Examples with AnnotationFeature de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature used on opensource projects

Example 26 with AnnotationFeature

use of de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature in project webanno by webanno.

the class TagSetEditorPanel method actionDelete.

private void actionDelete(AjaxRequestTarget aTarget) {
    confirmationDialog.setContentModel(new StringResourceModel("DeleteDialog.text", this).setParameters(selectedTagSet.getObject().getName()));
    confirmationDialog.show(aTarget);
    confirmationDialog.setConfirmAction((_target) -> {
        // the tagset is deleted!
        for (AnnotationFeature ft : annotationSchemaService.listAnnotationFeature(selectedProject.getObject())) {
            if (ft.getTagset() != null && ft.getTagset().equals(selectedTagSet.getObject())) {
                ft.setTagset(null);
                annotationSchemaService.createFeature(ft);
            }
        }
        annotationSchemaService.removeTagSet(selectedTagSet.getObject());
        _target.add(getPage());
        actionCancel(_target);
    });
}

Example 27 with AnnotationFeature

use of de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature in project webanno by webanno.

the class AutomationPage method createDetailEditor.

private AnnotationDetailEditorPanel createDetailEditor() {
    return new AnnotationDetailEditorPanel("annotationDetailEditorPanel", getModel()) {

        private static final long serialVersionUID = 2857345299480098279L;

        @Override
        protected void onChange(AjaxRequestTarget aTarget) {
            AnnotatorState state = getModelObject();
            aTarget.addChildren(getPage(), IFeedback.class);
            try {
                annotationEditor.requestRender(aTarget);
            } catch (Exception e) {
                handleException(this, aTarget, e);
                return;
            }
            try {
                SuggestionBuilder builder = new SuggestionBuilder(casStorageService, documentService, correctionDocumentService, curationDocumentService, annotationService, userRepository);
                curationContainer = builder.buildCurationContainer(state);
                setCurationSegmentBeginEnd(getEditorCas());
                curationContainer.setBratAnnotatorModel(state);
                suggestionView.updatePanel(aTarget, curationContainer, annotationSelectionByUsernameAndAddress, curationSegment);
                update(aTarget);
            } catch (Exception e) {
                handleException(this, aTarget, e);
            }
        }

        @Override
        public void onAnnotate(AjaxRequestTarget aTarget) {
            AnnotatorState state = getModelObject();
            if (state.isForwardAnnotation()) {
                return;
            }
            AnnotationLayer layer = state.getSelectedAnnotationLayer();
            int address = state.getSelection().getAnnotation().getId();
            try {
                JCas jCas = getEditorCas();
                AnnotationFS fs = selectByAddr(jCas, address);
                for (AnnotationFeature f : annotationService.listAnnotationFeature(layer)) {
                    Type type = CasUtil.getType(fs.getCAS(), layer.getName());
                    Feature feat = type.getFeatureByBaseName(f.getName());
                    if (!automationService.existsMiraTemplate(f)) {
                        continue;
                    }
                    if (!automationService.getMiraTemplate(f).isAnnotateAndRepeat()) {
                        continue;
                    }
                    TagSet tagSet = f.getTagset();
                    boolean isRepeatable = false;
                    // repeat only if the value is in the tagset
                    for (Tag tag : annotationService.listTags(tagSet)) {
                        if (fs.getFeatureValueAsString(feat) == null) {
                            // this is new annotation without values
                            break;
                        }
                        if (fs.getFeatureValueAsString(feat).equals(tag.getName())) {
                            isRepeatable = true;
                            break;
                        }
                    }
                    if (automationService.getMiraTemplate(f) != null && isRepeatable) {
                        if (layer.getType().endsWith(WebAnnoConst.RELATION_TYPE)) {
                            AutomationUtil.repeateRelationAnnotation(state, documentService, correctionDocumentService, annotationService, fs, f, fs.getFeatureValueAsString(feat));
                            update(aTarget);
                            break;
                        } else if (layer.getType().endsWith(WebAnnoConst.SPAN_TYPE)) {
                            AutomationUtil.repeateSpanAnnotation(state, documentService, correctionDocumentService, annotationService, fs.getBegin(), fs.getEnd(), f, fs.getFeatureValueAsString(feat));
                            update(aTarget);
                            break;
                        }
                    }
                }
            } catch (Exception e) {
                handleException(this, aTarget, e);
            }
        }

        @Override
        protected void onAutoForward(AjaxRequestTarget aTarget) {
            annotationEditor.requestRender(aTarget);
        }

