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elki-project/elki | elki-core-util/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/FormatUtil.java | FormatUtil.format | public static String format(float[] f) {
return (f == null) ? "null" : (f.length == 0) ? "" : //
formatTo(new StringBuilder(), f, ", ").toString();
} | java | public static String format(float[] f) {
return (f == null) ? "null" : (f.length == 0) ? "" : //
formatTo(new StringBuilder(), f, ", ").toString();
} | [
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elki-project/elki | elki-core-util/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/FormatUtil.java | FormatUtil.format | public static String format(int[] a, String sep) {
return (a == null) ? "null" : (a.length == 0) ? "" : //
formatTo(new StringBuilder(), a, sep).toString();
} | java | public static String format(int[] a, String sep) {
return (a == null) ? "null" : (a.length == 0) ? "" : //
formatTo(new StringBuilder(), a, sep).toString();
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elki-project/elki | elki-core-util/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/FormatUtil.java | FormatUtil.format | public static String format(boolean[] b, final String sep) {
return (b == null) ? "null" : (b.length == 0) ? "" : //
formatTo(new StringBuilder(), b, ", ").toString();
} | java | public static String format(boolean[] b, final String sep) {
return (b == null) ? "null" : (b.length == 0) ? "" : //
formatTo(new StringBuilder(), b, ", ").toString();
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elki-project/elki | elki-core-util/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/FormatUtil.java | FormatUtil.format | public static String format(double[][] d) {
return d == null ? "null" : (d.length == 0) ? "[]" : //
formatTo(new StringBuilder().append("[\n"), d, " [", "]\n", ", ", NF2).append(']').toString();
} | java | public static String format(double[][] d) {
return d == null ? "null" : (d.length == 0) ? "[]" : //
formatTo(new StringBuilder().append("[\n"), d, " [", "]\n", ", ", NF2).append(']').toString();
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elki-project/elki | elki-core-util/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/FormatUtil.java | FormatUtil.format | public static String format(double[][] m, int w, int d, String pre, String pos, String csep) {
DecimalFormat format = new DecimalFormat();
format.setDecimalFormatSymbols(new DecimalFormatSymbols(Locale.US));
format.setMinimumIntegerDigits(1);
format.setMaximumFractionDigits(d);
format.setMinimumFractionDigits(d);
format.setGroupingUsed(false);
StringBuilder msg = new StringBuilder();
for(int i = 0; i < m.length; i++) {
double[] row = m[i];
msg.append(pre);
for(int j = 0; j < row.length; j++) {
if(j > 0) {
msg.append(csep);
}
String s = format.format(row[j]); // format the number
whitespace(msg, w - s.length()).append(s);
}
msg.append(pos);
}
return msg.toString();
} | java | public static String format(double[][] m, int w, int d, String pre, String pos, String csep) {
DecimalFormat format = new DecimalFormat();
format.setDecimalFormatSymbols(new DecimalFormatSymbols(Locale.US));
format.setMinimumIntegerDigits(1);
format.setMaximumFractionDigits(d);
format.setMinimumFractionDigits(d);
format.setGroupingUsed(false);
StringBuilder msg = new StringBuilder();
for(int i = 0; i < m.length; i++) {
double[] row = m[i];
msg.append(pre);
for(int j = 0; j < row.length; j++) {
if(j > 0) {
msg.append(csep);
}
String s = format.format(row[j]); // format the number
whitespace(msg, w - s.length()).append(s);
}
msg.append(pos);
}
return msg.toString();
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elki-project/elki | elki-core-util/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/FormatUtil.java | FormatUtil.format | public static String format(double[][] m, NumberFormat nf) {
return formatTo(new StringBuilder().append("[\n"), m, " [", "]\n", ", ", nf).append("]").toString();
} | java | public static String format(double[][] m, NumberFormat nf) {
return formatTo(new StringBuilder().append("[\n"), m, " [", "]\n", ", ", nf).append("]").toString();
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elki-project/elki | elki-core-util/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/FormatUtil.java | FormatUtil.format | public static String format(Collection<String> d, String sep) {
if(d == null) {
return "null";
}
if(d.isEmpty()) {
return "";
}
if(d.size() == 1) {
return d.iterator().next();
}
int len = sep.length() * (d.size() - 1);
for(String s : d) {
len += s.length();
}
Iterator<String> it = d.iterator();
StringBuilder buffer = new StringBuilder(len) //
.append(it.next());
while(it.hasNext()) {
buffer.append(sep).append(it.next());
}
return buffer.toString();
} | java | public static String format(Collection<String> d, String sep) {
if(d == null) {
return "null";
}
if(d.isEmpty()) {
return "";
}
if(d.size() == 1) {
return d.iterator().next();
}
int len = sep.length() * (d.size() - 1);
for(String s : d) {
len += s.length();
}
Iterator<String> it = d.iterator();
StringBuilder buffer = new StringBuilder(len) //
.append(it.next());
while(it.hasNext()) {
buffer.append(sep).append(it.next());
}
return buffer.toString();
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elki-project/elki | elki-core-util/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/FormatUtil.java | FormatUtil.format | public static String format(String[] d, String sep) {
if(d == null) {
return "null";
}
if(d.length == 0) {
return "";
}
if(d.length == 1) {
return d[0];
}
int len = sep.length() * (d.length - 1);
for(String s : d) {
len += s.length();
}
StringBuilder buffer = new StringBuilder(len)//
.append(d[0]);
for(int i = 1; i < d.length; i++) {
buffer.append(sep).append(d[i]);
}
return buffer.toString();
} | java | public static String format(String[] d, String sep) {
if(d == null) {
return "null";
}
if(d.length == 0) {
return "";
}
if(d.length == 1) {
return d[0];
}
int len = sep.length() * (d.length - 1);
for(String s : d) {
len += s.length();
}
StringBuilder buffer = new StringBuilder(len)//
.append(d[0]);
for(int i = 1; i < d.length; i++) {
buffer.append(sep).append(d[i]);
}
return buffer.toString();
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elki-project/elki | elki-core-util/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/FormatUtil.java | FormatUtil.findSplitpoint | public static int findSplitpoint(String s, int width) {
// the newline (or EOS) is the fallback split position.
int in = s.indexOf(NEWLINE);
in = in < 0 ? s.length() : in;
// Good enough?
if(in < width) {
return in;
}
// otherwise, search for whitespace
int iw = s.lastIndexOf(' ', width);
// good whitespace found?
if(iw >= 0 && iw < width) {
return iw;
}
// sub-optimal splitpoint - retry AFTER the given position
int bp = nextPosition(s.indexOf(' ', width), s.indexOf(NEWLINE, width));
if(bp >= 0) {
return bp;
}
// even worse - can't split!
return s.length();
} | java | public static int findSplitpoint(String s, int width) {
// the newline (or EOS) is the fallback split position.
int in = s.indexOf(NEWLINE);
in = in < 0 ? s.length() : in;
// Good enough?
if(in < width) {
return in;
}
// otherwise, search for whitespace
int iw = s.lastIndexOf(' ', width);
// good whitespace found?
if(iw >= 0 && iw < width) {
return iw;
}
// sub-optimal splitpoint - retry AFTER the given position
int bp = nextPosition(s.indexOf(' ', width), s.indexOf(NEWLINE, width));
if(bp >= 0) {
return bp;
}
// even worse - can't split!
return s.length();
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elki-project/elki | elki-core-util/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/FormatUtil.java | FormatUtil.splitAtLastBlank | public static List<String> splitAtLastBlank(String s, int width) {
List<String> chunks = new ArrayList<>();
String tmp = s;
while(tmp.length() > 0) {
int index = findSplitpoint(tmp, width);
// store first part
chunks.add(tmp.substring(0, index));
// skip whitespace at beginning of line
while(index < tmp.length() && tmp.charAt(index) == ' ') {
index += 1;
}
// remove a newline
if(index < tmp.length() && tmp.regionMatches(index, NEWLINE, 0, NEWLINE.length())) {
index += NEWLINE.length();
}
if(index >= tmp.length()) {
break;
}
tmp = tmp.substring(index);
}
return chunks;
} | java | public static List<String> splitAtLastBlank(String s, int width) {
List<String> chunks = new ArrayList<>();
String tmp = s;
while(tmp.length() > 0) {
int index = findSplitpoint(tmp, width);
// store first part
chunks.add(tmp.substring(0, index));
// skip whitespace at beginning of line
while(index < tmp.length() && tmp.charAt(index) == ' ') {
index += 1;
}
// remove a newline
if(index < tmp.length() && tmp.regionMatches(index, NEWLINE, 0, NEWLINE.length())) {
index += NEWLINE.length();
}
if(index >= tmp.length()) {
break;
}
tmp = tmp.substring(index);
}
return chunks;
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elki-project/elki | elki-core-util/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/FormatUtil.java | FormatUtil.pad | public static String pad(String o, int len) {
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} | java | public static String pad(String o, int len) {
return o.length() >= len ? o : (o + whitespace(len - o.length()));
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elki-project/elki | elki-core-util/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/FormatUtil.java | FormatUtil.padRightAligned | public static String padRightAligned(String o, int len) {
return o.length() >= len ? o : (whitespace(len - o.length()) + o);
} | java | public static String padRightAligned(String o, int len) {
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elki-project/elki | elki-core-util/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/FormatUtil.java | FormatUtil.formatTimeDelta | public static String formatTimeDelta(long time, CharSequence sep) {
final StringBuilder sb = new StringBuilder();
final Formatter fmt = new Formatter(sb);
for(int i = TIME_UNIT_SIZES.length - 1; i >= 0; --i) {
// We do not include ms if we are in the order of minutes.
if(i == 0 && sb.length() > 4) {
continue;
}
// Separator
if(sb.length() > 0) {
sb.append(sep);
}
final long acValue = time / TIME_UNIT_SIZES[i];
time = time % TIME_UNIT_SIZES[i];
if(!(acValue == 0 && sb.length() == 0)) {
fmt.format("%0" + TIME_UNIT_DIGITS[i] + "d%s", Long.valueOf(acValue), TIME_UNIT_NAMES[i]);
}
}
fmt.close();
return sb.toString();
} | java | public static String formatTimeDelta(long time, CharSequence sep) {
final StringBuilder sb = new StringBuilder();
final Formatter fmt = new Formatter(sb);
for(int i = TIME_UNIT_SIZES.length - 1; i >= 0; --i) {
// We do not include ms if we are in the order of minutes.
if(i == 0 && sb.length() > 4) {
continue;
}
// Separator
if(sb.length() > 0) {
sb.append(sep);
}
final long acValue = time / TIME_UNIT_SIZES[i];
time = time % TIME_UNIT_SIZES[i];
if(!(acValue == 0 && sb.length() == 0)) {
fmt.format("%0" + TIME_UNIT_DIGITS[i] + "d%s", Long.valueOf(acValue), TIME_UNIT_NAMES[i]);
}
}
fmt.close();
return sb.toString();
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elki-project/elki | elki-core-util/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/FormatUtil.java | FormatUtil.appendZeros | public static StringBuilder appendZeros(StringBuilder buf, int zeros) {
for(int i = zeros; i > 0; i -= ZEROPADDING.length) {
buf.append(ZEROPADDING, 0, i < ZEROPADDING.length ? i : ZEROPADDING.length);
}
return buf;
} | java | public static StringBuilder appendZeros(StringBuilder buf, int zeros) {
for(int i = zeros; i > 0; i -= ZEROPADDING.length) {
buf.append(ZEROPADDING, 0, i < ZEROPADDING.length ? i : ZEROPADDING.length);
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elki-project/elki | elki-core-util/src/main/java/de/lmu/ifi/dbs/elki/utilities/io/FormatUtil.java | FormatUtil.appendSpace | public static StringBuilder appendSpace(StringBuilder buf, int spaces) {
for(int i = spaces; i > 0; i -= SPACEPADDING.length) {
buf.append(SPACEPADDING, 0, i < SPACEPADDING.length ? i : SPACEPADDING.length);
}
return buf;
} | java | public static StringBuilder appendSpace(StringBuilder buf, int spaces) {
for(int i = spaces; i > 0; i -= SPACEPADDING.length) {
buf.append(SPACEPADDING, 0, i < SPACEPADDING.length ? i : SPACEPADDING.length);
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elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/optics/AbstractOPTICSVisualization.java | AbstractOPTICSVisualization.makeLayerElement | protected void makeLayerElement() {
plotwidth = StyleLibrary.SCALE;
plotheight = StyleLibrary.SCALE / optics.getOPTICSPlot(context).getRatio();
final double margin = context.getStyleLibrary().getSize(StyleLibrary.MARGIN);
layer = SVGUtil.svgElement(svgp.getDocument(), SVGConstants.SVG_G_TAG);
final String transform = SVGUtil.makeMarginTransform(getWidth(), getHeight(), plotwidth, plotheight, margin * .5, margin * .5, margin * 1.5, margin * .5);
SVGUtil.setAtt(layer, SVGConstants.SVG_TRANSFORM_ATTRIBUTE, transform);
} | java | protected void makeLayerElement() {
plotwidth = StyleLibrary.SCALE;
plotheight = StyleLibrary.SCALE / optics.getOPTICSPlot(context).getRatio();
final double margin = context.getStyleLibrary().getSize(StyleLibrary.MARGIN);
layer = SVGUtil.svgElement(svgp.getDocument(), SVGConstants.SVG_G_TAG);
final String transform = SVGUtil.makeMarginTransform(getWidth(), getHeight(), plotwidth, plotheight, margin * .5, margin * .5, margin * 1.5, margin * .5);
SVGUtil.setAtt(layer, SVGConstants.SVG_TRANSFORM_ATTRIBUTE, transform);
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elki-project/elki | elki-input/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/LinearDiscriminantAnalysisFilter.java | LinearDiscriminantAnalysisFilter.computeCentroids | protected List<Centroid> computeCentroids(int dim, List<V> vectorcolumn, List<ClassLabel> keys, Map<ClassLabel, IntList> classes) {
final int numc = keys.size();
List<Centroid> centroids = new ArrayList<>(numc);
for(int i = 0; i < numc; i++) {
Centroid c = new Centroid(dim);
for(IntIterator it = classes.get(keys.get(i)).iterator(); it.hasNext();) {
c.put(vectorcolumn.get(it.nextInt()));
}
centroids.add(c);
}
return centroids;
} | java | protected List<Centroid> computeCentroids(int dim, List<V> vectorcolumn, List<ClassLabel> keys, Map<ClassLabel, IntList> classes) {
final int numc = keys.size();
List<Centroid> centroids = new ArrayList<>(numc);
for(int i = 0; i < numc; i++) {
Centroid c = new Centroid(dim);
for(IntIterator it = classes.get(keys.get(i)).iterator(); it.hasNext();) {
c.put(vectorcolumn.get(it.nextInt()));
}
centroids.add(c);
}
return centroids;
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elki-project/elki | elki-index-mtree/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxTreeNode.java | MkMaxTreeNode.kNNDistance | protected double kNNDistance() {
double knnDist = 0.;
for(int i = 0; i < getNumEntries(); i++) {
MkMaxEntry entry = getEntry(i);
knnDist = Math.max(knnDist, entry.getKnnDistance());
}
return knnDist;
} | java | protected double kNNDistance() {
double knnDist = 0.;
for(int i = 0; i < getNumEntries(); i++) {
MkMaxEntry entry = getEntry(i);
knnDist = Math.max(knnDist, entry.getKnnDistance());
}
return knnDist;
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elki-project/elki | elki-index-mtree/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxTreeNode.java | MkMaxTreeNode.adjustEntry | @Override
public boolean adjustEntry(MkMaxEntry entry, DBID routingObjectID, double parentDistance, AbstractMTree<O, MkMaxTreeNode<O>, MkMaxEntry, ?> mTree) {
super.adjustEntry(entry, routingObjectID, parentDistance, mTree);
// adjust knn distance
entry.setKnnDistance(kNNDistance());
return true; // TODO: improve
} | java | @Override
public boolean adjustEntry(MkMaxEntry entry, DBID routingObjectID, double parentDistance, AbstractMTree<O, MkMaxTreeNode<O>, MkMaxEntry, ?> mTree) {
super.adjustEntry(entry, routingObjectID, parentDistance, mTree);
// adjust knn distance
entry.setKnnDistance(kNNDistance());
return true; // TODO: improve
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elki-project/elki | elki-index-mtree/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxTreeNode.java | MkMaxTreeNode.integrityCheckParameters | @Override
protected void integrityCheckParameters(MkMaxEntry parentEntry, MkMaxTreeNode<O> parent, int index, AbstractMTree<O, MkMaxTreeNode<O>, MkMaxEntry, ?> mTree) {
super.integrityCheckParameters(parentEntry, parent, index, mTree);
// test if knn distance is correctly set
MkMaxEntry entry = parent.getEntry(index);
double knnDistance = kNNDistance();
if(Math.abs(entry.getKnnDistance() - knnDistance) > 0) {
throw new RuntimeException("Wrong knnDistance in node " + parent.getPageID() + " at index " + index + " (child " + entry + ")" + "\nsoll: " + knnDistance + ",\n ist: " + entry.getKnnDistance());
}
} | java | @Override
protected void integrityCheckParameters(MkMaxEntry parentEntry, MkMaxTreeNode<O> parent, int index, AbstractMTree<O, MkMaxTreeNode<O>, MkMaxEntry, ?> mTree) {
super.integrityCheckParameters(parentEntry, parent, index, mTree);
// test if knn distance is correctly set
MkMaxEntry entry = parent.getEntry(index);
double knnDistance = kNNDistance();
if(Math.abs(entry.getKnnDistance() - knnDistance) > 0) {
throw new RuntimeException("Wrong knnDistance in node " + parent.getPageID() + " at index " + index + " (child " + entry + ")" + "\nsoll: " + knnDistance + ",\n ist: " + entry.getKnnDistance());
}
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elki-project/elki | elki-database/src/main/java/de/lmu/ifi/dbs/elki/database/StaticArrayDatabase.java | StaticArrayDatabase.initialize | @Override
public void initialize() {
if(databaseConnection == null) {
return; // Supposedly we initialized already.
