pyclustering.container.tests.Test.templateDistanceCalculation() - Code Metrics - Inspection of "[.] Update README to display python code quality." - annoviko/pyclustering - Measure and Improve Code Quality continuously with Scrutinizer

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created 2016-03-31 09:37 UTC

pyclustering.container.tests.Test.templateDistanceCalculation() F

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'''

Unit-tests for CF-Tree.

Copyright (C) 2015    Andrei Novikov ([email protected])

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/>.

'''

import unittest;

import numpy;

from pyclustering.container.cftree import cfentry, cftree;
from pyclustering.container.cftree import measurement_type;

from pyclustering.utils import linear_sum, square_sum;
from pyclustering.utils import euclidean_distance_sqrt, manhattan_distance, average_inter_cluster_distance, average_intra_cluster_distance, variance_increase_distance;

from random import random;

class Test(unittest.TestCase):
    def templateCfClusterRepresentation(self, cluster, centroid, radius, diameter, tolerance):
        entry = cfentry(len(cluster), linear_sum(cluster), square_sum(cluster));
           
        assertion_centroid = centroid;
        if (type(centroid) != list):
            assertion_centroid = [ centroid ];
           
        if (type(centroid) == list):
            for dimension in range(0, len(assertion_centroid)):
                assert (assertion_centroid[dimension] - tolerance < ( entry.get_centroid() )[dimension]) and (( entry.get_centroid() )[dimension] < assertion_centroid[dimension] + tolerance);
           
        assert (radius - tolerance < entry.get_radius()) and (entry.get_radius() < radius + tolerance);
        assert (diameter - tolerance < entry.get_diameter()) and (entry.get_diameter() < diameter + tolerance);
           
    def testCfClusterRepresentationOneDimension2(self):
        cluster = [ [0.1], [0.2], [0.5], [0.4], [0.6] ];
        self.templateCfClusterRepresentation(cluster, 0.36, 0.18547, 0.29326, 0.0001);        
       
    def testCfClusterRepresentationTwoDimension(self):
        cluster = [ [0.1, 0.1], [0.2, 0.2], [0.5, 0.5], [0.4, 0.4], [0.6, 0.6] ];
        self.templateCfClusterRepresentation(cluster, [0.36, 0.36], 0.26230, 0.41473, 0.0001);
       
       
    def templateCfEntryValueDistance(self, cluster1, cluster2, value, tolerance, type_measurment):
        entry1 = cfentry(len(cluster1), linear_sum(cluster1), square_sum(cluster1));
        entry2 = cfentry(len(cluster2), linear_sum(cluster2), square_sum(cluster2));
           
        distance = entry1.get_distance(entry2, type_measurment);
        assert ( (value - tolerance < distance) and (value + tolerance > distance) );
           
    def testCfEntryTwoPoints1(self):
        self.templateCfEntryValueDistance([[0.0]], [[1.0]], 1.0, 0.0000001, measurement_type.CENTROID_EUCLIDIAN_DISTANCE);
   
    def testCfEntryTwoPoints2(self):
        self.templateCfEntryValueDistance([[0.0]], [[0.0]], 0.0, 0.0000001, measurement_type.CENTROID_EUCLIDIAN_DISTANCE);
           
    def testCfEntryTwoPoints3(self):
        self.templateCfEntryValueDistance([[-1.0]], [[0.0]], 1.0, 0.0000001, measurement_type.CENTROID_EUCLIDIAN_DISTANCE);
           
    def testCfEntryTwoPoints4(self):
        self.templateCfEntryValueDistance([[1.0, 0.0]], [[0.0, 1.0]], 2.0, 0.0000001, measurement_type.CENTROID_EUCLIDIAN_DISTANCE);
       
       
    def testCfEntryIncrease(self):
        tolerance = 0.00001;
        cluster = [ [0.1, 0.1], [0.2, 0.2], [0.5, 0.5], [0.4, 0.4], [0.6, 0.6] ];
           
        entry1 = cfentry(len(cluster), linear_sum(cluster), square_sum(cluster));
        entry2 = entry1 + entry1;
           
        assert cfentry(10, [3.6, 3.6], 3.28) == entry2;
           
