Examples with AnnotationSet gate.AnnotationSet used on opensource projects

Example 6 with AnnotationSet

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

the class AnnotationMerging method mergeAnnotation.

/**
 * Merge all annotationset from an array. If one annotation is in at least
 * numK annotation sets, then put it into the merging annotation set.
 */
public static void mergeAnnotation(AnnotationSet[] annsArr, String nameFeat, HashMap<Annotation, String> mergeAnns, int numMinK, boolean isTheSameInstances) {
    int numA = annsArr.length;
    // First copy the annotatioin sets into a temp array
    @SuppressWarnings({ "unchecked", "rawtypes" }) Set<Annotation>[] annsArrTemp = new Set[numA];
    for (int i = 0; i < numA; ++i) {
        if (annsArr[i] != null) {
            annsArrTemp[i] = new HashSet<Annotation>();
            for (Annotation ann : annsArr[i]) annsArrTemp[i].add(ann);
        }
    }
    HashSet<String> featSet = new HashSet<String>();
    if (nameFeat != null)
        featSet.add(nameFeat);
    if (numMinK < 1)
        numMinK = 1;
    for (int iA = 0; iA < numA - numMinK + 1; ++iA) {
        if (annsArrTemp[iA] != null) {
            for (Annotation ann : annsArrTemp[iA]) {
                int numContained = 1;
                StringBuffer featAdd = new StringBuffer();
                featAdd.append(iA);
                StringBuffer featDisa = new StringBuffer();
                if (iA > 0) {
                    featDisa.append("0");
                    for (int i = 1; i < iA; ++i) featDisa.append("-" + i);
                }
                int numDisagreed = iA;
                for (int i = iA + 1; i < numA; ++i) {
                    boolean isContained = false;
                    if (annsArrTemp[i] != null) {
                        Annotation annT = null;
                        for (Annotation ann0 : annsArrTemp[i]) {
                            if (ann0.isCompatible(ann, featSet)) {
                                ++numContained;
                                featAdd.append("-" + i);
                                annT = ann0;
                                isContained = true;
                                break;
                            }
                        }
                        if (isContained)
                            annsArrTemp[i].remove(annT);
                    }
                    if (!isContained) {
                        if (numDisagreed == 0)
                            featDisa.append(i);
                        else
                            featDisa.append("-" + i);
                        ++numDisagreed;
                    }
                }
                if (numContained >= numMinK) {
                    mergeAnns.put(ann, featAdd.toString());
                } else if (isTheSameInstances && nameFeat != null) {
                    ann.getFeatures().remove(nameFeat);
                    mergeAnns.put(ann, featAdd.toString());
                }
            }
        }
    }
    // Remove the annotation in the same place
    removeDuplicate(mergeAnns);
    return;
}

Example 7 with AnnotationSet

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

the class AnnotationMerging method mergeAnnotationMajority.

/**
 * Merge all annotationset from an array. If one annotation is agreed by
 * the majority of the annotators, then put it into the merging annotation set.
 */
public static void mergeAnnotationMajority(AnnotationSet[] annsArr, String nameFeat, HashMap<Annotation, String> mergeAnns, boolean isTheSameInstances) {
    int numA = annsArr.length;
    if (nameFeat == null) {
        mergeAnnogationMajorityNoFeat(annsArr, mergeAnns, isTheSameInstances);
        return;
    }
    // First copy the annotatioin sets into a temp array
    @SuppressWarnings({ "unchecked", "rawtypes" }) Set<Annotation>[] annsArrTemp = new Set[numA];
    for (int i = 0; i < numA; ++i) {
        if (annsArr[i] != null) {
            annsArrTemp[i] = new HashSet<Annotation>();
            for (Annotation ann : annsArr[i]) annsArrTemp[i].add(ann);
        }
    }
    for (int iA = 0; iA < numA; ++iA) {
        if (annsArrTemp[iA] != null) {
            for (Annotation ann : annsArrTemp[iA]) {
                int numDisagreed = 0;
                // Already the iA annotators don't agree the annotation
                numDisagreed = iA;
                StringBuffer featDisa = new StringBuffer();
                if (iA > 0) {
                    featDisa.append("0");
                    for (int i = 1; i < iA; ++i) featDisa.append("-" + i);
                }
                HashMap<String, String> featOthers = new HashMap<String, String>();
                String featTh = null;
                if (ann.getFeatures().get(nameFeat) != null)
                    featTh = ann.getFeatures().get(nameFeat).toString();
                featOthers.put(featTh, new Integer(iA).toString());
                HashMap<String, Annotation> annAll = new HashMap<String, Annotation>();
                annAll.put(featTh, ann);
                for (int i = iA + 1; i < numA; ++i) {
                    boolean isContained = false;
                    if (annsArrTemp[i] != null) {
                        Annotation annT = null;
                        for (Annotation ann0 : annsArrTemp[i]) {
                            if (ann0.coextensive(ann)) {
                                String featValue = null;
                                if (ann0.getFeatures().get(nameFeat) != null)
                                    featValue = ann0.getFeatures().get(nameFeat).toString();
                                if (!featOthers.containsKey(featValue)) {
                                    featOthers.put(featValue, new Integer(i).toString());
                                    annAll.put(featValue, ann0);
                                } else {
                                    String str = featOthers.get(featValue);
                                    featOthers.put(featValue, str + "-" + i);
                                }
                                annT = ann0;
                                isContained = true;
                                break;
                            }
                        }
                        if (isContained)
                            annsArrTemp[i].remove(annT);
                    }
                    if (!isContained) {
                        if (numDisagreed == 0)
                            featDisa.append(i);
                        else
                            featDisa.append("-" + i);
                        ++numDisagreed;
                    }
                }
                // end of the loop for the following annotation set
                int numAgreed = -1;
                String agreeFeat = null;
                for (String str : featOthers.keySet()) {
                    String str0 = featOthers.get(str);
                    int num = 1;
                    while (str0.contains("-")) {
                        ++num;
                        str0 = str0.substring(str0.indexOf('-') + 1);
                    }
                    if (numAgreed < num) {
                        numAgreed = num;
                        agreeFeat = str;
                    }
                }
                if (numAgreed >= numDisagreed) {
                    mergeAnns.put(annAll.get(agreeFeat), featOthers.get(agreeFeat));
                } else if (isTheSameInstances) {
                    if (ann.getFeatures().get(nameFeat) != null)
                        ann.getFeatures().remove(nameFeat);
                    mergeAnns.put(ann, featDisa.toString());
                }
            }
        // for each ann in the current annotation set
        }
    }
    return;
}

