/*
* $RCSfile: ArrayListDoubleDataTable.java,v $
* $Revision: 1.9 $
* $Date: 2009/02/23 09:49:23 $
* $Author: wojna $
*
* Copyright (C) 2002 - 2007 Logic Group, Institute of Mathematics, Warsaw University
*
* This file is part of Rseslib.
*
* Rseslib is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option) any later version.
*
* Rseslib 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package rseslib.structure.table;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Random;
import rseslib.structure.attribute.BadHeaderException;
import rseslib.structure.attribute.Header;
import rseslib.structure.attribute.NominalAttribute;
import rseslib.structure.attribute.formats.DataFormatRecognizer;
import rseslib.structure.attribute.formats.HeaderFormatException;
import rseslib.structure.data.DoubleData;
import rseslib.structure.data.formats.DataFormatException;
import rseslib.structure.data.formats.DoubleDataInput;
import rseslib.structure.data.formats.RsesDoubleDataInput;
import rseslib.structure.data.formats.RseslibDoubleDataInput;
import rseslib.system.Report;
import rseslib.system.progress.Progress;
import rseslib.util.random.RandomSelection;
/**
* Table of data objects with double values
* implemented with use of java.lang.ArrayList.
*
* @author Arkadiusz Wojna
*/
public class ArrayListDoubleDataTable implements DoubleDataTable
{
/** Random number generator. */
private static final Random RANDOM_GENERATOR = new Random();
/** Array of attribute types. */
private Header m_arrAttributes;
/** Array of data objects in this set. */
private ArrayList<DoubleData> m_DataObjects = new ArrayList<DoubleData>();
/** Array of numerical statistics for numerical attributes. */
private NumericalStatistics[] m_NumStats = null;
/**
* Array of sizes of particular decision classes.
* Array indices correspond to local decision codes from this data header.
* It is null if the decision distribution has not been requested yet.
*/
private int[][] m_ValueDistribution = null;
/**
* Constructor reading data from a file.
* Data format is recognized automatically.
*
* @param dataFile Data file to be loaded.
* @param prog Progress object for progress reporting.
* @throws IOException If error in data has occured.
* @throws InterruptedException If user has interrupted reading data.
*/
public ArrayListDoubleDataTable(File dataFile, Progress prog) throws IOException, HeaderFormatException, DataFormatException, InterruptedException
{
DoubleDataInput doi = null;
DataFormatRecognizer rec = new DataFormatRecognizer();
if (rec.isRses2xFormat(dataFile)) doi = new RsesDoubleDataInput(dataFile, prog);
else doi = new RseslibDoubleDataInput(dataFile, prog);
m_arrAttributes = doi.attributes();
while (doi.available())
{
DoubleData dObject = doi.readDoubleData();
m_DataObjects.add(dObject);
}
}
/**
* Constructor reading data from a file.
* Data format is recognized automatically.
* The constructor verifies compatibility of data
* with a given header.
*
* @param dataFile Data file to be loaded.
* @param hdr Header for data in a given file.
* @param prog Progress object for progress reporting.
* @throws IOException If error in data has occured.
* @throws InterruptedException If user has interrupted reading data.
*/
public ArrayListDoubleDataTable(File dataFile, Header hdr, Progress prog) throws IOException, HeaderFormatException, DataFormatException, BadHeaderException, InterruptedException
{
DoubleDataInput doi = null;
DataFormatRecognizer rec = new DataFormatRecognizer();
if (rec.isRses2xFormat(dataFile)) doi = new RsesDoubleDataInput(dataFile, hdr, prog);
else doi = new RseslibDoubleDataInput(dataFile, hdr, prog);
m_arrAttributes = doi.attributes();
while (doi.available())
{
DoubleData dObject = doi.readDoubleData();
m_DataObjects.add(dObject);
}
}
/**
* Constructs an empty table with attributes from a template table.
*
* @param attributes Header for the table.
*/
public ArrayListDoubleDataTable(Header attributes)
{
m_arrAttributes = attributes;
m_ValueDistribution = new int[m_arrAttributes.noOfAttr()][];
}
/**
* Constructs a table with attributes from an array of data objects.
*
* @param objects Array of data objects used to construct this table.
*/
public ArrayListDoubleDataTable(DoubleData[] objects)
{
if (objects.length <= 0) throw new RuntimeException("Data table initialized with empty set of objects");
m_arrAttributes = objects[0].attributes();
for (int obj = 0; obj < objects.length; obj++) m_DataObjects.add(objects[obj]);
}
/**
* Constructs a table with attributes from a collection of data objects.
*
* @param objects Collection of data objects used to construct this table.
