Example usage for org.apache.commons.math.linear RealMatrix getRowDimension

Introduction

In this page you can find the example usage for org.apache.commons.math.linear RealMatrix getRowDimension.

Prototype

int getRowDimension();

Source Link

Document

Returns the number of rows in the matrix.

Usage

From source file:math2605.gn_log.java

private static void setJ(List<String[]> pairs, double a, double b, double c, RealMatrix r, RealMatrix J) {
    for (int i = 0; i < r.getRowDimension(); i++) {
        double x = Double.parseDouble(pairs.get(i)[0]);
        for (int j = 0; j < 3; j++) {
            double entry = -1;
            if (j == 0) {
                entry = -(Math.log(x + b));
            } else if (j == 1) {
                entry = -a / (x + b);/*from   w  ww .  j  a va2 s  .  c  o  m*/
            }
            J.setEntry(i, j, entry);
        }
    }
}

From source file:math2605.gn_rat.java

private static void setJ(List<String[]> pairs, double a, double b, double c, RealMatrix r, RealMatrix J) {
    for (int i = 0; i < r.getRowDimension(); i++) {
        double x = Double.parseDouble(pairs.get(i)[0]);
        for (int j = 0; j < 3; j++) {
            double entry = -1;
            if (j == 0) {
                entry = -x / (x + b);// ww w.j a  va 2  s .c  o  m
            } else if (j == 1) {
                entry = (a * x) / Math.pow(x + b, 2);
            }
            J.setEntry(i, j, entry);
        }
    }
}

From source file:math2605.gn_exp.java

private static void setJ(List<String[]> pairs, double a, double b, double c, RealMatrix r, RealMatrix J) {
    for (int i = 0; i < r.getRowDimension(); i++) {
        double x = Double.parseDouble(pairs.get(i)[0]);
        for (int j = 0; j < 3; j++) {
            double entry = -1;
            if (j == 0) {
                entry = -(Math.pow(Math.E, b * x));
            } else if (j == 1) {
                entry = -a * x * Math.pow(Math.E, b * x);
            }//from  www.j a v a2 s .com
            J.setEntry(i, j, entry);
        }
    }
}

From source file:math2605.gn_qua.java

private static void setJ(List<String[]> pairs, double a, double b, double c, RealMatrix r, RealMatrix J) {
    for (int i = 0; i < r.getRowDimension(); i++) {
        double x = Double.parseDouble(pairs.get(i)[0]);
        for (int j = 0; j < 3; j++) {
            double entry = -1;
            if (j == 0) {
                entry = -x * x;//  www .j av  a  2  s .co m
            } else if (j == 1) {
                entry = -x;
            }
            J.setEntry(i, j, entry);
        }
    }
}

From source file:juicebox.tools.utils.juicer.arrowhead.DynamicProgrammingUtils.java

/**
 * Calculate cumulative sums across upper right matrix
 * iterative result is entry to left + entry below + orig value - diagonal down (else we double count)
 *
 * @param matrix/*from  w  w w.  j a v a  2s.c  om*/
 * @param superDiagonal
 * @return
 */
public static RealMatrix sum(RealMatrix matrix, int superDiagonal) {

    int n = Math.min(matrix.getRowDimension(), matrix.getColumnDimension());

    RealMatrix diagMatrix = MatrixTools.cleanArray2DMatrix(matrix.getRowDimension(),
            matrix.getColumnDimension());
    if (superDiagonal <= 0) {
        diagMatrix = MatrixTools.extractDiagonal(matrix);
        superDiagonal = 1;
    }

    // d = distance from diagonal
    for (int d = superDiagonal; d < n; d++) {
        // i = row, column is i +d;

        for (int i = 0; i < n - d; i++) {
            diagMatrix.setEntry(i, i + d, diagMatrix.getEntry(i, i + d - 1) + diagMatrix.getEntry(i + 1, i + d)
                    + matrix.getEntry(i, i + d) - diagMatrix.getEntry(i + 1, i + d - 1));
        }
    }
    return diagMatrix;
}

