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‎demo/dbscan-clustering-demo.nlogo‎

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‎libs/NetLogo/NetLogo/5.3.1/NetLogo-5.3.1.jar‎

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‎pom.xml‎

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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<groupId>org.nlogo.extensions.dbscan</groupId>
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<artifactId>dbscan</artifactId>
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<version>0.1</version>
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<packaging>jar</packaging>
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<repositories>
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<repository>
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<id>in-project</id>
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<name>In Project Repo</name>
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<url>file://${project.basedir}/libs</url>
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</repository>
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<repository>
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<id>jitpack.io</id>
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<url>https://jitpack.io</url>
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</repository>
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</repositories>
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<properties>
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<maven.compiler.source>1.8</maven.compiler.source>
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<maven.compiler.target>1.8</maven.compiler.target>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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</properties>
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<dependencies>
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<dependency>
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<groupId>NetLogo</groupId>
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<artifactId>NetLogo</artifactId>
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<version>5.3.1</version>
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</dependency>
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<dependency>
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<groupId>com.github.chrfrantz</groupId>
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<artifactId>DBSCAN</artifactId>
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<version>8f0532d80f775f9a27e811fa6c2901adbeae3ba9</version>
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</dependency>
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<dependency>
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<groupId>junit</groupId>
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<artifactId>junit</artifactId>
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<version>4.9</version>
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<scope>test</scope>
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</dependency>
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</dependencies>
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<build>
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<finalName>${project.name}</finalName>
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<plugins>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-compiler-plugin</artifactId>
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<executions>
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<!-- Prevent test compilation as of Scala dependency -->
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<execution>
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<id>default-testCompile</id>
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<phase>test-compile</phase>
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<configuration>
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<testExcludes>
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<exclude>**/TestNetLogoDBSCAN.java</exclude>
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</testExcludes>
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</configuration>
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<goals>
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<goal>testCompile</goal>
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</goals>
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</execution>
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</executions>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-jar-plugin</artifactId>
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<configuration>
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<archive>
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<manifestFile>src/main/resources/manifest.txt</manifestFile>
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</archive>
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</configuration>
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</plugin>
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</plugins>
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</build>
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</project>

