#include <itkAmoebaOptimizerv4.h>

Detailed Description

Wrap of the vnl_amoeba algorithm.

AmoebaOptimizerv4 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 amoeba 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 (SetNumberOfIterations) 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).

Definition at line 62 of file itkAmoebaOptimizerv4.h.

Inheritance diagram for itk::AmoebaOptimizerv4:

Collaboration diagram for itk::AmoebaOptimizerv4:

Public Types
using	ConstPointer = SmartPointer< const Self >

using	InternalParametersType = vnl_vector< double >

using	ParametersType = Superclass::ParametersType

using	Pointer = SmartPointer< Self >

using	Self = AmoebaOptimizerv4

using	Superclass = SingleValuedNonLinearVnlOptimizerv4

Public Types inherited from itk::SingleValuedNonLinearVnlOptimizerv4
using	CommandType = ReceptorMemberCommand< Self >

using	ConstPointer = SmartPointer< const Self >

using	DerivativeType = Superclass::DerivativeType

using	MetricType = Superclass::MetricType

using	ParametersType = Superclass::ParametersType

using	Pointer = SmartPointer< Self >

using	ScalesType = Superclass::ScalesType

using	Self = SingleValuedNonLinearVnlOptimizerv4

using	StopConditionDescriptionType = Superclass::StopConditionDescriptionType

using	StopConditionReturnStringType = Superclass::StopConditionReturnStringType

using	Superclass = ObjectToObjectOptimizerBase

Public Types inherited from itk::ObjectToObjectOptimizerBaseTemplate< double >
using	ConstPointer = SmartPointer< const Self >

using	DerivativeType = typename MetricType::DerivativeType

using	MeasureType = typename MetricType::MeasureType

using	MetricType = ObjectToObjectMetricBaseTemplate< double >

using	MetricTypePointer = typename MetricType::Pointer

using	NumberOfParametersType = typename MetricType::NumberOfParametersType

using	ParametersType = OptimizerParameters< double >

using	Pointer = SmartPointer< Self >

using	ScalesEstimatorType = OptimizerParameterScalesEstimatorTemplate< double >

using	ScalesType = OptimizerParameters< double >

using	Self = ObjectToObjectOptimizerBaseTemplate

using	StopConditionDescriptionType = std::ostringstream

using	StopConditionReturnStringType = std::string

using	Superclass = Object

Public Types inherited from itk::Object
using	ConstPointer = SmartPointer< const Self >

using	Pointer = SmartPointer< Self >

using	Self = Object

using	Superclass = LightObject

Public Types inherited from itk::LightObject
using	ConstPointer = SmartPointer< const Self >

using	Pointer = SmartPointer< Self >

using	Self = LightObject

Public Member Functions
const char *	GetNameOfClass () const override

vnl_amoeba *	GetOptimizer () const

std::string	GetStopConditionDescription () const override

void	SetMetric (MetricType *metric) override

void	StartOptimization (bool doOnlyInitialization=false) override


virtual void	SetAutomaticInitialSimplex (bool _arg)

virtual void	AutomaticInitialSimplexOn ()

virtual bool	GetAutomaticInitialSimplex () const


virtual void	SetOptimizeWithRestarts (bool _arg)

virtual void	OptimizeWithRestartsOn ()

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::SingleValuedNonLinearVnlOptimizerv4
const char *	GetNameOfClass () const override

StopConditionReturnStringType	GetStopConditionDescription () const override=0

void	SetMetric (MetricType *metric) override=0

void	StartOptimization (bool doOnlyInitialization=false) override

virtual const DerivativeType &	GetCachedDerivative () const

virtual const ParametersType &	GetCachedCurrentPosition () const

Public Member Functions inherited from itk::ObjectToObjectOptimizerBaseTemplate< double >
virtual bool	CanUseScales () const

virtual SizeValueType	GetCurrentIteration () const

virtual const MeasureType &	GetCurrentMetricValue () const

virtual const ParametersType &	GetCurrentPosition () const

const char *	GetNameOfClass () const override

virtual SizeValueType	GetNumberOfIterations () const

virtual const ThreadIdType &	GetNumberOfWorkUnits () const

virtual const ScalesType &	GetScales () const

virtual const bool &	GetScalesAreIdentity () const

bool	GetScalesInitialized () const

virtual StopConditionReturnStringType	GetStopConditionDescription () const=0

virtual const MeasureType &	GetValue () const

virtual const ScalesType &	GetWeights () const

virtual const bool &	GetWeightsAreIdentity () const

virtual void	SetNumberOfIterations (SizeValueType _arg)

virtual void	SetNumberOfWorkUnits (ThreadIdType number)

virtual void	SetScalesEstimator (ScalesEstimatorType *_arg)

virtual void	SetWeights (ScalesType _arg)

virtual void	StartOptimization (bool doOnlyInitialization=false)

virtual void	SetMetric (MetricType *_arg)

virtual MetricType *	GetModifiableMetric ()

virtual void	SetScales (const ScalesType &scales)

virtual void	SetDoEstimateScales (bool _arg)

virtual const bool &	GetDoEstimateScales () const

virtual void	DoEstimateScalesOn ()

