Package org.apache.ctakes.utils.tree

Examples of org.apache.ctakes.utils.tree.SimpleTree

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    List<Feature> features = new ArrayList<Feature>();
    // first get the root and print it out...
    TopTreebankNode root = AnnotationTreeUtils.getTreeCopy(jcas, AnnotationTreeUtils.getAnnotationTree(jcas, arg1));
   
    if(root == null){
      SimpleTree fakeTree = new SimpleTree("(S (NN null))");
      features.add(new TreeFeature(FEAT_NAME, fakeTree.toString()));
      return features;
    }
   
    // swap the order if necessary:
    if(arg2.getBegin() <= arg1.getBegin() && arg2.getEnd() <= arg1.getEnd()){
      IdentifiedAnnotation temp = arg1;
      arg1 = arg2;
      arg2 = temp;
    }
   
    String a1type="", a2type="";
    String eventModality="";
    String timeClass;
   
    if(arg1 instanceof EventMention){
      eventModality = ((EventMention)arg1).getEvent().getProperties().getContextualModality();
      a1type = "EVENT-"+eventModality;
    }else if(arg1 instanceof TimeMention){
      timeClass = ((TimeMention)arg1).getTimeClass();
      a1type = "TIMEX-"+timeClass;
    }
   
    if(arg2 instanceof EventMention){
      eventModality = ((EventMention)arg2).getEvent().getProperties().getContextualModality();
      a2type = "EVENT-"+eventModality;     
    }else if(arg2 instanceof TimeMention){
      timeClass = ((TimeMention)arg2).getTimeClass();
      a2type = "TIMEX-"+timeClass;     
    }
   
    TreebankNode t1 = AnnotationTreeUtils.insertAnnotationNode(jcas, root, arg1, "ARG1-"+a1type);
    TreebankNode t2 = AnnotationTreeUtils.insertAnnotationNode(jcas, root, arg2, "ARG2-"+a2type);

//    addOtherTimes(jcas,root, arg1, arg2);
       
    SimpleTree tree = null;
    if(t1.getBegin() <= t2.getBegin() && t1.getEnd() >= t2.getEnd()){
      // t1 encloses t2
      tree = TreeExtractor.getSimpleClone(t1);
    }else if(t2.getBegin() <= t1.getBegin() && t2.getEnd() >= t1.getEnd()){
      // t2 encloses t1
      tree = TreeExtractor.getSimpleClone(t2);
    }else{
//      tree = TreeExtractor.extractPathEnclosedTree(t1, t2, jcas);
      tree = TreeExtractor.getSimpleClone(root);
    }

    TemporalPETExtractor.moveTimexDownToNP(tree);
   
    features.add(new TreeFeature(FEAT_NAME, tree.toString()));
    return features;
  }
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    List<Feature> features = new ArrayList<Feature>();
    // first get the root and print it out...
    TopTreebankNode root = AnnotationTreeUtils.getTreeCopy(jcas, AnnotationTreeUtils.getAnnotationTree(jcas, arg1));
   
    if(root == null){
      SimpleTree fakeTree = new SimpleTree("(S (NN null))");
      features.add(new TreeFeature("TK_PET", fakeTree.toString()));
      return features;
    }
   
    // swap the order if necessary:
    if(arg2.getBegin() <= arg1.getBegin() && arg2.getEnd() <= arg1.getEnd()){
      IdentifiedAnnotation temp = arg1;
      arg1 = arg2;
      arg2 = temp;
    }
   
    String a1type="", a2type="";
    String eventModality="";
    String timeClass;
   
    if(arg1 instanceof EventMention){
      EventMention mention = (EventMention) arg1;
      if(mention.getEvent() != null && mention.getEvent().getProperties() != null){
        eventModality = mention.getEvent().getProperties().getContextualModality();
      }
      a1type = "EVENT-"+eventModality;
    }else if(arg1 instanceof TimeMention){
      timeClass = ((TimeMention)arg1).getTimeClass(); 
      a1type = "TIMEX-"+timeClass;
    }
   
    if(arg2 instanceof EventMention){
      EventMention mention = (EventMention) arg2;
      if(mention.getEvent() != null && mention.getEvent().getProperties() != null){
        eventModality = mention.getEvent().getProperties().getContextualModality();
      }
      a2type = "EVENT-"+eventModality;     
    }else if(arg2 instanceof TimeMention){
      timeClass = ((TimeMention)arg2).getTimeClass();
      a2type = "TIMEX-"+timeClass;     
    }
   
    TreebankNode t1 = AnnotationTreeUtils.insertAnnotationNode(jcas, root, arg1, "ARG1-"+a1type);
    TreebankNode t2 = AnnotationTreeUtils.insertAnnotationNode(jcas, root, arg2, "ARG2-"+a2type);

