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提交 5ae5ae3f 编写于 作者: E Eduardo Ramos
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Merge branch 0.9.1

上级 42c003ea 89d04c1b
隐藏空白更改
内联 并排
Showing with 112 addition and 78 deletion
modules/ImportPlugin/src/main/java/org/gephi/io/importer/plugin/file/ImporterCSV.java
浏览文件 @ 5ae5ae3f
......@@ -44,6 +44,7 @@ package org.gephi.io.importer.plugin.file;
import java.io.IOException;
import java.io.LineNumberReader;
import java.io.Reader;
import java.text.MessageFormat;
import java.util.ArrayList;
import java.util.List;
import java.util.regex.Matcher;
......@@ -126,7 +127,9 @@ public class ImporterCSV implements FileImporter, LongTask {
int size = lines.size();
if (size != labels.size()) {
throw new Exception("Inconsistent number of matrix lines compared to the number of labels.");
throw new Exception(
MessageFormat.format("Inconsistent number of matrix lines compared to the number of labels. {0} lines, {1} labels", size, labels.size())
);
}
for (int i = 0; i < size; i++) {
......
modules/LayoutAPI/src/main/java/org/gephi/layout/LayoutModelImpl.java
浏览文件 @ 5ae5ae3f
......@@ -55,6 +55,7 @@ import javax.xml.stream.XMLStreamReader;
import javax.xml.stream.XMLStreamWriter;
import javax.xml.stream.events.XMLEvent;
import org.gephi.graph.api.GraphController;
import org.gephi.graph.api.GraphModel;
import org.gephi.layout.api.LayoutModel;
import org.gephi.layout.spi.Layout;
import org.gephi.layout.spi.LayoutBuilder;
......@@ -79,7 +80,7 @@ public class LayoutModelImpl implements LayoutModel {
private final Map<LayoutPropertyKey, Object> savedProperties;
private Layout selectedLayout;
private LayoutBuilder selectedBuilder;
private Workspace workspace;
private final Workspace workspace;
//Util
private final LongTaskExecutor executor;
......@@ -116,6 +117,9 @@ public class LayoutModelImpl implements LayoutModel {
@Override
public Layout getLayout(LayoutBuilder layoutBuilder) {
Layout layout = layoutBuilder.buildLayout();
GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
GraphModel graphModel = graphController.getGraphModel(workspace);
layout.setGraphModel(graphModel);
selectedBuilder = layoutBuilder;
layout.resetPropertiesValues();
return layout;
......
modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/Modularity.java
浏览文件 @ 5ae5ae3f
......@@ -133,26 +133,27 @@ public class Modularity implements Statistics, LongTask {
Graph graph;
double[] weights;
double graphWeightSum;
LinkedList<ModEdge>[] topology;
LinkedList<Community> communities;
List<ModEdge>[] topology;
List<Community> communities;
int N;
HashMap<Integer, Community> invMap;
CommunityStructure(Graph hgraph) {
this.graph = hgraph;
N = hgraph.getNodeCount();
CommunityStructure(Graph graph) {
this.graph = graph;
N = graph.getNodeCount();
invMap = new HashMap<>();
nodeConnectionsWeight = new HashMap[N];
nodeConnectionsCount = new HashMap[N];
nodeCommunities = new Community[N];
map = new HashMap<>();
topology = new LinkedList[N];
communities = new LinkedList<>();
topology = new ArrayList[N];
communities = new ArrayList<>();
int index = 0;
weights = new double[N];
for (Node node : hgraph.getNodes()) {
for (Node node : graph.getNodes()) {
map.put(node, index);
nodeCommunities[index] = new Community(this);
nodeConnectionsWeight[index] = new HashMap<>();
nodeConnectionsCount[index] = new HashMap<>();
weights[index] = 0;
......@@ -167,34 +168,47 @@ public class Modularity implements Statistics, LongTask {
}
}
for (Node node : hgraph.getNodes()) {
for (Node node : graph.getNodes()) {
int node_index = map.get(node);
topology[node_index] = new LinkedList<>();
for (Edge edge : hgraph.getEdges(node)) {
Node neighbor = hgraph.getOpposite(node, edge);
topology[node_index] = new ArrayList<>();
Set<Node> uniqueNeighbors = new HashSet<>(graph.getNeighbors(node).toCollection());
for (Node neighbor : uniqueNeighbors) {
if (node == neighbor) {
continue;
}
int neighbor_index = map.get(neighbor);
float weight = 1;
if (useWeight) {
weight = (float) edge.getWeight(graph.getView());
float weight = 0;
//Sum all parallel edges weight:
