Namespaces
	Function

	Functor

	Statistics

Classes
class	AbsoluteManhattanDistancePointMetric
	Computes the sum of the absolute Manhattan Distance (L1-norm) between two point sets. More...

class	AddOneLayerOfGreyMatterFilter
	Assumes input is GM, WM, CSF labelled image, and adds 1 layer of GM to the WM, which means that the output will have the same size WM, only 1 voxel wide layer of GM, and the rest is then all CSF. More...

class	AddUpdateToTimeVaryingVelocityFieldFilter
	Adds a vector displacement field to a time varying velocity field. More...

class	AffineTransform2D3D

class	AnalyzeImageIO3160
	Class that defines how to read Analyze file format. Analyze IMAGE FILE FORMAT - As much information as I can determine from the Medical image formats web site, and the Analyze75.pdf file provided from the Mayo clinic. A special note of thanks to Dennis P. Hanson (dph@m.nosp@m.ayo..nosp@m.edu) for his generous contributions in getting this information correct. More...

class	BackwardImageProjector2Dto3D
	Class to project a 3D image into 2D. More...

class	BaseCTEFilter
	Base class for methods many CTE filters will need. More...

class	BaseCTESegmentationFilter
	Base class for classes that manipulate the segmented volume before it gets to the Cortical Thickness Estimation. More...

class	BaseCTEStreamlinesFilter
	Base class for filters that calculate thicknesses based on Laplacian streamlines. More...

class	BasicFiniteDifferenceBaseClassImageFilter
	Abstract base class to provide first, second, mixed derivatives, which can be subclassed for things like calculating Mean / Gaussian curvature. More...

class	BasicImageFeaturesImageFilter
	2D image filter class to compute basic image features (BIFs) on an image. More...

class	BinariseUsingPaddingImageFilter
	Binarise the image using using padding value. More...

class	BinariseVesselResponseFilter
	Binarises the vesselness response and keeps the largest objects. More...

class	BinaryIntersectWithPaddingImageFilter
	Calculate the intersection of two images using padding value. More...

class	BinaryShapeBasedSuperSamplingFilter
	Filter to super-sample a mask by a certain factor and apply the appropriate shape based interpolation. More...

class	BinaryThresholdSurfaceVoxelImageFunction
	Returns true is the value of an image lies within a range of thresholds This ImageFunction returns true (or false) if the pixel value lies within (outside) a lower and upper threshold value. The threshold range can be set with the ThresholdBelow, ThresholdBetween or ThresholdAbove methods. The input image is set via method SetInputImage(). More...

class	BinaryUnionWithPaddingImageFilter
	Calculate the union of two images using padding value. More...

class	BlockMatchingMethod
	Initial implementation of Seb Ourselin's block matching algorithm. More...

class	BoundaryShiftIntegralCalculator
	Calculate the boundary shift integral. More...

class	BoundaryValueRescaleIntensityImageFilter
	Applies a linear transformation to the intensity levels of the input Image, but takes into an upper and lower threshold, so we can reassign stuff thats above or below (respectively) these thresholds to a set OutputBoundaryValue. More...

class	BrainMaskFromCTFilter
	Filter to extract the brain from a CT image. Optionally, the filter can receive a T1 image, co-registered with the CT, to improve the brain extraction. More...

class	BreastMaskSegmentationFromMRI
	Base class for breast mask MRI segmentation methods. More...

class	BreastMaskSegmForBreastDensity
	Class to segment the breast mask from MRI for modelling purposes. More...

class	BreastMaskSegmForModelling
	Class to segment the breast mask from MRI for modelling purposes. More...

class	BSplineBendingEnergyConstraint
	Calculated the bending energy, to be used as regulariser in FFD. More...

class	BSplineCurveFitMetric
	Class to compute the goodness of fit of a BSpline to a set of data values. More...

class	BSplineOperator
	A NeighborhoodOperator whose coefficients are a one dimensional, discrete BSpline kernel. More...

class	BSplineSmoothVectorFieldFilter
	Class that takes a vector field, and applies BSpline smoothing. More...

class	CheckForThreeLevelsFilter
	Simply checks for 3 levels and passes data straight through. More...

class	CommandIterationUpdateSuperEllipseFit

class	ConjugateGradientMaxIterOptimizer
	Wrap of the vnl_conjugate_gradient. More...

class	Constraint
	Abstract Base class for constraints, which are objects that return a single double value, such as might be used for a regulariser in a deformable registration algorithm. In practice you create any subclass of this. Then the base similarity measure itkImageToImageMetricWithConstraint will evaluate the cost function, for example, the mutual information of your two images is X, then, if the itkImageToImageMetricWithConstraint has a pointer to a constraint, it will call EvaluateConstraint, which will return a value Y, then itkImageToImageMetricWithConstraint will combine those two numbers together. So, in principal, the itkImageToImageMetricWithConstraint (and derived subclasses) need not even know what or how a constraint works, only that it provides a number. More...

class	CorrectGMUsingNeighbourhoodFilter
	Implements section 2.3 in Acosta et al. doi:10.1016/j.media.2009.07.003. More...

class	CorrectGMUsingPVMapFilter
	Implements section 2.3.1 Correction Of Segmentation in Bourgeat MICCAI 2008. More...

class	CreateEulerAffineTransformMatrix
	Class to apply the affine transformation matrix to a 3D image. More...

class	CreateEulerAffineTransformMatrixBaseClass
	The base class for 3D-3D affine transformation matrix. More...

class	CreateForwardBackwardProjectionMatrix
	Class to project a 3D image into 2D. More...

class	CRImageToImageMetric
	Implements Correlation Ratio (Fixed \| Moving), without a histogram. More...

class	CropTargetImageWhereSourceImageNonZeroImageFilter
	Crops the target (second input) where the source image (first input) is non zero. More...

class	CrossCorrelationDerivativeForceFilter
	This class takes as input 2 input images, and outputs the registration force based on the derivative of cross correlation. More...

class	CurveFitRegistrationMethod

class	DasGradientFilter
	This class calculates the gradient as per equation 3 in Das et. al. Neuroimage 45 (2009) 867-879. More...

class	DasTransformImageFilter
	Transform an image using a vector field, where each vector represents the absolute sampling position, not a vector displacement. More...

struct	data_history

class	DBCImageFilter

class	DeformableTransform
	Base class for deformable transforms. More...

class	DisplacementFieldJacobianFilter
	This class calculates the Jacobian matrix of a deformation field. More...

class	DisplacementFieldJacobianVectorFilter
	This class calculates the Jacobian matrix of a deformation field and store in a row-major vector. More...

class	DivideOrZeroImageFilter
	Implements an operator for pixel-wise division of two images, and where divisor is zero, outputs zero. More...

class	DoubleWindowBoundaryShiftIntegralCalculator
	Calculate the boundary shift integral using double intensity window. More...

class	DRCAnalyzeImageIO
	Subclass of AnalyzeImageIO3160, to read Dementia Research Centre (DRC) Analyze format, which is incorrectly flipped. If you call this->SetDRCMode(true) (also default), it will do DRC specific functionality, and if you call SetDRCMode(false), it will revert to standard ITK functionality. More...

struct	dsr

class	DynamicContrastEnhancementAnalysisImageFilter
	Image filter to process a set of contrast enhancement images. More...

class	EulerAffineTransform
	Euler Affine transform. More...

class	EulerAffineTransformMatrixAndItsVariations
	Class to apply the affine transformation matrix to a 3D image. More...

class	ExcludeImageFilter
	Performs the connection breaker algorithm as in "Interactive Algorithms for the segmentation and quantification of 3-D MRI scans" Freeborough et. al. CMPB 53 (1997) 15-25. More...

class	ExtendedBrainMaskWithSmoothDropOffCompositeFilter
	Takes a mask, dilates outwards, blurs with a gaussian, then substitutes in the dilated mask, so you end up with a bigger mask than you started, with gaussian blurred edges (ie. smooth drop off to zero). More...

