Segment pixels with similar statistics using connectivity. More...

#include <sitkConfidenceConnectedImageFilter.h>

Inheritance diagram for itk::simple::ConfidenceConnectedImageFilter:

Collaboration diagram for itk::simple::ConfidenceConnectedImageFilter:

Detailed Description

Segment pixels with similar statistics using connectivity.

This filter extracts a connected set of pixels whose pixel intensities are consistent with the pixel statistics of a seed point. The mean and variance across a neighborhood (8-connected, 26-connected, etc.) are calculated for a seed point. Then pixels connected to this seed point whose values are within the confidence interval for the seed point are grouped. The width of the confidence interval is controlled by the "Multiplier" variable (the confidence interval is the mean plus or minus the "Multiplier" times the standard deviation). If the intensity variations across a segment were gaussian, a "Multiplier" setting of 2.5 would define a confidence interval wide enough to capture 99% of samples in the segment.

After this initial segmentation is calculated, the mean and variance are re-calculated. All the pixels in the previous segmentation are used to calculate the mean the standard deviation (as opposed to using the pixels in the neighborhood of the seed point). The segmentation is then recalculated using these refined estimates for the mean and variance of the pixel values. This process is repeated for the specified number of iterations. Setting the "NumberOfIterations" to zero stops the algorithm after the initial segmentation from the seed point.

NOTE: the lower and upper threshold are restricted to lie within the valid numeric limits of the input data pixel type. Also, the limits may be adjusted to contain the seed point's intensity.

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

Definition at line 45 of file sitkConfidenceConnectedImageFilter.h.

Public Types
using	PixelIDTypeList = BasicPixelIDTypeList

using	Self = ConfidenceConnectedImageFilter

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

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

Public Member Functions
Self &	AddSeed (std::vector< unsigned int > point)
	Add SeedList point. More...

Self &	ClearSeeds ()
	Remove all SeedList points. More...

	ConfidenceConnectedImageFilter ()

Image	Execute (const Image &image1)

unsigned int	GetInitialNeighborhoodRadius () const

double	GetMean () const

double	GetMultiplier () const

std::string	GetName () const

unsigned int	GetNumberOfIterations () const

uint8_t	GetReplaceValue () const

std::vector< std::vector< unsigned int > >	GetSeedList () const
	Get list of seeds. More...

double	GetVariance () const

Self &	SetInitialNeighborhoodRadius (unsigned int InitialNeighborhoodRadius)

Self &	SetMultiplier (double Multiplier)

Self &	SetNumberOfIterations (unsigned int NumberOfIterations)

Self &	SetReplaceValue (uint8_t ReplaceValue)

Self &	SetSeedList (std::vector< std::vector< unsigned int > > SeedList)
	Set list of image indexes for seeds. More...

std::string	ToString () const

virtual	~ConfidenceConnectedImageFilter ()

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 &image1)

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

Private Attributes
unsigned int	m_InitialNeighborhoodRadius {1u}

double	m_Mean {0.0}

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

double	m_Multiplier {4.5}

unsigned int	m_NumberOfIterations {4u}

uint8_t	m_ReplaceValue {1u}

std::vector< std::vector< unsigned int > >	m_SeedList {std::vector< std::vector<unsigned int > >()}

double	m_Variance {0.0}

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. 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::ConfidenceConnectedImageFilter::MemberFunctionType = Image (Self::*)( const Image& image1 )

private

Setup for member function dispatching

Definition at line 146 of file sitkConfidenceConnectedImageFilter.h.

◆ PixelIDTypeList

using itk::simple::ConfidenceConnectedImageFilter::PixelIDTypeList = BasicPixelIDTypeList

Define the pixels types supported by this filter

Definition at line 57 of file sitkConfidenceConnectedImageFilter.h.

◆ Self

using itk::simple::ConfidenceConnectedImageFilter::Self = ConfidenceConnectedImageFilter

Definition at line 47 of file sitkConfidenceConnectedImageFilter.h.

Constructor & Destructor Documentation

◆ ~ConfidenceConnectedImageFilter()

virtual itk::simple::ConfidenceConnectedImageFilter::~ConfidenceConnectedImageFilter ( )

virtual

Destructor

◆ ConfidenceConnectedImageFilter()

itk::simple::ConfidenceConnectedImageFilter::ConfidenceConnectedImageFilter ( )

Default Constructor that takes no arguments and initializes default parameters

Member Function Documentation

◆ AddSeed()

Self& itk::simple::ConfidenceConnectedImageFilter::AddSeed ( std::vector< unsigned int > point )

inline

Add SeedList point.

Definition at line 70 of file sitkConfidenceConnectedImageFilter.h.

References itk::point().

◆ ClearSeeds()

Self& itk::simple::ConfidenceConnectedImageFilter::ClearSeeds ( )

inline

Remove all SeedList points.

Definition at line 72 of file sitkConfidenceConnectedImageFilter.h.

◆ Execute()

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

Execute the filter on the input image

◆ ExecuteInternal()

template<class TImageType >

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

private

◆ GetInitialNeighborhoodRadius()

unsigned int itk::simple::ConfidenceConnectedImageFilter::GetInitialNeighborhoodRadius ( ) const

inline

Get/Set the radius of the neighborhood over which the statistics are evaluated

Definition at line 103 of file sitkConfidenceConnectedImageFilter.h.

◆ GetMean()

double itk::simple::ConfidenceConnectedImageFilter::GetMean ( ) const

inline

Method to get access to the mean of the pixels accepted in the output region. This method should only be invoked after the filter has been executed using the Update() method.

This is a measurement. Its value is updated in the Execute methods, so the value will only be valid after an execution.

Definition at line 120 of file sitkConfidenceConnectedImageFilter.h.

◆ GetMultiplier()

double itk::simple::ConfidenceConnectedImageFilter::GetMultiplier ( ) const

inline

Set/Get the multiplier to define the confidence interval. Multiplier can be anything greater than zero. A typical value is 2.5

Definition at line 93 of file sitkConfidenceConnectedImageFilter.h.

◆ GetName()

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

inlinevirtual

Name of this class

Implements itk::simple::ProcessObject.

Definition at line 132 of file sitkConfidenceConnectedImageFilter.h.

◆ GetNumberOfIterations()

unsigned int itk::simple::ConfidenceConnectedImageFilter::GetNumberOfIterations ( ) const

inline

Set/Get the number of iterations

Definition at line 83 of file sitkConfidenceConnectedImageFilter.h.

◆ GetReplaceValue()

uint8_t itk::simple::ConfidenceConnectedImageFilter::GetReplaceValue ( ) const

inline

Set/Get value to replace thresholded pixels

Definition at line 113 of file sitkConfidenceConnectedImageFilter.h.

◆ GetSeedList()

std::vector< std::vector< unsigned int > > itk::simple::ConfidenceConnectedImageFilter::GetSeedList ( ) const

inline

Get list of seeds.

Definition at line 68 of file sitkConfidenceConnectedImageFilter.h.

◆ GetVariance()

double itk::simple::ConfidenceConnectedImageFilter::GetVariance ( ) const

inline

Method to get access to the variance of the pixels accepted in the output region. This method should only be invoked after the filter has been executed using the Update() method.

This is a measurement. Its value is updated in the Execute methods, so the value will only be valid after an execution.

Definition at line 128 of file sitkConfidenceConnectedImageFilter.h.