diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox index 13d05fa1af..67ac20c7c5 100644 --- a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox +++ b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox @@ -1,67 +1,68 @@ /** \page PluginListPage MITK Plugin Manuals \section PluginListPageOverview Overview 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. The distinction between developer and end user use is for convenience only and mainly distinguishes which group a plugin is primarily aimed at. \section PluginListPageEndUserPluginList List of Plugins for End User Use \li \subpage org_blueberry_ui_qt_log \li \subpage org_mitk_views_basicimageprocessing \li \subpage org_mitk_views_cmdlinemodules \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_diffusionimaging \li \subpage org_mitk_gui_qt_imagecropper \li \subpage org_mitk_views_imagenavigator \li \subpage org_mitk_gui_qt_measurementtoolbox \li \subpage org_mitk_gui_qt_moviemaker \li \subpage org_mitk_views_screenshotmaker + \li \subpage org_mitk_gui_qt_photoacoustics_imageprocessing \li \subpage org_mitk_views_pointsetinteraction \li \subpage org_mitk_gui_qt_pointsetinteractionmultispectrum \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_spectrocamrecorder \li \subpage org_mitk_gui_qt_ultrasound \li \subpage org_mitk_gui_qt_viewnavigator \li \subpage org_mitk_views_volumevisualization \li \subpage org_mitk_gui_qt_xnat \li \subpage org_mitk_gui_qt_aicpregistration \li \subpage org_mitk_gui_qt_igtlplugin \li \subpage org_mitk_gui_qt_geometrytools \li \subpage org_mitk_gui_qt_classificationsegmentation \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_cest \section PluginListPageDevPluginList List of Plugins for Developer Use and Examples \li \subpage org_surfacematerialeditor \li \subpage org_toftutorial \li \subpage org_mitk_gui_qt_examples \li \subpage org_mitkexamplesopencv \li \subpage org_mitk_gui_qt_igtexample \li \subpage org_mitk_gui_qt_igttracking \li \subpage org_mitk_gui_qt_igt_app_echotrack \li \subpage org_blueberry_ui_qt_objectinspector \li \subpage org_mitk_gui_qt_eventrecorder \li \subpage org_mitk_gui_qt_overlaymanager \li \subpage org_mitk_example_gui_pcaexample \li \subpage org_mitk_gui_qt_renderwindowmanager \li \subpage org_mitk_gui_qt_lasercontrol \li \subpage org_mitk_gui_qt_photoacoustics_imageprocessing \li \subpage org_mitk_gui_qt_lasercontrol \li \subpage org_mitk_gui_qt_igttrackingsemiautomaticmeasurement */ diff --git a/Documentation/Doxygen/3-DeveloperManual/Toolkit/ModuleManuals/MITKModuleManualsList.dox b/Documentation/Doxygen/3-DeveloperManual/Toolkit/ModuleManuals/MITKModuleManualsList.dox index 204dd984fd..3d18e0605d 100644 --- a/Documentation/Doxygen/3-DeveloperManual/Toolkit/ModuleManuals/MITKModuleManualsList.dox +++ b/Documentation/Doxygen/3-DeveloperManual/Toolkit/ModuleManuals/MITKModuleManualsList.dox @@ -1,30 +1,31 @@ /** \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 ChartModule \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 */ diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/Manual.dox index 57374336c2..0aea28cd07 100644 --- a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/Manual.dox @@ -1,62 +1,62 @@ /** \page org_mitk_gui_qt_photoacoustics_imageprocessing The Photoacoustics Imageprocessing Plugin -\imageMacro{icon.png,"Icon of Imageprocessing",2.00} +\imageMacro{pai.png,"Icon of Imageprocessing",2.00} \tableofcontents \section org_mitk_gui_qt_photoacoustics_imageprocessingOverview Overview This plugin offers an interface to perform image processing on photoacoustic, as well as ultrasound images, i.e. to use beamforming and post-processing filters. For convenience, image processing can be done automatically for a whole batch of files containing PA or US data. \section org_mitk_gui_qt_photoacoustics_imageprocessingPrerequisites Prerequisites To use the much more performant openCL filters which run on the graphics card, MITK has to be able to use openCL, for which it is necessary to install the openCL implementation provided by your graphics card vendor. \section org_mitk_gui_qt_photoacoustics_imageprocessingFiltering Using the filters To perform image processing, simply load an image into MITK and select it in the Data manager. Only the selected image will be processed by the filters. \imageMacro{QmikPhotoacousticsImageProcessing_DataManager.png,"Select