agglomerative.py

"""!

@brief Cluster analysis algorithm: agglomerative algorithm.
@details Implementation based on paper @cite book::algorithms_for_clustering_data::1988.

@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

"""


from enum import IntEnum;

from pyclustering.cluster.encoder import type_encoding;

from pyclustering.utils import euclidean_distance_square;

from pyclustering.core.wrapper import ccore_library

import pyclustering.core.agglomerative_wrapper as wrapper;


class type_link(IntEnum):
    """!
    @brief Enumerator of types of link between clusters.
    
    """

    
    SINGLE_LINK = 0;
    
    
    COMPLETE_LINK = 1;
    
    
    AVERAGE_LINK = 2;
    
    
    CENTROID_LINK = 3;


class agglomerative:
    """!
    @brief Class represents agglomerative algorithm for cluster analysis.
    @details Agglomerative algorithm considers each data point (object) as a separate cluster at the beggining and
              step by step finds the best pair of clusters for merge until required amount of clusters is obtained.
            
            CCORE option can be used to use the pyclustering core - C/C++ shared library for processing that significantly increases performance.
    
    Example of agglomerative algorithm where centroid link is used:
    @code
        # sample for cluster analysis (represented by list)
        sample = read_sample(path_to_sample);
        
        # create object that uses python code only
        agglomerative_instance = agglomerative(sample, 2, link_type.CENTROID_LINK)
        
        # cluster analysis
        agglomerative_instance.process();
        
        # obtain results of clustering
        clusters = agglomerative_instance.get_clusters();  
    @endcode
    
    Algorithm performance can be improved if 'ccore' flag is on. In this case C++ library will be called for clustering.
    There is example of clustering 'LSUN' sample when usage of single or complete link will take a lot of resources and
    when core usage is prefereble.
    @code
        # sample Lsun for cluster analysis
        lsun_sample = read_sample(FCPS_SAMPLES.SAMPLE_LSUN);
        
        # create instance of the algorithm that will use ccore library (the last argument)
        agglomerative_instance = agglomerative(lsun_sample, 3, link_type.SINGLE_LINK, True);
        
        # start processing
        agglomerative_instance.process();
        
        # get result and visualize it
        lsun_clusters = agglomerative_instance.get_clusters();
        visualizer = cluster_visualizer();
        visualizer.append_clusters(lsun_clusters, lsun_sample);
        visualizer.show();
    @endcode
    
    Example of agglomerative clustering using different links:
    @image html agglomerative_lsun_clustering_single_link.png
    
    """
    
    def __init__(self, data, number_clusters, link = None, ccore = True):
        """!
        @brief Constructor of agglomerative hierarchical algorithm.
        
        @param[in] data (list): Input data that is presented as a list of points (objects), each point should be represented by list, for example
                    [[0.1, 0.2], [0.4, 0.5], [1.3, 0.9]].
        @param[in] number_clusters (uint): Number of clusters that should be allocated.
        @param[in] link (type_link): Link type that is used for calculation similarity between objects and clusters, if it is not specified centroid link will be used by default.
        @param[in] ccore (bool): Defines should be CCORE (C++ pyclustering library) used instead of Python code or not (by default it is 'False').
        
        """  
        
        self.__pointer_data = data;
        self.__number_clusters = number_clusters;
        self.__similarity = link;
        
        if (self.__similarity is None):
            self.__similarity = type_link.CENTROID_LINK;
        
        self.__clusters = [];
        self.__ccore = ccore;
        if (self.__ccore):
            self.__ccore = ccore_library.workable();
        
        if (self.__similarity == type_link.CENTROID_LINK):
            self.__centers = self.__pointer_data.copy();    # used in case of usage of centroid links
    
    
    def process(self):
        """!
        @brief Performs cluster analysis in line with rules of agglomerative algorithm and similarity.
        
        @see get_clusters()
        
        """
        
        if (self.__ccore is True):
            self.__clusters = wrapper.agglomerative_algorithm(self.__pointer_data, self.__number_clusters, self.__similarity);

        else:
            self.__clusters = [[index] for index in range(0, len(self.__pointer_data))];
            
            current_number_clusters = len(self.__clusters);
                
            while (current_number_clusters > self.__number_clusters):
                self.__merge_similar_clusters();
                current_number_clusters = len(self.__clusters);
    
    
    def get_clusters(self):
        """!
        @brief Returns list of allocated clusters, each cluster contains indexes of objects in list of data.
        
        @remark Results of clustering can be obtained using corresponding gets methods.
        
        @return (list) List of allocated clusters, each cluster contains indexes of objects in list of data.
        
        @see process()
        
        """
        
        return self.__clusters;
    
    
    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 __merge_similar_clusters(self):
        """!
        @brief Merges the most similar clusters in line with link type.
        
        """
        
        if (self.__similarity == type_link.AVERAGE_LINK):
            self.__merge_by_average_link();
        
        elif (self.__similarity == type_link.CENTROID_LINK):
            self.__merge_by_centroid_link();
        
        elif (self.__similarity == type_link.COMPLETE_LINK):
            self.__merge_by_complete_link();
        
        elif (self.__similarity == type_link.SINGLE_LINK):
            self.__merge_by_signle_link();
        
        else:
            raise NameError('Not supported similarity is used');
    
    
    def __merge_by_average_link(self):
        """!
        @brief Merges the most similar clusters in line with average link type.
        
