#include <elxConfiguration.h>

Detailed Description

A class that deals with user given parameters and command line arguments.

The Configuration class provides the functions ReadParameter() (to read parameters from the parameter file) and ReadCommandLineArgument(), and provides an easy way to get the current elastix level.

Parameters: PrintErrorMessages: defines if warnings and errors should be printed to screen, e.g. when a parameter cannot be found and the default is used. example: (PrintErrorMessages "false")
Default: "true"

Definition at line 50 of file elxConfiguration.h.

Inheritance diagram for elastix::Configuration:

[legend]

Public Types
using	CommandLineArgumentMapType = std::map<std::string, std::string>

using	CommandLineEntryType = CommandLineArgumentMapType::value_type

using	ConstPointer = itk::SmartPointer<const Self>

using	Pointer = itk::SmartPointer<Self>

using	Self = Configuration

using	Superclass1 = itk::Object

using	Superclass2 = BaseComponent

Public Member Functions
int	BeforeAll () override

int	BeforeAllTransformix ()

std::vcl_size_t	CountNumberOfParameterEntries (const std::string &parameterName) const

virtual const char *	GetClassName () const

std::string	GetCommandLineArgument (const std::string &key) const

virtual unsigned int	GetElastixLevel () const

virtual const char *	GetParameterFileName () const

bool	GetPrintErrorMessages () const

virtual unsigned int	GetTotalNumberOfElastixLevels () const

std::vector< std::string >	GetValuesOfParameter (const std::string &parameterName) const

bool	HasParameter (const std::string &parameterName) const

int	Initialize (const CommandLineArgumentMapType &_arg)

int	Initialize (const CommandLineArgumentMapType &_arg, const itk::ParameterFileParser::ParameterMapType &inputMap)

bool	IsInitialized () const

	ITK_DISALLOW_COPY_AND_MOVE (Configuration)

template<class T >
bool	ReadParameter (std::vector< T > &parameterValues, const std::string &parameterName, const unsigned int entry_nr_start, const unsigned int entry_nr_end, const bool produceWarningMessage) const

template<class T >
bool	ReadParameter (T &parameterValue, const std::string &parameterName, const std::string &prefix, const unsigned int entry_nr, const int default_entry_nr) const

template<class T >
bool	ReadParameter (T &parameterValue, const std::string &parameterName, const std::string &prefix, const unsigned int entry_nr, const int default_entry_nr, const bool produceWarningMessage) const

template<class T >
bool	ReadParameter (T &parameterValue, const std::string &parameterName, const unsigned int entry_nr) const

template<class T >
bool	ReadParameter (T &parameterValue, const std::string &parameterName, const unsigned int entry_nr, const bool produceWarningMessage) const

std::string	RetrieveParameterStringValue (const std::string &defaultParameterValue, const std::string &parameterName, const unsigned int entry_nr, const bool produceWarningMessage) const

template<typename T >
T	RetrieveParameterValue (const T &defaultParameterValue, const std::string &parameterName, const unsigned int entry_nr, const bool produceWarningMessage) const

template<typename T >
std::unique_ptr< std::vector< T > >	RetrieveValuesOfParameter (const std::string &parameterName) const

void	SetCommandLineArgument (const std::string &key, const std::string &value)

virtual void	SetElastixLevel (unsigned int _arg)

virtual void	SetParameterFileName (const char *_arg)

virtual void	SetTotalNumberOfElastixLevels (unsigned int _arg)

Public Member Functions inherited from elastix::BaseComponent
virtual void	AfterEachIteration ()

virtual void	AfterEachIterationBase ()

virtual void	AfterEachResolution ()

virtual void	AfterEachResolutionBase ()

virtual void	AfterRegistration ()

virtual void	AfterRegistrationBase ()

virtual int	BeforeAllBase ()

virtual void	BeforeEachResolution ()

virtual void	BeforeEachResolutionBase ()

virtual void	BeforeRegistration ()

virtual void	BeforeRegistrationBase ()

virtual const char *	elxGetClassName () const

const char *	GetComponentLabel () const

	ITK_DISALLOW_COPY_AND_MOVE (BaseComponent)

	itkTypeMacroNoParent (BaseComponent)

void	SetComponentLabel (const char *label, unsigned int idx)