        entry2 = entry2 + entry2;
        assert cfentry(20, [7.2, 7.2], 6.56) == entry2;
       
    def testCfEntryDecrease(self):
        entry1 = cfentry(10, [3.6, 3.6], 3.28);
        entry2 = cfentry(5, [1.8, 1.8], 1.64);
           
        assert entry2 == (entry1 - entry2);
       
       
    def templateCfEntryDistance(self, type_measurement):
        cluster1 = [[0.1, 0.1], [0.1, 0.2], [0.2, 0.1], [0.2, 0.2]];
        cluster2 = [[0.4, 0.4], [0.4, 0.5], [0.5, 0.4], [0.5, 0.5]];
        cluster3 = [[0.9, 0.9], [0.9, 1.0], [1.0, 0.9], [1.0, 1.0]];
           
        entry1 = cfentry(len(cluster1), linear_sum(cluster1), square_sum(cluster1));
        entry2 = cfentry(len(cluster2), linear_sum(cluster2), square_sum(cluster2));
        entry3 = cfentry(len(cluster3), linear_sum(cluster3), square_sum(cluster3));
           
        distance12 = entry1.get_distance(entry2, type_measurement);
        distance23 = entry2.get_distance(entry3, type_measurement);
        distance13 = entry1.get_distance(entry3, type_measurement);
        
        assert distance12 < distance23;
        assert distance23 < distance13;
       
    def testCfDistanceCentroidEuclidian(self):
        self.templateCfEntryDistance(measurement_type.CENTROID_EUCLIDIAN_DISTANCE);
           
    def testCfDistanceCentroidManhatten(self):
        self.templateCfEntryDistance(measurement_type.CENTROID_MANHATTAN_DISTANCE);
           
    def testCfDistanceAverageInterCluster(self):
        self.templateCfEntryDistance(measurement_type.AVERAGE_INTER_CLUSTER_DISTANCE);
   
    def testCfDistanceAverageIntraCluster(self):
        self.templateCfEntryDistance(measurement_type.AVERAGE_INTRA_CLUSTER_DISTANCE);
           
    def testCfDistanceVarianceIncrease(self):
        self.templateCfEntryDistance(measurement_type.VARIANCE_INCREASE_DISTANCE);
    
    
    def templateDistanceCalculation(self, cluster1, cluster2, type_measurement):
        entry1 = cfentry(len(cluster1), linear_sum(cluster1), square_sum(cluster1));
        entry2 = cfentry(len(cluster2), linear_sum(cluster2), square_sum(cluster2));
        
        # check that the same distance from 1 to 2 and from 2 to 1.
        distance12 = entry1.get_distance(entry2, type_measurement);
        distance21 = entry2.get_distance(entry1, type_measurement);
        
        assert distance12 == distance21;
        
        # check with utils calculation
        float_delta = 0.0000001;
        if (type_measurement == measurement_type.CENTROID_EUCLIDIAN_DISTANCE):
            assert distance12 == euclidean_distance_sqrt(entry1.get_centroid(), entry2.get_centroid());
        
        elif (type_measurement == measurement_type.CENTROID_MANHATTAN_DISTANCE):
            assert distance12 == manhattan_distance(entry1.get_centroid(), entry2.get_centroid());
        
        elif (type_measurement == measurement_type.AVERAGE_INTER_CLUSTER_DISTANCE):
            assert numpy.isclose(distance12, average_inter_cluster_distance(cluster1, cluster2)) == True;
        
        elif (type_measurement == measurement_type.AVERAGE_INTRA_CLUSTER_DISTANCE):
            assert numpy.isclose(distance12, average_intra_cluster_distance(cluster1, cluster2)) == True;
        
        elif (type_measurement == measurement_type.VARIANCE_INCREASE_DISTANCE):
            assert numpy.isclose(distance12, variance_increase_distance(cluster1, cluster2)) == True;
    
    def templateDistanceCalculationTheSimplestSample(self, type_measurement):
        cluster1 = [[0.1, 0.1], [0.1, 0.2], [0.2, 0.1], [0.2, 0.2]];
        cluster2 = [[0.4, 0.4], [0.4, 0.5], [0.5, 0.4], [0.5, 0.5]];
        
