Examples with Logging de.lmu.ifi.dbs.elki.logging.Logging used on opensource projects

Example 6 with Logging

use of de.lmu.ifi.dbs.elki.logging.Logging in project elki by elki-project.

the class IndexTree method initialize.

/**
 * Initializes the index.
 *
 * @param exampleLeaf an object that will be stored in the index
 */
protected final void initialize(E exampleLeaf) {
    initializeCapacities(exampleLeaf);
    // create empty root
    createEmptyRoot(exampleLeaf);
    final Logging log = getLogger();
    if (log.isStatistics()) {
        String cls = this.getClass().getName();
        log.statistics(new LongStatistic(cls + ".directory.capacity", dirCapacity));
        log.statistics(new LongStatistic(cls + ".directory.minfill", dirMinimum));
        log.statistics(new LongStatistic(cls + ".leaf.capacity", leafCapacity));
        log.statistics(new LongStatistic(cls + ".leaf.minfill", leafMinimum));
    }
    initialized = true;
}

Example 7 with Logging

use of de.lmu.ifi.dbs.elki.logging.Logging in project elki by elki-project.

the class MetricalIndexApproximationMaterializeKNNPreprocessor method preprocess.

@Override
protected void preprocess() {
    final Logging log = getLogger();
    DistanceQuery<O> distanceQuery = relation.getDistanceQuery(distanceFunction);
    MetricalIndexTree<O, N, E> index = getMetricalIndex(relation);
    createStorage();
    MeanVariance pagesize = new MeanVariance();
    MeanVariance ksize = new MeanVariance();
    if (log.isVerbose()) {
        log.verbose("Approximating nearest neighbor lists to database objects");
    }
    List<E> leaves = index.getLeaves();
    FiniteProgress progress = getLogger().isVerbose() ? new FiniteProgress("Processing leaf nodes", leaves.size(), getLogger()) : null;
    for (E leaf : leaves) {
        N node = index.getNode(leaf);
        int size = node.getNumEntries();
        pagesize.put(size);
        if (log.isDebuggingFinest()) {
            log.debugFinest("NumEntires = " + size);
        }
        // Collect the ids in this node.
        ArrayModifiableDBIDs ids = DBIDUtil.newArray(size);
        for (int i = 0; i < size; i++) {
            ids.add(((LeafEntry) node.getEntry(i)).getDBID());
        }
        Object2DoubleOpenHashMap<DBIDPair> cache = new Object2DoubleOpenHashMap<>((size * size * 3) >> 2);
        cache.defaultReturnValue(Double.NaN);
        for (DBIDIter id = ids.iter(); id.valid(); id.advance()) {
            KNNHeap kNN = DBIDUtil.newHeap(k);
            for (DBIDIter id2 = ids.iter(); id2.valid(); id2.advance()) {
                DBIDPair key = DBIDUtil.newPair(id, id2);
                double d = cache.removeDouble(key);
                if (d == d) {
                    // Not NaN
                    // consume the previous result.
                    kNN.insert(d, id2);
                } else {
                    // compute new and store the previous result.
                    d = distanceQuery.distance(id, id2);
                    kNN.insert(d, id2);
                    // put it into the cache, but with the keys reversed
                    key = DBIDUtil.newPair(id2, id);
                    cache.put(key, d);
                }
            }
            ksize.put(kNN.size());
            storage.put(id, kNN.toKNNList());
        }
        if (log.isDebugging() && cache.size() > 0) {
            log.warning("Cache should be empty after each run, but still has " + cache.size() + " elements.");
        }
        log.incrementProcessed(progress);
    }
    log.ensureCompleted(progress);
    if (log.isVerbose()) {
        log.verbose("Average page size = " + pagesize.getMean() + " +- " + pagesize.getSampleStddev());
        log.verbose("On average, " + ksize.getMean() + " +- " + ksize.getSampleStddev() + " neighbors returned.");
    }
}

Example 8 with Logging

use of de.lmu.ifi.dbs.elki.logging.Logging in project elki by elki-project.

the class AbstractMTree method insert.

