itk::AmoebaOptimizer Class Reference

#include <itkAmoebaOptimizer.h>

Inheritance diagram for itk::AmoebaOptimizer:

Collaboration diagram for itk::AmoebaOptimizer:

Detailed Description

Wrap of the vnl_amoeba algorithm.

AmoebaOptimizer is a wrapper around the vnl_amoeba algorithm which is an implementation of the Nelder-Meade downhill simplex problem. For most problems, it is a few times slower than a Levenberg-Marquardt algorithm but does not require derivatives of its cost function. It works by creating a simplex (n+1 points in ND space). The cost function is evaluated at each corner of the simplex. The simplex is then modified (by reflecting a corner about the opposite edge, by shrinking the entire simplex, by contracting one edge of the simplex, or by expanding the simplex) in searching for the minimum of the cost function.

The methods AutomaticInitialSimplex() and SetInitialSimplexDelta() control whether the optimizer defines the initial simplex automatically (by constructing a very small simplex around the initial position) or uses a user supplied simplex size.

The method SetOptimizeWithRestarts() indicates that the amoeabe algorithm should be rerun after if converges. This heuristic increases the chances of escaping from a local optimum. Each time the simplex is initialized with the best solution obtained by the previous runs. The edge length is half of that from the previous iteration. The heuristic is terminated if the total number of iterations is greater-equal than the maximal number of iterations (SetMaximumNumberOfIterations) or the difference between the current function value and the best function value is less than a threshold (SetFunctionConvergenceTolerance) and max(|best_parameters_i - current_parameters_i|) is less than a threshold (SetParametersConvergenceTolerance).

Examples:

RegistrationITKv3/ImageRegistration10.cxx, RegistrationITKv3/ImageRegistration16.cxx, RegistrationITKv3/ImageRegistration17.cxx, RegistrationITKv3/ImageRegistration19.cxx, RegistrationITKv4/ImageRegistration10.cxx, RegistrationITKv4/ImageRegistration16.cxx, RegistrationITKv4/ImageRegistration17.cxx, and RegistrationITKv4/ImageRegistration19.cxx.

Definition at line 61 of file itkAmoebaOptimizer.h.

Public Types
typedef SmartPointer< const Self >	ConstPointer
typedef vnl_vector< double >	InternalParametersType
typedef unsigned int	NumberOfIterationsType
typedef Superclass::ParametersType	ParametersType
typedef SmartPointer< Self >	Pointer
typedef AmoebaOptimizer	Self
typedef SingleValuedNonLinearVnlOptimizer	Superclass
Public Types inherited from itk::SingleValuedNonLinearVnlOptimizer
typedef ReceptorMemberCommand < Self >	CommandType
typedef SmartPointer< const Self >	ConstPointer
typedef SmartPointer< Self >	Pointer
typedef SingleValuedNonLinearVnlOptimizer	Self
typedef SingleValuedNonLinearOptimizer	Superclass
Public Types inherited from itk::SingleValuedNonLinearOptimizer
typedef SmartPointer< const Self >	ConstPointer
typedef CostFunctionType::Pointer	CostFunctionPointer
typedef SingleValuedCostFunction	CostFunctionType
typedef CostFunctionType::DerivativeType	DerivativeType
typedef CostFunctionType::MeasureType	MeasureType
typedef Superclass::ParametersType	ParametersType
typedef SmartPointer< Self >	Pointer
typedef SingleValuedNonLinearOptimizer	Self
typedef NonLinearOptimizer	Superclass
Public Types inherited from itk::NonLinearOptimizer
typedef SmartPointer< const Self >	ConstPointer
typedef Superclass::ParametersType	ParametersType
typedef SmartPointer< Self >	Pointer
typedef Superclass::ScalesType	ScalesType
typedef NonLinearOptimizer	Self
typedef Optimizer	Superclass
Public Types inherited from itk::Optimizer
typedef SmartPointer< const Self >	ConstPointer
typedef OptimizerParameters < double >	ParametersType
typedef SmartPointer< Self >	Pointer
typedef Array< double >	ScalesType
typedef Optimizer	Self
typedef Object	Superclass
Public Types inherited from itk::Object
typedef SmartPointer< const Self >	ConstPointer
typedef SmartPointer< Self >	Pointer
typedef Object	Self
typedef LightObject	Superclass
Public Types inherited from itk::LightObject
typedef SmartPointer< const Self >	ConstPointer
typedef SmartPointer< Self >	Pointer
typedef LightObject	Self

