Thin wrapper around a C-style nifti_image struct that allows C++-style destruction. More...

#include <NiftiImage.h>

Classes
struct	Block
	Inner class referring to a subset of an image. More...

class	Extension
	Inner class wrapping a NIfTI extension, a weakly-specified standard for attaching additional metadata to NIfTI-1 and NIfTI-2 images. More...

class	Xform
	Inner class representing an xform matrix, which indicates the orientation and other spatial properties of an image. More...

Public Member Functions
	NiftiImage ()
	Default constructor.

	NiftiImage (const NiftiImage &source, const bool copy=true)
	Copy constructor. More...

	NiftiImage (const Block &source)
	Initialise from a block, copying in the data. More...

	NiftiImage (nifti_image *const image, const bool copy=false)
	Initialise using an existing `nifti_image` pointer. More...

	NiftiImage (const std::vector< dim_t > &dim, const int datatype)
	Initialise from basic metadata, allocating and zeroing pixel data. More...

	NiftiImage (const std::vector< dim_t > &dim, const std::string &datatype)
	Initialise from basic metadata, allocating and zeroing pixel data. More...

	NiftiImage (const std::string &path, const bool readData=true)
	Initialise using a path string. More...

	NiftiImage (const std::string &path, const std::vector< dim_t > &volumes)
	Initialise using a path string and sequence of required volumes. More...

	NiftiImage (const SEXP object, const bool readData=true, const bool readOnly=false)
	Initialise from an R object, retrieving an existing image from an external pointer attribute if available; otherwise constructing a new one from the R object itself. More...

virtual	~NiftiImage ()
	Destructor which decrements the reference counter, and releases the wrapped pointer if the counter drops to zero.

	operator const nifti_image * () const
	Allows a `NiftiImage` object to be treated as a pointer to a `const` `nifti_image`.

	operator nifti_image * ()
	Allows a `NiftiImage` object to be treated as a pointer to a `nifti_image`.

const nifti_image *	operator-> () const
	Allows a `NiftiImage` object to be treated as a pointer to a `const` `nifti_image`.

nifti_image *	operator-> ()
	Allows a `NiftiImage` object to be treated as a pointer to a `nifti_image`.

NiftiImage &	operator= (const NiftiImage &source)
	Copy assignment operator, which copies from its argument. More...

NiftiImage &	operator= (const Block &source)
	Copy assignment operator, which allows a block to be used to replace the contents of a suitably sized image. More...

NiftiImage &	setPersistence (const bool persistent)
	Mark the image as persistent, so that it can be passed back to R. More...

bool	isNull () const
	Determine whether or not the wrapped pointer is `NULL`. More...

bool	isShared () const
	Determine whether the wrapped pointer is shared with another `NiftiImage`. More...

bool	isPersistent () const
	Determine whether or not the image is marked as persistent. More...

bool	isDataScaled () const
	Determine whether nontrivial scale and slope parameters are set. More...

int	nDims () const
	Return the number of dimensions in the image. More...

std::vector< dim_t >	dim () const
	Return the dimensions of the image. More...

std::vector< pixdim_t >	pixdim () const
	Return the dimensions of the pixels or voxels in the image. More...

NiftiImage &	drop ()
	Drop unitary dimensions. More...

const NiftiImageData	data () const
	Obtain the pixel data within the image. More...

NiftiImageData	data ()
	Obtain the pixel data within the image. More...

template<typename TargetType >
std::vector< TargetType >	getData (const bool useSlope=true) const
	Extract a vector of data from the image, casting it to any required element type. More...

NiftiImage &	changeDatatype (const int datatype, const bool useSlope=false)
	Change the datatype of the image, casting the pixel data if present. More...

NiftiImage &	changeDatatype (const std::string &datatype, const bool useSlope=false)
	Change the datatype of the image, casting the pixel data if present. More...

template<typename SourceType >
NiftiImage &	replaceData (const std::vector< SourceType > &data, const int datatype=DT_NONE)
	Replace the pixel data in the image with the contents of a vector. More...

