elastix::RandomCoordinateSampler< TElastix > Class Template Reference

#include <elxRandomCoordinateSampler.h>

Detailed Description

template<typename TElastix>
class elastix::RandomCoordinateSampler< TElastix >

An interpolator based on the itk::ImageRandomCoordinateSampler.

This image sampler randomly samples 'NumberOfSamples' coordinates in the InputImageRegion. If a mask is given, the sampler tries to find samples within the mask. If the mask is very sparse, this may take some time. The RandomCoordinate sampler samples not only positions that correspond to voxels, but also positions between voxels. An interpolator for the fixed image is thus required. A B-spline interpolator is used, the order of which can be specified by the user. Typically, the RandomCoordinate gives a smoother cost function, because the so-called 'grid-effect' is avoided.

This sampler is suitable to used in combination with the NewSamplesEveryIteration parameter (defined in the elx::OptimizerBase).

The parameters used in this class are:

Parameters

ImageSampler: Select this image sampler as follows:
(ImageSampler "RandomCoordinate")

NumberOfSpatialSamples: The number of image voxels used for computing the metric value and its derivative in each iteration. Must be given for each resolution.
example: (NumberOfSpatialSamples 2048 2048 4000)
The default is 5000.

UseRandomSampleRegion: Defines whether to randomly select a subregion of the image in each iteration. When set to "true", also specify the SampleRegionSize. By setting this option to "true", in combination with the NewSamplesEveryIteration parameter, a "localised" similarity measure is obtained. This can give better performance in case of the presence of large inhomogeneities in the image, for example.
example: (UseRandomSampleRegion "true")
Default: false.

SampleRegionSize: the size of the subregions that are selected when using the UseRandomSampleRegion option. The size should be specified in mm, for each dimension. As a rule of thumb, you may try a value ~1/3 of the image size.
example: (SampleRegionSize 50.0 50.0 50.0)
You can also specify one number, which will be used for all dimensions. Also, you can specify different values for each resolution:
example: (SampleRegionSize 50.0 50.0 50.0 30.0 30.0 30.0)
In this example, in the first resolution 50mm is used for each of the 3 dimensions, and in the second resolution 30mm.
Default: sampleRegionSize[i] = min ( fixedImageSize[i], max_i ( fixedImageSize[i]/3 ) ), with fixedImageSize in mm. So, approximately 1/3 of the fixed image size.

FixedImageBSplineInterpolationOrder: When using a RandomCoordinate sampler, the fixed image needs to be interpolated. This is done using a B-spline interpolator. With this option you can specify the order of interpolation.
example: (FixedImageBSplineInterpolationOrder 0 0 1)
Default value: 1. The parameter can be specified for each resolution.

Definition at line 78 of file elxRandomCoordinateSampler.h.

Inheritance diagram for elastix::RandomCoordinateSampler< TElastix >:

