Examples with DBIDRange de.lmu.ifi.dbs.elki.database.ids.DBIDRange used on opensource projects

Example 16 with DBIDRange

use of de.lmu.ifi.dbs.elki.database.ids.DBIDRange in project elki by elki-project.

the class ClusteringVectorDumper method dumpClusteringOutput.

/**
 * Dump a single clustering result.
 *
 * @param writer Output writer
 * @param hierarchy Cluster hierarchy to process
 * @param c Clustering result
 */
protected void dumpClusteringOutput(PrintStream writer, ResultHierarchy hierarchy, Clustering<?> c) {
    DBIDRange ids = null;
    for (It<Relation<?>> iter = hierarchy.iterParents(c).filter(Relation.class); iter.valid(); iter.advance()) {
        DBIDs pids = iter.get().getDBIDs();
        if (pids instanceof DBIDRange) {
            ids = (DBIDRange) pids;
            break;
        }
        LOG.warning("Parent result " + iter.get().getLongName() + " has DBID type " + pids.getClass());
    }
    // Fallback: try to locate a database.
    if (ids == null) {
        for (It<Database> iter = hierarchy.iterAll().filter(Database.class); iter.valid(); iter.advance()) {
            DBIDs pids = iter.get().getRelation(TypeUtil.ANY).getDBIDs();
            if (pids instanceof DBIDRange) {
                ids = (DBIDRange) pids;
                break;
            }
            LOG.warning("Parent result " + iter.get().getLongName() + " has DBID type " + pids.getClass());
        }
    }
    if (ids == null) {
        LOG.warning("Cannot dump cluster assignment, as I do not have a well-defined DBIDRange to use for a unique column assignment. DBIDs must be a continuous range.");
        return;
    }
    WritableIntegerDataStore map = DataStoreUtil.makeIntegerStorage(ids, DataStoreFactory.HINT_TEMP);
    int cnum = 0;
    for (Cluster<?> clu : c.getAllClusters()) {
        for (DBIDIter iter = clu.getIDs().iter(); iter.valid(); iter.advance()) {
            map.putInt(iter, cnum);
        }
        ++cnum;
    }
    for (DBIDArrayIter iter = ids.iter(); iter.valid(); iter.advance()) {
        if (iter.getOffset() > 0) {
            writer.append(' ');
        }
        writer.append(Integer.toString(map.intValue(iter)));
    }
    if (forceLabel != null) {
        if (forceLabel.length() > 0) {
            writer.append(' ').append(forceLabel);
        }
    } else {
        writer.append(' ').append(c.getLongName());
    }
    writer.append('\n');
}

Example 17 with DBIDRange

use of de.lmu.ifi.dbs.elki.database.ids.DBIDRange in project elki by elki-project.

the class PrecomputedSimilarityMatrix method initialize.

@Override
public void initialize() {
    DBIDs rids = relation.getDBIDs();
    if (!(rids instanceof DBIDRange)) {
        throw new AbortException("Similarity matrixes are currently only supported for DBID ranges (as used by static databases) for performance reasons (Patches welcome).");
    }
    ids = (DBIDRange) rids;
    size = ids.size();
    if (size > 65536) {
        throw new AbortException("Similarity 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.");
    }
    similarityQuery = similarityFunction.instantiate(relation);
    int msize = triangleSize(size);
    matrix = new double[msize];
    DBIDArrayIter ix = ids.iter(), iy = ids.iter();
    FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Precomputing similarity 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] = similarityQuery.similarity(ix, iy);
            pos++;
        }
        if (prog != null) {
            prog.setProcessed(prog.getProcessed() + ix.getOffset(), LOG);
        }
    }
    LOG.ensureCompleted(prog);
}

Example 18 with DBIDRange

use of de.lmu.ifi.dbs.elki.database.ids.DBIDRange 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 19 with DBIDRange

use of de.lmu.ifi.dbs.elki.database.ids.DBIDRange 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 20 with DBIDRange

use of de.lmu.ifi.dbs.elki.database.ids.DBIDRange in project elki by elki-project.

the class WeightedQuickUnionRangeDBIDsTest method testTree.

@Test
public void testTree() {
    DBIDRange range = DBIDUtil.generateStaticDBIDRange(8);
    UnionFind uf = new WeightedQuickUnionRangeDBIDs(range);
    DBIDArrayIter i1 = range.iter(), i2 = range.iter();
    assertFalse(uf.isConnected(i1.seek(0), i2.seek(7)));
    uf.union(i1.seek(0), i2.seek(1));
    assertTrue(uf.isConnected(i1.seek(0), i2.seek(1)));
    uf.union(i1.seek(2), i2.seek(3));
    assertFalse(uf.isConnected(i1.seek(0), i2.seek(2)));
    uf.union(i1.seek(0), i2.seek(2));
    assertTrue(uf.isConnected(i1.seek(3), i2.seek(1)));
    uf.union(i1.seek(4), i2.seek(5));
    uf.union(i1.seek(6), i2.seek(7));
    uf.union(i1.seek(4), i2.seek(6));
    assertFalse(uf.isConnected(i1.seek(0), i2.seek(4)));
    uf.union(i1.seek(0), i2.seek(4));
    for (int i = 0; i < 8; i++) {
        for (int j = 0; j < 8; j++) {
            assertTrue(uf.isConnected(i1.seek(i), i2.seek(j)));
        }
    }
}