NA-MIC National Alliance for Medical Image Computing 3D Slicer Interactive Modules Steve Pieper, PhD

National Alliance for Medical Image Computing 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 Application’s 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 2

National Alliance for Medical Image Computing This Session Discuss Implementation of Loadable and Scripted Modules –Module Architecture –Implementation Options –Issues to be Consider Example Interactive Modules Documentation: (Linked from the developer section of slicer.org) 3

National Alliance for Medical Image Computing 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) 4

National Alliance for Medical Image Computing C++ Superclasses Modules Inherit Much of their Behavior –Look and Feel –Application Settings –Common API, Wrapping 5

National Alliance for Medical Image Computing 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 6

National Alliance for Medical Image Computing 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 7

National Alliance for Medical Image Computing 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 8

National Alliance for Medical Image Computing Processing Events AddGUIObservers / RemoveGUIObservers –List Events to Watch –Inherited Callback Function Calls ProcessGUIEvents ProcessGUIEvents –Maps Events To Actions 9

National Alliance for Medical Image Computing 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 10

National Alliance for Medical Image Computing 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 11

National Alliance for Medical Image Computing 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->DisableModifiedEventOn(); /* set a series of parameter values */ node->DisableModifiedEventOff(); node->InvokePendingModifiedEvent(); 12

National Alliance for Medical Image Computing 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 13

National Alliance for Medical Image Computing 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 14

National Alliance for Medical Image Computing 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 15

National Alliance for Medical Image Computing 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 16