Events:Slicer4-Review-07-2011

RSNA 2011 Targeted Objectives

• Roadmap for the Slicer 4 release for the series of demos at the RSNA 3DSlicer Booth
• Most tasks need to be ready by end of September, to leave time to update tutorials, test and debug.
• List of open Mantis issues with RSNA Target

UI

Main GUI Cosmetics  % face lift for the Slice viewers: reduce permanent non-image components. Reduce the number and depth of submenus. (J2) done  % Main Gui 3D viewers should have similar appearance to slice viewers (J2) done  % scenview and screensnapshot icons move to the icon bar at the top of the main gui. (J2-> Nicole) done Module Cosmetics  % Volume Rendering (J2) (in progress)  % Models module (J2) done  % Editor, see picture to the right (Steve) (Done)  % Welcome Module (Wendy)  % Volumes Module (J2) Not part of the original plan, will be done if time permits (nice to have, low priority for RSNA), not a show stopper.  % Tractography Display Module (Isaiah) done  % Sceneviews module (Nicole)  % Stabilize annotations module (Nicole, Daniel, Alex) Update tutorials (Sonia)  % Volume rendering transfer function  %% Mac crash in transfer functions (J2) (in progress) stability and usability such as jittery, and gradient banding on MAC (J2) (gradient banding not started yet) %Threshold feature ->offset slider(J2) (in progress)  % Level of Detail (interrupt CPU VR when accessing the transfer function editor) + progress indicator during long renders (J2)  % Documentation on wiki (at least stubs)  % Linking and CompareView (Jim) ROI Slice Displayable Manager done  % Centering on the slice (Alex) done (Now implemented even better with ROI widget in slice view)  % Updated Icons (Annotations, HotLink, cursors, new layouts) (Wendy) all done except hotlink -- but I *like* the current hotlink icon. Can we keep it?  % Revised colors for ROI widget (Wendy) done  % Reorganization of the dMRI sections (Demian)

Mock-up of redesigned editor interface

Under the hood

• hierarchies
  •  % Collapsing Model Hierarchies controls display of children (Nicole) done
  •  % Collapsing Annotation Hierarchies controls display of children (Nicole and Daniel)
•  % Annotations (Nicole, Daniel)
  • vtkWidgets - bug fixes (Will)
    • 2D ruler tick spacing done
    • 3D ruler tick marks done
    • Widget performance (Michael) done
  •  % 3D Representations for all (ruler, bidimensional and maybe fiducials/caption) (Will, Nicole)
•  % CTK DICOM widget (Steve, Nicole) - interface done, some debugging to do.
  • % Implement Slicer Data Bundle (SDB a.k.a. lollipop): put the entire scene into a single folder, zip the folder, add a proper DICOM secondary capture header, which exposes the scenesnapshots. This should be the default save option. Everything else should be accessible through an "advanced" button. (Nicole) - prototype done, but not integrated with app. Zip is done by Nicole, Steve did secondary capture dicom.
  •  % Listener, Query, Retrieve, Send (Steve) - done except for Send (which is grayed out for now)
•  % Optimize Model Displayable Manager (Alex)
•  % Brainsfit: the slicer 3 brainsfit will be available in slicer 4 (Hans)
•  % Fix resize crash due to extent problem in reslice mask (J2) done

Infrastructure

Tk/Tcl  % Annotation/main interaction speedup (Steve) - replace SliceSWidget::updateAnnotation(s) with vtkMRMLSliceInformationDisplayableManager and vtkMRMLSliceLogic::CalculateInformationText - done as Data Probe - need to check windows performance Extensions  % ABC, SkullStripper, EMSegmenter, VMTK (?), Plastimatch, DVH extension (Jc)  % Support for superbuild (Jc) Web: minor updates and tweaks  % mobile skin for webkit rendering of the slicer wiki documentation pages (JC, Zack, others)  % Statistics on packages and on individual extensions (Jc with input from Zack)  % redirect links to slicer 4 dashboard (slicer.org download page, developer pages,....)  % Slicer 4 nightlies, snapshots (monthly) and stable versions are pulled from the factory machine  % Template for Slicer 4 documentation (JC)

ViewerInformation mock-up [1]

Snapshot of SliceAnnotationTree

What

Slicer 4 review and programming sprint

When

July 19, 10 am -21, 4pm 2011

Who

Slicer 4 core programmers

Where

Demo room, 2nd floor, 1249 Boylston Street, Boston, MA

Why

• Identify roadmap for a Slicer 4 product release for the Nov 27-Dec.2 RSNA demos at the 3DSlicer Booth
  • Main GUI and UI changes first, so that tutorial porting can begin
  • debugging the features used in the RSNA tutorials

Work on

Full List

Below is the complete list of items discussed. Items that are targeted for the RSNA 2011 events are preceded by a % sign, the person responsible is identified in parenthesis