NiftiImage &	replaceData (const NiftiImageData &data)
	Replace the pixel data in the image with the contents of a `NiftiImageData` object. More...

NiftiImage &	dropData ()
	Drop the data from the image, retaining only the metadata. More...

NiftiImage &	rescale (const std::vector< pixdim_t > &scales)
	Rescale the image, changing its image dimensions and pixel dimensions. More...

NiftiImage &	reorient (const int i, const int j, const int k)
	Reorient the image by permuting dimensions and potentially reversing some. More...

NiftiImage &	reorient (const std::string &orientation)
	Reorient the image by permuting dimensions and potentially reversing some. More...

NiftiImage &	update (const Rcpp::RObject &object)
	Update the image from an R array. More...

const Xform	xform (const bool preferQuaternion=true) const
	Obtain an xform matrix, indicating the orientation of the image. More...

const Xform	qform () const
	Access the qform matrix. More...

Xform	qform ()
	Access the qform matrix. More...

const Xform	sform () const
	Access the sform matrix. More...

Xform	sform ()
	Access the sform matrix. More...

dim_t	nBlocks () const
	Return the number of blocks in the image. More...

const Block	block (const int i) const
	Extract a block from the image. More...

Block	block (const int i)
	Extract a block from the image. More...

const Block	slice (const int i) const
	Extract a slice block from a 3D image. More...

Block	slice (const int i)
	Extract a slice block from a 3D image. More...

const Block	volume (const int i) const
	Extract a volume block from a 4D image. More...

Block	volume (const int i)
	Extract a volume block from a 4D image. More...

int	nChannels () const
	Return the number of colour channels used by the image. More...

size_t	nVoxels () const
	Return the number of voxels in the image. More...

int	nExtensions () const
	Return the number of extensions associated with the image. More...

std::list< Extension >	extensions (const int code=-1) const
	Return a list of the extensions associated with the image. More...

NiftiImage &	addExtension (const Extension &extension)
	Add an extension to the image. More...

NiftiImage &	replaceExtensions (const std::list< Extension > extensions)
	Replace all extensions with new ones. More...

NiftiImage &	dropExtensions ()
	Remove any extensions from the image. More...

std::pair< std::string, std::string >	toFile (const std::string fileName, const int datatype=DT_NONE, const int filetype=-1) const
	Write the image to a NIfTI-1 file. More...

std::pair< std::string, std::string >	toFile (const std::string fileName, const std::string &datatype, const int filetype=-1) const
	Write the image to a NIfTI-1 file. More...

Rcpp::RObject	toArray () const
	Create an R array from the image. More...

Rcpp::RObject	toPointer (const std::string label) const
	Create an internal image to pass back to R. More...

Rcpp::RObject	toArrayOrPointer (const bool internal, const std::string label) const
	A conditional method that calls either toArray or toPointer. More...

Static Public Member Functions
static int	sexpTypeToNiftiType (const int sexpType)
	Convert between R `SEXP` object type and `nifti_image` datatype codes. More...

static int	fileVersion (const std::string &path)
	Get the NIfTI format version used by the file at the specified path. More...

Protected Member Functions
void	acquire (nifti_image *const image)
	Acquire the specified pointer to a `nifti_image` `struct`, taking (possibly shared) responsibility for freeing the associated memory. More...

void	acquire (const NiftiImage &source)
	Acquire the same pointer as another `NiftiImage`, incrementing the shared reference count. More...

void	release ()
	Release the currently wrapped pointer, if it is not `NULL`, decrementing the reference count and releasing memory if there are no remaining references to the pointer.

void	copy (const nifti_image *source)
	Copy the contents of a `nifti_image` to create a new image, acquiring the new pointer. More...

void	copy (const NiftiImage &source)
	Copy the contents of another `NiftiImage` to create a new image, acquiring a new pointer. More...

