diff --git a/Documentation/Doxygen/DeveloperManual/Deployment.dox b/Documentation/Doxygen/DeveloperManual/Deployment.dox index e293d379ba..ea81e022c7 100644 --- a/Documentation/Doxygen/DeveloperManual/Deployment.dox +++ b/Documentation/Doxygen/DeveloperManual/Deployment.dox @@ -1,46 +1,46 @@ /** \page DeploymentPage Deployment \section DeploymentPageIntroduction Introduction \note This does not install the MITK headers (like an SDK). If you want to develop applications based on MITK you still have to compile MITK yourself. \section DeploymentPagePlatform Platform specific notes \subsection DeploymentPagePlatformLinux Linux You can create a tarball (.tar.gz) of your MITK application which includes all necessary non-system libraries by following these steps: \note Libraries in system locations (/lib/, /lib32/, /lib64/, /usr/lib/, /usr/lib32/,/usr/lib64/, and /usr/X11R6/) will not be included in the tarball. If you want to distribute Qt (for example), you have to do a custom Qt installation outside of these directories. \subsection DeploymentPagePlatformWindows Windows You can create a Zip file (.zip) or an NSIS installer (needs an installation of NSIS) for Windows platforms. Only "Release" builds are supported during packaging, the results of trying to package "Debug" builds are undefined. \note Building installers based on MinGW is not supported. On some systems, it might still be necessary to install the Microsoft Visual C++ Redistributable Package to start the installed application successfully. \subsection DeploymentPagePlatformMacOS MacOS You can create a drag'n drop disk image (.dmg) file for MacOS. The procedure is pretty much the same as for Linux. -Note that on MacOS, libraries in system locations as pointed out in the Linux section \b and \b libraries located in /System/Library will not be copied. If you want to distribute any libraries from these locations, you have to install them somewhere else prior to configuring your MITK build. +\note On MacOS, libraries in system locations as pointed out in the Linux section \b and libraries located in /System/Library will not be copied. If you want to distribute any libraries from these locations, you have to install them somewhere else prior to configuring your MITK build. */ \ No newline at end of file diff --git a/Documentation/Doxygen/DeveloperManual/HowToNewProject.dox b/Documentation/Doxygen/DeveloperManual/HowToNewProject.dox index bd0971db9d..d961d9c9e4 100644 --- a/Documentation/Doxygen/DeveloperManual/HowToNewProject.dox +++ b/Documentation/Doxygen/DeveloperManual/HowToNewProject.dox @@ -1,161 +1,161 @@ /** \page HowToNewProject Creating a new MITK project This page is intended to give a comprehensive guide to setting up your own MITK based project. It will use the application framework provided by MITK and is probably the preferred way for most users. -The first part of this document is a tutorial aimed at newcomers to MITK and possibly CMake and tries to give as much help as possible on setting up your own project. If you are looking for more technical information about customizing MITK, the structure of the superbuild or packaging you might want to read the \ref HowToNewProjectAdvancedInformation. +The first part of this document is a tutorial aimed at newcomers to MITK and possibly %CMake and tries to give as much help as possible on setting up your own project. If you are looking for more technical information about customizing MITK, the structure of the superbuild or packaging you might want to read the \ref HowToNewProjectAdvancedInformation. If you have set up your MITK project already and want to start developing you could take a look at \ref TutorialPage. \section HowToNewProjectGettingStarted Getting Started To bootstrap your project MITK offers two convenient options:
  1. Use the MITK Plugin Generator, a command line tool used to generate a customized MITK project and/or MITK plug-ins (available for download here).
