Morphological watershed transform from markers. More...

#include <sitkMorphologicalWatershedFromMarkersImageFilter.h>

Inheritance diagram for itk::simple::MorphologicalWatershedFromMarkersImageFilter:

Collaboration diagram for itk::simple::MorphologicalWatershedFromMarkersImageFilter:

Public Types
typedef ScalarPixelIDTypeList	PixelIDTypeList

typedef MorphologicalWatershedFromMarkersImageFilter	Self

Public Types inherited from itk::simple::ImageFilter< 0 >
typedef ImageFilter	Self

Public Types inherited from itk::simple::ProcessObject
typedef ProcessObject	Self

Public Member Functions
Image	Execute (const Image &image, const Image &markerImage)

Image	Execute (const Image &image, const Image &markerImage, bool markWatershedLine, bool fullyConnected)

Self &	FullyConnectedOff ()

Self &	FullyConnectedOn ()

bool	GetFullyConnected () const

bool	GetMarkWatershedLine () const

std::string	GetName () const

Self &	MarkWatershedLineOff ()

Self &	MarkWatershedLineOn ()

	MorphologicalWatershedFromMarkersImageFilter ()

Self &	SetFullyConnected (bool FullyConnected)

Self &	SetMarkWatershedLine (bool MarkWatershedLine)

std::string	ToString () const

virtual	~MorphologicalWatershedFromMarkersImageFilter ()

Public Member Functions inherited from itk::simple::ImageFilter< 0 >
	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 image, const Image markerImage)

Private Member Functions
template<class TImageType1 , class TImageType2 >
Image	DualExecuteInternal (const Image image, const Image markerImage)

Private Attributes
nsstd::auto_ptr< detail::DualMemberFunctionFactory< MemberFunctionType > >	m_DualMemberFactory

bool	m_FullyConnected

bool	m_MarkWatershedLine

Friends
struct	detail::DualExecuteInternalAddressor< 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< 0 >
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

Morphological watershed transform from markers.

The watershed transform is a tool for image segmentation that is fast and flexible and potentially fairly parameter free. It was originally derived from a geophysical model of rain falling on a terrain and a variety of more formal definitions have been devised to allow development of practical algorithms. If an image is considered as a terrain and divided into catchment basins then the hope is that each catchment basin would contain an object of interest.

The output is a label image. A label image, sometimes referred to as a categorical image, has unique values for each region. For example, if a watershed produces 2 regions, all pixels belonging to one region would have value A, and all belonging to the other might have value B. Unassigned pixels, such as watershed lines, might have the background value (0 by convention).

The simplest way of using the watershed is to preprocess the image we want to segment so that the boundaries of our objects are bright (e.g apply an edge detector) and compute the watershed transform of the edge image. Watershed lines will correspond to the boundaries and our problem will be solved. This is rarely useful in practice because there are always more regional minima than there are objects, either due to noise or natural variations in the object surfaces. Therefore, while many watershed lines do lie on significant boundaries, there are many that don't. Various methods can be used to reduce the number of minima in the image, like thresholding the smallest values, filtering the minima and/or smoothing the image.

This filter use another approach to avoid the problem of over segmentation: it let the user provide a marker image which mark the minima in the input image and give them a label. The minima are imposed in the input image by the markers. The labels of the output image are the label of the marker image.

The morphological watershed transform algorithm is described in Chapter 9.2 of Pierre Soille's book "Morphological Image Analysis: Principles and Applications", Second Edition, Springer, 2003.

This code was contributed in the Insight Journal paper: "The watershed transform in ITK - discussion and new developments" by Beare R., Lehmann G. https://hdl.handle.net/1926/202 http://www.insight-journal.org/browse/publication/92

Author: Gaetan Lehmann. Biologie du Developpement et de la Reproduction, INRA de Jouy-en-Josas, France.; Richard Beare. Department of Medicine, Monash University, Melbourne, Australia.

See also: WatershedImageFilter , MorphologicalWatershedImageFilter; itk::simple::MorphologicalWatershedFromMarkers for the procedural interface; itk::MorphologicalWatershedFromMarkersImageFilter for the Doxygen on the original ITK class.

