diff options
Diffstat (limited to 'src/de/lmu/ifi/dbs/elki/algorithm/outlier/OPTICSOF.java')
| -rw-r--r-- | src/de/lmu/ifi/dbs/elki/algorithm/outlier/OPTICSOF.java | 51 |
1 files changed, 27 insertions, 24 deletions
diff --git a/src/de/lmu/ifi/dbs/elki/algorithm/outlier/OPTICSOF.java b/src/de/lmu/ifi/dbs/elki/algorithm/outlier/OPTICSOF.java index b1ffae63..61d11935 100644 --- a/src/de/lmu/ifi/dbs/elki/algorithm/outlier/OPTICSOF.java +++ b/src/de/lmu/ifi/dbs/elki/algorithm/outlier/OPTICSOF.java @@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.algorithm.outlier; This file is part of ELKI:
Environment for Developing KDD-Applications Supported by Index-Structures - Copyright (C) 2013
+ Copyright (C) 2014
Ludwig-Maximilians-Universität München
Lehr- und Forschungseinheit für Datenbanksysteme
ELKI Development Team @@ -27,7 +27,7 @@ import java.util.ArrayList; import java.util.List;
import de.lmu.ifi.dbs.elki.algorithm.AbstractDistanceBasedAlgorithm;
-import de.lmu.ifi.dbs.elki.algorithm.clustering.OPTICS;
+import de.lmu.ifi.dbs.elki.algorithm.clustering.optics.OPTICS;
import de.lmu.ifi.dbs.elki.data.type.TypeInformation;
import de.lmu.ifi.dbs.elki.data.type.TypeUtil;
import de.lmu.ifi.dbs.elki.database.Database;
@@ -38,15 +38,15 @@ import de.lmu.ifi.dbs.elki.database.datastore.WritableDoubleDataStore; import de.lmu.ifi.dbs.elki.database.datastore.WritableIntegerDataStore;
import de.lmu.ifi.dbs.elki.database.ids.DBIDIter;
import de.lmu.ifi.dbs.elki.database.ids.DBIDs;
-import de.lmu.ifi.dbs.elki.database.ids.distance.DistanceDBIDListIter;
-import de.lmu.ifi.dbs.elki.database.ids.distance.KNNList;
+import de.lmu.ifi.dbs.elki.database.ids.DoubleDBIDListIter;
+import de.lmu.ifi.dbs.elki.database.ids.KNNList;
import de.lmu.ifi.dbs.elki.database.query.distance.DistanceQuery;
import de.lmu.ifi.dbs.elki.database.query.knn.KNNQuery;
import de.lmu.ifi.dbs.elki.database.query.range.RangeQuery;
-import de.lmu.ifi.dbs.elki.database.relation.MaterializedRelation;
+import de.lmu.ifi.dbs.elki.database.relation.DoubleRelation;
+import de.lmu.ifi.dbs.elki.database.relation.MaterializedDoubleRelation;
import de.lmu.ifi.dbs.elki.database.relation.Relation;
import de.lmu.ifi.dbs.elki.distance.distancefunction.DistanceFunction;
-import de.lmu.ifi.dbs.elki.distance.distancevalue.NumberDistance;
import de.lmu.ifi.dbs.elki.logging.Logging;
import de.lmu.ifi.dbs.elki.math.DoubleMinMax;
import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult;
@@ -60,8 +60,8 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameteriz import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter;
/**
- * OPTICSOF provides the Optics-of algorithm, an algorithm to find Local
- * Outliers in a database.
+ * Optics-OF outlier detection algorithm, an algorithm to find Local Outliers in
+ * a database based on ideas from {@link OPTICS} clustering.
* <p>
* Reference:<br>
* Markus M. Breunig, Hans-Peter Kriegel, Raymond T. N, Jörg Sander:<br />
@@ -79,8 +79,11 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.IntParameter; */
@Title("OPTICS-OF: Identifying Local Outliers")
@Description("Algorithm to compute density-based local outlier factors in a database based on the neighborhood size parameter 'minpts'")
-@Reference(authors = "M. M. Breunig, H.-P. Kriegel, R. Ng, and J. Sander", title = "OPTICS-OF: Identifying Local Outliers", booktitle = "Proc. of the 3rd European Conference on Principles of Knowledge Discovery and Data Mining (PKDD), Prague, Czech Republic", url = "http://springerlink.metapress.com/content/76bx6413gqb4tvta/")
-public class OPTICSOF<O, D extends NumberDistance<D, ?>> extends AbstractDistanceBasedAlgorithm<O, D, OutlierResult> implements OutlierAlgorithm {
+@Reference(authors = "M. M. Breunig, H.-P. Kriegel, R. Ng, and J. Sander", //
+title = "OPTICS-OF: Identifying Local Outliers", //
+booktitle = "Proc. of the 3rd European Conference on Principles of Knowledge Discovery and Data Mining (PKDD), Prague, Czech Republic", //
+url = "http://springerlink.metapress.com/content/76bx6413gqb4tvta/")
+public class OPTICSOF<O> extends AbstractDistanceBasedAlgorithm<O, OutlierResult> implements OutlierAlgorithm {
/**
* The logger for this class.