}
if(LOG.isDebugging()) {
LOG.debugFine("Loading data from database connection.");
}
MultipleObjectsBundle bundle = databaseConnection.loadData();
// Run at most once.
databaseConnection = null;
// Find DBIDs for bundle
{
DBIDs bids = bundle.getDBIDs();
if(bids instanceof ArrayStaticDBIDs) {
this.ids = (ArrayStaticDBIDs) bids;
}
else if(bids == null) {
this.ids = DBIDUtil.generateStaticDBIDRange(bundle.dataLength());
}
else {
this.ids = (ArrayStaticDBIDs) DBIDUtil.makeUnmodifiable(DBIDUtil.ensureArray(bids));
}
}
// Replace id representation (it would be nicer if we would not need
// DBIDView at all)
this.idrep = new DBIDView(this.ids);
relations.add(this.idrep);
getHierarchy().add(this, idrep);
DBIDArrayIter it = this.ids.iter();
int numrel = bundle.metaLength();
for(int i = 0; i < numrel; i++) {
SimpleTypeInformation<?> meta = bundle.meta(i);
@SuppressWarnings("unchecked")
SimpleTypeInformation<Object> ometa = (SimpleTypeInformation<Object>) meta;
WritableDataStore<Object> store = DataStoreUtil.makeStorage(ids, DataStoreFactory.HINT_DB, ometa.getRestrictionClass());
for(it.seek(0); it.valid(); it.advance()) {
store.put(it, bundle.data(it.getOffset(), i));
}
Relation<?> relation = new MaterializedRelation<>(ometa, ids, null, store);
relations.add(relation);
getHierarchy().add(this, relation);
// Try to add indexes where appropriate
for(IndexFactory<?> factory : indexFactories) {
if(factory.getInputTypeRestriction().isAssignableFromType(ometa)) {
@SuppressWarnings("unchecked")
final IndexFactory<Object> ofact = (IndexFactory<Object>) factory;
@SuppressWarnings("unchecked")
final Relation<Object> orep = (Relation<Object>) relation;
final Index index = ofact.instantiate(orep);
Duration duration = LOG.isStatistics() ? LOG.newDuration(index.getClass().getName() + ".construction").begin() : null;
index.initialize();
if(duration != null) {
LOG.statistics(duration.end());
}
getHierarchy().add(relation, index);
}
}
}
// fire insertion event
eventManager.fireObjectsInserted(ids);
} | java | @Override
public void initialize() {
if(databaseConnection == null) {
return; // Supposedly we initialized already.
}
if(LOG.isDebugging()) {
LOG.debugFine("Loading data from database connection.");
}
MultipleObjectsBundle bundle = databaseConnection.loadData();
// Run at most once.
databaseConnection = null;
// Find DBIDs for bundle
{
DBIDs bids = bundle.getDBIDs();
if(bids instanceof ArrayStaticDBIDs) {
this.ids = (ArrayStaticDBIDs) bids;
}
else if(bids == null) {
this.ids = DBIDUtil.generateStaticDBIDRange(bundle.dataLength());
}
else {
this.ids = (ArrayStaticDBIDs) DBIDUtil.makeUnmodifiable(DBIDUtil.ensureArray(bids));
}
}
// Replace id representation (it would be nicer if we would not need
// DBIDView at all)
this.idrep = new DBIDView(this.ids);
relations.add(this.idrep);
getHierarchy().add(this, idrep);
DBIDArrayIter it = this.ids.iter();
int numrel = bundle.metaLength();
for(int i = 0; i < numrel; i++) {
SimpleTypeInformation<?> meta = bundle.meta(i);
@SuppressWarnings("unchecked")
SimpleTypeInformation<Object> ometa = (SimpleTypeInformation<Object>) meta;
WritableDataStore<Object> store = DataStoreUtil.makeStorage(ids, DataStoreFactory.HINT_DB, ometa.getRestrictionClass());
for(it.seek(0); it.valid(); it.advance()) {
store.put(it, bundle.data(it.getOffset(), i));
}
Relation<?> relation = new MaterializedRelation<>(ometa, ids, null, store);
relations.add(relation);
getHierarchy().add(this, relation);
// Try to add indexes where appropriate
for(IndexFactory<?> factory : indexFactories) {
if(factory.getInputTypeRestriction().isAssignableFromType(ometa)) {
@SuppressWarnings("unchecked")
final IndexFactory<Object> ofact = (IndexFactory<Object>) factory;
@SuppressWarnings("unchecked")
final Relation<Object> orep = (Relation<Object>) relation;
final Index index = ofact.instantiate(orep);
Duration duration = LOG.isStatistics() ? LOG.newDuration(index.getClass().getName() + ".construction").begin() : null;
index.initialize();
if(duration != null) {
LOG.statistics(duration.end());
}
getHierarchy().add(relation, index);
}
}
}
// fire insertion event
eventManager.fireObjectsInserted(ids);
} | [
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elki-project/elki | elki-core-math/src/main/java/de/lmu/ifi/dbs/elki/math/spacefillingcurves/ZCurveSpatialSorter.java | ZCurveSpatialSorter.zSort | protected void zSort(List<? extends SpatialComparable> objs, int start, int end, double[] mms, int[] dims, int depth) {
final int numdim = (dims != null) ? dims.length : (mms.length >> 1);
final int edim = (dims != null) ? dims[depth] : depth;
// Find the splitting points.
final double min = mms[2 * edim], max = mms[2 * edim + 1];
double spos = (min + max) / 2.;
// Safeguard against duplicate points:
if(max - spos < STOPVAL || spos - min < STOPVAL) {
boolean ok = false;
for(int d = 0; d < numdim; d++) {
int d2 = ((dims != null) ? dims[d] : d) << 1;
if(mms[d2 + 1] - mms[d2] >= STOPVAL) {
ok = true;
break;
}
}
if(!ok) {
return;
}
}
int split = pivotizeList1D(objs, start, end, edim, spos, false);
assert (start <= split && split <= end);
int nextdim = (depth + 1) % numdim;
if(start < split - 1) {
mms[2 * edim] = min;
mms[2 * edim + 1] = spos;
zSort(objs, start, split, mms, dims, nextdim);
}
if(split < end - 1) {
mms[2 * edim] = spos;
mms[2 * edim + 1] = max;
zSort(objs, split, end, mms, dims, nextdim);
}
// Restore ranges
mms[2 * edim] = min;
mms[2 * edim + 1] = max;
} | java | protected void zSort(List<? extends SpatialComparable> objs, int start, int end, double[] mms, int[] dims, int depth) {
final int numdim = (dims != null) ? dims.length : (mms.length >> 1);
final int edim = (dims != null) ? dims[depth] : depth;
// Find the splitting points.
final double min = mms[2 * edim], max = mms[2 * edim + 1];
double spos = (min + max) / 2.;
// Safeguard against duplicate points:
if(max - spos < STOPVAL || spos - min < STOPVAL) {
boolean ok = false;
for(int d = 0; d < numdim; d++) {
int d2 = ((dims != null) ? dims[d] : d) << 1;
if(mms[d2 + 1] - mms[d2] >= STOPVAL) {
ok = true;
break;
}
}
if(!ok) {
return;
}
}
int split = pivotizeList1D(objs, start, end, edim, spos, false);
assert (start <= split && split <= end);
int nextdim = (depth + 1) % numdim;
if(start < split - 1) {
mms[2 * edim] = min;
mms[2 * edim + 1] = spos;
zSort(objs, start, split, mms, dims, nextdim);
}
if(split < end - 1) {
mms[2 * edim] = spos;
mms[2 * edim + 1] = max;
zSort(objs, split, end, mms, dims, nextdim);
}
// Restore ranges
mms[2 * edim] = min;
mms[2 * edim + 1] = max;
} | [
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elki-project/elki | elki-timeseries/src/main/java/de/lmu/ifi/dbs/elki/algorithm/timeseries/ChangePoint.java | ChangePoint.appendTo | public StringBuilder appendTo(StringBuilder buf) {
return buf.append(DBIDUtil.toString((DBIDRef) id)).append(" ").append(column).append(" ").append(score);
} | java | public StringBuilder appendTo(StringBuilder buf) {
return buf.append(DBIDUtil.toString((DBIDRef) id)).append(" ").append(column).append(" ").append(score);
} | [
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/DOC.java | DOC.runDOC | protected Cluster<SubspaceModel> runDOC(Database database, Relation<V> relation, ArrayModifiableDBIDs S, final int d, int n, int m, int r, int minClusterSize) {
// Best cluster for the current run.
DBIDs C = null;
// Relevant attributes for the best cluster.
long[] D = null;
// Quality of the best cluster.
double quality = Double.NEGATIVE_INFINITY;
// Bounds for our cluster.
// ModifiableHyperBoundingBox bounds = new ModifiableHyperBoundingBox(new
// double[d], new double[d]);
// Inform the user about the progress in the current iteration.
FiniteProgress iprogress = LOG.isVerbose() ? new FiniteProgress("Iteration progress for current cluster", m * n, LOG) : null;
Random random = rnd.getSingleThreadedRandom();
DBIDArrayIter iter = S.iter();
for(int i = 0; i < n; ++i) {
// Pick a random seed point.
iter.seek(random.nextInt(S.size()));
for(int j = 0; j < m; ++j) {
// Choose a set of random points.
DBIDs randomSet = DBIDUtil.randomSample(S, r, random);
// Initialize cluster info.
long[] nD = BitsUtil.zero(d);
// Test each dimension and build bounding box.
for(int k = 0; k < d; ++k) {
if(dimensionIsRelevant(k, relation, randomSet)) {
BitsUtil.setI(nD, k);
}
}
if(BitsUtil.cardinality(nD) > 0) {
DBIDs nC = findNeighbors(iter, nD, S, relation);
if(LOG.isDebuggingFiner()) {
LOG.finer("Testing a cluster candidate, |C| = " + nC.size() + ", |D| = " + BitsUtil.cardinality(nD));
}
// Is the cluster large enough?
if(nC.size() < minClusterSize) {
// Too small.
if(LOG.isDebuggingFiner()) {
LOG.finer("... but it's too small.");
}
continue;
}
// Better cluster than before?
double nQuality = computeClusterQuality(nC.size(), BitsUtil.cardinality(nD));
if(nQuality > quality) {
if(LOG.isDebuggingFiner()) {
LOG.finer("... and it's the best so far: " + nQuality + " vs. " + quality);
}
C = nC;
D = nD;
quality = nQuality;
}
else {
if(LOG.isDebuggingFiner()) {
LOG.finer("... but we already have a better one.");
}
}
}
LOG.incrementProcessed(iprogress);
}
}
LOG.ensureCompleted(iprogress);
return (C != null) ? makeCluster(relation, C, D) : null;
} | java | protected Cluster<SubspaceModel> runDOC(Database database, Relation<V> relation, ArrayModifiableDBIDs S, final int d, int n, int m, int r, int minClusterSize) {
// Best cluster for the current run.
DBIDs C = null;
// Relevant attributes for the best cluster.
long[] D = null;
// Quality of the best cluster.
double quality = Double.NEGATIVE_INFINITY;
// Bounds for our cluster.
// ModifiableHyperBoundingBox bounds = new ModifiableHyperBoundingBox(new
// double[d], new double[d]);
// Inform the user about the progress in the current iteration.
FiniteProgress iprogress = LOG.isVerbose() ? new FiniteProgress("Iteration progress for current cluster", m * n, LOG) : null;
Random random = rnd.getSingleThreadedRandom();
DBIDArrayIter iter = S.iter();
for(int i = 0; i < n; ++i) {
// Pick a random seed point.
iter.seek(random.nextInt(S.size()));
for(int j = 0; j < m; ++j) {
// Choose a set of random points.
DBIDs randomSet = DBIDUtil.randomSample(S, r, random);
// Initialize cluster info.
long[] nD = BitsUtil.zero(d);
// Test each dimension and build bounding box.
for(int k = 0; k < d; ++k) {
if(dimensionIsRelevant(k, relation, randomSet)) {
BitsUtil.setI(nD, k);
}
}
if(BitsUtil.cardinality(nD) > 0) {
DBIDs nC = findNeighbors(iter, nD, S, relation);
if(LOG.isDebuggingFiner()) {
LOG.finer("Testing a cluster candidate, |C| = " + nC.size() + ", |D| = " + BitsUtil.cardinality(nD));
}
// Is the cluster large enough?
if(nC.size() < minClusterSize) {
// Too small.
if(LOG.isDebuggingFiner()) {
LOG.finer("... but it's too small.");
}
continue;
}
// Better cluster than before?
double nQuality = computeClusterQuality(nC.size(), BitsUtil.cardinality(nD));
if(nQuality > quality) {
if(LOG.isDebuggingFiner()) {
LOG.finer("... and it's the best so far: " + nQuality + " vs. " + quality);
}
C = nC;
D = nD;
quality = nQuality;
}
else {
if(LOG.isDebuggingFiner()) {
LOG.finer("... but we already have a better one.");
}
}
}
LOG.incrementProcessed(iprogress);
}
}
LOG.ensureCompleted(iprogress);
return (C != null) ? makeCluster(relation, C, D) : null;
} | [
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@param d Dimensionality of the data set we're currently working on.
@param r Size of random samples.
@param m Number of inner iterations (per seed point).
@param n Number of outer iterations (seed points).
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/DOC.java | DOC.findNeighbors | protected DBIDs findNeighbors(DBIDRef q, long[] nD, ArrayModifiableDBIDs S, Relation<V> relation) {
// Weights for distance (= rectangle query)
DistanceQuery<V> dq = relation.getDistanceQuery(new SubspaceMaximumDistanceFunction(nD));
// TODO: add filtering capabilities into query API!
// Until then, using the range query API will be unnecessarily slow.
// RangeQuery<V> rq = relation.getRangeQuery(df, DatabaseQuery.HINT_SINGLE);
ArrayModifiableDBIDs nC = DBIDUtil.newArray();
for(DBIDIter it = S.iter(); it.valid(); it.advance()) {
if(dq.distance(q, it) <= w) {
nC.add(it);
}
}
return nC;
} | java | protected DBIDs findNeighbors(DBIDRef q, long[] nD, ArrayModifiableDBIDs S, Relation<V> relation) {
// Weights for distance (= rectangle query)
DistanceQuery<V> dq = relation.getDistanceQuery(new SubspaceMaximumDistanceFunction(nD));
// TODO: add filtering capabilities into query API!
// Until then, using the range query API will be unnecessarily slow.
// RangeQuery<V> rq = relation.getRangeQuery(df, DatabaseQuery.HINT_SINGLE);
ArrayModifiableDBIDs nC = DBIDUtil.newArray();
for(DBIDIter it = S.iter(); it.valid(); it.advance()) {
if(dq.distance(q, it) <= w) {
nC.add(it);
}
}
return nC;
} | [
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/DOC.java | DOC.makeCluster | protected Cluster<SubspaceModel> makeCluster(Relation<V> relation, DBIDs C, long[] D) {
DBIDs ids = DBIDUtil.newHashSet(C); // copy, also to lose distance values!
Cluster<SubspaceModel> cluster = new Cluster<>(ids);
cluster.setModel(new SubspaceModel(new Subspace(D), Centroid.make(relation, ids).getArrayRef()));
return cluster;
} | java | protected Cluster<SubspaceModel> makeCluster(Relation<V> relation, DBIDs C, long[] D) {
DBIDs ids = DBIDUtil.newHashSet(C); // copy, also to lose distance values!
