SpineData Class Reference

#include <SpinePlugin/include/ImFusion/Spine/SpineData.h>

Container for set of vertebrae and other spine-related metadata The SpineData class is the main Data type of the ImFusion SpinePlugin. More...

Inheritance diagram for SpineData:

Detailed Description

Container for set of vertebrae and other spine-related metadata The SpineData class is the main Data type of the ImFusion SpinePlugin.

The main functionality of the SpineData class is managing a vector of OrientedVertebra objects The SpineData class can also hold a single Sacrum and Ilium object

Public Member Functions
	SpineData (bool is2D=false)
std::unique_ptr< SpineData >	clone () const
std::unique_ptr< AnatomicalStructure >	construct () const override
std::unique_ptr< AnatomicalStructure >	cloneImpl () const override
	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.
std::string	identifier () const override
	A (machine-readable) name of the anatomy.
std::string	serializationID () const override
	String differentiating the type of Anatomical Structure For imfusion types, these strings should start with "imfusion." Used for (de)serialization.
Kind	kind () const override
	Return the kind of this data.
Geometry::AlignedBox	bounds () const override
	Returns the axis-aligned bounding box of this data in world space.
std::string	describe () const override
	A (human-readable) description of this anatomy.
void	setMatrix (const mat4 &other) override
	Set the transformation matrix.
void	setMatrix (const mat4 &other, bool syncWorld)
void	setMatrixToWorld (const mat4 &m, bool synchronize) override
	Set the local to world matrix of this object.
Properties const &	properties () const
Properties &	properties ()
virtual mat4	matrixToWorld () const
	Get matrix mapping from the data coordinate system to the world coordinate system.
virtual void	setMatrixToWorld (const mat4 &m)
	Set matrix mapping from the data coordinate system to the world coordinate system.
Public Member Functions inherited from AnatomicalStructureCollection
	AnatomicalStructureCollection (bool is2D=false)
	AnatomicalStructureCollection (const AnatomicalStructureCollection &)=delete
AnatomicalStructureCollection &	operator= (const AnatomicalStructureCollection &)=delete
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.
DataList	children () const override
	Returns the list of direct children of this group.
bool	enableChildren ()
void	setEnableChildren (bool enableChildren)
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.
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.
Public Member Functions inherited from AnatomicalStructure
	AnatomicalStructure (bool is2D=false)
	AnatomicalStructure (AnatomicalStructure &other)
	AnatomicalStructure (AnatomicalStructure &&other)
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.
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 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 void	setMatrixFromWorld (const mat4 &m)
	Set matrix mapping from the world coordinate system to the data 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.
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< const Data * >	signalMatrixChanged
	Signal emitted when the transformation of this Data has changed.
Public Attributes inherited from AnatomicalStructureCollection
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.

Signals
Signal< OrientedVertebra * >	signalVertebraToBeDeleted
	This signal is emitted with the previous value of a vertebra if the vertebra is being deleted.
Signal< Sacrum * >	signalSacrumToBeDeleted
Signal< Ilium * >	signalIliumToBeDeleted
Signal< OrientedVertebra * >	signalVertebraAdded
Signal< Sacrum * >	signalSacrumAdded
Signal< Ilium * >	signalIliumAdded

Functions implementing the AnatomicalStructureCollection interface for accessing stored AnatomicalStructure objects.
These are OrientedVertebra, Sacrum, and Ilium
int	numAnatomicalStructures () const override
const AnatomicalStructure &	anatomicalStructure (int index) const override
	Returns the anatomical structure at index index.
AnatomicalStructure &	anatomicalStructure (int index) override
	Returns the anatomical structure at index index.
int	anatomicalStructureIndex (const AnatomicalStructure *anatomicalStructure) const override
	Returns -1 if the structure is not included in this SpineData object.
bool	addAnatomicalStructure (std::unique_ptr< AnatomicalStructure > as) override
	Add an anatomical structure to this collection.
std::unique_ptr< AnatomicalStructure >	takeAnatomicalStructure (AnatomicalStructure *as) override
	Take an anatomical structure from this collection.

Functions for accessing and modifying stored OrientedVertebra objects
const std::vector< std::unique_ptr< OrientedVertebra > > &	vertebrae () const
	The entire vector of vertebrae.
std::vector< std::unique_ptr< OrientedVertebra > > &	vertebrae ()
OrientedVertebra &	vertebra (int index)
	Convenience function for accessing a single vertebra.
const OrientedVertebra &	vertebra (int index) const
IntervertebralDisc &	disc (int index)
const IntervertebralDisc &	disc (int index) const
size_t	numVertebrae () const
	Convenience function to get number of stored vertebrae.
size_t	numDiscs () const
int	vertebraIndex (const OrientedVertebra *v) const
	Convenience function for finding vertebrae.
OrientedVertebra *	vertebraByName (const std::string &name)
void	addVertebra (std::unique_ptr< OrientedVertebra > v)
	Push back a vertebra onto the list of owned vertebrae.
void	addDisc (std::unique_ptr< IntervertebralDisc > disc)
std::unique_ptr< Sacrum >	replaceSacrum (std::unique_ptr< Sacrum > sacrum)
	Replace Sacrum, and sets this as "parent" of sacrum. Returns the old sacrum.
std::unique_ptr< Ilium >	replaceIlium (std::unique_ptr< Ilium > ilium)
	Set Ilium. Returns the old ilium.
Sacrum &	sacrum ()
	Getter for the Sacrum.
const Sacrum &	sacrum () const
Ilium &	ilium ()
	Getter for the Ilium.
const Ilium &	ilium () const
std::unique_ptr< OrientedVertebra >	removeVertebra (OrientedVertebra *v)
	Remove the vertebra equal to v
std::unique_ptr< IntervertebralDisc >	removeDisc (IntervertebralDisc *disc)
void	sortVertebrae (const std::function< bool(const OrientedVertebra &, const OrientedVertebra &)> &cmp)
	Sort vertebrae using comparison function cmp.
void	sortVertebraeNN ()
	Sort vertebrae by identifying vertebra with highest z-coordinate, then iteratively selecting the closest vertebra.
bool	sortVertebraeSpline (int numSamplePoints=100, int numIterationsRANSAC=10000, double epsRANSAC=0.15, int sampleSizeRANSAC=4)
	Sort vertebrae by fitting a spline using RANSAC, then order them sequentially along the computed spline.
void	clearVertebrae ()
	Remove all vertebrae.
void	clearDiscs ()
void	clear () override
	Clear all data contained in this structure.
static bool	saveSpineData (SpineData *spineData, std::ostream &out)
static std::unique_ptr< SpineData >	loadSpineData (std::istream &in)

