elastix Namespace Reference

Namespaces
namespace	LibUtilities

Classes
class	AdaGrad
class	AdaptiveStochasticGradientDescent
class	AdaptiveStochasticLBFGS
class	AdaptiveStochasticVarianceReducedGradient
class	AdvancedAffineTransformElastix
class	AdvancedBSplineTransform
class	AdvancedKappaStatisticMetric
class	AdvancedMattesMutualInformationMetric
class	AdvancedMeanSquaresMetric
class	AdvancedNormalizedCorrelationMetric
class	AdvancedTransformAdapter
class	AffineDTITransformElastix
class	AffineLogStackTransform
class	AffineLogTransformElastix
class	BaseComponent
class	BaseComponentSE
class	BSplineInterpolator
class	BSplineInterpolatorFloat
class	BSplineResampleInterpolator
class	BSplineResampleInterpolatorFloat
class	BSplineStackTransform
class	BSplineTransformWithDiffusion
class	CMAEvolutionStrategy
class	ComponentDatabase
class	ComponentInstaller
class	ComponentInstaller< TComponent, NrOfSupportedImageTypes+1 >
class	ComponentLoader
class	Configuration
class	ConjugateGradient
class	ConjugateGradientFRPR
class	Conversion
class	CorrespondingPointsEuclideanDistanceMetric
class	DefaultConstruct
class	DefaultResampler
class	DeformationFieldTransform
class	DisplacementMagnitudePenalty
class	DistancePreservingRigidityPenalty
class	ELASTIX
class	ElastixBase
class	ElastixMain
class	ElastixTemplate
class	ElastixTypedef
class	EulerStackTransform
class	EulerTransformElastix
class	ExternalTransform
class	FiniteDifferenceGradientDescent
class	FixedGenericPyramid
struct	FixedImageDimensionSupport
struct	FixedImageDimensionSupport< maxSupportedImageDimension+1 >
class	FixedImagePyramidBase
class	FixedRecursivePyramid
class	FixedShrinkingPyramid
class	FixedSmoothingPyramid
class	FullSampler
class	FullSearch
class	GenericPyramidHelper
class	GradientDifferenceMetric
class	GridSampler
class	ImageSamplerBase
class	ImpactMetric
class	InstallFunctions
class	InterpolatorBase
class	IterationInfo
class	KNNGraphAlphaMutualInformationMetric
class	LinearInterpolator
class	LinearResampleInterpolator
class	log
class	MainBase
class	MetricBase
class	MissingStructurePenalty
class	MovingGenericPyramid
class	MovingImagePyramidBase
class	MovingRecursivePyramid
class	MovingShrinkingPyramid
class	MovingSmoothingPyramid
class	MultiBSplineTransformWithNormal
class	MultiInputRandomCoordinateSampler
class	MultiMetricMultiResolutionRegistration
class	MultiResolutionRegistration
class	MultiResolutionRegistrationWithFeatures
class	NearestNeighborInterpolator
class	NearestNeighborResampleInterpolator
class	NormalizedGradientCorrelationMetric
class	NormalizedMutualInformationMetric
class	OpenCLFixedGenericPyramid
class	OpenCLMovingGenericPyramid
class	OpenCLResampler
class	OptimizerBase
class	ParameterObject
class	PatternIntensityMetric
class	PCAMetric
class	PCAMetric2
class	PolydataDummyPenalty
class	Powell
class	PreconditionedStochasticGradientDescent
class	ProgressCommand
class	QuasiNewtonLBFGS
class	RandomCoordinateSampler
class	RandomSampler
class	RandomSamplerSparseMask
class	RayCastInterpolator
class	RayCastResampleInterpolator
class	RecursiveBSplineTransform
class	ReducedDimensionBSplineInterpolator
class	ReducedDimensionBSplineResampleInterpolator
class	RegistrationBase
class	RegularStepGradientDescent
class	ResampleInterpolatorBase
class	ResamplerBase
class	RSGDEachParameterApart
class	SimilarityTransformElastix
class	Simplex
class	SimultaneousPerturbation
class	SplineKernelTransform
class	StandardGradientDescent
class	StatisticalShapePenalty
class	SumOfPairwiseCorrelationCoefficientsMetric
class	SumSquaredTissueVolumeDifferenceMetric
class	TransformBase
class	TransformBendingEnergyPenalty
class	TransformFactoryRegistration
class	TransformIO
class	TransformixMain
class	TransformRigidityPenalty
class	TranslationStackTransform
class	TranslationTransformElastix
class	VarianceOverLastDimensionMetric
class	WeightedCombinationTransformElastix