Definition at line 60 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

Member Typedef Documentation

typedef Image(Self::* itk::simple::MorphologicalWatershedFromMarkersImageFilter::MemberFunctionType) (const Image *image, const Image *markerImage)

private

Setup for member function dispatching

Definition at line 120 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

typedef ScalarPixelIDTypeList itk::simple::MorphologicalWatershedFromMarkersImageFilter::PixelIDTypeList

Define the pixels types supported by this filter

Definition at line 72 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

typedef MorphologicalWatershedFromMarkersImageFilter itk::simple::MorphologicalWatershedFromMarkersImageFilter::Self

Definition at line 62 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

Constructor & Destructor Documentation

virtual itk::simple::MorphologicalWatershedFromMarkersImageFilter::~MorphologicalWatershedFromMarkersImageFilter ( )

virtual

Destructor

itk::simple::MorphologicalWatershedFromMarkersImageFilter::MorphologicalWatershedFromMarkersImageFilter ( )

Default Constructor that takes no arguments and initializes default parameters

Member Function Documentation

template<class TImageType1 , class TImageType2 >

Image itk::simple::MorphologicalWatershedFromMarkersImageFilter::DualExecuteInternal	(	const Image *	image,
		const Image *	markerImage
	)

private

Image itk::simple::MorphologicalWatershedFromMarkersImageFilter::Execute	(	const Image &	image,
		const Image &	markerImage
	)

Execute the filter on the input image

Image itk::simple::MorphologicalWatershedFromMarkersImageFilter::Execute	(	const Image &	image,
		const Image &	markerImage,
		bool	markWatershedLine,
		bool	fullyConnected
	)

Execute the filter on the input image with the given parameters

Self& itk::simple::MorphologicalWatershedFromMarkersImageFilter::FullyConnectedOff ( )

inline

Definition at line 97 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

Self& itk::simple::MorphologicalWatershedFromMarkersImageFilter::FullyConnectedOn ( )

inline

Set the value of FullyConnected to true or false respectfully.

Definition at line 96 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

bool itk::simple::MorphologicalWatershedFromMarkersImageFilter::GetFullyConnected ( ) const

inline

Set/Get whether the connected components are defined strictly by face connectivity or by face+edge+vertex connectivity. Default is FullyConnectedOff. For objects that are 1 pixel wide, use FullyConnectedOn.

Definition at line 102 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

bool itk::simple::MorphologicalWatershedFromMarkersImageFilter::GetMarkWatershedLine ( ) const

inline

Set/Get whether the watershed pixel must be marked or not. Default is true. Set it to false do not only avoid writing watershed pixels, it also decrease algorithm complexity.

Definition at line 88 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

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

inlinevirtual

Name of this class

Implements itk::simple::ProcessObject.

Definition at line 104 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

Self& itk::simple::MorphologicalWatershedFromMarkersImageFilter::MarkWatershedLineOff ( )

inline

Definition at line 83 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

Self& itk::simple::MorphologicalWatershedFromMarkersImageFilter::MarkWatershedLineOn ( )

inline

Set the value of MarkWatershedLine to true or false respectfully.

Definition at line 82 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

Self& itk::simple::MorphologicalWatershedFromMarkersImageFilter::SetFullyConnected ( bool FullyConnected )

inline

Set/Get whether the connected components are defined strictly by face connectivity or by face+edge+vertex connectivity. Default is FullyConnectedOff. For objects that are 1 pixel wide, use FullyConnectedOn.

Definition at line 93 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

Self& itk::simple::MorphologicalWatershedFromMarkersImageFilter::SetMarkWatershedLine ( bool MarkWatershedLine )

inline

Set/Get whether the watershed pixel must be marked or not. Default is true. Set it to false do not only avoid writing watershed pixels, it also decrease algorithm complexity.

Definition at line 79 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

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

virtual

Print ourselves out

Reimplemented from itk::simple::ProcessObject.

Friends And Related Function Documentation

friend struct detail::DualExecuteInternalAddressor< MemberFunctionType >

friend

Definition at line 122 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

Member Data Documentation

nsstd::auto_ptr<detail::DualMemberFunctionFactory<MemberFunctionType> > itk::simple::MorphologicalWatershedFromMarkersImageFilter::m_DualMemberFactory

private

Definition at line 126 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

bool itk::simple::MorphologicalWatershedFromMarkersImageFilter::m_FullyConnected

private

Definition at line 131 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

bool itk::simple::MorphologicalWatershedFromMarkersImageFilter::m_MarkWatershedLine

private

Definition at line 130 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

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