A class for shapes that have been discretised as a volume. More...

#include "stir/Shape/DiscretisedShape3D.h"

Inheritance diagram for stir::DiscretisedShape3D:

[legend]

Public Member Functions
	DiscretisedShape3D (const VoxelsOnCartesianGrid< float > &image)
	Constructor that will copy the image to an internal member. More...

	DiscretisedShape3D (const shared_ptr< const DiscretisedDensity< 3, float >> &density_sptr)
	Constructor that will copy the shared_ptr image. More...

bool	operator== (const Shape3D &) const override
	Compare shapes. More...

void	set_origin (const CartesianCoordinate3D< float > &) override
	set origin of the shape

void	scale (const CartesianCoordinate3D< float > &scale3D) override
	Scale shape. More...

bool	is_inside_shape (const CartesianCoordinate3D< float > &index) const override
	determine if a point is inside a non-zero voxel or not More...

float	get_voxel_weight (const CartesianCoordinate3D< float > &coord, const CartesianCoordinate3D< float > &voxel_size, const CartesianCoordinate3D< int > &num_samples) const override
	get weight for a voxel centred around coord More...

void	construct_volume (VoxelsOnCartesianGrid< float > &image, const CartesianCoordinate3D< int > &num_samples) const override
	Construct a new image from the underlying density. More...

Shape3D *	clone () const override
	Allocate a new Shape3D object which is a copy of the current one.

DiscretisedDensity< 3, float > &	get_discretised_density ()
	provide access to the underlying density

const DiscretisedDensity< 3, float > &	get_discretised_density () const
	provide (const) access to the underlying density

int	get_label_index () const
	Return label index.

void	set_label_index (int label_index)
	Set label index.

Public Member Functions inherited from stir::RegisteredParsingObject< DiscretisedShape3D, Shape3D, Shape3D >
std::string	get_registered_name () const override
	Returns Derived::registered_name.

std::string	parameter_info () override
	Returns a string with all parameters and their values, in a form suitable for parsing again.

Public Member Functions inherited from stir::Shape3D
bool	operator!= (const Shape3D &) const
	Compare shapes.

virtual void	translate (const CartesianCoordinate3D< float > &direction)
	translate the whole shape by shifting its origin More...

void	scale_around_origin (const CartesianCoordinate3D< float > &scale3D)
	scale the whole shape, keeping the centre at the same place

virtual float	get_geometric_volume () const
	Compute approximate volume. More...

CartesianCoordinate3D< float >	get_origin () const
	get the origin of the shape-coordinate system

Public Member Functions inherited from stir::ParsingObject
	ParsingObject (const ParsingObject &)

ParsingObject &	operator= (const ParsingObject &)

void	ask_parameters ()

bool	parse (std::istream &f)

bool	parse (const char *const filename)

Static Public Attributes
static const char *const	registered_name = "Discretised Shape3D"
	Name which will be used when parsing a Shape3D object.

Additional Inherited Members
Static Public Member Functions inherited from stir::RegisteredParsingObject< DiscretisedShape3D, Shape3D, Shape3D >
static Shape3D *	read_from_stream (std::istream *)
	Construct a new object (of type Derived) by parsing the istream. More...

Static Public Member Functions inherited from stir::RegisteredObject< Shape3D >
static Shape3D *	read_registered_object (std::istream *in, const std::string &registered_name)
	Construct a new object (of a type derived from Root, its actual type determined by the registered_name parameter) by parsing the istream. More...

static Shape3D *	ask_type_and_parameters ()
	ask the user for the type, and then calls read_registered_object(0, type) More...

static void	list_registered_names (std::ostream &stream)
	List all possible registered names to the stream. More...

Protected Types inherited from stir::RegisteredObject< Shape3D >
typedef Shape3D (	RootFactory) (std::istream *)
	The type of a root factory is a function, taking an istream* as argument, and returning a Root*.

typedef FactoryRegistry< std::string, RootFactory, interfile_less >	RegistryType
	The type of the registry.

Protected Member Functions inherited from stir::Shape3D
	Shape3D (const CartesianCoordinate3D< float > &origin)

void	set_defaults () override
	Set defaults before parsing.

void	initialise_keymap () override
	Initialise all keywords.

Protected Member Functions inherited from stir::ParsingObject
virtual void	set_key_values ()
	This will be called before parsing or parameter_info is called. More...

Static Protected Member Functions inherited from stir::RegisteredObject< Shape3D >
static RegistryType &	registry ()
	Static function returning the registry. More...

Protected Attributes inherited from stir::ParsingObject
KeyParser	parser

Detailed Description

A class for shapes that have been discretised as a volume.

Currently only supports discretisation via VoxelsOnCartesianGrid.

