Examples of weka.clusterers.forOPTICSAndDBScan.DataObjects.DataObject

Package weka.clusterers.forOPTICSAndDBScan.DataObjects

Examples of weka.clusterers.forOPTICSAndDBScan.DataObjects.DataObject

weka.clusterers.forOPTICSAndDBScan.DataObjects.DataObject

DataObject.java
Authors: Rainer Holzmann, Zhanna Melnikova-Albrecht, Matthias Schubert
Date: Aug 19, 2004
Time: 5:48:59 PM
$ Revision 1.4 $

@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: 1.2 $

        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++;
                }
            }

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            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--;

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        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";
    }

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        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();


        UpdateQueue seeds = new UpdateQueue();


        /** OPTICS-Begin */
        Iterator iterator = database.dataObjectIterator();
        while (iterator.hasNext()) {
            DataObject dataObject = (DataObject) iterator.next();
            if (!dataObject.isProcessed()) {
                expandClusterOrder(dataObject, seeds);
            }
        }


        long time_2 = System.currentTimeMillis();

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        if (dataObject.getCoreDistance() != DataObject.UNDEFINED) {
            update(seeds, epsilonRange_List, dataObject);
            while (seeds.hasNext()) {
                UpdateQueueElement updateQueueElement = seeds.next();
                DataObject currentDataObject = (DataObject) updateQueueElement.getObject();
                currentDataObject.setReachabilityDistance(updateQueueElement.getPriority());
                List list_1 = database.coreDistance(getMinPoints(), getEpsilon(), currentDataObject);
                List epsilonRange_List_1 = (List) list_1.get(1);
                currentDataObject.setCoreDistance(((Double) list_1.get(2)).doubleValue());
                currentDataObject.setProcessed(true);


                resultVector.addElement(currentDataObject);


                if (currentDataObject.getCoreDistance() != DataObject.UNDEFINED) {
                    update(seeds, epsilonRange_List_1, currentDataObject);
                }
            }
        }
    }

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        double coreDistance = centralObject.getCoreDistance();
        double new_r_dist = DataObject.UNDEFINED;


        for (int i = 0; i < epsilonRange_list.size(); i++) {
            EpsilonRange_ListElement listElement = (EpsilonRange_ListElement) epsilonRange_list.get(i);
            DataObject neighbourhood_object = listElement.getDataObject();
            if (!neighbourhood_object.isProcessed()) {
                new_r_dist = Math.max(coreDistance, listElement.getDistance());
                seeds.add(new_r_dist, neighbourhood_object, neighbourhood_object.getKey());
            }
        }
    }

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        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();


        UpdateQueue seeds = new UpdateQueue();


        /** OPTICS-Begin */
        Iterator iterator = database.dataObjectIterator();
        while (iterator.hasNext()) {
            DataObject dataObject = (DataObject) iterator.next();
            if (!dataObject.isProcessed()) {
                expandClusterOrder(dataObject, seeds);
            }
        }


        long time_2 = System.currentTimeMillis();

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        if (dataObject.getCoreDistance() != DataObject.UNDEFINED) {
            update(seeds, epsilonRange_List, dataObject);
            while (seeds.hasNext()) {
                UpdateQueueElement updateQueueElement = seeds.next();
                DataObject currentDataObject = (DataObject) updateQueueElement.getObject();
                currentDataObject.setReachabilityDistance(updateQueueElement.getPriority());
                List list_1 = database.coreDistance(getMinPoints(), getEpsilon(), currentDataObject);
                List epsilonRange_List_1 = (List) list_1.get(1);
                currentDataObject.setCoreDistance(((Double) list_1.get(2)).doubleValue());
                currentDataObject.setProcessed(true);


                resultVector.addElement(currentDataObject);


                if (currentDataObject.getCoreDistance() != DataObject.UNDEFINED) {
                    update(seeds, epsilonRange_List_1, currentDataObject);
                }
            }
        }
    }

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        double coreDistance = centralObject.getCoreDistance();
        double new_r_dist = DataObject.UNDEFINED;


        for (int i = 0; i < epsilonRange_list.size(); i++) {
            EpsilonRange_ListElement listElement = (EpsilonRange_ListElement) epsilonRange_list.get(i);
            DataObject neighbourhood_object = listElement.getDataObject();
            if (!neighbourhood_object.isProcessed()) {
                new_r_dist = Math.max(coreDistance, listElement.getDistance());
                seeds.add(new_r_dist, neighbourhood_object, neighbourhood_object.getKey());
            }
        }
    }

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        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++;
                }
            }

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