Java tutorial
package clusterer; /* * 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 <http://www.gnu.org/licenses/>. */ /* * Copyright (C) 2004 * & Matthias Schubert (schubert@dbs.ifi.lmu.de) * & Zhanna Melnikova-Albrecht (melnikov@cip.ifi.lmu.de) * & Rainer Holzmann (holzmann@cip.ifi.lmu.de) */ import weka.clusterers.AbstractClusterer; import weka.clusterers.forOPTICSAndDBScan.DataObjects.DataObject; import weka.clusterers.forOPTICSAndDBScan.Databases.Database; import weka.core.Capabilities; import weka.core.Instance; import weka.core.Instances; import weka.core.Option; import weka.core.OptionHandler; import weka.core.RevisionUtils; import weka.core.TechnicalInformation; import weka.core.TechnicalInformationHandler; import weka.core.Utils; import weka.core.Capabilities.Capability; import weka.core.TechnicalInformation.Field; import weka.core.TechnicalInformation.Type; import weka.filters.Filter; import weka.filters.unsupervised.attribute.ReplaceMissingValues; import java.lang.reflect.Constructor; import java.lang.reflect.InvocationTargetException; import java.text.DecimalFormat; import java.util.Enumeration; import java.util.Iterator; import java.util.List; import java.util.Vector; /** <!-- globalinfo-start --> * Basic implementation of DBSCAN clustering algorithm that should *not* be used as a reference for runtime benchmarks: more sophisticated implementations exist! Clustering of new instances is not supported. More info:<br/> * <br/> * Martin Ester, Hans-Peter Kriegel, Joerg Sander, Xiaowei Xu: A Density-Based Algorithm for Discovering Clusters in Large Spatial Databases with Noise. In: Second International Conference on Knowledge Discovery and Data Mining, 226-231, 1996. * <p/> <!-- globalinfo-end --> * <!-- technical-bibtex-start --> * BibTeX: * <pre> * @inproceedings{Ester1996, * author = {Martin Ester and Hans-Peter Kriegel and Joerg Sander and Xiaowei Xu}, * booktitle = {Second International Conference on Knowledge Discovery and Data Mining}, * editor = {Evangelos Simoudis and Jiawei Han and Usama M. Fayyad}, * pages = {226-231}, * publisher = {AAAI Press}, * title = {A Density-Based Algorithm for Discovering Clusters in Large Spatial Databases with Noise}, * year = {1996} * } * </pre> * <p/> <!-- technical-bibtex-end --> * <!-- options-start --> * Valid options are: <p/> * * <pre> -E <double> * epsilon (default = 0.9)</pre> * * <pre> -M <int> * minPoints (default = 6)</pre> * * <pre> -I <String> * index (database) used for DBSCAN (default = weka.clusterers.forOPTICSAndDBScan.Databases.SequentialDatabase)</pre> * * <pre> -D <String> * distance-type (default = weka.clusterers.forOPTICSAndDBScan.DataObjects.EuclideanDataObject)</pre> * <!-- options-end --> * * @author Matthias Schubert (schubert@dbs.ifi.lmu.de) * @author Zhanna Melnikova-Albrecht (melnikov@cip.ifi.lmu.de) * @author Rainer Holzmann (holzmann@cip.ifi.lmu.de) * @version $Revision: 9434 $ */ public class HaritsDBScan extends AbstractClusterer implements OptionHandler, TechnicalInformationHandler { /** for serialization */ static final long serialVersionUID = -1666498248451219728L; /** * Specifies the radius for a range-query */ private double epsilon = 0.9; /** * Specifies the density (the range-query must contain at least minPoints DataObjects) */ private int minPoints = 6; /** * Replace missing values in training instances */ private ReplaceMissingValues replaceMissingValues_Filter; /** * Holds the number of clusters generated */ private int numberOfGeneratedClusters; /** * Holds the distance-type that is used * (default = weka.clusterers.forOPTICSAndDBScan.DataObjects.EuclideanDataObject) */ private String database_distanceType = "weka.clusterers.forOPTICSAndDBScan.DataObjects.EuclideanDataObject"; /** * Holds the type of the used database * (default = weka.clusterers.forOPTICSAndDBScan.Databases.SequentialDatabase) */ private String database_Type = "weka.clusterers.forOPTICSAndDBScan.Databases.SequentialDatabase"; /** * The database that is used for DBSCAN */ private Database database; /** * Holds the current clusterID */ private int clusterID; /** * Counter for the processed instances */ private int processed_InstanceID; /** * Holds the time-value (seconds) for the duration of the clustering-process */ private double elapsedTime; /** * Returns default capabilities of the clusterer. * * @return the capabilities of this clusterer */ public Capabilities getCapabilities() { Capabilities result = super.getCapabilities(); result.disableAll(); result.enable(Capability.NO_CLASS); // attributes result.enable(Capability.NOMINAL_ATTRIBUTES); result.enable(Capability.NUMERIC_ATTRIBUTES); result.enable(Capability.DATE_ATTRIBUTES); result.enable(Capability.MISSING_VALUES); return