Examples with AbortException de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException used on opensource projects

Example 16 with AbortException

use of de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException in project elki by elki-project.

the class CheckParameterizables method checkParameterizables.

/**
 * Validate all "Parameterizable" objects for parts of the API contract that
 * cannot be specified in Java interfaces (such as constructors, static
 * methods)
 */
public void checkParameterizables() {
    LoggingConfiguration.setVerbose(Level.VERBOSE);
    knownParameterizables = new ArrayList<>();
    try {
        Enumeration<URL> us = getClass().getClassLoader().getResources(ELKIServiceLoader.RESOURCE_PREFIX);
        while (us.hasMoreElements()) {
            URL u = us.nextElement();
            if ("file".equals(u.getProtocol())) {
                for (String prop : new File(u.toURI()).list()) {
                    try {
                        knownParameterizables.add(Class.forName(prop));
                    } catch (ClassNotFoundException e) {
                        LOG.warning("Service file name is not a class name: " + prop);
                        continue;
                    }
                }
            } else if (("jar".equals(u.getProtocol()))) {
                JarURLConnection con = (JarURLConnection) u.openConnection();
                try (JarFile jar = con.getJarFile()) {
                    Enumeration<JarEntry> entries = jar.entries();
                    while (entries.hasMoreElements()) {
                        String prop = entries.nextElement().getName();
                        if (prop.startsWith(ELKIServiceLoader.RESOURCE_PREFIX)) {
                            prop = prop.substring(ELKIServiceLoader.RESOURCE_PREFIX.length());
                        } else if (prop.startsWith(ELKIServiceLoader.FILENAME_PREFIX)) {
                            prop = prop.substring(ELKIServiceLoader.FILENAME_PREFIX.length());
                        } else {
                            continue;
                        }
                        try {
                            knownParameterizables.add(Class.forName(prop));
                        } catch (ClassNotFoundException e) {
                            LOG.warning("Service file name is not a class name: " + prop);
                            continue;
                        }
                    }
                }
            }
        }
    } catch (IOException | URISyntaxException e) {
        throw new AbortException("Error enumerating service folders.", e);
    }
    final String internal = de.lmu.ifi.dbs.elki.utilities.optionhandling.Parameterizer.class.getPackage().getName();
    for (final Class<?> cls : ELKIServiceRegistry.findAllImplementations(Object.class, false, false)) {
        // Classes in the same package are special and don't cause warnings.
        if (cls.getName().startsWith(internal)) {
            continue;
        }
        try {
            State state = State.NO_CONSTRUCTOR;
            state = checkV3Parameterization(cls, state);
            if (state == State.ERROR) {
                continue;
            }
            state = checkDefaultConstructor(cls, state);
            if (state == State.ERROR) {
                continue;
            }
            boolean expectedParameterizer = checkSupertypes(cls);
            if (state == State.NO_CONSTRUCTOR && expectedParameterizer) {
                LOG.verbose(// 
                "Class " + cls.getName() + " implements a parameterizable interface, but doesn't have a public and parameterless constructor!");
            }
            if (state == State.INSTANTIABLE && !expectedParameterizer) {
                LOG.verbose(// 
                "Class " + cls.getName() + " has a parameterizer, but there is no service file for any of its interfaces.");
            }
        } catch (NoClassDefFoundError e) {
            LOG.verbose("Class discovered but not found: " + cls.getName() + " (missing: " + e.getMessage() + ")");
        }
    }
}

Example 17 with AbortException

use of de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException in project elki by elki-project.

the class PrecomputedDistanceMatrix method initialize.

@Override
public void initialize() {
    size = ids.size();
    if (size > 65536) {
        throw new AbortException("Distance matrixes currently have a limit of 65536 objects (~16 GB). After this, the array size exceeds the Java integer range, and a different data structure needs to be used.");
    }
    distanceQuery = distanceFunction.instantiate(relation);
    final int msize = triangleSize(size);
    matrix = new double[msize];
    DBIDArrayIter ix = ids.iter(), iy = ids.iter();
    FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Precomputing distance matrix", msize, LOG) : null;
    int pos = 0;
    for (ix.seek(0); ix.valid(); ix.advance()) {
        // y < x -- must match {@link #getOffset}!
        for (iy.seek(0); iy.getOffset() < ix.getOffset(); iy.advance()) {
            matrix[pos] = distanceQuery.distance(ix, iy);
            pos++;
        }
        if (prog != null) {
            prog.setProcessed(prog.getProcessed() + ix.getOffset(), LOG);
        }
    }
    LOG.ensureCompleted(prog);
}

Example 18 with AbortException

use of de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException in project elki by elki-project.

the class FlexibleLOF method doRunInTime.

