Examples with ResourceInstantiationException gate.creole.ResourceInstantiationException used on opensource projects

Example 6 with ResourceInstantiationException

use of gate.creole.ResourceInstantiationException in project gate-core by GateNLP.

the class CorpusBenchmarkTool method evaluateAllThree.

protected void evaluateAllThree(Document persDoc, Document cleanDoc, Document markedDoc, File errDir) throws ResourceInstantiationException {
    // first start the table and its header
    printTableHeader();
    // store annotation diff in .err file
    Writer errWriter = null;
    if (isMoreInfoMode && errDir != null) {
        StringBuffer docName = new StringBuffer(cleanDoc.getName());
        docName.replace(cleanDoc.getName().lastIndexOf("."), docName.length(), ".err");
        File errFile = new File(errDir, docName.toString());
        // String encoding = ( (gate.corpora.DocumentImpl) cleanDoc).getEncoding();
        try {
            errWriter = new FileWriter(errFile, false);
        /*
                 if(encoding == null) {
          errWriter = new OutputStreamWriter(
              new FileOutputStream(errFile, false));
                 } else {
          errWriter = new OutputStreamWriter(
              new FileOutputStream(errFile, false), encoding);
                 }*/
        } catch (Exception ex) {
            Out.prln("Exception when creating the error file " + errFile + ": " + ex.getMessage());
            errWriter = null;
        }
    }
    for (int jj = 0; jj < annotTypes.size(); jj++) {
        String annotType = annotTypes.get(jj);
        AnnotationDiffer annotDiffer = measureDocs(markedDoc, cleanDoc, annotType);
        // we don't have this annotation type in this document
        if (annotDiffer == null)
            continue;
        // increase the number of processed documents
        docNumber++;
        // add precison and recall to the sums
        updateStatistics(annotDiffer, annotType);
        AnnotationDiffer annotDiffer1 = measureDocs(markedDoc, persDoc, annotType);
        Out.prln("<TR>");
        if (isMoreInfoMode && annotDiffer1 != null && (annotDiffer1.getPrecisionAverage() != annotDiffer.getPrecisionAverage() || annotDiffer1.getRecallAverage() != annotDiffer.getRecallAverage()))
            Out.prln("<TD> " + annotType + "_new" + "</TD>");
        else
            Out.prln("<TD> " + annotType + "</TD>");
        if (isMoreInfoMode) {
            if (annotDiffer1 != null)
                updateStatisticsProc(annotDiffer1, annotType);
            Out.prln("<TD>" + annotDiffer.getCorrectMatches() + "</TD>");
            Out.prln("<TD>" + annotDiffer.getPartiallyCorrectMatches() + "</TD>");
            Out.prln("<TD>" + annotDiffer.getMissing() + "</TD>");
            Out.prln("<TD>" + annotDiffer.getSpurious() + "</TD>");
        }
        Out.prln("<TD>");
        // check the precision first
        if (annotDiffer1 != null) {
            if (annotDiffer1.getPrecisionAverage() < annotDiffer.getPrecisionAverage()) {
                Out.prln("<P><Font color=blue> ");
                Out.prln(annotDiffer.getPrecisionAverage());
                if (!isMoreInfoMode) {
                    Out.pr("<BR>Precision increase on human-marked from ");
                    Out.pr(annotDiffer1.getPrecisionAverage() + " to ");
                    Out.prln(annotDiffer.getPrecisionAverage());
                }
                Out.prln(" </Font></P>");
            } else if (annotDiffer1.getPrecisionAverage() > annotDiffer.getPrecisionAverage()) {
                Out.prln("<P><Font color=red> ");
                Out.prln(annotDiffer.getPrecisionAverage());
                if (!isMoreInfoMode) {
                    Out.pr("<BR>Precision decrease on human-marked from ");
                    Out.pr(annotDiffer1.getPrecisionAverage() + " to ");
                    Out.prln(annotDiffer.getPrecisionAverage());
                }
                Out.prln(" </Font></P>");
            } else
                Out.prln("<P> " + annotDiffer.getPrecisionAverage() + " </P>");
        } else
            Out.prln("<P> " + annotDiffer.getPrecisionAverage() + " </P>");
        Out.prln("</TD>");
        Out.prln("<TD>");
        // check the recall now
