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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/birch/ClusteringFeature.java | ClusteringFeature.addToStatistics | protected void addToStatistics(NumberVector nv) {
final int d = nv.getDimensionality();
assert (d == ls.length);
this.n++;
for(int i = 0; i < d; i++) {
double v = nv.doubleValue(i);
ls[i] += v;
ss += v * v;
}
} | java | protected void addToStatistics(NumberVector nv) {
final int d = nv.getDimensionality();
assert (d == ls.length);
this.n++;
for(int i = 0; i < d; i++) {
double v = nv.doubleValue(i);
ls[i] += v;
ss += v * v;
}
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/birch/ClusteringFeature.java | ClusteringFeature.addToStatistics | protected void addToStatistics(ClusteringFeature other) {
n += other.n;
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ss += other.ss;
} | java | protected void addToStatistics(ClusteringFeature other) {
n += other.n;
VMath.plusEquals(ls, other.ls);
ss += other.ss;
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/birch/ClusteringFeature.java | ClusteringFeature.sumOfSquaresOfSums | public double sumOfSquaresOfSums() {
double sum = 0.;
for(int i = 0; i < ls.length; i++) {
double v = ls[i];
sum += v * v;
}
return sum;
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double sum = 0.;
for(int i = 0; i < ls.length; i++) {
double v = ls[i];
sum += v * v;
}
return sum;
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/birch/ClusteringFeature.java | ClusteringFeature.sumOfSquares | public static double sumOfSquares(NumberVector v) {
final int dim = v.getDimensionality();
double sum = 0;
for(int d = 0; d < dim; d++) {
double x = v.doubleValue(d);
sum += x * x;
}
return sum;
} | java | public static double sumOfSquares(NumberVector v) {
final int dim = v.getDimensionality();
double sum = 0;
for(int d = 0; d < dim; d++) {
double x = v.doubleValue(d);
sum += x * x;
}
return sum;
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elki-project/elki | elki-core-util/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/arrays/IntegerArrayQuickSort.java | IntegerArrayQuickSort.insertionSort | private static void insertionSort(int[] data, final int start, final int end, IntComparator comp) {
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final int cur = data[i];
int j = i - 1;
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final int pre = data[j];
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// Classic insertion sort.
for(int i = start + 1; i < end; i++) {
final int cur = data[i];
int j = i - 1;
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elki-project/elki | elki-core/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/WeightedCovarianceMatrixBuilder.java | WeightedCovarianceMatrixBuilder.processIds | @Override
public double[][] processIds(DBIDs ids, Relation<? extends NumberVector> relation) {
final int dim = RelationUtil.dimensionality(relation);
final CovarianceMatrix cmat = new CovarianceMatrix(dim);
final Centroid centroid = Centroid.make(relation, ids);
// find maximum distance
double ma... | java | @Override
public double[][] processIds(DBIDs ids, Relation<? extends NumberVector> relation) {
final int dim = RelationUtil.dimensionality(relation);
final CovarianceMatrix cmat = new CovarianceMatrix(dim);
final Centroid centroid = Centroid.make(relation, ids);
// find maximum distance
double ma... | [
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elki-project/elki | elki-core/src/main/java/de/lmu/ifi/dbs/elki/math/linearalgebra/pca/WeightedCovarianceMatrixBuilder.java | WeightedCovarianceMatrixBuilder.processQueryResults | @Override
public double[][] processQueryResults(DoubleDBIDList results, Relation<? extends NumberVector> database, int k) {
final int dim = RelationUtil.dimensionality(database);
final CovarianceMatrix cmat = new CovarianceMatrix(dim);
// avoid bad parameters
k = k <= results.size() ? k : results.siz... | java | @Override
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final int dim = RelationUtil.dimensionality(database);
final CovarianceMatrix cmat = new CovarianceMatrix(dim);
// avoid bad parameters
k = k <= results.size() ? k : results.siz... | [
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/gdbscan/ERiCNeighborPredicate.java | ERiCNeighborPredicate.instantiate | public Instance instantiate(Database database, Relation<V> relation) {
DistanceQuery<V> dq = database.getDistanceQuery(relation, EuclideanDistanceFunction.STATIC);
KNNQuery<V> knnq = database.getKNNQuery(dq, settings.k);
WritableDataStore<PCAFilteredResult> storage = DataStoreUtil.makeStorage(relation.getD... | java | public Instance instantiate(Database database, Relation<V> relation) {
DistanceQuery<V> dq = database.getDistanceQuery(relation, EuclideanDistanceFunction.STATIC);
KNNQuery<V> knnq = database.getKNNQuery(dq, settings.k);
WritableDataStore<PCAFilteredResult> storage = DataStoreUtil.makeStorage(relation.getD... | [
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elki-project/elki | elki-docutil/src/main/java/de/lmu/ifi/dbs/elki/utilities/xml/HTMLUtil.java | HTMLUtil.writeXHTML | public static void writeXHTML(Document htmldoc, OutputStream out) throws IOException {
javax.xml.transform.Result result = new StreamResult(out);
// Use a transformer for pretty printing
Transformer xformer;
try {
xformer = TransformerFactory.newInstance().newTransformer();
xformer.setOutput... | java | public static void writeXHTML(Document htmldoc, OutputStream out) throws IOException {
javax.xml.transform.Result result = new StreamResult(out);
// Use a transformer for pretty printing
Transformer xformer;
try {
xformer = TransformerFactory.newInstance().newTransformer();
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elki-project/elki | elki-docutil/src/main/java/de/lmu/ifi/dbs/elki/utilities/xml/HTMLUtil.java | HTMLUtil.appendMultilineText | public static Element appendMultilineText(Document htmldoc, Element parent, String text) {
String[] parts = text != null ? text.split("\n") : null;
if(parts == null || parts.length == 0) {
return parent;
}
parent.appendChild(htmldoc.createTextNode(parts[0]));
for(int i = 1; i < parts.length; i... | java | public static Element appendMultilineText(Document htmldoc, Element parent, String text) {
String[] parts = text != null ? text.split("\n") : null;
if(parts == null || parts.length == 0) {
return parent;
}
parent.appendChild(htmldoc.createTextNode(parts[0]));
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elki-project/elki | elki-index/src/main/java/de/lmu/ifi/dbs/elki/index/tree/IndexTreePath.java | IndexTreePath.getPathCount | public int getPathCount() {
int result = 0;
for(IndexTreePath<E> path = this; path != null; path = path.parentPath) {
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return result;
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int result = 0;
for(IndexTreePath<E> path = this; path != null; path = path.parentPath) {
result++;
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return result;
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elki-project/elki | elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/clustering/CBLOF.java | CBLOF.run | public OutlierResult run(Database database, Relation<O> relation) {
StepProgress stepprog = LOG.isVerbose() ? new StepProgress("CBLOF", 3) : null;
DBIDs ids = relation.getDBIDs();
LOG.beginStep(stepprog, 1, "Computing clustering.");
