package de.lmu.ifi.dbs.elki.datasource.parser;
/*
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.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.BitSet;
import java.util.List;
import java.util.regex.Pattern;
import de.lmu.ifi.dbs.elki.data.BitVector;
import de.lmu.ifi.dbs.elki.data.LabelList;
import de.lmu.ifi.dbs.elki.data.type.TypeUtil;
import de.lmu.ifi.dbs.elki.data.type.VectorFieldTypeInformation;
import de.lmu.ifi.dbs.elki.datasource.bundle.MultipleObjectsBundle;
import de.lmu.ifi.dbs.elki.logging.Logging;
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;
/**
* Provides a parser for parsing one sparse BitVector per line, where the
* indices of the one-bits are separated by whitespace. The first index starts
* with zero.
* <p/>
* Several labels may be given per BitVector, a label must not be parseable as
* an Integer. Lines starting with "#" will be ignored.
*
* @author Elke Achtert
*
* @apiviz.has BitVector
*/
@Title("Sparse Bit Vector Label Parser")
@Description("Parser for the lines of the following format:\n" + "A single line provides a single sparse BitVector. The indices of the one-bits are " + "separated by whitespace. The first index starts with zero. Any substring not containing whitespace is tried to be read as an Integer. " + "If this fails, it will be appended to a label. (Thus, any label must not be parseable as an Integer.) " + "Empty lines and lines beginning with \"#\" will be ignored.")
public class SparseBitVectorLabelParser extends AbstractParser implements Parser {
/**
* Class logger
*/
private static final Logging logger = Logging.getLogger(SparseBitVectorLabelParser.class);
/**
* Constructor.
*
* @param colSep
* @param quoteChar
*/
public SparseBitVectorLabelParser(Pattern colSep, char quoteChar) {
super(colSep, quoteChar);
}
@Override
public MultipleObjectsBundle parse(InputStream in) {
BufferedReader reader = new BufferedReader(new InputStreamReader(in));
int lineNumber = 0;
int dimensionality = -1;
List<BitVector> vectors = new ArrayList<BitVector>();
List<LabelList> lblc = new ArrayList<LabelList>();
try {
List<BitSet> bitSets = new ArrayList<BitSet>();
List<LabelList> allLabels = new ArrayList<LabelList>();
for(String line; (line = reader.readLine()) != null; lineNumber++) {
if(!line.startsWith(COMMENT) && line.length() > 0) {
List<String> entries = tokenize(line);
BitSet bitSet = new BitSet();
LabelList labels = null;
for(String entry : entries) {
try {
Integer index = Integer.valueOf(entry);
bitSet.set(index);
dimensionality = Math.max(dimensionality, index);
}
catch(NumberFormatException e) {
if(labels == null) {
labels = new LabelList(1);
}
labels.add(entry);
}
}
bitSets.add(bitSet);
allLabels.add(labels);
}
}
dimensionality++;
for(int i = 0; i < bitSets.size(); i++) {
BitSet bitSet = bitSets.get(i);
LabelList labels = allLabels.get(i);
vectors.add(new BitVector(bitSet, dimensionality));
lblc.add(labels);
}
}
catch(IOException e) {
throw new IllegalArgumentException("Error while parsing line " + lineNumber + ".");
}
return MultipleObjectsBundle.makeSimple(getTypeInformation(dimensionality), vectors, TypeUtil.LABELLIST, lblc);
}
protected VectorFieldTypeInformation<BitVector> getTypeInformation(int dimensionality) {
return new VectorFieldTypeInformation<BitVector>(BitVector.class, dimensionality, new BitVector(new BitSet(), dimensionality));
}
@Override
protected Logging getLogger() {
return logger;
}
/**
* 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 SparseBitVectorLabelParser makeInstance() {
return new SparseBitVectorLabelParser(colSep, quoteChar);
}
}
}