Public Member Functions
virtual ::itk::LightObject::Pointer	CreateAnother (void) const
virtual const char *	GetNameOfClass () const
vnl_amoeba *	GetOptimizer (void) const
virtual const std::string	GetStopConditionDescription () const ITK_OVERRIDE
MeasureType	GetValue () const
virtual void	SetCostFunction (SingleValuedCostFunction *costFunction) ITK_OVERRIDE
virtual void	StartOptimization (void) ITK_OVERRIDE
virtual void	SetMaximumNumberOfIterations (NumberOfIterationsType _arg)
virtual NumberOfIterationsType	GetMaximumNumberOfIterations () const
virtual void	SetAutomaticInitialSimplex (bool _arg)
virtual void	AutomaticInitialSimplexOn ()
virtual void	AutomaticInitialSimplexOff ()
virtual bool	GetAutomaticInitialSimplex () const
virtual void	SetOptimizeWithRestarts (bool _arg)
virtual void	OptimizeWithRestartsOn ()
virtual void	OptimizeWithRestartsOff ()
virtual bool	GetOptimizeWithRestarts () const
void	SetInitialSimplexDelta (ParametersType initialSimplexDelta, bool automaticInitialSimplex=false)
virtual ParametersType	GetInitialSimplexDelta () const
virtual void	SetParametersConvergenceTolerance (double _arg)
virtual double	GetParametersConvergenceTolerance () const
virtual void	SetFunctionConvergenceTolerance (double _arg)
virtual double	GetFunctionConvergenceTolerance () const
Public Member Functions inherited from itk::SingleValuedNonLinearVnlOptimizer
virtual const bool &	GetMaximize () const
virtual void	SetMaximize (bool _arg)
virtual void	MaximizeOn ()
virtual void	MaximizeOff ()
bool	GetMinimize () const
void	SetMinimize (bool v)
void	MinimizeOn ()
void	MinimizeOff ()
virtual const MeasureType &	GetCachedValue () const
virtual const DerivativeType &	GetCachedDerivative () const
virtual const ParametersType &	GetCachedCurrentPosition () const
Public Member Functions inherited from itk::SingleValuedNonLinearOptimizer
virtual ::itk::LightObject::Pointer	CreateAnother (void) const
virtual const CostFunctionType *	GetCostFunction () const
virtual CostFunctionType *	GetModifiableCostFunction ()
MeasureType	GetValue (const ParametersType &parameters) const
virtual void	SetCostFunction (CostFunctionType *costFunction)
Public Member Functions inherited from itk::Optimizer
virtual const ParametersType &	GetCurrentPosition () const
virtual const ParametersType &	GetInitialPosition () const
virtual void	SetInitialPosition (const ParametersType &param)
void	SetScales (const ScalesType &scales)
virtual const ScalesType &	GetScales () const
virtual const ScalesType &	GetInverseScales () 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
Command *	GetCommand (unsigned long tag)
bool	GetDebug () const
MetaDataDictionary &	GetMetaDataDictionary (void)
const MetaDataDictionary &	GetMetaDataDictionary (void) const
virtual ModifiedTimeType	GetMTime () const
virtual const TimeStamp &	GetTimeStamp () const
bool	HasObserver (const EventObject &event) const
void	InvokeEvent (const EventObject &)
void	InvokeEvent (const EventObject &) const
virtual void	Modified () const
virtual void	Register () const ITK_OVERRIDE
void	RemoveAllObservers ()
void	RemoveObserver (unsigned long tag)
void	SetDebug (bool debugFlag) const
void	SetMetaDataDictionary (const MetaDataDictionary &rhs)
virtual void	SetReferenceCount (int) ITK_OVERRIDE
virtual void	UnRegister () const ITK_OVERRIDE
virtual void	SetObjectName (std::string _arg)
virtual const std::string &	GetObjectName () 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::SingleValuedNonLinearOptimizer
static Pointer	New ()
Static Public Member Functions inherited from itk::NonLinearOptimizer
static Pointer	New ()
Static Public Member Functions inherited from itk::Optimizer
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 Types
typedef Superclass::CostFunctionAdaptorType	CostFunctionAdaptorType
Protected Types inherited from itk::SingleValuedNonLinearVnlOptimizer
typedef SingleValuedVnlCostFunctionAdaptor	CostFunctionAdaptorType
Protected Types inherited from itk::LightObject
typedef int	InternalReferenceCountType

