Uniform volume. More...

#include <cmtkUniformVolume.h>

Inheritance diagram for cmtk::UniformVolume:

Collaboration diagram for cmtk::UniformVolume:

Classes
class	ResampleTaskInfo
	Thread parameter block for volume resampling. More...
Public Types
typedef UniformVolume	Self
	This class.
typedef Volume	Superclass
	Superclass.
typedef SmartPointer< Self >	SmartPtr
	Smart pointer to UniformVolume.
typedef SmartConstPointer< Self >	SmartConstPtr
	Smart pointer to const UniformVolume.
typedef Superclass::CoordinateRegionType	CoordinateRegionType
	Region type.
typedef Superclass::CoordinateVectorType	CoordinateVectorType
	Index type.
Public Member Functions
const CoordinateVectorType &	Deltas () const
	Get pixel size vector.
CoordinateVectorType &	Deltas ()
	Get pixel size vector.
virtual	~UniformVolume ()
	Destructor.
	UniformVolume (const UniformVolume &other, const Types::Coordinate resolution=0, const bool allowUpsampling=false)
	Resample other volume to given resolution.
	UniformVolume (const DataGrid::IndexType &dims, const Self::CoordinateVectorType &size, TypedArray::SmartPtr &data=TypedArray::SmartPtr::Null)
	Create uniform volume "from scratch".
	UniformVolume (const DataGrid::IndexType &dims, const Types::Coordinate deltaX, const Types::Coordinate deltaY, const Types::Coordinate deltaZ, TypedArray::SmartPtr &data=TypedArray::SmartPtr::Null)
	Create uniform volume "from scratch".
bool	GridMatches (const Self &other) const
	Test whether this grid matches another one, i.e., has the same pixel sizes.
virtual void	ChangeCoordinateSpace (const std::string &newSpace)
	Change volume coordinate space.
std::string	GetOrientationFromDirections () const
	Get anatomical orientation from space directions.
virtual void	CreateDefaultIndexToPhysicalMatrix ()
	Create a default index-to-physical transformation matrix.
virtual AffineXform::MatrixType	GetImageToPhysicalMatrix () const
	Get matrix that maps form image coordinates to physical space.
Self::SmartPtr	Clone (const bool copyData)
	Create a physical copy of this object.
Self::SmartPtr	Clone () const
Self::SmartPtr	CloneGrid () const
	Create igsUniformObject with identical geometry but no data.
virtual Types::Coordinate	GetDelta (const int axis) const
	Get delta (pixel size) in one dimension.
virtual Types::Coordinate	GetMinDelta () const
	Get minimum grid spacing for all dimensions.
virtual Types::Coordinate	GetMaxDelta () const
	Get maximum grid spacing for all dimensions.
virtual TypedArray::SmartPtr	Resample (const UniformVolume &) const
	Resample other volume.
const UniformVolume::SmartPtr	GetReoriented (const char *newOrientation=AnatomicalOrientation::ORIENTATION_STANDARD) const
	Get volume reoriented to a different anatomical axis alignment.
virtual UniformVolume *	GetDownsampledAndAveraged (const int downsample, const bool approxIsotropic=false) const
	Downsampling constructor function.
virtual UniformVolume *	GetDownsampledAndAveraged (const int(&downsample)[3]) const
	Downsampling constructor function.
UniformVolume *	GetInterleavedSubVolume (const int axis, const int factor, const int idx) const
	Get interleaved sub-volume along given axis and with given interleave offset.
UniformVolume *	GetInterleavedPaddedSubVolume (const int axis, const int factor, const int idx) const
	Get interleaved sub-volume along given axis and with given interleave offset, padded with empty image planes.
virtual void	Mirror (const int axis=AXIS_X)
	Mirror volume and associated data.
virtual ScalarImage *	GetOrthoSlice (const int axis, const unsigned int plane) const
	Return orthogonal slice.
Self::SmartPtr	ExtractSlice (const int axis, const int plane) const
	Extract orthogonal slice as a new volume.
virtual ScalarImage *	GetOrthoSliceInterp (const int axis, const Types::Coordinate location) const
	Return interpolated orthogonal slice.
virtual ScalarImage *	GetNearestOrthoSlice (const int axis, const Types::Coordinate location) const
	Return orthogonal slice by location.
virtual const Self::CoordinateVectorType	GetGradientAt (const int i, const int j, const int k)
	Get date gradient vector at pixel using central differences.
virtual void	GetHessianAt (Matrix3x3< Types::DataItem > &H, const int i, const int j, const int k)
	Get data Hessian matrix at pixel using central differences.
template<class TData >
bool	ProbeData (TData &result, const TData *dataPtr, const Self::CoordinateVectorType &location) const
