cmtkBase Library

This library provides classes for basic objects, such as volumes, transformations, vectors, functionals, and meta information. More...

Collaboration diagram for cmtkBase Library:

Classes
class	cmtk::ActiveDeformationModel< W >
	Active deformation model. More...
class	cmtk::ActiveShapeModel
	Class for a three-dimensional active shape model. More...
class	cmtk::AffineXform
	3D affine transformation. More...
class	cmtk::AffineXformUniformVolume
	Pre-compute transformation for grid locations in a uniform volume. More...
class	cmtk::AnatomicalOrientation
	Class with helper functions for handling anatomical image orientation. More...
class	cmtk::AnatomicalOrientationBase
	Base class for handling anatomical image orientation. More...
class	cmtk::BitVector
	Set of binary values. More...
class	cmtk::ControlPoint
	Class for control points in WarpXform and derived classes. More...
class	cmtk::ControlPointList
	List of several warp control points. More...
class	cmtk::CubicSpline
	Class computing cubic splines. More...
class	cmtk::DataGrid
	Grid topology of data arranged in a 3D lattice. More...
class	cmtk::DataGridFilter
	Filter operations for data on 3D grids. More...
class	cmtk::DataGridFilter::FilterThreadParameters
	Thread parameter for entropy evaluation. More...
class	cmtk::DataGridMorphologicalOperators
	Grid topology of data arranged in a 3D lattice. More...
class	cmtk::DataTypeTraits< TType >
	Data type traits. More...
class	cmtk::DataTypeTraits< float >
	Data type traits for single-precision floating point. More...
class	cmtk::DataTypeTraits< double >
	Data type traits for double-precision floating point. More...
class	cmtk::DataTypeTraits< byte >
	Data type traits for unsigned char (byte). More...
class	cmtk::DataTypeTraits< char >
	Data type traits for signed char. More...
class	cmtk::DataTypeTraits< signed short >
	Data type traits for signed short. More...
class	cmtk::DataTypeTraits< unsigned short >
	Data type traits for unsigned short. More...
class	cmtk::DataTypeTraits< int >
	Data type traits for unsigned short. More...
class	cmtk::DeformationField
	Class for pixel-wise deformation field. More...
class	cmtk::DirectionSet
	A set of directions in n-dimensional space. More...
class	cmtk::EigenSystemSymmetricMatrix3x3< TFloat >
	Compute the eigenvectors and eigenvalues of a symmetric 3x3 matrix. More...
class	cmtk::FilterMaskPixel< DIM >
	Filter mask pixel entry. More...
class	cmtk::FilterMask< DIM >
	Filter mask. More...
class	cmtk::FilterMask< DIM >::Gaussian
	Gaussian filter as an example of a concrete filter implementation. More...
class	cmtk::FilterVolume
	Class for filtering volume images. More...
class	cmtk::Functional
	Class defining a real-valued functional on a multi-dimensional domain. More...
class	cmtk::GeneralLinearModel
	Pixelwise linear modeling and t statistics of data. More...
class	cmtk::Histogram< T >
	Histogram of a distribution with bins of arbitrary types. More...
class	cmtk::HistogramBase
	Common (non-template) base class for all 1-D histograms. More...
class	cmtk::ImageInterpolator< TImageType, TInterpolationFunction >
	Class template for kernel-based volume interpolators. More...
class	cmtk::ImageTemplate< TPixelType >
	Uniform volume template. More...
class	cmtk::Intersection
	Utility Class for Intersection Computation. More...
class	cmtk::JointHistogram< T >
	Joint histogram of two distributions. More...
class	cmtk::JointHistogramBase
	Basic (non-template) 2-D histogram functions. More...
class	cmtk::Landmark
	Coordinates of an (anatomical) landmark. More...
class	cmtk::LandmarkList
	List of landmarks in 3-D. More...
class	cmtk::LogHistogram< T >
	Histogram of log intensities. More...
class	cmtk::MatchedLandmark
	Matched landmark (landmark with source and target location). More...
class	cmtk::MatchedLandmarkList
	List of matched landmarks in 3-D. More...
class	cmtk::MathUtil
	General-purpose mathematical functions and function templates. More...
class	cmtk::Matrix< TElement, NDim >
	Rekursive matrix template. More...
class	cmtk::Matrix< TElement, 1 >
class	cmtk::Matrix2D< T >
	Two-dimensional matrix template. More...
class	cmtk::Matrix3D< T >
	Three-dimensional matrix template. More...
class	cmtk::Matrix3x3< T >
	Homogeneous 3x3 transformation matrix. More...
class	cmtk::Matrix4x4< T >
	Homogeneous 4x4 transformation matrix. More...
class	cmtk::MetaInformationObject
	Meta-information associated with library objects. More...
class	cmtk::NumericTraits< TType >
	Base class for numeric traits definition for primitive data types.. More...
class	cmtk::NumericTraits< char >
class	cmtk::NumericTraits< unsigned char >
class	cmtk::NumericTraits< short >
class	cmtk::ParametricPlane
	Class for parameterized infinite planes. More...
class	cmtk::Polynomial< NDegree, TRealType >
	Generic class template for polynomials of arbitrary degrees. More...
class	cmtk::Polynomial< 0, TRealType >
	Generic class template for polynomials of degree 1. More...
class	cmtk::Polynomial< 1, TRealType >
	Generic class template for polynomials of degree 1. More...
class	cmtk::Polynomial< 2, TRealType >
	Generic class template for polynomials of degree 2. More...
class	cmtk::Polynomial< 3, TRealType >
	Generic class template for polynomials of degree 3. More...
class	cmtk::Polynomial< 4, TRealType >
	Generic class template for polynomials of degree 4. More...
class	cmtk::ProbeInfo
	Information on volume node data. More...
class	cmtk::QRDecomposition< TFloat >
	Compute the QRDecomposition of a matrix. More...
class	cmtk::ScalarImage
	Two-dimensional image with scalar pixel values. More...
class	cmtk::SegmentationLabel
	A label (class) in a segmentation. More...
class	cmtk::SplineWarpXform
	B-spline-based local deformation. More...
struct	cmtk::SplineWarpXform::JacobianConstraintThreadInfo
	Thread parameter block for volume resampling. More...
class	cmtk::SplineWarpXformUniformVolume
	Pre-compute transformation for grid locations in a uniform volume. More...
class	cmtk::SurfaceNormal
	Class that computes the surface normal. More...
class	cmtk::TemplateArray< T >
	Template for Variable-Typed Data Arrays. More...
class	cmtk::TransformChangeFromSpaceAffine
	Compute affine coordinate transformation in standard space from transformation in natrive reference and floating image coordinate spaces. More...
class	cmtk::TransformChangeToSpaceAffine
	Compute affine coordinate transformation between native spaces of reference and floating images. More...
class	cmtk::TransformedVolumeAxes
	Class that represents pre-transformed axes samples for 3D volumes. More...
class	cmtk::TypedArray
	Generic Variable-Typed Data Array. More...
class	cmtk::TypedArrayFunction
	Base class for lookup classes. More...
class	cmtk::TypedArrayFunctionHistogramEqualization
	Lookup class for histogram equalization. More...
class	cmtk::TypedArrayFunctionHistogramMatching
	Lookup class for histogram intensity matching. More...
class	cmtk::UniformDistanceMap< TDistanceDataType >
	Distance map on a uniform grid. More...
class	cmtk::UniformVolume
	Uniform volume. More...
class	cmtk::UniformVolumeFilter
	Filter operations for 3D uniform image data. More...
class	cmtk::UniformVolumeInterpolator< TInterpolationFunction >
	Class template for kernel-based volume interpolators. More...
class	cmtk::UniformVolumeInterpolatorBase
	Base class for kernel-based uniform volume. More...
class	cmtk::UniformVolumeInterpolatorPartialVolume
	Partial-volume interpolation class. More...
class	cmtk::UniformVolumePainter
	Class for painting in uniform volume objects. More...
class	cmtk::UnionFind< T >
	Class template for (relatively) efficient union-find algorithm. More...
class	cmtk::ValueSequence< T >
	Class for computing characteristic values of number sequences. More...
class	cmtk::Vector< T >
	Numerical vector class. More...
class	cmtk::Volume
	General 3D volume. More...
class	cmtk::VolumeClipping
	Utility class for volume clipping. More...
class	cmtk::VolumeGridToGridLookup
	Class for grid to grid lookup tables. More...
class	cmtk::WarpXform
	Common base class for free-form-deformation-based warps. More...
class	cmtk::Xform
	General 3D coordinate transformation. More...
class	cmtk::XformList
	A transformation list. More...
class	cmtk::XformListEntry
	An entry in a transformation sequence. More...
class	cmtk::XformUniformVolume
	Pre-compute transformation for grid locations in a uniform volume. More...
Namespaces
namespace	cmtk::Accumulators
	Helper classes that project a series of values into a single value.
namespace	cmtk::Interpolators
	Interpolation kernels to be used with UniformVolumeInterpolator.
namespace	cmtk
namespace	cmtk::MathUtil
namespace	cmtk::Types
	Define float type used for coordinates.
namespace	cmtk::Units
	Classes for type-safe values with physical units, and automatic conversions between them.
Defines
#define	TOL   1.0e-5
#define	CMTK_SCALARIMAGE_NOCLONEDATA   false
#define	CMTK_SCALARIMAGE_CLONEDATA   true
#define	CMTK_SCALARIMAGE_HORIZONTAL   true
#define	CMTK_SCALARIMAGE_VERTICAL   false
#define	CMTK_SCALARIMAGE_ABSOLUTE   true
#define	CMTK_SCALARIMAGE_SIGNED   false
#define	CMTK_ITEM_MAX   DBL_MAX
#define	CMTK_ITEM_MIN   DBL_MIN
#define	CMTK_ITEM_NAN   CMTK_DOUBLE_NAN
Typedefs
typedef ActiveDeformationModel < SplineWarpXform >	cmtk::SplineActiveDeformationModel
	Spline warp active deformation model.
typedef SmartPointer< Self >	cmtk::FilterMaskPixel::SmartPtr
	Smart pointer.
typedef std::vector < FilterMaskPixel< DIM > >	cmtk::FilterMask::Superclass
	Direct parent class.
typedef SmartPointer< Self >	cmtk::FilterMask::SmartPtr
	Smert pointer to this class.
typedef Matrix3x3 < Types::Coordinate >	cmtk::CoordinateMatrix3x3
	Define coordinate matrix.
typedef std::map< int, SegmentationLabel >	cmtk::SegmentationLabelMap
	Map from numerical IDs to labels.
typedef WarpXform	cmtk::SplineWarpXform::Superclass
	Parent class.
typedef SmartPointer< Self >	cmtk::SplineWarpXform::SmartPtr
	Smart pointer to SplineWarpXform.
typedef SmartConstPointer< Self >	cmtk::SplineWarpXform::SmartConstPtr
	Smart pointer to const SplineWarpXform.
typedef Vector< Types::Coordinate >	cmtk::CoordinateVector
	Shortcut definition.
typedef Vector< float >	cmtk::FloatVector
	Shortcut definition.
typedef FixedVector < 3, Types::Coordinate >	cmtk::Vector3D
	Convenience typedef: vectors in 3D coordinate space.
Enumerations
enum	{ cmtk::AXIS_X = 0, cmtk::AXIS_Y = 1, cmtk::AXIS_Z = 2 }
	Identifiers for coordinate axes. More...
enum	cmtk::DataClass { cmtk::DATACLASS_GREY, cmtk::DATACLASS_LABEL, cmtk::DATACLASS_UNKNOWN }
	Class of image data. More...
enum	cmtk::ScalarDataType {   cmtk::TYPE_BYTE = 0, cmtk::TYPE_CHAR = 1, cmtk::TYPE_SHORT = 2, cmtk::TYPE_USHORT = 3,   cmtk::TYPE_INT = 4, cmtk::TYPE_UINT = 5, cmtk::TYPE_FLOAT = 6, cmtk::TYPE_DOUBLE = 7,   cmtk::TYPE_NONE = -1 }
	Scalar data type identifiers. More...
Functions
void	cmtk::Accumulators::Avg::Reset ()
	Reset.
void	cmtk::Accumulators::Avg::AddValue (const TDataType &value)
	Add a value.
const TDataType	cmtk::Accumulators::Avg::GetResult () const
	Retrive accumulated result.
void	cmtk::Accumulators::Max::Reset ()
	Reset.
void	cmtk::Accumulators::Max::AddValue (const TDataType &value)
	Add a value.
const TDataType	cmtk::Accumulators::Max::GetResult () const
	Retrive accumulated result.
void	cmtk::Accumulators::Sum::Reset ()
	Reset.
void	cmtk::Accumulators::Sum::AddValue (const TDataType &value)
	Add a value.
const TDataType &	cmtk::Accumulators::Sum::GetResult () const
	Retrive accumulated result.
static Types::Coordinate	cmtk::CubicSpline::ApproxSpline1 (const Types::Coordinate t)
	Compute a value of the 1st approximating spline function.
static Types::Coordinate	cmtk::CubicSpline::ApproxSpline2 (const Types::Coordinate t)
	Compute a value of the 2nd approximating spline function.
static Types::Coordinate	cmtk::CubicSpline::ApproxSpline3 (const Types::Coordinate t)
	Compute a value of the 3rd approximating spline function.
static Types::Coordinate	cmtk::CubicSpline::ApproxSpline (const int k, const Types::Coordinate t)
	Compute the value of a given approximating spline function.
static Types::Coordinate	cmtk::CubicSpline::DerivApproxSpline0 (const Types::Coordinate t)
	Compute the derivative of the 0th approximating spline function.
static Types::Coordinate	cmtk::CubicSpline::DerivApproxSpline1 (const Types::Coordinate t)
	Compute derivative of the 1st approximating spline function.
static Types::Coordinate	cmtk::CubicSpline::DerivApproxSpline2 (const Types::Coordinate t)
	Compute derivative of the 2nd approximating spline function.
static Types::Coordinate	cmtk::CubicSpline::DerivApproxSpline3 (const Types::Coordinate t)
	Compute derivative of the 3rd approximating spline function.
static Types::Coordinate	cmtk::CubicSpline::DerivApproxSpline (const int k, const Types::Coordinate t)
	Compute the derivative of a given approximating spline function.
static Types::Coordinate	cmtk::CubicSpline::SecondDerivApproxSpline0 (const Types::Coordinate t)
	Compute the second derivative of the 0th approximating spline function.
static Types::Coordinate	cmtk::CubicSpline::SecondDerivApproxSpline1 (const Types::Coordinate t)
	Compute second derivative of the 1st approximating spline function.
static Types::Coordinate	cmtk::CubicSpline::SecondDerivApproxSpline2 (const Types::Coordinate t)
	Compute second derivative of the 2nd approximating spline function.
static Types::Coordinate	cmtk::CubicSpline::SecondDerivApproxSpline3 (const Types::Coordinate t)
	Compute second derivative of the 3rd approximating spline function.
static Types::Coordinate	cmtk::CubicSpline::SecondDerivApproxSpline (const int k, const Types::Coordinate t)
	Compute the second derivative of a given approximating spline function.
static Types::Coordinate	cmtk::CubicSpline::InterpSpline0 (const Types::Coordinate t)
	Compute a value of the 0th interpolating spline function.
static Types::Coordinate	cmtk::CubicSpline::InterpSpline1 (const Types::Coordinate t)
	Compute a value of the 1st interpolating spline function.
static Types::Coordinate	cmtk::CubicSpline::InterpSpline2 (const Types::Coordinate t)
	Compute a value of the 2nd interpolating spline function.
static Types::Coordinate	cmtk::CubicSpline::InterpSpline3 (const Types::Coordinate t)
	Compute a value of the 3rd interpolating spline function.
static Types::Coordinate	cmtk::CubicSpline::InterpSpline (const int k, const Types::Coordinate t)
	Compute the value of a given interpolating spline function.
static Types::Coordinate	cmtk::CubicSpline::DerivInterpSpline0 (const Types::Coordinate t)
	Compute derivative of the 0th interpolating spline function.
static Types::Coordinate	cmtk::CubicSpline::DerivInterpSpline1 (const Types::Coordinate t)
	Compute derivative of the 1st interpolating spline function.
static Types::Coordinate	cmtk::CubicSpline::DerivInterpSpline2 (const Types::Coordinate t)
	Compute derivative of the 2nd interpolating spline function.
static Types::Coordinate	cmtk::CubicSpline::DerivInterpSpline3 (const Types::Coordinate t)
	Compute derivative of the 3rd interpolating spline function.
static Types::Coordinate	cmtk::CubicSpline::DerivInterpSpline (const int k, const Types::Coordinate t)
	Compute derivative of a given interpolating spline function.
static Types::Coordinate	cmtk::CubicSpline::SecondDerivInterpSpline0 (const Types::Coordinate t)
	Compute second derivative of the 0th interpolating spline function.
static Types::Coordinate	cmtk::CubicSpline::SecondDerivInterpSpline1 (const Types::Coordinate t)
	Compute second derivative of the 1st interpolating spline function.
static Types::Coordinate	cmtk::CubicSpline::SecondDerivInterpSpline2 (const Types::Coordinate t)
	Compute second derivative of the 2nd interpolating spline function.
static Types::Coordinate	cmtk::CubicSpline::SecondDerivInterpSpline3 (const Types::Coordinate t)
	Compute second derivative of the 3rd interpolating spline function.
static Types::Coordinate	cmtk::CubicSpline::SecondDerivInterpSpline (const int k, const Types::Coordinate t)
	Compute second derivative of a given interpolating spline function.
	cmtk::DataGridFilter::DataGridFilter (DataGrid::SmartPtr dataGrid)
	Constructor: link to DataGrid object.
TypedArray::SmartPtr	cmtk::DataGridFilter::GetDataMedianFiltered (const int radius) const
	Return data after median-filtering with global filter radius (convenience function).
TypedArray::SmartPtr	cmtk::DataGridFilter::GetDataMedianFiltered (const int radiusX, const int radiusY, const int radiusZ) const
	Return data after median-filtering with per-dimension filter radius.
TypedArray::SmartPtr	cmtk::DataGridFilter::GetDataSobelFiltered () const
	Return data after median-filtering.
TypedArray::SmartPtr	cmtk::DataGridFilter::GetDataKernelFiltered (const std::vector< Types::DataItem > &filterX, const std::vector< Types::DataItem > &filterY, const std::vector< Types::DataItem > &filterZ) const
	Return after filtering with a separable kernel.
static void	cmtk::DataGridFilter::GetFilteredDataThreadX (void *args, const size_t taskIdx, const size_t taskCnt, const size_t threadIdx, const size_t)
	Thread function for separable filtering in x-direction.
static void	cmtk::DataGridFilter::GetFilteredDataThreadY (void *args, const size_t taskIdx, const size_t taskCnt, const size_t threadIdx, const size_t)
	Thread function for separable filtering in y-direction.
static void	cmtk::DataGridFilter::GetFilteredDataThreadZ (void *args, const size_t taskIdx, const size_t taskCnt, const size_t threadIdx, const size_t)
	Thread function for separable filtering in z-direction.
	cmtk::DataGridMorphologicalOperators::DataGridMorphologicalOperators (const DataGrid::SmartConstPtr &dataGrid)
	Constructor: link to DataGrid object.
bool	cmtk::DataGridMorphologicalOperators::EliminatePaddingVoting (const int iterations=1)
	Eliminating padding data by neighborhood voting.
TypedArray::SmartPtr	cmtk::DataGridMorphologicalOperators::GetBoundaryMap (const bool multiValued=false) const
	Return map of region boundaries.
TypedArray::SmartPtr	cmtk::DataGridMorphologicalOperators::GetEroded (const int iterations=1) const
	Get data after erosion operator.
TypedArray::SmartPtr	cmtk::DataGridMorphologicalOperators::GetDilated (const int iterations=1) const
	Get data after dilation operator.
TypedArray::SmartPtr	cmtk::DataGridMorphologicalOperators::GetBinaryConnectedComponents () const
	Get connected components of a binary image.
TypedArray::SmartPtr	cmtk::DataGridMorphologicalOperators::GetRegionsRenumberedBySize () const
	Get data with region labels renumbered by decreasing region size.
	cmtk::FilterMaskPixel::FilterMaskPixel ()
	Default constructor.
	cmtk::FilterMaskPixel::FilterMaskPixel (const FixedVector< DIM, int > &location, const int relativeIndex, const Types::DataItem coefficient)
	Explicit constructor.
template<class F >
	cmtk::FilterMask::FilterMask (const FixedVector< DIM, int > &dims, const FixedVector< DIM, Types::Coordinate > &deltas, const Types::Coordinate radius, F filter)
	Constructor.
Types::DataItem	cmtk::FilterMask::Gaussian::operator() (const FixedVector< DIM, Types::Coordinate > &relativePosition)
	Get filter coefficient at relative location from filter center.
void	cmtk::printBlock (Types::DataItem block[COUPE_BLOCK_SIZE])
template<class T >
Console &	cmtk::operator<< (Console &stream, const Matrix3x3< T > &m)
	Output object to console.
template<class T , class T2 >
FixedVector< 3, T2 > &	cmtk::operator*= (FixedVector< 3, T2 > &u, const Matrix4x4< T > &M)
	In-place multiplication with 3d vector operation (will implicitly be made homogeneous).
template<class T , class T2 >
FixedVector< 3, T2 >	cmtk::operator* (const FixedVector< 3, T2 > &u, const Matrix4x4< T > &M)
	Multiplication with 3d vector operation (will implicitly be made homogeneous).
template<class T >
Console &	cmtk::operator<< (Console &stream, const Matrix4x4< T > &m)
	Output object to console.
static Types::Coordinate	cmtk::Interpolators::NearestNeighbor::GetWeight (const int weight, const Types::Coordinate x)
	Get specific interpolation weight for relative coordinate.
ScalarImage *	cmtk::operator- (const ScalarImage &image0, const ScalarImage &image1)
void	cmtk::CreateSystemLabelColorMap (SegmentationLabelMap &map)
	Create system label map.
	cmtk::SplineWarpXform::SplineWarpXform ()
	Construct empty new warp.
	cmtk::SplineWarpXform::SplineWarpXform (const FixedVector< 3, Types::Coordinate > &domain, const Types::Coordinate delta, const AffineXform *initialXform=NULL, const bool exactDelta=false)
	Construct new warp from volume size and control grid density.
void	cmtk::SplineWarpXform::Init (const Self::SpaceVectorType &domain, const Types::Coordinate delta, const AffineXform *initialXform=NULL, const bool exactDelta=false)
	Initialize warp from volume size and control grid density.
	cmtk::SplineWarpXform::SplineWarpXform (const FixedVector< 3, Types::Coordinate > &domain, const Self::IndexType &dims, CoordinateVector::SmartPtr &parameters, const AffineXform *initialXform=NULL)
	Construct new warp from volume size, grid dimensions and parameters.
Self::SmartPtr	cmtk::SplineWarpXform::Clone () const
	Clone and return smart pointer.
void	cmtk::SplineWarpXform::InitControlPoints (const AffineXform *affineXform=NULL)
	Initialize control point positions, potentially with affine displacement.
virtual void	cmtk::SplineWarpXform::Update (const bool exactDelta=false)
	Update internal representation.
virtual SplineWarpXform *	cmtk::SplineWarpXform::MakeInverse () const
	Create inverse transformation.
virtual void	cmtk::SplineWarpXform::Refine ()
	Refine control point grid by a factor of two, but maintain transformation exactly.
virtual Types::Coordinate	cmtk::SplineWarpXform::GetGridEnergy () const
	Return grid bending energy.
virtual Types::Coordinate	cmtk::SplineWarpXform::GetGridEnergy (const Types::Coordinate *cp) const
	Return grid bending energy at one control point.
virtual Types::Coordinate	cmtk::SplineWarpXform::GetGridEnergy (const Self::SpaceVectorType &v) const
	Return grid bending energy at arbitrary location.
virtual void	cmtk::SplineWarpXform::GetGridEnergyDerivative (double &lower, double &upper, const int param, const Types::Coordinate step) const
	Return derivative of grid energy with respect to one parameter.
virtual Types::Coordinate	cmtk::SplineWarpXform::GetJacobianDeterminant (const Self::SpaceVectorType &v) const
	Compute Jacobian determinant at a certain location.
virtual Types::Coordinate	cmtk::SplineWarpXform::GetJacobianDeterminant (const int x, const int y, const int z) const
	Compute Jacobian determinant at a certain reference image pixel.
virtual void	cmtk::SplineWarpXform::GetJacobianDeterminantRow (double *const values, const int x, const int y, const int z, const size_t numberOfPoints=1) const
	Compute sequence of Jacobian determinants from given grid location.
Types::Coordinate	cmtk::SplineWarpXform::JacobianDeterminant (const Types::Coordinate *cp) const
	Compute Jacobian determinant at a certain control point.
virtual Types::Coordinate	cmtk::SplineWarpXform::GetJacobianConstraint () const
	Return Jacobian constraint of the current transformation grid.
virtual Types::Coordinate	cmtk::SplineWarpXform::GetJacobianFoldingConstraint () const
	Return Jacobian folding constraint of the current transformation grid.
virtual void	cmtk::SplineWarpXform::RelaxToUnfold ()
	Relax the deformation to unfold areas with negative Jacobian at the current image sampling.
virtual Types::Coordinate	cmtk::SplineWarpXform::GetRigidityConstraint () const
	Return rigidity constraint of the current transformation grid.
virtual Types::Coordinate	cmtk::SplineWarpXform::GetRigidityConstraint (const DataGrid *weightMap) const
	Return rigidity constraint of the current transformation grid with local weights.
virtual Types::Coordinate	cmtk::SplineWarpXform::GetJacobianConstraintSparse () const
	Return sparse Jacobian constraint of the current transformation grid.
virtual Types::Coordinate	cmtk::SplineWarpXform::GetRigidityConstraintSparse () const
	Return sparse rigidity constraint of the current transformation grid.
virtual void	cmtk::SplineWarpXform::GetJacobianConstraintDerivative (double &lower, double &upper, const int param, const UniformVolume::RegionType &, const Types::Coordinate step) const
	Return derivative of Jacobian constraint with respect to one parameter.
virtual void	cmtk::SplineWarpXform::GetJacobianFoldingConstraintDerivative (double &lower, double &upper, const int param, const UniformVolume::RegionType &, const Types::Coordinate step) const
	Return derivative of Jacobian constraint with respect to one parameter.
virtual void	cmtk::SplineWarpXform::GetJacobianConstraintDerivative (double &lower, double &upper, const int param, const Types::Coordinate step) const
	Return derivative of Jacobian constraint with respect to one parameter.
virtual void	cmtk::SplineWarpXform::GetRigidityConstraintDerivative (double &lower, double &upper, const int param, const UniformVolume::RegionType &, const Types::Coordinate step) const
	Return derivative of rigidity constraint with respect to one parameter.
virtual void	cmtk::SplineWarpXform::GetRigidityConstraintDerivative (double &lower, double &upper, const int param, const UniformVolume::RegionType &, const Types::Coordinate step, const DataGrid *weightMap) const
	Return derivative of rigidity constraint with respect to one parameter.
virtual void	cmtk::SplineWarpXform::GetRigidityConstraintDerivative (double &lower, double &upper, const int param, const Types::Coordinate step) const
	Return derivative of rigidity constraint with respect to one parameter.
virtual Types::Coordinate	cmtk::SplineWarpXform::GetInverseConsistencyError (const WarpXform *inverse, const UniformVolume *volume, const UniformVolume::RegionType *voi=NULL) const
	Return inverse consistency.
virtual bool	cmtk::SplineWarpXform::ApplyInverse (const Self::SpaceVectorType &v, Self::SpaceVectorType &u, const Types::Coordinate accuracy=0.01) const
	Return origin of warped vector.
virtual bool	cmtk::SplineWarpXform::ApplyInverseInPlace (Self::SpaceVectorType &v, const Types::Coordinate accuracy=0.01) const
	Return origin of warped vector.
virtual bool	cmtk::SplineWarpXform::ApplyInverseInPlaceWithInitial (Self::SpaceVectorType &v, const Self::SpaceVectorType &initial, const Types::Coordinate accuracy=0.01) const
	Return origin of warped vector.
virtual void	cmtk::SplineWarpXform::ApplyInPlace (Self::SpaceVectorType &v) const
	Replace existing vector with transformed location.
virtual void	cmtk::SplineWarpXform::GetVolumeOfInfluence (const size_t idx, const Self::SpaceVectorType &, const Self::SpaceVectorType &, Self::SpaceVectorType &, Self::SpaceVectorType &, const int=-1) const
	Get volume influenced by one parameter.
void	cmtk::SplineWarpXform::RegisterVolume (const UniformVolume *volume)
	Register the grid points of the deformed uniform or non-uniform volume.
void	cmtk::SplineWarpXform::UnRegisterVolume ()
	Unegister axes points, ie free all internal data structures.
void	cmtk::SplineWarpXform::GetTransformedGrid (Self::SpaceVectorType &v, const int idxX, const int idxY, const int idxZ) const
	Get a grid point from the deformed grid.
void	cmtk::SplineWarpXform::GetTransformedGridRow (const int numPoints, Self::SpaceVectorType *const v, const int idxX, const int idxY, const int idxZ) const
	Get a sequence of grid points from the deformed grid.
virtual Types::Coordinate	cmtk::SplineWarpXform::GetParamStep (const size_t idx, const Self::SpaceVectorType &volSize, const Types::Coordinate mmStep=1) const
	Get parameter stepping.
virtual Self::SpaceVectorType &	cmtk::SplineWarpXform::GetDeformedControlPointPosition (Self::SpaceVectorType &, const int, const int, const int) const
	Get the deformed position of a transformation control point.
Types::Coordinate *	cmtk::SplineWarpXform::GetPureDeformation (const bool includeScale=false) const
	Return array of pre deformation vectors.
virtual CoordinateMatrix3x3	cmtk::SplineWarpXform::GetJacobian (const Self::SpaceVectorType &v) const
	Get local Jacobian.
virtual void	cmtk::SplineWarpXform::GetJacobian (const Self::SpaceVectorType &v, CoordinateMatrix3x3 &J) const
	Get local Jacobian into existing matrix.
virtual void	cmtk::SplineWarpXform::GetJacobianAtControlPoint (const Types::Coordinate *cp, CoordinateMatrix3x3 &J) const
	Get local Jacobian at control point into existing matrix.
virtual void	cmtk::SplineWarpXform::GetJacobianRow (CoordinateMatrix3x3 *const array, const int x, const int y, const int z, const size_t numberOfPoints) const
	Get sequence of Jacobians for pixel row.
void	cmtk::SplineWarpXform::RegisterVolumePoints (const DataGrid::IndexType &, const Self::SpaceVectorType &)
	Register axes points of the volume to be deformed.
void	cmtk::SplineWarpXform::RegisterVolumePoints (const DataGrid::IndexType &, const Self::SpaceVectorType &, const Self::SpaceVectorType &)
	Register axes points of the volume to be deformed.
void	cmtk::SplineWarpXform::RegisterVolumeAxis (const DataGrid::IndexType::ValueType, const Types::Coordinate delta, const Types::Coordinate origin, const int, const Types::Coordinate, std::vector< int > &g, std::vector< Types::Coordinate > &spline, std::vector< Types::Coordinate > &dspline)
	Register a single axis of the uniform volume to be deformed.
Types::Coordinate	cmtk::SplineWarpXform::GetRigidityConstraint (const CoordinateMatrix3x3 &J) const
	Return rigidity constraint based on given Jacobian matrix.
virtual SplineWarpXform *	cmtk::SplineWarpXform::CloneVirtual () const
	Clone transformation.
void	cmtk::SplineWarpXform::Init ()
	Initialize internal data structures.
static void	cmtk::SplineWarpXform::GetJacobianConstraintThread (void *const args, const size_t taskIdx, const size_t taskCnt, const size_t, const size_t)
	Thread function for SMP Jacobian constraint computation.
static void	cmtk::SplineWarpXform::GetJacobianFoldingConstraintThread (void *const args, const size_t taskIdx, const size_t taskCnt, const size_t, const size_t)
	Thread function for SMP Jacobian folding constraint computation.
void	cmtk::SplineWarpXform::FindClosestControlPoint (const Self::SpaceVectorType &v, Self::SpaceVectorType &cp) const
	Find nearest (after deformation) control point.
DataClass	cmtk::StringToDataClass (const char *dataClassStr)
	Convert string to data class identifier.
const char *	cmtk::DataClassToString (const DataClass dataClass)
	Convert data class identifier to string.
size_t	cmtk::TypeItemSize (const ScalarDataType dtype)
	Return item size for given scalar data type.
ScalarDataType	cmtk::SelectDataTypeInteger (const byte itemSize, const bool signBit)
	Select integer data type based on item size and sign bit.
ScalarDataType	cmtk::GetSignedDataType (const ScalarDataType dtype)
	Return signed datatype ID corresponding to given datatype.
ScalarDataType	cmtk::GetDifferenceDataType (const ScalarDataType dtype1, const ScalarDataType dtype2)
	Return difference datatype ID for given pair of datatypes.
ScalarDataType	cmtk::GetUnsignedDataType (const ScalarDataType dtype)
	Return unsigned datatype ID corresponding to given datatype.
	cmtk::UniformVolumeFilter::UniformVolumeFilter (UniformVolume::SmartPtr volume)
	Constructor: link to UniformVolume object.
TypedArray::SmartPtr	cmtk::UniformVolumeFilter::GetDataGaussFiltered (const Units::GaussianSigma &sigma, const Types::Coordinate maxError=0.01) const
	Gaussian filter (using faster, separable filtering).
template<class T >
ValueSequence< T >	cmtk::operator+ (const ValueSequence< T > &a, const ValueSequence< T > &b)
template<class T >
Vector< T >	cmtk::operator+ (const Vector< T > &p, const Vector< T > &delta)
	Vector addition operator.
template<class T >
Vector< T >	cmtk::operator- (const Vector< T > &p, const Vector< T > &delta)
	Vector subtraction operator.
template<class T >
Vector< T >	cmtk::operator* (const T c, const Vector< T > &p)
	Scalar-to-vector multiplication operator.
template<class T >
Vector< T >	cmtk::CoordMult (const Vector< T > &p, const Vector< T > &q)
	Coordinatewise multiplication operator.
template<class T >
T	cmtk::operator* (const Vector< T > &p, const Vector< T > &q)
	Scalar product.
	cmtk::ActiveDeformationModel::ActiveDeformationModel (const std::list< SmartPointer< W > > deformationList, const unsigned int numberOfModes, const bool includeScaleInModel=true, const bool includeReferenceInModel=true)
	Build deformation model from list of deformations.
Types::Coordinate *	cmtk::ActiveDeformationModel::MakeSamplePointsReference (const W *deformation)
	Make ADM sample points from the undeformed c.p.g.
Types::Coordinate *	cmtk::ActiveDeformationModel::MakeSamplePoints (const W *deformation)
	Make ADM sample points from a given deformation.
W *	cmtk::ActiveDeformationModel::Compose (const Types::Coordinate *weights=NULL)
	Compose deformation from mean deformation and modes of variation.
float	cmtk::ActiveDeformationModel::Decompose (const W *input, Types::Coordinate *const weights=NULL) const
	Decompose a deformation into mean and modes of this model.
	cmtk::ActiveShapeModel::ActiveShapeModel (CoordinateVector::SmartPtr &mean, DirectionSet::SmartPtr &modes, CoordinateVector::SmartPtr &modeVariances)
	Construct using given mean and modes.
float	cmtk::ActiveShapeModel::Construct (const Types::Coordinate *const *trainingSet, const unsigned int numberOfSamples, const unsigned int numberOfPoints, const unsigned int numberOfModes)
	Construct model.
Types::Coordinate *	cmtk::ActiveShapeModel::Generate (Types::Coordinate *const instance, const Types::Coordinate *modeWeights) const
	Generate a model instance.
float	cmtk::ActiveShapeModel::Decompose (const CoordinateVector *input, Types::Coordinate *const weights=NULL) const
	Decompose a vector into mean and modes of this model.
void	cmtk::ActiveShapeModel::Allocate (const unsigned int numberOfPoints, const unsigned int numberOfModes)
	Allocate data structures.
void	cmtk::AffineXform::MakeIdentityXform ()
	Create identity transformation.
	cmtk::AffineXform::AffineXform (const AffineXform &other)
	Copy transform by reference.
	cmtk::AffineXform::AffineXform (const Types::Coordinate matrix[4][4], const Types::Coordinate *center=NULL)
	Create transformation from transformation matrix.
	cmtk::AffineXform::AffineXform (const MatrixType &matrix, const Types::Coordinate *center=NULL)
	Create transformation from transformation matrix.
	cmtk::AffineXform::AffineXform (const Types::Coordinate matrix[4][4], const Types::Coordinate xlate[3], const Types::Coordinate center[3])
	Create transformation from transformation matrix.
AffineXform &	cmtk::AffineXform::operator= (const AffineXform &other)
	Assignment operator.
virtual void	cmtk::AffineXform::SetNumberDOFs (const int numberDOFs=12)
	Set the number of degrees of freedom for this object.
void	cmtk::AffineXform::SetUseLogScaleFactors (const bool logScaleFactors)
	Switch between log and ordinary scale factors.
void	cmtk::AffineXform::ComposeMatrix ()
	Compose this object's transformation matrix from parameter vector.
bool	cmtk::AffineXform::DecomposeMatrix ()
	Decompose this object's transformation matrix into parameter vector.
Self::SpaceVectorType	cmtk::AffineXform::RotateScaleShear (const Self::SpaceVectorType &v) const
	Apply rotation, scaling, and shearing but no translation to vector.
virtual Self *	cmtk::AffineXform::MakeInverse () const
	Clone inverse of this transformation.
void	cmtk::AffineXform::ChangeCenter (const Self::SpaceVectorType &center)
	Create equivalent transformation with different rotational center.
template<>
void	cmtk::AffineXform::GetMatrix (float(&matrix)[4][4]) const
template<>
void	cmtk::AffineXform::GetMatrix (double(&matrix)[4][4]) const
virtual void	cmtk::AffineXform::SetParamVector (CoordinateVector &v)
	Set Xform by parameter vector.
virtual void	cmtk::AffineXform::SetParamVector (const CoordinateVector &v)
	Set Xform by constant parameter vector.
virtual void	cmtk::AffineXform::SetParameter (const size_t idx, const Types::Coordinate p)
	Set a single parameter value.
virtual Types::Coordinate	cmtk::AffineXform::GetParamStep (const size_t idx, const Self::SpaceVectorType &volSize, const Types::Coordinate step_mm=1) const
	Get parameter stepping.
virtual Self::SmartPtr	cmtk::AffineXform::GetDifference (const AffineXform &other) const
	Compute difference to another affine transformation.
void	cmtk::AffineXform::Concat (const AffineXform &other)
	Concatenate this transformation with another.
void	cmtk::AffineXform::Insert (const AffineXform &other)
	Insert another transformation before this one.
void	cmtk::AffineXform::RotateWXYZ (const Units::Radians angle, const Self::SpaceVectorType &direction, const Types::Coordinate *origin=NULL, Self::MatrixType *const accumulate=NULL)
	Rotate around axis.
const Self::SmartPtr	cmtk::AffineXform::GetInverse () const
	Get linked inverse of this transformation.
void	cmtk::AffineXform::UpdateInverse () const
	Update linked inverse transformation.
void	cmtk::AffineXform::CanonicalRotationRange ()
	Correct rotation parameters to canonical range -180 to 180.
virtual void	cmtk::AffineXform::Print () const
	Print object.
static void	cmtk::AnatomicalOrientation::GetOrientationFromDirections (char *orientation, const AffineXform::MatrixType &directions, const char *spaceAxes)
	Get closest anatomical orientation based on space dimensions and image direction vectors.
static void	cmtk::AnatomicalOrientation::GetImageToSpaceAxesPermutation (int(&imageToSpaceAxesPermutation)[3][3], const char *orientation, const char *spaceAxes)
	Get permutation table of coordinate axes from space axes and image orientation.
static const char *	cmtk::AnatomicalOrientationBase::GetClosestOrientation (const char *desiredOrientation, const char *const availableOrientations[])
	Get closest orientation from a list.
static bool	cmtk::AnatomicalOrientationBase::OnSameAxis (const char from, const char to)
	Return true if the direction corresponding to the character 'from' is on the same axis as that corresponding to 'to'.
	cmtk::AnatomicalOrientation::PermutationMatrix::PermutationMatrix (const FixedVector< 3, int > &sourceDims, const std::string &curOrientation, const char newOrientation[3])
	Constructor: determine axes permutation, flipping, and store local copy of reoriented dimensions array.
AffineXform::MatrixType	cmtk::AnatomicalOrientation::PermutationMatrix::GetPermutedMatrix (const AffineXform::MatrixType &inMatrix) const
	Permute index-to-physical matrix.
	cmtk::BitVector::BitVector (const size_t size, const bool initial=false)
	Constructor.
	cmtk::BitVector::BitVector (const size_t size, byte *const bitset)
	Constructor.
	cmtk::BitVector::~BitVector ()
	Destructor.
BitVector *	cmtk::BitVector::Clone () const
	Create copy of this object.
void	cmtk::BitVector::Set ()
	Set all bits to 1.
void	cmtk::BitVector::Set (const size_t pos, const bool val=true)
	Set one bit to a given value.
void	cmtk::BitVector::Reset (const bool value=false)
	Set all bits to given flag (default: clear all).
void	cmtk::BitVector::Reset (const size_t pos)
	Set one bit to 0.
void	cmtk::BitVector::Flip ()
	Flip (invert) the whole bitset.
void	cmtk::BitVector::Flip (const size_t pos)
	Flip (invert) one bit.
bool	cmtk::BitVector::operator[] (const size_t pos) const
	Return a given bit.
	cmtk::ControlPointList::~ControlPointList ()
	Destructor: Free all stored points.
const RegionType	cmtk::DataGrid::GetWholeImageRegion () const
	Get whole image region.
virtual TypedArray::SmartPtr	cmtk::DataGrid::CreateDataArray (const ScalarDataType dataType, const bool setToZero=false)
	Create data array.
virtual DataGrid *	cmtk::DataGrid::GetDownsampledAndAveraged (const int(&downsample)[3]) const
	Downsampling and pixel-averaging constructor function.
const DataGrid::SmartPtr	cmtk::DataGrid::GetReoriented (const char *newOrientation=AnatomicalOrientation::ORIENTATION_STANDARD) const
	Reorientation constructor function.
void	cmtk::DataGrid::SetDims (const Self::IndexType &dims)
	Set dimensions array.
bool	cmtk::DataGrid::TrilinearInterpolation (Types::DataItem &data, const int x, const int y, const int z, const Self::SpaceVectorType &location, const Types::Coordinate *cellFrom, const Types::Coordinate *cellTo) const
	Utility function for trilinear interpolation.
TypedArray::SmartPtr	cmtk::DataGrid::GetDataMirrorPlane (const int axis=AXIS_X) const
	Return data after mirroring.
void	cmtk::DataGrid::ApplyMirrorPlane (const int axis=AXIS_X)
	Replace data with mirrored version.
