This abstract class is the basis for all image representations. More...

#include "stir/DiscretisedDensity.h"

Inheritance diagram for stir::DiscretisedDensity< num_dimensions, elemT >:

[legend]

Public Types
typedef DiscretisedDensity< num_dimensions, elemT >	hierarchy_base_type
	A typedef that can be used what the base of the hierarchy is. More...

Public Types inherited from stir::Array< num_dimensions, elemT >
typedef base_type::value_type	value_type
	typedefs such that we do not need to have `typename` wherever we use these types defined in the base class

typedef base_type::reference	reference

typedef base_type::const_reference	const_reference

typedef base_type::difference_type	difference_type

typedef base_type::size_type	size_type

typedef base_type::iterator	iterator

typedef base_type::const_iterator	const_iterator

typedef elemT	full_value_type

typedef full_value_type *	full_pointer

typedef const full_value_type *	const_full_pointer

typedef full_value_type &	full_reference

typedef const full_value_type &	const_full_reference

typedef FullArrayIterator< typename base_type::iterator, typename Array< num_dimensions - 1, elemT >::full_iterator, elemT, full_reference, full_pointer >	full_iterator
	This defines an iterator type that iterates through all elements.

typedef FullArrayIterator< typename base_type::const_iterator, typename Array< num_dimensions - 1, elemT >::const_full_iterator, elemT, const_full_reference, const_full_pointer >	const_full_iterator
	As full_iterator, but for const objects.

Public Types inherited from stir::VectorWithOffset< Array< num_dimensions - 1, elemT > >
typedef size_t	size_type

typedef Array< num_dimensions - 1, elemT >	value_type

typedef value_type &	reference

typedef const value_type &	const_reference

typedef ptrdiff_t	difference_type

typedef Array< num_dimensions - 1, elemT > *	iterator

typedef Array< num_dimensions - 1, elemT > const *	const_iterator

typedef std::reverse_iterator< iterator >	reverse_iterator

typedef std::reverse_iterator< const_iterator >	const_reverse_iterator

Public Member Functions
	DiscretisedDensity ()
	Construct an empty DiscretisedDensity.

	DiscretisedDensity (const IndexRange< num_dimensions > &range, const CartesianCoordinate3D< float > &origin)
	Construct DiscretisedDensity from a given range of indices & origin.

	DiscretisedDensity (const shared_ptr< const ExamInfo > &exam_info_sptr, const IndexRange< num_dimensions > &range, const CartesianCoordinate3D< float > &origin)
	Construct DiscretisedDensity from ExamInfo and a given range of indices & origin.

const CartesianCoordinate3D< float > &	get_origin () const
	Return the origin.

void	set_origin (const CartesianCoordinate3D< float > &origin)
	Set the origin.

virtual DiscretisedDensity< num_dimensions, elemT > *	get_empty_copy () const =0
	Allocate a new DiscretisedDensity object with same characteristics as the current one.

virtual DiscretisedDensity< num_dimensions, elemT > *	clone () const =0
	Allocate a new DiscretisedDensity object which is a copy of the current one.

DiscretisedDensity< num_dimensions, elemT > *	get_empty_discretised_density () const
	Allocate a new DiscretisedDensity object with same characteristics as the current one.

Translation between indices and physical coordinates
CartesianCoordinate3D< float >	get_physical_coordinates_for_indices (const BasicCoordinate< num_dimensions, int > &indices) const
	Return the coordinates of the centre of the basis-function corresponding to `indices`. More...

CartesianCoordinate3D< float >	get_physical_coordinates_for_indices (const BasicCoordinate< num_dimensions, float > &indices) const
	Return the coordinates of the centre of the basis-function corresponding to non-integer coordinate in 'physical' coordinates. More...

CartesianCoordinate3D< float >	get_relative_coordinates_for_indices (const BasicCoordinate< num_dimensions, int > &indices) const
	Return the relative coordinates of the centre of the basis-function corresponding to `indices`. More...

CartesianCoordinate3D< float >	get_relative_coordinates_for_indices (const BasicCoordinate< num_dimensions, float > &indices) const
	Return the relative coordinates of the centre of the basis-function corresponding to the non-integer coordinates in 'index' coordinates. More...

BasicCoordinate< num_dimensions, int >	get_indices_closest_to_physical_coordinates (const CartesianCoordinate3D< float > &coords) const
	Return the indices of the basis-function closest to the given point. More...

