National Alliance for Medical Image Computing Slicer3 plugins Common architecture for interactive and batch processing

National Alliance for Medical Image Computing 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

National Alliance for Medical Image Computing 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

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 Example module

National Alliance for Medical Image Computing Configuring example modules … from a Slicer3 installation… from a Slicer3 build

National Alliance for Medical Image Computing Building the example modules

National Alliance for Medical Image Computing Adding example modules to Slicer3 … from a Slicer3ExampleModules installation … from a Slicer3ExampleModules build * Slicer3 restart required

National Alliance for Medical Image Computing Running the modules

National Alliance for Medical Image Computing ExampleModule.xml

National Alliance for Medical Image Computing ExampleModule.cxx

National Alliance for Medical Image Computing ExampleModule.cxx

National Alliance for Medical Image Computing CMakeLists.txt

National Alliance for Medical Image Computing 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

National Alliance for Medical Image Computing 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

National Alliance for Medical Image Computing 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

National Alliance for Medical Image Computing 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"]

National Alliance for Medical Image Computing 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

National Alliance for Medical Image Computing 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.

National Alliance for Medical Image Computing Slicer3 Plugins Common architecture for interactive and batch processing