ml.engine.LibSVM.java Source code

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package ml.engine;

/*
 *    This program 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 2 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 General Public License for more details.
 *
 *    You should have received a copy of the GNU General Public License
 *    along with this program; if not, write to the Free Software
 *    Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
 */

/*
 * LibSVM.java
 * Copyright (C) 2005 Yasser EL-Manzalawy (original code)
 * Copyright (C) 2005 University of Waikato, Hamilton, NZ (adapted code)
 * 
 */

import java.io.Serializable;
import java.lang.reflect.Array;
import java.lang.reflect.Field;
import java.lang.reflect.Method;
import java.util.Enumeration;
import java.util.Random;
import java.util.StringTokenizer;
import java.util.Vector;

import weka.classifiers.RandomizableClassifier;
import weka.core.Capabilities;
import weka.core.Capabilities.Capability;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.Option;
import weka.core.RevisionUtils;
import weka.core.SelectedTag;
import weka.core.Tag;
import weka.core.TechnicalInformation;
import weka.core.TechnicalInformation.Type;
import weka.core.TechnicalInformationHandler;
import weka.core.Utils;
import weka.filters.Filter;
import weka.filters.unsupervised.attribute.NominalToBinary;
import weka.filters.unsupervised.attribute.Normalize;
import weka.filters.unsupervised.attribute.ReplaceMissingValues;

/*
 * Modifications by FracPete:
 * - complete overhaul to make it useable in Weka
 * - accesses libsvm classes only via Reflection to make Weka compile without
 *   the libsvm classes
 * - uses more efficient code to transfer the data into the libsvm sparse format
 */

/**
 <!-- globalinfo-start --> 
 * A wrapper class for the libsvm tools (the libsvm
 * classes, typically the jar file, need to be in the classpath to use this
 * classifier).<br/>
 * LibSVM runs faster than SMO since it uses LibSVM to build the SVM classifier.<br/>
 * LibSVM allows users to experiment with One-class SVM, Regressing SVM, and
 * nu-SVM supported by LibSVM tool. LibSVM reports many useful statistics about
 * LibSVM classifier (e.g., confusion matrix,precision, recall, ROC score,
 * etc.).<br/>
 * <br/>
 * Yasser EL-Manzalawy (2005). WLSVM. URL
 * http://www.cs.iastate.edu/~yasser/wlsvm/.<br/>
 * <br/>
 * Chih-Chung Chang, Chih-Jen Lin (2001). LIBSVM - A Library for Support Vector
 * Machines. URL http://www.csie.ntu.edu.tw/~cjlin/libsvm/.
 * <p/>
 <!-- globalinfo-end -->
 * 
 <!-- technical-bibtex-start --> 
 * BibTeX:
 * 
 * <pre>
 * &#64;misc{EL-Manzalawy2005,
 *    author = {Yasser EL-Manzalawy},
 *    note = {You don't need to include the WLSVM package in the CLASSPATH},
 *    title = {WLSVM},
 *    year = {2005},
 *    URL = {http://www.cs.iastate.edu/\~yasser/wlsvm/}
 * }
 * 
 * &#64;misc{Chang2001,
 *    author = {Chih-Chung Chang and Chih-Jen Lin},
 *    note = {The Weka classifier works with version 2.82 of LIBSVM},
 *    title = {LIBSVM - A Library for Support Vector Machines},
 *    year = {2001},
 *    URL = {http://www.csie.ntu.edu.tw/\~cjlin/libsvm/}
 * }
 * </pre>
 * <p/>
 <!-- technical-bibtex-end -->
 * 
 <!-- options-start --> 
 * Valid options are:
 * <p/>
 * 
 * <pre>
 * -S &lt;int&gt;
 *  Set type of SVM (default: 0)
 *    0 = C-SVC
 *    1 = nu-SVC
 *    2 = one-class SVM
 *    3 = epsilon-SVR
 *    4 = nu-SVR
 * </pre>
 * 
 * <pre>
 * -K &lt;int&gt;
 *  Set type of kernel function (default: 2)
 *    0 = linear: u'*v
 *    1 = polynomial: (gamma*u'*v + coef0)^degree
 *    2 = radial basis function: exp(-gamma*|u-v|^2)
 *    3 = sigmoid: tanh(gamma*u'*v + coef0)
 * </pre>
 * 
 * <pre>
 * -D &lt;int&gt;
 *  Set degree in kernel function (default: 3)
 * </pre>
 * 
 * <pre>
 * -G &lt;double&gt;
 *  Set gamma in kernel function (default: 1/k)
 * </pre>
 * 
 * <pre>
 * -R &lt;double&gt;
 *  Set coef0 in kernel function (default: 0)
 * </pre>
 * 
 * <pre>
 * -C &lt;double&gt;
 *  Set the parameter C of C-SVC, epsilon-SVR, and nu-SVR
 *   (default: 1)
 * </pre>
 * 
 * <pre>
 * -N &lt;double&gt;
 *  Set the parameter nu of nu-SVC, one-class SVM, and nu-SVR
 *   (default: 0.5)
 * </pre>
 * 
 * <pre>
 * -Z
 *  Turns on normalization of input data (default: off)
 * </pre>
 * 
 * <pre>
 * -J
 *  Turn off nominal to binary conversion.
 *  WARNING: use only if your data is all numeric!
 * </pre>
 * 
 * <pre>
 * -V
 *  Turn off missing value replacement.
 *  WARNING: use only if your data has no missing values.
 * </pre>
 * 
 * <pre>
 * -P &lt;double&gt;
 *  Set the epsilon in loss function of epsilon-SVR (default: 0.1)
 * </pre>
 * 
 * <pre>
 * -M &lt;double&gt;
 *  Set cache memory size in MB (default: 40)
 * </pre>
 * 
 * <pre>
 * -E &lt;double&gt;
 *  Set tolerance of termination criterion (default: 0.001)
 * </pre>
 * 
 * <pre>
 * -H
 *  Turns the shrinking heuristics off (default: on)
 * </pre>
 * 
 * <pre>
 * -W &lt;double&gt;
 *  Set the parameters C of class i to weight[i]*C, for C-SVC
 *  E.g., for a 3-class problem, you could use "1 1 1" for equally
 *  weighted classes.
 *  (default: 1 for all classes)
 * </pre>
 * 
 * <pre>
 * -B
 *  Generate probability estimates for classification
 * </pre>
 * 
 * <pre>
 * -seed &lt;num&gt;
 *  Random seed
 *  (default = 1)
 * </pre>
 * 
 <!-- options-end -->
 * 
 * @author Yasser EL-Manzalawy
 * @author FracPete (fracpete at waikato dot ac dot nz)
 * @version $Revision: 10660 $
 * @see weka.core.converters.LibSVMLoader
 * @see weka.core.converters.LibSVMSaver
 */
public class LibSVM extends RandomizableClassifier implements TechnicalInformationHandler, Serializable {

