FastMarching semgentation tool. More...

#include <mitkFastMarchingTool3D.h>

Inheritance diagram for mitk::FastMarchingTool3D:

Collaboration diagram for mitk::FastMarchingTool3D:

Public Types
typedef float	InternalPixelType

typedef itk::Image< InternalPixelType, 3 >	InternalImageType

typedef mitk::Tool::DefaultSegmentationDataType	OutputPixelType

typedef itk::Image< OutputPixelType, 3 >	OutputImageType

typedef itk::BinaryThresholdImageFilter< InternalImageType, OutputImageType >	ThresholdingFilterType

typedef itk::CurvatureAnisotropicDiffusionImageFilter< InternalImageType, InternalImageType >	SmoothingFilterType

typedef itk::GradientMagnitudeRecursiveGaussianImageFilter< InternalImageType, InternalImageType >	GradientFilterType

typedef itk::SigmoidImageFilter< InternalImageType, InternalImageType >	SigmoidFilterType

typedef itk::FastMarchingImageFilter< InternalImageType, InternalImageType >	FastMarchingFilterType

typedef FastMarchingFilterType::NodeContainer	NodeContainer

typedef FastMarchingFilterType::NodeType	NodeType

Public Types inherited from mitk::Tool
typedef mitk::Label::PixelType	DefaultSegmentationDataType

Public Types inherited from mitk::EventStateMachine
typedef EventStateMachine	Self

typedef InteractionEventHandler	Superclass

typedef itk::SmartPointer< Self >	Pointer

typedef itk::SmartPointer< const Self >	ConstPointer

typedef std::map< std::string, TActionFunctor * >	ActionFunctionsMapType

typedef itk::SmartPointer< StateMachineState >	StateMachineStateType

Public Types inherited from mitk::InteractionEventHandler
typedef InteractionEventHandler	Self

typedef itk::Object	Superclass

typedef itk::SmartPointer< Self >	Pointer

typedef itk::SmartPointer< const Self >	ConstPointer

Public Member Functions
	mitkClassMacro (FastMarchingTool3D, AutoSegmentationTool) static Pointer New()

Pointer	Clone () const

bool	CanHandle (BaseData *referenceData) const override

virtual const char **	GetXPM () const override
	Returns an icon in the XPM format. More...

virtual const char *	GetName () const override
	Returns the name of this tool. Make it short! More...

us::ModuleResource	GetIconResource () const override
	Returns the tool button icon of the tool wrapped by a usModuleResource. More...

void	SetUpperThreshold (double)
	Set parameter used in Threshold filter. More...

void	SetLowerThreshold (double)
	Set parameter used in Threshold filter. More...

void	SetStoppingValue (double)
	Set parameter used in Fast Marching filter. More...

void	SetSigma (double)
	Set parameter used in Gradient Magnitude filter. More...

void	SetAlpha (double)
	Set parameter used in Fast Marching filter. More...

void	SetBeta (double)
	Set parameter used in Fast Marching filter. More...

virtual void	ConfirmSegmentation ()
	Adds the feedback image to the current working image. More...

virtual void	SetCurrentTimeStep (int t)
	Set the working time step. More...

void	ClearSeeds ()
	Clear all seed points. More...

void	Update ()
	Updates the itk pipeline and shows the result of FastMarching. More...

Public Member Functions inherited from mitk::AutoSegmentationTool
	mitkClassMacro (AutoSegmentationTool, Tool)

void	SetOverwriteExistingSegmentation (bool overwrite)

std::string	GetCurrentSegmentationName ()
	Gets the name of the currently selected segmentation node. More...

virtual mitk::DataNode *	GetTargetSegmentationNode ()
	Depending on the selected mode either returns the currently selected segmentation or creates a new one from the selected reference data and adds the new segmentation to the datastorage. More...