BasicCoordinate< num_dimensions, int >	get_indices_closest_to_relative_coordinates (const CartesianCoordinate3D< float > &coords) const
	Return the indices of the basis-function closest to the given point. More...

BasicCoordinate< num_dimensions, float >	get_index_coordinates_for_physical_coordinates (const CartesianCoordinate3D< float > &coords) const
	Return the indices of the basis-function closest to the given point. More...

BasicCoordinate< num_dimensions, float >	get_index_coordinates_for_relative_coordinates (const CartesianCoordinate3D< float > &coords) const
	Return the index-coordinates of the basis-function closest to the given point. More...

BasicCoordinate< num_dimensions, float >	get_index_coordinates_for_LPS_coordinates (const CartesianCoordinate3D< float > &coords) const
	Translation from LPS coordinates to continuous indices.

CartesianCoordinate3D< float >	get_LPS_coordinates_for_physical_coordinates (const CartesianCoordinate3D< float > &indices) const
	Translation from physical to LPS coordinates.

CartesianCoordinate3D< float >	get_LPS_coordinates_for_indices (const BasicCoordinate< num_dimensions, int > &indices) const
	Translation from indices to LPS coordinates.

CartesianCoordinate3D< float >	get_LPS_coordinates_for_indices (const BasicCoordinate< num_dimensions, float > &indices) const
	Translation from continuous indices to LPS coordinates.

CartesianCoordinate3D< float >	get_physical_coordinates_for_LPS_coordinates (const CartesianCoordinate3D< float > &coords) const
	Translation from LPS coordinates to physical coordinates.

BasicCoordinate< num_dimensions, int >	get_indices_closest_to_LPS_coordinates (const CartesianCoordinate3D< float > &coords) const
	Translation from LPS coordinates to indices.

Equality
bool	has_same_characteristics (self_type const &, std::string &explanation) const
	Checks if the 2 objects have the same type, index range, origin etc. More...

bool	has_same_characteristics (self_type const &) const
	Checks if the 2 objects have the same type, index range, origin etc. More...

bool	operator== (const self_type &) const
	check equality (data has to be identical) More...

bool	operator!= (const self_type &) const
	negation of operator==

Public Member Functions inherited from stir::ExamData
	ExamData ()
	ExamData. More...

	ExamData (const shared_ptr< const ExamInfo > &_this_exam)

virtual const ExamInfo &	get_exam_info () const

virtual shared_ptr< const ExamInfo >	get_exam_info_sptr () const
	Get shared pointer to exam info.

virtual void	set_exam_info (ExamInfo const &)
	change exam info More...

void	set_exam_info_sptr (shared_ptr< const ExamInfo > new_exam_info_sptr)

Public Member Functions inherited from stir::Array< num_dimensions, elemT >
	Array ()
	Construct an empty Array.

	Array (const IndexRange< num_dimensions > &)
	Construct an Array of given range of indices, elements are initialised to 0.

	Array (const IndexRange< num_dimensions > &range, shared_ptr< elemT[]> data_sptr)
	Construct an Array pointing to existing contiguous data. More...

	Array (const base_type &t)
	Construct an Array from an object of its base_type.

	Array (const self &t)
	Copy constructor.

	~Array () override
	virtual destructor, frees up any allocated memory

	Array (Array &&other) noexcept
	move constructor More...

Array &	operator= (Array other)
	assignment operator More...

IndexRange< num_dimensions >	get_index_range () const

size_t	size_all () const
	return the total number of elements in this array

virtual void	resize (const IndexRange< num_dimensions > &range)
	change the array to a new range of indices, new elements are set to 0 More...

virtual void	grow (const IndexRange< num_dimensions > &range)
	alias for resize()

elemT	sum () const
	return sum of all elements

elemT	sum_positive () const
	return sum of all positive elements

elemT	find_max () const
	return maximum of all the elements

elemT	find_min () const
	return minimum of all the elements

void	fill (const elemT &n)
	Fill elements with value `n`. More...

void	apply_lower_threshold (const elemT &l)
	Sets elements below value to the value.

void	apply_upper_threshold (const elemT &u)
	Sets elements above value to the value.

bool	is_regular () const
	checks if the index range is 'regular' More...

bool	get_regular_range (BasicCoordinate< num_dimensions, int > &min, BasicCoordinate< num_dimensions, int > &max) const
	find regular range, returns `false` if the range is not regular More...

