Derived class implementing a specific patch-based denoising algorithm, as detailed below. More...

#include <sitkPatchBasedDenoisingImageFilter.h>

Inheritance diagram for itk::simple::PatchBasedDenoisingImageFilter:

Collaboration diagram for itk::simple::PatchBasedDenoisingImageFilter:

Detailed Description

Derived class implementing a specific patch-based denoising algorithm, as detailed below.

This class is derived from the base class PatchBasedDenoisingBaseImageFilter ; please refer to the documentation of the base class first. This class implements a denoising filter that uses iterative non-local, or semi-local, weighted averaging of image patches for image denoising. The intensity at each pixel 'p' gets updated as a weighted average of intensities of a chosen subset of pixels from the image.

This class implements the denoising algorithm using a Gaussian kernel function for nonparametric density estimation. The class implements a scheme to automatically estimated the kernel bandwidth parameter (namely, sigma) using leave- one-out cross validation. It implements schemes for random sampling of patches non-locally (from the entire image) as well as semi-locally (from the spatial proximity of the pixel being denoised at the specific point in time). It implements a specific scheme for defining patch weights (mask) as described in Awate and Whitaker 2005 IEEE CVPR and 2006 IEEE TPAMI.

See also: PatchBasedDenoisingBaseImageFilter; itk::PatchBasedDenoisingImageFilter for the Doxygen on the original ITK class.

Definition at line 54 of file sitkPatchBasedDenoisingImageFilter.h.

Public Types
enum	NoiseModelType { NOMODEL , GAUSSIAN , RICIAN , POISSON }

using	PixelIDTypeList = BasicPixelIDTypeList

using	Self = PatchBasedDenoisingImageFilter

Public Types inherited from itk::simple::ImageFilter
using	Self = ImageFilter

Public Types inherited from itk::simple::ProcessObject
using	Self = ProcessObject

Public Member Functions
void	AlwaysTreatComponentsAsEuclideanOff ()

void	AlwaysTreatComponentsAsEuclideanOn ()

Image	Execute (const Image &image1)

bool	GetAlwaysTreatComponentsAsEuclidean () const

bool	GetKernelBandwidthEstimation () const

double	GetKernelBandwidthFractionPixelsForEstimation () const

double	GetKernelBandwidthMultiplicationFactor () const

double	GetKernelBandwidthSigma () const

uint32_t	GetKernelBandwidthUpdateFrequency () const

std::string	GetName () const

NoiseModelType	GetNoiseModel () const

double	GetNoiseModelFidelityWeight () const

double	GetNoiseSigma () const

uint32_t	GetNumberOfIterations () const

uint32_t	GetNumberOfSamplePatches () const

uint32_t	GetPatchRadius () const

double	GetSampleVariance () const

void	KernelBandwidthEstimationOff ()

void	KernelBandwidthEstimationOn ()

	PatchBasedDenoisingImageFilter ()

void	SetAlwaysTreatComponentsAsEuclidean (bool AlwaysTreatComponentsAsEuclidean)

void	SetKernelBandwidthEstimation (bool KernelBandwidthEstimation)

void	SetKernelBandwidthFractionPixelsForEstimation (double KernelBandwidthFractionPixelsForEstimation)

void	SetKernelBandwidthMultiplicationFactor (double KernelBandwidthMultiplicationFactor)

void	SetKernelBandwidthSigma (double KernelBandwidthSigma)

void	SetKernelBandwidthUpdateFrequency (uint32_t KernelBandwidthUpdateFrequency)

void	SetNoiseModel (NoiseModelType NoiseModel)

void	SetNoiseModelFidelityWeight (double NoiseModelFidelityWeight)

void	SetNoiseSigma (double NoiseSigma)

void	SetNumberOfIterations (uint32_t NumberOfIterations)

void	SetNumberOfSamplePatches (uint32_t NumberOfSamplePatches)

void	SetPatchRadius (uint32_t PatchRadius)

void	SetSampleVariance (double SampleVariance)

std::string	ToString () const

virtual	~PatchBasedDenoisingImageFilter ()

Public Member Functions inherited from itk::simple::ImageFilter
	ImageFilter ()

virtual	~ImageFilter ()=0

Public Member Functions inherited from itk::simple::ProcessObject
virtual void	Abort ()

virtual int	AddCommand (itk::simple::EventEnum event, const std::function< void()> &func)
	Directly add a callback to observe an event.

virtual int	AddCommand (itk::simple::EventEnum event, itk::simple::Command &cmd)
	Add a Command Object to observer the event.

virtual float	GetProgress () const
	An Active Measurement of the progress of execution.

virtual bool	HasCommand (itk::simple::EventEnum event) const
	Query of this object has any registered commands for event.