        if (annotDiffer1 != null) {
            if (annotDiffer1.getRecallAverage() < annotDiffer.getRecallAverage()) {
                Out.prln("<P><Font color=blue> ");
                Out.prln(annotDiffer.getRecallAverage());
                if (!isMoreInfoMode) {
                    Out.pr("<BR>Recall increase on human-marked from ");
                    Out.pr(annotDiffer1.getRecallAverage() + " to ");
                    Out.prln(annotDiffer.getRecallAverage());
                }
                Out.prln(" </Font></P>");
            } else if (annotDiffer1.getRecallAverage() > annotDiffer.getRecallAverage()) {
                Out.prln("<P><Font color=red> ");
                Out.prln(annotDiffer.getRecallAverage());
                if (!isMoreInfoMode) {
                    Out.pr("<BR>Recall decrease on human-marked from ");
                    Out.pr(annotDiffer1.getRecallAverage() + " to ");
                    Out.prln(annotDiffer.getRecallAverage());
                }
                Out.prln(" </Font></P>");
            } else
                Out.prln("<P> " + annotDiffer.getRecallAverage() + " </P>");
        } else
            Out.prln("<P> " + annotDiffer.getRecallAverage() + " </P>");
        Out.prln("</TD>");
        // check the recall now
        if (isVerboseMode) {
            Out.prln("<TD>");
            if (annotDiffer.getRecallAverage() < threshold || annotDiffer.getPrecisionAverage() < threshold) {
                printAnnotations(annotDiffer, markedDoc, cleanDoc);
            } else {
                Out.prln("&nbsp;");
            }
            Out.prln("</TD>");
        }
        Out.prln("</TR>");
        // show one more table line for processed document
        if (isMoreInfoMode && annotDiffer1 != null && (annotDiffer1.getPrecisionAverage() != annotDiffer.getPrecisionAverage() || annotDiffer1.getRecallAverage() != annotDiffer.getRecallAverage())) {
            Out.prln("<TR>");
            Out.prln("<TD> " + annotType + "_old" + "</TD>");
            Out.prln("<TD>" + annotDiffer1.getCorrectMatches() + "</TD>");
            Out.prln("<TD>" + annotDiffer1.getPartiallyCorrectMatches() + "</TD>");
            Out.prln("<TD>" + annotDiffer1.getMissing() + "</TD>");
            Out.prln("<TD>" + annotDiffer1.getSpurious() + "</TD>");
            Out.prln("<TD>");
            if (annotDiffer1.getPrecisionAverage() < annotDiffer.getPrecisionAverage())
                Out.prln("<P><Font color=blue> " + annotDiffer1.getPrecisionAverage() + "</Font></P>");
            else if (annotDiffer1.getPrecisionAverage() > annotDiffer.getPrecisionAverage())
                Out.prln("<P><Font color=red> " + annotDiffer1.getPrecisionAverage() + " </Font></P>");
            else
                Out.prln(annotDiffer1.getPrecisionAverage());
            Out.prln("</TD>");
            Out.prln("<TD>");
            if (annotDiffer1.getRecallAverage() < annotDiffer.getRecallAverage())
                Out.prln("<P><Font color=blue> " + annotDiffer1.getRecallAverage() + " </Font></P>");
            else if (annotDiffer1.getRecallAverage() > annotDiffer.getRecallAverage())
                Out.prln("<P><Font color=red> " + annotDiffer1.getRecallAverage() + " </Font></P>");
            else
                Out.prln(annotDiffer1.getRecallAverage());
            Out.prln("</TD>");
            // check the recall now
            if (isVerboseMode) {
                // create error file and start writing
                Out.prln("<TD>");
                if (annotDiffer.getRecallAverage() < threshold || annotDiffer.getPrecisionAverage() < threshold) {
                    printAnnotations(annotDiffer, markedDoc, cleanDoc);
                } else {
                    Out.prln("&nbsp;");
                }
                Out.prln("</TD>");
            }
            Out.prln("</TR>");
        }
        if (isMoreInfoMode && errDir != null)
            storeAnnotations(annotType, annotDiffer, markedDoc, cleanDoc, errWriter);
    }
    // for loop through annotation types
    Out.prln("</TABLE>");
    try {
        if (errWriter != null)
            errWriter.close();
    } catch (Exception ex) {
        Out.prln("Exception on close of error file " + errWriter + ": " + ex.getMessage());
    }
}