void	copy (const Block &source)
	Copy the contents of a Block to create a new image, acquiring a new pointer. More...

void	initFromNiftiS4 (const Rcpp::RObject &object, const bool copyData=true)
	Initialise the object from an S4 object of class `"nifti"`. More...

void	initFromMriImage (const Rcpp::RObject &object, const bool copyData=true)
	Initialise the object from a reference object of class `"MriImage"`. More...

void	initFromList (const Rcpp::RObject &object)
	Initialise the object from an R list with named elements, which can only contain metadata. More...

void	initFromArray (const Rcpp::RObject &object, const bool copyData=true)
	Initialise the object from an R array. More...

void	initFromDims (const std::vector< dim_t > &dim, const int datatype)
	Initialise an empty object from basic metadata. More...

void	updatePixdim (const std::vector< pixdim_t > &pixdim)
	Modify the pixel dimensions, and potentially the xform matrices to match. More...

void	setPixunits (const std::vector< std::string > &pixunits)
	Modify the pixel dimension units. More...

Protected Attributes
nifti_image *	image
	The wrapped `nifti_image` pointer.

int *	refCount
	A reference counter, shared with other objects wrapping the same pointer.

Detailed Description

Thin wrapper around a C-style nifti_image struct that allows C++-style destruction.

Reference counting is used to allow multiple NiftiImage objects to wrap the same nifti_image pointer, akin to a std::shared_ptr (but without requiring C++11).

Author: Jon Clayden (code@.nosp@m.clay.nosp@m.den.o.nosp@m.rg)

Constructor & Destructor Documentation

◆ NiftiImage() [1/8]

RNifti::NiftiImage::NiftiImage	(	const NiftiImage &	source,
		const bool	copy = `true`
	)

inline

Copy constructor.

Parameters

source	Another `NiftiImage` object
copy	If `true`, the underlying `nifti_image` will be copied; otherwise the new object wraps the same `nifti_image` and increments the shared reference count

◆ NiftiImage() [2/8]

RNifti::NiftiImage::NiftiImage ( const Block & source )

inline

Initialise from a block, copying in the data.

Parameters

source A Block object, referring to part of another NiftiImage

◆ NiftiImage() [3/8]

RNifti::NiftiImage::NiftiImage	(	nifti_image *const	image,
		const bool	copy = `false`
	)

inline

Initialise using an existing nifti_image pointer.

Parameters

image	An existing `nifti_image` pointer, possibly `NULL`
copy	If `true`, the image data will be copied; otherwise this object just wraps the pointer passed to it

◆ NiftiImage() [4/8]

RNifti::NiftiImage::NiftiImage	(	const std::vector< dim_t > &	dim,
		const int	datatype
	)

Initialise from basic metadata, allocating and zeroing pixel data.

Parameters

dim	A vector of image dimensions
datatype	A datatype code for the image data

◆ NiftiImage() [5/8]

RNifti::NiftiImage::NiftiImage	(	const std::vector< dim_t > &	dim,
		const std::string &	datatype
	)

Initialise from basic metadata, allocating and zeroing pixel data.

Parameters

dim	A vector of image dimensions
datatype	A datatype string for the image data

◆ NiftiImage() [6/8]

RNifti::NiftiImage::NiftiImage	(	const std::string &	path,
		const bool	readData = `true`
	)

Initialise using a path string.

Parameters

path	A string specifying a path to a valid NIfTI-1 file, possibly gzipped
readData	If `true`, the data will be read as well as the metadata

Exceptions

runtime_error If reading from the file fails

◆ NiftiImage() [7/8]

RNifti::NiftiImage::NiftiImage	(	const std::string &	path,
		const std::vector< dim_t > &	volumes
	)

Initialise using a path string and sequence of required volumes.

