experiment-2D-holes-analysis.py

import numpy as np
import matplotlib.pylab as plt

from persistence_diagram import persistence
from plot_persistent_homology import plot_diagrams


if __name__ == '__main__':
    seed = 12345
    num_neurons = 1024
    bc_base = './results/barcode-experiment-2D-holes-'
    h0_base = './results/homology0-experiment-2D-holes-'
    h1_base = './results/homology1-experiment-2D-holes-'

    n = 50_000
    X = np.random.uniform(0, 1, n)
    Y = np.random.uniform(0, 1, n)
    holes = 64
    for i in range(holes):
        x, y = np.random.uniform(0.1, 0.9, 2)
        r = 0.1 * np.random.uniform(0, 1)
        idx = ((X-x)**2 + (Y-y)**2) > r*r
        X, Y = X[idx], Y[idx]
    X = np.c_[X, Y]
    input_space = X

    regular_som = np.load("results/experiment-2D-holes-regular.npy")
    random_som = np.load("results/experiment-2D-holes-random.npy")
    data = [input_space, regular_som, random_som]
    case = ['input_space', 'regular', 'random']
    per = persistence(dimension=2, max_edge_length=1.5, max_alpha_square=2)
    for i, d in enumerate(data):
        per.compute_persistence(d, case='2D-holes-'+case[i])

    homology0_input = per.read_pdgm(h0_base+'input_space.dat')
    homology1_input = per.read_pdgm(h1_base+'input_space.dat')

    homology0_regular = per.read_pdgm(h0_base+'regular.dat')
    homology1_regular = per.read_pdgm(h1_base+'regular.dat')

    homology0_random = per.read_pdgm(h0_base+'random.dat')
    homology1_random = per.read_pdgm(h1_base+'random.dat')

    regDH0, regDH1 = per.compute_distances(homology0_input,
                                           homology1_input,
                                           homology0_regular,
                                           homology1_regular)

    ranDH0, ranDH1 = per.compute_distances(homology0_input,
                                           homology1_input,
                                           homology0_random,
                                           homology1_random)
    print("=" * 30)
    print("Bootstrap distance (Regular) - H0: %f, H1 %f" % (regDH0, regDH1))
    print("Bootstrap distance (Random) - H0: %f, H1 %f" % (ranDH0, ranDH1))
    print("=" * 30)

    dgm_input = per.read_pdgm(bc_base+'input_space.dat')
    dgm_regular = per.read_pdgm(bc_base+'regular.dat')
    dgm_random = per.read_pdgm(bc_base+'random.dat')

    plot_diagrams(dgm_input, dgm_regular, dgm_random)
    plt.savefig("experiment-2D-holes-analysis.pdf")
    plt.show()