Array< num_dimensions - 1, elemT > &	operator[] (int i)
	allow array-style access, read/write

const Array< num_dimensions - 1, elemT > &	operator[] (int i) const
	array access, read-only

elemT &	operator[] (const BasicCoordinate< num_dimensions, int > &c)
	allow array-style access given a BasicCoordinate to specify the indices, read/write

const elemT &	operator[] (const BasicCoordinate< num_dimensions, int > &c) const
	array access given a BasicCoordinate to specify the indices, read-only

template<typename elemT2 >
STIR_DEPRECATED void	axpby (const elemT2 a, const Array &x, const elemT2 b, const Array &y)

void	xapyb (const Array &x, const elemT a, const Array &y, const elemT b)
	set values of the array to xa+yb, where a and b are scalar

void	xapyb (const Array &x, const Array &a, const Array &y, const Array &b)
	set values of the array to xa+yb, where a and b are arrays

template<class T >
void	sapyb (const T &a, const Array &y, const T &b)
	set values of the array to selfa+yb where a and b are scalar or arrays

template<int num_dimensions, typename elemT>
	Array (Array< num_dimensions, elemT > &&other) noexcept

template<typename elemT2 >
void	axpby (const elemT2 a, const Array &x, const elemT2 b, const Array &y)

full_iterator	begin_all ()
	start value for iterating through all elements in the array, see full_iterator

const_full_iterator	begin_all () const
	start value for iterating through all elements in the (const) array, see full_iterator

const_full_iterator	begin_all_const () const
	start value for iterating through all elements in the array, see full_iterator

full_iterator	end_all ()
	end value for iterating through all elements in the array, see full_iterator

const_full_iterator	end_all () const
	end value for iterating through all elements in the (const) array, see full_iterator

const_full_iterator	end_all_const () const
	end value for iterating through all elements in the array, see full_iterator

Array< num_dimensions - 1, elemT > &	at (int i)

const Array< num_dimensions - 1, elemT > &	at (int i) const

elemT &	at (const BasicCoordinate< num_dimensions, int > &c)

const elemT &	at (const BasicCoordinate< num_dimensions, int > &c) const

bool	is_contiguous () const
	return if the array is contiguous in memory

elemT *	get_full_data_ptr ()
	member function for access to the data via a elemT* More...

const elemT *	get_const_full_data_ptr () const
	member function for access to the data via a const elemT* More...

void	release_full_data_ptr ()
	signal end of access to elemT* More...

void	release_const_full_data_ptr () const
	signal end of access to const elemT* More...

Public Member Functions inherited from stir::NumericVectorWithOffset< Array< num_dimensions - 1, elemT >, elemT >
	NumericVectorWithOffset (const VectorWithOffset< Array< num_dimensions - 1, elemT > > &t)
	Constructor from an object of this class' base_type.

	NumericVectorWithOffset (const NumericVectorWithOffset &t)
	Constructor from an object of this class' base_type.

	NumericVectorWithOffset (NumericVectorWithOffset &&other) noexcept
	move constructor More...

NumericVectorWithOffset &	operator= (const NumericVectorWithOffset &other)
	assignment

NumericVectorWithOffset	operator+ (const NumericVectorWithOffset &v) const
	adding vectors, element by element

NumericVectorWithOffset	operator+ (const elemT &v) const
	return a new vector with elements equal to the sum of the elements in the original and the `elemT`

NumericVectorWithOffset	operator- (const NumericVectorWithOffset &v) const
	subtracting vectors, element by element

NumericVectorWithOffset	operator- (const elemT &v) const
	return a new vector with elements equal to the difference of the elements in the original and the `elemT`

NumericVectorWithOffset	operator* (const NumericVectorWithOffset &v) const
	multiplying vectors, element by element

NumericVectorWithOffset	operator* (const elemT &v) const
	return a new vector with elements equal to the multiplication of the elements in the original and the `elemT`

NumericVectorWithOffset	operator/ (const NumericVectorWithOffset &v) const
	dividing vectors, element by element

NumericVectorWithOffset	operator/ (const elemT &v) const
	return a new vector with elements equal to the division of the elements in the original and the `elemT`

NumericVectorWithOffset &	operator+= (const NumericVectorWithOffset &v)
	adding elements of `v` to the current vector More...

