/** @return the largest connected component of the graph. */
public ArrayList<Cell> getLargestConnectedComponent() {
ArrayList<ArrayList<Cell>> components = new ArrayList<>();
boolean visited[][] = new boolean[rowCount][colCount];
for (int row = 0; row < rowCount; ++row)
for (int col = 0; col < colCount; ++col) visited[row][col] = false;
Queue<Cell> q;
Cell t = null, u = null;
for (Cell c : g.vertexSet()) {
if (!visited[c.getRow()][c.getCol()]) {
q = new LinkedList<Cell>();
ArrayList<Cell> component = new ArrayList<>();
visited[c.getRow()][c.getCol()] = true;
// Find all connected nodes
q.add(c);
component.add(c);
while (!q.isEmpty()) {
t = q.remove();
for (WeightedEdge e : g.edgesOf(t)) {
u = t.equals(g.getEdgeSource(e)) ? g.getEdgeTarget(e) : g.getEdgeSource(e);
if (!visited[u.getRow()][u.getCol()]) {
visited[u.getRow()][u.getCol()] = true;
q.add(u);
component.add(u);
}
}
}
components.add(component);
}
}
int largestSize = 0, largestIndex = 0;
for (int i = 0; i < components.size(); ++i) {
if (components.get(i).size() > largestSize) {
largestSize = components.get(i).size();
largestIndex = i;
}
}
filterGraph(components.get(largestIndex));
return components.get(largestIndex);
}
public Queue<Vector2> getPathToPoint(Vector2 origin, Vector2 destination) {
LinkedList<Vector2> steps = new LinkedList<Vector2>();
Vector2 originRounded = getClosestNode(Math.round(origin.x), Math.round(origin.y));
Vector2 destinationRounded =
getClosestNode(Math.round(destination.x), Math.round(destination.y));
try {
List<DefaultWeightedEdge> list =
DijkstraShortestPath.findPathBetween(movementGraph, originRounded, destinationRounded);
for (DefaultWeightedEdge edge : list) steps.add(movementGraph.getEdgeSource(edge));
steps.add(movementGraph.getEdgeTarget(list.get(list.size() - 1)));
} catch (Exception e) {
logger.warning(
"Error pathfinding for origin="
+ originRounded
+ " destination="
+ destinationRounded
+ " with message: "
+ e.getMessage());
}
return steps;
}
/**
* Links all the spots in the selection, in time-forward order.
*
* @param model the model to modify.
* @param selectionModel the selection that contains the spots to link.
*/
public static void linkSpots(final Model model, final SelectionModel selectionModel) {
/*
* Configure tracker
*/
final TrackableObjectCollection<Spot> spots =
new DefaultTOCollection<Spot>(selectionModel.getSpotSelection());
final Map<String, Object> settings = new HashMap<String, Object>(1);
settings.put(KEY_LINKING_MAX_DISTANCE, Double.POSITIVE_INFINITY);
final NearestNeighborTracker<Spot> tracker = new NearestNeighborTracker<Spot>(spots, settings);
tracker.setNumThreads(1);
/*
* Execute tracking
*/
if (!tracker.checkInput() || !tracker.process()) {
System.err.println("Problem while computing spot links: " + tracker.getErrorMessage());
return;
}
final SimpleWeightedGraph<Spot, DefaultWeightedEdge> graph = tracker.getResult();
/*
* Copy found links in source model
*/
model.beginUpdate();
try {
for (final DefaultWeightedEdge edge : graph.edgeSet()) {
final Spot source = graph.getEdgeSource(edge);
final Spot target = graph.getEdgeTarget(edge);
model.addEdge(source, target, graph.getEdgeWeight(edge));
}
} finally {
model.endUpdate();
}
}
private void createGraphVisible() {
if (graphVisibleBodies == null) graphVisibleBodies = new ArrayList<Body>();
for (int i = 0; i < graphVisibleBodies.size(); i++)
world.destroyBody(graphVisibleBodies.get(i));
graphVisibleBodies.clear();
if (nodesVisible)
for (Vector2 node : movementGraph.vertexSet())
PhysicsHelper.createCircle(world, BodyType.StaticBody, .1f, 1, FactionType.NEUTRAL)
.setTransform(node, 0);
if (edgesVisible)
for (DefaultWeightedEdge edge : movementGraph.edgeSet()) {
Vector2 source = movementGraph.getEdgeSource(edge),
target = movementGraph.getEdgeTarget(edge);
PhysicsHelper.createEdge(
world,
BodyType.StaticBody,
source.x,
source.y,
target.x,
target.y,
1,
FactionType.NEUTRAL);
}
}
/**
* Simulate next step for the given particle.