Protected Member Functions
	AmoebaOptimizer ()
virtual void	PrintSelf (std::ostream &os, Indent indent) const ITK_OVERRIDE
virtual	~AmoebaOptimizer ()
Protected Member Functions inherited from itk::SingleValuedNonLinearVnlOptimizer
const CostFunctionAdaptorType *	GetCostFunctionAdaptor (void) const
CostFunctionAdaptorType *	GetCostFunctionAdaptor (void)
CostFunctionAdaptorType *	GetNonConstCostFunctionAdaptor (void) const
void	SetCostFunctionAdaptor (CostFunctionAdaptorType *adaptor)
	SingleValuedNonLinearVnlOptimizer ()
virtual	~SingleValuedNonLinearVnlOptimizer ()
Protected Member Functions inherited from itk::SingleValuedNonLinearOptimizer
	SingleValuedNonLinearOptimizer ()
virtual	~SingleValuedNonLinearOptimizer ()
Protected Member Functions inherited from itk::NonLinearOptimizer
	NonLinearOptimizer ()
virtual	~NonLinearOptimizer ()
Protected Member Functions inherited from itk::Optimizer
	Optimizer ()
virtual void	SetCurrentPosition (const ParametersType &param)
virtual	~Optimizer ()
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 Member Functions
void	ValidateSettings ()
	AmoebaOptimizer (const Self &)
void	operator= (const Self &)

Private Attributes
bool	m_AutomaticInitialSimplex
CostFunctionType::MeasureType	m_FunctionConvergenceTolerance
ParametersType	m_InitialSimplexDelta
NumberOfIterationsType	m_MaximumNumberOfIterations
bool	m_OptimizeWithRestarts
ParametersType::ValueType	m_ParametersConvergenceTolerance
std::ostringstream	m_StopConditionDescription
vnl_amoeba *	m_VnlOptimizer

Additional Inherited Members
Protected Attributes inherited from itk::SingleValuedNonLinearOptimizer
CostFunctionPointer	m_CostFunction
Protected Attributes inherited from itk::Optimizer
ParametersType	m_CurrentPosition
bool	m_ScalesInitialized
Protected Attributes inherited from itk::LightObject
InternalReferenceCountType	m_ReferenceCount
SimpleFastMutexLock	m_ReferenceCountLock

Member Typedef Documentation

typedef SmartPointer< const Self > itk::AmoebaOptimizer::ConstPointer

Definition at line 69 of file itkAmoebaOptimizer.h.

typedef Superclass::CostFunctionAdaptorType itk::AmoebaOptimizer::CostFunctionAdaptorType

protected

Definition at line 159 of file itkAmoebaOptimizer.h.

typedef vnl_vector< double > itk::AmoebaOptimizer::InternalParametersType

InternalParameters typedef.

Definition at line 83 of file itkAmoebaOptimizer.h.

typedef unsigned int itk::AmoebaOptimizer::NumberOfIterationsType

Definition at line 70 of file itkAmoebaOptimizer.h.

typedef Superclass::ParametersType itk::AmoebaOptimizer::ParametersType

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

Definition at line 76 of file itkAmoebaOptimizer.h.

typedef SmartPointer< Self > itk::AmoebaOptimizer::Pointer

Definition at line 68 of file itkAmoebaOptimizer.h.

typedef AmoebaOptimizer itk::AmoebaOptimizer::Self

Standard "Self" typedef.

Definition at line 66 of file itkAmoebaOptimizer.h.

typedef SingleValuedNonLinearVnlOptimizer itk::AmoebaOptimizer::Superclass

Definition at line 67 of file itkAmoebaOptimizer.h.

Constructor & Destructor Documentation

itk::AmoebaOptimizer::AmoebaOptimizer ( )

protected

virtual itk::AmoebaOptimizer::~AmoebaOptimizer ( )

protectedvirtual

itk::AmoebaOptimizer::AmoebaOptimizer ( const Self &  )

private

Check that the settings are valid. If not throw an exception.