Example 7 with ResourceInstantiationException

use of gate.creole.ResourceInstantiationException in project gate-core by GateNLP.

the class ResourcePersistence method extractDataFromSource.

@Override
public void extractDataFromSource(Object source) throws PersistenceException {
    if (!(source instanceof Resource)) {
        throw new UnsupportedOperationException(getClass().getName() + " can only be used for " + Resource.class.getName() + " objects!\n" + source.getClass().getName() + " is not a " + Resource.class.getName());
    }
    Resource res = (Resource) source;
    resourceType = res.getClass().getName();
    resourceName = ((NameBearer) res).getName();
    ResourceData rData = Gate.getCreoleRegister().get(resourceType);
    if (rData == null)
        throw new PersistenceException("Could not find CREOLE data for " + resourceType);
    ParameterList params = rData.getParameterList();
    try {
        // get the values for the init time parameters
        initParams = Factory.newFeatureMap();
        // this is a list of lists
        Iterator<List<Parameter>> parDisjIter = params.getInitimeParameters().iterator();
        while (parDisjIter.hasNext()) {
            Iterator<Parameter> parIter = parDisjIter.next().iterator();
            while (parIter.hasNext()) {
                Parameter parameter = parIter.next();
                String parName = parameter.getName();
                Object parValue = res.getParameterValue(parName);
                if (storeParameterValue(parValue, parameter.getDefaultValue())) {
                    ((FeatureMap) initParams).put(parName, parValue);
                }
            }
        }
        initParams = PersistenceManager.getPersistentRepresentation(initParams);
        // get the features
        if (res.getFeatures() != null) {
            features = Factory.newFeatureMap();
            ((FeatureMap) features).putAll(res.getFeatures());
            features = PersistenceManager.getPersistentRepresentation(features);
        }
    } catch (ResourceInstantiationException | ParameterException rie) {
        throw new PersistenceException(rie);
    }
}

Example 8 with ResourceInstantiationException

use of gate.creole.ResourceInstantiationException in project gate-core by GateNLP.

the class CorpusAnnotationDiff method setParameterValue.

/**
 * Sets the value for a specified parameter.
 *
 * @param paramaterName the name for the parameteer
 * @param parameterValue the value the parameter will receive
 */
@Override
public void setParameterValue(String paramaterName, Object parameterValue) throws ResourceInstantiationException {
    // get the beaninfo for the resource bean, excluding data about Object
    BeanInfo resBeanInf = null;
    try {
        resBeanInf = Introspector.getBeanInfo(this.getClass(), Object.class);
    } catch (Exception e) {
        throw new ResourceInstantiationException("Couldn't get bean info for resource " + this.getClass().getName() + Strings.getNl() + "Introspector exception was: " + e);
    }
    AbstractResource.setParameterValue(this, resBeanInf, paramaterName, parameterValue);
}

Example 9 with ResourceInstantiationException

use of gate.creole.ResourceInstantiationException in project gate-core by GateNLP.

the class CorpusAnnotationDiff method init.

