Represents a cluster of indices of a WDataSetFiberVector. More...

#include <WFiberCluster.h>

Inheritance diagram for WFiberCluster:

Collaboration diagram for WFiberCluster:

Public Types
typedef std::shared_ptr< WFiberCluster >	SPtr
	Shared pointer abbreviation. More...

typedef std::shared_ptr< const WFiberCluster >	ConstSPtr
	Const shared pointer abbreviation. More...

typedef std::list< size_t >	IndexList
	This is the list of indices of fibers. More...

typedef IndexList::const_iterator	IndexListConstIterator
	Const iterator on the index list. More...

Public Member Functions
	WFiberCluster (size_t index)
	Constructs an cluster with one fiber and a reference to the fiber dataset to compute the intercluster distance. More...

	WFiberCluster (const IndexList &indices, const WColor &color=WColor(), std::string const &annotation=std::string())
	Constructs a cluster with the specified set of indices and the given color. More...

	WFiberCluster (IndexListConstIterator indicesBegin, IndexListConstIterator indicesEnd, const WColor &color=WColor(), std::string const &annotation=std::string())
	Constructs a clustering with the given set of indices. More...

	WFiberCluster (const WFiberCluster &other)
	Copies the specified WFiberCluster Instance. More...

	WFiberCluster ()
	Constructs an empty cluster. More...

virtual	~WFiberCluster ()
	Destructs. More...

bool	empty () const
	Returns true if there are no fibers in that cluster, false otherwise. More...

void	merge (WFiberCluster &other)
	Merge the fibers of the other cluster with the fibers of this cluster. More...

void	merge (IndexListConstIterator indicesBegin, IndexListConstIterator indicesEnd)
	Copy the elements denoted by the two iterators to this cluster. More...

const IndexList &	getIndices () const
	Returns a const reference of all indices inside this cluster. More...

void	setIndices (const IndexList &indices)
	Reset the indices belonging to that cluster. More...

void	sort ()
	Sort the indices of fibers associated with this cluster in ascending order. More...

size_t	size () const

void	clear ()
	Make this cluster empty. More...

void	setColor (WColor color)
	Sets the color of which all fibers of this clusters should be painted with. More...

WColor	getColor () const
	Gets the color of which all fibers of this clusters should be painted with. More...

void	setAnnotation (std::string const &anno)
	Set the annotation for this fiber cluster. More...

std::string const &	getAnnotation () const
	Get the annotation string. More...

void	setMainDirection (osg::Vec3 mainDirection)
	Sets the main direction of the cluster. More...

osg::Vec3	getMainDirection () const
	Gets the main direction of the cluster ( if set ) More...

virtual const std::string	getName () const
	The name of this transferable. More...

virtual const std::string	getDescription () const
	The description of this transferable. More...

bool	operator== (const WFiberCluster &other) const

bool	operator!= (const WFiberCluster &other) const
	The opposite of the operator==. More...

WFiberCluster &	operator= (const WFiberCluster &other)
	Copy assignment operator which does NOT copy the mutex's!!! More...

std::shared_ptr< WFiber >	getCenterLine () const
	Returns the center line of this cluster. More...

std::shared_ptr< WFiber >	getLongestLine () const
	Returns the center line of this cluster. More...

void	generateCenterLine () const
	Makes the hard work to compute the center line. More...

void	generateLongestLine () const
	Makes the hard work to find the longest line. More...

WBoundingBox	getBoundingBox () const
	Recomputes on every call the axis aligned bounding box incorporating all tracts in this cluster. More...

Public Member Functions inherited from WTransferable
	WTransferable ()
	Default constructor. More...

virtual	~WTransferable ()
	Destructor. More...

Public Member Functions inherited from WPrototyped
	WPrototyped ()
	Default constructor. More...

virtual	~WPrototyped ()
	Destructor. More...

template<typename T >
bool	isA ()
	Checks whether the actual prototype has the specified runtime type. More...

Static Public Member Functions
static std::shared_ptr< WPrototyped >	getPrototype ()
	Returns a prototype instantiated with the true type of the deriving class. More...

Protected Member Functions
void	unifyDirection (std::shared_ptr< WDataSetFiberVector > fibs) const
	Alings all fibers within the given dataset to be in one main direction. More...

Static Protected Attributes
static std::shared_ptr< WPrototyped >	m_prototype = std::shared_ptr< WPrototyped >()
	Prototype for this dataset. More...

Private Member Functions
void	elongateCenterLine () const
	The centerline may be shortened due to the averaging of outliers. More...

