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i3d::Image3d< VOXEL > Class Template Reference

The main template class which stores and manipulates the image data. More...

#include <image3d.h>

Inheritance diagram for i3d::Image3d< VOXEL >:

List of all members.

Public Member Functions
void	CopyFromVOI (const Image3d< VOXEL > &src, const VOI< size_t > &voi)
	function called by copy constructors
	Image3d (const Offset *off_=0, const Resolution *res_=0)
	Image3d (const char *fname, VOI< size_t > *voi=0, bool is_regex=false, int channel=-1, const Offset *off_=0, const Resolution *res_=0)
void	ReadImage (const char *fname, VOI< size_t > *voi=0, bool is_regex=false, int channel=-1, const Offset *off_=0, const Resolution *res_=0)
void	SaveImage (const char *fname, FileFormat ft=IMG_UNKNOWN, bool comp=true) const
	Image3d (const Image3d &, const VOI< size_t > *voi=0)
	Image3d (const Image3d &, const VOI< float > &voi)
virtual	~Image3d ()
Image3d &	operator= (const Image3d &)
VOXEL	GetVoxel (size_t x, size_t y, size_t z) const
VOXEL	GetVoxel (const Vector3d< size_t > &v) const
VOXEL	GetVoxel (size_t i) const
void	SetVoxel (size_t i, VOXEL voxel)
void	SetVoxel (size_t x, size_t y, size_t z, VOXEL voxel)
void	SetVoxel (const Vector3d< size_t > &v, VOXEL voxel)
VOXEL *	GetVoxelAddr (size_t x, size_t y, size_t z)
const VOXEL *	GetVoxelAddr (size_t x, size_t y, size_t z) const
VOXEL *	GetVoxelAddr (size_t i)
const VOXEL *	GetVoxelAddr (size_t i) const
VOXEL *	GetFirstVoxelAddr ()
VOXEL *	begin ()
VOXEL *	end ()
const VOXEL *	begin () const
const VOXEL *	end () const
const VOXEL *	GetFirstVoxelAddr () const
bool	IsEmpty () const
std::valarray< VOXEL > &	GetVoxelData ()
size_t	GetImageSize (void) const
	Get the number of voxels in image.
size_t	GetSliceSize (void) const
	Get the number of voxels per one slice.
size_t	GetWidth (void) const
	Get the width (horizontal axis) of the image.
size_t	GetHeight (void) const
	Get the height (vertical axis) of the image.
size_t	GetNumSlices (void) const
	Get number of slices per image.
size_t	GetSizeX (void) const
	Get the width (horizontal axis) of the image.
size_t	GetSizeY (void) const
	Get the height (vertical axis) of the image.
size_t	GetSizeZ (void) const
	Get number of slices per image.
size_t	GetX (size_t i) const
	Get the x-coordinate of the i-th voxel in the image data block.
size_t	GetY (size_t i) const
	Get the y-coordinate of the i-th voxel in the image data block.
size_t	GetZ (size_t i) const
	Get the z-coordinate of the i-th voxel in the image data block.
size_t	GetIndex (size_t x, size_t y, size_t z) const
Coords	GetCoords (size_t i) const
	get the coords from the position in the image buffer vector
bool	OnBorder (const Vector3d< size_t > v) const
	Is (x,y,z) on the border of the image?
bool	Include (int x, int y, int z) const
	Is the voxel [x,y,z] in this image?
bool	Include (Vector3d< int > v) const
	Is the voxel 'v' in this image?
void	GetRange (VOXEL &min, VOXEL &max)
	Returns minimal and maximal value in the Image. Returns minimum and maximum in red green and blue, if the image is RGB or RGB16.
VOI< float >	GetVOI (void) const
	Get this image 'voi'.
Offset	GetOffset () const
	Get the offset of this image.
Resolution	GetResolution () const
	Get the resolution of this image.
Vector3d< size_t >	GetSize () const
	Get the dimensions of the image.
void	SetOffset (const Offset &off_)
	Set the offset for this image.
void	SetResolution (const Resolution &res_)
	Set the resolution for this image.
HistDesc	GetOrigHisto () const
	return original intensity histogram of the image
void	SetOrigHisto (const HistDesc &h)
	set new intensity histogram for current image
void	ComputeHistDesc (byte histo_smooth=std_histo_smooth, float thres_factor=std_thres_factor)
void	DisposeData ()
void	MakeRoom (size_t width, size_t height, size_t slices)
void	MakeRoom (const Vector3d< size_t > &sz)
bool	TestConsistency (ImgVoxelType itype) const
ImgVoxelType	ConsistentVoxelType () const
Protected Attributes
Offset	offset
	position of the image in absolute coordinates in micrometers
Vector3d< size_t >	size
	size of the image (width x height x slices) in pixels
Resolution	resolution
	image resolution in pixels per micrometer
unsigned long	capacity
	size of memory allocated for data, in VOXELs
std::valarray< VOXEL >	data
	image data buffer
HistDesc	origHisto
	histogram of the original acquired image

---

Detailed Description

template<class VOXEL>
class i3d::Image3d< VOXEL >

The main template class which stores and manipulates the image data.

