diff --git a/Modules/SurfaceInterpolation/mitkComputeContourSetNormalsFilter.cpp b/Modules/SurfaceInterpolation/mitkComputeContourSetNormalsFilter.cpp index 9fdcd9f9af..08d36794b1 100644 --- a/Modules/SurfaceInterpolation/mitkComputeContourSetNormalsFilter.cpp +++ b/Modules/SurfaceInterpolation/mitkComputeContourSetNormalsFilter.cpp @@ -1,311 +1,317 @@ /*=================================================================== 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 "mitkComputeContourSetNormalsFilter.h" +#include "mitkImagePixelReadAccessor.h" + mitk::ComputeContourSetNormalsFilter::ComputeContourSetNormalsFilter() { m_MaxSpacing = 5; this->m_UseProgressBar = false; this->m_ProgressStepSize = 1; mitk::Surface::Pointer output = mitk::Surface::New(); this->SetNthOutput(0, output.GetPointer()); } mitk::ComputeContourSetNormalsFilter::~ComputeContourSetNormalsFilter() { } void mitk::ComputeContourSetNormalsFilter::GenerateData() { unsigned int numberOfInputs = this->GetNumberOfIndexedInputs(); this->CreateOutputsForAllInputs(numberOfInputs); //Iterating over each input for(unsigned int i = 0; i < numberOfInputs; i++) { //Getting the inputs polydata and polygons Surface* currentSurface = const_cast( this->GetInput(i) ); vtkPolyData* polyData = currentSurface->GetVtkPolyData(); vtkSmartPointer existingPolys = polyData->GetPolys(); vtkSmartPointer existingPoints = polyData->GetPoints(); existingPolys->InitTraversal(); vtkIdType* cell (NULL); vtkIdType cellSize (0); //The array that contains all the vertex normals of the current polygon vtkSmartPointer normals = vtkSmartPointer::New(); normals->SetNumberOfComponents(3); normals->SetNumberOfTuples(polyData->GetNumberOfPoints()); //If the current contour is an inner contour then the direction is -1 //A contour lies inside another one if the pixel values in the direction of the normal is 1 m_NegativeNormalCounter = 0; m_PositiveNormalCounter = 0; //Iterating over each polygon for( existingPolys->InitTraversal(); existingPolys->GetNextCell(cellSize, cell);) { if(cellSize < 3)continue; //First we calculate the current polygon's normal double polygonNormal[3] = {0.0}; double p1[3]; double p2[3]; double v1[3]; double v2[3]; existingPoints->GetPoint(cell[0], p1); unsigned int index = cellSize*0.5; existingPoints->GetPoint(cell[index], p2); v1[0] = p2[0]-p1[0]; v1[1] = p2[1]-p1[1]; v1[2] = p2[2]-p1[2]; for (unsigned int k = 2; k < cellSize; k++) { index = cellSize*0.25; existingPoints->GetPoint(cell[index], p1); index = cellSize*0.75; existingPoints->GetPoint(cell[index], p2); v2[0] = p2[0]-p1[0]; v2[1] = p2[1]-p1[1]; v2[2] = p2[2]-p1[2]; vtkMath::Cross(v1,v2,polygonNormal); if (vtkMath::Norm(polygonNormal) != 0) break; } vtkMath::Normalize(polygonNormal); //Now we start computing the normal for each vertex double vertexNormalTemp[3]; existingPoints->GetPoint(cell[0], p1); existingPoints->GetPoint(cell[1], p2); v1[0] = p2[0]-p1[0]; v1[1] = p2[1]-p1[1]; v1[2] = p2[2]-p1[2]; vtkMath::Cross(v1,polygonNormal,vertexNormalTemp); vtkMath::Normalize(vertexNormalTemp); double vertexNormal[3]; + for (unsigned j = 0; j < cellSize-2; j++) { existingPoints->GetPoint(cell[j+1], p1); existingPoints->GetPoint(cell[j+2], p2); v1[0] = p2[0]-p1[0]; v1[1] = p2[1]-p1[1]; v1[2] = p2[2]-p1[2]; vtkMath::Cross(v1,polygonNormal,vertexNormal); vtkMath::Normalize(vertexNormal); double finalNormal[3]; finalNormal[0] = (vertexNormal[0] + vertexNormalTemp[0])*0.5; finalNormal[1] = (vertexNormal[1] + vertexNormalTemp[1])*0.5; finalNormal[2] = (vertexNormal[2] + vertexNormalTemp[2])*0.5; //Here