Example usage for org.apache.commons.math3.ml.distance EarthMoversDistance EarthMoversDistance

Introduction

In this page you can find the example usage for org.apache.commons.math3.ml.distance EarthMoversDistance EarthMoversDistance.

Prototype

EarthMoversDistance

Source Link

Usage

From source file:GeMSE.GS.Analysis.Clustering.DistanceMatrix.java

public double[][] GetDistanceMatrix(double[][] space, Metrics metric, ClusteringDomains clusteringDomain) {
    euclideanDistance = new EuclideanDistance();
    manhattanDistance = new ManhattanDistance();
    earthMoversDistance = new EarthMoversDistance();
    chebyshevDistance = new ChebyshevDistance();
    canberraDistance = new CanberraDistance();

    double[][] rtv = null;

    int rowCount = space.length;
    int colCount = space[0].length;
    int rtvIndex = 0;

    switch (clusteringDomain) {
    case Rows:/*  ww w  .  j  a  va 2 s  .c o  m*/
        rtv = new double[1][(int) Math.floor((Math.pow(rowCount, 2) - rowCount) / 2f)];

        for (int i = 0; i < rowCount - 1; i++)
            for (int j = i + 1; j < rowCount; j++)
                // TODO: replace the following mess with the factory method. 
                switch (metric) {
                case EuclideanDistance:
                    rtv[0][rtvIndex++] = euclideanDistance.compute(space[i], space[j]);
                    break;

                case ManhattanDistance:
                    rtv[0][rtvIndex++] = manhattanDistance.compute(space[i], space[j]);
                    break;

                case EarthMoversDistance:
                    rtv[0][rtvIndex++] = earthMoversDistance.compute(space[i], space[j]);
                    break;

                case ChebyshevDistance:
                    rtv[0][rtvIndex++] = chebyshevDistance.compute(space[i], space[j]);
                    break;

                case CanberraDistance:
                    rtv[0][rtvIndex++] = canberraDistance.compute(space[i], space[j]);
                    break;

                case PearsonCorrelationCoefficient:
                    rtv[0][rtvIndex++] = ComputePCC(space[i], space[j]);
                    break;
                }

        break;

    case Columns:
        rtv = new double[1][(int) Math.floor((Math.pow(colCount, 2) - colCount) / 2f)];

        double[] col_i = new double[rowCount];
        double[] col_j = new double[rowCount];

        for (int i = 0; i < colCount - 1; i++) {
            for (int j = i + 1; j < colCount; j++) {
                for (int row = 0; row < rowCount; row++) {
                    col_i[row] = space[row][i];
                    col_j[row] = space[row][j];
                }

                // TODO: Replace the following mess with the factory pattern. 
                switch (metric) {
                case EuclideanDistance:
                    rtv[0][rtvIndex++] = euclideanDistance.compute(col_i, col_j);
                    break;

                case ManhattanDistance:
                    rtv[0][rtvIndex++] = manhattanDistance.compute(col_i, col_j);
                    break;

                case EarthMoversDistance:
                    rtv[0][rtvIndex++] = earthMoversDistance.compute(col_i, col_j);
                    break;

                case ChebyshevDistance:
                    rtv[0][rtvIndex++] = chebyshevDistance.compute(col_i, col_j);
                    break;

                case CanberraDistance:
                    rtv[0][rtvIndex++] = canberraDistance.compute(col_i, col_j);
                    break;

                case PearsonCorrelationCoefficient:
                    rtv[0][rtvIndex++] = ComputePCC(col_i, col_j);
                    break;
                }
            }
        }
        break;
    }

    return rtv;
}

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From source file:org.apache.solr.client.solrj.io.eval.DistanceEvaluator.java

@Override
public Object doWork(Object... values) throws IOException {

    if (values.length == 2) {
        Object first = values[0];
        Object second = values[1];

        if (null == first) {
            throw new IOException(
                    String.format(Locale.ROOT, "Invalid expression %s - null found for the first value",
                            toExpression(constructingFactory)));
        }//w ww  . ja va  2s.  c om
        if (null == second) {
            throw new IOException(
                    String.format(Locale.ROOT, "Invalid expression %s - null found for the second value",
                            toExpression(constructingFactory)));
        }
        if (!(first instanceof List<?>)) {
            throw new IOException(String.format(Locale.ROOT,
                    "Invalid expression %s - found type %s for the first value, expecting a list of numbers",
                    toExpression(constructingFactory), first.getClass().getSimpleName()));
        }
        if (!(second instanceof List<?>)) {
            throw new IOException(String.format(Locale.ROOT,
                    "Invalid expression %s - found type %s for the second value, expecting a list of numbers",
                    toExpression(constructingFactory), first.getClass().getSimpleName()));
        }

        if (type.equals(DistanceType.euclidean)) {
            EuclideanDistance euclideanDistance = new EuclideanDistance();
            return euclideanDistance.compute(
                    ((List) first).stream().mapToDouble(value -> ((Number) value).doubleValue()).toArray(),
                    ((List) second).stream().mapToDouble(value -> ((Number) value).doubleValue()).toArray());
        } else if (type.equals(DistanceType.manhattan)) {
            ManhattanDistance manhattanDistance = new ManhattanDistance();
            return manhattanDistance.compute(
                    ((List) first).stream().mapToDouble(value -> ((Number) value).doubleValue()).toArray(),
                    ((List) second).stream().mapToDouble(value -> ((Number) value).doubleValue()).toArray());

