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From tm...@apache.org
Subject svn commit: r1485222 - /ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java
Date Wed, 22 May 2013 14:22:46 GMT
Author: tmill
Date: Wed May 22 14:22:46 2013
New Revision: 1485222

URL: http://svn.apache.org/r1485222
Log:
addresses ctakes-154: Class to generate candidate feature trees for doing tree fragment feature
selection.

Added:
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java
  (with props)

Added: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java?rev=1485222&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java
(added)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java
Wed May 22 14:22:46 2013
@@ -0,0 +1,110 @@
+package org.apache.ctakes.assertion.pipelines;
+
+import static org.apache.ctakes.assertion.util.AssertionTreeUtils.extractAboveLeftConceptTree;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.PrintStream;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.List;
+
+import org.apache.ctakes.assertion.eval.XMIReader;
+import org.apache.ctakes.assertion.util.SemanticClasses;
+import org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils;
+import org.apache.ctakes.core.resource.FileLocator;
+import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.typesystem.type.constants.CONST;
+import org.apache.ctakes.typesystem.type.syntax.TopTreebankNode;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.utils.tree.SimpleTree;
+import org.apache.log4j.Logger;
+import org.apache.uima.UIMAException;
+import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.cleartk.util.Options_ImplBase;
+import org.kohsuke.args4j.Option;
+import org.uimafit.factory.CollectionReaderFactory;
+import org.uimafit.pipeline.JCasIterable;
+import org.uimafit.util.JCasUtil;
+
+public class GenerateTreeRepresentation{
+
+	public static class Options extends Options_ImplBase {
+
+		@Option(
+				name = "--train-dir",
+				usage = "specify the directory containing the XMI training files (for example, /NLP/Corpus/Relations/mipacq/xmi/train)",
+				required = true)
+		public File trainDirectory;
+		
+		@Option(
+				name = "--output",
+				usage = "The file to which the data points be written.",
+				required = true)
+		public File outFile;
+	}
+	
+	protected static Options options = new Options();
+	private static SemanticClasses sems = null; 
+	private static PrintStream out = null;
+	private static Logger log = Logger.getLogger(GenerateTreeRepresentation.class);
+	
+	/**
+	 * @param args
+	 * @throws IOException 
+	 * @throws UIMAException 
+	 */
+	public static void main(String[] args) throws UIMAException, IOException {
+	    options.parseOptions(args);
+	    
+	    out = new PrintStream(options.outFile);
+	    List<File> trainFiles = Arrays.asList(options.trainDirectory.listFiles());
+
+	    String[] paths = new String[trainFiles.size()];
+	    for (int i = 0; i < paths.length; ++i) {
+	      paths[i] = trainFiles.get(i).getPath();
+	    }
+	    CollectionReader reader = CollectionReaderFactory.createCollectionReader(
+	            XMIReader.class,
+	            XMIReader.PARAM_FILES,
+	            paths);
+	       
+	    JCasIterable casIter = new JCasIterable(reader);
+	    while(casIter.hasNext()){
+	    	JCas jcas = casIter.next();
+	    	processDocument(jcas);
+	    }
+	    out.close();
+	}
+
+	public static void processDocument(JCas jcas) throws ResourceInitializationException, FileNotFoundException
{
+		log.info("Processing document: " + DocumentIDAnnotationUtil.getDocumentID(jcas));
+		if(sems == null){
+			sems = new SemanticClasses(FileLocator.locateFile("org/apache/ctakes/assertion/models/semantic_classes").getAbsolutePath());
+		}
+		Collection<IdentifiedAnnotation> mentions = JCasUtil.select(jcas, IdentifiedAnnotation.class);
+		for(IdentifiedAnnotation mention : mentions){
+			TopTreebankNode orig = AnnotationTreeUtils.getAnnotationTree(jcas, mention);
+			if(orig == null){
+				log.warn("Tree for entity mention: " + mention.getCoveredText() + " (" + mention.getBegin()
+ "-" + mention.getEnd() + ") is null.");
+				continue;
+			}
+			SimpleTree tree = extractAboveLeftConceptTree(jcas, mention, sems);
+//			if(mention.getPolarity() == CONST.NE_POLARITY_NEGATION_PRESENT){
+			if(mention.getUncertainty() == CONST.NE_UNCERTAINTY_PRESENT){
+				out.print("+1 ");
+			}else{
+				out.print("-1 ");
+			}
+			
+			out.print("|BT| ");
+			out.print(tree.toString());
+			out.println(" |ET|");
+			out.flush();
+		}
+	}
+
+}

Propchange: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java
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