diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp index 8ad4dee7c7..c9d5bb5113 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp @@ -1,266 +1,266 @@ /*=================================================================== 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. ===================================================================*/ #ifndef __itkAddArtifactsToDwiImageFilter_txx #define __itkAddArtifactsToDwiImageFilter_txx #include #include #include #include "itkAddArtifactsToDwiImageFilter.h" #include #include #include #include #include #include #define _USE_MATH_DEFINES #include namespace itk { template< class TPixelType > AddArtifactsToDwiImageFilter< TPixelType > ::AddArtifactsToDwiImageFilter() : m_NoiseModel(NULL) , m_FrequencyMap(NULL) , m_kOffset(0) , m_tLine(1) , m_EddyGradientStrength(0.001) , m_SimulateEddyCurrents(false) , m_TE(100) , m_Upsampling(1) { this->SetNumberOfRequiredInputs( 1 ); } template< class TPixelType > AddArtifactsToDwiImageFilter< TPixelType >::ComplexSliceType::Pointer AddArtifactsToDwiImageFilter< TPixelType >::RearrangeSlice(ComplexSliceType::Pointer slice) { ImageRegion<2> region = slice->GetLargestPossibleRegion(); typename ComplexSliceType::Pointer rearrangedSlice = ComplexSliceType::New(); rearrangedSlice->SetLargestPossibleRegion( region ); rearrangedSlice->SetBufferedRegion( region ); rearrangedSlice->SetRequestedRegion( region ); rearrangedSlice->Allocate(); int xHalf = region.GetSize(0)/2; int yHalf = region.GetSize(1)/2; for (int y=0; y pix = slice->GetPixel(idx); if( idx[0] < xHalf ) idx[0] = idx[0] + xHalf; else idx[0] = idx[0] - xHalf; if( idx[1] < yHalf ) idx[1] = idx[1] + yHalf; else idx[1] = idx[1] - yHalf; rearrangedSlice->SetPixel(idx, pix); } return rearrangedSlice; } template< class TPixelType > void AddArtifactsToDwiImageFilter< TPixelType > ::GenerateData() { typename DiffusionImageType::Pointer inputImage = static_cast< DiffusionImageType * >( this->ProcessObject::GetInput(0) ); itk::ImageRegion<3> inputRegion = inputImage->GetLargestPossibleRegion(); typename itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage( inputImage ); duplicator->Update(); typename DiffusionImageType::Pointer outputImage = duplicator->GetOutput(); // is input slize size even? int x=inputRegion.GetSize(0); int y=inputRegion.GetSize(1); if ( x%2 == 1 ) x += 1; if ( y%2 == 1 ) y += 1; // create slice object typename SliceType::Pointer slice = SliceType::New(); ImageRegion<2> sliceRegion; sliceRegion.SetSize(0, x); sliceRegion.SetSize(1, y); slice->SetLargestPossibleRegion( sliceRegion ); slice->SetBufferedRegion( sliceRegion ); slice->SetRequestedRegion( sliceRegion ); slice->Allocate(); slice->FillBuffer(0.0); ImageRegion<2> upsampledSliceRegion; if (m_Upsampling>1.00001) { upsampledSliceRegion.SetSize(0, x*m_Upsampling); upsampledSliceRegion.SetSize(1, y*m_Upsampling); } // frequency map slice typename SliceType::Pointer fMap = NULL; if (m_FrequencyMap.IsNotNull()) { fMap = SliceType::New(); fMap->SetLargestPossibleRegion( sliceRegion ); fMap->SetBufferedRegion( sliceRegion ); fMap->SetRequestedRegion( sliceRegion ); fMap->Allocate(); fMap->FillBuffer(0.0); } if ( m_FrequencyMap.IsNotNull() || m_kOffset>0.0 || m_Upsampling>1.00001 || m_SimulateEddyCurrents) { MatrixType transform = inputImage->GetDirection(); for (int i=0; i<3; i++) for (int j=0; j<3; j++) transform[i][j] *= inputImage->GetSpacing()[j]; MITK_INFO << "Adjusting complex signal"; MITK_INFO << "line readout time: " << m_tLine; MITK_INFO << "line offset: " << m_kOffset; if (m_FrequencyMap.IsNotNull()) MITK_INFO << "frequency map is set"; else MITK_INFO << "no frequency map set"; if (m_Upsampling>1.00001) MITK_INFO << "Gibbs ringing enabled"; else MITK_INFO << "Gibbs ringing disabled"; if (m_SimulateEddyCurrents) MITK_INFO << "Simulating eddy currents"; boost::progress_display disp(inputImage->GetVectorLength()*inputRegion.GetSize(2)); for (int g=0; gGetVectorLength(); g++) for (int z=0; z compartmentSlices; // extract slice from channel g for (int y=0; yGetPixel(index3D)[g]; slice->SetPixel(index2D, pix2D); if (fMap.IsNotNull()) fMap->SetPixel(index2D, m_FrequencyMap->GetPixel(index3D)); } if (m_Upsampling>1.00001) { itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); resampler->SetInput(slice); resampler->SetOutputParametersFromImage(slice); resampler->SetSize(upsampledSliceRegion.GetSize()); resampler->SetOutputSpacing(slice->GetSpacing()/m_Upsampling); resampler->Update(); typename SliceType::Pointer upslice = resampler->GetOutput(); compartmentSlices.push_back(upslice); } else compartmentSlices.push_back(slice); // fourier transform slice typename ComplexSliceType::Pointer fSlice; itk::Size<2> outSize; outSize.SetElement(0, x); outSize.SetElement(1, y); typename itk::KspaceImageFilter< SliceType::PixelType >::Pointer idft = itk::KspaceImageFilter< SliceType::PixelType >::New(); idft->SetCompartmentImages(compartmentSlices); idft->SetkOffset(m_kOffset); idft->SettLine(m_tLine); idft->SetSimulateRelaxation(false); idft->SetFrequencyMap(fMap); idft->SetDiffusionGradientDirection(m_GradientList.at(g)); idft->SetSimulateEddyCurrents(m_SimulateEddyCurrents); idft->SetEddyGradientMagnitude(m_EddyGradientStrength); idft->SetTE(m_TE); idft->SetZ((double)z-(double)inputRegion.GetSize(2)/2.0); idft->SetDirectionMatrix(transform); idft->SetOutSize(outSize); idft->Update(); fSlice = idft->GetOutput(); // inverse fourier transform slice typename SliceType::Pointer newSlice; typename itk::DftImageFilter< SliceType::PixelType >::Pointer dft = itk::DftImageFilter< SliceType::PixelType >::New(); dft->SetInput(fSlice); dft->Update(); newSlice = dft->GetOutput(); // put slice back into channel g - for (int y=0; yGetPixel(index3D); typename SliceType::IndexType index2D; index2D[0]=x; index2D[1]=y; double signal = newSlice->GetPixel(index2D); if (signal>0) signal = floor(signal+0.5); else signal = ceil(signal-0.5); pix3D[g] = signal; outputImage->SetPixel(index3D, pix3D); } ++disp; } } if (m_NoiseModel!=NULL) { ImageRegionIterator it1 (outputImage, inputRegion); boost::progress_display disp2(inputRegion.GetNumberOfPixels()); while(!it1.IsAtEnd()) { ++disp2; typename DiffusionImageType::PixelType signal = it1.Get(); m_NoiseModel->AddNoise(signal); it1.Set(signal); ++it1; } } this->SetNthOutput(0, outputImage); } } #endif diff --git a/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/CommandLineModulesView.h b/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/CommandLineModulesView.h index 45449be50e..e42b2b5ed2 100644 --- a/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/CommandLineModulesView.h +++ b/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/CommandLineModulesView.h @@ -1,225 +1,225 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) University College London (UCL). 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. ===================================================================*/ #ifndef CommandLineModulesView_h #define CommandLineModulesView_h #include #include #include #include #include #include #include class ctkCmdLineModuleBackendLocalProcess; class ctkCmdLineModuleDirectoryWatcher; class CommandLineModulesViewControls; class QmitkCmdLineModuleProgressWidget; class QAction; class QVBoxLayout; namespace berry { - class IBerryPreferences; + struct IBerryPreferences; } /*! * \class CommandLineModulesView * \brief Provides basic GUI interface to the CTK command line modules. * \author Matt Clarkson (m.clarkson@ucl.ac.uk) * \ingroup org_mitk_gui_qt_cmdlinemodules_internal * \sa QmitkAbstractView */ class CommandLineModulesView : public QmitkAbstractView { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: CommandLineModulesView(); virtual ~CommandLineModulesView(); /** * \brief Main method, called by framework to create the GUI at the right time. * \param parent The parent QWidget, as this class itself is not a QWidget subclass. */ virtual void CreateQtPartControl(QWidget *parent); /** * \brief Called by the framework to indicate that the preferences have changed. * \param prefs not used, as we call RetrievePreferenceValues(). */ void OnPreferencesChanged(const berry::IBerryPreferences* prefs); protected Q_SLOTS: /** * \brief Called when the ctkMenuComboBox has the menu selection changed, * and causes the corresponding GUI to be displayed. */ void OnActionChanged(QAction*); /** * \brief Slot that is called when the restore defaults