	Get data value at specified coordinate.
bool	ProbeNoXform (ProbeInfo &, const Self::CoordinateVectorType &) const
	Return linearly interpolated voxel without applying a transformation.
bool	FindVoxel (const Self::CoordinateVectorType &location, int const idx, Types::Coordinate const from, Types::Coordinate *const to) const
	Find a voxel in the volume.
bool	FindVoxel (const Self::CoordinateVectorType &location, int *const idx) const
	Find a voxel in the volume.
void	GetVoxelIndexNoBounds (const Self::CoordinateVectorType &location, int *const idx) const
	Find a grid index inside or outside the volume.
bool	FindVoxelByIndex (const Self::CoordinateVectorType &fracIndex, int const idx, Types::Coordinate const frac) const
	Find a voxel in the volume by fractional index.
const UniformVolume::RegionType	GetGridRange (const Self::CoordinateVectorType &fromVOI, const Self::CoordinateVectorType &toVOI) const
	Get 3D grid region from continuous lower and upper corner.
virtual Types::Coordinate	GetPlaneCoord (const int axis, const int plane) const
	Get plane coordinate.
virtual int	GetCoordIndex (const int axis, const Types::Coordinate location) const
	Get grid index of slice with highest coordinate smaller than given.
virtual int	GetClosestCoordIndex (const int axis, const Types::Coordinate location) const
	Get grid index corresponding (as close as possible) to coordinate.
virtual bool	GetClosestGridPointIndex (const Self::CoordinateVectorType v, int *const xyz) const
	Get grid index corresponding (as close as possible) to coordinate.
virtual int	GetTruncCoordIndex (const int axis, const Types::Coordinate location) const
	Get grid index corresponding to coordinate by truncation, not rounding.
virtual bool	GetTruncGridPointIndex (const Self::CoordinateVectorType v, int *const xyz) const
	Get grid index corresponding to coordinate by truncation, not rounding.
virtual const Self::CoordinateVectorType	GetGridLocation (const int x, const int y, const int z) const
	Get a grid location in image coordinates.
virtual const Self::CoordinateVectorType	IndexToPhysical (const Self::CoordinateVectorType &idxV) const
	Get a grid location in physical coordinates.
virtual const Self::CoordinateVectorType	GetGridLocation (const size_t idx) const
	Get a grid coordinate by continuous pixel index.
void	SetHighResCropRegion (const Self::CoordinateRegionType &crop)
	Set cropping region in real-world coordinates.
const Self::CoordinateRegionType	GetHighResCropRegion () const
	Get cropped volume in real-world coordinates.
virtual void	SetCropRegion (const Self::RegionType &region)
	Catch calls to inherited SetCropRegion() and reset high-res crop region.
Self::CoordinateVectorType	GetCenterCropRegion () const
	Calculate volume center.
Self::SmartPtr	GetCroppedVolume () const
	Return cropped uniform volume.
template<class TAccumulator >
ScalarImage *	ComputeProjection (const int axis) const
	Return projection (e.g., MIP, sum) along one axis.
virtual Self::CoordinateVectorType	GetCenterOfMass () const
	Get center of mass of pixel data.
virtual Self::CoordinateVectorType	GetCenterOfMass (Self::CoordinateVectorType &firstOrderMoment) const
	Get center of mass of pixel data.
void	GetPrincipalAxes (Matrix3x3< Types::Coordinate > &directions, Self::CoordinateVectorType &centerOfMass) const
	Get principal axes.
Public Attributes
CoordinateVectorType	m_Delta
	Grid spacing for three dimensions.
AffineXform::MatrixType	m_IndexToPhysicalMatrix
	Coordinate transformation from index to physical position.
Protected Member Functions
virtual Self *	CloneVirtual (const bool copyData)
	Create a physical copy of this object.
virtual Self *	CloneVirtual () const
virtual Self *	CloneGridVirtual () const
	Virtual grid cloning constructor.
Private Member Functions
virtual Self *	ExtractSliceVirtual (const int axis, const int plane) const
	Extract orthogonal slice as a new volume.
Static Private Member Functions
static void	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.
static void	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).
Private Attributes
Self::CoordinateRegionType::SmartPtr	m_HighResCropRegion
	Optional high-resolution crop region.
Friends
class	WarpXform
	Friend declaration of WarpXform class.
class	VolumeAxesHash
	Make axes hash a friend.
class	VolumeGridToGridLookup
	Grid grid-to-grid lookup friend.
class	ResampleThreadInfo
	Give thread parameter class access to local types.

