diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginGeneralManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginGeneralManualsList.dox index 1bab9b4031..4a288bf3e8 100644 --- a/Documentation/Doxygen/2-UserManual/MITKPluginGeneralManualsList.dox +++ b/Documentation/Doxygen/2-UserManual/MITKPluginGeneralManualsList.dox @@ -1,32 +1,33 @@ /** \page PluginListGeneralPage List of General Purpose Plugins \li \subpage org_mitk_views_basicimageprocessing \li \subpage org_mitk_views_datamanager \li \subpage org_mitk_views_properties \li \subpage org_mitk_editors_dicombrowser \li \subpage org_mitk_views_dicominspector \li \subpage org_mitk_views_imagecropper \li \subpage org_mitk_views_imagenavigator \li \subpage org_blueberry_views_logview \li \subpage org_mitk_views_matchpoint_algorithm_browser \li \subpage org_mitk_views_matchpoint_algorithm_control \li \subpage org_mitk_views_matchpoint_evaluator \li \subpage org_mitk_views_matchpoint_framereg \li \subpage org_mitk_views_matchpoint_manipulator \li \subpage org_mitk_views_matchpoint_mapper \li \subpage org_mitk_views_matchpoint_visualizer \li \subpage org_mitk_gui_qt_measurementtoolbox \li \subpage org_mitk_views_moviemaker \li \subpage org_mitk_views_multilabelsegmentation \li \subpage org_mitk_views_pointsetinteraction \li \subpage org_mitk_views_python \li \subpage org_mitk_views_remeshing \li \subpage org_mitk_views_screenshotmaker \li \subpage org_mitk_views_segmentation \li \subpage org_mitk_views_deformableclippingplane \li \subpage org_mitk_gui_qt_flow_segmentation + \li \subpage org_mitk_editors_stdmultiwidget \li \subpage org_mitk_views_viewnavigatorview \li \subpage org_mitk_views_volumevisualization */ diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox index a85370db75..e65e793f8a 100644 --- a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox +++ b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox @@ -1,71 +1,72 @@ /** \page PluginListPage MITK Plugin Manuals The plugins and bundles provide much of the extended functionality of MITK. Each encapsulates a solution to a problem and associated features. This way one can easily assemble the necessary capabilites for a workflow without adding a lot of bloat, by combining plugins as needed. \subpage PluginListGeneralPage \subpage PluginListSpecificPage */ diff --git a/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual.dox b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual.dox index 9918cc73ad..78e691f83f 100644 --- a/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual.dox +++ b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual.dox @@ -1,98 +1,72 @@ /** \page MITKWorkbenchManualPage The MITK Workbench \tableofcontents -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. +Welcome to the basic MITK user manual. This document gives a concise overview of the basic functions of MITK and instructions how to use them. \section MITKWorkbenchManualPage_UserInterface 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. \imageMacro{MITKUserManual_GUICommented.png,"The Common MITK Application Graphical User Interface",16.00} -\section MITKWorkbenchManualPage_FourWindowView Four Window View - -\subsection MITKWorkbenchManualPage_FourWindowView_Overview 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 axial 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 MITKWorkbenchManualPage_FourWindowView_Navigation 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 MITKWorkbenchManualPage_FourWindowView_Customizing Customizing - -By moving the cursor to the upper right corner of any window you can activate the window menu. It consists of three buttons. - -\imageMacro{MITKUserManual_CrosshairModes.png,"Crosshair",8.72} - -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. - -\imageMacro{MITKUserManual_ViewsChoices.png,"Layout Choices",5.19} - -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 MITKWorkbenchManualPage_Menu Menu \subsection MITKWorkbenchManualPage_Menu_File File -This dialog allows you to save, load and clear entire projects, this includes any nodes in the data manager. +This dialogue allows you to save, load and clear entire projects. This includes any nodes in the data manager. \subsection MITKWorkbenchManualPage_Menu_Edit Edit -This dialog supports undo and redo operations as well as the image navigator, which gives you sliders to navigate through the data quickly. +This dialogue supports undo and redo operations. \subsection MITKWorkbenchManualPage_Menu_Window Window -This dialog allows you to open a new window, change between perspectives and reset your current one to default settings. +This dialogue allows you to change between the \ref