//    addOtherTimes(jcas,root, arg1, arg2);
       
    SimpleTree tree = null;
    if(t1.getBegin() <= t2.getBegin() && t1.getEnd() >= t2.getEnd()){
      // t1 encloses t2
      tree = TreeExtractor.getSimpleClone(t1);
    }else if(t2.getBegin() <= t1.getBegin() && t2.getEnd() >= t1.getEnd()){
      // t2 encloses t1
      tree = TreeExtractor.getSimpleClone(t2);
    }else{
      tree = TreeExtractor.extractPathEnclosedTree(t1, t2, jcas);
    }

    tree.setGeneralizeLeaf(true);
    moveTimexDownToNP(tree);
    simplifyGCG(tree);
   
    features.add(new TreeFeature("TK_PET", tree.toString()));
    return features;
  }
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    }
  }

  public static void moveTimexDownToNP(SimpleTree tree) {
    if(tree.cat.contains("-TIMEX-")){
      SimpleTree child = tree.children.get(0);
      // we've found the correct node: only correct clear violations: PP -> IN NP
      if(child.cat.contains("PP") && child.children.size() == 2 && child.children.get(0).cat.equals("IN") && child.children.get(1).cat.startsWith("NP")){
        // swap labels
        String fullCat = tree.cat;
        tree.cat = "PP";
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    String dtreeStr ="(TOP (EVENT " + focusAnnotation.getCoveredText().trim() + "))";
    //find the colldepnode covered by focusAnnotation:
    for(ConllDependencyNode node : JCasUtil.selectCovered(view, ConllDependencyNode.class, focusAnnotation)){
      //find if it has head:
      ConllDependencyNode head = node.getHead();
      SimpleTree curTree = null;
      SimpleTree headTree = null;
     
      if(head == null) { //if the current node is the root, then not right
        continue;
      }

//      curTree = SimpleTree.fromString(String.format("(%s %s)", node.getDeprel(), SimpleTree.escapeCat(node.getCoveredText().trim())));
      curTree = SimpleTree.fromString(String.format("(%s %s)", node.getDeprel(), node.getPostag()));



      while(head.getHead() != null){ //while head node is not the root
//              String token = node.getHead().getHead() == null ? "TOP" : node.getHead().getCoveredText();
//        headTree = SimpleTree.fromString(String.format("(%s %s)", head.getDeprel(), SimpleTree.escapeCat(head.getCoveredText().trim())));
        headTree = SimpleTree.fromString(String.format("(%s %s)", head.getDeprel(), head.getPostag()));
        curTree.parent = headTree.children.get(0);
        headTree.children.get(0).addChild(curTree);
        curTree = headTree;
        head = head.getHead();
      }
      if(headTree==null){
        curTree = SimpleTree.fromString(String.format("(%s (%s %s))",node.getDeprel(), node.getPostag(),"null"));
        dtreeStr = curTree.toString();
      }else{
        dtreeStr = headTree.toString();
      }
      break;
    }
   
    features.add(new TreeFeature(FEAT_NAME, dtreeStr));
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      IdentifiedAnnotation temp = arg1;
      arg1 = arg2;
      arg2 = temp;
    }
   
    SimpleTree bopTree = getTree(jcas, arg1, arg2, "BOP", new Function<BaseToken,String>(){public String apply(BaseToken t){ return t.getPartOfSpeech();}});
    SimpleTree bowTree = getTree(jcas, arg1, arg2, "BOW", new Function<BaseToken,String>(){public String apply(BaseToken t){ return t.getCoveredText();}});
   
    feats.add(new TreeFeature("TK_BOP_Tree", bopTree.toString()));
    feats.add(new TreeFeature("TK_BOW_Tree", bowTree.toString()));
    return feats;
  }
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    feats.add(new TreeFeature("TK_BOW_Tree", bowTree.toString()));
    return feats;
  }

  private static SimpleTree getTree(JCas jcas, IdentifiedAnnotation arg1, IdentifiedAnnotation arg2, String label, Function<BaseToken, String> leafFun) throws AnalysisEngineProcessException{
    SimpleTree tree = new SimpleTree(label);
    SimpleTree arg1Tree = null;
    SimpleTree arg2Tree = null;
    String eventModality="";
    String timeClass="";
 
    // make sure we have the right classes
    if(arg1 instanceof EventMention){
      EventMention mention = (EventMention) arg1;
      if(mention.getEvent() != null && mention.getEvent().getProperties() != null){
        eventModality = mention.getEvent().getProperties().getContextualModality();
      }
      arg1Tree = new SimpleTree("EVENT-"+eventModality);
    }else if(arg1 instanceof TimeMention){
      timeClass = ((TimeMention)arg1).getTimeClass();
      arg1Tree = new SimpleTree("TIMEX-"+timeClass);
    }else{
      throw new AnalysisEngineProcessException("Argument type not recognized (arg1) -- must be EventMention or TimeMention", null);
    }
   
    if(arg2 instanceof EventMention){
      EventMention mention = (EventMention) arg2;
      if(mention.getEvent() != null && mention.getEvent().getProperties() != null){
        eventModality = mention.getEvent().getProperties().getContextualModality();
      }
      arg2Tree = new SimpleTree("EVENT-"+eventModality);     
    }else if(arg2 instanceof TimeMention){
      timeClass = ((TimeMention)arg2).getTimeClass();
      arg2Tree = new SimpleTree("TIMEX-"+timeClass);     
    }else{
      throw new AnalysisEngineProcessException("Argument type not recognized (arg2) -- must be EventMention or TimeMention", null);
    }
   
    List<BaseToken> tokens = JCasUtil.selectCovered(jcas, BaseToken.class, arg1.getBegin(), arg2.getEnd());
    tree.addChild(arg1Tree);
    for(BaseToken token : tokens){
      SimpleTree tokenTree = new SimpleTree("TOK");
      tokenTree.addChild(new SimpleTree(leafFun.apply(token)));
     
      if(token.getEnd() <= arg1.getEnd()){
        arg1Tree.addChild(tokenTree);
      }else if(token.getBegin() >= arg2.getBegin()){
        arg2Tree.addChild(tokenTree);
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  }

  @Override
  public List<Feature> extract(JCas jcas, Annotation annotation) {
    List<Feature> features = new ArrayList<Feature>();
    SimpleTree tree = extractAboveRightConceptTree(jcas, annotation, sems);
   
    for(SimpleTree frag : frags){
      if(TreeUtils.containsIgnoreCase(tree, frag)){
        features.add(new Feature("TreeFrag_" + prefix, frag.toString()));
      }
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  }

  @Override
  public List<Feature> extract(JCas jcas, Annotation annotation) {
    List<Feature> features = new ArrayList<Feature>();
    SimpleTree tree = extractAboveLeftConceptTree(jcas, annotation, sems);
   
    for(SimpleTree frag : frags){
      if(TreeUtils.containsIgnoreCase(tree, frag)){
        features.add(new Feature("TreeFrag_" + prefix, frag.toString()));
      }
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  @Override
  public List<Feature> extract(JCas jcas, Annotation annotation)
      throws CleartkExtractorException {
    List<Feature> features = new ArrayList<Feature>();
    SimpleTree tree = extractAboveLeftConceptTree(jcas, annotation, sems);
    features.add(new TreeFeature("TK_AboveLeftTree", tree.toString()));
    return features;
  }
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      Sentence sent = sents.get(0);
      List<ConllDependencyNode> nodes = JCasUtil.selectCovered(ConllDependencyNode.class, sent);
   
      //treeString = AnnotationDepUtils.getTokenRelTreeString(jCas, nodes, new Annotation[]{arg1}, new String[]{"CONCEPT"}, true);
//      treeString = AssertionDepUtils.getTokenRelTreeString(jCas, nodes, arg1, "CONCEPT");
      SimpleTree tree = AssertionDepUtils.getTokenTreeString(jCas, nodes, arg1, GenerateDependencyRepresentation.UP_NODES);
     
      if(tree == null){
        treeString = "(S (no parse))";
      }else{
        AssertionTreeUtils.replaceDependencyWordsWithSemanticClasses(tree, sems);
        treeString = tree.toString();
//        treeString = treeString.replaceAll("\\(([^ ]+) \\)", "$1");
      }
    }

    f1 = new TreeFeature("TK_DW", treeString);  
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Related Classes of org.apache.ctakes.utils.tree.SimpleTree

  • org.apache.ctakes.assertion.medfacts.cleartk.extractors.AboveLeftFragmentExtractor
  • org.apache.ctakes.assertion.medfacts.cleartk.extractors.AboveRightFragmentExtractor
  • org.apache.ctakes.assertion.medfacts.cleartk.extractors.AssertionAboveLeftTreeExtractor
  • org.apache.ctakes.assertion.medfacts.cleartk.extractors.AssertionDependencyTreeExtractor
  • org.apache.ctakes.assertion.medfacts.cleartk.extractors.DependencyWordsFragmentExtractor
  • org.apache.ctakes.assertion.pipelines.GenerateDependencyRepresentation
  • org.apache.ctakes.assertion.pipelines.GenerateTreeRepresentation
  • org.apache.ctakes.assertion.util.AssertionDepUtils
  • org.apache.ctakes.assertion.util.AssertionTreeUtils
  • org.apache.ctakes.constituency.parser.treekernel.TreeExtractor
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