Detailed Description

Uniform volume.

This class handles 3D isotropic data of any scalar type.

Definition at line 58 of file cmtkUniformVolume.h.

Member Typedef Documentation

typedef Superclass:: CoordinateRegionType cmtk::UniformVolume::CoordinateRegionType

Region type.

Reimplemented from cmtk::Volume.

Reimplemented in cmtk::ImageTemplate< TPixelType >.

Definition at line 76 of file cmtkUniformVolume.h.

typedef Superclass::CoordinateVectorType cmtk::UniformVolume::CoordinateVectorType

Index type.

Reimplemented from cmtk::Volume.

Reimplemented in cmtk::ImageTemplate< TPixelType >.

Definition at line 79 of file cmtkUniformVolume.h.

typedef UniformVolume cmtk::UniformVolume::Self

This class.

Reimplemented from cmtk::Volume.

Reimplemented in cmtk::ImageTemplate< TPixelType >.

Definition at line 64 of file cmtkUniformVolume.h.

typedef SmartConstPointer<Self> cmtk::UniformVolume::SmartConstPtr

Smart pointer to const UniformVolume.

Reimplemented from cmtk::DataGrid.

Reimplemented in cmtk::ImageTemplate< TPixelType >.

Definition at line 73 of file cmtkUniformVolume.h.

typedef SmartPointer<Self> cmtk::UniformVolume::SmartPtr

Smart pointer to UniformVolume.

Reimplemented from cmtk::Volume.

Reimplemented in cmtk::ImageTemplate< TPixelType >.

Definition at line 70 of file cmtkUniformVolume.h.

typedef Volume cmtk::UniformVolume::Superclass

Superclass.

Reimplemented from cmtk::Volume.

Reimplemented in cmtk::ImageTemplate< TPixelType >.

Definition at line 67 of file cmtkUniformVolume.h.

Constructor & Destructor Documentation

virtual cmtk::UniformVolume::~UniformVolume ( ) [inline, virtual]

Destructor.

Definition at line 97 of file cmtkUniformVolume.h.

cmtk::UniformVolume::UniformVolume	(	const UniformVolume &	other,
		const Types::Coordinate	resolution = `0`,
		const bool	allowUpsampling = `false`
	)

Resample other volume to given resolution.

Parameters:

other	Original volume that will be resampled.
resolution	Resolution of the newly created volume in world units.
allowUpsampling	If true, then local upsampling is allowed in regions where the original image resolution (non-uniform) was coarser than the given resolution of the resampled volume.

Definition at line 75 of file cmtkUniformVolume.cxx.

References GetHighResCropRegion(), m_Delta, cmtk::DataGrid::m_Dims, m_IndexToPhysicalMatrix, cmtk::MetaInformationObject::m_MetaInformation, cmtk::Volume::m_Offset, and cmtk::Volume::Size.

cmtk::UniformVolume::UniformVolume	(	const DataGrid::IndexType &	dims,
		const Self::CoordinateVectorType &	size,
		TypedArray::SmartPtr &	data = `TypedArray::SmartPtr::Null`
	)

Create uniform volume "from scratch".

Parameters:

dims	Number of grid elements for the three spatial dimensions.
size	Size of the volume in real-world coordinates.
data	An existing TypedArray containing the scalar voxel data.

Definition at line 43 of file cmtkUniformVolume.cxx.

cmtk::UniformVolume::UniformVolume	(	const DataGrid::IndexType &	dims,
		const Types::Coordinate	deltaX,
		const Types::Coordinate	deltaY,
		const Types::Coordinate	deltaZ,
		TypedArray::SmartPtr &	data = `TypedArray::SmartPtr::Null`
	)

Create uniform volume "from scratch".

Parameters:

dims	Number of grid elements for the three spatial dimensions.
deltaX	Pixel size in x direction.
deltaY	Pixel size in y direction.
deltaZ	Pixel size in z direction.
data	An existing TypedArray containing the scalar voxel data.

Definition at line 58 of file cmtkUniformVolume.cxx.

Member Function Documentation

void cmtk::UniformVolume::ChangeCoordinateSpace ( const std::string & newSpace ) [virtual]

Change volume coordinate space.

Re-arrange volume's direction vectors to refer to a different coordinate space.