class	FFDConjugateGradientDescentOptimizer
	Class to perform FFD specific optimization using conjugate gradient descent. More...

class	FFDDerivativeBridge
	FFDDerivative bridge to enable plugging a whole pipeline into a similarity measure to measure the derivative of a cost function. More...

class	FFDGradientDescentOptimizer
	Class to perform FFD specific optimization. More...

class	FFDMultiResolutionMethod
	Extends MultiResolutionDeformableImageRegistrationMethod to sort out interpolating the BSpline grid in between resolution levels. More...

class	FFDSteepestGradientDescentOptimizer
	Class to perform FFD specific optimization using steepest gradient descent. More...

class	FiniteDifferenceGradientSimilarityMeasure
	AbstractBase class, just to implement the finite difference gradient method. More...

class	FiniteDifferenceVoxel
	Simple data type to hold a voxel value, and indexes that can be used to refer to other voxels. More...

class	FluidDeformableTransform
	Deformable transform using a fluid representation. More...

class	FluidMultiResolutionMethod
	Extends MultiResolutionDeformableImageRegistrationMethod to sort out interpolating the deformation fluid in between resolution levels. More...

class	FluidVelocityToDeformationFilter
	This class takes two inputs, the first is the current deformation vector field and the second is the fluid velocity vector field. The output is a vector field of deformation according to Christensens paper. More...

class	ForegroundFromBackgroundImageThresholdCalculator
	Computes the threshold required to separate an object or patient in the foreground of an image from a dark background. More...

class	ForwardAndBackProjectionDifferenceFilter
	Class to compute the difference between a reconstruction estimate and the target set of 2D projection images. More...

class	ForwardAndBackwardProjectionMatrix
	Class to apply the affine transformation matrix to a 3D image. More...

class	ForwardDifferenceDisplacementFieldJacobianDeterminantFilter

class	ForwardImageProjector3Dto2D
	Class to project a 3D image into 2D. More...

class	ForwardProjectionWithAffineTransformDifferenceFilter
	Class to compute the difference between a reconstruction estimate and the target set of 2D projection images. More...

class	FourthOrderRungeKuttaVelocityFieldIntegrationFilter
	This filter integrates a time varying velocity field, using fourth order Runge-Kutta. This filter is basically a tidied up version of that in ANTS: http://www.picsl.upenn.edu/ANTS/ However, ANTS has the four timepoints back to front. I don't know if this is intentional. More...

class	GaussianCurvatureImageFilter
	Class to calculate Gaussian curvature of a scalar image. More...

class	GaussianSmoothVectorFieldFilter
	Class that takes a vector field, and applies Gaussian smoothing. More...

class	GE5000_TomosynthesisGeometry
	Class to calculate the geometry of a GE tomosynthesis machine. More...

class	GE6000_TomosynthesisGeometry
	Class to calculate the geometry of a GE tomosynthesis machine. More...

class	GroupwiseRegistrationMethod
	A class to perform a generic group-wise registration. More...

struct	header_key

class	HighResLaplacianSolverImageFilter
	Solves Laplace equation over the cortical volume, but can be run at very high resolution, by setting the VoxelMultiplicationFactor to determine an effective voxel size. More...

class	HighResRelaxStreamlinesFilter
	Prototype high res version of RelaxStreamlines Filter. More...

class	HistogramSimilarityMeasure
	Computes similarity between two objects to be registered using Histogram. More...

struct	image_dimension

class	ImageAndArray

class	ImageMatrixFormReconstructionMethod
	Base class for Image Reconstruction Methods. More...

class	ImageMatrixFormReconstructionMetric
	Class to compute the difference between a reconstruction estimate and the target set of 2D projection images. More...

class	ImageMatrixFormReconTwoDataSetsWithoutRegMethod
	Base class for Image Reconstruction Methods. More...

class	ImageMatrixFormReconTwoDataSetsWithoutRegMetric
	Class to compute the difference between a reconstruction estimate and the target set of 2D projection images. More...

class	ImageProjectionBaseClass2D3D
	The base class for 2D-3D forward and back projection. More...

class	ImageProjector2D3D
	Class to project a 3D image into 2D. More...

class	ImageReconstructionMethod
	Base class for Image Reconstruction Methods. More...

class	ImageReconstructionMetric
	Class to compute the difference between a reconstruction estimate and the target set of 2D projection images. More...

class	ImageReconstructionOptimizer
	Base class for image reconstruction optimization methods. More...

class	ImageRegistrationFactory
	Parameterised Factory Pattern [2] for creating registration objects. More...

class	ImageRegistrationFilter
	Used to plug registration methods into a filter based pipeline. More...

class	ImageToImageMetricWithConstraint
	Abstract base class to provide functionality for adding arbitrary constraints, and also arbitrary ways of evaluating a derivative, both via Template Method pattern [2]. More...

class	ImageToVTKImageFilter
	Converts an ITK image into a VTK image and plugs a itk data pipeline to a VTK datapipeline. More...

class	InjectSourceImageGreaterThanZeroIntoTargetImageFilter
	If first input is != 0, then the first input is copied to output, otherwise, the second input pixel is copied to output. More...

struct	INRFileWrapper

class	INRImageIO
	ITK IO class to load INRIA image format. More...

class	IntegrateStreamlinesFilter
	Integrates streamlines using Eulers method (Lagrangian framework). More...

class	IntensityFilter

class	IntensityNormalisationCalculator
	Calculates the means to normalise the intensities of two scans. Calculate the means used to normalise the intensities of two scans acquired in different dates, using the following steps: More...

class	InterpolateVectorFieldFilter
	This class takes a vector field as input 1, and a vector field as input 2, and the output is a vector field, of the same dimensions as input 2, where the vector at each location is interpolated from input 1. More...

class	InvariantPointCalibrationCostFunction
	Base class for Ultrasound Pin/Cross-Wire calibration and Video Hand-Eye calibration cost functions. More...

class	InvertIntensityBetweenMaxAndMinImageFilter
	Invert intensity of an image. More...

class	InvNormalizedCorrelationImageToImageMetric

class	InvRayCastInterpolateImageFunction

class	InvResampleImageFilter

class	IsocentricConeBeamRotationGeometry
	Class to calculate the geometry of an isocentric cone beam projection CT or tomosynthesis machine. More...

class	IterationUpdateCommand
	Simply prints out the registration params, so we can track registration. More...

class	IterativeReconstructionAndRegistrationMethod
	Base class for iterative image reconstruction and registration methods. More...

class	JacobianGradientSimilarityMeasure
	AbstractBase class, just to implement a gradient method based on Jacobian. More...

class	JEImageToImageMetric
	Implements Joint Entropy of a histogram for a similarity measure. More...

class	JonesThicknessFilter
	Composite filter to implement Jones et. al. Human Brain Mapping 2005 11:12-32(2000). More...

class	JorgesInitializationRelaxStreamlinesFilter
	Implementation of Jorges method to initialize GM boundaries prior to cortical thickness calculations. More...

class	KnownCorEuclideanDistancePointMetric

class	LagrangianInitializedRelaxStreamlinesFilter
	Implements section 2.3.2 in Bourgeat et. al. ISBI 2008. More...

class	LaplacianSolverImageFilter
	Solves Laplace equation over the cortical volume. More...

class	LargestConnectedComponentFilter
	Does connected component analysis and outputs a binary volume of the largest connected component. More...

class	LeastTrimmedSquaresPointMetric
	Like sum of squared difference between point sets, except you throw away a certain percentage of outliers. More...

class	LewisGriffinRecursiveGaussianImageFilter
	Lewis Griffin's implementation of a recursive Gaussian filter which does not produce the oscillations that itk::RecursiveSeparableImageFilter does. More...

class	LightLineResponseImageFilter
	2D image filter class to compute the light line response of an image a specific scale. More...

