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Subject: svn commit: r1587731 -
 /ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/GoldRelationViewer.java
Date: Tue, 15 Apr 2014 21:04:19 -0000
To: commits@ctakes.apache.org
From: dligach@apache.org
Message-Id: <20140415210419.936BA238896F@eris.apache.org>

Author: dligach
Date: Tue Apr 15 21:04:19 2014
New Revision: 1587731

URL: http://svn.apache.org/r1587731
Log:
Print a sentence and all gold relations that are annotated in it.

Added:
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/GoldRelationViewer.java   (with props)

Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/GoldRelationViewer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/GoldRelationViewer.java?rev=1587731&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/GoldRelationViewer.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/GoldRelationViewer.java Tue Apr 15 21:04:19 2014
@@ -0,0 +1,192 @@
+/**
+ * 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.File;
+import java.io.FilenameFilter;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.ctakes.core.cr.XMIReader;
+import org.apache.ctakes.temporal.eval.CommandLine;
+import org.apache.ctakes.temporal.eval.THYMEData;
+import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+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.apache.uima.jcas.tcas.Annotation;
+import org.uimafit.component.JCasAnnotator_ImplBase;
+import org.uimafit.factory.AnalysisEngineFactory;
+import org.uimafit.factory.CollectionReaderFactory;
+import org.uimafit.pipeline.SimplePipeline;
+import org.uimafit.util.JCasUtil;
+
+import com.lexicalscope.jewel.cli.CliFactory;
+import com.lexicalscope.jewel.cli.Option;
+
+/**
+ * Print gold standard relations and their context.
+ * 
+ * @author dmitriy dligach
+ */
+public class GoldRelationViewer {
+  
+  static interface Options {
+
+    @Option(longName = "xmi-dir")
+    public File getInputDirectory();
+    
+    @Option(longName = "patients")
+    public CommandLine.IntegerRanges getPatients();
+  }
+  
+	public static void main(String[] args) throws Exception {
+		
+		Options options = CliFactory.parseArguments(Options.class, args);
+		
+		List<Integer> patientSets = options.getPatients().getList();
+		List<Integer> trainItems = THYMEData.getTrainPatientSets(patientSets);
+		List<File> trainFiles = getFilesFor(trainItems, options.getInputDirectory());
+    CollectionReader collectionReader = getCollectionReader(trainFiles);
+		
+    AnalysisEngine annotationConsumer = AnalysisEngineFactory.createPrimitive(
+    		RelationContextPrinter.class);
+    		
+		SimplePipeline.runPipeline(collectionReader, annotationConsumer);
+	}
+	  
+	private static CollectionReader getCollectionReader(List<File> inputFiles) throws Exception {
+
+	  List<String> fileNames = new ArrayList<>();
+	  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);
+	}
+
+	private static List<File> getFilesFor(List<Integer> patientSets, File inputDirectory) {
+	  
+	  List<File> files = new ArrayList<>();
+	  
+	  for (Integer set : patientSets) {
+	    final int setNum = set;
+	    for (File file : inputDirectory.listFiles(new FilenameFilter(){
+	      @Override
+	      public boolean accept(File dir, String name) {
+	        return name.contains(String.format("ID%03d", setNum));
+	      }})) {
+	      // skip hidden files like .svn
+	      if (!file.isHidden()) {
+	        files.add(file);
+	      } 
+	    }
+	  }
+	  
+	  return files;
+	}
+
+  /**
+   * Print gold standard relations and their context.
+   * 
+   * @author dmitriy dligach
+   */
+  public static class RelationContextPrinter extends JCasAnnotator_ImplBase {
+    
+    @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);
+      }
+
+      // can't iterate over binary text relations in a sentence, so need
+      // a lookup from pair of annotations to binary text relation
+      Map<List<Annotation>, BinaryTextRelation> relationLookup = new HashMap<>();
+      for(BinaryTextRelation relation : JCasUtil.select(goldView, BinaryTextRelation.class)) {
+        Annotation arg1 = relation.getArg1().getArgument();
+        Annotation arg2 = relation.getArg2().getArgument();
+        relationLookup.put(Arrays.asList(arg1, arg2), relation);
+      }
+
+      for(Sentence sentence : JCasUtil.select(systemView, Sentence.class)) {
+        List<String> formattedRelationsInSentence = new ArrayList<>();
+        List<EventMention> eventMentions = JCasUtil.selectCovered(goldView, EventMention.class, sentence);
+        for(EventMention mention1 : eventMentions) {
+          for(EventMention mention2 : eventMentions) {
+            if(mention1 == mention2) {
+              continue;
+            }
+            BinaryTextRelation relation = relationLookup.get(Arrays.asList(mention1, mention2));
+            if(relation != null) {
+              String text = String.format("%s(%s, %s)", relation.getCategory(), mention1.getCoveredText(), mention2.getCoveredText());
+              formattedRelationsInSentence.add(text);
+            }
+          }
+        }
+        if(formattedRelationsInSentence.size() > 0) {
+          System.out.println(sentence.getCoveredText());
+          for(String text : formattedRelationsInSentence) {
+            System.out.println(text);
+          }
+          System.out.println();
+        }
+      }
+    }
+    
+    @SuppressWarnings("unused")
+    private static String getTextBetweenAnnotations(JCas jCas, Annotation arg1, Annotation arg2) {
+      
+      final int windowSize = 15;
+      
+      String text = jCas.getDocumentText();
+      int leftArgBegin = Math.min(arg1.getBegin(), arg2.getBegin());
+      int rightArgEnd = Math.max(arg1.getEnd(), arg2.getEnd());
+      int begin = Math.max(0, leftArgBegin - windowSize);
+      int end = Math.min(text.length(), rightArgEnd + windowSize); 
+      
+      return text.substring(begin, end).replaceAll("[\r\n]", " ");
+    }
+  }
+}

Propchange: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/GoldRelationViewer.java
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