Cluster<SubspaceModel> cluster = new Cluster<>(ids);
cluster.setModel(new SubspaceModel(new Subspace(D), Centroid.make(relation, ids).getArrayRef()));
return cluster;
} | [
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elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/KeyVisualization.java | KeyVisualization.findDepth | protected static <M extends Model> int[] findDepth(Clustering<M> c) {
final Hierarchy<Cluster<M>> hier = c.getClusterHierarchy();
int[] size = { 0, 0 };
for(It<Cluster<M>> iter = c.iterToplevelClusters(); iter.valid(); iter.advance()) {
findDepth(hier, iter.get(), size);
}
return size;
} | java | protected static <M extends Model> int[] findDepth(Clustering<M> c) {
final Hierarchy<Cluster<M>> hier = c.getClusterHierarchy();
int[] size = { 0, 0 };
for(It<Cluster<M>> iter = c.iterToplevelClusters(); iter.valid(); iter.advance()) {
findDepth(hier, iter.get(), size);
}
return size;
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elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/KeyVisualization.java | KeyVisualization.findDepth | private static <M extends Model> void findDepth(Hierarchy<Cluster<M>> hier, Cluster<M> cluster, int[] size) {
if(hier.numChildren(cluster) > 0) {
for(It<Cluster<M>> iter = hier.iterChildren(cluster); iter.valid(); iter.advance()) {
findDepth(hier, iter.get(), size);
}
size[0] += 1; // Depth
}
else {
size[1] += 1; // Leaves
}
} | java | private static <M extends Model> void findDepth(Hierarchy<Cluster<M>> hier, Cluster<M> cluster, int[] size) {
if(hier.numChildren(cluster) > 0) {
for(It<Cluster<M>> iter = hier.iterChildren(cluster); iter.valid(); iter.advance()) {
findDepth(hier, iter.get(), size);
}
size[0] += 1; // Depth
}
else {
size[1] += 1; // Leaves
}
} | [
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elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/visualizers/visunproj/KeyVisualization.java | KeyVisualization.getPreferredColumns | protected static int getPreferredColumns(double width, double height, int numc, double maxwidth) {
// Maximum width (compared to height) of labels - guess.
// FIXME: do we really need to do this three-step computation?
// Number of rows we'd use in a squared layout:
final double rows = Math.ceil(FastMath.pow(numc * maxwidth, height / (width + height)));
// Given this number of rows (plus one for header), use this many columns:
return (int) Math.ceil(numc / (rows + 1));
} | java | protected static int getPreferredColumns(double width, double height, int numc, double maxwidth) {
// Maximum width (compared to height) of labels - guess.
// FIXME: do we really need to do this three-step computation?
// Number of rows we'd use in a squared layout:
final double rows = Math.ceil(FastMath.pow(numc * maxwidth, height / (width + height)));
// Given this number of rows (plus one for header), use this many columns:
return (int) Math.ceil(numc / (rows + 1));
} | [
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elki-project/elki | elki-core-util/src/main/java/de/lmu/ifi/dbs/elki/utilities/ELKIBuilder.java | ELKIBuilder.with | public ELKIBuilder<T> with(String opt, Object value) {
p.addParameter(opt, value);
return this;
} | java | public ELKIBuilder<T> with(String opt, Object value) {
p.addParameter(opt, value);
return this;
} | [
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elki-project/elki | elki-core-util/src/main/java/de/lmu/ifi/dbs/elki/utilities/ELKIBuilder.java | ELKIBuilder.build | @SuppressWarnings("unchecked")
public <C extends T> C build() {
if(p == null) {
throw new AbortException("build() may be called only once.");
}
final T obj = ClassGenericsUtil.parameterizeOrAbort(clazz, p);
if(p.hasUnusedParameters()) {
LOG.warning("Unused parameters: " + p.getRemainingParameters());
}
p = null; // Prevent build() from being called again.
return (C) obj;
} | java | @SuppressWarnings("unchecked")
public <C extends T> C build() {
if(p == null) {
throw new AbortException("build() may be called only once.");
}
final T obj = ClassGenericsUtil.parameterizeOrAbort(clazz, p);
if(p.hasUnusedParameters()) {
LOG.warning("Unused parameters: " + p.getRemainingParameters());
}
p = null; // Prevent build() from being called again.
return (C) obj;
} | [
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] | b54673327e76198ecd4c8a2a901021f1a9174498 | https://github.com/elki-project/elki/blob/b54673327e76198ecd4c8a2a901021f1a9174498/elki-core-util/src/main/java/de/lmu/ifi/dbs/elki/utilities/ELKIBuilder.java#L159-L170 | train |
elki-project/elki | elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/projection/TSNE.java | TSNE.randomInitialSolution | protected static double[][] randomInitialSolution(final int size, final int dim, Random random) {
double[][] sol = new double[size][dim];
for(int i = 0; i < size; i++) {
for(int j = 0; j < dim; j++) {
sol[i][j] = random.nextGaussian() * INITIAL_SOLUTION_SCALE;
}
}
return sol;
} | java | protected static double[][] randomInitialSolution(final int size, final int dim, Random random) {
double[][] sol = new double[size][dim];
for(int i = 0; i < size; i++) {
for(int j = 0; j < dim; j++) {
sol[i][j] = random.nextGaussian() * INITIAL_SOLUTION_SCALE;
}
}
return sol;
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] | b54673327e76198ecd4c8a2a901021f1a9174498 | https://github.com/elki-project/elki/blob/b54673327e76198ecd4c8a2a901021f1a9174498/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/projection/TSNE.java#L220-L228 | train |
elki-project/elki | elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/projection/TSNE.java | TSNE.sqDist | protected double sqDist(double[] v1, double[] v2) {
assert (v1.length == v2.length) : "Lengths do not agree: " + v1.length + " " + v2.length;
double sum = 0;
for(int i = 0; i < v1.length; i++) {
final double diff = v1[i] - v2[i];
sum += diff * diff;
}
++projectedDistances;
return sum;
} | java | protected double sqDist(double[] v1, double[] v2) {
assert (v1.length == v2.length) : "Lengths do not agree: " + v1.length + " " + v2.length;
double sum = 0;
for(int i = 0; i < v1.length; i++) {
final double diff = v1[i] - v2[i];
sum += diff * diff;
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++projectedDistances;
return sum;
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] | b54673327e76198ecd4c8a2a901021f1a9174498 | https://github.com/elki-project/elki/blob/b54673327e76198ecd4c8a2a901021f1a9174498/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/projection/TSNE.java#L296-L305 | train |
elki-project/elki | elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/projection/TSNE.java | TSNE.updateSolution | protected void updateSolution(double[][] sol, double[] meta, int it) {
final double mom = (it < momentumSwitch && initialMomentum < finalMomentum) ? initialMomentum : finalMomentum;
final int dim3 = dim * 3;
for(int i = 0, off = 0; i < sol.length; i++, off += dim3) {
final double[] sol_i = sol[i];
for(int k = 0; k < dim; k++) {
// Indexes in meta array
final int gradk = off + k, movk = gradk + dim, gaink = movk + dim;
// Adjust learning rate:
meta[gaink] = MathUtil.max(((meta[gradk] > 0) != (meta[movk] > 0)) ? (meta[gaink] + 0.2) : (meta[gaink] * 0.8), MIN_GAIN);
meta[movk] *= mom; // Dampening the previous momentum
meta[movk] -= learningRate * meta[gradk] * meta[gaink]; // Learn
sol_i[k] += meta[movk];
}
}
} | java | protected void updateSolution(double[][] sol, double[] meta, int it) {
final double mom = (it < momentumSwitch && initialMomentum < finalMomentum) ? initialMomentum : finalMomentum;
final int dim3 = dim * 3;
for(int i = 0, off = 0; i < sol.length; i++, off += dim3) {
final double[] sol_i = sol[i];
for(int k = 0; k < dim; k++) {
// Indexes in meta array
final int gradk = off + k, movk = gradk + dim, gaink = movk + dim;
// Adjust learning rate:
meta[gaink] = MathUtil.max(((meta[gradk] > 0) != (meta[movk] > 0)) ? (meta[gaink] + 0.2) : (meta[gaink] * 0.8), MIN_GAIN);
meta[movk] *= mom; // Dampening the previous momentum
meta[movk] -= learningRate * meta[gradk] * meta[gaink]; // Learn
sol_i[k] += meta[movk];
}
}
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elki-project/elki | elki-index/src/main/java/de/lmu/ifi/dbs/elki/index/distancematrix/PrecomputedSimilarityMatrix.java | PrecomputedSimilarityMatrix.getOffset | private int getOffset(int x, int y) {
return (y < x) ? (triangleSize(x) + y) : (triangleSize(y) + x);
} | java | private int getOffset(int x, int y) {
return (y < x) ? (triangleSize(x) + y) : (triangleSize(y) + x);
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] | b54673327e76198ecd4c8a2a901021f1a9174498 | https://github.com/elki-project/elki/blob/b54673327e76198ecd4c8a2a901021f1a9174498/elki-index/src/main/java/de/lmu/ifi/dbs/elki/index/distancematrix/PrecomputedSimilarityMatrix.java#L162-L164 | train |
elki-project/elki | elki-core-math/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/weightfunctions/QuadraticStddevWeight.java | QuadraticStddevWeight.getWeight | @Override
public double getWeight(double distance, double max, double stddev) {
if(stddev <= 0) {
return 1;
}
double scaleddistance = distance / (scaling * stddev);
// After this, the result would be negative.
if(scaleddistance >= 1.0) {
return 0.0;
}
return 1.0 - scaleddistance * scaleddistance;
} | java | @Override
public double getWeight(double distance, double max, double stddev) {
if(stddev <= 0) {
return 1;
}
double scaleddistance = distance / (scaling * stddev);
// After this, the result would be negative.
if(scaleddistance >= 1.0) {
return 0.0;
}
return 1.0 - scaleddistance * scaleddistance;
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elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/projector/OPTICSProjector.java | OPTICSProjector.getOPTICSPlot | public OPTICSPlot getOPTICSPlot(VisualizerContext context) {
if(plot == null) {
plot = OPTICSPlot.plotForClusterOrder(clusterOrder, context);
}
return plot;
} | java | public OPTICSPlot getOPTICSPlot(VisualizerContext context) {
if(plot == null) {
plot = OPTICSPlot.plotForClusterOrder(clusterOrder, context);
}
return plot;
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elki-project/elki | elki-core-util/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/Flag.java | Flag.setValue | public void setValue(boolean val) {
try {
super.setValue(Boolean.valueOf(val));
}
catch(ParameterException e) {
// We're pretty sure that any Boolean is okay, so this should never be
// reached.
throw new AbortException("Flag did not accept boolean value!", e);
}
} | java | public void setValue(boolean val) {
try {
super.setValue(Boolean.valueOf(val));
}
catch(ParameterException e) {
// We're pretty sure that any Boolean is okay, so this should never be
// reached.
throw new AbortException("Flag did not accept boolean value!", e);
}
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elki-project/elki | elki-outlier/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LoOP.java | LoOP.run | public OutlierResult run(Database database, Relation<O> relation) {
StepProgress stepprog = LOG.isVerbose() ? new StepProgress(5) : null;
Pair<KNNQuery<O>, KNNQuery<O>> pair = getKNNQueries(database, relation, stepprog);
KNNQuery<O> knnComp = pair.getFirst();
KNNQuery<O> knnReach = pair.getSecond();
// Assert we got something
if(knnComp == null) {
throw new AbortException("No kNN queries supported by database for comparison distance function.");
}
if(knnReach == null) {
throw new AbortException("No kNN queries supported by database for density estimation distance function.");
}
// FIXME: tie handling!
// Probabilistic distances
WritableDoubleDataStore pdists = DataStoreUtil.makeDoubleStorage(relation.getDBIDs(), DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_DB);
LOG.beginStep(stepprog, 3, "Computing pdists");
computePDists(relation, knnReach, pdists);
// Compute PLOF values.
WritableDoubleDataStore plofs = DataStoreUtil.makeDoubleStorage(relation.getDBIDs(), DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP);
LOG.beginStep(stepprog, 4, "Computing PLOF");
double nplof = computePLOFs(relation, knnComp, pdists, plofs);
// Normalize the outlier scores.
DoubleMinMax mm = new DoubleMinMax();
{// compute LOOP_SCORE of each db object
LOG.beginStep(stepprog, 5, "Computing LoOP scores");
FiniteProgress progressLOOPs = LOG.isVerbose() ? new FiniteProgress("LoOP for objects", relation.size(), LOG) : null;
final double norm = 1. / (nplof * MathUtil.SQRT2);
for(DBIDIter iditer = relation.iterDBIDs(); iditer.valid(); iditer.advance()) {
double loop = NormalDistribution.erf((plofs.doubleValue(iditer) - 1.) * norm);
plofs.putDouble(iditer, loop);
mm.put(loop);
LOG.incrementProcessed(progressLOOPs);
}
LOG.ensureCompleted(progressLOOPs);
}
LOG.setCompleted(stepprog);
// Build result representation.
DoubleRelation scoreResult = new MaterializedDoubleRelation("Local Outlier Probabilities", "loop-outlier", plofs, relation.getDBIDs());
OutlierScoreMeta scoreMeta = new ProbabilisticOutlierScore(mm.getMin(), mm.getMax(), 0.);
return new OutlierResult(scoreMeta, scoreResult);
} | java | public OutlierResult run(Database database, Relation<O> relation) {
StepProgress stepprog = LOG.isVerbose() ? new StepProgress(5) : null;
Pair<KNNQuery<O>, KNNQuery<O>> pair = getKNNQueries(database, relation, stepprog);
KNNQuery<O> knnComp = pair.getFirst();
KNNQuery<O> knnReach = pair.getSecond();
// Assert we got something
if(knnComp == null) {
throw new AbortException("No kNN queries supported by database for comparison distance function.");
}
if(knnReach == null) {
throw new AbortException("No kNN queries supported by database for density estimation distance function.");
}
// FIXME: tie handling!
// Probabilistic distances
WritableDoubleDataStore pdists = DataStoreUtil.makeDoubleStorage(relation.getDBIDs(), DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_DB);
LOG.beginStep(stepprog, 3, "Computing pdists");
computePDists(relation, knnReach, pdists);
// Compute PLOF values.
WritableDoubleDataStore plofs = DataStoreUtil.makeDoubleStorage(relation.getDBIDs(), DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP);
LOG.beginStep(stepprog, 4, "Computing PLOF");
double nplof = computePLOFs(relation, knnComp, pdists, plofs);
// Normalize the outlier scores.
DoubleMinMax mm = new DoubleMinMax();
{// compute LOOP_SCORE of each db object
LOG.beginStep(stepprog, 5, "Computing LoOP scores");
FiniteProgress progressLOOPs = LOG.isVerbose() ? new FiniteProgress("LoOP for objects", relation.size(), LOG) : null;
final double norm = 1. / (nplof * MathUtil.SQRT2);
for(DBIDIter iditer = relation.iterDBIDs(); iditer.valid(); iditer.advance()) {
double loop = NormalDistribution.erf((plofs.doubleValue(iditer) - 1.) * norm);
plofs.putDouble(iditer, loop);
mm.put(loop);
LOG.incrementProcessed(progressLOOPs);
}
LOG.ensureCompleted(progressLOOPs);
}
LOG.setCompleted(stepprog);
// Build result representation.
