Examples with BlockRealMatrix org.apache.commons.math3.linear.BlockRealMatrix used on opensource projects

Example 11 with BlockRealMatrix

use of org.apache.commons.math3.linear.BlockRealMatrix in project activityinfo by bedatadriven.

the class ScoreMatrix method computeScoreMatrix.

public BlockRealMatrix computeScoreMatrix() {
    // First compute the scores of all possible matches between the source and targets
    int numPairs = getRowCount() * getColumnCount();
    int numDimensions = getDimensionCount();
    BlockRealMatrix matrix = new BlockRealMatrix(numPairs, numDimensions);
    int rowIndex = 0;
    for (int i = 0; i < getRowCount(); ++i) {
        for (int j = 0; j < getColumnCount(); ++j) {
            matrix.setRow(rowIndex++, score(i, j));
        }
    }
    return matrix;
}

Example 12 with BlockRealMatrix

use of org.apache.commons.math3.linear.BlockRealMatrix in project MindsEye by SimiaCryptus.

the class PCAUtil method getCovariance.

/**
 * Forked from Apache Commons Math
 *
 * @param stream the stream
 * @return covariance covariance
 */
@Nonnull
public static RealMatrix getCovariance(@Nonnull final Supplier<Stream<double[]>> stream) {
    final int dimension = stream.get().findAny().get().length;
    final List<DoubleStatistics> statList = IntStream.range(0, dimension * dimension).mapToObj(i -> new DoubleStatistics()).collect(Collectors.toList());
    stream.get().forEach(array -> {
        for (int i = 0; i < dimension; i++) {
            for (int j = 0; j <= i; j++) {
                statList.get(i * dimension + j).accept(array[i] * array[j]);
            }
        }
        RecycleBin.DOUBLES.recycle(array, array.length);
    });
    @Nonnull final RealMatrix covariance = new BlockRealMatrix(dimension, dimension);
    for (int i = 0; i < dimension; i++) {
        for (int j = 0; j <= i; j++) {
            final double v = statList.get(i + dimension * j).getAverage();
            covariance.setEntry(i, j, v);
            covariance.setEntry(j, i, v);
        }
    }
    return covariance;
}

Example 13 with BlockRealMatrix

use of org.apache.commons.math3.linear.BlockRealMatrix in project tetrad by cmu-phil.

the class DataUtils method simpleTest.

public static void simpleTest() {
    double[][] d = new double[][] { { 1, 2 }, { 3, 4 }, { 5, 6 } };
    RealMatrix m = new BlockRealMatrix(d);
    System.out.println(m);
    System.out.println(times(m.transpose(), m));
    System.out.println(MatrixUtils.transposeWithoutCopy(m).multiply(m));
    TetradMatrix n = new TetradMatrix(m, m.getRowDimension(), m.getColumnDimension());
    System.out.println(n);
    RealMatrix q = n.getRealMatrix();
    RealMatrix q1 = MatrixUtils.transposeWithoutCopy(q);
    RealMatrix q2 = times(q1, q);
    System.out.println(new TetradMatrix(q2, q.getColumnDimension(), q.getColumnDimension()));
}

Example 14 with BlockRealMatrix

use of org.apache.commons.math3.linear.BlockRealMatrix in project tetrad by cmu-phil.

the class DataUtils method times.

private static RealMatrix times(final RealMatrix m, final RealMatrix n) {
    if (m.getColumnDimension() != n.getRowDimension())
        throw new IllegalArgumentException("Incompatible matrices.");
    final int rowDimension = m.getRowDimension();
    final int columnDimension = n.getColumnDimension();
    final RealMatrix out = new BlockRealMatrix(rowDimension, columnDimension);
    final int NTHREADS = Runtime.getRuntime().availableProcessors();
    ForkJoinPool pool = ForkJoinPoolInstance.getInstance().getPool();
    for (int t = 0; t < NTHREADS; t++) {
        final int _t = t;
        Runnable worker = new Runnable() {

            @Override
            public void run() {
                int chunk = rowDimension / NTHREADS + 1;
                for (int row = _t * chunk; row < Math.min((_t + 1) * chunk, rowDimension); row++) {
                    if ((row + 1) % 100 == 0)
                        System.out.println(row + 1);
                    for (int col = 0; col < columnDimension; ++col) {
                        double sum = 0.0D;
                        int commonDimension = m.getColumnDimension();
                        for (int i = 0; i < commonDimension; ++i) {
                            sum += m.getEntry(row, i) * n.getEntry(i, col);
                        }
                        // double sum = m.getRowVector(row).dotProduct(n.getColumnVector(col));
                        out.setEntry(row, col, sum);
                    }
                }
            }
        };
        pool.submit(worker);
    }
    while (!pool.isQuiescent()) {
    }
    return out;
}

Example 15 with BlockRealMatrix

use of org.apache.commons.math3.linear.BlockRealMatrix in project imagej-ops by imagej.

the class DefaultInertiaTensor3D method calculate.

@Override
public RealMatrix calculate(final IterableRegion<B> input) {
    final BlockRealMatrix output = new BlockRealMatrix(3, 3);
    Cursor<Void> c = input.localizingCursor();
    double[] pos = new double[3];
    double[] computedCentroid = new double[3];
    centroid.calculate(input).localize(computedCentroid);
    final double mX = computedCentroid[0];
    final double mY = computedCentroid[1];
    final double mZ = computedCentroid[2];
    while (c.hasNext()) {
        c.fwd();
        c.localize(pos);
        output.setEntry(0, 0, output.getEntry(0, 0) + (pos[0] - mX) * (pos[0] - mX));
        output.setEntry(1, 1, output.getEntry(1, 1) + (pos[1] - mX) * (pos[1] - mY));
        output.setEntry(2, 2, output.getEntry(2, 2) + (pos[2] - mX) * (pos[2] - mZ));
        output.setEntry(0, 1, output.getEntry(0, 1) + (pos[0] - mY) * (pos[1] - mY));
        output.setEntry(1, 0, output.getEntry(0, 1));
        output.setEntry(0, 2, output.getEntry(0, 2) + (pos[0] - mY) * (pos[2] - mZ));
        output.setEntry(2, 0, output.getEntry(0, 2));
        output.setEntry(1, 2, output.getEntry(1, 2) + (pos[1] - mZ) * (pos[2] - mZ));
        output.setEntry(2, 1, output.getEntry(1, 2));
    }
    final double size = input.size();
    output.setEntry(0, 0, output.getEntry(0, 0) / size);
    output.setEntry(0, 1, output.getEntry(0, 1) / size);
    output.setEntry(0, 2, output.getEntry(0, 2) / size);
    output.setEntry(1, 0, output.getEntry(1, 0) / size);
    output.setEntry(1, 1, output.getEntry(1, 1) / size);
    output.setEntry(1, 2, output.getEntry(1, 2) / size);
    output.setEntry(2, 0, output.getEntry(2, 0) / size);
    output.setEntry(2, 1, output.getEntry(2, 1) / size);
    output.setEntry(2, 2, output.getEntry(2, 2) / size);
    return output;
}