	ProcessObject ()

virtual void	RemoveAllCommands ()
	Remove all registered commands.

virtual	~ProcessObject ()

virtual void	DebugOn ()

virtual void	DebugOff ()

virtual bool	GetDebug () const

virtual void	SetDebug (bool debugFlag)

virtual void	SetNumberOfThreads (unsigned int n)

virtual unsigned int	GetNumberOfThreads () const

virtual void	SetNumberOfWorkUnits (unsigned int n)

virtual unsigned int	GetNumberOfWorkUnits () const

Private Types
using	MemberFunctionType = Image (Self::*)(const Image &image1)

Private Member Functions
template<class TImageType>
Image	ExecuteInternal (const Image &image1)

Static Private Member Functions
static const detail::MemberFunctionFactory< MemberFunctionType > &	GetMemberFunctionFactory ()

Private Attributes
bool	m_AlwaysTreatComponentsAsEuclidean { false }

bool	m_KernelBandwidthEstimation { false }

double	m_KernelBandwidthFractionPixelsForEstimation { 0.2 }

double	m_KernelBandwidthMultiplicationFactor { 1.0 }

double	m_KernelBandwidthSigma { 400.0 }

uint32_t	m_KernelBandwidthUpdateFrequency { 3u }

NoiseModelType	m_NoiseModel { itk::simple::PatchBasedDenoisingImageFilter::NOMODEL }

double	m_NoiseModelFidelityWeight { 0.0 }

double	m_NoiseSigma { 0.0 }

uint32_t	m_NumberOfIterations { 1u }

uint32_t	m_NumberOfSamplePatches { 200u }

uint32_t	m_PatchRadius { 4u }

double	m_SampleVariance { 400.0 }

Friends
struct	detail::MemberFunctionAddressor< MemberFunctionType >

Additional Inherited Members
Static Public Member Functions inherited from itk::simple::ProcessObject
static bool	GetGlobalDefaultDebug ()

static void	GlobalDefaultDebugOff ()

static void	GlobalDefaultDebugOn ()

static void	SetGlobalDefaultDebug (bool debugFlag)

static void	GlobalWarningDisplayOn ()

static void	GlobalWarningDisplayOff ()

static void	SetGlobalWarningDisplay (bool flag)

static bool	GetGlobalWarningDisplay ()

static double	GetGlobalDefaultCoordinateTolerance ()
	Access the global tolerance to determine congruent spaces.

static void	SetGlobalDefaultCoordinateTolerance (double)
	Access the global tolerance to determine congruent spaces.

static double	GetGlobalDefaultDirectionTolerance ()
	Access the global tolerance to determine congruent spaces.

static void	SetGlobalDefaultDirectionTolerance (double)
	Access the global tolerance to determine congruent spaces.

static bool	SetGlobalDefaultThreader (const std::string &threader)
	Set/Get the default threader used for process objects.

static std::string	GetGlobalDefaultThreader ()
	Set/Get the default threader used for process objects.

static void	SetGlobalDefaultNumberOfThreads (unsigned int n)

static unsigned int	GetGlobalDefaultNumberOfThreads ()
	Set/Get the default threader used for process objects.