        } else if (type.equals(DistanceType.canberra)) {
            CanberraDistance canberraDistance = new CanberraDistance();
            return canberraDistance.compute(
                    ((List) first).stream().mapToDouble(value -> ((Number) value).doubleValue()).toArray(),
                    ((List) second).stream().mapToDouble(value -> ((Number) value).doubleValue()).toArray());
        } else if (type.equals(DistanceType.earthMovers)) {
            EarthMoversDistance earthMoversDistance = new EarthMoversDistance();
            return earthMoversDistance.compute(
                    ((List) first).stream().mapToDouble(value -> ((Number) value).doubleValue()).toArray(),
                    ((List) second).stream().mapToDouble(value -> ((Number) value).doubleValue()).toArray());
        } else {
            return null;
        }
    } else if (values.length == 1) {
        if (values[0] instanceof Matrix) {
            Matrix matrix = (Matrix) values[0];
            if (type.equals(DistanceType.euclidean)) {
                EuclideanDistance euclideanDistance = new EuclideanDistance();
                return distance(euclideanDistance, matrix);
            } else if (type.equals(DistanceType.canberra)) {
                CanberraDistance canberraDistance = new CanberraDistance();
                return distance(canberraDistance, matrix);
            } else if (type.equals(DistanceType.manhattan)) {
                ManhattanDistance manhattanDistance = new ManhattanDistance();
                return distance(manhattanDistance, matrix);
            } else if (type.equals(DistanceType.earthMovers)) {
                EarthMoversDistance earthMoversDistance = new EarthMoversDistance();
                return distance(earthMoversDistance, matrix);
            } else {
                return null;
            }
        } else {
            throw new IOException(
                    "distance function operates on either two numeric arrays or a single matrix as parameters.");
        }
    } else {
        throw new IOException(
                "distance function operates on either two numeric arrays or a single matrix as parameters.");
    }
}

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From source file:org.apache.solr.client.solrj.io.eval.EarthMoversDistanceEvaluator.java

@Override
public Object doWork(Object first, Object second) throws IOException {
    if (null == first) {
        throw new IOException(String.format(Locale.ROOT,
                "Invalid expression %s - null found for the first value", toExpression(constructingFactory)));
    }/*from  w  w w  . j  ava2  s  .  c  o  m*/
    if (null == second) {
        throw new IOException(String.format(Locale.ROOT,
                "Invalid expression %s - null found for the second value", toExpression(constructingFactory)));
    }
    if (!(first instanceof List<?>)) {
        throw new IOException(String.format(Locale.ROOT,
                "Invalid expression %s - found type %s for the first value, expecting a list of numbers",
                toExpression(constructingFactory), first.getClass().getSimpleName()));
    }
    if (!(second instanceof List<?>)) {
        throw new IOException(String.format(Locale.ROOT,
                "Invalid expression %s - found type %s for the second value, expecting a list of numbers",
                toExpression(constructingFactory), first.getClass().getSimpleName()));
    }

    EarthMoversDistance distance = new EarthMoversDistance();
    return distance.compute(
            ((List) first).stream().mapToDouble(value -> ((BigDecimal) value).doubleValue()).toArray(),
            ((List) second).stream().mapToDouble(value -> ((BigDecimal) value).doubleValue()).toArray());
}

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From source file:org.apache.solr.client.solrj.io.eval.KnnEvaluator.java

public KnnEvaluator(StreamExpression expression, StreamFactory factory) throws IOException {
    super(expression, factory);

    DistanceEvaluator.DistanceType type = null;
    List<StreamExpressionNamedParameter> namedParams = factory.getNamedOperands(expression);
    if (namedParams.size() > 0) {
        if (namedParams.size() > 1) {
            throw new IOException("distance function expects only one named parameter 'distance'.");
        }//from  www.j  a v  a 2  s  . c o  m

        StreamExpressionNamedParameter namedParameter = namedParams.get(0);
        String name = namedParameter.getName();
        if (!name.equalsIgnoreCase("distance")) {
            throw new IOException("distance function expects only one named parameter 'distance'.");
        }

        String typeParam = namedParameter.getParameter().toString().trim();
        type = DistanceEvaluator.DistanceType.valueOf(typeParam);
    } else {
        type = DistanceEvaluator.DistanceType.euclidean;
    }

    if (type.equals(DistanceEvaluator.DistanceType.euclidean)) {
        distanceMeasure = new EuclideanDistance();
    } else if (type.equals(DistanceEvaluator.DistanceType.manhattan)) {
        distanceMeasure = new ManhattanDistance();
    } else if (type.equals(DistanceEvaluator.DistanceType.canberra)) {
        distanceMeasure = new CanberraDistance();
    } else if (type.equals(DistanceEvaluator.DistanceType.earthMovers)) {
        distanceMeasure = new EarthMoversDistance();
    }

}

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