public int testBfsDfs() {
int foo = 0;
// BFS from 1000 nodes
start = System.currentTimeMillis();
for (int i = 0; i < 1000; i++) {
Iterator<Node> bfsIt = g.getNode(nodeIds.get(i)).getBreadthFirstIterator();
while (bfsIt.hasNext()) {
Node node = bfsIt.next();
if (node.hasAttribute("foo")) foo++;
}
}
end = System.currentTimeMillis();
measureValues.put(Measures.BFS_IT, end - start);
// DFS from 1000 nodes - tested only for new implementations
// because of a bug in the old
start = System.currentTimeMillis();
if (g instanceof org.graphstream.graph.implementations.AbstractGraph) {
for (int i = 0; i < 1000; i++) {
Iterator<Node> dfsIt = g.getNode(nodeIds.get(i)).getDepthFirstIterator();
while (dfsIt.hasNext()) {
Node node = dfsIt.next();
if (node.hasAttribute("foo")) foo++;
}
}
}
end = System.currentTimeMillis();
measureValues.put(Measures.DFS_IT, end - start);
return foo;
}
public int testGraphIterators() {
int foo = 0;
// Iterating on all nodes
start = System.currentTimeMillis();
Iterator<Node> nodeIt = g.getNodeIterator();
while (nodeIt.hasNext()) {
Node n = nodeIt.next();
if (n.hasAttribute("foo")) foo++;
}
end = System.currentTimeMillis();
measureValues.put(Measures.GRAPH_NODE_IT, end - start);
// iterating on all edges
start = System.currentTimeMillis();
Iterator<Edge> edgeIt = g.getEdgeIterator();
while (edgeIt.hasNext()) {
Edge e = edgeIt.next();
if (e.hasAttribute("foo")) foo++;
}
end = System.currentTimeMillis();
measureValues.put(Measures.GRAPH_EDGE_IT, end - start);
return foo;
}
/**
* Like {@link #nodePosition(Graph,String,Point3)} but use an existing node as argument.
*
* @param node The node to consider.
* @param pos A point that will receive the node position.
*/
public static void nodePosition(Node node, Point3 pos) {
if (node.hasAttribute("xyz") || node.hasAttribute("xy")) {
Object o = node.getAttribute("xyz");
if (o == null) o = node.getAttribute("xy");
if (o != null) {
positionFromObject(o, pos);
}
} else if (node.hasAttribute("x")) {
pos.x = (double) node.getNumber("x");
if (node.hasAttribute("y")) pos.y = (double) node.getNumber("y");
if (node.hasAttribute("z")) pos.z = (double) node.getNumber("z");
}
// if (node.hasAttribute("xyz") || node.hasAttribute("xy")) {
// Object o = node.getAttribute("xyz");
//
// if (o == null)
// o = node.getAttribute("xy");
//
// if (o != null && o instanceof Object[]) {
// Object oo[] = (Object[]) o;
//
// if (oo.length > 0 && oo[0] instanceof Number) {
// pos.x = ((Number) oo[0]).doubleValue();
//
// if (oo.length > 1)
// pos.y = ((Number) oo[1]).doubleValue();
// if (oo.length > 2)
// pos.z = ((Number) oo[2]).doubleValue();
// }
// }
// } else if (node.hasAttribute("x")) {
// pos.x = (double) node.getNumber("x");
//
// if (node.hasAttribute("y"))
// pos.y = (double) node.getNumber("y");
//
// if (node.hasAttribute("z"))
// pos.z = (double) node.getNumber("z");
// }
}
/**
* Like {@link #nodePosition(Graph,String,double[])} but use an existing node as argument.
*
* @param node The node to consider.
* @param xyz An array of at least three cells.
*/
public static void nodePosition(Node node, double xyz[]) {
if (xyz.length < 3) return;
if (node.hasAttribute("xyz") || node.hasAttribute("xy")) {
Object o = node.getAttribute("xyz");
if (o == null) o = node.getAttribute("xy");
if (o != null) {
positionFromObject(o, xyz);
}
} else if (node.hasAttribute("x")) {
xyz[0] = (double) node.getNumber("x");
if (node.hasAttribute("y")) xyz[1] = (double) node.getNumber("y");
if (node.hasAttribute("z")) xyz[2] = (double) node.getNumber("z");
}
}
/**
* Compute the scores for all relevant communities for the selected node using Leung algorithm.
*
* @param u The node for which the scores computation is performed
* @complexity O(DELTA) where DELTA is is the average node degree in the network
*/
@Override
protected void communityScores(Node u) {
/*
* Reset the scores for each communities
*/
communityScores = new HashMap<Object, Double>();
/*
* Iterate over the nodes that this node "hears"
*/
for (Edge e : u.getEnteringEdgeSet()) {
Node v = e.getOpposite(u);
/*
* Update the count for this community
*/
if (v.hasAttribute(marker)) {
// Compute the neighbor node current score
Double score = (Double) v.getAttribute(marker + ".score") * Math.pow(v.getInDegree(), m);
/*
* The rest of the formula depends on the weighted status of the
* network
*/
Double weight;
if (e.hasAttribute(weightMarker))
if (e.isDirected()) {
Edge e2 = v.getEdgeToward(u.getId());
if (e2 != null && e2.hasAttribute(weightMarker))
weight =
(Double) e.getAttribute(weightMarker) + (Double) e2.getAttribute(weightMarker);
else weight = (Double) e.getAttribute(weightMarker);
} else weight = (Double) e.getAttribute(weightMarker);
else weight = 1.0;
// Update the score of the according community
if (communityScores.get(v.getAttribute(marker)) == null)
communityScores.put(v.getAttribute(marker), score * weight);
else
communityScores.put(
v.getAttribute(marker),
communityScores.get(v.getAttribute(marker)) + (score * weight));
}
}
}
@Override
public void computeNode(Node node) {
/*
* Recall and update the node current community and previous score
*/
Object previousCommunity = node.getAttribute(marker);
Double previousScore = (Double) node.getAttribute(marker + ".score");
super.computeNode(node);
/*
* Update the node label score
*/
// Handle first iteration
if (previousCommunity == null) {
previousCommunity = node.getAttribute(marker);
previousScore = (Double) node.getAttribute(marker + ".score");
}
/*
* The node is the originator of the community and hasn't changed
* community at this iteration (or we are at the first simulation step):
* keep the maximum label score
*/
if ((node.getAttribute(marker).equals(previousCommunity)) && (previousScore.equals(1.0)))
node.setAttribute(marker + ".score", 1.0);
/*
* Otherwise search for the highest score amongst neighbors and reduce
* it by decreasing factor
*/
else {
Double maxLabelScore = Double.NEGATIVE_INFINITY;
for (Edge e : node.getEnteringEdgeSet()) {
Node v = e.getOpposite(node);
if (v.hasAttribute(marker) && v.getAttribute(marker).equals(node.getAttribute(marker))) {
if ((Double) v.getAttribute(marker + ".score") > maxLabelScore)
maxLabelScore = (Double) v.getAttribute(marker + ".score");
}
}
node.setAttribute(marker + ".score", maxLabelScore - delta);
}
}
public int testAccessById() {
int foo = 0;
// access each node by id
start = System.currentTimeMillis();
for (String id : nodeIds) {
Node n = g.getNode(id);
if (n.hasAttribute("foo")) foo++;
}
end = System.currentTimeMillis();
measureValues.put(Measures.NODE_BY_ID, end - start);
// access each edge by id
start = System.currentTimeMillis();
for (String id : edgeIds) {
Edge e = g.getEdge(id);
if (e.hasAttribute("foo")) foo++;
}
end = System.currentTimeMillis();
measureValues.put(Measures.EDGE_BY_ID, end - start);
return foo;
}
public int testNodeIterators() {
int foo = 0;
// For each node n, iterating on all edges of n
start = System.currentTimeMillis();
Iterator<Node> nodeIt = g.getNodeIterator();
while (nodeIt.hasNext()) {
Node n = nodeIt.next();
Iterator<Edge> edgeIt = n.getEdgeIterator();
while (edgeIt.hasNext()) {
Edge e = edgeIt.next();
if (e.hasAttribute("foo")) foo++;
}
}
end = System.currentTimeMillis();
measureValues.put(Measures.NODE_EDGE_IT, end - start);
// For each node n, iterating on all entering edges of n
start = System.currentTimeMillis();
nodeIt = g.getNodeIterator();
while (nodeIt.hasNext()) {
Node n = nodeIt.next();
Iterator<Edge> edgeIt = n.getEnteringEdgeIterator();
while (edgeIt.hasNext()) {
Edge e = edgeIt.next();
if (e.hasAttribute("foo")) foo++;
}
}
end = System.currentTimeMillis();
measureValues.put(Measures.NODE_ENTERING_EDGE_IT, end - start);
// For each node n, iterating on all leaving edges of n
start = System.currentTimeMillis();
nodeIt = g.getNodeIterator();
while (nodeIt.hasNext()) {
Node n = nodeIt.next();
Iterator<Edge> edgeIt = n.getLeavingEdgeIterator();
while (edgeIt.hasNext()) {
Edge e = edgeIt.next();
if (e.hasAttribute("foo")) foo++;
}
}
end = System.currentTimeMillis();
measureValues.put(Measures.NODE_LEAVING_EDGE_IT, end - start);
// For each node n, iterating on all neighbors of n
start = System.currentTimeMillis();
nodeIt = g.getNodeIterator();
while (nodeIt.hasNext()) {
Node n = nodeIt.next();
Iterator<Node> neighborIt = n.getNeighborNodeIterator();
while (neighborIt.hasNext()) {
Node neighbor = neighborIt.next();
if (neighbor.hasAttribute("foo")) foo++;
}
}
end = System.currentTimeMillis();
measureValues.put(Measures.NODE_NEIGHBOR_IT, end - start);
// For each node n, iterating on all edges of n using n.getEdge(i)
start = System.currentTimeMillis();
nodeIt = g.getNodeIterator();
while (nodeIt.hasNext()) {
Node n = nodeIt.next();
for (int i = 0; i < n.getDegree(); i++) {
Edge e = n.getEdge(i);
if (e.hasAttribute("foo")) foo++;
}
}
end = System.currentTimeMillis();
measureValues.put(Measures.NODE_GET_EDGE, end - start);
return foo;
}