  2. Use the MITK project template as an example project.
Both options will provide you with a project which contains a "superbuild" mechanism to automatically download, configure, and build MITK as a dependency of your own project. The MITK Plugin Generator generates code using the supplied command line arguments, whereas the MITK project template needs immediate modifications to customize it to your naming schemes. However, the project template will potentially contain more code demonstrating features of MITK. \note Using the MITK Plugin Generator is recommended for beginners. \section HowToNewProjectPrerequisites Prerequisites What ever option you choose, a MITK-based project needs essentially the same prerequisites as MITK itself. Please see \ref BuildInstructions_Prerequisites for details. \note If you use one of the two options above you will \b not \b need to build MITK yourself. This will be done automatically. \section HowToNewProjectCreatingSourceDir Preparing your source directory In order to start developing with MITK, you first have to set up the source directory for your project. \subsection HowToNewProjectSourceUsingGenerator Using the MITK Plugin Generator The usage of the Plugin Generator for creating a new project is described in \ref NewPluginWithProject, please have a look there. \subsection HowToNewProjectSourceUsingTemplate Using the MITK Project Template Download the project as a tarball or zipball and extract it to your desired source directory. \note This is a \b template \b. You must modify it such that it fits the needs of your particular project. Especially you should do a global search and replace for the string "awesome" to rename the template application and plug-in. You may want to rename some files too. \section HowToNewProjectGeneratingCMake Generating your binary with CMake -After you have set up your source directory you can proceed to generate your binary directory using CMake. Depending on your operating system and preferences you might want to use "cmake-gui" or "ccmake" (shell). This document assumes you are using cmake-gui. +After you have set up your source directory you can proceed to generate your binary directory using %CMake. Depending on your operating system and preferences you might want to use "cmake-gui" or "ccmake" (shell). This document assumes you are using cmake-gui.
    -
  1. Start "cmake-gui" and enter your source (e.g. D:\AwesomeProject) and binary directory (e.g. D:\AwesomeProject-superbuild). -
  2. Upon first pressing "Configure" you will be prompted to select your generator. This determines what project files will be generated by CMake. Set this to the development tool you are intending to use (e.g. "Visual Studio 2010 64Bit" or "linux makefiles". +
  3. Start "cmake-gui" and enter your source (e.g. "D:\AwesomeProject") and binary directory (e.g. "D:\AwesomeProject-superbuild"). +
  4. Upon first pressing "Configure" you will be prompted to select your generator. This determines what project files will be generated by %CMake. Set this to the development tool you are intending to use (e.g. "Visual Studio 2010 64Bit" or "linux makefiles".
  5. Press "Configure" until no new variables appear and then "Generate". Now all project files have been generated into your binary directory.
  6. Double-check that the right Qt version is used.
Now you are ready to compile your code. Depending on your choice of tool this will be done differently, we cover two possibilities here. \subsection HowToNewProjectCompilingLinuxMakefiles Compiling using linux makefiles
  1. In the shell, switch to your binary directory.
  2. type "make" and hit enter
\subsection HowToNewProjectCompilingVisualStudio Compiling using visual studio We assume your application is called "AwesomeApp" and your project "AwesomeProject" and your binary directory is "D:\AwesomeProject-superbuild\". Replace names and paths accordingly.
    -
  1. Close CMake and open "D:\AwesomeProject-superbuild\AwesomeProject-superbuild.sln" . Your Visual Studio should appear and by pressing F7 you start the compilation. This will clone the MITK source code, build it, and then start building your own project. +
  2. Close %CMake and open "D:\AwesomeProject-superbuild\AwesomeProject-superbuild.sln" . Your Visual Studio should appear and by pressing F7 you start the compilation. This will clone the MITK source code, build it, and then start building your own project.
  3. After the superbuild compilation has finished, close the solution file and start the batch file "D:\AwesomeProject-superbuild\AwesomeProject-build\StartVS_debug.bat" (or _release.bat if you built in Release mode) which opens the "D:\AwesomeProject-superbuild\AweseomeProject-build\AwesomeProject.sln" solution.
  4. Set the "AwesomeApp" project as start-up project (right click > "Set as StartUp Project") and press "F5" to start your MITK AwesomeApp.
