Label pixels that are connected to one set of seeds but not another. More...

#include <sitkIsolatedConnectedImageFilter.h>

Inheritance diagram for itk::simple::IsolatedConnectedImageFilter:

Collaboration diagram for itk::simple::IsolatedConnectedImageFilter:

Public Types
typedef BasicPixelIDTypeList	PixelIDTypeList

typedef IsolatedConnectedImageFilter	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
Image	Execute (const Image &image1)

Image	Execute (const Image &image1, const std::vector< unsigned int > &seed1, const std::vector< unsigned int > &seed2, double lower, double upper, uint8_t replaceValue, double isolatedValueTolerance, bool findUpperThreshold)

Self &	FindUpperThresholdOff ()

Self &	FindUpperThresholdOn ()

bool	GetFindUpperThreshold () const

double	GetIsolatedValue () const

double	GetIsolatedValueTolerance () const

double	GetLower () const

std::string	GetName () const

uint8_t	GetReplaceValue () const

std::vector< unsigned int >	GetSeed1 () const

std::vector< unsigned int >	GetSeed2 () const

bool	GetThresholdingFailed () const

double	GetUpper () const

	IsolatedConnectedImageFilter ()

Self &	SetFindUpperThreshold (bool FindUpperThreshold)

Self &	SetIsolatedValueTolerance (double IsolatedValueTolerance)

Self &	SetLower (double Lower)

Self &	SetReplaceValue (uint8_t ReplaceValue)

Self &	SetSeed1 (const std::vector< unsigned int > &Seed1)

Self &	SetSeed2 (const std::vector< unsigned int > &Seed2)

Self &	SetUpper (double Upper)

std::string	ToString () const

virtual	~IsolatedConnectedImageFilter ()

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
bool	m_FindUpperThreshold

double	m_IsolatedValue

double	m_IsolatedValueTolerance

double	m_Lower

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

uint8_t	m_ReplaceValue

std::vector< unsigned int >	m_Seed1

std::vector< unsigned int >	m_Seed2

bool	m_ThresholdingFailed

double	m_Upper

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

Label pixels that are connected to one set of seeds but not another.

IsolatedConnectedImageFilter finds the optimal threshold to separate two regions. It has two modes, one to separate dark regions surrounded by bright regions by automatically finding a minimum isolating upper threshold, and another to separate bright regions surrounded by dark regions by automatically finding a maximum lower isolating threshold. The mode can be chosen by setting FindUpperThresholdOn() /Off(). In both cases, the isolating threshold is retrieved with GetIsolatedValue() .

The algorithm labels pixels with ReplaceValue that are connected to Seeds1 AND NOT connected to Seeds2. When finding the threshold to separate two dark regions surrounded by bright regions, given a fixed lower threshold, the filter adjusts the upper threshold until the two sets of seeds are not connected. The algorithm uses a binary search to adjust the upper threshold, starting at Upper. The reverse is true for finding the threshold to separate two bright regions. Lower defaults to the smallest possible value for the InputImagePixelType, and Upper defaults to the largest possible value for the InputImagePixelType.

The user can also supply the Lower and Upper values to restrict the search. However, if the range is too restrictive, it could happen that no isolating threshold can be found between the user specified Lower and Upper values. Therefore, unless the user is sure of the bounds to set, it is recommended that the user set these values to the lowest and highest intensity values in the image, respectively.

The user can specify more than one seed for both regions to separate. The algorithm will try find the threshold that ensures that all of the first seeds are contained in the resulting segmentation and all of the second seeds are not contained in the segmentation.

It is possible that the algorithm may not be able to find the isolating threshold because no such threshold exists. The user can check for this by querying the GetThresholdingFailed() flag.

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

Definition at line 50 of file sitkIsolatedConnectedImageFilter.h.

Member Typedef Documentation

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

private

Setup for member function dispatching

Definition at line 171 of file sitkIsolatedConnectedImageFilter.h.

typedef BasicPixelIDTypeList itk::simple::IsolatedConnectedImageFilter::PixelIDTypeList

Define the pixels types supported by this filter

Definition at line 62 of file sitkIsolatedConnectedImageFilter.h.

typedef IsolatedConnectedImageFilter itk::simple::IsolatedConnectedImageFilter::Self

Definition at line 52 of file sitkIsolatedConnectedImageFilter.h.

Constructor & Destructor Documentation

virtual itk::simple::IsolatedConnectedImageFilter::~IsolatedConnectedImageFilter ( )

virtual

Destructor

itk::simple::IsolatedConnectedImageFilter::IsolatedConnectedImageFilter ( )

Default Constructor that takes no arguments and initializes default parameters

Member Function Documentation

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

Execute the filter on the input image

Image itk::simple::IsolatedConnectedImageFilter::Execute	(	const Image &	image1,
		const std::vector< unsigned int > &	seed1,
		const std::vector< unsigned int > &	seed2,
		double	lower,
		double	upper,
		uint8_t	replaceValue,
		double	isolatedValueTolerance,
		bool	findUpperThreshold
	)

Execute the filter on the input image with the given parameters

template<class TImageType >

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

private

Self& itk::simple::IsolatedConnectedImageFilter::FindUpperThresholdOff ( )

inline

Definition at line 131 of file sitkIsolatedConnectedImageFilter.h.