        @Override
        public void onDelete(AjaxRequestTarget aTarget, AnnotationFS aFS) {
            AnnotatorState state = getModelObject();
            AnnotationLayer layer = state.getSelectedAnnotationLayer();
            for (AnnotationFeature f : annotationService.listAnnotationFeature(layer)) {
                if (!automationService.existsMiraTemplate(f)) {
                    continue;
                }
                if (!automationService.getMiraTemplate(f).isAnnotateAndRepeat()) {
                    continue;
                }
                try {
                    Type type = CasUtil.getType(aFS.getCAS(), layer.getName());
                    Feature feat = type.getFeatureByBaseName(f.getName());
                    if (layer.getType().endsWith(WebAnnoConst.RELATION_TYPE)) {
                        AutomationUtil.deleteRelationAnnotation(state, documentService, correctionDocumentService, annotationService, aFS, f, aFS.getFeatureValueAsString(feat));
                    } else {
                        AutomationUtil.deleteSpanAnnotation(state, documentService, correctionDocumentService, annotationService, aFS.getBegin(), aFS.getEnd(), f, aFS.getFeatureValueAsString(feat));
                    }
                    update(aTarget);
                } catch (Exception e) {
                    handleException(this, aTarget, e);
                }
            }
        }
    };
}

Example 28 with AnnotationFeature

use of de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature in project webanno by webanno.

the class AutomationUtil method generateFinalClassifier.

/**
 * Based on the other layer, predict features for the training document
 *
 * @param aTemplate
 *            the template.
 * @param aRepository
 *            the repository.
 * @return the prediction.
 * @throws UIMAException
 *             hum?
 * @throws ClassNotFoundException
 *             hum?
 * @throws IOException
 *             hum?
 * @throws AnnotationException
 *             hum?
 *
 * @throws AutomationException
 *             if an error occurs.
 */
public static String generateFinalClassifier(MiraTemplate aTemplate, DocumentService aRepository, CurationDocumentService aCurationDocumentService, AnnotationSchemaService aAnnotationService, AutomationService aAutomationService, UserDao aUserDao) throws UIMAException, ClassNotFoundException, IOException, AnnotationException, AutomationException {
    int frequency = 2;
    double sigma = 1;
    int iterations = 10;
    int beamSize = 0;
    boolean maxPosteriors = false;
    AnnotationFeature layerFeature = aTemplate.getTrainFeature();
    List<List<String>> predictions = new ArrayList<>();
    File miraDir = aAutomationService.getMiraDir(layerFeature);
    Mira mira = new Mira();
    File predFile = new File(miraDir, layerFeature.getLayer().getId() + "-" + layerFeature.getId() + ".train.ft");
    File predcitedFile = new File(predFile.getAbsolutePath() + "-pred");
    boolean trainingDocumentUpdated = false;
    // A. training document for other train layers were changed
    for (AnnotationFeature feature : aTemplate.getOtherFeatures()) {
        for (TrainingDocument document : aAutomationService.listTrainingDocuments(aTemplate.getTrainFeature().getProject())) {
            if (!document.isProcessed() && document.getFeature() != null && document.getFeature().equals(feature)) {
                trainingDocumentUpdated = true;
                break;
            }
        }
    }
    // B. Training document for the main training layer were changed
    for (TrainingDocument document : aAutomationService.listTrainingDocuments(layerFeature.getProject())) {
        if (!document.isProcessed() && (document.getFeature() != null && document.getFeature().equals(layerFeature))) {
            trainingDocumentUpdated = true;
            break;
        }
    }
    // C. New Curation document arrives
    for (SourceDocument document : aRepository.listSourceDocuments(layerFeature.getProject())) {
        if (document.getState().equals(SourceDocumentState.CURATION_FINISHED)) {
            trainingDocumentUpdated = true;
            break;
        }
    }
    // D. tab-sep training documents
    for (TrainingDocument document : aAutomationService.listTabSepDocuments(aTemplate.getTrainFeature().getProject())) {
        if (!document.isProcessed() && document.getFeature() != null && document.getFeature().equals(layerFeature)) {
            trainingDocumentUpdated = true;
            break;
        }
    }
    if (!trainingDocumentUpdated) {
        return aTemplate.getResult();
    }
    // if no other layer is used, use this as main train document,
    // otherwise, add all the
    // predictions and modify template
    File baseTrainFile = new File(miraDir, layerFeature.getLayer().getId() + "-" + layerFeature.getId() + ".train.base");
    File trainFile = new File(miraDir, layerFeature.getLayer().getId() + "-" + layerFeature.getId() + ".train");
    // generate final classifier, using all features generated
    String trainName = trainFile.getAbsolutePath();
    String finalClassifierModelName = aAutomationService.getMiraModel(layerFeature, false, null).getAbsolutePath();
    getFeatureOtherLayer(aTemplate, aRepository, aAutomationService, aAnnotationService, aUserDao, beamSize, maxPosteriors, predictions, mira, predFile, predcitedFile, null);
    getFeaturesTabSep(aTemplate, aAutomationService, beamSize, maxPosteriors, layerFeature, predictions, mira, predFile, predcitedFile);
    generateTrainDocument(aTemplate, aRepository, aCurationDocumentService, aAnnotationService, aAutomationService, aUserDao, false);
    String trainTemplate;
    if (predictions.size() == 0) {
        trainTemplate = createTemplate(aTemplate.getTrainFeature(), getMiraTemplateFile(layerFeature, aAutomationService), 0);
        FileUtils.copyFile(baseTrainFile, trainFile);
    } else {
        trainTemplate = createTemplate(aTemplate.getTrainFeature(), getMiraTemplateFile(layerFeature, aAutomationService), predictions.size());
        buildTrainFile(baseTrainFile, trainFile, predictions);
    }
    boolean randomInit = false;
    if (!layerFeature.getLayer().isLockToTokenOffset()) {
        mira.setIobScorer();
    }
    mira.loadTemplates(trainTemplate);
    mira.setClip(sigma);
    mira.maxPosteriors = maxPosteriors;
    mira.beamSize = beamSize;
    int numExamples = mira.count(trainName, frequency);
    mira.initModel(randomInit);
    String trainResult = "";
    for (int i = 0; i < iterations; i++) {
        trainResult = mira.train(trainName, iterations, numExamples, i);
        mira.averageWeights(iterations * numExamples);
    }
    mira.saveModel(finalClassifierModelName);
    // all training documents are processed by now
    for (TrainingDocument document : aAutomationService.listTrainingDocuments(layerFeature.getProject())) {
        document.setProcessed(true);
    }
    for (TrainingDocument document : aAutomationService.listTabSepDocuments(layerFeature.getProject())) {
        document.setProcessed(true);
    }
    return trainResult;
}

