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authorMatt A. Tobin <mattatobin@localhost.localdomain>2018-02-02 04:16:08 -0500
committerMatt A. Tobin <mattatobin@localhost.localdomain>2018-02-02 04:16:08 -0500
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+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+ * Class that can run the hierarchical clustering algorithm with the given
+ * parameters.
+ *
+ * @param distance
+ * Function that should return the distance between two items.
+ * Defaults to clusterlib.euclidean_distance.
+ * @param merge
+ * Function that should take in two items and return a merged one.
+ * Defaults to clusterlib.average_linkage.
+ * @param threshold
+ * The maximum distance between two items for which their clusters
+ * can be merged.
+ */
+function HierarchicalClustering(distance, merge, threshold) {
+ this.distance = distance || clusterlib.euclidean_distance;
+ this.merge = merge || clusterlib.average_linkage;
+ this.threshold = threshold == undefined ? Infinity : threshold;
+}
+
+HierarchicalClustering.prototype = {
+ /**
+ * Run the hierarchical clustering algorithm on the given items to produce
+ * a final set of clusters. Uses the parameters set in the constructor.
+ *
+ * @param items
+ * An array of "things" to cluster - this is the domain-specific
+ * collection you're trying to cluster (colors, points, etc.)
+ * @param snapshotGap
+ * How many iterations of the clustering algorithm to wait between
+ * calling the snapshotCallback
+ * @param snapshotCallback
+ * If provided, will be called as clusters are merged to let you view
+ * the progress of the algorithm. Passed the current array of
+ * clusters, cached distances, and cached closest clusters.
+ *
+ * @return An array of merged clusters. The represented item can be
+ * found in the "item" property of the cluster.
+ */
+ cluster: function HC_cluster(items, snapshotGap, snapshotCallback) {
+ // array of all remaining clusters
+ let clusters = [];
+ // 2D matrix of distances between each pair of clusters, indexed by key
+ let distances = [];
+ // closest cluster key for each cluster, indexed by key
+ let neighbors = [];
+ // an array of all clusters, but indexed by key
+ let clustersByKey = [];
+
+ // set up clusters from the initial items array
+ for (let index = 0; index < items.length; index++) {
+ let cluster = {
+ // the item this cluster represents
+ item: items[index],
+ // a unique key for this cluster, stays constant unless merged itself
+ key: index,
+ // index of cluster in clusters array, can change during any merge
+ index: index,
+ // how many clusters have been merged into this one
+ size: 1
+ };
+ clusters[index] = cluster;
+ clustersByKey[index] = cluster;
+ distances[index] = [];
+ neighbors[index] = 0;
+ }
+
+ // initialize distance matrix and cached neighbors
+ for (let i = 0; i < clusters.length; i++) {
+ for (let j = 0; j <= i; j++) {
+ var dist = (i == j) ? Infinity :
+ this.distance(clusters[i].item, clusters[j].item);
+ distances[i][j] = dist;
+ distances[j][i] = dist;
+
+ if (dist < distances[i][neighbors[i]]) {
+ neighbors[i] = j;
+ }
+ }
+ }
+
+ // merge the next two closest clusters until none of them are close enough
+ let next = null, i = 0;
+ for (; next = this.closestClusters(clusters, distances, neighbors); i++) {
+ if (snapshotCallback && (i % snapshotGap) == 0) {
+ snapshotCallback(clusters);
+ }
+ this.mergeClusters(clusters, distances, neighbors, clustersByKey,
+ clustersByKey[next[0]], clustersByKey[next[1]]);
+ }
+ return clusters;
+ },
+
+ /**
+ * Once we decide to merge two clusters in the cluster method, actually
+ * merge them. Alters the given state of the algorithm.
+ *
+ * @param clusters
+ * The array of all remaining clusters
+ * @param distances
+ * Cached distances between pairs of clusters
+ * @param neighbors
+ * Cached closest clusters
+ * @param clustersByKey
+ * Array of all clusters, indexed by key
+ * @param cluster1
+ * First cluster to merge
+ * @param cluster2
+ * Second cluster to merge
+ */
+ mergeClusters: function HC_mergeClus(clusters, distances, neighbors,
+ clustersByKey, cluster1, cluster2) {
+ let merged = { item: this.merge(cluster1.item, cluster2.item),
+ left: cluster1,
+ right: cluster2,
+ key: cluster1.key,
+ size: cluster1.size + cluster2.size };
+
+ clusters[cluster1.index] = merged;
+ clusters.splice(cluster2.index, 1);
+ clustersByKey[cluster1.key] = merged;
+
+ // update distances with new merged cluster
+ for (let i = 0; i < clusters.length; i++) {
+ var ci = clusters[i];
+ var dist;
+ if (cluster1.key == ci.key) {
+ dist = Infinity;
+ } else if (this.merge == clusterlib.single_linkage) {
+ dist = distances[cluster1.key][ci.key];
+ if (distances[cluster1.key][ci.key] >
+ distances[cluster2.key][ci.key]) {
+ dist = distances[cluster2.key][ci.key];
+ }
+ } else if (this.merge == clusterlib.complete_linkage) {
+ dist = distances[cluster1.key][ci.key];
+ if (distances[cluster1.key][ci.key] <
+ distances[cluster2.key][ci.key]) {
+ dist = distances[cluster2.key][ci.key];
+ }
+ } else if (this.merge == clusterlib.average_linkage) {
+ dist = (distances[cluster1.key][ci.key] * cluster1.size
+ + distances[cluster2.key][ci.key] * cluster2.size)
+ / (cluster1.size + cluster2.size);
+ } else {
+ dist = this.distance(ci.item, cluster1.item);
+ }
+
+ distances[cluster1.key][ci.key] = distances[ci.key][cluster1.key]
+ = dist;
+ }
+
+ // update cached neighbors
+ for (let i = 0; i < clusters.length; i++) {
+ var key1 = clusters[i].key;
+ if (neighbors[key1] == cluster1.key ||
+ neighbors[key1] == cluster2.key) {
+ let minKey = key1;
+ for (let j = 0; j < clusters.length; j++) {
+ var key2 = clusters[j].key;
+ if (distances[key1][key2] < distances[key1][minKey]) {
+ minKey = key2;
+ }
+ }
+ neighbors[key1] = minKey;
+ }
+ clusters[i].index = i;
+ }
+ },
+
+ /**
+ * Given the current state of the algorithm, return the keys of the two
+ * clusters that are closest to each other so we know which ones to merge
+ * next.
+ *
+ * @param clusters
+ * The array of all remaining clusters
+ * @param distances
+ * Cached distances between pairs of clusters
+ * @param neighbors
+ * Cached closest clusters
+ *
+ * @return An array of two keys of clusters to merge, or null if there are
+ * no more clusters close enough to merge
+ */
+ closestClusters: function HC_closestClus(clusters, distances, neighbors) {
+ let minKey = 0, minDist = Infinity;
+ for (let i = 0; i < clusters.length; i++) {
+ var key = clusters[i].key;
+ if (distances[key][neighbors[key]] < minDist) {
+ minKey = key;
+ minDist = distances[key][neighbors[key]];
+ }
+ }
+ if (minDist < this.threshold) {
+ return [minKey, neighbors[minKey]];
+ }
+ return null;
+ }
+};
+
+var clusterlib = {
+ hcluster: function hcluster(items, distance, merge, threshold, snapshotGap,
+ snapshotCallback) {
+ return (new HierarchicalClustering(distance, merge, threshold))
+ .cluster(items, snapshotGap, snapshotCallback);
+ },
+
+ single_linkage: function single_linkage(cluster1, cluster2) {
+ return cluster1;
+ },
+
+ complete_linkage: function complete_linkage(cluster1, cluster2) {
+ return cluster1;
+ },
+
+ average_linkage: function average_linkage(cluster1, cluster2) {
+ return cluster1;
+ },
+
+ euclidean_distance: function euclidean_distance(v1, v2) {
+ let total = 0;
+ for (let i = 0; i < v1.length; i++) {
+ total += Math.pow(v2[i] - v1[i], 2);
+ }
+ return Math.sqrt(total);
+ },
+
+ manhattan_distance: function manhattan_distance(v1, v2) {
+ let total = 0;
+ for (let i = 0; i < v1.length; i++) {
+ total += Math.abs(v2[i] - v1[i]);
+ }
+ return total;
+ },
+
+ max_distance: function max_distance(v1, v2) {
+ let max = 0;
+ for (let i = 0; i < v1.length; i++) {
+ max = Math.max(max, Math.abs(v2[i] - v1[i]));
+ }
+ return max;
+ }
+};