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 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

construct()

std::unique_ptr< AnatomicalStructure > construct ( ) const

overridevirtual

Implements AnatomicalStructure.

cloneImpl()

std::unique_ptr< AnatomicalStructure > cloneImpl ( ) const

overridevirtual

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.

This is done using the (virtual) construct function (see below).

Reimplemented from AnatomicalStructure.

identifier()

std::string identifier ( ) const

overridevirtual

A (machine-readable) name of the anatomy.

Implements AnatomicalStructure.

serializationID()

std::string serializationID ( ) const

overridevirtual

String differentiating the type of Anatomical Structure For imfusion types, these strings should start with "imfusion." Used for (de)serialization.

Implements AnatomicalStructure.

kind()

Kind kind ( ) const

inlineoverridevirtual

Return the kind of this data.

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.

Reimplemented from AnatomicalStructureCollection.

describe()

std::string describe ( ) const

overridevirtual

A (human-readable) description of this anatomy.

Reimplemented from AnatomicalStructure.

setMatrix()

void setMatrix ( const mat4 & m )

overridevirtual

Set the transformation matrix.

Note

The matrix convention expected for m depends on the concrete derived class implementation, with either a matrix mapping to or from the world coordinate system being expected. Only use if convention is explicitly known. Use methods setMatrixFromWorld or setMatrixToWorld to avoid inconsistencies. The default implementation sets m_matrix.

Reimplemented from Data.

setMatrixToWorld() [1/2]

void setMatrixToWorld ( const mat4 & m, bool synchronizeWorld )

overridevirtual

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 AnatomicalStructureCollection.

numAnatomicalStructures()

int numAnatomicalStructures ( ) const

overridevirtual

Implements AnatomicalStructureCollection.

anatomicalStructure() [1/2]

const AnatomicalStructure & anatomicalStructure ( int index ) const

overridevirtual

Returns the anatomical structure at index index.

Warning

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

Implements AnatomicalStructureCollection.

anatomicalStructure() [2/2]

AnatomicalStructure & anatomicalStructure ( int index )

overridevirtual

Returns the anatomical structure at index index.

Warning

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

Implements AnatomicalStructureCollection.

anatomicalStructureIndex()

int anatomicalStructureIndex ( const AnatomicalStructure * anatomicalStructure ) const

overridevirtual

Returns -1 if the structure is not included in this SpineData object.

Reimplemented from AnatomicalStructureCollection.

addAnatomicalStructure()

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

overridevirtual

Add an anatomical structure to this collection.

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

Reimplemented from AnatomicalStructureCollection.

takeAnatomicalStructure()

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

overridevirtual

Take an anatomical structure from this collection.

Reimplemented from AnatomicalStructureCollection.

vertebrae()

const std::vector< std::unique_ptr< OrientedVertebra > > & vertebrae ( ) const

inline

The entire vector of vertebrae.

No element in the returned vector may be nullptr. This vector is not guaranteed to be sorted in any way.

sacrum()

Sacrum & sacrum

(

)

Getter for the Sacrum.

In addition to global sacrum information this object provides an access to S1 and S2 from m_vertebrae in order to have a unified access to Sacrum related information.

clear()

void clear ( )

overridevirtual

Clear all data contained in this structure.

Reimplemented from AnatomicalStructureCollection.

matrixToWorld()

virtual mat4 matrixToWorld ( ) const

virtual

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 AnatomicalStructureCollection.

setMatrixToWorld() [2/2]

virtual void setMatrixToWorld ( const mat4 & m )

virtual

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

Note

Depending on how matrices are internally stored in concrete derived classes, m might be inverted before it is saved. The default implementation checks matrixConvention and accordingly calls setMatrix with either m or its inverse.

Reimplemented from Data.

Member Data Documentation

signalVertebraToBeDeleted

Signal<OrientedVertebra*> signalVertebraToBeDeleted

This signal is emitted with the previous value of a vertebra if the vertebra is being deleted.

The object being pointed to still exists, but is no longer part of vertebrae()

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

• SpinePlugin/include/ImFusion/Spine/SpineData.h