---

Constructor & Destructor Documentation

template<class VOXEL>

i3d::Image3d< VOXEL >::Image3d	(	const Offset *	off_ = 0,
		const Resolution *	res_ = 0
	)			[inline, explicit]

Empty image:

template<class T>

i3d::Image3d< T >::Image3d	(	const char *	fname,
		VOI< size_t > *	voi = 0,
		bool	is_regex = false,
		int	channel = -1,
		const Offset *	off_ = 0,
		const Resolution *	res_ = 0
	)

Read image from a specified file and constructs the Image3d object

parameters:

• voi ... if you want to read only specific rectangular par of the image
• 'is_regex' says, whether the input 'fname' is regular filename or can be expected as a mask for regular expansion.
• 'channel' chooses the channel order which is going to be read. If default value (-1) is chosen, all the channels are read. For the time being, only ICS format supports this parameter.
• offset and resolution set the image layout in the real scene. Both of them are optional: if not set, the values stored in the image data file is used (implicitly), otherwise the argument values are used (explicitly).

template<class VOXEL>

i3d::Image3d< VOXEL >::Image3d	(	const Image3d< VOXEL > &	,
		const VOI< size_t > *	voi = 0
	)

Copy constructor: copy of VOI, if VOI == 0, whole image is copied VOI is in pixels and is relative to origin of image offset is recomputed apropriately, if resolution is not defined offset is simply added (i.e. it's supposed 1 pixel = 1 micron)

template<class VOXEL>

i3d::Image3d< VOXEL >::Image3d	(	const Image3d< VOXEL > &	,
		const VOI< float > &	voi
	)

Copy constructor, VOI is in microns, Image in intersection of VOI and src image is returned

template<class VOXEL>

virtual i3d::Image3d< VOXEL >::~Image3d

(

)

[inline, virtual]

Destructor:

---

Member Function Documentation

template<class T>

void i3d::Image3d< T >::ReadImage	(	const char *	fname,
		VOI< size_t > *	voi = 0,
		bool	is_regex = false,
		int	channel = -1,
		const Offset *	off_ = 0,
		const Resolution *	res_ = 0
	)

Reads 3D image from specified file. Returns true on success.

parameters:

• voi ... if you want to read only specific rectangular par of the image
• 'is_regex' says, whether the input 'fname' is regular filename or can be expected as a mask for regular expansion.
• 'channel' chooses the channel order which is going to be read. If default value (-1) is chosen, all the channels are read. For the time being, only ICS format supports this parameter.
• offset and resolution set the image layout in the real scene. Both of them are optional: if not set, the values stored in the image data file is used (implicitly), otherwise the argument values are used (explicitly).

open image

read the basic image info to the predefined structures

verify if the required VOI is included in the image

fetch the image size

choose the channel to read if the default value is set (-1), then all the channels are read

test if image file is in the same colorspace as the prepared image structure

set some image characteristics, only if requested:

set the image offset (if set)

test whether the resolution is defined by the user

test whether the resolution is defined within the image format

allocate the memory

read the image data

template<class T>

void i3d::Image3d< T >::SaveImage	(	const char *	fname,
		FileFormat	ft = IMG_UNKNOWN,
		bool	comp = true
	)			const

SaveImage: Saves the image into a file(s) in specified format File format is guessed from extension of fname if ft == IMG_UNKNOWN

IOException is thrown

• if format for saving is not recognized or not supported
• if some disk problems occurred

create image writer

set the image dimensions

set the image voxel type (binary, gray8, rgb, ...)

set the image resolution (if it is even used)

set the referred image compression

set the image offset

save header info

save the data

template<class VOXEL>

Image3d& i3d::Image3d< VOXEL >::operator=

(

const Image3d< VOXEL > &

)

Asignment operator :

template<class VOXEL>

VOXEL i3d::Image3d< VOXEL >::GetVoxel	(	size_t	x,
		size_t	y,
		size_t	z
	)			const [inline]

Get a voxel value (voxels are numbered from 0):

template<class VOXEL>

VOXEL i3d::Image3d< VOXEL >::GetVoxel

(

const Vector3d< size_t > &

v

)

const [inline]