static void	cmtk::DataGrid::MirrorPlaneInPlace (TypedArray &data, const Self::IndexType &dims, const int axis=AXIS_X)
	Mirror about plane without allocating additional memory.
TypedArray::SmartPtr	cmtk::DataGrid::GetDataMirrored (const int axis=AXIS_X) const
	Return data after mirror operator.
virtual ScalarImage *	cmtk::DataGrid::GetOrthoSlice (const int axis, const unsigned int plane) const
	Return orthogonal slice as a 2D image.
virtual Self *	cmtk::DataGrid::ExtractSliceVirtual (const int axis, const int plane) const
	Extract orthogonal slice as a data grid object.
virtual void	cmtk::DataGrid::SetOrthoSlice (const int axis, const unsigned int idx, const ScalarImage *slice)
	Set orthogonal slice from a 2D image.
virtual FixedVector < 3, Types::Coordinate >	cmtk::DataGrid::GetCenterOfMassGrid () const
	Get center of mass of pixel data.
virtual FixedVector < 3, Types::Coordinate >	cmtk::DataGrid::GetCenterOfMassGrid (FixedVector< 3, Types::Coordinate > &firstOrderMoment) const
	Get center of mass and first-order moments of pixel data.
void	cmtk::DataGrid::Print () const
	Print object.
template<class TAccumulator >
ScalarImage *	cmtk::DataGrid::ComputeProjection (const int axis) const
	Return maximum-intensity projection MIP along one axis.
template<class TData >
TData	cmtk::DataGrid::TrilinearInterpolation (const TData *dataPtr, const int x, const int y, const int z, const Self::SpaceVectorType &gridPosition, const Types::Coordinate *cellFrom, const Types::Coordinate *cellTo) const
	Utility function for trilinear interpolation from a primitive data array.
template<class TData , class TOutputIterator >
void	cmtk::DataGrid::TrilinearInterpolation (TOutputIterator result, const std::vector< TData * > &dataPtr, const int x, const int y, const int z, const Types::Coordinate fracX, const Types::Coordinate fracY, const Types::Coordinate fracZ) const
	Utility function for trilinear interpolation from multiple primitive data arrays of identical grid structure.
void	cmtk::DeformationField::InitControlPoints (const AffineXform *affineXform=NULL)
	Initialize control point positions, potentially with affine displacement.
virtual void	cmtk::DeformationField::GetTransformedGrid (Self::SpaceVectorType &v, const int idxX, const int idxY, const int idxZ) const
	Get a grid point from the deformed grid.
virtual void	cmtk::DeformationField::GetTransformedGridRow (Self::SpaceVectorType *const v, const int numPoints, const int idxX, const int idxY, const int idxZ) const
	Get a sequence of grid points from the deformed grid.
virtual void	cmtk::DeformationField::ApplyInPlace (Self::SpaceVectorType &) const
	Apply transformation to vector in-place.
virtual void	cmtk::DeformationField::GetJacobian (const Self::SpaceVectorType &v, CoordinateMatrix3x3 &J) const
	Get Jacobian matrix.
void	cmtk::DirectionSet::NormalizeMaxNorm (const double value=1.0)
	Normalizes each direction vector to have max norm = value.
void	cmtk::DirectionSet::NormalizeEuclidNorm (const double value=1.0)
	Normalizes each direction vector to have euclid norm = value.
	cmtk::EigenSystemSymmetricMatrix3x3::EigenSystemSymmetricMatrix3x3 (const Matrix3x3< TFloat > &matrix, const bool sortAbsolute=true)
	Constructor: compute eigensystem of given matrix.
static TFloat	cmtk::EigenSystemSymmetricMatrix3x3::hypot2 (const TFloat &x, const TFloat &y)
	Helper function that computes the Euclidean length of (x,y).
static void	cmtk::EigenSystemSymmetricMatrix3x3::tred2 (TFloat V[3][3], TFloat d[3], TFloat e[3])
	Symmetric Householder reduction to tridiagonal form.
static void	cmtk::EigenSystemSymmetricMatrix3x3::tql2 (TFloat V[3][3], TFloat d[3], TFloat e[3], const bool sortAbsolute=true)
static TypedArray::SmartPtr	cmtk::FilterVolume::GaussianFilter (const UniformVolume *volume, const Units::GaussianSigma &width, const Types::Coordinate radius=1.0, const TypedArray *maskData=NULL)
	Apply Gaussian filter.
static TypedArray::SmartPtr	cmtk::FilterVolume::RohlfingFilter (const UniformVolume *volume, const TypedArray *subjectData, const TypedArray *maskData, const Units::GaussianSigma &iFilterSigma, const Units::GaussianSigma &filterWidth, const Types::Coordinate filterRadius)
	Apply Torsten Rohlfing's single-image intensity-consistent Gaussian filter.
static TypedArray::SmartPtr	cmtk::FilterVolume::StudholmeFilter (const UniformVolume *volume, const TypedArray *subjectData, const TypedArray *averageData, const TypedArray *maskData, std::list< TypedArray::SmartPtr > imgList, const Types::DataItem binWidth, const Units::GaussianSigma &filterWidth, const Types::Coordinate filterRadius)
	Apply Colin Studholme's Gaussian filter with registration-based weights.
static TypedArray::SmartPtr	cmtk::FilterVolume::StudholmeFilter (const UniformVolume *volume, std::list< TypedArray::SmartPtr > subjectData, const TypedArray *averageData, const TypedArray *maskData, std::list< TypedArray::SmartPtr > imgList, const Types::DataItem binWidth, const Units::GaussianSigma &filterWidth, const Types::Coordinate filterRadius)
	Apply Colin Studholme's Gaussian filter using multiple time points.
virtual Self::ReturnType	cmtk::Functional::EvaluateWithGradient (ParameterVectorType &v, ParameterVectorType &g, const Types::Coordinate step=1)
	Evaluate functional and also return its gradient.
	cmtk::GeneralLinearModel::GeneralLinearModel (const size_t nParameters, const size_t nData, const double *designMatrix)
	Constructor.
Matrix2D< double > *	cmtk::GeneralLinearModel::GetCorrelationMatrix () const
	Get the parameter correlation matrix from design matrix.
	cmtk::GeneralLinearModel::~GeneralLinearModel ()
	Destructor.
void	cmtk::GeneralLinearModel::InitResults (const size_t nPixels)
	Initialize results arrays with the correct number of pixels.
void	cmtk::GeneralLinearModel::FitModel (std::vector< TypedArray::SmartPtr > &y, const bool normalizeParameters=true)
	Model y[] distribution and return model parameters a[].
size_t	cmtk::Histogram::GetMaximumBinIndex () const
	Return index of bin with highest value.
double	cmtk::Histogram::GetEntropy () const
	Compute entropy of distribution.
void	cmtk::Histogram::AddHistogram (const Self &other)
	Add values from another histogram.
void	cmtk::Histogram::RemoveHistogram (const Self &other)
	Subtract bin values from another histogram.
void	cmtk::Histogram::Normalize (const T normalizeTo=1)
	Normalize histogram values by their total sum.
void	cmtk::Histogram::NormalizeMaximum (const T normalizeTo=1)
	Normalize histogram values by their maximum.
Types::DataItem	cmtk::Histogram::GetPercentile (const Types::DataItem percentile) const
	Compute approximate percentile value from histogram.
void	cmtk::Histogram::AddWeightedSymmetricKernel (const size_t bin, const size_t kernelRadius, const T *kernel, const T factor=1)
	Add weighted symmetric kernel to histogram.
void	cmtk::Histogram::AddWeightedSymmetricKernelFractional (const double bin, const size_t kernelRadius, const T *kernel, const T factor=1)
	Add weighted symmetric kernel to histogram, spreading contriubtions between adjacent bins.
double	cmtk::Histogram::GetKullbackLeiblerDivergence (const Self &other) const
	Get Kullback-Leibler divergence to other histogram.
static int	cmtk::Intersection::IntersectX (Types::Coordinate &fromFactor, Types::Coordinate &toFactor, const Vector3D &offset, const Vector3D &dX, const Types::Coordinate Size[3], const Types::Coordinate initFromFactor=0, const Types::Coordinate initToFactor=1, const int lowerClosed=0, const int upperClosed=0)
	Compute line-to-volume intersection.
static int	cmtk::Intersection::IntersectY (Types::Coordinate &fromFactor, Types::Coordinate &toFactor, const Vector3D &offset, const Vector3D &dX, const Vector3D &dY, const Types::Coordinate Size[3], const Types::Coordinate initFromFactor=0, const Types::Coordinate initToFactor=1)
	Compute plane-to-volume intersection.
static int	cmtk::Intersection::IntersectZ (Types::Coordinate &fromFactor, Types::Coordinate &toFactor, const Vector3D &offset, const Vector3D &dX, const Vector3D &dY, const Vector3D &dZ, const Types::Coordinate Size[3], const Types::Coordinate initFromFactor=0, const Types::Coordinate initToFactor=1)
	Compute volume-to-volume intersection.
void	cmtk::JointHistogram::GetMarginalEntropies (double &HX, double &HY) const
	Compute marginal entropies.
double	cmtk::JointHistogram::GetJointEntropy () const
	Compute joint entropy.
Histogram< T > *	cmtk::JointHistogram::GetMarginalX () const
	Get marginal X distribution as 1D histogram.
Histogram< T > *	cmtk::JointHistogram::GetMarginalY () const
	Get marginal Y distribution as 1D histogram.
	cmtk::Landmark::Landmark ()
	Default constructor.
	cmtk::Landmark::Landmark (const char *name, const Types::Coordinate location[3])
	Explicit constructor.
	cmtk::Landmark::~Landmark ()
	Destructor.
const Landmark::SmartPtr	cmtk::LandmarkList::FindByName (const char *name) const
	Find landmark by name and return constant pointer.
Landmark::SmartPtr	cmtk::LandmarkList::FindByName (const char *name)
	Find landmark by name.
void	cmtk::MatchedLandmarkList::AddLandmarkLists (const LandmarkList *sourceList, const LandmarkList *targetList)
	Initialize from two separate landmark lists.
const SmartPointer < MatchedLandmark >	cmtk::MatchedLandmarkList::FindByName (const char *name) const
	Find landmark by name and return constant pointer.
SmartPointer< MatchedLandmark >	cmtk::MatchedLandmarkList::FindByName (const char *name)
	Find landmark by name.
template<class T >
static void	cmtk::MathUtil::ComputeEigensystem (const Matrix2D< T > &matrix, Matrix2D< T > &eigensystem, std::vector< T > &eigenvalues)
	Compute eigensystem and eigenvalues for square real matrix using Jacobi rotation.
template<class T >
static void	cmtk::MathUtil::ComputeEigenvalues (const Matrix2D< T > &matrix, std::vector< T > &eigenvalues)
	Compute eigenvalues for square real matrix using Jacobi rotation.
static void	cmtk::MathUtil::SVD (Matrix2D< double > *U, size_t m, size_t n, std::vector< double > *W, Matrix2D< double > *V)
	Singular Value Decomposition.
static void	cmtk::MathUtil::SVDLinearRegression (Matrix2D< double > *U, size_t m, size_t n, std::vector< double > *W, Matrix2D< double > *V, double *b, std::vector< double > &lm_params)
	Linear Regression using SVD results.
template<class T >
static T	cmtk::MathUtil::CholeskyDeterminant (const Matrix2D< T > &matrix, int n)
	Determinant of an n x n square matrix.
static double	cmtk::MathUtil::UniformRandom ()
	Uniform random number generator.
static double	cmtk::MathUtil::TStatFromCorrelation (const double r, const size_t df)
	Compute t-statistic from coefficient of correlation.
static double	cmtk::MathUtil::ProbabilityFromTStat (const double t, const size_t df)
	Compute probability from T-statistic.
template<class T >
static T	cmtk::MathUtil::Mean (const unsigned int nValues, const T *values)
	Computes average of an array of float values.
template<class T >
static T	cmtk::MathUtil::Variance (const unsigned int nValues, const T *values, T mean, const bool unbiased=false)
	Computes variance of an array of float values.
template<class T >
static T	cmtk::MathUtil::Mean (const std::vector< T > &values)
	Computes average of a vector of float values.
template<class T >
static T	cmtk::MathUtil::Variance (const std::vector< T > &values, T mean, const bool unbiased=false)
	Computes variance of a vector of float values.
template<class T >
static T	cmtk::MathUtil::Correlation (const std::vector< T > &x, const std::vector< T > &y)
	Normalized correlation coefficient between two float vectors.
template<class T >
static T	cmtk::MathUtil::TTest (const std::vector< T > &valuesX, const std::vector< T > &valuesY, T &t)
	Performs two-tailed unpaired t-test on two distributions.
template<class T >
static T	cmtk::MathUtil::PairedTTest (const std::vector< T > &valuesX, const std::vector< T > &valuesY, T &t, T &avgX, T &avgY)
	Performs two-tailed paired t-test on two distributions.
template<class T >
static T	cmtk::MathUtil::TTest (const std::vector< T > &valuesX, const std::vector< T > &valuesY, T &t, T &avgX, T &avgY)
	Performs two-tailed unpaired t-test on two distributions.
template<class T >
static T	cmtk::MathUtil::TTest (const std::vector< T > &valuesX, T &t, T &avgX)
	Performs one-sample t-test on distribution to test for zero mean.
	cmtk::Matrix3x3::Matrix3x3 ()
	Default constructor: make identity matrix.
	cmtk::Matrix3x3::Matrix3x3 (const Self &other)
	Copy constructor.
Self &	cmtk::Matrix3x3::Set (const T *const values)
	Set from array of entries.
Self &	cmtk::Matrix3x3::Fill (const T value)
	Set to constant value.
Self &	cmtk::Matrix3x3::Compose (const Types::Coordinate params[8])
	Compose from canonical parameters.
bool	cmtk::Matrix3x3::Decompose (Types::Coordinate params[8], const Types::Coordinate *center=NULL) const
	Decompose into affine parameters.
Self	cmtk::Matrix3x3::GetTranspose () const
	Transpose operator.
Self &	cmtk::Matrix3x3::Invert2x2 ()
	Inversion operator (in place).
Self &	cmtk::Matrix3x3::Invert3x3 ()
	Inversion operator (in place) as a 3D non-homogeneous matrix.
Self &	cmtk::Matrix3x3::operator*= (const Self &other)
	In-place multiplication operator.
Self &	cmtk::Matrix3x3::operator*= (const T scalar)
	In-place scalar multiplication operator.
const Self	cmtk::Matrix3x3::operator* (const Self &other) const
	Multiplication operator.
Self &	cmtk::Matrix3x3::operator= (const Self &other)
	Assignment operator.
T	cmtk::Matrix3x3::FrobeniusNorm () const
	Get Frobenius norm.
void	cmtk::Matrix3x3::ComputeEigenvalues (T(&lambda)[3]) const
	Compute eigenvalues.
	cmtk::Matrix4x4::Matrix4x4 ()
	Default constructor: make identity matrix.
	cmtk::Matrix4x4::Matrix4x4 (const Matrix3x3< T > &other)
	Top left submatrix copy constructor.
Self &	cmtk::Matrix4x4::Set (const T *const values)
	Set from array of entries.
Self	cmtk::Matrix4x4::GetTranspose () const
	Transpose operator.
Self &	cmtk::Matrix4x4::Compose (const Types::Coordinate params[15], const bool logScaleFactors=false)
	Compose from canonical parameters.
bool	cmtk::Matrix4x4::Decompose (Types::Coordinate params[12], const Types::Coordinate *center=NULL, const bool logScaleFactors=false) const
	Decompose into affine parameters.
const Self	cmtk::Matrix4x4::GetInverse () const
	Inversion operator (in place).
Self &	cmtk::Matrix4x4::operator*= (const Self &other)
	In-place multiplication operator.
const Self	cmtk::Matrix4x4::operator* (const Self &other) const
	Multiplication operator.
Self &	cmtk::Matrix4x4::operator= (const Matrix3x3< T > &other)
	3x3 submatrix assignment operator.
Self &	cmtk::Matrix4x4::ChangeCoordinateSystem (const FixedVector< 3, T > &newX, const FixedVector< 3, T > &newY)
	Change reference coordinate system.
static Self	cmtk::Matrix4x4::RotateX (const T angle)
	Return rotation around x axis.
static Self	cmtk::Matrix4x4::RotateY (const T angle)
	Return rotation around y axis.
static Self	cmtk::Matrix4x4::RotateZ (const T angle)
	Return rotation around z axis.
T	cmtk::Matrix4x4::FrobeniusNorm () const
	Get Frobenius norm.
	cmtk::ParametricPlane::ParametricPlane ()
	Default constructor.
void	cmtk::ParametricPlane::Update ()
	Update internal fields after change of parameters.
void	cmtk::ParametricPlane::SetNormal (const Self::CoordinateVectorType &normal)
	Set normal vector and determine rotation angles from it.
AffineXform *	cmtk::ParametricPlane::GetAlignmentXform (const byte normalAxis=0) const
	Get transformation that aligns this plane with the coordinate system.
AffineXform::MatrixType	cmtk::ParametricPlane::GetMirrorXformMatrix () const
	Get affine transformation matrix of the mirror transform.
	cmtk::QRDecomposition::QRDecomposition (const Matrix2D< TFloat > &matrix)
	Constructor: compute QR decomposition of given matrix.
matrix2D &	cmtk::QRDecomposition::GetQ ()
	Get the Q factor.
matrix2D &	cmtk::QRDecomposition::GetR ()
	Get the R factor.
	cmtk::ScalarImage::ScalarImage ()
	Default constructor creates empty image.
	cmtk::ScalarImage::ScalarImage (const int dimsx, const int dimsy, const int numberOfFrames=1)
	Constructor with separate x and y dimensions.
	cmtk::ScalarImage::ScalarImage (const ScalarImage &source, const int *roiFrom=NULL, const int *roiTo=NULL)
	Get ROI as sub-image.
	cmtk::ScalarImage::ScalarImage (const ScalarImage &other, const Self::RegionType &roi)
	Get ROI as sub-image.
virtual ScalarImage *	cmtk::ScalarImage::InterpolateFrom (const ScalarImage *grid, const CoordinateMatrix3x3 *matrix, const cmtk::Interpolators::InterpolationEnum interpolation=cmtk::Interpolators::LINEAR) const
	Interpolate sub-image with affine transformation.
virtual void	cmtk::ScalarImage::ApplyBinaryMask (const ScalarImage *maskImage, const bool invert=false)
	Apply binary mask to image.
bool	cmtk::ScalarImage::GetPixelAt (Types::DataItem &value, const Types::Coordinate i, const Types::Coordinate j) const
	Get pixel at fractional 2-D index by bilinear interpolation.
bool	cmtk::ScalarImage::GetPixelAtCubic (Types::DataItem &value, const Types::Coordinate i, const Types::Coordinate j) const
	Get pixel at fractional 2-D index by bicubic interpolation.
Self::SpaceVectorType	cmtk::ScalarImage::GetImageOrigin (const int frame=0) const
	Get image origin of given frame (default: 0).
virtual ScalarImage *	cmtk::ScalarImage::Clone () const
	Clone (duplicate) this object.
virtual ScalarImage *	cmtk::ScalarImage::Clone (const bool clonePixelData)
	Clone (duplicate) this object.
ScalarImage *	cmtk::ScalarImage::Downsample (const int factorX, int factorY=0, ScalarImage *const target=NULL) const
	Create downsampled copy of this image.
TypedArray::SmartPtr	cmtk::ScalarImage::GetFilteredData (const std::vector< Types::DataItem > &filterX, const std::vector< Types::DataItem > &filterY) const
ScalarImage &	cmtk::ScalarImage::operator-= (const ScalarImage &)
	Subtract one image from another in place.
void	cmtk::ScalarImage::Mirror (const bool horizontal, const bool vertical)
	Mirror image horizontally and/or vertically.
void	cmtk::ScalarImage::AdjustToIsotropic (const Types::Coordinate pixelSize, const bool interpolate=false)
	Adjust aspect ratio.
void	cmtk::ScalarImage::AdjustAspect (const bool interpolate=false)
	Adjust aspect ratio.
void	cmtk::ScalarImage::AdjustAspectY (const bool interpolate=false)
	Adjust aspect ratio by stretching in Y-direction.
void	cmtk::ScalarImage::AdjustAspectX (const bool interpolate=false)
	Adjust aspect ratio by stretching in X-direction.
void	cmtk::ScalarImage::ProjectPixel (const Self::SpaceVectorType &v, int &i, int &j) const
	Project 3D coordinate onto image plane.
virtual void	cmtk::ScalarImage::Print () const
	Print object information.
virtual double	cmtk::TemplateArray::GetEntropy (const bool fractional=CMTK_HISTOGRAM_DISCRETE, const int numberOfBins=128) const
	Calculate entropy of distribution of values in this array.
virtual double	cmtk::TemplateArray::GetEntropy (Histogram< unsigned int > &histogram) const
	Calculate entropy of values in this array using existing histogram.
virtual double	cmtk::TemplateArray::GetEntropy (Histogram< double > &histogram, const bool fractional=CMTK_HISTOGRAM_DISCRETE) const
	Calculate entropy of values in this array using existing histogram.
virtual double	cmtk::TemplateArray::GetEntropy (Histogram< double > &histogram, const double *kernel, const size_t kernelRadius) const
	Calculate entropy of values in this array using existing histogram and kernel for Parzen windowing.
virtual const Types::DataItemRange	cmtk::TemplateArray::GetRange () const
	Calculate minimum and maximum data value.
virtual const Types::Range< T >	cmtk::TemplateArray::GetRangeTemplate () const
	Calculate minimum and maximum data value.
virtual TypedArray::SmartPtr	cmtk::TemplateArray::Convert (const ScalarDataType dtype) const
	Convert to typed array of any given template type.
virtual void *	cmtk::TemplateArray::ConvertSubArray (const ScalarDataType dtype, const size_t fromIdx, const size_t len) const
	Convert a sub-array to any given primitive data type.
virtual void	cmtk::TemplateArray::GammaCorrection (const Types::DataItem gamma)
	Apply gamma correction.
virtual void	cmtk::TemplateArray::ApplyFunctionFloat (typename Self::FunctionTypeFloat f)
	Apply real function to data.
virtual void	cmtk::TemplateArray::ApplyFunctionDouble (typename Self::FunctionTypeDouble f)
	Apply real function to data.
virtual void	cmtk::TemplateArray::ConvertSubArray (void *const destination, const ScalarDataType dtype, const size_t fromIdx, const size_t len) const
	Convert a sub-array to given primitive data type into existing array.
virtual void	cmtk::TemplateArray::ChangeEndianness ()
	Change endianness of data.
virtual void	cmtk::TemplateArray::ApplyFunctionObject (const TypedArrayFunction &f)
	Apply function class to the values of this array.
virtual void	cmtk::TemplateArray::BlockSet (const Types::DataItem value, const size_t fromOffset, const size_t toOffset)
	Set data block to constant value.
virtual size_t	cmtk::TemplateArray::GetStatistics (Types::DataItem &mean, Types::DataItem &variance) const
	Calculate statistics.
virtual Histogram< unsigned int >::SmartPtr	cmtk::TemplateArray::GetHistogram (const unsigned int numberOfBins, const bool centeredBins=false) const
	Get data histogram.
	cmtk::TransformedVolumeAxes::TransformedVolumeAxes (const UniformVolume &volume, const AffineXform *xform=NULL, const Types::Coordinate *deltas=NULL, const Types::Coordinate *otherOrigin=NULL)
	Constructor using affine transformation.
	cmtk::TransformedVolumeAxes::TransformedVolumeAxes (const UniformVolume &volume, const ParametricPlane &mirrorPlane, const Types::Coordinate *deltas=NULL)
	Constructor using mirror plane.
void	cmtk::TransformedVolumeAxes::MakeHash (const UniformVolume &volume, const UniformVolume::SpaceVectorType &offset, const UniformVolume::SpaceVectorType &dX, const UniformVolume::SpaceVectorType &dY, const UniformVolume::SpaceVectorType &dZ)
	Create the actual hash: allocate and fill according to given offset and delta vectors.
	cmtk::TransformedVolumeAxes::~TransformedVolumeAxes ()
	Free all storage.
virtual void	cmtk::TypedArray::RescaleToRange (const Types::DataItemRange &toRange)
	Scale values in the array to a given target range.
virtual void	cmtk::TypedArray::BlockSwap (const size_t fromOffset, const size_t toOffset, const size_t blockLength)
	Exchange two data blocks.
virtual void	cmtk::TypedArray::BlockReverse (const size_t fromOffset, const size_t blockLength)
	Revert order of items in a given range.
static Self::SmartPtr	cmtk::TypedArray::Create (const ScalarDataType dtype, void *const data, const size_t size, const bool freeArray=true, const bool paddingFlag=false, const void *paddingData=NULL)
	Create typed data array from existing array of values.
static Self::SmartPtr	cmtk::TypedArray::Create (const ScalarDataType dtype, const size_t size)
	Create typed data array, allocating new memory for the items array.
virtual void	cmtk::TypedArray::PruneHistogram (const bool pruneHi, const bool pruneLo, const size_t numberOfBinsTarget, const size_t numberOfBinsInternal=1024)
	Prune histogram to trim noise.
virtual Types::DataItem	cmtk::TypedArray::GetPercentile (const Types::DataItem percentile, const size_t nBins=256) const
	Compute approximate percentile value from histogram.
virtual std::vector < Types::DataItem >	cmtk::TypedArray::GetPercentileList (const std::vector< Types::DataItem > &percentileList, const size_t nBins=256) const
	Compute list of approximate percentile values from histogram.
	cmtk::UniformDistanceMap::UniformDistanceMap (const UniformVolume &volume, const byte flags=DEFAULT, const Types::DataItem value=0, const Types::DataItem window=0)
	Construct map from given volume.
void	cmtk::UniformDistanceMap::BuildDistanceMap (const UniformVolume &volume, const byte flags, const Types::DataItem value=0, const Types::DataItem window=0)
	Compute distance map.
void	cmtk::UniformDistanceMap::ComputeEDT (DistanceDataType *const distance)
	Compute 3-D Euclidean Distance Transformation.
static void	cmtk::UniformDistanceMap::ComputeEDTThreadPhase1 (void *const args, const size_t taskIdx, const size_t taskCnt, const size_t threadIdx, const size_t)
	Thread function for first phase (xy) of EDT computation.
static void	cmtk::UniformDistanceMap::ComputeEDTThreadPhase2 (void *const args, const size_t taskIdx, const size_t taskCnt, const size_t threadIdx, const size_t)
	Thread function for second phase (z) of EDT computation.
void	cmtk::UniformDistanceMap::ComputeEDT2D (DistanceDataType *const plane, std::vector< DistanceDataType > &gTemp, std::vector< DistanceDataType > &hTemp)
	Compute 2-D Euclidean Distance Transformation for one image plane.
bool	cmtk::UniformDistanceMap::VoronoiEDT (DistanceDataType *const lpY, const int nSize, const DistanceDataType delta, std::vector< DistanceDataType > &gTemp, std::vector< DistanceDataType > &hTemp)
	Compute 1-D Voronoi Euclidean Distance Transform.
template<class TData >
bool	cmtk::UniformVolume::ProbeData (TData &result, const TData *dataPtr, const Self::CoordinateVectorType &location) const
	Get data value at specified coordinate.
bool	cmtk::UniformVolume::ProbeNoXform (ProbeInfo &, const Self::CoordinateVectorType &) const
	Return linearly interpolated voxel without applying a transformation.
bool	cmtk::UniformVolume::FindVoxel (const Self::CoordinateVectorType &location, int *const idx, Types::Coordinate *const from, Types::Coordinate *const to) const
	Find a voxel in the volume.
bool	cmtk::UniformVolume::FindVoxel (const Self::CoordinateVectorType &location, int *const idx) const
	Find a voxel in the volume.
void	cmtk::UniformVolume::GetVoxelIndexNoBounds (const Self::CoordinateVectorType &location, int *const idx) const
	Find a grid index inside or outside the volume.
bool	cmtk::UniformVolume::FindVoxelByIndex (const Self::CoordinateVectorType &fracIndex, int *const idx, Types::Coordinate *const frac) const
	Find a voxel in the volume by fractional index.
template<class TAccumulator >
ScalarImage *	cmtk::UniformVolume::ComputeProjection (const int axis) const
	Return projection (e.g., MIP, sum) along one axis.
void	cmtk::UniformVolume::SetHighResCropRegion (const Self::CoordinateRegionType &crop)
	Set cropping region in real-world coordinates.
const Self::CoordinateRegionType	cmtk::UniformVolume::GetHighResCropRegion () const
	Get cropped volume in real-world coordinates.
Self::SmartPtr	cmtk::UniformVolume::GetCroppedVolume () const
	Return cropped uniform volume.
virtual TypedArray::SmartPtr	cmtk::UniformVolume::Resample (const UniformVolume &) const
	Resample other volume.
static void	cmtk::UniformVolume::ResampleThreadPoolExecuteLabels (void *const arg, const size_t taskIdx, const size_t taskCnt, const size_t threadIdx, const size_t threadCnt)
	Multi-threaded resampling for label data (using partial volume averaging).
static void	cmtk::UniformVolume::ResampleThreadPoolExecuteGrey (void *const arg, const size_t taskIdx, const size_t taskCnt, const size_t threadIdx, const size_t threadCnt)
	Multi-threaded resampling for grey data.
virtual bool	cmtk::UniformVolumeInterpolator::GetDataAt (const Vector3D &v, Types::DataItem &value) const
	Get data at location.
virtual Types::DataItem	cmtk::UniformVolumeInterpolator::GetDataDirect (const int *imageGridPoint, const Types::Coordinate *insidePixel) const
	Get data at a pre-computed relative pixel index.
virtual bool	cmtk::UniformVolumeInterpolatorPartialVolume::GetDataAt (const Vector3D &v, Types::DataItem &value) const
	Get data at location.
virtual Types::DataItem	cmtk::UniformVolumeInterpolatorPartialVolume::GetDataDirect (const int *imageGridPoint, const Types::Coordinate *insidePixel) const
	Get data at a pre-computed relative pixel index. This is faster if we already know the pixel index and fractional coordinate of a location.
ValueSequence< T > &	cmtk::ValueSequence::operator= (const ValueSequence< T > &other)
	Assignment operator.
bool	cmtk::Volume::GetTrilinear (ProbeInfo &, const int, const int, const int, const Vector3D &, const Types::Coordinate *, const Types::Coordinate *) const
	Get information needed for trilinear interpolation.
Vector3D	cmtk::Volume::GetCenter () const
	Calculate volume center.
void	cmtk::VolumeClipping::SetClippingBoundaries (const UniformVolume::CoordinateRegionType &region)
	Set clipping boundaries.
int	cmtk::VolumeClipping::ClipX (Types::Coordinate &fromFactor, Types::Coordinate &toFactor, const Vector3D &offset, const Types::Coordinate initFromFactor=0, const Types::Coordinate initToFactor=1, const bool lowerClosed=false, const bool upperClosed=false) const
	Compute line-to-volume intersection.
int	cmtk::VolumeClipping::ClipY (Types::Coordinate &fromFactor, Types::Coordinate &toFactor, const Vector3D &offset, const Types::Coordinate initFromFactor=0, const Types::Coordinate initToFactor=1) const
	Compute plane-to-volume intersection.
int	cmtk::VolumeClipping::ClipZ (Types::Coordinate &fromFactor, Types::Coordinate &toFactor, const Vector3D &offset, const Types::Coordinate initFromFactor=0, const Types::Coordinate initToFactor=1) const
	Compute volume-to-volume intersection.
	cmtk::VolumeGridToGridLookup::VolumeGridToGridLookup (const UniformVolume &fromGrid, const UniformVolume &toGrid)
	Constructor: takes original and new image grids.
virtual void	cmtk::WarpXform::InitGrid (const FixedVector< 3, Types::Coordinate > &domain, const Self::IndexType &dims)
	Initialized internal data structures for new control point grid.
virtual void	cmtk::WarpXform::Update (const bool exactDelta=false)
	Update internal representation.
virtual void	cmtk::WarpXform::GetDerivativeLandmarksMSD (double &lowerMSD, double &upperMSD, const MatchedLandmarkList *ll, const unsigned int idx, const Types::Coordinate step)
	Return derivative of registration error with respect to one parameter.
virtual Types::Coordinate	cmtk::WarpXform::GetInverseConsistencyError (const Self *inverse, const UniformVolume *volume, const UniformVolume::RegionType *voi=NULL) const
	Return inverse consistency.
virtual void	cmtk::WarpXform::GetDerivativeInverseConsistencyError (double &lower, double &upper, const Self *inverse, const UniformVolume *volume, const UniformVolume::RegionType *voi, const unsigned int idx, const Types::Coordinate step)
	Return derivative of inverse consistency.
virtual Types::Coordinate	cmtk::WarpXform::GetParamStep (const size_t, const Self::SpaceVectorType &volSize, const Types::Coordinate mmStep=1) const
	Get parameter step given a transformed volume size.
void	cmtk::WarpXform::SetParametersActive ()
	Set all parameters as active.
void	cmtk::WarpXform::SetParameterActive (const size_t index, const bool active=true)
	Set a particular parameter as active (or passive).
void	cmtk::WarpXform::SetParametersActive (const UniformVolume::RegionType &roi)
	Set only those parameters as active that influence a given ROI.
void	cmtk::WarpXform::SetParametersActive (const int axis, const bool active=true)
	Set parameters for one spatial dimension as active or inactive.
void	cmtk::WarpXform::SetParametersActive (const char *axes)
	Set parameters for spatial dimensions as active.
void	cmtk::WarpXform::SetParameterInactive (const size_t index)
	Set a particular parameter as inactive.
int	cmtk::WarpXform::GetParameterActive (const size_t index) const
	Test whether a particular parameter is active.
void	cmtk::WarpXform::DeleteParameterActiveFlags ()
	Free bitset for active parameter flags if it exists.
void	cmtk::WarpXform::ReplaceInitialAffine (const AffineXform *newAffineXform=NULL)
	Replace initial affine transformation.
void	cmtk::WarpXform::ConcatAffine (const AffineXform *affineXform)
	Concat affine transformation.
void	cmtk::Xform::AllocateParameterVector (const size_t numberOfParameters)
	Allocate parameter vector.
virtual void	cmtk::Xform::SetParamVector (CoordinateVector &v)
	Set Xform by parameter vector.
virtual void	cmtk::Xform::SetParamVector (const CoordinateVector &v)
	Set the parameter vector.
virtual CoordinateVector &	cmtk::Xform::GetParamVector (CoordinateVector &v, const size_t targetOffset=0) const
	Copy parameter vector to existing vector object.
virtual void	cmtk::Xform::GetVolumeOfInfluence (const size_t idx, const Self::SpaceVectorType &, const Self::SpaceVectorType &, Self::SpaceVectorType &, Self::SpaceVectorType &, const int=-1) const
	Get volume influenced by one parameter.
virtual Types::Coordinate	cmtk::Xform::GetLandmarksMSD (const MatchedLandmarkList *ll) const
	Return registration error for set of source/target landmarks.
Variables
TDataType	cmtk::Accumulators::Avg::m_Sum
	Current sum of values.
unsigned int	cmtk::Accumulators::Avg::m_Count
	Counter.
bool	cmtk::Accumulators::Max::m_Valid
	Flag whether there is a valid accumulated value.
TDataType	cmtk::Accumulators::Max::m_Maximum
	Current maximum.
TDataType	cmtk::Accumulators::Sum::m_Sum
	Current sum.
Vector3D	cmtk::ControlPoint::deformed
	Deformed control point position.
bool	cmtk::ControlPoint::active
	Is this an active (true) or passive (false) control point?
DataGrid::SmartPtr	cmtk::DataGridFilter::m_DataGrid
	The DataGrid object we're working on.
TypedArray::SmartPtr	cmtk::DataGridFilter::FilterThreadParameters::m_Result
	Pointer to result pixel data.
DataGrid::SmartConstPtr	cmtk::DataGridMorphologicalOperators::m_DataGrid
	The DataGrid object we're working on.
FixedVector< DIM, int >	cmtk::FilterMaskPixel::Location
	Relative location of this pixel.
int	cmtk::FilterMaskPixel::RelativeIndex
	Relative index of this pixel in source image from center of kernel.
Types::DataItem	cmtk::FilterMaskPixel::Coefficient
	Filter coefficient.
int	cmtk::FilterMaskPixel::PixelIndex
	Cached source index of image pixel for this element.
bool	cmtk::FilterMaskPixel::Valid
	Active flag.
Types::Coordinate	cmtk::FilterMask::Gaussian::InvStandardDeviation
	Standard deviation.
Types::Coordinate	cmtk::FilterMask::Gaussian::NormFactor
	Gaussian normalization factor.
const FPInitializeUnion	cmtk::MathUtil::FPInitializeInf
const void *	cmtk::MathUtil::FPInitializeNaN_P = &FPInitializeNaN
const void *	cmtk::MathUtil::FPInitializeInf_P = &FPInitializeInf
const void *	cmtk::MathUtil::FPInitializeNaN_fP = &FPInitializeNaN.f[1]
const void *	cmtk::MathUtil::FPInitializeInf_fP = &FPInitializeInf.f[1]
DataGrid::IndexType	cmtk::SplineWarpXform::VolumeDims
	Dimensions of the volume image linked to this transformation.
int	cmtk::SplineWarpXform::GridPointOffset [48]
	Relative offsets of all control points in a 4 x 4 x 4 neighborhood.
int	cmtk::SplineWarpXform::JacobianConstraintThreadInfo::ThisThreadIndex
	Unique index of this thread instance among all threads.
int	cmtk::SplineWarpXform::JacobianConstraintThreadInfo::NumberOfThreads
	Total number of threads created.
Types::Coordinate	cmtk::SplineWarpXform::JacobianConstraintThreadInfo::Constraint
	Constraint for subvolume handled by this thread.
const char *	cmtk::DataClassString []
const char *	cmtk::DataTypeName []
	Names of scalar data types.
const ScalarDataType	cmtk::TYPE_ITEM = TYPE_DOUBLE
const ScalarDataType	cmtk::TYPE_COORDINATE = TYPE_DOUBLE
UniformVolume::SmartPtr	cmtk::UniformVolumeFilter::m_UniformVolume
	The UniformVolume object we're working on.
static const char *const	cmtk::AnatomicalOrientationBase::ORIENTATION_STANDARD = "RAS"
	Orientation of standardized reoriented image axes (LR/AP/IS).
static const char *const	cmtk::AnatomicalOrientationBase::SPACE_CMTK = "RAS"
	Standard CMTK coordinate space (LR/PA/IS).
static const char *const	cmtk::AnatomicalOrientationBase::SPACE_ITK = "LPS"
	Standard ITK coordinate space (RL/AP/IS).
static const Types::DataItem	cmtk::DataTypeTraits< byte >::Min = 0
	Minimum value in this type.
static const Types::DataItem	cmtk::DataTypeTraits< byte >::Max = UCHAR_MAX
	Maximum value in this type.
static const Types::DataItem	cmtk::DataTypeTraits< char >::Min = SCHAR_MIN
	Minimum value in this type.
static const Types::DataItem	cmtk::DataTypeTraits< char >::Max = SCHAR_MAX
	Maximum value in this type.
static const Types::DataItem	cmtk::DataTypeTraits< signed short >::Min = SHRT_MIN
	Minimum value in this type.
static const Types::DataItem	cmtk::DataTypeTraits< signed short >::Max = SHRT_MAX
	Maximum value in this type.
static const Types::DataItem	cmtk::DataTypeTraits< unsigned short >::Min = 0
	Minimum value in this type.
static const Types::DataItem	cmtk::DataTypeTraits< unsigned short >::Max = USHRT_MAX
	Maximum value in this type.
static const Types::DataItem	cmtk::DataTypeTraits< int >::Min = INT_MIN
	Minimum value in this type.
static const Types::DataItem	cmtk::DataTypeTraits< int >::Max = INT_MAX
	Maximum value in this type.
static const Self	cmtk::Matrix4x4::IdentityMatrix
	Identity transformation matrix.
Friends
class	cmtk::SplineWarpXform::SplineWarpXformUniformVolume
	Friend declaration.
Shortcut class typedefs for typed arrays.
typedef TemplateArray< byte >	cmtk::ByteArray
	Array of (unsigned) byte values.
typedef TemplateArray< char >	cmtk::CharArray
	Array of (signed) char values.
typedef TemplateArray< short >	cmtk::ShortArray
	Array of signed short values.
typedef TemplateArray < unsigned short >	cmtk::UShortArray
	Array of unsigned short values.
typedef TemplateArray< int >	cmtk::IntArray
	Array of (signed) integer values.
typedef TemplateArray< float >	cmtk::FloatArray
	Array of single-precision float values.
typedef TemplateArray< double >	cmtk::DoubleArray
	Array of double-precision float values.
Precomputed grid indices.
These arrays hold the precomputed grid indices of the deformed grid's voxels with respect to the control point grid of this deformation.
std::vector< int >	cmtk::SplineWarpXform::gX
	x-axis.
std::vector< int >	cmtk::SplineWarpXform::gY
	y-axis.
std::vector< int >	cmtk::SplineWarpXform::gZ
	z-axis.
Precomputed spline coefficients.
These arrays hold the precomputed spline coefficients for deforming the voxel locations in the associated deformed grid.
std::vector< Types::Coordinate >	cmtk::SplineWarpXform::splineX
	x-axis.
std::vector< Types::Coordinate >	cmtk::SplineWarpXform::splineY
	y-axis.
std::vector< Types::Coordinate >	cmtk::SplineWarpXform::splineZ
	z-axis.
Precomputed derivative spline coefficients.
These arrays hold the precomputed derivatives of the spline coefficients. This allows for rapid evaluation of the Jacobian determinant.
std::vector< Types::Coordinate >	cmtk::SplineWarpXform::dsplineX
	x-axis.
std::vector< Types::Coordinate >	cmtk::SplineWarpXform::dsplineY
	y-axis.
std::vector< Types::Coordinate >	cmtk::SplineWarpXform::dsplineZ
	z-axis.
Matrix access.
void	cmtk::AffineXform::SetMatrix (const MatrixType &matrix)
void	cmtk::AffineXform::SetMatrix (const float matrix[4][4])
	Set transformation matrix.
void	cmtk::AffineXform::SetMatrix (const double matrix[4][4])
Image filter operators.
These functions perform various filter operations on the image data. For each filter, two functions are implemented: GetXXXFiltered and ApplyXXXFilter. The former returns a pointer to a newly allocated pixel data array that contains the filtered data. The latter replaces the current object's pixel data with the filtered data. Note: A complete new ScalarImage object with filtered pixel data can easily and efficiently be created by calling object->Clone( false )->ApplyXXXFilter().
TypedArray::SmartPtr	cmtk::ScalarImage::GetMedianFiltered (const byte range) const
	Return median-filtered image data.
TypedArray::SmartPtr	cmtk::ScalarImage::GetGaussFiltered (const Types::Coordinate stdDev) const
	Return Gauss-filtered (smoothed) image data.
TypedArray::SmartPtr	cmtk::ScalarImage::GetSobel2DFiltered () const
	Return Sobel-filtered (edge-enhanced) image data.
TypedArray::SmartPtr	cmtk::ScalarImage::GetSobelFiltered (const bool horizontal, const bool absolute=false) const
	Return Sobel-filtered (edge-enhanced) image data.
TypedArray::SmartPtr	cmtk::ScalarImage::GetLaplace2DFiltered () const
	Return Laplace-filtered (edge-enhanced) image data.
ScalarImage *	cmtk::ScalarImage::ApplyMedianFilter (const byte range)
	Replace pixel data with median-filtered data.
ScalarImage *	cmtk::ScalarImage::ApplyGaussFilter (const Types::Coordinate stdDev)
	Replace pixel data with Gauss-filtered data.
ScalarImage *	cmtk::ScalarImage::ApplySobel2DFilter ()
	Replace pixel data with Sobel-filtered data.
ScalarImage *	cmtk::ScalarImage::ApplyLaplace2DFilter ()
	Replace pixel data with Laplace-filtered data.
ScalarImage *	cmtk::ScalarImage::ApplySobelFilter (const bool horizontal, const bool absolute=false)
	Replace pixel data with 1-D Sobel-filtered data.

