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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) 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.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.regex.Pattern;
import de.lmu.ifi.dbs.elki.datasource.parser.AbstractParser;
import de.lmu.ifi.dbs.elki.logging.Logging;
import de.lmu.ifi.dbs.elki.logging.progress.IndefiniteProgress;
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.optionhandling.parameterization.Parameterization;
/**
* Parser for parsing one distance value per line.
*
* A line must have the following format: {@code id1 id2 distanceValue}, where
* id1 and id2 are integers representing the two ids belonging to the distance
* value. Lines starting with "#" will be ignored.
*
* @author Elke Achtert
* @author Erich Schubert
*/
@Title("Number Distance Parser")
@Description("Parser for the following line format:\n" //
+ "id1 id2 distanceValue, where id1 and is2 are integers representing the two ids belonging to the distance value.\n" //
+ "The ids and the distance value are separated by whitespace. Empty lines and lines beginning with \"#\" will be ignored.")
public class AsciiDistanceParser extends AbstractParser implements DistanceParser {
/**
* The logger for this class.
*/
private static final Logging LOG = Logging.getLogger(AsciiDistanceParser.class);
/**
* Constructor.
*
* @param colSep Column separator pattern
* @param quoteChars Quote characters
* @param comment Comment pattern
*/
public AsciiDistanceParser(Pattern colSep, String quoteChars, Pattern comment) {
super(colSep, quoteChars, comment);
}
@Override
public void parse(InputStream in, DistanceCacheWriter cache) {
BufferedReader reader = new BufferedReader(new InputStreamReader(in));
int lineNumber = 1;
int min = Integer.MAX_VALUE, max = Integer.MIN_VALUE;
IndefiniteProgress prog = LOG.isVerbose() ? new IndefiniteProgress("Parsing distance matrix", LOG) : null;
try {
for(String line; (line = reader.readLine()) != null; lineNumber++) {
LOG.incrementProcessed(prog);
// Skip empty lines and comments
if(line.length() <= 0 || isComment(line)) {
continue;
}
tokenizer.initialize(line, 0, lengthWithoutLinefeed(line));
if(!tokenizer.valid()) {
throw new IllegalArgumentException("Less than three values in line " + lineNumber);
}
int id1, id2;
try {
id1 = (int) tokenizer.getLongBase10();
tokenizer.advance();
}
catch(NumberFormatException e) {
throw new IllegalArgumentException("Error in line " + lineNumber + ": id1 is not an integer!");
}
if(!tokenizer.valid()) {
throw new IllegalArgumentException("Less than three values in line " + lineNumber);
}
try {
id2 = (int) tokenizer.getLongBase10();
tokenizer.advance();
}
catch(NumberFormatException e) {
throw new IllegalArgumentException("Error in line " + lineNumber + ": id2 is not an integer!");
}
if(!tokenizer.valid()) {
throw new IllegalArgumentException("Less than three values in line " + lineNumber);
}
// Track minimum and maximum
if(id1 < id2) {
min = (id1 < min) ? id1 : min;
max = (id2 > min) ? id2 : max;
}
else {
min = (id2 < min) ? id2 : min;
max = (id1 > min) ? id1 : max;
}
try {
double distance = tokenizer.getDouble();
cache.put(id1, id2, distance);
}
catch(IllegalArgumentException e) {
throw new IllegalArgumentException("Error in line " + lineNumber + ":" + e.getMessage(), e);
}
tokenizer.advance();
if(tokenizer.valid()) {
throw new IllegalArgumentException("More than three values in line " + lineNumber);
}
}
}
catch(IOException e) {
throw new IllegalArgumentException("Error while parsing line " + lineNumber + ".");
}
LOG.setCompleted(prog);
// check if all distance values are specified
for(int i1 = min; i1 <= max; i1++) {
for(int i2 = i1 + 1; i2 <= max; i2++) {
if(!cache.containsKey(i1, i2)) {
throw new IllegalArgumentException("Distance value for " + i1 + " to " + i2 + " is missing!");
}
}
}
}
@Override
protected Logging getLogger() {
return LOG;
}
/**
* Parameterization class.
*
* @author Erich Schubert
*
* @apiviz.exclude
*/
public static class Parameterizer extends AbstractParser.Parameterizer {
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
}
@Override
protected AsciiDistanceParser makeInstance() {
return new AsciiDistanceParser(colSep, quoteChars, comment);
}
}
}
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