weka.core.neighboursearch

## Class KDTree

- java.lang.Object
- - weka.core.neighboursearch.NearestNeighbourSearch
  - - weka.core.neighboursearch.KDTree

- All Implemented Interfaces:
    java.io.Serializable, AdditionalMeasureProducer, OptionHandler, RevisionHandler, TechnicalInformationHandler

      public class KDTree
      extends NearestNeighbourSearch
      implements TechnicalInformationHandler

  Class implementing the KDTree search algorithm for nearest neighbour search.
  The connection to dataset is only a reference. For the tree structure the indexes are stored in an array.
  Building the tree:
  If a node has <maximal-inst-number> (option -L) instances no further splitting is done. Also if the split would leave one side empty, the branch is not split any further even if the instances in the resulting node are more than <maximal-inst-number> instances.
  **PLEASE NOTE:** The algorithm can not handle missing values, so it is advisable to run ReplaceMissingValues filter if there are any missing values in the dataset.
  For more information see:
  Jerome H. Friedman, Jon Luis Bentley, Raphael Ari Finkel (1977). An Algorithm for Finding Best Matches in Logarithmic Expected Time. ACM Transactions on Mathematics Software. 3(3):209-226.
  Andrew Moore (1991). A tutorial on kd-trees.

  BibTeX:

       @article{Friedman1977,
          author = {Jerome H. Friedman and Jon Luis Bentley and Raphael Ari Finkel},
          journal = {ACM Transactions on Mathematics Software},
          month = {September},
          number = {3},
          pages = {209-226},
          title = {An Algorithm for Finding Best Matches in Logarithmic Expected Time},
          volume = {3},
          year = {1977}
       }

       @techreport{Moore1991,
          author = {Andrew Moore},
          booktitle = {University of Cambridge Computer Laboratory Technical Report No. 209},
          howpublished = {Extract from PhD Thesis},
          title = {A tutorial on kd-trees},
          year = {1991},
          HTTP = {Available from http://www.autonlab.org/autonweb/14665.html}
       }

  Valid options are:

       -S <classname and options>
        Node splitting method to use.
        (default: weka.core.neighboursearch.kdtrees.SlidingMidPointOfWidestSide)

       -W <value>
        Set minimal width of a box
        (default: 1.0E-2).

       -L
        Maximal number of instances in a leaf
        (default: 40).

       -N
        Normalizing will be done
        (Select dimension for split, with normalising to universe).

  Version:
    $Revision: 10141 $
  Author:
    Gabi Schmidberger (gabi[at-the-rate]cs[dot]waikato[dot]ac[dot]nz), Malcolm Ware (mfw4[at-the-rate]cs[dot]waikato[dot]ac[dot]nz), Ashraf M. Kibriya (amk14[at-the-rate]cs[dot]waikato[dot]ac[dot]nz)
  See Also:
    Serialized Form

- - ### Field Summary

    Fields
    Modifier and Type | Field and Description
    --- | ---
    `static int` | `MAX` The index of MAX value in attributes' range array.
    `static int` | `MIN` The index of MIN value in attributes' range array.
    `static int` | `WIDTH` The index of WIDTH (MAX-MIN) value in attributes' range array.

  - ### Constructor Summary

    Constructors
    Constructor and Description
    `KDTree()` Creates a new instance of KDTree.
    `KDTree(Instances insts)` Creates a new instance of KDTree.