DoubleRelation scoreResult = new MaterializedDoubleRelation("Local Outlier Probabilities", "loop-outlier", plofs, relation.getDBIDs());
OutlierScoreMeta scoreMeta = new ProbabilisticOutlierScore(mm.getMin(), mm.getMax(), 0.);
return new OutlierResult(scoreMeta, scoreResult);
} | [
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] | b54673327e76198ecd4c8a2a901021f1a9174498 | https://github.com/elki-project/elki/blob/b54673327e76198ecd4c8a2a901021f1a9174498/elki-outlier/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LoOP.java#L184-L232 | train |
elki-project/elki | elki-outlier/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LoOP.java | LoOP.computePDists | protected void computePDists(Relation<O> relation, KNNQuery<O> knn, WritableDoubleDataStore pdists) {
// computing PRDs
FiniteProgress prdsProgress = LOG.isVerbose() ? new FiniteProgress("pdists", relation.size(), LOG) : null;
for(DBIDIter iditer = relation.iterDBIDs(); iditer.valid(); iditer.advance()) {
final KNNList neighbors = knn.getKNNForDBID(iditer, kreach + 1); // +
// query
// point
// use first kref neighbors as reference set
int ks = 0;
double ssum = 0.;
for(DoubleDBIDListIter neighbor = neighbors.iter(); neighbor.valid() && ks < kreach; neighbor.advance()) {
if(DBIDUtil.equal(neighbor, iditer)) {
continue;
}
final double d = neighbor.doubleValue();
ssum += d * d;
ks++;
}
double pdist = ks > 0 ? FastMath.sqrt(ssum / ks) : 0.;
pdists.putDouble(iditer, pdist);
LOG.incrementProcessed(prdsProgress);
}
LOG.ensureCompleted(prdsProgress);
} | java | protected void computePDists(Relation<O> relation, KNNQuery<O> knn, WritableDoubleDataStore pdists) {
// computing PRDs
FiniteProgress prdsProgress = LOG.isVerbose() ? new FiniteProgress("pdists", relation.size(), LOG) : null;
for(DBIDIter iditer = relation.iterDBIDs(); iditer.valid(); iditer.advance()) {
final KNNList neighbors = knn.getKNNForDBID(iditer, kreach + 1); // +
// query
// point
// use first kref neighbors as reference set
int ks = 0;
double ssum = 0.;
for(DoubleDBIDListIter neighbor = neighbors.iter(); neighbor.valid() && ks < kreach; neighbor.advance()) {
if(DBIDUtil.equal(neighbor, iditer)) {
continue;
}
final double d = neighbor.doubleValue();
ssum += d * d;
ks++;
}
double pdist = ks > 0 ? FastMath.sqrt(ssum / ks) : 0.;
pdists.putDouble(iditer, pdist);
LOG.incrementProcessed(prdsProgress);
}
LOG.ensureCompleted(prdsProgress);
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] | b54673327e76198ecd4c8a2a901021f1a9174498 | https://github.com/elki-project/elki/blob/b54673327e76198ecd4c8a2a901021f1a9174498/elki-outlier/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LoOP.java#L241-L264 | train |
elki-project/elki | elki-outlier/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/lof/LoOP.java | LoOP.computePLOFs | protected double computePLOFs(Relation<O> relation, KNNQuery<O> knn, WritableDoubleDataStore pdists, WritableDoubleDataStore plofs) {
FiniteProgress progressPLOFs = LOG.isVerbose() ? new FiniteProgress("PLOFs for objects", relation.size(), LOG) : null;
double nplof = 0.;
for(DBIDIter iditer = relation.iterDBIDs(); iditer.valid(); iditer.advance()) {
final KNNList neighbors = knn.getKNNForDBID(iditer, kcomp + 1); // + query
// point
// use first kref neighbors as comparison set.
int ks = 0;
double sum = 0.;
for(DBIDIter neighbor = neighbors.iter(); neighbor.valid() && ks < kcomp; neighbor.advance()) {
if(DBIDUtil.equal(neighbor, iditer)) {
continue;
}
sum += pdists.doubleValue(neighbor);
ks++;
}
double plof = MathUtil.max(pdists.doubleValue(iditer) * ks / sum, 1.0);
if(Double.isNaN(plof) || Double.isInfinite(plof)) {
plof = 1.0;
}
plofs.putDouble(iditer, plof);
nplof += (plof - 1.0) * (plof - 1.0);
LOG.incrementProcessed(progressPLOFs);
}
LOG.ensureCompleted(progressPLOFs);
nplof = lambda * FastMath.sqrt(nplof / relation.size());
if(LOG.isDebuggingFine()) {
LOG.debugFine("nplof normalization factor is " + nplof);
}
return nplof > 0. ? nplof : 1.;
} | java | protected double computePLOFs(Relation<O> relation, KNNQuery<O> knn, WritableDoubleDataStore pdists, WritableDoubleDataStore plofs) {
FiniteProgress progressPLOFs = LOG.isVerbose() ? new FiniteProgress("PLOFs for objects", relation.size(), LOG) : null;
double nplof = 0.;
for(DBIDIter iditer = relation.iterDBIDs(); iditer.valid(); iditer.advance()) {
final KNNList neighbors = knn.getKNNForDBID(iditer, kcomp + 1); // + query
// point
// use first kref neighbors as comparison set.
int ks = 0;
double sum = 0.;
for(DBIDIter neighbor = neighbors.iter(); neighbor.valid() && ks < kcomp; neighbor.advance()) {
if(DBIDUtil.equal(neighbor, iditer)) {
continue;
}
sum += pdists.doubleValue(neighbor);
ks++;
}
double plof = MathUtil.max(pdists.doubleValue(iditer) * ks / sum, 1.0);
if(Double.isNaN(plof) || Double.isInfinite(plof)) {
plof = 1.0;
}
plofs.putDouble(iditer, plof);
nplof += (plof - 1.0) * (plof - 1.0);
LOG.incrementProcessed(progressPLOFs);
}
LOG.ensureCompleted(progressPLOFs);
nplof = lambda * FastMath.sqrt(nplof / relation.size());
if(LOG.isDebuggingFine()) {
LOG.debugFine("nplof normalization factor is " + nplof);
}
return nplof > 0. ? nplof : 1.;
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elki-project/elki | elki-core/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/TextWriterWriterInterface.java | TextWriterWriterInterface.writeObject | @SuppressWarnings("unchecked")
public final void writeObject(TextWriterStream out, String label, Object object) throws IOException {
write(out, label, (O) object);
} | java | @SuppressWarnings("unchecked")
public final void writeObject(TextWriterStream out, String label, Object object) throws IOException {
write(out, label, (O) object);
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elki-project/elki | elki-core-math/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/filter/ProgressiveEigenPairFilter.java | ProgressiveEigenPairFilter.filter | @Override
public int filter(double[] eigenValues) {
// determine sum of eigenvalues
double totalSum = 0;
for(int i = 0; i < eigenValues.length; i++) {
totalSum += eigenValues[i];
}
double expectedVariance = totalSum / eigenValues.length * walpha;
// determine strong and weak eigenpairs
double currSum = 0;
for(int i = 0; i < eigenValues.length - 1; i++) {
// weak Eigenvector?
if(eigenValues[i] < expectedVariance) {
break;
}
currSum += eigenValues[i];
// calculate progressive alpha level
double alpha = 1.0 - (1.0 - palpha) * (1.0 - (i + 1) / (double) eigenValues.length);
if(currSum / totalSum >= alpha) {
return i + 1;
}
}
// the code using this method doesn't expect an empty strong set,
// if we didn't find any strong ones, we make all vectors strong
return eigenValues.length;
} | java | @Override
public int filter(double[] eigenValues) {
// determine sum of eigenvalues
double totalSum = 0;
for(int i = 0; i < eigenValues.length; i++) {
totalSum += eigenValues[i];
}
double expectedVariance = totalSum / eigenValues.length * walpha;
// determine strong and weak eigenpairs
double currSum = 0;
for(int i = 0; i < eigenValues.length - 1; i++) {
// weak Eigenvector?
if(eigenValues[i] < expectedVariance) {
break;
}
currSum += eigenValues[i];
// calculate progressive alpha level
double alpha = 1.0 - (1.0 - palpha) * (1.0 - (i + 1) / (double) eigenValues.length);
if(currSum / totalSum >= alpha) {
return i + 1;
}
}
// the code using this method doesn't expect an empty strong set,
// if we didn't find any strong ones, we make all vectors strong
return eigenValues.length;
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elki-project/elki | elki-outlier/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/OutlierResult.java | OutlierResult.getOutlierResults | public static List<OutlierResult> getOutlierResults(Result r) {
if(r instanceof OutlierResult) {
List<OutlierResult> ors = new ArrayList<>(1);
ors.add((OutlierResult) r);
return ors;
}
if(r instanceof HierarchicalResult) {
return ResultUtil.filterResults(((HierarchicalResult) r).getHierarchy(), r, OutlierResult.class);
}
return Collections.emptyList();
} | java | public static List<OutlierResult> getOutlierResults(Result r) {
if(r instanceof OutlierResult) {
List<OutlierResult> ors = new ArrayList<>(1);
ors.add((OutlierResult) r);
return ors;
}
if(r instanceof HierarchicalResult) {
return ResultUtil.filterResults(((HierarchicalResult) r).getHierarchy(), r, OutlierResult.class);
}
return Collections.emptyList();
} | [
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elki-project/elki | elki-outlier/src/main/java/de/lmu/ifi/dbs/elki/result/outlier/OutlierResult.java | OutlierResult.evaluateBy | double evaluateBy(ScoreEvaluation eval) {
return eval.evaluate(new DBIDsTest(DBIDUtil.ensureSet(scores.getDBIDs())), new OutlierScoreAdapter(this));
} | java | double evaluateBy(ScoreEvaluation eval) {
return eval.evaluate(new DBIDsTest(DBIDUtil.ensureSet(scores.getDBIDs())), new OutlierScoreAdapter(this));
} | [
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elki-project/elki | elki-core-distance/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/minkowski/SquaredEuclideanDistanceFunction.java | SquaredEuclideanDistanceFunction.distance | public double distance(double[] v1, double[] v2) {
final int dim1 = v1.length, dim2 = v2.length;
final int mindim = dim1 < dim2 ? dim1 : dim2;
double agg = preDistance(v1, v2, 0, mindim);
if(dim1 > mindim) {
agg += preNorm(v1, mindim, dim1);
}
else if(dim2 > mindim) {
agg += preNorm(v2, mindim, dim2);
}
return agg;
} | java | public double distance(double[] v1, double[] v2) {
final int dim1 = v1.length, dim2 = v2.length;
final int mindim = dim1 < dim2 ? dim1 : dim2;
double agg = preDistance(v1, v2, 0, mindim);
if(dim1 > mindim) {
agg += preNorm(v1, mindim, dim1);
}
else if(dim2 > mindim) {
agg += preNorm(v2, mindim, dim2);
}
return agg;
} | [
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elki-project/elki | addons/3dpc/src/main/java/de/lmu/ifi/dbs/elki/visualization/parallel3d/layout/SimpleCircularMSTLayout3DPC.java | SimpleCircularMSTLayout3DPC.computeWeights | private void computeWeights(Node node) {
int wsum = 0;
for(Node child : node.children) {
computeWeights(child);
wsum += child.weight;
}
node.weight = Math.max(1, wsum);
} | java | private void computeWeights(Node node) {
int wsum = 0;
for(Node child : node.children) {
computeWeights(child);
wsum += child.weight;
}
node.weight = Math.max(1, wsum);
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/pairsegments/ClusterPairSegmentAnalysis.java | ClusterPairSegmentAnalysis.processNewResult | @Override
public void processNewResult(ResultHierarchy hier, Result result) {
// Get all new clusterings
// TODO: handle clusterings added later, too. Can we update the result?
List<Clustering<?>> clusterings = Clustering.getClusteringResults(result);
// Abort if not enough clusterings to compare
if(clusterings.size() < 2) {
return;
}
// create segments
Segments segments = new Segments(clusterings);
hier.add(result, segments);
} | java | @Override
public void processNewResult(ResultHierarchy hier, Result result) {
// Get all new clusterings
// TODO: handle clusterings added later, too. Can we update the result?
List<Clustering<?>> clusterings = Clustering.getClusteringResults(result);
// Abort if not enough clusterings to compare
if(clusterings.size() < 2) {
return;
}
// create segments
Segments segments = new Segments(clusterings);
hier.add(result, segments);
} | [
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elki-project/elki | elki-index-various/src/main/java/de/lmu/ifi/dbs/elki/index/vafile/VALPNormDistance.java | VALPNormDistance.getPartialMinDist | public double getPartialMinDist(int dimension, int vp) {
final int qp = queryApprox.getApproximation(dimension);
if(vp < qp) {
return lookup[dimension][vp + 1];
}
else if(vp > qp) {
return lookup[dimension][vp];
}
else {
return 0.0;
}
} | java | public double getPartialMinDist(int dimension, int vp) {
final int qp = queryApprox.getApproximation(dimension);
if(vp < qp) {
return lookup[dimension][vp + 1];
}
else if(vp > qp) {
return lookup[dimension][vp];
}
else {
return 0.0;
}
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elki-project/elki | elki-index-various/src/main/java/de/lmu/ifi/dbs/elki/index/vafile/VALPNormDistance.java | VALPNormDistance.getMinDist | public double getMinDist(VectorApproximation vec) {
final int dim = lookup.length;
double minDist = 0;
for(int d = 0; d < dim; d++) {
final int vp = vec.getApproximation(d);
minDist += getPartialMinDist(d, vp);
}
return FastMath.pow(minDist, onebyp);
} | java | public double getMinDist(VectorApproximation vec) {
final int dim = lookup.length;
double minDist = 0;
for(int d = 0; d < dim; d++) {
final int vp = vec.getApproximation(d);
minDist += getPartialMinDist(d, vp);
}
return FastMath.pow(minDist, onebyp);
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elki-project/elki | elki-index-various/src/main/java/de/lmu/ifi/dbs/elki/index/vafile/VALPNormDistance.java | VALPNormDistance.getPartialMaxDist | public double getPartialMaxDist(int dimension, int vp) {
final int qp = queryApprox.getApproximation(dimension);
if(vp < qp) {
return lookup[dimension][vp];
}
else if(vp > qp) {
return lookup[dimension][vp + 1];
}
else {
return Math.max(lookup[dimension][vp], lookup[dimension][vp + 1]);
}
} | java | public double getPartialMaxDist(int dimension, int vp) {
final int qp = queryApprox.getApproximation(dimension);
if(vp < qp) {
return lookup[dimension][vp];
}
else if(vp > qp) {
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elki-project/elki | elki-index-various/src/main/java/de/lmu/ifi/dbs/elki/index/vafile/VALPNormDistance.java | VALPNormDistance.initializeLookupTable | private void initializeLookupTable(double[][] splitPositions, NumberVector query, double p) {
final int dimensions = splitPositions.length;
final int bordercount = splitPositions[0].length;
lookup = new double[dimensions][bordercount];
for(int d = 0; d < dimensions; d++) {
final double val = query.doubleValue(d);
for(int i = 0; i < bordercount; i++) {
lookup[d][i] = FastMath.pow(splitPositions[d][i] - val, p);
}
}
} | java | private void initializeLookupTable(double[][] splitPositions, NumberVector query, double p) {
final int dimensions = splitPositions.length;
final int bordercount = splitPositions[0].length;
lookup = new double[dimensions][bordercount];
for(int d = 0; d < dimensions; d++) {
final double val = query.doubleValue(d);
for(int i = 0; i < bordercount; i++) {
lookup[d][i] = FastMath.pow(splitPositions[d][i] - val, p);
}
}
} | [
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elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizerContext.java | VisualizerContext.makeStyleResult | protected void makeStyleResult(StyleLibrary stylelib) {
final Database db = ResultUtil.findDatabase(hier);
stylelibrary = stylelib;
List<Clustering<? extends Model>> clusterings = Clustering.getClusteringResults(db);
if(!clusterings.isEmpty()) {
stylepolicy = new ClusterStylingPolicy(clusterings.get(0), stylelib);
}
else {
Clustering<Model> c = generateDefaultClustering();
stylepolicy = new ClusterStylingPolicy(c, stylelib);
}
} | java | protected void makeStyleResult(StyleLibrary stylelib) {
final Database db = ResultUtil.findDatabase(hier);
stylelibrary = stylelib;
List<Clustering<? extends Model>> clusterings = Clustering.getClusteringResults(db);
if(!clusterings.isEmpty()) {
stylepolicy = new ClusterStylingPolicy(clusterings.get(0), stylelib);
}
else {
Clustering<Model> c = generateDefaultClustering();
stylepolicy = new ClusterStylingPolicy(c, stylelib);
}
} | [
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] | b54673327e76198ecd4c8a2a901021f1a9174498 | https://github.com/elki-project/elki/blob/b54673327e76198ecd4c8a2a901021f1a9174498/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizerContext.java#L171-L182 | train |
elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizerContext.java | VisualizerContext.contentChanged | @Override
public void contentChanged(DataStoreEvent e) {
for(int i = 0; i < listenerList.size(); i++) {
listenerList.get(i).contentChanged(e);
}
} | java | @Override
public void contentChanged(DataStoreEvent e) {
for(int i = 0; i < listenerList.size(); i++) {
listenerList.get(i).contentChanged(e);
}
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elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/VisualizerContext.java | VisualizerContext.notifyFactories | private void notifyFactories(Object item) {
for(VisualizationProcessor f : factories) {
try {
f.processNewResult(this, item);
}
catch(Throwable e) {
LOG.warning("VisFactory " + f.getClass().getCanonicalName() + " failed:", e);
}
}
} | java | private void notifyFactories(Object item) {
for(VisualizationProcessor f : factories) {
try {
f.processNewResult(this, item);
}
catch(Throwable e) {
LOG.warning("VisFactory " + f.getClass().getCanonicalName() + " failed:", e);
}
}
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elki-project/elki | elki-index-rtree/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/AbstractBulkSplit.java | AbstractBulkSplit.chooseBulkSplitPoint | protected int chooseBulkSplitPoint(int numEntries, int minEntries, int maxEntries) {
if(numEntries < minEntries) {
throw new IllegalArgumentException("numEntries < minEntries!");
}
if(numEntries <= maxEntries) {
return numEntries;
}
else if(numEntries < maxEntries + minEntries) {
return (numEntries - minEntries);
}
else {
return maxEntries;
}
} | java | protected int chooseBulkSplitPoint(int numEntries, int minEntries, int maxEntries) {
if(numEntries < minEntries) {
throw new IllegalArgumentException("numEntries < minEntries!");
}
if(numEntries <= maxEntries) {
return numEntries;
}
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return (numEntries - minEntries);
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return maxEntries;
}
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elki-project/elki | elki-index-rtree/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/strategies/bulk/AbstractBulkSplit.java | AbstractBulkSplit.trivialPartition | protected <T> List<List<T>> trivialPartition(List<T> objects, int minEntries, int maxEntries) {
// build partitions
final int size = objects.size();
final int numberPartitions = (int) Math.ceil(((double) size) / maxEntries);
List<List<T>> partitions = new ArrayList<>(numberPartitions);
int start = 0;
for(int pnum = 0; pnum < numberPartitions; pnum++) {
int end = (int) ((pnum + 1.) * size / numberPartitions);
if(pnum == numberPartitions - 1) {
end = size;
}
assert ((end - start) >= minEntries && (end - start) <= maxEntries);
partitions.add(objects.subList(start, end));
start = end;
}
return partitions;
} | java | protected <T> List<List<T>> trivialPartition(List<T> objects, int minEntries, int maxEntries) {
// build partitions
final int size = objects.size();
final int numberPartitions = (int) Math.ceil(((double) size) / maxEntries);
List<List<T>> partitions = new ArrayList<>(numberPartitions);
int start = 0;
for(int pnum = 0; pnum < numberPartitions; pnum++) {
int end = (int) ((pnum + 1.) * size / numberPartitions);
if(pnum == numberPartitions - 1) {
end = size;
}
assert ((end - start) >= minEntries && (end - start) <= maxEntries);
partitions.add(objects.subList(start, end));
start = end;
}
return partitions;
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elki-project/elki | elki-database/src/main/java/de/lmu/ifi/dbs/elki/database/HashmapDatabase.java | HashmapDatabase.alignColumns | protected Relation<?>[] alignColumns(ObjectBundle pack) {
// align representations.