        self.templateDistanceCalculation(cluster1, cluster2, type_measurement);
    
    def testDistanceCalculationTheSimplestSampleCentroidEuclidian(self):
        self.templateDistanceCalculationTheSimplestSample(measurement_type.CENTROID_EUCLIDIAN_DISTANCE);

    def testDistanceCalculationTheSimplestSampleCentroidManhattan(self):
        self.templateDistanceCalculationTheSimplestSample(measurement_type.CENTROID_MANHATTAN_DISTANCE);

    def testDistanceCalculationTheSimplestSampleAverageInterClusterDistance(self):
        self.templateDistanceCalculationTheSimplestSample(measurement_type.AVERAGE_INTER_CLUSTER_DISTANCE);

    def testDistanceCalculationTheSimplestSampleAverageIntraClusterDistance(self):
        self.templateDistanceCalculationTheSimplestSample(measurement_type.AVERAGE_INTRA_CLUSTER_DISTANCE);

    def testDistanceCalculationTheSimplestSampleVarianceIncreaseDistance(self):
        self.templateDistanceCalculationTheSimplestSample(measurement_type.VARIANCE_INCREASE_DISTANCE);


    def testCfTreeCreationWithOneEntry(self):
        tree = cftree(2, 1, 1.0);
        entry = cfentry(5, [0.0, 0.1], 0.05);
           
        tree.insert(entry);
           
        assert 1 == tree.amount_nodes;
        assert 1 == tree.height;
        assert 1 == tree.amount_entries;
           
        assert entry == tree.root.feature;
        assert None == tree.root.parent;
           
       
    def testCfTreeCreationWithoutMerging(self):
        clusters = [ [ [random() + j, random() + j] for i in range(10) ] for j in range(10) ];
        tree = cftree(2, 1, 0.0);
           
        for cluster in clusters:
            tree.insert_cluster(cluster);
           
        assert tree.height >= 4;
        assert tree.amount_entries == 10;
        assert len(tree.leafes) == 10;
           
    def testCfTreeInserionOneLeafThreeEntries(self):
        cluster1 = [[0.1, 0.1], [0.1, 0.2], [0.2, 0.1], [0.2, 0.2]];
        cluster2 = [[0.4, 0.4], [0.4, 0.5], [0.5, 0.4], [0.5, 0.5]];
        cluster3 = [[0.9, 0.9], [0.9, 1.0], [1.0, 0.9], [1.0, 1.0]];
            
        tree = cftree(3, 4, 0.0);
        tree.insert_cluster(cluster1);
        tree.insert_cluster(cluster2);
        tree.insert_cluster(cluster3);
            
        entry1 = cfentry(len(cluster1), linear_sum(cluster1), square_sum(cluster1));
        entry2 = cfentry(len(cluster2), linear_sum(cluster2), square_sum(cluster2));
        entry3 = cfentry(len(cluster3), linear_sum(cluster3), square_sum(cluster3));
            
        assert tree.find_nearest_leaf(entry1) == tree.find_nearest_leaf(entry2);
        assert tree.find_nearest_leaf(entry2) == tree.find_nearest_leaf(entry3);
       
       
    def templateCfTreeLeafIntegrity(self, number_clusters, branching_factor, max_entries, threshold):
        clusters = [ [ [random() + j, random() + j] for i in range(10) ] for j in range(number_clusters) ];
        tree = cftree(branching_factor, max_entries, threshold);
           
        for index_cluster in range(0, len(clusters)):
            tree.insert_cluster(clusters[index_cluster]);
               
            result_searching = False;
            for leaf in tree.leafes:
                for node_entry in leaf.entries:
                    result_searching |= (node_entry == node_entry);
       
            assert True == result_searching;
                   
    def testCfTreeLeafIntegrity10_2_1(self):
        self.templateCfTreeLeafIntegrity(10, 2, 1, 0.0);
            
    def testCfTreeLeafIntegrity10_3_1(self):
        self.templateCfTreeLeafIntegrity(10, 3, 1, 0.0);
            
    def testCfTreeLeafIntegrity20_4_1(self):
        self.templateCfTreeLeafIntegrity(20, 4, 1, 0.0);
       
