二分k均值聚类

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 range(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 using k-means complete!')
    return centroids, clusterAssment


# bisecting k-means cluster
def biKmeans(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)))

    # step 1: the init cluster is the whole data set
    centroid = mean(dataSet, axis=0).tolist()[0]
    centList = [centroid]
    for i in range(numSamples):
        clusterAssment[i, 1] = euclDistance(mat(centroid), dataSet[i, :]) ** 2

    while len(centList) < k:
        # min sum of square error
        minSSE = 100000.0
        numCurrCluster = len(centList)
        # for each cluster
        for i in range(numCurrCluster):
            # step 2: get samples in cluster i
            pointsInCurrCluster = dataSet[nonzero(clusterAssment[:, 0].A == i)[0], :]

            # step 3: cluster it to 2 sub-clusters using k-means
            centroids, splitClusterAssment = kmeans(pointsInCurrCluster, 2)

            # step 4: calculate the sum of square error after split this cluster
            splitSSE = sum(splitClusterAssment[:, 1])
            notSplitSSE = sum(clusterAssment[nonzero(clusterAssment[:, 0].A != i)[0], 1])
            currSplitSSE = splitSSE + notSplitSSE

            # step 5: find the best split cluster which has the min sum of square error
            if currSplitSSE < minSSE:
                minSSE = currSplitSSE
                bestCentroidToSplit = i
                bestNewCentroids = centroids.copy()
                bestClusterAssment = splitClusterAssment.copy()

                # step 6: modify the cluster index for adding new cluster
        bestClusterAssment[nonzero(bestClusterAssment[:, 0].A == 1)[0], 0] = numCurrCluster
        bestClusterAssment[nonzero(bestClusterAssment[:, 0].A == 0)[0], 0] = bestCentroidToSplit

        # step 7: update and append the centroids of the new 2 sub-cluster
        centList[bestCentroidToSplit] = bestNewCentroids[0, :]
        centList.append(bestNewCentroids[1, :])

        # step 8: update the index and error of the samples whose cluster have been changed
        clusterAssment[nonzero(clusterAssment[:, 0].A == bestCentroidToSplit), :] = bestClusterAssment

    print('Congratulations, cluster using bi-kmeans complete!')
    return mat(centList), 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 range(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()


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

## step 1: load data
print("step 1: load data...")
dataSet = []
fileIn = open('/home/zengxl/PycharmProjects/test5.py/aaa/机器学习实战代码/Ch10/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 = biKmeans(dataSet, k)

## step 3: show the result
print("step 3: show the result...")
showCluster(dataSet, k, centroids, clusterAssment)