@Override
public void execute(GraphModel graphModel, AttributeModel attributeModel) {
// Graph graph = graphModel.getGraphVisible();
HierarchicalGraph graph = null;
// get visible graph
if (directed) {
graph = graphModel.getHierarchicalDirectedGraphVisible();
} else {
graph = graphModel.getHierarchicalUndirectedGraphVisible();
}
// lock graph
graph.readLock();
try {
Progress.start(progressTicket, graph.getNodeCount());
// all coefficients
nodeCoefficients = new double[graph.getNodeCount()];
// attribute column
AttributeTable nodeTable = attributeModel.getNodeTable();
AttributeColumn clusteringColumn = nodeTable.getColumn("newClusteringCoefficient");
if (clusteringColumn == null) {
clusteringColumn =
nodeTable.addColumn(
"newClusteringCoefficient",
"Local Clustering Coefficient",
AttributeType.DOUBLE,
AttributeOrigin.COMPUTED,
0.0);
}
int i = 0;
// for each node
for (Node e : graph.getNodes()) {
// compute coefficient
double coeficient = 0.0;
double denominator = (graph.getDegree(e) * (graph.getDegree(e) - 1));
if (!directed) {
denominator /= 2;
}
double numerator = 0.0;
// get neighbors as list
List<Node> n2 = Arrays.asList(graph.getNeighbors(e).toArray());
List<Node> neighbors2 = new ArrayList<Node>(n2);
for (Node neighbor1 : graph.getNeighbors(e)) {
neighbors2.remove(neighbor1);
// count edges betwwen neighbors
for (Node neighbor2 : neighbors2) {
if (graph.getEdge(neighbor1, neighbor2) != null
|| graph.getEdge(neighbor2, neighbor1) != null) {
numerator++;
}
}
}
// compute coefficient
if (denominator > 0) {
coeficient = numerator / denominator;
} else {
coeficient = 0.0;
}
averageCoefficient += coeficient;
nodeCoefficients[i] = coeficient;
i++;
// set attribute
AttributeRow row = (AttributeRow) e.getNodeData().getAttributes();
row.setValue(clusteringColumn, coeficient);
Progress.progress(progressTicket);
if (cancel) {
break;
}
}
if (graph.getNodeCount() > 0) {
averageCoefficient = averageCoefficient / graph.getNodeCount();
}
graph.readUnlockAll();
} catch (Exception e) {
e.printStackTrace();
// Unlock graph
graph.readUnlockAll();
}
}
public boolean execute() {
attributeModel = workspace.getLookup().lookup(AttributeModel.class);
graphModel = workspace.getLookup().lookup(GraphModel.class);
HierarchicalGraph graph = null;
if (exportVisible) {
graph = graphModel.getHierarchicalGraphVisible();
} else {
graph = graphModel.getHierarchicalGraph();
}
Progress.start(progress);
graph.readLock();
// Options
if (normalize) {
calculateMinMax(graph);
}
// Calculate progress units count
int max = 0;
if (exportHierarchy) {
for (Node n : graph.getNodesTree()) {
max++;
}
for (Edge e : graph.getEdgesTree()) {
max++;
}
} else {
max = graph.getNodeCount();
for (Edge e : graph.getEdgesAndMetaEdges()) {
max++;
}
}
Progress.switchToDeterminate(progress, max);
try {
XMLOutputFactory outputFactory = XMLOutputFactory.newInstance();
outputFactory.setProperty("javax.xml.stream.isRepairingNamespaces", Boolean.FALSE);
XMLStreamWriter xmlWriter = outputFactory.createXMLStreamWriter(writer);
xmlWriter = new IndentingXMLStreamWriter(xmlWriter);
xmlWriter.writeStartDocument("UTF-8", "1.0");
xmlWriter.setPrefix("", GEXF_NAMESPACE);
xmlWriter.writeStartElement(GEXF_NAMESPACE, GEXF);
xmlWriter.writeNamespace("", GEXF_NAMESPACE);
