Slicer3:Status Summary

New functionality is being added to the Slicer3 repository daily to flesh out and finish the features of the software. This page provides an overview of the major planned functionality together with a snapshot of the status in the current build. Use the 'history' tab for this page to see when the status changed for various parts of the project.

This list includes items that we expect to be functional as part of the 3.0 release.

MRML (Slicer scene description file format)

Done

• Core library and nodes -- done
• Save/Restore of Module Parameter Nodes

In Process

• Undo/Redo -- done, debugging
• Load/Save Scene -- done, debugging
• Import scenes into currently loaded scene

Not Done

• Slicer2.x MRML import as new scene
• SmartPointers

Deferred

Slices

Done

• Pixel to Physical space matrices -- done
• Slice display, FG/BG blend -- done
• pan/zoom/slice scroll -- done
• Slices visible in 3D
• Corner annotations -- coordinates and pixel values displayed
• Label map display, overlay
• Repacking, resizing slice windows -- done
• Volumes should be transparent outside of their boundaries done

In Process

• Oblique slice views -- No GUI yet, but supporte in nodes and logic
• Lookup tables -- displayed on images, no mrml or GUI yet

Not Done

• Keyboard and event bindings -- not done Slicer3:EventBindings

Deferred

• Display on Non-Linear Transforms
• Integration of wwidgets -- slicer will use non-standard widgets for 3.0, but will migrate to WWidgets for later releases

3D View

Done

• Display Models -- done
• Display Slices -- done
• MRML Nodes to store camera settings -- done

In Process

• Logo widget -- widget basically done, needs integration

Not Done

• Keyboard and mouse bindings -- not done
• Lighting nodes and GUI -- not done
• Orientation letters and FOV cube -- not done

Deferred

• Volume Rendering (IGT will be driver)
• Integration of wwidgets -- not done

Data GUI

Done

• Scene display -- done
• Cut and paste to edit transform hierarchy -- almost finished

In Process

• Property Editors -- in process

Not Done

Deferred

• Model Hierarchy (control visibility / display properties of subgroups) -- may get deferred.

Volumes

Done

• Load Volume -- done
• Export volumes in various formats -- done
• Drawing of Threshold
• optionally name a volume, set label flag, when loading -- done
• Auto Window/Level, Auto Threshold -- done
• GUI for Lookup tables -- done

In Process

• Display Control -- mostly done, debugging

Not Done

• Display of color/vector/tensor volumes -- not done

Deferred

Models

Done

• Load model -- done
• Display Control and Logic (material properties editor and nodes) -- done
• Load models from directory -- done
• Clipping Control and Logic -- done
• Hierarchy editor (transforms) -- done

In Process

Not Done

• Scalar fields selection, with lookup tables -- not done
• Apply (harden) transform to a model -- not done (command line module?)

Deferred

• Clipping of transformed models

Transforms

Done

• Matrix editor -- done
• Hierarchy of linear transforms can be applied to models and volumes

In Process

• Transform Node Manipulation -- done, but needs usability overhaul
• Non-linear transform support -- part done: plan to stick with linear only for first release of slicer3
• Interactive Transform editing -- in process

Not Done

• Automatic registration --- not done
• Resample volumes through transforms -- not done (command line module, also models and fiducials?)

Deferred

• Nonlinear transforms

Application GUI

Done

• Overall Look and Feel -- done
• New logo finalized.
• Module navigation and search -- done.
• Toolbar view configuration done.
• Module GUI appearance changes for visual clarity done.
• Module notebook and collapsing frame styles done.

In Process

Mostly a to-do list of little things:

• Menu: remove File->Close
• Toolbar
  • Fix mouse mode buttons to not have indicator but display mode with icon change
  • hook up undo/redo buttons
  • hook up load/save buttons
  • decrease width of Modules menubutton slightly
  • modify menu button text to truncate in middle with '...' if too long
  • modify 'fiducials' icon to match default fiducial point style.
  • improve module search functionality
• View and Navigation panel
  • Nav Zoom widget
  • remove slice opacity icon
  • add select camera icon
  • add background color options under visibility menu
  • implement fov and % entry widgets
  • check packing on linux
• Slices control panel
  • Add fit to window
  • Reduce padx in packing -- shifts when panel resizes
• Agree on final paradigm for mouse-mode and hot-keys for switching.

Not Done

• Ability to start up with stereo enabled, detect that, and activate the stereo menu options
• Check look&feel across build platform and adjust theme to ensure appearance is consistent as possible.