NumericVectorWithOffset &	operator+= (const elemT &v)
	adding an `elemT` to the elements of the current vector

NumericVectorWithOffset &	operator-= (const NumericVectorWithOffset &v)
	subtracting elements of `v` from the current vector More...

NumericVectorWithOffset &	operator-= (const elemT &v)
	subtracting an `elemT` from the elements of the current vector

NumericVectorWithOffset &	operator*= (const NumericVectorWithOffset &v)
	multiplying elements of the current vector with elements of `v` More...

NumericVectorWithOffset &	operator*= (const elemT &v)
	multiplying the elements of the current vector with an `elemT`

NumericVectorWithOffset &	operator/= (const NumericVectorWithOffset &v)
	dividing all elements of the current vector by elements of `v` More...

NumericVectorWithOffset &	operator/= (const elemT &v)
	dividing the elements of the current vector by an `elemT`

STIR_DEPRECATED void	axpby (const elemT2 a, const NumericVectorWithOffset &x, const elemT2 b, const NumericVectorWithOffset &y)

void	axpby (const NUMBER2 a, const NumericVectorWithOffset &x, const NUMBER2 b, const NumericVectorWithOffset &y)

void	xapyb (const NumericVectorWithOffset &x, const elemT a, const NumericVectorWithOffset &y, const elemT b)
	set values of the array to xa+yb, where a and b are scalar

void	xapyb (const NumericVectorWithOffset &x, const NumericVectorWithOffset &a, const NumericVectorWithOffset &y, const NumericVectorWithOffset &b)
	set the values of the array to xa+yb, where a and b are vectors

void	sapyb (const T2 &a, const NumericVectorWithOffset &y, const T2 &b)
	set the values of the array to selfa+yb, where a and b are scalar or vectors

Public Member Functions inherited from stir::VectorWithOffset< Array< num_dimensions - 1, elemT > >
	VectorWithOffset ()
	Default constructor: creates a vector of length 0.

	VectorWithOffset (const int hsz)
	Construct a VectorWithOffset of given length (initialised with `T()`)

	VectorWithOffset (const int min_index, const int max_index)
	Construct a VectorWithOffset with offset `min_index` (initialised with `T()`)

STIR_DEPRECATED	VectorWithOffset (const int hsz, Array< num_dimensions - 1, elemT > const data_ptr, Array< num_dimensions - 1, elemT > const end_of_data_ptr)
	Construct a VectorWithOffset of given length pointing to existing data. More...

STIR_DEPRECATED	VectorWithOffset (const int min_index, const int max_index, Array< num_dimensions - 1, elemT > const data_ptr, Array< num_dimensions - 1, elemT > const end_of_data_ptr)
	Construct a VectorWithOffset with offset `min_index` pointing to existing data. More...

	VectorWithOffset (const int hsz, const Array< num_dimensions - 1, elemT > *const data_ptr)
	Construct a VectorWithOffset of given length from a bare pointer (copying data)

	VectorWithOffset (const int min_index, const int max_index, const Array< num_dimensions - 1, elemT > *const data_ptr)
	Construct a VectorWithOffset with offset `min_index` from a bare pointer (copying data)

	VectorWithOffset (const int min_index, const int max_index, shared_ptr< Array< num_dimensions - 1, elemT > []> data_sptr)
	Construct a VectorWithOffset sharing existing data. More...

	VectorWithOffset (const int sz, shared_ptr< Array< num_dimensions - 1, elemT > []> data_sptr)
	Construct a VectorWithOffset sharing existing data. More...

	VectorWithOffset (const VectorWithOffset &il)
	copy constructor

	VectorWithOffset (VectorWithOffset &&other) noexcept
	move constructor More...

virtual	~VectorWithOffset ()
	Destructor.

void	recycle ()
	Free all memory and make object as if default-constructed. More...

VectorWithOffset &	operator= (const VectorWithOffset &il)
	assignment operator with another vector More...

Array< num_dimensions - 1, elemT > &	operator[] (int i)
	allow array-style access, read/write More...

const Array< num_dimensions - 1, elemT > &	operator[] (int i) const
	array access, read-only More...

