Ripser.py学习 (5)：稀疏距离矩阵

1 一些必须的库

关于如何在ripser中使用稀释矩阵，一些必须的库如下：

import numpy as np
import matplotlib.pyplot as plt
import tadasets
from sklearn import datasets
from sklearn.metrics.pairwise import pairwise_distances
from scipy import sparse
from ripser import ripser
from persim import plot_diagrams

2 测试数据

测试数据包含两个噪声圆：

data = np.concatenate([
    tadasets.dsphere(n=500, d=1, r=5, noise=0.5),
    tadasets.dsphere(n=100, d=1, r=1, noise=0.2)
])


plt.scatter(data[:, 0], data[:, 1])
plt.show()

输出如下：

3 稀疏距离矩阵

使用稀疏距离矩阵与否的计算结果对比：

def makeSparseDM(X, thresh):
    N = X.shape[0]
    D = pairwise_distances(X, metric='euclidean')
    [I, J] = np.meshgrid(np.arange(N), np.arange(N))
    I = I[D <= thresh]
    J = J[D <= thresh]
    V = D[D <= thresh]
    return sparse.coo_matrix((V, (I, J)), shape=(N, N)).tocsr()


thresh = 1.5
results0 = ripser(data, thresh=thresh, maxdim=1)

D = makeSparseDM(data, thresh)
results1 = ripser(D, distance_matrix=True)

print("%i edges added in the dense filtration" % results0['num_edges'])
print("%i edges added in the sparse filtration" % results1['num_edges'])

输出如下：

13217 edges added in the dense filtration
13217 edges added in the sparse filtration

4 持续同伦图

plt.figure(figsize=(12, 4))
plt.subplot(131)
plt.scatter(data[:, 0], data[:, 1])
plt.title("Point Cloud")
plt.subplot(132)
plot_diagrams(results0['dgms'], show=False)
plt.title("Dense Filtration")
plt.subplot(133)
plt.title("Sparse Filtration")
plot_diagrams(results1['dgms'], show=False)
plt.tight_layout()
plt.show()

输出如下，可以发现两者的结果几乎是一样的：