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
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
|
package de.lmu.ifi.dbs.elki.distance.distancefunction.external;
import java.io.BufferedInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import de.lmu.ifi.dbs.elki.database.ids.DBID;
import de.lmu.ifi.dbs.elki.database.ids.DBIDRange;
import de.lmu.ifi.dbs.elki.database.query.distance.DistanceQuery;
import de.lmu.ifi.dbs.elki.database.relation.Relation;
import de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractDBIDRangeDistanceFunction;
import de.lmu.ifi.dbs.elki.logging.Logging;
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.parameterization.Parameterization;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.FileParameter;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter;
import gnu.trove.impl.Constants;
/*
This file is part of ELKI:
Environment for Developing KDD-Applications Supported by Index-Structures
Copyright (C) 2015
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 gnu.trove.map.TLongFloatMap;
import gnu.trove.map.hash.TLongFloatHashMap;
/**
* Distance function that is based on float distances given by a distance matrix
* of an external ASCII file.
*
* Note: parsing an ASCII file is rather expensive.
*
* See {@link AsciiDistanceParser} for the default input format.
*
* TODO: use a {@code float[]} instead of the hash map.
*
* @author Elke Achtert
* @author Erich Schubert
* @since 0.2
*
* @apiviz.composedOf DistanceCacheWriter
*/
@Title("File based float distance for database objects.")
@Description("Loads float distance values from an external text file.")
public class FileBasedFloatDistanceFunction extends AbstractDBIDRangeDistanceFunction {
/**
* Class logger.
*/
private static final Logging LOG = Logging.getLogger(FileBasedFloatDistanceFunction.class);
/**
* The distance cache
*/
private TLongFloatMap cache;
/**
* Distance parser
*/
private DistanceParser parser;
/**
* Input file of distance matrix
*/
private File matrixfile;
/**
* Minimum and maximum IDs seen.
*/
private int min, max;
/**
* Constructor.
*
* @param parser Parser
* @param matrixfile input file
*/
public FileBasedFloatDistanceFunction(DistanceParser parser, File matrixfile) {
super();
this.parser = parser;
this.matrixfile = matrixfile;
}
@Override
public <O extends DBID> DistanceQuery<O> instantiate(Relation<O> database) {
if(cache == null) {
try {
loadCache(parser, matrixfile);
}
catch(IOException e) {
throw new AbortException("Could not load external distance file: " + matrixfile.toString(), e);
}
}
return super.instantiate(database);
}
@Override
public double distance(int i1, int i2) {
return (i1 == i2) ? 0. : cache.get(makeKey(i1 + min, i2 + min));
}
private void loadCache(DistanceParser parser, File matrixfile) throws IOException {
InputStream in = new BufferedInputStream(FileUtil.tryGzipInput(new FileInputStream(matrixfile)));
cache = new TLongFloatHashMap(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, -1L, Float.POSITIVE_INFINITY);
min = Integer.MAX_VALUE;
max = Integer.MIN_VALUE;
parser.parse(in, new DistanceCacheWriter() {
@Override
public void put(int id1, int id2, double distance) {
if(id1 < id2) {
min = id1 < min ? id1 : min;
max = id2 > max ? id2 : max;
}
else {
min = id2 < min ? id2 : min;
max = id1 > max ? id1 : max;
}
cache.put(makeKey(id1, id2), (float) distance);
}
@Override
public boolean containsKey(int id1, int id2) {
return cache.containsKey(makeKey(id1, id2));
}
});
if(min != 0) {
LOG.verbose("Distance matrix is supposed to be 0-indexed. Choosing offset " + min + " to compensate.");
}
}
/**
* Combine two integer ids into a long value.
*
* @param i1 First id
* @param i2 Second id
* @return Combined value
*/
protected static final long makeKey(int i1, int i2) {
return (i1 < i2) //
? ((((long) i1) << 32) | i2)//
: ((((long) i2) << 32) | i1);
}
@Override
public void checkRange(DBIDRange range) {
final int size = max + 1 - min;
if(size < range.size()) {
LOG.warning("Distance matrix has size " + size + " but range has size: " + range.size());
}
}
@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 {
/**
* Input file.
*/
protected File matrixfile = null;
/**
* Parser for input file.
*/
protected DistanceParser parser = null;
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
final FileParameter MATRIX_PARAM = new FileParameter(FileBasedDoubleDistanceFunction.Parameterizer.MATRIX_ID, FileParameter.FileType.INPUT_FILE);
if(config.grab(MATRIX_PARAM)) {
matrixfile = MATRIX_PARAM.getValue();
}
final ObjectParameter<DistanceParser> PARSER_PARAM = new ObjectParameter<>(FileBasedDoubleDistanceFunction.Parameterizer.PARSER_ID, DistanceParser.class, AsciiDistanceParser.class);
if(config.grab(PARSER_PARAM)) {
parser = PARSER_PARAM.instantiateClass(config);
}
}
@Override
protected FileBasedFloatDistanceFunction makeInstance() {
return new FileBasedFloatDistanceFunction(parser, matrixfile);
}
}
}
|