    /** the svm classname */
    protected final static String CLASS_SVM = "libsvm.svm";

    /** the svm_model classname */
    protected final static String CLASS_SVMMODEL = "libsvm.svm_model";

    /** the svm_problem classname */
    protected final static String CLASS_SVMPROBLEM = "libsvm.svm_problem";

    /** the svm_parameter classname */
    protected final static String CLASS_SVMPARAMETER = "libsvm.svm_parameter";

    /** the svm_node classname */
    protected final static String CLASS_SVMNODE = "libsvm.svm_node";

    /** serial UID */
    protected static final long serialVersionUID = 14172;

    /** LibSVM Model */
    protected Object m_Model;

    /** for normalizing the data */
    protected Filter m_Filter = null;

    /** for converting mult-valued nominal attributes to binary */
    protected Filter m_NominalToBinary;

    /** The filter used to get rid of missing values. */
    protected ReplaceMissingValues m_ReplaceMissingValues;

    /** normalize input data */
    protected boolean m_Normalize = false;

    /** If true, the replace missing values filter is not applied */
    private boolean m_noReplaceMissingValues;

    /** SVM type C-SVC (classification) */
    public static final int SVMTYPE_C_SVC = 0;
    /** SVM type nu-SVC (classification) */
    public static final int SVMTYPE_NU_SVC = 1;
    /** SVM type one-class SVM (classification) */
    public static final int SVMTYPE_ONE_CLASS_SVM = 2;
    /** SVM type epsilon-SVR (regression) */
    public static final int SVMTYPE_EPSILON_SVR = 3;
    /** SVM type nu-SVR (regression) */
    public static final int SVMTYPE_NU_SVR = 4;
    /** SVM types */
    public static final Tag[] TAGS_SVMTYPE = { new Tag(SVMTYPE_C_SVC, "C-SVC (classification)"),
            new Tag(SVMTYPE_NU_SVC, "nu-SVC (classification)"),
            new Tag(SVMTYPE_ONE_CLASS_SVM, "one-class SVM (classification)"),
            new Tag(SVMTYPE_EPSILON_SVR, "epsilon-SVR (regression)"),
            new Tag(SVMTYPE_NU_SVR, "nu-SVR (regression)") };

    /** the SVM type */
    protected int m_SVMType = SVMTYPE_C_SVC;

    /** kernel type linear: u'*v */
    public static final int KERNELTYPE_LINEAR = 0;
    /** kernel type polynomial: (gamma*u'*v + coef0)^degree */
    public static final int KERNELTYPE_POLYNOMIAL = 1;
    /** kernel type radial basis function: exp(-gamma*|u-v|^2) */
    public static final int KERNELTYPE_RBF = 2;
    /** kernel type sigmoid: tanh(gamma*u'*v + coef0) */
    public static final int KERNELTYPE_SIGMOID = 3;
    /** the different kernel types */
    public static final Tag[] TAGS_KERNELTYPE = { new Tag(KERNELTYPE_LINEAR, "linear: u'*v"),
            new Tag(KERNELTYPE_POLYNOMIAL, "polynomial: (gamma*u'*v + coef0)^degree"),
            new Tag(KERNELTYPE_RBF, "radial basis function: exp(-gamma*|u-v|^2)"),
            new Tag(KERNELTYPE_SIGMOID, "sigmoid: tanh(gamma*u'*v + coef0)") };

    /** the kernel type */
    protected int m_KernelType = KERNELTYPE_RBF;

    /**
     * for poly - in older versions of libsvm declared as a double. At least since
     * 2.82 it is an int.
     */
    protected int m_Degree = 3;

    /** for poly/rbf/sigmoid */
    protected double m_Gamma = 0;

    /** for poly/rbf/sigmoid (the actual gamma) */
    protected double m_GammaActual = 0;

    /** for poly/sigmoid */
    protected double m_Coef0 = 0;

    /** in MB */
    protected double m_CacheSize = 40;

    /** stopping criteria */
    protected double m_eps = 1e-3;

    /** cost, for C_SVC, EPSILON_SVR and NU_SVR */
    protected double m_Cost = 1;

    /** for C_SVC */
    protected int[] m_WeightLabel = new int[0];

    /** for C_SVC */
    protected double[] m_Weight = new double[0];

    /** for NU_SVC, ONE_CLASS, and NU_SVR */
    protected double m_nu = 0.5;

    /** loss, for EPSILON_SVR */
    protected double m_Loss = 0.1;

    /** use the shrinking heuristics */
    protected boolean m_Shrinking = true;

    /**
     * whether to generate probability estimates instead of +1/-1 in case of
     * classification problems
     */
    protected boolean m_ProbabilityEstimates = false;

    /** whether the libsvm classes are in the Classpath */
    protected static boolean m_Present = false;
    static {
        try {
            Class.forName(CLASS_SVM);
            m_Present = true;
        } catch (Exception e) {
            m_Present = false;
        }
    }

