Volume Class Reference

The Volume class represents a three-dimensional volume on a uniform grid. The volume can be located at arbitrary positions and orientations in space, and can represent most voxel types (float, unsigned char, etc.). A volume can also support multiple planes, which is used to hold three dimensional vector fields, or three-dimensional bitfields. More...

#include <volume.h>

Public Member Functions
	SMART_POINTER_SUPPORT (Volume)
	Volume ()
	Volume (const plm_long dim[3], const float origin[3], const float spacing[3], const float direction_cosines[9], enum Volume_pixel_type vox_type, int vox_planes)
	Volume (const plm_long dim[3], const float origin[3], const float spacing[3], const Direction_cosines &direction_cosines, enum Volume_pixel_type vox_type, int vox_planes)
	Volume (const Volume_header &vh, enum Volume_pixel_type vox_type, int vox_planes)
	~Volume ()
plm_long	index (plm_long i, plm_long j, plm_long k) const
	Return a linear index to a voxel.
plm_long	index (plm_long ijk[3]) const
	Return a linear index to a voxel.
void	create (const plm_long new_dim[3], const float origin[3], const float spacing[3], const float direction_cosines[9], enum Volume_pixel_type vox_type, int vox_planes=1)
	Initialize and allocate memory for the image.
void	create (const Volume_header &vh, enum Volume_pixel_type vox_type, int vox_planes=1)
	Initialize and allocate memory for the image.
Volume::Pointer	clone ()
	Make a copy of the volume.
Volume::Pointer	clone (Volume_pixel_type new_type) const
	Make a copy of the volume with the same geometry and same voxel values, but converted to a different data type.
Volume::Pointer	clone_empty ()
	Make a copy of the volume with the same geometry, but set all the voxel values to zero.
void	convert (Volume_pixel_type new_type)
	Convert the image voxels to a new data type.
const float *	get_origin (void) const
	Get a pointer to the origin of the volume. The origin is defined as the location in world coordinates of the center of the first voxel in the volume.
void	get_origin (float *) const
void	set_origin (const float origin[3])
	Set the origin. The origin is defined as the location in world coordinates of the center of the first voxel in the volume.
const plm_long *	get_dim (void)
	Get a pointer to the volume dimensions.
const float *	get_spacing (void) const
	Get a pointer to the spacing of the volume. The spacing is distance between voxels.
void	get_spacing (float *) const
void	set_spacing (const float spacing[3])
	Set the spacing. The spacing is distance between voxels.
Direction_cosines &	get_direction_cosines (void)
	Get a pointer to the direction cosines. Direction cosines hold the orientation of a volume. They are defined as the unit length direction vectors of the volume in world space as one traverses the pixels in the raw array of values.
const Direction_cosines &	get_direction_cosines (void) const
float *	get_direction_matrix (void)
const float *	get_direction_matrix (void) const
void	set_direction_cosines (const float direction_cosines[9])
	Set the direction cosines. Direction cosines hold the orientation of a volume. They are defined as the unit length direction vectors of the volume in world space as one traverses the pixels in the raw array of values.
void	set_header (const Volume_header &)
	Set the image header. This routine doesn't change any of the pixel values. It just changes the image geometry.
void	set_header (const Plm_image_header *)
template<class T>
T *	get_raw ()
	Get the raw image pointer as specified type. No error checking done.
template<class T>
const T *	get_raw () const
const float *	get_step (void) const
	Get the step matrix. The step matrix encodes the transform from voxel coordinates to world coordinates.
const float *	get_proj (void) const
	Get the proj matrix. The proj matrix encodes the transform from world coordinates to voxel coordinates.
void	position (float xyz[3], const plm_long ijk[3])
	Return a world coordinates of a voxel.
void	coordinates (plm_long ijk[3], plm_long idx)
	Return coordinates from index.
float	get_ijk_value (const float xyz[3]) const
	Get the value at a voxel coordinate, clamped and tri-linearly interpolated. Only applies to float volumes.
void	get_xyz_from_ijk (double xyz[3], const plm_long ijk[3])
plm_long	get_idx_from_xyz (const float xyz[3], bool *in)
void	get_ijk_from_xyz (plm_long ijk[3], const float xyz[3], bool *in)
void	get_ijk_from_xyz (float ijk[3], const float xyz[3], bool *in)
bool	is_inside (const float ijk[3]) const
	Return true if continuous index ijk is inside volume.
void	move_origin_to_idx (const plm_long ijk[3])
	Move the origin to the coordinate at a given index. This is used to correct itk images which have a non-zero region index.
void	scale_inplace (float scale)
	In-place (destructive) scaling of the image according to the supplied scale factor.
void	debug ()
void	direction_cosines_debug ()
Volume *	clone_raw ()

