Slicer Custom Modules

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Slicer Custom Modules

• Steve Pieper, PhD

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Overall Goals

• Allow Independent Development of Run-Time
  Loadable Modules
• Enforce code independence
• Allow modules delivered under different licenses
• Support development outside of main cvs prior to
  code sharing
• The SLICER_MODULES environment variable
• Space-separated list of directories containing
  slicer module directory trees
• Used by cmaker, launch, and tarup
• Allows you to keep your own code in a distinct
  cvs repository/working directory

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What is a Module?

• C code (optional)
• VTK Subclasses
• ITK Subclasses
• Extra Helper code (GSL, OpenGL, etc)
• Tcl code
• Application Logic
• User Interface Code

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Directory Organization

• Modules/vtkltModuleNamegt
• cxx
• CMakeListsLocal.txt lists the source files plus
  custom build directives
• tcl
• ltModuleNamegt.tcl has standard slicer entry points
• builds
• Platform specific binary directories
• Wrapping
• Standard tcl/java/python wrapping support
• data
• Additional files your module needs (will be
  included in distribution by tarup.tcl)

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Modules in Slicer CVS

• vtkCISGFile/ vtkITK/
• vtkCorCTA/ vtkIbrowser/
• BIRNDUP/ vtkCustomModule/
  vtkImageSmooth/
• vtkDTMRI/ vtkLevelSets/
• LDMMViewer/ vtkEMLocalSegment/
  vtkMIRIADSegment/
• MultiVolumeReader/ vtkEMPrivateSegment/
  vtkMorphometrics/
• vtkFMRIEngine/ vtkRealignResample/
• iSlicer/ vtkFSLReader/
  vtkRigidIntensityRegistration/
• vtkAffineSegment/ vtkFastMarching/
  vtkSubVolume/
• vtkAnalyze/ vtkFluxDiffusion/
  vtkTensorUtil/
• vtkBXH/ vtkFreeSurferReaders/
  vtkVolumeTextureMapping/

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vtkCustomModule

• A support script to help manage the many files
  that need to be created/customized when making a
  vtk loadable library source tree
• Modules/vtkCustomModule/README.txt describes the
  step-by-step process

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Module Making Steps

• Copy vtkCustomModule to vtkltModuleNamegt and cd to
  that dir
• Remove all CVS subdirs
• (e.g. with rm -r find . -name CVS )
• Run ./vtkNameModule
• Your ltModuleNamegt will be propagated to the
  various files

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Module Making Steps (cont)

• Add your source files to cxx directory
• Add references to files in CMakeListsLocal.txt
  (copy from SAMPLE)
• SET(LOCAL_MODULE_SRCS
• vtkMultiInputsSimpleImageToImageFilter.cxx
• vtkActivationVolumeGenerator.cxx
• vtkActivationDetector.cxx
• vtkCDF.cxx
• )

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Module Making Steps (cont)

• Set any classes not to be wrapped
• SET ( LOCAL_NO_WRAP_SRCS
• GeneralLinearModel.cxx
• )
• Set any Abstract classes
• SET_SOURCE_FILES_PROPERTIES (
• vtkMultiInputsSimpleImageToImageFilter.cxx
• ABSTRACT
• )

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Module Making Steps (cont)

• If your code subclasses Slicer classes, uncomment
  the include directories lines and add other
  modules you depend on if needed
• INCLUDE_DIRECTORIES(
• VTKSLICERBASE_SOURCE_DIR/cxx
• VTKSLICERBASE_BUILD_DIR
• VTKTENSORUTIL_SOURCE_DIR/cxx
• VTKTENSORUTIL_BUILD_DIR
• )
• LINK_LIBRARIES (VTKSLICERBASE_BUILD_LIB
  VTKTENSORUTIL_BUILD_LIB VTKTENSORUTIL_BUILD_T
  CL_LIB)

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Module Cxx Code

• To ensure Windows dll files will be built
  correctly, be sure your .h files have the
  following code
• include ltvtkModuleNameConfigure.hgt
• and
• class VTK_MODULENAME_EXPORT vtkTest ...

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Module Tcl Files

• vtkNameModule will create a tcl/ModuleName.tcl
  file for you with a default UI
• Comments in that file tell how to customize your
  interface for your application

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Module Tcl Wrapping

• In the Wrapping/Tcl/vtkltModuleNamegt/vtkltModuleName
  gt.tcl file
• Source all tcl files your module needs
• If your module depends on another module,
  include, for example
• package require vtkTensorUtil

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What you get for this work

• Cross-platform build and automatic detection at
  run time
• Spot in the slicer More menu
• Ability to interact with slicer scene

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ITK Based Modules

• Depend on vtkITK Module for build
• To allow subclassing the vtkITKImageToImageFilters
  
• Write vtkITK wrapper class (Raul will describe in
  the next section)
• Just use the filter as if it were a vtk class
• if info command vtkITKBSplineImageFilter
  ""
• DevErrorWindow "DTMRI\nERROR
  vtkITKBSplineImageFilter does not exist, cannot
  use bspline filter
• return
• DTMRIMakeVTKObject vtkITKBSplineImageFilter
  bspline(i)