weka.clusterers.SimpleKMeans.java Source code

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Here is the source code for weka.clusterers.SimpleKMeans.java

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/*
 *   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 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 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/>.
 */

/*
 *    SimpleKMeans.java
 *    Copyright (C) 2000-2012 University of Waikato, Hamilton, New Zealand
 *
 */
package weka.clusterers;

import java.util.ArrayList;
import java.util.Collections;
import java.util.Enumeration;
import java.util.HashMap;
import java.util.List;
import java.util.Random;
import java.util.Vector;
import java.util.concurrent.Callable;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Future;

import weka.classifiers.rules.DecisionTableHashKey;
import weka.core.Attribute;
import weka.core.Capabilities;
import weka.core.Capabilities.Capability;
import weka.core.DenseInstance;
import weka.core.DistanceFunction;
import weka.core.EuclideanDistance;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.ManhattanDistance;
import weka.core.Option;
import weka.core.RevisionUtils;
import weka.core.SelectedTag;
import weka.core.Tag;
import weka.core.TechnicalInformation;
import weka.core.TechnicalInformation.Field;
import weka.core.TechnicalInformation.Type;
import weka.core.TechnicalInformationHandler;
import weka.core.Utils;
import weka.core.WeightedInstancesHandler;
import weka.filters.Filter;
import weka.filters.unsupervised.attribute.ReplaceMissingValues;

/**
 * <!-- globalinfo-start --> Cluster data using the k means algorithm. Can use
 * either the Euclidean distance (default) or the Manhattan distance. If the
 * Manhattan distance is used, then centroids are computed as the component-wise
 * median rather than mean. For more information see:<br/>
 * <br/>
 * D. Arthur, S. Vassilvitskii: k-means++: the advantages of carefull seeding.
 * In: Proceedings of the eighteenth annual ACM-SIAM symposium on Discrete
 * algorithms, 1027-1035, 2007.
 * <p/>
 * <!-- globalinfo-end -->
 * 
 * <!-- technical-bibtex-start --> BibTeX:
 * 
 * <pre>
 * &#64;inproceedings{Arthur2007,
 *    author = {D. Arthur and S. Vassilvitskii},
 *    booktitle = {Proceedings of the eighteenth annual ACM-SIAM symposium on Discrete algorithms},
 *    pages = {1027-1035},
 *    title = {k-means++: the advantages of carefull seeding},
 *    year = {2007}
 * }
 * </pre>
 * <p/>
 * <!-- technical-bibtex-end -->
 * 
 * <!-- options-start --> Valid options are:
 * <p/>
 * 
 * <pre>
 * -N &lt;num&gt;
 *  Number of clusters.
 *  (default 2).
 * </pre>
 * 
 * <pre>
 * -init
 *  Initialization method to use.
 *  0 = random, 1 = k-means++, 2 = canopy, 3 = farthest first.
 *  (default = 0)
 * </pre>
 * 
 * <pre>
 * -C
 *  Use canopies to reduce the number of distance calculations.
 * </pre>
 * 
 * <pre>
 * -max-candidates &lt;num&gt;
 *  Maximum number of candidate canopies to retain in memory
 *  at any one time when using canopy clustering.
 *  T2 distance plus, data characteristics,
 *  will determine how many candidate canopies are formed before
 *  periodic and final pruning are performed, which might result
 *  in exceess memory consumption. This setting avoids large numbers
 *  of candidate canopies consuming memory. (default = 100)
 * </pre>
 * 
 * <pre>
 * -periodic-pruning &lt;num&gt;
 *  How often to prune low density canopies when using canopy clustering. 
 *  (default = every 10,000 training instances)
 * </pre>
 * 
 * <pre>
 * -min-density
 *  Minimum canopy density, when using canopy clustering, below which
 *   a canopy will be pruned during periodic pruning. (default = 2 instances)
 * </pre>
 * 
 * <pre>
 * -t2
 *  The T2 distance to use when using canopy clustering. Values &lt; 0 indicate that
 *  a heuristic based on attribute std. deviation should be used to set this.
 *  (default = -1.0)
 * </pre>
 * 
 * <pre>
 * -t1
 *  The T1 distance to use when using canopy clustering. A value &lt; 0 is taken as a
 *  positive multiplier for T2. (default = -1.5)
 * </pre>
 * 
 * <pre>
 * -V
 *  Display std. deviations for centroids.
 * </pre>
 * 
 * <pre>
 * -M
 *  Don't replace missing values with mean/mode.
 * </pre>
 * 
 * <pre>
 * -A &lt;classname and options&gt;
 *  Distance function to use.
 *  (default: weka.core.EuclideanDistance)
 * </pre>
 * 
 * <pre>
 * -I &lt;num&gt;
 *  Maximum number of iterations.
 * </pre>
 * 
 * <pre>
 * -O
 *  Preserve order of instances.
 * </pre>
 * 
 * <pre>
 * -fast
 *  Enables faster distance calculations, using cut-off values.
 *  Disables the calculation/output of squared errors/distances.
 * </pre>
 * 
 * <pre>
 * -num-slots &lt;num&gt;
 *  Number of execution slots.
 *  (default 1 - i.e. no parallelism)
 * </pre>
 * 
 * <pre>
 * -S &lt;num&gt;
 *  Random number seed.
 *  (default 10)
 * </pre>
 * 
 * <pre>
 * -output-debug-info
 *  If set, clusterer is run in debug mode and
 *  may output additional info to the console
 * </pre>
 * 
 * <pre>
 * -do-not-check-capabilities
 *  If set, clusterer capabilities are not checked before clusterer is built
 *  (use with caution).
 * </pre>
 * 
 * <!-- options-end -->
 * 
 * @author Mark Hall (mhall@cs.waikato.ac.nz)
 * @author Eibe Frank (eibe@cs.waikato.ac.nz)
 * @version $Revision$
 * @see RandomizableClusterer
 */
public class SimpleKMeans extends RandomizableClusterer
        implements NumberOfClustersRequestable, WeightedInstancesHandler, TechnicalInformationHandler {

    /** for serialization. */
    static final long serialVersionUID = -3235809600124455376L;

    /**
     * replace missing values in training instances.
     */
    protected ReplaceMissingValues m_ReplaceMissingFilter;

    /**
     * number of clusters to generate.
     */
    protected int m_NumClusters = 2;

    /**
     * Holds the initial start points, as supplied by the initialization method
     * used
     */
    protected Instances m_initialStartPoints;

    /**
     * holds the cluster centroids.
     */
    protected Instances m_ClusterCentroids;

    /**
     * Holds the standard deviations of the numeric attributes in each cluster.
     */
    protected Instances m_ClusterStdDevs;

    /**
     * For each cluster, holds the frequency counts for the values of each nominal
     * attribute.
     */
    protected double[][][] m_ClusterNominalCounts;
    protected double[][] m_ClusterMissingCounts;

    /**
     * Stats on the full data set for comparison purposes. In case the attribute
     * is numeric the value is the mean if is being used the Euclidian distance or
     * the median if Manhattan distance and if the attribute is nominal then it's
     * mode is saved.
     */
    protected double[] m_FullMeansOrMediansOrModes;
    protected double[] m_FullStdDevs;
    protected double[][] m_FullNominalCounts;
    protected double[] m_FullMissingCounts;

    /**
     * Display standard deviations for numeric atts.
     */
    protected boolean m_displayStdDevs;

    /**
     * Replace missing values globally?
     */
    protected boolean m_dontReplaceMissing = false;

    /**
     * The number of instances in each cluster.
     */
    protected double[] m_ClusterSizes;

    /**
     * Maximum number of iterations to be executed.
     */
    protected int m_MaxIterations = 500;

    /**
     * Keep track of the number of iterations completed before convergence.
     */
    protected int m_Iterations = 0;

    /**
     * Holds the squared errors for all clusters.
     */
    protected double[] m_squaredErrors;

    /** the distance function used. */
    protected DistanceFunction m_DistanceFunction = new EuclideanDistance();

    /**
     * Preserve order of instances.
     */
    protected boolean m_PreserveOrder = false;

    /**
     * Assignments obtained.
     */
    protected int[] m_Assignments = null;

    /** whether to use fast calculation of distances (using a cut-off). */
    protected boolean m_FastDistanceCalc = false;

    public static final int RANDOM = 0;
    public static final int KMEANS_PLUS_PLUS = 1;
    public static final int CANOPY = 2;
    public static final int FARTHEST_FIRST = 3;

    /** Initialization methods */
    public static final Tag[] TAGS_SELECTION = { new Tag(RANDOM, "Random"), new Tag(KMEANS_PLUS_PLUS, "k-means++"),
            new Tag(CANOPY, "Canopy"), new Tag(FARTHEST_FIRST, "Farthest first") };

    /** The initialization method to use */
    protected int m_initializationMethod = RANDOM;

    /**
     * Whether to reducet the number of distance calcs done by k-means with
     * canopies
     */
    protected boolean m_speedUpDistanceCompWithCanopies = false;

    /** Canopies that each centroid falls into (determined by T1 radius) */
    protected List<long[]> m_centroidCanopyAssignments;

