diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberBundleOperationsView.cpp b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberBundleOperationsView.cpp index 83e24bf4e7..11d3a6d2c5 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberBundleOperationsView.cpp +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberBundleOperationsView.cpp @@ -1,1829 +1,1823 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2010-03-31 16:40:27 +0200 (Mi, 31 Mrz 2010) $ Version: $Revision: 21975 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ // Blueberry #include #include // Qmitk #include "QmitkFiberBundleOperationsView.h" #include "QmitkStdMultiWidget.h" // Qt #include //MITK #include "mitkNodePredicateProperty.h" //#include "mitkNodePredicateAND.h" #include "mitkImageCast.h" #include "mitkPointSet.h" #include "mitkPlanarCircle.h" #include "mitkPlanarPolygon.h" #include #include "mitkPlanarFigureInteractor.h" #include "mitkGlobalInteraction.h" #include #include #include #include #include #include #include #include const std::string QmitkFiberBundleOperationsView::VIEW_ID = "org.mitk.views.fiberBundleOperations"; const std::string id_DataManager = "org.mitk.views.datamanager"; using namespace berry; using namespace mitk; QmitkFiberBundleOperationsView::QmitkFiberBundleOperationsView() : QmitkFunctionality() , m_Controls( 0 ) , m_MultiWidget( NULL ) , m_EllipseCounter(0) , m_PolygonCounter(0) //, m_SelectedFBNodes( NULL ) //, m_SelectedPFNodes(0) , m_UpsamplingFactor(5) { } // Destructor QmitkFiberBundleOperationsView::~QmitkFiberBundleOperationsView() { } void QmitkFiberBundleOperationsView::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::QmitkFiberBundleOperationsViewControls; m_Controls->setupUi( parent ); m_Controls->doExtractFibersButton->setDisabled(true); m_Controls->PFCompoANDButton->setDisabled(true); m_Controls->PFCompoORButton->setDisabled(true); m_Controls->PFCompoNOTButton->setDisabled(true); m_Controls->PFCompoDELButton->setDisabled(true); connect( m_Controls->doExtractFibersButton, SIGNAL(clicked()), this, SLOT(DoFiberExtraction()) ); //connect( m_Controls->comboBox_fiberAlgo, SIGNAL(selected()), this, SLOT(handleAlgoSelection() ); connect( m_Controls->m_CircleButton, SIGNAL( clicked() ), this, SLOT( ActionDrawEllipseTriggered() ) ); connect( m_Controls->m_PolygonButton, SIGNAL( clicked() ), this, SLOT( ActionDrawPolygonTriggered() ) ); connect(m_Controls->PFCompoANDButton, SIGNAL(clicked()), this, SLOT(generatePFCompo_AND()) ); connect(m_Controls->PFCompoORButton, SIGNAL(clicked()), this, SLOT(generatePFCompo_OR()) ); connect(m_Controls->PFCompoNOTButton, SIGNAL(clicked()), this, SLOT(generatePFCompo_NOT()) ); connect(m_Controls->PFCompoDELButton, SIGNAL(clicked()), this, SLOT(deletePFCompo()) ); connect(m_Controls->m_JoinBundles, SIGNAL(clicked()), this, SLOT(JoinBundles()) ); connect(m_Controls->m_SubstractBundles, SIGNAL(clicked()), this, SLOT(SubstractBundles()) ); connect(m_Controls->m_GenerateROIImage, SIGNAL(clicked()), this, SLOT(GenerateROIImage()) ); connect( m_Controls->m_GenerationStartButton, SIGNAL(clicked()), this, SLOT(GenerationStart()) ); } } void QmitkFiberBundleOperationsView::GenerateROIImage(){ if (m_Image.IsNull() || m_SelectedPF.empty()) return; mitk::Image* image = const_cast(m_Image.GetPointer()); MaskImage3DType::Pointer temp = MaskImage3DType::New(); mitk::CastToItkImage(m_Image, temp); m_PlanarFigureImage = MaskImage3DType::New(); m_PlanarFigureImage->SetSpacing( temp->GetSpacing() ); // Set the image spacing m_PlanarFigureImage->SetOrigin( temp->GetOrigin() ); // Set the image origin m_PlanarFigureImage->SetDirection( temp->GetDirection() ); // Set the image direction m_PlanarFigureImage->SetRegions( temp->GetLargestPossibleRegion() ); m_PlanarFigureImage->Allocate(); m_PlanarFigureImage->FillBuffer( 0 ); for (int i=0; i(m_SelectedPF.at(i)->GetData()), image); DataNode::Pointer node = DataNode::New(); Image::Pointer tmpImage = Image::New(); tmpImage->InitializeByItk(m_PlanarFigureImage.GetPointer()); tmpImage->SetVolume(m_PlanarFigureImage->GetBufferPointer()); node->SetData(tmpImage); node->SetName("planarFigureImage"); this->GetDefaultDataStorage()->Add(node); } void QmitkFiberBundleOperationsView::CompositeExtraction(mitk::PlanarFigure::Pointer planarFigure, mitk::Image* image) { if (dynamic_cast(planarFigure.GetPointer())){ mitk::PlanarFigureComposite::Pointer pfcomp = dynamic_cast(planarFigure.GetPointer()); for (int i=0; igetNumberOfChildren(); ++i) { CompositeExtraction(pfcomp->getChildAt(i), image); } } else { m_PlanarFigure = planarFigure; AccessFixedDimensionByItk_3( image, InternalReorientImagePlane, 3, image->GetGeometry(), m_PlanarFigure->GetGeometry(), -1); AccessFixedDimensionByItk_1( m_InternalImage, InternalCalculateMaskFromPlanarFigure, 3, 2 ); } } template < typename TPixel, unsigned int VImageDimension > void QmitkFiberBundleOperationsView::InternalReorientImagePlane( const itk::Image< TPixel, VImageDimension > *image, mitk::Geometry3D* imggeo, mitk::Geometry3D* planegeo3D, int additionalIndex ) { MITK_INFO << "InternalReorientImagePlane() start"; typedef itk::Image< TPixel, VImageDimension > ImageType; typedef itk::Image< float, VImageDimension > FloatImageType; typedef itk::ResampleImageFilter ResamplerType; typename ResamplerType::Pointer resampler = ResamplerType::New(); mitk::PlaneGeometry* planegeo = dynamic_cast(planegeo3D); float upsamp = m_UpsamplingFactor; float gausssigma = 0.5; // Spacing typename ResamplerType::SpacingType spacing = planegeo->GetSpacing(); spacing[0] = image->GetSpacing()[0] / upsamp; spacing[1] = image->GetSpacing()[1] / upsamp; spacing[2] = image->GetSpacing()[2]; resampler->SetOutputSpacing( spacing ); // Size typename ResamplerType::SizeType size; size[0] = planegeo->GetParametricExtentInMM(0) / spacing[0]; size[1] = planegeo->GetParametricExtentInMM(1) / spacing[1]; size[2] = 1; resampler->SetSize( size ); // Origin typename mitk::Point3D orig = planegeo->GetOrigin(); typename mitk::Point3D corrorig; planegeo3D->WorldToIndex(orig,corrorig); corrorig[0] += 0.5/upsamp; corrorig[1] += 0.5/upsamp; corrorig[2] += 0; planegeo3D->IndexToWorld(corrorig,corrorig); resampler->SetOutputOrigin(corrorig ); // Direction typename ResamplerType::DirectionType direction; typename mitk::AffineTransform3D::MatrixType matrix = planegeo->GetIndexToWorldTransform()->GetMatrix(); for(int c=0; cSetOutputDirection( direction ); // Gaussian interpolation if(gausssigma != 0) { double sigma[3]; for( unsigned int d = 0; d < 3; d++ ) { sigma[d] = gausssigma * image->GetSpacing()[d]; } double alpha = 2.0; typedef itk::GaussianInterpolateImageFunction GaussianInterpolatorType; typename GaussianInterpolatorType::Pointer interpolator = GaussianInterpolatorType::New(); interpolator->SetInputImage( image ); interpolator->SetParameters( sigma, alpha ); resampler->SetInterpolator( interpolator ); } else { // typedef typename itk::BSplineInterpolateImageFunction // InterpolatorType; typedef typename itk::LinearInterpolateImageFunction InterpolatorType; typename InterpolatorType::Pointer interpolator = InterpolatorType::New(); interpolator->SetInputImage( image ); resampler->SetInterpolator( interpolator ); } // Other resampling options resampler->SetInput( image ); resampler->SetDefaultPixelValue(0); MITK_INFO << "Resampling requested image plane ... "; resampler->Update(); MITK_INFO << " ... done"; if(additionalIndex < 0) { this->m_InternalImage = mitk::Image::New(); this->m_InternalImage->InitializeByItk( resampler->GetOutput() ); this->m_InternalImage->SetVolume( resampler->GetOutput()->GetBufferPointer() ); } } template < typename TPixel, unsigned int VImageDimension > void QmitkFiberBundleOperationsView::InternalCalculateMaskFromPlanarFigure( itk::Image< TPixel, VImageDimension > *image, unsigned int axis ) { MITK_INFO << "InternalCalculateMaskFromPlanarFigure() start"; typedef itk::Image< TPixel, VImageDimension > ImageType; typedef itk::CastImageFilter< ImageType, MaskImage3DType > CastFilterType; // Generate mask image as new image with same header as input image and // initialize with "1". MaskImage3DType::Pointer newMaskImage = MaskImage3DType::New(); newMaskImage->SetSpacing( image->GetSpacing() ); // Set the image spacing newMaskImage->SetOrigin( image->GetOrigin() ); // Set the image origin newMaskImage->SetDirection( image->GetDirection() ); // Set the image direction newMaskImage->SetRegions( image->GetLargestPossibleRegion() ); newMaskImage->Allocate(); newMaskImage->FillBuffer( 1 ); // Generate VTK polygon from (closed) PlanarFigure polyline // (The polyline points are shifted by -0.5 in z-direction to make sure // that the extrusion filter, which afterwards elevates all points by +0.5 // in z-direction, creates a 3D object which is cut by the the plane z=0) const Geometry2D *planarFigureGeometry2D = m_PlanarFigure->GetGeometry2D(); const PlanarFigure::PolyLineType planarFigurePolyline = m_PlanarFigure->GetPolyLine( 0 ); const Geometry3D *imageGeometry3D = m_InternalImage->GetGeometry( 0 ); vtkPolyData *polyline = vtkPolyData::New(); polyline->Allocate( 1, 1 ); // Determine x- and y-dimensions depending on principal axis int i0, i1; switch ( axis ) { case 0: i0 = 1; i1 = 2; break; case 1: i0 = 0; i1 = 2; break; case 2: default: i0 = 0; i1 = 1; break; } // Create VTK polydata object of polyline contour vtkPoints *points = vtkPoints::New(); PlanarFigure::PolyLineType::const_iterator it; std::vector indices; unsigned int numberOfPoints = 0; for ( it = planarFigurePolyline.begin(); it != planarFigurePolyline.end(); ++it ) { Point3D point3D; // Convert 2D point back to the local index coordinates of the selected // image Point2D point2D = it->Point; planarFigureGeometry2D->WorldToIndex(point2D, point2D); point2D[0] -= 0.5/m_UpsamplingFactor; point2D[1] -= 0.5/m_UpsamplingFactor; planarFigureGeometry2D->IndexToWorld(point2D, point2D); planarFigureGeometry2D->Map( point2D, point3D ); // Polygons (partially) outside of the image bounds can not be processed // further due to a bug in vtkPolyDataToImageStencil if ( !imageGeometry3D->IsInside( point3D ) ) { float bounds[2] = {0,0}; bounds[0] = this->m_InternalImage->GetLargestPossibleRegion().GetSize().GetElement(i0); bounds[1] = this->m_InternalImage->GetLargestPossibleRegion().GetSize().GetElement(i1); imageGeometry3D->WorldToIndex( point3D, point3D ); if (point3D[i0]<0) point3D[i0] = 0.5; else if (point3D[i0]>bounds[0]) point3D[i0] = bounds[0]-0.5; if (point3D[i1]<0) point3D[i1] = 0.5; else if (point3D[i1]>bounds[1]) point3D[i1] = bounds[1]-0.5; points->InsertNextPoint( point3D[i0], point3D[i1], -0.5 ); numberOfPoints++; } else { imageGeometry3D->WorldToIndex( point3D, point3D ); point3D[i0] += 0.5; point3D[i1] += 0.5; // Add point to polyline array points->InsertNextPoint( point3D[i0], point3D[i1], -0.5 ); numberOfPoints++; } } polyline->SetPoints( points ); points->Delete(); vtkIdType *ptIds = new vtkIdType[numberOfPoints]; for ( vtkIdType i = 0; i < numberOfPoints; ++i ) { ptIds[i] = i; } polyline->InsertNextCell( VTK_POLY_LINE, numberOfPoints, ptIds ); // Extrude the generated contour polygon vtkLinearExtrusionFilter *extrudeFilter = vtkLinearExtrusionFilter::New(); extrudeFilter->SetInput( polyline ); extrudeFilter->SetScaleFactor( 1 ); extrudeFilter->SetExtrusionTypeToNormalExtrusion(); extrudeFilter->SetVector( 0.0, 0.0, 1.0 ); // Make a stencil from the extruded polygon vtkPolyDataToImageStencil *polyDataToImageStencil = vtkPolyDataToImageStencil::New(); polyDataToImageStencil->SetInput( extrudeFilter->GetOutput() ); // Export from ITK to VTK (to use a VTK filter) typedef itk::VTKImageImport< MaskImage3DType > ImageImportType; typedef itk::VTKImageExport< MaskImage3DType > ImageExportType; typename ImageExportType::Pointer itkExporter = ImageExportType::New(); itkExporter->SetInput( newMaskImage ); vtkImageImport *vtkImporter = vtkImageImport::New(); this->ConnectPipelines( itkExporter, vtkImporter ); vtkImporter->Update(); // Apply the generated image stencil to the input image vtkImageStencil *imageStencilFilter = vtkImageStencil::New(); imageStencilFilter->SetInputConnection( vtkImporter->GetOutputPort() ); imageStencilFilter->SetStencil( polyDataToImageStencil->GetOutput() ); imageStencilFilter->ReverseStencilOff(); imageStencilFilter->SetBackgroundValue( 0 ); imageStencilFilter->Update(); // Export from VTK back to ITK vtkImageExport *vtkExporter = vtkImageExport::New(); vtkExporter->SetInputConnection( imageStencilFilter->GetOutputPort() ); vtkExporter->Update(); typename ImageImportType::Pointer itkImporter = ImageImportType::New(); this->ConnectPipelines( vtkExporter, itkImporter ); itkImporter->Update(); // calculate cropping bounding box m_InternalImageMask3D = itkImporter->GetOutput(); m_InternalImageMask3D->SetDirection(image->GetDirection()); itk::ImageRegionConstIterator itmask(m_InternalImageMask3D, m_InternalImageMask3D->GetLargestPossibleRegion()); itk::ImageRegionIterator itimage(image, image->GetLargestPossibleRegion()); itmask = itmask.Begin(); itimage = itimage.Begin(); typename ImageType::SizeType lowersize = {{9999999999,9999999999,9999999999}}; typename ImageType::SizeType uppersize = {{0,0,0}}; while( !itmask.IsAtEnd() ) { if(itmask.Get() == 0) { itimage.Set(0); } else { typename ImageType::IndexType index = itimage.GetIndex(); typename ImageType::SizeType signedindex; signedindex[0] = index[0]; signedindex[1] = index[1]; signedindex[2] = index[2]; lowersize[0] = signedindex[0] < lowersize[0] ? signedindex[0] : lowersize[0]; lowersize[1] = signedindex[1] < lowersize[1] ? signedindex[1] : lowersize[1]; lowersize[2] = signedindex[2] < lowersize[2] ? signedindex[2] : lowersize[2]; uppersize[0] = signedindex[0] > uppersize[0] ? signedindex[0] : uppersize[0]; uppersize[1] = signedindex[1] > uppersize[1] ? signedindex[1] : uppersize[1]; uppersize[2] = signedindex[2] > uppersize[2] ? signedindex[2] : uppersize[2]; } ++itmask; ++itimage; } typename ImageType::IndexType index; index[0] = lowersize[0]; index[1] = lowersize[1]; index[2] = lowersize[2]; typename ImageType::SizeType size; size[0] = uppersize[0] - lowersize[0] + 1; size[1] = uppersize[1] - lowersize[1] + 1; size[2] = uppersize[2] - lowersize[2] + 1; itk::ImageRegion<3> cropRegion = itk::ImageRegion<3>(index, size); // // crop internal image // typedef itk::RegionOfInterestImageFilter< ImageType, ImageType > ROIFilterType; // typename ROIFilterType::Pointer roi = ROIFilterType::New(); // roi->SetRegionOfInterest(cropRegion); // roi->SetInput(image); // roi->Update(); // m_InternalImage = mitk::Image::New(); // m_InternalImage->InitializeByItk(roi->GetOutput()); // m_InternalImage->SetVolume(roi->GetOutput()->GetBufferPointer()); // crop internal mask typedef itk::RegionOfInterestImageFilter< MaskImage3DType, MaskImage3DType > ROIMaskFilterType; typename ROIMaskFilterType::Pointer roi2 = ROIMaskFilterType::New(); roi2->SetRegionOfInterest(cropRegion); roi2->SetInput(m_InternalImageMask3D); roi2->Update(); m_InternalImageMask3D = roi2->GetOutput(); DataNode::Pointer node = DataNode::New(); Image::Pointer tmpImage = Image::New(); tmpImage->InitializeByItk(m_InternalImageMask3D.GetPointer()); tmpImage->SetVolume(m_InternalImageMask3D->GetBufferPointer()); node->SetData(tmpImage); this->GetDefaultDataStorage()->Add(node); Image::Pointer tmpImage2 = Image::New(); tmpImage2->InitializeByItk(m_PlanarFigureImage.GetPointer()); const Geometry3D *pfImageGeometry3D = tmpImage2->GetGeometry( 0 ); const Geometry3D *intImageGeometry3D = tmpImage->GetGeometry( 0 ); typedef itk::ImageRegionIteratorWithIndex IteratorType; IteratorType imageIterator (m_InternalImageMask3D, m_InternalImageMask3D->GetRequestedRegion()); imageIterator.GoToBegin(); while ( !imageIterator.IsAtEnd() ) { unsigned char val = imageIterator.Value(); if (val>0) { itk::Index<3> index = imageIterator.GetIndex(); Point3D point; point[0] = index[0]; point[1] = index[1]; point[2] = index[2]; intImageGeometry3D->IndexToWorld(point, point); pfImageGeometry3D->WorldToIndex(point, point); index[0] = point[0]; index[1] = point[1]; index[2] = point[2]; m_PlanarFigureImage->SetPixel(index, 1); } ++imageIterator; } // Clean up VTK objects polyline->Delete(); extrudeFilter->Delete(); polyDataToImageStencil->Delete(); vtkImporter->Delete(); imageStencilFilter->Delete(); //vtkExporter->Delete(); // TODO: crashes when outcommented; memory leak?? delete[] ptIds; } void QmitkFiberBundleOperationsView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkFiberBundleOperationsView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } /* OnSelectionChanged is registered to SelectionService, therefore no need to implement SelectionService Listener explicitly */ void QmitkFiberBundleOperationsView::OnSelectionChanged( std::vector nodes ) { if ( !this->IsVisible() ) { // do nothing if nobody wants to see me :-( return; } //reset existing Vectors containing FiberBundles and PlanarFigures from a previous selection m_SelectedFB.clear(); m_SelectedPF.clear(); m_Image = NULL; //differ between 2 scenarios... // 1) add PF to an existing Spaghetti // 2) BOOLEAN OPERATORS HANDLING ... selection of multiple PF, and or multiple Spaghetti //scenario 1 for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if ( dynamic_cast(node->GetData()) ) { // MITK_INFO << "onselectionchg(): " << node->GetData()->GetNameOfClass(); m_SelectedFB.push_back(node); mitk::FiberBundle::Pointer bundle = dynamic_cast(node->GetData()); QString numFibers; this->m_Controls->m_NumFibersLabel->setText(numFibers.setNum(bundle->GetNumTracts())); } else if (dynamic_cast(node->GetData())){ // MITK_INFO << "onselectionchg(): " << node->GetData()->GetNameOfClass(); m_SelectedPF.push_back(node); } else if (dynamic_cast(node->GetData())){ m_Image = dynamic_cast(node->GetData()); } } if (m_SelectedPF.size() >= 1 && m_Image.IsNotNull()) m_Controls->m_GenerateROIImage->setEnabled(true); else m_Controls->m_GenerateROIImage->setEnabled(false); //quick and dirty control structure for extraction ATM if (m_SelectedPF.size() == 1) { //############################################# //### PLANAR FIGURE COMPOSIT SelectionLOGIC ### //############################################# m_Controls->PFCompoANDButton->setDisabled(true); m_Controls->PFCompoORButton->setDisabled(true); m_Controls->PFCompoNOTButton->setEnabled(true); m_Controls->PFCompoDELButton->setDisabled(true); //if planarFigureComposite selected, activate DEL button if ( dynamic_cast(m_SelectedPF.at(0)->GetData()) ) { m_Controls->PFCompoDELButton->setEnabled(true); } } else if (m_SelectedPF.size() > 1) { //############################################# //### PLANAR FIGURE COMPOSIT SelectionLOGIC ### //############################################# // if 2 PlanarFigure objects (PFCircle, PFPoly, ..., PFComposite) selected, //then activate AND OR NOT PF Composite Buttons m_Controls->PFCompoANDButton->setEnabled(true); m_Controls->PFCompoORButton->setEnabled(true); m_Controls->PFCompoNOTButton->setDisabled(true); m_Controls->PFCompoDELButton->setDisabled(true); } if (m_SelectedFB.size() == 1 && m_SelectedPF.size() == 1) { //############################################# //##### EXTRACT FIBERBUNDLE SelectionLOGIC #### //############################################# m_Controls->doExtractFibersButton->setEnabled(true); } else if (nodes.size() > 1 ) { //scenario 2 } else if (nodes.empty()) { //############################################# //##### EXTRACT FIBERBUNDLE SelectionLOGIC #### //############################################# m_Controls->doExtractFibersButton->setDisabled(true); //############################################# //### PLANAR FIGURE COMPOSIT SelectionLOGIC ### //############################################# m_Controls->PFCompoANDButton->setDisabled(true); m_Controls->PFCompoORButton->setDisabled(true); m_Controls->PFCompoNOTButton->setDisabled(true); } if (m_SelectedFB.size() == 2) { //############################################# //##### JOIN/SUBSTRACT FIBERBUNDLES #### //############################################# m_Controls->m_JoinBundles->setEnabled(true); m_Controls->m_SubstractBundles->setEnabled(true); } else { m_Controls->m_JoinBundles->setEnabled(false); m_Controls->m_SubstractBundles->setEnabled(false); } } void QmitkFiberBundleOperationsView::ActionDrawPolygonTriggered() { // bool checked = m_Controls->m_PolygonButton->isChecked(); // if(!this->AssertDrawingIsPossible(checked)) // return; mitk::PlanarPolygon::Pointer figure = mitk::PlanarPolygon::New(); figure->ClosedOn(); this->AddFigureToDataStorage(figure, QString("Polygon%1").arg(++m_PolygonCounter)); MITK_INFO << "PlanarPolygon created ..."; mitk::DataStorage::SetOfObjects::ConstPointer _NodeSet = this->GetDefaultDataStorage()->GetAll(); mitk::DataNode* node = 0; mitk::PlanarFigureInteractor::Pointer figureInteractor = 0; mitk::PlanarFigure* figureP = 0; for(mitk::DataStorage::SetOfObjects::ConstIterator it=_NodeSet->Begin(); it!=_NodeSet->End() ; it++) { node = const_cast(it->Value().GetPointer()); figureP = dynamic_cast(node->GetData()); if(figureP) { figureInteractor = dynamic_cast(node->GetInteractor()); if(figureInteractor.IsNull()) figureInteractor = mitk::PlanarFigureInteractor::New("PlanarFigureInteractor", node); mitk::GlobalInteraction::GetInstance()->AddInteractor(figureInteractor); } } } void QmitkFiberBundleOperationsView::ActionDrawEllipseTriggered() { //bool checked = m_Controls->m_CircleButton->isChecked(); //if(!this->AssertDrawingIsPossible(checked)) // return; mitk::PlanarCircle::Pointer figure = mitk::PlanarCircle::New(); this->AddFigureToDataStorage(figure, QString("Circle%1").arg(++m_EllipseCounter)); this->GetDataStorage()->Modified(); MITK_INFO << "PlanarCircle created ..."; //call mitk::DataStorage::SetOfObjects::ConstPointer _NodeSet = this->GetDefaultDataStorage()->GetAll(); mitk::DataNode* node = 0; mitk::PlanarFigureInteractor::Pointer figureInteractor = 0; mitk::PlanarFigure* figureP = 0; for(mitk::DataStorage::SetOfObjects::ConstIterator it=_NodeSet->Begin(); it!=_NodeSet->End() ; it++) { node = const_cast(it->Value().GetPointer()); figureP = dynamic_cast(node->GetData()); if(figureP) { figureInteractor = dynamic_cast(node->GetInteractor()); if(figureInteractor.IsNull()) figureInteractor = mitk::PlanarFigureInteractor::New("PlanarFigureInteractor", node); mitk::GlobalInteraction::GetInstance()->AddInteractor(figureInteractor); } } } void QmitkFiberBundleOperationsView::Activated() { MITK_INFO << "FB OPerations ACTIVATED()"; /* mitk::DataStorage::SetOfObjects::ConstPointer _NodeSet = this->GetDefaultDataStorage()->GetAll(); mitk::DataNode* node = 0; mitk::PlanarFigureInteractor::Pointer figureInteractor = 0; mitk::PlanarFigure* figure = 0; for(mitk::DataStorage::SetOfObjects::ConstIterator it=_NodeSet->Begin(); it!