Template class that stores 3D voxel data. More...

#include <drawables.h>

Inheritance diagram for Voxels< T >:

Public Member Functions
	Voxels ()
	Constructor. More...

	~Voxels ()
	Destructor. More...

void	swap (Voxels< T > &v)
	Swap object contents with other voxel object. More...

void	clone (Voxels< T > &newClone) const
	Clone this into another object. More...

void	setPoint (const Point3D &pt, const T &val)
	Set the value of a point in the dataset. More...

T	getPointData (const Point3D &pt) const
	Retrieve the value of a datapoint, this is rounded to the nearest voxel. More...

void	getIndex (size_t &x, size_t &y, size_t &z, const Point3D &p) const
	Retrieve the XYZ voxel location associated with a given position. More...

void	getIndexWithUpper (size_t &x, size_t &y, size_t &z, const Point3D &p) const
	Retrieve the XYZ voxel location associated with a given position,. More...

Point3D	getPoint (size_t x, size_t y, size_t z) const
	Get the position associated with an XYZ voxel. More...

T	getData (size_t x, size_t y, size_t z) const
	Retrieve the value of a specific voxel. More...

T	getData (size_t *array) const

T	getData (size_t i) const
	Retrieve value of the nth voxel. More...

void	setEntry (size_t n, const T &val)

void	setData (size_t x, size_t y, size_t z, const T &val)
	Retrieve a reference to the data ata given position. More...

void	setData (size_t n, const T &val)
	Set the value of nth point in the dataset. More...

void	getInterpolatedData (const Point3D &pt, T &v) const

void	isotropicGaussianSmooth (float stdev, float windowRatio)

void	laplaceOfGaussian (float stdev, float windowRatio)

void	getInterpSlice (size_t normal, float offset, T *p, size_t interpMode=VOX_INTERP_NONE) const

void	getSlice (size_t normal, size_t offset, T *p) const

void	getSize (size_t &x, size_t &y, size_t &z) const
	Get the size of the data field. More...

size_t	getSize () const

size_t	resize (size_t newX, size_t newY, size_t newZ, const Point3D &newMinBound=Point3D(0.0f, 0.0f, 0.0f), const Point3D &newMaxBound=Point3D(1.0f, 1.0f, 1.0f))
	Resize the data field. More...

size_t	resize (const Voxels< T > &v)

size_t	resizeKeepData (size_t newX, size_t newY, size_t newZ, unsigned int direction=CLIP_LOWER_SOUTH_WEST, const Point3D &newMinBound=Point3D(0.0f, 0.0f, 0.0f), const Point3D &newMaxBound=Point3D(1.0f, 1.0f, 1.0f), const T &fill=T(0), bool doFill=false)
	Resize the data field, maintaining data as best as possible. More...

size_t	deprecatedGetEdgeUniqueIndex (size_t x, size_t y, size_t z, unsigned int edge) const
	DEPRECATED FUNCTION : Get a unique integer that corresponds to the edge index for the voxel; where edges are shared between voxels. More...

size_t	getCellUniqueEdgeIndex (size_t x, size_t y, size_t z, unsigned int edge) const
	Get a unique integer that corresponds to an edge index for the voxel; where edges are shared between voxels. More...

void	getEdgeEnds (size_t edgeIndex, Point3D &a, Point3D &b) const
	Convert the edge index (as generated by getEdgeUniqueIndex) into a cenre position. More...

void	getEdgeCell (size_t edgeUniqId, size_t &x, size_t &y, size_t &z, size_t &axis) const
	Convert edge index (only as generted by getCellUniqueEdgeIndex) into a cell & axis value. More...

void	getEdgeEndApproxVals (size_t edgeUniqId, T &a, T &b) const
	Return the values that are associated with the edge ends, as returned by getEdgeEnds. More...

void	rebin (Voxels< T > &dest, size_t rate, size_t clipMode=CLIP_NONE) const
	Rebin the data by a given rate. More...

T	getSum (const T &initialVal=T(0.0)) const
	Get the total value of the data field. More...

size_t	count (const T &minIntensity) const
	count the number of cells with at least this intensity More...

void	fill (const T &val)
	Fill all voxels with a given value. More...

Point3D	getMinBounds () const
	Get the bounding box vertex (min/max) More...

