class Inrimage : public BaseInrimage, public Pointed<Inrimage>

Inrimages

Inheritance:

Public Classes

enum	WORD_TYPE different handled inrimage types WT_UNSIGNED_CHAR unsigned 8 bits WT_SIGNED_CHAR signed 8 bits WT_UNSIGNED_SHORT unsigned 16 bits WT_SIGNED_SHORT signed 16 bits WT_UNSIGNED_INT unsigned 32 bits WT_SIGNED_INT signed 32 bits WT_UNSIGNED_LONG unsigned 64 bits WT_SIGNED_LONG signed 64 bits WT_FLOAT float 32 bits WT_DOUBLE float 64 bits WT_RGB R, G, B, 8 bits each WT_RGBA R, G, B, A, 8 bits each WT_FLOAT_VECTOR Vector of 32 bit floats WT_DOUBLE_VECTOR Vector of 64 bit floats
enum	SLICE_ORIENTATION the different geometry of a slice of a volumetric image SLICE_X slice with X (column) = constant SLICE_Y slice with Y (row) = constant SLICE_Z slice with Z (plane) = constant SLICE_ALPHA slice with alpha (angle in XY) = constant
enum	GEOMETRY the different image kinds CARTESIAN standard 3D image CYLINDRICAL cylindrical geometry (Z = plane angle, Y = elevation, Z = in plane radius) SPHERICAL spherical geometry (Z = plane angle, Y = in plane angle, X = radius)
enum	CompressType Compression type for writing CT_8BITS write using 8bits/voxel CT_16BITS write using 16bits/voxel
enum	Noise noise kinds WHITE_NOISE white Gaussian noise GAUSSIAN_NOISE Gaussian noise on image US_NOISE ultrasond-like

