anatomist Namespace Reference

Namespaces
	internal

Classes
class	AnatomistInfo
class	Anatomist
	The Anatomist class holds information about all data handled by Anatomist: the objects, the windows, and other application-wide lists. More...
class	GlobalConfiguration
	This class stores global configuration settings, read by default from $HOME/.anatomist/config/settings.cfg. More...
class	LocalConfiguration
	Local configurator: used by program parts (modules, ...) to setup their part of the global config. More...
class	Settings
class	Module
	Base class for dynamically loaded modules. More...
class	ModuleManager
	Manage Anatomist modules. More...
class	ModuleObserver
	Base class for objects interested in module changes notification. More...
class	ModuleInterface
	Represent the Anatomist internals made available to Modules. More...
class	SyntaxRepository
class	SelectBrowserControl
class	AttDescr
	Attributed object descriptor. More...
class	Bucket
	Bucket class. More...
class	ColorScalarPaletteTraits
class	ColorNoPaletteTraits
class	ColorTraits
	Converter value -> RGBA (high-level) More...
class	APaletteExtensionAction
class	APaletteWin
	Object color palette window. More...
class	APaletteWinFactory
	singleton "factory": always use this trick instead of "new APaletteWin" More...
class	AObjectPalette
class	PaletteList
class	APalette
class	Material
	This class has to be rewritten, it's really really a shame....... More...
class	Light
	Light used for OpenGL in 3D windows. More...
class	ActivateActionCommand
class	AddObjectCommand
	? More...
class	ApplyBuiltinReferentialCommand
	Assign builtin referentials and transformations to objects. More...
class	AskTexExtremaCommand
class	AssignReferentialCommand
	Assign a referential to objects and/or windows. More...
class	CameraCommand
class	ChangePaletteCommand
	Change a APalette RGB lookup in the main list. More...
class	ControlsParamsCommand
class	ClosePipeCommand
class	CloseWindowCommand
	? More...
class	CreateControlWindowCommand
	Command to open the control window. More...
class	CreateWindowCommand
	Window creation command. More...
class	DeleteAllCommand
	Deletes all elemets in the application (kind of reset): More...
class	DeleteElementCommand
	Deletes elemets given by their (un)serializer ID. More...
class	DeleteObjectCommand
	? More...
class	DuplicateObjectCommand
	Duplicate (clone or shallow-copy) an object when possible. More...
class	EventFilterCommand
	Set output stream for the current commands context. More...
class	ExitCommand
class	ExportTextureCommand
	Exports a texture of an object (fusion) to disk (texture file) More...
class	ExternalReferenceCommand
	Manages reference counting on elements for a remote application. More...
class	ExtractTextureCommand
	Extracts a texture of an object (fusion) to a texture object. More...
class	Fusion2DParamsCommand
class	Fusion3DParamsCommand
class	FusionInfoCommand
class	FusionObjectsCommand
class	GenerateTextureCommand
	Generates a texture corresponding to the geometry of another given object. More...
class	GetInfoCommand
	Writes information about Anatomist state in a file or pipe. More...
class	GraphDisplayPropertiesCommand
class	GraphParamsCommand
class	GroupObjectsCommand
	Group objects in an ObjectList. More...
class	LinkedCursorCommand
	Positioning the linked cursor. More...
class	LinkWindowsCommand
class	LoadGraphSubObjectsCommand
class	LoadObjectCommand
	Command to load an object from a file. More...
class	LoadTransformationCommand
	Load a transformation between two referentials. More...
class	LoadTransformationGraphCommand
	Load a transformations graph. More...
class	NewIdCommand
	Reserves an object/window/element ID in the context namespace. More...
class	NewPaletteCommand
	Add a new APalette to the common PaletteList (stored in Anatomist class). More...
class	ObjectInfoCommand
	Writes information about Anatomist state in a file or pipe. More...
class	OutputCommand
	Set output stream for the current commands context. More...
class	PopupPaletteCommand
class	ReloadObjectCommand
	? More...
class	RemoveObjectCommand
class	SaveObjectCommand
class	SaveTransformationCommand
	Save a transformation between two referentials. More...
class	SaveTransformationGraphCommand
	Save a transformations graph. More...
class	SelectCommand
class	SelectByHierarchyCommand
class	ServerCommand
	Launches a stream server or re-sets its parameters. More...
class	SetControlCommand
class	SetMaterialCommand
	Apply a material colors to objects. More...
class	SetObjectPaletteCommand
	Set an AObjectPalette to objects. More...
class	ShowObjectCommand
	Show an object in the control window if it is hidden. More...
class	SliceParamsCommand
class	TexturingParamsCommand
class	WindowBlockCommand
class	WindowConfigCommand
class	Hierarchy
	Nomenclature hierarchy object. More...
class	QSelectWidget
	A simple window to allow choosing between selected objects. More...
class	WSelectChooser
	Base class for selection chooser windows. More...
class	SelectFactory
	Central selection center. More...
class	Selector
class	LowestLevelSelector
class	PostSelector
	Performs an action after an object has been selected (fiber tracking, ...) More...
class	Observer
	A class can implement the Observer interface when it wants to be informed of changes in observable objects. More...