Relation<?>[] targets = new Relation<?>[pack.metaLength()];
long[] used = BitsUtil.zero(relations.size());
for(int i = 0; i < targets.length; i++) {
SimpleTypeInformation<?> meta = pack.meta(i);
// TODO: aggressively try to match exact metas first?
// Try to match unused representations only
for(int j = BitsUtil.nextClearBit(used, 0); j >= 0 && j < relations.size(); j = BitsUtil.nextClearBit(used, j + 1)) {
Relation<?> relation = relations.get(j);
if(relation.getDataTypeInformation().isAssignableFromType(meta)) {
targets[i] = relation;
BitsUtil.setI(used, j);
break;
}
}
if(targets[i] == null) {
targets[i] = addNewRelation(meta);
BitsUtil.setI(used, relations.size() - 1);
}
}
return targets;
} | java | protected Relation<?>[] alignColumns(ObjectBundle pack) {
// align representations.
Relation<?>[] targets = new Relation<?>[pack.metaLength()];
long[] used = BitsUtil.zero(relations.size());
for(int i = 0; i < targets.length; i++) {
SimpleTypeInformation<?> meta = pack.meta(i);
// TODO: aggressively try to match exact metas first?
// Try to match unused representations only
for(int j = BitsUtil.nextClearBit(used, 0); j >= 0 && j < relations.size(); j = BitsUtil.nextClearBit(used, j + 1)) {
Relation<?> relation = relations.get(j);
if(relation.getDataTypeInformation().isAssignableFromType(meta)) {
targets[i] = relation;
BitsUtil.setI(used, j);
break;
}
}
if(targets[i] == null) {
targets[i] = addNewRelation(meta);
BitsUtil.setI(used, relations.size() - 1);
}
}
return targets;
} | [
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elki-project/elki | elki-database/src/main/java/de/lmu/ifi/dbs/elki/database/HashmapDatabase.java | HashmapDatabase.addNewRelation | private Relation<?> addNewRelation(SimpleTypeInformation<?> meta) {
@SuppressWarnings("unchecked")
SimpleTypeInformation<Object> ometa = (SimpleTypeInformation<Object>) meta;
Relation<?> relation = new MaterializedRelation<>(ometa, ids);
relations.add(relation);
getHierarchy().add(this, relation);
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final IndexFactory<Object> ofact = (IndexFactory<Object>) factory;
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Index index = ofact.instantiate(orep);
index.initialize();
getHierarchy().add(relation, index);
}
}
return relation;
} | java | private Relation<?> addNewRelation(SimpleTypeInformation<?> meta) {
@SuppressWarnings("unchecked")
SimpleTypeInformation<Object> ometa = (SimpleTypeInformation<Object>) meta;
Relation<?> relation = new MaterializedRelation<>(ometa, ids);
relations.add(relation);
getHierarchy().add(this, relation);
// Try to add indexes where appropriate
for(IndexFactory<?> factory : indexFactories) {
if(factory.getInputTypeRestriction().isAssignableFromType(meta)) {
@SuppressWarnings("unchecked")
final IndexFactory<Object> ofact = (IndexFactory<Object>) factory;
@SuppressWarnings("unchecked")
final Relation<Object> orep = (Relation<Object>) relation;
Index index = ofact.instantiate(orep);
index.initialize();
getHierarchy().add(relation, index);
}
}
return relation;
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elki-project/elki | elki-database/src/main/java/de/lmu/ifi/dbs/elki/database/HashmapDatabase.java | HashmapDatabase.doDelete | private void doDelete(DBIDRef id) {
// Remove id
ids.remove(id);
// Remove from all representations.
for(Relation<?> relation : relations) {
// ID has already been removed, and this would loop...
if(relation == idrep) {
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throw new AbortException("Non-modifiable relations have been added to the database.");
}
((ModifiableRelation<?>) relation).delete(id);
}
DBIDFactory.FACTORY.deallocateSingleDBID(id);
} | java | private void doDelete(DBIDRef id) {
// Remove id
ids.remove(id);
// Remove from all representations.
for(Relation<?> relation : relations) {
// ID has already been removed, and this would loop...
if(relation == idrep) {
continue;
}
if(!(relation instanceof ModifiableRelation)) {
throw new AbortException("Non-modifiable relations have been added to the database.");
}
((ModifiableRelation<?>) relation).delete(id);
}
DBIDFactory.FACTORY.deallocateSingleDBID(id);
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/PROCLUS.java | PROCLUS.greedy | private ArrayDBIDs greedy(DistanceQuery<V> distFunc, DBIDs sampleSet, int m, Random random) {
ArrayModifiableDBIDs medoids = DBIDUtil.newArray(m);
ArrayModifiableDBIDs s = DBIDUtil.newArray(sampleSet);
DBIDArrayIter iter = s.iter();
DBIDVar m_i = DBIDUtil.newVar();
int size = s.size();
// Move a random element to the end, then pop()
s.swap(random.nextInt(size), --size);
medoids.add(s.pop(m_i));
if(LOG.isDebugging()) {
LOG.debugFiner("medoids " + medoids.toString());
}
// To track the current worst element:
int worst = -1;
double worstd = Double.NEGATIVE_INFINITY;
// compute distances between each point in S and m_i
WritableDoubleDataStore distances = DataStoreUtil.makeDoubleStorage(s, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP);
for(iter.seek(0); iter.getOffset() < size; iter.advance()) {
final double dist = distFunc.distance(iter, m_i);
distances.putDouble(iter, dist);
if(dist > worstd) {
worstd = dist;
worst = iter.getOffset();
}
}
for(int i = 1; i < m; i++) {
// choose medoid m_i to be far from previous medoids
s.swap(worst, --size);
medoids.add(s.pop(m_i));
// compute distances of each point to closest medoid; track worst.
worst = -1;
worstd = Double.NEGATIVE_INFINITY;
for(iter.seek(0); iter.getOffset() < size; iter.advance()) {
double dist_new = distFunc.distance(iter, m_i);
double dist_old = distances.doubleValue(iter);
double dist = (dist_new < dist_old) ? dist_new : dist_old;
distances.putDouble(iter, dist);
if(dist > worstd) {
worstd = dist;
worst = iter.getOffset();
}
}
if(LOG.isDebugging()) {
LOG.debugFiner("medoids " + medoids.toString());
}
}
return medoids;
} | java | private ArrayDBIDs greedy(DistanceQuery<V> distFunc, DBIDs sampleSet, int m, Random random) {
ArrayModifiableDBIDs medoids = DBIDUtil.newArray(m);
ArrayModifiableDBIDs s = DBIDUtil.newArray(sampleSet);
DBIDArrayIter iter = s.iter();
DBIDVar m_i = DBIDUtil.newVar();
int size = s.size();
// Move a random element to the end, then pop()
s.swap(random.nextInt(size), --size);
medoids.add(s.pop(m_i));
if(LOG.isDebugging()) {
LOG.debugFiner("medoids " + medoids.toString());
}
// To track the current worst element:
int worst = -1;
double worstd = Double.NEGATIVE_INFINITY;
// compute distances between each point in S and m_i
WritableDoubleDataStore distances = DataStoreUtil.makeDoubleStorage(s, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP);
for(iter.seek(0); iter.getOffset() < size; iter.advance()) {
final double dist = distFunc.distance(iter, m_i);
distances.putDouble(iter, dist);
if(dist > worstd) {
worstd = dist;
worst = iter.getOffset();
}
}
for(int i = 1; i < m; i++) {
// choose medoid m_i to be far from previous medoids
s.swap(worst, --size);
medoids.add(s.pop(m_i));
// compute distances of each point to closest medoid; track worst.
worst = -1;
worstd = Double.NEGATIVE_INFINITY;
for(iter.seek(0); iter.getOffset() < size; iter.advance()) {
double dist_new = distFunc.distance(iter, m_i);
double dist_old = distances.doubleValue(iter);
double dist = (dist_new < dist_old) ? dist_new : dist_old;
distances.putDouble(iter, dist);
if(dist > worstd) {
worstd = dist;
worst = iter.getOffset();
}
}
if(LOG.isDebugging()) {
LOG.debugFiner("medoids " + medoids.toString());
}
}
return medoids;
} | [
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/PROCLUS.java | PROCLUS.initialSet | private ArrayDBIDs initialSet(DBIDs sampleSet, int k, Random random) {
return DBIDUtil.ensureArray(DBIDUtil.randomSample(sampleSet, k, random));
} | java | private ArrayDBIDs initialSet(DBIDs sampleSet, int k, Random random) {
return DBIDUtil.ensureArray(DBIDUtil.randomSample(sampleSet, k, random));
} | [
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/PROCLUS.java | PROCLUS.computeM_current | private ArrayDBIDs computeM_current(DBIDs m, DBIDs m_best, DBIDs m_bad, Random random) {
ArrayModifiableDBIDs m_list = DBIDUtil.newArray(m);
m_list.removeDBIDs(m_best);
DBIDArrayMIter it = m_list.iter();
ArrayModifiableDBIDs m_current = DBIDUtil.newArray();
for(DBIDIter iter = m_best.iter(); iter.valid(); iter.advance()) {
if(m_bad.contains(iter)) {
int currentSize = m_current.size();
while(m_current.size() == currentSize) {
m_current.add(it.seek(random.nextInt(m_list.size())));
it.remove();
}
}
else {
m_current.add(iter);
}
}
return m_current;
} | java | private ArrayDBIDs computeM_current(DBIDs m, DBIDs m_best, DBIDs m_bad, Random random) {
ArrayModifiableDBIDs m_list = DBIDUtil.newArray(m);
m_list.removeDBIDs(m_best);
DBIDArrayMIter it = m_list.iter();
ArrayModifiableDBIDs m_current = DBIDUtil.newArray();
for(DBIDIter iter = m_best.iter(); iter.valid(); iter.advance()) {
if(m_bad.contains(iter)) {
int currentSize = m_current.size();
while(m_current.size() == currentSize) {
m_current.add(it.seek(random.nextInt(m_list.size())));
it.remove();
}
}
else {
m_current.add(iter);
}
}
return m_current;
} | [
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@param random random number generator
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/PROCLUS.java | PROCLUS.findDimensions | private long[][] findDimensions(ArrayDBIDs medoids, Relation<V> database, DistanceQuery<V> distFunc, RangeQuery<V> rangeQuery) {
// get localities
DataStore<DBIDs> localities = getLocalities(medoids, distFunc, rangeQuery);
// compute x_ij = avg distance from points in l_i to medoid m_i
final int dim = RelationUtil.dimensionality(database);
final int numc = medoids.size();
double[][] averageDistances = new double[numc][];
for(DBIDArrayIter iter = medoids.iter(); iter.valid(); iter.advance()) {
V medoid_i = database.get(iter);
DBIDs l_i = localities.get(iter);
double[] x_i = new double[dim];
for(DBIDIter qr = l_i.iter(); qr.valid(); qr.advance()) {
V o = database.get(qr);
for(int d = 0; d < dim; d++) {
x_i[d] += Math.abs(medoid_i.doubleValue(d) - o.doubleValue(d));
}
}
for(int d = 0; d < dim; d++) {
x_i[d] /= l_i.size();
}
averageDistances[iter.getOffset()] = x_i;
}
List<DoubleIntInt> z_ijs = computeZijs(averageDistances, dim);
return computeDimensionMap(z_ijs, dim, numc);
} | java | private long[][] findDimensions(ArrayDBIDs medoids, Relation<V> database, DistanceQuery<V> distFunc, RangeQuery<V> rangeQuery) {
// get localities
DataStore<DBIDs> localities = getLocalities(medoids, distFunc, rangeQuery);
// compute x_ij = avg distance from points in l_i to medoid m_i
final int dim = RelationUtil.dimensionality(database);
final int numc = medoids.size();
double[][] averageDistances = new double[numc][];
for(DBIDArrayIter iter = medoids.iter(); iter.valid(); iter.advance()) {
V medoid_i = database.get(iter);
DBIDs l_i = localities.get(iter);
double[] x_i = new double[dim];
for(DBIDIter qr = l_i.iter(); qr.valid(); qr.advance()) {
V o = database.get(qr);
for(int d = 0; d < dim; d++) {
x_i[d] += Math.abs(medoid_i.doubleValue(d) - o.doubleValue(d));
}
}
for(int d = 0; d < dim; d++) {
x_i[d] /= l_i.size();
}
averageDistances[iter.getOffset()] = x_i;
}
List<DoubleIntInt> z_ijs = computeZijs(averageDistances, dim);
return computeDimensionMap(z_ijs, dim, numc);
} | [
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@param distFunc the distance function
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/PROCLUS.java | PROCLUS.findDimensions | private List<Pair<double[], long[]>> findDimensions(ArrayList<PROCLUSCluster> clusters, Relation<V> database) {
// compute x_ij = avg distance from points in c_i to c_i.centroid
final int dim = RelationUtil.dimensionality(database);
final int numc = clusters.size();
double[][] averageDistances = new double[numc][];
for(int i = 0; i < numc; i++) {
PROCLUSCluster c_i = clusters.get(i);
double[] x_i = new double[dim];
for(DBIDIter iter = c_i.objectIDs.iter(); iter.valid(); iter.advance()) {
V o = database.get(iter);
for(int d = 0; d < dim; d++) {
x_i[d] += Math.abs(c_i.centroid[d] - o.doubleValue(d));
}
}
for(int d = 0; d < dim; d++) {
x_i[d] /= c_i.objectIDs.size();
}
averageDistances[i] = x_i;
}
List<DoubleIntInt> z_ijs = computeZijs(averageDistances, dim);
long[][] dimensionMap = computeDimensionMap(z_ijs, dim, numc);
// mapping cluster -> dimensions
List<Pair<double[], long[]>> result = new ArrayList<>(numc);
for(int i = 0; i < numc; i++) {
long[] dims_i = dimensionMap[i];
if(dims_i == null) {
continue;
}
result.add(new Pair<>(clusters.get(i).centroid, dims_i));
}
return result;
} | java | private List<Pair<double[], long[]>> findDimensions(ArrayList<PROCLUSCluster> clusters, Relation<V> database) {
// compute x_ij = avg distance from points in c_i to c_i.centroid
final int dim = RelationUtil.dimensionality(database);
final int numc = clusters.size();
double[][] averageDistances = new double[numc][];
for(int i = 0; i < numc; i++) {
PROCLUSCluster c_i = clusters.get(i);
double[] x_i = new double[dim];
for(DBIDIter iter = c_i.objectIDs.iter(); iter.valid(); iter.advance()) {
V o = database.get(iter);
for(int d = 0; d < dim; d++) {
x_i[d] += Math.abs(c_i.centroid[d] - o.doubleValue(d));
}
}
for(int d = 0; d < dim; d++) {
x_i[d] /= c_i.objectIDs.size();
}
averageDistances[i] = x_i;
}
List<DoubleIntInt> z_ijs = computeZijs(averageDistances, dim);
long[][] dimensionMap = computeDimensionMap(z_ijs, dim, numc);
// mapping cluster -> dimensions
List<Pair<double[], long[]>> result = new ArrayList<>(numc);
for(int i = 0; i < numc; i++) {
long[] dims_i = dimensionMap[i];
if(dims_i == null) {
continue;
}
result.add(new Pair<>(clusters.get(i).centroid, dims_i));
}
return result;
} | [
