niftk Namespace Reference

Namespaces
	ICPBasedRegistrationConstants
	impldetail
	PointBasedRegistrationConstants

Classes
union	ad
class	AffineTransformDataInteractor3D
	Affine data interaction with objects in 3D windows. More...
class	AffineTransformDataNodeProperty
	MITK data-node property suitable for holding affine transforms. More...
class	AffineTransformer
	Class to contain all the ITK/MITK logic for the Affine Transformation Plugin, to separate from AffineTransformationView to make unit testing easier. More...
class	AffineTransformParametersDataNodeProperty
class	AtomicStateTransitionTester
	Test class to ensure the atomic transition from one object state to another. More...
class	AuroraCubeTracker
	RAII object to connect to Aurora Cube tracker. More...
class	AuroraDomeTracker
	RAII object to connect to Aurora Dome tracker. More...
class	AuroraTableTopTracker
	RAII object to connect to Aurora Table Top tracker. More...
class	BackfaceCullingFilter
class	BaseApplication
	Abstract plugin class to start up an application. More...
class	BaseApplicationPluginActivator
	Abstract class that implements QT and CTK specific functionality to launch the application as a plugin. More...
class	BaseApplicationPreferencePage
	Preferences page for this plugin, providing application wide defaults. More...
class	BaseController
class	BaseControllerPrivate
class	BaseGUI
	Base class for GUI controls on BlueBerry views. More...
class	BaseSegmentorController
class	BaseSegmentorGUI
	Base class for GUI controls on MIDAS segmentor views. More...
class	BaseSegmentorView
	Base view component for MIDAS Segmentation widgets. More...
class	BaseView
	Base view component for plugins listening to visibility change events, focus changed events and so on. More...
class	BaseViewPrivate
class	BaseWorkbenchAdvisor
	Abstract advisor class to set up an initial workbench. More...
class	BaseWorkbenchWindowAdvisor
class	BasicMesh
	Simple mesh implementation that is used in the Surface Extraction and surface smoothing and decimation algorithms. This stores a list of vertices and another list of triangles (which references the vertex list) More...
class	BasicTriangle
	Simple triangle implementation that is used in the Surface Extraction and surface smoothing and decimation algorithms. It keeps hold of vertices, triangle index and has an active flag. More...
class	BasicVec3D
	Simple 3D Vector implementation that is used in the Surface Extraction and surface smoothing and decimation algorithms. More...
class	BasicVertex
	Simple vertex implementation that is used in the Surface Extraction and surface smoothing and decimation algorithms. It has both a position and a normal. More...
class	BitmapOverlay
	Used to draw a 2D image into the background of a VTK Render Window. More...
struct	Border
class	CameraCalView
	User interface to provide controls to do mono/stereo, video camera calibration. More...
class	CameraCalViewActivator
class	CameraCalViewPreferencePage
	Preferences page for the Video Camera Calibration View plugin. More...
class	CGALMesherBackEnd
class	CMC33
	Marching Cubes - CMC33 algorithm. More...
class	CMICLogo
struct	CommandLineArgumentDescription
class	CommandLineParser
	Parser for extracting program arguments from the command line. More...
class	CommonMIDASActivator
class	ContourTool
	Provides common functionality for DrawTool and PolyTool where these two tools enable drawing lines and poly-lines around voxel edges. More...
class	ContourToolEventInterface
	Interface class, simply to callback onto ContourTool for Undo/Redo purposes. More...
class	ContourToolOpAccumulateContour
	Operation class to hold data to pass back to this ContourTool, so that this ContourTool can execute the Undo/Redo command. More...
class	CoordinateAxesData
	Class to enable the data to represent coordinate axes to be added as a mitk::BaseData to the mitk::DataStorage. This class turns out to be very simple, as the BaseData contains the mitk::BaseGeometry, which contains all the information we need. So this class is effectively a dummy class. More...
class	CoordinateAxesDataOpUpdate
class	CoordinateAxesDataReaderService
	Loads a 4x4 Matrix into a niftk::CoordinateAxesData. More...
class	CoordinateAxesDataSerializer
	Serializes niftk::CoordinateAxesData for mitk::SceneIO. More...
class	CoordinateAxesDataWriterService
	Saves a niftk::CoordinateAxesData into a 4x4 Matrix text file. More...
class	CoordinateAxesVtkMapper3D
	Draws a representation of an niftk::CoordinateAxesData. More...
class	CoreIOActivator
	The CoreIOActivator class. More...
class	CoreIOMimeTypes
	The CoreIOMimeTypes class. More...
class	CoreIOObjectFactory
	Object factory class to create and register our IO classes. More...
class	CoreObjectFactory
	Object factory class to instantiate or set properties on our non-IO related classes. More...
class	CSVRow
	Comma separated value (CSV) row class used to parse rows from an input stream and split them into a vector of strin elements. More...
class	CUDAImage
class	CUDAImageProperty
class	CUDAManager
class	CustomVTKAxesActor
class	DataNodeBoolPropertyFilter
	A filter that contains a list of renderers, and returns true if the node has a specific boolean property set to true for those filters. More...
class	DataNodeFilter
	A class that tests a list of nodes, and returns true for "pass" and false otherwise. More...
class	DataNodePropertyListener
class	DataNodeStringPropertyFilter
	A filter that takes a named property, for example "name", and a list of strings to check against, and compares the node to see if its property (eg "name") matches any of the supplied strings, and if it does match, will return Pass=false, otherwise Pass=true. More...
class	DataNodeVisibilityTracker
class	DataSourcesView
	User interface to provide Image Guided Surgery functionality. More...
class	DataSourcesViewActivator
class	DataSourcesViewPreferencePage
	Preferences page for the surgical guidance plugin with choices for colours, default paths to save data etc. More...
class	DataStorageCheckableComboBox
class	DataStorageListener
	Base class for objects that Listen to data storage, and want to update a node. More...
class	DisplayGeometryModificationCommand
class	DnDDisplayInteractor
	Observer that manages the interaction with the display. More...
class	DnDDisplayPreferencePage
	Provides a preferences page for the NifTK DnD Display, including default number of rows, default number of columns, image interpolation, default window layout and background colour. More...
class	DrawTool
	Tool to draw lines around voxel edges like MIDAS does rather than through them as most of the MITK tools do. More...
class	DrawToolEventInterface
	Interface class, simply to callback onto DrawTool for Undo/Redo purposes. More...
class	DrawToolGUI
	GUI component for the DrawTool, providing a single slider to control the radius in millimetres of the "erase" function. More...
class	DrawToolOpEraseContour
	Operation class to hold data to pass back to this DrawTool, so that this DrawTool can execute the Undo/Redo command. More...
class	EditorLifeCycleListener
class	ExceptionObject
	Basic NIFTK exception class. More...
class	FastPointSetVtkMapper3D
	Vtk-based mapper for PointSet, that just displays a basic dot for each point. More...
class	FilteringStateMachine
	Common base class for segmentor tools and interactors. More...
class	FitPlaneToPointCloudWrapper
class	FixedLengthFileReader
	Reads a fixed number S of type T from a file. More...
class	GeneralSegmentorActivator
	CTK Plugin Activator class for niftkGeneralSegmentorView. More...
class	GeneralSegmentorController
	Provides the MIDAS general purpose, Irregular Volume Editor functionality originally developed at the Dementia Research Centre UCL (http://dementia.ion.ucl.ac.uk/). More...
class	GeneralSegmentorControllerPrivate
class	GeneralSegmentorEventInterface
	Interface class, simply to callback onto niftkGeneralSegmentorController class for Undo/Redo purposes. More...
class	GeneralSegmentorGUI
	Implements the Qt/Widget specific functionality pertaining to the General Segmentor View. More...
class	GeneralSegmentorPipeline
	A specific implementation of GeneralSegmentorPipelineInterface, based on ITK, called from MITK. More...
class	GeneralSegmentorPipelineCache
class	GeneralSegmentorPipelineInterface
	Abstract interface to plug the ITK pipeline into MITK framework. More...
class	GeneralSegmentorPipelineParams
	A simple parameters object to pass all parameters to the ITK based region growing pipeline. More...
class	GeneralSegmentorPreferencePage
	Preferences page for this plugin, enabling the choice of the default colour of the segmentation. More...
class	GeneralSegmentorView
	Provides a view for the MIDAS general purpose, Irregular Volume Editor functionality, originally developed at the Dementia Research Centre UCL (http://dementia.ion.ucl.ac.uk/). More...
class	HandeyeCalibrateUsingRegistration
	Computes hand-eye using registration. More...
class	HelpAboutDialog
	Prints out a useful About dialog with software version numbers. More...
class	IBaseView
	Public interface to QmitkBaseView. More...
class	ICPBasedRegistration
	Class to perform a surface based registration of two MITK Surfaces/PointSets, using VTKs ICP. More...
class	ICPRegService
	Implements niftk::SurfaceRegServiceI using niftk::ICPBasedRegistration. More...
class	ICPRegServiceActivator
	Activator to register instances of niftk::SurfaceRegServiceI, currently only niftk::ICPRegService. More...
class	ICPRegServiceRAII
	RAII object to run ICP Surface Based Registration. More...
class	IGIBufferedSaveableDataSourceI
	Abstract base class for data sources that can clean their own buffer. More...
class	IGICleanableDataSourceI
	Abstract base class for data sources that can clean their own buffer. More...
class	IGIConfigurationDialog
	Used to send parameters to and from the IGIDataSourceServiceI at runtime. More...
class	IGIDataItemInfo
	Info class to describe current state, so that GUI can display status. More...
class	IGIDataSource
	Abstract base class for IGI DataSources, such as objects that produce tracking data, video frames or ultrasound frames. More...
class	IGIDataSourceBackgroundDeleteThread
	Thread class, based on IGITimerBasedThread to simply call "CleanBuffer". More...
class	IGIDataSourceBackgroundSaveThread
	Thread class, based on IGITimerBasedThread to simply call "SaveBuffer". More...
class	IGIDataSourceBuffer
	Manages a buffer of niftk::IGIDataType. More...
class	IGIDataSourceFactoryServiceI
	Interface for a factory to create niftk::IGIDataSourceServiceI. More...
class	IGIDataSourceFactoryServiceRAII
	RAII object to retrieve a specific IGIDataSourceFactoryServiceI subclass. More...
class	IGIDataSourceGrabbingThread
class	IGIDataSourceI
	Interface for an IGI Data Source (e.g. video feed, ultrasound feed, tracker feed). More...
class	IGIDataSourceLocker
	Helper class to provide a class-level counter. More...
class	IGIDataSourceManager
	Class to manage a list of IGIDataSources (trackers, ultra-sound machines, video etc). More...
class	IGIDataSourceManagerWidget
	Widget class to manage a list of IGIDataSources (trackers, ultra-sound machines, video etc). More...
class	IGIDataType
	Abstract base class for IGI Data, such as objects containing tracking data, video frames or ultrasound frames. More...
class	IGIInitialisationDialog
	Initialisation dialogs must export their properties on completion. More...
class	IGILocalDataSourceI
	Abstract base class for local data sources. More...
class	IGIOverlayWidgetPartListener
	Used to handle interaction with the contained overlay editor widget when this IGIUltrasoundOverlayEditor is opened/closed etc. More...
class	IGIPerspective
	Perspective to arrange widgets as would be suitable for CMIC IGI applications.Note: We have to load at least one view component, to get an editor created. More...
class	IGISaveableDataSourceI
	Abstract base class for data sources that can save their own buffer. More...
class	IGITimerBasedThread
	Base class for threads that are simply triggered off of a QTimer. More...
class	IGITrackerDataType
	Class to represent tracker data. More...
class	IGIUltrasoundOverlayEditor
	Simple editor that delegates all functionality to a niftk::IGIUltrasoundOverlayWidget, and most methods are dummy or do-nothing implementations, as the widget is for a very specific purpose and most of the mitk::ILinkedRenderWindowPart are not needed. More...
class	IGIUltrasoundOverlayEditorActivator
	Activator class for the IGIUltrasoundOverlayEditor. More...
struct	IGIUltrasoundOverlayEditorPreferencePage
class	IGIUltrasoundOverlayEditorPrivate
	PIMPL pattern implementation of IGIUltrasoundOverlayEditor. More...
class	IGIUltrasoundOverlayWidget
	A widget that contains a niftk::SingleVideoWidget and a QmitkRenderWindow, (all set to render 3D mode), and several widgets for some basic controls. More...
class	IGIVideoOverlayEditor
	Simple editor that delegates all functionality to a niftk::IGIVideoOverlayWidget, and most methods are dummy or do-nothing implementations, as the widget is for a very specific purpose and most of the mitk::ILinkedRenderWindowPart are not needed. More...
class	IGIVideoOverlayEditorActivator
	Activator class for the IGIVideoOverlayEditor. More...
class	IGIVideoOverlayEditorPreferencePage
	Preference page for IGIVideoOverlayEditor, eg. setting the gradient background. More...
class	IGIVideoOverlayEditorPrivate
	PIMPL pattern implementation of IGIVideoOverlayEditor. More...
class	IGIVideoOverlayWidget
	A widget that contains 3 niftk::SingleVideoWidget (left video, right video, rendered data only no video) and a QmitkRenderWindow, (all set to render 3D mode), and several widgets for some basic controls. More...
struct	IGIVLOverlayWidgetPartListener
class	IGIVLVideoOverlayEditor
	Simple editor that delegates all functionality to a niftk::VLVideoOverlayWidget, and most methods are dummy or do-nothing implementations, as the widget is for a very specific purpose and most of the mitk::ILinkedRenderWindowPart are not needed. More...
class	IGIVLVideoOverlayEditorActivator
	Activator class for the IGIVLVideoOverlayEditor. More...
class	IGIVLVideoOverlayEditorPreferencePage
	Preference page for IGIVLVideoOverlayEditor, eg. setting the gradient background. More...
class	IGIVLVideoOverlayEditorPrivate
	PIMPL pattern implementation of IGIVLVideoOverlayEditor. More...
class	IGIWaitForSavedDataSourceBuffer
	Manages a buffer of niftk::IGIDataType, where the buffer will not delete things that have not yet been saved, thereby allowing for independent save/cleardown threads. More...
class	ImageLookupTablesPreferencePage
	Preferences page for this plugin, enabling choice of spin box precision. More...
class	ImageLookupTablesView
	Provides a simple GUI enabling the selection of window, level, min, max and a choice of lookup tables. More...
class	ImageToSurfaceFilter
	Converts pixel data to surface data by using a threshold The mitkNifTKImageToSurfaceFilter is used to create a new surface out of an mitk image. The filter uses a threshold to define the surface. It can use two algorithms for the extraction: the vtkMarchingCube algorithm (default) and the Corrected Marching Cubes 33 method: Custodio, Lis, et al. "Practical considerations on Marching Cubes 33 topological correctness." Computers & Graphics 37.7 (2013): 840-850. More...
class	InteractionEventObserverMutex
	Helper class to prevent unwanted simultaneous interactions. More...
class	InvalidArgumentException
	Exceptions for signalling invalid input. More...
class	IOException
	Exceptions for Filesystem, Network, ... I/O. More...
class	IPHostPortDialog
class	IPPortDialog
class	itkLogHelper
	This is a class to help with a few logging functions. More...
class	ITKRegionParametersDataNodeProperty
	MITK data-node property suitable for holding an ITK Region, consisting of a "valid" flag, plus 6 parameters containing the index and size, as a simple vector of integers. More...
class	ItkSignalCollector
	Class for collecting ITK signals and sending notifications of them to registered listeners. More...
class	ItkSignalListener
	Abstract class to be implemented by ITK signal listeners. More...
class	KeepTextOutputInShell
class	LabeledLookupTableProperty
	Provides a property so that each value/color has an associated name. More...
class	LabeledLookupTablePropertySerializer
	Serializes LabeledLookupTableProperty. More...
class	LabelMapReader
class	LabelMapWriter
	Writer to save labeled lookup tables in the format of Slicer v 4.4.0. More...
class	LagDialog
class	LightweightCUDAImage
class	LookupTableContainer
	Class to contain a vtkLookupTable and to store meta-data attributes like display name, which order to display it in in GUI, etc. More...
class	LookupTableManager
	Class to manage access to LookupTableContainers. More...
class	LookupTableProviderService
	Service to provide lookup tables. More...
class	LookupTableProviderServiceImpl
	Service implementation of LookupTableProviderService. More...
class	LookupTableSaxHandler
	SAX handler to load lookup tables into LookupTableContainer objects. More...
struct	Match
class	MeditMeshParser
	Parses a Medit mesh (.mesh) file. More...
class	MergePointClouds
class	MeshData
	Container class for passing around data structures containing a mesh. More...
class	MeshGenerator
	Creates a VTK mesh using CGAL as a back-end from any single-file image volume supported by ITK. More...
class	MeshMerger
class	MeshSmoother
	This class implements various mesh smoothing algorithms and it can be used to (re)compute surface and vertex normals of a BasicMesh structure. More...
struct	MethodDescription
class	MinimalPerspective
	Default Perspective, called 'Minimal' to discourage incrementally adding to it.Note: We have to load at least one view component, to get an editor created. More...
class	MITKAuroraCubeDataSourceFactory
	Class to create Aurora Cube trackers. More...
class	MITKAuroraDomeDataSourceFactory
	Class to create Aurora Dome trackers. More...
class	MITKAuroraTableTopDataSourceFactory
	Class to create Aurora Table Top trackers. More...
class	MITKNDITracker
	RAII wrapper for MITK interface to NDI trackers. More...
class	MITKPolarisSpectraDataSourceFactory
	Class to create Polaris Vicra trackers. More...
class	MITKPolarisVicraDataSourceFactory
	Class to create Polaris Vicra trackers. More...
class	MITKTrackerDataSourceActivator
	Activator to register all the MITK Tracker Factories. More...
class	MITKTrackerDataSourceFactory
	Abstract factory class to create MITKTrackerDataSources. More...
class	MITKTrackerDataSourceService
	Provides a local MITK implementation of a tracker interface, as an IGIDataSourceServiceI. The other class niftk::NDITracker provides the main tracking mechanism, utilising MITK to speak to the serial port and grab data etc. This class therefore is to coordinate threads, buffers, etc. and to function as a MicroService. More...
class	MITKTrackerDialog
struct	ml
class	MorphologicalSegmentorActivator
class	MorphologicalSegmentorController
class	MorphologicalSegmentorGUI
	Implements a few Qt specific things that are of no interest to the MITK view class. More...
class	MorphologicalSegmentorPipelineManager
	Class to contain all the ITK/MITK logic for the MIDAS Morphological Segmentor pipeline, to separate from MorphologicalSegmentationView to make unit testing easier. More...
class	MorphologicalSegmentorPipelineManagerTestClass
	Test class for niftkMorphologicalSegmentorPipelineManagerTest. More...
class	MorphologicalSegmentorPreferencePage
	Preferences page for this plugin, enabling choice volume rendering on/off. More...
class	MorphologicalSegmentorView
	Provides the plugin component for the MIDAS brain segmentation functionality, originally developed at the Dementia Research Centre UCL. More...
class	MouseEventEater
	Qt event filter to eat mouse events .... More...
class	MultiViewerControls
	Control panel for the DnD display. More...
class	MultiViewerEditor
	Provides a display with with multiple image viewers on up to 5 x 5 panes of equal size in a grid layout. More...
struct	MultiViewerEditorPartListener
class	MultiViewerEditorPrivate
class	MultiViewerVisibilityManager
	Maintains a list of SingleViewerWidgets and coordinates visibility properties by listening to AddNodeEvent, RemoveNodeEvent and listening directly to Modified events from the nodes "visible" property in DataStorage. More...
class	MultiViewerWidget
	Provides up to 5 x 5 image viewing panes, arranged as rows and columns. More...
class	MultiViewerWidgetTestClass
class	MultiViewerWidgetTestClassPrivate
class	MultiWindowWidget
	Subclass of QmitkStdMultiWidget to provide MIDAS specific functionality by having convenient methods to control geometry, background, cursors on/off etc. via calling methods in the base class QmitkStdMultiWidget. More...
class	NamedLookupTableProperty
	Provides a property so we can see the lookup table name in the property window. More...
class	NamedLookupTablePropertySerializer
	Serializes NamedLookupTableProperty. More...
class	NDICAPITracker
	Interface class for Northern Digital's tracking devices. More...
class	NDITracker
	Base class for NifTK interfaces to NDI trackers. More...
class	NewSegmentationDialog
	Derives from QmitkNewSegmentationDialog, to simply set the default colour to pure green. More...
class	NiftyCalVideoCalibrationManager
	Manager class to perform video calibration as provided by NiftyCal. More...
class	NiftyIGIApplication
	Plugin class to start up the NiftyIGI application. More...
class	NiftyIGIAppWorkbenchAdvisor
	Advisor class to set up the initial NiftyIGI workbench. More...
class	NiftyIGIWorkbenchWindowAdvisor
	Advisor class to set up NiftyIGI windows on startup. More...
class	NiftyLinkClientDataSourceFactory
	Factory class to create NiftyLinkClientDataSourceServices. More...
class	NiftyLinkClientDataSourceService
class	NiftyLinkDataSourceActivator
	Activator to register all the Nifty Link factories. (should just be a client one, and a server one). More...
class	NiftyLinkDataSourceService
	Abstract base class for both NiftyLink Client and Server sources. More...
class	NiftyLinkDataType
class	NiftyLinkServerDataSourceFactory
	Factory class to create NiftyLinkServerDataSourceServices. More...
class	NiftyLinkServerDataSourceService
class	NiftyMIDASApplication
	Plugin class to start up the NiftyMIDAS application. More...
class	NiftyMIDASWorkbenchAdvisor
	Advisor class to set up the initial NiftyMIDAS workbench. More...
class	NiftyMIDASWorkbenchWindowAdvisor
	Advisor class to set up NiftyMIDAS windows on startup. More...
class	NiftyViewApplication
	Plugin class to start up the NiftyView application. More...
class	NiftyViewAppWorkbenchAdvisor
	Advisor class to set up the initial NiftyView workbench. More...
class	NiftyViewPreferencePage
	Preferences page for the NiftyView application, providing application wide defaults. More...
class	NiftyViewWorkbenchWindowAdvisor
	Advisor class to set up NiftyView windows on startup. More...
class	NVidiaSDIConfigDialog
class	NVidiaSDIDataSourceActivator
	Activator to register the NVidiaSDIDataSourceFactory. More...
class	NVidiaSDIDataSourceFactory
	Factory class to create NVidiaSDIDataSources. More...
class	NVidiaSDIDataSourceImpl
class	NVidiaSDIDataSourceService
	Provides an NVidia SDI video feed, as an IGIDataSourceServiceI. More...
class	NVidiaSDIDataType
	Class to represent video frame data from NVidia SDI, to integrate within the niftkIGI framework. More...
class	NVidiaSDIInitDialog
class	OIGTLSystemTimeService
	Implements SystemTimeServiceI using igtl::TimeStamp. More...
class	OIGTLSystemTimeServiceActivator
	Activator to register instances of niftk::SystemTimeServiceI. More...
class	OpChangeSliceCommand
	Command class for changing slice. More...
class	OpClean
	Class to hold data for the MIDAS "clean" command, which filters the current contour set. More...
class	OpenCVVideoDataSourceActivator
	Activator to register the OpenCVVideoDataSourceFactory. More...
class	OpenCVVideoDataSourceFactory
	Factory class to create OpenCVVideoDataSources. More...
class	OpenCVVideoDataSourceService
	Provides an OpenCV video feed, as an IGIDataSourceServiceI. More...
class	OpenCVVideoDataType
	Class to represent video frame data from OpenCV. More...
class	OpGeneralSegmentorBaseCommand
	Base class for General Segmentor commands. More...
class	OpPropagate
	Class to hold data to do propagate up/down/3D. More...
class	OpPropagateSeeds
	Command class to store data for propagating seeds from one slice to the next. More...
class	OpRetainMarks
	Command class to store data to copy one slice to the next. More...
class	OpThresholdApply
	Class to hold data to apply the threshold region into the segmented image. More...
class	OpWipe
	Class to hold data to pass back to niftkGeneralSegmentorController to Undo/Redo the Wipe commands. More...
class	ordered_indexed_edge
	Utility class for storing an ordered edge. More...
class	ordered_size_t_pair
	Utility class for storing an ordered pair of vertex indices. More...
class	PaintbrushTool
	Paint brush tool used during editing on the morphological editor screen (a.k.a connection breaker). More...
class	PaintbrushToolClass
	Test class for niftkPaintbrushTool. More...
class	PaintbrushToolEventInterface
	Interface class, simply to callback operations onto the PaintbrushTool. More...
class	PaintbrushToolGUI
class	PaintbrushToolOpEditImage
	Operation class to hold data to pass back to this PaintbrushTool, so that this PaintbrushTool can execute the Undo/Redo command. More...
class	PaintEventEater
	Qt Event Filter to eat paint events. More...
class	PCLData
class	PluginActivator
	Plugin activator for the uk.ac.ucl.cmic.common plugin. More...
class	PLUSNDITracker
	RAII wrapper for PLUS/Atami interface to NDI trackers. More...
class	PNMReaderService
	The PNMReaderService class. More...
class	PNMWriterService
class	PointBasedRegistration
	Class to implement point based registration of two point sets. More...
class	PointRegServiceActivator
	Activator to register instances of niftk::PointRegServiceI, currently only niftk::PointRegServiceUsingSVD. More...
class	PointRegServiceI
	Interface for a Point Based Registration Service. More...
class	PointRegServiceRAII
	RAII object to run Point Based Registration via a PointRegServiceI implementation. More...
class	PointRegServiceUsingSVD
	Implements niftk::PointRegServiceI using niftk::PointBasedRegistrationUsingSVD. More...
class	PointSetDataInteractor
	Derived from mitk::PointSetDataInteractor so we can handle the mouse move event. More...
class	PointSetInteractor
	Derived from mitk::PointSetInteractor so we can handle the mouse move event. More...
class	PointSetUpdate
	Operation class to enable updating an mitk::PointSet with Undo/Redo. More...
class	PolyTool
	Tool to draw poly lines around voxel edges like MIDAS does rather than through them as most of the MITK tools do. More...
class	PolyToolEventInterface
	Interface class, simply to callback onto PolyTool for Undo/Redo purposes. More...
class	PolyToolOpAddToFeedbackContour
	Operation class to hold data to pass back to this PolyTool, so that the PolyTool can execute the Undo/Redo command. More...
class	PolyToolOpUpdateFeedbackContour
	Operation class to hold data to pass back to this PolyTool, so that the PolyTool can execute the Undo/Redo command. More...
class	PosnTool
	Dummy class, as the MIDAS posn tool, just enables you to change the position of the slices in 2 or 3 windows, which is the default behaviour of the MITK ortho-viewer anyway. More...
struct	PropagationParameters
class	PropertyChangedCommand
class	QCPerspective
	Perspective for doing scan quality control (QC). More...
class	QDSInterface
class	QImageToMitkImageFilter
	A basic interface to produce a 2D Mitk image from a 2D QImage. Currently only supports a QImage with format. More...
class	QtAudioDataDialog
class	QtAudioDataSourceActivator
	Activator to register the QtAudioDataSourceFactory. More...
class	QtAudioDataSourceFactory
	Factory class to create QtAudioDataSources. More...
class	QtAudioDataSourceService
	Provides a feed of images from QtAudio MDP, as an IGIDataSourceServiceI. More...
class	QtAudioDataType
	Class to represent audio data from QtAudio. More...
class	QtSignalCollector
	Class for collecting Qt signals and sending notifications of them to registered listeners. More...
class	QtSignalListener
	Abstract class to be implemented by Qt signal listeners. More...
class	QtSignalNotifier
	Helper class that implements a call back mechanism for Qt signals. More...
struct	ReadAccessor
struct	RefPoint
struct	RegisterNifTKCoreIOObjectFactory
struct	RegisterNifTKCoreObjectFactory
struct	ScopedCUDADevice
struct	ScopedOGLContext
	Utility class to activate a given OpenGL context, and restore the previous one on scope-exit. More...
class	SeedTool
	Seed tool for adding / removing / moving seeds. More...
class	SegmentationNodeAddedVisibilityTestClass
	Test class for niftkSegmentationNodeAddedVisibilityTest. More...
class	SegmentationPerspective
class	SegmentationSelectorWidget
	Implements the widget to select a reference image, and create a new segmentation. More...
class	SequentialCpuQds
class	ServiceConfigurationI
	Interface to describe how any service should be configured. More...
class	SharedOGLContext
class	SideViewerView
	Base view component for MIDAS Segmentation widgets. More...
class	SideViewerWidget
	Qt Widget to provide a single SingleViewerWidget, and some associated buttons controlling 2/3 view, vertical/horizontal and axial/coronal/sagittal/ortho. More...
class	Single3DViewWidget
	Base class widget containing a single 3D render window whose purpose is to render a 3D VTK scene, blended with image data, such as might be available from video or ultrasound. More...
class	SingleUltrasoundWidget
	Derived from niftk::Single3DViewWidget to provide a widget that given an image, will always position the camera to face the image and scale the image to maximally fill the window. In contrast to niftk::SingleVideoWidget the image plane is a plane in 3D space, not a projection through a camera model. Therefore, the image is modelled as a texture plane, so 3D geometry objects can appear infront or behind the plane. More...
class	SingleVideoWidget
	Derived from niftk::Single3DViewWidget to provide a widget that given a video image, will render it at video frame rate into both the foreground and the background layer, and additionally merge VTK renderings. More...
class	SingleViewerControls
	Control panel for the DnD display. More...
class	SingleViewerEditor
	Simple image viewer that supports cursor and magnification binding. More...
struct	SingleViewerEditorPartListener
class	SingleViewerEditorPrivate
class	SingleViewerWidget
	A widget to wrap a single MultiWindowWidget, providing methods for switching the render window layout, remembering the last slice, magnification and cursor position. More...
class	SingleViewerWidgetState
class	SingleViewerWidgetTestClass
class	SingleViewerWidgetTestClassPrivate
class	SpectraTracker
	RAII object to connect to Polaris Spectra tracker. More...
class	StateMachineEventFilter
	StateMachineEventFilter represents a condition that has to be fulfilled so that an event is processed by a tool or interactor that derives from niftk::FilteringStateMachine. More...
class	StateMachineRendererFilter
	StateMachineRendererFilter represents a condition that allows only the events coming from certain renderers to be processed. More...
class	SurfaceReconstruction
	Takes image data, and calculates a surface reconstruction, and write a point cloud to mitk::DataStorage. More...
class	SurfaceRegServiceI
	Interface for a Surface Based Registration Service. More...
class	SystemTimeServiceI
	Interface for a service that can return the system time. More...
class	SystemTimeServiceRAII
	RAII object to retrieve the system time via a SystemTimeServiceI implementation. More...
class	TestICPBasedRegistration
class	ThumbnailInteractor
	Observer that manages the interaction with the thumbnail window. More...
class	ThumbnailRenderWindow
	Subclass of QmitkRenderWindow to track to another QmitkRenderWindow and provide a zoomed-out view with an overlay of a bounding box to provide the current size of the currently tracked QmitkRenderWindow's view-port size. ....The client must. More...
class	ThumbnailView
	Provides a thumbnail view of the currently focused QmitkRenderWindow. ....Note: This class should basically just be a wrapper that instantiates the widget QmitkThumnailRenderWindow, and does almost nothing else. Do not try and add loads more functionality here, just do the necessary plumbing. More...
class	ThumbnailViewPreferencePage
	Preferences page for the ThumbnailView plugin, enabling the user to set line thickness, opacity, layer, and whether to respond to mouse events. More...
class	Tool
	Base class for segmentor tools that need access to the list of seeds for the current reference data volume registered with the ToolManager. More...
class	ToolKeyPressResponder
	Pure Virtual Interface to be implemented by classes that want to respond to MIDAS key events relevant to which tool is selected where events are passed through from the MIDASToolKeyPressStateMachine which is a subclass of StateMachine, and hence registered with the interaction loop. More...
class	ToolKeyPressStateMachine
class	ToolSelectorWidget
	Implements a widget containing the QmitkToolGUIArea and QmitkToolSelectionBox. More...
class	ToolWorkingDataNameFilter
	A filter that returns Pass=false if the name is in the following list, and true otherwise. More...
class	UltrasonixDataSourceActivator
	Activator to register the UltrasonixDataSourceFactory. More...
class	UltrasonixDataSourceFactory
	Factory class to create UltrasonixDataSources. More...
class	UltrasonixDataSourceService
	Provides a feed of images from Ultrasonix MDP, as an IGIDataSourceServiceI. More...
class	UltrasonixDataType
	Class to represent ultrasound frame data from Ultrasonix. More...
class	UltrasoundPointerBasedCalibration
	Calibrates an Ultrasound Probe using LM optimisation, as described in Muratore 2001. More...
class	UltrasoundPointerCalibrationCostFunction
	Cost function for Ultrasound Pointer based calibration, a la Muratore 2001. More...
class	Undistortion
class	UndistortionWorker
struct	vec_equal
class	VicraTracker
	RAII object to connect to Polaris Vicra tracker. More...
class	VisibilityChangedCommand
class	VisibilityChangeObserver
class	VL_Clip_Mode_Property
class	VL_Fog_Mode_Property
class	VL_Point_Mode_Property
class	VL_Render_Mode_Property
class	VL_Smart_Target_Property
class	VL_Surface_Mode_Property
class	VL_Volume_Mode_Property
class	VLDummyData
class	VLGlobalSettingsDataNode
class	VLMapper
	A VL representation of a mitk::DataNode for rendering purposes. More...
class	VLMapper2DImage
class	VLMapper3DImage
class	VLMapperCoordinateAxes
class	VLMapperPoints
class	VLMapperPointSet
class	VLMapperSurface
class	VLMapperVLGlobalSettings
class	VLSceneView
	A vl::UIEventListener bound to a QGLWidget (niftk::VLWidget) managing all VL/Vivid rendering and options and listening to mitk::DataStorage events. More...
class	VLStandardDisplayEditor
	Simple editor that delegates all functionality to a niftk::VLStandardDisplayWidget, and most methods are dummy or do-nothing implementations, as the widget is for a very specific purpose and most of the mitk::ILinkedRenderWindowPart are not needed. More...
class	VLStandardDisplayEditorActivator
	Activator class for the VLStandardDisplayEditor. More...
class	VLStandardDisplayEditorPreferencePage
	Preference page for VLStandardDisplayEditor, eg. setting the background colour. More...
class	VLStandardDisplayEditorPrivate
	PIMPL pattern implementation of VLStandardDisplayEditor. More...
class	VLStandardDisplayWidget
	Contains 4 coordinated VL views for radiological viewing purposes (e.g. EpiNav project). More...
class	VLTrackballManipulator
class	VLUserData
class	VLUtils
class	VLVideoOverlayWidget
	Contains 4 coordinated VL views for AR purposes (e.g. liver project). More...
class	VLWidget
	A QGLWidget containing a niftk::VLSceneView. More...
class	VTK4PointsReader
	Reads points to a polydata object. More...
class	VTKIGIGeometry
class	VTKIterativeClosestPoint
	Uses vtkIterativeClosestPointTransform to register two vtkPolyData sets. More...
class	WheelEventEater
	Qt event filter to eat wheel events. More...
class	WindowsHotkeyHandler
struct	WindowsHotkeyHandlerImpl
struct	WriteAccessor