button is pressed, * to reset the current GUI form to the default values, if the XML specifies defaults. */ void OnRestoreButtonPressed(); /** * \brief Slot that is called when the Run button is pressed to run the current module. */ void OnRunButtonPressed(); protected: /** * \brief Called by framework to set the focus on the right widget * when this view has focus, so currently, thats the ctkMenuCombo box. */ virtual void SetFocus(); private slots: /** * \brief Called when the user clicks to close a tab, and removes the front end from m_ListOfModules */ void OnTabCloseRequested(int tabNumber); /** * \brief Called from QmitkCmdLineModuleProgressWidget to indicate a job has started. */ void OnJobStarted(); /** * \brief Called from QmitkCmdLineModuleProgressWidget to indicate a job has finished. */ void OnJobFinished(); private: /** * \brief Called on startup and by OnPreferencesChanged to load all * preferences except the temporary folder into member variables. */ void RetrieveAndStorePreferenceValues(); /** * \brief Called on startup and by OnPreferencesChanged to load the temporary folder * preference into member variable m_TemporaryDirectoryName. */ void RetrieveAndStoreTemporaryDirectoryPreferenceValues(); /** * \brief Called on startup and by OnPreferencesChanged to set the validation mode, but will require a restart. */ void RetrieveAndStoreValidationMode(); /** * \brief Called to get hold of the actual preferences node. */ berry::IBerryPreferences::Pointer RetrievePreferences(); /** * \brief Search all modules for the one matching the given identifier. * \param fullName The "fullName" is the . from the XML. * \return ctkCmdLineModuleReference the reference corresponding to the fullName, or an invalid reference if non found. */ ctkCmdLineModuleReference GetReferenceByFullName(QString fullName); /** * \brief Raises a message box asking the user to select a module first. */ void AskUserToSelectAModule() const; /** * \brief Enables or Disables the Run Button. */ void UpdateRunButtonEnabledStatus(); /** * \brief The GUI controls contain a reset and run button, and a QWidget container, and the GUI component * for each command line module is added to the QWidget dynamically at run time. */ CommandLineModulesViewControls *m_Controls; /** * \brief We store the parent, passed in via CommandLineModulesView::CreateQtPartControl, * as this class itself is not a QWidget. */ QWidget *m_Parent; /** * \brief We keep a local layout, and arrange a display of QmitkCmdLineModuleProgressWidget, * where each QmitkCmdLineModuleProgressWidget represents a single running job. */ QVBoxLayout *m_Layout; /** * \brief The manager is responsible for loading and instantiating command line modules. */ ctkCmdLineModuleManager *m_ModuleManager; /** * \brief We are using a back-end that runs locally installed command line programs. */ ctkCmdLineModuleBackendLocalProcess *m_ModuleBackend; /** * \brief The ctkCmdLineModuleDirectoryWatcher maintains the list of directories * we are using to load modules, to provide automatic updates. */ ctkCmdLineModuleDirectoryWatcher *m_DirectoryWatcher; /** * \brief We store a temporary folder name, accessible via user preferences. */ QString m_TemporaryDirectoryName; /** * \brief We store an output folder name, accessible via user preferences for when * the file specified in a default output path is not within a writable directory. */ QString m_OutputDirectoryName; /** * \brief We store the validation mode, accessisble via user preferences. */ ctkCmdLineModuleManager::ValidationMode m_ValidationMode; /** * \brief We store the maximum number of concurrent processes, and disable the run button accordingly. */ int m_MaximumConcurrentProcesses; /** * \brief Counts the number of currently running processes. */ int m_CurrentlyRunningProcesses; /** * \brief Member variable, taken from preference page. */ bool m_DebugOutput; /** * \brief We keep a list of front ends to match the m_TabWidget. */ QList<ctkCmdLineModuleFrontend*> m_ListOfModules; }; #endif // CommandLineModulesView_h diff --git a/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/QmitkCmdLineModuleFactoryGui.h b/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/QmitkCmdLineModuleFactoryGui.h index f6e1f9d43b..58df0095ee 100644 --- a/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/QmitkCmdLineModuleFactoryGui.h +++ b/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/QmitkCmdLineModuleFactoryGui.h @@ -1,54 +1,54 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) University College London (UCL). 