cure.py

"""!
 
@brief Cluster analysis algorithm: CURE
@details Implementation based on paper @cite article::cure::1.
 
@authors Andrei Novikov (pyclustering@yandex.ru)
@date 2014-2020
@copyright BSD-3-Clause
 
"""
 
 
import numpy
 
from pyclustering.cluster.encoder import type_encoding
 
from pyclustering.utils import euclidean_distance_square
 
from pyclustering.container.kdtree import kdtree
 
from pyclustering.core.wrapper import ccore_library
 
import pyclustering.core.cure_wrapper as wrapper
 
 
class cure_cluster:
    """!
    @brief Represents data cluster in CURE term. 
    @details CURE cluster is described by points of cluster, representation points of the cluster and by the cluster center.
    
    """
    
    def __init__(self, point, index):
        """!
        @brief Constructor of CURE cluster.
        
        @param[in] point (list): Point represented by list of coordinates.
        @param[in] index (uint): Index point in dataset.
        
        """
        
        
        self.points = [ ]
        
        
        self.indexes = -1
        
        
        self.mean = None
        
        
        self.rep = [ ]
        
        if point is not None:
            self.points = [ point ]
            self.indexes = [ index ]
            self.mean = point
            self.rep = [ point ]
        
        
        self.closest = None
        
        
        self.distance = float('inf')      # calculation of distance is really complexity operation (even square distance), so let's store distance to closest cluster.
 
    def __repr__(self):
        """!
        @brief Displays distance to closest cluster and points that are contained by current cluster.
        
        """
        return "%s, %s" % (self.distance, self.points)
        
 
class cure:
    """!
    @brief Class represents clustering algorithm CURE with KD-tree optimization.
    @details CCORE option can be used to use the pyclustering core - C/C++ shared library for processing that significantly increases performance.
    
    Here is an example how to perform cluster analysis of sample 'Lsun':
    @code
        from pyclustering.cluster import cluster_visualizer;
        from pyclustering.cluster.cure import cure;
        from pyclustering.utils import read_sample;
        from pyclustering.samples.definitions import FCPS_SAMPLES;
 
        # Input data in following format [ [0.1, 0.5], [0.3, 0.1], ... ].
        input_data = read_sample(FCPS_SAMPLES.SAMPLE_LSUN);
 
        # Allocate three clusters.
        cure_instance = cure(input_data, 3);
        cure_instance.process();
        clusters = cure_instance.get_clusters();
 
        # Visualize allocated clusters.
        visualizer = cluster_visualizer();
        visualizer.append_clusters(clusters, input_data);
        visualizer.show();
    @endcode
    
    """
    
    def __init__(self, data, number_cluster, number_represent_points = 5, compression = 0.5, ccore = True):
        """!
        @brief Constructor of clustering algorithm CURE.
        
        @param[in] data (array_like): Input data that should be processed.
        @param[in] number_cluster (uint): Number of clusters that should be allocated.
        @param[in] number_represent_points (uint): Number of representative points for each cluster.
        @param[in] compression (double): Coefficient defines level of shrinking of representation points toward the mean of the new created cluster after merging on each step. Usually it destributed from 0 to 1.
        @param[in] ccore (bool): If True then CCORE (C++ solution) will be used for solving.
        
        """
        
        self.__pointer_data = self.__prepare_data_points(data)
        
        self.__clusters = None
        self.__representors = None
        self.__means = None
        
        self.__number_cluster = number_cluster
        self.__number_represent_points = number_represent_points
        self.__compression = compression
 
        self.__ccore = ccore
        if self.__ccore:
            self.__ccore = ccore_library.workable()
 
        self.__validate_arguments()
 
 
    def process(self):
        """!
        @brief Performs cluster analysis in line with rules of CURE algorithm.
        
        @return (cure) Returns itself (CURE instance).
        
        @see get_clusters()
        
        """
        
        if self.__ccore is True:
            self.__process_by_ccore()
            
        else:
            self.__process_by_python()
 
        return self
 
 
    def __process_by_ccore(self):
        """!
        @brief Performs cluster analysis using CCORE (C/C++ part of pyclustering library).
 
