svn commit: r1429860 - in /incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data: GoldAnnotationAnalysis.java GoldAnnotationStats.java

[dl...@apache.org]

Author: dligach
Date: Mon Jan  7 15:53:31 2013
New Revision: 1429860

URL: http://svn.apache.org/viewvc?rev=1429860&view=rev
Log:
added init version of two classes for analyzing gold standard annotations

Added:
    incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationAnalysis.java
    incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationStats.java

Added: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationAnalysis.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationAnalysis.java?rev=1429860&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationAnalysis.java (added)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationAnalysis.java Mon Jan  7 15:53:31 2013
@@ -0,0 +1,80 @@
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.ctakes.relationextractor.data;
+
+import java.io.File;
+import java.util.Arrays;
+import java.util.List;
+
+import org.apache.ctakes.relationextractor.eval.XMIReader;
+import org.apache.uima.analysis_engine.AnalysisEngine;
+import org.apache.uima.collection.CollectionReader;
+import org.cleartk.util.Options_ImplBase;
+import org.kohsuke.args4j.Option;
+import org.uimafit.factory.AnalysisEngineFactory;
+import org.uimafit.factory.CollectionReaderFactory;
+import org.uimafit.pipeline.SimplePipeline;
+
+/**
+ * 
+ * Pipeline for analyzing gold annotations.
+ *  
+ * @author dmitriy dligach
+ *
+ */
+public class GoldAnnotationAnalysis {
+
+  public static class Options extends Options_ImplBase {
+
+    @Option(
+        name = "--input-dir",
+        usage = "specify the path to the directory containing the clinical notes to be processed",
+        required = true)
+    public File inputDirectory;
+  }
+  
+	public static void main(String[] args) throws Exception {
+		
+		Options options = new Options();
+		options.parseOptions(args);
+
+		List<File> trainFiles = Arrays.asList(options.inputDirectory.listFiles());
+    CollectionReader collectionReader = getCollectionReader(trainFiles);
+		
+    AnalysisEngine relationExtractorConsumer = AnalysisEngineFactory.createPrimitive(
+    		GoldAnnotationStats.class);
+    		
+		SimplePipeline.runPipeline(collectionReader, relationExtractorConsumer);
+	}
+	
+  private static CollectionReader getCollectionReader(List<File> items) throws Exception {
+
+  	// convert the List<File> to a String[]
+    String[] paths = new String[items.size()];
+    for (int i = 0; i < paths.length; ++i) {
+      paths[i] = items.get(i).getPath();
+    }
+    
+    // return a reader that will load each of the XMI files
+    return CollectionReaderFactory.createCollectionReader(
+        XMIReader.class,
+        XMIReader.PARAM_FILES,
+        paths);
+  }
+}

Added: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationStats.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationStats.java?rev=1429860&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationStats.java (added)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationStats.java Mon Jan  7 15:53:31 2013
@@ -0,0 +1,104 @@
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.ctakes.relationextractor.data;
+
+import java.util.List;
+
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.cas.CAS;
+import org.apache.uima.cas.CASException;
+import org.apache.uima.jcas.JCas;
+import org.uimafit.component.JCasAnnotator_ImplBase;
+import org.uimafit.util.JCasUtil;
+
+import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+
+/**
+ * This is a sample relation annotation consumer. 
+ * Currently it displays the relation annotations.
+ * 
+ * @author dmitriy dligach
+ *
+ */
+public class GoldAnnotationStats extends JCasAnnotator_ImplBase {
+
+	// TODO: turn these into configuration parameters
+	public final boolean displayEntities = false;
+	public final boolean displayContext = false;
+	
+	@Override
+  public void process(JCas jCas) throws AnalysisEngineProcessException {
+
+    JCas systemView;
+    try {
+      systemView = jCas.getView(CAS.NAME_DEFAULT_SOFA);
+    } catch (CASException e) {
+      throw new AnalysisEngineProcessException(e);
+    }	  
+    
+    if(displayEntities) {
+    	System.out.println();
+    	for(IdentifiedAnnotation identifiedAnnotation : JCasUtil.select(systemView, IdentifiedAnnotation.class)) {
+    		String text = identifiedAnnotation.getCoveredText();
+    		int type = identifiedAnnotation.getTypeID();
+    		System.out.format("%s/%d\n", text, type);
+    	}
+    	System.out.println();
+    }
+
+    // print relations
+    System.out.println();
+    for(BinaryTextRelation binaryTextRelation : JCasUtil.select(systemView, BinaryTextRelation.class)) {
+    	    	
+    	String category = binaryTextRelation.getCategory();
+    	
+    	IdentifiedAnnotation entity1; // entity whose role is "Argument"
+    	IdentifiedAnnotation entity2; // entity whose role is "Related_to"
+    	
+    	if(binaryTextRelation.getArg1().getRole().equals("Argument")) {
+    		entity1 = (IdentifiedAnnotation) binaryTextRelation.getArg1().getArgument();
+    		entity2 = (IdentifiedAnnotation) binaryTextRelation.getArg2().getArgument();
+    	} else {
+    		entity1 = (IdentifiedAnnotation) binaryTextRelation.getArg2().getArgument();
+    		entity2 = (IdentifiedAnnotation) binaryTextRelation.getArg1().getArgument();
+    	}
+    	
+    	String arg1 = entity1.getCoveredText();
+    	String arg2 = entity2.getCoveredText();
+    	
+    	int type1 = entity1.getTypeID();
+    	int type2 = entity2.getTypeID();
+    	
+    	// print relation and its arguments: location_of(colon/6, colon cancer/2)
+    	System.out.format("%s(%s/%d, %s/%d)\n", category, arg1, type1, arg2, type2);
+
+    	if(displayContext) {
+    		List<Sentence> list = JCasUtil.selectCovering(jCas, Sentence.class, entity1.getBegin(), entity1.getEnd());
+    		
+    		// print the sentence containing this instance
+    		for(Sentence s : list) {
+    			System.out.println(s.getCoveredText());
+    		}
+    		System.out.println();
+    	}
+    }
+  }
+}