Slicer 3.0 Architecure

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Slicer 3.0 Architecure
User Desktop
Algorithms
ITK
VTK
Slicer Modules
Slicer 3.0
Scripts of Slicer Mods
VTK Apps Using ITK
Batch Programs
Non-NAMIC Cmd tools
LONI Pipeline
Birn Grid Data/Compute
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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

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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

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Program Flow
User Desktop
Slicer Modules
Slicer 3.0
prog.xml
GenerateCLP
progCLP.h
prog.cxx
Non-NAMIC Cmd tools
LONI Pipeline
Birn Grid Data/Compute
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Execution Model Documentation

• On the Wiki
• Slicer3Execution_Model_Documentation

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MedianImageFilter --xml
ltlabelgtNeighborhood Sizelt/labelgt
ltdefaultgt1,1,1lt/defaultgt lt/integer-vectorgt
lt/parametersgt ltparametersgt
ltlabelgtI/Olt/labelgt ltdescriptiongtInput/Output
parameterslt/descriptiongt ltimagegt
ltnamegtinputVolumelt/namegt ltlabelgtInput
Volumelt/labelgt ltchannelgtinputlt/channelgt
ltindexgt0lt/indexgt ltdescriptiongtInput
volume to be filteredlt/descriptiongt
lt/imagegt ltimagegt ltnamegtoutputVolumelt/n
amegt ltlabelgtOutput Volumelt/labelgt
ltchannelgtoutputlt/channelgt
ltindexgt1lt/indexgt ltdescriptiongtOutput
filteredlt/descriptiongt lt/imagegt
lt/parametersgt lt/executablegt

• lt?xml version"1.0" encoding"utf-8"?gt
• ltexecutablegt
• ltcategorygtFilteringlt/categorygt
• lttitlegtMedian Filterlt/titlegt
• ltdescriptiongt
• 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.
• lt/descriptiongt
• ltversiongt1.0lt/versiongt
• ltdocumentationurlgtlt/documentationurlgt
• ltlicensegtlt/licensegt
• ltcontributorgtBill Lorensenlt/contributorgt
• ltparametersgt
• ltlabelgtMedian Filter Parameterslt/labelgt
• ltdescriptiongt
• Parameters for the median filter
• lt/descriptiongt
• ltinteger-vectorgt
• ltnamegtneighborhoodlt/namegt
• ltlongflaggt--neighborhoodlt/longflaggt

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MedianImageFilter --help
USAGE d\lorensen\Projects\Slicer3-net\bin\Re
lWithDebInfo\MedianImageFilter
--xml --echo
--neighborhood
ltstdvectorltintgtgt --
--version -h
ltstdstringgt
ltstdstringgt Where --xml Produce
xml description of command line arguments
(default 0) --echo Echo the command line
arguments (default 0) --neighborhood
ltstdvectorltintgtgt 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. ltstdstringgt (required) Input
volume to be filtered ltstdstringgt
(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.
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MedianImageFilter GUI
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Building An Executable

• To use GenerateCLP from CMake include the
  following in your CMakeLists.txt file
• INCLUDE(Slicer3_SOURCE_DIR/Libs/GenerateCLP/Us
  eGenerateCLP.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.

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Execution Model Documentation
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Demo
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Converting Existing Modules

• Insight/Examples/Filtering/MedianImageFilter
• To
• Slicer3/Applications/CLI/MedianImageFilter