密度聚类算法python详解_密度峰值聚类算法总结及其python实现

密度峰值聚类算法总结及其python实现

先上代码：

#-*-coding:utf-8 -*-

from __future__ import division

import numpy as np

from sklearn import preprocessing

from scipy.special import comb

from sklearn.metrics import adjusted_rand_score,f1_score,accuracy_score,precision_score,precision_recall_fscore_support

from sklearn.datasets import *

import sys

import matplotlib.pyplot as plt

import matplotlib.colors as colors

import csv

import random

from time import time

from matplotlib.font_manager import FontProperties

defaultencoding = 'utf-8'

font = FontProperties(fname='/Library/Fonts/Songti.ttc')

if sys.getdefaultencoding() != defaultencoding:

reload(sys)

sys.setdefaultencoding(defaultencoding)

def calculate(data,percent):

#计算距离

distlist = []

dist = np.zeros((len(data), len(data)));

for i in range(len(data)-1):

for j in range(i+1,len(data)):

distance = np.sqrt(np.sum(np.square(data[i] - data[j])))

dist[i, j] = distance

dist[j, i] = distance

if(i != j):

distlist.append(distance)

# dc

# for i in range(len(dist) - 1):

# for j in range(len(dist) - 1):

# if(dist[i,j] != 0):

sortdist = sorted(distlist)

position = round(len(distlist) * percent / 100)

dc = sortdist[position]

print('dc',dc)

#计算局部密度

# 计算局部密度 rho (利用 Gaussian 核)

rho = np.zeros(len(dist))

# Gaussian kernel

for i in range(len(dist) - 1):

for j in range(i + 1, len(dist)):

rho[i] = rho[i] + np.exp(-(dist[i, j] / dc) * (dist[i, j] / dc))

rho[j] = rho[j] + np.exp(-(dist[i, j] / dc) * (dist[i, j] / dc))

rho = [item / max(rho) for item in rho]

# 生成 delta 和 nneigh 数组

# delta 距离数组

# nneigh 比本身密度大的最近的点

# 记录 rho 值更大的数据点中与 ordrho(ii) 距离最近的点的编号 ordrho(jj)

# 将 rho 按降序排列，ordrho 保持序

ordrho = np.flipud(np.argsort(rho))

delta = np.zeros(len(dist))

nneigh = np.zeros(len(dist),dtype=int)

delta[ordrho[0]] = -1.

nneigh[ordrho[0]] = 0

# 求最大距离

maxd = max(dist.flatten())

for ii in range(1,len(dist)):

delta[ordrho[ii]] = maxd

for jj in range(ii):

if dist[ordrho[ii], ordrho[jj]] < delta[ordrho[ii]]:

delta[ordrho[ii]] = dist[ordrho[ii], ordrho[jj]]

nneigh[ordrho[ii]] = ordrho[jj]

delta[ordrho[0]] = max(delta)

# delta = [item/max(delta) for item in delta]

gamma = [rho[i] * delta[i] for i in range(len(dist))]

plt.figure(1);

for index in range(len(dist)):

plt.plot(rho[index], delta[index], 'ko');

pos = plt.ginput(1)

rhomin = pos[0][0]

deltamin = pos[0][1]

cl = -1*np.ones(len(dist),dtype=int)

icl = []

NCLUST = 1

for i in range(len(dist)):

if rho[i]>rhomin and delta[i]>deltamin:

cl[i] = NCLUST #第 i 号数据点属于第 NCLUST 个 cluster

icl.append(i) # 逆映射,第 NCLUST 个 cluster 的中心为第 i 号数据点

NCLUST+=1

for i in range(len(dist)):

if cl[ordrho[i]] == -1:

cl[ordrho[i]] = cl[nneigh[ordrho[i]]]

print(cl)

color = ['bo', 'co', 'go', 'ko', 'mo', 'ro', 'wo', 'yo']

s = random.sample(color, NCLUST-1)

plt.close()

for i in range(len(data)):

plt.plot(data[i][0],data[i][1],s[cl[i]-1])

plt.show();

def loadData():

dataSet = []

# fileIn = open('C:/data/jain.txt')

fileIn = open('C:/data/jain.dat')

for line in fileIn.readlines():

lineArr = line.strip().split('\t')

dataSet.append([float(lineArr[0]), float(lineArr[1])])

data = np.array(dataSet);

return data;

#data,label = load_breast_cancer(True)

#min_max_scaler = preprocessing.MinMaxScaler()

#data = min_max_scaler.fit_transform(data)

def test():

data = loadData()

dataSet = np.array(data);

dist = calculate(dataSet,2)

# local_density(dist,2)

if __name__ == '__main__': test();

# len = len(data)

# # start = time()

# fsdp = FSDP(len,7.8605,data)

# fsdp.clustering(0.4703,0.7108)

# print (time() - start)/60.0

# print fsdp.cl

# print label

# print "f1_score"

# print f1_score(fsdp.cl,label,average="weighted")

# print "accary"

# print accuracy_score(fsdp.cl,label)

# print adjusted_rand_score(fsdp.cl,label)

# gamma = np.flipud(np.sort(fsdp.gamma))

# plt.figure("标准CS")

# plt.subplot(311)

# x = [t for t in range(0, len(gamma))]

# plt.plot(x, gamma, 'r*')

# plt.subplot(312)

# plt.plot(fsdp.rho, fsdp.delta, 'r*')

# plt.legend(loc='upper right', prop=font)

#

# plt.subplot(313)

# color = []

# for i in fsdp.cl:

# color.append(colors.cnames.values()[i])

# plt.scatter(data[:,0], data[:,1],marker=".",c=color)

# plt.legend(loc='upper right', prop=font)

# plt.show()