Connectivity matix object: fusions sparse matrix, white mesh, and optionally a gyrus patch texture. More...

#include <anatomist/sparsematrix/connectivitymatrix.h>

Inheritance diagram for anatomist::AConnectivityMatrix:

[legend]

Collaboration diagram for anatomist::AConnectivityMatrix:

[legend]

Public Types
enum	PatchMode { ONE, ALL_BUT_ONE, ALL_MESH, REDUCED }

Public Types inherited from anatomist::MObject
typedef AIterator	iterator

typedef AIterator	const_iterator

Public Types inherited from anatomist::AObject
enum	ObjectType { VOLUME, BUCKET, FACET, TRIANG, LIST, VECTOR, MAP, SET, GRAPH, GRAPHOBJECT, VOLSURF, MULTISURF, MULTIBUCKET, MULTIVOLUME, FUSION2D, FUSION3D, FASCICLE, FASCICLEGRAPH, TEXTURE, TEXSURFACE, FUSION2DMESH, VECTORFIELD, OTHER }
	Base object type identifiers. More...

typedef std::set< MObject * >	ParentList
	Storage type for parent objects (multi-objects containing this one) More...

typedef ObjectMenu (	ObjectMenuRegistrerFunction) (const AObject objtype, ObjectMenu menu)
	dynamic menu registration function More...

Public Types inherited from carto::RCObject
typedef int	RefCounterType

Signals
void	texturesUpdated (AConnectivityMatrix *)

void	processingProgress (AConnectivityMatrix *, int current, int count)

Public Member Functions
	AConnectivityMatrix (const std::vector< AObject *> &obj)

virtual	~AConnectivityMatrix ()

virtual int	MType () const
	Precise type of multi-object. More...

virtual bool	render (PrimList &, const ViewState &)
	rendering (generally 2D or 3D using OpenGL). More...

virtual void	update (const Observable observable, void arg)
	This class is an Observer of each of the AObject it groups. More...

void	buildTexture (int mesh_index, uint32_t vertex, float time_pos=0)

void	buildColumnTexture (int mesh_index, uint32_t vertex, float time_pos=0)

void	buildPatchTexture (int mesh_index, uint32_t vertex, float time_pos=0)

void	buildColumnPatchTexture (int mesh_index, uint32_t vertex, float time_pos=0)

std::vector< carto::rc_ptr< ATriangulated > >	meshes () const

std::vector< carto::rc_ptr< ATexture > >	textures () const

const carto::rc_ptr< ATriangulated >	marker () const

void	cancelThread ()

virtual bool	boundingBox (std::vector< float > &bmin, std::vector< float > &bmax) const
	Fills bmin and bmax with the N-D bounding box extrema in the object's referential coordinates. More...

Public Member Functions inherited from anatomist::ObjectVector
	ObjectVector ()

virtual	~ObjectVector ()

virtual bool	CanRemove (AObject *obj)

virtual Tree *	optionTree () const
	Menu tree for new options, see object/optionMatcher.h. More...

virtual size_t	size () const

virtual iterator	begin ()

virtual const_iterator	begin () const

virtual iterator	end ()

virtual const_iterator	end () const

virtual void	insert (AObject *)

virtual void	insert (AObject *, int pos)

virtual void	insert (const carto::shared_ptr< AObject > &, int pos=-1)

virtual const_iterator	find (const AObject *) const

virtual const_iterator	find (const carto::shared_ptr< AObject > &) const

virtual void	erase (iterator &)

Public Member Functions inherited from anatomist::MObject
	MObject ()

virtual	~MObject ()

virtual const MObject *	mObjectAPI () const

virtual MObject *	mObjectAPI ()

virtual void	setReferential (Referential *ref)

virtual void	setReferentialInheritance (AObject *)

virtual float	MinT () const
	Obsolete, deprecated. More...

virtual float	MaxT () const
	Obsolete, deprecated. More...

virtual bool	boundingBox2D (std::vector< float > &bmin, std::vector< float > &bmax) const
	Bounding box in 2D views mode. More...

virtual std::vector< float >	voxelSize () const
	Returns at least 4 sizes. For 3D objects, returns (1, 1, 1, 1) More...

virtual void	SetMaterial (const Material &mat)

virtual void	setPalette (const AObjectPalette &pal)

virtual bool	shouldRemoveChildrenWithMe () const
	tells whether children objects should be removed from views when this MObject is removed from a view. More...

virtual std::list< AObject * >	generativeChildren () const
	Children objects which have been used to build the current MObject. More...

