ITK  4.4.0
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itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree > Class Template Reference

#include <itkKdTreeBasedKmeansEstimator.h>

+ Inheritance diagram for itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >:
+ Collaboration diagram for itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >:

Detailed Description

template<class TKdTree>
class itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >

fast k-means algorithm implementation using k-d tree structure

It returns k mean vectors that are centroids of k-clusters using pre-generated k-d tree. k-d tree generation is done by the WeightedCentroidKdTreeGenerator. The tree construction needs to be done only once. The resulting k-d tree's non-terminal nodes that have their children nodes have vector sums of measurement vectors that belong to the nodes and the number of measurement vectors in addition to the typical node boundary information and pointers to children nodes. Instead of reassigning every measurement vector to the nearest cluster centroid and recalculating centroid, it maintain a set of cluster centroid candidates and using pruning algorithm that utilizes k-d tree, it updates the means of only relevant candidates at each iterations. It would be faster than traditional implementation of k-means algorithm. However, the k-d tree consumes a large amount of memory. The tree construction time and pruning algorithm's performance are important factors to the whole process's performance. If users want to use k-d tree for some purpose other than k-means estimation, they can use the KdTreeGenerator instead of the WeightedCentroidKdTreeGenerator. It will save the tree construction time and memory usage.

Note: There is a second implementation of k-means algorithm in ITK under the While the Kd tree based implementation is more time efficient, the GLA/LBG based algorithm is more memory efficient.

Recent API changes: The static const macro to get the length of a measurement vector, MeasurementVectorSize has been removed to allow the length of a measurement vector to be specified at run time. It is now obtained from the KdTree set as input. You may query this length using the function GetMeasurementVectorSize().

See Also
ImageKmeansModelEstimator
WeightedCentroidKdTreeGenerator, KdTree
Wiki Examples:

Definition at line 77 of file itkKdTreeBasedKmeansEstimator.h.

Classes

class  CandidateVector
 

Public Types

typedef
KdTreeNodeType::CentroidType 
CentroidType
 
typedef itksys::hash_map
< InstanceIdentifier, unsigned
int > 
ClusterLabelsType
 
typedef SmartPointer< const SelfConstPointer
 
typedef
DistanceToCentroidMembershipFunctionType::Pointer 
DistanceToCentroidMembershipFunctionPointer
 
typedef
DistanceToCentroidMembershipFunction
< MeasurementVectorType
DistanceToCentroidMembershipFunctionType
 
typedef TKdTree::InstanceIdentifier InstanceIdentifier
 
typedef std::vector
< ParameterType
InternalParametersType
 
typedef TKdTree::KdTreeNodeType KdTreeNodeType
 
typedef TKdTree::MeasurementType MeasurementType
 
typedef unsigned int MeasurementVectorSizeType
 
typedef
TKdTree::MeasurementVectorType 
MeasurementVectorType
 
typedef
MembershipFunctionType::ConstPointer 
MembershipFunctionPointer
 
typedef MembershipFunctionBase
< MeasurementVectorType
MembershipFunctionType
 
typedef
MembershipFunctionVectorObjectType::Pointer 
MembershipFunctionVectorObjectPointer
 
typedef
SimpleDataObjectDecorator
< MembershipFunctionVectorType
MembershipFunctionVectorObjectType
 
typedef std::vector
< MembershipFunctionPointer
MembershipFunctionVectorType
 
typedef Array< double > ParametersType
 
typedef Array< double > ParameterType
 
typedef SmartPointer< SelfPointer
 
typedef TKdTree::SampleType SampleType
 
typedef KdTreeBasedKmeansEstimator Self
 
typedef Object Superclass
 
- Public Types inherited from itk::Object
typedef SmartPointer< const SelfConstPointer
 
typedef SmartPointer< SelfPointer
 
typedef Object Self
 
typedef LightObject Superclass
 
- Public Types inherited from itk::LightObject
typedef SmartPointer< const SelfConstPointer
 
typedef SmartPointer< SelfPointer
 
typedef LightObject Self
 

Public Member Functions

virtual ::itk::LightObject::Pointer CreateAnother (void) const
 
virtual double GetCentroidPositionChanges () const
 
virtual double GetCentroidPositionChangesThreshold () const
 
virtual int GetCurrentIteration () const
 
const TKdTree * GetKdTree () const
 
virtual MeasurementVectorSizeType GetMeasurementVectorSize () const
 
virtual const char * GetNameOfClass () const
 
const
MembershipFunctionVectorObjectType
GetOutput () const
 
virtual bool GetUseClusterLabels () const
 
virtual void SetCentroidPositionChangesThreshold (double _arg)
 