MITKWorkbenchManualPage_Perspectives and reset your current ones 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. +If you want to use certain \ref MITKWorkbenchManualPage_Views within a 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 view works with every perspective in a meaningful way. -The Preferences dialog allows you to adjust and save your custom settings. +The Preferences dialogue allows you to adjust and save your general and view-specific custom settings. -\imageMacro{MITKUserManual_WindowDropdown.png,"Preferences",4.89} +\imageMacro{MITKUserManual_WindowDropdown.png,"Window dropdown menu",4.89} \subsection MITKWorkbenchManualPage_Menu_Help Help -This dialog contains this help, the welcome screen and information about MITK. +This dialogue contains the help perspective containing the view-specific documentation, the welcome screen and information about MITK. -\section MITKWorkbenchManualPage_Levelwindow 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. +\section MITKWorkbenchManualPage_Perspectives Perspectives -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. +The different tasks that arise in medical imaging need very different approaches. To acknowledge this circumstance MITK supplies a framework that can be build upon 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. -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. +It is possible to switch between the perspectives using the "Window"->"Open Perspective" dialogue. Available default perspective are "Research", "Viewer" and "Visualization". +Various views can be added to each perspective to tailor the chosen perspective to your specific requirements. -With line edit fields below you can directly adjust the levelwindow. The upper field describes the center of the levelwindow, the bottom the span of the window around the center. By selecting one of fields and typing any number you can set these two parameters. +\section MITKWorkbenchManualPage_Views Views -\section MITKWorkbenchManualPage_SystemLoadIndicator System Load Indicator +Each solution for a specific problem is realized as a self contained view. Thus you can create a workflow for your problem by combining the capabilities of different views to suit your needs within a perspective. -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. +By pressing and holding the left mouse button on a view tab you can move it around to suit your needs, even out of the application window. -\section MITKWorkbenchManualPage_Views Views +\section MITKWorkbenchManualPage_SystemLoadIndicator System Load Indicator/Memory Usage -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 perspectives. +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. -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 MITKWorkbenchManualPage_DataManager Data Manager +The Data Manager is the central component of MITK to manage medical data like images, segmentation masks, registrations, surfaces, point sets, annotations and measurements. +For a detailed description of the Data Manager please be referred to the view documentation: \ref org_mitk_views_datamanager. -\section MITKWorkbenchManualPage_Perspectives Perspectives +\section MITKWorkbenchManualPage_ImageNavigator Image Navigator +Fast movement through the available data can be achieved by using the Image Navigator. By moving the sliders around you can scroll through the slides and timesteps. +For a detailed description of the Image Navigator please be referred to the Image Navigator view documentation: \ref org_mitk_views_imagenavigator. + +\section MITKWorkbenchManualPage_FourWindowView Standard Display -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. +The four window view of the standard display is the heart of the MITK image viewing. For a detailed description of the four window view and the levelwindow please be referred to the standard display view documentation: \ref org_mitk_editors_stdmultiwidget. -It is possible to switch between the perspectives using the "Window"->"Open Perspective" dialog. -See menu for more information about switching perspectives. */ diff --git a/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual_CrosshairModes.png b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual_CrosshairModes.png deleted file mode 100644 index 264b2fcf63..0000000000 Binary files a/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual_CrosshairModes.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual_GUI.png b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual_GUI.png deleted file mode 100644 index f20495216b..0000000000 Binary files a/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual_GUI.