#include <AnatomyPlugin/include/ImFusion/AnatomyPlugin/AnatomicalStructureCollection.h>

Interface for managing collections of anatomical structures For a concrete implementation of this class, see GenericASC. More...

Inheritance diagram for AnatomicalStructureCollection:

Detailed Description

Interface for managing collections of anatomical structures For a concrete implementation of this class, see GenericASC.

Public Member Functions
	AnatomicalStructureCollection (bool is2D=false)

virtual int	numAnatomicalStructures () const =0

	AnatomicalStructureCollection (const AnatomicalStructureCollection &)=delete

AnatomicalStructureCollection &	operator= (const AnatomicalStructureCollection &)=delete

virtual const AnatomicalStructure &	anatomicalStructure (int index) const =0
	Returns the anatomical structure at index `index`.

virtual AnatomicalStructure &	anatomicalStructure (int index)=0
	Returns the anatomical structure at index `index`.

AnatomicalStructure *	anatomicalStructureByIdentifier (const std::string &identifier)

const AnatomicalStructure *	anatomicalStructureByIdentifier (const std::string &identifier) const

virtual std::vector< const AnatomicalStructure * >	anatomicalStructures () const
	Returns a vector of pointers to all anatomical structures.

virtual std::vector< AnatomicalStructure * >	anatomicalStructures ()

Pose::TransformationConvention	matrixConvention () const final override
	Defines whether the internally stored matrices in derived classes map from or to the world coordinate system.

Geometry::AlignedBox	bounds () const override
	Returns the axis-aligned bounding box of this data in world space.

DataList	children () const override
	Returns the list of direct children of this group.

bool	enableChildren ()

void	setEnableChildren (bool enableChildren)

virtual int	anatomicalStructureIndex (const AnatomicalStructure *anatomicalStructure) const
	Return the index corresponding to a given anatomical structure.

virtual bool	addAnatomicalStructure (std::unique_ptr< AnatomicalStructure > toAdd)
	Add an anatomical structure to this collection.

virtual std::unique_ptr< AnatomicalStructure >	takeAnatomicalStructure (AnatomicalStructure *a)
	Take an anatomical structure from this collection.

int	size () const override

bool	empty () const override
	Retuns true if all members are empty, i.e. this structure has no associated information.

void	merge (const AnatomicalStructureCollection &other, bool checkIdentifier=true)
	Merges the collection `other` into the current collection by adding all anatomical structures from `other`.

void	clear () override
	Clear all data contained in this structure.

ASCSet *	parent () const
	If the AnatomicalStructureCollection is part of an ASCSet, the parent ASCSet of the anatomical structure.

void	setParent (ASCSet *parent)
	Sets the parent ASCSet of the anatomical structure.

mat4	matrixToWorld () const
	Get matrix mapping from the data coordinate system to the world coordinate system.

virtual void	setMatrixToWorld (const mat4 &m, bool synchronizeWorld=true)
	Set the local to world matrix of this object.

Public Member Functions inherited from AnatomicalStructure
	AnatomicalStructure (bool is2D=false)

	AnatomicalStructure (AnatomicalStructure &other)

	AnatomicalStructure (AnatomicalStructure &&other)

virtual std::string	describe () const
	A (human-readable) description of this anatomy.

virtual std::string	identifier () const =0
	A (machine-readable) name of the anatomy.

virtual std::string	serializationID () const =0
	String differentiating the type of Anatomical Structure For imfusion types, these strings should start with "imfusion." Used for (de)serialization.

mat4	matrixToWorld () const

virtual Geometry::AlignedBox	bounds (const mat4 &orientation=mat4::Identity(), const std::vector< ContentType > &toConsider={ContentType::Keypoints, ContentType::PointClouds, ContentType::Meshes, ContentType::Splines, ContentType::Graphs}) const

Properties &	attributes ()

Properties const &	attributes () const

template<typename Derived>
std::unique_ptr< Derived >	clone () const
	Helper function for calling cloneImpl() and casting to a specific type.

void	configure (const Properties *p) override
	Configure attributes and parameters.

void	configuration (Properties *p) const override
	Retrieve configuration of attributes and parameters.

bool	is2D () const
	Returns true if the AnatomicalStructure is 2D or false if it is 3D.

virtual std::unique_ptr< AnatomicalStructure >	construct () const =0

KeyValueStore< vec3 > &	keypoints ()
	Getters for non-Data key/value stores.

const KeyValueStore< vec3 > &	keypoints () const

KeyValueStore< vec4 > &	planes ()

const KeyValueStore< vec4 > &	planes () const

KeyValueStore< std::unique_ptr< Spline > > &	splines ()

const KeyValueStore< std::unique_ptr< Spline > > &	splines () const

KeyValueStore< std::unique_ptr< SharedImageSet > > &	images ()
	Getters for Data key/value stores.

