1. National Alliance for Medical Image Computing http://na-mic.org Slicer3 plugins Common architecture for interactive and batch processing

2. National Alliance for Medical Image Computing http://na-mic.org The grand vision… User Desktop AlgorithmsITKVTK Slicer Modules VTK Apps Using ITK Scripts of Slicer Mods Batch Programs Non-NAMIC Cmd tools BatchMake BIRN Grid Wizard Slicer 3.0

3. National Alliance for Medical Image Computing http://na-mic.org Common architecture for interactive and batch processing User Desktop AlgorithmsITKVTK Slicer Modules VTK Apps Using ITK Scripts of Slicer Mods Batch Programs Non-NAMIC Cmd tools BatchMake BIRN Grid Wizard Slicer 3.0

4. National Alliance for Medical Image Computing http://na-mic.org Each module has … … an entry in the module menu … a panel of user interface controls

5. National Alliance for Medical Image Computing http://na-mic.org Example module http://www.nitrc.org/projects/slicer3examples/

6. National Alliance for Medical Image Computing http://na-mic.org Configuring example modules … from a Slicer3 installation… from a Slicer3 build

7. National Alliance for Medical Image Computing http://na-mic.org Building the example modules

8. National Alliance for Medical Image Computing http://na-mic.org Adding example modules to Slicer3 … from a Slicer3ExampleModules installation … from a Slicer3ExampleModules build * Slicer3 restart required

9. National Alliance for Medical Image Computing http://na-mic.org Running the modules

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

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

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

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

14. National Alliance for Medical Image Computing http://na-mic.org Communicating status (easy) #include "vtkPluginFilterWatcher.h"... vtkMarchingCubes *cubes = vtkMarchingCubes::New(); cubes->SetInput(reader->GetOutput()); vtkPluginFilterWatcher watchCubes(cubes, "Generate Isosurface", CLPProcessInformation,.5, 0.0); vtkDecimatePro *decimate = vtkDecimatePro::New(); decimate->SetInput(cubes->GetOutput()); vtkPluginFilterWatcher watchDecimate(decimate, "Reduce Triangle Count", CLPProcessInformation,.5, 0.5); decimate->Update(); VTK #include "itkPluginFilterWatcher.h... typedef itk::MedianImageFilter FilterType; FilterType::Pointer median = FilterType::New(); itk::PluginFilterWatcher watchMedian(median, "Denoise Image", CLPProcessInformation); Median->Update(); ITK

15. National Alliance for Medical Image Computing http://na-mic.org Communicating status (hard) name of program section or algorithm description of program section or algrotihm floating number from 0 to 1 name of program section or algorithm execution time Executable extern "C" { struct ModuleProcessInformation { /** Inputs from calling application to the module **/ unsigned char Abort; /** Outputs from the module to the calling application **/ float Progress; char ProgressMessage[1024]; void (*ProgressCallbackFunction)(void *); void *ProgressCallbackClientData; double ElapsedTime; } Shared object

16. National Alliance for Medical Image Computing http://na-mic.org Python modules XML = """ Filtering.Denoising... def toXML(): return XML; def Execute ( inputVolume, outputVolume, conductance=1.0, timeStep=0.0625, iterations=1 ): print "Executing Python Demo Application!" Slicer = __import__ ( "Slicer" ); slicer = Slicer.Slicer() in = slicer.MRMLScene.GetNodeByID ( inputVolume ); out = slicer.MRMLScene.GetNodeByID ( outputVolume ); filter = slicer.vtkITKGradientAnisotropicDiffusionImageFilter.New() filter.SetConductanceParameter ( conductance ) filter.SetTimeStep ( timeStep ) filter.SetNumberOfIterations ( iterations ) filter.SetInput ( in.GetImageData() ) filter.Update() out.SetAndObserveImageData(filter.GetOutput()) return

17. National Alliance for Medical Image Computing http://na-mic.org Parameters | | | | | | | | | | | [type="scalar|label|tensor|diffusion-weighted|vector|model"] | [type="fiberbundle|model"] | [multiple="true|false"] [coordinateSystem="lps|ras|ijk"] | [multiple="true|false"] [coordinateSystem="lps|ras|ijk"]

18. National Alliance for Medical Image Computing http://na-mic.org Parameter description * C++ variable name of the parameter * Help message for parameter * GUI label for the parameter Default value * Single character flag, e.g. –f * Single word flag, e.g. --outputImage Block around minimum/maximum/step. Trigger a slider to be used. Minimum parameter value Maximum parameter value Step size * Input or output parameter (image, geometry, file, directory) * Position of a parameter without a flag. Starts at 0 * Block around element * Choice value for an enumeration * Required tags * Required under certain conditions

19. National Alliance for Medical Image Computing http://na-mic.org Behind the scenes Tasks queued for processing thread Three types of modules: –executable, –shared object, and –Python modules Scalar images sent via files for executables and memory* for shared objects and python Vector images, tensor images, geometry, tables, transforms sent via files Scalars, file names, directories, fiducials, regions sent via command line * VTK-based modules using scalar images are only supported as executable (command line) modules.

20. National Alliance for Medical Image Computing http://na-mic.org Slicer3 Plugins Common architecture for interactive and batch processing