milxQtShapeModel Class Reference

Inheritance diagram for milxQtShapeModel:

Public Slots
void	LoadModel (const QString filename)
	Loads a model as an SSM (*.ssm) file. MILX-MSK like call. More...
virtual void	openModel (const QString filename)
	Loads a model as an SSM (*.ssm) file. Alias same as LoadModel(). More...
virtual void	SaveModel (const QString filename)
	Saves a model as an SSM (*.ssm) file. MILX-MSK like call. More...
virtual void	saveModel (const QString filename)
	Saves a model as an SSM (*.ssm) file. More...
virtual void	SetInputCollection (vtkPolyDataCollection *meshes)
	Uses the collection of polydata to create shape model. More...
virtual void	SetInputCollection (vtkPolyDataCollection *meshes, QStringList &filenames)
	Uses the collection of polydata to create shape model. More...
void	SetPrecision (float modePrecision)
	Assigns the reduction factor of the modes, i.e the number of modes required to quantify modePrecision percent of the model.
void	AddShape (vtkPolyData *shape)
	Adds the shape to the SSM, once done adding shapes, call generateSSM() to get the SSM.
vtkPolyData *	GetShape (unsigned int index)
	Gets the shape at index in the SSM.
vtkPolyData *	GetAlignedShape (unsigned int index)
	Gets the shape at index in the SSM.
vtkPolyData *	GetProcrustesAlignedSurface (unsigned int index)
	Gets the shape at index in the SSM. Same as GetAlignedShape().
vtkPolyData *	GetMeanShape ()
	Returns the mean shape of the Statistical Shape Model. Assumes SSM has been generated (via generateSSM()).
QPointer< milxQtModel >	getMeanModel ()
	Returns the mean model of the Statistical Shape Model. Assumes SSM has been generated (via generateSSM()). More...
int	GetNumberOfModes ()
	Returns the number of modes in the Statistical Shape Model according to the precision set. Assumes SSM has been generated (via generateSSM()).
int	GetNumberOfShapes ()
	Returns the number of shapes in the Statistical Shape Model. Assumes SSM has been generated (via generateSSM()).
QList< int >	getCaseIDs ()
	Returns the case IDs for the SSM. Assumes that an SSM has been loaded.
virtual vtkDataSet *	GetDataSet ()
	Get the data, depending on whats been generated, return that dataset.
virtual void	createMenu (QMenu *menu)
	Create the menu for the data in this object. Used for context menu and file menus. More...
virtual void	generateSSM ()
virtual void	generateMeanModel (vtkSmartPointer< vtkPolyData > shape=NULL)
void	generateModels (const bool display=true)
void	generateAlignedModels (const bool display=true)
virtual void	generateModes ()
virtual void	generateCollectionBasedOnMode ()
void	generateVectorField ()
void	generateTensorField ()
void	generateCorrespondences ()
void	mean ()
	Show the mean model in the window. More...
void	aligned ()
	Show the aligned models in the window as a set of coloured point clouds. More...
void	original ()
	Show the original models in the window as a set of coloured point clouds. More...
void	modesAsVectors ()
	Show the modes variation as a vector field.
void	modesAsTensors ()
	Show the modes variation as a ellipsoidal tensor field.
void	modesAsCollection ()
	Show the modes variation as a collection of surfaces.
void	procrustes ()
	Change the procrustes mode of the SSM (causes recomputation of the model).
void	alignment ()
	Output each aligned shape as a PNG image in a directory and prefix provided by the user (internally via file dialog). More...
void	alignedMeshes ()
	Output each aligned shape as a poly data file in a directory and prefix provided by the user (internally via file dialog). More...
void	originalMeshes ()
	Output each original shape as a poly data file in a directory and prefix provided by the user (internally via file dialog). More...
void	pointIds ()
	Output each aligned shape coloured by the point IDs as a PNG image in a directory and prefix provided by the user (internally via file dialog). More...
void	coordinates ()
	Output each aligned shape coloured by the coordinates as a PNG image in a directory and prefix provided by the user (internally via file dialog). More...
void	replaceOriginal ()
	Replace the original (unaligned) meshes with the aligned ones. The new meshes are unnormalised as compared to the aligned meshes which are normalised. More...
void	correspondences ()
	Compare points from each shape to measure the correspondence as a hedgehog plot. More...
void	compactness ()
	Plot the compactness of the SSM. More...
void	specificity ()
	Plot the specificity of the SSM. More...
void	generalisability ()
	Plot the generalisability of the SSM. More...
void	eigenvalues ()
	Plot the eigenvalues of the model. More...
void	eigenmodes ()
	Plot the primary eigenmodes of the model for each training shape. More...
void	parameters ()
	Plot the training shape parameters of the model for each training shape (leave 1 out). More...
Public Slots inherited from milxQtRenderWindow
void	addModelActor (vtkSmartPointer< vtkActor > mdlActor)
	Directly add model actor to generic view. More...
