Magnetic Resonance Image class. More...

#include <NiftiHeader.hpp>

Collaboration diagram for Bial::NiftiHeader:

Public Member Functions
	NiftiHeader ()
	Basic Constructor. More...

	NiftiHeader (const Vector< size_t > &new_dim, const Vector< float > &new_pixdim, NiftiType new_datatype=NiftiType::INT8, bool one_file=true)
	Basic Constructor. More...

template<class D >
	NiftiHeader (const Image< D > &img, bool one_file=true)
	Basic Constructor. More...

	NiftiHeader (const std::string &filename)
	Basic Constructor. More...

const Vector< size_t > &	Dim () const
	Returns a reference to dimension vector. More...

size_t	Size (size_t dms) const
	Returns the size of a given image dimension. More...

void	Size (size_t dms, size_t val)
	Updates image dimension size. More...

const Vector< float > &	PixelSize () const
	Returns a reference to pixel dimension vector. More...

float	PixelSize (size_t dms) const
	Returns the pixel size of a given image dimension. More...

void	PixelSize (size_t dms, float val)
	Updates Pixel dimension size. More...

short	BitPix () const
	Returns the number of bits per pixel. More...

NiftiType	DataType () const
	Returns data type code. More...

void	Write (OFile &file, bool one_file) const
	Writes this nifti header to file. More...

void	Write (const std::string &filename) const
	Writes this nifti header to file with filename 'filename'. More...

void	DataType (NiftiType type)
	Changes header information to support data of type 'type'. More...

void	QuaternToMat (const Vector< float > &pixel_dim)
	Translates quaterns to 4x4 matrix used to convert from xyz to ijk space. More...

void	MatToQuatern ()
	Translates 4x4 matrix used to convert from xyz to ijk space to quaterns. More...

std::string	Orientation (size_t row) const
	Returned std::string can be: LR, RL, SI, IS, AP, PA, or Undefined. More...

std::string	Orientation () const
	Returned std::string will be a composition of three values containing: LR, RL, SI, IS, AP, or PA, or Undefined std::string. More...

bool	UseQuatern ()
	Returns a boolean value indicating if this MR image uses quaternion orientation form or not. More...

bool	UseAffine ()
	Returns a boolean value indicating if this MR image uses affine orientation form or not. More...

void	QuaternMatrix (const Matrix< float > mat)
	Assigns mat data to qtm. More...

Matrix< float >	QuaternMatrix () const
	returns a copy of qtm. More...

void	QuaternOffset (float x, float y, float z)
	Sets quatern offset. More...

void	AffineMatrix (const Matrix< float > mat)
	Assigns mat data to stm. More...

Matrix< float >	AffineMatrix () const
	returns a copy of stm. More...

template<class O >
O &	PrintOrientation (O &os) const
	Prints nifti orientation information to output stream 'os'. More...

template<class O >
O &	Print (O &os) const
	Prints nifti header information to output stream 'os'. More...

Static Public Member Functions
static NiftiHeader	Read (const std::string &filename)
	Returns a nifti header read from file with filename 'filename'. More...

static bool	IsNiftiFile (const std::string &filename)
	Returns true if given file has nifti extension. More...

static std::string	HeaderFileName (const std::string &filename)
	Returns nifti header file name associated to filename. More...

static std::string	DataFileName (const std::string &filename)
	Returns nifti data file name associated to filename. More...

static std::string	ExistingHeaderFileName (const std::string &filename)
	Returns existing nifti header file name associated to filename. More...

static std::string	ExistingDataFileName (const std::string &filename)
	Returns existing nifti data file name associated to filename. More...

static size_t	AxialDimension (const std::string &orientation)
	Returns the number of the image dimension that corresponds to axial direction. More...

static size_t	CoronalDimension (const std::string &orientation)
	Returns the number of the image dimension that corresponds to coronal direction. More...

static size_t	SagittalDimension (const std::string &orientation)
	Returns the number of the image dimension that corresponds to sagittal direction. More...

static bool	SuperiorInferior (const std::string &orientation)
	Returns true if axial dimension direction is superior-inferior. More...

static bool	AnteriorPosterior (const std::string &orientation)
	Returns true if coronal dimension direction is anterior-posterior. More...

static void	SwapNBytes (size_t n, int siz, void *ar)
	Swaps bytes of data pointed by ar. Used to read data written by different architectures. More...

static bool	IsSwapped (const std::string filename)
	Verifies if header nifti file corresponding to filename must swap bytes order. More...

static NiftiType	DataType (const std::string &filename)
	Returns the type of the data in given file. More...

static void	DataTypeSizes (int datatype, size_t &nbyper, size_t &swapsize)
	Computes the number of bytes of each element and the bytes to be swapped. More...

