*full implementation, does not work!

*should start the debugging now

de.uniwue.ls6.rulelearning/.classpath

 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" output="target/classes" path="src/main/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>

de.uniwue.ls6.rulelearning/DataStructure/src/de/uniwue/ls6/datastructure/Instance.java

@@ -20,12 +20,12 @@ public class Instance {
 
 	public Instance(int nrRows, int nrCols) {
 		super();
-		featureArray = new int[nrRows][nrCols];
+		featureArray = new int[nrCols][nrRows];
 	}
 
 	public Instance(int nrRows, int nrCols, int label) {
 		super();
-		featureArray = new int[nrRows][nrCols];
+		featureArray = new int[nrCols][nrRows];
 		this.label = label;
 	}
 
@@ -33,6 +33,9 @@ public class Instance {
 		return label;
 	}
 
+	public void setFeatureAt(int col,int row, int value){
+		featureArray[col][row] = value;
+	}
 	public void setLabel(int label) {
 		this.label = label;
 	}

de.uniwue.ls6.rulelearning/InstanceLoading/.classpath

+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/J2SE-1.5">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

de.uniwue.ls6.rulelearning/InstanceLoading/.gitignore

+/target/

de.uniwue.ls6.rulelearning/InstanceLoading/.project

+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>InstanceLoading</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+	</natures>
+</projectDescription>

de.uniwue.ls6.rulelearning/InstanceLoading/.settings/org.eclipse.core.resources.prefs

+eclipse.preferences.version=1
+encoding/<project>=UTF-8

de.uniwue.ls6.rulelearning/InstanceLoading/.settings/org.eclipse.jdt.core.prefs

+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.5
+org.eclipse.jdt.core.compiler.compliance=1.5
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.source=1.5

de.uniwue.ls6.rulelearning/InstanceLoading/.settings/org.eclipse.m2e.core.prefs

+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1

de.uniwue.ls6.rulelearning/InstanceLoading/pom.xml

+<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>
+		<groupId>de.uniwue.ls6.rulelearning</groupId>
+		<relativePath>../</relativePath>
+		<artifactId>ruleLearningParent</artifactId>
+		<version>0.0.1-SNAPSHOT</version>
+	</parent>
+	<groupId>de.uniwue.ls6.rulelearning</groupId>
+	<artifactId>InstanceLoading</artifactId>
+	<version>0.0.1-SNAPSHOT</version>
+	<packaging>jar</packaging>
+
+	<name>InstanceLoading</name>
+	<url>http://maven.apache.org</url>
+
+	<properties>
+		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+	</properties>
+
+	<dependencies>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<version>3.8.1</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>de.uniwue.ls6.rulelearning</groupId>
+			<artifactId>DataStructure</artifactId>
+			<version>0.0.1-SNAPSHOT</version>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.uima</groupId>
+			<artifactId>uimaj-core</artifactId>
+			<version>2.9.0</version>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.uima</groupId>
+			<artifactId>uimafit-core</artifactId>
+			<version>2.2.0</version>
+		</dependency>
+
+	</dependencies>
+</project>

de.uniwue.ls6.rulelearning/InstanceLoading/src/de/uniwue/ls6/rulelearning/instanceloading/featuregenerator/AFeatureGenerator.java

+package de.uniwue.ls6.rulelearning.instanceloading.featuregenerator;
+
+import org.apache.uima.cas.text.AnnotationFS;
+
+public abstract class AFeatureGenerator {
+	
+	public abstract String[] generateFeatures(AnnotationFS token);
+
+}

de.uniwue.ls6.rulelearning/InstanceLoading/src/de/uniwue/ls6/rulelearning/instanceloading/featuregenerator/IsUppercaseFeatureGenerator.java

