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

Introduction

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

Prototype

int getColumnDimension();

Source Link

Document

Returns the number of columns in the matrix.

Usage

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 2  s .  co  m*/
 * @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;
}

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

/**
 * @param data/*  w w  w .jav  a2 s. c  o m*/
 * @return
 */
public static RealMatrix rankPercentile(RealMatrix data) {
    int n = data.getColumnDimension();
    StatPercentile percentile = new StatPercentile(MatrixTools.flattenedRowMajorOrderMatrix(data));

    RealMatrix matrix = new Array2DRowRealMatrix(n, n);
    for (int r = 0; r < n; r++) {
        for (int c = 0; c < n; c++) {
            double currValue = data.getEntry(r, c);
            if (currValue == 0) {
                matrix.setEntry(r, c, 0);
            } else {
                matrix.setEntry(r, c, percentile.evaluate(currValue));
            }
            //matrix.setEntry(r, c, percentile.evaluate());
        }
    }
    return matrix;
}

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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);
        }/*from w w  w  .  j a va  2 s .  c  om*/
    }
    return normalized;
}

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From source file:gda.images.camera.Utilities.java

public static RealMatrix createMatrixFromProperty(String propName) {

     RealMatrixPropertyEditor mpe = new RealMatrixPropertyEditor();
     mpe.setAsText(LocalProperties.get(propName));
     RealMatrix axisOrientationMatrix = mpe.getValue();
     if (axisOrientationMatrix.getRowDimension() != 3 || axisOrientationMatrix.getColumnDimension() != 3) {
         throw new IllegalArgumentException("Axis orientation matrix is not 33: " + axisOrientationMatrix);
     }/*from w w  w  .  java 2 s.  c o  m*/

     return axisOrientationMatrix;
 }

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From source file:juicebox.tools.utils.common.MatrixTools.java

/**
 * Flatten a 2D double matrix into a double array
 *
 * @param matrix/*w ww  .  ja v a 2 s. c  om*/
 * @return 1D double array in row major order
 */
public static double[] flattenedRowMajorOrderMatrix(RealMatrix matrix) {
    int n = matrix.getColumnDimension();
    int m = matrix.getRowDimension();
    int numElements = n * m;
    double[] flattenedMatrix = new double[numElements];

    int index = 0;
    for (int i = 0; i < m; i++) {
        System.arraycopy(matrix.getRow(i), 0, flattenedMatrix, index, n);
        index += n;
    }
    return flattenedMatrix;
}

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From source file:juicebox.tools.utils.common.MatrixTools.java

/**
 * Returns the values along the diagonal of the matrix
 *
 * @param matrix/*from   ww  w  . j  av  a 2 s .  c o  m*/
 * @return diagonal
 */
public static RealMatrix extractDiagonal(RealMatrix matrix) {
    int n = Math.min(matrix.getColumnDimension(), matrix.getRowDimension());
    RealMatrix diagonal = MatrixTools.cleanArray2DMatrix(n);
    for (int i = 0; i < n; i++) {
        diagonal.setEntry(i, i, matrix.getEntry(i, i));
    }
    return diagonal;
}

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From source file:juicebox.tools.utils.common.MatrixTools.java

/**
 * @return matrix flipped across the antidiagonal
 *///from   ww  w  . ja  va 2  s .  c  om
public static RealMatrix flipAcrossAntiDiagonal(RealMatrix matrix) {
    int n = Math.min(matrix.getColumnDimension(), matrix.getRowDimension());
    RealMatrix antiDiagFlippedMatrix = cleanArray2DMatrix(n, n);
    int maxIndex = n - 1;
    for (int i = 0; i < n; i++) {
        for (int j = 0; j < n; j++) {
            antiDiagFlippedMatrix.setEntry(maxIndex - j, maxIndex - i, matrix.getEntry(i, j));
        }
    }
    return antiDiagFlippedMatrix;
}

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From source file:juicebox.tools.utils.common.MatrixTools.java

/**
 * @return matrix flipped Left-Right// ww w .ja va  2 s .  com
 */
public static RealMatrix flipLeftRight(RealMatrix matrix) {
    int r = matrix.getRowDimension(), c = matrix.getColumnDimension();
    RealMatrix leftRightFlippedMatrix = cleanArray2DMatrix(r, c);
    for (int i = 0; i < r; i++) {
        for (int j = 0; j < c; j++) {
            leftRightFlippedMatrix.setEntry(i, c - 1 - j, matrix.getEntry(i, j));
        }
    }
    return leftRightFlippedMatrix;
}

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From source file:juicebox.tools.utils.common.MatrixTools.java

/**
 * @return matrix flipped Top-Bottom//from  www  . j av  a 2 s  .  c  o m
 */
public static RealMatrix flipTopBottom(RealMatrix matrix) {
    int r = matrix.getRowDimension(), c = matrix.getColumnDimension();
    RealMatrix topBottomFlippedMatrix = cleanArray2DMatrix(r, c);
    for (int i = 0; i < r; i++) {
        for (int j = 0; j < c; j++) {
            topBottomFlippedMatrix.setEntry(r - 1 - i, j, matrix.getEntry(i, j));
        }
    }
    return topBottomFlippedMatrix;
}

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From source file:juicebox.tools.utils.common.MatrixTools.java

/**
 * Return sign of values in matrix:/* w w  w.  ja v a  2  s.  co  m*/
 * val > 0 : 1
 * val = 0 : 0
 * val < 0 : -1
 */
public static RealMatrix sign(RealMatrix matrix) {
    int r = matrix.getRowDimension();
    int c = matrix.getColumnDimension();
    RealMatrix signMatrix = cleanArray2DMatrix(r, c);
    for (int i = 0; i < r; i++) {
        for (int j = 0; j < c; j++) {
            double val = matrix.getEntry(i, j);
            if (val > 0) {
                signMatrix.setEntry(i, j, 1);
            } else if (val < 0) {
                signMatrix.setEntry(i, j, -1);
            }
        }
    }
    return signMatrix;
}

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