we determine the direction of the normal if (j == 0 && m_SegmentationBinaryImage) { Point3D worldCoord; worldCoord[0] = p1[0]+finalNormal[0]*m_MaxSpacing; worldCoord[1] = p1[1]+finalNormal[1]*m_MaxSpacing; worldCoord[2] = p1[2]+finalNormal[2]*m_MaxSpacing; - double val = m_SegmentationBinaryImage->GetPixelValueByWorldCoordinate(worldCoord); + double val = 0.0; + mitk::ImagePixelReadAccessor readAccess(m_SegmentationBinaryImage); + val = readAccess.GetPixelByWorldCoordinates(worldCoord); + if (val == 1.0) { ++m_PositiveNormalCounter; } else { ++m_NegativeNormalCounter; } } vertexNormalTemp[0] = vertexNormal[0]; vertexNormalTemp[1] = vertexNormal[1]; vertexNormalTemp[2] = vertexNormal[2]; vtkIdType id = cell[j+1]; normals->SetTuple(id,finalNormal); } existingPoints->GetPoint(cell[0], p1); existingPoints->GetPoint(cell[1], p2); v1[0] = p2[0]-p1[0]; v1[1] = p2[1]-p1[1]; v1[2] = p2[2]-p1[2]; vtkMath::Cross(v1,polygonNormal,vertexNormal); vtkMath::Normalize(vertexNormal); vertexNormal[0] = (vertexNormal[0] + vertexNormalTemp[0])*0.5; vertexNormal[1] = (vertexNormal[1] + vertexNormalTemp[1])*0.5; vertexNormal[2] = (vertexNormal[2] + vertexNormalTemp[2])*0.5; vtkIdType id = cell[0]; normals->SetTuple(id,vertexNormal); id = cell[cellSize-1]; normals->SetTuple(id,vertexNormal); int normalDirection(-1); if(m_NegativeNormalCounter < m_PositiveNormalCounter) { normalDirection = 1; } for(unsigned int n = 0; n < normals->GetNumberOfTuples(); n++) { double normal[3]; normals->GetTuple(n,normal); normal[0] = normalDirection*normal[0]; normal[1] = normalDirection*normal[1]; normal[2] = normalDirection*normal[2]; } }//end for all cells Surface::Pointer surface = this->GetOutput(i); surface->GetVtkPolyData()->GetCellData()->SetNormals(normals); }//end for all inputs //Setting progressbar if (this->m_UseProgressBar) mitk::ProgressBar::GetInstance()->Progress(this->m_ProgressStepSize); } mitk::Surface::Pointer mitk::ComputeContourSetNormalsFilter::GetNormalsAsSurface() { //Just for debugging: vtkSmartPointer newPolyData = vtkSmartPointer::New(); vtkSmartPointer newLines = vtkSmartPointer::New(); vtkSmartPointer newPoints = vtkSmartPointer::New(); unsigned int idCounter (0); //Debug end for (unsigned int i = 0; i < this->GetNumberOfIndexedOutputs(); i++) { Surface* currentSurface = const_cast( this->GetOutput(i) ); vtkPolyData* polyData = currentSurface->GetVtkPolyData(); vtkSmartPointer currentCellNormals = vtkDoubleArray::SafeDownCast(polyData->GetCellData()->GetNormals()); vtkSmartPointer existingPolys = polyData->GetPolys(); vtkSmartPointer existingPoints = polyData->GetPoints(); existingPolys->InitTraversal(); vtkIdType* cell (NULL); vtkIdType cellSize (0); for( existingPolys->InitTraversal(); existingPolys->GetNextCell(cellSize, cell);) { for ( unsigned int j = 0; j < cellSize; j++ ) { double currentNormal[3]; currentCellNormals->GetTuple(cell[j], currentNormal); vtkSmartPointer line = vtkSmartPointer::New(); line->GetPointIds()->SetNumberOfIds(2); double newPoint[3]; double p0[3]; existingPoints->GetPoint(cell[j], p0); newPoint[0] = p0[0] + currentNormal[0]; newPoint[1] = p0[1] + currentNormal[1]; newPoint[2] = p0[2] + currentNormal[2]; line->GetPointIds()->SetId(0, idCounter); newPoints->InsertPoint(idCounter, p0); idCounter++; line->GetPointIds()->SetId(1, idCounter); newPoints->InsertPoint(idCounter, newPoint); idCounter++; newLines->InsertNextCell(line); }//end for all points }//end for all cells }//end for all outputs