public void newmanCluster(ItemRegistry registry) {
DoubleMatrix2D distance_matrix =
DoubleFactory2D.sparse.make(
registry.getGraph().getNodeCount(), registry.getGraph().getNodeCount());
DoubleMatrix1D a_matrix = DoubleFactory1D.dense.make(registry.getGraph().getNodeCount(), 0.);
Map<String, Cluster> cluster_map = new HashMap<String, Cluster>();
// construct the leaf node distance matrix
Iterator edge_iter = registry.getGraph().getEdges();
m_total_distances = 0.;
while (edge_iter.hasNext()) {
Edge edge = (Edge) edge_iter.next();
Cluster clust1 = (Cluster) edge.getFirstNode();
Cluster clust2 = (Cluster) edge.getSecondNode();
if (cluster_map.get(clust1.getAttribute("id")) == null) {
cluster_map.put(clust1.getAttribute("id"), clust1);
}
if (cluster_map.get(clust2.getAttribute("id")) == null) {
cluster_map.put(clust2.getAttribute("id"), clust2);
}
int n = Integer.parseInt(clust1.getAttribute("id"));
int m = Integer.parseInt(clust2.getAttribute("id"));
// make reciprocal (big values = good in newman, but not in our case)
double dist = 1 / clust1.getCenter().distance(clust2.getCenter());
distance_matrix.set(Math.max(n, m), Math.min(n, m), dist);
// m_total_distances += dist;
// a_matrix.setQuick( n, a_matrix.getQuick( n ) + dist );
// a_matrix.setQuick( m, a_matrix.getQuick( m ) + dist );
m_total_distances += 1;
a_matrix.setQuick(n, a_matrix.getQuick(n) + 1);
a_matrix.setQuick(m, a_matrix.getQuick(m) + 1);
}
// System.out.println(distance_matrix);
// System.out.println(count_matrix);
// agglomerate nodes until we reach a root node (or nodes)
boolean done = false;
int trash = 0;
QFinder qfinder = new QFinder();
qfinder.a_matrix = a_matrix;
QMerger qmerger = new QMerger();
while (!done) {
// find the minimum cluster distance
qfinder.reset();
distance_matrix.forEachNonZero(qfinder);
// done = true;
// System.out.println(distance_matrix);
// System.out.println(count_matrix);
if (qfinder.getVal() == -Double.MAX_VALUE) {
break;
}
// add a parent cluster to the graph
Cluster clust1 = cluster_map.get("" + qfinder.getM());
Cluster clust2 = cluster_map.get("" + qfinder.getN());
while (clust1.getParent() != null) {
clust1 = clust1.getParent();
}
while (clust2.getParent() != null) {
clust2 = clust2.getParent();
}
trash++;
double dist = Math.max(clust1.getHeight(), clust2.getHeight());
Cluster new_cluster =
new DefaultCluster(
(float) (clust1.getCenter().getX() + clust2.getCenter().getX()) / 2.f,
(float) (clust1.getCenter().getY() + clust2.getCenter().getY()) / 2.f,
(float)
Math.sqrt(
clust1.getRadius() * clust1.getRadius()
+ clust2.getRadius() * clust2.getRadius()),
clust1,
clust2,
dist);
registry.getGraph().addNode(new_cluster);
// merge the clusters distances / counts
int M = Math.max(qfinder.getM(), qfinder.getN());
int N = Math.min(qfinder.getM(), qfinder.getN());
a_matrix.set(N, a_matrix.getQuick(M) + a_matrix.getQuick(N));
a_matrix.set(M, 0);
// System.out.println("M = "+M+" N = "+N + " VAL=" + minfinder.getVal() );
qmerger.setM(M);
qmerger.setN(N);
qmerger.setParent(distance_matrix);
qmerger.setMode(true);
// System.out.println(distance_matrix.viewPart( 0, M, distance_matrix.rows(), 1));
distance_matrix.viewPart(0, M, distance_matrix.rows(), 1).forEachNonZero(qmerger);
qmerger.setMode(false);
// System.out.println(distance_matrix.viewPart( M, 0, 1, M ));
distance_matrix.viewPart(M, 0, 1, M).forEachNonZero(qmerger);
// System.out.println(distance_matrix);
// System.out.println(count_matrix);
// free any superfluous memory randomly ~ (1/20) times
if (Math.random() > 0.95) {
distance_matrix.trimToSize();
}
}
}
public void shortestDistance(ItemRegistry registry) {
// System.out.println(""+registry.getGraph().getNodeCount());
DoubleMatrix2D distance_matrix =
DoubleFactory2D.sparse.make(
registry.getGraph().getNodeCount(), registry.getGraph().getNodeCount());
DoubleMatrix2D count_matrix =
DoubleFactory2D.sparse.make(
registry.getGraph().getNodeCount(), registry.getGraph().getNodeCount());
Map<String, Cluster> cluster_map = new HashMap<String, Cluster>();
// construct the leaf node distance matrix
Iterator edge_iter = registry.getGraph().getEdges();
while (edge_iter.hasNext()) {
Edge edge = (Edge) edge_iter.next();
Cluster clust1 = (Cluster) edge.getFirstNode();
Cluster clust2 = (Cluster) edge.getSecondNode();
if (cluster_map.get(clust1.getAttribute("id")) == null) {
cluster_map.put(clust1.getAttribute("id"), clust1);
}
if (cluster_map.get(clust2.getAttribute("id")) == null) {
cluster_map.put(clust2.getAttribute("id"), clust2);
}
int n = Integer.parseInt(clust1.getAttribute("id"));
int m = Integer.parseInt(clust2.getAttribute("id"));
double dist = clust1.getCenter().distance(clust2.getCenter());
distance_matrix.set(Math.max(n, m), Math.min(n, m), dist);
count_matrix.set(Math.max(n, m), Math.min(n, m), 1);
}
// System.out.println(distance_matrix);
// System.out.println(count_matrix);
// agglomerate nodes until we reach a root node (or nodes)
boolean done = false;
MinFinder minfinder = new MinFinder();
minfinder.count_matrix = count_matrix;
Merger merger = new Merger();
while (!done) {
// find the minimum cluster distance
minfinder.reset();
distance_matrix.forEachNonZero(minfinder);
// done = true;
// System.out.println(distance_matrix);
// System.out.println(count_matrix);
if (minfinder.getVal() == Double.MAX_VALUE) {
break;
}
// add a parent cluster to the graph
Cluster clust1 = cluster_map.get("" + minfinder.getM());
Cluster clust2 = cluster_map.get("" + minfinder.getN());
while (clust1.getParent() != null) {
clust1 = clust1.getParent();
}
while (clust2.getParent() != null) {
clust2 = clust2.getParent();
}
// System.out.println("HERE!");
Cluster new_cluster =
new DefaultCluster(
(float) (clust1.getCenter().getX() + clust2.getCenter().getX()) / 2.f,
(float) (clust1.getCenter().getY() + clust2.getCenter().getY()) / 2.f,
(float)
Math.sqrt(
clust1.getRadius() * clust1.getRadius()
+ clust2.getRadius() * clust2.getRadius()),
clust1,
clust2,
minfinder.getVal());
registry.getGraph().addNode(new_cluster);
// merge the clusters distances / counts
int M = Math.max(minfinder.getM(), minfinder.getN());
int N = Math.min(minfinder.getM(), minfinder.getN());
// System.out.println("M = "+M+" N = "+N + " VAL=" + minfinder.getVal() );
merger.setM(M);
merger.setN(N);
merger.setParent(distance_matrix);
merger.setMode(true);
// System.out.println(distance_matrix.viewPart( 0, M, distance_matrix.rows(), 1));
distance_matrix.viewPart(0, M, distance_matrix.rows(), 1).forEachNonZero(merger);
merger.setMode(false);
// System.out.println(distance_matrix.viewPart( M, 0, 1, M ));
distance_matrix.viewPart(M, 0, 1, M).forEachNonZero(merger);
merger.setParent(count_matrix);
merger.setMode(true);
count_matrix.viewPart(0, M, count_matrix.rows(), 1).forEachNonZero(merger);
merger.setMode(false);
count_matrix.viewPart(M, 0, 1, M).forEachNonZero(merger);
// System.out.println(distance_matrix);
// System.out.println(count_matrix);
// free any superfluous memory randomly ~ (1/20) times
if (Math.random() > 0.95) {
distance_matrix.trimToSize();
}
}
}