    def testCfTreeLeafIntegrity20_4_2(self):
        self.templateCfTreeLeafIntegrity(20, 4, 2, 0.0);
           
    def testCfTreeLeafIntegrity40_10_5(self):
        self.templateCfTreeLeafIntegrity(40, 10, 5, 0.0);
          
          
    def testCfTreeEntryAbsorbing(self):
        tree = cftree(2, 1, 10000.0);
        absorbing_entry = cfentry(0, [0.0, 0.0], 0.0);
          
        for offset in range(0, 10):
            cluster = [ [random() + offset, random() + offset] for i in range(10)];
            entry = cfentry(len(cluster), linear_sum(cluster), square_sum(cluster));
              
            absorbing_entry += entry;
              
            tree.insert(entry);
              
            assert 1 == tree.amount_entries;
            assert 1 == tree.amount_nodes;
            assert 1 == tree.height;
              
            assert None == tree.root.parent;
            assert absorbing_entry == tree.root.feature;
             
     
    def templateCfTreeTotalNumberPoints(self, number_points, dimension, branching_factor, number_entries, diameter):
        tree = cftree(branching_factor, number_entries, diameter);
         
        for index_point in range(0, number_points):
            point = [ index_point for i in range(0, dimension) ];
             
            tree.insert_cluster([ point ]);
             
            number_points = 0;
            for leaf in tree.leafes:
                number_points += leaf.feature.number_points;
                 
            assert (index_point + 1) == number_points;
         
        number_leaf_points = 0;
        for leaf in tree.leafes:
            number_leaf_points += leaf.feature.number_points;
         
        assert number_points == tree.root.feature.number_points;
         
        if (number_points != number_leaf_points):
            print(number_points, number_leaf_points);
             
        assert number_points == number_leaf_points;
         
    def testCfTreeTotalNumberPoints10_1_5_5_NoDiameter(self):
        self.templateCfTreeTotalNumberPoints(10, 1, 5, 5, 0.0);
 
    def testCfTreeTotalNumberPoints10_1_5_5_WithDiameter(self):
        self.templateCfTreeTotalNumberPoints(10, 1, 5, 5, 100.0);
        
    def testCfTreeTotalNumberPoints10_1_5_5_WithSmallDiameter(self):
        self.templateCfTreeTotalNumberPoints(10, 1, 5, 5, 2.5);
         
    def testCfTreeTotalNumberPoints10_2_5_5_NoDiameter(self):
        self.templateCfTreeTotalNumberPoints(10, 2, 5, 5, 0.0);
  
    def testCfTreeTotalNumberPoints10_2_5_5_WithDiameter(self):
        self.templateCfTreeTotalNumberPoints(10, 2, 5, 5, 100.0);
  
    def testCfTreeTotalNumberPoints50_3_5_5_NoDiameter(self):
        self.templateCfTreeTotalNumberPoints(50, 3, 5, 5, 0.0);
          
    def testCfTreeTotalNumberPoints50_3_5_5_WithDiameter(self):
        self.templateCfTreeTotalNumberPoints(50, 3, 5, 5, 100.0);
          
    def testCfTreeTotalNumberPoints100_2_2_1_NoDiameter(self):
        self.templateCfTreeTotalNumberPoints(100, 2, 2, 1, 0.0);
          
    def testCfTreeTotalNumberPoints100_2_2_1_WithDiameter(self):
        self.templateCfTreeTotalNumberPoints(100, 2, 2, 1, 100.0);
         
    def testCfTreeTotalNumberPoints100_2_5_5_WithSmallDiameter(self):
        self.templateCfTreeTotalNumberPoints(100, 2, 5, 5, 10.0);
        
        
if __name__ == "__main__":
    unittest.main();