‎src/main/java/org/nlogo/extensions/dbscan/DBSCANExtension.java‎

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package org.nlogo.extensions.dbscan;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.Iterator;
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import org.christopherfrantz.dbscan.DBSCANClusterer;
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import org.christopherfrantz.dbscan.DBSCANClusteringException;
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import org.nlogo.agent.Agent;
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import org.nlogo.agent.Turtle;
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import org.nlogo.api.AgentSet;
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import org.nlogo.api.Argument;
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import org.nlogo.api.Context;
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import org.nlogo.api.DefaultReporter;
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import org.nlogo.api.ExtensionException;
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import org.nlogo.api.LogoException;
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import org.nlogo.api.LogoListBuilder;
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import org.nlogo.api.PrimitiveManager;
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import org.nlogo.api.Syntax;
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import org.nlogo.extensions.dbscan.metrics.DistanceMetricNetLogoAgents;
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import org.nlogo.extensions.dbscan.metrics.DistanceMetricNetLogoLocation;
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/**
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* NetLogo extension for clustering based on DBSCAN by agent variables or coordinates.
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*
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* @author Christopher Frantz <[email protected]>
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*
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*/
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public class DBSCANExtension extends org.nlogo.api.DefaultClassManager {
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@Override
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public void load(PrimitiveManager primitiveManager) throws ExtensionException {
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primitiveManager.addPrimitive("cluster-by-variable", new DbscanNetlogoVariableClusterer());
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primitiveManager.addPrimitive("cluster-by-location", new DbscanNetlogoCoordinateClusterer());
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}
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/**
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* Clusters based on agent variables
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* @author Christopher Frantz <[email protected]>
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*/
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public static class DbscanNetlogoVariableClusterer extends DefaultReporter {
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@Override
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public Syntax getSyntax() {
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//Inputs: values to be clustered, property to be clustered on, minimum number of elements, maximum distance
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int[] input = new int[] {Syntax.AgentsetType(), Syntax.StringType(), Syntax.NumberType(), Syntax.NumberType()};
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int ret = Syntax.ListType();
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return Syntax.reporterSyntax(input, ret);
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}
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@Override
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public Object report(Argument[] args, Context ctx)
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throws ExtensionException, LogoException {
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AgentSet inputValues = null;
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String field = null;
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int minNumberOfElements = -1;
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double maxDistance = -1;
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LogoListBuilder list = new LogoListBuilder();
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try {
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inputValues = args[0].getAgentSet();
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field = args[1].getString();
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minNumberOfElements = args[2].getIntValue();
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maxDistance = args[3].getDoubleValue();
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} catch (Exception e) {
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throw new ExtensionException(e.getMessage());
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}
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if (minNumberOfElements == -1) {
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throw new ExtensionException("Minimum number of cluster elements has not been defined.");
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}
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if (maxDistance == -1) {
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throw new ExtensionException("Maximum distance of cluster variable has not been defined.");
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}
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// Convert input agentset to collection
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Collection<Agent> inputCollection = new ArrayList<>();
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Iterator it = inputValues.agents().iterator();
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while (it.hasNext()) {
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inputCollection.add((Agent) it.next());
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}
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// Perform clustering
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ArrayList<ArrayList<Agent>> tmpList = null;
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try {
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DBSCANClusterer<Agent> clusterer = new DBSCANClusterer<Agent>(inputCollection, minNumberOfElements, maxDistance, new DistanceMetricNetLogoAgents(field.toUpperCase()));
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tmpList = clusterer.performClustering();
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} catch (DBSCANClusteringException e) {
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throw new ExtensionException(e);
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}
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// Convert generated lists of clusters to nested LogoList
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for (ArrayList<Agent> intList: tmpList) {
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LogoListBuilder internalBuilder = new LogoListBuilder();
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for (Agent agent: intList) {
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internalBuilder.add(agent);
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}
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list.add(internalBuilder.toLogoList());
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}
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return list.toLogoList();
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}
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}
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/**
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* Clusters based on coordinates
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* @author Christopher Frantz <[email protected]>
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*
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*/
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public static class DbscanNetlogoCoordinateClusterer extends DefaultReporter {
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@Override
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public Syntax getSyntax() {
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//Inputs: values to be clustered, minimum number of elements, maximum distance
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int[] input = new int[] {Syntax.AgentsetType(), Syntax.NumberType(), Syntax.NumberType()};
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int ret = Syntax.ListType();
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return Syntax.reporterSyntax(input, ret);
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}
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@Override
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public Object report(Argument[] args, Context ctx)
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throws ExtensionException, LogoException {
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AgentSet inputValues = null;
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int minNumberOfElements = -1;
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double maxDistance = -1;
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LogoListBuilder list = new LogoListBuilder();
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try {
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inputValues = args[0].getAgentSet();
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minNumberOfElements = args[1].getIntValue();
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maxDistance = args[2].getDoubleValue();
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} catch (Exception e) {
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throw new ExtensionException(e.getMessage());
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}
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if (minNumberOfElements == -1) {
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throw new ExtensionException("Minimum number of cluster elements has not been defined.");
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}
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if (maxDistance == -1) {
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throw new ExtensionException("Maximum distance of cluster variable has not been defined.");
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}
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// Convert input agentset to collection
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Collection<Turtle> inputCollection = new ArrayList<>();
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Iterator it = inputValues.agents().iterator();
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while (it.hasNext()) {
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inputCollection.add((Turtle) it.next());
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}
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// Perform clustering
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ArrayList<ArrayList<Turtle>> tmpList = null;
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try {
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DBSCANClusterer<Turtle> clusterer = new DBSCANClusterer<Turtle>(inputCollection, minNumberOfElements, maxDistance, new DistanceMetricNetLogoLocation());
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tmpList = clusterer.performClustering();
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} catch (DBSCANClusteringException e) {
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throw new ExtensionException(e);
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}
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// Convert generated lists of clusters to nested LogoList
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for (ArrayList<Turtle> intList: tmpList) {
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LogoListBuilder internalBuilder = new LogoListBuilder();
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for (Turtle agent: intList) {
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internalBuilder.add(agent);
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}
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list.add(internalBuilder.toLogoList());
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}
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return list.toLogoList();
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}
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}
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}

‎src/main/java/org/nlogo/extensions/dbscan/metrics/DistanceMetricNetLogoAgents.java‎

