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

#include <voxels.h>

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

	~Voxels ()
	Destructor. More...

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

void	copy (Voxels< T > &newCopy) const
	Clone data into another object. More...

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

T	getPointData (const AtomProbe::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 AtomProbe::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 AtomProbe::Point3D &p) const
	Retrieve the XYZ voxel location associated with a given position,. More...

AtomProbe::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 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 AtomProbe::Point3D &pt, T &v) const

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	resize (size_t newX, size_t newY, size_t newZ, const AtomProbe::Point3D &newMinBound=AtomProbe::Point3D(0.0f, 0.0f, 0.0f), const AtomProbe::Point3D &newMaxBound=AtomProbe::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 AtomProbe::Point3D &newMinBound=AtomProbe::Point3D(0.0f, 0.0f, 0.0f), const AtomProbe::Point3D &newMaxBound=AtomProbe::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, AtomProbe::Point3D &a, AtomProbe::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...

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...

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

AtomProbe::Point3D	getMaxBounds () const

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

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

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

void	setBounds (const BoundCube &b)

void	getBounds (AtomProbe::Point3D &pMin, AtomProbe::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...

void	threshold (const T &thresh, bool keepUpper, const T &newVal)
	Threshold the voxels, keeping either the lower or upper values above this threshold. More...

void	thresholdToBoolMask (const T &thresh, bool keepUpper, Voxels< bool > &result) const
	Generate a boolean voxel field stating whether the data is above or below the threshold specified. More...

void	applyMask (const Voxels< bool > &mask, const T &newVal, bool invert=false)
	Apply a mask to this dataset, where the mask is true (if not inverting), replace with specified val (newVal) More...

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

int	countIons (const std::vector< AtomProbe::IonHit > &ions, bool noWrap=true, bool doErase=true)
	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 AtomProbe::Voxels< T >

Template class that stores 3D voxel data.

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

Definition at line 106 of file voxels.h.

Constructor & Destructor Documentation

◆ Voxels()

template<class T >

AtomProbe::Voxels< T >::Voxels ( )

Constructor.

Definition at line 392 of file voxels.h.

◆ ~Voxels()

template<class T >

AtomProbe::Voxels< T >::~Voxels ( )

Destructor.

Definition at line 397 of file voxels.h.

Member Function Documentation

◆ applyMask()

template<class T >

void AtomProbe::Voxels< T >::applyMask	(	const Voxels< bool > &	mask,
		const T &	newVal,
		bool	invert = `false`
	)

Apply a mask to this dataset, where the mask is true (if not inverting), replace with specified val (newVal)

Definition at line 1297 of file voxels.h.

References ASSERT, AtomProbe::Voxels< T >::getData(), AtomProbe::Voxels< T >::getMaxBounds(), AtomProbe::Voxels< T >::getMinBounds(), AtomProbe::Voxels< T >::getSize(), and AtomProbe::Voxels< T >::size().

Referenced by AtomProbe::Voxels< T >::getBounds().

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◆ binarise()

template<class T >

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

Binarise the data into a result vector.

Definition at line 1330 of file voxels.h.

References AtomProbe::Voxels< T >::getData(), AtomProbe::Voxels< T >::resize(), and AtomProbe::Voxels< T >::setData().

Referenced by AtomProbe::Voxels< T >::sizeofType().

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◆ calculateDensity()

template<class T >

void AtomProbe::Voxels< T >::calculateDensity ( )

Convert voxel intensity into voxel density.

Definition at line 1469 of file voxels.h.

References AtomProbe::Voxels< T >::size().

Referenced by AtomProbe::Voxels< T >::clear().

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◆ clear()

template<class T>

void AtomProbe::Voxels< T >::clear ( )

inline

Empty the data.

Definition at line 314 of file voxels.h.