Parameters

path	A string specifying a path to a valid NIfTI-1 file, possibly gzipped
volumes	The volumes to read in (squashing all dimensions above the third together)

Exceptions

runtime_error If reading from the file fails, or volumes is empty

◆ NiftiImage() [8/8]

RNifti::NiftiImage::NiftiImage	(	const SEXP	object,
		const bool	readData = `true`,
		const bool	readOnly = `false`
	)

Initialise from an R object, retrieving an existing image from an external pointer attribute if available; otherwise constructing a new one from the R object itself.

Parameters

object	The source object
readData	If `true`, the data will be retrieved as well as the metadata
readOnly	If `true`, the caller asserts that its intent is read-only. Otherwise, if the `SEXP` may have multiple names at the R level (according to the `MAYBE_SHARED` R macro), an image retrieved from an external pointer will be duplicated to preserve R's usual semantics

Member Function Documentation

◆ acquire() [1/2]

void RNifti::NiftiImage::acquire ( const NiftiImage & source )

inlineprotected

Acquire the same pointer as another NiftiImage, incrementing the shared reference count.

Parameters

source A reference to a NiftiImage

◆ acquire() [2/2]

void RNifti::NiftiImage::acquire ( nifti_image *const image )

protected

Acquire the specified pointer to a nifti_image struct, taking (possibly shared) responsibility for freeing the associated memory.

If the object currently wraps another pointer, it will be released

Parameters

image The pointer to wrap

◆ addExtension()

NiftiImage& RNifti::NiftiImage::addExtension ( const Extension & extension )

inline

Add an extension to the image.

Parameters

The	new image extension, an Extension object

Returns: Self, with the extension appended

◆ block() [1/2]

Block RNifti::NiftiImage::block ( const int i )

inline

Extract a block from the image.

Parameters

i	The block number required

Returns: A Block object

Note: slice and volume are variants of this function specific to 3D and 4D images, respectively, which may be preferred in some cases for clarity

◆ block() [2/2]

const Block RNifti::NiftiImage::block ( const int i ) const

inline

Extract a block from the image.

Parameters

i	The block number required

Returns: A Block object

Note: slice and volume are variants of this function specific to 3D and 4D images, respectively, which may be preferred in some cases for clarity

◆ changeDatatype() [1/2]

NiftiImage& RNifti::NiftiImage::changeDatatype	(	const int	datatype,
		const bool	useSlope = `false`
	)

Change the datatype of the image, casting the pixel data if present.

Parameters

datatype	A NIfTI datatype code
useSlope	If `true`, and conversion is to an integer type, the data will be rescaled and the image's slope and intercept set to capture the full range of original values

Returns: Self, after changing the datatype

◆ changeDatatype() [2/2]

NiftiImage& RNifti::NiftiImage::changeDatatype	(	const std::string &	datatype,
		const bool	useSlope = `false`
	)

Change the datatype of the image, casting the pixel data if present.

Parameters

datatype	A string specifying the new datatype
useSlope	If `true`, and conversion is to an integer type, the data will be rescaled and the image's slope and intercept set to capture the full range of original values

Returns: Self, after changing the datatype

◆ copy() [1/3]

void RNifti::NiftiImage::copy ( const Block & source )

protected

Copy the contents of a Block to create a new image, acquiring a new pointer.

Parameters

source A reference to a Block

◆ copy() [2/3]

void RNifti::NiftiImage::copy ( const nifti_image * source )

protected

Copy the contents of a nifti_image to create a new image, acquiring the new pointer.

Parameters

source A pointer to a nifti_image

◆ copy() [3/3]

void RNifti::NiftiImage::copy ( const NiftiImage & source )

protected

Copy the contents of another NiftiImage to create a new image, acquiring a new pointer.

Parameters

source A reference to a NiftiImage

◆ data() [1/2]

NiftiImageData RNifti::NiftiImage::data ( )

inline

Obtain the pixel data within the image.

Returns: A mutable NiftiImageData object encapsulating the data

◆ data() [2/2]

const NiftiImageData RNifti::NiftiImage::data ( ) const

inline

Obtain the pixel data within the image.

Returns: A constant NiftiImageData object encapsulating the data

◆ dim()

std::vector<dim_t> RNifti::NiftiImage::dim ( ) const

inline

Return the dimensions of the image.

Returns: A vector of integers giving the width in each dimension

◆ drop()

NiftiImage& RNifti::NiftiImage::drop ( )

inline

Drop unitary dimensions.

Returns: Self, after possibly reducing the dimensionality of the image

Note: This function differs from its R equivalent in only dropping unitary dimensions after the last nonunitary one

◆ dropData()

NiftiImage& RNifti::NiftiImage::dropData ( )

inline

Drop the data from the image, retaining only the metadata.

This method invalidates any NiftiImageData objects referencing the old data

Returns: Self, after dropping the data

◆ dropExtensions()

NiftiImage& RNifti::NiftiImage::dropExtensions ( )

inline

Remove any extensions from the image.

Returns: Self, with extensions removed

◆ extensions()

std::list<Extension> RNifti::NiftiImage::extensions ( const int code = -1 ) const

inline

Return a list of the extensions associated with the image.

Parameters

code	Integer specifying the code corresponding to the extensions required. If -1, the default, all extensions are returned. There may be more than one extension with a given code

Returns: A list of Extension objects

◆ fileVersion()

static int RNifti::NiftiImage::fileVersion ( const std::string & path )

static

Get the NIfTI format version used by the file at the specified path.

Parameters

path	A string specifying a file path

Returns: An integer: -1 if the file is not present or not valid, 0 for ANALYZE-7.5, or a value greater than 0 for NIfTI

◆ getData()

template<typename TargetType >

std::vector<TargetType> RNifti::NiftiImage::getData ( const bool useSlope = true ) const

Extract a vector of data from the image, casting it to any required element type.

Parameters

useSlope If true, the default, then the data will be adjusted for the slope and intercept stored with the image, if any

Returns: A vector of data values, cast to the required type

Note: If the slope and intercept are applied, there is no guarantee that the adjusted values will fit within the requested type. No check is made for this

Deprecated:: Use of the (ultimately more flexible) data methods is now preferred

◆ initFromArray()

void RNifti::NiftiImage::initFromArray	(	const Rcpp::RObject &	object,
		const bool	copyData = `true`
	)

protected

Initialise the object from an R array.

Parameters

object	The source object
copyData	If `true`, the data are copied in; otherwise just the metadata is extracted

◆ initFromDims()

void RNifti::NiftiImage::initFromDims	(	const std::vector< dim_t > &	dim,
		const int	datatype
	)

protected

Initialise an empty object from basic metadata.

Parameters

dim	A vector of image dimensions
datatype	A datatype code for the image data

◆ initFromList()

void RNifti::NiftiImage::initFromList ( const Rcpp::RObject & object )

protected

Initialise the object from an R list with named elements, which can only contain metadata.

Parameters

object The source object

◆ initFromMriImage()

void RNifti::NiftiImage::initFromMriImage	(	const Rcpp::RObject &	object,
		const bool	copyData = `true`
	)

protected

Initialise the object from a reference object of class "MriImage".

Parameters

object	The source object
copyData	If `true`, the data are copied in; otherwise just the metadata is extracted

◆ initFromNiftiS4()

void RNifti::NiftiImage::initFromNiftiS4	(	const Rcpp::RObject &	object,
		const bool	copyData = `true`
	)

protected

Initialise the object from an S4 object of class "nifti".

Parameters

object	The source object
copyData	If `true`, the data are copied in; otherwise just the metadata is extracted

◆ isDataScaled()

bool RNifti::NiftiImage::isDataScaled ( ) const

inline

Determine whether nontrivial scale and slope parameters are set.