    /** Canopies that each training instance falls into (determined by T1 radius) */
    protected List<long[]> m_dataPointCanopyAssignments;

    /** The canopy clusterer (if being used) */
    protected Canopy m_canopyClusters;

    /**
     * The maximum number of candidate canopies to hold in memory at any one time
     * (if using canopy clustering)
     */
    protected int m_maxCanopyCandidates = 100;

    /**
     * Prune low-density candidate canopies after every x instances have been seen
     * (if using canopy clustering)
     */
    protected int m_periodicPruningRate = 10000;

    /**
     * The minimum cluster density (according to T2 distance) allowed. Used when
     * periodically pruning candidate canopies (if using canopy clustering)
     */
    protected double m_minClusterDensity = 2;

    /** The t2 radius to pass through to Canopy */
    protected double m_t2 = Canopy.DEFAULT_T2;

    /** The t1 radius to pass through to Canopy */
    protected double m_t1 = Canopy.DEFAULT_T1;

    /** Number of threads to run */
    protected int m_executionSlots = 1;

    /** For parallel execution mode */
    protected transient ExecutorService m_executorPool;

    /**
     * the default constructor.
     */
    public SimpleKMeans() {
        super();

        m_SeedDefault = 10;
        setSeed(m_SeedDefault);
    }

    /**
     * Start the pool of execution threads
     */
    protected void startExecutorPool() {
        if (m_executorPool != null) {
            m_executorPool.shutdownNow();
        }

        m_executorPool = Executors.newFixedThreadPool(m_executionSlots);
    }

    protected int m_completed;
    protected int m_failed;

    @Override
    public TechnicalInformation getTechnicalInformation() {
        TechnicalInformation result;

        result = new TechnicalInformation(Type.INPROCEEDINGS);
        result.setValue(Field.AUTHOR, "D. Arthur and S. Vassilvitskii");
        result.setValue(Field.TITLE, "k-means++: the advantages of carefull seeding");
        result.setValue(Field.BOOKTITLE,
                "Proceedings of the eighteenth annual " + "ACM-SIAM symposium on Discrete algorithms");
        result.setValue(Field.YEAR, "2007");
        result.setValue(Field.PAGES, "1027-1035");

        return result;
    }

    /**
     * Returns a string describing this clusterer.
     * 
     * @return a description of the evaluator suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String globalInfo() {
        return "Cluster data using the k means algorithm. Can use either "
                + "the Euclidean distance (default) or the Manhattan distance."
                + " If the Manhattan distance is used, then centroids are computed "
                + "as the component-wise median rather than mean." + " For more information see:\n\n"
                + getTechnicalInformation().toString();
    }

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

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

        return result;
    }

    private class KMeansComputeCentroidTask implements Callable<double[]> {

        protected Instances m_cluster;
        protected int m_centroidIndex;

        public KMeansComputeCentroidTask(int centroidIndex, Instances cluster) {
            m_cluster = cluster;
            m_centroidIndex = centroidIndex;
        }

        @Override
        public double[] call() {
            return moveCentroid(m_centroidIndex, m_cluster, true, false);
        }
    }

    /**
     * Launch the move centroids tasks
     * 
     * @param clusters the cluster centroids
     * @return the number of empty clusters
     */
    protected int launchMoveCentroids(Instances[] clusters) {
        int emptyClusterCount = 0;
        List<Future<double[]>> results = new ArrayList<Future<double[]>>();

        for (int i = 0; i < m_NumClusters; i++) {
            if (clusters[i].numInstances() == 0) {
                emptyClusterCount++;
            } else {
                Future<double[]> futureCentroid = m_executorPool
                        .submit(new KMeansComputeCentroidTask(i, clusters[i]));
                results.add(futureCentroid);
            }
        }

        try {
            for (Future<double[]> d : results) {
                m_ClusterCentroids.add(new DenseInstance(1.0, d.get()));
            }
        } catch (Exception ex) {
            ex.printStackTrace();
        }

        return emptyClusterCount;
    }

    private class KMeansClusterTask implements Callable<Boolean> {

        protected int m_start;
        protected int m_end;
        protected Instances m_inst;
        protected int[] m_clusterAssignments;

        public KMeansClusterTask(Instances inst, int start, int end, int[] clusterAssignments) {
            m_start = start;
            m_end = end;
            m_inst = inst;
            m_clusterAssignments = clusterAssignments;
        }

        @Override
        public Boolean call() {
            boolean converged = true;
            for (int i = m_start; i < m_end; i++) {
                Instance toCluster = m_inst.instance(i);
                long[] instanceCanopies = m_speedUpDistanceCompWithCanopies ? m_dataPointCanopyAssignments.get(i)
                        : null;
                int newC = clusterInstance(toCluster, instanceCanopies);
                if (newC != m_clusterAssignments[i]) {
                    converged = false;
                }
                m_clusterAssignments[i] = newC;
            }

            return converged;
        }

        protected int clusterInstance(Instance inst, long[] instanceCanopies) {
            double minDist = Integer.MAX_VALUE;
            int bestCluster = 0;
            for (int i = 0; i < m_NumClusters; i++) {
                double dist;

                if (m_speedUpDistanceCompWithCanopies && instanceCanopies != null && instanceCanopies.length > 0) {
                    try {
                        if (!Canopy.nonEmptyCanopySetIntersection(m_centroidCanopyAssignments.get(i),
                                instanceCanopies)) {
                            // System.err.println("Skipping distance calc... "
                            // + Canopy.printSingleAssignment(instanceCanopies));
                            continue;
                        }
                    } catch (Exception ex) {
                        ex.printStackTrace();
                    }
                }

                dist = m_DistanceFunction.distance(inst, m_ClusterCentroids.instance(i), minDist);

                if (dist < minDist) {
                    minDist = dist;
                    bestCluster = i;
                }
            }

            return bestCluster;
        }
    }

    /**
     * Launch the tasks that assign instances to clusters
     * 
     * @param insts the instances to be clustered
     * @param clusterAssignments the array of cluster assignments
     * @return true if k means has converged
     * @throws Exception if a problem occurs
     */
    protected boolean launchAssignToClusters(Instances insts, int[] clusterAssignments) throws Exception {
        int numPerTask = insts.numInstances() / m_executionSlots;

        List<Future<Boolean>> results = new ArrayList<Future<Boolean>>();
        for (int i = 0; i < m_executionSlots; i++) {
            int start = i * numPerTask;
            int end = start + numPerTask;
            if (i == m_executionSlots - 1) {
                end = insts.numInstances();
            }

            Future<Boolean> futureKM = m_executorPool
                    .submit(new KMeansClusterTask(insts, start, end, clusterAssignments));
            results.add(futureKM);
        }

        boolean converged = true;
        for (Future<Boolean> f : results) {
            if (!f.get()) {
                converged = false;
            }
        }

        return converged;
    }

    /**
     * Generates a clusterer. Has to initialize all fields of the clusterer that
     * are not being set via options.
     * 
     * @param data set of instances serving as training data
     * @throws Exception if the clusterer has not been generated successfully
     */
    @Override
    public void buildClusterer(Instances data) throws Exception {

        m_canopyClusters = null;

        // can clusterer handle the data?
        getCapabilities().testWithFail(data);

        m_Iterations = 0;

        m_ReplaceMissingFilter = new ReplaceMissingValues();
        Instances instances = new Instances(data);

        instances.setClassIndex(-1);
        if (!m_dontReplaceMissing) {
            m_ReplaceMissingFilter.setInputFormat(instances);
            instances = Filter.useFilter(instances, m_ReplaceMissingFilter);
        }

        m_ClusterNominalCounts = new double[m_NumClusters][instances.numAttributes()][];
        m_ClusterMissingCounts = new double[m_NumClusters][instances.numAttributes()];
        if (m_displayStdDevs) {
            m_FullStdDevs = instances.variances();
        }

        m_FullMeansOrMediansOrModes = moveCentroid(0, instances, true, false);

        m_FullMissingCounts = m_ClusterMissingCounts[0];
        m_FullNominalCounts = m_ClusterNominalCounts[0];
        double sumOfWeights = instances.sumOfWeights();
        for (int i = 0; i < instances.numAttributes(); i++) {
            if (instances.attribute(i).isNumeric()) {
                if (m_displayStdDevs) {
                    m_FullStdDevs[i] = Math.sqrt(m_FullStdDevs[i]);
                }
                if (m_FullMissingCounts[i] == sumOfWeights) {
                    m_FullMeansOrMediansOrModes[i] = Double.NaN; // mark missing as mean
                }
            } else {
                if (m_FullMissingCounts[i] > m_FullNominalCounts[i][Utils.maxIndex(m_FullNominalCounts[i])]) {
                    m_FullMeansOrMediansOrModes[i] = -1; // mark missing as most common
                                                         // value
                }
            }
        }

        m_ClusterCentroids = new Instances(instances, m_NumClusters);
        int[] clusterAssignments = new int[instances.numInstances()];

        if (m_PreserveOrder) {
            m_Assignments = clusterAssignments;
        }

        m_DistanceFunction.setInstances(instances);

