Inheritance diagram for niftk::MorphologicalSegmentorController:

Collaboration diagram for niftk::MorphologicalSegmentorController:

Public Member Functions
	MorphologicalSegmentorController (IBaseView *view)

virtual	~MorphologicalSegmentorController ()

virtual void	SetupGUI (QWidget *parent) override
	Sets up the GUI. This function has to be called from the CreateQtPartControl function of the view. More...

void	OnViewGetsClosed ()
	If the user hits the close icon, it is equivalent to a Cancel, and the segmentation is destroyed without warning. More...

virtual void	OnNodeVisibilityChanged (const mitk::DataNode node, const mitk::BaseRenderer renderer) override
	Called when the visibility of a data node has changed. More...

virtual void	OnNodeRemoved (const mitk::DataNode *node) override
	Called when a data node has been removed. More...

virtual void	OnSegmentationEdited (int imageIndex)
	Called when the segmentation is manually edited via the paintbrush tool. More...

Public Member Functions inherited from niftk::BaseSegmentorController
	BaseSegmentorController (IBaseView *view)

virtual	~BaseSegmentorController ()

mitk::ToolManager *	GetToolManager () const
	Returns the segmentation tool manager used by the segmentor. More...

template<class ToolType >
ToolType *	GetToolByType ()

virtual bool	EventFilter (const mitk::StateEvent *stateEvent) const override
	Returns true if the event should be filtered, i.e. not processed, otherwise false. More...

virtual bool	EventFilter (mitk::InteractionEvent *event) const override
	Returns true if the event should be filtered, i.e. not processed, otherwise false. More...

const QColor &	GetDefaultSegmentationColour () const
	Default colour to be displayed in the new segmentation dialog box. More...

void	SetDefaultSegmentationColour (const QColor &defaultSegmentationColour)
	Default colour to be displayed in the new segmentation dialog box. More...

virtual void	OnViewGetsActivated () override
	Called when the BlueBerry view that hosts the GUI for this controller gets activated. More...

Public Member Functions inherited from niftk::BaseController
	BaseController (IBaseView *view)
	Constructs a BaseController object. More...

virtual	~BaseController ()
	Destructs the BaseController object. More...

ImageOrientation	GetOrientation () const
	Returns the orientation of the selected render window. Returns IMAGE_ORIENTATION_UNKNOWN if no window is selected or the selected window is a 3D window. More...

int	GetSliceIndex () const
	Returns the index of the displayed slice in the currently selected window. Returns -1 if no window is selected or the selected window is a 3D window. More...

mitk::Point3D	GetSelectedPosition () const
	Returns the selected position in the current editor (render window part). The selected position is the voxel at the intersection of the crosshair planes. More...

virtual void	OnViewGetsDeactivated ()
	Called when the BlueBerry view that hosts the GUI for this controller gets deactivated. More...

virtual void	OnViewGetsVisible ()
	Called when the BlueBerry view that hosts the GUI for this controller becomes visible. More...

virtual void	OnViewGetsHidden ()
	Called when the BlueBerry view that hosts the GUI for this controller becomes hidden. More...

Public Member Functions inherited from niftk::StateMachineEventFilter
	mitkClassMacroNoParent (StateMachineEventFilter) StateMachineEventFilter()

virtual	~StateMachineEventFilter ()

Protected Slots
virtual void	OnNewSegmentationButtonClicked () override
	Called when the user hits the button "New segmentation", which creates the necessary reference data. More...

void	OnThresholdingValuesChanged (double lowerThreshold, double upperThreshold, int axialSliceNumber)
	Called from niftkMorphologicalSegmentorGUI when thresholding sliders or spin boxes changed. More...

void	OnErosionsValuesChanged (double upperThreshold, int numberOfErosions)
	Called from niftkMorphologicalSegmentorGUI when erosion sliders or spin boxes changed. More...

void	OnDilationsValuesChanged (double lowerPercentage, double upperPercentage, int numberOfDilations)
	Called from niftkMorphologicalSegmentorGUI when dilation sliders or spin boxes changed. More...

void	OnRethresholdingValuesChanged (int boxSize)
	Called from niftkMorphologicalSegmentorGUI when re-thresholding widgets changed. More...

void	OnTabChanged (int i)
	Called from niftkMorphologicalSegmentorGUI when a tab changes. More...

void	OnOKButtonClicked ()
	Called from niftkMorphologicalSegmentatorControls when OK button is clicked, which should finalise / finish and accept the segmentation. More...

void	OnRestartButtonClicked ()
	Called from niftkMorphologicalSegmentatorControls when Restart button is clicked, which means "back to start", like a "reset" button. More...

void	OnCancelButtonClicked ()
	Called from niftkMorphologicalSegmentorGUI when cancel button is clicked, which should mean "throw away" / "abandon" current segmentation. More...