Private Attributes
IndexList	m_memberIndices
	All indices in this set are members of this cluster. More...

std::shared_ptr< const WDataSetFiberVector >	m_fibs
	Reference to the real fibers of the brain this cluster belongs to. More...

WColor	m_color
	Color which is used to paint the members of this cluster. More...

std::string	m_annotation
	An annotation for the bundle, usually a name. More...

osg::Vec3	m_mainDirection
	The cluster's main direction. More...

std::shared_mutex *	m_centerLineCreationLock
	Lock the modification in the m_centerLine mutable. More...

std::shared_mutex *	m_longestLineCreationLock
	Lock the modification in the m_longestLine mutable. More...

std::shared_ptr< WFiber >	m_centerLine
	Average fiber for this cluster representing the main direction and curvature of this cluster. More...

std::shared_ptr< WFiber >	m_longestLine
	The longest fiber in the dataset. More...

Friends
class	WFiberClusterTest
	Access for test class. More...

Detailed Description

Represents a cluster of indices of a WDataSetFiberVector.

Definition at line 44 of file WFiberCluster.h.

Member Typedef Documentation

◆ ConstSPtr

typedef std::shared_ptr< const WFiberCluster > WFiberCluster::ConstSPtr

Const shared pointer abbreviation.

Definition at line 56 of file WFiberCluster.h.

◆ IndexList

typedef std::list< size_t > WFiberCluster::IndexList

This is the list of indices of fibers.

Definition at line 61 of file WFiberCluster.h.

◆ IndexListConstIterator

typedef IndexList::const_iterator WFiberCluster::IndexListConstIterator

Const iterator on the index list.

Definition at line 66 of file WFiberCluster.h.

◆ SPtr

typedef std::shared_ptr< WFiberCluster > WFiberCluster::SPtr

Shared pointer abbreviation.

Definition at line 51 of file WFiberCluster.h.

Constructor & Destructor Documentation

◆ WFiberCluster() [1/5]

WFiberCluster::WFiberCluster ( size_t index )

explicit

Constructs an cluster with one fiber and a reference to the fiber dataset to compute the intercluster distance.

Parameters

index The index of the first fiber belonging to this cluster

Definition at line 49 of file WFiberCluster.cpp.

References m_memberIndices.

◆ WFiberCluster() [2/5]

WFiberCluster::WFiberCluster	(	const IndexList &	indices,
		const WColor &	color = `WColor()`,
		std::string const &	annotation = `std::string()`
	)

Constructs a cluster with the specified set of indices and the given color.

Parameters

indices	the indices initially used for this clustering
color	the color of this cluster
annotation	an optional annotation string

Definition at line 57 of file WFiberCluster.cpp.

◆ WFiberCluster() [3/5]

WFiberCluster::WFiberCluster	(	WFiberCluster::IndexListConstIterator	indicesBegin,
		WFiberCluster::IndexListConstIterator	indicesEnd,
		const WColor &	color = `WColor()`,
		std::string const &	annotation = `std::string()`
	)

Constructs a clustering with the given set of indices.

The indexlist is generated using the given iterators. It copies the elements in [indicesBegin,indicesEnd).

Parameters

indicesBegin	begin iterator in the predefined index set
indicesEnd	end iterator in the predefined index set
color	the color of this cluster
annotation	an optional annotation string

Definition at line 68 of file WFiberCluster.cpp.

References m_memberIndices.

◆ WFiberCluster() [4/5]

WFiberCluster::WFiberCluster ( const WFiberCluster & other )

Copies the specified WFiberCluster Instance.

The copy does not contain a valid centerline or longest line.

Parameters

other the other instance to clone.

Definition at line 82 of file WFiberCluster.cpp.

References m_centerLine, and m_longestLine.

◆ WFiberCluster() [5/5]

WFiberCluster::WFiberCluster ( )

Constructs an empty cluster.

Definition at line 42 of file WFiberCluster.cpp.

Referenced by getPrototype().

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◆ ~WFiberCluster()

WFiberCluster::~WFiberCluster ( )

virtual

Destructs.

Frees used locks/mutex.

Definition at line 105 of file WFiberCluster.cpp.

References m_centerLineCreationLock, and m_longestLineCreationLock.

Member Function Documentation

◆ clear()

void WFiberCluster::clear ( )

inline

Make this cluster empty.

Note: The real fibers from fiber dataset are not deleted.

Definition at line 410 of file WFiberCluster.h.

References m_memberIndices.

