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

Example 61 with AbortException

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

the class LuceneDistanceRangeQuery method getRangeForObject.

@Override
public void getRangeForObject(DBID obj, double range, ModifiableDoubleDBIDList neighbors) {
    try {
        Query query = mlt.like(ids.getOffset(obj));
        is.search(query, new DocumentsCollector(ids, neighbors, range));
    } catch (IOException e) {
        throw new AbortException("I/O error in lucene.", e);
    }
}

Example 62 with AbortException

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

the class LuceneDistanceKNNQuery method getKNNForDBID.

@Override
public KNNList getKNNForDBID(DBIDRef id, int k) {
    try {
        Query query = mlt.like(range.getOffset(id));
        TopDocs topDocs = is.search(query, k);
        int rk = topDocs.scoreDocs.length;
        DoubleIntegerDBIDKNNList res = new DoubleIntegerDBIDKNNList(k, rk);
        DBIDArrayIter it = range.iter();
        for (ScoreDoc scoreDoc : topDocs.scoreDocs) {
            double dist = (scoreDoc.score > 0.) ? (1. / scoreDoc.score) : Double.POSITIVE_INFINITY;
            it.seek(scoreDoc.doc);
            res.add(dist, it);
        }
        return res;
    } catch (IOException e) {
        throw new AbortException("I/O error in lucene.", e);
    }
}

Example 63 with AbortException

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

the class AbstractXTree method initializeFromFile.

/**
 * To be called via the constructor if the tree is to be read from file.
 */
@Override
public void initializeFromFile(TreeIndexHeader hdr, PageFile<N> file) {
    XTreeHeader header = (XTreeHeader) hdr;
    super.dirCapacity = header.getDirCapacity();
    super.leafCapacity = header.getLeafCapacity();
    super.dirMinimum = header.getDirMinimum();
    super.leafMinimum = header.getLeafMinimum();
    settings.min_fanout = header.getMin_fanout();
    this.num_elements = header.getNumberOfElements();
    this.dimensionality = header.getDimensionality();
    settings.max_overlap = header.getMaxOverlap();
    long superNodeOffset = header.getSupernode_offset();
    if (getLogger().isDebugging()) {
        getLogger().debugFine(new StringBuilder(200).append(getClass()).append("\n file = ").append(file.getClass()).toString());
    }
    // reset page id maintenance
    file.setNextPageID((int) (superNodeOffset / header.getPageSize()));
    // read supernodes (if there are any)
    if (superNodeOffset > 0) {
        RandomAccessFile ra_file = ((PersistentPageFile<?>) file).getFile();
        long offset = header.getReservedPages() * file.getPageSize() + superNodeOffset;
        int bs = // omit this: 4 // EMPTY_PAGE or FILLED_PAGE ?
        0 + // id
        4 + // isLeaf
        1 + // isSupernode
        1 + // number of entries
        4 + // capacity
        4;
        byte[] buffer = new byte[bs];
        try {
            // go to supernode region
            ra_file.seek(offset);
            while (ra_file.getFilePointer() + file.getPageSize() <= ra_file.length()) {
                // file.countRead();
                ra_file.read(buffer);
                ObjectInputStream ois = new ObjectInputStream(new ByteArrayInputStream(buffer));
                int id = ois.readInt();
                // iLeaf
                ois.readBoolean();
                boolean supernode = ois.readBoolean();
                if (!supernode) {
                    throw new IllegalStateException("Non-supernode at supernode position '" + superNodeOffset + "'");
                }
                int numEntries = ois.readInt();
                int capacity = ois.readInt();
                ois.close();
                N page;
                try {
                    page = getNodeClass().newInstance();
                } catch (IllegalAccessException e) {
                    throw new AbortException("AccessException instantiating a supernode", e);
                } catch (InstantiationException e) {
                    throw new AbortException("InstantiationException instantiating a supernode", e);
                }
                // file.countRead();
                ra_file.seek(offset);
                byte[] superbuffer = new byte[file.getPageSize() * (int) Math.ceil((double) capacity / dirCapacity)];
                // increase offset for the next position seek
                offset += superbuffer.length;
                ra_file.read(superbuffer);
                ois = new ObjectInputStream(new ByteArrayInputStream(buffer));
                try {
                    // read from file and add to supernode map
                    page.readSuperNode(ois, this);
                } catch (ClassNotFoundException e) {
                    throw new AbortException("ClassNotFoundException when loading a supernode", e);
                }
                assert numEntries == page.getNumEntries();
                assert capacity == page.getCapacity();
                assert id == page.getPageID();
            }
        } catch (IOException e) {
            throw new RuntimeException("IOException caught when loading tree from file." + e);
        }
    }
    super.initialized = true;
    // compute height
    super.height = computeHeight();
    if (getLogger().isDebugging()) {
        getLogger().debugFine(new StringBuilder(100).append(getClass()).append("\n height = ").append(height).toString());
    }
}

Example 64 with AbortException

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

the class LibSVMOneClassOutlierDetection method run.