Clustering<MeanModel> clustering = clusteringAlgorithm.run(database);
... | java | public OutlierResult run(Database database, Relation<O> relation) {
StepProgress stepprog = LOG.isVerbose() ? new StepProgress("CBLOF", 3) : null;
DBIDs ids = relation.getDBIDs();
LOG.beginStep(stepprog, 1, "Computing clustering.");
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elki-project/elki | elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/clustering/CBLOF.java | CBLOF.getClusterBoundary | private int getClusterBoundary(Relation<O> relation, List<? extends Cluster<MeanModel>> clusters) {
int totalSize = relation.size();
int clusterBoundary = clusters.size() - 1;
int cumulativeSize = 0;
for(int i = 0; i < clusters.size() - 1; i++) {
cumulativeSize += clusters.get(i).size();
//... | java | private int getClusterBoundary(Relation<O> relation, List<? extends Cluster<MeanModel>> clusters) {
int totalSize = relation.size();
int clusterBoundary = clusters.size() - 1;
int cumulativeSize = 0;
for(int i = 0; i < clusters.size() - 1; i++) {
cumulativeSize += clusters.get(i).size();
//... | [
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elki-project/elki | elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/clustering/CBLOF.java | CBLOF.computeCBLOFs | private void computeCBLOFs(Relation<O> relation, NumberVectorDistanceFunction<? super O> distance, WritableDoubleDataStore cblofs, DoubleMinMax cblofMinMax, List<? extends Cluster<MeanModel>> largeClusters, List<? extends Cluster<MeanModel>> smallClusters) {
List<NumberVector> largeClusterMeans = new ArrayList<>(la... | java | private void computeCBLOFs(Relation<O> relation, NumberVectorDistanceFunction<? super O> distance, WritableDoubleDataStore cblofs, DoubleMinMax cblofMinMax, List<? extends Cluster<MeanModel>> largeClusters, List<? extends Cluster<MeanModel>> smallClusters) {
List<NumberVector> largeClusterMeans = new ArrayList<>(la... | [
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@param relation Data to process
@param distance The distance function
@param cblofs CBLOF scores
@param cblofMinMax Minimum/maximum score tracker
@param largeClusters Large clusters output
@param smallClusters Small clusters output | [
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elki-project/elki | elki-data-generator/src/main/java/de/lmu/ifi/dbs/elki/datasource/GeneratorXMLDatabaseConnection.java | GeneratorXMLDatabaseConnection.loadXMLSpecification | private GeneratorMain loadXMLSpecification() {
try {
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
dbf.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
URL url = ClassLoader.getSystemResource(GENERATOR_SCHEMA_FILE);
if(url != null) {
... | java | private GeneratorMain loadXMLSpecification() {
try {
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
dbf.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
URL url = ClassLoader.getSystemResource(GENERATOR_SCHEMA_FILE);
if(url != null) {
... | [
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elki-project/elki | elki-data-generator/src/main/java/de/lmu/ifi/dbs/elki/datasource/GeneratorXMLDatabaseConnection.java | GeneratorXMLDatabaseConnection.processElementDataset | private void processElementDataset(GeneratorMain gen, Node cur) {
// *** get parameters
String seedstr = ((Element) cur).getAttribute(ATTR_SEED);
if(clusterRandom != RandomFactory.DEFAULT && seedstr != null && seedstr.length() > 0) {
clusterRandom = new RandomFactory((long) (ParseUtil.parseIntBase10(s... | java | private void processElementDataset(GeneratorMain gen, Node cur) {
// *** get parameters
String seedstr = ((Element) cur).getAttribute(ATTR_SEED);
if(clusterRandom != RandomFactory.DEFAULT && seedstr != null && seedstr.length() > 0) {
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elki-project/elki | elki-data-generator/src/main/java/de/lmu/ifi/dbs/elki/datasource/GeneratorXMLDatabaseConnection.java | GeneratorXMLDatabaseConnection.processElementCluster | private void processElementCluster(GeneratorMain gen, Node cur) {
int size = -1;
double overweight = 1.0;
String sizestr = ((Element) cur).getAttribute(ATTR_SIZE);
if(sizestr != null && sizestr.length() > 0) {
size = (int) (ParseUtil.parseIntBase10(sizestr) * sizescale);
}
String name = ... | java | private void processElementCluster(GeneratorMain gen, Node cur) {
int size = -1;
double overweight = 1.0;
String sizestr = ((Element) cur).getAttribute(ATTR_SIZE);
if(sizestr != null && sizestr.length() > 0) {
size = (int) (ParseUtil.parseIntBase10(sizestr) * sizescale);
}
String name = ... | [
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elki-project/elki | elki-data-generator/src/main/java/de/lmu/ifi/dbs/elki/datasource/GeneratorXMLDatabaseConnection.java | GeneratorXMLDatabaseConnection.processElementUniform | private void processElementUniform(GeneratorSingleCluster cluster, Node cur) {
double min = 0.0;
double max = 1.0;
String minstr = ((Element) cur).getAttribute(ATTR_MIN);
if(minstr != null && minstr.length() > 0) {
min = ParseUtil.parseDouble(minstr);
}
String maxstr = ((Element) cur).get... | java | private void processElementUniform(GeneratorSingleCluster cluster, Node cur) {
double min = 0.0;
double max = 1.0;
String minstr = ((Element) cur).getAttribute(ATTR_MIN);
if(minstr != null && minstr.length() > 0) {
min = ParseUtil.parseDouble(minstr);
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elki-project/elki | elki-data-generator/src/main/java/de/lmu/ifi/dbs/elki/datasource/GeneratorXMLDatabaseConnection.java | GeneratorXMLDatabaseConnection.processElementNormal | private void processElementNormal(GeneratorSingleCluster cluster, Node cur) {
double mean = 0.0;
double stddev = 1.0;
String meanstr = ((Element) cur).getAttribute(ATTR_MEAN);
if(meanstr != null && meanstr.length() > 0) {
mean = ParseUtil.parseDouble(meanstr);
}
String stddevstr = ((Elemen... | java | private void processElementNormal(GeneratorSingleCluster cluster, Node cur) {
double mean = 0.0;
double stddev = 1.0;
String meanstr = ((Element) cur).getAttribute(ATTR_MEAN);
if(meanstr != null && meanstr.length() > 0) {
mean = ParseUtil.parseDouble(meanstr);
}
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elki-project/elki | elki-data-generator/src/main/java/de/lmu/ifi/dbs/elki/datasource/GeneratorXMLDatabaseConnection.java | GeneratorXMLDatabaseConnection.processElementGamma | private void processElementGamma(GeneratorSingleCluster cluster, Node cur) {
double k = 1.0;
double theta = 1.0;
String kstr = ((Element) cur).getAttribute(ATTR_K);
if(kstr != null && kstr.length() > 0) {
k = ParseUtil.parseDouble(kstr);
}
String thetastr = ((Element) cur).getAttribute(ATT... | java | private void processElementGamma(GeneratorSingleCluster cluster, Node cur) {
double k = 1.0;
double theta = 1.0;
String kstr = ((Element) cur).getAttribute(ATTR_K);
if(kstr != null && kstr.length() > 0) {
k = ParseUtil.parseDouble(kstr);
}
String thetastr = ((Element) cur).getAttribute(ATT... | [
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elki-project/elki | elki-data-generator/src/main/java/de/lmu/ifi/dbs/elki/datasource/GeneratorXMLDatabaseConnection.java | GeneratorXMLDatabaseConnection.processElementRotate | private void processElementRotate(GeneratorSingleCluster cluster, Node cur) {
int axis1 = 0;
int axis2 = 0;
double angle = 0.0;
String a1str = ((Element) cur).getAttribute(ATTR_AXIS1);