int	isMultiObject () const
	maybe not necessary ?: we can use dynamic_cast instead More...

void	eraseObject (AObject *obj)

virtual AObject *	objectAt (const std::vector< float > &pos, float tol=0)
	Find the object (sub-object) at given postion with a tolerence. More...

virtual bool	renderingIsObserverDependent () const
	true only if the rendering (openGL) of the object changes with the observer position/orientation of the view (which is rare, but typically needed for Volume Rendering) More...

virtual bool	Is2DObject ()
	Can be display in 2D windows. More...

virtual bool	Is3DObject ()
	Can be display in 3D windows. More...

virtual bool	isTransparent () const

virtual void	setContentChanged () const

bool	hasContentChanged () const

virtual void	clearHasChangedFlags () const
	Reset has-changed flags Must be called after a call to notifyObservers function to reset changes More...

Public Member Functions inherited from anatomist::AObject
	AObject (const std::string &filename="")

virtual	~AObject ()
	AObject subclasses must call cleanup() in their destructor. More...

virtual AObject *	clone (bool shallow=true)
	Makes a copy of the object, with a duplicated object structure, palette and material, but which may share the underlying low-level data object (Aims object). More...

virtual const GLComponent *	glAPI () const
	OpenGL objects const API. More...

virtual GLComponent *	glAPI ()
	OpenGL objects API. More...

int	type () const
	Object type identifier. More...

void	setType (int type)
	Method to set type id, because type() is not virtual. More...

int	id () const
	Unique ID assigned upon construction, but somewhat unused now... More...

std::string	name () const
	Name shown in control window. More...

std::string	fileName () const
	File name (if any) for loaded objects. More...

void	setName (const std::string &n)

void	setFileName (const std::string &filename)

void	setId (int id)

virtual void	setVoxelSize (const std::vector< float > &)

virtual void	internalUpdate ()
	Updates the state of the object. More...

virtual void	adjustPalette ()
	Creates or updates object palette according to object values (if needed) More...

virtual AObjectPalette *	palette ()
	Normally, getOrCreatePalette() should be used instead of this function in most cases. More...

virtual const AObjectPalette *	palette () const

virtual const AObjectPalette *	getOrCreatePalette () const
	User normally calls this function. More...

virtual void	createDefaultPalette (const std::string &name="")
	function called by getOrCreatePalette() - overloadable, need not be called directly More...

virtual Material &	GetMaterial ()

virtual const Material &	material () const

Referential *	getReferential () const

AObject *	referentialInheritance () const
	if not null, the object referential is inherited from this object More...

virtual AObject *	fallbackReferentialInheritance () const
	object to take referential from when no ref is assigned More...

const Referential *	previousReferential () const
	Referential that the object was in before the last change. More...

virtual ObjectMenu *	optionMenu () const

int	InMemory () const
	For objects loading only when needed (not used yet...) More...

int	Visible () const
	Visibility in control window. More...

void	SetVisibility (int v)

ParentList &	Parents ()
	List of multi-objects containing this one. Obsolete: use parents() More...

ParentList &	parents ()
	List of multi-objects containing this one. More...

const ParentList &	parents () const
	List of multi-objects containing this one. More...

virtual void	RegisterParent (MObject *pob)

virtual void	UnregisterParent (MObject *pob)

const std::set< AWindow * > &	WinList ()
	List of windows showing this object. More...

virtual void	registerWindow (AWindow *window)

virtual void	unregisterWindow (AWindow *window)

virtual bool	textured2D () const
	true if 2D rendering uses a textured plane (not a full openGL object) More...

virtual int	CanBeDestroyed ()
	Allows / unallows destruction of object. More...

virtual void	setReferenceChanged ()

bool	hasReferenceChanged () const

virtual void	setInternalsChanged ()
	Notifies some underlying lower-level objects have changed. More...

virtual AObject *	objectAt (const std::vector< float > &pos, float tol, const Referential *orgref, const Point3df &orggeom)
	Same with origin window referential. More...

virtual void	setGeomExtrema ()
	Scans the object internals and determines its geometry extrema. More...

virtual void	SetExtrema ()
	Scans the object internals and determines its (texture) extrema values. More...

virtual bool	hasTexture () const
	Textured objects have values associated with a geometric coordinate. More...

virtual unsigned	dimTexture () const
	Number of texture values for a point. More...

virtual float	mixedTexValue (const std::vector< float > &pos, const Referential *orgRef) const
	Gets a "mixed" texture value at a given space / time location. More...

virtual float	mixedTexValue (const std::vector< float > &pos) const
	Same as above except that coordinates are not transformed but taken in object coordinates system. More...