Public Methods

Inrimage&	operator= (const Inrimage& img) throw(Inrimage::InvalidSize, Inrimage::InvalidVectorialMode, Inrimage::InvalidVoxelSize, Inrimage::NotEnoughMemory) Make *this a replica of img
virtual Inrimage*	allocate (unsigned int xdim, unsigned int ydim, unsigned int zdim, WORD_TYPE wt, unsigned int vdim = 1, VECTORIAL_MODE vm = VM_INTERLACED, float vx = 1.0, float vy = 1.0, float vz = 1.0) const throw(Inrimage::InvalidSize, Inrimage::UnknownType, Inrimage::NotEnoughMemory, InvalidVoxelSize) Creates an inrimage from its size and its type
virtual Inrimage*	allocate (const Inrimage& img) const throw(Inrimage::InvalidSize, Inrimage::InvalidVectorialMode, Inrimage::InvalidVoxelSize, Inrimage::NotEnoughMemory) Created an inrimage identical to img
virtual void	resize (unsigned int xdim, unsigned int ydim, unsigned int zdim, unsigned int vdim = 1, unsigned int wdim = 1, WORD_KIND wordKind = WK_FIXED, SIGN sign = SGN_SIGNED) throw(Inrimage::InvalidSize, Inrimage::NotEnoughMemory) Changes image size
unsigned int	ncols (void) const returns number of columns
unsigned int	nrows (void) const returns number of rows
const TclString&	getName (void) const get inrimage file name
void	setName (const TclString& _name) set inrimage file name
WORD_TYPE	getType (void) const returns inrimage type
void	setType (WORD_TYPE type, unsigned int vdim = 1, VECTORIAL_MODE vm = VM_INTERLACED, bool resize = true) set inrimage type
void***	getArray (void) const returns pointer a 3D buffer for a scalar image or interleaved vectorial image
void****	getVarray (void) const returns a 4D buffer for a vectorial non-interleaved image
unsigned int	sizeofWords (void) const returns size of image words (each vector component size)
unsigned int	sizeofVoxels (void) const returns size of each voxel (a vector is one voxel)
void	write (const char *name) throw(Inrimage::UnableToCreateFile, Inrimage::UnableToWriteHeader, Inrimage::UnableToWriteData) Writes inrimage to file whose path is given as argument
void	write (const char *name, CompressType ct) throw(UnableToCreateFile, UnableToWriteHeader, UnableToWriteData, InvalidCompressType) Writes inrimage to file whose path is given as argument
virtual void	allocate (void) throw(Inrimage::NotEnoughMemory) Allocates and fills with zero image data buffer
virtual void	free (void) frees image data buffer
bool	inside (const int x, const int y, const int z) Tests if a voxel position is within the bounds of the image
virtual void*	setData (void *data) throw(NotEnoughMemory) Set a new data buffer
virtual void	setVectorialMode (VECTORIAL_MODE vm) throw(Inrimage::InvalidVectorialMode, Inrimage::NotEnoughMemory) Changes image vectorial mode
GEOMETRY	getGeometry (void) const returns image geometry
void	setGeometry (GEOMETRY g) set image geometry
Interpolator const*	getInterpolator () const set interpolator object
Extrapolator const*	getExtrapolator () const set extrapolator object
void	setInterpolator (Interpolator* i) set interpolator object
void	setExtrapolator (Extrapolator* e) set extrapolator object
ImageGeometry*	newConverter (void) const creates an image coordinates converter for this image geometry
Voxel*	getRealVoxel (double x, double y, double z) const Return image voxel at (x,y,z), using interpolation or extrapolation as appropriate
Voxel&	getRealVoxel (double x, double y, double z, Voxel& v) const Stores voxel (x, y, z) value in v, using interpolation or extrapolation as appropriate
Voxel*	getVoxel (unsigned int x, unsigned int y, unsigned int z) const returns a Voxel representing given image voxel
Voxel&	getVoxel (unsigned int x, unsigned int y, unsigned int z, Voxel& v) const stores voxel (x, y, z) value in v
void	setVoxel (unsigned int x, unsigned int y, unsigned int z, const Voxel& v) set given image voxel with transmitted voxel value
Voxel*	checkVoxel (unsigned int x, unsigned int y, unsigned int z) const Returns a Voxel representing given image voxel
void	line (int x1, int y1, int x2, int y2, unsigned int z, const Voxel& v) draw a 2D discrete line in given image plane
virtual void	setWords (WORD_KIND wordKind = WK_FIXED, SIGN sign = SGN_SIGNED) throw(Inrimage::NotEnoughMemory) Changes image word type
bool	in (unsigned int row, unsigned int col, unsigned int plane) indicates wether voxel lies in image bounds
bool	sameSize (Inrimage const& inr) const indicates wether inr has same size than this
void	crop (unsigned int x1, unsigned int y1, unsigned int z1, unsigned int x2, unsigned int y2, unsigned int z2) throw(Inrimage::InvalidArguments) crops region between (x1, y1, z1) and (x2, y2, z2) in inrimage Crop expects x1 < x2, y1 < y2 and z1 < z2
void	isolateRegion (unsigned int x1, unsigned int y1, unsigned int z1, unsigned int x2, unsigned int y2, unsigned int z2) throw(Inrimage::InvalidArguments) put to 0 all voxels outside region between (x1, y1, z1) and (x2, y2, z2) in inrimage it expects x1 < x2, y1 < y2 and z1 < z2
void	zeroRegion (unsigned int x1, unsigned int y1, unsigned int z1, unsigned int x2, unsigned int y2, unsigned int z2) throw(Inrimage::InvalidArguments) put to 0 all voxels inside region between (x1, y1, z1) and (x2, y2, z2) in inrimage it expects x1 < x2, y1 < y2 and z1 < z2
void	getBounds (Voxel *min, Voxel *max, bool vectorNorm = true) const compute inrimage grey level bounds
void	setBounds (Voxel *min, Voxel *max, int z = -1) Set inrimage grey level bounds (rescales GL window)
static bool	vectorial (WORD_TYPE) returns true if type is WT_FLOAT_VECTOR, WT_DOUBLE_VECTOR, WT_RGB or WT_RGBA, false otherwise
static bool	floating (WORD_TYPE) returns true if type is WT_FLOAT, WT_DOUBLE, WT_FLOAT_VECTOR or WT_DOUBLE_VECTOR, false otherwise
Inrimage**	splitVectors (void) const Split a vectorial inrimage in one inrimage per component
void	setComponentsFrom (Inrimage **inrs) throw(Inrimage::InvalidSize, InvalidArguments) Set vectorial components from an array of scalar inrimages
void	flip (SLICE_ORIENTATION geom) flip an inrimage in given direction
void	switchGeometry (SLICE_ORIENTATION geom1, SLICE_ORIENTATION geom2) switch two inrimage dimensions
void	mel (const Inrimage *inr, int xdest, int ydest, int zdest, int xorg, int yorg, int zorg, unsigned int dx, unsigned int dy, unsigned int dz) throw(Inrimage::InvalidArguments) mel given inrimage with this by substituing a box from this with a box from inr
GenericHistogram*	createHistogram () const creates and return the Histogram of this image
void	noise (unsigned int x1, unsigned int y1, unsigned int z1, unsigned int x2, unsigned int y2, unsigned int z2, Noise kind, double mean, double dev) throw(Inrimage::InvalidArguments ) creates a noisy cube inside this inrimage
void	convertCast (WORD_TYPE type) converts inrimage to any type
void	convertScale (WORD_TYPE type) converts inrimage to any type, resizing grey-levels
void	eval (char *func, int nmbr, Var_list *op) throw(Inrimage::InvalidArguments) Evaluates expression in function string
static Vec3 *	createDirectionArray (int frequency = DEFAULT_SPHERE_FREQUENCY) Creates a vector array corresponding to the position of unit vector on a spherical dome of frequency "frequency"
void	underSample (unsigned int sx = 2, unsigned int sy = 2, unsigned int sz = 1) Undersamples image by an integer coefficient
void	overSample (unsigned int sx, unsigned int sy, unsigned int sz) throw(Inrimage::InvalidSize) Oversample an image
void	resample (unsigned int sx, unsigned int sy, unsigned int sz) Resamples an image to given image size
void	setRegion (int x1, int y1, int z1, int x2, int y2, int z2) set region in which operations are performed
void	getRegion (int& x1, int& y1, int& z1, int& x2, int& y2, int& z2) get region in which operations are performed
void	getWorkRegion (unsigned int& x1, unsigned int& y1, unsigned int& z1, unsigned int& x2, unsigned int& y2, unsigned int& z2) const get region [(x1,y1,z1),(x2,y2,z2)) in which operations are should be performed
void	copyRegion (Inrimage const& img) copy region from another image
bool	regionIsWholeImage () const test if region is the whole image