        Random RandomO = new Random(getSeed());
        int instIndex;
        HashMap<DecisionTableHashKey, Integer> initC = new HashMap<DecisionTableHashKey, Integer>();
        DecisionTableHashKey hk = null;

        Instances initInstances = null;
        if (m_PreserveOrder) {
            initInstances = new Instances(instances);
        } else {
            initInstances = instances;
        }

        if (m_speedUpDistanceCompWithCanopies) {
            m_canopyClusters = new Canopy();
            m_canopyClusters.setNumClusters(m_NumClusters);
            m_canopyClusters.setSeed(getSeed());
            m_canopyClusters.setT2(getCanopyT2());
            m_canopyClusters.setT1(getCanopyT1());
            m_canopyClusters.setMaxNumCandidateCanopiesToHoldInMemory(getCanopyMaxNumCanopiesToHoldInMemory());
            m_canopyClusters.setPeriodicPruningRate(getCanopyPeriodicPruningRate());
            m_canopyClusters.setMinimumCanopyDensity(getCanopyMinimumCanopyDensity());
            m_canopyClusters.setDebug(getDebug());
            m_canopyClusters.buildClusterer(initInstances);
            // System.err.println(m_canopyClusters);
            m_centroidCanopyAssignments = new ArrayList<long[]>();
            m_dataPointCanopyAssignments = new ArrayList<long[]>();
        }

        if (m_initializationMethod == KMEANS_PLUS_PLUS) {
            kMeansPlusPlusInit(initInstances);

            m_initialStartPoints = new Instances(m_ClusterCentroids);
        } else if (m_initializationMethod == CANOPY) {
            canopyInit(initInstances);

            m_initialStartPoints = new Instances(m_canopyClusters.getCanopies());
        } else if (m_initializationMethod == FARTHEST_FIRST) {
            farthestFirstInit(initInstances);

            m_initialStartPoints = new Instances(m_ClusterCentroids);
        } else {
            // random
            for (int j = initInstances.numInstances() - 1; j >= 0; j--) {
                instIndex = RandomO.nextInt(j + 1);
                hk = new DecisionTableHashKey(initInstances.instance(instIndex), initInstances.numAttributes(),
                        true);
                if (!initC.containsKey(hk)) {
                    m_ClusterCentroids.add(initInstances.instance(instIndex));
                    initC.put(hk, null);
                }
                initInstances.swap(j, instIndex);

                if (m_ClusterCentroids.numInstances() == m_NumClusters) {
                    break;
                }
            }

            m_initialStartPoints = new Instances(m_ClusterCentroids);
        }

        if (m_speedUpDistanceCompWithCanopies) {
            // assign canopies to training data
            for (int i = 0; i < instances.numInstances(); i++) {
                m_dataPointCanopyAssignments.add(m_canopyClusters.assignCanopies(instances.instance(i)));
            }
        }

        m_NumClusters = m_ClusterCentroids.numInstances();

        // removing reference
        initInstances = null;

        int i;
        boolean converged = false;
        int emptyClusterCount;
        Instances[] tempI = new Instances[m_NumClusters];
        m_squaredErrors = new double[m_NumClusters];
        m_ClusterNominalCounts = new double[m_NumClusters][instances.numAttributes()][0];
        m_ClusterMissingCounts = new double[m_NumClusters][instances.numAttributes()];
        startExecutorPool();

        while (!converged) {
            if (m_speedUpDistanceCompWithCanopies) {
                // re-assign canopies to the current cluster centers
                m_centroidCanopyAssignments.clear();
                for (int kk = 0; kk < m_ClusterCentroids.numInstances(); kk++) {
                    m_centroidCanopyAssignments
                            .add(m_canopyClusters.assignCanopies(m_ClusterCentroids.instance(kk)));
                }
            }

            emptyClusterCount = 0;
            m_Iterations++;
            converged = true;

            if (m_executionSlots <= 1 || instances.numInstances() < 2 * m_executionSlots) {
                for (i = 0; i < instances.numInstances(); i++) {
                    Instance toCluster = instances.instance(i);
                    int newC = clusterProcessedInstance(toCluster, false, true,
                            m_speedUpDistanceCompWithCanopies ? m_dataPointCanopyAssignments.get(i) : null);
                    if (newC != clusterAssignments[i]) {
                        converged = false;
                    }
                    clusterAssignments[i] = newC;
                }
            } else {
                converged = launchAssignToClusters(instances, clusterAssignments);
            }

            // update centroids
            m_ClusterCentroids = new Instances(instances, m_NumClusters);
            for (i = 0; i < m_NumClusters; i++) {
                tempI[i] = new Instances(instances, 0);
            }
            for (i = 0; i < instances.numInstances(); i++) {
                tempI[clusterAssignments[i]].add(instances.instance(i));
            }
            if (m_executionSlots <= 1 || instances.numInstances() < 2 * m_executionSlots) {
                for (i = 0; i < m_NumClusters; i++) {
                    if (tempI[i].numInstances() == 0) {
                        // empty cluster
                        emptyClusterCount++;
                    } else {
                        moveCentroid(i, tempI[i], true, true);
                    }
                }
            } else {
                emptyClusterCount = launchMoveCentroids(tempI);
            }

            if (m_Iterations == m_MaxIterations) {
                converged = true;
            }

            if (emptyClusterCount > 0) {
                m_NumClusters -= emptyClusterCount;
                if (converged) {
                    Instances[] t = new Instances[m_NumClusters];
                    int index = 0;
                    for (int k = 0; k < tempI.length; k++) {
                        if (tempI[k].numInstances() > 0) {
                            t[index] = tempI[k];

                            for (i = 0; i < tempI[k].numAttributes(); i++) {
                                m_ClusterNominalCounts[index][i] = m_ClusterNominalCounts[k][i];
                            }
                            index++;
                        }
                    }
                    tempI = t;
                } else {
                    tempI = new Instances[m_NumClusters];
                }
            }

            if (!converged) {
                m_ClusterNominalCounts = new double[m_NumClusters][instances.numAttributes()][0];
            }
        }

        // calculate errors
        if (!m_FastDistanceCalc) {
            for (i = 0; i < instances.numInstances(); i++) {
                clusterProcessedInstance(instances.instance(i), true, false, null);
            }
        }

        if (m_displayStdDevs) {
            m_ClusterStdDevs = new Instances(instances, m_NumClusters);
        }
        m_ClusterSizes = new double[m_NumClusters];
        for (i = 0; i < m_NumClusters; i++) {
            if (m_displayStdDevs) {
                double[] vals2 = tempI[i].variances();
                for (int j = 0; j < instances.numAttributes(); j++) {
                    if (instances.attribute(j).isNumeric()) {
                        vals2[j] = Math.sqrt(vals2[j]);
                    } else {
                        vals2[j] = Utils.missingValue();
                    }
                }
                m_ClusterStdDevs.add(new DenseInstance(1.0, vals2));
            }
            m_ClusterSizes[i] = tempI[i].sumOfWeights();
        }

        m_executorPool.shutdown();

        // save memory!
        m_DistanceFunction.clean();
    }

    /**
     * Initialize with the canopy centers of the Canopy clustering method
     * 
     * @param data the training data
     * @throws Exception if a problem occurs
     */
    protected void canopyInit(Instances data) throws Exception {
        if (m_canopyClusters == null) {
            m_canopyClusters = new Canopy();
            m_canopyClusters.setNumClusters(m_NumClusters);
            m_canopyClusters.setSeed(getSeed());
            m_canopyClusters.setT2(getCanopyT2());
            m_canopyClusters.setT1(getCanopyT1());
            m_canopyClusters.setMaxNumCandidateCanopiesToHoldInMemory(getCanopyMaxNumCanopiesToHoldInMemory());
            m_canopyClusters.setPeriodicPruningRate(getCanopyPeriodicPruningRate());
            m_canopyClusters.setMinimumCanopyDensity(getCanopyMinimumCanopyDensity());
            m_canopyClusters.setDebug(getDebug());
            m_canopyClusters.buildClusterer(data);
        }
        m_ClusterCentroids = m_canopyClusters.getCanopies();
    }

    /**
     * Initialize with the fartherst first centers
     * 
     * @param data the training data
     * @throws Exception if a problem occurs
     */
    protected void farthestFirstInit(Instances data) throws Exception {
        FarthestFirst ff = new FarthestFirst();
        ff.setNumClusters(m_NumClusters);
        ff.buildClusterer(data);

        m_ClusterCentroids = ff.getClusterCentroids();
    }

    /**
     * Initialize using the k-means++ method
     * 
     * @param data the training data
     * @throws Exception if a problem occurs
     */
    protected void kMeansPlusPlusInit(Instances data) throws Exception {
        Random randomO = new Random(getSeed());
        HashMap<DecisionTableHashKey, String> initC = new HashMap<DecisionTableHashKey, String>();