Public Member Functions inherited from itk::Object
unsigned long	AddObserver (const EventObject &event, Command *cmd) const

unsigned long	AddObserver (const EventObject &event, std::function< void(const EventObject &)> function) const

LightObject::Pointer	CreateAnother () const override

virtual void	DebugOff () const

virtual void	DebugOn () const

Command *	GetCommand (unsigned long tag)

bool	GetDebug () const

MetaDataDictionary &	GetMetaDataDictionary ()

const MetaDataDictionary &	GetMetaDataDictionary () const

virtual ModifiedTimeType	GetMTime () const

const char *	GetNameOfClass () const override

virtual const TimeStamp &	GetTimeStamp () const

bool	HasObserver (const EventObject &event) const

void	InvokeEvent (const EventObject &)

void	InvokeEvent (const EventObject &) const

virtual void	Modified () const

void	Register () const override

void	RemoveAllObservers ()

void	RemoveObserver (unsigned long tag) const

void	SetDebug (bool debugFlag) const

void	SetReferenceCount (int) override

void	UnRegister () const noexcept override

void	SetMetaDataDictionary (const MetaDataDictionary &rhs)

void	SetMetaDataDictionary (MetaDataDictionary &&rrhs)

virtual void	SetObjectName (std::string _arg)

virtual const std::string &	GetObjectName () const

Public Member Functions inherited from itk::LightObject
Pointer	Clone () const

virtual Pointer	CreateAnother () const

virtual void	Delete ()

virtual const char *	GetNameOfClass () const

virtual int	GetReferenceCount () const

void	Print (std::ostream &os, Indent indent=0) const

virtual void	Register () const

virtual void	SetReferenceCount (int)

virtual void	UnRegister () const noexcept

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 val)

Static Public Member Functions inherited from itk::LightObject
static void	BreakOnError ()

static Pointer	New ()

Protected Types
using	CostFunctionAdaptorType = Superclass::CostFunctionAdaptorType

Protected Types inherited from itk::SingleValuedNonLinearVnlOptimizerv4
using	CostFunctionAdaptorType = SingleValuedVnlCostFunctionAdaptorv4

Protected Member Functions
	AmoebaOptimizerv4 ()

void	PrintSelf (std::ostream &os, Indent indent) const override

	~AmoebaOptimizerv4 () override

Protected Member Functions inherited from itk::SingleValuedNonLinearVnlOptimizerv4
CostFunctionAdaptorType *	GetCostFunctionAdaptor ()

const CostFunctionAdaptorType *	GetCostFunctionAdaptor () const

CostFunctionAdaptorType *	GetNonConstCostFunctionAdaptor () const

void	PrintSelf (std::ostream &os, Indent indent) const override

void	SetCostFunctionAdaptor (CostFunctionAdaptorType *adaptor)

	SingleValuedNonLinearVnlOptimizerv4 ()

	~SingleValuedNonLinearVnlOptimizerv4 () override

Protected Member Functions inherited from itk::ObjectToObjectOptimizerBaseTemplate< double >
void	PrintSelf (std::ostream &os, Indent indent) const override

	ObjectToObjectOptimizerBaseTemplate ()

	~ObjectToObjectOptimizerBaseTemplate () override

Protected Member Functions inherited from itk::Object
	Object ()

bool	PrintObservers (std::ostream &os, Indent indent) const

void	PrintSelf (std::ostream &os, Indent indent) const override

virtual void	SetTimeStamp (const TimeStamp &timeStamp)

	~Object () override

Protected Member Functions inherited from itk::LightObject
virtual LightObject::Pointer	InternalClone () const

	LightObject ()

virtual void	PrintHeader (std::ostream &os, Indent indent) const

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

virtual void	PrintTrailer (std::ostream &os, Indent indent) const

virtual	~LightObject ()

Private Member Functions
void	ValidateSettings ()