        """
        
        minimum_average_distance = float('Inf');
        
        for index_cluster1 in range(0, len(self.__clusters)):
            for index_cluster2 in range(index_cluster1 + 1, len(self.__clusters)):
                
                # Find farthest objects
                candidate_average_distance = 0.0;
                for index_object1 in self.__clusters[index_cluster1]:
                    for index_object2 in self.__clusters[index_cluster2]:
                        candidate_average_distance += euclidean_distance_square(self.__pointer_data[index_object1], self.__pointer_data[index_object2]);
                
                candidate_average_distance /= (len(self.__clusters[index_cluster1]) + len(self.__clusters[index_cluster2]));
                
                if (candidate_average_distance < minimum_average_distance):
                    minimum_average_distance = candidate_average_distance;
                    indexes = [index_cluster1, index_cluster2];
        
        self.__clusters[indexes[0]] += self.__clusters[indexes[1]];  
        self.__clusters.pop(indexes[1]);   # remove merged cluster.  
        
    
    def __merge_by_centroid_link(self):
        """!
        @brief Merges the most similar clusters in line with centroid link type.
        
        """
        
        minimum_centroid_distance = float('Inf');
        indexes = None;
        
        for index1 in range(0, len(self.__centers)):
            for index2 in range(index1 + 1, len(self.__centers)):
                distance = euclidean_distance_square(self.__centers[index1], self.__centers[index2]);
                if (distance < minimum_centroid_distance):
                    minimum_centroid_distance = distance;
                    indexes = [index1, index2];
        
        self.__clusters[indexes[0]] += self.__clusters[indexes[1]];
        self.__centers[indexes[0]] = self.__calculate_center(self.__clusters[indexes[0]]);
         
        self.__clusters.pop(indexes[1]);   # remove merged cluster.
        self.__centers.pop(indexes[1]);    # remove merged center.
    
    
    def __merge_by_complete_link(self):
        """!
        @brief Merges the most similar clusters in line with complete link type.
        
        """
        
        minimum_complete_distance = float('Inf');
        indexes = None;
        
        for index_cluster1 in range(0, len(self.__clusters)):
            for index_cluster2 in range(index_cluster1 + 1, len(self.__clusters)):
                candidate_maximum_distance = self.__calculate_farthest_distance(index_cluster1, index_cluster2);
                
                if (candidate_maximum_distance < minimum_complete_distance):
                    minimum_complete_distance = candidate_maximum_distance;
                    indexes = [index_cluster1, index_cluster2];

        self.__clusters[indexes[0]] += self.__clusters[indexes[1]];  
        self.__clusters.pop(indexes[1]);   # remove merged cluster.        
    
    
    def __calculate_farthest_distance(self, index_cluster1, index_cluster2):
        """!
        @brief Finds two farthest objects in two specified clusters in terms and returns distance between them.
        
        @param[in] (uint) Index of the first cluster.
        @param[in] (uint) Index of the second cluster.
        
        @return The farthest euclidean distance between two clusters.
        
        """
        candidate_maximum_distance = 0.0;
        for index_object1 in self.__clusters[index_cluster1]:
            for index_object2 in self.__clusters[index_cluster2]:
                distance = euclidean_distance_square(self.__pointer_data[index_object1], self.__pointer_data[index_object2]);
                
                if (distance > candidate_maximum_distance):
                    candidate_maximum_distance = distance;
    
        return candidate_maximum_distance;
    
    
    def __merge_by_signle_link(self):
        """!
        @brief Merges the most similar clusters in line with single link type.
        
        """
        
        minimum_single_distance = float('Inf');
        indexes = None;
        
        for index_cluster1 in range(0, len(self.__clusters)):
            for index_cluster2 in range(index_cluster1 + 1, len(self.__clusters)):
                candidate_minimum_distance = self.__calculate_nearest_distance(index_cluster1, index_cluster2);
                
                if (candidate_minimum_distance < minimum_single_distance):
                    minimum_single_distance = candidate_minimum_distance;
                    indexes = [index_cluster1, index_cluster2];

        self.__clusters[indexes[0]] += self.__clusters[indexes[1]];  
        self.__clusters.pop(indexes[1]);   # remove merged cluster.
    
    
    def __calculate_nearest_distance(self, index_cluster1, index_cluster2):
        """!
        @brief Finds two nearest objects in two specified clusters and returns distance between them.
        
        @param[in] (uint) Index of the first cluster.
        @param[in] (uint) Index of the second cluster.
        
        @return The nearest euclidean distance between two clusters.
        
        """
        candidate_minimum_distance = float('Inf');
        
        for index_object1 in self.__clusters[index_cluster1]:
            for index_object2 in self.__clusters[index_cluster2]:
                distance = euclidean_distance_square(self.__pointer_data[index_object1], self.__pointer_data[index_object2]);
                if (distance < candidate_minimum_distance):
                    candidate_minimum_distance = distance;
        
        return candidate_minimum_distance;
    
    
    def __calculate_center(self, cluster):
        """!
        @brief Calculates new center.
        
        @return (list) New value of the center of the specified cluster.
        
        """
         
        dimension = len(self.__pointer_data[cluster[0]]);
        center = [0] * dimension;
        for index_point in cluster:
            for index_dimension in range(0, dimension):
                center[index_dimension] += self.__pointer_data[index_point][index_dimension];
         
        for index_dimension in range(0, dimension):
            center[index_dimension] /= len(cluster);
             
        return center;