diff --git a/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/MITKExamples.dox b/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/MITKExamples.dox index bf7631f9a6..973ca1f272 100644 --- a/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/MITKExamples.dox +++ b/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/MITKExamples.dox @@ -1,18 +1,17 @@ /** -\page org_mitk_gui_qt_examples Examples for the use of MITK - +\page org_mitk_gui_qt_examples The MITK Examples \section QmitkExamplesUserManualSummary Summary This module is a collection of examples for developing with mitk. The following examples are included: */ diff --git a/Examples/Plugins/org.mitk.example.gui.opencv/documentation/UserManual/MITKExamplesOpenCV.dox b/Examples/Plugins/org.mitk.example.gui.opencv/documentation/UserManual/MITKExamplesOpenCV.dox index 68f2398d23..8def88044b 100644 --- a/Examples/Plugins/org.mitk.example.gui.opencv/documentation/UserManual/MITKExamplesOpenCV.dox +++ b/Examples/Plugins/org.mitk.example.gui.opencv/documentation/UserManual/MITKExamplesOpenCV.dox @@ -1,12 +1,11 @@ /** -\page org_mitkexamplesopencv OpenCV Examples for the use of MITK - +\page org_mitkexamplesopencv The OpenCV Examples \section QmitkExamplesOpenCVUserManualSummary Summary This module is a collection of examples for developing with mitk and openCV. The following examples are included: */ diff --git a/Examples/Plugins/org.mitk.example.gui.pcaexample/documentation/UserManual/Manual.dox b/Examples/Plugins/org.mitk.example.gui.pcaexample/documentation/UserManual/Manual.dox index 3cd8f72689..d7db668df3 100644 --- a/Examples/Plugins/org.mitk.example.gui.pcaexample/documentation/UserManual/Manual.dox +++ b/Examples/Plugins/org.mitk.example.gui.pcaexample/documentation/UserManual/Manual.dox @@ -1,17 +1,17 @@ /** -\page org_mitk_example_gui_pcaexample PCA example +\page org_mitk_example_gui_pcaexample The PCA example \imageMacro{icon.png,"Icon of Pcaexample",2.00} \tableofcontents \section org_mitk_example_gui_pcaexampleOverview Overview Describe the features of your awesome plugin here */ 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 63d2abcfc7..34290412a6 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 Logging Plugin +\page org_blueberry_ui_qt_log The 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 "Categories" adds a column for the category. The checkbox "Advanced Fields" 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.aicpregistration/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.aicpregistration/documentation/UserManual/Manual.dox index b1e0204f71..4da7b4f2b5 100644 --- a/Plugins/org.mitk.gui.qt.aicpregistration/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.aicpregistration/documentation/UserManual/Manual.dox @@ -1,80 +1,80 @@ /** -\page org_mitk_gui_qt_aicpregistration Anisotropic Iterative Closest Point Registration Plugin +\page org_mitk_gui_qt_aicpregistration The Anisotropic Iterative Closest Point Registration Plugin \imageMacro{"QmitkAICPRegistration_Icon.xpm","Icon of the A-ICP Registration Plugin",2} \tableofcontents \section org_mitk_gui_qt_aicpregistrationOverview Overview The Surfaceregistration plugin allows the user to compute a transformation between two surfaces and align them in 3D space. It performs the registration with the anisotropic iterative closest point algorithm (A-ICP) presented in L. Maier-Hein et al. "Convergent Iterative Closest-Point Algorithm to Accomodate Anisotropic and Inhomogenous Localization Error.", IEEE T Pattern Anal 34 (8), 1520-1532, 2012. With the plugin it's also possible to compute the target registration error (TRE) between the two aligned surfaces with a given set of target points. In order to register the surfaces they need to be initially aligned to be able to run the fine registration with the A-ICP algorithm. \imageMacro{"QmitkAICPRegistration_Plugin.png","Overview of the A-ICP Registration Plugin.",28} \section org_mitk_gui_qt_aicpregistrationUsage Usage In order to run a registration at least two surfaces need to be loaded into the data manager. Once the surfaces are loaded, a moving and a fixed surface can be selected in the associated combo boxes of the plugin. When the Register Surfaces button is pressed the registration is started and the moving surface is transformed onto the fixed surface. \imageMacro{"QmitkAICPRegistration_Input.png","Select the surfaces to register.",28} \section org_mitk_gui_qt_aicpregistrationTargetRegistrationErrorCalculation Target Registration Error Calculation To compute the target registration error, enable the calculation via the checkbox in the target registration view. Once the TRE computation is enabled the combo boxes are activated to select the according target point sets. \imageMacro{"QmitkAICPRegistration_TRECalculation.png","Usage of the TRE calculation view.",28} \section org_mitk_gui_qt_aicpregistrationRegistrationSettings Registration Settings The following additional settings are available in the plugin to configure the algorithm: \imageMacro{"QmitkAICPRegistration_Settings.png","Additional registration settings.",28} \subsection org_mitk_gui_qt_aicpregistrationTrimmedRegistration Trimmed Registration This option enables a trimmed version of the algorithm to register partial overlapping surfaces. Once the option is enabled the user can specify the overlapping part of the surface. Valid values for the overlapping part lie between 0 an 1. The trimmed version of the algorithm uses only a fixed percentage of all correspondences found during one iteration. Only the best correspondences will be used during the registration process. \subsection org_mitk_gui_qt_aicpregistrationThreshold Threshold The user can specify the threshold which is used as a termination constraint for the algorithm. When the the change of the fiducial registration error (FRE) between to registrations falls under the specified threshold the algorithm terminates. Larger values can speedup the registration process at the cost of a more accurate result. \subsection org_mitk_gui_qt_aicpregistrationMaximumIterations Maximum Iterations The maximum amount of iterations used by the algorithm can be specified by the user. Once the algorithm reaches the maximum amount of iterations it will stop the registration process. \subsection org_mitk_gui_qt_aicpregistrationSearchRadius Search Radius The user can specify the search radius in mm used during the correspondence search in a kd tree. The default value is 30 mm. A small radius can speedup the algorithm but can in addition also lead in bad correspondences and therefore in an incorrect alignment of the surfaces. */ 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 1c516ad9c0..e67b1b862b 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 The 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.cest/documentation/UserManual/org_mitk_gui_qt_cest.dox b/Plugins/org.mitk.gui.qt.cest/documentation/UserManual/org_mitk_gui_qt_cest.dox index 17c8d546fd..b559b0388e 100644 --- a/Plugins/org.mitk.gui.qt.cest/documentation/UserManual/org_mitk_gui_qt_cest.dox +++ b/Plugins/org.mitk.gui.qt.cest/documentation/UserManual/org_mitk_gui_qt_cest.dox @@ -1,66 +1,66 @@ /** -\page org_mitk_gui_qt_cest CEST View +\page org_mitk_gui_qt_cest The CEST View \imageMacro{icon.svg,"Icon of the cest view",2.00} \tableofcontents \section org_mitk_gui_qt_cestOverview Overview This view gives the option to explore and analyze CEST data. You can select a CEST data set together with either a segmentation or a point set in the datamanager. If a segmentation was selected (make sure the segmentation is the same in each time step, you can use the button at the top of the view to copy the first time step to all subsequent ones) a statistic for the selected region is shown. If a point set was selected each points grey value is plotted. \section org_mitk_gui_qt_cestDataLoading Data Loading CEST dicom data can be loaded either via file open or drag and drop. When a dicom file is loaded via MITK and it contains CEST meta information the CEST Dicom Reader is offered as an option. Selecting it will parse the CEST data as follows: An initial parsing determines whether the provided string belongs to CEST data at all. If the "tSequenceFileName" is of the format "{WHATEVER}CEST_Rev####" it is assumed that the data is indeed CEST data and was taken with revision #### (not limited to four digits). Which custom parameters to save and to which property name can be controlled by a json file. This file can be either provided as a resource for the MitkCEST module during compilation or placed next to the MitkCEST library in your binary folder. The expected format for the file "REVISIONNUMBER.json":
{
"REVISIONNUMBER" : "revision_json",
"sWiPMemBlock.alFree[1]" : "AdvancedMode",
"sWiPMemBlock.alFree[2]" : "RetreatMode"
}
where : If the sampling type is list it will try to access LIST.txt at the same location as the dicom files read the offsets. \section org_mitk_gui_qt_cestCreatingSegmentation Creating a segmentation You can use the segmentation view to create a segmentation for the CEST data. Drawing a segmentation will by default only add it to the first timestep. For more information check the help of the segmentation view. You can copy the segmentation on the first timestep to all following ones by using the copy timestep button in this view. \section org_mitk_gui_qt_cestCreatingPointSet Creating a point set You can use the point set interaction view to create a point set for the CEST data. For more information check the help of the point set interaction view. \section org_mitk_gui_qt_cestNormalizing Normalizing the CEST data Select the CEST image in the datamanager and hit the normalize button to create a new, normalized image. \section org_mitk_gui_qt_cestInspectProperties Investigate CEST meta data You can inspect the CEST meta data with the properties view. You need to enable the developer mode in the "Window->Preferences" Properties menu. When selecting a data node in the data manager with the properties view active you can change the Property List from "Data node: common" to "Base data". The cest meta data is grouped under CEST. */ diff --git a/Plugins/org.mitk.gui.qt.classificationsegmentation/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.classificationsegmentation/documentation/UserManual/Manual.dox index 7877e578d8..c1a5768584 100644 --- a/Plugins/org.mitk.gui.qt.classificationsegmentation/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.classificationsegmentation/documentation/UserManual/Manual.dox @@ -1,25 +1,25 @@ /** -\page org_mitk_gui_qt_classificationsegmentation Classificationsegmentation Plugin +\page org_mitk_gui_qt_classificationsegmentation The Classificationsegmentation Plugin \imageMacro{brain.png,"Icon of Classificationsegmentation Plugin",2.00} \tableofcontents \section org_mitk_gui_qt_classificationsegmentationOverview Overview Segmentation of the classes: using a random forest based approach. Credits (from the Noun Project): */ 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 e320592ac6..9e485fd10f 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 Command Line Modules View +\page org_mitk_views_cmdlinemodules The 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 d06d0340e4..08e636a260 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 DataManager +\page org_mitk_views_datamanager The 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 7e8e526781..136c56e93d 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 Dicom Plugin +\page org_mitk_gui_qt_dicom The 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 36aa96489c..f45e70d5e1 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 DICOM Inspector +\page org_mitk_gui_qt_dicominspector The 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.eventrecorder/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.eventrecorder/documentation/UserManual/Manual.dox index 4522d6cdf8..1ac1f69e7e 100644 --- a/Plugins/org.mitk.gui.qt.eventrecorder/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.eventrecorder/documentation/UserManual/Manual.dox @@ -1,17 +1,17 @@ /** -\page org_mitk_gui_qt_eventrecorder Event Recorder Plugin +\page org_mitk_gui_qt_eventrecorder The Event Recorder Plugin \imageMacro{icon.png,"Icon of Eventrecorder",2.00} \tableofcontents \section org_mitk_gui_qt_eventrecorderOverview Describe the features of your awesome plugin here */ diff --git a/Plugins/org.mitk.gui.qt.fit.demo/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.fit.demo/documentation/UserManual/Manual.dox index 0aa91d6bfb..9460060acb 100644 --- a/Plugins/org.mitk.gui.qt.fit.demo/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.fit.demo/documentation/UserManual/Manual.dox @@ -1,17 +1,17 @@ /** -\page org_mitk_gui_qt_fit_demo Model Fit Demo View +\page org_mitk_gui_qt_fit_demo The Model Fit Demo View \imageMacro{fit_demo_doc.svg,"Icon of the Fit Demo View",3.0} \tableofcontents \section FIT_DEMO_Introduction Introduction This plugin is a very simple demo plugin that allows 1) to generate a demo 3D+t image (with linear increasing values) and 2) to perform a linear fit on a selected node. It was/is use to demonstrate basic principle and to generate example fit sessions for demo and testing purposes (e.g. functionality of the fit inspector). \section FIT_DEMO_Contact Contact information This plug-in is being developed by the SIDT group (Software development for Integrated Diagnostics and Therapy) at the German Cancer Research Center (DKFZ). If you have any questions, need support, find a bug or have a feature request, feel free to contact us at www.mitk.org. */ diff --git a/Plugins/org.mitk.gui.qt.fit.genericfitting/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.fit.genericfitting/documentation/UserManual/Manual.dox index 9685f21f85..063fdf0dd9 100644 --- a/Plugins/org.mitk.gui.qt.fit.genericfitting/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.fit.genericfitting/documentation/UserManual/Manual.dox @@ -1,16 +1,16 @@ /** -\page org_mitk_gui_qt_fit_genericfitting Model Fit Generic Fitting View +\page org_mitk_gui_qt_fit_genericfitting The Model Fit Generic Fitting View \imageMacro{fit_generic_doc.svg,"Icon of the Generic Fitting View",3.0} \tableofcontents \section FIT_GENERIC_Introduction Introduction This plug-in offers a generic fitting component for time resolved image data. \section FIT_GENERIC_Contact Contact information This plug-in is being developed by the SIDT group (Software development for Integrated Diagnostics and Therapy) at the German Cancer Research Center (DKFZ). If you have any questions, need support, find a bug or have a feature request, feel free to contact us at www.mitk.org. */ diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/Manual.dox index 75a15aa1aa..4abb6951fd 100644 --- a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/Manual.dox @@ -1,78 +1,78 @@ /** -\page org_mitk_gui_qt_fit_inspector Model Fit Inspector View +\page org_mitk_gui_qt_fit_inspector The Model Fit Inspector View \imageMacro{fit_inspector_doc.svg,"Icon of the Model Fit Inspector View",3.0} \tableofcontents \section FIT_INSPECTOR_Introduction Introduction This view (Model Fit Inspector; MFI) offers the possibility to display the time course of the signal within an individual voxel (with or without fit). \section FIT_INSPECTOR_Contact Contact information This plug-in is being developed by the SIDT group (Software development for Integrated Diagnostics and Therapy) at the German Cancer Research Center (DKFZ). If you have any questions, need support, find a bug or have a feature request, feel free to contact us at www.mitk.org. \section FIT_INSPECTOR_Raw Viewing without a model fit \imageMacro{fit_inspect_raw.png, "Example screen shot showing the inspection of raw dynamic data without a fit.", 10} Open the view and select the dynamic image in the data manager. The graph plot will show the time course of image intensities (signal) in the selected voxel (cross hair) as red data points. The blue point indicates the frame currently displayed in the 4-window view. \section FIT_INSPECTOR_Fit Viewing without a model fit \imageMacro{fit_inspect_fit.png, "Example screen shot showing the inspection of dynamic data and an associated fit.", 10} Selecting a parameter map of the fit of interest in the Data Manager will display the raw data curve in red dots with corresponding fit as black line in the selected cross-hair position. If an AIF-based model was used, the utilized AIF (averaged over AIF mask) is also displayed (default in green). The color of the AIF display can be adjusted. For ROI based fits, the MFI will display both the current data curve in the selected voxel (in red) and the ROI-averaged fitted curve (in dark green, can be adjusted). Scrolling through the individual voxels will change the current data curve, but the ROI-based curve remains the same. If voxels outside the fitted area defined by the mask are selected, the raw data voxel values will be displayed, however no black fit line is visualized. Below the data plot, several options for data visualization can be selected: \subsection FIT_INSPECTOR_Fit_info Fit info tab \imageMacro{fit_inspect_info.png, "Details of the fit info tab.", 5} The Fit info tab displays meta-data for selected fits performed on the displayed data set. If no fit was performed and only raw data is visualized, the fields are empty. \subsection FIT_INSPECTOR_Fit_Parameter Fit parameter tab \imageMacro{fit_inspect_results.png, "Details of the fit parameter tab.", 5} The "fit parameter" tab shows fit related parameter estimate values, derived parameters, fit criterion values and (optional) debug parameter maps in the selected voxel (and all inspection positions; see also \ref FIT_INSPECTOR_Inspect "inspection positions") listed as a table. If no fit was performed and only raw data is visualized, the table is empty. The content of the table may by copied to clipboard or exported as csv file, by clicking the respective button below the table. \subsection FIT_INSPECTOR_Fit_Inspection Inspection positions tab \imageMacro{fit_inspect_positions.png, "Details of the inspection position tab.", 5} The tab allows to manage inspection positions (see here for more about \ref FIT_INSPECTOR_Inspect "inspection positions"). - (1) Shows the coordinates of the current selected position in the workbench. - (2) Press to make the current position a inspected position. It will be added at the bottom of the list (3). - (3) List of all inspection positions - (4) Toggle adding mode on/off. If on, you can add new positions by clicking into render windows with "SHIFT + left mouse button". - (5) Manually adding inspection positions by entering the coordinates. - (6) Remove the selected inspection positions. (Hot key: Del) - (7) Move the selected inspection position up in the list (3). - (8) Move the selected inspection position down in the list (3). - (9) Save inspection points to a file. - (10) Load inspection points from a file. \subsection FIT_INSPECTOR_Fit_Settings Settings tab \imageMacro{fit_inspect_settings.png, "Details of the settings tab.", 5} The View settings tab is used to adjust the plot display, namely, x and y axis scales and colors of displayed data plots (i.e. AIF). \subsection FIT_INSPECTOR_Fit_Export Plot data export tab \imageMacro{fit_inspect_export.png, "Details of the plot data export tab.", 5} Displays voxel data (input image) and corresponding time grid together with model fit values and additional curves (like AIF values) for each time point. The table will contain the position depended values of the current selected position as well as of all inspection positions (see also \ref FIT_INSPECTOR_Inspect "inspection positions"). The data in the table can also be copied to clipboard or exported to csv files, by clicking the respective button below the table. \section FIT_INSPECTOR_Inspect Inspection positions \imageMacro{fit_inspect_positions_example.png, "Example of the usage of inspection positions.", 5} The fit inspector allows to define positions in the world coordinate system that will be constantly displayed in addition to the current selected position. These inspected position will be shown in the following parts of the view: - The plot windows. See example image above; the plot shows the current position (raw data: red dots, fit: black line) and an additional inspection position (green). - The fit parameter tab (see example image above) - The plot data export tab. It will work with dynamic data with and without an model fit. See the \ref FIT_INSPECTOR_Fit_Inspection "inspection positions tab section" for more details on how to manage inspection positions. */ diff --git a/Plugins/org.mitk.gui.qt.flow.segmentation/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.flow.segmentation/documentation/UserManual/Manual.dox index 0c2786406c..b97c29b247 100644 --- a/Plugins/org.mitk.gui.qt.flow.segmentation/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.flow.segmentation/documentation/UserManual/Manual.dox @@ -1,8 +1,8 @@ /** -\page org_mitk_gui_qt_flow_segmentation Segmentation Flow +\page org_mitk_gui_qt_flow_segmentation The Segmentation Flow The view offers a simple way to directly save the first segmentation found in the data storage. The save location will be determined given the application argument flags (--flow.outputdir and --flow.outputextension). If no flags where set when starting the application the current working directory and "nrrd" as extensions will be used. */ diff --git a/Plugins/org.mitk.gui.qt.flowapplication/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.flowapplication/documentation/UserManual/Manual.dox