/** {@inheritDoc} */
 @Override
 public void onMatching(
     String docUri, Type type, SortedSet<Annotation> goldAnnos, SortedSet<Annotation> sysAnnos) {
   if (goldAnnos.size() == 1 && sysAnnos.size() == 1) {
     Annotation goldAnno = goldAnnos.iterator().next();
     Annotation sysAnno = sysAnnos.iterator().next();
     if (goldAnno.getBegin() == sysAnno.getBegin() && goldAnno.getEnd() == sysAnno.getEnd()) {
       printRow(
           type.getShortName(),
           "Exact",
           goldAnno.getCoveredText(),
           String.valueOf(goldAnno.getBegin()),
           sysAnno.getCoveredText(),
           String.valueOf(sysAnno.getBegin()),
           docUri);
       return;
     }
   }
   printRow(
       type.getShortName(),
       "Partial",
       Joiner.on(" /// ").join(transform(goldAnnos, annoToTxt)),
       Joiner.on(", ").join(transform(goldAnnos, annoToOffset)),
       Joiner.on(" /// ").join(transform(sysAnnos, annoToTxt)),
       Joiner.on(", ").join(transform(sysAnnos, annoToOffset)),
       docUri);
 }
Esempio n. 2
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 @Override
 public void process(JCas cas) throws AnalysisEngineProcessException {
   this.setSource(cas);
   this.setTarget(cas);
   AnnotationIndex<Annotation> index = cas.getAnnotationIndex(this.getSourceType());
   FSIterator<Annotation> iter = index.iterator();
   while (iter.hasNext()) {
     Annotation annotation = iter.next();
     String source = null;
     if (this.getSourceFeature() == null) {
       source = annotation.getCoveredText();
     } else {
       source = annotation.getStringValue(this.getSourceFeature());
     }
     if (source != null) {
       String target = this.getMapping().get(source);
       if (target != null) {
         if (this.update().booleanValue()) {
           this.update(cas, annotation, this.getTargetFeature(), target);
         } else {
           this.create(
               cas, this.getTargetFeature(), annotation.getBegin(), annotation.getEnd(), target);
         }
       }
     }
   }
 }
  @Override
  public void process(JCas jcas) throws AnalysisEngineProcessException {
    Type type = jcas.getCas().getTypeSystem().getType(TYPE_NAME);
    Feature entityFeature = type.getFeatureByBaseName(ENTITY_FEATURE);
    Feature nameFeature = type.getFeatureByBaseName(NAME_FEATURE);

    for (Annotation annotation : jcas.getAnnotationIndex(TokenAnnotation.type)) {
      String tokenPOS = ((TokenAnnotation) annotation).getPosTag();

      if (NP.equals(tokenPOS) || NPS.equals(tokenPOS)) {
        AnnotationFS entityAnnotation =
            jcas.getCas().createAnnotation(type, annotation.getBegin(), annotation.getEnd());

        entityAnnotation.setStringValue(entityFeature, annotation.getCoveredText());

        String name =
            "OTHER"; // "OTHER" makes no sense. In practice, "PERSON", "COUNTRY", "E-MAIL", etc.
        if (annotation.getCoveredText().equals("Apache")) name = "ORGANIZATION";
        entityAnnotation.setStringValue(nameFeature, name);

        jcas.addFsToIndexes(entityAnnotation);
      }
    }
  }
Esempio n. 4
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  /** Outputs Trigrams for an input Annotation. */
  public void extractNgramsFromAnnotation(Annotation annotation, JCas aJCas) {

    AnnotationIndex<Annotation> tokens = aJCas.getAnnotationIndex(Token.type);
    Iterator<Annotation> tIterator = tokens.subiterator(annotation);

    Annotation token = null;
    Annotation prev = null;
    Annotation prev_prev = null;

    while (tIterator.hasNext()) {

      prev_prev = prev;
      prev = token;
      token = tIterator.next();

      if (tokenIsInAnnotation(annotation, prev) && tokenIsInAnnotation(annotation, prev_prev)) {

        NGram ngram = new NGram(aJCas);
        FSArray ngArray = new FSArray(aJCas, 3);

        ngArray.set(0, prev_prev);
        ngArray.set(1, prev);
        ngArray.set(2, token);

        ngram.setBegin(prev_prev.getBegin());
        ngram.setEnd(token.getEnd());

        ngram.setElements(ngArray);
        ngram.setElementType("edu.cmu.deiis.types.Token");

        ngram.setConfidence(1D);
        ngram.setCasProcessorId(PROCESSOR_ID);
        ngram.addToIndexes();
      }
    }
  }
Esempio n. 5
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 public static boolean sameIndexes(Annotation anno1, Annotation anno2) {
   return anno1.getBegin() == anno2.getBegin() && anno1.getEnd() == anno2.getEnd();
 }
Esempio n. 6
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 public static boolean contains(Annotation container, Annotation subAnnotation) {
   return container.getBegin() <= subAnnotation.getBegin()
       && container.getEnd() >= subAnnotation.getEnd();
 }
Esempio n. 7
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  /**
   * Recreates a Stanford Tree from the StanfordParser annotations and saves all
   * non-StanfordParser-Annotations within the scope of the sentence in the label of the best
   * fitting node.
   *
   * <p><strong>CAUTION: </strong><i>This method is intended for the use by CAS Multipliers, which
   * create new CASes from this tree. The annotation-spans in the source-CAS will be changed!!!!!!
   * You do NOT want to use the source CAS after this method has been called. The
   * createStanfordTree()-method does not change the CAS, so use this instead, if the annotations do
   * not have to be recovered or accessed in the tree.</i>
   *
   * <p>TODO: This behavior could be changed by making COPIES of the annotations and changing the
   * copied instead of the originals. However, in order to being able to make copies, a dummy CAS
   * must be introduced to which the annotations can be copied. When they are recovered, they will
   * be copied to the new destination CAS anyway.
   *
   * @param root the ROOT annotation
   * @return an {@link Tree} object representing the syntax structure of the sentence
   * @throws CASException if the JCas cannot be accessed.
   */
  public static Tree createStanfordTreeWithAnnotations(Annotation root) throws CASException {
    JCas aJCas = root.getCAS().getJCas();

    // Create tree
    Tree tree = createStanfordTree(root);

    // Get all non-parser related annotations
    // and all tokens (needed for span-calculations later on)
    List<Annotation> nonParserAnnotations = new ArrayList<Annotation>();
    List<Token> tokens = new ArrayList<Token>();

    // Using getCoveredAnnotations instead of iterate, because subiterators did not work in all
    // cases
    List<Annotation> annosWithinRoot = JCasUtil.selectCovered(aJCas, Annotation.class, root);

    for (Annotation curAnno : annosWithinRoot) {
      if (!(curAnno instanceof POS)
          && !(curAnno instanceof Constituent)
          && !(curAnno instanceof Dependency)
          && !(curAnno instanceof PennTree)
          && !(curAnno instanceof Lemma)
          && !(curAnno instanceof Token)
          && !(curAnno instanceof DocumentMetaData)) {
        nonParserAnnotations.add(curAnno);
      } else if (curAnno instanceof Token) {
        tokens.add((Token) curAnno);
      }
    }

    // create wrapper for tree and its tokens
    TreeWithTokens annoTree = new TreeWithTokens(tree, tokens);

    /*
     * Add annotations to the best-fitting nodes. The best-fitting node for an annotation is the
     * deepest node in the tree that still completely contains the annotation.
     */
    for (Annotation curAnno : nonParserAnnotations) {
      // get best fitting node
      Tree bestFittingNode = annoTree.getBestFit(curAnno);

      // Add annotation to node
      if (bestFittingNode != null) {

        // translate annotation span to a value relative to the
        // node-span
        IntPair span = annoTree.getSpan(bestFittingNode);
        curAnno.setBegin(curAnno.getBegin() - span.getSource());
        curAnno.setEnd(curAnno.getEnd() - span.getSource());

        // get the collection from the label of the best-fitting node in which we store UIMA
        // annotations or create it, if it does not exist
        Collection<Annotation> annotations =
            ((CoreLabel) bestFittingNode.label()).get(UIMAAnnotations.class);
        if (annotations == null) {
          annotations = new ArrayList<Annotation>();
        }

        // add annotation + checksum of annotated text to list and write it back to node
        // label
        annotations.add(curAnno);

        ((CoreLabel) bestFittingNode.label()).set(UIMAAnnotations.class, annotations);
      }
    }

    return tree;
  }
 /**
  * Static method that changes the annotation passed by off-setting it offset from zero
  *
  * @param annotation
  * @param offset - The offset as computed by (copy - original)
  */
 private static void updateAnnotation(Annotation annotation, int offset) {
   if (annotation == null) return;
   annotation.setBegin(annotation.getBegin() + offset);
   annotation.setEnd(annotation.getEnd() + offset);
 }