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From dlig...@apache.org
Subject svn commit: r1762961 - /ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/EventTimeRelPositionPrinter.java
Date Fri, 30 Sep 2016 19:53:00 GMT
Author: dligach
Date: Fri Sep 30 19:53:00 2016
New Revision: 1762961

URL: http://svn.apache.org/viewvc?rev=1762961&view=rev
Log:
printing positions for the arguments

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

Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/EventTimeRelPositionPrinter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/EventTimeRelPositionPrinter.java?rev=1762961&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/EventTimeRelPositionPrinter.java
(added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/EventTimeRelPositionPrinter.java
Fri Sep 30 19:53:00 2016
@@ -0,0 +1,358 @@
+/**
+ * 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.data;
+
+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.Collections;
+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.relation.TemporalTextRelation;
+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 EventTimeRelPositionPrinter {
+
+  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());
+
+    // sort training files to eliminate platform specific dir listings
+    Collections.sort(trainFiles);
+    //    Collections.shuffle(trainFiles, new Random(100));  
+
+    // write training data to file
+    CollectionReader trainCollectionReader = Utils.getCollectionReader(trainFiles);
+    AnalysisEngine trainDataWriter = AnalysisEngineFactory.createEngine(
+        RelationSnippetPrinter.class,
+        "IsTraining",
+        true,
+        "OutputFile",
+        trainFile.getAbsoluteFile());
+    SimplePipeline.runPipeline(trainCollectionReader, trainDataWriter);
+
+    // write dev data to file
+    CollectionReader devCollectionReader = Utils.getCollectionReader(devFiles);
+    AnalysisEngine devDataWriter = AnalysisEngineFactory.createEngine(
+        RelationSnippetPrinter.class,
+        "IsTraining",
+        false,
+        "OutputFile",
+        devFile.getAbsolutePath());
+    SimplePipeline.runPipeline(devCollectionReader, devDataWriter);
+  }
+
+  /**
+   * Print gold standard relations and their context.
+   */
+  public static class RelationSnippetPrinter extends JCasAnnotator_ImplBase {
+
+    @ConfigurationParameter(
+        name = "IsTraining",
+        mandatory = true,
+        description = "are we training?")
+    private boolean isTraining;
+    
+    @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
+      Map<List<Annotation>, BinaryTextRelation> relationLookup = new HashMap<>();
+      if(isTraining) {
+        for(BinaryTextRelation relation : JCasUtil.select(goldView, TemporalTextRelation.class))
{
+          Annotation arg1 = relation.getArg1().getArgument();
+          Annotation arg2 = relation.getArg2().getArgument();
+
+          if(relationLookup.get(Arrays.asList(arg1, arg2)) != null) {
+            // there is already a relation between arg1 and arg2
+            // only store if it is 'contains' relation 
+            if(relation.getCategory().equals("CONTAINS")) {
+              relationLookup.put(Arrays.asList(arg1, arg2), relation);
+            } else {
+              System.out.println("skipping relation: " + arg1.getCoveredText() + " ... "
+ arg2.getCoveredText());
+            }
+          } else {
+            relationLookup.put(Arrays.asList(arg1, arg2), relation);
+          }
+        }
+      } else {
+        for(BinaryTextRelation relation : JCasUtil.select(goldView, TemporalTextRelation.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> eventTimeRelationsInSentence = 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));
+            BinaryTextRelation eventTimeRelation = relationLookup.get(Arrays.asList(event,
time));
+
+            String label = "none";
+            if(timeEventRelation != null) {
+              if(timeEventRelation.getCategory().equals("CONTAINS")) {
+                label = "contains";  // this is contains
+              }
+            }
+            // there is at least one instance where both event-time and time-event rels exist?
+            if(eventTimeRelation != null) {
+              if(eventTimeRelation.getCategory().equals("CONTAINS")) {
+                label = "contains-1"; // this is contains