Referenced by merge().

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◆ elongateCenterLine()

void WFiberCluster::elongateCenterLine ( ) const

private

The centerline may be shortened due to the averaging of outliers.

To nevertheless color almost the whole bundle surface we need a surface parameterization (given via the centerline) upto the endings of the bundle. Therefore the centerline is stepwise elongated with the last known direction, until no perpendicular plane intersects any of the tracts inside of the bundle.

Definition at line 240 of file WFiberCluster.cpp.

References WMixinVector< ValueT >::back(), WMixinVector< ValueT >::begin(), WPlane::getPosition(), WMixinVector< ValueT >::insert(), m_centerLine, m_fibs, m_memberIndices, WMixinVector< ValueT >::push_back(), WPlane::resetPosition(), and WMixinVector< ValueT >::size().

Referenced by generateCenterLine().

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◆ empty()

bool WFiberCluster::empty ( ) const

inline

Returns true if there are no fibers in that cluster, false otherwise.

Returns: true if empty

Definition at line 395 of file WFiberCluster.h.

References m_memberIndices.

Referenced by WFiberClusterTest::testMerge().

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◆ generateCenterLine()

void WFiberCluster::generateCenterLine ( ) const

Makes the hard work to compute the center line.

Definition at line 157 of file WFiberCluster.cpp.

References elongateCenterLine(), m_centerLine, m_centerLineCreationLock, m_fibs, m_memberIndices, and unifyDirection().

Referenced by getCenterLine().

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◆ generateLongestLine()

void WFiberCluster::generateLongestLine ( ) const

Makes the hard work to find the longest line.

Definition at line 202 of file WFiberCluster.cpp.

References m_fibs, m_longestLine, and m_longestLineCreationLock.

Referenced by getLongestLine().

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◆ getAnnotation()

std::string const & WFiberCluster::getAnnotation ( ) const

inline

Get the annotation string.

Returns: The annotation string.

Definition at line 430 of file WFiberCluster.h.

References m_annotation.

◆ getBoundingBox()

WBoundingBox WFiberCluster::getBoundingBox ( ) const

Recomputes on every call the axis aligned bounding box incorporating all tracts in this cluster.

Returns: AABB as WBoundingBox.

Definition at line 408 of file WFiberCluster.cpp.

References WBoundingBoxImpl< VT >::expandBy(), m_fibs, and m_memberIndices.

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◆ getCenterLine()

std::shared_ptr< WFiber > WFiberCluster::getCenterLine ( ) const

Returns the center line of this cluster.

The centerline gets calculated during the first call of this method.

Returns: Reference to the center line

Definition at line 390 of file WFiberCluster.cpp.

References generateCenterLine(), and m_centerLine.

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◆ getColor()

WColor WFiberCluster::getColor ( ) const

inline

Gets the color of which all fibers of this clusters should be painted with.

Returns: cluster color.

Definition at line 420 of file WFiberCluster.h.

References m_color.

◆ getDescription()

const std::string WFiberCluster::getDescription ( ) const

inlinevirtual

The description of this transferable.

This is useful information for the users.

Returns: A description

Implements WPrototyped.

Definition at line 450 of file WFiberCluster.h.

◆ getIndices()

const WFiberCluster::IndexList & WFiberCluster::getIndices ( ) const

inline

Returns a const reference of all indices inside this cluster.

Returns: the index list

Definition at line 465 of file WFiberCluster.h.

References m_memberIndices.

◆ getLongestLine()

std::shared_ptr< WFiber > WFiberCluster::getLongestLine ( ) const

Returns the center line of this cluster.

The longest line gets calculated during the first call if this method.

Returns: Reference to the longest line

Definition at line 399 of file WFiberCluster.cpp.

References generateLongestLine(), and m_longestLine.

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◆ getMainDirection()

osg::Vec3 WFiberCluster::getMainDirection ( ) const

inline

Gets the main direction of the cluster ( if set )

Returns: the cluster's main direction

Definition at line 440 of file WFiberCluster.h.

References m_mainDirection.

◆ getName()

const std::string WFiberCluster::getName ( ) const

inlinevirtual

The name of this transferable.

This is useful information for the users.

Returns: the name.

Implements WPrototyped.

Definition at line 445 of file WFiberCluster.h.

◆ getPrototype()

std::shared_ptr< WPrototyped > WFiberCluster::getPrototype ( )

static

Returns a prototype instantiated with the true type of the deriving class.

Returns: the prototype.

Definition at line 148 of file WFiberCluster.cpp.

