Finds the threshold value of an image based on maximizing the number of objects in the image that are larger than a given minimal size. More...

#include <sitkThresholdMaximumConnectedComponentsImageFilter.h>

Inheritance diagram for itk::simple::ThresholdMaximumConnectedComponentsImageFilter:

Collaboration diagram for itk::simple::ThresholdMaximumConnectedComponentsImageFilter:

Detailed Description

Finds the threshold value of an image based on maximizing the number of objects in the image that are larger than a given minimal size.

: This method is based on Topological Stable State Thresholding to calculate the threshold set point. This method is particularly effective when there are a large number of objects in a microscopy image. Compiling in Debug mode and enable the debug flag for this filter to print debug information to see how the filter focuses in on a threshold value. Please see the Insight Journal's MICCAI 2005 workshop for a complete description. References are below.

Parameters: The MinimumObjectSizeInPixels parameter is controlled through the class Get/SetMinimumObjectSizeInPixels() method. Similar to the standard itk::BinaryThresholdImageFilter the Get/SetInside and Get/SetOutside values of the threshold can be set. The GetNumberOfObjects() and GetThresholdValue() methods return the number of objects above the minimum pixel size and the calculated threshold value.

Automatic Thresholding in ITK: There are multiple methods to automatically calculate the threshold intensity value of an image. As of version 4.0, ITK has a Thresholding ( ITKThresholding ) module which contains numerous automatic thresholding methods.implements two of these. Topological Stable State Thresholding works well on images with a large number of objects to be counted.

References:: 1) Urish KL, August J, Huard J. "Unsupervised segmentation for myofiber counting in immunofluorescent microscopy images". Insight Journal. ISC/NA-MIC/MICCAI Workshop on Open-Source Software (2005) https://doi.org/10.54294/h1vbsl 2) Pikaz A, Averbuch, A. "Digital image thresholding based on topological stable-state". Pattern Recognition, 29(5): 829-843, 1996.

: Questions: email Ken Urish at ken.urish(at)gmail.com Please cc the itk list serve for archival purposes.

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

Definition at line 60 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

Public Types
using	PixelIDTypeList = ScalarPixelIDTypeList

using	Self = ThresholdMaximumConnectedComponentsImageFilter

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)

uint8_t	GetInsideValue () const

uint32_t	GetMinimumObjectSizeInPixels () const

std::string	GetName () const

uint8_t	GetOutsideValue () const

double	GetUpperBoundary () const

Self &	SetInsideValue (uint8_t InsideValue)

Self &	SetMinimumObjectSizeInPixels (uint32_t MinimumObjectSizeInPixels)

Self &	SetOutsideValue (uint8_t OutsideValue)

Self &	SetUpperBoundary (double UpperBoundary)

	ThresholdMaximumConnectedComponentsImageFilter ()

std::string	ToString () const

virtual	~ThresholdMaximumConnectedComponentsImageFilter ()

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
uint8_t	m_InsideValue {1u}

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

uint32_t	m_MinimumObjectSizeInPixels {0u}

uint8_t	m_OutsideValue {0u}

double	m_UpperBoundary {std::numeric_limits<double>::max()}

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

private

Setup for member function dispatching

Definition at line 130 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

◆ PixelIDTypeList

using itk::simple::ThresholdMaximumConnectedComponentsImageFilter::PixelIDTypeList = ScalarPixelIDTypeList

Define the pixels types supported by this filter

Definition at line 72 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

◆ Self

using itk::simple::ThresholdMaximumConnectedComponentsImageFilter::Self = ThresholdMaximumConnectedComponentsImageFilter

Definition at line 62 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

Constructor & Destructor Documentation

◆ ~ThresholdMaximumConnectedComponentsImageFilter()

virtual itk::simple::ThresholdMaximumConnectedComponentsImageFilter::~ThresholdMaximumConnectedComponentsImageFilter ( )

virtual

Destructor

◆ ThresholdMaximumConnectedComponentsImageFilter()

itk::simple::ThresholdMaximumConnectedComponentsImageFilter::ThresholdMaximumConnectedComponentsImageFilter ( )

Default Constructor that takes no arguments and initializes default parameters

Member Function Documentation

◆ Execute()

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

Execute the filter on the input image

◆ ExecuteInternal()

template<class TImageType >

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

private

◆ GetInsideValue()

uint8_t itk::simple::ThresholdMaximumConnectedComponentsImageFilter::GetInsideValue ( ) const

inline

The following Set/Get methods are for the binary threshold function. This class automatically calculates the lower threshold boundary. The upper threshold boundary, inside value, and outside value can be defined by the user, however the standard values are used as default if not set by the user. The default value of the: Inside value is the maximum pixel type intensity. Outside value is the minimum pixel type intensity. Upper threshold boundary is the maximum pixel type intensity.