Public Member Functions inherited from mitk::Tool
	mitkClassMacro (Tool, EventStateMachine)

virtual std::string	GetIconPath () const
	Returns the path of an icon. More...

virtual us::ModuleResource	GetCursorIconResource () const
	Returns the path of a cursor icon. More...

virtual void	InitializeStateMachine ()

virtual itk::Object::Pointer	GetGUI (const std::string &toolkitPrefix, const std::string &toolkitPostfix)
	Interface for GUI creation. More...

virtual NodePredicateBase::ConstPointer	GetReferenceDataPreference () const

virtual NodePredicateBase::ConstPointer	GetWorkingDataPreference () const

DataNode::Pointer	CreateEmptySegmentationNode (Image *original, const std::string &organName, const mitk::Color &color)

DataNode::Pointer	CreateSegmentationNode (Image *image, const std::string &organName, const mitk::Color &color)

Public Member Functions inherited from mitk::EventStateMachine
virtual std::vector< std::string >	GetClassHierarchy () const override

virtual const char *	GetClassName () const

bool	LoadStateMachine (const std::string &filename, const us::Module *module=nullptr)
	Loads XML resource. More...

bool	HandleEvent (InteractionEvent event, DataNode dataNode)

void	EnableUndo (bool enable)
	Enables or disabled Undo. More...

void	EnableInteraction (bool enable)
	Enables/disables the state machine. In un-enabled state it won't react to any events. More...

Public Member Functions inherited from mitk::InteractionEventHandler
bool	SetEventConfig (const std::string &filename, const us::Module *module=nullptr)
	Loads a configuration from an XML resource. More...

bool	SetEventConfig (const EventConfig &config)
	Loads a configuration from an EventConfig object. More...

EventConfig	GetEventConfig () const
	Returns the current configuration. More...

bool	AddEventConfig (const std::string &filename, const us::Module *module=nullptr)
	This method extends the configuration. More...

bool	AddEventConfig (const EventConfig &config)
	This method extends the configuration. The configuration from the EventConfig object is loaded and only the ones conflicting are replaced by the new one. This way several configurations can be combined. More...

Public Member Functions inherited from mitk::InteractionEventObserver
	InteractionEventObserver ()

virtual	~InteractionEventObserver ()

void	Disable ()

void	Enable ()

bool	IsEnabled () const

Protected Member Functions
	FastMarchingTool3D ()

virtual	~FastMarchingTool3D ()

virtual void	Activated () override
	Called when the tool gets activated. More...

virtual void	Deactivated () override
	Called when the tool gets deactivated. More...

virtual void	Initialize ()

virtual void	OnAddPoint ()
	Add point action of StateMachine pattern. More...

virtual void	OnDelete ()
	Delete action of StateMachine pattern. More...

void	Reset ()
	Reset all relevant inputs of the itk pipeline. More...

Protected Member Functions inherited from mitk::AutoSegmentationTool
	AutoSegmentationTool ()

virtual	~AutoSegmentationTool ()

virtual const char *	GetGroup () const override
	Name of a group. More...

virtual itk::SmartPointer< Image >	Get3DImage (itk::SmartPointer< Image > image, unsigned int timestep)

Protected Member Functions inherited from mitk::Tool
virtual void	SetToolManager (ToolManager *)

void	ConnectActionsAndFunctions () override

	Tool ()

	Tool (const char *)

virtual	~Tool ()

virtual void	Notify (InteractionEvent *interactionEvent, bool isHandled) override

bool	FilterEvents (InteractionEvent , DataNode ) override

Protected Member Functions inherited from mitk::EventStateMachine
	EventStateMachine ()

virtual	~EventStateMachine ()

void	AddActionFunction (const std::string &action, TActionFunctor *functor)

void	AddActionFunction (const std::string &action, const ActionFunctionDelegate &delegate)

void	AddConditionFunction (const std::string &condition, const ConditionFunctionDelegate &delegate)

StateMachineState *	GetCurrentState () const

void	ResetToStartState ()
	ResetToStartState Reset state machine to it initial starting state. More...

virtual bool	CheckCondition (const StateMachineCondition &condition, const InteractionEvent *interactionEvent)

virtual void	ExecuteAction (StateMachineAction action, InteractionEvent interactionEvent)

void	SetMouseCursor (const char *xpm[], int hotspotX, int hotspotY)
	Sets the specified mouse cursor. More...

void	ResetMouseCursor ()
	Resets the mouse cursor (if modified by the SlicesCoordinator) to its original state. More...