Public Types
using	ConstPointer = itk::SmartPointer<const Self>
using	ITKBaseType = typename Superclass2::ITKBaseType
using	Pointer = itk::SmartPointer<Self>
using	Self = RandomCoordinateSampler
using	Superclass1 = itk::ImageRandomCoordinateSampler<typename elx::ImageSamplerBase<TElastix>::InputImageType>
using	Superclass2 = elx::ImageSamplerBase<TElastix>
Public Types inherited from itk::ImageRandomCoordinateSampler< TInputImage >
using	ConstPointer = SmartPointer<const Self>
using	CoordinateType = double
using	DefaultInterpolatorType = BSplineInterpolateImageFunction<InputImageType, CoordinateType, double>
using	InputImageSpacingType = typename InputImageType::SpacingType
using	InterpolatorPointer = typename InterpolatorType::Pointer
using	InterpolatorType = InterpolateImageFunction<InputImageType, CoordinateType>
using	Pointer = SmartPointer<Self>
using	RandomGeneratorPointer = typename RandomGeneratorType::Pointer
using	RandomGeneratorType = itk::Statistics::MersenneTwisterRandomVariateGenerator
using	Self = ImageRandomCoordinateSampler
using	Superclass = ImageRandomSamplerBase<TInputImage>
Public Types inherited from itk::ImageRandomSamplerBase< TInputImage >
using	ConstPointer = SmartPointer<const Self>
using	ImageSampleContainerPointer
using	ImageSampleContainerType
using	ImageSampleType
using	InputImageConstPointer
using	InputImagePixelType
using	InputImagePointer
using	InputImageRegionType
using	InputImageType
using	MaskType
using	Pointer = SmartPointer<Self>
using	SeedIntegerType = Statistics::MersenneTwisterRandomVariateGenerator::IntegerType
using	Self = ImageRandomSamplerBase
using	Superclass = ImageSamplerBase<TInputImage>
Public Types inherited from itk::ImageSamplerBase< TInputImage >
using	ConstPointer = SmartPointer<const Self>
using	ImageSampleContainerPointer = typename ImageSampleContainerType::Pointer
using	ImageSampleContainerType = VectorDataContainer<ImageSampleType>
using	ImageSampleType = ImageSample<InputImageType>
using	ImageSampleValueType = typename ImageSampleType::RealType
using	InputImageConstPointer = typename InputImageType::ConstPointer
using	InputImageIndexType = typename InputImageType::IndexType
using	InputImagePixelType = typename InputImageType::PixelType
using	InputImagePointer = typename InputImageType::Pointer
using	InputImagePointType = typename InputImageType::PointType
using	InputImagePointValueType = typename InputImagePointType::ValueType
using	InputImageRegionType = typename InputImageType::RegionType
using	InputImageRegionVectorType = std::vector<InputImageRegionType>
using	InputImageSizeType = typename InputImageType::SizeType
using	InputImageType = TInputImage
using	MaskConstPointer = typename MaskType::ConstPointer
using	MaskPointer = typename MaskType::Pointer
using	MaskType = ImageMaskSpatialObject<Self::InputImageDimension>
using	MaskVectorType = std::vector<MaskConstPointer>
using	OutputVectorContainerPointer
using	OutputVectorContainerType
using	Pointer = SmartPointer<Self>
using	Self = ImageSamplerBase
using	Superclass = VectorContainerSource<VectorDataContainer<ImageSample<TInputImage>>>
Public Types inherited from itk::VectorContainerSource< VectorDataContainer< ImageSample< TInputImage > > >
using	ConstPointer
using	OutputVectorContainerPointer
using	OutputVectorContainerType
using	Pointer
using	Self
using	Superclass
Public Types inherited from itk::ImageSamplerBase< TElastix >
using	ConstPointer
using	ImageSampleContainerPointer
using	ImageSampleContainerType
using	ImageSampleType
using	ImageSampleValueType
using	InputImageConstPointer
using	InputImageIndexType
using	InputImagePixelType
using	InputImagePointer
using	InputImagePointType
using	InputImagePointValueType
using	InputImageRegionType
using	InputImageRegionVectorType
using	InputImageSizeType
using	InputImageType
using	MaskConstPointer
using	MaskPointer
using	MaskType
using	MaskVectorType
typedef typename OutputVectorContainerType::Pointer	OutputVectorContainerPointer
typedef VectorDataContainer< ImageSample< TElastix > >	OutputVectorContainerType
using	Pointer
using	Self
using	Superclass
Public Types inherited from itk::VectorContainerSource< TOutputVectorContainer >
using	ConstPointer = SmartPointer<const Self>
using	OutputVectorContainerPointer = typename OutputVectorContainerType::Pointer
using	OutputVectorContainerType = TOutputVectorContainer
using	Pointer = SmartPointer<Self>
using	Self = VectorContainerSource
using	Superclass = ProcessObject