Invariant:: This should keep the result of GetOrientationFromDirections invariant.

Definition at line 70 of file cmtkUniformVolume_Space.cxx.

References cmtk::META_SPACE.

Self::SmartPtr cmtk::UniformVolume::Clone ( const bool copyData ) [inline]

Create a physical copy of this object.

Parameters:

copyData If true, the associated data array is also copied.

Definition at line 163 of file cmtkUniformVolume.h.

Referenced by cmtk::ImageSymmetryPlaneFunctionalBase::ApplyThresholds(), cmtk::VoxelRegistration::ImagePreprocessor::GetProcessedImage(), cmtk::ImagePairRegistration::ImagePreprocessor::GetProcessedImage(), cmtk::VolumeFromFile::WriteAnalyzeHdr(), and cmtk::VolumeFromFile::WriteNifti().

Self::SmartPtr cmtk::UniformVolume::Clone ( ) const [inline]

Definition at line 168 of file cmtkUniformVolume.h.

Self::SmartPtr cmtk::UniformVolume::CloneGrid ( ) const [inline]

Create igsUniformObject with identical geometry but no data.

Definition at line 174 of file cmtkUniformVolume.h.

Referenced by cmtk::InverseInterpolationVolumeReconstruction< TInterpolator >::Interpolation(), cmtk::TransformChangeFromSpaceAffine::TransformChangeFromSpaceAffine(), cmtk::TransformChangeToSpaceAffine::TransformChangeToSpaceAffine(), and cmtk::VolumeInjectionReconstruction::VolumeInjectionReconstruction().

UniformVolume * cmtk::UniformVolume::CloneGridVirtual ( ) const [protected, virtual]

Virtual grid cloning constructor.

Definition at line 149 of file cmtkUniformVolume.cxx.

References m_IndexToPhysicalMatrix, cmtk::MetaInformationObject::m_MetaInformation, and cmtk::Volume::SetOffset().

UniformVolume * cmtk::UniformVolume::CloneVirtual ( const bool copyData ) [protected, virtual]

Create a physical copy of this object.

Parameters:

copyData If true, the associated data array is also copied.

Definition at line 115 of file cmtkUniformVolume.cxx.

UniformVolume * cmtk::UniformVolume::CloneVirtual ( ) const [protected, virtual]

Definition at line 131 of file cmtkUniformVolume.cxx.

void cmtk::UniformVolume::CreateDefaultIndexToPhysicalMatrix ( ) [virtual]

Create a default index-to-physical transformation matrix.

The new matrix is the identity matrix with diagonal elements scaled according to pixel size.

Definition at line 43 of file cmtkUniformVolume_Space.cxx.

CoordinateVectorType& cmtk::UniformVolume::Deltas ( ) [inline]

Get pixel size vector.

Definition at line 91 of file cmtkUniformVolume.h.

const CoordinateVectorType& cmtk::UniformVolume::Deltas ( ) const [inline]

Get pixel size vector.

Definition at line 85 of file cmtkUniformVolume.h.

Referenced by cmtk::FilterVolume::GaussianFilter(), cmtk::operator<<(), cmtk::FilterVolume::RohlfingFilter(), cmtk::UniformVolumeInterpolatorBase::SetVolume(), and cmtk::FilterVolume::StudholmeFilter().

Self::SmartPtr cmtk::UniformVolume::ExtractSlice	(	const int	axis,
		const int	plane
	)		const `[inline]`

Extract orthogonal slice as a new volume.

Reimplemented from cmtk::DataGrid.

Definition at line 255 of file cmtkUniformVolume.h.

UniformVolume * cmtk::UniformVolume::ExtractSliceVirtual	(	const int	axis,
		const int	plane
	)		const `[private, virtual]`

Extract orthogonal slice as a new volume.

Reimplemented from cmtk::DataGrid.

Definition at line 345 of file cmtkUniformVolume.cxx.

Self::CoordinateVectorType cmtk::UniformVolume::GetCenterCropRegion ( ) const [inline]

Calculate volume center.

Returns:: Returned is the center of the bounding box.

Definition at line 467 of file cmtkUniformVolume.h.

Referenced by cmtk::MakeInitialAffineTransformation::AlignDirectionVectors(), cmtk::MakeInitialAffineTransformation::AlignFieldsOfView(), and cmtk::QtTriplanarWindow::slotCenter().

virtual Self::CoordinateVectorType cmtk::UniformVolume::GetCenterOfMass ( ) const [inline, virtual]

Get center of mass of pixel data.

