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

Kilian

current week - week 3

week 2

week 1

Review list of widget and prioritize.

Sebastien

Work with Danielle on the workflow manager

Julien

Current week - Week 3

Week 2

Marcus (Kitware Inc.) has finished a pass on the design of vtkCharts (VTK trunk).

A local branch (github.com/finetjul/VTK) has been forked.

Added minor improvements/bug fixes into the VTK charts (on wait for contributing back to VTK trunk).

Week 1

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

Jc

Current week - Week 3

Define a clear agenda for the August 9th meeting

Design static UI panel

Port dynamic list of Input Channels to Qt. See DynamicListOfInputChannel

Enable CTK/PythonQt wrapping of QtModules (Gui, UITools, ... ). See 14448, 14449, CTK

Define python task skeleton

Week 2

Update QtModule to use EMSegment libraries. See 14250, 14251

Setup a priority list for the widget for Kilian to edit. See List of widget to prioritize

Updated logic to initialize properly. See 14353

Design static UI panel

Created corresponding UI files, header and cxx files. See 14350

Port Task selector to Qt. See TaskSelector

Week 1

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

Danielle

Current week - Week 3

In progress

ctkWorkflowWidgets based on QDialog

integrate workflow manager into EMSegment module

testing for ctkWorkflowManager / ctkWorkflowStep / ctkWorkflowWidget

example for using the workflow manager

jumping directly to "finish" state

specify validation/showUI/hideUI functions via callback

Finished

allow user to set layouts instead of hard-coding the layout type

Week 2

Develop the skeleton / API of the ctkWorkflowManager / ctkWorkflowStep / ctkWorkflowWidget

Implement core functionality of ctkWorkflowManager / ctkWorkflowStep / ctkWorkflowWidget

ctkWorkflowWidget convenience class with integrated Back/Next/Finish buttons

Clean up code, documentation - See WorkflowManager

Week 1

Get familiar with Git and how to contribute to CTK

Evaluate QtStateMachine and identify what are its limitation

Team meeting

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

Coming

• 8/03/2010 - Meeting / Weekly meeting #3
• 8/9/2010 - Meeting / Midterm meeting with Kilian

Past

• 7/27/2010 - Meeting / Weekly meeting #2
• 7/20/2010 - Meeting / Weekly meeting #1
• 7/14/2010 - WorkflowManager meeting
• 7/8/2010 - Kickoff meeting

Milestones

Please note that the current list may be refined

• 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, NodeAttributes, ProbabilityMapSelector
  • Python scripting: 10%

• August 6th
  • Port: AtlasToInputRegistration, Segmentation_Mode,InputChannelSelector, DynamicListOfInputChannel
  • Panel:Define Task, Define Input Channel (static version)
  • Python scripting: 50%

• August 13th
  • Port: AnatomicalTree 50%, IntensityDistribution
  • Workflow manager: Start integration with Static UI Panel
  • Panel: Define preprocessing, Edit registration parameter, Specify intensity distribution (without Manual sampling)
  • Python scripting: 75%

• August 20th
  • Port: WeightEditor, AnatomicalTree 100%, PlotClassDistribution1D
  • Panel: Define Anatomical tree
  • Python scripting: 100%

• August 27th
  • Port: WorkingDirSelector, ClassWeightsOverview, OutputLabelMapSelector
  • 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:
  • PrintConfig
  • ManualSampling, StoppingConditionsEditor
  • ColorMapViewOnly, Colormap selector
  • AdvancedNodeParameterEditor
  • PlotClassDistribution2D
  • Panel: Integrate Manual sampling to Define Anatomical tree panel

Project components

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

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>