Public Member Functions
void	BeforeEachResolution () override
	elxClassNameMacro ("RandomCoordinate")
	ITK_DISALLOW_COPY_AND_MOVE (RandomCoordinateSampler)
	itkOverrideGetNameOfClassMacro (RandomCoordinateSampler)
	itkStaticConstMacro (InputImageDimension, unsigned int, Superclass1::InputImageDimension)
Public Member Functions inherited from itk::ImageRandomCoordinateSampler< TInputImage >
virtual const InputImageSpacingType &	GetSampleRegionSize ()
virtual bool	GetUseRandomSampleRegion () const
	ITK_DISALLOW_COPY_AND_MOVE (ImageRandomCoordinateSampler)
	itkGetModifiableObjectMacro (Interpolator, InterpolatorType)
	itkOverrideGetNameOfClassMacro (ImageRandomCoordinateSampler)
	itkStaticConstMacro (InputImageDimension, unsigned int, Superclass::InputImageDimension)
virtual void	SetInterpolator (InterpolatorType *_arg)
virtual void	SetSampleRegionSize (InputImageSpacingType _arg)
virtual void	SetUseRandomSampleRegion (bool _arg)
Public Member Functions inherited from itk::ImageRandomSamplerBase< TInputImage >
std::optional< SeedIntegerType >	GetOptionalSeed () const
	ITK_DISALLOW_COPY_AND_MOVE (ImageRandomSamplerBase)
	itkOverrideGetNameOfClassMacro (ImageRandomSamplerBase)
	itkStaticConstMacro (InputImageDimension, unsigned int, Superclass::InputImageDimension)
void	SetOptionalSeed (const std::optional< SeedIntegerType > arg)
void	SetRandomVariateGenerator (Statistics::MersenneTwisterRandomVariateGenerator &randomVariateGenerator)
void	SetSeed (const SeedIntegerType arg)
Public Member Functions inherited from itk::ImageSamplerBase< TInputImage >
virtual const InputImageRegionType &	GetCroppedInputImageRegion ()
const InputImageType *	GetInput ()
const InputImageType *	GetInput (unsigned int idx)
virtual const InputImageRegionType &	GetInputImageRegion () const
virtual const InputImageRegionType &	GetInputImageRegion (unsigned int pos) const
virtual const MaskType *	GetMask () const
virtual const MaskType *	GetMask (unsigned int pos) const
virtual unsigned int	GetNumberOfInputImageRegions () const
virtual unsigned int	GetNumberOfMasks () const
virtual unsigned long	GetNumberOfSamples () const
OutputVectorContainerType *	GetOutput ()
	ITK_DISALLOW_COPY_AND_MOVE (ImageSamplerBase)
	itkOverrideGetNameOfClassMacro (ImageSamplerBase)
	itkStaticConstMacro (InputImageDimension, unsigned int, InputImageType::ImageDimension)
DataObject::Pointer	MakeOutput (ProcessObject::DataObjectPointerArraySizeType idx) override
virtual bool	SelectingNewSamplesOnUpdateSupported () const
virtual bool	SelectNewSamplesOnUpdate ()
void	SetInput (const InputImageType *input)
void	SetInput (unsigned int idx, const InputImageType *input)
virtual void	SetInputImageRegion (const InputImageRegionType _arg)
virtual void	SetInputImageRegion (const InputImageRegionType _arg, unsigned int pos)
virtual void	SetMask (const MaskType *_arg)
virtual void	SetMask (const MaskType *_arg, unsigned int pos)
virtual void	SetNumberOfInputImageRegions (const unsigned int _arg)
virtual void	SetNumberOfMasks (const unsigned int _arg)
virtual void	SetNumberOfSamples (unsigned long _arg)
virtual void	SetUseMultiThread (bool _arg)
Public Member Functions inherited from itk::VectorContainerSource< VectorDataContainer< ImageSample< TInputImage > > >
OutputVectorContainerType *	GetOutput ()
OutputVectorContainerType *	GetOutput (unsigned int idx)
virtual void	GraftNthOutput (unsigned int idx, DataObject *output)
virtual void	GraftOutput (DataObject *output)
	ITK_DISALLOW_COPY_AND_MOVE (VectorContainerSource)
	itkOverrideGetNameOfClassMacro (VectorContainerSource)
DataObjectPointer	MakeOutput (ProcessObject::DataObjectPointerArraySizeType idx) override
Public Member Functions inherited from itk::ImageSamplerBase< TElastix >
virtual const InputImageRegionType &	GetCroppedInputImageRegion ()
const InputImageType *	GetInput ()
const InputImageType *	GetInput (unsigned int idx)
virtual const InputImageRegionType &	GetInputImageRegion () const
virtual const InputImageRegionType &	GetInputImageRegion (unsigned int pos) const
virtual const MaskType *	GetMask () const
virtual const MaskType *	GetMask (unsigned int pos) const
virtual unsigned int	GetNumberOfInputImageRegions () const
virtual unsigned int	GetNumberOfMasks () const
virtual unsigned long	GetNumberOfSamples () const
OutputVectorContainerType *	GetOutput ()
	ITK_DISALLOW_COPY_AND_MOVE (ImageSamplerBase)
	itkOverrideGetNameOfClassMacro (ImageSamplerBase)
	itkStaticConstMacro (InputImageDimension, unsigned int, InputImageType::ImageDimension)
DataObject::Pointer	MakeOutput (ProcessObject::DataObjectPointerArraySizeType idx) override
virtual bool	SelectingNewSamplesOnUpdateSupported () const
virtual bool	SelectNewSamplesOnUpdate ()
void	SetInput (const InputImageType *input)
void	SetInput (unsigned int idx, const InputImageType *input)
virtual void	SetInputImageRegion (const InputImageRegionType _arg)
virtual void	SetInputImageRegion (const InputImageRegionType _arg, unsigned int pos)
virtual void	SetMask (const MaskType *_arg)
virtual void	SetMask (const MaskType *_arg, unsigned int pos)
virtual void	SetNumberOfInputImageRegions (const unsigned int _arg)
virtual void	SetNumberOfMasks (const unsigned int _arg)
virtual void	SetNumberOfSamples (unsigned long _arg)
virtual void	SetUseMultiThread (bool _arg)
Public Member Functions inherited from itk::VectorContainerSource< TOutputVectorContainer >
OutputVectorContainerType *	GetOutput ()
OutputVectorContainerType *	GetOutput (unsigned int idx)
virtual void	GraftNthOutput (unsigned int idx, DataObject *output)
virtual void	GraftOutput (DataObject *output)
	ITK_DISALLOW_COPY_AND_MOVE (VectorContainerSource)
	itkOverrideGetNameOfClassMacro (VectorContainerSource)
DataObjectPointer	MakeOutput (ProcessObject::DataObjectPointerArraySizeType idx) override