Definition at line 487 of file cmtkUniformVolume.h.

Referenced by cmtk::MakeInitialAffineTransformation::AlignCentersOfMass().

virtual Self::CoordinateVectorType cmtk::UniformVolume::GetCenterOfMass ( Self::CoordinateVectorType & firstOrderMoment ) const [inline, virtual]

Get center of mass of pixel data.

Definition at line 496 of file cmtkUniformVolume.h.

virtual int cmtk::UniformVolume::GetClosestCoordIndex	(	const int	axis,
		const Types::Coordinate	location
	)		const `[inline, virtual]`

Get grid index corresponding (as close as possible) to coordinate.

Parameters:

axis	The coordinate axis that the location parameters refers to.
location	The location along the selected coordinate axis in the range from 0 to Size[axis].

Definition at line 365 of file cmtkUniformVolume.h.

Referenced by cmtk::QtTriplanarWindow::slotMouse3D(), cmtk::QtTriplanarWindow::slotMouseAx(), cmtk::QtTriplanarWindow::slotMouseCo(), and cmtk::QtTriplanarWindow::slotMouseSa().

virtual bool cmtk::UniformVolume::GetClosestGridPointIndex	(	const Self::CoordinateVectorType	v,
		int *const	xyz
	)		const `[inline, virtual]`

Get grid index corresponding (as close as possible) to coordinate.

Returns:: True if given point is inside image, false if outside.

Definition at line 374 of file cmtkUniformVolume.h.

virtual int cmtk::UniformVolume::GetCoordIndex	(	const int	axis,
		const Types::Coordinate	location
	)		const `[inline, virtual]`

Get grid index of slice with highest coordinate smaller than given.

Parameters:

axis	The coordinate axis that the location parameters refers to.
location	The location along the selected coordinate axis in the range from 0 to Size[axis].

Definition at line 356 of file cmtkUniformVolume.h.

virtual Types::Coordinate cmtk::UniformVolume::GetDelta ( const int axis ) const [inline, virtual]

Get delta (pixel size) in one dimension.

Definition at line 180 of file cmtkUniformVolume.h.

UniformVolume * cmtk::UniformVolume::GetDownsampledAndAveraged	(	const int	downsample,
		const bool	approxIsotropic = `false`
	)		const `[virtual]`

Downsampling constructor function.

Parameters:

downsample	Downsampling factor.
approxIsotropic	If this is set (default: off), then the downsample factors per dimension are adjusted so that the resulting output volume is as close to isotropic as possible without interpolation.

Definition at line 159 of file cmtkUniformVolume.cxx.

UniformVolume * cmtk::UniformVolume::GetDownsampledAndAveraged ( const int(&) downsample[3] ) const [virtual]

Downsampling constructor function.

Parameters:

downsample Array of per-dimension downsampling factors.

Reimplemented from cmtk::DataGrid.

Definition at line 177 of file cmtkUniformVolume.cxx.

References m_IndexToPhysicalMatrix, cmtk::MetaInformationObject::m_MetaInformation, SetHighResCropRegion(), and cmtk::Volume::SetOffset().

const cmtk::UniformVolume::CoordinateVectorType cmtk::UniformVolume::GetGradientAt	(	const int	i,
		const int	j,
		const int	k
	)		`[virtual]`

Get date gradient vector at pixel using central differences.

This function cannot be called for pixels on the volume boundaries, i.e., we require that 0 < i,j,k < [Dims[0]-1,Dims[1]-1,Dims[2]-1].

Warning:: No parameter range checking is currently performed!

Definition at line 35 of file cmtkUniformVolume_Differential.cxx.

virtual const Self::CoordinateVectorType cmtk::UniformVolume::GetGridLocation	(	const int	x,
		const int	y,
		const int	z
	)		const `[inline, virtual]`

Get a grid location in image coordinates.

Parameters:

x,y,z The indices of the intended grid element with respect to the three coordinate axes. Valid range is from 0 to Dims[...]-1.

Returns:: The location in image coordinates of the given grid element as a Self::CoordinateVectorType.

Definition at line 415 of file cmtkUniformVolume.h.

Referenced by cmtk::InverseInterpolationVolumeReconstruction< TInterpolator >::ComputeErrorGradientImage(), cmtk::WarpXform::GetInverseConsistencyError(), cmtk::SplineWarpXform::GetInverseConsistencyError(), cmtk::InverseInterpolationVolumeReconstruction< TInterpolator >::GetPassImageDependentPixelRegion(), cmtk::InverseInterpolationVolumeReconstruction< TInterpolator >::Interpolation(), cmtk::ReformatVolume::ReformatMasked(), cmtk::ReformatVolume::ReformatUnmasked(), and cmtk::VolumeInjectionReconstruction::VolumeInjectionIsotropic().

virtual const Self::CoordinateVectorType cmtk::UniformVolume::GetGridLocation ( const size_t idx ) const [inline, virtual]

Get a grid coordinate by continuous pixel index.

This function directly calculates the grid location from the volume's grid deltas.

Parameters:

idx	The index of the intended grid element. Valid range is from 0 to (Dims[0]Dims[1]Dims[2])-1.

Returns:: The location of the given grid element as a Self::CoordinateVectorType.

Definition at line 439 of file cmtkUniformVolume.h.

const UniformVolume::RegionType cmtk::UniformVolume::GetGridRange	(	const Self::CoordinateVectorType &	fromVOI,
		const Self::CoordinateVectorType &	toVOI
	)		const

Get 3D grid region from continuous lower and upper corner.

Definition at line 282 of file cmtkUniformVolume.cxx.

void cmtk::UniformVolume::GetHessianAt	(	Matrix3x3< Types::DataItem > &	H,
		const int	i,
		const int	j,
		const int	k
	)		`[virtual]`

Get data Hessian matrix at pixel using central differences.

This function cannot be called for pixels within a two-pixel distance from the volume boundary, i.e., we require that 1 < i,j,k < [Dims[0]-2,Dims[1]-2,Dims[2]-2].

Warning:: No parameter range checking is currently performed!

Definition at line 46 of file cmtkUniformVolume_Differential.cxx.

AffineXform::MatrixType cmtk::UniformVolume::GetImageToPhysicalMatrix ( ) const [virtual]

Get matrix that maps form image coordinates to physical space.

The returned matrix is computed by removing pixel size from the one stored in m_IndexToPhysicalMatrix.

Definition at line 109 of file cmtkUniformVolume_Space.cxx.

Referenced by cmtk::MakeInitialAffineTransformation::AlignDirectionVectors(), cmtk::SplineWarpXformITKIO::Write(), and cmtk::VolumeFromFile::WriteMetaImage().

UniformVolume * cmtk::UniformVolume::GetInterleavedPaddedSubVolume	(	const int	axis,
		const int	factor,
		const int	idx
	)		const

Get interleaved sub-volume along given axis and with given interleave offset, padded with empty image planes.

Parameters:

axis	Coordinate axis along which the image is interleaved.
factor	Interleave factor, i.e., the number of interleaved sub-volumes.
idx	Index of interleaved sub-volume to extract.

Definition at line 259 of file cmtkUniformVolume.cxx.

References cmtk::DataGrid::CreateDataArray(), m_IndexToPhysicalMatrix, cmtk::MetaInformationObject::m_MetaInformation, cmtk::Volume::SetOffset(), and cmtk::DataGrid::SetOrthoSlice().

UniformVolume * cmtk::UniformVolume::GetInterleavedSubVolume	(	const int	axis,
		const int	factor,
		const int	idx
	)		const

Get interleaved sub-volume along given axis and with given interleave offset.

Parameters:

axis	Coordinate axis along which the image is interleaved.
factor	Interleave factor, i.e., the number of interleaved sub-volumes.
idx	Index of interleaved sub-volume to extract.

Definition at line 213 of file cmtkUniformVolume.cxx.

References m_IndexToPhysicalMatrix, cmtk::MetaInformationObject::m_MetaInformation, cmtk::Volume::SetOffset(), and cmtk::DataGrid::SetOrthoSlice().

Referenced by cmtk::VolumeInjectionReconstruction::VolumeInjectionReconstruction().

virtual Types::Coordinate cmtk::UniformVolume::GetMaxDelta ( ) const [inline, virtual]

Get maximum grid spacing for all dimensions.

For each dimension, the maximum delta is retrieved by a call to the derived class's corresponding method.

Definition at line 198 of file cmtkUniformVolume.h.

virtual Types::Coordinate cmtk::UniformVolume::GetMinDelta ( ) const [inline, virtual]

Get minimum grid spacing for all dimensions.

For each dimension, the minimum delta is retrieved by a call to the derived class's corresponding method.

Definition at line 189 of file cmtkUniformVolume.h.

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

ScalarImage * cmtk::UniformVolume::GetNearestOrthoSlice	(	const int	axis,
		const Types::Coordinate	location
	)		const `[virtual]`

Return orthogonal slice by location.

This function looks up a given orthogonal slice location and returns the nearest slice from this volume.

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.

Definition at line 358 of file cmtkUniformVolume.cxx.

std::string cmtk::UniformVolume::GetOrientationFromDirections ( ) const

Get anatomical orientation from space directions.

Definition at line 100 of file cmtkUniformVolume_Space.cxx.

References cmtk::META_SPACE.

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

Return orthogonal slice.

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 306 of file cmtkUniformVolume.cxx.

References cmtk::AXIS_X, cmtk::AXIS_Y, cmtk::AXIS_Z, and cmtk::ScalarImage::SetImageOrigin().

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

ScalarImage * cmtk::UniformVolume::GetOrthoSliceInterp	(	const int	axis,
		const Types::Coordinate	location
	)		const `[virtual]`

Return interpolated orthogonal slice.

This function calls its non-interpolating counterpart twice and performs a 1-D interpolation on the results to form the interpolated slice.

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.

Definition at line 365 of file cmtkUniformVolume.cxx.

References cmtk::ScalarImage::GetImageOrigin(), and cmtk::ScalarImage::SetImageOrigin().

virtual Types::Coordinate cmtk::UniformVolume::GetPlaneCoord	(	const int	axis,
		const int	plane
	)		const `[inline, virtual]`

Get plane coordinate.

Definition at line 347 of file cmtkUniformVolume.h.

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

void cmtk::UniformVolume::GetPrincipalAxes	(	Matrix3x3< Types::Coordinate > &	directions,
		Self::CoordinateVectorType &	centerOfMass
	)		const

Get principal axes.

Returns:: This function returns two types of information: the principal directions (axes) of the image data, and the relative scales. The principal axes are returned as a 3x3 array, such that directions[0] is the 3D array of the major principal direction, i.e. the one with the largest norm. Then, directions[0][1] is the y-component of that vector, etc. Accordingly, directions[1] and directions[2] are the two remaining principal directions, with the norm of directions[1] larger than, or equal to, the norm of directions[2].

Definition at line 410 of file cmtkUniformVolume.cxx.

References cmtk::AXIS_X, cmtk::AXIS_Y, cmtk::AXIS_Z, cmtk::Matrix3x3< T >::Determinant(), and cmtk::EigenSystemSymmetricMatrix3x3< TFloat >::GetNthEigenvector().

Referenced by cmtk::MakeInitialAffineTransformation::AlignPrincipalAxes().

const UniformVolume::SmartPtr cmtk::UniformVolume::GetReoriented ( const char * newOrientation = AnatomicalOrientation::ORIENTATION_STANDARD ) const

Get volume reoriented to a different anatomical axis alignment.

Reimplemented from cmtk::DataGrid.

Definition at line 52 of file cmtkUniformVolume_Space.cxx.

References cmtk::AnatomicalOrientation::PermutationMatrix::GetPermutedArray(), cmtk::AnatomicalOrientation::PermutationMatrix::GetPermutedMatrix(), and cmtk::META_IMAGE_ORIENTATION.

Referenced by cmtk::VolumeIO::Write(), and cmtk::VolumeFromFile::WriteAnalyzeHdr().

virtual int cmtk::UniformVolume::GetTruncCoordIndex	(	const int	axis,
		const Types::Coordinate	location
	)		const `[inline, virtual]`

Get grid index corresponding to coordinate by truncation, not rounding.

Parameters:

axis	The coordinate dimension that the location parameters refers to.
location	The location in the range from 0 to Size[axis].

Definition at line 389 of file cmtkUniformVolume.h.

virtual bool cmtk::UniformVolume::GetTruncGridPointIndex	(	const Self::CoordinateVectorType	v,
		int *const	xyz
	)		const `[inline, virtual]`

Get grid index corresponding to coordinate by truncation, not rounding.

Returns:: True if given point is inside image, false if outside.

Parameters:

v	Location to find in the grid.
xyz	Truncated grid point index (i.e., nearest grid point between location and grid coordinate origin.

Definition at line 398 of file cmtkUniformVolume.h.

bool cmtk::UniformVolume::GridMatches ( const Self & other ) const [inline]

Test whether this grid matches another one, i.e., has the same pixel sizes.

Reimplemented from cmtk::DataGrid.

Definition at line 125 of file cmtkUniformVolume.h.

virtual const Self::CoordinateVectorType cmtk::UniformVolume::IndexToPhysical ( const Self::CoordinateVectorType & idxV ) const [inline, virtual]

Get a grid location in physical coordinates.