class	Observable
	This class can be subclassed to represent an object that the programmer wants to have observed. More...
class	ObservableCreatedNotifier
	This is a manager for callbacks called when an new Observable is created. More...
class	Transformation
	Transformation between two referentials. More...
class	Referential
	Referential: marker for transformations, with an associated color. More...
class	Geometry
class	Referentiable
class	ReferentialObserver
class	ReferencePixmap
class	TransformationObserver
	Transformation observer. More...
class	ATransformSet
	List of all transformations. More...
class	RefWindow
class	CutMesh
class	Fusion2DMesh
	Anatomist object which contains several meshes: it displays the mesh polygons that intersect the current slice plane. More...
class	FusionTexSurfMethod
class	GLComponent
	Base class for all OpenGL objects in Anatomist (with OpenGL display lists) More...
class	AGLObject
class	AMTexture
	Multi-texture. More...
class	PlanarFusion3D
class	ASurface
	Template surface type. More...
class	TesselatedMesh
class	ATexSurfaceIterator
	Textured surface iterator. More...
class	const_ATexSurfaceIterator
	Textured surface const_iterator. More...
class	ATexSurface
	Fusion object merging a triangulation and a texture object. More...
class	TextObject
	A text object: displays text messages as textures in 3D objects. More...
class	ATexture
	High-level Texture object in Anatomist. More...
class	TransformedObject
	A container object which displays its children either with a fixed orientation, or at a fixed position in the window corner. More...
class	Shader
class	ANormalsMesh
	A mesh displaying normals for other meshes. More...
class	NormalsFusionMethod
class	NormalsSettingsPanel
	normals settings GUI More...
class	VectorField
class	AGraphIterator
class	const_AGraphIterator
class	PythonAObject
	Attributed objects wrapper. More...
class	AGraphObject
	Anatomist graph object: a list that manages destruction of its sub-elements. More...
class	AGraph
	AGraph object class. More...
class	ObjectActions
	Base callback functions for actions on the objects. More...
class	ClippedObject
class	AObjectLoadEvent
class	ObjectReaderNotifier
class	MObjectIO
class	ObjectMenuCallback
class	ObjectMenuCallbackFunc
class	ObjectMenu
class	ObjectMenuRegistrerClass
class	ObjectMenuRegistrerFuncClass
class	ObjectUtils
class	OptionMatcher
	Option menus registration mechanism (all static). More...
class	ObjectReader
	Object reader. More...
struct	AImage
class	AObject
	Base Anatomist object (abstract) More...
class	ObjectConverter
	Converts custom lower-level objects (generally aims objects) to Anatomist objects and vice versa. More...
class	SelfSliceable
	Self sliceable objects contain a plane (slice) information: slice position and orientation only depend on the object itself. More...
class	Sliceable
	Sliceable objects can draw themselves in a 2D texture. More...
class	SliceableObject
	AObject-inherited version of Sliceable. More...
class	ColoredPixmapCache
class	GraphParams
class	AWinConfigIO
class	AControlMenuHandler
	Menu of ControlWindow. More...
class	AbstractMenuHandler
	Base class for GUI-independant menu handling, using Trees. More...
class	ControlConfiguration
	Configuration stuff for main Anatomist (control window settings) More...
class	WhatsNew
class	QAObjectDrag
class	Action
class	ActionDictionary
class	ControlDictionary
class	ControlGroupDictionary
class	IconDictionary
class	ActionPool
struct	ControlMapEntry
struct	LessControlMap
class	ControlManager
class	Control
class	KeyAndMouseLongEvent
class	MouseLongEvent
class	LongActions
class	ControlSwitchObserver
class	View
class	QAWindowDrag
class	GLCaps
	OpenGL capabilities. More...
class	GLWidgetManager
	Base class for OpenGL-rendering widget. More...
struct	ViewState
	ViewState holds information about how a view wants to see an object. More...
struct	SliceViewState
	Specialization for a sliceable object. More...
class	AWindowCreator
	Virtual functor for AWindowFactory. More...
class	AWindowFactory
	Window creator: (string) type -> new window. More...
class	AWindowCreatorFunc
	Virtual functor for AWindowFactory, using a function pointer. More...
class	AWindow
	Abstract base class Anatomist window. More...
class	AnnotationAction
class	BoxViewSlice
class	ConnectivityMatrixAction
class	ConnectivityMatrixControl
class	OrientationAnnotation
class	Cursor
class	Control3D
class	Select3DControl
class	FlightControl
class	ObliqueControl
class	TransformControl
class	CutControl
class	WindowActions
class	LinkAction
class	MenuAction
class	SelectAction
class	Zoom3DAction
class	Translate3DAction
class	Sync3DAction
class	MovieAction
class	SliceAction
class	DragObjectAction
class	SortMeshesPolygonsAction
class	ObjectStatAction
class	LabelEditAction
class	Trackball
class	ContinuousTrackball
class	KeyFlightAction
class	TrackCutAction
class	CutSliceAction
class	TrackOblique
class	TrackObliqueSlice
class	Transformer
class	TranslaterAction
class	PlanarTransformer
class	ResizerAction
class	GLObjectList
class	GLObjectVector
class	GLMObject
	A Multi-object with OpenGL rendering capabilities. More...
class	ObjectVectorIterator
class	const_ObjectVectorIterator
class	ObjectVector
	it's a list, in fact... More...
class	BaseIterator
class	AIterator
	Multi-object generic iterator. More...