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. ===================================================================*/ #ifndef QmitkCmdLineModuleFactoryGui_h #define QmitkCmdLineModuleFactoryGui_h #include <ctkCmdLineModuleFrontendFactoryQtGui.h> #include <ctkCmdLineModuleReference.h> namespace mitk { class DataStorage; } -class QmitkCmdLineModuleFactoryGuiPrivate; +struct QmitkCmdLineModuleFactoryGuiPrivate; /** * \class QmitkCmdLineModuleFactoryGui * \brief Derived from ctkCmdLineModuleFactory to instantiate QmitkCmdLineModuleGui front ends. * \author Matt Clarkson (m.clarkson@ucl.ac.uk) * \ingroup org_mitk_gui_qt_cmdlinemodules_internal * \sa QmitkCmdLineModuleGui * \sa ctkCmdLineModuleFrontendFactoryQtGui */ class QmitkCmdLineModuleFactoryGui : public ctkCmdLineModuleFrontendFactoryQtGui { public: QmitkCmdLineModuleFactoryGui(const mitk::DataStorage* dataStorage); virtual ~QmitkCmdLineModuleFactoryGui(); /** * \brief Simply creates QmitkCmdLineModuleGui which is an MITK specific Qt front end. */ ctkCmdLineModuleFrontendQtGui* create(const ctkCmdLineModuleReference& moduleRef); private: QScopedPointer<QmitkCmdLineModuleFactoryGuiPrivate> d; }; #endif // QmitkCmdLineModuleFactoryGui_h diff --git a/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/QmitkCmdLineModuleGui.h b/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/QmitkCmdLineModuleGui.h index adea0c6bf4..c535f697e7 100644 --- a/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/QmitkCmdLineModuleGui.h +++ b/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/QmitkCmdLineModuleGui.h @@ -1,117 +1,117 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) University College London (UCL). 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. ===================================================================*/ #ifndef QmitkCmdLineModuleGui_h #define QmitkCmdLineModuleGui_h #include <QBuffer> #include <QUiLoader> #include <ctkCmdLineModuleReference.h> #include <ctkCmdLineModuleFrontendQtGui.h> namespace mitk { class DataStorage; } -class QmitkCmdLineModuleGuiPrivate; +struct QmitkCmdLineModuleGuiPrivate; class QWidget; /** * \class QmitkCmdLineModuleGui * \brief Derived from ctkCmdLineModuleQtGui to implement an MITK specific command line module, * that has access to the mitk::DataStorage, and also instantiates QmitkDataStorageComboBox * for any "imageInputWidget" type, and also provides QmitkDataStorageComboBox.xsl to override * the standard CTK xslt transformation. * \author Matt Clarkson (m.clarkson@ucl.ac.uk) * \ingroup org_mitk_gui_qt_cmdlinemodules_internal * \sa QmitkCmdLineModuleFactoryGui * \sa ctkCmdLineModuleFrontendQtGui */ class QmitkCmdLineModuleGui : public ctkCmdLineModuleFrontendQtGui { Q_OBJECT public: QmitkCmdLineModuleGui(const mitk::DataStorage* dataStorage, const ctkCmdLineModuleReference& moduleRef); virtual ~QmitkCmdLineModuleGui(); /** * \brief Returns the top level widget containing the whole GUI, and * should be used in preference to ctkCmdLineModuleFrontend::guiHandle. */ QWidget* getGui(); /** * \brief Copies the visible parameters from another QmitkCmdLineModuleGui; * \param another a QmitkCmdLineModuleGui frontend. */ void copyParameters(QmitkCmdLineModuleGui& another); /** * \brief A custom method to enable access to a mitk::DataNode::Pointer for input images. * \param parameter The name of the parameter as specified in XML. * \param role The role, \see ctkCmdLineModuleFrontend. * \return QVariant * * If role==UserRole and the parameter specified by parameter name is an * input image, will return a mitk::DataNode::Pointer wrapped in a QVariant. * * If role==UserRole and the parameter specified is not an input image, * returns an Empty QVariant. * * For any other scenario, calls base class. * * \sa ctkCmdLineModuleFrontend::value */ virtual QVariant value(const QString ¶meter, int role) const; /** * \brief