class	LinearlyInterpolatedDerivativeFilter
	This class takes as input 2 input images, the Fixed and Moving image, as you would have in a registration pipeline, and outputs the derivative of the moving image resampled by a transformation. More...

class	LocalHistogramDerivativeForceFilter

class	LocalSimilarityMeasureGradientDescentOptimizer
	Implement a gradient descent optimization suitable for FFD and Fluid deformation. More...

class	LogNonZeroIntensitiesImageFilter
	Computes the vcl_log(x) pixel-wise of non-zero intensities leaving zero-valued pixels unchanged. More...

class	LSDerivativesL0

class	LSDerivativesL1

class	LSDerivativesL2

struct	LSGradientsL0

struct	LSGradientsL1

struct	LSGradientsL2

class	MammogramAnalysis

class	MammogramFatEstimationFitMetric
	An abstract metric to compute the fit of a model of mammographic fat. More...

class	MammogramFatEstimationFitMetricForArray
	A metric to compute the similarity between an image and breast fat model. More...

class	MammogramFatEstimationFitMetricForImage
	A metric to compute the similarity between an image and breast fat model. More...

class	MammogramFatSubtractionImageFilter
	2D image filter class to subtract the fat signal from a mammogram. More...

class	MammogramLeftOrRightSideCalculator
	Computes whether a mammogram is of the left or right breast from the center of mass. More...

class	MammogramMaskSegmentationImageFilter
	2D image filter class to segment the breast area from a mammogram. More...

class	MammogramMLOorCCViewCalculator
	Computes whether a mammogram corresponds to a CC or an MLO view. More...

class	MammogramPectoralisFitMetric
	A metric to compute the similarity between an image and a pectoral shape model. More...

class	MammogramPectoralisSegmentationImageFilter
	2D image filter class to segment the pectoral muscle from a mammogram. More...

class	MammogramRegistrationFilter

class	MammographicTumourDistribution

class	MaskedImageRegistrationMethod
	Base class for NifTK Image Registration Methods employing a binary mask. More...

class	MatrixBasedSimulReconRegnMethod
	Base class for Image Reconstruction Methods. More...

class	MatrixBasedSimulReconRegnMetric
	Class to compute the difference between a reconstruction estimate and the target set of 2D projection images. More...

class	MatrixLinearCombinationFunctions

class	MaximumCurvatureImageFilter
	Calculates maximum curvature, assuming that the two inputs represent Gaussian Curvature on input 0, and Mean Curvature on input 1. More...

class	MeanCurvatureImageFilter
	Class to calculate mean curvature of a scalar image. More...

class	MeanVoxelwiseIntensityOfMultipleImages
	Image filter class to calculate the mean image on a voxel by voxel basis of multiple input images. More...

class	MetricDerivativeBridge

class	MIDASBaseConditionalMorphologyFilter
	Base class for MIDASConditionalErosionFilter and MIDASConditionalDilationFilter. More...

class	MIDASConditionalDilationFilter
	Performs the conditional dilation, described in step 4 of "Interactive Algorithms for the segmentation and quantification of 3-D MRI scans" Freeborough et. al. CMPB 53 (1997) 15-25. More...

class	MIDASConditionalErosionFilter
	Performs the conditional erosion, described in step 3 of "Interactive Algorithms for the segmentation and quantification of 3-D MRI scans" Freeborough et. al. CMPB 53 (1997) 15-25. More...

class	MIDASDownSamplingFilter
	Performs the down sampling described in step 5 of "Interactive Algorithms for the segmentation and quantification of 3-D MRI scans" Freeborough et. al. CMPB 53 (1997) 15-25. More...

class	MIDASImageUpdateClearRegionProcessor
	Class to support undo/redo of a clear operation (set value to zero), within a given region. More...

class	MIDASImageUpdateCopyRegionProcessor
	Class to support undo/redo of a copy operation, within a given region. More...

class	MIDASImageUpdatePasteRegionProcessor
	Class to support undo/redo of a paste operation, within a given region, where we take non-zero pixels in the source image, and write them to the destination image. More...

class	MIDASImageUpdatePixelWiseSingleValueProcessor
	Class to support undo/redo of an operation that takes a list of pixels, and sets them all to a given value. More...

class	MIDASImageUpdateProcessor
	Class that takes a pointer to a destination image, and applies changes directly to it and enablng undo/redo. In practice, this may result in large memory overhead, so, if we are using this for undo/redo we should consider using a small undo/redo stack or small regions. More...

class	MIDASImageUpdateRegionProcessor
	Provides methods to do Undo/Redo within a specific Region. More...

class	MIDASMaskByRegionImageFilter
	Class, developed for MIDAS migration, that outputs an image the same size as the input, but you can specify a region, and that region is kept, and anything outside that region, set to a single background value. Used for axial cut-off. More...

class	MIDASMeanIntensityWithinARegionFilter
	calculate the mean intensity within a binary mask (region). More...

class	MIDASMorphologicalSegmentorLargestConnectedComponentImageFilter
	Largest connected component filter. More...

class	MIDASRegionGrowingImageFilter
	Implements region growing limited by contours. More...

class	MIDASRegionOfInterestCalculator
	Class to calculate regions within an image according to MIDAS specifications, where for example we need to know (for Wipe+, Wipe- and PropUp and PropDown) that "plus" or "up" means anterior, right or superior and "minus" or "down" means posterior, left or inferior. More...

class	MIDASRetainMarksNoThresholdingProcessor
	Class to support the MIDAS Retain marks operation, specifically when thresholding is off, which means it copies from a given slice in the source image, to a given slice in the destination image. More...

class	MIDASRethresholdingFilter
	Performs the re-thresholding, described in step 5 of "Interactive Algorithms for the segmentation and quantification of 3-D MRI scans" Freeborough et. al. CMPB 53 (1997) 15-25. More...

class	MIDASUpSamplingFilter
	Performs the up sampling described in step 5 of "Interactive Algorithms for the segmentation and quantification of 3-D MRI scans" Freeborough et. al. CMPB 53 (1997) 15-25. More...

class	MIImageToImageMetric
	Implements Mutual Information of a histogram for a similarity measure. More...

class	MinimumCurvatureImageFilter
	Calculates minimum curvature, assuming that the two inputs represent Gaussian Curvature on input 0, and Mean Curvature on input 1. More...

class	MinimumImageFunction
	Calculate the minimum value in the neighborhood of a pixel. More...

class	MinimumInterpolateImageFunction
	Minimum interpolation of an image at specified positions. More...

class	MSDImageToImageMetric
	Implements Mean of Squared Difference similarity measure. More...

class	MultipleDilateImageFilter

class	MultipleErodeImageFilter

class	MultiResolutionBlockMatchingMethod
	Extends MultiResolutionImageRegistrationWrapper to provide setting up block matching method at each resolution level, which currently just means setting the percentage of points to keep. More...

class	MultiResolutionDeformableImageRegistrationMethod
	Extends MultiResolutionImageRegistrationWrapper to provide various common methods for FFD and Fluid, such as saving Jacobian images. More...

class	MultiResolutionImageRegistrationWrapper
	UCL Base class for multi-resolution image registration methods. More...

class	MultiScaleVesselnessFilter
	Gives tha maximum filter response using Sato's filter (Sato et al, MedIA 1998) per voxel, given a range of scales. More...

class	MultiStageImageRegistrationMethod
	Base Class specifically for doing multiple stage registrations. More...

class	NCCImageToImageMetric
	Implements Normalized Cross Correlation similarity measure. More...

class	NegateImageFilter
	Computes the -1.0 * x pixel-wise. More...

class	NiftiImageIO3201
	Class that defines how to read Nifti file format. Nifti IMAGE FILE FORMAT - As much information as I can determine from sourceforge.net/projects/Niftilib. More...

class	NifTKImageIOFactory
	Creates instances of NifTK specific image IO objects. More...

class	NLMFilter

class	NMIImageToImageMetric
	Implements Normalised Mutual Information of a histogram for a similarity measure. More...

