Transcript National Alliance for Medical Image Computing: Namic

NA-MIC
National Alliance for Medical Image Computing
http://na-mic.org
3D Slicer
Modules and Extensions
Steve Pieper, Ph.D.
How Modules Should Work
• Slicer 3.4 is a Stable Base for Many Medical
Image Computing Apps
– Core File I/O, Visualization, Interface…
– Tutorials and Other Resources to Get New Users Up to
Speed
• Developers of New Techniques can Draw on the
NA-MIC Kit to Implement Compatible Modules
– Consistent Framework for Deployment and User
Interface
– Several Styles of Development to Meet Varied
Requirements
National Alliance for Medical Image Computing
http://na-mic.org
Slicer3 data model
Provided by D. Gering
Provided by R. Kikinis
National Alliance for Medical Image Computing
http://na-mic.org
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
Modules Should Follow Same Conventions
National Alliance for Medical Image Computing
http://na-mic.org
GUI
Renderers
Widgets
Edit
Observe
Logic
Observe
Edit
Observe
Edit
MRML Nodes
“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.
Variety of levels of integration
Slicer Libs
•
•
•
•
Slicer Base
• Application logic
• Widgets
Common infrastructure for Slicer
applications
Built in modules
•
•
•
•
Slice viewers
Models
Fiducials
Transforms
Full access to Slicer internals
Loadable modules
•
•
•
•
•
Query Atlas
QDEC
Volume rendering
ChangeTracker
EMSegment
Full access to Slicer internals
Scripted modules
• Editor
• Teem Two Tensor Tractography
• VMTK
Limited access to Slicer internals
Command line modules
• Registration
Restricted access to Slicer internals
Daemon
• OpenIGTLink
• Stochastic Tractography
Access to MRML
ModuleDescriptionParser
GenerateCLP
vtkITK
MRML
National Alliance for Medical Image Computing
http://na-mic.org
Non-slicer specific support libraries
Base Features vs. Modules
Features
Base
Modules
Visualization
MRML: Models, Volumes, Volume Rendering, Fiducials,
Continuum Meshes, Labeled Data
Can create custom MRML Nodes and
behavior
Filtering
None
Implemented as Modules using ITK or
other Libraries
Registration
Transform Display and Edit, Save/Restore
Calculate Transforms, Resample Data
Segmentation
Label Maps, Parcellated Surfaces
Segmentation Algorithms in ITK or other
Libraries
Quantification
Label, Image, Volume Statistics; Numpy access to
MRML
Applications in Python or MATLAB
Real-time Integration
VTK Rendering, KWWidgets framework, Tracker
Support (as Transforms)
Direct Manipulation of the MRML
Scene; 2D/3D Widgets; Device
Interfaces, OpenIGTLink Module
Diffusion Imaging
DWI, DTI, Fiber Bundles
Tractography, Clustering, Atlases
Applications
“Bundles” of Modules in Distribution: Registration, Editor,
some Filters,
Customized Extensions, Domainspecific code, Optimized Interfaces…
National Alliance for Medical Image Computing
http://na-mic.org
Each module has …
… an entry in the module menu
… a panel of user interface controls
National Alliance for Medical Image Computing
http://na-mic.org
Built in module
Slicer provided
Module writer provided
vtkMRMLNode.h
vtkSlicerModuleGUI.h
vtkSlicerModuleLogic.h
vtkMRMLYourModuleNode.h
•GetNodeTagName()
•Copy()
•ReadXMLAttributes()
•WriteXML()
vtkSlicerYourModuleGUI.h
•BuildGUI()
•ProcessGUIEvents()
•ProcessLogicEvents()
•ProcessMRMLEvents()
vtkSlicerYourModuleLogic.h
•ProcessMRMLEvents()
•ProcessLogicEvents()
National Alliance for Medical Image Computing
http://na-mic.org
Loadable module
Slicer provided
Module writer provided
vtkMRMLNode.h
vtkSlicerModuleGUI.h
vtkSlicerModuleLogic.h
vtkMRMLYourModuleNode.h
•GetNodeTagName()
•Copy()
•ReadXMLAttributes()
•WriteXML()
vtkSlicerYourModuleGUI.h
•BuildGUI()
•ProcessGUIEvents()
•ProcessLogicEvents()
•ProcessMRMLEvents()
vtkSlicerYourModuleLogic.h
•ProcessMRMLEvents()
•ProcessLogicEvents()
YourModule.so
•GetLoadableModuleDescription()
•GetLoadableModuleLogic()
•GetLoadableModuleGUI()
National Alliance for Medical Image Computing
http://na-mic.org
Tcl scripted module
Slicer provided
Module writer provided
vtkMRMLScriptedModule
Node.h
vtkSlicerScriptedModule
GUI.h
vtkSlicerScriptedModule
Logic.h
YourModuleNode.tcl
YourModuleGUI.tcl