xmlWriter.writeAttribute(GEXF_VERSION, "1.1");
if (exportColors || exportPosition || exportSize) {
xmlWriter.writeNamespace(VIZ, VIZ_NAMESPACE);
}
xmlWriter.writeAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance");
xmlWriter.writeAttribute("xsi:schemaLocation", GEXF_NAMESPACE_LOCATION);
if (exportDynamic) {
DynamicController dynamicController = Lookup.getDefault().lookup(DynamicController.class);
dynamicModel = dynamicController != null ? dynamicController.getModel(workspace) : null;
visibleInterval =
dynamicModel == null
? null
: exportVisible
? dynamicModel.getVisibleInterval()
: new TimeInterval(Double.NEGATIVE_INFINITY, Double.POSITIVE_INFINITY);
}
writeMeta(xmlWriter);
writeGraph(xmlWriter, graph);
xmlWriter.writeEndElement();
xmlWriter.writeEndDocument();
xmlWriter.close();
} catch (Exception e) {
graph.readUnlockAll();
if (e instanceof RuntimeException) {
throw (RuntimeException) e;
}
throw new RuntimeException(e);
}
graph.readUnlock();
Progress.finish(progress);
return !cancel;
}
public void start(int iterations) {
Progress.start(progressTicket, iterations);
}
private void exportData(Graph graph) throws Exception {
int max = graph.getNodeCount();
Progress.start(progressTicket, max);
if (!list) {
if (header) {
writer.append(SEPARATOR);
Node[] nodes = graph.getNodes().toArray();
for (int i = 0; i < nodes.length; i++) {
writeMatrixNode(nodes[i], i < nodes.length - 1);
}
writer.append(EOL);
}
}
if (list) {
Node[] nodes = graph.getNodes().toArray();
for (int i = 0; i < nodes.length; i++) {
Node n = nodes[i];
List<Node> neighbours = new ArrayList<Node>();
for (Edge e : graph.getEdges(n)) {
if (!e.isDirected() || (e.isDirected() && n == e.getSource())) {
Node m = graph.getOpposite(n, e);
neighbours.add(m);
}
}
for (Edge e : ((HierarchicalGraph) graph).getMetaEdges(n)) {
if (!e.isDirected() || (e.isDirected() && n == e.getSource())) {
Node m = graph.getOpposite(n, e);
neighbours.add(m);
}
}
writeListNode(n, !neighbours.isEmpty());
for (int j = 0; j < neighbours.size(); j++) {
writeListNode(neighbours.get(j), j < neighbours.size() - 1);
}
writer.append(EOL);
}
} else {
if (graph instanceof DirectedGraph) {
DirectedGraph directedGraph = (DirectedGraph) graph;
Node[] nodes = graph.getNodes().toArray();
for (Node n : nodes) {
if (cancel) {
break;
}
writeMatrixNode(n, true);
for (int j = 0; j < nodes.length; j++) {
Node m = nodes[j];
Edge e = directedGraph.getEdge(n, m);
e = e == null ? ((HierarchicalDirectedGraph) directedGraph).getMetaEdge(n, m) : e;
writeEdge(e, j < nodes.length - 1);
}
Progress.progress(progressTicket);
writer.append(EOL);
}
} else if (graph instanceof UndirectedGraph) {
UndirectedGraph undirectedGraph = (UndirectedGraph) graph;
Node[] nodes = graph.getNodes().toArray();
for (Node n : nodes) {
if (cancel) {
break;
}
writeMatrixNode(n, true);
for (int j = 0; j < nodes.length; j++) {
Node m = nodes[j];
Edge e = undirectedGraph.getEdge(n, m);
e = e == null ? ((HierarchicalUndirectedGraph) undirectedGraph).getMetaEdge(n, m) : e;
writeEdge(e, j < nodes.length - 1);
}
Progress.progress(progressTicket);
writer.append(EOL);
}
} else {
MixedGraph mixedGraph = (MixedGraph) graph;
Node[] nodes = graph.getNodes().toArray();
for (Node n : graph.getNodes()) {
if (cancel) {
break;
}
