Package weka.core.neighboursearch
Class PCANNSearch
- java.lang.Object
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- weka.core.neighboursearch.NearestNeighbourSearch
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- weka.core.neighboursearch.NewNNSearch
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- weka.core.neighboursearch.PCANNSearch
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- All Implemented Interfaces:
Serializable
,weka.core.AdditionalMeasureProducer
,weka.core.OptionHandler
,weka.core.RevisionHandler
public class PCANNSearch extends NewNNSearch
Class implementing the brute force search algorithm for nearest neighbour search, filtered using PLS.
Valid options are:
-S Skip identical instances (distances equal to zero).
- Version:
- $Revision$
- Author:
- Dale
- See Also:
- Serialized Form
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Nested Class Summary
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Nested classes/interfaces inherited from class weka.core.neighboursearch.NewNNSearch
NewNNSearch.InstanceNode
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Nested classes/interfaces inherited from class weka.core.neighboursearch.NearestNeighbourSearch
weka.core.neighboursearch.NearestNeighbourSearch.MyHeap, weka.core.neighboursearch.NearestNeighbourSearch.MyHeapElement, weka.core.neighboursearch.NearestNeighbourSearch.NeighborList, weka.core.neighboursearch.NearestNeighbourSearch.NeighborNode
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Field Summary
Fields Modifier and Type Field Description protected double
m_CoverVariance
the amount of varaince to cover in the original data when retaining the best n PC's.protected int
m_MaxAttrsInName
maximum number of attributes in the transformed attribute name.protected weka.core.Instances
m_myInstances
protected PrincipalComponentsJ
m_pca
The neighbourhood of instances to find neighbours in.protected int
m_Preprocessing
the type of preprocessing-
Fields inherited from class weka.core.neighboursearch.NewNNSearch
m_Distances, m_neighbours, m_SkipIdentical
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Constructor Summary
Constructors Constructor Description PCANNSearch()
Constructor.PCANNSearch(weka.core.Instances insts)
Constructor that uses the supplied set of instances.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addInstanceInfo(weka.core.Instance ins)
Adds the given instance info.protected PrincipalComponentsJ
buildFilter(double cv, int maxatt)
int
getMaximumAttributeNames()
Gets maximum number of attributes to include in transformed attribute names.String[]
getOptions()
Gets the current settings.double
getVarianceCovered()
Gets the proportion of total variance to account for when retaining principal components.weka.core.Instances
kNearestNeighbours(weka.core.Instance target, int kNN)
Returns k nearest instances in the current neighbourhood to the supplied instance.Enumeration
listOptions()
Returns an enumeration describing the available options.void
setInstances(weka.core.Instances insts)
Sets the instances comprising the current neighbourhood.void
setMaximumAttributeNames(int value)
Sets maximum number of attributes to include in transformed attribute names.void
setOptions(String[] options)
Parses a given list of options.void
setPreprocessing(weka.core.SelectedTag value)
Sets the type of preprocessing to usevoid
setVarianceCovered(double value)
Sets the amount of variance to account for when retaining principal components.protected weka.core.Instance
transformInstance(weka.core.Instance in)
protected weka.core.Instances
transformInstances(weka.core.Instances in)
void
update(weka.core.Instance ins)
Updates the LinearNNSearch to cater for the new added instance.-
Methods inherited from class weka.core.neighboursearch.NewNNSearch
getDistances, getRevision, getSkipIdentical, globalInfo, nearestNeighbour, setSkipIdentical, skipIdenticalTipText
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Methods inherited from class weka.core.neighboursearch.NearestNeighbourSearch
combSort11, distanceFunctionTipText, enumerateMeasures, getDistanceFunction, getInstances, getMeasure, getMeasurePerformance, getPerformanceStats, measurePerformanceTipText, partition, quickSort, setDistanceFunction, setMeasurePerformance
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Field Detail
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m_pca
protected PrincipalComponentsJ m_pca
The neighbourhood of instances to find neighbours in.
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m_CoverVariance
protected double m_CoverVariance
the amount of varaince to cover in the original data when retaining the best n PC's.