+              } 
+            } 
+
+            String context = getPositionContext(systemView, sentence, time, event);  
+            String text = String.format("%s|%s", label, context);
+            eventTimeRelationsInSentence.add(text.toLowerCase());
+          }
+        }  
+
+        try {
+          Files.write(Paths.get(outputFile), eventTimeRelationsInSentence, StandardOpenOption.APPEND);
+        } catch (IOException e) {
+          e.printStackTrace();
+        }
+      }
+    }
+  }
+
+  /**
+   * Print words from left to right.
+   * @param contextSize number of tokens to include on the left of arg1 and on the right
of arg2
+   */
+  public static String getTokenContext(
+      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]", " ");
+  }
+
+  /**
+   * Print POS tags from left to right.
+   * @param contextSize number of tokens to include on the left of arg1 and on the right
of arg2
+   */
+  public static String getPosContext(
+      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.getPartOfSpeech()); 
+      }
+    }
+    tokens.add("<" + leftType + ">");
+    for(BaseToken baseToken : JCasUtil.selectCovered(jCas, BaseToken.class, left)) {
+      tokens.add(baseToken.getPartOfSpeech());
+    }
+    tokens.add("</" + leftType + ">");
+    for(BaseToken baseToken : JCasUtil.selectBetween(jCas, BaseToken.class, left, right))
{
+      tokens.add(baseToken.getPartOfSpeech());
+    }
+    tokens.add("<" + rightType + ">");
+    for(BaseToken baseToken : JCasUtil.selectCovered(jCas, BaseToken.class, right)) {
+      tokens.add(baseToken.getPartOfSpeech());
+    }
+    tokens.add("</" + rightType + ">");
+    for(BaseToken baseToken : JCasUtil.selectFollowing(jCas, BaseToken.class, right, contextSize))
{
+      if(baseToken.getEnd() <= sent.getEnd()) {
+        tokens.add(baseToken.getPartOfSpeech());
+      }
+    }
+
+    return String.join(" ", tokens).replaceAll("[\r\n]", " ");
+  }
+  
+  /**
+   * Print indices
+   * @param contextSize number of tokens to include on the left of arg1 and on the right
of arg2
+   */
+  public static String getPositionContext(
+      JCas jCas, 
+      Sentence sent, 
+      TimeMention time,
+      EventMention event) {
+
+    // get sentence as a list of tokens
+    List<String> tokens = new ArrayList<>();
+    for(BaseToken baseToken : JCasUtil.selectCovered(jCas, BaseToken.class, sent)) {
+      tokens.add(baseToken.getCoveredText());  
+    }
+    
+    // assume time consists of multipe words; event of one
+    int currentPosition = 0;       // current token index
+    int timeFirstPosition = -1000; // timex's start index
+    int timeLastPosition = -1000;  // timex's end index
+    int eventPosition = -1000;     // event's index
+    for(BaseToken token : JCasUtil.selectCovered(jCas, BaseToken.class, sent)) {
+      if(time.getBegin() == token.getBegin()) { 
+        timeFirstPosition = currentPosition; // start of time expression found
+      }
+      if(time.getEnd() == token.getEnd()) {
+        timeLastPosition = currentPosition;  // end of time expression found
+      }
+      if(event.getBegin() == token.getBegin()) { 
+        eventPosition = currentPosition;     // event postion found
+      } 
+      currentPosition++;
+    }
+
+    List<String> positionsWrtToTime = new ArrayList<>();
+    List<String> positionsWrtToEvent = new ArrayList<>();
+    int tokensInSentence = JCasUtil.selectCovered(jCas, BaseToken.class, sent).size();
+    for(int tokenIndex = 0; tokenIndex < tokensInSentence; tokenIndex++) {
+      if(tokenIndex < timeFirstPosition) {
+        positionsWrtToTime.add(Integer.toString(tokenIndex - timeFirstPosition));
+      } else if(tokenIndex >= timeFirstPosition && tokenIndex <= timeLastPosition)
{
+        positionsWrtToTime.add("0");
+      } else {
+        positionsWrtToTime.add(Integer.toString(tokenIndex - timeLastPosition));
+      }
+      positionsWrtToEvent.add(Integer.toString(tokenIndex - eventPosition));
+    }
+
+    String tokensAsString = String.join(" ", tokens).replaceAll("[\r\n]", " ");
+    String wrtToTimeAsString = String.join(" ", positionsWrtToTime);
+    String wrtToEventAsString = String.join(" ", positionsWrtToEvent);
+    
+    return tokensAsString + "|" + wrtToTimeAsString + "|" + wrtToEventAsString;
+  } 
+}



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