diff --git a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/documentation/UserManual/Manual.dox index 59a33479b0..9e454d636b 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/documentation/UserManual/Manual.dox @@ -1,21 +1,21 @@ /** \page org_mitk_gui_qt_matchpoint_algorithm_batch The MatchPoint Registration Batch Processor Plugin -\imageMacro{map-icon-batch.png, "Icon of the MatchPoint Algorithm Batch Processor",3} +\imageMacro{map-icon-batch.svg, "Icon of the MatchPoint Algorithm Batch Processor",3} \li \ref MAP_BATCH_Introduction \li \ref MAP_BATCH_Contact \li \ref MAP_BATCH_Usage \section MAP_BATCH_Introduction Introduction This plugin is very similar to the MatchPoint algorithm controller plugin, but allows to register a set of selected input images in one batch run onto one selected target image. \section MAP_BATCH_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_BATCH_Usage Usage Oops. Documentation is missing and to be done. */ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/documentation/UserManual/map-icon-batch.png b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/documentation/UserManual/map-icon-batch.png deleted file mode 100644 index ef52844a1b..0000000000 Binary files a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/documentation/UserManual/map-icon-batch.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/documentation/UserManual/map-icon-batch.svg b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/documentation/UserManual/map-icon-batch.svg new file mode 100644 index 0000000000..7280678b79 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/documentation/UserManual/map-icon-batch.svg @@ -0,0 +1,129 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/files.cmake b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/files.cmake index 4fcb45ce99..e2300f67e8 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/files.cmake +++ b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/files.cmake @@ -1,45 +1,45 @@ set(SRC_CPP_FILES ) set(INTERNAL_CPP_FILES org_mitk_gui_qt_matchpoint_algorithm_batch_Activator.cpp QmitkMatchPointBatchProcessor.cpp ) set(UI_FILES src/internal/QmitkMatchPointBatchProcessor.ui ) set(MOC_H_FILES src/internal/org_mitk_gui_qt_matchpoint_algorithm_batch_Activator.h src/internal/QmitkMatchPointBatchProcessor.h ) # list of resource files which can be used by the plug-in # system without loading the plug-ins shared library, # for example the icon used in the menu and tabs for the # plug-in views in the workbench set(CACHED_RESOURCE_FILES - resources/icon.png + resources/icon.svg resources/icon_lock.png resources/icon_unlock.png plugin.xml ) # list of Qt .qrc files which contain additional resources # specific to this plugin set(QRC_FILES ) set(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/plugin.xml b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/plugin.xml index 67f17a3b21..f57ae12923 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/plugin.xml +++ b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/plugin.xml @@ -1,12 +1,12 @@ + icon="resources/icon.svg" /> diff --git a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/resources/icon.png b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/resources/icon.png deleted file mode 100644 index ef52844a1b..0000000000 Binary files a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/resources/icon.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/resources/icon.svg b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/resources/icon.svg new file mode 100644 index 0000000000..7280678b79 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.batch/resources/icon.svg @@ -0,0 +1,129 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 4b34606932..d75c0e48be 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 @@ -1,58 +1,58 @@ /** \page org_mitk_gui_qt_matchpoint_algorithm_browser The MatchPoint Algorithm Browser View -\imageMacro{map-icon-browser.png, "Icon of the MatchPoint Algorithm Browser", 3} +\imageMacro{map-icon-browser.svg, "Icon of the MatchPoint Algorithm Browser", 3} \li \ref MAP_BROWSER_Introduction \li \ref MAP_BROWSER_Contact \li \ref MAP_BROWSER_Usage \li \ref MAP_BROWSER_Profile \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_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_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). DIPP-User: You should activate at least "scan installation directory" to see the algorithms delivered with the DIPP installer. 