Public Attributes
plm_long	dim [3]
plm_long	npix
float	origin [3]
float	spacing [3]
Direction_cosines	direction_cosines
enum Volume_pixel_type	pix_type
int	vox_planes
int	pix_size
void *	img
float	step [9]
float	proj [9]

Protected Member Functions
void	allocate (void)
void	init ()

Detailed Description

The Volume class represents a three-dimensional volume on a uniform grid. The volume can be located at arbitrary positions and orientations in space, and can represent most voxel types (float, unsigned char, etc.). A volume can also support multiple planes, which is used to hold three dimensional vector fields, or three-dimensional bitfields.

Constructor & Destructor Documentation

Volume() [1/4]

Volume::Volume

(

)

Volume() [2/4]

Volume::Volume	(	const plm_long	dim[3],
		const float	origin[3],
		const float	spacing[3],
		const float	direction_cosines[9],
		enum Volume_pixel_type	vox_type,
		int	vox_planes )

Volume() [3/4]

Volume::Volume	(	const plm_long	dim[3],
		const float	origin[3],
		const float	spacing[3],
		const Direction_cosines &	direction_cosines,
		enum Volume_pixel_type	vox_type,
		int	vox_planes )

Volume() [4/4]

Volume::Volume	(	const Volume_header &	vh,
		enum Volume_pixel_type	vox_type,
		int	vox_planes )

~Volume()

Volume::~Volume

(

)

Member Function Documentation

allocate()

void Volume::allocate ( void )

protected

clone() [1/2]

Volume::Pointer Volume::clone

(

)

Make a copy of the volume.

clone() [2/2]

Volume::Pointer Volume::clone

(

Volume_pixel_type

new_type

)

const

Make a copy of the volume with the same geometry and same voxel values, but converted to a different data type.

clone_empty()

Volume::Pointer Volume::clone_empty

(

)

Make a copy of the volume with the same geometry, but set all the voxel values to zero.

clone_raw()

Volume * Volume::clone_raw

(

)

convert()

void Volume::convert

(

Volume_pixel_type

new_type

)

Convert the image voxels to a new data type.

coordinates()

void Volume::coordinates ( plm_long ijk[3], plm_long idx )

inline

Return coordinates from index.

create() [1/2]

void Volume::create	(	const plm_long	new_dim[3],
		const float	origin[3],
		const float	spacing[3],
		const float	direction_cosines[9],
		enum Volume_pixel_type	vox_type,
		int	vox_planes = 1 )

Initialize and allocate memory for the image.

create() [2/2]

void Volume::create	(	const Volume_header &	vh,
		enum Volume_pixel_type	vox_type,
		int	vox_planes = 1 )

Initialize and allocate memory for the image.

debug()

void Volume::debug

(

)

direction_cosines_debug()

void Volume::direction_cosines_debug

(

)

get_dim()

const plm_long * Volume::get_dim ( void )

inline

Get a pointer to the volume dimensions.

get_direction_cosines() [1/2]

Direction_cosines & Volume::get_direction_cosines ( void )

inline

Get a pointer to the direction cosines.
Direction cosines hold the orientation of a volume. They are defined as the unit length direction vectors of the volume in world space as one traverses the pixels in the raw array of values.

