smile.clustering.linkage.Linkage Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of openchemlib Show documentation
Open Source Chemistry Library
There is a newer version: 2024.11.2
/*******************************************************************************
 * Copyright (c) 2010 Haifeng Li
 *   
 * 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 smile.clustering.linkage;

/**
 * A measure of dissimilarity between clusters (i.e. sets of observations).
 * 
 * References
 * 
 *  Anil K. Jain, Richard C. Dubes. Algorithms for clustering data. 1988. 
 * 
 * 
 * @see smile.clustering.HierarchicalClustering
 *
 * @author Haifeng Li
 */
public abstract class Linkage {
    /** The data size. */
    int size;

    /**
     * Linearized proximity matrix to store the pair-wise distance measure
     * as dissimilarity between clusters. To save space, we only need the
     * lower half of matrix. And we use float instead of double to save
     * more space, which also help speed performance. During the
     * clustering, this matrix will be updated to reflect the dissimilarity
     * of merged clusters.
     */
    float[] proximity;

    /** Initialize the linkage with the lower triangular proximity matrix. */
    void init(double[][] proximity) {
        size = proximity.length;
        this.proximity = new float[size * (size+1) / 2];

        // row wise
        /*
        for (int i = 0, k = 0; i < size; i++) {
            double[] pi = proximity[i];
            for (int j = 0; j <= i; j++, k++) {
                this.proximity[k] = (float) pi[j];
            }
        }
        */

        // column wise
        for (int j = 0, k = 0; j < size; j++) {
            for (int i = j; i < size; i++, k++) {
                this.proximity[k] = (float) proximity[i][j];
            }
        }
    }

    int index(int i, int j) {
        // row wise
        // return i > j ? i*(i+1)/2 + j : j*(j+1)/2 + i;
        // column wise
        return i > j ? proximity.length - (size-j)*(size-j+1)/2 + i - j : proximity.length - (size-i)*(size-i+1)/2 + j - i;
    }

    /** Returns the proximity matrix size. */
    public int size() {
        return size;
    }

    /**
     * Returns the distance/dissimilarity between two clusters/objects, which
     * are indexed by integers.
     */
    public float d(int i, int j) {
        return proximity[index(i, j)];
    }

    /**
     * Merge two clusters into one and update the proximity matrix.
     * @param i cluster id.
     * @param j cluster id.
     */
    public abstract void merge(int i, int j);
}