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 or \ref de_dkfz_dwi_gui_qt_crex) which use registration algorithms will be notified and allow to choose the selected algorithm for usage. \imageMacro{browser.png, "View of the browser with the list of available algorithm and the profile area",14} \remark You haven't found a fitting registration algorithm? Please have a look at the registration repository at our SBR share point (http://intracoop/sites/sbr/Lists/RegRepository/default.aspx) or contact us (dipp@dkfz.de). \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.browser/documentation/UserManual/map-icon-browser.png b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/documentation/UserManual/map-icon-browser.png deleted file mode 100644 index 980b776810..0000000000 Binary files a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/documentation/UserManual/map-icon-browser.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/documentation/UserManual/map-icon-browser.svg b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/documentation/UserManual/map-icon-browser.svg new file mode 100644 index 0000000000..25aaffc180 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/documentation/UserManual/map-icon-browser.svg @@ -0,0 +1,120 @@ + + + + + + + + + + + + + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/files.cmake b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/files.cmake index 280e75be68..e5f66edd7a 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/files.cmake +++ b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/files.cmake @@ -1,45 +1,45 @@ set(SRC_CPP_FILES ) set(INTERNAL_CPP_FILES org_mitk_gui_qt_matchpoint_algorithm_browser_Activator.cpp QmitkMatchPointBrowser.cpp mitkAlgorithmInfoSelectionProvider.cpp ) set(UI_FILES src/internal/QmitkMatchPointBrowserControls.ui ) set(MOC_H_FILES src/internal/org_mitk_gui_qt_matchpoint_algorithm_browser_Activator.h src/internal/QmitkMatchPointBrowser.h src/internal/mitkAlgorithmInfoSelectionProvider.h ) # list of resource files which can be used by the plug-in # system without loading the plug-ins shared library, # for example the icon used in the menu and tabs for the # plug-in views in the workbench set(CACHED_RESOURCE_FILES - resources/icon.xpm + resources/icon.svg plugin.xml ) # list of Qt .qrc files which contain additional resources # specific to this plugin set(QRC_FILES ) set(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/plugin.xml b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/plugin.xml index dc24da9a94..820ac77e1d 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/plugin.xml +++ b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/plugin.xml @@ -1,12 +1,12 @@ + icon="resources/icon.svg" /> diff --git a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/resources/icon.svg b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/resources/icon.svg new file mode 100644 index 0000000000..25aaffc180 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/resources/icon.svg @@ -0,0 +1,120 @@ + + + + + + + + + + + + + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/resources/icon.xpm b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/resources/icon.xpm deleted file mode 100644 index 5eda35daa7..0000000000 --- a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.browser/resources/icon.xpm +++ /dev/null @@ -1,230 +0,0 @@ -/* XPM */ -static char *mapiconbrowse[] = { -/* columns rows colors chars-per-pixel */ -"32 32 192 2", -" c #1B1A1B", -". c #2C2B2B", -"X c #2A3131", -"o c #3C3B3A", -"O c #623C3C", -"+ c #424243", -"@ c #4C4C4C", -"# c #514F4C", -"$ c #53514E", -"% c #525252", -"& c #585552", -"* c #5B5B5B", -"= c #666665", -"- c #696765", -"; c #6F6E6D", -": c #706D6A", -"> c #72716F", -", c #6E7170", -"< c #767574", -"1 c #7A7978", -"2 c #850100", -"3 c #8D0702", -"4 c #8C0801", -"5 c #9D0704", -"6 c #961207", -"7 c #B30000", -"8 c #A11D03", -"9 c #B22501", -"0 c #BB2602", -"q c #B12801", -"w c #B13216", -"e c #C60000", -"r c #C62000", -"t c #C12802", -"y c #BE4F22", -"u c #C1481F", -"i c #CB5712", -"p c #EC6D0B", -"a c #FB7909", -"s c #CC4622", -"d c #C74D21", -"f c #CC4B21", -"g c #D24D21", -"h c #DA4B28", -"j c #CF7628", -"k c #FF9917", -"l c #FF9619", -"z c #FFA025", -"x c #FFB332", -"c c #FFC738", -"v c #81807E", -"b c #F1C74F", -"n c #FAD04E", -"m c #FFE24E", -"M c #FFE450", -"N c #FFEA53", -"B c #FCEC5D", -"V c #FCEF60", -"C c #0027B5", -"Z c #042BB7", -"A c #0F34B9", -"S c #1E40BE", -"D c #2143BF", -"F c #677CA9", -"G c #627CB6", -"H c #2D4DC2", -"J c #3655C5", -"K c #3957C6", -"L c #425FC8", -"P c #4561C9", -"I c #546ECD", -"U c #637BD2", -"Y c #7E8892", -"T c #6C83B3", -"R c #7589C5", -"E c #6C82D4", -"W c #738DD4", -"Q c #7AA4DD", -"! 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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} 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.algorithm.control/documentation/UserManual/map-icon-run.png b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/documentation/UserManual/map-icon-run.png deleted file mode 100644 index 5a0011cc1c..0000000000 Binary files a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/documentation/UserManual/map-icon-run.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/documentation/UserManual/map-icon-run.svg b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/documentation/UserManual/map-icon-run.svg new file mode 100644 index 0000000000..5395b6f814 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/documentation/UserManual/map-icon-run.svg @@ -0,0 +1,133 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/files.cmake b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/files.cmake index aff465200d..72703626b0 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/files.cmake +++ b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/files.cmake @@ -1,43 +1,43 @@ set(SRC_CPP_FILES ) set(INTERNAL_CPP_FILES org_mitk_gui_qt_matchpoint_algorithmcontrol_Activator.cpp QmitkMatchPoint.cpp ) set(UI_FILES src/internal/QmitkMatchPointControls.ui ) set(MOC_H_FILES src/internal/org_mitk_gui_qt_matchpoint_algorithmcontrol_Activator.h src/internal/QmitkMatchPoint.h ) # list of resource files which can be used by the plug-in # system without loading the plug-ins shared library, # for example the icon used in the menu and tabs for the # plug-in views in the workbench set(CACHED_RESOURCE_FILES - resources/icon.png + resources/icon.svg plugin.xml ) # list of Qt .qrc files which contain additional resources # specific to this plugin set(QRC_FILES ) set(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/plugin.xml b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/plugin.xml index f0c8d9c5d4..136b6b9879 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/plugin.xml +++ b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/plugin.xml @@ -1,12 +1,12 @@ + icon="resources/icon.svg" /> diff --git a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/resources/icon.png b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/resources/icon.png deleted file mode 100644 index 5a0011cc1c..0000000000 Binary files a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/resources/icon.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/resources/icon.svg b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/resources/icon.svg new file mode 100644 index 0000000000..5395b6f814 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/resources/icon.svg @@ -0,0 +1,133 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + 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 db3620292a..5c967973c7 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{map-icon-regeval.png, "Icon of the MatchPoint Registration Evaluator", 3} +\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} 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} 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} \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} */ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/evaluator.svg b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/evaluator.svg new file mode 100644 index 0000000000..f04b510934 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/evaluator.svg @@ -0,0 +1,125 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map-icon-regeval.png b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map-icon-regeval.png deleted file mode 100644 index 1a3389dd0a..0000000000 Binary files a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/map-icon-regeval.