diff --git a/Modules/PlanarFigure/CMakeLists.txt b/Modules/PlanarFigure/CMakeLists.txt index ed698f46b8..3f37aaf0f2 100644 --- a/Modules/PlanarFigure/CMakeLists.txt +++ b/Modules/PlanarFigure/CMakeLists.txt @@ -1,9 +1,9 @@ MITK_CREATE_MODULE( INCLUDE_DIRS Algorithms DataManagement Interactions IO Rendering - DEPENDS MitkLegacyIO MitkSceneSerializationBase + DEPENDS MitkSceneSerializationBase # WARNINGS_AS_ERRORS ) IF( BUILD_TESTING ) add_subdirectory(Testing) ENDIF() diff --git a/Modules/PlanarFigureSegmentation/mitkPlanarFigureSegmentationController.cpp b/Modules/PlanarFigureSegmentation/mitkPlanarFigureSegmentationController.cpp index 6e44b799c5..c97b0301ef 100644 --- a/Modules/PlanarFigureSegmentation/mitkPlanarFigureSegmentationController.cpp +++ b/Modules/PlanarFigureSegmentation/mitkPlanarFigureSegmentationController.cpp @@ -1,315 +1,291 @@ /*=================================================================== 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 "mitkPlanarFigureSegmentationController.h" #include "mitkSurfaceToImageFilter.h" #include #include #include #include #include #include -#include "mitkImageWriter.h" -#include "mitkSurfaceVtkWriter.h" #include "mitkImageToSurfaceFilter.h" #include "mitkImageAccessByItk.h" #include "mitkImageCast.h" mitk::PlanarFigureSegmentationController::PlanarFigureSegmentationController() : itk::Object() , m_ReduceFilter( NULL ) , m_NormalsFilter( NULL ) , m_DistanceImageCreator( NULL ) , m_ReferenceImage( NULL ) , m_SegmentationAsImage( NULL ) { InitializeFilters(); } mitk::PlanarFigureSegmentationController::~PlanarFigureSegmentationController() { } void mitk::PlanarFigureSegmentationController::SetReferenceImage( mitk::Image::Pointer referenceImage ) { m_ReferenceImage = referenceImage; } void mitk::PlanarFigureSegmentationController::AddPlanarFigure( mitk::PlanarFigure::Pointer planarFigure ) { if ( planarFigure.IsNull() ) return; bool newFigure = true; std::size_t indexOfFigure = 0; for( std::size_t i=0; iCreateSurfaceFromPlanarFigure( planarFigure ); m_SurfaceList.push_back( figureAsSurface ); if (!m_PlanarFigureList.empty()) { indexOfFigure = m_PlanarFigureList.size() -1 ; } } else { figureAsSurface = this->CreateSurfaceFromPlanarFigure( planarFigure ); m_SurfaceList.at(indexOfFigure) = figureAsSurface; } if ( m_ReduceFilter.IsNull() ) { InitializeFilters(); } m_ReduceFilter->SetInput( indexOfFigure, figureAsSurface ); m_NormalsFilter->SetInput( indexOfFigure, m_ReduceFilter->GetOutput( indexOfFigure ) ); m_DistanceImageCreator->SetInput( indexOfFigure, m_NormalsFilter->GetOutput( indexOfFigure ) ); } void mitk::PlanarFigureSegmentationController::RemovePlanarFigure( mitk::PlanarFigure::Pointer planarFigure ) { if ( planarFigure.IsNull() ) return; bool figureFound = false; std::size_t indexOfFigure = 0; for( std::size_t i=0; iRemoveInputs( m_NormalsFilter->GetOutput( indexOfFigure ) ); // m_NormalsFilter->RemoveInput( m_ReduceFilter->GetOutput( indexOfFigure ) ); // m_ReduceFilter->RemoveInput( const_cast(m_ReduceFilter->GetInput(indexOfFigure)) ); } else { // this is not very nice! If the figure that has been removed is NOT the last // one in the list we have to create new filters and add all remaining // inputs again. // // Has to be done as the filters do not work when removing an input // other than the last one. // create new filters InitializeFilters(); // and add all existing surfaces SurfaceListType::iterator surfaceIter = m_SurfaceList.begin(); int index = 0; for ( surfaceIter = m_SurfaceList.begin(); surfaceIter!=m_SurfaceList.end(); surfaceIter++ ) { m_ReduceFilter->SetInput( index, (*surfaceIter) ); m_NormalsFilter->SetInput( index, m_ReduceFilter->GetOutput( index ) ); m_DistanceImageCreator->SetInput( index, m_NormalsFilter->GetOutput( index ) ); ++index; } } } template void mitk::PlanarFigureSegmentationController::GetImageBase(itk::Image* input, itk::ImageBase<3>::Pointer& result) { result = input; } mitk::Image::Pointer mitk::PlanarFigureSegmentationController::GetInterpolationResult() { m_SegmentationAsImage = NULL; if ( m_PlanarFigureList.size() == 0 ) { m_SegmentationAsImage = mitk::Image::New(); m_SegmentationAsImage->Initialize(mitk::MakeScalarPixelType() , *m_ReferenceImage->GetTimeGeometry()); return