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/PROCLUS.java | PROCLUS.computeZijs | private List<DoubleIntInt> computeZijs(double[][] averageDistances, final int dim) {
List<DoubleIntInt> z_ijs = new ArrayList<>(averageDistances.length * dim);
for(int i = 0; i < averageDistances.length; i++) {
double[] x_i = averageDistances[i];
// y_i
double y_i = 0;
for(int j = 0; j < dim; j++) {
y_i += x_i[j];
}
y_i /= dim;
// sigma_i
double sigma_i = 0;
for(int j = 0; j < dim; j++) {
double diff = x_i[j] - y_i;
sigma_i += diff * diff;
}
sigma_i /= (dim - 1);
sigma_i = FastMath.sqrt(sigma_i);
for(int j = 0; j < dim; j++) {
z_ijs.add(new DoubleIntInt((x_i[j] - y_i) / sigma_i, i, j));
}
}
Collections.sort(z_ijs);
return z_ijs;
} | java | private List<DoubleIntInt> computeZijs(double[][] averageDistances, final int dim) {
List<DoubleIntInt> z_ijs = new ArrayList<>(averageDistances.length * dim);
for(int i = 0; i < averageDistances.length; i++) {
double[] x_i = averageDistances[i];
// y_i
double y_i = 0;
for(int j = 0; j < dim; j++) {
y_i += x_i[j];
}
y_i /= dim;
// sigma_i
double sigma_i = 0;
for(int j = 0; j < dim; j++) {
double diff = x_i[j] - y_i;
sigma_i += diff * diff;
}
sigma_i /= (dim - 1);
sigma_i = FastMath.sqrt(sigma_i);
for(int j = 0; j < dim; j++) {
z_ijs.add(new DoubleIntInt((x_i[j] - y_i) / sigma_i, i, j));
}
}
Collections.sort(z_ijs);
return z_ijs;
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/PROCLUS.java | PROCLUS.computeDimensionMap | private long[][] computeDimensionMap(List<DoubleIntInt> z_ijs, final int dim, final int numc) {
// mapping cluster index -> dimensions
long[][] dimensionMap = new long[numc][((dim - 1) >> 6) + 1];
int max = Math.max(k * l, 2);
for(int m = 0; m < max; m++) {
DoubleIntInt z_ij = z_ijs.get(m);
long[] dims_i = dimensionMap[z_ij.dimi];
BitsUtil.setI(dims_i, z_ij.dimj);
if(LOG.isDebugging()) {
LOG.debugFiner(new StringBuilder().append("z_ij ").append(z_ij).append('\n') //
.append("D_i ").append(BitsUtil.toString(dims_i)).toString());
}
}
return dimensionMap;
} | java | private long[][] computeDimensionMap(List<DoubleIntInt> z_ijs, final int dim, final int numc) {
// mapping cluster index -> dimensions
long[][] dimensionMap = new long[numc][((dim - 1) >> 6) + 1];
int max = Math.max(k * l, 2);
for(int m = 0; m < max; m++) {
DoubleIntInt z_ij = z_ijs.get(m);
long[] dims_i = dimensionMap[z_ij.dimi];
BitsUtil.setI(dims_i, z_ij.dimj);
if(LOG.isDebugging()) {
LOG.debugFiner(new StringBuilder().append("z_ij ").append(z_ij).append('\n') //
.append("D_i ").append(BitsUtil.toString(dims_i)).toString());
}
}
return dimensionMap;
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@param numc Number of clusters
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/PROCLUS.java | PROCLUS.assignPoints | private ArrayList<PROCLUSCluster> assignPoints(ArrayDBIDs m_current, long[][] dimensions, Relation<V> database) {
ModifiableDBIDs[] clusterIDs = new ModifiableDBIDs[dimensions.length];
for(int i = 0; i < m_current.size(); i++) {
clusterIDs[i] = DBIDUtil.newHashSet();
}
DBIDArrayIter m_i = m_current.iter();
for(DBIDIter it = database.iterDBIDs(); it.valid(); it.advance()) {
V p = database.get(it);
double minDist = Double.NaN;
int best = -1, i = 0;
for(m_i.seek(0); m_i.valid(); m_i.advance(), i++) {
V m = database.get(m_i);
double currentDist = manhattanSegmentalDistance(p, m, dimensions[i]);
if(!(minDist <= currentDist)) {
minDist = currentDist;
best = i;
}
}
// add p to cluster with mindist
assert best >= 0;
clusterIDs[best].add(it);
}
ArrayList<PROCLUSCluster> clusters = new ArrayList<>(m_current.size());
for(int i = 0; i < dimensions.length; i++) {
ModifiableDBIDs objectIDs = clusterIDs[i];
if(!objectIDs.isEmpty()) {
long[] clusterDimensions = dimensions[i];
double[] centroid = Centroid.make(database, objectIDs).getArrayRef();
clusters.add(new PROCLUSCluster(objectIDs, clusterDimensions, centroid));
}
else {
clusters.add(null);
}
}
if(LOG.isDebugging()) {
LOG.debugFine(new StringBuilder().append("clusters ").append(clusters).toString());
}
return clusters;
} | java | private ArrayList<PROCLUSCluster> assignPoints(ArrayDBIDs m_current, long[][] dimensions, Relation<V> database) {
ModifiableDBIDs[] clusterIDs = new ModifiableDBIDs[dimensions.length];
for(int i = 0; i < m_current.size(); i++) {
clusterIDs[i] = DBIDUtil.newHashSet();
}
DBIDArrayIter m_i = m_current.iter();
for(DBIDIter it = database.iterDBIDs(); it.valid(); it.advance()) {
V p = database.get(it);
double minDist = Double.NaN;
int best = -1, i = 0;
for(m_i.seek(0); m_i.valid(); m_i.advance(), i++) {
V m = database.get(m_i);
double currentDist = manhattanSegmentalDistance(p, m, dimensions[i]);
if(!(minDist <= currentDist)) {
minDist = currentDist;
best = i;
}
}
// add p to cluster with mindist
assert best >= 0;
clusterIDs[best].add(it);
}
ArrayList<PROCLUSCluster> clusters = new ArrayList<>(m_current.size());
for(int i = 0; i < dimensions.length; i++) {
ModifiableDBIDs objectIDs = clusterIDs[i];
if(!objectIDs.isEmpty()) {
long[] clusterDimensions = dimensions[i];
double[] centroid = Centroid.make(database, objectIDs).getArrayRef();
clusters.add(new PROCLUSCluster(objectIDs, clusterDimensions, centroid));
}
else {
clusters.add(null);
}
}
if(LOG.isDebugging()) {
LOG.debugFine(new StringBuilder().append("clusters ").append(clusters).toString());
}
return clusters;
} | [
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/PROCLUS.java | PROCLUS.finalAssignment | private List<PROCLUSCluster> finalAssignment(List<Pair<double[], long[]>> dimensions, Relation<V> database) {
Map<Integer, ModifiableDBIDs> clusterIDs = new HashMap<>();
for(int i = 0; i < dimensions.size(); i++) {
clusterIDs.put(i, DBIDUtil.newHashSet());
}
for(DBIDIter it = database.iterDBIDs(); it.valid(); it.advance()) {
V p = database.get(it);
double minDist = Double.POSITIVE_INFINITY;
int best = -1;
for(int i = 0; i < dimensions.size(); i++) {
Pair<double[], long[]> pair_i = dimensions.get(i);
double currentDist = manhattanSegmentalDistance(p, pair_i.first, pair_i.second);
if(best < 0 || currentDist < minDist) {
minDist = currentDist;
best = i;
}
}
// add p to cluster with mindist
assert minDist >= 0.;
clusterIDs.get(best).add(it);
}
List<PROCLUSCluster> clusters = new ArrayList<>();
for(int i = 0; i < dimensions.size(); i++) {
ModifiableDBIDs objectIDs = clusterIDs.get(i);
if(!objectIDs.isEmpty()) {
long[] clusterDimensions = dimensions.get(i).second;
double[] centroid = Centroid.make(database, objectIDs).getArrayRef();
clusters.add(new PROCLUSCluster(objectIDs, clusterDimensions, centroid));
}
}
if(LOG.isDebugging()) {
LOG.debugFine(new StringBuilder().append("clusters ").append(clusters).toString());
}
return clusters;
} | java | private List<PROCLUSCluster> finalAssignment(List<Pair<double[], long[]>> dimensions, Relation<V> database) {
Map<Integer, ModifiableDBIDs> clusterIDs = new HashMap<>();
for(int i = 0; i < dimensions.size(); i++) {
clusterIDs.put(i, DBIDUtil.newHashSet());
}
for(DBIDIter it = database.iterDBIDs(); it.valid(); it.advance()) {
V p = database.get(it);
double minDist = Double.POSITIVE_INFINITY;
int best = -1;
for(int i = 0; i < dimensions.size(); i++) {
Pair<double[], long[]> pair_i = dimensions.get(i);
double currentDist = manhattanSegmentalDistance(p, pair_i.first, pair_i.second);
if(best < 0 || currentDist < minDist) {
minDist = currentDist;
best = i;
}
}
// add p to cluster with mindist
assert minDist >= 0.;
clusterIDs.get(best).add(it);
}
List<PROCLUSCluster> clusters = new ArrayList<>();
for(int i = 0; i < dimensions.size(); i++) {
ModifiableDBIDs objectIDs = clusterIDs.get(i);
if(!objectIDs.isEmpty()) {
long[] clusterDimensions = dimensions.get(i).second;
double[] centroid = Centroid.make(database, objectIDs).getArrayRef();
clusters.add(new PROCLUSCluster(objectIDs, clusterDimensions, centroid));
}
}
if(LOG.isDebugging()) {
LOG.debugFine(new StringBuilder().append("clusters ").append(clusters).toString());
}
return clusters;
} | [
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/PROCLUS.java | PROCLUS.manhattanSegmentalDistance | private double manhattanSegmentalDistance(NumberVector o1, double[] o2, long[] dimensions) {
double result = 0;
int card = 0;
for(int d = BitsUtil.nextSetBit(dimensions, 0); d >= 0; d = BitsUtil.nextSetBit(dimensions, d + 1)) {
result += Math.abs(o1.doubleValue(d) - o2[d]);
++card;
}
return result / card;
} | java | private double manhattanSegmentalDistance(NumberVector o1, double[] o2, long[] dimensions) {
double result = 0;
int card = 0;
for(int d = BitsUtil.nextSetBit(dimensions, 0); d >= 0; d = BitsUtil.nextSetBit(dimensions, d + 1)) {
result += Math.abs(o1.doubleValue(d) - o2[d]);
++card;
}
return result / card;
} | [
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@param o1 the first object
@param o2 the second object
@param dimensions the dimensions to be considered
@return the Manhattan segmental distance between o1 and o2 relative to the
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/PROCLUS.java | PROCLUS.evaluateClusters | private double evaluateClusters(ArrayList<PROCLUSCluster> clusters, long[][] dimensions, Relation<V> database) {
double result = 0;
for(int i = 0; i < dimensions.length; i++) {
PROCLUSCluster c_i = clusters.get(i);
double[] centroid_i = c_i.centroid;
long[] dims_i = dimensions[i];
double w_i = 0;
for(int d = BitsUtil.nextSetBit(dims_i, 0); d >= 0; d = BitsUtil.nextSetBit(dims_i, d + 1)) {
w_i += avgDistance(centroid_i, c_i.objectIDs, database, d);
}
w_i /= dimensions.length;
result += c_i.objectIDs.size() * w_i;
}
return result / database.size();
} | java | private double evaluateClusters(ArrayList<PROCLUSCluster> clusters, long[][] dimensions, Relation<V> database) {
double result = 0;
for(int i = 0; i < dimensions.length; i++) {
PROCLUSCluster c_i = clusters.get(i);
double[] centroid_i = c_i.centroid;
long[] dims_i = dimensions[i];
double w_i = 0;
for(int d = BitsUtil.nextSetBit(dims_i, 0); d >= 0; d = BitsUtil.nextSetBit(dims_i, d + 1)) {
w_i += avgDistance(centroid_i, c_i.objectIDs, database, d);
}
w_i /= dimensions.length;
result += c_i.objectIDs.size() * w_i;
}
return result / database.size();
} | [
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/PROCLUS.java | PROCLUS.avgDistance | private double avgDistance(double[] centroid, DBIDs objectIDs, Relation<V> database, int dimension) {
Mean avg = new Mean();
for(DBIDIter iter = objectIDs.iter(); iter.valid(); iter.advance()) {
V o = database.get(iter);
avg.put(Math.abs(centroid[dimension] - o.doubleValue(dimension)));
}
return avg.getMean();
} | java | private double avgDistance(double[] centroid, DBIDs objectIDs, Relation<V> database, int dimension) {
Mean avg = new Mean();
for(DBIDIter iter = objectIDs.iter(); iter.valid(); iter.advance()) {
V o = database.get(iter);
avg.put(Math.abs(centroid[dimension] - o.doubleValue(dimension)));
}
return avg.getMean();
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/PROCLUS.java | PROCLUS.computeBadMedoids | private DBIDs computeBadMedoids(ArrayDBIDs m_current, ArrayList<PROCLUSCluster> clusters, int threshold) {
ModifiableDBIDs badMedoids = DBIDUtil.newHashSet(m_current.size());
int i = 0;
for(DBIDIter it = m_current.iter(); it.valid(); it.advance(), i++) {
PROCLUSCluster c_i = clusters.get(i);
if(c_i == null || c_i.objectIDs.size() < threshold) {
badMedoids.add(it);
}
}
return badMedoids;
} | java | private DBIDs computeBadMedoids(ArrayDBIDs m_current, ArrayList<PROCLUSCluster> clusters, int threshold) {
ModifiableDBIDs badMedoids = DBIDUtil.newHashSet(m_current.size());
int i = 0;
for(DBIDIter it = m_current.iter(); it.valid(); it.advance(), i++) {
PROCLUSCluster c_i = clusters.get(i);
if(c_i == null || c_i.objectIDs.size() < threshold) {
badMedoids.add(it);
}
}
return badMedoids;
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elki-project/elki | elki-core-data/src/main/java/de/lmu/ifi/dbs/elki/data/Bit.java | Bit.valueOf | public static Bit valueOf(String bit) throws NumberFormatException {
final int i = ParseUtil.parseIntBase10(bit);
if(i != 0 && i != 1) {
throw new NumberFormatException("Input \"" + bit + "\" must be 0 or 1.");
}
return (i > 0) ? TRUE : FALSE;
} | java | public static Bit valueOf(String bit) throws NumberFormatException {
final int i = ParseUtil.parseIntBase10(bit);
if(i != 0 && i != 1) {
throw new NumberFormatException("Input \"" + bit + "\" must be 0 or 1.");
}
return (i > 0) ? TRUE : FALSE;
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elki-project/elki | elki-timeseries/src/main/java/de/lmu/ifi/dbs/elki/algorithm/timeseries/OfflineChangePointDetectionAlgorithm.java | OfflineChangePointDetectionAlgorithm.run | public ChangePoints run(Relation<DoubleVector> relation) {
if(!(relation.getDBIDs() instanceof ArrayDBIDs)) {
throw new AbortException("This implementation may only be used on static databases, with ArrayDBIDs to provide a clear order.");
}
return new Instance(rnd.getSingleThreadedRandom()).run(relation);
} | java | public ChangePoints run(Relation<DoubleVector> relation) {
if(!(relation.getDBIDs() instanceof ArrayDBIDs)) {
throw new AbortException("This implementation may only be used on static databases, with ArrayDBIDs to provide a clear order.");
}
return new Instance(rnd.getSingleThreadedRandom()).run(relation);
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elki-project/elki | elki-timeseries/src/main/java/de/lmu/ifi/dbs/elki/algorithm/timeseries/OfflineChangePointDetectionAlgorithm.java | OfflineChangePointDetectionAlgorithm.cusum | public static void cusum(double[] data, double[] out, int begin, int end) {
assert (out.length >= data.length);
// Use Kahan summation for better precision!