/**
 * Inserts the specified object into this M-Tree.
 *
 * @param entry the entry to be inserted
 * @param withPreInsert if this flag is true, the preInsert method will be
 *        called before inserting the object
 */
// todo: implement a bulk load for M-Tree and remove this method
public void insert(E entry, boolean withPreInsert) {
    final Logging log = getLogger();
    if (log.isDebugging()) {
        log.debugFine("insert " + entry.getRoutingObjectID());
    }
    if (!initialized) {
        initialize(entry);
    }
    // choose subtree for insertion
    IndexTreePath<E> subtree = settings.insertStrategy.choosePath(this, entry);
    if (log.isDebugging()) {
        log.debugFine("insertion-subtree " + subtree);
    }
    // determine parent distance
    E parentEntry = subtree.getEntry();
    entry.setParentDistance(distance(parentEntry.getRoutingObjectID(), entry.getRoutingObjectID()));
    // create leaf entry and do pre insert
    if (withPreInsert) {
        preInsert(entry);
    }
    // get parent node
    N parent = getNode(parentEntry);
    parent.addLeafEntry(entry);
    writeNode(parent);
    // adjust the tree from subtree to root
    adjustTree(subtree);
    // test
    if (EXTRA_INTEGRITY_CHECKS) {
        getRoot().integrityCheck(this, getRootEntry());
    }
}

Example 9 with Logging

use of de.lmu.ifi.dbs.elki.logging.Logging in project elki by elki-project.

the class ThumbnailVisualization method doThumbnail.

@Override
public synchronized void doThumbnail() {
    pendingThumbnail = null;
    try {
        VisualizationPlot plot = new VisualizationPlot();
        plot.getRoot().setAttribute(SVGConstants.SVG_VIEW_BOX_ATTRIBUTE, "0 0 " + getWidth() + " " + getHeight());
        // Work on a clone
        Visualization vis = visFactory.makeVisualization(context, task, plot, getWidth(), getHeight(), proj);
        plot.getRoot().appendChild(vis.getLayer());
        plot.updateStyleElement();
        final int tw = (int) (getWidth() * tresolution);
        final int th = (int) (getHeight() * tresolution);
        thumb = plot.makeAWTImage(tw, th);
        thumbid = ThumbnailRegistryEntry.registerImage(thumb);
        // The visualization will not be used anymore.
        vis.destroy();
        svgp.requestRedraw(this.task, this);
    } catch (Exception e) {
        final Logging logger = Logging.getLogger(task.getFactory().getClass());
        if (logger != null && logger.isDebugging()) {
            logger.exception("Thumbnail for " + task.getFactory() + " failed.", e);
        } else {
            LoggingUtil.warning("Thumbnail for " + task.getFactory() + " failed - enable debugging to see details.");
        }
    // TODO: hide the failed image?
    }
}

Example 10 with Logging

use of de.lmu.ifi.dbs.elki.logging.Logging in project elki by elki-project.

the class SLINK method run.

/**
 * Performs the SLINK algorithm on the given database.
 *
 * @param database Database to process
 * @param relation Data relation to use
 */
public PointerHierarchyRepresentationResult run(Database database, Relation<O> relation) {
    DBIDs ids = relation.getDBIDs();
    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);
    // Temporary storage for m.
    WritableDoubleDataStore m = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP);
    // To allow CLINK logger override
    final Logging log = getLogger();
    FiniteProgress progress = log.isVerbose() ? new FiniteProgress("Running SLINK", ids.size(), log) : null;
    ArrayDBIDs aids = DBIDUtil.ensureArray(ids);
    // First element is trivial/special:
    DBIDArrayIter id = aids.iter(), it = aids.iter();
    // Step 1: initialize
    for (; id.valid(); id.advance()) {
        // P(n+1) = n+1:
        pi.put(id, id);
    // L(n+1) = infinity already.
    }
    // First element is finished already (start at seek(1) below!)
    log.incrementProcessed(progress);
    // Optimized branch
    if (getDistanceFunction() instanceof PrimitiveDistanceFunction) {
        PrimitiveDistanceFunction<? super O> distf = (PrimitiveDistanceFunction<? super O>) getDistanceFunction();
        for (id.seek(1); id.valid(); id.advance()) {
            step2primitive(id, it, id.getOffset(), relation, distf, m);
            // SLINK or CLINK
            process(id, aids, it, id.getOffset(), pi, lambda, m);
            log.incrementProcessed(progress);
        }
    } else {
        // Fallback branch
        DistanceQuery<O> distQ = database.getDistanceQuery(relation, getDistanceFunction());
        for (id.seek(1); id.valid(); id.advance()) {
            step2(id, it, id.getOffset(), distQ, m);
            // SLINK or CLINK
            process(id, aids, it, id.getOffset(), pi, lambda, m);
            log.incrementProcessed(progress);
        }
    }
    log.ensureCompleted(progress);
    // We don't need m anymore.
    m.destroy();
    m = null;
    return new PointerHierarchyRepresentationResult(ids, pi, lambda, getDistanceFunction().isSquared());
}