m_SegmentationAsImage; } itk::ImageBase<3>::Pointer itkImage; AccessFixedDimensionByItk_1( m_ReferenceImage.GetPointer(), GetImageBase, 3, itkImage ); m_DistanceImageCreator->SetReferenceImage( itkImage.GetPointer() ); m_ReduceFilter->Update(); m_NormalsFilter->Update(); m_DistanceImageCreator->Update(); mitk::Image::Pointer distanceImage = m_DistanceImageCreator->GetOutput(); // Cleanup the pipeline distanceImage->DisconnectPipeline(); m_DistanceImageCreator = NULL; m_NormalsFilter = NULL; m_ReduceFilter = NULL; itkImage = NULL; - // If this bool flag is true, the distanceImage will be written to the - // filesystem as nrrd-image and as surface-representation. - bool debugOutput(false); - if ( debugOutput ) - { - mitk::ImageWriter::Pointer imageWriter = mitk::ImageWriter::New(); - imageWriter->SetInput( distanceImage ); - imageWriter->SetExtension( ".nrrd" ); - imageWriter->SetFileName( "v:/DistanceImage" ); - imageWriter->Update(); - } - mitk::ImageToSurfaceFilter::Pointer imageToSurfaceFilter = mitk::ImageToSurfaceFilter::New(); imageToSurfaceFilter->SetInput( distanceImage ); imageToSurfaceFilter->SetThreshold( 0 ); imageToSurfaceFilter->Update(); mitk::Surface::Pointer segmentationAsSurface = imageToSurfaceFilter->GetOutput(); // Cleanup the pipeline segmentationAsSurface->DisconnectPipeline(); imageToSurfaceFilter = NULL; - if ( debugOutput ) - { - mitk::SurfaceVtkWriter::Pointer surfaceWriter = mitk::SurfaceVtkWriter::New(); - surfaceWriter->SetInput( segmentationAsSurface ); - surfaceWriter->SetExtension( ".vtk" ); - surfaceWriter->SetFileName( "v:/DistanceImageAsSurface.vtk" ); - surfaceWriter->Update(); - } - - mitk::SurfaceToImageFilter::Pointer surfaceToImageFilter = mitk::SurfaceToImageFilter::New(); surfaceToImageFilter->SetInput( segmentationAsSurface ); surfaceToImageFilter->SetImage( m_ReferenceImage ); surfaceToImageFilter->SetMakeOutputBinary(true); surfaceToImageFilter->Update(); m_SegmentationAsImage = surfaceToImageFilter->GetOutput(); // Cleanup the pipeline m_SegmentationAsImage->DisconnectPipeline(); return m_SegmentationAsImage; } mitk::Surface::Pointer mitk::PlanarFigureSegmentationController::CreateSurfaceFromPlanarFigure( mitk::PlanarFigure::Pointer figure ) { if ( figure.IsNull() ) { MITK_ERROR << "Given PlanarFigure is NULL. Please provide valid PlanarFigure."; return NULL; } mitk::Surface::Pointer newSurface = mitk::Surface::New(); vtkSmartPointer points = vtkSmartPointer::New(); vtkSmartPointer polygon = vtkSmartPointer::New(); vtkSmartPointer cells = vtkSmartPointer::New(); vtkSmartPointer polyData = vtkSmartPointer::New(); const mitk::PlaneGeometry* figureGeometry = figure->GetPlaneGeometry(); // Get the polyline mitk::PlanarFigure::PolyLineType planarPolyLine = figure->GetPolyLine(0); mitk::PlanarFigure::PolyLineType::iterator iter; // iterate over the polyline, ... int pointCounter = 0; for( iter = planarPolyLine.begin(); iter != planarPolyLine.end(); iter++ ) { // ... determine the world-coordinates mitk::Point3D pointInWorldCoordiantes; figureGeometry->Map( *iter, pointInWorldCoordiantes ); // and add them as new points to the vtkPoints points->InsertNextPoint( pointInWorldCoordiantes[0], pointInWorldCoordiantes[1], pointInWorldCoordiantes[2] ); ++pointCounter; } // create a polygon with the points of the polyline polygon->GetPointIds()->SetNumberOfIds( pointCounter ); for(int i = 0; i < pointCounter; i++) { polygon->GetPointIds()->SetId(i,i); } // initialize the vtkCellArray and vtkPolyData cells->InsertNextCell(polygon); polyData->SetPoints(points); polyData->SetPolys( cells ); // set the polydata to the surface newSurface->SetVtkPolyData( polyData ); return newSurface; } mitk::PlanarFigureSegmentationController::PlanarFigureListType mitk::PlanarFigureSegmentationController::GetAllPlanarFigures() { return m_PlanarFigureList; } void mitk::PlanarFigureSegmentationController::InitializeFilters() { m_ReduceFilter = mitk::ReduceContourSetFilter::New(); m_ReduceFilter->SetReductionType(ReduceContourSetFilter::NTH_POINT); m_ReduceFilter->SetStepSize( 10 ); m_NormalsFilter = mitk::ComputeContourSetNormalsFilter::New(); m_DistanceImageCreator = mitk::CreateDistanceImageFromSurfaceFilter::New(); }