net.sf.maltcms.chromaui.features.spi.FeatureTable.java Source code

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Here is the source code for net.sf.maltcms.chromaui.features.spi.FeatureTable.java

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/* 
 * Maui, Maltcms User Interface. 
 * Copyright (C) 2008-2014, The authors of Maui. All rights reserved.
 *
 * Project website: http://maltcms.sf.net
 *
 * Maui may be used under the terms of either the
 *
 * GNU Lesser General Public License (LGPL)
 * http://www.gnu.org/licenses/lgpl.html
 *
 * or the
 *
 * Eclipse Public License (EPL)
 * http://www.eclipse.org/org/documents/epl-v10.php
 *
 * As a user/recipient of Maui, you may choose which license to receive the code 
 * under. Certain files or entire directories may not be covered by this 
 * dual license, but are subject to licenses compatible to both LGPL and EPL.
 * License exceptions are explicitly declared in all relevant files or in a 
 * LICENSE file in the relevant directories.
 *
 * Maui 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. Please consult the relevant license documentation
 * for details.
 */
package net.sf.maltcms.chromaui.features.spi;

import net.sf.maltcms.chromaui.features.api.IFeatureTable;
import java.util.HashMap;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.apache.commons.math.linear.MatrixUtils;
import org.apache.commons.math.linear.RealMatrix;
import org.apache.commons.math.stat.StatUtils;

/**
 *
 * @author nilshoffmann
 */
public class FeatureTable implements IFeatureTable {

    private final RealMatrix featureMatrix;
    private String[] factorNames;
    private String[] variableNames;

    /**
     * factors-> number of rows variables-> number of columns
     *
     * @param factors
     * @param variables
     *
     */
    public FeatureTable(int factors, int variables) {
        this.featureMatrix = MatrixUtils.createRealMatrix(factors, variables);
        this.factorNames = new String[factors];
        this.variableNames = new String[variables];
    }

    @Override
    public void setValue(int factor, int variable, double value) {
        this.featureMatrix.setEntry(factor, variable, value);
    }

    @Override
    public void setColumn(int variable, double[] values) {
        this.featureMatrix.setColumn(variable, values);
    }

    @Override
    public void setRow(int factor, double[] values) {
        this.featureMatrix.setRow(factor, values);
    }

    @Override
    public RealMatrix getMatrix() {
        return this.featureMatrix;
    }

    public static RealMatrix normalize(RealMatrix sourceMatrix) {
        return FeatureTable.normalize(sourceMatrix, true, true);
    }

    public static RealMatrix normalize(RealMatrix sourceMatrix, boolean center, boolean normalize) {
        RealMatrix normalized = MatrixUtils.createRealMatrix(sourceMatrix.getRowDimension(),
                sourceMatrix.getColumnDimension());
        for (int col = 0; col < sourceMatrix.getColumnDimension(); col++) {
            double[] columnVector = sourceMatrix.getColumn(col);
            double mean = StatUtils.mean(columnVector);
            double stdev = Math.sqrt(StatUtils.variance(columnVector, mean));
            Logger.getLogger(FeatureTable.class.getName()).log(Level.INFO, "column {0}, mean={1} stdev={2}",
                    new Object[] { col, mean, stdev });
            for (int j = 0; j < columnVector.length; j++) {
                normalized.setEntry(j, col, (sourceMatrix.getEntry(j, col) - mean) / stdev);
            }
        }
        return normalized;
    }

    @Override
    public void setFactorName(int factor, String name) {
        this.factorNames[factor] = name;
    }

    @Override
    public String getFactorName(int factor) {
        return this.factorNames[factor];
    }

    @Override
    public void setVariableName(int variable, String name) {
        this.variableNames[variable] = name;
    }

    @Override
    public String getVariableName(int variable) {
        return this.variableNames[variable];
    }
}