Point3D	getMaxBounds () const

void	getAxisBounds (size_t axis, float &minV, float &maxV) const

Point3D	getPitch () const
	! Get the spacing for a unit cell More...

void	setBounds (const Point3D &pMin, const Point3D &pMax)
	Set the bounding size. More...

void	getBounds (Point3D &pMin, Point3D &pMax) const
	Get the bounding size. More...

void	getBounds (BoundCube &bc) const

size_t	init (size_t nX, size_t nY, size_t nZ, const BoundCube &bound)
	Initialise the voxel storage. More...

size_t	init (size_t nX, size_t nY, size_t nZ)
	Initialise the voxel storage. More...

size_t	loadFile (const char *cpFilename, size_t nX, size_t nY, size_t nZ, bool silent=false)
	Load the voxels from file. More...

size_t	writeFile (const char *cpFilename) const
	Write the voxel objects in column major written out to file. More...

size_t	convolve (const Voxels< T > &templateVec, Voxels< T > &result, size_t boundMode=BOUND_CLIP) const
	Run convolution over this data, placing the correlation data into "result". More...

size_t	separableConvolve (const Voxels< T > &templateVec, Voxels< T > &result, size_t boundMode=BOUND_CLIP)
	Similar to convolve, but faster – only works with separable kernels. More...

void	thresholdForPosition (std::vector< Point3D > &p, const T &thresh, bool lowerEq=false) const
	Find the positions of the voxels that are above or below a given value. More...

void	binarise (Voxels< T > &result, const T &thresh, const T &onThresh, const T &offThresh) const
	Binarise the data into a result vector. More...

void	clear ()
	Empty the data. More...

T	min () const
	Find minimum in dataset. More...

T	max () const
	Find maximum in dataset. More...

void	minMax (T &min, T &max) const
	Find both min and max in dataset in the same loop. More...

int	countPoints (const std::vector< Point3D > &points, bool noWrap=true, bool doErase=false)
	Generate a dataset that consists of the counts of points in a given voxel. More...

T	trapezIntegral () const
	Integrate the datataset via the trapezoidal method. More...

void	calculateDensity ()
	Convert voxel intensity into voxel density. More...

float	getBinVolume () const

void	operator/= (const Voxels< T > &v)
	Element wise division. More...

void	operator/= (const T &v)

bool	operator== (const Voxels< T > &v) const

size_t	size () const

Static Public Member Functions
static size_t	sizeofType ()
	Return the sizeof value for the T type. More...

Detailed Description

template<class T>
class Voxels< T >

Template class that stores 3D voxel data.

To instantiate this class, objects must have basic mathematical operators, such as * + - and =

Constructor & Destructor Documentation

◆ Voxels()

template<class T >

Voxels< T >::Voxels ( )

Constructor.

◆ ~Voxels()

template<class T >

Voxels< T >::~Voxels ( )

Destructor.

Member Function Documentation

◆ binarise()

template<class T>

void Voxels< T >::binarise	(	Voxels< T > &	result,
		const T &	thresh,
		const T &	onThresh,
		const T &	offThresh
	)		const

Binarise the data into a result vector.

◆ calculateDensity()

template<class T >

void Voxels< T >::calculateDensity ( )

Convert voxel intensity into voxel density.

Referenced by VoxeliseFilter::refresh().

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◆ clear()

template<class T>

void Voxels< T >::clear ( )

inline

Empty the data.

Referenced by VoxelStreamData::clear(), VoxeliseFilter::clearCache(), and VoxeliseFilter::refresh().

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◆ clone()

template<class T>

void Voxels< T >::clone ( Voxels< T > & newClone ) const

Clone this into another object.

Referenced by VisController::updateScene().

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◆ convolve()

template<class T>

size_t Voxels< T >::convolve	(	const Voxels< T > &	templateVec,
		Voxels< T > &	result,
		size_t	boundMode = `BOUND_CLIP`
	)		const

Run convolution over this data, placing the correlation data into "result".

Datasets MUST have the same pitch (spacing) for the result to be defined template type must have a T(0.0) constructor that intialises it to some "zero"

◆ count()

template<class T>

size_t Voxels< T >::count ( const T & minIntensity ) const

count the number of cells with at least this intensity

◆ countPoints()

template<class T >

int Voxels< T >::countPoints	(	const std::vector< Point3D > &	points,
		bool	noWrap = `true`,
		bool	doErase = `false`
	)

Generate a dataset that consists of the counts of points in a given voxel.