References AtomProbe::Voxels< T >::calculateDensity(), AtomProbe::Voxels< T >::countIons(), AtomProbe::Voxels< T >::countPoints(), AtomProbe::Voxels< T >::getBinVolume(), AtomProbe::Voxels< T >::max(), AtomProbe::Voxels< T >::min(), AtomProbe::Voxels< T >::minMax(), AtomProbe::Voxels< T >::operator/=(), AtomProbe::Voxels< T >::operator==(), and AtomProbe::Voxels< T >::trapezIntegral().

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◆ copy()

template<class T >

void AtomProbe::Voxels< T >::copy ( Voxels< T > & newCopy ) const

Clone data into another object.

Definition at line 409 of file voxels.h.

◆ count()

template<class T >

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

count the number of cells with at least this intensity

Definition at line 1156 of file voxels.h.

Referenced by AtomProbe::Voxels< T >::setEntry().

◆ countIons()

template<class T >

int AtomProbe::Voxels< T >::countIons	(	const std::vector< AtomProbe::IonHit > &	ions,
		bool	noWrap = `true`,
		bool	doErase = `true`
	)

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

Definition at line 1418 of file voxels.h.

References AtomProbe::Voxels< T >::fill(), AtomProbe::Voxels< T >::getData(), AtomProbe::Voxels< T >::getIndex(), and AtomProbe::Voxels< T >::setData().

Referenced by AtomProbe::Voxels< T >::clear().

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◆ countPoints()

template<class T >

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

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

Definition at line 1382 of file voxels.h.

References AtomProbe::Voxels< T >::fill(), AtomProbe::Voxels< T >::getData(), AtomProbe::Voxels< T >::getIndex(), and AtomProbe::Voxels< T >::setData().

Referenced by AtomProbe::Voxels< T >::clear().

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◆ deprecatedGetEdgeUniqueIndex()

template<class T >

size_t AtomProbe::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

Definition at line 497 of file voxels.h.

Referenced by AtomProbe::marchingCubes(), and AtomProbe::Voxels< T >::setEntry().

◆ fill()

template<class T >

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

Fill all voxels with a given value.

Definition at line 1536 of file voxels.h.

Referenced by AtomProbe::Voxels< T >::countIons(), AtomProbe::Voxels< T >::countPoints(), main(), AtomProbe::marchingCubes(), and AtomProbe::Voxels< T >::setEntry().

◆ getAxisBounds()

template<class T >

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

Definition at line 828 of file voxels.h.

Referenced by AtomProbe::Voxels< T >::setEntry().

◆ getBinVolume()

template<class T >

float AtomProbe::Voxels< T >::getBinVolume ( ) const

Definition at line 1485 of file voxels.h.

References AtomProbe::Voxels< T >::size().

Referenced by AtomProbe::Voxels< T >::clear().

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◆ getBounds() [1/2]

template<class T>

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

inline

Get the bounding size.

Definition at line 252 of file voxels.h.

Referenced by main(), and AtomProbe::marchingCubes().

◆ getBounds() [2/2]

template<class T>

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

inline

Definition at line 253 of file voxels.h.

References AtomProbe::Voxels< T >::applyMask(), AtomProbe::Voxels< T >::init(), AtomProbe::Voxels< T >::loadFile(), AtomProbe::BoundCube::setBounds(), AtomProbe::Voxels< T >::threshold(), AtomProbe::Voxels< T >::thresholdForPosition(), AtomProbe::Voxels< T >::thresholdToBoolMask(), and AtomProbe::Voxels< T >::writeFile().

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◆ getCellUniqueEdgeIndex()

template<class T >

size_t AtomProbe::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

Definition at line 701 of file voxels.h.

Referenced by AtomProbe::Voxels< T >::setEntry().

◆ getData() [1/2]

template<class T >

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

inline

Retrieve the value of a specific voxel.

Definition at line 1186 of file voxels.h.

References ASSERT.

