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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) 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 gnu.trove.map.hash.TObjectIntHashMap;
import java.util.BitSet;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import de.lmu.ifi.dbs.elki.data.LabelList;
import de.lmu.ifi.dbs.elki.data.NumberVector;
import de.lmu.ifi.dbs.elki.logging.Logging;
import de.lmu.ifi.dbs.elki.utilities.datastructures.arraylike.ArrayLikeUtil;
import de.lmu.ifi.dbs.elki.utilities.documentation.Description;
/**
* A very simple parser for categorial data, which will then be encoded as
* numbers. This is closely modeled after the number vector parser.
*
* TODO: specify handling for numerical values.
*
* @author Erich Schubert
*
* @apiviz.landmark
* @apiviz.has NumberVector
*
* @param <V> the type of NumberVector used
*/
@Description("This parser expects data in roughly the same format as the NumberVectorLabelParser,\n"//
+ "except that it will enumerate all unique strings to always produce numerical values.\n"//
+ "This way, it can for example handle files that contain lines like 'y,n,y,y,n,y,n'.")
public class CategorialDataAsNumberVectorParser<V extends NumberVector> extends NumberVectorLabelParser<V> {
/**
* Logging class.
*/
private static final Logging LOG = Logging.getLogger(CategorialDataAsNumberVectorParser.class);
/**
* For String unification.
*/
TObjectIntHashMap<String> unique = new TObjectIntHashMap<>();
/**
* Base for enumerating unique values.
*/
int ustart = Math.max(unique.getNoEntryValue() + 1, 1);
/**
* Pattern for NaN values.
*/
Matcher nanpattern = Pattern.compile("\\?").matcher("Dummy text");
/**
* Constructor with defaults.
*
* @param factory Vector factory
*/
public CategorialDataAsNumberVectorParser(NumberVector.Factory<V> factory) {
this(Pattern.compile(DEFAULT_SEPARATOR), QUOTE_CHARS, Pattern.compile(COMMENT_PATTERN), null, factory);
}
/**
* Constructor.
*
* @param colSep Column separator
* @param quoteChars Quote character
* @param comment Comment pattern
* @param labelIndices Column indexes that are numeric.
* @param factory Vector factory
*/
public CategorialDataAsNumberVectorParser(Pattern colSep, String quoteChars, Pattern comment, BitSet labelIndices, NumberVector.Factory<V> factory) {
super(colSep, quoteChars, comment, labelIndices, factory);
}
@Override
public Event nextEvent() {
Event e = super.nextEvent();
if(e == Event.END_OF_STREAM) {
unique.clear();
}
return e;
}
@Override
protected boolean parseLineInternal() {
int i = 0;
for(/* Initialized by nextLineExceptComments */; tokenizer.valid(); tokenizer.advance(), i++) {
if(!isLabelColumn(i)) {
try {
double attribute = tokenizer.getDouble();
attributes.add(attribute);
continue;
}
catch(NumberFormatException e) {
String s = tokenizer.getSubstring();
if(nanpattern.reset(s).matches()) {
attributes.add(Double.NaN);
continue;
}
int id = unique.get(s);
if(id == unique.getNoEntryValue()) {
id = ustart + unique.size();
unique.put(s, id);
}
attributes.add(id);
continue;
}
}
// Else: labels.
haslabels = true;
labels.add(tokenizer.getSubstring());
}
// Pass outside via class variables
curvec = createDBObject(attributes, ArrayLikeUtil.TDOUBLELISTADAPTER);
curlbl = LabelList.make(labels);
attributes.reset();
labels.clear();
return true;
}
@Override
protected Logging getLogger() {
return LOG;
}
/**
* Parameterization class.
*
* @author Erich Schubert
*
* @apiviz.exclude
*/
public static class Parameterizer<V extends NumberVector> extends NumberVectorLabelParser.Parameterizer<V> {
@Override
protected CategorialDataAsNumberVectorParser<V> makeInstance() {
return new CategorialDataAsNumberVectorParser<>(colSep, quoteChars, comment, labelIndices, factory);
}
}
}
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