=_NodeSet->End() ; it++) { node = const_cast(it->Value().GetPointer()); figure = dynamic_cast(node->GetData()); if(figure) { figureInteractor = dynamic_cast(node->GetInteractor()); if(figureInteractor.IsNull()) figureInteractor = mitk::PlanarFigureInteractor::New("PlanarFigureInteractor", node); mitk::GlobalInteraction::GetInstance()->AddInteractor(figureInteractor); } } */ } void QmitkFiberBundleOperationsView::AddFigureToDataStorage(mitk::PlanarFigure* figure, const QString& name, const char *propertyKey, mitk::BaseProperty *property ) { //set desired data to DataNode where Planarfigure is stored mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetName(name.toStdString()); newNode->SetData(figure); newNode->AddProperty( "planarfigure.default.line.color", mitk::ColorProperty::New(1.0,0.0,0.0)); newNode->AddProperty( "planarfigure.line.width", mitk::FloatProperty::New(2.0)); newNode->AddProperty( "planarfigure.drawshadow", mitk::BoolProperty::New(true)); newNode->AddProperty( "selected", mitk::BoolProperty::New(true) ); newNode->AddProperty( "planarfigure.ishovering", mitk::BoolProperty::New(true) ); newNode->AddProperty( "planarfigure.drawoutline", mitk::BoolProperty::New(true) ); newNode->AddProperty( "planarfigure.drawquantities", mitk::BoolProperty::New(false) ); newNode->AddProperty( "planarfigure.drawshadow", mitk::BoolProperty::New(true) ); newNode->AddProperty( "planarfigure.line.width", mitk::FloatProperty::New(3.0) ); newNode->AddProperty( "planarfigure.shadow.widthmodifier", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.outline.width", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.helperline.width", mitk::FloatProperty::New(2.0) ); // PlanarFigureControlPointStyleProperty::Pointer styleProperty = // dynamic_cast< PlanarFigureControlPointStyleProperty* >( node->GetProperty( "planarfigure.controlpointshape" ) ); // if ( styleProperty.IsNotNull() ) // { // m_ControlPointShape = styleProperty->GetShape(); // } newNode->AddProperty( "planarfigure.default.line.color", mitk::ColorProperty::New(1.0,1.0,1.0) ); newNode->AddProperty( "planarfigure.default.line.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.default.outline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.default.outline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.default.helperline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.default.helperline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.default.markerline.color", mitk::ColorProperty::New(0.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.default.markerline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.default.marker.color", mitk::ColorProperty::New(1.0,1.0,1.0) ); newNode->AddProperty( "planarfigure.default.marker.opacity",mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.hover.line.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.hover.line.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.hover.outline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.hover.outline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.hover.helperline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.hover.helperline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.hover.markerline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.hover.markerline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.hover.marker.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.hover.marker.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.selected.line.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.selected.line.opacity",mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.selected.outline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.selected.outline.opacity", mitk::FloatProperty::New(2.0)); newNode->AddProperty( "planarfigure.selected.helperline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.selected.helperline.opacity",mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.selected.markerline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.selected.markerline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.selected.marker.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.selected.marker.opacity",mitk::FloatProperty::New(2.0)); // Add custom property, if available //if ( (propertyKey != NULL) && (property != NULL) ) //{ // newNode->AddProperty( propertyKey, property ); //} //get current selected DataNode -which should be a FiberBundle- and set PlanarFigure as child //this->GetDataStorage()->GetNodes() // mitk::FiberBundle::Pointer selectedFBNode = m_SelectedFBNodes.at(0); // figure drawn on the topmost layer / image this->GetDataStorage()->Add(newNode ); std::vector selectedNodes = GetDataManagerSelection(); for(unsigned int i = 0; i < selectedNodes.size(); i++) { selectedNodes[i]->SetSelected(false); } //selectedNodes = m_SelectedPlanarFigureNodes->GetNodes(); /*for(unsigned int i = 0; i < selectedNodes.size(); i++) { selectedNodes[i]->SetSelected(false); } */ newNode->SetSelected(true); //Select(newNode); } void QmitkFiberBundleOperationsView::DoFiberExtraction() { mitk::FiberBundle::Pointer selFB = dynamic_cast(m_SelectedFB.at(0)->GetData()); mitk::PlanarFigure::Pointer selPF = dynamic_cast (m_SelectedPF.at(0)->GetData()); std::vector extFBset = selFB->extractFibersByPF(selPF); //MITK_INFO << "returned vector in FBOperationsView: " << extFBset.size(); // for(std::vector::iterator dispIt = extFBset.begin(); dispIt != extFBset.end(); dispIt++) // { // MITK_INFO << "vector DTI ID: " << *dispIt; // // } mitk::FiberBundle::Pointer extFB = selFB->extractFibersById(extFBset); MITK_INFO << " Number Of Tracts in sourceFiberBundle: " << selFB->GetNumTracts(); MITK_INFO << " Number Of Tracts in extractedFiberBundle: " << extFB->GetNumTracts(); mitk::DataNode::Pointer fbNode; fbNode = mitk::DataNode::New(); fbNode->SetData(extFB); fbNode->SetName("extGroupFinberBundle"); fbNode->SetVisibility(true); GetDataStorage()->Add(fbNode); } void QmitkFiberBundleOperationsView::generatePFCompo_AND() { mitk::PlanarFigureComposite::Pointer PFCAnd = mitk::PlanarFigureComposite::New(); PFCAnd->setOperationType(mitk::PFCOMPOSITION_AND_OPERATION); for( std::vector::iterator it = m_SelectedPF.begin(); it != m_SelectedPF.end(); ++it ) { mitk::DataNode::Pointer nodePF = *it; mitk::PlanarFigure::Pointer tmpPF = dynamic_cast( nodePF->GetData() ); PFCAnd->addPlanarFigure( tmpPF ); PFCAnd->addDataNode( nodePF ); PFCAnd->setDisplayName("AND_COMPO"); // MITK_INFO << "PFCAND(): added to AND PF" << nodePF->GetName(); } debugPFComposition(PFCAnd, 0); this->addPFCompositionToDataStorage(PFCAnd, NULL /*parent*/); } void QmitkFiberBundleOperationsView::debugPFComposition(mitk::PlanarFigureComposite::Pointer pfc, int itLevelStatus) { int myLevel = itLevelStatus; if (myLevel == 0) { MITK_INFO << "############################################## " ; MITK_INFO << "######### DEBUG START ############## " ; MITK_INFO << "############################################## " ; } MITK_INFO << "############################################## " ; MITK_INFO << "Name: " << pfc->getDisplayName(); MITK_INFO << "iterationLevel: " << myLevel; MITK_INFO << "CompositionType: " << pfc->getOperationType(); MITK_INFO << "Number of children: " << pfc->getNumberOfChildren(); //iterate through pfcs children for(int i=0; igetNumberOfChildren(); ++i) { mitk::PlanarFigure::Pointer tmpPFchild = pfc->getChildAt(i); mitk::DataNode::Pointer savedPFchildNode = pfc->getDataNodeAt(i); if (tmpPFchild == savedPFchildNode->GetData()) { MITK_INFO << "[OK] Pointers point to same Data..."; }else{ MITK_INFO << "Pointers differ in equation"; } MITK_INFO << "Level: " << myLevel << " ChildNr.: " << i ; mitk::PlanarFigureComposite::Pointer pfcompcastNode= dynamic_cast(savedPFchildNode->GetData()); mitk::PlanarFigureComposite::Pointer pfcompcast= dynamic_cast(tmpPFchild.GetPointer()); if( !pfcompcast.IsNull() ) { // we have a composite as child if ( pfcompcastNode.IsNull() ) { MITK_INFO << "************** NODE DIFFER FROM PFC...ERROR! ***************"; } else { MITK_INFO << "[OK]...node contains right type "; } itLevelStatus++; MITK_INFO << "child is PFC...debug this PFC"; debugPFComposition(pfcompcast, itLevelStatus); } else { // we have a planarFigure as child // figure out which type mitk::PlanarCircle::Pointer circleName = mitk::PlanarCircle::New(); mitk::PlanarRectangle::Pointer rectName = mitk::PlanarRectangle::New(); mitk::PlanarPolygon::Pointer polyName = mitk::PlanarPolygon::New(); if (tmpPFchild->GetNameOfClass() == circleName->GetNameOfClass() ) { MITK_INFO << "a circle child of " << pfc->getDisplayName() ; } else if (tmpPFchild->GetNameOfClass() == rectName->GetNameOfClass() ){ MITK_INFO << "a rectangle child of " << pfc->getDisplayName() ; } else if (tmpPFchild->GetNameOfClass() == polyName->GetNameOfClass() ) { MITK_INFO << "a polygon child of " << pfc->getDisplayName() ; } MITK_INFO << "....................................................... " ; } } //end for if (myLevel == 0) { MITK_INFO << "############################################## " ; MITK_INFO << "######### DEBUG END ############## " ; MITK_INFO << "############################################## " ; } } void QmitkFiberBundleOperationsView::generatePFCompo_OR() { mitk::PlanarFigureComposite::Pointer PFCOr = mitk::PlanarFigureComposite::New(); PFCOr->setOperationType(mitk::PFCOMPOSITION_OR_OPERATION); for( std::vector::iterator it = m_SelectedPF.begin(); it != m_SelectedPF.end(); ++it ) { mitk::DataNode::Pointer nodePF = *it; mitk::PlanarFigure::Pointer tmpPF = dynamic_cast( nodePF->GetData() ); PFCOr->addPlanarFigure( tmpPF ); PFCOr->addDataNode( nodePF ); PFCOr->setDisplayName("OR_COMPO"); // MITK_INFO << "PFCAND(): added to AND PF" << nodePF->GetName(); } debugPFComposition(PFCOr, 0); this->addPFCompositionToDataStorage(PFCOr, NULL /*parent*/); } void QmitkFiberBundleOperationsView::generatePFCompo_NOT() { mitk::PlanarFigureComposite::Pointer PFCNot = mitk::PlanarFigureComposite::New(); PFCNot->setOperationType(mitk::PFCOMPOSITION_NOT_OPERATION); for( std::vector::iterator it = m_SelectedPF.begin(); it != m_SelectedPF.end(); ++it ) { mitk::DataNode::Pointer nodePF = *it; mitk::PlanarFigure::Pointer tmpPF = dynamic_cast( nodePF->GetData() ); PFCNot->addPlanarFigure( tmpPF ); PFCNot->addDataNode( nodePF ); PFCNot->setDisplayName("NOT_COMPO"); // MITK_INFO << "PFCAND(): added to AND PF" << nodePF->GetName(); } debugPFComposition(PFCNot, 0); this->addPFCompositionToDataStorage(PFCNot, NULL /*parent*/); } void QmitkFiberBundleOperationsView::deletePFCompo() { } void QmitkFiberBundleOperationsView::addPFCompositionToDataStorage(mitk::PlanarFigureComposite::Pointer pfcomp, mitk::DataNode::Pointer parentDataNode ) { //a new planarFigureComposition arrived //convert it into a dataNode mitk::DataNode::Pointer newPFCNode; newPFCNode = mitk::DataNode::New(); newPFCNode->SetName( pfcomp->getDisplayName() ); //MITK_INFO << "PFComp Name: " << pfcomp->getDisplayName() << " newPFCNodeName: " << newPFCNode->GetName(); newPFCNode->SetData(pfcomp); newPFCNode->SetVisibility(true); switch (pfcomp->getOperationType()) { case 0: { // AND PLANARFIGURECOMPOSITE // newPFCNode->SetName("AND_PFCombo"); if (!parentDataNode.IsNull()) { MITK_INFO << "adding " << newPFCNode->GetName() << " to " << parentDataNode->GetName() ; GetDataStorage()->Add(newPFCNode, parentDataNode); } else { MITK_INFO << "adding " << newPFCNode->GetName(); GetDataStorage()->Add(newPFCNode); } //iterate through its childs for(int i=0; igetNumberOfChildren(); ++i) { mitk::PlanarFigure::Pointer tmpPFchild = pfcomp->getChildAt(i); mitk::DataNode::Pointer savedPFchildNode = pfcomp->getDataNodeAt(i); mitk::PlanarFigureComposite::Pointer pfcompcast= dynamic_cast(tmpPFchild.GetPointer()); if ( !pfcompcast.IsNull() ) { // child is of type planar Figure composite // make new node of the child, cuz later the child has to be removed of its old position in datamanager // feed new dataNode with information of the savedDataNode, which is gonna be removed soon mitk::DataNode::Pointer newChildPFCNode; newChildPFCNode = mitk::DataNode::New(); newChildPFCNode->SetData(tmpPFchild); newChildPFCNode->SetName( savedPFchildNode->GetName() ); pfcompcast->setDisplayName( savedPFchildNode->GetName() ); //name might be changed in DataManager by user //update inside vector the dataNodePointer pfcomp->replaceDataNodeAt(i, newChildPFCNode); addPFCompositionToDataStorage(pfcompcast, newPFCNode); //the current PFCNode becomes the childs parent // remove savedNode here, cuz otherwise its children will change their position in the dataNodeManager // without having its parent anymore //GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_INFO << savedPFchildNode->GetName() << " exists in DS...trying to remove it"; }else{ MITK_INFO << "[ERROR] does NOT exist, but can I read its Name? " << savedPFchildNode->GetName(); } // remove old child position in dataStorage GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_INFO << savedPFchildNode->GetName() << " still exists"; } } else { // child is not of type PlanarFigureComposite, so its one of the planarFigures // create new dataNode containing the data of the old dataNode, but position in dataManager will be // modified cuz we re setting a (new) parent. mitk::DataNode::Pointer newPFchildNode = mitk::DataNode::New(); newPFchildNode->SetName(savedPFchildNode->GetName() ); newPFchildNode->SetData(tmpPFchild); newPFchildNode->SetVisibility(true); // replace the dataNode in PFComp DataNodeVector pfcomp->replaceDataNodeAt(i, newPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_INFO << savedPFchildNode->GetName() << " exists in DS...trying to remove it"; }else{ MITK_INFO << "[ERROR] does NOT exist, but can I read its Name? " << savedPFchildNode->GetName(); } // remove old child position in dataStorage GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_INFO << savedPFchildNode->GetName() << " still exists"; } MITK_INFO << "adding " << newPFchildNode->GetName() << " to " << newPFCNode->GetName(); //add new child to datamanager with its new position as child of newPFCNode parent GetDataStorage()->Add(newPFchildNode, newPFCNode); } } GetDataStorage()->Modified(); break; } case 1: { // AND PLANARFIGURECOMPOSITE // newPFCNode->SetName("AND_PFCombo"); if (!parentDataNode.IsNull()) { MITK_INFO << "adding " << newPFCNode->GetName() << " to " << parentDataNode->GetName() ; GetDataStorage()->Add(newPFCNode, parentDataNode); } else { MITK_INFO << "adding " << newPFCNode->GetName(); GetDataStorage()->Add(newPFCNode); } //iterate through its childs for(int i=0; igetNumberOfChildren(); ++i) { mitk::PlanarFigure::Pointer