*
* @param nextPts
* @param particleNum
*/
public void simulateForwardStep(ArrayList<Point> nextPts, Particle thisParticle) {
HashMap<Vertex, Point> thisObservedPosMap = new HashMap<Vertex, Point>();
HashMap<Vertex, AntPath> thisAntPathMap = new HashMap<Vertex, AntPath>();
thisParticle.currentFalsePositives = new ArrayList<Point>();
for (Point pt : nextPts) {
Vertex vx = new ObsVertex();
thisObservedPosMap.put(vx, pt);
}
for (AntPath ap : thisParticle.getPaths()) {
Vertex vx = new PathVertex();
thisAntPathMap.put(vx, ap);
}
/*
* Compute probability graph for this particle.
*/
SimpleWeightedGraph<Vertex, DefaultWeightedComparableEdge> probabilityGraph =
new SimpleWeightedGraph<Vertex, DefaultWeightedComparableEdge>(
DefaultWeightedComparableEdge.class);
ValueSortedMap<DefaultWeightedComparableEdge, Double> edgeMap =
new ValueSortedMap<DefaultWeightedComparableEdge, Double>(true);
computeLogProbabilityGraph(probabilityGraph, edgeMap, thisObservedPosMap, thisAntPathMap);
// displayLogProbabilityGraph(probabilityGraph,thisObservedPosMap,thisAntPathMap,vertexSums);
/*
* Generate new ant locations based on probability graph. We do this by sampling the most likely event,
* removing this event from the probability graph, updating the prob. graph, then repeating until all
* observations/causes are accounted for.
*
* To do this (relatively) efficiently, we maintain a sorted hash-map of possible observation/cause pairs.
* To avoid having to rescale the entire hash-map every step, we maintain the current sum of weights.
*
* We're also keeping track of the posterior log-probability of the simulated step.
*/
double logprob = 0;
int nfp = 0;
int nfn = 0;
int doOutput = 0;
while (edgeMap.size() > 0) {
/*
* Sample an event from the probability graph.
*/
DefaultWeightedComparableEdge event = sampleEdge(probabilityGraph, edgeMap);
edgeMap.remove(event);
double edgeWeight = probabilityGraph.getEdgeWeight(event);
double thisLogProb = edgeWeight;
logprob = logprob + thisLogProb;
Vertex v1 = probabilityGraph.getEdgeSource(event);
Vertex v2 = probabilityGraph.getEdgeTarget(event);
if (doOutput > 0) {
System.err.println("edgeWeight: " + edgeWeight);
doOutput = outputInterestingStuff(v1, v2, probabilityGraph);
}
if (v1.getClass().equals(ObsVertex.class)) {
assert (v2.getClass().equals(PathVertex.class));
Vertex tv = v1;
v1 = v2;
v2 = tv;
}
/*
* Update the probability graph.