Parameters:

idxV	The index of the intended grid element with respect to the three coordinate axes. Valid range is from 0 to Dims[...]-1. Fractional coordinates are permitted.

Returns:: The location in image coordinates of the given grid element as a Self::CoordinateVectorType.

Definition at line 426 of file cmtkUniformVolume.h.

Referenced by cmtk::QtTriplanarWindow::UpdateGridInfo().

void cmtk::UniformVolume::Mirror ( const int axis = AXIS_X ) [virtual]

Mirror volume and associated data.

Parameters:

axis	Mirror with respect to this coordinate axis.

Definition at line 296 of file cmtkUniformVolume.cxx.

virtual void cmtk::UniformVolume::SetCropRegion ( const Self::RegionType & region ) [inline, virtual]

Catch calls to inherited SetCropRegion() and reset high-res crop region.

Reimplemented from cmtk::DataGrid.

Definition at line 458 of file cmtkUniformVolume.h.

References NULL.

Friends And Related Function Documentation

friend class ResampleThreadInfo [friend]

Give thread parameter class access to local types.

Definition at line 548 of file cmtkUniformVolume.h.

friend class VolumeAxesHash [friend]

Make axes hash a friend.

Definition at line 543 of file cmtkUniformVolume.h.

friend class VolumeGridToGridLookup [friend]

Grid grid-to-grid lookup friend.

Definition at line 546 of file cmtkUniformVolume.h.

friend class WarpXform [friend]

Friend declaration of WarpXform class.

This allows direct access to Dims and Delta fields in RegisterVolumePoints member function of WarpXform.

Definition at line 540 of file cmtkUniformVolume.h.

Member Data Documentation

CoordinateVectorType cmtk::UniformVolume::m_Delta

Grid spacing for three dimensions.

Definition at line 82 of file cmtkUniformVolume.h.

Referenced by cmtk::AffineXformUniformVolume::AffineXformUniformVolume(), cmtk::DeblurringVolumeReconstruction< TPSF >::DeblurringVolumeReconstruction(), cmtk::DeviceUniformVolume::DeviceUniformVolume(), cmtk::SplineWarpXform::GetInverseConsistencyError(), cmtk::VolumeInjectionReconstruction::GuessInterleaveAxis(), cmtk::TransformedVolumeAxes::MakeHash(), cmtk::SplineWarpXformUniformVolume::RegisterVolume(), cmtk::SplineWarpXform::RegisterVolume(), UniformVolume(), cmtk::VolumeGridToGridLookup::VolumeGridToGridLookup(), and cmtk::VolumeFromFile::WriteMetaImage().

Self::CoordinateRegionType::SmartPtr cmtk::UniformVolume::m_HighResCropRegion [private]

Optional high-resolution crop region.

If this is unset (i.e., a NULL pointer), then calls to GetHighResCropRegion() will simply convert the grid-based crop region.

Note:: The crop region includes the volume offset, m_Offset. Its upper limit can, therefore, be larger than m_Size, which does NOT include m_Offset.

Definition at line 534 of file cmtkUniformVolume.h.

AffineXform::MatrixType cmtk::UniformVolume::m_IndexToPhysicalMatrix

Coordinate transformation from index to physical position.

This incorporates image axis directions and first pixel offset.

Note:: Strictly, this is not a transformation from the pixel index to physical coordinates, but from pixel index times pixel size to physical coordinates. This way, the transformation maps from physical space back into physical space.

Definition at line 137 of file cmtkUniformVolume.h.

Referenced by CloneGridVirtual(), GetDownsampledAndAveraged(), GetInterleavedPaddedSubVolume(), GetInterleavedSubVolume(), cmtk::UniformDistanceMap< TDistanceDataType >::UniformDistanceMap(), UniformVolume(), and cmtk::VolumeFromFile::WriteNifti().

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

libs/Base/cmtkUniformVolume.h
libs/Base/cmtkUniformVolume.cxx
libs/Base/cmtkUniformVolume.txx
libs/Base/cmtkUniformVolume_Crop.cxx
libs/Base/cmtkUniformVolume_Differential.cxx
libs/Base/cmtkUniformVolume_Resample.cxx
libs/Base/cmtkUniformVolume_Space.cxx

cmtk::UniformVolume Class Reference [cmtkBase Library]

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cmtk::UniformVolume Class Reference
[cmtkBase Library]