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Java example source code file (StorelessCovariance.java)

This example Java source code file (StorelessCovariance.java) is included in the alvinalexander.com "Java Source Code Warehouse" project. The intent of this project is to help you "Learn Java by Example" TM.

Learn more about this Java project at its project page.

Java - Java tags/keywords

dimensionmismatchexception, mathunsupportedoperationexception, numberistoosmallexception, override, realmatrix, storelessbivariatecovariance, storelesscovariance

The StorelessCovariance.java Java example source code

/*
 * Licensed to the Apache Software Foundation (ASF) under one or more
 * contributor license agreements.  See the NOTICE file distributed with
 * this work for additional information regarding copyright ownership.
 * The ASF licenses this file to You under the Apache License, Version 2.0
 * (the "License"); you may not use this file except in compliance with
 * the License.  You may obtain a copy of the License at
 *
 *      http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package org.apache.commons.math3.stat.correlation;

import org.apache.commons.math3.exception.DimensionMismatchException;
import org.apache.commons.math3.exception.MathUnsupportedOperationException;
import org.apache.commons.math3.exception.NumberIsTooSmallException;
import org.apache.commons.math3.linear.MatrixUtils;
import org.apache.commons.math3.linear.RealMatrix;

/**
 * Covariance implementation that does not require input data to be
 * stored in memory. The size of the covariance matrix is specified in the
 * constructor. Specific elements of the matrix are incrementally updated with
 * calls to incrementRow() or increment Covariance().
 *
 * <p>This class is based on a paper written by Philippe Pébay:
 * <a href="http://prod.sandia.gov/techlib/access-control.cgi/2008/086212.pdf">
 * Formulas for Robust, One-Pass Parallel Computation of Covariances and
 * Arbitrary-Order Statistical Moments</a>, 2008, Technical Report SAND2008-6212,
 * Sandia National Laboratories.</p>
 *
 * <p>Note: the underlying covariance matrix is symmetric, thus only the
 * upper triangular part of the matrix is stored and updated each increment.</p>
 *
 * @since 3.0
 */
public class StorelessCovariance extends Covariance {

    /** the square covariance matrix (upper triangular part) */
    private StorelessBivariateCovariance[] covMatrix;

    /** dimension of the square covariance matrix */
    private int dimension;

    /**
     * Create a bias corrected covariance matrix with a given dimension.
     *
     * @param dim the dimension of the square covariance matrix
     */
    public StorelessCovariance(final int dim) {
        this(dim, true);
    }

    /**
     * Create a covariance matrix with a given number of rows and columns and the
     * indicated bias correction.
     *
     * @param dim the dimension of the covariance matrix
     * @param biasCorrected if <code>true the covariance estimate is corrected
     * for bias, i.e. n-1 in the denominator, otherwise there is no bias correction,
     * i.e. n in the denominator.
     */
    public StorelessCovariance(final int dim, final boolean biasCorrected) {
        dimension = dim;
        covMatrix = new StorelessBivariateCovariance[dimension * (dimension + 1) / 2];
        initializeMatrix(biasCorrected);
    }

    /**
     * Initialize the internal two-dimensional array of
     * {@link StorelessBivariateCovariance} instances.
     *
     * @param biasCorrected if the covariance estimate shall be corrected for bias
     */
    private void initializeMatrix(final boolean biasCorrected) {
        for(int i = 0; i < dimension; i++){
            for(int j = 0; j < dimension; j++){
                setElement(i, j, new StorelessBivariateCovariance(biasCorrected));
            }
        }
    }

    /**
     * Returns the index (i, j) translated into the one-dimensional
     * array used to store the upper triangular part of the symmetric
     * covariance matrix.
     *
     * @param i the row index
     * @param j the column index
     * @return the corresponding index in the matrix array
     */
    private int indexOf(final int i, final int j) {
        return j < i ? i * (i + 1) / 2 + j : j * (j + 1) / 2 + i;
    }