Static Public Attributes
static const short	NIFTI_HEADER_SIZE = 348

static const short	ANALYZE_EXTENT = 16384

Friends
template<class D >
class	Image

Detailed Description

Magnetic Resonance Image class.

Definition at line 248 of file NiftiHeader.hpp.

Constructor & Destructor Documentation

Bial::NiftiHeader::NiftiHeader ( )

Basic Constructor.

Date: 2013/Fev/01

Parameters

none.

Returns: none.

Warning: All nifti fields are uninitialized or undefined.

Bial::NiftiHeader::NiftiHeader	(	const Vector< size_t > &	new_dim,
		const Vector< float > &	new_pixdim,
		NiftiType	new_datatype = `NiftiType::INT8`,
		bool	one_file = `true`
	)

Basic Constructor.

Date: 2012/Aug/02

Parameters

new_dim	Vector with MR image dimensions.
new_pixel_dim	array with pixel dimensions.
new_datatype	nifti header data type.
one_file	defines weather it is a header from one or two files image.

Returns: none.

Warning: All nifti fields, except dim, pixdim, and datatype, are uninitialized.

template<class D >

Bial::NiftiHeader::NiftiHeader	(	const Image< D > &	img,
		bool	one_file = `true`
	)

Basic Constructor.

Date: 2012/Aug/20

Parameters

img	base image to extract dimensions and datatype.
one_file	defines weather it is a header from one or two files image.

Returns: none.

Warning: All nifti fields, except dim, pixdim, and datatype, are uninitialized.

Bial::NiftiHeader::NiftiHeader ( const std::string & filename )

Basic Constructor.

Date: 2013/Aug/10

Parameters

filename File name.

Returns: none.

Warning: none.

Member Function Documentation

void Bial::NiftiHeader::AffineMatrix ( const Matrix< float > mat )

Assigns mat data to stm.

Date: 2012/Aug/03

Parameters

mat	a matrix to be set to affine transformation matrix.

Returns: none.

Warning: This method will change data orientation.

Matrix< float > Bial::NiftiHeader::AffineMatrix ( ) const

returns a copy of stm.

Date: 2012/Aug/03

Parameters

none.

Returns: A copy of stm.

Warning: none.

static bool Bial::NiftiHeader::AnteriorPosterior ( const std::string & orientation )

static

Returns true if coronal dimension direction is anterior-posterior.

Date: 2014/Mar/14

Parameters

orientation Image orientation. Must be a composition of three values containing: LR, RL, SI, IS, AP, or PA. Look for NiftiHeader::Orientation() function for examples.

Returns: True if coronal dimension direction is anterior-posterior.

Warning: none.

static size_t Bial::NiftiHeader::AxialDimension ( const std::string & orientation )

static

Returns the number of the image dimension that corresponds to axial direction.

Date: 2013/Aug/27

Parameters

orientation Image orientation. Must be a composition of three values containing: LR, RL, SI, IS, AP, or PA. Look for NiftiHeader::Orientation() function for examples.

Returns: The number of the image dimension that corresponds to axial direction.

Warning: none.

short Bial::NiftiHeader::BitPix ( ) const

Returns the number of bits per pixel.

Date: 2015/Oct/30

Parameters

none.

Returns: Number of bits per pixel.

Warning: none.

static size_t Bial::NiftiHeader::CoronalDimension ( const std::string & orientation )

static

Returns the number of the image dimension that corresponds to coronal direction.

Date: 2013/Aug/27

Parameters

orientation Image orientation. Must be a composition of three values containing: LR, RL, SI, IS, AP, or PA. Look for NiftiHeader::Orientation() function for examples.

Returns: The number of the image dimension that corresponds to coronal direction.

Warning: none.

static std::string Bial::NiftiHeader::DataFileName ( const std::string & filename )

static

Returns nifti data file name associated to filename.

Date: 2013/Sep/25

Parameters

filename A nifti extension file name.

Returns: Nifti data file name associated to filename.

Warning: none.

NiftiType Bial::NiftiHeader::DataType ( ) const

Returns data type code.

Date: 2015/Oct/30

Parameters

none.

Returns: The data type code.

Warning: none.

void Bial::NiftiHeader::DataType ( NiftiType type )

Changes header information to support data of type 'type'.

Date: 2013/Aug/20

Parameters

type	data type.

Returns: none.

Warning: none.

static NiftiType Bial::NiftiHeader::DataType ( const std::string & filename )

static

Returns the type of the data in given file.

