itk::simple::MorphologicalWatershedFromMarkersImageFilter Class Reference

Morphological watershed transform from markers. More...

#include <sitkMorphologicalWatershedFromMarkersImageFilter.h>

Inheritance diagram for itk::simple::MorphologicalWatershedFromMarkersImageFilter:

Collaboration diagram for itk::simple::MorphologicalWatershedFromMarkersImageFilter:

Public Types
using	PixelIDTypeList = ScalarPixelIDTypeList
using	Self = MorphologicalWatershedFromMarkersImageFilter
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 &image, const Image &markerImage)
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
	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 *image, const Image *markerImage)

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

Private Attributes
std::unique_ptr< detail::DualMemberFunctionFactory< MemberFunctionType > >	m_DualMemberFactory
bool	m_FullyConnected {false}
bool	m_MarkWatershedLine {true}

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 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)

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://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 61 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

Member Typedef Documentation

MemberFunctionType

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

private

Setup for member function dispatching

Definition at line 119 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

PixelIDTypeList

using itk::simple::MorphologicalWatershedFromMarkersImageFilter::PixelIDTypeList = ScalarPixelIDTypeList

Define the pixels types supported by this filter

Definition at line 73 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

Self

using itk::simple::MorphologicalWatershedFromMarkersImageFilter::Self = MorphologicalWatershedFromMarkersImageFilter

Definition at line 63 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

Constructor & Destructor Documentation

~MorphologicalWatershedFromMarkersImageFilter()

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

virtual

Destructor

MorphologicalWatershedFromMarkersImageFilter()

itk::simple::MorphologicalWatershedFromMarkersImageFilter::MorphologicalWatershedFromMarkersImageFilter

(

)

Default Constructor that takes no arguments and initializes default parameters

Member Function Documentation

DualExecuteInternal()

template<class TImageType1 , class TImageType2 >

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

private

Execute()

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

Execute the filter on the input image

FullyConnectedOff()

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

inline

Definition at line 98 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

FullyConnectedOn()

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

inline

Set the value of FullyConnected to true or false respectfully.

Definition at line 97 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

GetFullyConnected()

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 103 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

GetMarkWatershedLine()

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 89 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

GetName()

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

inlinevirtual

Name of this class

Implements itk::simple::ProcessObject.

Definition at line 106 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

MarkWatershedLineOff()

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

inline

Definition at line 84 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

MarkWatershedLineOn()

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

inline

Set the value of MarkWatershedLine to true or false respectfully.

Definition at line 83 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

SetFullyConnected()

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 94 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

SetMarkWatershedLine()

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 80 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

ToString()

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

virtual

Print ourselves out

Reimplemented from itk::simple::ProcessObject.

Friends And Related Function Documentation

detail::DualExecuteInternalAddressor< MemberFunctionType >

friend struct detail::DualExecuteInternalAddressor< MemberFunctionType >

friend

Definition at line 121 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

Member Data Documentation

m_DualMemberFactory

std::unique_ptr<detail::DualMemberFunctionFactory<MemberFunctionType> > itk::simple::MorphologicalWatershedFromMarkersImageFilter::m_DualMemberFactory

private

Definition at line 125 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

m_FullyConnected

bool itk::simple::MorphologicalWatershedFromMarkersImageFilter::m_FullyConnected {false}

private

Definition at line 131 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

m_MarkWatershedLine

bool itk::simple::MorphologicalWatershedFromMarkersImageFilter::m_MarkWatershedLine {true}

private

Definition at line 129 of file sitkMorphologicalWatershedFromMarkersImageFilter.h.

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

• sitkMorphologicalWatershedFromMarkersImageFilter.h