weka.clusterers.forOPTICSAndDBScan.Databases.SequentialDatabase Maven / Gradle / Ivy
/*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see
* SequentialDatabase.java
* Authors: Rainer Holzmann, Zhanna Melnikova-Albrecht, Matthias Schubert
* Date: Aug 20, 2004
* Time: 1:23:38 PM
* $ Revision 1.4 $
*
*
* @author Matthias Schubert ([email protected])
* @author Zhanna Melnikova-Albrecht ([email protected])
* @author Rainer Holzmann ([email protected])
* @version $Revision: 8108 $
*/
public class SequentialDatabase
implements Database, Serializable, RevisionHandler {
/** for serialization */
private static final long serialVersionUID = 787245523118665778L;
/**
* Internal, sorted Treemap for storing all the DataObjects
*/
private TreeMap treeMap;
/**
* Holds the original instances delivered from WEKA
*/
private Instances instances;
/**
* Holds the minimum value for each attribute
*/
private double[] attributeMinValues;
/**
* Holds the maximum value for each attribute
*/
private double[] attributeMaxValues;
// *****************************************************************************************************************
// constructors
// *****************************************************************************************************************
/**
* Constructs a new sequential database and holds the original instances
* @param instances
*/
public SequentialDatabase(Instances instances) {
this.instances = instances;
treeMap = new TreeMap();
}
// *****************************************************************************************************************
// methods
// *****************************************************************************************************************
/**
* Select a dataObject from the database
* @param key The key that is associated with the dataObject
* @return dataObject
*/
public DataObject getDataObject(String key) {
return (DataObject) treeMap.get(key);
}
/**
* Sets the minimum and maximum values for each attribute in different arrays
* by walking through every DataObject of the database
*/
public void setMinMaxValues() {
attributeMinValues = new double[getInstances().numAttributes()];
attributeMaxValues = new double[getInstances().numAttributes()];
//Init
for (int i = 0; i < getInstances().numAttributes(); i++) {
attributeMinValues[i] = attributeMaxValues[i] = Double.NaN;
}
Iterator iterator = dataObjectIterator();
while (iterator.hasNext()) {
DataObject dataObject = (DataObject) iterator.next();
for (int j = 0; j < getInstances().numAttributes(); j++) {
if (Double.isNaN(attributeMinValues[j])) {
attributeMinValues[j] = dataObject.getInstance().value(j);
attributeMaxValues[j] = dataObject.getInstance().value(j);
} else {
if (dataObject.getInstance().value(j) < attributeMinValues[j])
attributeMinValues[j] = dataObject.getInstance().value(j);
if (dataObject.getInstance().value(j) > attributeMaxValues[j])
attributeMaxValues[j] = dataObject.getInstance().value(j);
}
}
}
}
/**
* Returns the array of minimum-values for each attribute
* @return attributeMinValues
*/
public double[] getAttributeMinValues() {
return attributeMinValues;
}
/**
* Returns the array of maximum-values for each attribute
* @return attributeMaxValues
*/
public double[] getAttributeMaxValues() {
return attributeMaxValues;
}
/**
* Performs an epsilon range query for this dataObject
* @param epsilon Specifies the range for the query
* @param queryDataObject The dataObject that is used as query-object for epsilon range query
* @return List with all the DataObjects that are within the specified range
*/
public List epsilonRangeQuery(double epsilon, DataObject queryDataObject) {
ArrayList epsilonRange_List = new ArrayList();
Iterator iterator = dataObjectIterator();
while (iterator.hasNext()) {
DataObject dataObject = (DataObject) iterator.next();
double distance = queryDataObject.distance(dataObject);
if (distance < epsilon) {
epsilonRange_List.add(dataObject);
}
}
return epsilonRange_List;
}
/**
* Emits the k next-neighbours and performs an epsilon-range-query at the parallel.