    /**
     * Returns a string describing classifier
     * 
     * @return a description suitable for displaying in the explorer/experimenter
     *         gui
     */
    public String globalInfo() {
        return "A wrapper class for the libsvm tools (the libsvm classes, typically "
                + "the jar file, need to be in the classpath to use this classifier).\n"
                + "LibSVM runs faster than SMO since it uses LibSVM to build the SVM " + "classifier.\n"
                + "LibSVM allows users to experiment with One-class SVM, Regressing SVM, "
                + "and nu-SVM supported by LibSVM tool. LibSVM reports many useful "
                + "statistics about LibSVM classifier (e.g., confusion matrix,"
                + "precision, recall, ROC score, etc.).\n" + "\n" + getTechnicalInformation().toString();
    }

    /**
     * Returns an instance of a TechnicalInformation object, containing detailed
     * information about the technical background of this class, e.g., paper
     * reference or book this class is based on.
     * 
     * @return the technical information about this class
     */
    @Override
    public TechnicalInformation getTechnicalInformation() {
        TechnicalInformation result;
        TechnicalInformation additional;

        result = new TechnicalInformation(Type.MISC);
        result.setValue(TechnicalInformation.Field.AUTHOR, "Yasser EL-Manzalawy");
        result.setValue(TechnicalInformation.Field.YEAR, "2005");
        result.setValue(TechnicalInformation.Field.TITLE, "WLSVM");
        result.setValue(TechnicalInformation.Field.NOTE, "LibSVM was originally developed as 'WLSVM'");
        result.setValue(TechnicalInformation.Field.URL, "http://www.cs.iastate.edu/~yasser/wlsvm/");
        result.setValue(TechnicalInformation.Field.NOTE,
                "You don't need to include the WLSVM package in the CLASSPATH");

        additional = result.add(Type.MISC);
        additional.setValue(TechnicalInformation.Field.AUTHOR, "Chih-Chung Chang and Chih-Jen Lin");
        additional.setValue(TechnicalInformation.Field.TITLE, "LIBSVM - A Library for Support Vector Machines");
        additional.setValue(TechnicalInformation.Field.YEAR, "2001");
        additional.setValue(TechnicalInformation.Field.URL, "http://www.csie.ntu.edu.tw/~cjlin/libsvm/");
        additional.setValue(TechnicalInformation.Field.NOTE,
                "The Weka classifier works with version 2.82 of LIBSVM");

        return result;
    }

    /**
     * Returns an enumeration describing the available options.
     * 
     * @return an enumeration of all the available options.
     */
    @Override
    public Enumeration listOptions() {
        Vector result;

        result = new Vector();

        result.addElement(new Option(
                "\tSet type of SVM (default: 0)\n" + "\t\t 0 = C-SVC\n" + "\t\t 1 = nu-SVC\n"
                        + "\t\t 2 = one-class SVM\n" + "\t\t 3 = epsilon-SVR\n" + "\t\t 4 = nu-SVR",
                "S", 1, "-S <int>"));

        result.addElement(new Option("\tSet type of kernel function (default: 2)\n" + "\t\t 0 = linear: u'*v\n"
                + "\t\t 1 = polynomial: (gamma*u'*v + coef0)^degree\n"
                + "\t\t 2 = radial basis function: exp(-gamma*|u-v|^2)\n"
                + "\t\t 3 = sigmoid: tanh(gamma*u'*v + coef0)", "K", 1, "-K <int>"));

        result.addElement(new Option("\tSet degree in kernel function (default: 3)", "D", 1, "-D <int>"));

        result.addElement(new Option("\tSet gamma in kernel function (default: 1/k)", "G", 1, "-G <double>"));

        result.addElement(new Option("\tSet coef0 in kernel function (default: 0)", "R", 1, "-R <double>"));

        result.addElement(
                new Option("\tSet the parameter C of C-SVC, epsilon-SVR, and nu-SVR\n" + "\t (default: 1)", "C", 1,
                        "-C <double>"));

        result.addElement(
                new Option("\tSet the parameter nu of nu-SVC, one-class SVM, and nu-SVR\n" + "\t (default: 0.5)",
                        "N", 1, "-N <double>"));

        result.addElement(new Option("\tTurns on normalization of input data (default: off)", "Z", 0, "-Z"));

        result.addElement(new Option(
                "\tTurn off nominal to binary conversion." + "\n\tWARNING: use only if your data is all numeric!",
                "J", 0, "-J"));

        result.addElement(new Option("\tTurn off missing value replacement."
                + "\n\tWARNING: use only if your data has no missing " + "values.", "V", 0, "-V"));

        result.addElement(new Option("\tSet the epsilon in loss function of epsilon-SVR (default: 0.1)", "P", 1,
                "-P <double>"));

        result.addElement(new Option("\tSet cache memory size in MB (default: 40)", "M", 1, "-M <double>"));

        result.addElement(
                new Option("\tSet tolerance of termination criterion (default: 0.001)", "E", 1, "-E <double>"));

        result.addElement(new Option("\tTurns the shrinking heuristics off (default: on)", "H", 0, "-H"));

        result.addElement(new Option("\tSet the parameters C of class i to weight[i]*C, for C-SVC\n"
                + "\tE.g., for a 3-class problem, you could use \"1 1 1\" for equally\n" + "\tweighted classes.\n"
                + "\t(default: 1 for all classes)", "W", 1, "-W <double>"));

        result.addElement(new Option("\tGenerate probability estimates for classification", "B", 0, "-B"));

        result.addElement(new Option("\tRandom seed\n\t(default = 1)", "seed", 1, "-seed <num>"));