virtual std::vector< float >	texValues (const std::vector< float > &pos, const Referential *orgRef) const
	Gets the array of texture values at a given location. More...

virtual std::vector< float >	texValues (const std::vector< float > &pos) const

virtual bool	loadable () const

virtual bool	savable () const

virtual bool	reload (const std::string &filename)
	Re-reads objects from disk. More...

virtual std::string	objectFullTypeName (void) const
	Get Object Full Type Name. More...

virtual bool	save (const std::string &filename)

virtual bool	printTalairachCoord (const Point3df &, const Referential *) const
	should be replaced by a real referential More...

void	setHeaderOptions ()
	Set some object properties according to the header (.minf), such as material, palette etc. More...

virtual void	setProperties (carto::Object options)
	Same as setHeaderOptions() and used by it, allows passing a dictionary. More...

virtual void	storeHeaderOptions ()
	Store some object properties into the header (.minf), such as material, palette etc before saving the object. More...

virtual carto::Object	makeHeaderOptions () const
	get object properties into a generic object, such as material, palette etc before saving the object More...

long	loadDate () const
	Time the object was created, loaded or reloaded. More...

void	setLoadDate (long t)

bool	isCopy () const

void	setCopyFlag (bool x=true)

virtual std::string	toolTip () const
	tooltip displayed in 3D views (HTML). More...

carto::Object	aimsMeshFromGLComponent ()

Public Member Functions inherited from anatomist::Observable
	Observable ()
	Construct an Observable with zero observers. More...

virtual	~Observable ()
	does nothing More...

void	addObserver (Observer *observer)
	Adds an observer to the set of observers for this object. More...

void	deleteObserver (Observer *observer)
	Deletes an observer from the set of observers of this object. More...

void	deleteObservers ()
	Clears the observer list so that this object no longer has any observers (doesn't call any observer method - see notifyUnregisterObservers() for this ) More...

int	countObservers () const
	Returns the number of observers of this object. More...

virtual void	notifyObservers (void *arg=0)
	If this object has changed, as indicated by the hasChanged method, then notify all of its observers. More...

virtual void	notifyUnregisterObservers ()
	Notifies observable destruction to all observers and unregisters them. More...

bool	hasChanged () const
	Tests if this object has changed. More...

bool	obsHasChanged (int) const
	only valid during an Observer::update() More...

bool	obsHasChanged (const std::string &) const
	only valid during an Observer::update() More...

void	setChanged () const
	Indicates that this object has changed. More...

Public Member Functions inherited from carto::SharedObject
	SharedObject ()

	SharedObject (const SharedObject &x)

virtual	~SharedObject ()

SharedObject &	operator= (const SharedObject &)

bool	testDeletable ()

bool	tryDelete ()

Public Member Functions inherited from carto::WeakObject
void	attachWeakPtr (weak_ptr< T > &) const

void	detachWeakPtr (weak_ptr< T > &) const

void	attachWeakPtr (weak_shared_ptr< T > &) const

void	detachWeakPtr (weak_shared_ptr< T > &) const

virtual	~WeakObject ()

Public Member Functions inherited from carto::RCObject
	RCObject ()

	RCObject (const RCObject &)

RCObject &	operator= (const RCObject &)

virtual	~RCObject ()

Public Member Functions inherited from anatomist::Observer
virtual	~Observer ()

Static Public Member Functions
static bool	checkObjects (const std::set< AObject > &objects, AObject &matrix, std::list< ATriangulated > &meshes, std::list< ATexture > &patch_textures, std::list< ATexture *> &basin_textures, PatchMode &pmode, std::set< int > &patches, bool &transpose)

Static Public Member Functions inherited from anatomist::AObject
static std::list< AObject * >	load (const std::string &filename)
	Static object loader: creates an objects, loads its contents. More...

static bool	reload (AObject *object, bool onlyoutdated=false)
	Reads from disk again. More...

static int	registerObjectType (const std::string &id)
	Creates a new object type number and returns it. More...

static std::string	objectTypeName (int type)

static void	setObjectMenu (std::string type, carto::rc_ptr< ObjectMenu > om)

static carto::rc_ptr< ObjectMenu >	getObjectMenu (std::string type)

static std::map< std::string, carto::rc_ptr< ObjectMenu > > &	getObjectMenuMap ()

static void	addObjectMenuRegistration (ObjectMenuRegistrerFunction)

static void	addObjectMenuRegistration (ObjectMenuRegistrerClass *)

static void	cleanStatic ()
	cleanup static global variables (called when quitting anatomist) More...

