Examples with DoubleMatrix2D cern.colt.matrix.DoubleMatrix2D used on opensource projects

Example 46 with DoubleMatrix2D

use of cern.colt.matrix.DoubleMatrix2D in project tdq-studio-se by Talend.

the class Statistic method demo3.

/**
 * Demonstrates usage of this class.
 */
public static void demo3(VectorVectorFunction norm) {
    double[][] values = { { -0.9611052, -0.25421095 }, { 0.4308269, -0.69932648 }, { -1.2071029, 0.62030596 }, { 1.5345166, 0.02135884 }, { -1.1341542, 0.20388430 } };
    System.out.println("\n\ninitializing...");
    DoubleFactory2D factory = DoubleFactory2D.dense;
    DoubleMatrix2D A = factory.make(values).viewDice();
    System.out.println("\nA=" + A.viewDice());
    System.out.println("\ndist=" + distance(A, norm).viewDice());
}

Example 47 with DoubleMatrix2D

use of cern.colt.matrix.DoubleMatrix2D in project tdq-studio-se by Talend.

the class Stencil method stencil9.

/**
 *9 point stencil operation.
 *Applies a function to a moving <tt>3 x 3</tt> window.
 *@param A the matrix to operate on.
 *@param function the function to be applied to each window.
 *@param maxIterations the maximum number of times the stencil shall be applied to the matrix.
 *	Should be a multiple of 2 because two iterations are always done in one atomic step.
 *@param hasConverged Convergence condition; will return before maxIterations are done when <tt>hasConverged.apply(A)==true</tt>.
 *	Set this parameter to <tt>null</tt> to indicate that no convergence checks shall be made.
 *@param convergenceIterations the number of iterations to pass between each convergence check.
 *	(Since a convergence may be expensive, you may want to do it only every 2,4 or 8 iterations.)
 *@return the number of iterations actually executed.
 */
public static int stencil9(DoubleMatrix2D A, cern.colt.function.Double9Function function, int maxIterations, DoubleMatrix2DProcedure hasConverged, int convergenceIterations) {
    DoubleMatrix2D B = A.copy();
    if (convergenceIterations <= 1)
        convergenceIterations = 2;
    // odd -> make it even
    if (convergenceIterations % 2 != 0)
        convergenceIterations++;
    int i = 0;
    while (i < maxIterations) {
        // do two steps at a time for efficiency
        A.zAssign8Neighbors(B, function);
        B.zAssign8Neighbors(A, function);
        i = i + 2;
        if (i % convergenceIterations == 0 && hasConverged != null) {
            if (hasConverged.apply(A))
                return i;
        }
    }
    return i;
}

Example 48 with DoubleMatrix2D

use of cern.colt.matrix.DoubleMatrix2D in project Gemma by PavlidisLab.

the class MeanVarianceServiceImpl method calculateMeanVariance.

/**
 * @param matrix on which mean variance relation is computed with
 * @param mvr    object, if null, a new object is created
 * @return MeanVarianceRelation object
 */
private MeanVarianceRelation calculateMeanVariance(ExpressionDataDoubleMatrix matrix, MeanVarianceRelation mvr) {
    if (matrix == null) {
        log.warn("Experiment matrix is null");
        return null;
    }
    DoubleMatrix2D mat = new DenseDoubleMatrix2D(matrix.rows(), matrix.columns());
    for (int row = 0; row < mat.rows(); row++) {
        mat.viewRow(row).assign(matrix.getRawRow(row));
    }
    MeanVarianceEstimator mve = new MeanVarianceEstimator(mat);
    if (mvr == null) {
        mvr = MeanVarianceRelation.Factory.newInstance();
    }
    if (mve.getMeanVariance() != null) {
        mvr.setMeans(bac.doubleArrayToBytes(mve.getMeanVariance().viewColumn(0).toArray()));
        mvr.setVariances(bac.doubleArrayToBytes(mve.getMeanVariance().viewColumn(1).toArray()));
    }
    return mvr;
}

Example 49 with DoubleMatrix2D

use of cern.colt.matrix.DoubleMatrix2D in project Gemma by PavlidisLab.

the class ExpressionDataSVD method equalize.

/**
 * Implements the method described in the SPELL paper, alternative interpretation as related by Q. Morris. Set all
 * components to have equal weight (set all singular values to 1)
 *
 * @return the reconstructed matrix; values that were missing before are re-masked.
 */
public ExpressionDataDoubleMatrix equalize() {
    DoubleMatrix<Integer, Integer> copy = svd.getS().copy();
    for (int i = 0; i < copy.columns(); i++) {
        copy.set(i, i, 1.0);
    }
    double[][] rawU = svd.getU().getRawMatrix();
    double[][] rawS = copy.getRawMatrix();
    double[][] rawV = svd.getV().getRawMatrix();
    DoubleMatrix2D u = new DenseDoubleMatrix2D(rawU);
    DoubleMatrix2D s = new DenseDoubleMatrix2D(rawS);
    DoubleMatrix2D v = new DenseDoubleMatrix2D(rawV);
    Algebra a = new Algebra();
    DoubleMatrix<CompositeSequence, BioMaterial> reconstructed = new DenseDoubleMatrix<>(a.mult(a.mult(u, s), a.transpose(v)).toArray());
    reconstructed.setRowNames(this.expressionData.getMatrix().getRowNames());
    reconstructed.setColumnNames(this.expressionData.getMatrix().getColNames());
    // re-mask the missing values.
    for (int i = 0; i < reconstructed.rows(); i++) {
        for (int j = 0; j < reconstructed.columns(); j++) {
            if (Double.isNaN(this.missingValueInfo.get(i, j))) {
                reconstructed.set(i, j, Double.NaN);
            }
        }
    }
    return new ExpressionDataDoubleMatrix(this.expressionData, reconstructed);
}

Example 50 with DoubleMatrix2D

use of cern.colt.matrix.DoubleMatrix2D in project Gemma by PavlidisLab.

the class ComBat method getBatchData.

/**
 * @param sdata   data to be sliced
 * @param batchId which batch
 */
private DoubleMatrix2D getBatchData(DoubleMatrix2D sdata, String batchId) {
    Collection<C> sampleNames = batches.get(batchId);
    DoubleMatrix2D result = new DenseDoubleMatrix2D(sdata.rows(), sampleNames.size());
    int i = 0;
    for (C sname : sampleNames) {
        DoubleMatrix1D colInBatch = sdata.viewColumn(data.getColIndexByName(sname));
        for (int k = 0; k < colInBatch.size(); k++) {
            result.set(k, i, colInBatch.get(k));
        }
        i++;
    }
    // log.info( result );
    return result;
}