1. National Alliance for Medical Image Computing http://na-mic.org User Desktop Slicer 3.0 Architecure AlgorithmsITKVTK Slicer Modules VTK Apps Using ITK Scripts of Slicer Mods Batch Programs Non-NAMIC Cmd tools LONI Pipeline Birn Grid Data/Compute Slicer 3.0

2. National Alliance for Medical Image Computing http://na-mic.org Slicer 3 Execution Model: Goals Provide interface to batch programs –Simplify and unify command line processing Auto generate C++ command line processing –Simplify and unify GUI Auto generate GUI

3. National Alliance for Medical Image Computing http://na-mic.org Execution Model: Progress XML Interface Description –Describes command line options –Describes suggestions for GUI GenerateCLP –Generates C++ command line processing code from XML –Reports XML description GUI Generation –Discovers executables at Slicer start-up –Generates GUI from XML –Executes command line program

4. National Alliance for Medical Image Computing http://na-mic.org Program Flow User Desktop prog.xmlGenerateCLPprogCLP.h Slicer Modules prog.cxx Non-NAMIC Cmd tools LONI Pipeline Birn Grid Data/Compute Slicer 3.0

5. National Alliance for Medical Image Computing http://na-mic.org

6. On the Wiki: –Slicer3:Execution_Model_Documentation Execution Model Documentation

7. National Alliance for Medical Image Computing http://na-mic.org MedianImageFilter --xml Filtering Median Filter The MedianImageFilter is commonly used as a robust approach for noise reduction. This filter is particularly efficient against "salt-and-pepper" noise. In other words, it is robust to the presence of gray-level outliers. MedianImageFilter computes the value of each output pixel as the statistical median of the neighborhood of values around the corresponding input pixel. 1.0 Bill Lorensen Median Filter Parameters Parameters for the median filter neighborhood --neighborhood The size of the neighborhood in each dimension. The sizes are comma separated. Neighborhood Size 1,1,1 I/O Input/Output parameters inputVolume Input Volume input 0 Input volume to be filtered outputVolume Output Volume output 1 Output filtered

8. National Alliance for Medical Image Computing http://na-mic.org MedianImageFilter --help USAGE: d:\lorensen\Projects\Slicer3- net\bin\RelWithDebInfo\MedianImageFilter [--xml] [--echo] [--neighborhood >] [--] [--version] [-h] Where: --xml Produce xml description of command line arguments (default: 0) --echo Echo the command line arguments (default: 0) --neighborhood > The size of the neighborhood in each dimension (default: 1,1,1) --, --ignore_rest Ignores the rest of the labeled arguments following this flag. --version Displays version information and exits. -h, --help Displays usage information and exits. (required) Input volume to be filtered (required) Output filtered The MedianImageFilter is commonly used as a robust approach for noise reduction. This filter is particularly efficient against 'salt-and- pepper' noise. In other words, it is robust to the presence of gray-level outliers. MedianImageFilter computes the value of each output pixel as the statistical median of the neighborhood of values around the corresponding input pixel.

9. National Alliance for Medical Image Computing http://na-mic.org MedianImageFilter GUI

10. National Alliance for Medical Image Computing http://na-mic.org Building An Executable To use GenerateCLP from CMake include the following in your CMakeLists.txt file: INCLUDE(${Slicer3_SOURCE_DIR}/Libs/GenerateCLP/UseGenerateCLP.cmake) For each executable, include the following, replacing '''MyFilter''' with the name of your C++ source: SET ( '''MyFilter'''_SOURCE '''MyFilter'''.cxx GENERATECLP('''MyFilter'''_SOURCE '''MyFilter'''.xml) ADD_EXECUTABLE ( '''MyFilter''' ${'''MyFilter'''_SOURCE}) TARGET_LINK_LIBRARIES ( '''MyFilter''' ITKIO ITKBasicFilters ITKCommon) Although this example linked to ITK libraries, other libraries can be specified.

11. National Alliance for Medical Image Computing http://na-mic.org Execution Model Documentation

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

13. National Alliance for Medical Image Computing http://na-mic.org Converting Existing Modules Insight/Examples/Filtering/MedianImageFilter To Slicer3/Applications/CLI/MedianImageFilter