1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
|
package de.lmu.ifi.dbs.elki.utilities.referencepoints;
/*
This file is part of ELKI:
Environment for Developing KDD-Applications Supported by Index-Structures
Copyright (C) 2014
Ludwig-Maximilians-Universität München
Lehr- und Forschungseinheit für Datenbanksysteme
ELKI Development Team
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program 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 Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
import java.util.ArrayList;
import java.util.Collection;
import de.lmu.ifi.dbs.elki.data.NumberVector;
import de.lmu.ifi.dbs.elki.database.ids.DBIDIter;
import de.lmu.ifi.dbs.elki.database.relation.Relation;
import de.lmu.ifi.dbs.elki.database.relation.RelationUtil;
import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.CommonConstraints;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.DoubleParameter;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Flag;
/**
* Star-based strategy to pick reference points.
*
* @author Erich Schubert
*/
public class StarBasedReferencePoints implements ReferencePointsHeuristic {
/**
* Exclude the center vector.
*/
protected boolean nocenter;
/**
* Scaling factor.
*/
protected double scale;
/**
* Constructor.
*
* @param nocenter Do not include center point
* @param scale Scaling factor
*/
public StarBasedReferencePoints(boolean nocenter, double scale) {
super();
this.nocenter = nocenter;
this.scale = scale;
}
@Override
public Collection<? extends NumberVector> getReferencePoints(Relation<? extends NumberVector> db) {
int dim = RelationUtil.dimensionality(db);
// Compute minimum, maximum and centroid
double[] centroid = new double[dim];
double[] min = new double[dim];
double[] max = new double[dim];
for(int d = 0; d < dim; d++) {
centroid[d] = 0;
min[d] = Double.MAX_VALUE;
max[d] = -Double.MAX_VALUE;
}
for(DBIDIter iditer = db.iterDBIDs(); iditer.valid(); iditer.advance()) {
NumberVector obj = db.get(iditer);
for(int d = 0; d < dim; d++) {
double val = obj.doubleValue(d);
centroid[d] += val;
min[d] = Math.min(min[d], val);
max[d] = Math.max(max[d], val);
}
}
// finish centroid, scale min, max
for(int d = 0; d < dim; d++) {
centroid[d] = centroid[d] / db.size();
min[d] = (min[d] - centroid[d]) * scale + centroid[d];
max[d] = (max[d] - centroid[d]) * scale + centroid[d];
}
ArrayList<Vector> result = new ArrayList<>(2 * dim + 1);
if(!nocenter) {
result.add(new Vector(centroid));
}
// Plus axis end points through centroid
for(int i = 0; i < dim; i++) {
double[] vec = centroid.clone();
vec[i] = min[i];
result.add(new Vector(vec));
vec = centroid.clone();
vec[i] = max[i];
result.add(new Vector(vec));
}
return result;
}
/**
* Parameterization class.
*
* @author Erich Schubert
*
* @apiviz.exclude
*/
public static class Parameterizer extends AbstractParameterizer {
/**
* Parameter to specify the grid resolution.
* <p>
* Key: {@code -star.nocenter}
* </p>
*/
public static final OptionID NOCENTER_ID = new OptionID("star.nocenter", "Do not use the center as extra reference point.");
/**
* Parameter to specify the extra scaling of the space, to allow
* out-of-data-space reference points.
* <p>
* Key: {@code -star.scale}
* </p>
*/
public static final OptionID SCALE_ID = new OptionID("star.scale", "Scale the reference points by the given factor. This can be used to obtain reference points outside the used data space.");
/**
* Holds the value of {@link #NOCENTER_ID}.
*/
protected boolean nocenter;
/**
* Holds the value of {@link #SCALE_ID}.
*/
protected double scale;
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
Flag nocenterF = new Flag(NOCENTER_ID);
if(config.grab(nocenterF)) {
nocenter = nocenterF.getValue();
}
DoubleParameter scaleP = new DoubleParameter(SCALE_ID, 1.0) //
.addConstraint(CommonConstraints.GREATER_EQUAL_ZERO_DOUBLE);
if(config.grab(scaleP)) {
scale = scaleP.getValue();
}
}
@Override
protected StarBasedReferencePoints makeInstance() {
return new StarBasedReferencePoints(nocenter, scale);
}
}
}
|