Array< num_dimensions - 1, elemT > &	at (int i)
	allow array-style access, read/write, but with range checking (throws std::out_of_range)

const Array< num_dimensions - 1, elemT > &	at (int i) const
	array access, read-only, but with range checking (throws std::out_of_range)

bool	empty () const
	checks if the vector is empty

void	fill (const Array< num_dimensions - 1, elemT > &n)
	fill elements with value n

void	apply_lower_threshold (const Array< num_dimensions - 1, elemT > &lower)
	Sets elements below value to the value.

void	apply_upper_threshold (const Array< num_dimensions - 1, elemT > &upper)
	Sets elements above value to the value.

int	get_length () const
	return number of elements in this vector More...

size_t	size () const
	return number of elements in this vector

int	get_min_index () const
	get value of first valid index

int	get_max_index () const
	get value of last valid index

void	set_offset (const int min_index)
	change value of starting index

void	set_min_index (const int min_index)
	identical to set_offset()

virtual void	grow (const int min_index, const int max_index)
	grow the range of the vector, new elements are set to `T()` More...

void	grow (const unsigned int new_size)
	grow the range of the vector from 0 to new_size-1, new elements are set to `T()`

virtual void	resize (const int min_index, const int max_index)
	change the range of the vector, new elements are set to `T()` More...

void	resize (const unsigned int new_size)
	change the range of the vector from 0 to new_size-1, new elements are set to `T()`

void	reserve (const int min_index, const int max_index)
	make the allocated range at least from min_index to max_index

void	reserve (const unsigned int new_size)
	make the allocated range at least from 0 to new_size-1

size_t	capacity () const
	get allocated size

bool	owns_memory_for_data () const
	check if this object owns the memory for the data More...

int	get_capacity_min_index () const
	get min_index within allocated range More...

int	get_capacity_max_index () const
	get max_index within allocated range More...

bool	operator== (const VectorWithOffset &iv) const

bool	operator!= (const VectorWithOffset &iv) const

Array< num_dimensions - 1, elemT > *	get_data_ptr ()
	member function for access to the data via a T* More...

const Array< num_dimensions - 1, elemT > *	get_const_data_ptr () const
	member function for access to the data via a const T* More...

void	release_data_ptr ()
	signal end of access to T* More...

void	release_const_data_ptr () const
	signal end of access to const T* More...

iterator	begin ()
	use to initialise an iterator to the first element of the vector

const_iterator	begin () const
	use to initialise an iterator to the first element of the (const) vector

iterator	end ()
	iterator 'past' the last element of the vector

const_iterator	end () const
	iterator 'past' the last element of the (const) vector

reverse_iterator	rbegin ()

const_reverse_iterator	rbegin () const

reverse_iterator	rend ()

const_reverse_iterator	rend () const

VectorWithOffset &	operator+= (const VectorWithOffset &v)
	adding elements of `v` to the current vector

VectorWithOffset &	operator-= (const VectorWithOffset &v)
	subtracting elements of `v` from the current vector

VectorWithOffset &	operator*= (const VectorWithOffset &v)
	multiplying elements of the current vector with elements of `v`

VectorWithOffset &	operator/= (const VectorWithOffset &v)
	dividing all elements of the current vector by elements of `v`

VectorWithOffset	operator+ (const VectorWithOffset &v) const
	adding vectors, element by element

VectorWithOffset	operator- (const VectorWithOffset &v) const
	subtracting vectors, element by element

VectorWithOffset	operator* (const VectorWithOffset &v) const
	multiplying vectors, element by element

VectorWithOffset	operator/ (const VectorWithOffset &v) const
	dividing vectors, element by element

Static Public Member Functions
static DiscretisedDensity *	read_from_file (const std::string &filename)
	A static member to read an image from file. More...

Protected Member Functions
virtual bool	actual_has_same_characteristics (DiscretisedDensity< num_dimensions, elemT > const &, std::string &explanation) const
	Implementation used by has_same_characteristics. More...

virtual CartesianCoordinate3D< float >	actual_get_relative_coordinates_for_indices (const BasicCoordinate< num_dimensions, float > &indices) const =0
	Implementation used by get_relative_coordinates_for_indices. More...

virtual BasicCoordinate< num_dimensions, float >	actual_get_index_coordinates_for_relative_coordinates (const CartesianCoordinate3D< float > &coords) const =0

Protected Member Functions inherited from stir::VectorWithOffset< Array< num_dimensions - 1, elemT > >
void	check_state () const
	Called internally to see if all variables are consistent. More...

void	init (const int min_index, const int max_index, Array< num_dimensions - 1, elemT > *const data_ptr, bool copy_data)
	change vector with new index range and point to `data_ptr` More...

