diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginGeneralManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginGeneralManualsList.dox new file mode 100644 index 0000000000..9b387dea83 --- /dev/null +++ b/Documentation/Doxygen/2-UserManual/MITKPluginGeneralManualsList.dox @@ -0,0 +1,31 @@ +/** +\page PluginListGeneralPage List of General Purpose Plugins + + + \li \subpage org_mitk_views_basicimageprocessing + \li \subpage org_mitk_gui_qt_chartExample + \li \subpage org_mitk_views_datamanager + \li \subpage org_mitk_gui_qt_dicom + \li \subpage org_mitk_gui_qt_dicominspector + \li \subpage org_mitk_gui_qt_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_gui_qt_matchpoint_algorithm_browser + \li \subpage org_mitk_gui_qt_matchpoint_algorithm_control + \li \subpage org_mitk_gui_qt_matchpoint_evaluator + \li \subpage org_mitk_gui_qt_matchpoint_framereg + \li \subpage org_mitk_gui_qt_matchpoint_manipulator + \li \subpage org_mitk_gui_qt_matchpoint_mapper + \li \subpage org_mitk_gui_qt_matchpoint_visualizer + \li \subpage org_mitk_gui_qt_measurementtoolbox + \li \subpage org_mitk_gui_qt_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_viewnavigator + \li \subpage org_mitk_views_volumevisualization +*/ \ No newline at end of file diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox index 1728b2a49d..90d1400671 100644 --- a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox +++ b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox @@ -1,80 +1,81 @@ /** \page PluginListPage MITK Plugin Manuals The plugins and bundles provide much of the extended functionality of MITK. Each encapsulates a solution to a problem and associated features. This way one can easily assemble the necessary capabilites for a workflow without adding a lot of bloat, by combining plugins as needed. -\paragraph PluginListPageEndUserPluginList List of General Purpose Plugins +\subpage PluginListGeneralPage + +\subpage PluginListSpecificPage -\paragraph PluginListPageApplicationPluginList List of Application-specific Plugins - - \li \subpage org_mitk_gui_qt_aicpregistration - \li \subpage org_mitk_gui_qt_cest - \li \subpage org_mitk_gui_qt_classificationsegmentation - \li \subpage org_mitk_views_cmdlinemodules - \li \subpage org_mitk_gui_qt_eventrecorder - \li \subpage org_mitk_gui_qt_examples - \li \subpage org_mitk_gui_qt_fit_demo - \li \subpage org_mitk_gui_qt_fit_genericfitting - \li \subpage org_mitk_gui_qt_fit_inspector - \li \subpage org_mitk_gui_qt_geometrytools - \li \subpage org_mitk_gui_qt_igt_app_echotrack - \li \subpage org_mitk_gui_qt_igtexample - \li \subpage org_mitk_gui_qt_igtlplugin - \li \subpage org_mitk_gui_qt_igttracking - \li \subpage org_mitk_gui_qt_igttrackingsemiautomaticmeasurement - \li \subpage org_mitk_gui_qt_lasercontrol - \li \subpage org_mitk_gui_qt_matchpoint_algorithm_batch - \li \subpage org_mitk_gui_qt_matchpoint_algorithm_browser - \li \subpage org_mitk_gui_qt_matchpoint_algorithm_control - \li \subpage org_mitk_gui_qt_matchpoint_evaluator - \li \subpage org_mitk_gui_qt_matchpoint_framereg - \li \subpage org_mitk_gui_qt_matchpoint_manipulator - \li \subpage org_mitk_gui_qt_matchpoint_mapper - \li \subpage org_mitk_gui_qt_matchpoint_visualizer - \li \subpage org_mitk_gui_qt_overlaymanager - \li \subpage org_mitk_gui_qt_mitkphenotyping - \li \subpage org_mitk_gui_qt_photoacoustics_pausmotioncompensation - \li \subpage org_mitk_example_gui_pcaexample - \li \subpage org_mitk_gui_qt_pharmacokinetics_mri - \li \subpage org_mitk_gui_qt_pharmacokinetics_pet - \li \subpage org_mitk_gui_qt_pharmacokinetics_concentration_mri - \li \subpage org_mitk_gui_qt_pharmacokinetics_curvedescriptor - \li \subpage org_mitk_gui_qt_photoacoustics_imageprocessing - \li \subpage org_mitk_gui_qt_pharmacokinetics_simulation - \li \subpage org_mitk_gui_qt_photoacoustics_spectralunmixing - \li \subpage org_mitk_gui_qt_pointsetinteractionmultispectrum - \li \subpage org_mitk_gui_qt_renderwindowmanager - \li \subpage org_mitk_gui_qt_spectrocamrecorder - \li \subpage org_surfacematerialeditor - \li \subpage org_toftutorial - \li \subpage org_mitk_gui_qt_ultrasound - \li \subpage org_mitk_views_volumevisualization - \li \subpage org_mitk_gui_qt_xnat - - \li \subpage org_mitkexamplesopencv - \li \subpage org_blueberry_ui_qt_objectinspector - + */ \ No newline at end of file diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginSpecificManualsList.dox similarity index 50% copy from Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox copy to Documentation/Doxygen/2-UserManual/MITKPluginSpecificManualsList.dox