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/*
 * Copyright (c) 2010-2025 Haifeng Li. All rights reserved.
 *
 * Smile is free software: you can redistribute it and/or modify it
 * under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * Smile is distributed in the hope that it will be useful, but
 * WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with Smile. If not, see .
 */
package smile.clustering;

import java.io.Serial;
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
 *
 * @param tree the hierarchical cluster tree. 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 {@code j >= n} then the merge was with the cluster formed
 *             at the (earlier) stage j-n of the algorithm.
 * @param height the clustering height. A set of n-1 non-decreasing real values,
 *               which are the value of the criterion associated with the
 *               clustering method for the particular agglomeration.
 * @author Haifeng Li
 */
public record HierarchicalClustering(int[][] tree, double[] height) implements Serializable {
    @Serial
    private static final long serialVersionUID = 3L;

    /**
     * Fits 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.
     * @return the model.
     */
    public static HierarchicalClustering fit(Linkage linkage) {
        int n = linkage.size();

        int[][] merge = new int[n - 1][2];
        int[] id = new int[n];
        double[] 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, linkage);
        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 the 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]);
            }
        }

        return new HierarchicalClustering(merge, 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 = tree.length + 1;
        int[] membership = new int[n];

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

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

            int m2 = tree[i][1];

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