newPolyData->SetPoints(newPoints); newPolyData->SetLines(newLines); newPolyData->BuildCells(); mitk::Surface::Pointer surface = mitk::Surface::New(); surface->SetVtkPolyData(newPolyData); return surface; } void mitk::ComputeContourSetNormalsFilter::SetMaxSpacing(double maxSpacing) { m_MaxSpacing = maxSpacing; } void mitk::ComputeContourSetNormalsFilter::GenerateOutputInformation() { Superclass::GenerateOutputInformation(); } void mitk::ComputeContourSetNormalsFilter::Reset() { for (unsigned int i = 0; i < this->GetNumberOfIndexedInputs(); i++) { this->PopBackInput(); } this->SetNumberOfIndexedInputs(0); this->SetNumberOfIndexedOutputs(0); mitk::Surface::Pointer output = mitk::Surface::New(); this->SetNthOutput(0, output.GetPointer()); } void mitk::ComputeContourSetNormalsFilter::SetUseProgressBar(bool status) { this->m_UseProgressBar = status; } void mitk::ComputeContourSetNormalsFilter::SetProgressStepSize(unsigned int stepSize) { this->m_ProgressStepSize = stepSize; } diff --git a/Modules/SurfaceInterpolation/mitkSurfaceInterpolationController.cpp b/Modules/SurfaceInterpolation/mitkSurfaceInterpolationController.cpp index c44683b530..8c9375727a 100644 --- a/Modules/SurfaceInterpolation/mitkSurfaceInterpolationController.cpp +++ b/Modules/SurfaceInterpolation/mitkSurfaceInterpolationController.cpp @@ -1,317 +1,317 @@ /*=================================================================== 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 "mitkSurfaceInterpolationController.h" #include "mitkMemoryUtilities.h" #include "mitkImageAccessByItk.h" #include "mitkImageCast.h" #include "mitkImageToSurfaceFilter.h" mitk::SurfaceInterpolationController::SurfaceInterpolationController() :m_SelectedSegmentation(0) { m_ReduceFilter = ReduceContourSetFilter::New(); m_NormalsFilter = ComputeContourSetNormalsFilter::New(); m_InterpolateSurfaceFilter = CreateDistanceImageFromSurfaceFilter::New(); m_ReduceFilter->SetUseProgressBar(false); m_NormalsFilter->SetUseProgressBar(false); m_InterpolateSurfaceFilter->SetUseProgressBar(false); m_Contours = Surface::New(); m_PolyData = vtkSmartPointer::New(); m_PolyData->SetPoints(vtkPoints::New()); m_InterpolationResult = 0; m_CurrentNumberOfReducedContours = 0; } mitk::SurfaceInterpolationController::~SurfaceInterpolationController() { ContourListMap::iterator it = m_MapOfContourLists.begin(); for (; it != m_MapOfContourLists.end(); it++) { for (unsigned int j = 0; j < m_MapOfContourLists[(*it).first].size(); ++j) { delete(m_MapOfContourLists[(*it).first].at(j).position); } m_MapOfContourLists.erase(it); } //Removing all observers std::map::iterator dataIter = m_SegmentationObserverTags.begin(); for (; dataIter != m_SegmentationObserverTags.end(); ++dataIter ) { (*dataIter).first->GetProperty("visible")->RemoveObserver( (*dataIter).second ); } m_SegmentationObserverTags.clear(); } mitk::SurfaceInterpolationController* mitk::SurfaceInterpolationController::GetInstance() { static mitk::SurfaceInterpolationController* m_Instance; if ( m_Instance == 0) { m_Instance = new SurfaceInterpolationController(); } return m_Instance; } void mitk::SurfaceInterpolationController::AddNewContour (mitk::Surface::Pointer newContour ,RestorePlanePositionOperation* op) { AffineTransform3D::Pointer transform = AffineTransform3D::New(); transform = op->GetTransform(); mitk::Vector3D direction = op->GetDirectionVector(); int pos (-1); for (unsigned int i = 0; i < m_MapOfContourLists[m_SelectedSegmentation].size(); i++) { itk::Matrix diffM = transform->GetMatrix()-m_MapOfContourLists[m_SelectedSegmentation].at(i).position->GetTransform()->GetMatrix(); bool isSameMatrix(true); for (unsigned int j = 0; j < 3; j++) { if (fabs(diffM[j][0]) > 0.0001 && fabs(diffM[j][1]) > 0.0001 && fabs(diffM[j][2]) > 0.0001) { isSameMatrix = false; break; } } itk::Vector diffV = m_MapOfContourLists[m_SelectedSegmentation].at(i).position->GetTransform()->GetOffset()-transform->GetOffset(); if ( isSameMatrix && m_MapOfContourLists[m_SelectedSegmentation].at(i).position->GetPos() == op->GetPos() && (fabs(diffV[0]) < 0.0001 && fabs(diffV[1]) < 0.0001 && fabs(diffV[2]) < 0.0001) ) { pos = i; break; } } //Don't save a new empty contour if (pos == -1 && newContour->GetVtkPolyData()->GetNumberOfPoints() > 0) { mitk::RestorePlanePositionOperation* newOp = new mitk::RestorePlanePositionOperation (OpRESTOREPLANEPOSITION, op->GetWidth(), op->GetHeight(), op->GetSpacing(), op->GetPos(), direction, transform); ContourPositionPair newData; newData.contour = newContour; newData.position = newOp; m_ReduceFilter->SetInput(m_MapOfContourLists[m_SelectedSegmentation].size(), newContour); m_MapOfContourLists[m_SelectedSegmentation].push_back(newData); } //Edit a existing contour. If the contour is empty, edit it anyway so that the interpolation will always be consistent else if (pos != -1) { m_MapOfContourLists[m_SelectedSegmentation].at(pos).contour = newContour; m_ReduceFilter->SetInput(pos, newContour); } m_ReduceFilter->Update(); m_CurrentNumberOfReducedContours = m_ReduceFilter->GetNumberOfOutputs(); for (unsigned int i = 0; i < m_CurrentNumberOfReducedContours; i++) { m_NormalsFilter->SetInput(i, m_ReduceFilter->GetOutput(i)); m_InterpolateSurfaceFilter->SetInput(i, m_NormalsFilter->GetOutput(i)); } this->Modified(); } void mitk::SurfaceInterpolationController::Interpolate() { if (m_CurrentNumberOfReducedContours< 2) { //If no interpolation is possible reset the interpolation result m_InterpolationResult = 0; return; } //Setting up progress bar /* * Removed due to bug 12441. ProgressBar messes around with Qt event queue which is fatal for segmentation */ //mitk::ProgressBar::GetInstance()->AddStepsToDo(8); // update the filter and get teh resulting distance-image m_InterpolateSurfaceFilter->Update(); Image::Pointer distanceImage = m_InterpolateSurfaceFilter->GetOutput(); // create a surface from the distance-image mitk::ImageToSurfaceFilter::Pointer imageToSurfaceFilter = mitk::ImageToSurfaceFilter::New(); imageToSurfaceFilter->SetInput( distanceImage ); imageToSurfaceFilter->SetThreshold( 0 ); imageToSurfaceFilter->Update(); m_InterpolationResult = imageToSurfaceFilter->GetOutput(); vtkSmartPointer polyDataAppender = vtkSmartPointer::New(); for (unsigned int i = 0; i < m_ReduceFilter->GetNumberOfOutputs(); i++) { polyDataAppender->AddInput(m_ReduceFilter->GetOutput(i)->GetVtkPolyData()); } polyDataAppender->Update(); m_Contours->SetVtkPolyData(polyDataAppender->GetOutput()); //Last progress step /* * Removed due to bug 12441. ProgressBar messes around with Qt event queue which is fatal for segmentation */ //mitk::ProgressBar::GetInstance()->Progress(8); m_InterpolationResult->DisconnectPipeline(); } mitk::Surface::Pointer mitk::SurfaceInterpolationController::GetInterpolationResult() { return m_InterpolationResult; } mitk::Surface* mitk::SurfaceInterpolationController::GetContoursAsSurface() { return m_Contours; } void mitk::SurfaceInterpolationController::SetDataStorage(DataStorage::Pointer ds) { m_DataStorage = ds; } void mitk::SurfaceInterpolationController::SetMinSpacing(double