diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox index 03de23a0ea..1728b2a49d 100644 --- a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox +++ b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox @@ -1,80 +1,80 @@ /** \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. \paragraph PluginListPageEndUserPluginList List of General Purpose Plugins \li \subpage org_mitk_views_basicimageprocessing - \li \subpage org_mitk_views_cmdlinemodules \li \subpage org_mitk_gui_qt_chartExample \li \subpage org_mitk_views_datamanager \li \subpage org_mitk_gui_qt_dicom \li \subpage org_mitk_gui_qt_dicominspector \li \subpage org_mitk_gui_qt_imagecropper \li \subpage org_mitk_views_imagenavigator \li \subpage org_blueberry_ui_qt_log \li \subpage org_mitk_gui_qt_measurementtoolbox \li \subpage org_mitk_gui_qt_moviemaker \li \subpage org_mitk_views_screenshotmaker \li \subpage org_mitk_views_pointsetinteraction - \li \subpage org_mitk_gui_qt_pointsetinteractionmultispectrum \li \subpage org_mitk_gui_qt_python \li \subpage org_mitk_gui_qt_remeshing \li \subpage org_mitk_views_segmentation \li \subpage org_mitk_views_multilabelsegmentation \li \subpage org_mitk_gui_qt_viewnavigator \paragraph PluginListPageApplicationPluginList 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_eventrecorder \li \subpage org_mitk_gui_qt_examples \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_mitk_gui_qt_geometrytools \li \subpage org_mitk_gui_qt_igt_app_echotrack \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_matchpoint_algorithm_batch \li \subpage org_mitk_gui_qt_matchpoint_algorithm_browser \li \subpage org_mitk_gui_qt_matchpoint_algorithm_control \li \subpage org_mitk_gui_qt_matchpoint_evaluator \li \subpage org_mitk_gui_qt_matchpoint_framereg \li \subpage org_mitk_gui_qt_matchpoint_manipulator \li \subpage org_mitk_gui_qt_matchpoint_mapper \li \subpage org_mitk_gui_qt_matchpoint_visualizer \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_mri \li \subpage org_mitk_gui_qt_pharmacokinetics_pet \li \subpage org_mitk_gui_qt_pharmacokinetics_concentration_mri \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_photoacoustics_spectralunmixing + \li \subpage org_mitk_gui_qt_pointsetinteractionmultispectrum \li \subpage org_mitk_gui_qt_renderwindowmanager \li \subpage org_mitk_gui_qt_spectrocamrecorder \li \subpage org_surfacematerialeditor \li \subpage org_toftutorial \li \subpage org_mitk_gui_qt_ultrasound \li \subpage org_mitk_views_volumevisualization \li \subpage org_mitk_gui_qt_xnat \li \subpage org_mitkexamplesopencv \li \subpage org_blueberry_ui_qt_objectinspector */ \ No newline at end of file diff --git a/Plugins/org.blueberry.ui.qt.log/documentation/UserManual/blueberrylogview.dox b/Plugins/org.blueberry.ui.qt.log/documentation/UserManual/blueberrylogview.dox index 1487cb3947..cf91138549 100644 --- a/Plugins/org.blueberry.ui.qt.log/documentation/UserManual/blueberrylogview.dox +++ b/Plugins/org.blueberry.ui.qt.log/documentation/UserManual/blueberrylogview.dox @@ -1,16 +1,16 @@ /** -\page org_blueberry_ui_qt_log The Logging Plugin +\page org_blueberry_ui_qt_log Logging Plugin \imageMacro{logging.svg,"Icon of the Logging Plugin",2.00} This plug-in records all logging output of events and progress as specified in the source code with time of occurence, level of importance (Info, Warning, Error, Fatal, Debug), the message given and where it happens. The logging starts once the plug-is started. A screenshot of the provided Logging view is shown next. \imageMacro{LogView.png,"Screenshot of the Logging Module",16.00} There are different features available in the view. The filter text field allows for searching all log events containing a certain substring. Using the button "Copy to clipboard" on the bottom right you can copy the current content of the logging view to your clipboard. This enables you to insert the logging information to any text processing application. You can also show more information on every logging message by activating the two checkboxes. In the simple view, leaving both checkboxes unchecked, you'll see logging messages and logging levels. A brief description of the logging levels can be found in the \ref LoggingPage "logging concept documentation". The checkbox "Category" adds a column for the category. The checkbox "Show Advanced Field" shows method, filename and linenumber where the logging message was emitted as well as the running time of the application. The next figure shows all information which can be shown in the Logging Module. \imageMacro{LogViewExplain.png,"Details on the Vizualized Logging Information",16.00} */ 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 bff25497fa..ec66e4cca9 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 The Basic Image Processing Plugin +\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, 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). \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 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, 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. 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.chartExample/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.chartExample/documentation/UserManual/Manual.dox index 3ffaadb6c7..204d43d2c3 100644 --- a/Plugins/org.mitk.gui.qt.chartExample/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.chartExample/documentation/UserManual/Manual.dox @@ -1,17 +1,17 @@ /** -\page org_mitk_gui_qt_chartExample The ChartExample +\page org_mitk_gui_qt_chartExample ChartExample \imageMacro{icon.png,"Icon of ChartExample",2.00} \tableofcontents \section org_mitk_gui_qt_chartExampleOverview Overview Describe the features of your awesome plugin here */ diff --git a/Plugins/org.mitk.gui.qt.cmdlinemodules/documentation/UserManual/cmdlinemodules.dox b/Plugins/org.mitk.gui.qt.cmdlinemodules/documentation/UserManual/cmdlinemodules.dox index 9e485fd10f..e320592ac6 100644 --- a/Plugins/org.mitk.gui.qt.cmdlinemodules/documentation/UserManual/cmdlinemodules.dox +++ b/Plugins/org.mitk.gui.qt.cmdlinemodules/documentation/UserManual/cmdlinemodules.dox @@ -1,172 +1,172 @@ /** -\page org_mitk_views_cmdlinemodules The Command Line Modules View +\page org_mitk_views_cmdlinemodules Command Line Modules View \imageMacro{cmdlinemodules_Icon.png,"Icon of the Command Line Modules View",2.00} \tableofcontents \section CLIPrefix Contribution This plugin was developed at the Centre For Medical Image Computing (CMIC), part of University College London (UCL) and contributed back to the MITK community with thanks. \section CLIIntroduction Introduction This view provides the facility to run third party command line programs, and load the data back into the DataManager for immediate visualisation. All that is required is that the command line application can be called with an argument of --xml and respond with a valid XML description of the necessary parameters, and currently, that if the program requires images, they must be NifTI images. This view can then generate a Graphical User Interface (GUI) dynamically from the XML to enable the user to interact with the command line application. This provides an easy to use, and potentially very flexible way to integrate almost any third party, medical imaging, command line application. As a high level introduction, this view performs the following steps: \li The view searches for available programs to run, and for each valid module, stores the XML document describing the interface, and populates a searchable list of available programs. \li When a program is selected, the GUI is generated. \li The user can then set the necessary parameters and run the program. \li Multiple programs can be launched in succession and run simultaneously, and where available on the host platform, the user can pause, resume or cancel running jobs and see console output for each job. As a consequence of the very flexible nature of this plugin, these instructions can only describe how to launch command line modules in a general sense. The examples shown have been constructed by downloading the latest version (subversion commit 329) of the NiftyReg package, available here, and described further here. NiftyReg provides valid XML descriptors to enable the integration of the NiftyReg affine (RegAladin) and and non-rigid (RegF3D) image registration algorithms, as well as utility programs to resample an image, and calculate a Jacobian image. These same XML descriptors work within Slicer and MITK based applications. \section CLIPreferences Preferences The first time that the Command Line Modules View is launched, it is advisable to set the user preferences for the view. Please refer to Figure 1. \imageMacro{cmdlinemodules_Preferences.png,"Figure 1. The Command Line Modules Preferences Page",16.00} Each of these preferences is now explained in some detail. \li show debug output: If checked will output more messages to the console for debugging purposes. \li XML validation mode: The user may select a different mode for XML validation. If this is changed, the application will need to be restarted. There are 3 modes available. If the user selects "strict" mode, the XML schema produced by the command line application must exactly conform to this definition. For "none", there will be no validation. For "weak" validation, the application will report errors, but try to carry on and load as many modules as possible. The XML validation errors are available as tool-tips on the tab widget when the module is launched. Many third party modules included with Slicer currently have incorrect XML (typically, mis-ordered XML tags), and so the "weak" or "none" mode may assist in loading them. By default the "weak" mode is chosen so that only valid modules are loaded. \li max concurrent processes: Sets the maximum number of concurrent jobs that can be run via this interface. The default is 4. When the maximum number is reached, the green "Run" button is disabled until a job finishes. The next 7 preferences are to control where the view will search for valid command line programs. By default these are off as the searching process can take a long time and slow down the startup time of the GUI. The options provided are: \li scan home directory: Scan the users home directory. (See QDir::homePath().) \li scan home directory/cli-modules: Scans the sub-directory called cli-modules under the users home directory. \li scan current directory: Scan the current working directory. (See QDir::homePath().) \li scan current directory/cli-modules: Scans the sub-directory called cli-modules under the current working directory. \li scan installation directory: This is the directory where the actual application is stored. \li scan installation directory/cli-modules: Scans the sub-directory called cli-modules under the application installation directory. \li scan CTK_MODULE_LOAD_PATH: Scans the directory or list of directories defined by the environment variable CTK_MODULE_LOAD_PATH. A list is colon separated on Linux/Mac, and semi-colon separated on Windows. In most cases, it is suggested that the user will leave these options unchecked, as the user can also specify custom directories, and even cherry-pick specific command line programs to load. Figure 2 shows a selection box that enables the user to specify custom directories to scan, and Figure 3. shows a selection box that enables the user to select specific modules. Picking specific directories, and specific executables will most likely make the application quicker to launch. \imageMacro{cmdlinemodules_PreferencesAdditionalDirectories.png,"Figure 2. The User can specify specific directories to scan".",7.90} \imageMacro{cmdlinemodules_PreferencesAdditionalModules.png,"Figure 3. The User can specify specific command line programs to load".",7.92} These directory and file selection boxes enable directories or files to be added, removed and updated in a similar fashion. The user must make sure that the list of files selected in the "additional modules" section are not already contained within the directories specified in the "additional module directories" section. In addition, the preferences page provides: \li temporary directory: Images stored in the DataManager are first written to a temporary folder as Nifti images before being passed to each command line program. This temporary directory will default to a platform specific temporary folder, but the user may select their preferred choice of temporary workspace. \section CLIUsage Usage When the view is launched, a simple interface is presented, as shown in Figure 4. \imageMacro{cmdlinemodules_Initial.png,"Figure 4. The initial interface\, with no command line programs available.",8.66} In this example, all the above check-box preferences were off, and the "additional module directories" was empty, and the "additional modules" list was empty so no command line applications were found. The "Search" box displays zero entries, and there is nothing to search. If the available search paths contain programs that are compatible (i.e. runnable) with this view, the name of the programs are displayed in the "Search" box in a nested menu, shown in Figure 5. \imageMacro{cmdlinemodules_WithPrograms.png,"Figure 5. When valid paths are set\, and programs are discovered\, the menu is recalculated to show available programs.",10.54} When a program is selected, the relevant interface is displayed, by default as collapsed group boxes to save space. Each section can be individually expanded if necessary to see the parameters. \imageMacro{cmdlinemodules_NiftyReg.png,"Figure 6. An example program\, showing parameters for NiftyReg's program RegAladin.",10.24} In this example, the parameters are displayed for NiftyReg produced at UCL, and more specifically for the affine registration program called RegAladin. The interface can contain a wide variety of controls. If a parameter for a command line program is an input image, then the widget displayed is linked to the DataManager, so that as new images are loaded, the correct image can be easily selected from the combo box. At this stage, multiple tabs can be opened, with one tab for each command line program. Figure 7 shows 2 tabs, for the RegAladin and RegF3D programs. \imageMacro{cmdlinemodules_F3D.png,"Figure 7. Multiple tabs can be opened\, one for each command line program.",10.24} The main view provides some simple controls: \li Green arrow: Launch (run) the command line executable of the currently selected tab. \li Yellow undo arrow: Resets the GUI controls of the currently selected tab to default values, if and only if the original XML specified a default value. At this stage, nothing has been launched. When the user hits the green arrow button, a job is launched. Each running job is shown as a new progress reporting widget under the main tabbed widget, as shown in Figure 8. \imageMacro{cmdlinemodules_NiftyRegRunning2.png,"Figure 8. Multiple programs can be run\, each with individual controls and console output.",10.24} The controls for each running job are: \li Blue pause button: If supported on the host platform, this button will be enabled and can be toggled off (pause) or on (resume). \li Red square: If supported on the host platform, this button will kill the command line program. \li Black cross: Will remove the progress reporting widget from the GUI. When the user hits the green arrow in the main view: \li The currently selected tab is designated the "current" job, and contains the "current" set of parameters. \li A new progress reporting widget is created. \li The current parameters are copied to the progress reporting widget. In Figure 8. a parameters section is visible, and by default is collapsed, as they are simply for referring back to. \li All the output for the command line program is shown in the console widget, with a separate console for each job. \li Each new progress reporting widget is simply stacked vertically (newest is top-most), and it is up to the user to delete them when they are finished. It is easy to run multiple jobs. The green button simply launches the job corresponding to the current tab repeatedly. It is up to the user to make sure that any output file names are changed between successive invocations of the same command line module to avoid overwritting output data. In addition, each set of parameters contains an "About" section containing details of the contributors, the licence and acknowledgements and also a "Help" section containing a description and a link to any on-line documentation. These documentation features are provided by the developers of the third party plugin, and not by the host program. If information is missing, the user must contact the third party developers. \section CLITechnicalNotes Technical Notes From a technical perspective, the Command Line Modules View is a simple view, harnessing the power of the CTK command line modules framework. For technical information see: \li The doxygen generated manual page. \li The wiki page. and obviously the CTK code base. */ diff --git a/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox b/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox index 08e636a260..d06d0340e4 100644 --- a/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox +++ b/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox @@ -1,109 +1,109 @@ /** -\page org_mitk_views_datamanager The DataManager +\page org_mitk_views_datamanager DataManager \imageMacro{data-manager.svg,"Icon of the Data Manager",2.00} \tableofcontents \section QmitkDataManagerIntroduction Introduction The Datamanager is the central componenent to manage medical data like images, surfaces, etc.. After loading one or more data into the Datamanager the data are shown in the four-view window, the so called Standard View. The user can now start working on the data by just clicking into the standard view or by using the MITK-modules such as "Segmentation" or "Basic Image Processing". \imageMacro{QmitkDatamanager_Overview.png,"How MITK looks when started",16.00} \section QmitkDataManagerLoading Loading Data There are three ways of loading data into the Datamanager as so called Data-Elements. The user can just drag and drop data into the Datamanager or directly into one of the four parts of the Standard View. He can as well use the Open-Button in the right upper corner. Or he can use the standard "File->Open"-Dialog on the top. A lot of file-formats can be loaded into MITK, for example The user can also load a series of 2D images (e.g. image001.png, image002.png ...) to a MITK 3D volume. To do this, just drag and drop one of those 2D data files into the Datamanager by holding the ALT key. After loading one or more data into the Datamanager they appear as Data-Elements in a sorted list inside the Datamanager. Data-Elements can also be sorted hierarchically as a parent-child-relation. For example after using the Segmentation-Module on Data-Element1 the result is created as Data-Element2, which is a child of Data-Element1 (see Screenshot1). The order can be changed by drag and drop. \imageMacro{QmitkDatamanager_ParentChild.png,"Screenshot1",9.61} The listed Data-Elements are shown in the standard view. Here the user can scale or rotate the medical objects or he can change the cutting planes of the object by just using the mouse inside this view. \section QmitkDataManagerSaving Saving Data There are two ways of saving data from the Datamanger. The user can either save the whole project with all Data-Elements by clicking on "File"->"Save Project" or he can save single Data-Elements by right-clicking->"Save", directly on a Data-Element. When saving the whole project, the sorting of Data-Elements is saved as well. By contrast the sorting is lost, when saving a single Data-Element. \section QmitkDataManagerProperties Working with the Datamanager \subsection QmitkDataManagerPropertiesList List of Data-Elements The Data-Elements are listed in the Datamanager. As described above the elements can be sorted hierarchically as a parent-child-relation. For example after using the Segmentation-Module on Data-Element1 the result is created as Data-Element2, which is a child of Data-Element1 (see Screenshot1). By drag and drop the sorting of Data-Elements and their hierarchical relation can be changed. \subsection QmitkDataManagerPropertiesVisibility Visibility of Data-Elements By default all loaded Data-Elements are visible in the standard view. The visibility can be changed by right-clicking on the Data-Element and then choosing "Toogle visibility". The box in front of the Data-Element in the Datamanager shows the visibility. A green-filled box means a visible Data-Element, an empty box means an invisible Data-Element (see Screenshot1). \subsection QmitkDataManagerPropertiesRepresentation Representation of Data-Elements There are different types of representations how to show the Data-Element inside the standard view. By right-clicking on the Data-Element all options are listed (see Screenshot2 and Screenshot 3). \imageMacro{QmitkDatamanager_ImageProperties.png,"Screenshot2: Properties for images",10.56} \imageMacro{QmitkDatamanager_SurfaceProperties.png,"Screenshot3: Properties for surfaces",11.01} \subsection QmitkDataManagerPropertiesPreferences Preferences For the datamanager there are already some default hotkeys like the del-key for deleting a Data-Element. The whole list is seen in Screenshot4. From here the Hotkeys can also be changed. The preference page is found in "Window"->"Preferences". \imageMacro{QmitkDatamanager_Preferences.png,"Screenshot4",16.00} \section QmitkDataManagerPropertyList Property List The Property List displays all the properties the currently selected Data-Element has. Which properties these are depends on the Data-Element. Examples are opacity, shader, visibility. These properties can be changed by clicking on the appropriate field in the "value" column. \imageMacro{QmitkDatamanager_PropertyList.png,"Screenshot5: Property List",7.85} */ diff --git a/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicom.dox b/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicom.dox index 136c56e93d..7e8e526781 100644 --- a/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicom.dox +++ b/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicom.dox @@ -1,118 +1,118 @@ /** -\page org_mitk_gui_qt_dicom The Dicom Plugin +\page org_mitk_gui_qt_dicom Dicom Plugin \imageMacro{dicom.svg,"Icon of the DICOM Plugin",2.00} \note This article requires a basic knowledge of the DICOM Standard. \tableofcontents \section org_mitk_gui_qt_dicomOverview Overview The DICOM editor is an experimental editor which allows for loading of DICOM images as well as server communication. It features a highly experimental query/retrieve (you need to configure your PACS correspondingly) as well as a DICOM browser. The DICOM browser allows you to navigate the DICOM folder/cd depending on its metadata (patient/study/series) and import selected series for viewing in your MITK based application. It also allows you to store your dicom data in an internal database so you can easily access often used dicom images. It is based on the commonTK (CTK) DICOM funcionality. \section org_mitk_gui_qt_dicomDataHandling Data handling \imageMacro{QmitkDicom_PluginControls.png,"The dicom Plugin controls",7.37} In the image above you see the start page of the dicom plugin. On top of the start page you see four buttons. The Local Storage, the Import CD, the Import Folder and the Query Retrieve button. If you press one of these buttons, the dicom plugin will switch to your local dicom image storage or will start importing dicom images from CD or a folder on your hard drive or it will open the query retrieve screen. \subsection org_mitk_gui_qt_dicomStorage Data storage \imageMacro{QmitkDicom_PluginExtended.png,"The DICOM data storage",16.00} If you open the dicom plugin the dicom data storage will be displayed. You are able to see all your stored dicom image data. You can browse your data by clicking on the left arrow beside the name of your data. There are three levels available. The first level is the patient level where you can see the patient data. On the second level you can see the dicom studies for the patient. on the third level you can see all available series refering to it's study. You can delete the data by selecting it and pressing the delete button. Be careful if you have selected a patient or a study all refering data be deleted. So if you delete a patient the patient and all studies and series refered to the patient will be deleted. If you delete a study all series of the study will be deleted. If you want to view the dicom data you have to select a series and click on the View button. The data will appear in the DataManager and will be dispayed. \imageMacro{QmitkDicom_DisplayDataManager.png,"Viewed image",16.00} \subsection org_mitk_gui_qt_dicomImport Data import \imageMacro{QmitkDicom_ImportDialog.png,"The import dialog checked",9.53} There are two diffrent ways to import DICOM data. The First one is to directly imort it into your DICOM data storage. To achieve this you should toggle the checkbox 'Copy on import'. The second approach is, to have a look at the data first before importing it. To do that you simply don't check 'Copy on import'. This will leed you to the leed you to the 'External Dicom Data' screen which provides you a preview of the data containing in youre choosen folder. You can import the data here by selecting it and pressing the 'Download' button. It is also possible to view DICOM series directly in Mitk by selecting it here and pressing the 'View' button. \section org_mitk_gui_qt_dicomQueryRetrieve Query/Retrieve \warning This plugin is experimental and not all of the described features behave as expected. \note The query retrieve plugin only works if the PACS you are calling knows your machine settings. There are also issues when you are running a firewall. The query retrieve workflow allows you to get DICOM data from a server. \imageMacro{QmitkDicom_QueryRetrieve.png,"The query retrieve screen",16.00} \subsection org_mitk_gui_qt_dicomQuery Query \imageMacro{QmitkDicom_Nodes.png,"The DICOM network configuration",11.26} By performing a DICOM query you will ask a server for it's DICOM data. This requires to setup the DICOM network configuration of your system and the server. By clicking on 'Add Server' a new plain server field will appear. Now you can give it a name of your choice. Fill the servers "DICOM name" the AETitle. Type in it's url, it's port and the specific DICOM protocoll you want to use for image transfer. \note I recommend not to use CGET because most of the PACS systems (Image Servers) don't support that protocoll. You can configure the DICOM network configuration of your machine by editing the 'Calling AETiltle', the 'Storage AETitle' and The 'Storage Port' text fields. But normaly you don't have to change your configuration. \imageMacro{QmitkDicom_FilterWidget.png,"The DICOM search options",3.66} After you have finished your network configuration and before you start the query you should use the 'Search Options' to specify your query. Otherwise all data on the server will be queried and you will have to wait for a long time. You can specify your query by searching for a specific patient name or a study or a serie or a specific DICOM object by it's id. You are allowed to include or exclude DICOM modalities from your query and you can specify a specific time in which the DICOM images you are searching fo might been captured. When you finished that you can click the query button and the queried DICOM data will appear. \subsection org_mitk_gui_qt_dicomRetrieve Retrieve \imageMacro{QmitkDicom_Retrieve.png,"The queried DICOM data.",15.22} After the query you are able to select the queried data and click the 'Retrieve' button. This will store the queried DICOM data into your DICOM storage. Click on the 'Local Storage' button and work with your new data. */ diff --git a/Plugins/org.mitk.gui.qt.dicominspector/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.dicominspector/documentation/UserManual/Manual.dox index f45e70d5e1..36aa96489c 100644 --- a/Plugins/org.mitk.gui.qt.dicominspector/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.dicominspector/documentation/UserManual/Manual.dox @@ -1,12 +1,12 @@ /** -\page org_mitk_gui_qt_dicominspector The DICOM Inspector +\page org_mitk_gui_qt_dicominspector DICOM Inspector \imageMacro{ "inspector.png", "Icon of DICOM Inspector", 2} This is a simple view that displays all DICOM properties of the data of the currently selected node. DICOM properties are all properties that have a property name starting with "DICOM". The plugin will show the dicom values corresponding to the currently selected time point and z slice. E.G. the value of "acquesition time" will change with changing the time step of 3d+t image or the value of "slice position" will change with changing the current z slice of the image. */ diff --git a/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropper.dox b/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropper.dox index bbf0b99ee3..aeec51236c 100644 --- a/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropper.dox +++ b/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropper.dox @@ -1,37 +1,37 @@ /** -\page org_mitk_gui_qt_imagecropper The Image Cropper Plugin +\page org_mitk_gui_qt_imagecropper Image Cropper \imageMacro{crop.svg,"Icon of the Image Cropper Plugin.",20} \tableofcontents \section org_mitk_gui_qt_imagecropperUsage Usage The Image Cropper Plugin allows to crop subvolumes out of your original image volume by defining a cubic bounding box. This box can be placed at an arbitrary position in the volume and can be easily adjusted by using the handles on each of the faces. Touching the handles changes the size of the box whereas touching the box itself changes its position. As soon as the bounding box is placed at the desired position, pressing the button 'Crop' creates a new image assigned to the original image as child node containing only the selected subvolume. The size of the subvolume equals the size of the bounding box. Pressing the "Mask" button keeps the original image size but masks out the area not contained within the bounding box bounds. In case of 3D+t images the whole time series is cropped by default. \imageMacro{BoundingBox_ImageCropperView.png,"Bounding Box.",12.00} \imageMacro{Basic_ImageCropperView.png,"Basic Settings.",7.09} \section org_mitk_gui_qt_imagecropperAdvanced Advanced settings In the advanced settings view you find additional features to manipulate the bounding box. \imageMacro{Advanced_ImageCropperView.png,"Advanced Settings.",7.09} \subsection org_mitk_gui_qt_imagecropperAdvancedOverwrite Overwrite original image By enabling this checkbox the image is replaced by the cropped subvolume. Be careful to use this option since there is no undo action available. \subsection org_mitk_gui_qt_imagecropperAdvancedTimestep Crop current time step only If this checkbox is enabled the xD + t image is reduced to a xD image (e.g., 3D+t --> 3D) with the time step visible in the widget. This is useful if you want to extract a single image or its corresponding subvolume of the time series. The whole time series is cropped by default using the timeGeometry of the time step visible in the widget. \section org_mitk_gui_qt_imagecropperIssues Current issues Cropping 2D images is not supported unless the are 3D images containing only a single slice. The user will be notified by a warning and the input is handled as a single label image. Right now changing the shape or rotation of the bounding box is not supported but might be integrated in the future. */ \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.imagenavigator/documentation/UserManual/QmtikImageNavigator.dox b/Plugins/org.mitk.gui.qt.imagenavigator/documentation/UserManual/QmtikImageNavigator.dox index e158d98694..f72a663d43 100644 --- a/Plugins/org.mitk.gui.qt.imagenavigator/documentation/UserManual/QmtikImageNavigator.dox +++ b/Plugins/org.mitk.gui.qt.imagenavigator/documentation/UserManual/QmtikImageNavigator.dox @@ -1,15 +1,15 @@ /** -\page org_mitk_views_imagenavigator The Image Navigator +\page org_mitk_views_imagenavigator Image Navigator \imageMacro{image_navigator.svg,"Icon of the Image Navigator",2.00} \imageMacro{QmtikImageNavigator_ImageNavigator.png,"Image Navigator",7.47} Fast movement through the available data can be achieved by using the Image Navigator. By moving the sliders around you can scroll quickly through the slides and timesteps. By entering numbers in the relevant fields you can jump directly to your point of interest. The "Show detail" checkbox enables you to see the world coordinates in millimetres and the index/voxel coordinates. These may be edited to jump to a specific location. */ \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolbox.dox b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolbox.dox index e1fb8f97b2..8c5aa3850d 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolbox.dox +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurementToolbox.dox @@ -1,12 +1,12 @@ /** -\page org_mitk_gui_qt_measurementtoolbox The Measurement Toolbox Plugin +\page org_mitk_gui_qt_measurementtoolbox Measurement Toolbox \section QmitkmeasurementToolbox Manual This plugin contains all views that provide measurement and statistics functionality. */ \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMaker.dox b/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMaker.dox index cc8f00e9a7..ea26cae85b 100644 --- a/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMaker.dox +++ b/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMaker.dox @@ -1,64 +1,64 @@ /** -\page org_mitk_gui_qt_moviemaker The Movie Maker Plugin +\page org_mitk_gui_qt_moviemaker Movie Maker \imageMacro{video-camera.svg,"Icon of the Movie Maker Plugin.",2.00} \tableofcontents \section org_mitk_gui_qt_moviemakerOverview Overview The Movie Maker View allows you to create basic animations of your scene and to record them to video files. Individual animations are arranged in a timeline and can be played back sequential or in parallel. The Movie Maker View uses external FFmpeg/Libav command line utilities to write compressed video files. You have to manually install either FFmpeg or Libav and set the corresponding path in "External Programs" in the MITK Workbench Preferences (Ctrl+P) in order to record your movies to video files. \imageMacro{QmitkMovieMaker_Preferences.png,"The External Programs preferences page.",12.00} \section org_mitk_gui_qt_moviemakerUsage Usage \imageMacro{QmitkMovieMaker_MovieMakerView.png,"The Movie Maker View.",16.00} To create a movie you have to add an animation to the timeline by clicking the "Add animation" button. You can choose between the available types of animations, e.g., Orbit or Slice. The timeline surrounding bottons allow you to arrange, remove, or add further animations to your movie. Each animation can be set to either begin with the previous animation, i.e., run in parallel, or to start after the previous animation, i.e., run sequential. In combination with delays, rather complex animation arrangements are possible. To set animation specific parameters, select the corresponding animation in the timeline first. You can play back, pause and stop your movie with the according controls at the bottom of the Movie Maker View. Click the "Record" button to finally record your movie to a video file with the specified number of frames per second. You have to choose the render window which you want to record. \subsection org_mitk_gui_qt_moviemakerOrbitUsage Orbit Animation The Orbit animation rotates the camera in the 3D window around the scene. Align the camera directly in the 3D window and enter the number of degrees for the orbitting. If you are planning to have a specific view in the middle of your movie you can play the movie and pause it at the specific frame of interest. Adjust the camera in the 3D window and restart the animation. \imageMacro{QmitkMovieMaker_Orbit.png,"The Orbit animation.",12.00} \subsection org_mitk_gui_qt_moviemakerSliceUsage Slice Animation The Slice animation slices through an image. You can choose the image plane (axial, sagittal, or coronal), as well as the start and end points of the slicing. Use the image navigator in the bottom left of the Workbench to get an idea of the desired values. Check "Reverse" in order to slice from the higher slice number to the lower slice number. \imageMacro{QmitkMovieMaker_Slice.png,"The Slice animation.",12.00} \subsection org_mitk_gui_qt_moviemakerTimeUsage Time Animation The Time animation steps through the individual time steps of the current scene. You can specify the range of the animated time steps. Use the image navigator in the bottom left of the Workbench to get an idea of the desired values. Check "Reverse" in order to step from later time steps to previous time steps. \imageMacro{QmitkMovieMaker_Time.gif,"The Time animation.",12.00} */ diff --git a/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkScreenshotMaker.dox b/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkScreenshotMaker.dox index 71a6a17ed4..5635b65a1b 100644 --- a/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkScreenshotMaker.dox +++ b/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkScreenshotMaker.dox @@ -1,19 +1,19 @@ /** -\page org_mitk_views_screenshotmaker The Screenshot Maker +\page org_mitk_views_screenshotmaker Screenshot Maker This view provides the functionality to create and save screenshots of the data. Available sections: - \ref QmitkScreenshotMakerUserManualUse \imageMacro{QmitkMovieMaker_ScreenshotMakerInterface.png,"The Screenshot Maker User Interface",7.09} \section QmitkScreenshotMakerUserManualUse Usage The first section offers the option of creating a screenshot of the last activated render window (thus the one, which was last clicked into). Upon clicking the button, the Screenshot Maker asks for a filename in which the screenshot is to be stored. The multiplanar Screenshot button asks for a folder, where screenshots of the three 2D views will be stored with default names. The high resolution screenshot section works the same as the simple screenshot section, aside from the fact, that the user can choose a magnification factor. In the option section one can choose the background color for the screenshots, default is black. */ diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_gui_qt_multilabelsegmentation.dox b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_gui_qt_multilabelsegmentation.dox index a88b5f28fe..6d5bd1d481 100644 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_gui_qt_multilabelsegmentation.dox +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/org_mitk_gui_qt_multilabelsegmentation.dox @@ -1,114 +1,114 @@ /** -\page org_mitk_views_multilabelsegmentation The Multilabel Segmentation View +\page org_mitk_views_multilabelsegmentation Multilabel Segmentation \imageMacro{"multilabelsegmentation.svg", "Icon of the MultiLabelSegmentation Plugin", 12} Please reference \ref org_mitk_views_segmentation for the description of the general segmentation tools. \tableofcontents \section org_mitk_views_multilabelsegmentationUserManualCreateOpenSaveImportAdd Start Segmenting To start using the Segmentation Perspective you will have to either create a new segmentation session or load an existing one from disk. The Segmentation toolbar collects buttons for the these actions: \imageMacro{"org_mitk_views_multilabelsegmentationIMGtoolbar.png", "Segmentation toolbar", 12} \section org_mitk_views_multilabelsegmentationUserManualLabelTable The Label Table The following label properties are readily available to modify: The Label Table is shown below: \imageMacro{"org_mitk_views_multilabelsegmentationIMGlabeltable.png", "The Label Table showing all the labels in the current segmentation session", 12} \section org_mitk_views_multilabelsegmentationUserManualLabelCreation Creating a New Label Click the "New Label" button to add a new label. A dialog will show-up to enter the name and color. Preset organ names and corresponding colors are offered while you type in, but you can set any name. The new name if not known will be automatically remembered and made available the next time you create a new label. In the current implementation of the plugin, the maximum number of labels is restricted to 255. If you need more, you will have to create a new segmentation session. \section org_mitk_views_multilabelsegmentationUserManualLayerCreation Creating a New Layer A layer is a set of labels that occupy a non-overlapping anatomical space. The best way to describe them is by a real use case. Imagine you are working on a radiotherpay planning application. In the first layer of your segmentation session you would like to trace the contours of the liver and neighboring organs. You can accomodate all these segmentations in separate labels because they all occupy different anamical regions and do not overlap. Now say you would like to segment the arteries and veins inside the liver. If you don´t trace them in a different layer, you will overwrite the previous ones. You may also need a third layer for segmenting the different irrigation territories in the liver and a fourth layer to contain the lession you would like to treat. The next figure illustrates the Layer Manager . The buttons in it contained serve for adding a new layer, selecting the previous and the next one. The active layer is shown together with the buttons. \imageMacro{"org_mitk_views_multilabelsegmentationIMGlayerManager.png", "Correction Tool",12} \section org_mitk_views_multilabelsegmentationUserManualLabelSearch Searching a Label It may happen that many labels (e.g. > 200) are present in a segmentation session and therefore manual searching is time consuming. The Label Search edit box allows for quickly finding the label you want. Just start writing its name and and you will get assitance for completing its name. If the label you were searching is found, press enter and it will became the active one. \imageMacro{"org_mitk_views_multilabelsegmentationIMGsearchlabel.png", "Label search", 12} \section org_mitk_views_multilabelsegmentationUserManualLabelEditing Label Editing First of all, you have to select the active label by clicking on the corresponding row in the Label Table. Only one label can be active at the time. Then you can select an editing tool in the toolbox. \section org_mitk_views_multilabelsegmentationUserManualOperationsOnLabels Operations on Labels Depending on your selection in the Label Table , several actions are offered: \subsection org_mitk_views_multilabelsegmentationUserManualOperationsOnSingleSelection Single Label Selection If you right click on any label in the table, a menu will pop-up offering the following actions to be performed on the selected label: \imageMacro{"org_mitk_views_multilabelsegmentationIMGLabelTableSingleSelectionContextMenu.png", "Context menu for single label selection", 12} \subsection org_mitk_views_multilabelsegmentationUserManualOperationsOnMultipleSelection Multiple Label Selection If more than one label is selected, a different menu will show up: \imageMacro{"org_mitk_views_multilabelsegmentationIMGLabelTableMultipleSelectionContextMenu.png", "Context menu for multiple label selection", 12} */ 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 a65d740abe..f8641177dd 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 The Point Set Interaction View +\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 diff --git a/Plugins/org.mitk.gui.qt.python/documentation/UserManual/QmitkPython.dox b/Plugins/org.mitk.gui.qt.python/documentation/UserManual/QmitkPython.dox index 114be980c4..48d9f15f65 100644 --- a/Plugins/org.mitk.gui.qt.python/documentation/UserManual/QmitkPython.dox +++ b/Plugins/org.mitk.gui.qt.python/documentation/UserManual/QmitkPython.dox @@ -1,33 +1,33 @@ /** -\page org_mitk_gui_qt_python The Python Plugin +\page org_mitk_gui_qt_python Python Plugin Available sections: - \ref org_mitk_gui_qt_pythonOverview - \ref org_mitk_gui_qt_pythonUsage - \ref org_mitk_gui_qt_PythonConsole - \ref org_mitk_gui_qt_PythonSnippets \section org_mitk_gui_qt_pythonOverview Overview The Python view provides the graphical front end to run Python code through the mitkPython module. Furthermore the SimpleITK/VTK/OpenCV Python wrapping can be used. Images and surfaces in the DataManager can be transferred via a drag & drop mechanism into the MITK Python Console. \section org_mitk_gui_qt_pythonUsage Transfer data Images and surfaces can be tranferred from the data manger into the python console. To transfer an image or surface simply drag it from the data manager into the Variable Stack view, as shown in Figure. A new entry will appear in the Variable Stack, as soon as the data is transferred. As soon as the entry is available the object can be accessed and modified in the python console. Three dimensional images will be copied in-memory to python via numpy and a SimpleITK image object is created with the same properties. When a two dimensional image is transferred the user can choose to transfer it as an OpenCV image object. Surfaces are fully memory mapped as a vtkPolyData object. To transfer an image or surface from the python runtime to the data manager just double click on the corresponding entry in the Variable Stack View. \imageMacro{MitkPythonPluginView.png,"Screenshot of the MITK Python Plugin",6} \section org_mitk_gui_qt_PythonConsole Console The Python console can be used for interactive programming. All items in the data storage can be accessed in the python console. The console can also be used to load python scripts and run them. \section org_mitk_gui_qt_PythonSnippets Snippets The python plugin contains some code snippets of SimpleITK/VTK/OpenCV that can be run in the python console. Snippets can be modified and saved by the user. */ diff --git a/Plugins/org.mitk.gui.qt.remeshing/documentation/UserManual/QmitkRemeshing.dox b/Plugins/org.mitk.gui.qt.remeshing/documentation/UserManual/QmitkRemeshing.dox index 223aa31385..ada4d17731 100644 --- a/Plugins/org.mitk.gui.qt.remeshing/documentation/UserManual/QmitkRemeshing.dox +++ b/Plugins/org.mitk.gui.qt.remeshing/documentation/UserManual/QmitkRemeshing.dox @@ -1,19 +1,19 @@ /** -\page org_mitk_gui_qt_remeshing The Remeshing Plugin +\page org_mitk_gui_qt_remeshing Remeshing \imageMacro{RemeshingIcon.png,"Icon of the Remeshing Plugin.",2.00} \tableofcontents \section org_mitk_gui_qt_remeshingOverview Overview The Remeshing View allows you to remesh surfaces. If done right, remeshing can dramatically increase the quality of your surface mesh. However, you might lose precision if you reduce the vertex density of your surface mesh too strong. Even when you preserve the detail of your mesh, there might be a tiny distance between your original surface and the remeshed surface. Hence, be careful when using remeshed surfaces for evaluation purposes and always keep the original versions. \section org_mitk_gui_qt_remeshingUsage Usage The Remeshing View provides details on its parameters in its user interface. When in doubt, start with the default parameters and iterate to your desired result by reducing the density parameter. */ diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox index a508fb6260..5cad88bfd3 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox +++ b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox @@ -1,317 +1,317 @@ /** -\page org_mitk_views_segmentation The Segmentation Plugin +\page org_mitk_views_segmentation Segmentation \imageMacro{segmentation.svg,"Icon of the Segmentation Plugin",2.00} Some of the features described below are closed source additions to the open source toolkit MITK and are not available in every application. \tableofcontents \section org_mitk_gui_qt_segmentationUserManualOverview Overview The Segmentation plugin allows you to create segmentations of anatomical and pathological structures in medical images of the human body. The plugin consists of a number of view which can be used for: \imageMacro{QmitkSegmentation_IMGApplication.png,"Segmentation Plugin consisting of the Segmentation View the Segmentation Utilities View and the Clipping Plane View", 16.00} The segmentation plugin offers a number of preferences which can be set via the MITK Workbench application preference dialog: \imageMacro{QmitkSegmentation_IMGPreferences.png,"Segmentation Plugin consisting of the Segmentation View the Segmentation Utilities View and the Clipping Plane View", 10.00} The following preferences can be set: If you wonder what segmentations are good for, we shortly revisit the concept of a segmentation here. A CT or MR image is made up of volume of physical measurements (volume elements are called voxels). In CT images, for example, the gray value of each voxel corresponds to the mass absorbtion coefficient for X-rays in this voxel, which is similar in many %parts of the human body. The gray value does not contain any further information, so the computer does not know whether a given voxel is part of the body or the background, nor can it tell a brain from a liver. However, the distinction between a foreground and a background structure is required when: Creating this distinction between foreground and background is called segmentation. The Segmentation perspective of the MITK Workbench uses a voxel based approach to segmentation, i.e. each voxel of an image must be completely assigned to either foreground or background. This is in contrast to some other applications which might use an approach based on contours, where the border of a structure might cut a voxel into two %parts. The remainder of this document will summarize the features of the Segmentation perspective and how they are used. \section org_mitk_gui_qt_segmentationUserManualTechnical Technical Issues The Segmentation perspective makes a number of assumptions. To know what this view can be used for, it will help you to know that: \section org_mitk_gui_qt_segmentationUserManualImageSelection Image Selection The Segmentation perspective makes use of the Data Manager view to give you an overview of all images and segmentations. \imageMacro{QmitkSegmentation_IMGSelection.png,"Data Manager is used for selecting the current segmentation. The reference image is selected in the drop down box of the control area.",5.50} To select the reference image (e.g. the original CT/MR image) use the patient image drop down box in the control area of the Segmentation view. The segmentation image selected in the Data Manager is displayed below in the segmentation drop down box. By default the auto selection mode is enabled, which always keeps the selection of the segmentation drop down box in synch with the selection in the data manager. If you disable the auto selection mode the selection of the right segmentation image has to be done via the drop down box. If no segmentation image exists or none is selected create a new segmentation image by using the "New segmentation" button on the right of the Segmentation drop down box. Some items of the graphical user interface might be disabled when no image is selected or the selected image does not fit to the patient image's geoemtry. In any case, the application will give you hints if a selection is needed. \section org_mitk_gui_qt_segmentationUserManualToolOverview Tool overview MITK comes with a comprehensive set of segmentation tools. These tools can be differenciated between manual slice-based 2D segmentation tools and (semi-)automated 3D tools. The manual 2D tools require a big amount of user interaction and can only be applied to a single image slice whereas the 3D tools operate on the hole image. The 3D tools usually require a small amount of interaction like placin seedpoints of setting some parameters. You can switch between the different toolsets by switching the 2D/3D tab in the segmentation view. \imageMacro{QmitkSegmentation_ToolOverview.png,"An overview of the existing tools in MITK. There are interactive 2D tools as well as (semi-)automated 3D tools",5.50} \section org_mitk_gui_qt_segmentationUserManualManualKringeling Manual Contouring With manual contouring you define which voxels are part of the segmentation and which are not. This allows you to create segmentations of any structeres that you may find in an image, even if they are not part of the human body. You might also use manual contouring to correct segmentations that result from sub-optimal automatic methods. The drawback of manual contouring is that you might need to define contours on many 2D slices. However, this is moderated by the interpolation feature, which will make suggestions for a segmentation. \subsection org_mitk_gui_qt_segmentationUserManualManualKringeling1 Creating New Segmentations Unless you want to edit existing segmentations, you have to create a new, empty segmentation before you can edit it. To do so, click the "New manual segmentation" button. Input fields will appear where you can choose a name for the new segmentation and a color for its display. Click the checkmark button to confirm or the X button to cancel the new segmentation. Notice that the input field suggests names once you %start typing and that it also suggests colors for known organ names. If you use names that are not yet known to the application, it will automatically remember these names and consider them the next time you create a new segmentation. Once you created a new segmentation, you can notice a new item with the "binary mask" icon in the Data Manager tree view. This item is automatically selected for you, allowing you to %start editing the new segmentation right away. \subsection org_mitk_gui_qt_segmentationUserManualManualKringeling2 Selecting Segmentations for Editing As you might want to have segmentations of multiple structures in a single patient image, the application needs to know which of them to use for editing. You select a segmenation by clicking it in the tree view of Data Manager. Note that segmentations are usually displayed as sub-items of "their" patient image. In the rare case, where you need to edit a segmentation that is not displayed as a a sub-item, you can click both the original image AND the segmentation while holding down CTRL or for macOS the CMD on the keyboard. When a selection is made, the Segmentation View will hide all but the selected segmentation and the corresponding original image. When there are multiple segmentations, the unselected ones will remain in the Data Manager, you can make them visible at any time by selecting them. \subsection org_mitk_gui_qt_segmentationUserManualManualKringeling3 Selecting Editing Tools If you are familiar with the MITK Workbench, you know that clicking and moving the mouse in any of the 2D render windows will move around the crosshair that defines what part of the image is displayed. This behavior is disabled while any of the manual segmentation tools are active -- otherwise you might have a hard time concentrating on the contour you are drawing. To %start using one of the editing tools, click its button the the displayed toolbox. The selected editing tool will be active and its corresponding button will stay pressed until you click the button again. Selecting a different tool also deactivates the previous one. If you have to delineate a lot of images, you should try using shortcuts to switch tools. Just hit the first letter of each tool to activate it (A for Add, S for Subtract, etc.). \subsection org_mitk_gui_qt_segmentationUserManualManualKringeling4 Using Editing Tools All of the editing tools work by the same principle: you use the mouse (left button) to click anywhere in a 2D window (any of the orientations axial, sagittal, or frontal), move the mouse while holding the mouse button and release to finish the editing action. Multi-step undo and redo is fully supported by all editing tools. Use the application-wide undo button in the toolbar to revert erroneous %actions. \imageMacro{QmitkSegmentation_IMGIconAddSubtract.png,"Add and Subtract Tools",7.70} Use the left mouse button to draw a closed contour. When releasing the mouse button, the contour will be added (Add tool) to or removed from (Subtract tool) the current segmentation. Hold down the CTRL / CMD key to invert the operation (this will switch tools temporarily to allow for quick corrections). \imageMacro{QmitkSegmentation_IMGIconPaintWipe.png,"Paint and Wipe Tools",7.68} Use the slider below the toolbox to change the radius of these round paintbrush tools. Move the mouse in any 2D window and press the left button to draw or erase pixels. As the Add/Subtract tools, holding CTRL / CMD while drawing will invert the current tool's behavior. \imageMacro{QmitkSegmentation_IMGIconRegionGrowing.png,"Region Growing Tool",3.81} Click at one point in a 2D slice widget to add an image region to the segmentation with the region growing tool. Moving up the cursor while holding the left mouse button widens the range for the included grey values; moving it down narrows it. Moving the mouse left and right will shift the range. Region Growing selects all pixels around the mouse cursor that have a similar gray value as the pixel below the mouse cursor. This enables you to quickly create segmentations of structures that have a good contrast to surrounding tissue, e.g. the lungs. The tool will select more or less pixels (corresponding to a changing gray value interval width) when you move the mouse up or down while holding down the left mouse button. \if THISISNOTIMPLEMENTEDATTHEMOMENT A common issue with region growing is the so called "leakage" which happens when the structure of interest is connected to other pixels, of similar gray values, through a narrow "bridge" at the border of the structure. The Region Growing tool comes with a "leakage detection/removal" feature. If leakage happens, you can left-click into the leakage region and the tool will try to automatically remove this region (see illustration below). \imageMacro{QmitkSegmentation_IMGLeakage.png,"Leakage correction feature of the Region Growing tool",11.28} \endif
\imageMacro{QmitkSegmentation_IMGIconCorrection.png,"Correction Tool",3.77} You do not have to draw a closed contour to use the Correction tool and do not need to switch between the Add and Substract tool to perform small corrective changes. The following figure shows the usage of this tool: \imageMacro{QmitkSegmentation_IMGCorrectionActions.png,"%Actions of the Correction tool illustrated.",13.50}
\imageMacro{QmitkSegmentation_IMGIconFill.png,"Fill Tool",3.81} Left-click inside a segmentation with holes to completely fill all holes (left-click outside a segmentation). \imageMacro{QmitkSegmentation_IMGIconErase.png,"Erase Tool",3.79} This tool removes a connected part of pixels that form a segmentation. You may use it to remove so called islands (see picture) or to clear a whole slice at once (left-click outside a segmentation). \imageMacro{QmitkSegmentation_IMGIconLiveWire.png,"LiveWire Tool",3.01} The LiveWire Tool acts as a magnetic lasso with a contour snapping to edges of objects. \imageMacro{QmitkSegmentation_IMGLiveWireUsage.PNG,"Steps for using LiveWire Tool",16.00} The contour will be transfered to its binary image representation by deactivating the tool. \imageMacro{QmitkSegmentation_IMG2DFastMarchingUsage.png,"2D Fast Marching Tool",3.01} Provides a fast marching based 2D interaction segmentation tool. You start with setting seedpoints in an image slice. Via several sliders you can adapt parameters and see the fast marching result instantly. \subsection org_mitk_gui_qt_segmentationUserManualManualKringeling5 Interpolation Creating segmentations for modern CT volumes is very time-consuming, because structures of interest can easily cover a range of 50 or more slices. The Manual Segmentation View offers two helpful features for these cases:
