kmean对3d点聚类

效果一般

# -*- coding : UTF-8 -*-
# @file   : clustering_3d.py
# @Time   : 2021-12-22 10:01
# @Author : wmz

import random
from sklearn import datasets
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
import pandas as pd
import os


# 正规化数据集 X
def normalize(X, axis=-1, p=2):
    lp_norm = np.atleast_1d(np.linalg.norm(X, p, axis))
    lp_norm[lp_norm == 0] = 1
    return X / np.expand_dims(lp_norm, axis)


# 计算一个样本与数据集中所有样本的欧氏距离的平方
def euclidean_distance(one_sample, X):
    one_sample = one_sample.reshape(1, -1)
    X = X.reshape(X.shape[0], -1)
    distances = np.power(np.tile(one_sample, (X.shape[0], 1)) - X, 2).sum(axis=1)
    return distances



class Kmeans():
    """Kmeans聚类算法.

    Parameters:
    -----------
    k: int
        聚类的数目.
    max_iterations: int
        最大迭代次数.
    varepsilon: float
        判断是否收敛, 如果上一次的所有k个聚类中心与本次的所有k个聚类中心的差都小于varepsilon,
        则说明算法已经收敛
    """
    def __init__(self, k=2, max_iterations=500, varepsilon=0.0001):
        self.k = k
        self.max_iterations = max_iterations
        self.varepsilon = varepsilon

    # 从所有样本中随机选取self.k样本作为初始的聚类中心
    def init_random_centroids(self, X):
        n_samples, n_features = np.shape(X)
        centroids = np.zeros((self.k, n_features))
        for i in range(self.k):
            centroid = X[np.random.choice(range(n_samples))]
            centroids[i] = centroid
        return centroids

    # 返回距离该样本最近的一个中心索引[0, self.k)
    def _closest_centroid(self, sample, centroids):
        distances = euclidean_distance(sample, centroids)
        closest_i = np.argmin(distances)
        return closest_i

    # 将所有样本进行归类，归类规则就是将该样本归类到与其最近的中心
    def create_clusters(self, centroids, X):
        n_samples = np.shape(X)[0]
        clusters = [[] for _ in range(self.k)]
        for sample_i, sample in enumerate(X):
            centroid_i = self._closest_centroid(sample, centroids)
            clusters[centroid_i].append(sample_i)
        return clusters

    # 对中心进行更新
    def update_centroids(self, clusters, X):
        n_features = np.shape(X)[1]
        centroids = np.zeros((self.k, n_features))
        for i, cluster in enumerate(clusters):
            centroid = np.mean(X[cluster], axis=0)
            centroids[i] = centroid
        return centroids

    # 将所有样本进行归类，其所在的类别的索引就是其类别标签
    def get_cluster_labels(self, clusters, X):
        y_pred = np.zeros(np.shape(X)[0])
        for cluster_i, cluster in enumerate(clusters):
            for sample_i in cluster:
                y_pred[sample_i] = cluster_i
        return y_pred

    # 对整个数据集X进行Kmeans聚类，返回其聚类的标签
    def predict(self, X):
        # 从所有样本中随机选取self.k样本作为初始的聚类中心
        centroids = self.init_random_centroids(X)

        # 迭代，直到算法收敛(上一次的聚类中心和这一次的聚类中心几乎重合)或者达到最大迭代次数
        for _ in range(self.max_iterations):
            # 将所有进行归类，归类规则就是将该样本归类到与其最近的中心
            clusters = self.create_clusters(centroids, X)
            former_centroids = centroids