* The returned list contains two elements:
* At index=0 --> list with all k next-neighbours;
* At index=1 --> list with all dataObjects within epsilon;
* @param k number of next neighbours
* @param epsilon Specifies the range for the query
* @param dataObject the start object
* @return list with the k-next neighbours (PriorityQueueElements) and a list
* with candidates from the epsilon-range-query (EpsilonRange_ListElements)
*/
public List k_nextNeighbourQuery(int k, double epsilon, DataObject dataObject) {
Iterator iterator = dataObjectIterator();
List return_List = new ArrayList();
List nextNeighbours_List = new ArrayList();
List epsilonRange_List = new ArrayList();
PriorityQueue priorityQueue = new PriorityQueue();
while (iterator.hasNext()) {
DataObject next_dataObject = (DataObject) iterator.next();
double dist = dataObject.distance(next_dataObject);
if (dist <= epsilon) epsilonRange_List.add(new EpsilonRange_ListElement(dist, next_dataObject));
if (priorityQueue.size() < k) {
priorityQueue.add(dist, next_dataObject);
} else {
if (dist < priorityQueue.getPriority(0)) {
priorityQueue.next(); //removes the highest distance
priorityQueue.add(dist, next_dataObject);
}
}
}
while (priorityQueue.hasNext()) {
nextNeighbours_List.add(0, priorityQueue.next());
}
return_List.add(nextNeighbours_List);
return_List.add(epsilonRange_List);
return return_List;
}
/**
* Calculates the coreDistance for the specified DataObject.
* The returned list contains three elements:
* At index=0 --> list with all k next-neighbours;
* At index=1 --> list with all dataObjects within epsilon;
* At index=2 --> coreDistance as Double-value
* @param minPoints minPoints-many neighbours within epsilon must be found to have a non-undefined coreDistance
* @param epsilon Specifies the range for the query
* @param dataObject Calculate coreDistance for this dataObject
* @return list with the k-next neighbours (PriorityQueueElements) and a list
* with candidates from the epsilon-range-query (EpsilonRange_ListElements) and
* the double-value for the calculated coreDistance
*/
public List coreDistance(int minPoints, double epsilon, DataObject dataObject) {
List list = k_nextNeighbourQuery(minPoints, epsilon, dataObject);
if (((List) list.get(1)).size() < minPoints) {
list.add(new Double(DataObject.UNDEFINED));
return list;
} else {
List nextNeighbours_List = (List) list.get(0);
PriorityQueueElement priorityQueueElement =
(PriorityQueueElement) nextNeighbours_List.get(nextNeighbours_List.size() - 1);
if (priorityQueueElement.getPriority() <= epsilon) {
list.add(new Double(priorityQueueElement.getPriority()));
return list;
} else {
list.add(new Double(DataObject.UNDEFINED));
return list;
}
}
}
/**
* Returns the size of the database (the number of dataObjects in the database)
* @return size
*/
public int size() {
return treeMap.size();
}
/**
* Returns an iterator over all the keys
* @return iterator
*/
public Iterator keyIterator() {
return treeMap.keySet().iterator();
}
/**
* Returns an iterator over all the dataObjects in the database
* @return iterator
*/
public Iterator dataObjectIterator() {
return treeMap.values().iterator();
}
/**
* Tests if the database contains the dataObject_Query
* @param dataObject_Query The query-object
* @return true if the database contains dataObject_Query, else false
*/
public boolean contains(DataObject dataObject_Query) {
Iterator iterator = dataObjectIterator();
while (iterator.hasNext()) {
DataObject dataObject = (DataObject) iterator.next();
if (dataObject.equals(dataObject_Query)) return true;
}
return false;
}
/**
* Inserts a new dataObject into the database
* @param dataObject
*/
public void insert(DataObject dataObject) {
treeMap.put(dataObject.getKey(), dataObject);
}
/**
* Returns the original instances delivered from WEKA
* @return instances
*/
public Instances getInstances() {
return instances;
}
/**
* Returns the revision string.
*
* @return the revision
*/
public String getRevision() {
return RevisionUtils.extract("$Revision: 8108 $");
}
}
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