Slicer 3 plugins Common architecture for interactive and

Slicer 3 plugins Common architecture for interactive and batch processing National Alliance for Medical Image Computing http: //na-mic. org

The grand vision… Algorithms ITK VTK Slicer Modules Slicer 3. 0 Scripts of Slicer Mods VTK Apps Using ITK Batch Programs Non-NAMIC Cmd tools Batch. Make BIRN Grid Wizard National Alliance for Medical Image Computing http: //na-mic. org User Desktop

Common architecture for interactive and batch processing Algorithms ITK VTK Slicer Modules Slicer 3. 0 User Desktop Scripts of Slicer Mods VTK Apps Using ITK Batch Programs Non-NAMIC Cmd tools Batch. Make BIRN Grid Wizard 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 National Alliance for Medical Image Computing http: //na-mic. org

Example module http: //www. nitrc. org/projects/slicer 3 examples/ National Alliance for Medical Image Computing http: //na-mic. org

Configuring example modules … from a Slicer 3 installation National Alliance for Medical Image Computing http: //na-mic. org … from a Slicer 3 build

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

Adding example modules to Slicer 3 … from a Slicer 3 Example. Modules installation … from a Slicer 3 Example. Modules build * Slicer 3 restart required National Alliance for Medical Image Computing http: //na-mic. org

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

Example. Module. xml National Alliance for Medical Image Computing http: //na-mic. org

Example. Module. cxx National Alliance for Medical Image Computing http: //na-mic. org

Example. Module. cxx National Alliance for Medical Image Computing http: //na-mic. org

CMake. Lists. txt National Alliance for Medical Image Computing http: //na-mic. org

Communicating status (easy) VTK #include "vtk. Plugin. Filter. Watcher. h". . . vtk. Marching. Cubes *cubes = vtk. Marching. Cubes: : New(); cubes->Set. Input(reader->Get. Output()); vtk. Plugin. Filter. Watcher watch. Cubes(cubes, "Generate Isosurface", CLPProcess. Information, . 5, 0. 0); vtk. Decimate. Pro *decimate = vtk. Decimate. Pro: : New(); decimate->Set. Input(cubes->Get. Output()); vtk. Plugin. Filter. Watcher watch. Decimate(decimate, "Reduce Triangle Count", CLPProcess. Information, . 5, 0. 5); decimate->Update(); ITK #include "itk. Plugin. Filter. Watcher. h. . . typedef itk: : Median. Image. Filter<Image. Type, Image. Type> Filter. Type; Filter. Type: : Pointer median = Filter. Type: : New(); itk: : Plugin. Filter. Watcher watch. Median(median, "Denoise Image", CLPProcess. Information); Median->Update(); National Alliance for Medical Image Computing http: //na-mic. org

Communicating status (hard) Executable <filter-start> <filter-name> name of program section or algorithm </filter-name> <filter-comment> description of program section or algrotihm </filter-comment> </filter-start> <filter-progress> floating number from 0 to 1 </filter-progress> <filter-end> <filter-name> name of program section or algorithm </filter-name> <filter-time> execution time </filter-time> </filter-end> National Alliance for Medical Image Computing http: //na-mic. org Shared object extern "C" { struct Module. Process. Information { /** Inputs from calling application to the module **/ unsigned char Abort; /** Outputs from the module to the calling application **/ float Progress; char Progress. Message[1024]; void (*Progress. Callback. Function)(void *); void *Progress. Callback. Client. Data; double Elapsed. Time; } }

Python modules XML = """<? xml version="1. 0" encoding="utf-8"? > <executable> <category>Filtering. Denoising</category>. . . def to. XML(): return XML; def Execute ( input. Volume, output. Volume, conductance=1. 0, time. Step=0. 0625, iterations=1 ): print "Executing Python Demo Application!" Slicer = __import__ ( "Slicer" ); slicer = Slicer() in = slicer. MRMLScene. Get. Node. By. ID ( input. Volume ); out = slicer. MRMLScene. Get. Node. By. ID ( output. Volume ); filter = slicer. vtk. ITKGradient. Anisotropic. Diffusion. Image. Filter. New() filter. Set. Conductance. Parameter ( conductance ) filter. Set. Time. Step ( time. Step ) filter. Set. Number. Of. Iterations ( iterations ) filter. Set. Input ( in. Get. Image. Data() ) filter. Update() out. Set. And. Observe. Image. Data(filter. Get. Output()) return National Alliance for Medical Image Computing http: //na-mic. org

Parameters <integer> | <float> | <double> | <boolean> | <string> | <integer-vector> | <float-vector> | <double-vector> | <string-vector> | <integer-enumeration> | <float-enumeration> | <double-enumeration> | <string-enumeration> | <file> | <directory> | <image>[type="scalar|label|tensor|diffusion-weighted|vector|model"] | <geometry> [type="fiberbundle|model"] | <point>[multiple="true|false"] [coordinate. System="lps|ras|ijk"] | <region>[multiple="true|false"] [coordinate. System="lps|ras|ijk"] National Alliance for Medical Image Computing http: //na-mic. org

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

Slicer 3 Plugins Common architecture for interactive and batch processing National Alliance for Medical Image Computing http: //na-mic. org