        return result.elements();
    }

    /**
     * Sets the classifier options
     * <p/>
     * 
     <!-- options-start --> 
     * Valid options are:
     * <p/>
     * 
     * <pre>
     * -S &lt;int&gt;
     *  Set type of SVM (default: 0)
     *    0 = C-SVC
     *    1 = nu-SVC
     *    2 = one-class SVM
     *    3 = epsilon-SVR
     *    4 = nu-SVR
     * </pre>
     * 
     * <pre>
     * -K &lt;int&gt;
     *  Set type of kernel function (default: 2)
     *    0 = linear: u'*v
     *    1 = polynomial: (gamma*u'*v + coef0)^degree
     *    2 = radial basis function: exp(-gamma*|u-v|^2)
     *    3 = sigmoid: tanh(gamma*u'*v + coef0)
     * </pre>
     * 
     * <pre>
     * -D &lt;int&gt;
     *  Set degree in kernel function (default: 3)
     * </pre>
     * 
     * <pre>
     * -G &lt;double&gt;
     *  Set gamma in kernel function (default: 1/k)
     * </pre>
     * 
     * <pre>
     * -R &lt;double&gt;
     *  Set coef0 in kernel function (default: 0)
     * </pre>
     * 
     * <pre>
     * -C &lt;double&gt;
     *  Set the parameter C of C-SVC, epsilon-SVR, and nu-SVR
     *   (default: 1)
     * </pre>
     * 
     * <pre>
     * -N &lt;double&gt;
     *  Set the parameter nu of nu-SVC, one-class SVM, and nu-SVR
     *   (default: 0.5)
     * </pre>
     * 
     * <pre>
     * -Z
     *  Turns on normalization of input data (default: off)
     * </pre>
     * 
     * <pre>
     * -J
     *  Turn off nominal to binary conversion.
     *  WARNING: use only if your data is all numeric!
     * </pre>
     * 
     * <pre>
     * -V
     *  Turn off missing value replacement.
     *  WARNING: use only if your data has no missing values.
     * </pre>
     * 
     * <pre>
     * -P &lt;double&gt;
     *  Set the epsilon in loss function of epsilon-SVR (default: 0.1)
     * </pre>
     * 
     * <pre>
     * -M &lt;double&gt;
     *  Set cache memory size in MB (default: 40)
     * </pre>
     * 
     * <pre>
     * -E &lt;double&gt;
     *  Set tolerance of termination criterion (default: 0.001)
     * </pre>
     * 
     * <pre>
     * -H
     *  Turns the shrinking heuristics off (default: on)
     * </pre>
     * 
     * <pre>
     * -W &lt;double&gt;
     *  Set the parameters C of class i to weight[i]*C, for C-SVC
     *  E.g., for a 3-class problem, you could use "1 1 1" for equally
     *  weighted classes.
     *  (default: 1 for all classes)
     * </pre>
     * 
     * <pre>
     * -B
     *  Generate probability estimates for classification
     * </pre>
     * 
     * <pre>
     * -seed &lt;num&gt;
     *  Random seed
     *  (default = 1)
     * </pre>
     * 
     <!-- options-end -->
     * 
     * @param options the options to parse
     * @throws Exception if parsing fails
     */
    @Override
    public void setOptions(String[] options) throws Exception {
        String tmpStr;

        tmpStr = Utils.getOption('S', options);
        if (tmpStr.length() != 0) {
            setSVMType(new SelectedTag(Integer.parseInt(tmpStr), TAGS_SVMTYPE));
        } else {
            setSVMType(new SelectedTag(SVMTYPE_EPSILON_SVR, TAGS_SVMTYPE));
        }

        tmpStr = Utils.getOption('K', options);
        if (tmpStr.length() != 0) {
            setKernelType(new SelectedTag(Integer.parseInt(tmpStr), TAGS_KERNELTYPE));
        } else {
            setKernelType(new SelectedTag(KERNELTYPE_RBF, TAGS_KERNELTYPE));
        }

        tmpStr = Utils.getOption('D', options);
        if (tmpStr.length() != 0) {
            setDegree(Integer.parseInt(tmpStr));
        } else {
            setDegree(1);
        }

        tmpStr = Utils.getOption('G', options);
        if (tmpStr.length() != 0) {
            setGamma(Double.parseDouble(tmpStr));
        } else {
            setGamma(0.18);
        }

        tmpStr = Utils.getOption('R', options);
        if (tmpStr.length() != 0) {
            setCoef0(Double.parseDouble(tmpStr));
        } else {
            setCoef0(0);
        }

        tmpStr = Utils.getOption('N', options);
        if (tmpStr.length() != 0) {
            setNu(Double.parseDouble(tmpStr));
        } else {
            setNu(0.5);
        }

        tmpStr = Utils.getOption('M', options);
        if (tmpStr.length() != 0) {
            setCacheSize(Double.parseDouble(tmpStr));
        } else {
            setCacheSize(40);
        }

        tmpStr = Utils.getOption('C', options);
        if (tmpStr.length() != 0) {
            setCost(Double.parseDouble(tmpStr));
        } else {
            setCost(5);
        }

        tmpStr = Utils.getOption('E', options);
        if (tmpStr.length() != 0) {
            setEps(Double.parseDouble(tmpStr));
        } else {
            setEps(1e-3);
        }

        setNormalize(Utils.getFlag('Z', options));

        setDoNotReplaceMissingValues(Utils.getFlag("V", options));

        tmpStr = Utils.getOption('P', options);
        if (tmpStr.length() != 0) {
            setLoss(Double.parseDouble(tmpStr));
        } else {
            setLoss(0.1);
        }

        setShrinking(!Utils.getFlag('H', options));

        setWeights(Utils.getOption('W', options));

        setProbabilityEstimates(Utils.getFlag('B', options));

        String seedString = Utils.getOption("seed", options);
        if (seedString.length() > 0) {
            setSeed(Integer.parseInt(seedString.trim()));
        }
    }

    /**
     * Returns the current options
     * 
     * @return the current setup
     */
    @Override
    public String[] getOptions() {