Private Attributes
bool	m_AutomaticInitialSimplex {}

MeasureType	m_FunctionConvergenceTolerance {}

ParametersType	m_InitialSimplexDelta {}

bool	m_OptimizeWithRestarts {}

ParametersType::ValueType	m_ParametersConvergenceTolerance {}

std::ostringstream	m_StopConditionDescription {}

std::unique_ptr< vnl_amoeba >	m_VnlOptimizer

Additional Inherited Members
Protected Attributes inherited from itk::ObjectToObjectOptimizerBaseTemplate< double >
SizeValueType	m_CurrentIteration

MeasureType	m_CurrentMetricValue

bool	m_DoEstimateScales

MetricTypePointer	m_Metric

SizeValueType	m_NumberOfIterations

ThreadIdType	m_NumberOfWorkUnits

ScalesType	m_Scales

bool	m_ScalesAreIdentity

ScalesEstimatorType::Pointer	m_ScalesEstimator

ScalesType	m_Weights

bool	m_WeightsAreIdentity

Protected Attributes inherited from itk::LightObject
std::atomic< int >	m_ReferenceCount {}

Member Typedef Documentation

◆ ConstPointer

using itk::AmoebaOptimizerv4::ConstPointer = SmartPointer<const Self>

Definition at line 71 of file itkAmoebaOptimizerv4.h.

◆ CostFunctionAdaptorType

using itk::AmoebaOptimizerv4::CostFunctionAdaptorType = Superclass::CostFunctionAdaptorType

protected

Definition at line 155 of file itkAmoebaOptimizerv4.h.

◆ InternalParametersType

using itk::AmoebaOptimizerv4::InternalParametersType = vnl_vector<double>

InternalParameters type alias.

Definition at line 84 of file itkAmoebaOptimizerv4.h.

◆ ParametersType

using itk::AmoebaOptimizerv4::ParametersType = Superclass::ParametersType

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

Definition at line 81 of file itkAmoebaOptimizerv4.h.

◆ Pointer

using itk::AmoebaOptimizerv4::Pointer = SmartPointer<Self>

Definition at line 70 of file itkAmoebaOptimizerv4.h.

◆ Self

using itk::AmoebaOptimizerv4::Self = AmoebaOptimizerv4

Standard "Self" type alias.

Definition at line 68 of file itkAmoebaOptimizerv4.h.

◆ Superclass

using itk::AmoebaOptimizerv4::Superclass = SingleValuedNonLinearVnlOptimizerv4

Definition at line 69 of file itkAmoebaOptimizerv4.h.

Constructor & Destructor Documentation

◆ AmoebaOptimizerv4()

itk::AmoebaOptimizerv4::AmoebaOptimizerv4 ( )

protected

◆ ~AmoebaOptimizerv4()

itk::AmoebaOptimizerv4::~AmoebaOptimizerv4 ( )

overrideprotected

Member Function Documentation

◆ AutomaticInitialSimplexOn()

virtual void itk::AmoebaOptimizerv4::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]].

◆ GetAutomaticInitialSimplex()

virtual bool itk::AmoebaOptimizerv4::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]].

◆ GetFunctionConvergenceTolerance()

virtual double itk::AmoebaOptimizerv4::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().

◆ GetInitialSimplexDelta()

virtual ParametersType itk::AmoebaOptimizerv4::GetInitialSimplexDelta ( ) const

virtual

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

◆ GetNameOfClass()

const char * itk::AmoebaOptimizerv4::GetNameOfClass ( ) const

overridevirtual

See also: LightObject::GetNameOfClass()

Reimplemented from itk::Object.

◆ GetOptimizer()

vnl_amoeba * itk::AmoebaOptimizerv4::GetOptimizer ( ) const

Method for getting access to the internal optimizer.

◆ GetOptimizeWithRestarts()

virtual bool itk::AmoebaOptimizerv4::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.

◆ GetParametersConvergenceTolerance()

virtual double itk::AmoebaOptimizerv4::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().

◆ GetStopConditionDescription()

std::string itk::AmoebaOptimizerv4::GetStopConditionDescription ( ) const

overridevirtual

Report the reason for stopping.

Implements itk::SingleValuedNonLinearVnlOptimizerv4.

◆ New()

static Pointer itk::AmoebaOptimizerv4::New ( )

static

Method for creation through the object factory.

◆ OptimizeWithRestartsOn()

virtual void itk::AmoebaOptimizerv4::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.