Static Public Member Functions
static Pointer	New ()

Static Public Member Functions inherited from elastix::BaseComponent
template<typename TBaseComponent >
static auto	AsITKBaseType (TBaseComponent *const baseComponent) -> decltype(baseComponent->GetAsITKBaseType())

static void	InitializeElastixExecutable ()

static bool	IsElastixLibrary ()

Protected Member Functions
	Configuration ()

void	PrintParameterFile () const

	~Configuration () override=default

Protected Member Functions inherited from elastix::BaseComponent
	BaseComponent ()=default

virtual	~BaseComponent ()=default

Private Attributes
CommandLineArgumentMapType	m_CommandLineArgumentMap {}

unsigned int	m_ElastixLevel { 0 }

bool	m_IsInitialized { false }

std::string	m_ParameterFileName {}

const itk::ParameterFileParser::Pointer	m_ParameterFileParser { itk::ParameterFileParser::New() }

const itk::ParameterMapInterface::Pointer	m_ParameterMapInterface { itk::ParameterMapInterface::New() }

unsigned int	m_TotalNumberOfElastixLevels { 1 }

Member Typedef Documentation

◆ CommandLineArgumentMapType

using elastix::Configuration::CommandLineArgumentMapType = std::map<std::string, std::string>

Typedefs for the command line arguments.

Definition at line 71 of file elxConfiguration.h.

◆ CommandLineEntryType

using elastix::Configuration::CommandLineEntryType = CommandLineArgumentMapType::value_type

Definition at line 72 of file elxConfiguration.h.

◆ ConstPointer

using elastix::Configuration::ConstPointer = itk::SmartPointer<const Self>

Definition at line 62 of file elxConfiguration.h.

◆ Pointer

using elastix::Configuration::Pointer = itk::SmartPointer<Self>

Definition at line 61 of file elxConfiguration.h.

◆ Self

using elastix::Configuration::Self = Configuration

Standard itk.

Definition at line 58 of file elxConfiguration.h.

◆ Superclass1

using elastix::Configuration::Superclass1 = itk::Object

Definition at line 59 of file elxConfiguration.h.

◆ Superclass2

using elastix::Configuration::Superclass2 = BaseComponent

Definition at line 60 of file elxConfiguration.h.

Constructor & Destructor Documentation

◆ Configuration()

elastix::Configuration::Configuration ( )

protected

◆ ~Configuration()

elastix::Configuration::~Configuration ( )

overrideprotecteddefault

Member Function Documentation

◆ BeforeAll()

int elastix::Configuration::BeforeAll ( )

overridevirtual

Set/Get whether warnings are allowed to be printed, when reading a parameter. * itkSetMacro( Silent, bool ); itkGetConstMacro( Silent, bool ); Methods that is called at the very beginning of elastixTemplate::Run.

Prints the parameter file

Reimplemented from elastix::BaseComponent.

◆ BeforeAllTransformix()

int elastix::Configuration::BeforeAllTransformix ( )

Methods that is called at the very beginning of elastixTemplate::ApplyTransform.

Prints the parameter file

◆ CountNumberOfParameterEntries()

std::vcl_size_t elastix::Configuration::CountNumberOfParameterEntries ( const std::string & parameterName ) const

inline

Interface to the ParameterMapInterface. Count the number of parameters.

Definition at line 141 of file elxConfiguration.h.

◆ GetClassName()

virtual const char * elastix::Configuration::GetClassName ( ) const

virtual

Standard part of all itk objects.

◆ GetCommandLineArgument()

std::string elastix::Configuration::GetCommandLineArgument ( const std::string & key ) const

Get and Set CommandLine arguments into the argument map.

◆ GetElastixLevel()

virtual unsigned int elastix::Configuration::GetElastixLevel ( ) const

virtual

◆ GetParameterFileName()

virtual const char * elastix::Configuration::GetParameterFileName ( ) const

virtual

Get/Set the name of the parameterFileName.

◆ GetPrintErrorMessages()

bool elastix::Configuration::GetPrintErrorMessages ( ) const

inline

Definition at line 114 of file elxConfiguration.h.

