Examples with CasDiff de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.CasDiff used on opensource projects

Example 6 with CasDiff

use of de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.CasDiff in project webanno by webanno.

the class TwoPairedKappaTest method testThreeUserDiffArcAndSpanAnnotation.

@Test
public void testThreeUserDiffArcAndSpanAnnotation() throws Exception {
    Map<User, List<SourceDocument>> userDocs = new HashMap<>();
    userDocs.put(user1, asList(document));
    userDocs.put(user2, asList(document));
    userDocs.put(user3, asList(document));
    Map<User, CAS> userCases = new HashMap<>();
    userCases.put(user1, kappatestCas);
    userCases.put(user2, kappaspandiff);
    userCases.put(user3, kappaspanarcdiff);
    Map<SourceDocument, Map<User, CAS>> documentJCases = new HashMap<>();
    documentJCases.put(document, userCases);
    // Check against new impl
    CasDiff diff = doDiff(asList(POS_DIFF_ADAPTER, DEPENDENCY_DIFF_ADAPTER), LINK_TARGET_AS_LABEL, convert(userCases));
    DiffResult result = diff.toResult();
    Map<String, List<CAS>> user1and2 = convert(userCases);
    user1and2.remove("user3");
    AgreementResult agreement12 = getCohenKappaAgreement(diff, Dependency.class.getName(), "DependencyType", user1and2);
    Map<String, List<CAS>> user2and3 = convert(userCases);
    user2and3.remove("user1");
    AgreementResult agreement23 = getCohenKappaAgreement(diff, Dependency.class.getName(), "DependencyType", user2and3);
    Map<String, List<CAS>> user1and3 = convert(userCases);
    user1and3.remove("user2");
    AgreementResult agreement13 = getCohenKappaAgreement(diff, Dependency.class.getName(), "DependencyType", user1and3);
    // Asserts
    result.print(System.out);
    System.out.printf("New agreement 1/2: %s%n", agreement12.toString());
    System.out.printf("New agreement 2/3: %s%n", agreement23.toString());
    System.out.printf("New agreement 1/3: %s%n", agreement13.toString());
}

Example 7 with CasDiff

use of de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.CasDiff in project webanno by webanno.

the class AgreementUtils method makeCodingStudy.