Member Function Documentation

virtual void itk::AmoebaOptimizer::AutomaticInitialSimplexOff ( )

virtual

Set/Get the mode which determines how the amoeba algorithm defines the initial simplex. Default is AutomaticInitialSimplexOn. If AutomaticInitialSimplex is on, the initial simplex is created with a default size. If AutomaticInitialSimplex is off, then InitialSimplexDelta will be used to define the initial simplex, setting the ith corner of the simplex as [x0[0], x0[1], ..., x0[i]+InitialSimplexDelta[i], ..., x0[d-1]].

virtual void itk::AmoebaOptimizer::AutomaticInitialSimplexOn ( )

virtual

Set/Get the mode which determines how the amoeba algorithm defines the initial simplex. Default is AutomaticInitialSimplexOn. If AutomaticInitialSimplex is on, the initial simplex is created with a default size. If AutomaticInitialSimplex is off, then InitialSimplexDelta will be used to define the initial simplex, setting the ith corner of the simplex as [x0[0], x0[1], ..., x0[i]+InitialSimplexDelta[i], ..., x0[d-1]].

virtual::itk::LightObject::Pointer itk::AmoebaOptimizer::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.

virtual bool itk::AmoebaOptimizer::GetAutomaticInitialSimplex ( ) const

virtual

Set/Get the mode which determines how the amoeba algorithm defines the initial simplex. Default is AutomaticInitialSimplexOn. If AutomaticInitialSimplex is on, the initial simplex is created with a default size. If AutomaticInitialSimplex is off, then InitialSimplexDelta will be used to define the initial simplex, setting the ith corner of the simplex as [x0[0], x0[1], ..., x0[i]+InitialSimplexDelta[i], ..., x0[d-1]].

virtual double itk::AmoebaOptimizer::GetFunctionConvergenceTolerance ( ) const

virtual

The optimization algorithm will terminate when the simplex diameter and the difference in cost function values at the corners of the simplex falls below user specified thresholds. The cost function convergence threshold is set via SetFunctionConvergenceTolerance().

virtual ParametersType itk::AmoebaOptimizer::GetInitialSimplexDelta ( ) const

virtual

Set/Get the deltas that are used to define the initial simplex when AutomaticInitialSimplex is off.

virtual NumberOfIterationsType itk::AmoebaOptimizer::GetMaximumNumberOfIterations ( ) const

virtual

Set/Get the maximum number of iterations. The optimization algorithm will terminate after the maximum number of iterations has been reached. The default value is defined as DEFAULT_MAXIMAL_NUMBER_OF_ITERATIONS.

virtual const char* itk::AmoebaOptimizer::GetNameOfClass ( ) const

virtual

Run-time type information (and related methods).

Reimplemented from itk::SingleValuedNonLinearVnlOptimizer.

vnl_amoeba* itk::AmoebaOptimizer::GetOptimizer

(

void

)

const

Method for getting access to the internal optimizer.

virtual bool itk::AmoebaOptimizer::GetOptimizeWithRestarts ( ) const

virtual

Set/Get the mode that determines if we want to use multiple runs of the Amoeba optimizer. If true, then the optimizer is rerun after it converges. The additional runs are performed using a simplex initialized with the best solution obtained by the previous runs. The edge length is half of that from the previous iteration.

virtual double itk::AmoebaOptimizer::GetParametersConvergenceTolerance ( ) const

virtual

The optimization algorithm will terminate when the simplex diameter and the difference in cost function values at the corners of the simplex falls below user specified thresholds. The simplex diameter threshold is set via SetParametersConvergenceTolerance().

virtual const std::string itk::AmoebaOptimizer::GetStopConditionDescription ( ) const

virtual

Report the reason for stopping.

Reimplemented from itk::Optimizer.

MeasureType itk::AmoebaOptimizer::GetValue

(

)

const

Return Current Value

static Pointer itk::AmoebaOptimizer::New ( )

static

Method for creation through the object factory.

void itk::AmoebaOptimizer::operator= ( const Self &  )

private

Check that the settings are valid. If not throw an exception.

virtual void itk::AmoebaOptimizer::OptimizeWithRestartsOff ( )

virtual

Set/Get the mode that determines if we want to use multiple runs of the Amoeba optimizer. If true, then the optimizer is rerun after it converges. The additional runs are performed using a simplex initialized with the best solution obtained by the previous runs. The edge length is half of that from the previous iteration.

virtual void itk::AmoebaOptimizer::OptimizeWithRestartsOn ( )

virtual

Set/Get the mode that determines if we want to use multiple runs of the Amoeba optimizer. If true, then the optimizer is rerun after it converges. The additional runs are performed using a simplex initialized with the best solution obtained by the previous runs. The edge length is half of that from the previous iteration.