1			'''
2
3			Unit-tests for CF-Tree.
4
5			Copyright (C) 2015 Andrei Novikov ([email protected])
6
7			pyclustering is free software: you can redistribute it and/or modify
8			it under the terms of the GNU General Public License as published by
9			the Free Software Foundation, either version 3 of the License, or
10			(at your option) any later version.
11
12			pyclustering is distributed in the hope that it will be useful,
13			but WITHOUT ANY WARRANTY; without even the implied warranty of
14			MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15			GNU General Public License for more details.
16
17			You should have received a copy of the GNU General Public License
18			along with this program. If not, see <http://www.gnu.org/licenses/>.
19
20			'''
21
22			import unittest;
23
24			import numpy;
25
26			from pyclustering.container.cftree import cfentry, cftree;
27			from pyclustering.container.cftree import measurement_type;
28
29			from pyclustering.utils import linear_sum, square_sum;
30			from pyclustering.utils import euclidean_distance_sqrt, manhattan_distance, average_inter_cluster_distance, average_intra_cluster_distance, variance_increase_distance;
31
32			from random import random;
33
34			class Test(unittest.TestCase):
35			def templateCfClusterRepresentation(self, cluster, centroid, radius, diameter, tolerance):
36			entry = cfentry(len(cluster), linear_sum(cluster), square_sum(cluster));
37
38			assertion_centroid = centroid;
39			if (type(centroid) != list):
40			assertion_centroid = [ centroid ];
41
42			if (type(centroid) == list):
43			for dimension in range(0, len(assertion_centroid)):
44			assert (assertion_centroid[dimension] - tolerance < ( entry.get_centroid() )[dimension]) and (( entry.get_centroid() )[dimension] < assertion_centroid[dimension] + tolerance);
45
46			assert (radius - tolerance < entry.get_radius()) and (entry.get_radius() < radius + tolerance);
47			assert (diameter - tolerance < entry.get_diameter()) and (entry.get_diameter() < diameter + tolerance);
48
49			def testCfClusterRepresentationOneDimension2(self):
50			cluster = [ [0.1], [0.2], [0.5], [0.4], [0.6] ];
51			self.templateCfClusterRepresentation(cluster, 0.36, 0.18547, 0.29326, 0.0001);
52
53			def testCfClusterRepresentationTwoDimension(self):
54			cluster = [ [0.1, 0.1], [0.2, 0.2], [0.5, 0.5], [0.4, 0.4], [0.6, 0.6] ];
55			self.templateCfClusterRepresentation(cluster, [0.36, 0.36], 0.26230, 0.41473, 0.0001);
56
57
58			def templateCfEntryValueDistance(self, cluster1, cluster2, value, tolerance, type_measurment):
59			entry1 = cfentry(len(cluster1), linear_sum(cluster1), square_sum(cluster1));
60			entry2 = cfentry(len(cluster2), linear_sum(cluster2), square_sum(cluster2));
61
62			distance = entry1.get_distance(entry2, type_measurment);
63			assert ( (value - tolerance < distance) and (value + tolerance > distance) );
64
65			def testCfEntryTwoPoints1(self):
66			self.templateCfEntryValueDistance([[0.0]], [[1.0]], 1.0, 0.0000001, measurement_type.CENTROID_EUCLIDIAN_DISTANCE);
67
68			def testCfEntryTwoPoints2(self):
69			self.templateCfEntryValueDistance([[0.0]], [[0.0]], 0.0, 0.0000001, measurement_type.CENTROID_EUCLIDIAN_DISTANCE);
70
71			def testCfEntryTwoPoints3(self):
72			self.templateCfEntryValueDistance([[-1.0]], [[0.0]], 1.0, 0.0000001, measurement_type.CENTROID_EUCLIDIAN_DISTANCE);
73
74			def testCfEntryTwoPoints4(self):
75			self.templateCfEntryValueDistance([[1.0, 0.0]], [[0.0, 1.0]], 2.0, 0.0000001, measurement_type.CENTROID_EUCLIDIAN_DISTANCE);
