Examples with Annotation gate.Annotation used on opensource projects

Example 11 with Annotation

use of gate.Annotation in project gate-core by GateNLP.

the class TestDiffer method testDiffer.

// tearDown
public void testDiffer() throws Exception {
    Document doc = Factory.newDocument(new URL(gate.corpora.TestDocument.getTestServerName() + "tests/ft-bt-03-aug-2001.html"), "windows-1252");
    AnnotationSet annSet = doc.getAnnotations();
    // create 100 annotations
    FeatureMap features = Factory.newFeatureMap();
    features.put("type", "BAR");
    for (int i = 0; i < 100; i++) {
        annSet.add(new Long(i * 10), new Long((i + 1) * 10), "Foo", features);
    }
    List<Annotation> keySet = new ArrayList<Annotation>(annSet);
    List<Annotation> responseSet = new ArrayList<Annotation>(annSet);
    // check 100% Precision and recall
    AnnotationDiffer differ = new AnnotationDiffer();
    differ.setSignificantFeaturesSet(null);
    differ.calculateDiff(keySet, responseSet);
    differ.sanityCheck();
    if (DEBUG)
        differ.printMissmatches();
    double value = differ.getPrecisionStrict();
    Assert.assertEquals("Precision Strict: " + value + " instead of 1!", 1, value, 0);
    value = differ.getRecallStrict();
    Assert.assertEquals("Recall Strict: " + value + " instead of 1!", 1, value, 0);
    value = differ.getPrecisionLenient();
    Assert.assertEquals("Precision Lenient: " + value + " instead of 1!", 1, value, 0);
    value = differ.getRecallLenient();
    Assert.assertEquals("Recall Lenient: " + value + " instead of 1!", 1, value, 0);
    // check low precision
    Integer id = annSet.add(new Long(2), new Long(4), "Foo", features);
    Annotation falsePositive = annSet.get(id);
    responseSet.add(falsePositive);
    differ.calculateDiff(keySet, responseSet);
    differ.sanityCheck();
    if (DEBUG)
        differ.printMissmatches();
    value = differ.getPrecisionStrict();
    Assert.assertEquals("Precision Strict: " + value + " instead of .99!", .99, value, .001);
    // recall should still be 100%
    value = differ.getRecallStrict();
    Assert.assertEquals("Recall Strict: " + value + " instead of 1!", 1, value, 0);
    value = differ.getRecallLenient();
    Assert.assertEquals("Recall Lenient: " + value + " instead of 1!", 1, value, 0);
    // check low recall
    responseSet.remove(falsePositive);
    keySet.add(falsePositive);
    differ.calculateDiff(keySet, responseSet);
    differ.sanityCheck();
    if (DEBUG)
        differ.printMissmatches();
    value = differ.getRecallStrict();
    Assert.assertEquals("Recall Strict: " + value + " instead of .99!", .99, value, .001);
    // precision should still be 100%
    value = differ.getPrecisionStrict();
    Assert.assertEquals("Precision Strict: " + value + " instead of 1!", 1, value, 0);
    value = differ.getPrecisionLenient();
    Assert.assertEquals("Precision Lenient: " + value + " instead of 1!", 1, value, 0);
}

Example 12 with Annotation

use of gate.Annotation in project gate-core by GateNLP.

the class TestXml method verifyIDConsistency.

// End of verifyAnnotationIDGenerator()
/**
 * Verifies if the two maps hold annotations with the same ID. The only thing not checked
 * are the features, as some of them could be lost in the serialization/deserialization process
 * @param origAnnotMap A map by ID, containing the original annotations
 * @param reloadedAnnMap A map by ID, containing the recreated annotations
 */
private void verifyIDConsistency(Map<Integer, Annotation> origAnnotMap, Map<Integer, Annotation> reloadedAnnMap) {
    assertEquals("Found a different number of annot in both documents.", origAnnotMap.keySet().size(), reloadedAnnMap.keySet().size());
    for (Iterator<Integer> it = origAnnotMap.keySet().iterator(); it.hasNext(); ) {
        Integer id = it.next();
        Annotation origAnn = origAnnotMap.get(id);
        Annotation reloadedAnnot = reloadedAnnMap.get(id);
        assertTrue("Annotation with ID=" + id + " was not found in the reloaded document.", reloadedAnnot != null);
        compareAnnot(origAnn, reloadedAnnot);
    }
// End for
}

Example 13 with Annotation

use of gate.Annotation in project gate-core by GateNLP.

the class DocumentStaxUtils method readXces.

/**
 * Read XML data in <a href="http://www.xces.org/">XCES</a> format
 * from the given reader and add the corresponding annotations to the
 * given annotation set. The reader must be positioned on the starting
 * <code>cesAna</code> tag and will be left pointing to the
 * corresponding end tag.
 *
 * @param xsr the XMLStreamReader to read from.
 * @param as the annotation set to read into.
 * @throws XMLStreamException
 */
public static void readXces(XMLStreamReader xsr, AnnotationSet as) throws XMLStreamException {
    xsr.require(XMLStreamConstants.START_ELEMENT, XCES_NAMESPACE, "cesAna");
    // Set of all annotation IDs in this set.
    Set<Integer> allAnnotIds = new TreeSet<Integer>();
    // pre-populate with the IDs of any existing annotations in the set
    for (Annotation a : as) {
        allAnnotIds.add(a.getId());
    }
    // lists to collect the annotations in before adding them to the
    // set. We collect the annotations that specify and ID (via
    // struct/@n) in one list and those that don't in another, so we can
    // add the identified ones first, then the others will take the next
    // available ID
    List<AnnotationObject> collectedIdentifiedAnnots = new ArrayList<AnnotationObject>();
    List<AnnotationObject> collectedNonIdentifiedAnnots = new ArrayList<AnnotationObject>();
    while (xsr.nextTag() == XMLStreamConstants.START_ELEMENT) {
        xsr.require(XMLStreamConstants.START_ELEMENT, XCES_NAMESPACE, "struct");
        AnnotationObject annObj = new AnnotationObject();
        annObj.setElemName(xsr.getAttributeValue(null, "type"));
        try {
            annObj.setStart(Long.valueOf(xsr.getAttributeValue(null, "from")));
        } catch (NumberFormatException nfe) {
            throw new XMLStreamException("Non-integer value found for struct/@from", xsr.getLocation());
        }
        try {
            annObj.setEnd(Long.valueOf(xsr.getAttributeValue(null, "to")));
        } catch (NumberFormatException nfe) {
            throw new XMLStreamException("Non-integer value found for struct/@to", xsr.getLocation());
        }
        String annotIdString = xsr.getAttributeValue(null, "n");
        if (annotIdString != null) {
            try {
                Integer annotationId = Integer.valueOf(annotIdString);
                if (allAnnotIds.contains(annotationId)) {
                    throw new XMLStreamException("Annotation IDs must be unique " + "within an annotation set. Found duplicate ID", xsr.getLocation());
                }
                allAnnotIds.add(annotationId);
                annObj.setId(annotationId);
            } catch (NumberFormatException nfe) {
                throw new XMLStreamException("Non-integer annotation ID found", xsr.getLocation());
            }
        }
        // get the features of this annotation
        annObj.setFM(readXcesFeatureMap(xsr));
        // readFeatureMap leaves xsr on the </Annotation> tag
        if (annObj.getId() != null) {
            collectedIdentifiedAnnots.add(annObj);
        } else {
            collectedNonIdentifiedAnnots.add(annObj);
        }
    }
    // finished reading, add the annotations to the set
    AnnotationObject a = null;
    try {
        // first the ones that specify an ID
        Iterator<AnnotationObject> it = collectedIdentifiedAnnots.iterator();
        while (it.hasNext()) {
            a = it.next();
            as.add(a.getId(), a.getStart(), a.getEnd(), a.getElemName(), a.getFM());
        }
        // next the ones that don't
        it = collectedNonIdentifiedAnnots.iterator();
        while (it.hasNext()) {
            a = it.next();
            as.add(a.getStart(), a.getEnd(), a.getElemName(), a.getFM());
        }
    } catch (InvalidOffsetException ioe) {
        throw new XMLStreamException("Invalid offset when creating annotation " + a, ioe);
    }
}

Example 14 with Annotation

use of gate.Annotation in project gate-core by GateNLP.

the class DocumentStaxUtils method writeDocument.