Additional Inherited Members
Protected Attributes inherited from stir::ExamData
shared_ptr< const ExamInfo >	exam_info_sptr

Protected Attributes inherited from stir::VectorWithOffset< Array< num_dimensions - 1, elemT > >
Array< num_dimensions - 1, elemT > *	num
	pointer to (*this)[0] (taking get_min_index() into account that is).

Detailed Description

template<int num_dimensions, typename elemT>
class stir::DiscretisedDensity< num_dimensions, elemT >

This abstract class is the basis for all image representations.

This class is templated with the number of dimensions (should be 1, 2 or 3) and the type of the data.

It defines functionality common to all discretised densities: the data structure itself (Array) and an origin.

Warning: The origin is always a CartesianCoordinate3D<float>, independent of what coordinate system (or even dimension) this class represents. Similarly, the functions that translate from indices to physical coordinates assume that the later is 3D.

Iterative algorithms generally assume that the activity density can be discretised in some way. That is, the continuous density can be approximated by having a linear combination of some basis-functions. The reconstruction problem will try to estimate the coefficients $\lambda_{ijk}$ of the discretised density

$\sum_{ijk} \lambda_{ijk} b_{ijk}({\bar x})$

The base class corresponding to this kind of data is DiscretisedDensity. We assume that the set of basisfunctions can be characterised by 3 indices (ijk) such that i runs over a range of integers i1..i2, j runs over a similar range that can however depend on i, and k runs over a similar range that can depend on i and j. This concept of ranges is embodied in the IndexRange class. Multi-dimensional arrays which have such ranges are encoded by the Array class. This forms the data structure for the set of coefficients of the basisfunctions, hence DiscretisedDensity is derived from the Array class.

In most useful cases, the basisfunctions will be translations of a single function b(x) (although scaling etc could occur depending on ijk). This means that the discretisation has a certain grid, corresponding to the centre of the basisfunctions. This structure is the next level in the image hierarchy. Currently we have the class DiscretisedDensityOnCartesianGrid to implement the case where the grid is formed by an orthogonal set of vectors. Another case would be e.g. DiscretisedDensityOnCylindricalGrid, but we have not implemented this yet.

The next level in the hierarchy is then finally the specification of the basis functions themselves. We currently have only voxels and pixels, but another useful case would be to use Kaiser-Bessel functions (so called Blobs). This leads us to the image hierarchy as shown in the class diagram.

Member Typedef Documentation

◆ hierarchy_base_type

template<int num_dimensions, typename elemT>

typedef DiscretisedDensity<num_dimensions, elemT> stir::DiscretisedDensity< num_dimensions, elemT >::hierarchy_base_type

A typedef that can be used what the base of the hierarchy is.

For these purposes, we don't use Array (even though it's the base_type) as DiscretisedDensity is used in STIR as the type for any image.

This typedef is used in write_to_file().

Member Function Documentation

◆ read_from_file()

template<int num_dimensions, typename elemT >

DiscretisedDensity< num_dimensions, elemT > * stir::DiscretisedDensity< num_dimensions, elemT >::read_from_file ( const std::string & filename )

static

A static member to read an image from file.

Deprecated:: This function just calls stir::read_from_file.

◆ get_physical_coordinates_for_indices() [1/2]

template<int num_dimensions, typename elemT >

CartesianCoordinate3D< float > stir::DiscretisedDensity< num_dimensions, elemT >::get_physical_coordinates_for_indices ( const BasicCoordinate< num_dimensions, int > & indices ) const

inline

Return the coordinates of the centre of the basis-function corresponding to indices.

We distinguish between physical coordinates, relative coordinates (which are physical coordinates relative to the origin) and index coordinates (which run over the index range (but are allowed to have float values).

This class provides 3-way conversion functions. The derived classes have to implement the actual conversion between relative and index coordinates.

We distinguish also a fourth coordinate system, an LPS patient-based one. It is similar to the physical one, but the x (i.e. fastest-running) axis runs left-wards on the patient, the y-axis runs posterior-wards on the patient and the z-axis runs superior-wards on the patient. Conversion to this coordinate system depends on the patient position being recorded correctly. Only the most common patient positions are currently implemented.

The return value is in the same coordinate system as get_origin(). Implemented as

get_relative_coordinates_for_indices(indices)+get_origin()

◆ get_physical_coordinates_for_indices() [2/2]

template<int num_dimensions, typename elemT >

CartesianCoordinate3D< float > stir::DiscretisedDensity< num_dimensions, elemT >::get_physical_coordinates_for_indices ( const BasicCoordinate< num_dimensions, float > & indices ) const

inline

Return the coordinates of the centre of the basis-function corresponding to non-integer coordinate in 'physical' coordinates.

See also: get_physical_coordinates_for_indices(const BasicCoordinate<num_dimensions,int>&)

◆ get_relative_coordinates_for_indices() [1/2]

template<int num_dimensions, typename elemT >

CartesianCoordinate3D< float > stir::DiscretisedDensity< num_dimensions, elemT >::get_relative_coordinates_for_indices ( const BasicCoordinate< num_dimensions, int > & indices ) const

inline

Return the relative coordinates of the centre of the basis-function corresponding to indices.

Implementation uses actual_get_relative_coordinates_for_indices

◆ get_relative_coordinates_for_indices() [2/2]

template<int num_dimensions, typename elemT >

CartesianCoordinate3D< float > stir::DiscretisedDensity< num_dimensions, elemT >::get_relative_coordinates_for_indices ( const BasicCoordinate< num_dimensions, float > & indices ) const

inline

Return the relative coordinates of the centre of the basis-function corresponding to the non-integer coordinates in 'index' coordinates.

The return value is relative to the origin.

Implementation uses actual_get_relative_coordinates_for_indices

See also: get_physical_coordinates_for_indices()

◆ get_indices_closest_to_physical_coordinates()

template<int num_dimensions, typename elemT >

BasicCoordinate< num_dimensions, int > stir::DiscretisedDensity< num_dimensions, elemT >::get_indices_closest_to_physical_coordinates ( const CartesianCoordinate3D< float > & coords ) const

inline

Return the indices of the basis-function closest to the given point.

The input argument should be in the same coordinate system as get_origin(). Implemented as

get_indices_closest_to_relative_coordinates(coords-get_origin())

◆ get_indices_closest_to_relative_coordinates()

template<int num_dimensions, typename elemT >

BasicCoordinate< num_dimensions, int > stir::DiscretisedDensity< num_dimensions, elemT >::get_indices_closest_to_relative_coordinates ( const CartesianCoordinate3D< float > & coords ) const

inline

Return the indices of the basis-function closest to the given point.

The input argument should be in 'physical' coordinates relative to the origin. Implementation uses stir::round on the result of get_index_coordinates_for_relative_coordinates.

◆ get_index_coordinates_for_physical_coordinates()

template<int num_dimensions, typename elemT >

BasicCoordinate< num_dimensions, float > stir::DiscretisedDensity< num_dimensions, elemT >::get_index_coordinates_for_physical_coordinates ( const CartesianCoordinate3D< float > & coords ) const

inline

Return the indices of the basis-function closest to the given point.

The input argument should be in 'physical' coordinates. Implementation uses get_index_coordinates_for_relative_coordinates.

◆ get_index_coordinates_for_relative_coordinates()

template<int num_dimensions, typename elemT >

BasicCoordinate< num_dimensions, float > stir::DiscretisedDensity< num_dimensions, elemT >::get_index_coordinates_for_relative_coordinates ( const CartesianCoordinate3D< float > & coords ) const

inline

Return the index-coordinates of the basis-function closest to the given point.

The input argument should be in 'physical' coordinates relative to the origin. Implementation uses actual_get_index_coordinates_for_relative_coordinates.

◆ has_same_characteristics() [1/2]

template<int num_dimensions, typename elemT>

bool stir::DiscretisedDensity< num_dimensions, elemT >::has_same_characteristics	(	self_type const &	,
		std::string &	explanation
	)		const

inline

Checks if the 2 objects have the same type, index range, origin etc.

If they do not have the same characteristics, the string explanation explains why.

Referenced by stir::LogcoshPrior< elemT >::accumulate_Hessian_times_input(), stir::QuadraticPrior< float >::accumulate_Hessian_times_input(), stir::RelativeDifferencePrior< elemT >::accumulate_Hessian_times_input(), stir::QuadraticPrior< float >::add_multiplication_with_approximate_Hessian(), stir::QuadraticPrior< float >::compute_gradient(), stir::LogcoshPrior< elemT >::compute_gradient(), stir::RelativeDifferencePrior< elemT >::compute_gradient(), stir::BackProjectorByBin::get_output(), stir::QuadraticPrior< float >::parabolic_surrogate_curvature(), and stir::LogcoshPrior< elemT >::parabolic_surrogate_curvature().

◆ has_same_characteristics() [2/2]

template<int num_dimensions, typename elemT>

bool stir::DiscretisedDensity< num_dimensions, elemT >::has_same_characteristics ( self_type const & ) const

inline

Checks if the 2 objects have the same type, index range, origin etc.

Use this version if you do not need to know why they do not match.

◆ operator==()

template<int num_dimensions, typename elemT >

bool stir::DiscretisedDensity< num_dimensions, elemT >::operator== ( const self_type & that ) const

inline

check equality (data has to be identical)

Uses has_same_characteristics() and Array::operator==.

Warning: This function uses ==, which might not be what you need to check when elemT has data with float or double numbers.

◆ actual_has_same_characteristics()

template<int num_dimensions, typename elemT>

bool stir::DiscretisedDensity< num_dimensions, elemT >::actual_has_same_characteristics	(	DiscretisedDensity< num_dimensions, elemT > const &	other,
		std::string &	explanation
	)		const

protectedvirtual

Implementation used by has_same_characteristics.

Warning: Has to be overloaded by the derived classes to check for other parameters. Also, the overloaded function has to call the current one.

Developer's note

We need this function as C++ rules say that if you overload a function, you hide all functions of the same name.

Reimplemented in stir::DiscretisedDensityOnCartesianGrid< num_dimensions, elemT >, stir::DiscretisedDensityOnCartesianGrid< 2, elemT >, and stir::DiscretisedDensityOnCartesianGrid< 3, elemT >.

◆ actual_get_relative_coordinates_for_indices()

template<int num_dimensions, typename elemT>

virtual CartesianCoordinate3D<float> stir::DiscretisedDensity< num_dimensions, elemT >::actual_get_relative_coordinates_for_indices ( const BasicCoordinate< num_dimensions, float > & indices ) const

protectedpure virtual

Implementation used by get_relative_coordinates_for_indices.

Developer's note

We need this function as C++ rules say that if you overload a function, you hide all functions of the same name.

Implemented in stir::DiscretisedDensityOnCartesianGrid< num_dimensions, elemT >, stir::DiscretisedDensityOnCartesianGrid< 2, elemT >, and stir::DiscretisedDensityOnCartesianGrid< 3, elemT >.

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

/home/sirfuser/devel/STIRdistrib/STIR/src/include/stir/analytic/FBP2D/FBP2DReconstruction.h
/home/sirfuser/devel/STIRdistrib/STIR/src/include/stir/DiscretisedDensity.h
/home/sirfuser/devel/STIRdistrib/STIR/src/buildblock/DiscretisedDensity.cxx
/home/sirfuser/devel/STIRdistrib/STIR/src/include/stir/DiscretisedDensity.inl

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

template<int num_dimensions, typename elemT> class stir::DiscretisedDensity< num_dimensions, elemT >

Member Typedef Documentation

◆ hierarchy_base_type

Member Function Documentation

◆ read_from_file()

◆ get_physical_coordinates_for_indices() [1/2]

◆ get_physical_coordinates_for_indices() [2/2]

◆ get_relative_coordinates_for_indices() [1/2]

◆ get_relative_coordinates_for_indices() [2/2]

◆ get_indices_closest_to_physical_coordinates()

◆ get_indices_closest_to_relative_coordinates()

◆ get_index_coordinates_for_physical_coordinates()

◆ get_index_coordinates_for_relative_coordinates()

◆ has_same_characteristics() [1/2]

◆ has_same_characteristics() [2/2]

◆ operator==()

◆ actual_has_same_characteristics()

◆ actual_get_relative_coordinates_for_indices()

template<int num_dimensions, typename elemT>
class stir::DiscretisedDensity< num_dimensions, elemT >