Protected Member Functions inherited from itk::simple::ImageFilter
void	CheckImageMatchingDimension (const Image &image1, const Image &image2, const std::string &image2Name)

void	CheckImageMatchingPixelType (const Image &image1, const Image &image2, const std::string &image2Name)

void	CheckImageMatchingSize (const Image &image1, const Image &image2, const std::string &image2Name)

Protected Member Functions inherited from itk::simple::ProcessObject
virtual unsigned long	AddITKObserver (const itk::EventObject &, itk::Command *)

virtual itk::ProcessObject *	GetActiveProcess ()

virtual void	OnActiveProcessDelete ()

virtual void	onCommandDelete (const itk::simple::Command *cmd) noexcept

virtual void	PreUpdate (itk::ProcessObject *p)

virtual void	RemoveITKObserver (EventCommand &e)

Protected Member Functions inherited from itk::simple::NonCopyable
	NonCopyable ()=default

	NonCopyable (const NonCopyable &)=delete

NonCopyable &	operator= (const NonCopyable &)=delete

Static Protected Member Functions inherited from itk::simple::ImageFilter
template<class TImageType>
static void	FixNonZeroIndex (TImageType *img)

Static Protected Member Functions inherited from itk::simple::ProcessObject
template<class TImageType>
static TImageType::ConstPointer	CastImageToITK (const Image &img)

template<class TPixelType, unsigned int VImageDimension, unsigned int VLength, template< typename, unsigned int > class TVector>
static Image	CastITKToImage (itk::Image< TVector< TPixelType, VLength >, VImageDimension > *img)

template<unsigned int VImageDimension, unsigned int VLength, template< unsigned int > class TVector>
static Image	CastITKToImage (itk::Image< TVector< VLength >, VImageDimension > *img)

template<class TImageType>
static Image	CastITKToImage (TImageType *img)

static const itk::EventObject &	GetITKEventObject (EventEnum e)

template<typename T>
static std::ostream &	ToStringHelper (std::ostream &os, const T &v)

static std::ostream &	ToStringHelper (std::ostream &os, const char &v)

static std::ostream &	ToStringHelper (std::ostream &os, const signed char &v)

static std::ostream &	ToStringHelper (std::ostream &os, const unsigned char &v)

Member Typedef Documentation

◆ MemberFunctionType

using itk::simple::PatchBasedDenoisingImageFilter::MemberFunctionType = Image (Self::*)(const Image &image1)

private

Setup for member function dispatching

Definition at line 286 of file sitkPatchBasedDenoisingImageFilter.h.

◆ PixelIDTypeList

using itk::simple::PatchBasedDenoisingImageFilter::PixelIDTypeList = BasicPixelIDTypeList

Define the pixels types supported by this filter

Definition at line 66 of file sitkPatchBasedDenoisingImageFilter.h.

◆ Self

using itk::simple::PatchBasedDenoisingImageFilter::Self = PatchBasedDenoisingImageFilter

Definition at line 56 of file sitkPatchBasedDenoisingImageFilter.h.

Member Enumeration Documentation

◆ NoiseModelType

enum itk::simple::PatchBasedDenoisingImageFilter::NoiseModelType

Enumerator
NOMODEL
GAUSSIAN
RICIAN
POISSON

Definition at line 138 of file sitkPatchBasedDenoisingImageFilter.h.

Constructor & Destructor Documentation

◆ ~PatchBasedDenoisingImageFilter()

virtual itk::simple::PatchBasedDenoisingImageFilter::~PatchBasedDenoisingImageFilter ( )

virtual

Destructor

◆ PatchBasedDenoisingImageFilter()

itk::simple::PatchBasedDenoisingImageFilter::PatchBasedDenoisingImageFilter ( )

Default Constructor that takes no arguments and initializes default parameters

Member Function Documentation

◆ AlwaysTreatComponentsAsEuclideanOff()

void itk::simple::PatchBasedDenoisingImageFilter::AlwaysTreatComponentsAsEuclideanOff ( )

inline

Definition at line 194 of file sitkPatchBasedDenoisingImageFilter.h.

References SetAlwaysTreatComponentsAsEuclidean().

◆ AlwaysTreatComponentsAsEuclideanOn()

void itk::simple::PatchBasedDenoisingImageFilter::AlwaysTreatComponentsAsEuclideanOn ( )

inline

Set the value of AlwaysTreatComponentsAsEuclidean to true or false respectfully.

Definition at line 192 of file sitkPatchBasedDenoisingImageFilter.h.

References SetAlwaysTreatComponentsAsEuclidean().

◆ Execute()

Image itk::simple::PatchBasedDenoisingImageFilter::Execute ( const Image & image1 )

Execute the filter on the input image

◆ ExecuteInternal()

template<class TImageType>

Image itk::simple::PatchBasedDenoisingImageFilter::ExecuteInternal ( const Image & image1 )

private

Referenced by detail::MemberFunctionAddressor< MemberFunctionType >.