Date: 2013/Aug/20

Parameters

filename A nifti extension file name.

Returns: Type of data in given file.

Warning: none.

static void Bial::NiftiHeader::DataTypeSizes	(	int	datatype,
		size_t &	nbyper,
		size_t &	swapsize
	)

static

Computes the number of bytes of each element and the bytes to be swapped.

Date: 2012/jul/31

Parameters

datatype	type of image data.
nbyper	bytes by data element.
swapsize	size of datas that may be swapped.

Returns: none.

Warning: none.

const Vector< size_t >& Bial::NiftiHeader::Dim ( ) const

Returns a reference to dimension vector.

Date: 2015/Oct/30

Parameters

none.

Returns: Reference to dimension vector.

Warning: none.

static std::string Bial::NiftiHeader::ExistingDataFileName ( const std::string & filename )

static

Returns existing nifti data file name associated to filename.

Date: 2013/Aug/11

Parameters

filename A nifti extension file name.

Returns: Existing nifti data file name associated to filename.

Warning: none.

static std::string Bial::NiftiHeader::ExistingHeaderFileName ( const std::string & filename )

static

Returns existing nifti header file name associated to filename.

Date: 2013/Aug/11

Parameters

filename A nifti extension file name.

Returns: Existing nifti header file name associated to filename.

Warning: none.

static std::string Bial::NiftiHeader::HeaderFileName ( const std::string & filename )

static

Returns nifti header file name associated to filename.

Date: 2013/Sep/25

Parameters

filename A nifti extension file name.

Returns: Nifti header file name associated to filename.

Warning: none.

static bool Bial::NiftiHeader::IsNiftiFile ( const std::string & filename )

static

Returns true if given file has nifti extension.

Date: 2014/May/27

Parameters

filename A file name.

Returns: True if given file has nifti extension.

Warning: none.

static bool Bial::NiftiHeader::IsSwapped ( const std::string filename )

static

Verifies if header nifti file corresponding to filename must swap bytes order.

Date: 2013/Aug/21

Parameters

filename File name.

Returns: If header nifti file corresponding to filename must swap bytes order.

Warning: none.

void Bial::NiftiHeader::MatToQuatern ( )

Translates 4x4 matrix used to convert from xyz to ijk space to quaterns.

Date: 2012/Aug/03

Parameters

none.

Returns: none.

Warning: Quatern parameters must be set prior to this function call.

std::string Bial::NiftiHeader::Orientation ( size_t row ) const

Returned std::string can be: LR, RL, SI, IS, AP, PA, or Undefined.

Date: 2012/Sep/08

Parameters

row	The row of orientation.

Returns: A std::string with the orientation of the given row.

Warning: Looks for quatern form first. If it is undefined, searches in affine form.

std::string Bial::NiftiHeader::Orientation ( ) const

Returned std::string will be a composition of three values containing: LR, RL, SI, IS, AP, or PA, or Undefined std::string.

Date: 2012/Sep/08

Parameters

none.

Returns: A std::string with the orientation of the MR image.

Warning: Looks for quatern form first. If it is undefined, searches in affine form.

const Vector< float >& Bial::NiftiHeader::PixelSize ( ) const

Returns a reference to pixel dimension vector.

Date: 2015/Oct/30

Parameters

none.

Returns: Reference to pixel dimension vector.

Warning: none.

float Bial::NiftiHeader::PixelSize ( size_t dms ) const

Returns the pixel size of a given image dimension.

Date: 2016/Apr/14

Parameters

dms	The dimension of desired pixel size.

Returns: The pixel size of a given image dimension.

Warning: none.

void Bial::NiftiHeader::PixelSize	(	size_t	dms,
		float	val
	)

Updates Pixel dimension size.

Date: 2016/Apr/14

Parameters

dms	The dimension of desired size.
val	New size of the pixel dimension.

Returns: none.

Warning: none.

template<class O >

O& Bial::NiftiHeader::Print ( O & os ) const

Prints nifti header information to output stream 'os'.

Date: 2012/Aug/06

Parameters

os	An output stream.

Returns: A reference to the given output stream.

Warning: none.

template<class O >

O& Bial::NiftiHeader::PrintOrientation ( O & os ) const

Prints nifti orientation information to output stream 'os'.

Date: 2012/Aug/06

Parameters

os	An output stream.

Returns: A reference to the given output stream.

Warning: none.

void Bial::NiftiHeader::QuaternMatrix ( const Matrix< float > mat )

Assigns mat data to qtm.

Date: 2012/Aug/03

Parameters

mat	a matrix to be set to quatern matrix.