Static Public Member Functions
static Pointer	New ()
Static Public Member Functions inherited from itk::ImageRandomCoordinateSampler< TInputImage >
static Pointer	New ()
Static Public Member Functions inherited from itk::ImageRandomSamplerBase< TInputImage >
static Pointer	New ()
Static Public Member Functions inherited from itk::ImageSamplerBase< TInputImage >
static Pointer	New ()
Static Public Member Functions inherited from itk::VectorContainerSource< VectorDataContainer< ImageSample< TInputImage > > >
static Pointer	New ()
Static Public Member Functions inherited from itk::ImageSamplerBase< TElastix >
static Pointer	New ()
Static Public Member Functions inherited from itk::VectorContainerSource< TOutputVectorContainer >
static Pointer	New ()

Protected Member Functions
	RandomCoordinateSampler ()=default
	~RandomCoordinateSampler () override=default
Protected Member Functions inherited from itk::ImageRandomCoordinateSampler< TInputImage >
void	GenerateData () override
virtual void	GenerateRandomCoordinate (const InputImageContinuousIndexType &smallestContIndex, const InputImageContinuousIndexType &largestContIndex, InputImageContinuousIndexType &randomContIndex)
virtual void	GenerateSampleRegion (const InputImageContinuousIndexType &smallestImageContIndex, const InputImageContinuousIndexType &largestImageContIndex, InputImageContinuousIndexType &smallestContIndex, InputImageContinuousIndexType &largestContIndex)
	ImageRandomCoordinateSampler ()=default
void	PrintSelf (std::ostream &os, Indent indent) const override
	~ImageRandomCoordinateSampler () override=default
Protected Member Functions inherited from itk::ImageRandomSamplerBase< TInputImage >
void	GenerateRandomNumberList ()
Statistics::MersenneTwisterRandomVariateGenerator &	GetRandomVariateGenerator ()
	ImageRandomSamplerBase ()
void	PrintSelf (std::ostream &os, Indent indent) const override
	~ImageRandomSamplerBase () override=default
Protected Member Functions inherited from itk::ImageSamplerBase< TInputImage >
virtual bool	CheckInputImageRegions ()
void	CropInputImageRegion ()
void	GenerateInputRequestedRegion () override
	ImageSamplerBase ()
virtual bool	IsInsideAllMasks (const InputImagePointType &point) const
void	PrintSelf (std::ostream &os, Indent indent) const override
virtual void	UpdateAllMasks ()
	~ImageSamplerBase () override=default
Protected Member Functions inherited from itk::VectorContainerSource< VectorDataContainer< ImageSample< TInputImage > > >
void	PrintSelf (std::ostream &os, Indent indent) const override
	VectorContainerSource ()
	~VectorContainerSource () override=default
Protected Member Functions inherited from itk::ImageSamplerBase< TElastix >
virtual bool	CheckInputImageRegions ()
void	CropInputImageRegion ()
void	GenerateInputRequestedRegion () override
	ImageSamplerBase ()
virtual bool	IsInsideAllMasks (const InputImagePointType &point) const
void	PrintSelf (std::ostream &os, Indent indent) const override
virtual void	UpdateAllMasks ()
	~ImageSamplerBase () override=default
Protected Member Functions inherited from itk::VectorContainerSource< TOutputVectorContainer >
void	PrintSelf (std::ostream &os, Indent indent) const override
	VectorContainerSource ()
	~VectorContainerSource () override=default