        Vector result;

        result = new Vector();

        result.add("-S");
        result.add("" + m_SVMType);

        result.add("-K");
        result.add("" + m_KernelType);

        result.add("-D");
        result.add("" + getDegree());

        result.add("-G");
        result.add("" + getGamma());

        result.add("-R");
        result.add("" + getCoef0());

        result.add("-N");
        result.add("" + getNu());

        result.add("-M");
        result.add("" + getCacheSize());

        result.add("-C");
        result.add("" + getCost());

        result.add("-E");
        result.add("" + getEps());

        result.add("-P");
        result.add("" + getLoss());

        if (!getShrinking()) {
            result.add("-H");
        }

        if (getNormalize()) {
            result.add("-Z");
        }

        if (getDoNotReplaceMissingValues()) {
            result.add("-V");
        }

        if (getWeights().length() != 0) {
            result.add("-W");
            result.add("" + getWeights());
        }

        if (getProbabilityEstimates()) {
            result.add("-B");
        }

        result.add("-seed");
        result.add("" + getSeed());

        return (String[]) result.toArray(new String[result.size()]);
    }

    /**
     * returns whether the libsvm classes are present or not, i.e. whether the
     * classes are in the classpath or not
     * 
     * @return whether the libsvm classes are available
     */
    public static boolean isPresent() {
        return m_Present;
    }

    /**
     * Sets type of SVM (default SVMTYPE_C_SVC)
     * 
     * @param value the type of the SVM
     */
    public void setSVMType(SelectedTag value) {
        if (value.getTags() == TAGS_SVMTYPE) {
            m_SVMType = value.getSelectedTag().getID();
        }
    }

    /**
     * Gets type of SVM
     * 
     * @return the type of the SVM
     */
    public SelectedTag getSVMType() {
        return new SelectedTag(m_SVMType, TAGS_SVMTYPE);
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String SVMTypeTipText() {
        return "The type of SVM to use.";
    }

    /**
     * Sets type of kernel function (default KERNELTYPE_RBF)
     * 
     * @param value the kernel type
     */
    public void setKernelType(SelectedTag value) {
        if (value.getTags() == TAGS_KERNELTYPE) {
            m_KernelType = value.getSelectedTag().getID();
        }
    }

    /**
     * Gets type of kernel function
     * 
     * @return the kernel type
     */
    public SelectedTag getKernelType() {
        return new SelectedTag(m_KernelType, TAGS_KERNELTYPE);
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String kernelTypeTipText() {
        return "The type of kernel to use";
    }

    /**
     * Sets the degree of the kernel
     * 
     * @param value the degree of the kernel
     */
    public void setDegree(int value) {
        m_Degree = value;
    }

    /**
     * Gets the degree of the kernel
     * 
     * @return the degree of the kernel
     */
    public int getDegree() {
        return m_Degree;
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String degreeTipText() {
        return "The degree of the kernel.";
    }

    /**
     * Sets gamma (default = 1/no of attributes)
     * 
     * @param value the gamma value
     */
    public void setGamma(double value) {
        m_Gamma = value;
    }

    /**
     * Gets gamma
     * 
     * @return the current gamma
     */
    public double getGamma() {
        return m_Gamma;
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String gammaTipText() {
        return "The gamma to use, if 0 then 1/max_index is used.";
    }

    /**
     * Sets coef (default 0)
     * 
     * @param value the coef
     */
    public void setCoef0(double value) {
        m_Coef0 = value;
    }

    /**
     * Gets coef
     * 
     * @return the coef
     */
    public double getCoef0() {
        return m_Coef0;
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String coef0TipText() {
        return "The coefficient to use.";
    }

    /**
     * Sets nu of nu-SVC, one-class SVM, and nu-SVR (default 0.5)
     * 
     * @param value the new nu value
     */
    public void setNu(double value) {
        m_nu = value;
    }

    /**
     * Gets nu of nu-SVC, one-class SVM, and nu-SVR (default 0.5)
     * 
     * @return the current nu value
     */
    public double getNu() {
        return m_nu;
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String nuTipText() {
        return "The value of nu for nu-SVC, one-class SVM and nu-SVR.";
    }

    /**
     * Sets cache memory size in MB (default 40)
     * 
     * @param value the memory size in MB
     */
    public void setCacheSize(double value) {
        m_CacheSize = value;
    }

    /**
     * Gets cache memory size in MB
     * 
     * @return the memory size in MB
     */
    public double getCacheSize() {
        return m_CacheSize;
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String cacheSizeTipText() {
        return "The cache size in MB.";
    }

    /**
     * Sets the parameter C of C-SVC, epsilon-SVR, and nu-SVR (default 1)
     * 
     * @param value the cost value
     */
    public void setCost(double value) {
        m_Cost = value;
    }

    /**
     * Sets the parameter C of C-SVC, epsilon-SVR, and nu-SVR
     * 
     * @return the cost value
     */
    public double getCost() {
        return m_Cost;
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String costTipText() {
        return "The cost parameter C for C-SVC, epsilon-SVR and nu-SVR.";
    }

    /**
     * Sets tolerance of termination criterion (default 0.001)
     * 
     * @param value the tolerance
     */
    public void setEps(double value) {
        m_eps = value;
    }

    /**
     * Gets tolerance of termination criterion
     * 
     * @return the current tolerance
     */
    public double getEps() {
        return m_eps;
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String epsTipText() {
        return "The tolerance of the termination criterion.";
    }

    /**
     * Sets the epsilon in loss function of epsilon-SVR (default 0.1)
     * 
     * @param value the loss epsilon
     */
    public void setLoss(double value) {
        m_Loss = value;
    }

    /**
     * Gets the epsilon in loss function of epsilon-SVR
     * 
     * @return the loss epsilon
     */
    public double getLoss() {
        return m_Loss;
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String lossTipText() {
        return "The epsilon for the loss function in epsilon-SVR.";
    }

    /**
     * whether to use the shrinking heuristics
     * 
     * @param value true uses shrinking
     */
    public void setShrinking(boolean value) {
        m_Shrinking = value;
    }

    /**
     * whether to use the shrinking heuristics
     * 
     * @return true, if shrinking is used
     */
    public boolean getShrinking() {
        return m_Shrinking;
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String shrinkingTipText() {
        return "Whether to use the shrinking heuristic.";
    }