*/
public ArrayListDoubleDataTable(ArrayList<DoubleData> objects)
{
if (objects.size() <= 0) throw new RuntimeException("Data table initialized with empty set of objects");
m_arrAttributes = objects.get(0).attributes();
m_DataObjects = objects;
}
/**
* Saves this object to a file.
*
* @param outputFile File to be used for storing this object.
* @param prog Progress object for progress reporting.
* @throws IOException If an I/O error has occured.
* @throws InterruptedException If user has interrupted saving object.
*/
public void store(File outputFile, Progress prog) throws IOException, InterruptedException
{
BufferedWriter bw = new BufferedWriter(new FileWriter(outputFile));
prog.set("Saving data table to "+outputFile.getPath(), m_DataObjects.size());
m_arrAttributes.store(bw);
bw.newLine();
for (DoubleData obj : m_DataObjects)
{
obj.store(bw);
prog.step();
}
bw.close();
}
/**
* Saves this object to a file in arff format.
*
* @param outputFile File to be used for storing this object.
* @param prog Progress object for progress reporting.
* @throws IOException If an I/O error has occured.
* @throws InterruptedException If user has interrupted saving object.
*/
public void storeArff(String name, File outputFile, Progress prog) throws IOException, InterruptedException
{
BufferedWriter bw = new BufferedWriter(new FileWriter(outputFile));
prog.set("Saving data table to "+outputFile.getPath(), m_DataObjects.size());
m_arrAttributes.storeArff(name, bw);
bw.newLine();
bw.write("@DATA");
bw.newLine();
for (DoubleData obj : m_DataObjects)
{
obj.storeArff(bw);
prog.step();
}
bw.close();
}
/**
* Returns an array of attributes.
*
* @return Array of attributes.
*/
public Header attributes()
{
return m_arrAttributes;
}
/**
* Returns the number of objects.
*
* @return Number of objects.
*/
public int noOfObjects()
{
return m_DataObjects.size();
}
/**
* Adds a data object to this table.
*
* @param obj The object to be added.
*/
public void add(DoubleData obj)
{
m_DataObjects.add(obj);
m_NumStats = null;
if (m_ValueDistribution!=null)
for (int att = 0; att < m_ValueDistribution.length; att++)
if (m_ValueDistribution[att]!=null)
m_ValueDistribution[att][((NominalAttribute)m_arrAttributes.attribute(att)).localValueCode(obj.get(att))]++;
}
/**
* Removes a data object from this table.
*
* @param obj The object to be removed.
* @return True, if the object was found and removed from this table,
* false otherwise.
*/
public boolean remove(DoubleData obj)
{
for (DoubleData iterObj : m_DataObjects)
if (iterObj.equals(obj))
{
m_DataObjects.remove(iterObj);
if (m_ValueDistribution!=null)
for (int att = 0; att < m_ValueDistribution.length; att++)
if (m_ValueDistribution[att]!=null)
m_ValueDistribution[att][((NominalAttribute)m_arrAttributes.attribute(att)).localValueCode(obj.get(att))]--;
return true;
}
return false;
}
/**
* Returns collection of all objects from this table.
*
* @return Collection of all objects from this table.
*/
public ArrayList<DoubleData> getDataObjects()
{
return m_DataObjects;
}
/**
* Returns the basic statistics of a given numerical attribute.
*
* @return Statistics of a given numerical attribute.
*/
public NumericalStatistics getNumericalStatistics(int attr)
{
if (!m_arrAttributes.isNumeric(attr)) return null;
if (m_NumStats==null)
m_NumStats = new NumericalStatistics[m_arrAttributes.noOfAttr()];
if (m_NumStats[attr]==null)
m_NumStats[attr] = new NumericalStatistics(m_DataObjects,attr);
return m_NumStats[attr];
}
/**
* Returns the distribution of decision values in this table if the decision is nominal.
* Array indices correspond to local decision codes from this data header.
*
* @return Distribution of decisions in this table.
*/
public int[] getDecisionDistribution()
{
return getValueDistribution(m_arrAttributes.decision());
}
/**
* Returns the distribution of values in this table for a nominal attribute.
* Array indices correspond to local value codes for a given attibute.
*
* @param attrInd Index of the attribute.
* @return Distribution of values in this table.
