code stringlengths 73 34.1k | label stringclasses 1
value |
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public static int lengthWithoutLinefeed(CharSequence line) {
int length = line.length();
while(length > 0) {
char last = line.charAt(length - 1);
if(last != '\n' && last != '\r') {
break;
}
--length;
}
return length;
} | java |
public synchronized void logAndClearReportedErrors() {
for(ParameterException e : getErrors()) {
if(LOG.isDebugging()) {
LOG.warning(e.getMessage(), e);
}
else {
LOG.warning(e.getMessage());
}
}
clearErrors();
} | java |
public void addParameter(Object owner, Parameter<?> param, TrackParameters track) {
this.setBorder(new SoftBevelBorder(SoftBevelBorder.LOWERED));
ParameterConfigurator cfg = null;
{ // Find
Object cur = owner;
while(cur != null) {
cfg = childconfig.get(cur);
if(cfg != null) {
... | java |
protected static <E extends MTreeEntry, N extends AbstractMTreeNode<?, N, E>> double[][] computeDistanceMatrix(AbstractMTree<?, N, E, ?> tree, N node) {
final int n = node.getNumEntries();
double[][] distancematrix = new double[n][n];
// Build distance matrix
for(int i = 0; i < n; i++) {
E ei = no... | java |
protected static double sparsity(final int setsize, final int dbsize, final int k, final double phi) {
// calculate sparsity c
final double fK = MathUtil.powi(1. / phi, k);
return (setsize - (dbsize * fK)) / FastMath.sqrt(dbsize * fK * (1 - fK));
} | java |
protected DBIDs computeSubspace(int[] subspace, ArrayList<ArrayList<DBIDs>> ranges) {
HashSetModifiableDBIDs ids = DBIDUtil.newHashSet(ranges.get(subspace[0]).get(subspace[1]));
// intersect all selected dimensions
for(int i = 2, e = subspace.length - 1; i < e; i += 2) {
DBIDs current = ranges.get(sub... | java |
protected DBIDs computeSubspaceForGene(short[] gene, ArrayList<ArrayList<DBIDs>> ranges) {
HashSetModifiableDBIDs m = null;
// intersect all present restrictions
for(int i = 0; i < gene.length; i++) {
if(gene[i] != DONT_CARE) {
DBIDs current = ranges.get(i).get(gene[i] - GENE_OFFSET);
... | java |
private static void updateFilterSDASet(double mib, List<SteepDownArea> sdaset, double ixi) {
Iterator<SteepDownArea> iter = sdaset.iterator();
while(iter.hasNext()) {
SteepDownArea sda = iter.next();
if(sda.getMaximum() * ixi <= mib) {
iter.remove();
}
else {
// Update
... | java |
private static void sort5(double[] keys, int[] vals, final int m1, final int m2, final int m3, final int m4, final int m5) {
if(keys[m1] > keys[m2]) {
swap(keys, vals, m1, m2);
}
if(keys[m3] > keys[m4]) {
swap(keys, vals, m3, m4);
}
// Merge 1+2 and 3+4
if(keys[m2] > keys[m4]) {
... | java |
private static void swap(double[] keys, int[] vals, int j, int i) {
double td = keys[j];
keys[j] = keys[i];
keys[i] = td;
int ti = vals[j];
vals[j] = vals[i];
vals[i] = ti;
} | java |
public EvaluationResult.MeasurementGroup newGroup(String string) {
EvaluationResult.MeasurementGroup g = new MeasurementGroup(string);
groups.add(g);
return g;
} | java |
public EvaluationResult.MeasurementGroup findOrCreateGroup(String label) {
for(EvaluationResult.MeasurementGroup g : groups) {
if(label.equals(g.getName())) {
return g;
}
}
return newGroup(label);
} | java |
public int numLines() {
int r = header.size();
for(MeasurementGroup m : groups) {
r += 1 + m.measurements.size();
}
return r;
} | java |
public static EvaluationResult findOrCreate(ResultHierarchy hierarchy, Result parent, String name, String shortname) {
ArrayList<EvaluationResult> ers = ResultUtil.filterResults(hierarchy, parent, EvaluationResult.class);
EvaluationResult ev = null;
for(EvaluationResult e : ers) {
if(shortname.equals(... | java |
public Document cloneDocument(DOMImplementation domImpl, Document document) {
Element root = document.getDocumentElement();
// New document
Document result = domImpl.createDocument(root.getNamespaceURI(), root.getNodeName(), null);
