use of org.gephi.graph.api.Node in project gephi by gephi.
the class WeightedDegreeNGTest method testNullGraphDegree.
@Test
public void testNullGraphDegree() {
GraphModel graphModel = GraphGenerator.generateNullUndirectedGraph(5);
Graph graph = graphModel.getGraph();
Node n = graph.getNode("1");
WeightedDegree d = new WeightedDegree();
d.execute(graph);
double degree = (Double) n.getAttribute(WeightedDegree.WDEGREE);
double avDegree = d.getAverageDegree();
assertEquals(degree, 0.0);
assertEquals(avDegree, 0.0);
}
use of org.gephi.graph.api.Node in project gephi by gephi.
the class ModularityNGTest method testCyclicWithWeightsGraphModularity.
@Test
public void testCyclicWithWeightsGraphModularity() {
GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
Node node1 = graphModel.factory().newNode("0");
Node node2 = graphModel.factory().newNode("1");
Node node3 = graphModel.factory().newNode("2");
Node node4 = graphModel.factory().newNode("3");
Node node5 = graphModel.factory().newNode("4");
Node node6 = graphModel.factory().newNode("5");
Node node7 = graphModel.factory().newNode("6");
Node node8 = graphModel.factory().newNode("7");
undirectedGraph.addNode(node1);
undirectedGraph.addNode(node2);
undirectedGraph.addNode(node3);
undirectedGraph.addNode(node4);
undirectedGraph.addNode(node5);
undirectedGraph.addNode(node6);
undirectedGraph.addNode(node7);
undirectedGraph.addNode(node8);
//Test 3 parallel edges summing weight = 10
//Related issues ==> #1419 Getting null pointer error when trying to calculate modularity; #1526 NullPointerException on Modularity Statistics with gexf with kind / parallel nodes
Edge edge12_1 = graphModel.factory().newEdge(node1, node2, 1, 2.f, false);
Edge edge12_2 = graphModel.factory().newEdge(node1, node2, 2, 5.f, false);
Edge edge12_3 = graphModel.factory().newEdge(node1, node2, 2, 3.f, false);
Edge edge23 = graphModel.factory().newEdge(node2, node3, false);
Edge edge34 = graphModel.factory().newEdge(node3, node4, 0, 10.f, false);
Edge edge45 = graphModel.factory().newEdge(node4, node5, false);
Edge edge56 = graphModel.factory().newEdge(node5, node6, 0, 10.f, false);
Edge edge67 = graphModel.factory().newEdge(node6, node7, false);
//Test 2 parallel edges summing weight = 10
Edge edge78_1 = graphModel.factory().newEdge(node7, node8, 0, 5.f, false);
Edge edge78_2 = graphModel.factory().newEdge(node7, node8, 0, 5.f, false);
Edge edge81 = graphModel.factory().newEdge(node8, node1, false);
undirectedGraph.addEdge(edge12_1);
undirectedGraph.addEdge(edge12_2);
undirectedGraph.addEdge(edge12_3);
undirectedGraph.addEdge(edge23);
undirectedGraph.addEdge(edge34);
undirectedGraph.addEdge(edge45);
undirectedGraph.addEdge(edge56);
undirectedGraph.addEdge(edge67);
undirectedGraph.addEdge(edge78_1);
undirectedGraph.addEdge(edge78_2);
undirectedGraph.addEdge(edge81);
UndirectedGraph graph = graphModel.getUndirectedGraph();
Modularity mod = new Modularity();
Modularity.CommunityStructure theStructure = mod.new CommunityStructure(graph);
int[] comStructure = new int[graph.getNodeCount()];
HashMap<String, Double> modularityValues = mod.computeModularity(graph, theStructure, comStructure, 1., true, true);
int class1 = comStructure[0];
int class2 = comStructure[1];
int class4 = comStructure[3];
int class5 = comStructure[4];
int class7 = comStructure[6];
int class8 = comStructure[7];
assertEquals(class1, class2);
assertEquals(class7, class8);
assertNotEquals(class4, class5);
}
use of org.gephi.graph.api.Node in project gephi by gephi.
the class ModularityNGTest method testComputeBarbellGraphModularityHasHighWeight.
@Test
public void testComputeBarbellGraphModularityHasHighWeight() {
GraphModel graphModel = GraphGenerator.generateCompleteUndirectedGraph(4);
UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
Node[] nodes = new Node[4];
for (int i = 0; i < 4; i++) {
Node currentNode = graphModel.factory().newNode(((Integer) (i + 4)).toString());
nodes[i] = currentNode;
undirectedGraph.addNode(currentNode);
}
for (int i = 0; i < 3; i++) {
for (int j = i + 1; j < 4; j++) {
Edge currentEdge = graphModel.factory().newEdge(nodes[i], nodes[j], false);
undirectedGraph.addEdge(currentEdge);
}
}
Edge currentEdge = graphModel.factory().newEdge(undirectedGraph.getNode("0"), undirectedGraph.getNode("5"), 0, 100.f, false);
undirectedGraph.addEdge(currentEdge);
UndirectedGraph graph = graphModel.getUndirectedGraph();
Modularity mod = new Modularity();
Modularity.CommunityStructure theStructure = mod.new CommunityStructure(graph);
int[] comStructure = new int[graph.getNodeCount()];
HashMap<String, Double> modularityValues = mod.computeModularity(graph, theStructure, comStructure, 1., true, true);
int class4 = comStructure[0];
int class5 = comStructure[5];
assertEquals(class4, class5);
}
use of org.gephi.graph.api.Node in project gephi by gephi.
the class PageRankNGTest method testCyclicGraphPageRank.
@Test
public void testCyclicGraphPageRank() {
pc.newProject();
GraphModel graphModel = GraphGenerator.generateCyclicUndirectedGraph(6);
UndirectedGraph graph = graphModel.getUndirectedGraph();
PageRank pr = new PageRank();
double[] pageRank;
HashMap<Node, Integer> indicies = pr.createIndiciesMap(graph);
pageRank = pr.calculatePagerank(graph, indicies, false, false, 0.001, 0.6);
Node n4 = graph.getNode("3");
int index4 = indicies.get(n4);
double pr4 = pageRank[index4];
double res = 0.1667;
double diff4 = Math.abs(pr4 - res);
assertTrue(diff4 < 0.01);
}
use of org.gephi.graph.api.Node in project gephi by gephi.
the class PageRankNGTest method testPathDirectedGraphPageRank.
@Test
public void testPathDirectedGraphPageRank() {
pc.newProject();
GraphModel graphModel = GraphGenerator.generatePathDirectedGraph(4);
DirectedGraph graph = graphModel.getDirectedGraph();
PageRank pr = new PageRank();
double[] pageRank;
HashMap<Node, Integer> indicies = pr.createIndiciesMap(graph);
pageRank = pr.calculatePagerank(graph, indicies, true, false, 0.001, 0.85);
Node n1 = graph.getNode("0");
Node n2 = graph.getNode("1");
Node n3 = graph.getNode("2");
Node n4 = graph.getNode("3");
int index1 = indicies.get(n1);
int index2 = indicies.get(n2);
int index3 = indicies.get(n3);
int index4 = indicies.get(n4);
double pr1 = pageRank[index1];
double pr2 = pageRank[index2];
double pr3 = pageRank[index3];
double pr4 = pageRank[index4];
double res = 1.;
double diff = 0.01;
double sum = pr1 + pr2 + pr3 + pr4;
assertTrue(pr1 < pr2);
assertTrue(pr2 < pr4);
assertTrue(Math.abs(sum - res) < diff);
}
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