org.wallerlab.yoink.math.linear.CommonsMatrix.java Source code

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Here is the source code for org.wallerlab.yoink.math.linear.CommonsMatrix.java

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/*
 * Copyright 2014-2015 the original author or authors.
 *
 * Licensed 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.wallerlab.yoink.math.linear;

import org.apache.commons.math3.geometry.euclidean.threed.Vector3D;
import org.apache.commons.math3.linear.Array2DRowRealMatrix;
import org.apache.commons.math3.linear.ArrayRealVector;
import org.apache.commons.math3.linear.MatrixUtils;
import org.apache.commons.math3.linear.RealMatrix;
import org.apache.commons.math3.linear.RealVector;
import org.wallerlab.yoink.api.service.math.Matrix;

/**
 * Matrix Adaptor pattern.
 * 
 * this class i sto convert from our own implementation to the appache commons
 * maths lib.
 * 
 * @author Min Zheng
 *
 */

public class CommonsMatrix implements Matrix<RealMatrix> {

    private RealMatrix internalMatrix;

    // this matrix is used as intermediate matrix in internalMatrix operation.
    private RealMatrix tempMatrix;

    public CommonsMatrix() {
        this.internalMatrix = new Array2DRowRealMatrix();
    }

    public CommonsMatrix(int rowDimension, int columnDimension) {
        this.internalMatrix = MatrixUtils.createRealMatrix(rowDimension, columnDimension);
    }

    @Override
    public void array2DRowRealMatrix(double[][] d) {
        this.internalMatrix = new Array2DRowRealMatrix(d);

    }

    @Override
    public void setEntry(int row, int column, double value) {
        this.internalMatrix.setEntry(row, column, value);

    }

    @Override
    public void addToEntry(int row, int column, double value) {
        this.internalMatrix.addToEntry(row, column, value);

    }

    @Override
    public double getEntry(int row, int column) {

        return this.internalMatrix.getEntry(row, column);
    }

    @SuppressWarnings({ "rawtypes", "unchecked" })
    @Override
    public Matrix transpose() {

        tempMatrix = this.internalMatrix.transpose();
        Matrix newMatrix = new CommonsMatrix();
        newMatrix.setInternalMatrix(tempMatrix);
        return newMatrix;

    }

    @Override
    public Matrix add(Matrix m) {
        tempMatrix = this.internalMatrix.add((RealMatrix) m.getInternalMatrix());
        Matrix newMatrix = new CommonsMatrix();
        newMatrix.setInternalMatrix(tempMatrix);
        return newMatrix;
    }

    @Override
    public Matrix subtract(Matrix m) {
        tempMatrix = this.internalMatrix.subtract((RealMatrix) m.getInternalMatrix());
        Matrix newMatrix = new CommonsMatrix();
        newMatrix.setInternalMatrix(tempMatrix);
        return newMatrix;
    }

    @Override
    public Matrix scalarMultiply(double d) {
        tempMatrix = this.internalMatrix.scalarMultiply(d);
        Matrix newMatrix = new CommonsMatrix();
        newMatrix.setInternalMatrix(tempMatrix);
        return newMatrix;
    }

    // when the matrix is a 3D vector
    @Override
    public double dotProduct() {
        double[] v = this.internalMatrix.getRow(0);
        Vector3D vector = new Vector3D(v);
        return vector.dotProduct(vector);
    }

    @Override
    public double[][] getData() {
        return this.internalMatrix.getData();
    }

    @Override
    public double[] getRow(int i) {
        return this.internalMatrix.getRow(i);
    }

    public RealMatrix getInternalMatrix() {
        return internalMatrix;
    }

    public void setInternalMatrix(RealMatrix internalMatrix) {
        this.internalMatrix = internalMatrix;
    }

    /**
     * Element-by-element multiplication of two 3D vectors.
     */
    @Override
    public Matrix ebeMultiply(Matrix m) {
        double[] v1 = this.internalMatrix.getRow(0);
        RealVector vector1 = new ArrayRealVector(v1);
        double[] v2 = ((RealMatrix) m.getInternalMatrix()).getRow(0);
        RealVector vector2 = new ArrayRealVector(v2);
        RealVector vectorEBE = vector1.ebeMultiply(vector2);
        double[] vEBE = vectorEBE.toArray();
        tempMatrix = MatrixUtils.createRealMatrix(1, 3);
        tempMatrix.setRow(0, vEBE);
        Matrix newMatrix = new CommonsMatrix();
        newMatrix.setInternalMatrix(tempMatrix);
        return newMatrix;
    }

    // when the matrix is a 3D vector
    @Override
    public double distance(Matrix m) {
        double[] v1 = this.internalMatrix.getRow(0);
        Vector3D vector1 = new Vector3D(v1);
        double[] v2 = ((RealMatrix) m.getInternalMatrix()).getRow(0);
        Vector3D vector2 = new Vector3D(v2);
        return vector1.distance(vector2);
    }

    @Override
    public double getNorm() {
        double[] v1 = this.internalMatrix.getRow(0);
        Vector3D vector1 = new Vector3D(v1);
        return vector1.getNorm();
    }

    @Override
    public boolean equals(Matrix m) {
        return this.internalMatrix.equals(m.getInternalMatrix());
    }

}