index 1728b2a49d..a65603b45b 100644 --- a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox +++ b/Documentation/Doxygen/2-UserManual/MITKPluginSpecificManualsList.dox @@ -1,80 +1,42 @@ /** -\page PluginListPage MITK Plugin Manuals - -The plugins and bundles provide much of the extended functionality of MITK. Each encapsulates a solution to a problem and associated features. This way one can easily assemble the necessary capabilites for a workflow without adding a lot of bloat, by combining plugins as needed. - - -\paragraph PluginListPageEndUserPluginList List of General Purpose Plugins - - - \li \subpage org_mitk_views_basicimageprocessing - \li \subpage org_mitk_gui_qt_chartExample - \li \subpage org_mitk_views_datamanager - \li \subpage org_mitk_gui_qt_dicom - \li \subpage org_mitk_gui_qt_dicominspector - \li \subpage org_mitk_gui_qt_imagecropper - \li \subpage org_mitk_views_imagenavigator - \li \subpage org_blueberry_ui_qt_log - \li \subpage org_mitk_gui_qt_measurementtoolbox - \li \subpage org_mitk_gui_qt_moviemaker - \li \subpage org_mitk_views_screenshotmaker - \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_segmentation - \li \subpage org_mitk_views_multilabelsegmentation - \li \subpage org_mitk_gui_qt_viewnavigator - - -\paragraph PluginListPageApplicationPluginList List of Application-specific Plugins +\page PluginListSpecificPage List of Application-specific Plugins \li \subpage org_mitk_gui_qt_aicpregistration \li \subpage org_mitk_gui_qt_cest \li \subpage org_mitk_gui_qt_classificationsegmentation \li \subpage org_mitk_views_cmdlinemodules + \li \subpage org_mitk_gui_qt_pharmacokinetics_concentration_mri + \li \subpage org_mitk_gui_qt_pharmacokinetics_mri + \li \subpage org_mitk_gui_qt_pharmacokinetics_pet \li \subpage org_mitk_gui_qt_eventrecorder \li \subpage org_mitk_gui_qt_examples - \li \subpage org_mitk_gui_qt_fit_demo - \li \subpage org_mitk_gui_qt_fit_genericfitting - \li \subpage org_mitk_gui_qt_fit_inspector \li \subpage org_mitk_gui_qt_geometrytools - \li \subpage org_mitk_gui_qt_igt_app_echotrack \li \subpage org_mitk_gui_qt_igtexample \li \subpage org_mitk_gui_qt_igtlplugin \li \subpage org_mitk_gui_qt_igttracking \li \subpage org_mitk_gui_qt_igttrackingsemiautomaticmeasurement \li \subpage org_mitk_gui_qt_lasercontrol - \li \subpage org_mitk_gui_qt_matchpoint_algorithm_batch - \li \subpage org_mitk_gui_qt_matchpoint_algorithm_browser - \li \subpage org_mitk_gui_qt_matchpoint_algorithm_control - \li \subpage org_mitk_gui_qt_matchpoint_evaluator - \li \subpage org_mitk_gui_qt_matchpoint_framereg - \li \subpage org_mitk_gui_qt_matchpoint_manipulator - \li \subpage org_mitk_gui_qt_matchpoint_mapper - \li \subpage org_mitk_gui_qt_matchpoint_visualizer + \li \subpage org_mitk_gui_qt_fit_demo + \li \subpage org_mitk_gui_qt_fit_genericfitting + \li \subpage org_mitk_gui_qt_fit_inspector + \li \subpage org_mitkexamplesopencv \li \subpage org_mitk_gui_qt_overlaymanager \li \subpage org_mitk_gui_qt_mitkphenotyping \li \subpage org_mitk_gui_qt_photoacoustics_pausmotioncompensation \li \subpage org_mitk_example_gui_pcaexample - \li \subpage org_mitk_gui_qt_pharmacokinetics_mri - \li \subpage org_mitk_gui_qt_pharmacokinetics_pet - \li \subpage org_mitk_gui_qt_pharmacokinetics_concentration_mri \li \subpage org_mitk_gui_qt_pharmacokinetics_curvedescriptor \li \subpage org_mitk_gui_qt_photoacoustics_imageprocessing \li \subpage org_mitk_gui_qt_pharmacokinetics_simulation - \li \subpage org_mitk_gui_qt_photoacoustics_spectralunmixing \li \subpage org_mitk_gui_qt_pointsetinteractionmultispectrum \li \subpage org_mitk_gui_qt_renderwindowmanager + \li \subpage org_mitk_gui_qt_photoacoustics_spectralunmixing \li \subpage org_mitk_gui_qt_spectrocamrecorder \li \subpage org_surfacematerialeditor + \li \subpage org_blueberry_ui_qt_objectinspector \li \subpage org_toftutorial \li \subpage org_mitk_gui_qt_ultrasound - \li \subpage org_mitk_views_volumevisualization + \li \subpage org_mitk_gui_qt_igt_app_echotrack \li \subpage org_mitk_gui_qt_xnat - \li \subpage org_mitkexamplesopencv - \li \subpage org_blueberry_ui_qt_objectinspector - - */ \ No newline at end of file diff --git a/Documentation/Doxygen/2-UserManual/MiniApps.dox b/Documentation/Doxygen/2-UserManual/MiniApps.dox index b75d671971..8fd724a298 100644 --- a/Documentation/Doxygen/2-UserManual/MiniApps.dox +++ b/Documentation/Doxygen/2-UserManual/MiniApps.dox @@ -1,64 +1,65 @@ /** \page AdvancedTopicsPage Advanced MITK user topics \section MiniAppExplainPage MITK MiniApps

