national alliance for medical image computing slicer3 architecture

National Alliance for Medical Image Computing http://na-mic.org

Slicer3 Architecture


ScientistDesktop

NA-MIC Architecture

Algorithms ITK

VTK

SlicerModules

ExperimentControl

Workstation /Cluster /

Grid

Slicer 3.0

Python/TclMATLAB…

ExecutionModel

DatabasesLocal / BIRN

DataAcquisition

ExperimentResults

QueryPlot

Visualize


Slicer3 “Observer MVC” Pattern

• MRML (Model)– For Scene Description and Application

State– MRML Nodes are Persistent and

Undoable– Scene and Nodes are Observable

• Logic Encapsulate VTK and ITK Pipelines (Controller)– Observe MRML to Configure Pipelines– Help Create/Manage Nodes– No UI Components (no Widgets, Actors,

Mappers, Renderers or RenderWindows)• GUI (View)

– Observe and Edit MRML– Interact with User and Display Hardware

Logic

MRML Nodes

GUI

Widgets Renderers

EditObserve

Observe

Observe

Edit

Edit

“Observe” means generic event mechanisms are used to pass information.“Edit” means code can directly call methods.

Example: GUI can call methods in Logic classes,but Logic cannot call GUI methods.MRML cannot call Logic or GUI methods.

There can be many observers for any event.

MRML

BaseLogic

Links to: ITK

MRMLVTK (except Rendering)

GUILinks to:

VTK RenderingKWWidgets

LogicMRML

Observe ModifiedEvents

Edit Mrml Scene/Nodes

Mediators

Interactive ModuleLogic

Links to: Base Logic

ITKMRML

VTK (except Rendering)

GUILinks to:

VTK RenderingKWWidgets

LogicMRML

Mediators

Observe ModifiedEvents on ApplicationState

Edit Mrml Scene/Nodes

•Registers GUI Event Observers

Observe ModifiedEvents

Provides •Frames for Widgets,•Routing of User Events

CommandLineModule

LogicLinks to:

Base Logic,MRML

GUILinks to:

KWWidgets Mediators

Execution Model Modules• build as executables

or shared libraries• support –xml query

(Managed by Base and communicateslike other Modules)

Describe Input options (uses--xml option)

Formulates Command Lineand passes data

Back-door to MRML with MRMLIDImageIOITK IO Factory Library(Otherwise through files,command line options)

Slicer 3 Architecture Diagram (updated 2007-01-09)

Auto-Generated GUIs from XML Descriptions

Notes:•All classes in the Logic directory should be able to run ‘headless’ without OpenGL or window system for scripting and testing•Base Logic and GUI contain transient application state (cursor location, focus, mrml scene connection…)•Persistent and Undoable state in MRML Nodes•Interactive Modules are ones which interact with the VTK scene and/or User events•Interactive Modules interact with 3D scene by creating objects in MRML scene (not by direct manipulation of the Renderer)•Logic classes encapsulate and manage internal vtk/itk pipelines and provide helper routines to create/manage nodes•GUI classes are implemented as KWWidget subclasses•Each Logic class defines Get/Set methods for internal state and Modified Events that GUI classes can Observe•Code in Base implements “first order” Node types (Volumes, Models, Transforms, Fiducials, Colors, etc).•Code in Modules provides application-specific extensions

External Connections• Use socket connection directly

(e.g. MATLAB)• Use slicerget/slicerget utilities

(e.g. unu)

Slicer Daemoncommunication viaserver port


Slicer3 Slice Coordinates

XY Image Space CoordinatesIn RenderWindow

Slice Coordinates

RAS to RAS Coordinates

IJK Volume Coordinates

XYToSlice Matrix

SliceToRAS Matrix

RASToRAS Transforms

RASToIJK Matrix

IJK = RASToIJK * RASToRAS * SliceToRAS * XYToSlice * XY

SliceNode

XYToIJK Matrix Calculated by SliceLayerLogic Coordinates are Cell Centered (no VTK flip)

From GUI

IJK = XYToIJK * XY

TransformNodeVolumeNode


Slice Management

ForegroundSlice Layer Logic

Slice Node

Slice Composite Node

BackgroundSlice Layer Logic

Slice Logic

Volume Display NodeVolume Node


Slice GUI

MRML Nodes: Persistent, Undoable State

Logic: Encapsulate VTK Pipelines, Observe MRML Nodes

GUI: Manage Widgets and Rendering; Manipulated Nodes and Logic; Observe Nodes and Logic


Slice Management


Slice Node



Slice Logic



Slice GUI




Stores:

Window/Level

Lookup Table (Color Node)

Transparency Threshold


Slice Management


Slice Node



Slice Logic



Slice GUI




Stores:

RAS Location of Slice (Origin and Orientation)

Field of View

Pixel Dimensions


Slice Management


Slice Node



Slice Logic



Slice GUI




Stores:

Volume IDs per Layer

Opacity of Overlay


Slice Management


Slice Node



Slice Logic



Slice GUI




Stores:

Image Data

IJKToRAS Matrix

Name…


Slice Management


Slice Node



Slice Logic



Slice GUI




Pipeline with:

vtkImageReslice

vtkImageMapToWindowLevelColors

vtkImageMapToRGBA


Slice Management


Slice Node



Slice Logic



Slice GUI




Pipeline with:

vtkImageBlend


Slice Management


Slice Node



Slice Logic



Slice GUI




GUI:

SliceControllerWidget (Menus, Scale, Buttons…)

SliceViewer (RenderWidget, ImageMapper, ImageActor…)


Undo Architecture for Slicer3

• Versioning “Commit Aside” Strategy Encapsulated within MRML

• Store “Initial Scene” (from file) and “Delta Scenes” (scenes containing undoable changes)

• Delta Scenes ‘are’ MRML Scenes • Some Nodes are Reference Nodes• Setting the MRML scene in the Application Logic

causes the cascade of observer callbacks • => All Undoable operations must store their data

as MRML nodes


Undo Implementation

Initial Scene

MRML Scene

N1

N2

N3

Delta1 Scene

N4

Delta2 Scene

N5

Saved Scene

N1

N4

N5

Undo Stack

national alliance for medical image computing slicer3 architecture

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