void SetKdTree (TKdTree *tree)
 
virtual void SetUseClusterLabels (bool _arg)
 
void StartOptimization ()
 
virtual void SetParameters (ParametersType _arg)
 
virtual ParametersType GetParameters () const
 
virtual void SetMaximumIteration (int _arg)
 
virtual int GetMaximumIteration () const
 
- Public Member Functions inherited from itk::Object
unsigned long AddObserver (const EventObject &event, Command *)
 
unsigned long AddObserver (const EventObject &event, Command *) const
 
virtual void DebugOff () const
 
virtual void DebugOn () const
 
CommandGetCommand (unsigned long tag)
 
bool GetDebug () const
 
MetaDataDictionaryGetMetaDataDictionary (void)
 
const MetaDataDictionaryGetMetaDataDictionary (void) const
 
virtual ModifiedTimeType GetMTime () const
 
virtual const TimeStampGetTimeStamp () const
 
bool HasObserver (const EventObject &event) const
 
void InvokeEvent (const EventObject &)
 
void InvokeEvent (const EventObject &) const
 
virtual void Modified () const
 
virtual void Register () const
 
void RemoveAllObservers ()
 
void RemoveObserver (unsigned long tag)
 
void SetDebug (bool debugFlag) const
 
void SetMetaDataDictionary (const MetaDataDictionary &rhs)
 
virtual void SetReferenceCount (int)
 
virtual void UnRegister () const
 
- Public Member Functions inherited from itk::LightObject
virtual void Delete ()
 
virtual int GetReferenceCount () const
 
 itkCloneMacro (Self)
 
void Print (std::ostream &os, Indent indent=0) const
 

Static Public Member Functions

static Pointer New ()
 
- Static Public Member Functions inherited from itk::Object
static bool GetGlobalWarningDisplay ()
 
static void GlobalWarningDisplayOff ()
 
static void GlobalWarningDisplayOn ()
 
static Pointer New ()
 
static void SetGlobalWarningDisplay (bool flag)
 
- Static Public Member Functions inherited from itk::LightObject
static void BreakOnError ()
 
static Pointer New ()
 

Protected Member Functions

void CopyParameters (InternalParametersType &source, InternalParametersType &target)
 
void CopyParameters (ParametersType &source, InternalParametersType &target)
 
void CopyParameters (InternalParametersType &source, ParametersType &target)
 
void FillClusterLabels (KdTreeNodeType *node, int closestIndex)
 
void Filter (KdTreeNodeType *node, std::vector< int > validIndexes, MeasurementVectorType &lowerBound, MeasurementVectorType &upperBound)
 
int GetClosestCandidate (ParameterType &measurements, std::vector< int > &validIndexes)
 
void GetPoint (ParameterType &point, MeasurementVectorType measurements)
 
double GetSumOfSquaredPositionChanges (InternalParametersType &previous, InternalParametersType &current)
 
bool IsFarther (ParameterType &pointA, ParameterType &pointB, MeasurementVectorType &lowerBound, MeasurementVectorType &upperBound)
 
 KdTreeBasedKmeansEstimator ()
 
void PrintPoint (ParameterType &point)
 
void PrintSelf (std::ostream &os, Indent indent) const
 
virtual ~KdTreeBasedKmeansEstimator ()
 
- Protected Member Functions inherited from itk::Object
 Object ()
 
bool PrintObservers (std::ostream &os, Indent indent) const
 
virtual void SetTimeStamp (const TimeStamp &time)
 
virtual ~Object ()
 
- Protected Member Functions inherited from itk::LightObject
virtual LightObject::Pointer InternalClone () const
 
 LightObject ()
 
virtual void PrintHeader (std::ostream &os, Indent indent) const
 
virtual void PrintTrailer (std::ostream &os, Indent indent) const
 
virtual ~LightObject ()
 

Private Attributes

CandidateVector m_CandidateVector
 
double m_CentroidPositionChanges
 
double m_CentroidPositionChangesThreshold
 
ClusterLabelsType m_ClusterLabels
 
int m_CurrentIteration
 
EuclideanDistanceMetric
< ParameterType >::Pointer 
m_DistanceMetric
 
bool m_GenerateClusterLabels
 
TKdTree::Pointer m_KdTree
 
int m_MaximumIteration
 
MeasurementVectorSizeType m_MeasurementVectorSize
 
MembershipFunctionVectorObjectPointer m_MembershipFunctionsObject
 
ParametersType m_Parameters
 
ParameterType m_TempVertex
 
bool m_UseClusterLabels
 

Additional Inherited Members

- Protected Types inherited from itk::LightObject
typedef int InternalReferenceCountType
 
- Protected Attributes inherited from itk::LightObject
InternalReferenceCountType m_ReferenceCount
 
SimpleFastMutexLock m_ReferenceCountLock
 

Member Typedef Documentation

template<class TKdTree >
typedef KdTreeNodeType::CentroidType itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::CentroidType

Definition at line 99 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
typedef itksys::hash_map< InstanceIdentifier, unsigned int > itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::ClusterLabelsType

Definition at line 162 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
typedef SmartPointer< const Self > itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::ConstPointer

Definition at line 85 of file itkKdTreeBasedKmeansEstimator.h.

Definition at line 116 of file itkKdTreeBasedKmeansEstimator.h.

Typedef requried to generate dataobject decorated output that can be plugged into SampleClassifierFilter

Definition at line 113 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
typedef TKdTree::InstanceIdentifier itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::InstanceIdentifier

Definition at line 97 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
typedef std::vector< ParameterType > itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::InternalParametersType

Definition at line 107 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
typedef TKdTree::KdTreeNodeType itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::KdTreeNodeType

Types for the KdTree data structure

Definition at line 91 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
typedef TKdTree::MeasurementType itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::MeasurementType

Definition at line 95 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
typedef unsigned int itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::MeasurementVectorSizeType

Typedef for the length of a measurement vector

Definition at line 102 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
typedef TKdTree::MeasurementVectorType itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::MeasurementVectorType

Definition at line 96 of file itkKdTreeBasedKmeansEstimator.h.

Definition at line 119 of file itkKdTreeBasedKmeansEstimator.h.

Definition at line 118 of file itkKdTreeBasedKmeansEstimator.h.

Definition at line 124 of file itkKdTreeBasedKmeansEstimator.h.

Definition at line 122 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
typedef std::vector< MembershipFunctionPointer > itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::MembershipFunctionVectorType

Definition at line 120 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
typedef Array< double > itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::ParametersType

Definition at line 108 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
typedef Array< double > itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::ParameterType

Parameters type. It defines a position in the optimization search space.

Definition at line 106 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
typedef SmartPointer< Self > itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::Pointer

Definition at line 84 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
typedef TKdTree::SampleType itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::SampleType

Definition at line 98 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
typedef KdTreeBasedKmeansEstimator itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::Self

Standard Self typedef.

Definition at line 82 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
typedef Object itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::Superclass

Definition at line 83 of file itkKdTreeBasedKmeansEstimator.h.

Constructor & Destructor Documentation

template<class TKdTree >
itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::KdTreeBasedKmeansEstimator ( )
protected
template<class TKdTree >
virtual itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::~KdTreeBasedKmeansEstimator ( )
inlineprotectedvirtual

Definition at line 169 of file itkKdTreeBasedKmeansEstimator.h.

Member Function Documentation

template<class TKdTree >
void itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::CopyParameters ( InternalParametersType source,
InternalParametersType target 
)
protected

copies the source parameters (k-means) to the target

template<class TKdTree >
void itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::CopyParameters ( ParametersType source,
InternalParametersType target 
)
protected

copies the source parameters (k-means) to the target

template<class TKdTree >
void itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::CopyParameters ( InternalParametersType source,
ParametersType target 
)
protected

copies the source parameters (k-means) to the target

template<class TKdTree >
virtual::itk::LightObject::Pointer itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::CreateAnother ( void  ) const
virtual

Create an object from an instance, potentially deferring to a factory. This method allows you to create an instance of an object that is exactly the same type as the referring object. This is useful in cases where an object has been cast back to a base class.

Reimplemented from itk::Object.

template<class TKdTree >
void itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::FillClusterLabels ( KdTreeNodeType node,
int  closestIndex 
)
protected
template<class TKdTree >
void itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::Filter ( KdTreeNodeType node,
std::vector< int >  validIndexes,
MeasurementVectorType lowerBound,
MeasurementVectorType upperBound 
)
protected

recursive pruning algorithm. the validIndexes vector contains only the indexes of the surviving candidates for the node

template<class TKdTree >
virtual double itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::GetCentroidPositionChanges ( ) const
virtual
template<class TKdTree >
virtual double itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::GetCentroidPositionChangesThreshold ( ) const
virtual
template<class TKdTree >
int itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::GetClosestCandidate ( ParameterType measurements,
std::vector< int > &  validIndexes 
)
protected

get the index of the closest candidate to the measurements measurement vector

template<class TKdTree >
virtual int itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::GetCurrentIteration ( ) const
virtual
template<class TKdTree >
const TKdTree* itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::GetKdTree ( ) const
template<class TKdTree >
virtual int itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::GetMaximumIteration ( ) const
virtual

Set/Get maximum iteration limit.

template<class TKdTree >
virtual MeasurementVectorSizeType itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::GetMeasurementVectorSize ( ) const
virtual

Get the length of measurement vectors in the KdTree

template<class TKdTree >
virtual const char* itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::GetNameOfClass ( ) const
virtual

Run-time type information (and related methods).

Reimplemented from itk::Object.

template<class TKdTree >
const MembershipFunctionVectorObjectType* itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::GetOutput ( ) const

Output Membership function vector containing the membership functions with the final optimized parameters

template<class TKdTree >
virtual ParametersType itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::GetParameters ( ) const
virtual

Set the position to initialize the optimization.

template<class TKdTree >
void itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::GetPoint ( ParameterType point,
MeasurementVectorType  measurements 
)
protected

imports the measurements measurement vector data to the point

template<class TKdTree >
double itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::GetSumOfSquaredPositionChanges ( InternalParametersType previous,
InternalParametersType current 
)
protected

gets the sum of squared difference between the previous position and current position of all centroid. This is the primary termination condition for this algorithm. If the return value is less than the value that was set by the SetCentroidPositionChangesThreshold method.

template<class TKdTree >
virtual bool itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::GetUseClusterLabels ( ) const
virtual
template<class TKdTree >
bool itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::IsFarther ( ParameterType pointA,
ParameterType pointB,
MeasurementVectorType lowerBound,
MeasurementVectorType upperBound 
)
protected

returns true if the pointA is farther than pointB to the boundary

template<class TKdTree >
static Pointer itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::New ( )
static

Method for creation through the object factory.

template<class TKdTree >
void itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::PrintPoint ( ParameterType point)
protected
template<class TKdTree >
void itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::PrintSelf ( std::ostream &  os,
Indent  indent 
) const
protectedvirtual

Methods invoked by Print() to print information about the object including superclasses. Typically not called by the user (use Print() instead) but used in the hierarchical print process to combine the output of several classes.

Reimplemented from itk::Object.

template<class TKdTree >
virtual void itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::SetCentroidPositionChangesThreshold ( double  _arg)
virtual

Set/Get the termination threshold for the squared sum of changes in centroid postions after one iteration

template<class TKdTree >
void itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::SetKdTree ( TKdTree *  tree)

Set/Get the pointer to the KdTree

template<class TKdTree >
virtual void itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::SetMaximumIteration ( int  _arg)
virtual

Set/Get maximum iteration limit.

template<class TKdTree >
virtual void itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::SetParameters ( ParametersType  _arg)
virtual

Set the position to initialize the optimization.

template<class TKdTree >
virtual void itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::SetUseClusterLabels ( bool  _arg)
virtual
template<class TKdTree >
void itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::StartOptimization ( )

Start optimization Optimization will stop when it meets either of two termination conditions, the maximum iteration limit or epsilon (minimal changes in squared sum of changes in centroid positions)

Member Data Documentation

template<class TKdTree >
CandidateVector itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::m_CandidateVector
private

Definition at line 326 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
double itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::m_CentroidPositionChanges
private

sum of squared centroid position changes at the current iteration

Definition at line 311 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
double itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::m_CentroidPositionChangesThreshold
private

threshold for the sum of squared centroid position changes. termination criterion

Definition at line 315 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
ClusterLabelsType itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::m_ClusterLabels
private

Definition at line 332 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
int itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::m_CurrentIteration
private

current number of iteration

Definition at line 305 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
EuclideanDistanceMetric< ParameterType >::Pointer itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::m_DistanceMetric
private

pointer to the euclidean distance function

Definition at line 321 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
bool itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::m_GenerateClusterLabels
private

Definition at line 331 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
TKdTree::Pointer itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::m_KdTree
private

pointer to the k-d tree

Definition at line 318 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
int itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::m_MaximumIteration
private

maximum number of iteration. termination criterion

Definition at line 308 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
MeasurementVectorSizeType itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::m_MeasurementVectorSize
private

Definition at line 333 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
MembershipFunctionVectorObjectPointer itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::m_MembershipFunctionsObject
private

Definition at line 334 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
ParametersType itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::m_Parameters
private

k-means

Definition at line 324 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
ParameterType itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::m_TempVertex
private

Definition at line 328 of file itkKdTreeBasedKmeansEstimator.h.

template<class TKdTree >
bool itk::Statistics::KdTreeBasedKmeansEstimator< TKdTree >::m_UseClusterLabels
private

Definition at line 330 of file itkKdTreeBasedKmeansEstimator.h.


The documentation for this class was generated from the following file: