diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox index 90d1400671..679f5b479f 100644 --- a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox +++ b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox @@ -1,81 +1,81 @@ /** \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 PluginListGeneralPage -\subpage PluginListSpecificPage +\subpage PluginListSpecificPage */ \ No newline at end of file diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginSpecificManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginSpecificManualsList.dox index a65603b45b..8a15972540 100644 --- a/Documentation/Doxygen/2-UserManual/MITKPluginSpecificManualsList.dox +++ b/Documentation/Doxygen/2-UserManual/MITKPluginSpecificManualsList.dox @@ -1,42 +1,42 @@ /** -\page PluginListSpecificPage List of Application-specific Plugins +\page PluginListSpecificPage List of Application-specific Plugins \li \subpage org_mitk_gui_qt_aicpregistration \li \subpage org_mitk_gui_qt_cest \li \subpage org_mitk_gui_qt_classificationsegmentation \li \subpage org_mitk_views_cmdlinemodules \li \subpage org_mitk_gui_qt_pharmacokinetics_concentration_mri \li \subpage org_mitk_gui_qt_pharmacokinetics_mri \li \subpage org_mitk_gui_qt_pharmacokinetics_pet \li \subpage org_mitk_gui_qt_eventrecorder \li \subpage org_mitk_gui_qt_examples \li \subpage org_mitk_gui_qt_geometrytools \li \subpage org_mitk_gui_qt_igtexample \li \subpage org_mitk_gui_qt_igtlplugin \li \subpage org_mitk_gui_qt_igttracking \li \subpage org_mitk_gui_qt_igttrackingsemiautomaticmeasurement \li \subpage org_mitk_gui_qt_lasercontrol \li \subpage org_mitk_gui_qt_fit_demo \li \subpage org_mitk_gui_qt_fit_genericfitting \li \subpage org_mitk_gui_qt_fit_inspector \li \subpage org_mitkexamplesopencv \li \subpage org_mitk_gui_qt_overlaymanager \li \subpage org_mitk_gui_qt_mitkphenotyping \li \subpage org_mitk_gui_qt_photoacoustics_pausmotioncompensation \li \subpage org_mitk_example_gui_pcaexample \li \subpage org_mitk_gui_qt_pharmacokinetics_curvedescriptor \li \subpage org_mitk_gui_qt_photoacoustics_imageprocessing \li \subpage org_mitk_gui_qt_pharmacokinetics_simulation \li \subpage org_mitk_gui_qt_pointsetinteractionmultispectrum \li \subpage org_mitk_gui_qt_renderwindowmanager \li \subpage org_mitk_gui_qt_photoacoustics_spectralunmixing \li \subpage org_mitk_gui_qt_spectrocamrecorder \li \subpage org_surfacematerialeditor \li \subpage org_blueberry_ui_qt_objectinspector \li \subpage org_toftutorial \li \subpage org_mitk_gui_qt_ultrasound \li \subpage org_mitk_gui_qt_igt_app_echotrack \li \subpage org_mitk_gui_qt_xnat */ \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.basicimageprocessing/documentation/UserManual/QmitkBasicImageProcessing.dox b/Plugins/org.mitk.gui.qt.basicimageprocessing/documentation/UserManual/QmitkBasicImageProcessing.dox index ec66e4cca9..1c516ad9c0 100644 --- a/Plugins/org.mitk.gui.qt.basicimageprocessing/documentation/UserManual/QmitkBasicImageProcessing.dox +++ b/Plugins/org.mitk.gui.qt.basicimageprocessing/documentation/UserManual/QmitkBasicImageProcessing.dox @@ -1,126 +1,126 @@ /** -\page org_mitk_views_basicimageprocessing Basic Image Processing +\page org_mitk_views_basicimageprocessing Basic Image Processing \imageMacro{QmitkBasicImageProcessing_ImageProcessing_48.png,"Icon of the Basic Image Processing Plugin",2.00} \tableofcontents \section QmitkBasicImageProcessingUserManualSummary Summary This view provides an easy interface to fundamental image preprocessing and enhancement filters. -It offers filter operations on 3D and 4D images in the areas of noise suppression, morphological operations, edge detection and image arithmetics, +It offers filter operations on 3D and 4D images in the areas of noise suppression, morphological operations, edge detection and image arithmetics, as well as image inversion and downsampling. Please see \ref QmitkBasicImageProcessingUserManualOverview for more detailed information on usage and supported filters. If you encounter problems using the view, please have a look at the \ref QmitkBasicImageProcessingUserManualTrouble page. \section QmitkBasicImageProcessingUserManualOverview Overview This view provides an easy interface to fundamental image preprocessing and image enhancement filters. It offers a variety of filter operations in the areas of noise suppression, morphological operations, edge detection and image arithmetics. Currently the view can be used with all 3D and 4D image types loadable by MITK. 2D image support will be added in the future. -All filters are encapsulated from the Insight Segmentation and Registration Toolkit (ITK, www.itk.org). +All filters are encapsulated from the Insight Segmentation and Registration Toolkit (ITK, www.itk.org). \imageMacro{QmitkBasicImageProcessing_BIP_Overview.png,"MITK with the Basic Image Processing view",16.00} This document will tell you how to use this view, but it is assumed that you already know how to use MITK in general. \section QmitkBasicImageProcessingUserManualFilters Filters This section will not describe the fundamental functioning of the single filters in detail, though. -If you want to know more about a single filter, please have a look at http://www.itk.org/Doxygen316/html/classes.html +If you want to know more about a single filter, please have a look at http://www.itk.org/Doxygen316/html/classes.html or in any good digital image processing book. For total denoising filter, please see Tony F. Chan et al., "The digital TV filter and nonlinear denoising". Available filters are:

\a Single image operations

- +

\a Dual image operations

- \section QmitkBasicImageProcessingUserManualUsage Usage All you have to do to use a filter is to: A busy cursor appeares; when it vanishes, the operation is completed. Your filtered image is displayed and selected for further processing. -(If the checkbox "Hide original image" is not selected, you will maybe not see the filter result imideately, +(If the checkbox "Hide original image" is not selected, you will maybe not see the filter result imideately, because your filtered image is possibly hidden by the original.) For two image operations, please make sure that the correct second image is selected in the drop down menu, and the image order is correct. For sure, image order only plays a role for image subtraction and division. These are conducted (Image1 - Image2) or (Image1 / Image2), respectively. Please Note: When you select a 4D image, you can select the time step for the filter to work on via the time slider at the top of the GUI. The 3D image at this time step is extracted and processed. The result will also be a 3D image. This means, a true 4D filtering is not yet supported. \section QmitkBasicImageProcessingUserManualTrouble Troubleshooting I get an error when using a filter on a 2D image.
2D images are not yet supported... I use a filter on a 4D image, and the output is 3D.
When you select a 4D image, you can select the time step for the filter to work on via the time slider at the top of the GUI. The 3D image at this time step is extracted and processed. The result will also be a 3D image. This means, a true 4D filtering is not supported by now. A filter crashes during execution.
Maybe your image is too large. Some filter operations, like derivatives, take a lot of memory. -Try downsampling your image first. +Try downsampling your image first. All other problems.
Please report to the MITK mailing list. See http://www.mitk.org/wiki/Mailinglist on how to do this. */ 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 e188603c98..4c320da6eb 100644 --- a/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual.dox +++ b/Plugins/org.mitk.gui.qt.ext/documentation/UserManual/MITKUserManual.dox @@ -1,111 +1,111 @@ /** \page MITKWorkbenchManualPage The MITK Workbench -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 tries to give a concise overview of the basic functions of MITK and be an comprehensible guide on using them.

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} The datamanager and the \ref MITKUserManualPagePerspectives have their own help sections. This document explains the use of: - The \ref Four Window View - The \ref Menu - The \ref MITKUserManualPageLevelWindow - The \ref MITKUserManualPageMemoryUsage - The \ref MITKUserManualPageViews

Four Window View

- +

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.

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.

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. +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. - +

Menu

File

-This dialog allows you to save, load and clear entire projects, this includes any nodes in the data manager. +This dialog allows you to save, load and clear entire projects, this includes any nodes in the data manager.

Edit

This dialog supports undo and redo operations as well as the image navigator, which gives you sliders to navigate through the data quickly.

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. \imageMacro{MITKUserManual_WindowDropdown.png,"Preferences",4.89}

Help

This dialog contains this help, the welcome screen and information about MITK.

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. 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.

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.

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 perspectives. -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. +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.

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 menu for more information about switching perspectives. */ diff --git a/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteraction.dox b/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteraction.dox index f8641177dd..224f18ebbb 100644 --- a/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteraction.dox +++ b/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteraction.dox @@ -1,47 +1,47 @@ /** -\page org_mitk_views_pointsetinteraction Point Set Interaction +\page org_mitk_views_pointsetinteraction Point Set Interaction \imageMacro{pointset_interaction.svg,"Icon of the Point Set Interaction View",2.00} Available sections: - \ref QmitkPointSetInteractionUserManualOverview - \ref QmitkPointSetInteractionUserManualDetails \section QmitkPointSetInteractionUserManualOverview Overview This view allows you to define multiple sets of points, to fill them with points and to save them in so called PointSets. \imageMacro{QmitkPointSetInteraction_Screenshot.png,"MITK with the QmitkPointSetInteraction view",16.00} This document will tell you how to use this view, but it is assumed that you already know how to navigate through the slices of an image using the four window view. Please read the application manual for more information. \section QmitkPointSetInteractionUserManualDetails Details First of all you have to select a PointSet to use this view. Therefore, you have to select the point set in the data manager. If there are currently no point sets in the data tree, you have to first add a new point set to the data tree. This is done by clicking the "Add pointset..." button. \imageMacro{QmitkPointSetInteraction_AddPointSet.png,"The Add pointset... dialog",8.64} In the pop-up dialog, you have to specify a name for the new point set. This is also the node for the new data tree item. \imageMacro{QmitkPointSetInteraction_CurrentPointSetArea.png,"The Current pointset area",6.52} The "Current pointset" area contains a list of points. Within this area, all points for the current point set node are listed. To set points you have to toggle the "Set Points" button, the leftmost of the four buttons on the bottom of the view. Points can be defined by performing a left mouse button click while holding the "Shift"-key pressed in the four window view. To erase all points from the list press the next button. The user is prompted to confirm the decision. If you want to delete only a single point, left click on it in the list and then press delete on your keyboard. With the third button, a previously saved point set can be loaded and all of its points are shown in the list and the four window view. The user is prompted to select the file to be loaded. The file extension is ".mps". On the right of this button is the save button. With this function the entire point set can be saved to the harddrive. The user is prompted to select a filename. Pointsets are saved in XML fileformat but have to have a ".mps" file extension. You can select points in the render window, if the "Set Points" button is toggled, with a left mouse button click on them. If you keep the mouse button pressed, you can move the points by moving the mouse and then releasing the mouse button. With the delete key you can remove the selected points. */ \ No newline at end of file