◆ GetAlwaysTreatComponentsAsEuclidean()

bool itk::simple::PatchBasedDenoisingImageFilter::GetAlwaysTreatComponentsAsEuclidean ( ) const

inline

Set/Get flag indicating whether all components should always be treated as if they are in euclidean space regardless of pixel type. Defaults to false.

Definition at line 200 of file sitkPatchBasedDenoisingImageFilter.h.

References m_AlwaysTreatComponentsAsEuclidean.

◆ GetKernelBandwidthEstimation()

bool itk::simple::PatchBasedDenoisingImageFilter::GetKernelBandwidthEstimation ( ) const

inline

Set/Get flag indicating whether kernel-bandwidth should be estimated automatically from the image data. Defaults to true.

Definition at line 221 of file sitkPatchBasedDenoisingImageFilter.h.

References m_KernelBandwidthEstimation.

◆ GetKernelBandwidthFractionPixelsForEstimation()

double itk::simple::PatchBasedDenoisingImageFilter::GetKernelBandwidthFractionPixelsForEstimation ( ) const

inline

Set/Get the fraction of the image to use for kernel bandwidth sigma estimation. To reduce the computational burden for computing sigma, a small random fraction of the image pixels can be used.

Definition at line 270 of file sitkPatchBasedDenoisingImageFilter.h.

References m_KernelBandwidthFractionPixelsForEstimation.

◆ GetKernelBandwidthMultiplicationFactor()

double itk::simple::PatchBasedDenoisingImageFilter::GetKernelBandwidthMultiplicationFactor ( ) const

inline

Set/Get the kernel bandwidth sigma multiplication factor used to modify the automatically-estimated kernel bandwidth sigma. At times, it may be desirable to modify the value of the automatically-estimated sigma. Typically, this number isn't very far from 1. Note: This is used only when KernelBandwidthEstimation is True/On.

Definition at line 238 of file sitkPatchBasedDenoisingImageFilter.h.

References m_KernelBandwidthMultiplicationFactor.

◆ GetKernelBandwidthSigma()

double itk::simple::PatchBasedDenoisingImageFilter::GetKernelBandwidthSigma ( ) const

inline

Set/Get initial kernel bandwidth estimate. To prevent the class from automatically modifying this estimate, set KernelBandwidthEstimation to false in the base class.

Definition at line 83 of file sitkPatchBasedDenoisingImageFilter.h.

References m_KernelBandwidthSigma.

◆ GetKernelBandwidthUpdateFrequency()

uint32_t itk::simple::PatchBasedDenoisingImageFilter::GetKernelBandwidthUpdateFrequency ( ) const

inline

Set/Get the update frequency for the kernel bandwidth estimation. An optimal bandwidth will be re-estimated based on the denoised image after every 'n' iterations. Must be a positive integer. Defaults to 3, i.e. bandwidth updated after every 3 denoising iteration.

Definition at line 255 of file sitkPatchBasedDenoisingImageFilter.h.

References m_KernelBandwidthUpdateFrequency.

◆ GetMemberFunctionFactory()

static const detail::MemberFunctionFactory< MemberFunctionType > & itk::simple::PatchBasedDenoisingImageFilter::GetMemberFunctionFactory ( )

staticprivate

◆ GetName()

std::string itk::simple::PatchBasedDenoisingImageFilter::GetName ( ) const

inlinevirtual

Name of this class

Implements itk::simple::ProcessObject.

Definition at line 274 of file sitkPatchBasedDenoisingImageFilter.h.

◆ GetNoiseModel()

NoiseModelType itk::simple::PatchBasedDenoisingImageFilter::GetNoiseModel ( ) const

inline

Set/Get the noise model type. Defaults to GAUSSIAN. To use the noise model during denoising, FidelityWeight must be positive.

Definition at line 152 of file sitkPatchBasedDenoisingImageFilter.h.

References m_NoiseModel.

◆ GetNoiseModelFidelityWeight()

double itk::simple::PatchBasedDenoisingImageFilter::GetNoiseModelFidelityWeight ( ) const

inline

Set/Get the weight on the fidelity term (penalizes deviations from the noisy data). This option is used when a noise model is specified. This weight controls the balance between the smoothing and the closeness to the noisy data.