result; } // ***************************************************************************************************************** // constructors // ***************************************************************************************************************** // ***************************************************************************************************************** // methods // ***************************************************************************************************************** /** * Generate Clustering via DBSCAN * @param instances The instances that need to be clustered * @throws java.lang.Exception If clustering was not successful */ public void buildClusterer(Instances instances) throws Exception { // can clusterer handle the data? getCapabilities().testWithFail(instances); long time_1 = System.currentTimeMillis(); processed_InstanceID = 0; numberOfGeneratedClusters = 0; clusterID = 0; replaceMissingValues_Filter = new ReplaceMissingValues(); replaceMissingValues_Filter.setInputFormat(instances); Instances filteredInstances = Filter.useFilter(instances, replaceMissingValues_Filter); database = databaseForName(getDatabase_Type(), filteredInstances); for (int i = 0; i < database.getInstances().numInstances(); i++) { DataObject dataObject = dataObjectForName(getDatabase_distanceType(), database.getInstances().instance(i), Integer.toString(i), database); database.insert(dataObject); } database.setMinMaxValues(); Iterator iterator = database.dataObjectIterator(); while (iterator.hasNext()) { DataObject dataObject = (DataObject) iterator.next(); if (dataObject.getClusterLabel() == DataObject.UNCLASSIFIED) { if (expandCluster(dataObject)) { clusterID++; numberOfGeneratedClusters++; } } } long time_2 = System.currentTimeMillis(); elapsedTime = (double) (time_2 - time_1) / 1000.0; } /** * Assigns this dataObject to a cluster or remains it as NOISE * @param dataObject The DataObject that needs to be assigned * @return true, if the DataObject could be assigned, else false */ private boolean expandCluster(DataObject dataObject) { List seedList = database.epsilonRangeQuery(getEpsilon(), dataObject); /** dataObject is NO coreObject */ if (seedList.size() < getMinPoints()) { dataObject.setClusterLabel(DataObject.NOISE); return false; } /** dataObject is coreObject */ for (int i = 0; i < seedList.size(); i++) { DataObject seedListDataObject = (DataObject) seedList.get(i); /** label this seedListDataObject with the current clusterID, because it is in epsilon-range */ seedListDataObject.setClusterLabel(clusterID); if (seedListDataObject.equals(dataObject)) { seedList.remove(i); i--; } } /** Iterate the seedList of the startDataObject */ for (int j = 0; j < seedList.size(); j++) { DataObject seedListDataObject = (DataObject) seedList.get(j); List seedListDataObject_Neighbourhood = database.epsilonRangeQuery(getEpsilon(), seedListDataObject); /** seedListDataObject is coreObject */ if (seedListDataObject_Neighbourhood.size() >= getMinPoints()) { for (int i = 0; i < seedListDataObject_Neighbourhood.size(); i++) { DataObject p = (DataObject) seedListDataObject_Neighbourhood.get(i); if (p.getClusterLabel() == DataObject.UNCLASSIFIED || p.getClusterLabel() == DataObject.NOISE) { if (p.getClusterLabel() == DataObject.UNCLASSIFIED) { seedList.add(p); } p.setClusterLabel(clusterID); } } } seedList.remove(j); j--; } return true; } /** * Classifies a given instance. * * @param instance The instance to be assigned to a cluster * @return int The number of the assigned cluster as an integer * @throws java.lang.Exception If instance could not be clustered * successfully */ public int clusterInstance(Instance instance) throws Exception { if (processed_InstanceID >= database.size()) processed_InstanceID = 0; int cnum = (database.getDataObject(Integer.toString(processed_InstanceID++))).getClusterLabel(); if (cnum == DataObject.NOISE) throw new Exception(); else return cnum; } /** * Returns the number of clusters. * * @return int The number of clusters generated for a training dataset. * @throws java.lang.Exception if number of clusters could not be returned * successfully */ public int numberOfClusters() throws Exception { return numberOfGeneratedClusters; } /** * Returns an enumeration of all the available options.. * * @return Enumeration An enumeration of all available options. */ public Enumeration listOptions() { Vector vector = new Vector(); vector.addElement(new Option("\tepsilon (default = 0.9)", "E", 1, "-E <double>")); vector.addElement(new Option("\tminPoints (default = 6)", "M", 1, "-M <int>")); vector.addElement(new Option( "\tindex (database) used for DBSCAN (default = weka.clusterers.forOPTICSAndDBScan.Databases.SequentialDatabase)", "I", 1, "-I <String>")); vector.addElement(new Option( "\tdistance-type (default = weka.clusterers.forOPTICSAndDBScan.DataObjects.EuclideanDataObject)", "D", 1, "-D <String>")); return vector.elements(); } /** * Sets the OptionHandler's options using the given list. All options * will be set (or reset) during this call (i.e. incremental setting * of options is not possible). <p/> * <!