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

Example 1 with BlockRealMatrix

use of org.apache.commons.math3.linear.BlockRealMatrix in project gatk-protected by broadinstitute.

the class Nd4jApacheAdapterUtilsUnitTest method assertINDArrayToApacheMatrixCorrectness.

public void assertINDArrayToApacheMatrixCorrectness(final INDArray arr) {
    /* brute force result */
    final RealMatrix expected = new BlockRealMatrix(arr.rows(), arr.columns());
    for (int i = 0; i < arr.rows(); i++) {
        for (int j = 0; j < arr.columns(); j++) {
            expected.setEntry(i, j, arr.getDouble(i, j));
        }
    }
    final RealMatrix result = Nd4jApacheAdapterUtils.convertINDArrayToApacheMatrix(arr);
    Assert.assertEquals(result.getColumnDimension(), expected.getColumnDimension());
    Assert.assertEquals(result.getRowDimension(), expected.getRowDimension());
    for (int i = 0; i < expected.getRowDimension(); i++) {
        ArrayAsserts.assertArrayEquals(result.getData()[i], expected.getData()[i], EPS);
    }
}

Example 2 with BlockRealMatrix

use of org.apache.commons.math3.linear.BlockRealMatrix in project gatk by broadinstitute.

the class Nd4jApacheAdapterUtils method convertINDArrayToApacheMatrix.

/**
     * INDArray to Apache
     *
     * @param matrix rank-2 INDArray
     * @return Apache matrix
     */
public static RealMatrix convertINDArrayToApacheMatrix(@Nonnull final INDArray matrix) {
    Utils.validateArg(matrix.rank() == 2, "Input rank is not 2 (not matrix)");
    final int[] shape = matrix.shape();
    final INDArray concreteMatrix = matrix.isView() ? matrix.dup() : matrix;
    final double[] data = concreteMatrix.data().asDouble();
    final char ordering = concreteMatrix.ordering();
    if (ordering == 'c') {
        return new BlockRealMatrix(monoToBiDiArrayRowMajor(data, shape[0], shape[1]));
    } else {
        /* ordering == 'f' */
        return new BlockRealMatrix(monoToBiDiArrayColumnMajor(data, shape[0], shape[1]));
    }
}

Example 3 with BlockRealMatrix

use of org.apache.commons.math3.linear.BlockRealMatrix in project gatk by broadinstitute.

the class Nd4jApacheAdapterUtilsUnitTest method assertINDArrayToApacheMatrixCorrectness.

public void assertINDArrayToApacheMatrixCorrectness(final INDArray arr) {
    /* brute force result */
    final RealMatrix expected = new BlockRealMatrix(arr.rows(), arr.columns());
    for (int i = 0; i < arr.rows(); i++) {
        for (int j = 0; j < arr.columns(); j++) {
            expected.setEntry(i, j, arr.getDouble(i, j));
        }
    }
    final RealMatrix result = Nd4jApacheAdapterUtils.convertINDArrayToApacheMatrix(arr);
    Assert.assertEquals(result.getColumnDimension(), expected.getColumnDimension());
    Assert.assertEquals(result.getRowDimension(), expected.getRowDimension());
    for (int i = 0; i < expected.getRowDimension(); i++) {
        ArrayAsserts.assertArrayEquals(result.getData()[i], expected.getData()[i], EPS);
    }
}

Example 4 with BlockRealMatrix

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

the class DefaultInertiaTensor3DMesh method calculate.

@Override
public RealMatrix calculate(final Mesh input) {
    final RealLocalizable o = centroid.calculate(input);
    BlockRealMatrix tensor = new BlockRealMatrix(3, 3);
    final Iterator<Facet> c = input.getFacets().iterator();
    while (c.hasNext()) {
        final TriangularFacet tf = (TriangularFacet) c.next();
        tensor = tensor.add(tetrahedronInertiaTensor(tf.getVertex(0), tf.getVertex(1), tf.getVertex(2), o));
    }
    return tensor;
}

Example 5 with BlockRealMatrix

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

the class DefaultInertiaTensor3DMesh method tetrahedronInertiaTensor.

/**
 * The computations are based on this paper:
 * http://docsdrive.com/pdfs/sciencepublications/jmssp/2005/8-11.pdf
 *
 * Note: In the paper b' and c' are swapped.
 *
 * @param p1
 *            triangular facet point
 * @param p2
 *            triangular facet point
 * @param p3
 *            triangular facet point
 * @param cent
 *            of the mesh
 * @return inertia tensor of this tetrahedron
 */
private BlockRealMatrix tetrahedronInertiaTensor(final RealLocalizable p1, final RealLocalizable p2, final RealLocalizable p3, final RealLocalizable cent) {
    final double originX = cent.getDoublePosition(0);
    final double originY = cent.getDoublePosition(1);
    final double originZ = cent.getDoublePosition(2);
    final double x1 = p1.getDoublePosition(0) - originX;
    final double y1 = p1.getDoublePosition(1) - originY;
    final double z1 = p1.getDoublePosition(2) - originZ;
    final double x2 = p2.getDoublePosition(0) - originX;
    final double y2 = p2.getDoublePosition(1) - originY;
    final double z2 = p2.getDoublePosition(2) - originZ;
    final double x3 = p3.getDoublePosition(0) - originX;
    final double y3 = p3.getDoublePosition(1) - originY;
    final double z3 = p3.getDoublePosition(2) - originZ;
    final double volume = tetrahedronVolume(new Vector3D(x1, y1, z1), new Vector3D(x2, y2, z2), new Vector3D(x3, y3, z3));
    final double a = 6 * volume * (y1 * y1 + y1 * y2 + y2 * y2 + y1 * y3 + y2 * y3 + y3 * y3 + z1 * z1 + z1 * z2 + z2 * z2 + z1 * z3 + z2 * z3 + z3 * z3) / 60.0;
    final double b = 6 * volume * (x1 * x1 + x1 * x2 + x2 * x2 + x1 * x3 + x2 * x3 + x3 * x3 + z1 * z1 + z1 * z2 + z2 * z2 + z1 * z3 + z2 * z3 + z3 * z3) / 60.0;
    final double c = 6 * volume * (x1 * x1 + x1 * x2 + x2 * x2 + x1 * x3 + x2 * x3 + x3 * x3 + y1 * y1 + y1 * y2 + y2 * y2 + y1 * y3 + y2 * y3 + y3 * y3) / 60.0;
    final double aa = 6 * volume * (2 * y1 * z1 + y2 * z1 + y3 * z1 + y1 * z2 + 2 * y2 * z2 + y3 * z2 + y1 * z3 + y2 * z3 + 2 * y3 * z3) / 120.0;
    final double bb = 6 * volume * (2 * x1 * y1 + x2 * y1 + x3 * y1 + x1 * y2 + 2 * x2 * y2 + x3 * y2 + x1 * y3 + x2 * y3 + 2 * x3 * y3) / 120.0;
    final double cc = 6 * volume * (2 * x1 * z1 + x2 * z1 + x3 * z1 + x1 * z2 + 2 * x2 * z2 + x3 * z2 + x1 * z3 + x2 * z3 + 2 * x3 * z3) / 120.0;
    final BlockRealMatrix t = new BlockRealMatrix(3, 3);
    t.setRow(0, new double[] { a, -bb, -cc });
    t.setRow(1, new double[] { -bb, b, -aa });
    t.setRow(2, new double[] { -cc, -aa, c });
    return t;
}