Public

	Exception classes class UnknownType : public Exception unknown inrimage type class InvalidArguments : public Exception invalid arguments transmitted to method class InvalidCompressType : public Exception attempt to write image in an invalid compress type class MissingCompressInfo : public Exception missing compression information in header
	Constructors Inrimage (const TclString& name, bool headerOnly = false, VECTORIAL_MODE vm = VM_INTERLACED, VECTORIAL_MODE filevm = VM_INTERLACED) throw(ImageNotFound, UnknownImageType, InvalidHeader, InvalidData, UnknownType, InvalidVoxelSize) Reads inrimage from file whose path is given as argument Inrimage (unsigned int xdim, unsigned int ydim, unsigned int zdim, unsigned int vdim = 1, unsigned int wdim = 1, WORD_KIND wordKind = WK_FIXED, SIGN sign = SGN_SIGNED, float vx = 1.0, float vy = 1.0, float vz = 1.0) throw(InvalidSize, UnknownType, NotEnoughMemory, InvalidVoxelSize) Creates an inrimage with given size and word type Inrimage (unsigned int xdim, unsigned int ydim, unsigned int zdim, void *data, unsigned int vdim = 1, unsigned int wdim = 1, WORD_KIND wordKind = WK_FIXED, SIGN sign = SGN_SIGNED, float vx = 1.0, float vy = 1.0, float vz = 1.0) throw(InvalidSize, UnknownType, InvalidVoxelSize) Creates an inrimage with given size and word type Inrimage (unsigned int xdim, unsigned int ydim, unsigned int zdim, WORD_TYPE wt, unsigned int vdim = 1, VECTORIAL_MODE vm = VM_INTERLACED, float vx = 1.0, float vy = 1.0, float vz = 1.0) throw(InvalidSize, UnknownType, NotEnoughMemory, InvalidVoxelSize) Creates an inrimage from its size and its type Inrimage (unsigned int n, Inrimage **inrs, WORD_TYPE wt = WT_FLOAT_VECTOR, VECTORIAL_MODE vm = VM_INTERLACED, float vx = 1.0, float vy = 1.0, float vz = 1.0) throw(InvalidSize, InvalidArguments, NotEnoughMemory, InvalidVoxelSize) Creates a vectorial inrimage from scalar inrimages Inrimage (const Inrimage& img) throw(InvalidSize, InvalidVectorialMode, InvalidVoxelSize, NotEnoughMemory) Creates an replica of img
	Destructor virtual ~Inrimage () deallocates image buffer

Protected Fields

TclString	name image file name
WORD_TYPE	type inrimage type
GEOMETRY	geom inrimage geometry
Interpolator const*	interpolator interpolator object used for image values at real coordinates inside the image. void**** fourD 3D array on each image voxel -> array[z][y][x] 4D array on each vector component when vectors are not interlaced -> varray[v][z][y][x]
Extrapolator const*	extrapolator extrapolator object used for image values at real coordinates outside the image.
float	region [6] region in which operations are performed, in world coordinates. not used by all operations.

Private Fields

friend class

TclInrimage buffer convertion routine

Private Methods

void	setType (void) throw(Inrimage::UnknownType) set initial image type
void	index3D (void) throw(Inrimage::NotEnoughMemory) builds 3D index (array buffer, standard inrimage)
void	index4D (void) throw(Inrimage::NotEnoughMemory) builds 4D index (varray buffer, non-interlaced vectorial inrimage)
void	buildIndex () throw(Inrimage::NotEnoughMemory) builds 3D or 4D index depending on vectorial mode
void	deleteArray (void) deletes array buffer
void	queryGeometry (void) set image geometry field looking at inrimage header tags
void	convertFromRGBToRGBABuffer (void) buffer convertion routine
void	convertFromRGBAToRGBBuffer (void) buffer convertion routine

Inherited from BaseInrimage:

Public Methods

unsigned int getX() const

unsigned int getY() const

unsigned int getZ() const

void setX(const unsigned int x)

void setY(const unsigned int y)

void setZ(const unsigned int z)

void setVdim(const unsigned int v)

unsigned int getVdim(void) const

unsigned int getWdim(void) const

float getVX() const

float getVY() const

float getVZ() const

void* getData() const

unsigned int getWordSize() const

WORD_KIND getWordKind() const

SIGN getWordSign() const

VECTORIAL_MODE getVectorialMode() const

IMAGE_FORMAT getFileFormat(void) const

void setFileFormat(IMAGE_FORMAT f)

void setVoxelSize(float vx, float vy, float vz) throw(InvalidVoxelSize)

virtual void setInterlacedData(void)

virtual void setNonInterlacedData(void)

void setUserParams(unsigned int n, char **params)

static BaseInrimage* _image2BaseInrimage(const _image& img) throw(BaseInrimage::InvalidSize, BaseInrimage::InvalidVoxelSize, BaseInrimage::InvalidVectorialMode)

static _image* BaseInrimage2_image(const BaseInrimage& bimg)

bool userField(const char *name, char *val, unsigned int n) const

bool updateUserField(const char *name, const char *val) const

void addUserField(const char *name, const char *val)

bool removeUserField(const char *name)

template void rescaleBuffer(FROM, TO, double fmin, double fmax, double tmin, double tmax, double offset, BaseInrimage& img)