const KeyValueStore< std::unique_ptr< SharedImageSet > > &	images () const

KeyValueStore< std::unique_ptr< Mesh > > &	meshes ()

const KeyValueStore< std::unique_ptr< Mesh > > &	meshes () const

KeyValueStore< std::unique_ptr< PointCloud > > &	pointclouds ()

const KeyValueStore< std::unique_ptr< PointCloud > > &	pointclouds () const

KeyValueStore< std::unique_ptr< Graph > > &	graphs ()

const KeyValueStore< std::unique_ptr< Graph > > &	graphs () const

KeyValueStore< AnatomicalStructureDeformation > &	deformations ()

const KeyValueStore< AnatomicalStructureDeformation > &	deformations () const

Public Member Functions inherited from Configurable
virtual void	configureDefaults ()
	Retrieve the properties of this object, replaces values with their defaults and sets it again.

void	registerParameter (ParameterBase *param)
	Register the given Parameter or SubProperty, so that it will be configured during configure()/configuration().

void	unregisterParameter (const ParameterBase *param)
	Remove the given Parameter or SubProperty from the list of registered parameters.

	Configurable (const Configurable &rhs)

	Configurable (Configurable &&rhs) noexcept

Configurable &	operator= (const Configurable &)

Configurable &	operator= (Configurable &&) noexcept

Public Member Functions inherited from Data
	Data (const std::string &name="")

	Data (const Data &other)

Data &	operator= (const Data &other)

virtual	~Data ()
	Mandatory virtual destructor.

virtual Kind	kind () const =0
	Return the kind of this data.

virtual Modality	modality () const
	Return the modality of this data.

const std::string &	name () const
	Return the name of this data.

void	setName (const std::string &name)
	Sets the name of this data.

virtual bool	isAnnotationType () const
	Return whether this data type is visualized through an annotation (e.g. mesh)

const DataComponentList &	components () const
	Returns the list of DataComponents for this data.

DataComponentList &	components ()

virtual std::string	describe () const
	Human readable description of the data for showing in the info bar.

virtual void	setMatrixFromWorld (const mat4 &m)
	Set matrix mapping from the world coordinate system to the data coordinate system.

virtual void	setMatrixToWorld (const mat4 &m)
	Set matrix mapping from the data coordinate system to the world coordinate system.

virtual mat4	matrixFromWorld () const
	Get matrix mapping from the world coordinate system to the data coordinate system.

virtual mat4	matrix () const
	Return the transformation matrix.

virtual void	setMatrix (const mat4 &m)
	Set the transformation matrix.

Public Member Functions inherited from SignalReceiver
	SignalReceiver ()=default
	Default constructor.

	SignalReceiver (const SignalReceiver &other)
	Copy constructor, does not copy any existing signal connections from other.

SignalReceiver &	operator= (SignalReceiver rhs)
	Assignment operator, disconnects all existing connections, does not copy any existing signal connections from rhs.

virtual	~SignalReceiver ()
	Virtual destructor disconnects from all connected signals.

Public Member Functions inherited from Selectable
	Selectable (const Selectable &)

	Selectable (Selectable &&)

Selectable &	operator= (const Selectable &)

Selectable &	operator= (Selectable &&)

virtual Selection	selection () const

virtual int	focus () const

virtual void	setSelection (const Selection &sel)
	Set the underlying selection.

virtual void	setFocus (int index)
	Set focus of the selection.

Public Attributes
Signal< AnatomicalStructure * >	signalAnatomicalStructureToBeDeleted

Signal< AnatomicalStructure * >	signalAnatomicalStructureAdded

Signal	signalDataChanged
	This signal can be emitted after changing included anatomical structures or parameters owned by this object.

Signal	signalMatrixChanged

Public Attributes inherited from AnatomicalStructure
Signal	signalMatrixChanged

Signal	signalInDestructor
	This signal is called in the destructor. Classes that inherit from AnatomicalStructure may additionally emit this signal.

Public Attributes inherited from Configurable
Signal	signalParametersChanged
	Emitted whenever one of the registered Parameters' or SubPropertys' `signalValueChanged` signal was emitted.

Public Attributes inherited from Data
Signal< const Data * >	signalDeleted
	Signal emitted when this instance is deleted.

Signal< const Data * >	signalMatrixChanged
	Signal emitted when the transformation of this Data has changed.

Signal< std::string >	signalNameChanged
	Signal emitted when the name changed.