class	NMILocalHistogramDerivativeForceFilter

class	NondirectionalDerivativeOperator
	Construct a multi-directional n-th derivative operator. More...

class	NormaliseVectorFilter
	This class takes a vector field and normalises each vector to unit length. More...

class	OrderedTraversalStreamlinesFilter
	Calculates length between two boundaries, solving PDE by ordered traversal. More...

class	OrthogonalContourExtractor2DImageFilter
	Computes a list of PolyLineParametricPath objects from the contours in a 2D image. More...

class	ParzenWindowNMIDerivativeForceGenerator
	This class takes as input 2 input images, and outputs the registration force using Marc's Parzen window approach. (reference to follow). More...

class	Patch

class	PCADeformationModelTransform
	PCA deformation model transformation. More...

class	PerspectiveProjectionTransform
	PerspectiveProjectionTransform of a vector space (e.g. space coordinates) More...

class	PIUImageToImageMetric
	Implements Roger Woods PIU image similarity measure. More...

class	PointOnBoundary

class	PointSetToPointSetSingleValuedMetric
	Computes similarity between two point sets, but sums it up to a single value. More...

class	ProjectionGeometry
	Abstract class to calculate the geometry of a CT or tomo machine. More...

class	Ray
	Class to project a ray through a 3D volume. More...

class	ReconstructionAndRegistrationUpdateCommand
	Override this class to redefine DoExecute(). More...

class	ReconstructionUpdateCommand
	Override this class to redefine DoExecute(). More...

class	RegionalMammographicDensity

class	RegionGrowSurfacePoints
	Label pixels that are connected to a seed and lie within a range of values. More...

class	RegistrationBasedCorticalThicknessFilter

class	RegistrationBasedCTEFilter

class	RegistrationForceFilter
	This class takes as input 2 input images, and outputs the registration force. More...

class	RelaxStreamlinesFilter
	Calculates length between two boundaries, solving PDE by iterative relaxation. More...

class	ResampleImage
	Up/Down samples an image in the axial direction to reduce anistoropy. More...

class	RescaleImageUsingHistogramPercentilesFilter
	Filter to rescale an image, with the input limits being specified as percentiles of the input image histogram. More...

class	RigidPCADeformationModelTransform
	Rigid-body + PCA deformation model transformation. More...

class	RigidPlusScaleImageRegistrationMethod
	Class specifically for doing Rigid plus Scale registration. More...

class	RIUImageToImageMetric
	Implements Roger Woods Ratio Image Uniformity, but beware, its non-symetrical, as the base class doesn't compute it both ways round. So, we are only using a fixedMask, not a movingMask. More...

class	RoundImageFilter

class	SADImageToImageMetric
	Implements Sums of Absolute Differences similarity measure. More...

class	SampleImageFilter
	Filter to sub- or super-sample an image by a certain factor and apply the appropriate blurring (equivalent to voxel averaging for integer subsampling factors) when subsampling. More...

class	ScalarImageToNormalizedGradientVectorImageFilter
	This class takes scalar image as input, and outputs a vector field of image gradient. More...

class	ScaleVectorFieldFilter
	This class takes two inputs, the first is a vector field, such as the output from a registration force generator. The second is another vector field, such as the gradient of an image. The images must have the same size, and same vector dimensionality (enforced via template parameters). The output is the first field, scaled by the second. If ScaleByComponents is true, the vectors are simply multiplied componentwise. If ScaleByComponents is false, the vectors are simply multiplied by the individual magnitude of the second vector field. More...

class	SetBoundaryVoxelsToValueFilter
	Image filter class to set all voxels which are on the boundary of the image to a user specified value (or zero by default). More...

class	SetGreyBoundaryToWhiteOrCSFFilter
	Assumes input is GM, WM, CSF labelled image, where the GM is exaclty 1 voxel wide, we then set this GM voxel to WM or CSF depending on thickness, and the immediate neighbourhood. More...

class	SetOutputVectorToCurrentPositionFilter
	This class takes a vector image as input, and outputs a vector image, where the vector data value at each voxel is equal to the millimetre or voxel position of that voxel. More...

class	ShapeBasedAveragingImageFilter
	Combines several segmentations/shapes into an average shape according to the Shaped-Based Averaging, Rohlfing and Maurer, TMI, Jan 2007. More...

class	SiemensMammomat_TomosynthesisGeometry
	Class to calculate the geometry of a GE tomosynthesis machine. More...

class	SimilarityMeasure
	Abstract base class, implementing TemplateMethod [2] for similarity measures. More...

class	SimpleKMeansClusteringImageFilter

class	SimulateMammogramFromMRI
	Class to project a 3D image into 2D. More...

class	SimultaneousReconAndRegnUpdateCommand
	Override this class to redefine DoExecute(). More...

class	SimultaneousReconstructionAndRegistrationMethod
	Base class for Image Reconstruction Methods. More...

class	SimultaneousReconstructionRegistrationMetric
	Class to compute the difference between a reconstruction estimate and the target set of 2D projection images. More...

class	SimultaneousUnconstrainedMatrixReconRegnMethod
	Base class for Image Reconstruction Methods. More...

class	SimultaneousUnconstrainedMatrixReconRegnMetric
	Class to compute the difference between a reconstruction estimate and the target set of 2D projection images. More...

class	SingleDerivativeTermInfo
	Information about a single derivative term (derivative order and the multiplicative term). More...

class	SingleResolutionImageRegistrationBuilder
	Base class for NifTK Image Registration Builders. More...

class	SingleResolutionImageRegistrationMethod
	Base class for NifTK Image Registration Methods. More...

class	SliceBySliceImageFilter
	Apply a filter or a pipeline slice by slice on an image. More...

class	SmoothVectorFieldFilter
	Abstract base class that takes a vector field as input and smoothes it. More...

class	SquaredFunctionImageToImageMetric
	Dummy similarity measure, to enable testing of optimizers. More...

class	SSDImageToImageMetric
	Implements Sums of Squared Difference similarity measure. More...

class	SSDRegistrationForceFilter
	This class takes as input 2 input images, and outputs the registration force. More...

class	SubsampleImageFilter
	Filter to subsample an image by a certain factor and apply the appropriate blurring (equivalent to voxel averaging for integer subsampling factors). More...

class	Subtract2DImageFromVolumeSliceFilter
	Implements an operator for pixel-wise subtraction of a slice of a 3D volume from a 2D image. More...

class	SumLogJacobianDeterminantConstraint
	Calculated the sum of the log of the jacobian determinant of a BSpline transform, to be used as regulariser in FFD. More...

class	SumOfSquaredDifferencePointMetric
	Computes sum of the squared distance between two point sets. More...

class	SuperEllipseFitMetric

class	SwitchableAffineTransform
	Matrix transformations, with switchable Degrees Of Freedom. More...

class	ThinPlateSplineScatteredDataPointSetToImageFilter
	Image filter which provides a thin plate spline mask approximation to a set of landmarks. More...

class	ThresholdImageWithRespectToPlane
	Image filter class to set all voxels on one side of plane to a uer specified value (or zero by default). More...

class	Transform2D3D
	Transform2D3D of a vector space (e.g. space coordinates) More...

class	TranslateRotateScaleImageRegistrationMethod
	Class specifically for doing Translate, Rotate, Scale registration. More...

class	TranslationPCADeformationModelTransform
	Translation + PCA deformation model transformation. More...

class	TranslationThenRotationImageRegistrationMethod
	Class specifically for doing registration that alternately solves the translation components, then the rotation components. More...

class	TwinThresholdBoundaryFilter

class	UCLBaseTransform
	Our base transform class. Cant think of a better name. More...

class	UCLBSplineTransform
	Deformable transform using a BSpline representation. More...

class	UCLLabelVotingImageFilter

class	UCLMultiResolutionPyramidImageFilter
	Framework for creating images in a multi-resolution pyramid. More...