---

Detailed Description

This library provides classes for basic objects, such as volumes, transformations, vectors, functionals, and meta information.

---

Define Documentation

#define CMTK_ITEM_MAX   DBL_MAX

Definition at line 145 of file cmtkTypes.h.

#define CMTK_ITEM_MIN   DBL_MIN

Definition at line 146 of file cmtkTypes.h.

#define CMTK_ITEM_NAN   CMTK_DOUBLE_NAN

Definition at line 147 of file cmtkTypes.h.

#define CMTK_SCALARIMAGE_ABSOLUTE   true

Definition at line 386 of file cmtkScalarImage.h.

#define CMTK_SCALARIMAGE_CLONEDATA   true

Definition at line 380 of file cmtkScalarImage.h.

#define CMTK_SCALARIMAGE_HORIZONTAL   true

Definition at line 382 of file cmtkScalarImage.h.

Referenced by cmtk::ScalarImageSimilarity::GetGradientCorrelation(), and cmtk::ScalarImageSimilarity::GetGradientDifference().

#define CMTK_SCALARIMAGE_NOCLONEDATA   false

Definition at line 378 of file cmtkScalarImage.h.

#define CMTK_SCALARIMAGE_SIGNED   false

Definition at line 388 of file cmtkScalarImage.h.

#define CMTK_SCALARIMAGE_VERTICAL   false

Definition at line 384 of file cmtkScalarImage.h.

Referenced by cmtk::ScalarImageSimilarity::GetGradientCorrelation(), and cmtk::ScalarImageSimilarity::GetGradientDifference().

#define TOL   1.0e-5

Definition at line 54 of file cmtkGeneralLinearModel.cxx.

Referenced by cmtk::GeneralLinearModel::GeneralLinearModel().

---

Typedef Documentation

typedef TemplateArray<byte> cmtk::ByteArray

Array of (unsigned) byte values.

Definition at line 650 of file cmtkTemplateArray.h.

typedef TemplateArray<char> cmtk::CharArray

Array of (signed) char values.

Definition at line 653 of file cmtkTemplateArray.h.

typedef Matrix3x3<Types::Coordinate> cmtk::CoordinateMatrix3x3

Define coordinate matrix.

Definition at line 192 of file cmtkMatrix3x3.h.

typedef Vector<Types::Coordinate> cmtk::CoordinateVector

Shortcut definition.

This typedef defines a name for the frequently used vectors over the Types::Coordinate type. This is used for all kinds of parameters vectors etc.

Definition at line 415 of file cmtkVector.h.

typedef TemplateArray<double> cmtk::DoubleArray

Array of double-precision float values.

Definition at line 668 of file cmtkTemplateArray.h.

typedef TemplateArray<float> cmtk::FloatArray

Array of single-precision float values.

Definition at line 665 of file cmtkTemplateArray.h.

typedef Vector<float> cmtk::FloatVector

Shortcut definition.

This typedef defines a name for the frequently used vectors over the float type.

Definition at line 421 of file cmtkVector.h.

typedef TemplateArray<int> cmtk::IntArray

Array of (signed) integer values.

Definition at line 662 of file cmtkTemplateArray.h.

typedef std::map<int,SegmentationLabel> cmtk::SegmentationLabelMap

Map from numerical IDs to labels.

Definition at line 68 of file cmtkSegmentationLabel.h.

typedef TemplateArray<short> cmtk::ShortArray

Array of signed short values.

Definition at line 656 of file cmtkTemplateArray.h.

typedef SmartConstPointer<Self> cmtk::SplineWarpXform::SmartConstPtr [inherited]

Smart pointer to const SplineWarpXform.

Reimplemented from cmtk::WarpXform.

Definition at line 74 of file cmtkSplineWarpXform.h.

typedef SmartPointer<Self> cmtk::SplineWarpXform::SmartPtr [inherited]

Smart pointer to SplineWarpXform.

Reimplemented from cmtk::WarpXform.

Definition at line 71 of file cmtkSplineWarpXform.h.

template<int DIM>

typedef SmartPointer<Self> cmtk::FilterMaskPixel< DIM >::SmartPtr [inherited]

Smart pointer.

Definition at line 68 of file cmtkFilterMask.h.

template<int DIM>

typedef SmartPointer<Self> cmtk::FilterMask< DIM >::SmartPtr [inherited]

Smert pointer to this class.

Definition at line 119 of file cmtkFilterMask.h.

typedef ActiveDeformationModel<SplineWarpXform> cmtk::SplineActiveDeformationModel

Spline warp active deformation model.

Definition at line 107 of file cmtkActiveDeformationModel.h.

typedef WarpXform cmtk::SplineWarpXform::Superclass [inherited]

Parent class.

Definition at line 68 of file cmtkSplineWarpXform.h.

template<int DIM>

typedef std::vector< FilterMaskPixel<DIM> > cmtk::FilterMask< DIM >::Superclass [inherited]

Direct parent class.

Definition at line 116 of file cmtkFilterMask.h.

typedef TemplateArray<unsigned short> cmtk::UShortArray

Array of unsigned short values.

Definition at line 659 of file cmtkTemplateArray.h.

typedef FixedVector<3,Types::Coordinate> cmtk::Vector3D

Convenience typedef: vectors in 3D coordinate space.

Definition at line 49 of file cmtkVector3D.h.

---

Enumeration Type Documentation

anonymous enum

Identifiers for coordinate axes.

Note:

It is very important that the enumeration constants remain defined equal to the integer constants 0 through 2, since quite a bit of code depends on this for array indexing.

Enumerator:

AXIS_X	x-axis.
AXIS_Y	y-axis.
AXIS_Z	z-axis.

Definition at line 74 of file cmtkTypes.h.

enum cmtk::DataClass

Class of image data.

Enumerator:

DATACLASS_GREY	Grey-level data.
DATACLASS_LABEL	(Segmented) label data.
DATACLASS_UNKNOWN	Data type unknown.

Definition at line 85 of file cmtkTypes.h.

enum cmtk::ScalarDataType

Scalar data type identifiers.

Enumerator:

TYPE_BYTE	Unsigned byte data (8 bit, range 0-255).
TYPE_CHAR	Signed byte data (8 bit, range -128-127).
TYPE_SHORT	Signed byte data (16 bit, range -32768-32767).
TYPE_USHORT	Unsigned byte data (16 bit, range 0-65535).
TYPE_INT	Signed integer data (32 bit).
TYPE_UINT	Unsigned integer data (32 bits).
TYPE_FLOAT	Single precision float data (32 bits).
TYPE_DOUBLE	Double precision float data (64 bits).
TYPE_NONE	No data type defined.

Definition at line 102 of file cmtkTypes.h.

---

Function Documentation

template<class W >

cmtk::ActiveDeformationModel< W >::ActiveDeformationModel	(	const std::list< SmartPointer< W > >	deformationList,
		const unsigned int	numberOfModes,
		const bool	includeScaleInModel = true,
		const bool	includeReferenceInModel = true
	)		[inherited]

Build deformation model from list of deformations.

All deformations in the list must be of the same type, have the same arrangement of control points, and must be defined on the same domain (reference image).

Definition at line 49 of file cmtkActiveDeformationModel.cxx.

References cmtk::Memory::DeleteArray(), and cmtk::StdErr.

cmtk::ActiveShapeModel::ActiveShapeModel	(	CoordinateVector::SmartPtr &	mean,
		DirectionSet::SmartPtr &	modes,
		CoordinateVector::SmartPtr &	modeVariances
	)		[inherited]

Construct using given mean and modes.

Definition at line 51 of file cmtkActiveShapeModel.cxx.

template<class T >

void cmtk::Histogram< T >::AddHistogram

(

const Self &

other )

[inherited]

Add values from another histogram.

Adding is done by corresponding bins. The caller has to make sure that both histograms actually have the same number and arrangement of bins. It is also a good idea to ensure that the data range of these bins is the same in both objects. Both can be guaranteed if one histogram was created from the other by a call to Clone() for example.

Parameters:

other

A pointer to the other histogram. Its bin values are added to this object's bins.

Definition at line 87 of file cmtkHistogram.cxx.

References cmtk::Histogram< T >::GetNumBins(), and cmtk::Histogram< T >::m_Bins.

void cmtk::MatchedLandmarkList::AddLandmarkLists	(	const LandmarkList *	sourceList,
		const LandmarkList *	targetList
	)		[inherited]

Initialize from two separate landmark lists.

Definition at line 44 of file cmtkMatchedLandmarkList.cxx.

References cmtk::LandmarkList::FindByName().

template<class TDataType >

void cmtk::Accumulators::Avg< TDataType >::AddValue

(

const TDataType &

value )

[inline, inherited]

Add a value.

Definition at line 66 of file cmtkAccumulatorAvg.h.

template<class TDataType >

void cmtk::Accumulators::Max< TDataType >::AddValue

(

const TDataType &

value )

[inline, inherited]

Add a value.

Definition at line 65 of file cmtkAccumulatorMax.h.

template<class TDataType >

void cmtk::Accumulators::Sum< TDataType >::AddValue

(

const TDataType &

value )

[inline, inherited]

Add a value.

Definition at line 66 of file cmtkAccumulatorSum.h.

template<class T>

void cmtk::Histogram< T >::AddWeightedSymmetricKernel	(	const size_t	bin,
		const size_t	kernelRadius,
		const T *	kernel,
		const T	factor = 1
	)		[inherited]

Add weighted symmetric kernel to histogram.

Parameters:

bin	Histogram bin index
kernelRadius	Kernel radius
factor	Kernel multiplication factor

Definition at line 46 of file cmtkHistogram.txx.

Referenced by cmtk::CongealingFunctional< TXform >::EvaluateProbabilisticThread(), cmtk::CongealingFunctional< TXform >::EvaluateThread(), and cmtk::FilterVolume::RohlfingFilter().

template<class T>

void cmtk::Histogram< T >::AddWeightedSymmetricKernelFractional	(	const double	bin,
		const size_t	kernelRadius,
		const T *	kernel,
		const T	factor = 1
	)		[inherited]

Add weighted symmetric kernel to histogram, spreading contriubtions between adjacent bins.

Parameters:

bin	Histogram bin index
kernelRadius	Kernel radius
factor	Kernel multiplication factor

Definition at line 63 of file cmtkHistogram.txx.

Referenced by cmtk::TemplateArray< T >::GetEntropy().

void cmtk::ScalarImage::AdjustAspect

(

const bool

interpolate = false )

[inherited]

Adjust aspect ratio.

Definition at line 819 of file cmtkScalarImage.cxx.

References cmtk::ScalarImage::AdjustAspectX(), and cmtk::ScalarImage::AdjustAspectY().

void cmtk::ScalarImage::AdjustAspectX

(

const bool

interpolate = false )

[private, inherited]

Adjust aspect ratio by stretching in X-direction.

Definition at line 895 of file cmtkScalarImage.cxx.

References cmtk::TypedArray::Create(), and cmtk::ScalarImage::m_Dims.

Referenced by cmtk::ScalarImage::AdjustAspect().

void cmtk::ScalarImage::AdjustAspectY

(

const bool

interpolate = false )

[private, inherited]

Adjust aspect ratio by stretching in Y-direction.

Definition at line 829 of file cmtkScalarImage.cxx.

References cmtk::TypedArray::Create(), and cmtk::ScalarImage::m_Dims.

Referenced by cmtk::ScalarImage::AdjustAspect().

void cmtk::ScalarImage::AdjustToIsotropic	(	const Types::Coordinate	pixelSize,
		const bool	interpolate = false
	)		[inherited]

Adjust aspect ratio.

Definition at line 800 of file cmtkScalarImage.cxx.

Referenced by cmtk::QtTriplanarWindow::slotSwitchImageCo(), and cmtk::QtTriplanarWindow::slotSwitchImageSa().

cmtk::AffineXform::AffineXform

(

const AffineXform &

other )

[inherited]

Copy transform by reference.

Definition at line 59 of file cmtkAffineXform.cxx.

References cmtk::Xform::AllocateParameterVector(), cmtk::AffineXform::ComposeMatrix(), cmtk::AffineXform::m_LogScaleFactors, cmtk::Xform::m_ParameterVector, cmtk::AffineXform::NumberDOFs, and cmtk::AffineXform::TotalNumberOfParameters.

cmtk::AffineXform::AffineXform	(	const Types::Coordinate	matrix[4][4],
		const Types::Coordinate *	center = NULL
	)		[inherited]

Create transformation from transformation matrix.

Parameters:

matrix	The homogeneous 4x4 affine transformation matrix.
center	If non-NULL, this parameter points to a three-coordinate vector defining the rotation center of the constructed transformation. This does only effect the computation of the translation vector when decomposing the given matrix into its parameter representation.

Definition at line 73 of file cmtkAffineXform.cxx.

cmtk::AffineXform::AffineXform	(	const MatrixType &	matrix,
		const Types::Coordinate *	center = NULL
	)		[inherited]

Create transformation from transformation matrix.

Parameters:

matrix	The homogeneous 4x4 affine transformation matrix.
center	If non-NULL, this parameter points to a three-coordinate vector defining the rotation center of the constructed transformation. This does only effect the computation of the translation vector when decomposing the given matrix into its parameter representation.

Definition at line 88 of file cmtkAffineXform.cxx.

cmtk::AffineXform::AffineXform	(	const Types::Coordinate	matrix[4][4],
		const Types::Coordinate	xlate[3],
		const Types::Coordinate	center[3]
	)		[inherited]

Create transformation from transformation matrix.

Translation vector and rotation center are given in addition to the 4x4 transformation matrix..

Parameters:

matrix	The homogeneous 4x4 affine transformation matrix. If a translation is defined by this matrix, it is ignored.
xlate	Translation of the constructed transformation.
center	Rotation center of the constructed transformation.

Definition at line 103 of file cmtkAffineXform.cxx.

void cmtk::ActiveShapeModel::Allocate	(	const unsigned int	numberOfPoints,
		const unsigned int	numberOfModes
	)		[protected, inherited]

Allocate data structures.

If this instance already has data structures allocated, these are deallocated first.

Definition at line 238 of file cmtkActiveShapeModel.cxx.

void cmtk::Xform::AllocateParameterVector

(

const size_t

numberOfParameters )

[protected, inherited]

Allocate parameter vector.

Definition at line 49 of file cmtkXform.cxx.

References NULL.

Referenced by cmtk::AffineXform::AffineXform().

void cmtk::ScalarImage::ApplyBinaryMask	(	const ScalarImage *	maskImage,
		const bool	invert = false
	)		[virtual, inherited]

Apply binary mask to image.

Parameters:

maskImage	Binary mask image.
invert	If this flag is set, then all pixels are set to NULL where the mask image is zero. Otherwise (default) the pixels are set to NULL where the mask image is non-zero.

Definition at line 247 of file cmtkScalarImage.cxx.

References cmtk::TypedArray::Get().

template<class T >

void cmtk::TemplateArray< T >::ApplyFunctionDouble

(

typename Self::FunctionTypeDouble

f )

[virtual, inherited]

Apply real function to data.

Implements cmtk::TypedArray.

Definition at line 249 of file cmtkTemplateArray.txx.

template<class T >

void cmtk::TemplateArray< T >::ApplyFunctionFloat

(

typename Self::FunctionTypeFloat

f )

[virtual, inherited]

Apply real function to data.

Implements cmtk::TypedArray.

Definition at line 236 of file cmtkTemplateArray.txx.

template<class T >

void cmtk::TemplateArray< T >::ApplyFunctionObject

(

const TypedArrayFunction &

f )

[virtual, inherited]

Apply function class to the values of this array.

Implements cmtk::TypedArray.

Definition at line 336 of file cmtkTemplateArray.txx.

ScalarImage* cmtk::ScalarImage::ApplyGaussFilter

(

const Types::Coordinate

stdDev )

[inline, inherited]

Replace pixel data with Gauss-filtered data.

Definition at line 286 of file cmtkScalarImage.h.

void cmtk::DeformationField::ApplyInPlace

(

Self::SpaceVectorType &

v )

const [virtual, inherited]

Apply transformation to vector in-place.

Implements cmtk::Xform.

Definition at line 114 of file cmtkDeformationField.cxx.

virtual void cmtk::SplineWarpXform::ApplyInPlace

(

Self::SpaceVectorType &

v )

const [inline, virtual, inherited]

Replace existing vector with transformed location.

Implements cmtk::Xform.

Definition at line 244 of file cmtkSplineWarpXform.h.

Referenced by cmtk::Slicer::ExecuteSplineWarp().

bool cmtk::SplineWarpXform::ApplyInverse	(	const Self::SpaceVectorType &	v,
		Self::SpaceVectorType &	u,
		const Types::Coordinate	accuracy = 0.01
	)		const [virtual, inherited]

Return origin of warped vector.

Note that since this class of transformation is not closed under inversion this function computes only a more or less accurate numerical approximation to the actual origin of a warped vector. Note also that this computation is everything but computationally efficient.

Returns:

True is the given inverse was succesfully comuted, false if the given warped vector was outside the target domain of this transformation.

Implements cmtk::Xform.

Definition at line 46 of file cmtkSplineWarpXform_Inverse.cxx.

bool cmtk::SplineWarpXform::ApplyInverseInPlace	(	Self::SpaceVectorType &	v,
		const Types::Coordinate	accuracy = 0.01
	)		const [virtual, inherited]

Return origin of warped vector.

Note that since this class of transformation is not closed under inversion this function computes only a more or less accurate numerical approximation to the actual origin of a warped vector. Note also that this computation is everything but computationally efficient.

Returns:

True is the given inverse was succesfully comuted, false if the given warped vector was outside the target domain of this transformation.

Implements cmtk::Xform.

Definition at line 54 of file cmtkSplineWarpXform_Inverse.cxx.

Referenced by cmtk::ReformatVolume::GetTransformedReferenceGrey(), cmtk::ReformatVolume::GetTransformedReferenceGreyAvg(), cmtk::ReformatVolume::GetTransformedReferenceJacobianAvgThread(), and cmtk::ReformatVolume::GetTransformedReferenceLabel().

bool cmtk::SplineWarpXform::ApplyInverseInPlaceWithInitial	(	Self::SpaceVectorType &	v,
		const Self::SpaceVectorType &	initial,
		const Types::Coordinate	accuracy = 0.01
	)		const [virtual, inherited]

Return origin of warped vector.

Note that since this class of transformation is not closed under inversion this function computes only a more or less accurate numerical approximation to the actual origin of a warped vector. Note also that this computation is everything but computationally efficient.

Parameters:

v	Input location; is replaced with the inverse transformation applied to it upon return.
initial	Initial estimate for the original location. Search goes from here. This is useful for looking up the original locations of a large number of closely located vectors, for example all pixels in an image.
accuracy	Accuracy of the inversion, i.e., residual inverse consistency error threshold.

Returns:

True is the given inverse was succesfully comuted, false if the given warped vector was outside the target domain of this transformation.

Reimplemented from cmtk::Xform.

Definition at line 118 of file cmtkSplineWarpXform_Inverse.cxx.

References cmtk::Matrix3x3< T >::GetTranspose(), cmtk::Matrix3x3< T >::Invert3x3(), and cmtk::FixedVector< NDIM, T >::RootSumOfSquares().

ScalarImage* cmtk::ScalarImage::ApplyLaplace2DFilter

(

)

[inline, inherited]

Replace pixel data with Laplace-filtered data.

Definition at line 312 of file cmtkScalarImage.h.

ScalarImage* cmtk::ScalarImage::ApplyMedianFilter

(

const byte

range )

[inline, inherited]

Replace pixel data with median-filtered data.

Definition at line 272 of file cmtkScalarImage.h.

void cmtk::DataGrid::ApplyMirrorPlane

(

const int

axis = AXIS_X )

[inherited]

Replace data with mirrored version.

Definition at line 273 of file cmtkDataGrid.cxx.

ScalarImage* cmtk::ScalarImage::ApplySobel2DFilter

(

)

[inline, inherited]

Replace pixel data with Sobel-filtered data.

Definition at line 300 of file cmtkScalarImage.h.

ScalarImage* cmtk::ScalarImage::ApplySobelFilter	(	const bool	horizontal,
		const bool	absolute = false
	)		[inline, inherited]

Replace pixel data with 1-D Sobel-filtered data.

Definition at line 324 of file cmtkScalarImage.h.

static Types::Coordinate cmtk::CubicSpline::ApproxSpline	(	const int	k,
		const Types::Coordinate	t
	)		[inline, static, inherited]

Compute the value of a given approximating spline function.

Definition at line 81 of file cmtkCubicSpline.h.

Referenced by cmtk::SplineWarpXformUniformVolume::RegisterVolumeAxis().

static Types::Coordinate cmtk::CubicSpline::ApproxSpline1

(

const Types::Coordinate

t )

[inline, static, inherited]

Compute a value of the 1st approximating spline function.

Definition at line 63 of file cmtkCubicSpline.h.

static Types::Coordinate cmtk::CubicSpline::ApproxSpline2

(

const Types::Coordinate

t )

[inline, static, inherited]

Compute a value of the 2nd approximating spline function.

Definition at line 69 of file cmtkCubicSpline.h.

static Types::Coordinate cmtk::CubicSpline::ApproxSpline3

(

const Types::Coordinate

t )

[inline, static, inherited]

Compute a value of the 3rd approximating spline function.

Definition at line 75 of file cmtkCubicSpline.h.

cmtk::BitVector::BitVector	(	const size_t	size,
		const bool	initial = false
	)		[inherited]

Constructor.

Parameters:

size	Number of bits handled by this object.
initial	Initial value for the bits in the array.

Definition at line 46 of file cmtkBitVector.cxx.

References cmtk::Memory::Set().

cmtk::BitVector::BitVector	(	const size_t	size,
		byte *const	bitset
	)		[inherited]

Constructor.

Parameters:

size	Number of bits handled by this object.
bitset	Byte array that is used to initialize the array.

Definition at line 57 of file cmtkBitVector.cxx.

void cmtk::TypedArray::BlockReverse	(	const size_t	fromOffset,
		const size_t	blockLength
	)		[virtual, inherited]

Revert order of items in a given range.

Attention:

This implementation only works for item sizes up to 16 bytes (128 bits); above that, the internal buffer size needs to be increased.

Definition at line 93 of file cmtkTypedArray.cxx.

Referenced by cmtk::DataGrid::MirrorPlaneInPlace().

template<class T >

void cmtk::TemplateArray< T >::BlockSet	(	const Types::DataItem	value,
		const size_t	fromOffset,
		const size_t	toOffset
	)		[virtual, inherited]

Set data block to constant value.

Implements cmtk::TypedArray.

Definition at line 350 of file cmtkTemplateArray.txx.

void cmtk::TypedArray::BlockSwap	(	const size_t	fromOffset,
		const size_t	toOffset,
		const size_t	blockLength
	)		[virtual, inherited]

Exchange two data blocks.

Internally, the data is copied in chunks of up to 2KB (currently), using an 'automatic' intermediate buffer of that size.

Definition at line 60 of file cmtkTypedArray.cxx.

Referenced by cmtk::DataGrid::MirrorPlaneInPlace().

template<class TDistanceDataType >

void cmtk::UniformDistanceMap< TDistanceDataType >::BuildDistanceMap	(	const UniformVolume &	volume,
		const byte	flags,
		const Types::DataItem	value = 0,
		const Types::DataItem	window = 0
	)		[private, inherited]

Compute distance map.

Definition at line 65 of file cmtkUniformDistanceMap.cxx.

References cmtk::TypedArray::Get(), cmtk::DataGrid::GetNumberOfPixels(), cmtk::DataGrid::m_Dims, and cmtk::Volume::Size.

void cmtk::AffineXform::CanonicalRotationRange

(

)

[private, inherited]

Correct rotation parameters to canonical range -180 to 180.

Definition at line 490 of file cmtkAffineXform.cxx.

References cmtk::Xform::m_Parameters.

Referenced by cmtk::AffineXform::SetParameter(), and cmtk::AffineXform::SetParamVector().

void cmtk::AffineXform::ChangeCenter

(

const Self::SpaceVectorType &

center )

[inherited]

Create equivalent transformation with different rotational center.

In fact, this function only computes a new translation vector reflecting the changed rotation center. The transformation matrix itself is not changed.

Definition at line 222 of file cmtkAffineXform.cxx.

References cmtk::AffineXform::RetCenter(), cmtk::AffineXform::RetXlate(), and cmtk::AffineXform::RotateScaleShear().

Referenced by cmtk::MakeInitialAffineTransformation::AlignDirectionVectors(), cmtk::MakeInitialAffineTransformation::AlignPrincipalAxes(), cmtk::ParametricPlane::GetAlignmentXform(), and cmtk::AffineXform::MakeInverse().

template<class T>

Matrix4x4< T > & cmtk::Matrix4x4< T >::ChangeCoordinateSystem	(	const FixedVector< 3, T > &	newX,
		const FixedVector< 3, T > &	newY
	)		[inherited]

Change reference coordinate system.

Definition at line 487 of file cmtkMatrix4x4.cxx.

template<class T >

void cmtk::TemplateArray< T >::ChangeEndianness

(

)

[virtual, inherited]

Change endianness of data.

Implements cmtk::TypedArray.

Definition at line 315 of file cmtkTemplateArray.txx.

template<class T >

T cmtk::MathUtil::CholeskyDeterminant	(	const Matrix2D< T > &	matrix,
		int	n
	)		[static, inherited]

Determinant of an n x n square matrix.

