3D Slicer Interactive Modules

1
3D SlicerInteractive Modules

• Steve Pieper, PhD

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Review of Module Types

• Built-In Modules
• Few Core Features Linked to Slicer3.cxx
• Non-Core Modules becoming Loadable
• Loadable Modules
• Dynamically Discovered and Loaded
• Can Access Applications MRML Scene Instance and
  Call SlicerBaseGUI and Related APIs
  (vtkRendering, KWWidgets)
• Scripted Modules
• Like Loadable, but Written in Tcl or Python
• Command Line Modules
• Can Run as Stand Alone Executables
• Provide Standard Command Line Parsing, which
  Allows Slicer to Generate GUI Automatically
• Can be Compiled as Shared Library for Dynamic
  Link to Slicer

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This Session

• Discuss Implementation of Loadable and Scripted
  Modules
• Module Architecture
• Implementation Options
• Issues to be Consider
• Example Interactive Modules
• Documentation
• http//www.slicer.org/slicerWiki/index.php/Buildin
  g_a_Slicer_3_Module_GUI
• (Linked from the developer section of slicer.org)

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Why Interactve Modules

• Continuous Feedback
• Perform Calculation while Adjusting a Value
• Responding to Render Window Events (e.g. 3D
  Widgets)
• Periodic Updates / Animations
• Injecting New Data
• Connecting to Devices (e.g. OpenIGTLink)
• Connecting to Servers (e.g. QueryAtlas, FetchMI)
• Defining New Data Types and Storing State
• New MRML Nodes can be Displayable (e.g. Volume or
  Model Subclasses)
• Interaction State in Nodes is Serialized in MRML
  Scene
• Define Multi-Step Workflows (e.g. EMSegmenter)

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C Superclasses

• Modules Inherit Much of their Behavior
• Look and Feel
• Application Settings
• Common API, Wrapping

http//www.na-mic.org/Slicer/Documentation/Slicer3
/html/index.html
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Classes to Implement

• Subclasses of
• vtkMRMLNode
• vtkSlicerLogic
• vtkSlicerModuleGUI
• Default Behavior is Often Adequate
• Follows VTK Conventions for Object Management and
  Event Handling
• Use KWWidgets to Define GUI

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Constructor/Destructor

• Allocate Widgets in Constructor
• In Destructor, Set Parent to NULL to Avoid
  Reference Deadlock (and Leaks)
• Constructor Called at System Start
• Enter / Exit
• Called when Module Changes
• Can be used to Create GUI on the Fly

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Build GUI / TearDownGUI

• Initialize the Module
• Construct the Widgets and Layout of the Page
• Rely on Slicer-Custom KWWidgets like the
  vtkSlicerNodeSelectorWidget
• TearDownGUI (Optional) Unpacks

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Processing Events

• AddGUIObservers / RemoveGUIObservers
• List Events to Watch
• Inherited CallbackFunction CallsProcessGUIEvents
  
• ProcessGUIEvents
• Maps EventsTo Actions

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Manipulating MRML

• Modules Should Save Parameter State in MRML Nodes
• Supports Undo/Redo and Serialization of
  Parameters to Scene File
• Use of Node Selector Widgets Simplifies
  Input/Output
• Can be Configured to Allow Creation of New Output
  Nodes or Select Existing Nodes to Overwrite
• Typically there is a Logic Method to Apply
  Parameters using a VTK Pipeline
• Parameters Copied from MRML Node to Processing
  Classes
• End of Pipeline Connected to MRML Volume or Model
  Node

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Coordinate Issues

• MRML Volume Nodes
• Track the IJKtoRAS Transformation Explicitly
• Map from Pixel Space to Patient Space in
  Millimeters
• Hold Data in vtkImageData Instance Variable
• Origin is 0,0,0
• Spacing is 1,1,1
• vtkImageChangeInformation Filter is Sometimes
  Needed
• MRML Model Nodes
• Vertices are in RAS Millimeters
• Optionally Copy the TransformNodeID to Put Output
  Node in Same Spot of Transformation Hierarchy as
  Input Node

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Event Issues

• Avoid Event Loops
• VTK Events are Handled Synchronously (on the
  Stack)
• Modifed Event from Node May Cause GUI to Update
• GUI Update May Trigger Second Call to
  ProcessGUIEvents
• Can Use Guard Variables to Only Enter
  ProcessGUIEvents Once
• Can Perform Atomic Updates
• node-gtDisableModifiedEventOn()
• / set a series of parameter values /
• node-gtDisableModifiedEventOff()
• node-gtInvokePendingModifiedEvent()

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Calling Other Modules

• Interactive Modules
• Draw on the Public API of the MRML Nodes and
  Logic
• Command Line Modules
• Construct Appropriate Parameter Node
• Invoke Module in Separate Thread
• Observe Scene Events to Check for Completion
  Status

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Scripted Modules

• Map C Methods to Script Code
• Parameter Node Provides Keyword / Value Pair
  Serialization
• Code Can Often Be Reloaded
• Don't Need to Exit Slicer or Reload Data
• Can Be Significant Time Savings
• Slicer3/Modules/ScriptedModuleExample
• in Slicer3 svn trunk, not 3.2 or Stanford
  branches
• ScriptedModuleExampleClone Procedure
• Creates All Files Needed for New Module

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Example Modules

• Modules/GradientAnisotropicDiffusion (a.k.a GAD)
  is "Prototype" Module to Review
• Slicer3/Modules/Editor
• Complex Module with Many Features
• Interacts with MRML, and Volumes
• Applies Filter Operations
• Provides Real-Time Feedback to Mouse Events
• Available if Python Enabled in your Slicer3 Build
• PythonGADScriptedModule.py
• Modules/Python has Several Examples

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Module Considerations

• CommandLineModule is an Interactive Module that
  Wraps and Manages the Execution Model
• Command Line Modules
• Simpler to Program
• Pure ITK
• Any Executable (even MATLAB Wrapped with Shell
  Script)
• Can Run in Separate Thread
• Can be Packaged as Executable or Shared Library
• Can Used in Shell Scripts or Distributed
  Applications
• Interactive Modules Require Greater Effort but
  have More Flexibility