            # 计算新的聚类中心
            centroids = self.update_centroids(clusters, X)

            # 如果聚类中心几乎没有变化，说明算法已经收敛，退出迭代
            diff = centroids - former_centroids
            if diff.any() < self.varepsilon:
                break

        return self.get_cluster_labels(clusters, X)


def getFiles(path, suffix):
    return [os.path.join(root, file) for root, dirs, files in os.walk(path) for file in files if file.endswith(suffix)]


def read_info_from_csv(file):
    print(file)
    df = pd.read_csv(file)
    # print(df.head())
    anchors = []
    for v in df.values:
        # print(v)
        fid = v[0]
        if "Avg" in fid:
            continue
        anchors.append(v[1:].tolist())
    return anchors


def main():
    # Load the dataset
    lwh_list = []
    csv_folder = r"D:\Work\Data\Patient_Data\bbox_bfresample_spacing1mm\bone_info_statisitic"
    file_list = getFiles(csv_folder, '.csv')
    anchors_all = []
    for file in file_list:
        if not'femur' in file:
            continue
        anchors = read_info_from_csv(file)
        anchors_all.append(anchors)
        print(anchors)
    anchor_reshape1 = np.array(anchors_all).reshape(-1, 3)
    print(anchor_reshape1)
    # np.savetxt('anchor_reshape.txt', anchor_reshape)
    anchor_reshape = np.loadtxt('anchor_reshape.txt')

    # 用Kmeans算法进行聚类
    clf = Kmeans(k=3)
    y_pred = clf.predict(anchor_reshape)
    print(y_pred)
    print("anchor_reshape[y_pred == 0]")
    print(anchor_reshape[y_pred == 0])
    print("anchor_reshape[y_pred == 1]")
    print(anchor_reshape[y_pred == 1])
    print("anchor_reshape[y_pred == 2]")
    print(anchor_reshape[y_pred == 2])
    print("anchor_reshape[y_pred == 3]")
    print(anchor_reshape[y_pred == 3])


    # 可视化聚类效果
    fig = plt.figure()
    ax = Axes3D(fig)
    plt.scatter(anchor_reshape[y_pred == 0][:, 0], anchor_reshape[y_pred == 0][:, 1], anchor_reshape[y_pred == 0][:, 2], c="red", marker='*')
    plt.scatter(anchor_reshape[y_pred == 1][:, 0], anchor_reshape[y_pred == 1][:, 1], anchor_reshape[y_pred == 1][:, 2], c="green", marker='*')
    plt.scatter(anchor_reshape[y_pred == 2][:, 0], anchor_reshape[y_pred == 2][:, 1], anchor_reshape[y_pred == 2][:, 2], c="blue", marker='*')
    plt.scatter(anchor_reshape[y_pred == 3][:, 0], anchor_reshape[y_pred == 3][:, 1], anchor_reshape[y_pred == 3][:, 2], c="yellow", marker='*')
    plt.show()


if __name__ == "__main__":
    main()

调整后的代码

# -*- coding : UTF-8 -*-
# @file   : clustering_3d.py
# @Time   : 2021-12-22 10:01
# @Author : wmz

import random
from sklearn import datasets
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
import pandas as pd
import os


# 正规化数据集 X
def normalize(X, axis=-1, p=2):
    lp_norm = np.atleast_1d(np.linalg.norm(X, p, axis))
    lp_norm[lp_norm == 0] = 1
    return X / np.expand_dims(lp_norm, axis)


# 计算一个样本与数据集中所有样本的欧氏距离的平方
def euclidean_distance(one_sample, X):
    one_sample = one_sample.reshape(1, -1)
    X = X.reshape(X.shape[0], -1)
    distances = np.power(np.tile(one_sample, (X.shape[0], 1)) - X, 2).sum(axis=1)
    return distances



class Kmeans():
    """Kmeans聚类算法.

    Parameters:
    -----------
    k: int
        聚类的数目.
    max_iterations: int
        最大迭代次数.
    varepsilon: float
        判断是否收敛, 如果上一次的所有k个聚类中心与本次的所有k个聚类中心的差都小于varepsilon,
        则说明算法已经收敛
    """
    def __init__(self, k=2, max_iterations=500, varepsilon=0.0001):
        self.k = k
        self.max_iterations = max_iterations
        self.varepsilon = varepsilon

    # 从所有样本中随机选取self.k样本作为初始的聚类中心
    def init_random_centroids(self, X):
        n_samples, n_features = np.shape(X)
        centroids = np.zeros((self.k, n_features))
        for i in range(self.k):
            centroid = X[np.random.choice(range(n_samples))]
            centroids[i] = centroid
        return centroids