Definition at line 221 of file cmtkMathUtil_LinAlg.cxx.

int cmtk::VolumeClipping::ClipX	(	Types::Coordinate &	fromFactor,
		Types::Coordinate &	toFactor,
		const Vector3D &	offset,
		const Types::Coordinate	initFromFactor = 0,
		const Types::Coordinate	initToFactor = 1,
		const bool	lowerClosed = false,
		const bool	upperClosed = false
	)		const [inherited]

Compute line-to-volume intersection.

This function computes the part of a lines that lies within a given volume.

Returns:

This function returns 1 if and only if there is a non-empty intersection of line and volume. In this case, the intersection is described by fromFactor and toFactor.

Parameters:

fromFactor	If the function returned 1, this variable holds the relative distance to the entrance point of the line into the volume. 0 means the line's starting point, 1 means its end.
toFactor	If the function returned 1, this variable holds the relative distance to the exit point of the line from the volume. Possible values range from 0 to 1 and have the same meaning as fromFactor.
offset	This 3D vector is the line's starting point.
initFromFactor	The fromFactor parameter's value is initialized with this value. It is therefore the lower bound of the parameter range that is available for intersection.
initToFactor	The toFactor parameter's value is initialized with this value. It is therefore the upper bound of the parameter range that is available for intersection. One application for this parameter is to use a value bigger than 1, even if [0,1] is the allowed range. Then, by testing if toFactor == 1.0, it can be determined whether clipping set the value to 1. This, for example allows to tell closed from open intervals, which may be important for subsequent computation such as volume probing.
lowerClosed	This flag defines whether lower range boundaries are open (value 0, default) or closed (value 1). In case of an open range, the bounding value itself is not an element of the range. Thus, if an intersection is entirely on the boundary, then it is empty in case of an open range.
upperClosed	This flag has the same meaning and default as lowerClosed, but refers to the ranges' upper bounds.

Definition at line 54 of file cmtkVolumeClipping.cxx.

Referenced by cmtk::VoxelMatchingAffineFunctional::ClipX(), cmtk::ImagePairAffineRegistrationFunctional::ClipX(), and cmtk::AffineMultiChannelRegistrationFunctional< TMultiChannelMetricFunctional >::ClipX().

int cmtk::VolumeClipping::ClipY	(	Types::Coordinate &	fromFactor,
		Types::Coordinate &	toFactor,
		const Vector3D &	offset,
		const Types::Coordinate	initFromFactor = 0,
		const Types::Coordinate	initToFactor = 1
	)		const [inherited]

Compute plane-to-volume intersection.

This function computes the part of a plane that intersects with a given volume. The intersection is only tested with respect to the dY direction. for the range of relative positions returned by fromFactor and toFactor, IntersectX can be used to computed the exact 2D intersection.

Parameters and return value are identical to IntersectionX.

Definition at line 90 of file cmtkVolumeClipping.cxx.

Referenced by cmtk::VoxelMatchingAffineFunctional::ClipY(), cmtk::ImagePairAffineRegistrationFunctional::ClipY(), and cmtk::AffineMultiChannelRegistrationFunctional< TMultiChannelMetricFunctional >::ClipY().

int cmtk::VolumeClipping::ClipZ	(	Types::Coordinate &	fromFactor,
		Types::Coordinate &	toFactor,
		const Vector3D &	offset,
		const Types::Coordinate	initFromFactor = 0,
		const Types::Coordinate	initToFactor = 1
	)		const [inherited]

Compute volume-to-volume intersection.

This function computes the part of a volume that intersects with a given volume. The intersection is only tested with respect to the dZ direction. for the range of relative positions returned by fromFactor and toFactor, IntersectY and afterwards IntersectX can be used to computed the exact 3D intersection.

Parameters and return value are identical to IntersectionX.

Definition at line 131 of file cmtkVolumeClipping.cxx.

Referenced by cmtk::VoxelMatchingAffineFunctional::ClipZ(), cmtk::ImagePairAffineRegistrationFunctional::ClipZ(), and cmtk::AffineMultiChannelRegistrationFunctional< TMultiChannelMetricFunctional >::ClipZ().

Self::SmartPtr cmtk::SplineWarpXform::Clone

(

)

const [inline, inherited]

Clone and return smart pointer.

Reimplemented from cmtk::Xform.

Definition at line 95 of file cmtkSplineWarpXform.h.

ScalarImage * cmtk::ScalarImage::Clone

(

)

const [virtual, inherited]

Clone (duplicate) this object.

Definition at line 367 of file cmtkScalarImage.cxx.

References cmtk::ScalarImage::m_Dims, cmtk::ScalarImage::m_ImageOrigin, cmtk::ScalarImage::ScalarImage(), and cmtk::ScalarImage::SetImageOrigin().

Referenced by cmtk::ScalarImage::ScalarImage().

ScalarImage * cmtk::ScalarImage::Clone

(

const bool

clonePixelData )

[virtual, inherited]

Clone (duplicate) this object.

This function optionally allows to reference the original pixel data rather than duplicating it. This is useful when the cloned object is only generated as an intermediate object before the application of an in-place image filter. In this case, not cloning the pixel data saves significant heap operations.

Note:

Note that this function is not a const member since referencing the original image data requires modifying its reference counter.

Definition at line 383 of file cmtkScalarImage.cxx.

References cmtk::ScalarImage::m_Dims, cmtk::ScalarImage::m_ImageOrigin, cmtk::ScalarImage::ScalarImage(), and cmtk::ScalarImage::SetImageOrigin().

BitVector * cmtk::BitVector::Clone

(

)

const [inherited]

Create copy of this object.

Definition at line 69 of file cmtkBitVector.cxx.

SplineWarpXform * cmtk::SplineWarpXform::CloneVirtual

(

)

const [protected, virtual, inherited]

Clone transformation.

Implements cmtk::Xform.

Definition at line 197 of file cmtkSplineWarpXform.cxx.

References cmtk::WarpXform::Domain, cmtk::SplineWarpXform::dsplineX, cmtk::SplineWarpXform::dsplineY, cmtk::SplineWarpXform::dsplineZ, cmtk::WarpXform::GlobalScaling, cmtk::SplineWarpXform::GridPointOffset, cmtk::SplineWarpXform::gX, cmtk::SplineWarpXform::gY, cmtk::SplineWarpXform::gZ, cmtk::WarpXform::InverseSpacing, cmtk::WarpXform::m_Dims, cmtk::Xform::m_NumberOfParameters, cmtk::WarpXform::m_Offset, cmtk::Xform::m_Parameters, cmtk::Xform::m_ParameterVector, cmtk::WarpXform::nextI, cmtk::WarpXform::nextIJ, cmtk::WarpXform::nextIJK, cmtk::WarpXform::nextIK, cmtk::WarpXform::nextJ, cmtk::WarpXform::nextJK, cmtk::WarpXform::nextK, cmtk::WarpXform::NumberOfControlPoints, cmtk::WarpXform::Spacing, cmtk::SplineWarpXform::splineX, cmtk::SplineWarpXform::splineY, cmtk::SplineWarpXform::splineZ, and cmtk::SplineWarpXform::VolumeDims.

template<class T >

Matrix3x3< T > & cmtk::Matrix3x3< T >::Compose

(

const Types::Coordinate

params[8] )

[inherited]

Compose from canonical parameters.

Definition at line 81 of file cmtkMatrix3x3.cxx.

Referenced by cmtk::Registration2d2d::Register().

template<class W >

W * cmtk::ActiveDeformationModel< W >::Compose

(

const Types::Coordinate *

weights = NULL )

[inherited]

Compose deformation from mean deformation and modes of variation.

Definition at line 181 of file cmtkActiveDeformationModel.cxx.

template<class T >

Matrix4x4< T > & cmtk::Matrix4x4< T >::Compose	(	const Types::Coordinate	params[15],
		const bool	logScaleFactors = false
	)		[inherited]

Compose from canonical parameters.

Definition at line 101 of file cmtkMatrix4x4.cxx.

Referenced by cmtk::AffineXform::MakeInverse().

void cmtk::AffineXform::ComposeMatrix

(

)

[protected, inherited]

Compose this object's transformation matrix from parameter vector.

Definition at line 166 of file cmtkAffineXform.cxx.

References cmtk::AffineXform::m_LogScaleFactors, cmtk::Xform::m_Parameters, cmtk::AffineXform::NumberDOFs, and cmtk::AffineXform::UpdateInverse().

Referenced by cmtk::AffineXform::AffineXform(), cmtk::AffineXform::operator=(), cmtk::AffineXform::SetNumberDOFs(), cmtk::AffineXform::SetParameter(), and cmtk::AffineXform::SetParamVector().

template<class TDistanceDataType >

void cmtk::UniformDistanceMap< TDistanceDataType >::ComputeEDT

(

DistanceDataType *const

distance )

[private, inherited]

Compute 3-D Euclidean Distance Transformation.

Definition at line 153 of file cmtkUniformDistanceMap.cxx.

References cmtk::ThreadPool::GetNumberOfThreads(), and cmtk::ThreadPool::Run().

template<class TDistanceDataType >

void cmtk::UniformDistanceMap< TDistanceDataType >::ComputeEDT2D	(	DistanceDataType *const	plane,
		std::vector< DistanceDataType > &	gTemp,
		std::vector< DistanceDataType > &	hTemp
	)		[private, inherited]

Compute 2-D Euclidean Distance Transformation for one image plane.

Definition at line 239 of file cmtkUniformDistanceMap.cxx.

Referenced by cmtk::UniformDistanceMap< TDistanceDataType >::ComputeEDTThreadPhase1().

template<class TDistanceDataType >

void cmtk::UniformDistanceMap< TDistanceDataType >::ComputeEDTThreadPhase1	(	void *const	args,
		const size_t	taskIdx,
		const size_t	taskCnt,
		const size_t	threadIdx,
		const	size_t
	)		[static, private, inherited]

Thread function for first phase (xy) of EDT computation.

Definition at line 177 of file cmtkUniformDistanceMap.cxx.

References cmtk::UniformDistanceMap< TDistanceDataType >::ComputeEDT2D(), cmtk::UniformDistanceMap< TDistanceDataType >::ThreadParametersEDT::m_Distance, cmtk::UniformDistanceMap< TDistanceDataType >::m_DistanceMap, cmtk::UniformDistanceMap< TDistanceDataType >::m_G, cmtk::UniformDistanceMap< TDistanceDataType >::m_H, and cmtk::ThreadParameters< T >::thisObject.

template<class TDistanceDataType >

void cmtk::UniformDistanceMap< TDistanceDataType >::ComputeEDTThreadPhase2	(	void *const	args,
		const size_t	taskIdx,
		const size_t	taskCnt,
		const size_t	threadIdx,
		const	size_t
	)		[static, private, inherited]

Thread function for second phase (z) of EDT computation.

Definition at line 200 of file cmtkUniformDistanceMap.cxx.

References cmtk::UniformDistanceMap< TDistanceDataType >::ThreadParametersEDT::m_Distance, cmtk::UniformDistanceMap< TDistanceDataType >::m_DistanceMap, cmtk::UniformDistanceMap< TDistanceDataType >::m_G, cmtk::UniformDistanceMap< TDistanceDataType >::m_H, cmtk::ThreadParameters< T >::thisObject, and cmtk::UniformDistanceMap< TDistanceDataType >::VoronoiEDT().

template<class T >

void cmtk::MathUtil::ComputeEigensystem	(	const Matrix2D< T > &	matrix,
		Matrix2D< T > &	eigensystem,
		std::vector< T > &	eigenvalues
	)		[static, inherited]

Compute eigensystem and eigenvalues for square real matrix using Jacobi rotation.

Definition at line 56 of file cmtkMathUtil_LinAlg.cxx.

References cmtk::Matrix2D< T >::GetNumberOfColumns(), cmtk::Matrix2D< T >::GetNumberOfRows(), and cmtk::StdErr.

template<class T >

void cmtk::MathUtil::ComputeEigenvalues	(	const Matrix2D< T > &	matrix,
		std::vector< T > &	eigenvalues
	)		[static, inherited]

Compute eigenvalues for square real matrix using Jacobi rotation.

Definition at line 103 of file cmtkMathUtil_LinAlg.cxx.

References cmtk::Matrix2D< T >::GetNumberOfColumns(), cmtk::Matrix2D< T >::GetNumberOfRows(), and cmtk::StdErr.

template<class T>

void cmtk::Matrix3x3< T >::ComputeEigenvalues

(

T(&)

lambda[3] )

const [inherited]

Compute eigenvalues.

Definition at line 383 of file cmtkMatrix3x3.cxx.

References M_PI.

template<class TAccumulator >

ScalarImage * cmtk::UniformVolume::ComputeProjection

(

const int

axis )

const [inherited]

Return projection (e.g., MIP, sum) along one axis.

This function calls its equivalent in DataGrid and adds calibration info (i.e., correct pixel sizes) to the resulting image.

Note:

The pixel size if taken from the size of the first grid element along each axis -- non-uniform spacings will lead to incorrect results.

Reimplemented from cmtk::DataGrid.

Definition at line 171 of file cmtkUniformVolume.txx.

References cmtk::AXIS_X, cmtk::AXIS_Y, and cmtk::AXIS_Z.

template<class TAccumulator >

ScalarImage * cmtk::DataGrid::ComputeProjection

(

const int

axis )

const [inherited]

Return maximum-intensity projection MIP along one axis.

Reimplemented in cmtk::UniformVolume.

Definition at line 43 of file cmtkDataGrid.txx.

References cmtk::AXIS_X, cmtk::AXIS_Y, cmtk::AXIS_Z, cmtk::TypedArray::Get(), and cmtk::TypedArray::GetType().

void cmtk::AffineXform::Concat

(

const AffineXform &

other )

[inherited]

Concatenate this transformation with another.

Definition at line 360 of file cmtkAffineXform.cxx.

References cmtk::AffineXform::DecomposeMatrix(), and cmtk::AffineXform::Matrix.

Referenced by cmtk::MakeInitialAffineTransformation::AlignDirectionVectors(), and cmtk::WarpXform::ReplaceInitialAffine().

void cmtk::WarpXform::ConcatAffine

(

const AffineXform *

affineXform )

[inherited]

Concat affine transformation.

Definition at line 314 of file cmtkWarpXform.cxx.

References cmtk::AffineXform::ApplyInPlace().

float cmtk::ActiveShapeModel::Construct	(	const Types::Coordinate *const *	trainingSet,
		const unsigned int	numberOfSamples,
		const unsigned int	numberOfPoints,
		const unsigned int	numberOfModes
	)		[inherited]

Construct model.

Parameters:

trainingSet	The training set. This is a an array with size [numberOfSamples]. Each entry is a pointer to an array of size [numberOfPoints] Types::Coordinate values. Each of these latter arrays is a sample vector from the training set, for example a sequential concatenation of 2-D or 3-D point coordinates. The order of these values within the vectors is irrelevant, as long as the order is the same in all vectors. This order also defines the order of parameters in the generated model.
numberOfSamples	The number of samples in the training set. This is the size of the pointer array given as parameter "trainingSet".
numberOfPoints	This is the number of values in each array pointed to by a pointer in the "trainingSet" array.
numberOfModes	Number of modes in the generated model. This can be at most as many as "numberOfSamples", the number of samples in the training set. If the value of this parameter is to large, it will automatically be reduced to equal numberOfSamples.

Returns:

Percentage of the total variance of the training set that is explained by the generated model.

Definition at line 60 of file cmtkActiveShapeModel.cxx.

References cmtk::StdErr.

template<class T >

TypedArray::SmartPtr cmtk::TemplateArray< T >::Convert

(

const ScalarDataType

dtype )

const [virtual, inherited]

Convert to typed array of any given template type.

Todo:

This should somehow preserve PaddingFlag and Padding of the original array.

Implements cmtk::TypedArray.

Definition at line 192 of file cmtkTemplateArray.txx.

template<class T >

void * cmtk::TemplateArray< T >::ConvertSubArray	(	const ScalarDataType	dtype,
		const size_t	fromIdx,
		const size_t	len
	)		const [virtual, inherited]

Convert a sub-array to any given primitive data type.

Todo:

It would probably be a good idea to preserve PaddingData as much as possible during the conversion.

Implements cmtk::TypedArray.

Definition at line 202 of file cmtkTemplateArray.txx.

References cmtk::TypeItemSize().

template<class T >

void cmtk::TemplateArray< T >::ConvertSubArray	(	void *const	destination,
		const ScalarDataType	dtype,
		const size_t	fromIdx,
		const size_t	len
	)		const [virtual, inherited]

Convert a sub-array to given primitive data type into existing array.

Implements cmtk::TypedArray.

Definition at line 262 of file cmtkTemplateArray.txx.

References cmtk::TYPE_BYTE, cmtk::TYPE_CHAR, cmtk::TYPE_DOUBLE, cmtk::TYPE_FLOAT, cmtk::TYPE_INT, cmtk::TYPE_SHORT, and cmtk::TYPE_USHORT.

template<class T >

Vector<T> cmtk::CoordMult	(	const Vector< T > &	p,
		const Vector< T > &	q
	)

Coordinatewise multiplication operator.

Two vectors are multiplied element by element. The result is returned as an automatic variable.

Definition at line 98 of file cmtkVector.txx.

References cmtk::Vector< T >::Dim, and cmtk::Vector< T >::Elements.

template<class T >

T cmtk::MathUtil::Correlation	(	const std::vector< T > &	x,
		const std::vector< T > &	y
	)		[static, inherited]

Normalized correlation coefficient between two float vectors.

Definition at line 118 of file cmtkMathUtil_Statistics.txx.

TypedArray::SmartPtr cmtk::TypedArray::Create	(	const ScalarDataType	dtype,
		void *const	data,
		const size_t	size,
		const bool	freeArray = true,
		const bool	paddingFlag = false,
		const void *	paddingData = NULL
	)		[static, inherited]

Create typed data array from existing array of values.

Parameters:

dtype	Type specifier.
data	Pointer to the existing data array.
size	Number of data items in the array.
freeArray	On destruction, the created object will de-allocate the array's memory if and only if this flag is true.
paddingFlag	If this flag is not zero, padding data exists in the array.
paddingData	Value used for padding data.

Returns:

A pointer to a new typed array object, or NULL if an error occurred.

Definition at line 118 of file cmtkTypedArray.cxx.

References cmtk::TYPE_BYTE, cmtk::TYPE_CHAR, cmtk::TYPE_DOUBLE, cmtk::TYPE_FLOAT, cmtk::TYPE_INT, cmtk::TYPE_SHORT, and cmtk::TYPE_USHORT.

Referenced by cmtk::ScalarImage::AdjustAspectX(), cmtk::ScalarImage::AdjustAspectY(), cmtk::DataGridMorphologicalOperators::GetBinaryConnectedComponents(), cmtk::Image::GetData(), cmtk::ScalarImage::GetFilteredData(), cmtk::ScalarImage::GetLaplace2DFiltered(), cmtk::ScalarImage::GetMedianFiltered(), cmtk::DataGridMorphologicalOperators::GetRegionsRenumberedBySize(), cmtk::ScalarImage::GetSobel2DFiltered(), cmtk::ScalarImage::GetSobelFiltered(), cmtk::ReformatVolume::GetTransformedReference(), cmtk::ReformatVolume::GetTransformedReferenceJacobianAvg(), cmtk::operator-(), cmtk::ReformatVolume::PlainReformat(), cmtk::ImageSymmetryPlaneCommandLineBase::WriteAligned(), cmtk::ImageSymmetryPlaneCommandLineBase::WriteDifference(), and cmtk::ImageSymmetryPlaneCommandLineBase::WriteMirror().

TypedArray::SmartPtr cmtk::TypedArray::Create	(	const ScalarDataType	dtype,
		const size_t	size
	)		[static, inherited]

Create typed data array, allocating new memory for the items array.

Parameters:

dtype	Type specifier.
size	Number of items in the array to be allocated. Memory will be freed when the created object is destroyed. The values in the array are not initialized.

Returns:

A pointer to a new typed array object, or NULL if an error occurred.

Definition at line 153 of file cmtkTypedArray.cxx.

References cmtk::TYPE_BYTE, cmtk::TYPE_CHAR, cmtk::TYPE_DOUBLE, cmtk::TYPE_FLOAT, cmtk::TYPE_INT, cmtk::TYPE_SHORT, and cmtk::TYPE_USHORT.

TypedArray::SmartPtr cmtk::DataGrid::CreateDataArray	(	const ScalarDataType	dataType,
		const bool	setToZero = false
	)		[virtual, inherited]

Create data array.

Parameters:

dataType	ID of scalar data type for the array. This is the image pixel type.
setToZero	If this flag is set, all values in the newly created array will be initialized to zero.

Definition at line 55 of file cmtkDataGrid.cxx.

Referenced by cmtk::UniformVolume::GetInterleavedPaddedSubVolume(), and cmtk::DataGrid::GetReoriented().

void cmtk::CreateSystemLabelColorMap

(

SegmentationLabelMap &

map )

Create system label map.

Definition at line 43 of file cmtkSegmentationLabel.cxx.

Referenced by cmtk::Colormap::Colormap().

const char * cmtk::DataClassToString

(

const DataClass

dataClass )

Convert data class identifier to string.

Definition at line 75 of file cmtkTypes.cxx.

cmtk::DataGridFilter::DataGridFilter

(

DataGrid::SmartPtr

dataGrid )

[explicit, inherited]

Constructor: link to DataGrid object.

Definition at line 47 of file cmtkDataGridFilter.cxx.

cmtk::DataGridMorphologicalOperators::DataGridMorphologicalOperators

(

const DataGrid::SmartConstPtr &

dataGrid )

[inherited]

Constructor: link to DataGrid object.

Definition at line 45 of file cmtkDataGridMorphologicalOperators.cxx.

template<class W >

float cmtk::ActiveDeformationModel< W >::Decompose	(	const W *	input,
		Types::Coordinate *const	weights = NULL
	)		const [inherited]

Decompose a deformation into mean and modes of this model.

Parameters:

input	Input deformation.
weights	Weights of the modes that make up the given input vector. This parameter is optional. If not given, no weights will be returned.

Returns:

The value of the multivariate Gaussian PDF represented by this model atr the location of the input vector.

Definition at line 191 of file cmtkActiveDeformationModel.cxx.

template<class T >

bool cmtk::Matrix3x3< T >::Decompose	(	Types::Coordinate	params[8],
		const Types::Coordinate *	center = NULL
	)		const [inherited]

Decompose into affine parameters.

Todo:

Currently, we cannot correctly recover the parameters of a transformation that includes a mirroring. Rotation also gets messed up in this case. A possible solution may involve using the determinant to detect the mirror and then come up with something that respects this. Shear is not even supported yet.

Definition at line 123 of file cmtkMatrix3x3.cxx.

References IGS_EPSILON, cmtk::StdErr, and cmtk::Units::UnitBase::Value().

Referenced by cmtk::Registration2d2d::Register().

float cmtk::ActiveShapeModel::Decompose	(	const CoordinateVector *	input,
		Types::Coordinate *const	weights = NULL
	)		const [inherited]

Decompose a vector into mean and modes of this model.

Parameters:

input	Input vector.
weights	Weights of the modes that make up the given input vector. This parameter is optional. If not given, no weights will be returned.

Returns:

The value of the multivariate Gaussian PDF represented by this model atr the location of the input vector.

Definition at line 194 of file cmtkActiveShapeModel.cxx.

References cmtk::Vector< T >::EuclidNorm(), and M_PI.

template<class T >

bool cmtk::Matrix4x4< T >::Decompose	(	Types::Coordinate	params[12],
		const Types::Coordinate *	center = NULL,
		const bool	logScaleFactors = false
	)		const [inherited]

Decompose into affine parameters.

END OF ADOPTED VTK CODE

Definition at line 161 of file cmtkMatrix4x4.cxx.

References cmtk::Matrix4x4< T >::GetInverse(), cmtk::QRDecomposition< TFloat >::GetR(), cmtk::StdErr, cmtk::Units::UnitBase::Value(), and VTK_AXIS_EPSILON.

bool cmtk::AffineXform::DecomposeMatrix

(

)

[protected, inherited]

Decompose this object's transformation matrix into parameter vector.

Definition at line 179 of file cmtkAffineXform.cxx.

References cmtk::AffineXform::m_LogScaleFactors, cmtk::Xform::m_Parameters, and cmtk::AffineXform::RetCenter().

Referenced by cmtk::AffineXform::Concat(), cmtk::AffineXform::Insert(), cmtk::AffineXform::MakeInverse(), and cmtk::AffineXform::SetMatrix().

void cmtk::WarpXform::DeleteParameterActiveFlags

(

)

[inherited]

Free bitset for active parameter flags if it exists.

Definition at line 268 of file cmtkWarpXform.cxx.

static Types::Coordinate cmtk::CubicSpline::DerivApproxSpline	(	const int	k,
		const Types::Coordinate	t
	)		[inline, static, inherited]

Compute the derivative of a given approximating spline function.

Definition at line 121 of file cmtkCubicSpline.h.

Referenced by cmtk::SplineWarpXformUniformVolume::RegisterVolumeAxis().

static Types::Coordinate cmtk::CubicSpline::DerivApproxSpline0

(

const Types::Coordinate

t )

[inline, static, inherited]

Compute the derivative of the 0th approximating spline function.

Definition at line 97 of file cmtkCubicSpline.h.

static Types::Coordinate cmtk::CubicSpline::DerivApproxSpline1

(

const Types::Coordinate

t )

[inline, static, inherited]

Compute derivative of the 1st approximating spline function.

Definition at line 103 of file cmtkCubicSpline.h.

static Types::Coordinate cmtk::CubicSpline::DerivApproxSpline2

(

const Types::Coordinate

t )

[inline, static, inherited]

Compute derivative of the 2nd approximating spline function.

Definition at line 109 of file cmtkCubicSpline.h.

static Types::Coordinate cmtk::CubicSpline::DerivApproxSpline3

(

const Types::Coordinate

t )

[inline, static, inherited]

Compute derivative of the 3rd approximating spline function.

Definition at line 115 of file cmtkCubicSpline.h.

static Types::Coordinate cmtk::CubicSpline::DerivInterpSpline	(	const int	k,
		const Types::Coordinate	t
	)		[inline, static, inherited]

Compute derivative of a given interpolating spline function.

Definition at line 241 of file cmtkCubicSpline.h.

static Types::Coordinate cmtk::CubicSpline::DerivInterpSpline0

(

const Types::Coordinate

t )

[inline, static, inherited]

Compute derivative of the 0th interpolating spline function.

Definition at line 217 of file cmtkCubicSpline.h.

static Types::Coordinate cmtk::CubicSpline::DerivInterpSpline1

(

const Types::Coordinate

t )

[inline, static, inherited]

Compute derivative of the 1st interpolating spline function.

Definition at line 223 of file cmtkCubicSpline.h.

static Types::Coordinate cmtk::CubicSpline::DerivInterpSpline2

(

const Types::Coordinate

t )

[inline, static, inherited]

Compute derivative of the 2nd interpolating spline function.

Definition at line 229 of file cmtkCubicSpline.h.

static Types::Coordinate cmtk::CubicSpline::DerivInterpSpline3

(

const Types::Coordinate

t )

[inline, static, inherited]

Compute derivative of the 3rd interpolating spline function.

Definition at line 235 of file cmtkCubicSpline.h.

ScalarImage * cmtk::ScalarImage::Downsample	(	const int	factorX,
		int	factorY = 0,
		ScalarImage *const	target = NULL
	)		const [inherited]

Create downsampled copy of this image.

Definition at line 403 of file cmtkScalarImage.cxx.

References cmtk::ScalarImage::CreatePixelData(), cmtk::ScalarImage::SetImageOrigin(), and cmtk::ScalarImage::SetPixelAt().

template<class TFloat >

cmtk::EigenSystemSymmetricMatrix3x3< TFloat >::EigenSystemSymmetricMatrix3x3	(	const Matrix3x3< TFloat > &	matrix,
		const bool	sortAbsolute = true
	)		[inherited]

Constructor: compute eigensystem of given matrix.

Parameters:

matrix	Symmetric 3x3 matrix for which we are computing the eigenvalues and eigenvectors.
sortAbsolute	Flag for sorting by absolute eigenvalues (default) vs. sorting by actual eigenvalues.

Definition at line 41 of file cmtkEigenSystemSymmetricMatrix3x3.txx.

bool cmtk::DataGridMorphologicalOperators::EliminatePaddingVoting

(

const int

iterations = 1 )

[inherited]

Eliminating padding data by neighborhood voting.

Returns:

Returns "true" if data was actually changed, "false" if no change was necessary or possible.

Parameters:

iterations

Number of elimination iterations.

Definition at line 53 of file cmtkDataGridMorphologicalOperators.cxx.

References cmtk::TypedArray::Clone(), cmtk::TypedArray::GetData(), cmtk::TypedArray::GetPaddingFlag(), cmtk::TypedArray::GetPaddingValue(), and cmtk::TypedArray::PaddingDataAt().

Functional::ReturnType cmtk::Functional::EvaluateWithGradient	(	Self::ParameterVectorType &	v,
		Self::ParameterVectorType &	g,
		const Types::Coordinate	step = 1
	)		[virtual, inherited]

Evaluate functional and also return its gradient.

Definition at line 44 of file cmtkFunctional.cxx.

DataGrid * cmtk::DataGrid::ExtractSliceVirtual	(	const int	axis,
		const int	plane
	)		const [protected, virtual, inherited]

Extract orthogonal slice as a data grid object.

Parameters:

axis	Coordinate axis perpendicular to extracted plane
plane	Index of extracted plane

Reimplemented in cmtk::UniformVolume.

Definition at line 430 of file cmtkDataGrid.cxx.

References cmtk::AXIS_X, cmtk::AXIS_Y, cmtk::AXIS_Z, cmtk::TypedArray::GetDataPtr(), cmtk::TypedArray::GetItemSize(), cmtk::TypedArray::GetPaddingFlag(), cmtk::TypedArray::GetPaddingValue(), and cmtk::TypedArray::GetType().

template<class T>

Matrix3x3< T > & cmtk::Matrix3x3< T >::Fill

(

const T

value )

[inherited]

Set to constant value.

Definition at line 71 of file cmtkMatrix3x3.cxx.

Referenced by cmtk::DeformationField::GetJacobian(), and cmtk::SplineWarpXform::GetJacobianAtControlPoint().

template<int DIM>

template<class F >

cmtk::FilterMask< DIM >::FilterMask	(	const FixedVector< DIM, int > &	dims,
		const FixedVector< DIM, Types::Coordinate > &	deltas,
		const Types::Coordinate	radius,
		F	filter
	)		[inline, inherited]

Constructor.

Definition at line 123 of file cmtkFilterMask.h.

template<int DIM>

cmtk::FilterMaskPixel< DIM >::FilterMaskPixel

(

)

[inline, inherited]

Default constructor.

Definition at line 71 of file cmtkFilterMask.h.

template<int DIM>

cmtk::FilterMaskPixel< DIM >::FilterMaskPixel	(	const FixedVector< DIM, int > &	location,
		const int	relativeIndex,
		const Types::DataItem	coefficient
	)		[inline, inherited]

Explicit constructor.

Definition at line 75 of file cmtkFilterMask.h.

SmartPointer< Landmark > cmtk::LandmarkList::FindByName

(

const char *

name )

[inherited]

Find landmark by name.

Definition at line 59 of file cmtkLandmarkList.cxx.

References NULL.

Referenced by cmtk::MatchedLandmarkList::AddLandmarkLists(), and cmtk::QtTriplanarWindow::slotGoToLandmark().

const SmartPointer< MatchedLandmark > cmtk::MatchedLandmarkList::FindByName

(

const char *

name )

const [inherited]

Find landmark by name and return constant pointer.

Definition at line 63 of file cmtkMatchedLandmarkList.cxx.

References NULL.

SmartPointer< MatchedLandmark > cmtk::MatchedLandmarkList::FindByName

(

const char *

name )

[inherited]

Find landmark by name.

Definition at line 79 of file cmtkMatchedLandmarkList.cxx.

References NULL.

const SmartPointer< Landmark > cmtk::LandmarkList::FindByName

(

const char *

name )

const [inherited]

Find landmark by name and return constant pointer.

Definition at line 43 of file cmtkLandmarkList.cxx.

References NULL.

void cmtk::SplineWarpXform::FindClosestControlPoint	(	const Self::SpaceVectorType &	v,
		Self::SpaceVectorType &	cp
	)		const [protected, inherited]

Find nearest (after deformation) control point.

Definition at line 63 of file cmtkSplineWarpXform_Inverse.cxx.

References cmtk::FixedVector< NDIM, T >::RootSumOfSquares().

bool cmtk::UniformVolume::FindVoxel	(	const Self::CoordinateVectorType &	location,
		int *const	idx,
		Types::Coordinate *const	from,
		Types::Coordinate *const	to
	)		const [inline, inherited]

Find a voxel in the volume.

Parameters:

location	Real-world coordinates of the location that is to be found.
idx	This array is used to store the index components of the model voxel containing the given location. Values range from 0 to ModelDims[dim-1].
from	Real-world coordinate of the voxel's lower left corner.
to	Real-world coordinate of the voxel's upper right corner.

Returns:

A non-zero value is returned if and only if the given location lies within the model volume. If zero is returned, the location is outside and all other output values (see parameters) are invalid.

Definition at line 103 of file cmtkUniformVolume.txx.

Referenced by cmtk::InverseInterpolationVolumeReconstruction< TInterpolator >::ComputeErrorGradientImage().

bool cmtk::UniformVolume::FindVoxel	(	const Self::CoordinateVectorType &	location,
		int *const	idx
	)		const [inline, inherited]

Find a voxel in the volume.

Parameters:

location	Real-world coordinates of the location that is to be found.
idx	This array is used to store the index components of the model voxel containing the given location. Values range from 0 to ModelDims[dim-1].

Returns:

A non-zero value is returned if and only if the given location lies within the model volume. If zero is returned, the location is outside and all other output values (see parameters) are invalid.

Definition at line 124 of file cmtkUniformVolume.txx.

bool cmtk::UniformVolume::FindVoxelByIndex	(	const Self::CoordinateVectorType &	fracIndex,
		int *const	idx,
		Types::Coordinate *const	frac
	)		const [inline, inherited]

Find a voxel in the volume by fractional index.

Parameters:

fracIndex	Fractional 3D voxel index.
idx	Output: integer 3D voxel index.
frac	Output: fractional within-voxel location.

Returns:

True value is returned if and only if the given location lies within the model volume. If false is returned, the location is outside and all other output values (see parameters) are invalid.

Definition at line 153 of file cmtkUniformVolume.txx.

void cmtk::GeneralLinearModel::FitModel	(	std::vector< TypedArray::SmartPtr > &	y,
		const bool	normalizeParameters = true
	)		[inherited]

Model y[] distribution and return model parameters a[].

Parameters:

y	A vector of TypedArray smart pointers. Each object in this vector points to a pixel array from a different subject in a population.
normalizeParameters	If this flag is set (default), then the linear model parameters are normalized w.r.t. the maghnitudes of the respective measurements.

Definition at line 196 of file cmtkGeneralLinearModel.cxx.

void cmtk::BitVector::Flip

(

)

[inherited]

Flip (invert) the whole bitset.

Definition at line 111 of file cmtkBitVector.cxx.

void cmtk::BitVector::Flip

(

const size_t

pos )

[inherited]

Flip (invert) one bit.

Definition at line 118 of file cmtkBitVector.cxx.

template<class T >

T cmtk::Matrix3x3< T >::FrobeniusNorm

(

)

const [inherited]

Get Frobenius norm.

Definition at line 370 of file cmtkMatrix3x3.cxx.

template<class T >

T cmtk::Matrix4x4< T >::FrobeniusNorm

(

)

const [inherited]

Get Frobenius norm.

Definition at line 543 of file cmtkMatrix4x4.cxx.

template<class T >

void cmtk::TemplateArray< T >::GammaCorrection

(

const Types::DataItem

gamma )

[virtual, inherited]

Apply gamma correction.

Parameters:

gamma

The gamma correction coefficient.

Implements cmtk::TypedArray.

Definition at line 212 of file cmtkTemplateArray.txx.

References cmtk::Types::Range< T >::m_LowerBound, and cmtk::Types::Range< T >::m_UpperBound.

TypedArray::SmartPtr cmtk::FilterVolume::GaussianFilter	(	const UniformVolume *	volume,
		const Units::GaussianSigma &	width,
		const Types::Coordinate	radius = 1.0,
		const TypedArray *	maskData = NULL
	)		[static, inherited]

Apply Gaussian filter.

Parameters:

volume	Input 3D image.
width	Width (standard deviation) of the Gaussian kernel.
radius	Filter radius in multiples of the filter width. Outside the radius (Euclidean distance) the filter is truncated.
maskData	Optional binary mask data array.

Returns:

A newly allocated TypedArray object that can be used, for example, to replace the one held by the input image. The data type of the array is identical to the input array.

Definition at line 57 of file cmtkFilterVolume.cxx.

References cmtk::AXIS_X, cmtk::AXIS_Y, cmtk::AXIS_Z, cmtk::UniformVolume::Deltas(), cmtk::TypedArray::Get(), cmtk::TypedArray::GetDataSize(), cmtk::DataGrid::GetOffsetFromIndex(), cmtk::TypedArray::GetType(), and cmtk::DataGrid::m_Dims.

cmtk::GeneralLinearModel::GeneralLinearModel	(	const size_t	nParameters,
		const size_t	nData,
		const double *	designMatrix
	)		[inherited]

Constructor.

This will take care of SVD of the design matrix and perform all necessary pre-computations for the actual modeling.

Definition at line 56 of file cmtkGeneralLinearModel.cxx.