class	MObject
	Multi-object : base abstract class for objects that contain others. More...
class	Fusion2D
	Anatomist object which contains two volumes: one for the MRI anatomic image, and another for the functional data (fMRI, PET...) More...
class	Fusion3D
	Anatomist object which contains a volume of functional data (fMRI, PET...) and a surface of the MRI anatomic data. More...
class	ObjectListIterator
class	const_ObjectListIterator
class	ObjectList
	Multi-object : AObject containing children objects. More...
class	Slice
class	AVolumeBase
	VolumeBase object : use for generic dynamic_cast of all AVolume<T>, thus the visitor design pattern can be used. More...
class	AVolume
	Volume object. More...
class	AVolumeView
struct	CommandContext
	Context for commands processor readers (APipeReader etc) More...
class	ErrorMessage
	A wrapper for QMessageBox, but may use non-graphical message outputs. More...
class	OutputEvent
	This class holds events to send to output streams so that external programs are notified when something happens in Anatomist. More...
class	OutputEventFilter
	Filering of events sent to the external wolrd (output streams) More...
class	EventHandler
	Event handlers are called internally when the default context outputs an event. More...
class	APipeReader
	Handles async reads. More...
class	Unserializer
	Pointer decoder (or id to pointer map) More...
class	CommandServer
class	Command
	The abstract base class for commands. More...
class	RegularCommand
	The abstract base class for usual commands. More...
class	SerializingCommand
	The abstract base class used for commands that have to read/write pointers. More...
class	WaitCommand
	The abstract base class for commands that display a watch cursor. More...
class	Processor
	The command processor receives commands to manage and execute. More...
class	Registry
	Registry links all Command concrete subclasses with a function that will read the guts of the command and create an instance of the subclass. More...
class	CommandReader
	CommandReader replays history files. More...
class	CommandWriter
	CommandWriter is a helper class logging commands into a history file. More...
class	Serializer
	Serializer is a helper class for pointer serialization. More...
class	Fusion2dMethod
	Default fusion method for Fusion2D objects. More...
class	Fusion3dMethod
	Default fusion method for Fusion3D objects. More...
class	PlanarFusion3dMethod
class	FusionTextureMethod
class	FusionMultiTextureMethod
class	FusionCutMeshMethod
class	Fusion2DMeshMethod
class	FusionSliceMethod
class	FusionRGBAVolumeMethod
class	FusionClipMethod
class	FusionTesselationMethod
class	ConnectivityMatrixFusionMethod
class	VectorFieldFusionMethod
class	FusionMethod
	Fusion method interface. More...
class	FusionFactory
	Handles creation of various fusion objects. More...
class	StdModule
class	AConnectivityMatrix
	Connectivity matix object: fusions sparse matrix, white mesh, and optionally a gyrus patch texture. More...
class	ASparseMatrix
	Sparse matrix in Anatomist. More...
class	GLItem
	OpenGL item (display list, texture, ...) with reference counter and cleanup upon destruction. More...
class	Primitive
	Multiple display lists and texture objects. More...
class	GLList
class	GLTexture
class	GLItemList
class	GLNoExecItemList
class	ConstraintEditorWindow
class	NodeSelectionAction
class	NodeSelectionControl
class	HierarchyEditor
class	ErpReader
	.erp format reader More...
class	AInterpolerMethod
	Method to fusion surfaces & texture, to make an interpoler. More...
class	AInterpoler
	Interpoler object: associates a ATexSurface and a Triangulated to map the TexSurface's texture onto the Triangulated mesh, using interpolation (spheric spline for ex.). More...
class	ALandmarkFactory
	Simple class to create basic surfaces used as landmarks. More...
class	PlaneFusionMethod
	Simple tool top make a plane from 3 landmarks. More...
class	CylinderFusionMethod
	Simple tool top make a cylinder from 2 landmarks. More...
class	ASurfMatchMethod
	Method to fusion surfaces, to make a surface matcher. More...
class	ASurfMatcher
	Fusion object to match 2 surfaces. More...
class	AnaSurfMatch
class	SurfpaintModule
class	SurfpaintTools
class	SurfpaintToolsAction
class	SurfpaintToolsControl
class	VolRenderFusionMethod
class	VolRenderShaderFusionMethod
class	VolRenderModule
class	VolRender
class	VolRenderShader
class	ProfileModule
class	RoiLevelSetActionSharedData
class	RoiLevelSetAction
class	RoiLabelNamingAction
struct	ChangesItem
struct	ChangedBucketsItem
class	RoiChangeProcessor
class	PaintStrategy
class	PointPaintStrategy
class	SquarePaintStrategy
class	DiskPaintStrategy
class	BallPaintStrategy
class	PaintActionSharedData
class	PaintAction
class	RoiBlobSegmentationAction
class	PaintControl
class	RoiLevelSetControl
class	RoiLabelNamingControl
class	RoiManagementActionSharedData
class	RoiManagementAction
class	RoiManagementControl
class	RoiBaseModule
class	CreateGraphCommand
class	GetConnThresholdCommand
	Assign a referential to objects and/or windows. More...
class	SetConnThresholdCommand
	Assign a referential to objects and/or windows. More...
class	AddNodeCommand
class	PaintParamsCommand
class	RoiDynSegmentAction
class	RoiMorphoMathAction
class	RoiDynSegmentControl
class	RoiAlgoModule
class	HistogramModule