get_direction_cosines() [2/2]

const Direction_cosines & Volume::get_direction_cosines ( void ) const

inline

get_direction_matrix() [1/2]

float * Volume::get_direction_matrix ( void )

inline

get_direction_matrix() [2/2]

const float * Volume::get_direction_matrix ( void ) const

inline

get_idx_from_xyz()

plm_long Volume::get_idx_from_xyz	(	const float	xyz[3],
		bool *	in )

get_ijk_from_xyz() [1/2]

void Volume::get_ijk_from_xyz	(	float	ijk[3],
		const float	xyz[3],
		bool *	in )

get_ijk_from_xyz() [2/2]

void Volume::get_ijk_from_xyz	(	plm_long	ijk[3],
		const float	xyz[3],
		bool *	in )

get_ijk_value()

float Volume::get_ijk_value

(

const float

xyz[3]

)

const

Get the value at a voxel coordinate, clamped and tri-linearly interpolated. Only applies to float volumes.

get_origin() [1/2]

void Volume::get_origin

(

float *

origin

)

const

get_origin() [2/2]

const float * Volume::get_origin

(

void

)

const

Get a pointer to the origin of the volume.
The origin is defined as the location in world coordinates of the center of the first voxel in the volume.

get_proj()

const float * Volume::get_proj

(

void

)

const

Get the proj matrix. The proj matrix encodes the transform from world coordinates to voxel coordinates.

get_raw() [1/2]

template<class T>

template float * Volume::get_raw< float >

(

)

Get the raw image pointer as specified type. No error checking done.

get_raw() [2/2]

template<class T>

template const float * Volume::get_raw< float >

(

)

const

get_spacing() [1/2]

void Volume::get_spacing

(

float *

spacing

)

const

get_spacing() [2/2]

const float * Volume::get_spacing

(

void

)

const

Get a pointer to the spacing of the volume.
The spacing is distance between voxels.

get_step()

const float * Volume::get_step

(

void

)

const

Get the step matrix. The step matrix encodes the transform from voxel coordinates to world coordinates.

get_xyz_from_ijk()

void Volume::get_xyz_from_ijk	(	double	xyz[3],
		const plm_long	ijk[3] )

index() [1/2]

plm_long Volume::index ( plm_long i, plm_long j, plm_long k ) const

inline

Return a linear index to a voxel.

index() [2/2]

plm_long Volume::index ( plm_long ijk[3] ) const

inline

Return a linear index to a voxel.

init()

void Volume::init ( )

protected

is_inside()

bool Volume::is_inside

(

const float

ijk[3]

)

const

Return true if continuous index ijk is inside volume.

move_origin_to_idx()

void Volume::move_origin_to_idx

(

const plm_long

ijk[3]

)

Move the origin to the coordinate at a given index. This is used to correct itk images which have a non-zero region index.

position()

void Volume::position ( float xyz[3], const plm_long ijk[3] )

inline

Return a world coordinates of a voxel.

scale_inplace()

void Volume::scale_inplace

(

float

scale

)

In-place (destructive) scaling of the image according to the supplied scale factor.

set_direction_cosines()

void Volume::set_direction_cosines

(

const float

direction_cosines[9]

)

Set the direction cosines.
Direction cosines hold the orientation of a volume. They are defined as the unit length direction vectors of the volume in world space as one traverses the pixels in the raw array of values.

set_header() [1/2]

void Volume::set_header

(

const Plm_image_header *

pih

)

set_header() [2/2]

void Volume::set_header

(

const Volume_header &

vh

)

Set the image header. This routine doesn't change any of the pixel values. It just changes the image geometry.

set_origin()

void Volume::set_origin

(

const float

origin[3]

)

Set the origin. The origin is defined as the location in world coordinates of the center of the first voxel in the volume.

set_spacing()

void Volume::set_spacing

(

const float

spacing[3]

)

Set the spacing. The spacing is distance between voxels.

SMART_POINTER_SUPPORT()

Volume::SMART_POINTER_SUPPORT

(

Volume

)

Member Data Documentation

dim

plm_long Volume::dim[3]

direction_cosines

Direction_cosines Volume::direction_cosines

img

void* Volume::img

npix

plm_long Volume::npix

origin

float Volume::origin[3]

pix_size

int Volume::pix_size

pix_type

enum Volume_pixel_type Volume::pix_type

proj

float Volume::proj[9]

spacing

float Volume::spacing[3]

step

float Volume::step[9]

vox_planes

int Volume::vox_planes

---

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

• src/base/volume.h
• src/base/volume.cxx