functions and classes related to image data input/output More...

#include "image.h"

Inheritance diagram for MR::Image< ValueType >:

Classes
class	Buffer

Public Types
using	value_type = ValueType

Public Member Functions
void *	operator new (std::size_t size)

void *	operator new[] (std::size_t size)

void	operator delete (void *ptr)

void	operator delete[] (void *ptr)

	Image ()

	Image (const Image &)=default

	Image (Image &&)=default

Image &	operator= (const Image &image)=default

Image &	operator= (Image &&)=default

	~Image ()

	Image (const std::shared_ptr< Buffer > &, const Stride::List &=Stride::List())
	used internally to instantiate Image objects More...

bool	valid () const

bool	operator! () const

const KeyValues &	keyval () const
	get generic key/value text attributes More...

const std::string &	name () const

const transform_type &	transform () const

size_t	ndim () const

ssize_t	size (size_t axis) const

default_type	spacing (size_t axis) const

ssize_t	stride (size_t axis) const

size_t	offset () const
	offset to current voxel from start of data More...

void	reset ()
	reset index to zero (origin) More...

ssize_t	get_index (size_t axis) const
	get position of current voxel location along axis More...

void	move_index (size_t axis, ssize_t increment)
	move position of current voxel location along axis More...

bool	is_direct_io () const

ValueType	get_value () const
	get voxel value at current location More...

void	set_value (ValueType val)
	set voxel value at current location More...

std::string	dump_to_mrtrix_file (std::string filename, bool use_multi_threading=true) const
	write out the contents of a direct IO image to file More...

Image	with_direct_io (Stride::List with_strides=Stride::List())
	return a new Image using direct IO More...

Image	with_direct_io (int axis)
	return a new Image using direct IO More...

ValueType *	address () const
	return RAM address of current voxel More...

Static Public Member Functions
static Image	open (const std::string &image_name, bool read_write_if_existing=false)

static Image	create (const std::string &image_name, const Header &template_header, bool add_to_command_history=true)

static Image	scratch (const Header &template_header, const std::string &label="scratch image")

Public Attributes
std::shared_ptr< Buffer >	buffer
	shared reference to header/buffer More...

Protected Attributes
void *	data_pointer
	pointer to data address whether in RAM or MMap More...

vector< ssize_t >	x
	voxel indices More...

Stride::List	strides
	voxel indices More...

size_t	data_offset
	offset to currently pointed-to voxel More...

Friends
std::ostream &	operator<< (std::ostream &stream, const Image &V)
	use for debugging More...

Detailed Description

template<typename ValueType>
class MR::Image< ValueType >

functions and classes related to image data input/output

Definition at line 39 of file image.h.

Member Typedef Documentation

◆ value_type

template<typename ValueType >

using MR::Image< ValueType >::value_type = ValueType

Definition at line 43 of file image.h.

Constructor & Destructor Documentation

◆ Image() [1/4]

template<typename ValueType >

MR::Image< ValueType >::Image ( )

◆ Image() [2/4]

template<typename ValueType >

MR::Image< ValueType >::Image ( const Image< ValueType > & )

inlinedefault

◆ Image() [3/4]

template<typename ValueType >

MR::Image< ValueType >::Image ( Image< ValueType > && )

inlinedefault

◆ ~Image()

template<typename ValueType >

MR::Image< ValueType >::~Image ( )

◆ Image() [4/4]

template<typename ValueType >

MR::Image< ValueType >::Image	(	const std::shared_ptr< Buffer > &	,
		const Stride::List &	= `Stride::List()`
	)

used internally to instantiate Image objects

Member Function Documentation

◆ address()

template<typename ValueType >

ValueType * MR::Image< ValueType >::address ( ) const

inline

return RAM address of current voxel

Note: this will only work if image access is direct (i.e. for a scratch image, with preloading, or when the data type is native and without scaling.

Definition at line 185 of file image.h.

◆ create()

template<typename ValueType >

static Image MR::Image< ValueType >::create	(	const std::string &	image_name,
		const Header &	template_header,
		bool	add_to_command_history = `true`
	)

inlinestatic

Definition at line 192 of file image.h.

◆ dump_to_mrtrix_file()

template<typename ValueType >

std::string MR::Image< ValueType >::dump_to_mrtrix_file	(	std::string	filename,
		bool	use_multi_threading = `true`
	)		const

write out the contents of a direct IO image to file

returns the name of the image - needed by display() to get the name of the temporary file to supply to MRView.