if(a1str != null && a1str.length() > 0) {
axis1 = ParseUtil.parseIntBase10(a1str);
}
String a2str = ... | java | private void processElementRotate(GeneratorSingleCluster cluster, Node cur) {
int axis1 = 0;
int axis2 = 0;
double angle = 0.0;
String a1str = ((Element) cur).getAttribute(ATTR_AXIS1);
if(a1str != null && a1str.length() > 0) {
axis1 = ParseUtil.parseIntBase10(a1str);
}
String a2str = ... | [
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elki-project/elki | elki-data-generator/src/main/java/de/lmu/ifi/dbs/elki/datasource/GeneratorXMLDatabaseConnection.java | GeneratorXMLDatabaseConnection.processElementTranslate | private void processElementTranslate(GeneratorSingleCluster cluster, Node cur) {
double[] offset = null;
String vstr = ((Element) cur).getAttribute(ATTR_VECTOR);
if(vstr != null && vstr.length() > 0) {
offset = parseVector(vstr);
}
if(offset == null) {
throw new AbortException("No transl... | java | private void processElementTranslate(GeneratorSingleCluster cluster, Node cur) {
double[] offset = null;
String vstr = ((Element) cur).getAttribute(ATTR_VECTOR);
if(vstr != null && vstr.length() > 0) {
offset = parseVector(vstr);
}
if(offset == null) {
throw new AbortException("No transl... | [
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elki-project/elki | elki-data-generator/src/main/java/de/lmu/ifi/dbs/elki/datasource/GeneratorXMLDatabaseConnection.java | GeneratorXMLDatabaseConnection.processElementClipping | private void processElementClipping(GeneratorSingleCluster cluster, Node cur) {
double[] cmin = null, cmax = null;
String minstr = ((Element) cur).getAttribute(ATTR_MIN);
if(minstr != null && minstr.length() > 0) {
cmin = parseVector(minstr);
}
String maxstr = ((Element) cur).getAttribute(ATT... | java | private void processElementClipping(GeneratorSingleCluster cluster, Node cur) {
double[] cmin = null, cmax = null;
String minstr = ((Element) cur).getAttribute(ATTR_MIN);
if(minstr != null && minstr.length() > 0) {
cmin = parseVector(minstr);
}
String maxstr = ((Element) cur).getAttribute(ATT... | [
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elki-project/elki | elki-data-generator/src/main/java/de/lmu/ifi/dbs/elki/datasource/GeneratorXMLDatabaseConnection.java | GeneratorXMLDatabaseConnection.processElementStatic | private void processElementStatic(GeneratorMain gen, Node cur) {
String name = ((Element) cur).getAttribute(ATTR_NAME);
if(name == null) {
throw new AbortException("No cluster name given in specification file.");
}
ArrayList<double[]> points = new ArrayList<>();
// TODO: check for unknown att... | java | private void processElementStatic(GeneratorMain gen, Node cur) {
String name = ((Element) cur).getAttribute(ATTR_NAME);
if(name == null) {
throw new AbortException("No cluster name given in specification file.");
}
ArrayList<double[]> points = new ArrayList<>();
// TODO: check for unknown att... | [
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elki-project/elki | elki-data-generator/src/main/java/de/lmu/ifi/dbs/elki/datasource/GeneratorXMLDatabaseConnection.java | GeneratorXMLDatabaseConnection.parseVector | private double[] parseVector(String s) {
String[] entries = WHITESPACE_PATTERN.split(s);
double[] d = new double[entries.length];
for(int i = 0; i < entries.length; i++) {
try {
d[i] = ParseUtil.parseDouble(entries[i]);
}
catch(NumberFormatException e) {
throw new AbortExce... | java | private double[] parseVector(String s) {
String[] entries = WHITESPACE_PATTERN.split(s);
double[] d = new double[entries.length];
for(int i = 0; i < entries.length; i++) {
try {
d[i] = ParseUtil.parseDouble(entries[i]);
}
catch(NumberFormatException e) {
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/data/model/ModelUtil.java | ModelUtil.getPrototype | public static NumberVector getPrototype(Model model, Relation<? extends NumberVector> relation) {
// Mean model contains a numeric Vector
if(model instanceof MeanModel) {
return DoubleVector.wrap(((MeanModel) model).getMean());
}
// Handle medoid models
if(model instanceof MedoidModel) {
... | java | public static NumberVector getPrototype(Model model, Relation<? extends NumberVector> relation) {
// Mean model contains a numeric Vector
if(model instanceof MeanModel) {
return DoubleVector.wrap(((MeanModel) model).getMean());
}
// Handle medoid models
if(model instanceof MedoidModel) {
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elki-project/elki | elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/preference/DiSHPreferenceVectorIndex.java | DiSHPreferenceVectorIndex.determinePreferenceVectorByApriori | private long[] determinePreferenceVectorByApriori(Relation<V> relation, ModifiableDBIDs[] neighborIDs, StringBuilder msg) {
int dimensionality = neighborIDs.length;
// database for apriori
UpdatableDatabase apriori_db = new HashmapDatabase();
SimpleTypeInformation<?> bitmeta = VectorFieldTypeInformatio... | java | private long[] determinePreferenceVectorByApriori(Relation<V> relation, ModifiableDBIDs[] neighborIDs, StringBuilder msg) {
int dimensionality = neighborIDs.length;
// database for apriori
UpdatableDatabase apriori_db = new HashmapDatabase();
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elki-project/elki | elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/preference/DiSHPreferenceVectorIndex.java | DiSHPreferenceVectorIndex.determinePreferenceVectorByMaxIntersection | private long[] determinePreferenceVectorByMaxIntersection(ModifiableDBIDs[] neighborIDs, StringBuilder msg) {
int dimensionality = neighborIDs.length;
long[] preferenceVector = BitsUtil.zero(dimensionality);
Map<Integer, ModifiableDBIDs> candidates = new HashMap<>(dimensionality);
for(int i = 0; i < di... | java | private long[] determinePreferenceVectorByMaxIntersection(ModifiableDBIDs[] neighborIDs, StringBuilder msg) {
int dimensionality = neighborIDs.length;
long[] preferenceVector = BitsUtil.zero(dimensionality);
Map<Integer, ModifiableDBIDs> candidates = new HashMap<>(dimensionality);
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elki-project/elki | elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/preference/DiSHPreferenceVectorIndex.java | DiSHPreferenceVectorIndex.max | private int max(Map<Integer, ModifiableDBIDs> candidates) {
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int maxDim = -1, size = -1;
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elki-project/elki | elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/preference/DiSHPreferenceVectorIndex.java | DiSHPreferenceVectorIndex.maxIntersection | private int maxIntersection(Map<Integer, ModifiableDBIDs> candidates, ModifiableDBIDs set) {
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int maxDim = -1;
ModifiableDBIDs maxIntersection = null;
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elki-project/elki | elki/src/main/java/de/lmu/ifi/dbs/elki/index/preprocessed/preference/DiSHPreferenceVectorIndex.java | DiSHPreferenceVectorIndex.initRangeQueries | private RangeQuery<V>[] initRangeQueries(Relation<V> relation, int dimensionality) {
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RangeQuery<V>[] rangeQueries = (RangeQuery<V>[]) new RangeQuery[dimensionality];
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@SuppressWarnings("unchecked")
RangeQuery<V>[] rangeQueries = (RangeQuery<V>[]) new RangeQuery[dimensionality];