Typedefs
typedef enum QDir::Filter	FileFilterSpec
typedef enum QDir::SortFlag	FileSortSpec
typedef ASurface< 3 >	ATriangulated
typedef PythonAObject	AttributedAObject
typedef std::list< carto::rc_ptr< GLItem > >	PrimList
typedef Action *	ActionPtr
typedef std::map< std::string, std::set< std::string > >	ViewControls
typedef std::map< std::string, std::set< std::string > >	ObjectControls
typedef Control *	ControlPtr
typedef carto::rc_ptr< GLItem >	RefGLItem
typedef carto::rc_ptr< Primitive >	RefPrimitive
typedef carto::rc_ptr< GLList >	RefGLList
typedef carto::rc_ptr< GLTexture >	RefGLTexture
typedef carto::rc_ptr< GLItemList >	RefGLItemList
typedef std::list< RefGLItem >	GLPrimitives

Functions
QFileDialog &	fileDialog ()
std::list< std::string >	listDirectory (const std::string &dir, const std::string &filter="", int sortSpec=QDir::Name|QDir::IgnoreCase, int filterSpec=QDir::AllEntries)
	A utility function to scan a directory for files or directories, which will hide non-portable things. More...
std::istream &	operator>> (std::istream &, anatomist::Material &)
std::ostream &	operator<< (std::ostream &, const anatomist::Material &)
void	AError (const char *message)
void	AWarning (const char *message)
std::ostream &	operator<< (std::ostream &, const anatomist::Shader &)
void	initMenuObjects (void)
void	installBackgroundPixmap (QWidget *w)
void	setQtColorStyle (QWidget *w)
	fix KDE3 style bug, some styles don't allow changing colors, here we change if to one which is known to work More...