◆ GetTotalNumberOfElastixLevels()

virtual unsigned int elastix::Configuration::GetTotalNumberOfElastixLevels ( ) const

virtual

◆ GetValuesOfParameter()

std::vector< std::string > elastix::Configuration::GetValuesOfParameter ( const std::string & parameterName ) const

inline

Returns the values of the specified parameter (from the parameter file).

Definition at line 236 of file elxConfiguration.h.

◆ HasParameter()

bool elastix::Configuration::HasParameter ( const std::string & parameterName ) const

inline

Tells whether its parameter map has the parameter with the given name.

Definition at line 228 of file elxConfiguration.h.

◆ Initialize() [1/2]

int elastix::Configuration::Initialize ( const CommandLineArgumentMapType & _arg )

Pass the command line arguments as a map. One of the command line arguments should be either: -p <parameter_file> or -tp <transform_parameter_file>. The specified (transform) parameter file is read by the itk::ParameterFileParser and passed to the itk::ParameterMapInterface.

◆ Initialize() [2/2]

int elastix::Configuration::Initialize	(	const CommandLineArgumentMapType &	_arg,
		const itk::ParameterFileParser::ParameterMapType &	inputMap )

◆ IsInitialized()

bool elastix::Configuration::IsInitialized ( ) const

True, if Initialize was successfully called.

◆ ITK_DISALLOW_COPY_AND_MOVE()

elastix::Configuration::ITK_DISALLOW_COPY_AND_MOVE ( Configuration )

◆ New()

static Pointer elastix::Configuration::New ( )

static

Method for creation through the object factory.

◆ PrintParameterFile()

void elastix::Configuration::PrintParameterFile ( ) const

protected

Print the parameter file to the log file. Called by BeforeAll(). This function is not really generic. It's just added because it needs to be called by both BeforeAll and BeforeAllTransformix.

◆ ReadParameter() [1/5]

template<class T >

bool elastix::Configuration::ReadParameter	(	std::vector< T > &	parameterValues,
		const std::string &	parameterName,
		const unsigned int	entry_nr_start,
		const unsigned int	entry_nr_end,
		const bool	produceWarningMessage ) const

inline

Read a range of parameters from the parameter file.

Definition at line 284 of file elxConfiguration.h.

◆ ReadParameter() [2/5]

template<class T >

bool elastix::Configuration::ReadParameter	(	T &	parameterValue,
		const std::string &	parameterName,
		const std::string &	prefix,
		const unsigned int	entry_nr,
		const int	default_entry_nr ) const

inline

Read a parameter from the parameter file.

Definition at line 208 of file elxConfiguration.h.

◆ ReadParameter() [3/5]

template<class T >

bool elastix::Configuration::ReadParameter	(	T &	parameterValue,
		const std::string &	parameterName,
		const std::string &	prefix,
		const unsigned int	entry_nr,
		const int	default_entry_nr,
		const bool	produceWarningMessage ) const

inline

Read a parameter from the parameter file.

Definition at line 186 of file elxConfiguration.h.

◆ ReadParameter() [4/5]

template<class T >

bool elastix::Configuration::ReadParameter	(	T &	parameterValue,
		const std::string &	parameterName,
		const unsigned int	entry_nr ) const

inline

Read a parameter from the parameter file.

Definition at line 170 of file elxConfiguration.h.

◆ ReadParameter() [5/5]

template<class T >

bool elastix::Configuration::ReadParameter	(	T &	parameterValue,
		const std::string &	parameterName,
		const unsigned int	entry_nr,
		const bool	produceWarningMessage ) const

inline

Read a parameter from the parameter file.

Definition at line 150 of file elxConfiguration.h.

◆ RetrieveParameterStringValue()

std::string elastix::Configuration::RetrieveParameterStringValue	(	const std::string &	defaultParameterValue,
		const std::string &	parameterName,
		const unsigned int	entry_nr,
		const bool	produceWarningMessage ) const

inline

Retrieves the string value of the specified parameter (from the parameter file). Returns the specified default parameter value if the parameter cannot be found.

Definition at line 272 of file elxConfiguration.h.

◆ RetrieveParameterValue()

template<typename T >

T elastix::Configuration::RetrieveParameterValue	(	const T &	defaultParameterValue,
		const std::string &	parameterName,
		const unsigned int	entry_nr,
		const bool	produceWarningMessage ) const

inline

Retrieves the value of the specified parameter (from the parameter file). Returns the specified default parameter value if the parameter cannot be found.