Public

Destructors

virtual ~BaseInrimage()

frees image buffer

Protected Fields

unsigned int xdim

unsigned int ydim

unsigned int zdim

unsigned int vdim

float vx

float vy

float vz

void* data

unsigned int wdim

WORD_KIND wordKind

SIGN sign

VECTORIAL_MODE vectMode

char** user

unsigned int nuser

IMAGE_FORMAT imageFormat

ImageInformation* info

Private Methods

_image* readHeader(const char *name) throw(ImageNotFound, InvalidHeader, UnknownImageType)

Exception classes

class UnknownType: public Exception

unknown inrimage type

class InvalidArguments: public Exception

invalid arguments transmitted to method

class InvalidCompressType: public Exception

attempt to write image in an invalid compress type

class MissingCompressInfo: public Exception

missing compression information in header

enum WORD_TYPE

different handled inrimage types

WT_UNSIGNED_CHAR

unsigned 8 bits

WT_SIGNED_CHAR

signed 8 bits

WT_UNSIGNED_SHORT

unsigned 16 bits

WT_SIGNED_SHORT

signed 16 bits

WT_UNSIGNED_INT

unsigned 32 bits

WT_SIGNED_INT

signed 32 bits

WT_UNSIGNED_LONG

unsigned 64 bits

WT_SIGNED_LONG

signed 64 bits

WT_FLOAT

float 32 bits

WT_DOUBLE

float 64 bits

WT_RGB

R, G, B, 8 bits each

WT_RGBA

R, G, B, A, 8 bits each

WT_FLOAT_VECTOR

Vector of 32 bit floats

WT_DOUBLE_VECTOR

Vector of 64 bit floats

enum SLICE_ORIENTATION

the different geometry of a slice of a volumetric image

SLICE_X

slice with X (column) = constant

SLICE_Y

slice with Y (row) = constant

SLICE_Z

slice with Z (plane) = constant

SLICE_ALPHA

slice with alpha (angle in XY) = constant

enum GEOMETRY

the different image kinds

CARTESIAN

standard 3D image

CYLINDRICAL

cylindrical geometry (Z = plane angle, Y = elevation, Z = in plane radius)

SPHERICAL

spherical geometry (Z = plane angle, Y = in plane angle, X = radius)

enum CompressType

Compression type for writing

CT_8BITS

write using 8bits/voxel

CT_16BITS

write using 16bits/voxel

Constructors

Inrimage(const TclString& name, bool headerOnly = false, VECTORIAL_MODE vm = VM_INTERLACED, VECTORIAL_MODE filevm = VM_INTERLACED) throw(ImageNotFound, UnknownImageType, InvalidHeader, InvalidData, UnknownType, InvalidVoxelSize)

Reads inrimage from file whose path is given as argument. File can be an INRIMAGE(4) gzipped or not, an anlayse, a GIF or a RGB irix file. If image has a vectorial type, it can be read interlaced (default) or non interlaced by giving WM_NON_INTERLACED as third argument.

Throws:

ImageNotFound image file not found
UnknownImageType unknown image file format
InvalidHeader invalid inrimage header encountered
InvalidData invalid inrimage data encountered @excpetion UnknownType unsupported inrimage type

Parameters:

name - image file name
false - if true, only image header is read (data is set to 0)
vm - vectorial mode interleave
filevm - read file vectorial mode interleave

Inrimage(unsigned int xdim, unsigned int ydim, unsigned int zdim, unsigned int vdim = 1, unsigned int wdim = 1, WORD_KIND wordKind = WK_FIXED, SIGN sign = SGN_SIGNED, float vx = 1.0, float vy = 1.0, float vz = 1.0) throw(InvalidSize, UnknownType, NotEnoughMemory, InvalidVoxelSize)

Creates an inrimage with given size and word type. The inrimage data buffer is allocated

Throws:

InvalidSize image dimension should be > 0 @excpetion UnknownType unsupported inrimage type
NotEnoughMemory unable to allocate memory to store image
InvalidVoxelSize voxels size should be > 0.0

Parameters:

xdim - image number of columns
ydim - image number of rows
zdim - image number of planes
vdim - image vectorial dimension
wdim - image word size in bytes
wordKind - image word kind
sign - image word sign
vx - distance between voxels in the X direction
vy - distance between voxels in the Y direction
vz - distance between voxels in the Z direction

Inrimage(unsigned int xdim, unsigned int ydim, unsigned int zdim, void *data, unsigned int vdim = 1, unsigned int wdim = 1, WORD_KIND wordKind = WK_FIXED, SIGN sign = SGN_SIGNED, float vx = 1.0, float vy = 1.0, float vz = 1.0) throw(InvalidSize, UnknownType, InvalidVoxelSize)

Creates an inrimage with given size and word type. If data is 0, the image is not allocated. If data is non 0, image data points to it.