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package org.nlogo.extensions.dbscan.metrics;
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import org.christopherfrantz.dbscan.DBSCANClusteringException;
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import org.christopherfrantz.dbscan.DistanceMetric;
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import org.nlogo.agent.Agent;
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import org.nlogo.api.AgentException;
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public class DistanceMetricNetLogoAgents implements DistanceMetric<Agent>{
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private String field = null;
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public DistanceMetricNetLogoAgents(String field) {
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this.field = field;
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}
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@Override
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public double calculateDistance(Agent val1, Agent val2) throws DBSCANClusteringException {
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try {
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// Check on turtle level first ...
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Double val1Num = Double.parseDouble(val1.getTurtleOrLinkVariable(field).toString());
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Double val2Num = Double.parseDouble(val2.getTurtleOrLinkVariable(field).toString());
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return Math.abs(val1Num - val2Num);
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} catch (ArrayIndexOutOfBoundsException e) {
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try {
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// ... before looking at breed level
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Double val1Num = Double.parseDouble(val1.getBreedVariable(field).toString());
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Double val2Num = Double.parseDouble(val2.getBreedVariable(field).toString());
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return Math.abs(val1Num - val2Num);
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} catch (NumberFormatException | AgentException e1) {
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throw new DBSCANClusteringException(e1.getMessage());
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}
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} catch (NumberFormatException | AgentException e) {
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throw new DBSCANClusteringException(e.getMessage());
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}
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}
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}

‎src/main/java/org/nlogo/extensions/dbscan/metrics/DistanceMetricNetLogoLocation.java‎

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package org.nlogo.extensions.dbscan.metrics;
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import org.christopherfrantz.dbscan.DBSCANClusteringException;
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import org.christopherfrantz.dbscan.DistanceMetric;
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import org.nlogo.agent.Agent;
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import org.nlogo.agent.Turtle;
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import org.nlogo.api.AgentException;
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public class DistanceMetricNetLogoLocation implements DistanceMetric<Turtle>{
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private static final String X_COORDINATE = "XCOR";
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private static final String Y_COORDINATE = "YCOR";
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public DistanceMetricNetLogoLocation() {
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}
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@Override
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public double calculateDistance(Turtle val1, Turtle val2) throws DBSCANClusteringException {
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try {
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Double val1XNum = Double.parseDouble(val1.getTurtleOrLinkVariable(X_COORDINATE).toString());
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Double val1YNum = Double.parseDouble(val1.getTurtleOrLinkVariable(Y_COORDINATE).toString());
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Double val2XNum = Double.parseDouble(val2.getTurtleOrLinkVariable(X_COORDINATE).toString());
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Double val2YNum = Double.parseDouble(val2.getTurtleOrLinkVariable(Y_COORDINATE).toString());
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return StrictMath.sqrt(StrictMath.pow(val1YNum - val2YNum, 2.0) + StrictMath.pow(val1XNum - val2XNum, 2.0));
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} catch (NumberFormatException e) {
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throw new DBSCANClusteringException(e.getMessage());
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}
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}
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}

‎src/main/java/org/nlogo/extensions/dbscan/metrics/DistanceMetricNetLogoTurtles.java‎

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package org.nlogo.extensions.dbscan.metrics;
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import org.christopherfrantz.dbscan.DBSCANClusteringException;
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import org.christopherfrantz.dbscan.DistanceMetric;
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import org.nlogo.agent.Turtle;
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import org.nlogo.api.AgentException;
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public class DistanceMetricNetLogoTurtles implements DistanceMetric<Turtle>{
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private String field = null;
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public DistanceMetricNetLogoTurtles(String field) {
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this.field = field;
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}
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@Override
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public double calculateDistance(Turtle val1, Turtle val2) throws DBSCANClusteringException {
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try {
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// Check on turtle level first ...
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Double val1Num = Double.parseDouble(val1.getTurtleOrLinkVariable(field).toString());
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Double val2Num = Double.parseDouble(val2.getTurtleOrLinkVariable(field).toString());
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return Math.abs(val1Num - val2Num);
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} catch (ArrayIndexOutOfBoundsException e) {
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try {
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// ... before looking at breed level
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Double val1Num = Double.parseDouble(val1.getBreedVariable(field).toString());
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Double val2Num = Double.parseDouble(val2.getBreedVariable(field).toString());
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return Math.abs(val1Num - val2Num);
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} catch (NumberFormatException | AgentException e1) {
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throw new DBSCANClusteringException(e1.getMessage());
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}
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} catch (NumberFormatException e) {
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throw new DBSCANClusteringException(e.getMessage());
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}
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}
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}

‎src/main/resources/manifest.txt‎

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Manifest-Version: 1.0
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Extension-Name: dbscan
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Class-Manager: org.nlogo.extensions.dbscan.DBSCANExtension
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NetLogo-Extension-API-Version: 5.0

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