diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox
index c4d4470da7..86e8fa6f2c 100644
--- a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox
+++ b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox
@@ -1,84 +1,84 @@
/**
\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.
\subpage PluginListGeneralPage
- \ref org_mitk_views_basicimageprocessing
- \ref org_mitk_views_datamanager
- \ref org_mitk_editors_dicombrowser
- \ref org_mitk_gui_qt_dicominspector
- \ref org_mitk_gui_qt_flowapplication
- \ref org_mitk_views_imagecropper
- \ref org_mitk_views_imagenavigator
- \ref org_blueberry_views_logview
- \ref org_mitk_views_matchpoint_algorithm_browser
- \ref org_mitk_views_matchpoint_algorithm_control
- \ref org_mitk_views_matchpoint_evaluator
- \ref org_mitk_views_matchpoint_framereg
- \ref org_mitk_views_matchpoint_manipulator
- \ref org_mitk_views_matchpoint_mapper
- \ref org_mitk_views_matchpoint_visualizer
- \ref org_mitk_gui_qt_measurementtoolbox
- \ref org_mitk_views_moviemaker
- \ref org_mitk_views_multilabelsegmentation
- \ref org_mitk_views_pointsetinteraction
- \ref org_mitk_gui_qt_python
- \ref org_mitk_gui_qt_remeshing
- \ref org_mitk_views_screenshotmaker
- \ref org_mitk_views_segmentation
- \ref org_mitk_gui_qt_flow_segmentation
- \ref org_mitk_gui_qt_viewnavigator
- \ref org_mitk_views_volumevisualization
- \ref org_mitk_views_properties
\subpage PluginListSpecificPage
- \ref org_mitk_gui_qt_aicpregistration
- \ref org_mitk_gui_qt_cest
- \ref org_mitk_gui_qt_classificationsegmentation
- \ref org_mitk_views_cmdlinemodules
- \ref org_mitk_views_pharmacokinetics_concentration_mri
- \ref org_mitk_views_pharmacokinetics_mri
- \ref org_mitk_gui_qt_pharmacokinetics_pet
- \ref org_mitk_gui_qt_eventrecorder
- \ref org_mitk_gui_qt_examples
- \ref org_mitk_gui_qt_geometrytools
- \ref org_mitk_gui_qt_igtexample
- \ref org_mitk_gui_qt_igtlplugin
- \ref org_mitk_gui_qt_igttracking
- \ref org_mitk_gui_qt_igttrackingsemiautomaticmeasurement
- \ref org_mitk_views_imagestatistics
- \ref org_mitk_gui_qt_lasercontrol
- \ref org_mitk_views_fit_demo
- \ref org_mitk_gui_qt_fit_genericfitting
- \ref org_mitk_views_fit_inspector
- \ref org_mitkexamplesopencv
- \ref org_mitk_gui_qt_overlaymanager
- \ref org_mitk_gui_qt_mitkphenotyping
- \ref org_mitk_gui_qt_photoacoustics_pausmotioncompensation
- \ref org_mitk_example_gui_pcaexample
- \ref org_mitk_gui_qt_preprocessing_resampling
- \ref org_mitk_views_pharmacokinetics_curvedescriptor
- - \ref org_mitk_gui_qt_photoacoustics_imageprocessing
+ - \ref org_mitk_views_photoacoustics_imageprocessing
- \ref org_mitk_gui_qt_pharmacokinetics_simulation
- \ref org_mitk_gui_qt_pointsetinteractionmultispectrum
- \ref org_mitk_gui_qt_renderwindowmanager
- \ref org_mitk_gui_qt_photoacoustics_spectralunmixing
- \ref org_mitk_gui_qt_spectrocamrecorder
- \ref org_surfacematerialeditor
- \ref org_toftutorial
- \ref org_blueberry_ui_qt_objectinspector
- \ref org_mitk_gui_qt_ultrasound
- \ref org_mitk_gui_qt_igt_app_echotrack
- \ref org_mitk_gui_qt_xnat
*/
diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginSpecificManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginSpecificManualsList.dox
index c470916167..efa68b94a4 100644
--- a/Documentation/Doxygen/2-UserManual/MITKPluginSpecificManualsList.dox
+++ b/Documentation/Doxygen/2-UserManual/MITKPluginSpecificManualsList.dox
@@ -1,45 +1,45 @@
/**
\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_gui_qt_flowapplication
\li \subpage org_mitk_views_cmdlinemodules
\li \subpage org_mitk_views_pharmacokinetics_concentration_mri
\li \subpage org_mitk_views_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_geometrytools
\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_views_imagestatistics
\li \subpage org_mitk_gui_qt_lasercontrol
\li \subpage org_mitk_views_fit_demo
\li \subpage org_mitk_gui_qt_fit_genericfitting
\li \subpage org_mitk_views_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_preprocessing_resampling
\li \subpage org_mitk_views_pharmacokinetics_curvedescriptor
- \li \subpage org_mitk_gui_qt_photoacoustics_imageprocessing
+ \li \subpage org_mitk_views_photoacoustics_imageprocessing
\li \subpage org_mitk_gui_qt_pharmacokinetics_simulation
\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_gui_qt_igt_app_echotrack
\li \subpage org_mitk_gui_qt_xnat
*/
\ No newline at end of file
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 e13c48d0b5..ee77922748 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
@@ -1,66 +1,66 @@
/**
-\page org_mitk_gui_qt_photoacoustics_imageprocessing The Photoacoustics Imageprocessing Plugin
+\page org_mitk_views_photoacoustics_imageprocessing The Photoacoustics Imageprocessing Plugin
\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_imageprocessingImageDetails Image Details
To create the .nrrd images necessary for the plugin from raw data, one can use e.g. pynrrd, a python package for very straightforward creation of .nrrd images.
The Beamforming Filter is also able to read certain paramters, as the scan depth and the transducer pitch from the selected image. To this end, the image must have a time-axis spacing in µs and a horizontal spacing in mm.
\subsection org_mitk_gui_qt_photoacoustics_imageprocessingBeamforming The Beamforming Settings
For beamforming, three beamforming algorithms are available:
- DAS (Delay And Sum)
- DMAS (Delay Multiply And Sum)
- sDMAS (signed Delay Multiply And Sum)
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:
- Box (No apodization)
- Hamming
- Von Hann
Other Standard beamforming parameters are available, which have to be chosen depending on the source image to attain a correctly reconstructed image.
As mentioned above, 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:
- An absolute filter
- An envelope detection filter
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.
*/