minSpacing) { m_ReduceFilter->SetMinSpacing(minSpacing); } void mitk::SurfaceInterpolationController::SetMaxSpacing(double maxSpacing) { m_ReduceFilter->SetMaxSpacing(maxSpacing); m_NormalsFilter->SetMaxSpacing(maxSpacing); } void mitk::SurfaceInterpolationController::SetDistanceImageVolume(unsigned int distImgVolume) { m_InterpolateSurfaceFilter->SetDistanceImageVolume(distImgVolume); } void mitk::SurfaceInterpolationController::SetSegmentationImage(Image* workingImage) { m_NormalsFilter->SetSegmentationBinaryImage(workingImage); } mitk::Image* mitk::SurfaceInterpolationController::GetImage() { return m_InterpolateSurfaceFilter->GetOutput(); } double mitk::SurfaceInterpolationController::EstimatePortionOfNeededMemory() { double numberOfPointsAfterReduction = m_ReduceFilter->GetNumberOfPointsAfterReduction()*3; double sizeOfPoints = pow(numberOfPointsAfterReduction,2)*sizeof(double); double totalMem = mitk::MemoryUtilities::GetTotalSizeOfPhysicalRam(); double percentage = sizeOfPoints/totalMem; return percentage; } template void mitk::SurfaceInterpolationController::GetImageBase(itk::Image* input, itk::ImageBase<3>::Pointer& result) { - result = input; + result->Graft(input); } void mitk::SurfaceInterpolationController::SetCurrentSegmentationInterpolationList(mitk::Image* segmentation) { if (segmentation == m_SelectedSegmentation) return; m_ReduceFilter->Reset(); m_NormalsFilter->Reset(); m_InterpolateSurfaceFilter->Reset(); if (segmentation == 0) { m_SelectedSegmentation = 0; return; } ContourListMap::iterator it = m_MapOfContourLists.find(segmentation); m_SelectedSegmentation = segmentation; - itk::ImageBase<3>::Pointer itkImage; + itk::ImageBase<3>::Pointer itkImage = itk::ImageBase<3>::New(); AccessFixedDimensionByItk_1( m_SelectedSegmentation, GetImageBase, 3, itkImage ); m_InterpolateSurfaceFilter->SetReferenceImage( itkImage.GetPointer() ); if (it == m_MapOfContourLists.end()) { ContourPositionPairList newList; m_MapOfContourLists.insert(std::pair(segmentation, newList)); m_InterpolationResult = 0; m_CurrentNumberOfReducedContours = 0; itk::MemberCommand::Pointer command = itk::MemberCommand::New(); command->SetCallbackFunction(this, &SurfaceInterpolationController::OnSegmentationDeleted); m_SegmentationObserverTags.insert( std::pair( segmentation, segmentation->AddObserver( itk::DeleteEvent(), command ) ) ); } else { for (unsigned int i = 0; i < m_MapOfContourLists[m_SelectedSegmentation].size(); i++) { m_ReduceFilter->SetInput(i, m_MapOfContourLists[m_SelectedSegmentation].at(i).contour); } m_ReduceFilter->Update(); m_CurrentNumberOfReducedContours = m_ReduceFilter->GetNumberOfOutputs(); for (unsigned int i = 0; i < m_CurrentNumberOfReducedContours; i++) { m_NormalsFilter->SetInput(i, m_ReduceFilter->GetOutput(i)); m_InterpolateSurfaceFilter->SetInput(i, m_NormalsFilter->GetOutput(i)); } } Modified(); } void mitk::SurfaceInterpolationController::RemoveSegmentationFromContourList(mitk::Image *segmentation) { if (segmentation != 0) { m_MapOfContourLists.erase(segmentation); if (m_SelectedSegmentation == segmentation) { SetSegmentationImage(NULL); m_SelectedSegmentation = 0; } } } void mitk::SurfaceInterpolationController::OnSegmentationDeleted(const itk::Object *caller, const itk::EventObject &/*event*/) { mitk::Image* tempImage = dynamic_cast(const_cast(caller)); if (tempImage) { RemoveSegmentationFromContourList(tempImage); if (tempImage == m_SelectedSegmentation) { SetSegmentationImage(NULL); m_SelectedSegmentation = 0; } } }