Typedefs
typedef unsigned char	uchar
typedef signed char	schar
typedef float	real
typedef std::pair< int, std::string >	LabelType
typedef std::vector< LabelType >	LabelsListType
typedef std::vector< QColor >	ColorListType
typedef QMap< QString, QVariant >	IGIDataSourceProperties
typedef itk::PolyLineParametricPath< 3 >	ParametricPathType
typedef std::vector < ParametricPathType::Pointer >	ParametricPathVectorType
typedef ParametricPathType::VertexListType	ParametricPathVertexListType
typedef ParametricPathType::VertexType	ParametricPathVertexType
typedef itk::RGBPixel < unsigned char >	UCRGBPixelType
typedef itk::RGBAPixel < unsigned char >	UCRGBAPixelType
typedef mitk::GenericProperty < itk::Matrix< float, 4, 4 > >	MatrixProperty

Enumerations
enum	ImageOrientation { IMAGE_ORIENTATION_AXIAL = 0, IMAGE_ORIENTATION_SAGITTAL = 1, IMAGE_ORIENTATION_CORONAL = 2, IMAGE_ORIENTATION_UNKNOWN = 3 }
	Describes the different types of orientation, axial, sagittal, coronal, that can be achieved in the Drag&Drop Display windows. This is different from WindowOrientation. The orientation might be used to refer to the axis of an image, so an image can ONLY be sampled in AXIAL, SAGITTAL and CORONAL direction. More...
enum	WindowOrientation { WINDOW_ORIENTATION_AXIAL = 0, WINDOW_ORIENTATION_SAGITTAL = 1, WINDOW_ORIENTATION_CORONAL = 2, WINDOW_ORIENTATION_UNKNOWN = 3 }
	Describes the different types of orientation, axial, sagittal, coronal, that can be achieved in the Drag&Drop Display windows. This is different from the WindowLayout. The orientation might be used to refer to the axis of an image, so an image can ONLY be sampled in AXIAL, SAGITTAL and CORONAL direction. More...
enum	WindowLayout {   WINDOW_LAYOUT_AXIAL = 0, WINDOW_LAYOUT_SAGITTAL = 1, WINDOW_LAYOUT_CORONAL = 2, WINDOW_LAYOUT_ORTHO = 3,   WINDOW_LAYOUT_3D = 4, WINDOW_LAYOUT_3H = 5, WINDOW_LAYOUT_3V = 6, WINDOW_LAYOUT_AS_ACQUIRED = 7,   WINDOW_LAYOUT_UNKNOWN = 8, WINDOW_LAYOUT_COR_SAG_H = 9, WINDOW_LAYOUT_COR_SAG_V = 10, WINDOW_LAYOUT_COR_AX_H = 11,   WINDOW_LAYOUT_COR_AX_V = 12, WINDOW_LAYOUT_SAG_AX_H = 13, WINDOW_LAYOUT_SAG_AX_V = 14 }
	Describes the different render window layouts. So one WindowLayout could have multiple windows of different orientations, but most often will contain either axial, coronal or sagittal. This is different to the WindowLayout as a layout can contain multiple orientations. More...
enum	DnDDisplayDropType { DNDDISPLAY_DROP_SINGLE = 0, DNDDISPLAY_DROP_MULTIPLE = 1, DNDDISPLAY_DROP_ALL = 2 }
	Describes the different modes that can be used when drag and dropping into the DnD Display window. More...
enum	DnDDisplayInterpolationType { DNDDISPLAY_NO_INTERPOLATION, DNDDISPLAY_LINEAR_INTERPOLATION, DNDDISPLAY_CUBIC_INTERPOLATION }
	Describes what the interpolation type should be set to when an image is dropped. More...

