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b/Documentation/Doxygen/DeveloperManual/Application/BlueBerry/workbench-window-views.xcf similarity index 100% rename from Documentation/Doxygen/BlueBerry/workbench-window-views.xcf rename to Documentation/Doxygen/DeveloperManual/Application/BlueBerry/workbench-window-views.xcf diff --git a/Documentation/Doxygen/BlueBerry/workbench-window.jpg b/Documentation/Doxygen/DeveloperManual/Application/BlueBerry/workbench-window.jpg similarity index 100% rename from Documentation/Doxygen/BlueBerry/workbench-window.jpg rename to Documentation/Doxygen/DeveloperManual/Application/BlueBerry/workbench-window.jpg diff --git a/Documentation/Doxygen/BlueBerry/workbench.jpg b/Documentation/Doxygen/DeveloperManual/Application/BlueBerry/workbench.jpg similarity index 100% rename from Documentation/Doxygen/BlueBerry/workbench.jpg rename to Documentation/Doxygen/DeveloperManual/Application/BlueBerry/workbench.jpg diff --git a/Documentation/Doxygen/DeveloperManual/Deployment.dox b/Documentation/Doxygen/DeveloperManual/Application/Deployment.dox similarity index 100% rename from Documentation/Doxygen/DeveloperManual/Deployment.dox rename to Documentation/Doxygen/DeveloperManual/Application/Deployment.dox diff --git a/Documentation/Doxygen/DeveloperManual/Development.dox b/Documentation/Doxygen/DeveloperManual/DeveloperManual.dox similarity index 97% rename from Documentation/Doxygen/DeveloperManual/Development.dox rename to Documentation/Doxygen/DeveloperManual/DeveloperManual.dox index 5e1997f33c..f57eecbbec 100644 --- a/Documentation/Doxygen/DeveloperManual/Development.dox +++ b/Documentation/Doxygen/DeveloperManual/DeveloperManual.dox @@ -1,50 +1,50 @@ /** -\page Development Development with MITK +\page DeveloperManual Developer Manual The following items are concerned with the practical use of the MITK library for software development. Some abstract concepts of MITK are described in \ref Concepts \section DevelopmentSetup Setting Up MITK \li \subpage SupportedPlatformsPage \li \subpage BuildInstructionsPage \li \subpage thirdpartylibs \li \ref HowToNewProject \section DevelopmentGettingToKnow Getting To Know MITK \li \subpage DirectoryStructurePage \li \subpage TutorialPage \section DevelopmentWith Developing With MITK \li \subpage CMAKE_FAQ \li \subpage DICOMTesting \li \subpage NewPluginPage \li \subpage StatemachineEditor \li \subpage mitkExtPointsIndex \li \subpage DeploymentPage \li \subpage KnownProblemsPage \section DevelopmentContributing Contributing To MITK \li \subpage DocumentationGuide \li \subpage StyleGuideAndNotesPage \section DevelopmentGettingToKnowBlueberry Getting To Know BlueBerry \li \subpage BlueBerryExamples \section DevelopmentFurtherInfo Further Information This section lists some ressources you might want to look at if you could not find what you need in the \ref Development or \ref Concepts sections. We hold regular internal seminars which may or may not have something to do with MITK directly. The slides can be found here. If you have some problems with MITK you might want to take a look at the FAQ. If the above does not prove sufficient you can contact the Mailinglist. */ diff --git a/Core/Documentation/Doxygen/Concepts/Overview.dox b/Documentation/Doxygen/DeveloperManual/Starting/Architecture.dox similarity index 96% rename from Core/Documentation/Doxygen/Concepts/Overview.dox rename to Documentation/Doxygen/DeveloperManual/Starting/Architecture.dox index f5def8bb90..c1553fe018 100644 --- a/Core/Documentation/Doxygen/Concepts/Overview.dox +++ b/Documentation/Doxygen/DeveloperManual/Starting/Architecture.dox @@ -1,47 +1,47 @@ /** -\page OverviewPage Introduction: Overview on the Medical Imaging Interaction Toolkit (MITK) +\page Architecture The Architecture of MITK MITK is an open source software toolkit for medical image processing, subsequent data analysis and integration of medical hardware. It is designed with the aim of providing a modular and heavily reusable code base to enable rapid development of new features. Following this design philosophy MITK includes many different specialized modules e.g. the Segmentation Module. This document is aimed at giving an overview of the general structure of MITK. Furthermore it will give an introduction into the coding and design concepts behind this toolkit. \section OverviewPage_DesignOverview Design Overview MITK is designed to be used as a pure software library or as a complete application framework. Thus, a