\note Just opening AwesomeProject.sln from your explorer by double-cliking won`t allow you to start or debug your application because the required environment variables would be missing. Use the supplied batch files or set your PATH variable accordingly. \section HowToNewProjectAddingMITKFunctionality I want to use some MITK plugin but it is not available Due to the sheer number of MITK plugins not every plugin is activated by default. To activate a specific plugin (again replace paths as needed):
  1. Start "cmake-gui" and set the binary directory to "D:\AwesomeProject-superbuild\MITK-superbuild\MITK-build\", the source will adjust automatically and you will see new settings appear.
  2. Navigate to the plugin you want to use (e.g. "MITK_BUILD_org.mitk.gui.qt.segmentation") and tick the checkbox behind it
  3. Press "Configure" until no new variables appear and then "Generate".
  4. Build MITK using your development tool (as in \ref HowToNewProjectCompilingLinuxMakefiles or \ref HowToNewProjectCompilingVisualStudio only in the "D:\AwesomeProject-superbuild\MITK-superbuild\MITK-build\" directory )
  5. Start "cmake-gui" and set the binary directory to "D:\AwesomeProject-superbuild\AwesomeProject-build\", the source will adjust automatically and you will see new settings appear.
  6. Press "Configure" until no new variables appear and then "Generate".
  7. Build your project
  8. Start your application
\note If you want to use an application provided by MITK (e.g. MITK Workbench) you have to tick the appropriate checkbox as well (in this case MITK_BUILD_APP_mitkWorkbench ) and build MITK. Do note, that this application will be located in the bin directory of the "D:\AwesomeProject-superbuild\MITK-superbuild\MITK-build\" folder. \section HowToNewProjectAdvancedInformation Information for avanced users \subsection HowToNewProjectCustomizingMITK Customizing MITK -The CMake scripts from the Plugin Generator of the project template provide some handy options which allow you to customize the MITK build used in your project. You can either inject an already build MITK to be used by your project or configure some MITK options directly in your project's superbuild configuration if MITK is going to be build inside your project. +The %CMake scripts from the Plugin Generator of the project template provide some handy options which allow you to customize the MITK build used in your project. You can either inject an already build MITK to be used by your project or configure some MITK options directly in your project's superbuild configuration if MITK is going to be build inside your project. \subsubsection HowToNewProjectCustomizingMITKInjectMITK Inject a MITK build -By setting the \b EXTERNAL_MITK_DIR \b variable in your project's superbuild CMake configuration to a MITK build directory (containing the MITKConfig.cmake) you can skip the MITK build process. +By setting the \b EXTERNAL_MITK_DIR \b variable in your project's superbuild %CMake configuration to a MITK build directory (containing the MITKConfig.cmake) you can skip the MITK build process. -If MITK is the only external project in your project, you might want to disable the superbuild of your project completely (set _USE_SUPERBUILD to OFF or edit your CMakeLists.txt file to set it to OFF by default) and set the \b MITK_DIR \b CMake variable to your MITK build directory. +If MITK is the only external project in your project, you might want to disable the superbuild of your project completely (set _USE_SUPERBUILD to OFF or edit your CMakeLists.txt file to set it to OFF by default) and set the \b MITK_DIR \b %CMake variable to your MITK build directory. \subsubsection HowToNewProjectCustomizingMITKConfigure Configure the MITK superbuild If MITK is being build inside your project's superbuild process, you can enable the use of certain third-party libraries inside of MITK. The following variables control the MITK configuration: -You can also inject already build third-party libraries from inside your project's superbuild in the MITK superbuild by using any of the following CMake variables: +You can also inject already build third-party libraries from inside your project's superbuild in the MITK superbuild by using any of the following %CMake variables: If the corresponding \b MITK_USE_ \b option is set to on, the MITK superbuild will use the provided build directory instead of building the project itself. -You can also control the source code location for MITK in your project's superbuild configuration by using the following CMake variables: +You can also control the source code location for MITK in your project's superbuild configuration by using the following %CMake variables:
  • \b MITK_SOURCE_DIR The path to the MITK source directory. If the value for this variable is non-empty, the variables below are ignored.