Enumerations
enum class	MaskCondition { IsNull , HasSameImageDomain , HasDifferentImageDomain }
enum class	ParameterMapStringFormat { LegacyTxt , Toml }

Functions
	elxSupportedImageTypeMacro (float, 2, float, 2, 1)
	elxSupportedImageTypeMacro (float, 3, float, 3, 3)
	elxSupportedImageTypeMacro (float, 4, float, 4, 5)
	elxSupportedImageTypeMacro (short, 3, short, 3, 2)
	elxSupportedImageTypeMacro (short, 4, short, 4, 4)
template<typename TFunction>
void	ForEachSupportedImageType (const TFunction &func)
template<typename TFunction, std::vcl_size_t... VIndexSequence>
void	ForEachSupportedImageType (const TFunction &func, const std::index_sequence< VIndexSequence... > &)
template<typename TFunction>
bool	ForEachSupportedImageTypeUntilTrue (const TFunction &func)
template<typename TFunction, std::vcl_size_t... VIndexSequence>
bool	ForEachSupportedImageTypeUntilTrue (const TFunction &func, const std::index_sequence< VIndexSequence... > &)
std::vector< bool >	GetBooleanVectorFromString (std::string valueStr, bool defaultValue)
std::string	GetExtendedVersionInformation (const char *const executableName, const char *const indentation="")
template<typename T>
std::vector< std::vector< T > >	GroupByDimensions (const std::vector< T > &values, const std::vector< unsigned int > &dimensions)
std::string	MakeStringOfCommandLineArguments (const char *const *const arguments)
template<unsigned int VImageDimension>
bool	MaskHasSameImageDomain (const itk::ImageMaskSpatialObject< VImageDimension > &mask, const itk::ImageBase< VImageDimension > &inputImage)
template<typename TPixel>
std::string	PixelTypeToFixedWidthString ()
template<typename TPixel>
std::string	PixelTypeToString ()
void	ReportTerminatingException (const char *const executableName, const std::exception &stdException) noexcept
template<unsigned VDimension>
constexpr bool	SupportsFixedDimension ()
template<unsigned VDimension, std::vcl_size_t... VIndex>
constexpr bool	SupportsFixedDimensionByImageTypeIndexSequence (std::index_sequence< VIndex... >)
bool	ToLogLevel (const std::string &str, log::level &logLevel)

Variables
constexpr const char *	gitRevisionDate = ""
constexpr const char *	gitRevisionSha = ""
constexpr unsigned	maxSupportedImageDimension { 4 }
constexpr unsigned	minSupportedImageDimension { 2 }
const unsigned int	NrOfSupportedImageTypes = 5
const auto	SupportedFixedImageDimensionSequence

Detailed Description

Include itk transforms needed.

Include structure for the diffusion.

Include itk transforms needed. Include grid schedule computer and upsample filter.

Needed for the macros

Needed for the macros.

Needed for the macros Mask support.

******************* elxBaseComponent.h *************************

This file defines the class elx::BaseComponent, from which all elastix components should inherit. It contains some methods that each component is supposed to have.

The namespace alias elx is defined in this file. All elastix components should be in namespace elastix.

Enumeration Type Documentation

MaskCondition

enum class elastix::MaskCondition

strong

Enum to indicate that a mask is null, has the same domain as the input image, or has a different image domain.

