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:

Public Types
typedef ScalarPixelIDTypeList	PixelIDTypeList

typedef ThresholdMaximumConnectedComponentsImageFilter	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, uint32_t minimumObjectSizeInPixels, double upperBoundary, uint8_t insideValue, uint8_t outsideValue)

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< 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
uint8_t	m_InsideValue

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

uint32_t	m_MinimumObjectSizeInPixels

uint8_t	m_OutsideValue

double	m_UpperBoundary

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

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 immunoflourescent images". Insight Journal. ISC/NA-MIC/MICCAI Workshop on Open-Source Software (2005) Dspace handle: https://hdl.handle.net/1926/48 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 57 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

Member Typedef Documentation

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

private

Setup for member function dispatching

Definition at line 130 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

typedef ScalarPixelIDTypeList itk::simple::ThresholdMaximumConnectedComponentsImageFilter::PixelIDTypeList

Define the pixels types supported by this filter

Definition at line 69 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

typedef ThresholdMaximumConnectedComponentsImageFilter itk::simple::ThresholdMaximumConnectedComponentsImageFilter::Self

Definition at line 59 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

Constructor & Destructor Documentation

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

virtual

Destructor

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

Default Constructor that takes no arguments and initializes default parameters

Member Function Documentation

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

Execute the filter on the input image

Image itk::simple::ThresholdMaximumConnectedComponentsImageFilter::Execute	(	const Image &	image1,
		uint32_t	minimumObjectSizeInPixels,
		double	upperBoundary,
		uint8_t	insideValue,
		uint8_t	outsideValue
	)

Execute the filter on the input image with the given parameters

template<class TImageType >

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

private

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 101 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

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 81 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

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

inlinevirtual

Name of this class

Implements itk::simple::ProcessObject.

Definition at line 113 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

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 111 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

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 91 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

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 96 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

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 76 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

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 106 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

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 86 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

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

virtual

Print ourselves out

Reimplemented from itk::simple::ProcessObject.