*/
public int[] getValueDistribution(int attrInd)
{
if (!m_arrAttributes.isNominal(attrInd)) return null;
if (m_ValueDistribution==null)
m_ValueDistribution = new int[m_arrAttributes.noOfAttr()][];
if (m_ValueDistribution[attrInd]==null)
{
NominalAttribute attr = (NominalAttribute)m_arrAttributes.attribute(attrInd);
m_ValueDistribution[attrInd] = new int[attr.noOfValues()];
for (DoubleData dObj : m_DataObjects)
m_ValueDistribution[attrInd][attr.localValueCode(dObj.get(attrInd))]++;
}
return m_ValueDistribution[attrInd];
}
/**
* Random split of this table into 2 data collections
* with the splitting ratio noOfPartsForLeft to noOfPartsForRight.
*
* @param noOfPartsForLeft Number of parts for the table returned at the position 0.
* @param noOfPartsForRight Number of parts for the table returned at the position 1.
* @return Table splitted into 2 data collections.
*/
public ArrayList<DoubleData>[] randomSplit(int noOfPartsForLeft, int noOfPartsForRight)
{
ArrayList<DoubleData>[] parts = new ArrayList[2];
parts[0] = new ArrayList<DoubleData>();
parts[1] = new ArrayList<DoubleData>();
boolean[] assigned = RandomSelection.subset(m_DataObjects.size(), noOfPartsForLeft, noOfPartsForRight);
for (int ind = 0; ind < m_DataObjects.size(); ind++)
if (assigned[ind]) parts[0].add(m_DataObjects.get(ind));
else parts[1].add(m_DataObjects.get(ind));
return parts;
}
/**
* Random partition of this table into a given number of parts of equal sizes.
*
* @param noOfParts Number of parts to be generated.
* @return Table divided into noOfParts collections.
*/
public ArrayList<DoubleData>[] randomPartition(int noOfParts)
{
ArrayList<DoubleData>[] parts = new ArrayList[noOfParts];
for (int part = 0; part < parts.length; part++) parts[part] = new ArrayList<DoubleData>();
boolean[] assigned = new boolean[m_DataObjects.size()];
int noOfAssigned = 0;
int part = 0;
while (part < parts.length - 1)
{
int ind = RANDOM_GENERATOR.nextInt(m_DataObjects.size());
while (assigned[ind]) ind = RANDOM_GENERATOR.nextInt(m_DataObjects.size());
parts[part].add(m_DataObjects.get(ind));
assigned[ind] = true;
noOfAssigned++;
if (noOfAssigned*parts.length >= m_DataObjects.size()*(part+1)) part++;
}
for (int ind = 0; ind < m_DataObjects.size(); ind++)
if (!assigned[ind]) parts[parts.length-1].add(m_DataObjects.get(ind));
return parts;
}
/**
* Returns a string representation of this object.
*
* @return String representation of this object.
*/
public String toString()
{
StringBuffer buf = new StringBuffer(1024);
buf.append("Number of objects = " + m_DataObjects.size()+Report.lineSeparator);
buf.append(m_arrAttributes);
int dec = -1;
for (int i = 0; dec!=-2 && i < m_arrAttributes.noOfAttr(); i++)
if (m_arrAttributes.isDecision(i))
if (dec==-1) dec = i;
else dec = -2;
if (dec >= 0 && m_arrAttributes.isNominal(dec))
{
int[] decDistr = getDecisionDistribution();
NominalAttribute decAttr = m_arrAttributes.nominalDecisionAttribute();
buf.append("Decisions:"+Report.lineSeparator);
for (int i = 0; i < decDistr.length; i++)
if (decDistr[i] > 0)
buf.append(" number of objects with the decision " + NominalAttribute.stringValue(decAttr.globalValueCode(i)) + " is " + decDistr[i]+Report.lineSeparator);
}
return buf.toString();
}
/**
* Create and return a copy of this object.
*
* @return Copy of this object.
*/
public Object clone()
{
ArrayListDoubleDataTable tab = new ArrayListDoubleDataTable(m_arrAttributes);
if (m_DataObjects!=null)
{
tab.m_DataObjects = new ArrayList<DoubleData>(m_DataObjects.size());
for (DoubleData object : m_DataObjects)
tab.m_DataObjects.add((DoubleData)object.clone());
}
if (m_ValueDistribution!=null)
{
tab.m_ValueDistribution = new int[m_ValueDistribution.length][];
for (int att = 0; att < m_ValueDistribution.length; att++)
if (m_ValueDistribution[att]!=null)
tab.m_ValueDistribution[att] = m_ValueDistribution[att].clone();
}
if (m_NumStats!=null)
{
tab.m_NumStats = new NumericalStatistics[m_NumStats.length];
for (int att = 0; att < m_NumStats.length; att++)
if (m_NumStats[att]!=null)
tab.m_NumStats[att] = (NumericalStatistics)m_NumStats[att].clone();
}
return tab;
}
}