Definition at line 179 of file sitkPatchBasedDenoisingImageFilter.h.

References m_NoiseModelFidelityWeight.

◆ GetNoiseSigma()

double itk::simple::PatchBasedDenoisingImageFilter::GetNoiseSigma ( ) const

inline

Definition at line 164 of file sitkPatchBasedDenoisingImageFilter.h.

References m_NoiseSigma.

◆ GetNumberOfIterations()

uint32_t itk::simple::PatchBasedDenoisingImageFilter::GetNumberOfIterations ( ) const

inline

Set/Get the number of denoising iterations to perform. Must be a positive integer. Defaults to 1.

Definition at line 111 of file sitkPatchBasedDenoisingImageFilter.h.

References m_NumberOfIterations.

◆ GetNumberOfSamplePatches()

uint32_t itk::simple::PatchBasedDenoisingImageFilter::GetNumberOfSamplePatches ( ) const

inline

Definition at line 123 of file sitkPatchBasedDenoisingImageFilter.h.

References m_NumberOfSamplePatches.

◆ GetPatchRadius()

uint32_t itk::simple::PatchBasedDenoisingImageFilter::GetPatchRadius ( ) const

inline

Set/Get the patch radius specified in physical coordinates. Patch radius is preferably set to an even number. Currently, only isotropic patches in physical space are allowed; patches can be anisotropic in voxel space.

Definition at line 98 of file sitkPatchBasedDenoisingImageFilter.h.

References m_PatchRadius.

◆ GetSampleVariance()

double itk::simple::PatchBasedDenoisingImageFilter::GetSampleVariance ( ) const

inline

Set/Get the variance of the domain where patches are sampled.

Definition at line 136 of file sitkPatchBasedDenoisingImageFilter.h.

References m_SampleVariance.

◆ KernelBandwidthEstimationOff()

void itk::simple::PatchBasedDenoisingImageFilter::KernelBandwidthEstimationOff ( )

inline

Definition at line 215 of file sitkPatchBasedDenoisingImageFilter.h.

References SetKernelBandwidthEstimation().

◆ KernelBandwidthEstimationOn()

void itk::simple::PatchBasedDenoisingImageFilter::KernelBandwidthEstimationOn ( )

inline

Set the value of KernelBandwidthEstimation to true or false respectfully.

Definition at line 213 of file sitkPatchBasedDenoisingImageFilter.h.

References SetKernelBandwidthEstimation().

◆ SetAlwaysTreatComponentsAsEuclidean()

void itk::simple::PatchBasedDenoisingImageFilter::SetAlwaysTreatComponentsAsEuclidean ( bool AlwaysTreatComponentsAsEuclidean )

inline

Set/Get flag indicating whether all components should always be treated as if they are in euclidean space regardless of pixel type. Defaults to false.

Definition at line 187 of file sitkPatchBasedDenoisingImageFilter.h.

References m_AlwaysTreatComponentsAsEuclidean.

Referenced by AlwaysTreatComponentsAsEuclideanOff(), and AlwaysTreatComponentsAsEuclideanOn().

◆ SetKernelBandwidthEstimation()

void itk::simple::PatchBasedDenoisingImageFilter::SetKernelBandwidthEstimation ( bool KernelBandwidthEstimation )

inline

Set/Get flag indicating whether kernel-bandwidth should be estimated automatically from the image data. Defaults to true.

Definition at line 208 of file sitkPatchBasedDenoisingImageFilter.h.

References m_KernelBandwidthEstimation.

Referenced by KernelBandwidthEstimationOff(), and KernelBandwidthEstimationOn().

◆ SetKernelBandwidthFractionPixelsForEstimation()

void itk::simple::PatchBasedDenoisingImageFilter::SetKernelBandwidthFractionPixelsForEstimation ( double KernelBandwidthFractionPixelsForEstimation )

inline

Set/Get the fraction of the image to use for kernel bandwidth sigma estimation. To reduce the computational burden for computing sigma, a small random fraction of the image pixels can be used.

Definition at line 263 of file sitkPatchBasedDenoisingImageFilter.h.

References m_KernelBandwidthFractionPixelsForEstimation.

