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

Example 31 with ArrayModifiableDBIDs

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

the class KMLOutputHandler method writeOutlierResult.

private void writeOutlierResult(XMLStreamWriter xmlw, OutlierResult outlierResult, Database database) throws XMLStreamException {
    Relation<PolygonsObject> polys = database.getRelation(TypeUtil.POLYGON_TYPE);
    Relation<String> labels = DatabaseUtil.guessObjectLabelRepresentation(database);
    xmlw.writeStartDocument();
    xmlw.writeCharacters("\n");
    xmlw.writeStartElement("kml");
    xmlw.writeDefaultNamespace("http://earth.google.com/kml/2.2");
    xmlw.writeStartElement("Document");
    {
        // TODO: can we automatically generate more helpful data here?
        xmlw.writeStartElement("name");
        xmlw.writeCharacters("ELKI KML output for " + outlierResult.getLongName());
        // name
        xmlw.writeEndElement();
        writeNewlineOnDebug(xmlw);
        // TODO: e.g. list the settings in the description?
        xmlw.writeStartElement("description");
        xmlw.writeCharacters("ELKI KML output for " + outlierResult.getLongName());
        // description
        xmlw.writeEndElement();
        writeNewlineOnDebug(xmlw);
    }
    {
        // TODO: generate styles from color scheme
        for (int i = 0; i < NUMSTYLES; i++) {
            Color col = getColorForValue(i / (NUMSTYLES - 1.0));
            xmlw.writeStartElement("Style");
            xmlw.writeAttribute("id", "s" + i);
            writeNewlineOnDebug(xmlw);
            {
                xmlw.writeStartElement("LineStyle");
                xmlw.writeStartElement("width");
                xmlw.writeCharacters("0");
                // width
                xmlw.writeEndElement();
                // LineStyle
                xmlw.writeEndElement();
            }
            writeNewlineOnDebug(xmlw);
            {
                xmlw.writeStartElement("PolyStyle");
                xmlw.writeStartElement("color");
                // KML uses AABBGGRR format!
                xmlw.writeCharacters(String.format("%02x%02x%02x%02x", col.getAlpha(), col.getBlue(), col.getGreen(), col.getRed()));
                // color
                xmlw.writeEndElement();
                // out.writeStartElement("fill");
                // out.writeCharacters("1"); // Default 1
                // out.writeEndElement(); // fill
                xmlw.writeStartElement("outline");
                xmlw.writeCharacters("0");
                // outline
                xmlw.writeEndElement();
                // PolyStyle
                xmlw.writeEndElement();
            }
            writeNewlineOnDebug(xmlw);
            // Style
            xmlw.writeEndElement();
            writeNewlineOnDebug(xmlw);
        }
    }
    DoubleRelation scores = outlierResult.getScores();
    Collection<Relation<?>> otherrel = new LinkedList<>(database.getRelations());
    otherrel.remove(scores);
    otherrel.remove(polys);
    otherrel.remove(labels);
    otherrel.remove(database.getRelation(TypeUtil.DBID));
    ArrayModifiableDBIDs ids = DBIDUtil.newArray(scores.getDBIDs());
    scaling.prepare(outlierResult);
    for (DBIDIter iter = outlierResult.getOrdering().order(ids).iter(); iter.valid(); iter.advance()) {