Returns: true if the object wraps an image pointer, its slope is not zero and the slope and intercept are not exactly one and zero; false otherwise

◆ isNull()

bool RNifti::NiftiImage::isNull ( ) const

inline

Determine whether or not the wrapped pointer is NULL.

Returns: true if the wrapped pointer is NULL; false otherwise

◆ isPersistent()

bool RNifti::NiftiImage::isPersistent ( ) const

inline

Determine whether or not the image is marked as persistent.

Returns: false, always

Deprecated:: The persistence mechanism has been replaced with reference counting, so this function will always return false. Use isShared instead.

◆ isShared()

bool RNifti::NiftiImage::isShared ( ) const

inline

Determine whether the wrapped pointer is shared with another NiftiImage.

Returns: true if the reference count is greater than 1; false otherwise

◆ nBlocks()

dim_t RNifti::NiftiImage::nBlocks ( ) const

inline

Return the number of blocks in the image.

Returns: An integer giving the number of blocks in the image

◆ nChannels()

int RNifti::NiftiImage::nChannels ( ) const

inline

Return the number of colour channels used by the image.

Returns: An integer giving the number of channels: generally 1, exception for RGB datatypes, which have 3 or 4, or the empty datatype, which has 0. Also 0 for null images

◆ nDims()

int RNifti::NiftiImage::nDims ( ) const

inline

Return the number of dimensions in the image.

Returns: An integer giving the image dimensionality

◆ nExtensions()

int RNifti::NiftiImage::nExtensions ( ) const

inline

Return the number of extensions associated with the image.

Returns: An integer giving the number of extensions

◆ nVoxels()

size_t RNifti::NiftiImage::nVoxels ( ) const

inline

Return the number of voxels in the image.

Returns: An integer giving the number of voxels in the image

◆ operator=() [1/2]

NiftiImage& RNifti::NiftiImage::operator= ( const Block & source )

inline

Copy assignment operator, which allows a block to be used to replace the contents of a suitably sized image.

Parameters

source A reference to a suitable Block object

◆ operator=() [2/2]

NiftiImage& RNifti::NiftiImage::operator= ( const NiftiImage & source )

inline

Copy assignment operator, which copies from its argument.

Parameters

source Another NiftiImage

◆ pixdim()

std::vector<pixdim_t> RNifti::NiftiImage::pixdim ( ) const

inline

Return the dimensions of the pixels or voxels in the image.

Returns: A vector of floating-point values giving the pixel width in each dimension

◆ qform() [1/2]

Xform RNifti::NiftiImage::qform ( )

inline

Access the qform matrix.

Returns: An Xform object

◆ qform() [2/2]

const Xform RNifti::NiftiImage::qform ( ) const

inline

Access the qform matrix.

Returns: An Xform object

◆ reorient() [1/2]

NiftiImage& RNifti::NiftiImage::reorient	(	const int	i,
		const int	j,
		const int	k
	)

Reorient the image by permuting dimensions and potentially reversing some.

Parameters

i,j,k Constants such as NIFTI_L2R, NIFTI_P2A and NIFTI_I2S, giving the canonical axes to reorient to

Returns: Self, after reorientation

Note: The pixel data is reordered, but not resampled. The xform matrices will also be adjusted in line with the transformation

◆ reorient() [2/2]

NiftiImage& RNifti::NiftiImage::reorient ( const std::string & orientation )

Reorient the image by permuting dimensions and potentially reversing some.

Parameters

orientation A string containing some permutation of the letters L or R, P or A, I or S, giving the canonical axes to reorient to

Returns: Self, after reorientation

Note: The pixel data is reordered, but not resampled. The xform matrices will also be adjusted in line with the transformation

◆ replaceData() [1/2]

NiftiImage& RNifti::NiftiImage::replaceData ( const NiftiImageData & data )

Replace the pixel data in the image with the contents of a NiftiImageData object.