Get a voxel value (voxels are numbered from 0)

template<class VOXEL>

VOXEL i3d::Image3d< VOXEL >::GetVoxel

(

size_t

i

)

const [inline]

Get a voxel value (voxels are numbered from 0)

template<class VOXEL>

void i3d::Image3d< VOXEL >::SetVoxel	(	size_t	i,
		VOXEL	voxel
	)			[inline]

Set a voxel to value (voxels are numbered from 0)

template<class VOXEL>

void i3d::Image3d< VOXEL >::SetVoxel	(	size_t	x,
		size_t	y,
		size_t	z,
		VOXEL	voxel
	)			[inline]

Set a voxel to value (voxels are numbered from 0)

template<class VOXEL>

void i3d::Image3d< VOXEL >::SetVoxel	(	const Vector3d< size_t > &	v,
		VOXEL	voxel
	)			[inline]

Set a voxel to value (voxels are numbered from 0)

template<class VOXEL>

VOXEL* i3d::Image3d< VOXEL >::GetVoxelAddr	(	size_t	x,
		size_t	y,
		size_t	z
	)			[inline]

Get a voxel address (voxels are numbered from 0)

template<class VOXEL>

const VOXEL* i3d::Image3d< VOXEL >::GetVoxelAddr	(	size_t	x,
		size_t	y,
		size_t	z
	)			const [inline]

Get a voxel address (voxels are numbered from 0)

template<class VOXEL>

VOXEL* i3d::Image3d< VOXEL >::GetVoxelAddr

(

size_t

i

)

[inline]

Get a voxel address (voxels are numbered from 0)

template<class VOXEL>

const VOXEL* i3d::Image3d< VOXEL >::GetVoxelAddr

(

size_t

i

)

const [inline]

Get a voxel address (voxels are numbered from 0)

template<class VOXEL>

VOXEL* i3d::Image3d< VOXEL >::GetFirstVoxelAddr

(

)

[inline]

Get the first voxel address (voxels are numbered from 0)

template<class VOXEL>

VOXEL* i3d::Image3d< VOXEL >::begin

(

)

[inline]

Synonym for GetFirstVoxelAddr()

template<class VOXEL>

VOXEL* i3d::Image3d< VOXEL >::end

(

)

[inline]

Pointer beyond the last image element

template<class VOXEL>

const VOXEL* i3d::Image3d< VOXEL >::begin

(

)

const [inline]

Synonym for const GetFirstVoxelAddr()

template<class VOXEL>

const VOXEL* i3d::Image3d< VOXEL >::end

(

)

const [inline]

Const pointer beyond the last image element

template<class VOXEL>

const VOXEL* i3d::Image3d< VOXEL >::GetFirstVoxelAddr

(

)

const [inline]

Get the first voxel address (voxels are numbered from 0)

template<class VOXEL>

bool i3d::Image3d< VOXEL >::IsEmpty

(

)

const [inline]

Is the image empty?

template<class VOXEL>

std::valarray<VOXEL>& i3d::Image3d< VOXEL >::GetVoxelData

(

)

[inline]

Returns the reference the the object 'data', which is of the std::valarray data type

template<class VOXEL>

size_t i3d::Image3d< VOXEL >::GetIndex	(	size_t	x,
		size_t	y,
		size_t	z
	)			const [inline]

Get the position of the voxel in the image data block (first position is O.

template<class T>

void i3d::Image3d< T >::ComputeHistDesc	(	byte	histo_smooth = std_histo_smooth,
		float	thres_factor = std_thres_factor
	)

Compute histogram and its descriptionn for this image and store them to origHisto. Voxel lying at the border are not considered.

template<class VOXEL>

void i3d::Image3d< VOXEL >::DisposeData

(

)

[inline]

Free memory occupied by data and set size to (0,0,0)

template<class VOXEL>

void i3d::Image3d< VOXEL >::MakeRoom	(	size_t	width,
		size_t	height,
		size_t	slices
	)			[inline]

Allocate/reallocate voxel memory and set the image size. The input are three dimensions.

template<class VOXEL>

void i3d::Image3d< VOXEL >::MakeRoom

(

const Vector3d< size_t > &

sz

)

[inline]

Allocate/reallocate voxel memory and set the image size. The input is the dimension vector.

template<class T>

bool i3d::Image3d< T >::TestConsistency

(

ImgVoxelType

itype

)

const

Test, whether Image3d<T> can, in principle, be created from a file of type itype:

template<class T>

ImgVoxelType i3d::Image3d< T >::ConsistentVoxelType

(

)

const

Return a file type consistent with the voxel type T:

---

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

• image3d.h
• image3d.cc

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