Protected Slots inherited from niftk::BaseSegmentorController
virtual void	OnNewSegmentationButtonClicked ()=0
	Called from niftkSegmentationSelectorWidget when the 'Start/restart segmentation' button is clicked. More...

Protected Member Functions
virtual bool	IsASegmentationImage (const mitk::DataNode::Pointer node) override
	For Morphological Editing, a Segmentation image should have a grey scale parent, and two binary children called SUBTRACTIONS_IMAGE_NAME and ADDITIONS_IMAGE_NAME. More...

virtual bool	IsAWorkingImage (const mitk::DataNode::Pointer node) override
	For Morphological Editing, a Working image should be called either SUBTRACTIONS_IMAGE_NAME and ADDITIONS_IMAGE_NAME, and have a binary image parent. More...

virtual std::vector < mitk::DataNode * >	GetWorkingDataFromSegmentationNode (const mitk::DataNode::Pointer node) override
	Assumes input is a valid segmentation node, then searches for the derived children of the node, looking for binary images called SUBTRACTIONS_IMAGE_NAME and ADDITIONS_IMAGE_NAME. Returns empty list if both not found. More...

virtual mitk::DataNode *	GetSegmentationNodeFromWorkingData (const mitk::DataNode::Pointer node) override
	Assumes input is a valid working node, then searches for a binary parent node, returns NULL if not found. More...

virtual bool	CanStartSegmentationForBinaryNode (const mitk::DataNode::Pointer node) override
	For any binary image, we return true if the property midas.morph.stage is present, and false otherwise. More...

virtual BaseGUI *	CreateGUI (QWidget *parent) override
	Creates the morphological segmentor widget that holds the GUI components of the view. More...

virtual void	OnDataManagerSelectionChanged (const QList< mitk::DataNode::Pointer > &nodes) override
	Called when the selection changes in the data manager. More...

Protected Member Functions inherited from niftk::BaseSegmentorController
virtual void	OnActiveToolChanged ()
	Called from niftkToolSelectorWidget when a tool changes. More...

std::vector< mitk::DataNode * >	GetWorkingData ()
	Gets a vector of the working data nodes registered with the tool manager. The data nodes normally hold image, but could be surfaces etc. Empty list is returned if this can't be found. More...

mitk::Image *	GetWorkingImage (int index)
	Gets a single binary image registered with the ToolManager. Returns nullptr if it can't be found or is not an image. More...

mitk::DataNode *	GetReferenceNode ()
	Gets the reference node from the tool manager or nullptr if it can't be found. More...

mitk::Image *	GetReferenceImage ()
	Gets the reference image from the tool manager, or nullptr if this doesn't yet exist or is not an image. Assumes that a reference (grey scale) image is always registered with the tool manager. More...

mitk::DataNode *	FindReferenceNodeFromSegmentationNode (const mitk::DataNode::Pointer segmentationNode)
	Gets the reference node that the segmentation node belongs to. Assumes that the reference (grey scale) node is always the direct parent of the segmentation (binary) node, so we simply search for a non binary parent. More...

void	SetReferenceImageSelected ()
	Makes sure the reference image is the selected one. More...

virtual bool	IsAReferenceImage (const mitk::DataNode::Pointer node)
	Returns true if node represent an image that is non binary, and false otherwise. More...

virtual void	ApplyDisplayOptions (mitk::DataNode *node)
	Decorates a DataNode according to the user preference settings, or requirements for binary images. More...

int	GetReferenceImageSliceAxis ()
	Returns which image coordinate corresponds to the currently selected orientation. Retrieves the currently active QmitkRenderWindow, and the reference image registered with the ToolManager, and returns the Image axis that the current view is looking along, or -1 if it can not be worked out. More...

int	GetReferenceImageSliceAxis (ImageOrientation orientation)
	Returns which image coordinate corresponds to the given orientation. Looks up the ReferenceImage registered with ToolManager and returns the axis [0,1,2] that corresponds to the given orientation, or -1 if it can't be found. More...

int	GetReferenceImageSliceIndex ()
	Returns the slice index in the reference image that corresponds to the currently displayed slice. This might be different to the slice displayed in the viewer, depending on the up direction. More...

int	GetReferenceImageSliceUpDirection ()
	Returns the "Up" direction which is the anterior, superior or right direction depending on which orientation you are interested in. More...

virtual mitk::DataNode *	CreateNewSegmentation ()
	Creates from derived classes when the the user hits the "New segmentation", producing a dialog box, and on successful completion of the dialog box, will create a new segmentation image. More...

BaseSegmentorGUI *	GetSegmentorGUI () const
	Gets the segmentor widget that holds the GUI components of the view. More...

bool	HasInitialisedWorkingData ()
	Utility method to check that we have initialised all the working data such as contours, region growing images etc. More...

Protected Member Functions inherited from niftk::BaseController
mitk::DataStorage *	GetDataStorage () const

void	RequestRenderWindowUpdate () const

QList< mitk::DataNode::Pointer >	GetDataManagerSelection () const

mitk::SliceNavigationController *	GetSliceNavigationController () const

virtual void	OnSelectedSliceChanged (niftk::ImageOrientation orientation, int sliceIndex)
	Called when the selected slice changes. This happens when selected window changes in the current editor (render window part) or when the focus is on a 2D render window in the current editor and the selected slice changes, either through interaction (e.g. by scrolling with the mouse wheel) or through an API call. More...

BaseGUI *	GetGUI () const
	Gets the widget that holds the GUI components of the view. More...

IBaseView *	GetView () const
	Gets the segmentor BlueBerry view. More...

virtual void	OnFocusChanged ()
	Called when the window focus changes, and tracks the current mitk::BaseRenderer*. More...

virtual mitk::BaseRenderer *	GetFocused2DRenderer () const
	Returns the currently focused renderer, as this class is tracking the focus changes. More...

virtual void	OnNodeAdded (const mitk::DataNode *node)
	Called when a data node is added to the data storage. Empty implementation. Derived classes can override it. More...

virtual void	OnNodeChanged (const mitk::DataNode *node)
	Called when a data node in the data storage has changed. Empty implementation. Derived classes can override it. More...

virtual void	OnNodeDeleted (const mitk::DataNode *node)
	Called when a data node has been deleted that has previously been in the data storage. Empty implementation. Derived classes can override it. More...

void	WaitCursorOn ()
	Convenient method to set and reset a wait cursor ("hourglass") More...

void	WaitCursorOff ()
	Convenient method to restore the standard cursor. More...

void	BusyCursorOn ()
	Convenient method to set and reset a busy cursor. More...

void	BusyCursorOff ()
	Convenient method to restore the standard cursor. More...

Constructor & Destructor Documentation

niftk::MorphologicalSegmentorController::MorphologicalSegmentorController ( IBaseView * view )

niftk::MorphologicalSegmentorController::~MorphologicalSegmentorController ( )

virtual

Member Function Documentation

bool niftk::MorphologicalSegmentorController::CanStartSegmentationForBinaryNode ( const mitk::DataNode::Pointer node )

overrideprotectedvirtual

For any binary image, we return true if the property midas.morph.stage is present, and false otherwise.

Implements niftk::BaseSegmentorController.

BaseGUI * niftk::MorphologicalSegmentorController::CreateGUI ( QWidget * parent )

overrideprotectedvirtual

Creates the morphological segmentor widget that holds the GUI components of the view.

Implements niftk::BaseController.

mitk::DataNode * niftk::MorphologicalSegmentorController::GetSegmentationNodeFromWorkingData ( const mitk::DataNode::Pointer node )

overrideprotectedvirtual

Assumes input is a valid working node, then searches for a binary parent node, returns NULL if not found.

Reimplemented from niftk::BaseSegmentorController.

std::vector< mitk::DataNode * > niftk::MorphologicalSegmentorController::GetWorkingDataFromSegmentationNode ( const mitk::DataNode::Pointer node )

overrideprotectedvirtual

Assumes input is a valid segmentation node, then searches for the derived children of the node, looking for binary images called SUBTRACTIONS_IMAGE_NAME and ADDITIONS_IMAGE_NAME. Returns empty list if both not found.

Reimplemented from niftk::BaseSegmentorController.

bool niftk::MorphologicalSegmentorController::IsASegmentationImage ( const mitk::DataNode::Pointer node )

overrideprotectedvirtual

For Morphological Editing, a Segmentation image should have a grey scale parent, and two binary children called SUBTRACTIONS_IMAGE_NAME and ADDITIONS_IMAGE_NAME.

Reimplemented from niftk::BaseSegmentorController.

bool niftk::MorphologicalSegmentorController::IsAWorkingImage ( const mitk::DataNode::Pointer node )

overrideprotectedvirtual

For Morphological Editing, a Working image should be called either SUBTRACTIONS_IMAGE_NAME and ADDITIONS_IMAGE_NAME, and have a binary image parent.

Reimplemented from niftk::BaseSegmentorController.

void niftk::MorphologicalSegmentorController::OnCancelButtonClicked ( )

protectedslot

Called from niftkMorphologicalSegmentorGUI when cancel button is clicked, which should mean "throw away" / "abandon" current segmentation.

void niftk::MorphologicalSegmentorController::OnDataManagerSelectionChanged ( const QList< mitk::DataNode::Pointer > & nodes )

overrideprotectedvirtual

Called when the selection changes in the data manager.

See also: QmitkAbstractView::OnSelectionChanged.

Reimplemented from niftk::BaseSegmentorController.

void niftk::MorphologicalSegmentorController::OnDilationsValuesChanged	(	double	lowerPercentage,
		double	upperPercentage,
		int	numberOfDilations
	)

protectedslot

Called from niftkMorphologicalSegmentorGUI when dilation sliders or spin boxes changed.

void niftk::MorphologicalSegmentorController::OnErosionsValuesChanged	(	double	upperThreshold,
		int	numberOfErosions
	)

protectedslot

Called from niftkMorphologicalSegmentorGUI when erosion sliders or spin boxes changed.

void niftk::MorphologicalSegmentorController::OnNewSegmentationButtonClicked ( )

overrideprotectedvirtualslot

Called when the user hits the button "New segmentation", which creates the necessary reference data.

Note: The 'new segmentation' button is enabled only when a reference image is selected. A reference image gets selected when the selection in the data manager changes to a valid reference image or a segmentation that was created by this segmentor. Hence, we can assume that we have a valid tool manager, paintbrush tool and reference image.

Create the new segmentation, either using a previously selected one, or create a new volume.

Note: The tool selection box tracks the events when the working data changes, and enables and disables the tool buttons accordingly. However, we want to enable the buttons only in the second and third step of the workflow (erosion and dilation). So, since we are at the first step, we have to disable the tool selector that was enabled at the previous call when setting the working data.

void niftk::MorphologicalSegmentorController::OnNodeRemoved ( const mitk::DataNode * node )

overridevirtual

Called when a data node has been removed.

Reimplemented from niftk::BaseController.

void niftk::MorphologicalSegmentorController::OnNodeVisibilityChanged	(	const mitk::DataNode *	node,
		const mitk::BaseRenderer *	renderer
	)

overridevirtual

Called when the visibility of a data node has changed.

Reimplemented from niftk::BaseController.

void niftk::MorphologicalSegmentorController::OnOKButtonClicked ( )

protectedslot

Called from niftkMorphologicalSegmentatorControls when OK button is clicked, which should finalise / finish and accept the segmentation.

Remove the axial cut-off plane node from the data storage.

void niftk::MorphologicalSegmentorController::OnRestartButtonClicked ( )

protectedslot

Called from niftkMorphologicalSegmentatorControls when Restart button is clicked, which means "back to start", like a "reset" button.

Reset the axial cut-off plane to the bottom of the image.

void niftk::MorphologicalSegmentorController::OnRethresholdingValuesChanged ( int boxSize )

protectedslot

Called from niftkMorphologicalSegmentorGUI when re-thresholding widgets changed.

void niftk::MorphologicalSegmentorController::OnSegmentationEdited ( int imageIndex )

virtual

Called when the segmentation is manually edited via the paintbrush tool.

Parameters

imageIndex tells which image has been modified: erosion addition / subtraction or dilation addition / subtraction.

void niftk::MorphologicalSegmentorController::OnTabChanged ( int i )

protectedslot

Called from niftkMorphologicalSegmentorGUI when a tab changes.

void niftk::MorphologicalSegmentorController::OnThresholdingValuesChanged	(	double	lowerThreshold,
		double	upperThreshold,
		int	axialSliceNumber
	)

protectedslot

Called from niftkMorphologicalSegmentorGUI when thresholding sliders or spin boxes changed.

void niftk::MorphologicalSegmentorController::OnViewGetsClosed ( )

If the user hits the close icon, it is equivalent to a Cancel, and the segmentation is destroyed without warning.

TODO this is not invoked at all. This function was called "ClosePart" before it was moved here from niftkMorphologicalSegmentorView. It was not invoked there, either. I leave this here to remind me that the segmentation should be discarded when the view is closed.

void niftk::MorphologicalSegmentorController::SetupGUI ( QWidget * parent )

overridevirtual

Sets up the GUI. This function has to be called from the CreateQtPartControl function of the view.

Reimplemented from niftk::BaseSegmentorController.

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

Public Member Functions

Protected Slots

Protected Member Functions

Constructor & Destructor Documentation

Member Function Documentation