Wrapper class encapsulating a NIfTI data blob, with responsibility for handling data scaling and polymorphism. More...

#include <NiftiImage.h>

Classes
struct	ConcreteTypeHandler
	Concrete inner class template defining behaviour specific to individual data types. More...

struct	ConcreteTypeHandler< rgba32_t, alpha >

struct	ConcreteTypeHandler< std::complex< ElementType >, false >

struct	Element
	Inner class representing a single element in the data blob. More...

class	Iterator
	Iterator type for `NiftiImageData`, with `Element` as its value type. More...

struct	TypeHandler
	Abstract inner class defining the type-specific functions required in concrete subclasses. More...

Public Member Functions
	NiftiImageData ()
	Default constructor, creating an empty data object.

	NiftiImageData (void *data, const size_t length, const int datatype, const double slope=1.0, const double intercept=0.0)
	Primary constructor. More...

	NiftiImageData (nifti_image *image)
	Convenience constructor for a `nifti_image`. More...

	NiftiImageData (const NiftiImageData &source, const int datatype=DT_NONE)
	Copy constructor with optional type conversion. More...

template<class InputIterator >
	NiftiImageData (InputIterator from, InputIterator to, const int datatype)
	Iterator-based constructor. More...

virtual	~NiftiImageData ()
	Destructor which frees the type handler, and the data blob if it is owned by this object.

NiftiImageData &	operator= (const NiftiImageData &source)
	Copy assignment operator. More...

void *	blob () const
	Return an opaque pointer to the blob.

int	datatype () const
	Return stored datatype code.

size_t	length () const
	Return the number of elements in the data.

size_t	size () const
	Return the number of elements in the data.

size_t	bytesPerPixel () const
	Return the number of bytes used per element, or zero if the datatype is undefined or the blob is `NULL`.

size_t	totalBytes () const
	Return the total size of the data blob, in bytes.

bool	isEmpty () const
	Determine whether or not the object is empty. More...

bool	isScaled () const
	Determine whether the object uses data scaling. More...

bool	isComplex () const
	Determine whether the datatype is complex. More...

bool	isFloatingPoint () const
	Determine whether the datatype is floating point. More...

bool	isInteger () const
	Determine whether the datatype is an integer type. More...

bool	isRgb () const
	Determine whether the datatype corresponds to an RGB type. More...

NiftiImageData	unscaled () const
	Return a similar object to the callee, but with the slope and intercept values reset. More...

NiftiImageData &	disown ()
	Disown the data blob, removing responsibility for freeing it upon destruction. More...

const Iterator	begin () const
	Obtain a constant iterator corresponding to the start of the blob.

const Iterator	end () const
	Obtain a constant iterator corresponding to the end of the blob.

Iterator	begin ()
	Obtain a mutable iterator corresponding to the start of the blob.

Iterator	end ()
	Obtain a mutable iterator corresponding to the end of the blob.

const Element	operator[] (const size_t i) const
	Indexing operator, returning a constant element. More...

Element	operator[] (const size_t i)
	Indexing operator, returning a mutable element. More...

void	minmax (double min, double max) const
	Calculate the minimum and maximum values in the blob, as doubles. More...

Public Attributes
double	slope
	The slope term used to scale data values. More...

double	intercept
	The intercept term used to scale data values.

Protected Member Functions
TypeHandler *	createHandler ()
	Create a concrete type handler appropriate to the datatype code stored with the data. More...

void	init (void *data, const size_t length, const int datatype, const double slope, const double intercept, const bool alloc=true)
	Initialiser method, used by constructors. More...

void	calibrateFrom (const NiftiImageData &data)
	Update the slope and intercept to cover the range of another data object. More...

Protected Attributes
void *	dataPtr
	Opaque pointer to the underlying data blob.

int	_datatype
	Datatype code indicating the actual type of the elements.

TypeHandler *	handler
	Type handler, which is created to match the datatype.

size_t	_length
	The number of data elements in the blob.

bool	owner
	An indicator of whether this object is responsible for cleaning up the data.

Detailed Description

Wrapper class encapsulating a NIfTI data blob, with responsibility for handling data scaling and polymorphism.

This class provides read/write data access, iterators, etc., which internally handle conversion to and from the data's native type. It can be linked to the data in a nifti_image or used independently.

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

Constructor & Destructor Documentation

◆ NiftiImageData() [1/4]

RNifti::NiftiImageData::NiftiImageData	(	void *	data,
		const size_t	length,
		const int	datatype,
		const double	slope = `1.0`,
		const double	intercept = `0.0`
	)

inline

Primary constructor.

Parameters

data	A pointer to a pre-allocated data blob, or `NULL`. In the latter case, memory will be allocated by the object, and cleaned up at destruction unless it is disowned
length	The number of elements in the blob
datatype	The NIfTI datatype code corresponding to the type of the data elements
slope	The slope parameter to use for data scaling, if any
intercept	The intercept parameter to use for data scaling, if any

◆ NiftiImageData() [2/4]

RNifti::NiftiImageData::NiftiImageData ( nifti_image * image )

inline

Convenience constructor for a nifti_image.

Parameters

image The image struct whose data the object will wrap

◆ NiftiImageData() [3/4]

RNifti::NiftiImageData::NiftiImageData	(	const NiftiImageData &	source,
		const int	datatype = `DT_NONE`
	)

inline

Copy constructor with optional type conversion.

Parameters

source	Another `NiftiImageData` object to copy data from
datatype	The datatype to convert to, or `DT_NONE`, the default, for no conversion. If the range of the source data cannot be represented by the chosen type, the slope and intercept parameters will be set to adjust the range

◆ NiftiImageData() [4/4]

template<class InputIterator >

RNifti::NiftiImageData::NiftiImageData	(	InputIterator	from,
		InputIterator	to,
		const int	datatype
	)

inline

Iterator-based constructor.

Parameters

from	Iterator type representing the start of the source data to be copied
to	Iterator type representing the end of the source data to be copied
datatype	The NIfTI datatype to use within the data blob

Member Function Documentation

◆ calibrateFrom()

void RNifti::NiftiImageData::calibrateFrom ( const NiftiImageData & data )

inlineprotected

Update the slope and intercept to cover the range of another data object.

If the current object's datatype can capture the required range without scaling, the slope and intercept are simply reset

Parameters

data	Another data object

◆ createHandler()

TypeHandler* RNifti::NiftiImageData::createHandler ( )

inlineprotected

Create a concrete type handler appropriate to the datatype code stored with the data.

Returns: The newly allocated type handler, or NULL

Exceptions

runtime_error If the current datatype is unsupported

◆ disown()

NiftiImageData& RNifti::NiftiImageData::disown ( )

inline

Disown the data blob, removing responsibility for freeing it upon destruction.

Returns: A reference to the modified callee

◆ init()

void RNifti::NiftiImageData::init	(	void *	data,
		const size_t	length,
		const int	datatype,
		const double	slope,
		const double	intercept,
		const bool	alloc = `true`
	)

inlineprotected

Initialiser method, used by constructors.

Parameters

data	Pointer to a preallocated data blob, or `NULL`
length	Number of elements in the blob
datatype	NIfTI datatype code appropriate to the blob
slope	Slope parameter for scaling values
intercept	Intercept parameter for scaling values
alloc	If `true`, the default, and `data` is `NULL`, memory will be allocated for the blob. If `false`, the blob will be `NULL` in this case

◆ isComplex()

bool RNifti::NiftiImageData::isComplex ( ) const

inline

Determine whether the datatype is complex.

Returns: true if the data represents complex floating point values; false otherwise

◆ isEmpty()

bool RNifti::NiftiImageData::isEmpty ( ) const

inline

Determine whether or not the object is empty.

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

◆ isFloatingPoint()

bool RNifti::NiftiImageData::isFloatingPoint ( ) const

inline

Determine whether the datatype is floating point.

Returns: true if the data represents 32-bit or 64-bit floating point values; false otherwise

◆ isInteger()

bool RNifti::NiftiImageData::isInteger ( ) const

inline

Determine whether the datatype is an integer type.

Returns: true if the data represents integers; false otherwise

◆ isRgb()

bool RNifti::NiftiImageData::isRgb ( ) const

inline

Determine whether the datatype corresponds to an RGB type.

Returns: true if the data represents RGB colour values; false otherwise

◆ isScaled()

bool RNifti::NiftiImageData::isScaled ( ) const

inline

Determine whether the object uses data scaling.

Returns: true if the slope and intercept parameters are set to nontrivial values; false otherwise

◆ minmax()

void RNifti::NiftiImageData::minmax	(	double *	min,
		double *	max
	)		const

inline

Calculate the minimum and maximum values in the blob, as doubles.

Parameters

min	Pointer to the minimum value (output parameter). Will be set to zero if the datatype is unknown or the data is empty
max	Pointer to the maximum value (output parameter). Will be set to zero if the datatype is unknown or the data is empty

◆ operator=()

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

inline

Copy assignment operator.

Parameters

source Another NiftiImageData object, from which the data and metadata are copied

Returns: A reference to the callee

◆ operator[]() [1/2]

Element RNifti::NiftiImageData::operator[] ( const size_t i )

inline

Indexing operator, returning a mutable element.

Parameters

i	Index value, where the first dimension moves fastest

Returns: Mutable element proxy type

◆ operator[]() [2/2]

const Element RNifti::NiftiImageData::operator[] ( const size_t i ) const

inline

Indexing operator, returning a constant element.

Parameters

i	Index value, where the first dimension moves fastest

Returns: Constant element proxy type

◆ unscaled()

NiftiImageData RNifti::NiftiImageData::unscaled ( ) const

inline

Return a similar object to the callee, but with the slope and intercept values reset.

Returns: A new NiftiImageData object, pointing to the same memory as the callee

Member Data Documentation

◆ slope

double RNifti::NiftiImageData::slope

The slope term used to scale data values.

Ignored if zero.

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

inst/include/RNifti/NiftiImage.h

Classes

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ NiftiImageData() [1/4]

◆ NiftiImageData() [2/4]

◆ NiftiImageData() [3/4]

◆ NiftiImageData() [4/4]

Member Function Documentation

◆ calibrateFrom()

◆ createHandler()

◆ disown()

◆ init()

◆ isComplex()

◆ isEmpty()

◆ isFloatingPoint()

◆ isInteger()

◆ isRgb()

◆ isScaled()

◆ minmax()

◆ operator=()

◆ operator[]() [1/2]

◆ operator[]() [2/2]

◆ unscaled()

Member Data Documentation

◆ slope