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

#include <sitkConfidenceConnectedImageFilter.h>

Inheritance diagram for itk::simple::ConfidenceConnectedImageFilter:

Collaboration diagram for itk::simple::ConfidenceConnectedImageFilter:

Public Types
typedef BasicPixelIDTypeList	PixelIDTypeList

typedef ConfidenceConnectedImageFilter	Self

Public Types inherited from itk::simple::ImageFilter< 1 >
typedef ImageFilter	Self

Public Types inherited from itk::simple::ProcessObject
typedef ProcessObject	Self

Public Member Functions
Self &	AddSeed (const std::vector< unsigned int > &idx)

Self &	ClearSeeds ()

	ConfidenceConnectedImageFilter ()

Image	Execute (const Image &image1)

Image	Execute (const Image &image1, const std::vector< std::vector< unsigned int > > &seedList, unsigned int numberOfIterations, double multiplier, unsigned int initialNeighborhoodRadius, uint8_t replaceValue)

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

double	GetVariance () const

Self &	SetInitialNeighborhoodRadius (unsigned int InitialNeighborhoodRadius)

Self &	SetMultiplier (double Multiplier)

Self &	SetNumberOfIterations (unsigned int NumberOfIterations)

Self &	SetReplaceValue (uint8_t ReplaceValue)

Self &	SetSeed (const std::vector< unsigned int > &idx)

Self &	SetSeedList (const std::vector< std::vector< unsigned int > > &t)

std::string	ToString () const

virtual	~ConfidenceConnectedImageFilter ()

Public Member Functions inherited from itk::simple::ImageFilter< 1 >
	ImageFilter ()

virtual	~ImageFilter ()=0

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

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

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

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

Private Attributes
unsigned int	m_InitialNeighborhoodRadius

double	m_Mean

nsstd::auto_ptr< detail::MemberFunctionFactory< MemberFunctionType > >	m_MemberFactory

double	m_Multiplier

unsigned int	m_NumberOfIterations

uint8_t	m_ReplaceValue

std::vector< std::vector< unsigned int > >	m_SeedList

double	m_Variance

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 void	SetGlobalDefaultNumberOfThreads (unsigned int n)

static unsigned int	GetGlobalDefaultNumberOfThreads ()

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...

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) SITK_NOEXCEPT

virtual void	PreUpdate (itk::ProcessObject *p)

virtual void	RemoveITKObserver (EventCommand &e)

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

Static Protected Member Functions inherited from itk::simple::ImageFilter< 1 >
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 TImageType >
static Image	CastITKToImage (TImageType *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)

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)

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 46 of file sitkConfidenceConnectedImageFilter.h.

Member Typedef Documentation

typedef Image(Self::* itk::simple::ConfidenceConnectedImageFilter::MemberFunctionType) (const Image &image1)

private

Setup for member function dispatching

Definition at line 169 of file sitkConfidenceConnectedImageFilter.h.

typedef BasicPixelIDTypeList itk::simple::ConfidenceConnectedImageFilter::PixelIDTypeList

Define the pixels types supported by this filter

Definition at line 58 of file sitkConfidenceConnectedImageFilter.h.

typedef ConfidenceConnectedImageFilter itk::simple::ConfidenceConnectedImageFilter::Self

Definition at line 48 of file sitkConfidenceConnectedImageFilter.h.

Constructor & Destructor Documentation

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

virtual

Destructor

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

Default Constructor that takes no arguments and initializes default parameters

Member Function Documentation

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

inline

AddSeed - Add a seed to the end of the list

Definition at line 145 of file sitkConfidenceConnectedImageFilter.h.

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

inline

ClearSeeds - Clear out all seeds in the list

Definition at line 130 of file sitkConfidenceConnectedImageFilter.h.

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

Execute the filter on the input image

Image itk::simple::ConfidenceConnectedImageFilter::Execute	(	const Image &	image1,
		const std::vector< std::vector< unsigned int > > &	seedList,
		unsigned int	numberOfIterations,
		double	multiplier,
		unsigned int	initialNeighborhoodRadius,
		uint8_t	replaceValue
	)

Execute the filter on the input image with the given parameters

template<class TImageType >

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

private

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

inline

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

Definition at line 90 of file sitkConfidenceConnectedImageFilter.h.

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 107 of file sitkConfidenceConnectedImageFilter.h.

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 80 of file sitkConfidenceConnectedImageFilter.h.

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

inlinevirtual

Name of this class

Implements itk::simple::ProcessObject.

Definition at line 152 of file sitkConfidenceConnectedImageFilter.h.

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

inline

Set/Get the number of iterations

Definition at line 70 of file sitkConfidenceConnectedImageFilter.h.

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

inline

Set/Get value to replace thresholded pixels

Definition at line 100 of file sitkConfidenceConnectedImageFilter.h.

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

inline

Get SeedList

Definition at line 124 of file sitkConfidenceConnectedImageFilter.h.

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 115 of file sitkConfidenceConnectedImageFilter.h.

Self& itk::simple::ConfidenceConnectedImageFilter::SetInitialNeighborhoodRadius ( unsigned int InitialNeighborhoodRadius )

inline

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

Definition at line 85 of file sitkConfidenceConnectedImageFilter.h.

Self& itk::simple::ConfidenceConnectedImageFilter::SetMultiplier ( double Multiplier )

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 75 of file sitkConfidenceConnectedImageFilter.h.

Self& itk::simple::ConfidenceConnectedImageFilter::SetNumberOfIterations ( unsigned int NumberOfIterations )

inline