diff --git a/Documentation/Doxygen/UserManual/MITKUserManual.dox b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual.dox similarity index 99% rename from Documentation/Doxygen/UserManual/MITKUserManual.dox rename to Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual.dox index 8fd660c38f..65f6223227 100644 --- a/Documentation/Doxygen/UserManual/MITKUserManual.dox +++ b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual.dox @@ -1,118 +1,118 @@ /** -\page MITKUserManualPage The MITK User Manual +\bundlemainpage{MITKUserManualPage} The MITK User Manual Welcome to the basic MITK user manual. This document tries to give a concise overview of the basic functions of MITK and be an comprehensible guide on using them. Available sections: - \ref MITKUserManualPageOverview - \ref MITKUserManualPageUserInterface - \ref MITKUserManualPagePerspectives \section MITKUserManualPageOverview About MITK MITK is an open-source framework that was originally developed as a common framework for Ph.D. students in the Division of Medical and Biological Informatics (MBI) at the German Cancer Research Center. MITK aims at supporting the development of leading-edge medical imaging software with a high degree of interaction. 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 features not supported by VTK or ITK. Research institutes, medical professionals and companies alike can use MITK as a basic framework for their research and even commercial (thorough code research needed) software due to the BSD-like software license. Research institutes will profit from the high level of integration of ITK and VTK enhanced with data management, advanced visualization and interaction functionality in a single framework that is supported by a wide variety of researchers and developers. You will not have to reinvent the wheel over and over and can concentrate on your work. Medical Professionals will profit from MITK and the MITK applications by using its basic functionalities for research projects. But nonetheless they will be better off, unless they are programmers themselves, to cooperate with a research institute developing with MITK to get the functionalitiy they need. MITK and the MITK applications are not certified medical products and may be used in a research setting only. They must not be used in patient care. \section MITKUserManualPageUserInterface The User Interface The layout of the MITK applications is designed to give a clear distinction between the different work areas. The following figure gives an overview of the main sections of the user interface. \image html GUI_Commented.png "The Common MITK Application Graphical User Interface" The datamanager and the \ref MITKUserManualPagePerspectives have their own help sections. This document explains the use of: - The \ref MITKUserManualPageMultiWidget - The \ref MITKUserManualPageMenu - The \ref MITKUserManualPageLevelWindow - The \ref MITKUserManualPageMemoryUsage - The \ref MITKUserManualPageViews \section MITKUserManualPageMultiWidget Four Window View \subsection MITKUserManualPageMultiWidgetOverview Overview The four window view is the heart of the MITK image viewing. The standard layout is three 2D windows and one 3D window, with the transversal window in the top left quarter, the sagittal window in the top right quarter, the coronal window in the lower left quarter and the 3D window in the lower right quarter. The different planes form a crosshair that can be seen in the 3D window. Once you select a point within the picture, informations about it are displayed at the bottom of the screen. \subsection MITKUserManualPageMultiWidgetNavigation Navigation Left click in any of the 2D windows centers the crosshair on that point. Pressing the right mouse button and moving the mouse zooms in and out. By scrolling with the mouse wheel you can navigate through the slices of the active window and pressing the mouse wheel while moving the mouse pans the image section. In the 3D window you can rotate the object by pressing the left mouse button and moving the mouse, zoom either with the right mouse button as in 2D or with the mouse wheel, and pan the object by moving the mouse while the mouse wheel is pressed. Placing the cursor within the 3D window and holding the "F" key allows free flight into the 3D view. \subsection MITKUserManualPageMultiWidgetCustomizingViews Customizing By moving the cursor to the upper right corner of any window you can activate the window menu. It consists of three buttons. \image html Crosshair_Modes.png "Crosshair" The crosshair button allows you toggle the crosshair, reset the view and change the behaviour of the planes. Activating either of the rotation modes allows you to rotate the planes visible in a 2D window by moving the mouse cursor close to them and click and dragging once it changes to indicate that rotation can be done. The swivel mode is recommended only for advanced users as the planes can be moved freely by clicking and dragging anywhere within a 2D window. The middle button expands the corresponding window to fullscreen within the four window view. \image html Views_Choices.png "Layout Choices" The right button allows you to choose between many different layouts of the four window view to use the one most suited to your task. \section MITKUserManualPageMenu Menu \subsection MITKUserManualPageFile File This dialog allows you to save, load and