    /**
     * whether to normalize input data
     * 
     * @param value whether to normalize the data
     */
    public void setNormalize(boolean value) {
        m_Normalize = value;
    }

    /**
     * whether to normalize input data
     * 
     * @return true, if the data is normalized
     */
    public boolean getNormalize() {
        return m_Normalize;
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String normalizeTipText() {
        return "Whether to normalize the data.";
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String doNotReplaceMissingValuesTipText() {
        return "Whether to turn off automatic replacement of missing "
                + "values. WARNING: set to true only if the data does not " + "contain missing values.";
    }

    /**
     * Whether to turn off automatic replacement of missing values. Set to true
     * only if the data does not contain missing values.
     * 
     * @param b true if automatic missing values replacement is to be disabled.
     */
    public void setDoNotReplaceMissingValues(boolean b) {
        m_noReplaceMissingValues = b;
    }

    /**
     * Gets whether automatic replacement of missing values is disabled.
     * 
     * @return true if automatic replacement of missing values is disabled.
     */
    public boolean getDoNotReplaceMissingValues() {
        return m_noReplaceMissingValues;
    }

    /**
     * Sets the parameters C of class i to weight[i]*C, for C-SVC (default 1).
     * Blank separated list of doubles.
     * 
     * @param weightsStr the weights (doubles, separated by blanks)
     */
    public void setWeights(String weightsStr) {
        StringTokenizer tok;
        int i;

        tok = new StringTokenizer(weightsStr, " ");
        m_Weight = new double[tok.countTokens()];
        m_WeightLabel = new int[tok.countTokens()];

        if (m_Weight.length == 0) {
            System.out.println("Zero Weights processed. Default weights will be used");
        }

        for (i = 0; i < m_Weight.length; i++) {
            m_Weight[i] = Double.parseDouble(tok.nextToken());
            m_WeightLabel[i] = i;
        }
    }

    /**
     * Gets the parameters C of class i to weight[i]*C, for C-SVC (default 1).
     * Blank separated doubles.
     * 
     * @return the weights (doubles separated by blanks)
     */
    public String getWeights() {
        String result;
        int i;

        result = "";
        for (i = 0; i < m_Weight.length; i++) {
            if (i > 0) {
                result += " ";
            }
            result += Double.toString(m_Weight[i]);
        }

        return result;
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String weightsTipText() {
        return "The weights to use for the classes (blank-separated list, eg, \"1 1 1\" for a 3-class problem), if empty 1 is used by default.";
    }

    /**
     * Returns whether probability estimates are generated instead of -1/+1 for
     * classification problems.
     * 
     * @param value whether to predict probabilities
     */
    public void setProbabilityEstimates(boolean value) {
        m_ProbabilityEstimates = value;
    }

    /**
     * Sets whether to generate probability estimates instead of -1/+1 for
     * classification problems.
     * 
     * @return true, if probability estimates should be returned
     */
    public boolean getProbabilityEstimates() {
        return m_ProbabilityEstimates;
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String probabilityEstimatesTipText() {
        return "Whether to generate probability estimates instead of -1/+1 for classification problems.";
    }

    /**
     * sets the specified field
     * 
     * @param o the object to set the field for
     * @param name the name of the field
     * @param value the new value of the field
     */
    protected void setField(Object o, String name, Object value) {
        Field f;

        try {
            f = o.getClass().getField(name);
            f.set(o, value);
        } catch (Exception e) {
            e.printStackTrace();
        }
    }

    /**
     * sets the specified field in an array
     * 
     * @param o the object to set the field for
     * @param name the name of the field
     * @param index the index in the array
     * @param value the new value of the field
     */
    protected void setField(Object o, String name, int index, Object value) {
        Field f;

        try {
            f = o.getClass().getField(name);
            Array.set(f.get(o), index, value);
        } catch (Exception e) {
            e.printStackTrace();
        }
    }

    /**
     * returns the current value of the specified field
     * 
     * @param o the object the field is member of
     * @param name the name of the field
     * @return the value
     */
    protected Object getField(Object o, String name) {
        Field f;
        Object result;

        try {
            f = o.getClass().getField(name);
            result = f.get(o);
        } catch (Exception e) {
            e.printStackTrace();
            result = null;
        }

        return result;
    }

    /**
     * sets a new array for the field
     * 
     * @param o the object to set the array for
     * @param name the name of the field
     * @param type the type of the array
     * @param length the length of the one-dimensional array
     */
    protected void newArray(Object o, String name, Class type, int length) {
        newArray(o, name, type, new int[] { length });
    }

    /**
     * sets a new array for the field
     * 
     * @param o the object to set the array for
     * @param name the name of the field
     * @param type the type of the array
     * @param dimensions the dimensions of the array
     */
    protected void newArray(Object o, String name, Class type, int[] dimensions) {
        Field f;

        try {
            f = o.getClass().getField(name);
            f.set(o, Array.newInstance(type, dimensions));
        } catch (Exception e) {
            e.printStackTrace();
        }
    }

    /**
     * executes the specified method and returns the result, if any
     * 
     * @param o the object the method should be called from
     * @param name the name of the method
     * @param paramClasses the classes of the parameters
     * @param paramValues the values of the parameters
     * @return the return value of the method, if any (in that case null)
     */
    protected Object invokeMethod(Object o, String name, Class[] paramClasses, Object[] paramValues) {
        Method m;
        Object result;

        result = null;

        try {
            m = o.getClass().getMethod(name, paramClasses);
            result = m.invoke(o, paramValues);
        } catch (Exception e) {
            e.printStackTrace();
            result = null;
        }

        return result;
    }

    /**
     * transfers the local variables into a svm_parameter object
     * 
     * @return the configured svm_parameter object
     */
    protected Object getParameters() {
        Object result;
        int i;

        try {
            result = Class.forName(CLASS_SVMPARAMETER).newInstance();

