Slicer3:Status Summary

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Slicer3

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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/Import Scene -- done, debugging
  • Slicer2.x MRML import as new scene (supports volumes, models, transforms, fiducials)
Not Done


Deferred
  • SmartPointers


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
  • Color Nodes and Lookup tables
In Process
  • Oblique slice views -- No GUI yet, but supporte in nodes and logic


Not Done


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.
  • modify 'fiducials' icon to match default fiducial point style.
  • Added new method to create a Help&About frame in each ModuleGUI
In Process

Mostly a to-do list of little things:

  • Toolbar
    • Fix mouse mode buttons to not have indicator but display mode with icon change (tried -- can we keep relief flat when button is selected, and only rely on image change to show state?)
    • hook up load/save buttons
    • modify menu button text to truncate in middle with '...' if too long
    • improve module search functionality
  • View and Navigation panel
    • Nav Zoom widget
    • implement ability to toggle Fiducial visibility in 3D viewer
    • implement fov and % entry widgets
    • check packing on linux
    • if rocking/spinning, can we resume rock/spin after view reconfiguration? (seems no, not reliably...)
  • Slices control panel
    • implement ability to toggle Fiducial visibility in slice windows
  • 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)