References TOL.

Types::Coordinate * cmtk::ActiveShapeModel::Generate	(	Types::Coordinate *const	instance,
		const Types::Coordinate *	modeWeights
	)		const [inherited]

Generate a model instance.

Definition at line 167 of file cmtkActiveShapeModel.cxx.

AffineXform * cmtk::ParametricPlane::GetAlignmentXform

(

const byte

normalAxis = 0 )

const [inherited]

Get transformation that aligns this plane with the coordinate system.

The object returned by this function represents a rigid transformation that aligns the normal vector of this object with one of the coordinate axes.

Parameters:

normalAxis

The index of the axis to align the normal vector with (0, 1, or 2 for x, y, or z, respectively).

Definition at line 82 of file cmtkParametricPlane.cxx.

References cmtk::MathUtil::ArcTan2(), cmtk::AffineXform::ChangeCenter(), cmtk::ParametricPlane::Normal, cmtk::ParametricPlane::Rho, cmtk::AffineXform::SetAngles(), cmtk::AffineXform::SetXlate(), cmtk::MathUtil::Sign(), and cmtk::Units::UnitBase::Value().

cmtk::TypedArray::SmartPtr cmtk::DataGridMorphologicalOperators::GetBinaryConnectedComponents

(

)

const [inherited]

Get connected components of a binary image.

All pixels with non-zero values are considered "foreground," and the result of this function is a partitioning of the foreground into connected components. Connectivity is determined based on 8 neighbours in the 3D grid.

Definition at line 40 of file cmtkDataGridConnectedComponents.cxx.

References cmtk::TypedArray::Create(), cmtk::UnionFind< T >::Find(), cmtk::UnionFind< T >::FindKey(), cmtk::UnionFind< T >::Insert(), cmtk::DataGridMorphologicalOperators::m_DataGrid, cmtk::TYPE_INT, and cmtk::UnionFind< T >::Union().

Referenced by cmtk::ImageOperationConnectedComponents::Apply().

TypedArray::SmartPtr cmtk::DataGridMorphologicalOperators::GetBoundaryMap

(

const bool

multiValued = false )

const [inherited]

Return map of region boundaries.

This function returns a byte data array where each pixel is one if it is a boundary pixel, i.e., if one of its neighbours in this object has a different value than it has itself. All other pixels are set to zero.

Parameters:

multiValued

If this is set (default: false), then the resulting boundary map is multi valued, i.e., instead of setting boundary pixels to "1", they are set to the value present in the image at that location.

Note:

The boundary contours are at least 2 pixels wide since "boundaryness" is a symmetric relationship.

Definition at line 237 of file cmtkDataGridMorphologicalOperators.cxx.

Referenced by cmtk::ImageOperationBoundaryMap::Apply().

Vector3D cmtk::Volume::GetCenter

(

)

const [inherited]

Calculate volume center.

Returns:

Returned is the center of the bounding box.

Definition at line 98 of file cmtkVolume.cxx.

FixedVector< 3, Types::Coordinate > cmtk::DataGrid::GetCenterOfMassGrid

(

)

const [virtual, inherited]

Get center of mass of pixel data.

Definition at line 565 of file cmtkDataGrid.cxx.

FixedVector< 3, Types::Coordinate > cmtk::DataGrid::GetCenterOfMassGrid

(

FixedVector< 3, Types::Coordinate > &

firstOrderMoment )

const [virtual, inherited]

Get center of mass and first-order moments of pixel data.

Definition at line 591 of file cmtkDataGrid.cxx.

const char * cmtk::AnatomicalOrientationBase::GetClosestOrientation	(	const char *	desiredOrientation,
		const char *const	availableOrientations[]
	)		[static, inherited]

Get closest orientation from a list.

This function is used to determine which orientation to bring an image into so it can be written to a file format with limited orientation support (e.g., Analyze).

Definition at line 52 of file cmtkAnatomicalOrientationBase.cxx.

References NULL.

Matrix2D< double > * cmtk::GeneralLinearModel::GetCorrelationMatrix

(

)

const [inherited]

Get the parameter correlation matrix from design matrix.

Definition at line 130 of file cmtkGeneralLinearModel.cxx.

UniformVolume::SmartPtr cmtk::UniformVolume::GetCroppedVolume

(

)

const [inherited]

Return cropped uniform volume.

Definition at line 83 of file cmtkUniformVolume_Crop.cxx.

References cmtk::META_IMAGE_ORIENTATION, cmtk::META_IMAGE_ORIENTATION_ORIGINAL, and cmtk::META_SPACE.

template<class TInterpolationFunction >

bool cmtk::UniformVolumeInterpolator< TInterpolationFunction >::GetDataAt	(	const Vector3D &	v,
		Types::DataItem &	value
	)		const [virtual, inherited]

Get data at location.

This function performs interpolation of one value from m_Volume at location v using the interpolation function given as the class template parameter.

This function should return true if a value can be interpolated from m_Volume at v, and it should return false if v is outside the range where a value can be interpolated (i.e., outside the volume boundaries).

Implements cmtk::UniformVolumeInterpolatorBase.

Definition at line 46 of file cmtkUniformVolumeInterpolator.txx.

bool cmtk::UniformVolumeInterpolatorPartialVolume::GetDataAt	(	const Vector3D &	v,
		Types::DataItem &	value
	)		const [virtual, inherited]

Get data at location.

This function performs interpolation of one value from m_Volume at location v using the interpolation function given as the class template parameter.

This function should return true if a value can be interpolated from m_Volume at v, and it should return false if v is outside the range where a value can be interpolated (i.e., outside the volume boundaries).

Implements cmtk::UniformVolumeInterpolatorBase.

Definition at line 49 of file cmtkUniformVolumeInterpolatorPartialVolume.cxx.

template<class TInterpolationFunction >

Types::DataItem cmtk::UniformVolumeInterpolator< TInterpolationFunction >::GetDataDirect	(	const int *	imageGridPoint,
		const Types::Coordinate *	insidePixel
	)		const [virtual, inherited]

Get data at a pre-computed relative pixel index.

This is faster if we already know the pixel index and fractional coordinate of a location.

Returns:

Interpolated value.

Implements cmtk::UniformVolumeInterpolatorBase.

Definition at line 115 of file cmtkUniformVolumeInterpolator.txx.

Types::DataItem cmtk::UniformVolumeInterpolatorPartialVolume::GetDataDirect	(	const int *	imageGridPoint,
		const Types::Coordinate *	insidePixel
	)		const [virtual, inherited]

Get data at a pre-computed relative pixel index. This is faster if we already know the pixel index and fractional coordinate of a location.

Implements cmtk::UniformVolumeInterpolatorBase.

Definition at line 130 of file cmtkUniformVolumeInterpolatorPartialVolume.cxx.

TypedArray::SmartPtr cmtk::UniformVolumeFilter::GetDataGaussFiltered	(	const Units::GaussianSigma &	sigma,
		const Types::Coordinate	maxError = 0.01
	)		const [inherited]

Gaussian filter (using faster, separable filtering).

Parameters:

sigma	Kernel parameter "sigma" (standard deviation)
maxError	Maximum approximation error: the kernel is truncated when it falls below this threshold

Definition at line 48 of file cmtkUniformVolumeFilter.cxx.

Referenced by cmtk::GroupwiseRegistrationFunctionalBase::PrepareSingleImage().

TypedArray::SmartPtr cmtk::DataGridFilter::GetDataKernelFiltered	(	const std::vector< Types::DataItem > &	filterX,
		const std::vector< Types::DataItem > &	filterY,
		const std::vector< Types::DataItem > &	filterZ
	)		const [inherited]

Return after filtering with a separable kernel.

Definition at line 189 of file cmtkDataGridFilter.cxx.

TypedArray::SmartPtr cmtk::DataGridFilter::GetDataMedianFiltered	(	const int	radiusX,
		const int	radiusY,
		const int	radiusZ
	)		const [inherited]

Return data after median-filtering with per-dimension filter radius.

Definition at line 55 of file cmtkDataGridFilter.cxx.

References cmtk::Memory::DeleteArray(), cmtk::TypedArray::Get(), cmtk::TypedArray::GetData(), cmtk::TypedArray::GetDataSize(), cmtk::TypedArray::GetType(), and NULL.

TypedArray::SmartPtr cmtk::DataGridFilter::GetDataMedianFiltered

(

const int

radius )

const [inline, inherited]

Return data after median-filtering with global filter radius (convenience function).

Definition at line 63 of file cmtkDataGridFilter.h.

TypedArray::SmartPtr cmtk::DataGrid::GetDataMirrored

(

const int

axis = AXIS_X )

const [inherited]

Return data after mirror operator.

Definition at line 316 of file cmtkDataGrid.cxx.

References cmtk::AXIS_X, cmtk::AXIS_Y, cmtk::AXIS_Z, cmtk::TypedArray::BlockCopy(), cmtk::TypedArray::GetDataSize(), cmtk::TypedArray::GetType(), and cmtk::StdErr.

TypedArray::SmartPtr cmtk::DataGrid::GetDataMirrorPlane

(

const int

axis = AXIS_X )

const [inherited]

Return data after mirroring.

Parameters:

axis	Coordinate axis normal to mirror plane. Default is AXIS_X (mirror about mid-sagittal plane).

Definition at line 264 of file cmtkDataGrid.cxx.

TypedArray::SmartPtr cmtk::DataGridFilter::GetDataSobelFiltered

(

)

const [inherited]

Return data after median-filtering.

Definition at line 128 of file cmtkDataGridFilter.cxx.

References cmtk::TypedArray::Get(), cmtk::TypedArray::GetData(), cmtk::TypedArray::GetDataSize(), and cmtk::TypedArray::GetType().

SplineWarpXform::SpaceVectorType & cmtk::SplineWarpXform::GetDeformedControlPointPosition	(	Self::SpaceVectorType &	v,
		const int	x,
		const int	y,
		const int	z
	)		const [virtual, inherited]

Get the deformed position of a transformation control point.

Note:

This function does not return the shifted control point position, but rather it applies the current transformation to the given control point. It does so more efficiently than applying the transformation to the explicit 3D coordinate of the control point, because most spline coefficients vanish at control points and need not be considered.

Definition at line 481 of file cmtkSplineWarpXform.cxx.

void cmtk::WarpXform::GetDerivativeInverseConsistencyError	(	double &	lower,
		double &	upper,
		const Self *	inverse,
		const UniformVolume *	volume,
		const UniformVolume::RegionType *	voi,
		const unsigned int	idx,
		const Types::Coordinate	step
	)		[virtual, inherited]

Return derivative of inverse consistency.

Definition at line 149 of file cmtkWarpXform.cxx.

Referenced by cmtk::ImagePairNonrigidRegistrationFunctional::WeightedDerivative().

void cmtk::WarpXform::GetDerivativeLandmarksMSD	(	double &	lowerMSD,
		double &	upperMSD,
		const MatchedLandmarkList *	ll,
		const unsigned int	idx,
		const Types::Coordinate	step
	)		[virtual, inherited]

Return derivative of registration error with respect to one parameter.

Definition at line 75 of file cmtkWarpXform.cxx.

Referenced by cmtk::ImagePairNonrigidRegistrationFunctional::WeightedDerivative().

AffineXform::SmartPtr cmtk::AffineXform::GetDifference

(

const AffineXform &

other )

const [virtual, inherited]

Compute difference to another affine transformation.

Todo:

It is probably not a good idea to return a dynamically allocated object here.

Definition at line 352 of file cmtkAffineXform.cxx.

References cmtk::AffineXform::MakeInverse().

ScalarDataType cmtk::GetDifferenceDataType	(	const ScalarDataType	dtype1,
		const ScalarDataType	dtype2
	)

Return difference datatype ID for given pair of datatypes.

Definition at line 140 of file cmtkTypes.cxx.

References cmtk::TYPE_BYTE, cmtk::TYPE_CHAR, cmtk::TYPE_DOUBLE, cmtk::TYPE_FLOAT, cmtk::TYPE_INT, cmtk::TYPE_SHORT, cmtk::TYPE_UINT, and cmtk::TYPE_USHORT.

TypedArray::SmartPtr cmtk::DataGridMorphologicalOperators::GetDilated

(

const int

iterations = 1 )

const [inherited]

Get data after dilation operator.

Parameters:

iterations

Number of dilation iterations.

Definition at line 181 of file cmtkDataGridMorphologicalOperators.cxx.

References cmtk::TYPE_BYTE.

Referenced by cmtk::ImageOperationErodeDilate::Apply().

DataGrid * cmtk::DataGrid::GetDownsampledAndAveraged

(

const int(&)

downsample[3] )

const [virtual, inherited]

Downsampling and pixel-averaging constructor function.

Reimplemented in cmtk::UniformVolume.

Definition at line 65 of file cmtkDataGrid.cxx.

References cmtk::TypedArray::Get(), cmtk::TypedArray::GetType(), cmtk::META_IMAGE_ORIENTATION, cmtk::META_IMAGE_ORIENTATION_ORIGINAL, and cmtk::DataGrid::SetDims().

template<class T >

double cmtk::TemplateArray< T >::GetEntropy	(	Histogram< double > &	histogram,
		const bool	fractional = CMTK_HISTOGRAM_DISCRETE
	)		const [virtual, inherited]

Calculate entropy of values in this array using existing histogram.

See also:

TypedArray::GetEntropy

Implements cmtk::TypedArray.

Definition at line 91 of file cmtkTemplateArray.txx.

References cmtk::Histogram< T >::GetEntropy(), cmtk::Histogram< T >::Increment(), cmtk::Histogram< T >::IncrementFractional(), cmtk::Histogram< T >::Reset(), cmtk::HistogramBase::ValueToBin(), and cmtk::HistogramBase::ValueToBinFractional().

template<class T >

double cmtk::TemplateArray< T >::GetEntropy	(	const bool	fractional = CMTK_HISTOGRAM_DISCRETE,
		const int	numberOfBins = 128
	)		const [virtual, inherited]

Calculate entropy of distribution of values in this array.

Implements cmtk::TypedArray.

Definition at line 51 of file cmtkTemplateArray.txx.

References cmtk::Histogram< T >::GetEntropy(), cmtk::Histogram< T >::Increment(), cmtk::Histogram< T >::IncrementFractional(), cmtk::HistogramBase::SetRange(), cmtk::HistogramBase::ValueToBin(), and cmtk::HistogramBase::ValueToBinFractional().

template<class T >

double cmtk::TemplateArray< T >::GetEntropy

(

Histogram< unsigned int > &

histogram )

const [virtual, inherited]

Calculate entropy of values in this array using existing histogram.

By using an already existing histogram, this function ensures that the same numbers and sizes of bins are used for repeated calls of this function, even when the actual data in this array has changed. On the other hand, there is of course a risk that the data may have changed in such a way that the old histogram arrangement does not fit it anymore.

In the process of entropy computation, the histogram is also filled with the data from this array. It is therefore available for subsequent operations after returning from this function.

Implements cmtk::TypedArray.

Definition at line 80 of file cmtkTemplateArray.txx.

References cmtk::Histogram< T >::GetEntropy(), cmtk::Histogram< T >::Increment(), cmtk::Histogram< T >::Reset(), and cmtk::HistogramBase::ValueToBin().

template<class T >

double cmtk::TemplateArray< T >::GetEntropy	(	Histogram< double > &	histogram,
		const double *	kernel,
		const size_t	kernelRadius
	)		const [virtual, inherited]

Calculate entropy of values in this array using existing histogram and kernel for Parzen windowing.

See also:

TypedArray::GetEntropy

Implements cmtk::TypedArray.

Definition at line 111 of file cmtkTemplateArray.txx.

References cmtk::Histogram< T >::AddWeightedSymmetricKernelFractional(), cmtk::Histogram< T >::GetEntropy(), cmtk::Histogram< T >::Reset(), and cmtk::HistogramBase::ValueToBinFractional().

template<class T >

double cmtk::Histogram< T >::GetEntropy

(

)

const [inherited]

Compute entropy of distribution.

From the bin counts, the entropy of the distribution of values is estimated.

Definition at line 64 of file cmtkHistogram.cxx.

Referenced by cmtk::CongealingFunctional< TXform >::EvaluateProbabilisticThread(), cmtk::CongealingFunctional< TXform >::EvaluateThread(), cmtk::TemplateArray< T >::GetEntropy(), and cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::UpdateTransformationFixedControlPoints().

TypedArray::SmartPtr cmtk::DataGridMorphologicalOperators::GetEroded

(

const int

iterations = 1 )

const [inherited]

Get data after erosion operator.

Parameters:

iterations

Number of erosion iterations.

Definition at line 124 of file cmtkDataGridMorphologicalOperators.cxx.

References cmtk::TYPE_BYTE.

Referenced by cmtk::ImageOperationErodeDilate::Apply().

TypedArray::SmartPtr cmtk::ScalarImage::GetFilteredData	(	const std::vector< Types::DataItem > &	filterX,
		const std::vector< Types::DataItem > &	filterY
	)		const [private, inherited]

Definition at line 522 of file cmtkScalarImage.cxx.

References cmtk::TypedArray::Create().

Referenced by cmtk::ScalarImage::GetGaussFiltered().

void cmtk::DataGridFilter::GetFilteredDataThreadX	(	void *	args,
		const size_t	taskIdx,
		const size_t	taskCnt,
		const size_t	threadIdx,
		const	size_t
	)		[static, private, inherited]

Thread function for separable filtering in x-direction.

Definition at line 224 of file cmtkDataGridFilter.cxx.

References cmtk::DataGridFilter::m_DataGrid, cmtk::DataGridFilter::FilterThreadParameters::m_Filter, cmtk::DataGridFilter::FilterThreadParameters::m_Result, and cmtk::ThreadParameters< T >::thisObject.

void cmtk::DataGridFilter::GetFilteredDataThreadY	(	void *	args,
		const size_t	taskIdx,
		const size_t	taskCnt,
		const size_t	threadIdx,
		const	size_t
	)		[static, private, inherited]

Thread function for separable filtering in y-direction.

Definition at line 287 of file cmtkDataGridFilter.cxx.

References cmtk::DataGridFilter::m_DataGrid, cmtk::DataGridFilter::FilterThreadParameters::m_Filter, cmtk::DataGridFilter::FilterThreadParameters::m_Result, and cmtk::ThreadParameters< T >::thisObject.

void cmtk::DataGridFilter::GetFilteredDataThreadZ	(	void *	args,
		const size_t	taskIdx,
		const size_t	taskCnt,
		const size_t	threadIdx,
		const	size_t
	)		[static, private, inherited]

Thread function for separable filtering in z-direction.

Definition at line 341 of file cmtkDataGridFilter.cxx.

References cmtk::DataGridFilter::m_DataGrid, cmtk::DataGridFilter::FilterThreadParameters::m_Filter, cmtk::DataGridFilter::FilterThreadParameters::m_Result, and cmtk::ThreadParameters< T >::thisObject.

TypedArray::SmartPtr cmtk::ScalarImage::GetGaussFiltered

(

const Types::Coordinate

stdDev )

const [inherited]

Return Gauss-filtered (smoothed) image data.

Parameters:

stdDev

Standard deviation of the smoothing kernel in world coordinates. This value is internally converted to the effective kernel size in pixels.

Definition at line 494 of file cmtkScalarImage.cxx.

References cmtk::ScalarImage::GetFilteredData(), cmtk::ScalarImage::m_Dims, M_PI, and cmtk::MathUtil::Square().

Types::Coordinate cmtk::SplineWarpXform::GetGridEnergy

(

)

const [virtual, inherited]

Return grid bending energy.

Definition at line 643 of file cmtkSplineWarpXform.cxx.

Referenced by cmtk::ImagePairNonrigidRegistrationFunctional::WeightedTotal().

Types::Coordinate cmtk::SplineWarpXform::GetGridEnergy

(

const Types::Coordinate *

cp )

const [virtual, inherited]

Return grid bending energy at one control point.

Parameters:

cp	The control point where the bending energy is to be evaluated.

Definition at line 761 of file cmtkSplineWarpXform.cxx.

Types::Coordinate cmtk::SplineWarpXform::GetGridEnergy

(

const Self::SpaceVectorType &

v )

const [virtual, inherited]

Return grid bending energy at arbitrary location.

Definition at line 665 of file cmtkSplineWarpXform.cxx.

void cmtk::SplineWarpXform::GetGridEnergyDerivative	(	double &	lower,
		double &	upper,
		const int	param,
		const Types::Coordinate	step
	)		const [virtual, inherited]

Return derivative of grid energy with respect to one parameter.

Definition at line 844 of file cmtkSplineWarpXform.cxx.

Referenced by cmtk::SplineWarpCongealingFunctional::EvaluateLocalGradientThreadFunc(), and cmtk::ImagePairNonrigidRegistrationFunctional::WeightedDerivative().

const UniformVolume::CoordinateRegionType cmtk::UniformVolume::GetHighResCropRegion

(

)

const [inherited]

Get cropped volume in real-world coordinates.

Definition at line 61 of file cmtkUniformVolume_Crop.cxx.

References cmtk::Region< NDIM, T >::From(), and cmtk::Region< NDIM, T >::To().

Referenced by cmtk::UniformVolume::UniformVolume().

template<class T >

Histogram< unsigned int >::SmartPtr cmtk::TemplateArray< T >::GetHistogram	(	const unsigned int	numberOfBins,
		const bool	centeredBins = false
	)		const [virtual, inherited]

Get data histogram.

Returns:

A histogram object filled with the relative frequencies of values in this array.

Parameters:

numberOfBins	Number of histogram bins
centeredBins	Flag for bins centered around the samples

Implements cmtk::TypedArray.

Definition at line 71 of file cmtkTemplateArray_Statistics.txx.

References cmtk::Histogram< T >::Increment(), cmtk::HistogramBase::SetRange(), cmtk::HistogramBase::SetRangeCentered(), and cmtk::HistogramBase::ValueToBin().

ScalarImage::SpaceVectorType cmtk::ScalarImage::GetImageOrigin

(

const int

frame = 0 )

const [inherited]

Get image origin of given frame (default: 0).

Definition at line 350 of file cmtkScalarImage.cxx.

References cmtk::SurfaceNormal::Get(), cmtk::ScalarImage::m_ImageOrigin, and cmtk::FixedVector< NDIM, T >::RootSumOfSquares().

Referenced by cmtk::VolumeFromSlices::CheckImage(), cmtk::UniformVolume::GetOrthoSliceInterp(), cmtk::VolumeFromSlices::InitSequence(), cmtk::ScalarImage::ScalarImage(), and cmtk::Image::SetFromScalarImage().

void cmtk::AnatomicalOrientation::GetImageToSpaceAxesPermutation	(	int(&)	imageToSpaceAxesPermutation[3][3],
		const char *	orientation,
		const char *	spaceAxes
	)		[static, inherited]

Get permutation table of coordinate axes from space axes and image orientation.

Definition at line 98 of file cmtkAnatomicalOrientation.cxx.

template<class T >

const Matrix4x4< T > cmtk::Matrix4x4< T >::GetInverse

(

)

const [inherited]

Inversion operator (in place).

Definition at line 378 of file cmtkMatrix4x4.cxx.

References cmtk::Matrix4x4< T >::Matrix.

Referenced by cmtk::Matrix4x4< T >::Decompose(), cmtk::AnatomicalOrientation::PermutationMatrix::GetPermutedMatrix(), cmtk::AffineXform::RotateWXYZ(), cmtk::TransformChangeFromSpaceAffine::TransformChangeFromSpaceAffine(), and cmtk::TransformChangeToSpaceAffine::TransformChangeToSpaceAffine().

const AffineXform::SmartPtr cmtk::AffineXform::GetInverse

(

)

const [inherited]

Get linked inverse of this transformation.

Definition at line 463 of file cmtkAffineXform.cxx.

References cmtk::AffineXform::InverseXform, cmtk::AffineXform::MakeInverse(), and cmtk::AffineXform::UpdateInverse().

Referenced by cmtk::MakeInitialAffineTransformation::AlignDirectionVectors(), cmtk::InverseInterpolationVolumeReconstruction< TInterpolator >::ComputeErrorGradientImage(), cmtk::GroupwiseRegistrationFunctionalXformTemplate< SplineWarpXform >::ForceZeroSumGradient(), and cmtk::TypedStreamStudylist::Write().

Types::Coordinate cmtk::SplineWarpXform::GetInverseConsistencyError	(	const WarpXform *	inverse,
		const UniformVolume *	volume,
		const UniformVolume::RegionType *	voi = NULL
	)		const [virtual, inherited]

Return inverse consistency.

Definition at line 896 of file cmtkSplineWarpXform.cxx.

References cmtk::Xform::ApplyInPlace(), cmtk::AXIS_X, cmtk::AXIS_Y, cmtk::AXIS_Z, cmtk::Region< NDIM, T >::From(), cmtk::UniformVolume::GetGridLocation(), cmtk::DataGrid::GetWholeImageRegion(), cmtk::WarpXform::InDomain(), cmtk::UniformVolume::m_Delta, cmtk::FixedVector< NDIM, T >::RootSumOfSquares(), and cmtk::Region< NDIM, T >::To().

Referenced by cmtk::ImagePairNonrigidRegistrationFunctional::WeightedTotal().

Types::Coordinate cmtk::WarpXform::GetInverseConsistencyError	(	const Self *	inverse,
		const UniformVolume *	volume,
		const UniformVolume::RegionType *	voi = NULL
	)		const [virtual, inherited]

Return inverse consistency.

Definition at line 111 of file cmtkWarpXform.cxx.

References cmtk::Xform::ApplyInPlace(), cmtk::Region< NDIM, T >::From(), cmtk::UniformVolume::GetGridLocation(), cmtk::DataGrid::GetWholeImageRegion(), cmtk::WarpXform::InDomain(), cmtk::FixedVector< NDIM, T >::RootSumOfSquares(), and cmtk::Region< NDIM, T >::To().

CoordinateMatrix3x3 cmtk::SplineWarpXform::GetJacobian

(

const Self::SpaceVectorType &

v )

const [virtual, inherited]

Get local Jacobian.

Definition at line 50 of file cmtkSplineWarpXform_Jacobian.cxx.

void cmtk::DeformationField::GetJacobian	(	const Self::SpaceVectorType &	v,
		CoordinateMatrix3x3 &	J
	)		const [virtual, inherited]

Get Jacobian matrix.

Definition at line 46 of file cmtkDeformationField_Jacobian.cxx.

References cmtk::Matrix3x3< T >::Fill().

void cmtk::SplineWarpXform::GetJacobian	(	const Self::SpaceVectorType &	v,
		CoordinateMatrix3x3 &	J
	)		const [virtual, inherited]

Get local Jacobian into existing matrix.

Definition at line 212 of file cmtkSplineWarpXform_Jacobian.cxx.

void cmtk::SplineWarpXform::GetJacobianAtControlPoint	(	const Types::Coordinate *	cp,
		CoordinateMatrix3x3 &	J
	)		const [virtual, inherited]

Get local Jacobian at control point into existing matrix.

Definition at line 170 of file cmtkSplineWarpXform_Jacobian.cxx.

References cmtk::Matrix3x3< T >::Fill().

Types::Coordinate cmtk::SplineWarpXform::GetJacobianConstraint

(

)

const [virtual, inherited]

Return Jacobian constraint of the current transformation grid.

Definition at line 584 of file cmtkSplineWarpXform_Jacobian.cxx.

References cmtk::ThreadPool::GetNumberOfThreads(), and cmtk::ThreadPool::Run().

Referenced by cmtk::ImagePairNonrigidRegistrationFunctional::WeightedTotal().

void cmtk::SplineWarpXform::GetJacobianConstraintDerivative	(	double &	lower,
		double &	upper,
		const int	param,
		const UniformVolume::RegionType &	voi,
		const Types::Coordinate	step
	)		const [virtual, inherited]

Return derivative of Jacobian constraint with respect to one parameter.

Definition at line 655 of file cmtkSplineWarpXform_Jacobian.cxx.

References cmtk::Region< NDIM, T >::From(), cmtk::Region< NDIM, T >::Size(), and cmtk::Region< NDIM, T >::To().

Referenced by cmtk::SplineWarpCongealingFunctional::EvaluateLocalGradientThreadFunc(), and cmtk::ImagePairNonrigidRegistrationFunctional::WeightedDerivative().

void cmtk::SplineWarpXform::GetJacobianConstraintDerivative	(	double &	lower,
		double &	upper,
		const int	param,
		const Types::Coordinate	step
	)		const [virtual, inherited]

Return derivative of Jacobian constraint with respect to one parameter.

Definition at line 754 of file cmtkSplineWarpXform_Jacobian.cxx.

Types::Coordinate cmtk::SplineWarpXform::GetJacobianConstraintSparse

(

)

const [virtual, inherited]

Return sparse Jacobian constraint of the current transformation grid.

Unlike GetJacobianConstraint(), this function does not evaluate the Jacobian constraint at each voxel of the registered reference image; it merely performs the evaluation at the control points of the deformation, thereby greatly increasing computational performance at the cost of less accurate and stable computation.

Definition at line 638 of file cmtkSplineWarpXform_Jacobian.cxx.

void cmtk::SplineWarpXform::GetJacobianConstraintThread	(	void *const	args,
		const size_t	taskIdx,
		const size_t	taskCnt,
		const	size_t,
		const	size_t
	)		[static, protected, inherited]

Thread function for SMP Jacobian constraint computation.

Definition at line 511 of file cmtkSplineWarpXform_Jacobian.cxx.

References cmtk::SplineWarpXform::JacobianConstraintThreadInfo::Constraint, cmtk::SplineWarpXform::GetJacobianDeterminantRow(), cmtk::WarpXform::GlobalScaling, cmtk::SplineWarpXform::JacobianConstraintThreadInfo::thisObject, and cmtk::SplineWarpXform::VolumeDims.

Types::Coordinate cmtk::SplineWarpXform::GetJacobianDeterminant

(

const Self::SpaceVectorType &

v )

const [virtual, inherited]

Compute Jacobian determinant at a certain location.

Implements cmtk::Xform.

Definition at line 326 of file cmtkSplineWarpXform_Jacobian.cxx.

Referenced by cmtk::ReformatVolume::GetTransformedReferenceJacobianAvgThread().

Types::Coordinate cmtk::SplineWarpXform::GetJacobianDeterminant	(	const int	x,
		const int	y,
		const int	z
	)		const [virtual, inherited]

Compute Jacobian determinant at a certain reference image pixel.

Definition at line 280 of file cmtkSplineWarpXform_Jacobian.cxx.

void cmtk::SplineWarpXform::GetJacobianDeterminantRow	(	double *const	values,
		const int	x,
		const int	y,
		const int	z,
		const size_t	numberOfPoints = 1
	)		const [virtual, inherited]

Compute sequence of Jacobian determinants from given grid location.

Definition at line 384 of file cmtkSplineWarpXform_Jacobian.cxx.

Referenced by cmtk::SplineWarpXform::GetJacobianConstraintThread(), and cmtk::SplineWarpXform::GetJacobianFoldingConstraintThread().

Types::Coordinate cmtk::SplineWarpXform::GetJacobianFoldingConstraint

(

)

const [virtual, inherited]

Return Jacobian folding constraint of the current transformation grid.

Definition at line 611 of file cmtkSplineWarpXform_Jacobian.cxx.

References cmtk::ThreadPool::GetNumberOfThreads(), and cmtk::ThreadPool::Run().

void cmtk::SplineWarpXform::GetJacobianFoldingConstraintDerivative	(	double &	lower,
		double &	upper,
		const int	param,
		const UniformVolume::RegionType &	voi,
		const Types::Coordinate	step
	)		const [virtual, inherited]

Return derivative of Jacobian constraint with respect to one parameter.

Definition at line 704 of file cmtkSplineWarpXform_Jacobian.cxx.

References cmtk::Region< NDIM, T >::From(), cmtk::Region< NDIM, T >::Size(), and cmtk::Region< NDIM, T >::To().

void cmtk::SplineWarpXform::GetJacobianFoldingConstraintThread	(	void *const	args,
		const size_t	taskIdx,
		const size_t	taskCnt,
		const	size_t,
		const	size_t
	)		[static, protected, inherited]

Thread function for SMP Jacobian folding constraint computation.

Definition at line 548 of file cmtkSplineWarpXform_Jacobian.cxx.

References cmtk::SplineWarpXform::JacobianConstraintThreadInfo::Constraint, cmtk::SplineWarpXform::GetJacobianDeterminantRow(), cmtk::WarpXform::GlobalScaling, cmtk::SplineWarpXform::JacobianConstraintThreadInfo::thisObject, and cmtk::SplineWarpXform::VolumeDims.

void cmtk::SplineWarpXform::GetJacobianRow	(	CoordinateMatrix3x3 *const	array,
		const int	x,
		const int	y,
		const int	z,
		const size_t	numberOfPoints
	)		const [virtual, inherited]

Get sequence of Jacobians for pixel row.

Definition at line 59 of file cmtkSplineWarpXform_Jacobian.cxx.

References cmtk::Matrix3x3< T >::Set().

template<class T >

double cmtk::JointHistogram< T >::GetJointEntropy

(

)

const [inherited]

Compute joint entropy.

From the joint bins, an estimate to the joint entropy of both, reference and model image is computed.

Returns:

The estimated joint entropy.

Definition at line 73 of file cmtkJointHistogram.cxx.

template<class T >

double cmtk::Histogram< T >::GetKullbackLeiblerDivergence

(

const Self &

other )

const [inherited]

Get Kullback-Leibler divergence to other histogram.

The second histogram must have the same number of bins, because the function assumes bin-to-bin correspondence between the two distributions.

Note:

Any bin value ranges set in derived classes are ignored here!

Definition at line 97 of file cmtkHistogram.txx.

References cmtk::Histogram< T >::GetNumBins(), cmtk::Histogram< T >::m_Bins, and cmtk::Histogram< T >::SampleCount().

Types::Coordinate cmtk::Xform::GetLandmarksMSD

(

const MatchedLandmarkList *

ll )

const [virtual, inherited]

Return registration error for set of source/target landmarks.

What is actually returned is the mean squared distance of source landmark after transformation and desired target landmark.

Definition at line 110 of file cmtkXform.cxx.

Referenced by cmtk::ImagePairNonrigidRegistrationFunctional::WeightedTotal().

TypedArray::SmartPtr cmtk::ScalarImage::GetLaplace2DFiltered

(

)

const [inherited]

Return Laplace-filtered (edge-enhanced) image data.

This function implements the 2-D Laplace edge operator.

Definition at line 693 of file cmtkScalarImage.cxx.

References cmtk::TypedArray::Create(), and cmtk::ScalarImage::m_Dims.

template<class T >

void cmtk::JointHistogram< T >::GetMarginalEntropies	(	double &	HX,
		double &	HY
	)		const [inherited]

Compute marginal entropies.

From the bin counts, the marginal entropies of both, reference and model data are estimated.

Parameters:

HX	Upon return, this reference holds the estimated marginal entropy of the X random variable, i.e. the reference image.
HY	Upon return, this reference holds the estimated marginal entropy of the Y random variable, i.e. the model image.

Definition at line 45 of file cmtkJointHistogram.cxx.

template<class T >

Histogram< T > * cmtk::JointHistogram< T >::GetMarginalX

(

)

const [inherited]

Get marginal X distribution as 1D histogram.

Definition at line 92 of file cmtkJointHistogram.cxx.

References cmtk::HistogramBase::SetRange().

Referenced by cmtk::FilterVolume::StudholmeFilter().

template<class T >

Histogram< T > * cmtk::JointHistogram< T >::GetMarginalY

(

)

const [inherited]

Get marginal Y distribution as 1D histogram.

Definition at line 105 of file cmtkJointHistogram.cxx.

References cmtk::HistogramBase::SetRange().

template<>

void cmtk::AffineXform::GetMatrix

(

float(&)

matrix[4][4] )

const [inherited]

Definition at line 270 of file cmtkAffineXform.cxx.

template<>

void cmtk::AffineXform::GetMatrix

(

double(&)

matrix[4][4] )

const [inherited]

Definition at line 279 of file cmtkAffineXform.cxx.

template<class T >

size_t cmtk::Histogram< T >::GetMaximumBinIndex

(

)

const [inherited]

Return index of bin with highest value.

Definition at line 45 of file cmtkHistogram.cxx.

TypedArray::SmartPtr cmtk::ScalarImage::GetMedianFiltered

(

const byte

range )

const [inherited]

Return median-filtered image data.

Parameters:

range

Field of view of the median operator.

Definition at line 450 of file cmtkScalarImage.cxx.

References cmtk::MathUtil::CompareDouble(), cmtk::MathUtil::CompareFloat(), cmtk::TypedArray::Create(), cmtk::Memory::DeleteArray(), and cmtk::ScalarImage::m_Dims.

AffineXform::MatrixType cmtk::ParametricPlane::GetMirrorXformMatrix

(

)

const [inherited]

Get affine transformation matrix of the mirror transform.

Definition at line 138 of file cmtkParametricPlane.cxx.

References cmtk::Matrix4x4< Types::Coordinate >::IdentityMatrix, cmtk::ParametricPlane::Normal, cmtk::ParametricPlane::Rho, and cmtk::ParametricPlane::SquareNormal.

void cmtk::AnatomicalOrientation::GetOrientationFromDirections	(	char *	orientation,
		const AffineXform::MatrixType &	directions,
		const char *	spaceAxes
	)		[static, inherited]

Get closest anatomical orientation based on space dimensions and image direction vectors.

