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/*******************************************************************************
 * 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;

import java.io.Serializable;
import java.util.LinkedList;
import java.util.Queue;
import smile.clustering.linkage.Linkage;
import smile.clustering.linkage.UPGMCLinkage;
import smile.clustering.linkage.WPGMCLinkage;
import smile.clustering.linkage.WardLinkage;
import smile.sort.IntHeapSelect;

/**
 * Agglomerative Hierarchical Clustering. Hierarchical agglomerative clustering
 * seeks to build a hierarchy of clusters in a bottom up approach: each
 * observation starts in its own cluster, and pairs of clusters are merged as
 * one moves up the hierarchy. The results of hierarchical clustering are
 * usually presented in a dendrogram.
 * 
 * In general, the merges are determined in a greedy manner. In order to decide
 * which clusters should be combined, a measure of dissimilarity between sets
 * of observations is required. In most methods of hierarchical clustering,
 * this is achieved by use of an appropriate metric, and a linkage criteria
 * which specifies the dissimilarity of sets as a function of the pairwise
 * distances of observations in the sets.
 * 

 * Hierarchical clustering has the distinct advantage that any valid measure
 * of distance can be used. In fact, the observations themselves are not
 * required: all that is used is a matrix of distances.
 * 
 * 
References
 * 
 * David Eppstein. Fast hierarchical clustering and other applications of dynamic closest pairs. SODA 1998.
 * 
 * 
 * @see Linkage
 * 
 * @author Haifeng Li
 */
public class HierarchicalClustering implements Serializable {
    private static final long serialVersionUID = 1L;

    /**
     * An n-1 by 2 matrix of which row i describes the merging of clusters at
     * step i of the clustering. If an element j in the row is less than n, then
     * observation j was merged at this stage. If j ≥ n then the merge
     * was with the cluster formed at the (earlier) stage j-n of the algorithm.
     */
    private int[][] merge;
    /**
     * A set of n-1 non-decreasing real values, which are the clustering height,
     * i.e., the value of the criterion associated with the clustering method
     * for the particular agglomeration.
     */
    private double[] height;

    /**
     * Constructor.
     * Learn the Agglomerative Hierarchical Clustering with given linkage
     * method, which includes proximity matrix.
     * @param linkage a linkage method to merge clusters. The linkage object
     * includes the proximity matrix of data.
     */
    public HierarchicalClustering(Linkage linkage) {
        double[][] proximity = linkage.getProximity();
        int n = proximity.length;

        merge = new int[n - 1][2];
        int[] id = new int[n];
        height = new double[n - 1];

        int[] points = new int[n];
        for (int i = 0; i < n; i++) {
            points[i] = i;
            id[i] = i;
        }

        FastPair fp = new FastPair(points, proximity);
        for (int i = 0; i < n - 1; i++) {
            height[i] = fp.getNearestPair(merge[i]);
            linkage.merge(merge[i][0], merge[i][1]);     // merge clusters into one
            fp.remove(merge[i][1]);           // drop b
            fp.updatePoint(merge[i][0]);      // and tell closest pairs about merger

            int p = merge[i][0];
            int q = merge[i][1];
            merge[i][0] = Math.min(id[p], id[q]);
            merge[i][1] = Math.max(id[p], id[q]);
            id[p] = n + i;
        }

        if (linkage instanceof UPGMCLinkage || linkage instanceof WPGMCLinkage || linkage instanceof WardLinkage) {
            for (int i = 0; i < height.length; i++) {
                height[i] = Math.sqrt(height[i]);
            }
        }
    }

    /**
     * Returns an n-1 by 2 matrix of which row i describes the merging of clusters at
     * step i of the clustering. If an element j in the row is less than n, then
     * observation j was merged at this stage. If j ≥ n then the merge
     * was with the cluster formed at the (earlier) stage j-n of the algorithm.
     */
    public int[][] getTree() {
        return merge;
    }

    /**
     * Returns a set of n-1 non-decreasing real values, which are the clustering height,
     * i.e., the value of the criterion associated with the clustering method
     * for the particular agglomeration.
     */
    public double[] getHeight() {
        return height;
    }

    /**
     * Cuts a tree into several groups by specifying the desired number.
     * @param k the number of clusters.
     * @return the cluster label of each sample.
     */
    public int[] partition(int k) {
        int n = merge.length + 1;
        int[] membership = new int[n];

        IntHeapSelect heap = new IntHeapSelect(k);
        for (int i = 2; i <= k; i++) {
            heap.add(merge[n - i][0]);
            heap.add(merge[n - i][1]);
        }

        for (int i = 0; i < k; i++) {
            bfs(membership, heap.get(i), i);
        }

        return membership;
    }

    /**
     * Cuts a tree into several groups by specifying the cut height.
     * @param h the cut height.
     * @return the cluster label of each sample.
     */
    public int[] partition(double h) {
        for (int i = 0; i < height.length - 1; i++) {
            if (height[i] > height[i + 1]) {
                throw new IllegalStateException("Non-monotonic cluster tree -- the linkage is probably not appropriate!");
            }
        }

        int n = merge.length + 1;
        int k = 2;
        for (; k <= n; k++) {
            if (height[n - k] < h) {
                break;
            }
        }

        if (k <= 2) {
            throw new IllegalArgumentException("The parameter h is too large.");
        }

        return partition(k - 1);
    }

    /**
     * BFS the merge tree and identify cluster membership.
     * @param membership the cluster membership array.
     * @param cluster the last merge point of cluster.
     * @param id the cluster ID.
     */
    private void bfs(int[] membership, int cluster, int id) {
        int n = merge.length + 1;
        Queue queue = new LinkedList<>();
        queue.offer(cluster);

        for (Integer i = queue.poll(); i != null; i = queue.poll()) {
            if (i < n) {
                membership[i] = id;
                continue;
            }

            i -= n;

            int m1 = merge[i][0];

            if (m1 >= n) {
                queue.offer(m1);
            } else {
                membership[m1] = id;
            }

            int m2 = merge[i][1];

            if (m2 >= n) {
                queue.offer(m2);
            } else {
                membership[m2] = id;
            }
        }
    }
}