index 4296137ae7..866972cb6d 100644 --- a/Plugins/org.mitk.gui.qt.flowapplication/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.flowapplication/documentation/UserManual/Manual.dox @@ -1,6 +1,6 @@ /** -\page org_mitk_gui_qt_flowapplication Flow application +\page org_mitk_gui_qt_flowapplication The Flow application */ diff --git a/Plugins/org.mitk.gui.qt.geometrytools/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.geometrytools/documentation/UserManual/Manual.dox index 41cc6fa9a3..66bc02d803 100644 --- a/Plugins/org.mitk.gui.qt.geometrytools/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.geometrytools/documentation/UserManual/Manual.dox @@ -1,18 +1,18 @@ /** -\page org_mitk_gui_qt_geometrytools Geometry Tools +\page org_mitk_gui_qt_geometrytools The Geometry Tools \imageMacro{icon.png,"Icon of Geometry Tools",2.00} \tableofcontents \section org_mitk_gui_qt_geometrytoolsOverview Overview A plugin to modify geometry of mitkBaseData via interaction. Currently, the following operations can be performed: */ diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/documentation/UserManual/Manual.dox index aca0042001..4e25a77184 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/documentation/UserManual/Manual.dox @@ -1,16 +1,16 @@ /** -\page org_mitk_gui_qt_igt_app_echotrack Ultrasound Navigation Plugin +\page org_mitk_gui_qt_igt_app_echotrack The Ultrasound Navigation Plugin Available sections: - \ref org_mitk_gui_qt_igt_app_echotrackOverview \section org_mitk_gui_qt_igt_app_echotrackOverview Overview Describe the features of your awesome plugin here */ diff --git a/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTExamples.dox b/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTExamples.dox index 0bc225644e..e52ecd3d69 100644 --- a/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTExamples.dox +++ b/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTExamples.dox @@ -1,14 +1,14 @@ /** -\page org_mitk_gui_qt_igtexample IGT Examples +\page org_mitk_gui_qt_igtexample The IGT Examples This plugin includes views with examples and help applications for IGT. The different views are described on the pages below: */ diff --git a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTracking.dox b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTracking.dox index 67326607a3..e94957da24 100644 --- a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTracking.dox +++ b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTracking.dox @@ -1,20 +1,20 @@ /** -\page org_mitk_gui_qt_igttracking IGT Tracking Plugin +\page org_mitk_gui_qt_igttracking The IGT Tracking Plugin This plugin offers basic tracking functionalities. This includes connecting to a tracking system, logging and recording of tracking data, managing tracking tools and playing recorded tracking data. The plugin includes different views, which are described on different pages in detail. As part of the tutorial, it is recommended to get familiar with each of the following views as they lead you through the main functionality of the IGT plugin. Please read the following pages to get familiar with them: \ref Return to the \ref TrackingPlugins "[IGT Tutorial Overview]" */ \ No newline at end of file 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 aeec51236c..2bcd21d2bb 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 Image Cropper +\page org_mitk_gui_qt_imagecropper The 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 f72a663d43..e158d98694 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 Image Navigator +\page org_mitk_views_imagenavigator The 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.lasercontrol/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.lasercontrol/documentation/UserManual/Manual.dox index b709022b24..d94dda6a62 100644 --- a/Plugins/org.mitk.gui.qt.lasercontrol/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.lasercontrol/documentation/UserManual/Manual.dox @@ -1,17 +1,17 @@ /** -\page org_mitk_gui_qt_lasercontrol Laser Control +\page org_mitk_gui_qt_lasercontrol The Laser Control \imageMacro{icon.png,"Icon of Lasercontrol",2.00} \tableofcontents \section org_mitk_gui_qt_lasercontrolOverview Overview Describe the features of your awesome plugin here */ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/documentation/UserManual/Manual.dox index a1348a0788..3d911805f2 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/documentation/UserManual/Manual.dox @@ -1,46 +1,46 @@ /** -\page org_mitk_gui_qt_matchpoint_algorithm_browser MatchPoint Algorithm Browser View +\page org_mitk_gui_qt_matchpoint_algorithm_browser The MatchPoint Algorithm Browser View \imageMacro{map_icon_browser_doc.svg, "Icon of the MatchPoint Algorithm Browser", 3} \tableofcontents \section MAP_BROWSER_Introduction Introduction This view offers the user a way to search for available registration algorithms and select them for further usage by other views (e.g. MatchPoint Algorithm Control \ref org_mitk_gui_qt_algorithm_control). \section MAP_BROWSER_Usage Usage \remark If you see no algorithms available by the browser, please check the search paths which can be configured at the MatchPoint preference page (Ctrl+P). The basic idea of the browser is that you can use this view as central place to search for suitable algorithms. If you select an algorithm you can see its profile in the lower part of the view. If a algorithm is selected all other views (e.g. \ref org_mitk_gui_qt_algorithm_control) which use registration algorithms will be notified and allow to choose the selected algorithm for usage. \imageMacro{map_browser.png, "View of the browser with the list of available algorithm and the profile area",14} \section MAP_BROWSER_Profile Profile info In the following a short information about the different properties classified in the profile.\n */ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/documentation/UserManual/Manual.dox index d442184af4..fcc483e40c 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/documentation/UserManual/Manual.dox @@ -1,39 +1,39 @@ /** -\page org_mitk_gui_qt_matchpoint_algorithm_control MatchPoint Algorithm Control View +\page org_mitk_gui_qt_matchpoint_algorithm_control The MatchPoint Algorithm Control View \imageMacro{map_icon_run_doc.svg,"Icon of the MatchPoint Algorithm Control",3.0} \tableofcontents \section MAP_RUN_Introduction Introduction This plugin offers the user a way to use a selected registration algorithm in order to determine a registration for two selected images. For the selection of an algorithm please see MatchPoint Algorithm Browser (\ref org_mitk_gui_qt_matchpoint_algorithm_browser). \section MAP_RUN_Contact Contact information This plug-in is being developed by the SIDT group (Software development for Integrated Diagnostics and Therapy) at the German Cancer Research Center (DKFZ). If you have any questions, need support, find a bug or have a feature request, feel free to contact us at www.mitk.org. \section MAP_RUN_Usage Usage \imageMacro{map_control_example.png, "Example screenshot showing the control plugin in use.", 10} To use the plugin a registration algorithm must be loaded and a moving as well as a target image must be selected.\n The moving image is registered onto the target image. Thus the result is a mapped input image in the geometry (field of view, orientation, spacing) defined by the target image.\n All images are selected in the data manager using multi select (press the CTRL-key while selecting the nodes in the data manager). The first selection is the moving image, the second is the target image.\n If an algorithm is loaded and input images are selected, the plugin will automatically switch to the "Execution" tab. \subsection MAP_RUN_Usage_selection Selection tab \imageMacro{map_control_step1_selection.png, "Details of the selection tab.", 5} In this tab registration algorithms that are selected in the MatchPoint Algorithm Browser can be chosen. In the tab you see the ID of the algorithm selected by the browser and its profile information.\n If you press "Load selected algorithm", the algorithm will be used by the control plugin. The name of the algorithm occurs in the text field "Loaded algorithm" (at the top of the plugin view).\n At this point, it has no effect if you change the selection in the browser. The control plugin will keep the loaded algorithm until you choose to load another one. \subsection MAP_RUN_Usage_exec Execution tab \imageMacro{map_control_step2_execution.png, "Details of the execution tab.", 5} In this tab you can specify a name for the registration job (this will determine the names of the result nodes in the data manager).\n You can also choose to "store registration" (which is normally the goal of the whole process, because this is the very result of the algorithm ;).\n Additionally you can choose "Generate + store mapped result". This is a convenience feature which often saves you the time to use the mapper plugin afterwards. It will do the same like using the mapper plugin with the moving and target image, setting padding value "0" and using "linear interpolation". If you need other settings, skip the convenience generation and use the MatchPoint mapper plugin directly.\n "Start" will trigger the registration process. Some algorithms can be stopped while processing takes place. In those cases, there is a "Stop" button enabled, as soon as the registration process starts. \subsection MAP_RUN_Usage_settings Settings tab \imageMacro{map_control_step3_settings.png, "Details of the settings tab.", 5} In this tab, you can change the parametrization of the loaded algorithm (before it starts), if it offers any possibility to do so. */ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/Manual.dox index 472e54d16c..93f1b219bb 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/Manual.dox @@ -1,50 +1,50 @@ /** -\page org_mitk_gui_qt_matchpoint_evaluator MatchPoint Registration Evaluation View +\page org_mitk_gui_qt_matchpoint_evaluator The MatchPoint Registration Evaluation View \imageMacro{map_evaluator_doc.svg, "Icon of the MatchPoint Registration Evaluator", 3} \tableofcontents \section MAP_REGEVAL_Introduction Introduction This view offers the possibility to evaluate the quality of the registration/mapping of two given images by visual inspection. One may select no registration. Then the images will be displayed in evaluation mode assuming an identity transform (so no mapping). It is one of several MatchPoint registration plug-ins.\n \section MAP_REGEVAL_Contact Contact information This plug-in is being developed by the SIDT group (Software development for Integrated Diagnostics and Therapy) at the German Cancer Research Center (DKFZ). If you have any questions, need support, find a bug or have a feature request, feel free to contact us at www.mitk.org. \section MAP_REGEVAL_Usage Usage \imageMacro{map_view_example.png, "Example screenshot showing the plug-in in use.", 14} To use the evaluation view you must have selected at least the moving and the target image you want to use to evaluate. If you select a registration with referenced target and moving image (the normal state if you generate registrations with the MatchPoint plugins) these images will be auto selected by just clicking on the registration. If you select no registration the view will assume that an identity transform should be used.\n As long as no valid set of data is selected the "Start evaluation" button will be disabled. If its enabled you may start the evaluation mode with it. \imageMacro{map_no_data_selected.png, "Example screenshot showing the state if no data is selected", 5} If the evaluation view is active you can choose between different modes of visualization. For more details see \ref MAP_REGEVAL_Styles.\n To stop the evaluation mode, you may use the "Stop evaluation" button or just close the evaluation view. \remark The evaluation view will use the level window settings of the used images. So to changes the level windowing of the evaluation view, you must change the level windowing of the respective images. \section MAP_REGEVAL_Styles Visualization styles You can choose from the following visualization styles to evaluate the registration/mapping quality:\n \li "Blend": Blends the images with a user defined weight. Default is 50:50. \imageMacro{map_style_blend.png, "Example for mode: Blend", 5} \li "Checkerboard": Checkerboard style that composes both images. You may define the resolution of the checkerboard. \imageMacro{map_style_checkerboard.png, "Example for mode: Checkerboard", 5} \li "Color blend": Color blend of the images (blue: target image; yellow: moving). Areas where you see no color implies good intensity matchings. \imageMacro{map_style_color_blend.png, "Example for mode: Color blend", 5} \li "Contour": Blend mode that display one image as blue "background" and the other image in yellow contours. You may choose the role of the images. \imageMacro{map_style_contour.png, "Example for mode: Contour", 5} \li "Difference": Displays the absolute difference of both images. \li "Wipe": Blend mode that makes a rectilinear combination of the images. You can choose the mode how the images are splitted. The split is synchronized with the current selection. So you may interact with the split border to position it on interesting areas. \imageMacro{map_style_wipe_cross.png, "Example for mode: Wipe cross", 5} \imageMacro{map_style_wipe_horizontal.png, "Example for mode: Wipe horizontal", 5} */ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/Manual.dox index 32216586ad..ac1d07d340 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/Manual.dox @@ -1,64 +1,64 @@ /** -\page org_mitk_gui_qt_matchpoint_framereg MatchPoint Motion/Frame Correction View +\page org_mitk_gui_qt_matchpoint_framereg The MatchPoint Motion/Frame Correction View \imageMacro{"map_framereg_icon_doc.svg", "Icon of the MatchPoint Algorithm Control", 3} \tableofcontents \section MAP_FRAME_Introduction Introduction This plugin offers the user a way to use a selected registration algorithm in order to make a frame/motion correction for a selected 3D+t images. The plugin is for example helpfull if you have a dynamic image with motion artifacts in same time points and you want to reduce/remove this motion artifacts. For the selection of an algorithm please see MatchPoint Algorithm Browser (\ref de_dkfz_matchpoint_mitk_gui_qt_algorithm_browser). \section MAP_FRAME_Contact Contact information This plug-in is being developed by the SIDT group (Software development for Integrated Diagnostics and Therapy) at the German Cancer Research Center (DKFZ). If you have any questions, need support, find a bug or have a feature request, feel free to contact us at www.mitk.org. \section MAP_FRAME_Usage Usage \imageMacro{"map_framereg_example.png" , "Example screenshot showing the plugin in use.", 15} To use the plugin a registration algorithm must be loaded and the image must be selected, that should be corrected.\n The correction is performed that every frame/timpoint of the image is registered to the first frame. And the corrected frames is mapped in the same geometry then the first frame.\n If an algorithm is loaded and input images are selected, the plugin will automatically switch to the "Execution" tab. \subsection MAP_FRAME_Usage_selection Algorithm selection tab \imageMacro{map_step1_selection.png, "Details of the algorithm selection tab.", 6} In this tab you can load/"book" the algorithm selected in the MatchPoint Algorithm Browser. In the tab you see the ID of the algorithm selected by the browser and its profile information.\n If you press "Load selected algorithm", the algorithm will be used by the plugin for the frame correction and the name of the algorithm occurs in the text field "Loaded algorithm" (at the top of the plugin view).\n At this point, it has no effect if you change the the selection in the browser. The plugin will keep the loaded algorithm until you choose to load another one. \subsection MAP_FRAME_Usage_exec Execution tab \imageMacro{map_step2_execution.png, "Details of the execution tab.", 6} In this tab you can specify a name for the correction job (this will determine the names of the result nodes in the data manager).\n "Start" will trigger the correction process. \subsection MAP_FRAME_Usage_settings Settings tab \imageMacro{map_step3_settings.png, "Details of the settings tab.", 6} In this tab, you can (1) define the mapping settings \ref MAP_FRAME_Mapper_Settings "(See details)", used for the corrected frames, or (2) parametrize the loaded algorithm (before it starts), if it offers any possibility to do so. \subsubsection MAP_FRAME_Mapper_Settings Mapper settings For the mapping of corrected images, you have several settings available:\n \li "Allow undefined pixels": Activate to handle pixels of the result image that are not in the field of view of the input image. This pixel will get the "padding value". \li "Allow error pixels": Activate to handle pixels of the result image that can not be mapped because the registration does not support this part of the output image. This pixel will get the "error value". \li "Interpolator": Set to choose the interpolation strategy that should be used for mapping. \ref MAP_FRAME_Interpolation "(see details)" \subsubsection MAP_FRAME_Interpolation Interpolation You can choose from the following interpolation strategies:\n \li "nearest neighbour": Use the value of the nearest pixel. Fastest, but high interpolation errors for gray value images. Right choice for label images or masks. \li "Linear": Fast linear interpolation with often sufficient quality. Tends to blur edges. \li "BSpline (3rd order)": Good trade off between time and quality. \li "Windowed Sinc (Hamming)": Good interpolation quality but very time consuming. \li "Windowed Sinc (Welch)": Good interpolation quality but very time consuming. \subsection MAP_FRAME_Usage_frame_selection Frame selection tab \imageMacro{map_step4_frameselection.png, "Details of the frame selection tab.", 6} In this tab you can specify the frames of the currently selected image that should be corrected. As default all frames of an image will be corrected. If you only select specific frames, these frames will be corrected all other frames will be just copied unchanged. */ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/Manual.dox index 988b5eaf6f..d4af889568 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/Manual.dox @@ -1,69 +1,69 @@ /** -\page org_mitk_gui_qt_matchpoint_manipulator MatchPoint Registration Manipulator View +\page org_mitk_gui_qt_matchpoint_manipulator The MatchPoint Registration Manipulator View \imageMacro{map_manipulator_icon_doc.svg, "Icon of the MatchPoint Registration Manipulator", 3} \tableofcontents \section MAP_REGMANIP_Introduction Introduction This view offers the possibility to manually manipulate a registration to establish a good mapping between data. The effect of manipulation is visualized with to user defined images to allow visual inspection.\n It is one of several MatchPoint registration plug-ins.\n \imageMacro{map_view_example.png, "Example screenshot showing the plug-in in use", 10} \section MAP_REGMANIP_Contact Contact information This plug-in is being developed by the SIDT group (Software development for Integrated Diagnostics and Therapy) at the German Cancer Research Center (DKFZ). If you have any questions, need support, find a bug or have a feature request, feel free to contact us at www.mitk.org. \section MAP_REGMANIP_Usage Usage \imageMacro{map_view_steps.png, "Illustration of the workflow steps.", 7} The typical workflow with the manipulator has following steps/sections: 1. Source selection: You can choose between starting a new registration and using a selected registration. For later option, the registration must be selected in the data manager. \remark If you choose a new registration, the manipulator will automatically pre initialize this new transform to align the centers of the used images and therefore starts with sensible settings. \remark If you choose an existing registration, the registration will *not* be altered. It serves as template/baseline for the manipulation, which will be "on top" of the existing registration. 2. Image selection: To allow visual inspection of the manipulation to images are needed. If you have selected a registration (independent from the source selection mode) the manipulator will use the moving and target images used to determine the selected registration as images for the manipulation. You can also explicitly select images in the data manager (press shift while selecting for multi select). 3. Start manual registration: If all settings are valid, you can start the manipulation. The render windows will automatically switch to the visual inspection mode. The views will be reinitialized to the field of view of the target image. 4. Generation settings: You may choose to give the resulting registration a special name. Additionally you can choose the convenience option to map the moving image with the confirmed registration automatically. 5. Settings: You can alter the settings of the transform (\ref MAP_REGMANIP_TransSettings) and the rendering settings (\ref MAP_REGMANIP_EvalSettings) for the visual inspection. 6. Cancel or confirmation: You may cancel the manipulation process (Closing the view equals cancelation) or confirm the determined registration and store it in the data storage with the given name.\n \section MAP_REGMANIP_TransSettings Transformation settings You can alter the translation and the rotation of the transform. In addition you may choose the center of rotation type. You have the following options:\n - Moving image center: Rotate around the center of the moving image. - World origin: Rotate around (0.0,0.0,0.0), the world origin. - Current navigator position: Rotate around the current navigator position in the render views. \remark FAQ: Why are the translation values "jumping" when I change the center mode or when I am rotating?\n The reason is the relation between center, rotation, and translation.\n A transformation is defined as x' = R (x - C) + C + T\n where x': transformed point; x: point to transform; R: rotation matrix; C: center point; T: translation vector.\n The offset of a transform is defined as O = -RC + C + T\n The offset as well as the rotation matrix stay constant if the center point changes, therefore the translation has to be altered. \note To ease the orientation, the edit fields have background colours which resemble the colours of the plane the changes will "happen".\n For translation, the translation vector will be perpendicular to the indicated plane (The image moves "through" the plane). For rotation, the rotation axis will be perpendicular to the indicated plane. \section MAP_REGMANIP_EvalSettings Evaluation settings The settings you can choose are equal to the settings of the evaluation view (\ref org_mitk_gui_qt_matchpoint_evaluator). Please see the documentation of the MatchPoint Registration Evaluator view for more details. */ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.mapper/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.matchpoint.mapper/documentation/UserManual/Manual.dox index e076a1795b..76b20f6419 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.mapper/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.matchpoint.mapper/documentation/UserManual/Manual.dox @@ -1,85 +1,85 @@ /** -\page org_mitk_gui_qt_matchpoint_mapper MatchPoint Image Mapper View +\page org_mitk_gui_qt_matchpoint_mapper The MatchPoint Image Mapper View \imageMacro{map_mapper_icon_doc.svg, "Icon of the MatchPoint Image Mapper",3} \tableofcontents \section MAP_MAPPER_Introduction Introduction This view offers the possibility to map any image or point set in the data manager using a user selected registration object. Using the Mapper to map images the user can control the field of view (image geometry) the image should be mapped into, as well as interpolation strategy that should be used.\n It is one of several MatchPoint registration plugins.\n Typical usage scenarios\n \li You have registered image I1 onto image I2. Now you want to transfer the segmentation of I1 to I2 in order to evaluate I2 within this mapped segmentation using \ref org_mitk_views_imagestatistics . \li You have registered image I1 onto image I2. Now you want to map I3 (e.g. an other MRI sequence of the same session) also onto I2 with the same registration. \li You have registered image I1 onto image I2. Now you want to map a segmentation done on I1 also onto I2 with the same registration. \li You have registered image I1 onto image I2. Now you want to map a point set of image I1 also onto I2 with the same registration. \section MAP_MAPPER_Contact Contact information This plug-in is being developed by the SIDT group (Software development for Integrated Diagnostics and Therapy) at the German Cancer Research Center (DKFZ). If you have any questions, need support, find a bug or have a feature request, feel free to contact us at www.mitk.org. \section MAP_MAPPER_Usage Usage \imageMacro{map_mapper-examplescreen.png, "Example screenshot showing the Mapper plugin in use.", 14} To use the mapper at least an input data (image or point set) must be selected. Additionally you may select a registration object and a reference image. Registration objects are marked with a small blue icon (e.g. the data "Registration" in the data manager of the screen shot above). The Reference image defines the geometry (field of view, orientation, spacing) that should be used for the result image. By default the view will try to automatically determine the reference image (by default it is the target image of the selected registration). If auto selection cannot determine the reference it will choose the input image as reference. The reference image can be also defined by the user explicitly by activating manual selection.\n REMARK: If you map point sets you can ignore the reference image slot. It has no affect.\n You can multi select registration and data (press the CTRL-key while selecting the nodes in the data manager). The Mapper will automatically sort the selections in the correct "slots" of the view.\n REMARK: The mapping results will be added as child nodes to the used input node.\n REMARK: If you do not select an registration the view will assume that you make an identity transform. This is a convenient way if you just want to resample an image into the geometry of an other image (when no registration is needed). Also in this use case you can take advantage of the different interpolation and sub/super sampling strategies. \imageMacro{map_mapper.png, "Details of the mapper view.", 8} (1) The currently selected registration, that will be used for mapping.\n (2) The currently selected input data, that will be mapped.\n (3) The currently (automatically or by user) selected reference image, that defines the geometry of the result.\n (4) The name of the result data in the data manger.\n (5) The start button(s) to commence the mapping process. For details regarding the two options see \ref MAP_MAPPER_Refine.\n (6) Log windows with messages regarding the mapping process.\n\n Every "slot" has the ability to be locked. If locked the last selection will be kept, regardless the current selection in the data manager. You can use this for example to lock the registration, if you want to map multiple images. Doing so it is enough to just select the next image in the data manager. To lock a slot, click at the "lock" button at the right side (see example images below). \imageMacro{map_node-unlocked.png, "Unlocked slot/node (default state). Changes with the selections in the data manager.",6} \imageMacro{map_node-locked.png, "Locked slot/node. Stays, regardless the selections in the data manager.",6} \section MAP_MAPPER_Refine Mapping or geometry refinement The mapper view offers two options to map images:\n \li "Map" (default) \li "Refine geometry" For images "Map" fills the pixels of the output image by interpolating input image pixels using the registration object. This option always works. But may take longer and introduces interpolation errors, because a new image is resampled.\n The second option "Refine geometry" is only offered, if the registration (more precise its inverse kernel) is matrix based and the selected data is an image. In this case it just clones the image and refines its image geometry (origin and orientation) to project it to the position indicated by the registration; thus no interpolation artefacts are introduced. \remark If you want to use a mapped image in conjunction with the statistic plugin and an mask of the reference image (or you want to proceed any other computation that expects the voxel to be in the same grid for direct numeric comparison), you must use "Map" to ensure the same geometry (including the same image grid; including same spacing and resolution). Otherwise operations like the statistic plugin will fail. \section MAP_MAPPER_Settings Settings If you map the image (and not just refine the geometry), you have several settings available:\n \li "Allow undefined pixels": Activate to handle pixels of the result image that are not in the field of view of the input image. This pixel will get the "padding value". \li "Allow error pixels": Activate to handle pixels of the result image that can not be mapped because the registration does not support this part of the output image. This pixel will get the "error value". \li "Interpolator": Set to choose the interpolation strategy that should be used for mapping. \li "Activate super/sub sampling": Activate if you want to use origin and orientation of the reference image but want to alter the spacing. \section MAP_MAPPER_Interpolation Interpolation You can choose from the following interpolation strategies:\n \li "nearest neighbor": Use the value of the nearest pixel. Fastest, but high interpolation errors for gray value images. Right choice for label images or masks. \li "Linear": Fast linear interpolation with often sufficient quality. Tends to blur edges. \li "BSpline (3rd order)": Good trade off between time and quality. \li "Windowed Sinc (Hamming)": Good interpolation quality but very time consuming. \li "Windowed Sinc (Welch)": Good interpolation quality but very time consuming. \section MAP_MAPPER_Masks Handling of masks/segmentations If you select an mask as input image, the plugin will be automatically reconfigured to settings that are suitable for the task of mapping masks. Most importantly the interpolator will be set to "nearest neighbor". */ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/Manual.dox index c365a8713a..1a23e3e98a 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/Manual.dox @@ -1,21 +1,21 @@ /** -\page org_mitk_gui_qt_matchpoint_visualizer MatchPoint Registration Visualizer View +\page org_mitk_gui_qt_matchpoint_visualizer The MatchPoint Registration Visualizer View \imageMacro{map_vis_icon_doc.svg, "Icon of the Registration Visualizer",3} \tableofcontents \section MAP_VIS_Introduction Introduction This view is in development to offer the user a way to visualize MatchPoint registrations in a MITK scene. Currently only a simple grid visualization and glyph visualization is implemented.\n \remark This is an experimental version and work in progress. So please excuse errors or usage issues and report them. This view will be improved and polished with the next releases. \section MAP_VIS_Contact Contact information This plug-in is being developed by the SIDT group (Software development for Integrated Diagnostics and Therapy) at the German Cancer Research Center (DKFZ). If you have any questions, need support, find a bug or have a feature request, feel free to contact us at www.mitk.org. \section MAP_VIS_Usage Usage Oops. Documentation is missing and to be done. */ diff --git a/Plugins/org.mitk.gui.qt.materialeditor/documentation/UserManual/QmitkSurfaceMaterialEditor.dox b/Plugins/org.mitk.gui.qt.materialeditor/documentation/UserManual/QmitkSurfaceMaterialEditor.dox index d748264e16..1a6935a94d 100644 --- a/Plugins/org.mitk.gui.qt.materialeditor/documentation/UserManual/QmitkSurfaceMaterialEditor.dox +++ b/Plugins/org.mitk.gui.qt.materialeditor/documentation/UserManual/QmitkSurfaceMaterialEditor.dox @@ -1,10 +1,10 @@ /** -\page org_surfacematerialeditor Surface Material Editor +\page org_surfacematerialeditor The Surface Material Editor \imageMacro{QmitkSurfaceMaterialEditor_Icon.png,"Icon of the Surface Material Editor",2.00} The Surface Material Editor shows the properties of the selected data that are relevant for the selected shader. These properties can be filtered to find a specific property. The preview window shows the representation of a neutral 3D object with the currently selected settings. \imageMacro{QmitkSurfaceMaterialEditor_Gui.png,"The Surface Material Editor",10.92} */ \ 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 8c5aa3850d..811c479e3e 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 Measurement Toolbox +\page org_mitk_gui_qt_measurementtoolbox The 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 ea26cae85b..4c8c0f3c7c 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 Movie Maker +\page org_mitk_gui_qt_moviemaker The 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 5635b65a1b..71a6a17ed4 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 Screenshot Maker +\page org_mitk_views_screenshotmaker The 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 6d5bd1d481..5259fa5e35 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 Multilabel Segmentation +\page org_mitk_views_multilabelsegmentation The 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.openigtlink/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.openigtlink/documentation/UserManual/Manual.dox index d60a2c51fd..f063230e77 100644 --- a/Plugins/org.mitk.gui.qt.openigtlink/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.openigtlink/documentation/UserManual/Manual.dox @@ -1,17 +1,17 @@ /** -\page org_mitk_gui_qt_igtlplugin IGT Plugin +\page org_mitk_gui_qt_igtlplugin The IGT Plugin \imageMacro{icon.png,"Icon of Igtlplugin",2.00} \tableofcontents \section org_mitk_gui_qt_igtlpluginOverview Overview Describe the features of your awesome plugin here */ diff --git a/Plugins/org.mitk.gui.qt.overlaymanager/documentation/UserManual/QmitkOverlayManager.dox b/Plugins/org.mitk.gui.qt.overlaymanager/documentation/UserManual/QmitkOverlayManager.dox index 0d52ed9311..8520e79ce4 100644 --- a/Plugins/org.mitk.gui.qt.overlaymanager/documentation/UserManual/QmitkOverlayManager.dox +++ b/Plugins/org.mitk.gui.qt.overlaymanager/documentation/UserManual/QmitkOverlayManager.dox @@ -1,11 +1,11 @@ /** -\page org_mitk_gui_qt_overlaymanager Overlay Manager Plugin +\page org_mitk_gui_qt_overlaymanager The Overlay Manager Plugin \imageMacro{icon.png,"Icon of Overlaymanager",2.00} \tableofcontents \section org_mitk_gui_qt_overlaymanagerOverview Overview The OverlayManager plugin allows to view all annotations currently managed. Properties of added annotations can be modified. Additionally it is possible to create some basic overlays and register them. */ diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/Manual.dox index 340092ff68..79c3c04ad5 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/Manual.dox @@ -1,16 +1,16 @@ /** -\page org_mitk_gui_qt_pharmacokinetics_concentration_mri Concentration Curve Converter View +\page org_mitk_gui_qt_pharmacokinetics_concentration_mri The Concentration Curve Converter View \imageMacro{pharmacokinetics_concentration_doc.svg,"Icon of the Concentration Curve Converter View",3.0} \tableofcontents \section org_mitk_gui_qt_pharmacokinetics_concentration_mri_overview Overview Stand-alone conversion of image signal intensities to contrast agent concentration units can be performed with a dedicated plugin. The plugin distinguishes between T1 weighted and T2 weighted sequences. T1 conversion can be performed in terms of absolute and relative signal enhancement as well as turbo flash sequences for both 3D images (baseline images S0 without contrast enhancement (pre-contrast) input required) and 4D sequences (baseline selected as first frame of time series). \section org_mitk_gui_qt_pharmacokinetics_concentration_mri_Contact Contact information This plug-in is being developed by Charlotte Debus and the SIDT group (Software development for Integrated Diagnostics and Therapy) at the German Cancer Research Center (DKFZ). If you have any questions, need support, find a bug or have a feature request, feel free to contact us at www.mitk.org. */ diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/documentation/UserManual/Manual.dox index 4536863bb9..d5ece877b8 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/documentation/UserManual/Manual.dox @@ -1,26 +1,26 @@ /** -\page org_mitk_gui_qt_pharmacokinetics_curvedescriptor Perfusion Curve Description Parameters View +\page org_mitk_gui_qt_pharmacokinetics_curvedescriptor The Perfusion Curve Description Parameters View \imageMacro{pharmacokinetics_curve_desc_doc.svg,"Icon of the Perfusion Curve Description Parameters View",3.0} \tableofcontents \section org_mitk_gui_qt_pharmacokinetics_curvedescriptor_overview Overview In cases where data quality is not sufficient for dedicated pharmacokinetic analysis, or if global scouting of the overall image should be performed to identify regions of interest, it is often advisable to use semi-quantitative measures that describe the general shape and type of the curve. The Perfusion Curve Description Parameters plugin can be used to voxelwise calculate these parameters. Currently the following parameters are offered by the tool: - area-under-the-curve (AUC) - area-under the first moment curve (AUMC), - mean-residence-time (MRT; AUMC/AUC) - time to peak and maximum signal These parameters are calculated directly from the sampled data. AUC and AUMC are calculated by step-wise integration with linear interpolation between sampling points. Maximum and time to peak are derived from the highest intensity value (overall maximum) of all data points. Note: If semi-quantitative parameters should be calculated from concentration time curves rather than raw data signal intensities, use the concentration n curve converter view (See 5) Parameters of interest can be selected from the list. Selecting a 4D image in the Data manager enables the Calculate Parameters button. Resulting parameter maps will afterwards be added to the data manager as subnodes to the analyzed 4D image. \section org_mitk_gui_qt_pharmacokinetics_curvedescriptor_Contact Contact information This plug-in is being developed by Charlotte Debus and the SIDT group (Software development for Integrated Diagnostics and Therapy) at the German Cancer Research Center (DKFZ). If you have any questions, need support, find a bug or have a feature request, feel free to contact us at www.mitk.org. */ diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.simulation/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.pharmacokinetics.simulation/documentation/UserManual/Manual.dox index f495f3409c..667143d2b5 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.simulation/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.simulation/documentation/UserManual/Manual.dox @@ -1,5 +1,5 @@ /** -\page org_mitk_gui_qt_pharmacokinetics_simulation Perfusion Data Simulation View +\page org_mitk_gui_qt_pharmacokinetics_simulation The Perfusion Data Simulation View */ diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/documentation/UserManual/Manual.dox index 719631874f..4497cf1a23 100644 --- a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/documentation/UserManual/Manual.dox @@ -1,17 +1,17 @@ /** -\page org_mitk_gui_qt_photoacoustics_pausmotioncompensation Pausmotioncompensation +\page org_mitk_gui_qt_photoacoustics_pausmotioncompensation The Pausmotioncompensation \imageMacro{icon.png,"Icon of Pausmotioncompensation",2.00} \tableofcontents \section org_mitk_gui_qt_photoacoustics_pausmotioncompensationOverview Overview Describe the features of your awesome plugin here */ 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 224f18ebbb..aeeced827a 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 The 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.pointsetinteractionmultispectrum/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/documentation/UserManual/Manual.dox index a3df95b4f8..d9fee1b600 100644 --- a/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/documentation/UserManual/Manual.dox @@ -1,17 +1,17 @@ /** -\page org_mitk_gui_qt_pointsetinteractionmultispectrum Point Set Interaction Multispectrum +\page org_mitk_gui_qt_pointsetinteractionmultispectrum The Point Set Interaction Multispectrum \imageMacro{icon.png,"Icon of Pointsetinteractionmultispectrum",2.00} \tableofcontents \section org_mitk_gui_qt_pointsetinteractionmultispectrumOverview Overview Describe the features of your awesome plugin here */ diff --git a/Plugins/org.mitk.gui.qt.preprocessing.resampling/documentation/UserManual/QmitkBasicImageProcessing_resampling.dox b/Plugins/org.mitk.gui.qt.preprocessing.resampling/documentation/UserManual/QmitkBasicImageProcessing_resampling.dox index 23475f73c1..159087be57 100644 --- a/Plugins/org.mitk.gui.qt.preprocessing.resampling/documentation/UserManual/QmitkBasicImageProcessing_resampling.dox +++ b/Plugins/org.mitk.gui.qt.preprocessing.resampling/documentation/UserManual/QmitkBasicImageProcessing_resampling.dox @@ -1,5 +1,5 @@ /** -\page org_mitk_gui_qt_preprocessing_resampling Preprocessing and Resampling +\page org_mitk_gui_qt_preprocessing_resampling The Preprocessing and Resampling */ 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 48d9f15f65..114be980c4 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 Python Plugin +\page org_mitk_gui_qt_python The 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.radiomics/documentation/UserManual/QmitkPhenotypingPortalPage.dox b/Plugins/org.mitk.gui.qt.radiomics/documentation/UserManual/QmitkPhenotypingPortalPage.dox index 090d76edd3..a2cc0e7284 100644 --- a/Plugins/org.mitk.gui.qt.radiomics/documentation/UserManual/QmitkPhenotypingPortalPage.dox +++ b/Plugins/org.mitk.gui.qt.radiomics/documentation/UserManual/QmitkPhenotypingPortalPage.dox @@ -1,41 +1,41 @@ /** -\page org_mitk_gui_qt_mitkphenotyping Phenotyping +\page org_mitk_gui_qt_mitkphenotyping The Phenotyping \tableofcontents MITK Phenotyping is a selection of algorithms that can be used to extract image-based phenotypes, for example using a radiomics approach. The software is part of the research of the Division of Medical Image Computing of the German Cancer Research Center (DKFZ). MITK Phenotyping is not intended to be a single application, it is rather a collection of the necessary plugins within the offical MITK releases. The functionality of MITK Phenotyping can be accessed in different ways: Using the graphical interface using the Plugins listed below, using command line applications, or using one of the programming interfaces. \section org_mitk_gui_qt_mitkphenotyping_Tutorials Tutorials \li \subpage org_mitk_views_radiomicstutorial_gui_portal A tutorial on how to use the grapical interface of MITK Phenotying \section org_mitk_gui_qt_mitkphenotyping_Views Views \subsection sub2 Specific Views: Views that were developed with the main focus on Radiomics. They still might be used in other use-cases as well: \li \subpage org_mitk_views_radiomicstransformationview : Image transformations like Resampling, Laplacian of Gaussian, and Wavelet Transformations \li \subpage org_mitk_views_radiomicsmaskprocessingview : Processing and Cleaning of Masks \li \subpage org_mitk_views_radiomicsarithmetricview : Processing images using mathematical operations \li \subpage org_mitk_views_radiomicsstatisticview : Calculate Radiomics Features \subsection sub1 Non-Specific Views: This section contains views that are included within MITK Phenotyping, but were developed with a broader application in mind. \li \subpage org_mitk_views_basicimageprocessing : Deprecated plugin for performing different image-related tasks like subtraction, mutliplaction, filtering etc. \li \subpage org_mitk_gui_qt_matchpoint_algorithm_browser : Selection of MatchPoint (Registration) Algorithm \li \subpage org_mitk_gui_qt_matchpoint_algorithm_control : Configuring and Controlling MatchPoint (Registration) Algorithm \li \subpage org_mitk_gui_qt_matchpoint_evaluator : Evaluate the Registration performance using MatchPoint \li \subpage org_mitk_gui_qt_matchpoint_manipulator : Adapt a registration calculated using MatchPoint \li \subpage org_mitk_gui_qt_matchpoint_mapper : Apply a MatchPoint Registration to a specific image \li \subpage org_mitk_gui_qt_matchpoint_visualizer : Visualize a Registration obtained with MatchPoint \li \subpage org_mitk_gui_qt_matchpoint_algorithm_batch : Running MatchPoint over multiple images (BatchMode) \li \subpage org_mitk_views_multilabelsegmentation : Create and editing of Multilabel-Segmentations. \li \subpage org_mitk_views_segmentation : Create simple segmentations \li \subpage org_mitk_views_segmentationutilities : Utilities for the processing of simple segmentations. \section radiomics_miniapps MiniApps (Command line Tools) \li \subpage MiniAppExplainPage Explanation of the Command Line App concept in MITK \li \subpage mitkBasicImageProcessingMiniAppsPortalPage : List of common preprocessing MiniApps \li \subpage mitkClassificationMiniAppsPortalPage : (Incomplete) list of MITK Classification MiniApps */ 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 ada4d17731..4f609da6ec 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 Remeshing +\page org_mitk_gui_qt_remeshing The 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.renderwindowmanager/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.renderwindowmanager/documentation/UserManual/Manual.dox index 5b00c3db4f..62b08443be 100644 --- a/Plugins/org.mitk.gui.qt.renderwindowmanager/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.renderwindowmanager/documentation/UserManual/Manual.dox @@ -1,17 +1,17 @@ /** -\page org_mitk_gui_qt_renderwindowmanager Renderwindowmanager +\page org_mitk_gui_qt_renderwindowmanager The Renderwindowmanager \imageMacro{icon.png,"Icon of Renderwindowmanager",2.00} \tableofcontents \section org_mitk_gui_qt_renderwindowmanagerOverview Overview Describe the features of your awesome plugin here */ 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 5cad88bfd3..8465c4c126 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 Segmentation +\page org_mitk_views_segmentation The 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.spectrocamrecorder/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.spectrocamrecorder/documentation/UserManual/Manual.dox index dbdd4f158e..994c6468d9 100644 --- a/Plugins/org.mitk.gui.qt.spectrocamrecorder/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.spectrocamrecorder/documentation/UserManual/Manual.dox @@ -1,17 +1,17 @@ /** -\page org_mitk_gui_qt_spectrocamrecorder Spectrocamrecorder +\page org_mitk_gui_qt_spectrocamrecorder The Spectrocamrecorder \imageMacro{icon.png,"Icon of Spectrocamrecorder",2.00} \tableofcontents \section org_mitk_gui_qt_spectrocamrecorderOverview Overview Describe the features of your awesome plugin here */ diff --git a/Plugins/org.mitk.gui.qt.toftutorial/documentation/Manual/Manual.dox b/Plugins/org.mitk.gui.qt.toftutorial/documentation/Manual/Manual.dox index c1d1db20c4..00b0777dde 100644 --- a/Plugins/org.mitk.gui.qt.toftutorial/documentation/Manual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.toftutorial/documentation/Manual/Manual.dox @@ -1,13 +1,13 @@ /** -\page org_toftutorial ToF Tutorial +\page org_toftutorial The ToF Tutorial \imageMacro{icon.png,"Icon of ToFTutorial",2} Available sections: - \ref ToFTutorialOverview \section ToFTutorialOverview This is the description for the ToFTutorial. */ diff --git a/Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/QmitkUltrasound.dox b/Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/QmitkUltrasound.dox index b07ad8ca3d..4abc2ba488 100644 --- a/Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/QmitkUltrasound.dox +++ b/Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/QmitkUltrasound.dox @@ -1,95 +1,95 @@ /** -\page org_mitk_gui_qt_ultrasound Ultrasound Plugin +\page org_mitk_gui_qt_ultrasound The Ultrasound Plugin \imageMacro{QmitkUltrasound_Icon.png,"Icon of the Ultrasound Plugin",2.12} \tableofcontents \section org_mitk_gui_qt_ultrasoundOverview Overview This plugin offers a simple interface to create and manage ultrasound devices. Devices, once configured, will be stored and loaded on the next start of MITK. One can configure several aspects of the images acquired. Last but not least, this plugin makes the configured devices available as a microservice, exposing them for further usage in other plugins. \section org_mitk_gui_qt_ultrasoundPrerequisites Prerequisites To make use of this plugin, you obviously require an ultrasound device. The device must have a video output or must be one of the supported API devices (at the moment only Telemed LogicScan 128 is supported as an API device. Typical video outputs are: HDMI, DVI, VGA and S-Video. You also need a Video-Grabber that can acquire the image data from the ultrasound device. In principal, this plugin is compatible with any grabber that allows the operating system to access it's functionality. However, not all grabbers are created equal. Make sure your grabber supports the video-out offered by your ultrasound device and that it can achieve a satisfying framerate. We have made good experiences with epiphan Grabbers and currently recommend the Epiphan DVI2USB 3.0 device which supports HDMI, DVI and VGA, but less costly grabbers certainly are an option. \section org_mitk_gui_qt_ultrasoundCreateDevice Creating an Device To configure an ultrasound device as a video device, connect it to the grabber and the grabber to the computer. Start the ultrasound device and open the ultrasound plugin. The devicemanager will open. \imageMacro{QmitkUltrasound_DeviceManagement.png,"MITK Screenshot With the Device Manager Activated",7.54} Any currently configured devices are listed in the box, which accordingly is empty now. The creation of API devices depends on the device. A Telemed device would be listed in the box if this version of MITK was compiled with support for Telemed devices (see \link USHardwareTelemedPage\endlink). Such a device requires no configuration. Click "New Video Device" if you want to create a new video device. \imageMacro{QmitkUltrasound_NewVideoDevice.png,"The 'New Device' form",7.62} In the appearing form, enter descriptive data on your device in the corresponding fields. Manufacturer and model will be used to display the device in MITK. You may choose the video source ID if more than one is available (as is the case on laptops with built-in webcams). Try 0 and 1. If the wrong camera is addressed, simply try the next ID. Most ultrasound images are grey scale, so using a grey scale conversion doesn't take information away from the image, but makes processing images significantly faster. Only uncheck this box if you require color. Click "Add Video Device" to save your changes. \imageMacro{QmitkUltrasound_DeviceManagement2.png,"Devicemanager With a Configured Device",7.64} An ultrasound device in MITK can be activated or removed. Removing may not be available for some API devices. The device you just created is available to all other plugins in MITK, but does not yet generate image data. Activating the device will start image generating. \section org_mitk_gui_qt_ultrasoundUseDevice Using an Ultrasound Device Click the device, then click "Activate Device". The device is now activated and generates image data continuously. The device is listed in the box on the bottom of the view now. Viewing of the image data can be started by selecting the device in this list and click the "Start Viewing" button. \imageMacro{QmitkUltrasound_Imaging.png,"US Imaging Tab for a Video Device",7.60} You can adjust the cropping parameters to reduce the acquired image size which will further increase speed and remove unnecessary information. All changes are saved and restored whenever MITK is started. If an API device was selected, buttons for controlling the b mode imaging may be available. This depends on the implementation of a control interface for this specific device in MITK. \imageMacro{QmikUltrasound_BModeControls.png,"B Mode Controls for an API Device",7} */ 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 8ca5f20e0a..e44be368d5 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 View Navigator +\page org_mitk_gui_qt_viewnavigator The 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} */ diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization.dox b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization.dox index 786233b54b..49360ff183 100644 --- a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization.dox +++ b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization.dox @@ -1,154 +1,154 @@ /** -\page org_mitk_views_volumevisualization Volume Visualization Plugin +\page org_mitk_views_volumevisualization The Volume Visualization Plugin \imageMacro{volume_visualization.svg,"Icon of the Volume Visualization Plugin",2.00} \tableofcontents \section QVV_Overview Overview The Volume Visualization Plugin is a basic tool for visualizing three dimensional medical images. MITK provides generic transfer function presets for medical CT data. These functions, that map the gray-value to color and opacity, can be interactively edited. Additionally, there are controls to quickly generate common used transfer function shapes like the threshold and bell curve to help identify a range of grey-values. \imageMacro{QmitkVolumeVisualization_Overview.png,"",16.00} \section QVV_EnableVRPage Enable Volume Rendering \subsection QVV_LoadingImage Loading an image into the application Load an