  • \b MITK_GIT_REPOSITORY The Git repository containing the MITK source code.
  • \b MITK_GIT_TAG The hash id, tag or branch name used for a checkout from MITK_GIT_REPOSITORY.
\subsubsection HowToNewProjectProjectStructure Project Structure -If you are using the superbuild feature of the generated project (the default), you might want to familiarise yourself with the layout of your build tree. The top-level build directory which you specified in CMake when configuring your project will contain all the required dependencies. +If you are using the superbuild feature of the generated project (the default), you might want to familiarise yourself with the layout of your build tree. The top-level build directory which you specified in %CMake when configuring your project will contain all the required dependencies. -Suppose we call our project MyProject and the build directory is C:\MyProject-superbuild. Then the layout looks something like this: +Suppose we call our project MyProject and the build directory is "C:\MyProject-superbuild". Then the layout looks something like this: -MyProjectLayout.png The top-level directory contains the source code and the build directories from the dependencies of your project. In the current case, the only dependency of MyProject is MITK, which in turn has downloaded and built its own dependencies (CTK, DCMTK, ITK, etc.). The "real" build tree for your project is located in MyProject-superbuild/MyProject-build, so point the CMake-GUI to this build directory if you want to change the set of enabled plug-ins for example. +MyProjectLayout.png The top-level directory contains the source code and the build directories from the dependencies of your project. In the current case, the only dependency of MyProject is MITK, which in turn has downloaded and built its own dependencies (CTK, DCMTK, ITK, etc.). The "real" build tree for your project is located in MyProject-superbuild/MyProject-build, so point the %CMake-GUI to this build directory if you want to change the set of enabled plug-ins for example. Further, you should open the MyProject.sln solution file (for Visual Studio) or execute "make" in the MyProject-superbuild/MyProject-build/ directory. Only for the very first time or if you want to update and newly build the project's dependencies should you use the project files in the MyProject-superbuild directory directly. -The same applies for the MyProject-superbuild/MITK-superbuild directory. This directory contains the MITK superbuild, nested inside your project's superbuild. If you want to change CMake options for MITK, use the MyProject-superbuild/MITK-superbuild/MITK-build build directory. +The same applies for the MyProject-superbuild/MITK-superbuild directory. This directory contains the MITK superbuild, nested inside your project's superbuild. If you want to change %CMake options for MITK, use the MyProject-superbuild/MITK-superbuild/MITK-build build directory. \image html HowToNewProject-MyProjectLayout.png "Layout of MyProject" \subsubsection HowToNewProjectPackaging Packaging The project template and the generated projects by the Plugin Generator come with full packaging support. You can create deployable packages of your project for all supported operating systems my building the PACKAGE target. On Linux, this will create a tarball, on MacOS a .dmg file, and on Windows a zipball and an NSIS installer (if NSIS is installed and found). You can read more about deployment \ref DeploymentPage "here". */ \ No newline at end of file diff --git a/Documentation/Doxygen/DeveloperManual/NewPlugin.dox b/Documentation/Doxygen/DeveloperManual/NewPlugin.dox index e664deaada..d937ffa225 100644 --- a/Documentation/Doxygen/DeveloperManual/NewPlugin.dox +++ b/Documentation/Doxygen/DeveloperManual/NewPlugin.dox @@ -1,97 +1,97 @@ /** \page NewPluginPage How to create a new MITK Plug-in The MITK Plugin Generator is a command line tool to simplify the process of creating your own MITK project (optional) and plug-ins. It can either be downloaded here or used from an existing MITK build. The Plugin Generator takes the following command line arguments: \verbatim ./MITKPluginGenerator -h A CTK plug-in generator for MITK (version 1.2.0) -h, --help Show this help text -o, --out-dir Output directory (default: /tmp) -l, --license Path to a file containing license information (default: :/MITKLicense.txt) -v, --vendor The vendor of the generated code (default: DKFZ, Medical and Biological Informatics) -q, --quiet Do