Public Attributes inherited from CompoundData
Signal< Data * >	signalChildAdded
	Signal emitted when a new Data instance has been added to children()

Signal< Data * >	signalChildMoved
	Signal emitted when a Data instance has changed its position in children()

Signal< Data * >	signalChildAboutToBeRemoved
	Signal emitted when a Data instance is about to be removed or taken from children()

Public Attributes inherited from Selectable
ProtectedSignal	signalSelectionChanged
	Signals that the selection or size might have changed.

Additional Inherited Members
Public Types inherited from AnatomicalStructure
using	ContentType = AnatomyPlugin::ContentType

Public Types inherited from Data
enum	Kind { UNKNOWN = 0 , IMAGE = 1 , VOLUME = 2 , IMAGESET = 3 , VOLUMESET = 4 , IMAGESTREAM = 5 , VOLUMESTREAM = 6 , POINTSET = 7 , SURFACE = 8 , TRACKINGSTREAM = 9 , LIVETRACKINGSTREAM = TRACKINGSTREAM , TRACKINGDATA = 10 , TREE = 11 , TENSOR = 12 , POLYDATASTREAM = 13 , STEREOIMAGESET = 14 , STEREOIMAGESTREAM = 15 , VOLUMETRICMESH = 16 }
	Kind of data. More...

enum	Modality { NA = 0 , XRAY = 1 , CT = 2 , MRI = 3 , ULTRASOUND = 4 , VIDEO = 5 , NM = 6 , OCT = 7 , LABEL = 8 , DISTANCE = 9 }
	Image modality of the data. More...

Static Public Member Functions inherited from Data
static std::string	modalityString (Data::Modality m)
	Return the name of an image modality.

static Data::Modality	stringToModality (const std::string &s)
	Returns the modality corresponding to a modality string or NA if nothing matches.

Protected Member Functions inherited from AnatomicalStructure
virtual std::unique_ptr< AnatomicalStructure >	cloneImpl () const
	Derived classes may override this, but should call the base class `cloneImpl` to obtain a (unique-ptr) which they may assume to point to an object of the derived class.

Protected Member Functions inherited from NotCopyable
	NotCopyable (NotCopyable &&) noexcept=default

NotCopyable &	operator= (NotCopyable &&) noexcept=default

	NotCopyable (const NotCopyable &)=delete

NotCopyable &	operator= (const NotCopyable &)=delete

Protected Member Functions inherited from Data
void	swapWith (Data &other)
	Swaps the data and emits a matrix and name changed signal for both.

Protected Member Functions inherited from SignalReceiver
void	disconnectAll ()
	Disconnects all existing connections.

Protected Attributes inherited from AnatomicalStructure
mat4	m_matrixToWorld = mat4::Identity()

KeyValueStore< vec3 >	m_keypoints {m_matrixToWorld}

KeyValueStore< vec4 >	m_planes {m_matrixToWorld}

KeyValueStore< std::unique_ptr< Spline > >	m_splines {m_matrixToWorld}

KeyValueStore< std::unique_ptr< SharedImageSet > >	m_images {m_matrixToWorld}

KeyValueStore< std::unique_ptr< Mesh > >	m_meshes {m_matrixToWorld}

KeyValueStore< std::unique_ptr< PointCloud > >	m_pointClouds {m_matrixToWorld}

KeyValueStore< std::unique_ptr< Graph > >	m_graphs {m_matrixToWorld}

KeyValueStore< AnatomicalStructureDeformation >	m_deformations {m_matrixToWorld}

Properties	m_attributes
	General properties object for the Anatomical Structure.

bool	m_is2D
	Indicates if the AnatomicalStructure information is in 2D or, if false, in 3D.

Protected Attributes inherited from Configurable
std::vector< Param >	m_params
	List of all registered Parameter and SubProperty instances.

Protected Attributes inherited from Data
mat4	m_matrix
	Transformation matrix.

std::recursive_mutex *	m_matrixMutex
	Used to internally synchronize access to the matrix of data.

DataComponentList	m_dataComponentList
	The list of DataComponents for this data.

Protected Attributes inherited from Selectable
std::mutex	m_selectionMutex
	Mutex protecting the selection.

Selection	m_sel

Member Function Documentation

◆ numAnatomicalStructures()

virtual int numAnatomicalStructures ( ) const

pure virtual

Implemented in GenericASC.

◆ anatomicalStructure() [1/2]

virtual const AnatomicalStructure & anatomicalStructure ( int index ) const

pure virtual

Returns the anatomical structure at index index.

Warning: the index must be non-negative and smaller than the result of numAnatomicalStructures

Implemented in GenericASC, and SpineData.

◆ anatomicalStructure() [2/2]

virtual AnatomicalStructure & anatomicalStructure ( int index )

pure virtual

Returns the anatomical structure at index index.

