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From dlig...@apache.org
Subject svn commit: r1511067 - /ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventPrinterPipeline.java
Date Tue, 06 Aug 2013 18:37:43 GMT
Author: dligach
Date: Tue Aug  6 18:37:43 2013
New Revision: 1511067

URL: http://svn.apache.org/r1511067
Log:
Script for printing gold standard events of a given UMLS semantic type

Added:
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventPrinterPipeline.java

Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventPrinterPipeline.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventPrinterPipeline.java?rev=1511067&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventPrinterPipeline.java
(added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventPrinterPipeline.java
Tue Aug  6 18:37:43 2013
@@ -0,0 +1,235 @@
+/**
+ * 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.temporal.data.analysis;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.ctakes.relationextractor.eval.XMIReader;
+import org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
+import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.uima.analysis_engine.AnalysisEngine;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.cas.CASException;
+import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.util.Options_ImplBase;
+import org.kohsuke.args4j.Option;
+import org.uimafit.component.JCasAnnotator_ImplBase;
+import org.uimafit.descriptor.ConfigurationParameter;
+import org.uimafit.factory.AnalysisEngineFactory;
+import org.uimafit.factory.CollectionReaderFactory;
+import org.uimafit.pipeline.SimplePipeline;
+import org.uimafit.util.JCasUtil;
+
+import com.google.common.base.Function;
+import com.google.common.base.Functions;
+import com.google.common.collect.Ordering;
+
+/**
+ * Print events of given UMLS semantic type.
+ * 
+ * @author dmitriy dligach
+ */
+public class EventPrinterPipeline {
+
+  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;
+
+    @Option(
+        name = "--umls-type",
+        usage = "specify the UMLS semantic type (e.g. 5, i.e. procedure)",
+        required = true)
+    public int umlsSemanticType;
+
+    @Option(
+        name = "--event-output-file",
+        usage = "specify the path to the directory containing the clinical notes to be processed",
+        required = true)
+    public File eventOutputFile;
+  }
+  
+	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 annotationConsumer = AnalysisEngineFactory.createPrimitive(
+    		EventAndTokenContextWriter.class,
+    		"UmlsSemanticType",
+    		options.umlsSemanticType,
+    		"EventOutputFile",
+    		options.eventOutputFile);
+    		
+		SimplePipeline.runPipeline(collectionReader, annotationConsumer);
+	}
+
+	/**
+	 * Print events with a given UMLS semantic type.
+	 */
+	public static class EventAndTokenContextWriter extends JCasAnnotator_ImplBase {
+
+	  @ConfigurationParameter(
+	      name = "EventOutputFile",
+	      mandatory = true,
+	      description = "path to the file that stores the events")
+	  private String eventOutputFile;
+
+	  @ConfigurationParameter(
+	      name = "UmlsSemanticType",
+	      mandatory = true,
+	      description = "umls semantic type")
+	  private int umlsSemanticType;
+	  
+	  @Override
+	  public void process(JCas jCas) throws AnalysisEngineProcessException {
+	    
+	    JCas goldView;
+	    try {
+	      goldView = jCas.getView("GoldView");
+	    } catch (CASException e) {
+	      throw new AnalysisEngineProcessException(e);
+	    }
+	    
+	    JCas systemView;
+	    try {
+	      systemView = jCas.getView("_InitialView");
+	    } catch (CASException e) {
+	      throw new AnalysisEngineProcessException(e);
+	    }
+
+	    BufferedWriter eventWriter = getWriter(eventOutputFile, true);
+	    try {
+	      for(EventMention eventMention : JCasUtil.select(goldView, EventMention.class)) {
+	        
+	        List<EntityMention> coveringEntityMentions = JCasUtil.selectCovered(
+	            systemView, 
+	            EntityMention.class, 
+	            eventMention.getBegin(), 
+	            eventMention.getEnd());
+	        
+	        for(EntityMention entityMention : coveringEntityMentions) {
+	          if(entityMention.getTypeID() == umlsSemanticType) { 
+	            String output = String.format(
+	                "%s|%s\n", 
+	                entityMention.getCoveredText().toLowerCase(),
+	                expandToNP(systemView, eventMention).toLowerCase());
+	            try {
+	              eventWriter.write(output);
+	            } catch (IOException e) {
+	              throw new AnalysisEngineProcessException(e);
+	            }
+	          }
+	        }
+	      }
+	    } finally {
+	      try {
+	        eventWriter.close();
+	      } catch (IOException e) {
+	        throw new AnalysisEngineProcessException(e);
+	      }
+	    }
+	  }
+	}
+
+  public static BufferedWriter getWriter(String filePath, boolean append) {
+
+    BufferedWriter bufferedWriter = null;
+    try {
+      FileWriter fileWriter = new FileWriter(filePath, append);
+      bufferedWriter = new BufferedWriter(fileWriter);
+    } catch (IOException e) {
+      e.printStackTrace();
+    }
+
+    return bufferedWriter;
+  }
+  
+	public static CollectionReader getCollectionReader(List<File> inputFiles) throws Exception
{
+
+	  List<String> fileNames = new ArrayList<String>();
+	  for(File file : inputFiles) {
+	    if(! (file.isHidden())) {
+	      fileNames.add(file.getPath());
+	    }
+	  }
+
+	  String[] paths = new String[fileNames.size()];
+	  fileNames.toArray(paths);
+
+	  return CollectionReaderFactory.createCollectionReader(
+	      XMIReader.class,
+	      XMIReader.PARAM_FILES,
+	      paths);
+	}
+
+	public static String expandToNP(JCas jCas, IdentifiedAnnotation identifiedAnnotation) {
+
+	  // map each covering treebank node to its character length
+	  Map<TreebankNode, Integer> treebankNodeSizes = new HashMap<TreebankNode, Integer>();
+	  for(TreebankNode treebankNode : JCasUtil.selectCovering(
+	      jCas, 
+	      TreebankNode.class, 
+	      identifiedAnnotation.getBegin(), 
+	      identifiedAnnotation.getEnd())) {
+
+	    // only expand nouns (and not verbs or adjectives)
+	    if(treebankNode instanceof TerminalTreebankNode) {
+	      if(! treebankNode.getNodeType().startsWith("N")) {
+	        return identifiedAnnotation.getCoveredText();
+	      }
+	    }
+
+	    // because only nouns are expanded, look for covering NPs
+	    if(treebankNode.getNodeType().equals("NP")) {
+	      treebankNodeSizes.put(treebankNode, treebankNode.getCoveredText().length());
+	    }
+	  }
+
+	  // find the shortest covering treebank node
+	  List<TreebankNode> sortedTreebankNodes = new ArrayList<TreebankNode>(treebankNodeSizes.keySet());
+	  Function<TreebankNode, Integer> getValue = Functions.forMap(treebankNodeSizes);
+	  Collections.sort(sortedTreebankNodes, Ordering.natural().onResultOf(getValue));
+
+	  if(sortedTreebankNodes.size() > 0) {
+	    return sortedTreebankNodes.get(0).getCoveredText();
+	  } 
+
+	  return identifiedAnnotation.getCoveredText();
+	}
+}



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