References m_prototype, and WFiberCluster().

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◆ merge() [1/2]

void WFiberCluster::merge	(	WFiberCluster::IndexListConstIterator	indicesBegin,
		WFiberCluster::IndexListConstIterator	indicesEnd
	)

Copy the elements denoted by the two iterators to this cluster.

In contrast to the other merge() methods, this will not clean the source list.

Parameters

indicesBegin	begin iterator in the predefined index set
indicesEnd	end iterator in the predefined index set

Definition at line 124 of file WFiberCluster.cpp.

References m_memberIndices.

◆ merge() [2/2]

void WFiberCluster::merge ( WFiberCluster & other )

Merge the fibers of the other cluster with the fibers of this cluster.

Afterwards the other cluster is empty.

Parameters

other The other WFiberCluster which should merged into this one

Definition at line 111 of file WFiberCluster.cpp.

References clear(), m_centerLine, m_longestLine, and m_memberIndices.

Referenced by WFiberClusterTest::testMerge().

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◆ operator!=()

bool WFiberCluster::operator!= ( const WFiberCluster & other ) const

inline

The opposite of the operator==.

Parameters

other The other fiber which should be compared

Returns: false If both clusters having same fibers IN SAME ORDER!

Definition at line 460 of file WFiberCluster.h.

References m_memberIndices.

◆ operator=()

WFiberCluster& WFiberCluster::operator= ( const WFiberCluster & other )

inline

Copy assignment operator which does NOT copy the mutex's!!!

Parameters

other The instance to copy.

Returns: itself

Definition at line 249 of file WFiberCluster.h.

References m_centerLine, m_centerLineCreationLock, m_color, m_fibs, m_longestLine, m_longestLineCreationLock, and m_memberIndices.

◆ operator==()

bool WFiberCluster::operator== ( const WFiberCluster & other ) const

inline

Parameters

other The other fiber which should be compared

Returns: true If both clusters having same fibers IN SAME ORDER!

Definition at line 455 of file WFiberCluster.h.

References m_memberIndices.

◆ setAnnotation()

void WFiberCluster::setAnnotation ( std::string const & anno )

inline

Set the annotation for this fiber cluster.

Parameters

anno	The new annotation.

Definition at line 425 of file WFiberCluster.h.

References m_annotation.

◆ setColor()

void WFiberCluster::setColor ( WColor color )

inline

Sets the color of which all fibers of this clusters should be painted with.

Parameters

color The color for all fibers of this cluster.

Definition at line 415 of file WFiberCluster.h.

References m_color.

◆ setIndices()

void WFiberCluster::setIndices ( const IndexList & indices )

inline

Reset the indices belonging to that cluster.

Parameters

indices list of indices

Definition at line 470 of file WFiberCluster.h.

References m_memberIndices.

◆ setMainDirection()

void WFiberCluster::setMainDirection ( osg::Vec3 mainDirection )

inline

Sets the main direction of the cluster.

Parameters

mainDirection the cluster's main direction

Definition at line 435 of file WFiberCluster.h.

References m_mainDirection.

◆ size()

size_t WFiberCluster::size ( ) const

inline

Returns: Number of fibers associated with this cluster.

Definition at line 405 of file WFiberCluster.h.

References m_memberIndices.

◆ sort()

void WFiberCluster::sort ( )

inline

Sort the indices of fibers associated with this cluster in ascending order.

Definition at line 400 of file WFiberCluster.h.

References m_memberIndices.

◆ unifyDirection()

void WFiberCluster::unifyDirection ( std::shared_ptr< WDataSetFiberVector > fibs ) const

protected

Alings all fibers within the given dataset to be in one main direction.

But Alignment only may swap the ordering of the fibers but not the positions or something similar. We need this only for the centerline generation.

Parameters

fibs	The dataset

Definition at line 354 of file WFiberCluster.cpp.

References WMixinVector< ValueT >::at(), WMixinVector< ValueT >::back(), WMixinVector< ValueT >::front(), and WMixinVector< ValueT >::size().

Referenced by generateCenterLine().

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Friends And Related Function Documentation

◆ WFiberClusterTest

friend class WFiberClusterTest

friend

Access for test class.

Definition at line 46 of file WFiberCluster.h.

Member Data Documentation

◆ m_annotation

std::string WFiberCluster::m_annotation

private

An annotation for the bundle, usually a name.

Definition at line 363 of file WFiberCluster.h.

Referenced by getAnnotation(), and setAnnotation().