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/files.cmake b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/files.cmake index dbf00eb6df..f278150a77 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/files.cmake +++ b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/files.cmake @@ -1,43 +1,43 @@ set(SRC_CPP_FILES ) set(INTERNAL_CPP_FILES org_mitk_gui_qt_matchpoint_evaluator_Activator.cpp QmitkMatchPointRegistrationEvaluator.cpp ) set(UI_FILES src/internal/QmitkMatchPointRegistrationEvaluator.ui ) set(MOC_H_FILES src/internal/org_mitk_gui_qt_matchpoint_evaluator_Activator.h src/internal/QmitkMatchPointRegistrationEvaluator.h ) # list of resource files which can be used by the plug-in # system without loading the plug-ins shared library, # for example the icon used in the menu and tabs for the # plug-in views in the workbench set(CACHED_RESOURCE_FILES - resources/evaluator.png + resources/evaluator.svg plugin.xml ) # list of Qt .qrc files which contain additional resources # specific to this plugin set(QRC_FILES ) set(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/plugin.xml b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/plugin.xml index 1fc9db506c..015b7372b2 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 @@ + icon="resources/evaluator.svg" /> diff --git a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/resources/evaluator.png b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/resources/evaluator.png deleted file mode 100644 index 1a3389dd0a..0000000000 Binary files a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/resources/evaluator.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/resources/evaluator.svg b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/resources/evaluator.svg new file mode 100644 index 0000000000..f04b510934 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/resources/evaluator.svg @@ -0,0 +1,125 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 f70bda38f4..5f545f2e62 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{"map-icon-run.png", "Icon of the MatchPoint Algorithm Control", 3} +\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} 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.framereg/documentation/UserManual/icon.svg b/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/icon.svg new file mode 100644 index 0000000000..c75d640660 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/icon.svg @@ -0,0 +1,125 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/map-icon-run.png b/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/map-icon-run.png deleted file mode 100644 index 5a0011cc1c..0000000000 Binary files a/Plugins/org.mitk.gui.qt.matchpoint.framereg/documentation/UserManual/map-icon-run.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.framereg/files.cmake b/Plugins/org.mitk.gui.qt.matchpoint.framereg/files.cmake index 40758303ee..e4cfa9aa6b 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.framereg/files.cmake +++ b/Plugins/org.mitk.gui.qt.matchpoint.framereg/files.cmake @@ -1,43 +1,43 @@ set(SRC_CPP_FILES ) set(INTERNAL_CPP_FILES org_mitk_gui_qt_matchpoint_framereg_Activator.cpp QmitkMatchPointFrameCorrection.cpp ) set(UI_FILES src/internal/QmitkMatchPointFrameCorrectionControls.ui ) set(MOC_H_FILES src/internal/org_mitk_gui_qt_matchpoint_framereg_Activator.h src/internal/QmitkMatchPointFrameCorrection.h ) # list of resource files which can be used by the plug-in # system without loading the plug-ins shared library, # for example the icon used in the menu and tabs for the # plug-in views in the workbench set(CACHED_RESOURCE_FILES - resources/icon.png + resources/icon.svg plugin.xml ) # list of Qt .qrc files which contain additional resources # specific to this plugin set(QRC_FILES ) set(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.matchpoint.framereg/plugin.xml b/Plugins/org.mitk.gui.qt.matchpoint.framereg/plugin.xml index 80506cd356..0386b0c385 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.framereg/plugin.xml +++ b/Plugins/org.mitk.gui.qt.matchpoint.framereg/plugin.xml @@ -1,12 +1,12 @@ + icon="resources/icon.svg" /> diff --git a/Plugins/org.mitk.gui.qt.matchpoint.framereg/resources/icon.png b/Plugins/org.mitk.gui.qt.matchpoint.framereg/resources/icon.png deleted file mode 100644 index 5a0011cc1c..0000000000 Binary files a/Plugins/org.mitk.gui.qt.matchpoint.framereg/resources/icon.