user of MITK can decide if he simply wants to add a new plug-in to the existing application framework or if he needs to implement his own application and wants to use MITK as a software library. Depending on the type of use MITK uses different software libraries, which is shown in the next figure for overview. \image html MitkOverview.png "Overview of MITK" Like shown above, MITK uses the following libraries. These are the main libraries MITK is based on. For further functionality you can optionally include others, a list can be found \ref thirdpartylibs "here" . Based on these libraries, MITK includes the following features: */ diff --git a/Documentation/Doxygen/DeveloperManual/Starting/FirstSteps/NewModule.dox b/Documentation/Doxygen/DeveloperManual/Starting/FirstSteps/NewModule.dox new file mode 100644 index 0000000000..ac64bbafbe --- /dev/null +++ b/Documentation/Doxygen/DeveloperManual/Starting/FirstSteps/NewModule.dox @@ -0,0 +1,4 @@ +/** +\page NewModulePage How to create a new MITK Module + +*/ diff --git a/Documentation/Doxygen/DeveloperManual/NewPlugin.dox b/Documentation/Doxygen/DeveloperManual/Starting/FirstSteps/NewPlugin.dox similarity index 100% rename from Documentation/Doxygen/DeveloperManual/NewPlugin.dox rename to Documentation/Doxygen/DeveloperManual/Starting/FirstSteps/NewPlugin.dox diff --git a/Documentation/Doxygen/StatemachineEditor/StatemachineEditor.dox b/Documentation/Doxygen/DeveloperManual/Starting/FirstSteps/StatemachineEditor/StatemachineEditor.dox similarity index 100% rename from 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Documentation/Doxygen/DeveloperManual/Starting/SettingUpMITK/HowToNewProject.dox diff --git a/Documentation/Doxygen/DeveloperManual/SupportedPlatforms.md b/Documentation/Doxygen/DeveloperManual/Starting/SettingUpMITK/SupportedPlatforms.md similarity index 100% rename from Documentation/Doxygen/DeveloperManual/SupportedPlatforms.md rename to Documentation/Doxygen/DeveloperManual/Starting/SettingUpMITK/SupportedPlatforms.md diff --git a/Documentation/Doxygen/DeveloperManual/ThirdPartyLibs.dox b/Documentation/Doxygen/DeveloperManual/Starting/SettingUpMITK/ThirdPartyLibs.dox similarity index 100% rename from Documentation/Doxygen/DeveloperManual/ThirdPartyLibs.dox rename to Documentation/Doxygen/DeveloperManual/Starting/SettingUpMITK/ThirdPartyLibs.dox diff --git a/Core/Documentation/Doxygen/Concepts/images/introduction/MitkOverview.png b/Documentation/Doxygen/DeveloperManual/images/MitkOverview.png similarity index 100% rename from Core/Documentation/Doxygen/Concepts/images/introduction/MitkOverview.png rename to Documentation/Doxygen/DeveloperManual/images/MitkOverview.png diff --git a/Documentation/Doxygen/MainPage.dox.in b/Documentation/Doxygen/MainPage.dox.in index 05d7565451..4fe57a1f1e 100644 --- a/Documentation/Doxygen/MainPage.dox.in +++ b/Documentation/Doxygen/MainPage.dox.in @@ -1,57 +1,17 @@ /** -\mainpage Medical Imaging Interaction Toolkit +\mainpage Medical Imaging Interaction Toolkit - Documentation Portal \image html mitkLogo.jpg -\section intro Introduction +This page acts as a portal to the three different parts of the MITK-Documentation. -Welcome to the Medical Imaging Interaction Toolkit (MITK). -Currently under active development, MITK aims at supporting the -development of leading-edge medical imaging software -with a high degree of interaction. It combines VTK, -ITK and the pic-based-libraries of the -Div. Medical and Biological Informatics -of the DKFZ and adds those features that are most important -for developing interactive medical imaging software covered neither by VTK nor ITK, i.e: -\li multiple, consistent views on the same data. For example, when you have three orthogonal -2D-views and a 3D view and data consisting of a green surface, the surface will be visible and green -in all views (as contour lines in 2D, as a surface in 3D), and when you move the surface, it will -move in all views. When you try to implement this with basic VTK, you will need to coordinate the -position/orientation/color/... of all the views somewhere in your program - exactly this can MITK -do for you. -\li interactions that create and/or modify data (not only actors as in basic VTK) -\li complex interactions with multiple states, e.g., for interaction with active contours -\li undo/redo of interactions -\li organization of data objects in a tree at run-time, e.g., to represent logical dependencies (e.g., -a heart cavity is a part of the heart) or