public Graph createGraph(Clustering[] clusts) {
Clustering c = clusts[0];
// total number of items
int n = c.instancesCount();
Graph graph = new AdjListGraph();
Object2LongOpenHashMap<Instance> mapping = new Object2LongOpenHashMap();
Instance a, b;
Node na, nb;
// cluster membership
int ca, cb;
int x = 0;
Edge edge;
// accumulate evidence
for (Clustering clust : clusts) {
System.out.println("reducing " + (x++));
for (int i = 1; i < n; i++) {
a = clust.instance(i);
na = fetchNode(graph, mapping, a);
ca = clust.assignedCluster(a.getIndex());
for (int j = 0; j < i; j++) {
b = clust.instance(j);
nb = fetchNode(graph, mapping, b);
// for each pair of instances check if placed in the same cluster
cb = clust.assignedCluster(b.getIndex());
if (ca == cb) {
edge = graph.getEdge(na, nb);
// check if exists
if (edge == null) {
edge = graph.getFactory().newEdge(na, nb, 0, 0, false);
graph.addEdge(edge);
}
// increase weight by 1
edge.setWeight(edge.getWeight() + 1.0);
}
}
}
}
return graph;
}
@Override
public Clustering updateCutoff(double cutoff) {
this.cutoff = cutoff;
int[] assign = new int[dataset.size()];
int estClusters = (int) Math.sqrt(dataset.size());
colorGenerator.reset();
num = 0; // human readable
Clustering clusters = new ClusterList(estClusters);
DendroNode root = treeData.getRoot();
if (root != null) {
checkCutoff(root, cutoff, clusters, assign);
if (clusters.size() > 0) {
mapping = assign;
} else {
LOG.info("failed to cutoff dendrogram, cut = {}", cutoff);
}
}
// add input dataset to clustering lookup
if (noise != null) {
Cluster clust = new BaseCluster<>(noise.size());
clust.setColor(colorGenerator.next());
clust.setClusterId(num++);
clust.setParent(getDataset());
clust.setName("Noise");
clust.setAttributes(getDataset().getAttributes());
for (Instance ins : noise) {
clust.add(ins);
mapping[ins.getIndex()] = num - 1;
}
clusters.add(clust);
}
clusters.lookupAdd(dataset);
if (dendroMapping != null) {
clusters.lookupAdd(dendroMapping);
}
clusters.lookupAdd(this);
return clusters;
}