        double score = scores.doubleValue(iter);
        PolygonsObject poly = polys.get(iter);
        String label = labels.get(iter);
        if (Double.isNaN(score)) {
            LOG.warning("No score for object " + DBIDUtil.toString(iter));
        }
        if (poly == null) {
            LOG.warning("No polygon for object " + DBIDUtil.toString(iter) + " - skipping.");
            continue;
        }
        xmlw.writeStartElement("Placemark");
        {
            xmlw.writeStartElement("name");
            xmlw.writeCharacters(score + " " + label);
            // name
            xmlw.writeEndElement();
            StringBuilder buf = makeDescription(otherrel, iter);
            xmlw.writeStartElement("description");
            xmlw.writeCData("<div>" + buf.toString() + "</div>");
            // description
            xmlw.writeEndElement();
            xmlw.writeStartElement("styleUrl");
            int style = (int) (scaling.getScaled(score) * NUMSTYLES);
            style = Math.max(0, Math.min(style, NUMSTYLES - 1));
            xmlw.writeCharacters("#s" + style);
            // styleUrl
            xmlw.writeEndElement();
        }
        {
            xmlw.writeStartElement("Polygon");
            writeNewlineOnDebug(xmlw);
            if (compat) {
                xmlw.writeStartElement("altitudeMode");
                xmlw.writeCharacters("relativeToGround");
                // close altitude mode
                xmlw.writeEndElement();
                writeNewlineOnDebug(xmlw);
            }
            // First polygon clockwise?
            boolean first = true;
            for (Polygon p : poly.getPolygons()) {
                if (first) {
                    xmlw.writeStartElement("outerBoundaryIs");
                } else {
                    xmlw.writeStartElement("innerBoundaryIs");
                }
                xmlw.writeStartElement("LinearRing");
                xmlw.writeStartElement("coordinates");
                // Reverse anti-clockwise polygons.
                boolean reverse = (p.testClockwise() >= 0);
                ArrayListIter<double[]> it = p.iter();
                if (reverse) {
                    it.seek(p.size() - 1);
                }
                while (it.valid()) {
                    double[] v = it.get();
                    xmlw.writeCharacters(FormatUtil.format(v, ","));
                    if (compat && (v.length == 2)) {
                        xmlw.writeCharacters(",50");
                    }
                    xmlw.writeCharacters(" ");
                    if (!reverse) {
                        it.advance();
                    } else {
                        it.retract();
                    }
                }
                // close coordinates
                xmlw.writeEndElement();
                // close LinearRing
                xmlw.writeEndElement();
                // close *BoundaryIs
                xmlw.writeEndElement();
                first = false;
            }
            writeNewlineOnDebug(xmlw);
            // Polygon
            xmlw.writeEndElement();
        }
        // Placemark
        xmlw.writeEndElement();
        writeNewlineOnDebug(xmlw);
    }
    // Document
    xmlw.writeEndElement();
    // kml
    xmlw.writeEndElement();
    xmlw.writeEndDocument();
}

Example 32 with ArrayModifiableDBIDs

use of de.lmu.ifi.dbs.elki.database.ids.ArrayModifiableDBIDs 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 33 with ArrayModifiableDBIDs

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

the class HiCS method calculateContrast.

/**
 * Calculates the actual contrast of a given subspace.
 *
 * @param relation Relation to process
 * @param subspace Subspace
 * @param subspaceIndex Subspace indexes
 */
private void calculateContrast(Relation<? extends NumberVector> relation, HiCSSubspace subspace, ArrayList<ArrayDBIDs> subspaceIndex, Random random) {
    final int card = subspace.cardinality();
    final double alpha1 = FastMath.pow(alpha, (1.0 / card));
    final int windowsize = (int) (relation.size() * alpha1);
    final FiniteProgress prog = LOG.isDebugging() ? new FiniteProgress("Monte-Carlo iterations", m, LOG) : null;
    int retries = 0;
    double deviationSum = 0.0;
    for (int i = 0; i < m; i++) {
        // Choose a random set bit.
        int chosen = -1;
        for (int tmp = random.nextInt(card); tmp >= 0; tmp--) {
            chosen = subspace.nextSetBit(chosen + 1);
        }
        // initialize sample
        DBIDs conditionalSample = relation.getDBIDs();
        for (int j = subspace.nextSetBit(0); j >= 0; j = subspace.nextSetBit(j + 1)) {
            if (j == chosen) {
                continue;
            }
            ArrayDBIDs sortedIndices = subspaceIndex.get(j);
            ArrayModifiableDBIDs indexBlock = DBIDUtil.newArray(windowsize);
            // initialize index block
            DBIDArrayIter iter = sortedIndices.iter();
            iter.seek(random.nextInt(relation.size() - windowsize));
            for (int k = 0; k < windowsize; k++, iter.advance()) {
                // select index block
                indexBlock.add(iter);
            }
            conditionalSample = DBIDUtil.intersection(conditionalSample, indexBlock);
        }
        if (conditionalSample.size() < 10) {
            retries++;
            if (LOG.isDebugging()) {
                LOG.debug("Sample size very small. Retry no. " + retries);
            }
            if (retries >= MAX_RETRIES) {
                LOG.warning("Too many retries, for small samples: " + retries);
            } else {
                i--;
                continue;
            }
        }
        // Project conditional set
        double[] sampleValues = new double[conditionalSample.size()];
        {
            int l = 0;
            for (DBIDIter iter = conditionalSample.iter(); iter.valid(); iter.advance()) {
                sampleValues[l] = relation.get(iter).doubleValue(chosen);
                l++;
            }
        }
        // Project full set
        double[] fullValues = new double[relation.size()];
        {
            int l = 0;
            for (DBIDIter iter = subspaceIndex.get(chosen).iter(); iter.valid(); iter.advance()) {
                fullValues[l] = relation.get(iter).doubleValue(chosen);
                l++;
            }
        }
        double contrast = statTest.deviation(fullValues, sampleValues);
        if (Double.isNaN(contrast)) {
            i--;
            LOG.warning("Contrast was NaN");
            continue;
        }
        deviationSum += contrast;
        LOG.incrementProcessed(prog);
    }
    LOG.ensureCompleted(prog);
    subspace.contrast = deviationSum / m;
}

Example 34 with ArrayModifiableDBIDs

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

the class AbstractAggarwalYuOutlier method buildRanges.

/**
 * Grid discretization of the data:<br />
 * Each attribute of data is divided into phi equi-depth ranges.<br />
 * Each range contains a fraction f=1/phi of the records.
 *
 * @param relation Relation to process
 * @return range map
 */
protected ArrayList<ArrayList<DBIDs>> buildRanges(Relation<V> relation) {
    final int dim = RelationUtil.dimensionality(relation);
    final int size = relation.size();
    final ArrayList<ArrayList<DBIDs>> ranges = new ArrayList<>();
    ArrayModifiableDBIDs ids = DBIDUtil.newArray(relation.getDBIDs());
    SortDBIDsBySingleDimension sorter = new SortDBIDsBySingleDimension(relation);
    // Split into cells
    final double part = size * 1.0 / phi;
    for (int d = 0; d < dim; d++) {
        sorter.setDimension(d);
        ids.sort(sorter);
        ArrayList<DBIDs> dimranges = new ArrayList<>(phi + 1);
        int start = 0;
        DBIDArrayIter iter = ids.iter();
        for (int r = 1; r <= phi; r++) {
            int end = (r < phi) ? (int) (part * r) : size;
            ArrayModifiableDBIDs currange = DBIDUtil.newArray(end - start);
            for (iter.seek(start); iter.getOffset() < end; iter.advance()) {
                currange.add(iter);
            }
            start = end;
            dimranges.add(currange);
        }
        ranges.add(dimranges);
    }
    return ranges;
}

Example 35 with ArrayModifiableDBIDs

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

the class OrderingFromRelation method order.

@Override
public ArrayModifiableDBIDs order(DBIDs ids) {
    ArrayModifiableDBIDs sorted = DBIDUtil.newArray(ids);
    sorted.sort(// 
    ascending ? // 
    new RelationUtil.AscendingByDoubleRelation(scores) : new RelationUtil.DescendingByDoubleRelation(scores));
    return sorted;
}