        // choose initial center uniformly at random
        int index = randomO.nextInt(data.numInstances());
        m_ClusterCentroids.add(data.instance(index));
        DecisionTableHashKey hk = new DecisionTableHashKey(data.instance(index), data.numAttributes(), true);
        initC.put(hk, null);

        int iteration = 0;
        int remainingInstances = data.numInstances() - 1;
        if (m_NumClusters > 1) {
            // proceed with selecting the rest

            // distances to the initial randomly chose center
            double[] distances = new double[data.numInstances()];
            double[] cumProbs = new double[data.numInstances()];
            for (int i = 0; i < data.numInstances(); i++) {
                distances[i] = m_DistanceFunction.distance(data.instance(i),
                        m_ClusterCentroids.instance(iteration));
            }

            // now choose the remaining cluster centers
            for (int i = 1; i < m_NumClusters; i++) {

                // distances converted to probabilities
                double[] weights = new double[data.numInstances()];
                System.arraycopy(distances, 0, weights, 0, distances.length);
                Utils.normalize(weights);

                double sumOfProbs = 0;
                for (int k = 0; k < data.numInstances(); k++) {
                    sumOfProbs += weights[k];
                    cumProbs[k] = sumOfProbs;
                }

                cumProbs[data.numInstances() - 1] = 1.0; // make sure there are no
                                                         // rounding issues

                // choose a random instance
                double prob = randomO.nextDouble();
                for (int k = 0; k < cumProbs.length; k++) {
                    if (prob < cumProbs[k]) {
                        Instance candidateCenter = data.instance(k);
                        hk = new DecisionTableHashKey(candidateCenter, data.numAttributes(), true);
                        if (!initC.containsKey(hk)) {
                            initC.put(hk, null);
                            m_ClusterCentroids.add(candidateCenter);
                        } else {
                            // we shouldn't get here because any instance that is a duplicate
                            // of
                            // an already chosen cluster center should have zero distance (and
                            // hence
                            // zero probability of getting chosen) to that center.
                            System.err.println("We shouldn't get here....");
                        }
                        remainingInstances--;
                        break;
                    }
                }
                iteration++;

                if (remainingInstances == 0) {
                    break;
                }

                // prepare to choose the next cluster center.
                // check distances against the new cluster center to see if it is closer
                for (int k = 0; k < data.numInstances(); k++) {
                    if (distances[k] > 0) {
                        double newDist = m_DistanceFunction.distance(data.instance(k),
                                m_ClusterCentroids.instance(iteration));
                        if (newDist < distances[k]) {
                            distances[k] = newDist;
                        }
                    }
                }
            }
        }
    }

    /**
     * Move the centroid to it's new coordinates. Generate the centroid
     * coordinates based on it's members (objects assigned to the cluster of the
     * centroid) and the distance function being used.
     * 
     * @param centroidIndex index of the centroid which the coordinates will be
     *          computed
     * @param members the objects that are assigned to the cluster of this
     *          centroid
     * @param updateClusterInfo if the method is supposed to update the m_Cluster
     *          arrays
     * @param addToCentroidInstances true if the method is to add the computed
     *          coordinates to the Instances holding the centroids
     * @return the centroid coordinates
     */
    protected double[] moveCentroid(int centroidIndex, Instances members, boolean updateClusterInfo,
            boolean addToCentroidInstances) {

        double[] vals = new double[members.numAttributes()];
        double[][] nominalDists = new double[members.numAttributes()][];
        double[] weightMissing = new double[members.numAttributes()];
        double[] weightNonMissing = new double[members.numAttributes()];

        // Quickly calculate some relevant statistics 
        for (int j = 0; j < members.numAttributes(); j++) {
            if (members.attribute(j).isNominal()) {
                nominalDists[j] = new double[members.attribute(j).numValues()];
            }
        }
        for (Instance inst : members) {
            for (int j = 0; j < members.numAttributes(); j++) {
                if (inst.isMissing(j)) {
                    weightMissing[j] += inst.weight();
                } else {
                    weightNonMissing[j] += inst.weight();
                    if (members.attribute(j).isNumeric()) {
                        vals[j] += inst.weight() * inst.value(j); // Will be overwritten in Manhattan case
                    } else {
                        nominalDists[j][(int) inst.value(j)] += inst.weight();
                    }
                }
            }
        }
        for (int j = 0; j < members.numAttributes(); j++) {
            if (members.attribute(j).isNumeric()) {
                if (weightNonMissing[j] > 0) {
                    vals[j] /= weightNonMissing[j];
                } else {
                    vals[j] = Utils.missingValue();
                }
            } else {
                double max = -Double.MAX_VALUE;
                double maxIndex = -1;
                for (int i = 0; i < nominalDists[j].length; i++) {
                    if (nominalDists[j][i] > max) {
                        max = nominalDists[j][i];
                        maxIndex = i;
                    }
                    if (max < weightMissing[j]) {
                        vals[j] = Utils.missingValue();
                    } else {
                        vals[j] = maxIndex;
                    }
                }
            }
        }

        if (m_DistanceFunction instanceof ManhattanDistance) {

            // Need to replace means by medians
            Instances sortedMembers = null;
            int middle = (members.numInstances() - 1) / 2;
            boolean dataIsEven = ((members.numInstances() % 2) == 0);
            if (m_PreserveOrder) {
                sortedMembers = members;
            } else {
                sortedMembers = new Instances(members);
            }
            for (int j = 0; j < members.numAttributes(); j++) {
                if ((weightNonMissing[j] > 0) && members.attribute(j).isNumeric()) {
                    // singleton special case
                    if (members.numInstances() == 1) {
                        vals[j] = members.instance(0).value(j);
                    } else {
                        vals[j] = sortedMembers.kthSmallestValue(j, middle + 1);
                        if (dataIsEven) {
                            vals[j] = (vals[j] + sortedMembers.kthSmallestValue(j, middle + 2)) / 2;
                        }
                    }
                }
            }
        }

        if (updateClusterInfo) {
            for (int j = 0; j < members.numAttributes(); j++) {
                m_ClusterMissingCounts[centroidIndex][j] = weightMissing[j];
                m_ClusterNominalCounts[centroidIndex][j] = nominalDists[j];
            }
        }

        if (addToCentroidInstances) {
            m_ClusterCentroids.add(new DenseInstance(1.0, vals));
        }

        return vals;
    }

    /**
     * clusters an instance that has been through the filters.
     * 
     * @param instance the instance to assign a cluster to
     * @param updateErrors if true, update the within clusters sum of errors
     * @param useFastDistCalc whether to use the fast distance calculation or not
     * @param instanceCanopies the canopies covering the instance to be clustered,
     *          or null if not using the option to reduce the number of distance
     *          computations via canopies
     * @return a cluster number
     */
    private int clusterProcessedInstance(Instance instance, boolean updateErrors, boolean useFastDistCalc,
            long[] instanceCanopies) {
        double minDist = Integer.MAX_VALUE;
        int bestCluster = 0;
        for (int i = 0; i < m_NumClusters; i++) {
            double dist;
            if (useFastDistCalc) {
                if (m_speedUpDistanceCompWithCanopies && instanceCanopies != null && instanceCanopies.length > 0) {
                    try {
                        if (!Canopy.nonEmptyCanopySetIntersection(m_centroidCanopyAssignments.get(i),
                                instanceCanopies)) {
                            continue;
                        }
                    } catch (Exception ex) {
                        ex.printStackTrace();
                    }
                    dist = m_DistanceFunction.distance(instance, m_ClusterCentroids.instance(i), minDist);
                } else {
                    dist = m_DistanceFunction.distance(instance, m_ClusterCentroids.instance(i), minDist);
                }
            } else {
                dist = m_DistanceFunction.distance(instance, m_ClusterCentroids.instance(i));
            }
            if (dist < minDist) {
                minDist = dist;
                bestCluster = i;
            }
        }
        if (updateErrors) {
            if (m_DistanceFunction instanceof EuclideanDistance) {
                // Euclidean distance to Squared Euclidean distance
                minDist *= minDist * instance.weight();
            }
            m_squaredErrors[bestCluster] += minDist;
        }
        return bestCluster;
    }

    /**
     * Classifies a given instance.
     * 
     * @param instance the instance to be assigned to a cluster
     * @return the number of the assigned cluster as an interger if the class is
     *         enumerated, otherwise the predicted value
     * @throws Exception if instance could not be classified successfully
     */
    @Override
    public int clusterInstance(Instance instance) throws Exception {
        Instance inst = null;
        if (!m_dontReplaceMissing) {
            m_ReplaceMissingFilter.input(instance);
            m_ReplaceMissingFilter.batchFinished();
            inst = m_ReplaceMissingFilter.output();
        } else {
            inst = instance;
        }

        return clusterProcessedInstance(inst, false, true, null);
    }

    /**
     * Returns the number of clusters.
     * 
     * @return the number of clusters generated for a training dataset.
     * @throws Exception if number of clusters could not be returned successfully
     */
    @Override
    public int numberOfClusters() throws Exception {
        return m_NumClusters;
    }

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

        result.addElement(new Option("\tNumber of clusters.\n" + "\t(default 2).", "N", 1, "-N <num>"));

        result.addElement(new Option("\tInitialization method to use.\n\t0 = random, 1 = k-means++, "
                + "2 = canopy, 3 = farthest first.\n\t(default = 0)", "init", 1, "-init"));

        result.addElement(
                new Option("\tUse canopies to reduce the number of distance calculations.", "C", 0, "-C"));

        result.addElement(new Option(
                "\tMaximum number of candidate canopies to retain in memory\n\t"
                        + "at any one time when using canopy clustering.\n\t"
                        + "T2 distance plus, data characteristics,\n\t"
                        + "will determine how many candidate canopies are formed before\n\t"
                        + "periodic and final pruning are performed, which might result\n\t"
                        + "in exceess memory consumption. This setting avoids large numbers\n\t"
                        + "of candidate canopies consuming memory. (default = 100)",
                "-max-candidates", 1, "-max-candidates <num>"));

        result.addElement(new Option(
                "\tHow often to prune low density canopies when using canopy clustering. \n\t"
                        + "(default = every 10,000 training instances)",
                "periodic-pruning", 1, "-periodic-pruning <num>"));

        result.addElement(new Option(
                "\tMinimum canopy density, when using canopy clustering, below which\n\t"
                        + " a canopy will be pruned during periodic pruning. (default = 2 instances)",
                "min-density", 1, "-min-density"));

        result.addElement(
                new Option("\tThe T2 distance to use when using canopy clustering. Values < 0 indicate that\n\t"
                        + "a heuristic based on attribute std. deviation should be used to set this.\n\t"
                        + "(default = -1.0)", "t2", 1, "-t2"));

        result.addElement(
                new Option("\tThe T1 distance to use when using canopy clustering. A value < 0 is taken as a\n\t"
                        + "positive multiplier for T2. (default = -1.5)", "t1", 1, "-t1"));

        result.addElement(new Option("\tDisplay std. deviations for centroids.\n", "V", 0, "-V"));
        result.addElement(new Option("\tDon't replace missing values with mean/mode.\n", "M", 0, "-M"));

        result.add(new Option("\tDistance function to use.\n" + "\t(default: weka.core.EuclideanDistance)", "A", 1,
                "-A <classname and options>"));

        result.add(new Option("\tMaximum number of iterations.\n", "I", 1, "-I <num>"));

        result.addElement(new Option("\tPreserve order of instances.\n", "O", 0, "-O"));

        result.addElement(new Option("\tEnables faster distance calculations, using cut-off values.\n"
                + "\tDisables the calculation/output of squared errors/distances.\n", "fast", 0, "-fast"));

        result.addElement(new Option("\tNumber of execution slots.\n" + "\t(default 1 - i.e. no parallelism)",
                "num-slots", 1, "-num-slots <num>"));

        result.addAll(Collections.list(super.listOptions()));

        return result.elements();
    }

    /**
     * Returns the tip text for this property.
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String numClustersTipText() {
        return "set number of clusters";
    }

    /**
     * set the number of clusters to generate.
     * 
     * @param n the number of clusters to generate
     * @throws Exception if number of clusters is negative
     */
    @Override
    public void setNumClusters(int n) throws Exception {
        if (n <= 0) {
            throw new Exception("Number of clusters must be > 0");
        }
        m_NumClusters = n;
    }

    /**
     * gets the number of clusters to generate.
     * 
     * @return the number of clusters to generate
     */
    public int getNumClusters() {
        return m_NumClusters;
    }

    /**
     * Returns the tip text for this property.
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String initializationMethodTipText() {
        return "The initialization method to use. Random, k-means++, Canopy or farthest first";
    }

    /**
     * Set the initialization method to use
     * 
     * @param method the initialization method to use
     */
    public void setInitializationMethod(SelectedTag method) {
        if (method.getTags() == TAGS_SELECTION) {
            m_initializationMethod = method.getSelectedTag().getID();
        }
    }

    /**
     * Get the initialization method to use
     * 
     * @return method the initialization method to use
     */
    public SelectedTag getInitializationMethod() {
        return new SelectedTag(m_initializationMethod, TAGS_SELECTION);
    }

    /**
     * Returns the tip text for this property.
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String reduceNumberOfDistanceCalcsViaCanopiesTipText() {
        return "Use canopy clustering to reduce the number of distance calculations " + "performed by k-means";
    }

    /**
     * Set whether to use canopies to reduce the number of distance computations
     * required
     * 
     * @param c true if canopies are to be used to reduce the number of distance
     *          computations
     */
    public void setReduceNumberOfDistanceCalcsViaCanopies(boolean c) {
        m_speedUpDistanceCompWithCanopies = c;
    }

    /**
     * Get whether to use canopies to reduce the number of distance computations
     * required
     * 
     * @return true if canopies are to be used to reduce the number of distance
     *         computations
     */
    public boolean getReduceNumberOfDistanceCalcsViaCanopies() {
        return m_speedUpDistanceCompWithCanopies;
    }

    /**
     * Returns the tip text for this property.
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String canopyPeriodicPruningRateTipText() {
        return "If using canopy clustering for initialization and/or speedup "
                + "this is how often to prune low density canopies during training";
    }

    /**
     * Set the how often to prune low density canopies during training (if using
     * canopy clustering)
     * 
     * @param p how often (every p instances) to prune low density canopies
     */
    public void setCanopyPeriodicPruningRate(int p) {
        m_periodicPruningRate = p;
    }

    /**
     * Get the how often to prune low density canopies during training (if using
     * canopy clustering)
     * 
     * @return how often (every p instances) to prune low density canopies
     */
    public int getCanopyPeriodicPruningRate() {
        return m_periodicPruningRate;
    }

    /**
     * Returns the tip text for this property.
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String canopyMinimumCanopyDensityTipText() {
        return "If using canopy clustering for initialization and/or speedup "
                + "this is the minimum T2-based density "
                + "below which a canopy will be pruned during periodic pruning";
    }

    /**
     * Set the minimum T2-based density below which a canopy will be pruned during
     * periodic pruning.
     * 
     * @param dens the minimum canopy density
     */
    public void setCanopyMinimumCanopyDensity(double dens) {
        m_minClusterDensity = dens;
    }

    /**
     * Get the minimum T2-based density below which a canopy will be pruned during
     * periodic pruning.
     * 
     * @return the minimum canopy density
     */
    public double getCanopyMinimumCanopyDensity() {
        return m_minClusterDensity;
    }

    /**
     * Returns the tip text for this property.
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String canopyMaxNumCanopiesToHoldInMemoryTipText() {
        return "If using canopy clustering for initialization and/or speedup "
                + "this is the maximum number of candidate canopies to "
                + "retain in main memory during training of the canopy clusterer. "
                + "T2 distance and data characteristics determine how many candidate "
                + "canopies are formed before periodic and final pruning are performed. There "
                + "may not be enough memory available if T2 is set too low.";
    }

    /**
     * Set the maximum number of candidate canopies to retain in memory during
     * training. T2 distance and data characteristics determine how many candidate
     * canopies are formed before periodic and final pruning are performed. There
     * may not be enough memory available if T2 is set too low.
     * 
     * @param max the maximum number of candidate canopies to retain in memory
     *          during training
     */
    public void setCanopyMaxNumCanopiesToHoldInMemory(int max) {
        m_maxCanopyCandidates = max;
    }

    /**
     * Get the maximum number of candidate canopies to retain in memory during
     * training. T2 distance and data characteristics determine how many candidate
     * canopies are formed before periodic and final pruning are performed. There
     * may not be enough memory available if T2 is set too low.
     * 
     * @return the maximum number of candidate canopies to retain in memory during
     *         training
     */
    public int getCanopyMaxNumCanopiesToHoldInMemory() {
        return m_maxCanopyCandidates;
    }

    /**
     * Tip text for this property
     * 
     * @return the tip text for this property
     */
    public String canopyT2TipText() {
        return "The T2 distance to use when using canopy clustering. Values < 0 indicate that this should be set using "
                + "a heuristic based on attribute standard deviation";
    }

    /**
     * Set the t2 radius to use when canopy clustering is being used as start
     * points and/or to reduce the number of distance calcs
     * 
     * @param t2 the t2 radius to use
     */
    public void setCanopyT2(double t2) {
        m_t2 = t2;
    }

    /**
     * Get the t2 radius to use when canopy clustering is being used as start
     * points and/or to reduce the number of distance calcs
     * 
     * @return the t2 radius to use
     */
    public double getCanopyT2() {
        return m_t2;
    }

    /**
     * Tip text for this property
     * 
     * @return the tip text for this property
     */
    public String canopyT1TipText() {
        return "The T1 distance to use when using canopy clustering. Values < 0 are taken as a positive "
                + "multiplier for the T2 distance";
    }

    /**
     * Set the t1 radius to use when canopy clustering is being used as start
     * points and/or to reduce the number of distance calcs
     * 
     * @param t1 the t1 radius to use
     */
    public void setCanopyT1(double t1) {
        m_t1 = t1;
    }

    /**
     * Get the t1 radius to use when canopy clustering is being used as start
     * points and/or to reduce the number of distance calcs
     * 
     * @return the t1 radius to use
     */
    public double getCanopyT1() {
        return m_t1;
    }