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.framereg/resources/icon.svg b/Plugins/org.mitk.gui.qt.matchpoint.framereg/resources/icon.svg new file mode 100644 index 0000000000..c75d640660 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.matchpoint.framereg/resources/icon.svg @@ -0,0 +1,125 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 7cfe7e1d94..c40d45597c 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{map-icon-manipulator.png, "Icon of the MatchPoint Registration Manipulator", 3} +\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} \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} 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. */ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/manipulator.svg b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/manipulator.svg new file mode 100644 index 0000000000..11f89f36bd --- /dev/null +++ b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/manipulator.svg @@ -0,0 +1,123 @@ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map-icon-manipulator.png b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map-icon-manipulator.png deleted file mode 100644 index 4ef51ce0e2..0000000000 Binary files a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/documentation/UserManual/map-icon-manipulator.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/files.cmake b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/files.cmake index f5c494bf11..7b7b6b953c 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/files.cmake +++ b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/files.cmake @@ -1,43 +1,43 @@ set(SRC_CPP_FILES ) set(INTERNAL_CPP_FILES org_mitk_gui_qt_matchpoint_manipulator_Activator.cpp QmitkMatchPointRegistrationManipulator.cpp ) set(UI_FILES src/internal/QmitkMatchPointRegistrationManipulator.ui ) set(MOC_H_FILES src/internal/org_mitk_gui_qt_matchpoint_manipulator_Activator.h src/internal/QmitkMatchPointRegistrationManipulator.h ) # list of resource files which can be used by the plug-in # system without loading the plug-ins shared library, # for example the icon used in the menu and tabs for the # plug-in views in the workbench set(CACHED_RESOURCE_FILES - resources/manipulator.png + resources/manipulator.svg plugin.xml ) # list of Qt .qrc files which contain additional resources # specific to this plugin set(QRC_FILES ) set(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/plugin.xml b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/plugin.xml index c59b268f78..0bd72dc8bc 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/plugin.xml +++ b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/plugin.xml @@ -1,12 +1,12 @@ + icon="resources/manipulator.svg" /> diff --git a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/resources/manipulator.png b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/resources/manipulator.png deleted file mode 100644 index 4ef51ce0e2..0000000000 Binary files a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/resources/manipulator.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/resources/manipulator.svg b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/resources/manipulator.svg new file mode 100644 index 0000000000..11f89f36bd --- /dev/null +++ b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/resources/manipulator.svg @@ -0,0 +1,123 @@ + + + + + + + + + + + + + + + + + + + + + + + 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 7ca6d839bb..58371aca7a 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 @@ -1,87 +1,87 @@ /** \page org_mitk_gui_qt_matchpoint_mapper The MatchPoint Image Mapper View -\imageMacro{map-icon-map.png, "Icon of the MatchPoint Image Mapper",3} +\imageMacro{icon.svg, "Icon of the MatchPoint Image Mapper",3} \li \ref MAP_MAPPER_Introduction \li \ref MAP_MAPPER_Contact \li \ref MAP_MAPPER_Usage \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 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_MAPPER_Usage Usage \imageMacro{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 multiselect 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 convinient 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 adventage of the different interpolation and sub/super sampling strategies. \imageMacro{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{node-unlocked.png, "Unlocked slot/node (default state). Changes with the selections in the data manager.",6} \imageMacro{ 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 the image geometry (origin, orientation, ...); 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, you must use "Map" to ensure the same geometry. Otherwise 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 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. \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 neighbour". */ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.mapper/documentation/UserManual/icon.svg b/Plugins/org.mitk.gui.qt.matchpoint.mapper/documentation/UserManual/icon.svg new file mode 100644 index 0000000000..61b42a5b9f --- /dev/null +++ b/Plugins/org.mitk.gui.qt.matchpoint.mapper/documentation/UserManual/icon.svg @@ -0,0 +1,120 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.matchpoint.mapper/documentation/UserManual/map-icon-map.png b/Plugins/org.mitk.gui.qt.matchpoint.mapper/documentation/UserManual/map-icon-map.png deleted file mode 100644 index 9fa3a54865..0000000000 Binary files a/Plugins/org.mitk.gui.qt.matchpoint.mapper/documentation/UserManual/map-icon-map.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.mapper/files.cmake b/Plugins/org.mitk.gui.qt.matchpoint.mapper/files.cmake index f414101888..2700970a3a 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.mapper/files.cmake +++ b/Plugins/org.mitk.gui.qt.matchpoint.mapper/files.cmake @@ -1,45 +1,45 @@ set(SRC_CPP_FILES ) set(INTERNAL_CPP_FILES org_mitk_gui_qt_matchpoint_mapper_Activator.cpp QmitkMatchPointMapper.cpp ) set(UI_FILES src/internal/QmitkMatchPointMapper.ui ) set(MOC_H_FILES src/internal/org_mitk_gui_qt_matchpoint_mapper_Activator.h src/internal/QmitkMatchPointMapper.h ) # list of resource files which can be used by the plug-in # system without loading the plug-ins shared library, # for example the icon used in the menu and tabs for the # plug-in views in the workbench set(CACHED_RESOURCE_FILES - resources/icon.xpm + resources/icon.svg resources/icon_lock.png resources/icon_unlock.png plugin.xml ) # list of Qt .qrc files which contain additional resources # specific to this plugin set(QRC_FILES ) set(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.matchpoint.mapper/plugin.xml b/Plugins/org.mitk.gui.qt.matchpoint.mapper/plugin.xml index 64a25ac2d3..70800adf8f 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.mapper/plugin.xml +++ b/Plugins/org.mitk.gui.qt.matchpoint.mapper/plugin.xml @@ -1,12 +1,12 @@ + icon="resources/icon.svg" /> diff --git a/Plugins/org.mitk.gui.qt.matchpoint.mapper/resources/icon.svg b/Plugins/org.mitk.gui.qt.matchpoint.mapper/resources/icon.svg new file mode 100644 index 0000000000..61b42a5b9f --- /dev/null +++ b/Plugins/org.mitk.gui.qt.matchpoint.mapper/resources/icon.svg @@ -0,0 +1,120 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.matchpoint.mapper/resources/icon.xpm b/Plugins/org.mitk.gui.qt.matchpoint.mapper/resources/icon.xpm deleted file mode 100644 index 37d18007f9..0000000000 --- a/Plugins/org.mitk.gui.qt.matchpoint.mapper/resources/icon.xpm +++ /dev/null @@ -1,251 +0,0 @@ -/* XPM */ -static char *mapiconmap[] = { -/* columns rows colors chars-per-pixel */ -"32 32 213 2", -" c #163C01", -". c #173E01", -"X c #163E04", -"o c #173D07", -"O c #183E03", -"+ c #253001", -"@ c #1E3831", -"# c #333D37", -"$ c #5E0101", -"% c #580601", -"& c #510B01", -"* c #560D08", -"= c #560B0F", -"- c #471401", -"; c #561201", -": c #550D11", -"> c #4C191F", -", c #511312", -"< c #610101", -"1 c #650101", -"2 c #660101", -"3 c #680101", -"4 c #6F0101", -"5 c #710101", -"6 c #740101", -"7 c #770101", -"8 c #7A0101", -"9 c #7C0101", -"0 c #452601", -"q c #402F01", -"w c #5F2401", -"e c #542801", -"r c #472316", -"t c #632303", -"y c #612401", -"u c #652603", -"i c #662703", -"p c #6D2001", -"a c #4A153D", -"s c #194001", -"d c #1A4201", -"f c #1C4301", -"g c #1D4209", -"h c #174011", -"j c #174216", -"k c #1C411D", -"l c #204902", -"z c #244E02", -"x c #275202", -"c c #254910", -"v c #2C4E1E", -"b c #326103", -"n c #386804", -"m c #3C6E04", -"M c #3F7104", -"N c #184426", -"B c #154D27", -"V c #18472C", -"C c #135226", -"Z c #125524", -"A c #314F3D", -"S c #487E05", -"D c #7A7F07", -"F c #425F39", -"G c #4A683A", -"H c #2A4557", -"J c #116B5D", -"K c #0B7B57", -"L c #0A7D55", -"P c #097F54", -"I c #0A7E55", -"U c #0A7C57", -"Y c #0B7C57", -"T c #0C7759", -"R c #0D775A", -"E c #0F735E", -"W c #0B7B58", -"Q c #0C7959", -"! 