kmeans 算法，python

重点内容#################################################

kmeans: k-means cluster

Author : zouxy

Date : 2013-12-25

HomePage : http://blog.csdn.net/zouxy09

Email : zouxy09@qq.com

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from numpy import *
import time
import matplotlib.pyplot as plt

calculate Euclidean distance

def euclDistance(vector1, vector2):
return sqrt(sum(power(vector2 - vector1, 2)))

init centroids with random samples

def initCentroids(dataSet, k):
numSamples, dim = dataSet.shape
centroids = zeros((k, dim))
for i in range(k):
index = int(random.uniform(0, numSamples))
centroids[i, :] = dataSet[index, :]
return centroids

k-means cluster

def kmeans(dataSet, k):
numSamples = dataSet.shape[0]
# first column stores which cluster this sample belongs to,
# second column stores the error between this sample and its centroid
clusterAssment = mat(zeros((numSamples, 2)))
clusterChanged = True

## step 1: init centroids
centroids = initCentroids(dataSet, k)

while clusterChanged:
    clusterChanged = False
    ## for each sample
    for i in xrange(numSamples):
        minDist  = 100000.0
        minIndex = 0
        ## for each centroid
        ## step 2: find the centroid who is closest
        for j in range(k):
            distance = euclDistance(centroids[j, :], dataSet[i, :])
            if distance < minDist:
                minDist  = distance
                minIndex = j

        ## step 3: update its cluster
        if clusterAssment[i, 0] != minIndex:
            clusterChanged = True
            clusterAssment[i, :] = minIndex, minDist**2

    ## step 4: update centroids
    for j in range(k):
        pointsInCluster = dataSet[nonzero(clusterAssment[:, 0].A == j)[0]]
        centroids[j, :] = mean(pointsInCluster, axis = 0)

print 'Congratulations, cluster complete!'
return centroids, clusterAssment

show your cluster only available with 2-D data

def showCluster(dataSet, k, centroids, clusterAssment):
numSamples, dim = dataSet.shape
if dim != 2:
print “Sorry! I can not draw because the dimension of your data is not 2!”
return 1

mark = ['or', 'ob', 'og', 'ok', '^r', '+r', 'sr', 'dr', '<r', 'pr']
if k > len(mark):
    print "Sorry! Your k is too large! please contact Zouxy"
    return 1

# draw all samples
for i in xrange(numSamples):
    markIndex = int(clusterAssment[i, 0])
    plt.plot(dataSet[i, 0], dataSet[i, 1], mark[markIndex])

mark = ['Dr', 'Db', 'Dg', 'Dk', '^b', '+b', 'sb', 'db', '<b', 'pb']
# draw the centroids
for i in range(k):
    plt.plot(centroids[i, 0], centroids[i, 1], mark[i], markersize = 12)

plt.show()

step 1: load data

print “step 1: load data…”
dataSet = []
fileIn = open(‘E:/Dataset/testSet.txt’)
for line in fileIn.readlines():
lineArr = line.strip().split(‘\t’)
dataSet.append([float(lineArr[0]), float(lineArr[1])])

step 2: clustering…

print “step 2: clustering…”
dataSet = mat(dataSet)
k = 4
centroids, clusterAssment = kmeans(dataSet, k)

step 3: show the result

print “step 3: show the result…”
showCluster(dataSet, k, centroids, clusterAssment)