    /**
     * Returns the tip text for this property.
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String maxIterationsTipText() {
        return "set maximum number of iterations";
    }

    /**
     * set the maximum number of iterations to be executed.
     * 
     * @param n the maximum number of iterations
     * @throws Exception if maximum number of iteration is smaller than 1
     */
    public void setMaxIterations(int n) throws Exception {
        if (n <= 0) {
            throw new Exception("Maximum number of iterations must be > 0");
        }
        m_MaxIterations = n;
    }

    /**
     * gets the number of maximum iterations to be executed.
     * 
     * @return the number of clusters to generate
     */
    public int getMaxIterations() {
        return m_MaxIterations;
    }

    /**
     * Returns the tip text for this property.
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String displayStdDevsTipText() {
        return "Display std deviations of numeric attributes " + "and counts of nominal attributes.";
    }

    /**
     * Sets whether standard deviations and nominal count. Should be displayed in
     * the clustering output.
     * 
     * @param stdD true if std. devs and counts should be displayed
     */
    public void setDisplayStdDevs(boolean stdD) {
        m_displayStdDevs = stdD;
    }

    /**
     * Gets whether standard deviations and nominal count. Should be displayed in
     * the clustering output.
     * 
     * @return true if std. devs and counts should be displayed
     */
    public boolean getDisplayStdDevs() {
        return m_displayStdDevs;
    }

    /**
     * Returns the tip text for this property.
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String dontReplaceMissingValuesTipText() {
        return "Replace missing values globally with mean/mode.";
    }

    /**
     * Sets whether missing values are to be replaced.
     * 
     * @param r true if missing values are to be replaced
     */
    public void setDontReplaceMissingValues(boolean r) {
        m_dontReplaceMissing = r;
    }

    /**
     * Gets whether missing values are to be replaced.
     * 
     * @return true if missing values are to be replaced
     */
    public boolean getDontReplaceMissingValues() {
        return m_dontReplaceMissing;
    }

    /**
     * Returns the tip text for this property.
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String distanceFunctionTipText() {
        return "The distance function to use for instances comparison "
                + "(default: weka.core.EuclideanDistance). ";
    }

    /**
     * returns the distance function currently in use.
     * 
     * @return the distance function
     */
    public DistanceFunction getDistanceFunction() {
        return m_DistanceFunction;
    }

    /**
     * sets the distance function to use for instance comparison.
     * 
     * @param df the new distance function to use
     * @throws Exception if instances cannot be processed
     */
    public void setDistanceFunction(DistanceFunction df) throws Exception {
        if (!(df instanceof EuclideanDistance) && !(df instanceof ManhattanDistance)) {
            throw new Exception("SimpleKMeans currently only supports the Euclidean and Manhattan distances.");
        }
        m_DistanceFunction = df;
    }

    /**
     * Returns the tip text for this property.
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String preserveInstancesOrderTipText() {
        return "Preserve order of instances.";
    }

    /**
     * Sets whether order of instances must be preserved.
     * 
     * @param r true if missing values are to be replaced
     */
    public void setPreserveInstancesOrder(boolean r) {
        m_PreserveOrder = r;
    }

    /**
     * Gets whether order of instances must be preserved.
     * 
     * @return true if missing values are to be replaced
     */
    public boolean getPreserveInstancesOrder() {
        return m_PreserveOrder;
    }

    /**
     * Returns the tip text for this property.
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String fastDistanceCalcTipText() {
        return "Uses cut-off values for speeding up distance calculation, but "
                + "suppresses also the calculation and output of the within cluster sum "
                + "of squared errors/sum of distances.";
    }

    /**
     * Sets whether to use faster distance calculation.
     * 
     * @param value true if faster calculation to be used
     */
    public void setFastDistanceCalc(boolean value) {
        m_FastDistanceCalc = value;
    }

    /**
     * Gets whether to use faster distance calculation.
     * 
     * @return true if faster calculation is used
     */
    public boolean getFastDistanceCalc() {
        return m_FastDistanceCalc;
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String numExecutionSlotsTipText() {
        return "The number of execution slots (threads) to use. "
                + "Set equal to the number of available cpu/cores";
    }

    /**
     * Set the degree of parallelism to use.
     * 
     * @param slots the number of tasks to run in parallel when computing the
     *          nearest neighbors and evaluating different values of k between the
     *          lower and upper bounds
     */
    public void setNumExecutionSlots(int slots) {
        m_executionSlots = slots;
    }

    /**
     * Get the degree of parallelism to use.
     * 
     * @return the number of tasks to run in parallel when computing the nearest
     *         neighbors and evaluating different values of k between the lower
     *         and upper bounds
     */
    public int getNumExecutionSlots() {
        return m_executionSlots;
    }

    /**
     * Parses a given list of options.
     * <p/>
     * 
     * <!-- options-start --> Valid options are:
     * <p/>
     * 
     * <pre>
     * -N &lt;num&gt;
     *  Number of clusters.
     *  (default 2).
     * </pre>
     * 
     * <pre>
     * -init
     *  Initialization method to use.
     *  0 = random, 1 = k-means++, 2 = canopy, 3 = farthest first.
     *  (default = 0)
     * </pre>
     * 
     * <pre>
     * -C
     *  Use canopies to reduce the number of distance calculations.
     * </pre>
     * 
     * <pre>
     * -max-candidates &lt;num&gt;
     *  Maximum number of candidate canopies to retain in memory
     *  at any one time when using canopy clustering.
     *  T2 distance plus, data characteristics,
     *  will determine how many candidate canopies are formed before
     *  periodic and final pruning are performed, which might result
     *  in exceess memory consumption. This setting avoids large numbers
     *  of candidate canopies consuming memory. (default = 100)
     * </pre>
     * 
     * <pre>
     * -periodic-pruning &lt;num&gt;
     *  How often to prune low density canopies when using canopy clustering. 
     *  (default = every 10,000 training instances)
     * </pre>
     * 
     * <pre>
     * -min-density
     *  Minimum canopy density, when using canopy clustering, below which
     *   a canopy will be pruned during periodic pruning. (default = 2 instances)
     * </pre>
     * 
     * <pre>
     * -t2
     *  The T2 distance to use when using canopy clustering. Values &lt; 0 indicate that
     *  a heuristic based on attribute std. deviation should be used to set this.
     *  (default = -1.0)
     * </pre>
     * 
     * <pre>
     * -t1
     *  The T1 distance to use when using canopy clustering. A value &lt; 0 is taken as a
     *  positive multiplier for T2. (default = -1.5)
     * </pre>
     * 
     * <pre>
     * -V
     *  Display std. deviations for centroids.
     * </pre>
     * 
     * <pre>
     * -M
     *  Don't replace missing values with mean/mode.
     * </pre>
     * 
     * <pre>
     * -A &lt;classname and options&gt;
     *  Distance function to use.
     *  (default: weka.core.EuclideanDistance)
     * </pre>
     * 
     * <pre>
     * -I &lt;num&gt;
     *  Maximum number of iterations.
     * </pre>
     * 
     * <pre>
     * -O
     *  Preserve order of instances.
     * </pre>
     * 
     * <pre>
     * -fast
     *  Enables faster distance calculations, using cut-off values.
     *  Disables the calculation/output of squared errors/distances.
     * </pre>
     * 
     * <pre>
     * -num-slots &lt;num&gt;
     *  Number of execution slots.
     *  (default 1 - i.e. no parallelism)
     * </pre>
     * 
     * <pre>
     * -S &lt;num&gt;
     *  Random number seed.
     *  (default 10)
     * </pre>
     * 
     * <pre>
     * -output-debug-info
     *  If set, clusterer is run in debug mode and
     *  may output additional info to the console
     * </pre>
     * 
     * <pre>
     * -do-not-check-capabilities
     *  If set, clusterer capabilities are not checked before clusterer is built
     *  (use with caution).
     * </pre>
     * 
     * <!-- options-end -->
     * 
     * @param options the list of options as an array of strings
     * @throws Exception if an option is not supported
     */
    @Override
    public void setOptions(String[] options) throws Exception {

        m_displayStdDevs = Utils.getFlag("V", options);
        m_dontReplaceMissing = Utils.getFlag("M", options);

        String initM = Utils.getOption("init", options);
        if (initM.length() > 0) {
            setInitializationMethod(new SelectedTag(Integer.parseInt(initM), TAGS_SELECTION));
        }

        m_speedUpDistanceCompWithCanopies = Utils.getFlag('C', options);

        String temp = Utils.getOption("max-candidates", options);
        if (temp.length() > 0) {
            setCanopyMaxNumCanopiesToHoldInMemory(Integer.parseInt(temp));
        }

        temp = Utils.getOption("periodic-pruning", options);
        if (temp.length() > 0) {
            setCanopyPeriodicPruningRate(Integer.parseInt(temp));
        }

        temp = Utils.getOption("min-density", options);
        if (temp.length() > 0) {
            setCanopyMinimumCanopyDensity(Double.parseDouble(temp));
        }

        temp = Utils.getOption("t2", options);
        if (temp.length() > 0) {
            setCanopyT2(Double.parseDouble(temp));
        }

        temp = Utils.getOption("t1", options);
        if (temp.length() > 0) {
            setCanopyT1(Double.parseDouble(temp));
        }