Definition at line 103 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

◆ GetMinimumObjectSizeInPixels()

uint32_t itk::simple::ThresholdMaximumConnectedComponentsImageFilter::GetMinimumObjectSizeInPixels ( ) const

inline

The pixel type must support comparison operators. Set the minimum pixel area used to count objects on the image. Thus, only objects that have a pixel area greater than the minimum pixel area will be counted as an object in the optimization portion of this filter. Essentially, it eliminates noise from being counted as an object. The default value is zero.

Definition at line 83 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

◆ GetName()

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

inlinevirtual

Name of this class

Implements itk::simple::ProcessObject.

Definition at line 116 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

◆ GetOutsideValue()

uint8_t itk::simple::ThresholdMaximumConnectedComponentsImageFilter::GetOutsideValue ( ) const

inline

The following Set/Get methods are for the binary threshold function. This class automatically calculates the lower threshold boundary. The upper threshold boundary, inside value, and outside value can be defined by the user, however the standard values are used as default if not set by the user. The default value of the: Inside value is the maximum pixel type intensity. Outside value is the minimum pixel type intensity. Upper threshold boundary is the maximum pixel type intensity.

Definition at line 113 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

◆ GetUpperBoundary()

double itk::simple::ThresholdMaximumConnectedComponentsImageFilter::GetUpperBoundary ( ) const

inline

The following Set/Get methods are for the binary threshold function. This class automatically calculates the lower threshold boundary. The upper threshold boundary, inside value, and outside value can be defined by the user, however the standard values are used as default if not set by the user. The default value of the: Inside value is the maximum pixel type intensity. Outside value is the minimum pixel type intensity. Upper threshold boundary is the maximum pixel type intensity.

Definition at line 93 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

◆ SetInsideValue()

Self& itk::simple::ThresholdMaximumConnectedComponentsImageFilter::SetInsideValue ( uint8_t InsideValue )

inline

The following Set/Get methods are for the binary threshold function. This class automatically calculates the lower threshold boundary. The upper threshold boundary, inside value, and outside value can be defined by the user, however the standard values are used as default if not set by the user. The default value of the: Inside value is the maximum pixel type intensity. Outside value is the minimum pixel type intensity. Upper threshold boundary is the maximum pixel type intensity.

Definition at line 98 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

◆ SetMinimumObjectSizeInPixels()

Self& itk::simple::ThresholdMaximumConnectedComponentsImageFilter::SetMinimumObjectSizeInPixels ( uint32_t MinimumObjectSizeInPixels )

inline

The pixel type must support comparison operators. Set the minimum pixel area used to count objects on the image. Thus, only objects that have a pixel area greater than the minimum pixel area will be counted as an object in the optimization portion of this filter. Essentially, it eliminates noise from being counted as an object. The default value is zero.

Definition at line 78 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

◆ SetOutsideValue()

Self& itk::simple::ThresholdMaximumConnectedComponentsImageFilter::SetOutsideValue ( uint8_t OutsideValue )

inline

The following Set/Get methods are for the binary threshold function. This class automatically calculates the lower threshold boundary. The upper threshold boundary, inside value, and outside value can be defined by the user, however the standard values are used as default if not set by the user. The default value of the: Inside value is the maximum pixel type intensity. Outside value is the minimum pixel type intensity. Upper threshold boundary is the maximum pixel type intensity.

Definition at line 108 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

◆ SetUpperBoundary()

Self& itk::simple::ThresholdMaximumConnectedComponentsImageFilter::SetUpperBoundary ( double UpperBoundary )

inline

The following Set/Get methods are for the binary threshold function. This class automatically calculates the lower threshold boundary. The upper threshold boundary, inside value, and outside value can be defined by the user, however the standard values are used as default if not set by the user. The default value of the: Inside value is the maximum pixel type intensity. Outside value is the minimum pixel type intensity. Upper threshold boundary is the maximum pixel type intensity.

Definition at line 88 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.