/**
* Positions the nodes on the layout according to the results of numerous iterations of the
* Kamada-Kawai spring-embedding algorithm. Essentially, the network is modeled as a collection of
* nodes connected by springs with resting lengths proportional to the length of the shortest path
* distance between each node pair. Nodes are normally positioned in a circle, and then each node
* in sequence is repositioned until the "energy" of all of its springs are minimized to a
* parameter value epsilon. The location of the local minima for each node is estimated with
* iterations of a Newtown-Raphson steepest descent method. Repositioning ceases when all nodes
* have energy below epsilon. In this implementation, epsilon is initialized at a high value, and
* than decreased as in simulated annealing. the layout SHOULD stop when a low value (epsilon < 1)
* is reached or when energies of nodes can now longer be decreased.
*
* <p>Note: In the current implementation the layout may not always converge! however, the
* maxPasses parameter can be set lower to interrupt cycling layouts. Also has not been tested/
* implemented on weighted graphs. The Kamada-Kawai algorithm was not intended to run on
* disconnected graphs (graphs with multiple components. The kludgy solution implemented here is
* to run the algorithm independently on each of the components (of size > 1). This is somewhat
* unsatisfactory as the components will often overlap.
*
* <p>The KK algorithm is relatively slow, especially on the first round. However, it often
* discovers layouts of regularly structured graphs which are "better" and more repeatable than
* the Fruchmen-Reingold technique. Implementation of the numerics of the Newton-Raphson method
* follows Shawn Lorae Stutzman, Auburn University, 12/12/96 <A
* href="http://mathcs.mta.ca/research/rosebrugh/gdct/javasource.htm">
* http://mathcs.mta.ca/research/rosebrugh/gdct/javasource.htm</A>
*
* <p>Kamada, Tomihisa and Satoru Kawai (1989) "An Algorithm for Drawing Undirected Graphs" <CITE>
* Information Processing Letters</CITE> 31:7-15
*/
public void updateLayout() {
// check that layout should be drawn
if (update) {
isEventThread = SwingUtilities.isEventDispatchThread();
stop = false;
if (circleLayout) {
// give nodes circular initial coord to begin with
circleLayout();
}
if (firstLayout) {
firstLayout = false;
circleLayout();
}
// runs kk algorithm on each component individualy
ArrayList components = NetUtilities.getComponents(nodeList);
Iterator compIter = components.iterator();
while (compIter.hasNext() && !stop) {
ArrayList comp = (ArrayList) compIter.next();
if (comp.size() > 1) runKamadaOn(comp);
}
// rescale node positions to fit in window
if (rescaleLayout) rescalePositions(nodeList);
}
}
// RENORM COORDS TO 0-1 range before running ?
private void runKamadaOn(ArrayList componentNodes) {
int nNodes = componentNodes.size();
// sets up the matrix of path distances
DenseDoubleMatrix2D distMatrix = NetUtilities.getAllShortPathMatrix(componentNodes);
// sets up kmatrix of forces
DenseDoubleMatrix2D kMatrix = calcKMatrix(distMatrix, springConst);
// calc desired distance between nodes
double optDist = Math.min(width, height) / Math.max(getDiam(distMatrix), 1);
// sets up lMatrix of distance between nodes pairs
DenseDoubleMatrix2D lMatrix = calcLMatrix(distMatrix, optDist);
// arrays for quick acess to node coords
double[] xPos = new double[nNodes];
double[] yPos = new double[nNodes];
int numEdges = 0;
for (int i = 0; i < nNodes; i++) {
DrawableNonGridNode workNode = (DrawableNonGridNode) componentNodes.get(i);
xPos[i] = workNode.getX();
yPos[i] = workNode.getY();
numEdges += ((ArrayList) workNode.getOutEdges()).size();
}
// calc value to start minimization from (should be based on previous?)
// epsilon = (nNodes * numEdges)/2;
// figure out the initial stat to compare to at the end
double initialEnergy = getEnergy(lMatrix, kMatrix, xPos, yPos);
double epsilon = initialEnergy / nNodes;
// figure out which node to start moving first
double deltaM;
int maxDeltaMIndex = 0;
double maxDeltaM = getDeltaM(0, lMatrix, kMatrix, xPos, yPos);
for (int i = 1; i < nNodes; i++) {
deltaM = getDeltaM(i, lMatrix, kMatrix, xPos, yPos);
if (deltaM > maxDeltaM) {
maxDeltaM = deltaM;
maxDeltaMIndex = i;
}
}
int passes = 0;
int subPasses = 0;
// epsilon minimizing loop
while ((epsilon > minEpsilon) && !stop) {
double previousMaxDeltaM = maxDeltaM + 1;
// KAMADA-KAWAI LOOP: while the deltaM of the node with
// the largest deltaM > epsilon..
while ((maxDeltaM > epsilon) && ((previousMaxDeltaM - maxDeltaM) > 0.1) && !stop) {
double[] deltas;
double moveNodeDeltaM = maxDeltaM;
// double previousDeltaM = moveNodeDeltaM + 1;
// KK INNER LOOP while the node with the largest energy > epsilon...
while ((moveNodeDeltaM > epsilon) && !stop) {
// get the deltas which will move node towards the local minima
deltas = getDeltas(maxDeltaMIndex, lMatrix, kMatrix, xPos, yPos);
// set coords of node to old coords + changes
xPos[maxDeltaMIndex] += deltas[0];
yPos[maxDeltaMIndex] += deltas[1];
// previousDeltaM = moveNodeDeltaM;
// recalculate the deltaM of the node w/ new vals
moveNodeDeltaM = getDeltaM(maxDeltaMIndex, lMatrix, kMatrix, xPos, yPos);
subPasses++;
if (subPasses > maxPasses) stop = true;
}
// previousDeltaM = maxDeltaM;
// recalculate deltaMs and find node with max
maxDeltaMIndex = 0;
maxDeltaM = getDeltaM(0, lMatrix, kMatrix, xPos, yPos);
for (int i = 1; i < nNodes; i++) {
deltaM = getDeltaM(i, lMatrix, kMatrix, xPos, yPos);
if (deltaM > maxDeltaM) {
maxDeltaM = deltaM;
maxDeltaMIndex = i;
}
}
// if set to update display, update on every nth pass
if (updates > 0) {
if ((passes % updates) == 0) {
for (int i = 0; i < nNodes; i++) {
DrawableNonGridNode node = (DrawableNonGridNode) componentNodes.get(i);
node.setX(xPos[i]);
node.setY(yPos[i]);
}
updateDisplay();
}
}
passes++;
}
epsilon -= epsilon / 4;
}
if (animate) animateTransition(8, componentNodes, xPos, yPos);
else {
// set positions of nodes to coord array vals
for (int i = 0; i < nNodes; i++) {
DrawableNonGridNode node = (DrawableNonGridNode) componentNodes.get(i);
node.setX(xPos[i]);
node.setY(yPos[i]);
}
}
}