diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginGeneralManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginGeneralManualsList.dox index 78f1b417e2..f580efdfcc 100644 --- a/Documentation/Doxygen/2-UserManual/MITKPluginGeneralManualsList.dox +++ b/Documentation/Doxygen/2-UserManual/MITKPluginGeneralManualsList.dox @@ -1,32 +1,32 @@ /** \page PluginListGeneralPage List of General Purpose Plugins \li \subpage org_mitk_views_basicimageprocessing \li \subpage org_mitk_views_datamanager \li \subpage org_mitk_views_properties \li \subpage org_mitk_editors_dicombrowser \li \subpage org_mitk_gui_qt_dicominspector \li \subpage org_mitk_views_imagecropper \li \subpage org_mitk_views_imagenavigator \li \subpage org_blueberry_ui_qt_log \li \subpage org_mitk_gui_qt_matchpoint_algorithm_batch - \li \subpage org_mitk_views_qt_matchpoint_algorithm_browser - \li \subpage org_mitk_views_qt_matchpoint_algorithm_control + \li \subpage org_mitk_views_matchpoint_algorithm_browser + \li \subpage org_mitk_views_matchpoint_algorithm_control \li \subpage org_mitk_views_matchpoint_evaluator - \li \subpage org_mitk_views_qt_matchpoint_framereg - \li \subpage org_mitk_views_qt_matchpoint_manipulator + \li \subpage org_mitk_views_matchpoint_framereg + \li \subpage org_mitk_views_matchpoint_manipulator \li \subpage org_mitk_views_matchpoint_mapper - \li \subpage org_mitk_views_qt_matchpoint_visualizer + \li \subpage org_mitk_views_matchpoint_visualizer \li \subpage org_mitk_gui_qt_measurementtoolbox \li \subpage org_mitk_views_moviemaker \li \subpage org_mitk_views_multilabelsegmentation \li \subpage org_mitk_views_pointsetinteraction \li \subpage org_mitk_gui_qt_python \li \subpage org_mitk_gui_qt_remeshing \li \subpage org_mitk_views_screenshotmaker \li \subpage org_mitk_views_segmentation \li \subpage org_mitk_gui_qt_flow_segmentation \li \subpage org_mitk_gui_qt_viewnavigator \li \subpage org_mitk_views_volumevisualization */ 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 c00ab5da9b..6a9058e5ca 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 +1,77 @@ /** -\page org_mitk_gui_qt_matchpoint_manipulator The MatchPoint Registration Manipulator View +\page org_mitk_views_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 +The effect of manipulation is visualized with two 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. +\imageMacro{map_view_manipulator_example.png, "Example screenshot showing the main elements of the view used to start a manipulation.", 14} +The typical workflow with the manipulator has following steps/sections:\n\n +(1) Source selection: You can choose between starting a new registration and using a selected registration. For later option, +the registration must be selected (see (2)). \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. +(2) Registration slot: Shows the currently selected registration that serves as base line. Only active if (1) is selected appropriately. Click to change.\n\n + +(3) Auto select option: If active the view will try to deduce and automatically select (if loaded in the application) the moving and target image when the base line registration changes. The view assumes that the moving and target images used to determine the registration should be used to illustrate the effects of the manipulation.\n\n + +(4) Moving image slot: To allow visual inspection of the manipulation a moving image must be specified. This image is mapped by the manipulated registration to illustrate the effects of the manipulation. Click to change the image.\n\n + +(5) Target image slot: To allow visual inspection of the manipulation a target image must be specified. This image is used to compare against the mapped moving image to illustrate the effects of the manipulation. Click to change the image.\n\n + +(6) 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.\n\n\n + +\imageMacro{map_view_manipulator_started.png, "Controls after the manipulation session is started.", 14} + +(7) New registration name: You may choose to give the resulting registration a special name.\n\n + +(8) Additionally you can choose the convenience +option to map the moving image with the confirmed registration automatically and also store the mapped image.\n\n + +(9) 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.\n\n + +(10) Translation parameters: You can alter the translation parameter of the transform by using the sliders or the spinboxes. For more details see transform settings section (\ref MAP_REGMANIP_TransSettings).\n\n + +(11) Rotation parameters: You can alter the rotation parameter of the transform by using the sliders or the spinboxes. For more details see transform settings section (\ref MAP_REGMANIP_TransSettings).\n\n -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. +(12) Center of rotation: You may choose the center of rotation for your manipulation. For more details see transform settings section (\ref MAP_REGMANIP_TransSettings).\n\n -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. +(13) Confirmation: You may confirm the determined registration and store it in the data storage with the given name. The manipulation session will be automatically closed.\n\n -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 +(14) Cancel: You may cancel the session any time. No changes will be stored and the manipulation session will be automatically closed.\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 +\note To ease the orientation, the edit fields have background colors which resemble the colors 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_views_matchpoint_evaluator). Please see the documentation of the MatchPoint Registration Evaluator view for more details. */ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_example.png b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_example.png deleted file mode 100644 index ab8d6e5d1f..0000000000 Binary files a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_example.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_example.png b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_example.png new file mode 100644 index 0000000000..d3dbb5e430 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_example.png differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_example.svg b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_example.svg new file mode 100644 index 0000000000..cf290b44e4 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_example.svg @@ -0,0 +1,377 @@ + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (1) Source selection + (2) Registration slot + (4) Moving image slot + (5) Target image slot + (6) Start button + + (3) Auto select option + diff --git a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_example_raw.png b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_example_raw.png new file mode 100644 index 0000000000..b3afbb095f Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_example_raw.png differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_started.png b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_started.png new file mode 100644 index 0000000000..b467ba42bc Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_started.png differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_started.svg b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_started.svg new file mode 100644 index 0000000000..ee1a78f1dc --- /dev/null +++ b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_started.svg @@ -0,0 +1,455 @@ + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (7) New registration name + (10) Translation parameters + (11) Rotation parameters + (13) Confirm registration + (12) Center of rotation type + + (8) Auto image mapping + + (9) Setting tabs + + (14) Cancel manipulation + diff --git a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_started_raw.png b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_started_raw.png new file mode 100644 index 0000000000..ffac708563 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_manipulator_started_raw.png differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_steps.png b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_steps.png deleted file mode 100644 index 1ddf20fc83..0000000000 Binary files a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map_view_steps.png and /dev/null differ