for (Edge edge : graph.getEdges(node, neighbor)) {
if (useWeight) {
weight += edge.getWeight(graph.getView());
} else {
weight += 1;
}
}
//Finally add a single edge with the summed weight of all parallel edges:
//Fixes issue #1419 Getting null pointer error when trying to calculate modularity
weights[node_index] += weight;
Modularity.ModEdge me = new ModEdge(node_index, neighbor_index, weight);
topology[node_index].add(me);
Community adjCom = nodeCommunities[neighbor_index];
nodeConnectionsWeight[node_index].put(adjCom, weight);
nodeConnectionsCount[node_index].put(adjCom, 1);
nodeCommunities[node_index].connectionsWeight.put(adjCom, weight);
nodeCommunities[node_index].connectionsCount.put(adjCom, 1);
nodeConnectionsWeight[neighbor_index].put(nodeCommunities[node_index], weight);
nodeConnectionsCount[neighbor_index].put(nodeCommunities[node_index], 1);
nodeCommunities[neighbor_index].connectionsWeight.put(nodeCommunities[node_index], weight);
nodeCommunities[neighbor_index].connectionsCount.put(nodeCommunities[node_index], 1);
Community nodeCom = nodeCommunities[node_index];
nodeCom.connectionsWeight.put(adjCom, weight);
nodeCom.connectionsCount.put(adjCom, 1);
nodeConnectionsWeight[neighbor_index].put(nodeCom, weight);
nodeConnectionsCount[neighbor_index].put(nodeCom, 1);
adjCom.connectionsWeight.put(nodeCom, weight);
adjCom.connectionsCount.put(nodeCom, 1);
graphWeightSum += weight;
}
......@@ -206,7 +220,7 @@ public class Modularity implements Statistics, LongTask {
}
private void addNodeTo(int node, Community to) {
to.add(new Integer(node));
to.add(node);
nodeCommunities[node] = to;
for (ModEdge e : topology[node]) {
......@@ -276,8 +290,7 @@ public class Modularity implements Statistics, LongTask {
}
}
private void removeNodeFrom(int node, Community from) {
private void removeNodeFromItsCommunity(int node) {
Community community = nodeCommunities[node];
for (ModEdge e : topology[node]) {
int neighbor = e.target;
......@@ -334,18 +347,17 @@ public class Modularity implements Statistics, LongTask {
}
}
from.remove(new Integer(node));
community.remove(node);
}
private void moveNodeTo(int node, Community to) {
Community from = nodeCommunities[node];
removeNodeFrom(node, from);
removeNodeFromItsCommunity(node);
addNodeTo(node, to);
}
private void zoomOut() {
int M = communities.size();
LinkedList<ModEdge>[] newTopology = new LinkedList[M];
ArrayList<ModEdge>[] newTopology = new ArrayList[M];
int index = 0;
nodeCommunities = new Community[M];
nodeConnectionsWeight = new HashMap[M];
......@@ -355,7 +367,8 @@ public class Modularity implements Statistics, LongTask {
Community com = communities.get(i);
nodeConnectionsWeight[index] = new HashMap<>();
nodeConnectionsCount[index] = new HashMap<>();
newTopology[index] = new LinkedList<>();
newTopology[index] = new ArrayList<>();
nodeCommunities[index] = new Community(com);
Set<Community> iter = com.connectionsWeight.keySet();
double weightSum = 0;
......@@ -406,7 +419,7 @@ public class Modularity implements Statistics, LongTask {
double weightSum;
CommunityStructure structure;
LinkedList<Integer> nodes;
List<Integer> nodes;
HashMap<Modularity.Community, Float> connectionsWeight;
HashMap<Modularity.Community, Integer> connectionsCount;
......@@ -418,7 +431,7 @@ public class Modularity implements Statistics, LongTask {
structure = com.structure;
connectionsWeight = new HashMap<>();
connectionsCount = new HashMap<>();
nodes = new LinkedList<>();
nodes = new ArrayList<>();
//mHidden = pCom.mHidden;
}
......@@ -426,7 +439,7 @@ public class Modularity implements Statistics, LongTask {
this.structure = structure;
connectionsWeight = new HashMap<>();
connectionsCount = new HashMap<>();
nodes = new LinkedList<>();
nodes = new ArrayList<>();
}
public void seed(int node) {
......@@ -435,13 +448,13 @@ public class Modularity implements Statistics, LongTask {
}
public boolean add(int node) {
nodes.addLast(new Integer(node));
nodes.add(node);
weightSum += structure.weights[node];
return true;
}
public boolean remove(int node) {
boolean result = nodes.remove(new Integer(node));
boolean result = nodes.remove((Integer) node);