A custom method to enable the setting of mitk::DataNode::Pointer for input images. * \param parameter The name of the parameter as specified in XML. * \param value QVariant containing a mitk::DataNode::Pointer * \param role The role, \see ctkCmdLineModuleFrontend. * * If role==UserRole and the parameter specified by parameter name is an * input image, will set the value for that parameter. * * * For any other scenario, calls base class. * * \sa ctkCmdLineModuleFrontend::setValue */ virtual void setValue(const QString& parameter, const QVariant& value, int role = DisplayRole); protected: /** * \brief Virtual getter. * \see ctkCmdLineModuleFrontendQtGui::uiLoader() */ virtual QUiLoader* uiLoader() const; /** * \brief Virtual getter. * \see ctkCmdLineModuleFrontendQtGui::xslTransform() */ virtual ctkCmdLineModuleXslTransform* xslTransform() const; private: QScopedPointer<QmitkCmdLineModuleGuiPrivate> d; }; // end class #endif // QmitkCmdLineModuleGui_h diff --git a/Plugins/org.mitk.gui.qt.datamanagerlight/documentation/UserManual/QmitkDatamanagerLight.dox b/Plugins/org.mitk.gui.qt.datamanagerlight/documentation/UserManual/QmitkDatamanagerLight.dox deleted file mode 100644 index 8d95aeb632..0000000000 --- a/Plugins/org.mitk.gui.qt.datamanagerlight/documentation/UserManual/QmitkDatamanagerLight.dox +++ /dev/null @@ -1,108 +0,0 @@ -/** - -\page org_mitk_views_datamanager The DataManager - -\image html DataManager_48.png "Icon of the Module" - -\section QmitkDataManagerIntroduction Introduction - -The Datamanager is the central componenent to manage medical data like images, surfaces, etc.. -After loading one or more data into the Datamanager the data are shown in the four-view window, the so called Standard View. -The user can now start working on the data by just clicking into the standard view or by using the MITK-modules such as "Segmentation" or "Basic Image Processing". - -Available sections: - - \ref QmitkDataManagerIntroduction - - \ref QmitkDataManagerLoading - - \ref QmitkDataManagerSaving - - \ref QmitkDataManagerProperties - - \ref QmitkDataManagerPropertiesList - - \ref QmitkDataManagerPropertiesVisibility - - \ref QmitkDataManagerPropertiesRepresentation - - \ref QmitkDataManagerPropertiesPreferences - - \ref QmitkDataManagerPropertyList - - -\image html Overview.png "How MITK looks when starting" - - -\section QmitkDataManagerLoading Loading Data - -There are three ways of loading data into the Datamanager as so called Data-Elements. - -The user can just drag and drop data into the Datamanager or directly into one of the four parts of the Standard View. -He can as well use the Open-Button in the right upper corner. Or he can use the standard "File->Open"-Dialog on the top. - -A lot of file-formats can be loaded into MITK, for example - -<ul> -<li> 2D-images/3D-volumes with or without several timesteps (*.dcm, *.ima, *.pic, ...) -<li> Surfaces (*.stl, *.vtk, ...) -<li> Pointsets (*.mps) -<li> ... -</ul> - -The user can also load a series of 2D images (e.g. image001.png, image002.png ...) to a MITK 3D volume. -To do this, just drag and drop one of those 2D data files into the Datamanager by holding the ALT key. - -After loading one or more data into the Datamanager they appear as Data-Elements in a sorted list inside the Datamanager. -Data-Elements can also be sorted hierarchically as a parent-child-relation. -For example after using the Segmentation-Module on Data-Element1 the result is created as Data-Element2, which is a child of Data-Element1 (see Screenshot1). -The order can be changed by drag and drop. - -\image html Parent-Child.png "Screenshot1" - -The listed Data-Elements are shown in the standard view. -Here the user can scale or rotate the medical objects or he can change the cutting planes of the object by just using the mouse inside this view. - -\section QmitkDataManagerSaving Saving Data - -There are two ways of saving data from the Datamanger. The user can either save the whole project with all Data-Elements by clicking on "File"->"Save Project" -or he can save single Data-Elements by right-clicking->"Save", directly on a Data-Element. -When saving the whole project, the sorting of Data-Elements is saved as