Friends
class	anatomist::ConnectivityMatrixProcessingThread

Additional Inherited Members
Static Public Attributes inherited from anatomist::ObjectVector
static Tree *	_optionTree

Protected Types inherited from anatomist::ObjectVector
typedef std::list< carto::shared_ptr< AObject > >	datatype

Protected Member Functions inherited from anatomist::MObject
virtual void	_insertObject (AObject *o)
	must be called by all subclasses in their insert() implementation More...

virtual void	_eraseObject (AObject *o)
	must be called by all subclasses if they reimplement erase() More...

virtual void	updateSubObjectReferential (const AObject *o)

virtual void	clearReferentialInheritance ()
	sets the object to get referential from to null, unregister it More...

Protected Member Functions inherited from anatomist::AObject
const PrimList &	primitives () const

PrimList &	primitives ()

virtual void	cleanup ()
	must be called by objects destructors - Must be explicitly called by each object destructor since it can call virtual functions More...

AObject *&	_referentialInheritance ()
	provide access to derived classes More...

virtual void	unregisterObservable (Observable *)
	Called when an observable is destroyed, only called by Observable: don't use this function directly. More...

	AObject (const AObject &)
	copy constructor, protected and used only to reimplement clone() More...

Protected Member Functions inherited from anatomist::Observable
void	clearChanged () const
	Indicates that this object has no longer changed, or that it has already notified all of its observers of its most recent change. More...

void	obsSetChanged (int, bool=true) const
	int-based change flags (use enums to address them) More...

void	obsSetChanged (const std::string &, bool=true) const
	string-based change flags More...

Protected Member Functions inherited from carto::SharedObject
void	disableRefCount ()

Protected Member Functions inherited from carto::WeakObject
	WeakObject ()

	WeakObject (const WeakObject &)

WeakObject &	operator= (const WeakObject &)

Protected Member Functions inherited from anatomist::Observer
virtual void	cleanupObserver ()
	call this function from inherited classes destructors. More...

virtual void	registerObservable (Observable *)
	only called by Observable: don't use this function directly More...

const std::set< Observable * > &	observed () const

Protected Attributes inherited from anatomist::ObjectVector
datatype	_data

Protected Attributes inherited from anatomist::MObject
bool	_contentHasChanged

Protected Attributes inherited from anatomist::AObject
int	_type
	Should be static in each object class. More...

int	_id

std::string	_name

std::string	_filename

std::set< AWindow * >	_winList

int	_inMemory

int	_visible

ParentList	_parents

Material	_material
	Should be a pointer: some objects don't have a material (2D objects) More...

Referential *	_referential
	Referentiel. More...

bool	_referenceHasChanged
	Reference has-changed flag. More...

AObjectPalette *	_palette
	Palette. More...

Static Protected Attributes inherited from anatomist::AObject
static std::map< std::string, int >	_objectTypes
	name-to-type map More...

static std::map< int, std::string >	_objectTypeNames
	type-to-name map More...

static std::map< std::string, carto::rc_ptr< ObjectMenu > >	_objectmenu_map
	Object Menu Map. More...

Detailed Description

Connectivity matix object: fusions sparse matrix, white mesh, and optionally a gyrus patch texture.

The gyrus patch texture may be:

a binary texture
a label texture where the patch is one label
a label texture where the patch is all but one label (typically, all but 0) In this latter case, sub-patch connectivity may be displayed using ctrl+left click
a label texture for a reduced matrix (region-region)

Definition at line 63 of file connectivitymatrix.h.

Member Enumeration Documentation

◆ PatchMode

enum anatomist::AConnectivityMatrix::PatchMode

Enumerator
ONE
ALL_BUT_ONE
ALL_MESH
REDUCED

Definition at line 68 of file connectivitymatrix.h.

Constructor & Destructor Documentation

◆ AConnectivityMatrix()

anatomist::AConnectivityMatrix::AConnectivityMatrix ( const std::vector< AObject *> & obj )

◆ ~AConnectivityMatrix()

virtual anatomist::AConnectivityMatrix::~AConnectivityMatrix ( )

virtual

Member Function Documentation

◆ boundingBox()

virtual bool anatomist::AConnectivityMatrix::boundingBox	(	std::vector< float > &	bmin,
		std::vector< float > &	bmax
	)		const

virtual

Fills bmin and bmax with the N-D bounding box extrema in the object's referential coordinates.

Changed in Anatomist 4.6. The older API was using Point3df instead of vector and informed only the spatial dimensions.