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X,X9X&XA b !.!.!.!.!.!.s. q q.q.q.q.q.9.$ 0X", -"0X9X4X]./././././.).#X9XY.c f.T.d.d.d.u.u.u.l 6.q.q.q.q.7.$ 0X", -"9X8X[././././././././.;X3XG e q.q.q.q.q.4.$ 0X", -"9X=X/././././././././.'.9XoXk o h j + w y y =.q.q.q.q.q.q.1.$ 0X", -"9X X/./././././././././.1X9X0X' / H 8 q.q.q.q.q.q.q.q.q.q.,.$ 0X", -"9X|././././././././././.>X9X0X0X0X` 2 ;.0.q.q.q.q.q.q.q.q.>.$ 0X", -"9XXX/././././././././.(.5X9X0X0X0X( 0X$ 4 >.q.q.q.q.q.q.q.:.$ 0X", -"9XThis is an experimental version and work in progress. So please excuse errors or usage issues and report them. This plugin 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 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_VIS_Usage Usage Oops. Documentation is missing and to be done. */ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/icon.svg b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/icon.svg new file mode 100644 index 0000000000..81c461e166 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/icon.svg @@ -0,0 +1,126 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map-icon-regvis.png b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map-icon-regvis.png deleted file mode 100644 index 29c4ccf332..0000000000 Binary files a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map-icon-regvis.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/files.cmake b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/files.cmake index 96ce8a2852..7964f05c25 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/files.cmake +++ b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/files.cmake @@ -1,45 +1,45 @@ set(SRC_CPP_FILES ) set(INTERNAL_CPP_FILES org_mitk_gui_qt_matchpoint_visualizer_Activator.cpp QmitkMatchPointRegistrationVisualizer.cpp ) set(UI_FILES src/internal/QmitkMatchPointRegistrationVisualizer.ui ) set(MOC_H_FILES src/internal/org_mitk_gui_qt_matchpoint_visualizer_Activator.h src/internal/QmitkMatchPointRegistrationVisualizer.h ) # list of resource files which can be used by the plug-in # system without loading the plug-ins shared library, # for example the icon used in the menu and tabs for the # plug-in views in the workbench set(CACHED_RESOURCE_FILES - resources/icon.png + resources/icon.svg resources/icon_lock.png resources/icon_unlock.png plugin.xml ) # list of Qt .qrc files which contain additional resources # specific to this plugin set(QRC_FILES ) set(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/plugin.xml b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/plugin.xml index 5248d2b270..01fc9fe0e1 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/plugin.xml +++ b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/plugin.xml @@ -1,12 +1,12 @@ + icon="resources/icon.svg" /> diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/resources/icon.png b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/resources/icon.png deleted file mode 100644 index 29c4ccf332..0000000000 Binary files a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/resources/icon.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/resources/icon.svg b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/resources/icon.svg new file mode 100644 index 0000000000..81c461e166 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/resources/icon.svg @@ -0,0 +1,126 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/Plugins/org.mitk.matchpoint.core.helper/files.cmake b/Plugins/org.mitk.matchpoint.core.helper/files.cmake index 4fca84b3fa..17656d6808 100644 --- a/Plugins/org.mitk.matchpoint.core.helper/files.cmake +++ b/Plugins/org.mitk.matchpoint.core.helper/files.cmake @@ -1,56 +1,55 @@ set(SRC_CPP_FILES mitkMAPAlgorithmInfoSelection.cpp mitkMAPAlgorithmInfoObject.cpp ) set(INTERNAL_CPP_FILES org_mitk_matchpoint_core_helper_Activator.cpp MatchPointBrowserPreferencesPage.cpp MatchPointBrowserConstants.cpp QmitkDirectoryListWidget.cpp QmitkFileListWidget.cpp ) set(UI_FILES src/internal/QmitkPathListWidget.ui ) set(H_FILES src/MatchPointBrowserConstants.h src/mitkMAPAlgorithmInfoSelection.h src/mitkMAPAlgorithmInfoObject.h ) set(MOC_H_FILES src/internal/org_mitk_matchpoint_core_helper_Activator.h src/internal/MatchPointBrowserPreferencesPage.h src/internal/QmitkDirectoryListWidget.h src/internal/QmitkFileListWidget.h ) # list of resource files which can be used by