YourModuleLogic.tcl
•proc YourModuleBuildGUI
•proc YourModuleProcessGUIEvents
•proc YourModuleProcessLogicEvents
•proc YourModuleProcessLogicEvents
YourModule.tcl
•package provide YourModule x.y
National Alliance for Medical Image Computing
http://na-mic.org
Python scripted module
Slicer provided
Module writer provided
vtkMRMLScriptedModule
Node.h
vtkSlicerScriptedModule
GUI.h
vtkSlicerScriptedModule
Logic.h
YourModuleGUI.py
YourModuleNode.py
• Optional State Management
•def BuildGUI()
•def ProcessGUIEvents()
•def ProcessLogicEvents()
•def ProcessLogicEvents()
National Alliance for Medical Image Computing
http://na-mic.org
YourModuleLogic.py
• Optional Helper Code
Command line module
Slicer provided
Module writer provided
vtkMRMLCommandLine
ModuleNode.h
vtkCommandLine
ModuleGUI.h
vtkCommandLine
ModuleLogic.h
YourModule.xml
•<image>
•<geometry>
•<integer>
•<double>
•<file>
YourModule.so
•XMLModuleDescription
•GetXMLModuleDescription()
•ModelEntryPoint()
or
YourModule (exe)
•YourModule –xml
National Alliance for Medical Image Computing
http://na-mic.org
or
YourModule.py
•XML
•def toXML()
•def Execute()
All modules are created equal…
… an entry in the module menu
… a panel of user interface controls
National Alliance for Medical Image Computing
http://na-mic.org
Daemons
slicerget.tcl name > image.nrrd
SlicerDaemon
YourTool
(exernal
process
such as
MATLAB)
cat image.nrrd | slicerput.tcl name
OpenIGTLink Protocol
OpenIGTLinkIF
National Alliance for Medical Image Computing
http://na-mic.org
YourTool
(exernal
process
such as
Tracker or
Scanner)
Variety of levels of integration
Slicer Libs
•
•
•
•
Slicer Base
• Application logic
• Widgets
Common infrastructure for Slicer
applications
Built in modules
•
•
•
•
Slice viewers
Models
Fiducials
Transforms
Full access to Slicer internals
Loadable modules
•
•
•
•
•
Query Atlas
QDEC
Volume rendering
ChangeTracker
EMSegment
Full access to Slicer internals
Scripted modules
• Editor
• Teem Two Tensor Tractography
• VMTK
Limited access to Slicer internals
Command line modules
• Registration
Restricted access to Slicer internals
Daemon
• OpenIGTLink
• Stochastic Tractography
Access to MRML
ModuleDescriptionParser
GenerateCLP
vtkITK
MRML
National Alliance for Medical Image Computing
http://na-mic.org
Non-slicer specific support libraries
Extension Goals
•
•
Keep the base package “lean and mean”
Modules have individual identity
– Per-module web site, svn, downloads, mailing lists, wiki…
•
Allow users to assemble their own set of tools
– Customized ‘Bundles’ by task or application
•
Easy to download compatible extensions
– Analogous to Firefox extensions
– Integrate extension builds into developer/nightly/release process
•
NITRC Supplement to NA-MIC helping to pay for needed
infrastructure (Neuroimaging Informatics Tools and Resources
Clearinghouse)
– NITRC can host neuroimaging projects (gforge implementation)
•
Other repositories can also be used
– NAMICSandBox, Institution’s svn, Google Code, etc…
National Alliance for Medical Image Computing
http://na-mic.org
Extension Management Wizard*
* Under development
National Alliance for Medical Image Computing
http://na-mic.org
NITRC
http://www.nitrc.org/projects/slicer3examples/
Sample Code for CommandLine, Loadable, and Scripted
Extension Modules
National Alliance for Medical Image Computing
http://na-mic.org
Extension Process
• Write your module following the examples
on nitrc.org
• Create .s3ext description file
– http://viewvc.slicer.org/viewcvs.cgi/trunk/Extensions/
– Svn path, dependencies, homepage, category,
status, description…
• Nightly builds create compatible sets of
extension binaries that correspond to the
slicer builds (windows, linux, mac)
– Correct lib versions, compiler versions, etc
• Users can install from Extension Manager
National Alliance for Medical Image Computing
http://na-mic.org
CTK Issues
• Can some or all Slicer Module types
be interoperable with other CTK
Tools
– Automatic Adaptors?
• What will be the CTK Preferred
Module Implementation?
– Web Services? daemons? OSGi?...
National Alliance for Medical Image Computing
http://na-mic.org