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:

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 49 of file sitkIsolatedConnectedImageFilter.h.

Public Types
using	PixelIDTypeList = BasicPixelIDTypeList

using	Self = IsolatedConnectedImageFilter

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 &image1)

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 (std::vector< unsigned int > Seed1)

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

Self &	SetUpper (double Upper)

std::string	ToString () const

virtual	~IsolatedConnectedImageFilter ()

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
bool	m_FindUpperThreshold {true}

double	m_IsolatedValue {0.0}

double	m_IsolatedValueTolerance {1.0}

double	m_Lower {0}

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

uint8_t	m_ReplaceValue {1u}

std::vector< unsigned int >	m_Seed1 {std::vector<unsigned int>(3, 0)}

std::vector< unsigned int >	m_Seed2 {std::vector<unsigned int>(3, 0)}

bool	m_ThresholdingFailed {false}

double	m_Upper {1}

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::IsolatedConnectedImageFilter::MemberFunctionType = Image (Self::*)( const Image& image1 )

private

Setup for member function dispatching

Definition at line 171 of file sitkIsolatedConnectedImageFilter.h.

◆ PixelIDTypeList

using itk::simple::IsolatedConnectedImageFilter::PixelIDTypeList = BasicPixelIDTypeList

Define the pixels types supported by this filter

Definition at line 61 of file sitkIsolatedConnectedImageFilter.h.

◆ Self

using itk::simple::IsolatedConnectedImageFilter::Self = IsolatedConnectedImageFilter

Definition at line 51 of file sitkIsolatedConnectedImageFilter.h.

Constructor & Destructor Documentation

◆ ~IsolatedConnectedImageFilter()

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

virtual

Destructor

◆ IsolatedConnectedImageFilter()

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

Default Constructor that takes no arguments and initializes default parameters

Member Function Documentation

◆ Execute()

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

Execute the filter on the input image

◆ ExecuteInternal()

template<class TImageType >

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

private

◆ FindUpperThresholdOff()

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

inline

Definition at line 133 of file sitkIsolatedConnectedImageFilter.h.

◆ FindUpperThresholdOn()

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

inline

Set the value of FindUpperThreshold to true or false respectfully.

Definition at line 132 of file sitkIsolatedConnectedImageFilter.h.

◆ GetFindUpperThreshold()

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 138 of file sitkIsolatedConnectedImageFilter.h.

◆ GetIsolatedValue()

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 153 of file sitkIsolatedConnectedImageFilter.h.

◆ GetIsolatedValueTolerance()

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

inline

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

Definition at line 124 of file sitkIsolatedConnectedImageFilter.h.

◆ GetLower()

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 94 of file sitkIsolatedConnectedImageFilter.h.

◆ GetName()

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

inlinevirtual

Name of this class

Implements itk::simple::ProcessObject.

Definition at line 157 of file sitkIsolatedConnectedImageFilter.h.

◆ GetReplaceValue()

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 114 of file sitkIsolatedConnectedImageFilter.h.

◆ GetSeed1()

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

inline

Definition at line 73 of file sitkIsolatedConnectedImageFilter.h.

◆ GetSeed2()

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

inline

Definition at line 84 of file sitkIsolatedConnectedImageFilter.h.

◆ GetThresholdingFailed()

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 145 of file sitkIsolatedConnectedImageFilter.h.

◆ GetUpper()

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 104 of file sitkIsolatedConnectedImageFilter.h.

◆ SetFindUpperThreshold()

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 129 of file sitkIsolatedConnectedImageFilter.h.

◆ SetIsolatedValueTolerance()

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 119 of file sitkIsolatedConnectedImageFilter.h.

◆ SetLower()

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 89 of file sitkIsolatedConnectedImageFilter.h.

◆ SetReplaceValue()

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 109 of file sitkIsolatedConnectedImageFilter.h.

◆ SetSeed1()

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

inline

     Set a single seed point 1.

This seed will be isolated from Seed2 (if possible). All pixels connected to this seed will be replaced with ReplaceValue.

Definition at line 69 of file sitkIsolatedConnectedImageFilter.h.

◆ SetSeed2()

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

inline

     Set a single seed point 2.

This seed will be isolated from Seed1 (if possible).

Definition at line 80 of file sitkIsolatedConnectedImageFilter.h.