writeMatrixNode(n, true);
for (int j = 0; j < nodes.length; j++) {
Node m = nodes[j];
Edge e = mixedGraph.getEdge(n, m);
e = e == null ? ((HierarchicalMixedGraph) mixedGraph).getMetaEdge(n, m) : e;
writeEdge(e, j < nodes.length - 1);
}
Progress.progress(progressTicket);
writer.append(EOL);
}
}
}
graph.readUnlockAll();
Progress.finish(progressTicket);
}
protected void process(ContainerUnloader container, Workspace workspace) {
// Architecture
GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
graphModel = graphController.getGraphModel(workspace);
// Get graph
Graph graph = graphModel.getGraph();
GraphFactory factory = graphModel.factory();
// Time Format & Time zone
graphModel.setTimeFormat(container.getTimeFormat());
graphModel.setTimeZone(container.getTimeZone());
// Progress
Progress.start(progressTicket, container.getNodeCount() + container.getEdgeCount());
// Attributes - Creates columns for properties
flushColumns(container);
// Counters
int addedNodes = 0, addedEdges = 0;
// Create all nodes
ElementIdType elementIdType = container.getElementIdType();
for (NodeDraft draftNode : container.getNodes()) {
String idString = draftNode.getId();
Object id = toElementId(elementIdType, idString);
Node node = graph.getNode(id);
if (node == null) {
node = factory.newNode(id);
addedNodes++;
}
flushToNode(draftNode, node);
graph.addNode(node);
Progress.progress(progressTicket);
}
// Create all edges and push to data structure
for (EdgeDraft draftEdge : container.getEdges()) {
String idString = draftEdge.getId();
Object id = toElementId(elementIdType, idString);
String sourceId = draftEdge.getSource().getId();
String targetId = draftEdge.getTarget().getId();
Node source = graph.getNode(toElementId(elementIdType, sourceId));
Node target = graph.getNode(toElementId(elementIdType, targetId));
Object type = draftEdge.getType();
int edgeType = graphModel.addEdgeType(type);
Edge edge = graph.getEdge(source, target, edgeType);
if (edge == null) {
switch (container.getEdgeDefault()) {
case DIRECTED:
edge = factory.newEdge(id, source, target, edgeType, draftEdge.getWeight(), true);
break;
case UNDIRECTED:
edge = factory.newEdge(id, source, target, edgeType, draftEdge.getWeight(), false);
break;
case MIXED:
boolean directed =
draftEdge.getDirection() == null
|| !draftEdge.getDirection().equals(EdgeDirection.UNDIRECTED);
edge = factory.newEdge(id, source, target, edgeType, draftEdge.getWeight(), directed);
break;
}
addedEdges++;
}
flushToEdge(draftEdge, edge);
graph.addEdge(edge);
Progress.progress(progressTicket);
}
// Report
int touchedNodes = container.getNodeCount();
int touchedEdges = container.getEdgeCount();
if (touchedNodes != addedNodes || touchedEdges != addedEdges) {
Logger.getLogger(getClass().getSimpleName())
.log(
Level.INFO,
"# Nodes loaded: {0} ({1} added)",
new Object[] {touchedNodes, addedNodes});
Logger.getLogger(getClass().getSimpleName())
.log(
Level.INFO,
"# Edges loaded: {0} ({1} added)",
new Object[] {touchedEdges, addedEdges});
} else {
Logger.getLogger(getClass().getSimpleName())
.log(Level.INFO, "# Nodes loaded: {0}", new Object[] {touchedNodes});
Logger.getLogger(getClass().getSimpleName())
.log(Level.INFO, "# Edges loaded: {0}", new Object[] {touchedEdges});
}
Progress.finish(progressTicket);
}