Parameters:

orientation	The resulting orientation string (three characters plus terminating zero) will be put into this string.
directions	The image direction vectors. "directions[0]" is the 3-D vector of the in-plane x image direction, "directions[1]" is in-plane y, and "directions[2]" is the vector from one plane origin to the origin of the next plane.
spaceAxes	Six-character string that defines the orientation of the underlying space. The first two characters relate to the x coordinate, the second two to the y coordinate, and the final two to the z coordinate.

Definition at line 48 of file cmtkAnatomicalOrientation.cxx.

References cmtk::StdErr.

ScalarImage * cmtk::DataGrid::GetOrthoSlice	(	const int	axis,
		const unsigned int	plane
	)		const [virtual, inherited]

Return orthogonal slice as a 2D image.

Reimplemented in cmtk::UniformVolume.

Definition at line 357 of file cmtkDataGrid.cxx.

References cmtk::AXIS_X, cmtk::AXIS_Y, cmtk::AXIS_Z, cmtk::TypedArray::GetDataPtr(), cmtk::TypedArray::GetItemSize(), cmtk::TypedArray::GetPaddingFlag(), cmtk::TypedArray::GetPaddingValue(), and cmtk::TypedArray::GetType().

int cmtk::WarpXform::GetParameterActive

(

const size_t

index )

const [inherited]

Test whether a particular parameter is active.

Parameters:

index

Index of the parameter.

Returns:

Non-zero if and only if the given parameter is active.

Definition at line 259 of file cmtkWarpXform.cxx.

Types::Coordinate cmtk::WarpXform::GetParamStep	(	const size_t	idx,
		const Self::SpaceVectorType &	volSize,
		const Types::Coordinate	mmStep = 1
	)		const [virtual, inherited]

Get parameter step given a transformed volume size.

Reimplemented from cmtk::Xform.

Reimplemented in cmtk::DeformationField, and cmtk::SplineWarpXform.

Definition at line 167 of file cmtkWarpXform.cxx.

Types::Coordinate cmtk::AffineXform::GetParamStep	(	const size_t	idx,
		const Self::SpaceVectorType &	volSize,
		const Types::Coordinate	step_mm = 1
	)		const [virtual, inherited]

Get parameter stepping.

Reimplemented from cmtk::Xform.

Definition at line 314 of file cmtkAffineXform.cxx.

References M_PI, cmtk::FixedVector< NDIM, T >::MaxValue(), and cmtk::MathUtil::Square().

virtual Types::Coordinate cmtk::SplineWarpXform::GetParamStep	(	const size_t	idx,
		const Self::SpaceVectorType &	volSize,
		const Types::Coordinate	mmStep = 1
	)		const [inline, virtual, inherited]

Get parameter stepping.

Reimplemented from cmtk::WarpXform.

Definition at line 318 of file cmtkSplineWarpXform.h.

CoordinateVector & cmtk::Xform::GetParamVector	(	CoordinateVector &	v,
		const size_t	targetOffset = 0
	)		const [virtual, inherited]

Copy parameter vector to existing vector object.

Definition at line 94 of file cmtkXform.cxx.

References cmtk::Vector< T >::AdjustDimension(), cmtk::Vector< T >::CopyToOffset(), and cmtk::Vector< T >::Dim.

Referenced by cmtk::TemplateMultiChannelRegistrationFunctional< SplineWarpXform, TMetricFunctional >::GetParamVector().

Types::DataItem cmtk::TypedArray::GetPercentile	(	const Types::DataItem	percentile,
		const size_t	nBins = 256
	)		const [virtual, inherited]

Compute approximate percentile value from histogram.

Parameters:

percentile	The percentile to be computed. Value must be between 0 and 1.
nBins	Number of histogram bins for percentile estimation.

Definition at line 45 of file cmtkTypedArray_Statistics.cxx.

References cmtk::Histogram< T >::GetPercentile().

Referenced by cmtk::Study::ReadVolume(), and cmtk::Study::UpdateFromVolume().

template<class T >

Types::DataItem cmtk::Histogram< T >::GetPercentile

(

const Types::DataItem

percentile )

const [inherited]

Compute approximate percentile value from histogram.

Parameters:

percentile

The percentile to be computed. Value must be between 0 and 1.

Definition at line 137 of file cmtkHistogram.cxx.

Referenced by cmtk::TypedArray::GetPercentile(), and cmtk::TypedArray::GetPercentileList().

std::vector< Types::DataItem > cmtk::TypedArray::GetPercentileList	(	const std::vector< Types::DataItem > &	percentileList,
		const size_t	nBins = 256
	)		const [virtual, inherited]

Compute list of approximate percentile values from histogram.

This function calls GetPercentile for each value in the given input vector and puts all resulting values into the output vector in the same order. The main advantage of using this function is that it is more efficient as a single histogram is created to compute all percentiles.

Parameters:

percentileList	The list of percentiles to be computed. Each value must be between 0 and 1.
nBins	Number of histogram bins for percentile estimation.

Definition at line 54 of file cmtkTypedArray_Statistics.cxx.

References cmtk::Histogram< T >::GetPercentile().

AffineXform::MatrixType cmtk::AnatomicalOrientation::PermutationMatrix::GetPermutedMatrix

(

const AffineXform::MatrixType &

inMatrix )

const [inherited]

Permute index-to-physical matrix.

Definition at line 74 of file cmtkAnatomicalOrientationPermutationMatrix.cxx.

References cmtk::Matrix4x4< T >::GetInverse().

Referenced by cmtk::UniformVolume::GetReoriented().

bool cmtk::ScalarImage::GetPixelAt	(	Types::DataItem &	value,
		const Types::Coordinate	i,
		const Types::Coordinate	j
	)		const [inherited]

Get pixel at fractional 2-D index by bilinear interpolation.

Returns:

True if value is valid; false if at least one of the four neighbor pixels was invalid or outside the image.

Definition at line 267 of file cmtkScalarImage.cxx.

bool cmtk::ScalarImage::GetPixelAtCubic	(	Types::DataItem &	value,
		const Types::Coordinate	i,
		const Types::Coordinate	j
	)		const [inherited]

Get pixel at fractional 2-D index by bicubic interpolation.

Returns:

True if value is valid; false if at least one of the source pixels was invalid or outside the image.

Definition at line 302 of file cmtkScalarImage.cxx.

References cmtk::TypedArray::Get(), and cmtk::CubicSpline::InterpSpline().

Types::Coordinate * cmtk::SplineWarpXform::GetPureDeformation

(

const bool

includeScale = false )

const [inherited]

Return array of pre deformation vectors.

The newly alocated data array contains the control point positions after deformation without affine components.

Parameters:

includeScale

If this flag is set (default: off), then the scale components of the affine transformation remain in the deformation.

Definition at line 955 of file cmtkSplineWarpXform.cxx.

template<class TFloat >

Matrix2D< TFloat > & cmtk::QRDecomposition< TFloat >::GetQ

(

)

[inherited]

Get the Q factor.

Definition at line 79 of file cmtkQRDecomposition.txx.

template<class TFloat >

Matrix2D< TFloat > & cmtk::QRDecomposition< TFloat >::GetR

(

)

[inherited]

Get the R factor.

Definition at line 101 of file cmtkQRDecomposition.txx.

Referenced by cmtk::Matrix4x4< T >::Decompose(), and cmtk::SplineWarpXform::GetRigidityConstraint().

template<class T >

const Types::DataItemRange cmtk::TemplateArray< T >::GetRange

(

)

const [virtual, inherited]

Calculate minimum and maximum data value.

Implements cmtk::TypedArray.

Definition at line 123 of file cmtkTemplateArray.txx.

template<class T >

const Types::Range< T > cmtk::TemplateArray< T >::GetRangeTemplate

(

)

const [virtual, inherited]

Calculate minimum and maximum data value.

Definition at line 131 of file cmtkTemplateArray.txx.

References cmtk::Types::Range< T >::m_LowerBound, and cmtk::Types::Range< T >::m_UpperBound.

cmtk::TypedArray::SmartPtr cmtk::DataGridMorphologicalOperators::GetRegionsRenumberedBySize

(

)

const [inherited]

Get data with region labels renumbered by decreasing region size.

This is typically run after GetBinaryConnectedComponents() to order the components and be able to easily select, say, the largest k components.

Definition at line 128 of file cmtkDataGridConnectedComponents.cxx.

References cmtk::TypedArray::Create(), and cmtk::TYPE_INT.

Referenced by cmtk::ImageOperationConnectedComponents::Apply().

const DataGrid::SmartPtr cmtk::DataGrid::GetReoriented

(

const char *

newOrientation = AnatomicalOrientation::ORIENTATION_STANDARD )

const [inherited]

Reorientation constructor function.

Parameters:

newOrientation

Three letter orientation code that specifies the anatomically-based orientation of the reoriented volume. Each letter can be one of the following: R, L, A, P, I, S. These stand for Right, Left, Anterior, Posterior, Inferior, Superior.

The three letters in the orientation string define the directions of the positive x, y, and z axes, in this order. For example, "RAS", the standard orientation for this software, means that the pixels along the x axis are arranged from the subject's Left to the Right side, along the y axis from the subject's Posterior (back) to Anterior (front), and along the z axis from Inferior (feet) to Superior (head).

The current orientation of this volume is to be taken from its meta information, as this->m_MetaInformation[CMTK_META_IMAGE_ORIENTATION]. This is also a three-letter string of the same form as the one given to this function as a parameter.

If the current orientation is not set, a warning message should be printed to StdErr, and a NULL pointer returned.

Returns:

Reoriented data grid with permuted pixels in this->Data and permuted grid dimensions in this->Dims. The returned pointers points to a newly allocated object, which can be wrapped in an SmartPointer.

Reimplemented in cmtk::UniformVolume.

Definition at line 128 of file cmtkDataGrid.cxx.

References cmtk::DataGrid::CreateDataArray(), cmtk::TypedArray::GetDataPtr(), cmtk::TypedArray::GetItemSize(), cmtk::TypedArray::GetPaddingFlag(), cmtk::TypedArray::GetPaddingValue(), cmtk::AnatomicalOrientation::PermutationMatrix::GetPermutedArray(), cmtk::TypedArray::GetType(), cmtk::MetaInformationObject::m_MetaInformation, cmtk::META_IMAGE_ORIENTATION, cmtk::META_IMAGE_ORIENTATION_ORIGINAL, cmtk::AnatomicalOrientation::PermutationMatrix::NewOffsetFromPoint(), and cmtk::TypedArray::SetPaddingValue().

template<class TDataType >

const TDataType cmtk::Accumulators::Avg< TDataType >::GetResult

(

)

const [inline, inherited]

Retrive accumulated result.

Definition at line 73 of file cmtkAccumulatorAvg.h.

template<class TDataType >

const TDataType& cmtk::Accumulators::Sum< TDataType >::GetResult

(

)

const [inline, inherited]

Retrive accumulated result.

Definition at line 72 of file cmtkAccumulatorSum.h.

template<class TDataType >

const TDataType cmtk::Accumulators::Max< TDataType >::GetResult

(

)

const [inline, inherited]

Retrive accumulated result.

Definition at line 75 of file cmtkAccumulatorMax.h.

Types::Coordinate cmtk::SplineWarpXform::GetRigidityConstraint

(

)

const [virtual, inherited]

Return rigidity constraint of the current transformation grid.

Definition at line 229 of file cmtkSplineWarpXform_Rigidity.cxx.

Types::Coordinate cmtk::SplineWarpXform::GetRigidityConstraint

(

const DataGrid *

weightMap )

const [virtual, inherited]

Return rigidity constraint of the current transformation grid with local weights.

Definition at line 251 of file cmtkSplineWarpXform_Rigidity.cxx.

References cmtk::DataGrid::GetDataAt().

Types::Coordinate cmtk::SplineWarpXform::GetRigidityConstraint

(

const CoordinateMatrix3x3 &

J )

const [private, inherited]

Return rigidity constraint based on given Jacobian matrix.

Definition at line 273 of file cmtkSplineWarpXform_Rigidity.cxx.

References cmtk::QRDecomposition< TFloat >::GetR().

void cmtk::SplineWarpXform::GetRigidityConstraintDerivative	(	double &	lower,
		double &	upper,
		const int	param,
		const Types::Coordinate	step
	)		const [virtual, inherited]

Return derivative of rigidity constraint with respect to one parameter.

Definition at line 171 of file cmtkSplineWarpXform_Rigidity.cxx.

void cmtk::SplineWarpXform::GetRigidityConstraintDerivative	(	double &	lower,
		double &	upper,
		const int	param,
		const UniformVolume::RegionType &	voi,
		const Types::Coordinate	step
	)		const [virtual, inherited]

Return derivative of rigidity constraint with respect to one parameter.

Definition at line 68 of file cmtkSplineWarpXform_Rigidity.cxx.

References cmtk::Region< NDIM, T >::From(), and cmtk::Region< NDIM, T >::To().

void cmtk::SplineWarpXform::GetRigidityConstraintDerivative	(	double &	lower,
		double &	upper,
		const int	param,
		const UniformVolume::RegionType &	voi,
		const Types::Coordinate	step,
		const DataGrid *	weightMap
	)		const [virtual, inherited]

Return derivative of rigidity constraint with respect to one parameter.

Definition at line 119 of file cmtkSplineWarpXform_Rigidity.cxx.

References cmtk::Region< NDIM, T >::From(), cmtk::DataGrid::GetDataAt(), cmtk::Region< NDIM, T >::Size(), and cmtk::Region< NDIM, T >::To().

Types::Coordinate cmtk::SplineWarpXform::GetRigidityConstraintSparse

(

)

const [virtual, inherited]

Return sparse rigidity constraint of the current transformation grid.

Definition at line 47 of file cmtkSplineWarpXform_Rigidity.cxx.

ScalarDataType cmtk::GetSignedDataType

(

const ScalarDataType

dtype )

Return signed datatype ID corresponding to given datatype.

Definition at line 123 of file cmtkTypes.cxx.

References cmtk::TYPE_BYTE, cmtk::TYPE_CHAR, cmtk::TYPE_INT, cmtk::TYPE_SHORT, cmtk::TYPE_UINT, and cmtk::TYPE_USHORT.

Referenced by cmtk::TypedArraySimilarity::GetDifferenceArray(), cmtk::ScalarImage::GetSobelFiltered(), cmtk::operator-(), and cmtk::ImageSymmetryPlaneCommandLineBase::WriteDifference().

TypedArray::SmartPtr cmtk::ScalarImage::GetSobel2DFiltered

(

)

const [inherited]

Return Sobel-filtered (edge-enhanced) image data.

This function implements the 2-D Sobel edge operator. In particular, it computed the gradient magnitude at a certian location as the square root of the squared horizontal and vertical Sobel operators.

Definition at line 610 of file cmtkScalarImage.cxx.

References cmtk::TypedArray::Create(), cmtk::ScalarImage::m_Dims, and cmtk::MathUtil::Square().

TypedArray::SmartPtr cmtk::ScalarImage::GetSobelFiltered	(	const bool	horizontal,
		const bool	absolute = false
	)		const [inherited]

Return Sobel-filtered (edge-enhanced) image data.

This function implements the 1-D Sobel edge operator.

Definition at line 641 of file cmtkScalarImage.cxx.

References cmtk::TypedArray::Create(), cmtk::GetSignedDataType(), cmtk::GetUnsignedDataType(), and cmtk::ScalarImage::m_Dims.

Referenced by cmtk::ScalarImageSimilarity::GetGradientCorrelation(), and cmtk::ScalarImageSimilarity::GetGradientDifference().

template<class T >

size_t cmtk::TemplateArray< T >::GetStatistics	(	Types::DataItem &	mean,
		Types::DataItem &	variance
	)		const [virtual, inherited]

Calculate statistics.

Results will be both zero if there is not data in the array.

Returns:

The number of valid (i.e., non-padding) values that constitute the given results.

Implements cmtk::TypedArray.

Definition at line 42 of file cmtkTemplateArray_Statistics.txx.

void cmtk::SplineWarpXform::GetTransformedGrid	(	Self::SpaceVectorType &	v,
		const int	idxX,
		const int	idxY,
		const int	idxZ
	)		const [inherited]

Get a grid point from the deformed grid.

Definition at line 525 of file cmtkSplineWarpXform.cxx.

void cmtk::DeformationField::GetTransformedGrid	(	Self::SpaceVectorType &	v,
		const int	idxX,
		const int	idxY,
		const int	idxZ
	)		const [virtual, inherited]

Get a grid point from the deformed grid.

Definition at line 84 of file cmtkDeformationField.cxx.

void cmtk::SplineWarpXform::GetTransformedGridRow	(	const int	numPoints,
		Self::SpaceVectorType *const	v,
		const int	idxX,
		const int	idxY,
		const int	idxZ
	)		const [inherited]

Get a sequence of grid points from the deformed grid.

Definition at line 559 of file cmtkSplineWarpXform.cxx.

Referenced by cmtk::ParallelElasticFunctional< VM >::EvaluateCompleteThread(), cmtk::ImagePairNonrigidRegistrationFunctionalTemplate< VM >::EvaluateCompleteThread(), cmtk::VoxelMatchingElasticFunctional_Template< VM >::EvaluateIncremental(), cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::EvaluateIncremental(), cmtk::ParallelElasticFunctional< VM >::EvaluateIncremental(), cmtk::ImagePairNonrigidRegistrationFunctionalTemplate< VM >::EvaluateIncremental(), cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::EvaluateThreadFunction(), and cmtk::GroupwiseRegistrationFunctionalXformTemplate< SplineWarpXform >::InterpolateImageThread().

void cmtk::DeformationField::GetTransformedGridRow	(	Self::SpaceVectorType *const	v,
		const int	numPoints,
		const int	idxX,
		const int	idxY,
		const int	idxZ
	)		const [virtual, inherited]

Get a sequence of grid points from the deformed grid.

Definition at line 95 of file cmtkDeformationField.cxx.

template<class T >

Matrix3x3< T > cmtk::Matrix3x3< T >::GetTranspose

(

)

const [inherited]

Transpose operator.

Definition at line 189 of file cmtkMatrix3x3.cxx.

Referenced by cmtk::MakeInitialAffineTransformation::AlignPrincipalAxes(), and cmtk::SplineWarpXform::ApplyInverseInPlaceWithInitial().

template<class T >

Matrix4x4< T > cmtk::Matrix4x4< T >::GetTranspose

(

)

const [inherited]

Transpose operator.

Definition at line 87 of file cmtkMatrix4x4.cxx.

bool cmtk::Volume::GetTrilinear	(	ProbeInfo &	probeInfo,
		const int	X,
		const int	Y,
		const int	Z,
		const Vector3D &	Location,
		const Types::Coordinate *	from,
		const Types::Coordinate *	to
	)		const [protected, inherited]

Get information needed for trilinear interpolation.

Returns:

1 if operation was successful, 0 if no valid data could be found at the given location.

Definition at line 44 of file cmtkVolume.cxx.

References cmtk::ProbeInfo::Deltas, cmtk::TypedArray::Get(), cmtk::ProbeInfo::Location, cmtk::ProbeInfo::Offsets, and cmtk::ProbeInfo::Values.

ScalarDataType cmtk::GetUnsignedDataType

(

const ScalarDataType

dtype )

Return unsigned datatype ID corresponding to given datatype.

Definition at line 166 of file cmtkTypes.cxx.

References cmtk::TYPE_BYTE, cmtk::TYPE_CHAR, cmtk::TYPE_INT, cmtk::TYPE_SHORT, cmtk::TYPE_UINT, and cmtk::TYPE_USHORT.

Referenced by cmtk::ScalarImage::GetSobelFiltered().

void cmtk::SplineWarpXform::GetVolumeOfInfluence	(	const size_t	idx,
		const Self::SpaceVectorType &	fromVol,
		const Self::SpaceVectorType &	toVol,
		Self::SpaceVectorType &	fromVOI,
		Self::SpaceVectorType &	toVOI,
		const int	fastMode = -1
	)		const [virtual, inherited]

Get volume influenced by one parameter.

Reimplemented from cmtk::Xform.

Definition at line 390 of file cmtkSplineWarpXform.cxx.

Referenced by cmtk::GroupwiseRegistrationFunctionalXformTemplate< SplineWarpXform >::UpdateVolumesOfInfluence().

void cmtk::Xform::GetVolumeOfInfluence	(	const size_t	idx,
		const Self::SpaceVectorType &	fromVol,
		const Self::SpaceVectorType &	toVol,
		Self::SpaceVectorType &	fromVOI,
		Self::SpaceVectorType &	toVOI,
		const	int = -1
	)		const [virtual, inherited]

Get volume influenced by one parameter.

Reimplemented in cmtk::SplineWarpXform.

Definition at line 103 of file cmtkXform.cxx.

void cmtk::UniformVolume::GetVoxelIndexNoBounds	(	const Self::CoordinateVectorType &	location,
		int *const	idx
	)		const [inline, inherited]

Find a grid index inside or outside the volume.

Parameters:

location	Real-world coordinates of the location that is to be found.
idx	This array is used to store the index components of the model voxel containing the given location. Values range from 0 to ModelDims[dim-1].

Definition at line 143 of file cmtkUniformVolume.txx.

Referenced by cmtk::InverseInterpolationVolumeReconstruction< TInterpolator >::GetPassImageDependentPixelRegion(), and cmtk::VolumeInjectionReconstruction::VolumeInjectionAnisotropic().

static Types::Coordinate cmtk::Interpolators::NearestNeighbor::GetWeight	(	const int	weight,
		const Types::Coordinate	x
	)		[inline, static, inherited]

Get specific interpolation weight for relative coordinate.

Definition at line 55 of file cmtkNearestNeighborInterpolator.h.

const DataGrid::RegionType cmtk::DataGrid::GetWholeImageRegion

(

)

const [inherited]

Get whole image region.

Definition at line 48 of file cmtkDataGrid.cxx.

Referenced by cmtk::WarpXform::GetInverseConsistencyError(), and cmtk::SplineWarpXform::GetInverseConsistencyError().

template<class TFloat >

TFloat cmtk::EigenSystemSymmetricMatrix3x3< TFloat >::hypot2	(	const TFloat &	x,
		const TFloat &	y
	)		[static, private, inherited]

Helper function that computes the Euclidean length of (x,y).

Definition at line 58 of file cmtkEigenSystemSymmetricMatrix3x3.txx.

void cmtk::SplineWarpXform::Init	(	const Self::SpaceVectorType &	domain,
		const Types::Coordinate	delta,
		const AffineXform *	initialXform = NULL,
		const bool	exactDelta = false
	)		[inherited]

Initialize warp from volume size and control grid density.

Definition at line 67 of file cmtkSplineWarpXform.cxx.

References cmtk::AffineXform::Clone().

void cmtk::SplineWarpXform::Init

(

)

[protected, inherited]

Initialize internal data structures.

This function is called from the various destructors to avoid unnecessary duplication of code.

Definition at line 53 of file cmtkSplineWarpXform.cxx.

void cmtk::DeformationField::InitControlPoints

(

const AffineXform *

affineXform = NULL )

[inherited]

Initialize control point positions, potentially with affine displacement.

Definition at line 43 of file cmtkDeformationField.cxx.

References cmtk::AffineXform::ApplyInPlace(), cmtk::AffineXform::GetGlobalScaling(), and cmtk::AffineXform::GetScales().

void cmtk::SplineWarpXform::InitControlPoints

(

const AffineXform *

affineXform = NULL )

[inherited]

Initialize control point positions, potentially with affine displacement.

Definition at line 128 of file cmtkSplineWarpXform.cxx.

References cmtk::AffineXform::ApplyInPlace(), cmtk::AffineXform::GetGlobalScaling(), and cmtk::AffineXform::GetScales().

void cmtk::WarpXform::InitGrid	(	const FixedVector< 3, Types::Coordinate > &	domain,
		const Self::IndexType &	dims
	)		[virtual, inherited]

Initialized internal data structures for new control point grid.

Definition at line 50 of file cmtkWarpXform.cxx.

void cmtk::GeneralLinearModel::InitResults

(

const size_t

nPixels )

[private, inherited]

Initialize results arrays with the correct number of pixels.

Definition at line 178 of file cmtkGeneralLinearModel.cxx.

References cmtk::TYPE_FLOAT.

void cmtk::AffineXform::Insert

(

const AffineXform &

other )

[inherited]

Insert another transformation before this one.

Definition at line 367 of file cmtkAffineXform.cxx.

References cmtk::AffineXform::DecomposeMatrix(), and cmtk::AffineXform::Matrix.

ScalarImage * cmtk::ScalarImage::InterpolateFrom	(	const ScalarImage *	grid,
		const CoordinateMatrix3x3 *	matrix,
		const cmtk::Interpolators::InterpolationEnum	interpolation = cmtk::Interpolators::LINEAR
	)		const [virtual, inherited]

Interpolate sub-image with affine transformation.

Definition at line 160 of file cmtkScalarImage.cxx.

References cmtk::ScalarImage::CreatePixelData(), cmtk::Interpolators::CUBIC, cmtk::Interpolators::LINEAR, cmtk::ScalarImage::m_Dims, cmtk::Matrix3x3< T >::Multiply(), cmtk::TypedArray::Set(), and cmtk::TypedArray::SetPaddingAt().

static Types::Coordinate cmtk::CubicSpline::InterpSpline	(	const int	k,
		const Types::Coordinate	t
	)		[inline, static, inherited]

Compute the value of a given interpolating spline function.

Definition at line 201 of file cmtkCubicSpline.h.

Referenced by cmtk::ScalarImage::GetPixelAtCubic().

static Types::Coordinate cmtk::CubicSpline::InterpSpline0

(

const Types::Coordinate

t )

[inline, static, inherited]

Compute a value of the 0th interpolating spline function.

Definition at line 177 of file cmtkCubicSpline.h.

static Types::Coordinate cmtk::CubicSpline::InterpSpline1

(

const Types::Coordinate

t )

[inline, static, inherited]

Compute a value of the 1st interpolating spline function.

Definition at line 183 of file cmtkCubicSpline.h.

static Types::Coordinate cmtk::CubicSpline::InterpSpline2

(

const Types::Coordinate

t )

[inline, static, inherited]

Compute a value of the 2nd interpolating spline function.

Definition at line 189 of file cmtkCubicSpline.h.

static Types::Coordinate cmtk::CubicSpline::InterpSpline3

(

const Types::Coordinate

t )

[inline, static, inherited]

Compute a value of the 3rd interpolating spline function.

Definition at line 195 of file cmtkCubicSpline.h.

int cmtk::Intersection::IntersectX	(	Types::Coordinate &	fromFactor,
		Types::Coordinate &	toFactor,
		const Vector3D &	offset,
		const Vector3D &	dX,
		const Types::Coordinate	Size[3],
		const Types::Coordinate	initFromFactor = 0,
		const Types::Coordinate	initToFactor = 1,
		const int	lowerClosed = 0,
		const int	upperClosed = 0
	)		[static, inherited]

Compute line-to-volume intersection.

This function computes the part of a lines that lies within a given volume.

Returns:

This function returns 1 if and only if there is a non-empty intersection of line and volume. In this case, the intersection is described by fromFactor and toFactor.

Parameters:

fromFactor	If the function returned 1, this variable holds the relative distance to the entrance point of the line into the volume. 0 means the line's starting point, 1 means its end.
toFactor	If the function returned 1, this variable holds the relative distance to the exit point of the line from the volume. Possible values range from 0 to 1 and have the same meaning as fromFactor.
offset	This 3D vector is the line's starting point.
dX	This is the vector spanning from the starting point of the line to its end.
Size	This is the size of the volume. It is always rectilinear with faces parallel to the coordinate axes and its lower left front corner identical to the coordinate origin. If affine transformed volumes are to be tested, the inverse affine transformation has to be applied to the line's endpoints instead.
initFromFactor	The fromFactor parameter's value is initialized with this value. It is therefore the lower bound of the parameter range that is available for intersection.
initToFactor	The toFactor parameter's value is initialized with this value. It is therefore the upper bound of the parameter range that is available for intersection. One application for this parameter is to use a value bigger than 1, even if [0,1] is the allowed range. Then, by testing if toFactor == 1.0, it can be determined whether clipping set the value to 1. This, for example allows to tell closed from open intervals, which may be important for subsequent computation such as volume probing.
lowerClosed	This flag defines whether lower range boundaries are open (value 0, default) or closed (value 1). In case of an open range, the bounding value itself is not an element of the range. Thus, if an intersection is entirely on the boundary, then it is empty in case of an open range.
upperClosed	This flag has the same meaning and default as lowerClosed, but refers to the ranges' upper bounds.

Definition at line 46 of file cmtkIntersection.cxx.

int cmtk::Intersection::IntersectY	(	Types::Coordinate &	fromFactor,
		Types::Coordinate &	toFactor,
		const Vector3D &	offset,
		const Vector3D &	dX,
		const Vector3D &	dY,
		const Types::Coordinate	Size[3],
		const Types::Coordinate	initFromFactor = 0,
		const Types::Coordinate	initToFactor = 1
	)		[static, inherited]

Compute plane-to-volume intersection.

This function computes the part of a plane that intersects with a given volume. The intersection is only tested with respect to the dY direction. for the range of relative positions returned by fromFactor and toFactor, IntersectX can be used to computed the exact 2D intersection.

Parameters and return value are identical to IntersectionX.

Parameters:

fromFactor	If the function returned 1, this variable holds the relative distance to the entrance point of the line into the volume. 0 means the line's starting point, 1 means its end.
toFactor	If the function returned 1, this variable holds the relative distance to the exit point of the line from the volume. Possible values range from 0 to 1 and have the same meaning as fromFactor.
offset	This 3D vector is the line's starting point.
dX	This is the vector spanning from the starting point of the line to its end.
dY	This is the second vector in addition to dX spanning the plane under consideration. In general, dX and dY should be orthogonal, and dY should be defined in the way just as dX is, i.e. as the difference of two plane corner vectors.
Size	This is the size of the volume. It is always rectilinear with faces parallel to the coordinate axes and its lower left front corner identical to the coordinate origin. If affine transformed volumes are to be tested, the inverse affine transformation has to be applied to the line's endpoints instead.
initFromFactor	The fromFactor parameter's value is initialized with this value. It is therefore the lower bound of the parameter range that is available for intersection.
initToFactor	The toFactor parameter's value is initialized with this value. It is therefore the upper bound of the parameter range that is available for intersection. One application for this parameter is to use a value bigger than 1, even if [0,1] is the allowed range. Then, by testing if toFactor == 1.0, it can be determined whether clipping set the value to 1. This, for example allows to tell closed from open intervals, which may be important for subsequent computation such as volume probing.

Definition at line 85 of file cmtkIntersection.cxx.

int cmtk::Intersection::IntersectZ	(	Types::Coordinate &	fromFactor,
		Types::Coordinate &	toFactor,
		const Vector3D &	offset,
		const Vector3D &	dX,
		const Vector3D &	dY,
		const Vector3D &	dZ,
		const Types::Coordinate	Size[3],
		const Types::Coordinate	initFromFactor = 0,
		const Types::Coordinate	initToFactor = 1
	)		[static, inherited]

Compute volume-to-volume intersection.

This function computes the part of a volume that intersects with a given volume. The intersection is only tested with respect to the dZ direction. for the range of relative positions returned by fromFactor and toFactor, IntersectY and afterwards IntersectX can be used to computed the exact 3D intersection.

Parameters and return value are identical to IntersectionX.

Parameters:

fromFactor	If the function returned 1, this variable holds the relative distance to the entrance point of the line into the volume. 0 means the line's starting point, 1 means its end.
toFactor	If the function returned 1, this variable holds the relative distance to the exit point of the line from the volume. Possible values range from 0 to 1 and have the same meaning as fromFactor.
offset	This 3D vector is the line's starting point.
dX	This is the vector spanning from the starting point of the line to its end.
dY	This is the second vector in addition to dX spanning the plane under consideration. In general, dX and dY should be orthogonal, and dY should be defined in the way just as dX is, i.e. as the difference of two plane corner vectors.
dZ	This is the third vector in addition to dX and dY spanning the volume under consideration. In general, dX, dY, and dZ should be orthogonal, and dZ should be defined in the same way as dX and dY are, i.e. as the difference of two plane corner vectors where one is the volume origin.
Size	This is the size of the volume. It is always rectilinear with faces parallel to the coordinate axes and its lower left front corner identical to the coordinate origin. If affine transformed volumes are to be tested, the inverse affine transformation has to be applied to the line's endpoints instead.
initFromFactor	The fromFactor parameter's value is initialized with this value. It is therefore the lower bound of the parameter range that is available for intersection.
initToFactor	The toFactor parameter's value is initialized with this value. It is therefore the upper bound of the parameter range that is available for intersection. One application for this parameter is to use a value bigger than 1, even if [0,1] is the allowed range. Then, by testing if toFactor == 1.0, it can be determined whether clipping set the value to 1. This, for example allows to tell closed from open intervals, which may be important for subsequent computation such as volume probing.

Definition at line 123 of file cmtkIntersection.cxx.

template<class T >

Matrix3x3< T > & cmtk::Matrix3x3< T >::Invert2x2

(

)

[inherited]

Inversion operator (in place).

Definition at line 202 of file cmtkMatrix3x3.cxx.

template<class T >

Matrix3x3< T > & cmtk::Matrix3x3< T >::Invert3x3

(

)

[inherited]

Inversion operator (in place) as a 3D non-homogeneous matrix.

Definition at line 263 of file cmtkMatrix3x3.cxx.

Referenced by cmtk::MakeInitialAffineTransformation::AlignPrincipalAxes(), and cmtk::SplineWarpXform::ApplyInverseInPlaceWithInitial().

Types::Coordinate cmtk::SplineWarpXform::JacobianDeterminant

(

const Types::Coordinate *

cp )

const [inherited]

Compute Jacobian determinant at a certain control point.

As we evaluate the spline polynomials and their derivatives at a known control point, they reduce to constants which allows for a particularly efficient computation.

Parameters:

cp	Pointer to the spline control point at which the Jacobian determinant is to be evaluated. This pointer is assumed to be pointing to the 0th-component (ie, x) of a non-peripheral control point. Callers have to make sure that this is true.

Definition at line 498 of file cmtkSplineWarpXform_Jacobian.cxx.

cmtk::Landmark::Landmark

(

)

[inherited]

Default constructor.

Definition at line 42 of file cmtkLandmark.cxx.

References NULL.

cmtk::Landmark::Landmark	(	const char *	name,
		const Types::Coordinate	location[3]
	)		[inherited]

Explicit constructor.

Definition at line 47 of file cmtkLandmark.cxx.

void cmtk::TransformedVolumeAxes::MakeHash	(	const UniformVolume &	volume,
		const UniformVolume::SpaceVectorType &	offset,
		const UniformVolume::SpaceVectorType &	dX,
		const UniformVolume::SpaceVectorType &	dY,
		const UniformVolume::SpaceVectorType &	dZ
	)		[private, inherited]

Create the actual hash: allocate and fill according to given offset and delta vectors.

Definition at line 120 of file cmtkTransformedVolumeAxes.cxx.

References cmtk::UniformVolume::m_Delta, cmtk::DataGrid::m_Dims, and NULL.

void cmtk::AffineXform::MakeIdentityXform

(

)

[inherited]

Create identity transformation.

Definition at line 50 of file cmtkAffineXform.cxx.

AffineXform * cmtk::AffineXform::MakeInverse

(

)

const [virtual, inherited]

Clone inverse of this transformation.

Definition at line 197 of file cmtkAffineXform.cxx.

References cmtk::AffineXform::AffineXform(), cmtk::AffineXform::ChangeCenter(), cmtk::Matrix4x4< T >::Compose(), cmtk::AffineXform::DecomposeMatrix(), cmtk::AffineXform::m_LogScaleFactors, cmtk::MetaInformationObject::m_MetaInformation, cmtk::Xform::m_Parameters, cmtk::AffineXform::Matrix, cmtk::META_SPACE, cmtk::META_XFORM_FIXED_IMAGE_PATH, cmtk::META_XFORM_MOVING_IMAGE_PATH, cmtk::AffineXform::NumberDOFs, cmtk::AffineXform::RetCenter(), and cmtk::AffineXform::SetNumberDOFs().

Referenced by cmtk::ClassStream::Get(), cmtk::AffineXform::GetDifference(), and cmtk::AffineXform::GetInverse().

virtual SplineWarpXform* cmtk::SplineWarpXform::MakeInverse

(

)

const [inline, virtual, inherited]

Create inverse transformation.

This function returns NULL as there is no explicit inverse of a spline warp transformation.

Definition at line 110 of file cmtkSplineWarpXform.h.

References NULL.

template<class W >

Types::Coordinate * cmtk::ActiveDeformationModel< W >::MakeSamplePoints

(

const W *

deformation )

[private, inherited]

Make ADM sample points from a given deformation.

This function applies the inverse affine transformation of the given deformation to all of its control points. This brings all deformations into the same reference system, which is a necessary condition for model building. Note that otherwise all control point positions are in the coordinate system of the respective floating image, which varies from deformation to deformation.

Definition at line 148 of file cmtkActiveDeformationModel.cxx.

template<class W >

Types::Coordinate * cmtk::ActiveDeformationModel< W >::MakeSamplePointsReference

(

const W *

deformation )

[private, inherited]

Make ADM sample points from the undeformed c.p.g.

of a given deformation. This is for inclusion of the reference individual into the model by putting the identity transformation into the sample set.

Definition at line 126 of file cmtkActiveDeformationModel.cxx.

template<class T >

cmtk::Matrix3x3< T >::Matrix3x3

(

)

[inherited]

Default constructor: make identity matrix.

Note:

In order to create an uninitialized matrix (for speed), use Matrix3x3<>( NULL ).

Todo:

We do not actually support shear yet.