Self& itk::simple::IsolatedConnectedImageFilter::FindUpperThresholdOn ( )

inline

Set the value of FindUpperThreshold to true or false respectfully.

Definition at line 130 of file sitkIsolatedConnectedImageFilter.h.

bool itk::simple::IsolatedConnectedImageFilter::GetFindUpperThreshold ( ) const

inline

Set/Get whether to find an upper threshold (separating two dark regions) or a lower threshold (separating two bright regions).

Definition at line 136 of file sitkIsolatedConnectedImageFilter.h.

double itk::simple::IsolatedConnectedImageFilter::GetIsolatedValue ( ) const

inline

Get value that isolates the two seeds.

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 151 of file sitkIsolatedConnectedImageFilter.h.

double itk::simple::IsolatedConnectedImageFilter::GetIsolatedValueTolerance ( ) const

inline

Set/Get the precision required for the intensity threshold value. The default is 1.

Definition at line 122 of file sitkIsolatedConnectedImageFilter.h.

double itk::simple::IsolatedConnectedImageFilter::GetLower ( ) const

inline

Set/Get the limit on the lower threshold value. The default is the NonpositiveMin() for the InputPixelType.

Definition at line 92 of file sitkIsolatedConnectedImageFilter.h.

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

inlinevirtual

Name of this class

Implements itk::simple::ProcessObject.

Definition at line 154 of file sitkIsolatedConnectedImageFilter.h.

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

inline

Set/Get value to replace thresholded pixels. Pixels that lie within the thresholds will be replaced with this value. The default is 1.

Definition at line 112 of file sitkIsolatedConnectedImageFilter.h.

std::vector<unsigned int> itk::simple::IsolatedConnectedImageFilter::GetSeed1 ( ) const

inline

Definition at line 73 of file sitkIsolatedConnectedImageFilter.h.

std::vector<unsigned int> itk::simple::IsolatedConnectedImageFilter::GetSeed2 ( ) const

inline

Definition at line 82 of file sitkIsolatedConnectedImageFilter.h.

bool itk::simple::IsolatedConnectedImageFilter::GetThresholdingFailed ( ) const

inline

Get the flag that tells whether the algorithm failed to find a threshold.

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 143 of file sitkIsolatedConnectedImageFilter.h.

double itk::simple::IsolatedConnectedImageFilter::GetUpper ( ) const

inline

Set/Get the limit on the upper threshold value. The default is the max() for the InputPixelType.

Definition at line 102 of file sitkIsolatedConnectedImageFilter.h.

Self& itk::simple::IsolatedConnectedImageFilter::SetFindUpperThreshold ( bool FindUpperThreshold )

inline

Set/Get whether to find an upper threshold (separating two dark regions) or a lower threshold (separating two bright regions).

Definition at line 127 of file sitkIsolatedConnectedImageFilter.h.

Self& itk::simple::IsolatedConnectedImageFilter::SetIsolatedValueTolerance ( double IsolatedValueTolerance )

inline

Set/Get the precision required for the intensity threshold value. The default is 1.

Definition at line 117 of file sitkIsolatedConnectedImageFilter.h.

Self& itk::simple::IsolatedConnectedImageFilter::SetLower ( double Lower )

inline

Set/Get the limit on the lower threshold value. The default is the NonpositiveMin() for the InputPixelType.

Definition at line 87 of file sitkIsolatedConnectedImageFilter.h.

Self& itk::simple::IsolatedConnectedImageFilter::SetReplaceValue ( uint8_t ReplaceValue )

inline

Set/Get value to replace thresholded pixels. Pixels that lie within the thresholds will be replaced with this value. The default is 1.

Definition at line 107 of file sitkIsolatedConnectedImageFilter.h.

Self& itk::simple::IsolatedConnectedImageFilter::SetSeed1 ( const std::vector< unsigned int > & Seed1 )

inline

DeprecatedSet seed point 1. This seed will be isolated from Seed2 (if possible). All pixels connected to this seed will be replaced with ReplaceValue. This method is deprecated, please use AddSeed1() .

Definition at line 69 of file sitkIsolatedConnectedImageFilter.h.

Self& itk::simple::IsolatedConnectedImageFilter::SetSeed2 ( const std::vector< unsigned int > & Seed2 )

inline

DeprecatedSet seed point 2. This seed will be isolated from Seed1 (if possible). This method is deprecated, please use AddSeed2() .

Definition at line 78 of file sitkIsolatedConnectedImageFilter.h.

Self& itk::simple::IsolatedConnectedImageFilter::SetUpper ( double Upper )

inline

Set/Get the limit on the upper threshold value. The default is the max() for the InputPixelType.

Definition at line 97 of file sitkIsolatedConnectedImageFilter.h.

std::string itk::simple::IsolatedConnectedImageFilter::ToString ( ) const

virtual

Print ourselves out