*/
@@ -97,7 +100,7 @@ public class OPTICSOF<O, D extends NumberDistance<D, ?>> extends AbstractDistanc * @param distanceFunction distance function
* @param minpts minPts parameter
*/
- public OPTICSOF(DistanceFunction<? super O, D> distanceFunction, int minpts) {
+ public OPTICSOF(DistanceFunction<? super O> distanceFunction, int minpts) {
super(distanceFunction);
this.minpts = minpts;
}
@@ -110,13 +113,13 @@ public class OPTICSOF<O, D extends NumberDistance<D, ?>> extends AbstractDistanc * @return Outlier detection result
*/
public OutlierResult run(Database database, Relation<O> relation) {
- DistanceQuery<O, D> distQuery = database.getDistanceQuery(relation, getDistanceFunction());
- KNNQuery<O, D> knnQuery = database.getKNNQuery(distQuery, minpts);
- RangeQuery<O, D> rangeQuery = database.getRangeQuery(distQuery);
+ DistanceQuery<O> distQuery = database.getDistanceQuery(relation, getDistanceFunction());
+ KNNQuery<O> knnQuery = database.getKNNQuery(distQuery, minpts);
+ RangeQuery<O> rangeQuery = database.getRangeQuery(distQuery);
DBIDs ids = relation.getDBIDs();
// FIXME: implicit preprocessor.
- WritableDataStore<KNNList<D>> nMinPts = DataStoreUtil.makeStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP, KNNList.class);
+ WritableDataStore<KNNList> nMinPts = DataStoreUtil.makeStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP, KNNList.class);
WritableDoubleDataStore coreDistance = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP);
WritableIntegerDataStore minPtsNeighborhoodSize = DataStoreUtil.makeIntegerStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP, -1);
@@ -124,10 +127,10 @@ public class OPTICSOF<O, D extends NumberDistance<D, ?>> extends AbstractDistanc // N_minpts(id) and core-distance(id)
for(DBIDIter iditer = relation.iterDBIDs(); iditer.valid(); iditer.advance()) {
- KNNList<D> minptsNeighbours = knnQuery.getKNNForDBID(iditer, minpts);
- D d = minptsNeighbours.getKNNDistance();
+ KNNList minptsNeighbours = knnQuery.getKNNForDBID(iditer, minpts);
+ double d = minptsNeighbours.getKNNDistance();
nMinPts.put(iditer, minptsNeighbours);
- coreDistance.putDouble(iditer, d.doubleValue());
+ coreDistance.putDouble(iditer, d);
minPtsNeighborhoodSize.put(iditer, rangeQuery.getRangeForDBID(iditer, d).size());
}
@@ -138,9 +141,9 @@ public class OPTICSOF<O, D extends NumberDistance<D, ?>> extends AbstractDistanc List<Double> core = new ArrayList<>();
double lrd = 0;
// TODO: optimize for double distances
- for(DistanceDBIDListIter<D> neighbor = nMinPts.get(iditer).iter(); neighbor.valid(); neighbor.advance()) {
+ for(DoubleDBIDListIter neighbor = nMinPts.get(iditer).iter(); neighbor.valid(); neighbor.advance()) {
double coreDist = coreDistance.doubleValue(neighbor);
- double dist = distQuery.distance(iditer, neighbor).doubleValue();
+ double dist = distQuery.distance(iditer, neighbor);
double rd = Math.max(coreDist, dist);
lrd = rd + lrd;
core.add(rd);
@@ -166,7 +169,7 @@ public class OPTICSOF<O, D extends NumberDistance<D, ?>> extends AbstractDistanc ofminmax.put(of);
}
// Build result representation.
- Relation<Double> scoreResult = new MaterializedRelation<>("OPTICS Outlier Scores", "optics-outlier", TypeUtil.DOUBLE, ofs, relation.getDBIDs());
+ DoubleRelation scoreResult = new MaterializedDoubleRelation("OPTICS Outlier Scores", "optics-outlier", ofs, relation.getDBIDs());
OutlierScoreMeta scoreMeta = new QuotientOutlierScoreMeta(ofminmax.getMin(), ofminmax.getMax(), 0.0, Double.POSITIVE_INFINITY, 1.0);
return new OutlierResult(scoreMeta, scoreResult);
}
@@ -188,13 +191,13 @@ public class OPTICSOF<O, D extends NumberDistance<D, ?>> extends AbstractDistanc *
* @apiviz.exclude
*/
- public static class Parameterizer<O, D extends NumberDistance<D, ?>> extends AbstractDistanceBasedAlgorithm.Parameterizer<O, D> {
+ public static class Parameterizer<O> extends AbstractDistanceBasedAlgorithm.Parameterizer<O> {
protected int minpts = 0;
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
- final IntParameter param = new IntParameter(OPTICS.MINPTS_ID);
+ final IntParameter param = new IntParameter(OPTICS.Parameterizer.MINPTS_ID);
param.addConstraint(CommonConstraints.GREATER_THAN_ONE_INT);
if(config.grab(param)) {
minpts = param.getValue();
@@ -202,7 +205,7 @@ public class OPTICSOF<O, D extends NumberDistance<D, ?>> extends AbstractDistanc }
@Override
- protected OPTICSOF<O, D> makeInstance() {
+ protected OPTICSOF<O> makeInstance() {
return new OPTICSOF<>(distanceFunction, minpts);
}
}
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