Throws:

InvalidSize image dimension should be > 0 @excpetion UnknownType unsupported inrimage type
InvalidVoxelSize voxels size should be > 0.0

Parameters:

xdim - image number of columns
ydim - image number of rows
zdim - image number of planes
data - image data buffer
vdim - image vectorial dimension
wdim - image word size in bytes
wordKind - image word kind
sign - image word sign
vx - distance between voxels in the X direction
vy - distance between voxels in the Y direction
vz - distance between voxels in the Z direction

Inrimage(unsigned int xdim, unsigned int ydim, unsigned int zdim, WORD_TYPE wt, unsigned int vdim = 1, VECTORIAL_MODE vm = VM_INTERLACED, float vx = 1.0, float vy = 1.0, float vz = 1.0) throw(InvalidSize, UnknownType, NotEnoughMemory, InvalidVoxelSize)

Creates an inrimage from its size and its type

Throws:

InvalidSize image dimension should be > 0 @excpetion UnknownType unsupported inrimage type
NotEnoughMemory unable to allocate image buffer
InvalidVoxelSize voxels size should be > 0.0

Parameters:

xdim - image number of columns
ydim - image number of rows
zdim - image number of planes
wt - inrimage word type
vdim - vectorial dimension (for WT_FLOAT_VECTOR and WT_DOUBLE_VECTOR only, ignored otherwise)
vectorial - mode (for WT_FLOAT_VECTOR and WT_DOUBLE_VECTOR only, ignored otherwise)
vx - distance between voxels in the X direction
vy - distance between voxels in the Y direction
vz - distance between voxels in the Z direction

Inrimage(unsigned int n, Inrimage **inrs, WORD_TYPE wt = WT_FLOAT_VECTOR, VECTORIAL_MODE vm = VM_INTERLACED, float vx = 1.0, float vy = 1.0, float vz = 1.0) throw(InvalidSize, InvalidArguments, NotEnoughMemory, InvalidVoxelSize)

Creates a vectorial inrimage from scalar inrimages

Throws:

InvalidSize image dimension should be > 0 @excpetion InvalidArguments there should be at least one image and wt should be WT_FLOAT_VECTOR or WT_DOUBLE_VECTOR
NotEnoughMemory unable to allocate image buffer
InvalidVoxelSize voxels size should be > 0.0

Parameters:

n - number of inrimages
inrs - inrimages array
wt - type (only WT_FLOAT_VECTOR and WT_DOUBLE_VECTOR)
vm - vectorial mode
vx - distance between voxels in the X direction
vy - distance between voxels in the Y direction
vz - distance between voxels in the Z direction

Inrimage(const Inrimage& img) throw(InvalidSize, InvalidVectorialMode, InvalidVoxelSize, NotEnoughMemory)

Creates an replica of img

Throws:

InvalidSize image dimension should be > 0
InvalidVectorialMode img has scalar vectorial mode for vectorial image or opposite
InvalidVoxelSize img has <= 0 voxel size
NotEnoughMemory unable to allocate image buffer

Parameters:

img - image to copy

Destructor

virtual ~Inrimage()

deallocates image buffer

Inrimage& operator=(const Inrimage& img) throw(Inrimage::InvalidSize, Inrimage::InvalidVectorialMode, Inrimage::InvalidVoxelSize, Inrimage::NotEnoughMemory)

Make *this a replica of img

Throws:

InvalidSize image dimension should be > 0
InvalidVectorialMode img has scalar vectorial mode for vectorial image or opposite
InvalidVoxelSize img has <= 0 voxel size
NotEnoughMemory unable to allocate image buffer

Parameters:

img - image to copy

virtual Inrimage* allocate(unsigned int xdim, unsigned int ydim, unsigned int zdim, WORD_TYPE wt, unsigned int vdim = 1, VECTORIAL_MODE vm = VM_INTERLACED, float vx = 1.0, float vy = 1.0, float vz = 1.0) const throw(Inrimage::InvalidSize, Inrimage::UnknownType, Inrimage::NotEnoughMemory, InvalidVoxelSize)

Creates an inrimage from its size and its type

Throws:

InvalidSize image dimension should be > 0 @excpetion UnknownType unsupported inrimage type
NotEnoughMemory unable to allocate image buffer
InvalidVoxelSize voxels size should be > 0.0

Parameters:

xdim - image number of columns
ydim - image number of rows
zdim - image number of planes
wt - inrimage word type
vdim - vectorial dimension (for WT_FLOAT_VECTOR and WT_DOUBLE_VECTOR only, ignored otherwise)
vectorial - mode (for WT_FLOAT_VECTOR and WT_DOUBLE_VECTOR only, ignored otherwise)
vx - distance between voxels in the X direction
vy - distance between voxels in the Y direction
vz - distance between voxels in the Z direction

virtual Inrimage* allocate(const Inrimage& img) const throw(Inrimage::InvalidSize, Inrimage::InvalidVectorialMode, Inrimage::InvalidVoxelSize, Inrimage::NotEnoughMemory)

Created an inrimage identical to img

Throws:

InvalidSize image dimension should be > 0
InvalidVectorialMode img has scalar vectorial mode for vectorial image or opposite
InvalidVoxelSize img has <= 0 voxel size
NotEnoughMemory unable to allocate image buffer

Parameters:

img - image to copy

virtual void resize(unsigned int xdim, unsigned int ydim, unsigned int zdim, unsigned int vdim = 1, unsigned int wdim = 1, WORD_KIND wordKind = WK_FIXED, SIGN sign = SGN_SIGNED) throw(Inrimage::InvalidSize, Inrimage::NotEnoughMemory)

Changes image size. If image data buffer existed it is fried and reallocated.

