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

Example 11 with AbortException

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

the class KMeansPlusPlusInitialMeans method chooseInitialMeans.

@Override
public <T extends NumberVector> double[][] chooseInitialMeans(Database database, Relation<T> relation, int k, NumberVectorDistanceFunction<? super T> distanceFunction) {
    DistanceQuery<T> distQ = database.getDistanceQuery(relation, distanceFunction);
    DBIDs ids = relation.getDBIDs();
    WritableDoubleDataStore weights = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP, 0.);
    // Chose first mean
    List<NumberVector> means = new ArrayList<>(k);
    if (ids.size() <= k) {
        throw new AbortException("Don't use k-means with k >= data set size.");
    }
    Random random = rnd.getSingleThreadedRandom();
    DBIDRef first = DBIDUtil.randomSample(ids, random);
    T firstvec = relation.get(first);
    means.add(firstvec);
    // Initialize weights
    double weightsum = initialWeights(weights, ids, firstvec, distQ);
    while (true) {
        if (weightsum > Double.MAX_VALUE) {
            LoggingUtil.warning("Could not choose a reasonable mean for k-means++ - too many data points, too large squared distances?");
        }
        if (weightsum < Double.MIN_NORMAL) {
            LoggingUtil.warning("Could not choose a reasonable mean for k-means++ - to few data points?");
        }
        double r = random.nextDouble() * weightsum, s = 0.;
        DBIDIter it = ids.iter();
        for (; s < r && it.valid(); it.advance()) {
            s += weights.doubleValue(it);
        }
        if (!it.valid()) {
            // Rare case, but happens due to floating math
            // Decrease
            weightsum -= (r - s);
            // Retry
            continue;
        }
        // Add new mean:
        final T newmean = relation.get(it);
        means.add(newmean);
        if (means.size() >= k) {
            break;
        }
        // Update weights:
        weights.putDouble(it, 0.);
        // Choose optimized version for double distances, if applicable.
        weightsum = updateWeights(weights, ids, newmean, distQ);
    }
    // Explicitly destroy temporary data.
    weights.destroy();
    return unboxVectors(means);
}

Example 12 with AbortException

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

the class PAMInitialMeans method chooseInitialMeans.

@Override
public <T extends NumberVector> double[][] chooseInitialMeans(Database database, Relation<T> relation, int k, NumberVectorDistanceFunction<? super T> distanceFunction) {
    if (relation.size() < k) {
        throw new AbortException("Database has less than k objects.");
    }
    // Ugly cast; but better than code duplication.
    @SuppressWarnings("unchecked") Relation<O> rel = (Relation<O>) relation;
    // Get a distance query
    @SuppressWarnings("unchecked") final PrimitiveDistanceFunction<? super O> distF = (PrimitiveDistanceFunction<? super O>) distanceFunction;
    final DistanceQuery<O> distQ = database.getDistanceQuery(rel, distF);
    DBIDs medids = chooseInitialMedoids(k, rel.getDBIDs(), distQ);
    double[][] medoids = new double[k][];
    DBIDIter iter = medids.iter();
    for (int i = 0; i < k; i++, iter.advance()) {
        medoids[i] = relation.get(iter).toArray();
    }
    return medoids;
}

Example 13 with AbortException

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

the class BundleWriter method writeBundleStream.

/**
 * Write a bundle stream to a file output channel.
 *
 * @param source Data source
 * @param output Output channel
 * @throws IOException on IO errors
 */
public void writeBundleStream(BundleStreamSource source, WritableByteChannel output) throws IOException {
    ByteBuffer buffer = ByteBuffer.allocateDirect(INITIAL_BUFFER);
    DBIDVar var = DBIDUtil.newVar();
    ByteBufferSerializer<?>[] serializers = null;
    loop: while (true) {
        BundleStreamSource.Event ev = source.nextEvent();
        switch(ev) {
            case NEXT_OBJECT:
                if (serializers == null) {
                    serializers = writeHeader(source, buffer, output);
                }
                if (serializers[0] != null) {
                    if (!source.assignDBID(var)) {
                        throw new AbortException("An object did not have an DBID assigned.");
                    }
                    DBID id = DBIDUtil.deref(var);
                    @SuppressWarnings("unchecked") ByteBufferSerializer<DBID> ser = (ByteBufferSerializer<DBID>) serializers[0];
                    int size = ser.getByteSize(id);
                    buffer = ensureBuffer(size, buffer, output);
                    ser.toByteBuffer(buffer, id);
                }
                for (int i = 1, j = 0; i < serializers.length; ++i, ++j) {
                    @SuppressWarnings("unchecked") ByteBufferSerializer<Object> ser = (ByteBufferSerializer<Object>) serializers[i];
                    int size = ser.getByteSize(source.data(j));
                    buffer = ensureBuffer(size, buffer, output);
                    ser.toByteBuffer(buffer, source.data(j));
                }
                // switch
                break;
            case META_CHANGED:
                if (serializers != null) {
                    throw new AbortException("Meta changes are not supported, once the block header has been written.");
                }
                // switch
                break;
            case END_OF_STREAM:
                break loop;
            default:
                LOG.warning("Unknown bundle stream event. API inconsistent? " + ev);
                // switch
                break;
        }
    }
    if (buffer.position() > 0) {
        flushBuffer(buffer, output);
    }
}

Example 14 with AbortException

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

the class TrivialDBIDFactory method generateSingleDBID.

@Override
public DBID generateSingleDBID() {
    final int id = next.getAndIncrement();
    if (id == Integer.MAX_VALUE) {
        throw new AbortException("DBID allocation error - too many objects allocated!");
    }
    DBID ret = new IntegerDBID(id);
    return ret;
}

Example 15 with AbortException

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

the class SimpleDBIDFactory method generateStaticDBIDRange.

@Override
public synchronized DBIDRange generateStaticDBIDRange(int size) {
    if (rangestart >= Integer.MAX_VALUE - size) {
        throw new AbortException("DBID range allocation error - too many objects allocated!");
    }
    DBIDRange alloc = new IntegerDBIDRange(rangestart, size);
    rangestart += size;
    return alloc;
}