This class supports 2 options:

a label-image with associated label index (an integer), suitable for multiple ROIs in a single file.
a "weight" image, with (potentially) smooth edges, where voxel values vary between 0 and 1.

Parameters for parsing

Discretised Shape3D Parameters:=
input filename := <filename>
label index := -1 ; if less than 1 (default), we will use "weights"
END:=

where filename needs to specify a volume that can be read by STIR.

Constructor & Destructor Documentation

◆ DiscretisedShape3D() [1/2]

stir::DiscretisedShape3D::DiscretisedShape3D ( const VoxelsOnCartesianGrid< float > & image )

Constructor that will copy the image to an internal member.

The filename member is set to "FROM MEMORY" such that parameter_info() returns somewhat useful info. This has a consequence that the object cannot be constructed from its own parameter_info(). This is in contrast with most other shapes.

References stir::DiscretisedDensity< num_dimensions, elemT >::get_origin(), and set_origin().

◆ DiscretisedShape3D() [2/2]

stir::DiscretisedShape3D::DiscretisedShape3D ( const shared_ptr< const DiscretisedDensity< 3, float >> & density_sptr )

Constructor that will copy the shared_ptr image.

The filename member is set to "FROM MEMORY" such that parameter_info() returns somewhat useful info. This has a consequence that the object cannot be constructed from its own parameter_info(). This is in contrast with most other shapes.

References stir::KeyParser::add_key(), stir::KeyParser::add_start_key(), stir::KeyParser::add_stop_key(), stir::error(), stir::Shape3D::get_origin(), stir::Shape3D::initialise_keymap(), stir::ParsingObject::post_processing(), registered_name, stir::Shape3D::set_defaults(), set_origin(), and stir::warning().

Member Function Documentation

◆ operator==()

bool stir::DiscretisedShape3D::operator== ( const Shape3D & ) const

inlineoverridevirtual

Compare shapes.

Todo:: currently not implemented (will call error()

Implements stir::Shape3D.

References stir::error().

◆ scale()

void stir::DiscretisedShape3D::scale ( const CartesianCoordinate3D< float > & scale3D )

inlineoverridevirtual

Scale shape.

Todo:: Not implemented (will call error())

Implements stir::Shape3D.

References stir::error().

◆ is_inside_shape()

bool stir::DiscretisedShape3D::is_inside_shape ( const CartesianCoordinate3D< float > & index ) const

overridevirtual

determine if a point is inside a non-zero voxel or not

Warning: For voxels at the edges, it is somewhat ill-defined if a point in the voxel is inside the shape. The current implementation will return true for every point in the voxel, even if the voxel value is .001. In particular, this means that this definition of is_inside_shape() cannot be used to find the voxel_weight. So, we have to redefine get_voxel_weight() in the present class.

Implements stir::Shape3D.

◆ get_voxel_weight()

float stir::DiscretisedShape3D::get_voxel_weight	(	const CartesianCoordinate3D< float > &	coord,
		const CartesianCoordinate3D< float > &	voxel_size,
		const CartesianCoordinate3D< int > &	num_samples
	)		const

overridevirtual

get weight for a voxel centred around coord

Warning: Presently only works when coord is the centre of a voxel and voxel_size is identical to the image's voxel_size

The argument num_samples is ignored.

If get_label_index() >= 0, the weight will be 1 for those voxels whose value is equal to the label_index and zero otherwise. If get_label_index() < 0 (default), the weight will be the actual voxel value.

Reimplemented from stir::Shape3D.

References stir::round().

◆ construct_volume()

void stir::DiscretisedShape3D::construct_volume	(	VoxelsOnCartesianGrid< float > &	image,
		const CartesianCoordinate3D< int > &	num_samples
	)		const

overridevirtual

Construct a new image from the underlying density.

If get_label_index() >= 0, the imags need to have the same characteristics, but in the other case, zoom_image is called for interpolation. The result is then scaled such that mean ROI values remain the same (at least for ROIs which avoid edges).

The argument num_samples is ignored.

Reimplemented from stir::Shape3D.

References stir::Array< num_dimensions, elemT >::begin_all(), stir::Array< num_dimensions, elemT >::end_all(), stir::error(), stir::round(), and stir::zoom_image().

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

/home/sirfuser/devel/STIRdistrib/STIR/src/include/stir/Shape/DiscretisedShape3D.h
/home/sirfuser/devel/STIRdistrib/STIR/src/include/stir/Shape/DiscretisedShape3D.inl
/home/sirfuser/devel/STIRdistrib/STIR/src/Shape_buildblock/DiscretisedShape3D.cxx

Public Member Functions

Static Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ DiscretisedShape3D() [1/2]

◆ DiscretisedShape3D() [2/2]

Member Function Documentation

◆ operator==()

◆ scale()

◆ is_inside_shape()

◆ get_voxel_weight()

◆ construct_volume()