  - ### Method Summary

    Methods
    Modifier and Type | Method and Description
    --- | ---
    `void` | `addInstanceInfo(Instance instance)` Adds one instance to KDTree loosly.
    `void` | `assignSubToCenters(KDTreeNode node, Instances centers, int[] centList, int[] assignments)` Assigns instances of this node to center.
    `void` | `centerInstances(Instances centers, int[] assignments, double pc)` Assigns instances to centers using KDTree.
    `java.util.Enumeration<java.lang.String>` | `enumerateMeasures()` Returns an enumeration of the additional measure names.
    `DistanceFunction` | `getDistanceFunction()` returns the distance function currently in use.
    `double[]` | `getDistances()` Returns the distances to the kNearest or 1 nearest neighbour currently found with either the kNearestNeighbours or the nearestNeighbour method.
    `int` | `getMaxInstInLeaf()` Get the maximum number of instances in a leaf.
    `double` | `getMeasure(java.lang.String additionalMeasureName)` Returns the value of the named measure.
    `double` | `getMinBoxRelWidth()` Gets the minimum relative box width.
    `KDTreeNodeSplitter` | `getNodeSplitter()` Returns the splitting method currently in use to split the nodes of the KDTree.
    `boolean` | `getNormalizeNodeWidth()` Gets the normalize flag.
    `java.lang.String[]` | `getOptions()` Gets the current settings of KDtree.
    `java.lang.String` | `getRevision()` Returns the revision string.
    `TechnicalInformation` | `getTechnicalInformation()` 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.
    `java.lang.String` | `globalInfo()` Returns a string describing this nearest neighbour search algorithm.
    `Instances` | `kNearestNeighbours(Instance target, int k)` Returns the k nearest neighbours of the supplied instance.
    `java.util.Enumeration<Option>` | `listOptions()` Returns an enumeration describing the available options.
    `java.lang.String` | `maxInstInLeafTipText()` Tip text for this property.
    `double` | `measureMaxDepth()` Returns the depth of the tree.
    `double` | `measureNumLeaves()` Returns the number of leaves.
    `double` | `measureTreeSize()` Returns the size of the tree.
    `java.lang.String` | `minBoxRelWidthTipText()` Tip text for this property.
    `Instance` | `nearestNeighbour(Instance target)` Returns the nearest neighbour of the supplied target instance.
    `java.lang.String` | `nodeSplitterTipText()` Returns the tip text for this property.
    `java.lang.String` | `normalizeNodeWidthTipText()` Tip text for this property.
    `void` | `setDistanceFunction(DistanceFunction df)` sets the distance function to use for nearest neighbour search.
    `void` | `setInstances(Instances instances)` Builds the KDTree on the given set of instances.
    `void` | `setMaxInstInLeaf(int i)` Sets the maximum number of instances in a leaf.
    `void` | `setMeasurePerformance(boolean measurePerformance)` Sets whether to calculate the performance statistics or not.
    `void` | `setMinBoxRelWidth(double i)` Sets the minimum relative box width.
    `void` | `setNodeSplitter(KDTreeNodeSplitter splitter)` Sets the splitting method to use to split the nodes of the KDTree.
    `void` | `setNormalizeNodeWidth(boolean n)` Sets the flag for normalizing the widths of a KDTree Node by the width of the dimension in the universe.
    `void` | `setOptions(java.lang.String[] options)` Parses a given list of options.
    `void` | `update(Instance instance)` Adds one instance to the KDTree.

    - ### Methods inherited from class weka.core.neighboursearch.NearestNeighbourSearch

      `combSort11, distanceFunctionTipText, getInstances, getMeasurePerformance, getPerformanceStats, measurePerformanceTipText, quickSort`

    - ### Methods inherited from class java.lang.Object

      `equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

- - ### Field Detail

    - #### MIN

          public static final int MIN

      The index of MIN value in attributes' range array.
      See Also:
        Constant Field Values

    - #### MAX

          public static final int MAX

      The index of MAX value in attributes' range array.
      See Also:
        Constant Field Values

    - #### WIDTH

          public static final int WIDTH

      The index of WIDTH (MAX-MIN) value in attributes' range array.
      See Also:
        Constant Field Values

  - ### Constructor Detail

    - #### KDTree

          public KDTree()

      Creates a new instance of KDTree.

    - #### KDTree

          public KDTree(Instances insts)

      Creates a new instance of KDTree. It also builds the tree on supplied set of Instances.
      Parameters:
        `insts` - The instances/points on which the BallTree should be built on.

  - ### Method Detail

    - #### getTechnicalInformation

          public TechnicalInformation getTechnicalInformation()

      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.
      Specified by:
        `getTechnicalInformation` in interface `TechnicalInformationHandler`
      Returns:
        the technical information about this class

    - #### kNearestNeighbours

          public Instances kNearestNeighbours(Instance target,
                                     int k)
                                       throws java.lang.Exception

      Returns the k nearest neighbours of the supplied instance. >k neighbours are returned if there are more than one neighbours at the kth boundary.
      Specified by:
        `kNearestNeighbours` in class `NearestNeighbourSearch`
      Parameters:
        `target` - The instance to find the nearest neighbours for.
        `k` - The number of neighbours to find.
      Returns:
        The k nearest neighbours (or >k if more there are than one neighbours at the kth boundary).
      Throws:
        `java.lang.Exception` - if the nearest neighbour could not be found.

    - #### nearestNeighbour

          public Instance nearestNeighbour(Instance target)
                                    throws java.lang.Exception

      Returns the nearest neighbour of the supplied target instance.
      Specified by:
        `nearestNeighbour` in class `NearestNeighbourSearch`
      Parameters:
        `target` - The instance to find the nearest neighbour for.
      Returns:
        The nearest neighbour from among the previously supplied training instances.
      Throws:
        `java.lang.Exception` - if the neighbours could not be found.

    - #### getDistances

          public double[] getDistances()
                                throws java.lang.Exception

      Returns the distances to the kNearest or 1 nearest neighbour currently found with either the kNearestNeighbours or the nearestNeighbour method.
      Specified by:
        `getDistances` in class `NearestNeighbourSearch`
      Returns:
        array containing the distances of the nearestNeighbours. The length and ordering of the array is the same as that of the instances returned by nearestNeighbour functions.
      Throws:
        `java.lang.Exception` - if called before calling kNearestNeighbours or nearestNeighbours.

    - #### setInstances

          public void setInstances(Instances instances)
                            throws java.lang.Exception

      Builds the KDTree on the given set of instances.
      Overrides:
        `setInstances` in class `NearestNeighbourSearch`
      Parameters:
        `instances` - The insts on which the KDTree is to be built.
      Throws:
        `java.lang.Exception` - If some error occurs while building the KDTree

    - #### update

          public void update(Instance instance)
                      throws java.lang.Exception

      Adds one instance to the KDTree. This updates the KDTree structure to take into account the newly added training instance.
      Specified by:
        `update` in class `NearestNeighbourSearch`
      Parameters:
        `instance` - the instance to be added. Usually the newly added instance in the training set.
      Throws:
        `java.lang.Exception` - If the instance cannot be added.

    - #### addInstanceInfo

          public void addInstanceInfo(Instance instance)

      Adds one instance to KDTree loosly. It only changes the ranges in EuclideanDistance, and does not affect the structure of the KDTree.
      Overrides:
        `addInstanceInfo` in class `NearestNeighbourSearch`
      Parameters:
        `instance` - the new instance. Usually this is the test instance supplied to update the range of attributes in the distance function.

    - #### measureTreeSize

          public double measureTreeSize()

      Returns the size of the tree.
      Returns:
        the size of the tree

    - #### measureNumLeaves

          public double measureNumLeaves()

      Returns the number of leaves.
      Returns:
        the number of leaves

    - #### measureMaxDepth

          public double measureMaxDepth()

      Returns the depth of the tree.
      Returns:
        The depth of the tree

    - #### enumerateMeasures

          public java.util.Enumeration<java.lang.String> enumerateMeasures()

      Returns an enumeration of the additional measure names.
      Specified by:
        `enumerateMeasures` in interface `AdditionalMeasureProducer`
      Overrides:
        `enumerateMeasures` in class `NearestNeighbourSearch`
      Returns:
        an enumeration of the measure names

    - #### getMeasure

          public double getMeasure(java.lang.String additionalMeasureName)

      Returns the value of the named measure.
      Specified by:
        `getMeasure` in interface `AdditionalMeasureProducer`
      Overrides:
        `getMeasure` in class `NearestNeighbourSearch`
      Parameters:
        `additionalMeasureName` - the name of the measure to query for its value.
      Returns:
        The value of the named measure
      Throws:
        `java.lang.IllegalArgumentException` - If the named measure is not supported.

    - #### setMeasurePerformance

          public void setMeasurePerformance(boolean measurePerformance)

      Sets whether to calculate the performance statistics or not.
      Overrides:
        `setMeasurePerformance` in class `NearestNeighbourSearch`
      Parameters:
        `measurePerformance` - Should be true if performance statistics are to be measured.

    - #### centerInstances

          public void centerInstances(Instances centers,
                             int[] assignments,
                             double pc)
                               throws java.lang.Exception

      Assigns instances to centers using KDTree.
      Parameters:
        `centers` - the current centers
        `assignments` - the centerindex for each instance
        `pc` - the threshold value for pruning.
      Throws:
        `java.lang.Exception` - If there is some problem assigning instances to centers.

    - #### assignSubToCenters

          public void assignSubToCenters(KDTreeNode node,
                                Instances centers,
                                int[] centList,
                                int[] assignments)
                                  throws java.lang.Exception

      Assigns instances of this node to center. Center to be assign to is decided by the distance function.
      Parameters:
        `node` - The KDTreeNode whose instances are to be assigned.
        `centers` - all the input centers
        `centList` - the list of centers to work with
        `assignments` - index list of last assignments
      Throws:
        `java.lang.Exception` - If there is error assigning the instances.

    - #### minBoxRelWidthTipText

          public java.lang.String minBoxRelWidthTipText()

      Tip text for this property.
      Returns:
        the tip text for this property

    - #### setMinBoxRelWidth

          public void setMinBoxRelWidth(double i)

      Sets the minimum relative box width.
      Parameters:
        `i` - the minimum relative box width

    - #### getMinBoxRelWidth

          public double getMinBoxRelWidth()

      Gets the minimum relative box width.
      Returns:
        the minimum relative box width

    - #### maxInstInLeafTipText

          public java.lang.String maxInstInLeafTipText()

      Tip text for this property.
      Returns:
        the tip text for this property

    - #### setMaxInstInLeaf

          public void setMaxInstInLeaf(int i)

      Sets the maximum number of instances in a leaf.
      Parameters:
        `i` - the maximum number of instances in a leaf

    - #### getMaxInstInLeaf

          public int getMaxInstInLeaf()

      Get the maximum number of instances in a leaf.
      Returns:
        the maximum number of instances in a leaf

    - #### normalizeNodeWidthTipText

          public java.lang.String normalizeNodeWidthTipText()

      Tip text for this property.
      Returns:
        the tip text for this property

    - #### setNormalizeNodeWidth

          public void setNormalizeNodeWidth(boolean n)

      Sets the flag for normalizing the widths of a KDTree Node by the width of the dimension in the universe.
      Parameters:
        `n` - true to use normalizing.

    - #### getNormalizeNodeWidth

          public boolean getNormalizeNodeWidth()

      Gets the normalize flag.
      Returns:
        True if normalizing

    - #### getDistanceFunction

          public DistanceFunction getDistanceFunction()

      returns the distance function currently in use.
      Overrides:
        `getDistanceFunction` in class `NearestNeighbourSearch`
      Returns:
        the distance function

    - #### setDistanceFunction

          public void setDistanceFunction(DistanceFunction df)
                                   throws java.lang.Exception

      sets the distance function to use for nearest neighbour search.
      Overrides:
        `setDistanceFunction` in class `NearestNeighbourSearch`
      Parameters:
        `df` - the distance function to use
      Throws:
        `java.lang.Exception` - if not EuclideanDistance

    - #### nodeSplitterTipText

          public java.lang.String nodeSplitterTipText()

      Returns the tip text for this property.
      Returns:
        tip text for this property suitable for displaying in the explorer/experimenter gui

    - #### getNodeSplitter

          public KDTreeNodeSplitter getNodeSplitter()

      Returns the splitting method currently in use to split the nodes of the KDTree.
      Returns:
        The KDTreeNodeSplitter currently in use.

    - #### setNodeSplitter

          public void setNodeSplitter(KDTreeNodeSplitter splitter)

      Sets the splitting method to use to split the nodes of the KDTree.
      Parameters:
        `splitter` - The KDTreeNodeSplitter to use.

    - #### globalInfo

          public java.lang.String globalInfo()

      Returns a string describing this nearest neighbour search algorithm.
      Overrides:
        `globalInfo` in class `NearestNeighbourSearch`
      Returns:
        a description of the algorithm for displaying in the explorer/experimenter gui

    - #### listOptions

          public java.util.Enumeration<Option> listOptions()

      Returns an enumeration describing the available options.
      Specified by:
        `listOptions` in interface `OptionHandler`
      Overrides:
        `listOptions` in class `NearestNeighbourSearch`
      Returns:
        an enumeration of all the available options.

    - #### setOptions

          public void setOptions(java.lang.String[] options)
                          throws java.lang.Exception

      Parses a given list of options.

      Valid options are:

           -S <classname and options>
            Node splitting method to use.
            (default: weka.core.neighboursearch.kdtrees.SlidingMidPointOfWidestSide)

           -W <value>
            Set minimal width of a box
            (default: 1.0E-2).

           -L
            Maximal number of instances in a leaf
            (default: 40).

           -N
            Normalizing will be done
            (Select dimension for split, with normalising to universe).

      Specified by:
        `setOptions` in interface `OptionHandler`
      Overrides:
        `setOptions` in class `NearestNeighbourSearch`
      Parameters:
        `options` - the list of options as an array of strings
      Throws:
        `java.lang.Exception` - if an option is not supported

    - #### getOptions

          public java.lang.String[] getOptions()

      Gets the current settings of KDtree.
      Specified by:
        `getOptions` in interface `OptionHandler`
      Overrides:
        `getOptions` in class `NearestNeighbourSearch`
      Returns:
        an array of strings suitable for passing to setOptions

    - #### getRevision

          public java.lang.String getRevision()

      Returns the revision string.
      Specified by:
        `getRevision` in interface `RevisionHandler`
      Returns:
        the revision