Package org.apache.ctakes.typesystem.type.textspan

Examples of org.apache.ctakes.typesystem.type.textspan.Segment

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    JFSIndexRepository indexes = jcas.getJFSIndexRepository();
    Iterator<?> sectionItr = indexes.getAnnotationIndex(Segment.type)
        .iterator();
    while (sectionItr.hasNext()) {
      Segment sa = (Segment) sectionItr.next();
      String sectionID = sa.getId();
      if (!skipSegmentsSet.contains(sectionID)) {
        sentenceCount = annotateRange(jcas, text, sa, sentenceCount);
      }
    }
  }
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        .getAnnotationIndex(Segment.type);
    Iterator<Annotation> iter = mentions.iterator();
    Set<String> uniqueSegments = new HashSet<String>();
    int emCount = 0;
    while (iter.hasNext()) {
      Segment em = (Segment) iter.next();
      uniqueSegments.add(em.getId());
      System.out.println(em.getId() + " [" + em.getCoveredText() + "]");
      emCount++;
    }
    // should be 4 segments - default/title/default/history
    Assert.assertTrue(emCount == 4);
    // should be 3 unique segments
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    ner.initRegexMap(Arrays.asList(nerex));
   
      JCas jCas = JCasFactory.createJCasFromPath("src/main/resources/org/apache/ctakes/ytex/types/TypeSystem.xml");
      String text = "Dr. Doolitle asked patient\nto take a deep breath\nand exhale slowly.  Patient coughed.";
      jCas.setDocumentText(text);
      Segment s = new Segment(jCas);
      s.setBegin(0);
      s.setEnd(text.length());
      s.setId("DEFAULT");
      s.addToIndexes();
      ner.process(jCas);
      // run the analysis engine
      AnnotationIndex<Annotation> mentions = jCas.getAnnotationIndex(EntityMention.type);
    Iterator<Annotation> iter =mentions.iterator();
    int emCount = 0;
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    @Override
    public void process(JCas jCas) throws AnalysisEngineProcessException {
      Matcher matcher = SECTION_PATTERN.matcher(jCas.getDocumentText());
      while (matcher.find()) {
        Segment segment = new Segment(jCas);
        segment.setBegin(matcher.start() + matcher.group(1).length());
        segment.setEnd(matcher.end() - matcher.group(3).length());
        segment.setId(matcher.group(2));
        segment.addToIndexes();
      }
    }
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      source = new XMLInputSource(file);
      builder.add(parser.parseAnalysisEngineDescription(source));
      AnalysisEngine engine = builder.createAggregate();
      JCas jCas = engine.newJCas();
      jCas.setDocumentText(text);
      Segment s = new Segment(jCas);
      s.setBegin(0);
      s.setEnd(text.length());
      s.setId("DEFAULT");
      s.addToIndexes();
      // run the analysis engine
      engine.process(jCas);
      AnnotationIndex<Annotation> sentences = jCas.getAnnotationIndex(Sentence.type);
    Iterator<Annotation> iter =sentences.iterator();
    int sentCount = 0;
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  @Test
    public void testSimpleSegment() throws ResourceInitializationException {
    AnalysisEngine ae = TestUtil.getAE(new File("desc/test/analysis_engine/SimpleSegmentAnnotator.xml"));
    JCas jCas = TestUtil.processAE(ae, "data/test/mother_goose/OneMistyMorning.txt");
    Segment segment = TestUtil.getFeatureStructureAtIndex(jCas, Segment.class, 0);
    assertEquals(0, segment.getBegin());
    assertEquals(42, segment.getEnd());
    assertEquals("seg1234", segment.getId());
  }
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    String doc = "Patient suffers from a shattered tibia and facial contusions. Recommend bed rest, aspirin, and ice.";
    jcas.setDocumentText(doc);
    SimplePipeline.runPipeline(jcas, SimpleSegmentAnnotator.createAnnotatorDescription());
    Collection<Segment> segs = JCasUtil.select(jcas, Segment.class);
    assertEquals(segs.size(), 1);
    Segment seg = segs.toArray(new Segment[]{})[0];
    assert(seg.getId().equals("SIMPLE_SEGMENT"));
   
    jcas = JCasFactory.createJCas();
    jcas.setDocumentText(doc);
    SimplePipeline.runPipeline(jcas, SimpleSegmentAnnotator.createAnnotatorDescription("TestId"));
    segs = JCasUtil.select(jcas, Segment.class);
    assertEquals(segs.size(), 1);
    seg = segs.toArray(new Segment[]{})[0];
    assertEquals("Segment ids do not match!", seg.getId(), "TestId"); 
  }
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      prepareSubSection(jcas, indexes,
          iv_subMedSectionFSM.execute(baseTokenList));

      while (segmentItr.hasNext())
      {
        Segment seg = (Segment) segmentItr.next();
        if (iv_medicationRelatedSections.contains(seg.getId()))
          generateDrugMentions(jcas, seg, false);
        else
          generateDrugMentions(jcas, seg, true);
      }
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    List sortedSubSecInds = sortSubSectionInd(subSectionIndSet.toArray());

    for (int i = 0, endBodyOffset = 0; i < sortedSubSecInds.size(); i++, endBodyOffset = 0)
    {
      SubSectionIndicator ssi = (SubSectionIndicator) sortedSubSecInds.get(i);
      Segment segment = getSegmentContainingOffsets(jcas, ssi.getStartOffset(),
          ssi.getEndOffset());
      endBodyOffset = segment.getEnd(); // backup

      SubSectionAnnotation ssa = new SubSectionAnnotation(jcas);

      ssa.setBegin(ssi.getStartOffset());
      // header is marked by the indicator
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    JFSIndexRepository indexes = jcas.getJFSIndexRepository();
    Iterator segmentItr = indexes.getAnnotationIndex(Segment.type).iterator();

    while (segmentItr.hasNext())
    {
      Segment seg = (Segment) segmentItr.next();

      if (seg.getBegin() <= start && seg.getEnd() >= end)
        return seg;
    }

    return null; // did not find a segment - cannot happen - we always have
    // segments
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Related Classes of org.apache.ctakes.typesystem.type.textspan.Segment

  • org.apache.ctakes.clinicalpipeline.ae.ExtractionPrepAnnotator
  • org.apache.ctakes.core.ae.CDASegmentAnnotator
  • org.apache.ctakes.core.ae.SectionSegmentAnnotator
  • org.apache.ctakes.core.ae.SentenceDetector
  • org.apache.ctakes.core.ae.SimpleSegmentAnnotator
  • org.apache.ctakes.core.ae.SimpleSegmentAnnotatorTests
  • org.apache.ctakes.core.ae.SimpleSegmentWithTagsAnnotator
  • org.apache.ctakes.core.ae.TokenizerAnnotator
  • org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
  • org.apache.ctakes.drugner.ae.DrugMentionAnnotator
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