elastix::Configuration Class Reference

#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:

Public Types
typedef std::map< std::string, std::string >	CommandLineArgumentMapType
typedef CommandLineArgumentMapType::value_type	CommandLineEntryType
typedef itk::SmartPointer< const Self >	ConstPointer
typedef ParameterFileParserType::Pointer	ParameterFileParserPointer
typedef itk::ParameterFileParser	ParameterFileParserType
typedef ParameterMapInterfaceType::Pointer	ParameterMapInterfacePointer
typedef itk::ParameterMapInterface	ParameterMapInterfaceType
typedef itk::SmartPointer< Self >	Pointer
typedef Configuration	Self
typedef itk::Object	Superclass1
typedef BaseComponent	Superclass2

Public Member Functions
int	BeforeAll (void) override
virtual int	BeforeAllTransformix (void)
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
virtual bool	GetPrintErrorMessages (void)
virtual unsigned int	GetTotalNumberOfElastixLevels () const
virtual int	Initialize (const CommandLineArgumentMapType &_arg)
virtual int	Initialize (const CommandLineArgumentMapType &_arg, const ParameterFileParserType::ParameterMapType &inputMap)
virtual bool	IsInitialized (void) const
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 printThisErrorMessage) 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 printThisErrorMessage) const
template<class T >
bool	ReadParameter (T &parameterValue, const std::string &parameterName, const unsigned int entry_nr)
template<class T >
bool	ReadParameter (T &parameterValue, const std::string &parameterName, const unsigned int entry_nr, const bool printThisErrorMessage)
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 (void)
virtual void	AfterEachIterationBase (void)
virtual void	AfterEachResolution (void)
virtual void	AfterEachResolutionBase (void)
virtual void	AfterRegistration (void)
virtual void	AfterRegistrationBase (void)
virtual int	BeforeAll (void)
virtual int	BeforeAllBase (void)
virtual void	BeforeEachResolution (void)
virtual void	BeforeEachResolutionBase (void)
virtual void	BeforeRegistration (void)
virtual void	BeforeRegistrationBase (void)
virtual const char *	elxGetClassName (void) const
const char *	GetComponentLabel (void) const
	ITK_DISALLOW_COPY_AND_ASSIGN (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
static std::string	ConvertSecondsToDHMS (const double totalSeconds, const unsigned int precision)
static void	InitializeElastixExecutable ()
static bool	IsElastixLibrary ()

Protected Member Functions
	Configuration ()
virtual void	PrintParameterFile (void) const
	~Configuration () override
Protected Member Functions inherited from elastix::BaseComponent
	BaseComponent ()=default
virtual	~BaseComponent ()=default

Private Member Functions
	Configuration (const Self &)
void	operator= (const Self &)

Private Attributes
CommandLineArgumentMapType	m_CommandLineArgumentMap
unsigned int	m_ElastixLevel
bool	m_IsInitialized
std::string	m_ParameterFileName
ParameterFileParserPointer	m_ParameterFileParser
ParameterMapInterfacePointer	m_ParameterMapInterface
unsigned int	m_TotalNumberOfElastixLevels

Member Typedef Documentation

CommandLineArgumentMapType

typedef std::map< std::string, std::string > elastix::Configuration::CommandLineArgumentMapType

Typedefs for the command line arguments.

Definition at line 68 of file elxConfiguration.h.

CommandLineEntryType

typedef CommandLineArgumentMapType::value_type elastix::Configuration::CommandLineEntryType

Definition at line 69 of file elxConfiguration.h.

ConstPointer

typedef itk::SmartPointer< const Self > elastix::Configuration::ConstPointer

Definition at line 59 of file elxConfiguration.h.

ParameterFileParserPointer

typedef ParameterFileParserType::Pointer elastix::Configuration::ParameterFileParserPointer

Definition at line 73 of file elxConfiguration.h.

ParameterFileParserType

typedef itk::ParameterFileParser elastix::Configuration::ParameterFileParserType

Typedefs for the parameter file.

Definition at line 72 of file elxConfiguration.h.

ParameterMapInterfacePointer

typedef ParameterMapInterfaceType::Pointer elastix::Configuration::ParameterMapInterfacePointer

Definition at line 75 of file elxConfiguration.h.

ParameterMapInterfaceType

typedef itk::ParameterMapInterface elastix::Configuration::ParameterMapInterfaceType

Definition at line 74 of file elxConfiguration.h.

Pointer

typedef itk::SmartPointer< Self > elastix::Configuration::Pointer

Definition at line 58 of file elxConfiguration.h.

Self

typedef Configuration elastix::Configuration::Self

Standard itk.

Definition at line 55 of file elxConfiguration.h.

Superclass1

typedef itk::Object elastix::Configuration::Superclass1

Definition at line 56 of file elxConfiguration.h.

Superclass2

typedef BaseComponent elastix::Configuration::Superclass2

Definition at line 57 of file elxConfiguration.h.

Constructor & Destructor Documentation

Configuration() [1/2]

elastix::Configuration::Configuration ( )

protected

~Configuration()

elastix::Configuration::~Configuration ( )

inlineoverrideprotected

Definition at line 242 of file elxConfiguration.h.

Configuration() [2/2]

elastix::Configuration::Configuration ( const Self &  )

private

Member Function Documentation

BeforeAll()

int elastix::Configuration::BeforeAll ( void  )

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()

virtual int elastix::Configuration::BeforeAllTransformix ( void  )

virtual

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 136 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()

virtual bool elastix::Configuration::GetPrintErrorMessages ( void  )

inlinevirtual

Definition at line 112 of file elxConfiguration.h.

GetTotalNumberOfElastixLevels()

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

virtual

Initialize() [1/2]

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

virtual

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]

virtual int elastix::Configuration::Initialize ( const CommandLineArgumentMapType &  _arg, const ParameterFileParserType::ParameterMapType &  inputMap  )

virtual

IsInitialized()

virtual bool elastix::Configuration::IsInitialized ( void  ) const

virtual

True, if Initialize was successfully called.

New()

static Pointer elastix::Configuration::New ( )

static

Method for creation through the object factory.

operator=()

void elastix::Configuration::operator= ( const Self &  )

private

PrintParameterFile()

virtual void elastix::Configuration::PrintParameterFile ( void  ) const

protectedvirtual

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  printThisErrorMessage  ) const

inline

Read a range of parameters from the parameter file.

Definition at line 220 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 201 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  printThisErrorMessage  ) const

inline

Read a parameter from the parameter file.

Definition at line 181 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  )

inline

Read a parameter from the parameter file.

Definition at line 164 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  printThisErrorMessage  )

inline

Read a parameter from the parameter file.

Definition at line 146 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 255 of file elxConfiguration.h.

m_ElastixLevel

unsigned int elastix::Configuration::m_ElastixLevel

private

Definition at line 261 of file elxConfiguration.h.

m_IsInitialized

bool elastix::Configuration::m_IsInitialized

private

Definition at line 260 of file elxConfiguration.h.

m_ParameterFileName

std::string elastix::Configuration::m_ParameterFileName

private

Definition at line 256 of file elxConfiguration.h.

m_ParameterFileParser

ParameterFileParserPointer elastix::Configuration::m_ParameterFileParser

private

Definition at line 257 of file elxConfiguration.h.

m_ParameterMapInterface

ParameterMapInterfacePointer elastix::Configuration::m_ParameterMapInterface

private

Definition at line 258 of file elxConfiguration.h.

m_TotalNumberOfElastixLevels

unsigned int elastix::Configuration::m_TotalNumberOfElastixLevels

private

Definition at line 262 of file elxConfiguration.h.