image into the application by Volume Visualization imposes following restrictions on images: \subsection QVV_EnableVR Enable Volumerendering \imageMacro{QmitkVolumeVisualization_Checkboxen.png,"",8.21} Select an image in datamanager and click on the checkbox left of "Volumerendering". Please be patient, while the image is prepared for rendering, which can take up to a half minute. \subsection QVV_LODGPU Dropdown menus for the rendering and blend modes Two dropdown menus allow selection of rendering mode (Default, RayCast, GPU) and the blend mode (Composite, Max, Min, Avg, Add). Any Volume Rendering mode requires a lot of computing resources including processor, memory and often also graphics card. The Default selection usually finds the best rendering mode for the available hardware. Alternatively, it is possible to manually specify the selections RayCast and GPU. The RayCast selection is based on CPU computation and therefore typically slow, but allows to render without hardware acceleration. The GPU selection uses computing resources on the graphics card to accelerate volume rendering. It requires a powerful graphics card and OpenGL hardware support for shaders, but achieves much higher frame rates than software-rendering. Blend modes define how the volume voxels intersected by the rendering rays are pooled. The composite mode specifies standard volume rendering, for which each voxel contributes equally with opacity and color. Other blend modes simply visualize the voxel of maximum / minimum intensity and average / add the intentities along the rendering ray. \section QVV_PresetPage Applying premade presets \subsection QVV_Preset Internal presets There are some internal presets given, that can be used with normal CT data (given in Houndsfield units). A large set of medical data has been tested with that presets, but it may not suit on some special cases. Click on the "Preset" tab for using internal or custom presets. \imageMacro{QmitkVolumeVisualization_InternalPresets.png,"",8.30} \subsection QVV_CustomPreset Saving and loading custom presets After creating or editing a transferfunction (see \ref QVV_Editing or \ref QVV_ThresholdBell), the custom transferfunction can be stored and later retrieved on the filesystem. Click "Save" (respectively "Load") button to save (load) the threshold-, color- and gradient function combined in a single .xml file. \section QVV_ThresholdBell Interactively create transferfunctions Beside the possibility to directly edit the transferfunctions (\ref QVV_Editing), a one-click generation of two commonly known shapes is given. Both generators have two parameters, that can be modified by first clicking on the cross and then moving the mouse up/down and left/right. The first parameter "center" (controlled by horizontal movement of the mouse) specifies the gravalue where the center of the shape will be located. The second parameter "width" (controlled by vertical movement of the mouse) specifies the width (or steepness) of the shape. \subsection Threshold Click on the "Threshold" tab to active the threshold function generator. \imageMacro{QmitkVolumeVisualization_Threshold.png,"",8.21} A threshold shape begins with zero and raises to one across the "center" parameter. Lower widths results in steeper threshold functions. \subsection Bell Click on the "Bell" tab to active the threshold function generator. \imageMacro{QmitkVolumeVisualization_Bell.png,"",8.23} A threshold shape begins with zero and raises to one at the "center" parameter and the lowers agains to zero. The "width" parameter correspondens to the width of the bell. \section QVV_Editing Customize transferfunctions in detail \subsection QVV_Navigate Choosing grayvalue interval to edit \imageMacro{QmitkVolumeVisualization_Slider.png,"",8.23} To navigate across the grayvalue range or to zoom in some ranges use the "range"-slider. All three function editors have in common following: There are three transferfunctions to customize: \subsection QVV_GO Grayvalue -> Opacity \imageMacro{QmitkVolumeVisualization_Opacity.png,"grayvalues will be mapped to opacity.",8.04} An opacity of 0 means total transparent, an opacity of 1 means total opaque. \subsection QVV_GC Grayvalue -> Color \imageMacro{QmitkVolumeVisualization_Color.png,"grayvalues will be mapped to color.",8.81} The color transferfunction editor also allows by double-clicking a point to change its color. \subsection QVV_GGO Grayvalue and Gradient -> Opacity \imageMacro{QmitkVolumeVisualization_Gradient.png,"",8.85} Here the influence of the gradient is controllable at specific grayvalues. */ diff --git a/Plugins/org.mitk.gui.qt.xnat/documentation/UserManual/QmitkXnatPluginManual.dox b/Plugins/org.mitk.gui.qt.xnat/documentation/UserManual/QmitkXnatPluginManual.dox index 7af2120575..c83dcee11d 100644 --- a/Plugins/org.mitk.gui.qt.xnat/documentation/UserManual/QmitkXnatPluginManual.dox +++ b/Plugins/org.mitk.gui.qt.xnat/documentation/UserManual/QmitkXnatPluginManual.dox @@ -1,113 +1,113 @@ /** -\page org_mitk_gui_qt_xnat XNAT Plugin +\page org_mitk_gui_qt_xnat The XNAT Plugin \imageMacro{xnat-docu-icon.png,"Icon of XNAT Plugin",1.00} \tableofcontents \section org_mitk_gui_qt_xnatOverview Overview This plug-in is allows the communication with a XNAT server from within MITK. The benefits of this plug-in are: \imageMacro{QmitkXnat_IMGTreeBrowser.png,"The XNAT tree-browser plugin", 6.00} \section org_mitk_gui_qt_xnatConnection Connect to XNAT For communicating with XNAT you have to connect to your XNAT instance. \subsection org_mitk_gui_qt_xnatPreferences XNAT preferences In order to establish the connection to XNAT you have to specify the XNAT server address, username and password in the XNAT preference page. It is also possible to specify a network proxy if you are behind one (this could lead to connection errors). Via the download path you can tell MITK where to save the data that is uploaded or downloaded. A screenshot of the preference page can be seen below. \imageMacro{QmitkXnat_IMGPreferences.png,"The XNAT preference page", 10.00} \subsection org_mitk_gui_qt_xnatSessionHandling Session time-out handling Once you are connected to XNAT, MITK takes care about the session handling. A existing XNAT session times out after a certain period of inactivity, usually after 15 minutes. One minute before session time-out MITK asks you to renew the session: \imageMacro{QmitkXnat_IMGSessionAboutToTimeOut.png,"Notification that the session will time-out in a minute", 6.00} If you do not renew the session MITK notifies you if the session has expired: \imageMacro{QmitkXnat_IMGSessionExpired.png,"Notification that the session has expired", 6.00} \section org_mitk_gui_qt_xnatBrowsing Browse data Once you are connected to XNAT, MITK displays the XNAT data hierachy as a tree within the XNAT tree browser. You can browse through the data by expanding the tree items ( which ist also possible via double click). If you hover the mouse cursor over an item you will see a tool tip with detailed information. The following table gives an overview about the icons of the treeview and the related XNAT objects
XNAT Icon Overview
Icon XNAT object
\imageMacro{xnat-server.png, "" ,0.50} XNAT Server
\imageMacro{xnat-project.png, "" ,0.50} XNAT Project
\imageMacro{xnat-subject.png, "" ,0.50} XNAT Subject
\imageMacro{xnat-experiment.png, "" ,0.50} XNAT Experiment
\imageMacro{xnat-folder-icon.png, "" ,0.50} XNAT Scan top-level folder
\imageMacro{xnat-scan.png, "" ,0.50} XNAT Scan
\imageMacro{xnat-folder-icon.png, "" ,0.50} XNAT Resource top-level folder
\imageMacro{xnat-resource.png, "" ,0.50} XNAT Resource folder
\imageMacro{xnat-file.png, "" ,0.50} XNAT File
If you have selected a XNAT project, subject or experiment, MITK displays detailed information in a separate info area below the tree browser \section org_mitk_gui_qt_xnatDownload Download data MITK allows you to download your data from XNAT. You can either simply download the data to your file system or your can download it and open it immediately in the workbench. \subsection org_mitk_gui_qt_xnatDownload_file_system Download data to file system If you just want to download data, simply right-click on a XNAT file or scan on the tree brower and select "Download". The data will be stored in the specified download location. \subsection org_mitk_gui_qt_xnatDownload_in_MITK Download data and open it in MITK You can download and open data in three ways: \imageMacro{QmitkXnat_IMGDownloadButton.png,"The XNAT dowload button", 16.00} \section org_mitk_gui_qt_xnatUpload Upload data You can also upload data to XNAT from within the workbench. Please note that it is currently only possible to upload files as resources. Uploading DICOMs is not yet available. \subsection org_mitk_gui_qt_xnatUpload1 Upload from file system If you just want to upload a local file, right-click on a resource and select "Upload". A file dialog will open, which allows you to select a file for upload. \subsection org_mitk_gui_qt_xnatUpload2 Upload via data manager If you want to upload data from within the MITK Workbench you can simply right-click on the data node in the data manager and select "Upload to XNAT". An "XNAT Upload dialog" will appear: \imageMacro{QmitkXnat_IMGUploadDialog.png,"The XNAT upload dialog", 16.00} You can then either select a existing resource folder if MITK is able to find ones or you can select the upload destination in a tree view. \subsection org_mitk_gui_qt_xnatUpload3 Upload via drag and drop Another way to upload the data is to drag the data node on the XNAT resource where you want to upload it to. \subsection org_mitk_gui_qt_xnatUpload4 Upload via XNAT Plugin Finally, if you select a data node and you select a XNAT resource, the upload button of the XNAT plugin will be enabled. If you click on that, the data will be uploaded. \imageMacro{QmitkXnat_IMGUploadButton.png,"The XNAT upload button", 16.00} \section org_mitk_gui_qt_xnatAddResourceFolder Create a resource folder You can also create new resources (i.e. folders to group your files in XNAT). Therefor you can either right-click on a project, subject, experiment or scan and enter the name of the folder in the appearing dialog. Or you simply select one of these items and click on the "Add folder button" above the tree browser. \imageMacro{QmitkXnat_IMGAddFolderButton.png,"The XNAT add folder button", 16.00} \subsection org_mitk_gui_qt_xnatCreateSubject Create a subject You can create subjects by right-clicking on a project and selecting "Create new subject". A dialog will appear where you have to enter the subject information. \subsection org_mitk_gui_qt_xnatCreateExperiment Create a experiment You can create experiments by right-clicking on a subject and selecting "Create new experiment". A dialog will appear where you have to enter the experiment information. */