Definition at line 49 of file cmtkMatrix3x3.cxx.

template<class T >

cmtk::Matrix3x3< T >::Matrix3x3

(

const Self &

other )

[inherited]

Copy constructor.

Definition at line 56 of file cmtkMatrix3x3.cxx.

References cmtk::Matrix3x3< T >::Matrix.

template<class T >

cmtk::Matrix4x4< T >::Matrix4x4

(

)

[inherited]

Default constructor: make identity matrix.

Note:

In order to create an uninitialized matrix (for speed), use Matrix4x4<>( NULL ).

Definition at line 53 of file cmtkMatrix4x4.cxx.

template<class T>

cmtk::Matrix4x4< T >::Matrix4x4

(

const Matrix3x3< T > &

other )

[inherited]

Top left submatrix copy constructor.

Definition at line 60 of file cmtkMatrix4x4.cxx.

template<class T >

T cmtk::MathUtil::Mean	(	const unsigned int	nValues,
		const T *	values
	)		[static, inherited]

Computes average of an array of float values.

Definition at line 46 of file cmtkMathUtil_Statistics.txx.

template<class T >

T cmtk::MathUtil::Mean

(

const std::vector< T > &

values )

[static, inherited]

Computes average of a vector of float values.

Definition at line 81 of file cmtkMathUtil_Statistics.txx.

void cmtk::ScalarImage::Mirror	(	const bool	horizontal,
		const bool	vertical
	)		[inherited]

Mirror image horizontally and/or vertically.

Definition at line 775 of file cmtkScalarImage.cxx.

References cmtk::ScalarImage::m_Dims, and cmtk::ScalarImage::m_ImageOrigin.

Referenced by cmtk::QtTriplanarWindow::slotSwitchImageCo(), and cmtk::QtTriplanarWindow::slotSwitchImageSa().

void cmtk::DataGrid::MirrorPlaneInPlace	(	TypedArray &	data,
		const Self::IndexType &	dims,
		const int	axis = AXIS_X
	)		[static, private, inherited]

Mirror about plane without allocating additional memory.

Definition at line 280 of file cmtkDataGrid.cxx.

References cmtk::AXIS_X, cmtk::AXIS_Y, cmtk::AXIS_Z, cmtk::TypedArray::BlockReverse(), and cmtk::TypedArray::BlockSwap().

template<class T>

void cmtk::Histogram< T >::Normalize

(

const T

normalizeTo = 1 )

[inherited]

Normalize histogram values by their total sum.

Parameters:

normalizeTo

All histogram bins are scaled by a common factor so that their sum matches the value of this parameter.

Definition at line 116 of file cmtkHistogram.cxx.

void cmtk::DirectionSet::NormalizeEuclidNorm

(

const double

value = 1.0 )

[inherited]

Normalizes each direction vector to have euclid norm = value.

Definition at line 54 of file cmtkDirectionSet.cxx.

template<class T>

void cmtk::Histogram< T >::NormalizeMaximum

(

const T

normalizeTo = 1 )

[inherited]

Normalize histogram values by their maximum.

Parameters:

normalizeTo

All histogram bins are scaled by a common factor so that their maximum matches the value of this parameter.

Definition at line 127 of file cmtkHistogram.cxx.

void cmtk::DirectionSet::NormalizeMaxNorm

(

const double

value = 1.0 )

[inherited]

Normalizes each direction vector to have max norm = value.

Definition at line 43 of file cmtkDirectionSet.cxx.

bool cmtk::AnatomicalOrientationBase::OnSameAxis	(	const char	from,
		const char	to
	)		[static, inherited]

Return true if the direction corresponding to the character 'from' is on the same axis as that corresponding to 'to'.

Parameters:

from	Either L, R, A, P, I, or S
to	Either L, R, A, P, I, or S

Definition at line 84 of file cmtkAnatomicalOrientationBase.cxx.

template<int DIM>

Types::DataItem cmtk::FilterMask< DIM >::Gaussian::operator()

(

const FixedVector< DIM, Types::Coordinate > &

relativePosition )

[inline, inherited]

Get filter coefficient at relative location from filter center.

Definition at line 192 of file cmtkFilterMask.h.

template<class T >

T cmtk::operator*	(	const Vector< T > &	p,
		const Vector< T > &	q
	)		[inline]

Scalar product.

This operator computes the standard scalar product of two vectors over the same primitive type. As only a primitive object is returned as the result of this operator, it is time- and memory-efficient.

Definition at line 116 of file cmtkVector.txx.

References cmtk::Vector< T >::Dim, and cmtk::Vector< T >::Elements.

template<class T >

const Matrix3x3< T > cmtk::Matrix3x3< T >::operator*

(

const Self &

other )

const [inherited]

Multiplication operator.

Definition at line 343 of file cmtkMatrix3x3.cxx.

References cmtk::Matrix< TElement, NDim >::Matrix(), and NULL.

template<class T >

const Matrix4x4< T > cmtk::Matrix4x4< T >::operator*

(

const Self &

other )

const [inherited]

Multiplication operator.

Definition at line 446 of file cmtkMatrix4x4.cxx.

References cmtk::Matrix< TElement, NDim >::Matrix(), and NULL.

template<class T >

Vector<T> cmtk::operator*	(	const T	c,
		const Vector< T > &	p
	)

Scalar-to-vector multiplication operator.

Every element of a vector is multiplies by the same scalar factor. The result is returned as an automatically created object. This operator is rather inefficient in terms of allocation and destruction of objects; use *= instead if possible.

Definition at line 83 of file cmtkVector.txx.

References cmtk::Vector< T >::Dim, and cmtk::Vector< T >::Elements.

template<class T , class T2 >

FixedVector<3,T2> cmtk::operator*	(	const FixedVector< 3, T2 > &	u,
		const Matrix4x4< T > &	M
	)

Multiplication with 3d vector operation (will implicitly be made homogeneous).

Definition at line 168 of file cmtkMatrix4x4.h.

template<class T >

Matrix3x3< T > & cmtk::Matrix3x3< T >::operator*=

(

const Self &

other )

[inherited]

In-place multiplication operator.

Definition at line 321 of file cmtkMatrix3x3.cxx.

template<class T , class T2 >

FixedVector<3,T2>& cmtk::operator*=	(	FixedVector< 3, T2 > &	u,
		const Matrix4x4< T > &	M
	)

In-place multiplication with 3d vector operation (will implicitly be made homogeneous).

Definition at line 160 of file cmtkMatrix4x4.h.

template<class T>

Matrix3x3< T > & cmtk::Matrix3x3< T >::operator*=

(

const T

scalar )

[inherited]

In-place scalar multiplication operator.

Definition at line 328 of file cmtkMatrix3x3.cxx.

template<class T >

Matrix4x4< T > & cmtk::Matrix4x4< T >::operator*=

(

const Self &

other )

[inherited]

In-place multiplication operator.

Definition at line 438 of file cmtkMatrix4x4.cxx.

template<class T >

ValueSequence<T> cmtk::operator+	(	const ValueSequence< T > &	a,
		const ValueSequence< T > &	b
	)

Definition at line 56 of file cmtkValueSequence.txx.

References cmtk::ValueSequence< T >::Maximum, cmtk::ValueSequence< T >::MaximumAbs, cmtk::ValueSequence< T >::Minimum, cmtk::ValueSequence< T >::MinimumAbs, cmtk::ValueSequence< T >::NValues, cmtk::ValueSequence< T >::Sum, cmtk::ValueSequence< T >::SumAbs, and cmtk::ValueSequence< T >::SumOfSquares.

template<class T >

Vector<T> cmtk::operator+	(	const Vector< T > &	p,
		const Vector< T > &	delta
	)

Vector addition operator.

Two vectors are added elementwise. A newly created vector object is returned. This operator is rather inefficient in terms of allocation and destruction of objects; use -= instead if possible.

Definition at line 45 of file cmtkVector.txx.

References cmtk::Vector< T >::Dim, and cmtk::Vector< T >::Elements.

ScalarImage* cmtk::operator-	(	const ScalarImage &	image0,
		const ScalarImage &	image1
	)

Definition at line 722 of file cmtkScalarImage.cxx.

References cmtk::TypedArray::Create(), cmtk::TypedArray::Get(), cmtk::ScalarImage::GetNumberOfPixels(), cmtk::GetSignedDataType(), cmtk::TypedArray::GetType(), and cmtk::ScalarImage::m_Dims.

template<class T >

Vector<T> cmtk::operator-	(	const Vector< T > &	p,
		const Vector< T > &	delta
	)		[inline]

Vector subtraction operator.

Two vectors are subtracted elementwise. A newly created vector object is returned. This operator is rather inefficient in terms of allocation and destruction of objects; use += instead if possible.

Definition at line 64 of file cmtkVector.txx.

References cmtk::Vector< T >::Dim, and cmtk::Vector< T >::Elements.

ScalarImage & cmtk::ScalarImage::operator-=

(

const ScalarImage &

source )

[inherited]

Subtract one image from another in place.

Definition at line 753 of file cmtkScalarImage.cxx.

References cmtk::TypedArray::Get(), cmtk::TypedArray::Set(), and cmtk::TypedArray::SetPaddingAt().

template<class T >

Console& cmtk::operator<<	(	Console &	stream,
		const Matrix3x3< T > &	m
	)		[inline]

Output object to console.

Definition at line 197 of file cmtkMatrix3x3.h.

template<class T >

Console& cmtk::operator<<	(	Console &	stream,
		const Matrix4x4< T > &	m
	)		[inline]

Output object to console.

Definition at line 179 of file cmtkMatrix4x4.h.

AffineXform & cmtk::AffineXform::operator=

(

const AffineXform &

other )

[inherited]

Assignment operator.

Definition at line 126 of file cmtkAffineXform.cxx.

References cmtk::AffineXform::ComposeMatrix(), cmtk::AffineXform::m_LogScaleFactors, cmtk::Xform::m_ParameterVector, and cmtk::AffineXform::NumberDOFs.

template<class T >

Matrix3x3< T > & cmtk::Matrix3x3< T >::operator=

(

const Self &

other )

[inherited]

Assignment operator.

Definition at line 362 of file cmtkMatrix3x3.cxx.

References cmtk::Matrix3x3< T >::Matrix.

template<class T >

ValueSequence< T > & cmtk::ValueSequence< T >::operator=

(

const ValueSequence< T > &

other )

[inherited]

Assignment operator.

Definition at line 41 of file cmtkValueSequence.txx.

References cmtk::ValueSequence< T >::Maximum, cmtk::ValueSequence< T >::MaximumAbs, cmtk::ValueSequence< T >::Minimum, cmtk::ValueSequence< T >::MinimumAbs, cmtk::ValueSequence< T >::NValues, cmtk::ValueSequence< T >::Sum, cmtk::ValueSequence< T >::SumAbs, and cmtk::ValueSequence< T >::SumOfSquares.

template<class T>

Matrix4x4< T > & cmtk::Matrix4x4< T >::operator=

(

const Matrix3x3< T > &

other )

[inherited]

3x3 submatrix assignment operator.

Definition at line 465 of file cmtkMatrix4x4.cxx.

bool cmtk::BitVector::operator[]

(

const size_t

pos )

const [inherited]

Return a given bit.

Definition at line 124 of file cmtkBitVector.cxx.

template<class T >

T cmtk::MathUtil::PairedTTest	(	const std::vector< T > &	valuesX,
		const std::vector< T > &	valuesY,
		T &	t,
		T &	avgX,
		T &	avgY
	)		[static, inherited]

Performs two-tailed paired t-test on two distributions.

Also return average value for each distribution.

Definition at line 157 of file cmtkMathUtil_Statistics.txx.

cmtk::ParametricPlane::ParametricPlane

(

)

[inherited]

Default constructor.

Definition at line 46 of file cmtkParametricPlane.cxx.

References cmtk::ParametricPlane::Update().

cmtk::AnatomicalOrientation::PermutationMatrix::PermutationMatrix	(	const FixedVector< 3, int > &	sourceDims,
		const std::string &	curOrientation,
		const char	newOrientation[3]
	)		[inherited]

Constructor: determine axes permutation, flipping, and store local copy of reoriented dimensions array.

Definition at line 46 of file cmtkAnatomicalOrientationPermutationMatrix.cxx.

void cmtk::AffineXform::Print

(

)

const [virtual, inherited]

Print object.

Definition at line 502 of file cmtkAffineXform.cxx.

References cmtk::Xform::m_Parameters, cmtk::AffineXform::NumberDOFs, cmtk::Console::printf(), and cmtk::StdErr.

void cmtk::DataGrid::Print

(

)

const [inherited]

Print object.

Definition at line 617 of file cmtkDataGrid.cxx.

References cmtk::Console::printf(), and cmtk::StdErr.

void cmtk::ScalarImage::Print

(

)

const [virtual, inherited]

Print object information.

Definition at line 982 of file cmtkScalarImage.cxx.

References cmtk::Console::indent(), cmtk::ScalarImage::m_Dims, cmtk::ScalarImage::m_ImageOrigin, cmtk::Console::printf(), cmtk::StdErr, and cmtk::Console::unindent().

void cmtk::printBlock

(

Types::DataItem

block[COUPE_BLOCK_SIZE] )

Definition at line 134 of file cmtkFilterVolume.cxx.

References COUPE_BLOCK_SIZE.

double cmtk::MathUtil::ProbabilityFromTStat	(	const double	t,
		const size_t	df
	)		[static, inherited]

Compute probability from T-statistic.

Parameters:

t	T-statistic as returned for example from MathUtil::TStatFromCorrelation function.
df	Number of degrees of freedom.

Definition at line 55 of file cmtkMathUtil_Statistics.cxx.

template<class TData >

bool cmtk::UniformVolume::ProbeData	(	TData &	result,
		const TData *	dataPtr,
		const Self::CoordinateVectorType &	location
	)		const [inline, inherited]

Get data value at specified coordinate.

Definition at line 45 of file cmtkUniformVolume.txx.

Referenced by cmtk::SplineWarpGroupwiseRegistrationRMIFunctional::EvaluateLocalGradientThreadFunc(), cmtk::SplineWarpCongealingFunctional::EvaluateLocalGradientThreadFunc(), cmtk::GroupwiseRegistrationFunctionalXformTemplate< AffineXform >::InterpolateImageProbabilisticThread(), cmtk::GroupwiseRegistrationFunctionalXformTemplate< TXform >::InterpolateImageProbabilisticThread(), cmtk::GroupwiseRegistrationFunctionalXformTemplate< SplineWarpXform >::InterpolateImageThread(), cmtk::GroupwiseRegistrationFunctionalXformTemplate< AffineXform >::InterpolateImageThread(), and cmtk::GroupwiseRegistrationFunctionalXformTemplate< TXform >::InterpolateImageThread().

bool cmtk::UniformVolume::ProbeNoXform	(	ProbeInfo &	probeInfo,
		const Self::CoordinateVectorType &	location
	)		const [inline, inherited]

Return linearly interpolated voxel without applying a transformation.

Definition at line 75 of file cmtkUniformVolume.txx.

void cmtk::ScalarImage::ProjectPixel	(	const Self::SpaceVectorType &	v,
		int &	i,
		int &	j
	)		const [inherited]

Project 3D coordinate onto image plane.

Parameters:

v	Original coordinate.
i	Index of projected pixel in x direction.
j	Index of projected pixel in y direction.

Definition at line 972 of file cmtkScalarImage.cxx.

References cmtk::MathUtil::Round().

void cmtk::TypedArray::PruneHistogram	(	const bool	pruneHi,
		const bool	pruneLo,
		const size_t	numberOfBinsTarget,
		const size_t	numberOfBinsInternal = 1024
	)		[virtual, inherited]

Prune histogram to trim noise.

This function trims values on the upper and lower end of the value range by thresholding in such a way that the trimmed number of samples on either side amounts to the relative fraction of samples based on a target histogram bin count.

Definition at line 189 of file cmtkTypedArray.cxx.

References cmtk::Types::Range< T >::m_LowerBound, and cmtk::Types::Range< T >::m_UpperBound.

template<class TFloat >

cmtk::QRDecomposition< TFloat >::QRDecomposition

(

const Matrix2D< TFloat > &

matrix )

[inherited]

Constructor: compute QR decomposition of given matrix.

Definition at line 45 of file cmtkQRDecomposition.txx.

References cmtk::Matrix2D< T >::GetNumberOfColumns(), and cmtk::Matrix2D< T >::GetNumberOfRows().

void cmtk::SplineWarpXform::Refine

(

)

[virtual, inherited]

Refine control point grid by a factor of two, but maintain transformation exactly.

Reimplemented from cmtk::WarpXform.

Definition at line 254 of file cmtkSplineWarpXform.cxx.

void cmtk::SplineWarpXform::RegisterVolume

(

const UniformVolume *

volume )

[inline, inherited]

Register the grid points of the deformed uniform or non-uniform volume.

Definition at line 303 of file cmtkSplineWarpXform.h.

References cmtk::UniformVolume::m_Delta, cmtk::DataGrid::m_Dims, and cmtk::Volume::m_Offset.

Referenced by cmtk::GroupwiseRegistrationFunctionalXformTemplate< SplineWarpXform >::RefineTransformationGrids(), and cmtk::GroupwiseRegistrationFunctionalXformTemplate< SplineWarpXform >::SetTemplateGrid().

void cmtk::SplineWarpXform::RegisterVolumeAxis	(	const DataGrid::IndexType::ValueType	dim,
		const Types::Coordinate	delta,
		const Types::Coordinate	origin,
		const int	cpgDim,
		const Types::Coordinate	invCpgSpacing,
		std::vector< int > &	g,
		std::vector< Types::Coordinate > &	spline,
		std::vector< Types::Coordinate > &	dspline
	)		[private, inherited]

Register a single axis of the uniform volume to be deformed.

Definition at line 427 of file cmtkSplineWarpXform.cxx.

void cmtk::SplineWarpXform::RegisterVolumePoints	(	const DataGrid::IndexType &	,
		const Self::SpaceVectorType &
	)		[private, inherited]

Register axes points of the volume to be deformed.

void cmtk::SplineWarpXform::RegisterVolumePoints	(	const DataGrid::IndexType &	volDims,
		const Self::SpaceVectorType &	delta,
		const Self::SpaceVectorType &	origin
	)		[private, inherited]

Register axes points of the volume to be deformed.

Definition at line 451 of file cmtkSplineWarpXform.cxx.

void cmtk::SplineWarpXform::RelaxToUnfold

(

)

[virtual, inherited]

Relax the deformation to unfold areas with negative Jacobian at the current image sampling.

Note:

This requires a uniform pixel grid to be registered with this transformation.

See also:

RegisterVolume

Definition at line 802 of file cmtkSplineWarpXform_Jacobian.cxx.

References cmtk::FixedVector< NDIM, T >::SumOfSquares().

template<class T >

void cmtk::Histogram< T >::RemoveHistogram

(

const Self &

other )

[inherited]

Subtract bin values from another histogram.

Subtraction is done by corresponding bins. The caller has to make sure that both histograms actually have the same number of bins. It is also a good idea to ensure that the data ranges of these bins are the same in both objects. Both can be guaranteed if one histogram was created from the other by a call to Clone() for example.

Parameters:

other

A pointer to the other histogram. Its bin values are subtracted this object's bins.

Definition at line 101 of file cmtkHistogram.cxx.

References cmtk::Histogram< T >::GetNumBins(), and cmtk::Histogram< T >::m_Bins.

void cmtk::WarpXform::ReplaceInitialAffine

(

const AffineXform *

newAffineXform = NULL )

[inherited]

Replace initial affine transformation.

If the new transformation is not given (or a NULL pointer), then the new initial affine transformation is the identity transformation. This means that the transformation is converted into its pure nonrigid form.

Definition at line 274 of file cmtkWarpXform.cxx.

References cmtk::AffineXform::ApplyInPlace(), cmtk::AffineXform::Clone(), cmtk::AffineXform::Concat(), cmtk::META_XFORM_FIXED_IMAGE_PATH, and cmtk::META_XFORM_MOVING_IMAGE_PATH.

TypedArray::SmartPtr cmtk::UniformVolume::Resample

(

const UniformVolume &

other )

const [virtual, inherited]

Resample other volume.

Resampling is done by a sliding window algorithm combining both interpolation and averaging, even within one volume.

Returns:

Pointer to a newly created TypedArray object holding the resampled volume data. NULL is returned if sufficient memory is not available.

Definition at line 47 of file cmtkUniformVolume_Resample.cxx.

References cmtk::DATACLASS_GREY, cmtk::DATACLASS_LABEL, cmtk::Memory::DeleteArray(), cmtk::ThreadPool::GetNumberOfThreads(), cmtk::TypedArray::GetPaddingFlag(), cmtk::TypedArray::GetPaddingValue(), cmtk::TypedArray::GetType(), and cmtk::ThreadPool::Run().

void cmtk::UniformVolume::ResampleThreadPoolExecuteGrey	(	void *const	arg,
		const size_t	taskIdx,
		const size_t	taskCnt,
		const size_t	threadIdx,
		const size_t	threadCnt
	)		[static, private, inherited]

Multi-threaded resampling for grey data.

Definition at line 165 of file cmtkUniformVolume_Resample.cxx.

References cmtk::DataGrid::GetDataAt(), cmtk::VolumeGridToGridLookup::GetFromIndex(), cmtk::VolumeGridToGridLookup::GetLength(), cmtk::VolumeGridToGridLookup::GetSourceCount(), cmtk::VolumeGridToGridLookup::GetWeight(), cmtk::UniformVolume::ResampleTaskInfo::GridLookup, cmtk::DataGrid::m_Dims, cmtk::UniformVolume::ResampleTaskInfo::OtherVolume, cmtk::UniformVolume::ResampleTaskInfo::ResampledData, and cmtk::ThreadParameters< T >::thisObject.

void cmtk::UniformVolume::ResampleThreadPoolExecuteLabels	(	void *const	arg,
		const size_t	taskIdx,
		const size_t	taskCnt,
		const size_t	threadIdx,
		const size_t	threadCnt
	)		[static, private, inherited]

Multi-threaded resampling for label data (using partial volume averaging).

Definition at line 99 of file cmtkUniformVolume_Resample.cxx.

References cmtk::DataGrid::GetDataAt(), cmtk::VolumeGridToGridLookup::GetFromIndex(), cmtk::VolumeGridToGridLookup::GetSourceCount(), cmtk::VolumeGridToGridLookup::GetWeight(), cmtk::UniformVolume::ResampleTaskInfo::GridLookup, cmtk::DataGrid::m_Dims, cmtk::UniformVolume::ResampleTaskInfo::OtherVolume, cmtk::UniformVolume::ResampleTaskInfo::ResampledData, and cmtk::ThreadParameters< T >::thisObject.

void cmtk::TypedArray::RescaleToRange

(

const Types::DataItemRange &

toRange )

[virtual, inherited]

Scale values in the array to a given target range.

Definition at line 47 of file cmtkTypedArray.cxx.

References cmtk::Types::Range< T >::m_LowerBound, and cmtk::Types::Range< T >::Width().

template<class TDataType >

void cmtk::Accumulators::Avg< TDataType >::Reset

(

)

[inline, inherited]

Reset.

Definition at line 59 of file cmtkAccumulatorAvg.h.

template<class TDataType >

void cmtk::Accumulators::Max< TDataType >::Reset

(

)

[inline, inherited]

Reset.

Definition at line 59 of file cmtkAccumulatorMax.h.

void cmtk::BitVector::Reset

(

const size_t

pos )

[inherited]

Set one bit to 0.

Definition at line 105 of file cmtkBitVector.cxx.

template<class TDataType >

void cmtk::Accumulators::Sum< TDataType >::Reset

(

)

[inline, inherited]

Reset.

Definition at line 60 of file cmtkAccumulatorSum.h.

void cmtk::BitVector::Reset

(

const bool

value = false )

[inherited]

Set all bits to given flag (default: clear all).

Definition at line 96 of file cmtkBitVector.cxx.

TypedArray::SmartPtr cmtk::FilterVolume::RohlfingFilter	(	const UniformVolume *	volume,
		const TypedArray *	subjectData,
		const TypedArray *	maskData,
		const Units::GaussianSigma &	iFilterSigma,
		const Units::GaussianSigma &	filterWidth,
		const Types::Coordinate	filterRadius
	)		[static, inherited]

Apply Torsten Rohlfing's single-image intensity-consistent Gaussian filter.

Parameters:

volume	Input 3D image.
subjectData	Pixel array of the individual grey image from this subject.
maskData	Optional binary mask data array.
iFilterSigma	Width (standard deviation of the Gaussian kernel.
filterWidth	Width (standard deviation of the Gaussian kernel.
filterRadius	Filter radius in multiples of the filter width. Outside the radius (Euclidean distance) the filter is truncated.

Returns:

A newly allocated TypedArray object that can be used, for example, to replace the one held by the input image. The data type of the array is identical to the input array.

Definition at line 143 of file cmtkFilterVolume.cxx.

References cmtk::Histogram< T >::AddWeightedSymmetricKernel(), cmtk::AXIS_X, cmtk::AXIS_Y, cmtk::AXIS_Z, cmtk::UniformVolume::Deltas(), cmtk::TypedArray::Get(), cmtk::TypedArray::GetDataSize(), cmtk::DataGrid::GetDims(), cmtk::TypedArray::GetRange(), cmtk::TypedArray::GetType(), M_PI, cmtk::Histogram< T >::Reset(), cmtk::HistogramBase::SetRange(), cmtk::Units::UnitBase::Value(), and cmtk::HistogramBase::ValueToBin().

AffineXform::SpaceVectorType cmtk::AffineXform::RotateScaleShear

(

const Self::SpaceVectorType &

v )

const [inherited]

Apply rotation, scaling, and shearing but no translation to vector.

This function only used the upper left 3x3 sub-matrix of Matrix to transform a given vector. This is needed for rotation-center changes.

Note:

It is safe to use the same address for source and destination of this operation.

Returns:

The rotated, scaled, and sheared vector.

Parameters:

v	The vector to be rotated, scaled, and sheared.

Definition at line 186 of file cmtkAffineXform.cxx.

Referenced by cmtk::AffineXform::ChangeCenter(), and cmtk::GroupwiseRegistrationFunctionalXformTemplate< SplineWarpXform >::ForceZeroSumGradient().

void cmtk::AffineXform::RotateWXYZ	(	const Units::Radians	angle,
		const Self::SpaceVectorType &	direction,
		const Types::Coordinate *	origin = NULL,
		Self::MatrixType *const	accumulate = NULL
	)		[inherited]

Rotate around axis.

Parameters:

angle	Rotation angle.
direction	Direction vector of the rotation axis.
origin	If this parameter is given, it defines the 3D coordinates of a point on the rotation axis. If this parameter is not given, the rotation axis goes through the rotation center of this transformation.
accumulate	This parameter, if given, points to a 4x4 transformation matrix that can accumulate successive rotations. If given, two things happen: a) the current rotation axis is rotated according to the accumulated transformation, and b) the new rotation is concatenated onto the accumulated matrix by multiplication.

Definition at line 377 of file cmtkAffineXform.cxx.

References cmtk::MathUtil::Cos(), cmtk::Matrix4x4< T >::GetInverse(), and cmtk::MathUtil::Sin().

template<class T>

Matrix4x4< T > cmtk::Matrix4x4< T >::RotateX

(

const T

angle )

[static, inherited]

Return rotation around x axis.

Definition at line 510 of file cmtkMatrix4x4.cxx.

template<class T>

Matrix4x4< T > cmtk::Matrix4x4< T >::RotateY

(

const T

angle )

[static, inherited]

Return rotation around y axis.

Definition at line 521 of file cmtkMatrix4x4.cxx.

template<class T>

Matrix4x4< T > cmtk::Matrix4x4< T >::RotateZ

(

const T

angle )

[static, inherited]

Return rotation around z axis.

Definition at line 532 of file cmtkMatrix4x4.cxx.

cmtk::ScalarImage::ScalarImage	(	const ScalarImage &	other,
		const Self::RegionType &	roi
	)		[inherited]

Get ROI as sub-image.

Definition at line 125 of file cmtkScalarImage.cxx.

References cmtk::AXIS_X, cmtk::AXIS_Y, cmtk::TypedArray::ConvertSubArray(), cmtk::Region< NDIM, T >::From(), cmtk::ScalarImage::GetImageOrigin(), cmtk::TypedArray::GetPaddingFlag(), cmtk::TypedArray::GetPaddingPtr(), cmtk::TypedArray::GetType(), cmtk::ScalarImage::m_Dims, and cmtk::Region< NDIM, T >::To().

cmtk::ScalarImage::ScalarImage	(	const ScalarImage &	source,
		const int *	roiFrom = NULL,
		const int *	roiTo = NULL
	)		[inherited]

Get ROI as sub-image.

Parameters:

source	The source image to copy an ROI from.
roiFrom	The (x,y) pixel of the original image that will make up the top left (0,0) pixel of this image.
roiTo	The (x,y) pixel of the original image that will make up the bottom right (dimx-1,dimy-1) pixel of this image.

Note:

Note that the ROI given by roiFrom and roiTo is an inclusive boundary, i.e., the indexed row and column will still be part of the cropped image. The cropped image dimension is therefore (1+roiTo[0]-roiFrom[0],1+roiTo[0]-roiFrom[0]).

Definition at line 77 of file cmtkScalarImage.cxx.

References cmtk::AXIS_X, cmtk::AXIS_Y, cmtk::ScalarImage::Clone(), cmtk::TypedArray::ConvertSubArray(), cmtk::ScalarImage::GetImageOrigin(), cmtk::TypedArray::GetPaddingFlag(), cmtk::TypedArray::GetPaddingPtr(), cmtk::TypedArray::GetType(), cmtk::ScalarImage::HasROI, cmtk::ScalarImage::m_Dims, and cmtk::ScalarImage::ROI.

cmtk::ScalarImage::ScalarImage

(

)

[inherited]

Default constructor creates empty image.

Definition at line 52 of file cmtkScalarImage.cxx.

References cmtk::ScalarImage::m_Dims.

Referenced by cmtk::ScalarImage::Clone().

cmtk::ScalarImage::ScalarImage	(	const int	dimsx,
		const int	dimsy,
		const int	numberOfFrames = 1
	)		[inherited]

Constructor with separate x and y dimensions.

Definition at line 63 of file cmtkScalarImage.cxx.

static Types::Coordinate cmtk::CubicSpline::SecondDerivApproxSpline	(	const int	k,
		const Types::Coordinate	t
	)		[inline, static, inherited]

Compute the second derivative of a given approximating spline function.

Definition at line 161 of file cmtkCubicSpline.h.

static Types::Coordinate cmtk::CubicSpline::SecondDerivApproxSpline0

(

const Types::Coordinate

t )

[inline, static, inherited]

Compute the second derivative of the 0th approximating spline function.

Definition at line 137 of file cmtkCubicSpline.h.

static Types::Coordinate cmtk::CubicSpline::SecondDerivApproxSpline1

(

const Types::Coordinate

t )

[inline, static, inherited]

Compute second derivative of the 1st approximating spline function.

Definition at line 143 of file cmtkCubicSpline.h.

static Types::Coordinate cmtk::CubicSpline::SecondDerivApproxSpline2

(

const Types::Coordinate

t )

[inline, static, inherited]

Compute second derivative of the 2nd approximating spline function.

Definition at line 149 of file cmtkCubicSpline.h.

static Types::Coordinate cmtk::CubicSpline::SecondDerivApproxSpline3

(

const Types::Coordinate

t )

[inline, static, inherited]

Compute second derivative of the 3rd approximating spline function.

Definition at line 155 of file cmtkCubicSpline.h.

static Types::Coordinate cmtk::CubicSpline::SecondDerivInterpSpline	(	const int	k,
		const Types::Coordinate	t
	)		[inline, static, inherited]

Compute second derivative of a given interpolating spline function.

Definition at line 281 of file cmtkCubicSpline.h.

static Types::Coordinate cmtk::CubicSpline::SecondDerivInterpSpline0

(

const Types::Coordinate

t )

[inline, static, inherited]

Compute second derivative of the 0th interpolating spline function.

Definition at line 257 of file cmtkCubicSpline.h.

static Types::Coordinate cmtk::CubicSpline::SecondDerivInterpSpline1

(

const Types::Coordinate

t )

[inline, static, inherited]

Compute second derivative of the 1st interpolating spline function.

Definition at line 263 of file cmtkCubicSpline.h.

static Types::Coordinate cmtk::CubicSpline::SecondDerivInterpSpline2

(

const Types::Coordinate

t )

[inline, static, inherited]

Compute second derivative of the 2nd interpolating spline function.

Definition at line 269 of file cmtkCubicSpline.h.

static Types::Coordinate cmtk::CubicSpline::SecondDerivInterpSpline3

(

const Types::Coordinate

t )

[inline, static, inherited]

Compute second derivative of the 3rd interpolating spline function.

Definition at line 275 of file cmtkCubicSpline.h.

ScalarDataType cmtk::SelectDataTypeInteger	(	const byte	itemSize,
		const bool	signBit
	)

Select integer data type based on item size and sign bit.

Definition at line 98 of file cmtkTypes.cxx.

References cmtk::TYPE_BYTE, cmtk::TYPE_CHAR, cmtk::TYPE_INT, cmtk::TYPE_NONE, cmtk::TYPE_SHORT, and cmtk::TYPE_USHORT.

Referenced by cmtk::VolumeFromSlices::FinishVolume().

template<class T>

Matrix3x3< T > & cmtk::Matrix3x3< T >::Set

(

const T *const

values )

[inherited]

Set from array of entries.

Definition at line 63 of file cmtkMatrix3x3.cxx.

Referenced by cmtk::SplineWarpXform::GetJacobianRow().

template<class T>

Matrix4x4< T > & cmtk::Matrix4x4< T >::Set

(

const T *const

values )

[inherited]

Set from array of entries.

Definition at line 79 of file cmtkMatrix4x4.cxx.

void cmtk::BitVector::Set	(	const size_t	pos,
		const bool	val = true
	)		[inherited]

Set one bit to a given value.

Definition at line 83 of file cmtkBitVector.cxx.

void cmtk::BitVector::Set

(

)

[inherited]

Set all bits to 1.

Definition at line 77 of file cmtkBitVector.cxx.

void cmtk::VolumeClipping::SetClippingBoundaries

(

const UniformVolume::CoordinateRegionType &

region )

[inherited]

Set clipping boundaries.

This function sets the boundaries by which clipping is performed.

Parameters:

region

The clipping region in image coordinates

Definition at line 48 of file cmtkVolumeClipping.cxx.

void cmtk::DataGrid::SetDims

(

const Self::IndexType &

dims )

[inherited]

Set dimensions array.

This function updates the internal offsets for fast access to adjacent voxel rows, columns, planes etc.

Definition at line 185 of file cmtkDataGrid.cxx.

Referenced by cmtk::DataGrid::GetDownsampledAndAveraged().

void cmtk::UniformVolume::SetHighResCropRegion

(

const Self::CoordinateRegionType &

crop )

[inherited]

Set cropping region in real-world coordinates.

Definition at line 44 of file cmtkUniformVolume_Crop.cxx.

Referenced by cmtk::UniformVolume::GetDownsampledAndAveraged().

void cmtk::AffineXform::SetMatrix

(

const MatrixType &

matrix )

[inherited]

Definition at line 241 of file cmtkAffineXform.cxx.

References cmtk::AffineXform::DecomposeMatrix(), and cmtk::AffineXform::UpdateInverse().

void cmtk::AffineXform::SetMatrix

(

const double

matrix[4][4] )

[inherited]

Definition at line 259 of file cmtkAffineXform.cxx.

References cmtk::AffineXform::DecomposeMatrix(), and cmtk::AffineXform::UpdateInverse().

void cmtk::AffineXform::SetMatrix

(

const float

matrix[4][4] )

[inherited]

Set transformation matrix.

Definition at line 249 of file cmtkAffineXform.cxx.

References cmtk::AffineXform::DecomposeMatrix(), and cmtk::AffineXform::UpdateInverse().

void cmtk::ParametricPlane::SetNormal

(

const Self::CoordinateVectorType &

normal )

[inherited]

Set normal vector and determine rotation angles from it.

Definition at line 66 of file cmtkParametricPlane.cxx.

References cmtk::MathUtil::ArcCos(), cmtk::MathUtil::ArcSin(), cmtk::ParametricPlane::Normal, cmtk::ParametricPlane::Phi, cmtk::FixedVector< NDIM, T >::RootSumOfSquares(), cmtk::MathUtil::Sin(), cmtk::ParametricPlane::SquareNormal, and cmtk::ParametricPlane::Theta.

void cmtk::AffineXform::SetNumberDOFs

(

const int

numberDOFs = 12 )

[virtual, inherited]

Set the number of degrees of freedom for this object.

Definition at line 136 of file cmtkAffineXform.cxx.

References cmtk::AffineXform::ComposeMatrix(), cmtk::Xform::m_Parameters, and cmtk::AffineXform::NumberDOFs.

Referenced by cmtk::AffineXform::MakeInverse().

void cmtk::DataGrid::SetOrthoSlice	(	const int	axis,
		const unsigned int	idx,
		const ScalarImage *	slice
	)		[virtual, inherited]

Set orthogonal slice from a 2D image.

Definition at line 502 of file cmtkDataGrid.cxx.

References cmtk::AXIS_X, cmtk::AXIS_Y, cmtk::AXIS_Z, cmtk::TypedArray::BlockCopy(), and cmtk::TypedArray::GetType().

Referenced by cmtk::UniformVolume::GetInterleavedPaddedSubVolume(), and cmtk::UniformVolume::GetInterleavedSubVolume().

void cmtk::AffineXform::SetParameter	(	const size_t	idx,
		const Types::Coordinate	p
	)		[virtual, inherited]

Set a single parameter value.

