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 e1e7cdcc4e..bfea90f9b4 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 @@ -1,37 +1,37 @@ /** \page org_mitk_gui_qt_matchpoint_algorithm_control The MatchPoint Algorithm Control Plugin \imageMacro{map-icon-run.svg, "Icon of the MatchPoint Algorithm Control", 3} \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_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 DKFZ (German Cancer Research Center). If you have any questions, need support, find a bug or have a feature request, feel free to contact us at dipp@dkfz.de. \section MAP_RUN_Usage Usage \imageMacro{control_example.png, "Example screenshot showing the control plugin in use.", 14} 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{step1_selection.png, "Details of the selection tab.", 8} 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{step2_execution.png, "Details of the execution tab.", 8} 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{step3_settings.png, "Details of the settings tab.", 8} +\imageMacro{step3_settings.PNG, "Details of the settings tab.", 8} 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 5c967973c7..dcdbcac6c0 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 @@ -1,52 +1,52 @@ /** \page org_mitk_gui_qt_matchpoint_evaluator The MatchPoint Registration Evaluation View \imageMacro{evaluator.svg, "Icon of the MatchPoint Registration Evaluator", 3} \li \ref MAP_REGEVAL_Introduction \li \ref MAP_REGEVAL_Contact \li \ref MAP_REGEVAL_Usage \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 DKFZ (German Cancer Research Center). 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{view_example.png, "Example screenshot showing the plug-in in use.", 14} +\imageMacro{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{no_data_selected.png, "Example screenshot showing the state if no data is selected", 5} +\imageMacro{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 differnt 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{style_blend.png, "Example for mode: Blend", 5} +\imageMacro{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{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{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{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{style_wipe_cross.png, "Example for mode: Wipe cross", 5} -\imageMacro{style_wipe_horizontal.png, "Example for mode: Wipe horizontal", 5} +\imageMacro{style_wipe_cross.PNG, "Example for mode: Wipe cross", 5} +\imageMacro{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 5f545f2e62..c61143c921 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 The MatchPoint Motion/Frame Correction Plugin \imageMacro{"icon.svg", "Icon of the MatchPoint Algorithm Control", 3} \li \ref MAP_FRAME_Introduction \li \ref MAP_FRAME_Contact \li \ref MAP_FRAME_Usage \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 DKFZ (German Cancer Research Center). If you have any questions, need support, find a bug or have a feature request, feel free to contact us at dipp@dkfz.de. \section MAP_FRAME_Usage Usage \imageMacro{"control_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{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{step2_execution.png, "Details of the execution tab.", 8} 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{step3_settings.png, "Details of the settings tab.", 8} +\imageMacro{step3_settings.PNG, "Details of the settings tab.", 8} 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. */ \section 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)" \section 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{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 c40d45597c..763f3ece18 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 @@ -1,75 +1,75 @@ /** \page org_mitk_gui_qt_matchpoint_manipulator The MatchPoint Registration Manipulator View \imageMacro{manipulator.svg, "Icon of the MatchPoint Registration Manipulator", 3} \li \ref MAP_REGMANIP_Introduction \li \ref MAP_REGMANIP_Contact \li \ref MAP_REGMANIP_Usage \li \ref MAP_REGMANIP_TransSettings \li \ref MAP_REGMANIP_EvalSettings \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{view_example.png, "Example screenshot showing the plug-in in use", 10} +\imageMacro{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 DKFZ (German Cancer Research Center). 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{view_steps.png, "Illustration of the workflow steps.", 7} +\imageMacro{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. \remark For more advanced mapping options please see the MatchPoint Mapper (\ref org_mitk_gui_qt_matchpoint_mapper). 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, those 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 evaluator for more details. */