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-mlpy for use of k-medoid : D. Albanese, R. Visintainer, S. Merler, S. Riccadonna, G. Jurman, C. Furlanello. mlpy: Machine Learning Python, 2012. arXiv:1202.6548 [bib] 

doc/doc_kmedoids.py

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-"""!
-
-@brief Cluster analysis algorithm: K-Medoids.
-@details Implementation based on papers @cite book::algorithms_for_clustering_data, @cite book::finding_groups_in_data.
-
-@authors Andrei Novikov (pyclustering@yandex.ru)
-@date 2014-2019
-@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
-
-from pyclustering.cluster.encoder import type_encoding
-
-from pyclustering.utils import medoid
-from pyclustering.utils.metric import distance_metric, type_metric
-
-import pyclustering.core.kmedoids_wrapper as wrapper
-
-from pyclustering.core.wrapper import ccore_library
-from pyclustering.core.metric_wrapper import metric_wrapper
-
-
-class kmedoids:
-    """!
-    @brief Class represents clustering algorithm K-Medoids.
-    @details The algorithm is less sensitive to outliers tham K-Means. The principle difference between K-Medoids and K-Medians is that
-             K-Medoids uses existed points from input data space as medoids, but median in K-Medians can be unreal object (not from
-             input data space).
-    
-    Clustering example:
-    @code
-        from pyclustering.cluster.kmedoids import kmedoids
-        from pyclustering.cluster import cluster_visualizer
-        from pyclustering.utils import read_sample
-        from pyclustering.samples.definitions import FCPS_SAMPLES
-
-        # Load list of points for cluster analysis.
-        sample = read_sample(FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS)
-
-        # Set random initial medoids.
-        initial_medoids = [1, 500]
-
-        # Create instance of K-Medoids algorithm.
-        kmedoids_instance = kmedoids(sample, initial_medoids)
-
-        # Run cluster analysis and obtain results.
-        kmedoids_instance.process()
-        clusters = kmedoids_instance.get_clusters()
-
-        # Show allocated clusters.
-        print(clusters)
-
-        # Display clusters.
-        visualizer = cluster_visualizer()
-        visualizer.append_clusters(clusters, sample)
-        visualizer.show()
-    @endcode
-
-    Metric for calculation distance between points can be specified by parameter additional 'metric':
-    @code
-        # create Minkowski distance metric with degree equals to '2'
-        metric = distance_metric(type_metric.MINKOWSKI, degree=2)
-
-        # create K-Medoids algorithm with specific distance metric
-        kmedoids_instance = kmedoids(sample, initial_medoids, metric=metric)
-
-        # run cluster analysis and obtain results
-        kmedoids_instance.process()
-        clusters = kmedoids_instance.get_clusters()
-    @endcode
-
-    Distance matrix can be used instead of sequence of points to increase performance and for that purpose parameter 'data_type' should be used:
-    @code
-        # calculate distance matrix for sample
-        sample = read_sample(path_to_sample)
-        matrix = calculate_distance_matrix(sample)
-
-        # create K-Medoids algorithm for processing distance matrix instead of points
-        kmedoids_instance = kmedoids(matrix, initial_medoids, data_type='distance_matrix')
-
-        # run cluster analysis and obtain results
-        kmedoids_instance.process()
-
-        clusters = kmedoids_instance.get_clusters()
-        medoids = kmedoids_instance.get_medoids()
-    @endcode
-
-    """
-    
-    
-    def __init__(self, data, initial_index_medoids, tolerance=0.001, ccore=True, **kwargs):
-        """!
-        @brief Constructor of clustering algorithm K-Medoids.
-        
-        @param[in] data (list): Input data that is presented as list of points (objects), each point should be represented by list or tuple.
-        @param[in] initial_index_medoids (list): Indexes of intial medoids (indexes of points in input data).
-        @param[in] tolerance (double): Stop condition: if maximum value of distance change of medoids of clusters is less than tolerance than algorithm will stop processing.
-        @param[in] ccore (bool): If specified than CCORE library (C++ pyclustering library) is used for clustering instead of Python code.
-        @param[in] **kwargs: Arbitrary keyword arguments (available arguments: 'metric', 'data_type', 'itermax').
-
-        <b>Keyword Args:</b><br>
-            - metric (distance_metric): Metric that is used for distance calculation between two points.
-            - data_type (string): Data type of input sample 'data' that is processed by the algorithm ('points', 'distance_matrix').
-            - itermax (uint): Maximum number of iteration for cluster analysis.
-
-        """
-        self.__pointer_data = data
-        self.__clusters = []
-        self.__medoid_indexes = initial_index_medoids
-        self.__tolerance = tolerance
-
-        self.__metric = kwargs.get('metric', distance_metric(type_metric.EUCLIDEAN_SQUARE))
-        self.__data_type = kwargs.get('data_type', 'points')
-        self.__itermax = kwargs.get('itermax', 200)
-
-        self.__distance_calculator = self.__create_distance_calculator()
-
-        self.__ccore = ccore and self.__metric.get_type() != type_metric.USER_DEFINED
-        if self.__ccore:
-            self.__ccore = ccore_library.workable()
-
-        #self.__verify_instance()
-
-
-    def process(self):
-        """!
-        @brief Performs cluster analysis in line with rules of K-Medoids algorithm.
-
-        @return (kmedoids) Returns itself (K-Medoids instance).
-
-        @remark Results of clustering can be obtained using corresponding get methods.
-        
-        @see get_clusters()
-        @see get_medoids()
-        
-        """
-        
-        if self.__ccore is True:
-            ccore_metric = metric_wrapper.create_instance(self.__metric)
-            self.__clusters, self.__medoid_indexes = wrapper.kmedoids(self.__pointer_data, self.__medoid_indexes, self.__tolerance, self.__itermax, ccore_metric.get_pointer(), self.__data_type)
-        
-        else:
-            changes = float('inf')
-            iterations = 0
-
-            while changes > self.__tolerance and iterations < self.__itermax:
-                self.__clusters = self.__update_clusters()
-                update_medoid_indexes = self.__update_medoids()
-
-                changes = max([self.__distance_calculator(self.__medoid_indexes[index], update_medoid_indexes[index]) for index in range(len(update_medoid_indexes))])
-
-                self.__medoid_indexes = update_medoid_indexes
-
-                iterations += 1
-
-        return self
-
-
-    def predict(self, points):
-        """!
-        @brief Calculates the closest cluster to each point.
-
-        @param[in] points (array_like): Points for which closest clusters are calculated.
-
-        @return (list) List of closest clusters for each point. Each cluster is denoted by index. Return empty
-                 collection if 'process()' method was not called.
-
-        An example how to calculate (or predict) the closest cluster to specified points.
-        @code
-            from pyclustering.cluster.kmedoids import kmedoids
-            from pyclustering.samples.definitions import SIMPLE_SAMPLES
-            from pyclustering.utils import read_sample
-
-            # Load list of points for cluster analysis.
-            sample = read_sample(SIMPLE_SAMPLES.SAMPLE_SIMPLE3)
-
-            # Initial medoids for sample 'Simple3'.
-            initial_medoids = [4, 12, 25, 37]
-
-            # Create instance of K-Medoids algorithm with prepared centers.
-            kmedoids_instance = kmedoids(sample, initial_medoids)
-
-            # Run cluster analysis.
-            kmedoids_instance.process()
-
-            # Calculate the closest cluster to following two points.
-            points = [[0.35, 0.5], [2.5, 2.0]]
-            closest_clusters = kmedoids_instance.predict(points)
-            print(closest_clusters)
-        @endcode
-
-        """
-
-        if len(self.__clusters) == 0:
-            return []
-
-        medoids = [ self.__pointer_data[index] for index in self.__medoid_indexes ]
-        differences = numpy.zeros((len(points), len(medoids)))
-        for index_point in range(len(points)):
-            differences[index_point] = [ self.__metric(points[index_point], center) for center in medoids ]
-
-        return numpy.argmin(differences, axis=1)
-
-
-    def get_clusters(self):
-        """!
-        @brief Returns list of allocated clusters, each cluster contains indexes of objects in list of data.
-        
-        @see process()
-        @see get_medoids()
-        
-        """
-        
-        return self.__clusters
-    
-    
-    def get_medoids(self):
-        """!
-        @brief Returns list of medoids of allocated clusters represented by indexes from the input data.
-        
-        @see process()
-        @see get_clusters()
-        
-        """
-
-        return self.__medoid_indexes
-
-
-    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 __verify_instance(self):
-        pass
-
-
-    def __create_distance_calculator(self):
-        """!
-        @brief Creates distance calculator in line with algorithms parameters.
-
-        @return (callable) Distance calculator.
-
-        """
-        if self.__data_type == 'points':
-            return lambda index1, index2: self.__metric(self.__pointer_data[index1], self.__pointer_data[index2])
-
-        elif self.__data_type == 'distance_matrix':
-            if isinstance(self.__pointer_data, numpy.matrix):
-                return lambda index1, index2: self.__pointer_data.item((index1, index2))
-
-            return lambda index1, index2: self.__pointer_data[index1][index2]
-
-        else:
-            raise TypeError("Unknown type of data is specified '%s'" % self.__data_type)
-
-
-    def __update_clusters(self):
-        """!
-        @brief Calculate distance to each point from the each cluster. 
-        @details Nearest points are captured by according clusters and as a result clusters are updated.
-        
-        @return (list) updated clusters as list of clusters where each cluster contains indexes of objects from data.
-        
-        """
-        
-        clusters = [[self.__medoid_indexes[i]] for i in range(len(self.__medoid_indexes))]
-        for index_point in range(len(self.__pointer_data)):
-            if index_point in self.__medoid_indexes:
-                continue
-
-            index_optim = -1
-            dist_optim = float('Inf')
-            
-            for index in range(len(self.__medoid_indexes)):
-                dist = self.__distance_calculator(index_point, self.__medoid_indexes[index])
-                
-                if dist < dist_optim:
-                    index_optim = index
-                    dist_optim = dist
-            
-            clusters[index_optim].append(index_point)
-        
-        return clusters
-    
-    
-    def __update_medoids(self):
-        """!
-        @brief Find medoids of clusters in line with contained objects.
-        
-        @return (list) list of medoids for current number of clusters.
-        
-        """
-
-        medoid_indexes = [-1] * len(self.__clusters)
-        
-        for index in range(len(self.__clusters)):
-            medoid_index = medoid(self.__pointer_data, self.__clusters[index], metric=self.__metric, data_type=self.__data_type)
-            medoid_indexes[index] = medoid_index
-             
-        return medoid_indexes