Throws:

InvalidSize image dimension should be > 0
NotEnoughMemory unable to allocate image buffer

Parameters:

xdim - image number of columns
ydim - image number of rows
zdim - image number of planes
vdim - image vectorial dimension
wdim - image word size in bytes

unsigned int ncols(void) const

returns number of columns

unsigned int nrows(void) const

returns number of rows

const TclString& getName(void) const

get inrimage file name

void setName(const TclString& _name)

set inrimage file name

Parameters:

_name - new file name

WORD_TYPE getType(void) const

returns inrimage type

void setType(WORD_TYPE type, unsigned int vdim = 1, VECTORIAL_MODE vm = VM_INTERLACED, bool resize = true)

set inrimage type

Parameters:

type - new image type
vdim - vectorial dimension (for WT_FLOAT_VECTOR and WT_DOUBLE_VECTOR types only)
resize - whether image should be resized (and buffer reallocated to new image size)

void*** getArray(void) const

returns pointer a 3D buffer for a scalar image or interleaved vectorial image

void**** getVarray(void) const

returns a 4D buffer for a vectorial non-interleaved image

unsigned int sizeofWords(void) const

returns size of image words (each vector component size)

unsigned int sizeofVoxels(void) const

returns size of each voxel (a vector is one voxel)

void write(const char *name) throw(Inrimage::UnableToCreateFile, Inrimage::UnableToWriteHeader, Inrimage::UnableToWriteData)

Writes inrimage to file whose path is given as argument. If file name ends with '.gz' suffix, file is gzipped.

Throws:

UnableToCreateFile file creation failed for writting
UnableToWriteHeader write error encountered while writting header
UnableToWriteData write error encountered while writting data

Parameters:

name - inrimage file name

void write(const char *name, CompressType ct) throw(UnableToCreateFile, UnableToWriteHeader, UnableToWriteData, InvalidCompressType)

Writes inrimage to file whose path is given as argument. If file name ends with '.gz' suffix, file is gzipped.

Throws:

UnableToCreateFile file creation failed for writting
UnableToWriteHeader write error encountered while writting header
UnableToWriteData write error encountered while writting data

Parameters:

name - inrimage file name
ct - number of bits to convert image to before writing.

virtual void allocate(void) throw(Inrimage::NotEnoughMemory)

Allocates and fills with zero image data buffer. If data is not null, buffer is first fried.

Throws:

NotEnoughMemory unable to allocate image buffer

virtual void free(void)

frees image data buffer

bool inside(const int x, const int y, const int z)

Tests if a voxel position is within the bounds of the image

Returns:

true is the voxel is inside the image and false otherwise

Parameters:

x - the x coordinate of the voxel position
y - the y coordinate of the voxel position
z - the z coordinate of the voxel position

virtual void* setData(void *data) throw(NotEnoughMemory)

Set a new data buffer. If image data is not 0, it is first fried. Use setVectorialMode(VECTORIAL_MODE vm) if vectMode has changed

Throws:

NotEnoughMemory unable to allocate image buffer

Returns:

old image data buffer

Parameters:

data - new image data buffer

virtual void setVectorialMode(VECTORIAL_MODE vm) throw(Inrimage::InvalidVectorialMode, Inrimage::NotEnoughMemory)

Changes image vectorial mode. A vectorial image buffer can be stored either interlaced (default) or non interlaced.

Throws:

InvalidVectorialMode attempt to set a scalar mode to a vectorial image or opposite
NotEnoughMemory unable to allocate temporary buffer to swap vectors

Parameters:

vm - new vectorial mode

GEOMETRY getGeometry(void) const

returns image geometry

void setGeometry(GEOMETRY g)

set image geometry

Interpolator const* getInterpolator() const

set interpolator object

Returns:

old interpolator object

Parameters:

i - new interpolator object

Extrapolator const* getExtrapolator() const

set extrapolator object

Returns:

old extrapolator object

Parameters:

e - new extrapolator object

void setInterpolator(Interpolator* i)

set interpolator object

Returns:

old interpolator object

Parameters:

i - new interpolator object

void setExtrapolator(Extrapolator* e)

set extrapolator object

Returns:

old extrapolator object

Parameters:

e - new extrapolator object

ImageGeometry* newConverter(void) const

creates an image coordinates converter for this image geometry

Returns:

image coordinates converter

Voxel* getRealVoxel(double x, double y, double z) const

Return image voxel at (x,y,z), using interpolation or extrapolation as appropriate

Returns:

s Voxel representing given image voxel

Parameters:

x - X voxel coordinate
y - Y voxel coordinate
z - Z voxel coordinate

Voxel& getRealVoxel(double x, double y, double z, Voxel& v) const

Stores voxel (x, y, z) value in v, using interpolation or extrapolation as appropriate

Parameters:

x - X voxel coordinate
y - Y voxel coordinate
z - Z voxel coordinate
v - voxel to store value

Voxel* getVoxel(unsigned int x, unsigned int y, unsigned int z) const

returns a Voxel representing given image voxel

Parameters:

x - X voxel coordinate
y - Y voxel coordinate
z - Z voxel coordinate

Voxel& getVoxel(unsigned int x, unsigned int y, unsigned int z, Voxel& v) const

stores voxel (x, y, z) value in v

Parameters:

x - X voxel coordinate
y - Y voxel coordinate
z - Z voxel coordinate
v - voxel to store value

void setVoxel(unsigned int x, unsigned int y, unsigned int z, const Voxel& v)

set given image voxel with transmitted voxel value

Parameters:

x - X voxel coordinate
y - Y voxel coordinate
z - Z voxel coordinate
v - voxel value

Voxel* checkVoxel(unsigned int x, unsigned int y, unsigned int z) const

Returns a Voxel representing given image voxel. Check that given coordinates do not exceed image size.

Parameters:

x - X voxel coordinate
y - Y voxel coordinate
z - Z voxel coordinate

void line(int x1, int y1, int x2, int y2, unsigned int z, const Voxel& v)

draw a 2D discrete line in given image plane

Parameters:

x1 - first pixel X coordinate
y1 - first pixel Y coordinate
x2 - last pixel X coordinate
y2 - last pixel Y coordinate
z - image plane
v - line voxels value

virtual void setWords(WORD_KIND wordKind = WK_FIXED, SIGN sign = SGN_SIGNED) throw(Inrimage::NotEnoughMemory)

Changes image word type. If image data buffer existed it is fried and reallocated.

Throws:

NotEnoughMemory unable to allocate image buffer

Parameters:

wordKind - image word kind
sign - image word sign

bool in(unsigned int row, unsigned int col, unsigned int plane)

indicates wether voxel lies in image bounds

Parameters:

row - voxel row (Y)
col - voxel column (X)
plane - voxel plane (Z)

bool sameSize(Inrimage const& inr) const

indicates wether inr has same size than this

Parameters:

inr - image to compare

void crop(unsigned int x1, unsigned int y1, unsigned int z1, unsigned int x2, unsigned int y2, unsigned int z2) throw(Inrimage::InvalidArguments)

crops region between (x1, y1, z1) and (x2, y2, z2) in inrimage Crop expects x1 < x2, y1 < y2 and z1 < z2

Throws:

InvalidArgument x1 >= x2 or y1 >= y2 or z1 >= z2 or x2 >= xdim or y2 >= ydim or z2 >= zdim

Parameters:

x1 - first crop box corner X coordinate
y1 - first crop box corner Y coordinate
z1 - first crop box corner Z coordinate
x2 - second crop box corner X coordinate (x1 should be < x2)
y2 - secont crop box corner Y coordinate (y1 should be < y2)
z2 - second crop box corner Z coordinate (z1 should be < z2)

void isolateRegion(unsigned int x1, unsigned int y1, unsigned int z1, unsigned int x2, unsigned int y2, unsigned int z2) throw(Inrimage::InvalidArguments)

put to 0 all voxels outside region between (x1, y1, z1) and (x2, y2, z2) in inrimage it expects x1 < x2, y1 < y2 and z1 < z2

Throws:

InvalidArgument x1 >= x2 or y1 >= y2 or z1 >= z2 or x2 >= xdim or y2 >= ydim or z2 >= zdim

Parameters:

x1 - first crop box corner X coordinate
y1 - first crop box corner Y coordinate
z1 - first crop box corner Z coordinate
x2 - second crop box corner X coordinate (x1 should be < x2)
y2 - secont crop box corner Y coordinate (y1 should be < y2)
z2 - second crop box corner Z coordinate (z1 should be < z2)

void zeroRegion(unsigned int x1, unsigned int y1, unsigned int z1, unsigned int x2, unsigned int y2, unsigned int z2) throw(Inrimage::InvalidArguments)

put to 0 all voxels inside region between (x1, y1, z1) and (x2, y2, z2) in inrimage it expects x1 < x2, y1 < y2 and z1 < z2

Throws:

InvalidArgument x1 >= x2 or y1 >= y2 or z1 >= z2 or x2 >= xdim or y2 >= ydim or z2 >= zdim

Parameters:

x1 - first crop box corner X coordinate
y1 - first crop box corner Y coordinate
z1 - first crop box corner Z coordinate
x2 - second crop box corner X coordinate (x1 should be < x2)
y2 - secont crop box corner Y coordinate (y1 should be < y2)
z2 - second crop box corner Z coordinate (z1 should be < z2)

void getBounds(Voxel *min, Voxel *max, bool vectorNorm = true) const

compute inrimage grey level bounds

Parameters:

min - min GL voxel value (min should have been allocated with inrimage dynamic type)
max - max GL voxel value (max should have been allocated with inrimage dynamic type)
vectorNorm - if true, this method returns min and max vector norm for vectorial inrimages, otherwise it returns min and max vector component

void setBounds(Voxel *min, Voxel *max, int z = -1)

Set inrimage grey level bounds (rescales GL window). If z is >= 0, only one slice is set, otherwise the wall image buffer is set.

Parameters:

min - min GL value (min should have been allocated with inrimage dynamic type)
max - max GL value (max should have been allocated with inrimage dynamic type)
z - (if >= 0) slice number to modify

static bool vectorial(WORD_TYPE)

returns true if type is WT_FLOAT_VECTOR, WT_DOUBLE_VECTOR, WT_RGB or WT_RGBA, false otherwise

static bool floating(WORD_TYPE)

returns true if type is WT_FLOAT, WT_DOUBLE, WT_FLOAT_VECTOR or WT_DOUBLE_VECTOR, false otherwise

Inrimage** splitVectors(void) const

Split a vectorial inrimage in one inrimage per component. The inrimage array returned is a WT_FLOAT inrimages array if input image is WT_FLOAT_VECTOR, a WT_DOUBLE inrimages array if input is WT_DOUBLE_VECTOR, and WT_UNSIGNED_CHAR if input image is WT_RGB or WT_RGBA. Non vectorial inrimages lead to a copy. Input image is not modified