// FIXME: this should be unit tested.
double m = 0., carry = 0.;
for(int i = begin; i < end; i++) {
double v = data[i] - carry; // Compensation
double n = out[i] = (m + v); // May lose small digits of v.
carry = (n - m) - v; // Recover lost bits
m = n;
}
} | java | public static void cusum(double[] data, double[] out, int begin, int end) {
assert (out.length >= data.length);
// Use Kahan summation for better precision!
// FIXME: this should be unit tested.
double m = 0., carry = 0.;
for(int i = begin; i < end; i++) {
double v = data[i] - carry; // Compensation
double n = out[i] = (m + v); // May lose small digits of v.
carry = (n - m) - v; // Recover lost bits
m = n;
}
} | [
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elki-project/elki | elki-timeseries/src/main/java/de/lmu/ifi/dbs/elki/algorithm/timeseries/OfflineChangePointDetectionAlgorithm.java | OfflineChangePointDetectionAlgorithm.bestChangeInMean | public static DoubleIntPair bestChangeInMean(double[] sums, int begin, int end) {
final int len = end - begin, last = end - 1;
final double suml = begin > 0 ? sums[begin - 1] : 0.;
final double sumr = sums[last];
int bestpos = begin;
double bestscore = Double.NEGATIVE_INFINITY;
// Iterate elements k=2..n-1 in math notation_
for(int j = begin, km1 = 1; j < last; j++, km1++) {
assert (km1 < len); // FIXME: remove eventually
final double sumj = sums[j]; // Sum _inclusive_ j'th element.
// Derive the left mean and right mean from the precomputed aggregates:
final double lmean = (sumj - suml) / km1;
final double rmean = (sumr - sumj) / (len - km1);
// Equation 2.6.17 from the Basseville book
final double dm = lmean - rmean;
final double score = km1 * (double) (len - km1) * dm * dm;
if(score > bestscore) {
bestpos = j + 1;
bestscore = score;
}
}
return new DoubleIntPair(bestscore, bestpos);
} | java | public static DoubleIntPair bestChangeInMean(double[] sums, int begin, int end) {
final int len = end - begin, last = end - 1;
final double suml = begin > 0 ? sums[begin - 1] : 0.;
final double sumr = sums[last];
int bestpos = begin;
double bestscore = Double.NEGATIVE_INFINITY;
// Iterate elements k=2..n-1 in math notation_
for(int j = begin, km1 = 1; j < last; j++, km1++) {
assert (km1 < len); // FIXME: remove eventually
final double sumj = sums[j]; // Sum _inclusive_ j'th element.
// Derive the left mean and right mean from the precomputed aggregates:
final double lmean = (sumj - suml) / km1;
final double rmean = (sumr - sumj) / (len - km1);
// Equation 2.6.17 from the Basseville book
final double dm = lmean - rmean;
final double score = km1 * (double) (len - km1) * dm * dm;
if(score > bestscore) {
bestpos = j + 1;
bestscore = score;
}
}
return new DoubleIntPair(bestscore, bestpos);
} | [
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elki-project/elki | elki-timeseries/src/main/java/de/lmu/ifi/dbs/elki/algorithm/timeseries/OfflineChangePointDetectionAlgorithm.java | OfflineChangePointDetectionAlgorithm.shuffle | public static void shuffle(double[] bstrap, int len, Random rnd) {
int i = len;
while(i > 0) {
final int r = rnd.nextInt(i);
--i;
// Swap
double tmp = bstrap[r];
bstrap[r] = bstrap[i];
bstrap[i] = tmp;
}
} | java | public static void shuffle(double[] bstrap, int len, Random rnd) {
int i = len;
while(i > 0) {
final int r = rnd.nextInt(i);
--i;
// Swap
double tmp = bstrap[r];
bstrap[r] = bstrap[i];
bstrap[i] = tmp;
}
} | [
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elki-project/elki | elki-core/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/ObjHistogram.java | ObjHistogram.get | @SuppressWarnings("unchecked")
public T get(double coord) {
if(coord == Double.NEGATIVE_INFINITY) {
return getSpecial(0);
}
if(coord == Double.POSITIVE_INFINITY) {
return getSpecial(1);
}
if(Double.isNaN(coord)) {
return getSpecial(2);
}
int bin = getBinNr(coord);
if(bin < 0) {
if(size - bin > data.length) {
// Reallocate. TODO: use an arraylist-like grow strategy!
Object[] tmpdata = new Object[growSize(data.length, size - bin)];
System.arraycopy(data, 0, tmpdata, -bin, size);
data = tmpdata;
}
else {
// Shift in place
System.arraycopy(data, 0, data, -bin, size);
}
for(int i = 0; i < -bin; i++) {
data[i] = supplier.make();
}
// Note that bin is negative, -bin is the shift offset!
offset -= bin;
size -= bin;
// TODO: modCounter++; and have iterators fast-fail
// Unset max value when resizing
max = Double.MAX_VALUE;
return (T) data[0];
}
else if(bin >= size) {
if(bin >= data.length) {
Object[] tmpdata = new Object[growSize(data.length, bin + 1)];
System.arraycopy(data, 0, tmpdata, 0, size);
data = tmpdata;
}
for(int i = size; i <= bin; i++) {
data[i] = supplier.make();
}
size = bin + 1;
// TODO: modCounter++; and have iterators fast-fail
// Unset max value when resizing
max = Double.MAX_VALUE;
return (T) data[bin];
}
else {
return (T) data[bin];
}
} | java | @SuppressWarnings("unchecked")
public T get(double coord) {
if(coord == Double.NEGATIVE_INFINITY) {
return getSpecial(0);
}
if(coord == Double.POSITIVE_INFINITY) {
return getSpecial(1);
}
if(Double.isNaN(coord)) {
return getSpecial(2);
}
int bin = getBinNr(coord);
if(bin < 0) {
if(size - bin > data.length) {
// Reallocate. TODO: use an arraylist-like grow strategy!
Object[] tmpdata = new Object[growSize(data.length, size - bin)];
System.arraycopy(data, 0, tmpdata, -bin, size);
data = tmpdata;
}
else {
// Shift in place
System.arraycopy(data, 0, data, -bin, size);
}
for(int i = 0; i < -bin; i++) {
data[i] = supplier.make();
}
// Note that bin is negative, -bin is the shift offset!
offset -= bin;
size -= bin;
// TODO: modCounter++; and have iterators fast-fail
// Unset max value when resizing
max = Double.MAX_VALUE;
return (T) data[0];
}
else if(bin >= size) {
if(bin >= data.length) {
Object[] tmpdata = new Object[growSize(data.length, bin + 1)];
System.arraycopy(data, 0, tmpdata, 0, size);
data = tmpdata;
}
for(int i = size; i <= bin; i++) {
data[i] = supplier.make();
}
size = bin + 1;
// TODO: modCounter++; and have iterators fast-fail
// Unset max value when resizing
max = Double.MAX_VALUE;
return (T) data[bin];
}
else {
return (T) data[bin];
}
} | [
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elki-project/elki | elki-precomputed/src/main/java/de/lmu/ifi/dbs/elki/distance/distancefunction/external/FileBasedSparseFloatDistanceFunction.java | FileBasedSparseFloatDistanceFunction.loadCache | protected void loadCache(int size, InputStream in) throws IOException {
// Expect a sparse matrix here
cache = new Long2FloatOpenHashMap(size * 20);
cache.defaultReturnValue(Float.POSITIVE_INFINITY);
min = Integer.MAX_VALUE;
max = Integer.MIN_VALUE;
parser.parse(in, new DistanceCacheWriter() {
@Override
public void put(int id1, int id2, double distance) {
if(id1 < id2) {
min = id1 < min ? id1 : min;
max = id2 > max ? id2 : max;
}
else {
min = id2 < min ? id2 : min;
max = id1 > max ? id1 : max;
}
cache.put(makeKey(id1, id2), (float) distance);
}
});
if(min != 0) {
LOG.verbose("Distance matrix is supposed to be 0-indexed. Choosing offset " + min + " to compensate.");
}
if(max + 1 - min != size) {
LOG.warning("ID range is not consistent with relation size.");
}
} | java | protected void loadCache(int size, InputStream in) throws IOException {
// Expect a sparse matrix here
cache = new Long2FloatOpenHashMap(size * 20);
cache.defaultReturnValue(Float.POSITIVE_INFINITY);
min = Integer.MAX_VALUE;
max = Integer.MIN_VALUE;
parser.parse(in, new DistanceCacheWriter() {
@Override
public void put(int id1, int id2, double distance) {
if(id1 < id2) {
min = id1 < min ? id1 : min;
max = id2 > max ? id2 : max;
}
else {
min = id2 < min ? id2 : min;
max = id1 > max ? id1 : max;
}
cache.put(makeKey(id1, id2), (float) distance);
}
});
if(min != 0) {
LOG.verbose("Distance matrix is supposed to be 0-indexed. Choosing offset " + min + " to compensate.");
}
if(max + 1 - min != size) {
LOG.warning("ID range is not consistent with relation size.");
}
} | [
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elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java | SVGPlot.svgElement | public Element svgElement(String name, String cssclass) {
Element elem = SVGUtil.svgElement(document, name);
if(cssclass != null) {
elem.setAttribute(SVGConstants.SVG_CLASS_ATTRIBUTE, cssclass);
}
return elem;
} | java | public Element svgElement(String name, String cssclass) {
Element elem = SVGUtil.svgElement(document, name);
if(cssclass != null) {
elem.setAttribute(SVGConstants.SVG_CLASS_ATTRIBUTE, cssclass);
}
return elem;
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elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java | SVGPlot.svgRect | public Element svgRect(double x, double y, double w, double h) {
return SVGUtil.svgRect(document, x, y, w, h);
} | java | public Element svgRect(double x, double y, double w, double h) {
return SVGUtil.svgRect(document, x, y, w, h);
} | [
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] | b54673327e76198ecd4c8a2a901021f1a9174498 | https://github.com/elki-project/elki/blob/b54673327e76198ecd4c8a2a901021f1a9174498/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java#L254-L256 | train |
elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java | SVGPlot.svgCircle | public Element svgCircle(double cx, double cy, double r) {
return SVGUtil.svgCircle(document, cx, cy, r);
} | java | public Element svgCircle(double cx, double cy, double r) {
return SVGUtil.svgCircle(document, cx, cy, r);
} | [
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@param r radius
@return new element | [
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elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java | SVGPlot.svgLine | public Element svgLine(double x1, double y1, double x2, double y2) {
return SVGUtil.svgLine(document, x1, y1, x2, y2);
} | java | public Element svgLine(double x1, double y1, double x2, double y2) {
return SVGUtil.svgLine(document, x1, y1, x2, y2);
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@param x2 second point x
@param y2 second point y
@return new element | [
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] | b54673327e76198ecd4c8a2a901021f1a9174498 | https://github.com/elki-project/elki/blob/b54673327e76198ecd4c8a2a901021f1a9174498/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java#L279-L281 | train |
elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java | SVGPlot.elementCoordinatesFromEvent | public SVGPoint elementCoordinatesFromEvent(Element tag, Event evt) {
return SVGUtil.elementCoordinatesFromEvent(document, tag, evt);
} | java | public SVGPoint elementCoordinatesFromEvent(Element tag, Event evt) {
return SVGUtil.elementCoordinatesFromEvent(document, tag, evt);
} | [
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] | b54673327e76198ecd4c8a2a901021f1a9174498 | https://github.com/elki-project/elki/blob/b54673327e76198ecd4c8a2a901021f1a9174498/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java#L302-L304 | train |
elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java | SVGPlot.addCSSClassOrLogError | public void addCSSClassOrLogError(CSSClass cls) {
try {
cssman.addClass(cls);
}
catch(CSSNamingConflict e) {
LoggingUtil.exception(e);
}
} | java | public void addCSSClassOrLogError(CSSClass cls) {
try {
cssman.addClass(cls);
}
catch(CSSNamingConflict e) {
LoggingUtil.exception(e);
}
} | [
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] | b54673327e76198ecd4c8a2a901021f1a9174498 | https://github.com/elki-project/elki/blob/b54673327e76198ecd4c8a2a901021f1a9174498/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java#L361-L368 | train |
elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java | SVGPlot.updateStyleElement | public void updateStyleElement() {
// TODO: this should be sufficient - why does Batik occasionally not pick up
// the changes unless we actually replace the style element itself?
// cssman.updateStyleElement(document, style);
Element newstyle = cssman.makeStyleElement(document);
style.getParentNode().replaceChild(newstyle, style);
style = newstyle;
} | java | public void updateStyleElement() {
// TODO: this should be sufficient - why does Batik occasionally not pick up
// the changes unless we actually replace the style element itself?
// cssman.updateStyleElement(document, style);
Element newstyle = cssman.makeStyleElement(document);
style.getParentNode().replaceChild(newstyle, style);
style = newstyle;
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elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java | SVGPlot.saveAsSVG | public void saveAsSVG(File file) throws IOException, TransformerFactoryConfigurationError, TransformerException {
OutputStream out = new BufferedOutputStream(new FileOutputStream(file));
// TODO embed linked images.
javax.xml.transform.Result result = new StreamResult(out);
SVGDocument doc = cloneDocument();
// Use a transformer for pretty printing
Transformer xformer = TransformerFactory.newInstance().newTransformer();
xformer.setOutputProperty(OutputKeys.INDENT, "yes");
xformer.transform(new DOMSource(doc), result);
out.flush();
out.close();
} | java | public void saveAsSVG(File file) throws IOException, TransformerFactoryConfigurationError, TransformerException {
OutputStream out = new BufferedOutputStream(new FileOutputStream(file));
// TODO embed linked images.
javax.xml.transform.Result result = new StreamResult(out);
SVGDocument doc = cloneDocument();
// Use a transformer for pretty printing
Transformer xformer = TransformerFactory.newInstance().newTransformer();
xformer.setOutputProperty(OutputKeys.INDENT, "yes");
xformer.transform(new DOMSource(doc), result);
out.flush();
out.close();
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@throws TransformerFactoryConfigurationError Transformation error
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] | b54673327e76198ecd4c8a2a901021f1a9174498 | https://github.com/elki-project/elki/blob/b54673327e76198ecd4c8a2a901021f1a9174498/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java#L394-L405 | train |
elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java | SVGPlot.transcode | protected void transcode(File file, Transcoder transcoder) throws IOException, TranscoderException {
// Disable validation, performance is more important here (thumbnails!)
transcoder.addTranscodingHint(XMLAbstractTranscoder.KEY_XML_PARSER_VALIDATING, Boolean.FALSE);
SVGDocument doc = cloneDocument();
TranscoderInput input = new TranscoderInput(doc);
OutputStream out = new BufferedOutputStream(new FileOutputStream(file));
TranscoderOutput output = new TranscoderOutput(out);
transcoder.transcode(input, output);
out.flush();
out.close();
} | java | protected void transcode(File file, Transcoder transcoder) throws IOException, TranscoderException {
// Disable validation, performance is more important here (thumbnails!)