            setField(result, "svm_type", new Integer(m_SVMType));
            setField(result, "kernel_type", new Integer(m_KernelType));
            setField(result, "degree", new Integer(m_Degree));
            setField(result, "gamma", new Double(m_GammaActual));
            setField(result, "coef0", new Double(m_Coef0));
            setField(result, "nu", new Double(m_nu));
            setField(result, "cache_size", new Double(m_CacheSize));
            setField(result, "C", new Double(m_Cost));
            setField(result, "eps", new Double(m_eps));
            setField(result, "p", new Double(m_Loss));
            setField(result, "shrinking", new Integer(m_Shrinking ? 1 : 0));
            setField(result, "nr_weight", new Integer(m_Weight.length));
            setField(result, "probability", new Integer(m_ProbabilityEstimates ? 1 : 0));

            newArray(result, "weight", Double.TYPE, m_Weight.length);
            newArray(result, "weight_label", Integer.TYPE, m_Weight.length);
            for (i = 0; i < m_Weight.length; i++) {
                setField(result, "weight", i, new Double(m_Weight[i]));
                setField(result, "weight_label", i, new Integer(m_WeightLabel[i]));
            }
        } catch (Exception e) {
            e.printStackTrace();
            result = null;
        }

        return result;
    }

    /**
     * returns the svm_problem
     * 
     * @param vx the x values
     * @param vy the y values
     * @return the svm_problem object
     */
    protected Object getProblem(Vector vx, Vector vy) {
        Object result;

        try {
            result = Class.forName(CLASS_SVMPROBLEM).newInstance();

            setField(result, "l", new Integer(vy.size()));

            newArray(result, "x", Class.forName(CLASS_SVMNODE), new int[] { vy.size(), 0 });
            for (int i = 0; i < vy.size(); i++) {
                setField(result, "x", i, vx.elementAt(i));
            }

            newArray(result, "y", Double.TYPE, vy.size());
            for (int i = 0; i < vy.size(); i++) {
                setField(result, "y", i, vy.elementAt(i));
            }
        } catch (Exception e) {
            e.printStackTrace();
            result = null;
        }

        return result;
    }

    /**
     * returns an instance into a sparse libsvm array
     * 
     * @param instance the instance to work on
     * @return the libsvm array
     * @throws Exception if setup of array fails
     */
    protected Object instanceToArray(Instance instance) throws Exception {
        int index;
        int count;
        int i;
        Object result;

        // determine number of non-zero attributes
        /*
         * for (i = 0; i < instance.numAttributes(); i++) { if (i ==
         * instance.classIndex()) continue; if (instance.value(i) != 0) count++; }
         */
        count = 0;
        for (i = 0; i < instance.numValues(); i++) {
            if (instance.index(i) == instance.classIndex()) {
                continue;
            }
            if (instance.valueSparse(i) != 0) {
                count++;
            }
        }

        // fill array
        /*
         * result = Array.newInstance(Class.forName(CLASS_SVMNODE), count); index =
         * 0; for (i = 0; i < instance.numAttributes(); i++) { if (i ==
         * instance.classIndex()) continue; if (instance.value(i) == 0) continue;
         * 
         * Array.set(result, index, Class.forName(CLASS_SVMNODE).newInstance());
         * setField(Array.get(result, index), "index", new Integer(i + 1));
         * setField(Array.get(result, index), "value", new
         * Double(instance.value(i))); index++; }
         */

        result = Array.newInstance(Class.forName(CLASS_SVMNODE), count);
        index = 0;
        for (i = 0; i < instance.numValues(); i++) {

            int idx = instance.index(i);
            if (idx == instance.classIndex()) {
                continue;
            }
            if (instance.valueSparse(i) == 0) {
                continue;
            }

            Array.set(result, index, Class.forName(CLASS_SVMNODE).newInstance());
            setField(Array.get(result, index), "index", new Integer(idx + 1));
            setField(Array.get(result, index), "value", new Double(instance.valueSparse(i)));
            index++;
        }

        return result;
    }

    /**
     * Computes the distribution for a given instance. In case of 1-class
     * classification, 1 is returned at index 0 if libsvm returns 1 and NaN (=
     * missing) if libsvm returns -1.
     * 
     * @param instance the instance for which distribution is computed
     * @return the distribution
     * @throws Exception if the distribution can't be computed successfully
     */
    @Override
    public double[] distributionForInstance(Instance instance) throws Exception {
        int[] labels = new int[instance.numClasses()];
        double[] prob_estimates = null;

        if (m_ProbabilityEstimates) {
            invokeMethod(Class.forName(CLASS_SVM).newInstance(), "svm_get_labels",
                    new Class[] { Class.forName(CLASS_SVMMODEL),
                            Array.newInstance(Integer.TYPE, instance.numClasses()).getClass() },
                    new Object[] { m_Model, labels });

            prob_estimates = new double[instance.numClasses()];
        }

        if (!getDoNotReplaceMissingValues()) {
            m_ReplaceMissingValues.input(instance);
            m_ReplaceMissingValues.batchFinished();
            instance = m_ReplaceMissingValues.output();
        }

        if (m_Filter != null) {
            m_Filter.input(instance);
            m_Filter.batchFinished();
            instance = m_Filter.output();
        }

        m_NominalToBinary.input(instance);
        m_NominalToBinary.batchFinished();
        instance = m_NominalToBinary.output();

        Object x = instanceToArray(instance);
        double v;
        double[] result = new double[instance.numClasses()];
        if (m_ProbabilityEstimates && ((m_SVMType == SVMTYPE_C_SVC) || (m_SVMType == SVMTYPE_NU_SVC))) {
            v = ((Double) invokeMethod(Class.forName(CLASS_SVM).newInstance(), "svm_predict_probability",
                    new Class[] { Class.forName(CLASS_SVMMODEL),
                            Array.newInstance(Class.forName(CLASS_SVMNODE), Array.getLength(x)).getClass(),
                            Array.newInstance(Double.TYPE, prob_estimates.length).getClass() },
                    new Object[] { m_Model, x, prob_estimates })).doubleValue();

