National Alliance for Medical Image Computing Integrating with Slicer3.

Slides:



Advertisements
Similar presentations
National Alliance for Medical Image Computing Integrating with Slicer3.
Advertisements

National Alliance for Medical Image Computing Slicer3 plugins Common architecture for interactive and batch processing.
National Alliance for Medical Image Computing User Desktop Slicer 3.0 Architecure AlgorithmsITKVTK Slicer Modules VTK Apps Using ITK.
National Alliance for Medical Image Computing Slicer3 Architecture.
NA-MIC National Alliance for Medical Image Computing National Alliance for Medical Image Computing: NAMIC Ron Kikinis, M.D.
National Alliance for Medical Image Computing Slicer3 plugins Common architecture for interactive and batch processing.
National Alliance for Medical Image Computing Slicer MRML MRML Library provides API for managing medical image data types (Volumes, Models,
NA-MIC National Alliance for Medical Image Computing 3D Slicer Version 4 Architecture and Status Steve Pieper, Ph.D.
National Alliance for Medical Image Computing Anatomy of a plugin Common architecture for interactive and batch processing.
MITK Diffusion (under the hood)
NA-MIC National Alliance for Medical Image Computing 3D Slicer Interactive Modules Steve Pieper, PhD.
Presented by IBM developer Works ibm.com/developerworks/ 2006 January – April © 2006 IBM Corporation. Making the most of Creating Eclipse plug-ins.
1 ParaView Current Architecture and History Current Architecture and History Issues with the Current Design Issues with the Current Design.
NA-MIC National Alliance for Medical Image Computing Slicer4 Guided Tour Steve Pieper, Ph.D.
NA-MIC National Alliance for Medical Image Computing Slicer Custom Modules Steve Pieper, PhD.
NA-MIC National Alliance for Medical Image Computing Core 1b – Engineering End-user Platform Steve Pieper Isomics, Inc.
NA-MIC National Alliance for Medical Image Computing Core 1b – Engineering End-user Platform Steve Pieper Isomics, Inc.
JavaServer Faces: The Fundamentals Compiled from Sun TechDays workshops (JSF Basics, Web-Tier Codecamp: JavaServer Faces, Java Studio Creator; IBM RAD)
NA-MIC National Alliance for Medical Image Computing IGT Software Design and Process Bill Lorensen GE Research.
3D Slicer Architecture and Implementation
Core 1b – Engineering Dynamic Coding a.k.a. Python in Slicer
NA-MIC National Alliance for Medical Image Computing NAMIC-Kit Update Will Schroeder Jim Miller Bill Lorensen.
© 2012 LogiGear Corporation. All Rights Reserved Robot framework.
NA-MIC National Alliance for Medical Image Computing NA-MIC Software Engineering Bill Lorensen GE Research NA-MIC Engineering Core PI.
Capture and Replay Often used for regression test development –Tool used to capture interactions with the system under test. –Inputs must be captured;
NA-MIC National Alliance for Medical Image Computing Why NITRC Matters to NA-MIC Steve Pieper, PhD.
DTIAtlasBuilder Adrien Kaiser Neuro Image Research and Analysis Laboratories University of North Carolina at Chapel Hill A tool to create an atlas from.
NA-MIC National Alliance for Medical Image Computing Slicer 3.4 Update Summer NA-MIC Project Week 2009 Steve Pieper, Ph.D.
9 Chapter Nine Compiled Web Server Programs. 9 Chapter Objectives Learn about Common Gateway Interface (CGI) Create CGI programs that generate dynamic.
NA-MIC National Alliance for Medical Image Computing Slicer4 CLI Slicer Execution Model.
BLU-ICE and the Distributed Control System Constraints for Software Development Strategies Timothy M. McPhillips Stanford Synchrotron Radiation Laboratory.
National Alliance for Medical Image Computing Slicer3 Status Update.
Contents 1.Introduction, architecture 2.Live demonstration 3.Extensibility.
Ch 1. A Python Q&A Session Spring Why do people use Python? Software quality Developer productivity Program portability Support libraries Component.
NA-MIC National Alliance for Medical Image Computing Slicer Building and Deployment Steve Pieper, PhD.
William Schroeder, Ph.D. §, Andy Cedilnik §, Sebastien Barré, Ph.D. §, William Lorensen ‡, James Miller, Ph.D. ‡, Daniel Blezek, Ph.D. ‡ § Kitware Inc.,
Tool Integration with Data and Computation Grid GWE - “Grid Wizard Enterprise”
NA-MIC National Alliance for Medical Image Computing Core 1b – Engineering Software Process Stephen R. Aylward Kitware, Inc.
NA-MIC National Alliance for Medical Image Computing ParaView Server Manager Berk Geveci Andy Cedilnik.
NA-MIC National Alliance for Medical Image Computing National Alliance for Medical Image Computing: NAMIC Ron Kikinis, M.D.
NA-MIC National Alliance for Medical Image Computing Core 1b – Engineering Components Jim Miller GE Research.
Slicer3 for developers – S.Pujol -1- National Alliance for Medical Image Computing Slicer3 Course for developers Sonia Pujol, Ph.D. Surgical Planning Laboratory.
NA-MIC National Alliance for Medical Image Computing Using Annotations in Slicer 4.0 Yong Zhang, Kilian Pohl June 2010.
NA-MIC National Alliance for Medical Image Computing 3D Slicer and the NA-MIC Kit for IGT Research Steve Pieper, PhD NAC, SPL, NA-MIC,
NA-MIC National Alliance for Medical Image Computing Diffusion Tensor Imaging tutorial Sonia Pujol, PhD Surgical Planning Laboratory.
NA-MIC National Alliance for Medical Image Computing Slicer 2010: Past, Present, and Future Steve Pieper, Ph.D.
© FPT SOFTWARE – TRAINING MATERIAL – Internal use 04e-BM/NS/HDCV/FSOFT v2/3 JSP Application Models.
August 2003 At A Glance The IRC is a platform independent, extensible, and adaptive framework that provides robust, interactive, and distributed control.
Neuroimage Analysis Center An NCRR National Resource Center NAC Engineering Core Steve Pieper, Core PI SPL; Isomics, Inc.
Slicer 3 Ron Kikinis, Steve Pieper. CTK Workshop Heidelberg, June 29/30, 2009 Slicer Goals  Stable, Usable, Cross Platform, End-User Software for Medical.
NA-MIC National Alliance for Medical Image Computing 3D Slicer Modules and Extensions Steve Pieper, Ph.D.
Sonia Pujol, PhD -1- National Alliance for Medical Image Computing Neuroimage Analysis Center Diffusion Tensor Imaging tutorial Sonia Pujol, Ph.D. Surgical.
NA-MIC National Alliance for Medical Image Computing Non-Interactive Tools Stephen Aylward, Kitware
Tool Integration with Data and Computation Grid “Grid Wizard 2”
NA-MIC National Alliance for Medical Image Computing Slicer 2010: Past, Present, and Future Steve Pieper, Ph.D.
NA-MIC National Alliance for Medical Image Computing Engineering a Segmentation Framework Marcel Prastawa.
NA-MIC National Alliance for Medical Image Computing Slicer3 Update
National Alliance for Medical Image Computing User Desktop Slicer 3.0 Architecure AlgorithmsITKVTK Slicer Modules VTK Apps Using ITK.
NA-MIC National Alliance for Medical Image Computing Slicer Progress in 2009 Steve Pieper, Ph.D.
Wednesday NI Vision Sessions
NA-MIC National Alliance for Medical Image Computing Core 1b – Engineering Data Management Daniel Marcus Washington University.
3D Slicer module programming
3D Slicer Architecture and Implementation
Pipeline Execution Environment
Core 1b – Engineering Data and Clinical Interface
Slicer3 Architecture.
3D Slicer Architecture and Implementation
JavaServer Faces: The Fundamentals
Ron Kikinis, MD Professor of Radiology, Harvard Medical School
Android Platform, Android App Basic Components
Presentation transcript:

National Alliance for Medical Image Computing Integrating with Slicer3

National Alliance for Medical Image Computing NA-MIC Kit Goals Software and Methodologies for Medical Image Computing –Facilitate Research –Promote Interoperability Stable, Cross-Platform Run Time Environment –Full Set of Core Features –Avoid Duplicated Effort Flexible Module Architecture –Plug-ins should be As Simple As Possible

National Alliance for Medical Image Computing Provided by D. Gering Slicer3 data model

National Alliance for Medical Image Computing Slicer3 “Observer MVC” Pattern MRML (Model) –For Scene Description and Application State –MRML Nodes are Persistent and Undoable –Scene and Nodes are Observable Logic Encapsulate VTK and ITK Pipelines (Controller) –Observe MRML to Configure Pipelines –Help Create/Manage Nodes –No UI Components (no Widgets, Actors, Mappers, Renderers or RenderWindows) GUI (View) –Observe and Edit MRML –Interact with User and Display Hardware Modules Should Follow Same Conventions Logic MRML Nodes GUI WidgetsRenderers Edit Observe Edit “Observe” means generic event mechanisms are used to pass information. “Edit” means code can directly call methods. Example: GUI can call methods in Logic classes, but Logic cannot call GUI methods. MRML cannot call Logic or GUI methods. There can be many observers for any event.

National Alliance for Medical Image Computing Variety of levels of integration Slicer Libs ModuleDescriptionParser GenerateCLP vtkITK MRML Non-slicer specific support libraries Slicer Base Application logic Widgets Common infrastructure for Slicer applications Built in modules Slice viewers Models Fiducials Transforms Full access to Slicer internals Loadable modules Query Atlas QDEC Volume rendering ChangeTracker EMSegment Full access to Slicer internals Scripted modules Editor Teem Two Tensor Tractography VMTK Limited access to Slicer internals Command line modules RegistrationRestricted access to Slicer internals Daemon OpenIGTLink Stochastic Tractography Access to MRML

National Alliance for Medical Image Computing Base Features vs. Modules FeaturesBaseModules VisualizationMRML: Models, Volumes, Volume Rendering, Fiducials, Continuum Meshes, Labeled Data Can create custom MRML Nodes and behavior FilteringNoneImplemented as Modules using ITK or other Libraries RegistrationTransform Display and Edit, Save/RestoreCalculate Transforms, Resample Data SegmentationLabel Maps, Parcellated SurfacesSegmentation Algorithms in ITK or other Libraries QuantificationLabel, Image, Volume Statistics; Numpy access to MRML Applications in Python or MATLAB Real-time IntegrationVTK Rendering, KWWidgets framework, Tracker Support (as Transforms) Direct Manipulation of the MRML Scene; 2D/3D Widgets; Device Interfaces, OpenIGTLink Module Diffusion ImagingDWI, DTI, Fiber BundlesTractography, Clustering, Atlases Applications“Bundles” of Modules in Distribution: Registration, Editor, some Filters, Customized Extensions, Domain- specific code, Optimized Interfaces…

National Alliance for Medical Image Computing Each module has … … an entry in the module menu … a panel of user interface controls

National Alliance for Medical Image Computing Built in module vtkMRMLNode.hvtkSlicerModuleGUI.h vtkSlicerModuleLogic.h vtkMRMLYourModuleNode.h GetNodeTagName() Copy() ReadXMLAttributes() WriteXML() vtkSlicerYourModuleGUI.h BuildGUI() ProcessGUIEvents() ProcessLogicEvents() ProcessMRMLEvents() vtkSlicerYourModuleLogic.h ProcessMRMLEvents() ProcessLogicEvents() Slicer provided Module writer provided

National Alliance for Medical Image Computing Loadable module vtkMRMLNode.hvtkSlicerModuleGUI.h vtkSlicerModuleLogic.h vtkMRMLYourModuleNode.h GetNodeTagName() Copy() ReadXMLAttributes() WriteXML() vtkSlicerYourModuleGUI.h BuildGUI() ProcessGUIEvents() ProcessLogicEvents() ProcessMRMLEvents() vtkSlicerYourModuleLogic.h ProcessMRMLEvents() ProcessLogicEvents() YourModule.so GetLoadableModuleDescription() GetLoadableModuleLogic() GetLoadableModuleGUI() Slicer provided Module writer provided

National Alliance for Medical Image Computing Tcl scripted module vtkMRMLScriptedModule Node.h vtkSlicerScriptedModule GUI.h vtkSlicerScriptedModule Logic.h YourModuleNode.tcl YourModuleGUI.tcl proc YourModuleBuildGUI proc YourModuleProcessGUIEvents proc YourModuleProcessLogicEvents YourModuleLogic.tcl YourModule.tcl package provide YourModule x.y Slicer provided Module writer provided

National Alliance for Medical Image Computing Python scripted module vtkMRMLScriptedModule Node.h vtkSlicerScriptedModule GUI.h vtkSlicerScriptedModule Logic.h YourModuleGUI.py def BuildGUI() def ProcessGUIEvents() def ProcessLogicEvents() Slicer provided Module writer provided

National Alliance for Medical Image Computing Command line module vtkMRMLCommandLine ModuleNode.h vtkCommandLine ModuleGUI.h vtkCommandLine ModuleLogic.h YourModule.xml YourModule.so XMLModuleDescription GetXMLModuleDescription() ModelEntryPoint() Slicer provided Module writer provided YourModule (exe) YourModule –xml YourModule.py XML def toXML() def Execute() or

National Alliance for Medical Image Computing All modules are created equal… … an entry in the module menu … a panel of user interface controls

National Alliance for Medical Image Computing Modularity Goals Keep the base package “lean and mean” Modules have individual identity –Per-module web site, svn, downloads, mailing lists, wiki… Allow users to assemble their own set of tools –Customized ‘Bundles’ by task or application Easy to download compatible extensions –Analogous to Firefox extensions –Integrate extension builds into developer/nightly/release processs NITRC Supplement to NA-MIC helping to pay for needed infrastructure (Neuroimaging Informatics Tools and Resources Clearinghouse) –NITRC can host neuroimaging projects (gforge implementation)

National Alliance for Medical Image Computing Module distribution* * Under development

National Alliance for Medical Image Computing NITRC

National Alliance for Medical Image Computing Daemon slicerget.tcl name > image.nrrd cat image.nrrd | slicerput.tcl name YourTool

National Alliance for Medical Image Computing Variety of levels of integration Slicer Libs ModuleDescriptionParser GenerateCLP vtkITK MRML Non-slicer specific support libraries Slicer Base Application logic Widgets Common infrastructure for Slicer applications Built in modules Slice viewers Models Fiducials Transforms Full access to Slicer internals Loadable modules Query Atlas QDEC Volume rendering ChangeTracker EMSegment Full access to Slicer internals Scripted modules Editor Teem Two Tensor Tractography VMTK Limited access to Slicer internals Command line modules RegistrationRestricted access to Slicer internals Daemon OpenIGTLink Stochastic Tractography Access to MRML

National Alliance for Medical Image Computing Module Terminology 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

National Alliance for Medical Image Computing Loadable Modules mplement_an_Interactive_Module_GUIhttp:// mplement_an_Interactive_Module_GUI Modules:HOWTOhttp:// Modules:HOWTO Create vtkSlicerModuleGUI Subclass –Override Virtual Methods for CreateGUI, ProcessMRMLEvents, etc. Provide Custom vtkMRMLNode Subclass(es) to Represent, Save and Restore state Create Logic Classes to Implement Module Functionality Create CMake Configuration Files to Build and Install Shared Libraries for Runtime Discovery and Packaging

National Alliance for Medical Image Computing Scripted Modules A Generic ScriptedModule Module Provides Mapping of C++ Method Entry Points to a Corresponding Naming Convention for Scripts –vtkMRMLScriptedModuleNode, vtkSlicerScriptedModuleLogic, vtkSlicerScriptedModuleGUI Scripts are Dynamically Discovered at Runtime A Generic ScriptedModuleNode Allows Save/Restore of Keyword / Value Pairs to Represent Module State Full API of Slicer, MRML, KWWidgets, VTK, available (except where not wrappable; these APIs have been designed for scriptability) Editor is extensive Tcl-based Module Several Python examples are included in current svn trunk –Python modules can also access Numpy routines for Numerical processing (Volumes and other DataArrays are directly mapped to Numpy arrays for easy manipulation)

National Alliance for Medical Image Computing Command Line Modules Use the GenerateCLP command (provided with Slicer) to convert XML description of program arguments into a C++.h file Main program of module uses PARSE_ARGS macro provided by.h file to instance variables corresponding to parameters defined in XML file PARSE_ARGS also defines a --xml argument that returns original XML string on stdout Slicer parses the XML to create GUI for each module Are Covered Extensively in the HelloWorld Tutorial Note: Command Line Modules can be written in any language. C++ utilities are provided, but can be emulated / recreated as needed.