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

Example 26 with RealMatrix

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

the class GATKProtectedMathUtils method rowVariances.

public static double[] rowVariances(final RealMatrix matrix) {
    Utils.nonNull(matrix);
    final Variance varianceEvaluator = new Variance();
    return IntStream.range(0, matrix.getRowDimension()).mapToDouble(r -> varianceEvaluator.evaluate(matrix.getRow(r))).toArray();
}

Example 27 with RealMatrix

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

the class SparkConverter method convertSparkMatrixToRealMatrix.

/**
     * Convert a local (not distributed) Spark Matrix to an Apache Commons matrix.
     *
     * @param r Never {@code null}
     * @return Not {@code null}
     */
public static RealMatrix convertSparkMatrixToRealMatrix(final Matrix r) {
    final RealMatrix result = new Array2DRowRealMatrix(r.numRows(), r.numCols());
    final double[] columnMajorMat = r.toArray();
    for (int i = 0; i < r.numRows(); i++) {
        result.setRow(i, Arrays.copyOfRange(columnMajorMat, i * r.numCols(), i * r.numCols() + r.numCols()));
    }
    return result;
}

Example 28 with RealMatrix

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

the class MatrixSummaryUtils method getColumnMedians.

/**
     * Return an array containing the median for each column in the given matrix.
     * @param m Not {@code null}.  Size MxN, where neither dimension is zero.  If any entry is NaN, it is disregarded
     *          in the calculation.
     * @return array of size N.  Never {@code null}
     */
public static double[] getColumnMedians(final RealMatrix m) {
    Utils.nonNull(m, "Cannot calculate medians on a null matrix.");
    final Median medianCalculator = new Median();
    return IntStream.range(0, m.getColumnDimension()).boxed().mapToDouble(i -> medianCalculator.evaluate(m.getColumn(i))).toArray();
}

Example 29 with RealMatrix

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

the class MatrixSummaryUtils method getRowMedians.

/**
     * Return an array containing the median for each row in the given matrix.
     * @param m Not {@code null}.  Size MxN.    If any entry is NaN, it is disregarded
     *          in the calculation.
     * @return array of size M.  Never {@code null}
     */
public static double[] getRowMedians(final RealMatrix m) {
    Utils.nonNull(m, "Cannot calculate medians on a null matrix.");
    final Median medianCalculator = new Median();
    return IntStream.range(0, m.getRowDimension()).boxed().mapToDouble(i -> medianCalculator.evaluate(m.getRow(i))).toArray();
}

Example 30 with RealMatrix

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

the class HDF5PCACoveragePoNCreationUtilsUnitTest method testSubtractMedianOfMedians.

@Test(dataProvider = "readCountOnlyData")
public void testSubtractMedianOfMedians(final ReadCountCollection readCounts) {
    final RealMatrix counts = readCounts.counts();
    final Median median = new Median();
    final double[] columnMedians = IntStream.range(0, counts.getColumnDimension()).mapToDouble(i -> median.evaluate(counts.getColumn(i))).toArray();
    final double center = median.evaluate(columnMedians);
    final double[][] expected = new double[counts.getRowDimension()][];
    for (int i = 0; i < expected.length; i++) {
        expected[i] = counts.getRow(i).clone();
        for (int j = 0; j < expected[i].length; j++) {
            expected[i][j] -= center;
        }
    }
    HDF5PCACoveragePoNCreationUtils.subtractMedianOfMedians(readCounts, NULL_LOGGER);
    final RealMatrix newCounts = readCounts.counts();
    Assert.assertEquals(newCounts.getColumnDimension(), expected[0].length);
    Assert.assertEquals(newCounts.getRowDimension(), expected.length);
    for (int i = 0; i < expected.length; i++) {
        for (int j = 0; j < expected[i].length; j++) {
            Assert.assertEquals(newCounts.getEntry(i, j), expected[i][j], 0.000001);
        }
    }
}