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m_MaxAttrsInName
protected int m_MaxAttrsInName
maximum number of attributes in the transformed attribute name.
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m_myInstances
protected weka.core.Instances m_myInstances
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m_Preprocessing
protected int m_Preprocessing
the type of preprocessing
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Method Detail
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setVarianceCovered
public void setVarianceCovered(double value)
Sets the amount of variance to account for when retaining principal components.- Parameters:
value
- the proportion of total variance to account for
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getVarianceCovered
public double getVarianceCovered()
Gets the proportion of total variance to account for when retaining principal components.- Returns:
- the proportion of variance to account for
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setMaximumAttributeNames
public void setMaximumAttributeNames(int value)
Sets maximum number of attributes to include in transformed attribute names.- Parameters:
value
- the maximum number of attributes
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getMaximumAttributeNames
public int getMaximumAttributeNames()
Gets maximum number of attributes to include in transformed attribute names.- Returns:
- the maximum number of attributes
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transformInstances
protected weka.core.Instances transformInstances(weka.core.Instances in) throws Exception
- Throws:
Exception
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transformInstance
protected weka.core.Instance transformInstance(weka.core.Instance in) throws Exception
- Throws:
Exception
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buildFilter
protected PrincipalComponentsJ buildFilter(double cv, int maxatt)
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kNearestNeighbours
public weka.core.Instances kNearestNeighbours(weka.core.Instance target, int kNN) throws Exception
Returns k nearest instances in the current neighbourhood to the supplied instance.- Overrides:
kNearestNeighbours
in classNewNNSearch
- Parameters:
target
- The instance to find the k nearest neighbours for.kNN
- The number of nearest neighbours to find.- Returns:
- the k nearest neighbors
- Throws:
Exception
- if the neighbours could not be found.
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setInstances
public void setInstances(weka.core.Instances insts) throws Exception
Sets the instances comprising the current neighbourhood.- Overrides:
setInstances
in classNewNNSearch
- Parameters:
insts
- The set of instances on which the nearest neighbour search is carried out. Usually this set is the training set.- Throws:
Exception
- if setting of instances fails
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update
public void update(weka.core.Instance ins) throws Exception
Updates the LinearNNSearch to cater for the new added instance. This implementation only updates the ranges of the DistanceFunction class, since our set of instances is passed by reference and should already have the newly added instance.- Overrides:
update
in classNewNNSearch
- Parameters:
ins
- The instance to add. Usually this is the instance that is added to our neighbourhood i.e. the training instances.- Throws:
Exception
- if the given instances are null
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addInstanceInfo
public void addInstanceInfo(weka.core.Instance ins)
Adds the given instance info. This implementation updates the range datastructures of the DistanceFunction class.- Overrides:
addInstanceInfo
in classNewNNSearch
- Parameters:
ins
- The instance to add the information of. Usually this is the test instance supplied to update the range of attributes in the distance function.
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listOptions
public Enumeration listOptions()
Description copied from class:NewNNSearch
Returns an enumeration describing the available options.- Specified by:
listOptions
in interfaceweka.core.OptionHandler
- Overrides:
listOptions
in classNewNNSearch
- Returns:
- an enumeration of all the available options.
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setPreprocessing
public void setPreprocessing(weka.core.SelectedTag value)
Sets the type of preprocessing to use- Parameters:
value
- the preprocessing type
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setOptions
public void setOptions(String[] options) throws Exception
Description copied from class:NewNNSearch
Parses a given list of options.
Valid options are:
-S Skip identical instances (distances equal to zero).
- Specified by:
setOptions
in interfaceweka.core.OptionHandler
- Overrides:
setOptions
in classNewNNSearch
- Parameters:
options
- the list of options as an array of strings- Throws:
Exception
- if an option is not supported
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getOptions
public String[] getOptions()
Description copied from class:NewNNSearch
Gets the current settings.- Specified by:
getOptions
in interfaceweka.core.OptionHandler
- Overrides:
getOptions
in classNewNNSearch
- Returns:
- an array of strings suitable for passing to setOptions()
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