-- options-start --> * Valid options are: <p/> * * <pre> -E <double> * epsilon (default = 0.9)</pre> * * <pre> -M <int> * minPoints (default = 6)</pre> * * <pre> -I <String> * index (database) used for DBSCAN (default = weka.clusterers.forOPTICSAndDBScan.Databases.SequentialDatabase)</pre> * * <pre> -D <String> * distance-type (default = weka.clusterers.forOPTICSAndDBScan.DataObjects.EuclideanDataObject)</pre> * <!-- options-end --> * * @param options The list of options as an array of strings * @throws java.lang.Exception If an option is not supported */ public void setOptions(String[] options) throws Exception { String optionString = Utils.getOption('E', options); if (optionString.length() != 0) { setEpsilon(Double.parseDouble(optionString)); } optionString = Utils.getOption('M', options); if (optionString.length() != 0) { setMinPoints(Integer.parseInt(optionString)); } optionString = Utils.getOption('I', options); if (optionString.length() != 0) { setDatabase_Type(optionString); } optionString = Utils.getOption('D', options); if (optionString.length() != 0) { setDatabase_distanceType(optionString); } } /** * Gets the current option settings for the OptionHandler. * * @return String[] The list of current option settings as an array of strings */ public String[] getOptions() { String[] options = new String[8]; int current = 0; options[current++] = "-E"; options[current++] = "" + getEpsilon(); options[current++] = "-M"; options[current++] = "" + getMinPoints(); options[current++] = "-I"; options[current++] = "" + getDatabase_Type(); options[current++] = "-D"; options[current++] = "" + getDatabase_distanceType(); return options; } /** * Returns a new Class-Instance of the specified database * @param database_Type String of the specified database * @param instances Instances that were delivered from WEKA * @return Database New constructed Database */ public Database databaseForName(String database_Type, Instances instances) { Object o = null; Constructor co = null; try { co = (Class.forName(database_Type)).getConstructor(new Class[] { Instances.class }); o = co.newInstance(new Object[] { instances }); } catch (NoSuchMethodException e) { e.printStackTrace(); } catch (SecurityException e) { e.printStackTrace(); } catch (ClassNotFoundException e) { e.printStackTrace(); } catch (InstantiationException e) { e.printStackTrace(); } catch (IllegalAccessException e) { e.printStackTrace(); } catch (InvocationTargetException e) { e.printStackTrace(); } return (Database) o; } /** * Returns a new Class-Instance of the specified database * @param database_distanceType String of the specified distance-type * @param instance The original instance that needs to hold by this DataObject * @param key Key for this DataObject * @param database Link to the database * @return DataObject New constructed DataObject */ public DataObject dataObjectForName(String database_distanceType, Instance instance, String key, Database database) { Object o = null; Constructor co = null; try { co = (Class.forName(database_distanceType)) .getConstructor(new Class[] { Instance.class, String.class, Database.class }); o = co.newInstance(new Object[] { instance, key, database }); } catch (NoSuchMethodException e) { e.printStackTrace(); } catch (SecurityException e) { e.printStackTrace(); } catch (ClassNotFoundException e) { e.printStackTrace(); } catch (InstantiationException e) { e.printStackTrace(); } catch (IllegalAccessException e) { e.printStackTrace(); } catch (InvocationTargetException e) { e.printStackTrace(); } return (DataObject) o; } /** * Sets a new value for minPoints * @param minPoints MinPoints */ public void setMinPoints(int minPoints) { this.minPoints = minPoints; } /** * Sets a new value for epsilon * @param epsilon Epsilon */ public void setEpsilon(double epsilon) { this.epsilon = epsilon; } /** * Returns the value of epsilon * @return double Epsilon */ public double getEpsilon() { return epsilon; } /** * Returns the value of minPoints * @return int MinPoints */ public int getMinPoints() { return minPoints; } /** * Returns the distance-type * @return String Distance-type */ public String getDatabase_distanceType() { return database_distanceType; } /** * Returns the type of the used index (database) * @return String Index-type */ public String getDatabase_Type() { return database_Type; } /** * Sets a new distance-type * @param database_distanceType The new distance-type */ public void setDatabase_distanceType(String database_distanceType) { this.database_distanceType = database_distanceType; } /** * Sets a new database-type * @param database_Type The new database-type */ public void setDatabase_Type(String database_Type) { this.database_Type = database_Type; } /** * Returns the tip text for this property * @return tip text for this property suitable for * displaying in the explorer/experimenter gui */ public String epsilonTipText() { return "radius of the epsilon-range-queries"; } /** * Returns the tip text for this property * @return tip text for this property suitable for * displaying in the explorer/experimenter gui */ public String minPointsTipText() { return "minimun number of DataObjects required in an epsilon-range-query"; } /** * Returns the tip text for this property * @return tip text for this property suitable for * displaying in the explorer/experimenter gui */ public String database_TypeTipText() { return "used database"; } /** * Returns the tip text for this property * @return tip text for this property suitable for * displaying in the explorer/experimenter gui */ public String database_distanceTypeTipText() { return "used distance-type"; } /** * Returns a string describing this DataMining-Algorithm * @return String Information for the gui-explorer */ public String globalInfo() { return "Basic implementation of DBSCAN clustering algorithm that should " + "*not* be used as a reference for runtime benchmarks: more sophisticated " + "implementations exist! Clustering of new instances is not supported. More info:\n\n " + getTechnicalInformation().toString(); } /** * Returns an instance of a TechnicalInformation object, containing * detailed information about the technical background of this class, * e.g., paper reference or book this class is based on. * * @return the technical information about this class */ public TechnicalInformation getTechnicalInformation() { TechnicalInformation result; result = new TechnicalInformation(Type.INPROCEEDINGS); result.setValue(Field.AUTHOR, "Martin Ester and Hans-Peter Kriegel and Joerg Sander and Xiaowei Xu"); result.setValue(Field.TITLE, "A Density-Based Algorithm for Discovering Clusters in Large Spatial Databases with Noise"); result.setValue(Field.BOOKTITLE, "Second International Conference on Knowledge Discovery and Data Mining"); result.setValue(Field.EDITOR, "Evangelos Simoudis and Jiawei Han and Usama M. Fayyad"); result.setValue(Field.YEAR, "1996"); result.setValue(Field.PAGES, "226-231"); result.setValue(Field.PUBLISHER, "AAAI Press"); return result; } /** * Returns a description of the clusterer * * @return a string representation of the clusterer */ public String toString() { StringBuffer stringBuffer = new StringBuffer(); stringBuffer.append("DBSCAN clustering results\n" + "========================================================================================\n\n"); stringBuffer.append("Clustered DataObjects: " + database.size() + "\n"); stringBuffer.append("Number of attributes: " + database.getInstances().numAttributes() + "\n"); stringBuffer.append("Epsilon: " + getEpsilon() + "; minPoints: " + getMinPoints() + "\n"); stringBuffer.append("Index: " + getDatabase_Type() + "\n"); stringBuffer.append("Distance-type: " + getDatabase_distanceType() + "\n"); stringBuffer.append("Number of generated clusters: " + numberOfGeneratedClusters + "\n"); DecimalFormat decimalFormat = new DecimalFormat(".##"); stringBuffer.append("Elapsed time: " + decimalFormat.format(elapsedTime) + "\n\n"); for (int i = 0; i < database.size(); i++) { DataObject dataObject = database.getDataObject(Integer.toString(i)); stringBuffer.append("(" + Utils.doubleToString(Double.parseDouble(dataObject.getKey()), (Integer.toString(database.size()).length()), 0) + ".) " + Utils.padRight(dataObject.toString(), 69) + " --> " + ((dataObject.getClusterLabel() == DataObject.NOISE) ? "NOISE\n" : dataObject.getClusterLabel() + "\n")); } return stringBuffer.toString() + "\n"; } /** * Returns the revision string. * * @return the revision */ public String getRevision() { return RevisionUtils.extract("$Revision: 9434 $"); } /** * Main Method for testing DBSCAN * @param args Valid parameters are: 'E' epsilon (default = 0.9); 'M' minPoints (default = 6); * 'I' index-type (default = weka.clusterers.forOPTICSAndDBScan.Databases.SequentialDatabase); * 'D' distance-type (default = weka.clusterers.forOPTICSAndDBScan.DataObjects.EuclideanDataObject); */ public static void main(String[] args) { runClusterer(new HaritsDBScan(), args); } }