Referenced by AtomProbe::Voxels< T >::applyMask(), AtomProbe::Voxels< T >::binarise(), AtomProbe::Voxels< T >::countIons(), AtomProbe::Voxels< T >::countPoints(), AtomProbe::Voxels< T >::getInterpolatedData(), AtomProbe::Voxels< T >::getSlice(), AtomProbe::marchingCubes(), AtomProbe::Voxels< T >::resizeKeepData(), AtomProbe::sumVoxels(), AtomProbe::Voxels< T >::threshold(), AtomProbe::Voxels< T >::thresholdForPosition(), and AtomProbe::Voxels< T >::thresholdToBoolMask().

◆ getData() [2/2]

template<class T>

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

inline

Retrieve value of the nth voxel.

Definition at line 156 of file voxels.h.

◆ getEdgeCell()

template<class T >

void AtomProbe::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.

Definition at line 751 of file voxels.h.

References ASSERT.

Referenced by AtomProbe::Voxels< T >::getEdgeEnds(), and AtomProbe::Voxels< T >::setEntry().

◆ getEdgeEndApproxVals()

template<class T >

void AtomProbe::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.

Definition at line 813 of file voxels.h.

References AtomProbe::Voxels< T >::getEdgeEnds(), AtomProbe::Voxels< T >::getIndex(), and AtomProbe::Voxels< T >::getPointData().

Referenced by AtomProbe::marchingCubes(), and AtomProbe::Voxels< T >::setEntry().

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◆ getEdgeEnds()

template<class T >

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

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

Definition at line 771 of file voxels.h.

References ASSERT, AtomProbe::BoundCube::containsPt(), AtomProbe::BoundCube::expand(), AtomProbe::Voxels< T >::getEdgeCell(), AtomProbe::Voxels< T >::getMaxBounds(), AtomProbe::Voxels< T >::getMinBounds(), AtomProbe::Voxels< T >::getPitch(), AtomProbe::Voxels< T >::getPoint(), and AtomProbe::BoundCube::setBounds().

Referenced by AtomProbe::Voxels< T >::getEdgeEndApproxVals(), AtomProbe::marchingCubes(), and AtomProbe::Voxels< T >::setEntry().

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◆ getIndex()

template<class T >

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

Retrieve the XYZ voxel location associated with a given position.

Definition at line 1496 of file voxels.h.

References ASSERT.

Referenced by AtomProbe::Voxels< T >::countIons(), AtomProbe::Voxels< T >::countPoints(), AtomProbe::Voxels< T >::getEdgeEndApproxVals(), AtomProbe::Voxels< T >::getIndexWithUpper(), and AtomProbe::Voxels< T >::getInterpolatedData().

◆ getIndexWithUpper()

template<class T >

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

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

Definition at line 1515 of file voxels.h.

References AtomProbe::Voxels< T >::getIndex().

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◆ getInterpolatedData()

template<class T >

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

Definition at line 1678 of file voxels.h.

References ASSERT, AtomProbe::BoundCube::containsPt(), AtomProbe::Voxels< T >::getData(), AtomProbe::Voxels< T >::getIndex(), and AtomProbe::Voxels< T >::getPitch().

Referenced by AtomProbe::Voxels< T >::setEntry().

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◆ getInterpSlice()

template<class T >

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

Definition at line 1614 of file voxels.h.

References ASSERT, AtomProbe::Voxels< T >::getSlice(), AtomProbe::VOX_INTERP_LINEAR, and AtomProbe::VOX_INTERP_NONE.

Referenced by AtomProbe::Voxels< T >::setEntry().

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◆ getMaxBounds()

template<class T >

AtomProbe::Point3D AtomProbe::Voxels< T >::getMaxBounds ( ) const

Definition at line 954 of file voxels.h.

References ASSERT.

Referenced by AtomProbe::Voxels< T >::applyMask(), AtomProbe::Voxels< T >::getEdgeEnds(), AtomProbe::marchingCubes(), and AtomProbe::Voxels< T >::setEntry().

