Projects:ARRA:SlicerEM:Developer

Back to SlicerEM page

Kitware Team

• Sebastien Barre - Workflow manager - 50%
• Julien Finet - Chart/Plot export - work in // with vtkChart folks - 10%
• Jean-Christophe Fillion-Robin (Project Lead) - Infrastructure / Python - 50%
• Danielle Pace - Workflow manager - 100%

Unassigned Items

lists tasks that need to be done

Work in Progress

What do you plan to do this week

Sebastien

• Work with Danielle on the workflow manager

Julien

• Discuss with vtkChart folks and see how existing CTK Charting [1] classes can be moved to VTKChart [2]

Jc

• Create initial directory structure and QtModule skeleton. See 14138
• Review UI - Added help and button (next, back, etc..) See 14195
• Write down Developer page
• Milestones for project at next weeks meeting. See Projects:ARRA:SlicerEM:Developer#Milestones
• Review which widgets should be converted. See Projects:ARRA:SlicerEM:Developer:WidgetsToPort
• Convert EMSegment/{Algorithm,Graph,MRML,Registration} to shared library. See 14245, 14428, 14258
• Update QtModule to use EMSegment libraries. See 14250, 14251
• Design static UI panel

Danielle

• Get familiar with Git and how to contribute to CTK
• Evaluate QtStateMachine and identify what are its limitation
• Develop the skeleton / API of the ctkWorkflowManager / ctkWorkflowStep

Team meeting

lists the team meeting and includes a pointer to the associated notes

Coming

• 7/20/2010 - Meeting / Weekly meeting #1
• 8/9/2010 - Meeting / Midterm meeting with Kilian

Past

• 7/14/2010 - WorkflowManager meeting
• 7/8/2010 - Kickoff meeting

Milestones

• July 16th
  • Create QtModule skeleton
  • Write developer documentation

• July 23th
  • Factor out EMSegment{Algorithm, Graph, MRML, Registration} libraries
  • Workflow manager: Class skeletons (ctkWorkflowManager, ctkWorkflowStep)

• July 30th
  • Port: TaskSelector, Segmentation_Mode,InputChannelSelector, NodeAttributes, ProbabilityMapSelector
  • Panel: Define Task, Define Input Channel (static version)

• August 6th
  • Port: AnatomicalTree 50%, IntensityDistribution
  • Panel: Define preprocessing

• August 13th
  • Port: AnatomicalTree 100%, AtlasToInputRegistration, ColorMapViewOnly
  • Workflow manager: Start integration with Static UI Panel
  • Panel: Define Anatomical tree, Edit registration parameter, Specify intensity distribution (without Manual sampling)

• August 20th
  • Port: ManualSampling, WeightEditor, PrintConfig, StoppingConditionsEditor
  • Panel: Integrate Manual sampling to Define Anatomical tree panel

• August 27th
  • Port: WorkingDirSelector, ClassWeightsOverview, OutputLabelMapSelector, AdvancedNodeParameterEditor
  • Workflow manager: Complete integration
  • Panel: Edit node-based parameters (Need to define exactly content of Advanced Tab)

• September 3rd
  • Port: VOIEditor
  • Panel:Run segmentation
  • Green dashboard expected

• September 10th
  • Polish
  • Review Doxygen, Style

• If time permit:
  • Projects:ARRA:SlicerEM:Developer:WidgetsToPort#DynamicListOfInputChannel DynamicListOfInputChannel

Project components

• Example workflow: MRI Human brain
• Workflow manager
• Widgets to port

Development environment

Contributing to CTK

• Each developer should fork CTK official repository (github.com/commontk/CTK). Doing so will allow to:
  • backup its work before integration with CTK master.
  • publish and share its work

• Refer to the follow document: http://www.commontk.org/index.php/Contributing_to_CTK.

• WorkflowManager code should be added to ctkWorkflowManager branch.
  • That branch has been created on http://github.com/jcfr/CTK.
  • See [3] to obtain details on how to checkout a branch from a different fork

Working on Slicer / CTK in parallel

• Step1: Build slicer following these instruction. Enable both Slicer3_USE_KWWIDGETS and Slicer3_USE_QT.
• Step2: Create a github user [4] and fork CTK (http://github.com/commontk/CTK).
• Step3: Build CTK - See these instructions - Consider also the instruction below to configure CTK as expected by Slicer
  • Make sure you set the following options
    • PluginFramework should be disable: CTK_LIB_PluginFramework:BOOL=OFF and CTK_PLUGIN_org.commontk.eventbus:BOOL=OFF
    • Enable VTK: CTK_LIB_Visualization/VTK/Widgets:BOOL=ON, VTK_DIR:PATH=<SlicerVTK_Binary_DIR>

cd MyProjects
git clone http://github.com/me/CTK
mkdir CTK-Superbuild
cd CTK-Superbuild
ccmake -DCTK_LIB_PluginFramework:BOOL=OFF -DCTK_PLUGIN_org.commontk.eventbus:BOOL=OFF -DCTK_LIB_Visualization/VTK/Widgets:BOOL=ON -DVTK_DIR:PATH=/home/me/MyProjects/Slicer3-SuperBuild/VTK-build ../CTK
make

• Step4: Re-configure slicer4 passing CTK_DIR

cd MyProjects/Slicer3-Superbuild
ccmake -DCTK_DIR:PATH=/home/me/MyProjects/CTK-Superbuild .

EMSegment source code

• The name of the Qt module is EMSegment.
• The associated source code, hosted on slicer3 repository (trunk) is located in the following directory: <SRC>/QTModules/EMSegment
• Every commit related to EMSegment should be prefixed with either:
  • ENH: EMSegment - <Message summary>
  • COMP: EMSegment - <Message summary>
  • BUG: EMSegment - <Message summary>
  • STYLE: EMSegment - <Message summary>