*/
if (!v1.equals(falsePositive)) {
Set<DefaultWeightedComparableEdge> es = probabilityGraph.edgesOf(v1);
for (DefaultWeightedComparableEdge ed : es) edgeMap.remove(ed);
boolean tt = probabilityGraph.removeVertex(v1);
assert (tt);
} else {
nfp += 1;
thisParticle.currentFalsePositives.add(thisObservedPosMap.get(v2));
}
if (!v2.equals(falseNegative)) {
Set<DefaultWeightedComparableEdge> es = probabilityGraph.edgesOf(v2);
for (DefaultWeightedComparableEdge ed : es) edgeMap.remove(ed);
boolean tt = probabilityGraph.removeVertex(v2);
assert (tt);
} else nfn += 1;
// Utils.computeVertexSums(probabilityGraph,vertexSums);
/*
* Update AntPath trajectory.
*/
if (!v1.equals(falsePositive)) {
AntPath ap = thisAntPathMap.get(v1);
assert (ap != null);
Point obs = thisObservedPosMap.get(v2);
Point newPos = new Point();
double thislp = sampleConditionalPos(ap, obs, newPos) + thisLogProb;
ap.updatePosition(newPos, obs, thislp);
}
/*
* Compute likelihoods.
*/
}
}
public EdgeBetweennessGraph(WeightedMultigraph<String, DefaultWeightedEdge> originalGraph) {
super(DefaultWeightedEdge.class); // Constructor inherented from parent class
// 1. Initialize the edge betweenness digraph
// 1.1. Add vertices
for (String thisVertex : originalGraph.vertexSet()) this.addVertex(thisVertex);
// 1.2. Add edges
for (DefaultWeightedEdge thisEdge : originalGraph.edgeSet()) {
DefaultWeightedEdge newEdge = new DefaultWeightedEdge();
String sendingName = originalGraph.getEdgeSource(thisEdge);
String receivingName = originalGraph.getEdgeTarget(thisEdge);
this.addEdge(sendingName, receivingName, newEdge);
this.setEdgeWeight(newEdge, 0.0);
}
// 1.3. Create corresponding unweighted graph
// 1.3.1. Add vertices
WeightedMultigraph<String, DefaultWeightedEdge> originalUnweightedGraph =
new WeightedMultigraph<String, DefaultWeightedEdge>(DefaultWeightedEdge.class);
for (String thisVertex : originalGraph.vertexSet())
originalUnweightedGraph.addVertex(thisVertex);
// 1.3.2. Add edges
for (DefaultWeightedEdge thisEdge : originalGraph.edgeSet()) {
DefaultWeightedEdge newEdge = new DefaultWeightedEdge();
String sendingName = originalGraph.getEdgeSource(thisEdge);
String receivingName = originalGraph.getEdgeTarget(thisEdge);
originalUnweightedGraph.addEdge(sendingName, receivingName, newEdge);
originalUnweightedGraph.setEdgeWeight(newEdge, 1.0);
}
for (String thisVertex : this.vertexSet()) {
// 2. Create shortest-path graph for every vertex by Dijkstra algorithm
Multigraph<String, DefaultEdge> shortestPathDigraph =
DijkstraAlgorithm(originalUnweightedGraph, thisVertex);
// 3. Calculate the contribution of current vertex's shortest-path graph to final edge
// betweenness (Newman algorithm)
SimpleWeightedGraph<String, DefaultWeightedEdge> edgeBetweennessDigraph =
NewmanAlgorithm(shortestPathDigraph, thisVertex);
// 4. Update final edge betweenness digraph with current vertex's shortest-path graph
if (edgeBetweennessDigraph != null)
for (DefaultWeightedEdge thisEdge : edgeBetweennessDigraph.edgeSet()) {
String sourceVertex = edgeBetweennessDigraph.getEdgeSource(thisEdge);
String targetVertex = edgeBetweennessDigraph.getEdgeTarget(thisEdge);
double betweennessWeight = edgeBetweennessDigraph.getEdgeWeight(thisEdge);
DefaultWeightedEdge edgeInWholeGraph = this.getEdge(sourceVertex, targetVertex);
double newWeight = this.getEdgeWeight(edgeInWholeGraph) + betweennessWeight;
this.setEdgeWeight(edgeInWholeGraph, newWeight);
}
}
// 5. Revise the edge betweenness digraph with the original active power digraph
for (DefaultWeightedEdge thisEdge : this.edgeSet()) {
String sourceVertex = this.getEdgeSource(thisEdge);
String targetVertex = this.getEdgeTarget(thisEdge);
double betweennessWeight = this.getEdgeWeight(thisEdge);
DefaultWeightedEdge edgeInWholeGraph = originalGraph.getEdge(sourceVertex, targetVertex);
double newWeight = betweennessWeight / originalGraph.getEdgeWeight(edgeInWholeGraph);
this.setEdgeWeight(thisEdge, newWeight);
// System.out.println("Final edge betweenness between " + sourceVertex + " and " +
// targetVertex + ": " + newWeight);
}
}
// Create shortest-path graph for every vertex by depth-first traversal algorithm
private Multigraph<String, DefaultEdge> DijkstraAlgorithm(
WeightedMultigraph<String, DefaultWeightedEdge> originalGraph, String thisVertex) {
// 1. Simplify the multi-graph of the active power flow into a simple graph
SimpleWeightedGraph<String, DefaultWeightedEdge> originalSimpleGraph =
new SimpleWeightedGraph<String, DefaultWeightedEdge>(DefaultWeightedEdge.class);
for (String curVertex : originalGraph.vertexSet()) originalSimpleGraph.addVertex(curVertex);
for (DefaultWeightedEdge curEdge : originalGraph.edgeSet()) {
String sourceVertex = originalGraph.getEdgeSource(curEdge);
String targetVertex = originalGraph.getEdgeTarget(curEdge);
if (originalSimpleGraph.containsEdge(sourceVertex, targetVertex)) {
DefaultWeightedEdge modifiedEdge = originalSimpleGraph.getEdge(sourceVertex, targetVertex);
double newEdgeWeight =
originalSimpleGraph.getEdgeWeight(modifiedEdge) + originalGraph.getEdgeWeight(curEdge);
originalSimpleGraph.setEdgeWeight(modifiedEdge, newEdgeWeight);
} else {
DefaultWeightedEdge newEdge = new DefaultWeightedEdge();
originalSimpleGraph.addEdge(sourceVertex, targetVertex, newEdge);
originalSimpleGraph.setEdgeWeight(newEdge, originalGraph.getEdgeWeight(curEdge));
}
}
// Issue (2010/10/25): Maybe larger amount of active power transfer still means weaker
// relationship between the two terminal buses of a certain branch,
// thus originalSimpleGraph other than inverseGraph should be used here.
// Use the inverse of active power to build a new weighted directed graph (the larger the active
// power is, the close the two buses will be)
// SimpleDirectedWeightedGraph<String, DefaultWeightedEdge> inverseGraph =
// new SimpleDirectedWeightedGraph<String, DefaultWeightedEdge>(DefaultWeightedEdge.class);
// for (String curVertex : originalSimpleGraph.vertexSet())
// inverseGraph.addVertex(curVertex);
// for (DefaultWeightedEdge curEdge : originalSimpleGraph.edgeSet()) {
// String sourceVertex = originalSimpleGraph.getEdgeSource(curEdge);
// String targetVertex = originalSimpleGraph.getEdgeTarget(curEdge);
// DefaultWeightedEdge newEdge = new DefaultWeightedEdge();
// inverseGraph.addEdge(sourceVertex, targetVertex, newEdge);
// inverseGraph.setEdgeWeight(newEdge, 1 / originalSimpleGraph.getEdgeWeight(curEdge));
// }
// 2. Initialize the map of vertices and the corresponding weights (distance from current vertex
// to the first vertex)
HashMap<String, Double> mapVertexShortestDistance = new HashMap<String, Double>();
// for (String thisOriginalVertex : inverseGraph.vertexSet())
for (String thisOriginalVertex : originalSimpleGraph.vertexSet())