        String optionString = Utils.getOption('N', options);

        if (optionString.length() != 0) {
            setNumClusters(Integer.parseInt(optionString));
        }

        optionString = Utils.getOption("I", options);
        if (optionString.length() != 0) {
            setMaxIterations(Integer.parseInt(optionString));
        }

        String distFunctionClass = Utils.getOption('A', options);
        if (distFunctionClass.length() != 0) {
            String distFunctionClassSpec[] = Utils.splitOptions(distFunctionClass);
            if (distFunctionClassSpec.length == 0) {
                throw new Exception("Invalid DistanceFunction specification string.");
            }
            String className = distFunctionClassSpec[0];
            distFunctionClassSpec[0] = "";

            setDistanceFunction(
                    (DistanceFunction) Utils.forName(DistanceFunction.class, className, distFunctionClassSpec));
        } else {
            setDistanceFunction(new EuclideanDistance());
        }

        m_PreserveOrder = Utils.getFlag("O", options);

        m_FastDistanceCalc = Utils.getFlag("fast", options);

        String slotsS = Utils.getOption("num-slots", options);
        if (slotsS.length() > 0) {
            setNumExecutionSlots(Integer.parseInt(slotsS));
        }

        super.setOptions(options);

        Utils.checkForRemainingOptions(options);
    }

    /**
     * Gets the current settings of SimpleKMeans.
     * 
     * @return an array of strings suitable for passing to setOptions()
     */
    @Override
    public String[] getOptions() {

        Vector<String> result = new Vector<String>();

        result.add("-init");
        result.add("" + getInitializationMethod().getSelectedTag().getID());

        if (m_speedUpDistanceCompWithCanopies) {
            result.add("-C");
        }

        result.add("-max-candidates");
        result.add("" + getCanopyMaxNumCanopiesToHoldInMemory());
        result.add("-periodic-pruning");
        result.add("" + getCanopyPeriodicPruningRate());
        result.add("-min-density");
        result.add("" + getCanopyMinimumCanopyDensity());
        result.add("-t1");
        result.add("" + getCanopyT1());
        result.add("-t2");
        result.add("" + getCanopyT2());

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

        if (m_dontReplaceMissing) {
            result.add("-M");
        }

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

        result.add("-A");
        result.add(
                (m_DistanceFunction.getClass().getName() + " " + Utils.joinOptions(m_DistanceFunction.getOptions()))
                        .trim());

        result.add("-I");
        result.add("" + getMaxIterations());

        if (m_PreserveOrder) {
            result.add("-O");
        }

        if (m_FastDistanceCalc) {
            result.add("-fast");
        }

        result.add("-num-slots");
        result.add("" + getNumExecutionSlots());

        Collections.addAll(result, super.getOptions());

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

    /**
     * return a string describing this clusterer.
     * 
     * @return a description of the clusterer as a string
     */
    @Override
    public String toString() {
        if (m_ClusterCentroids == null) {
            return "No clusterer built yet!";
        }

        int maxWidth = 0;
        int maxAttWidth = 0;
        boolean containsNumeric = false;
        for (int i = 0; i < m_NumClusters; i++) {
            for (int j = 0; j < m_ClusterCentroids.numAttributes(); j++) {
                if (m_ClusterCentroids.attribute(j).name().length() > maxAttWidth) {
                    maxAttWidth = m_ClusterCentroids.attribute(j).name().length();
                }
                if (m_ClusterCentroids.attribute(j).isNumeric()) {
                    containsNumeric = true;
                    double width = Math.log(Math.abs(m_ClusterCentroids.instance(i).value(j))) / Math.log(10.0);

                    if (width < 0) {
                        width = 1;
                    }
                    // decimal + # decimal places + 1
                    width += 6.0;
                    if ((int) width > maxWidth) {
                        maxWidth = (int) width;
                    }
                }
            }
        }

        for (int i = 0; i < m_ClusterCentroids.numAttributes(); i++) {
            if (m_ClusterCentroids.attribute(i).isNominal()) {
                Attribute a = m_ClusterCentroids.attribute(i);
                for (int j = 0; j < m_ClusterCentroids.numInstances(); j++) {
                    String val = a.value((int) m_ClusterCentroids.instance(j).value(i));
                    if (val.length() > maxWidth) {
                        maxWidth = val.length();
                    }
                }
                for (int j = 0; j < a.numValues(); j++) {
                    String val = a.value(j) + " ";
                    if (val.length() > maxAttWidth) {
                        maxAttWidth = val.length();
                    }
                }
            }
        }

        if (m_displayStdDevs) {
            // check for maximum width of maximum frequency count
            for (int i = 0; i < m_ClusterCentroids.numAttributes(); i++) {
                if (m_ClusterCentroids.attribute(i).isNominal()) {
                    int maxV = Utils.maxIndex(m_FullNominalCounts[i]);
                    /*
                     * int percent = (int)((double)m_FullNominalCounts[i][maxV] /
                     * Utils.sum(m_ClusterSizes) * 100.0);
                     */
                    int percent = 6; // max percent width (100%)
                    String nomV = "" + m_FullNominalCounts[i][maxV];
                    // + " (" + percent + "%)";
                    if (nomV.length() + percent > maxWidth) {
                        maxWidth = nomV.length() + 1;
                    }
                }
            }
        }

        // check for size of cluster sizes
        for (double m_ClusterSize : m_ClusterSizes) {
            String size = "(" + m_ClusterSize + ")";
            if (size.length() > maxWidth) {
                maxWidth = size.length();
            }
        }

        if (m_displayStdDevs && maxAttWidth < "missing".length()) {
            maxAttWidth = "missing".length();
        }

        String plusMinus = "+/-";
        maxAttWidth += 2;
        if (m_displayStdDevs && containsNumeric) {
            maxWidth += plusMinus.length();
        }
        if (maxAttWidth < "Attribute".length() + 2) {
            maxAttWidth = "Attribute".length() + 2;
        }

        if (maxWidth < "Full Data".length()) {
            maxWidth = "Full Data".length() + 1;
        }

        if (maxWidth < "missing".length()) {
            maxWidth = "missing".length() + 1;
        }

        StringBuffer temp = new StringBuffer();
        temp.append("\nkMeans\n======\n");
        temp.append("\nNumber of iterations: " + m_Iterations);

        if (!m_FastDistanceCalc) {
            temp.append("\n");
            if (m_DistanceFunction instanceof EuclideanDistance) {
                temp.append("Within cluster sum of squared errors: " + Utils.sum(m_squaredErrors));
            } else {
                temp.append("Sum of within cluster distances: " + Utils.sum(m_squaredErrors));
            }
        }

        temp.append("\n\nInitial starting points (");
        switch (m_initializationMethod) {
        case FARTHEST_FIRST:
            temp.append("farthest first");
            break;
        case KMEANS_PLUS_PLUS:
            temp.append("k-means++");
            break;
        case CANOPY:
            temp.append("canopy");
            break;
        default:
            temp.append("random");
        }
        temp.append("):\n");
        if (m_initializationMethod != CANOPY) {
            temp.append("\n");
            for (int i = 0; i < m_initialStartPoints.numInstances(); i++) {
                temp.append("Cluster " + i + ": " + m_initialStartPoints.instance(i)).append("\n");
            }
        } else {
            temp.append(m_canopyClusters.toString(false));
        }

        if (m_speedUpDistanceCompWithCanopies) {
            temp.append("\nReduced number of distance calculations by using canopies.");
            if (m_initializationMethod != CANOPY) {
                temp.append("\nCanopy T2 radius: " + String.format("%-10.3f", m_canopyClusters.getActualT2()));
                temp.append("\nCanopy T1 radius: " + String.format("%-10.3f", m_canopyClusters.getActualT1()))
                        .append("\n");
            }
        }

        if (!m_dontReplaceMissing) {
            temp.append("\nMissing values globally replaced with mean/mode");
        }

        temp.append("\n\nFinal cluster centroids:\n");
        temp.append(pad("Cluster#", " ", (maxAttWidth + (maxWidth * 2 + 2)) - "Cluster#".length(), true));

        temp.append("\n");
        temp.append(pad("Attribute", " ", maxAttWidth - "Attribute".length(), false));

        temp.append(pad("Full Data", " ", maxWidth + 1 - "Full Data".length(), true));

        // cluster numbers
        for (int i = 0; i < m_NumClusters; i++) {
            String clustNum = "" + i;
            temp.append(pad(clustNum, " ", maxWidth + 1 - clustNum.length(), true));
        }
        temp.append("\n");