76
77
78			def testCfEntryIncrease(self):
79			tolerance = 0.00001;
80			cluster = [ [0.1, 0.1], [0.2, 0.2], [0.5, 0.5], [0.4, 0.4], [0.6, 0.6] ];
81
82			entry1 = cfentry(len(cluster), linear_sum(cluster), square_sum(cluster));
83			entry2 = entry1 + entry1;
84
85			assert cfentry(10, [3.6, 3.6], 3.28) == entry2;
86
87			entry2 = entry2 + entry2;
88			assert cfentry(20, [7.2, 7.2], 6.56) == entry2;
89
90			def testCfEntryDecrease(self):
91			entry1 = cfentry(10, [3.6, 3.6], 3.28);
92			entry2 = cfentry(5, [1.8, 1.8], 1.64);
93
94			assert entry2 == (entry1 - entry2);
95
96
97			def templateCfEntryDistance(self, type_measurement):
98			cluster1 = [[0.1, 0.1], [0.1, 0.2], [0.2, 0.1], [0.2, 0.2]];
99			cluster2 = [[0.4, 0.4], [0.4, 0.5], [0.5, 0.4], [0.5, 0.5]];
100			cluster3 = [[0.9, 0.9], [0.9, 1.0], [1.0, 0.9], [1.0, 1.0]];
101
102			entry1 = cfentry(len(cluster1), linear_sum(cluster1), square_sum(cluster1));
103			entry2 = cfentry(len(cluster2), linear_sum(cluster2), square_sum(cluster2));
104			entry3 = cfentry(len(cluster3), linear_sum(cluster3), square_sum(cluster3));
105
106			distance12 = entry1.get_distance(entry2, type_measurement);
107			distance23 = entry2.get_distance(entry3, type_measurement);
108			distance13 = entry1.get_distance(entry3, type_measurement);
109
110			assert distance12 < distance23;
111			assert distance23 < distance13;
112
113			def testCfDistanceCentroidEuclidian(self):
114			self.templateCfEntryDistance(measurement_type.CENTROID_EUCLIDIAN_DISTANCE);
115
116			def testCfDistanceCentroidManhatten(self):
117			self.templateCfEntryDistance(measurement_type.CENTROID_MANHATTAN_DISTANCE);
118
119			def testCfDistanceAverageInterCluster(self):
120			self.templateCfEntryDistance(measurement_type.AVERAGE_INTER_CLUSTER_DISTANCE);
121
122			def testCfDistanceAverageIntraCluster(self):
123			self.templateCfEntryDistance(measurement_type.AVERAGE_INTRA_CLUSTER_DISTANCE);
124
125			def testCfDistanceVarianceIncrease(self):
126			self.templateCfEntryDistance(measurement_type.VARIANCE_INCREASE_DISTANCE);
127
128
129			def templateDistanceCalculation(self, cluster1, cluster2, type_measurement):
130			entry1 = cfentry(len(cluster1), linear_sum(cluster1), square_sum(cluster1));
131			entry2 = cfentry(len(cluster2), linear_sum(cluster2), square_sum(cluster2));
132
133			# check that the same distance from 1 to 2 and from 2 to 1.
134			distance12 = entry1.get_distance(entry2, type_measurement);
135			distance21 = entry2.get_distance(entry1, type_measurement);
136
137			assert distance12 == distance21;
138
139			# check with utils calculation
140			float_delta = 0.0000001;
141			if (type_measurement == measurement_type.CENTROID_EUCLIDIAN_DISTANCE):
142			assert distance12 == euclidean_distance_sqrt(entry1.get_centroid(), entry2.get_centroid());
143
144			elif (type_measurement == measurement_type.CENTROID_MANHATTAN_DISTANCE):
145			assert distance12 == manhattan_distance(entry1.get_centroid(), entry2.get_centroid());
146
147			elif (type_measurement == measurement_type.AVERAGE_INTER_CLUSTER_DISTANCE):
148			assert numpy.isclose(distance12, average_inter_cluster_distance(cluster1, cluster2)) == True;
149
150			elif (type_measurement == measurement_type.AVERAGE_INTRA_CLUSTER_DISTANCE):
151			assert numpy.isclose(distance12, average_intra_cluster_distance(cluster1, cluster2)) == True;
152
153			elif (type_measurement == measurement_type.VARIANCE_INCREASE_DISTANCE):
154			assert numpy.isclose(distance12, variance_increase_distance(cluster1, cluster2)) == True;
155
156			def templateDistanceCalculationTheSimplestSample(self, type_measurement):
157			cluster1 = [[0.1, 0.1], [0.1, 0.2], [0.2, 0.1], [0.2, 0.2]];
158			cluster2 = [[0.4, 0.4], [0.4, 0.5], [0.5, 0.4], [0.5, 0.5]];
159
160			self.templateDistanceCalculation(cluster1, cluster2, type_measurement);
161
162			def testDistanceCalculationTheSimplestSampleCentroidEuclidian(self):
163			self.templateDistanceCalculationTheSimplestSample(measurement_type.CENTROID_EUCLIDIAN_DISTANCE);
164
165			def testDistanceCalculationTheSimplestSampleCentroidManhattan(self):
166			self.templateDistanceCalculationTheSimplestSample(measurement_type.CENTROID_MANHATTAN_DISTANCE);
167
168			def testDistanceCalculationTheSimplestSampleAverageInterClusterDistance(self):
169			self.templateDistanceCalculationTheSimplestSample(measurement_type.AVERAGE_INTER_CLUSTER_DISTANCE);
170
171			def testDistanceCalculationTheSimplestSampleAverageIntraClusterDistance(self):
172			self.templateDistanceCalculationTheSimplestSample(measurement_type.AVERAGE_INTRA_CLUSTER_DISTANCE);
173
174			def testDistanceCalculationTheSimplestSampleVarianceIncreaseDistance(self):
175			self.templateDistanceCalculationTheSimplestSample(measurement_type.VARIANCE_INCREASE_DISTANCE);
176
177
178			def testCfTreeCreationWithOneEntry(self):
179			tree = cftree(2, 1, 1.0);
180			entry = cfentry(5, [0.0, 0.1], 0.05);
181
182			tree.insert(entry);
183
184			assert 1 == tree.amount_nodes;
185			assert 1 == tree.height;
186			assert 1 == tree.amount_entries;
187
188			assert entry == tree.root.feature;
189			assert None == tree.root.parent;
190
191
192			def testCfTreeCreationWithoutMerging(self):
193			clusters = [ [ [random() + j, random() + j] for i in range(10) ] for j in range(10) ];
194			tree = cftree(2, 1, 0.0);
195
196			for cluster in clusters:
197			tree.insert_cluster(cluster);
198
199			assert tree.height >= 4;
200			assert tree.amount_entries == 10;
201			assert len(tree.leafes) == 10;
202
203			def testCfTreeInserionOneLeafThreeEntries(self):
204			cluster1 = [[0.1, 0.1], [0.1, 0.2], [0.2, 0.1], [0.2, 0.2]];
205			cluster2 = [[0.4, 0.4], [0.4, 0.5], [0.5, 0.4], [0.5, 0.5]];
206			cluster3 = [[0.9, 0.9], [0.9, 1.0], [1.0, 0.9], [1.0, 1.0]];
207
208			tree = cftree(3, 4, 0.0);
209			tree.insert_cluster(cluster1);
210			tree.insert_cluster(cluster2);
211			tree.insert_cluster(cluster3);
212
213			entry1 = cfentry(len(cluster1), linear_sum(cluster1), square_sum(cluster1));
214			entry2 = cfentry(len(cluster2), linear_sum(cluster2), square_sum(cluster2));
215			entry3 = cfentry(len(cluster3), linear_sum(cluster3), square_sum(cluster3));
216
217			assert tree.find_nearest_leaf(entry1) == tree.find_nearest_leaf(entry2);
218			assert tree.find_nearest_leaf(entry2) == tree.find_nearest_leaf(entry3);
219
220
221			def templateCfTreeLeafIntegrity(self, number_clusters, branching_factor, max_entries, threshold):
222			clusters = [ [ [random() + j, random() + j] for i in range(10) ] for j in range(number_clusters) ];
223			tree = cftree(branching_factor, max_entries, threshold);
224
225			for index_cluster in range(0, len(clusters)):
226			tree.insert_cluster(clusters[index_cluster]);
227
228			result_searching = False;
229			for leaf in tree.leafes:
230			for node_entry in leaf.entries:
231			result_searching \|= (node_entry == node_entry);
232
233			assert True == result_searching;
234
235			def testCfTreeLeafIntegrity10_2_1(self):
236			self.templateCfTreeLeafIntegrity(10, 2, 1, 0.0);