Ensure that the voxel scaling factors are set by calling ::setBounds() with the appropriate parameters for your data. Disabling nowrap allows you to "saturate" your data field in the case of dense regions, rather than let wrap-around errors occur

◆ deprecatedGetEdgeUniqueIndex()

template<class T >

size_t Voxels< T >::deprecatedGetEdgeUniqueIndex	(	size_t	x,
		size_t	y,
		size_t	z,
		unsigned int	edge
	)		const

DEPRECATED FUNCTION : Get a unique integer that corresponds to the edge index for the voxel; where edges are shared between voxels.

Each voxel has 12 edges. These are shared (except voxels that on zero or positive boundary). Return a unique index that corresponds to a specified edge (0->11). Index CANNOT be inverted to yield cell

Referenced by marchingCubes().

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◆ fill()

template<class T>

void Voxels< T >::fill ( const T & val )

Fill all voxels with a given value.

Referenced by Voxels< float >::countPoints(), marchingCubes(), and VoxeliseFilter::refresh().

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◆ getAxisBounds()

template<class T >

void Voxels< T >::getAxisBounds	(	size_t	axis,
		float &	minV,
		float &	maxV
	)		const

Referenced by VoxeliseFilter::getRefreshUseMask().

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◆ getBinVolume()

template<class T >

float Voxels< T >::getBinVolume ( ) const

◆ getBounds() [1/2]

template<class T>

void Voxels< T >::getBounds	(	Point3D &	pMin,
		Point3D &	pMax
	)		const

inline

Get the bounding size.

Referenced by VoxeliseFilter::getRefreshUseMask(), marchingCubes(), and VoxeliseFilter::refresh().

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◆ getBounds() [2/2]

template<class T>

void Voxels< T >::getBounds ( BoundCube & bc ) const

inline

◆ getCellUniqueEdgeIndex()

template<class T >

size_t Voxels< T >::getCellUniqueEdgeIndex	(	size_t	x,
		size_t	y,
		size_t	z,
		unsigned int	edge
	)		const

Get a unique integer that corresponds to an edge index for the voxel; where edges are shared between voxels.

Each voxel has 12 edges. These are shared (except voxels that on zero or positive boundary). Return a NON-unique index that corresponds to a specified edge (0->11) Index can be inverted to yield cell

◆ getData() [1/3]

template<class T >

T Voxels< T >::getData	(	size_t	x,
		size_t	y,
		size_t	z
	)		const

inline

Retrieve the value of a specific voxel.

Referenced by Voxels< float >::binarise(), countPoints(), DrawField3D::draw(), Voxels< float >::getInterpolatedData(), VoxeliseFilter::getRefreshUseMask(), Voxels< float >::getSlice(), marchingCubes(), Voxels< float >::resizeKeepData(), sumVoxels(), Voxels< float >::thresholdForPosition(), and vtk_write_legacy().

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◆ getData() [2/3]

template<class T>

T Voxels< T >::getData ( size_t * array ) const

inline

◆ getData() [3/3]

template<class T>

T Voxels< T >::getData ( size_t i ) const

inline

Retrieve value of the nth voxel.

◆ getEdgeCell()

template<class T >

void Voxels< T >::getEdgeCell	(	size_t	edgeUniqId,
		size_t &	x,
		size_t &	y,
		size_t &	z,
		size_t &	axis
	)		const

Convert edge index (only as generted by getCellUniqueEdgeIndex) into a cell & axis value.

Referenced by Voxels< float >::getEdgeEnds().

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◆ getEdgeEndApproxVals()

template<class T>

void Voxels< T >::getEdgeEndApproxVals	(	size_t	edgeUniqId,
		T &	a,
		T &	b
	)		const

Return the values that are associated with the edge ends, as returned by getEdgeEnds.

Referenced by marchingCubes().

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◆ getEdgeEnds()

template<class T >

void Voxels< T >::getEdgeEnds	(	size_t	edgeIndex,
		Point3D &	a,
		Point3D &	b
	)		const

Convert the edge index (as generated by getEdgeUniqueIndex) into a cenre position.