UI

SlicerColorSelector using CTK color dialog

• Reformat capabilities: We need a widget and possibly a slider based interface. (Nicole, Will)
• Cosmetics
  •  % Volume Rendering (J2)
  •  % Models module (J2)
  •  % Editor (Steve)
  •  % Main GUI face lift for the Slice viewers: reduce permanent non-image components. Reduce the number and depth of submenus. (J2)
  •  % Main Gui 3D viewers should have similar appearance to slice viewers (J2)
  •  % Stabilize annotations module (Nicole)
• Update tutorials (Sonia)
  • After Facelift of Main Gui and some core modules
  • Using GUI Testing?
•  % Volume rendering transfer function (J2)
  •  %% Mac crash in transfer functions
  • stability
  • Jittery, and banding on MAC
  • %Threshold
  • Better appearance of the elements of the transfer function. They look ugly and are not antialiased. Check the graph in Ohloh and mouse over it. Looks much nicer! (according to the page source, the charts are made with HighCharts)
  • Level of Detail (interrupt CPU VR when accessing the transfer function editor) + progress indicator during long renders
  • Group selection and shifting
•  % Color selector
  •  % the default color selector should be THE CTK color dialog (see picture to the right). (J2)
  • add search function to the labels (J2)
•  % Documentation on wiki (at least stubs)
•  % Linking and CompareView (Jim)
• ROI Slice Displayable Manager
  •  % Centering on the slice (Alex)
•  % Updated Icons (Annotations, HotLink, cursors, new layouts) (Wendy) done, i believe.

Under the hood

Possible Treeview variation

• GPU Volume Rendering
  • Support for ATI and MAC
  • How many GPU render engines to support/provide?
    • Ron says: I just need a single one that works for flythroughs and can handle the combination of volume rendering, cross-sections, surface models, annotations
• hierarchies
  • display: the current display is confusing. Image shows a possible modification
  •  % Collapsing Model Hierarchies controls display of children (Nicole)
  •  % Collapsing Annotation Hierarchies controls display of children (Nicole and Daniel)
  • drag and drop capability
•  % Annotations (Nicole, Daniel)
  • vtkWidgets - bug fixes (Will)
  • GUI layout (Nicole)
  • compositing with volume rendering does not work properly
    •  % 3D Representations for all (ruler, bidimensional and maybe fiducials/caption) (Will, Nicole)
•  % CTK DICOM widget (Steve, Nicole)
  • % Implement Slicer Data Bundle (SDB a.k.a. lollipop): put the entire scene into a single folder, zip the folder, add a proper DICOM secondary capture header, which exposes the scenesnapshots. (Nicole)
  •  % Listener, Query, Retrieve, Send (Steve)
  • use DICOM widget local database as default mechanism for load/save
  • everything else is import/export
  • Slicer should have a single location for these operations
• DisplayModule
  • Draft of the DisplayModule
•  % Optimize Model Displayable Manager (Alex)

Infrastructure

• Move to git/gerrit (TBD - can it be used with git-svn or is the suggestion to retire svn?)
• GUI Testing
  • Instrumenting CTK widgets
  • Conversion of tutorials to tests
  • What will this provide that Sikuli does not? Sonia is ready to use Sikuli unless there is a good reason not to.
• Tk/Tcl
  • Removing the last dependencies in core interaction loops - see Slicer4:SliceInteractions
  •  % Annotation/main interaction speedup (Steve)
  • Maintain improve/functionality for Editor
• Performance optimization
  • Module for profiling events
• Extensions
  •  % ABC, EMSegmenter, VMTK (Jc)
  •  % Support for superbuild (Jc)
  • Requirements for testing, documentation, tutorials, and continued support from developers
    • How to name different levels of compliance
• Downloads
  •  % Statistics on packages and on individual extensions (Jc)
  • Web pages
  • Technologies
• Charts
  • Reference Implementation (Marcus)
• MIDAS
  • sceneviews support
• Interactive CLI modules

Compilation

• issues with win64 debug build - these impact developers more than users - we will prioritize getting nightly binary builds working on all platforms for RSNA before streamlining the developer process
  • Fix numpy builds on win64
    • Need to embed manifests in numpy pyd files
  • Fix win64 tcl version
    • currently permission issue with dlls in win64 slicerlib mirror
    • currently using tcl8.4 on win32 and elsewhere but tcl8.5 on win64 (should use the same everywhere if possible - we may want to switch to the active tcl pre-built distributions for windows)

• Slicer4 dashboard

Attending

1. Ron Kikinis
2. Steve Pieper
3. Nicole Aucoin
4. Julien Finet
5. Daniel Haehn (only 07/19)
6. Jean-Christophe Fillion-Robin
7. Stephen Aylward
8. Will Schroeder
9. Jim Miller
10. Suares Tamekue Tatuebu
11. Luping Fang
12. Mike Halle
13. Andrey Fedorov