Projects:ARRA:SlicerEM:Developer

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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 7

week 6

Comments and suggestions associated with EMSegment-QtPort preview

week 5

week 4

week 3

week 2

week 1

Review list of widget and prioritize.

Sebastien

Work with Danielle on the workflow manager

Julien

Current - Week 7

ToBeDone

Plot2D

Week 6

Week 5

Graph panel design

Plot1D

Week 4

Charts now work in CTK

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 - Week7

ToBeDone

Define python task skeleton

Week6

Refine Anatomical tree widget

Work with Danielle to integrate workflow manager

Week 5

Update anatomical tree to support editing of label + support of update checkbox

connect workflow manager

port the validation code

Week 4

Port dynamic list of Input Channels to Qt. See DynamicListOfInputChannel

Review workflowManager and integrate to CTK

Initial port of Anatomical tree widget

Week 3

Define a clear agenda for the August 9th meeting

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

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 - Week7

Week6

RunSegmentation panel

Finish integrating workflow manager with Qt designer

Week 5

Started to port RunSegmentation panel (complete with the exception of the ROI widget)

Started to integrate workflow manager with Qt Designer

Port DefinePreprocessing panel (without tcl scripts)

Ported "startSegmentation" mechanism.

Integrate workflow manager into EMSegment module

Enable branching workflows in workflow manager, for use with "simple" and "advanced" EM Segment workflows

Week 4

Integrate workflow manager into EMSegment module

jumping directly to "finish" state

Week 3

Should provide a high-level and a low-level API

The High-level API should be very simple

All method related to QState should be protected.

Add a method lastStep()

Make sure it's possible to configure step (Test associated with button, should Next be enabled)

Remove any UI related function from CTKCore

Review API to review API validateForward / validateBackward / enter / exit

Specify validation, entryProcessing, exitProcessing, populateStepWidgetsList, showUI, hideUI function for custom steps via signal-slot mechanism, instead of requiring derivation of ctkWorkflowStep

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

testing for ctkWorkflowManager / ctkWorkflowStep / ctkWorkflowWidget

example for using the workflow manager

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

Johan

Current - Week7

Week6

Week 5

Create a widget qMRMLLabelComboBox able to display a vtkMRMLTableColorNode. See 14702

Compile slicer

Start to port vtkMRMLColoreTableNode selector

Team meeting

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

Coming

• 9/07/2010 - Meeting Week #7

Past

• 8/31/2010 - Meeting Week #6
• 8/30/2010 - Meeting / EMSegment-QtPort Review
• 8/24/2010 - Meeting Week #5
• 8/19/2010 - Meeting Week #4
• 8/9/2010 - Midterm meeting with Kilian
• 8/3/2010 - Meeting Week #3
• 7/27/2010 - Meeting Week #2
• 7/20/2010 - Meeting Week #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, Specify intensity distribution (without Manual sampling)
  • Python scripting 60%

• August 20th
  • Port: WeightEditor 20%, AnatomicalTree 85%, PlotClassDistribution1D 50%
  • Panel: Define Anatomical tree, Define Atlas

• August 27th
  • Port: AnatomicalTree 85%, OutputLabelMapSelector 50%, PlotClassDistribution1D 100%, WeightEditor 60%, WorkingDirSelector
  • Workflow manager: Complete integration
  • Panel: Edit node-based parameters 50%, Run segmentation 35%, Define Input Channel 100%, Edit registration parameter

• September 3rd
  • Port: AnatomicalTree 100%, ClassWeightsOverview, StoppingConditionsEditor, VOIEditor (just UI part), WeightEditor 100%, OutputLabelMapSelector 100%
  • Panel: Run segmentation 100%, Edit node-based parameters 100%
  • Python scripting ???%
  • Green dashboard expected

• September 10th
  • Polish
  • Review Doxygen, Style

• If time permit:
  • Python scripting - complete integration
  • PrintConfig
  • ManualSampling
  • 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
• Image gallery

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: /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>