/**
 * Write the specified GATE Document to an XMLStreamWriter. This
 * method writes just the GateDocument element - the XML declaration
 * must be filled in by the caller if required.
 *
 * @param doc the Document to write
 * @param annotationSets the annotations to include. If the map
 *          contains an entry for the key <code>null</code>, this
 *          will be treated as the default set. All other entries are
 *          treated as named annotation sets.
 * @param xsw the StAX XMLStreamWriter to use for output
 * @throws GateException if an error occurs during writing
 */
public static void writeDocument(Document doc, Map<String, Collection<Annotation>> annotationSets, XMLStreamWriter xsw, String namespaceURI) throws XMLStreamException {
    xsw.setDefaultNamespace(namespaceURI);
    xsw.writeStartElement(namespaceURI, "GateDocument");
    xsw.writeAttribute("version", GATE_XML_VERSION);
    if (namespaceURI.length() > 0) {
        xsw.writeDefaultNamespace(namespaceURI);
    }
    newLine(xsw);
    // features
    xsw.writeComment(" The document's features");
    newLine(xsw);
    newLine(xsw);
    xsw.writeStartElement(namespaceURI, "GateDocumentFeatures");
    newLine(xsw);
    writeFeatures(doc.getFeatures(), xsw, namespaceURI);
    // GateDocumentFeatures
    xsw.writeEndElement();
    newLine(xsw);
    // text with nodes
    xsw.writeComment(" The document content area with serialized nodes ");
    newLine(xsw);
    newLine(xsw);
    writeTextWithNodes(doc, annotationSets.values(), xsw, namespaceURI);
    newLine(xsw);
    // Serialize as XML all document's annotation sets
    // Serialize the default AnnotationSet
    StatusListener sListener = (StatusListener) gate.Gate.getListeners().get("gate.event.StatusListener");
    if (annotationSets.containsKey(null)) {
        if (sListener != null)
            sListener.statusChanged("Saving the default annotation set ");
        xsw.writeComment(" The default annotation set ");
        newLine(xsw);
        newLine(xsw);
        writeAnnotationSet(annotationSets.get(null), null, xsw, namespaceURI);
        newLine(xsw);
    }
    // while(iter.hasNext()) {
    for (Map.Entry<String, Collection<Annotation>> entry : annotationSets.entrySet()) {
        // iter.next();
        String annotationSetName = entry.getKey();
        // above
        if (annotationSetName != null) {
            // annotationSets.get(annotationSetName);
            Collection<Annotation> annots = entry.getValue();
            xsw.writeComment(" Named annotation set ");
            newLine(xsw);
            newLine(xsw);
            // Serialize it as XML
            if (sListener != null)
                sListener.statusChanged("Saving " + annotationSetName + " annotation set ");
            writeAnnotationSet(annots, annotationSetName, xsw, namespaceURI);
            newLine(xsw);
        }
    // End if
    }
    // End while
    Iterator<String> iter = annotationSets.keySet().iterator();
    while (iter.hasNext()) {
        writeRelationSet(doc.getAnnotations(iter.next()).getRelations(), xsw, namespaceURI);
    }
    // close the GateDocument element
    xsw.writeEndElement();
    newLine(xsw);
}

Example 15 with Annotation

use of gate.Annotation in project gate-core by GateNLP.

the class AnnotationSetImpl method getContained.

// get(type, constraints, offset)
/**
 * Select annotations contained within an interval, i.e.
 * those annotations whose start position is
 * >= <code>startOffset</code> and whose end position is &lt;=
 * <code>endOffset</code>.
 */
@Override
public AnnotationSet getContained(Long startOffset, Long endOffset) {
    // check the range
    if (endOffset < startOffset)
        return emptyAS();
    // ensure index
    if (annotsByStartNode == null)
        indexByStartOffset();
    List<Annotation> annotationsToAdd = null;
    Iterator<Node> nodesIter;
    Node currentNode;
    Iterator<Annotation> annotIter;
    // find all the annots that start at or after the start offset but
    // strictly
    // before the end offset
    nodesIter = nodesByOffset.subMap(startOffset, endOffset).values().iterator();
    while (nodesIter.hasNext()) {
        currentNode = nodesIter.next();
        Collection<Annotation> objFromPoint = getAnnotsByStartNode(currentNode.getId());
        if (objFromPoint == null)
            continue;
        // loop through the annotations and find only those that
        // also end before endOffset
        annotIter = objFromPoint.iterator();
        while (annotIter.hasNext()) {
            Annotation annot = annotIter.next();
            if (annot.getEndNode().getOffset().compareTo(endOffset) <= 0) {
                if (annotationsToAdd == null)
                    annotationsToAdd = new ArrayList<Annotation>();
                annotationsToAdd.add(annot);
            }
        }
    }
    return new ImmutableAnnotationSetImpl(doc, annotationsToAdd);
}