The 3D interpolation is activated by default when using the manual segmentation tools. That means if you start contouring, from the second contour onwards, the surface of the segmented area will be interpolated based on the given contour information. The interpolation works with all available manual tools. Please note that this is currently a pure mathematical interpolation, i.e. image intensity information is not taken into account. With each further contour the interpolation result will be improved, but the more contours you provide the longer the recalculation will take. To achieve an optimal interpolation result and in this way a most accurate segmentation you should try to describe the surface with sparse contours by segmenting in arbitrary oriented planes. The 3D interpolation is not meant to be used for parallel slice-wise segmentation. \imageMacro{QmitkSegmentation_3DInterpolationWrongRight.png,"3D Interpolation HowTo",16.00} You can accept the interpolation result by clicking the "Accept" - button below the tool buttons. In this case the 3D interpolation will be deactivated automatically so that the result can be postprocessed without any interpolation running in background. During recalculation the interpolated surface is blinking yellow/white. When the interpolation has finished the surface is shown yellow with a small opacity. Additional to the surface, black contours are shown in the 3D render window. They mark the positions of all the drawn contours which were used for the interpolation. You can navigate between the drawn contours by clicking on the „Position“ - Nodes in the datamanager which are located below the selected segmentation. If you don't want to see these nodes just unckeck the „Show Position Nodes“ Checkbox and these nodes will be hidden. If you want to delete a drawn contour we recommend to use the Erase-Tool since Redo/Undo is not yet working for 3D interpolation. The current state of the 3D interpolation can be saved accross application restart. Therefor just click on save project during the interpolation is active. After restarting the application and load your project you can click on "Reinit Interpolation" within the 3D interpolation GUI area.
The 2D Interpolation creates suggestions for a segmentation whenever you have a slice that Interpolated suggestions are displayed in a different way than manual segmentations are, until you "accept" them as part of the segmentation. To accept single slices, click the "Accept" button below the toolbox. If you have segmented a whole organ in every-x-slice, you may also review the interpolations and then accept all of them at once by clicking "... all slices". \section org_mitk_gui_qt_segmentationUserManual3DSegmentationTools 3D Segmenation tools The 3D tools operate on the hole image and require usually a small amount of interaction like placing seed-points or specifying certain parameters. All 3D tools provide an immediate segmentation feedback, which is displayed as a transparent green overlay. For accepting a preview you have to press the "Comfirm" button of the selected tool. The following 3D tools are at your disposal: \subsection org_mitk_gui_qt_segmentationUserManual3DThresholdTool 3D Threshold tool The Thresholding tool simply applies a 3D threshold to the patient image. All pixels with values equal or above the selected threshold are labeled. You can change the threshold by either moving the slider of setting a certain value in the spinbox. \imageMacro{QmitkSegmentation_3DThresholdTool.png,"3D Threshold tool",10.00} \subsection org_mitk_gui_qt_segmentationUserManual3DULTool 3D Upper/Lower Threshold tool The Upper/Lower Thresholding tool works similar to the simple 3D threshold tool but allows you to define an upper and lower threshold. All pixels with values within this threshold intervall will be labeled \imageMacro{QmitkSegmentation_3DULThresholdTool.png,"3D Upper/Lower Threshold tool",10.00} \subsection org_mitk_gui_qt_segmentationUserManual3DOtsuTool 3D Otsu tool The 3D Otsu tool provides a more sophisticated thresholding algorithm. It allows you to define a number of regions. Based on the image histogram the pixels will then divided into different regions. There more regions you define the longer will the calculation take. \imageMacro{QmitkSegmentation_3DOtsuTool.png,"3D Otsu tool",10.00} \subsection org_mitk_gui_qt_segmentationUserManual3DFMTool 3D Fast Marching tool The 3D Fast Marching tools works similar to the 2D pendant but on the hole image. Depending on you image's size the calculation will take some time. You can interactive set the parameters of the algorithm via the tool GUI. \imageMacro{QmitkSegmentation_3DFMTool.png,"3D Fast Marching tool",10.00} \subsection org_mitk_gui_qt_segmentationUserManual3DRGTool 3D Region Growing tool The 3D Region Growing tool works similar to the 2D pendant. At the beginning you have to place a seedpoint and define a threshold intervall. If you press "Run segmentation" a preview is calculated, if the "3D preview" box is checked you will also see the result in 3D. By moving the "Adapt region growing slider" you can interactively adapt the result to you image. \imageMacro{QmitkSegmentation_3DRGTool.png,"3D Region Growing tool",10.00} +\subsection org_mitk_gui_qt_segmentationUserManual3DWatershedTool 3D Watershed tool This tool provides a watershed based segmentation algorithm. \imageMacro{QmitkSegmentation_3DWatershedTool.png,"3D Watershed tool",10.00} \subsection org_mitk_gui_qt_segmentationUserManualPickingTool Picking tool The Picking tool allows you to select islands within your segmentation. This is especially usefull if e.g. a thresholding delivered your several areas within your image but you are just interested in one special region. \imageMacro{QmitkSegmentation_PickingTool.png,"Picking tool",10.00} \section org_mitk_gui_qt_segmentationUserManualPostprocessing Things you can do with segmentations As mentioned in the introduction, segmentations are never an end in themselves. Consequently, the Segmentation view adds a couple of "post-processing" %actions to the Data Manager. These %actions are accessible through the context-menu of segmentations in Data Manager's list view \imageMacro{QmitkSegmentation_IMGDataManagerContextMenu.png,"Context menu items for segmentations.",10.58} \section QmitkSegmentation_UserManualSurfaceMasking Surface Masking You can use the surface masking tool to create binary images from a surface which is used used as a mask on an image. This task is demonstrated below: \imageMacro{QmitkSegmentation_FromSurfaceBefore.png,"Load an image and a surface.",16.00} Select the image and the surface in the corresponding drop-down boxes (both are selected automatically if there is just one image and one surface) \imageMacro{QmitkSegmentation_FromSurfaceAfter.png,"Create segmentation from surface",16.00} After clicking "Create segmentation from surface" the newly created binary image is inserted in the DataManager and can be used for further processing \section org_mitk_gui_qt_segmentationUserManualTechnicalDetail Technical Information for Developers For technical specifications see \subpage QmitkSegmentationTechnicalPage and for information on the extensions of the tools system \subpage toolextensions . */ diff --git a/Plugins/org.mitk.gui.qt.viewnavigator/documentation/UserManual/QmitkViewNavigator.dox b/Plugins/org.mitk.gui.qt.viewnavigator/documentation/UserManual/QmitkViewNavigator.dox index e44be368d5..8ca5f20e0a 100644 --- a/Plugins/org.mitk.gui.qt.viewnavigator/documentation/UserManual/QmitkViewNavigator.dox +++ b/Plugins/org.mitk.gui.qt.viewnavigator/documentation/UserManual/QmitkViewNavigator.dox @@ -1,43 +1,43 @@ /** -\page org_mitk_gui_qt_viewnavigator The View Navigator +\page org_mitk_gui_qt_viewnavigator View Navigator \imageMacro{view-manager.png,"Icon of the view navigator",2.00} \tableofcontents \section org_mitk_gui_qt_viewnavigatorOverview Overview This view allows for the easy navigation of the available views. You can select which view to open by double-clicking the name of the view in the view navigator. It provides a keyworded, grouped and searchable list of views. \section org_mitk_gui_qt_viewnavigatorUsage Usage You can toggle the View Navigator on and off by clicking on its icon in the menu bar. Alternatively it is also available via the Window->Show Views dialog. \imageMacro{QmitkViewNavigatorGUI.png,"The View Navigator GUI",6.00} Once the View Navigator has been opened you will see a list divided in workflows/perspectives and views. Via this list you can access any view or perspective provided by the application. They are further organized based on their associated category. An entry on the list is opened by a double left-click. \subsection org_mitk_gui_qt_viewnavigatorSearch Search You can search the lists for view/workflow names, keywords or categories. \imageMacro{QmitkViewNavigatorSearch.png,"Search the View Navigator",4.00} \subsection org_mitk_gui_qt_viewnavigatorCustomWorkflows Custom Workflows \imageMacro{QmitkViewNavigatorContextMenuWorkflows.png,"The workflow context menu",4.00} A right click on a workflow opens a context menu that allows you to copy that workflow to create your own custom one. \note The duplicated workflow will look like the basic state of the original workflow. Any changes to the original workflow will not be copied. \imageMacro{QmitkViewNavigatorNewWorkflow.png,"Custom workflow creation dialog",4.00} Your new workflow will appear in the list and you can modify it independently of the original workflow. Any changes will be stored for future sessions unless the workflow is deleted. \note Resetting a custom perspective will return it to the original state after duplicating. \imageMacro{QmitkViewNavigatorContextMenuCustomWorkflow.png,"Custom workflow context menu",4.00} */