◆ PrintSelf()

void itk::AmoebaOptimizerv4::PrintSelf	(	std::ostream &	os,
		Indent	indent
	)		const

overrideprotectedvirtual

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.

◆ SetAutomaticInitialSimplex()

virtual void itk::AmoebaOptimizerv4::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]].

◆ SetFunctionConvergenceTolerance()

virtual void itk::AmoebaOptimizerv4::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().

◆ SetInitialSimplexDelta()

void itk::AmoebaOptimizerv4::SetInitialSimplexDelta	(	ParametersType	initialSimplexDelta,
		bool	automaticInitialSimplex = `false`
	)

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

◆ SetMetric()

void itk::AmoebaOptimizerv4::SetMetric ( MetricType * metric )

overridevirtual

Plug in a Cost Function into the optimizer

Implements itk::SingleValuedNonLinearVnlOptimizerv4.

◆ SetOptimizeWithRestarts()

virtual void itk::AmoebaOptimizerv4::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.

◆ SetParametersConvergenceTolerance()

virtual void itk::AmoebaOptimizerv4::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().

◆ StartOptimization()

void itk::AmoebaOptimizerv4::StartOptimization ( bool doOnlyInitialization = false )

overridevirtual

Start optimization with an initial value.

Reimplemented from itk::ObjectToObjectOptimizerBaseTemplate< double >.

◆ ValidateSettings()

void itk::AmoebaOptimizerv4::ValidateSettings ( )

private

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

Member Data Documentation

◆ m_AutomaticInitialSimplex

bool itk::AmoebaOptimizerv4::m_AutomaticInitialSimplex {}

private

Definition at line 164 of file itkAmoebaOptimizerv4.h.

◆ m_FunctionConvergenceTolerance

MeasureType itk::AmoebaOptimizerv4::m_FunctionConvergenceTolerance {}

private

Definition at line 163 of file itkAmoebaOptimizerv4.h.

◆ m_InitialSimplexDelta

ParametersType itk::AmoebaOptimizerv4::m_InitialSimplexDelta {}

private

Definition at line 165 of file itkAmoebaOptimizerv4.h.

◆ m_OptimizeWithRestarts

bool itk::AmoebaOptimizerv4::m_OptimizeWithRestarts {}

private

Definition at line 166 of file itkAmoebaOptimizerv4.h.

◆ m_ParametersConvergenceTolerance

ParametersType::ValueType itk::AmoebaOptimizerv4::m_ParametersConvergenceTolerance {}

private

Definition at line 162 of file itkAmoebaOptimizerv4.h.

◆ m_StopConditionDescription

std::ostringstream itk::AmoebaOptimizerv4::m_StopConditionDescription {}

private

Definition at line 169 of file itkAmoebaOptimizerv4.h.

◆ m_VnlOptimizer

std::unique_ptr<vnl_amoeba> itk::AmoebaOptimizerv4::m_VnlOptimizer

private

Definition at line 167 of file itkAmoebaOptimizerv4.h.

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

itkAmoebaOptimizerv4.h

Detailed Description

Public Types

Public Member Functions

Static Public Member Functions

Protected Types

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ ConstPointer

◆ CostFunctionAdaptorType

◆ InternalParametersType

◆ ParametersType

◆ Pointer

◆ Self

◆ Superclass

Constructor & Destructor Documentation

◆ AmoebaOptimizerv4()

◆ ~AmoebaOptimizerv4()

Member Function Documentation

◆ AutomaticInitialSimplexOn()

◆ GetAutomaticInitialSimplex()

◆ GetFunctionConvergenceTolerance()

◆ GetInitialSimplexDelta()

◆ GetNameOfClass()

◆ GetOptimizer()

◆ GetOptimizeWithRestarts()

◆ GetParametersConvergenceTolerance()

◆ GetStopConditionDescription()

◆ New()

◆ OptimizeWithRestartsOn()

◆ PrintSelf()

◆ SetAutomaticInitialSimplex()

◆ SetFunctionConvergenceTolerance()

◆ SetInitialSimplexDelta()

◆ SetMetric()

◆ SetOptimizeWithRestarts()

◆ SetParametersConvergenceTolerance()

◆ StartOptimization()

◆ ValidateSettings()

Member Data Documentation

◆ m_AutomaticInitialSimplex

◆ m_FunctionConvergenceTolerance

◆ m_InitialSimplexDelta

◆ m_OptimizeWithRestarts

◆ m_ParametersConvergenceTolerance

◆ m_StopConditionDescription

◆ m_VnlOptimizer