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
171
172
173
174
175
176
177
178
179
180
|
package de.lmu.ifi.dbs.elki.distance.distancefunction.external;
/*
This file is part of ELKI:
Environment for Developing KDD-Applications Supported by Index-Structures
Copyright (C) 2012
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.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.Map;
import de.lmu.ifi.dbs.elki.database.ids.DBID;
import de.lmu.ifi.dbs.elki.database.ids.DBIDPair;
import de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractDBIDDistanceFunction;
import de.lmu.ifi.dbs.elki.distance.distancevalue.FloatDistance;
import de.lmu.ifi.dbs.elki.utilities.FileUtil;
import de.lmu.ifi.dbs.elki.utilities.documentation.Description;
import de.lmu.ifi.dbs.elki.utilities.documentation.Title;
import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException;
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.parameterization.ChainedParameterization;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.FileParameter;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter;
import de.lmu.ifi.dbs.elki.utilities.pairs.Pair;
/**
* Provides a DistanceFunction that is based on float distances given by a
* distance matrix of an external file.
*
* @author Elke Achtert
*/
@Title("File based float distance for database objects.")
@Description("Loads float distance values from an external text file.")
public class FileBasedFloatDistanceFunction extends AbstractDBIDDistanceFunction<FloatDistance> {
/**
* Parameter that specifies the name of the distance matrix file.
* <p>
* Key: {@code -distance.matrix}
* </p>
*/
public static final OptionID MATRIX_ID = OptionID.getOrCreateOptionID("distance.matrix", "The name of the file containing the distance matrix.");
/**
* Optional parameter to specify the parsers to provide a database, must
* extend {@link DistanceParser}. If this parameter is not set,
* {@link NumberDistanceParser} is used as parser for all input files.
* <p>
* Key: {@code -distance.parser}
* </p>
*/
public static final OptionID PARSER_ID = OptionID.getOrCreateOptionID("distance.parser", "Parser used to load the distance matrix.");
/**
* The distance cache
*/
private Map<DBIDPair, FloatDistance> cache;
/**
* Constructor.
*
* @param parser Parser
* @param matrixfile input file
*/
public FileBasedFloatDistanceFunction(DistanceParser<FloatDistance> parser, File matrixfile) {
super();
try {
loadCache(parser, matrixfile);
}
catch(IOException e) {
throw new AbortException("Could not load external distance file: " + matrixfile.toString(), e);
}
}
/**
* Returns the distance between the two objects specified by their objects
* ids. If a cache is used, the distance value is looked up in the cache. If
* the distance does not yet exists in cache, it will be computed an put to
* cache. If no cache is used, the distance is computed.
*
* @param id1 first object id
* @param id2 second object id
* @return the distance between the two objects specified by their objects ids
*/
@Override
public FloatDistance distance(DBID id1, DBID id2) {
if(id1 == null) {
return getDistanceFactory().undefinedDistance();
}
if(id2 == null) {
return getDistanceFactory().undefinedDistance();
}
// the smaller id is the first key
if(id1.getIntegerID() > id2.getIntegerID()) {
return distance(id2, id1);
}
return cache.get(new Pair<DBID, DBID>(id1, id2));
}
private void loadCache(DistanceParser<FloatDistance> parser, File matrixfile) throws IOException {
InputStream in = FileUtil.tryGzipInput(new FileInputStream(matrixfile));
DistanceParsingResult<FloatDistance> res = parser.parse(in);
cache = res.getDistanceCache();
}
@Override
public FloatDistance getDistanceFactory() {
return FloatDistance.FACTORY;
}
@Override
public boolean equals(Object obj) {
if(obj == null) {
return false;
}
if(getClass() != obj.getClass()) {
return false;
}
FileBasedFloatDistanceFunction other = (FileBasedFloatDistanceFunction) obj;
return this.cache.equals(other.cache);
}
/**
* Parameterization class.
*
* @author Erich Schubert
*
* @apiviz.exclude
*/
public static class Parameterizer extends AbstractParameterizer {
protected File matrixfile = null;
protected DistanceParser<FloatDistance> parser = null;
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
final FileParameter MATRIX_PARAM = new FileParameter(MATRIX_ID, FileParameter.FileType.INPUT_FILE);
if(config.grab(MATRIX_PARAM)) {
matrixfile = MATRIX_PARAM.getValue();
}
final ObjectParameter<DistanceParser<FloatDistance>> PARSER_PARAM = new ObjectParameter<DistanceParser<FloatDistance>>(PARSER_ID, DistanceParser.class, NumberDistanceParser.class);
if(config.grab(PARSER_PARAM)) {
ListParameterization parserConfig = new ListParameterization();
parserConfig.addParameter(DistanceParser.DISTANCE_ID, FloatDistance.class);
ChainedParameterization combinedConfig = new ChainedParameterization(parserConfig, config);
combinedConfig.errorsTo(config);
parser = PARSER_PARAM.instantiateClass(config);
}
}
@Override
protected FileBasedFloatDistanceFunction makeInstance() {
return new FileBasedFloatDistanceFunction(parser, matrixfile);
}
}
}
|