            // Return order of probabilities to canonical weka attribute order
            for (int k = 0; k < prob_estimates.length; k++) {
                result[labels[k]] = prob_estimates[k];
            }
        } else {
            v = ((Double) invokeMethod(Class.forName(CLASS_SVM).newInstance(), "svm_predict",
                    new Class[] { Class.forName(CLASS_SVMMODEL),
                            Array.newInstance(Class.forName(CLASS_SVMNODE), Array.getLength(x)).getClass() },
                    new Object[] { m_Model, x })).doubleValue();

            if (instance.classAttribute().isNominal()) {
                if (m_SVMType == SVMTYPE_ONE_CLASS_SVM) {
                    if (v > 0) {
                        result[0] = 1;
                    } else {
                        // outlier (interface for Classifier specifies that unclassified
                        // instances
                        // should return a distribution of all zeros)
                        result[0] = 0;
                    }
                } else {
                    result[(int) v] = 1;
                }
            } else {
                result[0] = v;
            }
        }

        return result;
    }

    /**
     * Returns default capabilities of the classifier.
     * 
     * @return the capabilities of this classifier
     */
    @Override
    public Capabilities getCapabilities() {
        Capabilities result = super.getCapabilities();
        result.disableAll();

        // attributes
        result.enable(Capability.NOMINAL_ATTRIBUTES);
        result.enable(Capability.NUMERIC_ATTRIBUTES);
        result.enable(Capability.DATE_ATTRIBUTES);
        result.enable(Capability.MISSING_VALUES);

        // class
        result.enableDependency(Capability.UNARY_CLASS);
        result.enableDependency(Capability.NOMINAL_CLASS);
        result.enableDependency(Capability.NUMERIC_CLASS);
        result.enableDependency(Capability.DATE_CLASS);

        switch (m_SVMType) {
        case SVMTYPE_C_SVC:
        case SVMTYPE_NU_SVC:
            result.enable(Capability.NOMINAL_CLASS);
            break;

        case SVMTYPE_ONE_CLASS_SVM:
            result.enable(Capability.UNARY_CLASS);
            break;

        case SVMTYPE_EPSILON_SVR:
        case SVMTYPE_NU_SVR:
            result.enable(Capability.NUMERIC_CLASS);
            result.enable(Capability.DATE_CLASS);
            break;

        default:
            throw new IllegalArgumentException("SVMType " + m_SVMType + " is not supported!");
        }
        result.enable(Capability.MISSING_CLASS_VALUES);

        return result;
    }

    /**
     * builds the classifier
     * 
     * @param insts the training instances
     * @throws Exception if libsvm classes not in classpath or libsvm encountered
     *           a problem
     */
    @Override
    public void buildClassifier(Instances insts) throws Exception {
        m_Filter = null;

        if (!isPresent()) {
            throw new Exception("libsvm classes not in CLASSPATH!");
        }

        // remove instances with missing class
        insts = new Instances(insts);
        insts.deleteWithMissingClass();

        if (!getDoNotReplaceMissingValues()) {
            m_ReplaceMissingValues = new ReplaceMissingValues();
            m_ReplaceMissingValues.setInputFormat(insts);
            insts = Filter.useFilter(insts, m_ReplaceMissingValues);
        }

        // can classifier handle the data?
        // we check this here so that if the user turns off
        // replace missing values filtering, it will fail
        // if the data actually does have missing values
        getCapabilities().testWithFail(insts);

        if (getNormalize()) {
            m_Filter = new Normalize();
            m_Filter.setInputFormat(insts);
            insts = Filter.useFilter(insts, m_Filter);
        }

        // nominal to binary
        m_NominalToBinary = new NominalToBinary();
        m_NominalToBinary.setInputFormat(insts);
        insts = Filter.useFilter(insts, m_NominalToBinary);

        Vector vy = new Vector();
        Vector vx = new Vector();
        int max_index = 0;

        for (int d = 0; d < insts.numInstances(); d++) {
            Instance inst = insts.instance(d);
            Object x = instanceToArray(inst);
            int m = Array.getLength(x);

            if (m > 0) {
                max_index = Math.max(max_index, ((Integer) getField(Array.get(x, m - 1), "index")).intValue());
            }
            vx.addElement(x);
            vy.addElement(new Double(inst.classValue()));
        }

        // calculate actual gamma
        if (getGamma() == 0) {
            m_GammaActual = 1.0 / max_index;
        } else {
            m_GammaActual = m_Gamma;
        }

        // check parameter
        String error_msg = (String) invokeMethod(Class.forName(CLASS_SVM).newInstance(), "svm_check_parameter",
                new Class[] { Class.forName(CLASS_SVMPROBLEM), Class.forName(CLASS_SVMPARAMETER) },
                new Object[] { getProblem(vx, vy), getParameters() });

        if (error_msg != null) {
            throw new Exception("Error: " + error_msg);
        }

        // make probability estimates deterministic from run to run
        Class svmClass = Class.forName(CLASS_SVM);
        Field randF = svmClass.getField("rand");
        Random rand = (Random) randF.get(null); // static field
        rand.setSeed(m_Seed);

        // train model
        m_Model = invokeMethod(Class.forName(CLASS_SVM).newInstance(), "svm_train",
                new Class[] { Class.forName(CLASS_SVMPROBLEM), Class.forName(CLASS_SVMPARAMETER) },
                new Object[] { getProblem(vx, vy), getParameters() });
    }

    /**
     * returns a string representation
     * 
     * @return a string representation
     */
    @Override
    public String toString() {
        return "LibSVM wrapper, original code by Yasser EL-Manzalawy (= WLSVM)";
    }

    /**
     * Returns the revision string.
     * 
     * @return the revision
     */
    @Override
    public String getRevision() {
        return RevisionUtils.extract("$Revision: 10660 $");
    }

    /**
     * Main method for testing this class.
     * 
     * @param args the options
     */
    public static void main(String[] args) {
        runClassifier(new LibSVM(), args);
    }
}