+package de.uniwue.ls6.rulelearning.instanceloading.featuregenerator;
+
+import org.apache.uima.cas.text.AnnotationFS;
+
+public class IsUppercaseFeatureGenerator extends AFeatureGenerator {
+
+	public static final String LOWERCASE = "Lowercase";
+	public static final String UPPERCASE = "Uppercase";
+
+	@Override
+	public String[] generateFeatures(AnnotationFS token) {
+		
+		return new String[]{Character.isUpperCase(token.getCoveredText().charAt(0))?UPPERCASE:LOWERCASE};
+	}
+
+}

de.uniwue.ls6.rulelearning/InstanceLoading/src/de/uniwue/ls6/rulelearning/instanceloading/featuregenerator/WordFeaturegenerator.java

+package de.uniwue.ls6.rulelearning.instanceloading.featuregenerator;
+
+import org.apache.uima.cas.text.AnnotationFS;
+
+public class WordFeaturegenerator extends AFeatureGenerator{
+
+	@Override
+	public String[] generateFeatures(AnnotationFS token) {
+		return new String[]{token.getCoveredText()};
+	}
+
+}

de.uniwue.ls6.rulelearning/InstanceLoading/src/de/uniwue/ls6/rulelearning/instanceloading/io/InstanceCreationFactory.java

+package de.uniwue.ls6.rulelearning.instanceloading.io;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Queue;
+
+import org.apache.uima.cas.CAS;
+import org.apache.uima.cas.Type;
+import org.apache.uima.cas.impl.XmiCasDeserializer;
+import org.apache.uima.cas.text.AnnotationFS;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.apache.uima.resource.metadata.TypeSystemDescription;
+import org.apache.uima.util.CasCreationUtils;
+import org.xml.sax.SAXException;
+
+import de.uniwue.ls6.datastructure.Instance;
+import de.uniwue.ls6.datastructure.LabelAlphabet;
+import de.uniwue.ls6.rulelearning.instanceloading.featuregenerator.AFeatureGenerator;
+
+public class InstanceCreationFactory {
+
+	public static List<Instance> createWindowedInstancesFromUIMA(File fileToDocument, int leftWindowsize,
+			int rightWindowSize, String tokentypeS, TypeSystemDescription typesystem, AFeatureGenerator goldGenerator,
+			AFeatureGenerator... generators) throws ResourceInitializationException, SAXException, IOException {
+
+		// deserialize
+		CAS cas = CasCreationUtils.createCas(typesystem, null, null);
+		FileInputStream fis = new FileInputStream(fileToDocument);
+		XmiCasDeserializer.deserialize(fis, cas);
+		Type tokentype = cas.getTypeSystem().getType(tokentypeS);
+		fis.close();
+
+		//
+		List<Instance> instances = new ArrayList<Instance>();
+		int windowSize = leftWindowsize + 1 + rightWindowSize;
+		Queue<List<String>> windowQueue = new LinkedList<List<String>>();
+		List<String> labelList = new ArrayList<String>();
+		// init leftWindowsize empty lists
+		for (int i = 0; i < leftWindowsize; i++) {
+			windowQueue.add(new LinkedList<String>());
+		}
+		int tokenIndex = 0;
+		for (AnnotationFS token : cas.getAnnotationIndex(tokentype)) {
+
+			String goldFeature = goldGenerator.generateFeatures(token)[0];
+			labelList.add(goldFeature);
+			List<String> featureForToken = generateFeatureForToken(token, generators);
+			// generate the instance with the help of the queue
+
+			// update the queue
+			if (windowQueue.size() >= windowSize) {
+				Instance inst = generateInstanceFromQueue(windowQueue, windowSize, labelList.get(tokenIndex));
+				instances.add(inst);
+				windowQueue.poll();
+				tokenIndex++;
+			}
+			windowQueue.add(featureForToken);
+		}
+		// add remaining tokens at the end of the token stream
+		for (int i = 0; i < rightWindowSize; i++) {
+			windowQueue.poll();
+			windowQueue.add(new LinkedList<String>());
+			Instance inst = generateInstanceFromQueue(windowQueue, windowSize, labelList.get(tokenIndex));
+			instances.add(inst);
+			tokenIndex++;
+		}
+
+		return instances;
+
+	}
+
+	private static Instance generateInstanceFromQueue(Queue<List<String>> windowQueue, int windowSize,
+			String goldfeature) {
+		int maxNrRows = 0;
+		for (List<String> features : windowQueue) {
+			if (features.size() > maxNrRows)
+				maxNrRows = features.size();
+		}
+
+		int idToFeature = LabelAlphabet.getIdToFeature(goldfeature);
+		Instance instance = new Instance(maxNrRows, windowSize, idToFeature);
+		//fill the data
+		int colNr =0;
+		for(List<String> tokenFeatures : windowQueue){
+			for(int i =0;i<tokenFeatures.size();i++){
+				instance.setFeatureAt(colNr, i, LabelAlphabet.getIdToFeature(tokenFeatures.get(i)));
+			}
+		colNr++;
+		}
+
+		return instance;
+	}
+
+	private static List<String> generateFeatureForToken(AnnotationFS token, AFeatureGenerator[] generators) {
+		List<String> features = new ArrayList<String>();
+		for (AFeatureGenerator generator : generators) {
+			features.addAll(Arrays.asList(generator.generateFeatures(token)));
+		}
+		return features;
+	}
+}