Reimplemented from cmtk::Xform.

Definition at line 304 of file cmtkAffineXform.cxx.

References cmtk::AffineXform::CanonicalRotationRange(), cmtk::AffineXform::ComposeMatrix(), and cmtk::Xform::SetParameter().

void cmtk::WarpXform::SetParameterActive	(	const size_t	index,
		const bool	active = true
	)		[inherited]

Set a particular parameter as active (or passive).

Parameters:

index	Index of the parameter.
active	Flag whether to set the parameter as active (non-zero) or passive (zero).

Definition at line 200 of file cmtkWarpXform.cxx.

void cmtk::WarpXform::SetParameterInactive

(

const size_t

index )

[inherited]

Set a particular parameter as inactive.

Definition at line 249 of file cmtkWarpXform.cxx.

void cmtk::WarpXform::SetParametersActive

(

const UniformVolume::RegionType &

roi )

[inherited]

Set only those parameters as active that influence a given ROI.

Definition at line 210 of file cmtkWarpXform.cxx.

void cmtk::WarpXform::SetParametersActive

(

const char *

axes )

[inherited]

Set parameters for spatial dimensions as active.

Parameters:

axes

This parameter defiend the activated dimensions in this transformation. If it contains the characters x, y, or z, then the x, y, and z-directions, respectively, are activated. The remaining directions (if any) are deativated. The order of the axes is not relevant. Both upper- and lowercase characters will be accepted.

Definition at line 231 of file cmtkWarpXform.cxx.

References cmtk::AXIS_X, cmtk::AXIS_Y, and cmtk::AXIS_Z.

void cmtk::WarpXform::SetParametersActive	(	const int	axis,
		const bool	active = true
	)		[inherited]

Set parameters for one spatial dimension as active or inactive.

Definition at line 220 of file cmtkWarpXform.cxx.

void cmtk::WarpXform::SetParametersActive

(

)

[inherited]

Set all parameters as active.

Definition at line 189 of file cmtkWarpXform.cxx.

void cmtk::AffineXform::SetParamVector

(

const CoordinateVector &

v )

[virtual, inherited]

Set Xform by constant parameter vector.

Other than setting the transformation from a non-constant vector object, this function does not update the given parameter vector to match the internal representation of the igsAfffineXform object. It is therefore not guaranteed that subsequent calls to GetParamVector() will yield the same parameters.

Reimplemented from cmtk::Xform.

Definition at line 296 of file cmtkAffineXform.cxx.

References cmtk::AffineXform::CanonicalRotationRange(), cmtk::AffineXform::ComposeMatrix(), and cmtk::Xform::SetParamVector().

void cmtk::Xform::SetParamVector

(

CoordinateVector &

v )

[virtual, inherited]

Set Xform by parameter vector.

Be careful: This is NOT a one-way function. The Xform object may change the parameter vector in order to ensure internal consistency (AffineXform) or to enhance efficiency.

Reimplemented in cmtk::AffineXform.

Definition at line 65 of file cmtkXform.cxx.

Referenced by cmtk::ParallelElasticFunctional< VM >::EvaluateGradientThread(), cmtk::ImagePairNonrigidRegistrationFunctionalTemplate< VM >::EvaluateGradientThread(), and cmtk::AffineXform::SetParamVector().

void cmtk::Xform::SetParamVector

(

const CoordinateVector &

v )

[virtual, inherited]

Set the parameter vector.

Reimplemented in cmtk::AffineXform.

Definition at line 79 of file cmtkXform.cxx.

void cmtk::AffineXform::SetParamVector

(

CoordinateVector &

v )

[virtual, inherited]

Set Xform by parameter vector.

Reimplemented from cmtk::Xform.

Definition at line 287 of file cmtkAffineXform.cxx.

References cmtk::AffineXform::CanonicalRotationRange(), cmtk::AffineXform::ComposeMatrix(), cmtk::Xform::m_ParameterVector, and cmtk::Xform::SetParamVector().

Referenced by cmtk::operator>>().

void cmtk::AffineXform::SetUseLogScaleFactors

(

const bool

logScaleFactors )

[inherited]

Switch between log and ordinary scale factors.

Definition at line 147 of file cmtkAffineXform.cxx.

References cmtk::AffineXform::m_LogScaleFactors, and cmtk::Xform::m_Parameters.

Referenced by cmtk::operator>>().

cmtk::SplineWarpXform::SplineWarpXform	(	const FixedVector< 3, Types::Coordinate > &	domain,
		const Self::IndexType &	dims,
		CoordinateVector::SmartPtr &	parameters,
		const AffineXform *	initialXform = NULL
	)		[inherited]

Construct new warp from volume size, grid dimensions and parameters.

Definition at line 96 of file cmtkSplineWarpXform.cxx.

References cmtk::AffineXform::Clone(), and NULL.

cmtk::SplineWarpXform::SplineWarpXform

(

)

[inherited]

Construct empty new warp.

This is mostly useful for the Clone() function that can subsequently copy all data structures into a newly created empty object.

Definition at line 48 of file cmtkSplineWarpXform.cxx.

cmtk::SplineWarpXform::SplineWarpXform	(	const FixedVector< 3, Types::Coordinate > &	domain,
		const Types::Coordinate	delta,
		const AffineXform *	initialXform = NULL,
		const bool	exactDelta = false
	)		[inherited]

Construct new warp from volume size and control grid density.

Definition at line 59 of file cmtkSplineWarpXform.cxx.

DataClass cmtk::StringToDataClass

(

const char *

dataClassStr )

Convert string to data class identifier.

Definition at line 60 of file cmtkTypes.cxx.

References cmtk::DATACLASS_UNKNOWN.

Referenced by cmtk::VoxelRegistration::ImagePreprocessor::GetProcessedImage(), and cmtk::ImagePairRegistration::ImagePreprocessor::GetProcessedImage().

TypedArray::SmartPtr cmtk::FilterVolume::StudholmeFilter	(	const UniformVolume *	volume,
		std::list< TypedArray::SmartPtr >	subjectData,
		const TypedArray *	averageData,
		const TypedArray *	maskData,
		std::list< TypedArray::SmartPtr >	imgList,
		const Types::DataItem	binWidth,
		const Units::GaussianSigma &	filterWidth,
		const Types::Coordinate	filterRadius
	)		[static, inherited]

Apply Colin Studholme's Gaussian filter using multiple time points.

Parameters:

volume	Input 3D image.
subjectData	List of pixel arrays of the individual grey images from this subject. Each list item corresponds to one time point. Ideally, there are two items in the list, which correspond to the time points between which the Jacobian map in "volume" was computed.
averageData	Pixel array of the population average grey image.
maskData	Optional binary mask data array.
imgList	List of pixel arrays from matched 3D images. The consistency between these pixel arrays determines the relative weights of the otherwise Gaussian kernel. Consult Colin's NeuroImage (2003) paper for details.
binWidth	Bin width of the intensity histogram used to quantify the matching between all individuals.
filterWidth	Width (standard deviation of the Gaussian kernel.
filterRadius	Filter radius in multiples of the filter width. Outside the radius (Euclidean distance) the filter is truncated.

Returns:

A newly allocated TypedArray object that can be used, for example, to replace the one held by the input image. The data type of the array is identical to the input array.

Definition at line 408 of file cmtkFilterVolume.cxx.

References cmtk::AXIS_X, cmtk::AXIS_Y, cmtk::AXIS_Z, cmtk::UniformVolume::Deltas(), cmtk::TypedArray::Get(), cmtk::JointHistogram< T >::GetBin(), cmtk::TypedArray::GetDataSize(), cmtk::DataGrid::GetDims(), cmtk::JointHistogram< T >::GetMarginalX(), cmtk::DataGrid::GetOffsetFromIndex(), cmtk::TypedArray::GetRange(), cmtk::TypedArray::GetType(), cmtk::JointHistogram< T >::Increment(), cmtk::JointHistogram< T >::Reset(), cmtk::JointHistogram< T >::SetRangeX(), cmtk::JointHistogram< T >::SetRangeY(), cmtk::JointHistogram< T >::ValueToBinX(), cmtk::JointHistogram< T >::ValueToBinY(), and cmtk::Types::Range< T >::Width().

TypedArray::SmartPtr cmtk::FilterVolume::StudholmeFilter	(	const UniformVolume *	volume,
		const TypedArray *	subjectData,
		const TypedArray *	averageData,
		const TypedArray *	maskData,
		std::list< TypedArray::SmartPtr >	imgList,
		const Types::DataItem	binWidth,
		const Units::GaussianSigma &	filterWidth,
		const Types::Coordinate	filterRadius
	)		[static, inherited]

Apply Colin Studholme's Gaussian filter with registration-based weights.

Parameters:

volume	Input 3D image.
subjectData	Pixel array of the individual grey image from this subject.
averageData	Pixel array of the population average grey image.
maskData	Optional binary mask data array.
imgList	List of pixel arrays from matched 3D images. The consistency between these pixel arrays determines the relative weights of the otherwise Gaussian kernel. Consult Colin's NeuroImage (2003) paper for details.
binWidth	Bin width of the intensity histogram used to quantify the matching between all individuals.
filterWidth	Width (standard deviation of the Gaussian kernel.
filterRadius	Filter radius in multiples of the filter width. Outside the radius (Euclidean distance) the filter is truncated.

Returns:

A newly allocated TypedArray object that can be used, for example, to replace the one held by the input image. The data type of the array is identical to the input array.

Definition at line 264 of file cmtkFilterVolume.cxx.

References cmtk::AXIS_X, cmtk::AXIS_Y, cmtk::AXIS_Z, cmtk::UniformVolume::Deltas(), cmtk::TypedArray::Get(), cmtk::JointHistogram< T >::GetBin(), cmtk::TypedArray::GetDataSize(), cmtk::DataGrid::GetDims(), cmtk::Threads::GetNumberOfThreads(), cmtk::TypedArray::GetRange(), cmtk::TypedArray::GetType(), cmtk::JointHistogram< T >::Increment(), cmtk::JointHistogram< T >::ProjectToX(), cmtk::JointHistogram< T >::Reset(), cmtk::JointHistogram< T >::ValueToBinX(), cmtk::JointHistogram< T >::ValueToBinY(), and cmtk::Types::Range< T >::Width().

void cmtk::MathUtil::SVD	(	Matrix2D< double > *	U,
		size_t	m,
		size_t	n,
		std::vector< double > *	W,
		Matrix2D< double > *	V
	)		[static, inherited]

Singular Value Decomposition.

Definition at line 146 of file cmtkMathUtil_LinAlg.cxx.

void cmtk::MathUtil::SVDLinearRegression	(	Matrix2D< double > *	U,
		size_t	m,
		size_t	n,
		std::vector< double > *	W,
		Matrix2D< double > *	V,
		double *	b,
		std::vector< double > &	lm_params
	)		[static, inherited]

Linear Regression using SVD results.

TODO: move this someplace more logical than the linear-algebra module.

Definition at line 183 of file cmtkMathUtil_LinAlg.cxx.

template<class TFloat >

void cmtk::EigenSystemSymmetricMatrix3x3< TFloat >::tql2	(	TFloat	V[3][3],
		TFloat	d[3],
		TFloat	e[3],
		const bool	sortAbsolute = true
	)		[static, private, inherited]

Definition at line 206 of file cmtkEigenSystemSymmetricMatrix3x3.txx.

cmtk::TransformedVolumeAxes::TransformedVolumeAxes	(	const UniformVolume &	volume,
		const ParametricPlane &	mirrorPlane,
		const Types::Coordinate *	deltas = NULL
	)		[inherited]

Constructor using mirror plane.

Parameters:

volume	The volume whose axes we are transforming.
mirrorPlane	Mirror plane with respect to which the coordinates of this volume and thus all hash values are mirrored.
deltas	If this parameter is given, it is used as a pointer to a 3 element coordinate array defining the voxel size in the other volume to obtain fractional voxel indices rather than actual coordinates.

Alternatively, this parameter can also be used to provide the volume size (Volume::Size), which creates normalized coordinates (0..1) for each volume axis.

Definition at line 88 of file cmtkTransformedVolumeAxes.cxx.

References cmtk::Volume::m_Offset, and cmtk::ParametricPlane::MirrorInPlace().

cmtk::TransformedVolumeAxes::TransformedVolumeAxes	(	const UniformVolume &	volume,
		const AffineXform *	xform = NULL,
		const Types::Coordinate *	deltas = NULL,
		const Types::Coordinate *	otherOrigin = NULL
	)		[inherited]

Constructor using affine transformation.

Parameters:

volume	The volume for which we are constructing an axes hash.
xform	Coordinate transformation. If this pointer is NULL, identity is assumed.
deltas	If this parameter is given, it is used as a pointer to a three-element coordinate array defining the voxel size in the other volume to obtain fractional voxel indices rather than actual coordinates.

Alternatively, this parameter can also be used to provide the volume size (Volume::Size), which creates normalized coordinates (0..1) for each volume axis.

Parameters:

otherOrigin

If this parameter is given, it is used as a pointer to a three-element coordinate array defining an m_Origin vector for the transformed coordinates.

Returns:

Pointer to an array of three pointers. Each of these points to an array of Vector3D objects that contain the vector hashes for the X-, Y-, and Z-axis.

Definition at line 45 of file cmtkTransformedVolumeAxes.cxx.

References cmtk::AffineXform::ApplyInPlace(), and cmtk::Volume::m_Offset.

template<class TFloat >

void cmtk::EigenSystemSymmetricMatrix3x3< TFloat >::tred2	(	TFloat	V[3][3],
		TFloat	d[3],
		TFloat	e[3]
	)		[static, private, inherited]

Symmetric Householder reduction to tridiagonal form.

Definition at line 66 of file cmtkEigenSystemSymmetricMatrix3x3.txx.

template<class TData , class TOutputIterator >

void cmtk::DataGrid::TrilinearInterpolation	(	TOutputIterator	result,
		const std::vector< TData * > &	dataPtr,
		const int	x,
		const int	y,
		const int	z,
		const Types::Coordinate	fracX,
		const Types::Coordinate	fracY,
		const Types::Coordinate	fracZ
	)		const [inline, protected, inherited]

Utility function for trilinear interpolation from multiple primitive data arrays of identical grid structure.

This function is provided for computational efficiency when a large number of interpolations from a given data volume of known pixel type are required.

Parameters:

result	Output iterator to store interpolated values.
dataPtr	Vector of data arrays to interpolate from
x	Grid position x
y	Grid position y
z	Grid position z
fracX	Fractional coordinate X within pixel
fracY	Fractional coordinate Y within pixel
fracZ	Fractional coordinate Z within pixel

Definition at line 142 of file cmtkDataGrid.txx.

bool cmtk::DataGrid::TrilinearInterpolation	(	Types::DataItem &	data,
		const int	x,
		const int	y,
		const int	z,
		const Self::SpaceVectorType &	location,
		const Types::Coordinate *	cellFrom,
		const Types::Coordinate *	cellTo
	)		const [protected, inherited]

Utility function for trilinear interpolation.

Parameters:

data	This reference is set to the interpolated data value. It is valid if and only if this function returns 1.
location	3D coordinate to interpolate data at.
x	Grid index x.
y	Grid index y.
z	Grid index z.
location	Location within grid cell.
cellFrom	3D coordinate of the lower-left-front voxel of the cell enclosing the given location.
cellTo	3D coordinate of the upper-right-rear voxel of the cell enclosing the given location.

Returns:

True if there is valid data for all eight voxels enclosing the given location, so that the interpolation could be completed successfully, False otherwise.

Definition at line 201 of file cmtkDataGrid.cxx.

References cmtk::TypedArray::Get().

template<class TData >

TData cmtk::DataGrid::TrilinearInterpolation	(	const TData *	dataPtr,
		const int	x,
		const int	y,
		const int	z,
		const Self::SpaceVectorType &	gridPosition,
		const Types::Coordinate *	cellFrom,
		const Types::Coordinate *	cellTo
	)		const [inline, protected, inherited]

Utility function for trilinear interpolation from a primitive data array.

This function is provided for computational efficiency when a large number of interpolations from a given data volume of known pixel type are required.

Parameters:

dataPtr	Pointer to the primitive data array.
x	Grid index x.
y	Grid index y.
z	Grid index z.
gridPosition	(x,y,z) indices of the voxel containing the given location.
cellFrom	3D coordinate of the lower-left-front voxel of the cell enclosing the given location.
cellTo	3D coordinate of the upper-right-rear voxel of the cell enclosing the given location.

Returns:

The interpolated data value..

Definition at line 115 of file cmtkDataGrid.txx.

double cmtk::MathUtil::TStatFromCorrelation	(	const double	r,
		const size_t	df
	)		[static, inherited]

Compute t-statistic from coefficient of correlation.

Parameters:

r	Coefficient of correlation as computed by MathUtil::Correlation function.
df	Number of degrees of freedom

Definition at line 48 of file cmtkMathUtil_Statistics.cxx.

template<class T >

T cmtk::MathUtil::TTest	(	const std::vector< T > &	valuesX,
		const std::vector< T > &	valuesY,
		T &	t,
		T &	avgX,
		T &	avgY
	)		[static, inherited]

Performs two-tailed unpaired t-test on two distributions.

Two-sample t-test.

Also return average value for each distribution.

Definition at line 181 of file cmtkMathUtil_Statistics.txx.

template<class T >

T cmtk::MathUtil::TTest	(	const std::vector< T > &	valuesX,
		T &	t,
		T &	avgX
	)		[static, inherited]

Performs one-sample t-test on distribution to test for zero mean.

One-sample t-test.

Also return average value for each distribution.

Definition at line 213 of file cmtkMathUtil_Statistics.txx.

template<class T >

T cmtk::MathUtil::TTest	(	const std::vector< T > &	valuesX,
		const std::vector< T > &	valuesY,
		T &	t
	)		[static, inherited]

Performs two-tailed unpaired t-test on two distributions.

Definition at line 148 of file cmtkMathUtil_Statistics.txx.

size_t cmtk::TypeItemSize

(

const ScalarDataType

dtype )

Return item size for given scalar data type.

Definition at line 81 of file cmtkTypes.cxx.

References cmtk::TYPE_BYTE, cmtk::TYPE_CHAR, cmtk::TYPE_DOUBLE, cmtk::TYPE_FLOAT, cmtk::TYPE_INT, cmtk::TYPE_SHORT, cmtk::TYPE_UINT, and cmtk::TYPE_USHORT.

Referenced by cmtk::TemplateArray< T >::ConvertSubArray().

template<class TDistanceDataType >

cmtk::UniformDistanceMap< TDistanceDataType >::UniformDistanceMap	(	const UniformVolume &	volume,
		const byte	flags = DEFAULT,
		const Types::DataItem	value = 0,
		const Types::DataItem	window = 0
	)		[inherited]

Construct map from given volume.

Parameters:

volume	3-D feature image.
flags	Computation flags.
value	Feature value
window	Window radius around feature value.

Definition at line 51 of file cmtkUniformDistanceMap.cxx.

References cmtk::UniformVolume::m_IndexToPhysicalMatrix, cmtk::MetaInformationObject::m_MetaInformation, and cmtk::Volume::m_Offset.

double cmtk::MathUtil::UniformRandom

(

)

[static, inherited]

Uniform random number generator.

Definition at line 47 of file cmtkMathUtil_Random.cxx.

Referenced by cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::SetForegroundMask().

cmtk::UniformVolumeFilter::UniformVolumeFilter

(

UniformVolume::SmartPtr

volume )

[inline, explicit, inherited]

Constructor: link to UniformVolume object.

Definition at line 60 of file cmtkUniformVolumeFilter.h.

void cmtk::SplineWarpXform::UnRegisterVolume

(

)

[inherited]

Unegister axes points, ie free all internal data structures.

Definition at line 464 of file cmtkSplineWarpXform.cxx.

void cmtk::WarpXform::Update

(

const bool

exactDelta = false )

[virtual, inherited]

Update internal representation.

Reimplemented in cmtk::SplineWarpXform.

Definition at line 62 of file cmtkWarpXform.cxx.

void cmtk::SplineWarpXform::Update

(

const bool

exactDelta = false )

[virtual, inherited]

Update internal representation.

Reimplemented from cmtk::WarpXform.

Definition at line 170 of file cmtkSplineWarpXform.cxx.

void cmtk::ParametricPlane::Update

(

)

[private, inherited]

Update internal fields after change of parameters.

Definition at line 56 of file cmtkParametricPlane.cxx.

References cmtk::MathUtil::Cos(), cmtk::ParametricPlane::Normal, cmtk::ParametricPlane::Phi, cmtk::MathUtil::Sin(), cmtk::ParametricPlane::SquareNormal, and cmtk::ParametricPlane::Theta.

Referenced by cmtk::ParametricPlane::ParametricPlane().

void cmtk::AffineXform::UpdateInverse

(

)

const [private, inherited]

Update linked inverse transformation.

Definition at line 478 of file cmtkAffineXform.cxx.

References cmtk::AffineXform::InverseXform, cmtk::AffineXform::m_LogScaleFactors, and cmtk::AffineXform::NumberDOFs.

Referenced by cmtk::AffineXform::ComposeMatrix(), cmtk::AffineXform::GetInverse(), and cmtk::AffineXform::SetMatrix().

template<class T >

T cmtk::MathUtil::Variance	(	const unsigned int	nValues,
		const T *	values,
		T	mean,
		const bool	unbiased = false
	)		[static, inherited]

Computes variance of an array of float values.

Parameters:

nValues	Number of values in "values" array.
values	The array of values to compute the variance of.
mean	Previously calculated mean of the array values.
unbiased	If this flag is set (default: unset), then the variance will be computed over nValues-1; otherwise over nValues.

Definition at line 60 of file cmtkMathUtil_Statistics.txx.

template<class T >

T cmtk::MathUtil::Variance	(	const std::vector< T > &	values,
		T	mean,
		const bool	unbiased = false
	)		[static, inherited]

Computes variance of a vector of float values.

Parameters:

values	Vector of values to compute variance from.
mean	Previously computed mean of vector values.
unbiased	If this flag is set (default: unset), then the variance will be computed over nValues-1; otherwise over nValues.

Definition at line 96 of file cmtkMathUtil_Statistics.txx.

cmtk::VolumeGridToGridLookup::VolumeGridToGridLookup	(	const UniformVolume &	fromGrid,
		const UniformVolume &	toGrid
	)		[inherited]

Constructor: takes original and new image grids.

Definition at line 45 of file cmtkVolumeGridToGridLookup.cxx.

References cmtk::UniformVolume::m_Delta, cmtk::DataGrid::m_Dims, and cmtk::Volume::Size.

template<class TDistanceDataType >

bool cmtk::UniformDistanceMap< TDistanceDataType >::VoronoiEDT	(	DistanceDataType *const	lpY,
		const int	nSize,
		const DistanceDataType	delta,
		std::vector< DistanceDataType > &	gTemp,
		std::vector< DistanceDataType > &	hTemp
	)		[private, inherited]

Compute 1-D Voronoi Euclidean Distance Transform.

Definition at line 341 of file cmtkUniformDistanceMap.cxx.

Referenced by cmtk::UniformDistanceMap< TDistanceDataType >::ComputeEDTThreadPhase2().

cmtk::BitVector::~BitVector

(

)

[inherited]

Destructor.

Definition at line 63 of file cmtkBitVector.cxx.

References cmtk::Memory::DeleteArray().

cmtk::ControlPointList::~ControlPointList

(

)

[inherited]

Destructor: Free all stored points.

Definition at line 42 of file cmtkControlPoint.cxx.

cmtk::GeneralLinearModel::~GeneralLinearModel

(

)

[inherited]

Destructor.

Definition at line 164 of file cmtkGeneralLinearModel.cxx.

cmtk::Landmark::~Landmark

(

)

[inherited]

Destructor.

Definition at line 53 of file cmtkLandmark.cxx.

cmtk::TransformedVolumeAxes::~TransformedVolumeAxes

(

)

[inherited]

Free all storage.

Definition at line 144 of file cmtkTransformedVolumeAxes.cxx.

References cmtk::Memory::DeleteArray(), and NULL.

---

Variable Documentation

bool cmtk::ControlPoint::active [inherited]

Is this an active (true) or passive (false) control point?

Definition at line 55 of file cmtkControlPoint.h.

template<int DIM>

Types::DataItem cmtk::FilterMaskPixel< DIM >::Coefficient [inherited]

Filter coefficient.

Definition at line 88 of file cmtkFilterMask.h.

Types::Coordinate cmtk::SplineWarpXform::JacobianConstraintThreadInfo::Constraint [inherited]

Constraint for subvolume handled by this thread.

Definition at line 435 of file cmtkSplineWarpXform.h.

Referenced by cmtk::SplineWarpXform::GetJacobianConstraintThread(), and cmtk::SplineWarpXform::GetJacobianFoldingConstraintThread().

const char* cmtk::DataClassString[]

Initial value:

 
{ "grey", "label", "unknown",
  NULL }

Definition at line 44 of file cmtkTypes.cxx.

const char * cmtk::DataTypeName

Initial value:

 
{ "byte (8bit unsigned)",
  "char (8bit signed)",
  "short (16bit signed)",
  "ushort (16bit unsigned)",
  "int (32bit signed)",
  "uint (32bit unsigned)",
  "float (32bit)",
  "double (64bit)"
}

Names of scalar data types.

Definition at line 48 of file cmtkTypes.cxx.

Referenced by cmtk::VolumeIO::Read().

Vector3D cmtk::ControlPoint::deformed [inherited]

Deformed control point position.

Definition at line 52 of file cmtkControlPoint.h.

std::vector<Types::Coordinate> cmtk::SplineWarpXform::dsplineX [protected, inherited]

x-axis.

Definition at line 405 of file cmtkSplineWarpXform.h.

Referenced by cmtk::SplineWarpXform::CloneVirtual().

std::vector<Types::Coordinate> cmtk::SplineWarpXform::dsplineY [protected, inherited]

y-axis.

Definition at line 407 of file cmtkSplineWarpXform.h.

Referenced by cmtk::SplineWarpXform::CloneVirtual().

std::vector<Types::Coordinate> cmtk::SplineWarpXform::dsplineZ [protected, inherited]

z-axis.

Definition at line 409 of file cmtkSplineWarpXform.h.

Referenced by cmtk::SplineWarpXform::CloneVirtual().

const FPInitializeUnion cmtk::MathUtil::FPInitializeInf [inherited]

Initial value:

 {
}

Definition at line 50 of file cmtkMathUtil_NaNInf.cxx.

const void* cmtk::MathUtil::FPInitializeInf_fP = &FPInitializeInf.f[1] [inherited]

Definition at line 61 of file cmtkMathUtil_NaNInf.cxx.

const void* cmtk::MathUtil::FPInitializeInf_P = &FPInitializeInf [inherited]

Definition at line 54 of file cmtkMathUtil_NaNInf.cxx.

const void* cmtk::MathUtil::FPInitializeNaN_fP = &FPInitializeNaN.f[1] [inherited]

Definition at line 60 of file cmtkMathUtil_NaNInf.cxx.

const void* cmtk::MathUtil::FPInitializeNaN_P = &FPInitializeNaN [inherited]

Definition at line 53 of file cmtkMathUtil_NaNInf.cxx.

int cmtk::SplineWarpXform::GridPointOffset[48] [protected, inherited]

Relative offsets of all control points in a 4 x 4 x 4 neighborhood.

Definition at line 413 of file cmtkSplineWarpXform.h.

Referenced by cmtk::SplineWarpXform::CloneVirtual().

std::vector<int> cmtk::SplineWarpXform::gX [protected, inherited]

x-axis.

Definition at line 379 of file cmtkSplineWarpXform.h.

Referenced by cmtk::SplineWarpXform::CloneVirtual().

std::vector<int> cmtk::SplineWarpXform::gY [protected, inherited]

y-axis.

Definition at line 381 of file cmtkSplineWarpXform.h.

Referenced by cmtk::SplineWarpXform::CloneVirtual().

std::vector<int> cmtk::SplineWarpXform::gZ [protected, inherited]

z-axis.

Definition at line 383 of file cmtkSplineWarpXform.h.

Referenced by cmtk::SplineWarpXform::CloneVirtual().

template<class T = Types::Coordinate>

const Matrix4x4< T > cmtk::Matrix4x4< T >::IdentityMatrix [static, inherited]

Identity transformation matrix.

Definition at line 64 of file cmtkMatrix4x4.h.

template<int DIM>

Types::Coordinate cmtk::FilterMask< DIM >::Gaussian::InvStandardDeviation [private, inherited]

Standard deviation.

Definition at line 202 of file cmtkFilterMask.h.

template<int DIM>

FixedVector<DIM,int> cmtk::FilterMaskPixel< DIM >::Location [inherited]

Relative location of this pixel.

Definition at line 82 of file cmtkFilterMask.h.

template<class TDataType >

unsigned int cmtk::Accumulators::Avg< TDataType >::m_Count [private, inherited]

Counter.

Definition at line 83 of file cmtkAccumulatorAvg.h.

DataGrid::SmartPtr cmtk::DataGridFilter::m_DataGrid [private, inherited]

The DataGrid object we're working on.

Definition at line 79 of file cmtkDataGridFilter.h.

Referenced by cmtk::DataGridFilter::GetFilteredDataThreadX(), cmtk::DataGridFilter::GetFilteredDataThreadY(), and cmtk::DataGridFilter::GetFilteredDataThreadZ().

DataGrid::SmartConstPtr cmtk::DataGridMorphologicalOperators::m_DataGrid [private, inherited]

The DataGrid object we're working on.

Definition at line 105 of file cmtkDataGridMorphologicalOperators.h.

Referenced by cmtk::DataGridMorphologicalOperators::GetBinaryConnectedComponents().

template<class TDataType >

TDataType cmtk::Accumulators::Max< TDataType >::m_Maximum [private, inherited]

Current maximum.

Definition at line 85 of file cmtkAccumulatorMax.h.

TypedArray::SmartPtr cmtk::DataGridFilter::FilterThreadParameters::m_Result [inherited]

Pointer to result pixel data.

Definition at line 91 of file cmtkDataGridFilter.h.

Referenced by cmtk::DataGridFilter::GetFilteredDataThreadX(), cmtk::DataGridFilter::GetFilteredDataThreadY(), and cmtk::DataGridFilter::GetFilteredDataThreadZ().

template<class TDataType >

TDataType cmtk::Accumulators::Avg< TDataType >::m_Sum [private, inherited]

Current sum of values.

Definition at line 80 of file cmtkAccumulatorAvg.h.

template<class TDataType >

TDataType cmtk::Accumulators::Sum< TDataType >::m_Sum [private, inherited]

Current sum.

Definition at line 79 of file cmtkAccumulatorSum.h.

UniformVolume::SmartPtr cmtk::UniformVolumeFilter::m_UniformVolume [private, inherited]

The UniformVolume object we're working on.

Definition at line 68 of file cmtkUniformVolumeFilter.h.

template<class TDataType >

bool cmtk::Accumulators::Max< TDataType >::m_Valid [private, inherited]

Flag whether there is a valid accumulated value.

Definition at line 82 of file cmtkAccumulatorMax.h.

const Types::DataItem cmtk::DataTypeTraits< unsigned short >::Max = USHRT_MAX [static, inherited]

Maximum value in this type.

Definition at line 298 of file cmtkDataTypeTraits.h.

const Types::DataItem cmtk::DataTypeTraits< byte >::Max = UCHAR_MAX [static, inherited]

Maximum value in this type.

Definition at line 160 of file cmtkDataTypeTraits.h.

const Types::DataItem cmtk::DataTypeTraits< char >::Max = SCHAR_MAX [static, inherited]

Maximum value in this type.

Definition at line 206 of file cmtkDataTypeTraits.h.

const Types::DataItem cmtk::DataTypeTraits< int >::Max = INT_MAX [static, inherited]

Maximum value in this type.

Definition at line 344 of file cmtkDataTypeTraits.h.

const Types::DataItem cmtk::DataTypeTraits< signed short >::Max = SHRT_MAX [static, inherited]

Maximum value in this type.

Definition at line 252 of file cmtkDataTypeTraits.h.

const Types::DataItem cmtk::DataTypeTraits< int >::Min = INT_MIN [static, inherited]

Minimum value in this type.

Definition at line 341 of file cmtkDataTypeTraits.h.

const Types::DataItem cmtk::DataTypeTraits< char >::Min = SCHAR_MIN [static, inherited]

Minimum value in this type.

Definition at line 203 of file cmtkDataTypeTraits.h.

const Types::DataItem cmtk::DataTypeTraits< signed short >::Min = SHRT_MIN [static, inherited]

Minimum value in this type.

Definition at line 249 of file cmtkDataTypeTraits.h.

const Types::DataItem cmtk::DataTypeTraits< byte >::Min = 0 [static, inherited]

Minimum value in this type.

Definition at line 157 of file cmtkDataTypeTraits.h.

const Types::DataItem cmtk::DataTypeTraits< unsigned short >::Min = 0 [static, inherited]

Minimum value in this type.

Definition at line 295 of file cmtkDataTypeTraits.h.

template<int DIM>

Types::Coordinate cmtk::FilterMask< DIM >::Gaussian::NormFactor [private, inherited]

Gaussian normalization factor.

Definition at line 205 of file cmtkFilterMask.h.

int cmtk::SplineWarpXform::JacobianConstraintThreadInfo::NumberOfThreads [inherited]

Total number of threads created.

Definition at line 433 of file cmtkSplineWarpXform.h.

const char *const cmtk::AnatomicalOrientationBase::ORIENTATION_STANDARD = "RAS" [static, inherited]

Orientation of standardized reoriented image axes (LR/AP/IS).

Definition at line 53 of file cmtkAnatomicalOrientationBase.h.

Referenced by cmtk::AffineRegistrationCommandLine::AffineRegistrationCommandLine(), cmtk::ImagePairAffineRegistrationCommandLine::ImagePairAffineRegistrationCommandLine(), cmtk::QtTriplanarViewer::slotReloadData(), cmtk::QtTriplanarWindow::slotSwitchToStudy(), cmtk::QtTriplanarWindow::slotSwitchToStudyInternal(), and cmtk::Xform::Xform().

template<int DIM>

int cmtk::FilterMaskPixel< DIM >::PixelIndex [inherited]

Cached source index of image pixel for this element.

Definition at line 91 of file cmtkFilterMask.h.

template<int DIM>

int cmtk::FilterMaskPixel< DIM >::RelativeIndex [inherited]

Relative index of this pixel in source image from center of kernel.

Definition at line 85 of file cmtkFilterMask.h.

const char *const cmtk::AnatomicalOrientationBase::SPACE_CMTK = "RAS" [static, inherited]

Standard CMTK coordinate space (LR/PA/IS).

Definition at line 56 of file cmtkAnatomicalOrientationBase.h.

const char *const cmtk::AnatomicalOrientationBase::SPACE_ITK = "LPS" [static, inherited]

Standard ITK coordinate space (RL/AP/IS).

Definition at line 59 of file cmtkAnatomicalOrientationBase.h.

Referenced by cmtk::ImagePairAffineRegistrationCommandLine::OutputResult(), and cmtk::AffineRegistrationCommandLine::OutputResult().

std::vector<Types::Coordinate> cmtk::SplineWarpXform::splineX [protected, inherited]

x-axis.

Definition at line 392 of file cmtkSplineWarpXform.h.

Referenced by cmtk::SplineWarpXform::CloneVirtual().

std::vector<Types::Coordinate> cmtk::SplineWarpXform::splineY [protected, inherited]

y-axis.

Definition at line 394 of file cmtkSplineWarpXform.h.

Referenced by cmtk::SplineWarpXform::CloneVirtual().

std::vector<Types::Coordinate> cmtk::SplineWarpXform::splineZ [protected, inherited]

z-axis.

Definition at line 396 of file cmtkSplineWarpXform.h.

Referenced by cmtk::SplineWarpXform::CloneVirtual().

int cmtk::SplineWarpXform::JacobianConstraintThreadInfo::ThisThreadIndex [inherited]

Unique index of this thread instance among all threads.

Definition at line 431 of file cmtkSplineWarpXform.h.

const ScalarDataType cmtk::TYPE_COORDINATE = TYPE_DOUBLE

Definition at line 201 of file cmtkTypes.h.

Referenced by cmtk::ImageOperationMedialSkeleton::Apply().

const ScalarDataType cmtk::TYPE_ITEM = TYPE_DOUBLE

Definition at line 144 of file cmtkTypes.h.

Referenced by cmtk::ImagePairNonrigidRegistrationFunctionalTemplate< VM >::MatchRefFltIntensities(), and cmtk::ImagePairSimilarityJointHistogram::PrescaleData().

template<int DIM>

bool cmtk::FilterMaskPixel< DIM >::Valid [inherited]

Active flag.

This flag can be used in client code to flag pixels in the filter mask as either valid (i.e., inside domain) or invalid (outsside domain). This eliminates repeated range checking in cases where there are multiple iterations over the filter mask at one location.

Definition at line 99 of file cmtkFilterMask.h.

DataGrid::IndexType cmtk::SplineWarpXform::VolumeDims [protected, inherited]

Dimensions of the volume image linked to this transformation.

Definition at line 371 of file cmtkSplineWarpXform.h.

Referenced by cmtk::SplineWarpXform::CloneVirtual(), cmtk::SplineWarpXform::GetJacobianConstraintThread(), and cmtk::SplineWarpXform::GetJacobianFoldingConstraintThread().

---

Friends

friend class SplineWarpXformUniformVolume [friend, inherited]

Friend declaration.

Reimplemented from cmtk::WarpXform.

Definition at line 448 of file cmtkSplineWarpXform.h.