public Graph copy() {
WeightedArcSet list = new WeightedArcSet();
Constructor[] cons = WeightedArc.class.getDeclaredConstructors();
for (int i = 0; i < cons.length; i++) cons[i].setAccessible(true);
ArcLabelledNodeIterator it = graph.nodeIterator();
while (it.hasNext()) {
Integer aux1 = it.nextInt();
Integer aux2 = null;
ArcLabelledNodeIterator.LabelledArcIterator suc = it.successors();
while ((aux2 = suc.nextInt()) != null && aux2 >= 0 && (aux2 < graph.numNodes()))
try {
if (commit++ % COMMIT_SIZE == 0) {
list.commit();
}
WeightedArc arc = (WeightedArc) cons[0].newInstance(aux2, aux1, suc.label().getFloat());
list.add(arc);
} catch (Exception ex) {
throw new Error(ex);
}
}
Graph result = new Graph(list.toArray(new WeightedArc[0]));
result.nodes.clear();
result.nodesReverse.clear();
for (Integer n : this.nodes.keySet()) {
if (commit++ % COMMIT_SIZE == 0) {
result.commit();
}
result.nodesReverse.put(this.nodes.get(n), n);
result.nodes.put(n, this.nodes.get(n));
}
return result;
}
public Graph(WeightedBVGraph graph, String[] names) {
org.apache.log4j.Logger logger =
org.apache.log4j.Logger.getLogger("it.unimi.dsi.webgraph.ImmutableGraph");
logger.setLevel(org.apache.log4j.Level.FATAL);
if (names.length != graph.numNodes())
throw new Error("Problem with the list of names for the nodes in the graph.");
try {
File auxFile = File.createTempFile("graph-maps-" + System.currentTimeMillis(), "aux");
auxFile.deleteOnExit();
RecordManager recMan = RecordManagerFactory.createRecordManager(auxFile.getAbsolutePath());
nodes = recMan.hashMap("nodes");
nodesReverse = recMan.hashMap("nodesReverse");
} catch (IOException ex) {
throw new Error(ex);
}
nodes.clear();
nodesReverse.clear();
Constructor[] cons = WeightedArc.class.getDeclaredConstructors();
for (int i = 0; i < cons.length; i++) cons[i].setAccessible(true);
this.graph = graph;
WeightedArcSet list = new WeightedArcSet();
ArcLabelledNodeIterator it = graph.nodeIterator();
while (it.hasNext()) {
if (commit++ % COMMIT_SIZE == 0) {
commit();
list.commit();
}
Integer aux1 = it.nextInt();
Integer aux2 = null;
ArcLabelledNodeIterator.LabelledArcIterator suc = it.successors();
while ((aux2 = suc.nextInt()) != null && aux2 >= 0 && (aux2 < graph.numNodes()))
try {
WeightedArc arc = (WeightedArc) cons[0].newInstance(aux2, aux1, suc.label().getFloat());
list.add(arc);
this.nodes.put(aux1, names[aux1]);
this.nodes.put(aux2, names[aux2]);
this.nodesReverse.put(names[aux1], aux1);
this.nodesReverse.put(names[aux2], aux2);
} catch (Exception ex) {
throw new Error(ex);
}
}
reverse = new WeightedBVGraph(list.toArray(new WeightedArc[0]));
numArcs = list.size();
iterator = nodeIterator();
try {
File auxFile = File.createTempFile("graph" + System.currentTimeMillis(), "aux");
auxFile.deleteOnExit();
String basename = auxFile.getAbsolutePath();
store(basename);
} catch (IOException ex) {
throw new Error(ex);
}
commit();
}
public static Graph merge(Graph g1, Graph g2) {
int commit = 0;
WeightedArcSet list = new WeightedArcSet();
Constructor[] cons = WeightedArc.class.getDeclaredConstructors();
for (int i = 0; i < cons.length; i++) cons[i].setAccessible(true);
ArcLabelledNodeIterator it1 = g1.graph.nodeIterator();
while (it1.hasNext()) {
Integer aux1 = it1.nextInt();
ArcLabelledNodeIterator.LabelledArcIterator suc = it1.successors();
Integer aux2 = null;
while ((aux2 = suc.nextInt()) != null && aux2 >= 0 && (aux2 < g1.graph.numNodes()))
try {
WeightedArc arc = (WeightedArc) cons[0].newInstance(aux1, aux2, suc.label().getFloat());
list.add(arc);
if (commit++ % COMMIT_SIZE == 0) {
list.commit();
}
} catch (Exception ex) {
throw new Error(ex);
}
}
ArcLabelledNodeIterator it2 = g2.graph.nodeIterator();
while (it2.hasNext()) {
Integer aux1 = it2.nextInt();
ArcLabelledNodeIterator.LabelledArcIterator suc = it2.successors();
Integer aux2 = null;
while ((aux2 = suc.nextInt()) != null && aux2 >= 0 && (aux2 < g2.graph.numNodes()))
try {
int aaux1 = aux1 + g1.numNodes();
int aaux2 = aux2 + g1.numNodes();
if (g1.nodes.get(aux1) != null && g1.nodes.get(aux1).equals(g2.nodes.get(aux1)))
aaux1 = g1.nodesReverse.get(g2.nodes.get(aux1));
if (g1.nodes.get(aux2) != null && g1.nodes.get(aux2).equals(g2.nodes.get(aux2)))
aaux2 = g1.nodesReverse.get(g2.nodes.get(aux2));
WeightedArc arc = (WeightedArc) cons[0].newInstance(aux1, aux2, suc.label().getFloat());
list.add(arc);
if (commit++ % COMMIT_SIZE == 0) {
list.commit();
}
} catch (Exception ex) {
throw new Error(ex);
}
}
Graph result = new Graph(list.toArray(new WeightedArc[0]));
result.nodes.clear();
result.nodesReverse.clear();
for (Integer n : g1.nodes.keySet()) {
result.nodesReverse.put(g1.nodes.get(n), n);
result.nodes.put(n, g1.nodes.get(n));
if (commit++ % COMMIT_SIZE == 0) {
result.commit();
}
}
for (Integer n : g2.nodes.keySet()) {
int nn = n + g1.numNodes();
if (g1.nodes.get(n) != null && g1.nodes.get(n).equals(g2.nodes.get(n)))
nn = g1.nodesReverse.get(g2.nodes.get(n));
result.nodesReverse.put(g2.nodes.get(n), nn);
result.nodes.put(nn, g2.nodes.get(n));
if (commit++ % COMMIT_SIZE == 0) {
result.commit();
}
}
result.iterator = result.nodeIterator();
return result;
}
/** Computes the next step of the Power Method. */
public void step() throws IOException {
double[] oldRank = rank, newRank = previousRank;
DoubleArrays.fill(newRank, 0.0);
// for each node, calculate its outdegree and redistribute its rank among pointed nodes
double accum = 0.0;
progressLogger.expectedUpdates = numNodes;
progressLogger.start("Iteration " + (++iterationNumber) + "...");
final ArcLabelledNodeIterator nodeIterator = g.nodeIterator();
int i, outdegree, j, n = numNodes;
int[] succ;
Label[] lab;
while (n-- != 0) {
i = nodeIterator.nextInt();
outdegree = nodeIterator.outdegree();
if (outdegree == 0 || buckets != null && buckets.get(i)) accum += oldRank[i];
else {
j = outdegree;
succ = nodeIterator.successorArray();
lab = nodeIterator.labelArray();
while (j-- != 0) {
newRank[succ[j]] += (oldRank[i] * lab[j].getFloat()) / sumoutweight[i];
}
}
progressLogger.update();
}
progressLogger.done();
final double accumOverNumNodes = accum / numNodes;
final double oneOverNumNodes = 1.0 / numNodes;
if (preference != null)
if (preferentialAdjustment == null)
for (i = numNodes; i-- != 0; )
newRank[i] =
alpha * newRank[i]
+ (1 - alpha) * preference.getDouble(i)
+ alpha * accumOverNumNodes;
else
for (i = numNodes; i-- != 0; )
newRank[i] =
alpha * newRank[i]
+ (1 - alpha) * preference.getDouble(i)
+ alpha * accum * preferentialAdjustment.getDouble(i);
else if (preferentialAdjustment == null)
for (i = numNodes; i-- != 0; )
newRank[i] = alpha * newRank[i] + (1 - alpha) * oneOverNumNodes + alpha * accumOverNumNodes;
else
for (i = numNodes; i-- != 0; )
newRank[i] =
alpha * newRank[i]
+ (1 - alpha) * oneOverNumNodes
+ alpha * accum * preferentialAdjustment.getDouble(i);
// make the rank just computed the new rank
rank = newRank;
previousRank = oldRank;
// Compute derivatives.
n = iterationNumber;
if (subset == null) {
for (i = 0; i < order.length; i++) {
final int k = order[i];
final double alphak = Math.pow(alpha, k);
final double nFallingK = Util.falling(n, k);
for (j = 0; j < numNodes; j++)
derivative[i][j] += nFallingK * (rank[j] - previousRank[j]) / alphak;
}
} else {
for (i = 0; i < order.length; i++) {
final int k = order[i];
final double alphak = Math.pow(alpha, k);
final double nFallingK = Util.falling(n, k);
for (int t : subset) derivative[i][t] += nFallingK * (rank[t] - previousRank[t]) / alphak;
}
}
// Compute coefficients, if required.
if (coeffBasename != null) {
final DataOutputStream coefficients =
new DataOutputStream(
new FastBufferedOutputStream(
new FileOutputStream(coeffBasename + "-" + (iterationNumber))));
final double alphaN = Math.pow(alpha, n);
for (i = 0; i < numNodes; i++) coefficients.writeDouble((rank[i] - previousRank[i]) / alphaN);
coefficients.close();
}
}