Returns:

inrimage array (one inrimage per vectorial dimension

void setComponentsFrom(Inrimage **inrs) throw(Inrimage::InvalidSize, InvalidArguments)

Set vectorial components from an array of scalar inrimages

Throws:

InvalidSize one of the inrimages size does not match this size
InvalidArguments one of the inrimages is vectorial

Parameters:

inrs - inrimages array (there should be one inrimage per vectorial dimension of this)

void flip(SLICE_ORIENTATION geom)

flip an inrimage in given direction

Parameters:

geom - flip axis

void switchGeometry(SLICE_ORIENTATION geom1, SLICE_ORIENTATION geom2)

switch two inrimage dimensions

Parameters:

geom1 - first dimension to switch
geom2 - second dimension to switch

void mel(const Inrimage *inr, int xdest, int ydest, int zdest, int xorg, int yorg, int zorg, unsigned int dx, unsigned int dy, unsigned int dz) throw(Inrimage::InvalidArguments)

mel given inrimage with this by substituing a box from this with a box from inr

Throws:

InvalidArguments inr type does not match this type or xorg > inr->xdim or yorg > inr->ydim or zorg > inr->zdim or xdest > xdim or ydest > ydim or zdest > zdim

Parameters:

inr - inrimage to mel with this
xdest - X coordinate of destination box
ydest - Y coordinate of destination box
zdest - Z coordinate of destination box
xorg - X coordinate of source box
yorg - Y coordinate of source box
zorg - Z coordinate of source box
dx - X size of box to mel
dy - Y size of box to mel
dz - Z size of box to mel

GenericHistogram* createHistogram() const

creates and return the Histogram of this image

enum Noise

noise kinds

WHITE_NOISE

white Gaussian noise

GAUSSIAN_NOISE

Gaussian noise on image

US_NOISE

ultrasond-like

void noise(unsigned int x1, unsigned int y1, unsigned int z1, unsigned int x2, unsigned int y2, unsigned int z2, Noise kind, double mean, double dev) throw(Inrimage::InvalidArguments )

creates a noisy cube inside this inrimage

Throws:

InvalidArguments given box exceeds image size

Parameters:

x1 - first noisy box corner X coordinate
y1 - first noisy box corner Y coordinate
z1 - first noisy box corner Z coordinate
x2 - second noisy box corner X coordinate
y2 - second noisy box corner Y coordinate
z2 - second noisy box corner Z coordinate
kind - noise kind
mean - noise value (if fromImage == false)
dev - mean dev value

void convertCast(WORD_TYPE type)

converts inrimage to any type

Parameters:

type - new inrimage type

void convertScale(WORD_TYPE type)

converts inrimage to any type, resizing grey-levels

Parameters:

type - new inrimage type

void eval(char *func, int nmbr, Var_list *op) throw(Inrimage::InvalidArguments)

Evaluates expression in function string. Supports the following arithmetic operators in the following order: ^(power),/(division) or *(multiplication) and +(addition) or -(subtraction) Operators with the same priority are processed from left to right. All other operators have lowest priority and therefor processed from left to right as well. Special operators: |<(minimum), |>(maximum) Logical Operators(returns 1=true,0=false): <=(Smaller or equal), >=(Larger or equal), ==(equal), >(larger), <(smaller), &&(and), ||(or). Standard functions (angles are in radians): abs(), exp(), ceil()(rounds upwards), floor()(rounds downwards), log(), sqrt(), sin(), cos(), tan(), asin(), acos(), atan(), sinh(), cosh(), tanh(). Global functions (returns a scalar and calculates value based on the expression given as input to the function)): mean, min(minimum value), max(maximum value), m ed(median), std(estimated standard deviation), var(estimated variance). Variables: x,y,z (pixel positions), inrX(X can be any number of a valid image). Examples: inr3 -eval inr1|

static Vec3 * createDirectionArray(int frequency = DEFAULT_SPHERE_FREQUENCY)

void underSample(unsigned int sx = 2, unsigned int sy = 2, unsigned int sz = 1)

void overSample(unsigned int sx, unsigned int sy, unsigned int sz) throw(Inrimage::InvalidSize)

void resample(unsigned int sx, unsigned int sy, unsigned int sz)

void setRegion(int x1, int y1, int z1, int x2, int y2, int z2)

void getRegion(int& x1, int& y1, int& z1, int& x2, int& y2, int& z2)

void getWorkRegion(unsigned int& x1, unsigned int& y1, unsigned int& z1, unsigned int& x2, unsigned int& y2, unsigned int& z2) const

void copyRegion(Inrimage const& img)

bool regionIsWholeImage() const

TclString name

WORD_TYPE type

GEOMETRY geom

Interpolator const* interpolator

Extrapolator const* extrapolator

float region[6]

void setType(void) throw(Inrimage::UnknownType)

void index3D(void) throw(Inrimage::NotEnoughMemory)

void index4D(void) throw(Inrimage::NotEnoughMemory)

void buildIndex() throw(Inrimage::NotEnoughMemory)

void deleteArray(void)

void queryGeometry(void)

void convertFromRGBToRGBABuffer(void)

void convertFromRGBAToRGBBuffer(void)

friend class TclInrimage

buffer convertion routine

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This class has no child classes.

alphabetic index hierarchy of classes

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