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

• Undo/Redo -- done, debugging
• Load/Save/Import Scene -- done, debugging
• Slicer2.x MRML import as new scene (supports volumes, models, transforms, fiducials)

In Process

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
• Oblique slice views -- specified interactively with slice viewers
• Integration of wwidgets -- used for fiducials and volume rendering
• Keyboard and event bindings -- Slicer3:EventBindings

In Process

Not Done

Deferred

• Display on Non-Linear Transforms

3D View

Done

• Display Models -- done
• Display Slices -- done
• MRML Nodes to store camera settings -- done
• Orientation letters and FOV cube
• Volume Rendering -- done

In Process

• Logo widget -- widget basically done, needs integration

Not Done

Deferred

• Integration of wwidgets -- not done
• Lighting nodes and GUI -- not done

Data GUI

Done

• Scene display -- done
• Cut and paste to edit transform hierarchy
• Drag and drop editing
• Model Hierarchy (control visibility / display properties of subgroups)
• Property Editors

In Process

Not Done

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
• Display Control
• Tensor volume display -- done

In Process

Not Done

Deferred

• Vector (color) volumes -- 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
• Scalar fields selection, with lookup tables -- done (testing for Tractography)
• Apply (harden) transform to a model and volume (context menu in Data Module)

In Process

Not Done

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
• Automatic registration --- rigid and affine modules take/return transforms on the TransformIO branch
• Nonlinear transforms
• Resample volumes through transforms -- in transform branch, so be merged April 2008

Not Done

Deferred

• Interactive Transform editing -- in process

Application GUI

Done

• Overall Look and Feel -- done
• New logo finalized.
• Module navigation and search -- done.
• Toolbar view configuration done (lightbox deferred).
• Module GUI appearance modifications for visual clarity -- done.
• Module notebook and collapsing frame styles -- done.
• Update icons and remove unused icons -- done.
• Added new method to create a Help&About frame in each ModuleGUI
• lightbox view not implemented

In Process

Mostly a to-do list of little things:

• Toolbar
  • Mouse mode selection and hot-key decisions, and finalize toolbar
  • modify menu button text to truncate in middle with '...' if module name too long
  • improve module search functionality (not required, but nice)
• View and Navigation panel
  • Nav Zoom widget -- in progress.
  • design logic for Fiducial visibility, and implement toggle in 3D viewer
  • implement fov and % zoom entry widgets
  • check packing across all platforms (problem on linux?
  • if rocking/spinning, find way to pause, resume rock/spin after view reconfiguration
  • once multiple views and multiple cameras can be created, activate the icons for saving and selecting views and cameras.
• Slices control panel
  • implement Fiducial visibility toggle in slice windows
• Implement base classes for "pop-up help windows" and icon to be used application-wide.

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

Fiducials

Done

• MRML nodes for individual fiducials and fiducial lists -- done
• Fiducials GUI -- done
• Display of fiducials in 3D -- done
• widget fiducial display/edit in slices -- done
• 3D widget interaction -- done

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
• Module caching
• 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++
• Module packaging for safe discovery mechanism
• Lazy gui construction
• Serialize parameter nodes
• Vector, tensor images, diffusion weighted images
• Contributor logos per module
• Linear transforms (available on TransformIO branch)
• Color nodes
• Model hierarchys returning from CLI (shallow hierarchies)

In Process

• Deformable transforms
• Resampling module
• Model hierachies (to CLI, deeper hierarchies from CLI)
• Fiducials -- orientation needs to added to XML spec
• Collapsing transformation to world

Not Done

• DWI/DTI use MRMLIDImageIO
• Passing scenes to command line modules (needs definition, transforms and model hierarchies can be passed in scenes currently)
• Other data types i/o
• Reloading of modules
• Separate value and default in ModuleDescription
• 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
• colors for models scalar fields -- done
• Color Module GUI

In Process

Not Done

Deferred

Model Maker

Done

• Implemented as command line module
• Tie in to Colors -- to be done when colors module is ready
• Data passing via mrml scene files

In Process

Not Done

Deferred

Editor

Done

• Basic Paint functionality
• Basic Draw functionality
• Paint/Draw with threshold
• Paint/Draw option not to draw over existing non-zero values
• Paint radius control
• Paint 'eye dropper' mode for quick color changes

In Process

• Speed improvements
• Draw mode preview shown in IJK rather than XY space

Not Done

Deferred

• Painting on Models
• 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

Slicer2 Modules

Done

• ModelMaker
• Fiducials
• FreeSurfer readers - curv surfaces, scalar overlays, annotations can load (some debugging still to do)

In Process

• EMSegment
• DTMRI

Not Done

Deferred

• 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)

Build/Package

Done

• CPack based installers for all platforms -- being optimized
• Nightly build installers uploaded to web site -- done
• Stable branches of vtk,itk,kwwidgets for slicer3 -- done

In Process

• Building plugins from an installation

Not Done

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://na-mic.org/Mantis/main_page.php

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
• Slicer3 BatchMake Module

Not Done

Deferred

System

Done

• Doxygen for Slicer3 - now being generated nightly
• splash screen
• about box

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 2008)
• User tutorials and documentation
• GUI Tracing
• Need to clean up Applications/Slicer3.cxx to unify discovery/initialization of built-in modules more like Slicer2 Underway Slicer3:Loadable Modules

Deferred

TODO/Notes

• Unify the observer code for use in MRML, Logic, and GUI See Slicer3:EventBroker
  • 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)