weightSum -= structure.weights[node];
if (nodes.isEmpty()) {
structure.communities.remove(this);
......@@ -452,29 +465,33 @@ public class Modularity implements Statistics, LongTask {
@Override
public void execute(GraphModel graphModel) {
Graph hgraph = graphModel.getUndirectedGraphVisible();
execute(hgraph);
Graph graph = graphModel.getUndirectedGraphVisible();
execute(graph);
}
public void execute(Graph hgraph) {
public void execute(Graph graph) {
isCanceled = false;
hgraph.readLock();
structure = new Modularity.CommunityStructure(hgraph);
int[] comStructure = new int[hgraph.getNodeCount()];
graph.readLock();
HashMap<String, Double> computedModularityMetrics = computeModularity(hgraph, structure, comStructure, resolution, isRandomized, useWeight);
structure = new Modularity.CommunityStructure(graph);
int[] comStructure = new int[graph.getNodeCount()];
modularity = computedModularityMetrics.get("modularity");
modularityResolution = computedModularityMetrics.get("modularityResolution");
if (graph.getNodeCount() > 0) {//Fixes issue #713 Modularity Calculation Throws Exception On Empty Graph
HashMap<String, Double> computedModularityMetrics = computeModularity(graph, structure, comStructure, resolution, isRandomized, useWeight);
modularity = computedModularityMetrics.get("modularity");
modularityResolution = computedModularityMetrics.get("modularityResolution");
} else {
modularity = 0;
modularityResolution = 0;
}
saveValues(comStructure, hgraph, structure);
saveValues(comStructure, graph, structure);
hgraph.readUnlock();
graph.readUnlock();
}
protected HashMap<String, Double> computeModularity(Graph hgraph, CommunityStructure theStructure, int[] comStructure,
protected HashMap<String, Double> computeModularity(Graph graph, CommunityStructure theStructure, int[] comStructure,
double currentResolution, boolean randomized, boolean weighted) {
isCanceled = false;
Progress.start(progress);
......@@ -486,7 +503,7 @@ public class Modularity implements Statistics, LongTask {
HashMap<String, Double> results = new HashMap<>();
if (isCanceled) {
hgraph.readUnlockAll();
graph.readUnlockAll();
return results;
}
boolean someChange = true;
......@@ -508,13 +525,13 @@ public class Modularity implements Statistics, LongTask {
localChange = true;
}
if (isCanceled) {
hgraph.readUnlockAll();
graph.readUnlockAll();
return results;
}
}
someChange = localChange || someChange;
if (isCanceled) {
hgraph.readUnlockAll();
graph.readUnlockAll();
return results;
}
}
......@@ -524,11 +541,11 @@ public class Modularity implements Statistics, LongTask {
}
}
fillComStructure(hgraph, theStructure, comStructure);
double[] degreeCount = fillDegreeCount(hgraph, theStructure, comStructure, nodeDegrees, weighted);
fillComStructure(graph, theStructure, comStructure);
double[] degreeCount = fillDegreeCount(graph, theStructure, comStructure, nodeDegrees, weighted);
double computedModularity = finalQ(comStructure, degreeCount, hgraph, theStructure, totalWeight, 1., weighted);
double computedModularityResolution = finalQ(comStructure, degreeCount, hgraph, theStructure, totalWeight, currentResolution, weighted);
double computedModularity = finalQ(comStructure, degreeCount, graph, theStructure, totalWeight, 1., weighted);
double computedModularityResolution = finalQ(comStructure, degreeCount, graph, theStructure, totalWeight, currentResolution, weighted);
results.put("modularity", computedModularity);
results.put("modularityResolution", computedModularityResolution);
......@@ -536,12 +553,12 @@ public class Modularity implements Statistics, LongTask {
return results;
}
Community updateBestCommunity(CommunityStructure theStructure, int i, double currentResolution) {
private Community updateBestCommunity(CommunityStructure theStructure, int node_id, double currentResolution) {
double best = 0.;
Community bestCommunity = null;
Set<Community> iter = theStructure.nodeConnectionsWeight[i].keySet();
Set<Community> iter = theStructure.nodeConnectionsWeight[node_id].keySet();
for (Community com : iter) {
double qValue = q(i, com, theStructure, currentResolution);