An object with no spatial information (a texture for instance) may still have time information. For this reason, the resulting bounding box should always have 4 components (at least), then 4th and additional ones should be valid, even if the function returns false (no spatial bounding box).

Returns: true if object has a "spatial" bounding box (x, y, z coordinates)

Reimplemented from anatomist::MObject.

Referenced by MType().

◆ buildColumnPatchTexture()

void anatomist::AConnectivityMatrix::buildColumnPatchTexture	(	int	mesh_index,
		uint32_t	vertex,
		float	time_pos = `0`
	)

Referenced by MType().

◆ buildColumnTexture()

void anatomist::AConnectivityMatrix::buildColumnTexture	(	int	mesh_index,
		uint32_t	vertex,
		float	time_pos = `0`
	)

Referenced by MType().

◆ buildPatchTexture()

void anatomist::AConnectivityMatrix::buildPatchTexture	(	int	mesh_index,
		uint32_t	vertex,
		float	time_pos = `0`
	)

Referenced by MType().

◆ buildTexture()

void anatomist::AConnectivityMatrix::buildTexture	(	int	mesh_index,
		uint32_t	vertex,
		float	time_pos = `0`
	)

Referenced by MType().

◆ cancelThread()

void anatomist::AConnectivityMatrix::cancelThread ( )

Referenced by MType().

◆ checkObjects()

static bool anatomist::AConnectivityMatrix::checkObjects	(	const std::set< AObject *> &	objects,
		AObject *&	matrix,
		std::list< ATriangulated *> &	meshes,
		std::list< ATexture *> &	patch_textures,
		std::list< ATexture *> &	basin_textures,
		PatchMode &	pmode,
		std::set< int > &	patches,
		bool &	transpose
	)

static

Referenced by MType().

◆ marker()

const carto::rc_ptr<ATriangulated> anatomist::AConnectivityMatrix::marker ( ) const

Referenced by MType().

◆ meshes()

std::vector<carto::rc_ptr<ATriangulated> > anatomist::AConnectivityMatrix::meshes ( ) const

Referenced by MType().

◆ MType()

virtual int anatomist::AConnectivityMatrix::MType ( ) const

inlinevirtual

Precise type of multi-object.

Reimplemented from anatomist::ObjectVector.

Definition at line 79 of file connectivitymatrix.h.

References boundingBox(), buildColumnPatchTexture(), buildColumnTexture(), buildPatchTexture(), buildTexture(), cancelThread(), checkObjects(), marker(), meshes(), render(), textures(), transpose(), anatomist::AObject::type(), and update().

◆ processingProgress

void anatomist::AConnectivityMatrix::processingProgress	(	AConnectivityMatrix *	,
		int	current,
		int	count
	)

signal

◆ render()

virtual bool anatomist::AConnectivityMatrix::render	(	PrimList &	,
		const ViewState &
	)

virtual

rendering (generally 2D or 3D using OpenGL).

Calls GLComponent API ig glAPI() is not null, otherwise nothing is done and this method should be overloaded.

Reimplemented from anatomist::MObject.

Referenced by MType().

◆ textures()

std::vector<carto::rc_ptr<ATexture> > anatomist::AConnectivityMatrix::textures ( ) const

Referenced by MType().

◆ texturesUpdated

void anatomist::AConnectivityMatrix::texturesUpdated ( AConnectivityMatrix * )

signal

◆ update()

virtual void anatomist::AConnectivityMatrix::update	(	const Observable *	observable,
		void *	arg
	)

virtual

This class is an Observer of each of the AObject it groups.

Reimplemented from anatomist::MObject.

Referenced by MType().

Friends And Related Function Documentation

◆ anatomist::ConnectivityMatrixProcessingThread

friend class anatomist::ConnectivityMatrixProcessingThread

friend

Definition at line 109 of file connectivitymatrix.h.

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

anatomist/sparsematrix/connectivitymatrix.h

Public Types

Signals

Public Member Functions

Static Public Member Functions

Friends

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ PatchMode

Constructor & Destructor Documentation

◆ AConnectivityMatrix()

◆ ~AConnectivityMatrix()

Member Function Documentation

◆ boundingBox()

◆ buildColumnPatchTexture()

◆ buildColumnTexture()

◆ buildPatchTexture()

◆ buildTexture()

◆ cancelThread()

◆ checkObjects()

◆ marker()

◆ meshes()

◆ MType()

◆ processingProgress

◆ render()

◆ textures()

◆ texturesUpdated

◆ update()

Friends And Related Function Documentation

◆ anatomist::ConnectivityMatrixProcessingThread