Examples with OnDiskUpperTriangleMatrix de.lmu.ifi.dbs.elki.persistent.OnDiskUpperTriangleMatrix used on opensource projects

Example 1 with OnDiskUpperTriangleMatrix

use of de.lmu.ifi.dbs.elki.persistent.OnDiskUpperTriangleMatrix in project elki by elki-project.

the class CacheDoubleDistanceInOnDiskMatrix 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, DiskCacheBasedDoubleDistanceFunction.DOUBLE_CACHE_MAGIC, 0, ByteArrayUtil.SIZE_DOUBLE, size)) {
        DBIDArrayIter id1 = ids.iter(), id2 = ids.iter();
        for (; id1.valid(); id1.advance()) {
            for (id2.seek(id1.getOffset()); 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!");
                    }
                }
                try {
                    matrix.getRecordBuffer(id1.getOffset(), id2.getOffset()).putDouble(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);
    }
    LOG.ensureCompleted(prog);
}

Example 2 with OnDiskUpperTriangleMatrix

use of de.lmu.ifi.dbs.elki.persistent.OnDiskUpperTriangleMatrix 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);
}