class	UCLN4BiasFieldCorrectionFilter
	N4 bias field correction algorithm contributed to ITK by Nicholas J. Tustison and James C. Gee. program runs the ITK N4BiasFieldCorrectionImageFilter on an image to correct nonuniformity commonly associated with MR images. The algorithm assumes a simple parametric model (Gaussian) for the bias field and does not require tissue class segmentation. References: J.G. Sled, A.P. Zijdenbos and A.C. Evans. "A Nonparametric Method for Automatic Correction of Intensity Nonuniformity in Data" IEEE Transactions on Medical Imaging, Vol 17, No 1. Feb. More...

class	UCLPowellOptimizer

class	UCLRecursiveMultiResolutionPyramidImageFilter
	Creates a multi-resolution pyramid using a recursive implementation. More...

class	UCLRegularStepGradientDescentOptimizer

class	UCLRegularStepOptimizer
	Implement a Regular Step Size optimizer. More...

class	UCLSimplexOptimizer
	Subclass itkAmoebaOptimizer to fix bug in SetCostFunction. More...

struct	uINRFileWrapper

class	UltrasoundPinCalibrationCostFunction
	Minimises the RMS error around a stationary invariant point. More...

class	VectorPhiPlusDeltaTTimesVFilter
	This class basically takes two vector images as input (Phi and V) and calculates Phi + (dt * V). More...

class	VectorVPlusLambdaUImageFilter
	This class takes two vector images as input (V and U), and calculates V + (lambda * U). More...

class	VelocityFieldMultiResolutionMethod
	Extends MultiResolutionDeformableImageRegistrationMethod to sort out interpolating the deformation fluid in between resolution levels. More...

class	VideoHandEyeCalibrationCostFunction
	Minimises the RMS error around a stationary invariant point. More...

class	VnlIterationUpdateCommand
	Simply prints out the registration params, so we can track registration. More...

Typedefs
typedef vnl_matrix< double >	MatrixType

typedef vnl_vector< double >	VectorType

typedef struct itk::LSGradientsL0	LSGradientsL0

typedef struct itk::LSGradientsL1	LSGradientsL1

typedef struct itk::LSGradientsL2	LSGradientsL2

Enumerations
enum	IsocentricConeBeamRotationTypeEnum { ISOCENTRIC_CONE_BEAM_ROTATION_IN_X, ISOCENTRIC_CONE_BEAM_ROTATION_IN_Y, ISOCENTRIC_CONE_BEAM_ROTATION_IN_Z }

enum	InterpolationTypeEnum { UNKNOWN_INTERP, NEAREST, LINEAR, BSPLINE, SINC }

enum	MetricTypeEnum { UNKNOWN_METRIC, SSD, MSD, SAD, NCC, RIU, PIU, JE, MI, NMI, CR }

enum	TransformTypeEnum { UNKNOWN_TRANSFORM, TRANSLATION, RIGID, RIGID_SCALE, AFFINE }

enum	OptimizerTypeEnum { UNKNOWN_OPTIMIZER, SIMPLEX, GRADIENT_DESCENT, REGSTEP_GRADIENT_DESCENT, CONJUGATE_GRADIENT_DESCENT, POWELL, SIMPLE_REGSTEP, UCLPOWELL }

enum	SingleResRegistrationMethodTypeEnum { UNKNOWN_METHOD, SINGLE_RES_MASKED, SINGLE_RES_TRANS_ROTATE, SINGLE_RES_TRANS_ROTATE_SCALE, SINGLE_RES_RIGID_SCALE, SINGLE_RES_BLOCK_MATCH }

enum	MultiResRegistrationMethodTypeEnum { UNKNOWN_MULTI, MULTI_RES_NORMAL }

enum	Orientation { ORIENTATION_AXIAL = 0, ORIENTATION_SAGITTAL = 1, ORIENTATION_CORONAL = 2, ORIENTATION_UNKNOWN = -1 }

enum	DataTypeKeyValues { ANALYZE_DT_UNKNOWN =0, ANALYZE_DT_BINARY =1, ANALYZE_DT_UNSIGNED_CHAR =2, ANALYZE_DT_SIGNED_SHORT =4, ANALYZE_DT_SIGNED_INT =8, ANALYZE_DT_FLOAT =16, ANALYZE_DT_COMPLEX =32, ANALYZE_DT_DOUBLE =64, ANALYZE_DT_RGB =128, ANALYZE_DT_ALL =255, SPMANALYZE_DT_UNSIGNED_SHORT =132, SPMANALYZE_DT_UNSIGNED_INT =136 }

enum	DataTypeIndex { ANALYZE_DT_INDEX_UNKNOWN =0, ANALYZE_DT_INDEX_BINARY =1, ANALYZE_DT_INDEX_UNSIGNED_CHAR =2, ANALYZE_DT_INDEX_SIGNED_SHORT =3, ANALYZE_DT_INDEX_SIGNED_INT =4, ANALYZE_DT_INDEX_FLOAT =5, ANALYZE_DT_INDEX_COMPLEX =6, ANALYZE_DT_INDEX_DOUBLE =7, ANALYZE_DT_INDEX_RGB =8, ANALYZE_DT_INDEX_ALL =9, SPMANALYZE_DT_INDEX_UNSIGNED_SHORT =10, SPMANALYZE_DT_INDEX_UNSIGNED_INT =11 }

Functions
template<class TInputImage1 , class TInputImage2 >
ITK_EXPORT bool	IsSameRegionSize (typename TInputImage1::Pointer image1, typename TInputImage2::Pointer image2)

template<class TInputImage1 , class TInputImage2 >
ITK_EXPORT bool	IsSameVoxelSize (typename TInputImage1::Pointer image1, typename TInputImage2::Pointer image2)

void	SetTag (itk::MetaDataDictionary &dictionary, std::string tagID, std::string newTagValue)

void	ModifyTag (itk::MetaDataDictionary &dictionary, std::string tagID, std::string newTagValue)

template<typename TImage >
void	CreatePositiveMammogram (typename TImage::Pointer &image, itk::MetaDataDictionary &dictionary, bool flgInvert=false)
	Create a positive version of a DICOM mammogram. More...

template<typename TImage >
bool	ConvertMammogramFromRawToPresentation (typename TImage::Pointer &image, itk::MetaDataDictionary &dictionary)
	Convert a raw DICOM mammogram to a presentation version by log inverting it. More...

int	SuperEllipseFit (SuperEllipseFitMetric::DataType &data, bool useGradient=true, double fTolerance=1e-2, double gTolerance=1e-2, double xTolerance=1e-5, double epsilonFunction=1e-9, int maxIterations=200)

std::string	GetExceptionString (itk::ExceptionObject &err)

void	InitialiseImageIO (std::string filename, ImageIOBase::Pointer &imageIO)

int	PeekAtImageDimension (std::string filename)

ImageIOBase::IOComponentType	PeekAtComponentType (std::string filename)

ImageIOBase::IOPixelType	PeekAtPixelType (std::string filename)

int	PeekAtImageDimensionFromSizeInVoxels (std::string filename)

NIFTKITK_WINEXPORT ITK_EXPORT std::string	GetExceptionString (ExceptionObject &err)

std::string	ConvertSpatialOrientationToString (const SpatialOrientation::ValidCoordinateOrientationFlags &code)

SpatialOrientation::ValidCoordinateOrientationFlags	ConvertStringToSpatialOrientation (std::string code)

std::string	ModifyFilenameSuffix (std::string filename, std::string suffix)

std::string	ExtractSuffix (std::string filename)

NIFTKITK_WINEXPORT ITK_EXPORT std::string	ExtractSuffix (std::string filename, std::string suffix)

template<typename TImage >
bool	IsImageBinary (typename TImage::Pointer image)
	Return whether an image is binary or not. More...

template<typename TImage >
bool	IsImageBinary (typename TImage::Pointer image, typename TImage::PixelType &intensity1, typename TImage::PixelType &intensity2)
	Return whether an image is binary or not. More...