Referenced by Voxels< float >::getEdgeEndApproxVals(), and marchingCubes().

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◆ getIndex()

template<class T >

void Voxels< T >::getIndex	(	size_t &	x,
		size_t &	y,
		size_t &	z,
		const Point3D &	p
	)		const

Retrieve the XYZ voxel location associated with a given position.

Referenced by Voxels< float >::getEdgeEndApproxVals(), Voxels< float >::getIndexWithUpper(), and Voxels< float >::getInterpolatedData().

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◆ getIndexWithUpper()

template<class T >

void Voxels< T >::getIndexWithUpper	(	size_t &	x,
		size_t &	y,
		size_t &	z,
		const Point3D &	p
	)		const

Retrieve the XYZ voxel location associated with a given position,.

Referenced by countPoints().

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◆ getInterpolatedData()

template<class T>

void Voxels< T >::getInterpolatedData	(	const Point3D &	pt,
		T &	v
	)		const

Referenced by VoxeliseFilter::refresh().

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◆ getInterpSlice()

template<class T>

void Voxels< T >::getInterpSlice	(	size_t	normal,
		float	offset,
		T *	p,
		size_t	interpMode = `VOX_INTERP_NONE`
	)		const

Referenced by VoxeliseFilter::getRefreshUseMask().

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◆ getMaxBounds()

template<class T >

Point3D Voxels< T >::getMaxBounds ( ) const

Referenced by DrawField3D::draw(), DrawField3D::getBoundingBox(), DrawIsoSurface::getBoundingBox(), Voxels< float >::getEdgeEnds(), and marchingCubes().

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◆ getMinBounds()

template<class T >

Point3D Voxels< T >::getMinBounds ( ) const

Get the bounding box vertex (min/max)

Referenced by DrawField3D::draw(), DrawField3D::getBoundingBox(), DrawIsoSurface::getBoundingBox(), Voxels< float >::getEdgeEnds(), and marchingCubes().

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◆ getPitch()

template<class T >

Point3D Voxels< T >::getPitch ( ) const

! Get the spacing for a unit cell

Referenced by DrawField3D::draw(), Voxels< float >::getEdgeEnds(), Voxels< float >::getInterpolatedData(), marchingCubes(), and VoxeliseFilter::refresh().

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◆ getPoint()

template<class T >

Point3D Voxels< T >::getPoint	(	size_t	x,
		size_t	y,
		size_t	z
	)		const

Get the position associated with an XYZ voxel.

Referenced by DrawField3D::draw(), Voxels< float >::getEdgeEnds(), marchingCubes(), Voxels< float >::thresholdForPosition(), and vtk_write_legacy().

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◆ getPointData()

template<class T >

T Voxels< T >::getPointData ( const Point3D & pt ) const

Retrieve the value of a datapoint, this is rounded to the nearest voxel.

Referenced by Voxels< float >::getEdgeEndApproxVals().

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◆ getSize() [1/2]

template<class T >

void Voxels< T >::getSize	(	size_t &	x,
		size_t &	y,
		size_t &	z
	)		const

Get the size of the data field.

Referenced by countPoints(), DrawField3D::draw(), VoxelStreamData::getNumBasicObjects(), VoxeliseFilter::getRefreshUseMask(), marchingCubes(), VoxeliseFilter::refresh(), sumVoxels(), and vtk_write_legacy().

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◆ getSize() [2/2]

template<class T>

size_t Voxels< T >::getSize ( ) const

inline

◆ getSlice()

template<class T>

void Voxels< T >::getSlice	(	size_t	normal,
		size_t	offset,
		T *	p
	)		const

Referenced by Voxels< float >::getInterpSlice().

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◆ getSum()

template<class T>

T Voxels< T >::getSum ( const T & initialVal = T(0.0) ) const

Get the total value of the data field.

An "initial value" is provided to provide the definition of a zero value

◆ init() [1/2]

template<class T >

size_t Voxels< T >::init	(	size_t	nX,
		size_t	nY,
		size_t	nZ,
		const BoundCube &	bound
	)

Initialise the voxel storage.

Referenced by Voxels< float >::init(), and VoxeliseFilter::refresh().

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◆ init() [2/2]

template<class T >

size_t Voxels< T >::init	(	size_t	nX,
		size_t	nY,
		size_t	nZ
	)

Initialise the voxel storage.

◆ isotropicGaussianSmooth()

template<class T >

void Voxels< T >::isotropicGaussianSmooth	(	float	stdev,
		float	windowRatio
	)

Referenced by VoxeliseFilter::refresh().

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◆ laplaceOfGaussian()

template<class T >

void Voxels< T >::laplaceOfGaussian	(	float	stdev,
		float	windowRatio
	)

Referenced by VoxeliseFilter::refresh().

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◆ loadFile()

template<class T >

size_t Voxels< T >::loadFile	(	const char *	cpFilename,
		size_t	nX,
		size_t	nY,
		size_t	nZ,
		bool	silent = `false`
	)

Load the voxels from file.

Format is flat size_ts in column major return codes: 1: File open error 2: Data size error

◆ max()

template<class T >

T Voxels< T >::max ( ) const

Find maximum in dataset.

Referenced by VoxeliseFilter::getRefreshUseMask(), and DrawField3D::setColourMinMax().

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◆ min()

template<class T >

T Voxels< T >::min ( ) const

Find minimum in dataset.

Referenced by VoxeliseFilter::getRefreshUseMask(), and DrawField3D::setColourMinMax().

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◆ minMax()

template<class T>

void Voxels< T >::minMax	(	T &	min,
		T &	max
	)		const

Find both min and max in dataset in the same loop.

Referenced by VoxeliseFilter::refresh().

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◆ operator/=() [1/2]

template<class T>

void Voxels< T >::operator/= ( const Voxels< T > & v )

Element wise division.

◆ operator/=() [2/2]

template<class T>

void Voxels< T >::operator/= ( const T & v )

◆ operator==()

template<class T>

bool Voxels< T >::operator== ( const Voxels< T > & v ) const

◆ rebin()

template<class T>

void Voxels< T >::rebin	(	Voxels< T > &	dest,
		size_t	rate,
		size_t	clipMode = `CLIP_NONE`
	)		const

Rebin the data by a given rate.

This will perform a quick and dirty rebin operation, where groups of datablocks are binned into a single cell. Number of blocks binned is rate^3. Field must be larger than rate in all directions. Currently only CLIP_NONE is supported.

◆ resize() [1/2]

template<class T >

size_t Voxels< T >::resize	(	size_t	newX,
		size_t	newY,
		size_t	newZ,
		const Point3D &	newMinBound = `Point3D(0.0f,0.0f,0.0f)`,
		const Point3D &	newMaxBound = `Point3D(1.0f,1.0f,1.0f)`
	)

Resize the data field.

This will destroy any data that was already in place If the data needs to be preserved use "resizeKeepData" Data will not be initialised

Referenced by Voxels< float >::binarise(), Voxels< float >::loadFile(), marchingCubes(), Voxels< float >::resize(), Voxels< float >::resizeKeepData(), and vtk_write_legacy().

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◆ resize() [2/2]

template<class T>

size_t Voxels< T >::resize ( const Voxels< T > & v )

◆ resizeKeepData()

template<class T>

size_t Voxels< T >::resizeKeepData	(	size_t	newX,
		size_t	newY,
		size_t	newZ,
		unsigned int	direction = `CLIP_LOWER_SOUTH_WEST`,
		const Point3D &	newMinBound = `Point3D(0.0f,0.0f,0.0f)`,
		const Point3D &	newMaxBound = `Point3D(1.0f,1.0f,1.0f)`,
		const T &	fill = `T(0)`,
		bool	doFill = `false`
	)

Resize the data field, maintaining data as best as possible.

This will preserve data by resizing as much as possible about the origin. If the bounds are extended, the "fill" value is used by default iff doFill is set to true.

◆ separableConvolve()

template<class T>

size_t Voxels< T >::separableConvolve	(	const Voxels< T > &	templateVec,
		Voxels< T > &	result,
		size_t	boundMode = `BOUND_CLIP`
	)

Similar to convolve, but faster – only works with separable kernels.

Datasets MUST have the same pitch (spacing) for the result to be defined template type must have a T(0.0) constructor that intialises it to some "zero"

◆ setBounds()

template<class T >

void Voxels< T >::setBounds	(	const Point3D &	pMin,
		const Point3D &	pMax
	)

Set the bounding size.

◆ setData() [1/2]

template<class T>

void Voxels< T >::setData	(	size_t	x,
		size_t	y,
		size_t	z,
		const T &	val
	)

Retrieve a reference to the data ata given position.

Set the value of a point in the dataset

Referenced by Voxels< float >::binarise(), countPoints(), marchingCubes(), Voxels< float >::resizeKeepData(), and vtk_write_legacy().

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◆ setData() [2/2]

template<class T>

void Voxels< T >::setData	(	size_t	n,
		const T &	val
	)

inline

Set the value of nth point in the dataset.

◆ setEntry()

template<class T>

void Voxels< T >::setEntry	(	size_t	n,
		const T &	val
	)

inline

◆ setPoint()

template<class T>

void Voxels< T >::setPoint	(	const Point3D &	pt,
		const T &	val
	)

Set the value of a point in the dataset.

◆ size()

template<class T>

size_t Voxels< T >::size ( ) const

inline

Referenced by Voxels< float >::calculateDensity(), Voxels< float >::getBinVolume(), sumVoxels(), and vtk_write_legacy().

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◆ sizeofType()

template<class T>

static size_t Voxels< T >::sizeofType ( )

inlinestatic

Return the sizeof value for the T type.

Maybe there is a better way to do this, I don't know

◆ swap()

template<class T>

void Voxels< T >::swap ( Voxels< T > & v )

Swap object contents with other voxel object.

Referenced by VisController::updateScene().

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◆ thresholdForPosition()

template<class T>

void Voxels< T >::thresholdForPosition	(	std::vector< Point3D > &	p,
		const T &	thresh,
		bool	lowerEq = `false`
	)		const

Find the positions of the voxels that are above or below a given value.

Returns the positions of the voxels' centroids for voxels that have, by default, a value greater than that of thresh. This behaviour can by reversed to "lesser than" by setting lowerEq to false

◆ trapezIntegral()

template<class T >

T Voxels< T >::trapezIntegral ( ) const

Integrate the datataset via the trapezoidal method.

◆ writeFile()

template<class T >

size_t Voxels< T >::writeFile ( const char * cpFilename ) const

Write the voxel objects in column major written out to file.

Format is flat objects ("T"s) in column major format. Returns nonzero on failure

Referenced by MainWindowFrame::OnFileExportFilterVideo().

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

Public Member Functions

Static Public Member Functions

Detailed Description

template<class T> class Voxels< T >

Constructor & Destructor Documentation

◆ Voxels()

◆ ~Voxels()

Member Function Documentation

◆ binarise()

◆ calculateDensity()

◆ clear()

◆ clone()

◆ convolve()

◆ count()

◆ countPoints()

◆ deprecatedGetEdgeUniqueIndex()

◆ fill()

◆ getAxisBounds()

◆ getBinVolume()

◆ getBounds() [1/2]

◆ getBounds() [2/2]

◆ getCellUniqueEdgeIndex()

◆ getData() [1/3]

◆ getData() [2/3]

◆ getData() [3/3]

◆ getEdgeCell()

◆ getEdgeEndApproxVals()

◆ getEdgeEnds()

◆ getIndex()

◆ getIndexWithUpper()

◆ getInterpolatedData()

◆ getInterpSlice()

◆ getMaxBounds()

◆ getMinBounds()

◆ getPitch()

◆ getPoint()

◆ getPointData()

◆ getSize() [1/2]

◆ getSize() [2/2]

◆ getSlice()

◆ getSum()

◆ init() [1/2]

◆ init() [2/2]

◆ isotropicGaussianSmooth()

◆ laplaceOfGaussian()

◆ loadFile()

◆ max()

◆ min()

◆ minMax()

◆ operator/=() [1/2]

◆ operator/=() [2/2]

◆ operator==()

◆ rebin()

◆ resize() [1/2]

◆ resize() [2/2]

◆ resizeKeepData()

◆ separableConvolve()

◆ setBounds()

◆ setData() [1/2]

◆ setData() [2/2]

◆ setEntry()

◆ setPoint()

◆ size()

◆ sizeofType()

◆ swap()

◆ thresholdForPosition()

◆ trapezIntegral()

◆ writeFile()

template<class T>
class Voxels< T >