clear entire projects, this includes any nodes in the data manager. \subsection MITKUserManualPageEdit Edit This dialog supports undo and redo operations as well as the image navigator, which gives you sliders to navigate through the data quickly. \subsection MITKUserManualPageWindow Window This dialog allows you to open a new window, change between perspectives and reset your current one to default settings. If you want to use an operation of a certain perspective within another perspective the "Show View" menu allows to select a specific function that is opened and can be moved within the working areas according to your wishes. Be aware that not every function works with every perspective in a meaningful way. The Preferences dialog allows you to adjust and save your custom settings. \image html Window_Dropdown.png "Preferences" \subsection MITKUserManualPageHelp Help This dialog contains this help, the welcome screen and information about MITK. \section MITKUserManualPageLevelWindow Levelwindow Once an image is loaded the levelwindow appears to the right hand side of the four window view. With this tool you can adjust the range of grey values displayed and the gradient between them. Moving the lower boundary up results in any pixels having a value lower than that boundary to be displayed as black. Lowering the upper boundary causes all pixels having a value higher than it to be displayed as white. The pixels with a value between the lower and upper boundary are displayed in different shades of grey. This way a smaller levelwindow results in higher contrasts while cutting of the information outside its range whereas a larger levelwindow displays more information at the cost of contrast and detail. You can pick the levelwindow with the mouse to move it up and down, while moving the mouse cursor to the left or right to change its size. Picking one of the boundaries with a left click allows you to change the size symmetrically. Holding CTRL and clicking a boundary adjusts only that value. \section MITKUserManualPageMemoryUsage System Load Indicator The System Load Indicator in the lower right hand corner of the screen gives information about the memory currently required by the MITK application. Keep in mind that image processing is a highly memory intensive task and monitor the indicator to avoid your system freezing while constantly swapping to the hard drive. \section MITKUserManualPageViews Views Each solution for a specific problem that is self contained is realized as a single view. Thus you can create a workflow for your problem by combining the capabilities of different views to suit your needs. One elegant way to do this is by combining views in \ref MITKUserManualPagePerspectives. By pressing and holding the left mouse button on a views tab you can move it around to suit your needs, even out of the application window. \section MITKUserManualPagePerspectives Perspectives The different tasks that arise in medical imaging need very different approaches. To acknowledge this circumstance MITK supplies a framework that can be build uppon by very different solutions to those tasks. These solutions are called perspectives, each of them works independently of others although they might be used in sequence to achieve the solution of more difficult problems. It is possible to switch between the perspectives using the "Window"->"Open Perspective" dialog. See \ref MITKUserManualPageMenu for more information about switching perspectives. */ diff --git a/Documentation/Doxygen/UserManual/images/Crosshair_Modes.png b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/Crosshair_Modes.png similarity index 100% rename from Documentation/Doxygen/UserManual/images/Crosshair_Modes.png rename to Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/Crosshair_Modes.png diff --git a/Documentation/Doxygen/UserManual/images/GUI.png b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/GUI.png similarity index 100% rename from Documentation/Doxygen/UserManual/images/GUI.png rename to Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/GUI.png diff --git a/Documentation/Doxygen/UserManual/images/GUI_Commented.png b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/GUI_Commented.png similarity index 100% rename from Documentation/Doxygen/UserManual/images/GUI_Commented.png rename to Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/GUI_Commented.png diff --git a/Documentation/Doxygen/UserManual/images/Top_Right_Corner_Menu.png b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/Top_Right_Corner_Menu.png similarity index 100% rename from Documentation/Doxygen/UserManual/images/Top_Right_Corner_Menu.png rename to Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/Top_Right_Corner_Menu.png diff --git a/Documentation/Doxygen/UserManual/images/Views_Choices.png b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/Views_Choices.png similarity index 100% rename from Documentation/Doxygen/UserManual/images/Views_Choices.png rename to Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/Views_Choices.png diff --git a/Documentation/Doxygen/UserManual/images/Window_Dropdown.png b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/Window_Dropdown.png similarity index 100% rename from Documentation/Doxygen/UserManual/images/Window_Dropdown.png rename to Plugins/org.mitk.gui.qt.ext/documentation/UserManual/images/Window_Dropdown.png