private static CodingAgreementResult makeCodingStudy(CasDiff aDiff, Collection<String> aUsers, String aType, String aFeature, boolean aExcludeIncomplete, boolean aNullLabelsAsEmpty, Map<String, List<CAS>> aCasMap) {
    List<String> users = new ArrayList<>(aUsers);
    Collections.sort(users);
    List<ConfigurationSet> completeSets = new ArrayList<>();
    List<ConfigurationSet> setsWithDifferences = new ArrayList<>();
    List<ConfigurationSet> incompleteSetsByPosition = new ArrayList<>();
    List<ConfigurationSet> incompleteSetsByLabel = new ArrayList<>();
    List<ConfigurationSet> pluralitySets = new ArrayList<>();
    List<ConfigurationSet> irrelevantSets = new ArrayList<>();
    CodingAnnotationStudy study = new CodingAnnotationStudy(users.size());
    // Check if the feature we are looking at is a primitive feature or a link feature
    // We do this by looking it up in the first available CAS. Mind that at this point all
    // CASes should have exactly the same typesystem.
    CAS someCas = findSomeCas(aCasMap);
    if (someCas == null) {
        // Well... there is NOTHING here!
        // All positions are irrelevant
        aDiff.getPositions().forEach(p -> irrelevantSets.add(aDiff.getConfigurationSet(p)));
        return new CodingAgreementResult(aType, aFeature, aDiff.toResult(), study, users, completeSets, irrelevantSets, setsWithDifferences, incompleteSetsByPosition, incompleteSetsByLabel, pluralitySets, aExcludeIncomplete);
    }
    TypeSystem ts = someCas.getTypeSystem();
    // We should just do the right thing here which is: do nothing
    if (ts.getType(aType) == null) {
        // All positions are irrelevant
        aDiff.getPositions().forEach(p -> irrelevantSets.add(aDiff.getConfigurationSet(p)));
        return new CodingAgreementResult(aType, aFeature, aDiff.toResult(), study, users, completeSets, irrelevantSets, setsWithDifferences, incompleteSetsByPosition, incompleteSetsByLabel, pluralitySets, aExcludeIncomplete);
    }
    // Check that the feature really exists instead of just getting a NPE later
    if (ts.getType(aType).getFeatureByBaseName(aFeature) == null) {
        throw new IllegalArgumentException("Type [" + aType + "] has no feature called [" + aFeature + "]");
    }
    boolean isPrimitiveFeature = ts.getType(aType).getFeatureByBaseName(aFeature).getRange().isPrimitive();
    nextPosition: for (Position p : aDiff.getPositions()) {
        ConfigurationSet cfgSet = aDiff.getConfigurationSet(p);
        // Only calculate agreement for the given layer
        if (!cfgSet.getPosition().getType().equals(aType)) {
            // We don't even consider these as irrelevant, they are just filtered out
            continue;
        }
        // If the feature on a position is set, then it is a subposition
        boolean isSubPosition = p.getFeature() != null;
        // this is an inverted XOR!
        if (!(isPrimitiveFeature ^ isSubPosition)) {
            irrelevantSets.add(cfgSet);
            continue;
        }
        // feature
        if (isSubPosition && !aFeature.equals(cfgSet.getPosition().getFeature())) {
            irrelevantSets.add(cfgSet);
            continue nextPosition;
        }
        // If non of the current users has made any annotation at this position, then skip it
        if (users.stream().filter(u -> cfgSet.getCasGroupIds().contains(u)).count() == 0) {
            irrelevantSets.add(cfgSet);
            continue nextPosition;
        }
        Object[] values = new Object[users.size()];
        int i = 0;
        for (String user : users) {
            // this configuration set.
            if (!cfgSet.getCasGroupIds().contains(user)) {
                incompleteSetsByPosition.add(cfgSet);
                if (aExcludeIncomplete) {
                    // Record as incomplete
                    continue nextPosition;
                } else {
                    // Record as missing value
                    values[i] = null;
                    i++;
                    continue;
                }
            }
            // Make sure a single user didn't do multiple alternative annotations at a single
            // position. So there is currently no support for calculating agreement on stacking
            // annotations.
            List<Configuration> cfgs = cfgSet.getConfigurations(user);
            if (cfgs.size() > 1) {
                pluralitySets.add(cfgSet);
                continue nextPosition;
            }
            Configuration cfg = cfgs.get(0);
            // Check if source and/or targets of a relation are stacked
            if (cfg.getPosition() instanceof RelationPosition) {
                RelationPosition pos = (RelationPosition) cfg.getPosition();
                FeatureStructure arc = cfg.getFs(user, pos.getCasId(), aCasMap);
                RelationDiffAdapter adapter = (RelationDiffAdapter) aDiff.getTypeAdapters().get(pos.getType());
                // Check if the source of the relation is stacked
                AnnotationFS source = FSUtil.getFeature(arc, adapter.getSourceFeature(), AnnotationFS.class);
                List<AnnotationFS> sourceCandidates = CasUtil.selectAt(arc.getCAS(), source.getType(), source.getBegin(), source.getEnd());
                if (sourceCandidates.size() > 1) {
                    pluralitySets.add(cfgSet);
                    continue nextPosition;
                }
                // Check if the target of the relation is stacked
                AnnotationFS target = FSUtil.getFeature(arc, adapter.getTargetFeature(), AnnotationFS.class);
                List<AnnotationFS> targetCandidates = CasUtil.selectAt(arc.getCAS(), target.getType(), target.getBegin(), target.getEnd());
                if (targetCandidates.size() > 1) {
                    pluralitySets.add(cfgSet);
                    continue nextPosition;
                }
            }
            // Only calculate agreement for the given feature
            FeatureStructure fs = cfg.getFs(user, cfg.getPosition().getCasId(), aCasMap);
            values[i] = extractValueForAgreement(fs, aFeature, cfg.getAID(user).index, cfg.getPosition().getLinkCompareBehavior());
            // agreement calculation. The empty label is still a valid label.
            if (aNullLabelsAsEmpty && values[i] == null) {
                values[i] = "";
            }
            // "null" cannot be used in agreement calculations. We treat these as incomplete
            if (values[i] == null) {
                incompleteSetsByLabel.add(cfgSet);
                if (aExcludeIncomplete) {
                    continue nextPosition;
                }
            }
            i++;
        }
        if (ObjectUtils.notEqual(values[0], values[1])) {
            setsWithDifferences.add(cfgSet);
        }
        // are calculating agreement over
        assert cfgSet.getPosition().getFeature() == null || cfgSet.getPosition().getFeature().equals(aFeature);
        completeSets.add(cfgSet);
        study.addItemAsArray(values);
    }
    return new CodingAgreementResult(aType, aFeature, aDiff.toResult(), study, users, completeSets, irrelevantSets, setsWithDifferences, incompleteSetsByPosition, incompleteSetsByLabel, pluralitySets, aExcludeIncomplete);
}

