pyfibre.model.tools.base_kmeans_filter module

PyFibre BD RGB clustering routine

Created by: Frank Longford Created on: 20/10/2019

class pyfibre.model.tools.base_kmeans_filter.BaseKmeansFilter(n_runs=2, n_clusters=10, p_intensity=(2, 98), sm_size=5, min_size=20, init_size=10000, reassignment_ratio=0.99, max_no_improvement=15)[source]

Bases: abc.ABC

Performs segmentation filtering using k-means clustering on RGB colour channels. Adapted from CurveAlign BDcreationHE routine.

Developers need to implement a cellular_classifier method that processes raw Kmeans clusters

abstract cellular_classifier(label_image, centres, **kwargs)[source]

Uses labels and centroids generated by K-means clusterer to assign each pixel as a cellular region

filter_image(image, **kwargs)[source]

Performs BD filtering on image

pyfibre.model.tools.base_kmeans_filter.pad(*args, **kwargs)