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Slicer 3.0 Architecure

Slicer 3.0 Architecure. User Desktop. Slicer 3.0. Algorithms. ITK. VTK. Slicer Modules. Scripts of Slicer Mods. VTK Apps Using ITK. Batch Programs. Non-NAMIC Cmd tools. LONI Pipeline. Birn Grid Data/Compute. Slicer 3 Architecture Diagram (2006-01-26). Execution Model Manager.

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Slicer 3.0 Architecure

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  1. Slicer 3.0 Architecure User Desktop Slicer3.0 Algorithms ITK VTK Slicer Modules Scripts of Slicer Mods VTK Apps Using ITK Batch Programs Non-NAMIC Cmd tools LONI Pipeline Birn Grid Data/Compute

  2. Slicer 3 Architecture Diagram (2006-01-26) Execution Model Manager Base (Managed by Base and communicats like other Modules) Auto-Generated GUIs from JSON Descriptions Logic Links to: Base Logic GUI Links to: KWWidgets Logic Links to: ITK MRML VTK (except Rendering) GUI Links to: VTK Rendering KWWidgets Mediators Mediators Observe Modified Events MRML • Provides • Frames for Widgets, • Routing of User Events Observe Modified Events on Application State Formulates Command Line and possibly stages data Edit Mrml Scene/Nodes • Registers GUI Event Observers Interactive Module Describe Input options Observe Modified Events Logic Links to: Base Logic ITK MRML VTK (except Rendering) GUI Links to: VTK Rendering KWWidgets Mediators Edit Mrml Scene/Nodes • External • Processes (Grid/Pipeline) • Speak MRML • (link to libmrml • or have data staged by slicer) • Uses the JSON interface MRML Aware Processes Can Edit Mrml Scene/Nodes and Observe Modified Events • Notes: • All classes in the Logic directory should be able to run ‘headless’ without OpenGL or window system for scripting and testing • Base/Logic contains transient application state (cursor location, focus, mrml scene connection…) • 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 • GUI classes are implemented as KWWidget subclasses • Each Logic class defines a set of Get/Set methods for internal state and Modified Events that GUI classes can Observe

  3. Main program; Bootstrap application logic, Create application gui data layer data mediator logic layer gui mediator gui layer (VTK, ITK, no KWWidgets, no VTKRendering) vtkObject vtkSlicerLogic - Undo manager, - tracing vtkSlicerApplicationLogic - MRML slice # - “transient state” - open views, slices, modules (and active) - cursor location - version - focus, event routing vtkSlicerViewLogic vtkSlicerLinkedSliceLogic vtkSliceLogic - vtkImageReslice - vtkImageComposite vtkSlicerSliceLayerLogic - MRML node - Opacity - Compositing - Window/level vtkSlicerViewLogic vtkSlicerModuleLogic - Undo/tracing helpers vtkSlicerEditorLogic vtkSlicerMRMLLogic vtkSlicerCustomModuleLogic vtkKWWidget vtkSlicerGUI - look & feel? - set command helpers? vtkSlicerApplicationGUI - connect to window system - vtkKWApplication - vtkKWWindow vtkSlicerViewGUI - Render windows - mappers, actors vtkSlicerSliceGUI - vtkImageMapper - vtkKWRenderWindow vtkSlicerSliceLogicGUI vtkSlicerModuleGUI vtkSlicerCustomModuleGUI GUI code adds observers to modified events generated by/to logic Logic code adds modified event observers to MRML scene and MRML nodes. MRML data model Apply methods from GUI classes call set method in logic to change state Logic methods apply changes to the MRML scene. VTK pipeline VTK pipeline

  4. Slicer Daemon • Slicerd listens on local socket • slicerget<id> • gets volume and writes to stdout in nrrd • slicerput[name] • reads nrrd on stdin and puts in slicer • % slicerget 0 | unu 1op exp - | slicerput

  5. ITK IO and Slicer Daemon AntiAliasBinaryImageFilter.exe bunny.z.nrrd "| sh slicerput.tcl"

  6. 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

  7. Undo 1st Pass Application Logic Undo Stack Initial Scene Delta1 Scene Delta2 Scene Saved Scene N1 R R N1 N2 N4 R N4 N3 R N5 N5

  8. Undo Current MRML Scene Undo Stack Initial Scene Delta1 Scene Delta2 Scene Saved Scene N1 N1 N2 N4 N4 N3 N5 N5

  9. 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 Volume Display Node Volume Node Foreground Slice Layer Logic Volume Display Node Volume Node Background Slice Layer Logic Slice Node Slice GUI Slice Logic Slice Composite Node

  10. SliceNode XYToIJK Matrix Calculated by SliceLayerLogic From GUI Slice Coordinates RASToRAS Transforms SliceToRAS Matrix XYToSlice Matrix RASToIJK Matrix RAS to RAS Coordinates Slice Coordinates XY Image Space Coordinates IJK = RASToIJK * RASToRAS * SliceToRAS * XYToSlice * XY IJK Volume Coordinates

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