Definition at line 258 of file elxConfiguration.h.

◆ RetrieveValuesOfParameter()

template<typename T >

std::unique_ptr< std::vector< T > > elastix::Configuration::RetrieveValuesOfParameter ( const std::string & parameterName ) const

inline

Retrieves the values of the specified parameter (from the parameter file). Returns null when the parameter map does not contain the specified parameter. Throws an exception when it fails to convert each of the parameter values to the specified type T.

Definition at line 249 of file elxConfiguration.h.

◆ SetCommandLineArgument()

void elastix::Configuration::SetCommandLineArgument	(	const std::string &	key,
		const std::string &	value )

◆ SetElastixLevel()

virtual void elastix::Configuration::SetElastixLevel ( unsigned int _arg )

virtual

Other elastix related information. Get and Set the elastix level.

◆ SetParameterFileName()

virtual void elastix::Configuration::SetParameterFileName ( const char * _arg )

virtual

◆ SetTotalNumberOfElastixLevels()

virtual void elastix::Configuration::SetTotalNumberOfElastixLevels ( unsigned int _arg )

virtual

Get and Set the total number of elastix levels.

Field Documentation

◆ m_CommandLineArgumentMap

CommandLineArgumentMapType elastix::Configuration::m_CommandLineArgumentMap {}

private

Definition at line 314 of file elxConfiguration.h.

◆ m_ElastixLevel

unsigned int elastix::Configuration::m_ElastixLevel { 0 }

private

Definition at line 320 of file elxConfiguration.h.

◆ m_IsInitialized

bool elastix::Configuration::m_IsInitialized { false }

private

Definition at line 319 of file elxConfiguration.h.

◆ m_ParameterFileName

std::string elastix::Configuration::m_ParameterFileName {}

private

Definition at line 315 of file elxConfiguration.h.

◆ m_ParameterFileParser

const itk::ParameterFileParser::Pointer elastix::Configuration::m_ParameterFileParser { itk::ParameterFileParser::New() }

private

Definition at line 316 of file elxConfiguration.h.

◆ m_ParameterMapInterface

const itk::ParameterMapInterface::Pointer elastix::Configuration::m_ParameterMapInterface { itk::ParameterMapInterface::New() }

private

Definition at line 317 of file elxConfiguration.h.

◆ m_TotalNumberOfElastixLevels

unsigned int elastix::Configuration::m_TotalNumberOfElastixLevels { 1 }

private

Definition at line 321 of file elxConfiguration.h.

Detailed Description

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Member Typedef Documentation

◆ CommandLineArgumentMapType

◆ CommandLineEntryType

◆ ConstPointer

◆ Pointer

◆ Self

◆ Superclass1

◆ Superclass2

Constructor & Destructor Documentation

◆ Configuration()

◆ ~Configuration()

Member Function Documentation

◆ BeforeAll()

◆ BeforeAllTransformix()

◆ CountNumberOfParameterEntries()

◆ GetClassName()

◆ GetCommandLineArgument()

◆ GetElastixLevel()

◆ GetParameterFileName()

◆ GetPrintErrorMessages()

◆ GetTotalNumberOfElastixLevels()

◆ GetValuesOfParameter()

◆ HasParameter()

◆ Initialize() [1/2]

◆ Initialize() [2/2]

◆ IsInitialized()

◆ ITK_DISALLOW_COPY_AND_MOVE()

◆ New()

◆ PrintParameterFile()

◆ ReadParameter() [1/5]

◆ ReadParameter() [2/5]

◆ ReadParameter() [3/5]

◆ ReadParameter() [4/5]

◆ ReadParameter() [5/5]

◆ RetrieveParameterStringValue()

◆ RetrieveParameterValue()

◆ RetrieveValuesOfParameter()

◆ SetCommandLineArgument()

◆ SetElastixLevel()

◆ SetParameterFileName()

◆ SetTotalNumberOfElastixLevels()

Field Documentation

◆ m_CommandLineArgumentMap

◆ m_ElastixLevel

◆ m_IsInitialized

◆ m_ParameterFileName

◆ m_ParameterFileParser

◆ m_ParameterMapInterface

◆ m_TotalNumberOfElastixLevels