transcoder.addTranscodingHint(XMLAbstractTranscoder.KEY_XML_PARSER_VALIDATING, Boolean.FALSE);
SVGDocument doc = cloneDocument();
TranscoderInput input = new TranscoderInput(doc);
OutputStream out = new BufferedOutputStream(new FileOutputStream(file));
TranscoderOutput output = new TranscoderOutput(out);
transcoder.transcode(input, output);
out.flush();
out.close();
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elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java | SVGPlot.cloneDocument | protected SVGDocument cloneDocument() {
return (SVGDocument) new CloneInlineImages() {
@Override
public Node cloneNode(Document doc, Node eold) {
// Skip elements with noexport attribute set
if(eold instanceof Element) {
Element eeold = (Element) eold;
String vis = eeold.getAttribute(NO_EXPORT_ATTRIBUTE);
if(vis != null && vis.length() > 0) {
return null;
}
}
return super.cloneNode(doc, eold);
}
}.cloneDocument(getDomImpl(), document);
} | java | protected SVGDocument cloneDocument() {
return (SVGDocument) new CloneInlineImages() {
@Override
public Node cloneNode(Document doc, Node eold) {
// Skip elements with noexport attribute set
if(eold instanceof Element) {
Element eeold = (Element) eold;
String vis = eeold.getAttribute(NO_EXPORT_ATTRIBUTE);
if(vis != null && vis.length() > 0) {
return null;
}
}
return super.cloneNode(doc, eold);
}
}.cloneDocument(getDomImpl(), document);
} | [
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elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java | SVGPlot.saveAsPDF | public void saveAsPDF(File file) throws IOException, TranscoderException, ClassNotFoundException {
try {
Object t = Class.forName("org.apache.fop.svg.PDFTranscoder").newInstance();
transcode(file, (Transcoder) t);
}
catch(InstantiationException | IllegalAccessException e) {
throw new ClassNotFoundException("Could not instantiate PDF transcoder - is Apache FOP installed?", e);
}
} | java | public void saveAsPDF(File file) throws IOException, TranscoderException, ClassNotFoundException {
try {
Object t = Class.forName("org.apache.fop.svg.PDFTranscoder").newInstance();
transcode(file, (Transcoder) t);
}
catch(InstantiationException | IllegalAccessException e) {
throw new ClassNotFoundException("Could not instantiate PDF transcoder - is Apache FOP installed?", e);
}
} | [
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elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java | SVGPlot.saveAsPNG | public void saveAsPNG(File file, int width, int height) throws IOException, TranscoderException {
PNGTranscoder t = new PNGTranscoder();
t.addTranscodingHint(PNGTranscoder.KEY_WIDTH, new Float(width));
t.addTranscodingHint(PNGTranscoder.KEY_HEIGHT, new Float(height));
transcode(file, t);
} | java | public void saveAsPNG(File file, int width, int height) throws IOException, TranscoderException {
PNGTranscoder t = new PNGTranscoder();
t.addTranscodingHint(PNGTranscoder.KEY_WIDTH, new Float(width));
t.addTranscodingHint(PNGTranscoder.KEY_HEIGHT, new Float(height));
transcode(file, t);
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elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java | SVGPlot.saveAsANY | public void saveAsANY(File file, int width, int height, float quality) throws IOException, TranscoderException, TransformerFactoryConfigurationError, TransformerException, ClassNotFoundException {
String extension = FileUtil.getFilenameExtension(file);
if("svg".equals(extension)) {
saveAsSVG(file);
}
else if("pdf".equals(extension)) {
saveAsPDF(file);
}
else if("ps".equals(extension)) {
saveAsPS(file);
}
else if("eps".equals(extension)) {
saveAsEPS(file);
}
else if("png".equals(extension)) {
saveAsPNG(file, width, height);
}
else if("jpg".equals(extension) || "jpeg".equals(extension)) {
saveAsJPEG(file, width, height, quality);
}
else {
throw new IOException("Unknown file extension: " + extension);
}
} | java | public void saveAsANY(File file, int width, int height, float quality) throws IOException, TranscoderException, TransformerFactoryConfigurationError, TransformerException, ClassNotFoundException {
String extension = FileUtil.getFilenameExtension(file);
if("svg".equals(extension)) {
saveAsSVG(file);
}
else if("pdf".equals(extension)) {
saveAsPDF(file);
}
else if("ps".equals(extension)) {
saveAsPS(file);
}
else if("eps".equals(extension)) {
saveAsEPS(file);
}
else if("png".equals(extension)) {
saveAsPNG(file, width, height);
}
else if("jpg".equals(extension) || "jpeg".equals(extension)) {
saveAsJPEG(file, width, height, quality);
}
else {
throw new IOException("Unknown file extension: " + extension);
}
} | [
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@param width Width (for pixel formats)
@param height Height (for pixel formats)
@param quality Quality (for lossy compression)
@throws IOException on file write errors or unrecognized file extensions
@throws TranscoderException on transcoding errors
@throws TransformerFactoryConfigurationError on transcoding errors
@throws TransformerException on transcoding errors
@throws ClassNotFoundException when the transcoder was not installed | [
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] | b54673327e76198ecd4c8a2a901021f1a9174498 | https://github.com/elki-project/elki/blob/b54673327e76198ecd4c8a2a901021f1a9174498/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java#L567-L590 | train |
elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java | SVGPlot.makeAWTImage | public BufferedImage makeAWTImage(int width, int height) throws TranscoderException {
ThumbnailTranscoder t = new ThumbnailTranscoder();
t.addTranscodingHint(PNGTranscoder.KEY_WIDTH, new Float(width));
t.addTranscodingHint(PNGTranscoder.KEY_HEIGHT, new Float(height));
// Don't clone. Assume this is used safely.
TranscoderInput input = new TranscoderInput(document);
t.transcode(input, null);
return t.getLastImage();
} | java | public BufferedImage makeAWTImage(int width, int height) throws TranscoderException {
ThumbnailTranscoder t = new ThumbnailTranscoder();
t.addTranscodingHint(PNGTranscoder.KEY_WIDTH, new Float(width));
t.addTranscodingHint(PNGTranscoder.KEY_HEIGHT, new Float(height));
// Don't clone. Assume this is used safely.
TranscoderInput input = new TranscoderInput(document);
t.transcode(input, null);
return t.getLastImage();
} | [
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@param width Width of thumbnail
@param height Height of thumbnail
@return Buffered image | [
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] | b54673327e76198ecd4c8a2a901021f1a9174498 | https://github.com/elki-project/elki/blob/b54673327e76198ecd4c8a2a901021f1a9174498/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java#L599-L607 | train |
elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java | SVGPlot.dumpDebugFile | public void dumpDebugFile() {
try {
File f = File.createTempFile("elki-debug", ".svg");
f.deleteOnExit();
this.saveAsSVG(f);
LoggingUtil.warning("Saved debug file to: " + f.getAbsolutePath());
}
catch(Throwable err) {
// Ignore.
}
} | java | public void dumpDebugFile() {
try {
File f = File.createTempFile("elki-debug", ".svg");
f.deleteOnExit();
this.saveAsSVG(f);
LoggingUtil.warning("Saved debug file to: " + f.getAbsolutePath());
}
catch(Throwable err) {
// Ignore.
}
} | [
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] | b54673327e76198ecd4c8a2a901021f1a9174498 | https://github.com/elki-project/elki/blob/b54673327e76198ecd4c8a2a901021f1a9174498/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java#L612-L622 | train |
elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java | SVGPlot.putIdElement | public void putIdElement(String id, Element obj) {
objWithId.put(id, new WeakReference<>(obj));
} | java | public void putIdElement(String id, Element obj) {
objWithId.put(id, new WeakReference<>(obj));
} | [
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@param id ID
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] | b54673327e76198ecd4c8a2a901021f1a9174498 | https://github.com/elki-project/elki/blob/b54673327e76198ecd4c8a2a901021f1a9174498/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java#L630-L632 | train |
elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java | SVGPlot.getIdElement | public Element getIdElement(String id) {
WeakReference<Element> ref = objWithId.get(id);
return (ref != null) ? ref.get() : null;
} | java | public Element getIdElement(String id) {
WeakReference<Element> ref = objWithId.get(id);
return (ref != null) ? ref.get() : null;
} | [
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@param id ID
@return Element | [
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] | b54673327e76198ecd4c8a2a901021f1a9174498 | https://github.com/elki-project/elki/blob/b54673327e76198ecd4c8a2a901021f1a9174498/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGPlot.java#L640-L643 | train |
elki-project/elki | elki-outlier/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/JudgeOutlierScores.java | JudgeOutlierScores.computeScore | protected ScoreResult computeScore(DBIDs ids, DBIDs outlierIds, OutlierResult or) throws IllegalStateException {
if(scaling instanceof OutlierScaling) {
OutlierScaling oscaling = (OutlierScaling) scaling;
oscaling.prepare(or);
}
final ScalingFunction innerScaling;
// If we have useful (finite) min/max, use these for binning.
double min = scaling.getMin();
double max = scaling.getMax();
if(Double.isInfinite(min) || Double.isNaN(min) || Double.isInfinite(max) || Double.isNaN(max)) {
innerScaling = new IdentityScaling();
// TODO: does the outlier score give us this guarantee?
LOG.warning("JudgeOutlierScores expects values between 0.0 and 1.0, but we don't have such a guarantee by the scaling function: min:" + min + " max:" + max);
}
else {
if(min == 0.0 && max == 1.0) {
innerScaling = new IdentityScaling();
}
else {
innerScaling = new LinearScaling(1.0 / (max - min), -min);
}
}
double posscore = 0.0;
double negscore = 0.0;
// fill histogram with values of each object
for(DBIDIter iter = ids.iter(); iter.valid(); iter.advance()) {
double result = or.getScores().doubleValue(iter);
result = innerScaling.getScaled(scaling.getScaled(result));
posscore += (1.0 - result);
}
for(DBIDIter iter = outlierIds.iter(); iter.valid(); iter.advance()) {
double result = or.getScores().doubleValue(iter);
result = innerScaling.getScaled(scaling.getScaled(result));
negscore += result;
}
posscore /= ids.size();
negscore /= outlierIds.size();
LOG.verbose("Scores: " + posscore + " " + negscore);
ArrayList<double[]> s = new ArrayList<>(1);
s.add(new double[] { (posscore + negscore) * .5, posscore, negscore });
return new ScoreResult(s);
} | java | protected ScoreResult computeScore(DBIDs ids, DBIDs outlierIds, OutlierResult or) throws IllegalStateException {
if(scaling instanceof OutlierScaling) {
OutlierScaling oscaling = (OutlierScaling) scaling;
oscaling.prepare(or);
}
final ScalingFunction innerScaling;
// If we have useful (finite) min/max, use these for binning.
double min = scaling.getMin();
double max = scaling.getMax();
if(Double.isInfinite(min) || Double.isNaN(min) || Double.isInfinite(max) || Double.isNaN(max)) {
innerScaling = new IdentityScaling();
// TODO: does the outlier score give us this guarantee?
LOG.warning("JudgeOutlierScores expects values between 0.0 and 1.0, but we don't have such a guarantee by the scaling function: min:" + min + " max:" + max);
}
else {
if(min == 0.0 && max == 1.0) {
innerScaling = new IdentityScaling();
}
else {
innerScaling = new LinearScaling(1.0 / (max - min), -min);
}
}
double posscore = 0.0;
double negscore = 0.0;
// fill histogram with values of each object
for(DBIDIter iter = ids.iter(); iter.valid(); iter.advance()) {
double result = or.getScores().doubleValue(iter);
result = innerScaling.getScaled(scaling.getScaled(result));
posscore += (1.0 - result);
}
for(DBIDIter iter = outlierIds.iter(); iter.valid(); iter.advance()) {
double result = or.getScores().doubleValue(iter);
result = innerScaling.getScaled(scaling.getScaled(result));
negscore += result;
}
posscore /= ids.size();
negscore /= outlierIds.size();
LOG.verbose("Scores: " + posscore + " " + negscore);
ArrayList<double[]> s = new ArrayList<>(1);
s.add(new double[] { (posscore + negscore) * .5, posscore, negscore });
return new ScoreResult(s);
} | [
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... | Evaluate a single outlier score result.
@param ids Inlier IDs
@param outlierIds Outlier IDs
@param or Outlier Result to evaluate
@return Outlier score result
@throws IllegalStateException | [
"Evaluate",
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"."
] | b54673327e76198ecd4c8a2a901021f1a9174498 | https://github.com/elki-project/elki/blob/b54673327e76198ecd4c8a2a901021f1a9174498/elki-outlier/src/main/java/de/lmu/ifi/dbs/elki/evaluation/outlier/JudgeOutlierScores.java#L100-L145 | train |
elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/FastDOC.java | FastDOC.runDOC | @Override
protected Cluster<SubspaceModel> runDOC(Database database, Relation<V> relation, ArrayModifiableDBIDs S, int d, int n, int m, int r, int minClusterSize) {
// Relevant attributes of highest cardinality.
long[] D = null;
// The seed point for the best dimensions.
DBIDVar dV = DBIDUtil.newVar();
// Inform the user about the progress in the current iteration.
FiniteProgress iprogress = LOG.isVerbose() ? new FiniteProgress("Iteration progress for current cluster", m * n, LOG) : null;
Random random = rnd.getSingleThreadedRandom();
DBIDArrayIter iter = S.iter();
outer: for(int i = 0; i < n; ++i) {
// Pick a random seed point.
iter.seek(random.nextInt(S.size()));
for(int j = 0; j < m; ++j) {
// Choose a set of random points.
DBIDs randomSet = DBIDUtil.randomSample(S, r, random);
// Initialize cluster info.
long[] nD = BitsUtil.zero(d);
// Test each dimension.
for(int k = 0; k < d; ++k) {
if(dimensionIsRelevant(k, relation, randomSet)) {
BitsUtil.setI(nD, k);
}
}
if(D == null || BitsUtil.cardinality(nD) > BitsUtil.cardinality(D)) {
D = nD;
dV.set(iter);
if(BitsUtil.cardinality(D) >= d_zero) {
if(iprogress != null) {
iprogress.setProcessed(iprogress.getTotal(), LOG);
}
break outer;
}
}
LOG.incrementProcessed(iprogress);
}
}
LOG.ensureCompleted(iprogress);
// If no relevant dimensions were found, skip it.
if(D == null || BitsUtil.cardinality(D) == 0) {
return null;
}
// Get all points in the box.
DBIDs C = findNeighbors(dV, D, S, relation);
// If we have a non-empty cluster, return it.
return (C.size() >= minClusterSize) ? makeCluster(relation, C, D) : null;
} | java | @Override
protected Cluster<SubspaceModel> runDOC(Database database, Relation<V> relation, ArrayModifiableDBIDs S, int d, int n, int m, int r, int minClusterSize) {
// Relevant attributes of highest cardinality.
long[] D = null;
// The seed point for the best dimensions.
DBIDVar dV = DBIDUtil.newVar();
// Inform the user about the progress in the current iteration.
FiniteProgress iprogress = LOG.isVerbose() ? new FiniteProgress("Iteration progress for current cluster", m * n, LOG) : null;
Random random = rnd.getSingleThreadedRandom();
DBIDArrayIter iter = S.iter();
outer: for(int i = 0; i < n; ++i) {
// Pick a random seed point.
iter.seek(random.nextInt(S.size()));
for(int j = 0; j < m; ++j) {
// Choose a set of random points.
DBIDs randomSet = DBIDUtil.randomSample(S, r, random);
// Initialize cluster info.
long[] nD = BitsUtil.zero(d);
// Test each dimension.
for(int k = 0; k < d; ++k) {
if(dimensionIsRelevant(k, relation, randomSet)) {
BitsUtil.setI(nD, k);
}
}
if(D == null || BitsUtil.cardinality(nD) > BitsUtil.cardinality(D)) {
D = nD;
dV.set(iter);
if(BitsUtil.cardinality(D) >= d_zero) {
if(iprogress != null) {
iprogress.setProcessed(iprogress.getTotal(), LOG);
}
break outer;
}
}
LOG.incrementProcessed(iprogress);
}
}
LOG.ensureCompleted(iprogress);
// If no relevant dimensions were found, skip it.
if(D == null || BitsUtil.cardinality(D) == 0) {
return null;
}
// Get all points in the box.
DBIDs C = findNeighbors(dV, D, S, relation);
// If we have a non-empty cluster, return it.
return (C.size() >= minClusterSize) ? makeCluster(relation, C, D) : null;
} | [
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@param database Database context
@param relation used to get actual values for DBIDs.
@param S The set of points we're working on.
@param d Dimensionality of the data set we're currently working on.
@param r Size of random samples.
@param m Number of inner iterations (per seed point).
@param n Number of outer iterations (seed points).
@param minClusterSize Minimum size a cluster must have to be accepted.
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] | b54673327e76198ecd4c8a2a901021f1a9174498 | https://github.com/elki-project/elki/blob/b54673327e76198ecd4c8a2a901021f1a9174498/elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/subspace/FastDOC.java#L101-L158 | train |
elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/VoronoiDraw.java | VoronoiDraw.drawDelaunay | public static SVGPath drawDelaunay(Projection2D proj, List<SweepHullDelaunay2D.Triangle> delaunay, List<double[]> means) {
final SVGPath path = new SVGPath();
for(SweepHullDelaunay2D.Triangle del : delaunay) {
path.moveTo(proj.fastProjectDataToRenderSpace(means.get(del.a)));
path.drawTo(proj.fastProjectDataToRenderSpace(means.get(del.b)));
path.drawTo(proj.fastProjectDataToRenderSpace(means.get(del.c)));
path.close();
}
return path;
} | java | public static SVGPath drawDelaunay(Projection2D proj, List<SweepHullDelaunay2D.Triangle> delaunay, List<double[]> means) {
final SVGPath path = new SVGPath();
for(SweepHullDelaunay2D.Triangle del : delaunay) {
path.moveTo(proj.fastProjectDataToRenderSpace(means.get(del.a)));
path.drawTo(proj.fastProjectDataToRenderSpace(means.get(del.b)));
path.drawTo(proj.fastProjectDataToRenderSpace(means.get(del.c)));
path.close();
}
return path;
} | [
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@param proj Projection
@param delaunay Triangulation
@param means Means
@return Path | [
"Draw",
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"triangulation",
"."
] | b54673327e76198ecd4c8a2a901021f1a9174498 | https://github.com/elki-project/elki/blob/b54673327e76198ecd4c8a2a901021f1a9174498/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/VoronoiDraw.java#L57-L66 | train |
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