Logging Example

In this example we demonstrate how to enable logging in zen mapper. The bulk of the example is taken from Basic Use, see that for discussion about the mapper bit.

Enable logging

We use the builtin python logging library to log internal activity. The simplest way to enable logging is to use basicConfig. A complete breakdown of the logging library is beyond the scope of this example however the official logging documentation is rather complete. Zen mapper logs to the zen_mapper logger.

import logging

logging.basicConfig(level=logging.INFO)

Generating data

import numpy as np
import matplotlib.pyplot as plt

theta = np.linspace(0, 2 * np.pi, 50)
data = np.c_[np.cos(theta), np.sin(theta)]
plt.scatter(data[:, 0], data[:, 1])
plt.show()

Running mapper

import networkx as nx
from zen_mapper.adapters import to_networkx
from sklearn.cluster import AgglomerativeClustering
from zen_mapper.adapters import sk_learn
from zen_mapper import mapper, Width_Balanced_Cover

projection = data[:, 0]

cover_scheme = Width_Balanced_Cover(n_elements=3, percent_overlap=0.4)
cover = cover_scheme(projection)

sk = AgglomerativeClustering(
    linkage="single",
    n_clusters=None,
    distance_threshold=0.2,
)
clusterer = sk_learn(sk)


result = mapper(
    data=data,
    projection=projection,
    cover_scheme=cover_scheme,
    clusterer=clusterer,
    dim=1,
)

INFO:zen_mapper:Computing the width balanced cover
INFO:zen_mapper:Computing the width balanced cover
INFO:zen_mapper:Clustering cover element 0
INFO:zen_mapper:Found 1 clusters
INFO:zen_mapper:Clustering cover element 1
INFO:zen_mapper:Found 2 clusters
INFO:zen_mapper:Clustering cover element 2
INFO:zen_mapper:Found 1 clusters
INFO:zen_mapper:Computing the nerve
INFO:zen_mapper:Found 4 0-complexes
INFO:zen_mapper:Searching for 1-complexes
INFO:zen_mapper:Found 4 1-complexes

Visualizing the mapper graph

graph = to_networkx(result.nerve)
nx.draw(graph)