    /**
     * Gets the element at index (i, j) from the covariance matrix
     * @param i the row index
     * @param j the column index
     * @return the {@link StorelessBivariateCovariance} element at the given index
     */
    private StorelessBivariateCovariance getElement(final int i, final int j) {
        return covMatrix[indexOf(i, j)];
    }

    /**
     * Sets the covariance element at index (i, j) in the covariance matrix
     * @param i the row index
     * @param j the column index
     * @param cov the {@link StorelessBivariateCovariance} element to be set
     */
    private void setElement(final int i, final int j,
                            final StorelessBivariateCovariance cov) {
        covMatrix[indexOf(i, j)] = cov;
    }

    /**
     * Get the covariance for an individual element of the covariance matrix.
     *
     * @param xIndex row index in the covariance matrix
     * @param yIndex column index in the covariance matrix
     * @return the covariance of the given element
     * @throws NumberIsTooSmallException if the number of observations
     * in the cell is < 2
     */
    public double getCovariance(final int xIndex,
                                final int yIndex)
        throws NumberIsTooSmallException {

        return getElement(xIndex, yIndex).getResult();

    }

    /**
     * Increment the covariance matrix with one row of data.
     *
     * @param data array representing one row of data.
     * @throws DimensionMismatchException if the length of <code>rowData
     * does not match with the covariance matrix
     */
    public void increment(final double[] data)
        throws DimensionMismatchException {

        int length = data.length;
        if (length != dimension) {
            throw new DimensionMismatchException(length, dimension);
        }

        // only update the upper triangular part of the covariance matrix
        // as only these parts are actually stored
        for (int i = 0; i < length; i++){
            for (int j = i; j < length; j++){
                getElement(i, j).increment(data[i], data[j]);
            }
        }

    }

    /**
     * Appends {@code sc} to this, effectively aggregating the computations in {@code sc}
     * with this.  After invoking this method, covariances returned should be close
     * to what would have been obtained by performing all of the {@link #increment(double[])}
     * operations in {@code sc} directly on this.
     *
     * @param sc externally computed StorelessCovariance to add to this
     * @throws DimensionMismatchException if the dimension of sc does not match this
     * @since 3.3
     */
    public void append(StorelessCovariance sc) throws DimensionMismatchException {
        if (sc.dimension != dimension) {
            throw new DimensionMismatchException(sc.dimension, dimension);
        }

        // only update the upper triangular part of the covariance matrix
        // as only these parts are actually stored
        for (int i = 0; i < dimension; i++) {
            for (int j = i; j < dimension; j++) {
                getElement(i, j).append(sc.getElement(i, j));
            }
        }
    }

    /**
     * {@inheritDoc}
     * @throws NumberIsTooSmallException if the number of observations
     * in a cell is < 2
     */
    @Override
    public RealMatrix getCovarianceMatrix() throws NumberIsTooSmallException {
        return MatrixUtils.createRealMatrix(getData());
    }

    /**
     * Return the covariance matrix as two-dimensional array.
     *
     * @return a two-dimensional double array of covariance values
     * @throws NumberIsTooSmallException if the number of observations
     * for a cell is < 2
     */
    public double[][] getData() throws NumberIsTooSmallException {
        final double[][] data = new double[dimension][dimension];
        for (int i = 0; i < dimension; i++) {
            for (int j = 0; j < dimension; j++) {
                data[i][j] = getElement(i, j).getResult();
            }
        }
        return data;
    }

    /**
     * This {@link Covariance} method is not supported by a {@link StorelessCovariance},
     * since the number of bivariate observations does not have to be the same for different
     * pairs of covariates - i.e., N as defined in {@link Covariance#getN()} is undefined.
     *
     * @return nothing as this implementation always throws a
     * {@link MathUnsupportedOperationException}
     * @throws MathUnsupportedOperationException in all cases
     */
    @Override
    public int getN()
        throws MathUnsupportedOperationException {
        throw new MathUnsupportedOperationException();
    }
}

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