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With inspiration from other libraries
/*
* 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().
*
* This class is based on a paper written by Philippe Pébay:
*
* Formulas for Robust, One-Pass Parallel Computation of Covariances and
* Arbitrary-Order Statistical Moments, 2008, Technical Report SAND2008-6212,
* Sandia National Laboratories.
*
* Note: the underlying covariance matrix is symmetric, thus only the
* upper triangular part of the matrix is stored and updated each increment.
*
* @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 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 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();
}
}