◆ m_centerLine

std::shared_ptr< WFiber > WFiberCluster::m_centerLine

mutableprivate

Average fiber for this cluster representing the main direction and curvature of this cluster.

Note: This member is mutable as it needs to be modified during a const getter.

Definition at line 385 of file WFiberCluster.h.

Referenced by elongateCenterLine(), generateCenterLine(), getCenterLine(), merge(), operator=(), and WFiberCluster().

◆ m_centerLineCreationLock

std::shared_mutex* WFiberCluster::m_centerLineCreationLock

private

Lock the modification in the m_centerLine mutable.

The lock is stored as pointer to avoid copy construction problems.

Definition at line 373 of file WFiberCluster.h.

Referenced by generateCenterLine(), operator=(), and ~WFiberCluster().

◆ m_color

WColor WFiberCluster::m_color

private

Color which is used to paint the members of this cluster.

Definition at line 358 of file WFiberCluster.h.

Referenced by getColor(), operator=(), and setColor().

◆ m_fibs

std::shared_ptr< const WDataSetFiberVector > WFiberCluster::m_fibs

private

Reference to the real fibers of the brain this cluster belongs to.

Definition at line 353 of file WFiberCluster.h.

Referenced by elongateCenterLine(), generateCenterLine(), generateLongestLine(), getBoundingBox(), and operator=().

◆ m_longestLine

std::shared_ptr< WFiber > WFiberCluster::m_longestLine

mutableprivate

The longest fiber in the dataset.

Note: This member is mutable as it needs to be modified during a const getter.

Definition at line 392 of file WFiberCluster.h.

Referenced by generateLongestLine(), getLongestLine(), merge(), operator=(), and WFiberCluster().

◆ m_longestLineCreationLock

std::shared_mutex* WFiberCluster::m_longestLineCreationLock

private

Lock the modification in the m_longestLine mutable.

The lock is stored as pointer to avoid copy construction problems.

Definition at line 378 of file WFiberCluster.h.

Referenced by generateLongestLine(), operator=(), and ~WFiberCluster().

◆ m_mainDirection

osg::Vec3 WFiberCluster::m_mainDirection

private

The cluster's main direction.

Definition at line 368 of file WFiberCluster.h.

Referenced by getMainDirection(), and setMainDirection().

◆ m_memberIndices

IndexList WFiberCluster::m_memberIndices

private

All indices in this set are members of this cluster.

Definition at line 344 of file WFiberCluster.h.

Referenced by clear(), elongateCenterLine(), empty(), generateCenterLine(), getBoundingBox(), getIndices(), merge(), operator!=(), operator=(), operator==(), setIndices(), size(), sort(), WFiberClusterTest::testMerge(), and WFiberCluster().

◆ m_prototype

std::shared_ptr< WPrototyped > WFiberCluster::m_prototype = std::shared_ptr< WPrototyped >()

staticprotected

Prototype for this dataset.

Definition at line 320 of file WFiberCluster.h.

Referenced by getPrototype().

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

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Static Protected Attributes

Private Member Functions

Private Attributes

Friends

Detailed Description

Member Typedef Documentation

◆ ConstSPtr

◆ IndexList

◆ IndexListConstIterator

◆ SPtr

Constructor & Destructor Documentation

◆ WFiberCluster() [1/5]

◆ WFiberCluster() [2/5]

◆ WFiberCluster() [3/5]

◆ WFiberCluster() [4/5]

◆ WFiberCluster() [5/5]

◆ ~WFiberCluster()

Member Function Documentation

◆ clear()

◆ elongateCenterLine()

◆ empty()

◆ generateCenterLine()

◆ generateLongestLine()

◆ getAnnotation()

◆ getBoundingBox()

◆ getCenterLine()

◆ getColor()

◆ getDescription()

◆ getIndices()

◆ getLongestLine()

◆ getMainDirection()

◆ getName()

◆ getPrototype()

◆ merge() [1/2]

◆ merge() [2/2]

◆ operator!=()

◆ operator=()

◆ operator==()

◆ setAnnotation()

◆ setColor()

◆ setIndices()

◆ setMainDirection()

◆ size()

◆ sort()

◆ unifyDirection()

Friends And Related Function Documentation

◆ WFiberClusterTest

Member Data Documentation

◆ m_annotation

◆ m_centerLine

◆ m_centerLineCreationLock

◆ m_color

◆ m_fibs

◆ m_longestLine

◆ m_longestLineCreationLock

◆ m_mainDirection

◆ m_memberIndices

◆ m_prototype