kmeans_visualizer

Complexity

Total Complexity

19

Size/Duplication

Total Lines	100
Duplicated Lines	0 %

Importance

Changes

0

6 Methods

Rating	Name	Duplication	Size	Complexity
A	__draw_rays()	0	7	2
A	__draw_centers()	0	10	3
A	__draw_center()	0	10	4
B	show_clusters()	0	34	3
A	__get_argument()	0	6	2
B	__draw_cluster_rays()	0	12	5

"""!


@brief Cluster analysis algorithm: K-Means

@details Based on book description:

         - J.B.MacQueen. Some Methods for Classification and Analysis of Multivariate Observations. 1967.


@authors Andrei Novikov (pyclustering@yandex.ru)

@date 2014-2018

@copyright GNU Public License


@cond GNU_PUBLIC_LICENSE

    PyClustering is free software: you can redistribute it and/or modify

    it under the terms of the GNU General Public License as published by

    the Free Software Foundation, either version 3 of the License, or

    (at your option) any later version.

    

    PyClustering is distributed in the hope that it will be useful,

    but WITHOUT ANY WARRANTY; without even the implied warranty of

    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

    GNU General Public License for more details.

    

    You should have received a copy of the GNU General Public License

    along with this program.  If not, see <http://www.gnu.org/licenses/>.

@endcond


"""



import numpy;

The import numpy could not be resolved.

import matplotlib.pyplot as plt;

The import matplotlib.pyplot could not be resolved.

import pyclustering.core.kmeans_wrapper as wrapper;


from pyclustering.core.wrapper import ccore_library;


from pyclustering.cluster.encoder import type_encoding;

from pyclustering.cluster import cluster_visualizer;



class kmeans_observer:

    """!

    @brief Observer of K-Means algorithm that is used to collect information about clustering process on each iteration of the algorithm.

    

    @see kmeans

    

    """

    

    def __init__(self, evolution_clusters = [], evolution_centers = []):

The default value [] might cause unintended side-effects.

The argument evolution_centers seems to be unused.

The argument evolution_clusters seems to be unused.

        """!

        @brief Initializer of observer of K-Means algorithm.

        

        @param[in] evolution_clusters (array_like): Evolution of clusters changes during clustering process.

        @param[in] evolution_centers (array_like): Evolution of centers changes during clustering process.

        

        """

        self.__evolution_clusters   = [];

        self.__evolution_centers    = [];



    def __len__(self):

        """!

        @brief Returns amount of steps that were observer during clustering process in K-Means algorithm.

        

        """

        return len(self.__evolution_clusters);



    def notify(self, clusters, centers):

        """!

        @brief This method is called by K-Means algorithm to notify about changes.

        

        @param[in] clusters (array_like): Allocated clusters by K-Means algorithm.

        @param[in] centers (array_like): Allocated centers by K-Means algorithm.

        

        """

        self.__evolution_clusters.append(clusters);

        self.__evolution_clusters.append(centers);



    def get_centers(self, iteration):

        """!

        @brief Get method to return centers at specific iteration of clustering process.

        

        @param[in] iteration (uint): Clustering process iteration at which centers are required.

        

        @return (array_like) Centers at specific iteration.

        

        """

        return self.__evolution_centers[iteration];



    def get_clusters(self, iteration):

        """!

        @brief Get method to return allocated clusters at specific iteration of clustering process.

        

        @param[in] iteration (uint): Clustering process iteration at which clusters are required.

        

        @return (array_like) Clusters at specific iteration.

        

        """

        return self.__evolution_clusters[iteration];




class kmeans_visualizer:

    """!

    @brief Visualizer of K-Means algorithm's results.

    @details K-Means visualizer provides visualization services that are specific for K-Means algorithm.

    

    """

    

    __default_2d_marker_size = 15;

    __default_3d_marker_size = 70;

    

    

    @staticmethod

    def show_clusters(sample, clusters, centers, initial_centers = None, **kwargs):

        """!

        @brief 

        

        @param[in] sample (list): Dataset that were used for clustering.

        @param[in] clusters (array_like): Clusters that were allocated by the algorithm.

        @param[in] centers (array_like): Centers that were allocated by the algorithm.

        @param[in] initial_centers (array_like): Initial centers that were used by the algorithm, if 'None' then initial centers are not displyed.

        @param[in] **kwargs: Arbitrary keyword arguments (available arguments: 'figure', 'display').

        

        Keyword Args:

            figure (figure): If 'None' then new is figure is creater, otherwise specified figure is used for visualization.

            display (bool): If 'True' then figure will be shown by the method, otherwise it should be shown manually using matplotlib function 'plt.show()'.

        

        @return (figure) Figure where clusters were drawn.

        

        """


        visualizer = cluster_visualizer();

        visualizer.append_clusters(clusters, sample);

        

        if (kmeans_visualizer.__get_argument('figure', None, **kwargs) is None):

            figure = visualizer.show(display = False);

        else:

            visualizer.show(figure = figure, display = False);

        

        kmeans_visualizer.__draw_centers(figure, visualizer, centers, initial_centers);

        kmeans_visualizer.__draw_rays(figure, visualizer, sample, clusters, centers);

        

        if (kmeans_visualizer.__get_argument('display', True, **kwargs) is True):

            plt.show();


        return figure;



    @staticmethod

    def __draw_rays(figure, visualizer, sample, clusters, centers):

        ax = figure.get_axes()[0];

        

        for index_cluster in range(len(clusters)):

            color = visualizer.get_cluster_color(index_cluster, 0);

            kmeans_visualizer.__draw_cluster_rays(ax, color, sample, clusters[index_cluster], centers[index_cluster])



    @staticmethod

    def __draw_cluster_rays(ax, color, sample, cluster, center):

        dimension = len(sample[0]);

        

        for index_point in cluster:

            point = sample[index_point];

            if (dimension == 1):

                ax.plot([point[0], center[0]], [0.0, 0.0], '-', color=color, linewidth=0.5);

            elif (dimension == 2):

                ax.plot([point[0], center[0]], [point[1], center[1]], '-', color=color, linewidth=0.5);

            elif (dimension == 3):

                ax.plot([point[0], center[0]], [point[1], center[1]], [point[2], center[2]], '-', color=color, linewidth=0.5)



    @staticmethod

    def __draw_center(ax, center, color, marker, alpha):

        dimension = len(center);

        

        if (dimension == 1):

            ax.plot(center[0], 0.0, color=color, alpha=alpha, marker=marker, markersize=kmeans_visualizer.__default_2d_marker_size);

        elif (dimension == 2):

            ax.plot(center[0], center[1], color=color, alpha=alpha, marker=marker, markersize=kmeans_visualizer.__default_2d_marker_size);

        elif (dimension == 3):

            ax.scatter(center[0], center[1], center[2], c=color, alpha=alpha, marker=marker, s=kmeans_visualizer.__default_3d_marker_size);



    @staticmethod

    def __draw_centers(figure, visualizer, centers, initial_centers):

        ax = figure.get_axes()[0];

        

        for index_center in range(len(centers)):

            color = visualizer.get_cluster_color(index_center, 0);

            kmeans_visualizer.__draw_center(ax, centers[index_center], color, '*', 1.0);

            

            if initial_centers:

                kmeans_visualizer.__draw_center(ax, initial_centers[index_center], color, '*', 0.4);



    @staticmethod

    def __get_argument(argument_name, default_value, **kwargs):

        if (argument_name in kwargs):

            return kwargs[argument_name];

        

        return default_value;




class kmeans:

    """!

    @brief Class represents clustering algorithm K-Means.

    @details CCORE option can be used to use the pyclustering core - C/C++ shared library for processing that significantly increases performance.

    

             CCORE implementation of the algorithm uses thread pool to parallelize the clustering process.

             

             K-Means clustering results depend on initial centers. Algorithm K-Means++ can used for initialization 

             initial centers from module 'pyclustering.cluster.center_initializer'.

    

    Example #1 - Trivial clustering:

    @code

        # load list of points for cluster analysis

        sample = read_sample(path);

        

        # create instance of K-Means algorithm

        kmeans_instance = kmeans(sample, [ [0.0, 0.1], [2.5, 2.6] ]);

        

        # run cluster analysis and obtain results

        kmeans_instance.process();

        clusters = kmeans_instance.get_clusters();

    @endcode

    

    Example #2 - Clustering using K-Means++ for center initialization:

    @code

        # load list of points for cluster analysis

        sample = read_sample(SIMPLE_SAMPLES.SAMPLE_SIMPLE2);

        

        # initialize initial centers using K-Means++ method

        initial_centers = kmeans_plusplus_initializer(sample, 3).initialize();

        

        # create instance of K-Means algorithm with prepared centers

        kmeans_instance = kmeans(sample, initial_centers);

        

        # run cluster analysis and obtain results

        kmeans_instance.process();

        clusters = kmeans_instance.get_clusters();

        final_centers = kmeans_instance.get_centers();

    @endcode

    

    @see center_initializer

    

    """

    

    def __init__(self, data, initial_centers, tolerance = 0.001, ccore = True, **kwargs):

        """!

        @brief Constructor of clustering algorithm K-Means.

        @details Center initializer can be used for creating initial centers, for example, K-Means++ method.

        

        @param[in] data (array_like): Input data that is presented as array of points (objects), each point should be represented by array_like data structure.

        @param[in] initial_centers (array_like): Initial coordinates of centers of clusters that are represented by array_like data structure: [center1, center2, ...].

        @param[in] tolerance (double): Stop condition: if maximum value of change of centers of clusters is less than tolerance then algorithm stops processing.

        @param[in] ccore (bool): Defines should be CCORE library (C++ pyclustering library) used instead of Python code or not.

        @param[in] **kwargs: Arbitrary keyword arguments (available arguments: 'observer').

        

        Keyword Args:

            observer (kmeans_observer): Observer of the algorithm to collect information about clustering process on each iteration.

        

        @see center_initializer

        

        """

        self.__pointer_data = numpy.matrix(data);

        self.__clusters = [];

        self.__centers = numpy.matrix(initial_centers);

        self.__tolerance = tolerance;

        

        self.__observer = None;

        if 'observer' in kwargs:

            self.__observer = kwargs['observer'];

        

        self.__ccore = ccore;

        if (self.__ccore):

            self.__ccore = ccore_library.workable();



    def process(self):

        """!

        @brief Performs cluster analysis in line with rules of K-Means algorithm.

        

        @remark Results of clustering can be obtained using corresponding get methods.

        

        @see get_clusters()

        @see get_centers()

        

        """

        

        if (self.__ccore is True):

            results = wrapper.kmeans(self.__pointer_data, self.__centers, self.__tolerance, (self.__observer is not None));

            self.__clusters = results[0];

            self.__centers  = results[1];

            

            if self.__observer:

                self.__observer = kmeans_observer(results[2], results[3]);

        else:

            maximum_change = float('inf');

             

            stop_condition = self.__tolerance * self.__tolerance;   # Fast solution

            #stop_condition = self.__tolerance;              # Slow solution

             

            # Check for dimension

            if (len(self.__pointer_data[0]) != len(self.__centers[0])):

                raise NameError('Dimension of the input data and dimension of the initial cluster centers must be equal.');

             

            while (maximum_change > stop_condition):

                self.__clusters = self.__update_clusters();

                updated_centers = self.__update_centers();  # changes should be calculated before asignment

                

                if self.__observer:

                    self.__observer.notify(self.__clusters, updated_centers);

                

                if (len(self.__centers) != len(updated_centers)):

                    maximum_change = float('inf');

                

                else:

                    changes = numpy.sum(numpy.square(self.__centers - updated_centers), axis=1);

                    maximum_change = numpy.max(changes);

                

                self.__centers = updated_centers;



    def get_clusters(self):

        """!

        @brief Returns list of allocated clusters, each cluster contains indexes of objects in list of data.

        

        @see process()

        @see get_centers()

        

        """

        

        return self.__clusters;

    

    

    def get_centers(self):

        """!

        @brief Returns list of centers of allocated clusters.

        

        @see process()

        @see get_clusters()

        

        """


        return self.__centers.tolist();



    def get_cluster_encoding(self):

        """!

        @brief Returns clustering result representation type that indicate how clusters are encoded.

        

        @return (type_encoding) Clustering result representation.

        

        @see get_clusters()

        

        """

        

        return type_encoding.CLUSTER_INDEX_LIST_SEPARATION;



    def __update_clusters(self):

        """!

        @brief Calculate Euclidean distance to each point from the each cluster. Nearest points are captured by according clusters and as a result clusters are updated.

        

        @return (list) updated clusters as list of clusters. Each cluster contains indexes of objects from data.

        

        """

        

        clusters = [[] for _ in range(len(self.__centers))];

        

        dataset_differences = numpy.zeros((len(clusters), len(self.__pointer_data)));

        for index_center in range(len(self.__centers)):

            dataset_differences[index_center] = numpy.sum(numpy.square(self.__pointer_data - self.__centers[index_center]), axis=1).T;

        

        optimum_indexes = numpy.argmin(dataset_differences, axis=0);

        for index_point in range(len(optimum_indexes)):

            index_cluster = optimum_indexes[index_point];

            clusters[index_cluster].append(index_point);

        

        clusters = [cluster for cluster in clusters if len(cluster) > 0];

        

        return clusters;

    

    

    def __update_centers(self):

        """!

        @brief Calculate centers of clusters in line with contained objects.

        

        @return (numpy.matrix) Updated centers as list of centers.

        

        """

        

        dimension = self.__pointer_data.shape[1];

        centers = numpy.zeros((len(self.__clusters), dimension));

        

        for index in range(len(self.__clusters)):

            cluster_points = self.__pointer_data[self.__clusters[index], :];

            centers[index] = cluster_points.mean(axis=0);


        return numpy.matrix(centers);