BigCLAM plugin for Gephi

modules/BigCLAM/README.md

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+

modules/BigCLAM/pom.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+    <parent>
+        <artifactId>gephi-plugin-parent</artifactId>
+        <groupId>org.gephi</groupId>
+        <version>0.10.0</version>
+    </parent>
+
+    <groupId>ir.urmia</groupId>
+    <artifactId>bigclam</artifactId>
+    <version>1.0.0</version>
+    <packaging>nbm</packaging>
+
+    <name>Big CLAM Plugin for Gephi</name>
+
+    <dependencies>
+        <!-- Insert dependencies here -->
+        <dependency>
+            <groupId>org.gephi</groupId>
+            <artifactId>gephi-toolkit</artifactId>
+            <version>0.10.0</version>
+        </dependency>
+        <dependency>
+            <groupId>org.netbeans.api</groupId>
+            <artifactId>org-openide-util-lookup</artifactId>
+            <version>RELEASE160</version>
+        </dependency>
+        <dependency>
+            <groupId>org.gephi</groupId>
+            <artifactId>utils-longtask</artifactId>
+            <version>0.10.0</version>
+        </dependency>
+        <dependency>
+            <groupId>org.gephi</groupId>
+            <artifactId>graph-api</artifactId>
+            <version>0.10.0</version>
+        </dependency>
+        <dependency>
+            <groupId>org.gephi</groupId>
+            <artifactId>statistics-api</artifactId>
+            <version>0.10.0</version>
+        </dependency>
+
+    </dependencies>
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.netbeans.utilities</groupId>
+                <artifactId>nbm-maven-plugin</artifactId>
+                <configuration>
+                    <licenseName>Apache 2.0</licenseName>
+                    <author>Mir Saman Tajbakhsh, Ebrahim Shami</author>
+                    <authorEmail>[email protected]</authorEmail>
+                    <authorUrl>https://mstajbakhsh.ir</authorUrl>
+                    <sourceCodeUrl>https://github.com/mirsamantajbakhsh/BigCLAM.git</sourceCodeUrl>
+                    <publicPackages>
+                        <!-- Insert public packages -->
+                    </publicPackages>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+
+    <!-- Snapshot Repositories (only needed if developing against a SNAPSHOT version) -->
+    <repositories>
+        <repository>
+            <id>oss-sonatype</id>
+            <name>oss-sonatype</name>
+            <url>https://oss.sonatype.org/content/repositories/snapshots/</url>
+            <snapshots>
+                <enabled>true</enabled>
+            </snapshots>
+        </repository>
+    </repositories>
+</project>
+
+

modules/BigCLAM/src/main/java/ir/urmia/bigclam/BigCLAM.java

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+
+package ir.urmia.bigclam;
+
+import org.gephi.graph.api.Graph;
+import org.gephi.graph.api.GraphModel;
+import org.gephi.graph.api.Node;
+import org.gephi.utils.longtask.spi.LongTask;
+import org.gephi.utils.progress.ProgressTicket;
+
+public class BigCLAM implements org.gephi.statistics.spi.Statistics, LongTask {
+    private StringBuilder reportSB = new StringBuilder();
+    private boolean cancel = false;
+    private int k = 3;
+    private int iterations = 100;
+    double[][] adjacencyMatrix;
+    Node[] nodes = null;
+
+    public void createAdjacencyMatrix(Graph g) {
+        adjacencyMatrix = new double[nodes.length][nodes.length];
+
+        for (int i = 0; i < nodes.length; i++) {
+            Node n1 = nodes[i];
+            for (int j = 0; j < nodes.length; j++) {
+                Node n2 = nodes[j];
+                adjacencyMatrix[i][j] = (g.getEdge(n1, n2) != null || g.getEdge(n2, n1) != null) ?
+                        1 : 0;
+            }
+        }
+
+        reportSB.append("Adjacency Matrix:\n");
+
+        for (double[] row : adjacencyMatrix) {
+            reportSB.append("\n");
+            for (double element : row) {
+                reportSB.append(String.format("%d", (int) element));
+                reportSB.append(" ");
+            }
+            reportSB.delete(reportSB.length() - 3, reportSB.length());
+
+        }
+    }
+
+    @Override
+    public void execute(GraphModel gm) {
+        Graph g = gm.getGraphVisible();
+        g.readLock();
+        nodes = g.getNodes().toArray();
+
+        createAdjacencyMatrix(g);
+        int communitiesCount = k;
+        int iterationsCount = iterations;
+        double learningRate = 0.01;
+
+        double[][] F = Utils.bigclam(adjacencyMatrix, communitiesCount, iterationsCount, learningRate);
+
+        reportSB.append("\n\nF:\n\n");
+
+        for (int i = 0; i < F.length; i++) {
+            double[] row = F[i];
+            reportSB.append(nodes[i].getLabel());
+            reportSB.append("\t");
+
+            for (double element : row) {
+                reportSB.append(String.format("%2.2f", element));
+                reportSB.append(" | ");
+            }
+            reportSB.delete(reportSB.length() - 3, reportSB.length());
+            reportSB.append("\n");
+        }
+        g.readUnlock();
+    }
+
+    @Override
+    public String getReport() {
+        reportSB.insert(0, "<pre>");
+        reportSB.append("</pre>");
+        return reportSB.toString();
+    }
+
+    @Override
+    public boolean cancel() {
+        cancel = true;
+        return true;
+    }
+
+    @Override
+    public void setProgressTicket(ProgressTicket pt) {
+    }
+
+    public int getK() {
+        return k;
+    }
+
+    public int getIterations() {
+        return iterations;
+    }
+
+    public void setK(int k) {
+        this.k = k;
+    }
+
+    public void setIterations(int iterations) {
+        this.iterations = iterations;
+    }
+
+}

