com.clust4j.metrics.pairwise.Pairwise.java Source code

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Here is the source code for com.clust4j.metrics.pairwise.Pairwise.java

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/*******************************************************************************
 *    Copyright 2015, 2016 Taylor G Smith
 *
 *    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 com.clust4j.metrics.pairwise;

import org.apache.commons.math3.linear.AbstractRealMatrix;

public abstract class Pairwise {
    public static double[][] getDistance(AbstractRealMatrix a, GeometricallySeparable geo, boolean upperTriang,
            boolean partial) {
        return getDistance(a.getData(), geo, upperTriang, partial);
    }

    public static double[][] getDistance(double[][] a, GeometricallySeparable geo, boolean upperTriang,
            boolean partial) {

        return pairwise(a, geo, upperTriang, partial, 1.0);
    }

    public static double[][] getSimilarity(AbstractRealMatrix a, GeometricallySeparable geo, boolean upperTriang,
            boolean partial) {
        return getSimilarity(a.getData(), geo, upperTriang, partial);
    }

    public static double[][] getSimilarity(double[][] a, GeometricallySeparable geo, boolean upperTriang,
            boolean partial) {

        return pairwise(a, geo, upperTriang, partial, -1.0);
    }

    private static double[][] pairwise(double[][] a, GeometricallySeparable geo, boolean upper, boolean partial,
            double scalar) {

        /*
         * Don't need to check dims, because that happens in each
         * getDistance call. Any non-uniformity should be handled 
         * there.
         */

        final int m = a.length;
        final double[][] out = new double[m][m];
        double dist;

        /*
         * First loop: O(M choose 2). Do computations
         */
        for (int i = 0; i < m - 1; i++) {
            for (int j = i + 1; j < m; j++) {

                dist = scalar * (partial ? geo.getPartialDistance(a[i], a[j]) : geo.getDistance(a[i], a[j]));
                out[i][j] = dist;

                // We want the full matrix
                if (!upper) {
                    out[j][i] = dist;
                }
            }
        }

        /*
         *  If we want the full matrix, we need to compute the diagonal...
         *  O(M) -- just the diagonal elements
         */
        if (!upper) {
            for (int i = 0; i < m; i++) {
                out[i][i] = scalar * (partial ? geo.getPartialDistance(a[i], a[i]) : geo.getDistance(a[i], a[i]));
            }
        }

        return out;
    }
}