◆ SetUpper()

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 99 of file sitkIsolatedConnectedImageFilter.h.

◆ ToString()

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

virtual

Print ourselves out

Reimplemented from itk::simple::ProcessObject.

Friends And Related Function Documentation

◆ detail::MemberFunctionAddressor< MemberFunctionType >

friend struct detail::MemberFunctionAddressor< MemberFunctionType >

friend

Definition at line 175 of file sitkIsolatedConnectedImageFilter.h.

Member Data Documentation

◆ m_FindUpperThreshold

bool itk::simple::IsolatedConnectedImageFilter::m_FindUpperThreshold {true}

private

Definition at line 193 of file sitkIsolatedConnectedImageFilter.h.

◆ m_IsolatedValue

double itk::simple::IsolatedConnectedImageFilter::m_IsolatedValue {0.0}

private

Definition at line 198 of file sitkIsolatedConnectedImageFilter.h.

◆ m_IsolatedValueTolerance

double itk::simple::IsolatedConnectedImageFilter::m_IsolatedValueTolerance {1.0}

private

Definition at line 190 of file sitkIsolatedConnectedImageFilter.h.

◆ m_Lower

double itk::simple::IsolatedConnectedImageFilter::m_Lower {0}

private

Definition at line 184 of file sitkIsolatedConnectedImageFilter.h.

◆ m_MemberFactory

std::unique_ptr<detail::MemberFunctionFactory<MemberFunctionType> > itk::simple::IsolatedConnectedImageFilter::m_MemberFactory

private

Definition at line 177 of file sitkIsolatedConnectedImageFilter.h.

◆ m_ReplaceValue

uint8_t itk::simple::IsolatedConnectedImageFilter::m_ReplaceValue {1u}

private

Definition at line 188 of file sitkIsolatedConnectedImageFilter.h.

◆ m_Seed1

std::vector<unsigned int> itk::simple::IsolatedConnectedImageFilter::m_Seed1 {std::vector<unsigned int>(3, 0)}

private

Definition at line 180 of file sitkIsolatedConnectedImageFilter.h.

◆ m_Seed2

std::vector<unsigned int> itk::simple::IsolatedConnectedImageFilter::m_Seed2 {std::vector<unsigned int>(3, 0)}

private

Definition at line 182 of file sitkIsolatedConnectedImageFilter.h.

◆ m_ThresholdingFailed

bool itk::simple::IsolatedConnectedImageFilter::m_ThresholdingFailed {false}

private

Definition at line 196 of file sitkIsolatedConnectedImageFilter.h.

◆ m_Upper

double itk::simple::IsolatedConnectedImageFilter::m_Upper {1}

private

Definition at line 186 of file sitkIsolatedConnectedImageFilter.h.

The documentation for this class was generated from the following file:

sitkIsolatedConnectedImageFilter.h

Detailed Description

Public Types

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Member Typedef Documentation

◆ MemberFunctionType

◆ PixelIDTypeList

◆ Self

Constructor & Destructor Documentation

◆ ~IsolatedConnectedImageFilter()

◆ IsolatedConnectedImageFilter()

Member Function Documentation

◆ Execute()

◆ ExecuteInternal()

◆ FindUpperThresholdOff()

◆ FindUpperThresholdOn()

◆ GetFindUpperThreshold()

◆ GetIsolatedValue()

◆ GetIsolatedValueTolerance()

◆ GetLower()

◆ GetName()

◆ GetReplaceValue()

◆ GetSeed1()

◆ GetSeed2()

◆ GetThresholdingFailed()

◆ GetUpper()

◆ SetFindUpperThreshold()

◆ SetIsolatedValueTolerance()

◆ SetLower()

◆ SetReplaceValue()

◆ SetSeed1()

◆ SetSeed2()

◆ SetUpper()

◆ ToString()

Friends And Related Function Documentation

◆ detail::MemberFunctionAddressor< MemberFunctionType >

Member Data Documentation

◆ m_FindUpperThreshold

◆ m_IsolatedValue

◆ m_IsolatedValueTolerance

◆ m_Lower

◆ m_MemberFactory

◆ m_ReplaceValue

◆ m_Seed1

◆ m_Seed2

◆ m_ThresholdingFailed

◆ m_Upper