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Posted to commits@ctakes.apache.org by tm...@apache.org on 2013/05/22 16:22:46 UTC
svn commit: r1485222 -
/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java
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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