Slicer 3'4 Update

1
Slicer 3.4 Update

• Summer NA-MIC Project Week 2009
• Steve Pieper, Ph.D.

2
Topics

• Slicer 3.4 Development Highlights
• Modules and Extensions
• Extensions and You

3
Slicer Goals

• Stable, Usable, Cross Platform, End-User Software
  for Medical Image Analysis
• 3D Slicer Role in NA-MIC and NCIGT
• Translation Platform to Deliver Medical Computing
  Technology to DBP Researchers
• Provide Reference Implementation using NA-MIC Kit
  (End-to-End Open Source)
• Outreach to New Applications
• First Slicer3 svn commit January 26, 2006

4
Progress Since Jan 2009

• Numbers Jan 2009
• Subversion Commits 8,317
• Lines of Code 735,536
• Bugs Features
• 239 Submitted
• 129 Fixed
• Active Developers 53
• 3D Slicer Version 3.2
• Released August 8, 2008

• Numbers June 2009
• Subversion Commits 9,732 (1,415)
• Lines of Code 791,101
• Bugs Features
• 605 Submitted
• 323 Fixed
• Active Developers 59
• 3D Slicer Version 3.4
• Released May 2009

find . -iname \.h -o -iname \.cxx -o -iname
\.tcl -o -iname \.java -o -name \.py grep -v
svn xargs wc (does not include libraries or
modules in external repositories) svn log
grep "r" cut -d " " -f 3 sort uniq wc
5
Whats New in 3.4

• Many fixes in performance, usability,
  functionality
• Editor, CompareView, Diffusion Tools, Load/Save,
  Welcome Module, Fiducials, FetchMI (XNAT
  interface)
• New Modules
• Change Tracker (Tumor Metrics), IA_FEMesh
  (Meshing), OpenIGTLink (Image Guided Therapy),
  RegisterImages, Stochastic Tractograpy
• New Infrastructure
• Python in Binary Distributions (More from Demian
  at 11)
• Extension Modules

6
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
• Next Few Slides are Updated from Jims January
  Presentation on Module Types

7
Integrating with Slicer3
8
Slicer3 data model
Provided by D. Gering
Provided by R. Kikinis
9
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

GUI
Widgets
Renderers
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.
10
Variety of levels of integration
11
Base Features vs. Modules
12
Each module has
an entry in the module menu
a panel of user interface controls
13
Module Terminology

• Built-In Modules
• Few Core Features Linked to Slicer3.cxx
• Non-Core Modules becoming Loadable
• Loadable Modules
• Dynamically Discovered and Loaded
• Can Access Applications MRML Scene Instance and
  Call SlicerBaseGUI and Related APIs
  (vtkRendering, KWWidgets)
• Scripted Modules
• Like Loadable, but Written in Tcl or Python
• Command Line Modules
• Can Run as Stand Alone Executables
• Provide Standard Command Line Parsing, which
  Allows Slicer to Generate GUI Automatically
• Can be Compiled as Shared Library for Dynamic
  Link to Slicer

14
Built in module
vtkMRMLNode.h
vtkSlicerModuleGUI.h
vtkSlicerModuleLogic.h

• vtkSlicerYourModuleGUI.h
• BuildGUI()
• ProcessGUIEvents()
• ProcessLogicEvents()
• ProcessMRMLEvents()

• vtkMRMLYourModuleNode.h
• GetNodeTagName()
• Copy()
• ReadXMLAttributes()
• WriteXML()

• vtkSlicerYourModuleLogic.h
• ProcessMRMLEvents()
• ProcessLogicEvents()

15
Loadable Modules

• http//www.slicer.org/slicerWiki/index.php/Slicer3
  How_to_implement_an_Interactive_Module_GUI
• http//www.slicer.org/slicerWiki/index.php/Slicer3
  Loadable_ModulesHOWTO
• Create vtkSlicerModuleGUI Subclass
• Override Virtual Methods for CreateGUI,
  ProcessMRMLEvents, etc.
• Provide Custom vtkMRMLNode Subclass(es) to
  Represent, Save and Restore state
• Create Logic Classes to Implement Module
  Functionality
• Create CMake Configuration Files to Build and
  Install Shared Libraries for Runtime Discovery
  and Packaging

16
Loadable module
vtkMRMLNode.h
vtkSlicerModuleGUI.h
vtkSlicerModuleLogic.h

• vtkSlicerYourModuleGUI.h
• BuildGUI()
• ProcessGUIEvents()
• ProcessLogicEvents()
• ProcessMRMLEvents()

• vtkMRMLYourModuleNode.h
• GetNodeTagName()
• Copy()
• ReadXMLAttributes()
• WriteXML()

• vtkSlicerYourModuleLogic.h
• ProcessMRMLEvents()
• ProcessLogicEvents()

• YourModule.so
• GetLoadableModuleDescription()
• GetLoadableModuleLogic()
• GetLoadableModuleGUI()

17
Scripted Modules

• A Generic ScriptedModule Module Provides Mapping
  of C Method Entry Points to a Corresponding
  Naming Convention for Scripts
• vtkMRMLScriptedModuleNode, vtkSlicerScriptedModule
  Logic, vtkSlicerScriptedModuleGUI
• Scripts are Dynamically Discovered at Runtime
• A Generic ScriptedModuleNode Allows Save/Restore
  of Keyword / Value Pairs to Represent Module
  State
• Full API of Slicer, MRML, KWWidgets, VTK,
  available (except where not wrappable these APIs
  have been designed for scriptability)
• Editor is extensive Tcl-based Module
• Several Python examples are included in current
  svn trunk
• Python modules can also access Numpy routines for
  Numerical processing (Volumes and other
  DataArrays are directly mapped to Numpy arrays
  for easy manipulation)

18
Tcl scripted module
vtkMRMLScriptedModuleNode.h
vtkSlicerScriptedModuleGUI.h
vtkSlicerScriptedModuleLogic.h
YourModuleNode.tcl

• YourModuleGUI.tcl
• proc YourModuleBuildGUI
• proc YourModuleProcessGUIEvents
• proc YourModuleProcessLogicEvents
• proc YourModuleProcessLogicEvents

YourModuleLogic.tcl

• YourModule.tcl
• package provide YourModule x.y

19
Python scripted module
vtkMRMLScriptedModuleNode.h
vtkSlicerScriptedModuleGUI.h
vtkSlicerScriptedModuleLogic.h

• YourModuleGUI.py
• def BuildGUI()
• def ProcessGUIEvents()
• def ProcessLogicEvents()
• def ProcessLogicEvents()

• YourModuleNode.py
• Optional State Management

• YourModuleLogic.py
• Optional Helper Code

20
Command Line Modules

• Use the GenerateCLP command (provided with
  Slicer) to convert XML description of program
  arguments into a C .h file
• Main program of module uses PARSE_ARGS macro
  provided by .h file to instance variables
  corresponding to parameters defined in XML file
• PARSE_ARGS also defines a --xml argument that
  returns original XML string on stdout
• Slicer parses the XML to create GUI for each
  module
• Are Covered Extensively in the HelloWorld
  Tutorial
• Note Command Line Modules can be written in any
  language. C utilities are provided, but can be
  emulated / recreated as needed.

21
Command line module
vtkMRMLCommandLineModuleNode.h
vtkCommandLineModuleGUI.h
vtkCommandLineModuleLogic.h

• YourModule.xml
• ltimagegt
• ltgeometrygt
• ltintegergt
• ltdoublegt
• ltfilegt

• YourModule.py
• XML
• def toXML()
• def Execute()

• YourModule (exe)
• YourModule xml

• YourModule.so
• XMLModuleDescription
• GetXMLModuleDescription()
• ModelEntryPoint()

or
or
22
All modules are created equal
an entry in the module menu
a panel of user interface controls
23
Daemons
YourTool (exernal process such as MATLAB)
slicerget.tcl name gt image.nrrd
SlicerDaemon
cat image.nrrd slicerput.tcl name
YourTool (exernal process such as Tracker or
Scanner)
OpenIGTLink Protocol
OpenIGTLinkIF
24
Variety of levels of integration
25
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, Institutions svn, Google Code, etc

26
Extension Management Wizard
Under development
27
NITRC
http//www.nitrc.org/projects/slicer3examples/ Sam
ple Code for CommandLine, Loadable, and Scripted
Extension Modules
28
Extension Process

• Write your module following the examples on
  nitrc.org
• Create .s3ext description file
• http//viewvc.slicer.org/viewcvs.cgi/trunk/Extensi
  ons/
• 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

29
Next Steps

• Work with Terry, Katie, and me to get your code
  working as an extension
• We will be integrating the .s3ext files to the
  Slicer 3.4 branch and enabling nightly builds of
  your modules
• Please give feedback - we will be refining this
  process based on experience (3.4 patch releases
  if needed)