Note: this is not the recommended way to save an image - only use this function when you absolutely need to minimise RAM usage on write-out (this avoids any further buffering before write-out).; this will only work for images accessed using direct IO (i.e. opened as a scratch image, or using with_direct_io(), and only supports output to MRtrix format images (*.mif / *.mih). There is a chance that images opened in other ways may also use direct IO (e.g. if the datatype & strides match, and the image is single-file), you can check using the is_direct_io() method. If there is any possibility that this image might use indirect IO, you should use the save() function instead (and even then, it should only be used for debugging purposes).

◆ get_index()

template<typename ValueType >

ssize_t MR::Image< ValueType >::get_index ( size_t axis ) const

inline

get position of current voxel location along axis

Definition at line 80 of file image.h.

◆ get_value()

template<typename ValueType >

ValueType MR::Image< ValueType >::get_value ( ) const

inline

get voxel value at current location

Definition at line 87 of file image.h.

◆ is_direct_io()

template<typename ValueType >

bool MR::Image< ValueType >::is_direct_io ( ) const

inline

Definition at line 84 of file image.h.

◆ keyval()

template<typename ValueType >

const KeyValues & MR::Image< ValueType >::keyval ( ) const

inline

get generic key/value text attributes

Definition at line 60 of file image.h.

◆ move_index()

template<typename ValueType >

void MR::Image< ValueType >::move_index	(	size_t	axis,
		ssize_t	increment
	)

inline

move position of current voxel location along axis

Definition at line 82 of file image.h.

◆ name()

template<typename ValueType >

const std::string & MR::Image< ValueType >::name ( ) const

inline

Definition at line 62 of file image.h.

◆ ndim()

template<typename ValueType >

size_t MR::Image< ValueType >::ndim ( ) const

inline

Definition at line 65 of file image.h.

◆ offset()

template<typename ValueType >

size_t MR::Image< ValueType >::offset ( ) const

inline

offset to current voxel from start of data

Definition at line 71 of file image.h.

◆ open()

template<typename ValueType >

static Image MR::Image< ValueType >::open	(	const std::string &	image_name,
		bool	read_write_if_existing = `false`
	)

inlinestatic

Definition at line 189 of file image.h.

◆ operator delete()

template<typename ValueType >

void MR::Image< ValueType >::operator delete ( void * ptr )

inline

Definition at line 41 of file image.h.

◆ operator delete[]()

template<typename ValueType >

void MR::Image< ValueType >::operator delete[] ( void * ptr )

inline

Definition at line 41 of file image.h.

◆ operator new()

template<typename ValueType >

void * MR::Image< ValueType >::operator new ( std::size_t size )

inline

Definition at line 41 of file image.h.

◆ operator new[]()

template<typename ValueType >

void * MR::Image< ValueType >::operator new[] ( std::size_t size )

inline

Definition at line 41 of file image.h.

◆ operator!()

template<typename ValueType >

bool MR::Image< ValueType >::operator! ( ) const

inline

Definition at line 57 of file image.h.

◆ operator=() [1/2]

template<typename ValueType >

Image & MR::Image< ValueType >::operator= ( const Image< ValueType > & image )

inlinedefault

◆ operator=() [2/2]

template<typename ValueType >

Image & MR::Image< ValueType >::operator= ( Image< ValueType > && )

inlinedefault

◆ reset()

template<typename ValueType >

void MR::Image< ValueType >::reset ( )

inline

reset index to zero (origin)

Definition at line 74 of file image.h.

◆ scratch()

template<typename ValueType >

static Image MR::Image< ValueType >::scratch	(	const Header &	template_header,
		const std::string &	label = `"scratch image"`
	)

inlinestatic

Definition at line 195 of file image.h.

◆ set_value()

template<typename ValueType >

void MR::Image< ValueType >::set_value ( ValueType val )

inline

set voxel value at current location

Definition at line 92 of file image.h.

◆ size()

template<typename ValueType >

ssize_t MR::Image< ValueType >::size ( size_t axis ) const

inline

Definition at line 66 of file image.h.

◆ spacing()

template<typename ValueType >

default_type MR::Image< ValueType >::spacing ( size_t axis ) const

inline

Definition at line 67 of file image.h.

◆ stride()

template<typename ValueType >

ssize_t MR::Image< ValueType >::stride ( size_t axis ) const

inline

Definition at line 68 of file image.h.

◆ transform()

template<typename ValueType >

const transform_type & MR::Image< ValueType >::transform ( ) const

inline

Definition at line 63 of file image.h.

◆ valid()

template<typename ValueType >

bool MR::Image< ValueType >::valid ( ) const

inline

Definition at line 56 of file image.h.

◆ with_direct_io() [1/2]

template<typename ValueType >

Image MR::Image< ValueType >::with_direct_io ( int axis )

inline

return a new Image using direct IO

this is a convenience function, performing the same function as with_direct_io(Stride::List). The difference is that the axis argument specifies which axis should be contiguous, or if axis is negative, that the spatial axes should be contiguous (the SpatiallyContiguous constexpr, set to -1, is provided for clarity). In other words:

auto image = Image<float>::open (filename).with_direct_io (3);

MR::Image::with_direct_io

Image with_direct_io(Stride::List with_strides=Stride::List())

return a new Image using direct IO

MR::Image::open

static Image open(const std::string &image_name, bool read_write_if_existing=false)

Definition: image.h:189

is equivalent to:

auto header = Header::open (filename);

auto image = header.get_image<float>().with_direct_io (Stride::contiguous_along_axis (3, header));

MR::Stride::contiguous_along_axis

List contiguous_along_axis(size_t axis)

convenience function to get volume-contiguous strides

Definition: stride.h:386

and

auto image = Image<float>::open (filename).with_direct_io (-1);
// or;
auto image = Image<float>::open (filename).with_direct_io (SpatiallyContiguous);

is equivalent to:

auto header = Header::open (filename);

auto image = header.get_image<float>().with_direct_io (Stride::contiguous_along_spatial_axes (header));

MR::Stride::contiguous_along_spatial_axes

List contiguous_along_spatial_axes(const HeaderType &header)

convenience function to get spatially contiguous strides

Definition: stride.h:402

Definition at line 174 of file image.h.

◆ with_direct_io() [2/2]

template<typename ValueType >

Image MR::Image< ValueType >::with_direct_io ( Stride::List with_strides = Stride::List() )

return a new Image using direct IO

this will preload the data into RAM if the datatype on file doesn't match that on file (or if any scaling is applied to the data). The optional with_strides argument is used to additionally enforce preloading if the strides aren't compatible with those specified.

Example:

auto image = Header::open (argument[0]).get_image().with_direct_io();

MR::App::argument

vector< ParsedArgument > argument

the list of arguments parsed from the command-line

Note: this invalidate the invoking Image - do not use the original image in subsequent code.

Friends And Related Function Documentation

◆ operator<<

template<typename ValueType >

std::ostream & operator<<	(	std::ostream &	stream,
		const Image< ValueType > &	V
	)

friend

use for debugging

Definition at line 98 of file image.h.

Member Data Documentation

◆ buffer

template<typename ValueType >

std::shared_ptr<Buffer> MR::Image< ValueType >::buffer

shared reference to header/buffer

Definition at line 200 of file image.h.

◆ data_offset

template<typename ValueType >

size_t MR::Image< ValueType >::data_offset

protected

offset to currently pointed-to voxel

Definition at line 209 of file image.h.

◆ data_pointer

template<typename ValueType >

void* MR::Image< ValueType >::data_pointer

protected

pointer to data address whether in RAM or MMap

Definition at line 203 of file image.h.

◆ strides

template<typename ValueType >

Stride::List MR::Image< ValueType >::strides

protected

voxel indices

Definition at line 207 of file image.h.

◆ x

template<typename ValueType >

vector<ssize_t> MR::Image< ValueType >::x

protected

voxel indices

Definition at line 205 of file image.h.

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

core/header.h
core/image.h

Classes

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Attributes

Friends

Detailed Description

Member Typedef Documentation

◆ value_type

Constructor & Destructor Documentation

◆ Image() [1/4]

◆ Image() [2/4]

◆ Image() [3/4]

◆ ~Image()

◆ Image() [4/4]

Member Function Documentation

◆ address()

◆ create()

◆ dump_to_mrtrix_file()

◆ get_index()

◆ get_value()

◆ is_direct_io()

◆ keyval()

◆ move_index()

◆ name()

◆ ndim()

◆ offset()

◆ open()

◆ operator delete()

◆ operator delete[]()

◆ operator new()

◆ operator new[]()

◆ operator!()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ reset()

◆ scratch()

◆ set_value()

◆ size()

◆ spacing()

◆ stride()

◆ transform()

◆ valid()

◆ with_direct_io() [1/2]

◆ with_direct_io() [2/2]

Friends And Related Function Documentation

◆ operator<<

Member Data Documentation

◆ buffer

◆ data_offset

◆ data_pointer

◆ strides

◆ x