Functions
std::string	ConvertToString (int x)
std::string	ConvertToString (unsigned int x)
std::string	ConvertToString (unsigned long long x)
std::string	ConvertToString (long int x)
std::string	ConvertToString (long unsigned int x)
std::string	ConvertToString (double x)
std::string	ConvertToString (bool x)
std::string	ConvertToString (float x)
int	ConvertToInt (const std::string &x)
double	ConvertToDouble (const std::string &x)
bool	ConvertToBool (const std::string &x)
double	CalculateVarianceFromFWHM (double fwhm)
double	CalculateStdDevFromFWHM (double fwhm)
double	ConvertFirstVoxelCoordinateToMiddleOfImageCoordinate (double millimetreCoordinateOfFirstVoxel, int numberOfVoxelsInThatAxis, double voxelSpacingInThatAxis)
double	ConvertMiddleOfImageCoordinateToFirstVoxelCoordinate (double millimetreCoordinateOfMiddleVoxel, int numberOfVoxelsInThatAxis, double voxelSpacingInThatAxis)
double	fixRangeTo1 (double d)
int	Round (double d)
double	Round (double d, int numberDecimalPlaces)
std::string	GetLastNCharacters (std::string s, int n)
std::istream &	operator>> (std::istream &str, CSVRow &data)
std::ostream &	operator<< (std::ostream &os, const CSVRow &data)
std::string	GetHomeDirectory ()
std::string	GetWorkingDirectory ()
std::string	GetNifTKHome ()
std::string	GetEnvVar (const std::string &variableName)
std::string	GetFileSeparator ()
std::string	ConcatenatePath (const std::string &path, const std::string &name)
fs::path	ConvertToFullPath (const std::string &pathName)
std::string	ConvertToFullNativePath (const std::string &pathName)
std::string	Basename (const std::string &pathName)
	Returns the basename. More...
std::string	CreateUniqueTempFileName (const std::string &prefix, const std::string &suffix)
bool	DirectoryExists (const std::string &directoryPath)
bool	CreateDirAndParents (const std::string &directoryPath)
bool	FileExists (const std::string &fileName)
bool	FileDelete (const std::string &fileName)
int	FileSize (const std::string &fileName)
bool	FileIsEmpty (const std::string &fileName)
bool	FilenameHasPrefixAndExtension (const std::string &filename, const std::string &prefix, const std::string &extension)
bool	FilenameMatches (const std::string &filename, const std::string &prefix, const std::string &middle, const std::string &extension)
std::string	GetImagesDirectory ()
std::vector< std::string >	GetFilesInDirectory (const std::string &fullDirectoryName)
std::vector< std::string >	GetDirectoriesInDirectory (const std::string &fullDirectoryName)
void	GetRecursiveFilesInDirectory (const std::string &directoryName, std::vector< std::string > &fileNames)
bool	NumericStringCompare (const std::string &string1, const std::string &string2)
std::vector< std::string >	FindVideoData (const std::string &directory)
std::string	FindVideoFile (const std::string &directory, const std::string &mask)
std::vector< std::string >	FindFilesWithGivenExtension (const std::string &fullDirectoryName, const std::string &extension)
std::string	ExtractImageFileSuffix (const std::string &fileName)
std::string	ExtractImageFileSuffix (const std::string &fileName, std::string &fileNameWithoutSuffix)
std::string	AddStringToImageFileSuffix (const std::string &fileName, std::string stringToAdd)
std::string	ModifyImageFileSuffix (const std::string &fileName, std::string newSuffix)
std::string	GetFilenameStem (const std::string &fileName)
std::string	ModifyFileSuffix (const std::string &fileName, std::string newSuffix)
bool	IsCloseToZero (const double &value, const double &tolerance=0.000001)
	Returns true if fabs(value) is less than a small tolerance, which defaults to 0.000001. More...
std::pair< double, double >	FindMinimumValues (std::vector< std::pair< double, double > > inputValues, std::pair< unsigned int, unsigned int > *indexes=NULL)
	Takes a vector of pairs and finds the minimum value in each dimension. Returns the minimum values. Optionally returns the indexes of the minium values. More...
double	RMS (const std::vector< double > &input)
	Assuming input contains squared errors, will sum them, divide by N, and take sqrt for an RMS measure. More...
double	Mean (const std::vector< double > &input)
	To return the sample mean of a vector. More...
double	StdDev (const std::vector< double > &input)
	To return the sample standard deviation of a vector. More...
double	ModifiedSignum (double value)
	Returns -1.0 if value < 0 or 1.0 if value >= 0. More...
double	SafeSQRT (double value)
	Returns 0.0 of value < 0 or sqrt(value) if value >= 0. More...
void NIFTKCUDAKERNELS_WINEXPORT	RunUndistortionKernel (char *outputRGBA, int width, int height, cudaTextureObject_t srcTexture, const float *intrinsic3x3, const float *distortion4, cudaStream_t stream)
	Provides 2D image undistortion, given a cameras intrinsic and distortion co-efficients. More...
static void	HandleCUDAError (cudaError_t err, const char *file, int line)
	Static method (only available to same T.U.) to print error. More...
int NIFTKCUDAKERNELS_WINEXPORT	AddTwoIntegers (int a, int b)
	Pointless minimal function, mainly just to test if anything at all could be run on a device. More...
void NIFTKCUDAKERNELS_WINEXPORT	RunEdgeDetectionKernel (char *outputRGBA, unsigned int outputBytePitch, const char *inputRGBA, unsigned int inputBytePitch, int width, int height, cudaStream_t stream)
	Basic example kernel to do some edge detection, but is not yet implemented. More...
void NIFTKCUDAKERNELS_WINEXPORT	RunFlipImageKernel (char *output, int widthInBytes, int height, int outputpitchInBytes, const char *input, int inputpitchInBytes, cudaStream_t stream)
	Flips image in y-axis. More...
int *	UpperToLowerOrder (int dim)
int *	LowerToUpperOrder (int dim)
int	SymMatDim (int count)
	vtkStandardNewMacro (VTK4PointsReader)
	vtkStandardNewMacro (BackfaceCullingFilter) BackfaceCullingFilter
double	GetEuclideanDistanceBetweenTwo3DPoints (const double *a, const double *b)
double	GetLength (const double *a)
void	ScaleVector (const double &scaleFactor, const double *a, double *b)
void	SubtractTwo3DPoints (const double *a, const double *b, double *output)
void	AddTwo3DPoints (const double *a, const double *b, double *output)
void	Normalise3DPoint (const double *a, const double length, double *output)
void	NormaliseToUnitLength (const double *a, double *output)
void	CrossProductTwo3DVectors (const double *a, const double *b, double *c)
void	CalculateUnitVector (const double *a, const double *b, double *output)
double	AngleBetweenTwoUnitVectors (const double *a, const double *b)
double	AngleBetweenTwoUnitVectorsInDegrees (const double *a, const double *b)
bool	ClipPointToWithinBoundingBox (const double *bounds, double *point)
double	GetBoundingBoxDiagonalLength (const double *boundingBoxVector6)
void	CopyDoubleVector (int n, const double *a, double *b)
void	RandomTransform (vtkTransform *transform, double xtrans, double ytrans, double ztrans, double xrot, double yrot, double zrot, vtkRandomSequence *rng)
	Creates a randomly determined vtkTransform, using existing random number geneterator. More...
void	TranslatePolyData (vtkPolyData *polydata, vtkTransform *transform)
	Translates a polydata object using a transform. More...
void	PerturbPolyDataAlongNormal (vtkPolyData *polydata, double stdDev, vtkRandomSequence *rng)
void	PerturbPolyData (vtkPolyData *polydata, double xerr, double yerr, double zerr, vtkRandomSequence *rng)
	Perturbs the points in a polydata object by random values, using existing random number generator. More...
void	PerturbPolyData (vtkPolyData *polydata, double xerr, double yerr, double zerr)
	Perturbs the points in a polydata object by with random values, intialising and using it's own random number generator. More...
void	RandomTransform (vtkTransform *transform, double xtrans, double ytrans, double ztrans, double xrot, double yrot, double zrot)
	Creates a randomly determined vtktransform, using it's own random number generator. More...
double	NormalisedRNG (vtkRandomSequence *rng)
	Normalises the values returned by a vtk random sequence to be centred on zero. More...
bool	DistancesToColorMap (vtkPolyData *source, vtkPolyData *target)
	Measures the euclidean distances between the points in two polydata, and sets the. More...
double	DistanceToSurface (double point[3], vtkPolyData *target)
	Returns the euclidean distance (in 3D) between a point and the closest point on a polydata mesh. More...
double	DistanceToSurface (double point[3], vtkCellLocator *targetLocator, vtkGenericCell *cell=NULL)
	Returns the euclidean distance (in 3D) between a point and the closest point on a polydata mesh. More...
void	DistanceToSurface (vtkPolyData *source, vtkPolyData *target, vtkSmartPointer< vtkDoubleArray > &result)
	Calculates the euclidean distance (in 3D) between each point in the source polydata and the closest point on the target polydata mesh. The result distances are stored in the scalar values passed in. More...
void	DistanceToSurface (vtkPolyData *source, vtkPolyData *target)
	Calculates the euclidean distance (in 3D) between each point in the source polydata and the closest point on the target polydata mesh. The result are stored the distances in the scalar values of the source. More...
std::string	WriteMatrix4x4ToString (const vtkMatrix4x4 &matrix)
	Writes matrix out as a string, for use in SaveMatrix4x4ToFile. More...
bool	SaveMatrix4x4ToFile (const std::string &fileName, const vtkMatrix4x4 &matrix, const bool &silent=false)
	Save the matrix to a plain text file of 4 rows of 4 space separated numbers. More...
vtkSmartPointer< vtkMatrix4x4 >	LoadMatrix4x4FromFile (const std::string &fileName, const bool &silent=false)
	Loads the matrix from file, or else creates an Identity matrix, and the caller is responsible for deallocation. More...
bool	MatricesAreEqual (const vtkMatrix4x4 &m1, const vtkMatrix4x4 &m2, const double &tolerance=0.01)
	Checks matrices for equality. More...
void	SetCameraParallelTo2DImage (const int *imageSize, const int *windowSize, const double *origin, const double *spacing, const double *xAxis, const double *yAxis, const double *clippingRange, const bool &flipYAxis, vtkCamera &camera, const double &distanceToFocalPoint=-1000)
	Used to set a vtkCamera to track a 2D image, and sets the camera to parallel projection mode. More...
bool	CropPointsFromPolyData (vtkPolyData *PolyData, int Points=200)
	Randomly removes points from the passed polydata until the passed number of points Any cells or surfaces will be deleted as part of the process, leaving only points. More...
void	MatrixToQuaternion (const vtkMatrix4x4 &matrix, double *quaternion)
	Extracts the rotation matrix, and converts to quaternion. More...
void	InterpolateRotation (const double *beforeRotation, const double *afterRotation, const double &weight, double *outputRotation, bool adjustSign)
	Performs spherical linear interpolation. More...
void	InterpolateTransformationMatrix (const vtkMatrix4x4 &before, const vtkMatrix4x4 &after, const double &proportion, vtkMatrix4x4 &interpolated)
	Interpolates between two matrices. More...
itk::Orientation	GetItkOrientation (ImageOrientation orientation)
	Converts an MITK orientation enum to an ITK orientation enum, and ideally these types should be merged. More...
ImageOrientation	GetMitkOrientation (itk::Orientation orientation)
	Converts an ITK orientation enum to an MITK orientation enum, and ideally these types should be merged. More...
std::string	GetOrientationName (ImageOrientation orientation)
	Returns the name of the given orientation. More...
int	GetUpDirection (const mitk::BaseGeometry *geometry, itk::Orientation orientation)
	Returns either +1, or -1 to indicate in which direction you should change the slice number to go "up". More...
int	GetUpDirection (const mitk::Image *image, ImageOrientation orientation)
	See GetUpDirection as in effect, we are only using the direction cosines from the geometry. More...
int	GetThroughPlaneAxis (const mitk::Image *image, ImageOrientation orientation)
	Returns either -1 (unknown), or [0,1,2] for the x, y, or z axis corresponding to the through plane direction for the specified orientation. More...
std::string	GetOrientationString (const mitk::Image *image)
	Returns the Orientation String (RPI, RAS etc). More...
void	GetAxesInWorldCoordinateOrder (const mitk::Image *mitkImage, int axes[3])
	Converts between voxel coordinate order and world coordinate order. The function writes the axes of the sagittal, coronal and axial dimensions to axes, in this order: More...
void	GetSpacingInWorldCoordinateOrder (const mitk::Image *mitkImage, mitk::Vector3D &spacing)
	Gets the spacing of the image in world coordinate order. More...
void	GetExtentsInVxInWorldCoordinateOrder (const mitk::Image *mitkImage, mitk::Vector3D &extentsInVx)
	Gets the extents (number of voxels) of the image in world coordinate order. More...
void	GetExtentsInMmInWorldCoordinateOrder (const mitk::Image *mitkImage, mitk::Vector3D &extentsInMm)
	Gets the extents of the image in millimetres in world coordinate order. More...
template<typename TPixel , unsigned int VImageDimension>
NIFTKCORE_EXPORT void	GetAxesInWorldCoordinateOrder (const itk::Image< TPixel, VImageDimension > *itkImage, int axes[3])
	Converts between voxel coordinate order and world coordinate order. The function writes the axes of the sagittal, coronal and axial dimensions to axes, in this order: More...
template<typename TPixel , unsigned int VImageDimension>
NIFTKCORE_EXPORT void	GetSpacingInWorldCoordinateOrder (const itk::Image< TPixel, VImageDimension > *itkImage, mitk::Vector3D &spacing)
	Gets the spacing of the image in world coordinate order. More...
template<typename TPixel , unsigned int VImageDimension>
NIFTKCORE_EXPORT void	GetExtentsInVxInWorldCoordinateOrder (const itk::Image< TPixel, VImageDimension > *itkImage, mitk::Vector3D &extentsInVx)
	Gets the extents (number of voxels) of the image in world coordinate order. More...
template<typename TPixel , unsigned int VImageDimension>
NIFTKCORE_EXPORT void	GetExtentsInMmInWorldCoordinateOrder (const itk::Image< TPixel, VImageDimension > *itkImage, mitk::Vector3D &extentsInMm)
	Gets the extents of the image in millimetres in world coordinate order. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKGetAsAcquiredOrientation (const itk::Image< TPixel, VImageDimension > *itkImage, ImageOrientation &outputOrientation)
	ITK method that given an image, returns the ImageOrientation for the XY plane. More...
ImageOrientation	GetAsAcquiredOrientation (ImageOrientation defaultOrientation, const mitk::Image *image)
	Returns the ImageOrientation corresponding to the XY plane, or else returns the supplied default. More...
bool	IsImage (const mitk::DataNode *node)
	Simply returns true if a node contains an image, and false otherwise. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKImagesHaveEqualIntensities (const itk::Image< TPixel, VImageDimension > *itkImage, const mitk::Image *image2, bool &output)
bool	ImagesHaveEqualIntensities (const mitk::Image *image1, const mitk::Image *image2)
	Utility method that compares if images have the same intensity values. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKImagesHaveSameSpatialExtent (const itk::Image< TPixel, VImageDimension > *itkImage, const mitk::Image *image2, bool &output)
bool	ImagesHaveSameSpatialExtent (const mitk::Image *image1, const mitk::Image *image2)
	Utility method that compares if images have the same spatial extent. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKFillImage (itk::Image< TPixel, VImageDimension > *itkImage, float &value)
void	FillImage (mitk::Image *image, float value)
	Simply iterates through a whole image, filling it with the specified value which is cast to the appropriate pixel type. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKCountBetweenThreshold (const itk::Image< TPixel, VImageDimension > *itkImage, const float &lower, const float &upper, unsigned long int &outputCount)
NIFTKCORE_EXPORT unsigned long int	CountBetweenThreshold (const mitk::Image *image, float lower, float upper)
	Simply iterates through a whole image, counting how many intensity values are >= lower and <= upper. More...
unsigned long int	GetNumberOfVoxels (const mitk::Image *image)
	Returns the number of voxels in an image. More...
mitk::Point3D	GetMiddlePointInVoxels (const mitk::Image *image)
	Returns the middle voxel of an image. More...
double	GetVolume (const mitk::Image *image)
	Returns the volume of non-zero voxels in an image. More...
void	UpdateVolumeProperty (const mitk::Image *image, mitk::DataNode *node)
	Calculates the volume of non-zero voxels in image, and creates a property "midas.volume" on the data node. More...
template<typename TPixel1 , unsigned int VImageDimension1, typename TPixel2 , unsigned int VImageDimension2>
void	ITKCopyIntensityData (const itk::Image< TPixel1, VImageDimension1 > *itkImage1, itk::Image< TPixel2, VImageDimension2 > *itkImage2)
	ITK function to copy image data, performing C-style casting between data types. More...
void	CopyIntensityData (const mitk::Image *input, mitk::Image *output)
	Assumes same size image, and same data type, and copies data from the input image to the output image. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKDumpImage (const itk::Image< TPixel, VImageDimension > *itkImage, const std::string &filename)
	Writes the image to file. More...
void	DumpImage (const mitk::Image *input, const std::string &fileName)
	Writes the image to file. More...
mitk::Vector3D	GetXYAspectRatio (const mitk::Image::Pointer image)
	Utility method to calculate the aspect ratio. More...
double	CalculateStepSize (double *spacing)
	Given a double[3] of x,y,z voxel spacing, calculates a step size along a ray, as 1/3 of the smallest voxel dimension. More...
bool	AreDifferent (const mitk::Point3D &a, const mitk::Point3D &b)
	Returns true if a and b are different (up to a given tolerance, currently 0.01), and false otherwise. More...
double	GetSquaredDistanceBetweenPoints (const mitk::Point3D &a, const mitk::Point3D &b)
	Returns the squared Euclidean distance between a and b. More...
double	GetRMSErrorBetweenPoints (const mitk::PointSet &fixed, const mitk::PointSet &moving, const CoordinateAxesData *const transform=NULL)
	Gets the RMS error between fixed point set and a moving point set, with optional transform specified. More...
void	GetDifference (const mitk::Point3D &a, const mitk::Point3D &b, mitk::Point3D &output)
	Returns as output the vector difference of a-b. More...
double	Length (mitk::Point3D &vector)
	Given a vector, will calculate the length. More...
void	Normalise (mitk::Point3D &vector)
	Given a vector, will normalise it to unit length. More...
double	FindLargestDistanceBetweenTwoPoints (const mitk::PointSet &input)
	Computes the largest Euclidean Distance between any two points. More...
int	CopyPointSets (const mitk::PointSet &input, mitk::PointSet &output)
	Copies input to output, i.e. the output is erased, and re-populated. More...
void	ScalePointSets (const mitk::PointSet &input, mitk::PointSet &output, double scaleFactor)
	Copies input to output, i.e. the output is erased, and re-populated, multiplying by a scale factor. More...
void	CopyValues (const mitk::Point3D &a, mitk::Point3D &b)
	Copies a into b. More...
void	CrossProduct (const mitk::Point3D &a, const mitk::Point3D &b, mitk::Point3D &c)
	Computes c = a x b, and will normalise a and b to unit length first. More...
void	ComputeNormalFromPoints (const mitk::Point3D &a, const mitk::Point3D &b, const mitk::Point3D &c, mitk::Point3D &output)
	Computes the normal by calculating cross product of (a-b) and (c-b). More...
void	TransformPointByVtkMatrix (const vtkMatrix4x4 *matrix, const bool &isNormal, mitk::Point3D &pointOrNormal)
	Simple method to multiply a mitk::Point3D by a vtkMatrix, if the matrix is not NULL, and otherwise if matrix is NULL, will simply leave the point un-altered. More...
void	TransformPointsByVtkMatrix (const mitk::PointSet &input, const vtkMatrix4x4 &matrix, mitk::PointSet &output)
	Multiplies one point set by a matrix. More...
int	FilterMatchingPoints (const mitk::PointSet &fixedPointsIn, const mitk::PointSet &movingPointsIn, mitk::PointSet &fixedPointsOut, mitk::PointSet &movingPointsOut)
	Takes fixed and moving points, and scans for matching ID's and returns 2 point sets with ordered and corresponding points. More...
int	RemoveNaNPoints (const mitk::PointSet &pointsIn, mitk::PointSet &pointsOut)
	Takes a point set and scans for matching NaN's and returns a point set with the offending points removed. More...
bool	CheckForNaNPoint (const mitk::PointSet::PointType &point)
	Checks if the point contains a NaN value. More...
mitk::Point3D	ComputeCentroid (const mitk::PointSet &input)
	Computes the mean/centroid of an mitk::PointSet. More...
std::ostream &	operator<< (std::ostream &os, const BasicTriangle &to)
std::ostream &	operator<< (std::ostream &os, const BasicVec3D &vo)
std::ostream &	operator<< (std::ostream &os, const BasicVertex &vo)
mitk::DataNode::Pointer	FindFirstParentImage (const mitk::DataStorage *storage, const mitk::DataNode::Pointer node, bool lookForBinary)
mitk::DataStorage::SetOfObjects::Pointer	FindDerivedVisibleNonHelperChildren (const mitk::DataStorage *storage, const mitk::DataNode::Pointer node)
mitk::DataStorage::SetOfObjects::Pointer	FindDerivedImages (const mitk::DataStorage *storage, const mitk::DataNode::Pointer node, bool lookForBinary)
bool	IsNodeAHelperObject (const mitk::DataNode *node)
bool	IsNodeAGreyScaleImage (const mitk::DataNode::Pointer node)
bool	IsNodeABinaryImage (const mitk::DataNode::Pointer node)
mitk::DataNode::Pointer	FindNthImage (const std::vector< mitk::DataNode * > &nodes, int n, bool lookForBinary)
mitk::DataNode::Pointer	FindNthGreyScaleImage (const std::vector< mitk::DataNode * > &nodes, int n)
mitk::DataNode::Pointer	FindNthBinaryImage (const std::vector< mitk::DataNode * > &nodes, int n)
mitk::DataNode::Pointer	FindFirstGreyScaleImage (const std::vector< mitk::DataNode * > &nodes)
mitk::DataNode::Pointer	FindFirstBinaryImage (const std::vector< mitk::DataNode * > &nodes)
mitk::DataNode::Pointer	FindFirstParent (const mitk::DataStorage *storage, const mitk::DataNode::Pointer node)
mitk::DataNode::Pointer	FindParentGreyScaleImage (const mitk::DataStorage *storage, const mitk::DataNode::Pointer node)
mitk::TimeGeometry::Pointer	GetPreferredGeometry (const mitk::DataStorage *dataStorage, const std::vector< mitk::DataNode * > &nodes, const int &nodeIndex=-1)
	GetPreferedGeometry will return the geometry to use by picking one from the list of nodes, or NULL, if none can be found. More...
void	LoadMatrixOrCreateDefault (const std::string &fileName, const std::string &nodeName, const bool &helperObject, mitk::DataStorage *dataStorage)
	Loads a 4x4 matrix from a plain textfile, and puts in data storage with the given nodeName, or else creates Identity matrix. More...
void	GetCurrentTransformFromNode (const mitk::DataNode::Pointer &node, vtkMatrix4x4 &outputMatrix)
	Retrieves the current tranform from the mitk::Geometry object of an mitk::DataNode. More...
void	ComposeTransformWithNode (const vtkMatrix4x4 &transform, mitk::DataNode::Pointer &node)
	Composes (pre-multiplies) the given transform with the given node. More...
void	ApplyTransformToNode (const vtkMatrix4x4 &transform, mitk::DataNode::Pointer &node)
	Applies (sets, i.e. copies) the given transform to the given node. More...
bool	LoadDoublesFromFile (const std::string &fileName, std::vector< double > &output)
bool	Load2DPointFromFile (const std::string &fileName, mitk::Point2D &point)
	Loads a 2D point from file, returning true if successful and false otherwise. More...
bool	Load3DPointFromFile (const std::string &fileName, mitk::Point3D &point)
	Loads a 3D point from file, returning true if successful and false otherwise. More...
vtkSmartPointer< vtkMatrix4x4 >	LoadVtkMatrix4x4FromFile (const std::string &fileName)
	Load a plain text file of 4 rows of 4 space separated numbers into a vtkMatrix4x4. More...
bool	SaveVtkMatrix4x4ToFile (const std::string &fileName, const vtkMatrix4x4 &matrix)
	Save the matrix to a plain text file of 4 rows of 4 space separated numbers. More...
std::vector < mitk::PointSet::Pointer >	LoadPointSetsFromDirectory (const std::string fullDirectoryName)
	Loads all point sets from directory. More...
void	LoadTimeStampData (const std::string &fileName, std::set< unsigned long long > &outputTimeStamps)
	Loads a list of timestamps from a file. More...
vtkLookupTable *	ChangeColor (vtkLookupTable *lut, int value, const QColor &newColor)
	Replace the color in the LookupTable at the given index. More...
vtkLookupTable *	SwapColors (vtkLookupTable *lut, int value1, int value2)
	Swap colors in the LookupTable at the given indices. More...
vtkLookupTable *	ResizeLookupTable (vtkLookupTable *lut, double newMaximum)
	Resize the LookupTable while retaining all of the previously set values. Newly added values are assigned the nan color. More...
vtkLookupTable *	CreateEmptyLookupTable (const QColor &lowColor, const QColor &highColor)
void	TestInstantiation ()
void	TestIdentity ()
void	TestSetGet ()
void	TestErrorConditions ()
void	TestSimpleCases ()
void	TestCalculateStepSize ()
void	TestAreDifferent ()
void	TestGetSquaredDistanceBetweenPoints ()
void	TestGetDifference ()
void	TestNormalise ()
void	TestFindLargestDistanceBetweenTwoPoints ()
void	TestScalePointSets ()
void	TestComputeNormalFromPoints ()
void	TestFilterMatchingPoints ()
void	TestRemoveNaNPoints ()
void	TestCheckForNaNPoint ()
void	TestRMS ()
void	UndistortionLauncher (char *hostInputImageData, int width, int height, int widthStep, float *intrinsics, float *distortion, char *hostOutputImageData)
	Runs the CUDA based image undistortion. More...
static bool	CUDADelayLoadCheck ()
void	EdgeDetectionExampleLauncher (mitk::DataStorage *dataStorage, mitk::DataNode *node, const mitk::BaseRenderer *renderer)
	Runs edge detection on an MITK DataNode containing a niftk::CUDAImage. More...
void	FlipImageLauncher (const WriteAccessor &src, WriteAccessor &dest, cudaStream_t stream)
	Flips the image upside down. This implementation is likely not very efficient. More...
void	FlipImageLauncher (const ReadAccessor &src, WriteAccessor &dest, cudaStream_t stream)
	Flips the image upside down. This implementation is likely not very efficient. More...
void	Producer (const mitk::StandaloneDataStorage::Pointer &datastorage)
void	Consumer (const mitk::StandaloneDataStorage::Pointer &datastorage)
void	AnotherConsumer (const mitk::StandaloneDataStorage::Pointer &datastorage)
void	WaitForResult (const mitk::StandaloneDataStorage::Pointer &datastorage)
void	RefcountTest (const mitk::StandaloneDataStorage::Pointer &datastorage)
bool	IsSingleWindowLayout (WindowLayout layout)
	Returns true if the layout contains only one window, otherwise false. More...
bool	IsMultiWindowLayout (WindowLayout layout)
	Returns true if the layout contains multiple windows, otherwise false. More...
WindowLayout	GetWindowLayout (const std::string &windowLayoutName)
static bool	EqualsWithTolerance1 (const mitk::Point3D &worldPosition1, const mitk::Point3D &worldPosition2, double tolerance=0.001)
static bool	EqualsWithTolerance (const mitk::Vector2D &cursorPosition1, const mitk::Vector2D &cursorPosition2, double tolerance=0.01)
QString	GetPreferredSlash ()
	Returns the platform specific directory separator. More...
void	ProbeTimeStampFiles (QDir path, const QString &suffix, std::set< niftk::IGIDataType::IGITimeType > &timeStamps)
	Scans the path for individual files that match a timestamp pattern and suffix. More...
void	ProbeTimeStampFiles (QDir path, const QString &suffix, std::set< niftk::IGIDataType::IGITimeType > &timeStamps, QHash< niftk::IGIDataType::IGITimeType, QString > &timeStampToFileName)
	Scans the path for individual files that match a timestamp pattern and suffix. More...
void	GetPlaybackIndex (const QString &directory, const QString &fileExtension, QMap< QString, std::set< niftk::IGIDataType::IGITimeType > > &bufferToTimeStamp, QMap< QString, QHash< niftk::IGIDataType::IGITimeType, QStringList > > &bufferToTimeStampToFileNames)
	Returns the list of timestamps, by source name. More...
bool	ProbeRecordedData (const QString &path, const QString &fileExtension, niftk::IGIDataType::IGITimeType *firstTimeStampInStore, niftk::IGIDataType::IGITimeType *lastTimeStampInStore)
	Returns the minimum and maximum timestamped of all files under the specified path, with the specified fileExtension, that look like they are timestamped. More...
void	ConvertMITKSeedsAndAppendToITKSeeds (const mitk::PointSet *seeds, itk::PointSet< float, 3 > *points)
	This file contains functions that convert between ITK and MITK contour representations. More...
void	ConvertMITKContoursAndAppendToITKContours (mitk::ContourModelSet *mitkContours, std::vector< ParametricPathType::Pointer > &itkContours, const mitk::Vector3D &spacingInWorldCoordinateOrder)
void NIFTKMIDAS_EXPORT	ConvertMITKContoursAndAppendToITKContours (mitk::ContourModelSet *mitkContours, ParametricPathVectorType &itkContours, const mitk::Vector3D &spacing)
	Converts MITK contours from to ITK contours and appends them to a list. More...
void	GenerateOutlineFromBinaryImage (mitk::Image::Pointer image, int sliceAxis, int sliceIndex, int projectedSliceNumber, mitk::ContourModelSet *outputContourSet)
	Used to generate a contour outline round a binary segmentation image, and refreshes the outputSurface. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKFillRegion (itk::Image< TPixel, VImageDimension > *itkImage, const typename itk::Image< TPixel, VImageDimension >::RegionType &region, TPixel fillValue)
	Fills the itkImage region with the fillValue. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKClearImage (itk::Image< TPixel, VImageDimension > *itkImage)
	Clears an image by setting all voxels to zero using ITKFillRegion. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKCopyImage (const itk::Image< TPixel, VImageDimension > *input, itk::Image< TPixel, VImageDimension > *output)
	Copies an image from input to output, assuming input and output already allocated and of the same size. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKCopyRegion (const itk::Image< TPixel, VImageDimension > *input, int sliceAxis, int sliceIndex, itk::Image< TPixel, VImageDimension > *output)
	Copies the region from input to output, assuming both images are the same size, and contain the region. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKCalculateSliceRegion (const itk::Image< TPixel, VImageDimension > *itkImage, int sliceAxis, int sliceIndex, typename itk::Image< TPixel, VImageDimension >::RegionType &outputRegion)
	Calculates the region corresponding to a single slice. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKCalculateSliceRegionAsVector (const itk::Image< TPixel, VImageDimension > *itkImage, int sliceAxis, int sliceIndex, std::vector< int > &outputRegion)
	Calculates the region corresponding to a single slice. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKClearSlice (itk::Image< TPixel, VImageDimension > *itkImage, int sliceAxis, int sliceIndex)
	Clears a slice by setting all voxels to zero for a given slice and axis. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKFilterSeedsToCurrentSlice (const itk::Image< TPixel, VImageDimension > *itkImage, const mitk::PointSet *inputSeeds, int sliceAxis, int sliceIndex, mitk::PointSet *outputSeeds)
	Takes the inputSeeds and filters them so that outputSeeds contains just those seeds contained within the current slice. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKRecalculateMinAndMaxOfSeedValues (const itk::Image< TPixel, VImageDimension > *itkImage, const mitk::PointSet *inputSeeds, int sliceAxis, int sliceIndex, double &min, double &max)
	Called from RecalculateMinAndMaxOfSeedValues(), the actual method in ITK that recalculates the min and max intensity value of all the voxel locations given by the seeds. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKFilterInputPointSetToExcludeRegionOfInterest (const itk::Image< TPixel, VImageDimension > *itkImage, const typename itk::Image< TPixel, VImageDimension >::RegionType &regionOfInterest, const mitk::PointSet *inputSeeds, mitk::PointSet *outputCopyOfInputSeeds, mitk::PointSet *outputNewSeedsNotInRegionOfInterest)
	Takes the inputSeeds and copies them to outputCopyOfInputSeeds, and also copies seeds to outputNewSeedsNotInRegionOfInterest if the seed is not within the region of interest. More...
template<typename TPixel , unsigned int VImageDimension>
bool	ITKSliceDoesHaveSeeds (const itk::Image< TPixel, VImageDimension > *itkImage, const mitk::PointSet *seeds, int sliceAxis, int sliceIndex)
	Will return true if the given slice has seeds within that slice. More...
template<typename TPixel , unsigned int VImageDimension>
bool	ITKSliceIsEmpty (const itk::Image< TPixel, VImageDimension > *itkImage, int sliceAxis, int sliceIndex, bool &outputSliceIsEmpty)
	Creates a region of interest within itkImage corresponding to the given slice, and checks if it is empty returning true if it is all zero. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKUpdateRegionGrowing (const itk::Image< TPixel, VImageDimension > *itkImage, bool skipUpdate, const mitk::Image *workingImage, const mitk::PointSet *seeds, mitk::ContourModelSet *segmentationContours, mitk::ContourModelSet *drawContours, mitk::ContourModelSet *polyContours, int sliceAxis, int sliceIndex, double lowerThreshold, double upperThreshold, mitk::Image *outputRegionGrowingImage)
	Called from UpdateRegionGrowing(), updates the interactive ITK single 2D slice region growing pipeline. Note: segmentationContours, drawContours and polyContours could be const pointers, but some const functions are missing from mitk::ContourModelSet. They are not modified from within this function (including transitive calls). More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKPropagateToRegionGrowingImage (const itk::Image< TPixel, VImageDimension > *itkImage, const mitk::PointSet *inputSeeds, int sliceAxis, int sliceIndex, int direction, double lowerThreshold, double upperThreshold, mitk::PointSet *outputCopyOfInputSeeds, mitk::PointSet *outputNewSeeds, std::vector< int > &outputRegion, mitk::Image *outputRegionGrowingImage)
	Method takes all the input, and calculates the 3D propagated region (up or down or 3D), and stores it in the region growing node. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKPropagateUpOrDown (const itk::Image< TPixel, VImageDimension > *itkImage, const mitk::PointSet *seeds, int sliceAxis, int sliceIndex, int direction, double lowerThreshold, double upperThreshold, mitk::Image *outputRegionGrowingImage)
	Called from ITKPropagateToRegionGrowingImage to propagate up or down. More...
template<typename TGreyScalePixel , unsigned int VImageDimension>
void	ITKPropagateToSegmentationImage (const itk::Image< TGreyScalePixel, VImageDimension > *itkImage, mitk::Image *segmentedImage, mitk::Image *regionGrowingImage, OpPropagate *op)
	Called from the ExecuteOperate (i.e. undo/redo framework) to actually apply the calculated propagated region to the current segmentation. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKGenerateOutlineFromBinaryImage (const itk::Image< TPixel, VImageDimension > *itkImage, int sliceAxis, int sliceIndex, int projectedSliceIndex, mitk::ContourModelSet *contourSet)
	Called to extract a contour set from a binary image, as might be used for "See Prior", "See Next", or the outlining a binary segmentation. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKGetLargestMinimumDistanceSeedLocation (const itk::Image< TPixel, VImageDimension > *itkImage, TPixel foregroundPixelValue, typename itk::Image< TPixel, VImageDimension >::IndexType &outputSeedIndex, int &outputDistance)
	Works out the largest minimum distance to the edge of the image data, filtered on a given foregroundPixelValue. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKAddNewSeedsToPointSet (const itk::Image< TPixel, VImageDimension > *itkImage, const typename itk::Image< TPixel, VImageDimension >::RegionType &regionOfInterest, int sliceAxis, mitk::PointSet *outputNewSeeds)
	For the given input itkImage (assumed to always be binary), and regionOfInterest, will iterate on a slice by slice basis, recalculating new seeds. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKPreprocessingOfSeedsForChangingSlice (const itk::Image< TPixel, VImageDimension > *itkImage, const mitk::PointSet *inputSeeds, int oldSliceAxis, int oldSliceIndex, int newSliceAxis, int newSliceIndex, bool optimiseSeedPosition, bool newSliceIsEmpty, mitk::PointSet *outputCopyOfInputSeeds, mitk::PointSet *outputNewSeeds, std::vector< int > &outputRegion)
	Does any pre-processing of seeds necessary to facilitate Undo/Redo for Threshold Apply, and also changing slice. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKPreprocessingForWipe (const itk::Image< TPixel, VImageDimension > *itkImage, const mitk::PointSet *inputSeeds, int sliceAxis, int sliceIndex, int direction, mitk::PointSet *outputCopyOfInputSeeds, mitk::PointSet *outputNewSeeds, std::vector< int > &outputRegion)
	Does any pre-processing necessary to facilitate Undo/Redo for Wipe commands, which in this case means computing a new list of seeds, and the region of interest to be wiped. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKDoWipe (itk::Image< TPixel, VImageDimension > *itkImage, mitk::PointSet *currentSeeds, OpWipe *op)
	Does the wipe command for Wipe, Wipe+, Wipe-. More...
template<typename TPixel , unsigned int VImageDimension>
bool	ITKImageHasNonZeroEdgePixels (const itk::Image< TPixel, VImageDimension > *itkImage)
	Returns true if the image has non-zero edge pixels, and false otherwise. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKSliceDoesHaveUnenclosedSeeds (const itk::Image< TPixel, VImageDimension > *itkImage, const mitk::PointSet *seeds, mitk::ContourModelSet *segmentationContours, mitk::ContourModelSet *polyToolContours, mitk::ContourModelSet *drawToolContours, const mitk::Image *workingImage, double lowerThreshold, double upperThreshold, bool useThresholds, int sliceAxis, int sliceIndex, bool &sliceDoesHaveUnenclosedSeeds)
	Will return true if slice has unenclosed seeds, and false otherwise. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKFilterContours (const itk::Image< TPixel, VImageDimension > *itkImage, const mitk::Image *workingImage, const mitk::PointSet *seeds, mitk::ContourModelSet *segmentationContours, mitk::ContourModelSet *drawContours, mitk::ContourModelSet *polyContours, int sliceAxis, int sliceIndex, double lowerThreshold, double upperThreshold, bool isThresholding, mitk::ContourModelSet *outputCopyOfInputContours, mitk::ContourModelSet *outputContours)
	Extracts a new contour set, for doing "Clean" operation. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKPropagateSeedsToNewSlice (const itk::Image< TPixel, VImageDimension > *itkImage, const mitk::PointSet *currentSeeds, mitk::PointSet *newSeeds, int sliceAxis, int oldSliceIndex, int newSliceIndex)
	Given an image, and a set of seeds, will append new seeds in the new slice if necessary. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKDestroyPipeline (const itk::Image< TPixel, VImageDimension > *itkImage)
	Completely removes the current 2D region growing pipeline that is stored in the map m_TypeToPipelineMap. More...
template<typename TPixel , unsigned int VImageDimension>
void	ITKInitialiseSeedsForSlice (const itk::Image< TPixel, VImageDimension > *itkImage, mitk::PointSet *seeds, int sliceAxis, int sliceIndex)
	Creates seeds for each distinct 4-connected region for a given slice. More...
	NIFTK_TOOL_MACRO (NIFTKMIDAS_EXPORT, PosnTool,"Posn Tool")
static bool	CUDADelayLoadCheck ()
static void	check_oglerror (const std::string &detailedmsg)
template<typename PropType >
static void	CopyProp (const mitk::DataNode::Pointer source, mitk::Image::Pointer target, const char *name)
template<typename ITKPixelType >
static mitk::Image::Pointer	CreateMitkImageInternal (const IplImage *image)
mitk::Image::Pointer	CreateMitkImage (const IplImage *image)
mitk::Image::Pointer	CreateMitkImage (const cv::Mat *image)
cv::Mat	MitkImageToOpenCVMat (const mitk::Image::Pointer image)
void	BuildTextureDescriptor (const boost::gil::gray8c_view_t src, const boost::gil::gray8_view_t dst)
float	Zncc_C1 (int p0x, int p0y, int p1x, int p1y, int w, boost::gil::gray8c_view_t img0, boost::gil::gray8c_view_t img1, boost::gil::gray32sc_view_t integral0, boost::gil::gray32sc_view_t integral1, boost::gil::gray64fc_view_t square0, boost::gil::gray64fc_view_t square1)
static bool	CheckBorder (const Match &m, int bx, int by, int w, int h)
template<typename ITKPixelType >
static mitk::Image::Pointer	CreateMitkImageInternal (const IplImage *image)
cv::Matx33d	CalculateCrossCovarianceH (const std::vector< cv::Point3d > &q, const std::vector< cv::Point3d > &qPrime)
	Calculates 1/N Sum (q_i * qPrime_i^t) where q_i and qPrime_i are column vectors, so the product is a 3x3 matrix. More...
double	DoSVDPointBasedRegistration (const std::vector< cv::Point3d > &fixedPoints, const std::vector< cv::Point3d > &movingPoints, cv::Matx33d &H, cv::Point3d &p, cv::Point3d &pPrime, cv::Matx44d &outputMatrix)
	Does the main SVD bit of the point based registration, and handles the degenerate conditions mentioned in Aruns paper. More...
double	CalculateFiducialRegistrationError (const std::vector< cv::Point3d > &fixedPoints, const std::vector< cv::Point3d > &movingPoints, const cv::Matx44d &matrix)
	Calculates Fiducial Registration Error by multiplying the movingPoints by the matrix, and comparing with fixedPoints. More...
double	CalculateFiducialRegistrationError (const mitk::PointSet::Pointer &fixedPointSet, const mitk::PointSet::Pointer &movingPointSet, vtkMatrix4x4 &vtkMatrix)
	Converts format of input to call the other CalculateFiducialRegistrationError method. More...
double	PointBasedRegistrationUsingSVD (const std::vector< cv::Point3d > &fixedPoints, const std::vector< cv::Point3d > &movingPoints, cv::Matx44d &outputMatrix)
	Does Point Based Registration of two same sized, corresponding, ordered point sets. More...
double	PointBasedRegistrationUsingSVD (const mitk::PointSet::Pointer fixedPoints, const mitk::PointSet::Pointer movingPoints, vtkMatrix4x4 &matrix)
	Overloaded method for MITK and VTK data types. More...
double	PointAndNormalBasedRegistrationUsingSVD (const std::vector< cv::Point3d > &fixedPoints, const std::vector< cv::Point3d > &fixedNormals, const std::vector< cv::Point3d > &movingPoints, const std::vector< cv::Point3d > &movingNormals, cv::Matx44d &outputMatrix)
	Does Point Based Registration of two same sized, corresponding point sets. More...
double	PointAndNormalBasedRegistrationUsingSVD (const mitk::PointSet::Pointer fixedPoints, const mitk::PointSet::Pointer fixedNormals, const mitk::PointSet::Pointer movingPoints, const mitk::PointSet::Pointer movingNormals, vtkMatrix4x4 &matrix)
	Overloaded method for MITK and VTK data types. More...

Variables
static const char *	type []
int	tunnelOrientation = 0
static RegisterNifTKCoreObjectFactory	registerNifTKCoreObjectFactory
static RegisterNifTKCoreIOObjectFactory	registerNifTKCoreIOObjectFactory
impldetail::ModuleCleanup	s_ModuleCleaner
const int	WINDOW_ORIENTATION_NUMBER = 4
	The number of the possible orientations. More...
const int	WINDOW_LAYOUT_NUMBER = 15
	The number of the possible window layouts. More...
const mitk::OperationType	OP_CHANGE_SLICE = 9320411
const mitk::OperationType	OP_PROPAGATE_SEEDS = 9320412
const mitk::OperationType	OP_RETAIN_MARKS = 9320413
const mitk::OperationType	OP_THRESHOLD_APPLY = 9320414
const mitk::OperationType	OP_CLEAN = 9320415
const mitk::OperationType	OP_WIPE = 9320416
const mitk::OperationType	OP_PROPAGATE = 9320417
const int	VIRTUAL_SROM_SIZE =1024
static const MethodDescription	s_AvailableMethods []
const QString	IMAGE_INITIALISATION_METHOD_NAME
const QString	IMAGE_INITIALISATION_MIDAS
const QString	IMAGE_INITIALISATION_LEVELWINDOW
const QString	IMAGE_INITIALISATION_PERCENTAGE
const QString	IMAGE_INITIALISATION_PERCENTAGE_NAME
const QString	IMAGE_INITIALISATION_RANGE
const QString	IMAGE_INITIALISATION_RANGE_LOWER_BOUND_NAME
const QString	IMAGE_INITIALISATION_RANGE_UPPER_BOUND_NAME

Typedef Documentation

typedef std::vector<QColor> niftk::ColorListType

typedef QMap<QString, QVariant> niftk::IGIDataSourceProperties

typedef std::vector<LabelType> niftk::LabelsListType

typedef std::pair<int, std::string> niftk::LabelType

Basic label typedefs

typedef mitk::GenericProperty<itk::Matrix<float, 4, 4> > niftk::MatrixProperty

typedef itk::PolyLineParametricPath<3> niftk::ParametricPathType

typedef std::vector<ParametricPathType::Pointer> niftk::ParametricPathVectorType

typedef ParametricPathType::VertexListType niftk::ParametricPathVertexListType

typedef ParametricPathType::VertexType niftk::ParametricPathVertexType

typedef float niftk::real

isovalue alias

typedef signed char niftk::schar

signed char alias

typedef unsigned char niftk::uchar

unsigned char alias

typedef itk::RGBAPixel< unsigned char > niftk::UCRGBAPixelType

typedef itk::RGBPixel< unsigned char > niftk::UCRGBPixelType

Enumeration Type Documentation

enum niftk::DnDDisplayDropType

Describes the different modes that can be used when drag and dropping into the DnD Display window.

Enumerator
DNDDISPLAY_DROP_SINGLE
DNDDISPLAY_DROP_MULTIPLE	This means that multiple nodes are dropped into a single window.
DNDDISPLAY_DROP_ALL	This means that multiple nodes are dropped across multiple windows.

enum niftk::DnDDisplayInterpolationType

Describes what the interpolation type should be set to when an image is dropped.

Enumerator
DNDDISPLAY_NO_INTERPOLATION
DNDDISPLAY_LINEAR_INTERPOLATION
DNDDISPLAY_CUBIC_INTERPOLATION

enum niftk::ImageOrientation

Describes the different types of orientation, axial, sagittal, coronal, that can be achieved in the Drag&Drop Display windows. This is different from WindowOrientation. The orientation might be used to refer to the axis of an image, so an image can ONLY be sampled in AXIAL, SAGITTAL and CORONAL direction.

Enumerator
IMAGE_ORIENTATION_AXIAL
IMAGE_ORIENTATION_SAGITTAL
IMAGE_ORIENTATION_CORONAL
IMAGE_ORIENTATION_UNKNOWN

enum niftk::WindowLayout

Describes the different render window layouts. So one WindowLayout could have multiple windows of different orientations, but most often will contain either axial, coronal or sagittal. This is different to the WindowLayout as a layout can contain multiple orientations.

Enumerator
WINDOW_LAYOUT_AXIAL
WINDOW_LAYOUT_SAGITTAL
WINDOW_LAYOUT_CORONAL
WINDOW_LAYOUT_ORTHO
WINDOW_LAYOUT_3D
WINDOW_LAYOUT_3H
WINDOW_LAYOUT_3V
WINDOW_LAYOUT_AS_ACQUIRED
WINDOW_LAYOUT_UNKNOWN
WINDOW_LAYOUT_COR_SAG_H
WINDOW_LAYOUT_COR_SAG_V
WINDOW_LAYOUT_COR_AX_H
WINDOW_LAYOUT_COR_AX_V
WINDOW_LAYOUT_SAG_AX_H
WINDOW_LAYOUT_SAG_AX_V

enum niftk::WindowOrientation

Describes the different types of orientation, axial, sagittal, coronal, that can be achieved in the Drag&Drop Display windows. This is different from the WindowLayout. The orientation might be used to refer to the axis of an image, so an image can ONLY be sampled in AXIAL, SAGITTAL and CORONAL direction.

Enumerator
WINDOW_ORIENTATION_AXIAL
WINDOW_ORIENTATION_SAGITTAL
WINDOW_ORIENTATION_CORONAL
WINDOW_ORIENTATION_UNKNOWN

Function Documentation

NIFTKCOMMON_WINEXPORT std::string niftk::AddStringToImageFileSuffix	(	const std::string &	fileName,
		std::string	stringToAdd
	)

Add a string just before the image suffix of a file name including the .gz or .zip extension if present.

Parameters

fileName	The input image file name.
stringToAdd	The string to add just before the image suffix.

Returns

The image file name with the text added just before the image suffix.

NIFTKVTK_WINEXPORT void niftk::AddTwo3DPoints	(	const double *	a,
		const double *	b,
		double *	output
	)

Adds two 3D points, so a, b and output must be arrays of length 3.

int NIFTKCUDAKERNELS_WINEXPORT niftk::AddTwoIntegers	(	int	a,
		int	b
	)

Pointless minimal function, mainly just to test if anything at all could be run on a device.

NIFTKVTK_WINEXPORT double niftk::AngleBetweenTwoUnitVectors	(	const double *	a,
		const double *	b
	)

Calculates the angle in radians between two vectors a and b, which must be of length 3.

NIFTKVTK_WINEXPORT double niftk::AngleBetweenTwoUnitVectorsInDegrees	(	const double *	a,
		const double *	b
	)

Calculates the angle in degrees between two vectors a and b, which must be of length 3.

void niftk::AnotherConsumer

(

const mitk::StandaloneDataStorage::Pointer &

datastorage

)

NIFTKCORE_EXPORT void niftk::ApplyTransformToNode	(	const vtkMatrix4x4 &	transform,
		mitk::DataNode::Pointer &	node
	)

Applies (sets, i.e. copies) the given transform to the given node.

Parameters

In]	transform a VTK transformation
Out]	node a non-NULL data node, and as each node has a mitk::BaseGeometry in the mitk::BaseData, we can transform anything.

Exceptions

mitk::Exception

if node points to null object

NIFTKCORE_EXPORT bool niftk::AreDifferent	(	const mitk::Point3D &	a,
		const mitk::Point3D &	b
	)

Returns true if a and b are different (up to a given tolerance, currently 0.01), and false otherwise.

NIFTKCOMMON_WINEXPORT std::string niftk::Basename

(

const std::string &

pathName

)

Returns the basename.

void NIFTKOPENCV_EXPORT niftk::BuildTextureDescriptor	(	const boost::gil::gray8c_view_t	src,
		const boost::gil::gray8_view_t	dst
	)

This is some kind of corner detector. If the output image has a low/zero value for a given pixel then the same pixel coordinate in your input image will have little to no texture suitable for tracking/matching.

Exceptions

std::runtime_error

if src and dst dimensions are different

NIFTKPOINTREG_EXPORT cv::Matx33d niftk::CalculateCrossCovarianceH	(	const std::vector< cv::Point3d > &	q,
		const std::vector< cv::Point3d > &	qPrime
	)

Calculates 1/N Sum (q_i * qPrime_i^t) where q_i and qPrime_i are column vectors, so the product is a 3x3 matrix.

See also

Least-Squares Fitting of two, 3-D Point Sets, Arun, 1987, DOI=10.1109/TPAMI.1987.4767965, where this calculates matrix H.

NIFTKPOINTREG_EXPORT double niftk::CalculateFiducialRegistrationError	(	const std::vector< cv::Point3d > &	fixedPoints,
		const std::vector< cv::Point3d > &	movingPoints,
		const cv::Matx44d &	matrix
	)

Calculates Fiducial Registration Error by multiplying the movingPoints by the matrix, and comparing with fixedPoints.

NIFTKPOINTREG_EXPORT double niftk::CalculateFiducialRegistrationError	(	const mitk::PointSet::Pointer &	fixedPointSet,
		const mitk::PointSet::Pointer &	movingPointSet,
		vtkMatrix4x4 &	vtkMatrix
	)

Converts format of input to call the other CalculateFiducialRegistrationError method.

NIFTKCOMMON_WINEXPORT double niftk::CalculateStdDevFromFWHM

(

double

fwhm

)

For Gaussian blurring and similar.

NIFTKCORE_EXPORT double niftk::CalculateStepSize

(

double *

spacing

)

Given a double[3] of x,y,z voxel spacing, calculates a step size along a ray, as 1/3 of the smallest voxel dimension.

NIFTKVTK_WINEXPORT void niftk::CalculateUnitVector	(	const double *	a,
		const double *	b,
		double *	output
	)

Calculates a unit vector from (a-b), so a, b and output must be arrays of length 3.

NIFTKCOMMON_WINEXPORT double niftk::CalculateVarianceFromFWHM

(

double

fwhm

)

For Gaussian blurring and similar.

NIFTKCORE_EXPORT vtkLookupTable * niftk::ChangeColor	(	vtkLookupTable *	lut,
		int	value,
		const QColor &	newColor
	)

Replace the color in the LookupTable at the given index.

static void niftk::check_oglerror ( const std::string &  detailedmsg )

static

static bool niftk::CheckBorder ( const Match &  m, int  bx, int  by, int  w, int  h  )

static

NIFTKCORE_EXPORT bool niftk::CheckForNaNPoint

(

const mitk::PointSet::PointType &

point

)

Checks if the point contains a NaN value.

Returns

true if NaN

NIFTKVTK_WINEXPORT bool niftk::ClipPointToWithinBoundingBox	(	const double *	boundingBoxVector6,
		double *	point
	)

Makes sure that the supplied point is within the VTK bounding box, by independently clipping the x, y, z coordinate to be within range of the bounds. Returns true if point was clipped and false otherwise.

NIFTKCORE_EXPORT void niftk::ComposeTransformWithNode	(	const vtkMatrix4x4 &	transform,
		mitk::DataNode::Pointer &	node
	)

Composes (pre-multiplies) the given transform with the given node.

Parameters

In]	transform a VTK transformation
Out]	node a non-NULL data node, and as each node has a mitk::BaseGeometry in the mitk::BaseData, we can transform anything.

Exceptions

mitk::Exception

if node points to null object

NIFTKCORE_EXPORT mitk::Point3D niftk::ComputeCentroid

(

const mitk::PointSet &

input

)

Computes the mean/centroid of an mitk::PointSet.

NIFTKCORE_EXPORT void niftk::ComputeNormalFromPoints	(	const mitk::Point3D &	a,
		const mitk::Point3D &	b,
		const mitk::Point3D &	c,
		mitk::Point3D &	output
	)

Computes the normal by calculating cross product of (a-b) and (c-b).

NIFTKCOMMON_WINEXPORT std::string niftk::ConcatenatePath	(	const std::string &	path,
		const std::string &	name
	)

Concatenates name onto path, taking care of file separator, its just string concatenation, we don't check if the resulting value actually exists.

Parameters

path	a string representing the path
name	a string representing a file or directory to be appended.

void niftk::Consumer

(

const mitk::StandaloneDataStorage::Pointer &

datastorage

)

NIFTKCOMMON_WINEXPORT double niftk::ConvertFirstVoxelCoordinateToMiddleOfImageCoordinate	(	double	millimetreCoordinateOfFirstVoxel,
		int	numberOfVoxelsInThatAxis,
		double	voxelSpacingInThatAxis
	)

Converts first voxel origin to middle of image origin.

NIFTKCOMMON_WINEXPORT double niftk::ConvertMiddleOfImageCoordinateToFirstVoxelCoordinate	(	double	millimetreCoordinateOfMiddleVoxel,
		int	numberOfVoxelsInThatAxis,
		double	voxelSpacingInThatAxis
	)

Converts middle of image origin to first voxel origin.

void niftk::ConvertMITKContoursAndAppendToITKContours	(	mitk::ContourModelSet *	mitkContours,
		std::vector< ParametricPathType::Pointer > &	itkContours,
		const mitk::Vector3D &	spacingInWorldCoordinateOrder
	)

TODO Contours should not be empty. Currently, the draw tool can create empty contours. We skip them for now, but this should be fixed in the draw tool. The empty contours are probably created when points are deleted from the contour.

Contours must not be empty. (Contour sets can be empty but if they contain contours, none of them can.)

Find the axis of the running coordinate.

Only one coordinate can differ at this point, otherwise the representation is incorrect. The contour can turn only at voxel corners.

In debug builds we do not break here, so that the assertion above can fail if two adjacent points of the contour is not on a line along voxel boundaries.

A contour must not contain the same point twice, one directly after the other. (The start and end point of a contour can be the same for closed contours, but they must contain other points in between.)

If the MITK contour stores several subsequent points along the same line, we skip the intermediate points and keep only the first and last one.

TODO This should be a simple '!=' operator, but the draw tool does not save perfect corner coordinates now.

The next point was on the line of the same contour edge, so we discard the previous end point, the end of the edge is this new point.

The contour has turned, so there is no more point on the same line, no more intermediate point to skip.

TODO Contours should not contain the same point multiple times, subsequently. The draw tool currently creates such contours, so here we just silently skip the duplicated points.

We should not arrive here, otherwise the contour is incorrectly represented. Contours must be on a single slice, and they must go along the boundary of voxels. Only the start and end point can be equal.

void NIFTKMIDAS_EXPORT niftk::ConvertMITKContoursAndAppendToITKContours	(	mitk::ContourModelSet *	mitkContours,
		ParametricPathVectorType &	itkContours,
		const mitk::Vector3D &	spacing
	)

Converts MITK contours from to ITK contours and appends them to a list.

The input MITK contours should be in one of the following representations:

o-------+-------+-------o
|       |       |       |
|       |       |       |
|       |       |       |
o-------+-------+-------o

or

o-------o-------o-------o
|       |       |       |
|       |       |       |
|       |       |       |
o-------o-------o-------o

The function creates ITK contours in this representation:

o---o---+---o---+---o---o
|       |       |       |
o       |       |       o
|       |       |       |
o---o---+---o---+---o---o

and appends them to the ITK contour list.

The function needs to know the spacing of the original image. Note that the geometry of the MITK contours cannot be set to the same as that of the reference image or the segmentation image, otherwise the contours would be rendered to a wrong location in space. Therefore, the spacing has to be retrieved from either the MITK or ITK image and passed to this function.

Note that the spacing must be in world coordinate order, not in voxel coordinate order. That is, the elements of have to be the spacing along the sagittal, coronal then axial axis, in this order. ITK images and MITK geometries store the spacing in voxel coordinate order.

You can translate between the two coordinate systems with the utility functions in niftkImageOrientationUtils.h.

void NIFTKMIDAS_EXPORT niftk::ConvertMITKSeedsAndAppendToITKSeeds	(	const mitk::PointSet *	seeds,
		itk::PointSet< float, 3 > *	points
	)

This file contains functions that convert between ITK and MITK contour representations.

Contours can be represented in similar way in ITK and MITK, but for the purposes of the MIDAS segmentation tools we restrict the representation according to the following terms.

ITK filters expect a contour in which there is a point on the side of every pixel, but not necessarily in the corners.

E.g. a contour around three adjacent pixels can be stored like this:

(1)

+---o---+---o---+---o---+
|       |       |       |
o       |       |       o
|       |       |       |
+---o---+---o---+---o---+

Note that there are no 'corner points' in the contour. If we simply copied these points to an MITK contour, it would be rendered like this:

---

/ \ < >

\ /

That is, the adjacent contour points would be connected by a straight line, cutting off the corners. To get around this, we use a modified version of the contour extraction filter that keeps the corners, i.e. creates a contour of a segmentation like this:

(2)

o---o---+---o---+---o---o
|       |       |       |
o       |       |       o
|       |       |       |
o---o---+---o---+---o---o

Note that the corner points are stored only when the contour "turns", not at at every pixel corner. The intermediate points are still at the side of the pixels.

If we copy this to an MITK contour set as it is, it is rendered as a rectangle:

+-----------------------+
|                       |
|                       |
|                       |
+-----------------------+

However, the following MITK contour would render to the same rectangle:

(3)

o-------+-------+-------o
|       |       |       |
|       |       |       |
|       |       |       |
o-------+-------+-------o

Reducing the number of contour points can significantly speed up the rendering. Moreover, the MITK contours are often cloned because of the undo-redo operations, so it is good to minimise the number of contour points for memory efficiency as well.

Currently, the draw tool creates a contour that stores every contour point, like this:

(4)

o-------o-------o-------o
|       |       |       |
|       |       |       |
|       |       |       |
o-------o-------o-------o

There should be only two kinds of representations.

ITK contours should be in the form (2), i.e.:

a) The start point of any contour must be a corner point.
b) The end point of any contour must be a corner point.
c) The contour must contain a point at the middle of the side of every pixel along the contour path, and
d) one at each pixel corner where the direction of the contour path changes.
e) The contour must not contain any other corner point along the path.

MITK contours should be in the form (3), i.e.:

f) The start point of any contour must be a corner point.
g) The end point of any contour must be a corner point.
h) The contour must not contain any point on the side of a pixel.
i) The contour must contain a point at each pixel corner where the direction of the contour path changes.
j) The contour must not contain any other corner point along the path.

Moreover,

k) Any contour must contain at least two (different) points.

Converts Points from MITK to ITK.

NIFTKCOMMON_WINEXPORT bool niftk::ConvertToBool

(

const std::string &

x

)

NIFTKCOMMON_WINEXPORT double niftk::ConvertToDouble

(

const std::string &

x

)

NIFTKCOMMON_WINEXPORT std::string niftk::ConvertToFullNativePath

(

const std::string &

pathName

)

Converts pathName to a full string by calling the above method.

Parameters

pathName

a string representing the path

Returns

a string representing the path

fs::path niftk::ConvertToFullPath

(

const std::string &

pathName

)

NIFTKCOMMON_WINEXPORT int niftk::ConvertToInt

(

const std::string &

x

)

NIFTKCOMMON_WINEXPORT std::string niftk::ConvertToString

(

int

x

)

NIFTKCOMMON_WINEXPORT std::string niftk::ConvertToString

(

unsigned int

x

)

NIFTKCOMMON_WINEXPORT std::string niftk::ConvertToString

(

unsigned long long

x

)

NIFTKCOMMON_WINEXPORT std::string niftk::ConvertToString

(

long int

x

)

NIFTKCOMMON_WINEXPORT std::string niftk::ConvertToString

(

long unsigned int

x

)

NIFTKCOMMON_WINEXPORT std::string niftk::ConvertToString

(

double

x

)

NIFTKCOMMON_WINEXPORT std::string niftk::ConvertToString

(

bool

x

)

NIFTKCOMMON_WINEXPORT std::string niftk::ConvertToString

(

float

x

)

NIFTKVTK_WINEXPORT void niftk::CopyDoubleVector	(	int	n,
		const double *	a,
		double *	b
	)

Copies n doubles from a to b, which must be allocated, and at least of length n.

NIFTKCORE_EXPORT void niftk::CopyIntensityData	(	const mitk::Image *	input,
		mitk::Image *	output
	)

Assumes same size image, and same data type, and copies data from the input image to the output image.

Parameters

input	Input MITK image, not NULL.
output	Output MITK image, not NULL, same size as input.

NIFTKCORE_EXPORT int niftk::CopyPointSets	(	const mitk::PointSet &	input,
		mitk::PointSet &	output
	)

Copies input to output, i.e. the output is erased, and re-populated.

template<typename PropType >

static void niftk::CopyProp ( const mitk::DataNode::Pointer  source, mitk::Image::Pointer  target, const char *  name  )

static

NIFTKCORE_EXPORT void niftk::CopyValues	(	const mitk::Point3D &	a,
		mitk::Point3D &	b
	)

Copies a into b.

NIFTKCORE_EXPORT unsigned long int niftk::CountBetweenThreshold	(	const mitk::Image *	image,
		float	lower,
		float	upper
	)

Simply iterates through a whole image, counting how many intensity values are >= lower and <= upper.

Parameters

lower	A lower threshold for intensity values
upper	An upper threshold for intensity values

Returns

unsigned long int The number of voxels.

Parameters

image	An MITK Image.
lower	A lower threshold for intensity values
upper	An upper threshold for intensity values

Returns

unsigned long int The number of voxels.

NIFTKCOMMON_WINEXPORT bool niftk::CreateDirAndParents

(

const std::string &

directoryPath

)

Creates a directory including all parents that don't exist.

Parameters

the	directory name

Returns

true if creation was successfull

NIFTKCORE_EXPORT vtkLookupTable * niftk::CreateEmptyLookupTable	(	const QColor &	lowColor,
		const QColor &	highColor
	)

mitk::Image::Pointer NIFTKOPENCVIMAGECONVERSION_EXPORT niftk::CreateMitkImage

(

const IplImage *

image

)

Supports RGB, RGBA and grayscale images, currently 8-bit per channel only!. Known bug: does not take care of different channel layouts: BGR vs RGB!

mitk::Image::Pointer NIFTKOPENCVIMAGECONVERSION_EXPORT niftk::CreateMitkImage

(

const cv::Mat *

image

)

Same as above but takes cv:Mat

template<typename ITKPixelType >

static mitk::Image::Pointer niftk::CreateMitkImageInternal ( const IplImage *  image )

static

template<typename ITKPixelType >

static mitk::Image::Pointer niftk::CreateMitkImageInternal ( const IplImage *  image )

static

NIFTKCOMMON_WINEXPORT std::string niftk::CreateUniqueTempFileName	(	const std::string &	prefix,
		const std::string &	suffix = ""
	)

Creates a unique file name for a file located in the O/S temporary directory.

Parameters

prefix	file basename prefix
suffix	file basename suffix

Returns

a unique file name

NIFTKVTK_WINEXPORT bool niftk::CropPointsFromPolyData	(	vtkPolyData *	PolyData,
		int	Points
	)

Randomly removes points from the passed polydata until the passed number of points Any cells or surfaces will be deleted as part of the process, leaving only points.

NIFTKCORE_EXPORT void niftk::CrossProduct	(	const mitk::Point3D &	a,
		const mitk::Point3D &	b,
		mitk::Point3D &	c
	)

Computes c = a x b, and will normalise a and b to unit length first.

NIFTKVTK_WINEXPORT void niftk::CrossProductTwo3DVectors	(	const double *	a,
		const double *	b,
		double *	output
	)

Takes the cross product of 2 vectors, so a, b and output must be arrays of length 3.

static bool niftk::CUDADelayLoadCheck ( )

static

static bool niftk::CUDADelayLoadCheck ( )

static

NIFTKCOMMON_WINEXPORT bool niftk::DirectoryExists

(

const std::string &

directoryPath

)

Returns

True if directory exists, and false otherwise.

NIFTKVTK_WINEXPORT bool niftk::DistancesToColorMap	(	vtkPolyData *	source,
		vtkPolyData *	target
	)

Measures the euclidean distances between the points in two polydata, and sets the.

scalars in both polydata to a color map to show the differences, min distance red, max distance is blue. Mid distance is green

Parameters

source,target

the two polydata, they need the same number of points

Returns

true if Ok, false if error

NIFTKVTK_WINEXPORT double niftk::DistanceToSurface	(	double	point[3],
		vtkPolyData *	target
	)

Returns the euclidean distance (in 3D) between a point and the closest point on a polydata mesh.

Parameters

point	the point
target	and the polydata

Returns

the euclidean distance

NIFTKVTK_WINEXPORT double niftk::DistanceToSurface	(	double	point[3],
		vtkCellLocator *	targetLocator,
		vtkGenericCell *	cell = NULL
	)

Returns the euclidean distance (in 3D) between a point and the closest point on a polydata mesh.

Parameters

point	the point
targetLocator	a vtkCellLocator, built from the polydata
cell	and optionally a vtkGenericCell

Returns

the euclidean distance

NIFTKVTK_WINEXPORT void niftk::DistanceToSurface	(	vtkPolyData *	source,
		vtkPolyData *	target,
		vtkSmartPointer< vtkDoubleArray > &	result
	)

Calculates the euclidean distance (in 3D) between each point in the source polydata and the closest point on the target polydata mesh. The result distances are stored in the scalar values passed in.

Parameters

source,target

the source and target polydata.

NIFTKVTK_WINEXPORT void niftk::DistanceToSurface	(	vtkPolyData *	source,
		vtkPolyData *	target
	)

Calculates the euclidean distance (in 3D) between each point in the source polydata and the closest point on the target polydata mesh. The result are stored the distances in the scalar values of the source.

Parameters

source,target

the source and target polydata.

NIFTKPOINTREG_EXPORT double niftk::DoSVDPointBasedRegistration	(	const std::vector< cv::Point3d > &	fixedPoints,
		const std::vector< cv::Point3d > &	movingPoints,
		cv::Matx33d &	H,
		cv::Point3d &	p,
		cv::Point3d &	pPrime,
		cv::Matx44d &	outputMatrix
	)

Does the main SVD bit of the point based registration, and handles the degenerate conditions mentioned in Aruns paper.

NIFTKCORE_EXPORT void niftk::DumpImage	(	const mitk::Image *	image,
		const std::string &	fileName
	)

Writes the image to file.

void NIFTKCUDA_EXPORT niftk::EdgeDetectionExampleLauncher	(	mitk::DataStorage *	dataStorage,
		mitk::DataNode *	node,
		const mitk::BaseRenderer *	renderer
	)

Runs edge detection on an MITK DataNode containing a niftk::CUDAImage.

See also

niftk::RunEdgeDetectionKernel

static bool niftk::EqualsWithTolerance ( const mitk::Vector2D &  cursorPosition1, const mitk::Vector2D &  cursorPosition2, double  tolerance = 0.01  )

static

static bool niftk::EqualsWithTolerance1 ( const mitk::Point3D &  worldPosition1, const mitk::Point3D &  worldPosition2, double  tolerance = 0.001  )

static

NIFTKCOMMON_WINEXPORT std::string niftk::ExtractImageFileSuffix

(

const std::string &

fileName

)

Extract common image suffixes from a file name including the .gz or .zip extension if present.

Parameters

fileName

The input image file name.

Returns

The image file extension, including the dot and .gz or .zip extension.

NIFTKCOMMON_WINEXPORT std::string niftk::ExtractImageFileSuffix	(	const std::string &	fileName,
		std::string &	fileNameWithoutSuffix
	)

Extract common image suffixes from a file name including the .gz or .zip extension if present.

Parameters

fileName	The input image file name.
fileNameWithoutSuffix	Output image file name without the suffix.

Returns

The image file extension, including the dot and .gz or .zip extension.

NIFTKCOMMON_WINEXPORT bool niftk::FileDelete

(

const std::string &

fileName

)

Returns

Delete a file and return true if successfull, false otherwise.

NIFTKCOMMON_WINEXPORT bool niftk::FileExists

(

const std::string &

fileName

)

Returns

True if file exists, and false otherwise.

NIFTKCOMMON_WINEXPORT bool niftk::FileIsEmpty

(

const std::string &

fileName

)

Returns

True if file has size of zero, and false otherwise.

NIFTKCOMMON_WINEXPORT bool niftk::FilenameHasPrefixAndExtension	(	const std::string &	filename,
		const std::string &	prefix,
		const std::string &	extension
	)

This method is used to find the plugin config files. So you look for stuff with a given prefix (usually blank) and the correct filename extension. ie. *.plg

Parameters

a	filename
normally	blank
extension	for example ".plg"

Returns

true for a match and false otherwise

NIFTKCOMMON_WINEXPORT bool niftk::FilenameMatches	(	const std::string &	filename,
		const std::string &	prefix,
		const std::string &	middle,
		const std::string &	extension
	)

Then this is used to find a library, as it must specifically have a prefix, then the library name, and also the correct extension.

Parameters

filename	a filename
prefix	for example "lib" on unix and nothing on windows
middle	for example "niftkonlinehelp" as specified in plugin config file
extension	for example .so on Unix and .dll on Windows.

Returns

true for a match and false otherwise

NIFTKCOMMON_WINEXPORT int niftk::FileSize

(

const std::string &

fileName

)

Returns

the file size in bytes.

NIFTKCORE_EXPORT void niftk::FillImage	(	mitk::Image *	image,
		float	value
	)

Simply iterates through a whole image, filling it with the specified value which is cast to the appropriate pixel type.

Parameters

image	A non NULL MITK image.
value	A single scalar value that will be cast.

NIFTKCORE_EXPORT int niftk::FilterMatchingPoints	(	const mitk::PointSet &	fixedPointsIn,
		const mitk::PointSet &	movingPointsIn,
		mitk::PointSet &	fixedPointsOut,
		mitk::PointSet &	movingPointsOut
	)

Takes fixed and moving points, and scans for matching ID's and returns 2 point sets with ordered and corresponding points.

Returns

the number of points in the output

NIFTKCORE_EXPORT mitk::DataStorage::SetOfObjects::Pointer niftk::FindDerivedImages	(	const mitk::DataStorage *	storage,
		const mitk::DataNode::Pointer	node,
		bool	lookForBinary
	)

NIFTKCORE_EXPORT mitk::DataStorage::SetOfObjects::Pointer niftk::FindDerivedVisibleNonHelperChildren	(	const mitk::DataStorage *	storage,
		const mitk::DataNode::Pointer	node
	)

NIFTKCOMMON_WINEXPORT std::vector< std::string > niftk::FindFilesWithGivenExtension	(	const std::string &	fullDirectoryName,
		const std::string &	extension
	)

Non-recursively searches a directory, looking for files with the specified extension.

Parameters

fullDirectoryName	Directory name
extension	file extension including the dot.

NIFTKCORE_EXPORT mitk::DataNode::Pointer niftk::FindFirstBinaryImage

(

const std::vector< mitk::DataNode * > &

nodes

)

NIFTKCORE_EXPORT mitk::DataNode::Pointer niftk::FindFirstGreyScaleImage

(

const std::vector< mitk::DataNode * > &

nodes

)

NIFTKCORE_EXPORT mitk::DataNode::Pointer niftk::FindFirstParent	(	const mitk::DataStorage *	storage,
		const mitk::DataNode::Pointer	node
	)

NIFTKCORE_EXPORT mitk::DataNode::Pointer niftk::FindFirstParentImage	(	const mitk::DataStorage *	storage,
		const mitk::DataNode::Pointer	node,
		bool	lookForBinary
	)

NIFTKCORE_EXPORT double niftk::FindLargestDistanceBetweenTwoPoints

(

const mitk::PointSet &

input

)

Computes the largest Euclidean Distance between any two points.

NIFTKCOMMON_WINEXPORT std::pair< double, double > niftk::FindMinimumValues	(	std::vector< std::pair< double, double > >	inputValues,
		std::pair< unsigned int, unsigned int > *	indexes
	)

Takes a vector of pairs and finds the minimum value in each dimension. Returns the minimum values. Optionally returns the indexes of the minium values.

NIFTKCORE_EXPORT mitk::DataNode::Pointer niftk::FindNthBinaryImage	(	const std::vector< mitk::DataNode * > &	nodes,
		int	n
	)

NIFTKCORE_EXPORT mitk::DataNode::Pointer niftk::FindNthGreyScaleImage	(	const std::vector< mitk::DataNode * > &	nodes,
		int	n
	)

NIFTKCORE_EXPORT mitk::DataNode::Pointer niftk::FindNthImage	(	const std::vector< mitk::DataNode * > &	nodes,
		int	n,
		bool	lookForBinary
	)

NIFTKCORE_EXPORT mitk::DataNode::Pointer niftk::FindParentGreyScaleImage	(	const mitk::DataStorage *	storage,
		const mitk::DataNode::Pointer	node
	)

NIFTKCOMMON_WINEXPORT std::vector< std::string > niftk::FindVideoData

(

const std::string &

directory

)

Recursively searches a directory looking for video files

Parameters

fullDirectoryName

Returns

vector of matching files

NIFTKCOMMON_WINEXPORT std::string niftk::FindVideoFile	(	const std::string &	directory,
		const std::string &	mask = ""
	)

Recursively searches a directory looking for video files

Parameters

fullDirectoryName
optional	mask

Returns

either the first one or the one that matches the optional input name mask

NIFTKCOMMON_WINEXPORT double niftk::fixRangeTo1

(

double

d

)

void NIFTKCUDA_EXPORT niftk::FlipImageLauncher	(	const WriteAccessor &	src,
		WriteAccessor &	dest,
		cudaStream_t	stream
	)

Flips the image upside down. This implementation is likely not very efficient.

Exceptions

std::runtime_error

TODO: Should not use WriteAccessor, cudaStream in API. Should throw mitk::Exception.

void NIFTKCUDA_EXPORT niftk::FlipImageLauncher	(	const ReadAccessor &	src,
		WriteAccessor &	dest,
		cudaStream_t	stream
	)

Flips the image upside down. This implementation is likely not very efficient.

Exceptions

std::runtime_error

TODO: Should not use ReadAccessor, WriteAccessor, cudaStream in API. Should throw mitk::Exception.

void NIFTKMIDAS_EXPORT niftk::GenerateOutlineFromBinaryImage	(	mitk::Image::Pointer	image,
		int	sliceAxis,
		int	sliceIndex,
		int	projectedSliceNumber,
		mitk::ContourModelSet *	outputContourSet
	)

Used to generate a contour outline round a binary segmentation image, and refreshes the outputSurface.

Called for generating the "See Prior", "See Next" and also the outline contour of the current segmentation.

NIFTKCORE_EXPORT ImageOrientation niftk::GetAsAcquiredOrientation	(	ImageOrientation	defaultOrientation,
		const mitk::Image *	image
	)

Returns the ImageOrientation corresponding to the XY plane, or else returns the supplied default.

Parameters

defaultOrientation	A default ImageOrientation that will be returned if we can't work out the As Acquired orientation.
image	An image to check.

Returns

ImageOrientation the As Acquired orientation, or the defaultOrientation.

template<typename TPixel , unsigned int VImageDimension>

NIFTKCORE_EXPORT void niftk::GetAxesInWorldCoordinateOrder	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		int	axes[3]
	)

Converts between voxel coordinate order and world coordinate order. The function writes the axes of the sagittal, coronal and axial dimensions to axes, in this order:

axes[0]: axis of sagittal dimension axes[1]: axis of coronal dimension axes[2]: axis of axial dimension

NIFTKCORE_EXPORT void niftk::GetAxesInWorldCoordinateOrder	(	const mitk::Image *	mitkImage,
		int	axes[3]
	)

Converts between voxel coordinate order and world coordinate order. The function writes the axes of the sagittal, coronal and axial dimensions to axes, in this order:

axes[0]: axis of sagittal dimension axes[1]: axis of coronal dimension axes[2]: axis of axial dimension

NIFTKVTK_WINEXPORT double niftk::GetBoundingBoxDiagonalLength

(

const double *

boundingBoxVector6

)

Calculates the bounding box diagonal length.

NIFTKCORE_EXPORT void niftk::GetCurrentTransformFromNode	(	const mitk::DataNode::Pointer &	node,
		vtkMatrix4x4 &	outputMatrix
	)

Retrieves the current tranform from the mitk::Geometry object of an mitk::DataNode.

Parameters

In]	node a non-NULL mitk::DataNode
Out]	outputMatrix a matrix that is updated

Exceptions

mitk::Exception

if node points to null object

NIFTKCORE_EXPORT void niftk::GetDifference	(	const mitk::Point3D &	a,
		const mitk::Point3D &	b,
		mitk::Point3D &	output
	)

Returns as output the vector difference of a-b.

NIFTKCOMMON_WINEXPORT std::vector< std::string > niftk::GetDirectoriesInDirectory

(

const std::string &

fullDirectoryName

)

Returns all directories in a given directory, or empty list if none found.

Parameters

fullDirectoryName

Directory name

Exceptions

logic_error

if directory name is invalid

Returns

a list of directories within that folder.

NIFTKCOMMON_WINEXPORT std::string niftk::GetEnvVar

(

const std::string &

variableName

)

NIFTKVTK_WINEXPORT double niftk::GetEuclideanDistanceBetweenTwo3DPoints	(	const double *	a,
		const double *	b
	)

Returns the Euclidean distance between two 3D points, so a and b must be arrays of length 3.

template<typename TPixel , unsigned int VImageDimension>

NIFTKCORE_EXPORT void niftk::GetExtentsInMmInWorldCoordinateOrder	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		mitk::Vector3D &	extentsInMm
	)

Gets the extents of the image in millimetres in world coordinate order.

extentsInMm[0]: extent of sagittal dimension in millimetres extentsInMm[1]: extent of coronal dimension in millimetres extentsInMm[2]: extent of axial dimension in millimetres

NIFTKCORE_EXPORT void niftk::GetExtentsInMmInWorldCoordinateOrder	(	const mitk::Image *	mitkImage,
		mitk::Vector3D &	extentsInMm
	)

Gets the extents of the image in millimetres in world coordinate order.

extentsInMm[0]: extent of sagittal dimension in millimetres extentsInMm[1]: extent of coronal dimension in millimetres extentsInMm[2]: extent of axial dimension in millimetres

template<typename TPixel , unsigned int VImageDimension>

NIFTKCORE_EXPORT void niftk::GetExtentsInVxInWorldCoordinateOrder	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		mitk::Vector3D &	extentsInVx
	)

Gets the extents (number of voxels) of the image in world coordinate order.

extentsInVx[0]: extent of sagittal dimension extentsInVx[1]: extent of coronal dimension extentsInVx[2]: extent of axial dimension

NIFTKCORE_EXPORT void niftk::GetExtentsInVxInWorldCoordinateOrder	(	const mitk::Image *	mitkImage,
		mitk::Vector3D &	extentsInVx
	)

Gets the extents (number of voxels) of the image in world coordinate order.

extentsInVx[0]: extent of sagittal dimension as number of voxels extentsInVx[1]: extent of coronal dimension as number of voxels extentsInVx[2]: extent of axial dimension as number of voxels

std::string niftk::GetFilenameStem

(

const std::string &

fileName

)

NIFTKCOMMON_WINEXPORT std::string niftk::GetFileSeparator

(

)

Converts pathName to a boost::filesystem::path. We throw std::logic_error if you pass an empty pathName.

Parameters

pathName

a string representing the path

Returns

boost path type

Returns the file separator.

Returns

a / or a \ depending on OS

NIFTKCOMMON_WINEXPORT std::vector< std::string > niftk::GetFilesInDirectory

(

const std::string &

fullDirectoryName

)

Returns all files in a given directory, or empty list if none found.

Parameters

fullDirectoryName

Directory name

Exceptions

logic_error

if directory name is invalid

Returns

a list of files within that folder.

NIFTKCOMMON_WINEXPORT std::string niftk::GetHomeDirectory

(

)

NIFTKCOMMON_WINEXPORT std::string niftk::GetImagesDirectory

(

)

Helper method to get the image directory, as it works off an environment variable.

Returns

NIFTK_HOME/images

NIFTKCORE_EXPORT itk::Orientation niftk::GetItkOrientation

(

ImageOrientation

orientation

)

Converts an MITK orientation enum to an ITK orientation enum, and ideally these types should be merged.

NIFTKCOMMON_WINEXPORT std::string niftk::GetLastNCharacters	(	std::string	s,
		int	n
	)

Returns the last n characters from s.

NIFTKVTK_WINEXPORT double niftk::GetLength

(

const double *

a

)

Returns the length of a 3D vector, so a must be an array of length 3.

NIFTKCORE_EXPORT mitk::Point3D niftk::GetMiddlePointInVoxels

(

const mitk::Image *

image

)

Returns the middle voxel of an image.

Parameters

image

An MITK image.

Returns

If the image has odd numbers of voxels in an axis, the returned voxel is the middle one, whereas if the image has even number of voxels in an axis, the returned voxel is (int)(number vox - 1)/2.0

NIFTKCORE_EXPORT ImageOrientation niftk::GetMitkOrientation

(

itk::Orientation

orientation

)

Converts an ITK orientation enum to an MITK orientation enum, and ideally these types should be merged.

NIFTKCOMMON_WINEXPORT std::string niftk::GetNifTKHome

(

)

NIFTKCORE_EXPORT unsigned long int niftk::GetNumberOfVoxels

(

const mitk::Image *

image

)

Returns the number of voxels in an image.

Parameters

image

An MITK Image.

Returns

unsigned long int The number of voxels.

NIFTKCORE_EXPORT std::string niftk::GetOrientationName

(

ImageOrientation

orientation

)

Returns the name of the given orientation.

Returns

the name of the orientation that can be "axial", "sagittal", "coronal" or "unknown".

NIFTKCORE_EXPORT std::string niftk::GetOrientationString

(

const mitk::Image *

image

)

Returns the Orientation String (RPI, RAS etc).

Parameters

image

An MITK image, not NULL.

NOTE: MIDAS Analyze are flipped in the MITK GUI. This means if you use the default ITK reader which is used for example in the command line app niftkImageInfo, you will get a different answer to this method, as this method will be run from within the MITK GUI, and hence will be using itkDRCAnalyzeImageIO.

NIFTKIGIDATASOURCES_EXPORT void niftk::GetPlaybackIndex	(	const QString &	directory,
		const QString &	fileExtension,
		QMap< QString, std::set< niftk::IGIDataType::IGITimeType > > &	bufferToTimeStamp,
		QMap< QString, QHash< niftk::IGIDataType::IGITimeType, QStringList > > &	bufferToTimeStampToFileNames
	)

Returns the list of timestamps, by source name.

NIFTKCORE_EXPORT mitk::TimeGeometry::Pointer niftk::GetPreferredGeometry	(	const mitk::DataStorage *	dataStorage,
		const std::vector< mitk::DataNode * > &	nodes,
		const int &	nodeIndex = -1
	)

GetPreferedGeometry will return the geometry to use by picking one from the list of nodes, or NULL, if none can be found.

Parameters

nodes	A vector of mitk::DataNode pointers where we assume each node has a Geometry (which should always be the case).
nodeIndex	if we specify a node number/index that is a valid node in the vector nodes we just short-cut the search and pick that one.

Returns

mitk::TimeGeometry::Pointer A pointer to the chosen TimeGeometry or NULL if we didn't find one.

The algorithm is:

If nodeIndex < 0,
  use the first Image geometry in the list, or failing that, the first available geometry.
else if nodeIndex is a valid node index
  pick that geometry regardless of what it belongs to
else (user specified a useless index)
  pick the first available geometry.

If the node we found was not a grey-scale image
 Try to find a parent grey-scale image, and if successful return that geometry.

NIFTKIGIDATASOURCES_EXPORT QString niftk::GetPreferredSlash

(

)

Returns the platform specific directory separator.

NIFTKCOMMON_WINEXPORT void niftk::GetRecursiveFilesInDirectory	(	const std::string &	fullDirectoryName,
		std::vector< std::string > &	fileNames
	)

Returns all files in a given directory and recursively in all sub-directories, or empty list if none found.

Parameters

fullDirectoryName	Directory name
fileNames	The list of files found

Exceptions

logic_error

if directory name is invalid

NIFTKCORE_EXPORT double niftk::GetRMSErrorBetweenPoints	(	const mitk::PointSet &	fixed,
		const mitk::PointSet &	moving,
		const CoordinateAxesData *const	transform = NULL
	)

Gets the RMS error between fixed point set and a moving point set, with optional transform specified.

Iterates through the moving point set, and if the corresponding point exists in the fixed point set, will compute the squared distance error, and accumulate this into the RMS error.

template<typename TPixel , unsigned int VImageDimension>

NIFTKCORE_EXPORT void niftk::GetSpacingInWorldCoordinateOrder	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		mitk::Vector3D &	spacing
	)

Gets the spacing of the image in world coordinate order.

spacing[0]: spacing along sagittal dimension spacing[1]: spacing along coronal dimension spacing[2]: spacing axial dimension

NIFTKCORE_EXPORT void niftk::GetSpacingInWorldCoordinateOrder	(	const mitk::Image *	mitkImage,
		mitk::Vector3D &	spacing
	)

Gets the spacing of the image in world coordinate order.

spacing[0]: spacing along sagittal dimension spacing[1]: spacing along coronal dimension spacing[2]: spacing axial dimension

NIFTKCORE_EXPORT double niftk::GetSquaredDistanceBetweenPoints	(	const mitk::Point3D &	a,
		const mitk::Point3D &	b
	)

Returns the squared Euclidean distance between a and b.

NIFTKCORE_EXPORT int niftk::GetThroughPlaneAxis	(	const mitk::Image *	image,
		ImageOrientation	orientation
	)

Returns either -1 (unknown), or [0,1,2] for the x, y, or z axis corresponding to the through plane direction for the specified orientation.

Parameters

image	An MITK image, not NULL.
orientation	an ImageOrientation corresponding to Axial, Coronal or Sagittal.

Returns

-1=unknown, or the axis number [0,1,2].

NIFTKCORE_EXPORT int niftk::GetUpDirection	(	const mitk::BaseGeometry *	geometry,
		itk::Orientation	orientation
	)

Returns either +1, or -1 to indicate in which direction you should change the slice number to go "up".

Parameters

geometry	An MITK geometry, not NULL.
orientation	an ImageOrientation corresponding to Axial, Coronal or Sagittal.

Returns

-1 or +1 telling you to either increase of decrease the slice number or 0 for "unknown".

So, the MIDAS spec is: Shortcut key A=Up, Z=Down which means:

Axial: A=Superior, Z=Inferior
Coronal: A=Anterior, Z=Posterior
Sagittal: A=Right, Z=Left

NIFTKCORE_EXPORT int niftk::GetUpDirection	(	const mitk::Image *	image,
		ImageOrientation	orientation
	)

See GetUpDirection as in effect, we are only using the direction cosines from the geometry.

NIFTKCORE_EXPORT double niftk::GetVolume

(

const mitk::Image *

image

)

Returns the volume of non-zero voxels in an image.

Parameters

image

An MITK image.

Returns

double The volume in millimetres cubed.

WindowLayout niftk::GetWindowLayout ( const std::string &  windowLayoutName )

inline

NIFTKCOMMON_WINEXPORT std::string niftk::GetWorkingDirectory

(

)

NIFTKCORE_EXPORT mitk::Vector3D niftk::GetXYAspectRatio

(

const mitk::Image::Pointer

image

)

Utility method to calculate the aspect ratio.

Retrieves the image scaling, and if X dimension has largest voxels e.g. 2.1mm compared with Y having 1.1mm, will calculate the aspect ratio for X, so that you can rescale the number of pixels in the X direction and leave Y un-altered. And vice-versa for Y.

eg. given X = 2.2mm, Y = 1.1mm, will return mitk::Vector3D with vector[0]=2 and vector[1] = 1;

i.e. the x axis is twice as big as the y axis.

static void niftk::HandleCUDAError ( cudaError_t  err, const char *  file, int  line  )

static

Static method (only available to same T.U.) to print error.

NIFTKCORE_EXPORT bool niftk::ImagesHaveEqualIntensities	(	const mitk::Image *	image1,
		const mitk::Image *	image2
	)

Utility method that compares if images have the same intensity values.

Parameters

image1	an MITK image
image2	an MITK image

Returns

true if images have the same intensity values, and false otherwise.

NIFTKCORE_EXPORT bool niftk::ImagesHaveSameSpatialExtent	(	const mitk::Image *	image1,
		const mitk::Image *	image2
	)

Utility method that compares if images have the same spatial extent.

Parameters

image1	an MITK image.
image2	an MITK image.

Returns

true if images have the same spatial extent, and false otherwise.

NIFTKVTK_WINEXPORT void niftk::InterpolateRotation	(	const double *	beforeRotation,
		const double *	afterRotation,
		const double &	weight,
		double *	outputRotation,
		bool	adjustSign
	)

Performs spherical linear interpolation.

Parameters

beforeRotation	quaternion as 4-vector, already allocated.
afterRotation	quaternion as 4-vector, already allocated.
outputRotation	quaternion as 4-vector, already allocated.
weight	between 0 and 1.

NIFTKVTK_WINEXPORT void niftk::InterpolateTransformationMatrix	(	const vtkMatrix4x4 &	before,
		const vtkMatrix4x4 &	after,
		const double &	proportion,
		vtkMatrix4x4 &	interpolated
	)

Interpolates between two matrices.

Parameters

proportion

is defined as between [0 and 1], where 0 gives exactly the before matrix, 1 gives exactly the after matrix, and the proportion is a linear proportion between them to interpolate.

NIFTKCOMMON_WINEXPORT bool niftk::IsCloseToZero	(	const double &	value,
		const double &	tolerance
	)

Returns true if fabs(value) is less than a small tolerance, which defaults to 0.000001.

NIFTKCORE_EXPORT bool niftk::IsImage

(

const mitk::DataNode *

node

)

Simply returns true if a node contains an image, and false otherwise.

Parameters

node	An MITK DataNode.

Returns

true if node contains an mitk::Image and false otherwise

bool niftk::IsMultiWindowLayout ( WindowLayout  layout )

inline

Returns true if the layout contains multiple windows, otherwise false.

NIFTKCORE_EXPORT bool niftk::IsNodeABinaryImage

(

const mitk::DataNode::Pointer

node

)

NIFTKCORE_EXPORT bool niftk::IsNodeAGreyScaleImage

(

const mitk::DataNode::Pointer

node

)

NIFTKCORE_EXPORT bool niftk::IsNodeAHelperObject

(

const mitk::DataNode *

node

)

bool niftk::IsSingleWindowLayout ( WindowLayout  layout )

inline

Returns true if the layout contains only one window, otherwise false.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKAddNewSeedsToPointSet	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		const typename itk::Image< TPixel, VImageDimension >::RegionType &	regionOfInterest,
		int	sliceAxis,
		mitk::PointSet *	outputNewSeeds
	)

For the given input itkImage (assumed to always be binary), and regionOfInterest, will iterate on a slice by slice basis, recalculating new seeds.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKCalculateSliceRegion	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		int	sliceAxis,
		int	sliceIndex,
		typename itk::Image< TPixel, VImageDimension >::RegionType &	outputRegion
	)

Calculates the region corresponding to a single slice.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKCalculateSliceRegionAsVector	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		int	sliceAxis,
		int	sliceIndex,
		std::vector< int > &	outputRegion
	)

Calculates the region corresponding to a single slice.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKClearImage

(

itk::Image< TPixel, VImageDimension > *

itkImage

)

Clears an image by setting all voxels to zero using ITKFillRegion.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKClearSlice	(	itk::Image< TPixel, VImageDimension > *	itkImage,
		int	sliceAxis,
		int	sliceIndex
	)

Clears a slice by setting all voxels to zero for a given slice and axis.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKCopyImage	(	const itk::Image< TPixel, VImageDimension > *	input,
		itk::Image< TPixel, VImageDimension > *	output
	)

Copies an image from input to output, assuming input and output already allocated and of the same size.

template<typename TPixel1 , unsigned int VImageDimension1, typename TPixel2 , unsigned int VImageDimension2>

void niftk::ITKCopyIntensityData	(	const itk::Image< TPixel1, VImageDimension1 > *	itkImage1,
		itk::Image< TPixel2, VImageDimension2 > *	itkImage2
	)

ITK function to copy image data, performing C-style casting between data types.

Parameters

itkImage1	An ITK image.
itkImage2	An ITK image.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKCopyRegion	(	const itk::Image< TPixel, VImageDimension > *	input,
		int	sliceAxis,
		int	sliceIndex,
		itk::Image< TPixel, VImageDimension > *	output
	)

Copies the region from input to output, assuming both images are the same size, and contain the region.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKCountBetweenThreshold	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		const float &	lower,
		const float &	upper,
		unsigned long int &	outputCount
	)

See also

CountBetweenThreshold

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKDestroyPipeline

(

const itk::Image< TPixel, VImageDimension > *

itkImage

)

Completely removes the current 2D region growing pipeline that is stored in the map m_TypeToPipelineMap.

Parameters

itkImage

pass in the reference image (grey scale image being segmented), just as a dummy parameter, as it is called via the MITK ImageAccess macros.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKDoWipe	(	itk::Image< TPixel, VImageDimension > *	itkImage,
		mitk::PointSet *	currentSeeds,
		OpWipe *	op
	)

Does the wipe command for Wipe, Wipe+, Wipe-.

Most of the logic is contained within the OpWipe command and the processing is done with itk::MIDASImageUpdateClearRegionProcessor which basically fills a given region (contained on OpWipe) with zero. The seed processing is done elsewhere.

See also

DoWipe.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKDumpImage	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		const std::string &	filename
	)

Writes the image to file.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKFillImage	(	itk::Image< TPixel, VImageDimension > *	itkImage,
		float &	value
	)

See also

FillImage

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKFillRegion	(	itk::Image< TPixel, VImageDimension > *	itkImage,
		const typename itk::Image< TPixel, VImageDimension >::RegionType &	region,
		TPixel	fillValue
	)

Fills the itkImage region with the fillValue.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKFilterContours	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		const mitk::Image *	workingImage,
		const mitk::PointSet *	seeds,
		mitk::ContourModelSet *	segmentationContours,
		mitk::ContourModelSet *	drawContours,
		mitk::ContourModelSet *	polyContours,
		int	sliceAxis,
		int	sliceIndex,
		double	lowerThreshold,
		double	upperThreshold,
		bool	isThresholding,
		mitk::ContourModelSet *	outputCopyOfInputContours,
		mitk::ContourModelSet *	outputContours
	)

Extracts a new contour set, for doing "Clean" operation.

This method creates a local GeneralSegmentorPipeline pipeline for region growing, and does a standard region growing, then for each point on each contour on the input contour sets will filter the contours to only retain contours that are touching (i.e. on the boundary of) the region growing image.

Parameters

isThreshold

if true, we use the lowerThreshold and upperThreshold, whereas if false, we use the min and maximum limit of the pixel data type of the itkImage.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKFilterInputPointSetToExcludeRegionOfInterest	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		const typename itk::Image< TPixel, VImageDimension >::RegionType &	regionOfInterest,
		const mitk::PointSet *	inputSeeds,
		mitk::PointSet *	outputCopyOfInputSeeds,
		mitk::PointSet *	outputNewSeedsNotInRegionOfInterest
	)

Takes the inputSeeds and copies them to outputCopyOfInputSeeds, and also copies seeds to outputNewSeedsNotInRegionOfInterest if the seed is not within the region of interest.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKFilterSeedsToCurrentSlice	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		const mitk::PointSet *	inputSeeds,
		int	sliceAxis,
		int	sliceIndex,
		mitk::PointSet *	outputSeeds
	)

Takes the inputSeeds and filters them so that outputSeeds contains just those seeds contained within the current slice.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKGenerateOutlineFromBinaryImage	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		int	sliceAxis,
		int	sliceIndex,
		int	projectedSliceIndex,
		mitk::ContourModelSet *	contourSet
	)

Called to extract a contour set from a binary image, as might be used for "See Prior", "See Next", or the outlining a binary segmentation.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKGetAsAcquiredOrientation	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		ImageOrientation &	outputOrientation
	)

ITK method that given an image, returns the ImageOrientation for the XY plane.

Parameters

itkImage	an ITK image
outputOrientation	the output ImageOrientation as either IMAGE_ORIENTATION_AXIAL, IMAGE_ORIENTATION_CORONAL or IMAGE_ORIENTATION_SAGITTAL, or else is unchanged from the input.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKGetLargestMinimumDistanceSeedLocation	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		TPixel	foregroundPixelValue,
		typename itk::Image< TPixel, VImageDimension >::IndexType &	outputSeedIndex,
		int &	outputDistance
	)

Works out the largest minimum distance to the edge of the image data, filtered on a given foregroundPixelValue.

For each foreground voxel, search along the +/- x,y, (z if 3D) direction to find the minimum distance to the edge. Returns the largest minimum distance over the whole of the foreground region.

template<typename TPixel , unsigned int VImageDimension>

bool niftk::ITKImageHasNonZeroEdgePixels

(

const itk::Image< TPixel, VImageDimension > *

itkImage

)

Returns true if the image has non-zero edge pixels, and false otherwise.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKImagesHaveEqualIntensities	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		const mitk::Image *	image2,
		bool &	output
	)

See also

ImagesHaveEqualIntensities

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKImagesHaveSameSpatialExtent	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		const mitk::Image *	image2,
		bool &	output
	)

See also

ImagesHaveSameSpatialExtent

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKInitialiseSeedsForSlice	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		mitk::PointSet *	seeds,
		int	sliceAxis,
		int	sliceIndex
	)

Creates seeds for each distinct 4-connected region for a given slice.

This methods creates a region for the given slice and calls ITKAddNewSeedsToPointSet to create new seeds.

Parameters

sliceAxis	through slice axis, which should be [0|1|2].
sliceIndex	the index of the slice along the given axis.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKPreprocessingForWipe	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		const mitk::PointSet *	inputSeeds,
		int	sliceAxis,
		int	sliceIndex,
		int	direction,
		mitk::PointSet *	outputCopyOfInputSeeds,
		mitk::PointSet *	outputNewSeeds,
		std::vector< int > &	outputRegion
	)

Does any pre-processing necessary to facilitate Undo/Redo for Wipe commands, which in this case means computing a new list of seeds, and the region of interest to be wiped.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKPreprocessingOfSeedsForChangingSlice	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		const mitk::PointSet *	inputSeeds,
		int	oldSliceAxis,
		int	oldSliceIndex,
		int	newSliceAxis,
		int	newSliceIndex,
		bool	optimiseSeedPosition,
		bool	newSliceIsEmpty,
		mitk::PointSet *	outputCopyOfInputSeeds,
		mitk::PointSet *	outputNewSeeds,
		std::vector< int > &	outputRegion
	)

Does any pre-processing of seeds necessary to facilitate Undo/Redo for Threshold Apply, and also changing slice.

In this case means calculating the region of interest as a slice and if we are changing slice we propagate the seeds on the current slice to the new slice, and if we are doing threshold apply, we re-calculate seeds for the current slice based on the connected component analysis described in the class header at the top of this file.

Notice how this is similar to the preprocessing required for Propagate, seen in PropagateToRegionGrowingImageUsingITK. Also note that itkImage input should be the binary region growing image.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKPropagateSeedsToNewSlice	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		const mitk::PointSet *	currentSeeds,
		mitk::PointSet *	newSeeds,
		int	sliceAxis,
		int	oldSliceIndex,
		int	newSliceIndex
	)

Given an image, and a set of seeds, will append new seeds in the new slice if necessary.

When MIDAS switches slice, if the current slice has seeds, and the new slice has none, it will auto-generate them. This is useful for things like quick region growing, as you simply switch slices, and the new region propagates forwards.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKPropagateToRegionGrowingImage	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		const mitk::PointSet *	inputSeeds,
		int	sliceAxis,
		int	sliceIndex,
		int	direction,
		double	lowerThreshold,
		double	upperThreshold,
		mitk::PointSet *	outputCopyOfInputSeeds,
		mitk::PointSet *	outputNewSeeds,
		std::vector< int > &	outputRegion,
		mitk::Image *	outputRegionGrowingImage
	)

Method takes all the input, and calculates the 3D propagated region (up or down or 3D), and stores it in the region growing node.

template<typename TGreyScalePixel , unsigned int VImageDimension>

void niftk::ITKPropagateToSegmentationImage	(	const itk::Image< TGreyScalePixel, VImageDimension > *	itkImage,
		mitk::Image *	segmentedImage,
		mitk::Image *	regionGrowingImage,
		OpPropagate *	op
	)

Called from the ExecuteOperate (i.e. undo/redo framework) to actually apply the calculated propagated region to the current segmentation.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKPropagateUpOrDown	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		const mitk::PointSet *	seeds,
		int	sliceAxis,
		int	sliceIndex,
		int	direction,
		double	lowerThreshold,
		double	upperThreshold,
		mitk::Image *	outputRegionGrowingImage
	)

Called from ITKPropagateToRegionGrowingImage to propagate up or down.

This is basically a case of taking the seeds on the current slice, and calculating the up/down region (which should include the currrent slice), and then perform 5D region growing in the correct direction.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKRecalculateMinAndMaxOfSeedValues	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		const mitk::PointSet *	inputSeeds,
		int	sliceAxis,
		int	sliceIndex,
		double &	min,
		double &	max
	)

Called from RecalculateMinAndMaxOfSeedValues(), the actual method in ITK that recalculates the min and max intensity value of all the voxel locations given by the seeds.

template<typename TPixel , unsigned int VImageDimension>

bool niftk::ITKSliceDoesHaveSeeds	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		const mitk::PointSet *	seeds,
		int	sliceAxis,
		int	sliceIndex
	)

Will return true if the given slice has seeds within that slice.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKSliceDoesHaveUnenclosedSeeds	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		const mitk::PointSet *	seeds,
		mitk::ContourModelSet *	segmentationContours,
		mitk::ContourModelSet *	polyToolContours,
		mitk::ContourModelSet *	drawToolContours,
		const mitk::Image *	workingImage,
		double	lowerThreshold,
		double	upperThreshold,
		bool	useThresholds,
		int	sliceAxis,
		int	sliceIndex,
		bool &	sliceDoesHaveUnenclosedSeeds
	)

Will return true if slice has unenclosed seeds, and false otherwise.

This works by region growing. We create a local GeneralSegmentorPipeline and perform region growing, and then check if the region has his the edge of the image. If the region growing hits the edge of the image, then the seeds must have been un-enclosed, and true is returned, and false otherwise.

Parameters

useThreshold

if true will use lowerThreshold and upperThreshold and if false will use the min and maximum limit of the pixel data type of the itkImage.

template<typename TPixel , unsigned int VImageDimension>

bool niftk::ITKSliceIsEmpty	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		int	sliceAxis,
		int	sliceIndex,
		bool &	outputSliceIsEmpty
	)

Creates a region of interest within itkImage corresponding to the given slice, and checks if it is empty returning true if it is all zero.

template<typename TPixel , unsigned int VImageDimension>

void niftk::ITKUpdateRegionGrowing	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		bool	skipUpdate,
		const mitk::Image *	workingImage,
		const mitk::PointSet *	seeds,
		mitk::ContourModelSet *	segmentationContours,
		mitk::ContourModelSet *	drawContours,
		mitk::ContourModelSet *	polyContours,
		int	sliceAxis,
		int	sliceIndex,
		double	lowerThreshold,
		double	upperThreshold,
		mitk::Image *	outputRegionGrowingImage
	)

Called from UpdateRegionGrowing(), updates the interactive ITK single 2D slice region growing pipeline. Note: segmentationContours, drawContours and polyContours could be const pointers, but some const functions are missing from mitk::ContourModelSet. They are not modified from within this function (including transitive calls).

NIFTKCORE_EXPORT double niftk::Length

(

mitk::Point3D &

vector

)

Given a vector, will calculate the length.

NIFTKCORE_EXPORT bool niftk::Load2DPointFromFile	(	const std::string &	fileName,
		mitk::Point2D &	point
	)

Loads a 2D point from file, returning true if successful and false otherwise.

NIFTKCORE_EXPORT bool niftk::Load3DPointFromFile	(	const std::string &	fileName,
		mitk::Point3D &	point
	)

Loads a 3D point from file, returning true if successful and false otherwise.

bool niftk::LoadDoublesFromFile	(	const std::string &	fileName,
		std::vector< double > &	output
	)

NIFTKVTK_WINEXPORT vtkSmartPointer< vtkMatrix4x4 > niftk::LoadMatrix4x4FromFile	(	const std::string &	fileName,
		const bool &	silent = false
	)

Loads the matrix from file, or else creates an Identity matrix, and the caller is responsible for deallocation.

Parameters

fileName

NIFTKCORE_EXPORT void niftk::LoadMatrixOrCreateDefault	(	const std::string &	fileName,
		const std::string &	nodeName,
		const bool &	helperObject,
		mitk::DataStorage *	dataStorage
	)

Loads a 4x4 matrix from a plain textfile, and puts in data storage with the given nodeName, or else creates Identity matrix.

Parameters

fileName	full file name
helperObject	if true the node is created in DataStorage as a helper object, and so by default will normally be invisible

NIFTKCORE_EXPORT std::vector< mitk::PointSet::Pointer > niftk::LoadPointSetsFromDirectory

(

const std::string

fullDirectoryName

)

Loads all point sets from directory.

NIFTKCORE_EXPORT void niftk::LoadTimeStampData	(	const std::string &	fileName,
		std::set< unsigned long long > &	outputTimeStamps
	)

Loads a list of timestamps from a file.

NIFTKCORE_EXPORT vtkSmartPointer< vtkMatrix4x4 > niftk::LoadVtkMatrix4x4FromFile

(

const std::string &

fileName

)

Load a plain text file of 4 rows of 4 space separated numbers into a vtkMatrix4x4.

Parameters

fileName

full path of file name

Returns

vtkSmartPointer<vtkMatrix4x4> that the caller is responsible for

int* niftk::LowerToUpperOrder

(

int

dim

)

NIFTKVTK_WINEXPORT bool niftk::MatricesAreEqual	(	const vtkMatrix4x4 &	m1,
		const vtkMatrix4x4 &	m2,
		const double &	tolerance = 0.01
	)

Checks matrices for equality.

Parameters

tolerance

absolute difference between corresponding elements must be less than this number.

NIFTKVTK_WINEXPORT void niftk::MatrixToQuaternion	(	const vtkMatrix4x4 &	matrix,
		double *	quaternion
	)

Extracts the rotation matrix, and converts to quaternion.

Parameters

quaternion

must be a pointer to an array of 4 doubles that is already allocated.

NIFTKCOMMON_WINEXPORT double niftk::Mean

(

const std::vector< double > &

input

)

To return the sample mean of a vector.

cv::Mat NIFTKOPENCVIMAGECONVERSION_EXPORT niftk::MitkImageToOpenCVMat

(

const mitk::Image::Pointer

)

mitk::Image::Pointer to cv::Mat* , supports 8 bit per channel RGB, RGBA and gray

NIFTKCOMMON_WINEXPORT double niftk::ModifiedSignum

(

double

value

)

Returns -1.0 if value < 0 or 1.0 if value >= 0.

NIFTKCOMMON_WINEXPORT std::string niftk::ModifyFileSuffix	(	const std::string &	fileName,
		std::string	newSuffix
	)

Modify the suffix of a file name, or append if no suffix present. It is up to the user to ensure that 'newSuffix' contains a '.' if required.

Parameters

fileName	The input file name.
newSuffix	The text to replace the suffix with.

Returns

The file name with the modified or appended suffix.

NIFTKCOMMON_WINEXPORT std::string niftk::ModifyImageFileSuffix	(	const std::string &	fileName,
		std::string	newSuffix
	)

Modify the image suffix of a file name, or append if no image suffix present.

Parameters

fileName	The input image file name.
newSuffix	The text to replace the image suffix with.

Returns

The image file name with the modified, or appended, image suffix.

niftk::NIFTK_TOOL_MACRO	(	NIFTKMIDAS_EXPORT	,
		PosnTool	,
		"Posn Tool"
	)

NIFTKCORE_EXPORT void niftk::Normalise

(

mitk::Point3D &

vector

)

Given a vector, will normalise it to unit length.

NIFTKVTK_WINEXPORT void niftk::Normalise3DPoint	(	const double *	a,
		const double	length,
		double *	output
	)

Divides a 3D point by a length, so a and output must be arrays of length 3.

NIFTKVTK_WINEXPORT double niftk::NormalisedRNG

(

vtkRandomSequence *

rng

)

Normalises the values returned by a vtk random sequence to be centred on zero.

Parameters

rng	the random number sequence

Returns

The normalised value

NIFTKVTK_WINEXPORT void niftk::NormaliseToUnitLength	(	const double *	a,
		double *	output
	)

Normalises a to unit length.

NIFTKCOMMON_WINEXPORT bool niftk::NumericStringCompare	(	const std::string &	string1,
		const std::string &	string2
	)

A numeric string comparison operator, useful for sorting filenames into numeric order

Parameters

string1
string2

Returns

comparison result

std::ostream& niftk::operator<<	(	std::ostream &	os,
		const CSVRow &	data
	)

Specialisation of 'operator<<' for the niftk::CSVRow class

std::ostream& niftk::operator<<	(	std::ostream &	os,
		const BasicVec3D &	vo
	)

std::ostream& niftk::operator<<	(	std::ostream &	os,
		const BasicVertex &	vo
	)

std::ostream& niftk::operator<<	(	std::ostream &	os,
		const BasicTriangle &	to
	)

std::istream& niftk::operator>>	(	std::istream &	str,
		CSVRow &	data
	)

Specialisation of 'operator>>' for the niftk::CSVRow class

NIFTKVTK_WINEXPORT void niftk::PerturbPolyData	(	vtkPolyData *	polydata,
		double	xerr,
		double	yerr,
		double	zerr,
		vtkRandomSequence *	rng
	)

Perturbs the points in a polydata object by random values, using existing random number generator.

Parameters

polydata	the polydata
xerr,yerr,zerr	the multipliers for the random number generator in each direction.
rng	the random number generator

Returns

void

NIFTKVTK_WINEXPORT void niftk::PerturbPolyData	(	vtkPolyData *	polydata,
		double	xerr,
		double	yerr,
		double	zerr
	)

Perturbs the points in a polydata object by with random values, intialising and using it's own random number generator.

Parameters

polydata	the polydata
xerr,yerr,zerr	the multipliers for the random number generator in each direction.

Returns

void

NIFTKVTK_WINEXPORT void niftk::PerturbPolyDataAlongNormal	(	vtkPolyData *	polydata,
		double	stdDev,
		vtkRandomSequence *	rng
	)

Perturbs a vtkPolyData, by moving each point along its normal.

NIFTKPOINTREG_EXPORT double niftk::PointAndNormalBasedRegistrationUsingSVD	(	const std::vector< cv::Point3d > &	fixedPoints,
		const std::vector< cv::Point3d > &	fixedNormals,
		const std::vector< cv::Point3d > &	movingPoints,
		const std::vector< cv::Point3d > &	movingNormals,
		cv::Matx44d &	outputMatrix
	)

Does Point Based Registration of two same sized, corresponding point sets.

Parameters

fixedPoints	fixed point set.
movingPoints	moving point set.
outputMatrix	output 4 x 4 homogeneous rigid body transformation.

Returns

fiducial registration error

NIFTKPOINTREG_EXPORT double niftk::PointAndNormalBasedRegistrationUsingSVD	(	const mitk::PointSet::Pointer	fixedPoints,
		const mitk::PointSet::Pointer	fixedNormals,
		const mitk::PointSet::Pointer	movingPoints,
		const mitk::PointSet::Pointer	movingNormals,
		vtkMatrix4x4 &	matrix
	)

Overloaded method for MITK and VTK data types.

Calls the above method. Converts (copies) the point sets from the mitk::PointSet into a vector of cv::Point3D in order. The PointID in mitk::PointSet is not used, so the points must be in the right order, and corresponding.

NIFTKPOINTREG_EXPORT double niftk::PointBasedRegistrationUsingSVD	(	const std::vector< cv::Point3d > &	fixedPoints,
		const std::vector< cv::Point3d > &	movingPoints,
		cv::Matx44d &	outputMatrix
	)

Does Point Based Registration of two same sized, corresponding, ordered point sets.

Parameters

fixedPoints	fixed point set.
movingPoints	moving point set.
outputMatrix	output 4 x 4 homogeneous rigid body transformation.

Returns

fiducial registration error

NIFTKPOINTREG_EXPORT double niftk::PointBasedRegistrationUsingSVD	(	const mitk::PointSet::Pointer	fixedPoints,
		const mitk::PointSet::Pointer	movingPoints,
		vtkMatrix4x4 &	matrix
	)

Overloaded method for MITK and VTK data types.

Calls the above method. Converts (copies) the point sets from the mitk::PointSet into a vector of cv::Point3D in order. The PointID in mitk::PointSet is not used, so the points must be in the right order, and corresponding.

NIFTKIGIDATASOURCES_EXPORT bool niftk::ProbeRecordedData	(	const QString &	path,
		const QString &	fileExtension,
		niftk::IGIDataType::IGITimeType *	firstTimeStampInStore,
		niftk::IGIDataType::IGITimeType *	lastTimeStampInStore
	)

Returns the minimum and maximum timestamped of all files under the specified path, with the specified fileExtension, that look like they are timestamped.

NIFTKIGIDATASOURCES_EXPORT void niftk::ProbeTimeStampFiles	(	QDir	path,
		const QString &	suffix,
		std::set< niftk::IGIDataType::IGITimeType > &	timeStamps
	)

Scans the path for individual files that match a timestamp pattern and suffix.

Parameters

suffix

for example ".jpg" or "-ultrasoundImage.nii".

NIFTKIGIDATASOURCES_EXPORT void niftk::ProbeTimeStampFiles	(	QDir	path,
		const QString &	suffix,
		std::set< niftk::IGIDataType::IGITimeType > &	timeStamps,
		QHash< niftk::IGIDataType::IGITimeType, QString > &	timeStampToFileName
	)

Scans the path for individual files that match a timestamp pattern and suffix.

Parameters

suffix

for example ".jpg" or "-ultrasoundImage.nii".

void niftk::Producer

(

const mitk::StandaloneDataStorage::Pointer &

datastorage

)

NIFTKVTK_WINEXPORT void niftk::RandomTransform	(	vtkTransform *	transform,
		double	xtrans,
		double	ytrans,
		double	ztrans,
		double	xrot,
		double	yrot,
		double	zrot,
		vtkRandomSequence *	rng
	)

Creates a randomly determined vtkTransform, using existing random number geneterator.

Parameters

transform	the transform to hold the result
xtrans,ytrans,ztrans,xrot,yrot,zrot	the multipliers in each of the 6 degrees of freedom
rng	the random number generator

Returns

void

NIFTKVTK_WINEXPORT void niftk::RandomTransform	(	vtkTransform *	transform,
		double	xtrans,
		double	ytrans,
		double	ztrans,
		double	xrot,
		double	yrot,
		double	zrot
	)

Creates a randomly determined vtktransform, using it's own random number generator.

Parameters

transform	the transform to hold the result
xtrans,ytrans,ztrans,xrot,yrot,zrot	the multipliers in each of the 6 degrees of freedom

Returns

void

void niftk::RefcountTest

(

const mitk::StandaloneDataStorage::Pointer &

datastorage

)

NIFTKCORE_EXPORT int niftk::RemoveNaNPoints	(	const mitk::PointSet &	pointsIn,
		mitk::PointSet &	pointsOut
	)

Takes a point set and scans for matching NaN's and returns a point set with the offending points removed.

Returns

the number of points removed

NIFTKCORE_EXPORT vtkLookupTable * niftk::ResizeLookupTable	(	vtkLookupTable *	lut,
		double	newMaximum
	)

Resize the LookupTable while retaining all of the previously set values. Newly added values are assigned the nan color.

NIFTKCOMMON_WINEXPORT double niftk::RMS

(

const std::vector< double > &

input

)

Assuming input contains squared errors, will sum them, divide by N, and take sqrt for an RMS measure.

NIFTKCOMMON_WINEXPORT int niftk::Round

(

double

d

)

NIFTKCOMMON_WINEXPORT double niftk::Round	(	double	d,
		int	numberDecimalPlaces
	)

void NIFTKCUDAKERNELS_WINEXPORT niftk::RunEdgeDetectionKernel	(	char *	outputRGBA,
		unsigned int	outputBytePitch,
		const char *	inputRGBA,
		unsigned int	inputBytePitch,
		int	width,
		int	height,
		cudaStream_t	stream
	)

Basic example kernel to do some edge detection, but is not yet implemented.

void NIFTKCUDAKERNELS_WINEXPORT niftk::RunFlipImageKernel	(	char *	output,
		int	widthInBytes,
		int	height,
		int	outputpitchInBytes,
		const char *	input,
		int	inputpitchInBytes,
		cudaStream_t	stream
	)

Flips image in y-axis.

Width and pitch are in bytes. Pitch has to be a multiple of 4.

void NIFTKCUDAKERNELS_WINEXPORT niftk::RunUndistortionKernel	(	char *	outputRGBA,
		int	width,
		int	height,
		cudaTextureObject_t	srcTexture,
		const float *	intrinsic3x3,
		const float *	distortion4,
		cudaStream_t	stream
	)

Provides 2D image undistortion, given a cameras intrinsic and distortion co-efficients.

NIFTKCOMMON_WINEXPORT double niftk::SafeSQRT

(

double

value

)

Returns 0.0 of value < 0 or sqrt(value) if value >= 0.

NIFTKVTK_WINEXPORT bool niftk::SaveMatrix4x4ToFile	(	const std::string &	fileName,
		const vtkMatrix4x4 &	matrix,
		const bool &	silent = false
	)

Save the matrix to a plain text file of 4 rows of 4 space separated numbers.

Parameters

fileName	full path of file name
matrix	a matrix
bool	true if successful and false otherwise

NIFTKCORE_EXPORT bool niftk::SaveVtkMatrix4x4ToFile	(	const std::string &	fileName,
		const vtkMatrix4x4 &	matrix
	)

Save the matrix to a plain text file of 4 rows of 4 space separated numbers.

Parameters

fileName	full path of file name
matrix	a matrix

Returns

true if successful and false otherwise

NIFTKCORE_EXPORT void niftk::ScalePointSets	(	const mitk::PointSet &	input,
		mitk::PointSet &	output,
		double	scaleFactor
	)

Copies input to output, i.e. the output is erased, and re-populated, multiplying by a scale factor.

NIFTKVTK_WINEXPORT void niftk::ScaleVector	(	const double &	scaleFactor,
		const double *	a,
		double *	b
	)

Scales the unit vector a by scaleFactor, and writes to b, so a and be must be an array of length 3.

NIFTKVTK_WINEXPORT void niftk::SetCameraParallelTo2DImage	(	const int *	imageSize,
		const int *	windowSize,
		const double *	origin,
		const double *	spacing,
		const double *	xAxis,
		const double *	yAxis,
		const double *	clippingRange,
		const bool &	flipYAxis,
		vtkCamera &	camera,
		const double &	distanceToFocalPoint = -1000
	)

Used to set a vtkCamera to track a 2D image, and sets the camera to parallel projection mode.

Parameters

imageSize	array of 2 integers containing imageSize[0]=number of pixels in x, imageSize[1]=number of pixels in y of the image
windowSize	array of 2 integers containing width and height of the current window.
origin	array of 3 doubles containing the x,y,z coordinates in 3D space of the origin of the image, presumed to be the centre of the first (0,0) voxel.
spacing	array of 2 doubles containing the x and y spacing in mm.
xAxis	array of 3 doubles containing the x,y,z direction vector describing the x-axis.
yAxis	array of 3 doubles containing the x,y,z direction vector describing the y-axis.
clippingRange	array of 2 doubles containing the near and far clipping range.
flipYAxis	if true we flip the y-axis.

NIFTKCOMMON_WINEXPORT double niftk::StdDev

(

const std::vector< double > &

input

)

To return the sample standard deviation of a vector.

NIFTKVTK_WINEXPORT void niftk::SubtractTwo3DPoints	(	const double *	a,
		const double *	b,
		double *	output
	)

Subtracts two 3D points, so a, b and output must be arrays of length 3.

NIFTKCORE_EXPORT vtkLookupTable * niftk::SwapColors	(	vtkLookupTable *	lut,
		int	value1,
		int	value2
	)

Swap colors in the LookupTable at the given indices.

int niftk::SymMatDim

(

int

count

)

void niftk::TestAreDifferent

(

)

void niftk::TestCalculateStepSize

(

)

void niftk::TestCheckForNaNPoint

(

)

void niftk::TestComputeNormalFromPoints

(

)

void niftk::TestErrorConditions

(

)

void niftk::TestFilterMatchingPoints

(

)

void niftk::TestFindLargestDistanceBetweenTwoPoints

(

)

void niftk::TestGetDifference

(

)

void niftk::TestGetSquaredDistanceBetweenPoints

(

)

void niftk::TestIdentity

(

)

void niftk::TestInstantiation

(

)

void niftk::TestNormalise

(

)

void niftk::TestRemoveNaNPoints

(

)

void niftk::TestRMS

(

)

void niftk::TestScalePointSets

(

)

void niftk::TestSetGet

(

)

void niftk::TestSimpleCases

(

)

NIFTKCORE_EXPORT void niftk::TransformPointByVtkMatrix	(	const vtkMatrix4x4 *	matrix,
		const bool &	isNormal,
		mitk::Point3D &	pointOrNormal
	)

Simple method to multiply a mitk::Point3D by a vtkMatrix, if the matrix is not NULL, and otherwise if matrix is NULL, will simply leave the point un-altered.

Parameters

isNormal

if true, will transform the mitk::Point3D as if it was a surface normal.

NIFTKCORE_EXPORT void niftk::TransformPointsByVtkMatrix	(	const mitk::PointSet &	input,
		const vtkMatrix4x4 &	matrix,
		mitk::PointSet &	output
	)

Multiplies one point set by a matrix.

NIFTKVTK_WINEXPORT void niftk::TranslatePolyData	(	vtkPolyData *	polydata,
		vtkTransform *	transform
	)

Translates a polydata object using a transform.

Parameters

polydata	the polydata
transform	the transform

Returns

void

void NIFTKCUDA_EXPORT niftk::UndistortionLauncher	(	char *	hostInputImageData,
		int	width,
		int	height,
		int	widthStep,
		float *	intrinsics,
		float *	distortion,
		char *	hostOutputImageData
	)

Runs the CUDA based image undistortion.

See also

niftk::RunUndistortionKernel

Parameters

hostInputImageData	host-side input 4-channel image data, such as might be obtained from an IplImage
width	the width of the image in pixels
height	the height of the image in pixels
widthStep	= width * channels (4)
intrinsics	array of 9 floats containing camera intrinsics
distortion	array of 4 floats containing distortion coefficients

NIFTKCORE_EXPORT void niftk::UpdateVolumeProperty	(	const mitk::Image *	image,
		mitk::DataNode *	node
	)

Calculates the volume of non-zero voxels in image, and creates a property "midas.volume" on the data node.

Parameters

image	An MITK image, not NULL.
node	An MITK DataNode, not NULL.

int* niftk::UpperToLowerOrder

(

int

dim

)

niftk::vtkStandardNewMacro

(

VTK4PointsReader

)

niftk::vtkStandardNewMacro

(

BackfaceCullingFilter

)

void niftk::WaitForResult

(

const mitk::StandaloneDataStorage::Pointer &

datastorage

)

NIFTKVTK_WINEXPORT std::string niftk::WriteMatrix4x4ToString

(

const vtkMatrix4x4 &

matrix

)

Writes matrix out as a string, for use in SaveMatrix4x4ToFile.

float NIFTKOPENCV_EXPORT niftk::Zncc_C1	(	int	p0x,
		int	p0y,
		int	p1x,
		int	p1y,
		int	w,
		boost::gil::gray8c_view_t	img0,
		boost::gil::gray8c_view_t	img1,
		boost::gil::gray32sc_view_t	integral0,
		boost::gil::gray32sc_view_t	integral1,
		boost::gil::gray64fc_view_t	square0,
		boost::gil::gray64fc_view_t	square1
	)

Variable Documentation

const QString niftk::IMAGE_INITIALISATION_LEVELWINDOW

const QString niftk::IMAGE_INITIALISATION_METHOD_NAME

const QString niftk::IMAGE_INITIALISATION_MIDAS

const QString niftk::IMAGE_INITIALISATION_PERCENTAGE

const QString niftk::IMAGE_INITIALISATION_PERCENTAGE_NAME

const QString niftk::IMAGE_INITIALISATION_RANGE

const QString niftk::IMAGE_INITIALISATION_RANGE_LOWER_BOUND_NAME

const QString niftk::IMAGE_INITIALISATION_RANGE_UPPER_BOUND_NAME

const mitk::OperationType niftk::OP_CHANGE_SLICE = 9320411

const mitk::OperationType niftk::OP_CLEAN = 9320415

const mitk::OperationType niftk::OP_PROPAGATE = 9320417

const mitk::OperationType niftk::OP_PROPAGATE_SEEDS = 9320412

const mitk::OperationType niftk::OP_RETAIN_MARKS = 9320413

const mitk::OperationType niftk::OP_THRESHOLD_APPLY = 9320414

const mitk::OperationType niftk::OP_WIPE = 9320416

RegisterNifTKCoreIOObjectFactory niftk::registerNifTKCoreIOObjectFactory

static

RegisterNifTKCoreObjectFactory niftk::registerNifTKCoreObjectFactory

static

const MethodDescription niftk::s_AvailableMethods[]

static

Initial value:

=
{
  
  {"Sequential Quasi-Dense CPU", SurfaceReconstruction::SEQUENTIAL_CPU}
}

impldetail::ModuleCleanup niftk::s_ModuleCleaner

int niftk::tunnelOrientation = 0

const char* niftk::type[]

static

Initial value:

= {
   "",        
   "(int) ",      
   "(float) ",      
   "(string) ",     
   "(var) ",      
   "",        
   "(double) ",     
   "(long) ",     
   "(intx2) ",      
   "(intx3) ",      
   "(intx4) ",      
   "(floatx2) ",    
   "(floatx3) ",    
   "(floatx4) ",    
   "(doublex2) ",   
   "(doublex3) ",   
   "(doublex4) ",   
}

const int niftk::VIRTUAL_SROM_SIZE =1024

const int niftk::WINDOW_LAYOUT_NUMBER = 15

The number of the possible window layouts.

const int niftk::WINDOW_ORIENTATION_NUMBER = 4

The number of the possible orientations.