StateMachineTransition *	GetExecutableTransition (InteractionEvent *event)
	Returns the executable transition for the given event. More...

Protected Member Functions inherited from mitk::InteractionEventHandler
	InteractionEventHandler ()

virtual	~InteractionEventHandler ()

PropertyList::Pointer	GetAttributes () const

std::string	MapToEventVariant (InteractionEvent *interactionEvent)

virtual void	ConfigurationChanged ()

Protected Attributes
mitk::ToolCommand::Pointer	m_ProgressCommand

Image::Pointer	m_ReferenceImage

bool	m_NeedUpdate

int	m_CurrentTimeStep

float	m_LowerThreshold

float	m_UpperThreshold

float	m_StoppingValue

float	m_Sigma

float	m_Alpha

float	m_Beta

NodeContainer::Pointer	m_SeedContainer

InternalImageType::Pointer	m_ReferenceImageAsITK

mitk::DataNode::Pointer	m_ResultImageNode

mitk::DataNode::Pointer	m_SeedsAsPointSetNode

mitk::PointSet::Pointer	m_SeedsAsPointSet

mitk::PointSetDataInteractor::Pointer	m_SeedPointInteractor

unsigned int	m_PointSetAddObserverTag

unsigned int	m_PointSetRemoveObserverTag

ThresholdingFilterType::Pointer	m_ThresholdFilter

SmoothingFilterType::Pointer	m_SmoothFilter

GradientFilterType::Pointer	m_GradientMagnitudeFilter

SigmoidFilterType::Pointer	m_SigmoidFilter

FastMarchingFilterType::Pointer	m_FastMarchingFilter

Protected Attributes inherited from mitk::AutoSegmentationTool
bool	m_OverwriteExistingSegmentation

Protected Attributes inherited from mitk::Tool
std::string	m_EventConfig
	Let subclasses change their event configuration. More...

ToolManager *	m_ToolManager

Protected Attributes inherited from mitk::EventStateMachine
bool	m_IsActive

UndoController *	m_UndoController

bool	m_UndoEnabled

Additional Inherited Members
Static Public Member Functions inherited from mitk::EventStateMachine
static const char *	GetStaticNameOfClass ()

Static Public Member Functions inherited from mitk::InteractionEventHandler
static const char *	GetStaticNameOfClass ()

Public Attributes inherited from mitk::Tool
Message	GUIProcessEventsMessage
	To let GUI process new events (e.g. qApp->processEvents() ) More...

Message1< std::string >	ErrorMessage
	To send error messages (to be shown by some GUI) More...

Message1< bool >	CurrentlyBusy
	To send whether the tool is busy (to be shown by some GUI) More...

Message1< std::string >	GeneralMessage
	To send general messages (to be shown by some GUI) More...

Protected Types inherited from mitk::EventStateMachine
typedef MessageAbstractDelegate2< StateMachineAction , InteractionEvent , void >	ActionFunctionDelegate

typedef MessageAbstractDelegate1< const InteractionEvent *, bool >	ConditionFunctionDelegate

Detailed Description

FastMarching semgentation tool.

The segmentation is done by setting one or more seed points on the image and adapting the time range and threshold. The pipeline is: Smoothing->GradientMagnitude->SigmoidFunction->FastMarching->Threshold The resulting binary image is seen as a segmentation of an object.

For detailed documentation see ITK Software Guide section 9.3.1 Fast Marching Segmentation.

Definition at line 56 of file mitkFastMarchingTool3D.h.

Member Typedef Documentation

typedef itk::FastMarchingImageFilter<InternalImageType, InternalImageType> mitk::FastMarchingTool3D::FastMarchingFilterType

Definition at line 73 of file mitkFastMarchingTool3D.h.

typedef itk::GradientMagnitudeRecursiveGaussianImageFilter<InternalImageType, InternalImageType> mitk::FastMarchingTool3D::GradientFilterType

Definition at line 71 of file mitkFastMarchingTool3D.h.

typedef itk::Image<InternalPixelType, 3> mitk::FastMarchingTool3D::InternalImageType

Definition at line 65 of file mitkFastMarchingTool3D.h.

typedef float mitk::FastMarchingTool3D::InternalPixelType

Definition at line 64 of file mitkFastMarchingTool3D.h.

typedef FastMarchingFilterType::NodeContainer mitk::FastMarchingTool3D::NodeContainer

Definition at line 74 of file mitkFastMarchingTool3D.h.

typedef FastMarchingFilterType::NodeType mitk::FastMarchingTool3D::NodeType

Definition at line 75 of file mitkFastMarchingTool3D.h.

typedef itk::Image<OutputPixelType, 3> mitk::FastMarchingTool3D::OutputImageType

Definition at line 67 of file mitkFastMarchingTool3D.h.

typedef mitk::Tool::DefaultSegmentationDataType mitk::FastMarchingTool3D::OutputPixelType

Definition at line 66 of file mitkFastMarchingTool3D.h.

typedef itk::SigmoidImageFilter<InternalImageType, InternalImageType> mitk::FastMarchingTool3D::SigmoidFilterType

Definition at line 72 of file mitkFastMarchingTool3D.h.

typedef itk::CurvatureAnisotropicDiffusionImageFilter<InternalImageType, InternalImageType> mitk::FastMarchingTool3D::SmoothingFilterType

Definition at line 70 of file mitkFastMarchingTool3D.h.

typedef itk::BinaryThresholdImageFilter<InternalImageType, OutputImageType> mitk::FastMarchingTool3D::ThresholdingFilterType

Definition at line 69 of file mitkFastMarchingTool3D.h.

Constructor & Destructor Documentation

mitk::FastMarchingTool3D::FastMarchingTool3D ( )

protected

Definition at line 39 of file mitkFastMarchingTool3D.cpp.

mitk::FastMarchingTool3D::~FastMarchingTool3D ( )

protectedvirtual

Definition at line 52 of file mitkFastMarchingTool3D.cpp.

Member Function Documentation

void mitk::FastMarchingTool3D::Activated ( )

overrideprotectedvirtual

Called when the tool gets activated.

Derived tools should call their parents implementation at the beginning of the overriding function.

Reimplemented from mitk::Tool.

Definition at line 146 of file mitkFastMarchingTool3D.cpp.

References mitk::ToolCommand::New(), mitk::New(), mitk::PointSetDataInteractor::New(), mitk::DataNode::New(), mitk::PointSet::New(), OnAddPoint(), and OnDelete().

bool mitk::FastMarchingTool3D::CanHandle ( BaseData * referenceData ) const

overridevirtual

Reimplemented from mitk::Tool.

Definition at line 56 of file mitkFastMarchingTool3D.cpp.

References mitk::Image::GetDimension().

void mitk::FastMarchingTool3D::ClearSeeds ( )

Clear all seed points.

Definition at line 406 of file mitkFastMarchingTool3D.cpp.

References mitk::New(), mitk::PointSet::New(), OnAddPoint(), and OnDelete().

Pointer mitk::FastMarchingTool3D::Clone ( ) const

void mitk::FastMarchingTool3D::ConfirmSegmentation ( )

virtual

Adds the feedback image to the current working image.

Definition at line 276 of file mitkFastMarchingTool3D.cpp.

References mitk::CastToItkImage(), mitk::RenderingManager::GetInstance(), mitk::ImageTimeSelector::New(), mitk::New(), and mitk::RenderingManager::RequestUpdateAll().

void mitk::FastMarchingTool3D::Deactivated ( )

overrideprotectedvirtual

Called when the tool gets deactivated.

Derived tools should call their parents implementation at the end of the overriding function.

Reimplemented from mitk::Tool.

Definition at line 231 of file mitkFastMarchingTool3D.cpp.

References mitk::RenderingManager::GetInstance(), mitk::OpREMOVE, and mitk::RenderingManager::RequestUpdateAll().

us::ModuleResource mitk::FastMarchingTool3D::GetIconResource ( ) const

overridevirtual

Returns the tool button icon of the tool wrapped by a usModuleResource.

Returns: a valid ModuleResource or an invalid if this function is not reimplemented

Reimplemented from mitk::Tool.

Definition at line 77 of file mitkFastMarchingTool3D.cpp.

References ModuleContext::GetModule(), us::GetModuleContext(), and us::Module::GetResource().

const char * mitk::FastMarchingTool3D::GetName ( ) const

overridevirtual

Returns the name of this tool. Make it short!

This name has to fit into some kind of button in most applications, so take some time to think of a good name!

Implements mitk::Tool.

Definition at line 84 of file mitkFastMarchingTool3D.cpp.

const char ** mitk::FastMarchingTool3D::GetXPM ( ) const

overridevirtual

Returns an icon in the XPM format.

This icon has to fit into some kind of button in most applications, so make it smaller than 25x25 pixels.

XPM is e.g. supported by The Gimp. But if you open any XPM file in your text editor, you will see that you could also "draw" it with an editor.

Implements mitk::Tool.

Definition at line 72 of file mitkFastMarchingTool3D.cpp.

void mitk::FastMarchingTool3D::Initialize ( )

protectedvirtual

Definition at line 260 of file mitkFastMarchingTool3D.cpp.

References mitk::CastToItkImage(), and mitk::ImageTimeSelector::New().

mitk::FastMarchingTool3D::mitkClassMacro	(	FastMarchingTool3D	,
		AutoSegmentationTool
	)

void mitk::FastMarchingTool3D::OnAddPoint ( )

protectedvirtual

Add point action of StateMachine pattern.

Definition at line 317 of file mitkFastMarchingTool3D.cpp.

References mitk::RenderingManager::GetInstance(), mitk::RenderingManager::RequestUpdateAll(), and Update().

Referenced by Activated(), and ClearSeeds().

void mitk::FastMarchingTool3D::OnDelete ( )

protectedvirtual

Delete action of StateMachine pattern.

Definition at line 345 of file mitkFastMarchingTool3D.cpp.

References mitk::RenderingManager::GetInstance(), mitk::RenderingManager::RequestUpdateAll(), and Update().

Referenced by Activated(), and ClearSeeds().

void mitk::FastMarchingTool3D::Reset ( void )

protected

Reset all relevant inputs of the itk pipeline.

Definition at line 444 of file mitkFastMarchingTool3D.cpp.

References mitk::RenderingManager::GetInstance(), and mitk::RenderingManager::RequestUpdateAll().

void mitk::FastMarchingTool3D::SetAlpha ( double value )

Set parameter used in Fast Marching filter.

Definition at line 126 of file mitkFastMarchingTool3D.cpp.

void mitk::FastMarchingTool3D::SetBeta ( double value )

Set parameter used in Fast Marching filter.

Definition at line 103 of file mitkFastMarchingTool3D.cpp.

void mitk::FastMarchingTool3D::SetCurrentTimeStep ( int t )

virtual

Set the working time step.

Definition at line 454 of file mitkFastMarchingTool3D.cpp.

void mitk::FastMarchingTool3D::SetLowerThreshold ( double value )

Set parameter used in Threshold filter.

Definition at line 96 of file mitkFastMarchingTool3D.cpp.

void mitk::FastMarchingTool3D::SetSigma ( double value )

Set parameter used in Gradient Magnitude filter.

Definition at line 113 of file mitkFastMarchingTool3D.cpp.

void mitk::FastMarchingTool3D::SetStoppingValue ( double value )

Set parameter used in Fast Marching filter.

Definition at line 136 of file mitkFastMarchingTool3D.cpp.

void mitk::FastMarchingTool3D::SetUpperThreshold ( double value )

Set parameter used in Threshold filter.

Definition at line 89 of file mitkFastMarchingTool3D.cpp.

void mitk::FastMarchingTool3D::Update ( )

Updates the itk pipeline and shows the result of FastMarching.

