OrientedVertebra Class Reference

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

A representation of a vertebra, containing orientation, classification keypoints, segmentations, meshes and all other related information. More...

Inheritance diagram for OrientedVertebra:

Detailed Description

A representation of a vertebra, containing orientation, classification keypoints, segmentations, meshes and all other related information.

Public Member Functions
	OrientedVertebra (const KeyValueStore< vec3 > &keypoints)
	Vertebra Constructor that takes a map of keypoints for initialization.
	OrientedVertebra (vec3 center)
	OrientedVertebra (OrientedVertebra &&other)
std::string	describe () const override
	A (human-readable) description of this anatomy.
	OrientedVertebra (std::vector< vec3 > keypoints)
	Vertebra Constructor that takes a vector of keypoints for initialization The order is either a single {body_keypoint}, or a set {body, left_pedicle, right_pedicle}.
vec3	position () const
	Returns the estimated position of the vertebra as was previously calculated by calculatePosition().
vec3	body () const
	Returns the body keypoint. If this keypoint is not available, a vec3(Nan, Nan, Nan) is returned.
vec3	posterior () const
	Returns the posterior keypoint. If this keypoint is not available, a vec3(Nan, Nan, Nan) is returned.
vec3	rightPedicle () const
	Returns the right pedicle keypoint. If this keypoint is not available, a vec3(Nan, Nan, Nan) is returned.
vec3	leftPedicle () const
	Returns the left pedicle keypoint. If this keypoint is not available, a vec3(Nan, Nan, Nan) is returned.
vec3	rightKeypoint () const
vec3	leftKeypoint () const
mat4	estimateMatrix (bool centerOnPedicles=false)
std::string	name () const
	Return name of the vertebra If the type is known it will be in the name ("T12", "L1", etc) Otherwise it will simply be "Vertebra".
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.
std::string	getName () const
VertebraType	getType () const
int	getRelativeIndex () const
void	setMeshes (std::vector< std::unique_ptr< Mesh > > &meshes_)
	Store a vector of meshes in the vertebra class If there is a single mesh it is stored under Keys::Spine::Vertebra::key for legacy reasons Otherwise, the meshes are stored under their given mesh->name()
Eigen::Quaternion< double >	calculateOrientation ()
std::vector< double > &	getTypeProbabilities ()
const std::vector< double > &	getTypeProbabilities () const
int	getTypeId () const
void	setTypeId (int t)
int	getPinnedTypeId () const
void	setPinnedTypeId (int t)
void	calculatePosition ()
	Estimates the vertebra "position" from keypoints If pedicle keypoints are present the estimate at the center of the vertebra, If only the body keypoint is present, this position will be returned.
Public Member Functions inherited from AnatomicalStructure
	AnatomicalStructure (bool is2D=false)
	AnatomicalStructure (AnatomicalStructure &other)
	AnatomicalStructure (AnatomicalStructure &&other)
virtual void	setMatrixToWorld (const mat4 &m, bool synchronizeWorld=true)
	Set the local to world matrix of this object.
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
virtual bool	empty () const
	Retuns true if all members are empty, i.e. this structure has no associated information.
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.
virtual void	clear ()
	Clear all data contained in this structure.
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 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.

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

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

Constructor & Destructor Documentation

OrientedVertebra() [1/2]

OrientedVertebra

(

const KeyValueStore< vec3 > &

keypoints

)

Vertebra Constructor that takes a map of keypoints for initialization.

This clones the key/value store. If Keys::Spine::Vertebra::Body::Center::key is present, this will be used to set the position If Keys::Spine::Vertebra::Body::Center::key, Keys::Spine::Vertebra::LeftPedicle::Center::key and Keys::Spine::Vertebra::RightPedicle::Center::key are present, the orientation will also be estimated

OrientedVertebra() [2/2]

OrientedVertebra

(

std::vector< vec3 >

keypoints

)

Vertebra Constructor that takes a vector of keypoints for initialization The order is either a single {body_keypoint}, or a set {body, left_pedicle, right_pedicle}.

Deprecated

"OrientedVertebra(std::vector<vec3> keypoints) is deprecated, use OrientedVertebra(std::map<std::string, vec3> keypoints);"

Member Function Documentation

describe()

std::string describe ( ) const

inlineoverridevirtual

A (human-readable) description of this anatomy.

Reimplemented from AnatomicalStructure.

position()

vec3 position

(

)

const

Returns the estimated position of the vertebra as was previously calculated by calculatePosition().

If this is not available, retruns vec3(Nan,Nan,Nan)

rightKeypoint()

vec3 rightKeypoint

(

)

const

Deprecated

"rightKeypoint() is deprecated, use rightPedicle() instead"

leftKeypoint()

vec3 leftKeypoint

(

)

const

Deprecated

"leftKeypoint() is deprecated, use leftPedicle() instead"

identifier()

std::string identifier ( ) const

overridevirtual

A (machine-readable) name of the anatomy.

Implements AnatomicalStructure.

serializationID()

std::string serializationID ( ) const

inlineoverridevirtual

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

Implements AnatomicalStructure.

getName()

std::string getName

(

)

const

Deprecated

"getName() is deprecated, Use name() instead"

setMeshes()

void setMeshes

(

std::vector< std::unique_ptr< Mesh > > &

meshes_

)

Store a vector of meshes in the vertebra class If there is a single mesh it is stored under Keys::Spine::Vertebra::key for legacy reasons Otherwise, the meshes are stored under their given mesh->name()

Deprecated

"setMeshes() is deprecated, use setMesh(std::string name, std::unique_ptr<Mesh>) instead."

construct()

std::unique_ptr< AnatomicalStructure > construct ( ) const

overrideprotectedvirtual

Implements AnatomicalStructure.

cloneImpl()

std::unique_ptr< AnatomicalStructure > cloneImpl ( ) const

overrideprotectedvirtual

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.

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

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