Example 8 with CasDiff

use of de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.CasDiff in project webanno by webanno.

the class CohenKappaAgreementMeasure method calculatePairAgreement.

@Override
public CodingAgreementResult calculatePairAgreement(Map<String, List<CAS>> aCasMap) {
    AnnotationFeature feature = getFeature();
    DefaultAgreementTraits traits = getTraits();
    List<DiffAdapter> adapters = getDiffAdapters(annotationService, asList(feature.getLayer()));
    CasDiff diff = doDiff(adapters, traits.getLinkCompareBehavior(), aCasMap);
    CodingAgreementResult agreementResult = makeCodingStudy(diff, feature.getLayer().getName(), feature.getName(), true, aCasMap);
    IAgreementMeasure agreement = new CohenKappaAgreement(agreementResult.getStudy());
    if (agreementResult.getStudy().getItemCount() > 0) {
        agreementResult.setAgreement(agreement.calculateAgreement());
    } else {
        agreementResult.setAgreement(Double.NaN);
    }
    return agreementResult;
}

Example 9 with CasDiff

use of de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.CasDiff in project webanno by webanno.

the class FleissKappaAgreementMeasure method calculatePairAgreement.

@Override
public CodingAgreementResult calculatePairAgreement(Map<String, List<CAS>> aCasMap) {
    AnnotationFeature feature = getFeature();
    DefaultAgreementTraits traits = getTraits();
    List<DiffAdapter> adapters = getDiffAdapters(annotationService, asList(feature.getLayer()));
    CasDiff diff = doDiff(adapters, traits.getLinkCompareBehavior(), aCasMap);
    CodingAgreementResult agreementResult = makeCodingStudy(diff, feature.getLayer().getName(), feature.getName(), true, aCasMap);
    IAgreementMeasure agreement = new FleissKappaAgreement(agreementResult.getStudy());
    if (agreementResult.getStudy().getItemCount() > 0) {
        agreementResult.setAgreement(agreement.calculateAgreement());
    } else {
        agreementResult.setAgreement(Double.NaN);
    }
    return agreementResult;
}

Example 10 with CasDiff

use of de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.CasDiff in project webanno by webanno.

the class KrippendorffAlphaAgreementMeasure method calculatePairAgreement.

@Override
public CodingAgreementResult calculatePairAgreement(Map<String, List<CAS>> aCasMap) {
    AnnotationFeature feature = getFeature();
    KrippendorffAlphaAgreementTraits traits = getTraits();
    List<DiffAdapter> adapters = getDiffAdapters(annotationService, asList(feature.getLayer()));
    CasDiff diff = doDiff(adapters, traits.getLinkCompareBehavior(), aCasMap);
    CodingAgreementResult agreementResult = makeCodingStudy(diff, feature.getLayer().getName(), feature.getName(), traits.isExcludeIncomplete(), aCasMap);
    IAgreementMeasure agreement = new KrippendorffAlphaAgreement(agreementResult.getStudy(), new NominalDistanceFunction());
    if (agreementResult.getStudy().getItemCount() > 0) {
        try {
            agreementResult.setAgreement(agreement.calculateAgreement());
        } catch (InsufficientDataException e) {
            agreementResult.setAgreement(NaN);
        }
    } else {
        agreementResult.setAgreement(NaN);
    }
    return agreementResult;
}