void	removeModelActor (vtkSmartPointer< vtkActor > mdlActor)
	Directly remove model actor from generic view. More...
void	addActor (vtkSmartPointer< vtkActor > imgActor, vtkMatrix4x4 *transformMatrix=NULL)
	Directly add actor to generic view with transform matrix. More...
void	addImageActor (vtkSmartPointer< vtkImageActor > imgActor, vtkMatrix4x4 *transformMatrix=NULL)
	Directly add image actor to generic view. More...
void	removeImageActor (vtkSmartPointer< vtkImageActor > imgActor)
	Directly remove image actor from generic view. More...
void	importFrom (milxQtRenderWindow *windowToImportFrom)
	Import actors/scene directly from another renderwindow. More...
void	importViewFrom (milxQtRenderWindow *windowToImportFrom)
	Same as importFrom()
virtual void	updateTextActor (vtkObject *obj, unsigned long, void *client_data, void *, vtkCommand *command)
	Update any text actors in display to current slice.
virtual void	updateImageActor (vtkObject *obj, unsigned long, void *client_data, void *, vtkCommand *command)
	Update any image actors in display to current slice when slice number changes.
virtual void	updateImageActor (vtkSmartPointer< vtkImageActor > actor)
void	userEvent (QMouseEvent *event=NULL)
void	userEvent (QKeyEvent *event)
void	userEvent (QWheelEvent *event)
void	refresh ()
	Refresh the display of the model including widgets. Camera remains as is.
vtkSmartPointer< vtkMatrix4x4 >	getTransformMatrix ()
	Internal transform matrix used to transform actors appropriately for direction and coordinate systems.
void	reset ()
	Reset the rendering, camera and windowing.
bool	isLoaded ()
	Is the data successfully loaded? Use this to check if all is ok with data display.
void	linkProgressEventOf (vtkObject *obj)
	Link the progress of filters etc to keep the UI responsive.
virtual void	updateCoords (vtkObject *obj)
	Picks the coordinates and pixel value from the current mouse position in the window. More...
virtual void	contour ()
	Draw contour interactively.
void	contourAsPolyData ()
	Save contour as polydata/model. This saves all intermediate points, not just what the user places.
void	contourAsNodePolyData ()
	Save contour as polydata/model. This only saves the points the user has placed.
void	contourInitFromPolyData (QString filename="")
	Load contour from polydata/model. More...
void	enableAxes (float xScale=1.0, float yScale=1.0, float zScale=1.0)
	Enable axes display with each arrow for dimension scaled as provided.
void	disableAxes ()
	Disables the axes display.
void	axesDisplay ()
	Toggles the axes display.
void	disableOrient ()
	Disables orientation marker.
void	orientDisplay ()
	Toggles orientation marker.
virtual void	background (bool white=false)
	Changes background to white.
void	lighting ()
	Toggles two sided lighting in display.
void	textDisplay ()
	Toggles text in display.
void	crosshair ()
	Toggles corsshair.
virtual void	viewToXYPlane ()
	Change view to xy-plane.
void	viewToAxial ()
virtual void	viewToZXPlane ()
	Change view to zx-plane.
void	viewToCoronal ()
virtual void	viewToZYPlane ()
	Change view to zy-plane.
void	viewToSagittal ()
int	getDefaultOrientation ()
	Get the orientation mode to one of the supported standards. More...
void	setDefaultOrientation (int orientMode)
	Change orientation mode to one of the supported standards. Default: Radiological. More...
int	getView ()
	Return current view mode identified by number. 0-axial, 1-coronal, 2-sagittal.
void	setView (int viewMode)
	Change view to view mode identified by number. 0-axial, 1-coronal, 2-sagittal. More...
void	enableActionBasedOnView ()
	Enables the view actions corresponding to current view set.
void	disableDefaultView ()
	Disables the default view whenever data is process or displayed. Enabled by default. More...
void	enableDefaultView ()
void	setDefaultView (int viewMode)
	Change default view to view mode identified by number. 0-axial, 1-coronal, 2-sagittal.
void	saveView (QString filename="")
void	saveViewFile ()
void	loadView (QString filename="")
	Saves the camera details to internal variables that can be restore anytime with loadView().
void	loadViewFile ()
virtual void	enableScale (QString title="", const bool quiet=false, double minRange=0.0, double maxRange=0.0, int noOfLabels=3)
	Enable scale bar display with the title provided. More...
virtual void	disableScale ()
	Disables the scale bar display.
virtual void	enableCrosshair ()
	Enables the mouse pointer as a crosshair instead. Scene must be rendered before calling.
virtual void	disableCrosshair ()
	Restores the mouse pointer to default.
virtual void	scaleDisplay (const bool forceDisplay=false)
	Toggles the scale bar display. More...
virtual void	colourMapToRainbow (double minRange=0.0, double maxRange=0.0)
	Change the colour map to default VTK which is rainbow.
virtual void	colourMapToVTK (double minRange=0.0, double maxRange=0.0)
	Change the colour map to inverse of default VTK.
virtual void	colourMapToGray (double minRange=0.0, double maxRange=0.0)
	Change the colour map to Gray.
virtual void	colourMapToSeismic (double minRange=0.0, double maxRange=0.0)
	Change the colour map to Seismic.
virtual void	colourMapToLogGray (double minRange=0.0, double maxRange=0.0)
	Change the colour map to Logarithmic (base 10) Gray.
virtual void	colourMapToJet (double minRange=0.0, double maxRange=0.0)
	Change the colour map to Jet.
virtual void	colourMapToNIH (double minRange=0.0, double maxRange=0.0)
	Change the colour map to NIH.
virtual void	colourMapToNIH_Fire (double minRange=0.0, double maxRange=0.0)
	Change the colour map to NIH Fire.
virtual void	colourMapToAAL (double minRange=0.0, double maxRange=0.0)
	Change the colour map to AAL.
virtual void	colourMapToFS (double minRange=0.0, double maxRange=0.0)
	Change the colour map to FS (FreeSurfer)
virtual void	colourMapToHOT (double minRange=0.0, double maxRange=0.0)
	Change the colour map to HOT.
virtual void	colourMapToCOOL (double minRange=0.0, double maxRange=0.0)
	Change the colour map to COOL.
virtual void	colourMapToCOOLWARM (double minRange=0.0, double maxRange=0.0)
	Change the colour map to COOL.
virtual void	colourMapToKnee (double minRange=0.0, double maxRange=0.0)
	Change the colour map to Knee.
virtual void	colourMapToBone (double minRange=0.0, double maxRange=0.0)
	Change the colour map to Bone.
virtual void	colourMapToSpectral (double minRange=0.0, double maxRange=0.0)
	Change the colour map to Spectral.
virtual void	colourMapToGNUPlot (double minRange=0.0, double maxRange=0.0)
	Change the colour map to GNUPlot.
virtual void	colourMapToCubeHelix (double minRange=0.0, double maxRange=0.0)
	Change the colour map to CubeHelix.
virtual void	colourMapToHSV (double minRange=0.0, double maxRange=0.0)
	Change the colour map to HSV.
void	generateRender ()
	Generate the render so it is ready for display. Should be called before showing the window. More...
void	setCustomActionGroup (QActionGroup *actionGrp)
	Set the action group for the menu with custom connections.
void	createCustomConnections (QList< QAction *> actionsInMenu)
void	createCustomConnections (QMenu *fromMenu)
	Create a series of connections on each action in group which will be placed into the context menu.
virtual void	customOperation ()
	Custom operation, data dependent for viewing in unified environment. By default, this allows importing of actors into the current views. More...
virtual void	createMenu (QMenu *menu)
	Create the menu for the data in this object. Used for context menu and file menus. More...
bool	openModelUsingQt (const QString filename, vtkSmartPointer< vtkPolyData > &data)
	Opens a model file using Qt file objects, which can be a Wavefront Object file (*.obj) only. This member is intended to be used with the Qt resource system. More...
Public Slots inherited from milxQtWindow
void	setName (const QString filename)
	Set the name of the data.
QString	getName ()
	Returns the name of the data.
void	rename ()
	Renames the data.
QString	strippedName ()
	Returns the stripped (path removed) name of the data.
QString	strippedBaseName ()
	Returns the stripped (path removed) base (no suffix) name of the data.
virtual QString	strippedNamePrefix ()
	Returns the stripped (path removed) name of the data with "Generic" prefix. More...
void	setNamePrefix (const QString newPrefix)
	Sets the prefix of the name of the data provided.
void	addToContextMenu (QAction *act)
	Adds (prepends) the action to the context menu. Connections are assumed to be made before hand.
void	appendToContextMenu (QAction *act)
	Adds (appends) the action to the context menu. Connections are assumed to be made before hand.
void	addToContextMenu (QMenu *newMenu)
	Adds the menu to the context menu. Connections are assumed to be made before hand.
void	addExtensionAction (QAction *act)
	Adds (in extension section) the action as an extension action. Connections are assumed to be made before hand.
void	addMenuToContextMenu (QMenu *newMenu)
	Adds (prepends) the menu to the context menu. Connections are assumed to be made before hand.
void	appendMenuToContextMenu (QMenu *newMenu)
	Adds (appends) the menu to the context menu. Connections are assumed to be made before hand.
virtual void	copyToContextMenu (QMenu *copyMenu)
	Copies the menu, by duplicating the entries, to the context menu. Connections are assumed to be made before hand.
void	setVerboseMode (bool verbose)
	Verbose mode for message output.
void	setDeletableOnClose (bool delOnClose)
	Set if the window deletable on close. Default is true.
bool	isDeletableOnClose ()
	Is the window deletable on close?
void	setConsole (milxQtConsole *con)
	Set the console for log output.
void	consumeVTKEvent (vtkObject *obj, unsigned long, void *client_data, void *, vtkCommand *command)
	Consume the event so that VTK interactor style doesn't get it. Safeguard for if remove observer directives have missed some bindings.
void	updateQtEvents ()
	Update the Qt events, used to keep UI responsive.

Signals
void	collectionAvailable (vtkPolyDataCollection *, QStringList &)
void	resultAvailable (milxQtRenderWindow *)
	Send signal that Resultant render window is available for showing.
void	resultAvailable (milxQtModel *)
	Send signal that Resultant model is available for showing.
Signals inherited from milxQtRenderWindow
void	imageAvailable (vtkImageData *, QString)
	Send signal that an image is available for showing.
void	modelAvailable (vtkPolyData *, QString)
	Send signal that an surface etc. is available for showing.
void	tableToPlot (vtkSmartPointer< vtkTable >, QString)
	Emit signal to show the table as a plot.
void	modified (vtkSmartPointer< vtkImageActor >)
	Emit signal to allow updating of image actors if present.
Signals inherited from milxQtWindow
void	closing (QWidget *win)
	Send signal that the window is closing.
void	nameChanged (const QString newName)
	Send signal that the data has been renamed.
void	working (int value)
	Send signal that computation is in progress. Value carries the progress,.
void	done (int value)
	Send signal that computation is done. Value carries the progress,.

Public Member Functions
	milxQtShapeModel (QWidget *theParent=0, bool contextSystem=true)
virtual	~milxQtShapeModel ()
virtual bool	isLoaded ()
	Is the model loaded successfully?
Public Member Functions inherited from milxQtRenderWindow
	milxQtRenderWindow (QWidget *theParent=0, bool contextSystem=true)
	The standard constructor. More...
virtual	~milxQtRenderWindow ()
	The standard destructor.
void	contextMenuSystem (bool context)
	Disable/enable context menu system, should be on by default otherwise VTK will steal all right click events. More...
void	AddActor (vtkSmartPointer< vtkProp > actor)
	Add a VTK actor to this window.
void	AddVolume (vtkSmartPointer< vtkVolume > actor)
	Add a VTK volume to this window.
void	AddActor2D (vtkSmartPointer< vtkProp > actor)
	Add a VTK actor to this window.
void	SetActor (vtkSmartPointer< vtkProp > actor)
	Add a VTK actor to this window. Alias for AddActor.
void	SetActor2D (vtkSmartPointer< vtkProp > actor)
	Add a VTK actor to this window. Alias for AddActor2D.
void	SetBackground (double red, double green, double blue)
	Set the background of the display window.
void	SetSize (int height, int width)
	Set the size of the display window.
void	SetLookupTable (vtkSmartPointer< vtkLookupTable > lut)
	Set the lookup table of the colours in display window.
void	RemoveAllActors ()
	Remove all VTK actors from this window.
void	RemoveActor (vtkSmartPointer< vtkProp > actor)
	Remove the VTK actor from this window.
void	RemoveActor2D (vtkSmartPointer< vtkProp > actor)
	Remove the VTK 2D actor from this window.
vtkActorCollection *	GetActors ()
	Get all the actors in the render window.
vtkVolumeCollection *	GetVolumes ()
	Get all the actors in the render window.
virtual vtkImageActor *	GetImageActor ()
	Get the image actors, Implement in derived class that uses images.
vtkLookupTable *	GetLookupTable ()
	Get the lookup table of the colours in display window.
void	SetScalarBar (vtkScalarBarActor *bar)
	Get the scalar bar of the display window.
vtkScalarBarActor *	GetScalarBar ()
	Get the scalar bar of the display window.
void	GetBackground (double &red, double &green, double &blue)
	Get the background of the display window.
virtual vtkDataSet *	GetDataSet ()
	Get the data, Implement in derived class that uses data derived from vtkDataSet, like vtkPolyData or vtkImageData. More...
void	SetRenderer (vtkRenderer *rnder)
	Assigns a VTK Renderer object.
vtkRenderer *	GetRenderer ()
	Returns the VTK Renderer object.
virtual vtkRenderWindowInteractor *	GetVTKInteractor ()
	Get the interactor associated with the view rendering.
void	OffScreenRenderingOn ()
	Enable off-screen rendering, which is faster for large datasets in some instances.
void	OffScreenRenderingOff ()
	Disable off-screen rendering, which is faster for large datasets in some instances.
void	Render ()
	Force Render or Update of the display.
void	enableUpdates (QStatusBar *bar)
	Enables the update of coordinates to the status bar provided directly. Update is done on mouse movement.
Public Member Functions inherited from milxQtWindow
	milxQtWindow (QWidget *theParent=0)
	The standard constructor. More...
virtual	~milxQtWindow ()
	The standard destructor.

Protected Member Functions
virtual void	updateLookupTable ()
	Update the colour maps depending on whats been generated for the model.
virtual void	reset ()
void	outputSnapshots (const QString filename)
void	createActions ()
	Create the actions for context menu etc. More...
void	createConnections ()
	Create the connections for context menu etc.
void	setupTooltips ()
	Assign tooltips to each action for users benefit. The tooltips explains the function of each action.
void	contextMenuEvent (QContextMenuEvent *event)
	The context menu setup member.
Protected Member Functions inherited from milxQtRenderWindow
void	createActions ()
	Create the actions for context menu etc.
void	createConnections ()
	Create the connections for context menu etc.
void	contextMenuEvent (QContextMenuEvent *event)
	The context menu setup member. More...
QMenu *	colourMapsMenu ()
	Return the colourmaps menu with the milxQtRenderWindow class ordering. This is for the benefit of derived class context menus and/or extensions.
void	dragMoveEvent (QDragMoveEvent *event)
	Part of the Drag and Drop feature members. Accepts drags.
void	dragLeaveEvent (QDragLeaveEvent *event)
	Part of the Drag and Drop feature members. Accepts drags.
void	dragEnterEvent (QDragEnterEvent *event)
	Part of the Drag and Drop feature members. Tells what drags to accept.
void	mouseDoubleClickEvent (QMouseEvent *event)
	Part of the Drag and Drop feature members. Triggers the dragging on double click.
void	dropEvent (QDropEvent *event)
	Part of the Drag and Drop feature members. Opens the dropped files.
virtual void	SetupWidgets (vtkRenderWindowInteractor *interactor)
	Update the interactor so that the widgets are usable. Call this if you change the render window or interator manually.
void	setupHumanGlyph (vtkSmartPointer< vtkMatrix4x4 > mat=NULL)
	Setup the human orientation glyph even if some transform if present between glyph and view.
Protected Member Functions inherited from milxQtWindow
void	createConnections ()
	Create the connections for context menu etc.
void	closeEvent (QCloseEvent *clEvent)
	When closing, execute this member.
void	printError (QString msg)
	Error message wrapper for console.
void	printWarning (QString msg)
	Warning message wrapper for console.
void	printDebug (QString msg)
	Debug message wrapper for console.
void	printInfo (QString msg)
	Info message wrapper for console.

Protected Attributes
bool	m_loaded
	Shapes loaded?
bool	m_modelled
	SSM Modelled?
bool	m_meaned
	Mean generated?
bool	m_shapesModelled
	Shapes were generated?
bool	m_alignedShapesModelled
	Shapes were generated?
bool	m_modes
	Modes been generated?
bool	m_vector
	Vectors generated?
bool	m_tensor
	Tensors generated?
bool	m_correspond
	Hedgehog generated?
int	m_mode
	Mode being viewed.
QAction *	actionMean
	mean action
QAction *	actionAligned
	aligned points action
QAction *	actionOriginal
	original points action
QAction *	actionModesAsVectors
	modes action
QAction *	actionModesAsTensors
	modes action
QAction *	actionModesAsCollection
	modes collection action
QAction *	actionAlignment
	alignment check action
QAction *	actionOriginalMeshes
	original meshes output action
QAction *	actionAlignedMeshes
	alignmed meshes output action
QAction *	actionPointIDs
	point ids check action
QAction *	actionCoordinates
	coordinates check action
QAction *	actionCorrespond
	correspondence check action
QAction *	actionReplaceOriginal
	correspondence check action
QMenu *	plotMenu
	Plot menu for SSM analysis.
QAction *	actionCompact
	compactness plot action
QAction *	actionSpecificity
	specificity plot action
QAction *	actionGeneralise
	generalisibility error plot action
QAction *	actionValues
	primary modes plot action
QAction *	actionModes
	primary modes plot action
QAction *	actionParameters
	training shape parameters plot action
QMenu *	alignMenu
	Plot menu for SSM alignment.
QActionGroup *	alignGroup
	Procrustes align gp action.
QAction *	actionRigid
	rigid Procrustes action
QAction *	actionSimilarity
	similarity Procrustes action
QAction *	actionAffine
	affine Procrustes action
ShapeModelType::Pointer	m_StandardSSM
	The Statistical Shape Model.
ShapeModelBaseType::Pointer	m_SSM
	The Statistical Shape Model Base Class.
QList< int >	m_caseIDs
	A list of case IDs corresponding to the models in the SSM.
QList< QPointer< milxQtModel > >	m_models
	Original Models in the SSM.
QList< QPointer< milxQtModel > >	m_alignedModels
	Aligned Models in the SSM.
QPointer< milxQtModel >	m_meanModel
	Model of the mean.
QPointer< milxQtModel >	m_modesVectorModel
	Vector Model of the modes.
QPointer< milxQtModel >	m_modesTensorModel
	Tensor Model of the modes.
QPointer< milxQtModel >	m_correspondences
	Hedgehog display of the correspondences.
Protected Attributes inherited from milxQtRenderWindow
bool	loaded
	Loaded Image from file?
bool	rendered
	Scene as been setup for rendering? (by generateRender())
bool	axesBefore
	Axes displayed?
bool	scaleBefore
	scale displayed?
bool	customScalarBar
bool	logScale
	Using custom scalar bar?
bool	useDefaultView
	Using log scalar map? More...
bool	orientationAxes
	Display orientation (posterior etc.) axes?
bool	contextMenuEnabled
	Display orientation (posterior etc.) axes?
int	defaultView
	Default view for data (default is axial)
int	currentView
	Current view for data.
int	orientationView
	view orientation standard
QMenu *	windowPropertiesMenu
	Context Menu.
QAction *	backgroundAct
	Action for axes of the display.
QAction *	axesAct
	Action for axes of the display.
QAction *	lightingAct
	Action for two-sided lighting of the display.
QAction *	lineAct
	Action for distance measuring display.
QAction *	distanceAct
	Action for distance measuring display.
QAction *	biDirectionAct
	Action for cross distance measuring display.
QAction *	angleAct
	Action for angle measuring display.
QAction *	planeAct
	Action for drawing planes.
QAction *	boxAct
	Action for box drawing display.
QAction *	sphereAct
	Action for sphere annotate display.
QAction *	humanAct
	Show human view orientation glyph?
QAction *	textAct
	Action for angle measuring display.
QAction *	crosshairAct
	Action for crosshair.
QMenu *	contourMenu
	Contour Menu.
QAction *	contourAct
	Action for contouring surface points using Dijkstras algorithm.
QAction *	contourPolyDataAct
	Save contour surface points as polydata.
QAction *	contourNodePolyDataAct
	Save contour surface nodes as polydata.
QAction *	contourInitAct
	Load contour surface points from polydata.
QMenu *	viewMenu
	Context Menu.
QActionGroup *	viewGroup
	Grouping for check boxes.
QAction *	viewXY
	Change view to xy-plane (Axial)
QAction *	viewZY
	Change view to zy-plane (Coronal)
QAction *	viewZX
	Change view to zx-plane (Sagittal)
QAction *	saveViewAct
	Save camera view.
QAction *	loadViewAct
	Load camera view.
QAction *	saveViewFileAct
	Save camera view to file.
QAction *	loadViewFileAct
	Load camera view to file.
QAction *	scaleAct
	Action for the scale bar of the display.
QMenu *	colourMapMenu
	Colour map menu.
QActionGroup *	mapGroup
	Grouping for check boxes.
QAction *	actionDefault
	Default colours.
QAction *	actionJet
	Jet colours.
QAction *	actionRainbow
	Default colours.
QAction *	actionInvRainbow
	Inv Default colours.
LabelledAction *	actionGray
	Gray colours.
LabelledAction *	actionSeismic
	Gray2 colours.
QAction *	actionLogGray
	Logarithmic Gray colours.
QAction *	actionNIH
	NIH colours.
QAction *	actionNIH_FIRE
	NIH_FIRE colours.
QAction *	actionAAL
	AAL colours.
QAction *	actionFS
	FS colours.
LabelledAction *	actionHOT
	HOT colours.
QAction *	actionCOOL
	COOL colours.
LabelledAction *	actionCOOLWARM
	COOL colours.
QAction *	actionKnee
	Knee colours.
LabelledAction *	actionBone
	Spectral colours.
LabelledAction *	actionSpectral
	Spectral colours.
LabelledAction *	actionGNUPlot
	GNUPlot colours.
LabelledAction *	actionCubeHelix
	Cube Helix colours.
LabelledAction *	actionHSV
	Cube Helix colours.
QAction *	resetAct
	Action for refreshing the display.
QAction *	refreshAct
	Action for refreshing the display.
QPoint	dragStartPosition
	Dragging helper variable.
vtkSmartPointer< vtkEventQtSlotConnect >	Connector
	VTK Events to slots convertor.
vtkSmartPointer< vtkMatrix4x4 >	transformMatrix
	Transform matrix for actor(s)
vtkSmartPointer< vtkRenderer >	renderer
	Renderer for the data.
vtkSmartPointer< vtkRenderWindow >	renderWindow
	Render Window used if no other set, only for deletion, access through QVTKWidget members.
vtkSmartPointer< vtkLookupTable >	lookupTable
	Lookup table for the shapes/images, base class is used to allow references to different look up table types.
vtkSmartPointer< vtkCamera >	camera
	camera for the view
vtkSmartPointer< vtkScalarBarActor >	scale
	Scale for the display.
vtkSmartPointer< vtkScalarBarWidget >	scalarBar
	Scalar Bar Widget for the display.
vtkSmartPointer< vtkAxesActor >	axes
	Axes for the model.
vtkSmartPointer< vtkAxesActor >	orientAxes
	Orientation (posterior etc.) axes for the orientation marker.
vtkSmartPointer< vtkPointPicker >	dataPicker
	For determining coordinates and points from the window.
vtkSmartPointer< vtkContourWidget >	contourWidget
	contour interaction
vtkSmartPointer< vtkLineWidget2 >	lineWidget
	Used for drawing lines.
vtkSmartPointer< vtkDistanceWidget >	distanceWidget
	Used for measuring distances.
vtkSmartPointer< vtkBiDimensionalWidget >	biDirectionWidget
	Used for measuring cross distances.
vtkSmartPointer< vtkAngleWidget >	angleWidget
	Used for measuring angles.
vtkSmartPointer< vtkPlaneWidget >	planeWidget
	Used for drawing planes.
vtkSmartPointer< vtkBoxWidget2 >	boxWidget
	Used for measuring angles.
vtkSmartPointer< vtkSphereRepresentation >	sphereRep
	Sphere for widgets.
vtkSmartPointer< vtkSphereWidget2 >	sphereWidget
	Used for measuring angles.
vtkSmartPointer< vtkOrientationMarkerWidget >	humanGlyph
	Glyph for showing equivalent view on human.
QList< vtkSmartPointer< vtkTextWidget > >	textWidgets
	Used for displaying movable texts in render window.
QList< vtkSmartPointer< vtkTextActor > >	textActors
	text actors for text widgets
QList< ImageActorItem >	imageActors
	Images actors being displayed in model view.
QStatusBar *	updateBar
	Pointer to bar, not allocated or deleted. To be passed to only.
QActionGroup *	windowActionGroup
	used for the custom menu
Protected Attributes inherited from milxQtWindow
QString	name
	Name of the data.
QString	prefix
	Prefix of the data.
bool	verboseMode
	Verbose message output mode.
bool	deletableOnClose
	Delete on close allowed? Allowed by default.
bool	consoleAssigned
	Console assigned for output?
QMenu *	contextMenu
	Context Menu.
QList< QAction * >	actionsToAdd
	Context actions to add.
QList< QAction * >	actionsToAppend
	Context actions to append.
QList< QAction * >	extActionsToAdd
	Extension actions to add.
QList< QMenu * >	menusToAdd
	Context Menu's to add.
QList< QMenu * >	menusToAppend
	Context Menu's to append.
milxQtConsole *	console
	Console for log outputs.

Detailed Description

Definition at line 31 of file milxQtShapeModel.h.

Constructor & Destructor Documentation

milxQtShapeModel()

milxQtShapeModel::milxQtShapeModel	(	QWidget *	theParent = 0,
		bool	contextSystem = true
	)

Default constructor

Set strings

Definition at line 41 of file milxQtShapeModel.cpp.

~milxQtShapeModel()

milxQtShapeModel::~milxQtShapeModel ( )

virtual

Default destructor

Definition at line 61 of file milxQtShapeModel.cpp.

Member Function Documentation

aligned

milxQtShapeModel::aligned ( )

slot

Show the aligned models in the window as a set of coloured point clouds.

< Add data to general display

Definition at line 782 of file milxQtShapeModel.cpp.

alignedMeshes

milxQtShapeModel::alignedMeshes ( )

slot

Output each aligned shape as a poly data file in a directory and prefix provided by the user (internally via file dialog).

< Strip the extension

For all shapes

Show as surface

Keep UI responsive

Definition at line 1338 of file milxQtShapeModel.cpp.

alignment

milxQtShapeModel::alignment ( )

slot

Output each aligned shape as a PNG image in a directory and prefix provided by the user (internally via file dialog).

<Pause interaction so camera position is fixed

<Resume interaction

< Strip the extension

For all shapes

Show as surface

Keep UI responsive

<Resume interaction

Definition at line 1282 of file milxQtShapeModel.cpp.

compactness

milxQtShapeModel::compactness ( )

slot

Plot the compactness of the SSM.

The compactness is basically how many modes are needed to represent what proportion of the model. High compactness is having a small number of modes representing a large amount of the model.

Init table

Set column names

Compute total of eigenvalues

Compute compactness

Definition at line 909 of file milxQtShapeModel.cpp.

coordinates

milxQtShapeModel::coordinates ( )

slot

Output each aligned shape coloured by the coordinates as a PNG image in a directory and prefix provided by the user (internally via file dialog).

Same regions (i.e. regions with correspondences) will have the same colour so that mis-matched points show up as coloured points in the wrong areas of the model.

<Pause interaction so camera position is fixed

<Resume interaction

< Strip the extension

Create scalars based on the point ids

For all shapes

Set the point ID colours

Show as surface

Keep UI responsive

<Resume interaction

Definition at line 1528 of file milxQtShapeModel.cpp.

correspondences

milxQtShapeModel::correspondences ( )

slot

Compare points from each shape to measure the correspondence as a hedgehog plot.

< Add data to general display

Definition at line 888 of file milxQtShapeModel.cpp.

createActions()

milxQtShapeModel::createActions ( )

protected

Create the actions for context menu etc.

< Only exists for the duration of the context selection

Definition at line 1734 of file milxQtShapeModel.cpp.

createMenu

milxQtShapeModel::createMenu ( QMenu *  menu )

virtualslot

Create the menu for the data in this object. Used for context menu and file menus.

Change View of Volume

Definition at line 195 of file milxQtShapeModel.cpp.

eigenmodes

milxQtShapeModel::eigenmodes ( )

slot

Plot the primary eigenmodes of the model for each training shape.

Init table

Definition at line 1166 of file milxQtShapeModel.cpp.

eigenvalues

milxQtShapeModel::eigenvalues ( )

slot

Plot the eigenvalues of the model.

Init table

Set column names

Compute total of eigenvalues

Compute compactness

Definition at line 1109 of file milxQtShapeModel.cpp.

generalisability

milxQtShapeModel::generalisability ( )

slot

Plot the generalisability of the SSM.

The generalisability is basically how good the model is at reconstruction using leave-one-out approach.

Init table

Set column names

Leave one out experiment

Definition at line 1042 of file milxQtShapeModel.cpp.

generateAlignedModels

milxQtShapeModel::generateAlignedModels ( const bool  display = true )

slot

Generate the display of the aligned Models within the SSM framework. Assumes generateSSM() has already been called.

If display is true, all the models are rendered into window. Could be slow for a large set of models.

< Pull colour for data

Build model

< Add data to general display

Keep UI responsive

Definition at line 383 of file milxQtShapeModel.cpp.

generateCollectionBasedOnMode

void milxQtShapeModel::generateCollectionBasedOnMode ( )

virtualslot

< View mode

Definition at line 593 of file milxQtShapeModel.cpp.

generateCorrespondences

milxQtShapeModel::generateCorrespondences ( )

slot

Generate the display of the correspondences within the SSM framework as a hedgehog plot. Assumes atleast generateSSM() has already been called.

Todo:

Assume all shapes have the smae number of points

Initialise deviation array

For all shapes

For all shapes

For each shape

For all shapes

Keep UI responsive

Definition at line 695 of file milxQtShapeModel.cpp.

generateMeanModel

milxQtShapeModel::generateMeanModel ( vtkSmartPointer< vtkPolyData >  shape = NULL )

virtualslot

Generates the display of the mean Model. Assumes generateSSM() has already been called.

< Add data to general display

Definition at line 307 of file milxQtShapeModel.cpp.

generateModels

milxQtShapeModel::generateModels ( const bool  display = true )

slot

Generate the display of the original Models. Assumes generateSSM() has already been called.

< Pull colour for data

Build model

< Add data to general display

Keep UI responsive

Definition at line 339 of file milxQtShapeModel.cpp.

generateModes

milxQtShapeModel::generateModes ( )

virtualslot

Generate the display of the PCA modes within the SSM framework. Assumes atleast generateSSM() has already been called.

Code for this member was contributed by Kaikai Shen, 2010.

Code contributed by Kaikai Shen, 2010. Smart Pointered and Modified by Shekhar Chandra, 2010.

< View mode

Keep UI responsive

Definition at line 432 of file milxQtShapeModel.cpp.

generateSSM

milxQtShapeModel::generateSSM ( )

virtualslot

Generate the Statistical Shape Model. Assumes SetInputCollection() has already been called.

Compute SSM

Compute the sum of eigenvalues, which is a measure of the variation of the modelling

Build colour lookup table

Definition at line 247 of file milxQtShapeModel.cpp.

generateTensorField

milxQtShapeModel::generateTensorField ( )

slot

Generate the display of the PCA modes within the SSM framework as a tensor field. Assumes atleast generateModes() has already been called.

Code for this member was contributed by Kaikai Shen, 2010.

Definition at line 670 of file milxQtShapeModel.cpp.

generateVectorField

milxQtShapeModel::generateVectorField ( )

slot

Generate the display of the PCA modes within the SSM framework as a vector field. Assumes atleast generateModes() has already been called.

Code for this member was contributed by Kaikai Shen, 2010.

Definition at line 643 of file milxQtShapeModel.cpp.

getMeanModel

milxQtShapeModel::getMeanModel ( )

slot

Returns the mean model of the Statistical Shape Model. Assumes SSM has been generated (via generateSSM()).

Displays Mean mesh so

Dont display mean mesh

Definition at line 168 of file milxQtShapeModel.cpp.

LoadModel

milxQtShapeModel::LoadModel ( const QString  filename )

slot

Loads a model as an SSM (*.ssm) file. MILX-MSK like call.

See itkStatisticalShapeModel.h for SSM file format details.

Definition at line 66 of file milxQtShapeModel.cpp.

mean

milxQtShapeModel::mean ( )

slot

Show the mean model in the window.

< Add data to general display

Definition at line 761 of file milxQtShapeModel.cpp.

openModel

milxQtShapeModel::openModel ( const QString  filename )

inlinevirtualslot

Loads a model as an SSM (*.ssm) file. Alias same as LoadModel().

See itkStatisticalShapeModel.h for SSM file format details.

Definition at line 62 of file milxQtShapeModel.h.

original

milxQtShapeModel::original ( )

slot

Show the original models in the window as a set of coloured point clouds.

< Add data to general display

Definition at line 809 of file milxQtShapeModel.cpp.

originalMeshes

milxQtShapeModel::originalMeshes ( )

slot

Output each original shape as a poly data file in a directory and prefix provided by the user (internally via file dialog).

< Strip the extension

For all shapes

Show as surface

Keep UI responsive

Definition at line 1388 of file milxQtShapeModel.cpp.

outputSnapshots()

void milxQtShapeModel::outputSnapshots ( const QString  filename )

protected

<transfer fixed camera setup

For all shapes

< Add data to general display

Keep UI responsive

< Write PNG image

< Remove data from general display

Keep UI responsive

Definition at line 1697 of file milxQtShapeModel.cpp.

parameters

milxQtShapeModel::parameters ( )

slot

Plot the training shape parameters of the model for each training shape (leave 1 out).

Init table

Definition at line 1213 of file milxQtShapeModel.cpp.

pointIds

milxQtShapeModel::pointIds ( )

slot

Output each aligned shape coloured by the point IDs as a PNG image in a directory and prefix provided by the user (internally via file dialog).

<Pause interaction so camera position is fixed

<Resume interaction

< Strip the extension

Create scalars based on the point ids

For all shapes

Set the point ID colours

Show as surface

Keep UI responsive

For all shapes

Revert to points

Keep UI responsive

<Resume interaction

Definition at line 1438 of file milxQtShapeModel.cpp.

replaceOriginal

milxQtShapeModel::replaceOriginal ( )

slot

Replace the original (unaligned) meshes with the aligned ones. The new meshes are unnormalised as compared to the aligned meshes which are normalised.

Useful when aligned meshes are accessed by GetShape() of the SSM class or unnormalised results are required. The rescaling of each aligned mesh is done based on the centroid size of the corresponding original mesh.

< Set model to shape filter

Keep UI responsive

Definition at line 1623 of file milxQtShapeModel.cpp.

SaveModel

milxQtShapeModel::SaveModel ( const QString  filename )

inlinevirtualslot

Saves a model as an SSM (*.ssm) file. MILX-MSK like call.

See itkStatisticalShapeModel.h for SSM file format details.

Definition at line 72 of file milxQtShapeModel.h.

saveModel

milxQtShapeModel::saveModel ( const QString  filename )

inlinevirtualslot

Saves a model as an SSM (*.ssm) file.

See itkStatisticalShapeModel.h for SSM file format details.

Definition at line 83 of file milxQtShapeModel.h.

SetInputCollection [1/2]

milxQtShapeModel::SetInputCollection ( vtkPolyDataCollection *  meshes )

virtualslot

Uses the collection of polydata to create shape model.

< Set model to shape filter

Keep UI responsive

Definition at line 81 of file milxQtShapeModel.cpp.

SetInputCollection [2/2]

milxQtShapeModel::SetInputCollection ( vtkPolyDataCollection *  meshes, QStringList &  filenames  )

virtualslot

Uses the collection of polydata to create shape model.

This version extracts case IDs from the filenames provided and displays them in the case browser.

Setup temporary combo widget for selecting case ids when there are Multiple integer matches in the filename

Capture integer expression

Read all integers from filename and save in list

If more than one integer in filename, ask user to select correct integer

< Extract case ID from filename by using integer user provided (or only one present)

< Add case ID to list

< Set model to shape filter

Keep UI responsive

Definition at line 100 of file milxQtShapeModel.cpp.

specificity

milxQtShapeModel::specificity ( )

slot

Plot the specificity of the SSM.

The specificity is given a randoming generated b-vector (shape parameters), how close would it be to the training population?

Init table

Set column names

Definition at line 966 of file milxQtShapeModel.cpp.

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

• plugin/ssm/milxQtShapeModel.h
• plugin/ssm/milxQtShapeModel.cpp