Deferred

• lightbox view not implemented

Fiducials

Done

• MRML nodes for individual fiducials and fiducial lists -- done
• Fiducials GUI -- done
• Display of fiducials in 3D -- done

In Process

• wwidget fiducial display/edit in slices -- in process
• wwidget fiducial edit in 3d view -- in process

Not Done

Slicer3:Transition_of_Slicer2.x_Modules:Fiducials

Deferred

Execution Model

Done

• Command Line Modules base implementation
• Executable and Shared library detection/loading
• Auto generated GUI
• File based and memory based volume i/o
• Executing module in separate thread
• Progress/abort events
• Category navigation
• Models
• Logging to a slicer window
• Runtime-selection of image types
• Access to XML fields from C++

In Process

• Module Functionality -- many useful filters in place, more to come
• Fiducials -- orientation needs to added to XML spec
• Vector and tensor images - waiting on Slicer IO

Not Done

• Other data types i/o (transforms, etc)
• Serialize parameter nodes
• Module packaging for safe discovery mechanism
• Reloading of modules
• Lazy gui construction
• Separate value and default in ModuleDescription
• Don't emit file and directory command line options if values not set
• Contributor logos per module
• Shared memory volume i/o to unu

Deferred

• Nonlinear transforms
• Steering optimizers
• Auto generated wwidgets
• Workflow (modules with several steps)

Colors

Done

• Nodes and Logic for managing color tables -- done for volumes

In Process

• Color Module GUI in process

Not Done

• colors for models scalar fields -- not done

Deferred

Model Maker

Done

• Implemented as command line module -- done

In Process

Not Done

• Tie in to Colors -- to be done when colors module is ready

Deferred

Editor

Done

• Basic Paint functionality

In Process

• Basic Draw functionality ported from slicer2, converted to wwidgets -- not done

Not Done

• Math Morphology, threshold, and other tools -- not done (may be pushed to slicer3.1)
• Auto Save Mode (save label map every minute)
• Oversample Label map mode
• Volume Math/Logic functions

Deferred

• Painting on Models

Slicer2 Modules

Done

• ModelMaker

In Process

• Fiducials
• FreeSurfer readers - curv surfaces, scalar overlays, annotations can load

Not Done

• EMSegment
• DTMRI
• Compatibility layer to allow some slicer2 modules to run inside slicer3 -- not done (priority on modules currently used heavily by clinical collaborators and/or modules ported by the original module developers)

Deferred

Build/Package

Done

In Process

• CPack based installers for all platforms -- in process

Not Done

• Nightly build installers uploaded to web site -- not done
• Stable branches of vtk,itk,kwwidgets for slicer3 -- to be done during final test phase

Deferred

Testing

Done

In Process

• Dart dashboard -- set up, but being debugged

Not Done

• Nightly build and test on major platforms -- not done
• Test suite for MRML API -- not done
• Test suite for Logic API -- not done
• Test suite for GUI API -- not done
• Test suites for Modules -- not done

Deferred

Bug Tracking

Done

• Slicer3 bug tracker -- done

http://www.na-mic.org/Bug/index.php - go to Slicer3 project

In Process

Not Done

Deferred

Pipeline Integration

Done

In Process

• LONI Pipeline can now be called on the command line with workflows with pre-bound parameters
• Provides the output results according to bound parameters and the logs are useful to track progress

Pending

• Ability to bind parameters on the command line
• Ability to showcase status messages for the user to track progress

Deferred

Grid Interface

Done

In Process

• Uniform job submission format for remote execution command line modules -- underway

Not Done

Deferred

System

Done

• Doxygen for Slicer3 - now being generated nightly
• Debug memory leaks -- no memory leaks currently, tested as part of nightly builds

In Process

• Optimize event/observer flows -- ongoing
• Optimize launcher, startup times -- ongoing
• Code reviews for:
  • Coding style -- ongoing
  • In line documentation -- ongoing
  • Consistent naming conventions and patterns -- ongoing
• Implement / clean up command line arguments

Not Done

• Overall software documentation (the Slicer3 book? - maybe in 2007)
• User tutorials and documentation
• GUI Tracing
• splash screen

Deferred

TODO/Notes

• Unify the observer code for use in MRML, Logic, and GUI
  • currently there is much duplication of the command callback structures
  • perhaps this needs to be a separate library that can be used by all?
  • we should be specifically observing DeleteEvent to avoid observing events invoked during destructors
  • The SetAndObserve* calls should also have a signature where they accept an event to observe
  • Perhaps this layer could also allow us to disable all the callbacks (not clear this is needed)