Element rroot = result.getDocumentElement();
// Cloning the document... | java |
public Node cloneNode(Document doc, Node eold) {
return doc.importNode(eold, true);
} | java |
public void copyAttributes(Document doc, Element eold, Element enew) {
if(eold.hasAttributes()) {
NamedNodeMap attr = eold.getAttributes();
int len = attr.getLength();
for(int i = 0; i < len; i++) {
enew.setAttributeNode((Attr) doc.importNode(attr.item(i), true));
}
}
} | java |
protected String getFilename(Object result, String filenamepre) {
if(filenamepre == null || filenamepre.length() == 0) {
filenamepre = "result";
}
for(int i = 0;; i++) {
String filename = i > 0 ? filenamepre + "-" + i : filenamepre;
Object existing = filenames.get(filename);
if(exist... | java |
@SuppressWarnings("unchecked")
public void output(Database db, Result r, StreamFactory streamOpener, Pattern filter) throws IOException {
List<Relation<?>> ra = new LinkedList<>();
List<OrderingResult> ro = new LinkedList<>();
List<Clustering<?>> rc = new LinkedList<>();
List<IterableResult<?>> ri = n... | java |
@Override
public void writeExternal(ObjectOutput out) throws IOException {
super.writeExternal(out);
out.writeObject(approximation);
} | java |
@Override
public void readExternal(ObjectInput in) throws IOException, ClassNotFoundException {
super.readExternal(in);
approximation = (PolynomialApproximation) in.readObject();
} | java |
private WritableIntegerDataStore computeSubtreeSizes(DBIDs order) {
WritableIntegerDataStore siz = DataStoreUtil.makeIntegerStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP, 1);
DBIDVar v1 = DBIDUtil.newVar();
for(DBIDIter it = order.iter(); it.valid(); it.advance()) {
if(DBIDUtil.e... | java |
private WritableDoubleDataStore computeMaxHeight() {
WritableDoubleDataStore maxheight = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP, 0.);
DBIDVar v1 = DBIDUtil.newVar();
for(DBIDIter it = ids.iter(); it.valid(); it.advance()) {
double d = parentDistance... | java |
public ArrayDBIDs topologicalSort() {
ArrayModifiableDBIDs ids = DBIDUtil.newArray(this.ids);
if(mergeOrder != null) {
ids.sort(new DataStoreUtil.AscendingByIntegerDataStore(mergeOrder));
WritableDoubleDataStore maxheight = computeMaxHeight();
ids.sort(new Sorter(maxheight));
maxheight.d... | java |
public static int[] range(int start, int end) {
int[] out = new int[end - start];
for(int i = 0, j = start; j < end; i++, j++) {
out[i] = j;
}
return out;
} | java |
private void doReverseKNNQuery(int k, DBIDRef q, ModifiableDoubleDBIDList result, ModifiableDBIDs candidates) {
final ComparableMinHeap<MTreeSearchCandidate> pq = new ComparableMinHeap<>();
// push root
pq.add(new MTreeSearchCandidate(0., getRootID(), null, Double.NaN));
// search in tree
while(!p... | java |
protected void expirePage(P page) {
if(LOG.isDebuggingFine()) {
LOG.debugFine("Write to backing:" + page.getPageID());
}
if (page.isDirty()) {
file.writePage(page);
}
} | java |
public void setCacheSize(int cacheSize) {
this.cacheSize = cacheSize;
long toDelete = map.size() - this.cacheSize;
if(toDelete <= 0) {
return;
}
List<Integer> keys = new ArrayList<>(map.keySet());
Collections.reverse(keys);
for(Integer id : keys) {
P page = map.remove(id);
... | java |
public static String getFilenameExtension(String name) {
if(name == null) {
return null;
}
int index = name.lastIndexOf('.');
return index < 0 ? null : name.substring(index + 1).toLowerCase();
} | java |
public static InputStream tryGzipInput(InputStream in) throws IOException {
// try autodetecting gzip compression.
if(!in.markSupported()) {
PushbackInputStream pb = new PushbackInputStream(in, 16);
// read a magic from the file header, and push it back
byte[] magic = { 0, 0 };
int r = p... | java |
public static File locateFile(String name, String basedir) {
// Try exact match first.
File f = new File(name);
if(f.exists()) {
return f;
}
// Try with base directory
if(basedir != null) {
if((f = new File(basedir, name)).exists()) {
return f;
}
}
// try stripp... | java |
protected void addInternal(double dist, int id) {
if(size == dists.length) {
grow();
}
dists[size] = dist;
ids[size] = id;
++size;
} | java |
protected void grow() {
if(dists == EMPTY_DISTS) {
dists = new double[INITIAL_SIZE];
ids = new int[INITIAL_SIZE];
return;
}
final int len = dists.length;
final int newlength = len + (len >> 1) + 1;
double[] odists = dists;
dists = new double[newlength];
System.arraycopy(odi... | java |
protected void reverse() {
for(int i = 0, j = size - 1; i < j; i++, j--) {
double tmpd = dists[j];
dists[j] = dists[i];
dists[i] = tmpd;
int tmpi = ids[j];
ids[j] = ids[i];
ids[i] = tmpi;
}
} | java |
public void truncate(int newsize) {
if(newsize < size) {
double[] odists = dists;
dists = new double[newsize];
System.arraycopy(odists, 0, dists, 0, newsize);
int[] oids = ids;
ids = new int[newsize];
System.arraycopy(oids, 0, ids, 0, newsize);
size = newsize;
}
} | java |
private RectangleArranger<PlotItem> arrangeVisualizations(double width, double height) {
if(!(width > 0. && height > 0.)) {
LOG.warning("No size information during arrange()", new Throwable());
return new RectangleArranger<>(1., 1.);
}
RectangleArranger<PlotItem> plotmap = new RectangleArranger<... | java |
public void initialize(double ratio) {
if(!(ratio > 0 && ratio < Double.POSITIVE_INFINITY)) {
LOG.warning("Invalid ratio: " + ratio, new Throwable());
ratio = 1.4;
}
this.ratio = ratio;
if(plot != null) {
LOG.warning("Already initialized.");
lazyRefresh();
return;
}
... | java |
private void initializePlot() {
plot = new VisualizationPlot();
{ // Add a background element:
CSSClass cls = new CSSClass(this, "background");
final String bgcol = context.getStyleLibrary().getBackgroundColor(StyleLibrary.PAGE);
cls.setStatement(SVGConstants.CSS_FILL_PROPERTY, bgcol);
p... | java |
private Visualization embedOrThumbnail(final int thumbsize, PlotItem it, VisualizationTask task, Element parent) {
final Visualization vis;
if(!single) {
vis = task.getFactory().makeVisualizationOrThumbnail(context, task, plot, it.w, it.h, it.proj, thumbsize);
}
else {
vis = task.getFactory(... | java |
protected boolean visibleInOverview(VisualizationTask task) {
return task.isVisible() && !task.has(single ? RenderFlag.NO_EMBED : RenderFlag.NO_THUMBNAIL);
} | java |
private void recalcViewbox() {
final Element root = plot.getRoot();
// Reset plot attributes
SVGUtil.setAtt(root, SVGConstants.SVG_WIDTH_ATTRIBUTE, "20cm");
SVGUtil.setAtt(root, SVGConstants.SVG_HEIGHT_ATTRIBUTE, SVGUtil.fmt(20 * plotmap.getHeight() / plotmap.getWidth()) + "cm");
String vb = "0 0 " ... | java |
protected void triggerSubplotSelectEvent(PlotItem it) {
// forward event to all listeners.
for(ActionListener actionListener : actionListeners) {
actionListener.actionPerformed(new DetailViewSelectedEvent(this, ActionEvent.ACTION_PERFORMED, null, 0, it));
}
} | java |
public static double cdf(double val, double mu, double sigma, double xi) {
val = (val - mu) / sigma;
// Check support:
if(val < 0) {
return 0.;
}
if(xi < 0 && val > -1. / xi) {
return 1.;
}
return 1 - FastMath.pow(1 + xi * val, -1. / xi);
} | java |
public static double quantile(double val, double mu, double sigma, double xi) {
if(val < 0.0 || val > 1.0) {
return Double.NaN;
}
if(xi == 0.) {
return mu - sigma * FastMath.log(1 - val);
}
return mu - sigma / xi * (1 - FastMath.pow(1 - val, -xi));
} | java |
public Result run(Database database, Relation<O> relation, Relation<NumberVector> radrel) {
if(queries != null) {
throw new AbortException("This 'run' method will not use the given query set!");
}
// Get a distance and kNN query instance.
