Fuzzy c-means clustering

[Fox Red]

Hello dear colleagues!

When I run the 'Fuzzy c-means clustering' example. I get uniform colored dots instead three color dots.

Can somebody help me to get three colored dots in the figures?

"""
========================
Fuzzy c-means clustering
========================

Fuzzy logic principles can be used to cluster multidimensional data, assigning
each point a *membership* in each cluster center from 0 to 100 percent. This
can be very powerful compared to traditional hard-thresholded clustering where
every point is assigned a crisp, exact label.

Fuzzy c-means clustering is accomplished via ``skfuzzy.cmeans``, and the
output from this function can be repurposed to classify new data according to
the calculated clusters (also known as *prediction*) via
``skfuzzy.cmeans_predict``

Data generation and setup
-------------------------

In this example we will first undertake necessary imports, then define some
test data to work with.

"""
from __future__ import division, print_function
import numpy as np
import matplotlib.pyplot as plt
import skfuzzy as fuzz

colors = ['b', 'orange', 'g', 'r', 'c', 'm', 'y', 'k', 'Brown', 'ForestGreen']

# Define three cluster centers
centers = [[4, 2],
           [1, 7],
           [5, 6]]

# Define three cluster sigmas in x and y, respectively
sigmas = [[0.8, 0.3],
          [0.3, 0.5],
          [1.1, 0.7]]

# Generate test data
np.random.seed(42)  # Set seed for reproducibility
xpts = np.empty(1)
ypts = np.empty(1)
labels = np.empty(1)
for i, ((xmu, ymu), (xsigma, ysigma)) in enumerate(zip(centers, sigmas)):
    xpts = np.hstack((xpts, np.random.standard_normal(200) * xsigma + xmu))
    ypts = np.hstack((ypts, np.random.standard_normal(200) * ysigma + ymu))
    labels = np.hstack((labels, np.ones(200) * i))

# Visualize the test data
fig0, ax0 = plt.subplots()
for label in range(3):
    ax0.plot(xpts[labels == label], ypts[labels == label], '.',
             color=colors[label])
ax0.set_title('Test data: 200 points x3 clusters.')

"""
.. image:: PLOT2RST.current_figure

Clustering
----------

Above is our test data. We see three distinct blobs. However, what would happen
if we didn't know how many clusters we should expect? Perhaps if the data were
not so clearly clustered?

Let's try clustering our data several times, with between 2 and 9 clusters.

"""
# Set up the loop and plot
fig1, axes1 = plt.subplots(3, 3, figsize=(8, 8))
alldata = np.vstack((xpts, ypts))
fpcs = []

for ncenters, ax in enumerate(axes1.reshape(-1), 2):
    cntr, u, u0, d, jm, p, fpc = fuzz.cluster.cmeans(
        alldata, ncenters, 2, error=0.005, maxiter=1000, init=None)

    # Store fpc values for later
    fpcs.append(fpc)

    # Plot assigned clusters, for each data point in training set
    cluster_membership = np.argmax(u, axis=0)
    for j in range(ncenters):
        ax.plot(xpts[cluster_membership == j],
                ypts[cluster_membership == j], '.', color=colors[j])

    # Mark the center of each fuzzy cluster
    for pt in cntr:
        ax.plot(pt[0], pt[1], 'rs')

    ax.set_title('Centers = {0}; FPC = {1:.2f}'.format(ncenters, fpc))
    ax.axis('off')

fig1.tight_layout()

"""
.. image:: PLOT2RST.current_figure

The fuzzy partition coefficient (FPC)
-------------------------------------

The FPC is defined on the range from 0 to 1, with 1 being best. It is a metric
which tells us how cleanly our data is described by a certain model. Next we
will cluster our set of data - which we know has three clusters - several
times, with between 2 and 9 clusters. We will then show the results of the
clustering, and plot the fuzzy partition coefficient. When the FPC is
maximized, our data is described best.

"""

fig2, ax2 = plt.subplots()
ax2.plot(np.r_[2:11], fpcs)
ax2.set_xlabel("Number of centers")
ax2.set_ylabel("Fuzzy partition coefficient")

"""
.. image:: PLOT2RST.current_figure

As we can see, the ideal number of centers is 3. This isn't news for our
contrived example, but having the FPC available can be very useful when the
structure of your data is unclear.

Note that we started with *two* centers, not one; clustering a dataset with
only one cluster center is the trivial solution and will by definition return
FPC == 1.


====================
Classifying New Data
====================

Now that we can cluster data, the next step is often fitting new points into
an existing model. This is known as prediction. It requires both an existing
model and new data to be classified.

Building the model
------------------

We know our best model has three cluster centers. We'll rebuild a 3-cluster
model for use in prediction, generate new uniform data, and predict which
cluster to which each new data point belongs.

"""
# Regenerate fuzzy model with 3 cluster centers - note that center ordering
# is random in this clustering algorithm, so the centers may change places
cntr, u_orig, _, _, _, _, _ = fuzz.cluster.cmeans(
    alldata, 3, 2, error=0.005, maxiter=1000)

# Show 3-cluster model
fig2, ax2 = plt.subplots()
ax2.set_title('Trained model')
for j in range(3):
    ax2.plot(alldata[0, u_orig.argmax(axis=0) == j],
             alldata[1, u_orig.argmax(axis=0) == j], 'o',
             label='series ' + str(j))
ax2.legend()

"""
.. image:: PLOT2RST.current_figure

Prediction
----------

Finally, we generate uniformly sampled data over this field and classify it
via ``cmeans_predict``, incorporating it into the pre-existing model.

"""

# Generate uniformly sampled data spread across the range [0, 10] in x and y
newdata = np.random.uniform(0, 1, (1100, 2)) * 10

# Predict new cluster membership with `cmeans_predict` as well as
# `cntr` from the 3-cluster model
u, u0, d, jm, p, fpc = fuzz.cluster.cmeans_predict(
    newdata.T, cntr, 2, error=0.005, maxiter=1000)

# Plot the classified uniform data. Note for visualization the maximum
# membership value has been taken at each point (i.e. these are hardened,
# not fuzzy results visualized) but the full fuzzy result is the output
# from cmeans_predict.
cluster_membership = np.argmax(u, axis=0)  # Hardening for visualization

fig3, ax3 = plt.subplots()
ax3.set_title('Random points classifed according to known centers')
for j in range(3):
    ax3.plot(newdata[cluster_membership == j, 0],
             newdata[cluster_membership == j, 1], 'o',
             label='series ' + str(j))
ax3.legend()

plt.show()

"""
.. image:: PLOT2RST.current_figure

"""

[Josh Warner]

​I cannot reproduce - copy/pasting this exact script gives me the results shown in the online docs here.​

There is an Issue raised about this (#80). I'd encourage discussion to continue there as GitHub has a better interface than Google Groups.

My suggestion is that custom matplotlib parameters are set, or a custom color cycler got in the way, because it definitely works as expected in a clean Anaconda virtualenv.

[JDWarner]

For posterity, see discussion around GitHub Issue #80. This is believed solved by reinstalling matplotlib or installing a new Python distribution designed for scientific computing.