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

Example 1 with LUDecomposition

use of org.apache.commons.math3.linear.LUDecomposition in project jstructure by JonStargaryen.

the class SVDSuperimposer method align.

@Override
public StructureAlignmentResult align(AtomContainer reference, AtomContainer query) {
    AtomContainer originalReference = reference;
    AtomContainer originalCandidate = query;
    Pair<GroupContainer, GroupContainer> atomContainerPair = AbstractAlignmentAlgorithm.comparableGroupContainerPair(reference, query, minimalSetOfAtomNames, maximalSetOfAtomNames);
    reference = atomContainerPair.getLeft();
    query = atomContainerPair.getRight();
    // calculate centroids
    double[] centroid1 = reference.calculate().centroid().getValue();
    double[] centroid2 = query.calculate().centroid().getValue();
    // center atoms
    reference.calculate().center();
    query.calculate().center();
    // compose covariance matrix and calculate SVD
    RealMatrix matrix1 = convertToMatrix(reference);
    RealMatrix matrix2 = convertToMatrix(query);
    RealMatrix covariance = matrix2.transpose().multiply(matrix1);
    SingularValueDecomposition svd = new SingularValueDecomposition(covariance);
    // R = (V * U')'
    RealMatrix ut = svd.getU().transpose();
    RealMatrix rotationMatrix = svd.getV().multiply(ut).transpose();
    // check if reflection
    if (new LUDecomposition(rotationMatrix).getDeterminant() < 0) {
        RealMatrix v = svd.getV().transpose();
        v.setEntry(2, 0, (0 - v.getEntry(2, 0)));
        v.setEntry(2, 1, (0 - v.getEntry(2, 1)));
        v.setEntry(2, 2, (0 - v.getEntry(2, 2)));
        rotationMatrix = v.transpose().multiply(ut).transpose();
    }
    double[][] rotation = rotationMatrix.getData();
    // calculate translation
    double[] translation = LinearAlgebra.on(centroid1).subtract(LinearAlgebra.on(centroid2).multiply(rotation)).getValue();
    logger.trace("rotation matrix\n{}\ntranslation vector\n{}", Arrays.deepToString(rotationMatrix.getData()), Arrays.toString(translation));
    /* transform 2nd atom select - employ neutral translation (3D vector of zeros), because the atoms are already
        * centered and calculate RMSD */
    query.calculate().transform(new Transformation(rotation));
    double rmsd = calculateRmsd(reference, query);
    // return alignment
    return new StructureAlignmentResult(originalReference, originalCandidate, query, rmsd, translation, rotation);
}

Example 2 with LUDecomposition

use of org.apache.commons.math3.linear.LUDecomposition in project incubator-systemml by apache.

the class LibCommonsMath method computeLU.

/**
	 * Function to perform LU decomposition on a given matrix.
	 * 
	 * @param in matrix object
	 * @return array of matrix blocks
	 * @throws DMLRuntimeException if DMLRuntimeException occurs
	 */
private static MatrixBlock[] computeLU(MatrixObject in) throws DMLRuntimeException {
    if (in.getNumRows() != in.getNumColumns()) {
        throw new DMLRuntimeException("LU Decomposition can only be done on a square matrix. Input matrix is rectangular (rows=" + in.getNumRows() + ", cols=" + in.getNumColumns() + ")");
    }
    Array2DRowRealMatrix matrixInput = DataConverter.convertToArray2DRowRealMatrix(in);
    // Perform LUP decomposition
    LUDecomposition ludecompose = new LUDecomposition(matrixInput);
    RealMatrix P = ludecompose.getP();
    RealMatrix L = ludecompose.getL();
    RealMatrix U = ludecompose.getU();
    // Read the results into native format
    MatrixBlock mbP = DataConverter.convertToMatrixBlock(P.getData());
    MatrixBlock mbL = DataConverter.convertToMatrixBlock(L.getData());
    MatrixBlock mbU = DataConverter.convertToMatrixBlock(U.getData());
    return new MatrixBlock[] { mbP, mbL, mbU };
}