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From dlig...@apache.org
Subject svn commit: r1750125 - /ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eventTimeRelationPrinter.java
Date Fri, 24 Jun 2016 15:44:44 GMT
Author: dligach
Date: Fri Jun 24 15:44:44 2016
New Revision: 1750125

URL: http://svn.apache.org/viewvc?rev=1750125&view=rev
Log:
printing event-time relations for nn experiments

Added:
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eventTimeRelationPrinter.java

Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eventTimeRelationPrinter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eventTimeRelationPrinter.java?rev=1750125&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eventTimeRelationPrinter.java
(added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eventTimeRelationPrinter.java
Fri Jun 24 15:44:44 2016
@@ -0,0 +1,254 @@
+/**
+ * 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.nn;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+import java.nio.file.StandardOpenOption;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.ctakes.temporal.duration.Utils;
+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.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.TimeMention;
+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.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+
+import com.lexicalscope.jewel.cli.CliFactory;
+import com.lexicalscope.jewel.cli.Option;
+
+/**
+ * Print gold standard relations and their context.
+ * 
+ * @author dmitriy dligach
+ */
+public class eventTimeRelationPrinter {
+
+  static interface Options {
+
+    @Option(longName = "xmi-dir")
+    public File getInputDirectory();
+
+    @Option(longName = "patients")
+    public CommandLine.IntegerRanges getPatients();
+
+    @Option(longName = "output-train")
+    public File getTrainOutputDirectory();
+
+    @Option(longName = "output-test")
+    public File getTestOutputDirectory();
+  }
+
+  public static void main(String[] args) throws Exception {
+
+    Options options = CliFactory.parseArguments(Options.class, args);
+
+    File trainFile = options.getTrainOutputDirectory();
+    if(trainFile.exists()) {
+      trainFile.delete();
+    }
+    trainFile.createNewFile();
+    File devFile = options.getTestOutputDirectory();
+    if(devFile.exists()) {
+      devFile.delete();
+    }
+    devFile.createNewFile();
+
+    List<Integer> patientSets = options.getPatients().getList();
+    List<Integer> trainItems = THYMEData.getPatientSets(patientSets, THYMEData.TRAIN_REMAINDERS);
+    List<Integer> devItems = THYMEData.getPatientSets(patientSets, THYMEData.DEV_REMAINDERS);
+
+    List<File> trainFiles = Utils.getFilesFor(trainItems, options.getInputDirectory());
+    List<File> devFiles = Utils.getFilesFor(devItems, options.getInputDirectory());
+
+    // write training data to file
+    CollectionReader trainCollectionReader = Utils.getCollectionReader(trainFiles);
+    AnalysisEngine trainDataWriter = AnalysisEngineFactory.createEngine(
+        RelationSnippetPrinter.class,
+        "OutputFile",
+        trainFile.getAbsoluteFile());
+    SimplePipeline.runPipeline(trainCollectionReader, trainDataWriter);
+
+    // write dev data to file
+    CollectionReader devCollectionReader = Utils.getCollectionReader(devFiles);
+    AnalysisEngine devDataWriter = AnalysisEngineFactory.createEngine(
+        RelationSnippetPrinter.class,
+        "OutputFile",
+        devFile.getAbsolutePath());
+    SimplePipeline.runPipeline(devCollectionReader, devDataWriter);
+  }
+
+  /**
+   * Print gold standard relations and their context.
+   * 
+   * @author dmitriy dligach
+   */
+  public static class RelationSnippetPrinter extends JCasAnnotator_ImplBase {
+
+    @ConfigurationParameter(
+        name = "OutputFile",
+        mandatory = true,
+        description = "path to the output file")
+    private String outputFile;
+
+    @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);
+      }
+
+      // go over sentences, extracting event-event relation instances
+      for(Sentence sentence : JCasUtil.select(systemView, Sentence.class)) {
+        List<String> eventEventRelationsInSentence = new ArrayList<>();
+
+        // retrieve event-time relations in this sentence
+        for(EventMention event : JCasUtil.selectCovered(goldView, EventMention.class, sentence))
{
+          for(TimeMention time : JCasUtil.selectCovered(goldView, TimeMention.class, sentence))
{
+            BinaryTextRelation timeEventRelation = relationLookup.get(Arrays.asList(time,
event));
+
+            String label;
+            if(timeEventRelation != null) {
+              if(timeEventRelation.getCategory().equals("CONTAINS")) {
+                label = "contains"; 
+              } else {
+                label = "none"; // e.g. before or overlap
+              }
+            } else {
+              label = "none";   // no relation between this time and event
+            }
+            
+            String context;
+            if(time.getBegin() < event.getBegin()) {
+              // ... time ... event ... scenario
+              context = getTokensBetween(systemView, sentence, time, "t", event, "e", 2);
 
+            } else {
+              // ... event ... time ... scenario
+              context = getTokensBetween(systemView, sentence, event, "e", time, "t", 2);
+            }
+            
+            String text = String.format("%s|%s", label, context);
+            eventEventRelationsInSentence.add(text.toLowerCase());
+          }
+        }  
+        
+        //            BinaryTextRelation eventTimeRelation = relationLookup.get(Arrays.asList(event,
time));
+
+        //
+        //            String label;            
+        //            if(forwardRelation != null) {
+        //              if(forwardRelation.getCategory().equals("CONTAINS")) {
+        //                label = "contains";   // this is contains relation
+        //              } else {
+        //                label = "none";       // this is some other relation
+        //              }
+        //            } else if(reverseRelation != null) {
+        //              if(reverseRelation.getCategory().equals("CONTAINS")) {
+        //                label = "contains-1"; // this is contains relation
+        //              } else {
+        //                label = "none";       // this is some other relation
+        //              }
+        //            } else {
+        //              label = "none";         // no relation between mentions
+        //            }
+
+        try {
+          Files.write(Paths.get(outputFile), eventEventRelationsInSentence, StandardOpenOption.APPEND);
+        } catch (IOException e) {
+          e.printStackTrace();
+        }
+      }
+    }
+  }
+
+  /**
+   * Return tokens between arg1 and arg2 as string 
+   * @param contextSize number of tokens to include on the left of arg1 and on the right
of arg2
+   */
+  public static String getTokensBetween(
+      JCas jCas, 
+      Sentence sent, 
+      Annotation left,
+      String leftType,
+      Annotation right,
+      String rightType,
+      int contextSize) {
+
+    List<String> tokens = new ArrayList<>();
+    for(BaseToken baseToken :  JCasUtil.selectPreceding(jCas, BaseToken.class, left, contextSize))
{
+      if(sent.getBegin() <= baseToken.getBegin()) {
+        tokens.add(baseToken.getCoveredText()); 
+      }
+    }
+    tokens.add("<" + leftType + ">");
+    tokens.add(left.getCoveredText());
+    tokens.add("</" + leftType + ">");
+    for(BaseToken baseToken : JCasUtil.selectBetween(jCas, BaseToken.class, left, right))
{
+      tokens.add(baseToken.getCoveredText());
+    }
+    tokens.add("<" + rightType + ">");
+    tokens.add(right.getCoveredText());
+    tokens.add("</" + rightType + ">");
+    for(BaseToken baseToken : JCasUtil.selectFollowing(jCas, BaseToken.class, right, contextSize))
{
+      if(baseToken.getEnd() <= sent.getEnd()) {
+        tokens.add(baseToken.getCoveredText());
+      }
+    }
+
+    return String.join(" ", tokens).replaceAll("[\r\n]", " ");
+  }
+}



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