1. Doxygen

2. Links http://www.itk.org/Doxygen/html/classes.html http://www.itk.org/Doxygen/html/classitk_1_1Image.html http://www.itk.org/Doxygen/html/modules.html http://www.stack.nl/~dimitri/doxygen/commands.html

3. Documentation Generation Requirements: –Doxygen –Dot (recommended) –LaTeX it is not tested if installed (=> JIRA)

4. Documentation Generation Process –CMake time When scanning modules –generate dot file for each module for dependency »TODO: use doxygen dot command instead (=>JIRA) –generate a dox file for each module »each module MUST be documented after keyword DESCRIPTION in itk_module.cmake »dependency documented

5. Documentation Generation Turn ON BUILD_DOCUMENTATION –Check Doxygen / Dot if are installed –Generate doxygen.config from doxygen.config.in –Create an additional target Documentation which is added to all Make Documentation or make all o at first generate all html pages (single threaded) o From *.h o generate all graphs (multi threaded and use all core on your machines)

6. Documentation Generation Turn ON BUILD_DOCUMENTATION –Once to generate the configuration file –Configure & Generate (CMake) Turn OFF BUILD_DOCUMENTATION cd build directory $ /path/to/source/ITK/Utilities/Maintenance/sin gle-doxygen.sh /path/to/source/ITK/Modules/Core/Common/i nclude firefox temp/html/index.html (=> JIRA)

7. Documentation Generation Turn ON BUILD_DOCUMENTATION –Once to generate the configuration file –Configure & Generate (CMake) Turn OFF BUILD_DOCUMENTATION cd build directory $ /path/to/source/ITK/Utilities/Maintenance/sin gle-doxygen.sh /path/to/source/ITK/Modules/Core/Common/i nclude/itkImage.h firefox temp/html/index.html (=> JIRA)

8. Errors / Warnings Doxygen can –Fail (rare) –Warn about inconsistencies!! Nightly Dashboard –Check snapper.megason-lab.hms –All doxygen warnings appear as a single 1

9. Module Documentation set(DOCUMENTATION "This module contains the central classes of the ITK toolkit. They include, basic data structures \(such as Points, Vectors, Images, Regions\) the core of the process objects \(such as base classes for image filters\) the pipeline infrastructure classes, the support for multi-threading, and a collection of classes that isolate ITK from platform specific features. It is anticipated that most other ITK modules will depend on this one.)

10. Module Documentation itk_module(ITK-Common DEPENDS ITK-VNLInstantiation ITK-KWSys TEST_DEPENDS ITK-TestKernel ITK-Mesh ITK-ImageIntensity ITK-IO-Base DESCRIPTION "${DOCUMENTATION} ) Automated generation of a dependency graph image Description of a module

11. Module Documentation For each class in ITK, the Module Name MUST be provided \ingroup ITK-Common If not => Test failure

12. Crowd Sourcing Online editing of doxygen documentation –To be connected (Kitware) (=>JIRA) Wiki Examples

13. Automated script which add links in header files \wiki \wikiexample{SimpleOperations/SetPixels,Set specified pixels to specified values} \endwiki

14. Few Commands \class \brief \tparam \param \return \code \li \sa \ingroup \class Image \brief Templated n-dimensional image class. \tparam TPixel Pixel Type \tparam VImageDimension Image Dimension template< class TPixel, unsigned int VImageDimension > class Image

15. Few Commands \class \brief \tparam \param \return \code \li \sa \ingroup \class Image \brief Templated n-dimensional image class. \tparam TPixel Pixel Type \tparam VImageDimension Image Dimension template< class TPixel, unsigned int VImageDimension > class Image

16. Few Commands \class \brief \tparam \param \return \code \li \sa \ingroup \class Image \brief Templated n-dimensional image class. \tparam TPixel Pixel Type \tparam VImageDimension Image Dimension template< class TPixel, unsigned int VImageDimension > class Image

17. Few Commands \class \brief \tparam \param \return \code \li \sa \ingroup \param[in] Parameter description \param[out] Parameter description \param[in,out] Parameter description

18. Few Commands \class \brief \tparam \param \return \code \li \sa \ingroup \return Description of the return value

19. Few Commands \class \brief \tparam \param \return \code \li \sa \ingroup \code typedef itk::Image ImageType; … \endcode

20. Few Commands \class \brief \tparam \param \return \code \li \sa \ingroup

21. Tweaks (needs) Font Size Font etc. Firefox with Firebug extension (consensus)