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

Example 11 with DBIDVar

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

the class DiSH method extractClusters.

/**
 * Extracts the clusters from the cluster order.
 *
 * @param relation the database storing the objects
 * @param clusterOrder the cluster order to extract the clusters from
 * @return the extracted clusters
 */
private Object2ObjectOpenCustomHashMap<long[], List<ArrayModifiableDBIDs>> extractClusters(Relation<V> relation, DiSHClusterOrder clusterOrder) {
    FiniteProgress progress = LOG.isVerbose() ? new FiniteProgress("Extract Clusters", relation.size(), LOG) : null;
    Object2ObjectOpenCustomHashMap<long[], List<ArrayModifiableDBIDs>> clustersMap = new Object2ObjectOpenCustomHashMap<>(BitsUtil.FASTUTIL_HASH_STRATEGY);
    // Note clusterOrder currently contains DBID objects anyway.
    WritableDataStore<Pair<long[], ArrayModifiableDBIDs>> entryToClusterMap = DataStoreUtil.makeStorage(relation.getDBIDs(), DataStoreFactory.HINT_TEMP | DataStoreFactory.HINT_HOT, Pair.class);
    for (DBIDIter iter = clusterOrder.iter(); iter.valid(); iter.advance()) {
        V object = relation.get(iter);
        long[] preferenceVector = clusterOrder.getCommonPreferenceVector(iter);
        // get the list of (parallel) clusters for the preference vector
        List<ArrayModifiableDBIDs> parallelClusters = clustersMap.get(preferenceVector);
        if (parallelClusters == null) {
            parallelClusters = new ArrayList<>();
            clustersMap.put(preferenceVector, parallelClusters);
        }
        // look for the proper cluster
        ArrayModifiableDBIDs cluster = null;
        for (ArrayModifiableDBIDs c : parallelClusters) {
            NumberVector c_centroid = ProjectedCentroid.make(preferenceVector, relation, c);
            long[] commonPreferenceVector = BitsUtil.andCMin(preferenceVector, preferenceVector);
            int subspaceDim = subspaceDimensionality(object, c_centroid, preferenceVector, preferenceVector, commonPreferenceVector);
            if (subspaceDim == clusterOrder.getCorrelationValue(iter)) {
                double d = weightedDistance(object, c_centroid, commonPreferenceVector);
                if (d <= 2 * epsilon) {
                    cluster = c;
                    break;
                }
            }
        }
        if (cluster == null) {
            cluster = DBIDUtil.newArray();
            parallelClusters.add(cluster);
        }
        cluster.add(iter);
        entryToClusterMap.put(iter, new Pair<>(preferenceVector, cluster));
        LOG.incrementProcessed(progress);
    }
    LOG.ensureCompleted(progress);
    if (LOG.isDebuggingFiner()) {
        int dim = RelationUtil.dimensionality(relation);
        StringBuilder msg = new StringBuilder("Step 0");
        for (Map.Entry<long[], List<ArrayModifiableDBIDs>> clusterList : clustersMap.entrySet()) {
            for (ArrayModifiableDBIDs c : clusterList.getValue()) {
                msg.append('\n').append(BitsUtil.toStringLow(clusterList.getKey(), dim)).append(" ids ").append(c.size());
            }
        }
        LOG.debugFiner(msg.toString());
    }
    // add the predecessor to the cluster
    DBIDVar cur = DBIDUtil.newVar(), pre = DBIDUtil.newVar();
    for (long[] pv : clustersMap.keySet()) {
        List<ArrayModifiableDBIDs> parallelClusters = clustersMap.get(pv);
        for (ArrayModifiableDBIDs cluster : parallelClusters) {
            if (cluster.isEmpty()) {
                continue;
            }
            cluster.assignVar(0, cur);
            clusterOrder.getPredecessor(cur, pre);
            if (!pre.isSet() || DBIDUtil.equal(pre, cur)) {
                continue;
            }
            // parallel cluster
            if (BitsUtil.equal(clusterOrder.getCommonPreferenceVector(pre), clusterOrder.getCommonPreferenceVector(cur))) {
                continue;
            }
            if (// 
            clusterOrder.getCorrelationValue(pre) < clusterOrder.getCorrelationValue(cur) || clusterOrder.getReachability(pre) < clusterOrder.getReachability(cur)) {
                continue;
            }
            Pair<long[], ArrayModifiableDBIDs> oldCluster = entryToClusterMap.get(pre);
            oldCluster.second.remove(pre);
            cluster.add(pre);
            entryToClusterMap.put(pre, new Pair<>(pv, cluster));
        }
    }
    return clustersMap;
}

Example 12 with DBIDVar

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

the class HashmapDatabase method insert.

@Override
public DBIDs insert(ObjectBundle objpackages) {
    if (objpackages.dataLength() == 0) {
        return DBIDUtil.EMPTYDBIDS;
    }
    // insert into db
    ArrayModifiableDBIDs newids = DBIDUtil.newArray(objpackages.dataLength());
    Relation<?>[] targets = alignColumns(objpackages);
    DBIDVar var = DBIDUtil.newVar();
    for (int j = 0; j < objpackages.dataLength(); j++) {
        // insert object
        if (!objpackages.assignDBID(j, var)) {
            var.set(DBIDUtil.generateSingleDBID());
        }
        if (ids.contains(var)) {
            throw new AbortException("Duplicate DBID conflict.");
        }
        ids.add(var);
        for (int i = 0; i < targets.length; i++) {
            if (!(targets[i] instanceof ModifiableRelation)) {
                throw new AbortException("Non-modifiable relations have been added to the database.");
            }
            @SuppressWarnings("unchecked") final ModifiableRelation<Object> relation = (ModifiableRelation<Object>) targets[i];
            relation.insert(var, objpackages.data(j, i));
        }
        newids.add(var);
    }
    // fire insertion event
    eventManager.fireObjectsInserted(newids);
    return newids;
}

Example 13 with DBIDVar

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

the class PointerPrototypeHierarchyRepresentationResult method findPrototype.

/**
 * Extract the prototype of a given cluster. When the argument is not a valid
 * cluster of this Pointer Hierarchy, the return value is unspecified.
 *
 * @param members Cluster members
 * @return The prototype of the cluster
 */
public DBID findPrototype(DBIDs members) {
    // Find the last merge within the cluster.
    // The object with maximum priority will merge outside of the cluster,
    // So we need the second largest priority.
    DBIDIter it = members.iter();
    DBIDVar proto = DBIDUtil.newVar(it), last = DBIDUtil.newVar(it);
    int maxprio = Integer.MIN_VALUE, secprio = Integer.MIN_VALUE;
    for (; it.valid(); it.advance()) {
        int prio = mergeOrder.intValue(it);
        if (prio > maxprio) {
            secprio = maxprio;
            proto.set(last);
            maxprio = prio;
            last.set(it);
        } else if (prio > secprio) {
            secprio = prio;
            proto.set(it);
        }
    }
    return DBIDUtil.deref(prototypes.assignVar(proto, proto));
}

Example 14 with DBIDVar

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

the class SLINKHDBSCANLinearMemory method step4.

/**
 * Fourth step: Actualize the clusters if necessary
 *
 * @param id the id of the current object
 * @param pi Pi data store
 * @param lambda Lambda data store
 * @param processedIDs the already processed ids
 */
private void step4(DBIDRef id, WritableDBIDDataStore pi, WritableDoubleDataStore lambda, DBIDs processedIDs) {
    DBIDVar p_i = DBIDUtil.newVar();
    // for i = 1..n
    for (DBIDIter it = processedIDs.iter(); it.valid(); it.advance()) {
        double l_i = lambda.doubleValue(it);
        // p_i = pi(it)
        pi.assignVar(it, p_i);
        double lp_i = lambda.doubleValue(p_i);
        // if L(i) >= L(P(i))
        if (l_i >= lp_i) {
            // P(i) = n+1
            pi.put(it, id);
        }
    }
}

Example 15 with DBIDVar

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

the class SLINKHDBSCANLinearMemory method step3.

/**
 * Third step: Determine the values for P and L
 *
 * @param id the id of the object to be inserted into the pointer
 *        representation
 * @param pi Pi data store
 * @param lambda Lambda data store
 * @param processedIDs the already processed ids
 * @param m Data store
 */
private void step3(DBIDRef id, WritableDBIDDataStore pi, WritableDoubleDataStore lambda, DBIDs processedIDs, WritableDoubleDataStore m) {
    DBIDVar p_i = DBIDUtil.newVar();
    // for i = 1..n
    for (DBIDIter it = processedIDs.iter(); it.valid(); it.advance()) {
        double l_i = lambda.doubleValue(it);
        double m_i = m.doubleValue(it);
        // p_i = pi(it)
        pi.assignVar(it, p_i);
        double mp_i = m.doubleValue(p_i);
        // if L(i) >= M(i)
        if (l_i >= m_i) {
            // M(P(i)) = min { M(P(i)), L(i) }
            if (l_i < mp_i) {
                m.putDouble(p_i, l_i);
            }
            // L(i) = M(i)
            lambda.putDouble(it, m_i);
            // P(i) = n+1;
            pi.put(it, id);
        } else {
            // M(P(i)) = min { M(P(i)), M(i) }
            if (m_i < mp_i) {
                m.putDouble(p_i, m_i);
            }
        }
    }
}