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 fee72e6aca..39073f4f70 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 +1,55 @@ /** -\page org_mitk_views_matchpoint_framereg The MatchPoint Motion/Frame Correction View +\page org_mitk_views_matchpoint_framereg The MatchPoint 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). +This view offers the user a way to use a selected registration algorithm in order to apply a frame correction to a selected 3D+t image. +This is for example useful if you have a dynamic image with motion artifacts in some time points and you want to reduce/remove these motion artifacts. -\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. +\imageMacro{"map_framereg_example.png" , "Example screenshot of the view.", 15} +To use the view, a 3D+t image must be selected and a registration algorithm must be loaded. For the selection of an algorithm please see \ref org_mitk_views_matchpoint_algorithm_browser.\n +The correction is performed such that every time frame of the image is registered to the first time frame. And the corrected time frames are mapped to the same geometry as the first frame.\n +If an algorithm is loaded and an input images is selected, the view 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. +In this tab, you can load the algorithm selected in the MatchPoint Algorithm Browser. In the area below the selection button the profile information of the registration algorithm is displayed. +For a detailed description of the profile characteristics the user is referred to \ref org_mitk_views_matchpoint_algorithm_browser .\n +When clicking the Load selected algorithm button, the selected algorithm will be used by the view for the frame correction and the name of the algorithm will be displayed in the text field Loaded algorithm at the top of the view.\n +At this point, it has no effect if you change the the selection in the algorithm browser. The view 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. +Clicking the Start button 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. +In this tab, you can configure the \ref MAP_FRAME_Mapper_Settings which are used for the corrected frames, or parameterize the loaded algorithm (before it starts), if it offers any possibility to do so. -\subsubsection MAP_FRAME_Mapper_Settings Mapper settings +\subsubsection MAP_FRAME_Mapper_Settings Mapping 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)" +\li Allow undefined pixels Activate to handle pixels of the result image that are not in the field of view of the input image. These pixels 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. These pixels will get the error value. +\li Interpolator Set to choose the interpolation strategy that should be used for mapping. See details at \ref MAP_FRAME_Interpolation . \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. +\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. +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 selected. +If you only select specific frames, these frames will be corrected whilst all other frames will be just copied unchanged. */