well. By contrast the sorting is lost, when saving a single Data-Element. - -\section QmitkDataManagerProperties Working with the Datamanager - -\subsection QmitkDataManagerPropertiesList List of Data-Elements - -The Data-Elements are listed in the Datamanager. -As described above the elements can be sorted hierarchically as a parent-child-relation. -For example after using the Segmentation-Module on Data-Element1 the result is created as Data-Element2, which is a child of Data-Element1 (see Screenshot1). -By drag and drop the sorting of Data-Elements and their hierarchical relation can be changed. - -\subsection QmitkDataManagerPropertiesVisibility Visibility of Data-Elements - -By default all loaded Data-Elements are visible in the standard view. -The visibility can be changed by right-clicking on the Data-Element and then choosing "Toogle visibility". -The box in front of the Data-Element in the Datamanager shows the visibility. -A green-filled box means a visible Data-Element, an empty box means an invisible Data-Element (see Screenshot1). - -\subsection QmitkDataManagerPropertiesRepresentation Representation of Data-Elements - -There are different types of representations how to show the Data-Element inside the standard view. By right-clicking on the Data-Element all options are listed (see Screenshot2 and Screenshot 3). - -<ul> -<li> An arbitrary color can be chosen -<li> The opacity can be changed with a slide control -<li> In case of images a texture interpolation can be switched on or off. The texture interpolation smoothes the image, so that no single pixels are visible anymore. -<li> In case of surfaces the surface representation can be changed between points, wireframe or surface. -<li> Global reinit updates all windows to contain all the current data. Reinit updates a single data item fits the windows to contain this data item. -</ul> - -\image html Image_properties.png "Screenshot2: Properties for images" -\image html Surface_Properties.png "Screenshot3: Properties for surfaces" - - -\subsection QmitkDataManagerPropertiesPreferences Preferences - -For the datamanager there are already some default hotkeys like the del-key for deleting a Data-Element. The whole list is seen in Screenshot4. -From here the Hotkeys can also be changed. The preference page is found in "Window"->"Preferences". - -\image html Preferences.png "Screenshot4" - -\section QmitkDataManagerPropertyList Property List - -The Property List displays all the properties the currently selected Data-Element has. Which properties these are depends on the Data-Element. Examples are opacity, shader, visibility. These properties can be changed by clicking on the appropriate field in the "value" column. - -\image html PropertyList.png "Screenshot5: Property List" - -*/ diff --git a/Plugins/org.mitk.gui.qt.ultrasound/documentation/doxygen/devicemanagement.png b/Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/devicemanagement.png similarity index 100% rename from Plugins/org.mitk.gui.qt.ultrasound/documentation/doxygen/devicemanagement.png rename to Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/devicemanagement.png diff --git a/Plugins/org.mitk.gui.qt.ultrasound/documentation/doxygen/devicemanagement_2.png b/Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/devicemanagement_2.png similarity index 100% rename from Plugins/org.mitk.gui.qt.ultrasound/documentation/doxygen/devicemanagement_2.png rename to Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/devicemanagement_2.png diff --git a/Plugins/org.mitk.gui.qt.ultrasound/documentation/doxygen/newvideodevice.png b/Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/newvideodevice.png similarity index 100% rename from Plugins/org.mitk.gui.qt.ultrasound/documentation/doxygen/newvideodevice.png rename to Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/newvideodevice.png diff --git a/Plugins/org.mitk.gui.qt.ultrasound/documentation/doxygen/usimaging.png b/Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/usimaging.png similarity index 100% rename from Plugins/org.mitk.gui.qt.ultrasound/documentation/doxygen/usimaging.png rename to Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/usimaging.png