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/internal/EvaluateConcordantPairs.java | EvaluateConcordantPairs.computeTau | @Reference(authors = "F. J. Rohlf", title = "Methods of comparing classifications", //
booktitle = "Annual Review of Ecology and Systematics", //
url = "https://doi.org/10.1146/annurev.es.05.110174.000533", //
bibkey = "doi:10.1146/annurev.es.05.110174.000533")
public double computeTau(long c, long ... | java | @Reference(authors = "F. J. Rohlf", title = "Methods of comparing classifications", //
booktitle = "Annual Review of Ecology and Systematics", //
url = "https://doi.org/10.1146/annurev.es.05.110174.000533", //
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elki-project/elki | elki-core-util/src/main/java/de/lmu/ifi/dbs/elki/application/internal/CheckELKIServices.java | CheckELKIServices.checkServices | public void checkServices(String update) {
TreeSet<String> props = new TreeSet<>();
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TreeSet<String> props = new TreeSet<>();
Enumeration<URL> us;
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}
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elki-project/elki | elki-core-util/src/main/java/de/lmu/ifi/dbs/elki/application/internal/CheckELKIServices.java | CheckELKIServices.checkAliases | @SuppressWarnings("unchecked")
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if... | java | @SuppressWarnings("unchecked")
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elki-project/elki | elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/CorrelationAnalysisSolution.java | CorrelationAnalysisSolution.getNormalizedLinearEquationSystem | public LinearEquationSystem getNormalizedLinearEquationSystem(Normalization<?> normalization) throws NonNumericFeaturesException {
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re... | java | public LinearEquationSystem getNormalizedLinearEquationSystem(Normalization<?> normalization) throws NonNumericFeaturesException {
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lq.solveByTotalPivotSearch();
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elki-project/elki | elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/CorrelationAnalysisSolution.java | CorrelationAnalysisSolution.squaredDistance | public double squaredDistance(V p) {
// V_affin = V + a
// dist(p, V_affin) = d(p-a, V) = ||p - a - proj_V(p-a) ||
double[] p_minus_a = minusEquals(p.toArray(), centroid);
return squareSum(minusEquals(p_minus_a, times(strongEigenvectors, transposeTimes(strongEigenvectors, p_minus_a))));
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// V_affin = V + a
// dist(p, V_affin) = d(p-a, V) = ||p - a - proj_V(p-a) ||
double[] p_minus_a = minusEquals(p.toArray(), centroid);
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elki-project/elki | elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/CorrelationAnalysisSolution.java | CorrelationAnalysisSolution.errorVector | public double[] errorVector(V p) {
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elki-project/elki | elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/CorrelationAnalysisSolution.java | CorrelationAnalysisSolution.dataVector | public double[] dataVector(V p) {
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elki-project/elki | elki/src/main/java/de/lmu/ifi/dbs/elki/data/model/CorrelationAnalysisSolution.java | CorrelationAnalysisSolution.writeToText | @Override
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out.commentPrintLn(label);
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elki-project/elki | elki-core/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/AbstractStaticHistogram.java | AbstractStaticHistogram.getBinNr | protected int getBinNr(double coord) {
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}
if (coord == max) {
// System.err.println("Triggered special case: "+ (Math.floor((coord -
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throw new UnsupportedOperationException("Encountered non-finite value in Histogram: " + coord);
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elki-project/elki | elki-core/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/histogram/AbstractStaticHistogram.java | AbstractStaticHistogram.growSize | protected static int growSize(int current, int requiredSize) {
// Double until 64, then increase by 50% each time.
int newCapacity = ((current < 64) ? ((current + 1) << 1) : ((current >> 1) * 3));
// overflow?
if (newCapacity < 0) {
throw new OutOfMemoryError();
}
if (requiredSize > newCap... | java | protected static int growSize(int current, int requiredSize) {
// Double until 64, then increase by 50% each time.
int newCapacity = ((current < 64) ? ((current + 1) << 1) : ((current >> 1) * 3));
// overflow?
if (newCapacity < 0) {
throw new OutOfMemoryError();
}
if (requiredSize > newCap... | [
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elki-project/elki | elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/DeLiClu.java | DeLiClu.expandNodes | private void expandNodes(DeLiCluTree index, SpatialPrimitiveDistanceFunction<V> distFunction, SpatialObjectPair nodePair, DataStore<KNNList> knns) {
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DeLiCluNode node2 = index.getNode(((SpatialDirectoryEntry) nodePair.entry... | java | private void expandNodes(DeLiCluTree index, SpatialPrimitiveDistanceFunction<V> distFunction, SpatialObjectPair nodePair, DataStore<KNNList> knns) {
DeLiCluNode node1 = index.getNode(((SpatialDirectoryEntry) nodePair.entry1).getPageID());
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elki-project/elki | elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/DeLiClu.java | DeLiClu.expandDirNodes | private void expandDirNodes(SpatialPrimitiveDistanceFunction<V> distFunction, DeLiCluNode node1, DeLiCluNode node2) {
if(LOG.isDebuggingFinest()) {
LOG.debugFinest("ExpandDirNodes: " + node1.getPageID() + " + " + node2.getPageID());
}
int numEntries_1 = node1.getNumEntries();
int numEntries_2 = no... | java | private void expandDirNodes(SpatialPrimitiveDistanceFunction<V> distFunction, DeLiCluNode node1, DeLiCluNode node2) {
if(LOG.isDebuggingFinest()) {
LOG.debugFinest("ExpandDirNodes: " + node1.getPageID() + " + " + node2.getPageID());
}
int numEntries_1 = node1.getNumEntries();
int numEntries_2 = no... | [
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elki-project/elki | elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/DeLiClu.java | DeLiClu.expandLeafNodes | private void expandLeafNodes(SpatialPrimitiveDistanceFunction<V> distFunction, DeLiCluNode node1, DeLiCluNode node2, DataStore<KNNList> knns) {
if(LOG.isDebuggingFinest()) {
LOG.debugFinest("ExpandLeafNodes: " + node1.getPageID() + " + " + node2.getPageID());
}
int numEntries_1 = node1.getNumEntries()... | java | private void expandLeafNodes(SpatialPrimitiveDistanceFunction<V> distFunction, DeLiCluNode node1, DeLiCluNode node2, DataStore<KNNList> knns) {
if(LOG.isDebuggingFinest()) {
LOG.debugFinest("ExpandLeafNodes: " + node1.getPageID() + " + " + node2.getPageID());
}
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elki-project/elki | elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/optics/DeLiClu.java | DeLiClu.reinsertExpanded | private void reinsertExpanded(SpatialPrimitiveDistanceFunction<V> distFunction, DeLiCluTree index, IndexTreePath<DeLiCluEntry> path, DataStore<KNNList> knns) {
int l = 0; // Count the number of components.