Enumerator
IsNull
HasSameImageDomain
HasDifferentImageDomain

Definition at line 29 of file elxMaskHasSameImageDomain.h.

ParameterMapStringFormat

enum class elastix::ParameterMapStringFormat

strong

Enumerator
LegacyTxt
Toml

Definition at line 38 of file elxConversion.h.

Function Documentation

elxSupportedImageTypeMacro() [1/5]

elastix::elxSupportedImageTypeMacro	(	float	,
		2	,
		float	,
		2	,
		1	)

elxSupportedImageTypeMacro() [2/5]

elastix::elxSupportedImageTypeMacro	(	float	,
		3	,
		float	,
		3	,
		3	)

elxSupportedImageTypeMacro() [3/5]

elastix::elxSupportedImageTypeMacro	(	float	,
		4	,
		float	,
		4	,
		5	)

elxSupportedImageTypeMacro() [4/5]

elastix::elxSupportedImageTypeMacro	(	short	,
		3	,
		short	,
		3	,
		2	)

elxSupportedImageTypeMacro() [5/5]

elastix::elxSupportedImageTypeMacro	(	short	,
		4	,
		short	,
		4	,
		4	)

ForEachSupportedImageType() [1/2]

template<typename TFunction>

void elastix::ForEachSupportedImageType

(

const TFunction &

func

)

Runs a function func(ElastixTypedef<VIndex>{}), for each supported image type from "elxSupportedImageTypes.h".

Definition at line 44 of file elxForEachSupportedImageType.h.

ForEachSupportedImageType() [2/2]

template<typename TFunction, std::vcl_size_t... VIndexSequence>

void elastix::ForEachSupportedImageType	(	const TFunction &	func,
		const std::index_sequence< VIndexSequence... > &	)

Definition at line 32 of file elxForEachSupportedImageType.h.

ForEachSupportedImageTypeUntilTrue() [1/2]

template<typename TFunction>

bool elastix::ForEachSupportedImageTypeUntilTrue

(

const TFunction &

func

)

Runs a function func(ElastixTypedef<VIndex>{}), for each supported image type from "elxSupportedImageTypes.h", until the function returns true.

Definition at line 62 of file elxForEachSupportedImageType.h.

ForEachSupportedImageTypeUntilTrue() [2/2]

template<typename TFunction, std::vcl_size_t... VIndexSequence>

bool elastix::ForEachSupportedImageTypeUntilTrue	(	const TFunction &	func,
		const std::index_sequence< VIndexSequence... > &	)

Definition at line 51 of file elxForEachSupportedImageType.h.

GetBooleanVectorFromString()

std::vector< bool > elastix::GetBooleanVectorFromString ( std::string valueStr, bool defaultValue )

inline

Parse a string into typed values using a custom delimiter.

If delimiter == '\0', characters are split one by one. Otherwise, the string is split using the given delimiter. Uses GetValueFromString<T>() for each token.

Template Parameters

T	The type to parse.

Parameters

valueStr	The input string.
defaultValue	The fallback value.
delimiter	The token delimiter or \0 for char-splitting.

Returns

A vector of parsed values.

Definition at line 317 of file elxImpactMetric.h.

GetExtendedVersionInformation()

std::string elastix::GetExtendedVersionInformation	(	const char *const	executableName,
		const char *const	indentation = "" )

Prints extended version information to standard output.

GroupByDimensions()

template<typename T>

std::vector< std::vector< T > > elastix::GroupByDimensions	(	const std::vector< T > &	values,
		const std::vector< unsigned int > &	dimensions )

Groups a flat vector into sub-vectors based on given dimension sizes.

Splits the input vector values into multiple groups, where the size of each group is specified by the corresponding entry in dimensions. If there are not enough elements in values to fill a group, the last available value is repeated to complete it.