        """
        cure_data_pointer = wrapper.cure_algorithm(self.__pointer_data, self.__number_cluster,
                                                   self.__number_represent_points, self.__compression)
 
        self.__clusters = wrapper.cure_get_clusters(cure_data_pointer)
        self.__representors = wrapper.cure_get_representors(cure_data_pointer)
        self.__means = wrapper.cure_get_means(cure_data_pointer)
 
        wrapper.cure_data_destroy(cure_data_pointer)
 
 
    def __process_by_python(self):
        """!
        @brief Performs cluster analysis using python code.
 
        """
        self.__create_queue()  # queue
        self.__create_kdtree()  # create k-d tree
 
        while len(self.__queue) > self.__number_cluster:
            cluster1 = self.__queue[0]  # cluster that has nearest neighbor.
            cluster2 = cluster1.closest  # closest cluster.
 
            self.__queue.remove(cluster1)
            self.__queue.remove(cluster2)
 
            self.__delete_represented_points(cluster1)
            self.__delete_represented_points(cluster2)
 
            merged_cluster = self.__merge_clusters(cluster1, cluster2)
 
            self.__insert_represented_points(merged_cluster)
 
            # Pointers to clusters that should be relocated is stored here.
            cluster_relocation_requests = []
 
            # Check for the last cluster
            if len(self.__queue) > 0:
                merged_cluster.closest = self.__queue[0]  # arbitrary cluster from queue
                merged_cluster.distance = self.__cluster_distance(merged_cluster, merged_cluster.closest)
 
                for item in self.__queue:
                    distance = self.__cluster_distance(merged_cluster, item)
                    # Check if distance between new cluster and current is the best than now.
                    if distance < merged_cluster.distance:
                        merged_cluster.closest = item
                        merged_cluster.distance = distance
 
                    # Check if current cluster has removed neighbor.
                    if (item.closest is cluster1) or (item.closest is cluster2):
                        # If previous distance was less then distance to new cluster then nearest cluster should
                        # be found in the tree.
                        if item.distance < distance:
                            (item.closest, item.distance) = self.__closest_cluster(item, distance)
 
                            # TODO: investigation is required. There is assumption that itself and merged cluster
                            # should be always in list of neighbors in line with specified radius. But merged cluster
                            # may not be in list due to error calculation, therefore it should be added manually.
                            if item.closest is None:
                                item.closest = merged_cluster
                                item.distance = distance
 
                        else:
                            item.closest = merged_cluster
                            item.distance = distance
 
                        cluster_relocation_requests.append(item)
 
            # New cluster and updated clusters should relocated in queue
            self.__insert_cluster(merged_cluster)
            for item in cluster_relocation_requests:
                self.__relocate_cluster(item)
 
        # Change cluster representation
        self.__clusters = [cure_cluster_unit.indexes for cure_cluster_unit in self.__queue]
        self.__representors = [cure_cluster_unit.rep for cure_cluster_unit in self.__queue]
        self.__means = [cure_cluster_unit.mean for cure_cluster_unit in self.__queue]
 
 
    def get_clusters(self):
        """!
        @brief Returns list of allocated clusters, each cluster contains indexes of objects in list of data.
        
        @return (list) List of allocated clusters.
        
        @see process()
        @see get_representors()
        @see get_means()
        
        """
        
        return self.__clusters
    
    
    def get_representors(self):
        """!
        @brief Returns list of point-representors of each cluster.
        @details Cluster index should be used for navigation between lists of point-representors.
        
        @return (list) List of point-representors of each cluster.
        
        @see get_clusters()
        @see get_means()
        
        """
        
        return self.__representors
    
    
    def get_means(self):
        """!
        @brief Returns list of mean values of each cluster.
        @details Cluster index should be used for navigation between mean values.
        
        @return (list) List of mean values of each cluster.
        
        @see get_clusters()
        @see get_representors()
        
        """
        
        return self.__means
 
 
    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 __prepare_data_points(self, sample):
        """!
        @brief Prepare data points for clustering.
        @details In case of numpy.array there are a lot of overloaded basic operators, such as __contains__, __eq__.
 
        @return (list) Returns sample in list format.
 
        """
        if isinstance(sample, numpy.ndarray):
            return sample.tolist()
 
        return sample
 
 
    def __validate_arguments(self):
        """!
        @brief Check input arguments of BANG algorithm and if one of them is not correct then appropriate exception
                is thrown.
 
        """
 
        if len(self.__pointer_data) == 0:
            raise ValueError("Empty input data. Data should contain at least one point.")
 
        if self.__number_cluster <= 0:
            raise ValueError("Incorrect amount of clusters '%d'. Amount of cluster should be greater than 0." % self.__number_cluster)
 
        if self.__compression < 0:
            raise ValueError("Incorrect compression level '%f'. Compression should not be negative." % self.__compression)
 
        if self.__number_represent_points <= 0:
            raise ValueError("Incorrect amount of representatives '%d'. Amount of representatives should be greater than 0." % self.__number_cluster)
 
 
    def __insert_cluster(self, cluster):
        """!
        @brief Insert cluster to the list (sorted queue) in line with sequence order (distance).
        
        @param[in] cluster (cure_cluster): Cluster that should be inserted.
        
        """
        
        for index in range(len(self.__queue)):
            if cluster.distance < self.__queue[index].distance:
                self.__queue.insert(index, cluster)
                return
    
        self.__queue.append(cluster)
 
 
    def __relocate_cluster(self, cluster):
        """!
        @brief Relocate cluster in list in line with distance order.
        
        @param[in] cluster (cure_cluster): Cluster that should be relocated in line with order.
        
        """
        
        self.__queue.remove(cluster)
        self.__insert_cluster(cluster)
 
 
    def __closest_cluster(self, cluster, distance):
        """!
        @brief Find closest cluster to the specified cluster in line with distance.
        
        @param[in] cluster (cure_cluster): Cluster for which nearest cluster should be found.
        @param[in] distance (double): Closest distance to the previous cluster.
        
        @return (tuple) Pair (nearest CURE cluster, nearest distance) if the nearest cluster has been found, otherwise None is returned.
        
        """
        
        nearest_cluster = None
        nearest_distance = float('inf')
 
        real_euclidean_distance = distance ** 0.5
 
        for point in cluster.rep:
            # Nearest nodes should be returned (at least it will return itself).
            nearest_nodes = self.__tree.find_nearest_dist_nodes(point, real_euclidean_distance)
            for (candidate_distance, kdtree_node) in nearest_nodes:
                if (candidate_distance < nearest_distance) and (kdtree_node is not None) and (kdtree_node.payload is not cluster):
                    nearest_distance = candidate_distance
                    nearest_cluster = kdtree_node.payload
                    
        return (nearest_cluster, nearest_distance)
 
 
    def __insert_represented_points(self, cluster):
        """!
        @brief Insert representation points to the k-d tree.
        
        @param[in] cluster (cure_cluster): Cluster whose representation points should be inserted.
        
        """
        
        for point in cluster.rep:
            self.__tree.insert(point, cluster)
 
 
    def __delete_represented_points(self, cluster): 
        """!
        @brief Remove representation points of clusters from the k-d tree
        
        @param[in] cluster (cure_cluster): Cluster whose representation points should be removed.
        
        """
        
        for point in cluster.rep:
            self.__tree.remove(point, payload=cluster)
 
 
    def __merge_clusters(self, cluster1, cluster2):
        """!
        @brief Merges two clusters and returns new merged cluster. Representation points and mean points are calculated for the new cluster.
        
        @param[in] cluster1 (cure_cluster): Cluster that should be merged.
        @param[in] cluster2 (cure_cluster): Cluster that should be merged.
        
        @return (cure_cluster) New merged CURE cluster.
        
        """
        
        merged_cluster = cure_cluster(None, None)
        
        merged_cluster.points = cluster1.points + cluster2.points
        merged_cluster.indexes = cluster1.indexes + cluster2.indexes
        
        # merged_cluster.mean = ( len(cluster1.points) * cluster1.mean + len(cluster2.points) * cluster2.mean ) / ( len(cluster1.points) + len(cluster2.points) );
        dimension = len(cluster1.mean)
        merged_cluster.mean = [0] * dimension
        if merged_cluster.points[1:] == merged_cluster.points[:-1]:
            merged_cluster.mean = merged_cluster.points[0]
        else:
            for index in range(dimension):
                merged_cluster.mean[index] = ( len(cluster1.points) * cluster1.mean[index] + len(cluster2.points) * cluster2.mean[index] ) / ( len(cluster1.points) + len(cluster2.points) );
        
        temporary = list()
        
        for index in range(self.__number_represent_points):
            maximal_distance = 0
            maximal_point = None
            
            for point in merged_cluster.points:
                minimal_distance = 0
                if index == 0:
                    minimal_distance = euclidean_distance_square(point, merged_cluster.mean)
                    #minimal_distance = euclidean_distance_sqrt(point, merged_cluster.mean);
                else:
                    minimal_distance = min([euclidean_distance_square(point, p) for p in temporary])
                    #minimal_distance = cluster_distance(cure_cluster(point), cure_cluster(temporary[0]));
                    
                if minimal_distance >= maximal_distance:
                    maximal_distance = minimal_distance
                    maximal_point = point
        
            if maximal_point not in temporary:
                temporary.append(maximal_point)
                
        for point in temporary:
            representative_point = [0] * dimension
            for index in range(dimension):
                representative_point[index] = point[index] + self.__compression * (merged_cluster.mean[index] - point[index])
                
            merged_cluster.rep.append(representative_point)
        
        return merged_cluster
 
 
    def __create_queue(self):
        """!
        @brief Create queue of sorted clusters by distance between them, where first cluster has the nearest neighbor. At the first iteration each cluster contains only one point.
        
        @param[in] data (list): Input data that is presented as list of points (objects), each point should be represented by list or tuple.
        
        @return (list) Create queue of sorted clusters by distance between them.
        
        """
        
        self.__queue = [cure_cluster(self.__pointer_data[index_point], index_point) for index_point in range(len(self.__pointer_data))]
        
        # set closest clusters
        for i in range(0, len(self.__queue)):
            minimal_distance = float('inf')
            closest_index_cluster = -1
            
            for k in range(0, len(self.__queue)):
                if i != k:
                    dist = self.__cluster_distance(self.__queue[i], self.__queue[k])
                    if dist < minimal_distance:
                        minimal_distance = dist
                        closest_index_cluster = k
            
            self.__queue[i].closest = self.__queue[closest_index_cluster]
            self.__queue[i].distance = minimal_distance
        
        # sort clusters
        self.__queue.sort(key=lambda x: x.distance, reverse = False)
    
 
    def __create_kdtree(self):
        """!
        @brief Create k-d tree in line with created clusters. At the first iteration contains all points from the input data set.
        
        @return (kdtree) k-d tree that consist of representative points of CURE clusters.
        
        """
 
        representatives, payloads = [], []
        for current_cluster in self.__queue:
            for representative_point in current_cluster.rep:
                representatives.append(representative_point)
                payloads.append(current_cluster)
 
        # initialize it using constructor to have balanced tree at the beginning to ensure the highest performance
        # when we have the biggest amount of nodes in the tree.
        self.__tree = kdtree(representatives, payloads)
 
 
    def __cluster_distance(self, cluster1, cluster2):
        """!
        @brief Calculate minimal distance between clusters using representative points.
        
        @param[in] cluster1 (cure_cluster): The first cluster.
        @param[in] cluster2 (cure_cluster): The second cluster.
        
        @return (double) Euclidean distance between two clusters that is defined by minimum distance between representation points of two clusters.
        
        """
        
        distance = float('inf')
        for i in range(0, len(cluster1.rep)):
            for k in range(0, len(cluster2.rep)):
                dist = euclidean_distance_square(cluster1.rep[i], cluster2.rep[k])   # Fast mode
                if dist < distance:
                    distance = dist
                    
        return distance