        // cluster sizes
        String cSize = "(" + Utils.sum(m_ClusterSizes) + ")";
        temp.append(pad(cSize, " ", maxAttWidth + maxWidth + 1 - cSize.length(), true));
        for (int i = 0; i < m_NumClusters; i++) {
            cSize = "(" + m_ClusterSizes[i] + ")";
            temp.append(pad(cSize, " ", maxWidth + 1 - cSize.length(), true));
        }
        temp.append("\n");

        temp.append(pad("", "=", maxAttWidth
                + (maxWidth * (m_ClusterCentroids.numInstances() + 1) + m_ClusterCentroids.numInstances() + 1),
                true));
        temp.append("\n");

        for (int i = 0; i < m_ClusterCentroids.numAttributes(); i++) {
            String attName = m_ClusterCentroids.attribute(i).name();
            temp.append(attName);
            for (int j = 0; j < maxAttWidth - attName.length(); j++) {
                temp.append(" ");
            }

            String strVal;
            String valMeanMode;
            // full data
            if (m_ClusterCentroids.attribute(i).isNominal()) {
                if (m_FullMeansOrMediansOrModes[i] == -1) { // missing
                    valMeanMode = pad("missing", " ", maxWidth + 1 - "missing".length(), true);
                } else {
                    valMeanMode = pad(
                            (strVal = m_ClusterCentroids.attribute(i).value((int) m_FullMeansOrMediansOrModes[i])),
                            " ", maxWidth + 1 - strVal.length(), true);
                }
            } else {
                if (Double.isNaN(m_FullMeansOrMediansOrModes[i])) {
                    valMeanMode = pad("missing", " ", maxWidth + 1 - "missing".length(), true);
                } else {
                    valMeanMode = pad(
                            (strVal = Utils.doubleToString(m_FullMeansOrMediansOrModes[i], maxWidth, 4).trim()),
                            " ", maxWidth + 1 - strVal.length(), true);
                }
            }
            temp.append(valMeanMode);

            for (int j = 0; j < m_NumClusters; j++) {
                if (m_ClusterCentroids.attribute(i).isNominal()) {
                    if (m_ClusterCentroids.instance(j).isMissing(i)) {
                        valMeanMode = pad("missing", " ", maxWidth + 1 - "missing".length(), true);
                    } else {
                        valMeanMode = pad(
                                (strVal = m_ClusterCentroids.attribute(i)
                                        .value((int) m_ClusterCentroids.instance(j).value(i))),
                                " ", maxWidth + 1 - strVal.length(), true);
                    }
                } else {
                    if (m_ClusterCentroids.instance(j).isMissing(i)) {
                        valMeanMode = pad("missing", " ", maxWidth + 1 - "missing".length(), true);
                    } else {
                        valMeanMode = pad((strVal = Utils
                                .doubleToString(m_ClusterCentroids.instance(j).value(i), maxWidth, 4).trim()), " ",
                                maxWidth + 1 - strVal.length(), true);
                    }
                }
                temp.append(valMeanMode);
            }
            temp.append("\n");

            if (m_displayStdDevs) {
                // Std devs/max nominal
                String stdDevVal = "";

                if (m_ClusterCentroids.attribute(i).isNominal()) {
                    // Do the values of the nominal attribute
                    Attribute a = m_ClusterCentroids.attribute(i);
                    for (int j = 0; j < a.numValues(); j++) {
                        // full data
                        String val = "  " + a.value(j);
                        temp.append(pad(val, " ", maxAttWidth + 1 - val.length(), false));
                        double count = m_FullNominalCounts[i][j];
                        int percent = (int) ((double) m_FullNominalCounts[i][j] / Utils.sum(m_ClusterSizes)
                                * 100.0);
                        String percentS = "" + percent + "%)";
                        percentS = pad(percentS, " ", 5 - percentS.length(), true);
                        stdDevVal = "" + count + " (" + percentS;
                        stdDevVal = pad(stdDevVal, " ", maxWidth + 1 - stdDevVal.length(), true);
                        temp.append(stdDevVal);

                        // Clusters
                        for (int k = 0; k < m_NumClusters; k++) {
                            percent = (int) ((double) m_ClusterNominalCounts[k][i][j] / m_ClusterSizes[k] * 100.0);
                            percentS = "" + percent + "%)";
                            percentS = pad(percentS, " ", 5 - percentS.length(), true);
                            stdDevVal = "" + m_ClusterNominalCounts[k][i][j] + " (" + percentS;
                            stdDevVal = pad(stdDevVal, " ", maxWidth + 1 - stdDevVal.length(), true);
                            temp.append(stdDevVal);
                        }
                        temp.append("\n");
                    }
                    // missing (if any)
                    if (m_FullMissingCounts[i] > 0) {
                        // Full data
                        temp.append(pad("  missing", " ", maxAttWidth + 1 - "  missing".length(), false));
                        double count = m_FullMissingCounts[i];
                        int percent = (int) ((double) m_FullMissingCounts[i] / Utils.sum(m_ClusterSizes) * 100.0);
                        String percentS = "" + percent + "%)";
                        percentS = pad(percentS, " ", 5 - percentS.length(), true);
                        stdDevVal = "" + count + " (" + percentS;
                        stdDevVal = pad(stdDevVal, " ", maxWidth + 1 - stdDevVal.length(), true);
                        temp.append(stdDevVal);

                        // Clusters
                        for (int k = 0; k < m_NumClusters; k++) {
                            percent = (int) ((double) m_ClusterMissingCounts[k][i] / m_ClusterSizes[k] * 100.0);
                            percentS = "" + percent + "%)";
                            percentS = pad(percentS, " ", 5 - percentS.length(), true);
                            stdDevVal = "" + m_ClusterMissingCounts[k][i] + " (" + percentS;
                            stdDevVal = pad(stdDevVal, " ", maxWidth + 1 - stdDevVal.length(), true);
                            temp.append(stdDevVal);
                        }

                        temp.append("\n");
                    }

                    temp.append("\n");
                } else {
                    // Full data
                    if (Double.isNaN(m_FullMeansOrMediansOrModes[i])) {
                        stdDevVal = pad("--", " ", maxAttWidth + maxWidth + 1 - 2, true);
                    } else {
                        stdDevVal = pad(
                                (strVal = plusMinus + Utils.doubleToString(m_FullStdDevs[i], maxWidth, 4).trim()),
                                " ", maxWidth + maxAttWidth + 1 - strVal.length(), true);
                    }
                    temp.append(stdDevVal);

                    // Clusters
                    for (int j = 0; j < m_NumClusters; j++) {
                        if (m_ClusterCentroids.instance(j).isMissing(i)) {
                            stdDevVal = pad("--", " ", maxWidth + 1 - 2, true);
                        } else {
                            stdDevVal = pad((strVal = plusMinus + Utils
                                    .doubleToString(m_ClusterStdDevs.instance(j).value(i), maxWidth, 4).trim()),
                                    " ", maxWidth + 1 - strVal.length(), true);
                        }
                        temp.append(stdDevVal);
                    }
                    temp.append("\n\n");
                }
            }
        }

        temp.append("\n\n");
        return temp.toString();
    }

    private String pad(String source, String padChar, int length, boolean leftPad) {
        StringBuffer temp = new StringBuffer();

        if (leftPad) {
            for (int i = 0; i < length; i++) {
                temp.append(padChar);
            }
            temp.append(source);
        } else {
            temp.append(source);
            for (int i = 0; i < length; i++) {
                temp.append(padChar);
            }
        }
        return temp.toString();
    }

    /**
     * Gets the the cluster centroids.
     * 
     * @return the cluster centroids
     */
    public Instances getClusterCentroids() {
        return m_ClusterCentroids;
    }

    /**
     * Gets the standard deviations of the numeric attributes in each cluster.
     * 
     * @return the standard deviations of the numeric attributes in each cluster
     */
    public Instances getClusterStandardDevs() {
        return m_ClusterStdDevs;
    }

    /**
     * Returns for each cluster the weighted frequency counts for the values of each
     * nominal attribute.
     * 
     * @return the counts
     */
    public double[][][] getClusterNominalCounts() {
        return m_ClusterNominalCounts;
    }

    /**
     * Gets the squared error for all clusters.
     * 
     * @return the squared error, NaN if fast distance calculation is used
     * @see #m_FastDistanceCalc
     */
    public double getSquaredError() {
        if (m_FastDistanceCalc) {
            return Double.NaN;
        } else {
            return Utils.sum(m_squaredErrors);
        }
    }

    /**
     * Gets the sum of weights for all the instances in each cluster.
     * 
     * @return The number of instances in each cluster
     */
    public double[] getClusterSizes() {
        return m_ClusterSizes;
    }

    /**
     * Gets the assignments for each instance.
     * 
     * @return Array of indexes of the centroid assigned to each instance
     * @throws Exception if order of instances wasn't preserved or no assignments
     *           were made
     */
    public int[] getAssignments() throws Exception {
        if (!m_PreserveOrder) {
            throw new Exception("The assignments are only available when order of instances is preserved (-O)");
        }
        if (m_Assignments == null) {
            throw new Exception("No assignments made.");
        }
        return m_Assignments;
    }

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

    /**
     * Main method for executing this class.
     * 
     * @param args use -h to list all parameters
     */
    public static void main(String[] args) {
        runClusterer(new SimpleKMeans(), args);
    }
}