DistanceQuery<O> distQuery = database.getDistanceQuery(rela... | java |
public static long[] random(int card, int capacity, Random random) {
if(card < 0 || card > capacity) {
throw new IllegalArgumentException("Cannot set " + card + " out of " + capacity + " bits.");
}
// FIXME: Avoid recomputing the cardinality.
if(card < capacity >>> 1) {
long[] bitset = BitsU... | java |
public static long[] copy(long[] v, int mincap) {
int words = ((mincap - 1) >>> LONG_LOG2_SIZE) + 1;
if(v.length == words) {
return Arrays.copyOf(v, v.length);
}
long[] ret = new long[words];
System.arraycopy(v, 0, ret, 0, Math.min(v.length, words));
return ret;
} | java |
public static boolean isZero(long[] v) {
for(int i = 0; i < v.length; i++) {
if(v[i] != 0) {
return false;
}
}
return true;
} | java |
public static long[] setI(long[] v, long[] o) {
assert (o.length <= v.length) : "Bit set sizes do not agree.";
final int max = Math.min(v.length, o.length);
for(int i = 0; i < max; i++) {
v[i] = o[i];
}
return v;
} | java |
public static void onesI(long[] v, int bits) {
final int fillWords = bits >>> LONG_LOG2_SIZE;
final int fillBits = bits & LONG_LOG2_MASK;
Arrays.fill(v, 0, fillWords, LONG_ALL_BITS);
if(fillBits > 0) {
v[fillWords] = (1L << fillBits) - 1;
}
if(fillWords + 1 < v.length) {
Arrays.fill(... | java |
public static long[] xorI(long[] v, long[] o) {
assert (o.length <= v.length) : "Bit set sizes do not agree.";
for(int i = 0; i < o.length; i++) {
v[i] ^= o[i];
}
return v;
} | java |
public static long[] orI(long[] v, long[] o) {
assert (o.length <= v.length) : "Bit set sizes do not agree.";
final int max = Math.min(v.length, o.length);
for(int i = 0; i < max; i++) {
v[i] |= o[i];
}
return v;
} | java |
public static long[] andI(long[] v, long[] o) {
int i = 0;
for(; i < o.length; i++) {
v[i] &= o[i];
}
// Zero higher words
Arrays.fill(v, i, v.length, 0);
return v;
} | java |
public static long[] nandI(long[] v, long[] o) {
int i = 0;
for(; i < o.length; i++) {
v[i] &= ~o[i];
}
return v;
} | java |
public static long[] invertI(long[] v) {
for(int i = 0; i < v.length; i++) {
v[i] = ~v[i];
}
return v;
} | java |
public static long cycleLeftC(long v, int shift, int len) {
return shift == 0 ? v : shift < 0 ? cycleRightC(v, -shift, len) : //
(((v) << (shift)) | ((v) >>> ((len) - (shift)))) & ((1 << len) - 1);
} | java |
public static long[] cycleLeftI(long[] v, int shift, int len) {
long[] t = copy(v, len, shift);
return orI(shiftRightI(v, len - shift), truncateI(t, len));
} | java |
public static int numberOfTrailingZerosSigned(long[] v) {
for(int p = 0;; p++) {
if(p == v.length) {
return -1;
}
if(v[p] != 0) {
return Long.numberOfTrailingZeros(v[p]) + p * Long.SIZE;
}
}
} | java |
public static int numberOfLeadingZerosSigned(long[] v) {
for(int p = 0, ip = v.length - 1; p < v.length; p++, ip--) {
if(v[ip] != 0) {
return Long.numberOfLeadingZeros(v[ip]) + p * Long.SIZE;
}
}
return -1;
} | java |
public static int previousClearBit(long v, int start) {
if(start < 0) {
return -1;
}
start = start < Long.SIZE ? start : Long.SIZE - 1;
long cur = ~v & (LONG_ALL_BITS >>> -(start + 1));
return cur == 0 ? -1 : 63 - Long.numberOfLeadingZeros(cur);
} | java |
public static int nextSetBit(long v, int start) {
if(start >= Long.SIZE) {
return -1;
}
start = start < 0 ? 0 : start;
long cur = v & (LONG_ALL_BITS << start);
return cur == 0 ? -1 : cur == LONG_ALL_BITS ? 0 : Long.numberOfTrailingZeros(cur);
} | java |
public static boolean intersect(long[] x, long[] y) {
final int min = (x.length < y.length) ? x.length : y.length;
for(int i = 0; i < min; i++) {
if((x[i] & y[i]) != 0L) {
return true;
}
}
return false;
} | java |
public static int intersectionSize(long[] x, long[] y) {
final int lx = x.length, ly = y.length;
final int min = (lx < ly) ? lx : ly;
int res = 0;
for(int i = 0; i < min; i++) {
res += Long.bitCount(x[i] & y[i]);
}
return res;
} | java |
public static int unionSize(long[] x, long[] y) {
final int lx = x.length, ly = y.length;
final int min = (lx < ly) ? lx : ly;
int i = 0, res = 0;
for(; i < min; i++) {
res += Long.bitCount(x[i] | y[i]);
}
for(; i < lx; i++) {
res += Long.bitCount(x[i]);
}
for(; i < ly; i++) ... | java |
public static boolean equal(long[] x, long[] y) {
if(x == null || y == null) {
return (x == null) && (y == null);
}
int p = Math.min(x.length, y.length) - 1;
for(int i = x.length - 1; i > p; i--) {
if(x[i] != 0L) {
return false;
}
}
for(int i = y.length - 1; i > p; i--)... | java |
public static int compare(long[] x, long[] y) {
if(x == null) {
return (y == null) ? 0 : -1;
}
if(y == null) {
return +1;
}
int p = Math.min(x.length, y.length) - 1;
for(int i = x.length - 1; i > p; i--) {
if(x[i] != 0) {
return +1;
}
}
for(int i = y.lengt... | java |
@Override
public int compareTo(DistanceEntry<E> o) {
int comp = Double.compare(distance, o.distance);
return comp;
// return comp != 0 ? comp :
// entry.getEntryID().compareTo(o.entry.getEntryID());
} | java |
private double[] knnDistances(O object) {
KNNList knns = knnq.getKNNForObject(object, getKmax() - 1);
double[] distances = new double[getKmax()];
int i = 0;
for(DoubleDBIDListIter iter = knns.iter(); iter.valid() && i < getKmax(); iter.advance(), i++) {
distances[i] = iter.doubleValue();
}
... | java |
protected double downsample(double[] data, int start, int end, int size) {
double sum = 0;
for (int i = start; i < end; i++) {
sum += data[i];
}
return sum;
} | java |
public void setRotationZ(double rotationZ) {
this.rotationZ = rotationZ;
this.cosZ = FastMath.cos(rotationZ);
this.sinZ = FastMath.sin(rotationZ);
fireCameraChangedEvent();
} | java |
public void apply(GL2 gl) {
// 3D projection
gl.glMatrixMode(GL2.GL_PROJECTION);
gl.glLoadIdentity();
// Perspective.
glu.gluPerspective(35, ratio, 1, 1000);
glu.gluLookAt(distance * sinZ, distance * -cosZ, height, // pos
0, 0, .5, // center
0, 0, 1 // up
);
// Change bac... | java |
public void project(double x, double y, double z, double[] out) {
glu.gluProject(x, y, z, modelview, 0, projection, 0, viewp, 0, out, 0);
} | java |
public void addCameraListener(CameraListener lis) {
if (listeners == null) {
listeners = new ArrayList<>(5);
}
listeners.add(lis);
} | java |
public static AffineTransformation axisProjection(int dim, int ax1, int ax2) {
// setup a projection to get the data into the interval -1:+1 in each
// dimension with the intended-to-see dimensions first.