Parameters

data	A data object, whose elements will be case to match the datatype of the image

Exceptions

runtime_error If the length of the new data does not match the image

Returns: Self, after replacing the data

◆ replaceData() [2/2]

template<typename SourceType >

NiftiImage& RNifti::NiftiImage::replaceData	(	const std::vector< SourceType > &	data,
		const int	datatype = `DT_NONE`
	)

Replace the pixel data in the image with the contents of a vector.

Parameters

data	A data vector, whose elements will be used to replace the image data
datatype	The final datatype required. By default the existing datatype of the image is used

Exceptions

runtime_error If the length of the new data does not match the image

Returns: Self, after replacing the data

◆ replaceExtensions()

NiftiImage& RNifti::NiftiImage::replaceExtensions ( const std::list< Extension > extensions )

inline

Replace all extensions with new ones.

Parameters

A	list of Extension objects

Returns: Self, with the new extensions attached

◆ rescale()

NiftiImage& RNifti::NiftiImage::rescale ( const std::vector< pixdim_t > & scales )

Rescale the image, changing its image dimensions and pixel dimensions.

Parameters

scales Vector of scale factors along each dimension

Returns: Self, after rescaling the metadata

Note: No interpolation is performed on the pixel data, which is simply dropped

◆ setPersistence()

NiftiImage& RNifti::NiftiImage::setPersistence ( const bool persistent )

inline

Mark the image as persistent, so that it can be passed back to R.

Parameters

persistent The new persistence state of the object

Returns: A reference to the callee.

Deprecated:: The persistence mechanism has been replaced with reference counting, so this function no longer has any effect. Instead it returns *this, unmodified.

◆ setPixunits()

void RNifti::NiftiImage::setPixunits ( const std::vector< std::string > & pixunits )

protected

Modify the pixel dimension units.

Parameters

pixunits Vector of new pixel units, specified using their standard abbreviations

◆ sexpTypeToNiftiType()

static int RNifti::NiftiImage::sexpTypeToNiftiType ( const int sexpType )

inlinestatic

Convert between R SEXP object type and nifti_image datatype codes.

Parameters

sexpType A numeric R SEXP type code

Returns: A nifti_image datatype code

Exceptions

runtime_error If a non-numeric type is passed

◆ sform() [1/2]

Xform RNifti::NiftiImage::sform ( )

inline

Access the sform matrix.

Returns: An Xform object

◆ sform() [2/2]

const Xform RNifti::NiftiImage::sform ( ) const

inline

Access the sform matrix.

Returns: An Xform object

◆ slice() [1/2]

Block RNifti::NiftiImage::slice ( const int i )

inline

Extract a slice block from a 3D image.

Parameters

i	The slice number required

Returns: A Block object

◆ slice() [2/2]

const Block RNifti::NiftiImage::slice ( const int i ) const

inline

Extract a slice block from a 3D image.

Parameters

i	The slice number required

Returns: A Block object

◆ toArray()

Rcpp::RObject RNifti::NiftiImage::toArray ( ) const

Create an R array from the image.

Returns: A numeric array object with an external pointer attribute

◆ toArrayOrPointer()

Rcpp::RObject RNifti::NiftiImage::toArrayOrPointer	(	const bool	internal,
		const std::string	label
	)		const

A conditional method that calls either toArray or toPointer.

Parameters

internal	If `true`, toPointer will be called; otherwise toArray
label	A string labelling the image

Returns: An R object

◆ toFile() [1/2]

std::pair<std::string,std::string> RNifti::NiftiImage::toFile	(	const std::string	fileName,
		const int	datatype = `DT_NONE`,
		const int	filetype = `-1`
	)		const

Write the image to a NIfTI-1 file.

Parameters

fileName	The file name to write to, with appropriate suffix (e.g. ".nii.gz")
datatype	The datatype to use when writing the file
filetype	The file type to create: a `NIFTI_FTYPE` constant or -1. In the latter case the file name is used to determine the file type

Returns: A pair of strings, giving the final header and image paths in that order

◆ toFile() [2/2]

std::pair<std::string,std::string> RNifti::NiftiImage::toFile	(	const std::string	fileName,
		const std::string &	datatype,
		const int	filetype = `-1`
	)		const

Write the image to a NIfTI-1 file.

Parameters

fileName	The file name to write to, with appropriate suffix (e.g. ".nii.gz")
datatype	The datatype to use when writing the file, or "auto"
filetype	The file type to create: a `NIFTI_FTYPE` constant or -1. In the latter case the file name is used to determine the file type

Returns: A pair of strings, giving the final header and image paths in that order

◆ toPointer()

Rcpp::RObject RNifti::NiftiImage::toPointer ( const std::string label ) const

Create an internal image to pass back to R.

Parameters

label A string labelling the image

Returns: An R character string with additional attributes

◆ update()

NiftiImage& RNifti::NiftiImage::update ( const Rcpp::RObject & object )

Update the image from an R array.

Parameters

object An R array or list object

Returns: Self, after updating data and/or metadata

◆ updatePixdim()

void RNifti::NiftiImage::updatePixdim ( const std::vector< pixdim_t > & pixdim )

protected

Modify the pixel dimensions, and potentially the xform matrices to match.

Parameters

pixdim Vector of new pixel dimensions

◆ volume() [1/2]

Block RNifti::NiftiImage::volume ( const int i )

inline

Extract a volume block from a 4D image.

Parameters

i	The volume number required

Returns: A Block object

◆ volume() [2/2]

const Block RNifti::NiftiImage::volume ( const int i ) const

inline

Extract a volume block from a 4D image.

Parameters

i	The volume number required

Returns: A Block object

◆ xform()

const Xform RNifti::NiftiImage::xform ( const bool preferQuaternion = true ) const

Obtain an xform matrix, indicating the orientation of the image.

Parameters

preferQuaternion If true, use the qform matrix in preference to the sform; otherwise prefer the sform

Returns: An Xform object

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

inst/include/RNifti/NiftiImage.h

Classes

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ NiftiImage() [1/8]

◆ NiftiImage() [2/8]

◆ NiftiImage() [3/8]

◆ NiftiImage() [4/8]

◆ NiftiImage() [5/8]

◆ NiftiImage() [6/8]

◆ NiftiImage() [7/8]

◆ NiftiImage() [8/8]

Member Function Documentation

◆ acquire() [1/2]

◆ acquire() [2/2]

◆ addExtension()

◆ block() [1/2]

◆ block() [2/2]

◆ changeDatatype() [1/2]

◆ changeDatatype() [2/2]

◆ copy() [1/3]

◆ copy() [2/3]

◆ copy() [3/3]

◆ data() [1/2]

◆ data() [2/2]

◆ dim()

◆ drop()

◆ dropData()

◆ dropExtensions()

◆ extensions()

◆ fileVersion()

◆ getData()

◆ initFromArray()

◆ initFromDims()

◆ initFromList()

◆ initFromMriImage()

◆ initFromNiftiS4()

◆ isDataScaled()

◆ isNull()

◆ isPersistent()

◆ isShared()

◆ nBlocks()

◆ nChannels()

◆ nDims()

◆ nExtensions()

◆ nVoxels()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ pixdim()

◆ qform() [1/2]

◆ qform() [2/2]

◆ reorient() [1/2]

◆ reorient() [2/2]

◆ replaceData() [1/2]

◆ replaceData() [2/2]

◆ replaceExtensions()

◆ rescale()

◆ setPersistence()

◆ setPixunits()

◆ sexpTypeToNiftiType()

◆ sform() [1/2]

◆ sform() [2/2]

◆ slice() [1/2]

◆ slice() [2/2]

◆ toArray()

◆ toArrayOrPointer()

◆ toFile() [1/2]

◆ toFile() [2/2]

◆ toPointer()

◆ update()

◆ updatePixdim()

◆ volume() [1/2]

◆ volume() [2/2]

◆ xform()