virtual void itk::AmoebaOptimizer::PrintSelf ( std::ostream &  os, Indent  indent  ) const

protectedvirtual

Print out internal state

Reimplemented from itk::SingleValuedNonLinearVnlOptimizer.

virtual void itk::AmoebaOptimizer::SetAutomaticInitialSimplex ( bool  _arg )

virtual

Set/Get the mode which determines how the amoeba algorithm defines the initial simplex. Default is AutomaticInitialSimplexOn. If AutomaticInitialSimplex is on, the initial simplex is created with a default size. If AutomaticInitialSimplex is off, then InitialSimplexDelta will be used to define the initial simplex, setting the ith corner of the simplex as [x0[0], x0[1], ..., x0[i]+InitialSimplexDelta[i], ..., x0[d-1]].

virtual void itk::AmoebaOptimizer::SetCostFunction ( SingleValuedCostFunction *  costFunction )

virtual

Plug in a Cost Function into the optimizer

Implements itk::SingleValuedNonLinearVnlOptimizer.

virtual void itk::AmoebaOptimizer::SetFunctionConvergenceTolerance ( double  _arg )

virtual

The optimization algorithm will terminate when the simplex diameter and the difference in cost function values at the corners of the simplex falls below user specified thresholds. The cost function convergence threshold is set via SetFunctionConvergenceTolerance().

void itk::AmoebaOptimizer::SetInitialSimplexDelta	(	ParametersType	initialSimplexDelta,
		bool	automaticInitialSimplex = false
	)

Set/Get the deltas that are used to define the initial simplex when AutomaticInitialSimplex is off.

virtual void itk::AmoebaOptimizer::SetMaximumNumberOfIterations ( NumberOfIterationsType  _arg )

virtual

Set/Get the maximum number of iterations. The optimization algorithm will terminate after the maximum number of iterations has been reached. The default value is defined as DEFAULT_MAXIMAL_NUMBER_OF_ITERATIONS.

virtual void itk::AmoebaOptimizer::SetOptimizeWithRestarts ( bool  _arg )

virtual

Set/Get the mode that determines if we want to use multiple runs of the Amoeba optimizer. If true, then the optimizer is rerun after it converges. The additional runs are performed using a simplex initialized with the best solution obtained by the previous runs. The edge length is half of that from the previous iteration.

virtual void itk::AmoebaOptimizer::SetParametersConvergenceTolerance ( double  _arg )

virtual

The optimization algorithm will terminate when the simplex diameter and the difference in cost function values at the corners of the simplex falls below user specified thresholds. The simplex diameter threshold is set via SetParametersConvergenceTolerance().

virtual void itk::AmoebaOptimizer::StartOptimization ( void  )

virtual

Start optimization with an initial value.

Reimplemented from itk::Optimizer.

void itk::AmoebaOptimizer::ValidateSettings ( )

private

Check that the settings are valid. If not throw an exception.

Member Data Documentation

bool itk::AmoebaOptimizer::m_AutomaticInitialSimplex

private

Definition at line 173 of file itkAmoebaOptimizer.h.

CostFunctionType::MeasureType itk::AmoebaOptimizer::m_FunctionConvergenceTolerance

private

Definition at line 172 of file itkAmoebaOptimizer.h.

ParametersType itk::AmoebaOptimizer::m_InitialSimplexDelta

private

Definition at line 174 of file itkAmoebaOptimizer.h.

NumberOfIterationsType itk::AmoebaOptimizer::m_MaximumNumberOfIterations

private

Definition at line 170 of file itkAmoebaOptimizer.h.

bool itk::AmoebaOptimizer::m_OptimizeWithRestarts

private

Definition at line 175 of file itkAmoebaOptimizer.h.

ParametersType::ValueType itk::AmoebaOptimizer::m_ParametersConvergenceTolerance

private

Definition at line 171 of file itkAmoebaOptimizer.h.

std::ostringstream itk::AmoebaOptimizer::m_StopConditionDescription

private

Definition at line 178 of file itkAmoebaOptimizer.h.

vnl_amoeba* itk::AmoebaOptimizer::m_VnlOptimizer

private

Definition at line 176 of file itkAmoebaOptimizer.h.

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

• itkAmoebaOptimizer.h