template<typename TInputImage >
bool	ReadImageFromFile (const char fileInput, const char description, typename TInputImage::Pointer &image)
	Read an ITK image to a file and print a message. More...

template<typename TInputImage >
bool	ReadImageFromFile (const char fileInput, const char description, typename TInputImage::ConstPointer &image)
	Read an ITK image to a file and print a message. More...

template<typename TInputImage >
bool	ReadImageFromFile (std::string fileInput, typename TInputImage::Pointer &image, std::string *description=0)
	Read an ITK image to a file and print a message. More...

template<typename TInputImage >
bool	ReadImageFromFile (std::string fileInput, typename TInputImage::ConstPointer &image, std::string *description=0)
	Read an ITK image to a file and print a message. More...

template<typename TOutputImage >
void	WriteImageToFile (const char fileOutput, const char description, typename TOutputImage::Pointer image)
	Write an ITK image to a file and print a message. More...

template<typename TOutputImage >
void	WriteImageToFile (const char fileOutput, const char description, typename TOutputImage::ConstPointer image)
	Write an ITK image to a file and print a message. More...

template<typename TOutputImage >
void	WriteImageToFile (std::string fileOutput, typename TOutputImage::Pointer image, std::string *description=0)
	Write an ITK image to a file and print a message. More...

template<typename TOutputImage >
void	WriteImageToFile (std::string fileOutput, typename TOutputImage::ConstPointer image, std::string *description=0)
	Write an ITK image to a file and print a message. More...

template<class TPixel , unsigned int VDimension, class TContainer >
std::ostream &	operator<< (std::ostream &os, const BSplineOperator< TPixel, VDimension, TContainer > &bspline)

int	GetAxisFromOrientationString (const std::string &orientationString, const itk::Orientation &orientation)
	Works out the axis of interest from the orientationString (normally derived from direction cosines), and the requested orientation. More...

int	GetUpDirection (const std::string &orientationString, const int &axisOfInterest)
	Returns either +1, or -1 to indicate in which direction you should change the slice number to go "up". More...

std::string	GetMajorAxisFromPatientRelativeDirectionCosine (double x, double y, double z)
	Returns the orientation string based on the the major axis. More...

template<class TImage >
NIFTKITK_WINEXPORT ITK_EXPORT void	LimitMaskByRegion (TImage *mask, typename TImage::RegionType &region, typename TImage::PixelType outValue)
	Used to mask an image within a region. More...

template<typename TPixel , unsigned int VImageDimension>
NIFTKITK_WINEXPORT ITK_EXPORT void	GetVolumeFromITKImage (const itk::Image< TPixel, VImageDimension > *itkImage, double &imageVolume)
	Returns the volume (number of voxels * voxel volume), of the number of voxels above zero. More...

template<unsigned int VImageDimension>
NIFTKITK_WINEXPORT ITK_EXPORT void	GetOrientationString (const itk::Matrix< double, VImageDimension, VImageDimension > &directionMatrix, std::string &orientationString)
	Gets the orientation string from direction cosines, but only works for 3D. More...

template<typename TPixel , unsigned int VImageDimension>
NIFTKITK_WINEXPORT ITK_EXPORT void	GetOrientationStringFromITKImage (const itk::Image< TPixel, VImageDimension > *itkImage, std::string &orientationString)
	Gets the orientation string for a 3D image. More...

template<typename TPixel , unsigned int VImageDimension>
NIFTKITK_WINEXPORT ITK_EXPORT void	GetAxisFromITKImage (const itk::Image< TPixel, VImageDimension > *itkImage, const itk::Orientation orientation, int &outputAxis)
	Returns the axis [0=x, 1=y, 2=z, -1=UNKNOWN] corresponding to the specified orientation for the given image. More...

template<typename TPixel , unsigned int VImageDimension>
NIFTKITK_WINEXPORT ITK_EXPORT void	GetUpDirectionFromITKImage (const itk::Image< TPixel, VImageDimension > *itkImage, const itk::Orientation orientation, int &upDirection)
	Returns +1 or -1 (or 0 if unknown) to indicate which way from the centre of the volume is considered "Up", which means anterior in coronal view, superior in axial view and right in sagittal view. More...

template<typename TPixel , unsigned int VImageDimension>
NIFTKITK_WINEXPORT ITK_EXPORT void	GetOrientationLabelFromITKImage (const itk::Image< TPixel, VImageDimension > *itkImage, std::string &label)
	Get Image Orientation Label (Axial/Coronal/Sagittal) based on Direction Cosines of the input image. More...

static std::string	GetExtension (const std::string &filename)

static std::string	GetRootName (const std::string &filename)

static std::string	GetHeaderFileName (const std::string &filename)

static std::string	GetImageFileName (const std::string &filename)

static std::string	GetExtension (const std::string &filename)

static std::string	GetRootName (const std::string &filename)

static std::string	GetHeaderFileName (const std::string &filename)

template<class TBuffer >
void	RescaleFunction (TBuffer *buffer, double slope, double intercept, vcl_size_t size)

template<typename PixelType >
void	CastCopy (float to, void from, vcl_size_t pixelcount)

Variables
const char	DataTypes [12][10]

const short int	DataTypeSizes [12] = { 0, 1, 8, 16, 32, 32, 64, 64, 24, 0, 16, 32 }

const short int	DataTypeKey [12]

Detailed Description

The specification for this file format is taken from the web site http://www.mayo.edu/bir/PDF/ANALYZE75.pdf.

Author: Hans J. Johnson The University of Iowa 2002

Typedef Documentation

typedef struct itk::LSGradientsL0 itk::LSGradientsL0

typedef struct itk::LSGradientsL1 itk::LSGradientsL1

typedef struct itk::LSGradientsL2 itk::LSGradientsL2

typedef vnl_matrix<double> itk::MatrixType

typedef vnl_vector<double> itk::VectorType

Enumeration Type Documentation

enum itk::DataTypeIndex

The index into the DataTypes array for each type.

Enumerator
ANALYZE_DT_INDEX_UNKNOWN
ANALYZE_DT_INDEX_BINARY
ANALYZE_DT_INDEX_UNSIGNED_CHAR
ANALYZE_DT_INDEX_SIGNED_SHORT
ANALYZE_DT_INDEX_SIGNED_INT
ANALYZE_DT_INDEX_FLOAT
ANALYZE_DT_INDEX_COMPLEX
ANALYZE_DT_INDEX_DOUBLE
ANALYZE_DT_INDEX_RGB
ANALYZE_DT_INDEX_ALL
SPMANALYZE_DT_INDEX_UNSIGNED_SHORT
SPMANALYZE_DT_INDEX_UNSIGNED_INT

enum itk::DataTypeKeyValues

Acceptable values for hdr.dime.datatype

Enumerator
ANALYZE_DT_UNKNOWN	Deontes that the data type is unknon
ANALYZE_DT_BINARY	Deontes that the data type is binary
ANALYZE_DT_UNSIGNED_CHAR	Deontes that the data type is unsigned char
ANALYZE_DT_SIGNED_SHORT	Deontes that the data type is signed short
ANALYZE_DT_SIGNED_INT	Deontes that the data type is signed int
ANALYZE_DT_FLOAT	Deontes that the data type is single precision floating point
ANALYZE_DT_COMPLEX	Deontes that the data type is pairs of single precision floating point numbers
ANALYZE_DT_DOUBLE	Deontes that the data type is double precision floating point
ANALYZE_DT_RGB	Deontes that the data type is triples of unsigned char
ANALYZE_DT_ALL	Deontes that the data type is unknon
SPMANALYZE_DT_UNSIGNED_SHORT	Deontes that the data type is unsigned short in SPM analyze extensions
SPMANALYZE_DT_UNSIGNED_INT	Deontes that the data type is unsigned int in SPM analyze extensions

enum itk::InterpolationTypeEnum

Enumerator
UNKNOWN_INTERP
NEAREST
LINEAR
BSPLINE
SINC

enum itk::IsocentricConeBeamRotationTypeEnum

Enumerator
ISOCENTRIC_CONE_BEAM_ROTATION_IN_X
ISOCENTRIC_CONE_BEAM_ROTATION_IN_Y
ISOCENTRIC_CONE_BEAM_ROTATION_IN_Z

enum itk::MetricTypeEnum

Enumerator
UNKNOWN_METRIC
SSD
MSD
SAD
NCC
RIU
PIU
JE
MI
NMI
CR

enum itk::MultiResRegistrationMethodTypeEnum

Enumerator
UNKNOWN_MULTI
MULTI_RES_NORMAL

enum itk::OptimizerTypeEnum

Enumerator
UNKNOWN_OPTIMIZER
SIMPLEX
GRADIENT_DESCENT
REGSTEP_GRADIENT_DESCENT
CONJUGATE_GRADIENT_DESCENT
POWELL
SIMPLE_REGSTEP
UCLPOWELL

enum itk::Orientation

Enum to define the concept of orientation directions.

Enumerator
ORIENTATION_AXIAL
ORIENTATION_SAGITTAL
ORIENTATION_CORONAL
ORIENTATION_UNKNOWN

enum itk::SingleResRegistrationMethodTypeEnum

Enumerator
UNKNOWN_METHOD
SINGLE_RES_MASKED
SINGLE_RES_TRANS_ROTATE
SINGLE_RES_TRANS_ROTATE_SCALE
SINGLE_RES_RIGID_SCALE
SINGLE_RES_BLOCK_MATCH

enum itk::TransformTypeEnum

Enumerator
UNKNOWN_TRANSFORM
TRANSLATION
RIGID
RIGID_SCALE
AFFINE

Function Documentation

template<typename PixelType >

void itk::CastCopy	(	float *	to,
		void *	from,
		vcl_size_t	pixelcount
	)

template<typename TImage >

bool itk::ConvertMammogramFromRawToPresentation	(	typename TImage::Pointer &	image,
		itk::MetaDataDictionary &	dictionary
	)

Convert a raw DICOM mammogram to a presentation version by log inverting it.

NIFTKITK_WINEXPORT ITK_EXPORT std::string itk::ConvertSpatialOrientationToString ( const SpatialOrientation::ValidCoordinateOrientationFlags & code )

Converts a SpatialOrientation code into a string. eg. ITK_COORDINATE_ORIENTATION_RAS to RAS.

NIFTKITK_WINEXPORT ITK_EXPORT SpatialOrientation::ValidCoordinateOrientationFlags itk::ConvertStringToSpatialOrientation ( std::string code )

Converts a code (3 letters, uppercase, made from L/R, I/S, A/P), into a ValidCoordinateOrientationFlags.

template<typename TImage >

void itk::CreatePositiveMammogram	(	typename TImage::Pointer &	image,
		itk::MetaDataDictionary &	dictionary,
		bool	flgInvert = `false`
	)

Create a positive version of a DICOM mammogram.

NIFTKITK_WINEXPORT ITK_EXPORT std::string itk::ExtractSuffix	(	std::string	filename,
		std::string	suffix
	)

Extract and return the suffix (taking into account .Z or .gz)

std::string itk::ExtractSuffix ( std::string filename )

template<typename TPixel , unsigned int VImageDimension>

NIFTKITK_WINEXPORT ITK_EXPORT void itk::GetAxisFromITKImage	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		const itk::Orientation	orientation,
		int &	outputAxis
	)

Returns the axis [0=x, 1=y, 2=z, -1=UNKNOWN] corresponding to the specified orientation for the given image.

NIFTKITK_WINEXPORT ITK_EXPORT int itk::GetAxisFromOrientationString	(	const std::string &	orientationString,
		const itk::Orientation &	orientation
	)

Works out the axis of interest from the orientationString (normally derived from direction cosines), and the requested orientation.

std::string itk::GetExceptionString ( itk::ExceptionObject & err )

NIFTKITK_WINEXPORT ITK_EXPORT std::string itk::GetExceptionString ( ExceptionObject & err )

Prints out a reasonable message from an exception, so we can log it, but ideally, you should probably rethrow it aswell.

Parameters

typename itk::ExceptionObject err the exception

Returns: std::string a formatted exception string

static std::string itk::GetExtension ( const std::string & filename )

static

This should be declared public in base class, but unfortunately isn't, so it's a cut and paste.

static std::string itk::GetExtension ( const std::string & filename )

static

static std::string itk::GetHeaderFileName ( const std::string & filename )

static

This should be declared public in base class, but unfortunately isn't, so it's a cut and paste.

static std::string itk::GetHeaderFileName ( const std::string & filename )

static

static std::string itk::GetImageFileName ( const std::string & filename )

static

NIFTKITK_WINEXPORT ITK_EXPORT std::string itk::GetMajorAxisFromPatientRelativeDirectionCosine	(	double	x,
		double	y,
		double	z
	)

Returns the orientation string based on the the major axis.

template<typename TPixel , unsigned int VImageDimension>

NIFTKITK_WINEXPORT ITK_EXPORT void itk::GetOrientationLabelFromITKImage	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		std::string &	label
	)

Get Image Orientation Label (Axial/Coronal/Sagittal) based on Direction Cosines of the input image.

template<unsigned int VImageDimension>

NIFTKITK_WINEXPORT ITK_EXPORT void itk::GetOrientationString	(	const itk::Matrix< double, VImageDimension, VImageDimension > &	directionMatrix,
		std::string &	orientationString
	)

Gets the orientation string from direction cosines, but only works for 3D.

template<typename TPixel , unsigned int VImageDimension>

NIFTKITK_WINEXPORT ITK_EXPORT void itk::GetOrientationStringFromITKImage	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		std::string &	orientationString
	)

Gets the orientation string for a 3D image.

static std::string itk::GetRootName ( const std::string & filename )

static

This should be declared public in base class, but unfortunately isn't, so it's a cut and paste.

static std::string itk::GetRootName ( const std::string & filename )

static

NIFTKITK_WINEXPORT ITK_EXPORT int itk::GetUpDirection	(	const std::string &	orientationString,
		const int &	axisOfInterest
	)

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

Parameters

orientationString	The orientation string such as "RAS", "LPI" etc.
axisOfInterest	Which axis are we looking at within the orientationString.

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

template<typename TPixel , unsigned int VImageDimension>

NIFTKITK_WINEXPORT ITK_EXPORT void itk::GetUpDirectionFromITKImage	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		const itk::Orientation	orientation,
		int &	upDirection
	)

Returns +1 or -1 (or 0 if unknown) to indicate which way from the centre of the volume is considered "Up", which means anterior in coronal view, superior in axial view and right in sagittal view.

template<typename TPixel , unsigned int VImageDimension>

NIFTKITK_WINEXPORT ITK_EXPORT void itk::GetVolumeFromITKImage	(	const itk::Image< TPixel, VImageDimension > *	itkImage,
		double &	imageVolume
	)

Returns the volume (number of voxels * voxel volume), of the number of voxels above zero.

NIFTKITK_WINEXPORT ITK_EXPORT void itk::InitialiseImageIO	(	std::string	filename,
		ImageIOBase::Pointer &	imageIO
	)

Helper method called by above.

template<typename TImage >

bool itk::IsImageBinary ( typename TImage::Pointer image )

Return whether an image is binary or not.

template<typename TImage >

bool itk::IsImageBinary	(	typename TImage::Pointer	image,
		typename TImage::PixelType &	intensity1,
		typename TImage::PixelType &	intensity2
	)

Return whether an image is binary or not.

template<class TInputImage1 , class TInputImage2 >

ITK_EXPORT bool itk::IsSameRegionSize	(	typename TInputImage1::Pointer	image1,
		typename TInputImage2::Pointer	image2
	)

Check if the two images have the same size.

Parameters

typename	TInputImage1::Pointer image1 The first image.
typename	TInputImage2::Pointer image2 The second image.

Returns: true if the two images have the same size, false if otherwise.

template<class TInputImage1 , class TInputImage2 >

ITK_EXPORT bool itk::IsSameVoxelSize	(	typename TInputImage1::Pointer	image1,
		typename TInputImage2::Pointer	image2
	)

Check if the two images have the same voxel sizes, within a relative error of 0.00005 in each dimension.

Parameters

typename	TInputImage1::Pointer image1 The first image.
typename	TInputImage2::Pointer image2 The second image.

Returns: true if the two images have the same voxel size, false if otherwise.

template<class TImage >

NIFTKITK_WINEXPORT ITK_EXPORT void itk::LimitMaskByRegion	(	TImage *	mask,
		typename TImage::RegionType &	region,
		typename TImage::PixelType	outValue
	)

Used to mask an image within a region.

Takes an input mask, and region, and iterates through the whole mask, checking that if a pixel is on (it's not the 'outValue'), it is within the specified region. If not, that pixel is set to the outValue. We assume, and don't check that the region is entirely within the mask.

NIFTKITK_WINEXPORT ITK_EXPORT std::string itk::ModifyFilenameSuffix	(	std::string	filename,
		std::string	suffix
	)

Modifies the suffix (taking into account .Z or .gz)

void itk::ModifyTag	(	itk::MetaDataDictionary &	dictionary,
		std::string	tagID,
		std::string	newTagValue
	)

template<class TPixel , unsigned int VDimension, class TContainer >

std::ostream& itk::operator<<	(	std::ostream &	os,
		const BSplineOperator< TPixel, VDimension, TContainer > &	bspline
	)

NIFTKITK_WINEXPORT ITK_EXPORT ImageIOBase::IOComponentType itk::PeekAtComponentType ( std::string filename )

Take a peek at an image to determine the component type (eg. float, short etc. )

Parameters

typename std::string filename the filename of the image

Returns: IOComponentType

Exceptions

typename itk::ExceptionObject if it fails for any reason.

NIFTKITK_WINEXPORT ITK_EXPORT int itk::PeekAtImageDimension ( std::string filename )

Take a peek at an image to determine the number of dimensions (eg. 2D or 3D).

Parameters

typename std::string filename the filename of the image

Returns: int the number of dimensions

Exceptions

typename itk::ExceptionObject if it fails for any reason.

NIFTKITK_WINEXPORT ITK_EXPORT int itk::PeekAtImageDimensionFromSizeInVoxels ( std::string filename )

Take a peek at an image to determine the dimension of an image based on the number of voxels (e.g. Nx,Ny,1 is a 2D image).

Parameters

typename std::string filename the filename of the image

Returns: SizeType

Exceptions

typename itk::ExceptionObject if it fails for any reason.

NIFTKITK_WINEXPORT ITK_EXPORT ImageIOBase::IOPixelType itk::PeekAtPixelType ( std::string filename )

Take a peek at an image to determine the pixel type (scalar, vector etc).

Parameters

typename std::string filename the filename of the image

Returns: IOPixelType

Exceptions

typename itk::ExceptionObject if it fails for any reason.

template<typename TInputImage >

bool itk::ReadImageFromFile	(	const char *	fileInput,
		const char *	description,
		typename TInputImage::Pointer &	image
	)

Read an ITK image to a file and print a message.

template<typename TInputImage >

bool itk::ReadImageFromFile	(	const char *	fileInput,
		const char *	description,
		typename TInputImage::ConstPointer &	image
	)

Read an ITK image to a file and print a message.

template<typename TInputImage >

bool itk::ReadImageFromFile	(	std::string	fileInput,
		typename TInputImage::Pointer &	image,
		std::string *	description = `0`
	)

Read an ITK image to a file and print a message.

template<typename TInputImage >

bool itk::ReadImageFromFile	(	std::string	fileInput,
		typename TInputImage::ConstPointer &	image,
		std::string *	description = `0`
	)

Read an ITK image to a file and print a message.

template<class TBuffer >

void itk::RescaleFunction	(	TBuffer *	buffer,
		double	slope,
		double	intercept,
		vcl_size_t	size
	)

void itk::SetTag	(	itk::MetaDataDictionary &	dictionary,
		std::string	tagID,
		std::string	newTagValue
	)

int itk::SuperEllipseFit	(	SuperEllipseFitMetric::DataType &	data,
		bool	useGradient = `true`,
		double	fTolerance = `1e-2`,
		double	gTolerance = `1e-2`,
		double	xTolerance = `1e-5`,
		double	epsilonFunction = `1e-9`,
		int	maxIterations = `200`
	)

template<typename TOutputImage >

void itk::WriteImageToFile	(	const char *	fileOutput,
		const char *	description,
		typename TOutputImage::Pointer	image
	)

Write an ITK image to a file and print a message.

template<typename TOutputImage >

void itk::WriteImageToFile	(	const char *	fileOutput,
		const char *	description,
		typename TOutputImage::ConstPointer	image
	)

Write an ITK image to a file and print a message.

template<typename TOutputImage >

void itk::WriteImageToFile	(	std::string	fileOutput,
		typename TOutputImage::Pointer	image,
		std::string *	description = `0`
	)

Write an ITK image to a file and print a message.

template<typename TOutputImage >

void itk::WriteImageToFile	(	std::string	fileOutput,
		typename TOutputImage::ConstPointer	image,
		std::string *	description = `0`
	)

Write an ITK image to a file and print a message.

Variable Documentation

const short int itk::DataTypeKey

Initial value:

=
  {
  ANALYZE_DT_UNKNOWN,
  ANALYZE_DT_BINARY,
  ANALYZE_DT_UNSIGNED_CHAR,
  ANALYZE_DT_SIGNED_SHORT,
  ANALYZE_DT_SIGNED_INT,
  ANALYZE_DT_FLOAT,
  ANALYZE_DT_COMPLEX,
  ANALYZE_DT_DOUBLE,
  ANALYZE_DT_RGB,
  ANALYZE_DT_ALL,
  SPMANALYZE_DT_UNSIGNED_SHORT,
  SPMANALYZE_DT_UNSIGNED_INT
  }

An array with Data type key sizes

0–>ANALYZE_DT_UNKNOWN
1–>ANALYZE_DT_BINARY
2–>ANALYZE_DT_UNSIGNED_CHAR
3–>ANALYZE_DT_SIGNED_SHORT
4–>ANALYZE_DT_SIGNED_INT
5–>ANALYZE_DT_FLOAT
6–>ANALYZE_DT_COMPLEX
7–>ANALYZE_DT_DOUBLE
8–>ANALYZE_DT_RGB
9–>ANALYZE_DT_ALL
10–>SPMANALYZE_DT_UNSIGNED_SHORT
11–>SPMANALYZE_DT_UNSIGNED_INT
See also
DataTypes

DataTypeSizes

DataTypeKey

const char itk::DataTypes

Initial value:

=
  {
  "UNKNOWN", "BINARY", "CHAR", "SHORT", "INT", "FLOAT",
  "COMPLEX", "DOUBLE", "RGB", "ALL", "USHORT", "UINT"
  }

An array of the Analyze v7.5 known DataTypes

0–>"UNKNOWN"
1–>"BINARY"
2–>"CHAR"
3–>"SHORT"
4–>"INT"
5–>"FLOAT"
6–>"COMPLEX"
7–>"DOUBLE"
8–>"RGB"
9–>"ALL"
10–>"USHORT"
11–>"UINT"
See also
DataTypes

DataTypeSizes

DataTypeKey

const short int itk::DataTypeSizes = { 0, 1, 8, 16, 32, 32, 64, 64, 24, 0, 16, 32 }

An array with the corresponding number of bits for each image type.

0–>0
1–>1
2–>8
3–>16
4–>32
5–>32
6–>64
7–>64
8–>24
9–>0
10–>16
11->32
See also
DataTypes

DataTypeSizes

DataTypeKey

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Detailed Description

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation