Examples with DoubleLongHeap de.lmu.ifi.dbs.elki.utilities.datastructures.heap.DoubleLongHeap used on opensource projects

Example 1 with DoubleLongHeap

use of de.lmu.ifi.dbs.elki.utilities.datastructures.heap.DoubleLongHeap in project elki by elki-project.

the class HDBSCANLinearMemory method run.

/**
 * Run the algorithm
 *
 * @param db Database
 * @param relation Relation
 * @return Clustering hierarchy
 */
public PointerDensityHierarchyRepresentationResult run(Database db, Relation<O> relation) {
    final DistanceQuery<O> distQ = db.getDistanceQuery(relation, getDistanceFunction());
    final KNNQuery<O> knnQ = db.getKNNQuery(distQ, minPts);
    // We need array addressing later.
    final ArrayDBIDs ids = DBIDUtil.ensureArray(relation.getDBIDs());
    // 1. Compute the core distances
    // minPts + 1: ignore query point.
    final WritableDoubleDataStore coredists = computeCoreDists(ids, knnQ, minPts);
    final int numedges = ids.size() - 1;
    DoubleLongHeap heap = new DoubleLongMinHeap(numedges);
    // 2. Build spanning tree.
    FiniteProgress mprog = LOG.isVerbose() ? new FiniteProgress("Computing minimum spanning tree (n-1 edges)", numedges, LOG) : null;
    // 
    PrimsMinimumSpanningTree.processDense(// 
    ids, // 
    new HDBSCANAdapter(ids, coredists, distQ), new HeapMSTCollector(heap, mprog, LOG));
    LOG.ensureCompleted(mprog);
    // Storage for pointer representation:
    WritableDBIDDataStore pi = DataStoreUtil.makeDBIDStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_STATIC);
    WritableDoubleDataStore lambda = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_STATIC, Double.POSITIVE_INFINITY);
    convertToPointerRepresentation(ids, heap, pi, lambda);
    return new PointerDensityHierarchyRepresentationResult(ids, pi, lambda, distQ.getDistanceFunction().isSquared(), coredists);
}