the plug-in # system without loading the plug-ins shared library, # for example the icon used in the menu and tabs for the # plug-in views in the workbench set(CACHED_RESOURCE_FILES plugin.xml - - resources/MAPRegData.png + resources/MAPRegData.svg ) # list of Qt .qrc files which contain additional resources # specific to this plugin set(QRC_FILES resources/QmitkMatchPointCore.qrc ) set(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.matchpoint.core.helper/manifest_headers.cmake b/Plugins/org.mitk.matchpoint.core.helper/manifest_headers.cmake index fda5847d5e..ee920f4935 100644 --- a/Plugins/org.mitk.matchpoint.core.helper/manifest_headers.cmake +++ b/Plugins/org.mitk.matchpoint.core.helper/manifest_headers.cmake @@ -1,5 +1,6 @@ SET(Plugin-Name "MAP MITK Core Helper") SET(Plugin-Version "0.1") set(Plugin-Vendor "DKFZ, Medical and Biological Informatics") set(Plugin-ContactAddress "http://www.mitk.org") -set(Require-Plugin org.mitk.gui.qt.common org.mitk.gui.qt.datamanager) +set(Require-Plugin org.mitk.gui.common) +set(Plugin-ActivationPolicy eager) diff --git a/Plugins/org.mitk.matchpoint.core.helper/resources/MAPRegData.png b/Plugins/org.mitk.matchpoint.core.helper/resources/MAPRegData.png deleted file mode 100644 index dc84e450fe..0000000000 Binary files a/Plugins/org.mitk.matchpoint.core.helper/resources/MAPRegData.png and /dev/null differ diff --git a/Plugins/org.mitk.matchpoint.core.helper/resources/MAPRegData.svg b/Plugins/org.mitk.matchpoint.core.helper/resources/MAPRegData.svg new file mode 100644 index 0000000000..e1d2643863 --- /dev/null +++ b/Plugins/org.mitk.matchpoint.core.helper/resources/MAPRegData.svg @@ -0,0 +1,66 @@ + + + + + + diff --git a/Plugins/org.mitk.matchpoint.core.helper/resources/QmitkMatchPointCore.qrc b/Plugins/org.mitk.matchpoint.core.helper/resources/QmitkMatchPointCore.qrc index 9674bf8181..8674df5c1e 100644 --- a/Plugins/org.mitk.matchpoint.core.helper/resources/QmitkMatchPointCore.qrc +++ b/Plugins/org.mitk.matchpoint.core.helper/resources/QmitkMatchPointCore.qrc @@ -1,5 +1,5 @@ - MAPRegData.png + MAPRegData.svg diff --git a/Plugins/org.mitk.matchpoint.core.helper/src/internal/org_mitk_matchpoint_core_helper_Activator.cpp b/Plugins/org.mitk.matchpoint.core.helper/src/internal/org_mitk_matchpoint_core_helper_Activator.cpp index 3fe9c64d4e..a17a102da9 100644 --- a/Plugins/org.mitk.matchpoint.core.helper/src/internal/org_mitk_matchpoint_core_helper_Activator.cpp +++ b/Plugins/org.mitk.matchpoint.core.helper/src/internal/org_mitk_matchpoint_core_helper_Activator.cpp @@ -1,69 +1,72 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "org_mitk_matchpoint_core_helper_Activator.h" #include "MatchPointBrowserPreferencesPage.h" #include "QmitkNodeDescriptorManager.h" +#include "QmitkStyleManager.h" #include "mitkNodePredicateDataType.h" ctkPluginContext* org_mitk_matchpoint_core_helper_Activator::m_Context = nullptr; org_mitk_matchpoint_core_helper_Activator* org_mitk_matchpoint_core_helper_Activator::m_Instance = nullptr; org_mitk_matchpoint_core_helper_Activator::org_mitk_matchpoint_core_helper_Activator() { m_Instance = this; } org_mitk_matchpoint_core_helper_Activator::~org_mitk_matchpoint_core_helper_Activator() { m_Instance = nullptr; } void org_mitk_matchpoint_core_helper_Activator::start(ctkPluginContext* context) { BERRY_REGISTER_EXTENSION_CLASS(MatchPointBrowserPreferencesPage, context) this->m_Context = context; QmitkNodeDescriptorManager* manager = QmitkNodeDescriptorManager::GetInstance(); mitk::NodePredicateDataType::Pointer isMITKRegistrationWrapper = mitk::NodePredicateDataType::New("MAPRegistrationWrapper"); - manager->AddDescriptor(new QmitkNodeDescriptor(QObject::tr("MAPRegistrationWrapper"), - QString(":/QmitkMatchPointCore/MAPRegData.png"), isMITKRegistrationWrapper, manager)); + auto desc = new QmitkNodeDescriptor(QObject::tr("MAPRegistrationWrapper"), + QmitkStyleManager::ThemeIcon(QStringLiteral(":/QmitkMatchPointCore/MAPRegData.svg")), isMITKRegistrationWrapper, manager); + + manager->AddDescriptor(desc); } void org_mitk_matchpoint_core_helper_Activator::stop(ctkPluginContext* context) { Q_UNUSED(context) this->m_Context = nullptr; } ctkPluginContext* org_mitk_matchpoint_core_helper_Activator::getContext() { return m_Context; } org_mitk_matchpoint_core_helper_Activator* org_mitk_matchpoint_core_helper_Activator::getDefault() { return m_Instance; }