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual_GUICommented.png b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual_GUICommented.png index 6523f71664..538ed8540d 100644 Binary files a/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual_GUICommented.png and b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual_GUICommented.png differ diff --git a/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual_TopRightCornerMenu.png b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual_TopRightCornerMenu.png deleted file mode 100644 index 493bfef682..0000000000 Binary files a/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual_TopRightCornerMenu.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual_ViewsChoices.png b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual_ViewsChoices.png deleted file mode 100644 index c1b74ef1ec..0000000000 Binary files a/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual_ViewsChoices.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual_WindowDropdown.png b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual_WindowDropdown.png index 74e0c9cba8..60bfaba64a 100644 Binary files a/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual_WindowDropdown.png and b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual_WindowDropdown.png differ diff --git a/Plugins/org.mitk.gui.qt.stdmultiwidgeteditor/documentation/UserManual/QmitkStdmultiwidget.dox b/Plugins/org.mitk.gui.qt.stdmultiwidgeteditor/documentation/UserManual/QmitkStdmultiwidget.dox new file mode 100644 index 0000000000..5f7e3139e7 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.stdmultiwidgeteditor/documentation/UserManual/QmitkStdmultiwidget.dox @@ -0,0 +1,53 @@ +/** +\page org_mitk_editors_stdmultiwidget The Standard Display + +\tableofcontents + +\section org_mitk_editors_stdmultiwidget_F1Help General remark on F1 help +This is the help window of the standard display. To display the help windows of other plugins, press F1 when the plugin of interest is active (please make sure the tab of the plugin of interest is highlighted). +Alternatively, go to the Help menu and select Open Help Perspective. A help window opens from which you can select the documentation of the plugin of interest. + +\section org_mitk_editors_stdmultiwidget_FourWindowView Four Window View + +\subsection org_mitk_editors_stdmultiwidget_FourWindowView_Overview 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 axial 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, information about it is displayed at the bottom of the screen. + +\subsection org_mitk_editors_stdmultiwidget_FourWindowView_Navigation 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 org_mitk_editors_stdmultiwidget_FourWindowView_Customizing Customizing + +By moving the cursor to the upper right corner of any window you can activate the window menu. It consists of three buttons. + +\imageMacro{org_mitk_editors_stdmultiwidget_CrosshairModes.png,"Crosshair",8.72} + +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. + +\imageMacro{org_mitk_editors_stdmultiwidget_ViewsChoices.png,"Layout Choices",5.19} + +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 org_mitk_editors_stdmultiwidget_Levelwindow 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 off the information outside its range whereas a larger levelwindow displays more information with a higher detail level at the cost of contrast. + +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. + +With line edit fields below you can directly adjust the levelwindow. The upper field describes the center of the levelwindow, the bottom the span of the window around the center. By selecting one of fields and typing any number you can set these two parameters. + + +*/ diff --git a/Plugins/org.mitk.gui.qt.stdmultiwidgeteditor/documentation/UserManual/org_mitk_editors_stdmultiwidget_CrosshairModes.png b/Plugins/org.mitk.gui.qt.stdmultiwidgeteditor/documentation/UserManual/org_mitk_editors_stdmultiwidget_CrosshairModes.png new file mode 100644 index 0000000000..17db28ee43 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.stdmultiwidgeteditor/documentation/UserManual/org_mitk_editors_stdmultiwidget_CrosshairModes.png differ diff --git a/Plugins/org.mitk.gui.qt.stdmultiwidgeteditor/documentation/UserManual/org_mitk_editors_stdmultiwidget_ViewsChoices.png b/Plugins/org.mitk.gui.qt.stdmultiwidgeteditor/documentation/UserManual/org_mitk_editors_stdmultiwidget_ViewsChoices.png new file mode 100644 index 0000000000..3fb71d353b Binary files /dev/null and b/Plugins/org.mitk.gui.qt.stdmultiwidgeteditor/documentation/UserManual/org_mitk_editors_stdmultiwidget_ViewsChoices.png differ