tmpPFchild = pfcomp->getChildAt(i); mitk::DataNode::Pointer savedPFchildNode = pfcomp->getDataNodeAt(i); mitk::PlanarFigureComposite::Pointer pfcompcast= dynamic_cast(tmpPFchild.GetPointer()); if ( !pfcompcast.IsNull() ) { // child is of type planar Figure composite // make new node of the child, cuz later the child has to be removed of its old position in datamanager // feed new dataNode with information of the savedDataNode, which is gonna be removed soon mitk::DataNode::Pointer newChildPFCNode; newChildPFCNode = mitk::DataNode::New(); newChildPFCNode->SetData(tmpPFchild); newChildPFCNode->SetName( savedPFchildNode->GetName() ); pfcompcast->setDisplayName( savedPFchildNode->GetName() ); //name might be changed in DataManager by user //update inside vector the dataNodePointer pfcomp->replaceDataNodeAt(i, newChildPFCNode); addPFCompositionToDataStorage(pfcompcast, newPFCNode); //the current PFCNode becomes the childs parent // remove savedNode here, cuz otherwise its children will change their position in the dataNodeManager // without having its parent anymore //GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_INFO << savedPFchildNode->GetName() << " exists in DS...trying to remove it"; }else{ MITK_INFO << "[ERROR] does NOT exist, but can I read its Name? " << savedPFchildNode->GetName(); } // remove old child position in dataStorage GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_INFO << savedPFchildNode->GetName() << " still exists"; } } else { // child is not of type PlanarFigureComposite, so its one of the planarFigures // create new dataNode containing the data of the old dataNode, but position in dataManager will be // modified cuz we re setting a (new) parent. mitk::DataNode::Pointer newPFchildNode = mitk::DataNode::New(); newPFchildNode->SetName(savedPFchildNode->GetName() ); newPFchildNode->SetData(tmpPFchild); newPFchildNode->SetVisibility(true); // replace the dataNode in PFComp DataNodeVector pfcomp->replaceDataNodeAt(i, newPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_INFO << savedPFchildNode->GetName() << " exists in DS...trying to remove it"; }else{ MITK_INFO << "[ERROR] does NOT exist, but can I read its Name? " << savedPFchildNode->GetName(); } // remove old child position in dataStorage GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_INFO << savedPFchildNode->GetName() << " still exists"; } MITK_INFO << "adding " << newPFchildNode->GetName() << " to " << newPFCNode->GetName(); //add new child to datamanager with its new position as child of newPFCNode parent GetDataStorage()->Add(newPFchildNode, newPFCNode); } } GetDataStorage()->Modified(); break; } case 2: { // AND PLANARFIGURECOMPOSITE // newPFCNode->SetName("AND_PFCombo"); if (!parentDataNode.IsNull()) { MITK_INFO << "adding " << newPFCNode->GetName() << " to " << parentDataNode->GetName() ; GetDataStorage()->Add(newPFCNode, parentDataNode); } else { MITK_INFO << "adding " << newPFCNode->GetName(); GetDataStorage()->Add(newPFCNode); } //iterate through its childs for(int i=0; igetNumberOfChildren(); ++i) { mitk::PlanarFigure::Pointer tmpPFchild = pfcomp->getChildAt(i); mitk::DataNode::Pointer savedPFchildNode = pfcomp->getDataNodeAt(i); mitk::PlanarFigureComposite::Pointer pfcompcast= dynamic_cast(tmpPFchild.GetPointer()); if ( !pfcompcast.IsNull() ) { // child is of type planar Figure composite // makeRemoveBundle new node of the child, cuz later the child has to be removed of its old position in datamanager // feed new dataNode with information of the savedDataNode, which is gonna be removed soon mitk::DataNode::Pointer newChildPFCNode; newChildPFCNode = mitk::DataNode::New(); newChildPFCNode->SetData(tmpPFchild); newChildPFCNode->SetName( savedPFchildNode->GetName() ); pfcompcast->setDisplayName( savedPFchildNode->GetName() ); //name might be changed in DataManager by user //update inside vector the dataNodePointer pfcomp->replaceDataNodeAt(i, newChildPFCNode); addPFCompositionToDataStorage(pfcompcast, newPFCNode); //the current PFCNode becomes the childs parent // remove savedNode here, cuz otherwise its children will change their position in the dataNodeManager // without having its parent anymore //GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_INFO << savedPFchildNode->GetName() << " exists in DS...trying to remove it"; }else{ MITK_INFO << "[ERROR] does NOT exist, but can I read its Name? " << savedPFchildNode->GetName(); } // remove old child position in dataStorage GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_INFO << savedPFchildNode->GetName() << " still exists"; } } else { // child is not of type PlanarFigureComposite, so its one of the planarFigures // create new dataNode containing the data of the old dataNode, but position in dataManager will be // modified cuz we re setting a (new) parent. mitk::DataNode::Pointer newPFchildNode = mitk::DataNode::New(); newPFchildNode->SetName(savedPFchildNode->GetName() ); newPFchildNode->SetData(tmpPFchild); newPFchildNode->SetVisibility(true); // replace the dataNode in PFComp DataNodeVector pfcomp->replaceDataNodeAt(i, newPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_INFO << savedPFchildNode->GetName() << " exists in DS...trying to remove it"; }else{ MITK_INFO << "[ERROR] does NOT exist, but can I read its Name? " << savedPFchildNode->GetName(); } // remove old child position in dataStorage GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_INFO << savedPFchildNode->GetName() << " still exists"; } MITK_INFO << "adding " << newPFchildNode->GetName() << " to " << newPFCNode->GetName(); //add new child to datamanager with its new position as child of newPFCNode parent GetDataStorage()->Add(newPFchildNode, newPFCNode); } } GetDataStorage()->Modified(); break; } default: MITK_INFO << "we have an UNDEFINED composition... ERROR" ; break; } } void QmitkFiberBundleOperationsView::JoinBundles() { mitk::FiberBundle::Pointer bundle1 = dynamic_cast(m_SelectedFB.at(0)->GetData()); mitk::FiberBundle::Pointer bundle2 = dynamic_cast(m_SelectedFB.at(1)->GetData()); mitk::FiberBundle::Pointer newBundle = bundle1->JoinBundle(bundle2); mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(m_SelectedFB.at(0)->GetName()+"+"+m_SelectedFB.at(1)->GetName()); fbNode->SetVisibility(true); GetDataStorage()->Add(fbNode); } void QmitkFiberBundleOperationsView::SubstractBundles() { mitk::FiberBundle::Pointer bundle1 = dynamic_cast(m_SelectedFB.at(0)->GetData()); mitk::FiberBundle::Pointer bundle2 = dynamic_cast(m_SelectedFB.at(1)->GetData()); mitk::FiberBundle::Pointer newBundle = bundle1->SubstractBundle(bundle2); mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(m_SelectedFB.at(0)->GetName()+"-"+m_SelectedFB.at(1)->GetName()); fbNode->SetVisibility(true); GetDataStorage()->Add(fbNode); } void QmitkFiberBundleOperationsView::GenerationStart() { int generationMethod = m_Controls->m_GenerationBox->currentIndex(); std::vector nodes = GetDataManagerSelection(); if (nodes.empty()){ QMessageBox::information( NULL, "Warning", "No data object selected!"); MITK_WARN("QmitkFiberBundleOperationsView") << "no data object selected"; return; } for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if (node.IsNotNull() && dynamic_cast(node->GetData())) { m_FiberBundle = dynamic_cast(node->GetData()); m_FiberBundleNode = node; switch(generationMethod){ case 0: GenerateGreyscaleHeatmap(true); break; case 1: GenerateGreyscaleHeatmap(false); break; case 2: GenerateColorHeatmap(); break; case 3: GenerateFiberEndingsImage(); break; case 4: GenerateFiberEndingsPointSet(); break; case 5: DWIGenerationStart(); break; } } } } // generate pointset displaying the fiber endings void QmitkFiberBundleOperationsView::GenerateFiberEndingsPointSet() { if(m_FiberBundle.IsNull()){ QMessageBox::information( NULL, "Warning", "No fiber bundle selected!"); MITK_WARN("QmitkGlobalFiberTrackingView") << "no fiber bundle selected"; return; } mitk::Geometry3D::Pointer geometry = m_FiberBundle->GetGeometry(); mitk::PointSet::Pointer pointSet = mitk::PointSet::New(); int numTracts = m_FiberBundle->GetNumTracts(); int count = 0; for( int i=0; iGetNumPoints(i); itk::Point start = m_FiberBundle->GetPoint(i,0); itk::Point world1; geometry->IndexToWorld(start, world1); pointSet->InsertPoint(count, world1); count++; // get fiber end point if(numVertices>1) { itk::Point end = m_FiberBundle->GetPoint(i,numVertices-1); itk::Point world; geometry->IndexToWorld(end, world); pointSet->InsertPoint(count, world); count++; } } mitk::DataNode::Pointer pointSetNode = mitk::DataNode::New(); pointSetNode->SetData( pointSet ); QString name(m_FiberBundleNode->GetName().c_str()); name += "_fiber_endings"; pointSetNode->SetName(name.toStdString()); pointSetNode->SetProperty( "opacity", mitk::FloatProperty::New( 1 ) ); pointSetNode->SetProperty( "pointsize", mitk::FloatProperty::New( 0.3) ); pointSetNode->SetColor( 1.0, 1.0, 1.0 ); GetDefaultDataStorage()->Add(pointSetNode); } // generate image displaying the fiber endings void QmitkFiberBundleOperationsView::GenerateFiberEndingsImage() { if(m_FiberBundle.IsNull()){ QMessageBox::information( NULL, "Warning", "No fiber bundle selected!"); MITK_WARN("QmitkGlobalFiberTrackingView") << "no fiber bundle selected"; return; } - typedef itk::RGBAPixel OutPixType; + typedef unsigned char OutPixType; // run generator typedef itk::TractsToFiberEndingsImageFilter ImageGeneratorType; ImageGeneratorType::Pointer generator = ImageGeneratorType::New(); generator->SetFiberBundle(m_FiberBundle); generator->SetUpsamplingFactor(m_Controls->m_UpsamplingSpinBox->value()); generator->Update(); // get result typedef itk::Image OutType; OutType::Pointer outImg = generator->GetOutput(); mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); // to datastorage mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(img); QString name(m_FiberBundleNode->GetName().c_str()); name += "_fiber_endings"; node->SetName(name.toStdString()); node->SetVisibility(true); - mitk::LevelWindow opaclevwin; - opaclevwin.SetRangeMinMax(0,255); - opaclevwin.SetWindowBounds(0,0); - mitk::LevelWindowProperty::Pointer prop = mitk::LevelWindowProperty::New(opaclevwin); - node->AddProperty( "opaclevelwindow", prop ); - GetDataStorage()->Add(node); } // generate rgba heatmap from fiber bundle void QmitkFiberBundleOperationsView::GenerateColorHeatmap() { if(m_FiberBundle.IsNull() || m_FiberBundleNode.IsNull()) { QMessageBox::information( NULL, "Warning", "No fiber bundle selected!"); MITK_WARN("QmitkGlobalFiberTrackingView") << "no fiber bundle selected"; return; } typedef itk::RGBAPixel OutPixType; // run generator typedef itk::TractsToProbabilityImageFilter ImageGeneratorType; ImageGeneratorType::Pointer generator = ImageGeneratorType::New(); //generator->SetInput(NULL); generator->SetFiberBundle(m_FiberBundle); generator->SetUpsamplingFactor(m_Controls->m_UpsamplingSpinBox->value()); generator->Update(); // get result typedef itk::Image OutType; OutType::Pointer outImg = generator->GetOutput(); mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); // to datastorage mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(img); QString name(m_FiberBundleNode->GetName().c_str()); name += "_rgba_heatmap"; node->SetName(name.toStdString()); node->SetVisibility(true); mitk::LevelWindow opaclevwin; opaclevwin.SetRangeMinMax(0,255); opaclevwin.SetWindowBounds(0,0); mitk::LevelWindowProperty::Pointer prop = mitk::LevelWindowProperty::New(opaclevwin); node->AddProperty( "opaclevelwindow", prop ); GetDataStorage()->Add(node); } // generate greyscale heatmap from fiber bundle void QmitkFiberBundleOperationsView::GenerateGreyscaleHeatmap(bool binary) { if(m_FiberBundle.IsNull() || m_FiberBundleNode.IsNull()) { QMessageBox::information( NULL, "Warning", "No fiber bundle selected!"); MITK_WARN("QmitkGlobalFiberTrackingView") << "no fiber bundle selected"; return; } typedef unsigned char OutPixType; // run generator typedef itk::TractsToProbabilityImageFilter ImageGeneratorType; ImageGeneratorType::Pointer generator = ImageGeneratorType::New(); generator->SetFiberBundle(m_FiberBundle); generator->SetInvertImage(m_Controls->m_InvertCheckbox->isChecked()); generator->SetUpsamplingFactor(m_Controls->m_UpsamplingSpinBox->value()); if (binary) generator->SetBinaryEnvelope(true); else generator->SetBinaryEnvelope(false); generator->Update(); // get result typedef itk::Image OutType; OutType::Pointer outImg = generator->GetOutput(); mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); // to datastorage mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(img); QString name(m_FiberBundleNode->GetName().c_str()); if(binary) name += "_enveloppe"; else name += "_heatmap"; node->SetName(name.toStdString()); node->SetVisibility(true); mitk::LevelWindow opaclevwin2; opaclevwin2.SetRangeMinMax(0,255); opaclevwin2.SetWindowBounds(0,0); mitk::LevelWindowProperty::Pointer prop2 = mitk::LevelWindowProperty::New(opaclevwin2); node->AddProperty( "opaclevelwindow", prop2 ); GetDataStorage()->Add(node); } // generate dwi from fiber bundle (experimental) void QmitkFiberBundleOperationsView::DWIGenerationStart() { // get fiber bundle and dwi image from data manager typedef mitk::DiffusionImage DiffVolumesType; std::vector nodes = GetDataManagerSelection(); DiffVolumesType::Pointer originalDWI = NULL; mitk::FiberBundle::Pointer fiberBundle = NULL; for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if (node.IsNotNull() && dynamic_cast(node->GetData())) { originalDWI = dynamic_cast(node->GetData()); continue; } if (node.IsNotNull() && dynamic_cast(node->GetData())) { fiberBundle = dynamic_cast(node->GetData()); } } if(fiberBundle.IsNull() || originalDWI.IsNull()){ QMessageBox::information( NULL, "Warning", "Please load and select a dwi image and a fiber bundle."); MITK_WARN("QmitkGlobalFiberTrackingView") << "please select a fiber bundle and a diffusion image"; return; } // CONSTRUCT CONTAINER WITH DIRECTIONS typedef vnl_vector_fixed< double, 3 > GradientDirectionType; typedef itk::VectorContainer< unsigned int, GradientDirectionType > GradientDirectionContainerType; GradientDirectionContainerType::Pointer directions = originalDWI->GetDirections(); float bVal = originalDWI->GetB_Value(); typedef itk::VectorImage< short, 3 > DWIImageType; DWIImageType::Pointer vectorImage = DWIImageType::New(); itk::TractsToDWIImageFilter::Pointer filter = itk::TractsToDWIImageFilter::New(); filter->SetInput(originalDWI->GetVectorImage()); filter->SetFiberBundle(fiberBundle); filter->SetbD(m_Controls->m_UpsamplingSpinBox->value()); filter->SetGradientDirections(directions); filter->SetParticleWidth(0.2); filter->GenerateData(); vectorImage = filter->GetOutput(); DiffVolumesType::Pointer diffImage = DiffVolumesType::New(); diffImage->SetDirections(directions); diffImage->SetOriginalDirections(directions); diffImage->SetVectorImage(vectorImage); diffImage->SetB_Value(bVal); diffImage->InitializeFromVectorImage(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( diffImage ); QString name(m_FiberBundleNode->GetName().c_str()); name += "_dwi"; GetDefaultDataStorage()->Add(node); } diff --git a/Modules/DiffusionImaging/Algorithms/itkTractsToFiberEndingsImageFilter.cpp b/Modules/DiffusionImaging/Algorithms/itkTractsToFiberEndingsImageFilter.cpp index a7148a7ef7..ef2a544a25 100644 --- a/Modules/DiffusionImaging/Algorithms/itkTractsToFiberEndingsImageFilter.cpp +++ b/Modules/DiffusionImaging/Algorithms/itkTractsToFiberEndingsImageFilter.cpp @@ -1,253 +1,136 @@ #include "itkTractsToFiberEndingsImageFilter.h" #include "itkBSplineUpsampleImageFilter.h" #define __CEIL_UCHAR__(val) (val) = \ ( (val) < 0 ) ? ( 0 ) : ( ( (val)>255 ) ? ( 255 ) : ( (val) ) ); namespace itk{ template< class TInputImage, class TOutputPixelType > TractsToFiberEndingsImageFilter< TInputImage, TOutputPixelType > ::TractsToFiberEndingsImageFilter() { this->SetNumberOfRequiredInputs(0); } template< class TInputImage, class TOutputPixelType > TractsToFiberEndingsImageFilter< TInputImage, TOutputPixelType > ::~TractsToFiberEndingsImageFilter() { } template< class TInputImage, class TOutputPixelType > void TractsToFiberEndingsImageFilter< TInputImage, TOutputPixelType > ::GenerateData() { MITK_INFO << "Generating 2D fiber endings image"; - bool isRgba = false; - if(&typeid(TOutputPixelType) == &typeid(itk::RGBAPixel)) - { - isRgba = true; - } - else if(&typeid(TOutputPixelType) != &typeid(unsigned char)) + if(&typeid(TOutputPixelType) != &typeid(unsigned char)) { MITK_INFO << "Only 'unsigned char' and 'itk::RGBAPixel supported as OutputPixelType"; return; } - mitk::Geometry3D::Pointer geometry = m_FiberBundle->GetGeometry(); typename OutputImageType::Pointer outImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0)); outImage->SetSpacing( geometry->GetSpacing()/m_UpsamplingFactor ); // Set the image spacing mitk::Point3D origin = geometry->GetOrigin(); mitk::Point3D indexOrigin; geometry->WorldToIndex(origin, indexOrigin); indexOrigin[0] = indexOrigin[0] - .5 * (1.0-1.0/m_UpsamplingFactor); indexOrigin[1] = indexOrigin[1] - .5 * (1.0-1.0/m_UpsamplingFactor); indexOrigin[2] = indexOrigin[2] - .5 * (1.0-1.0/m_UpsamplingFactor); mitk::Point3D newOrigin; geometry->IndexToWorld(indexOrigin, newOrigin); outImage->SetOrigin( newOrigin ); // Set the image origin itk::Matrix matrix; for (int i=0; i<3; i++) for (int j=0; j<3; j++) matrix[j][i] = geometry->GetMatrixColumn(i)[j]; outImage->SetDirection( matrix ); // Set the image direction float* bounds = m_FiberBundle->GetBounds(); ImageRegion<3> upsampledRegion; upsampledRegion.SetSize(0, bounds[0]); upsampledRegion.SetSize(1, bounds[1]); upsampledRegion.SetSize(2, bounds[2]); typename InputImageType::RegionType::SizeType upsampledSize = upsampledRegion.GetSize(); for (unsigned int n = 0; n < 3; n++) { upsampledSize[n] = upsampledSize[n] * m_UpsamplingFactor; } upsampledRegion.SetSize( upsampledSize ); outImage->SetRegions( upsampledRegion ); outImage->Allocate(); - // itk::RGBAPixel pix; - // pix.Set(0,0,0,0); - // outImage->FillBuffer(pix); int w = upsampledSize[0]; int h = upsampledSize[1]; int d = upsampledSize[2]; unsigned char* accuout; - float* accu; - accuout = reinterpret_cast(outImage->GetBufferPointer()); + for (int i=0; iGetTractContainer(); - // for each tract - int numTracts = m_FiberBundle->GetNumTracts(); - for( int i=0; iSize(); i++) { - std::vector< itk::Point > vertices; - - // get fiber start point - int numVertices = m_FiberBundle->GetNumPoints(i); - itk::Point start = m_FiberBundle->GetPoint(i,0); - vertices.push_back(start); + ContainerTractType::Pointer tract = tractContainer->GetElement(i); + int tractsize = tract->Size(); - // get fiber end point - if(numVertices>1) + if (tractsize>1) { - itk::Point end = m_FiberBundle->GetPoint(i,numVertices-1); - vertices.push_back(end); - } - - //////////////////// - // fill output image + ContainerPointType start = tract->GetElement(0); + ContainerPointType end = tract->GetElement(tractsize-1); - // for each vertex - for( int j=0; j vertex = vertices.at(j); - - // scaling coordinates (index coords scale with upsampling) - vertex[0] = (vertex[0]+0.5) * m_UpsamplingFactor; - vertex[1] = (vertex[1]+0.5) * m_UpsamplingFactor; - vertex[2] = (vertex[2]+0.5) * m_UpsamplingFactor; + start[0] = (start[0]+0.5) * m_UpsamplingFactor; + start[1] = (start[1]+0.5) * m_UpsamplingFactor; + start[2] = (start[2]+0.5) * m_UpsamplingFactor; // int coordinates inside image? - int px = (int) (vertex[0]); + int px = (int) (start[0]); if (px < 0 || px >= w) continue; - int py = (int) (vertex[1]); + int py = (int) (start[1]); if (py < 0 || py >= h) continue; - int pz = (int) (vertex[2]); + int pz = (int) (start[2]); if (pz < 0 || pz >= d) continue; - // float fraction of coordinates - float frac_x = vertex[0] - px; - float frac_y = vertex[1] - py; - float frac_z = vertex[2] - pz; - - float scale = 100 * pow((float)m_UpsamplingFactor,3); - - if(isRgba) - { - // add to r-channel in output image - accu[0+4*( px + w*(py + h*pz ))] += (1-frac_x)*(1-frac_y)*(1-frac_z) * scale; - accu[0+4*( px + w*(py+1+ h*pz ))] += (1-frac_x)*( frac_y)*(1-frac_z) * scale; - accu[0+4*( px + w*(py + h*pz+h))] += (1-frac_x)*(1-frac_y)*( frac_z) * scale; - accu[0+4*( px + w*(py+1+ h*pz+h))] += (1-frac_x)*( frac_y)*( frac_z) * scale; - accu[0+4*( px+1 + w*(py + h*pz ))] += ( frac_x)*(1-frac_y)*(1-frac_z) * scale; - accu[0+4*( px+1 + w*(py + h*pz+h))] += ( frac_x)*(1-frac_y)*( frac_z) * scale; - accu[0+4*( px+1 + w*(py+1+ h*pz ))] += ( frac_x)*( frac_y)*(1-frac_z) * scale; - accu[0+4*( px+1 + w*(py+1+ h*pz+h))] += ( frac_x)*( frac_y)*( frac_z) * scale; - - // add to a-channel in output image - accu[3+4*( px + w*(py + h*pz ))] = 1; - accu[3+4*( px + w*(py+1+ h*pz ))] = 1; - accu[3+4*( px + w*(py + h*pz+h))] = 1; - accu[3+4*( px + w*(py+1+ h*pz+h))] = 1; - accu[3+4*( px+1 + w*(py + h*pz ))] = 1; - accu[3+4*( px+1 + w*(py + h*pz+h))] = 1; - accu[3+4*( px+1 + w*(py+1+ h*pz ))] = 1; - accu[3+4*( px+1 + w*(py+1+ h*pz+h))] = 1; - } - else - { - accu[( px + w*(py + h*pz ))] += (1-frac_x)*(1-frac_y)*(1-frac_z) * scale; - accu[( px + w*(py+1+ h*pz ))] += (1-frac_x)*( frac_y)*(1-frac_z) * scale; - accu[( px + w*(py + h*pz+h))] += (1-frac_x)*(1-frac_y)*( frac_z) * scale; - accu[( px + w*(py+1+ h*pz+h))] += (1-frac_x)*( frac_y)*( frac_z) * scale; - accu[( px+1 + w*(py + h*pz ))] += ( frac_x)*(1-frac_y)*(1-frac_z) * scale; - accu[( px+1 + w*(py + h*pz+h))] += ( frac_x)*(1-frac_y)*( frac_z) * scale; - accu[( px+1 + w*(py+1+ h*pz ))] += ( frac_x)*( frac_y)*(1-frac_z) * scale; - accu[( px+1 + w*(py+1+ h*pz+h))] += ( frac_x)*( frac_y)*( frac_z) * scale; - } - - } - } - - float maxRgb = 0.000000001; - float maxInt = 0.000000001; - int numPix; - - if(isRgba) - { - numPix = w*h*d*4; + accuout[( px + w*(py + h*pz ))] += 1; - // calc maxima - for(int i=0; i maxRgb) - { - maxRgb = accu[i]; - } - } - else - { - if(accu[i] > maxInt) - { - maxInt = accu[i]; - } - } - } - // write output, normalized uchar 0..255 - for(int i=0; i maxInt) - { - maxInt = accu[i]; - } - } + end[0] = (end[0]+0.5) * m_UpsamplingFactor; + end[1] = (end[1]+0.5) * m_UpsamplingFactor; + end[2] = (end[2]+0.5) * m_UpsamplingFactor; - // write output, normalized uchar 0..255 - for(int i=0; i= w) + continue; + py = (int) (end[1]); + if (py < 0 || py >= h) + continue; + pz = (int) (end[2]); + if (pz < 0 || pz >= d) + continue; + accuout[( px + w*(py + h*pz ))] += 1; } } - delete[] accu; MITK_INFO << "2D fiber endings image generated"; } }