for(IndexTreePath<DeLiCluEntry> it = path; it != null; it = it.getParentPath()) {
l++;
}
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int l = 0; // Count the number of components.
for(IndexTreePath<DeLiCluEntry> it = path; it != null; it = it.getParentPath()) {
l++;
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elki-project/elki | elki-core-api/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialUtil.java | SpatialUtil.assertSameDimensionality | public static int assertSameDimensionality(SpatialComparable box1, SpatialComparable box2) {
final int dim = box1.getDimensionality();
if(dim != box2.getDimensionality()) {
throw new IllegalArgumentException("The spatial objects do not have the same dimensionality!");
}
return dim;
} | java | public static int assertSameDimensionality(SpatialComparable box1, SpatialComparable box2) {
final int dim = box1.getDimensionality();
if(dim != box2.getDimensionality()) {
throw new IllegalArgumentException("The spatial objects do not have the same dimensionality!");
}
return dim;
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elki-project/elki | elki-core-api/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialUtil.java | SpatialUtil.getMin | public static double[] getMin(SpatialComparable box) {
final int dim = box.getDimensionality();
double[] min = new double[dim];
for(int i = 0; i < dim; i++) {
min[i] = box.getMin(i);
}
return min;
} | java | public static double[] getMin(SpatialComparable box) {
final int dim = box.getDimensionality();
double[] min = new double[dim];
for(int i = 0; i < dim; i++) {
min[i] = box.getMin(i);
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return min;
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elki-project/elki | elki-core-api/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialUtil.java | SpatialUtil.getMax | public static double[] getMax(SpatialComparable box) {
final int dim = box.getDimensionality();
double[] max = new double[dim];
for(int i = 0; i < dim; i++) {
max[i] = box.getMax(i);
}
return max;
} | java | public static double[] getMax(SpatialComparable box) {
final int dim = box.getDimensionality();
double[] max = new double[dim];
for(int i = 0; i < dim; i++) {
max[i] = box.getMax(i);
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return max;
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elki-project/elki | elki-core-api/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialUtil.java | SpatialUtil.intersects | public static boolean intersects(SpatialComparable box1, SpatialComparable box2) {
final int dim = assertSameDimensionality(box1, box2);
for(int i = 0; i < dim; i++) {
if(box2.getMax(i) < box1.getMin(i) || box1.getMax(i) < box2.getMin(i)) {
return false;
}
}
return true;
} | java | public static boolean intersects(SpatialComparable box1, SpatialComparable box2) {
final int dim = assertSameDimensionality(box1, box2);
for(int i = 0; i < dim; i++) {
if(box2.getMax(i) < box1.getMin(i) || box1.getMax(i) < box2.getMin(i)) {
return false;
}
}
return true;
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elki-project/elki | elki-core-api/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialUtil.java | SpatialUtil.contains | public static boolean contains(SpatialComparable box, double[] point) {
final int dim = box.getDimensionality();
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}
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final int dim = box.getDimensionality();
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elki-project/elki | elki-core-api/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialUtil.java | SpatialUtil.enlargement | public static double enlargement(SpatialComparable exist, SpatialComparable addit) {
final int dim = assertSameDimensionality(exist, addit);
double v1 = 1.;
double v2 = 1.;
for(int i = 0; i < dim; i++) {
final double emin = exist.getMin(i);
final double emax = exist.getMax(i);
final do... | java | public static double enlargement(SpatialComparable exist, SpatialComparable addit) {
final int dim = assertSameDimensionality(exist, addit);
double v1 = 1.;
double v2 = 1.;
for(int i = 0; i < dim; i++) {
final double emin = exist.getMin(i);
final double emax = exist.getMax(i);
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elki-project/elki | elki-core-api/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialUtil.java | SpatialUtil.perimeter | public static double perimeter(SpatialComparable box) {
final int dim = box.getDimensionality();
double perimeter = 0.;
for(int i = 0; i < dim; i++) {
perimeter += box.getMax(i) - box.getMin(i);
}
return perimeter;
} | java | public static double perimeter(SpatialComparable box) {
final int dim = box.getDimensionality();
double perimeter = 0.;
for(int i = 0; i < dim; i++) {
perimeter += box.getMax(i) - box.getMin(i);
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return perimeter;
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elki-project/elki | elki-core-api/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialUtil.java | SpatialUtil.overlap | public static double overlap(SpatialComparable box1, SpatialComparable box2) {
final int dim = assertSameDimensionality(box1, box2);
// the maximal and minimal value of the overlap box.
double omax, omin;
// the overlap volume
double overlap = 1.;
for(int i = 0; i < dim; i++) {
// The m... | java | public static double overlap(SpatialComparable box1, SpatialComparable box2) {
final int dim = assertSameDimensionality(box1, box2);
// the maximal and minimal value of the overlap box.
double omax, omin;
// the overlap volume
double overlap = 1.;
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elki-project/elki | elki-core-api/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialUtil.java | SpatialUtil.relativeOverlap | public static double relativeOverlap(SpatialComparable box1, SpatialComparable box2) {
final int dim = assertSameDimensionality(box1, box2);
// the overlap volume
double overlap = 1.;
double vol1 = 1.;
double vol2 = 1.;
for(int i = 0; i < dim; i++) {
final double box1min = box1.getMin(i)... | java | public static double relativeOverlap(SpatialComparable box1, SpatialComparable box2) {
final int dim = assertSameDimensionality(box1, box2);
// the overlap volume
double overlap = 1.;
double vol1 = 1.;
double vol2 = 1.;
for(int i = 0; i < dim; i++) {
final double box1min = box1.getMin(i)... | [
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elki-project/elki | elki-core-api/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialUtil.java | SpatialUtil.unionTolerant | public static ModifiableHyperBoundingBox unionTolerant(SpatialComparable mbr1, SpatialComparable mbr2) {
if(mbr1 == null && mbr2 == null) {
return null;
}
if(mbr1 == null) {
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return new ModifiableHyperBoundingBox(mbr2);