de.uniwue.ls6.rulelearning/RuleLearning/pom.xml

@@ -9,6 +9,11 @@
   		<artifactId>DataStructure</artifactId>
   		<version>0.0.1-SNAPSHOT</version>
   	</dependency>
+  	<dependency>
+  		<groupId>de.uniwue.ls6.rulelearning</groupId>
+  		<artifactId>InstanceLoading</artifactId>
+  		<version>0.0.1-SNAPSHOT</version>
+  	</dependency>
   </dependencies>
     <parent>
   	<groupId>de.uniwue.ls6.rulelearning</groupId>

de.uniwue.ls6.rulelearning/RuleLearning/src/test/FirstTest.java

+package test;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+
+import org.apache.uima.fit.factory.TypeSystemDescriptionFactory;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.apache.uima.resource.metadata.TypeSystemDescription;
+import org.xml.sax.SAXException;
+
+import de.uniwue.ls6.datastructure.Instance;
+import de.uniwue.ls6.datastructure.LabelAlphabet;
+import de.uniwue.ls6.rulelearning.algorithm.impl.BinaryRepresentationRuleLearningAlgorithm;
+import de.uniwue.ls6.rulelearning.instanceloading.featuregenerator.IsUppercaseFeatureGenerator;
+import de.uniwue.ls6.rulelearning.instanceloading.featuregenerator.WordFeaturegenerator;
+import de.uniwue.ls6.rulelearning.instanceloading.io.InstanceCreationFactory;
+
+public class FirstTest {
+
+	public static void main(String[] args) throws Exception {
+
+		File document = new File("C:\\Users\\mkrug\\annoTest\\TestProject\\input\\Aston,-Louise__Lydia.xmi.xmi.xmi");
+		File typesystem = new File("C:\\Users\\mkrug\\annoTest\\TestProject\\descriptor\\MiKalliTypesystem.xml");
+
+		BinaryRepresentationRuleLearningAlgorithm algorithm = new BinaryRepresentationRuleLearningAlgorithm(
+				LabelAlphabet.getIdToFeature(IsUppercaseFeatureGenerator.LOWERCASE),
+				LabelAlphabet.getIdToFeature(IsUppercaseFeatureGenerator.UPPERCASE));
+		
+		TypeSystemDescription tsd = TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath(typesystem.toURL().toString());
+		List<Instance> instances = InstanceCreationFactory.createWindowedInstancesFromUIMA(document, 2, 2, "de.uniwue.kalimachos.coref.type.POS", tsd, new IsUppercaseFeatureGenerator(), new WordFeaturegenerator());
+		
+		System.out.println(instances.size());
+		
+		algorithm.learn(instances.toArray(new Instance[0]));
+
+	}
+
+}

de.uniwue.ls6.rulelearning/pom.xml

@@ -8,5 +8,6 @@
   	<module>DataStructure</module>
   	<module>Evaluation</module>
   	<module>RuleLearning</module>
+  	<module>InstanceLoading</module>
   </modules>
 </project>
\ No newline at end of file