Transcript Slicer 3.0 Architecure Algorithms ITK VTK Slicer Modules Slicer 3.0 Scripts of Slicer Mods VTK Apps Using ITK Batch Programs Non-NAMIC Cmd tools LONI Pipeline Birn Grid Data/Compute National Alliance for Medical Image Computing http://na-mic.org User Desktop.

Slicer 3.0 Architecure
Algorithms
ITK
VTK
Slicer
Modules
Slicer 3.0
Scripts of
Slicer Mods
VTK Apps
Using ITK
Batch
Programs
Non-NAMIC
Cmd tools
LONI
Pipeline
Birn Grid
Data/Compute
National Alliance for Medical Image Computing
http://na-mic.org
User
Desktop
Slicer 3 Architecture Diagram (2006-01-26)
Execution Model Manager
Auto-Generated
GUIs from JSON
Descriptions
Logic
Links to:
Base Logic
Mediators
Base
(Managed by
Base and communicats
like other Modules)
GUI
Links to:
KWWidgets
Observe Modified
Events
Formulates
Command Line
and possibly
stages data
Logic
Links to:
ITK
MRML
VTK (except
Rendering)
Edit Mrml
Scene/Nodes
Mediators
GUI
Links to:
VTK Rendering
KWWidgets
Provides
•Frames for Widgets,
•Routing of User Events
Observe Modified
Events on Application
State
•Registers GUI
Event Observers
MRML
Describe Input
options
External
Processes (Grid/Pipeline)
• Speak MRML
(link to libmrml
or have data staged by slicer)
•Uses the JSON interface
Interactive Module
Observe Modified
Events
MRML
Aware Processes
Can Edit Mrml
Scene/Nodes
and Observe
Modified Events
Edit Mrml
Scene/Nodes
Logic
Links to:
Base Logic
ITK
MRML
VTK (except
Rendering)
Mediators
GUI
Links to:
VTK Rendering
KWWidgets
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
Main program;
Bootstrap application logic,
Create application gui
data layer
data mediator
Logic code adds
modified event
observers to MRML
scene and MRML
nodes.
MRML
data
model
Logic methods
apply changes to
the MRML scene.
VTK pipeline
logic layer
gui mediator
gui layer
(VTK, ITK, no
KWWidgets, no
VTKRendering)
vtkKWWidget
vtkObject
vtkSlicerGUI
- look & feel?
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
GUI code adds
observers to modified
events generated
by/to logic
Apply
methods from
GUI classes
call set
method in
logic to
change state
- set command helpers?
vtkSlicerApplicationGUI
- connect to window system
- vtkKWApplication
- vtkKWWindow
vtkSlicerViewGUI
- Render windows
- mappers, actors
vtkSlicerSliceGUI
- vtkImageMapper
- vtkKWRenderWindow
vtkSlicerSliceLogicGUI
VTK pipeline
vtkSlicerModuleGUI
vtkSlicerCustomModuleGUI
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
National Alliance for Medical Image Computing
http://na-mic.org
ITK IO and Slicer Daemon
AntiAliasBinaryImageFilter.exe bunny.z.nrrd "| sh slicerput.tcl"
National Alliance for Medical Image Computing
http://na-mic.org
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
National Alliance for Medical Image Computing
http://na-mic.org
Undo 1st Pass
Undo Stack
Application Logic
Initial Scene
Delta1 Scene
Delta2 Scene
Saved Scene
N1
R
R
N1
N2
N4
R
N4
N3
R
N5
N5
National Alliance for Medical Image Computing
http://na-mic.org
Undo Current
Undo Stack
Initial Scene
Delta1 Scene
MRML Scene
Delta2 Scene
N1
N2
Saved Scene
N1
N4
N3
National Alliance for Medical Image Computing
http://na-mic.org
N4
N5
N5
Slice Management
Volume Display Node
Volume Node
Foreground
Slice Layer Logic
Volume Display Node
Volume Node
Background
Slice Layer Logic
Slice Node
Slice Logic
Slice Composite Node
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
National Alliance for Medical Image Computing
http://na-mic.org
Slice GUI
Slice Coordinates
RASToRAS Transforms
SliceToRAS Matrix
XYToSlice Matrix
RASToIJK Matrix
RAS to RAS Coordinates
Slice Coordinates
XY Image Space Coordinates
IJK Volume Coordinates
IJK = RASToIJK * RASToRAS * SliceToRAS * XYToSlice * XY
From GUI
SliceNode
XYToIJK Matrix Calculated by SliceLayerLogic
National Alliance for Medical Image Computing
http://na-mic.org