modules/BigCLAM/src/main/java/ir/urmia/bigclam/Builder.java

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+
+package ir.urmia.bigclam;
+
+import org.gephi.statistics.spi.Statistics;
+import org.gephi.statistics.spi.StatisticsBuilder;
+import org.openide.util.lookup.ServiceProvider;
+
+@ServiceProvider(service = StatisticsBuilder.class)
+public class Builder implements StatisticsBuilder {
+
+    @Override
+    public String getName() {
+        return "BigCLAM";
+    }
+
+    @Override
+    public Statistics getStatistics() {
+        return new BigCLAM();
+    }
+
+    @Override
+    public Class<? extends Statistics> getStatisticsClass() {
+        return BigCLAM.class;
+    }
+
+}

modules/BigCLAM/src/main/java/ir/urmia/bigclam/Panel.java

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+
+package ir.urmia.bigclam;
+
+import javax.swing.*;
+import java.awt.*;
+
+
+public class Panel extends JPanel {
+
+    private JTextField iterationsValue;
+    private JTextField kValue;
+    public Panel() {
+        JPanel panel = this;
+        panel.setPreferredSize(new Dimension(300, 100));
+
+        JLabel labelK = new JLabel("Number of communities:");
+        JLabel labelIterations = new JLabel("Number of iterations:");
+        kValue = new JTextField();
+        iterationsValue = new JTextField();
+
+        labelK.setAlignmentX(0.0f);
+        kValue.setAlignmentX(0.0f);
+        labelIterations.setAlignmentX(0.0f);
+        iterationsValue.setAlignmentX(0.0f);
+
+        this.add(labelK);
+        this.add(kValue);
+        this.add(labelIterations);
+        this.add(iterationsValue);
+
+        BoxLayout layout = new BoxLayout(panel, BoxLayout.Y_AXIS);
+        panel.setLayout(layout);
+
+        panel.add(labelK);
+        panel.add(kValue);
+        panel.add(labelIterations);
+        panel.add(iterationsValue);
+    }
+
+    public int getK() {
+        int i = 0;
+        try {
+            i = Integer.valueOf(kValue.getText());
+        } catch (Exception ex) {
+            return 0;
+        }
+        return i;
+    }
+
+    public void setK(int k) {
+        this.kValue.setText(String.valueOf(k));
+    }
+
+    public void setIterations(int i) {
+        this.iterationsValue.setText(String.valueOf(i));
+    }
+
+    public int getIterations() {
+        int i = 0;
+        try {
+            i = Integer.valueOf(iterationsValue.getText());
+        } catch (Exception ex) {
+            return 0;
+        }
+        return i;
+    }
+}

modules/BigCLAM/src/main/java/ir/urmia/bigclam/UI.java

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+
+package ir.urmia.bigclam;
+
+import javax.swing.JPanel;
+
+import org.gephi.statistics.spi.Statistics;
+import org.gephi.statistics.spi.StatisticsUI;
+import org.openide.util.lookup.ServiceProvider;
+
+@ServiceProvider(service = StatisticsUI.class)
+public class UI implements StatisticsUI {
+    private Panel panel;
+    private BigCLAM myMetric;
+
+    @Override
+    public JPanel getSettingsPanel() {
+        panel = new Panel();
+        return panel;
+    }
+
+    @Override
+    public void setup(Statistics ststcs) {
+        this.myMetric = (BigCLAM) ststcs;
+        if (panel != null) {
+            panel.setK(myMetric.getK());
+            panel.setIterations(myMetric.getIterations());
+        }
+    }
+
+    @Override
+    public void unsetup() {
+        if (panel != null) {
+            myMetric.setK(panel.getK());
+            myMetric.setIterations(panel.getIterations());
+        }
+        panel = null;
+    }
+
+    @Override
+    public Class<? extends Statistics> getStatisticsClass() {
+        return BigCLAM.class;
+    }
+
+    @Override
+    public String getValue() {
+        return null;
+    }
+
+    @Override
+    public String getDisplayName() {
+        return "BigCLAM";
+    }
+
+    @Override
+    public String getShortDescription() {
+        return "BigCLAM Algorithm";
+    }
+
+    @Override
+    public String getCategory() {
+        return CATEGORY_NETWORK_OVERVIEW;
+    }
+
+    @Override
+    public int getPosition() {
+        return 800;
+    }
+
+}