double qValue = q(node_id, com, theStructure, currentResolution);
if (qValue > best) {
best = qValue;
bestCommunity = com;
......@@ -550,8 +567,7 @@ public class Modularity implements Statistics, LongTask {
return bestCommunity;
}
int[] fillComStructure(Graph hgraph, CommunityStructure theStructure, int[] comStructure) {
// int[] comStructure = new int[hgraph.getNodeCount()];
private int[] fillComStructure(Graph graph, CommunityStructure theStructure, int[] comStructure) {
int count = 0;
for (Community com : theStructure.communities) {
......@@ -566,37 +582,37 @@ public class Modularity implements Statistics, LongTask {
return comStructure;
}
double[] fillDegreeCount(Graph hgraph, CommunityStructure theStructure, int[] comStructure, double[] nodeDegrees, boolean weighted) {
private double[] fillDegreeCount(Graph graph, CommunityStructure theStructure, int[] comStructure, double[] nodeDegrees, boolean weighted) {
double[] degreeCount = new double[theStructure.communities.size()];
for (Node node : hgraph.getNodes()) {
for (Node node : graph.getNodes()) {
int index = theStructure.map.get(node);
if (weighted) {
degreeCount[comStructure[index]] += nodeDegrees[index];
} else {
degreeCount[comStructure[index]] += hgraph.getDegree(node);
degreeCount[comStructure[index]] += graph.getDegree(node);
}
}
return degreeCount;
}
private double finalQ(int[] struct, double[] degrees, Graph hgraph,
private double finalQ(int[] struct, double[] degrees, Graph graph,
CommunityStructure theStructure, double totalWeight, double usedResolution, boolean weighted) {
double res = 0;
double[] internal = new double[degrees.length];
for (Node n : hgraph.getNodes()) {
for (Node n : graph.getNodes()) {
int n_index = theStructure.map.get(n);
for (Edge edge : hgraph.getEdges(n)) {
Node neighbor = hgraph.getOpposite(n, edge);
for (Edge edge : graph.getEdges(n)) {
Node neighbor = graph.getOpposite(n, edge);
if (n == neighbor) {
continue;
}
int neigh_index = theStructure.map.get(neighbor);
if (struct[neigh_index] == struct[n_index]) {
if (weighted) {
internal[struct[neigh_index]] += edge.getWeight(hgraph.getView());
internal[struct[neigh_index]] += edge.getWeight(graph.getView());
} else {
internal[struct[neigh_index]]++;
}
......@@ -610,13 +626,13 @@ public class Modularity implements Statistics, LongTask {
return res;
}
private void saveValues(int[] struct, Graph hgraph, CommunityStructure theStructure) {
Table nodeTable = hgraph.getModel().getNodeTable();
private void saveValues(int[] struct, Graph graph, CommunityStructure theStructure) {
Table nodeTable = graph.getModel().getNodeTable();
Column modCol = nodeTable.getColumn(MODULARITY_CLASS);
if (modCol == null) {
modCol = nodeTable.addColumn(MODULARITY_CLASS, "Modularity Class", Integer.class, new Integer(0));
modCol = nodeTable.addColumn(MODULARITY_CLASS, "Modularity Class", Integer.class, 0);
}
for (Node n : hgraph.getNodes()) {
for (Node n : graph.getNodes()) {
int n_index = theStructure.map.get(n);
n.setAttribute(modCol, struct[n_index]);
}
......
modules/StatisticsPlugin/src/test/java/org/gephi/statistics/plugin/ModularityNGTest.java
浏览文件 @ 5ae5ae3f
......@@ -250,22 +250,33 @@ public class ModularityNGTest {
undirectedGraph.addNode(node7);
undirectedGraph.addNode(node8);
Edge edge12 = graphModel.factory().newEdge(node1, node2, 0, 10.f, false);
//Test 3 parallel edges summing weight = 10
//Related issue ==> #1419 Getting null pointer error when trying to calculate modularity
Edge edge12_1 = graphModel.factory().newEdge(node1, node2, 0, 2.f, false);
Edge edge12_2 = graphModel.factory().newEdge(node1, node2, 0, 5.f, false);
Edge edge12_3 = graphModel.factory().newEdge(node1, node2, 0, 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);
Edge edge78 = graphModel.factory().newEdge(node7, node8, 0, 10.f, 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);
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);
undirectedGraph.addEdge(edge78_1);
undirectedGraph.addEdge(edge78_2);
undirectedGraph.addEdge(edge81);
UndirectedGraph hgraph = graphModel.getUndirectedGraph();
......
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