itk::simple::IsolatedConnectedImageFilter Class Reference

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 66 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)
void	FindUpperThresholdOff ()
void	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 ()
void	SetFindUpperThreshold (bool FindUpperThreshold)
void	SetIsolatedValueTolerance (double IsolatedValueTolerance)
void	SetLower (double Lower)
void	SetReplaceValue (uint8_t ReplaceValue)
void	SetSeed1 (std::vector< unsigned int > Seed1)
void	SetSeed2 (std::vector< unsigned int > Seed2)
void	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.
virtual int	AddCommand (itk::simple::EventEnum event, itk::simple::Command &cmd)
	Add a Command Object to observer the event.
virtual float	GetProgress () const
	An Active Measurement of the progress of execution.
virtual bool	HasCommand (itk::simple::EventEnum event) const
	Query of this object has any registered commands for event.
	ProcessObject ()
virtual void	RemoveAllCommands ()
	Remove all registered commands.
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)

Static Private Member Functions
static const detail::MemberFunctionFactory< MemberFunctionType > &	GetMemberFunctionFactory ()

Private Attributes
bool	m_FindUpperThreshold { true }
double	m_IsolatedValue { 0.0 }
double	m_IsolatedValueTolerance { 1.0 }
double	m_Lower { 0 }
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.
static void	SetGlobalDefaultCoordinateTolerance (double)
	Access the global tolerance to determine congruent spaces.
static double	GetGlobalDefaultDirectionTolerance ()
	Access the global tolerance to determine congruent spaces.
static void	SetGlobalDefaultDirectionTolerance (double)
	Access the global tolerance to determine congruent spaces.
static bool	SetGlobalDefaultThreader (const std::string &threader)
	Set/Get the default threader used for process objects.
static std::string	GetGlobalDefaultThreader ()
	Set/Get the default threader used for process objects.
static void	SetGlobalDefaultNumberOfThreads (unsigned int n)
static unsigned int	GetGlobalDefaultNumberOfThreads ()
	Set/Get the default threader used for process objects.
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 216 of file sitkIsolatedConnectedImageFilter.h.

PixelIDTypeList

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

Define the pixels types supported by this filter

Definition at line 78 of file sitkIsolatedConnectedImageFilter.h.

Self

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

Definition at line 68 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

Referenced by detail::MemberFunctionAddressor< MemberFunctionType >.

FindUpperThresholdOff()

void itk::simple::IsolatedConnectedImageFilter::FindUpperThresholdOff ( )

inline

Definition at line 178 of file sitkIsolatedConnectedImageFilter.h.

References SetFindUpperThreshold().

FindUpperThresholdOn()

void itk::simple::IsolatedConnectedImageFilter::FindUpperThresholdOn ( )

inline

Set the value of FindUpperThreshold to true or false respectfully.

Definition at line 176 of file sitkIsolatedConnectedImageFilter.h.

References SetFindUpperThreshold().

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 184 of file sitkIsolatedConnectedImageFilter.h.

References m_FindUpperThreshold.

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 201 of file sitkIsolatedConnectedImageFilter.h.

References m_IsolatedValue.

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 163 of file sitkIsolatedConnectedImageFilter.h.

References m_IsolatedValueTolerance.

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 122 of file sitkIsolatedConnectedImageFilter.h.

References m_Lower.

GetMemberFunctionFactory()

static const detail::MemberFunctionFactory< MemberFunctionType > & itk::simple::IsolatedConnectedImageFilter::GetMemberFunctionFactory ( )

staticprivate

GetName()

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

inlinevirtual

Name of this class

Implements itk::simple::ProcessObject.

Definition at line 204 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 150 of file sitkIsolatedConnectedImageFilter.h.

References m_ReplaceValue.

GetSeed1()

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

inline

Definition at line 95 of file sitkIsolatedConnectedImageFilter.h.

References m_Seed1.

GetSeed2()

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

inline

Definition at line 109 of file sitkIsolatedConnectedImageFilter.h.

References m_Seed2.

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 193 of file sitkIsolatedConnectedImageFilter.h.

References m_ThresholdingFailed.

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 135 of file sitkIsolatedConnectedImageFilter.h.

References m_Upper.

SetFindUpperThreshold()

void 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 171 of file sitkIsolatedConnectedImageFilter.h.

References m_FindUpperThreshold.

Referenced by FindUpperThresholdOff(), and FindUpperThresholdOn().

SetIsolatedValueTolerance()

void itk::simple::IsolatedConnectedImageFilter::SetIsolatedValueTolerance ( double IsolatedValueTolerance )

inline

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

Definition at line 157 of file sitkIsolatedConnectedImageFilter.h.

References m_IsolatedValueTolerance.

SetLower()

void 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 116 of file sitkIsolatedConnectedImageFilter.h.

References m_Lower.

SetReplaceValue()

void 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 143 of file sitkIsolatedConnectedImageFilter.h.

References m_ReplaceValue.

SetSeed1()

void 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 90 of file sitkIsolatedConnectedImageFilter.h.

References m_Seed1.

SetSeed2()

void 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 104 of file sitkIsolatedConnectedImageFilter.h.

References m_Seed2.

SetUpper()

void 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 129 of file sitkIsolatedConnectedImageFilter.h.

References m_Upper.

ToString()

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

virtual

Print ourselves out

Reimplemented from itk::simple::ProcessObject.

Friends And Related Symbol Documentation

detail::MemberFunctionAddressor< MemberFunctionType >

friend struct detail::MemberFunctionAddressor< MemberFunctionType >

friend

Definition at line 217 of file sitkIsolatedConnectedImageFilter.h.

References ExecuteInternal().

Member Data Documentation

m_FindUpperThreshold

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

private

Definition at line 234 of file sitkIsolatedConnectedImageFilter.h.

Referenced by GetFindUpperThreshold(), and SetFindUpperThreshold().

m_IsolatedValue

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

private

Definition at line 239 of file sitkIsolatedConnectedImageFilter.h.

Referenced by GetIsolatedValue().

m_IsolatedValueTolerance

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

private

Definition at line 232 of file sitkIsolatedConnectedImageFilter.h.

Referenced by GetIsolatedValueTolerance(), and SetIsolatedValueTolerance().

m_Lower

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

private

Definition at line 226 of file sitkIsolatedConnectedImageFilter.h.

Referenced by GetLower(), and SetLower().

m_ReplaceValue

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

private

Definition at line 230 of file sitkIsolatedConnectedImageFilter.h.

Referenced by GetReplaceValue(), and SetReplaceValue().

m_Seed1

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

private

Definition at line 222 of file sitkIsolatedConnectedImageFilter.h.

Referenced by GetSeed1(), and SetSeed1().

m_Seed2

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

private

Definition at line 224 of file sitkIsolatedConnectedImageFilter.h.

Referenced by GetSeed2(), and SetSeed2().

m_ThresholdingFailed

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

private

Definition at line 238 of file sitkIsolatedConnectedImageFilter.h.

Referenced by GetThresholdingFailed().

m_Upper

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

private

Definition at line 228 of file sitkIsolatedConnectedImageFilter.h.

Referenced by GetUpper(), and SetUpper().

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

• sitkIsolatedConnectedImageFilter.h