tracingfuncs

class topostats.tracingfuncs.getSkeleton(image_data, binary_map, number_of_columns, number_of_rows, pixel_size)

Skeltonisation algorithm based on the paper “A Fast Parallel Algorithm for Thinning Digital Patterns” by Zhang et al., 1984

doSkeletonising()

Simple while loop to check if the skeletonising is finished

finalSkeletonisationIteration()

A final skeletonisation iteration that removes “hanging” pixels. Examples of such pixels are:

[0, 0, 0] [0, 1, 0] [0, 0, 0] [0, 1, 1] [0, 1, 1] [0, 1, 1]

case 1: [0, 1, 0] or case 2: [0, 1, 0] or case 3: [1, 1, 0]

This is useful for the future functions that rely on local pixel environment to make assessments about the overall shape/structure of traces

pruneSkeleton()

Function to remove the hanging branches from the skeletons - these are a persistent problem in the overall tracing process.