What are MiniApps?

MiniApps are small command line tools. Generally the purpose of each of these tools is designed to fulfill one simple task, e.g. resample an image or extract image statistics of a given region of interest (ROI). They are intended to provide command line access to a variety of features of MITK, thus facilitating batched processing of data.

Usage

Each MiniApp should provide information about its usage. If it is called without parameters it will output help information about expected inputs, outputs and parameters. Below you can see the help output of the MitkGibbsTracking MiniApp: \code $./MitkGibbsTracking -i, --input, input image (tensor, ODF or FSL/MRTrix SH-coefficient image) -p, --parameters, parameter file (.gtp) -m, --mask, binary mask image (optional) -s, --shConvention, sh coefficient convention (FSL, MRtrix) (optional), (default: FSL) -o, --outFile, output fiber bundle (.fib) -f, --noFlip, do not flip input image to match MITK coordinate convention (optional) \endcode

Integrating a command line tool into MITK Workbench

The executable file has be to be announced in MITK Workbench. This can be done in Preferences window: Click 'Window' -> 'Preferences', and select 'Command Line Modules'. You can add directories containing executable files or you can select single executable files. Click 'OK' button. The configured command line tools are now available via the drop-down box of the Command Line Modules tab. \warning The build configuration of your MiniApp should match the build configuration of your MITK application. This is especially relevant for developers. Combining a Release application and Debug MiniApp or vice versa might not work.

Available MiniApps in MITK

-\li \subpage mitkBasicImageProcessingMiniAppsPortalPage -\li \subpage mitkClassificationMiniAppsPortalPage - +

Technical Information

MiniApps follow the Slicer Execution Model in describing themselves via xml: \code $./GibbsTracking --xml Fiber Tracking and Processing Methods Gibbs Tracking MBI ... \endcode \note Full conformity is still a work in progress. */ diff --git a/Documentation/Doxygen/3-DeveloperManual/Toolkit/ModuleManuals/MITKModuleManualsList.dox b/Documentation/Doxygen/3-DeveloperManual/Toolkit/ModuleManuals/MITKModuleManualsList.dox index 8b3b910830..82b108ddcd 100644 --- a/Documentation/Doxygen/3-DeveloperManual/Toolkit/ModuleManuals/MITKModuleManualsList.dox +++ b/Documentation/Doxygen/3-DeveloperManual/Toolkit/ModuleManuals/MITKModuleManualsList.dox @@ -1,34 +1,32 @@ /** \page MITKModuleManualsListPage MITK Module Manuals \section MITKModuleManualsListPageOverview Overview The modules are shared libraries that provide functionality that can be used by developers. \section MITKModuleManualsListPageModuleManualList List of Module Manuals \li \subpage NavigationGeneralModulePage \li \subpage MitkOpenCL_Overview \li \subpage LegacyGLModule \li \subpage GeneratingDeviceModulesPage \li \subpage mitkPython_Overview \li \subpage USModulePage \li \subpage PAModulePage \li \subpage AnnotationModulePage \li \subpage IGTConcepts \li \subpage IGTTutorialOverview \li \subpage ChartModule \li \subpage RESTModule \section MITKModuleManualsListPageAdditionalInformation Additional Information on Certain Modules \li \ref PlanarPropertiesPage - \li \subpage DiffusionImagingPropertiesPage - \li \subpage ConnectomicsRenderingPropertiesPage \section MITKMigrationGuides Migration Guides \li \subpage InteractionMigration \li \subpage GeometryMigration \li \subpage OverlayMigration */