}
if(mbr2 == null) {
// Clone - ... | java | public static ModifiableHyperBoundingBox unionTolerant(SpatialComparable mbr1, SpatialComparable mbr2) {
if(mbr1 == null && mbr2 == null) {
return null;
}
if(mbr1 == null) {
// Clone - intentionally
return new ModifiableHyperBoundingBox(mbr2);
}
if(mbr2 == null) {
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elki-project/elki | elki-core-api/src/main/java/de/lmu/ifi/dbs/elki/data/spatial/SpatialUtil.java | SpatialUtil.centroid | public static double[] centroid(SpatialComparable obj) {
final int dim = obj.getDimensionality();
double[] centroid = new double[dim];
for(int d = 0; d < dim; d++) {
centroid[d] = (obj.getMax(d) + obj.getMin(d)) * .5;
}
return centroid;
} | java | public static double[] centroid(SpatialComparable obj) {
final int dim = obj.getDimensionality();
double[] centroid = new double[dim];
for(int d = 0; d < dim; d++) {
centroid[d] = (obj.getMax(d) + obj.getMin(d)) * .5;
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return centroid;
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elki-project/elki | elki-core/src/main/java/de/lmu/ifi/dbs/elki/utilities/scaling/LinearScaling.java | LinearScaling.fromMinMax | public static LinearScaling fromMinMax(double min, double max) {
double zoom = 1.0 / (max - min);
return new LinearScaling(zoom, -min * zoom);
} | java | public static LinearScaling fromMinMax(double min, double max) {
double zoom = 1.0 / (max - min);
return new LinearScaling(zoom, -min * zoom);
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/PairCounting.java | PairCounting.fMeasure | public double fMeasure(double beta) {
final double beta2 = beta * beta;
double fmeasure = ((1 + beta2) * pairconfuse[0]) / ((1 + beta2) * pairconfuse[0] + beta2 * pairconfuse[1] + pairconfuse[2]);
return fmeasure;
} | java | public double fMeasure(double beta) {
final double beta2 = beta * beta;
double fmeasure = ((1 + beta2) * pairconfuse[0]) / ((1 + beta2) * pairconfuse[0] + beta2 * pairconfuse[1] + pairconfuse[2]);
return fmeasure;
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elki-project/elki | elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterObjectComment.java | TextWriterObjectComment.write | @Override
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}
if(object != null) {
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out.commentPrintLn(buf);
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elki-project/elki | elki-input/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/transform/ClassicMultidimensionalScalingTransform.java | ClassicMultidimensionalScalingTransform.computeSquaredDistanceMatrix | protected static <I> double[][] computeSquaredDistanceMatrix(final List<I> col, PrimitiveDistanceFunction<? super I> dist) {
final int size = col.size();
double[][] imat = new double[size][size];
boolean squared = dist.isSquared();
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final int size = col.size();
double[][] imat = new double[size][size];
boolean squared = dist.isSquared();
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elki-project/elki | elki-outlier/src/main/java/de/lmu/ifi/dbs/elki/algorithm/outlier/meta/RescaleMetaOutlierAlgorithm.java | RescaleMetaOutlierAlgorithm.getOutlierResult | private OutlierResult getOutlierResult(ResultHierarchy hier, Result result) {
List<OutlierResult> ors = ResultUtil.filterResults(hier, result, OutlierResult.class);
if(!ors.isEmpty()) {
return ors.get(0);
}
throw new IllegalStateException("Comparison algorithm expected at least one outlier result.... | java | private OutlierResult getOutlierResult(ResultHierarchy hier, Result result) {
List<OutlierResult> ors = ResultUtil.filterResults(hier, result, OutlierResult.class);
if(!ors.isEmpty()) {
return ors.get(0);
}
throw new IllegalStateException("Comparison algorithm expected at least one outlier result.... | [
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elki-project/elki | elki-index-mtree/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTreeNode.java | MkAppTreeNode.knnDistanceApproximation | protected PolynomialApproximation knnDistanceApproximation() {
int p_max = 0;
double[] b = null;
for(int i = 0; i < getNumEntries(); i++) {
MkAppEntry entry = getEntry(i);
PolynomialApproximation approximation = entry.getKnnDistanceApproximation();
if(b == null) {
p_max = approxima... | java | protected PolynomialApproximation knnDistanceApproximation() {
int p_max = 0;
double[] b = null;
for(int i = 0; i < getNumEntries(); i++) {
MkAppEntry entry = getEntry(i);
PolynomialApproximation approximation = entry.getKnnDistanceApproximation();
if(b == null) {
p_max = approxima... | [
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elki-project/elki | elki-database/src/main/java/de/lmu/ifi/dbs/elki/database/ProxyDatabase.java | ProxyDatabase.setDBIDs | public void setDBIDs(DBIDs ids) {
this.idrep.setDBIDs(ids);
// Update relations.
for (Relation<?> orel : this.relations) {
if (orel instanceof ProxyView) {
((ProxyView<?>) orel).setDBIDs(this.idrep.getDBIDs());
}
}
} | java | public void setDBIDs(DBIDs ids) {
this.idrep.setDBIDs(ids);
// Update relations.
for (Relation<?> orel : this.relations) {
if (orel instanceof ProxyView) {
((ProxyView<?>) orel).setDBIDs(this.idrep.getDBIDs());
}
}
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elki-project/elki | elki-logging/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/ProgressTracker.java | ProgressTracker.getProgresses | public synchronized Collection<Progress> getProgresses() {
List<Progress> list = new ArrayList<>(progresses.size());
Iterator<WeakReference<Progress>> iter = progresses.iterator();
while(iter.hasNext()) {
WeakReference<Progress> ref = iter.next();
if(ref.get() == null) {
iter.remove();
... | java | public synchronized Collection<Progress> getProgresses() {
List<Progress> list = new ArrayList<>(progresses.size());
Iterator<WeakReference<Progress>> iter = progresses.iterator();
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WeakReference<Progress> ref = iter.next();
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elki-project/elki | elki-logging/src/main/java/de/lmu/ifi/dbs/elki/logging/progress/ProgressTracker.java | ProgressTracker.addProgress | public synchronized void addProgress(Progress p) {
// Don't add more than once.
Iterator<WeakReference<Progress>> iter = progresses.iterator();
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WeakReference<Progress> ref = iter.next();
// since we are at it anyway, remove old links.
if(ref.get() == null) {
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// Don't add more than once.
Iterator<WeakReference<Progress>> iter = progresses.iterator();
while(iter.hasNext()) {
WeakReference<Progress> ref = iter.next();
// since we are at it anyway, remove old links.