the image to be processed",7.62} Before performing reconstruction or using other filters those can be configured using the plugin's settings panel. \imageMacro{QmikPhotoacousticsImageProcessing_Settings.png,"The plugin's GUI",7.62} \subsection org_mitk_gui_qt_photoacoustics_imageprocessingBeamforming The Beamforming Settings For beamforming, three beamforming algorithms are available: Each of those can be coupled with either spherical delay calculation or a quadratic approximation for the delays. To supress noise, one of the following apodizations can be chosen to be used when beamforming: Other Standard beamforming parameters are available, which have to be chosen depending on the source image to attain a correctly reconstructed image. The Plugin is able to calculate the used scan depth as well as the transducer pitch from the selected image if the time-axis spacing is in microseconds, and the horizontal spacing in mm. If such a spacing is given, check the box "Auto Get Depth" to make the plugin read those values by itself. If the US source or the laser used for imaging is not located at the top of the image, an option is given to cut off pixels at the top of the image until the source. This value should be calibrated by the user to match the used hardware. If one wishes to beamform only certain slices of a given image, those can be selected by checking "select slices" and setting the "min" and "max" values accordingly, which are to be understood as closed interval boundaries. \subsection org_mitk_gui_qt_photoacoustics_imageprocessingBandpass The Bandpass Settings The bandpass uses an itk implementation of an 1D Fast Fourier Transform (FFT) to transform the image vertically, then filters the image using a Tukey window in the frequency domain and performs an inverse 1D FFT to get the filtered image. The "smoothness" of the tukey window can be chosen by using the "Tukey window alpha" parameter. The Tukey window interpolates between a Box window (alpha = 0) and a Von Hann window (alpha = 1). The filtered frequencies can be set by defining the High and Low pass frequencies. \subsection org_mitk_gui_qt_photoacoustics_imageprocessingCrop The Crop Filter Settings The crop filter cuts off parts of the image at the top and the bottom. The amount of pixels cut off can be configured using the "Cut Top" and "Cut Bottom" parameters. \subsection org_mitk_gui_qt_photoacoustics_imageprocessingBMode The BMode Filter Settings The B-mode filters available are: If desired, the filter can also resample the image to a given spacing; to do this, check the "Do Resampling" box and set the desired spacing in mm. Afterwards a logarithmic filter can be applied, if "Add Logfilter" is checked. \subsection org_mitk_gui_qt_photoacoustics_imageprocessingBatch Batch Processing When processing large amounts of data, an option is available to automatically process multiple images by applying all filters in order to those images and saving the resulting images. In the first row of the Batch Processing Panel one can select which filters should be applied to the image; in the second row one can select whether the resulting image from the filter should be saved. After pressing the "Start Batch Processing" button, one can choose first the images to be processed, and then the folder where they will be saved. -*/ \ No newline at end of file +*/ diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/icon.xpm b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/icon.xpm deleted file mode 100644 index 9057c20bc6..0000000000 --- a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/icon.xpm +++ /dev/null @@ -1,21 +0,0 @@ -/* XPM */ -static const char * icon_xpm[] = { -"16 16 2 1", -" c #FF0000", -". c #000000", -" ", -" ", -" ", -" ", -" ", -" ", -" ", -" ", -" ", -" ", -" ", -" ", -" ", -" ", -" ", -" "}; diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/pai.png b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/pai.png new file mode 100644 index 0000000000..1b8dc34c11 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/pai.png differ diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/resources/pai.png b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/resources/pai.png new file mode 100644 index 0000000000..1b8dc34c11 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/resources/pai.png differ