diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging/files.cmake index 4778152042..e422eff8ae 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/files.cmake +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/files.cmake @@ -1,178 +1,180 @@ set(SRC_CPP_FILES QmitkODFDetailsWidget.cpp QmitkODFRenderWidget.cpp QmitkPartialVolumeAnalysisWidget.cpp QmitkIVIMWidget.cpp QmitkTbssRoiAnalysisWidget.cpp QmitkResidualAnalysisWidget.cpp QmitkResidualViewWidget.cpp QmitkTensorModelParametersWidget.cpp QmitkZeppelinModelParametersWidget.cpp QmitkStickModelParametersWidget.cpp QmitkDotModelParametersWidget.cpp QmitkBallModelParametersWidget.cpp QmitkAstrosticksModelParametersWidget.cpp ) set(INTERNAL_CPP_FILES mitkPluginActivator.cpp QmitkQBallReconstructionView.cpp QmitkPreprocessingView.cpp QmitkDiffusionDicomImportView.cpp QmitkDiffusionQuantificationView.cpp QmitkTensorReconstructionView.cpp QmitkDiffusionImagingPublicPerspective.cpp QmitkControlVisualizationPropertiesView.cpp QmitkODFDetailsView.cpp QmitkGibbsTrackingView.cpp QmitkStochasticFiberTrackingView.cpp QmitkStreamlineTrackingView.cpp QmitkFiberProcessingView.cpp # QmitkFiberBundleDeveloperView.cpp QmitkPartialVolumeAnalysisView.cpp QmitkIVIMView.cpp QmitkTractbasedSpatialStatisticsView.cpp QmitkTbssTableModel.cpp QmitkTbssMetaTableModel.cpp QmitkTbssSkeletonizationView.cpp Connectomics/QmitkConnectomicsDataView.cpp Connectomics/QmitkConnectomicsNetworkOperationsView.cpp Connectomics/QmitkConnectomicsStatisticsView.cpp Connectomics/QmitkNetworkHistogramCanvas.cpp QmitkDwiSoftwarePhantomView.cpp QmitkOdfMaximaExtractionView.cpp QmitkFiberfoxView.cpp QmitkFiberExtractionView.cpp QmitkFieldmapGeneratorView.cpp QmitkDiffusionRegistrationView.cpp + QmitkDenoisingView.cpp ) set(UI_FILES src/internal/QmitkQBallReconstructionViewControls.ui src/internal/QmitkPreprocessingViewControls.ui src/internal/QmitkDiffusionDicomImportViewControls.ui src/internal/QmitkDiffusionQuantificationViewControls.ui src/internal/QmitkTensorReconstructionViewControls.ui src/internal/QmitkControlVisualizationPropertiesViewControls.ui src/internal/QmitkODFDetailsViewControls.ui src/internal/QmitkGibbsTrackingViewControls.ui src/internal/QmitkStochasticFiberTrackingViewControls.ui src/internal/QmitkStreamlineTrackingViewControls.ui src/internal/QmitkFiberProcessingViewControls.ui # src/internal/QmitkFiberBundleDeveloperViewControls.ui src/internal/QmitkPartialVolumeAnalysisViewControls.ui src/internal/QmitkIVIMViewControls.ui src/internal/QmitkTractbasedSpatialStatisticsViewControls.ui src/internal/QmitkTbssSkeletonizationViewControls.ui src/internal/Connectomics/QmitkConnectomicsDataViewControls.ui src/internal/Connectomics/QmitkConnectomicsNetworkOperationsViewControls.ui src/internal/Connectomics/QmitkConnectomicsStatisticsViewControls.ui src/internal/QmitkDwiSoftwarePhantomViewControls.ui src/internal/QmitkOdfMaximaExtractionViewControls.ui src/internal/QmitkFiberfoxViewControls.ui src/internal/QmitkFiberExtractionViewControls.ui src/QmitkTensorModelParametersWidgetControls.ui src/QmitkZeppelinModelParametersWidgetControls.ui src/QmitkStickModelParametersWidgetControls.ui src/QmitkDotModelParametersWidgetControls.ui src/QmitkBallModelParametersWidgetControls.ui src/QmitkAstrosticksModelParametersWidgetControls.ui src/internal/QmitkFieldmapGeneratorViewControls.ui src/internal/QmitkDiffusionRegistrationViewControls.ui - + src/internal/QmitkDenoisingViewControls.ui ) set(MOC_H_FILES src/internal/mitkPluginActivator.h src/internal/QmitkQBallReconstructionView.h src/internal/QmitkPreprocessingView.h src/internal/QmitkDiffusionDicomImportView.h src/internal/QmitkDiffusionImagingPublicPerspective.h src/internal/QmitkDiffusionQuantificationView.h src/internal/QmitkTensorReconstructionView.h src/internal/QmitkControlVisualizationPropertiesView.h src/internal/QmitkODFDetailsView.h src/QmitkODFRenderWidget.h src/QmitkODFDetailsWidget.h src/internal/QmitkGibbsTrackingView.h src/internal/QmitkStochasticFiberTrackingView.h src/internal/QmitkStreamlineTrackingView.h src/internal/QmitkFiberProcessingView.h # src/internal/QmitkFiberBundleDeveloperView.h src/internal/QmitkPartialVolumeAnalysisView.h src/QmitkPartialVolumeAnalysisWidget.h src/internal/QmitkIVIMView.h src/internal/QmitkTractbasedSpatialStatisticsView.h src/internal/QmitkTbssSkeletonizationView.h src/QmitkTbssRoiAnalysisWidget.h src/QmitkResidualAnalysisWidget.h src/QmitkResidualViewWidget.h src/internal/Connectomics/QmitkConnectomicsDataView.h src/internal/Connectomics/QmitkConnectomicsNetworkOperationsView.h src/internal/Connectomics/QmitkConnectomicsStatisticsView.h src/internal/Connectomics/QmitkNetworkHistogramCanvas.h src/internal/QmitkDwiSoftwarePhantomView.h src/internal/QmitkOdfMaximaExtractionView.h src/internal/QmitkFiberfoxView.h src/internal/QmitkFiberExtractionView.h src/QmitkTensorModelParametersWidget.h src/QmitkZeppelinModelParametersWidget.h src/QmitkStickModelParametersWidget.h src/QmitkDotModelParametersWidget.h src/QmitkBallModelParametersWidget.h src/QmitkAstrosticksModelParametersWidget.h src/internal/QmitkFieldmapGeneratorView.h src/internal/QmitkDiffusionRegistrationView.h + src/internal/QmitkDenoisingView.h ) set(CACHED_RESOURCE_FILES # 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 plugin.xml resources/preprocessing.png resources/dwiimport.png resources/quantification.png resources/reconodf.png resources/recontensor.png resources/vizControls.png resources/OdfDetails.png resources/GibbsTracking.png resources/FiberBundleOperations.png resources/PartialVolumeAnalysis_24.png resources/IVIM_48.png resources/stochFB.png resources/tbss.png resources/connectomics/QmitkConnectomicsDataViewIcon_48.png resources/connectomics/QmitkConnectomicsNetworkOperationsViewIcon_48.png resources/connectomics/QmitkConnectomicsStatisticsViewIcon_48.png resources/arrow.png resources/qball_peaks.png resources/phantom.png resources/tensor.png resources/qball.png resources/StreamlineTracking.png resources/dwi2.png resources/odf.png resources/refresh.xpm resources/diffusionregistration.png ) set(QRC_FILES # uncomment the following line if you want to use Qt resources resources/QmitkDiffusionImaging.qrc #resources/QmitkTractbasedSpatialStatisticsView.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.gui.qt.diffusionimaging/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging/plugin.xml index 38c63b5d05..5d045e7c0d 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/plugin.xml +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/plugin.xml @@ -1,181 +1,188 @@ + + + + diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDenoisingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDenoisingView.cpp new file mode 100644 index 0000000000..c8c4c39811 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDenoisingView.cpp @@ -0,0 +1,366 @@ +/*=================================================================== + +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. + +===================================================================*/ + +// Blueberry +#include +#include + +// Qmitk +#include "QmitkDenoisingView.h" +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include + +const std::string QmitkDenoisingView::VIEW_ID = "org.mitk.views.denoisingview"; + +QmitkDenoisingView::QmitkDenoisingView() + : QmitkFunctionality() + , m_Controls( 0 ) + , m_MultiWidget( NULL ) + , m_OdfNormalization(0) + , m_ImageNode(NULL) +{ + m_VtkActor = vtkActor::New(); + m_VtkMapper = vtkPolyDataMapper::New(); + m_Renderer = vtkRenderer::New(); + m_VtkRenderWindow = vtkRenderWindow::New(); + m_RenderWindowInteractor = vtkRenderWindowInteractor::New(); + m_Camera = vtkCamera::New(); + m_VtkRenderWindow->SetSize(300,300); +} + +QmitkDenoisingView::~QmitkDenoisingView() +{ + +} + +void QmitkDenoisingView::CreateQtPartControl( QWidget *parent ) +{ + // build up qt view, unless already done + if ( !m_Controls ) + { + // create GUI widgets from the Qt Designer's .ui file + m_Controls = new Ui::QmitkDenoisingViewControls; + m_Controls->setupUi( parent ); + m_Controls->m_OdfBox->setVisible(false); + m_Controls->m_ODFRenderWidget->setVisible(false); + } +} + +void QmitkDenoisingView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) +{ + m_MultiWidget = &stdMultiWidget; + + { + mitk::SliceNavigationController* slicer = m_MultiWidget->mitkWidget1->GetSliceNavigationController(); + itk::ReceptorMemberCommand::Pointer command = itk::ReceptorMemberCommand::New(); + command->SetCallbackFunction( this, &QmitkDenoisingView::OnSliceChanged ); + m_SliceObserverTag1 = slicer->AddObserver( mitk::SliceNavigationController::GeometrySliceEvent(NULL, 0), command ); + } + + { + mitk::SliceNavigationController* slicer = m_MultiWidget->mitkWidget2->GetSliceNavigationController(); + itk::ReceptorMemberCommand::Pointer command = itk::ReceptorMemberCommand::New(); + command->SetCallbackFunction( this, &QmitkDenoisingView::OnSliceChanged ); + m_SliceObserverTag2 = slicer->AddObserver( mitk::SliceNavigationController::GeometrySliceEvent(NULL, 0), command ); + } + + { + mitk::SliceNavigationController* slicer = m_MultiWidget->mitkWidget3->GetSliceNavigationController(); + itk::ReceptorMemberCommand::Pointer command = itk::ReceptorMemberCommand::New(); + command->SetCallbackFunction( this, &QmitkDenoisingView::OnSliceChanged ); + m_SliceObserverTag3 = slicer->AddObserver( mitk::SliceNavigationController::GeometrySliceEvent(NULL, 0), command ); + } +} + +void QmitkDenoisingView::StdMultiWidgetNotAvailable() +{ + + { + mitk::SliceNavigationController* slicer = m_MultiWidget->mitkWidget1->GetSliceNavigationController(); + slicer->RemoveObserver( m_SliceObserverTag1 ); + } + + { + mitk::SliceNavigationController* slicer = m_MultiWidget->mitkWidget2->GetSliceNavigationController(); + slicer->RemoveObserver( m_SliceObserverTag2 ); + } + + { + mitk::SliceNavigationController* slicer = m_MultiWidget->mitkWidget3->GetSliceNavigationController(); + slicer->RemoveObserver( m_SliceObserverTag3 ); + } + + m_MultiWidget = NULL; +} + +void QmitkDenoisingView::OnSelectionChanged( std::vector nodes ) +{ + if (m_ImageNode.IsNotNull()) + m_ImageNode->RemoveObserver( m_PropertyObserverTag ); + + m_Controls->m_InputData->setTitle("Please Select Input Data"); + m_Controls->m_InputImageLabel->setText("mandatory"); + + m_ImageNode = NULL; + + // iterate selection + for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) + { + mitk::DataNode::Pointer node = *it; + + if( node.IsNotNull() && (dynamic_cast(node->GetData()) || dynamic_cast(node->GetData())) ) + { + m_Controls->m_InputImageLabel->setText(node->GetName().c_str()); + m_ImageNode = node; + } + } + + UpdateOdf(); + if (m_ImageNode.IsNotNull()) + { + itk::ReceptorMemberCommand::Pointer command = itk::ReceptorMemberCommand::New(); + command->SetCallbackFunction( this, &QmitkDenoisingView::OnSliceChanged ); + m_PropertyObserverTag = m_ImageNode->AddObserver( itk::ModifiedEvent(), command ); + + m_Controls->m_InputData->setTitle("Input Data"); + } +} + +void QmitkDenoisingView::UpdateOdf() +{ + + try + { + m_Controls->m_OverviewBox->setVisible(true); + if (m_ImageNode.IsNull() || !m_MultiWidget) + { + m_Controls->m_ODFRenderWidget->setVisible(false); + m_Controls->m_OdfBox->setVisible(false); + m_Controls->m_OverviewBox->setVisible(false); + return; + } + + // restore the input image label ( needed in case the last run resulted into an exception ) + m_Controls->m_InputImageLabel->setText(m_ImageNode->GetName().c_str()); + + // ODF Normalization Property + mitk::OdfNormalizationMethodProperty* nmp = dynamic_cast(m_ImageNode->GetProperty( "Normalization" )); + if(nmp) + m_OdfNormalization = nmp->GetNormalization(); + + m_TemplateOdf = itk::OrientationDistributionFunction::GetBaseMesh(); + m_OdfTransform = vtkSmartPointer::New(); + m_OdfTransform->Identity(); + m_OdfVals = vtkSmartPointer::New(); + m_OdfSource = vtkSmartPointer::New(); + itk::OrientationDistributionFunction odf; + + mitk::Point3D world = m_MultiWidget->GetCrossPosition(); + mitk::Point3D index; + mitk::Image::Pointer img = dynamic_cast(m_ImageNode->GetData()); + unsigned int *img_dimension = img->GetDimensions(); +// img->GetTimeSlicedGeometry()->WorldToIndex(world, index); + + float sum = 0; + float max = itk::NumericTraits::NonpositiveMin(); + float min = itk::NumericTraits::max(); + QString values; + QString overviewText; + + // check if dynamic_cast successfull and if the crosshair position is inside of the geometry of the ODF data + // otherwise possible crash for a scenario with multiple nodes + if (dynamic_cast(m_ImageNode->GetData()) && ( m_ImageNode->GetData()->GetGeometry()->IsInside(world) ) ) + { + m_Controls->m_ODFRenderWidget->setVisible(true); + m_Controls->m_OdfBox->setVisible(true); + + try + { + mitk::QBallImage* qball_image = dynamic_cast< mitk::QBallImage* >( m_ImageNode->GetData() ); + + // get access to the qball image data with explicitely allowing exceptions if memory locked + mitk::ImageReadAccessor readAccess( qball_image, qball_image->GetVolumeData(0), mitk::ImageAccessorBase::ExceptionIfLocked ); + const float* qball_cPtr = static_cast< const float*>(readAccess.GetData()); + + OdfVectorImgType::IndexType ind; + ind[0] = (int)(index[0]+0.5); + ind[1] = (int)(index[1]+0.5); + ind[2] = (int)(index[2]+0.5); + + // pixel size = QBALL_ODFSIZE + // position offset = standard offset + unsigned int offset_to_data = QBALL_ODFSIZE * (ind[2] * img_dimension[1] * img_dimension[0] + ind[1] * img_dimension[0] + ind[0]); + const float *pixel_data = qball_cPtr + offset_to_data; + + for (int i=0; imax) + max = val; + if (val pd = odf.GetDirection(odf.GetPrincipleDiffusionDirection()); + overviewText += "Main Diffusion:\n "+QString::number(pd[0])+"\n "+QString::number(pd[1])+"\n "+QString::number(pd[2])+"\n"; + + m_Controls->m_OdfValuesTextEdit->setText(values); + m_Controls->m_OverviewTextEdit->setVisible(true); + } + catch( mitk::Exception &e ) + { + MITK_WARN << "LOCKED : " << e.what(); + m_Controls->m_ODFRenderWidget->setVisible(false); + m_Controls->m_OdfBox->setVisible(false); + m_Controls->m_OverviewTextEdit->setVisible(false); + + // reset the selection + m_Controls->m_InputImageLabel->setText("Click image to restore rendering!"); + } + } + else if (dynamic_cast(m_ImageNode->GetData())) + { + m_Controls->m_ODFRenderWidget->setVisible(true); + m_Controls->m_OdfBox->setVisible(false); + + + mitk::TensorImage* qball_image = dynamic_cast< mitk::TensorImage*>(m_ImageNode->GetData()); + + // pixel access block + try + { + // get access to the qball image data with explicitely allowing exceptions if memory locked + mitk::ImageReadAccessor readAccess( qball_image, qball_image->GetVolumeData(0), mitk::ImageAccessorBase::ExceptionIfLocked ); + const float* qball_cPtr = static_cast< const float*>(readAccess.GetData()); + + TensorImageType::IndexType ind; + ind[0] = (int)(index[0]+0.5); + ind[1] = (int)(index[1]+0.5); + ind[2] = (int)(index[2]+0.5); + + // 6 - tensorsize + // remaining computation - standard offset + unsigned int offset_to_data = 6 * (ind[2] * img_dimension[1] * img_dimension[0] + ind[1] * img_dimension[0] + ind[0]); + const float *pixel_data = qball_cPtr + offset_to_data; + + float tensorelems[6] = { + *(pixel_data ), + *(pixel_data + 1), + *(pixel_data + 2), + *(pixel_data + 3), + *(pixel_data + 4), + *(pixel_data + 5), + }; + + itk::DiffusionTensor3D tensor(tensorelems); + odf.InitFromTensor(tensor); + + /** Array of eigen-values. */ + typedef itk::FixedArray EigenValuesArrayType; + /** Matrix of eigen-vectors. */ + typedef itk::Matrix MatrixType; + typedef itk::Matrix EigenVectorsMatrixType; + + EigenValuesArrayType eigenValues; + EigenVectorsMatrixType eigenVectors; + + QString pos = QString::number(ind[0])+", "+QString::number(ind[1])+", "+QString::number(ind[2]); + overviewText += "Coordinates: "+pos+"\n"; + overviewText += "FA: "+QString::number(tensor.GetFractionalAnisotropy())+"\n"; + overviewText += "RA: "+QString::number(tensor.GetRelativeAnisotropy())+"\n"; + overviewText += "Trace: "+QString::number(tensor.GetTrace())+"\n"; + tensor.ComputeEigenAnalysis(eigenValues,eigenVectors); + overviewText += "Eigenvalues:\n "+QString::number(eigenValues[2])+"\n "+QString::number(eigenValues[1])+"\n "+QString::number(eigenValues[0])+"\n"; + overviewText += "Main Diffusion:\n "+QString::number(eigenVectors[0][0])+"\n "+QString::number(eigenVectors[1][0])+"\n "+QString::number(eigenVectors[2][0])+"\n"; + overviewText += "Values:\n "+QString::number(tensorelems[0])+"\n "+QString::number(tensorelems[1])+"\n "+QString::number(tensorelems[2])+"\n "+QString::number(tensorelems[3])+"\n "+QString::number(tensorelems[4])+"\n "+QString::number(tensorelems[5])+"\n "+"\n"; + m_Controls->m_OverviewTextEdit->setVisible(true); + } + // end pixel access block + catch(mitk::Exception &e ) + { + MITK_WARN << "LOCKED : " << e.what(); + m_Controls->m_ODFRenderWidget->setVisible(false); + m_Controls->m_OdfBox->setVisible(false); + m_Controls->m_OverviewTextEdit->setVisible(false); + + // reset the selection + m_Controls->m_InputImageLabel->setText("Click image to restore rendering!"); + } + } + else + { + m_Controls->m_ODFRenderWidget->setVisible(false); + m_Controls->m_OdfBox->setVisible(false); + overviewText += "Please reinit image geometry.\n"; + } + + // proceed only if the render widget is visible which indicates that the + // predecessing computations were successfull + if( m_Controls->m_ODFRenderWidget->isVisible() ) + { + m_Controls->m_ODFDetailsWidget->SetParameters(odf); + + switch(m_OdfNormalization) + { + case 0: + odf = odf.MinMaxNormalize(); + break; + case 1: + odf = odf.MaxNormalize(); + break; + case 2: + odf = odf.MaxNormalize(); + break; + default: + odf = odf.MinMaxNormalize(); + } + + m_Controls->m_ODFRenderWidget->GenerateODF(odf); + m_Controls->m_OverviewTextEdit->setText(overviewText.toStdString().c_str()); + } + } + catch(...) + { + QMessageBox::critical(0, "Error", "Data could not be analyzed. The image might be corrupted."); + } +} + +void QmitkDenoisingView::OnSliceChanged(const itk::EventObject& /*e*/) +{ + UpdateOdf(); +} diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDenoisingView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDenoisingView.h new file mode 100644 index 0000000000..27e67c36c5 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDenoisingView.h @@ -0,0 +1,114 @@ +/*=================================================================== + +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 _QMITKQmitkDenoisingView_H_INCLUDED +#define _QMITKQmitkDenoisingView_H_INCLUDED + +#include + +#include + +#include "ui_QmitkDenoisingViewControls.h" + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +/*! + \brief View displaying details of the orientation distribution function in the voxel at the current crosshair position. + + \sa QmitkFunctionality + \ingroup Functionalities +*/ + +class QmitkDenoisingView : public QmitkFunctionality +{ + // 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: + + static const std::string VIEW_ID; + + QmitkDenoisingView(); + virtual ~QmitkDenoisingView(); + + typedef float TOdfPixelType; + typedef itk::Vector OdfVectorType; + typedef itk::Image OdfVectorImgType; + + typedef itk::DiffusionTensor3D< TOdfPixelType > TensorPixelType; + typedef itk::Image< TensorPixelType, 3 > TensorImageType; + + virtual void CreateQtPartControl(QWidget *parent); + + virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget); + virtual void StdMultiWidgetNotAvailable(); + + void OnSliceChanged(const itk::EventObject& e); + +protected slots: + +protected: + + /// \brief called by QmitkFunctionality when DataManager's selection has changed + virtual void OnSelectionChanged( std::vector nodes ); + + void UpdateOdf(); ///< called if slice position or datamanager selection has changed + + Ui::QmitkDenoisingViewControls* m_Controls; + QmitkStdMultiWidget* m_MultiWidget; + + /** observer flags */ + int m_SliceObserverTag1; + int m_SliceObserverTag2; + int m_SliceObserverTag3; + int m_PropertyObserverTag; + + /** ODF related variables like mesh structure, values etc. */ + vtkPolyData* m_TemplateOdf; ///< spherical base mesh + vtkSmartPointer m_OdfTransform; + vtkSmartPointer m_OdfVals; + vtkSmartPointer m_OdfSource; + + int m_OdfNormalization; ///< normalization method defined in the visualization view + + /** rendering of the ODF */ + vtkActor* m_VtkActor; + vtkPolyDataMapper* m_VtkMapper; + vtkRenderer* m_Renderer; + vtkRenderWindow* m_VtkRenderWindow; + vtkRenderWindowInteractor* m_RenderWindowInteractor; + vtkCamera* m_Camera; + + mitk::DataNode::Pointer m_ImageNode; +}; + + + +#endif // _QmitkDenoisingView_H_INCLUDED diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDenoisingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDenoisingViewControls.ui new file mode 100644 index 0000000000..7002f48242 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDenoisingViewControls.ui @@ -0,0 +1,208 @@ + + + QmitkDenoisingViewControls + + + + 0 + 0 + 351 + 734 + + + + + 0 + 0 + + + + QmitkTemplate + + + + 6 + + + 9 + + + + + Please Select Input Data + + + + + + DTI/QBI: + + + + + + + <html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html> + + + true + + + + + + + + + + Overview + + + + 0 + + + 9 + + + 0 + + + 0 + + + + + + 0 + 0 + + + + + 0 + 0 + + + + true + + + + + + + + 0 + 0 + + + + + 200 + 200 + + + + + + + + + + + + 0 + 0 + + + + + 0 + 0 + + + + QFrame::NoFrame + + + QFrame::Raised + + + + 0 + + + 0 + + + + + + + + ODF Values + + + + + + true + + + + + + + + 0 + 0 + + + + + 0 + 200 + + + + + + + + + + + Qt::Vertical + + + QSizePolicy::Expanding + + + + 20 + 220 + + + + + + + + + + QmitkODFDetailsWidget + QWidget +
QmitkODFDetailsWidget.h
+ 1 + + + QmitkODFRenderWidget + QWidget +
QmitkODFRenderWidget.h