Definition at line 362 of file mitkFastMarchingTool3D.cpp.

References mitk::CastToMitkImage(), mitk::RenderingManager::GetInstance(), MITK_ERROR, mitk::Image::New(), and mitk::RenderingManager::RequestUpdateAll().

Member Data Documentation

float mitk::FastMarchingTool3D::m_Alpha

protected

Definition at line 143 of file mitkFastMarchingTool3D.h.

float mitk::FastMarchingTool3D::m_Beta

protected

Definition at line 144 of file mitkFastMarchingTool3D.h.

int mitk::FastMarchingTool3D::m_CurrentTimeStep

protected

Definition at line 137 of file mitkFastMarchingTool3D.h.

FastMarchingFilterType::Pointer mitk::FastMarchingTool3D::m_FastMarchingFilter

protected

Definition at line 162 of file mitkFastMarchingTool3D.h.

GradientFilterType::Pointer mitk::FastMarchingTool3D::m_GradientMagnitudeFilter

protected

Definition at line 160 of file mitkFastMarchingTool3D.h.

float mitk::FastMarchingTool3D::m_LowerThreshold

protected

Definition at line 139 of file mitkFastMarchingTool3D.h.

bool mitk::FastMarchingTool3D::m_NeedUpdate

protected

Definition at line 135 of file mitkFastMarchingTool3D.h.

unsigned int mitk::FastMarchingTool3D::m_PointSetAddObserverTag

protected

Definition at line 155 of file mitkFastMarchingTool3D.h.

unsigned int mitk::FastMarchingTool3D::m_PointSetRemoveObserverTag

protected

Definition at line 156 of file mitkFastMarchingTool3D.h.

mitk::ToolCommand::Pointer mitk::FastMarchingTool3D::m_ProgressCommand

protected

Definition at line 131 of file mitkFastMarchingTool3D.h.

Image::Pointer mitk::FastMarchingTool3D::m_ReferenceImage

protected

Definition at line 133 of file mitkFastMarchingTool3D.h.

InternalImageType::Pointer mitk::FastMarchingTool3D::m_ReferenceImageAsITK

protected

Definition at line 148 of file mitkFastMarchingTool3D.h.

mitk::DataNode::Pointer mitk::FastMarchingTool3D::m_ResultImageNode

protected

Definition at line 150 of file mitkFastMarchingTool3D.h.

NodeContainer::Pointer mitk::FastMarchingTool3D::m_SeedContainer

protected

Definition at line 146 of file mitkFastMarchingTool3D.h.

mitk::PointSetDataInteractor::Pointer mitk::FastMarchingTool3D::m_SeedPointInteractor

protected

Definition at line 154 of file mitkFastMarchingTool3D.h.

mitk::PointSet::Pointer mitk::FastMarchingTool3D::m_SeedsAsPointSet

protected

Definition at line 153 of file mitkFastMarchingTool3D.h.

mitk::DataNode::Pointer mitk::FastMarchingTool3D::m_SeedsAsPointSetNode

protected

Definition at line 152 of file mitkFastMarchingTool3D.h.

float mitk::FastMarchingTool3D::m_Sigma

protected

Definition at line 142 of file mitkFastMarchingTool3D.h.

SigmoidFilterType::Pointer mitk::FastMarchingTool3D::m_SigmoidFilter

protected

Definition at line 161 of file mitkFastMarchingTool3D.h.

SmoothingFilterType::Pointer mitk::FastMarchingTool3D::m_SmoothFilter

protected

Definition at line 159 of file mitkFastMarchingTool3D.h.

float mitk::FastMarchingTool3D::m_StoppingValue

protected

Definition at line 141 of file mitkFastMarchingTool3D.h.

ThresholdingFilterType::Pointer mitk::FastMarchingTool3D::m_ThresholdFilter

protected

Definition at line 158 of file mitkFastMarchingTool3D.h.

float mitk::FastMarchingTool3D::m_UpperThreshold

protected

Definition at line 140 of file mitkFastMarchingTool3D.h.

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

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation