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Push — 0.7.dev ( 4c996b...97a20f )

by Andrei

created 2017-09-15 16:26 UTC

kmedoids.get_clusters() A

↳ Parent: kmedoids

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"""!

@brief Cluster analysis algorithm: K-Medoids (PAM - Partitioning Around Medoids).
@details Based on book description:
         - A.K. Jain, R.C Dubes, Algorithms for Clustering Data. 1988.
         - L. Kaufman, P.J. Rousseeuw, Finding Groups in Data: an Introduction to Cluster Analysis. 1990.

@authors Andrei Novikov ([email protected])
@date 2014-2017
@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 pyclustering.cluster.encoder import type_encoding;

from pyclustering.utils import euclidean_distance_sqrt, median;

import pyclustering.core.kmedoids_wrapper as wrapper;


class kmedoids:
    """!
    @brief Class represents clustering algorithm K-Medoids (another one title is PAM - Parti).
    @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).
    
    Example:
    @code
        # load list of points for cluster analysis
        sample = read_sample(path);
        
        # create instance of K-Medoids algorithm
        kmedoids_instance = kmedoids(sample, [1, 10]);
        
        # run cluster analysis and obtain results
        kmedoids_instance.process();
        kmedoids_instance.get_clusters();
    @endcode
    
    """
    
    
    def __init__(self, data, initial_index_medoids, tolerance = 0.25, ccore = False):
        """!
        @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.
        
        """
        self.__pointer_data = data;
        self.__clusters = [];
        self.__medoids = [ data[medoid_index] for medoid_index in initial_index_medoids ];
        self.__medoid_indexes = initial_index_medoids;
        self.__tolerance = tolerance;
        self.__ccore = ccore;


    def process(self):
        """!
        @brief Performs cluster analysis in line with rules of K-Medoids algorithm.
        
        @remark Results of clustering can be obtained using corresponding get methods.
        
        @see get_clusters()
        @see get_medoids()
        
        """
        
        if (self.__ccore is True):
            self.__clusters = wrapper.kmedoids(self.__pointer_data, self.__medoid_indexes, self.__tolerance);
            self.__medoids, self.__medoid_indexes = self.__update_medoids();
        
        else:
            changes = float('inf');
             
            stop_condition = self.__tolerance * self.__tolerance;   # Fast solution
            #stop_condition = self.__tolerance;              # Slow solution
             
            while (changes > stop_condition):
                self.__clusters = self.__update_clusters();
                updated_medoids, update_medoid_indexes = self.__update_medoids();  # changes should be calculated before asignment
             
                changes = max([euclidean_distance_sqrt(self.__medoids[index], updated_medoids[index]) for index in range(len(updated_medoids))]);    # Fast solution
                 
                self.__medoids = updated_medoids;
                self.__medoid_indexes = update_medoid_indexes;


    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.
        
        @see process()
        @see get_clusters()
        
        """

        return self.__medoids;


    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 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.__medoids))];
        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.__medoids)):
                dist = euclidean_distance_sqrt(self.__pointer_data[index_point], self.__medoids[index]);
                
                if ( (dist < dist_optim) or (index is 0)):
                    index_optim = index;
                    dist_optim = dist;
                
            clusters[index_optim].append(index_point);
        
        # If cluster is not able to capture object it should be removed
        clusters = [cluster for cluster in clusters if len(cluster) > 0];
        
        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.
        
        """
         
        medoids = [[] for _ in range(len(self.__clusters))];
        medoid_indexes = [-1] * len(self.__clusters);
        
        for index in range(len(self.__clusters)):
            medoid_index = median(self.__pointer_data, self.__clusters[index]);
            medoids[index] = self.__pointer_data[medoid_index];
            medoid_indexes[index] = medoid_index;
             
        return medoids, medoid_indexes;

