diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginGeneralManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginGeneralManualsList.dox index a34c39f999..78f1b417e2 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_qt_matchpoint_evaluator + \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_mapper \li \subpage org_mitk_views_qt_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.evaluator/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/Manual.dox index 93f1b219bb..f2e003fa4c 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 +1,56 @@ /** -\page org_mitk_gui_qt_matchpoint_evaluator The MatchPoint Registration Evaluation View +\page org_mitk_views_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). +This can either by used to assess the visual quality of a registration or to assess how well the image contents are already aligned +by default. To achieve the later, 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} +\imageMacro{map_view_example.png, "Example screenshot showing the main elements of the view.", 14} +(1) The currently selected registration that should be used to map the moving image for evaluation. Click to change. If no registration is selected, a direct evaluation will be performed.\n +(2) Reset button will remove the currently selected registration.\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 registration changes. The view assumes that the moving and target images used to determin the registration should be used.\n +(4) The currently selected moving data. Click to change.\n +(5) The currently selected target data. Click to change.\n +(6) Start/Stop button used to activate/deactivate the evaluation. This button become active when at least the moving and the target image are selected.\n +(7) Selection of the visualization style. (only visible if evaluation is active)\n +(8) Style specific settings. (only visible if evaluation is active)\n 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. +level windowing of the respective input images (moving image and target image). + +\section MAP_REGEVAL_Accuracy Evaluating accuracy +Important note: Please be aware, that a visual inspection of registration quality is only a weak surrogate for a thorough accuracy analysis based on representative and suitable ground truth data. From a visually good mapping you can not deduce a correct registration. This is especially true if the degrees of freedom of the registration increases. For a rigid registration it might by feasible to discern correct and incorrect registration. But for none rigid registrations you definitely you should use this view only for things like first visual inspection (to check if it SEEMS to do the right thing and is worth further exploration) or illustrating the registration effect for registration you have assessed in a sound way. \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} +\imageMacro{map_view_blend_settings.png, "Settings of the Blend style", 8} +(1) Click to set the weights to 100% target image.\n +(2) Click to set the weights to 50:50 (equal blend).\n +(3) Slider to adjust the weights between target image and the mapped input image. The spin box shows the weight of the mapped input image.\n +(4) Click to set the weights to 100% mapped input image.\n +(5) Click to toggle the weight between both images.\n +\imageMacro{map_style_blend.png, "Example for mode: Blend (50:50)", 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.evaluator/documentation/UserManual/map_no_data_selected.png b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_no_data_selected.png deleted file mode 100644 index 2a72cfa281..0000000000 Binary files a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_no_data_selected.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_blend_settings.png b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_blend_settings.png new file mode 100644 index 0000000000..ff4c1c314a Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_blend_settings.png differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_blend_settings.svg b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_blend_settings.svg new file mode 100644 index 0000000000..002060caab --- /dev/null +++ b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_blend_settings.svg @@ -0,0 +1,398 @@ + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (3) Slider to adjust weighting + (4) Set to 100% mapped visibility + (5) Toggle weighting + + (2) Set to 50:50 visibility + + (1) Set to 100% target visibility + diff --git a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_example.png b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_example.png index 496925adee..cdcfabe79d 100644 Binary files a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_example.png and b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_example.png differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_example.svg b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_example.svg new file mode 100644 index 0000000000..dd5a4ee8e2 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_example.svg @@ -0,0 +1,409 @@ + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (1) Registration slot + (7) Evaluation styles + (2) Registration reset + (4) Moving image slot + (5) Target image slot + (6) Start/Stop button + (8) Style specific settings + + (3) Auto select option + diff --git a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_example_raw.png b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_example_raw.png new file mode 100644 index 0000000000..ce373edb1b Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map_view_example_raw.png differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/plugin.xml b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/plugin.xml index 015b7372b2..ab99f800b2 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/plugin.xml +++ b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/plugin.xml @@ -1,12 +1,12 @@ - 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 d4af889568..c00ab5da9b 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 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). +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. */