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

Example 76 with AbortException

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

the class CacheDoubleDistanceRangeQueries method run.

@Override
public void run() {
    database.initialize();
    Relation<O> relation = database.getRelation(distance.getInputTypeRestriction());
    DistanceQuery<O> distanceQuery = database.getDistanceQuery(relation, distance);
    RangeQuery<O> rangeQ = database.getRangeQuery(distanceQuery, radius, DatabaseQuery.HINT_HEAVY_USE);
    LOG.verbose("Performing range queries with radius " + radius);
    // open file.
    try (RandomAccessFile file = new RandomAccessFile(out, "rw");
        FileChannel channel = file.getChannel();
        // and acquire a file write lock
        FileLock lock = channel.lock()) {
        // write magic header
        file.writeInt(RANGE_CACHE_MAGIC);
        // write the query radius.
        file.writeDouble(radius);
        // Initial size, enough for 100.
        int bufsize = 100 * 12 * 2 + 10;
        ByteBuffer buffer = ByteBuffer.allocateDirect(bufsize);
        FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Computing range queries", relation.size(), LOG) : null;
        ModifiableDoubleDBIDList nn = DBIDUtil.newDistanceDBIDList();
        DoubleDBIDListIter ni = nn.iter();
        for (DBIDIter it = relation.iterDBIDs(); it.valid(); it.advance()) {
            nn.clear();
            rangeQ.getRangeForDBID(it, radius, nn);
            nn.sort();
            final int nnsize = nn.size();
            // Grow the buffer when needed:
            if (nnsize * 12 + 10 > bufsize) {
                while (nnsize * 12 + 10 > bufsize) {
                    bufsize <<= 1;
                }
                LOG.verbose("Resizing buffer to " + bufsize + " to store " + nnsize + " results:");
                buffer = ByteBuffer.allocateDirect(bufsize);
            }
            buffer.clear();
            ByteArrayUtil.writeUnsignedVarint(buffer, it.internalGetIndex());
            ByteArrayUtil.writeUnsignedVarint(buffer, nnsize);
            int c = 0;
            for (ni.seek(0); ni.valid(); ni.advance(), c++) {
                ByteArrayUtil.writeUnsignedVarint(buffer, ni.internalGetIndex());
                buffer.putDouble(ni.doubleValue());
            }
            if (c != nn.size()) {
                throw new AbortException("Sizes did not agree. Cache is invalid.");
            }
            buffer.flip();
            channel.write(buffer);
            LOG.incrementProcessed(prog);
        }
        LOG.ensureCompleted(prog);
        lock.release();
    } catch (IOException e) {
        LOG.exception(e);
    }
// FIXME: close!
}

Example 77 with AbortException

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

the class PrecomputeDistancesAsciiApplication method run.

@Override
public void run() {
    database.initialize();
    Relation<O> relation = database.getRelation(distance.getInputTypeRestriction());
    DistanceQuery<O> distanceQuery = database.getDistanceQuery(relation, distance);
    DBIDRange ids = DBIDUtil.assertRange(relation.getDBIDs());
    final int size = ids.size();
    FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Precomputing distances", (int) (((size - 1) * (long) size) >>> 1), LOG) : null;
    try (PrintStream fout = openStream(out)) {
        DBIDArrayIter id1 = ids.iter(), id2 = ids.iter();
        for (; id1.valid(); id1.advance()) {
            String idstr1 = Integer.toString(id1.getOffset());
            if (debugExtraCheckSymmetry && distanceQuery.distance(id1, id1) != 0.) {
                LOG.warning("Distance function doesn't satisfy d(0,0) = 0.");
            }
            for (id2.seek(id1.getOffset() + 1); id2.valid(); id2.advance()) {
                double d = distanceQuery.distance(id1, id2);
                if (debugExtraCheckSymmetry) {
                    double d2 = distanceQuery.distance(id2, id1);
                    if (Math.abs(d - d2) > 0.0000001) {
                        LOG.warning("Distance function doesn't appear to be symmetric!");
                    }
                }
                // 
                fout.append(idstr1).append('\t').append(Integer.toString(id2.getOffset())).append(// 
                '\t').append(Double.toString(d)).append('\n');
            }
            if (prog != null) {
                prog.setProcessed(prog.getProcessed() + (size - id1.getOffset() - 1), LOG);
            }
        }
    } catch (IOException e) {
        throw new AbortException("Could not write to output file.", e);
    }
    LOG.ensureCompleted(prog);
}

Example 78 with AbortException

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

the class CacheDoubleDistanceKNNLists method run.

@Override
public void run() {
    database.initialize();
    Relation<O> relation = database.getRelation(distance.getInputTypeRestriction());
    DistanceQuery<O> distanceQuery = database.getDistanceQuery(relation, distance);
    KNNQuery<O> knnQ = database.getKNNQuery(distanceQuery, DatabaseQuery.HINT_HEAVY_USE);
    // open file.
    try (RandomAccessFile file = new RandomAccessFile(out, "rw");
        FileChannel channel = file.getChannel();
        // and acquire a file write lock
        FileLock lock = channel.lock()) {
        // write magic header
        file.writeInt(KNN_CACHE_MAGIC);
        // Initial size, enough for 2 kNN.
        int bufsize = k * 12 * 2 + 10;
        ByteBuffer buffer = ByteBuffer.allocateDirect(bufsize);
        FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Computing kNN", relation.size(), LOG) : null;
        for (DBIDIter it = relation.iterDBIDs(); it.valid(); it.advance()) {
            final KNNList nn = knnQ.getKNNForDBID(it, k);
            final int nnsize = nn.size();
            // Grow the buffer when needed:
            if (nnsize * 12 + 10 > bufsize) {
                while (nnsize * 12 + 10 > bufsize) {
                    bufsize <<= 1;
                }
                buffer = ByteBuffer.allocateDirect(bufsize);
            }
            buffer.clear();
            ByteArrayUtil.writeUnsignedVarint(buffer, it.internalGetIndex());
            ByteArrayUtil.writeUnsignedVarint(buffer, nnsize);
            int c = 0;
            for (DoubleDBIDListIter ni = nn.iter(); ni.valid(); ni.advance(), c++) {
                ByteArrayUtil.writeUnsignedVarint(buffer, ni.internalGetIndex());
                buffer.putDouble(ni.doubleValue());
            }
            if (c != nn.size()) {
                throw new AbortException("Sizes did not agree. Cache is invalid.");
            }
            buffer.flip();
            channel.write(buffer);
            LOG.incrementProcessed(prog);
        }
        LOG.ensureCompleted(prog);
        lock.release();
    } catch (IOException e) {
        LOG.exception(e);
    }
// FIXME: close!
}

Example 79 with AbortException

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

the class CacheFloatDistanceInOnDiskMatrix method run.

@Override
public void run() {
    database.initialize();
    Relation<O> relation = database.getRelation(distance.getInputTypeRestriction());
    DistanceQuery<O> distanceQuery = database.getDistanceQuery(relation, distance);
    DBIDRange ids = DBIDUtil.assertRange(relation.getDBIDs());
    int size = ids.size();
    FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Precomputing distances", (int) (((size + 1) * (long) size) >>> 1), LOG) : null;
    try (// 
    OnDiskUpperTriangleMatrix matrix = new OnDiskUpperTriangleMatrix(out, DiskCacheBasedFloatDistanceFunction.FLOAT_CACHE_MAGIC, 0, ByteArrayUtil.SIZE_FLOAT, size)) {
        DBIDArrayIter id1 = ids.iter(), id2 = ids.iter();
        for (; id1.valid(); id1.advance()) {
            for (id2.seek(id1.getOffset()); id2.valid(); id2.advance()) {
                float d = (float) distanceQuery.distance(id1, id2);
                if (debugExtraCheckSymmetry) {
                    float d2 = (float) distanceQuery.distance(id2, id1);
                    if (Math.abs(d - d2) > 0.0000001) {
                        LOG.warning("Distance function doesn't appear to be symmetric!");
                    }
                }
                try {
                    matrix.getRecordBuffer(id1.getOffset(), id2.getOffset()).putFloat(d);
                } catch (IOException e) {
                    throw new AbortException("Error writing distance record " + DBIDUtil.toString(id1) + "," + DBIDUtil.toString(id2) + " to matrix.", e);
                }
            }
            if (prog != null) {
                prog.setProcessed(prog.getProcessed() + (size - id1.getOffset()), LOG);
            }
        }
    } catch (IOException e) {
        throw new AbortException("Error precomputing distance matrix.", e);
    }
    prog.ensureCompleted(LOG);
}

Example 80 with AbortException

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

the class RankingPseudoOutlierScaling method prepare.

@Override
public void prepare(OutlierResult or) {
    // collect all outlier scores
    DoubleRelation oscores = or.getScores();
    scores = new double[oscores.size()];
    int pos = 0;
    if (or.getOutlierMeta() instanceof InvertedOutlierScoreMeta) {
        inverted = true;
    }
    for (DBIDIter iditer = oscores.iterDBIDs(); iditer.valid(); iditer.advance()) {
        scores[pos] = oscores.doubleValue(iditer);
        pos++;
    }
    if (pos != oscores.size()) {
        throw new AbortException("Database size is incorrect!");
    }
    // sort them
    Arrays.sort(scores);
}