◆ SetKernelBandwidthMultiplicationFactor()

void itk::simple::PatchBasedDenoisingImageFilter::SetKernelBandwidthMultiplicationFactor ( double KernelBandwidthMultiplicationFactor )

inline

Set/Get the kernel bandwidth sigma multiplication factor used to modify the automatically-estimated kernel bandwidth sigma. At times, it may be desirable to modify the value of the automatically-estimated sigma. Typically, this number isn't very far from 1. Note: This is used only when KernelBandwidthEstimation is True/On.

Definition at line 230 of file sitkPatchBasedDenoisingImageFilter.h.

References m_KernelBandwidthMultiplicationFactor.

◆ SetKernelBandwidthSigma()

void itk::simple::PatchBasedDenoisingImageFilter::SetKernelBandwidthSigma ( double KernelBandwidthSigma )

inline

Set/Get initial kernel bandwidth estimate. To prevent the class from automatically modifying this estimate, set KernelBandwidthEstimation to false in the base class.

Definition at line 76 of file sitkPatchBasedDenoisingImageFilter.h.

References m_KernelBandwidthSigma.

◆ SetKernelBandwidthUpdateFrequency()

void itk::simple::PatchBasedDenoisingImageFilter::SetKernelBandwidthUpdateFrequency ( uint32_t KernelBandwidthUpdateFrequency )

inline

Set/Get the update frequency for the kernel bandwidth estimation. An optimal bandwidth will be re-estimated based on the denoised image after every 'n' iterations. Must be a positive integer. Defaults to 3, i.e. bandwidth updated after every 3 denoising iteration.

Definition at line 247 of file sitkPatchBasedDenoisingImageFilter.h.

References m_KernelBandwidthUpdateFrequency.

◆ SetNoiseModel()

void itk::simple::PatchBasedDenoisingImageFilter::SetNoiseModel ( NoiseModelType NoiseModel )

inline

Set/Get the noise model type. Defaults to GAUSSIAN. To use the noise model during denoising, FidelityWeight must be positive.

Definition at line 145 of file sitkPatchBasedDenoisingImageFilter.h.

References m_NoiseModel.

◆ SetNoiseModelFidelityWeight()

void itk::simple::PatchBasedDenoisingImageFilter::SetNoiseModelFidelityWeight ( double NoiseModelFidelityWeight )

inline

Set/Get the weight on the fidelity term (penalizes deviations from the noisy data). This option is used when a noise model is specified. This weight controls the balance between the smoothing and the closeness to the noisy data.

Definition at line 172 of file sitkPatchBasedDenoisingImageFilter.h.

References m_NoiseModelFidelityWeight.

◆ SetNoiseSigma()

void itk::simple::PatchBasedDenoisingImageFilter::SetNoiseSigma ( double NoiseSigma )

inline

Set/Get the noise sigma. Used by the noise model where appropriate, defaults to 5% of the image intensity range

Definition at line 159 of file sitkPatchBasedDenoisingImageFilter.h.

References m_NoiseSigma.

◆ SetNumberOfIterations()

void itk::simple::PatchBasedDenoisingImageFilter::SetNumberOfIterations ( uint32_t NumberOfIterations )

inline

Set/Get the number of denoising iterations to perform. Must be a positive integer. Defaults to 1.

Definition at line 105 of file sitkPatchBasedDenoisingImageFilter.h.

References m_NumberOfIterations.

◆ SetNumberOfSamplePatches()

void itk::simple::PatchBasedDenoisingImageFilter::SetNumberOfSamplePatches ( uint32_t NumberOfSamplePatches )

inline

Set/Get the number of patches to sample for each pixel.

Definition at line 118 of file sitkPatchBasedDenoisingImageFilter.h.

References m_NumberOfSamplePatches.

◆ SetPatchRadius()

void itk::simple::PatchBasedDenoisingImageFilter::SetPatchRadius ( uint32_t PatchRadius )

inline

Set/Get the patch radius specified in physical coordinates. Patch radius is preferably set to an even number. Currently, only isotropic patches in physical space are allowed; patches can be anisotropic in voxel space.

Definition at line 91 of file sitkPatchBasedDenoisingImageFilter.h.

References m_PatchRadius.