Private Attributes
	elxOverrideGetSelfMacro

Additional Inherited Members
Protected Types inherited from itk::ImageRandomCoordinateSampler< TInputImage >
using	InputImageContinuousIndexType = typename InterpolatorType::ContinuousIndexType
Static Protected Member Functions inherited from itk::ImageSamplerBase< TInputImage >
static std::vector< InputImageRegionType >	SplitRegion (const InputImageRegionType &inputRegion, const vcl_size_t requestedNumberOfSubregions)
Static Protected Member Functions inherited from itk::ImageSamplerBase< TElastix >
static std::vector< InputImageRegionType >	SplitRegion (const InputImageRegionType &inputRegion, const vcl_size_t requestedNumberOfSubregions)
Protected Attributes inherited from itk::ImageRandomCoordinateSampler< TInputImage >
InterpolatorPointer	m_Interpolator
InputImageSpacingType	m_SampleRegionSize { itk::MakeFilled<InputImageSpacingType>(1.0) }
Protected Attributes inherited from itk::ImageRandomSamplerBase< TInputImage >
std::vector< double >	m_RandomNumberList {}
Protected Attributes inherited from itk::ImageSamplerBase< TInputImage >
unsigned long	m_NumberOfSamples { 0 }
bool	m_UseMultiThread { true }
Protected Attributes inherited from itk::ImageSamplerBase< TElastix >
unsigned long	m_NumberOfSamples
bool	m_UseMultiThread

Member Typedef Documentation

ConstPointer

template<typename TElastix>

using elastix::RandomCoordinateSampler< TElastix >::ConstPointer = itk::SmartPointer<const Self>

Definition at line 90 of file elxRandomCoordinateSampler.h.

ITKBaseType

template<typename TElastix>

using elastix::RandomCoordinateSampler< TElastix >::ITKBaseType = typename Superclass2::ITKBaseType

Definition at line 135 of file elxRandomCoordinateSampler.h.

Pointer

template<typename TElastix>

using elastix::RandomCoordinateSampler< TElastix >::Pointer = itk::SmartPointer<Self>

Definition at line 89 of file elxRandomCoordinateSampler.h.

Self

template<typename TElastix>

using elastix::RandomCoordinateSampler< TElastix >::Self = RandomCoordinateSampler

Standard ITK-stuff.

Definition at line 86 of file elxRandomCoordinateSampler.h.

Superclass1

template<typename TElastix>

using elastix::RandomCoordinateSampler< TElastix >::Superclass1 = itk::ImageRandomCoordinateSampler<typename elx::ImageSamplerBase<TElastix>::InputImageType>

Definition at line 87 of file elxRandomCoordinateSampler.h.

Superclass2

template<typename TElastix>

using elastix::RandomCoordinateSampler< TElastix >::Superclass2 = elx::ImageSamplerBase<TElastix>

Definition at line 88 of file elxRandomCoordinateSampler.h.

Constructor & Destructor Documentation

RandomCoordinateSampler()

template<typename TElastix>

elastix::RandomCoordinateSampler< TElastix >::RandomCoordinateSampler ( )

protecteddefault

The constructor.

~RandomCoordinateSampler()

template<typename TElastix>

elastix::RandomCoordinateSampler< TElastix >::~RandomCoordinateSampler ( )

overrideprotecteddefault

The destructor.

Member Function Documentation

BeforeEachResolution()

template<typename TElastix>

void elastix::RandomCoordinateSampler< TElastix >::BeforeEachResolution ( )

override

Execute stuff before each resolution:

• Set the number of samples.
• Set the fixed image interpolation order
• Set the UseRandomSampleRegion flag and the SampleRegionSize

elxClassNameMacro()

template<typename TElastix>

elastix::RandomCoordinateSampler< TElastix >::elxClassNameMacro

(

"RandomCoordinate"

)

Name of this class. Use this name in the parameter file to select this specific interpolator.
example: (ImageSampler "RandomCoordinate")

ITK_DISALLOW_COPY_AND_MOVE()

template<typename TElastix>

elastix::RandomCoordinateSampler< TElastix >::ITK_DISALLOW_COPY_AND_MOVE

(

RandomCoordinateSampler< TElastix >

)

itkOverrideGetNameOfClassMacro()

template<typename TElastix>

elastix::RandomCoordinateSampler< TElastix >::itkOverrideGetNameOfClassMacro

(

RandomCoordinateSampler< TElastix >

)

Run-time type information (and related methods).

itkStaticConstMacro()

template<typename TElastix>

elastix::RandomCoordinateSampler< TElastix >::itkStaticConstMacro	(	InputImageDimension	,
		unsigned int	,
		Superclass1::InputImageDimension	)

The input image dimension.

New()

template<typename TElastix>

Pointer elastix::RandomCoordinateSampler< TElastix >::New ( )

static

Method for creation through the object factory.

Member Data Documentation

elxOverrideGetSelfMacro

template<typename TElastix>

elastix::RandomCoordinateSampler< TElastix >::elxOverrideGetSelfMacro

private

Definition at line 152 of file elxRandomCoordinateSampler.h.