1		"""!
2
3		@brief Cluster analysis algorithm: K-Medoids (PAM - Partitioning Around Medoids).
4		@details Based on book description:
5		- A.K. Jain, R.C Dubes, Algorithms for Clustering Data. 1988.
6		- L. Kaufman, P.J. Rousseeuw, Finding Groups in Data: an Introduction to Cluster Analysis. 1990.
7
8		@authors Andrei Novikov ([email protected])
9		@date 2014-2017
10		@copyright GNU Public License
11
12		@cond GNU_PUBLIC_LICENSE
13		PyClustering is free software: you can redistribute it and/or modify
14		it under the terms of the GNU General Public License as published by
15		the Free Software Foundation, either version 3 of the License, or
16		(at your option) any later version.
17
18		PyClustering is distributed in the hope that it will be useful,
19		but WITHOUT ANY WARRANTY; without even the implied warranty of
20		MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21		GNU General Public License for more details.
22
23		You should have received a copy of the GNU General Public License
24		along with this program. If not, see <http://www.gnu.org/licenses/>.
25		@endcond
26
27		"""
28
29
30		from pyclustering.cluster.encoder import type_encoding;
31
32		from pyclustering.utils import euclidean_distance_sqrt, median;
33
34		import pyclustering.core.kmedoids_wrapper as wrapper;
35
36
37		class kmedoids:
38		"""!
39		@brief Class represents clustering algorithm K-Medoids (another one title is PAM - Parti).
40		@details The algorithm is less sensitive to outliers tham K-Means. The principle difference between K-Medoids and K-Medians is that
41		K-Medoids uses existed points from input data space as medoids, but median in K-Medians can be unreal object (not from
42		input data space).
43
44		Example:
45		@code
46		# load list of points for cluster analysis
47		sample = read_sample(path);
48
49		# create instance of K-Medoids algorithm
50		kmedoids_instance = kmedoids(sample, [1, 10]);
51
52		# run cluster analysis and obtain results
53		kmedoids_instance.process();
54		kmedoids_instance.get_clusters();
55		@endcode
56
57		"""
58
59
60		def __init__(self, data, initial_index_medoids, tolerance = 0.25, ccore = False):
61		"""!
62		@brief Constructor of clustering algorithm K-Medoids.
63
64		@param[in] data (list): Input data that is presented as list of points (objects), each point should be represented by list or tuple.
65		@param[in] initial_index_medoids (list): Indexes of intial medoids (indexes of points in input data).
66		@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.
67		@param[in] ccore (bool): If specified than CCORE library (C++ pyclustering library) is used for clustering instead of Python code.
68
69		"""
70		self.__pointer_data = data;
71		self.__clusters = [];
72		self.__medoids = [ data[medoid_index] for medoid_index in initial_index_medoids ];
73		self.__medoid_indexes = initial_index_medoids;
74		self.__tolerance = tolerance;
75		self.__ccore = ccore;
76
77
78		def process(self):
79		"""!
80		@brief Performs cluster analysis in line with rules of K-Medoids algorithm.
81
82		@remark Results of clustering can be obtained using corresponding get methods.
83
84		@see get_clusters()
85		@see get_medoids()
86
87		"""
88
89		if (self.__ccore is True):
90		self.__clusters = wrapper.kmedoids(self.__pointer_data, self.__medoid_indexes, self.__tolerance);
91		self.__medoids, self.__medoid_indexes = self.__update_medoids();
92
93		else:
94		changes = float('inf');
95
96		stop_condition = self.__tolerance * self.__tolerance; # Fast solution
97		#stop_condition = self.__tolerance; # Slow solution
98
99		while (changes > stop_condition):
100		self.__clusters = self.__update_clusters();
101		updated_medoids, update_medoid_indexes = self.__update_medoids(); # changes should be calculated before asignment
102
103		changes = max([euclidean_distance_sqrt(self.__medoids[index], updated_medoids[index]) for index in range(len(updated_medoids))]); # Fast solution
104
105		self.__medoids = updated_medoids;
106		self.__medoid_indexes = update_medoid_indexes;
107
108
109		def get_clusters(self):
110		"""!
111		@brief Returns list of allocated clusters, each cluster contains indexes of objects in list of data.
112
113		@see process()
114		@see get_medoids()
115
116		"""
117
118		return self.__clusters;
119
120
121		def get_medoids(self):
122		"""!
123		@brief Returns list of medoids of allocated clusters.
124
125		@see process()
126		@see get_clusters()
127
128		"""
129
130		return self.__medoids;
131
132
133		def get_cluster_encoding(self):
134		"""!
135		@brief Returns clustering result representation type that indicate how clusters are encoded.
136
137		@return (type_encoding) Clustering result representation.
138
139		@see get_clusters()
140
141		"""
142
143		return type_encoding.CLUSTER_INDEX_LIST_SEPARATION;
144
145
146	View Code Duplication	def __update_clusters(self):
		0 ignored issues – show Duplication introduced 2017-08-07 16:14 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
147		"""!
148		@brief Calculate distance to each point from the each cluster.
149		@details Nearest points are captured by according clusters and as a result clusters are updated.
150
151		@return (list) updated clusters as list of clusters where each cluster contains indexes of objects from data.
152
153		"""
154
155		clusters = [[self.__medoid_indexes[i]] for i in range(len(self.__medoids))];
156		for index_point in range(len(self.__pointer_data)):
157		if (index_point in self.__medoid_indexes):
158		continue;
159
160		index_optim = -1;
161		dist_optim = float('Inf');
162
163		for index in range(len(self.__medoids)):
164		dist = euclidean_distance_sqrt(self.__pointer_data[index_point], self.__medoids[index]);
165
166		if ( (dist < dist_optim) or (index is 0)):
167		index_optim = index;
168		dist_optim = dist;
169
170		clusters[index_optim].append(index_point);
171
172		# If cluster is not able to capture object it should be removed
173		clusters = [cluster for cluster in clusters if len(cluster) > 0];
174
175		return clusters;
176
177
178	View Code Duplication	def __update_medoids(self):
		0 ignored issues – show Duplication introduced 2017-08-07 16:14 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
179		"""!
180		@brief Find medoids of clusters in line with contained objects.
181
182		@return (list) list of medoids for current number of clusters.
183
184		"""
185
186		medoids = [[] for _ in range(len(self.__clusters))];
187		medoid_indexes = [-1] * len(self.__clusters);
188
189		for index in range(len(self.__clusters)):
190		medoid_index = median(self.__pointer_data, self.__clusters[index]);
191		medoids[index] = self.__pointer_data[medoid_index];
192		medoid_indexes[index] = medoid_index;
193
194		return medoids, medoid_indexes;

annoviko / pyclustering

Push — 0.7.dev ( 4c996b...97a20f )

kmedoids.get_clusters() A

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