	Check if there are jumps (large movements in the axis)
has_no_narrow_neurite_section	Check if the neuron has dendrites with narrow sections
has_no_narrow_start	Check if neurites have a narrow start
has_no_root_node_jumps	Check that the neurites have their first point not further than
has_nonzero_soma_radius	Check if soma radius not above threshold