◆ getMinBounds()

template<class T >

AtomProbe::Point3D AtomProbe::Voxels< T >::getMinBounds ( ) const

Get the bounding box vertex (min/max)

Definition at line 947 of file voxels.h.

References ASSERT.

Referenced by AtomProbe::Voxels< T >::applyMask(), AtomProbe::Voxels< T >::getEdgeEnds(), AtomProbe::marchingCubes(), and AtomProbe::Voxels< T >::setEntry().

◆ getPitch()

template<class T >

AtomProbe::Point3D AtomProbe::Voxels< T >::getPitch ( ) const

! Get the spacing for a unit cell

Definition at line 480 of file voxels.h.

Referenced by AtomProbe::Voxels< T >::getEdgeEnds(), AtomProbe::Voxels< T >::getInterpolatedData(), AtomProbe::marchingCubes(), and AtomProbe::Voxels< T >::setEntry().

◆ getPoint()

template<class T >

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

Get the position associated with an XYZ voxel.

Definition at line 470 of file voxels.h.

Referenced by AtomProbe::Voxels< T >::getEdgeEnds(), main(), and AtomProbe::Voxels< T >::thresholdForPosition().

◆ getPointData()

template<class T >

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

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

Definition at line 454 of file voxels.h.

References ASSERT.

Referenced by AtomProbe::Voxels< T >::getEdgeEndApproxVals().

◆ getSize()

template<class T >

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

Get the size of the data field.

Definition at line 488 of file voxels.h.

References ASSERT.

Referenced by AtomProbe::Voxels< T >::applyMask(), AtomProbe::marchingCubes(), AtomProbe::Voxels< T >::setEntry(), and AtomProbe::sumVoxels().

◆ getSlice()

template<class T >

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

Definition at line 1545 of file voxels.h.

References ASSERT, and AtomProbe::Voxels< T >::getData().

Referenced by AtomProbe::Voxels< T >::getInterpSlice(), and AtomProbe::Voxels< T >::setEntry().

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◆ getSum()

template<class T >

T AtomProbe::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

Definition at line 1117 of file voxels.h.

References ASSERT.

Referenced by AtomProbe::Voxels< T >::setEntry().

◆ init() [1/2]

template<class T >

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

Initialise the voxel storage.

Definition at line 982 of file voxels.h.

References AtomProbe::BoundCube::getBounds().

Referenced by AtomProbe::Voxels< T >::getBounds(), and AtomProbe::Voxels< T >::init().

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◆ init() [2/2]

template<class T >

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

Initialise the voxel storage.

Definition at line 997 of file voxels.h.

References AtomProbe::Voxels< T >::init().

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◆ loadFile()

template<class T >

size_t AtomProbe::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

Definition at line 1006 of file voxels.h.

References AtomProbe::Voxels< T >::resize(), AtomProbe::VOXELS_BAD_FILE_OPEN, AtomProbe::VOXELS_BAD_FILE_READ, and AtomProbe::VOXELS_BAD_FILE_SIZE.

Referenced by AtomProbe::Voxels< T >::getBounds().

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◆ max()

template<class T >

T AtomProbe::Voxels< T >::max ( ) const

Find maximum in dataset.

Definition at line 1364 of file voxels.h.

References ASSERT.

Referenced by AtomProbe::Voxels< T >::clear().

◆ min()

template<class T >

T AtomProbe::Voxels< T >::min ( ) const

Find minimum in dataset.

Definition at line 1357 of file voxels.h.

References ASSERT.

Referenced by AtomProbe::Voxels< T >::clear().

◆ minMax()

template<class T >

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

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

Definition at line 1372 of file voxels.h.

References ASSERT.

Referenced by AtomProbe::Voxels< T >::clear().

◆ operator/=() [1/2]

template<class T >

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

Element wise division.

Definition at line 1736 of file voxels.h.

References ASSERT.

Referenced by AtomProbe::Voxels< T >::clear().