From source file:juicebox.tools.utils.juicer.arrowhead.DynamicProgrammingUtils.java

/**
 * Dynamic programming to calculate "right" matrix
 * Initialize by setting the diagonal to the diagonal of original
 * Iterate to the right and up.//from ww  w. j  a  va 2  s. com
 *
 * @param matrix
 * @param maxSize
 * @return rightMatrix
 */
public static RealMatrix right(RealMatrix matrix, int maxSize) {

    RealMatrix rightMatrix = MatrixTools.extractDiagonal(matrix);
    int n = rightMatrix.getRowDimension();

    // j is column, i is row
    for (int j = 1; j < n; j++) {
        int endPoint = Math.max(j - 1 - maxSize, 0);
        for (int i = j - 1; i >= endPoint; i--) {
            rightMatrix.setEntry(i, j, matrix.getEntry(i, j) + rightMatrix.getEntry(i + 1, j));
        }
    }
    return rightMatrix;
}

From source file:juicebox.tools.utils.juicer.arrowhead.DynamicProgrammingUtils.java

/**
 * Dynamic programming to calculate "upper" matrix
 * Initialize by setting the diagonal to the diagonal of original
 * Iterate down (for each row) and to the left.
 *
 * @param matrix/*w ww.ja  v a2s .  co m*/
 * @param maxSize
 * @return upperMatrix
 */
public static RealMatrix upper(RealMatrix matrix, int maxSize) {

    RealMatrix upperMatrix = MatrixTools.extractDiagonal(matrix);
    int n = upperMatrix.getRowDimension();

    // j is column, i is row
    for (int i = 0; i < n; i++) {
        int endPoint = Math.min(i + 1 + maxSize, n - 1);
        for (int j = i + 1; j <= endPoint; j++) {
            upperMatrix.setEntry(i, j, matrix.getEntry(i, j) + upperMatrix.getEntry(i, j - 1));
        }
    }
    return upperMatrix;
}

From source file:juicebox.tools.utils.juicer.apa.APAUtils.java

public static double peakEnhancement(RealMatrix matrix) {
    int rows = matrix.getRowDimension();
    int center = rows / 2;
    double centerVal = matrix.getEntry(center, center);
    double remainingSum = APARegionStatistics.sum(matrix.getData()) - centerVal;
    double remainingAverage = remainingSum / (rows * rows - 1);
    return centerVal / remainingAverage;
}

From source file:juicebox.tools.utils.juicer.apa.APAUtils.java

public static RealMatrix centerNormalization(RealMatrix matrix) {

    int center = matrix.getRowDimension() / 2;
    double centerVal = matrix.getEntry(center, center);

    if (centerVal == 0) {
        centerVal = MatrixTools.minimumPositive(matrix);
        if (centerVal == 0)
            centerVal = 1;/*w w w.  ja v a 2 s.  c  o m*/
    }

    return matrix.copy().scalarMultiply(1. / centerVal);
}

From source file:net.sf.maltcms.chromaui.features.spi.FeatureTable.java

public static RealMatrix normalize(RealMatrix sourceMatrix, boolean center, boolean normalize) {
    RealMatrix normalized = MatrixUtils.createRealMatrix(sourceMatrix.getRowDimension(),
            sourceMatrix.getColumnDimension());
    for (int col = 0; col < sourceMatrix.getColumnDimension(); col++) {
        double[] columnVector = sourceMatrix.getColumn(col);
        double mean = StatUtils.mean(columnVector);
        double stdev = Math.sqrt(StatUtils.variance(columnVector, mean));
        Logger.getLogger(FeatureTable.class.getName()).log(Level.INFO, "column {0}, mean={1} stdev={2}",
                new Object[] { col, mean, stdev });
        for (int j = 0; j < columnVector.length; j++) {
            normalized.setEntry(j, col, (sourceMatrix.getEntry(j, col) - mean) / stdev);
        }/* ww  w  .jav a2 s . c  o m*/
    }
    return normalized;
}