Returns: none.

Warning: This method will change data orientation.

Matrix< float > Bial::NiftiHeader::QuaternMatrix ( ) const

returns a copy of qtm.

Date: 2012/Aug/03

Parameters

none.

Returns: A copy of qtm.

Warning: none.

void Bial::NiftiHeader::QuaternOffset	(	float	x,
		float	y,
		float	z
	)

Sets quatern offset.

Date: 2012/Aug/03

Parameters

x	x quatern offset.
y	y quatern offset.
z	z quatern offset.

Returns: none.

Warning: none.

void Bial::NiftiHeader::QuaternToMat ( const Vector< float > & pixel_dim )

Translates quaterns to 4x4 matrix used to convert from xyz to ijk space.

Date: 2012/jul/31

Parameters

pixel_dim dimensions of the pixel.

Returns: none.

Warning: Quatern parameters must be set prior to this function call.

static NiftiHeader Bial::NiftiHeader::Read ( const std::string & filename )

static

Returns a nifti header read from file with filename 'filename'.

Date: 2013/Aug/20

Parameters

filename A nifti extension file name.

Returns: Nifti header object.

Warning: none.

static size_t Bial::NiftiHeader::SagittalDimension ( const std::string & orientation )

static

Returns the number of the image dimension that corresponds to sagittal direction.

Date: 2013/Aug/27

Parameters

orientation Image orientation. Must be a composition of three values containing: LR, RL, SI, IS, AP, or PA. Look for NiftiHeader::Orientation() function for examples.

Returns: The number of the image dimension that corresponds to sagittal direction.

Warning: none.

size_t Bial::NiftiHeader::Size ( size_t dms ) const

Returns the size of a given image dimension.

Date: 2016/Apr/14

Parameters

dms	The dimension of desired size.

Returns: The size of a given image dimension.

Warning: none.

void Bial::NiftiHeader::Size	(	size_t	dms,
		size_t	val
	)

Updates image dimension size.

Date: 2016/Apr/14

Parameters

dms	The dimension of desired size.
val	New size of the dimension.

Returns: none.

Warning: none.

static bool Bial::NiftiHeader::SuperiorInferior ( const std::string & orientation )

static

Returns true if axial dimension direction is superior-inferior.

Date: 2013/Aug/27

Parameters

orientation Image orientation. Must be a composition of three values containing: LR, RL, SI, IS, AP, or PA. Look for NiftiHeader::Orientation() function for examples.

Returns: True if axial dimension direction is superior-inferior.

Warning: none.

static void Bial::NiftiHeader::SwapNBytes	(	size_t	n,
		int	siz,
		void *	ar
	)

static

Swaps bytes of data pointed by ar. Used to read data written by different architectures.

Date: 2012/Jul/31

Parameters

n	number of bytes to be swapped.
siz	size of the swapped data.
ar	pointer to data.

Returns: none.

Warning: none.

bool Bial::NiftiHeader::UseAffine ( )

Returns a boolean value indicating if this MR image uses affine orientation form or not.

Date: 2012/Sep/08

Parameters

none.

Returns: Boolean value indicating if this MR image uses affine orientation form or not.

Warning: none.

bool Bial::NiftiHeader::UseQuatern ( )

Returns a boolean value indicating if this MR image uses quaternion orientation form or not.

Date: 2012/Sep/08

Parameters

none.

Returns: Boolean value indicating if this MR image uses quaternion orientation form or not.

Warning: none.

void Bial::NiftiHeader::Write	(	OFile &	file,
		bool	one_file
	)		const

Writes this nifti header to file.

Date: 2013/Aug/20

Parameters

file	Opened file for outputting.
one_file	If it is nii or hdr+img file.

Returns: none.

Warning: 'file' is not closed. This function is necessary because gzstream does not have random access.

void Bial::NiftiHeader::Write ( const std::string & filename ) const

Writes this nifti header to file with filename 'filename'.

Date: 2013/Aug/20

Parameters

filename A nifti extension file name.

Returns: none.

Warning: none.

Friends And Related Function Documentation

template<class D >

friend class Image

friend

Definition at line 250 of file NiftiHeader.hpp.

Member Data Documentation

const short Bial::NiftiHeader::ANALYZE_EXTENT = 16384

static

Definition at line 253 of file NiftiHeader.hpp.

const short Bial::NiftiHeader::NIFTI_HEADER_SIZE = 348

static

Definition at line 252 of file NiftiHeader.hpp.

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

bial/inc/NiftiHeader.hpp

Public Member Functions

Static Public Member Functions

Static Public Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation