NA-MICNational Alliance for Medical Image Computing http://na-mic.org

Slicer4Guided Tour

Steve Pieper, Ph.D.

National Alliance for Medical Image Computing http://na-mic.org

Goals

• Understanding the Lay of the Land• Developing our Common Language• Highlighting the Points of Interest

http://www.slicer.org/slicerWiki/index.php/Slicer4

National Alliance for Medical Image Computing http://na-mic.org

The Big Picture

• Model / View / Controller Style– MRML / GUI / Logic

• Rules:– MRML: Things that get loaded with a

scene file.– GUI: Things that depend on a display.– Logic: Things that operate on MRML.

National Alliance for Medical Image Computing http://na-mic.org

Overview

National Alliance for Medical Image Computing http://na-mic.org

MRML Concepts: Nodes

• Data Containers and Data Helpers– XML (De)Serializable– Issue Events when Changed– Have Pointers to Bulk Data

• E.g. vtkImageData, vtkPolyData…

• Have Unique IDs

• Exist in only one MRML Scene– One MRML Scene for the Application

National Alliance for Medical Image Computing http://na-mic.org

Coordinate Systems

http://www.slicer.org/slicerWiki/index.php/Coordinate_systems

• Interface Works in Millimeters, Patient Space

• Volume Nodes have IJKToRAS– IJK is Index Space of Image– RAS is Right/Anterior/Superior

• vtkImageData is pixel container with origin 0,0,0 and spacing 1,1,1

• Annotations, PolyData are RAS mm

National Alliance for Medical Image Computing http://na-mic.org

MRML: Storable

• Storable Nodes Reference Storage Nodes

• Storage Nodes: Bulk Data I/O

• Storage Nodes allow RemoteIO (URL access to Bulk Data)– HTTP download supported now– Upload handlers still experimental– Scene files can contain URLs

National Alliance for Medical Image Computing http://na-mic.org

MRML: Displayable

• Has List of Display Nodes– Tagged by ViewNode IDs: each display

node on/off in each view– E.g. FiberBundles with Lines + Glyphs

• DisplayNode has Parameters and Pipelines to Implement Visualization of Displayable

National Alliance for Medical Image Computing http://na-mic.org

MRML Transformable

• Has Reference to TransformNode defining Transform To Parent

• Transforms are RAS to RAS

• Linear Transforms are Handled On-the-fly

• Non-Linear Transforms must be applied using modules

National Alliance for Medical Image Computing http://na-mic.org

MRML: Hierarchies

• Grouping Concept Independent of Transform Hierarchy– E.g. Vascular Tree Levels of Detail

• In Slicer3, Parent Model Display Parameters Override when Collapsed

• In Slicer4, Plans to Use Hierarchies for Time Series, DICOM, etc.

National Alliance for Medical Image Computing http://na-mic.org

• (Were SceneSnapShots in Slicer3)

• Retains State of MRML Nodes– Included in MRML Scene File– Optional Image and Text Description

• Bulk Data Not Copied– Load all Bulk Data Before Making

SceneViews– Use Visibility to Control what is Shown

MRML: SceneViews

National Alliance for Medical Image Computing http://na-mic.org

Module GUIs

• qSlicerAbstractModuleWidget subclasses (are QWidgets)

• setup()

• enter()

• exit()

• Are MRMLNode Editors– Synchronize MRML Events

to/from Widgets

National Alliance for Medical Image Computing http://na-mic.org

Modules

• Slicer Loadable Modules– Shared Libraries Discovered at Run-

Time– Can use Qt, MRML, VTK, ITK, Teem,

etc.– Best Choice for Full Control,

Interactivity, Optimized Computation

• Requires Familiarity with C++ APIs

National Alliance for Medical Image Computing http://na-mic.org

Command Line Interface (CLI) Modules

• Just Like Slicer3

• Any Executable that Works with –xml can be used (even via wrapper scripts)

• Shared Library CLI for Better Performance

• No Slicer API Knowledge Required

• Interface is Consistent, but Limited

National Alliance for Medical Image Computing http://na-mic.org

Scripted Modules

• Most of Qt, VTK, Slicer API Exposed– Only Python Supported– Tcl Legacy Mode to Ease Transition

• Very Rapid Development Iterations

• Requires Some Familiarity with APIs

• More about Slicer4 Python Later…

National Alliance for Medical Image Computing http://na-mic.org

Extensions

• Any Module Type can be an Extension

• Optional User Install– Built to Match Slicer Version– Network Download from within Slicer

• NA-MIC DBPs, Collaborations are Expected to Deliver Extensions

• Extension Writing Tutorial Later…

National Alliance for Medical Image Computing http://na-mic.org

Slicer4 Views

• LayoutNode Defines Interface

• Layout Manager Creates View Widget Instances to Match Layout

• ViewNodes Describe 3D Views

• SliceNodes + SliceCompositeNodes Describe 2D Slice Views

National Alliance for Medical Image Computing http://na-mic.org

DisplayableManagers

• DisplaybleManagers Link DisplayableNodes to VTK Actors/Mappers/Props/Widgets– Must Synchronize Events from Either

Source (like Module GUIs)

• Modules Can Register DisplayableManagers with Factory– DisplayableManagers are Instanced as

Views are Created

National Alliance for Medical Image Computing http://na-mic.org

Overview Revisited

National Alliance for Medical Image Computing http://na-mic.org

Functional Decomposition

• Reusable Components with Only Needed Dependencies– CTK for Non-Slicer-Specific Qt+DICOM (+VTK)– Reusable MRML: MRMLLogic, qMRMLWidgets– Module Support: SlicerExecutionModel, QTCLI– Slicer: QTCore, QTGUI– Modules: QTCoreModules, QTModules,

QTScriptedModules

• Extensions

National Alliance for Medical Image Computing http://na-mic.org

DICOM Interface

• Slicer3– File Based, Limited Write– Special Purpose Converters (e.g. DWI)

• Slicer4 (in Development)– Networking and Database (Q/R, Store)– Ron’s “Lollipop” Model (MRMLScene in

Private Tags)

• Community Input Needed

National Alliance for Medical Image Computing http://na-mic.org

Collaborating Groups

• CTK, DCMTK, ITKv4, VTK, CMake, Python, Qt…

• “SuperBuild Philosophy”– Slicer Organization on github.com

• patched versions as needed

– Edits “Belonging” in Package Go in git– Avoid Workarounds/Duplicates in Slicer

National Alliance for Medical Image Computing http://na-mic.org

svn and git

• http://svn.slicer.org/Slicer4/trunk– For Nightly builds, releases,

collaboration

• http://www.slicer.org/slicerWiki/index.php/Slicer:git-svn– Developers can choose to use git for

topic branches

• Extensions can use git/svn/cvs

National Alliance for Medical Image Computing http://na-mic.org

Coding Conventions

• http://www.slicer.org/slicerWiki/index.php/Slicer:Style_and_Conventions– Use Style of Parent Class

• VTK Classes use VTK Style• Qt Classes use Qt Style• Python Code uses Python Style

– Comments and Testing– Communicate with your Colleagues

National Alliance for Medical Image Computing http://na-mic.org

Python in Slicer4

• Scripted Modules as Slicelets

• Python Console

• PythonQt

• Slicer in External Python

• .slicerrc.py

• Python testing

• Scripted Access to Modules

National Alliance for Medical Image Computing http://na-mic.org

Slicer4: What Works (mostly)

• Main GUI, Toolbars, Menus• Scene/Data Load/Save• Slice and 3D Visualization (pan/zoom, overlays, models…)• Command Line Modules• Python Wrapping, Python Scripted Modules• Loadable Modules• Editor• Annotations (Evolution of Fiducials and Measurements)• Nightly Builds• Volume Rendering• Many things…

National Alliance for Medical Image Computing http://na-mic.org

Slicer4: What’s Missing

• Some Core Modules Need Work• Hierarchies Need Elaboration• IGT Modules• Performance Optimization• Your Extensions!

Please help identify what is needed to support your work.

National Alliance for Medical Image Computing http://na-mic.org

Developer Decision Tree

• Working on the Slicer Core?– Focus on Qt Transition

• Working on a Module?– Build it as an Extension

• Command Line Module?– Develop and Test with Slicer3.6 or Slicer4

• GUI Project with Deadlines in early 2011?– Develop with KWWidgets for 3.6.X– Keep your Logic and MRML Distinct from the GUI– Ongoing Support will be Provided

• Longer-Term Project that Needs a Custom GUI?– Start working with developer builds of Slicer4– Talk with dev team about any key missing features– Consider doing some or all coding in Python

Just use Slicer4 for New Projects

National Alliance for Medical Image Computing http://na-mic.org

Implementation Strategies

• Non-Interactive Algorithm– Write ITK Class– Use Slicer Execution Model– Add as Extension

• Interactive Segmentation– Add Effect to Editor Module– Add as Extension (coming soon)

• Custom GUI?– Loadable Module