237
238			def testCfTreeLeafIntegrity10_3_1(self):
239			self.templateCfTreeLeafIntegrity(10, 3, 1, 0.0);
240
241			def testCfTreeLeafIntegrity20_4_1(self):
242			self.templateCfTreeLeafIntegrity(20, 4, 1, 0.0);
243
244			def testCfTreeLeafIntegrity20_4_2(self):
245			self.templateCfTreeLeafIntegrity(20, 4, 2, 0.0);
246
247			def testCfTreeLeafIntegrity40_10_5(self):
248			self.templateCfTreeLeafIntegrity(40, 10, 5, 0.0);
249
250
251			def testCfTreeEntryAbsorbing(self):
252			tree = cftree(2, 1, 10000.0);
253			absorbing_entry = cfentry(0, [0.0, 0.0], 0.0);
254
255			for offset in range(0, 10):
256			cluster = [ [random() + offset, random() + offset] for i in range(10)];
257			entry = cfentry(len(cluster), linear_sum(cluster), square_sum(cluster));
258
259			absorbing_entry += entry;
260
261			tree.insert(entry);
262
263			assert 1 == tree.amount_entries;
264			assert 1 == tree.amount_nodes;
265			assert 1 == tree.height;
266
267			assert None == tree.root.parent;
268			assert absorbing_entry == tree.root.feature;
269
270
271			def templateCfTreeTotalNumberPoints(self, number_points, dimension, branching_factor, number_entries, diameter):
272			tree = cftree(branching_factor, number_entries, diameter);
273
274			for index_point in range(0, number_points):
275			point = [ index_point for i in range(0, dimension) ];
276
277			tree.insert_cluster([ point ]);
278
279			number_points = 0;
280			for leaf in tree.leafes:
281			number_points += leaf.feature.number_points;
282
283			assert (index_point + 1) == number_points;
284
285			number_leaf_points = 0;
286			for leaf in tree.leafes:
287			number_leaf_points += leaf.feature.number_points;
288
289			assert number_points == tree.root.feature.number_points;
290
291			if (number_points != number_leaf_points):
292			print(number_points, number_leaf_points);
293
294			assert number_points == number_leaf_points;
295
296			def testCfTreeTotalNumberPoints10_1_5_5_NoDiameter(self):
297			self.templateCfTreeTotalNumberPoints(10, 1, 5, 5, 0.0);
298
299			def testCfTreeTotalNumberPoints10_1_5_5_WithDiameter(self):
300			self.templateCfTreeTotalNumberPoints(10, 1, 5, 5, 100.0);
301
302			def testCfTreeTotalNumberPoints10_1_5_5_WithSmallDiameter(self):
303			self.templateCfTreeTotalNumberPoints(10, 1, 5, 5, 2.5);
304
305			def testCfTreeTotalNumberPoints10_2_5_5_NoDiameter(self):
306			self.templateCfTreeTotalNumberPoints(10, 2, 5, 5, 0.0);
307
308			def testCfTreeTotalNumberPoints10_2_5_5_WithDiameter(self):
309			self.templateCfTreeTotalNumberPoints(10, 2, 5, 5, 100.0);
310
311			def testCfTreeTotalNumberPoints50_3_5_5_NoDiameter(self):
312			self.templateCfTreeTotalNumberPoints(50, 3, 5, 5, 0.0);
313
314			def testCfTreeTotalNumberPoints50_3_5_5_WithDiameter(self):
315			self.templateCfTreeTotalNumberPoints(50, 3, 5, 5, 100.0);
316
317			def testCfTreeTotalNumberPoints100_2_2_1_NoDiameter(self):
318			self.templateCfTreeTotalNumberPoints(100, 2, 2, 1, 0.0);
319
320			def testCfTreeTotalNumberPoints100_2_2_1_WithDiameter(self):
321			self.templateCfTreeTotalNumberPoints(100, 2, 2, 1, 100.0);
322
323			def testCfTreeTotalNumberPoints100_2_5_5_WithSmallDiameter(self):
324			self.templateCfTreeTotalNumberPoints(100, 2, 5, 5, 10.0);
325
326
327			if __name__ == "__main__":
328			unittest.main();

annoviko / pyclustering

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pyclustering.container.tests.Test.templateDistanceCalculation() F

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