Warning: the index must be non-negative and smaller than the result of numAnatomicalStructures

Implemented in GenericASC, and SpineData.

◆ matrixConvention()

Pose::TransformationConvention matrixConvention ( ) const

inlinefinaloverridevirtual

Defines whether the internally stored matrices in derived classes map from or to the world coordinate system.

Changes the behavior of the default implementations of matrixToWorld and matrixFromWorld.

Implements Data.

◆ bounds()

Geometry::AlignedBox bounds ( ) const

overridevirtual

Returns the axis-aligned bounding box of this data in world space.

Warning: Depending on the underlying data type this calling function may be computationally expensive! Do not call this method more often than needed, unless it is known that the caching behavior is implemented.

Implements Data.

Reimplemented in GenericASC, and SpineData.

◆ children()

DataList children ( ) const

overridevirtual

Returns the list of direct children of this group.

Implements CompoundData.

◆ anatomicalStructureIndex()

virtual int anatomicalStructureIndex ( const AnatomicalStructure * anatomicalStructure ) const

virtual

Return the index corresponding to a given anatomical structure.

If the anatomical structure is not included in this AnatomicalStructureCollection object, -1 is returned.

Reimplemented in GenericASC, and SpineData.

◆ addAnatomicalStructure()

virtual bool addAnatomicalStructure ( std::unique_ptr< AnatomicalStructure > toAdd )

inlinevirtual

Add an anatomical structure to this collection.

Returns false if the anatomical structure that is being added is not supported

Reimplemented in GenericASC, and SpineData.

◆ takeAnatomicalStructure()

virtual std::unique_ptr< AnatomicalStructure > takeAnatomicalStructure ( AnatomicalStructure * a )

inlinevirtual

Take an anatomical structure from this collection.

Reimplemented in GenericASC, and SpineData.

◆ size()

int size ( ) const

overridevirtual

Returns: Total number of elements.

Implements Selectable.

◆ empty()

bool empty ( ) const

overridevirtual

Retuns true if all members are empty, i.e. this structure has no associated information.

Reimplemented from AnatomicalStructure.

◆ merge()

void merge	(	const AnatomicalStructureCollection &	other,
		bool	checkIdentifier = true )

Merges the collection other into the current collection by adding all anatomical structures from other.

If an anatomical structure with the same identifier exists in both collections, the current one is kept. The identifier check can be disabled by setting checkIdentifier to false.

◆ clear()

void clear ( )

overridevirtual

Clear all data contained in this structure.

Reimplemented from AnatomicalStructure.

Reimplemented in SpineData.

◆ parent()

ASCSet * parent ( ) const

inline

If the AnatomicalStructureCollection is part of an ASCSet, the parent ASCSet of the anatomical structure.

Warning: Users should never rely on an AnatomicalStructureCollection to have a parent. This coupling is only intended for display synchronization and may be removed in future versions of this plugin.

◆ setParent()

void setParent ( ASCSet * parent )

inline

Sets the parent ASCSet of the anatomical structure.

See also: the documentation of the parent() method for some warnings on the usage of this method.

◆ matrixToWorld()

mat4 matrixToWorld ( ) const

inlinevirtual

Get matrix mapping from the data coordinate system to the world coordinate system.

Inverse of matrixFromWorld.

Note: Depending on how matrices are internally stored in concrete derived classes, a matrix inversion might be necessary to obtain this mapping. The default implementation checks matrixConvention and accordingly returns matrix or its inverse.

Reimplemented from Data.

Reimplemented in SpineData.

◆ setMatrixToWorld()

virtual void setMatrixToWorld	(	const mat4 &	m,
		bool	synchronizeWorld = true )

virtual

Set the local to world matrix of this object.

If synchronizeWorld is true, then the local representation of all objects owned by this class are used to update the "world" representations. If synchronizeWorld is false, then the local representations are updated based on the "world" representations,

See also: ImpliedImageCoordinates Derived classes should call the parent version.

Reimplemented from AnatomicalStructure.

Reimplemented in GenericASC, and SpineData.

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

AnatomyPlugin/include/ImFusion/AnatomyPlugin/AnatomicalStructureCollection.h

Detailed Description

Public Member Functions

Public Attributes

Additional Inherited Members

Member Function Documentation

◆ numAnatomicalStructures()

◆ anatomicalStructure() [1/2]

◆ anatomicalStructure() [2/2]

◆ matrixConvention()

◆ bounds()

◆ children()

◆ anatomicalStructureIndex()

◆ addAnatomicalStructure()

◆ takeAnatomicalStructure()

◆ size()

◆ empty()

◆ merge()

◆ clear()

◆ parent()

◆ setParent()

◆ matrixToWorld()

◆ setMatrixToWorld()