/**
 * Performs the Generalized LOF_SCORE algorithm on the given database and
 * returns a {@link FlexibleLOF.LOFResult} encapsulating information that may
 * be needed by an OnlineLOF algorithm.
 *
 * @param ids Object ids
 * @param kNNRefer the kNN query w.r.t. reference neighborhood distance
 *        function
 * @param kNNReach the kNN query w.r.t. reachability distance function
 * @param stepprog Progress logger
 * @return LOF result
 */
protected LOFResult<O> doRunInTime(DBIDs ids, KNNQuery<O> kNNRefer, KNNQuery<O> kNNReach, StepProgress stepprog) {
    // Assert we got something
    if (kNNRefer == null) {
        throw new AbortException("No kNN queries supported by database for reference neighborhood distance function.");
    }
    if (kNNReach == null) {
        throw new AbortException("No kNN queries supported by database for reachability distance function.");
    }
    // Compute LRDs
    LOG.beginStep(stepprog, 2, "Computing LRDs.");
    WritableDoubleDataStore lrds = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP);
    computeLRDs(kNNReach, ids, lrds);
    // compute LOF_SCORE of each db object
    LOG.beginStep(stepprog, 3, "Computing LOFs.");
    WritableDoubleDataStore lofs = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_STATIC);
    // track the maximum value for normalization.
    DoubleMinMax lofminmax = new DoubleMinMax();
    computeLOFs(kNNRefer, ids, lrds, lofs, lofminmax);
    LOG.setCompleted(stepprog);
    // Build result representation.
    DoubleRelation scoreResult = new MaterializedDoubleRelation("Local Outlier Factor", "lof-outlier", lofs, ids);
    OutlierScoreMeta scoreMeta = new QuotientOutlierScoreMeta(lofminmax.getMin(), lofminmax.getMax(), 0.0, Double.POSITIVE_INFINITY, 1.0);
    OutlierResult result = new OutlierResult(scoreMeta, scoreResult);
    return new LOFResult<>(result, kNNRefer, kNNReach, lrds, lofs);
}

Example 19 with AbortException

use of de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException in project elki by elki-project.

the class ExternalDoubleOutlierScore method run.

/**
 * Run the algorithm.
 *
 * @param database Database to use
 * @param relation Relation to use
 * @return Result
 */
public OutlierResult run(Database database, Relation<?> relation) {
    WritableDoubleDataStore scores = DataStoreUtil.makeDoubleStorage(relation.getDBIDs(), DataStoreFactory.HINT_STATIC);
    DoubleMinMax minmax = new DoubleMinMax();
    try (// 
    InputStream in = FileUtil.tryGzipInput(new FileInputStream(file));
        TokenizedReader reader = CSVReaderFormat.DEFAULT_FORMAT.makeReader()) {
        Tokenizer tokenizer = reader.getTokenizer();
        CharSequence buf = reader.getBuffer();
        Matcher mi = idpattern.matcher(buf), ms = scorepattern.matcher(buf);
        reader.reset(in);
        while (reader.nextLineExceptComments()) {
            Integer id = null;
            double score = Double.NaN;
            for (; /* initialized by nextLineExceptComments */
            tokenizer.valid(); tokenizer.advance()) {
                mi.region(tokenizer.getStart(), tokenizer.getEnd());
                ms.region(tokenizer.getStart(), tokenizer.getEnd());
                final boolean mif = mi.find();
                final boolean msf = ms.find();
                if (mif && msf) {
                    throw new AbortException("ID pattern and score pattern both match value: " + tokenizer.getSubstring());
                }
                if (mif) {
                    if (id != null) {
                        throw new AbortException("ID pattern matched twice: previous value " + id + " second value: " + tokenizer.getSubstring());
                    }
                    id = ParseUtil.parseIntBase10(buf, mi.end(), tokenizer.getEnd());
                }
                if (msf) {
                    if (!Double.isNaN(score)) {
                        throw new AbortException("Score pattern matched twice: previous value " + score + " second value: " + tokenizer.getSubstring());
                    }
                    score = ParseUtil.parseDouble(buf, ms.end(), tokenizer.getEnd());
                }
            }
            if (id != null && !Double.isNaN(score)) {
                scores.putDouble(DBIDUtil.importInteger(id), score);
                minmax.put(score);
            } else if (id == null && Double.isNaN(score)) {
                LOG.warning("Line did not match either ID nor score nor comment: " + reader.getLineNumber());
            } else {
                throw new AbortException("Line matched only ID or only SCORE patterns: " + reader.getLineNumber());
            }
        }
    } catch (IOException e) {
        throw new AbortException("Could not load outlier scores: " + e.getMessage() + " when loading " + file, e);
    }
    OutlierScoreMeta meta;
    if (inverted) {
        meta = new InvertedOutlierScoreMeta(minmax.getMin(), minmax.getMax());
    } else {
        meta = new BasicOutlierScoreMeta(minmax.getMin(), minmax.getMax());
    }
    DoubleRelation scoresult = new MaterializedDoubleRelation("External Outlier", "external-outlier", scores, relation.getDBIDs());
    OutlierResult or = new OutlierResult(meta, scoresult);
    // Apply scaling
    if (scaling instanceof OutlierScalingFunction) {
        ((OutlierScalingFunction) scaling).prepare(or);
    }
    DoubleMinMax mm = new DoubleMinMax();
    for (DBIDIter iditer = relation.iterDBIDs(); iditer.valid(); iditer.advance()) {
        double val = scoresult.doubleValue(iditer);
        val = scaling.getScaled(val);
        scores.putDouble(iditer, val);
        mm.put(val);
    }
    meta = new BasicOutlierScoreMeta(mm.getMin(), mm.getMax());
    or = new OutlierResult(meta, scoresult);
    return or;
}

Example 20 with AbortException

use of de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException in project elki by elki-project.

the class ReferenceBasedOutlierDetection method run.

/**
 * Run the algorithm on the given relation.
 *
 * @param database Database
 * @param relation Relation to process
 * @return Outlier result
 */
public OutlierResult run(Database database, Relation<? extends NumberVector> relation) {
    @SuppressWarnings("unchecked") PrimitiveDistanceQuery<? super NumberVector> distq = (PrimitiveDistanceQuery<? super NumberVector>) database.getDistanceQuery(relation, distanceFunction);
    Collection<? extends NumberVector> refPoints = refp.getReferencePoints(relation);
    if (refPoints.isEmpty()) {
        throw new AbortException("Cannot compute ROS without reference points!");
    }
    DBIDs ids = relation.getDBIDs();
    if (k >= ids.size()) {
        throw new AbortException("k must not be chosen larger than the database size!");
    }
    // storage of distance/score values.
    WritableDoubleDataStore rbod_score = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_STATIC | DataStoreFactory.HINT_HOT, Double.NaN);
    // Compute density estimation:
    for (NumberVector refPoint : refPoints) {
        DoubleDBIDList referenceDists = computeDistanceVector(refPoint, relation, distq);
        updateDensities(rbod_score, referenceDists);
    }
    // compute maximum density
    DoubleMinMax mm = new DoubleMinMax();
    for (DBIDIter iditer = relation.iterDBIDs(); iditer.valid(); iditer.advance()) {
        mm.put(rbod_score.doubleValue(iditer));
    }
    // compute ROS
    double scale = mm.getMax() > 0. ? 1. / mm.getMax() : 1.;
    // Reuse
    mm.reset();
    for (DBIDIter iditer = relation.iterDBIDs(); iditer.valid(); iditer.advance()) {
        double score = 1 - (rbod_score.doubleValue(iditer) * scale);
        mm.put(score);
        rbod_score.putDouble(iditer, score);
    }
    DoubleRelation scoreResult = new MaterializedDoubleRelation("Reference-points Outlier Scores", "reference-outlier", rbod_score, relation.getDBIDs());
    OutlierScoreMeta scoreMeta = new BasicOutlierScoreMeta(mm.getMin(), mm.getMax(), 0., 1., 0.);
    OutlierResult result = new OutlierResult(scoreMeta, scoreResult);
    // adds reference points to the result. header information for the
    // visualizer to find the reference points in the result
    result.addChildResult(new ReferencePointsResult<>("Reference points", "reference-points", refPoints));
    return result;
}