Example: values = {1, 2, 3, 4, 5} dimensions = {2, 3} result = {{1, 2}, {3, 4, 5}}

Template Parameters

T	The type of elements in the input vector.

Parameters

values	The flat input vector to be grouped.
dimensions	A list of sizes specifying how to group the values.

Returns

A vector of groups, each being a sub-vector of values.

Definition at line 357 of file elxImpactMetric.h.

MakeStringOfCommandLineArguments()

std::string elastix::MakeStringOfCommandLineArguments

(

const char *const *const

arguments

)

Makes a string of all command-line arguments.

MaskHasSameImageDomain()

template<unsigned int VImageDimension>

bool elastix::MaskHasSameImageDomain	(	const itk::ImageMaskSpatialObject< VImageDimension > &	mask,
		const itk::ImageBase< VImageDimension > &	inputImage )

Returns true, if and only if the mask has exactly the same image domain (image region, origin, spacing, direction) as the specified input image.

Definition at line 40 of file elxMaskHasSameImageDomain.h.

PixelTypeToFixedWidthString()

template<typename TPixel>

std::string elastix::PixelTypeToFixedWidthString

(

)

Definition at line 33 of file elxPixelTypeToString.h.

PixelTypeToString()

template<typename TPixel>

std::string elastix::PixelTypeToString

(

)

Definition at line 58 of file elxPixelTypeToString.h.

ReportTerminatingException()

void elastix::ReportTerminatingException ( const char *const executableName, const std::exception & stdException )

noexcept

Reports the exception that is terminating the process to the user.

SupportsFixedDimension()

template<unsigned VDimension>

bool elastix::SupportsFixedDimension ( )

constexpr

Definition at line 55 of file elxSupportedImageDimensions.h.

SupportsFixedDimensionByImageTypeIndexSequence()

template<unsigned VDimension, std::vcl_size_t... VIndex>

bool elastix::SupportsFixedDimensionByImageTypeIndexSequence ( std::index_sequence< VIndex... > )

constexpr

Definition at line 37 of file elxSupportedImageDimensions.h.

ToLogLevel()

bool elastix::ToLogLevel	(	const std::string &	str,
		log::level &	logLevel )

Variable Documentation

gitRevisionDate

const char* elastix::gitRevisionDate = ""

constexpr

Definition at line 26 of file elxGitRevisionInfo.h.

gitRevisionSha

const char* elastix::gitRevisionSha = ""

constexpr

Definition at line 25 of file elxGitRevisionInfo.h.

maxSupportedImageDimension

unsigned elastix::maxSupportedImageDimension { 4 }

constexpr

The maximum possible supported image dimension (for either fixed or moving images).

Definition at line 32 of file elxSupportedImageDimensions.h.

minSupportedImageDimension

unsigned elastix::minSupportedImageDimension { 2 }

constexpr

The minimum possible supported image dimension (for either fixed or moving images).

Definition at line 29 of file elxSupportedImageDimensions.h.

NrOfSupportedImageTypes

const unsigned int elastix::NrOfSupportedImageTypes = 5

******************** SupportedImageTypes *********************

Add here the combinations of ImageTypes that elastix should support.

Syntax:

elxSupportedImageTypeMacro( FixedImagePixelType, FixedImageDimension, MovingImagePixelType, MovingImageDimension, Index )

Each combination of image types has as 'ID', the Index. Duplicate indices are not allowed. Index 0 is not allowed. The indices must form a "continuous series": ( index_{i} - index_{i-1} == 1 ).

The NrOfSupportedImageTypes must also be set to the right value.

elastix, and all its components, must be recompiled after adding a line in this file.

Definition at line 53 of file elxSupportedImageTypes.h.

SupportedFixedImageDimensionSequence

const auto elastix::SupportedFixedImageDimensionSequence

Initial value:

=
  FixedImageDimensionSupport<>::AddSupportedDimensions(std::index_sequence<>())

A sequence of the dimensions of supported fixed images

Definition at line 92 of file elxSupportedImageDimensions.h.