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elki-project/elki | elki-index-rtree/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluTreeIndex.java | DeLiCluTreeIndex.setHandled | public synchronized IndexTreePath<DeLiCluEntry> setHandled(DBID id, O obj) {
if(LOG.isDebugging()) {
LOG.debugFine("setHandled " + id + ", " + obj + "\n");
}
// find the leaf node containing o
IndexTreePath<DeLiCluEntry> pathToObject = findPathToObject(getRootPath(), obj, id);
if(pathToObjec... | java | public synchronized IndexTreePath<DeLiCluEntry> setHandled(DBID id, O obj) {
if(LOG.isDebugging()) {
LOG.debugFine("setHandled " + id + ", " + obj + "\n");
}
// find the leaf node containing o
IndexTreePath<DeLiCluEntry> pathToObject = findPathToObject(getRootPath(), obj, id);
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elki-project/elki | elki-index-rtree/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/deliclu/DeLiCluTreeIndex.java | DeLiCluTreeIndex.delete | @Override
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// find the leaf node containing o
O obj = relation.get(id);
IndexTreePath<DeLiCluEntry> deletionPath = findPathToObject(getRootPath(), obj, id);
if(deletionPath == null) {
return false;
}
deletePath(deletionPath);
return true;
} | java | @Override
public final boolean delete(DBIDRef id) {
// find the leaf node containing o
O obj = relation.get(id);
IndexTreePath<DeLiCluEntry> deletionPath = findPathToObject(getRootPath(), obj, id);
if(deletionPath == null) {
return false;
}
deletePath(deletionPath);
return true;
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elki-project/elki | elki/src/main/java/de/lmu/ifi/dbs/elki/application/experiments/EvaluateIntrinsicDimensionalityEstimators.java | EvaluateIntrinsicDimensionalityEstimators.makeSample | protected double[] makeSample(int maxk) {
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final Random rnd = this.rnd.getSingleThreadedRandom();
double[] dists = new double[maxk + 1];
final double e = 1. / dim;
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elki-project/elki | elki-index-mtree/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/MTreeDirectoryEntry.java | MTreeDirectoryEntry.setRoutingObjectID | @Override
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this.routingObjectID = objectID;
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elki-project/elki | elki-index-mtree/src/main/java/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/MTreeDirectoryEntry.java | MTreeDirectoryEntry.writeExternal | @Override
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public void writeExternal(ObjectOutput out) throws IOException {
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elki-project/elki | elki/src/main/java/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterTextWriteable.java | TextWriterTextWriteable.write | @Override
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public void write(TextWriterStream out, String label, TextWriteable obj) {
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/EvaluateClustering.java | EvaluateClustering.evaluteResult | protected void evaluteResult(Database db, Clustering<?> c, Clustering<?> refc) {
ClusterContingencyTable contmat = new ClusterContingencyTable(selfPairing, noiseSpecialHandling);
contmat.process(refc, c);
ScoreResult sr = new ScoreResult(contmat);
sr.addHeader(c.getLongName());
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ClusterContingencyTable contmat = new ClusterContingencyTable(selfPairing, noiseSpecialHandling);
contmat.process(refc, c);
ScoreResult sr = new ScoreResult(contmat);
sr.addHeader(c.getLongName());
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/evaluation/clustering/EvaluateClustering.java | EvaluateClustering.isReferenceResult | private boolean isReferenceResult(Clustering<?> t) {
// FIXME: don't hard-code strings
return "bylabel-clustering".equals(t.getShortName()) //
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// FIXME: don't hard-code strings
return "bylabel-clustering".equals(t.getShortName()) //
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elki-project/elki | elki-persistent/src/main/java/de/lmu/ifi/dbs/elki/persistent/AbstractPageFile.java | AbstractPageFile.writePage | @Override
public final synchronized int writePage(P page) {
int pageid = setPageID(page);
writePage(pageid, page);
return pageid;
} | java | @Override
public final synchronized int writePage(P page) {
int pageid = setPageID(page);
writePage(pageid, page);
return pageid;
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elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGHyperSphere.java | SVGHyperSphere.drawManhattan | public static Element drawManhattan(SVGPlot svgp, Projection2D proj, NumberVector mid, double radius) {
final double[] v_mid = mid.toArray(); // a copy
final long[] dims = proj.getVisibleDimensions2D();
SVGPath path = new SVGPath();
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final double[] v_mid = mid.toArray(); // a copy
final long[] dims = proj.getVisibleDimensions2D();
SVGPath path = new SVGPath();
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elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/svg/SVGHyperSphere.java | SVGHyperSphere.drawCross | public static Element drawCross(SVGPlot svgp, Projection2D proj, NumberVector mid, double radius) {
final double[] v_mid = mid.toArray();
final long[] dims = proj.getVisibleDimensions2D();
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final double[] v_mid = mid.toArray();
final long[] dims = proj.getVisibleDimensions2D();
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elki-project/elki | elki-index-rtree/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/query/RStarTreeUtil.java | RStarTreeUtil.getRangeQuery | @SuppressWarnings({ "cast", "unchecked" })
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// Can we support this distance function - spatial distances only!
SpatialPrimitiveDistanceFunction<? su... | java | @SuppressWarnings({ "cast", "unchecked" })
public static <O extends SpatialComparable> RangeQuery<O> getRangeQuery(AbstractRStarTree<?, ?, ?> tree, SpatialDistanceQuery<O> distanceQuery, Object... hints) {
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elki-project/elki | elki-index-rtree/src/main/java/de/lmu/ifi/dbs/elki/index/tree/spatial/rstarvariants/query/RStarTreeUtil.java | RStarTreeUtil.getKNNQuery | @SuppressWarnings({ "cast", "unchecked" })
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// Can we support this distance function - spatial distances only!
SpatialPrimitiveDistanceFunction<? super ... | java | @SuppressWarnings({ "cast", "unchecked" })
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elki-project/elki | elki-logging/src/main/java/de/lmu/ifi/dbs/elki/logging/LoggingConfiguration.java | LoggingConfiguration.privateReconfigureLogging | private void privateReconfigureLogging(String pkg, final String name) {
LogManager logManager = LogManager.getLogManager();
Logger logger = Logger.getLogger(LoggingConfiguration.class.getName());
// allow null as package name.
if(pkg == null) {
pkg = "";
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LogManager logManager = LogManager.getLogManager();
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// allow null as package name.
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elki-project/elki | elki-logging/src/main/java/de/lmu/ifi/dbs/elki/logging/LoggingConfiguration.java | LoggingConfiguration.openSystemFile | private static InputStream openSystemFile(String filename) throws FileNotFoundException {
try {
return new FileInputStream(filename);
}
catch(FileNotFoundException e) {
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String resname = File.separatorChar != '/' ? filename.replace(File.separatorChar, '/') : filename... | java | private static InputStream openSystemFile(String filename) throws FileNotFoundException {
try {
return new FileInputStream(filename);
}
catch(FileNotFoundException e) {
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elki-project/elki | elki-logging/src/main/java/de/lmu/ifi/dbs/elki/logging/LoggingConfiguration.java | LoggingConfiguration.setVerbose | public static void setVerbose(java.util.logging.Level verbose) {
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elki-project/elki | elki-logging/src/main/java/de/lmu/ifi/dbs/elki/logging/LoggingConfiguration.java | LoggingConfiguration.setStatistics | public static void setStatistics() {
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// decrease to INFO if it was higher
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elki-project/elki | elki-logging/src/main/java/de/lmu/ifi/dbs/elki/logging/LoggingConfiguration.java | LoggingConfiguration.replaceDefaultHandler | public static void replaceDefaultHandler(Handler handler) {
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rootlogger.removeHandler(h);
}
}
addHandler(handler);
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Logger rootlogger = LogManager.getLogManager().getLogger("");
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rootlogger.removeHandler(h);
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elki-project/elki | elki-logging/src/main/java/de/lmu/ifi/dbs/elki/logging/LoggingConfiguration.java | LoggingConfiguration.setDefaultLevel | public static void setDefaultLevel(java.util.logging.Level level) {
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elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/batikutil/BatikUtil.java | BatikUtil.getRelativeCoordinates | public static double[] getRelativeCoordinates(Event evt, Element reference) {
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elki-project/elki | elki-clustering/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/birch/BIRCHLeafClustering.java | BIRCHLeafClustering.run | public Clustering<MeanModel> run(Relation<NumberVector> relation) {
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elki-project/elki | addons/tutorial/src/main/java/tutorial/outlier/DistanceStddevOutlier.java | DistanceStddevOutlier.run | public OutlierResult run(Database database, Relation<O> relation) {
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elki-project/elki | elki/src/main/java/de/lmu/ifi/dbs/elki/application/ELKILauncher.java | ELKILauncher.main | public static void main(String[] args) {
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elki-project/elki | elki-core-util/src/main/java/de/lmu/ifi/dbs/elki/utilities/ClassGenericsUtil.java | ClassGenericsUtil.getParameterizer | public static Parameterizer getParameterizer(Class<?> c) {
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elki-project/elki | elki-core-util/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/HashMapHierarchy.java | HashMapHierarchy.putRec | private void putRec(O obj, Rec<O> rec) {
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graph.put(obj, rec);
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return;
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elki-project/elki | elki-core-util/src/main/java/de/lmu/ifi/dbs/elki/utilities/datastructures/hierarchy/HashMapHierarchy.java | HashMapHierarchy.removeRec | private void removeRec(O obj) {
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elki-project/elki | elki-gui-minigui/src/main/java/de/lmu/ifi/dbs/elki/gui/util/TreePopup.java | TreePopup.createTree | protected JTree createTree() {
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JTree tree = new JTree(model);
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tree.setFont(getFont());
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elki-project/elki | elki-gui-minigui/src/main/java/de/lmu/ifi/dbs/elki/gui/util/TreePopup.java | TreePopup.createScroller | protected JScrollPane createScroller() {
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sp.setHorizontalScrollBar(null);
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sp.setFocusable(false);
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JScrollPane sp = new JScrollPane(tree, ScrollPaneConstants.VERTICAL_SCROLLBAR_AS_NEEDED, ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
sp.setHorizontalScrollBar(null);
sp.setName("TreePopup.scrollPane");
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elki-project/elki | elki-gui-minigui/src/main/java/de/lmu/ifi/dbs/elki/gui/util/TreePopup.java | TreePopup.show | public void show(Component parent) {
Dimension parentSize = parent.getSize();
Insets insets = getInsets();
// reduce the width of the scrollpane by the insets so that the popup
// is the same width as the combo box.
parentSize.setSize(parentSize.width - (insets.right + insets.left), 10 * parentSize... | java | public void show(Component parent) {
Dimension parentSize = parent.getSize();
Insets insets = getInsets();
// reduce the width of the scrollpane by the insets so that the popup
// is the same width as the combo box.
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] | b54673327e76198ecd4c8a2a901021f1a9174498 | https://github.com/elki-project/elki/blob/b54673327e76198ecd4c8a2a901021f1a9174498/elki-gui-minigui/src/main/java/de/lmu/ifi/dbs/elki/gui/util/TreePopup.java#L195-L210 | train |
elki-project/elki | elki-gui-minigui/src/main/java/de/lmu/ifi/dbs/elki/gui/util/TreePopup.java | TreePopup.fireActionPerformed | protected void fireActionPerformed(ActionEvent event) {
Object[] listeners = listenerList.getListenerList();
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if(listeners[i] == ActionListener.class) {
((ActionListener) listeners[i + 1]).actionPerformed(event);
}
}
} | java | protected void fireActionPerformed(ActionEvent event) {
Object[] listeners = listenerList.getListenerList();
for(int i = listeners.length - 2; i >= 0; i -= 2) {
if(listeners[i] == ActionListener.class) {
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] | b54673327e76198ecd4c8a2a901021f1a9174498 | https://github.com/elki-project/elki/blob/b54673327e76198ecd4c8a2a901021f1a9174498/elki-gui-minigui/src/main/java/de/lmu/ifi/dbs/elki/gui/util/TreePopup.java#L262-L269 | train |
elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/PropertiesBasedStyleLibrary.java | PropertiesBasedStyleLibrary.setCached | private <T> void setCached(String prefix, String postfix, T data) {
cache.put(prefix + '.' + postfix, data);
} | java | private <T> void setCached(String prefix, String postfix, T data) {
cache.put(prefix + '.' + postfix, data);
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] | b54673327e76198ecd4c8a2a901021f1a9174498 | https://github.com/elki-project/elki/blob/b54673327e76198ecd4c8a2a901021f1a9174498/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/PropertiesBasedStyleLibrary.java#L181-L183 | train |
elki-project/elki | addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/PropertiesBasedStyleLibrary.java | PropertiesBasedStyleLibrary.getPropertyValue | protected String getPropertyValue(String prefix, String postfix) {
String ret = properties.getProperty(prefix + "." + postfix);
if (ret != null) {
// logger.debugFine("Found property: "+prefix + "." +
// postfix+" for "+prefix);
return ret;
}
int pos = prefix.length();
while (pos >... | java | protected String getPropertyValue(String prefix, String postfix) {
String ret = properties.getProperty(prefix + "." + postfix);
if (ret != null) {
// logger.debugFine("Found property: "+prefix + "." +
// postfix+" for "+prefix);
return ret;
}
int pos = prefix.length();
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] | b54673327e76198ecd4c8a2a901021f1a9174498 | https://github.com/elki-project/elki/blob/b54673327e76198ecd4c8a2a901021f1a9174498/addons/batikvis/src/main/java/de/lmu/ifi/dbs/elki/visualization/style/PropertiesBasedStyleLibrary.java#L192-L218 | train |
elki-project/elki | elki-input/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/FilterUtil.java | FilterUtil.guessFactory | @SuppressWarnings("unchecked")
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NumberVector.Factory<V> factory = null;
if(in instanceof VectorTypeInformation) {
factory = (NumberVector.Factory<V>) ((VectorTypeInformation<V>) in).getFactory();
... | java | @SuppressWarnings("unchecked")
public static <V extends NumberVector> NumberVector.Factory<V> guessFactory(SimpleTypeInformation<V> in) {
NumberVector.Factory<V> factory = null;
if(in instanceof VectorTypeInformation) {
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] | b54673327e76198ecd4c8a2a901021f1a9174498 | https://github.com/elki-project/elki/blob/b54673327e76198ecd4c8a2a901021f1a9174498/elki-input/src/main/java/de/lmu/ifi/dbs/elki/datasource/filter/FilterUtil.java#L54-L71 | train |
elki-project/elki | elki-core-api/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/MultipleObjectsBundle.java | MultipleObjectsBundle.appendSimple | public void appendSimple(Object... data) {
if(data.length != meta.size()) {
throw new AbortException("Invalid number of attributes in 'append'.");
}
for(int i = 0; i < data.length; i++) {
@SuppressWarnings("unchecked")
final List<Object> col = (List<Object>) columns.get(i);
col.add(d... | java | public void appendSimple(Object... data) {
if(data.length != meta.size()) {
throw new AbortException("Invalid number of attributes in 'append'.");
}
for(int i = 0; i < data.length; i++) {
@SuppressWarnings("unchecked")
final List<Object> col = (List<Object>) columns.get(i);
col.add(d... | [
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elki-project/elki | elki-core-api/src/main/java/de/lmu/ifi/dbs/elki/datasource/bundle/MultipleObjectsBundle.java | MultipleObjectsBundle.fromStream | public static MultipleObjectsBundle fromStream(BundleStreamSource source) {
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boolean stop = false;
DBIDVar var = null;
ArrayModifiableDBIDs ids = null;
int size = 0;
while(!stop) {
BundleStreamSource.Event ev = source.nextEvent();
... | java | public static MultipleObjectsBundle fromStream(BundleStreamSource source) {
MultipleObjectsBundle bundle = new MultipleObjectsBundle();
boolean stop = false;
DBIDVar var = null;
ArrayModifiableDBIDs ids = null;
int size = 0;
while(!stop) {
BundleStreamSource.Event ev = source.nextEvent();
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