AffineTransformation proj = AffineTransformation.reorderAxesTransformation(dim, ax1, ax2);
// Assum... | java |
protected ApproximationLine conservativeKnnDistanceApproximation(int k_max) {
// determine k_0, y_1, y_kmax
int k_0 = k_max;
double y_1 = Double.NEGATIVE_INFINITY;
double y_kmax = Double.NEGATIVE_INFINITY;
for(int i = 0; i < getNumEntries(); i++) {
MkCoPEntry entry = getEntry(i);
Approx... | java |
protected ApproximationLine progressiveKnnDistanceApproximation(int k_max) {
if(!isLeaf()) {
throw new UnsupportedOperationException("Progressive KNN-distance approximation " + "is only vailable in leaf nodes!");
}
// determine k_0, y_1, y_kmax
int k_0 = 0;
double y_1 = Double.POSITIVE_INFINI... | java |
public CSSClass addClass(CSSClass clss) throws CSSNamingConflict {
CSSClass existing = store.get(clss.getName());
if (existing != null && existing.getOwner() != null && existing.getOwner() != clss.getOwner()) {
throw new CSSNamingConflict("CSS class naming conflict between "+clss.getOwner().toString()+" a... | java |
public synchronized void removeClass(CSSClass clss) {
CSSClass existing = store.get(clss.getName());
if (existing == clss) {
store.remove(existing.getName());
}
} | java |
public CSSClass getClass(String name, Object owner) throws CSSNamingConflict {
CSSClass existing = store.get(name);
// Not found.
if (existing == null) {
return null;
}
// Different owner
if (owner != null && existing.getOwner() != owner) {
throw new CSSNamingConflict("CSS class nami... | java |
public void serialize(StringBuilder buf) {
for (CSSClass clss : store.values()) {
clss.appendCSSDefinition(buf);
}
} | java |
public boolean mergeCSSFrom(CSSClassManager other) throws CSSNamingConflict {
for (CSSClass clss : other.getClasses()) {
this.addClass(clss);
}
return true;
} | java |
public void updateStyleElement(Document document, Element style) {
StringBuilder buf = new StringBuilder();
serialize(buf);
Text cont = document.createTextNode(buf.toString());
while (style.hasChildNodes()) {
style.removeChild(style.getFirstChild());
}
style.appendChild(cont);
} | java |
private static double calculate_MDEF_norm(Node sn, Node cg) {
// get the square sum of the counting neighborhoods box counts
long sq = sn.getSquareSum(cg.getLevel() - sn.getLevel());
/*
* if the square sum is equal to box count of the sampling Neighborhood then
* n_hat is equal one, and as cg need... | java |
public void writeBundleStream(BundleStreamSource source, WritableByteChannel output) throws IOException {
ByteBuffer buffer = ByteBuffer.allocateDirect(INITIAL_BUFFER);
DBIDVar var = DBIDUtil.newVar();
ByteBufferSerializer<?>[] serializers = null;
loop: while(true) {
BundleStreamSource.Event ev =... | java |
private void flushBuffer(ByteBuffer buffer, WritableByteChannel output) throws IOException {
buffer.flip();
output.write(buffer);
buffer.flip();
buffer.limit(buffer.capacity());
} | java |
private ByteBuffer ensureBuffer(int size, ByteBuffer buffer, WritableByteChannel output) throws IOException {
if(buffer.remaining() >= size) {
return buffer;
}
flushBuffer(buffer, output);
if(buffer.remaining() >= size) {
return buffer;
}
// Aggressively grow the buffer
return By... | java |
private ByteBufferSerializer<?>[] writeHeader(BundleStreamSource source, ByteBuffer buffer, WritableByteChannel output) throws IOException {
final BundleMeta meta = source.getMeta();
final int nummeta = meta.size();
@SuppressWarnings("rawtypes")
final ByteBufferSerializer[] serializers = new ByteBufferS... | java |
protected void runDBSCAN(Relation<O> relation, RangeQuery<O> rangeQuery) {
final int size = relation.size();
FiniteProgress objprog = LOG.isVerbose() ? new FiniteProgress("Processing objects", size, LOG) : null;
IndefiniteProgress clusprog = LOG.isVerbose() ? new IndefiniteProgress("Number of clusters", LOG... | java |
protected void expandCluster(Relation<O> relation, RangeQuery<O> rangeQuery, DBIDRef startObjectID, ArrayModifiableDBIDs seeds, FiniteProgress objprog, IndefiniteProgress clusprog) {
DoubleDBIDList neighbors = rangeQuery.getRangeForDBID(startObjectID, epsilon);
ncounter += neighbors.size();
// startObject ... | java |
private void processNeighbors(DoubleDBIDListIter neighbor, ModifiableDBIDs currentCluster, ArrayModifiableDBIDs seeds) {
final boolean ismetric = getDistanceFunction().isMetric();
for(; neighbor.valid(); neighbor.advance()) {
if(processedIDs.add(neighbor)) {
if(!ismetric || neighbor.doubleValue() ... | java |
private double loglikelihoodAnomalous(DBIDs anomalousObjs) {
return anomalousObjs.isEmpty() ? 0 : anomalousObjs.size() * -FastMath.log(anomalousObjs.size());
} | java |
private double loglikelihoodNormal(DBIDs objids, SetDBIDs anomalous, CovarianceMatrix builder, Relation<V> relation) {
double[] mean = builder.getMeanVector();
final LUDecomposition lu = new LUDecomposition(builder.makeSampleMatrix());
double[][] covInv = lu.inverse();
// for each object compute probabi... | java |
private DoubleMinMax exactMinMax(Relation<O> relation, DistanceQuery<O> distFunc) {
final FiniteProgress progress = LOG.isVerbose() ? new FiniteProgress("Exact fitting distance computations", relation.size(), LOG) : null;
DoubleMinMax minmax = new DoubleMinMax();
// find exact minimum and maximum first.
... | java |
@Override
protected void preInsert(RdKNNEntry entry) {
KNNHeap knns_o = DBIDUtil.newHeap(settings.k_max);
preInsert(entry, getRootEntry(), knns_o);
} | java |
@Override
protected void postDelete(RdKNNEntry entry) {
// reverse knn of o
ModifiableDoubleDBIDList rnns = DBIDUtil.newDistanceDBIDList();
doReverseKNN(getRoot(), ((RdKNNLeafEntry) entry).getDBID(), rnns);
// knn of rnn
ArrayModifiableDBIDs ids = DBIDUtil.newArray(rnns);
ids.sort();
List... | java |
private void doReverseKNN(RdKNNNode node, DBID oid, ModifiableDoubleDBIDList result) {
if(node.isLeaf()) {
for(int i = 0; i < node.getNumEntries(); i++) {
RdKNNLeafEntry entry = (RdKNNLeafEntry) node.getEntry(i);
double distance = distanceQuery.distance(entry.getDBID(), oid);
if(distan... | java |
private void doBulkReverseKNN(RdKNNNode node, DBIDs ids, Map<DBID, ModifiableDoubleDBIDList> result) {
if(node.isLeaf()) {
for(int i = 0; i < node.getNumEntries(); i++) {
RdKNNLeafEntry entry = (RdKNNLeafEntry) node.getEntry(i);
for(DBIDIter iter = ids.iter(); iter.valid(); iter.advance()) {
... | java |
private void checkDistanceFunction(SpatialPrimitiveDistanceFunction<? super O> distanceFunction) {
if(!settings.distanceFunction.equals(distanceFunction)) {
throw new IllegalArgumentException("Parameter distanceFunction must be an instance of " + this.distanceQuery.getClass() + ", but is " + distanceFunction.... | java |
@Override
public final void insertAll(DBIDs ids) {
if(ids.isEmpty() || (ids.size() == 1)) {
return;
}
// Make an example leaf
if(canBulkLoad()) {
List<RdKNNEntry> leafs = new ArrayList<>(ids.size());
for(DBIDIter iter = ids.iter(); iter.valid(); iter.advance()) {
leafs.add(c... | java |
public int correlationDistance(PCAFilteredResult pca1, PCAFilteredResult pca2, int dimensionality) {
// TODO: Can we delay copying the matrixes?
// pca of rv1
double[][] v1t = copy(pca1.getEigenvectors());
double[][] v1t_strong = pca1.getStrongEigenvectors();
int lambda1 = pca1.getCorrelationDimensi... | java |
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