mapVertexShortestDistance.put(thisOriginalVertex, 10E10);
// The weight of the first vertex is zero
mapVertexShortestDistance.put(thisVertex, 0.0);
// 3. Depth-first traversing, update the shortest-path values
Stack<String> bfiVertices =
new Stack<String>(); // Stack to store passed vertices in a breadth-first traversing
// The map of a weighted edge and the flag of having been visited
// HashMap<DefaultWeightedEdge, Boolean> mapEdgeVisited = new HashMap<DefaultWeightedEdge,
// Boolean>();
// for (DefaultWeightedEdge thisEdge : inverseGraph.edgeSet())
// mapEdgeVisited.put(thisEdge, false);
String currentVertex = thisVertex;
bfiVertices.push(currentVertex);
// System.out.println(bfiVertices.toString());
while (!bfiVertices.isEmpty()) {
// Operate the following codes for those edges started with current vertex
boolean hasNewEdge = false;
// for (DefaultWeightedEdge curEdge : inverseGraph.outgoingEdgesOf(currentVertex)) {
for (DefaultWeightedEdge curEdge : originalSimpleGraph.edgesOf(currentVertex)) {
// if (!mapEdgeVisited.get(curEdge)) { // Used for those edges that have not been treated
// yet
// 3.1. Mark current edge as already been visited
// mapEdgeVisited.put(curEdge, true);
// String nextVertex = inverseGraph.getEdgeTarget(curEdge);
String nextVertex = originalSimpleGraph.getEdgeTarget(curEdge);
// 3.2. Update shortest-path values
double curSD = mapVertexShortestDistance.get(currentVertex);
// double edgeWeight = inverseGraph.getEdgeWeight(curEdge);
double edgeWeight = originalSimpleGraph.getEdgeWeight(curEdge);
double newSD = curSD + edgeWeight;
if (mapVertexShortestDistance.get(nextVertex) > newSD) {
hasNewEdge = true;
mapVertexShortestDistance.put(nextVertex, newSD);
// 3.3. Push the target vertex of current edge into the stack
bfiVertices.push(nextVertex);
// System.out.println(bfiVertices.toString());
break;
// System.out.println("New shortest path [" + nextVertex + "]: " + newSD);
}
// }
}
if (!hasNewEdge) {
bfiVertices.pop();
}
if (!bfiVertices.isEmpty()) currentVertex = bfiVertices.peek();
}
// 4. Create shortest-path digraph of current vertex
// 4.1. Initialize the shortest-path digraph
Multigraph<String, DefaultEdge> shortestPathGraph =
new Multigraph<String, DefaultEdge>(DefaultEdge.class);
// 4.2. Add all qualified edges
// for (DefaultWeightedEdge curEdge : inverseGraph.edgeSet()) {
for (DefaultWeightedEdge curEdge : originalSimpleGraph.edgeSet()) {
// 4.2.1. Evaluate if current edge is suitable
// String sourceVertex = inverseGraph.getEdgeSource(curEdge);
// String targetVertex = inverseGraph.getEdgeTarget(curEdge);
String sourceVertex = originalSimpleGraph.getEdgeSource(curEdge);
String targetVertex = originalSimpleGraph.getEdgeTarget(curEdge);
// if (Math.abs(inverseGraph.getEdgeWeight(curEdge) -
if (originalSimpleGraph.getEdgeWeight(curEdge) > 1.0E-5) {
if (Math.abs(
originalSimpleGraph.getEdgeWeight(curEdge)
- (mapVertexShortestDistance.get(targetVertex)
- mapVertexShortestDistance.get(sourceVertex)))
< 1.0E-5) {
// 4.2.2. Add suitable edge that found just now
DefaultEdge newEdge = new DefaultEdge();
if (!shortestPathGraph.containsVertex(sourceVertex))
shortestPathGraph.addVertex(sourceVertex);
if (!shortestPathGraph.containsVertex(targetVertex))
shortestPathGraph.addVertex(targetVertex);
shortestPathGraph.addEdge(sourceVertex, targetVertex, newEdge);
}
}
}
return shortestPathGraph;
}