not print additional information -y, --confirm-all Answer all questions with 'yes' -u, --check-update Check for updates and exit -n, --no-networking Disable all network requests Plug-in View options -vc, --view-class The View's' class name -vn, --view-name * The View's human readable name Plug-in options -ps, --plugin-symbolic-name * The plugin's symbolic name -pn, --plugin-name The plug-in's human readable name Project options --project-copyright Path to a file containing copyright information (default: :/LICENSE.txt) --project-name The project name --project-app-name The application name [* - options are required] \endverbatim If a project name is provided via the --project-name argument, the new plug-in will be generated as part of a new project. \section NewPluginOnly Creating a new MITK plug-in Here is an example call to the Plugin Generator, creating one plug-in with the symbolic name com.mycompany.myplugin and a View named My View: \verbatim ./MITKPluginGenerator --plugin-symbolic-name org.mycompany.myplugin --view-name "My View" \endverbatim If you did not already specify the final location of the plug-in via the --out-dir argument, move the directory (in our example /tmp/org.mycompany.myplugin) to your existing project. Do not forget to add the plug-in in your project's build system (usually in the file <your-project>/Plugins/Plugins.cmake). \section NewPluginWithProject Creating a new MITK project \subsection NewPluginProjectPrerequisites Prerequisites MITK-based projects created with the Plugin Generator need the same prerequisites as MITK itself. See the \ref BuildInstructionsPage for MITK for details. Here is an example call to the Plugin Generator, creating the same plug-in as above but integrated in a new project: \verbatim ./MITKPluginGenerator --plugin-symbolic-name org.mycompany.myplugin --view-name "My View" --project-name "MyProject" --project-app-name "MyApp" \endverbatim The generated project is completely self-contained and can be configured via CMake immediately. When building the generated project, it will first download all required dependencies (like MITK itself). For an explanation of the project's build directory layout and how to configure MITK from your project's superbuild CMake configuration, -see SetupAMITKBasedProject. +see \ref HowToNewProject. \subsection NewPluginLimitations Limitations The Plugin Generator supports only a very limited set of possible configuration options. For more customizations of your project or plug-in, you must familiarize yourself with CMake and the generated build system. Further, the generator is not able to modify existing projects, it can only create new ones. \section NewPluginBuildSystem Build system for plug-ins Just put new files in your plug-in's \c src or \c src/internal directory and edit the \c files.cmake file there. If you have any fancy stuff like external libraries and include directories you should have a look at the CMake manual and general MITK build system documentation. \section NewPluginTroubleshooting Troubleshooting \par I get "Could not find library" messages and similar stuff when I try to start my project's executable. This is mostly due to wrong environment settings. On Windows, make sure that you use the supplied batch files to start Visual Studio or your project's executable. If you still get errors, double check the value of the PATH variable in your batch files (it must contain MITK's binary directory and paths to the ITK, VTK and Qt libraries. \par On Linux, set your LD_LIBRARY_PATH variable accordingly. */ diff --git a/Documentation/Doxygen/MainPage.dox.in b/Documentation/Doxygen/MainPage.dox.in index e2a96c1b86..363fee2509 100644 --- a/Documentation/Doxygen/MainPage.dox.in +++ b/Documentation/Doxygen/MainPage.dox.in @@ -1,53 +1,55 @@ /** \mainpage Medical Imaging Interaction Toolkit \image html mitkLogo.jpg \section intro Introduction -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 +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 +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 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 +\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 +\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. -MITK re-uses virtually anything from VTK and ITK. Thus, it is not at all a competitor to VTK or ITK, but +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. \section FurtherReading Further Reading -\ref Concepts +\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 */