/**
 * This method does the diff, Precision,Recall,FalsePositive
 * calculation and so on.
 */
@Override
public Resource init() throws ResourceInstantiationException {
    colors[DEFAULT_TYPE] = WHITE;
    colors[CORRECT_TYPE] = GREEN;
    colors[SPURIOUS_TYPE] = RED;
    colors[PARTIALLY_CORRECT_TYPE] = BLUE;
    colors[MISSING_TYPE] = YELLOW;
    // Initialize the partially sets...
    keyPartiallySet = new HashSet<Annotation>();
    responsePartiallySet = new HashSet<Annotation>();
    // Do the diff, P&R calculation and so on
    AnnotationSet keyAnnotSet = null;
    AnnotationSet responseAnnotSet = null;
    if (annotationSchema == null)
        throw new ResourceInstantiationException("No annotation schema defined !");
    if (keyCorpus == null || 0 == keyCorpus.size())
        throw new ResourceInstantiationException("No key corpus or empty defined !");
    if (responseCorpus == null || 0 == responseCorpus.size())
        throw new ResourceInstantiationException("No response corpus or empty defined !");
    // init counters and do difference for documents by pairs
    for (int type = 0; type < MAX_TYPES; type++) typeCounter[type] = 0;
    diffSet = new HashSet<DiffSetElement>();
    for (int i = 0; i < keyCorpus.size(); ++i) {
        keyDocument = keyCorpus.get(i);
        // find corresponding responce document if any
        Document doc;
        responseDocument = null;
        for (int j = 0; j < responseCorpus.size(); ++j) {
            doc = responseCorpus.get(j);
            if (0 == doc.getName().compareTo(keyDocument.getName()) || 0 == doc.getSourceUrl().getFile().compareTo(keyDocument.getSourceUrl().getFile())) {
                responseDocument = doc;
                // response corpus loop
                break;
            }
        // if
        }
        if (null == responseDocument) {
            Out.prln("There is no mach in responce corpus for document '" + keyDocument.getName() + "' from key corpus");
            // key corpus loop
            continue;
        }
        if (keyAnnotationSetName == null) {
            // Get the default key AnnotationSet from the keyDocument
            keyAnnotSet = keyDocument.getAnnotations().get(annotationSchema.getAnnotationName());
        } else {
            keyAnnotSet = keyDocument.getAnnotations(keyAnnotationSetName).get(annotationSchema.getAnnotationName());
        }
        if (keyAnnotSet == null)
            // The diff will run with an empty set.All annotations from response
            // would be spurious.
            keyAnnotList = new LinkedList<Annotation>();
        else
            // The alghoritm will modify this annotation set. It is better to make a
            // separate copy of them.
            keyAnnotList = new LinkedList<Annotation>(keyAnnotSet);
        if (responseAnnotationSetName == null)
            // Get the response AnnotationSet from the default set
            responseAnnotSet = responseDocument.getAnnotations().get(annotationSchema.getAnnotationName());
        else
            responseAnnotSet = responseDocument.getAnnotations(responseAnnotationSetName).get(annotationSchema.getAnnotationName());
        if (responseAnnotSet == null)
            // The diff will run with an empty set.All annotations from key
            // would be missing.
            responseAnnotList = new LinkedList<Annotation>();
        else
            // The alghoritm will modify this annotation set. It is better to make a
            // separate copy of them.
            responseAnnotList = new LinkedList<Annotation>(responseAnnotSet);
        // Sort them ascending on Start offset (the comparator does that)
        AnnotationSetComparator asComparator = new AnnotationSetComparator();
        Collections.sort(keyAnnotList, asComparator);
        Collections.sort(responseAnnotList, asComparator);
        // Calculate the diff Set. This set will be used later with graphic
        // visualisation.
        doDiff(keyAnnotList, responseAnnotList);
    }
    // If it runs under text mode just stop here.
    if (textMode)
        return this;
    // Show it
    // Configuring the formatter object. It will be used later to format
    // precision and recall
    formatter.setMaximumIntegerDigits(1);
    formatter.setMinimumFractionDigits(4);
    formatter.setMinimumFractionDigits(4);
    // Create an Annotation diff table model
    AnnotationDiffTableModel diffModel = new AnnotationDiffTableModel(diffSet);
    // Create a XJTable based on this model
    diffTable = new XJTable(diffModel);
    diffTable.setAlignmentX(Component.LEFT_ALIGNMENT);
    // Set the cell renderer for this table.
    AnnotationDiffCellRenderer cellRenderer = new AnnotationDiffCellRenderer();
    diffTable.setDefaultRenderer(java.lang.String.class, cellRenderer);
    diffTable.setDefaultRenderer(java.lang.Long.class, cellRenderer);
    // Put the table into a JScroll
    // Arange all components on a this JPanel
    SwingUtilities.invokeLater(new Runnable() {

        @Override
        public void run() {
            arangeAllComponents();
        }
    });
    if (DEBUG)
        printStructure(diffSet);
    return this;
}

Example 10 with ResourceInstantiationException

use of gate.creole.ResourceInstantiationException in project gate-core by GateNLP.

the class CreoleProxy method defaultDuplicate.

/**
 * Implementation of the default duplication algorithm described in
 * the comment for {@link #duplicate(Resource)}. This method is public
 * for the benefit of resources that implement
 * {@link CustomDuplication} but only need to do some post-processing
 * after the default duplication algorithm; they can call this method
 * to obtain an initial duplicate and then post-process it before
 * returning. If they need to duplicate child resources they should
 * call {@link #duplicate(Resource, DuplicationContext)} in the normal
 * way. Calls to this method made outside the context of a
 * {@link CustomDuplication#duplicate CustomDuplication.duplicate}
 * call will fail with a runtime exception.
 *
 * @param res the resource to duplicate
 * @param ctx the current context
 * @return a duplicate of the given resource, constructed using the
 *         default algorithm. In particular, if <code>res</code>
 *         implements {@link CustomDuplication} its own duplicate
 *         method will <i>not</i> be called.
 * @throws ResourceInstantiationException if an error occurs while
 *           duplicating the given resource.
 */
public static Resource defaultDuplicate(Resource res, DuplicationContext ctx) throws ResourceInstantiationException {
    checkDuplicationContext(ctx);
    String className = res.getClass().getName();
    ResourceData resData = Gate.getCreoleRegister().get(className);
    if (resData == null) {
        throw new ResourceInstantiationException("Could not find CREOLE data for " + className);
    }
    String resName = res.getName();
    FeatureMap newResFeatures = duplicate(res.getFeatures(), ctx);
    // init parameters
    FeatureMap initParams = AbstractResource.getInitParameterValues(res);
    // remove parameters that are also sharable properties
    for (String propName : resData.getSharableProperties()) {
        initParams.remove(propName);
    }
    // duplicate any Resources in the params map (excluding sharable
    // ones)
    initParams = duplicate(initParams, ctx);
    // may be registered parameters but others may not be.
    for (String propName : resData.getSharableProperties()) {
        initParams.put(propName, res.getParameterValue(propName));
    }
    // create the new resource
    Resource newResource = createResource(className, initParams, newResFeatures, resName);
    if (newResource instanceof ProcessingResource) {
        // runtime params
        FeatureMap runtimeParams = AbstractProcessingResource.getRuntimeParameterValues(res);
        // remove parameters that are also sharable properties
        for (String propName : resData.getSharableProperties()) {
            runtimeParams.remove(propName);
        }
        // duplicate any Resources in the params map (excluding sharable
        // ones)
        runtimeParams = duplicate(runtimeParams, ctx);
        // do not need to add sharable properties here, they have already
        // been injected by createResource
        newResource.setParameterValues(runtimeParams);
    }
    return newResource;
}