Variables
Processor *	theProcessor
	Pointer to the command processor of the application. More...

Typedef Documentation

ActionPtr

typedef Action * anatomist::ActionPtr

Definition at line 47 of file action.h.

ATriangulated

typedef ASurface< 3 > anatomist::ATriangulated

Definition at line 42 of file triangulated.h.

AttributedAObject

typedef PythonAObject anatomist::AttributedAObject

Definition at line 44 of file attribAObject.h.

ControlPtr

typedef Control* anatomist::ControlPtr

Definition at line 62 of file control.h.

FileFilterSpec

typedef enum QDir::Filter anatomist::FileFilterSpec

Definition at line 1 of file listDir.h.

FileSortSpec

typedef enum QDir::SortFlag anatomist::FileSortSpec

Definition at line 1 of file listDir.h.

GLPrimitives

typedef std::list<RefGLItem> anatomist::GLPrimitives

Definition at line 156 of file primitive.h.

ObjectControls

typedef std::map< std::string, std::set< std::string > > anatomist::ObjectControls

Definition at line 66 of file controlmanager.h.

PrimList

typedef std::list<carto::rc_ptr<GLItem> > anatomist::PrimList

Definition at line 73 of file Object.h.

RefGLItem

typedef carto::rc_ptr<GLItem> anatomist::RefGLItem

Definition at line 129 of file primitive.h.

RefGLItemList

typedef carto::rc_ptr<GLItemList> anatomist::RefGLItemList

Definition at line 155 of file primitive.h.

RefGLList

typedef carto::rc_ptr<GLList> anatomist::RefGLList

Definition at line 153 of file primitive.h.

RefGLTexture

typedef carto::rc_ptr<GLTexture> anatomist::RefGLTexture

Definition at line 154 of file primitive.h.

RefPrimitive

typedef carto::rc_ptr<Primitive> anatomist::RefPrimitive

Definition at line 152 of file primitive.h.

ViewControls

typedef std::map< std::string, std::set< std::string > > anatomist::ViewControls

Definition at line 65 of file controlmanager.h.

Function Documentation

AError()

void anatomist::AError

(

const char *

message

)

AWarning()

void anatomist::AWarning

(

const char *

message

)

fileDialog()

QFileDialog& anatomist::fileDialog

(

)

initMenuObjects()

void anatomist::initMenuObjects

(

void

)

installBackgroundPixmap()

void anatomist::installBackgroundPixmap

(

QWidget *

w

)

listDirectory()

std::list<std::string> anatomist::listDirectory	(	const std::string &	dir,
		const std::string &	filter = "",
		int	sortSpec = QDir::Name|QDir::IgnoreCase,
		int	filterSpec = QDir::AllEntries
	)

A utility function to scan a directory for files or directories, which will hide non-portable things.

Uses Qt's QDir - see the doc...

Parameters

dir	directory to scan
filter	files filter
sortSpec	sorting orger specifications, using QDir::SortSpec
filterSpec	attributes to filter files with, bitwise OR of anatomist::FileAttrib which are just a typedef from QDir::FilterSpec

operator<<() [1/2]

std::ostream& anatomist::operator<<	(	std::ostream &	,
		const anatomist::Material &
	)

operator<<() [2/2]

std::ostream& anatomist::operator<<	(	std::ostream &	,
		const anatomist::Shader &
	)

operator>>()

std::istream& anatomist::operator>>	(	std::istream &	,
		anatomist::Material &
	)

setQtColorStyle()

void anatomist::setQtColorStyle

(

QWidget *

w

)

fix KDE3 style bug, some styles don't allow changing colors, here we change if to one which is known to work

Variable Documentation

theProcessor

Processor* anatomist::theProcessor

extern

Pointer to the command processor of the application.