Example 8 with AnnotationSet

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

the class CorpusBenchmarkTool method measureDocs.

// calculateAvgTotal
protected AnnotationDiffer measureDocs(Document keyDoc, Document respDoc, String annotType) throws ResourceInstantiationException {
    if (keyDoc == null || respDoc == null)
        return null;
    if (annotSetName != null && keyDoc.getAnnotations(annotSetName).get(annotType) == null)
        return null;
    else if ((annotSetName == null || annotSetName.equals("")) && keyDoc.getAnnotations().get(annotType) == null)
        return null;
    // create an annotation diff
    AnnotationDiffer annotDiffer = new AnnotationDiffer();
    // set the feature names set for annotation differ
    annotDiffer.setSignificantFeaturesSet(diffFeaturesSet);
    // we need to find the sets
    AnnotationSet keys, responses;
    if (annotSetName == null || annotSetName.equals("")) {
        keys = keyDoc.getAnnotations().get(annotType);
        responses = respDoc.getAnnotations().get(annotType);
    } else {
        keys = keyDoc.getAnnotations(annotSetName).get(annotType);
        responses = respDoc.getAnnotations(outputSetName).get(annotType);
    }
    // we have annotation sets so call the annotationDiffer
    annotDiffer.calculateDiff(keys, responses);
    return annotDiffer;
}

Example 9 with AnnotationSet

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

the class TestAnnotationMerging method testWithfeat.

/**
 * The actual method for testing.
 */
public void testWithfeat(String nameAnnSets, String nameAnnType, String nameAnnFeat, Corpus data, boolean isUsingMajority) {
    // get the annotation sets
    String[] annSetsN = nameAnnSets.split(";");
    int numJudges = annSetsN.length;
    int numDocs = data.size();
    AnnotationSet[][] annArr2 = new AnnotationSet[numDocs][numJudges];
    for (int i = 0; i < numDocs; ++i) {
        Document doc = data.get(i);
        for (int j = 0; j < numJudges; ++j) {
            // Get the annotation
            annArr2[i][j] = doc.getAnnotations(annSetsN[j]).get(nameAnnType);
        }
    }
    // Annotation merging
    boolean isTheSameInstances = true;
    for (int i = 0; i < annArr2.length; ++i) if (!AnnotationMerging.isSameInstancesForAnnotators(annArr2[i], 1)) {
        isTheSameInstances = false;
        break;
    }
    HashMap<Annotation, String> mergeInfor = new HashMap<Annotation, String>();
    if (isUsingMajority)
        AnnotationMerging.mergeAnnotationMajority(annArr2[0], nameAnnFeat, mergeInfor, isTheSameInstances);
    else
        AnnotationMerging.mergeAnnotation(annArr2[0], nameAnnFeat, mergeInfor, 2, isTheSameInstances);
    int numAnns = 0;
    if (isTheSameInstances) {
        for (Annotation ann : mergeInfor.keySet()) {
            if (ann.getFeatures().get(nameAnnFeat) != null)
                ++numAnns;
        }
    } else {
        numAnns = mergeInfor.size();
    }
    checkNumbers(numAnns);
}

Example 10 with AnnotationSet

use of gate.AnnotationSet 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);
}