to control the rendering process -\li additional properties of arbitrary type can be assigned to data objects contained in the data tree -\li visualization and interaction with 3D+t data (basic VTK can handle only 3D data and ITK is not -for visualization and interaction) -\li although MITK is mainly a toolkit and not an application, it offers some support on the -application-level, e.g, for structured combination of modules (so-called functionalities), e.g., for -combining and switching between one functionality for segmentation and another for registration. +If this is your first time around here and you are interested in learning more about MITK, please read \ref Overview -MITK re-uses virtually anything from VTK and ITK. Thus, it is not at all a competitor to VTK or ITK, but -an extension, which tries to ease the combination of both and to add the features outlined above. +If you are a MITK end-user, please refer to the \ref UserManual -\section FurtherReading Further Reading +If you are a developer looking for a developer's guide, please see \ref DeveloperManual -\subpage ShortIntroductionToMITK - -\ref Concepts - -\ref Development - -\ref HowToNewProject "A comprehensive newcomers guide to setting up your own MITK project" - -@MITK_XP_LINK@ - -@BLUEBERRY_DOXYGEN_LINK@ - -\ref thirdpartylibs - - */ diff --git a/Documentation/Doxygen/Modules/ModuleGeometryFigures.zip b/Documentation/Doxygen/Modules/ModuleGeometryFigures.zip deleted file mode 100644 index 434c701fb9..0000000000 Binary files a/Documentation/Doxygen/Modules/ModuleGeometryFigures.zip and /dev/null differ diff --git a/Documentation/Doxygen/DeveloperManual/ShortIntroductionToMITK.dox b/Documentation/Doxygen/Overview/Overview.dox similarity index 96% rename from Documentation/Doxygen/DeveloperManual/ShortIntroductionToMITK.dox rename to Documentation/Doxygen/Overview/Overview.dox index 9b03af2ba5..565f32e6f2 100644 --- a/Documentation/Doxygen/DeveloperManual/ShortIntroductionToMITK.dox +++ b/Documentation/Doxygen/Overview/Overview.dox @@ -1,29 +1,29 @@ /** -\page ShortIntroductionToMITK A short introduction to MITK +\page Overview MITK: An Overview The Medical Imaging Interaction Toolkit (MITK) can be used in several different ways. If you are a new user to MITK the first question is in what manner you intend to use it. The following options are simplified and condensed versions of the most common usage scenarios. \tableofcontents \section ShortIntroductionToMITKAsToolkit I want to develop my own software framework, but use some of MITK's data structures and algorithms You will use MITK as a toolkit and probably benefit most from the \ref BuildInstructionsPage and MITK API Documentation. \section ShortIntroductionToMITKAsFramework I want to use the MITK and BlueBerry software framework to develop my own software Here you have again two options. \subsection ShortIntroductionToMITKAsFrameworkExtendingWorkbench I want use the MITK Workbench and extend its capabilities You are using MITK as software framework and writing your own modules and plugins for MITK. You want to read the \ref BuildInstructionsPage and further on \ref Development. Also you might want to take a look at our \ref CMAKE_FAQ. \subsection ShortIntroductionToMITKAsFrameworkExternalProject I want to create my own application based on MITK but with major customizations and changes This is probably the most common way to use MITK. You are using MITK as software framework and building your own project and application using MITK. You want to read \ref HowToNewProject and the general information in \ref Development. Also you might want to take a look at our \ref CMAKE_FAQ. \section ShortIntroductionToMITKAsFrameworkEndUser I want to use the MITK Workbench to do image processing You are using MITK and the MITK Workbench as an end user and will find user manuals in \ref MITKUserManualPage and \ref PluginListPage. */ \ No newline at end of file diff --git a/Documentation/Doxygen/UserManual/UserManual.dox b/Documentation/Doxygen/UserManual/UserManual.dox new file mode 100644 index 0000000000..a74dcc373e --- /dev/null +++ b/Documentation/Doxygen/UserManual/UserManual.dox @@ -0,0 +1,5 @@ +/** +\page UserManual MITK: User Manual + + +*/ \ No newline at end of file diff --git a/Documentation/Doxygen/ExampleCode/DocumentationExample.h b/Examples/DocumentationExample.h similarity index 100% rename from Documentation/Doxygen/ExampleCode/DocumentationExample.h rename to Examples/DocumentationExample.h