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"""!
@brief Examples of usage and demonstration of abilities of OPTICS algorithm in cluster analysis.
@authors Andrei Novikov (pyclustering@yandex.ru)
@date 2014-2020
@copyright BSD-3-Clause
"""
import random
from pyclustering.cluster import cluster_visualizer
from pyclustering.cluster.optics import optics, ordering_analyser, ordering_visualizer
from pyclustering.utils import read_sample, timedcall
from pyclustering.samples.definitions import SIMPLE_SAMPLES, FCPS_SAMPLES
def template_clustering(path_sample, eps, minpts, amount_clusters = None, visualize = True, ccore = False):
sample = read_sample(path_sample)
optics_instance = optics(sample, eps, minpts, amount_clusters, ccore)
(ticks, _) = timedcall(optics_instance.process)
print("Sample: ", path_sample, "\t\tExecution time: ", ticks, "\n")
if (visualize is True):
clusters = optics_instance.get_clusters()
noise = optics_instance.get_noise()
visualizer = cluster_visualizer()
visualizer.append_clusters(clusters, sample)
visualizer.append_cluster(noise, sample, marker = 'x')
visualizer.show()
ordering = optics_instance.get_ordering()
analyser = ordering_analyser(ordering)
ordering_visualizer.show_ordering_diagram(analyser, amount_clusters)
def cluster_sample1():
template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 0.5, 3)
def cluster_sample2():
template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, 3.0, 3)
def cluster_sample3():
template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, 0.7, 3)
def cluster_sample4():
template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE4, 0.7, 3)
def cluster_sample5():
template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, 0.7, 3)
def cluster_sample6():
template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE6, 1.0, 3)
def cluster_elongate():
template_clustering(SIMPLE_SAMPLES.SAMPLE_ELONGATE, 0.5, 3)
def cluster_lsun():
template_clustering(FCPS_SAMPLES.SAMPLE_LSUN, 0.5, 3)
def cluster_lsun_radius_calculation():
template_clustering(FCPS_SAMPLES.SAMPLE_LSUN, 1.0, 3, 3)
def cluster_target():
template_clustering(FCPS_SAMPLES.SAMPLE_TARGET, 0.5, 2)
def cluster_target_radius_calculation():
template_clustering(FCPS_SAMPLES.SAMPLE_TARGET, 10.0, 2, 6)
def cluster_two_diamonds():
template_clustering(FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS, 0.15, 7)
def cluster_two_diamonds_radius_calculation():
template_clustering(FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS, 1.0, 7, 2)
def cluster_wing_nut():
template_clustering(FCPS_SAMPLES.SAMPLE_WING_NUT, 0.25, 2)
def cluster_wing_nut_radius_calculation():
template_clustering(FCPS_SAMPLES.SAMPLE_WING_NUT, 1.0, 2, 2)
def cluster_chainlink():
template_clustering(FCPS_SAMPLES.SAMPLE_CHAINLINK, 0.15, 3)
def cluster_hepta():
template_clustering(FCPS_SAMPLES.SAMPLE_HEPTA, 1, 3)
def cluster_golf_ball():
template_clustering(FCPS_SAMPLES.SAMPLE_GOLF_BALL, 0.5, 3)
def cluster_atom():
template_clustering(FCPS_SAMPLES.SAMPLE_ATOM, 15, 3)
def cluster_tetra():
template_clustering(FCPS_SAMPLES.SAMPLE_TETRA, 0.4, 3)
def cluster_engy_time():
template_clustering(FCPS_SAMPLES.SAMPLE_ENGY_TIME, 0.2, 20)
def experiment_execution_time(ccore):
template_clustering(FCPS_SAMPLES.SAMPLE_LSUN, 1.0, 3, 3, False, ccore)
template_clustering(FCPS_SAMPLES.SAMPLE_TARGET, 10.0, 2, 6, False, ccore)
template_clustering(FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS, 1.0, 7, 2, False, ccore)
template_clustering(FCPS_SAMPLES.SAMPLE_CHAINLINK, 2.0, 3, 2, False, ccore)
template_clustering(FCPS_SAMPLES.SAMPLE_WING_NUT, 1.0, 2, 2, False, ccore)
template_clustering(FCPS_SAMPLES.SAMPLE_HEPTA, 1, 3, None, False, ccore)
template_clustering(FCPS_SAMPLES.SAMPLE_TETRA, 1.0, 3, 4, False, ccore)
template_clustering(FCPS_SAMPLES.SAMPLE_ATOM, 30, 3, 2, False, ccore)
def clustering_random_points(amount, ccore):
sample = [ [ random.random(), random.random() ] for _ in range(amount) ]
optics_instance = optics(sample, 0.05, 20, None, ccore)
(ticks, _) = timedcall(optics_instance.process)
print("Execution time ("+ str(amount) +" 2D-points):", ticks)
def performance_measure_random_points(ccore):
clustering_random_points(1000, ccore)
clustering_random_points(2000, ccore)
clustering_random_points(3000, ccore)
clustering_random_points(4000, ccore)
clustering_random_points(5000, ccore)
clustering_random_points(10000, ccore)
clustering_random_points(20000, ccore)
cluster_sample1()
cluster_sample2()
cluster_sample3()
cluster_sample4()
cluster_sample5()
cluster_sample6()
cluster_elongate()
cluster_lsun()
cluster_lsun_radius_calculation()
cluster_target()
cluster_target_radius_calculation()
cluster_two_diamonds()
cluster_two_diamonds_radius_calculation()
cluster_wing_nut()
cluster_wing_nut_radius_calculation()
cluster_chainlink()
cluster_hepta()
cluster_golf_ball()
cluster_atom()
cluster_tetra()
cluster_engy_time()
experiment_execution_time(False)
experiment_execution_time(True)
performance_measure_random_points(False)
performance_measure_random_points(True)
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