    # 返回距离该样本最近的一个中心索引[0, self.k)
    def _closest_centroid(self, sample, centroids):
        distances = euclidean_distance(sample, centroids)
        closest_i = np.argmin(distances)
        return closest_i

    # 将所有样本进行归类，归类规则就是将该样本归类到与其最近的中心
    def create_clusters(self, centroids, X):
        n_samples = np.shape(X)[0]
        clusters = [[] for _ in range(self.k)]
        for sample_i, sample in enumerate(X):
            centroid_i = self._closest_centroid(sample, centroids)
            clusters[centroid_i].append(sample_i)
        return clusters

    # 对中心进行更新
    def update_centroids(self, clusters, X):
        n_features = np.shape(X)[1]
        centroids = np.zeros((self.k, n_features))
        for i, cluster in enumerate(clusters):
            centroid = np.mean(X[cluster], axis=0)
            centroids[i] = centroid
        return centroids

    # 将所有样本进行归类，其所在的类别的索引就是其类别标签
    def get_cluster_labels(self, clusters, X):
        y_pred = np.zeros(np.shape(X)[0])
        for cluster_i, cluster in enumerate(clusters):
            for sample_i in cluster:
                y_pred[sample_i] = cluster_i
        return y_pred

    # 对整个数据集X进行Kmeans聚类，返回其聚类的标签
    def predict(self, X):
        # 从所有样本中随机选取self.k样本作为初始的聚类中心
        centroids = self.init_random_centroids(X)

        # 迭代，直到算法收敛(上一次的聚类中心和这一次的聚类中心几乎重合)或者达到最大迭代次数
        for _ in range(self.max_iterations):
            # 将所有进行归类，归类规则就是将该样本归类到与其最近的中心
            clusters = self.create_clusters(centroids, X)
            former_centroids = centroids

            # 计算新的聚类中心
            centroids = self.update_centroids(clusters, X)

            # 如果聚类中心几乎没有变化，说明算法已经收敛，退出迭代
            diff = centroids - former_centroids
            if diff.any() < self.varepsilon:
                break

        return self.get_cluster_labels(clusters, X)


def getFiles(path, suffix):
    return [os.path.join(root, file) for root, dirs, files in os.walk(path) for file in files if file.endswith(suffix)]


def read_info_from_csv(file):
    print(file)
    df = pd.read_csv(file)
    # print(df.head())
    anchors = []
    for v in df.values:
        # print(v)
        fid = v[0]
        if "Avg" in fid:
            continue
        anchors.append(v[1:].tolist())
    return anchors


def main():
    # Load the dataset
    lwh_list = []
    csv_folder = r"D:\Work\Data\Patient_Data\bbox_bfresample_spacing1mm\bone_info_statisitic"
    file_list = getFiles(csv_folder, '.csv')
    anchors_all = []
    for file in file_list:
        # if not'hip' in file:
        #     continue
        anchors = read_info_from_csv(file)
        anchors_all.append(anchors)
        print(anchors)
    anchor_reshape1 = np.array(anchors_all).reshape(-1, 3)
    print(anchor_reshape1)
    np.savetxt('anchor_reshape.txt', anchor_reshape1)
    anchor_reshape = np.loadtxt('anchor_reshape.txt')
    print(anchor_reshape.shape)

    # 用Kmeans算法进行聚类
    classes = 8
    clf = Kmeans(k=classes)
    y_pred = clf.predict(anchor_reshape)
    print(y_pred)
    for i in range(classes):
        print("anchor_reshape[y_pred == ]", i)
        # print(anchor_reshape[y_pred == i])
        print(np.mean(anchor_reshape[y_pred == i], axis=0))


    # 可视化聚类效果
    clolrs = ["red", "green", "blue", "yellow", "black", "cyan", "gold", "gray"]
    fig = plt.figure()
    ax = Axes3D(fig)
    for i in range(classes):
        plt.scatter(anchor_reshape[y_pred == i][:, 0], anchor_reshape[y_pred == i][:, 1],
                    anchor_reshape[y_pred == i][:, 2], c=clolrs[i], marker='*')

    plt.show()


if __name__ == "__main__":
    main()

pycharm下的显示效果（只能2D显示）：

终端命令行执行时显示效果（3D显示，支持旋转）