◆ operator/=() [2/2]

template<class T >

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

Definition at line 1756 of file voxels.h.

◆ operator==()

template<class T >

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

Definition at line 1773 of file voxels.h.

Referenced by AtomProbe::Voxels< T >::clear().

◆ resize() [1/2]

template<class T >

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

Definition at line 835 of file voxels.h.

Referenced by AtomProbe::Voxels< T >::binarise(), AtomProbe::Voxels< T >::loadFile(), main(), AtomProbe::marchingCubes(), AtomProbe::Voxels< T >::resize(), AtomProbe::Voxels< T >::resizeKeepData(), AtomProbe::Voxels< T >::setEntry(), and AtomProbe::Voxels< T >::thresholdToBoolMask().

◆ resize() [2/2]

template<class T >

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

Definition at line 858 of file voxels.h.

References AtomProbe::Voxels< T >::resize().

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◆ resizeKeepData()

template<class T >

size_t AtomProbe::Voxels< T >::resizeKeepData	(	size_t	newX,
		size_t	newY,
		size_t	newZ,
		unsigned int	direction = `CLIP_LOWER_SOUTH_WEST`,
		const AtomProbe::Point3D &	newMinBound = `AtomProbe::Point3D(0.0f,0.0f,0.0f)`,
		const AtomProbe::Point3D &	newMaxBound = `AtomProbe::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.

Definition at line 864 of file voxels.h.

References ASSERT, AtomProbe::CLIP_LOWER_SOUTH_WEST, AtomProbe::Voxels< T >::getData(), AtomProbe::Voxels< T >::resize(), AtomProbe::Voxels< T >::setData(), and AtomProbe::Voxels< T >::swap().

Referenced by AtomProbe::Voxels< T >::setEntry().

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◆ setBounds() [1/2]

template<class T >

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

Set the bounding size.

Definition at line 961 of file voxels.h.

References ASSERT.

Referenced by main(), AtomProbe::Voxels< T >::setBounds(), and AtomProbe::Voxels< T >::setEntry().

◆ setBounds() [2/2]

template<class T >

void AtomProbe::Voxels< T >::setBounds ( const BoundCube & b )

Definition at line 976 of file voxels.h.

References AtomProbe::BoundCube::max(), AtomProbe::BoundCube::min(), and AtomProbe::Voxels< T >::setBounds().

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◆ setData() [1/2]

template<class T >

void AtomProbe::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

Definition at line 435 of file voxels.h.

References ASSERT.

Referenced by AtomProbe::Voxels< T >::binarise(), AtomProbe::Voxels< T >::countIons(), AtomProbe::Voxels< T >::countPoints(), main(), AtomProbe::marchingCubes(), AtomProbe::Voxels< T >::resizeKeepData(), AtomProbe::Voxels< T >::setEntry(), AtomProbe::Voxels< T >::threshold(), and AtomProbe::Voxels< T >::thresholdToBoolMask().

◆ setData() [2/2]

template<class T >

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

inline

Set the value of nth point in the dataset.

Definition at line 445 of file voxels.h.

References ASSERT.

◆ setEntry()

template<class T>

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

inline

Definition at line 158 of file voxels.h.

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◆ setPoint()

template<class T >

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

Set the value of a point in the dataset.

Definition at line 423 of file voxels.h.

References ASSERT.

◆ size()

template<class T>

size_t AtomProbe::Voxels< T >::size ( ) const

inline

Definition at line 361 of file voxels.h.

Referenced by AtomProbe::Voxels< T >::applyMask(), AtomProbe::Voxels< T >::calculateDensity(), AtomProbe::Voxels< T >::getBinVolume(), and AtomProbe::sumVoxels().

◆ sizeofType()

template<class T>

static size_t AtomProbe::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

Definition at line 300 of file voxels.h.

References AtomProbe::Voxels< T >::binarise().

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◆ swap()

template<class T >

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

Swap object contents with other voxel object.

