// 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]);
}
}
}