Example 29 with AnnotationFeature

use of de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature in project webanno by webanno.

the class AutomationUtil method addOtherFeatureToPredictDocument.

/**
 * Based on the other layer, add features for the prediction document
 *
 * @param aTemplate
 *            the template.
 * @param aRepository
 *            the repository.
 * @throws UIMAException
 *             hum?
 * @throws ClassNotFoundException
 *             hum?
 * @throws IOException
 *             hum?
 * @throws AnnotationException
 *             hum?
 * @throws AutomationException
 *             hum?
 */
public static void addOtherFeatureToPredictDocument(MiraTemplate aTemplate, DocumentService aRepository, AnnotationSchemaService aAnnotationService, AutomationService aAutomationService, UserDao aUserDao) throws UIMAException, ClassNotFoundException, IOException, AnnotationException, AutomationException {
    AnnotationFeature layerFeature = aTemplate.getTrainFeature();
    File miraDir = aAutomationService.getMiraDir(layerFeature);
    for (SourceDocument document : aRepository.listSourceDocuments(layerFeature.getProject())) {
        List<List<String>> predictions = new ArrayList<>();
        File predFtFile = new File(miraDir, document.getId() + ".pred.ft");
        Mira mira = new Mira();
        int beamSize = 0;
        boolean maxPosteriors = false;
        File predcitedFile = new File(predFtFile.getAbsolutePath() + "-pred");
        getFeatureOtherLayer(aTemplate, aRepository, aAutomationService, aAnnotationService, aUserDao, beamSize, maxPosteriors, predictions, mira, predFtFile, predcitedFile, document);
        getFeaturesTabSep(aTemplate, aAutomationService, beamSize, maxPosteriors, layerFeature, predictions, mira, predFtFile, predcitedFile);
        File basePredFile = new File(miraDir, document.getId() + ".pred");
        if (predictions.size() == 0) {
            createTemplate(aTemplate.getTrainFeature(), getMiraTemplateFile(layerFeature, aAutomationService), 0);
            FileUtils.copyFile(predFtFile, basePredFile);
        } else {
            createTemplate(aTemplate.getTrainFeature(), getMiraTemplateFile(layerFeature, aAutomationService), predictions.size());
            buildPredictFile(predFtFile, basePredFile, predictions, aTemplate.getTrainFeature());
        }
    }
}

Example 30 with AnnotationFeature

use of de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature in project webanno by webanno.

the class AutomationUtil method generatePredictDocument.

// TODO: rename to predictDocument
public static void generatePredictDocument(MiraTemplate aTemplate, DocumentService aRepository, CorrectionDocumentService aCorrectionDocumentService, AnnotationSchemaService aAnnotationService, AutomationService aAutomationService, UserDao aUserDao) throws IOException, UIMAException, ClassNotFoundException {
    File miraDir = aAutomationService.getMiraDir(aTemplate.getTrainFeature());
    if (!miraDir.exists()) {
        FileUtils.forceMkdir(miraDir);
    }
    User user = aUserDao.getCurrentUser();
    AnnotationFeature feature = aTemplate.getTrainFeature();
    AutomationTypeAdapter adapter = (AutomationTypeAdapter) aAnnotationService.getAdapter(feature.getLayer());
    for (SourceDocument document : aRepository.listSourceDocuments(feature.getProject())) {
        File predFile = new File(miraDir, document.getId() + ".pred.ft");
        BufferedWriter predOut = new BufferedWriter(new FileWriter(predFile));
        JCas jCas;
        try {
            jCas = aCorrectionDocumentService.readCorrectionCas(document);
        } catch (Exception e) {
            AnnotationDocument annoDoc = aRepository.createOrGetAnnotationDocument(document, user);
            jCas = aRepository.readAnnotationCas(annoDoc);
        }
        for (Sentence sentence : select(jCas, Sentence.class)) {
            predOut.append(getMiraLine(sentence, null, adapter).toString()).append("\n");
        }
        predOut.close();
    }
}