+ 1 + + + + + diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.cpp index 9c69c931d3..c2db49d785 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.cpp @@ -1,87 +1,89 @@ /*=================================================================== 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 "mitkPluginActivator.h" #include #include "src/internal/QmitkDiffusionImagingPublicPerspective.h" #include "src/internal/QmitkQBallReconstructionView.h" #include "src/internal/QmitkPreprocessingView.h" #include "src/internal/QmitkDiffusionDicomImportView.h" #include "src/internal/QmitkDiffusionQuantificationView.h" #include "src/internal/QmitkTensorReconstructionView.h" #include "src/internal/QmitkControlVisualizationPropertiesView.h" #include "src/internal/QmitkODFDetailsView.h" #include "src/internal/QmitkGibbsTrackingView.h" #include "src/internal/QmitkStochasticFiberTrackingView.h" #include "src/internal/QmitkFiberProcessingView.h" //#include "src/internal/QmitkFiberBundleDeveloperView.h" #include "src/internal/QmitkPartialVolumeAnalysisView.h" #include "src/internal/QmitkIVIMView.h" #include "src/internal/QmitkTractbasedSpatialStatisticsView.h" #include "src/internal/QmitkTbssSkeletonizationView.h" #include "src/internal/QmitkStreamlineTrackingView.h" #include "src/internal/Connectomics/QmitkConnectomicsDataView.h" #include "src/internal/Connectomics/QmitkConnectomicsNetworkOperationsView.h" #include "src/internal/Connectomics/QmitkConnectomicsStatisticsView.h" #include "src/internal/QmitkOdfMaximaExtractionView.h" #include "src/internal/QmitkFiberfoxView.h" #include "src/internal/QmitkFiberExtractionView.h" #include "src/internal/QmitkFieldmapGeneratorView.h" #include "src/internal/QmitkDiffusionRegistrationView.h" +#include "src/internal/QmitkDenoisingView.h" namespace mitk { void PluginActivator::start(ctkPluginContext* context) { BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionImagingPublicPerspective, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkQBallReconstructionView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkPreprocessingView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionDicomImport, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionQuantificationView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkTensorReconstructionView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkControlVisualizationPropertiesView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkODFDetailsView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkGibbsTrackingView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkStochasticFiberTrackingView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberProcessingView, context) // BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberBundleDeveloperView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkPartialVolumeAnalysisView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkIVIMView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkTractbasedSpatialStatisticsView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkTbssSkeletonizationView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkConnectomicsDataView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkConnectomicsNetworkOperationsView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkConnectomicsStatisticsView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkStreamlineTrackingView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkOdfMaximaExtractionView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberfoxView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberExtractionView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkFieldmapGeneratorView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionRegistrationView, context) + BERRY_REGISTER_EXTENSION_CLASS(QmitkDenoisingView, context) } void PluginActivator::stop(ctkPluginContext* context) { Q_UNUSED(context) } } Q_EXPORT_PLUGIN2(org_mitk_gui_qt_diffusionimaging, mitk::PluginActivator)