Normalize the grayscale values for a source image by matching the shape of the source image histogram to a reference histogram. More...

#include <sitkHistogramMatchingImageFilter.h>

Inheritance diagram for itk::simple::HistogramMatchingImageFilter:

Collaboration diagram for itk::simple::HistogramMatchingImageFilter:

Detailed Description

Normalize the grayscale values for a source image by matching the shape of the source image histogram to a reference histogram.

HistogramMatchingImageFilter normalizes the grayscale values of a source image based on the grayscale values of either a reference image or a reference histogram. This filter uses a histogram matching technique where the histograms of the are matched only at a specified number of quantile values.

This filter was originally designed to normalize MR images of the same MR protocol and same body part. The algorithm works best if background pixels are excluded from both the source and reference histograms. A simple background exclusion method is to exclude all pixels whose grayscale values are smaller than the mean grayscale value. ThresholdAtMeanIntensityOn() switches on this simple background exclusion method. With ThresholdAtMeanIntensityOn() , The reference histogram returned from this filter will expand the first and last bin bounds to include the minimum and maximum intensity values of the entire reference image, but only intensity values greater than the mean will be used to populate the histogram.

The source image can be set via either SetInput() or SetSourceImage(). The reference object used is selected with can be set via SetReferenceImage() or SetReferenceHistogram().

SetNumberOfHistogramLevels() sets the number of bins used when creating histograms of the source and reference images. SetNumberOfMatchPoints() governs the number of quantile values to be matched.

This filter assumes that both the source and reference are of the same type and that the input and output image type have the same number of dimension and have scalar pixel types.

REFERENCE: Laszlo G. Nyul, Jayaram K. Udupa, and Xuan Zhang, "New Variants of a Method of MRI Scale Standardization", IEEE Transactions on Medical Imaging, 19(2):143-150, 2000.

See also: itk::simple::HistogramMatching for the procedural interface; itk::HistogramMatchingImageFilter for the Doxygen on the original ITK class.

Examples: DemonsRegistration1/DemonsRegistration1.cxx, and DemonsRegistration2/DemonsRegistration2.cxx.

Definition at line 53 of file sitkHistogramMatchingImageFilter.h.

Public Types
using	PixelIDTypeList = BasicPixelIDTypeList

using	Self = HistogramMatchingImageFilter

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

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

Public Member Functions
Image	Execute (const Image &image, const Image &referenceImage)

std::string	GetName () const

uint32_t	GetNumberOfHistogramLevels () const

uint32_t	GetNumberOfMatchPoints () const

bool	GetThresholdAtMeanIntensity () const

	HistogramMatchingImageFilter ()

Self &	SetNumberOfHistogramLevels (uint32_t NumberOfHistogramLevels)

Self &	SetNumberOfMatchPoints (uint32_t NumberOfMatchPoints)

Self &	SetThresholdAtMeanIntensity (bool ThresholdAtMeanIntensity)

Self &	ThresholdAtMeanIntensityOff ()

Self &	ThresholdAtMeanIntensityOn ()

std::string	ToString () const

virtual	~HistogramMatchingImageFilter ()

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. More...

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

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

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

	ProcessObject ()

virtual void	RemoveAllCommands ()
	Remove all registered commands. More...

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 image, const Image *referenceImage)

Private Member Functions
template<class TImageType >
Image	ExecuteInternal (const Image image, const Image referenceImage)

Private Attributes
std::unique_ptr< detail::MemberFunctionFactory< MemberFunctionType > >	m_MemberFactory

uint32_t	m_NumberOfHistogramLevels {256u}

uint32_t	m_NumberOfMatchPoints {1u}

bool	m_ThresholdAtMeanIntensity {true}

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. More...

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

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

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

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

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

static void	SetGlobalDefaultNumberOfThreads (unsigned int n)

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

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::HistogramMatchingImageFilter::MemberFunctionType = Image (Self::*)( const Image * image, const Image * referenceImage )

private

Setup for member function dispatching

Definition at line 117 of file sitkHistogramMatchingImageFilter.h.