Definition at line 1173 of file voxels.h.

Referenced by AtomProbe::Voxels< T >::resizeKeepData().

◆ threshold()

template<class T >

void AtomProbe::Voxels< T >::threshold	(	const T &	thresh,
		bool	keepUpper,
		const T &	newVal
	)

Threshold the voxels, keeping either the lower or upper values above this threshold.

Definition at line 1238 of file voxels.h.

References AtomProbe::Voxels< T >::getData(), and AtomProbe::Voxels< T >::setData().

Referenced by AtomProbe::Voxels< T >::getBounds().

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◆ thresholdForPosition()

template<class T >

void AtomProbe::Voxels< T >::thresholdForPosition	(	std::vector< AtomProbe::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

Definition at line 1193 of file voxels.h.

References AtomProbe::Voxels< T >::getData(), and AtomProbe::Voxels< T >::getPoint().

Referenced by AtomProbe::Voxels< T >::getBounds().

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◆ thresholdToBoolMask()

template<class T >

void AtomProbe::Voxels< T >::thresholdToBoolMask	(	const T &	thresh,
		bool	keepUpper,
		Voxels< bool > &	result
	)		const

Generate a boolean voxel field stating whether the data is above or below the threshold specified.

Definition at line 1274 of file voxels.h.

References AtomProbe::Voxels< T >::getData(), AtomProbe::Voxels< T >::resize(), AtomProbe::Voxels< T >::setData(), and XOR.

Referenced by AtomProbe::Voxels< T >::getBounds().

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◆ trapezIntegral()

template<class T >

T AtomProbe::Voxels< T >::trapezIntegral ( ) const

Integrate the datataset via the trapezoidal method.

Definition at line 1130 of file voxels.h.

Referenced by AtomProbe::Voxels< T >::clear().

◆ writeFile()

template<class T >

size_t AtomProbe::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

Definition at line 1093 of file voxels.h.

References ASSERT.

Referenced by AtomProbe::Voxels< T >::getBounds().

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

include/atomprobe/helper/voxels.h

Public Member Functions

Static Public Member Functions

Detailed Description

template<class T> class AtomProbe::Voxels< T >

Constructor & Destructor Documentation

◆ Voxels()

◆ ~Voxels()

Member Function Documentation

◆ applyMask()

◆ binarise()

◆ calculateDensity()

◆ clear()

◆ copy()

◆ count()

◆ countIons()

◆ countPoints()

◆ deprecatedGetEdgeUniqueIndex()

◆ fill()

◆ getAxisBounds()

◆ getBinVolume()

◆ getBounds() [1/2]

◆ getBounds() [2/2]

◆ getCellUniqueEdgeIndex()

◆ getData() [1/2]

◆ getData() [2/2]

◆ getEdgeCell()

◆ getEdgeEndApproxVals()

◆ getEdgeEnds()

◆ getIndex()

◆ getIndexWithUpper()

◆ getInterpolatedData()

◆ getInterpSlice()

◆ getMaxBounds()

◆ getMinBounds()

◆ getPitch()

◆ getPoint()

◆ getPointData()

◆ getSize()

◆ getSlice()

◆ getSum()

◆ init() [1/2]

◆ init() [2/2]

◆ loadFile()

◆ max()

◆ min()

◆ minMax()

◆ operator/=() [1/2]

◆ operator/=() [2/2]

◆ operator==()

◆ resize() [1/2]

◆ resize() [2/2]

◆ resizeKeepData()

◆ setBounds() [1/2]

◆ setBounds() [2/2]

◆ setData() [1/2]

◆ setData() [2/2]

◆ setEntry()

◆ setPoint()

◆ size()

◆ sizeofType()

◆ swap()

◆ threshold()

◆ thresholdForPosition()

◆ thresholdToBoolMask()

◆ trapezIntegral()

◆ writeFile()

template<class T>
class AtomProbe::Voxels< T >