Persistence graphical tools benchmark

bench_persistence_graphical_tools.py

import numpy as np
import gudhi
import matplotlib.pyplot as plt
from timeit import default_timer as timer
from datetime import timedelta

def randpers(nb_elts):
    a = np.random.random(size=(nb_elts, 2))
    # birth = column 0 | death = column 0 + column 1
    return np.concatenate(((a[:,0]).reshape(nb_elts,1), (a[:,0] + a[:,1]).reshape(nb_elts,1)), axis=1)

nb_plots = 1000
for func in [gudhi.plot_persistence_diagram, gudhi.plot_persistence_barcode, gudhi.plot_persistence_density]:
    while True:
        start = timer()
        func(randpers(nb_plots), max_intervals=nb_plots)
        # Do not get stuck on matplotlib GUI
        plt.ion()
        plt.show()
        chrono = timedelta(seconds=timer()-start)
        print(func, "\t", nb_plots, "\t in ", chrono)
        plt.close('all')
        nb_plots = nb_plots * 2
        if chrono.total_seconds() > 10:
            nb_plots = 1000
            break