◆ PixelIDTypeList

using itk::simple::HistogramMatchingImageFilter::PixelIDTypeList = BasicPixelIDTypeList

Define the pixels types supported by this filter

Definition at line 65 of file sitkHistogramMatchingImageFilter.h.

◆ Self

using itk::simple::HistogramMatchingImageFilter::Self = HistogramMatchingImageFilter

Definition at line 55 of file sitkHistogramMatchingImageFilter.h.

Constructor & Destructor Documentation

◆ ~HistogramMatchingImageFilter()

virtual itk::simple::HistogramMatchingImageFilter::~HistogramMatchingImageFilter ( )

virtual

Destructor

◆ HistogramMatchingImageFilter()

itk::simple::HistogramMatchingImageFilter::HistogramMatchingImageFilter ( )

Default Constructor that takes no arguments and initializes default parameters

Member Function Documentation

◆ Execute()

Image itk::simple::HistogramMatchingImageFilter::Execute	(	const Image &	image,
		const Image &	referenceImage
	)

Execute the filter on the input image

Examples: DemonsRegistration1/DemonsRegistration1.cxx, and DemonsRegistration2/DemonsRegistration2.cxx.

◆ ExecuteInternal()

template<class TImageType >

Image itk::simple::HistogramMatchingImageFilter::ExecuteInternal	(	const Image *	image,
		const Image *	referenceImage
	)

private

◆ GetName()

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

inlinevirtual

Name of this class

Implements itk::simple::ProcessObject.

Definition at line 103 of file sitkHistogramMatchingImageFilter.h.

◆ GetNumberOfHistogramLevels()

uint32_t itk::simple::HistogramMatchingImageFilter::GetNumberOfHistogramLevels ( ) const

inline

Set/Get the number of histogram levels used.

Definition at line 76 of file sitkHistogramMatchingImageFilter.h.

◆ GetNumberOfMatchPoints()

uint32_t itk::simple::HistogramMatchingImageFilter::GetNumberOfMatchPoints ( ) const

inline

Set/Get the number of match points used.

Definition at line 86 of file sitkHistogramMatchingImageFilter.h.

◆ GetThresholdAtMeanIntensity()

bool itk::simple::HistogramMatchingImageFilter::GetThresholdAtMeanIntensity ( ) const

inline

Set/Get the threshold at mean intensity flag. If true, only source (reference) pixels which are greater than the mean source (reference) intensity is used in the histogram matching. If false, all pixels are used.

Definition at line 100 of file sitkHistogramMatchingImageFilter.h.

◆ SetNumberOfHistogramLevels()

Self& itk::simple::HistogramMatchingImageFilter::SetNumberOfHistogramLevels ( uint32_t NumberOfHistogramLevels )

inline

Set/Get the number of histogram levels used.

Examples: DemonsRegistration1/DemonsRegistration1.cxx, and DemonsRegistration2/DemonsRegistration2.cxx.

Definition at line 71 of file sitkHistogramMatchingImageFilter.h.

◆ SetNumberOfMatchPoints()

Self& itk::simple::HistogramMatchingImageFilter::SetNumberOfMatchPoints ( uint32_t NumberOfMatchPoints )

inline

Set/Get the number of match points used.

Examples: DemonsRegistration1/DemonsRegistration1.cxx, and DemonsRegistration2/DemonsRegistration2.cxx.

Definition at line 81 of file sitkHistogramMatchingImageFilter.h.

◆ SetThresholdAtMeanIntensity()

Self& itk::simple::HistogramMatchingImageFilter::SetThresholdAtMeanIntensity ( bool ThresholdAtMeanIntensity )

inline

Set/Get the threshold at mean intensity flag. If true, only source (reference) pixels which are greater than the mean source (reference) intensity is used in the histogram matching. If false, all pixels are used.

Definition at line 91 of file sitkHistogramMatchingImageFilter.h.