/**
 * Run one-class SVM.
 *
 * @param relation Data relation
 * @return Outlier result.
 */
public OutlierResult run(Relation<V> relation) {
    final int dim = RelationUtil.dimensionality(relation);
    final ArrayDBIDs ids = DBIDUtil.ensureArray(relation.getDBIDs());
    svm.svm_set_print_string_function(LOG_HELPER);
    svm_parameter param = new svm_parameter();
    param.svm_type = svm_parameter.ONE_CLASS;
    param.kernel_type = svm_parameter.LINEAR;
    param.degree = 3;
    switch(kernel) {
        case LINEAR:
            param.kernel_type = svm_parameter.LINEAR;
            break;
        case QUADRATIC:
            param.kernel_type = svm_parameter.POLY;
            param.degree = 2;
            break;
        case CUBIC:
            param.kernel_type = svm_parameter.POLY;
            param.degree = 3;
            break;
        case RBF:
            param.kernel_type = svm_parameter.RBF;
            break;
        case SIGMOID:
            param.kernel_type = svm_parameter.SIGMOID;
            break;
        default:
            throw new AbortException("Invalid kernel parameter: " + kernel);
    }
    // TODO: expose additional parameters to the end user!
    param.nu = nu;
    param.coef0 = 0.;
    param.cache_size = 10000;
    param.C = 1;
    // not used by one-class?
    param.eps = 1e-4;
    // not used by one-class?
    param.p = 0.1;
    param.shrinking = 0;
    param.probability = 0;
    param.nr_weight = 0;
    param.weight_label = new int[0];
    param.weight = new double[0];
    param.gamma = 1. / dim;
    // Transform data:
    svm_problem prob = new svm_problem();
    prob.l = relation.size();
    prob.x = new svm_node[prob.l][];
    prob.y = new double[prob.l];
    {
        DBIDIter iter = ids.iter();
        for (int i = 0; i < prob.l && iter.valid(); iter.advance(), i++) {
            V vec = relation.get(iter);
            // TODO: support compact sparse vectors, too!
            svm_node[] x = new svm_node[dim];
            for (int d = 0; d < dim; d++) {
                x[d] = new svm_node();
                x[d].index = d + 1;
                x[d].value = vec.doubleValue(d);
            }
            prob.x[i] = x;
            prob.y[i] = +1;
        }
    }
    if (LOG.isVerbose()) {
        LOG.verbose("Training one-class SVM...");
    }
    String err = svm.svm_check_parameter(prob, param);
    if (err != null) {
        LOG.warning("svm_check_parameter: " + err);
    }
    svm_model model = svm.svm_train(prob, param);
    if (LOG.isVerbose()) {
        LOG.verbose("Predicting...");
    }
    WritableDoubleDataStore scores = DataStoreUtil.makeDoubleStorage(relation.getDBIDs(), DataStoreFactory.HINT_DB);
    DoubleMinMax mm = new DoubleMinMax();
    {
        DBIDIter iter = ids.iter();
        double[] buf = new double[svm.svm_get_nr_class(model)];
        for (int i = 0; i < prob.l && iter.valid(); iter.advance(), i++) {
            V vec = relation.get(iter);
            svm_node[] x = new svm_node[dim];
            for (int d = 0; d < dim; d++) {
                x[d] = new svm_node();
                x[d].index = d + 1;
                x[d].value = vec.doubleValue(d);
            }
            svm.svm_predict_values(model, x, buf);
            // / param.gamma; // Heuristic rescaling, sorry.
            double score = -buf[0];
            // Unfortunately, libsvm one-class currently yields a binary decision.
            scores.putDouble(iter, score);
            mm.put(score);
        }
    }
    DoubleRelation scoreResult = new MaterializedDoubleRelation("One-Class SVM Decision", "svm-outlier", scores, ids);
    OutlierScoreMeta scoreMeta = new BasicOutlierScoreMeta(mm.getMin(), mm.getMax(), Double.NEGATIVE_INFINITY, Double.POSITIVE_INFINITY, 0.);
    return new OutlierResult(scoreMeta, scoreResult);
}

Example 65 with AbortException

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

the class LuceneDatabase method initialize.

@Override
public void initialize() {
    try {
        reader = IndexReader.open(directory);
        ids = DBIDUtil.generateStaticDBIDRange(reader.maxDoc());
        // ID relation:
        idrep = new DBIDView(ids);
        relations.add(idrep);
        getHierarchy().add(this, idrep);
        // Documents relation:
        docrep = new LuceneDocumentRelation(ids, reader);
        relations.add(docrep);
        getHierarchy().add(this, docrep);
        eventManager.fireObjectsInserted(ids);
    } catch (CorruptIndexException e) {
        throw new AbortException("Index is corrupt.", e);
    } catch (IOException e) {
        throw new AbortException("I/O error reading index.", e);
    }
}